Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1374
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: 7885
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Found at i:634 original size:15 final size:15
Alignment explanation
Indices: 616--646 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
606 TAATTACTAA
616 TAAGTTAAATTCTAT
1 TAAGTTAAATTCTAT
*
631 TAAGTTATATTCTAT
1 TAAGTTAAATTCTAT
646 T
1 T
647 TTGATTGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (15 bp):
TAAGTTAAATTCTAT
Found at i:699 original size:15 final size:15
Alignment explanation
Indices: 679--741 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 15
669 AATTTATTTA
* *
679 AATTTAATATATATT
1 AATTTAAAATAAATT
694 AATTTAAAATAAATT
1 AATTTAAAATAAATT
* **
709 TA-TTAAAATATTTT
1 AATTTAAAATAAATT
*
723 TATTT-AAATAAATT
1 AATTTAAAATAAATT
737 AATTT
1 AATTT
742 TTATTATTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 23 0.59
15 16 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTTAAAATAAATT
Found at i:3245 original size:2 final size:2
Alignment explanation
Indices: 3240--3284 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
3230 AATACTATAT
* * * *
3240 AC AC AC AC AC AT AC AC AC AC GC AC AC AC AC AC GC GC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
3282 AC A
1 AC A
3285 TACCAACTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.47, G:0.07, T:0.02
Consensus pattern (2 bp):
AC
Found at i:3272 original size:12 final size:12
Alignment explanation
Indices: 3240--3283 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
3230 AATACTATAT
* *
3240 ACACACACACAT
1 ACACACACGCAC
3252 ACACACACGCAC
1 ACACACACGCAC
*
3264 ACACACACGCGC
1 ACACACACGCAC
3276 ACACACAC
1 ACACACAC
3284 ATACCAACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.43, C:0.48, G:0.07, T:0.02
Consensus pattern (12 bp):
ACACACACGCAC
Found at i:3276 original size:14 final size:14
Alignment explanation
Indices: 3240--3284 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
3230 AATACTATAT
* *
3240 ACACACACACATAC
1 ACACACGCACACAC
3254 ACACACGCACACAC
1 ACACACGCACACAC
*
3268 ACACGCGCACACAC
1 ACACACGCACACAC
3282 ACA
1 ACA
3285 TACCAACTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.44, C:0.47, G:0.07, T:0.02
Consensus pattern (14 bp):
ACACACGCACACAC
Found at i:5252 original size:26 final size:25
Alignment explanation
Indices: 5221--5301 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 25
5211 ACATCTTTAA
5221 AATTAAACTATATAATATAAAAAAAT
1 AATTAAA-TATATAATATAAAAAAAT
*
5247 AATTAAA-ATATAATATAAAATAAAA
1 AATTAAATATATAATATAAAA-AAAT
* *
5272 AATATAAATATACTAAATATATAAATAT
1 AAT-TAAATATA-T-AATATAAAAAAAT
5300 AA
1 AA
5302 AAAAAATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
24 13 0.28
25 6 0.13
26 11 0.24
27 3 0.07
28 5 0.11
29 8 0.17
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
AATTAAATATATAATATAAAAAAAT
Found at i:5258 original size:19 final size:18
Alignment explanation
Indices: 5234--5308 Score: 66
Period size: 17 Copynumber: 4.2 Consensus size: 18
5224 TAAACTATAT
5234 AATATAAA-AAAATAATTAA
1 AATATAAATAAAATAA--AA
5253 AATATAATATAAAATAAAA
1 AATATAA-ATAAAATAAAA
* *
5272 AATATAAATATACT-AAA
1 AATATAAATAAAATAAAA
* *
5289 TATATAAATATAA-AAAA
1 AATATAAATAAAATAAAA
5306 AAT
1 AAT
5309 TTATAAAACA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
17 19 0.40
18 5 0.10
19 16 0.33
20 1 0.02
21 7 0.15
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (18 bp):
AATATAAATAAAATAAAA
Found at i:5298 original size:8 final size:8
Alignment explanation
Indices: 5259--5300 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
5249 TTAAAATATA
5259 ATATAAA-
1 ATATAAAT
*
5266 ATA-AAAA
1 ATATAAAT
5273 ATATAAAT
1 ATATAAAT
5281 ATACTAAAT
1 ATA-TAAAT
5290 ATATAAAT
1 ATATAAAT
5298 ATA
1 ATA
5301 AAAAAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
6 3 0.10
7 6 0.19
8 14 0.45
9 8 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (8 bp):
ATATAAAT
Found at i:5304 original size:31 final size:31
Alignment explanation
Indices: 5218--5306 Score: 94
Period size: 30 Copynumber: 2.9 Consensus size: 31
5208 GTTACATCTT
*
5218 TAAAATTAAACTATAT-AATATAAAAAAATAAT
1 TAAAA-TAAA-TATATAAATATAAAAAAATAAA
*
5250 TAAAATATAATATA-AAATA-AAAAATATAAA
1 TAAAATA-AATATATAAATATAAAAAAATAAA
* *
5280 TATACTAAATATATAAATATAAAAAAA
1 TAAAATAAATATATAAATATAAAAAAA
5307 ATTTATAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
29 6 0.12
30 19 0.40
31 16 0.33
32 7 0.15
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (31 bp):
TAAAATAAATATATAAATATAAAAAAATAAA
Found at i:5313 original size:19 final size:19
Alignment explanation
Indices: 5229--5324 Score: 54
Period size: 19 Copynumber: 4.8 Consensus size: 19
5219 AAAATTAAAC
*
5229 TATATAATATAAAAAAATAAT
1 TATA-AATATAAAAAAA-ATT
*
5250 TA-AAATATAATATAAAA-T
1 TATAAATATAA-AAAAAATT
* * *
5268 AAAAAATATAAATATACTAAATA
1 TATAAATATAAA-A-A--AAATT
5291 TATAAATATAAAAAAAATT
1 TATAAATATAAAAAAAATT
*
5310 TATAAA-ACAAAAAAA
1 TATAAATATAAAAAAA
5325 TATTACAGAC
Statistics
Matches: 60, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
18 11 0.18
19 26 0.43
20 6 0.10
21 3 0.05
22 4 0.07
23 10 0.17
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
TATAAATATAAAAAAAATT
Done.