Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold581
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: 29674
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:5500 original size:4 final size:4
Alignment explanation
Indices: 5493--5580 Score: 56
Period size: 4 Copynumber: 22.0 Consensus size: 4
5483 AAAAAAAAAG
* * * * * * *
5493 TAAA TAAA TGAA T-AA TATA TAAA TAAA TAAG TAAG TAAG TAAG TATA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
*
5540 TGAA TAAAA TAAA -AGGAA T-AA TAAA TAAA TAAA TAAA TAAA
1 TAAA T-AAA TAAA TA--AA TAAA TAAA TAAA TAAA TAAA TAAA
5581 AGGAAACCGT
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
3 7 0.10
4 57 0.83
5 5 0.07
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:5517 original size:8 final size:8
Alignment explanation
Indices: 5457--5580 Score: 60
Period size: 8 Copynumber: 15.4 Consensus size: 8
5447 AAGGAATAAC
5457 AAATAAAT
1 AAATAAAT
* *
5465 GAATAAAGG
1 AAATAAA-T
*
5474 AATTAAAGT
1 AAATAAA-T
5483 AAA-AAA-
1 AAATAAAT
5489 AAAGTAAAT
1 AAA-TAAAT
*
5498 AAATGAAT
1 AAATAAAT
*
5506 -AATATAT
1 AAATAAAT
5513 AAATAAAT
1 AAATAAAT
* *
5521 AAGTAAGT
1 AAATAAAT
* *
5529 AAGTAAGT
1 AAATAAAT
* *
5537 ATATGAAT
1 AAATAAAT
5545 AAAATAAA-
1 -AAATAAAT
5553 AGGAAT-AAT
1 A--AATAAAT
5562 AAATAAAT
1 AAATAAAT
5570 AAATAAAT
1 AAATAAAT
5578 AAA
1 AAA
5581 AGGAAACCGT
Statistics
Matches: 88, Mismatches: 18, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
6 3 0.03
7 9 0.10
8 56 0.64
9 20 0.23
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.23
Consensus pattern (8 bp):
AAATAAAT
Found at i:5574 original size:12 final size:12
Alignment explanation
Indices: 5457--5580 Score: 60
Period size: 12 Copynumber: 10.2 Consensus size: 12
5447 AAGGAATAAC
*
5457 AAATAAATGAAT
1 AAATAAATAAAT
* *
5469 AAAGGAATTAAAGT
1 AAA-TAAATAAA-T
5483 AAA-AAA-AAAGT
1 AAATAAATAAA-T
*
5494 AAATAAATGAAT
1 AAATAAATAAAT
*
5506 -AATATATAAAT
1 AAATAAATAAAT
* *
5517 AAATAAGTAAGT
1 AAATAAATAAAT
* * *
5529 AAGTAAGTATAT
1 AAATAAATAAAT
*
5541 GAATAAAATAAA-
1 AAAT-AAATAAAT
5553 AGGAAT-AATAAAT
1 A--AATAAATAAAT
5566 AAATAAATAAAT
1 AAATAAATAAAT
5578 AAA
1 AAA
5581 AGGAAACCGT
Statistics
Matches: 84, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
11 20 0.24
12 44 0.52
13 13 0.15
14 7 0.08
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.23
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:9714 original size:10 final size:10
Alignment explanation
Indices: 9648--9715 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 10
9638 TTTTTTTTTA
9648 TTTATATATATT
1 TTTATA-AT-TT
9660 TTTATATATTT
1 TTTATA-ATTT
9671 GTTTATAATTT
1 -TTTATAATTT
*
9682 ATTAGT--TTT
1 TTTA-TAATTT
*
9691 TTATATAAGTT
1 TT-TATAATTT
9702 TTTATAATTT
1 TTTATAATTT
9712 TTTA
1 TTTA
9716 AAAAAAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
9 5 0.11
10 16 0.34
11 11 0.23
12 15 0.32
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.66
Consensus pattern (10 bp):
TTTATAATTT
Found at i:17969 original size:18 final size:18
Alignment explanation
Indices: 17948--18006 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 18
17938 TTATAAAAAA
*
17948 ATTATATTAATTATATAT
1 ATTAAATTAATTATATAT
17966 ATTAAATT-ATT-TATAT
1 ATTAAATTAATTATATAT
* * *
17982 -TTATATTTA-TATTTAT
1 ATTAAATTAATTATATAT
17998 ATTAAATTA
1 ATTAAATTA
18007 CTAACCCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
15 7 0.21
16 10 0.30
17 9 0.27
18 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTAAATTAATTATATAT
Found at i:17984 original size:6 final size:6
Alignment explanation
Indices: 17973--18000 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
17963 TATATTAAAT
17973 TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATT
18001 AAATTACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:26213 original size:21 final size:21
Alignment explanation
Indices: 26187--26251 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
26177 GGCAATATAA
26187 AAAAATGTATATATATAATAT
1 AAAAATGTATATATATAATAT
* *
26208 AAAAATGTGTAT-TTTGAAT-T
1 AAAAATGTATATATAT-AATAT
*
26228 ATAAAATGTAAATATAT-ATAT
1 A-AAAATGTATATATATAATAT
26249 AAA
1 AAA
26252 TGTGTGTACA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
20 8 0.23
21 25 0.71
22 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (21 bp):
AAAAATGTATATATATAATAT
Found at i:26512 original size:21 final size:20
Alignment explanation
Indices: 26482--26523 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
26472 AATAGAAATA
* *
26482 ATAATAATAATAAATATAAC
1 ATAATAATAAAAAATAAAAC
26502 ATAATTAATAAAAAATAAAAC
1 ATAA-TAATAAAAAATAAAAC
26523 A
1 A
26524 ACGAATTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (20 bp):
ATAATAATAAAAAATAAAAC
