Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1534
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: 28409
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:10615 original size:21 final size:22
Alignment explanation
Indices: 10584--10632 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 22
10574 TATTTTCAGG
10584 ACACCATAACTTATACCCTTTT
1 ACACCATAACTTATACCCTTTT
10606 ACACC-TAACTTATACCCTTTT
1 ACACCATAACTTATACCCTTTT
10627 ACACCA
1 ACACCA
10633 GCTTTATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (22 bp):
ACACCATAACTTATACCCTTTT
Found at i:13506 original size:31 final size:30
Alignment explanation
Indices: 13450--13507 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
13440 CATCTAAGTA
*
13450 AATTAATTAATTTTTTAATTAAATAAATTT
1 AATTAATTAATTTTCTAATTAAATAAATTT
13480 AATTAATTGAATTTTCTAGATT-AATAAA
1 AATTAATT-AATTTTCTA-ATTAAATAAA
13508 AGGAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 14 0.56
32 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (30 bp):
AATTAATTAATTTTCTAATTAAATAAATTT
Found at i:19376 original size:26 final size:26
Alignment explanation
Indices: 19346--19453 Score: 207
Period size: 26 Copynumber: 4.2 Consensus size: 26
19336 TGAAATTCCC
19346 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
19372 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
19398 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
19424 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
19450 ATCA
1 ATCA
19454 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:20764 original size:26 final size:26
Alignment explanation
Indices: 20725--20832 Score: 155
Period size: 26 Copynumber: 4.2 Consensus size: 26
20715 TGGTACAAAT
20725 TGATAAT-GAGTTAGGTAAATGTTCCA
1 TGATAATGGA-TTAGGTAAATGTTCCA
* *
20751 TAATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
* *
20777 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGATTAGGTAAATGTTCCA
*
20803 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
20829 TGAT
1 TGAT
20833 GGGCATTTCA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 71 0.97
27 2 0.03
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.37
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:20809 original size:52 final size:52
Alignment explanation
Indices: 20725--20832 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
20715 TGGTACAAAT
20725 TGATAATGAGTTAGGTAAATGTTCCATAATAATGGATTAGGTAAATATTCCA
1 TGATAATGAGTTAGGTAAATGTTCCATAATAATGGATTAGGTAAATATTCCA
* * * * *
20777 TGATAATGGGTTAGGTAAATGTTCTATGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGAGTTAGGTAAATGTTCCATAATAATGGATTAGGTAAATATTCCA
20829 TGAT
1 TGAT
20833 GGGCATTTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.37
Consensus pattern (52 bp):
TGATAATGAGTTAGGTAAATGTTCCATAATAATGGATTAGGTAAATATTCCA
Found at i:22346 original size:26 final size:26
Alignment explanation
Indices: 22317--22369 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
22307 TTTACAATTT
22317 TACCCCTAGGAGATAAATT-ACCAAAA
1 TACCCCTAGG-GATAAATTGACCAAAA
* *
22343 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCAAAA
22369 T
1 T
22370 GCATATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCAAAA
Found at i:27711 original size:51 final size:49
Alignment explanation
Indices: 27651--27754 Score: 172
Period size: 51 Copynumber: 2.1 Consensus size: 49
27641 ATGTACAAAT
*
27651 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCC
1 TGATAATGGGTTAGGTAAATGTT-CATGATAATGG-TTAGGTAAATATTCA
*
27702 TGATAATGGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCA
1 TGATAATGGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATATTCA
27751 TGAT
1 TGAT
27755 GGGCATTTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
49 17 0.33
50 11 0.22
51 23 0.45
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.37
Consensus pattern (49 bp):
TGATAATGGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATATTCA
Found at i:27715 original size:25 final size:25
Alignment explanation
Indices: 27651--27754 Score: 165
Period size: 25 Copynumber: 4.2 Consensus size: 25
27641 ATGTACAAAT
27651 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTT-CA
* * *
27677 TGATAATGGATTAGGTAAATATTCC
1 TGATAATGGGTTAGGTAAATGTTCA
27702 TGATAATGGGTTAGGTAAATGTTCA
1 TGATAATGGGTTAGGTAAATGTTCA
27727 TGATAAT-GGTTAGGTAAATGTTCA
1 TGATAATGGGTTAGGTAAATGTTCA
27751 TGAT
1 TGAT
27755 GGGCATTTCA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
24 21 0.29
25 30 0.42
26 21 0.29
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.37
Consensus pattern (25 bp):
TGATAATGGGTTAGGTAAATGTTCA
Done.