Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006797.1 Corchorus capsularis cultivar CVL-1 contig06818, 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: 63713
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:105 original size:36 final size:38
Alignment explanation
Indices: 47--126 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 38
37 GTTTCCGATT
* *
47 TTTTTTTGAAAAAAAATAATTTTTCTTTTCCGTTTTTCC
1 TTTTTTT-AAAAAAAATAATTTTTATTTGCCGTTTTTCC
* *
86 TTTTTTT-AAAAAAAT-ATTTTTATTTGCTGTTTTTGC
1 TTTTTTTAAAAAAAATAATTTTTATTTGCCGTTTTTCC
122 TTTTT
1 TTTTT
127 ATTCTATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 22 0.59
37 8 0.22
39 7 0.19
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.61
Consensus pattern (38 bp):
TTTTTTTAAAAAAAATAATTTTTATTTGCCGTTTTTCC
Found at i:4106 original size:36 final size:34
Alignment explanation
Indices: 4059--4177 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 34
4049 TCTTTTCTAG
* *
4059 ATTAAGCTCTTTATTGACTTCACTTTATTACCTTGA
1 ATTAAGTTCTTTATTGAC-TCACTTAATTACC-TGA
4095 ATTAAGTTCTTTATT--CT-ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCACTTAATTA-CCTGA
**
4127 ATTAA-ACCTTTTATTGACCTCACTTAATTACACTGA
1 ATTAAGTTC-TTTATTGA-CTCACTTAATTAC-CTGA
4163 ATTAAGTTCTTTATT
1 ATTAAGTTCTTTATT
4178 TTACTTAATT
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
31 1 0.01
32 22 0.32
33 3 0.04
34 1 0.01
35 3 0.04
36 38 0.55
37 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (34 bp):
ATTAAGTTCTTTATTGACTCACTTAATTACCTGA
Found at i:4128 original size:32 final size:32
Alignment explanation
Indices: 4080--4187 Score: 110
Period size: 32 Copynumber: 3.2 Consensus size: 32
4070 TATTGACTTC
* *
4080 ACTTTATTACCTTGAATTAAGTTCTTTATTCT
1 ACTTAATTACCCTGAATTAAGTTCTTTATTCT
**
4112 ACTTAATTACCCTGAATTAA-ACCTTTTATTGACCT
1 ACTTAATTACCCTGAATTAAGTTC-TTTATT---CT
* *
4147 CACTTAATTACACTGAATTAAGTTCTTTATTTT
1 -ACTTAATTACCCTGAATTAAGTTCTTTATTCT
4180 ACTTAATT
1 ACTTAATT
4188 TCCTTGCTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
31 1 0.02
32 32 0.52
33 1 0.02
35 2 0.03
36 25 0.40
37 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.47
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAGTTCTTTATTCT
Found at i:4265 original size:36 final size:36
Alignment explanation
Indices: 4194--4498 Score: 350
Period size: 36 Copynumber: 8.6 Consensus size: 36
4184 AATTTCCTTG
* * * * *
4194 CTTGAAATTAAGTCTGTGTCTT-TTTACTTAATTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
*
4229 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* * * *
4265 CTCGAAACTAAG-CACTGCTTTTCTTTACTTAATTTC
1 CTTGAAATTAAGCCAGT-CTTTTCTTTACCTAATTTC
*
4301 CTTGAAATTAAGCCAGTC-TATCTTTACCTAATTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* * *
4336 TTTGAAATTAAGTCAGTCTTTTCTTTACTTAATTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
*
4372 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* * * * *
4408 TTTGAAACTAAGCTAGTCTTTTTTTTTACTTAATTTC
