Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1842
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: 26131
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Found at i:1098 original size:57 final size:59
Alignment explanation
Indices: 1034--1153 Score: 192
Period size: 59 Copynumber: 2.1 Consensus size: 59
1024 ATTTGGTTGA
1034 TTTTATATGGGAAA-TTGCTAT-ATTGATTAGTGTCAAAGTTTA-GGGTAAAATCGGAAT
1 TTTTATATGGGAAAGTTGCTATAATTGATTAGTGTCAAAG-TTAGGGGTAAAATCGGAAT
* *
1091 TTTTATATGGGAAAGTTGCTATAATTGATTAGTGTCAAAGTTAGGGGTAAATTCTGAAT
1 TTTTATATGGGAAAGTTGCTATAATTGATTAGTGTCAAAGTTAGGGGTAAAATCGGAAT
1150 TTTT
1 TTTT
1154 GTCTTATTTC
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
57 14 0.24
58 10 0.17
59 34 0.59
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.41
Consensus pattern (59 bp):
TTTTATATGGGAAAGTTGCTATAATTGATTAGTGTCAAAGTTAGGGGTAAAATCGGAAT
Found at i:1392 original size:35 final size:36
Alignment explanation
Indices: 1353--1426 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 36
1343 GATTACTAGC
1353 TAACAGTCTTCTAACACTTCCTTTCATGCT-GAGAA
1 TAACAGTCTTCTAACACTTCCTTTCATGCTGGAGAA
1388 TAACAGTCTTCTAACACTTCCTTTCATGCTGGAGAA
1 TAACAGTCTTCTAACACTTCCTTTCATGCTGGAGAA
1424 TAA
1 TAA
1427 GTATCTTTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 30 0.79
36 8 0.21
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (36 bp):
TAACAGTCTTCTAACACTTCCTTTCATGCTGGAGAA
Found at i:3303 original size:18 final size:18
Alignment explanation
Indices: 3255--3375 Score: 68
Period size: 18 Copynumber: 6.7 Consensus size: 18
3245 TGACTCAGCC
3255 TGGTTTTGAGACTTAGAT
1 TGGTTTTGAGACTTAGAT
* * * *
3273 T-GTGGTAGTGACTTAGCT
1 TGGT-TTTGAGACTTAGAT
* *
3291 TGGTTTTGAGACTCAGAA
1 TGGTTTTGAGACTTAGAT
* * *
3309 T-GTGTTAGTGACTTAGCT
1 TGGT-TTTGAGACTTAGAT
* *
3327 TGGTTTTGAGACTCAGAA
1 TGGTTTTGAGACTTAGAT
* * *
3345 T-GTGTTAGTGACTTAGCT
1 TGGT-TTTGAGACTTAGAT
3363 TGGTTTTGAGACT
1 TGGTTTTGAGACT
3376 CAGAATGTGT
Statistics
Matches: 70, Mismatches: 27, Indels: 12
0.64 0.25 0.11
Matches are distributed among these distances:
17 6 0.09
18 58 0.83
19 6 0.09
ACGTcount: A:0.21, C:0.10, G:0.29, T:0.40
Consensus pattern (18 bp):
TGGTTTTGAGACTTAGAT
Found at i:3406 original size:36 final size:36
Alignment explanation
Indices: 3242--3392 Score: 257
Period size: 36 Copynumber: 4.2 Consensus size: 36
3232 GGGACAAAGG
* * * * *
3242 TAGTGACTCAGCCTGGTTTTGAGACTTAGATTGTGG
1 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
3278 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
1 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
3314 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
1 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
3350 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
1 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
3386 TAGTGAC
1 TAGTGAC
3393 AGATTTTGTT
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 110 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (36 bp):
TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
Found at i:6482 original size:11 final size:11
Alignment explanation
Indices: 6456--6485 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
6446 CCCCCCCCCC
6456 AAAAA-AAAAA
1 AAAAAGAAAAA
6466 AAAAAGAAAAA
1 AAAAAGAAAAA
6477 AAAAAGAAA
1 AAAAAGAAA
6486 TGTTAGTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:23376 original size:1 final size:1
Alignment explanation
Indices: 23370--23394 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
23360 TCCACCTGCC
23370 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
23395 GCAATTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:23503 original size:1 final size:1
Alignment explanation
Indices: 23497--23618 Score: 244
Period size: 1 Copynumber: 122.0 Consensus size: 1
23487 GTTAAATCCG
23497 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
23562 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
23619 TTTTCTGGCC
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 121 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Done.