[Bioperl-l] Grail Tool
Alan R Williams
alanrw at cs.manchester.ac.uk
Mon May 16 10:43:40 EDT 2005
Hello,
I am trying to use Bio::Tools::Grail to parse a Grail output file. It
reads the file OK but does not produce any predictions. Is there a
particular part of the Grail output that it understands? I've attached
one of the test Grail outputs I'm using.
Thanks in advance,
Alan
-------------- next part --------------
gc_object_start: gene_grailexp --organism human --output pretty --dbpat grailexp_v3
# Service: gene_grailexp
# Version: 3.3
# Description: GAT GrailEXP Gene Prediction Service
# Last Modified: October, 2001
# Tool: GrailEXP 3.3 from ORNL. Last updated: October, 2001.
# Database: GrailEXP Database Thu Feb 27 16:15:37 EST 2003 from NCBI/TIGR/Baylor/Riken (15960696 entries). Last updated: Thu Feb 27 16:15:37 2003.
# Sequence Name: >gene_grailexp|PID=9167
# Sequence Length: 18553
# Output_begin: pretty
--------------------------------------------------------------------------------
GrailEXP v3.31 [March, 2002] http://compbio.ornl.gov/grailexp/
Authors: Doug Hyatt, Manesh Shah, Victor Olman, Richard Mural, Ying Xu, and
Edward C. Uberbacher, 1996-2001
Reference: "Automated Gene Identification in Large-Scale Genomic Sequences",
Xu, Y. and Uberbacher, E.C., Journal of Computational Biology, Volume 4,
Number 3, 1997
Sequence: >gene_grailexp|PID=9167 (18553 bp)
--------------------------------------------------------------------------------
GAWAIN Gene Predictions (1 predicted, 1 with database similarity)
Genes with Database Similarity (1 predicted, 0 with alternative splices)
Gene 1, Variant 1 Strand: + Bounds: 1-393 Exons: 1
Start Codon: No Stop Codon: Yes
Top-Scoring Reference: BF958402.1 (542 bp) (89% id, 1-393)
>human|BF958402.1|est_human|dbEST - gi|12375677|gb|BF958402.1|BF958402
QV4-NN1148-291100-616-h10 NN1148 Homo sapiens cDNA
Reference Path: BF958402.1 (542 bp) (89%, 1-393)
---Index---- --------Exons-------- ---------CDS--------- -Ph- -Fr- -Len- -Scr-
1.1.1 1 393 1 259 2 1 393 90
>GrailEXP Gene 1, Var 1 mRNA|Similar to BF958402.1
tgaattcagtgttaccactgcatatccagcccatctgacaccttcagatatgaagctgctcccatcagta
aagtattcgacatctgggtcttttaagggctggtcctttatgtcttttcggcttgagaaaacctcatcca
gtatttccacacaacagtcatacccagggccacacaacatgggctttccatgctctacccattctattgg
cagcagtgtggctggatttagagtattcacaatctccaaggttatgtaggggttttcacacaaaagccct
tgatatcttaacatcctagggttagaaagccagcgatgcccactctgctccatcagggtgatgaccgtgt
ggggaacccgaattatcaacctttgtcccaatttgagcttgtt
>GrailEXP Gene 1, Var 1 protein|Derived from similarity to BF958402.1
EFSVTTAYPAHLTPSDMKLLPSVKYSTSGSFKGWSFMSFRLEKTSSSISTQQSYPGPHNMGFPCSTHSIG
SSVAGFRVFTISKVM*
Genes with No Database Evidence (0 predicted)
--------------------------------------------------------------------------------
GALAHAD Gene Alignments (4 located: 3 displayed, 1 redundant)
Index Std Begin End Accession Database Organism Length
1 + 1 393 BF958402.1 est_human human 542
1 piece Seq exons = (1..393)
89% ident Ref exons = (148..542)
2 + 402 676 BF906163.1 est_human human 354
1 piece Seq exons = (402..676)
88% ident Ref exons = (4..277)
3 + 402 676 BI020262.1 est_human human 355
1 piece Seq exons = (402..676)
88% ident Ref exons = (5..278)
--------------------------------------------------------------------------------
PERCEVAL Exon Candidates (6 predicted)
Index Std Begin End Frm Type Len Scr Quality
1 + 337 481 2 Terminal 145 63 Marginal
2 - 1362 1482 2 Internal 121 19 Poor
3 + 6947 7042 0 Initial 96 41 Marginal
4 - 7856 7943 0 Initial 88 16 Poor
5 - 14834 15109 0 Internal 276 69 Marginal
6 - 15364 15448 0 Initial 85 59 Marginal
--------------------------------------------------------------------------------
# Output_end: pretty
gc_object_end: gene_grailexp --organism human --output pretty --dbpat grailexp_v3
