geneid samples: genes
1. geneid (default) format 
## date Thu Sep 27 15:54:45 2003
## source-version: geneid v 1.2 -- geneid@imim.es
## Sequence test - Length = 198285 bps
# Optimal Gene Structure. 7 genes. Score = 164.188676 
# Gene 1 (Forward). 8 exons. 525 aa. Score = 25.246988 
Internal     3698     3982	 8.69	+ 2 1	 5.39	 1.69	23.61	 0.00	AA   1: 96 gene_1
Internal     4612     4890	 5.95	+ 2 1	 3.01	 2.36	19.33	 0.00	AA  96:189 gene_1
Internal     5102     5230	 1.03	+ 2 1	 0.20	 2.06	11.69	 0.00	AA 189:232 gene_1
Internal    13675    13737	 0.26	+ 2 1	 2.23	 5.66	 1.33	 0.00	AA 232:253 gene_1
Internal    15525    15806	 4.26	+ 2 1	 5.61	 2.81	11.79	 0.00	AA 253:347 gene_1
Internal    17034    17318	 3.80	+ 2 1	 5.76	 1.67	12.10	 0.00	AA 347:442 gene_1
Internal    21599    21618	 0.64	+ 2 0	 4.61	 5.66	-0.07	 0.00	AA 442:448 gene_1
Terminal    23145    23375	 0.61	+ 0 0	 5.33	 0.00	 7.28	 0.00	AA 449:525 gene_1

>test|geneid_v1.2_predicted_protein_1|525_AA
ctPTPMWPDDLQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADW
AQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCF
VSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEI
DRYTAIAYWVPRNALPSDLLENVLCGVAFGLGVLGIIVGIVLIIYFRKPCSGEQSMITFL
PLLLGLSLGCTGAGGFVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCE
FGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPF
NTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPS
YGDTYTCVVEHIGAPEPILRDWRKAVPFQADAGSKKKPGSMGAIQCHAGQHLRQTPGAEV
LRVGPEGQMEDRKYIHNKKEKRQCCGVEREVQNLGFFWPWTMTSA*

# Gene 2 (Forward). 2 exons. 181 aa. Score = 10.263193 
   First    74617    74854	 6.35	+ 0 1	 5.56	-0.98	22.75	 0.00	AA   1: 80 gene_2
Terminal    74929    75233	 3.91	+ 2 0	-6.70	 0.00	33.58	 0.00	AA  80:181 gene_2

>test|geneid_v1.2_predicted_protein_2|181_AA
MAASTASQRPLKGILKDNTSTTSSMVASAEHPRGSVHEQLSKKSQKWDEMNILATYRPAD
KDYGLMKIDEPSTPYHSTMAAAEGLEPKYQVQEQESSGEEDSDLSPEEREKKRQFEMRRT
LHYNEGLNIKLARQLISKDLHDDDKVEEMLETAHGESMNTEESNQGSTASDQQQNKSRSS
*

# Gene 3 (Reverse). 5 exons. 203 aa. Score = 5.699872 
Terminal    86249    86417	 1.51	- 1 0	 0.00	 4.28	 9.84	 0.00	AA 147:203 gene_3
Internal    94859    94977	-1.65	- 0 2	 2.22	 2.55	 2.46	 0.00	AA 108:147 gene_3
Internal    96314    96443	 3.31	- 1 0	 5.34	 4.11	 7.85	 0.00	AA  64:107 gene_3
Internal    97054    97185	 2.74	- 1 2	 0.34	 2.74	15.98	 0.00	AA  20: 64 gene_3
   First    98244    98302	-0.20	- 0 2	 3.60	 1.52	 5.57	 0.00	AA   1: 20 gene_3

>test|geneid_v1.2_predicted_protein_3|203_AA
MAVEFDGGVVMGSDSRVSAGEAVVNRVFDKLSPLHERIYCALSGSAADAQAVADMAAYQL
ELHGIELEEPPLVLAAANVVRNISYKYREDLSAHLMVAGWDQREGGQLPVWTIESSWAMN
CQNSMMSEPSPDFSFLFCNKLSRAKTWAKPRSKIFFKMNVLTVTMPDLEYEQEHPFTLTE
TYVVTKTYINNIFNLDKINLEN*

# Gene 4 (Reverse). 1 exons. 104 aa. Score = 4.755478 
  Single   100629   100940	 4.76	- 0 0	 0.00	 0.42	25.01	 0.00	AA   1:104 gene_4

>test|geneid_v1.2_predicted_protein_4|104_AA
MRGSAVRSSTQSARSSSTVPSHAREAPGRQRHPRGAGHLELAIGTRTPSRSRPGLGLSAP
RWGLKLRVPPSPPLLAAGGGNEGGALGKSQEQADPALARSSAI*

# Gene 5 (Forward). 15 exons. 766 aa. Score = 46.549015 
   First   101952   102061	-1.42	+ 0 2	 1.16	 0.34	 6.71	 0.00	AA   1: 37 gene_5
Internal   102210   102340	-0.15	+ 1 1	 4.04	-1.92	 8.94	 0.00	AA  37: 81 gene_5
Internal   103300   103505	 3.34	+ 2 0	 4.52	 4.14	 7.86	 0.00	AA  81:149 gene_5
Internal   103932   104129	 4.76	+ 0 0	 3.85	-0.04	18.67	 0.00	AA 150:215 gene_5
Internal   105331   105459	 4.56	+ 0 0	 5.35	 3.92	10.00	 0.00	AA 216:258 gene_5
Internal   105609   105797	 3.81	+ 0 0	 5.64	 0.78	12.40	 0.00	AA 259:321 gene_5
Internal   106357   106530	 5.45	+ 0 0	 3.90	 3.52	15.00	 0.00	AA 322:379 gene_5
Internal   106774   106936	 1.28	+ 0 1	 3.56	 0.52	 9.56	 0.00	AA 380:434 gene_5
Internal   107245   107381	 2.61	+ 2 0	 3.85	 4.71	 6.19	 0.00	AA 434:479 gene_5
Internal   108664   108840	 2.52	+ 0 0	 4.41	-1.36	14.21	 0.00	AA 480:538 gene_5
Internal   111360   111507	 1.14	+ 0 1	 4.01	 0.44	 8.68	 0.00	AA 539:588 gene_5
Internal   111666   111777	 4.83	+ 2 2	 4.40	 5.44	 9.82	 0.00	AA 588:625 gene_5
Internal   112186   112315	 4.80	+ 1 0	 3.55	 3.50	13.92	 0.00	AA 625:668 gene_5
Internal   112714   112918	 6.00	+ 0 1	 2.72	 1.65	20.97	 0.00	AA 669:737 gene_5
Terminal   113402   113490	 3.02	+ 2 0	 5.19	 0.00	12.26	 0.00	AA 737:766 gene_5

>test|geneid_v1.2_predicted_protein_5|766_AA
MAIPFFTGRLTDWILQDGSADTFTRNLTLMSILTIASAVLEFVGDGIYNNTMGHVHSHLQ
GEVFGAVLRQETEFFQQNQTGNIMSRVTEDTSTLSDSLSENLSLFLWYLVRGLCLLGIML
WGSVSLTMVTLITLPLLFLLPKKVGKWYQLLEVQVRESLAKSSQVAIEALSAMPTVRSFA
NEEGEAQKFREKLQEIKTLNQKEAVAYAVNSWTTSISGMLLKVGILYIGGQLVTSGAVSS
GNLVTFVLYQMQFTQAVEVLLSIYPRVQKAVGSSEKIFEYLDRTPRCPPSGLLTPLHLEG
LVQFQDVSFAYPNRPDVLVLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQ
LLLDGKPLPQYEHRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGA
HSFISGLPQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQV
EQLLYESPERYSRSVLLITQHLSLVEQADHILFLEGGAIREGGTHQQLMEKKGCYWAMPT
EFFQSLGGDGERNVQIEMAHGTTTLAFKFQHGVIAAVDSRASAGSYISALRVNKVIEINP
YLLGTMSGCAADCQYWERLLAKECRLYYLRNGERISVSAASKLLSNMMCQYRGMGLSMGS
MICGWDKKGPGLYYVDEHGTRLSGNMFSTGSGNTYAYGVMDSGYRPNLSPEEAYDLGRRA
IAYATHRDSYSGGVVNMYHMKEDGWVKVESTDVSDLLHQYREANQ*

# Gene 6 (Forward). 15 exons. 1040 aa. Score = 51.141949 
   First   116217   116709	 1.18	+ 0 1	 4.46	 2.44	 5.09	 0.00	AA   1:165 gene_6
Internal   116799   116913	 4.26	+ 2 2	 5.85	 4.63	 7.42	 0.00	AA 165:203 gene_6
Internal   117437   117484	 0.05	+ 1 2	 6.31	 3.70	-1.13	 0.00	AA 203:219 gene_6
Internal   118677   118807	 3.22	+ 1 1	 5.18	 3.05	 8.20	 0.00	AA 219:263 gene_6
Internal   119091   119296	 7.73	+ 2 0	 5.08	 4.49	17.47	 0.00	AA 263:331 gene_6
Internal   121626   121823	 6.17	+ 0 0	 4.30	 3.64	17.26	 0.00	AA 332:397 gene_6
Internal   121989   122117	 2.09	+ 0 0	 7.47	 4.49	 1.03	 0.00	AA 398:440 gene_6
Internal   123644   123832	 2.08	+ 0 0	 4.08	 0.30	11.14	 0.00	AA 441:503 gene_6
Internal   124010   124183	 7.03	+ 0 0	 5.53	 3.68	16.25	 0.00	AA 504:561 gene_6
Internal   124361   124520	 3.46	+ 0 1	 4.54	 1.41	12.22	 0.00	AA 562:615 gene_6
Internal   132128   132308	 2.65	+ 2 2	 6.44	 3.78	 5.05	 0.00	AA 615:675 gene_6
Internal   137494   137585	 1.72	+ 1 1	 5.36	 5.38	 1.95	 0.00	AA 675:706 gene_6
Internal   139123   139392	 4.46	+ 2 1	 2.30	 4.31	14.99	 0.00	AA 706:796 gene_6
Internal   139835   140116	 3.25	+ 2 1	 5.08	-0.18	13.27	 0.00	AA 796:890 gene_6
Terminal   150538   150989	 1.80	+ 2 0	 1.12	 0.00	16.56	 0.00	AA 890:1040 gene_6

