Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011867.1 Corchorus capsularis cultivar CVL-1 contig11888, whole genome shotgun sequence
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: 50249
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:1739 original size:15 final size:15
Alignment explanation
Indices: 1719--1751 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1709 GTTATCGGAT
*
1719 TTGCTGGATTTGAGA
1 TTGCTGAATTTGAGA
1734 TTGCTGAATTTGAGA
1 TTGCTGAATTTGAGA
1749 TTG
1 TTG
1752 AGATTTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.30, T:0.42
Consensus pattern (15 bp):
TTGCTGAATTTGAGA
Found at i:2015 original size:32 final size:32
Alignment explanation
Indices: 1973--2039 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
1963 ACTTTGCTTC
*
1973 AGATTGGCTTTGCTTGATGGAGATGTTGATGG
1 AGATTGGCTTTGCTTGATGAAGATGTTGATGG
*
2005 AGATTTGCTTTGCTTGATGAAGATGTTGATGG
1 AGATTGGCTTTGCTTGATGAAGATGTTGATGG
2037 AGA
1 AGA
2040 AGAACTTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.06, G:0.34, T:0.37
Consensus pattern (32 bp):
AGATTGGCTTTGCTTGATGAAGATGTTGATGG
Found at i:2048 original size:32 final size:32
Alignment explanation
Indices: 1980--2073 Score: 99
Period size: 32 Copynumber: 3.1 Consensus size: 32
1970 TTCAGATTGG
* ****
1980 CTTTGCTTGATGGAGATGTTGATGGAGATTTG
1 CTTTGCTTGATGAAGATGTTGATGGAGAAGAA
2012 CTTTGCTTGATGAAGATGTTGATGGAGAAGAA
1 CTTTGCTTGATGAAGATGTTGATGGAGAAGAA
*
2044 CTTTGC-T--T-CAGAT-TTGATGGAGAAGAA
1 CTTTGCTTGATGAAGATGTTGATGGAGAAGAA
2071 CTT
1 CTT
2074 GGAGAAGAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 17 0.30
28 4 0.07
29 1 0.02
31 1 0.02
32 33 0.59
ACGTcount: A:0.26, C:0.09, G:0.30, T:0.36
Consensus pattern (32 bp):
CTTTGCTTGATGAAGATGTTGATGGAGAAGAA
Found at i:2078 original size:12 final size:12
Alignment explanation
Indices: 2061--2085 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2051 TCAGATTTGA
2061 TGGAGAAGAACT
1 TGGAGAAGAACT
2073 TGGAGAAGAACT
1 TGGAGAAGAACT
2085 T
1 T
2086 TGCCTTGCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.32, T:0.20
Consensus pattern (12 bp):
TGGAGAAGAACT
Found at i:5040 original size:16 final size:14
Alignment explanation
Indices: 5004--5031 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4994 TAGAGATCCA
5004 CCCCTTGTCTACTC
1 CCCCTTGTCTACTC
5018 CCCCTTGTCTACTC
1 CCCCTTGTCTACTC
5032 TTGCCCTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.50, G:0.07, T:0.36
Consensus pattern (14 bp):
CCCCTTGTCTACTC
Found at i:5146 original size:47 final size:46
Alignment explanation
Indices: 5089--5240 Score: 223
Period size: 46 Copynumber: 3.3 Consensus size: 46
5079 AGCTTTGTCT
* *
5089 TCGGCTTCTTGGCGGGGTTGATTTTTTTATCACCCTCTACCTTTGCA
1 TCGGCCTCTTGGCGGGGTTGA-TTTTTTATCACCCTCTACCTCTGCA
* * *
5136 TCGGCCTCTTGGTGGGGTTGATTTTTAATCACCTTCTACCTCTGCA
1 TCGGCCTCTTGGCGGGGTTGATTTTTTATCACCCTCTACCTCTGCA
* *
5182 TCAGCCTCTTGGCGGGGTTGATCTTTTATCACCCTCTACCTCTGCA
1 TCGGCCTCTTGGCGGGGTTGATTTTTTATCACCCTCTACCTCTGCA
*
5228 TCGGCGTCTTGGC
1 TCGGCCTCTTGGC
5241 AGGCCATGAG
Statistics
Matches: 93, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
46 74 0.80
47 19 0.20
ACGTcount: A:0.11, C:0.28, G:0.22, T:0.38
Consensus pattern (46 bp):
TCGGCCTCTTGGCGGGGTTGATTTTTTATCACCCTCTACCTCTGCA
Found at i:8315 original size:15 final size:15
Alignment explanation
Indices: 8295--8327 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