gc_object_start: cpg_grailexp --output pretty
# Service: cpg_grailexp
# Version: 3.0
# Description: GAT GrailEXP CpG Island Locator
# Last Modified: December 4, 2000
# Tool: GrailEXP 3.3 from ORNL. Last updated: October, 2001.
# Sequence Name: >cpg_grailexp|PID=9476
# Sequence Length: 18553
# Output_begin: pretty
--------------------------------------------------------------------------------
GrailEXP v3.31 [March, 2002] http://compbio.ornl.gov/grailexp/
Authors: Doug Hyatt, Manesh Shah, Victor Olman, Richard Mural, Ying Xu, and
Edward C. Uberbacher, 1996-2001
Reference: "Automated Gene Identification in Large-Scale Genomic Sequences",
Xu, Y. and Uberbacher, E.C., Journal of Computational Biology, Volume 4,
Number 3, 1997
Sequence: >cpg_grailexp|PID=9476 (18553 bp)
--------------------------------------------------------------------------------
PERCEVAL CpG Islands (2 predicted)
Index Begin End Ratio Pct_GC
1 5791 6610 0.90 67.32
2 7044 7412 0.85 58.88
--------------------------------------------------------------------------------
# Output_end: pretty
gc_object_end: cpg_grailexp --output pretty
gc_object_start: repeat_grailexp --output pretty
# Service: repeat_grailexp
# Version: 2.0
# Description: GAT GrailEXP Repetitive Element Locator
# Last Modified: December 4, 2000
# Tool: GrailEXP 3.3 from ORNL. Last updated: October, 2001.
# Database: Repeatmasker Repetitive Database Apr 20 from GIRI (4760 entries). Last updated: Fri Feb 28 13:12:30 2003.
# Sequence Name: >repeat_grailexp|PID=9508
# Sequence Length: 18553
# Output_begin: pretty
--------------------------------------------------------------------------------
GrailEXP v3.31 [March, 2002] http://compbio.ornl.gov/grailexp/
Authors: Doug Hyatt, Manesh Shah, Victor Olman, Richard Mural, Ying Xu, and
Edward C. Uberbacher, 1996-2001
Reference: "Automated Gene Identification in Large-Scale Genomic Sequences",
Xu, Y. and Uberbacher, E.C., Journal of Computational Biology, Volume 4,
Number 3, 1997
Sequence: >repeat_grailexp|PID=9508 (18553 bp)
--------------------------------------------------------------------------------
PERCEVAL Repeats (11 located: 2 simple, 9 complex)
Simple Repeats (2 located)
Index Begin End Score 1st 10 Bases
1 12069 12175 76 ttttctgttt...
2 14222 14323 58 atggagataa...
Complex Repeats (9 located)
Index Std Begin End E-Val Element Names
1 + 16656 16793 2e-218 FAM#SINE/Alu/FAM#SINE/Alu_/7SL...
2 - 8079 8186 6e-154 L1PA14#LINE/L1/L1PA13#LINE/L1/...
3 - 3319 3360 0.006 HERV15#LTR/ERV1___LTR15_5%...
4 - 3081 3147 7e-18 HERV3#LTR/ERV1___15%_div,_with...
5 - 2559 2927 5e-32 HERV15#LTR/ERV1___LTR15_5%...
6 - 1791 1867 4e-07 HERV15#LTR/ERV1___LTR15_5%...
7 - 1154 1254 2e-05 HERV3#LTR/ERV1___15%_div,_with...
8 - 581 849 4e-29 HERV3#LTR/ERV1___15%_div,_with...
9 - 49 90 2e-05 HERV3#LTR/ERV1___15%_div,_with...
