Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2463
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: 12827
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:3021 original size:90 final size:92
Alignment explanation
Indices: 2925--3107 Score: 244
Period size: 90 Copynumber: 2.0 Consensus size: 92
2915 GATTTTATGT
** * *
2925 GATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCAA-TGATGAATGTGAACATGC-A
1 GATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAAGTGATGAATATGAACATGCAA
*
2988 TATGTGATAAGGCCGAATGGCCAATGC
66 TATGTGATAAAGCCGAATGGCCAATGC
* * *
3015 GATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATATGAACATGCA
1 GATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAA-GTGATGAATATGAACATGCA
* *
3080 TATATGTGGTAAAGCCGAATGGCTAATG
65 -ATATGTGATAAAGCCGAATGGCCAATG
3108 TGAATATGTA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
90 38 0.48
92 17 0.22
94 24 0.30
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (92 bp):
GATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAAGTGATGAATATGAACATGCAA
TATGTGATAAAGCCGAATGGCCAATGC
Found at i:3108 original size:47 final size:47
Alignment explanation
Indices: 2921--3110 Score: 253
Period size: 47 Copynumber: 4.1 Consensus size: 47
2911 TTAGGATTTT
** * *
2921 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
2968 A--TGATGAATGTGAACATGC--ATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
3011 ATGCGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
3058 ATGTGATGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
3105 ATGTGA
1 ATGTGA
3111 ATATGTATGA
Statistics
Matches: 125, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
43 24 0.19
45 31 0.25
47 70 0.56
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:3190 original size:51 final size:52
Alignment explanation
Indices: 3079--3190 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 52
3069 ATGAACATGC
* *
3079 ATATATGTGGTAAAGCCGAATGGCTAATGTGAATATGTATGAGATATGTATGT
1 ATAT-TGTGGTAAAGCCGAATGGCTAATGTGAATATGTATGAGAGATGTACGT
* * *
3132 ATA-TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA-G-GCGATGTGCGT
1 ATATTGTGGTAAAGCCGAATGGCTAATGTG-AATATGTATGAGAGATGTACGT
3182 ATATTGTGG
1 ATATTGTGG
3191 CGAACGACCA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
50 10 0.19
51 31 0.60
52 8 0.15
53 3 0.06
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.32
Consensus pattern (52 bp):
ATATTGTGGTAAAGCCGAATGGCTAATGTGAATATGTATGAGAGATGTACGT
Found at i:3423 original size:37 final size:37
Alignment explanation
Indices: 3315--3423 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
3305 GGAAATATAT
*
3315 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
3352 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
3389 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
3424 CGTTGAGCTA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:5302 original size:78 final size:81
Alignment explanation
Indices: 5181--5362 Score: 230
Period size: 78 Copynumber: 2.3 Consensus size: 81
5171 TACTCGTTCA
* *
5181 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
5244 ATTTAGTAAC-TCGCAC
65 ATATAGTAACTTAGCAC
* **
5260 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
5323 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
5339 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
5363 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
77 3 0.03
78 46 0.52
79 29 0.33
80 11 0.12
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:5362 original size:40 final size:40
Alignment explanation
Indices: 5160--5362 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
5150 CGGAATTTAA
** *
5160 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5200 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
5240 CCGGATTTAGTAACTCGCAC-AATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5278 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
5318 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
5358 CCGGA
1 CCGGA
5363 CATCATTCGA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
38 24 0.17
39 22 0.16
40 81 0.58
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:6556 original size:56 final size:56
Alignment explanation
Indices: 6489--6608 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
6479 TATTAGTTTA
6489 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
6545 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
6601 TTGCCCAT
1 TTGCCCAT
6609 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:12403 original size:38 final size:38
Alignment explanation
Indices: 12359--12447 Score: 112
Period size: 38 Copynumber: 2.3 Consensus size: 38
12349 GCTACTCGTT
*
12359 CAAATGCCTTCGGG-TCAAG-CCGG-TTTAGTAACTCGCA
1 CAAATGCCTTCGGGCT-AAGCCCGGAATTAGT-ACTCGCA
*
12396 CCAAATGCCTTCGGGCTTAGCCCGGAATTAGTACTCGCA
1 -CAAATGCCTTCGGGCTAAGCCCGGAATTAGTACTCGCA
12435 CAAATGCCTTCGG
1 CAAATGCCTTCGG
12448 ATCTTAGTCC
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
38 29 0.63
39 12 0.26
40 5 0.11
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (38 bp):
CAAATGCCTTCGGGCTAAGCCCGGAATTAGTACTCGCA
Found at i:12454 original size:39 final size:39
Alignment explanation
Indices: 12359--12499 Score: 132
Period size: 39 Copynumber: 3.7 Consensus size: 39
12349 GCTACTCGTT
* * *
12359 CAAATGCCTTCGGGTC-AAG-CCGGTTTAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGCCCGGATTAGTAACTCGCA
*
12396 CCAAATGCCTTCGG-GCTTAGCCCGGAATTAGT-ACTCGCA
1 -CAAATGCCTTCGGATCTTAGCCCGG-ATTAGTAACTCGCA
* * * *
12435 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGATCTTAGCCCGGAT-TAGTAAC-TCGCA
12476 CAAA-GCCTTCGGA-CTTAGCCCGGA
1 CAAATGCCTTCGGATCTTAGCCCGGA
12500 CATCATTCGA
Statistics
Matches: 88, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
37 1 0.01
38 30 0.34
39 33 0.38
40 16 0.18
41 8 0.09
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGATCTTAGCCCGGATTAGTAACTCGCA
Done.