Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014437.1 Corchorus capsularis cultivar CVL-1 contig14458, 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: 199098
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3937 original size:2 final size:2
Alignment explanation
Indices: 3930--3965 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3920 ATCTGTCACA
3930 AT AT 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 AT AT
3966 CAGCCCCCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5566 original size:2 final size:2
Alignment explanation
Indices: 5559--5588 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5549 GCTCAAAGTC
5559 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
5589 GGCTTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5899 original size:2 final size:2
Alignment explanation
Indices: 5884--6001 Score: 53
Period size: 2 Copynumber: 64.0 Consensus size: 2
5874 ACCGACCGAT
* *
5884 TA TA T- TA T- TA TA TA TA -A AA TA TA TT TA TGA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* * *
5923 AA TA TA TA TA -A TA TA TT TA -A T- TA TT TA TGA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* * * *
5962 TA TA TG TA -A AA TA TA TA AA T- TA TA TT TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6000 TA
1 TA
6002 AAATATACTC
Statistics
Matches: 87, Mismatches: 15, Indels: 28
0.67 0.12 0.22
Matches are distributed among these distances:
1 12 0.14
2 71 0.82
3 4 0.05
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5916 original size:11 final size:11
Alignment explanation
Indices: 5901--5977 Score: 51
Period size: 11 Copynumber: 7.6 Consensus size: 11
5891 TTATATATAA
5901 AATATATTTAT
1 AATATATTTAT
*
5912 GATATA--TAT
1 AATATATTTAT
* *
5921 AAAATATATAT
1 AATATATTTAT
5932 AATATA-TT-T
1 AATATATTTAT
5941 AAT-TATTTAT
1 AATATATTTAT
*
5951 GATATA--TAT
1 AATATATTTAT
* *
5960 AATATATGTAA
1 AATATATTTAT
5971 AATATAT
1 AATATAT
5978 AAATTATATT
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
8 2 0.04
9 21 0.41
10 4 0.08
11 24 0.47
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (11 bp):
AATATATTTAT
Found at i:5949 original size:39 final size:40
Alignment explanation
Indices: 5893--6008 Score: 146
Period size: 39 Copynumber: 2.9 Consensus size: 40
5883 TTATATTATT
* *
5893 ATATATAAAATATATTTATGATATATATAAAATATATATA
1 ATATATAAATTATATTTATGATATATATAAAATATATAAA
* * *
5933 ATATATTTAA-T-TATTTATGATATATATAATATATGTAAA
1 ATATA-TAAATTATATTTATGATATATATAAAATATATAAA
*
5972 ATATATAAATTATATTTATTATTATATATAAAATATA
1 ATATATAAATTATATTTATGA-TATATATAAAATATA
6009 CTCCCTCCCA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
38 3 0.05
39 31 0.48
40 14 0.22
41 16 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (40 bp):
ATATATAAATTATATTTATGATATATATAAAATATATAAA
Found at i:5973 original size:48 final size:45
Alignment explanation
Indices: 5902--6008 Score: 130
Period size: 48 Copynumber: 2.4 Consensus size: 45
5892 TATATATAAA
* *
5902 ATATATTTATGATATATATAAAATATATATAA-TATATTTAATTATTT
1 ATATATATATAATATATATAAAATATATA-AATTATATTT-ATTA-TT
*
5949 ATGATATATATAATATATGTAAAATATATAAATTATATTTATTATT
1 AT-ATATATATAATATATATAAAATATATAAATTATATTTATTATT
5995 ATATATA-A-AATATA
1 ATATATATATAATATA
6009 CTCCCTCCCA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
43 6 0.11
44 1 0.02
45 5 0.09
46 4 0.07
47 8 0.15
48 31 0.56
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.48
Consensus pattern (45 bp):
