Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2365
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: 37898
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Found at i:5378 original size:28 final size:28
Alignment explanation
Indices: 5315--5465 Score: 205
Period size: 28 Copynumber: 5.4 Consensus size: 28
5305 ATATTAAGTC
*
5315 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
5342 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
5370 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
5398 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
5426 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
5455 CGCACACTTAG
1 CGCACACTTAG
5466 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.19
28 76 0.67
29 15 0.13
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:10022 original size:25 final size:25
Alignment explanation
Indices: 9988--10036 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
9978 GGTAGGGTTG
9988 TAACGCCCCAAAAATCTAAGTATTA
1 TAACGCCCCAAAAATCTAAGTATTA
10013 TAACGCCCCAAAAATCTAAGTATT
1 TAACGCCCCAAAAATCTAAGTATT
10037 TACTGTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.24
Consensus pattern (25 bp):
TAACGCCCCAAAAATCTAAGTATTA
Found at i:11358 original size:24 final size:24
Alignment explanation
Indices: 11322--11369 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
11312 CTGAAAAATA
11322 TGTCTATTAACATTACACGAGCGT
1 TGTCTATTAACATTACACGAGCGT
*
11346 TGTCTATTGACATTACACGAGCGT
1 TGTCTATTAACATTACACGAGCGT
11370 GCGCTCACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (24 bp):
TGTCTATTAACATTACACGAGCGT
Found at i:22571 original size:20 final size:20
Alignment explanation
Indices: 22505--22571 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
22495 ATCTTAGTTA
*
22505 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
22525 ACATGACATGTATGCTATGC
1 ACATGATATGTATGATATGC
*
22545 ACATGATATGTATGATATAC
1 ACATGATATGTATGATATGC
22565 ACATGAT
1 ACATGAT
22572 GTATTCATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:22714 original size:47 final size:46
Alignment explanation
Indices: 22622--22717 Score: 165
Period size: 47 Copynumber: 2.1 Consensus size: 46
22612 AAGAAGTGCA
22622 AAAGGGCTTATGCCCCAATTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAATTATTAAAGGGCTTATGCCCCAGTTATT
* *
22668 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAATTATT-AAAGGGCTTATGCCCCAGTTATT
22715 AAA
1 AAA
22718 AGAGGCTAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 22 0.47
47 25 0.53
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAATTATTAAAGGGCTTATGCCCCAGTTATT
Found at i:22734 original size:25 final size:24
Alignment explanation
Indices: 22621--22738 Score: 170
Period size: 23 Copynumber: 5.0 Consensus size: 24
22611 AAAGAAGTGC
*
22621 AAAAGGGCTTATGCCCCAATTATT
1 AAAAGGGCTTATGCCCCAGTTATT
22645 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
22668 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
22691 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
22715 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
22739 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
23 45 0.52
24 31 0.36
25 11 0.13
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:30258 original size:20 final size:20
Alignment explanation
Indices: 30192--30258 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
30182 TGGGATTTTA
*
30192 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
30212 ACATGACATGTATGCTATGC
1 ACATGATATGTATGATATGC
30232 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
30252 ACATGAT
1 ACATGAT
30259 GTATTCATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:30339 original size:23 final size:23
Alignment explanation
Indices: 30309--30381 Score: 128
Period size: 23 Copynumber: 3.1 Consensus size: 23
30299 AGGAAGTGCA
30309 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
30332 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
30355 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
30379 AAA
1 AAA
30382 AGAGGCTAGG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
23 26 0.54
24 22 0.46
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:30398 original size:25 final size:24
Alignment explanation
Indices: 30308--30402 Score: 140
Period size: 24 Copynumber: 4.0 Consensus size: 24
30298 GAGGAAGTGC
30308 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
30332 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
30355 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
30379 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
30403 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.35
24 31 0.48
25 11 0.17
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:30634 original size:31 final size:31
Alignment explanation
Indices: 30599--30660 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
30589 TTACAGTAAA
30599 GGCTTCGGCCCAGTAATATGAAATATGAAAT
1 GGCTTCGGCCCAGTAATATGAAATATGAAAT
**
30630 GGCTTCGGCCCAGTGTTATGAAATATGAAAT
1 GGCTTCGGCCCAGTAATATGAAATATGAAAT
30661 ATGAAAAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (31 bp):
GGCTTCGGCCCAGTAATATGAAATATGAAAT
Found at i:31512 original size:88 final size:88
Alignment explanation
Indices: 31409--31591 Score: 348
Period size: 88 Copynumber: 2.1 Consensus size: 88
31399 TTTATTGTAT
* *
31409 ACACATGAATCATATTCTACACTCCAAACATACATGCCATCCGTCCCACTCATCAACCATAATCA
1 ACACATTAATCATATTCTACACTCCAAACATACATGCCATCCATCCCACTCATCAACCATAATCA
31474 ACCATAACCACATTCAAGCATAA
66 ACCATAACCACATTCAAGCATAA
31497 ACACATTAATCATATTCTACACTCCAAACATACATGCCATCCATCCCACTCATCAACCATAATCA
1 ACACATTAATCATATTCTACACTCCAAACATACATGCCATCCATCCCACTCATCAACCATAATCA
31562 ACCATAACCACATTCAAGCATAA
66 ACCATAACCACATTCAAGCATAA
31585 ACACATT
1 ACACATT
31592 TGTATGGATG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 93 1.00
ACGTcount: A:0.40, C:0.34, G:0.03, T:0.22
Consensus pattern (88 bp):
ACACATTAATCATATTCTACACTCCAAACATACATGCCATCCATCCCACTCATCAACCATAATCA
ACCATAACCACATTCAAGCATAA
Found at i:33755 original size:46 final size:48
Alignment explanation
Indices: 33702--33832 Score: 205
Period size: 48 Copynumber: 2.8 Consensus size: 48
33692 TGTAACCCGC
* * *
33702 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-GC-GTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTATTCGCAT
33748 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTATTCGCAT
33796 CCATAAGTGAA-TCGGAACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGG-ACTCAACTCAACGAGTTCGGA
33833 TGCTCAACCA
Statistics
Matches: 79, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
46 35 0.44
47 5 0.06
48 39 0.49
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (48 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTATTCGCAT
Found at i:34285 original size:30 final size:30
Alignment explanation
Indices: 34251--34310 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
34241 ATTTAATACG
34251 AACTTTAGAAAAATTACACTTTTGCCCCTA
1 AACTTTAGAAAAATTACACTTTTGCCCCTA
* * *
34281 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAGAAAAATTACACTTTTGCCCCTA
34311 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTAGAAAAATTACACTTTTGCCCCTA
Done.