Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_33739
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, 495
Length: 825
ACGTcount: A:0.23, C:0.09, G:0.40, T:0.28
Found at i:222 original size:57 final size:56
Alignment explanation
Indices: 97--461 Score: 291
Period size: 57 Copynumber: 6.4 Consensus size: 56
87 AGTGGCTTCG
* * * * *
97 TATACACTGGAACCTGG-GGAGGTAGTGGTTTGTTGTATACAGGAACTGGAGGGGGCT
1 TATAGACTGGAA-CTGGTGGAGG-ACTGGTTTCTTGTATACTGGAACTGGAGGAGGCT
* * * * * *
154 TGTAGATTGGAACCGGAGGAGGGACTCGTTTCTTGTATACCGGAACTGGAGGAGGCT
1 TATAGACTGGAACTGGTGGA-GGACTGGTTTCTTGTATACTGGAACTGGAGGAGGCT
* * * **
211 TATGGACTGGAACTGGTGGAGGA-T-G----TGGT-T-CCGGAACTGGAGGAGATT
1 TATAGACTGGAACTGGTGGAGGACTGGTTTCTTGTATACTGGAACTGGAGGAGGCT
*
259 TATAGACTGGAACTGGGGGAGGACATGGTTTCTTGTATACTGGAACTGGAGGTGGATGTGGTTTC
1 TATAGACTGGAACTGGTGGAGGAC-TGGTTTCTTGTATACTGGAACTGGA---GGA---GG---C
324 T
56 T
* * **
325 TATAGACTGGAACTGGAGGAGGA-TGCGGTTTCTTGTATACTGGAACCGGAGGAGATT
1 TATAGACTGGAACTGGTGGAGGACT--GGTTTCTTGTATACTGGAACTGGAGGAGGCT
* * *
382 TATAGACTGGAACTGGTGGAGGACATGGTTTCTTATATACTGGAACTGGTGGAGGTT
1 TATAGACTGGAACTGGTGGAGGAC-TGGTTTCTTGTATACTGGAACTGGAGGAGGCT
*
439 TATAGACTGGAACAGGTGGAGGA
1 TATAGACTGGAACTGGTGGAGGA
462 TGTGGTTTTT
Statistics
Matches: 251, Mismatches: 33, Indels: 48
0.76 0.10 0.14
Matches are distributed among these distances:
48 37 0.15
49 1 0.00
50 4 0.02
51 1 0.00
54 1 0.00
55 4 0.02
56 7 0.03
57 138 0.55
58 2 0.01
59 1 0.00
60 4 0.02
63 4 0.02
64 1 0.00
66 46 0.18
ACGTcount: A:0.24, C:0.12, G:0.37, T:0.27
Consensus pattern (56 bp):
TATAGACTGGAACTGGTGGAGGACTGGTTTCTTGTATACTGGAACTGGAGGAGGCT
Found at i:267 original size:48 final size:48
Alignment explanation
Indices: 195--703 Score: 282
Period size: 48 Copynumber: 9.8 Consensus size: 48
185 CTTGTATACC
* * * *
195 GGAACTGGAGGAGGCTTATGGACTGGAACTGGTGGAGGATGTGGTTCC
1 GGAACTGGAGGAGGTTTATAGACTGGAACAGGTGGAGGATGTGGTTCT
* * * *
243 GGAACTGGAGGAGATTTATAGACTGGAACTGGGGGAGGACATGGTTTCTTGTATACT
1 GGAACTGGAGGAGGTTTATAGACTGGAACAGGTGGAGG--AT-G----TGGT-T-CT
* * *
300 GGAACTGGAGGTGGATGTGGTTTCTTATAGACTGGAACTGGAGGAGGATGCGGTTTCTT
1 GGAACTGGA---GGA---GG--T-TTATAGACTGGAACAGGTGGAGGATGTGG-TTC-T
* * **
359 GTATACTGGAACCGGAGGAGATTTATAGACTGGAACTGGTGGAGGACATGGTTTCTT
