Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2171
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: 14695
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Found at i:1508 original size:39 final size:40
Alignment explanation
Indices: 1371--1553 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
1361 GCTACTCGTT
*
1371 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
1411 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
1451 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
1489 CAAATGCCTTC-GGATCTTAG-TCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
1529 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1554 CATCATTCGA
Statistics
Matches: 124, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
37 2 0.02
38 24 0.19
39 33 0.27
40 63 0.51
41 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:1547 original size:78 final size:81
Alignment explanation
Indices: 1371--1553 Score: 209
Period size: 78 Copynumber: 2.3 Consensus size: 81
1361 GCTACTCGTT
* *
1371 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* *
1435 GATTTAGTAACTCGCAC
65 GATATAGTAACTAGCAC
* **
1452 CAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ACTCGCACAAATGCCTTC-GGATCTT-AGTCG
1 CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* *
1512 GATATGGTCACTTAGCA-
65 GATATAGTAAC-TAGCAC
1529 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
1554 CATCATTCGA
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
77 26 0.30
78 36 0.41
79 13 0.15
80 10 0.11
81 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTAGCAC
Found at i:2789 original size:55 final size:56
Alignment explanation
Indices: 2683--2801 Score: 222
Period size: 55 Copynumber: 2.1 Consensus size: 56
2673 TATTAGTTTA
*
2683 TTGCCCATGCTTCTTATTTTATTCTTCCTTTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
2739 TTGCCCATGCTTCTTATTTTATT-TTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
2794 TTGCCCAT
1 TTGCCCAT
2802 CATCCCTTGT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 39 0.63
56 23 0.37
ACGTcount: A:0.22, C:0.24, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:9337 original size:40 final size:40
Alignment explanation
Indices: 9255--9478 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
9245 GCTACTCGTT
*
9255 CAAATGCCTTCGGGACATAGCCC-G-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
9294 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
9334 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
9374 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
9413 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
9454 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9479 CATCATTCGA
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 53 0.33
40 94 0.58
41 13 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:9397 original size:79 final size:80
Alignment explanation
Indices: 9255--9478 Score: 269
Period size: 79 Copynumber: 2.8 Consensus size: 80
9245 GCTACTCGTT
* * *
9255 CAAATGCCTTCGGGACATAGCCC-G-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCG
*
9318 GATTTAGTAACTCACA
65 GAATTAGTAACTCACA
*
9334 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGG
* *
9398 AATTAGTATCTCGCA
66 AATTAGTAACTCACA
* * * * * *
9413 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACCAATGCCTTCGGGACTTAGCCC
9476 GGA
64 GGA
9479 CATCATTCGA
Statistics
Matches: 126, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
78 3 0.02
79 80 0.63
80 41 0.33
81 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCACA
Found at i:9438 original size:119 final size:119
Alignment explanation
Indices: 9257--9478 Score: 297
Period size: 119 Copynumber: 1.9 Consensus size: 119
9247 TACTCGTTCA
** *
9257 AATGCCTTCGGGACATAGCCCGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACATAGCCCGGAATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATA
9322 TAGTAACTCA-CACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 TAGTAACTCAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
9376 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGA
1 AATGCCTTCGGGACATAGCCCGGAA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
* * * *
9439 TATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 TATAGTAACTCAGCACAAAGCCTTCGGGACTTAACCCGGA
9479 CATCATTCGA
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
118 12 0.13
119 71 0.80
120 6 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAGCCCGGAATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATA
TAGTAACTCAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:10704 original size:55 final size:56
Alignment explanation
Indices: 10603--10721 Score: 231
Period size: 55 Copynumber: 2.1 Consensus size: 56
10593 TATTAGTTTA
10603 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
10659 TTGCCCATGCTTCTTATTTTATT-TTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
10714 TTGCCCAT
1 TTGCCCAT
10722 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 40 0.63
56 23 0.37
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:11832 original size:39 final size:40
Alignment explanation
Indices: 11731--11912 Score: 182
Period size: 39 Copynumber: 4.7 Consensus size: 40
11721 TCGAGTGATG
* *
11731 TCCGGGCTCAGTCCCGAAGGC-TTTGTGCTA-AGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTG--AGAGTTACTATA
*
11771 TCCGGACTAAGAT-CCGAAGGCATTTGTGAGAGTTACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGAGAGTTACTATA
* * *
11810 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACTATA
* *
11850 TCC-GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACTATA
* *
11889 ACC-GGCTATGT-CCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
11913 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
38 19 0.15
39 62 0.50
40 35 0.28
41 7 0.06
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACTATA
Found at i:11876 original size:78 final size:80
Alignment explanation
Indices: 11731--11886 Score: 203
Period size: 78 Copynumber: 2.0 Consensus size: 80
11721 TCGAGTGATG
* * *
11731 TCCGGGCTCAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
11796 GTGAGAGTTACTAAT
66 GTGAGAGTTACTAAT
* * *
11811 TCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGG-TTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTGGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCAT
*
11872 TTGTGCGAGTTACTA
64 TTGTGAGAGTTACTA
11887 TAACCGGCTA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
77 1 0.01
78 28 0.42
79 22 0.33
80 16 0.24
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
GTGAGAGTTACTAAT
Found at i:11930 original size:77 final size:78
Alignment explanation
Indices: 11765--11935 Score: 197
Period size: 77 Copynumber: 2.2 Consensus size: 78
11755 GTGCTAAGTG
* *
11765 ACTATATCCGGACTAAGATCCGAAGGCATTTGTGAGAGTTACTAATTCCGGGCTAAGCCCGAAGG
1 ACTATATCCGG-TTAAGATCCGAAGGCATTTGTGAGAGTTACTAATACCGGGCTAAGCCCGAAGG
**
11830 CATTGGTGCGAGTT
65 CATTGGAACGAGTT
* * * *
11844 ACTAAATCCGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACT-ATAACC-GGCTATGTCCGAAG
1 ACTATATCCGGTTAAGAT-CCGAAGGCATTTGTGAGAGTTACTAAT-ACCGGGCTAAGCCCGAAG
*
11906 GCATTTGAACGAG-T
64 GCATTGGAACGAGTT
11920 AGCTATATCCGGTTAA
1 A-CTATATCCGGTTAA
11936 ATTTCGAAGG
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
76 2 0.03
77 38 0.48
78 29 0.37
79 10 0.13
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (78 bp):
ACTATATCCGGTTAAGATCCGAAGGCATTTGTGAGAGTTACTAATACCGGGCTAAGCCCGAAGGC
ATTGGAACGAGTT
Done.