Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2427
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: 19302
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:5811 original size:12 final size:13
Alignment explanation
Indices: 5796--5825 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
5786 AAAAAAACTC
5796 AAAAAAATTC-AA
1 AAAAAAATTCGAA
5808 AAAAAAATTCGAA
1 AAAAAAATTCGAA
5821 AAAAA
1 AAAAA
5826 CTAGTTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:5882 original size:14 final size:14
Alignment explanation
Indices: 5863--5904 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
5853 GGATATCAAG
5863 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
5877 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
5891 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
5905 GAGAGCTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:7333 original size:20 final size:20
Alignment explanation
Indices: 7310--7356 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7300 GGGTTAAGAT
*
7310 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
7330 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
7350 TGAGCTG
1 TGAGCTG
7357 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:10357 original size:48 final size:48
Alignment explanation
Indices: 10305--10410 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
10295 TTGTCTTTTC
*
10305 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
10353 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
10401 TTTCTTTTTC
1 TTTCTTTTTC
10411 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:11606 original size:11 final size:11
Alignment explanation
Indices: 11592--11620 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
11582 TCCAACTCAA
11592 TTTTTTTTGA-
1 TTTTTTTTGAC
11602 TTTTTTTTGAC
1 TTTTTTTTGAC
11613 TTTTTTTT
1 TTTTTTTT
11621 ACGTTACGAA
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
Found at i:12332 original size:10 final size:10
Alignment explanation
Indices: 12316--12373 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
12306 CAACTCCGAC
12316 CAGCTCAATT
1 CAGCTCAATT
* *
12326 GAGCTCATTT
1 CAGCTCAATT
12336 CAGCTCAA-T
1 CAGCTCAATT
12345 CGAGCTCAATT
1 C-AGCTCAATT
*
12356 TAGCTACAATT
1 CAGCT-CAATT
12367 CAGCTCA
1 CAGCTCA
12374 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:12339 original size:20 final size:20
Alignment explanation
Indices: 12316--12376 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
12306 CAACTCCGAC
12316 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
12336 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
12357 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
12377 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:13751 original size:11 final size:12
Alignment explanation
Indices: 13735--13802 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 12
13725 TTGGAGTAAC
13735 AAAAAAA-TCAA
1 AAAAAAATTCAA
*
13746 AAAAAAATTGAAA
1 AAAAAAATT-CAA
*
13759 AAAAAATTGATTGAA
1 AAAAAA---ATTCAA
13774 AAAAAAATTC-A
1 AAAAAAATTCAA
*
13785 AAAAAAAGTCAA
1 AAAAAAATTCAA
13797 AAAAAA
1 AAAAAA
13803 TTGAGCAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
11 17 0.36
12 11 0.23
13 8 0.17
15 8 0.17
16 3 0.06
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:13771 original size:16 final size:16
Alignment explanation
Indices: 13752--13782 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13742 TCAAAAAAAA
13752 ATTGAAAAAAAAATTG
1 ATTGAAAAAAAAATTG
13768 ATTGAAAAAAAAATT
1 ATTGAAAAAAAAATT
13783 CAAAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (16 bp):
ATTGAAAAAAAAATTG
Found at i:13814 original size:38 final size:39
Alignment explanation
Indices: 13735--13817 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 39
13725 TTGGAGTAAC
*
13735 AAAAAAATCAAAAAAAAATTGAAAAAAAAATTGATTG-AAA
1 AAAAAAATCAAAAAAAAAGTGAAAAAAAAATTGA--GCAAA
* *
13775 AAAAAATTC-AAAAAAAAGT-CAAAAAAAATTGAGCAAA
1 AAAAAAATCAAAAAAAAAGTGAAAAAAAAATTGAGCAAA
13812 AAAAAA
1 AAAAAA
13818 GAAAAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
36 1 0.03
37 9 0.23
38 12 0.31
39 9 0.23
40 8 0.21
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.14
Consensus pattern (39 bp):
AAAAAAATCAAAAAAAAAGTGAAAAAAAAATTGAGCAAA
Found at i:14752 original size:18 final size:18
Alignment explanation
Indices: 14731--14765 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
14721 AGAAAAGAAA
14731 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
14749 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
14766 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:16850 original size:10 final size:10
Alignment explanation
Indices: 16834--16891 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
16824 CAACTCCGAC
16834 CAGCTCAATT
1 CAGCTCAATT
* *
16844 GAGCTCATTT
1 CAGCTCAATT
16854 CAGCTCAA-T
1 CAGCTCAATT
16863 CGAGCTCAATT
1 C-AGCTCAATT
*
16874 TAGCTACAATT
1 CAGCT-CAATT
16885 CAGCTCA
1 CAGCTCA
16892 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:16857 original size:20 final size:20
Alignment explanation
Indices: 16834--16894 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
16824 CAACTCCGAC
16834 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
16854 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
16875 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
16895 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:19069 original size:20 final size:20
Alignment explanation
Indices: 19046--19092 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19036 GGGTTAAGAT
*
19046 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
19066 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
19086 TGAGCTG
1 TGAGCTG
19093 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
Done.