ATATATATATAATATATATAAAATATATAAATTATATTTATTATT
Found at i:6737 original size:13 final size:14
Alignment explanation
Indices: 6714--6745 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
6704 TAATTACTTT
6714 AAAAAAGAGAAAAG
1 AAAAAAGAGAAAAG
6728 AAAAAA-AGAAAAG
1 AAAAAAGAGAAAAG
6741 AAAAA
1 AAAAA
6746 GAATTACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAGAGAAAAG
Found at i:7031 original size:6 final size:6
Alignment explanation
Indices: 7023--7055 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
7013 CAGCTGCTGC
*
7023 TCTCTC TCTCTT TCTCTT TCTCTT TCTCTT TCT
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCT
7056 GTCTGTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
TCTCTT
Found at i:7474 original size:14 final size:15
Alignment explanation
Indices: 7438--7466 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7428 ATACGAGTAT
7438 TATAATATTAATTAA
1 TATAATATTAATTAA
7453 TATAATATT-ATTAA
1 TATAATATTAATTAA
7467 ATGAATATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATATTAATTAA
Found at i:10095 original size:2 final size:2
Alignment explanation
Indices: 10088--10119 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10078 TATTATATTA
10088 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
10120 TAACCATATC
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:31551 original size:1 final size:1
Alignment explanation
Indices: 31545--31581 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
31535 ATGGGCCTTG
*
31545 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
31582 GTTGTTGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:31582 original size:6 final size:6
Alignment explanation
Indices: 31542--31602 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
31532 CCAATGGGCC
* *
31542 TTGTTT TT-TTT TT-TTT TT-TTT TT-TTT TTTTTT TTGTTT TTGTTG
1 TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT
* *
31586 TTGTTG TTGTTG TTGTT
1 TTGTTT TTGTTT TTGTT
31603 GTTGATGTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
5 20 0.38
6 32 0.62
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTGTTT
Found at i:31586 original size:3 final size:3
Alignment explanation
Indices: 31574--31612 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
31564 TTTTTTTTTT
* *
31574 TTG TTT TTG TTG TTG TTG TTG TTG TTG TTG TTG ATG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
31613 CATGTGTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.31, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:31586 original size:9 final size:9
Alignment explanation
Indices: 31542--31605 Score: 55
Period size: 9 Copynumber: 7.6 Consensus size: 9
31532 CCAATGGGCC
31542 TTGTTTTT-
1 TTGTTTTTG
31550 TT-TTTTT-
1 TTGTTTTTG
*
31557 TT-TTTTTT
1 TTGTTTTTG
* *
31565 TTTTTTTTT
1 TTGTTTTTG
31574 TTGTTTTTG
1 TTGTTTTTG
*
31583 TTGTTGTTG
1 TTGTTTTTG
*
31592 TTGTTGTTG
1 TTGTTTTTG
31601 TTGTT
1 TTGTT
31606 GATGTTGCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
7 12 0.24
8 4 0.08
9 35 0.69
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (9 bp):
TTGTTTTTG
Found at i:42938 original size:2 final size:2
Alignment explanation
Indices: 42931--42956 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42921 AGAAGACAAA
42931 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
42957 TGTTAAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46503 original size:23 final size:23
