Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3751
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: 40877
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:10094 original size:19 final size:18
Alignment explanation
Indices: 10058--10097 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
10048 TTTCCACTCG
*
10058 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
10076 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
10095 TTT
1 TTT
10098 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:11171 original size:11 final size:12
Alignment explanation
Indices: 11154--11200 Score: 69
Period size: 13 Copynumber: 3.8 Consensus size: 12
11144 TAGCTCTCTC
11154 TTTTTTTTCAAA
1 TTTTTTTTCAAA
11166 TTTTTTTTTCACAA
1 -TTTTTTTTCA-AA
11180 TTTTTTTTC-AA
1 TTTTTTTTCAAA
11191 TTTTTTTTCA
1 TTTTTTTTCA
11201 CAACTTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.34
13 19 0.59
14 2 0.06
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:11190 original size:26 final size:24
Alignment explanation
Indices: 11154--11203 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
11144 TAGCTCTCTC
11154 TTTTTTTTCAAATTTTTTTTTCACAA
1 TTTTTTTTC-AA-TTTTTTTTCACAA
11180 TTTTTTTTCAATTTTTTTTCACAA
1 TTTTTTTTCAATTTTTTTTCACAA
11204 CTTGATATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 13 0.54
25 2 0.08
26 9 0.38
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTTTTTTCAATTTTTTTTCACAA
Found at i:11258 original size:11 final size:11
Alignment explanation
Indices: 11242--11282 Score: 73
Period size: 11 Copynumber: 3.6 Consensus size: 11
11232 GGAAACTAGT
11242 TTTTTTTTGAA
1 TTTTTTTTGAA
11253 TTTTTTTTTGAA
1 -TTTTTTTTGAA
11265 TTTTTTTTGAA
1 TTTTTTTTGAA
11276 TTTTTTT
1 TTTTTTT
11283 CGAGAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:11258 original size:12 final size:12
Alignment explanation
Indices: 11241--11282 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
11231 TGGAAACTAG
11241 TTTTTTTTTGAA
1 TTTTTTTTTGAA
11253 TTTTTTTTTGAA
1 TTTTTTTTTGAA
11265 -TTTTTTTTGAA
1 TTTTTTTTTGAA
11276 TTTTTTT
1 TTTTTTT
11283 CGAGAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.38
12 18 0.62
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:13734 original size:22 final size:23
Alignment explanation
Indices: 13709--13757 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
13699 ATCAGCTTCT
13709 TTAATAC-ACCTATTAAGACACA
1 TTAATACGACCTATTAAGACACA
* *
13731 TTAA-ACGACTTATTAGGACACA
1 TTAATACGACCTATTAAGACACA
13753 TTAAT
1 TTAAT
13758 CATACCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (23 bp):
TTAATACGACCTATTAAGACACA
Found at i:14214 original size:18 final size:20
Alignment explanation
Indices: 14170--14219 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
14160 CTCGTATCAA
14170 TCTCTTTTTGCTATTTTTCAT
1 TCTCTTTTT-CTATTTTTCAT
*
14191 TCTCTTTTTCT-TTTTTGAT
1 TCTCTTTTTCTATTTTTCAT
14210 T-TCTTTTTCT
1 TCTCTTTTTCT
14220 GTCTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 2 0.07
21 9 0.32
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (20 bp):
TCTCTTTTTCTATTTTTCAT
Found at i:19728 original size:20 final size:20
Alignment explanation
Indices: 19705--19751 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19695 GGGTTAAGAT
*
19705 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
19725 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
19745 TGAGCTG
1 TGAGCTG
19752 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:20203 original size:22 final size:22
Alignment explanation
Indices: 20173--20216 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20163 TTTGGTATTT
20173 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
20195 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
20217 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:22723 original size:14 final size:14
Alignment explanation
Indices: 22706--22757 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
22696 AAAAAAAGTG
22706 AAAAAAAATCGAGC
1 AAAAAAAATCGAGC
*** *
22720 AAAAAAAAGAAAGA
1 AAAAAAAATCGAGC
22734 AAAAAAAAGT-GAGC
1 AAAAAAAA-TCGAGC
22748 AAAAAAAATC
1 AAAAAAAATC
22758 AAGTTAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 1 0.03
14 28 0.97
ACGTcount: A:0.73, C:0.08, G:0.13, T:0.06
Consensus pattern (14 bp):
AAAAAAAATCGAGC
Found at i:22726 original size:28 final size:29
Alignment explanation
Indices: 22695--22775 Score: 96
Period size: 28 Copynumber: 2.8 Consensus size: 29
22685 AAAAGAATTC
*
22695 AAAAA-AAAGTGAAAAAAAA-TCGAGCAAA
1 AAAAAGAAAGTAAAAAAAAAGT-GAGCAAA
22723 AAAAAGAAAG-AAAAAAAAAGTGAGCAAA
1 AAAAAGAAAGTAAAAAAAAAGTGAGCAAA
**
22751 AAAAATCAAGTTAAAAAAAAAGTGA
1 AAAAAGAAAG-TAAAAAAAAAGTGA
22776 AAAGTCTTGC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 28 0.61
29 5 0.11
30 13 0.28
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.09
Consensus pattern (29 bp):
AAAAAGAAAGTAAAAAAAAAGTGAGCAAA
Found at i:33952 original size:16 final size:15
Alignment explanation
Indices: 33931--33970 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
33921 CCGTATGCAA
33931 TTTTTTTTTCAATTT
1 TTTTTTTTTCAATTT
*
33946 TTTTTTTTTCGATTT
1 TTTTTTTTTCAATTT
33961 TTTTTATTTT
1 TTTTT-TTTT
33971 TTTTGAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.10, C:0.05, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTCAATTT
Done.