Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2223
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: 44055
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Found at i:12803 original size:12 final size:12
Alignment explanation
Indices: 12786--12810 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12776 TGACATCTCG
12786 TATGATATTTGA
1 TATGATATTTGA
12798 TATGATATTTGA
1 TATGATATTTGA
12810 T
1 T
12811 GCATTTCCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TATGATATTTGA
Found at i:13106 original size:28 final size:28
Alignment explanation
Indices: 13066--13135 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
13056 ATAGTAAGTC
*
13066 CGCACACTTAGTGCT-TAATAATCAAACT
1 CGCACACTTAGTGCTAT-ACAATCAAACT
*
13094 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
*
13122 CGCACAGTTAGTGC
1 CGCACACTTAGTGC
13136 CAATCTCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 37 0.97
29 1 0.03
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:14447 original size:33 final size:33
Alignment explanation
Indices: 14405--14471 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
14395 TTACATATTC
14405 CCCTATCATATTTTCTTAAGTTCTCAACTAAGT
1 CCCTATCATATTTTCTTAAGTTCTCAACTAAGT
14438 CCCTATCATATTTTCTTAAGTTCTCAACTAAGT
1 CCCTATCATATTTTCTTAAGTTCTCAACTAAGT
14471 C
1 C
14472 AATCACATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.42
Consensus pattern (33 bp):
CCCTATCATATTTTCTTAAGTTCTCAACTAAGT
Found at i:20618 original size:12 final size:12
Alignment explanation
Indices: 20601--20625 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20591 TGACATCTCG
20601 TATGATATTTGA
1 TATGATATTTGA
20613 TATGATATTTGA
1 TATGATATTTGA
20625 T
1 T
20626 GCATTTCCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TATGATATTTGA
Found at i:26546 original size:40 final size:39
Alignment explanation
Indices: 26448--26708 Score: 260
Period size: 40 Copynumber: 6.6 Consensus size: 39
26438 TCCTCGTTCA
* * * * *
26448 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
* ** *
26487 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
26526 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
* *
26566 AAAGGCCTTCGGGGCTTAACCCGGATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
*
26605 AATGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 AATGCCTTCGGGACTTAACCCGG-ATTTAGTATCTCGCAC
** * * *
26644 AAATGCCTTC-GGATCTTAGTCCGGATATATTCA-CTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGT-ATC-TCGCAC
* *
26685 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
26709 CAGCATTCAA
Statistics
Matches: 193, Mismatches: 21, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
38 22 0.11
39 65 0.34
40 97 0.50
41 9 0.05
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
Found at i:26668 original size:118 final size:119
Alignment explanation
Indices: 26413--26708 Score: 293
Period size: 118 Copynumber: 2.5 Consensus size: 119
26403 AAATCACGTA
* * ** * *
26413 CCTTCGGGATTTAA-CCGGATATAGCTC-C-TCGTTCAAATGCCTTCGGGACATAGCCCGGTTTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGATTT
*
26475 AGTAACTCACACAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
64 AGTAACTCACACAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACAAATG
* * * *
26531 CCTTCGGGACTTAACCCGGATTTAGT-A-TCTCGCACAAAGGCCTTCGGGGCTTAACCCGGATTT
1 CCTTCGGGACTTAACCCGGATATAGTCACT-TAGCACAAA-GCCTTCGGGACTTAGCCCGGATTT
* * * * ** *
26594 -GTATCTCGCACAATGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACAAATG
64 AGTAACTCACACAATGCCTTCGGGACATAACCCGG-ATTTAACAACTCGCACAAATG
** *
26649 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
26709 CAGCATTCAA
Statistics
Matches: 146, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
117 3 0.02
118 93 0.64
119 49 0.34
120 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (119 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGATTTAG
TAACTCACACAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACAAATG
Found at i:26669 original size:78 final size:79
Alignment explanation
Indices: 26448--26661 Score: 247
Period size: 78 Copynumber: 2.7 Consensus size: 79
26438 TCCTCGTTCA
* * * * * * *
26448 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGG-GACATAACCCGGA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGAG-CTTAACCCGGA
