Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_35340
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, 592
Length: 987
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Found at i:98 original size:51 final size:51
Alignment explanation
Indices: 31--179 Score: 190
Period size: 51 Copynumber: 2.9 Consensus size: 51
21 TGAATTGCCT
* * * * *
31 AAAGTTCCGGAGTTGCCAAAGCCCGAATTGCCTGAGGTTCCCAAGTTTCCG
1 AAAGTTCCAGAGTTGCCAAAGCCAGAATTACCTAAGGTTCCCGAGTTTCCG
* * * *
82 AAAGTTCCAGAATTGCCAAAACCAGAATTACCCAAGGTTCCTGAGTTTCCG
1 AAAGTTCCAGAGTTGCCAAAGCCAGAATTACCTAAGGTTCCCGAGTTTCCG
* * *
133 AAAGTTCCAGAGTTGCCAAAGCCTGAATTTCCTAAGATTCCCGAGTT
1 AAAGTTCCAGAGTTGCCAAAGCCAGAATTACCTAAGGTTCCCGAGTT
180 GAAAAAACCT
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 82 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.25
Consensus pattern (51 bp):
AAAGTTCCAGAGTTGCCAAAGCCAGAATTACCTAAGGTTCCCGAGTTTCCG
Found at i:145 original size:18 final size:18
Alignment explanation
Indices: 74--146 Score: 53
Period size: 18 Copynumber: 4.2 Consensus size: 18
64 GAGGTTCCCA
74 AGTTTCCGAAAGTTCCAG
1 AGTTTCCGAAAGTTCCAG
* * *
92 AATTGCC-AAA--ACCAG
1 AGTTTCCGAAAGTTCCAG
* * * * *
107 AATTACCCAAGGTTCCTG
1 AGTTTCCGAAAGTTCCAG
125 AGTTTCCGAAAGTTCCAG
1 AGTTTCCGAAAGTTCCAG
143 AGTT
1 AGTT
147 GCCAAAGCCT
Statistics
Matches: 40, Mismatches: 12, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
15 10 0.25
16 2 0.05
17 3 0.08
18 25 0.62
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (18 bp):
AGTTTCCGAAAGTTCCAG
Found at i:305 original size:33 final size:33
Alignment explanation
Indices: 265--599 Score: 273
Period size: 33 Copynumber: 10.2 Consensus size: 33
255 TCCGGAGTTA
* *
265 CCAAAGCCAGAATTTCCTAAAGTTCCTGAAGTG
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG
* * * *
298 CCCAAGCCTGAATTACCCAAAGCTCCTG-AGTTG
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAG-TG
* * * * *
331 CCAAAACCTGAATTACCAAAAGTTCCTG-AGTTA
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAG-TG
* *
364 CCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTG
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG
* * * *
397 CCTAAGCCAGAATTGCCTAAAGTTCCTGAGGTA
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG
* * * *
430 CCTAAGTCGGAATTGCCCAAAGCTCCTGAAGTG
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG
* * * * *
463 CCCAAGCCTGAATTACCCAAAGCTCCCG-AGTTG
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAG-TG
* ** ** * *
496 CCAAAACTTGAATCACCAAAAGTTCCTG-AGTTA
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAG-TG
*
529 CCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTG
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG
* * *
562 CCTAAGCCAGAATTGCCCAAAGCTCCTGAATTG