8285 GTTGTCGGAT
8295 TTGCTGGATTTGAGA
1 TTGCTGGATTTGAGA
8310 TTGCTGGATTTGAGA
1 TTGCTGGATTTGAGA
8325 TTG
1 TTG
8328 AGATTTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.33, T:0.42
Consensus pattern (15 bp):
TTGCTGGATTTGAGA
Found at i:8536 original size:78 final size:78
Alignment explanation
Indices: 8441--8593 Score: 288
Period size: 78 Copynumber: 2.0 Consensus size: 78
8431 CTATAGATCG
*
8441 GCTGGATTTGATAGAGAAACTTTGGTAGGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTGGC
1 GCTGGATTTGATAGAGAAACTTTCGTAGGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTGGC
8506 TTTGCTTGATTCA
66 TTTGCTTGATTCA
*
8519 GCTGGATTTGATGGAGAAACTTTCGTAGGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTGGC
1 GCTGGATTTGATAGAGAAACTTTCGTAGGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTGGC
8584 TTTGCTTGAT
66 TTTGCTTGAT
8594 GGAGATGTTG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.37
Consensus pattern (78 bp):
GCTGGATTTGATAGAGAAACTTTCGTAGGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTGGC
TTTGCTTGATTCA
Found at i:8618 original size:32 final size:32
Alignment explanation
Indices: 8576--8642 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
8566 ACTTTGCTTC
*
8576 AGATTGGCTTTGCTTGATGGAGATGTTGATGG
1 AGATTGGCTTTGCTTGATGAAGATGTTGATGG
*
8608 AGATTTGCTTTGCTTGATGAAGATGTTGATGG
1 AGATTGGCTTTGCTTGATGAAGATGTTGATGG
8640 AGA
1 AGA
8643 AGAATTTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.06, G:0.34, T:0.37
Consensus pattern (32 bp):
AGATTGGCTTTGCTTGATGAAGATGTTGATGG
Found at i:8652 original size:32 final size:32
Alignment explanation
Indices: 8583--8676 Score: 90
Period size: 32 Copynumber: 3.1 Consensus size: 32
8573 TTCAGATTGG
* ****
8583 CTTTGCTTGATGGAGATGTTGATGGAGATTTG
1 CTTTGCTTGATGAAGATGTTGATGGAGAAGAA
8615 CTTTGCTTGATGAAGATGTTGATGGAGAAGAA
1 CTTTGCTTGATGAAGATGTTGATGGAGAAGAA
* *
8647 TTTTGC-T--T-CAGAT-TTGATGGAGAAGAA
1 CTTTGCTTGATGAAGATGTTGATGGAGAAGAA
8674 CTT
1 CTT
8677 GGAGAAGAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
27 16 0.30
28 4 0.07
29 1 0.02
31 1 0.02
32 32 0.59
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (32 bp):
CTTTGCTTGATGAAGATGTTGATGGAGAAGAA
Found at i:8679 original size:12 final size:12
Alignment explanation
Indices: 8664--8688 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8654 TCAGATTTGA
8664 TGGAGAAGAACT
1 TGGAGAAGAACT
8676 TGGAGAAGAACT
1 TGGAGAAGAACT
8688 T
1 T
8689 TGCCTTGTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.32, T:0.20
Consensus pattern (12 bp):
TGGAGAAGAACT
Found at i:9406 original size:14 final size:14
Alignment explanation
Indices: 9389--9415 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9379 TTACATAACA
9389 ATAATTAATTTTAG
1 ATAATTAATTTTAG
9403 ATAATTAATTTTA
1 ATAATTAATTTTA
9416 AATTCAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
ATAATTAATTTTAG
Found at i:9572 original size:9 final size:9
Alignment explanation
Indices: 9537--9581 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
9527 TAGTTTTATA
9537 ATAACATA-
1 ATAACATAT
9545 ATAACATAT
1 ATAACATAT
*
9554 AT-ATATAT
1 ATAACATAT
9562 ATAACATAT
1 ATAACATAT
9571 ATAACATAT
1 ATAACATAT
9580 AT
1 AT
9582 TAAAGTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
8 15 0.45
9 18 0.55
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (9 bp):
ATAACATAT
Found at i:10691 original size:21 final size:21
Alignment explanation
