Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold540
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: 39918
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6236 original size:18 final size:18
Alignment explanation
Indices: 6193--6237 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
6183 CTTTCTCCTA
6193 TCTTTTTCTTTTTCAATT
1 TCTTTTTCTTTTTCAATT
*
6211 T-TTGTTTCTTTTTCAGTT
1 TCTT-TTTCTTTTTCAATT
6229 TCTTTTTCT
1 TCTTTTTCT
6238 CTCGTCACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.73
Consensus pattern (18 bp):
TCTTTTTCTTTTTCAATT
Found at i:7167 original size:15 final size:14
Alignment explanation
Indices: 7148--7174 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7138 CTAGCTCTCT
7148 TTTTTTTTTCAAAA
1 TTTTTTTTTCAAAA
7162 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
7175 CTTGATATCC
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:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTTTTCAAAA
Found at i:7228 original size:12 final size:12
Alignment explanation
Indices: 7211--7240 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
7201 GGAAACTAGC
7211 TTTTTTTCGAAT
1 TTTTTTTCGAAT
*
7223 TTTTTTTTGAAT
1 TTTTTTTCGAAT
7235 TTTTTT
1 TTTTTT
7241 CGAGAACTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.07, T:0.77
Consensus pattern (12 bp):
TTTTTTTCGAAT
Found at i:10984 original size:23 final size:23
Alignment explanation
Indices: 10958--11001 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
10948 CCACGTCTTT
*
10958 TTTCATTTGTT-TCTTTTTTCTAA
1 TTTCA-TTGTTCTCTTCTTTCTAA
10981 TTTCATTGTTCTCTTCTTTCT
1 TTTCATTGTTCTCTTCTTTCT
11002 TCATTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.09, C:0.18, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTCATTGTTCTCTTCTTTCTAA
Found at i:13961 original size:12 final size:13
Alignment explanation
Indices: 13944--13973 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
13934 TAGTTTCTCG
13944 AAAAAAATTC-AA
1 AAAAAAATTCGAA
13956 AAAAAAATTCGAA
1 AAAAAAATTCGAA
13969 AAAAA
1 AAAAA
13974 GCTAGTTTCC
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:14986 original size:18 final size:17
Alignment explanation
Indices: 14965--15009 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
14955 GAGTGACGAG
14965 AGAAAAAGAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
14983 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
15001 AGAGAAAAA
1 AGA-AAAAA
15010 GATAGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Found at i:23325 original size:23 final size:22
Alignment explanation
Indices: 23273--23325 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
23263 TCCACGTCTT
*
23273 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
23295 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
23318 TTTCTTTT
1 TTTCTTTT
23326 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:28306 original size:11 final size:11
Alignment explanation
Indices: 28290--28338 Score: 66
Period size: 10 Copynumber: 4.6 Consensus size: 11
28280 ACGGTATTGT
28290 AAAAAAAAT-A
1 AAAAAAAATCA
*
28300 AAAAAAATTC-
1 AAAAAAAATCA
28310 AAAAAAAATCA
1 AAAAAAAATCA
*
28321 AAAAAAATTCA
1 AAAAAAAATCA
28332 AAAAAAA
1 AAAAAAA
28339 GTTTGTGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
10 17 0.50
11 17 0.50
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (11 bp):
AAAAAAAATCA
Found at i:28316 original size:21 final size:21
Alignment explanation
Indices: 28290--28338 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
28280 ACGGTATTGT
28290 AAAAAAAAT-AAAAAAAATTC
1 AAAAAAAATCAAAAAAAATTC
28310 AAAAAAAATCAAAAAAAATTC
1 AAAAAAAATCAAAAAAAATTC
28331 AAAAAAAA
1 AAAAAAAA
28339 GTTTGTGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAAAAAATCAAAAAAAATTC
Found at i:29834 original size:20 final size:20
Alignment explanation
Indices: 29811--29856 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
29801 CCAGCTCGAA
*
29811 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
29831 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
29851 TTAGCT
1 TTAGCT
29857 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:29838 original size:30 final size:30
Alignment explanation
Indices: 29803--29876 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
29793 AGTTTTTCCC
29803 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
29833 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
29863 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
29877 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:31479 original size:12 final size:12
Alignment explanation
Indices: 31462--31500 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
31452 AAAAAAATTG
31462 AAATTCAAAAAA
1 AAATTCAAAAAA
31474 AAATTC-AAAAA
1 AAATTCAAAAAA
* *
31485 AAAGTGAAAAAA
1 AAATTCAAAAAA
31497 AAAT
1 AAAT
31501 CGAGCAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.15
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:31509 original size:14 final size:13
Alignment explanation
Indices: 31479--31539 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 13
31469 AAAAAAAATT
31479 CAAAAAAAAGTGA-
1 CAAAAAAAA-TGAG
31492 -AAAAAAAATCGAG
1 CAAAAAAAAT-GAG
*
31505 CAAAAAAAATAAAG
1 CAAAAAAAAT-GAG
31519 -AAAAAAAAGTGAG
1 CAAAAAAAA-TGAG
31532 CAAAAAAA
1 CAAAAAAA
31540 TCAAGTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
11 1 0.03
12 10 0.25
13 10 0.25
14 19 0.47
ACGTcount: A:0.74, C:0.07, G:0.13, T:0.07
Consensus pattern (13 bp):
CAAAAAAAATGAG
Found at i:31555 original size:28 final size:28
Alignment explanation
Indices: 31480--31558 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 28
31470 AAAAAAATTC
*
31480 AAAAA-AAAGTGAAAAAAAAATCGAGCAAA
1 AAAAATAAAGT-AAAAAAAAGT-GAGCAAA
31509 AAAAATAAAG-AAAAAAAAGTGAGC-AA
