Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_5165
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: 12024
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:2083 original size:57 final size:57
Alignment explanation
Indices: 2021--2181 Score: 232
Period size: 57 Copynumber: 2.8 Consensus size: 57
2011 CTGACTGATT
* * * *
2021 TCGCACACATAGCGCTCGATTAAAGAACTCACACACATAGTGCCTCAATTACCAATC
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
**
2078 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
* * * *
2135 TGGCACACATAGTGCTCGGTTGAAGAACTTGCACACACAGTGCCTCA
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCA
2182 TAACTCCAGC
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 94 1.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (57 bp):
TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
Found at i:2085 original size:29 final size:29
Alignment explanation
Indices: 2052--2149 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
2042 AAAGAACTCA
2052 CACACATAGTGCCTCAATTACCAATCTCG
1 CACACATAGTGCCTCAATTACCAATCTCG
* **
2081 CACACATAGTG-CTCGATTGAAGAA-CTCG
1 CACACATAGTGCCTCAATT-ACCAATCTCG
* ** *
2109 CACACATAGTGCCTCAACTACTGATCTGG
1 CACACATAGTGCCTCAATTACCAATCTCG
2138 CACACATAGTGC
1 CACACATAGTGC
2150 TCGGTTGAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
28 23 0.40
29 34 0.60
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (29 bp):
CACACATAGTGCCTCAATTACCAATCTCG
Found at i:2116 original size:28 final size:27
Alignment explanation
Indices: 2021--2177 Score: 134
Period size: 28 Copynumber: 5.6 Consensus size: 27
2011 CTGACTGATT
*
2021 TCGCACACATAGCGCTCGATTAAAGAAC
1 TCGCACACATAGTGCTCGATT-AAGAAC
* * **
2049 TCACACACATAGTGCCTCAATTACCAATC
1 TCGCACACATAGTG-CTCGATTAAGAA-C
2078 TCGCACACATAGTGCTCGATTGAAGAAC
1 TCGCACACATAGTGCTCGATT-AAGAAC
* * * *
2106 TCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTG-CTCGATTA-AGAAC
* *
2135 TGGCACACATAGTGCTCGGTTGAAGAAC
1 TCGCACACATAGTGCTCGATT-AAGAAC
* *
2163 TTGCACACACAGTGC
1 TCGCACACATAGTGC
2178 CTCATAACTC
Statistics
Matches: 102, Mismatches: 21, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
28 57 0.56
29 45 0.44
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (27 bp):
TCGCACACATAGTGCTCGATTAAGAAC
Found at i:2253 original size:40 final size:40
Alignment explanation
Indices: 2208--2498 Score: 503
Period size: 40 Copynumber: 7.3 Consensus size: 40
2198 GCCTTCGAGT
* *
2208 TTAGCCCGGATATATCACTAGCACGAATGCTTTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
* *
2248 TTAGCCCGGATACATTACTAGCATGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
2288 TTAGCCCGGATACATTACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
2328 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
2368 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
2408 TTAGCCCGGATTCATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
2448 TTAGCCCGGATACATCACTAGCATGAATGCTCTTCGG-AC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
2487 TTAGCCTGGATA
1 TTAGCCCGGATA
2499 TATATAACTC
Statistics
Matches: 241, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
39 13 0.05
40 228 0.95
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
Found at i:3567 original size:1 final size:1
Alignment explanation
Indices: 3561--3602 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
3551 CATAAAAGAC
3561 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3603 TTTGACAGCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5311 original size:27 final size:27
Alignment explanation
Indices: 5255--5428 Score: 190
Period size: 27 Copynumber: 6.4 Consensus size: 27
5245 ATTGTACAGT
*
5255 ACTAAGTGTGCG-ATTGACTATGTTGC
