Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3409
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: 13532
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Found at i:2699 original size:117 final size:119
Alignment explanation
Indices: 2519--2739 Score: 297
Period size: 117 Copynumber: 1.9 Consensus size: 119
2509 TCCTCGTTCA
**
2519 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
2584 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * **
2638 AATGCCTTCGGG-CTTAGCCCGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGA
1 AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
* * *
2700 TATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
65 TATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
2740 CATCATTCAA
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
116 3 0.03
117 57 0.64
118 17 0.19
119 12 0.13
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:2739 original size:40 final size:40
Alignment explanation
Indices: 2517--2739 Score: 285
Period size: 40 Copynumber: 5.7 Consensus size: 40
2507 GCTCCTCGTT
* *
2517 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
2557 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
2597 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
2637 C-AATGCCTTCGGG-CTTAGCCCGAAT-TAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
2674 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
2715 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
2740 CATCATTCAA
Statistics
Matches: 163, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
37 14 0.09
38 19 0.12
39 22 0.13
40 97 0.60
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:8613 original size:118 final size:119
Alignment explanation
Indices: 8432--8653 Score: 299
Period size: 118 Copynumber: 1.9 Consensus size: 119
8422 TCCTCGTTCA
*
8432 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
8497 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * **
8551 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
8613 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
8654 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
117 4 0.04
118 66 0.73
119 20 0.22
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:8653 original size:40 final size:40
Alignment explanation
Indices: 8430--8653 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
8420 GCTCCTCGTT
* *
8430 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
8470 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
8510 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
8550 C-AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
8588 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
8629 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
8654 CATCATTCAA
Statistics
Matches: 164, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
38 24 0.15
39 21 0.13
40 107 0.65
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:12470 original size:40 final size:40
Alignment explanation
Indices: 12274--12456 Score: 207
Period size: 39 Copynumber: 4.6 Consensus size: 40
12264 TGAATGATGT
* * * *
12274 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
12314 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
12354 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
12392 TCC-GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
12432 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
12457 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
38 6 0.05
39 56 0.45
40 54 0.44
41 8 0.06
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:12474 original size:79 final size:78
Alignment explanation
Indices: 12326--12489 Score: 215
Period size: 79 Copynumber: 2.1 Consensus size: 78
12316 GGACTAAGAT
* **
12326 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
12391 ATCCGGTTAAGTC
66 ATCCGGTTAAATC
* *
12404 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
12467 TATATCCGGTTAAATT
63 TAAATCCGGTTAAATC
12483 CCGAAGG
1 CCGAAGG
12490 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
77 2 0.03
78 34 0.45
79 39 0.52
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGTTAAATC
Done.