Masked Sequence
>repeat_grailexp|PID=9508, masked
tgaattcagtgttaccactgcatatccagcccatctgacaccttcagannnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttttaagggctggtcctttatgtcttttcg
gcttgagaaaacctcatccagtatttccacacaacagtcatacccagggccacacaacat
gggctttccatgctctacccattctattggcagcagtgtggctggatttagagtattcac
aatctccaaggttatgtaggggttttcacacaaaagcccttgatatcttaacatcctagg
gttagaaagccagcgatgcccactctgctccatcagggtgatgaccgtgtggggaacccg
aattatcaacctttgtcccaatttgagcttgttagcatcttctgctaacaggacagtggc
tgccaatgccttgaaacacagtggccatcccatagccaccaagtctagccctttggacta
atatgccatgggccaataccatgaccctagtatttgtaccaagactcctgtagctattcc
ttaactttcatgaacatataggtaaaaaggctttttcatgnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnntacagaagcctaaatactggacacttttaaagcagatttgagcctttttta
cctgacactttatatcctgccttccacagcaggtgcagaaggttttgggtttttcccggg
tgcagtagcccttggccagtggctttcttataccatggtcctgaccattttccttattct
cttgacattcatcctttcagtgtcctttccttttgcaccattcacattaatctttttcta
gccttggccagctcttaaatccctgtccagactggcctctttcatgactgcacccacgcc
tccttgcaaagtcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgtagc
cactttagtaagctgagtatcactcacgcctgtggagcttctaacttctggaatttatgc
ctgatatttccctgggcctgccttacaaatgccatatttaccatgtactgtttttcagca
gcctcagggtcaaatggcatatgaagccgataagcctcgcagagcctctcgtaaaattca
ccgggactttcatctggcttctggtggacctctgagacctttctgatattggtggccttt
ttccctccagcctttattccatttaggagtgcctctcaataccactgcaaactttgtggc
ccttgagcctggttagggtcccagcctgggacagcctctatcagaagtgcttgttgtgca
tactgcctgatatctcctgtgcctgcaggctcattgttctcgagccactggagagcagct
tgtataactctttggtgctcttccatatcaaataatgacagaagaagttgtttgcaatca
acccaggtaggattgtgcattaggaaaatgggctgcattaaatctataagnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnntgaagagccattctcccccttggacttcattctgtgcattcaaataaatttgt
ccccatgtttatcggagggacatctgcattgcttgggcatgacctgacctaagatagcca
acctcatccccctggaattcctcccttgggttttcaggtaagggctctgacttctgtctg
cgtggtgttgcctgagggatgctttcttctgagtctgagcctccagaggcagccagggca
gcctcctgtctaagccttgccaaggatggataaattggtgcatagggggtagagtttcta
actcttcagatggggcctgtaggacaggttttttctgcttttcctgtgactctttttctt
tttctgatgacttgcagtctctttctattgttcctggttttgtccaagccattaaagtct
tatggtaggtctcaaagcaggtctgcagccacttagggcgggtctgaattacacttagct
gggagtctgtatacgggaactgatctgggtgcctgggctattctccaagcccagtgacca
cctgaaacacttggccaattatctccttgtgtattgtcccctcggccagccaccctacat
taaaagacagccggtttatctcacaaaaggttctcagtttctgtggagttagcttaacca
tttaatcaccatttaaaccttttgtaaaagtttttcagnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnattcctgttacagctagctgcagccatggtggatgctgcttagccaggagagtac
cttaattcctgttacagctagctgcagccatacnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnacacacctccccc
gtccctgaaactgttttcctttctgactgacgtgcgagccccacctgcatctggtgtcgg
ttagggcgtgagttttgtctgaatcaatgggcctctcccattgtcccaaccccctcgggt
cagatcagtcatcatgccctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnntggttcagatggctgtgcgctgctcccgtgacc
atcctgcaaccccttccactggttccatttgtgctgtcgggggaaggccccagaacgcgg
gagggcagttctccttctgggctgaaactctcctggtggtgccaaggaccccagatctcc
catgtcctggggctgtagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
ggatgagcccccagaaatgttacaagacaatcaaagactggagagactgaaaaaggttca
