Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold670
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: 17175
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:4612 original size:17 final size:17
Alignment explanation
Indices: 4572--4614 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
4562 CGCCTCTTTC
*
4572 TTTTCTTTCCAATATTT
1 TTTTCTTTTCAATATTT
*
4589 TTCTCTTTTCAAT-TTT
1 TTTTCTTTTCAATATTT
4605 TGTTTCTTTT
1 T-TTTCTTTT
4615 TTCAGTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.12, C:0.16, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTTCTTTTCAATATTT
Found at i:4629 original size:19 final size:18
Alignment explanation
Indices: 4586--4632 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
4576 CTTTCCAATA
4586 TTTTTCTCTTTTCAATTT
1 TTTTTCTCTTTTCAATTT
* *
4604 TTGTTTCTTTTTTCAGTTT
1 TT-TTTCTCTTTTCAATTT
4623 CTTTTTCTCT
1 -TTTTTCTCT
4633 CGTCACTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 20 0.83
20 2 0.08
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.72
Consensus pattern (18 bp):
TTTTTCTCTTTTCAATTT
Found at i:5565 original size:14 final size:14
Alignment explanation
Indices: 5546--5573 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5536 ACTAGCTCTC
5546 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
5560 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
5574 CTTGATATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:5628 original size:12 final size:12
Alignment explanation
Indices: 5611--5658 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
5601 TGGAAACTAG
5611 TTTTTTTTCAAA
1 TTTTTTTTCAAA
* *
5623 TTTTTTTTTGAAT
1 -TTTTTTTTCAAA
* *
5636 TTTTTTTTCGAG
1 TTTTTTTTCAAA
5648 TTTTTTTTCAA
1 TTTTTTTTCAA
5659 GAAACTACTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:5629 original size:13 final size:13
Alignment explanation
Indices: 5611--5655 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
5601 TGGAAACTAG
*
5611 TTTTTTTTCAAAT
1 TTTTTTTTCGAAT
5624 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
*
5636 TTTTTTTTCGAGT
1 TTTTTTTTCGAAT
5649 TTTTTTT
1 TTTTTTT
5656 CAAGAAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:9900 original size:21 final size:22
Alignment explanation
Indices: 9858--9903 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
9848 ATAAACCATT
9858 AAGGCATCAAGGGTACCAAACC
1 AAGGCATCAAGGGTACCAAACC
9880 AAGGCATCAAGGGTA-CAAACC
1 AAGGCATCAAGGGTACCAAACC
9901 AAG
1 AAG
9904 AAAACATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.43, C:0.24, G:0.24, T:0.09
Consensus pattern (22 bp):
AAGGCATCAAGGGTACCAAACC
Found at i:10579 original size:22 final size:24
Alignment explanation
Indices: 10547--10590 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
10537 GATTCATTAA
*
10547 TTTTTAGTTAT-TT-TAGTTTGTG
1 TTTTTAATTATGTTATAGTTTGTG
10569 TTTTTAATTATGTTATAGTTTG
1 TTTTTAATTATGTTATAGTTTG
10591 CACATCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 2 0.11
24 7 0.37
ACGTcount: A:0.18, C:0.00, G:0.16, T:0.66
Consensus pattern (24 bp):
TTTTTAATTATGTTATAGTTTGTG
Found at i:11911 original size:13 final size:12
Alignment explanation
Indices: 11891--11927 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
11881 TATGTAGTTC
*
11891 TCAAAAAAAACT
1 TCAAAAAAAAAT
*
11903 TGAAAAAAAAAT
1 TCAAAAAAAAAT
11915 TCAAAAAAAAAT
1 TCAAAAAAAAAT
11927 T
1 T
11928 TTTTTTGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.70, C:0.08, G:0.03, T:0.19
Consensus pattern (12 bp):
TCAAAAAAAAAT
Found at i:11989 original size:12 final size:13
Alignment explanation
Indices: 11969--12012 Score: 65
Period size: 12 Copynumber: 3.5 Consensus size: 13
11959 GGATATCAAG
11969 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
11982 TT-TGAAAAAAAAA
1 TTGTG-AAAAAAAA
11995 TTGTG-AAAAAAA
1 TTGTGAAAAAAAA
12007 TTGTGA
1 TTGTGA
12013 TTGTGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 14 0.50
13 12 0.43
14 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.27
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:11992 original size:13 final size:14
Alignment explanation
Indices: 11969--12006 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
11959 GGATATCAAG
11969 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
11982 TT-TGAAAAAAAAA
1 TTGTGAAAAAAAAA
11995 TTGTGAAAAAAA
1 TTGTGAAAAAAA
12007 TTGTGATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 12 0.52
14 9 0.39
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:12985 original size:16 final size:17
Alignment explanation
Indices: 12955--12998 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
12945 AAAAGAAACC
12955 GAAAAAGAAACAAAATT
1 GAAAAAGAAACAAAATT
*
12972 GAAAAAGAGA-AAAATT
1 GAAAAAGAAACAAAATT
*
12988 GGAGAAAGAAA
1 -GAAAAAGAAA
12999 GAAAGAGTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.68, C:0.02, G:0.20, T:0.09
Consensus pattern (17 bp):
GAAAAAGAAACAAAATT
Done.