Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold559
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: 54056
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1127 original size:13 final size:14
Alignment explanation
Indices: 1109--1141 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1099 TATAATTTAA
1109 TTTAATTTTCT-TT
1 TTTAATTTTCTATT
*
1122 TTTAATTTTTTATT
1 TTTAATTTTCTATT
1136 TTTAAT
1 TTTAAT
1142 GGCTTTCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTAATTTTCTATT
Found at i:3162 original size:23 final size:23
Alignment explanation
Indices: 3136--3203 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
3126 ATAAATACTC
3136 ATATTTATATTATTAAAATTAAA
1 ATATTTATATTATTAAAATTAAA
* *
3159 ATATTCATATT-TTAAACTATAAA
1 ATATTTATATTATTAAAAT-TAAA
* *
3182 ATATTTA-ATGATTAAAAATAAA
1 ATATTTATATTATTAAAATTAAA
3204 TATGCATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
22 12 0.32
23 25 0.68
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (23 bp):
ATATTTATATTATTAAAATTAAA
Found at i:7187 original size:2 final size:2
Alignment explanation
Indices: 7180--7216 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
7170 AACAACTCAT
7180 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
7217 TTGTAAGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:9446 original size:5 final size:5
Alignment explanation
Indices: 9436--9466 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
9426 TGACCTAGGA
9436 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
9467 GGATGAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTAAT
Found at i:16058 original size:71 final size:71
Alignment explanation
Indices: 15977--16114 Score: 276
Period size: 71 Copynumber: 1.9 Consensus size: 71
15967 TAAAGTACAA
15977 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
1 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
16042 AAAAGG
66 AAAAGG
16048 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
1 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
16113 AA
66 AA
16115 GAGGAAATTG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (71 bp):
TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
AAAAGG
Found at i:24216 original size:30 final size:31
Alignment explanation
Indices: 24180--24247 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
24170 GTTTCATTTC
*
24180 AGTCACTCAAC-TTTTAAAAAA-TAACAAAAT
1 AGTCACT-AACGTTATAAAAAAGTAACAAAAT
*
24210 AGTCACTAACGTTATAAAAAAGTGACAAAAT
1 AGTCACTAACGTTATAAAAAAGTAACAAAAT
24241 AGTCACT
1 AGTCACT
24248 GATTAACAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 3 0.09
30 16 0.47
31 15 0.44
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (31 bp):
AGTCACTAACGTTATAAAAAAGTAACAAAAT
Found at i:24512 original size:3 final size:3
Alignment explanation
Indices: 24504--24529 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
24494 ACGTCTTTGC
24504 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
24530 ATGGCTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:25095 original size:14 final size:14
Alignment explanation
Indices: 25078--25115 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
25068 CTTCTTTTTC
*
25078 TTCTTTTCTTCCTT
1 TTCTTTTCTTCATT
25092 TTCTTTTCTTCATT
1 TTCTTTTCTTCATT
*
25106 TTCTCTTCTT
1 TTCTTTTCTT
25116 AAACCCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (14 bp):
TTCTTTTCTTCATT
Found at i:36422 original size:25 final size:24
Alignment explanation
Indices: 36386--36432 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
36376 CTCATGTTTT
36386 AAAAAATAAATCAT-AAAATTAATA
1 AAAAAATAAATC-TCAAAATTAATA
*
36410 AAAAAATTTAATCTCAAAATTAA
1 AAAAAA-TAAATCTCAAAATTAA
36433 AAATAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAAAATAAATCTCAAAATTAATA
Found at i:39171 original size:21 final size:21
Alignment explanation
Indices: 39145--39184 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
39135 ATCGGTTGGA
39145 TAAGCTCTTACGAGCTTCTGT
1 TAAGCTCTTACGAGCTTCTGT
39166 TAAGCTCTTACGAGCTTCT
1 TAAGCTCTTACGAGCTTCT
39185 ACTGGAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TAAGCTCTTACGAGCTTCTGT
Found at i:53285 original size:24 final size:22
Alignment explanation
Indices: 53233--53287 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
53223 AAAAATGTTA
* *
53233 TCATTGTAGCTAATACTTTTAG
1 TCATTGTAGATAATACTTTTAC
* *
53255 TCCTTGTAGATAGGATATTTTTAC
1 TCATTGTAGATA--ATACTTTTAC
53279 TCATTGTAG
1 TCATTGTAG
53288 CTATACTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 10 0.38
24 16 0.62
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (22 bp):
TCATTGTAGATAATACTTTTAC
Done.