ggagagtctattaaggtgatcaccggcccagccggacatatgtccagaaagtatgagccc
caaactaagggcttttcctacttttaaacattttaaggcaggaactacatgaggtgggaa
gcaagttacagaagcgagaaacaaaggcagttaatcaagcattacaacatttcttacatc
ttgagaaaaacatgtcttgcaacctaaacttattggtcttgtgactgcagctgtgcagga
gcttgctggcctgtaataaacttgagtaatttggagttggggagtatagataaggtccac
tgtccacagagacaggacaggctgttaacattctcctttaacttgagtgtaagggggcag
ggatcacactttgcagaaactttaagaggattttaaaatttctattactactactattaa
gttacgtttgatttcattaatttcttcttcaaattctaggaagtctgatcccagagttaa
tggtgaatgattacaaaacttatataatatctcacatatggttgtttatattttccaata
aagttatatggggtgaataattataacaagtatttctgaaaaaaataacaattgagaata
ctgatatatatagtccacagaaataatgagggaattttaataccatactccacattggct
gaaactttctcactgcaggctatgctgtcccattcaacattctataaactaaagatgata
gggagaatcttgtttaatctgaatgggagcttgaaggatacattaaatatggaaaatatg
catccttccttaaagagaagtagcaaatgttttcattattcatttattcaaccacttagc
caataatgttaacaattaaaggtgggagcattaaaaaaaggaaaagtggggtggggcggt
gaaatgaacctcactgatttcttgcttttatcatttcaaactccaaaagtgtatttcaac
tattcatatgatgattgaataaacttgttttacattatggaacacccttactgtgtagag
ctgtgagaaattcaataatcagtatttaatgtggacaaaaatagatagattagagaaaca
ataaacatggacatatctacacataatatatactccttttctatccaaaaatctgacaaa
aaccttacacaatggtcagtttacaccattttaaggacaaggatgtggtgaaacaatttt
aaacatttttatataataaaagaaaaaagttgttttaattgctaatgatcaagtttttac
caagaatttacatatgcatcatcaaacagtagcttgaaactgaagcttgacctttgagaa
ataaagcttttaaagtaaatgtctaaattctcttttctttattatgttacatttcattta
ctttaggttttctagtgcaatttaaataagaaataaatagagagtatggtaatcaggtac
aaaggctgtgaaaatattccctgcattttgcacagggaatatgttcaaattcctaatctg
caaagaagaaaagtgcattttcttttttgaaatggcatttgaagatctctccatccatga
acattcttgagcatatggattttacaataacagcagtgtatattagttttttaatttatc
attaactgataacatatacagtaaaatataatttccgttttcttatctaagggcagaaaa
tcccaacctatttctgaatctcactttggaacaaggacagaatgacctgacatggcattt
ttgatttccaacgtttaaacgcataacgtttgtgtgctatggaagcatcttagcttctgg
aatttatgctcgacacgaaacataaacaataaacaattcagtccacgttatatagacata
tctcatatatatatgagatatatatatataaaatatcttacgcacatgcacacttagact
ttctcggttttcatgaaactcacaatctacctcaggcgctcaaaggcactcggcctctca
ggtctgaggcaccacagagaggcttccttgggcacagttgcttgctggtcaagacgccaa
cttggcaaggttatgctgctggcaaaggcagattcgtcagaataaagtcgccacaggctc
aaccaggcaaatcatgaatggccctttcagcaggagcctgagaggagggatgttattcag
cccagcaaccctatttactttttttcaggatccccaaactcgcgttttttaaggctttcc
gctacaagagagccagaattgaagcctgggttggcggcagtgcaggtacctgctcaccta
agcatccctcttttaattttcctaactcctccacccacttgcccaagtataacttttgaa
tggattcagcagaagtgaggcaggaaaggcaggaagatgagaaaaggcgcgacatcaaca
cgcagagctcactgagccgccttgatgataaaaggcgggcacagggactacgtgggtggt
ggcagaaagggcgcgggacacgcctcgcaaagagggaagagtgggcggggccacgtgccg
ttgtcagagttcgcaactcgagcgcccagagggctcgcgaaaagtcccagcctgcaagcc
aacctcgctcagcggacgactggccggatcccaacgcgctgccccttgcccagcctgcga
gcgcgtggtacgaaggcgcgtctgcatccatgccccagcccggggagctggaggcgctcg
cagtcagaggcgagtgatgctaggctgagcgcgtggcggcccgtgtcgtgccccgctgag
ccaagtgcggaagggcagcggcgcgctccgactctgctcgccgcacgcagggcggggcgc
ggctggggggcggggggcctggccgcccgctgggagctgcggacgagcaggcgcgctgag
gacccgagggaggacacggttaaagcattgctatcaactgtgaacccagagagccctcct
tagccaacacgctaactccgaagcctcccttacgcccccgaaccaccgaaggcggcgaca
cctgattcagcgcacaaacacaggtcccttctgtcccggatacaattacgcggcagacac
