Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01334.F5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4268
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Found at i:750 original size:282 final size:282
Alignment explanation
Indices: 246--1627 Score: 1808
Period size: 282 Copynumber: 4.9 Consensus size: 282
236 CATTGTTTAC
* * * * ** * * * *
246 ACCTGAAGAATGCGGCAGCTTAGCTGGATCAGATTCCCGG-CCTTGTTGGACAGCATTATGTA-A
1 ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATT-TCGGAAGTTGTCGAACAGCTTTATCTATA
* * * *** *
309 TTCCTTCAGAGATCTTGCCTCCACAACAGGTAATTTTGATTTGTTACCTGTGTCATCCTGTG--G
65 -TCCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGAT-CTG-GCAG
* * * * * *
372 TTCCACAATCATACTTGGAACAATTACTTCCTCAACATCAGCTCCTTCATGCAGTTGCTTAAAAG
127 TTTCTCAATCATACTCGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAG
*
437 CCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAATCTCAGTCTTC
192 CCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAGTCTTC
*
502 ATATCTTTTGATGGTTCATTCCTTGA
257 ATATCTTTTGATGATTCATTCCTTGA
* * * *
528 ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTTCGGAAGTTGTTGAATAGCTTTGTCTATGT
1 ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTTCGGAAGTTGTCGAACAGCTTTATCTATAT
*
593 CCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGGTCTGGCAGTTTC
66 CCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTC
*
658 TCAATCATACTCGGAACAATTACTTCCTCAATGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAA
131 TCAATCATACTCGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAA
* * * ** **
723 ATCAATATCTTCGGCTGGTCTTGCTTCAAAAACTGGCAGCACCACATTAGTCTTGGTCTTCGCAT
196 ATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAGTCTTCATAT
*
788 CTTTTGATGATTCAATCCTTGA
261 CTTTTGATGATTCATTCCTTGA
* ** * * * *
810 GCCTGAAGAA--T---A--T--GCTGGATTAGATTTCACAAGTTGTTGAATAGCTTTGTCTAAAT
1 ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTTCGGAAGTTGTCGAACAGCTTTATCTATAT
* *
866 CCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCCAAGATCTGGCAGTTTC
66 CCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTC
* * **
931 TCAATCATACTCGGAACAATTACTTCCTCGACATTGACTCCTTCATGAAGTTGCTTAAAAGCCAA
131 TCAATCATACTCGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAA
* * * * * *
996 ATCAATATCTTCTGCTGACCTTGTTTCAAGAACTGGAAGCACCACATTAGTCTCAGTATCCTTAT
196 ATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAGTCTTCATAT
* *
1061 CTGTTAATGATTCATTCCTT-A
261 CTTTTGATGATTCATTCCTTGA
* *
1082 AGCCTGAAGAATGTGGCGGCTCAGCTGGATTAGA-TTCTGGAAGTTGTCGAACAGCTTTATGTAT
1 A-CCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTTC-GGAAGTTGTCGAACAGCTTTATCTAT
*
1146 ATCCTCCAGAGATCTTGCCTCGACAATAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTT
64 ATCCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTT
* *
1211 TCTCGATCATACTTGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCC
129 TCTCAATCATACTCGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCC
* * * *
1276 AAATCAATATCTTCAGCTGATCTTGGTTCAAGAA-TAGGCAGCACCACATTAGTCTCAGTTTTCG
194 AAATCAATATCTTCTGCTGATCTTGCTTCAAGAACT-GGCAGCACCACATTAGTCTCAGTCTTCA
1340 TATCTTTTGATGATTCATTCCTTGA
258 TATCTTTTGATGATTCATTCCTTGA
* * * *
1365 GCCTGAAGAATGTGGCGGCTCAGCTGGATTAGATTCCGGAAGTTGTCGAACAGCTTTATGTATAT
1 ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTTCGGAAGTTGTCGAACAGCTTTATCTATAT
* * *
1430 CCTCCAGAGACCTTGCCTCGAAAACAGGTAATTTTGATTTGTTACCTCCATGATCTGGCAGTTTC
66 CCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTC
** * * *
1495 TTGATCATACTCGGAACAGTTACTTCCTCAACGTCGACTCCTTCATGAAGTTGCTTAAAAGTCAA
131 TCAATCATACTCGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAA
* ** *
1560 ATAAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACTGCATTAGTCTTC-GCCTTCATA
196 ATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTC-TCAGTCTTCATA
1624 TCTT
260 TCTT
1628 CCTGTAACAA
Statistics
Matches: 969, Mismatches: 111, Indels: 40
0.87 0.10 0.04
Matches are distributed among these distances:
272 1 0.00
273 240 0.25
275 2 0.00
277 1 0.00
280 3 0.00
281 10 0.01
282 706 0.73
283 6 0.01
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (282 bp):
ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTTCGGAAGTTGTCGAACAGCTTTATCTATAT
CCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTC
TCAATCATACTCGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAA
ATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAGTCTTCATAT
CTTTTGATGATTCATTCCTTGA
Found at i:1318 original size:555 final size:558
Alignment explanation
Indices: 295--1612 Score: 1855
Period size: 555 Copynumber: 2.4 Consensus size: 558
285 GCCTTGTTGG
* * * * * **
295 ACAGCATTATGTAATTCCTTCAGAGATCTTGCCTCCACAACAGGTAATTTTGATTTGTTACCTGT
1 ACAGCTTTATCTAAATCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTACCTCC
* * * * * *
360 GTCATCCTGTG--GTTCCACAATCATACTTGGAACAATTACTTCCTCAACA-TCAGCTCCTTCAT
66 ATGAT-CTG-GCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCAACATTGA-CTCCTTCAT
*
422 GCAGTTGCTTAAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACA
128 GAAGTTGCTTAAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACA
* * * * * *
487 TTAATCTCAGTCTTCATATCTTTTGATGGTTCATTCCTTGAACCTGAAGAATGTGGCAGCTCAGC
193 TTAGTCTCAGTATCCATATCTGTTAATGATTCATTCCTTGAACCTGAAGAATGTGGCAGCTCAGC
* * * *
552 TGGATTAGATTTCGGAAGTTGTTGAATAGCTTTGTCTATGTCCTCCAGAGATCTTGCCTCGACAA
258 TGGATTAGATTTCGGAAGTTGTCGAACAGCTTTATCTATATCCTCCAGAGATCTTGCCTCGACAA
*
617 CAGGTAATTTTGATTTGTTATCTCCATGGTCTGGCAGTTTCTCAATCATACTCGGAACAATTACT
323 CAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACT
* * *
682 TCCTCAATGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCGGCTGGTCTTGC
388 TCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAGCTGATCTTGC
**
747 TTCAAAAACTGGCAGCACCACATTAGTCTTGGTCTTCGCATCTTTTGATGATTCAATCCTTGAGC
453 TTCAAAAACTGGCAGCACCACATTAGTCTCAGTCTTCGCATCTTTTGATGATTCAATCCTTGAGC
* *
812 CTGAAGAA-T-AT-GCTGGATTAGATTTCACAAGTTGTTGA
518 CTGAAGAAGTGATAGCTGGATTAGATTCCACAAGTTGTCGA
* * *
850 ATAGCTTTGTCTAAATCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCC
1 ACAGCTTTATCTAAATCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTACCTCC
* *
915 AAGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCGACATTGACTCCTTCATGAA
66 ATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCAACATTGACTCCTTCATGAA
* * *
980 GTTGCTTAAAAGCCAAATCAATATCTTCTGCTGACCTTGTTTCAAGAACTGGAAGCACCACATTA
131 GTTGCTTAAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTA
* *
1045 GTCTCAGTATCCTTATCTGTTAATGATTCATTCCTT-AAGCCTGAAGAATGTGGCGGCTCAGCTG
196 GTCTCAGTATCCATATCTGTTAATGATTCATTCCTTGAA-CCTGAAGAATGTGGCAGCTCAGCTG
* *
1109 GATTAGA-TTCTGGAAGTTGTCGAACAGCTTTATGTATATCCTCCAGAGATCTTGCCTCGACAAT
260 GATTAGATTTC-GGAAGTTGTCGAACAGCTTTATCTATATCCTCCAGAGATCTTGCCTCGACAAC
* *
1173 AGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTCTCGATCATACTTGGAACAATTACTT
324 AGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTT
*
1238 CCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAGCTGATCTTGGT
389 CCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAGCTGATCTTGCT
* * * *
1303 TCAAGAA-TAGGCAGCACCACATTAGTCTCAGTTTTCGTATCTTTTGATGATTCATTCCTTGAGC
454 TCAAAAACT-GGCAGCACCACATTAGTCTCAGTCTTCGCATCTTTTGATGATTCAATCCTTGAGC
* **
1367 CTGAAGAATGTGGCGGCTCAGCTGGATTAGATTCCGGAAGTTGTCGA
518 CTGAAGAA-GT----GAT-AGCTGGATTAGATTCCACAAGTTGTCGA
* * *
1414 ACAGCTTTATGTATATCCTCCAGAGACCTTGCCTCGAA-AACAGGTAATTTTGATTTGTTACCTC
1 ACAGCTTTATCTAAATCCTCCAGAGATCTTGCCTC-AACAACAGGTAATTTTGATTTGTTACCTC
** * * *
1478 CATGATCTGGCAGTTTCTTGATCATACTCGGAACAGTTACTTCCTCAACGTCGACTCCTTCATGA
65 CATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCAACATTGACTCCTTCATGA
* * **
1543 AGTTGCTTAAAAGTCAAATAAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACTGCATT
130 AGTTGCTTAAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATT
1608 AGTCT
195 AGTCT
1613 TCGCCTTCAT
Statistics
Matches: 673, Mismatches: 74, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
553 1 0.00
554 9 0.01
555 458 0.68
556 2 0.00
557 1 0.00
562 1 0.00
564 199 0.30
565 2 0.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (558 bp):
ACAGCTTTATCTAAATCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTACCTCC
ATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCAACATTGACTCCTTCATGAA
GTTGCTTAAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTA
GTCTCAGTATCCATATCTGTTAATGATTCATTCCTTGAACCTGAAGAATGTGGCAGCTCAGCTGG
ATTAGATTTCGGAAGTTGTCGAACAGCTTTATCTATATCCTCCAGAGATCTTGCCTCGACAACAG
GTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCC
TCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAGCTGATCTTGCTTC
AAAAACTGGCAGCACCACATTAGTCTCAGTCTTCGCATCTTTTGATGATTCAATCCTTGAGCCTG
AAGAAGTGATAGCTGGATTAGATTCCACAAGTTGTCGA
Done.