Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2744
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: 5733
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:3650 original size:2 final size:2
Alignment explanation
Indices: 3643--3670 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3633 CCGCAGAGTG
3643 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
3671 GATCATAAAT
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:4253 original size:3 final size:3
Alignment explanation
Indices: 4245--4295 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
4235 TTTCATTAGG
4245 TTA TTA TTA TTA TTA TTA TT- TT- TTA TTA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
4289 TTA TTA T
1 TTA TTA T
4296 ATAAACTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4272 original size:13 final size:13
Alignment explanation
Indices: 4245--4295 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
4235 TTTCATTAGG
4245 TTATTA-TTATTA
1 TTATTATTTATTA
*
4257 TTATTATTTTTTA
1 TTATTATTTATTA
*
4270 TTATTATATATTA
1 TTATTATTTATTA
4283 TTATTA-TTATTA
1 TTATTATTTATTA
4295 T
1 T
4296 ATAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 12 0.35
13 22 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTATTTATTA
Found at i:4272 original size:16 final size:17
Alignment explanation
Indices: 4246--4297 Score: 81
Period size: 16 Copynumber: 3.2 Consensus size: 17
4236 TTCATTAGGT
4246 TATTATTATTATTATTA
1 TATTATTATTATTATTA
*
4263 T-TTTTTATTATTA-TA
1 TATTATTATTATTATTA
4278 TATTATTATTATTATTA
1 TATTATTATTATTATTA
4295 TAT
1 TAT
4298 AAACTATTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 3 0.10
16 22 0.71
17 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:4296 original size:19 final size:19
Alignment explanation
Indices: 4245--4298 Score: 87
Period size: 19 Copynumber: 3.0 Consensus size: 19
4235 TTTCATTAGG
4245 TTATTATTATTATTAT-TA
1 TTATTATTATTATTATATA
4263 TT-TT-TTATTATTATATA
1 TTATTATTATTATTATATA
4280 TTATTATTATTATTATATA
1 TTATTATTATTATTATATA
4299 AACTATTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.30
17 6 0.18
18 4 0.12
19 13 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTATTATTATTATATA
Found at i:5491 original size:10 final size:10
Alignment explanation
Indices: 5458--5504 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
5448 ATGACATATC
*
5458 ATATTTAATT
1 ATATTTTATT
*
5468 TTATTTATATT
1 ATATTT-TATT
5479 AT-TTTT-TT
1 ATATTTTATT
5487 ATATTTTATT
1 ATATTTTATT
5497 ATATTTTA
1 ATATTTTA
5505 ATCATTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
8 4 0.13
9 5 0.16
10 18 0.58
11 4 0.13
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATATTTTATT
Found at i:5511 original size:19 final size:18
Alignment explanation
Indices: 5469--5515 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
5459 TATTTAATTT
* *
5469 TATTTATATTATTTTTTTA
1 TATTT-TATTATATTTTAA
5488 TATTTTATTATATTTTAA
1 TATTTTATTATATTTTAA
5506 TCATTTTATT
1 T-ATTTTATT
5516 TCATCCTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTTTATTATATTTTAA
Done.