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG
595 CCAAA
1 CCAAA
600 AATTCCTGAG
Statistics
Matches: 249, Mismatches: 49, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
32 4 0.02
33 242 0.97
34 3 0.01
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (33 bp):
CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG
Found at i:329 original size:66 final size:66
Alignment explanation
Indices: 250--599 Score: 319
Period size: 66 Copynumber: 5.3 Consensus size: 66
240 TGAAGCACCA
* * * * * * *
250 AAAGTTCCGGAGTTACCAAAGCCAGAATTTCCTAAAGTTCCTGAAGTGCCCAAGCCTGAATTACC
1 AAAGCTCCTGAGTTGCCAAAGCCAGAATTACCTAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCC
315 C
66 C
* * * *
316 AAAGCTCCTGAGTTGCCAAAACCTGAATTACCAAAAGTTCCTG-AGTTACCAAAGCCAGAATTGC
1 AAAGCTCCTGAGTTGCCAAAGCCAGAATTACCTAAAGTTCCTGAAG-TGCCAAAGCCAGAATTGC
*
380 CT
65 CC
* * * * * * * * *
382 AAAGTTCCTGAGGTGCCTAAGCCAGAATTGCCTAAAGTTCCTGAGGTACCTAAGTCGGAATTGCC
1 AAAGCTCCTGAGTTGCCAAAGCCAGAATTACCTAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCC
447 C
66 C
* * * * * * ** **
448 AAAGCTCCTGAAG-TGCCCAAGCCTGAATTACCCAAAGCTCCCG-AGTTGCCAAAACTTGAATCA
1 AAAGCTCCTG-AGTTGCCAAAGCCAGAATTACCTAAAGTTCCTGAAG-TGCCAAAGCCAGAATTG
*
511 CCA
64 CCC
* * * *
514 AAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTGCCTAAGCCAGAATTGCC
1 AAAGCTCCTGAGTTGCCAAAGCCAGAATTACCTAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCC
579 C
66 C
*
580 AAAGCTCCTGAATTGCCAAA
1 AAAGCTCCTGAGTTGCCAAA
600 AATTCCTGAG
Statistics
Matches: 219, Mismatches: 59, Indels: 12
0.76 0.20 0.04
Matches are distributed among these distances:
65 5 0.02
66 209 0.95
67 5 0.02
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (66 bp):
AAAGCTCCTGAGTTGCCAAAGCCAGAATTACCTAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCC
C
Found at i:342 original size:99 final size:99
Alignment explanation
Indices: 214--426 Score: 291
Period size: 99 Copynumber: 2.2 Consensus size: 99
204 TCCAGAGATG
* * * * *
214 CCCAATGCTCCTAAATTGTCAAAATCTGAAGCACCAAAAGTTCCGGAGTTACCAAAGCCAGAATT
1 CCCAAAGCTCCTGAGTTGCCAAAACCTGAAGCACCAAAAGTTCCGGAGTTACCAAAGCCAGAATT
* *
279 TCCTAAAGTTCCTGAAGTGCCCAAGCCTGAATTA
66 GCCTAAAGTTCCTGAAGTGCCCAAGCCAGAATTA
** *
313 CCCAAAGCTCCTGAGTTGCCAAAACCTGAATTACCAAAAGTTCCTGAGTTACCAAAGCCAGAATT
1 CCCAAAGCTCCTGAGTTGCCAAAACCTGAAGCACCAAAAGTTCCGGAGTTACCAAAGCCAGAATT
* * *
378 GCCTAAAGTTCCTGAGGTGCCTAAGCCAGAATTG
66 GCCTAAAGTTCCTGAAGTGCCCAAGCCAGAATTA
* *
412 CCTAAAGTTCCTGAG
1 CCCAAAGCTCCTGAG
427 GTACCTAAGT
Statistics
Matches: 99, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (99 bp):
CCCAAAGCTCCTGAGTTGCCAAAACCTGAAGCACCAAAAGTTCCGGAGTTACCAAAGCCAGAATT
GCCTAAAGTTCCTGAAGTGCCCAAGCCAGAATTA
Found at i:364 original size:18 final size:17