>test|geneid_v1.2_predicted_protein_6|1040_AA
MRLPDLRPWTSLLLVDAALLWLLQGPLGTLLPQGLPGLWLEGTLRLGGLWGLLKLRGLLG
FVGTLLLPLCLATPLTVSLRALVAGASRAPPARVASAPWSWLLVGYGAAGLSWSLWAVLS
PPGAQEKEQDQVNNKVLMWRLLKLSRPDLPLLVAAFFFLVLAVLGETLIPHYSGRVIDIL
GGDFDPHAFASAIFFMCLFSFGRHTQTNKLFDKAGTGMSSLSAGCRGGCFTYTMSRINLR
IREQLFSSLLRQDLGFFQETKTGELNSRLSSDTTLMSNWLPLNANVLLRSLVKVVGLYGF
MLSISPRLTLLSLLHMPFTIAAEKVYNTRHQEVLREIQDAVARAGQVVREAVGGLQTVRS
FGAEEHEVCRYKEALEQCRQLYWRRDLERALYLLVRRVLHLGVQMLMLSCGLQQMQDGEL
TQGSLLSFMIYQESVGSYVQTLVYIYGDMLSNVGAAEKVFSYMDRQPNLPSPGTLAPTTL
QGVVKFQDVSFAYPNRPDRPVLKGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTG
GQVLLDEKPISQYEHCYLHSQVVSVGQEPVLFSGSVRNNIAYGLQSCEDDKVMAAAQAAH
ADDFIQEMEHGIYTENPLEVHDILNFSGYFLGIMSSNERICGTKHHQHLFFQDEVMDKTI
TGKLRQIVHVKQYFGMGSGWVPWVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTN
GTEKVQFVVRFIFNLEEYVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVC
RHNYRLGAPFTVGRKVQPEVTVYPERTPLLHQHNLLHCSVTGFYPGDIKIKWFLNGQEER
AGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHSSLLSPVSVEWNAEKSSDKIQH
SFMLKTLDKLVIEGTYVKIVRAIYDKPAANIILNGQNLEAFPLKTGRRQECPLSLLLFNI
VLEVLARAIRQEKRIKSSQIGKEEVKVFLFADDMIIYLENPIVSAQKLLKLINNFSKVSG
YKINVQKLLIFLYTNNSQA*

# Gene 7 (Forward). 6 exons. 314 aa. Score = 20.532181 
   First   159435   159556	 0.89	+ 0 2	 1.25	 6.11	 4.94	 0.00	AA   1: 41 gene_7
Internal   177915   177947	 0.49	+ 1 2	 5.67	 4.44	-0.19	 0.00	AA  41: 52 gene_7
Internal   190046   190173	-1.22	+ 1 1	 2.30	 0.25	 6.88	 0.00	AA  52: 95 gene_7
Internal   192477   192743	17.00	+ 2 1	 4.16	 4.31	42.30	 0.00	AA  95:184 gene_7
Internal   195269   195550	 1.81	+ 2 1	 3.07	 1.41	11.56	 0.00	AA 184:278 gene_7
Internal   196514   196624	 1.56	+ 2 1	 2.68	 4.53	 5.59	 0.00	AA 278:314 gene_7

>test|geneid_v1.2_predicted_protein_7|314_AA
MRDKSSAWPHHQQSCYYNEDEGTEKRGRDGIHQTTVLIHTRDSMTFIHLVPRCTCFMVQG
GFKQLKNLQEKSQQILSLEEHECNTFLHNKESLAKDFLVQFKGMCYFTNGTERVRGVARY
IYNREEYGRFDSDVGEFQAVTELGRSIEDWNNYKDFLEQERAAVDKVCRHNYEAELRTTL
QRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTSLIRNG
DWTFQILVMLEITPQRGDIYTCQVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVLGLI
FLGLGLIIRHRGQKag
% bin/geneid -vP param/human3iso.param test.fa


2. gff format 
## gff-version 2
## date Thu Sep 27 17:16:16 2003
## source-version: geneid v 1.2 -- geneid@imim.es
## Sequence test - Length = 198285 bps
# Optimal Gene Structure. 7 genes. Score = 164.188676
# Gene 1 (Forward). 8 exons. 525 aa. Score = 25.246988
test    geneid_v1.2     Internal          3698    3982   8.69   +       2       gene_1
test    geneid_v1.2     Internal          4612    4890   5.95   +       2       gene_1
test    geneid_v1.2     Internal          5102    5230   1.03   +       2       gene_1
test    geneid_v1.2     Internal         13675    1373   0.26   +       2       gene_1
test    geneid_v1.2     Internal         15525    1580   4.26   +       2       gene_1
test    geneid_v1.2     Internal         17034    1731   3.80   +       2       gene_1
test    geneid_v1.2     Internal         21599   21618   0.64   +       2       gene_1
test    geneid_v1.2     Terminal         23145   23375   0.61   +       0       gene_1
# Gene 2 (Forward). 2 exons. 181 aa. Score = 10.263193
test    geneid_v1.2        First         74617   74854   6.35   +       0       gene_2
test    geneid_v1.2     Terminal         74929   75233   3.91   +       2       gene_2
# Gene 3 (Reverse). 5 exons. 203 aa. Score = 5.699872
test    geneid_v1.2     Terminal         86249   86417   1.51   -       1       gene_3
test    geneid_v1.2     Internal         94859   94977  -1.65   -       0       gene_3
test    geneid_v1.2     Internal         96314   96443   3.31   -       1       gene_3
test    geneid_v1.2     Internal         97054   97185   2.74   -       1       gene_3
test    geneid_v1.2        First         98244   98302  -0.20   -       0       gene_3   
# Gene 4 (Reverse). 1 exons. 104 aa. Score = 4.755478
test    geneid_v1.2       Single        100629  100940   4.76   -       0       gene_4
# Gene 5 (Forward). 15 exons. 766 aa. Score = 46.549015
test    geneid_v1.2        First        101952  102061  -1.42   +       0       gene_5
test    geneid_v1.2     Internal        102210  102340  -0.15   +       1       gene_5
test    geneid_v1.2     Internal        103300  103505   3.34   +       2       gene_5
test    geneid_v1.2     Internal        103932  104129   4.76   +       0       gene_5
test    geneid_v1.2     Internal        105331  105459   4.56   +       0       gene_5
test    geneid_v1.2     Internal        105609  105797   3.81   +       0       gene_5
test    geneid_v1.2     Internal        106357  106530   5.45   +       0       gene_5
test    geneid_v1.2     Internal        106774  106936   1.28   +       0       gene_5
test    geneid_v1.2     Internal        107245  107381   2.61   +       2       gene_5
test    geneid_v1.2     Internal        108664  108840   2.52   +       0       gene_5
test    geneid_v1.2     Internal        111360  111507   1.14   +       0       gene_5
test    geneid_v1.2     Internal        111666  111777   4.83   +       2       gene_5
test    geneid_v1.2     Internal        112186  112315   4.80   +       1       gene_5
test    geneid_v1.2     Internal        112714  112918   6.00   +       0       gene_5
test    geneid_v1.2     Terminal        113402  113490   3.02   +       2       gene_5
# Gene 6 (Forward). 15 exons. 1040 aa. Score = 51.141949
test    geneid_v1.2        First        116217  116709   1.18   +       0       gene_6
test    geneid_v1.2     Internal        116799  116913   4.26   +       2       gene_6
test    geneid_v1.2     Internal        117437  117484   0.05   +       1       gene_6
test    geneid_v1.2     Internal        118677  118807   3.22   +       1       gene_6
test    geneid_v1.2     Internal        119091  119296   7.73   +       2       gene_6
test    geneid_v1.2     Internal        121626  121823   6.17   +       0       gene_6
test    geneid_v1.2     Internal        121989  122117   2.09   +       0       gene_6
test    geneid_v1.2     Internal        123644  123832   2.08   +       0       gene_6
test    geneid_v1.2     Internal        124010  124183   7.03   +       0       gene_6
test    geneid_v1.2     Internal        124361  124520   3.46   +       0       gene_6
test    geneid_v1.2     Internal        132128  132308   2.65   +       2       gene_6
test    geneid_v1.2     Internal        137494  137585   1.72   +       1       gene_6
test    geneid_v1.2     Internal        139123  139392   4.46   +       2       gene_6
test    geneid_v1.2     Internal        139835  140116   3.25   +       2       gene_6
test    geneid_v1.2     Terminal        150538  150989   1.80   +       2       gene_6
# Gene 7 (Forward). 6 exons. 314 aa. Score = 20.532181
test    geneid_v1.2        First        159435  159556   0.89   +       0       gene_7
test    geneid_v1.2     Internal        177915  177947   0.49   +       1       gene_7
test    geneid_v1.2     Internal        190046  190173  -1.22   +       1       gene_7
test    geneid_v1.2     Internal        192477  192743  17.00   +       2       gene_7
test    geneid_v1.2     Internal        195269  195550   1.81   +       2       gene_7
test    geneid_v1.2     Internal        196514  196624   1.56   +       2       gene_7
% bin/geneid -vGP param/human3iso.param test.fa