Indices: 10665--10708 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
10655 TAGCACAGCT
* *
10665 CACCTGGGTGATCAGACGAAC
1 CACCTGGGTCATCAGACAAAC
*
10686 CACCTGGGTCTTCAGACAAAC
1 CACCTGGGTCATCAGACAAAC
10707 CA
1 CA
10709 TGTGGGCGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.32, G:0.23, T:0.16
Consensus pattern (21 bp):
CACCTGGGTCATCAGACAAAC
Found at i:13302 original size:11 final size:11
Alignment explanation
Indices: 13288--13314 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
13278 CTGGGGCGGG
13288 CCAGCCATGGC
1 CCAGCCATGGC
13299 CCAGCCATGGC
1 CCAGCCATGGC
13310 CCAGC
1 CCAGC
13315 GCCCAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.48, G:0.26, T:0.07
Consensus pattern (11 bp):
CCAGCCATGGC
Found at i:14250 original size:24 final size:24
Alignment explanation
Indices: 14223--14268 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
14213 CTTGGTTTTG
* *
14223 GATTGATTATCTTGATTTTACTAT
1 GATTGATGATCATGATTTTACTAT
* *
14247 GATTTATGATCATGGTTTTACT
1 GATTGATGATCATGATTTTACT
14269 GATTTTCCTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (24 bp):
GATTGATGATCATGATTTTACTAT
Found at i:15647 original size:12 final size:12
Alignment explanation
Indices: 15630--15654 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15620 ATTCTAAACC
15630 TGTTACTCTTCT
1 TGTTACTCTTCT
15642 TGTTACTCTTCT
1 TGTTACTCTTCT
15654 T
1 T
15655 AGAGATTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (12 bp):
TGTTACTCTTCT
Found at i:16790 original size:32 final size:32
Alignment explanation
Indices: 16705--16782 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
16695 GTCCCTTGTC
*
16705 CCCTTGGCCTTGGCGTCGGCATTTCCCGATGG
1 CCCTTGGCCTTGGCATCGGCATTTCCCGATGG
** * * * *
16737 CCGATGGTCTTGGCATCGGCATTTGCTGATGT
1 CCCTTGGCCTTGGCATCGGCATTTCCCGATGG
16769 CCCTTGGCCTTGGC
1 CCCTTGGCCTTGGC
16783 CTTGGCATCA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.08, C:0.31, G:0.31, T:0.31
Consensus pattern (32 bp):
CCCTTGGCCTTGGCATCGGCATTTCCCGATGG
Found at i:19618 original size:11 final size:10
Alignment explanation
Indices: 19601--19656 Score: 58
Period size: 11 Copynumber: 5.2 Consensus size: 10
19591 AGCTCGATTA
19601 ATGTTCGTTT
1 ATGTTCGTTT
19611 AGTGTTCGTTT
1 A-TGTTCGTTT
*
19622 AATAGATCGTTT
1 -AT-GTTCGTTT
*
19634 ATCGCTCGTTT
1 AT-GTTCGTTT
19645 ATGTTCGTTT
1 ATGTTCGTTT
19655 AT
1 AT
19657 ATTGTATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 10 0.26
11 21 0.54
12 8 0.21
ACGTcount: A:0.16, C:0.12, G:0.20, T:0.52
Consensus pattern (10 bp):
ATGTTCGTTT
Found at i:20190 original size:29 final size:30
Alignment explanation
Indices: 20144--20216 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
20134 TTCGGAAAAC
* **
20144 TCCAACTTAGTATGAAACCTTTTATT-TCG
1 TCCAATTTAGTACCAAACCTTTTATTATCG
* * *
20173 TCCAATTTGGTACCAAACGTTTTATTAATGG
1 TCCAATTTAGTACCAAACCTTTTATT-ATCG
20204 TCCAATTTAGTAC
1 TCCAATTTAGTAC
20217 TTTTTCAGGT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
29 21 0.60
31 14 0.40
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (30 bp):
TCCAATTTAGTACCAAACCTTTTATTATCG
Found at i:20303 original size:11 final size:10
Alignment explanation
Indices: 20285--20359 Score: 88
Period size: 10 Copynumber: 7.9 Consensus size: 10
20275 CCTACGTGGC
20285 ATTTTTAAAT
1 ATTTTTAAAT
20295 ATCTTTTAAAT
1 AT-TTTTAAAT
20306 ATTTTT-AAT
1 ATTTTTAAAT
20315 -TTTTTAAAT
1 ATTTTTAAAT
*