1 CTTGAAATTAAGCCAGTC-TTTTCTTTACCTAATTTC
*
4445 CTTGAAATTAAGCCAGTC--TTCTTTACCTAGTTTC
1 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
* *
4479 CTTGAAACTAAGTCAGTCTT
1 CTTGAAATTAAGCCAGTCTT
4499 CTTTCAGTCT
Statistics
Matches: 225, Mismatches: 38, Indels: 13
0.82 0.14 0.05
Matches are distributed among these distances:
34 29 0.13
35 52 0.23
36 111 0.49
37 33 0.15
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.46
Consensus pattern (36 bp):
CTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTC
Found at i:4308 original size:107 final size:106
Alignment explanation
Indices: 4194--4498 Score: 373
Period size: 107 Copynumber: 2.8 Consensus size: 106
4184 AATTTCCTTG
* *
4194 CTTGAAATTAAGTCTGTGTCTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCT
1 CTTGAAATTAAG-CTGTCTATTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCT
* * *
4259 AGTTTCCTCGAAACTAAG-CACTGCTTTTCTTTACTTAATTTC
65 AGTTTCCTTGAAACTAAGCCAGT-CTTTTCTTTACCTAATTTC
* * * * * *
4301 CTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCTTTGAAATTAAGTCAGTCTTTTCTTTACTT
1 CTTGAAATTAAG-CTGTCTATTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCT
* * *
4366 AATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTC
65 AGTTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTC
* * *
4408 TTTGAAACTAAGCTAGTCTTTTTTTTTACTTAATTTCCTTGAAATTAAGCCAGTC--TTCTTTAC
1 CTTGAAATTAAGCT-GTC--TATTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTAC
*
4471 CTAGTTTCCTTGAAACTAAGTCAGTCTT
63 CTAGTTTCCTTGAAACTAAGCCAGTCTT
4499 CTTTCAGTCT
Statistics
Matches: 167, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
106 1 0.01
107 133 0.80
108 3 0.02
109 30 0.18
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.46
Consensus pattern (106 bp):
CTTGAAATTAAGCTGTCTATTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTA
GTTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTC
Found at i:4366 original size:71 final size:72
Alignment explanation
Indices: 4194--4498 Score: 433
Period size: 71 Copynumber: 4.3 Consensus size: 72
4184 AATTTCCTTG
* * * *
4194 CTTGAAATTAAGTCTGTGTCTT-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACC
1 CTTGAAACTAAGTCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACC
4258 TAGTTTC
66 TAGTTTC
* * *
4265 CTCGAAACTAAG-CACTGCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTC-TATCTTTAC
1 CTTGAAACTAAGTCAGT-CTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTAC
*
4328 CTAATTTC
65 CTAGTTTC
* *
4336 TTTGAAATTAAGTCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACC
1 CTTGAAACTAAGTCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACC
4401 TAGTTTC
66 TAGTTTC
* *
4408 TTTGAAACTAAG-CTAGTCTTTTTTTTTACTTAATTTCCTTGAAATTAAGCCAGTC--TTCTTTA
1 CTTGAAACTAAGTC-AGTC-TTTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTA
4470 CCTAGTTTC
64 CCTAGTTTC
4479 CTTGAAACTAAGTCAGTCTT
1 CTTGAAACTAAGTCAGTCTT
4499 CTTTCAGTCT
Statistics