3. eXtended format (default) 
## date Thu Sep 27 17:27:29 2003
## source-version: geneid v 1.2 -- geneid@imim.es
## Sequence test - Length = 198285 bps
# Optimal Gene Structure. 7 genes. Score = 164.188676 
# Gene 1 (Forward). 8 exons. 525 aa. Score = 25.246988 
Acceptor     3697     3698	 5.39	+	AACCTCACCCTGTGTCCTTTGCAGCTC
Internal     3698     3982	 8.69	+ 2 1	 5.39	 1.69	23.61	 0.00	AA   1: 96 gene_1
   Donor     3982     3983	 1.69	+	GAGGTCAGG
Acceptor     4611     4612	 3.01	+	CCTACACTTCAATCCCCCCACCAGGGT
Internal     4612     4890	 5.95	+ 2 1	 3.01	 2.36	19.33	 0.00	AA  96:189 gene_1
   Donor     4890     4891	 2.36	+	GGGGTGAGG
Acceptor     5101     5102	 0.20	+	GGCTGAGCCACTCATTTCCTCCAGTAC
Internal     5102     5230	 1.03	+ 2 1	 0.20	 2.06	11.69	 0.00	AA 189:232 gene_1
   Donor     5230     5231	 2.06	+	GTGGTATGT
Acceptor    13674    13675	 2.23	+	ACTGAACTCCCGGCATCTTTACAGAGC
Internal    13675    13737	 0.26	+ 2 1	 2.23	 5.66	 1.33	 0.00	AA 232:253 gene_1
   Donor    13737    13738	 5.66	+	CAGGTAAGG
Acceptor    15524    15525	 5.61	+	TTCTCCCTTCCCTGGCTCCTCTAGGTG
Internal    15525    15806	 4.26	+ 2 1	 5.61	 2.81	11.79	 0.00	AA 253:347 gene_1
   Donor    15806    15807	 2.81	+	CACGTGAGG
Acceptor    17033    17034	 5.76	+	AACATGTTTTTTTCTCCTATGCAGGGC
Internal    17034    17318	 3.80	+ 2 1	 5.76	 1.67	12.10	 0.00	AA 347:442 gene_1
   Donor    17318    17319	 1.67	+	GGAGTAAGT
Acceptor    21598    21599	 4.61	+	CTTTGTAGGTTTTTTGTTTTATAGGAA
Internal    21599    21618	 0.64	+ 2 0	 4.61	 5.66	-0.07	 0.00	AA 442:448 gene_1
   Donor    21618    21619	 5.66	+	CAGGTAAGG
Acceptor    23144    23145	 5.33	+	CTCCCCTCTTCCCTCTGCTCTTAGGCT
Terminal    23145    23375	 0.61	+ 0 0	 5.33	 0.00	 7.28	 0.00	AA 449:525 gene_1
    Stop    23373    23375	 0.00	+	ATAG

>test|geneid_v1.2_predicted_protein_1|525_AA
ctPTPMWPDDLQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADW
AQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCF
VSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEI
DRYTAIAYWVPRNALPSDLLENVLCGVAFGLGVLGIIVGIVLIIYFRKPCSGEQSMITFL
PLLLGLSLGCTGAGGFVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCE
FGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPF
NTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPS
YGDTYTCVVEHIGAPEPILRDWRKAVPFQADAGSKKKPGSMGAIQCHAGQHLRQTPGAEV
LRVGPEGQMEDRKYIHNKKEKRQCCGVEREVQNLGFFWPWTMTSA*

# Gene 2 (Forward). 2 exons. 181 aa. Score = 10.263193 
   Start    74617    74619	 5.56	+	CGGAGCACCCGGCAATGGCG
   First    74617    74854	 6.35	+ 0 1	 5.56	-0.98	22.75	 0.00	AA   1: 80 gene_2
   Donor    74854    74855	-0.98	+	TGGGTGATG
Acceptor    74928    74929	-6.70	+	ACAGATAGCTTGCTAAGAACTTAGCTG
Terminal    74929    75233	 3.91	+ 2 0	-6.70	 0.00	33.58	 0.00	AA  80:181 gene_2
    Stop    75231    75233	 0.00	+	ATAG

>test|geneid_v1.2_predicted_protein_2|181_AA
MAASTASQRPLKGILKDNTSTTSSMVASAEHPRGSVHEQLSKKSQKWDEMNILATYRPAD
KDYGLMKIDEPSTPYHSTMAAAEGLEPKYQVQEQESSGEEDSDLSPEEREKKRQFEMRRT
LHYNEGLNIKLARQLISKDLHDDDKVEEMLETAHGESMNTEESNQGSTASDQQQNKSRSS
*

# Gene 3 (Reverse). 5 exons. 203 aa. Score = 5.699872 
    Stop    86249    86251	 0.00	-	TTGA
Terminal    86249    86417	 1.51	- 1 0	 0.00	 4.28	 9.84	 0.00	AA 147:203 gene_3
Acceptor    86417    86418	 4.28	-	TCGTCTCTATTTGGCCTGTTTTAGGGC
   Donor    94858    94859	 2.22	-	CTGGTATGG
Internal    94859    94977	-1.65	- 0 2	 2.22	 2.55	 2.46	 0.00	AA 108:147 gene_3
Acceptor    94977    94978	 2.55	-	TCATCTACCTGGTCACTATTACAGCTG
   Donor    96313    96314	 5.34	-	CAGGTGAGT
Internal    96314    96443	 3.31	- 1 0	 5.34	 4.11	 7.85	 0.00	AA  64:107 gene_3
Acceptor    96443    96444	 4.11	-	CTTTATTCCTAATATTTCCCTCAGGAT
   Donor    97053    97054	 0.34	-	TGGGTATGA
Internal    97054    97185	 2.74	- 1 2	 0.34	 2.74	15.98	 0.00	AA  20: 64 gene_3
Acceptor    97185    97186	 2.74	-	TGACTGTTGACTCCCTCCTGACAGCGA
   Donor    98243    98244	 3.60	-	AGGGTGAGT
   First    98244    98302	-0.20	- 0 2	 3.60	 1.52	 5.57	 0.00	AA   1: 20 gene_3
   Start    98300    98302	 1.52	-	TGCAGACCACCATCATGGCA

>test|geneid_v1.2_predicted_protein_3|203_AA
MAVEFDGGVVMGSDSRVSAGEAVVNRVFDKLSPLHERIYCALSGSAADAQAVADMAAYQL
ELHGIELEEPPLVLAAANVVRNISYKYREDLSAHLMVAGWDQREGGQLPVWTIESSWAMN
CQNSMMSEPSPDFSFLFCNKLSRAKTWAKPRSKIFFKMNVLTVTMPDLEYEQEHPFTLTE
TYVVTKTYINNIFNLDKINLEN*

# Gene 4 (Reverse). 1 exons. 104 aa. Score = 4.755478 
    Stop   100629   100631	 0.00	-	TTAG
  Single   100629   100940	 4.76	- 0 0	 0.00	 0.42	25.01	 0.00	AA   1:104 gene_4
   Start   100938   100940	 0.42	-	CCAGCAGGGAGAATATGCGG

>test|geneid_v1.2_predicted_protein_4|104_AA
MRGSAVRSSTQSARSSSTVPSHAREAPGRQRHPRGAGHLELAIGTRTPSRSRPGLGLSAP
RWGLKLRVPPSPPLLAAGGGNEGGALGKSQEQADPALARSSAI*

# Gene 5 (Forward). 15 exons. 766 aa. Score = 46.549015 
   Start   101952   101954	 1.16	+	TTTCTCCAGGGGAGATGGCC
   First   101952   102061	-1.42	+ 0 2	 1.16	 0.34	 6.71	 0.00	AA   1: 37 gene_5
   Donor   102061   102062	 0.34	+	CAGGTCTGG
Acceptor   102209   102210	 4.04	+	CCTTTTTTTCCGGGTTCTTTATAGTGC
Internal   102210   102340	-0.15	+ 1 1	 4.04	-1.92	 8.94	 0.00	AA  37: 81 gene_5
   Donor   102340   102341	-1.92	+	CAGGTTTCT
Acceptor   103299   103300	 4.52	+	ACTCTCTTCTCCCCAACCCTGCAGGTA
Internal   103300   103505	 3.34	+ 2 0	 4.52	 4.14	 7.86	 0.00	AA  81:149 gene_5
   Donor   103505   103506	 4.14	+	CAGGTATGT
Acceptor   103931   103932	 3.85	+	CATCTCTTGTCCATGTATCCACAGTTG
Internal   103932   104129	 4.76	+ 0 0	 3.85	-0.04	18.67	 0.00	AA 150:215 gene_5
   Donor   104129   104130	-0.04	+	AGTGTGAGC
Acceptor   105330   105331	 5.35	+	CCTTTTTTTGTGGTCTCTTTATAGATT
Internal   105331   105459	 4.56	+ 0 0	 5.35	 3.92	10.00	 0.00	AA 216:258 gene_5
   Donor   105459   105460	 3.92	+	GAGGTGAGG
Acceptor   105608   105609	 5.64	+	TTCACTATTCTTACCTCCCTCTAGGTA
Internal   105609   105797	 3.81	+ 0 0	 5.64	 0.78	12.40	 0.00	AA 259:321 gene_5
   Donor   105797   105798	 0.78	+	CAGGTACAA
Acceptor   106356   106357	 3.90	+	ATCGTGTGCTTCTCTGGCCTCTAGGGG
Internal   106357   106530	 5.45	+ 0 0	 3.90	 3.52	15.00	 0.00	AA 322:379 gene_5
   Donor   106530   106531	 3.52	+	CAGGTATGG
Acceptor   106773   106774	 3.56	+	ACTCTTCATCATATTTCATCTCAGGTG
Internal   106774   106936	 1.28	+ 0 1	 3.56	 0.52	 9.56	 0.00	AA 380:434 gene_5
   Donor   106936   106937	 0.52	+	CAGGTACTC
Acceptor   107244   107245	 3.85	+	TCATCTTGGCCCTTTGCTCTGCAGAGG
Internal   107245   107381	 2.61	+ 2 0	 3.85	 4.71	 6.19	 0.00	AA 434:479 gene_5
   Donor   107381   107382	 4.71	+	CAGGTGAGG
Acceptor   108663   108664	 4.41	+	TGACGGTCCGATGTCTTTCCTCAGGTG
Internal   108664   108840	 2.52	+ 0 0	 4.41	-1.36	14.21	 0.00	AA 480:538 gene_5
   Donor   108840   108841	-1.36	+	ATGGTGCAG
Acceptor   111359   111360	 4.01	+	TCTCAACCTCTTTTCTCTTATCAGCCC
Internal   111360   111507	 1.14	+ 0 1	 4.01	 0.44	 8.68	 0.00	AA 539:588 gene_5
   Donor   111507   111508	 0.44	+	TTAGTGAGT
Acceptor   111665   111666	 4.40	+	TCCCAAAGCTCCATCTTCTTCCAGGTG
Internal   111666   111777	 4.83	+ 2 2	 4.40	 5.44	 9.82	 0.00	AA 588:625 gene_5
   Donor   111777   111778	 5.44	+	CAGGTAAGC
Acceptor   112185   112186	 3.55	+	TCACTCCACCTTGTCCTCACCCAGGCT
Internal   112186   112315	 4.80	+ 1 0	 3.55	 3.50	13.92	 0.00	AA 625:668 gene_5
   Donor   112315   112316	 3.50	+	AAGGTGGGT
Acceptor   112713   112714	 2.72	+	AGCCTGAAATCTTTCATCTTATAGGGT
Internal   112714   112918	 6.00	+ 0 1	 2.72	 1.65	20.97	 0.00	AA 669:737 gene_5
   Donor   112918   112919	 1.65	+	ATAGTAAGA
Acceptor   113401   113402	 5.19	+	TGTTCTTTTCTCATTTGTCCACAGTGT
Terminal   113402   113490	 3.02	+ 2 0	 5.19	 0.00	12.26	 0.00	AA 737:766 gene_5
    Stop   113488   113490	 0.00	+	ATAA

