Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold467
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: 10867
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Found at i:37 original size:14 final size:15
Alignment explanation
Indices: 18--47 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
8 TTTAAAATTA
18 TAAATATT-ATTTTT
1 TAAATATTAATTTTT
32 TAAATATTAATTTTT
1 TAAATATTAATTTTT
47 T
1 T
48 TTAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TAAATATTAATTTTT
Found at i:158 original size:22 final size:22
Alignment explanation
Indices: 133--194 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
123 AATAAACATT
*
133 TAAATTTTTAAATAAATTTGTA
1 TAAATTTTTAAATAAATATGTA
**
155 TAAAAATTTAAA-AAA-ATGTA
1 TAAATTTTTAAATAAATATGTA
*
175 AAATATTTTTAAAATAAATA
1 TAA-ATTTTT-AAATAAATA
195 AAAATTATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
20 6 0.20
21 7 0.23
22 13 0.43
23 3 0.10
24 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
TAAATTTTTAAATAAATATGTA
Found at i:266 original size:19 final size:18
Alignment explanation
Indices: 244--316 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 18
234 ATTTAAATCA
244 TTTAAATATTAAAAAATAT
1 TTTAAATATT-AAAAATAT
** *
263 TTTAAATCATTTTAAATGT
1 TTTAAAT-ATTAAAAATAT
282 TTTATAATATTAAAAATAT
1 TTTA-AATATTAAAAATAT
301 ATTT-AATATTTAAAAA
1 -TTTAAATA-TTAAAAA
317 ATAATTTGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 4 0.09
19 31 0.70
20 9 0.20
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (18 bp):
TTTAAATATTAAAAATAT
Found at i:274 original size:10 final size:9
Alignment explanation
Indices: 235--311 Score: 50
Period size: 9 Copynumber: 8.2 Consensus size: 9
225 ATTTAAAAAA
235 TTTAAATCA-
1 TTTAAAT-AT
244 TTTAAATAT
1 TTTAAATAT
**
253 TAAAAAATAT
1 T-TTAAATAT
263 TTTAAATCAT
1 TTTAAAT-AT
*
273 TTTAAATGT
1 TTTAAATAT
282 TTTATAATAT
1 TTTA-AATAT
**
292 TAAAAATAT
1 TTTAAATAT
301 ATTT-AATAT
1 -TTTAAATAT
310 TT
1 TT
312 AAAAAATAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
8 3 0.06
9 27 0.51
10 23 0.43
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (9 bp):
TTTAAATAT
Found at i:337 original size:31 final size:31
Alignment explanation
Indices: 285--369 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 31
275 TAAATGTTTT
*
285 ATAATATTAAAAATATATTTAATATTTA-AAAA
1 ATAAT-TT-AAAATATTTTTAATATTTATAAAA
317 ATAATTTGAAAATATTTTTAATATTTATAAAA
1 ATAATTT-AAAATATTTTTAATATTTATAAAA
349 A-ATATTATAAAATATTTTTAA
1 ATA-ATT-TAAAATATTTTTAA
370 AAATACATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
31 21 0.44
32 26 0.54
33 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (31 bp):
ATAATTTAAAATATTTTTAATATTTATAAAA
Found at i:3834 original size:30 final size:30
Alignment explanation
Indices: 3798--3918 Score: 158
Period size: 30 Copynumber: 4.1 Consensus size: 30
3788 GGTCAAATGG
* *
3798 ACTCGAACCGCCTATATCCGGGTGATATGA
1 ACTCGAACCACCTATGTCCGGGTGATATGA
*
3828 ACTCGAACCACCCATGT-CGGGTGATATGA
1 ACTCGAACCACCTATGTCCGGGTGATATGA
* *
3857 ACTTGAACCATAC-ATGTCCGGGTGATATGA
1 ACTCGAACCA-CCTATGTCCGGGTGATATGA
*
3887 ACTCGAACCACCTATGTCC-GGTTATATGA
1 ACTCGAACCACCTATGTCCGGGTGATATGA
3916 ACT
1 ACT
3919 GCTCTGGGAC
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
29 38 0.47
30 42 0.52
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (30 bp):
ACTCGAACCACCTATGTCCGGGTGATATGA
Found at i:9207 original size:18 final size:18
Alignment explanation
Indices: 9172--9214 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
9162 TAAAAAATAT
*
9172 ATTTAATATATATTTTTAA
1 ATTT-ATATATATATTTAA
*
9191 ATTTATATTTATATTTAA
1 ATTTATATATATATTTAA
