Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2086
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: 25502
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1733 original size:14 final size:14
Alignment explanation
Indices: 1716--1744 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1706 CTTTTTTTCC
1716 TTTTTTTT-TGAAT
1 TTTTTTTTCTGAAT
1729 TTTTTTTTCTGAAT
1 TTTTTTTTCTGAAT
1743 TT
1 TT
1745 CTTCTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (14 bp):
TTTTTTTTCTGAAT
Found at i:1837 original size:12 final size:13
Alignment explanation
Indices: 1820--1848 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1810 TCCAACTCAA
1820 TTTTTTTGA-TTT
1 TTTTTTTGACTTT
1832 TTTTTTTGACTTT
1 TTTTTTTGACTTT
1845 TTTT
1 TTTT
1849 ACGTTACGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTTTTGACTTT
Found at i:6068 original size:24 final size:25
Alignment explanation
Indices: 6024--6070 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
6014 ACAACTTCTA
* *
6024 AAGAAAACTCAAGAGAGAATTCTTG
1 AAGAAAACCCAAGAGAAAATTCTTG
6049 AAGAAAACCCAA-AGAAAATTCT
1 AAGAAAACCCAAGAGAAAATTCT
6071 GCACTCAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.53, C:0.15, G:0.15, T:0.17
Consensus pattern (25 bp):
AAGAAAACCCAAGAGAAAATTCTTG
Found at i:9151 original size:13 final size:13
Alignment explanation
Indices: 9122--9155 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
9112 TCATTTTCTC
9122 TTCTTTCTTCAACT
1 TTCTTT-TTCAACT
*
9136 TTCTTTTTCAATT
1 TTCTTTTTCAACT
9149 TTCTTTT
1 TTCTTTT
9156 CTCATTCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.68
Consensus pattern (13 bp):
TTCTTTTTCAACT
Found at i:16755 original size:21 final size:21
Alignment explanation
Indices: 16729--16785 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
16719 TTGGTATTTG
*
16729 GGAATTGGTTCGAAATAGTAT
1 GGAATTGGTACGAAATAGTAT
*
16750 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATAGTAT
*
16771 GGTATTGGGTACGAA
1 GGAATT-GGTACGAA
16786 TTGGTAATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 24 0.75
22 8 0.25
ACGTcount: A:0.32, C:0.05, G:0.33, T:0.30
Consensus pattern (21 bp):
GGAATTGGTACGAAATAGTAT
Found at i:16784 original size:22 final size:21
Alignment explanation
Indices: 16732--16796 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
16722 GTATTTGGGA
* * *
16732 ATTGGTTCGAAATAGTATGGA
1 ATTGGTACGAAATGGTATGGT
16753 ATTGGTACGAAATGGTATGGT
1 ATTGGTACGAAATGGTATGGT
*
16774 ATTGGGTACGAATTGGTAATGGT
1 ATT-GGTACGAAATGGT-ATGGT
16797 TCAAAAGGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (21 bp):
ATTGGTACGAAATGGTATGGT
Found at i:22477 original size:33 final size:33
Alignment explanation
Indices: 22439--22501 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
22429 GATTACTCAC
22439 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
22472 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
22502 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:22533 original size:14 final size:13
Alignment explanation
Indices: 22498--22554 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
22488 TCAAGCTCTC
22498 TTTCAA-TTTCTT
1 TTTCAATTTTCTT
**
22510 TTTCGCTTTTTCTT
1 TTTC-AATTTTCTT
22524 TTTCAATTTTCTTT
1 TTTCAATTTTC-TT
22538 TCTTC-ATTTTCTT
1 T-TTCAATTTTCTT
22551 TTTC
1 TTTC
22555 TCTCACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 7 0.19
13 8 0.22
14 19 0.51
15 3 0.08
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTCAATTTTCTT
Found at i:22606 original size:11 final size:11
Alignment explanation
Indices: 22587--22621 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
22577 TCTTTTGCAA
*
22587 TTTCTTTTTCT
1 TTTCGTTTTCT
22598 TTTCGTTTTCT
1 TTTCGTTTTCT
*
22609 TTTTGTTTTCT
1 TTTCGTTTTCT
22620 TT
1 TT
22622 CAATTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (11 bp):
TTTCGTTTTCT
Found at i:22634 original size:6 final size:6
Alignment explanation
Indices: 22504--22621 Score: 69
Period size: 6 Copynumber: 19.2 Consensus size: 6
22494 TCTCTTTCAA
* * *
22504 TTTCTT TTTCGCTT TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC
1 TTTCTT TTT--CTT TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT
** ** * ** *
22557 TCACTT TTTCGA TTTCTT TTTCTT TTGCAA TTTCTT TTTC-T TTTCGT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
*
22604 TTTCTT TTT-GT TTTCTT T
1 TTTCTT TTTCTT TTTCTT T
22622 CAATTTCTTT
Statistics
Matches: 82, Mismatches: 24, Indels: 12
0.69 0.20 0.10
Matches are distributed among these distances:
5 9 0.11
6 55 0.67
7 9 0.11
8 9 0.11
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:22653 original size:80 final size:82
Alignment explanation
Indices: 22501--22653 Score: 177
Period size: 80 Copynumber: 1.9 Consensus size: 82
22491 AGCTCTCTTT
* * ** *
22501 CAATTTCTTTTTCGCTTTTTCTTTTTCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCACTTTTT
1 CAATTTCTTTTTC-CTTTTTCGTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCACTTTCT
*
22566 CGATTTCTTTTTCTTTTG
65 CCATTTCTTTTTCTTTTG
* * *
22584 CAATTTCTTTTT-C-TTTTCGTTTTC-TTTTTGTTTTCTTTCAATTTCTTTTTCAATCTCTTTCT
1 CAATTTCTTTTTCCTTTTTCGTTTTCAATTTTCTTTTC-TTCAATTTCTTTTTCAATCACTTTCT
*
22646 CCTTTTCT
65 CCATTTCT
22654 CGCTCAATGG
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
79 9 0.15
80 37 0.63
81 1 0.02
83 12 0.20
ACGTcount: A:0.08, C:0.21, G:0.03, T:0.67
Consensus pattern (82 bp):
CAATTTCTTTTTCCTTTTTCGTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCACTTTCTC
CATTTCTTTTTCTTTTG
Found at i:23647 original size:20 final size:19
Alignment explanation
Indices: 23619--23678 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
23609 CTCGCAAGAC
23619 TTTTCACTTTTTTTTGTTTT
1 TTTTCACTTTTTTTT-TTTT
*
23639 TTTTTACTTTTTTTCTTTTT
1 TTTTCACTTTTTTT-TTTTT
**
23659 TGCTCACTTTTTTTTTTTT
1 TTTTCACTTTTTTTTTTTT
23678 T
1 T
23679 GAATTTTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.17
20 28 0.80
21 1 0.03
ACGTcount: A:0.05, C:0.12, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTTCACTTTTTTTTTTTT
Found at i:23649 original size:17 final size:16
Alignment explanation
Indices: 23629--23713 Score: 71
Period size: 17 Copynumber: 4.9 Consensus size: 16
23619 TTTTCACTTT
23629 TTTTTGTTTTTTTTTAC
1 TTTTT-TTTTTTTTTAC
23646 TTTTTTTCTTTTTTGCTCAC
1 TTTTTTT-TTTTTT--T-AC
* *
23666 TTTTTTTTTTTTTGAA
1 TTTTTTTTTTTTTTAC
* * *
23682 TTTTGATTTTTTTTGAA
1 TTTT-TTTTTTTTTTAC
23699 TTTTTTTTTTTTTTA
1 TTTTTTTTTTTTTTA
23714 AATCCAATAC
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
16 16 0.28
17 26 0.45
19 7 0.12
20 9 0.16
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.79
Consensus pattern (16 bp):
TTTTTTTTTTTTTTAC
Found at i:23784 original size:11 final size:11
Alignment explanation
Indices: 23770--23798 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
23760 TCCAACTCAA
23770 TTTTTTTTGA-
1 TTTTTTTTGAC
23780 TTTTTTTTGAC
1 TTTTTTTTGAC
23791 TTTTTTTT
1 TTTTTTTT
23799 CATTACGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Done.