Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1065
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: 10409
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Found at i:123 original size:8 final size:8
Alignment explanation
Indices: 110--140 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
100 TAAATTTAAT
110 TATAAAAA
1 TATAAAAA
118 TATAAAAA
1 TATAAAAA
*
126 TACAAAAA
1 TATAAAAA
134 TATAAAA
1 TATAAAA
141 TATTAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (8 bp):
TATAAAAA
Found at i:189 original size:50 final size:49
Alignment explanation
Indices: 135--489 Score: 249
Period size: 50 Copynumber: 7.2 Consensus size: 49
125 ATACAAAAAT
*
135 ATAAAATATTAATAATTTTTTATTATTTTTAAATAG-AATTTTGAGATTTA
1 ATAAAATATT-TTAATTTTTTATTATTTTTAAATAGTAA-TTTGAGATTTA
185 ATAAAATAAGTTTTAA-TTTTTATTA-TTTTAAATAGTAATTTGAGATTTA
1 ATAAAAT-A-TTTTAATTTTTTATTATTTTTAAATAGTAATTTGAGATTTA
* * * *
234 ATAAAGT-TTTTAATTTTTTATTATTTTTAAATAGTAA-CTAAGGTTT-
1 ATAAAATATTTTAATTTTTTATTATTTTTAAATAGTAATTTGAGATTTA
** * *
280 -T-TCA-A----AATCTTTTGTTA-TTTTAAATAGTAATTTGAGATTTGA
1 ATAAAATATTTTAATTTTTTATTATTTTTAAATAGTAATTTGAGATTT-A
* * ** *
322 TATAAAAATATCTTT-A-TCTTT-TTATTTTTAAATAGTAGTTCAAAATTTAA
1 -AT-AAAATAT-TTTAATTTTTTATTATTTTTAAATAGTAATTTGAGATTT-A
*
372 TATAAAATATTTTTTAATTTTTTATTATTTTTAAATAGTAATTAGAGATTTAA
1 -ATAAAATA--TTTTAATTTTTTATTATTTTTAAATAGTAATTTGAGATTT-A
* * **
425 TATAAAATATTTTTAAATTTTTTTGTTATTTTTAAATAGTGATTAAAGATTTA
1 -ATAAAATA-TTTT-AA-TTTTTTATTATTTTTAAATAGTAATTTGAGATTTA
478 TTATAAAATATT
1 --ATAAAATATT
490 ATTTTAATAG
Statistics
Matches: 247, Mismatches: 30, Indels: 53
0.75 0.09 0.16
Matches are distributed among these distances:
39 13 0.05
40 16 0.06
44 1 0.00
45 1 0.00
46 7 0.03
47 16 0.06
48 13 0.05
49 36 0.15
50 47 0.19
51 7 0.03
52 11 0.04
53 39 0.16
54 40 0.16
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (49 bp):
ATAAAATATTTTAATTTTTTATTATTTTTAAATAGTAATTTGAGATTTA
Found at i:410 original size:103 final size:105
Alignment explanation
Indices: 289--497 Score: 268
Period size: 107 Copynumber: 2.0 Consensus size: 105
279 TTTCAAAATC
* * *
289 TTTTGTTATTTTAAATAGTAATTTGAGATTTGATATAAAAATATCTTT-A-TCTTT-TTATTTTT
1 TTTTATTATTTTAAATAGTAATTAGAGATTTAATAT-AAAATATCTTTAATTCTTTGTTATTTTT
351 AAATAGT-AGTTCAAA-ATTTAATATAAAATATT-TTTTAATT
65 AAATAGTGA-TT-AAAGATTTAATATAAAATATTATTTTAATT
* *
391 TTTTATTATTTTTAAATAGTAATTAGAGATTTAATATAAAATATTTTTAAATTTTTTTGTTATTT
1 TTTTATTA-TTTTAAATAGTAATTAGAGATTTAATATAAAATATCTTT-AA-TTCTTTGTTATTT
*
456 TTAAATAGTGATTAAAGATTTATTATAAAATATTATTTTAAT
63 TTAAATAGTGATTAAAGATTTAATATAAAATATTATTTTAAT
498 AGAGAATTGG
Statistics
Matches: 92, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
102 17 0.18
103 26 0.28
104 1 0.01
106 7 0.08
107 33 0.36
108 8 0.09
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (105 bp):
TTTTATTATTTTAAATAGTAATTAGAGATTTAATATAAAATATCTTTAATTCTTTGTTATTTTTA
AATAGTGATTAAAGATTTAATATAAAATATTATTTTAATT
Found at i:411 original size:53 final size:52
Alignment explanation
Indices: 343--497 Score: 204
Period size: 53 Copynumber: 2.9 Consensus size: 52
333 CTTTATCTTT
343 TTATTTTTAAATAGTAGTTCAAAATTTAATATAAAATATTTTTTAATTTTTTA
1 TTATTTTTAAATAGTAGTT-AAAATTTAATATAAAATATTTTTTAATTTTTTA
* * * *
396 TTATTTTTAAATAGTAATTAGAGATTTAATATAAAATATTTTTAAATTTTTTTG
1 TTATTTTTAAATAGTAGTTA-AAATTTAATATAAAATATTTTTTAA-TTTTTTA
*
450 TTATTTTTAAATAGT-GATTAAAGATTTATTATAAAATATTATTTTAAT
1 TTATTTTTAAATAGTAG-TTAAA-ATTTAATATAAAATATT-TTTTAAT
498 AGAGAATTGG