acactcaaactcgcgcggggcagccaagagacgaggtgagcggagggaccacgccgttcc
agagggcggaagggggggcggtctgggtggaggagaggggcgttgtttgctccctgaggt
gagtgccgggcgaatggctgctgtccaggggcgggggggtgggaattagaaagcacagac
agggttgggctgaggaagttagaagtggttagtgggggttggcggggtagggagaaaggc
taggggttgagggggtgtgaaggagatctttttaggctggcccctcatagcgcccgcgat
cctgtttctgccatatggcatccgttcgagggttctctcgcgtttgtgcgctcaaggcag
agggagggtataacggggaggcgattcggccgaggaccttgtacttgacccctgaaggga
tgggcaccgcggagcccagaggccagagccagctgccagggcagggatggaggtggggga
ccaggaggagcttcgggacctcttcaactcccctttactccgtcttccccctaaggagga
acaagagcgggatgtgttgggggtggggaatgtcttggggctgtacaagctcgctgagac
ttttcggggcccgccgtttccgcgtgcccgcgcgactctcgacaatggacagtgtacagt
ggtggcagggtttcacgggtccccgcgccgatttgggaatggtacggggtgcccttgcat
tagagaagcctgtgcgggcccccgggattagagaagaggtgagcgcctgcgggcggggag
agaaggacgcgctgctggcaaaaagaagggcgccttccatggactggaggagcggcgagg
gagcctggtatgtgtgttttggatttgaaggaggcaaaccgcatcggagagtgcaagtag
atgcagtgcgtcggggcaaaaggacaatctgaggaggtgggcggggtacccaatctctat
atacaagctttctggtttaattgagggtttataaaattgagtacggtaaacctgccattg
tgcagcacttccttaggaaaggaatagcctctgtacctgtaccgcgagttcccatcacct
ttcagcatctaggcggggagaggagagaaggtagagaacttctgagagagttctgagaac
taacgcgaatggctggattgcgctaactaggcgttcttagcaggaaaatgtcgccaaggg
aaggagtgggtggcggtatcaaaccaggcgtgctctggagaatcacctttattatgagcc
agtgttagcagtgacgatagagtcttttatttctggggatcctattggtaaaaattagaa
aaaaaccacactactccaaatactccaaaaatcttcagtcccctcaggctgtcaccttgt
actaccagtttttcagtatcaatgacgtgaatgttagggagtttggctagatgccaaatt
gttatcatttctgataatttcatgttcaaaaacgtctatattcactcaaaattggcgtgc
ttctgacatatccccagaaaaaaatcaccaccatttgaaggaaggatagaaagtgccctt
ttttcttttcttttttaaaaacttttattttaggttttnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnaaccaatattttaatagtgttaagagtaaccata
ctttgtccccaggagattttaaaattagagtcatgcatcttaatattatatggtaaagga
gaccagaactttgtgttacttgaattaaatcttagccagcttagttttctcctatagaaa
ctgtctcttggtggtttgaggttttgctttaggaatgtgtctgtgttcagcaactcttct
agataatgccagagaaaaacactctagtattgtatgatttgcctgccacctacaaggtta
agttgacatctagtgttgtgtgacttagtattatacaagtctttaaaaactacaataaag
catagtgccccgatatttagtaaaggcttgatactctattaggaggttgggcataactga
acagaaactatacttctgactttttccaggtaatactactatacaggttcaaactctttt
taaatctaagatttccagaggactatgcttgttgtatttaagcttggtacgcgtcttaga
ataaataaaccaatgcagtaaataaagatgcttatgacaatttttttggataaaaactac
ttttcgtttaaagattttgacagtttacatttcccaataatttaaattaaaacattttat
tgcaccttatgaacaactatcagcttcattaccatttaaatattgctaaaaatcccatct
tcaatcctcaaatcctttttaaaatcatgcacctgtttatcaaataatatcaatttgttg
ctttttaattcatactaggattttccaacatacacctgggaatttctaagatatccttgg
agagtgagaactttgattatttatgcaagatatagtatctcatttatttgacctcatctg
cattggtacttatttacataagcacattttctcggtagctgactcttcacaccgtttatt
actgaaacttaaaaaaaaagagccattataacccacaagcaatttctaaatcttactgtc
ttccttgttcccttggagaatattggatataagttattctttcttgttgggttgtcttta
tgaattcataaagaattgaatagtgctattcgctgaggtgtatagagctgtttttgttta
tagtaaatggtctcagcctgctgggttgaaatactagaatagagacagaagtaccattct
tctttttatgttttttttttttttctgggtcctctttctgttattggctatcactttctg
ctgctgtcagactgtgagtgggccctgctgctctattatctgttgtctttttttccatca
aatgatgtgggctattgcccgagtgtaaatcctgtagactttgtgacagacactttcagt
