Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2977
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: 30375
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Found at i:5240 original size:56 final size:56
Alignment explanation
Indices: 5154--5273 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
5144 ACAAGGGATG
5154 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
5210 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
5266 ATGGGCAA
1 ATGGGCAA
5274 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:6549 original size:40 final size:40
Alignment explanation
Indices: 6401--6585 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
6391 TCGAATGATG
* * * *
6401 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
6441 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TTACTAAA
*
6482 TCCGGG-TAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
6520 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
6561 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
6586 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
38 13 0.10
39 22 0.17
40 72 0.57
41 19 0.15
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:6607 original size:79 final size:79
Alignment explanation
Indices: 6454--6618 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
6444 GGACTAAGAT
* **
6454 CCGAAGGCATTTGTGCGAGATTACTAATTCCGGGTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATTACTAATACCGGGTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
6519 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
6533 CCGAAGGCATTTGTGCGAG-TTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAG
1 CCGAAGGCATTTGTGCGAGATTACTAAT-ACCGGG-TAAG-CCCGAAGGCATTGGAACGAGTTA-
* *
6595 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
6612 CCGAAGG
1 CCGAAGG
6619 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
77 2 0.03
78 10 0.14
79 38 0.51
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATTACTAATACCGGGTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:13127 original size:56 final size:56
Alignment explanation
Indices: 13041--13160 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
13031 ACAAGGGATG
13041 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
13097 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
13153 ATGGGCAA
1 ATGGGCAA
13161 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:14372 original size:40 final size:38
Alignment explanation
Indices: 14327--14424 Score: 106
Period size: 38 Copynumber: 2.5 Consensus size: 38
14317 AAGTGACCAT
*
14327 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGACTAAG-CCCGAAGGCA-TTGTGCGAGATACTAA
* ** *
14367 TTCCGGGTTAAGCCCGAAGGCATTGTGCGAGTTACTAA
1 ATCCGGACTAAGCCCGAAGGCATTGTGCGAGATACTAA
**
14405 ATCCGGGTTAAGTCCCGAAG
1 ATCCGGACTAAG-CCCGAAG
14425 TTACTATAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
38 26 0.51
39 16 0.31
40 9 0.18
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (38 bp):
ATCCGGACTAAGCCCGAAGGCATTGTGCGAGATACTAA
Found at i:14403 original size:38 final size:40
Alignment explanation
Indices: 14288--14424 Score: 140
Period size: 40 Copynumber: 3.5 Consensus size: 40
14278 TCGAATGATG
* * * *
14288 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
** *
14328 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
14368 TCCGGGTTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
14406 TCCGGGTTAAGTCCCGAAG
1 TCCGGGTTAAGTCCCGAAG
14425 TTACTATAAC
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
38 26 0.31
39 16 0.19
40 30 0.36
41 10 0.12
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:14437 original size:27 final size:27
Alignment explanation
Indices: 14396--14451 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
14386 GCATTGTGCG
*
14396 AGTTACTAAATCCGGGTTAAGTCCCGA
1 AGTTACTAAATCCGGGCTAAGTCCCGA
*
14423 AGTTACTATAA-CCGGGCTATGTCCCGA
1 AGTTACTA-AATCCGGGCTAAGTCCCGA
14450 AG
1 AG
14452 GCATTTGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (27 bp):
AGTTACTAAATCCGGGCTAAGTCCCGA
Found at i:18948 original size:40 final size:40
Alignment explanation
Indices: 18882--18958 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
18872 ATGTTTAAAG
* *
18882 TCAGTGAGTTACACAGTCTAGCACACGACCGTGTGACAAC
1 TCAGAGAGTTACACAATCTAGCACACGACCGTGTGACAAC
* *
18922 TCAGAGAGTTACACAATCTA-CGACACGGCTGTGTGAC
1 TCAGAGAGTTACACAATCTAGC-ACACGACCGTGTGAC
18959 CCTACTCAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.03
40 31 0.97
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (40 bp):
TCAGAGAGTTACACAATCTAGCACACGACCGTGTGACAAC
Found at i:20150 original size:54 final size:58
Alignment explanation
Indices: 20065--20177 Score: 198
Period size: 56 Copynumber: 2.0 Consensus size: 58
20055 GGGATGAGGC
20065 AAACATGTCATGAAACATGTTGTGTTAATGGAA-AAAT-AAAATAAGAAGCATGGGCA
1 AAACATGTCATGAAACATGTTGTGTTAATGGAAGAAATAAAAATAAGAAGCATGGGCA
20121 AAACATGTCATG-AACA-GTTGTGTTAATGGAAGAAATAAAAATAAGAAGCATGGGCA
1 AAACATGTCATGAAACATGTTGTGTTAATGGAAGAAATAAAAATAAGAAGCATGGGCA
20177 A
1 A
20178 TAAACTAATA
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
54 15 0.27
55 8 0.15
56 32 0.58
ACGTcount: A:0.47, C:0.09, G:0.22, T:0.22
Consensus pattern (58 bp):
AAACATGTCATGAAACATGTTGTGTTAATGGAAGAAATAAAAATAAGAAGCATGGGCA
Found at i:21427 original size:79 final size:81
Alignment explanation
Indices: 21291--21475 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
21281 TCGAATGATG
*
21291 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
21355 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
21370 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
21432 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
21450 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
21476 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:21489 original size:40 final size:40
Alignment explanation
Indices: 21292--21475 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
21282 CGAATGATGT
* * * *
21292 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
21332 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
21372 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
21410 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
21451 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
21476 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:21497 original size:79 final size:79
Alignment explanation
Indices: 21344--21508 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
21334 GGACTAAGAT
* **
21344 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
21409 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
21423 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
21486 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
21502 CCGAAGG
1 CCGAAGG
21509 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.