Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1230
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: 41954
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:249 original size:12 final size:11
Alignment explanation
Indices: 235--269 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
225 TCAATTTCTT
*
235 TTTTCATTTTC
1 TTTTCTTTTTC
246 TTTTCTTTTTC
1 TTTTCTTTTTC
257 ATTTTCTTTTTC
1 -TTTTCTTTTTC
269 T
1 T
270 CTCACTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:256 original size:17 final size:18
Alignment explanation
Indices: 229--266 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
219 CCAATCTCAA
229 TTTCTTTTTTCATTTTCT
1 TTTCTTTTTTCATTTTCT
247 TTTC-TTTTTCATTTTCT
1 TTTCTTTTTTCATTTTCT
264 TTT
1 TTT
267 TCTCTCACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTCTTTTTTCATTTTCT
Found at i:8067 original size:15 final size:13
Alignment explanation
Indices: 8047--8106 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 13
8037 AATGAGATAG
*
8047 AAAAAATAAC-AC
1 AAAAAAAAACAAC
*
8059 ACAAAAAAACAAC
1 AAAAAAAAACAAC
8072 AAAAAAAAA-AA-
1 AAAAAAAAACAAC
8083 AAAAAAAACACCAAAC
1 AAAAAAAA-A-C-AAC
8099 AAAAAAAA
1 AAAAAAAA
8107 GGAATAAACG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 8 0.21
12 11 0.28
13 10 0.26
15 2 0.05
16 8 0.21
ACGTcount: A:0.83, C:0.15, G:0.00, T:0.02
Consensus pattern (13 bp):
AAAAAAAAACAAC
Found at i:8087 original size:23 final size:23
Alignment explanation
Indices: 8061--8106 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
8051 AATAACACAC
8061 AAAAAAACAACAAAAAAAAAAAA
1 AAAAAAACAACAAAAAAAAAAAA
* *
8084 AAAAAAACACCAAACAAAAAAAA
1 AAAAAAACAACAAAAAAAAAAAA
8107 GGAATAAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (23 bp):
AAAAAAACAACAAAAAAAAAAAA
Found at i:18805 original size:20 final size:20
Alignment explanation
Indices: 18758--18805 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
18748 AGTAAGCTCG
18758 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
18778 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
18798 GTTGAGCT
1 GTTGAGCT
18806 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:33711 original size:13 final size:13
Alignment explanation
Indices: 33695--33738 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
33685 TAAAAAAAAG
33695 AAAAAAAAATTC-
1 AAAAAAAAATTCA
33707 AAAAAAAAATTCA
1 AAAAAAAAATTCA
* *
33720 AAAAAAAATTTTA
1 AAAAAAAAATTCA
33733 AAAAAA
1 AAAAAA
33739 TTGTATTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 12 0.41
13 17 0.59
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:33738 original size:12 final size:12
Alignment explanation
Indices: 33695--33729 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
33685 TAAAAAAAAG
33695 AAAAAAAAATTC
1 AAAAAAAAATTC
33707 AAAAAAAAATTC
1 AAAAAAAAATTC
33719 AAAAAAAAATT
1 AAAAAAAAATT
33730 TTAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:34548 original size:52 final size:52
Alignment explanation
Indices: 34465--34565 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
34455 TAAGGAAACG
* *
34465 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTAAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTAAAGCTCAAACAA
*
34517 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTAAAGCTCAAA
34566 TATGTGCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTAAAGCTCAAACAA
Found at i:35921 original size:20 final size:20
Alignment explanation
Indices: 35898--35951 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
35888 AGTTTTTCCC
*
35898 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
35918 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
35938 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
35952 TACTTTAGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:38639 original size:6 final size:6
Alignment explanation
Indices: 38630--38748 Score: 69
Period size: 6 Copynumber: 19.2 Consensus size: 6
38620 GAAAGAGATT
** * * **
38630 GAAAAA GAAATT GAAAGAA AAAAAAA GAAAAC GAAAAA GAAAAA GAAATT
1 GAAAAA GAAAAA GAAA-AA GAA-AAA GAAAAA GAAAAA GAAAAA GAAAAA
* ** ** * *
38680 GCAAAA GAAAAA GAAATC GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAA-AAA
38729 -AAAAA TTGAAAAA GAAAAA G
1 GAAAAA --GAAAAA GAAAAA G
38749 CGAAAAAAGA
Statistics
Matches: 81, Mismatches: 26, Indels: 12
0.68 0.22 0.10
Matches are distributed among these distances:
5 3 0.04
6 64 0.79
7 8 0.10
8 6 0.07
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.08
Consensus pattern (6 bp):
GAAAAA
Found at i:38667 original size:7 final size:6
Alignment explanation
Indices: 38643--38748 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
38633 AAAGAAATTG
* ** *
38643 AAAG-A AAA-AA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * *
38689 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAA GAAA-AA AAATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA -AAAGAA AAA--GAA
38739 AAAGAA AAAG
1 AAAGAA AAAG
38749 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 20, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
5 10 0.13
6 58 0.77
7 2 0.03
8 5 0.07
ACGTcount: A:0.73, C:0.03, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:38704 original size:18 final size:18
Alignment explanation
Indices: 38630--38704 Score: 87
Period size: 18 Copynumber: 4.1 Consensus size: 18
38620 GAAAGAGATT
*
38630 GAAAAAGAAATTGAAAGAAA
1 GAAAAAGAAATCG-AA-AAA
* *
38650 AAAAAAGAAAACGAAAAA
1 GAAAAAGAAATCGAAAAA
* *
38668 GAAAAAGAAATTGCAAAA
1 GAAAAAGAAATCGAAAAA
38686 GAAAAAGAAATCGAAAAA
1 GAAAAAGAAATCGAAAAA
38704 G
1 G
38705 TGAGAGAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
18 34 0.74
19 2 0.04
20 10 0.22
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAATCGAAAAA
Found at i:38747 original size:27 final size:26
Alignment explanation
Indices: 38710--38766 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
38700 AAAAGTGAGA
*
38710 GAAAAAGAAAA-TGAAGAAAAAAAATT
1 GAAAAAGAAAAGCGAA-AAAAAAAATT
*
38736 GAAAAAGAAAAAGCGAAAAAAGAAATT
1 GAAAAAG-AAAAGCGAAAAAAAAAATT
38763 GAAA
1 GAAA
38767 GAGAGCTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 7 0.26
27 17 0.63
28 3 0.11
ACGTcount: A:0.72, C:0.02, G:0.18, T:0.09
Consensus pattern (26 bp):
GAAAAAGAAAAGCGAAAAAAAAAATT
Found at i:38800 original size:33 final size:33
Alignment explanation
Indices: 38763--38825 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
38753 AAAAGAAATT
38763 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
38796 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
38826 GTGAGTAATC
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:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:40623 original size:20 final size:20
Alignment explanation
Indices: 40600--40653 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
40590 AGTTTTTCCC
*
40600 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
40620 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
40640 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
40654 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:40635 original size:30 final size:30
Alignment explanation
Indices: 40600--40673 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
40590 AGTTTTTCCC
40600 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
40630 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
40660 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
40674 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:40663 original size:20 final size:20
Alignment explanation
Indices: 40600--40664 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
40590 AGTTTTTCCC
* * * *
40600 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
40620 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
40639 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
40660 AGCTC
1 AGCTC
40665 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Done.