Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold539
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: 19402
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Found at i:1424 original size:39 final size:40
Alignment explanation
Indices: 1379--1600 Score: 240
Period size: 39 Copynumber: 5.7 Consensus size: 40
1369 GCTCCTCGTT
* * * *
1379 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
1419 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
1458 CGAATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
1497 CAAAGGCCTTCGGG-CTTAACCCGGAATT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
1535 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
1576 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
1601 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 20, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
37 4 0.03
38 29 0.19
39 63 0.41
40 48 0.31
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:1482 original size:79 final size:77
Alignment explanation
Indices: 1379--1600 Score: 250
Period size: 79 Copynumber: 2.8 Consensus size: 77
1369 GCTCCTCGTT
* * *
1379 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCACACAAAGCCTTCGGGACTTAACCCGGA
*
1444 TTTAATAACTCGCA
65 ATT-ATAACTCGCA
* * *
1458 CGAATGCCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAAGGCCTTCGGG-CTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCACACAAA-GCCTTCGGGACTTAACCCGGA
* *
1522 ATTGTATCTCGCA
65 ATTATAACTCGCA
* * * * *
1535 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-ACTCA-CACAAAGCCTTCGGGACTTAACCCG
1599 GA
63 GA
1601 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
76 3 0.02
77 31 0.26
78 34 0.28
79 53 0.44
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCACACAAAGCCTTCGGGACTTAACCCGGAA
TTATAACTCGCA
Found at i:1533 original size:38 final size:39
Alignment explanation
Indices: 1346--1600 Score: 234
Period size: 39 Copynumber: 6.5 Consensus size: 39
1336 AAATCACGTA
* * * **
1346 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCAAATG
1 CCTTCGGGACTTAACCCGGATTTAG-TACTCGCACAAATG
* * * *
1385 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAAATG
* *
1424 CCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAAATG
*
1464 CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
*
1503 CCTTCGGG-CTTAACCCGGAATT-GTATCTCGCACAAATG
1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCACAAATG
** * * *
1541 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAA-G
1 CCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAAATG
*
1581 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
1601 CAGCATTCAA
Statistics
Matches: 180, Mismatches: 26, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
37 5 0.03
38 29 0.16
39 75 0.42
40 59 0.33
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
Found at i:1609 original size:41 final size:41
Alignment explanation
Indices: 1532--1609 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
1522 ATTGTATCTC
* * *
1532 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
1573 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
1610 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:4390 original size:19 final size:20
Alignment explanation
Indices: 4353--4391 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4343 GCTCGTAATC
4353 TTTCAACAACTCAAAGCCAA
1 TTTCAACAACTCAAAGCCAA
4373 TTTCAACAACTC-AAGCCAA
1 TTTCAACAACTCAAAGCCAA
4392 CGTCTTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.44, C:0.31, G:0.05, T:0.21
Consensus pattern (20 bp):
TTTCAACAACTCAAAGCCAA
Found at i:8977 original size:78 final size:78
Alignment explanation
Indices: 8841--9009 Score: 209
Period size: 77 Copynumber: 2.2 Consensus size: 78
8831 GCTCCTCGTT
* * *
8841 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCAACAATGCCTTCGGGACTTAACCCGG-A
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCAACAAGGCCTTCGGGACTTAACCCGGAA
8905 TTTA-ATACTCGCA
66 TTTATAT-CTCGCA
* * * * *
8918 CGAATGCCTTCGGGACTTAACCCGGATTTA-TATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTC-AAC-AAGGCCTTCGGGACTTAACCCGG
*
8982 AATTTGTATCTCGCA
64 AATTTATATCTCGCA
8997 CAAATGCCTTCGG
1 CAAATGCCTTCGG
9010 ATCTTAGTCC
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
76 5 0.06
77 28 0.36
78 21 0.27
79 22 0.28
80 2 0.03
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCAACAAGGCCTTCGGGACTTAACCCGGAA
TTTATATCTCGCA
Found at i:9006 original size:40 final size:38
Alignment explanation
Indices: 8841--9062 Score: 195
