Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold804
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: 36451
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:10714 original size:54 final size:54
Alignment explanation
Indices: 10612--10719 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
10602 TGGATTTATA
* * * *
10612 CACTTAATAATTTTAAATCAAATTTTATTTAAAAAAGGTATTTTAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAGGGATTTCAATCTTAAAT
* *
10666 CACTTAATAATCTTAAATCGAATTTGA-TTAGAAACAGGGATTTCAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTA-AAAAAGGGATTTCAATCTTAAAT
10720 TAGTGACGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 3 0.06
54 44 0.94
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (54 bp):
CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAGGGATTTCAATCTTAAAT
Found at i:12516 original size:17 final size:17
Alignment explanation
Indices: 12495--12528 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
12485 TTATTATTAA
12495 ATAT-ATTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12512 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12529 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:16186 original size:6 final size:6
Alignment explanation
Indices: 16175--16221 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
16165 TTGAGCTCTT
*
16175 TTTTTC TTTTTC -TTTT- TTTTTC TTTTCCC TTTTTC TTTTT- TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTT-TC TTTTTC TTTTTC TTTTTC
16221 T
1 T
16222 ACTATTGGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
5 13 0.37
6 17 0.49
7 5 0.14
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:16355 original size:13 final size:13
Alignment explanation
Indices: 16337--16361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16327 CTGCTGTTGT
16337 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
16350 TTTTTTTCTTTT
1 TTTTTTTCTTTT
16362 TTCTGCTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:16434 original size:19 final size:21
Alignment explanation
Indices: 16395--16434 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
16385 GGATGCCTAC
*
16395 TGCTGGGCTGTCTGGCCTGCT
1 TGCTGGGCTGTCTGGCATGCT
16416 TGCTGGG-TG-CTGGCATGCT
1 TGCTGGGCTGTCTGGCATGCT
16435 GTTAAGGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.03, C:0.25, G:0.40, T:0.33
Consensus pattern (21 bp):
TGCTGGGCTGTCTGGCATGCT
Found at i:16605 original size:6 final size:6
Alignment explanation
Indices: 16596--16669 Score: 53
Period size: 6 Copynumber: 11.7 Consensus size: 6
16586 TTGCTCTTCT
* * *
16596 TTTTTC TTTTTA TTTTTC TTTCTTTC TTTTGT- TTTCTCTC TCTTTC TTCTTCC
1 TTTTTC TTTTTC TTTTTC -TT-TTTC TTTT-TC TTT-T-TC TTTTTC TT-TTTC
16649 TTTTTC TTTTTC TTTTT- TTTT
1 TTTTTC TTTTTC TTTTTC TTTT
16670 CAAACCCTAG
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
5 4 0.07
6 32 0.58
7 13 0.24
8 6 0.11
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:16605 original size:19 final size:20
Alignment explanation
Indices: 16583--16625 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
16573 ATATTTTTAT
*
16583 TTTTTGCTCTTCTTT-TTTC
1 TTTTTACTCTTCTTTCTTTC
* *
16602 TTTTTATTTTTCTTTCTTTC
1 TTTTTACTCTTCTTTCTTTC
16622 TTTT
1 TTTT
16626 GTTTTCTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTTACTCTTCTTTCTTTC
Found at i:17310 original size:29 final size:30
Alignment explanation
Indices: 17276--17385 Score: 118
Period size: 29 Copynumber: 3.7 Consensus size: 30
17266 CACAACTTTT
*
17276 GAGGTCAAAATGTAATTTTAAGAAAATTTA
1 GAGGTCAAAATATAATTTTAAGAAAATTTA
* *
17306 G-GGTCAAAATATAATTTTAAGAAAGTTGA
1 GAGGTCAAAATATAATTTTAAGAAAATTTA
* *
17335 GATGTCAAAATATAATTTT-A-AAAAGTTA
1 GAGGTCAAAATATAATTTTAAGAAAATTTA
* *
17363 GGTGGTCAAAATGTAAATTTTAA
1 -GAGGTCAAAATAT-AATTTTAA
17386 ATTTTATATT
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
28 5 0.08
29 37 0.56
30 23 0.35
31 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (30 bp):
GAGGTCAAAATATAATTTTAAGAAAATTTA
Found at i:29380 original size:18 final size:18
Alignment explanation
Indices: 29357--29391 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29347 CGAGGCTTGA
*
29357 ATTTTCAAGCTCGAGCCT
1 ATTTTCAAGCTCAAGCCT
29375 ATTTTCAAGCTCAAGCC
1 ATTTTCAAGCTCAAGCC
29392 CGACCCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (18 bp):
ATTTTCAAGCTCAAGCCT
Done.