Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold853
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: 14722
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:3655 original size:28 final size:26
Alignment explanation
Indices: 3602--3665 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 26
3592 TACTAGTTTC
3602 ATGTATCGATACAATGAACATGTATCG
1 ATGTATCGATACAA-GAACATGTATCG
*
3629 AATGTATCGATACAA-AGCATGATTATCG
1 -ATGTATCGATACAAGAACATG--TATCG
*
3657 ATATATCGA
1 ATGTATCGA
3666 GATATGTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 5 0.16
27 8 0.25
28 19 0.59
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (26 bp):
ATGTATCGATACAAGAACATGTATCG
Found at i:3715 original size:1 final size:1
Alignment explanation
Indices: 3709--3744 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
3699 GAGTCCTTTG
**
3709 TTTTTTTTTTTTTTTTTTAGTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3745 AATGTATCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.03, T:0.94
Consensus pattern (1 bp):
T
Found at i:3734 original size:18 final size:18
Alignment explanation
Indices: 3711--3745 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3701 GTCCTTTGTT
3711 TTTTTTTTTTTTTTTTAG
1 TTTTTTTTTTTTTTTTAG
3729 TTTTTTTTTTTTTTTTA
1 TTTTTTTTTTTTTTTTA
3746 ATGTATCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.03, T:0.91
Consensus pattern (18 bp):
TTTTTTTTTTTTTTTTAG
Found at i:3987 original size:11 final size:11
Alignment explanation
Indices: 3973--4022 Score: 75
Period size: 11 Copynumber: 4.5 Consensus size: 11
3963 CAATCCATAG
3973 TTTTTTTTTCA
1 TTTTTTTTTCA
3984 TTTTCTTTTTCA
1 TTTT-TTTTTCA
3996 -TTTTTTTTCA
1 TTTTTTTTTCA
*
4006 TTTTTTTCTCA
1 TTTTTTTTTCA
4017 TTTTTT
1 TTTTTT
4023 GAACATCACC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
10 7 0.19
11 22 0.61
12 7 0.19
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:4649 original size:18 final size:20
Alignment explanation
Indices: 4617--4659 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
4607 GTTCATAGCA
*
4617 AAAAAATAAATAAATAACCT
1 AAAAAATAAATAAATAACAT
*
4637 AAAAAAT-AA-AAATTACAT
1 AAAAAATAAATAAATAACAT
4655 AAAAA
1 AAAAA
4660 CAAACTAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 12 0.57
19 2 0.10
20 7 0.33
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAAAATAAATAAATAACAT
Found at i:4777 original size:118 final size:120
Alignment explanation
Indices: 4644--4870 Score: 332
Period size: 122 Copynumber: 1.9 Consensus size: 120
4634 CCTAAAAAAT
* * * * *
4644 AAAAATTACATAAAAACAAACT-AACATAAACTAATTTGACATAAAAAA-ATAAAGACTTTCCCT
1 AAAAATTACACAAAAACAAACTAAACATAAACTAATTCGACATAAAAAATAGAAAAACCTTCCCT
4707 CAAAGTTAAAACAAACATTATCCTCAATGTTTATAAATAAAAGAGAAGGAATAAG
66 CAAAGTTAAAACAAACATTATCCTCAATGTTTATAAATAAAAGAGAAGGAATAAG
* *
4762 AAAAATTACACAAAAATAAACTAAAACGTAAACTAATTCGACATAAAAAATTAGAAAAACCTTCC
1 AAAAATTACACAAAAACAAACT-AAACATAAACTAATTCGACATAAAAAA-TAGAAAAACCTTCC
* * *
4827 CTCAAAGTTAAAACAAATATTGTCCTTAATGTTTATAAATAAAA
64 CTCAAAGTTAAAACAAACATTATCCTCAATGTTTATAAATAAAA
4871 AAATAACAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
118 20 0.21
120 24 0.25
122 51 0.54
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.25
Consensus pattern (120 bp):
AAAAATTACACAAAAACAAACTAAACATAAACTAATTCGACATAAAAAATAGAAAAACCTTCCCT
CAAAGTTAAAACAAACATTATCCTCAATGTTTATAAATAAAAGAGAAGGAATAAG
Found at i:6317 original size:9 final size:10
Alignment explanation
Indices: 6295--6331 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
6285 AAATTACCTG
*
6295 AAAA-AAATA
1 AAAATAAATT
6304 AAAATAAATT
1 AAAATAAATT
6314 -AAATAAATT
1 AAAATAAATT
6323 AAAATAAAT
1 AAAATAAAT
6332 AATAAATAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 13 0.52
10 12 0.48
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAATAAATT
Found at i:6350 original size:25 final size:25
Alignment explanation
Indices: 6298--6350 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
6288 TTACCTGAAA
*
6298 AAAATAAAAATAAATTAAATAAATT
1 AAAATAAAAATAAATTAAATAAAGT
6323 AAAATAAATAATAAA-TAAGA-AAAGT
1 AAAATAAA-AATAAATTAA-ATAAAGT
6348 AAA
1 AAA
6351 GTATGAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (25 bp):
