Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3218
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: 19674
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3399 original size:20 final size:20
Alignment explanation
Indices: 3353--3399 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3343 AGCTCGTTTC
*
3353 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
3373 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
3393 CAGCTCA
1 CAGCTCA
3400 ATCTTAACCC
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:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:4890 original size:10 final size:10
Alignment explanation
Indices: 4875--4914 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
4865 GAAGAAATTC
4875 AAAAAAAATG
1 AAAAAAAATG
4885 AAAAAAAATCGG
1 AAAAAAAAT--G
*
4897 AAAAAAAAAG
1 AAAAAAAATG
4907 AAAAAAAA
1 AAAAAAAA
4915 AGGAAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 18 0.67
12 9 0.33
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:4893 original size:21 final size:20
Alignment explanation
Indices: 4855--4914 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
4845 ATTGGATTTT
* *
4855 AAAAAAAAGAGAAGAAATTC-
1 AAAAAAAAGA-AAAAAAATCG
4875 AAAAAAAATGAAAAAAAATCGG
1 AAAAAAAA-GAAAAAAAATC-G
4897 AAAAAAAAAGAAAAAAAA
1 -AAAAAAAAGAAAAAAAA
4915 AGGAAGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 15 0.44
21 2 0.06
22 9 0.26
23 8 0.24
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAAATCG
Found at i:4902 original size:24 final size:24
Alignment explanation
Indices: 4875--4937 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 24
4865 GAAGAAATTC
**
4875 AAAAAAAATGAAAAAAAATCG-GA
1 AAAAAAAATGAAAAAAAAAGGAGA
4898 AAAAAAAA-GAAAAAAAAAGGAAGA
1 AAAAAAAATGAAAAAAAAAGG-AGA
4922 AAAAAAAAGTGAAAAA
1 AAAAAAAA-TGAAAAA
4938 GTCTTGCGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 10 0.29
23 8 0.24
24 10 0.29
26 6 0.18
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (24 bp):
AAAAAAAATGAAAAAAAAAGGAGA
Found at i:4915 original size:10 final size:10
Alignment explanation
Indices: 4875--4927 Score: 52
Period size: 10 Copynumber: 4.9 Consensus size: 10
4865 GAAGAAATTC
*
4875 AAAAAAAATG
1 AAAAAAAAAG
*
4885 AAAAAAAATCGG
1 AAAAAAAA--AG
4897 AAAAAAAAAG
1 AAAAAAAAAG
4907 AAAAAAAAAGG
1 AAAAAAAAA-G
4918 AAGAAAAAAA
1 AA-AAAAAAA
4928 AAGTGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
10 18 0.49
11 3 0.08
12 16 0.43
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:4930 original size:14 final size:14
Alignment explanation
Indices: 4904--4930 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4894 CGGAAAAAAA
4904 AAGAAAAAAAAAGG
1 AAGAAAAAAAAAGG
4918 AAGAAAAAAAAAG
1 AAGAAAAAAAAAG
4931 TGAAAAAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAAGG
Found at i:5867 original size:47 final size:47
Alignment explanation
Indices: 5752--5872 Score: 135
Period size: 47 Copynumber: 2.6 Consensus size: 47
5742 CCATGAGCGA
*
5752 GAAAAGGAGAAAG-AATTGAAAAAGAAATTGAGATTGAAAAAGGATGT
1 GAAAA-GAGAAAGAAATTGAAAAAGAAATTGAGATTGAAAAAAGATGT
*
5799 GAAAAGAGAAAGAAATCGAAAAAGAAATTG-GATTGAACAAAAG-TGT
1 GAAAAGAGAAAGAAATTGAAAAAGAAATTGAGATTGAA-AAAAGATGT
*
5845 GAGGGAAA-AGAGA-AAATTGAAAAAGAAA
1 GA---AAAGAGAAAGAAATTGAAAAAGAAA
5873 GAAAAGACAT
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
46 19 0.29
47 39 0.60
48 4 0.06
49 3 0.05
ACGTcount: A:0.58, C:0.02, G:0.26, T:0.14
Consensus pattern (47 bp):
GAAAAGAGAAAGAAATTGAAAAAGAAATTGAGATTGAAAAAAGATGT
Found at i:7559 original size:20 final size:20
Alignment explanation
Indices: 7513--7559 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7503 AGCTCGTTTC
*