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
52 1 0.01
53 42 0.47
54 41 0.46
55 5 0.06
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.54
Consensus pattern (52 bp):
TTATTTTTAAATAGTAGTTAAAATTTAATATAAAATATTTTTTAATTTTTTA
Found at i:475 original size:54 final size:52
Alignment explanation
Indices: 289--489 Score: 232
Period size: 54 Copynumber: 3.9 Consensus size: 52
279 TTTCAAAATC
** * *
289 TTTTGTTA-TTTTAAATAGTAATTTGAGATTTGATATAAAAATATCTTT-A-T
1 TTTTGTTATTTTTAAATAGTAATTAAAGATTTAATAT-AAAATATTTTTAATT
* *
339 CTTT-TTATTTTTAAATAGTAGTTCAAA-ATTTAATATAAAATATTTTTTAATT
1 TTTTGTTATTTTTAAATAGTAATT-AAAGATTTAATATAAAATA-TTTTTAATT
* *
391 TTTTATTATTTTTAAATAGTAATTAGAGATTTAATATAAAATATTTTTAAATTT
1 TTTTGTTATTTTTAAATAGTAATTAAAGATTTAATATAAAATATTTTT-AA-TT
* *
445 TTTTGTTATTTTTAAATAGTGATTAAAGATTTATTATAAAATATT
1 TTTTGTTATTTTTAAATAGTAATTAAAGATTTAATATAAAATATT
490 ATTTTAATAG
Statistics
Matches: 129, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
49 9 0.07
50 29 0.22
51 2 0.02
52 11 0.09
53 35 0.27
54 43 0.33
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.53
Consensus pattern (52 bp):
TTTTGTTATTTTTAAATAGTAATTAAAGATTTAATATAAAATATTTTTAATT
Found at i:1425 original size:2 final size:2
Alignment explanation
Indices: 1418--1463 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1408 ATTGTTAATA
1418 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1460 AG AG
1 AG AG
1464 TGACTCCCAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1653 original size:2 final size:2
Alignment explanation
Indices: 1648--1687 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1638 TCTGTTTCTT
*
1648 TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1688 CTCCTATGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2661 original size:2 final size:2
Alignment explanation
Indices: 2654--2678 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2644 TCTGCTTAAT
2654 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 T
2679 GTTCCTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:8143 original size:2 final size:2
Alignment explanation
Indices: 8136--8163 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8126 AACCTTTCTC
8136 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8164 TTATGAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9370 original size:11 final size:11
Alignment explanation
Indices: 9354--9397 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
9344 AAAATTTTTA
9354 TATATTTATAT
1 TATATTTATAT
9365 TATATTTATAT
1 TATATTTATAT
*
9376 TAT-TTTTTAT
1 TATATTTATAT
*
9386 TATACTTATAT
1 TATATTTATAT
9397 T
1 T
9398 TAAGTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (11 bp):
TATATTTATAT
Found at i:9386 original size:21 final size:20
Alignment explanation
Indices: 9350--9397 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
9340 ATAAAAAATT
9350 TTTATA-TATTTATATTATA
1 TTTATATTATTTATATTATA
*
9369 TTTATATTATTTTTTATTATA
1 TTTATATTA-TTTATATTATA
*
9390 CTTATATT
1 TTTATATT
9398 TAAGTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.24
20 2 0.08
21 17 0.68
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATATTATTTATATTATA
Found at i:9495 original size:18 final size:17
Alignment explanation
Indices: 9472--9509 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
9462 TTTATTCGTA
*
9472 TTATATTATTATTATTTT
1 TTATATTA-TATTATATT
9490 TTATATTATATTATATT
1 TTATATTATATTATATT
9507 TTA
1 TTA
9510 GTCATGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATATTATATTATATT
Done.