1 AAAAATAAAGTAAAAAAAAGTGAGCAAA
*
31535 AAAAATCAAGTTAAAAAAAAGTGA
1 AAAAATAAAG-TAAAAAAAAGTGA
31559 CAAGTCTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
26 11 0.24
27 4 0.09
28 21 0.47
29 5 0.11
30 4 0.09
ACGTcount: A:0.71, C:0.05, G:0.14, T:0.10
Consensus pattern (28 bp):
AAAAATAAAGTAAAAAAAAGTGAGCAAA
Found at i:32589 original size:11 final size:11
Alignment explanation
Indices: 32573--32602 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
32563 AAAGAAATTG
32573 AAAGAAAACAA
1 AAAGAAAACAA
*
32584 AAAGAAAAGAA
1 AAAGAAAACAA
32595 AAAGAAAA
1 AAAGAAAA
32603 AGAAATTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAAACAA
Found at i:32597 original size:6 final size:6
Alignment explanation
Indices: 32573--32681 Score: 78
Period size: 6 Copynumber: 18.0 Consensus size: 6
32563 AAAGAAATTG
* ** *
32573 AAAG-A AAACAA AAAG-A AAAGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
32619 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
32670 AAAGAA AAAGAA
1 AAAGAA AAAGAA
32682 GAAAAATTGA
Statistics
Matches: 77, Mismatches: 22, Indels: 9
0.71 0.20 0.08
Matches are distributed among these distances:
5 8 0.10
6 58 0.75
7 7 0.09
8 4 0.05
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:32633 original size:18 final size:18
Alignment explanation
Indices: 32577--32681 Score: 86
Period size: 18 Copynumber: 5.7 Consensus size: 18
32567 AAATTGAAAG
*
32577 AAAACAAAAAGAAA-AGA
1 AAAAGAAAAAGAAATAGA
* *
32594 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATAGA
*
32612 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATAGA
** * *
32630 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAATAGA
* *
32648 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAG-AAATAGA
32669 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
32682 GAAAAATTGA
Statistics
Matches: 67, Mismatches: 17, Indels: 7
0.74 0.19 0.08
Matches are distributed among these distances:
17 13 0.19
18 36 0.54
19 5 0.07
20 4 0.06
21 9 0.13
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATAGA
Found at i:32659 original size:15 final size:15
Alignment explanation
Indices: 32639--32687 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 15
32629 AAAAAGTGAG
32639 AGAAAAAGAAAATGA
1 AGAAAAAGAAAATGA
32654 AG-AAAAGAAAAT--
1 AGAAAAAGAAAATGA
* *
32666 TGAAAAAGAAAAAGA
1 AGAAAAAGAAAATGA
32681 AGAAAAA
1 AGAAAAA
32688 TTGAAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 1 0.04
13 9 0.32
14 10 0.36
15 8 0.29
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (15 bp):
AGAAAAAGAAAATGA
Found at i:32674 original size:13 final size:12
Alignment explanation
Indices: 32559--32677 Score: 72
Period size: 12 Copynumber: 10.0 Consensus size: 12
32549 AGAAAGAGAT
*
32559 TGAAAAAGAAAT
1 TGAAAAAGAAAA
32571 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
32581 -CAAAAAGAAAA
1 TGAAAAAGAAAA
32592 -GAAAAAGAAAA
1 TGAAAAAGAAAA
* **
32603 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
32616 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* *
32626 TCGAAAAAGTGAGA
1 T-GAAAAAG-AAAA
32640 -GAAAAAGAAAA
1 TGAAAAAGAAAA
32651 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
32665 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
32678 AGAAGAAAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
10 10 0.12
11 20 0.24
12 27 0.32
13 14 0.16
14 12 0.14
15 2 0.02
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:32740 original size:33 final size:33
Alignment explanation
Indices: 32703--32765 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
32693 AGAAAGAATT
32703 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
32736 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
32766 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:34565 original size:20 final size:20
Alignment explanation
Indices: 34542--34595 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
34532 AGTTTTTCCC
*
34542 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
34562 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
34582 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
34596 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:34577 original size:30 final size:30
Alignment explanation
Indices: 34542--34615 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
34532 AGTTTTTCCC
34542 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
34572 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
34602 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
34616 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:34605 original size:20 final size:20
Alignment explanation
Indices: 34542--34606 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
34532 AGTTTTTCCC
* * * *
34542 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
34562 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
34581 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
34602 AGCTC
1 AGCTC
34607 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
Found at i:38333 original size:20 final size:20
Alignment explanation
Indices: 38308--38356 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
38298 GTCCAAACTG
38308 AATTAATT-AGACTTAGTTTT
1 AATTAATTGAG-CTTAGTTTT
* *
38328 AATTAATTGAGTTTTGTTTT
1 AATTAATTGAGCTTAGTTTT
38348 AATTAATTG
1 AATTAATTG
38357 GATTAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (20 bp):
AATTAATTGAGCTTAGTTTT
Found at i:39241 original size:22 final size:22
Alignment explanation
Indices: 39216--39259 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
39206 CTGACCTTTT
39216 TAAA-CGCATTACCATTTCGTAC
1 TAAATCGC-TTACCATTTCGTAC
*
39238 TAAATCTCTTACCATTTCGTAC
1 TAAATCGCTTACCATTTCGTAC
39260 CAATTCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (22 bp):
TAAATCGCTTACCATTTCGTAC
Done.