Alignment explanation
Indices: 46458--46504 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
46448 TGAATCCAAA
* *
46458 TTAATTAGATTTTTAAAGGAAAT
1 TTAATTAGATTGTTAAAGAAAAT
46481 TTAATTAGATTCGTTAAA-AAAAT
1 TTAATTAGATT-GTTAAAGAAAAT
46504 T
1 T
46505 ATTTGCAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.43
Consensus pattern (23 bp):
TTAATTAGATTGTTAAAGAAAAT
Found at i:56621 original size:7 final size:7
Alignment explanation
Indices: 56609--56640 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
56599 AAGAATAGGA
56609 AAAAAAC
1 AAAAAAC
56616 AAAAAAC
1 AAAAAAC
56623 AAAAAAC
1 AAAAAAC
56630 AAAAAAC
1 AAAAAAC
56637 AAAA
1 AAAA
56641 GAAATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:69372 original size:23 final size:23
Alignment explanation
Indices: 69337--69380 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
69327 TATTACTTTG
**
69337 TTTTTAATCACTCTTTATAATTT
1 TTTTTAAGAACTCTTTATAATTT
69360 TTTTTAAGAACTCTTTATAAT
1 TTTTTAAGAACTCTTTATAAT
69381 CATTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTTAAGAACTCTTTATAATTT
Found at i:69386 original size:23 final size:23
Alignment explanation
Indices: 69337--69386 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
69327 TATTACTTTG
** **
69337 TTTTTAATCACTCTTTATAATTT
1 TTTTTAAGAACTCTTTATAATCA
69360 TTTTTAAGAACTCTTTATAATCA
1 TTTTTAAGAACTCTTTATAATCA
69383 TTTT
1 TTTT
69387 AAATTCACTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTTTAAGAACTCTTTATAATCA
Found at i:84121 original size:174 final size:173
Alignment explanation
Indices: 83796--84122 Score: 512
Period size: 174 Copynumber: 1.9 Consensus size: 173
83786 TCTAGCTGTA
*
83796 AGTCTCTTTGGAAACTCTCTTTGATTTTGTGTTTGATTTTGGTTTTCAGAGACAGAAAACCAAAA
1 AGTCTCTTTGGAAACTCTCTTTGATTTTGTGTTTGATTTTGGTTTTCAGAGAAAGAAAACCAAAA
* *
83861 AGAATAAAAGATTTTGCCTTGAGCGAATGAAAAATGTAACCTTTTTCCTTTTATCTTTATTCATT
66 AAAAAAAAAGATTTTGCCTTGAGCGAATGAAAAATGTAACCTTTTTCCTTTTATCTTTATTCATT
*
83926 CTCTTGTTCTTTCTTAGTTTTCCTTCAATGGGTCGTAGCAGTG
131 CTCTTGCTCTTTCTTAGTTTTCCTTCAATGGGTCGTAGCAGTG
* * * *
83969 AGTCTCTTTGGGAACTCTCTTTGCTTTTGTGTTTGTTTTTGTTTTTCAGAGAAAGAAAACCAAAA
1 AGTCTCTTTGGAAACTCTCTTTGATTTTGTGTTTGATTTTGGTTTTCAGAGAAAGAAAACCAAAA
* * * * *
84034 AAAAAAAAATGATTTTGGCTTGAGGGACTGAAAAATGTTACCTTTTTCCTTTTATCTTTGTTCAT
66 AAAAAAAAA-GATTTTGCCTTGAGCGAATGAAAAATGTAACCTTTTTCCTTTTATCTTTATTCAT
84099 TCTCTTGCTCTTT-TTAAGTTTTCC
130 TCTCTTGCTCTTTCTT-AGTTTTCC
84123 ACTTTTCCTT
Statistics
Matches: 139, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
173 69 0.50
174 70 0.50
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (173 bp):
AGTCTCTTTGGAAACTCTCTTTGATTTTGTGTTTGATTTTGGTTTTCAGAGAAAGAAAACCAAAA
AAAAAAAAAGATTTTGCCTTGAGCGAATGAAAAATGTAACCTTTTTCCTTTTATCTTTATTCATT
CTCTTGCTCTTTCTTAGTTTTCCTTCAATGGGTCGTAGCAGTG
Found at i:87440 original size:18 final size:17
Alignment explanation
Indices: 87417--87450 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
87407 GTCCAGACCA
*
87417 CGGTTTCAGTTTCGGTTT
1 CGGTTTC-GGTTCGGTTT
87435 CGGTTTCGGTTCGGTT
1 CGGTTTCGGTTCGGTT
87451 CTTGAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.03, C:0.18, G:0.32, T:0.47
Consensus pattern (17 bp):
CGGTTTCGGTTCGGTTT
Found at i:87451 original size:5 final size:6
Alignment explanation
Indices: 87417--87450 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
87407 GTCCAGACCA
*
87417 CGGTTT CAGTTT CGGTTT CGGTTT CGG-TT CGGTT
1 CGGTTT CGGTTT CGGTTT CGGTTT CGGTTT CGGTT