Matches: 210, Mismatches: 17, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
70 4 0.02
71 106 0.50
72 65 0.31
73 35 0.17
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.46
Consensus pattern (72 bp):
CTTGAAACTAAGTCAGTCTTTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACC
TAGTTTC
Found at i:4507 original size:11 final size:11
Alignment explanation
Indices: 4491--4651 Score: 160
Period size: 11 Copynumber: 13.7 Consensus size: 11
4481 TGAAACTAAG
4491 TCAGTCTTCTT
1 TCAGTCTTCTT
4502 TCAGTCTTTCTT
1 TCAGTC-TTCTT
* *
4514 TCAATCTTTTT
1 TCAGTCTTCTT
*
4525 TCAGTCTTGTT
1 TCAGTCTTCTT
4536 TCAGTCTTCTCTT
1 TCAGTC-T-TCTT
*
4549 TCAGTCTTGTT
1 TCAGTCTTCTT
4560 TCAGTCTTCTTTT
1 TCAGTCTTC--TT
*
4573 TCAGTCTTGTT
1 TCAGTCTTCTT
* *
4584 TCAGACTTTTT
1 TCAGTCTTCTT
4595 TCAGTCTTCTTCTTT
1 TCAG---TCTTC-TT
4610 TCAGTCTTCTTT
1 TCAGTCTTC-TT
4622 TCAGTCTTCTT
1 TCAGTCTTCTT
*
4633 TCAGTATTCTT
1 TCAGTCTTCTT
4644 TCAGTCTT
1 TCAGTCTT
4652 TTGCTTAATT
Statistics
Matches: 127, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
11 70 0.55
12 29 0.23
13 19 0.15
14 3 0.02
15 6 0.05
ACGTcount: A:0.11, C:0.23, G:0.10, T:0.57
Consensus pattern (11 bp):
TCAGTCTTCTT
Found at i:4555 original size:24 final size:22
Alignment explanation
Indices: 4491--4651 Score: 160
Period size: 24 Copynumber: 6.9 Consensus size: 22
4481 TGAAACTAAG
* *
4491 TCAGTCTTCTTTCAGTCTTTCTT
1 TCAGTCTTTTTTCAGTC-TTGTT
*
4514 TCAATCTTTTTTCAGTCTTGTT
1 TCAGTCTTTTTTCAGTCTTGTT
4536 TCAGTCTTCTCTTTCAGTCTTGTT
1 TCAGTCTT-T-TTTCAGTCTTGTT
4560 TCAGTCTTCTTTTTCAGTCTTGTT
1 TCAGTC-T-TTTTTCAGTCTTGTT
* *
4584 TCAGACTTTTTTCAGTCTTCTTCTTT
1 TCAGTCTTTTTTCAG---TCTT-GTT
*
4610 TCAGTCTTCTTTTCAGTCTTCTT
1 TCAGTCTT-TTTTCAGTCTTGTT
* *
4633 TCAGTATTCTTTCAGTCTT
1 TCAGTCTTTTTTCAGTCTT
4652 TTGCTTAATT
Statistics
Matches: 119, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
22 29 0.24
23 26 0.22
24 41 0.34
25 6 0.05
26 10 0.08
27 7 0.06
ACGTcount: A:0.11, C:0.23, G:0.10, T:0.57
Consensus pattern (22 bp):
TCAGTCTTTTTTCAGTCTTGTT
Found at i:4562 original size:35 final size:34
Alignment explanation
Indices: 4491--4652 Score: 175
Period size: 35 Copynumber: 4.6 Consensus size: 34
4481 TGAAACTAAG
*
4491 TCAGTCTTCTTTCAGTCTTTCTTTCAATCTTTTT
1 TCAGTCTTCTTTCAGTCTTTCTTTCAGTCTTTTT
* *
4525 TCAGTCTTGTTTCAGTCTTCTCTTTCAGTCTTGTT
1 TCAGTCTTCTTTCAGTCTT-TCTTTCAGTCTTTTT
* *
4560 TCAGTCTTCTTTTTCAGTC-TTGTTTCAGACTTTTT
1 TCAGTCTTC--TTTCAGTCTTTCTTTCAGTCTTTTT
*
4595 TCAGTCTTCTTCTTTTCAGTC-TTCTTTTCAGTCTTCTT
1 TCAG---TCTTC-TTTCAGTCTTTC-TTTCAGTCTTTTT
*
4633 TCAGTATTCTTTCAGTCTTT
1 TCAGTCTTCTTTCAGTCTTT
4653 TGCTTAATTT
Statistics
Matches: 109, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
34 26 0.24
35 43 0.39
36 1 0.01
37 19 0.17
38 20 0.18
ACGTcount: A:0.10, C:0.23, G:0.10, T:0.57
Consensus pattern (34 bp):
TCAGTCTTCTTTCAGTCTTTCTTTCAGTCTTTTT
Found at i:4612 original size:15 final size:15
Alignment explanation
Indices: 4592--4632 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 15
