Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold457
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: 35769
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:15336 original size:39 final size:39
Alignment explanation
Indices: 15229--15502 Score: 417
Period size: 39 Copynumber: 7.1 Consensus size: 39
15219 AATTTTATTA
*
15229 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
*
15268 CCAGCACAAAGCCT--GGGTCTTTAGTCCGGATACATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
* * * *
15305 CAAGCACGAAGCCTGCGGGTCTTTGGCCCGGATATATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
* * *
15344 CCAGCACAAATCCTGCGGGACTTTAGCCCAGATACATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
15383 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
* * *
15422 CCAGCACGAAGCCTGCGGGTCTTTGGCCCGGATATATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
*
15461 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATATATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
15500 CCA
1 CCA
15503 TACACATTTC
Statistics
Matches: 211, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
37 33 0.16
39 178 0.84
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.24
Consensus pattern (39 bp):
CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
Found at i:15452 original size:117 final size:115
Alignment explanation
Indices: 15224--15502 Score: 477
Period size: 117 Copynumber: 2.4 Consensus size: 115
15214 CCCGAAATTT
*
15224 TATTACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACAAAGCCTGGGTCTT
1 TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACAAAGCCTGGGTCTT
*
15289 TAGTCCGGATACATTTCAAGCACGAAGCCTGCGGGTCTTTGGCCCGGATA
66 TAGCCCGGATACATTTCAAGCACGAAGCCTGCGGGTCTTTGGCCCGGATA
* *
15339 TATTTCCAGCACAAATCCTGCGGGACTTTAGCCCAGATACATTTCCAGCACAAAGCCTGCGGGTC
1 TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACAAAGCCT--GGGTC
*
15404 TTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGTCTTTGGCCCGGATA
64 TTTAGCCCGGATACATTTCAAGCACGAAGCCTGCGGGTCTTTGGCCCGGATA
* *
15456 TATTTCCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATATATTTCCA
1 TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCA
15503 TACACATTTC
Statistics
Matches: 153, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
115 55 0.36
117 98 0.64
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.25
Consensus pattern (115 bp):
TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACAAAGCCTGGGTCTT
TAGCCCGGATACATTTCAAGCACGAAGCCTGCGGGTCTTTGGCCCGGATA
Found at i:21365 original size:39 final size:39
Alignment explanation
Indices: 21255--21372 Score: 191
Period size: 39 Copynumber: 3.0 Consensus size: 39
21245 TTTTATTACT
* * *
21255 AGCACAAAGCCTGCGGGTCTTTAGCCCAGATACATCTCC
1 AGCACAAAGCCTGCGGGTCTTTAGCCCGGATATATTTCC
* *
21294 AGCACGAAGCCTGCGGGTCTTTGGCCCGGATATATTTCC
1 AGCACAAAGCCTGCGGGTCTTTAGCCCGGATATATTTCC
21333 AGCACAAAGCCTGCGGGTCTTTAGCCCGGATATATTTCC
1 AGCACAAAGCCTGCGGGTCTTTAGCCCGGATATATTTCC
21372 A
1 A
21373 TACACATTTC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.23, C:0.30, G:0.24, T:0.24
Consensus pattern (39 bp):
AGCACAAAGCCTGCGGGTCTTTAGCCCGGATATATTTCC
Found at i:25533 original size:55 final size:53
Alignment explanation
Indices: 25468--25582 Score: 149
Period size: 54 Copynumber: 2.1 Consensus size: 53
25458 TGGGGGAAGC
* * **
25468 GTTCTGGTGGCTATGCCATAATTATCTGTTTCTGGTGGTTATGCCACAAATATCT
