Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold400
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: 34715
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Found at i:272 original size:34 final size:34
Alignment explanation
Indices: 233--299 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
223 CATGCAGAAC
233 CATTATTTCTAAACCTTGTTTTATGGATATCTAA
1 CATTATTTCTAAACCTTGTTTTATGGATATCTAA
* *
267 CATTATTTCTAAACCTTGTTTTGTGGATGTCTA
1 CATTATTTCTAAACCTTGTTTTATGGATATCTA
300 CTCTGAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (34 bp):
CATTATTTCTAAACCTTGTTTTATGGATATCTAA
Found at i:12028 original size:39 final size:39
Alignment explanation
Indices: 11942--12104 Score: 129
Period size: 39 Copynumber: 4.2 Consensus size: 39
11932 ACTTGAAACC
* *
11942 AATTACCAGCAC-AAGCCTGCGGGAATTTAAACCCGG-TAT
1 AATT-CCAGCACGAAGCCTGCGGGACTTT-AGCCCGGATAT
* * *
11981 AATACCAGCTCGAAGCCTGCGGGACTTTAGCCCGGACAT
1 AATTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATAT
* * * *
12020 ATTTCCAGCACGTAGCCTGC-GGACCTTAAGTCCGGATAT
1 AATTCCAGCACGAAGCCTGCGGGA-CTTTAGCCCGGATAT
* * * *
12059 AATTCCAGCAC-ATAGCCTAC-GGACCCTAAGTCCGGATAT
1 AATTCCAGCACGA-AGCCTGCGGGA-CTTTAGCCCGGATAT
12098 AATTCCA
1 AATTCCA
12105 ACACATAGCT
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
38 15 0.14
39 89 0.86
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (39 bp):
AATTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATAT
Found at i:12110 original size:39 final size:39
Alignment explanation
Indices: 12012--12137 Score: 189
Period size: 39 Copynumber: 3.2 Consensus size: 39
12002 GGACTTTAGC
* * * *
12012 CCGGACATATTTCCAGCACGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
*
12051 CCGGATATAATTCCAGCACATAGCCTACGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
* *
12090 CCGGATATAATTCCAACACATAGCTTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
12129 CCGGATATA
1 CCGGATATA
12138 CATCACTGAA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:19376 original size:17 final size:17
Alignment explanation
Indices: 19354--19387 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19344 TATATACAAA
*
19354 TATATATATGTGTGTGT
1 TATATATATGTATGTGT
19371 TATATATATGTATGTGT
1 TATATATATGTATGTGT
19388 AATTGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (17 bp):
TATATATATGTATGTGT
Found at i:20636 original size:38 final size:38
Alignment explanation
Indices: 20545--20674 Score: 152
Period size: 38 Copynumber: 3.4 Consensus size: 38
20535 CGAGGTATAA
* * * * *
20545 AACCCGAACATAACACCAGCACGAAGCCTACGGCACTTT
1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGA-TTT
* * * * *
20584 AAACTCAGATATAATACCAGCACTAGGCCTTCGGGATTT
1 -AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
20623 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
20661 AACCCGGATATAAT
1 AACCCGGATATAAT
20675 TCCATCAAAT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
38 47 0.62
39 3 0.04
40 26 0.34
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (38 bp):
AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
Found at i:20689 original size:38 final size:38
Alignment explanation
Indices: 20545--20694 Score: 140
Period size: 38 Copynumber: 3.9 Consensus size: 38
20535 CGAGGTATAA
* * * * * *
20545 AACCCGAACATAACACCAGCACGAAGCCTACGGCACTTT
1 AACCCGGATATAATACCAGCACAAAGCCTGCGGGA-TTT
* * * * *
20584 AAACTCAGATATAATACCAGCACTAGGCCTTCGGGATTT
1 -AACCCGGATATAATACCAGCACAAAGCCTGCGGGATTT
*
20623 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
1 AACCCGGATATAATACCAGCACAAAGCCTGCGGGATTT
* *
20661 AACCCGGATATAATTCCATCA-AATAGCCTGCGGG
1 AACCCGGATATAATACCAGCACAA-AGCCTGCGGG
20695 TCTTTAAGCC
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
37 1 0.01
38 62 0.67
39 3 0.03
40 26 0.28
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.19
Consensus pattern (38 bp):
AACCCGGATATAATACCAGCACAAAGCCTGCGGGATTT
Found at i:20710 original size:78 final size:78
Alignment explanation
Indices: 20545--20694 Score: 171
Period size: 78 Copynumber: 1.9 Consensus size: 78
20535 CGAGGTATAA
* * * *
20545 AACCCGAACATAACACCAGCACGAAGCCTACGGCACTTTAAACTCAGATATAATACCAGCACTAG
1 AACCCGGATATAACACCAGCACGAAGCCTACGGCACTTTAAACCCAGATATAATACCAGCAATAG
*
20610 GCCTTCGGGATTT
66 GCCTGCGGGATTT
* * * * * *
20623 AACCCGGATATAATACCAGCACGAAGCCTGCGGGA-TTT-AACCCGGATATAATTCCATCAAATA
1 AACCCGGATATAACACCAGCACGAAGCCTACGGCACTTTAAACCCAGATATAATACCAGC-AATA
20686 -GCCTGCGGG
65 GGCCTGCGGG
20695 TCTTTAAGCC
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
76 24 0.40
77 6 0.10
78 30 0.50
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.19
Consensus pattern (78 bp):
AACCCGGATATAACACCAGCACGAAGCCTACGGCACTTTAAACCCAGATATAATACCAGCAATAG
GCCTGCGGGATTT
Found at i:22393 original size:40 final size:40
Alignment explanation
Indices: 22362--22540 Score: 288
Period size: 40 Copynumber: 4.5 Consensus size: 40
22352 CGCTCGAATA
*
22362 CCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGA-ACTAGTAACTCGCACAAATG
22402 CCTTCGGGACTTAGCCCGGAACTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAACTAGTAACTCGCACAAATG
*
22442 CCTTCGAGACTTAGCCCGGAACTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAACTAGTAACTCGCACAAATG
* * * *
22482 CCTTCGGGACTTAGCCCGAAACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGAACTAGTAACTCGCACAAATG
22522 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
22541 TTATCATCCA
Statistics
Matches: 130, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 1 0.01
40 129 0.99
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGAACTAGTAACTCGCACAAATG
Done.