Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1838
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: 35051
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:4717 original size:14 final size:15
Alignment explanation
Indices: 4698--4736 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
4688 GAAATAGAGA
4698 AAAGAAAAAAAA-TG
1 AAAGAAAAAAAATTG
4712 AAAGAAAAAGAAATTG
1 AAAGAAAAA-AAATTG
4728 AAA-AAAAAA
1 AAAGAAAAAA
4737 GAGTGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.43
15 8 0.35
16 5 0.22
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (15 bp):
AAAGAAAAAAAATTG
Found at i:4735 original size:16 final size:15
Alignment explanation
Indices: 4696--4738 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
4686 ATGAAATAGA
4696 GAAAAGAAAAA-AAAT
1 GAAAA-AAAAAGAAAT
*
4711 GAAAGAAAAAGAAATT
1 GAAAAAAAAAGAAA-T
4727 GAAAAAAAAAGA
1 GAAAAAAAAAGA
4739 GTGAGAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.21
15 7 0.29
16 12 0.50
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (15 bp):
GAAAAAAAAAGAAAT
Found at i:7290 original size:79 final size:81
Alignment explanation
Indices: 7166--7349 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
7156 GCTACTCGTT
* *
7166 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTC-GGATCTTAACCCG
* *
7229 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
7245 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCAC-AATGCCTTCGGATCTTAACCCG
* *
7308 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
7325 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
7350 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 48 0.53
80 19 0.21
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:7349 original size:40 final size:40
Alignment explanation
Indices: 7147--7349 Score: 229
Period size: 39 Copynumber: 5.1 Consensus size: 40
7137 CGGAATTTAA
** *
7147 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
7187 CCGGTTATAGTAACTCGCAC-AATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
7226 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
7265 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
7305 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
7345 CCGGA
1 CCGGA
7350 CATCATTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.01
39 68 0.49
40 57 0.41
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:14656 original size:47 final size:47
Alignment explanation
Indices: 14585--14688 Score: 127
Period size: 47 Copynumber: 2.2 Consensus size: 47
14575 TGGAACATGC
* * * *
14585 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGT
* * **
14632 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGGTGTGAAAGTGT
1 ATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGT
*
14679 ATAAATGTGA
1 ATATATGTGA
14689 TAAGTCCCGA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.31, C:0.10, G:0.33, T:0.27
Consensus pattern (47 bp):
ATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGT
Found at i:14866 original size:37 final size:37
Alignment explanation
Indices: 14810--14888 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
14800 CCGAGCTCTA
* * *
14810 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
14847 AAGACCCGATAACCT-CGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAA-CTACGTGTGGAGATTATGTCCGGGT
14884 AAGAC
1 AAGAC
14889 TTCATAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:19748 original size:79 final size:82
Alignment explanation
Indices: 19637--19821 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
19627 GCTACTCGTT
* * *
19637 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
19700 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
19717 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
19780 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
19797 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
19822 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:19821 original size:40 final size:40
Alignment explanation
Indices: 19618--19821 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
19608 CGGAATTTAA
** *
19618 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
19658 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
19698 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
19737 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
19777 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
19817 CCGGA
1 CCGGA
19822 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:24255 original size:4 final size:4
Alignment explanation
Indices: 24248--24272 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
24238 TAAAAAAAAA
24248 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
24273 TTAGTAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:25629 original size:12 final size:13
Alignment explanation
Indices: 25591--25629 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
25581 AAATATTTGA
25591 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
25604 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
25618 CTTGTT-TTAATT
1 CTTGTTCTTAATT
25630 TTCCAGGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 5 0.22
14 12 0.52
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (13 bp):
CTTGTTCTTAATT
Done.