87451 CTTGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.03, C:0.18, G:0.32, T:0.47
Consensus pattern (6 bp):
CGGTTT
Found at i:87673 original size:13 final size:13
Alignment explanation
Indices: 87655--87686 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
87645 GTCTATTAAT
87655 ATTAATTAAGAAA
1 ATTAATTAAGAAA
87668 ATTAATTAAGAAA
1 ATTAATTAAGAAA
*
87681 ACTAAT
1 ATTAAT
87687 ATATATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (13 bp):
ATTAATTAAGAAA
Found at i:87830 original size:18 final size:18
Alignment explanation
Indices: 87807--87845 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
87797 CCAACAAAGA
87807 TTCCGATTCCGATT-ACGG
1 TTCCGATT-CGATTCACGG
87825 TTCCGATTCGATTCACGG
1 TTCCGATTCGATTCACGG
87843 TTC
1 TTC
87846 GAACCGAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.15, C:0.28, G:0.21, T:0.36
Consensus pattern (18 bp):
TTCCGATTCGATTCACGG
Found at i:88420 original size:16 final size:16
Alignment explanation
Indices: 88399--88432 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
88389 GTAATCCTGG
88399 CATTATAAACCAATAC
1 CATTATAAACCAATAC
88415 CATTATAAACCAATAC
1 CATTATAAACCAATAC
88431 CA
1 CA
88433 GTTACTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (16 bp):
CATTATAAACCAATAC
Found at i:90634 original size:27 final size:27
Alignment explanation
Indices: 90596--90648 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
90586 CAATCGAGAG
90596 GAGGGTCACCAGGTCACAAACCAAGAT
1 GAGGGTCACCAGGTCACAAACCAAGAT
*
90623 GAGGGTCACCAGGTCGCAAACCAAGA
1 GAGGGTCACCAGGTCACAAACCAAGA
90649 GGAAGACTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.26, G:0.28, T:0.09
Consensus pattern (27 bp):
GAGGGTCACCAGGTCACAAACCAAGAT
Found at i:97995 original size:1 final size:1
Alignment explanation
Indices: 97989--98014 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
97979 AGCAAACATT
97989 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
98015 GTCGGATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:99103 original size:27 final size:27
Alignment explanation
Indices: 99067--99137 Score: 142
Period size: 27 Copynumber: 2.6 Consensus size: 27
99057 CCCGTCTGTA
99067 GCCTTGCCCTTCTGCTCGTGAATAGCC
1 GCCTTGCCCTTCTGCTCGTGAATAGCC
99094 GCCTTGCCCTTCTGCTCGTGAATAGCC
1 GCCTTGCCCTTCTGCTCGTGAATAGCC
99121 GCCTTGCCCTTCTGCTC
1 GCCTTGCCCTTCTGCTC
99138 CACTCACCTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.08, C:0.39, G:0.21, T:0.31
Consensus pattern (27 bp):
GCCTTGCCCTTCTGCTCGTGAATAGCC
Found at i:106637 original size:202 final size:197
Alignment explanation
Indices: 106289--107081 Score: 878
Period size: 188 Copynumber: 4.0 Consensus size: 197
106279 TTGGTTTAAA
* * * * * **
106289 ATAAGAAAAGTTATACAATATA-TCGTCAGTGGAGTTTAGAAGACTACACGTGCGGGGTTTAACT
1 ATAAGAAAAATTATGCAATACACT-GTCAGTGGAGTTTAGCAGACTGCACGTGCAAGG----AC-
106353 TTATAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAAT
60 TT-TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAA-
* * * * * *
106418 AT-GGTATGTCTCAACTTTTTAACCCGCTTATGGAGTTCAAAATTTTATACTGATAGTGTATTGA
123 ATGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAA-TTTACACTGACAGTGTATTGT
*
106482 AAAATAATCCT
187 ATAATAATCCT
* * * *
106493 ATAAGAAAAATTATGCGATACCCTGTCACTGGAGTTTAGCAGACTGCATGTGCAAGGTTTAACTT
1 ATAAGAAAAATTATGCAATACACTGTCAGTGGAGTTTAGCAGACTGCACGTGCAAGG----ACTT
106558 TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTAT-AAAATGG
