Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold873
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: 41518
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:3904 original size:17 final size:16
Alignment explanation
Indices: 3877--3924 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
3867 TCTTTTTCTT
*
3877 TCTTTTCTTTTCC-CAC
1 TCTTTTTTTTTCCTC-C
3893 TCTTTTTGTTTTCCTCC
1 TCTTTTT-TTTTCCTCC
3910 TCTTTTTTTTTCCTC
1 TCTTTTTTTTTCCTC
3925 TCGATCAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 14 0.48
17 14 0.48
18 1 0.03
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (16 bp):
TCTTTTTTTTTCCTCC
Found at i:5921 original size:17 final size:17
Alignment explanation
Indices: 5901--5935 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5891 CACTTTCTCT
*
5901 TTTTTTTTAATTCTGAA
1 TTTTTTTTAATACTGAA
5918 TTTTTTTTAATACTGAA
1 TTTTTTTTAATACTGAA
5935 T
1 T
5936 ACACAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.63
Consensus pattern (17 bp):
TTTTTTTTAATACTGAA
Found at i:10269 original size:21 final size:21
Alignment explanation
Indices: 10224--10286 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
10214 TTTGAACCAT
* *
10224 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
10246 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
10267 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
10287 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:10613 original size:18 final size:17
Alignment explanation
Indices: 10582--10626 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
10572 ATAGGTACAT
* *
10582 AAAAAAAGTCAAAATCAA
1 AAAAAAATTGAAAA-CAA
*
10600 AAAAAAATTGAAAAGAA
1 AAAAAAATTGAAAACAA
10617 AAAAAAATTG
1 AAAAAAATTG
10627 CATACGGTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.13
Consensus pattern (17 bp):
AAAAAAATTGAAAACAA
Found at i:12860 original size:17 final size:17
Alignment explanation
Indices: 12815--12868 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
12805 AGAAAAGAGC
* *
12815 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
12832 GAAAAATGAAAAAAAAA
1 GAAAATTCAAAAAAAAA
*
12849 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
12866 GAA
1 GAA
12869 TGAAAAGAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:14773 original size:12 final size:12
Alignment explanation
Indices: 14758--14812 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
14748 ATTGTAGATT
14758 AAAAAAATC-AA
1 AAAAAAATCGAA
14769 AAAAAAATCGAA
1 AAAAAAATCGAA
*
14781 AAAAAAATTGAA
1 AAAAAAATCGAA
* *
14793 AAAAAATTTGAA
1 AAAAAAATCGAA
14805 AAAAAAAT
1 AAAAAAAT
14813 TGCGTACGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
11 9 0.22
12 31 0.77
ACGTcount: A:0.76, C:0.04, G:0.05, T:0.15
Consensus pattern (12 bp):
AAAAAAATCGAA
Found at i:14774 original size:11 final size:11
Alignment explanation
Indices: 14758--14799 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
14748 ATTGTAGATT
14758 AAAAAAATCAA
1 AAAAAAATCAA
14769 AAAAAAATCGAA
1 AAAAAAATC-AA
**
14781 AAAAAAATTGA
1 AAAAAAATCAA
14792 AAAAAAAT
1 AAAAAAAT
14800 TTGAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.12
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:17084 original size:17 final size:18
Alignment explanation
Indices: 17045--17086 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
17035 AAGAAGAAAA
17045 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
17062 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
17079 TCAAAAGA
1 ACAAAAGA
17087 AAAAGAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:28969 original size:15 final size:15
Alignment explanation
Indices: 28949--28978 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28939 AGACCGTATA
28949 CAATTTTTTTCATTT
1 CAATTTTTTTCATTT
*
28964 CAATTTTTTTGATTT
1 CAATTTTTTTCATTT
28979 TTTTTTCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.67
Consensus pattern (15 bp):
CAATTTTTTTCATTT
Found at i:28982 original size:12 final size:13
Alignment explanation
Indices: 28952--28998 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
28942 CCGTATACAA
*
28952 TTTTTTTCATTTC
1 TTTTTTTGATTTC
28965 AATTTTTTTGATTT-
1 --TTTTTTTGATTTC
*
28979 TTTTTTCGATTTC
1 TTTTTTTGATTTC
28992 TTTTTTT
1 TTTTTTT
28999 TCAAATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 11 0.39
13 6 0.21
15 11 0.39
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTTTTTGATTTC
Found at i:29007 original size:27 final size:26
Alignment explanation
Indices: 28952--29013 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
28942 CCGTATACAA
* *
28952 TTTTTTTCATTTCAATTTTTTTGATT
1 TTTTTTTCATTTCAATTTTTTTAAAT
*
28978 TTTTTTTCGATTTC-TTTTTTTTCAAAT
1 TTTTTTTC-ATTTCAATTTTTTT-AAAT
29005 TTTTTTTCA
1 TTTTTTTCA
29014 CGAATCTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 16 0.52
27 15 0.48
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.73
Consensus pattern (26 bp):
TTTTTTTCATTTCAATTTTTTTAAAT
Found at i:35556 original size:24 final size:25
Alignment explanation
Indices: 35503--35556 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
35493 AACAAATTCT
* *
35503 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
35528 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
35551 TTTTTT
1 TTTTTT
35557 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:37837 original size:15 final size:14
Alignment explanation
Indices: 37808--37836 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
37798 CTAGACCGTA
37808 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
37822 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
37836 T
1 T
37837 TTTTTTCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:37870 original size:21 final size:19
Alignment explanation
Indices: 37813--37874 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
37803 CCGTATGCAA
*
37813 TTTTTTTTTTGCAATTTTT
1 TTTTTTTTTTTCAATTTTT
*
37832 TTTTTTTTTTTCGATTTTT
1 TTTTTTTTTTTCAATTTTT
*
37851 TTTTCTTTTTTTTAACTTTTT
1 TTTT-TTTTTTTCAA-TTTTT
37872 TTT
1 TTT
37875 CGAAGCTACG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 21 0.57
20 8 0.22
21 8 0.22
ACGTcount: A:0.08, C:0.06, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTTTTTTTTCAATTTTT
Found at i:37875 original size:20 final size:21
Alignment explanation
Indices: 37815--37875 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
37805 GTATGCAATT
37815 TTTTTTTTGCAA-TTTTTTTT-
1 TTTTTTTT-CAACTTTTTTTTC
* *
37835 TTTTTTTTCGATTTTTTTTTC
1 TTTTTTTTCAACTTTTTTTTC
37856 TTTTTTTT-AACTTTTTTTTC
1 TTTTTTTTCAACTTTTTTTTC
37876 GAAGCTACGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 2 0.06
20 26 0.72
21 8 0.22
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.80
Consensus pattern (21 bp):
TTTTTTTTCAACTTTTTTTTC
Done.