>test|geneid_v1.2_predicted_protein_5|766_AA
MAIPFFTGRLTDWILQDGSADTFTRNLTLMSILTIASAVLEFVGDGIYNNTMGHVHSHLQ
GEVFGAVLRQETEFFQQNQTGNIMSRVTEDTSTLSDSLSENLSLFLWYLVRGLCLLGIML
WGSVSLTMVTLITLPLLFLLPKKVGKWYQLLEVQVRESLAKSSQVAIEALSAMPTVRSFA
NEEGEAQKFREKLQEIKTLNQKEAVAYAVNSWTTSISGMLLKVGILYIGGQLVTSGAVSS
GNLVTFVLYQMQFTQAVEVLLSIYPRVQKAVGSSEKIFEYLDRTPRCPPSGLLTPLHLEG
LVQFQDVSFAYPNRPDVLVLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQ
LLLDGKPLPQYEHRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGA
HSFISGLPQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQV
EQLLYESPERYSRSVLLITQHLSLVEQADHILFLEGGAIREGGTHQQLMEKKGCYWAMPT
EFFQSLGGDGERNVQIEMAHGTTTLAFKFQHGVIAAVDSRASAGSYISALRVNKVIEINP
YLLGTMSGCAADCQYWERLLAKECRLYYLRNGERISVSAASKLLSNMMCQYRGMGLSMGS
MICGWDKKGPGLYYVDEHGTRLSGNMFSTGSGNTYAYGVMDSGYRPNLSPEEAYDLGRRA
IAYATHRDSYSGGVVNMYHMKEDGWVKVESTDVSDLLHQYREANQ*

# Gene 6 (Forward). 15 exons. 1040 aa. Score = 51.141949 
   Start   116217   116219	 4.46	+	CCGTTGACAGAGCCATGCGG
   First   116217   116709	 1.18	+ 0 1	 4.46	 2.44	 5.09	 0.00	AA   1:165 gene_6
   Donor   116709   116710	 2.44	+	TGGGTGAGT
Acceptor   116798   116799	 5.85	+	TGTTATTTTTCATGCCTCTTTCAGGTG
Internal   116799   116913	 4.26	+ 2 2	 5.85	 4.63	 7.42	 0.00	AA 165:203 gene_6
   Donor   116913   116914	 4.63	+	CAGGTAGGT
Acceptor   117436   117437	 6.31	+	ACTTGCTTTCCTTTCTCTTTCTAGACA
Internal   117437   117484	 0.05	+ 1 2	 6.31	 3.70	-1.13	 0.00	AA 203:219 gene_6
   Donor   117484   117485	 3.70	+	GAGGTGAGC
Acceptor   118676   118677	 5.18	+	CCCTCTTATTCTCCTACCCCACAGCTC
Internal   118677   118807	 3.22	+ 1 1	 5.18	 3.05	 8.20	 0.00	AA 219:263 gene_6
   Donor   118807   118808	 3.05	+	CAGGTGGGG
Acceptor   119090   119091	 5.08	+	CCTCACCTGCTCTGTCCTTCTTAGGGG
Internal   119091   119296	 7.73	+ 2 0	 5.08	 4.49	17.47	 0.00	AA 263:331 gene_6
   Donor   119296   119297	 4.49	+	CAGGTGAGC
Acceptor   121625   121626	 4.30	+	GTGTTTGCTGGCCCTCTTTTCCAGGAA
Internal   121626   121823	 6.17	+ 0 0	 4.30	 3.64	17.26	 0.00	AA 332:397 gene_6
   Donor   121823   121824	 3.64	+	AGGGTAAGA
Acceptor   121988   121989	 7.47	+	CATCTCTTTCTTCTCCTCTTCCAGGTG
Internal   121989   122117	 2.09	+ 0 0	 7.47	 4.49	 1.03	 0.00	AA 398:440 gene_6
   Donor   122117   122118	 4.49	+	CAGGTGAGC
Acceptor   123643   123644	 4.08	+	GGCTCTCCCATTCCTGTTTTCCAGACC
Internal   123644   123832	 2.08	+ 0 0	 4.08	 0.30	11.14	 0.00	AA 441:503 gene_6
   Donor   123832   123833	 0.30	+	AAGGTGCCT
Acceptor   124009   124010	 5.53	+	TTAACTCTTTTTCTGGTTTTCTAGGGG
Internal   124010   124183	 7.03	+ 0 0	 5.53	 3.68	16.25	 0.00	AA 504:561 gene_6
   Donor   124183   124184	 3.68	+	CAGGTGGGT
Acceptor   124360   124361	 4.54	+	TCTGCCCCTGTCCCTGCTGCACAGGTG
Internal   124361   124520	 3.46	+ 0 1	 4.54	 1.41	12.22	 0.00	AA 562:615 gene_6
   Donor   124520   124521	 1.41	+	CAGGTATCT
Acceptor   132127   132128	 6.44	+	GTTTTTTTTGTTTTTTTTTTCTAGAAA
Internal   132128   132308	 2.65	+ 2 2	 6.44	 3.78	 5.05	 0.00	AA 615:675 gene_6
   Donor   132308   132309	 3.78	+	CGGGTGAGT
Acceptor   137493   137494	 5.36	+	ATCTCATTTTTTTCCTTTCTCCAGAAT
Internal   137494   137585	 1.72	+ 1 1	 5.36	 5.38	 1.95	 0.00	AA 675:706 gene_6
   Donor   137585   137586	 5.38	+	CAGGTAAGA
Acceptor   139122   139123	 2.30	+	ATGGTTTTGGTTTTGGTTTTCCAGAAG
Internal   139123   139392	 4.46	+ 2 1	 2.30	 4.31	14.99	 0.00	AA 706:796 gene_6
   Donor   139392   139393	 4.31	+	AAGGTGAGC
Acceptor   139834   139835	 5.08	+	GTCTCATTTTTCCTCCCTTCCTAGTGC
Internal   139835   140116	 3.25	+ 2 1	 5.08	-0.18	13.27	 0.00	AA 796:890 gene_6
   Donor   140116   140117	-0.18	+	GGAGTGAGA
Acceptor   150537   150538	 1.12	+	AAACCCACATGATTATCTCAATAGATG
Terminal   150538   150989	 1.80	+ 2 0	 1.12	 0.00	16.56	 0.00	AA 890:1040 gene_6
    Stop   150987   150989	 0.00	+	CTAG

>test|geneid_v1.2_predicted_protein_6|1040_AA
MRLPDLRPWTSLLLVDAALLWLLQGPLGTLLPQGLPGLWLEGTLRLGGLWGLLKLRGLLG
FVGTLLLPLCLATPLTVSLRALVAGASRAPPARVASAPWSWLLVGYGAAGLSWSLWAVLS
PPGAQEKEQDQVNNKVLMWRLLKLSRPDLPLLVAAFFFLVLAVLGETLIPHYSGRVIDIL
GGDFDPHAFASAIFFMCLFSFGRHTQTNKLFDKAGTGMSSLSAGCRGGCFTYTMSRINLR
IREQLFSSLLRQDLGFFQETKTGELNSRLSSDTTLMSNWLPLNANVLLRSLVKVVGLYGF
MLSISPRLTLLSLLHMPFTIAAEKVYNTRHQEVLREIQDAVARAGQVVREAVGGLQTVRS
FGAEEHEVCRYKEALEQCRQLYWRRDLERALYLLVRRVLHLGVQMLMLSCGLQQMQDGEL
TQGSLLSFMIYQESVGSYVQTLVYIYGDMLSNVGAAEKVFSYMDRQPNLPSPGTLAPTTL
QGVVKFQDVSFAYPNRPDRPVLKGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTG
GQVLLDEKPISQYEHCYLHSQVVSVGQEPVLFSGSVRNNIAYGLQSCEDDKVMAAAQAAH
ADDFIQEMEHGIYTENPLEVHDILNFSGYFLGIMSSNERICGTKHHQHLFFQDEVMDKTI
TGKLRQIVHVKQYFGMGSGWVPWVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTN
GTEKVQFVVRFIFNLEEYVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVC
RHNYRLGAPFTVGRKVQPEVTVYPERTPLLHQHNLLHCSVTGFYPGDIKIKWFLNGQEER
AGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHSSLLSPVSVEWNAEKSSDKIQH
SFMLKTLDKLVIEGTYVKIVRAIYDKPAANIILNGQNLEAFPLKTGRRQECPLSLLLFNI
VLEVLARAIRQEKRIKSSQIGKEEVKVFLFADDMIIYLENPIVSAQKLLKLINNFSKVSG
YKINVQKLLIFLYTNNSQA*