9209 ATTTAT
1 ATTTAT
9215 TAATCATCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTATATATATATTTAA
Found at i:9350 original size:21 final size:24
Alignment explanation
Indices: 9320--9365 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
9310 AAAAAGAATT
9320 AAAATAATATT-TAAA-ATTGTAA
1 AAAATAATATTATAAACATTGTAA
*
9342 AAAAT-ATATTATAAACATTTTAA
1 AAAATAATATTATAAACATTGTAA
9365 A
1 A
9366 TATACATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 9 0.43
23 7 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
AAAATAATATTATAAACATTGTAA
Found at i:9413 original size:13 final size:13
Alignment explanation
Indices: 9393--9434 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
9383 TTAAAATTAT
9393 AAAAAAT-AAATA
1 AAAAAATAAAATA
9405 AACAAAATAAAATA
1 AA-AAAATAAAATA
9419 AAAAAA-AAACATA
1 AAAAAATAAA-ATA
9432 AAA
1 AAA
9435 TTTCAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.19
13 15 0.56
14 7 0.26
ACGTcount: A:0.83, C:0.05, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAATA
Found at i:9416 original size:18 final size:18
Alignment explanation
Indices: 9395--9435 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
9385 AAAATTATAA
*
9395 AAAATAAATAAACAAA-AT
1 AAAATAAA-AAAAAAACAT
9413 AAAATAAAAAAAAAACAT
1 AAAATAAAAAAAAAACAT
9431 AAAAT
1 AAAAT
9436 TTCAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAATAAAAAAAAAACAT
Found at i:9549 original size:25 final size:26
Alignment explanation
Indices: 9480--9543 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
9470 TTTAAAAAAA
* * *
9480 TATTTAAATATTATGATTTCTTATAT
1 TATTTAAAAATTATAATTTCTTAAAT
*
9506 TATTAAAAAATTATAATTT-TTAAAT
1 TATTTAAAAATTATAATTTCTTAAAT
9531 GTATTTAAAAATT
1 -TATTTAAAAATT
9544 GTATTTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 5 0.16
26 27 0.84
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
TATTTAAAAATTATAATTTCTTAAAT
Found at i:9762 original size:18 final size:17
Alignment explanation
Indices: 9727--9764 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
9717 TAATATTTAA
9727 TATATTTTTTTAAAATT
1 TATATTTTTTTAAAATT
9744 TATATTTATATTT-AAATT
1 TATATTT-T-TTTAAAATT
9762 TAT
1 TAT
9765 TAATAGTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 9 0.47
19 3 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATATTTTTTTAAAATT
Found at i:10142 original size:38 final size:38
Alignment explanation
Indices: 10095--10171 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 38
10085 CAAATTTTTT
*
10095 AAAATTAATATATAAA-TTAAATAAGCAAAATAAAT-TAAG
1 AAAATTAATATA-AAACTTAAAAAAG-AAAA-AAATCTAAG
10134 AAAA-TAATATAAAACTTAAAAAAGAAAAAAATCTAAG
1 AAAATTAATATAAAACTTAAAAAAGAAAAAAATCTAAG
10171 A
1 A
10172 GAGAGACAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 4 0.11
37 12 0.34
38 15 0.43
39 4 0.11
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (38 bp):
AAAATTAATATAAAACTTAAAAAAGAAAAAAATCTAAG
Found at i:10203 original size:9 final size:9
Alignment explanation
Indices: 10189--10219 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
10179 AAAATATAAG
10189 AAAAAAAGT
1 AAAAAAAGT
10198 -AAAAAAGT
1 AAAAAAAGT
10206 AAAAAAAGT
1 AAAAAAAGT
10215 AAAAA
1 AAAAA
10220 TAATATAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAAAAAGT
Found at i:10209 original size:7 final size:8
Alignment explanation
Indices: 10190--10219 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
10180 AAATATAAGA
10190 AAAAAAGT
1 AAAAAAGT
10198 AAAAAAGT
1 AAAAAAGT
10206 AAAAAAAGT
1 -AAAAAAGT
10215 AAAAA
1 AAAAA
10220 TAATATAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (8 bp):
AAAAAAGT
Done.