ttacgtgctttatttgtggtttggactgtgaactgaaatgtttaggtttccagaagggtg
acctctatataaaaggttttaatgtaccttttatagaaaaaatttgtgtatgagatcttt
aggagggtgtattaatttcagacaattcagtcttctggaatatcttggtgtttctgagaa
actgaagcagcctttaaaaaaaagtttactttcttatgataggcccagatcgtctttgtt
taggaatatgtatactagaatattttacatattactttctgccattgaaacttactaact
ataatgtagtgtagttaatatttttctaccccggaagtccagaataagaagtatgatttg
agaatcctgctaaccatacttgaggctacatgaattatttaaatattattttgcaaatct
acttatggaggaggtacataatcaaatacatatgattaaaatggtttaatttgatcttga
aaacagtggtaatcatatctccttaatctgaagcatttcacaaacattcattcttttatt
caacaaatatttgttaaaagcatactgtgtgccaagcactgtgctctggggatgtgcata
caattaaggccctgggagggctctaggtttaaaagggggagacaaggaggaaacaggcta
ttttcaatatctacagtatagtgctggctgttctgtaagtgccgtgatagagatacacac
acagtaccctgagcagaaatttggaagtggtcaattctgtgtggggacaggagatttgag
ggtttcttagagggtgacataaaagatgaatcactggaggcaggagcaagatcatggagg
gctgtttgccattctcaggagtatggactattttcagtttaaggttgttttaaacagagg
agctatgtgatgagaaaacagctcttacagcaagcaatctagaaggatggatctgaggaa
tgtgagatttggatggtagtttagaagatattggggtggctttggtaagagaggttgagg
tccttgtaccaaagtgttggcagtgggatgaaaaaaaggggtttggttacaacgatattc
aggtggtagaacctctaagattaggtgaccaatttggttggaggattgggagtgggtggt
ataggaggatgggatgggaacttaaaaggagatccagatttgagagcaagagtgatagag
ttcagttttagacatgtagaacttgaagtgcttatagaaaatcgaactggagatgtgtgt
ccagtgaatcattgtatgtgagttctgagcacagaggtcctgggctagataggcaggtag
ataaatggtaggtagataaatggatagacacacagaaacatttaggagttttcagtgtat
aggtaattataaaccgtgaaagttgataggttttccagggcaagtaccaaaagttaatag
ggaaacagaggcctggggagatcctaaaatttaagagttgggtagagaaataggaagcaa
taaagaaaaacgagaaggtacagaacaagagaggcaagaggagagttaggagggtgtaac
ttttaaaagcagctgaaaactgagaaaatttcagaaagtgagaaggtcaggtactgaaat
gagggggtgttagacagtctcggttcccaccccctctcgagccccgaatagctctgtgac
cttgagctcacaatttagtttcatttcctcatttagcaaatgaggggagaagcacctact
ttatagggctactgtgaggatcagatgagataaaatctatcaagcacaatgcctgggagg
ttactcctttgtgtttaacaaatgctacctgttttatggaaaccaggacttggatttgtg
attagaaggtccgtagtcatttttgctttcacaagtactcgctctcagaattcacagaga
gtgattgaaaatatatttttaagatgaaaatttgatcatacttttaacttttttggttag
aggccagtagaatagcagccattgaaagttttgaagggagcagagggagccaactgaaca
aaagtccttgaagagagagtggaagttgcctcaagagcgttgcagagatgttgggtttct
caggacaatccatgcttccgccagtcaggagggtctggtggcatatgcattgtgtttaaa
aagcacctggtaattaaacctccaggtttctaatgtcttgtttaaagtactcttagtatt
ttaagtgtgttctagttccttagataatctataaggacattgattatacattttagtatt
agctgaaaataaactcagaaaacaatacagatgatttcaaaatttaacaaaatgtaattt
aatatttgatgattccaaaggcacctctatacctcatagggtcttaaaaatcaacatgtg
aaaaataattattagcctgtgtaataggggaaggactgatttgtagaggtttgtttgctt
tttttttttttttcccccaattaagactactatggtaatatttaaatatacctacttttt
tcctaggattttctgtttggatgaagtgatgctttatattagagattaataaacatttta
aattagatttctattttaatatgtgtataagttttttactctgtaattactgcataattt
gagaaaatgtttacatctatgcagtggtttggaagtcaaccaacaattgcacatagtaca
tattgtttactaattggttataaggcatataataaatatttgttgtcccaatacatgttt
gttgaataaaacaaaattagatattccatatttttaagatgaaatgaattttatatctgt
agttttaatatttaatcatattctttacctgaaaatcgctagccatacttttcgttttca
gcacttctctattttgcagttgtgtttcagtgcttttttttttcccactgtgcttagtcc
ttcacgatttatggccctgttatttgtaaagcatagtaatctaagcaggtgattttcagt
ttaggatttcttctagttccatgttgtatattcaccaagtcagttttagactatatattg