1 ACTAAGTGTGCGAATTGACTATGTAGC
* *
5281 ACTAAGTGTGCGAAATGAATATG-ATGC
1 ACTAAGTGTGCGAATTGACTATGTA-GC
* **
5308 ACTAAGTGTGCGAATTGACCATGCGGC
1 ACTAAGTGTGCGAATTGACTATGTAGC
*
5335 ACTAAGTGTGCGAGTTTGACTATGTAGC
1 ACTAAGTGTGCGA-ATTGACTATGTAGC
* * *
5363 ACTAAGTGTGCGATTTGATTACGTAGC
1 ACTAAGTGTGCGAATTGACTATGTAGC
* * *
5390 ACTAAGTGTGCGAGTTGATTATATAGC
1 ACTAAGTGTGCGAATTGACTATGTAGC
*
5417 ACTGAGTGTGCG
1 ACTAAGTGTGCG
5429 GACTCAATAT
Statistics
Matches: 127, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
26 12 0.09
27 92 0.72
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
ACTAAGTGTGCGAATTGACTATGTAGC
Found at i:5365 original size:82 final size:80
Alignment explanation
Indices: 5255--5407 Score: 218
Period size: 82 Copynumber: 1.9 Consensus size: 80
5245 ATTGTACAGT
* *
5255 ACTAAGTGTGCGATTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTGC
1 ACTAAGTGTGCGATTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTGTGC
5319 GAATTGACCATGCGGC
65 GAATTGACCATGCGGC
** *
5335 ACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTG
1 ACTAAGTGTGCGA--TTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTG
*
5400 CGAGTTGA
64 CGAATTGA
5408 TTATATAGCA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
80 13 0.20
82 50 0.78
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (80 bp):
ACTAAGTGTGCGATTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTGCG
AATTGACCATGCGGC
Found at i:5419 original size:82 final size:80
Alignment explanation
Indices: 5249--5428 Score: 209
Period size: 82 Copynumber: 2.2 Consensus size: 80
5239 GATTAAATTG
* * *
5249 TACAGTACTAAGTGTGCGATTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAG
1 TACAGCACTAAGTGTGCGATTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAG
5314 TGTGCGAATTGACCA
66 TGTGCGAATTGACCA
* * ** *
5329 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA--TTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
5393 AAGTGTGCGAGTTGATTA
63 AAGTGTGCGAATTGACCA
* *
5411 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
5429 GACTCAATAT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
80 16 0.20
81 1 0.01
82 65 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (80 bp):
TACAGCACTAAGTGTGCGATTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAG
TGTGCGAATTGACCA
Found at i:6873 original size:34 final size:34
Alignment explanation
Indices: 6827--6914 Score: 119
Period size: 34 Copynumber: 2.6 Consensus size: 34
6817 GAATAGTCCC
*
6827 CACGTGTTATCGGTCTTACCCGGACAAAATCTCCA
1 CACGTGTCATCGGTCTTACCCGGAC-AAATCTCCA
*
6862 C-CGTGTCATCGGTCTTACCCGGACATATCTCCA
1 CACGTGTCATCGGTCTTACCCGGACAAATCTCCA
*
6895 CACGTATCATC-GTC-TACCCG
1 CACGTGTCATCGGTCTTACCCG
6915 AATATATTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
32 6 0.12
33 12 0.24
34 30 0.61
35 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (34 bp):
CACGTGTCATCGGTCTTACCCGGACAAATCTCCA
Found at i:7128 original size:48 final size:48
Alignment explanation
Indices: 7055--7358 Score: 551
Period size: 48 Copynumber: 6.4 Consensus size: 48
7045 ATATACACAC
*
7055 ATCTCCTACATA-TTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
7102 ATCTCATACATATTTCACATTAGCCATT--GCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
7148 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
7196 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
7244 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
7292 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
7340 ATCTCATACATATTTCACA
1 ATCTCATACATATTTCACA
7359 GTACATCAAT
Statistics
Matches: 247, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
46 45 0.18
47 11 0.04
48 191 0.77
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Done.