Found at i:28356 original size:174 final size:175
Alignment explanation
Indices: 28064--28407 Score: 489
Period size: 174 Copynumber: 2.0 Consensus size: 175
28054 CTTCAATATA
* * *
28064 CTCCACTGCAACTTCAAGGAGGTAAAATCTGCCGTCTACGATCTGCTTCGCTGTCTATGCAGGAA
1 CTCCACTGCAACTTCAAGGAGGTAAAATCTACCATCTACGATCTGCTTCGCTATCTATGCAGGAA
* * * *
28129 GGTAAGATCTAAAATCTTCAGTCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAAT
66 GATAAGATCTAAAATCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAAT
28194 GTACTCCACTGTAACATCAGGGAGGTAAAATCCGCCATCTACCTG
131 GTACTCCACTGTAACATCAGGGAGGTAAAATCCGCCATCTACCTG
* *
28239 CTCCACTGCAACTTCAGGGAGGTAAAATCTACCATCTTCGATCTGC-TC-C-AT-TACTGCTTAG
1 CTCCACTGCAACTTCAAGGAGGTAAAATCTACCATCTACGATCTGCTTCGCTATCTA-TGC--AG
* ** *
28300 GGAGATAAGATCTGTAATTTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTC
63 GAAGATAAGATCTAAAATCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTC
* * *
28365 AATGTAGTCCATTGTAACCTCAGGGAGGTAAAATCCGCCATCT
128 AATGTACTCCACTGTAACATCAGGGAGGTAAAATCCGCCATCT
28408 TCGATCTGCT
Statistics
Matches: 150, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
171 2 0.01
172 4 0.03
173 1 0.01
174 101 0.67
175 42 0.28
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (175 bp):
CTCCACTGCAACTTCAAGGAGGTAAAATCTACCATCTACGATCTGCTTCGCTATCTATGCAGGAA
GATAAGATCTAAAATCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAAT
GTACTCCACTGTAACATCAGGGAGGTAAAATCCGCCATCTACCTG
Found at i:28512 original size:50 final size:50
Alignment explanation
Indices: 28450--28916 Score: 348
Period size: 50 Copynumber: 9.4 Consensus size: 50
28440 GATCTGTAAA
* * * * *
28450 CTTCAATTTGTTCAACTGCAATGTCGGGGAAACCAGATCCTCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATATCAGGGAAACAAGATCCGCCGTCGTAG
* * * ** * * *
28500 CTTCAATCTGTTCCACTGCACTGTCAGGGAAGTAAGATCCACCGTTGTGG
1 CTTCAATCTGTTCAACTGCAATATCAGGGAAACAAGATCCGCCGTCGTAG
* * * * * *
28550 CTTCAATCTTTTTAATTGTAATATCAGGGAAACTAGATCTGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATATCAGGGAAACAAGATCCGCCGTCGTAG
* * * * ** * *
28600 CTTCAATCTGTTCCACTACACTA-CTAAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAACTGCAATATC-AGGGAAACAAGATCCGCCGTCGTAG
* * * * *
28650 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCTGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATATCAGGGAAACAAGATCCGCCGTCGTAG
* * ** ** * *
28700 CTTCAATCTGTTCCACTGCACTA-CTAAAGAATTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAACTGCAATATC-AGGGAAACAAGATCCGCCGTCGTAG
* * * *
28750 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATATCAGGGAAACAAGATCCGCCGTCGTAG
* ** * * ** * * *
28800 CTTCAATCTGTTCCACTGCGCT-GCTAAGGAATTAAG-TCCGCTGTTGTGG
1 CTTCAATCTGTTCAACTGCAATATC-AGGGAAACAAGATCCGCCGTCGTAG
* * * *
28849 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATATCAGGGAAACAAGATCCGCCGTCGTAG
*
28899 CTTCAATCTGTTCCACTG
1 CTTCAATCTGTTCAACTG
28917 TACTGCTAAG
Statistics
Matches: 302, Mismatches: 108, Indels: 14
0.71 0.25 0.03
Matches are distributed among these distances:
49 36 0.12
50 264 0.87
51 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (50 bp):
CTTCAATCTGTTCAACTGCAATATCAGGGAAACAAGATCCGCCGTCGTAG
Found at i:28598 original size:100 final size:100
Alignment explanation
Indices: 28466--28980 Score: 793
Period size: 100 Copynumber: 5.2 Consensus size: 100
28456 TTTGTTCAAC
* * *
28466 TGCAATGTCGGGGAAACCAGATCCT-CCGTCGTAGCTTCAATCTGTTCCACTGCACTG-TCAGGG
1 TGCAATATCAGGGAAACCAGAT-CTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCT-AAGG
*
28529 AAGTAAGATCCACCGTTGTGGCTTCAATCTTTTTAAT
64 AAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * *
28566 TGTAATATCAGGGAAACTAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTACACTACTAAGGAA
1 TGCAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
28631 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* *
28666 TGCAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTACTAAAGAA
1 TGCAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
*
28731 TTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* *
28766 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCGCTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
* *
28831 TTAAG-TCCGCTGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* *
28865 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
* * *
28930 GTAAGATCCGCCGCTGTGGCTTTAATCTTTTTTAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* *
28965 TTCAATATCAAGGAAA
1 TGCAATATCAGGGAAA
28981 GGTAAGGTTG
Statistics
Matches: 385, Mismatches: 27, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
99 97 0.25
100 287 0.75
101 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (100 bp):
TGCAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
Done.