4582 TTTCAGACTT
4592 TTTTCAGTCTTCTTC
1 TTTTCAGTCTTCTTC
4607 TTTTCAG---TCTTC
1 TTTTCAGTCTTCTTC
4619 TTTTCAGTCTTCTT
1 TTTTCAGTCTTCTT
4633 TCAGTATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 12 0.52
15 11 0.48
ACGTcount: A:0.07, C:0.24, G:0.07, T:0.61
Consensus pattern (15 bp):
TTTTCAGTCTTCTTC
Found at i:4985 original size:36 final size:36
Alignment explanation
Indices: 4709--4906 Score: 301
Period size: 36 Copynumber: 5.5 Consensus size: 36
4699 CATCTTTTGG
* * * *
4709 ATTAAATCTTTGCTGACTTTATTTAATTCTCGTGAA
1 ATTAAGTCTTTGCTAATTTTACTTAATTCTCGTGAA
4745 ATTAAGTCTTTGCTAATTTTACTTAATTCTCGTGAA
1 ATTAAGTCTTTGCTAATTTTACTTAATTCTCGTGAA
4781 ATTAAGTCTTTGCTAATTTTACTTAATTCTCGTGAA
1 ATTAAGTCTTTGCTAATTTTACTTAATTCTCGTGAA
* *
4817 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGCGAA
1 ATTAAGTCTTTGCTAATTTTACTTAATTCTCGTGAA
* *
4853 ATTAAGTCTTTGAC-AA-TTTACTTAACTCTTGTGAA
1 ATTAAGTCTTTG-CTAATTTTACTTAATTCTCGTGAA
4888 ATTAAGTCTTTGCTAATTT
1 ATTAAGTCTTTGCTAATTT
4907 CTTTCCTTGA
Statistics
Matches: 151, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
34 1 0.01
35 31 0.21
36 118 0.78
37 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (36 bp):
ATTAAGTCTTTGCTAATTTTACTTAATTCTCGTGAA
Found at i:5054 original size:34 final size:35
Alignment explanation
Indices: 5010--5232 Score: 263
Period size: 34 Copynumber: 6.3 Consensus size: 35
5000 CCTAAAACTG
*
5010 AGCCAGTC-TTTTTTACTTAATTTCTTTGAAATTA
1 AGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTA
* * *
5044 AGCCAATCTTTTCTTTACCTAATCTCCTTTCTTGAAATTA
1 AGCCAGTCTTTT-TTTACTTAA--T--TTCCTTGAAATTA
*
5084 AGCCATTC-TTTTTTACTTAATTTCCTTGAAATTA
1 AGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTA
5118 AGCCAGTC-TTTTTTACTTAATTTCCTTGAAATTA
1 AGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTA
* * *
5152 AGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTA
1 AGCCAGTCTTTT-TTTACTTAATTTCCTTGAAATTA
** *
5188 AGCCAGTCAATCTTTACTTAATTTCCTTGAAATTA
1 AGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTA
*
5223 AGTCAGTCTT
1 AGCCAGTCTT
5233 CTAATGTTCT
Statistics
Matches: 161, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
34 60 0.37
35 33 0.20
36 38 0.24
38 9 0.06
39 3 0.02
40 18 0.11
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.45
Consensus pattern (35 bp):
AGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTA
Found at i:5104 original size:74 final size:68
Alignment explanation
Indices: 5010--5232 Score: 248
Period size: 74 Copynumber: 3.1 Consensus size: 68
5000 CCTAAAACTG
* *
5010 AGCCAGTCTTTTTTACTTAATTTCTTTGAAATTAAGCCAATCTTTTCTTTACCTAATCTCCTTTC
1 AGCCAGTCTTTTTTACTTAATTTCCTTGAAATTAAGCCAATC-TTT-TTTACCTAA--T--TTCC
5075 TTGAAATTA
60 TTGAAATTA
* * *
5084 AGCCATTCTTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTTTACTTAATTTCCTTGAAA
1 AGCCAGTCTTTTTTACTTAATTTCCTTGAAATTAAGCCAATCTTTTTTACCTAATTTCCTTGAAA
5149 TTA
66 TTA
* * * * * * *
5152 AGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCAATCTTTACTTAATTTCCTTG
1 AGCCAGTC-TTT-TTTACTTAATTTCCTTGAAATTAAGCCAATC-TTTTTTACCTAATTTCCTTG
5217 AAATTA
63 AAATTA
*
5223 AGTCAGTCTT
1 AGCCAGTCTT
5233 CTAATGTTCT
Statistics
Matches: 134, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
68 19 0.14
69 3 0.02
70 31 0.23
71 31 0.23
72 8 0.06
73 3 0.02
74 39 0.29
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.45
Consensus pattern (68 bp):
AGCCAGTCTTTTTTACTTAATTTCCTTGAAATTAAGCCAATCTTTTTTACCTAATTTCCTTGAAA
TTA
Found at i:5132 original size:108 final size:105
Alignment explanation
Indices: 5010--5232 Score: 322
Period size: 108 Copynumber: 2.1 Consensus size: 105
5000 CCTAAAACTG
* *
5010 AGCCAGTCTTTTTTACTTAATTTCTTTGAAATTAAGCCAATCTTTTCTTTACCTAATCTCCTTTC
1 AGCCAGTCTTTTTTACTTAATTTCCTTGAAATTAAGCCAATCTTTTCTTTACCT-A-CT--TTCC
* * * *
5075 TTGAAATTAAGCCATTC-TTTTTTACTTAATTTCCTTGAAATTA
62 TTGAAACTAAGCCAGTCAATCTTTACTTAATTTCCTTGAAATTA
* *
5118 AGCCAGTCTTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGA
1 AGCCAGTCTTTTTTACTTAATTTCCTTGAAATTAAGCCAATCTTTTCTTTACCTACTTTCCTTGA
5183 AACTAAGCCAGTCAATCTTTACTTAATTTCCTTGAAATTA
66 AACTAAGCCAGTCAATCTTTACTTAATTTCCTTGAAATTA
*
5223 AGTCAGTCTT
1 AGCCAGTCTT
5233 CTAATGTTCT
Statistics
Matches: 105, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
104 18 0.17
105 33 0.31
106 1 0.01
107 1 0.01
108 52 0.50
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.45
Consensus pattern (105 bp):
AGCCAGTCTTTTTTACTTAATTTCCTTGAAATTAAGCCAATCTTTTCTTTACCTACTTTCCTTGA
AACTAAGCCAGTCAATCTTTACTTAATTTCCTTGAAATTA
Found at i:5330 original size:40 final size:40
Alignment explanation
Indices: 5201--5345 Score: 127
Period size: 40 Copynumber: 3.6 Consensus size: 40
5191 CAGTCAATCT
* * *
5201 TTACTTAATTTCCT-TGAAATTAAGTCAGTC-TTCTAATGTTC
1 TTACTTAATTT-CTATG-AATTAAGTC-TTCAATCTATTGTTC
* * * *
5242 TTACTTAATTGCCATGAATTAAGCCTTCTATCTATTGCTTC
1 TTACTTAATTTCTATGAATTAAGTCTTCAATCTATTG-TTC
* * *
5283 -CATTTAATTTCTATGAATTAAGTCTTCAAAT-TGTTGTTC
1 TTACTTAATTTCTATGAATTAAGTCTTC-AATCTATTGTTC
5322 TTACTTAATTTCTATGAATTAAGT
1 TTACTTAATTTCTATGAATTAAGT
5346 TCTTTAACTA
Statistics
Matches: 84, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
39 5 0.06
40 62 0.74
41 17 0.20
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.47
Consensus pattern (40 bp):
TTACTTAATTTCTATGAATTAAGTCTTCAATCTATTGTTC
Found at i:20356 original size:51 final size:51
Alignment explanation
Indices: 20299--20570 Score: 346
Period size: 51 Copynumber: 5.3 Consensus size: 51
20289 ATCAAGACTC
* * * *
20299 AATTTTTATTGTTAGAATTACTAAAACCCAACTCTTACTACATAAAGATTT
1 AATTTTTATTGTTAAAATTACTAGAACTCAACCCTTACTACATAAAGATTT
* * * * * *
20350 AATTTTTATTATTAAAATTACTAGCACTTAACCTTTACTACATAAAGACTC
1 AATTTTTATTGTTAAAATTACTAGAACTCAACCCTTACTACATAAAGATTT
* * * * *
20401 AATTTTTATGGCTAAAATTACTAGAACTCAACCCTTACTATACAAAGATTC
1 AATTTTTATTGTTAAAATTACTAGAACTCAACCCTTACTACATAAAGATTT
* *
20452 AATTTTTATGGCTAAAATTACTAGAACTCAACCCTTACTACATAAAGATTT