Alignment explanation
Indices: 304--368 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 17
294 AGTGCCCAAG
*
304 CCTGAATTACCCAAAGCT
1 CCTGAATTACCAAAAG-T
* *
322 CCTGAGTTGCCAAAA--
1 CCTGAATTACCAAAAGT
337 CCTGAATTACCAAAAGTT
1 CCTGAATTACCAAAAG-T
*
355 CCTGAGTTACCAAA
1 CCTGAATTACCAAA
369 GCCAGAATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 13 0.34
18 25 0.66
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (17 bp):
CCTGAATTACCAAAAGT
Found at i:400 original size:18 final size:18
Alignment explanation
Indices: 377--434 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
367 AAGCCAGAAT
377 TGCCTAAAGTTCCTGAGG
1 TGCCTAAAGTTCCTGAGG
* **
395 TGCCT-AAG--CCAGAAT
1 TGCCTAAAGTTCCTGAGG
410 TGCCTAAAGTTCCTGAGG
1 TGCCTAAAGTTCCTGAGG
*
428 TACCTAA
1 TGCCTAA
435 GTCGGAATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
15 9 0.30
16 3 0.10
17 3 0.10
18 15 0.50
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (18 bp):
TGCCTAAAGTTCCTGAGG
Found at i:466 original size:18 final size:18
Alignment explanation
Indices: 443--488 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 18
433 AAGTCGGAAT
443 TGCCCAAAGCTCCTGAAG
1 TGCCCAAAGCTCCTGAAG
*
461 TGCCC-AAG--CCTGAAT
1 TGCCCAAAGCTCCTGAAG
*
476 TACCCAAAGCTCC
1 TGCCCAAAGCTCC
489 CGAGTTGCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
15 10 0.43
16 3 0.13
17 3 0.13
18 7 0.30
ACGTcount: A:0.28, C:0.37, G:0.17, T:0.17
Consensus pattern (18 bp):
TGCCCAAAGCTCCTGAAG
Found at i:600 original size:99 final size:99
Alignment explanation
Indices: 247--600 Score: 327
Period size: 99 Copynumber: 3.6 Consensus size: 99
237 ATCTGAAGCA
* * * * * * *
247 CCAAAAGTTCC-GGAGTTACCAAAGCCAGAATTTCCTAAAGTTCCTGAAGTGCCCAAGCCTGAAT
1 CCAAAAGTTCCTGAAG-TGCCAAAGCCAGAATTGCCCAAAGCTCCTGAAGTGCCAAAACCTGAAT
* * * * * *
311 TACCCAAAGCTCCTGAGTTGCCAAAACCTGAATTA
65 TACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTG
* * * * * * *
346 CCAAAAGTTCCTG-AGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAGCCAGAAT
1 CCAAAAGTTCCTGAAG-TGCCAAAGCCAGAATTGCCCAAAGCTCCTGAAGTGCCAAAACCTGAAT
* * * * * *
410 TGCCTAAAGTTCCTGAGGTACCTAAGTCGGAATTG
65 TACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTG
* * * * * * *
445 CCCAAAGCTCCTGAAGTGCCCAAGCCTGAATTACCCAAAGCTCCCG-AGTTGCCAAAACTTGAAT
1 CCAAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCCCAAAGCTCCTGAAG-TGCCAAAACCTGAAT
*
509 CACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTG
65 TACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTG
* * *
544 CCTAAAGTTCCTGAAGTGCCTAAGCCAGAATTGCCCAAAGCTCCTGAATTGCCAAAA
1 CCAAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCCCAAAGCTCCTGAAGTGCCAAAA
601 ATTCCTGAGT
Statistics
