Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold286
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: 58240
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--30 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
*
1 AAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31 GGAAAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:5970 original size:40 final size:40
Alignment explanation
Indices: 5818--5963 Score: 206
Period size: 40 Copynumber: 3.6 Consensus size: 40
5808 TTGAATGATG
* * * *
5818 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
5858 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
5898 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
5939 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
5964 AACGAGTAGC
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
40 89 0.91
41 9 0.09
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:5970 original size:80 final size:80
Alignment explanation
Indices: 5818--5996 Score: 204
Period size: 80 Copynumber: 2.2 Consensus size: 80
5808 TTGAATGATG
* *
5818 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGGCTAAGTCCCGAAGGCATTT
**
5883 GTGCGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
* * * *
5898 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA-CCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCA-AATCCGGGCTAAGTCCCGAAGGCAT
*
5961 TTGAACGAGTAGCTATA
64 TTGAACGAGTAGCTAAA
* *
5978 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
5997 TACGTGATTT
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
79 16 0.19
80 60 0.71
81 9 0.11
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGGCTAAGTCCCGAAGGCATTT
GAACGAGTAGCTAAA
Found at i:10978 original size:18 final size:18
Alignment explanation
Indices: 10945--10979 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10935 ATGATGTGCC
*
10945 AAACTATTTTCTTGCTTG
1 AAACTATTTTCATGCTTG
*
10963 AAACTATTTTGATGCTT
1 AAACTATTTTCATGCTT
10980 ACCATTCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (18 bp):
AAACTATTTTCATGCTTG
Found at i:11795 original size:15 final size:15
Alignment explanation
Indices: 11775--11806 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11765 ATAGGCACTA
*
11775 GGGTGTCACGACATC
1 GGGTGTCACGAAATC
11790 GGGTGTCACGAAATC
1 GGGTGTCACGAAATC
11805 GG
1 GG
11807 TCCTTTACGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.38, T:0.19
Consensus pattern (15 bp):
GGGTGTCACGAAATC
Found at i:19369 original size:34 final size:34
Alignment explanation
Indices: 19326--19412 Score: 108
Period size: 34 Copynumber: 2.6 Consensus size: 34
19316 GGCTTAAGCA
19326 CATAT-CAGTAGCAGTATCAGTGTGAGCCTTAACC
1 CATATACAGTA-CAGTATCAGTGTGAGCCTTAACC
* *
19360 CA-ATACAGTAACAGTATCAGTGTGGGCCTTAGCC
1 CATATACAGT-ACAGTATCAGTGTGAGCCTTAACC
*
19394 CATTTA-AGTACAGTATCAG
1 CATATACAGTACAGTATCAG
19413 AAATGCATAC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
33 12 0.26
34 32 0.68
35 3 0.06
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (34 bp):
CATATACAGTACAGTATCAGTGTGAGCCTTAACC
Found at i:27047 original size:12 final size:12
Alignment explanation
Indices: 27026--27055 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
27016 TTATTTTTCA
27026 ATTC-AATCTAG
1 ATTCTAATCTAG
27037 ATTCTAATCTAG
1 ATTCTAATCTAG
27049 ATTCTAA
1 ATTCTAA
27056 CTTTTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.40
Consensus pattern (12 bp):
ATTCTAATCTAG
Found at i:53036 original size:30 final size:30
Alignment explanation
Indices: 53002--53062 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52992 TCCTTAACTC
53002 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
53032 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
53062 A
1 A
53063 GGCTCGGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:53358 original size:13 final size:13
Alignment explanation
Indices: 53340--53366 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53330 TATTGCTAAG
53340 CTAAATCAAGTTA
1 CTAAATCAAGTTA
53353 CTAAATCAAGTTA
1 CTAAATCAAGTTA
53366 C
1 C
53367 CGGGACTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (13 bp):
CTAAATCAAGTTA
Done.