Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1436
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: 33198
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:1343 original size:40 final size:39
Alignment explanation
Indices: 1294--1536 Score: 255
Period size: 40 Copynumber: 6.1 Consensus size: 39
1284 CAGAATTTAA
* ** *
1294 CCGGATATAGCTCCTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGC
* * *
1334 CCGGTTATAGTAATCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGC
1373 CCGGACT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGA-TATAGT-ACTCGCACAAATGCCTTCGGGACTTAGC
*
1413 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTA-CTCGCACAAATGCCTTCGGGA-CTTAGC
*
1453 CCGGAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTA-CTCGCACAAATGCCTTCGGGA-CTTAGC
* *
1492 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGT-AC-TCGCACAAATGCCTTCGGGACTTAGC
1532 CCGGA
1 CCGGA
1537 CATCATTCAA
Statistics
Matches: 178, Mismatches: 14, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
39 74 0.42
40 92 0.52
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:1413 original size:79 final size:79
Alignment explanation
Indices: 1313--1537 Score: 264
Period size: 79 Copynumber: 2.8 Consensus size: 79
1303 GCTCCTCGTT
* *
1313 CAAATGCCTTCGGGACATAGCCCGGTTATAGTA-ATCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTACATCGCACAAATGCCTTCGGGACTTAGCCCGG
1377 ACTTAGTAACTCGCA
65 ACTTAGTAACTCGCA
* *
1392 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATC-TCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTA-CATCGCACAAATGCCTTCGGGA-CTTAGCCC
*
1455 GGA-TTAGTATCTCGCA
63 GGACTTAGTAACTCGCA
* * * *
1471 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TATAGT-ACATCGCACAAATGCCTTCGGGACTTAGCCC
1534 GGAC
63 GGAC
1538 ATCATTCAAA
Statistics
Matches: 126, Mismatches: 10, Indels: 19
0.81 0.06 0.12
Matches are distributed among these distances:
78 4 0.03
79 84 0.67
80 38 0.30
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTACATCGCACAAATGCCTTCGGGACTTAGCCCGGA
CTTAGTAACTCGCA
Found at i:12611 original size:27 final size:27
Alignment explanation
Indices: 12553--12611 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
12543 GAGTACCTGA
* ***
12553 ACCCTTATGTGATAAAATGACGATTTT
1 ACCCTTATGTGATAAAATGACCAAAAT
*
12580 TCCCTTATGTGATAAAATGACCAAAAT
1 ACCCTTATGTGATAAAATGACCAAAAT
12607 ACCCT
1 ACCCT
12612 CATAGGGTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (27 bp):
ACCCTTATGTGATAAAATGACCAAAAT
Found at i:12624 original size:27 final size:26
Alignment explanation
Indices: 12594--12691 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 26
12584 TTATGTGATA
12594 AAATGACCAAAATACCCTCATAGGGT
1 AAATGACCAAAATACCCTCATAGGGT
* *
12620 GAAATGATCGAAATACCCTCATAGGGT
1 -AAATGACCAAAATACCCTCATAGGGT
* * *
12647 AGAATGACCGAAATACCCT-GTGGGGT
1 A-AATGACCAAAATACCCTCATAGGGT
* *
12673 AAAATGACTATAATACCCT
1 -AAATGACCAAAATACCCT
12692 GGTAAGGTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
26 20 0.33
27 41 0.67
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (26 bp):
AAATGACCAAAATACCCTCATAGGGT
Found at i:12706 original size:53 final size:54
Alignment explanation
Indices: 12592--12707 Score: 128
Period size: 53 Copynumber: 2.2 Consensus size: 54
12582 CCTTATGTGA
* *
12592 TAAAATGACCAAAATACCCTCATAGGGTGAAATGATCGAAATACCCTCATAGGG
1 TAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCTCATAAGG
* * * * * **
12646 TAGAATGACCGAAATACCCT-GTGGGGTAAAATGA-CTATAATACCCTGGTAAGG
1 TAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGA-AATACCCTCATAAGG
12699 TAAAATGAC
1 TAAAATGAC
12708 AGATTTGTTC
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
52 2 0.04
53 31 0.61
54 18 0.35
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (54 bp):
TAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCTCATAAGG
Found at i:22867 original size:15 final size:15
Alignment explanation
Indices: 22831--22868 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
22821 AAAATCACTC
*
22831 CAAAAGAATACTTAT
1 CAAAAGGATACTTAT
22846 CAAAAGGATACTTAT
1 CAAAAGGATACTTAT
22861 CAAAAGGA
1 CAAAAGGA
22869 ATTCTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (15 bp):
CAAAAGGATACTTAT
Found at i:24483 original size:19 final size:20
Alignment explanation
Indices: 24459--24496 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
24449 GGTACCACCA
24459 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
24478 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
24497 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:24893 original size:46 final size:46
Alignment explanation
Indices: 24721--24893 Score: 163
Period size: 46 Copynumber: 3.7 Consensus size: 46
24711 AACCCGCCCC
* * * * *
24721 TAAGTTAACTCGGACTCAACTCAATGAGCTTGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
* * * * *
24767 TAAATGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCATCCA
* * *
24815 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
*
24860 TAAGTGAACTTGGACTCAACTCAACGAGCTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
24894 TGCTCAACCA
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 56 0.54
47 28 0.27
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
Found at i:24893 original size:93 final size:93
Alignment explanation
Indices: 24727--24896 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
24717 CCCCTAAGTT
* * *
24727 AACTCGGACTCAACTCAATGAGCTTGGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAAT
1 AACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
*
24792 GAGTTCGGATGCCTAGTTACATCTCACG
66 GAGCTCGGATGCCTAGTTACATCTCACG
* * *
24820 AACTCGGACTCAACTCAACGAG-TTCGGACATTTGCATCCATAAGTGAACTTGGACTCAACTCAA
1 AACTCGGACTCAACTCAACGAGCTT-GGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
24884 CGAGCTCGGATGC
65 CGAGCTCGGATGC
24897 TCAACCATCC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
92 2 0.03
93 67 0.97
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCACG
Found at i:29443 original size:13 final size:13
Alignment explanation
Indices: 29425--29452 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29415 CATAAATTCT
29425 GTGTTCTCAACAG
1 GTGTTCTCAACAG
29438 GTGTTCTCAACAG
1 GTGTTCTCAACAG
29451 GT
1 GT
29453 ATATTCATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.32
Consensus pattern (13 bp):
GTGTTCTCAACAG
Done.