** *
26511 TTTAACAACTCGCACG
65 TTT-GTATCTCGCACG
*
26527 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGAGCTTAACCCGGAT
26592 TTGTATCTCGCAC-
66 TTGTATCTCGCACG
* * *
26605 AATGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACAAATGCCTTCGGATCTTA
1 AATGCCTTCGGGACTTAACCCGG-ATTTAGTATCTCGCACAAAGGCCTTCGGAGCTTA
26662 GTCCGGATAT
Statistics
Matches: 118, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
78 48 0.41
79 46 0.39
80 23 0.19
81 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGAGCTTAACCCGGAT
TTGTATCTCGCACG
Found at i:26717 original size:41 final size:41
Alignment explanation
Indices: 26640--26717 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
26630 TTTGTATCTC
* * *
26640 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
26681 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
26718 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:34391 original size:39 final size:40
Alignment explanation
Indices: 34346--34602 Score: 257
Period size: 39 Copynumber: 6.7 Consensus size: 40
34336 GCTCCTCGTT
* * * *
34346 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
34386 C-AATGCCTTCGGGACTTAACCCGGATTTA-AAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
34424 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCG--
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
34462 CAAAGGCCTTCGGG-CTTAACCCGGATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
34500 CAAATGCCTTC-GG-CTTAACCCGGAATT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
34537 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
34578 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
34603 CAGCATTCAA
Statistics
Matches: 188, Mismatches: 20, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
36 8 0.04
37 52 0.28
38 30 0.16
39 63 0.34
40 24 0.13
41 11 0.06
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:34562 original size:76 final size:78
Alignment explanation
Indices: 34346--34602 Score: 249
Period size: 76 Copynumber: 3.3 Consensus size: 78
34336 GCTCCTCGTT
* * ** * *
34346 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAATGCCTTC-GGACTTAACCCGG
34410 ATTTAAAACTCGCA
65 ATTTAAAACTCGCA
* * * *
34424 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCG--CAAAGGCCTTCGGGCTTAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAATGCCTTCGGACTTAACCCGGA
** *
34487 TTTGTATCTCGCA
66 TTTAAAACTCGCA
**
34500 CAAATGCCTTC-GG-CTTAACCCGGAATT-GTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAATGCCTTCGGA-CTTAACCCGG
* ** *
34562 ATATATTCACTTAGCA
65 ATTTA-AAAC-TCGCA
*
34578 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
34603 CAGCATTCAA
Statistics
Matches: 148, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
73 8 0.05
74 13 0.09
75 14 0.09
76 45 0.30
77 16 0.11
78 42 0.28
79 10 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAATGCCTTCGGACTTAACCCGGA
TTTAAAACTCGCA
Found at i:34611 original size:41 final size:41
Alignment explanation
Indices: 34534--34611 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
34524 ATTGTATCTC
* * *
34534 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
34575 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
34612 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:37455 original size:39 final size:38
Alignment explanation
Indices: 37253--37457 Score: 191
Period size: 39 Copynumber: 5.3 Consensus size: 38
37243 GGACTAAGAT
* * * *
37253 CCGAAGGCATTGTGCGAGATACAAAATTCGTGGTTAAGCC
1 CCGAAGGCATTGTGCGAGATACTAAA-TC-CGGTTATGTC
*
37293 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTA-GCC
1 CCGAAGGCA-TTGTGCGAGATACTAAA-TCC-GGTTATGTC
* *
37332 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGTTAAGTC
1 CCGAAGG-CATTGTGCGAGATACTAAATCCGGTTATGTC
* * **
37371 CCGAAGGCATTCTGCGAGTTTGTAAATCCGGTTATGT-
1 CCGAAGGCATTGTGCGAGATACTAAATCCGGTTATGTC
* * * *
37408 CCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTGTGCGAGATACTAAATCC-GGTTATGTC
37447 CCGAAGGCATT
1 CCGAAGGCATT
37458 TGAACGAGGA
Statistics
Matches: 143, Mismatches: 15, Indels: 15
0.83 0.09 0.09
Matches are distributed among these distances:
37 24 0.17
38 36 0.25
39 46 0.32
40 24 0.17
41 13 0.09
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (38 bp):
CCGAAGGCATTGTGCGAGATACTAAATCCGGTTATGTC
Done.