Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3714
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: 16683
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Found at i:1474 original size:79 final size:82
Alignment explanation
Indices: 1363--1547 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
1353 GCTACTCGTT
* *
1363 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
1426 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
1443 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
1506 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
1523 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1548 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:1547 original size:40 final size:40
Alignment explanation
Indices: 1344--1547 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
1334 CGGAATTTAA
** *
1344 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
1384 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
1424 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
1463 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
1503 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
1543 CCGGA
1 CCGGA
1548 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:8710 original size:22 final size:22
Alignment explanation
Indices: 8682--8733 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
8672 CCTTGTTAAG
8682 CATATCCACACCTCTCAATAAC
1 CATATCCACACCTCTCAATAAC
8704 CATATCCACACCTCTCAATAAC
1 CATATCCACACCTCTCAATAAC
8726 CATATCCA
1 CATATCCA
8734 TATCAAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.23
Consensus pattern (22 bp):
CATATCCACACCTCTCAATAAC
Found at i:9393 original size:39 final size:40
Alignment explanation
Indices: 9306--9529 Score: 253
Period size: 40 Copynumber: 5.7 Consensus size: 40
9296 GCTACTCGTT
* *
9306 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
9346 CAAATGCCTTCGGGACTTAACCCGAATTTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
9385 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** *
9425 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
** * * * *
9465 CAAATG-CTTC-GGATCTTAGTCCGGATATGGTCAGCTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGT-AACTCGCA
*
9505 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
9530 CATCATTCGA
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
39 65 0.39
40 95 0.58
41 5 0.03
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:9409 original size:79 final size:80
Alignment explanation
Indices: 9306--9527 Score: 267
Period size: 79 Copynumber: 2.8 Consensus size: 80
9296 GCTACTCGTT
* *
9306 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
9371 ATTTAGT-ACTCGCA
66 ATTTAGTAACTCGCA
* *
9385 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCC
* *
9448 GGATTTAGTAACTCGTA
64 GAATTTAGTAACTCGCA
* * * * *
9465 CAAATG-CTTC-GGATCTTAGTCCGGATATGGTCAGCTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGT-AACTCGCACAAATGCCTTCGGGACTTAGCCC
9527 G
64 G
9528 GACATCATTC
Statistics
Matches: 123, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
78 7 0.06
79 89 0.72
80 27 0.22
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
ATTTAGTAACTCGCA
Found at i:15275 original size:79 final size:81
Alignment explanation
Indices: 15139--15321 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
15129 TCGAATGATG
* *
15139 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
15203 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
15218 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
15280 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
15298 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
15322 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:15337 original size:40 final size:40
Alignment explanation
Indices: 15140--15323 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
15130 CGAATGATGT
* * * *
15140 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
15180 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
15220 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
15258 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
15299 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
15324 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:15345 original size:79 final size:79
Alignment explanation
Indices: 15192--15356 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
15182 GGACTAAGAT
* **
15192 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
15257 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
15271 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
15334 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
15350 CCGAAGG
1 CCGAAGG
15357 TACGTGATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.