Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold408
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: 59160
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1424 original size:39 final size:40
Alignment explanation
Indices: 1318--1541 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
1308 GCTCCTCGTT
*
1318 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
1358 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
1398 CAAATGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
1437 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
1476 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
1517 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1542 CATCATTCAA
Statistics
Matches: 163, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 70 0.43
40 78 0.48
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:1429 original size:79 final size:79
Alignment explanation
Indices: 1318--1541 Score: 292
Period size: 79 Copynumber: 2.8 Consensus size: 79
1308 GCTCCTCGTT
* *
1318 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
1382 GATTTAGTAACTCGCA
64 GAATTAGTAACTCGCA
* *
1398 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
1462 ATTAGTATCTCGCA
66 ATTAGTAACTCGCA
* * * * *
1476 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
1540 GA
64 GA
1542 CATCATTCAA
Statistics
Matches: 127, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
78 36 0.28
79 60 0.47
80 31 0.24
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:9448 original size:39 final size:40
Alignment explanation
Indices: 9342--9565 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
9332 GCTCCTCGTT
*
9342 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
9382 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
9422 CAAATGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
9461 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
9500 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
9541 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9566 CATCATTCAA
Statistics
Matches: 163, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 70 0.43
40 78 0.48
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:9453 original size:79 final size:79
Alignment explanation
Indices: 9342--9565 Score: 292
Period size: 79 Copynumber: 2.8 Consensus size: 79
9332 GCTCCTCGTT
* *
9342 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
9406 GATTTAGTAACTCGCA
64 GAATTAGTAACTCGCA
* *
9422 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
9486 ATTAGTATCTCGCA
66 ATTAGTAACTCGCA
* * * * *
9500 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
9564 GA
64 GA
9566 CATCATTCAA
Statistics
Matches: 127, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
78 36 0.28
79 60 0.47
80 31 0.24
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:23078 original size:23 final size:22
Alignment explanation
Indices: 23026--23078 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
23016 TCCACGTCTT
*
23026 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
23048 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
23071 TTTCTTTT
1 TTTCTTTT
23079 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:25438 original size:12 final size:12
Alignment explanation
Indices: 25416--25447 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
25406 CACAAAAATT
25416 TAAACTAAGTAAA
1 TAAA-TAAGTAAA
25429 TAAATAAGTAAA
1 TAAATAAGTAAA
25441 TAAATAA
1 TAAATAA
25448 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (12 bp):
TAAATAAGTAAA
Found at i:28730 original size:13 final size:13
Alignment explanation
Indices: 28703--28763 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 13
28693 TTTTGCTCGA
*
28703 TTTTTTTTC-ACT
1 TTTTTTTTCGAAT
*
28715 TTTTTTTTGGAAT
1 TTTTTTTTCGAAT
*
28728 TTTTTTTTCAATCAAT
1 TTTTTTTTC---GAAT
28744 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
28757 TTTTTTT
1 TTTTTTT
28764 GATTTTTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
12 8 0.20
13 20 0.50
16 12 0.30
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:32989 original size:11 final size:11
Alignment explanation
Indices: 32973--33001 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
32963 ACTTCAAAAA
32973 TTTTTTTCGAT
1 TTTTTTTCGAT
32984 TTTTTTT-GAT
1 TTTTTTTCGAT
32994 TTTTTTTC
1 TTTTTTTC
33002 AAATTTCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTCGAT
Found at i:41532 original size:18 final size:18
Alignment explanation
Indices: 41511--41554 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
41501 AAAAGAAGAC
41511 AGAAAAAGA-AATTGAAAA
1 AGAAAAAGAGAA-TGAAAA
41529 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
41547 AGAGAAAA
1 AGA-AAAA
41555 AAGAGATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:44821 original size:22 final size:22
Alignment explanation
Indices: 44791--44834 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
44781 TTTGGTATTT
*
44791 GGGAATTGGTACGAATTGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
44813 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
44835 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.36, T:0.27
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:46902 original size:23 final size:23
Alignment explanation
Indices: 46849--46925 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
46839 GATTAATTAA
*
46849 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGATTTGGTAC
** *
46872 -ATTTTGGTATTTGGAATTGGTAC
1 GA-AATGGTATTTGGATTTGGTAC
**
46895 GAAATGGTA-AGGGATTTGGTAC
1 GAAATGGTATTTGGATTTGGTAC
46917 GAAATGGTA
1 GAAATGGTA
46926 ATGGTTCAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
22 20 0.47
23 22 0.51
24 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.31, T:0.38
Consensus pattern (23 bp):
GAAATGGTATTTGGATTTGGTAC
Found at i:48112 original size:30 final size:30
Alignment explanation
Indices: 48054--48112 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
48044 TTGAAAATGT
* *
48054 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
48084 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
48113 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:51662 original size:22 final size:22
Alignment explanation
Indices: 51631--51692 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
51621 ACCTTTTTGA
*
51631 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
51654 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
51676 TCCATACCATTTCGTAC
1 ACCATACCATTTCGTAC
51693 TAATTCCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 32 0.89
23 4 0.11
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:53865 original size:17 final size:17
Alignment explanation
Indices: 53843--53937 Score: 68
Period size: 18 Copynumber: 5.4 Consensus size: 17
53833 TATCATATCA
*
53843 CTCATTTCTTTTGCACT
1 CTCATTTCTTTTTCACT
*
53860 CTCATTTCTTTCTTCATT
1 CTCATTTCTTT-TTCACT
* *
53878 CTCAATCTCTTTTTCAGTT
1 CTC-ATTTCTTTTTCA-CT
* *
53897 CTCTTTTC-TTTTCACA
1 CTCATTTCTTTTTCACT
*
53913 CTCATTT-TTATTCTCAAT
1 CTCATTTCTT-TT-TCACT
53931 CTCATTT
1 CTCATTT
53938 TCAATTTTCT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
16 7 0.11
17 19 0.31
18 24 0.39
19 12 0.19
ACGTcount: A:0.15, C:0.27, G:0.02, T:0.56
Consensus pattern (17 bp):
CTCATTTCTTTTTCACT
Found at i:53928 original size:47 final size:48
Alignment explanation
Indices: 53875--53965 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
53865 TTCTTTCTTC
* * *
53875 ATTCTCAATCTCTTTTTCAGTTCTCTTTTCT-TTTCACACTCATTTTT
1 ATTCTCAATCTCATTTTCAATTCTCTTTTCTATCTCACACTCATTTTT
*
53922 ATTCTCAATCTCATTTTCAATTTTCTTTTCTATCTCACACTCAT
1 ATTCTCAATCTCATTTTCAATTCTCTTTTCTATCTCACACTCAT
53966 CTTCTTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 28 0.72
48 11 0.28
ACGTcount: A:0.19, C:0.26, G:0.01, T:0.54
Consensus pattern (48 bp):
ATTCTCAATCTCATTTTCAATTCTCTTTTCTATCTCACACTCATTTTT
Found at i:53987 original size:15 final size:16
Alignment explanation
Indices: 53962--53993 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
53952 TATCTCACAC
53962 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
53978 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
53993 T
1 T
53994 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:54998 original size:12 final size:11
Alignment explanation
Indices: 54981--55010 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
54971 GAATACAAAC
54981 TTTTTTTTTGAA
1 TTTTTTTTTG-A
54993 TTTTTTTTTGA
1 TTTTTTTTTGA
55004 TTTTTTT
1 TTTTTTT
55011 ACAATACCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTGA
Done.