1 GGA-ACTGG-A--GGA-G-G-TTTATAGACTGGAACAGGTGGAGGATGTGG-TTC-T
** *
416 ATATACTGGAACTGGTGGAGGTTTATAGACTGGAACAGGTGGAGGATGTGGTTTT
1 GGA-ACTGG-A---G-G-AGGTTTATAGACTGGAACAGGTGGAGGATGTGGTTCT
** * * *
471 TCAACTGGTGGAGGTTTATAAACTGGAACAGGTGGAGGATGTGGTTTT
1 GGAACTGGAGGAGGTTTATAGACTGGAACAGGTGGAGGATGTGGTTCT
** * * * *
519 TCAACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTT
1 GGAACTGGAGGAGGTTTATAGACTGGAACAGGTGGAGGATGTGGTTCT
** * * * *
567 TCAACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTT
1 GGAACTGGAGGAGGTTTATAGACTGGAACAGGTGGAGGATGTGGTTCT
** * * *
615 TCAACTGGTGGAGGTTTGTAGA-TCGGAACAGGTGGAGGAAGTGGTTTTACT
1 GGAACTGGAGGAGGTTTATAGACT-GGAACAGGTGGAGGATGTGG--TT-CT
*
666 GGAACTGGAGGAGGTTTATAGACTGGAACTGGTGGAGG
1 GGAACTGGAGGAGGTTTATAGACTGGAACAGGTGGAGG
704 TTTATAGATT
Statistics
Matches: 390, Mismatches: 40, Indels: 59
0.80 0.08 0.12
Matches are distributed among these distances:
47 1 0.00
48 204 0.52
49 1 0.00
50 5 0.01
51 33 0.08
52 1 0.00
54 5 0.01
55 5 0.01
56 3 0.01
57 78 0.20
58 5 0.01
59 8 0.02
60 13 0.03
61 1 0.00
63 2 0.01
64 2 0.01
65 1 0.00
66 22 0.06
ACGTcount: A:0.24, C:0.09, G:0.38, T:0.29
Consensus pattern (48 bp):
GGAACTGGAGGAGGTTTATAGACTGGAACAGGTGGAGGATGTGGTTCT
Found at i:306 original size:33 final size:33
Alignment explanation
Indices: 258--436 Score: 160
Period size: 33 Copynumber: 5.7 Consensus size: 33
248 TGGAGGAGAT
* *
258 TTATAGACTGGAACTGGGGGAGGACATGGTTTC
1 TTATATACTGGAACTGGAGGAGGACATGGTTTC
* * **
291 TTGTATACTGGAACTGGAGGTGGATGTGGTTTC
1 TTATATACTGGAACTGGAGGAGGACATGGTTTC
* ***
324 TTATAGACTGGAACTGGAGGAGGATGCGGTTTC
1 TTATATACTGGAACTGGAGGAGGACATGGTTTC
* *
357 TTGTATACTGGAACCGGAGGA-G--A-----T-
1 TTATATACTGGAACTGGAGGAGGACATGGTTTC
* *
381 TTATAGACTGGAACTGGTGGAGGACATGGTTTC
1 TTATATACTGGAACTGGAGGAGGACATGGTTTC
*
414 TTATATACTGGAACTGGTGGAGG
1 TTATATACTGGAACTGGAGGAGG
437 TTTATAGACT
Statistics
Matches: 118, Mismatches: 19, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
24 17 0.14
25 2 0.02
27 1 0.01
32 2 0.02
33 96 0.81
ACGTcount: A:0.24, C:0.11, G:0.35, T:0.30
Consensus pattern (33 bp):
TTATATACTGGAACTGGAGGAGGACATGGTTTC
Found at i:594 original size:96 final size:96
Alignment explanation
Indices: 425--703 Score: 441
Period size: 96 Copynumber: 2.9 Consensus size: 96