tcatgctcagcactcccttacagagataacagatgccaagttgaaattgacttatacaga
atgccacacttaggtaagtgtttaggagtgcatagccaaaataaaaatggtacctttggt
ttatgaatggcagggcatctaggacagtgtaggtcagttcgtattctctggatggacatt
tatgtaaatattaaaacatttagattagatggaaagatgtatagtaggaacatttcagag
atactgtttccttgtagcattgtactatttatctgaattgttaatttggaataatcacta
tattgattttattttgaagatataatttatttccattgacttgatataaataacagaaat
gcatctgcaaggaatccagttcattaaagaaatttacattcgtatctgatttggtaaata
tgtgcttgatttgggaatattatataacaaaatatttgtgaaatcattttgtacttttta
attgttttgaagaaatttaatactcaaaatatttcaagacaccaaatcatgactttttag
ttattacattaagctataacttgctttaatgagtaaaaactgtggggctaattttcttcc
aagtgaaacatcaagtttaaataatgtgcacatgaatttacaaagtagaatcaagtgtgc
aaatatgctatatgttctgtaataggttcttgaaaagctgtatataaactcagcttttat
aagttgagtcatatttatagaataagaaaatagggcaaacatttaacacttcttaaatat
taagtgatgggcatacagatgtttgttatgttaatctttatatttttctgtatgttagaa
atagtttacagaaaaaaattgtggttagtgacattaaagcacattatatattaaatatac
tcagggactttgaaatttaaagcaatatcaacatacaatttaccatagaaaaaatcctat
tctgattttattaatacctgttttgcaaattcagaatttttaatgggtttaattaagcag
atacacacacaacaacaacaacaacaaaaaacttggacacacttctgtaacacatcttga
atatagtctcatctgttggaattttttaaacttctacacttaagtcttaatctgattctc
cctcatcctcataatattcattattcagaggagaggcatcaacaggaagaattcaatttt
acttaaataaaaattttttactagcaacggaatgagtgattcagtggtggtgtcttcctg
ctttgagagagctgttctaagactaggcagttagtcttaggcctaagactaggcagttag
tctaggggctccacagcaggcccttcctctgggttctctttatgaagaaggcctttgtgt
tttacatagattttgcatttgtgctgctgtccctattgagttgttctcaccaagccaatc
tggggagtagctcttaggggaaaactagtcaaacaggtttgcctgtctattcaaaaggag
ggaagaacggtgaaatgtatggataaaggccaagagtaaaactgttttaagtaatattca
tgctaatcactgactgttggttttgaaaatactttgtagacatttgtgagaatgtatctt
aatggagataaagtaagagagaaactggaaggggaagtagtttagaagcaggggataagg
acaagatggggagaaggaagggaaaaacaatggaggcaaaataagctcaagaaggaaaga
atagtgtttcagtgtcatatctgggctttatgtaaactgggtgtgttatagcaggaaacc
atggtattgatctgagaatgaatttaattaaaacaaacaaaaaacccccacatgcctgtg
atcctcaatgtccaaaatagggagcgtcttgccagggcagggctgaagtttactaggaat
attggtgggaaaatgttatagttaaccatctctgatactaatcttatattagagataata
cttggtttcccctagtaaagtgttagagtcatacagctttattgtagtttgcaaatctat
tacacatatatttctactgtttagttctcattctgcccctgaagcatagccctataggta
gtagcattttacagctcataacttggtagagtcccaagtaacctttggaagtcaaaatga
caatccagtctggggaatttgatgttaaaactaaagcttcttgcctagaacaagttttgg
aactatagctcaccacctgcctcatgttctgggaatgctgaaccttgatcccactgaaat
tacctttaagtagtctttctgtagtcctcagtaatctcctcctttgctccatgcttcttc
cctgctccttgagagttccttctcctttctcatctgtaatggtaactccccatctgatct
ttggttgtgcctcttcttccttcctggcatttttattaacatcttttgtcccagcacctc
tcctcttctctattctcactcctttggtgtagttattcatgcccatagactggattttta
tttatatatagatgattcaaaaagctgtatttctaattgtgatttcttctatactctcaa
gagcttagagttcccagctcaacttcctaactcagatctgacatccccatttgcctcagt
cttcgaagacagattttggtgttgtggaattcacttttttaccctttatatctaatctat
tcctaattgatcactatgtccttcatgaagaccttcttcccttgcctgagtctttccatt
cacctcctgatgtcttggtgtagtcccacatcacttcttcaccagtggtactaaatgact
cattttcaccattacctgggccttccatcacctcctactgcccacaaccatcagtcactt
gtccttactgacccacttgccttctttgagtgtgatttgactatgcgtttattttcacat
ggggatccaaaatttttagcatggctttcgaggctgtctattgtctagctgctttctgat
