Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1281
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: 18802
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Found at i:3214 original size:25 final size:25
Alignment explanation
Indices: 3164--3214 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
3154 ATGTGTACAA
* *
3164 CAAATGAATAGGGGCACTATATGTG
1 CAAATGAATAGAGGCACTAGATGTG
*
3189 CAAATGATTAGAGGCACTGAGA-GTG
1 CAAATGAATAGAGGCACT-AGATGTG
3214 C
1 C
3215 GAGTTCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.35, C:0.14, G:0.29, T:0.22
Consensus pattern (25 bp):
CAAATGAATAGAGGCACTAGATGTG
Found at i:6355 original size:48 final size:48
Alignment explanation
Indices: 6293--6669 Score: 673
Period size: 48 Copynumber: 7.9 Consensus size: 48
6283 TATATATGTG
*
6293 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
*
6341 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATAAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
6389 TGTGGTAAAGCTGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
*
6437 TGTGGTAAAGCCGAGTGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
6485 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
6533 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
6581 TGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
6629 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
6670 GTGTGTATAT
Statistics
Matches: 314, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 314 1.00
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
Found at i:6863 original size:37 final size:37
Alignment explanation
Indices: 6813--6949 Score: 238
Period size: 37 Copynumber: 3.7 Consensus size: 37
6803 AATGTATTCT
6813 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
*
6850 GGGTAAGACCCGATGACTATGTGTGGAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
* *
6887 GGGTAAGACCCGATGACTATGTGTGGAGATTTTGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
*
6924 GGGTAAGACCCGATAACTACGTGTGG
1 GGGTAAGACCCGATGACTACGTGTGG
6950 GGACTATTCG
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 96 1.00
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.26
Consensus pattern (37 bp):
GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
Found at i:8752 original size:28 final size:28
Alignment explanation
Indices: 8720--8811 Score: 150
Period size: 28 Copynumber: 3.3 Consensus size: 28
8710 TGTACTAGGG
*
8720 TACCCTTATGTATGCAAAATTACCATTA
1 TACCCCTATGTATGCAAAATTACCATTA
8748 TACCCCTATGTATGCAAAATTACCATTA
1 TACCCCTATGTATGCAAAATTACCATTA
*
8776 TACCCCTATGTATGCAAAATGACC-TCTA
1 TACCCCTATGTATGCAAAATTACCAT-TA
8804 TACCCCTA
1 TACCCCTA
8812 GGGTTAATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
27 1 0.02
28 60 0.98
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.32
Consensus pattern (28 bp):
TACCCCTATGTATGCAAAATTACCATTA
Found at i:9018 original size:29 final size:28
Alignment explanation
Indices: 8917--9007 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
8907 AGGAAGCGTC
8917 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAATTATCTGTT
*
8945 CTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCACTGCCACAAATTATCTGTT
*
8973 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAATTATCTGT-T
9002 CTGGTG
1 CTGGTG
9008 ACTCTGTCAC
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
28 51 0.88
29 7 0.12
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAATTATCTGTT
Found at i:9032 original size:56 final size:55
Alignment explanation
Indices: 8917--9032 Score: 128
Period size: 56 Copynumber: 2.1 Consensus size: 55
8907 AGGAAGCGTC
* * *
8917 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCAC-AATTATATGTT
* * *
8973 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCAC-ATTTTATGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACAATTATATGT-T
9029 CTGG
1 CTGG
9033 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
55 8 0.16
56 29 0.57
57 14 0.27
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (55 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACAATTATATGTT
Found at i:10383 original size:12 final size:12
Alignment explanation
Indices: 10344--10377 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
10334 GCGAGCAGCT
10344 CGAGGAAGAGGC
1 CGAGGAAGAGGC
* *
10356 CGTGGACGAGGC
1 CGAGGAAGAGGC
10368 CGAGGAAGAG
1 CGAGGAAGAG
10378 CTCGAGCGGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.50, T:0.03
Consensus pattern (12 bp):
CGAGGAAGAGGC
Found at i:16644 original size:23 final size:23
Alignment explanation
Indices: 16609--16653 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
16599 TGTACTAGAA
16609 TATGTATCAAAATTACCATTATG
1 TATGTATCAAAATTACCATTATG
16632 TATGTATGC-AAATTACCATTAT
1 TATGTAT-CAAAATTACCATTAT
16654 ACCCTATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (23 bp):
TATGTATCAAAATTACCATTATG
Found at i:16835 original size:27 final size:28
Alignment explanation
Indices: 16786--16874 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
16776 AGGAAGCGTC
*
16786 CTGGTGGCTA-TG-CACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* *
16813 CTGGTGGCCCTGCCAC-ATATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
16840 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
16869 CTGGTG
1 CTGGTG
16875 ACTCTGTCAC
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
27 34 0.64
28 12 0.23
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:16893 original size:55 final size:55
Alignment explanation
Indices: 16786--16899 Score: 135
Period size: 56 Copynumber: 2.1 Consensus size: 55
16776 AGGAAGCGTC
* *
16786 CTGGTGGCTATGCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
16840 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TG-CACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
16896 CTGG
1 CTGG
16900 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
53 1 0.02
54 10 0.20
55 19 0.37
56 21 0.41
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (55 bp):
CTGGTGGCTATGCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:18609 original size:47 final size:48
Alignment explanation
Indices: 18492--18691 Score: 314
Period size: 47 Copynumber: 4.2 Consensus size: 48
18482 GGATAGGGGT
* * *
18492 AAATATATATGAGATATGTATATGTGGTAAAGCGGAATGGCTAGTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
18540 AAATATGTATGAGATATGTATATGTGGTAAAGTCGAATGGC-AATATG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
18587 AAATATGTATGAGATATATATATGTGGTAAAGCCGAATGGCTAATGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
18635 AAATATATATGAGATATGTATATGT-GTAAAGCCGAATGGCTAGTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
18682 AAATATGTAT
1 AAATATGTAT
18692 CTCATACATA
Statistics
Matches: 139, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
47 73 0.53
48 66 0.47
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.32
Consensus pattern (48 bp):
AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
Found at i:18655 original size:95 final size:95
Alignment explanation
Indices: 18492--18691 Score: 312
Period size: 95 Copynumber: 2.1 Consensus size: 95
18482 GGATAGGGGT
* * * * *
18492 AAATATATATGAGATATGTATATGTGGTAAAGCGGAATGGCTAGTGTGAAATATGTATGAGATAT
1 AAATATGTATGAGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATAT
*
18557 GTATATGTGGTAAAGTCGAATGGC-AATATG
66 GTATATGT-GTAAAGCCGAATGGCTAATATG
18587 AAATATGTATGAGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATAT
1 AAATATGTATGAGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATAT
* *
18652 GTATATGTGTAAAGCCGAATGGCTAGTGTG
66 GTATATGTGTAAAGCCGAATGGCTAATATG
18682 AAATATGTAT
1 AAATATGTAT
18692 CTCATACATA
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
94 14 0.15
95 82 0.85
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.32
Consensus pattern (95 bp):
AAATATGTATGAGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATAT
GTATATGTGTAAAGCCGAATGGCTAATATG
Done.