Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold814
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: 31488
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6364 original size:23 final size:23
Alignment explanation
Indices: 6346--6402 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
6336 AAAAAATATG
6346 ATATAAAAATAAATTAAAACATA
1 ATATAAAAATAAATTAAAACATA
**
6369 ATATAAAAATAAA-TATCACATAA
1 ATATAAAAATAAATTAAAACAT-A
6392 ATATAAAAATA
1 ATATAAAAATA
6403 TATAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 6 0.19
23 25 0.81
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (23 bp):
ATATAAAAATAAATTAAAACATA
Found at i:6369 original size:12 final size:12
Alignment explanation
Indices: 6320--6402 Score: 77
Period size: 11 Copynumber: 7.2 Consensus size: 12
6310 TATACTACTT
*
6320 TAAATATATAAA
1 TAAATATAAAAA
6332 -AAATA-AAAAA
1 TAAATATAAAAA
*
6342 TATGATATAAAAA
1 TA-AATATAAAAA
6355 TAAAT-TAAAACA
1 TAAATATAAAA-A
6367 T-AATATAAAAA
1 TAAATATAAAAA
* *
6378 TAAATAT-CACA
1 TAAATATAAAAA
6389 TAAATATAAAAA
1 TAAATATAAAAA
6401 TA
1 TA
6403 TATAAATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
10 4 0.07
11 25 0.44
12 21 0.37
13 7 0.12
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.27
Consensus pattern (12 bp):
TAAATATAAAAA
Found at i:6663 original size:18 final size:20
Alignment explanation
Indices: 6620--6664 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
6610 TTATGTGGTT
6620 AATTTTATATTATCAATAAA
1 AATTTTATATTATCAATAAA
6640 AA-TTTA-ATTAT-AA-AATA
1 AATTTTATATTATCAATAA-A
6657 AATTTTAT
1 AATTTTAT
6665 TAAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.09
17 5 0.23
18 9 0.41
19 4 0.18
20 2 0.09
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTTTATATTATCAATAAA
Found at i:6673 original size:17 final size:18
Alignment explanation
Indices: 6623--6674 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
6613 TGTGGTTAAT
6623 TTTATATTATCAATAA-AAA
1 TTTA-ATTAT-AATAATAAA
6642 TTTAATTATAA-AATAAA
1 TTTAATTATAATAATAAA
*
6659 TTTTATTA-AATAATAA
1 TTTAATTATAATAATAA
6675 TTATGTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.13
17 17 0.57
18 5 0.17
19 4 0.13
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAATTATAATAATAAA
Found at i:7451 original size:24 final size:22
Alignment explanation
Indices: 7423--7477 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
7413 AATGAAAATG
*
7423 ATTAATACATGAATATAGTCAAAA
1 ATTAATA-ATGAATAT-GTAAAAA
*
7447 ATTAATAATTAATATGTAAAAA
1 ATTAATAATGAATATGTAAAAA
7469 ATTAGATAA
1 ATTA-ATAA
7478 ATTTATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 10 0.36
23 11 0.39
24 7 0.25
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (22 bp):
ATTAATAATGAATATGTAAAAA
Found at i:7810 original size:19 final size:19
Alignment explanation
Indices: 7773--7812 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
7763 TATAATATTT
*
7773 TAAATATAAAAAAATAATA
1 TAAATATAAAAAAAGAATA
* *
7792 TAAATATAAACACAGAATA
1 TAAATATAAAAAAAGAATA
7811 TA
1 TA
7813 TTTTAAAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (19 bp):
TAAATATAAAAAAAGAATA
Found at i:7900 original size:19 final size:19
Alignment explanation
Indices: 7863--7919 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
7853 TAATTCATTT
*
7863 TAGATATAGTAG-CAGATAG
1 TAGAT-TAGTAGATAGATAG
* *
7882 TAGGTTAGTGGATAGATAG
1 TAGATTAGTAGATAGATAG
*
7901 TAGATTAGTAGATACATAG
1 TAGATTAGTAGATAGATAG
7920 GATTAATTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 5 0.16
19 26 0.84
ACGTcount: A:0.39, C:0.04, G:0.28, T:0.30
Consensus pattern (19 bp):
TAGATTAGTAGATAGATAG
Found at i:9452 original size:20 final size:18
Alignment explanation
Indices: 9416--9455 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
9406 AATTAGTCGT
*
9416 ATATTATTTATATTAATA
1 ATATTATTTAAATTAATA
9434 ATATTATATTAAATGTAATA
1 ATATTAT-TTAAAT-TAATA
9454 AT
1 AT
9456 TGATAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
ATATTATTTAAATTAATA
Found at i:15351 original size:2 final size:2
Alignment explanation
Indices: 15344--15376 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15334 TCTAGCCATA
15344 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15377 AATAGTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21123 original size:5 final size:5
Alignment explanation
Indices: 21113--21142 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
21103 GTATTTCAAC
*
21113 CTAAT CTAAT CTAAT CTAAT CTGAT CTAAT
1 CTAAT CTAAT CTAAT CTAAT CTAAT CTAAT
21143 ATTATAGTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (5 bp):
CTAAT
Found at i:21758 original size:12 final size:12
Alignment explanation
Indices: 21743--21774 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
21733 CTCTTCACTG
21743 TCACAATCACAC
1 TCACAATCACAC
*
21755 TCACACTCACAC
1 TCACAATCACAC
21767 TCACAATC
1 TCACAATC
21775 CATTTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.19
Consensus pattern (12 bp):
TCACAATCACAC
Found at i:26584 original size:52 final size:52
Alignment explanation
Indices: 26506--26605 Score: 182
Period size: 52 Copynumber: 1.9 Consensus size: 52
26496 AACATCTTGA
*
26506 ATACTTGATTCTAATCCTATCAGCTCAATCAATTTAAGTCCTCATTTCATTC
1 ATACTTGATCCTAATCCTATCAGCTCAATCAATTTAAGTCCTCATTTCATTC
*
26558 ATACTTGATCCTAATCCTATCAGCTCAATCAATTTAATTCCTCATTTC
1 ATACTTGATCCTAATCCTATCAGCTCAATCAATTTAAGTCCTCATTTC
26606 CCGTCAAGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.29, C:0.26, G:0.05, T:0.40
Consensus pattern (52 bp):
ATACTTGATCCTAATCCTATCAGCTCAATCAATTTAAGTCCTCATTTCATTC
Done.