Period size: 39 Copynumber: 5.7 Consensus size: 38
8831 GCTCCTCGTT
* * *
8841 CAAATGCCTTCGGGACATAGCCCGG-TTTTAGTAACTC-AA
1 CAAATGCCTTCGGGACTTAACCCGGATTTTA-T--CTCGCA
*
8880 C-AATGCCTTCGGGACTTAACCCGGATTTAATACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTTAT-CTCGCA
*
8918 CGAATGCCTTCGGGACTTAACCCGGATTTATATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTT-TATCTCGCA
* *
8957 CAAAGGCCTTCGGGGCTTAACCCGGAATTTGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTT-TATCTCGCA
** *
8997 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-T-TT-ATC-TCGCA
*
9038 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
9063 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 15, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
37 4 0.03
38 24 0.15
39 64 0.41
40 52 0.33
41 13 0.08
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (38 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTTATCTCGCA
Found at i:9022 original size:79 final size:79
Alignment explanation
Indices: 8879--9062 Score: 207
Period size: 79 Copynumber: 2.3 Consensus size: 79
8869 TAGTAACTCA
* *
8879 ACAATGCCTTCGGGACTTAACCCGG-ATTTAATACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 ACAAAGCCTTCGGGACTTAACCCGGAATTTAATACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
8943 ATTTA-TA-TCTCGC
66 ATATATTACT-TAGC
* * **
8956 ACAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 ACAAA-GCCTTCGGGACTTAACCCGGAATTTAATA-CTCGCACAAATGCCTTCGGGA-CTTAACC
9019 CGGATATATTCACTTAGC
63 CGGATATATT-ACTTAGC
*
9037 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
9063 CAGCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
77 4 0.04
78 24 0.27
79 32 0.36
80 20 0.22
81 9 0.10
82 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (79 bp):
ACAAAGCCTTCGGGACTTAACCCGGAATTTAATACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATATTACTTAGC
Found at i:9071 original size:41 final size:41
Alignment explanation
Indices: 8994--9071 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
8984 TTTGTATCTC
* * *
8994 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
9035 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
9072 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:12262 original size:27 final size:27
Alignment explanation
Indices: 12224--12277 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
12214 CACAAACCAC
* *
12224 TGGTACCGATTCAAGTTTCTTTTCTGA
1 TGGTACCGATTCAAATCTCTTTTCTGA
12251 TGGTACCGATTCAAATCTCTTTTCTGA
1 TGGTACCGATTCAAATCTCTTTTCTGA
12278 CTCTATTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (27 bp):
TGGTACCGATTCAAATCTCTTTTCTGA
Found at i:15551 original size:39 final size:39
Alignment explanation
Indices: 15504--15676 Score: 265
Period size: 39 Copynumber: 4.4 Consensus size: 39
15494 ATCGCAACTC
*
15504 GCACAAATGCCTTCGGGTCTTAGCCCGATATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGATATAGTCACTA
* **
15543 GCATAAATGCCTTCGGGACTTAGCCCGATATAGTTGCTA
1 GCACAAATGCCTTCGGGACTTAGCCCGATATAGTCACTA
*
15582 GCACAAATGCCTTCGGGACTTAGCCCGGTATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGATATAGTCACTA
* * *
15621 GCATAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTC
1 GCACAAATGCCTTCGGGACTTAGCCC-GATATAGTCACTA
15661 GCACAAATGCCTTCGG
1 GCACAAATGCCTTCGG
15677 ATCTTAGTCC
Statistics
Matches: 120, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 95 0.79
40 25 0.21
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (39 bp):
GCACAAATGCCTTCGGGACTTAGCCCGATATAGTCACTA
Found at i:15589 original size:78 final size:79
Alignment explanation
Indices: 15476--15683 Score: 305
Period size: 78 Copynumber: 2.7 Consensus size: 79
15466 ACCCAAGTAT
* * * *
15476 CTTCGGGATTTAG--CGGATATCGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGATATAGTC
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGTCTTAGCCCGATATAGTC
15539 ACTAGCATAAATGC
66 ACTAGCATAAATGC
** * *
15553 CTTCGGGACTTAGCCC-GATATAGTTGCTAGCACAAATGCCTTCGGGACTTAGCCCGGTATAGTC
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGTCTTAGCCCGATATAGTC
15617 ACTAGCATAAATGC
66 ACTAGCATAAATGC
* *
15631 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAG
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGTCTTAG
15684 TCCGTTATCA
Statistics
Matches: 115, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
77 12 0.10
78 71 0.62
79 32 0.28
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (79 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGTCTTAGCCCGATATAGTC
ACTAGCATAAATGC
Done.