# Gene 7 (Forward). 6 exons. 314 aa. Score = 20.532181 
   Start   159435   159437	 1.25	+	GAGGTGGAAAGAACATGAGG
   First   159435   159556	 0.89	+ 0 2	 1.25	 6.11	 4.94	 0.00	AA   1: 41 gene_7
   Donor   159556   159557	 6.11	+	AAGGTAAGT
Acceptor   177914   177915	 5.67	+	GTGCTTCCCTGTCTCTATCCCCAGGGA
Internal   177915   177947	 0.49	+ 1 2	 5.67	 4.44	-0.19	 0.00	AA  41: 52 gene_7
   Donor   177947   177948	 4.44	+	CAGGTGAGA
Acceptor   190045   190046	 2.30	+	GTATTGTGCCTTTGCTCATATCAGATG
Internal   190046   190173	-1.22	+ 1 1	 2.30	 0.25	 6.88	 0.00	AA  52: 95 gene_7
   Donor   190173   190174	 0.25	+	CCAGTAGGG
Acceptor   192476   192477	 4.16	+	CTGACCCGCCGTGATTCTCCGCAGAGG
Internal   192477   192743	17.00	+ 2 1	 4.16	 4.31	42.30	 0.00	AA  95:184 gene_7
   Donor   192743   192744	 4.31	+	AAGGTGAGC
Acceptor   195268   195269	 3.07	+	TTCCCTGTCTGTTACTGCCCTCAGTGG
Internal   195269   195550	 1.81	+ 2 1	 3.07	 1.41	11.56	 0.00	AA 184:278 gene_7
   Donor   195550   195551	 1.41	+	GGCGTAAGG
Acceptor   196513   196514	 2.68	+	CTCACACTCAGTTCTGCTCCTTAGGGG
Internal   196514   196624	 1.56	+ 2 1	 2.68	 4.53	 5.59	 0.00	AA 278:314 gene_7
   Donor   196624   196625	 4.53	+	AAGGTGAGG

>test|geneid_v1.2_predicted_protein_7|314_AA
MRDKSSAWPHHQQSCYYNEDEGTEKRGRDGIHQTTVLIHTRDSMTFIHLVPRCTCFMVQG
GFKQLKNLQEKSQQILSLEEHECNTFLHNKESLAKDFLVQFKGMCYFTNGTERVRGVARY
IYNREEYGRFDSDVGEFQAVTELGRSIEDWNNYKDFLEQERAAVDKVCRHNYEAELRTTL
QRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTSLIRNG
DWTFQILVMLEITPQRGDIYTCQVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVLGLI
FLGLGLIIRHRGQKag
% bin/geneid -XP param/human3iso.param test.fa


