Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold796
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: 19803
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:5525 original size:28 final size:28
Alignment explanation
Indices: 5424--5527 Score: 129
Period size: 28 Copynumber: 3.7 Consensus size: 28
5414 CTTCGGCTAT
* *
5424 GTATGGCATTTAGTGTGTGAGATACTGA
1 GTATGGCACTTAGTGTGCGAGATACTGA
* *
5452 GTGTGGCACTTAGTGTGCGAGATACCGA
1 GTATGGCACTTAGTGTGCGAGATACTGA
* * *
5480 GTGTGGCACTTAATGTGC-AGGATATTGA
1 GTATGGCACTTAGTGTGCGA-GATACTGA
5508 GTATGGCACTTAGTGTGCGA
1 GTATGGCACTTAGTGTGCGA
5528 AGCATTGAGT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 1 0.02
28 63 0.97
29 1 0.02
ACGTcount: A:0.23, C:0.12, G:0.34, T:0.31
Consensus pattern (28 bp):
GTATGGCACTTAGTGTGCGAGATACTGA
Found at i:8324 original size:20 final size:20
Alignment explanation
Indices: 8278--8324 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
8268 AGCTTGTTTC
*
8278 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
8298 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
8318 CAGCTCA
1 CAGCTCA
8325 ATCTTAACCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:8388 original size:26 final size:26
Alignment explanation
Indices: 8359--8410 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
8349 AGCTTTCTTT
8359 AGCTTGCATTTATTTTCCTGAAATAA
1 AGCTTGCATTTATTTTCCTGAAATAA
8385 AGCTTGCATTTATTTTCCTGAAATAA
1 AGCTTGCATTTATTTTCCTGAAATAA
8411 TCATTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (26 bp):
AGCTTGCATTTATTTTCCTGAAATAA
Found at i:9858 original size:17 final size:17
Alignment explanation
Indices: 9805--9863 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
9795 TTGGAGTATC
* *
9805 AAAAAAAAAAGAAATTC
1 AAAAAAAAAAGAAAGTA
** *
9822 AAAAAAAAAAGTGAGCA
1 AAAAAAAAAAGAAAGTA
*
9839 AAAAAAAAAAAAAAGTA
1 AAAAAAAAAAGAAAGTA
9856 AAAGAAAA
1 AAA-AAAA
9864 GAACAAAAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
17 28 0.88
18 4 0.12
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (17 bp):
AAAAAAAAAAGAAAGTA
Found at i:9863 original size:22 final size:23
Alignment explanation
Indices: 9822--9882 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
9812 AAAGAAATTC
*
9822 AAAAAAAAAAGT--GAGCAAAAA
1 AAAAAAAAAAGTAAAAGCAAAAA
*
9843 AAAAAAAAAAGTAAAAG-AAAAG
1 AAAAAAAAAAGTAAAAGCAAAAA
*
9865 AACAAAAAAAGTGAAAAG
1 AAAAAAAAAAGT-AAAAG
9883 TATTGCGAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.35
22 15 0.44
23 7 0.21
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (23 bp):
AAAAAAAAAAGTAAAAGCAAAAA
Found at i:10976 original size:48 final size:47
Alignment explanation
Indices: 10897--11002 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
10887 GAGTGTCATG
*
10897 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
10945 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
10993 GAAAAAGAAA
1 GAAAAAGAAA
11003 AAAAAGACAA
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:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:12678 original size:20 final size:20
Alignment explanation
Indices: 12632--12678 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
12622 AGCTTGTTTC
*
12632 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
12652 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
12672 CAGCTCA
1 CAGCTCA
12679 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:16340 original size:11 final size:11
Alignment explanation
Indices: 16324--16383 Score: 61
Period size: 11 Copynumber: 5.3 Consensus size: 11
16314 AGAAAGAGAT
16324 TGAAAAAGAAA
1 TGAAAAAGAAA
16335 TGAAAAAG-AA
1 TGAAAAAGAAA
16345 -GAAAAAGAAAA
1 TGAAAAAG-AAA
*
16356 TGAAGAAAAAAAA
1 TG-A-AAAAGAAA
16369 TTGAAAAAGAAA
1 -TGAAAAAGAAA
16381 TGA
1 TGA
16384 GAATGAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
9 7 0.17
10 2 0.05
11 13 0.32
12 8 0.20
13 5 0.12
14 6 0.15
ACGTcount: A:0.72, C:0.00, G:0.18, T:0.10
Consensus pattern (11 bp):
TGAAAAAGAAA
Found at i:16360 original size:15 final size:15
Alignment explanation
Indices: 16336--16395 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
16326 AAAAAGAAAT
*
16336 GAAAAAGAAGAAAAA
1 GAAAATGAAGAAAAA
16351 GAAAATGAAGAAAAA
1 GAAAATGAAGAAAAA
* *
16366 -AAATTGAAAAAGAAA
1 GAAAATGAAGAA-AAA
*
16381 TGAGAATGAA-AAAAA
1 -GAAAATGAAGAAAAA
16396 AATTGAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
14 9 0.24
15 20 0.54
16 2 0.05
17 6 0.16
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.08
Consensus pattern (15 bp):
GAAAATGAAGAAAAA
Found at i:16390 original size:17 final size:18
Alignment explanation
Indices: 16365--16412 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
16355 ATGAAGAAAA
16365 AAAATTGAAAAAGAAA-TG
1 AAAA-TGAAAAAGAAATTG
* *
16383 AGAATGAAAAAAAAATTG
1 AAAATGAAAAAGAAATTG
*
16401 AAAAAGAAAAAG
1 AAAATGAAAAAG
16413 CGAAAAAAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (18 bp):
AAAATGAAAAAGAAATTG
Found at i:16464 original size:33 final size:33
Alignment explanation
Indices: 16427--16489 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
16417 AAAAGAAATT
16427 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
16460 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
16490 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:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Done.