Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold407
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: 38272
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:10390 original size:13 final size:13
Alignment explanation
Indices: 10372--10396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10362 TACCCTTTTC
10372 TTGTCTTTTTCTT
1 TTGTCTTTTTCTT
10385 TTGTCTTTTTCT
1 TTGTCTTTTTCT
10397 AACTTATTTT
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:0.16, G:0.08, T:0.76
Consensus pattern (13 bp):
TTGTCTTTTTCTT
Found at i:10452 original size:30 final size:31
Alignment explanation
Indices: 10403--10464 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
10393 TTCTAACTTA
*
10403 TTTTCTCTTCTTTCTTCAATTTCCTTTTCAC
1 TTTTCTCTTCTGTCTTCAATTTCCTTTTCAC
*
10434 TTTTCTTTTCTGT-TTCAATTTCCTTTTCAC
1 TTTTCTCTTCTGTCTTCAATTTCCTTTTCAC
10464 T
1 T
10465 CTCAATCCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.10, C:0.26, G:0.02, T:0.63
Consensus pattern (31 bp):
TTTTCTCTTCTGTCTTCAATTTCCTTTTCAC
Found at i:10496 original size:13 final size:13
Alignment explanation
Indices: 10478--10502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10468 AATCCCTTTT
10478 TTTCTCTTTTTCA
1 TTTCTCTTTTTCA
10491 TTTCTCTTTTTC
1 TTTCTCTTTTTC
10503 GTTTTTTCCA
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:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTCTTTTTCA
Found at i:13831 original size:9 final size:10
Alignment explanation
Indices: 13810--13842 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
13800 AAAAGAGAAG
13810 AAATTCAAAA
1 AAATTCAAAA
13820 AAATTCAAAA
1 AAATTCAAAA
13830 AAA-TCGAAAA
1 AAATTC-AAAA
13840 AAA
1 AAA
13843 AGAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 2 0.09
10 20 0.91
ACGTcount: A:0.73, C:0.09, G:0.03, T:0.15
Consensus pattern (10 bp):
AAATTCAAAA
Found at i:21120 original size:20 final size:20
Alignment explanation
Indices: 21097--21143 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
21087 GGGTTAAGAT
*
21097 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
21117 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
21137 TGAGCTG
1 TGAGCTG
21144 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:22872 original size:18 final size:18
Alignment explanation
Indices: 22851--22890 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
22841 GATTGAGAGT
* * *
22851 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
22869 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
22887 GAAA
1 GAAA
22891 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:25697 original size:10 final size:10
Alignment explanation
Indices: 25682--25719 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
25672 ATTTGGGAAT
25682 TGGTATGAAA
1 TGGTATGAAA
*
25692 TGGTATGGAAT
1 TGGTAT-GAAA
25703 TGGTATGAAA
1 TGGTATGAAA
25713 TGGTATG
1 TGGTATG
25720 GTATTTGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (10 bp):
TGGTATGAAA
Found at i:25703 original size:21 final size:21
Alignment explanation
Indices: 25677--25739 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
25667 TTGGTATTTG
25677 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTATGAAATGGTAT
25698 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTATGAAATGGTAT
* * *
25719 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTATGAAATGGTA
25740 ATGGTTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 23 0.61
22 15 0.39
ACGTcount: A:0.30, C:0.02, G:0.33, T:0.35
Consensus pattern (21 bp):
GGAATTGGTATGAAATGGTAT
Found at i:30696 original size:14 final size:14
Alignment explanation
Indices: 30679--30729 Score: 75
Period size: 14 Copynumber: 3.5 Consensus size: 14
30669 AATTTTCAAA
30679 AAAAAAATTTCGTG
1 AAAAAAATTTCGTG
*
30693 AAAAAAAATTCGTG
1 AAAAAAATTTCGTG
30707 AAAAAAAAATTTCGTG
1 --AAAAAAATTTCGTG
30723 AAAAAAA
1 AAAAAAA
30730 AAGAAGAAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 20 0.61
16 13 0.39
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.22
Consensus pattern (14 bp):
AAAAAAATTTCGTG
Found at i:30696 original size:16 final size:16
Alignment explanation
Indices: 30677--30731 Score: 96
Period size: 15 Copynumber: 3.6 Consensus size: 16
30667 AGAATTTTCA
30677 AAAAAAAAATTTCGTG
1 AAAAAAAAATTTCGTG
30693 -AAAAAAAA-TTCGTG
1 AAAAAAAAATTTCGTG
30707 AAAAAAAAATTTCGTG
1 AAAAAAAAATTTCGTG
30723 AAAAAAAAA
1 AAAAAAAAA
30732 GAAGAAGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.16
15 16 0.43
16 15 0.41
ACGTcount: A:0.64, C:0.05, G:0.11, T:0.20
Consensus pattern (16 bp):
AAAAAAAAATTTCGTG
Done.