Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1047
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: 23803
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:7084 original size:79 final size:81
Alignment explanation
Indices: 6960--7143 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
6950 GCTACTCGTT
* *
6960 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTC-GGATCTTAACCCG
* *
7023 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
7039 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCAC-AATGCCTTCGGATCTTAACCCG
* *
7102 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
7119 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
7144 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 48 0.53
80 19 0.21
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:7143 original size:40 final size:40
Alignment explanation
Indices: 6941--7143 Score: 229
Period size: 39 Copynumber: 5.1 Consensus size: 40
6931 CGGAATTTAA
** *
6941 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
6981 CCGGTTATAGTAACTCGCAC-AATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
7020 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
7059 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
7099 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
7139 CCGGA
1 CCGGA
7144 CATCATTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.01
39 68 0.49
40 57 0.41
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:12018 original size:19 final size:19
Alignment explanation
Indices: 11966--12018 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
11956 ATATCAATTT
*
11966 TCTTTCACAAAATTTCTCA
1 TCTTTCATAAAATTTCTCA
* * *
11985 TC-TGCGTAAATTTTCTCA
1 TCTTTCATAAAATTTCTCA
12003 TCTTTCATAAAATTTC
1 TCTTTCATAAAATTTC
12019 ATATCAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (19 bp):
TCTTTCATAAAATTTCTCA
Found at i:12669 original size:22 final size:23
Alignment explanation
Indices: 12616--12669 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
12606 TTATATGTTA
*
12616 TAAG-AATAATAGAACACTTTTT
1 TAAGAAATAATAGAACACTTTTG
*
12638 TATATAAAATAATAGAACAC-TTTG
1 TA-A-GAAATAATAGAACACTTTTG
12662 TAAGAAAT
1 TAAGAAAT
12670 TTAGTTCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
22 6 0.23
23 2 0.08
24 5 0.19
25 13 0.50
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.33
Consensus pattern (23 bp):
TAAGAAATAATAGAACACTTTTG
Found at i:14632 original size:14 final size:12
Alignment explanation
Indices: 14605--14635 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
14595 CAATATTTTT
14605 ATAATATTAAAA
1 ATAATATTAAAA
14617 ATAATATTAAAA
1 ATAATATTAAAA
14629 A-AATATT
1 ATAATATT
14636 CTTGATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATATTAAAA
Found at i:19047 original size:27 final size:28
Alignment explanation
Indices: 18938--19060 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
18928 GAGATTGGCG
* * *
18938 CTAAGTGTGCGGGTTTAAATTATATAGAA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
18967 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
18995 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
19023 CTAAGTGTGCAAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
19050 CTGAGTGTGCG
1 CTAAGTGTGCG
19061 GACTTAATAT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
27 23 0.27
28 48 0.56
29 15 0.17
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:19057 original size:55 final size:57
Alignment explanation
Indices: 18938--19060 Score: 178
Period size: 55 Copynumber: 2.2 Consensus size: 57
18928 GAGATTGGCG
* * *
18938 CTAAGTGTGCGGGTTTAAATTATATAGAACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATATAGAACTAAGTGTGCAAGTTTGATTATATAGCA
* *
18995 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCAAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATATAGAACTAAGTGTGCAAGTTTGATTATATAGCA
*
19050 CTGAGTGTGCG
1 CTAAGTGTGCG
19061 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.34
Consensus pattern (57 bp):
CTAAGTGTGCGAGTTTAAATTATATAGAACTAAGTGTGCAAGTTTGATTATATAGCA
Found at i:19071 original size:27 final size:27
Alignment explanation
Indices: 18958--19073 Score: 90
Period size: 28 Copynumber: 4.2 Consensus size: 27
18948 GGGTTTAAAT
* ** *
18958 TATATAGAACTAAGTGTGCGAGTTTGAT
1 TATATAGCACTAAGTGTGC-AACTTGAA
* ** *
18986 TATGTAGCACTAAGTGTGCGAGTTTGAT
1 TATATAGCACTAAGTGTGC-AACTTGAA
* *
19014 TATATAGCACTAAGTGTGCAAGTTGAT
1 TATATAGCACTAAGTGTGCAACTTGAA
* *
19041 TATATAGCACTGAGTGTGCGGACTT-AA
1 TATATAGCACTAAGTGTGC-AACTTGAA
19068 TATATA
1 TATATA
19074 CTTTTGAATC
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
27 31 0.40
28 47 0.60
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34
Consensus pattern (27 bp):
TATATAGCACTAAGTGTGCAACTTGAA
Done.