1 AATTTTTATTGTTAAAATTACTAGAACTCAACCCTTACTACATAAAGATTT
* * * *
20503 AATCTTTATTATTAAAATCATTAGAACTCAACCCTTACTACATAAAGATTT
1 AATTTTTATTGTTAAAATTACTAGAACTCAACCCTTACTACATAAAGATTT
*
20554 AATTTTTATTATTAAAA
1 AATTTTTATTGTTAAAA
20571 ACCTATAAAC
Statistics
Matches: 192, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 192 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.38
Consensus pattern (51 bp):
AATTTTTATTGTTAAAATTACTAGAACTCAACCCTTACTACATAAAGATTT
Found at i:23235 original size:13 final size:13
Alignment explanation
Indices: 23217--23273 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
23207 AATACCAAAT
23217 TACTAAATGAAAA
1 TACTAAATGAAAA
*
23230 TACTAATTGAAAA
1 TACTAAATGAAAA
* * *
23243 CACCATAATGTCAAA
1 TACTA-AATG-AAAA
23258 TCACTAAATGAAAA
1 T-ACTAAATGAAAA
23272 TA
1 TA
23274 TGCAAAAACT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
13 16 0.48
14 7 0.21
15 7 0.21
16 3 0.09
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (13 bp):
TACTAAATGAAAA
Found at i:23403 original size:27 final size:27
Alignment explanation
Indices: 23373--23459 Score: 115
Period size: 27 Copynumber: 3.2 Consensus size: 27
23363 AGATGAACTT
23373 AAAAATGACTAAAATGCCCCT-GAGTGC
1 AAAAATGACTAAAATGCCCCTAGA-TGC
*
23400 AAAAATGACCAAAATGCCCCTAGATGC
1 AAAAATGACTAAAATGCCCCTAGATGC
*
23427 AAAAAAT-AATCAAAATGCCCCTAGATGC
1 -AAAAATGACT-AAAATGCCCCTAGATGC
23455 AAAAA
1 AAAAA
23460 ATGATCAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
27 29 0.54
28 25 0.46
ACGTcount: A:0.48, C:0.22, G:0.14, T:0.16
Consensus pattern (27 bp):
AAAAATGACTAAAATGCCCCTAGATGC
Found at i:23440 original size:28 final size:28
Alignment explanation
Indices: 23373--23470 Score: 139
Period size: 28 Copynumber: 3.5 Consensus size: 28
23363 AGATGAACTT
23373 AAAAATGA-CTAAAATGCCCCT-GAGTGC-
1 AAAAATGATC-AAAATGCCCCTAGA-TGCA
*
23400 AAAAATGACCAAAATGCCCCTAGATGCA
1 AAAAATGATCAAAATGCCCCTAGATGCA
*
23428 AAAAATAATCAAAATGCCCCTAGATGCA
1 AAAAATGATCAAAATGCCCCTAGATGCA
23456 AAAAATGATCAAAAT
1 AAAAATGATCAAAAT
23471 ACCCTTGGGC
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
27 22 0.34
28 43 0.66
ACGTcount: A:0.49, C:0.20, G:0.13, T:0.17
Consensus pattern (28 bp):
AAAAATGATCAAAATGCCCCTAGATGCA
Found at i:25033 original size:22 final size:22
Alignment explanation
Indices: 25005--25050 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
24995 CAGGTTAGAG
25005 AAACCACAGTTAATTTCGGTAA
1 AAACCACAGTTAATTTCGGTAA
*
25027 AAACCACAGTTAATTTTGGTAA
1 AAACCACAGTTAATTTCGGTAA
25049 AA
1 AA
25051 TAAAAAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (22 bp):
AAACCACAGTTAATTTCGGTAA
Found at i:26703 original size:48 final size:48
Alignment explanation
Indices: 26635--26999 Score: 460
Period size: 48 Copynumber: 7.6 Consensus size: 48
26625 TCAATTCCCT
* * * * *
26635 GTTTTGCCCTTCTCTGTCGGAAGGTGCTATATTCAGTGTTTCTTTCCT
1 GTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCAGTGTTTATTTCCA
* * * * *
