Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3465
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: 18515
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:220 original size:40 final size:40
Alignment explanation
Indices: 146--329 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
136 GCTCCTCATT
*
146 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
185 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
225 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
264 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
305 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
330 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.02
39 44 0.35
40 67 0.53
41 13 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:262 original size:79 final size:81
Alignment explanation
Indices: 146--329 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 81
136 GCTCCTCATT
* * *
146 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
209 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
225 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
289 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
305 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
330 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
78 3 0.03
79 68 0.75
80 20 0.22
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:3079 original size:11 final size:12
Alignment explanation
Indices: 3063--3129 Score: 93
Period size: 12 Copynumber: 5.7 Consensus size: 12
3053 CATAAATCAC
3063 TTTTTTTTC-AA
1 TTTTTTTTCGAA
3074 TTTTTTTT-GAA
1 TTTTTTTTCGAA
*
3085 TTTTTTTTCGAT
1 TTTTTTTTCGAA
3097 TTTTTTTTCGAA
1 TTTTTTTTCGAA
*
3109 TTTTTTTTTCAAA
1 -TTTTTTTTCGAA
3122 TTTTTTTT
1 TTTTTTTT
3130 TCAAACTTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
11 18 0.36
12 21 0.42
13 11 0.22
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:3134 original size:13 final size:12
Alignment explanation
Indices: 3063--3133 Score: 92
Period size: 13 Copynumber: 5.9 Consensus size: 12
3053 CATAAATCAC
3063 TTTTTTTTCAA-
1 TTTTTTTTCAAT
*
3074 TTTTTTTTGAA-
1 TTTTTTTTCAAT
*
3085 TTTTTTTTCGAT
1 TTTTTTTTCAAT
3097 TTTTTTTTCGAAT
1 TTTTTTTTC-AAT
3110 TTTTTTTTCAAAT
1 TTTTTTTTC-AAT
3123 TTTTTTTTCAA
1 TTTTTTTTCAA
3134 ACTTGTATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
11 19 0.36
12 11 0.21
13 23 0.43
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:9510 original size:6 final size:6
Alignment explanation
Indices: 9501--9563 Score: 117
Period size: 6 Copynumber: 10.5 Consensus size: 6
9491 AATAAAATTG
*
9501 AAATGA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
9549 AAATAA AAATAA AAA
1 AAATAA AAATAA AAA
9564 GATAGGAGGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:12784 original size:40 final size:40
Alignment explanation
Indices: 12711--13178 Score: 803
Period size: 40 Copynumber: 11.7 Consensus size: 40
12701 TGAGCATTGG
12711 AATATATCCGGGCTAAGA-CCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
12750 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
12790 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
12830 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
12870 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
12910 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
12950 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
12990 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
13030 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* * **
13070 AATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGAC
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* * *
13110 GATATATCCGGGCTAAGACCCGAAGGCAATTAGGCAAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* * *
13150 GATATGTCCGGGTTAAGACCCGAAGGCAA
1 AATATATCCGGGCTAAGACCCGAAGGCAA
13179 GTGTGTTTGC
Statistics
Matches: 407, Mismatches: 21, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
39 18 0.04
40 389 0.96
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
Done.