Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2202
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: 31084
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4867 original size:24 final size:25
Alignment explanation
Indices: 4840--4891 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
4830 GCCTAGCCTC
4840 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
* *
4864 TTTTGATAAACTGGGGCATAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
4889 TTT
1 TTT
4892 AGCACTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:7176 original size:11 final size:10
Alignment explanation
Indices: 7137--7169 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
7127 AAATCGAGTT
7137 AAAAGAAAAA
1 AAAAGAAAAA
7147 AAAAGAAAAA
1 AAAAGAAAAA
7157 AAAAGAAAAA
1 AAAAGAAAAA
7167 AAA
1 AAA
7170 GTGAAAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:8069 original size:18 final size:18
Alignment explanation
Indices: 8048--8082 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
8038 AGAAAAGAAA
8048 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
8066 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
8083 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:15012 original size:1 final size:1
Alignment explanation
Indices: 15006--15043 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
14996 CGTAGCTTCG
15006 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15044 TTGCATACGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17326 original size:24 final size:25
Alignment explanation
Indices: 17299--17352 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
17289 ATGAGTGATA
*
17299 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
17323 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
17347 AAAAAA
1 AAAAAA
17353 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:22446 original size:13 final size:13
Alignment explanation
Indices: 22428--22453 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22418 CTAGCTCTCT
22428 TTTTTTTTCACAA
1 TTTTTTTTCACAA
22441 TTTTTTTTCACAA
1 TTTTTTTTCACAA
22454 CTTGATATCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTTTCACAA
Found at i:22508 original size:11 final size:11
Alignment explanation
Indices: 22492--22535 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
22482 GGAAACTAGT
22492 TTTTTTTTCGA
1 TTTTTTTTCGA
22503 TTTTTTTT-GAA
1 TTTTTTTTCG-A
*
22514 TTTTTTTTTGA
1 TTTTTTTTCGA
*
22525 ATTTTTTTCGA
1 TTTTTTTTCGA
22536 GAAACTACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 1 0.03
11 27 0.93
12 1 0.03
ACGTcount: A:0.14, C:0.05, G:0.09, T:0.73
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:22508 original size:12 final size:12
Alignment explanation
Indices: 22491--22532 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
22481 TGGAAACTAG
22491 TTTTTTTTTCG-A
1 TTTTTTTTT-GAA
22503 -TTTTTTTTGAA
1 TTTTTTTTTGAA
22514 TTTTTTTTTGAA
1 TTTTTTTTTGAA
22526 TTTTTTT
1 TTTTTTT
22533 CGAGAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 9 0.32
12 18 0.64
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:25608 original size:19 final size:18
Alignment explanation
Indices: 25572--25611 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25562 TTTCCACTCG
*
25572 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
25590 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
25609 TTT
1 TTT
25612 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:26684 original size:13 final size:14
Alignment explanation
Indices: 26666--26719 Score: 76
Period size: 13 Copynumber: 3.9 Consensus size: 14
26656 AAACTAGCTC
26666 TTTTTTTT-ACAAT
1 TTTTTTTTCACAAT
26679 TTTTTTTTCACAATT
1 TTTTTTTTCACAA-T
*
26694 TTTTTTTTCA-AAA
1 TTTTTTTTCACAAT
26707 TTTTTTTTCACAA
1 TTTTTTTTCACAA
26720 CTTGATATCC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
13 18 0.49
14 8 0.22
15 11 0.30
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:26685 original size:14 final size:14
Alignment explanation
Indices: 26666--26714 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
26656 AAACTAGCTC
26666 TTTTTTTTACAATT
1 TTTTTTTTACAATT
*
26680 TTTTTTTCACAATT
1 TTTTTTTTACAATT
*
26694 TTTTTTTTCAAAATT
1 TTTTTTTT-ACAATT
26709 TTTTTT
1 TTTTTT
26715 CACAACTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTTTACAATT
Found at i:26686 original size:15 final size:15
Alignment explanation
Indices: 26666--26714 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
26656 AAACTAGCTC
26666 TTTTTTTT-ACAA-T
1 TTTTTTTTCACAATT
26679 TTTTTTTTCACAATT
1 TTTTTTTTCACAATT
*
26694 TTTTTTTTCAAAATT
1 TTTTTTTTCACAATT
26709 TTTTTT
1 TTTTTT
26715 CACAACTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
13 8 0.24
14 4 0.12
15 21 0.64
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTTTTCACAATT
Found at i:26772 original size:11 final size:11
Alignment explanation
Indices: 26756--26795 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
26746 GGAAACTGTT
26756 TTTTTTTCGAA
1 TTTTTTTCGAA
*
26767 TTTTTTTTGAA
1 TTTTTTTCGAA
26778 TTTTTTTC-AA
1 TTTTTTTCGAA
26788 GTTTTTTT
1 -TTTTTTT
26796 TGAGAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 2 0.08
11 24 0.92
ACGTcount: A:0.15, C:0.05, G:0.07, T:0.72
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:26772 original size:12 final size:12
Alignment explanation
Indices: 26755--26796 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
26745 TGGAAACTGT
26755 TTTTTTTTCGAA
1 TTTTTTTTCGAA
26767 TTTTTTTT-GAA
1 TTTTTTTTCGAA
26778 -TTTTTTTC-AA
1 TTTTTTTTCGAA
26788 GTTTTTTTT
1 -TTTTTTTT
26797 GAGAAACTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.33
11 3 0.11
12 15 0.56
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:26781 original size:22 final size:22
Alignment explanation
Indices: 26756--26798 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
26746 GGAAACTGTT
26756 TTTTTTTCGAA-TTTTTTTTGAA
1 TTTTTTTC-AAGTTTTTTTTGAA
26778 TTTTTTTCAAGTTTTTTTTGA
1 TTTTTTTCAAGTTTTTTTTGA
26799 GAAACTACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTTTTCAAGTTTTTTTTGAA
Done.