20324 ATTTTT-TAT
1 ATTTTTAAAT
20333 ATTTTT--AT
1 ATTTTTAAAT
*
20341 ATTTTTTAAT
1 ATTTTTAAAT
20351 ATTTTTAAA
1 ATTTTTAAA
20360 CCAGCTCAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
8 13 0.22
9 14 0.24
10 21 0.36
11 10 0.17
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTAAAT
Found at i:20320 original size:8 final size:9
Alignment explanation
Indices: 20285--20358 Score: 80
Period size: 9 Copynumber: 7.9 Consensus size: 9
20275 CCTACGTGGC
20285 ATTTTTAAAT
1 ATTTTT-AAT
20295 ATCTTTTAAAT
1 AT-TTTT-AAT
20306 ATTTTTAAT
1 ATTTTTAAT
20315 -TTTTTAAAT
1 ATTTTT-AAT
*
20324 ATTTTTTAT
1 ATTTTTAAT
20333 ATTTTT-AT
1 ATTTTTAAT
20341 ATTTTTTAAT
1 A-TTTTTAAT
20351 ATTTTTAA
1 ATTTTTAA
20359 ACCAGCTCAA
Statistics
Matches: 58, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
8 8 0.14
9 26 0.45
10 14 0.24
11 10 0.17
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:20321 original size:18 final size:19
Alignment explanation
Indices: 20285--20359 Score: 100
Period size: 18 Copynumber: 3.9 Consensus size: 19
20275 CCTACGTGGC
20285 ATTTTTAAATATCTTTTAAAT
1 ATTTTT-AATAT-TTTTAAAT
20306 ATTTTTAAT-TTTTTAAAT
1 ATTTTTAATATTTTTAAAT
* *
20324 ATTTTTTATATTTTTATAT
1 ATTTTTAATATTTTTAAAT
20343 -TTTTTAATATTTTTAAA
1 ATTTTTAATATTTTTAAA
20360 CCAGCTCAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
18 31 0.63
19 9 0.18
20 3 0.06
21 6 0.12
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTAATATTTTTAAAT
Found at i:20356 original size:27 final size:27
Alignment explanation
Indices: 20285--20359 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 27
20275 CCTACGTGGC
*
20285 ATTTTTAAATATCTTTTAAATATTTTTA
1 ATTTTTTAATAT-TTTTAAATATTTTTA
*
20313 ATTTTTTAAATATTTTT-TATATTTTTA
1 ATTTTTT-AATATTTTTAAATATTTTTA
20340 TATTTTTTAATATTTTTAAA
1 -ATTTTTTAATATTTTTAAA
20360 CCAGCTCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 18 0.44
28 18 0.44
29 5 0.12
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (27 bp):
ATTTTTTAATATTTTTAAATATTTTTA
Found at i:20411 original size:31 final size:31
Alignment explanation
Indices: 20373--20435 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
20363 GCTCAAATAG
20373 GTGCTAAACGTTTCAAAATTAGATCAATTTA
1 GTGCTAAACGTTTCAAAATTAGATCAATTTA
*
20404 GTGCTAAACGTTTCAAAATTGGATCAATTTA
1 GTGCTAAACGTTTCAAAATTAGATCAATTTA
20435 G
1 G
20436 ATTTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (31 bp):
GTGCTAAACGTTTCAAAATTAGATCAATTTA
Found at i:22937 original size:23 final size:23
Alignment explanation
Indices: 22909--22957 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
22899 CATTTTGGTC
22909 AATTCATAGTTCATTTTTAAGTA
1 AATTCATAGTTCATTTTTAAGTA
*
22932 AATTCATAGTTTATTTTTAAGTA
1 AATTCATAGTTCATTTTTAAGTA
22955 AAT
1 AAT
22958 CCGTTCCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (23 bp):
AATTCATAGTTCATTTTTAAGTA
Found at i:25753 original size:49 final size:50
Alignment explanation
Indices: 25694--25823 Score: 133
Period size: 50 Copynumber: 2.6 Consensus size: 50
25684 TTTTACTTGT
* * *
25694 TATTTCCCAAATTGCTCTT-GCGAACGGAAGGCAT-TCT-TTTTTTACCTAC
1 TATTTCCCAAAATGCCCTTCCCGAACGGAA-G-ATGTCTATTTTTTACCTAC
* * *
25743 TATTTCCCAAAATGCCCTTCCCGGACGGAAGATGTTTATTTTTTACCTGC
1 TATTTCCCAAAATGCCCTTCCCGAACGGAAGATGTCTATTTTTTACCTAC
**
25793 TATTTCCCAAAACACCCTTCCC-AGACGGAAG
1 TATTTCCCAAAATGCCCTTCCCGA-ACGGAAG
25824 CCACTTATTT
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