62 TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAAATGG
* * * * *
106622 GATATGTGTCAACTTTTTAACCCGTTTATGGAGTCCAAAATTTATACTGACAGCGTATTTTATAA
127 G-TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAA
106687 TAATCCT
191 TAATCCT
* * * **
106694 ATAAGAAAATTTATGCAATACATTGTCAGTGGAGTTTAGCAGACTGCACGT--ACGGGGTTTAAG
1 ATAAGAAAAATTATGCAATACACTGTCAGTGGAGTTTAGCAGACTGCACGTGCAAGGACTTTAAG
* *
106757 GGTTGACATGTGTCCCCTTAGGGATTAT-T-TT-ATATT--A-A-TTAATTATG-AAATGGGGTA
66 GGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAAAT-GGGTA
* * * * *
106814 TGTGTCAACTTCTTAACCCGCTCATGGAGTTCAAAATTTACACCGATAGTTTATTGTATAATAAT
130 TGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAAT
106879 CCT
195 CCT
* * * * * * *
106882 ATAAAAAAAATTATACAATACACAGTTATTGGAGTTTAGCAGACTGCATGTGCATGG-C-TTAAG
1 ATAAGAAAAATTATGCAATACACTGTCAGTGGAGTTTAGCAGACTGCACGTGCAAGGACTTTAAG
* *
106945 GGTTGACATGTGTCCCCTTAAGGAATATGTATTAATATTAAATATTTAATTAATTATGAAAATGG
66 GGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATA--T--TTAATTATGAAAATGG
* * *
107010 TGTATGTATCAACTTCTTAACCCGTTTATGGAGTCCAAAATTTACATTGACAGTGTATTGTATAA
127 -GTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAA
107075 TAATCCT
191 TAATCCT
107082 TATTATAAAG
Statistics
Matches: 509, Mismatches: 60, Indels: 44
0.83 0.10 0.07
Matches are distributed among these distances:
188 146 0.29
189 5 0.01
190 6 0.01
191 5 0.01
192 5 0.01
193 3 0.01
194 2 0.00
195 32 0.06
199 14 0.03
200 69 0.14
201 77 0.15
202 92 0.18
203 2 0.00
204 50 0.10
205 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (197 bp):
ATAAGAAAAATTATGCAATACACTGTCAGTGGAGTTTAGCAGACTGCACGTGCAAGGACTTTAAG
GGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAAATGGGTAT
GTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATC
CT
Found at i:107444 original size:16 final size:16
Alignment explanation
Indices: 107419--107449 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
107409 CTACAAATTT
107419 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
*
107435 ATAAATATTTAGTAA
1 ATAAAGATTTAGTAA
107450 TATTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Found at i:108117 original size:21 final size:22
Alignment explanation
Indices: 108074--108121 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
108064 AAAGATAATT
*
108074 AAAGTGGAGTAGCATTGAAAAAA
1 AAAGTGGAGTAGCA-TAAAAAAA
108097 AAAGTGGAGTAGCA-AAAAAAA
1 AAAGTGGAGTAGCATAAAAAAA
108118 AAAG
1 AAAG
108122 ATAATTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 10 0.42
23 14 0.58
ACGTcount: A:0.58, C:0.04, G:0.25, T:0.12
Consensus pattern (22 bp):
AAAGTGGAGTAGCATAAAAAAA
Found at i:108420 original size:72 final size:72
Alignment explanation
Indices: 108331--108473 Score: 241
Period size: 72 Copynumber: 2.0 Consensus size: 72
108321 ACACCCATGG
* * * *
108331 CATTGGACTCTAACAAGTTCTTCAAATTATTTGGAGTTCTCATAGGATTTCATAATCTTCATTCA
1 CATTAGACTCTAACAAGTTCTTCAAATCATTTGGAGTTCCCATAAGATTTCATAATCTTCATTCA
108396 TCTCACC
66 TCTCACC
*
108403 CATTAGACTCTGACAAGTTCTTCAAATCATTTGGAGTTCCCATAAGATTTCATAATCTTCATTCA
1 CATTAGACTCTAACAAGTTCTTCAAATCATTTGGAGTTCCCATAAGATTTCATAATCTTCATTCA
108468 TCTCAC
66 TCTCAC
108474 ACAAGTTTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (72 bp):
CATTAGACTCTAACAAGTTCTTCAAATCATTTGGAGTTCCCATAAGATTTCATAATCTTCATTCA
TCTCACC
Found at i:111036 original size:114 final size:114
Alignment explanation
Indices: 110848--111055 Score: 353
