Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2041
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: 19981
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2125 original size:46 final size:46
Alignment explanation
Indices: 2075--2250 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
2065 TGGTTGAGCA
2075 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2121 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
2166 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2214 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2251 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:2231 original size:93 final size:93
Alignment explanation
Indices: 2072--2243 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
2062 GGATGGTTGA
* *
2072 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2137 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
2165 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2230 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
2244 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:5705 original size:15 final size:15
Alignment explanation
Indices: 5685--5715 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5675 AATTATGAAA
5685 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
5700 GATATGTTTTGTATT
1 GATATGTTTTGGATT
5715 G
1 G
5716 GAATTTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:9653 original size:11 final size:10
Alignment explanation
Indices: 9637--9666 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
9627 TTCGTAACGA
9637 AAAAAAAAGTC
1 AAAAAAAA-TC
9648 AAAAAAAATC
1 AAAAAAAATC
9658 AAAAAAAAT
1 AAAAAAAAT
9667 TTTGAGTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:14181 original size:20 final size:20
Alignment explanation
Indices: 14158--14204 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
14148 GGGTTAAGAT
*
14158 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
14178 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
14198 TGAGCTG
1 TGAGCTG
14205 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:15945 original size:47 final size:47
Alignment explanation
Indices: 15868--15972 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 47
15858 TTGTCTTTTC
* *
15868 TTTCTTTTTCAATTTTCTCTTTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTTCTCTCTTT-CTCACATCCTTT-TTCAATCTCAA
* *
15916 TTTCTTTTTCGATTTCTTTCTCTTT-TCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTT-TCTCTCTTTCTCACATCCTTTTTCAATCTCAA
15963 TTTCTTTTTC
1 TTTCTTTTTC
15973 CATGACACTC
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
47 26 0.51
48 18 0.35
49 7 0.14
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (47 bp):
TTTCTTTTTCAATTTTCTCTCTTTCTCACATCCTTTTTCAATCTCAA
Found at i:17004 original size:12 final size:12
Alignment explanation
Indices: 16982--17072 Score: 88
Period size: 11 Copynumber: 8.2 Consensus size: 12
16972 CTCGCAAGAC
16982 TTTTCACTTTTT
1 TTTTCACTTTTT
16994 TTTT--CTTTTT
1 TTTTCACTTTTT
17004 TTTTCAC-TTTT
1 TTTTCACTTTTT
17015 TTTTCA--TTTT
1 TTTTCACTTTTT
17025 TTTTCACTTTTT
1 TTTTCACTTTTT
* *
17037 TTTTGA-ATTTT
1 TTTTCACTTTTT
*
17048 TTTT-AATTTTT
1 TTTTCACTTTTT
* *
17059 TTTTGAATTTTT
1 TTTTCACTTTTT
17071 TT
1 TT
17073 GATTTTTTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
10 21 0.30
11 26 0.37
12 23 0.33
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTCACTTTTT
Found at i:17007 original size:22 final size:22
Alignment explanation
Indices: 16982--17082 Score: 118
Period size: 21 Copynumber: 4.7 Consensus size: 22
16972 CTCGCAAGAC
*
16982 TTTTCACTTTTTTTTTCTTTTT
1 TTTTCACTTTTTTTTTCATTTT
17004 TTTTCAC-TTTTTTTTCATTTT
1 TTTTCACTTTTTTTTTCATTTT
*
17025 TTTTCACTTTTTTTTTGAATTTT
1 TTTTCACTTTTTTTTT-CATTTT
* * *
17048 TTTT-AATTTTTTTTTGAATTT
1 TTTTCACTTTTTTTTTCATTTT
*
17069 TTTTGA-TTTTTTTT
1 TTTTCACTTTTTTTT
17083 ACTCCAATAC
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
21 36 0.51
22 26 0.37
23 9 0.13
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.78
Consensus pattern (22 bp):
TTTTCACTTTTTTTTTCATTTT
Found at i:17082 original size:10 final size:10
Alignment explanation
Indices: 16990--17082 Score: 87
Period size: 10 Copynumber: 8.8 Consensus size: 10
16980 ACTTTTCACT
*
16990 TTTTTTTTCT
1 TTTTTTTTCA
17000 TTTTTTTTCA
1 TTTTTTTTCA
17010 CTTTTTTTTCA
1 -TTTTTTTTCA
17021 TTTTTTTTCA
1 TTTTTTTTCA
*
17031 CTTTTTTTTTGAA
1 --TTTTTTTT-CA
*
17044 TTTTTTTTAA
1 TTTTTTTTCA
*
17054 TTTTTTTTTGA
1 -TTTTTTTTCA
* *
17065 ATTTTTTTGA
1 TTTTTTTTCA
17075 TTTTTTTT
1 TTTTTTTT
17083 ACTCCAATAC
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
10 37 0.51
11 27 0.37
12 8 0.11
13 1 0.01
ACGTcount: A:0.11, C:0.06, G:0.03, T:0.80
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:18573 original size:20 final size:21
Alignment explanation
Indices: 18550--18597 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
18540 GGGTTAAGAT
*
18550 TGAGCTGAATTGAGCT-TGAG
1 TGAGCTGAATTGAGCTCGGAG
* *
18570 TGAGTTGACTTGAGCTCGGAG
1 TGAGCTGAATTGAGCTCGGAG
18591 TGAGCTG
1 TGAGCTG
18598 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.21, C:0.12, G:0.38, T:0.29
Consensus pattern (21 bp):
TGAGCTGAATTGAGCTCGGAG
Done.