4. eXtended format (gff) 
## gff-version 2
## date Thu Sep 27 17:28:38 2003
## source-version: geneid v 1.2 -- geneid@imim.es
## Sequence test - Length = 198285 bps
# Optimal Gene Structure. 7 genes. Score = 164.188676 
# Gene 1 (Forward). 8 exons. 525 aa. Score = 25.246988 
test  geneid_v1.2  Acceptor    3697    3698   5.39  +  .  # AACCTCACCCTGTGTCCTTTGCAGCTC
test  geneid_v1.2  Internal    3698    3982   8.69  +  2  gene_1
test  geneid_v1.2     Donor    3982    3983   1.69  +  .  # GAGGTCAGG
test  geneid_v1.2  Acceptor    4611    4612   3.01  +  .  # CCTACACTTCAATCCCCCCACCAGGGT
test  geneid_v1.2  Internal    4612    4890   5.95  +  2  gene_1
test  geneid_v1.2     Donor    4890    4891   2.36  +  .  # GGGGTGAGG
test  geneid_v1.2  Acceptor    5101    5102   0.20  +  .  # GGCTGAGCCACTCATTTCCTCCAGTAC
test  geneid_v1.2  Internal    5102    5230   1.03  +  2  gene_1
test  geneid_v1.2     Donor    5230    5231   2.06  +  .  # GTGGTATGT
test  geneid_v1.2  Acceptor   13674   13675   2.23  +  .  # ACTGAACTCCCGGCATCTTTACAGAGC
test  geneid_v1.2  Internal   13675   13737   0.26  +  2  gene_1
test  geneid_v1.2     Donor   13737   13738   5.66  +  .  # CAGGTAAGG
test  geneid_v1.2  Acceptor   15524   15525   5.61  +  .  # TTCTCCCTTCCCTGGCTCCTCTAGGTG
test  geneid_v1.2  Internal   15525   15806   4.26  +  2  gene_1
test  geneid_v1.2     Donor   15806   15807   2.81  +  .  # CACGTGAGG
test  geneid_v1.2  Acceptor   17033   17034   5.76  +  .  # AACATGTTTTTTTCTCCTATGCAGGGC
test  geneid_v1.2  Internal   17034   17318   3.80  +  2  gene_1
test  geneid_v1.2     Donor   17318   17319   1.67  +  .  # GGAGTAAGT
test  geneid_v1.2  Acceptor   21598   21599   4.61  +  .  # CTTTGTAGGTTTTTTGTTTTATAGGAA
test  geneid_v1.2  Internal   21599   21618   0.64  +  2  gene_1
test  geneid_v1.2     Donor   21618   21619   5.66  +  .  # CAGGTAAGG
test  geneid_v1.2  Acceptor   23144   23145   5.33  +  .  # CTCCCCTCTTCCCTCTGCTCTTAGGCT
test  geneid_v1.2  Terminal   23145   23375   0.61  +  0  gene_1
test  geneid_v1.2      Stop   23373   23375   0.00  +  .  # ATAG
# Gene 2 (Forward). 2 exons. 181 aa. Score = 10.263193 
test  geneid_v1.2     Start   74617   74619   5.56  +  .  # CGGAGCACCCGGCAATGGCG
test  geneid_v1.2     First   74617   74854   6.35  +  0  gene_2
test  geneid_v1.2     Donor   74854   74855  -0.98  +  .  # TGGGTGATG
test  geneid_v1.2  Acceptor   74928   74929  -6.70  +  .  # ACAGATAGCTTGCTAAGAACTTAGCTG
test  geneid_v1.2  Terminal   74929   75233   3.91  +  2  gene_2
test  geneid_v1.2      Stop   75231   75233   0.00  +  .  # ATAG
# Gene 3 (Reverse). 5 exons. 203 aa. Score = 5.699872 
test  geneid_v1.2      Stop   86249   86251   0.00  -  .  # TTGA
test  geneid_v1.2  Terminal   86249   86417   1.51  -  1  gene_3
test  geneid_v1.2  Acceptor   86417   86418   4.28  -  .  # TCGTCTCTATTTGGCCTGTTTTAGGGC
test  geneid_v1.2     Donor   94858   94859   2.22  -  .  # CTGGTATGG
test  geneid_v1.2  Internal   94859   94977  -1.65  -  0  gene_3
test  geneid_v1.2  Acceptor   94977   94978   2.55  -  .  # TCATCTACCTGGTCACTATTACAGCTG
test  geneid_v1.2     Donor   96313   96314   5.34  -  .  # CAGGTGAGT
test  geneid_v1.2  Internal   96314   96443   3.31  -  1  gene_3
test  geneid_v1.2  Acceptor   96443   96444   4.11  -  .  # CTTTATTCCTAATATTTCCCTCAGGAT
test  geneid_v1.2     Donor   97053   97054   0.34  -  .  # TGGGTATGA
test  geneid_v1.2  Internal   97054   97185   2.74  -  1  gene_3
test  geneid_v1.2  Acceptor   97185   97186   2.74  -  .  # TGACTGTTGACTCCCTCCTGACAGCGA
test  geneid_v1.2     Donor   98243   98244   3.60  -  .  # AGGGTGAGT
test  geneid_v1.2     First   98244   98302  -0.20  -  0  gene_3
test  geneid_v1.2     Start   98300   98302   1.52  -  .  # TGCAGACCACCATCATGGCA
# Gene 4 (Reverse). 1 exons. 104 aa. Score = 4.755478 
test  geneid_v1.2      Stop  100629  100631   0.00  -  .  # TTAG
test  geneid_v1.2    Single  100629  100940   4.76  -  0  gene_4
test  geneid_v1.2     Start  100938  100940   0.42  -  .  # CCAGCAGGGAGAATATGCGG
# Gene 5 (Forward). 15 exons. 766 aa. Score = 46.549015 
test  geneid_v1.2     Start  101952  101954   1.16  +  .  # TTTCTCCAGGGGAGATGGCC
test  geneid_v1.2     First  101952  102061  -1.42  +  0  gene_5
test  geneid_v1.2     Donor  102061  102062   0.34  +  .  # CAGGTCTGG
test  geneid_v1.2  Acceptor  102209  102210   4.04  +  .  # CCTTTTTTTCCGGGTTCTTTATAGTGC
test  geneid_v1.2  Internal  102210  102340  -0.15  +  1  gene_5
test  geneid_v1.2     Donor  102340  102341  -1.92  +  .  # CAGGTTTCT
test  geneid_v1.2  Acceptor  103299  103300   4.52  +  .  # ACTCTCTTCTCCCCAACCCTGCAGGTA
test  geneid_v1.2  Internal  103300  103505   3.34  +  2  gene_5
test  geneid_v1.2     Donor  103505  103506   4.14  +  .  # CAGGTATGT
test  geneid_v1.2  Acceptor  103931  103932   3.85  +  .  # CATCTCTTGTCCATGTATCCACAGTTG
test  geneid_v1.2  Internal  103932  104129   4.76  +  0  gene_5
test  geneid_v1.2     Donor  104129  104130  -0.04  +  .  # AGTGTGAGC
test  geneid_v1.2  Acceptor  105330  105331   5.35  +  .  # CCTTTTTTTGTGGTCTCTTTATAGATT
test  geneid_v1.2  Internal  105331  105459   4.56  +  0  gene_5
test  geneid_v1.2     Donor  105459  105460   3.92  +  .  # GAGGTGAGG
test  geneid_v1.2  Acceptor  105608  105609   5.64  +  .  # TTCACTATTCTTACCTCCCTCTAGGTA
test  geneid_v1.2  Internal  105609  105797   3.81  +  0  gene_5
test  geneid_v1.2     Donor  105797  105798   0.78  +  .  # CAGGTACAA
test  geneid_v1.2  Acceptor  106356  106357   3.90  +  .  # ATCGTGTGCTTCTCTGGCCTCTAGGGG
test  geneid_v1.2  Internal  106357  106530   5.45  +  0  gene_5
test  geneid_v1.2     Donor  106530  106531   3.52  +  .  # CAGGTATGG
test  geneid_v1.2  Acceptor  106773  106774   3.56  +  .  # ACTCTTCATCATATTTCATCTCAGGTG
test  geneid_v1.2  Internal  106774  106936   1.28  +  0  gene_5
test  geneid_v1.2     Donor  106936  106937   0.52  +  .  # CAGGTACTC
test  geneid_v1.2  Acceptor  107244  107245   3.85  +  .  # TCATCTTGGCCCTTTGCTCTGCAGAGG
test  geneid_v1.2  Internal  107245  107381   2.61  +  2  gene_5
test  geneid_v1.2     Donor  107381  107382   4.71  +  .  # CAGGTGAGG
test  geneid_v1.2  Acceptor  108663  108664   4.41  +  .  # TGACGGTCCGATGTCTTTCCTCAGGTG
test  geneid_v1.2  Internal  108664  108840   2.52  +  0  gene_5
test  geneid_v1.2     Donor  108840  108841  -1.36  +  .  # ATGGTGCAG
test  geneid_v1.2  Acceptor  111359  111360   4.01  +  .  # TCTCAACCTCTTTTCTCTTATCAGCCC
test  geneid_v1.2  Internal  111360  111507   1.14  +  0  gene_5
test  geneid_v1.2     Donor  111507  111508   0.44  +  .  # TTAGTGAGT
test  geneid_v1.2  Acceptor  111665  111666   4.40  +  .  # TCCCAAAGCTCCATCTTCTTCCAGGTG
test  geneid_v1.2  Internal  111666  111777   4.83  +  2  gene_5
test  geneid_v1.2     Donor  111777  111778   5.44  +  .  # CAGGTAAGC
test  geneid_v1.2  Acceptor  112185  112186   3.55  +  .  # TCACTCCACCTTGTCCTCACCCAGGCT
test  geneid_v1.2  Internal  112186  112315   4.80  +  1  gene_5
test  geneid_v1.2     Donor  112315  112316   3.50  +  .  # AAGGTGGGT
test  geneid_v1.2  Acceptor  112713  112714   2.72  +  .  # AGCCTGAAATCTTTCATCTTATAGGGT
test  geneid_v1.2  Internal  112714  112918   6.00  +  0  gene_5
test  geneid_v1.2     Donor  112918  112919   1.65  +  .  # ATAGTAAGA
test  geneid_v1.2  Acceptor  113401  113402   5.19  +  .  # TGTTCTTTTCTCATTTGTCCACAGTGT
test  geneid_v1.2  Terminal  113402  113490   3.02  +  2  gene_5
test  geneid_v1.2      Stop  113488  113490   0.00  +  .  # ATAA
# Gene 6 (Forward). 15 exons. 1040 aa. Score = 51.141949 
test  geneid_v1.2     Start  116217  116219   4.46  +  .  # CCGTTGACAGAGCCATGCGG
test  geneid_v1.2     First  116217  116709   1.18  +  0  gene_6
test  geneid_v1.2     Donor  116709  116710   2.44  +  .  # TGGGTGAGT
test  geneid_v1.2  Acceptor  116798  116799   5.85  +  .  # TGTTATTTTTCATGCCTCTTTCAGGTG
test  geneid_v1.2  Internal  116799  116913   4.26  +  2  gene_6
test  geneid_v1.2     Donor  116913  116914   4.63  +  .  # CAGGTAGGT
test  geneid_v1.2  Acceptor  117436  117437   6.31  +  .  # ACTTGCTTTCCTTTCTCTTTCTAGACA
test  geneid_v1.2  Internal  117437  117484   0.05  +  1  gene_6
test  geneid_v1.2     Donor  117484  117485   3.70  +  .  # GAGGTGAGC
test  geneid_v1.2  Acceptor  118676  118677   5.18  +  .  # CCCTCTTATTCTCCTACCCCACAGCTC
test  geneid_v1.2  Internal  118677  118807   3.22  +  1  gene_6
test  geneid_v1.2     Donor  118807  118808   3.05  +  .  # CAGGTGGGG
test  geneid_v1.2  Acceptor  119090  119091   5.08  +  .  # CCTCACCTGCTCTGTCCTTCTTAGGGG
test  geneid_v1.2  Internal  119091  119296   7.73  +  2  gene_6
test  geneid_v1.2     Donor  119296  119297   4.49  +  .  # CAGGTGAGC
test  geneid_v1.2  Acceptor  121625  121626   4.30  +  .  # GTGTTTGCTGGCCCTCTTTTCCAGGAA
test  geneid_v1.2  Internal  121626  121823   6.17  +  0  gene_6
test  geneid_v1.2     Donor  121823  121824   3.64  +  .  # AGGGTAAGA
test  geneid_v1.2  Acceptor  121988  121989   7.47  +  .  # CATCTCTTTCTTCTCCTCTTCCAGGTG
test  geneid_v1.2  Internal  121989  122117   2.09  +  0  gene_6
test  geneid_v1.2     Donor  122117  122118   4.49  +  .  # CAGGTGAGC
test  geneid_v1.2  Acceptor  123643  123644   4.08  +  .  # GGCTCTCCCATTCCTGTTTTCCAGACC
test  geneid_v1.2  Internal  123644  123832   2.08  +  0  gene_6
test  geneid_v1.2     Donor  123832  123833   0.30  +  .  # AAGGTGCCT
test  geneid_v1.2  Acceptor  124009  124010   5.53  +  .  # TTAACTCTTTTTCTGGTTTTCTAGGGG
test  geneid_v1.2  Internal  124010  124183   7.03  +  0  gene_6
test  geneid_v1.2     Donor  124183  124184   3.68  +  .  # CAGGTGGGT
test  geneid_v1.2  Acceptor  124360  124361   4.54  +  .  # TCTGCCCCTGTCCCTGCTGCACAGGTG
test  geneid_v1.2  Internal  124361  124520   3.46  +  0  gene_6
test  geneid_v1.2     Donor  124520  124521   1.41  +  .  # CAGGTATCT
test  geneid_v1.2  Acceptor  132127  132128   6.44  +  .  # GTTTTTTTTGTTTTTTTTTTCTAGAAA
test  geneid_v1.2  Internal  132128  132308   2.65  +  2  gene_6
test  geneid_v1.2     Donor  132308  132309   3.78  +  .  # CGGGTGAGT
test  geneid_v1.2  Acceptor  137493  137494   5.36  +  .  # ATCTCATTTTTTTCCTTTCTCCAGAAT
test  geneid_v1.2  Internal  137494  137585   1.72  +  1  gene_6
test  geneid_v1.2     Donor  137585  137586   5.38  +  .  # CAGGTAAGA
test  geneid_v1.2  Acceptor  139122  139123   2.30  +  .  # ATGGTTTTGGTTTTGGTTTTCCAGAAG
test  geneid_v1.2  Internal  139123  139392   4.46  +  2  gene_6
test  geneid_v1.2     Donor  139392  139393   4.31  +  .  # AAGGTGAGC
test  geneid_v1.2  Acceptor  139834  139835   5.08  +  .  # GTCTCATTTTTCCTCCCTTCCTAGTGC
test  geneid_v1.2  Internal  139835  140116   3.25  +  2  gene_6
test  geneid_v1.2     Donor  140116  140117  -0.18  +  .  # GGAGTGAGA
test  geneid_v1.2  Acceptor  150537  150538   1.12  +  .  # AAACCCACATGATTATCTCAATAGATG
test  geneid_v1.2  Terminal  150538  150989   1.80  +  2  gene_6
test  geneid_v1.2      Stop  150987  150989   0.00  +  .  # CTAG
# Gene 7 (Forward). 6 exons. 314 aa. Score = 20.532181 
test  geneid_v1.2     Start  159435  159437   1.25  +  .  # GAGGTGGAAAGAACATGAGG
test  geneid_v1.2     First  159435  159556   0.89  +  0  gene_7
test  geneid_v1.2     Donor  159556  159557   6.11  +  .  # AAGGTAAGT
test  geneid_v1.2  Acceptor  177914  177915   5.67  +  .  # GTGCTTCCCTGTCTCTATCCCCAGGGA
test  geneid_v1.2  Internal  177915  177947   0.49  +  1  gene_7
test  geneid_v1.2     Donor  177947  177948   4.44  +  .  # CAGGTGAGA
test  geneid_v1.2  Acceptor  190045  190046   2.30  +  .  # GTATTGTGCCTTTGCTCATATCAGATG
test  geneid_v1.2  Internal  190046  190173  -1.22  +  1  gene_7
test  geneid_v1.2     Donor  190173  190174   0.25  +  .  # CCAGTAGGG
test  geneid_v1.2  Acceptor  192476  192477   4.16  +  .  # CTGACCCGCCGTGATTCTCCGCAGAGG
test  geneid_v1.2  Internal  192477  192743  17.00  +  2  gene_7
test  geneid_v1.2     Donor  192743  192744   4.31  +  .  # AAGGTGAGC
test  geneid_v1.2  Acceptor  195268  195269   3.07  +  .  # TTCCCTGTCTGTTACTGCCCTCAGTGG
test  geneid_v1.2  Internal  195269  195550   1.81  +  2  gene_7
test  geneid_v1.2     Donor  195550  195551   1.41  +  .  # GGCGTAAGG
test  geneid_v1.2  Acceptor  196513  196514   2.68  +  .  # CTCACACTCAGTTCTGCTCCTTAGGGG
test  geneid_v1.2  Internal  196514  196624   1.56  +  2  gene_7
test  geneid_v1.2     Donor  196624  196625   4.53  +  .  # AAGGTGAGG
% bin/geneid -XGP param/human3iso.param test.fa


