Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_35339
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, 572
Length: 954
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
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: 248
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 CCTAAGCCAGAATTGCCTAAAGTTCCTGAGGTG
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG
* *** *
430 CCTAAGTTGGAATTGCCCAAAGCTCCTGAAGTG
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG
* * * * *
463 CCCAAGCCTGAATTACCCAAAGCTCCCG-AGTTG
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAG-TG
** ** * *
496 CCAAAGCTTGAATCACCAAAAGTTCCTG-AGTTA
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAG-TG
* * *
529 TCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTG
1 CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG
* * *
562 CCTAAG-CAGAAATTGCCCAAAGCTCCTGAATTG
1 CCAAAGCCAG-AATTGCCCAAAGTTCCTGAAGTG
595 CCAAA
1 CCAAA
600 AATTCCTGAG
Statistics
Matches: 246, Mismatches: 51, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
32 7 0.03
33 237 0.96
34 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (33 bp):
CCAAAGCCAGAATTGCCCAAAGTTCCTGAAGTG
Found at i:342 original size:99 final size:99
Alignment explanation
Indices: 214--431 Score: 292
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 CCTAAAGTTCCTGAGGTGCC
1 CCCAAAGCTCCTGAGTTGCC
432 TAAGTTGGAA
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
99 103 1.00
ACGTcount: A:0.32, C:0.27, 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: 68
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 TGCCTAA
1 TGCCTAA
435 GTTGGAATTG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 9 0.29
16 3 0.10
17 3 0.10
18 16 0.52
ACGTcount: A:0.26, C:0.24, G:0.24, 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 AAGTTGGAAT
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:494 original size:132 final size:132
Alignment explanation
Indices: 245--600 Score: 464
Period size: 132 Copynumber: 2.7 Consensus size: 132
235 AAATCTGAAG
* * * *
245 CACCAAAAGTTCCGGAGTTACCAAAGCCAGAATTTCCTAAAGTTCCTGAAGTGCCCAAGCCT-GA
1 CACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAG-CTGGA
* * *
309 ATTACCCAAAGCTCCTG-AGTTGCCAAAACCTGAATTACCAAAAGTTCCTGAGTTACCAAAGCCA
65 ATTGCCCAAAGCTCCTGAAG-TGCCAAAACCTGAATTACCAAAAGCTCCCGAGTTACCAAAGCCA
373 GAAT
129 GAAT
** * * * * *
377 TGCCTAAAGTTCCTGAGGTGCCTAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAGTTGGAA
1 CACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAGCTGGAA
* * * * **
442 TTGCCCAAAGCTCCTGAAGTGCCCAAGCCTGAATTACCCAAAGCTCCCGAGTTGCCAAAGCTTGA
66 TTGCCCAAAGCTCCTGAAGTGCCAAAACCTGAATTACCAAAAGCTCCCGAGTTACCAAAGCCAGA
507 AT
131 AT
* * *
509 CACCAAAAGTTCCTGAGTTATCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAGCAGAAA
1 CACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAGCTGGAA
*
574 TTGCCCAAAGCTCCTGAATTGCCAAAA
66 TTGCCCAAAGCTCCTGAAGTGCCAAAA
601 ATTCCTGAGG
Statistics
Matches: 189, Mismatches: 33, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
131 1 0.01
132 186 0.98
133 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (132 bp):
CACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAGCTGGAA
TTGCCCAAAGCTCCTGAAGTGCCAAAACCTGAATTACCAAAAGCTCCCGAGTTACCAAAGCCAGA
AT
Found at i:606 original size:51 final size:51
Alignment explanation
Indices: 538--635 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
528 ATCAAAGCCA
* * * * *
538 GAATTGCCTAAAGTTCCTGAGGTGCC-TAAGCAGAAATTGCCCAAAGCTCCT
1 GAATTGCCAAAAATTCCTGAGGTACCAAAACCAG-AATTGCCCAAAGCTCCT
589 GAATTGCCAAAAATTCCTGAGGTACCAAAACCAGAATTGCCCAAAGC
1 GAATTGCCAAAAATTCCTGAGGTACCAAAACCAGAATTGCCCAAAGC