1 GTTCTGGTGGCTACGCCATAA-TATCTGTATCTGGTGACTATGCCAC-AATATCT
* * *
25523 GTTCTGGTGGCTCCGCCATAATATCTGTATCTGGTGACTCTGTCACAATATCT
1 GTTCTGGTGGCTACGCCATAATATCTGTATCTGGTGACTATGCCACAATATCT
25576 GTTCTGG
1 GTTCTGG
25583 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
53 14 0.26
54 20 0.38
55 19 0.36
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (53 bp):
GTTCTGGTGGCTACGCCATAATATCTGTATCTGGTGACTATGCCACAATATCT
Found at i:25540 original size:27 final size:27
Alignment explanation
Indices: 25468--25582 Score: 117
Period size: 27 Copynumber: 4.3 Consensus size: 27
25458 TGGGGGAAGC
* *
25468 GTTCTGGTGGCTATGCCATAATTATCT
1 GTTCTGGTGGCTATGCCACAAATATCT
*
25495 GTTTCTGGTGGTTATGCCACAAATATCT
1 G-TTCTGGTGGCTATGCCACAAATATCT
** *
25523 GTTCTGGTGGCTCCGCCA-TAATATCT
1 GTTCTGGTGGCTATGCCACAAATATCT
* * *
25549 GTATCTGGTGACTCTGTCAC-AATATCT
1 GT-TCTGGTGGCTATGCCACAAATATCT
25576 GTTCTGG
1 GTTCTGG
25583 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
26 14 0.19
27 37 0.49
28 24 0.32
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (27 bp):
GTTCTGGTGGCTATGCCACAAATATCT
Found at i:27531 original size:39 final size:39
Alignment explanation
Indices: 27469--27586 Score: 143
Period size: 39 Copynumber: 3.0 Consensus size: 39
27459 GAAATGTGTA
*
27469 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCTGGGCTAAAGACCCGCAGGCTTTGTGC
* *
27508 TGGAAAATATATC-GCGGC-CAAGACCCGCAGGCTTCGTGGC
1 TGG-AAATATATCTG-GGCTAAAGACCCGCAGGCTTTGT-GC
* *
27548 TGGAGATGTATCTGGGCTAAAGACCC-CAGGCTTTGTGC
1 TGGAAATATATCTGGGCTAAAGACCCGCAGGCTTTGTGC
27586 T
1 T
27587 AGTAATAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
38 3 0.04
39 40 0.59
40 25 0.37
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.23
Consensus pattern (39 bp):
TGGAAATATATCTGGGCTAAAGACCCGCAGGCTTTGTGC
Found at i:31598 original size:14 final size:14
Alignment explanation
Indices: 31579--31607 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31569 CTATGTTTGT
31579 TATATGTGAAAATA
1 TATATGTGAAAATA
31593 TATATGTGAAAATA
1 TATATGTGAAAATA
31607 T
1 T
31608 CGTGTTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (14 bp):
TATATGTGAAAATA
Found at i:33485 original size:38 final size:39
Alignment explanation
Indices: 33305--33575 Score: 322
Period size: 39 Copynumber: 7.1 Consensus size: 39
33295 GAAATGTGTA
*
33305 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTT-TGGC
1 TGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTTGT-GC
* * *
33344 TGGAAATATATCCGGGCCAAAGACCCGCAGGCTTCGTGC
1 TGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTTGTGC
*
33383 TGGAAATGTATCCGGGC-AAAGACCCGCA-GCTTGGTGC
1 TGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * *
33420 TGG-AATGTATCTGGGCTAAAG-TCCGCAGGATTTGTGC
1 TGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * * *
33457 TGAAAATAT-TCCGGGCCAAAGACCCGCAGGCTTCGTGC
1 TGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * *
33495 TTGAAATGTATCCGGACTAAAGACCCACAGGCTTTG-GC
1 TGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* *
33533 TGGAAATGTATCCGGGCTAAAGTCCCTCAGGCTCTTGTGC
1 TGGAAATGTATCCGGGCTAAAGACCCGCAGGCT-TTGTGC
33573 TGG
1 TGG
33576 TAATAAAATT
Statistics
Matches: 198, Mismatches: 26, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
36 17 0.09
37 34 0.17
38 65 0.33
39 76 0.38
40 6 0.03
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23
Consensus pattern (39 bp):
TGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTTGTGC
Done.