5. XML format 
<?xml version="1.0" ?>
<!DOCTYPE prediction SYSTEM "geneid.dtd">
<prediction locus="test" length="198285" source="geneid_v1.2" 
date="Thu Sep 27 17:44:50 2003" genes="7" score ="164.19">
   <gene idGene="test.G1" strand ="fwd" exons="8" score="25.25">
      <exon idExon="test.G1E1" type="Internal" frame="2" score="8.69">
         <site idSite="test.G1E1S1" type="Acceptor" position="3698" score="5.39" />
         <site idSite="test.G1E1S2" type="Donor" position="3982" score="1.69" />
      </exon>
      <exon idExon="test.G1E2" type="Internal" frame="2" score="5.95">
         <site idSite="test.G1E2S1" type="Acceptor" position="4612" score="3.01" />
         <site idSite="test.G1E2S2" type="Donor" position="4890" score="2.36" />
      </exon>
      <exon idExon="test.G1E3" type="Internal" frame="2" score="1.03">
         <site idSite="test.G1E3S1" type="Acceptor" position="5102" score="0.20" />
         <site idSite="test.G1E3S2" type="Donor" position="5230" score="2.06" />
      </exon>
      <exon idExon="test.G1E4" type="Internal" frame="2" score="0.26">
         <site idSite="test.G1E4S1" type="Acceptor" position="13675" score="2.23" />
         <site idSite="test.G1E4S2" type="Donor" position="13737" score="5.66" />
      </exon>
      <exon idExon="test.G1E5" type="Internal" frame="2" score="4.26">
         <site idSite="test.G1E5S1" type="Acceptor" position="15525" score="5.61" />
         <site idSite="test.G1E5S2" type="Donor" position="15806" score="2.81" />
      </exon>
      <exon idExon="test.G1E6" type="Internal" frame="2" score="3.80">
         <site idSite="test.G1E6S1" type="Acceptor" position="17034" score="5.76" />
         <site idSite="test.G1E6S2" type="Donor" position="17318" score="1.67" />
      </exon>
      <exon idExon="test.G1E7" type="Internal" frame="2" score="0.64">
         <site idSite="test.G1E7S1" type="Acceptor" position="21599" score="4.61" />
         <site idSite="test.G1E7S2" type="Donor" position="21618" score="5.66" />
      </exon>
      <exon idExon="test.G1E8" type="Terminal" frame="0" score="0.61">
         <site idSite="test.G1E8S1" type="Acceptor" position="23145" score="5.33" />
         <site idSite="test.G1E8S2" type="Stop" position="23375" score="0.00" />
      </exon>
      <protein length="525">
	ctPTPMWPDDLQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADW
	AQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCF
	VSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEI
	DRYTAIAYWVPRNALPSDLLENVLCGVAFGLGVLGIIVGIVLIIYFRKPCSGEQSMITFL
	PLLLGLSLGCTGAGGFVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCE
	FGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPF
	NTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPS
	YGDTYTCVVEHIGAPEPILRDWRKAVPFQADAGSKKKPGSMGAIQCHAGQHLRQTPGAEV
	LRVGPEGQMEDRKYIHNKKEKRQCCGVEREVQNLGFFWPWTMTSA*
      </protein>
   </gene>
   <gene idGene="test.G2" strand ="fwd" exons="2" score="10.26">
      <exon idExon="test.G2E1" type="First" frame="0" score="6.35">
         <site idSite="test.G2E1S1" type="Start" position="74617" score="5.56" />
         <site idSite="test.G2E1S2" type="Donor" position="74854" score="-0.98" />
      </exon>
      <exon idExon="test.G2E2" type="Terminal" frame="2" score="3.91">
         <site idSite="test.G2E2S1" type="Acceptor" position="74929" score="-6.70" />
         <site idSite="test.G2E2S2" type="Stop" position="75233" score="0.00" />
      </exon>
      <protein length="181">
	MAASTASQRPLKGILKDNTSTTSSMVASAEHPRGSVHEQLSKKSQKWDEMNILATYRPAD
	KDYGLMKIDEPSTPYHSTMAAAEGLEPKYQVQEQESSGEEDSDLSPEEREKKRQFEMRRT
	LHYNEGLNIKLARQLISKDLHDDDKVEEMLETAHGESMNTEESNQGSTASDQQQNKSRSS
	*
      </protein>
   </gene>
   <gene idGene="test.G3" strand ="rvs" exons="5" score="5.70">
      <exon idExon="test.G3E1" type="Terminal" frame="1" score="1.51">
         <site idSite="test.G3E1S1" type="Stop" position="86249" score="0.00" />
         <site idSite="test.G3E1S2" type="Acceptor" position="86417" score="4.28" />
      </exon>
      <exon idExon="test.G3E2" type="Internal" frame="0" score="-1.65">
         <site idSite="test.G3E2S1" type="Donor" position="94859" score="2.22" />
         <site idSite="test.G3E2S2" type="Acceptor" position="94977" score="2.55" />
      </exon>
      <exon idExon="test.G3E3" type="Internal" frame="1" score="3.31">
         <site idSite="test.G3E3S1" type="Donor" position="96314" score="5.34" />
         <site idSite="test.G3E3S2" type="Acceptor" position="96443" score="4.11" />
      </exon>
      <exon idExon="test.G3E4" type="Internal" frame="1" score="2.74">
         <site idSite="test.G3E4S1" type="Donor" position="97054" score="0.34" />
         <site idSite="test.G3E4S2" type="Acceptor" position="97185" score="2.74" />
      </exon>
      <exon idExon="test.G3E5" type="First" frame="0" score="-0.20">
         <site idSite="test.G3E5S1" type="Donor" position="98244" score="3.60" />
         <site idSite="test.G3E5S2" type="Start" position="98302" score="1.52" />
      </exon>
      <protein length="203">
	MAVEFDGGVVMGSDSRVSAGEAVVNRVFDKLSPLHERIYCALSGSAADAQAVADMAAYQL
	ELHGIELEEPPLVLAAANVVRNISYKYREDLSAHLMVAGWDQREGGQLPVWTIESSWAMN
	CQNSMMSEPSPDFSFLFCNKLSRAKTWAKPRSKIFFKMNVLTVTMPDLEYEQEHPFTLTE
	TYVVTKTYINNIFNLDKINLEN*
      </protein>
   </gene>
   <gene idGene="test.G4" strand ="rvs" exons="1" score="4.76">
      <exon idExon="test.G4E1" type="Single" frame="0" score="4.76">
         <site idSite="test.G4E1S1" type="Stop" position="100629" score="0.00" />
         <site idSite="test.G4E1S2" type="Start" position="100940" score="0.42" />
      </exon>
      <protein length="104">
	MRGSAVRSSTQSARSSSTVPSHAREAPGRQRHPRGAGHLELAIGTRTPSRSRPGLGLSAP
	RWGLKLRVPPSPPLLAAGGGNEGGALGKSQEQADPALARSSAI*
      </protein>
   </gene>
   <gene idGene="test.G5" strand ="fwd" exons="15" score="46.55">
      <exon idExon="test.G5E1" type="First" frame="0" score="-1.42">
         <site idSite="test.G5E1S1" type="Start" position="101952" score="1.16" />
         <site idSite="test.G5E1S2" type="Donor" position="102061" score="0.34" />
      </exon>
      <exon idExon="test.G5E2" type="Internal" frame="1" score="-0.15">
         <site idSite="test.G5E2S1" type="Acceptor" position="102210" score="4.04" />
         <site idSite="test.G5E2S2" type="Donor" position="102340" score="-1.92" />
      </exon>
      <exon idExon="test.G5E3" type="Internal" frame="2" score="3.34">
         <site idSite="test.G5E3S1" type="Acceptor" position="103300" score="4.52" />
         <site idSite="test.G5E3S2" type="Donor" position="103505" score="4.14" />
      </exon>
      <exon idExon="test.G5E4" type="Internal" frame="0" score="4.76">
         <site idSite="test.G5E4S1" type="Acceptor" position="103932" score="3.85" />
         <site idSite="test.G5E4S2" type="Donor" position="104129" score="-0.04" />
      </exon>
      <exon idExon="test.G5E5" type="Internal" frame="0" score="4.56">
         <site idSite="test.G5E5S1" type="Acceptor" position="105331" score="5.35" />
         <site idSite="test.G5E5S2" type="Donor" position="105459" score="3.92" />
      </exon>
      <exon idExon="test.G5E6" type="Internal" frame="0" score="3.81">
         <site idSite="test.G5E6S1" type="Acceptor" position="105609" score="5.64" />
         <site idSite="test.G5E6S2" type="Donor" position="105797" score="0.78" />
      </exon>
      <exon idExon="test.G5E7" type="Internal" frame="0" score="5.45">
         <site idSite="test.G5E7S1" type="Acceptor" position="106357" score="3.90" />
         <site idSite="test.G5E7S2" type="Donor" position="106530" score="3.52" />
      </exon>
      <exon idExon="test.G5E8" type="Internal" frame="0" score="1.28">
         <site idSite="test.G5E8S1" type="Acceptor" position="106774" score="3.56" />
         <site idSite="test.G5E8S2" type="Donor" position="106936" score="0.52" />
      </exon>
      <exon idExon="test.G5E9" type="Internal" frame="2" score="2.61">
         <site idSite="test.G5E9S1" type="Acceptor" position="107245" score="3.85" />
         <site idSite="test.G5E9S2" type="Donor" position="107381" score="4.71" />
      </exon>
      <exon idExon="test.G5E10" type="Internal" frame="0" score="2.52">
         <site idSite="test.G5E10S1" type="Acceptor" position="108664" score="4.41" />
         <site idSite="test.G5E10S2" type="Donor" position="108840" score="-1.36" />
      </exon>
      <exon idExon="test.G5E11" type="Internal" frame="0" score="1.14">
         <site idSite="test.G5E11S1" type="Acceptor" position="111360" score="4.01" />
         <site idSite="test.G5E11S2" type="Donor" position="111507" score="0.44" />
      </exon>
      <exon idExon="test.G5E12" type="Internal" frame="2" score="4.83">
         <site idSite="test.G5E12S1" type="Acceptor" position="111666" score="4.40" />
         <site idSite="test.G5E12S2" type="Donor" position="111777" score="5.44" />