cagacttatttattttctcatattgctcaataggattctatcctgtttacccactggggc
attcatttcaggatatccccccgcttgagatgtcctgccttttttttcttctgcacttcc
aaattctcacccaaggttttgacactcaagtcccacctcagactgtggcttcccagtctc
tgtcacttttctgtgactttgatttgtacatatattgatgttagcaattaggtttcattc
tccctctaaggagagtatgaactcttagagggtggagtctcttgtctcctcatacacctt
ggacaaacactattgatcagagagaagatattcaaacatgattgaatggtatctttagtt
tgtcatgaggcaataagggtaagtttcctaattttctatacgtattttgattttttcctg
ttgttttttccagaactgcatcattcaaacttgaaacattcccctatttttttttaacaa
ggtgttctatataggaacaacatatcttatagggattgctacattatttagtcacaatgg
aaaaaaaagtttgatatatagaaagattatataatagttacatggaactctactataaaa
ttataatggtttagtgggttttcttttttaaatttacctggggcttctataggtggatgt
gcattcacaactaattctaggtaatgctaataaaagaaaataatcacggtgataattaac
tgtatttagtttttattttgtatttacatttcaatgtaagtatgcctaatgtcatgaaac
catagttggagaaaataatgattatatgcatgaggaagataacttaggaagcattctaat
tgtccaactccccacttccccatagaccttttataacaattaaatcaaagcaccagccca
ggaataattcttttttccattctttgtgcctatttcctcctttgataattgctgaattct
tctggtcagaatatctccctttccatctccctctgagcagagcaataggaataggaatat
attttaagccaggtgaagtggtgcaggtctgaggtnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaaaa
gaatatattttaagaaaattcctcagctaaagtaaaaagaaaagagagataagctaggta
agattattaatcagaagtaatgcttgtctgtttaatttgccagttttaaataattcttga
aggcatttgagaggtcattatattcttttaatcagttagactttatctgaatatatgctt
tggaatatactttttcttcaaacttctaaactatgtgcaatatacagaaacaaggtcctc
tggctgtcctgctttctgcttgctttttttctctccctttcacttttctggagataattt
ttctgcctcttgtagggaattcagaggagggatcctagtgattggctttacaaatttgtg
tgggggagggattggatagagtggagatgggataggcatctgcccatcagtaggatttgg
ttgtttgtccagcctctatatgggctttaaatgctttatactttctgaccattatttttg
ccagcaaaaatgatgtagcttattttgatactacttaaatgcagtcctgtccttattcta
cccctactactccatccaaagggagactgaaggggagacattttgaaccagacatgttga
tttcctggtggcctgtacagtgagtattttgtaacatttagaattaattcagtcattcat
ttaataagtaacctaatatatgctagaaatcttctgtcttagagccaaaatatattgtaa
ttttttcatggtctaagtatctaaggctttacagtataaaagtttaataaagtcatgacc
aaggctttacaaagactgctattttgattcatgtatcacagaattcaataaaaagtcaaa
ctattatctgacatatggcagtgacaactttggagggtgtttatatggtacaaatagaag
atgctggattaggacctaggaaacctgaatgctggttccgactctgccagcgaataactg
aactagctgtgtaatgcaaagacaaccaccccatagagactttgcccctttctctacaaa
tgaggggtttgaaatcacctatctttagtttttaaattgtgactcatttatttaatgaaa
atatatggtttttaaaattttgatatcattttggtacaaatatattgtgtcaatgtttaa
atatatttatcttattttcacaagacaatggcaatgatatacaaaagactttctctggac
ttgcctcattgtggtgaatatcggttataatcatagatacttagaagacacaaaattata
cattcttacctgttagtaaaggaacatcaaagaaattcattctgtttttctgcagaaact
atcaaaatttttccacttctggggattaagataacttctgttttttatctaatactcaac
ctatctaatacaaccttgtcctagtgatgatggtagaattttataaaatagggaagtttg
ttatttgttcacctgtgaagaccttcaaggaattgaataggaaaatacctagagttttgt
ttcttgttctgatttgcttgtttatatttggccagttttgtcctgaaaatatgtttgaga
gattacatgaaaatttattttgtgactcttaatataaatgttaaaaatacatttaaacta
gtgatagtaaagaaagaatatcttaattagtgggggaaataatcccatgatcttttgtga
ttctacaacattactgtagccttaagaatctctactaatgttgtattgaaaagctgtttc
tcctacatgtgaa
--------------------------------------------------------------------------------
# Output_end: pretty
gc_object_end: repeat_grailexp --output pretty
More information about the Bioperl-l
mailing list