Matches: 209, Mismatches: 42, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
98 1 0.00
99 204 0.98
100 4 0.02
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (99 bp):
CCAAAAGTTCCTGAAGTGCCAAAGCCAGAATTGCCCAAAGCTCCTGAAGTGCCAAAACCTGAATT
ACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTG
Found at i:606 original size:18 final size:18
Alignment explanation
Indices: 571--641 Score: 51
Period size: 18 Copynumber: 4.1 Consensus size: 18
561 GCCTAAGCCA
* **
571 GAATTGCCCAAAGCTCCT
1 GAATTGCCAAAAATTCCT
589 GAATTGCCAAAAATTCCT
1 GAATTGCCAAAAATTCCT
* *
607 GAGTT--CACAAAA--CCA
1 GAATTGCCA-AAAATTCCT
*
622 GAATTGCCTAAAATTCCT
1 GAATTGCCAAAAATTCCT
640 GA
1 GA
642 GGTACCAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
15 6 0.15
16 6 0.15
17 5 0.12
18 23 0.57
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (18 bp):
GAATTGCCAAAAATTCCT
Found at i:606 original size:51 final size:51
Alignment explanation
Indices: 551--750 Score: 146
Period size: 51 Copynumber: 4.0 Consensus size: 51
541 TTGCCTAAAG
* *
551 TTCCTGAAGTGCCTAAGCCAGAATTGCCCAAAGCTCCTGAATTGCCAAAAA
1 TTCCTGAAGTGCCTAAGCCAGAATTGCCCAAAACTCCTGAATTACCAAAAA
* * * * * **
602 TTCCTG-AGTTCACAAAACCAGAATTGCCTAAAATTCCTGAGGTACC-AAAA
1 TTCCTGAAGTGC-CTAAGCCAGAATTGCCCAAAACTCCTGAATTACCAAAAA
* * * * * *
652 --CCAGAATTGCCTAAAGTGACTGAGTTG-CCAAAACT--TGAATTACCAAAAG
1 TTCCTGAAGTGCCT-AA--GCCAGAATTGCCCAAAACTCCTGAATTACCAAAAA
* *
701 TTTCTGAGGTGCCTAAGCCAGAATTG-CCAAAAGCTCCTGAATTACCAAAA
1 TTCCTGAAGTGCCTAAGCCAGAATTGCCCAAAA-CTCCTGAATTACCAAAA
751 CCTCAATTAC
Statistics
Matches: 109, Mismatches: 29, Indels: 22
0.68 0.18 0.14
Matches are distributed among these distances:
48 24 0.22
49 10 0.09
50 16 0.15
51 59 0.54
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (51 bp):
TTCCTGAAGTGCCTAAGCCAGAATTGCCCAAAACTCCTGAATTACCAAAAA
Found at i:607 original size:150 final size:150
Alignment explanation
Indices: 439--750 Score: 329
Period size: 150 Copynumber: 2.1 Consensus size: 150
429 ACCTAAGTCG
* * * * * * * *
439 GAATTGCCCAAAGCTCCTGAAGTGC-CCAAGCCTGAATTACCCAAAGCTCCCGAGTTGCCAAAAC
1 GAATTGCCAAAAACTCCTG-AGTGCACAAAACCAGAATTACCCAAAACTCCCGAGGTACCAAAAC
** ** * * *
503 TTGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAAGTGCCTAAG
65 CAGAATCACCAAAAGTGACTGAGTTACCAAAACCAGAATTACCAAAAGTTCCTGAAGTGCCTAAG
*
568 CCAGAATTGCCCAAAGCTCCT
130 CCAGAATTGCCAAAAGCTCCT
* * * * * *
589 GAATTGCCAAAAATTCCTGAGTTCACAAAACCAGAATTGCCTAAAATTCCTGAGGTACCAAAACC
1 GAATTGCCAAAAACTCCTGAGTGCACAAAACCAGAATTACCCAAAACTCCCGAGGTACCAAAACC
** * * ** * *
654 AGAATTGCCTAAAGTGACTGAGTTGCCAAAACTTGAATTACCAAAAGTTTCTGAGGTGCCTAAGC
66 AGAATCACCAAAAGTGACTGAGTTACCAAAACCAGAATTACCAAAAGTTCCTGAAGTGCCTAAGC
719 CAGAATTGCCAAAAGCTCCT
131 CAGAATTGCCAAAAGCTCCT
*
739 GAATTACCAAAA