      </exon>
      <exon idExon="test.G5E13" type="Internal" frame="1" score="4.80">
         <site idSite="test.G5E13S1" type="Acceptor" position="112186" score="3.55" />
         <site idSite="test.G5E13S2" type="Donor" position="112315" score="3.50" />
      </exon>
      <exon idExon="test.G5E14" type="Internal" frame="0" score="6.00">
         <site idSite="test.G5E14S1" type="Acceptor" position="112714" score="2.72" />
         <site idSite="test.G5E14S2" type="Donor" position="112918" score="1.65" />
      </exon>
      <exon idExon="test.G5E15" type="Terminal" frame="2" score="3.02">
         <site idSite="test.G5E15S1" type="Acceptor" position="113402" score="5.19" />
         <site idSite="test.G5E15S2" type="Stop" position="113490" score="0.00" />
      </exon>
      <protein length="766">
	MAIPFFTGRLTDWILQDGSADTFTRNLTLMSILTIASAVLEFVGDGIYNNTMGHVHSHLQ
	GEVFGAVLRQETEFFQQNQTGNIMSRVTEDTSTLSDSLSENLSLFLWYLVRGLCLLGIML
	WGSVSLTMVTLITLPLLFLLPKKVGKWYQLLEVQVRESLAKSSQVAIEALSAMPTVRSFA
	NEEGEAQKFREKLQEIKTLNQKEAVAYAVNSWTTSISGMLLKVGILYIGGQLVTSGAVSS
	GNLVTFVLYQMQFTQAVEVLLSIYPRVQKAVGSSEKIFEYLDRTPRCPPSGLLTPLHLEG
	LVQFQDVSFAYPNRPDVLVLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQ
	LLLDGKPLPQYEHRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGA
	HSFISGLPQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQV
	EQLLYESPERYSRSVLLITQHLSLVEQADHILFLEGGAIREGGTHQQLMEKKGCYWAMPT
	EFFQSLGGDGERNVQIEMAHGTTTLAFKFQHGVIAAVDSRASAGSYISALRVNKVIEINP
	YLLGTMSGCAADCQYWERLLAKECRLYYLRNGERISVSAASKLLSNMMCQYRGMGLSMGS
	MICGWDKKGPGLYYVDEHGTRLSGNMFSTGSGNTYAYGVMDSGYRPNLSPEEAYDLGRRA
	IAYATHRDSYSGGVVNMYHMKEDGWVKVESTDVSDLLHQYREANQ*
      </protein>
   </gene>
   <gene idGene="test.G6" strand ="fwd" exons="15" score="51.14">
      <exon idExon="test.G6E1" type="First" frame="0" score="1.18">
         <site idSite="test.G6E1S1" type="Start" position="116217" score="4.46" />
         <site idSite="test.G6E1S2" type="Donor" position="116709" score="2.44" />
      </exon>
      <exon idExon="test.G6E2" type="Internal" frame="2" score="4.26">
         <site idSite="test.G6E2S1" type="Acceptor" position="116799" score="5.85" />
         <site idSite="test.G6E2S2" type="Donor" position="116913" score="4.63" />
      </exon>
      <exon idExon="test.G6E3" type="Internal" frame="1" score="0.05">
         <site idSite="test.G6E3S1" type="Acceptor" position="117437" score="6.31" />
         <site idSite="test.G6E3S2" type="Donor" position="117484" score="3.70" />
      </exon>
      <exon idExon="test.G6E4" type="Internal" frame="1" score="3.22">
         <site idSite="test.G6E4S1" type="Acceptor" position="118677" score="5.18" />
         <site idSite="test.G6E4S2" type="Donor" position="118807" score="3.05" />
      </exon>
      <exon idExon="test.G6E5" type="Internal" frame="2" score="7.73">
         <site idSite="test.G6E5S1" type="Acceptor" position="119091" score="5.08" />
         <site idSite="test.G6E5S2" type="Donor" position="119296" score="4.49" />
      </exon>
      <exon idExon="test.G6E6" type="Internal" frame="0" score="6.17">
         <site idSite="test.G6E6S1" type="Acceptor" position="121626" score="4.30" />
         <site idSite="test.G6E6S2" type="Donor" position="121823" score="3.64" />
      </exon>
      <exon idExon="test.G6E7" type="Internal" frame="0" score="2.09">
         <site idSite="test.G6E7S1" type="Acceptor" position="121989" score="7.47" />
         <site idSite="test.G6E7S2" type="Donor" position="122117" score="4.49" />
      </exon>
      <exon idExon="test.G6E8" type="Internal" frame="0" score="2.08">
         <site idSite="test.G6E8S1" type="Acceptor" position="123644" score="4.08" />
         <site idSite="test.G6E8S2" type="Donor" position="123832" score="0.30" />
      </exon>
      <exon idExon="test.G6E9" type="Internal" frame="0" score="7.03">
         <site idSite="test.G6E9S1" type="Acceptor" position="124010" score="5.53" />
         <site idSite="test.G6E9S2" type="Donor" position="124183" score="3.68" />
      </exon>
      <exon idExon="test.G6E10" type="Internal" frame="0" score="3.46">
         <site idSite="test.G6E10S1" type="Acceptor" position="124361" score="4.54" />
         <site idSite="test.G6E10S2" type="Donor" position="124520" score="1.41" />
      </exon>
      <exon idExon="test.G6E11" type="Internal" frame="2" score="2.65">
         <site idSite="test.G6E11S1" type="Acceptor" position="132128" score="6.44" />
         <site idSite="test.G6E11S2" type="Donor" position="132308" score="3.78" />
      </exon>
      <exon idExon="test.G6E12" type="Internal" frame="1" score="1.72">
         <site idSite="test.G6E12S1" type="Acceptor" position="137494" score="5.36" />
         <site idSite="test.G6E12S2" type="Donor" position="137585" score="5.38" />
      </exon>
      <exon idExon="test.G6E13" type="Internal" frame="2" score="4.46">
         <site idSite="test.G6E13S1" type="Acceptor" position="139123" score="2.30" />
         <site idSite="test.G6E13S2" type="Donor" position="139392" score="4.31" />
      </exon>
      <exon idExon="test.G6E14" type="Internal" frame="2" score="3.25">
         <site idSite="test.G6E14S1" type="Acceptor" position="139835" score="5.08" />
         <site idSite="test.G6E14S2" type="Donor" position="140116" score="-0.18" />
      </exon>
      <exon idExon="test.G6E15" type="Terminal" frame="2" score="1.80">
         <site idSite="test.G6E15S1" type="Acceptor" position="150538" score="1.12" />
         <site idSite="test.G6E15S2" type="Stop" position="150989" score="0.00" />
      </exon>
      <protein length="1040">
	MRLPDLRPWTSLLLVDAALLWLLQGPLGTLLPQGLPGLWLEGTLRLGGLWGLLKLRGLLG
	FVGTLLLPLCLATPLTVSLRALVAGASRAPPARVASAPWSWLLVGYGAAGLSWSLWAVLS
	PPGAQEKEQDQVNNKVLMWRLLKLSRPDLPLLVAAFFFLVLAVLGETLIPHYSGRVIDIL
	GGDFDPHAFASAIFFMCLFSFGRHTQTNKLFDKAGTGMSSLSAGCRGGCFTYTMSRINLR
	IREQLFSSLLRQDLGFFQETKTGELNSRLSSDTTLMSNWLPLNANVLLRSLVKVVGLYGF
	MLSISPRLTLLSLLHMPFTIAAEKVYNTRHQEVLREIQDAVARAGQVVREAVGGLQTVRS
	FGAEEHEVCRYKEALEQCRQLYWRRDLERALYLLVRRVLHLGVQMLMLSCGLQQMQDGEL
	TQGSLLSFMIYQESVGSYVQTLVYIYGDMLSNVGAAEKVFSYMDRQPNLPSPGTLAPTTL
	QGVVKFQDVSFAYPNRPDRPVLKGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTG
	GQVLLDEKPISQYEHCYLHSQVVSVGQEPVLFSGSVRNNIAYGLQSCEDDKVMAAAQAAH
	ADDFIQEMEHGIYTENPLEVHDILNFSGYFLGIMSSNERICGTKHHQHLFFQDEVMDKTI
	TGKLRQIVHVKQYFGMGSGWVPWVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTN
	GTEKVQFVVRFIFNLEEYVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVC
	RHNYRLGAPFTVGRKVQPEVTVYPERTPLLHQHNLLHCSVTGFYPGDIKIKWFLNGQEER
	AGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHSSLLSPVSVEWNAEKSSDKIQH
	SFMLKTLDKLVIEGTYVKIVRAIYDKPAANIILNGQNLEAFPLKTGRRQECPLSLLLFNI
	VLEVLARAIRQEKRIKSSQIGKEEVKVFLFADDMIIYLENPIVSAQKLLKLINNFSKVSG
	YKINVQKLLIFLYTNNSQA*
      </protein>
   </gene>
   <gene idGene="test.G7" strand ="fwd" exons="6" score="20.53">
      <exon idExon="test.G7E1" type="First" frame="0" score="0.89">
         <site idSite="test.G7E1S1" type="Start" position="159435" score="1.25" />
         <site idSite="test.G7E1S2" type="Donor" position="159556" score="6.11" />
      </exon>
      <exon idExon="test.G7E2" type="Internal" frame="1" score="0.49">
         <site idSite="test.G7E2S1" type="Acceptor" position="177915" score="5.67" />
         <site idSite="test.G7E2S2" type="Donor" position="177947" score="4.44" />
      </exon>
      <exon idExon="test.G7E3" type="Internal" frame="1" score="-1.22">
         <site idSite="test.G7E3S1" type="Acceptor" position="190046" score="2.30" />
         <site idSite="test.G7E3S2" type="Donor" position="190173" score="0.25" />
      </exon>
      <exon idExon="test.G7E4" type="Internal" frame="2" score="17.00">
         <site idSite="test.G7E4S1" type="Acceptor" position="192477" score="4.16" />
         <site idSite="test.G7E4S2" type="Donor" position="192743" score="4.31" />
      </exon>
      <exon idExon="test.G7E5" type="Internal" frame="2" score="1.81">
         <site idSite="test.G7E5S1" type="Acceptor" position="195269" score="3.07" />
         <site idSite="test.G7E5S2" type="Donor" position="195550" score="1.41" />
      </exon>
      <exon idExon="test.G7E6" type="Internal" frame="2" score="1.56">
         <site idSite="test.G7E6S1" type="Acceptor" position="196514" score="2.68" />
         <site idSite="test.G7E6S2" type="Donor" position="196624" score="4.53" />
      </exon>
      <protein length="314">
	MRDKSSAWPHHQQSCYYNEDEGTEKRGRDGIHQTTVLIHTRDSMTFIHLVPRCTCFMVQG
	GFKQLKNLQEKSQQILSLEEHECNTFLHNKESLAKDFLVQFKGMCYFTNGTERVRGVARY
	IYNREEYGRFDSDVGEFQAVTELGRSIEDWNNYKDFLEQERAAVDKVCRHNYEAELRTTL
	QRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTSLIRNG
	DWTFQILVMLEITPQRGDIYTCQVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVLGLI
	FLGLGLIIRHRGQKag
      </protein>
   </gene>
</prediction>
% bin/geneid -MP param/human3iso.param test.fa





Enrique Blanco Garcia © 2003