636 GACTGAGCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 36 0.88
52 5 0.12
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (51 bp):
GAATTGCCAAAAATTCCTGAGGTACCAAAACCAGAATTGCCCAAAGCTCCT
Found at i:626 original size:33 final size:33
Alignment explanation
Indices: 589--839 Score: 191
Period size: 33 Copynumber: 7.6 Consensus size: 33
579 CAAAGCTCCT
*
589 GAATTGCCAAAAATTCCTGAGGTACCAAAACCA
1 GAATTGCCAAAAGTTCCTGAGGTACCAAAACCA
* *** * * *
622 GAATTGCCCAAAGCGACTGAGCTGCCAAAACCT
1 GAATTGCCAAAAGTTCCTGAGGTACCAAAACCA
* * * *
655 GAATTACCAAAAGTTCCTGAGGTGCCTAAGCCA
1 GAATTGCCAAAAGTTCCTGAGGTACCAAAACCA
* * ** *
688 GAATTGCCAAAAGCTCCTAAATTACCAAAACCT
1 GAATTGCCAAAAGTTCCTGAGGTACCAAAACCA
* * * * *
721 CAATTACCTAAAA-TTCCCGAGTTAACAAAACCA
1 GAATTGCC-AAAAGTTCCTGAGGTACCAAAACCA
* * *
754 GAATTGCCTAAAGTTCCAGAGGTACCGAAACCA
1 GAATTGCCAAAAGTTCCTGAGGTACCAAAACCA
* * * *
787 GAATTGCCCAAAA-CTCCTGAGTTGCCAAAACCT
1 GAATTG-CCAAAAGTTCCTGAGGTACCAAAACCA
* *
820 GAATTACCTAAAGTTCCTGA
1 GAATTGCCAAAAGTTCCTGA
840 ATTGCCTAGC
Statistics
Matches: 163, Mismatches: 51, Indels: 8
0.73 0.23 0.04
Matches are distributed among these distances:
32 8 0.05
33 146 0.90
34 9 0.06
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (33 bp):
GAATTGCCAAAAGTTCCTGAGGTACCAAAACCA
Found at i:629 original size:132 final size:128
Alignment explanation
Indices: 239--635 Score: 425
Period size: 132 Copynumber: 3.0 Consensus size: 128
229 TTGTCAAAAT
* * * * *
239 CTGAAGCACCAAAAGTTCCGGAGTTACCAAAGCCAGAATTTCCTAAAGTTCCTGAAGTGCCCAAG
1 CTGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAG
* * * *
304 CCTGAATTACCCAAAGCTCCTGAGTTGCCAAAACCTGAATTACCAAAAGTTCCTGAGTTACCAAA
66 -CTGAATTGCCCAAAGCTCCTGAATTGCCAAAACCTGAATTACCAAAA---CCAGAGTTGCCAAA
369 GC
127 GC
* ** * * * *
371 CAGAATTGCCTAAAGTTCCTGAGGTGCCTAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAG
1 CTGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAG
* * * * * *
436 TTGGAATTGCCCAAAGCTCCTGAAGTGCCCAAGCCTGAATTACCCAAAGCTCCCGAGTTGCCAAA
66 CT-GAATTGCCCAAAGCTCCTGAATTGCCAAAACCTGAATTA-CCAAA--ACCAGAGTTGCCAAA
501 GC
127 GC
* *
503 TTGAATCACCAAAAGTTCCTGAGTTATCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAG
1 CTGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAG
* ** *
568 CAGAAATTGCCCAAAGCTCCTGAATTGCCAAAAATTCCTGAGGTACCAAAACCAGAATTGCCCAA
66 CTG-AATTGCCCAAAGCTCCTGAATTGCC-AAAA--CCTGAATTACCAAAACCAGAGTTG-CCAA
633 AGC
126 AGC
636 GACTGAGCTG
Statistics
Matches: 216, Mismatches: 40, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
131 2 0.01
132 188 0.87
133 14 0.06
134 5 0.02
135 7 0.03
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (128 bp):
CTGAATCACCAAAAGTTCCTGAGTTACCAAAGCCAGAATTGCCTAAAGTTCCTGAGGTGCCTAAG
CTGAATTGCCCAAAGCTCCTGAATTGCCAAAACCTGAATTACCAAAACCAGAGTTGCCAAAGC
Found at i:767 original size:99 final size:99
Alignment explanation
Indices: 647--836 Score: 256
Period size: 99 Copynumber: 1.9 Consensus size: 99
637 ACTGAGCTGC
* * * * *
647 CAAAACCTGAATTACCAAAAGTTCCTGAGGTGCCTAAGCCAGAATTG-CCAAAAGCTCCTAAATT
1 CAAAACCAGAATTACCAAAAGTTCCAGAGGTACCGAAACCAGAATTGCCCAAAA-CTCCTAAATT
711 ACCAAAACCTCAATTACCTAAAATTCCCGAGTTAA
65 ACCAAAACCTCAATTACCTAAAATTCCCGAGTTAA
* * * * *
746 CAAAACCAGAATTGCCTAAAGTTCCAGAGGTACCGAAACCAGAATTGCCCAAAACTCCTGAGTTG
1 CAAAACCAGAATTACCAAAAGTTCCAGAGGTACCGAAACCAGAATTGCCCAAAACTCCTAAATTA
* *
811 CCAAAACCTGAATTACCTAAAGTTCC
66 CCAAAACCTCAATTACCTAAAATTCC
837 TGAATTGCCT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 72 0.92
100 6 0.08
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (99 bp):
CAAAACCAGAATTACCAAAAGTTCCAGAGGTACCGAAACCAGAATTGCCCAAAACTCCTAAATTA
CCAAAACCTCAATTACCTAAAATTCCCGAGTTAA
Done.