48 2 0.03
49 20 0.29
50 46 0.68
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.33
Consensus pattern (50 bp):
TATTTCCCAAAATGCCCTTCCCGAACGGAAGATGTCTATTTTTTACCTAC
Found at i:25859 original size:48 final size:48
Alignment explanation
Indices: 25684--26499 Score: 779
Period size: 48 Copynumber: 16.9 Consensus size: 48
25674 AATTTTCAGT
* ** * * * * *
25684 TTTTACTTGTTATTTCCCAAATTGCTCTTGCGA-ACGGAAGGCATTCTTT
1 TTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA--CTTA
* * * * ****
25733 TTTTACCTACTATTTCCCAAAATGCCCTTCCCGGACGGAAGATGTTTA
1 TTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTA
* *
25781 TTTTTTACCTGCTATTTCCCAAAACACCCTTCCCAGACGGAAGCCACTTA
1 --TTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTA
* * * *
25831 TTTTACTTGCTATTTCCCAAAGCGCCCTTCCCATATGGAAGCCATTTA
1 TTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTA
* * * * *
25879 TTTTCGCTTGCTATCTCCCCAAAACACCCTTTCCAGACGGAAGCCATTTA
1 TTTT-ACTTGCTAT-TTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTA
* * *
25929 TTTTTGCTTGCTATCTCCCCAAAATGCCCTTCCCAGACGGAAGCCA-TTCA
1 -TTTTACTTGCTAT-TTCCCAAAACGCCCTTCCCAGACGGAAGCCACTT-A
* * * *
25979 TTTTTACTTGCTATTTCCCAAAGCACCCTTCCCAAACGGAAGCCATTTA
1 -TTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTA
* * *
26028 TTTTTACGTGCTATCTCCCAAAACACCCTTCCCAGACGGAAGCCACTTA
1 -TTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTA
** *
26077 TTTTACTTGCTATTTCCCAAAGTGCCCTTCCCAAACGGAAGCCACTTA
1 TTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTA
* * *
26125 ATTTACTTGCTATTTCCCAAAGCGCCCTTCCCAAACGGAAGCCACTTA
1 TTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTA
* ** *
26173 TTTTACTTGTTATTTCCCAAAGTGCCCTTCCCAAACGGAAGCCACTTA
1 TTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTA
* * *
26221 TTTTACTTGCTATTTCCCAAAGCGCCCTTCCTAGACGGAAGCCATTTA
1 TTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTA
* * *
26269 TTTTGCTTGCTATTTCCCAAAGC-CCCATTCCCAGACGGAAGCCATTTA
1 TTTTACTTGCTATTTCCCAAAACGCCC-TTCCCAGACGGAAGCCACTTA
* * * *
26317 TTTTTGCTTGCTATCTCCCCAAAACGCCCTTCCCGGACGGAAG-C-CGTA
1 -TTTTACTTGCTAT-TTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTA
* * * *
26365 -TAT-CTTGCTATTTTCCAAAACGCCCTTCCCGGACGGAAGGCACTTA
1 TTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTA
* * * *
26411 TTATTACATG-TTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCA-TTAA
1 TT-TTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTT-A
* * * * *
26459 TTTTTACCTG-TTTTTCCTAAAACGCTCTTCCCGGACGGAAG
1 -TTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAG
26500 GCACCATTCT
Statistics
Matches: 666, Mismatches: 82, Indels: 39
0.85 0.10 0.05
Matches are distributed among these distances:
44 26 0.04
45 9 0.01
46 5 0.01
47 6 0.01
48 337 0.51
49 125 0.19
50 151 0.23
51 7 0.01
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.32
Consensus pattern (48 bp):
TTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTA
Found at i:30925 original size:2 final size:2
Alignment explanation
Indices: 30918--30944 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30908 TAATATGTAG
30918 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
30945 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30949 original size:2 final size:2
Alignment explanation
Indices: 30944--30977 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30934 TATATATATA