Period size: 114 Copynumber: 1.8 Consensus size: 114
110838 GTCCTCGTAT
* *
110848 AAAGAATCTTCATTTTGTCGTGTTATTATGGGTTGTTTGTCCTCATCGTGACCCTTTAATGAATA
1 AAAGAATCTTCATTTTGTCGTGTTATTATGGGTTGTTTGTCCTCATCGTGACCCTTTAACGAAAA
**
110913 ACGTTGGTACCAAATCATCAAACTATTCTTTTTGTAGATTTCTTCATAG
66 ACGGCGGTACCAAATCATCAAACTATTCTTTTTGTAGATTTCTTCATAG
* **
110962 AAAGAATCTTCATTTTGTCGTGTTATTATGGGTTGTTTGTTCTTGTCGTGACCCTTTAACGAAAA
1 AAAGAATCTTCATTTTGTCGTGTTATTATGGGTTGTTTGTCCTCATCGTGACCCTTTAACGAAAA
111027 ACGGCGGTACCAAATCATCAAACTATTCT
66 ACGGCGGTACCAAATCATCAAACTATTCT
111056 ATTACGTAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 87 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (114 bp):
AAAGAATCTTCATTTTGTCGTGTTATTATGGGTTGTTTGTCCTCATCGTGACCCTTTAACGAAAA
ACGGCGGTACCAAATCATCAAACTATTCTTTTTGTAGATTTCTTCATAG
Found at i:113633 original size:22 final size:23
Alignment explanation
Indices: 113605--113648 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
113595 CTAATATAGG
* *
113605 ATGTCCCT-TTTTTTTTCTTTTA
1 ATGTCCCTAGTTTTTCTCTTTTA
113627 ATGTCCCTAGTTTTTCTCTTTT
1 ATGTCCCTAGTTTTTCTCTTTT
113649 TTGTCTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.09, C:0.20, G:0.07, T:0.64
Consensus pattern (23 bp):
ATGTCCCTAGTTTTTCTCTTTTA
Found at i:117022 original size:2 final size:2
Alignment explanation
Indices: 117005--117045 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
116995 AAGCACCTCT
117005 TA TA TA -A TA TA CTA 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 TA TA TA TA TA TA TA T
117046 TAACTTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:122126 original size:21 final size:21
Alignment explanation
Indices: 122102--122143 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
122092 TTTTACACTG
122102 AGCCTCCCCACTAGGACGGCT
1 AGCCTCCCCACTAGGACGGCT
* *
122123 AGCCTCCCCACTGGGGCGGCT
1 AGCCTCCCCACTAGGACGGCT
122144 TCACCACGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.43, G:0.29, T:0.14
Consensus pattern (21 bp):
AGCCTCCCCACTAGGACGGCT
Found at i:122165 original size:33 final size:33
Alignment explanation
Indices: 122127--122208 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
122117 ACGGCTAGCC
122127 TCCCCACTGGGGCGGCTTCACCACGGGCAGGCCG
1 TCCCCACTGGGGCGGCTTCACCAC-GGCAGGCCG
*
122161 -CCCCACTGGGGCGGCTTCGCCACGGCAGGCCG
1 TCCCCACTGGGGCGGCTTCACCACGGCAGGCCG
*
122193 TCCTCA-TGGGGCGGCT
1 TCCCCACTGGGGCGGCT
122209 AGACCAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 19 0.42
33 26 0.58
ACGTcount: A:0.10, C:0.40, G:0.37, T:0.13
Consensus pattern (33 bp):
TCCCCACTGGGGCGGCTTCACCACGGCAGGCCG
Found at i:122970 original size:9 final size:9
Alignment explanation
Indices: 122952--122983 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
122942 AATTAACCTG
122952 AAAA-AAAA
1 AAAAGAAAA
122960 AAAAGAAAA
1 AAAAGAAAA
122969 AAAAGAAAA
1 AAAAGAAAA
122978 AAAAGA
1 AAAAGA
122984 CAAAGTCCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:123798 original size:24 final size:24
Alignment explanation
Indices: 123770--123816 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
123760 TCAGCCTTCC
*
123770 TCTGTTTCTCATTCACTCTGTTTT
1 TCTGTTTCTCACTCACTCTGTTTT
123794 TCTGTTTCTCACTCACTCTGTTT
1 TCTGTTTCTCACTCACTCTGTTT
123817 CAAAACCAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.09, C:0.28, G:0.09, T:0.55
Consensus pattern (24 bp):
TCTGTTTCTCACTCACTCTGTTTT
Found at i:159224 original size:21 final size:21
Alignment explanation
