Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3074
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: 35441
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Found at i:9354 original size:40 final size:40
Alignment explanation
Indices: 9317--9502 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
9307 GCTACTCGTT
* *
9317 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
9357 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
9397 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
9437 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
9478 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
9503 CATCATTCAA
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 3 0.02
40 117 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:12927 original size:27 final size:27
Alignment explanation
Indices: 12897--12958 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
12887 ATTTACTAAA
12897 ATACCCCTAAGCATG-AAAATTACCATT
1 ATACCCCTAAG-ATGCAAAATTACCATT
* *
12924 ATACCTCT-AGGTGCAAAATTACCATT
1 ATACCCCTAAGATGCAAAATTACCATT
12950 ATACCCCTA
1 ATACCCCTA
12959 CGGTTAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 2 0.07
26 21 0.70
27 7 0.23
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.27
Consensus pattern (27 bp):
ATACCCCTAAGATGCAAAATTACCATT
Found at i:13129 original size:28 final size:28
Alignment explanation
Indices: 13064--13176 Score: 117
Period size: 27 Copynumber: 4.2 Consensus size: 28
13054 GAGGAAGCGT
* *
13064 TCTGGTTGCTCTGCGACAAATATCTA-A
1 TCTGGTGGCTCTGCCACAAATATCTATA
* *
13091 TCTGGTGGCTCTACCACAAATATCTATT
1 TCTGGTGGCTCTGCCACAAATATCTATA
* *
13119 TCTGGTGGCTCTGCCA-TAATATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTATA
* * *
13146 TCTGGTGACTCTGTCAC-GATATCTAT-
1 TCTGGTGGCTCTGCCACAAATATCTATA
13172 TCTGG
1 TCTGG
13177 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
26 5 0.07
27 52 0.72
28 15 0.21
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (28 bp):
TCTGGTGGCTCTGCCACAAATATCTATA
Found at i:20721 original size:27 final size:26
Alignment explanation
Indices: 20686--20748 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
20676 AAATAGTTAA
20686 ATACCCCTATGTATG-AAAATTACCATT
1 ATACCCCTA-G-ATGCAAAATTACCATT
* *
20713 ATACACCTAGGTGCAAAATTACCATT
1 ATACCCCTAGATGCAAAATTACCATT
20739 ATACCCCTAG
1 ATACCCCTAG
20749 GGTTAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.06
26 22 0.69
27 8 0.25
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.29
Consensus pattern (26 bp):
ATACCCCTAGATGCAAAATTACCATT
Found at i:20955 original size:27 final size:28
Alignment explanation
Indices: 20853--20953 Score: 143
Period size: 27 Copynumber: 3.7 Consensus size: 28
20843 GAGGAAGCGT
*
20853 TCTGATGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACAAATATCTGTA
*
20880 TCTGGTGGCTCTGCCACAAATATCTGTT
1 TCTGGTGGCTCTGCCACAAATATCTGTA
*
20908 TCTAGTGGCTCTGCCAC-AATATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTGTA
* *
20935 TCTGGTGACTCTGTCACAA
1 TCTGGTGGCTCTGCCACAA
20954 TAGGATTCCC
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
27 48 0.74
28 17 0.26
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.33
Consensus pattern (28 bp):
TCTGGTGGCTCTGCCACAAATATCTGTA
Found at i:24285 original size:40 final size:40
Alignment explanation
Indices: 24123--24271 Score: 280
Period size: 40 Copynumber: 3.7 Consensus size: 40
24113 TATTCGGATG
*
24123 ATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
24163 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
24203 ATAACTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
24243 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
24272 AGCAAGTAGC
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 106 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:32205 original size:39 final size:39
Alignment explanation
Indices: 32141--32280 Score: 250
Period size: 39 Copynumber: 3.7 Consensus size: 39
32131 TCGGATGATA
32141 ACCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
32179 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
32218 A-C-GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
*
32255 AACGGGCTAAGTCCCGAAGGCATTTG
1 ACCGGGCTAAGTCCCGAAGGCATTTG
32281 AGCAAGTAGC
Statistics
Matches: 99, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
37 36 0.36
38 14 0.14
39 49 0.49
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (39 bp):
ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
Found at i:32294 original size:76 final size:76
Alignment explanation
Indices: 32145--32313 Score: 252
Period size: 76 Copynumber: 2.2 Consensus size: 76
32135 ATGATAACCG
* * *
32145 GGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATACCGGGCTAAGTCCCGAAGGCATTTGTGCGA
1 GGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAACGGGCTAAGTCCCGAAGGCATTTGAGCAA
32210 GTTACTATA-C
66 GTTACTATACC
32220 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACGGGCTAAGTCCCGAAGGCATTTGAGCA
1 GGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAACGGGCTAAGTCCCGAAGGCATTTGAGCA
32285 AG-TAGCTATATCC
65 AGTTA-CTATA-CC
*
32298 GGCTAAATTCCGAAGG
1 GGCT-AAGTCCGAAGG
32314 TACTTGGTTT
Statistics
Matches: 85, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
75 10 0.12
76 60 0.71
78 12 0.14
79 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (76 bp):
GGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAACGGGCTAAGTCCCGAAGGCATTTGAGCAA
GTTACTATACC
Found at i:32302 original size:39 final size:38
Alignment explanation
Indices: 32145--32313 Score: 236
Period size: 39 Copynumber: 4.4 Consensus size: 38
32135 ATGATAACCG
32145 GGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATACC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATACC
32182 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-C
1 -GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATACC
*
32220 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-ACC
* *
32259 GGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATA-CC
* *
32298 GGCTAAATTCCGAAGG
1 GGCTAAGTCCCGAAGG
32314 TACTTGGTTT
Statistics
Matches: 120, Mismatches: 6, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
37 35 0.29
38 13 0.11
39 72 0.60
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (38 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATACC
Done.