30944 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
30978 AACAATCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:35634 original size:23 final size:23
Alignment explanation
Indices: 35608--35655 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
35598 CATGTCCCGA
35608 ATGGATTTCGCAGCATATTGAAG
1 ATGGATTTCGCAGCATATTGAAG
35631 ATGGATTTCGCAGCATATTGAAG
1 ATGGATTTCGCAGCATATTGAAG
35654 AT
1 AT
35656 ATCTTGATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (23 bp):
ATGGATTTCGCAGCATATTGAAG
Found at i:35740 original size:67 final size:67
Alignment explanation
Indices: 35661--35793 Score: 257
Period size: 67 Copynumber: 2.0 Consensus size: 67
35651 AAGATATCTT
35661 GATAGTTTTTTGCAAATTGCAGCTTCATCATCCTTTACGCGTGGCTTTCTGCGTTTTAAGGTTTG
1 GATAGTTTTTTGCAAATTGCAGCTTCATCATCCTTTACGCGTGGCTTTCTGCGTTTTAAGGTTTG
35726 AG
66 AG
*
35728 GATAGTTTTTTGCAAATTGCAGCTTCATCATCCTTTAGGCGTGGCTTTCTGCGTTTTAAGGTTTG
1 GATAGTTTTTTGCAAATTGCAGCTTCATCATCCTTTACGCGTGGCTTTCTGCGTTTTAAGGTTTG
35793 A
66 A
35794 TGTCTTCTGC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (67 bp):
GATAGTTTTTTGCAAATTGCAGCTTCATCATCCTTTACGCGTGGCTTTCTGCGTTTTAAGGTTTG
AG
Found at i:36708 original size:2 final size:2
Alignment explanation
Indices: 36701--36732 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36691 CCATAATGAA
36701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36733 TTACCCTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49217 original size:49 final size:49
Alignment explanation
Indices: 49145--49532 Score: 415
Period size: 49 Copynumber: 7.9 Consensus size: 49
49135 AACTTGCCTT
* * *
49145 AATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGTAAGTAAAGATG
1 AATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATG
* * * *
49194 AATGGCTTCCGTCTGGGAAGGGCGCTCTGGGAAATAGCAAGTAAAAATA
1 AATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATG
** *
49243 AATGGCTTCCGTCTGGGAAGGGCACTTTGGGAAATAGCAAGTAAAAATG
1 AATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATG
* * * *
49292 AATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCTAGCAAAAATA
1 AATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATG
* * *
49341 AATGGCTTCCGTCTGGGAAGGGCATTTTAGGAAAAAGCAAAT-AAAA-G
1 AATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATG
* ** * *
49388 AAGTGACTTCCGTCCAGGAAGGGCGTTTAGGGAAAAAGCAAATAAAAATTG
1 AA-TGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAA-TG
* * * * * * *
49439 AGTGTCTTCCGTCCGGGAATGGCGTTTTGGGAAAAAGTTAA-TGAAAATA
1 AATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAG-CAAGTAAAAATG
* * * *
49488 AACGCCTTCCATCCGGGAAGGGCGTTTTGGGAAAAAG-AAGGTAAA
1 AATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAA-GTAAA
49533 GACTGAAAAT
Statistics
Matches: 292, Mismatches: 40, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
47 4 0.01
48 38 0.13
49 210 0.72
50 36 0.12
51 4 0.01
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (49 bp):
AATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATG
Found at i:50221 original size:27 final size:26
Alignment explanation
Indices: 50168--50221 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
50158 TCATTAGGAA
*** *
50168 AAATTAAAAGCCCAATTGTTTAGAAG
1 AAATTAAAAGCCCAATTAAATAAAAG
50194 AAATTAAAAGCCCAAATTAAATAAAAG
1 AAATTAAAAGCCC-AATTAAATAAAAG
50221 A
1 A
50222 TTTGAAGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (26 bp):
AAATTAAAAGCCCAATTAAATAAAAG
Done.