415 TATATACTGG
* *
425 AACTGGTGGAGGTTTATAGACTGGAACAGGTGGAGGATGTGGTTTTTCAACTGGTGGAGGTTTAT
1 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTCAACTGGTGGAGGTTTAT
*
490 AAACTGGAACAGGTGGAGGATGTGGTTTTTC
66 AGACTGGAACAGGTGGAGGATGTGGTTTTTC
*
521 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTCAACTGGTGGAGGTTTGT
1 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTCAACTGGTGGAGGTTTAT
*
586 AGATTGGAACAGGTGGAGGATGTGGTTTTTC
66 AGACTGGAACAGGTGGAGGATGTGGTTTTTC
* * * *
617 AACTGGTGGAGGTTTGTAGATCGGAACAGGTGGAGGAAGTGGTTTTACTGGAACTGGAGGAGGTT
1 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTT--T-CAACTGGTGGAGGTT
*
682 TATAGACTGGAACTGGTGGAGG
63 TATAGACTGGAACAGGTGGAGG
704 TTTATAGATT
Statistics
Matches: 168, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
96 135 0.80
98 1 0.01
99 32 0.19
ACGTcount: A:0.23, C:0.08, G:0.39, T:0.30
Consensus pattern (96 bp):
AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTCAACTGGTGGAGGTTTAT
AGACTGGAACAGGTGGAGGATGTGGTTTTTC
Found at i:723 original size:24 final size:24
Alignment explanation
Indices: 422--724 Score: 146
Period size: 24 Copynumber: 12.5 Consensus size: 24
412 TCTTATATAC
* *
422 TGGAACTGGTGGAGGTTTATAGAC
1 TGGAACTGGTGGAGGTTTGTAGAT
* * * *
446 TGGAACAGGTGGAGG-ATGTGGTTT
1 TGGAACTGGTGGAGGTTTGTAG-AT
** * * *
470 TTCAACTGGTGGAGGTTTATAAAC
1 TGGAACTGGTGGAGGTTTGTAGAT
* * * *
494 TGGAACAGGTGGAGG-ATGTGGTTT
1 TGGAACTGGTGGAGGTTTGTAG-AT
**
518 TTCAACTGGTGGAGGTTTGTAGAT
1 TGGAACTGGTGGAGGTTTGTAGAT
* * * *
542 TGGAACAGGTGGAGG-ATGTGGTTT
1 TGGAACTGGTGGAGGTTTGTAG-AT
**
566 TTCAACTGGTGGAGGTTTGTAGAT
1 TGGAACTGGTGGAGGTTTGTAGAT
* * * *
590 TGGAACAGGTGGAGG-ATGTGGTTT
1 TGGAACTGGTGGAGGTTTGTAG-AT
**
614 TTCAACTGGTGGAGGTTTGTAGAT
1 TGGAACTGGTGGAGGTTTGTAGAT
* * * * ** *
638 CGGAACAGGTGGAGGAAGTGGTTTTAC
1 TGGAACTGGTGGAGG--TTTG-TAGAT
* * *
665 TGGAACTGGAGGAGGTTTATAGAC
1 TGGAACTGGTGGAGGTTTGTAGAT
*
689 TGGAACTGGTGGAGGTTTATAGAT
1 TGGAACTGGTGGAGGTTTGTAGAT
*
713 TGGAACAGGTGG
1 TGGAACTGGTGG
725 GTTTACGGGA
Statistics
Matches: 194, Mismatches: 74, Indels: 22
0.67 0.26 0.08
Matches are distributed among these distances:
23 13 0.07
24 150 0.77
25 15 0.08
26 2 0.01
27 14 0.07
ACGTcount: A:0.23, C:0.07, G:0.39, T:0.30
Consensus pattern (24 bp):
TGGAACTGGTGGAGGTTTGTAGAT
Done.