AAAATAAAAATAAATTAAATAAAGT
Found at i:7775 original size:28 final size:28
Alignment explanation
Indices: 7725--7795 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
7715 AAAATTACAG
* *
7725 AATAGTCCTTAAATACATGAAATTATGT-
1 AATAGTCCTAAAATACATGAAATGAT-TA
7753 AATAGTCCTAAAAT-CATGAAAATGATTA
1 AATAGTCCTAAAATACATG-AAATGATTA
*
7781 AATGGTCCTAAAATA
1 AATAGTCCTAAAATA
7796 GTCCTAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.14
28 32 0.86
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (28 bp):
AATAGTCCTAAAATACATGAAATGATTA
Found at i:7806 original size:67 final size:69
Alignment explanation
Indices: 7725--7862 Score: 174
Period size: 67 Copynumber: 2.0 Consensus size: 69
7715 AAAATTACAG
* ** * *
7725 AATAGTCCTTAAATACATGAAATTATGTAATAGT-CCTAAAATCAT-GAAAATGAT-TAAATGGT
1 AATAGTCCTAAAATACATGAAATTACATAATAGTCCCTAAAAT-ATAGAAAATGATCTAAATAGC
7787 CCTAA
65 CCTAA
* * *
7792 AATAGTCCTAAAATATATGAAATTACATAATAGTCCCTATAATATAGAAAATGTTCTAAATAGCC
1 AATAGTCCTAAAATACATGAAATTACATAATAGTCCCTAAAATATAGAAAATGATCTAAATAGCC
7857 CTAA
66 CTAA
7861 AA
1 AA
7863 ATCATGGAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
67 32 0.53
68 15 0.25
69 13 0.22
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.30
Consensus pattern (69 bp):
AATAGTCCTAAAATACATGAAATTACATAATAGTCCCTAAAATATAGAAAATGATCTAAATAGCC
CTAA
Found at i:7873 original size:59 final size:58
Alignment explanation
Indices: 7791--7943 Score: 159
Period size: 59 Copynumber: 2.6 Consensus size: 58
7781 AATGGTCCTA
* * *
7791 AAATAGTCCTAAAATAT-ATGAAATTACATAATAGTCCCTATAATATAGAAAATGTTCT
1 AAATAGACCTAAAA-ATCATGAAATTACATAATAGTCCCTATAACATAGAAAAGGTTCT
* * * * * *
7849 AAATAGCCCTAAAAATCATGGAAATTACATGATAGGCCCTATAGCATGGAAAAGGTTTT
1 AAATAGACCTAAAAATCAT-GAAATTACATAATAGTCCCTATAACATAGAAAAGGTTCT
*
7908 ATA-AGAACCT-AAAATACATGAAATTACATAATAGTC
1 AAATAG-ACCTAAAAAT-CATGAAATTACATAATAGTC
7944 AATACATCAT
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
57 2 0.03
58 37 0.47
59 40 0.51
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (58 bp):
AAATAGACCTAAAAATCATGAAATTACATAATAGTCCCTATAACATAGAAAAGGTTCT
Found at i:8040 original size:57 final size:57
Alignment explanation
Indices: 7916--8076 Score: 146
Period size: 57 Copynumber: 2.8 Consensus size: 57
7906 TTATAAGAAC
* * * * * * * *
7916 CTAAAATACATGAAATTACATAATAGTCAATACATCATAAAAAATGA-CTAAATAGCT
1 CTAAAATGCATAAAATAACATAATAATC-CTAAATCATGAAAAATGACCAAAATAGCT
* * * ** *
7973 TTAAAATGCATAAAATAGCATCATGGTCCTTAAATCATG-AAAATGACCAAAATGGCT
1 CTAAAATGCATAAAATAACATAATAATCC-TAAATCATGAAAAATGACCAAAATAGCT
* *
8030 CTAAAGTGCATGAAATAACATAATAATCCTAAATCATGAAAAATGAC
1 CTAAAATGCATAAAATAACATAATAATCCTAAATCATGAAAAATGAC
8077 TAGCATAACT
Statistics
Matches: 82, Mismatches: 19, Indels: 6
0.77 0.18 0.06
Matches are distributed among these distances:
56 16 0.20
57 66 0.80
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.25
Consensus pattern (57 bp):
CTAAAATGCATAAAATAACATAATAATCCTAAATCATGAAAAATGACCAAAATAGCT
Found at i:10532 original size:27 final size:27
Alignment explanation
Indices: 10494--10546 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
10484 TATTATAAGT
10494 AATTCGCCACTTCAAGGAATCTAACTA
1 AATTCGCCACTTCAAGGAATCTAACTA
10521 AATTCGCCACTTCAAGGAATCTAACT
1 AATTCGCCACTTCAAGGAATCTAACT
10547 TGAACTGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.26
Consensus pattern (27 bp):
AATTCGCCACTTCAAGGAATCTAACTA
Found at i:12569 original size:15 final size:15
Alignment explanation
Indices: 12559--12588 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12549 TTTTAAAGAC
12559 TTAA-TAATTAAAAA
1 TTAACTAATTAAAAA
12573 TTAACTAATTAAAAA
1 TTAACTAATTAAAAA
12588 T
1 T
12589 AAAAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAACTAATTAAAAA
Found at i:14173 original size:16 final size:16
Alignment explanation
Indices: 14152--14208 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
14142 TAAAATTTTC
*
14152 GGATCATTTTAGGTTT
1 GGATCATTTCAGGTTT
*
14168 GGATCATTTCGGGTTT
1 GGATCATTTCAGGTTT
*
14184 GGATCATTTCAGGTTC
1 GGATCATTTCAGGTTT
*
14200 AGATCATTT
1 GGATCATTT
14209 TGGATTTTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (16 bp):
GGATCATTTCAGGTTT
Done.