Indices: 159185--159226 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
159175 GGATAATTGA
*
159185 ACCCCAAGAACTACCATTTCT
1 ACCCCAAGAACCACCATTTCT
* *
159206 ACCCCAAGGACCACTATTTCT
1 ACCCCAAGAACCACCATTTCT
159227 TCCATCGTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.38, G:0.07, T:0.24
Consensus pattern (21 bp):
ACCCCAAGAACCACCATTTCT
Found at i:161009 original size:31 final size:29
Alignment explanation
Indices: 160937--161014 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
160927 ACTTGTAGCG
* *
160937 TTTGGACGTTCTGCTCAATAAACTTCAAT
1 TTTGGACGTTTTGCCCAATAAACTTCAAT
* *
160966 TTTGGACATTTTGCCCACTAAACTCTCAATT
1 TTTGGACGTTTTGCCCAATAAACT-TCAA-T
*
160997 TTTGGATGTTTTGTCCCA
1 TTTGGACGTTTTG-CCCA
161015 TCTCAAACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 20 0.50
30 4 0.10
31 12 0.30
32 4 0.10
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCAATAAACTTCAAT
Found at i:164420 original size:10 final size:10
Alignment explanation
Indices: 164407--164440 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
164397 AAATCTCGAT
164407 ATATCCGTAA
1 ATATCCGTAA
*
164417 ATATCCATAA
1 ATATCCGTAA
164427 ATATCCGTAA
1 ATATCCGTAA
164437 ATAT
1 ATAT
164441 GCATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:164430 original size:20 final size:20
Alignment explanation
Indices: 164407--164445 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
164397 AAATCTCGAT
164407 ATATCCGTAAATATCCATAA
1 ATATCCGTAAATATCCATAA
*
164427 ATATCCGTAAATATGCATA
1 ATATCCGTAAATATCCATA
164446 TTAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (20 bp):
ATATCCGTAAATATCCATAA
Found at i:165292 original size:9 final size:10
Alignment explanation
Indices: 165267--165291 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
165257 TTCGCAGTAC
165267 AAAAAATAAA
1 AAAAAATAAA
165277 AAAAAATAAA
1 AAAAAATAAA
165287 AAAAA
1 AAAAA
165292 TGTCTACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:165482 original size:13 final size:12
Alignment explanation
Indices: 165452--165494 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
165442 CATCGATACC
*
165452 TCGATATATCCA
1 TCGATATATCCG
165464 TCGATATATCCG
1 TCGATATATCCG
165476 TTCGATATATCCG
1 -TCGATATATCCG
165489 TCGATA
1 TCGATA
165495 CATGTATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:175512 original size:23 final size:24
Alignment explanation
Indices: 175486--175536 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
175476 ATCTTATATA
175486 AATTGTTT-CTTTCTTTTGCAAGG
1 AATTGTTTACTTTCTTTTGCAAGG
* *
175509 AATT-TTTATTTTTTTTTGCAAGG
1 AATTGTTTACTTTCTTTTGCAAGG
175532 AATTG
1 AATTG
175537 AATATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.55
Consensus pattern (24 bp):
AATTGTTTACTTTCTTTTGCAAGG
Found at i:184760 original size:3 final size:3
Alignment explanation
Indices: 184754--184783 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
184744 TTGAATCAAA
184754 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
184784 GAAAGGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:193082 original size:23 final size:23
Alignment explanation
Indices: 193052--193096 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
193042 TTTGATGAAA
193052 TGAAAATCATGAGAAAATCCTCG
1 TGAAAATCATGAGAAAATCCTCG
*
193075 TGAAAATCATGAGCAAATCCTC
1 TGAAAATCATGAGAAAATCCTC
193097 AGCATTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (23 bp):
TGAAAATCATGAGAAAATCCTCG
Done.