Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1459
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: 30171
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Found at i:2603 original size:40 final size:40
Alignment explanation
Indices: 2548--2722 Score: 305
Period size: 40 Copynumber: 4.4 Consensus size: 40
2538 TATGTGCATA
2548 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
2588 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCAAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
2628 GCATTCGTGTGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
2668 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCTCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
2708 GCATTCATGCTGGTT
1 GCATTCGTGCGGGTT
2723 GTTACATCCG
Statistics
Matches: 128, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 128 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:2746 original size:80 final size:80
Alignment explanation
Indices: 2548--2746 Score: 238
Period size: 80 Copynumber: 2.5 Consensus size: 80
2538 TATGTGCATA
* * * * * *
2548 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCG
1 GCATTCATGTGGGTTATTACAACCGAGTCAAATCCCGAAGGCATTCGTGCGGGTTATTATAACCG
2613 GGTTAAGTCCCAAAG
66 GGTTAAGTCCCAAAG
* * * * *
2628 GCATTCGTGTGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCG
1 GCATTCATGTGGGTTATTACAACCGAGTCAAATCCCGAAGGCATTCGTGCGGGTTATTATAACCG
* *
2693 GGTTAAGTCTCGAAG
66 GGTTAAGTCCCAAAG
* * *
2708 GCATTCATGCT-GGTTGTTACATCCGAGTCAAATTCCGAA
1 GCATTCATG-TGGGTTATTACAACCGAGTCAAATCCCGAA
2747 AGTATTTATG
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 106 0.99
81 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (80 bp):
GCATTCATGTGGGTTATTACAACCGAGTCAAATCCCGAAGGCATTCGTGCGGGTTATTATAACCG
GGTTAAGTCCCAAAG
Found at i:5860 original size:52 final size:52
Alignment explanation
Indices: 5782--5884 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
5772 ATTAAAGGAC
*
5782 TGACAGAGTGTCTTGATTAGATATAGGTTTGGTGCTCGTTGGCTTCTGCGCT
1 TGACAGAGTGTCTTGATTAGATATAGGTTTGGTGCTCATTGGCTTCTGCGCT
*
5834 TGACAGAGTGTCTTGATTGGATATAGGTTTGGTGCTCATTGGCTTCTGCGC
1 TGACAGAGTGTCTTGATTAGATATAGGTTTGGTGCTCATTGGCTTCTGCGC
5885 CTTTTTACAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.16, C:0.16, G:0.31, T:0.38
Consensus pattern (52 bp):
TGACAGAGTGTCTTGATTAGATATAGGTTTGGTGCTCATTGGCTTCTGCGCT
Found at i:14588 original size:40 final size:40
Alignment explanation
Indices: 14533--14747 Score: 376
Period size: 40 Copynumber: 5.4 Consensus size: 40
14523 TATGTGCATA
*
14533 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCTCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
14573 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
14613 GCATTCGTGCGGGTTATTATAACCGAGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
14653 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
14693 GCATTCGTGCGGGTTACTATAACCAGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
14733 GCATTCATGCTGGTT
1 GCATTCGTGCGGGTT
14748 GTTACATCCG
Statistics
Matches: 168, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 168 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:14771 original size:120 final size:120
Alignment explanation
Indices: 14533--14771 Score: 379
Period size: 120 Copynumber: 2.0 Consensus size: 120
14523 TATGTGCATA
* * *
14533 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCTCGAAGGCATTCGTGCGGGTTATTATAACCG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTACTATAACCA
* * * *
14598 GGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCGAGTTAAGTCCCGAAG
66 GGTTAAGTCCCGAAGGCATTCATGCGGGTTATTACAACCGAGTCAAATCCCGAAG
14653 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTACTATAACCA
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTACTATAACCA
* * * *
14718 GGTTAAGTCCCGAAGGCATTCATGCTGGTTGTTACATCCGAGTCAAATTCCGAA
66 GGTTAAGTCCCGAAGGCATTCATGCGGGTTATTACAACCGAGTCAAATCCCGAA
14772 AGTATTTATG
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (120 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTACTATAACCA
GGTTAAGTCCCGAAGGCATTCATGCGGGTTATTACAACCGAGTCAAATCCCGAAG
Found at i:21529 original size:48 final size:48
Alignment explanation
Indices: 21466--21562 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
21456 GATTAAGGTA
21466 TGTTCAATGTTACTTTTGGAAGTTTATACATCCTTTGGATGATTAGTC
1 TGTTCAATGTTACTTTTGGAAGTTTATACATCCTTTGGATGATTAGTC
21514 TGTTCAATGTTACTTTTGGAAGTTTATACATCCTTTGGATGATTAGTC
1 TGTTCAATGTTACTTTTGGAAGTTTATACATCCTTTGGATGATTAGTC
21562 T
1 T
21563 AAATTCTATC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (48 bp):
TGTTCAATGTTACTTTTGGAAGTTTATACATCCTTTGGATGATTAGTC
Found at i:23145 original size:40 final size:40
Alignment explanation
Indices: 23090--23184 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 40
23080 TATGTGCATA
23090 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
23130 GCATTCGTGTGGGTTATTATAACCGGGTTAAGTCTCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
23170 GCATTCATGCTGGTT
1 GCATTCGTGCGGGTT
23185 GTTACATCCG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:26326 original size:52 final size:52
Alignment explanation
Indices: 26248--26350 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
26238 ATTAAAGGAC
*
26248 TGACAGAGTGTCTTGATTAGATATAGGTTTGGTGCTCGTTGGCTTCTGCGCT
1 TGACAGAGTGTCTTGATTAGATATAGGTTTGGTGCTCATTGGCTTCTGCGCT
*
26300 TGACAGAGTGTCTTGATTGGATATAGGTTTGGTGCTCATTGGCTTCTGCGC
1 TGACAGAGTGTCTTGATTAGATATAGGTTTGGTGCTCATTGGCTTCTGCGC
26351 CTTTTTACAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.16, C:0.16, G:0.31, T:0.38
Consensus pattern (52 bp):
TGACAGAGTGTCTTGATTAGATATAGGTTTGGTGCTCATTGGCTTCTGCGCT
Done.