Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3337
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: 58761
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:9123 original size:4 final size:4
Alignment explanation
Indices: 9104--9140 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
9094 GTTGTAAAGT
*
9104 TTTA TTTT TATTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
9141 CTTAGTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:15397 original size:14 final size:16
Alignment explanation
Indices: 15367--15398 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
15357 AGAAATCGGC
15367 AAAGTATAAGCAAAGA
1 AAAGTATAAGCAAAGA
15383 AAAGTA-AAG-AAAGA
1 AAAGTATAAGCAAAGA
15397 AA
1 AA
15399 TCGAAAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.09
Consensus pattern (16 bp):
AAAGTATAAGCAAAGA
Found at i:17513 original size:22 final size:21
Alignment explanation
Indices: 17463--17514 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
17453 TTCCACGTCT
* * *
17463 TTTCTTTTGTTTCTTTTTTAA
1 TTTCTTTTCTTTCTTTCTCAA
17484 -TTCATTTTCTCTTCTTTCTCAA
1 TTTC-TTTTCT-TTCTTTCTCAA
17506 TTTCTTTTC
1 TTTCTTTTC
17515 ACTCTCAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 14 0.56
23 3 0.12
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTCTTTTCTTTCTTTCTCAA
Found at i:19245 original size:11 final size:11
Alignment explanation
Indices: 19229--19267 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
19219 GTATGCAAAT
19229 TTTTTTTTCAA
1 TTTTTTTTCAA
*
19240 TTTTTTTTCGA
1 TTTTTTTTCAA
19251 TTTTTTTT-AA
1 TTTTTTTTCAA
19261 TTTTTTT
1 TTTTTTT
19268 GAATCTACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:26163 original size:17 final size:18
Alignment explanation
Indices: 26141--26181 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
26131 CGTTTCTTTT
26141 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
26158 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
26176 T-TTTTG
1 TCTTTTG
26182 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:26165 original size:24 final size:25
Alignment explanation
Indices: 26112--26165 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
26102 AACAAATTCT
* *
26112 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
26137 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
26160 TTTTTT
1 TTTTTT
26166 ATCACTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:28439 original size:14 final size:13
Alignment explanation
Indices: 28412--28438 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28402 CTAGACCGTA
28412 TGCAATTTTTTTT
1 TGCAATTTTTTTT
28425 TGCAATTTTTTTT
1 TGCAATTTTTTTT
28438 T
1 T
28439 TTCTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (13 bp):
TGCAATTTTTTTT
Found at i:32719 original size:30 final size:30
Alignment explanation
Indices: 32623--32719 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
32613 AGCTCACTCC
* *
32623 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
32653 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
**
32683 CGGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
32713 TAGCTCA
1 TAGCTCA
32720 TTTTAGTTTA
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 2 0.04
30 39 0.81
31 7 0.15
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:34330 original size:18 final size:19
Alignment explanation
Indices: 34307--34345 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
34297 TTTATCTCAA
*
34307 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
34325 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
34344 TT
1 TT
34346 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:34384 original size:18 final size:18
Alignment explanation
Indices: 34363--34412 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
34353 AAACTCTTTT
34363 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* * *
34381 TCATTTTCTTTTTGACTC
1 TCATTCTCTTTTTCAATC
*
34399 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
34413 TTTTTCTTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.14, C:0.26, G:0.02, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:34479 original size:42 final size:42
Alignment explanation
Indices: 34416--34512 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
34406 CTTTTTCTTT
* * *
34416 TTCTTTCA-TTTCTTTGTTTCTTTTCTCGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
34457 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
34499 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
34513 CTCATAATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 7 0.14
42 44 0.86
ACGTcount: A:0.14, C:0.24, G:0.05, T:0.57
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:34490 original size:21 final size:21
Alignment explanation
Indices: 34423--34490 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
34413 TTTTTCTTTC
*
34423 ATTTCTTTGTTTCTTTTCTCG
1 ATTTCTTTGTTTCTTCTCTCG
* *****
34444 ATTTCATTCAAGATTCTCTC-
1 ATTTCTTTGTTTCTTCTCTCG
34464 ATTTTCTTTGTTTCTTCTCTCG
1 A-TTTCTTTGTTTCTTCTCTCG
34486 ATTTC
1 ATTTC
34491 ATTCAAAATC
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.07, T:0.59
Consensus pattern (21 bp):
ATTTCTTTGTTTCTTCTCTCG
Found at i:38338 original size:23 final size:22
Alignment explanation
Indices: 38286--38339 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
38276 TCCACGTCTT
*
38286 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
38308 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
38331 TTTCTTTTC
1 TTTCTTTTC
38340 ACTCTCAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 3 0.11
22 5 0.19
23 13 0.48
24 6 0.22
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39648 original size:30 final size:30
Alignment explanation
Indices: 39604--39661 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
39594 CCGCTGAATC
*
39604 TTTTTTTAAATTTTT-ATTGAATTTTTTTTT
1 TTTTTTTAAATTTTTGACTG-ATTTTTTTTT
* *
39634 TTTTTTTGACTTTTTGACTGATTTTTTT
1 TTTTTTTAAATTTTTGACTGATTTTTTT
39662 GCGGAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.16, C:0.03, G:0.07, T:0.74
Consensus pattern (30 bp):
TTTTTTTAAATTTTTGACTGATTTTTTTTT
Found at i:42759 original size:10 final size:10
Alignment explanation
Indices: 42746--42783 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
42736 AAAAAACCGA
42746 AAAAAAATTC
1 AAAAAAATTC
42756 AAAAAAAATTC
1 -AAAAAAATTC
*
42767 AAAAAAATTG
1 AAAAAAATTC
42777 AAAAAAA
1 AAAAAAA
42784 AGTGATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:42759 original size:11 final size:11
Alignment explanation
Indices: 42745--42784 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
42735 AAAAAAACCG
42745 AAAAAAAATTC
1 AAAAAAAATTC
42756 AAAAAAAATTC
1 AAAAAAAATTC
*
42767 -AAAAAAATTG
1 AAAAAAAATTC
42777 AAAAAAAA
1 AAAAAAAA
42785 GTGATTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:43133 original size:15 final size:15
Alignment explanation
Indices: 43113--43160 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
43103 TCAAAGATGG
43113 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
43128 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
43142 GTTTATGGATATAAA
1 GTTTATGGATATGAA
43157 GTTT
1 GTTT
43161 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:43140 original size:29 final size:29
Alignment explanation
Indices: 43107--43166 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
43097 AAGGATTCAA
*
43107 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
43136 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
43165 AG
1 AG
43167 GTTTGCTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:43147 original size:14 final size:14
Alignment explanation
Indices: 43107--43150 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
43097 AAGGATTCAA
43107 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
43121 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
43136 AGATGGGTTTATGG
1 AGATGGGTTTATGG
43150 A
1 A
43151 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:45478 original size:20 final size:20
Alignment explanation
Indices: 45455--45508 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
45445 AGTTTTTCCC
*
45455 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
45475 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
45495 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
45509 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:45490 original size:30 final size:30
Alignment explanation
Indices: 45455--45528 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
45445 AGTTTTTCCC
45455 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
45485 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
45515 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
45529 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:45518 original size:20 final size:20
Alignment explanation
Indices: 45455--45519 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
45445 AGTTTTTCCC
* * * *
45455 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
45475 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
45494 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
45515 AGCTC
1 AGCTC
45520 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:48566 original size:23 final size:22
Alignment explanation
Indices: 48515--48566 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
48505 CCTCGTCTTT
*
48515 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
48537 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
48560 TTCTTTT
1 TTCTTTT
48567 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Done.