Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1932
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: 40818
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:11042 original size:20 final size:20
Alignment explanation
Indices: 11019--11065 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
11009 GGGTTAAGAT
*
11019 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
11039 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
11059 TGAGCTG
1 TGAGCTG
11066 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:12786 original size:48 final size:48
Alignment explanation
Indices: 12734--12839 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
12724 TTGTCTTTTC
*
12734 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
12782 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
12830 TTTCTTTTTC
1 TTTCTTTTTC
12840 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:15428 original size:20 final size:20
Alignment explanation
Indices: 15405--15451 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
15395 GGGTTAAGAT
*
15405 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
15425 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
15445 TGAGCTG
1 TGAGCTG
15452 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:21354 original size:21 final size:21
Alignment explanation
Indices: 21309--21371 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
21299 TTTGAACCAT
* *
21309 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
21331 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
21352 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
21372 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:25082 original size:10 final size:11
Alignment explanation
Indices: 25063--25106 Score: 79
Period size: 11 Copynumber: 4.0 Consensus size: 11
25053 TAGTAGTTTC
25063 TTCAAAAAAAA
1 TTCAAAAAAAA
25074 TTCAAAAAAAA
1 TTCAAAAAAAA
*
25085 ATCAAAAAAAA
1 TTCAAAAAAAA
25096 TTCAAAAAAAA
1 TTCAAAAAAAA
25107 AAATTTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:25083 original size:12 final size:12
Alignment explanation
Indices: 25066--25107 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
25056 TAGTTTCTTC
25066 AAAAAAAATTCA
1 AAAAAAAATTCA
25078 AAAAAAAA-TC-
1 AAAAAAAATTCA
25088 AAAAAAAATTCA
1 AAAAAAAATTCA
25100 AAAAAAAA
1 AAAAAAAA
25108 AATTTGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.29
11 4 0.14
12 16 0.57
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:25092 original size:22 final size:22
Alignment explanation
Indices: 25064--25107 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
25054 AGTAGTTTCT
25064 TCAAAAAAAATTCAAAAAAAAA
1 TCAAAAAAAATTCAAAAAAAAA
25086 TCAAAAAAAATTCAAAAAAAAA
1 TCAAAAAAAATTCAAAAAAAAA
25108 AATTTGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (22 bp):
TCAAAAAAAATTCAAAAAAAAA
Found at i:25172 original size:16 final size:16
Alignment explanation
Indices: 25151--25207 Score: 105
Period size: 16 Copynumber: 3.5 Consensus size: 16
25141 TATCAAGTTG
25151 AAAAAAAATTTCGTGA
1 AAAAAAAATTTCGTGA
25167 AAAAAAAATTTCGTGAA
1 AAAAAAAATTTCGTG-A
25184 AAAAAAAATTTCGTGA
1 AAAAAAAATTTCGTGA
25200 AAAAAAAA
1 AAAAAAAA
25208 GAAGCTAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 24 0.60
17 16 0.40
ACGTcount: A:0.63, C:0.05, G:0.11, T:0.21
Consensus pattern (16 bp):
AAAAAAAATTTCGTGA
Found at i:25173 original size:17 final size:17
Alignment explanation
Indices: 25151--25207 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
25141 TATCAAGTTG
25151 AAAAAAAATTTCGTG-A
1 AAAAAAAATTTCGTGAA
25167 AAAAAAAATTTCGTGAA
1 AAAAAAAATTTCGTGAA
25184 AAAAAAAATTTCGTGAA
1 AAAAAAAATTTCGTGAA
25201 AAAAAAA
1 AAAAAAA
25208 GAAGCTAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
16 15 0.38
17 25 0.62
ACGTcount: A:0.63, C:0.05, G:0.11, T:0.21
Consensus pattern (17 bp):
AAAAAAAATTTCGTGAA
Found at i:31577 original size:22 final size:22
Alignment explanation
Indices: 31547--31589 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
31537 TTTGGTATTT
31547 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
31569 GGGATTTGGTACGAAATGGTA
1 GGGAATTGGTACGAAATGGTA
31590 GTGGTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.37, T:0.26
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:33410 original size:23 final size:23
Alignment explanation
Indices: 33380--33433 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
33370 TGTAGATTCA
33380 AAAAAAAATCGAAAAAAAAATCG
1 AAAAAAAATCGAAAAAAAAATCG
* *
33403 AAAAAAAATTGAAAAAAAAATTG
1 AAAAAAAATCGAAAAAAAAATCG
33426 AAAAAAAA
1 AAAAAAAA
33434 ATTGCATACG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.78, C:0.04, G:0.07, T:0.11
Consensus pattern (23 bp):
AAAAAAAATCGAAAAAAAAATCG
Found at i:33436 original size:12 final size:12
Alignment explanation
Indices: 33379--33437 Score: 93
Period size: 12 Copynumber: 5.0 Consensus size: 12
33369 TTGTAGATTC
*
33379 AAAAAAAAATCG
1 AAAAAAAAATTG
*
33391 AAAAAAAAATCG
1 AAAAAAAAATTG
33403 -AAAAAAAATTG
1 AAAAAAAAATTG
33414 AAAAAAAAATTG
1 AAAAAAAAATTG
33426 AAAAAAAAATTG
1 AAAAAAAAATTG
33438 CATACGGTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
11 10 0.22
12 35 0.78
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTG
Done.