1 GAATTGCCAAAA
751 CCTCAATTAC
Statistics
Matches: 130, Mismatches: 31, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
149 4 0.03
150 126 0.97
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (150 bp):
GAATTGCCAAAAACTCCTGAGTGCACAAAACCAGAATTACCCAAAACTCCCGAGGTACCAAAACC
AGAATCACCAAAAGTGACTGAGTTACCAAAACCAGAATTACCAAAAGTTCCTGAAGTGCCTAAGC
CAGAATTGCCAAAAGCTCCT
Found at i:764 original size:99 final size:98
Alignment explanation
Indices: 616--866 Score: 268
Period size: 99 Copynumber: 2.5 Consensus size: 98
606 TGAGTTCACA
* * * * * **
616 AAACCAGAATTGCCTAAAATTCCTGAGGTACCAAAACCAGAATTGCCTAAAGTGACTGAGTTGCC
1 AAACCAGAATTGCC-AAAACTCCTGAGTTACCAAAACCTGAATTACCTAAAGTGACCGAGTTAAC
** * * * *
681 AAAACTTGAATTACCAAAAGTTTCTGAGGTGCCT
65 AAAACCAGAATTACCAAAAGTTCCAGAGGTACCG
* * * * ** *
715 AAGCCAGAATTGCCAAAAGCTCCTGAATTACCAAAACCTCAATTACCTAAAATTCCCGGGTTAAC
1 AAACCAGAATTGCCAAAA-CTCCTGAGTTACCAAAACCTGAATTACCTAAAGTGACCGAGTTAAC
* *
780 AAAACCAGAATTGCCTAAAGTTCCAGAGGTACCG
65 AAAACCAGAATTACCAAAAGTTCCAGAGGTACCG
*
814 AAACCAGAATTGCCCAAAACTCCTGAGTTGCCAAAACCTGAATTACCTAAAGT
1 AAACCAGAATTG-CCAAAACTCCTGAGTTACCAAAACCTGAATTACCTAAAGT
867 TCCTGAATTG
Statistics
Matches: 123, Mismatches: 27, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
98 4 0.03
99 113 0.92
100 6 0.05
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (98 bp):
AAACCAGAATTGCCAAAACTCCTGAGTTACCAAAACCTGAATTACCTAAAGTGACCGAGTTAACA
AAACCAGAATTACCAAAAGTTCCAGAGGTACCG
Found at i:878 original size:33 final size:33
Alignment explanation
Indices: 589--872 Score: 237
Period size: 33 Copynumber: 8.6 Consensus size: 33
579 CAAAGCTCCT
* *
589 GAATTGCCAAAAATTCCTGAGTT-CACAAAACCA
1 GAATTGCCTAAAGTTCCTGAGTTAC-CAAAACCA
* *
622 GAATTGCCTAAAATTCCTGAGGTACCAAAACCA
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
** * **
655 GAATTGCCTAAAGTGACTGAGTTGCCAAAACTT
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
* * * * * * *
688 GAATTACCAAAAGTTTCTGAGGTGCCTAAGCCA
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
* * * *
721 GAATTGCCAAAAGCTCCTGAATTACCAAAACCT
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
* * * * * *
754 CAATTACCTAAAATTCCCGGGTTAACAAAACCA
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
* * *
787 GAATTGCCTAAAGTTCCAGAGGTACCGAAACCA
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
* ** * *
820 GAATTGCCCAAAACTCCTGAGTTGCCAAAACCT
1 GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
*
853 GAATTACCTAAAGTTCCTGA
1 GAATTGCCTAAAGTTCCTGA
873 ATTGCCTAGC
Statistics
Matches: 193, Mismatches: 57, Indels: 2
0.77 0.23 0.01
Matches are distributed among these distances:
33 192 0.99
34 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (33 bp):
GAATTGCCTAAAGTTCCTGAGTTACCAAAACCA
Done.