7513 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
7533 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
7553 CAGCTCA
1 CAGCTCA
7560 ATCTTAACCC
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:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:9358 original size:18 final size:19
Alignment explanation
Indices: 9314--9358 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
9304 ATTAACACAC
*
9314 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
9333 -ATTCATAAAAATATAA-T
1 AATTAATAAAAATATAACT
9350 AATTAATAA
1 AATTAATAA
9359 TTACACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:9686 original size:19 final size:19
Alignment explanation
Indices: 9662--9701 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9652 AGCTCCCATG
9662 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
9681 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
9700 TA
1 TA
9702 TCATCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:11300 original size:10 final size:10
Alignment explanation
Indices: 11276--11311 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
11266 GCAAGCTCGT
*
11276 TGAGCTGAAA
1 TGAGCTCAAA
*
11286 CGAGCTCAAA
1 TGAGCTCAAA
11296 TGAGCTCAAA
1 TGAGCTCAAA
11306 TGAGCT
1 TGAGCT
11312 GAGTTTGCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.19
Consensus pattern (10 bp):
TGAGCTCAAA
Found at i:13001 original size:20 final size:19
Alignment explanation
Indices: 12976--13025 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
12966 AACAATAAAA
12976 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCG-ATTG-AGC
*
12996 TAAATGACCTCGATTGAGC
1 TAAATGAGCTCGATTGAGC
*
13015 GAAATGAGCTC
1 TAAATGAGCTC
13026 AATGAGCTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 12 0.46
20 13 0.50
21 1 0.04
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (19 bp):
TAAATGAGCTCGATTGAGC
Found at i:16092 original size:11 final size:12
Alignment explanation
Indices: 16076--16107 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
16066 CTACATAACG
16076 AAAAATAA-AAA
1 AAAAATAATAAA
16087 AAAAATAATAAA
1 AAAAATAATAAA
16099 AAAAA-AATA
1 AAAAATAATA
16108 GATAGTAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAATAATAAA
Found at i:16098 original size:14 final size:14
Alignment explanation
Indices: 16079--16107 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16069 CATAACGAAA
16079 AATAAAAAAAAAAT
1 AATAAAAAAAAAAT
16093 AATAAAAAAAAAAT
1 AATAAAAAAAAAAT
16107 A
1 A
16108 GATAGTAGCT
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AATAAAAAAAAAAT
Found at i:17431 original size:20 final size:19
Alignment explanation
Indices: 17372--17432 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 19
17362 TCAATTCTCA
17372 TTTTCTTTTTCACTCTCAATCTCT
1 TTTTCTTTTTCA-T-TC-AT-T-T
*
17396 TTTTCTTTTTCTTTCATTT
1 TTTTCTTTTTCATTCATTT
17415 TTTTCTTTTTCGATTCAT
1 TTTTCTTTTTC-ATTCAT
17433 CAAGATTCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 12 0.35
20 6 0.18
21 2 0.06
22 2 0.06
23 1 0.03
24 11 0.32
ACGTcount: A:0.10, C:0.21, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTCTTTTTCATTCATTT
Found at i:17467 original size:36 final size:34
Alignment explanation
Indices: 17414--17484 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 34
17404 TTCTTTCATT
* *
17414 TTTTTCTTTTTCGATTCATCAAGATTCTCTCATTTTC
1 TTTTTCTTTCTCGATTCA-CAA-ATCCTCT-ATTTTC
17451 TTTTTC-TTCTCGATTCACAAATCCTCTATTTTC
1 TTTTTCTTTCTCGATTCACAAATCCTCTATTTTC
17484 T
1 T
17485 CATAATCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 7 0.22
34 6 0.19
35 3 0.09
36 10 0.31
37 6 0.19
ACGTcount: A:0.17, C:0.24, G:0.04, T:0.55
Consensus pattern (34 bp):
TTTTTCTTTCTCGATTCACAAATCCTCTATTTTC
Done.