26683 GTTTTGCCCTTCCTGGTCGGAAGATGCTATTTTCAGTATCTATTTCCC
1 GTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCAGTGTTTATTTCCA
* * ** *
26731 GTTTTGCCCTTCCCGGTCGAAAGGTGCTATCTTCAGTGTCAATTTCCT
1 GTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCAGTGTTTATTTCCA
*** *
26779 GTTTTGCCCTTCTTAGTCGGAAGGTGCTATTTTCGGTGTTTATTTCCA
1 GTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCAGTGTTTATTTCCA
* *
26827 GTTTTGCCCTTCCCGGTCAGAAGGTGCAATTTTCAGTGTTTATTTCCA
1 GTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCAGTGTTTATTTCCA
** *
26875 GTTTCACCCTTCCCGGTCGGAAGGTGCTGTTTTCAGTGTTTATTTCCA
1 GTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCAGTGTTTATTTCCA
* * **
26923 GTCTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCATTGTCCATTTCCA
1 GTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCAGTGTTTATTTCCA
* *
26971 ATTTTGCCCTCCCCGGTCGGAAGGTGCTA
1 GTTTTGCCCTTCCCGGTCGGAAGGTGCTA
27000 GATTTGTCTC
Statistics
Matches: 271, Mismatches: 46, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 271 1.00
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.40
Consensus pattern (48 bp):
GTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCAGTGTTTATTTCCA
Found at i:28261 original size:21 final size:21
Alignment explanation
Indices: 28228--28276 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
28218 AAGAATTGTA
**
28228 GCTT-CTTGGAAATGGTTCTT
1 GCTTCCTTGGAAATCCTTCTT
*
28248 GCTTCCTTTGAAATCCTTCTT
1 GCTTCCTTGGAAATCCTTCTT
28269 GCATTCCT
1 GC-TTCCT
28277 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.45
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCTTCTT
Found at i:31156 original size:21 final size:21
Alignment explanation
Indices: 31130--31178 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
31120 GCGCTGGGCG
* *
31130 CCCATGTGGCATGCTTGGCAC
1 CCCATGTGGCATGCCTCGCAC
**
31151 CCCATGTGGTTTGCCTCGCAC
1 CCCATGTGGCATGCCTCGCAC
31172 CCCATGT
1 CCCATGT
31179 ACTCCAATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.12, C:0.37, G:0.24, T:0.27
Consensus pattern (21 bp):
CCCATGTGGCATGCCTCGCAC
Found at i:37661 original size:12 final size:12
Alignment explanation
Indices: 37644--37668 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37634 AGCATTACAC
37644 TTTACAGGGATA
1 TTTACAGGGATA
37656 TTTACAGGGATA
1 TTTACAGGGATA
37668 T
1 T
37669 GAATTTTTCT
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:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (12 bp):
TTTACAGGGATA
Found at i:39348 original size:10 final size:9
Alignment explanation
Indices: 39333--39366 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
39323 TTTTCGCAAC
*
39333 AAAAAATAT
1 AAAAAAAAT
39342 AAAAAAAAT
1 AAAAAAAAT
39351 AAAAAAAAAT
1 -AAAAAAAAT
39361 AAAAAA
1 AAAAAA
39367 TAATGTCTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:39349 original size:11 final size:10
Alignment explanation
Indices: 39333--39366 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
39323 TTTTCGCAAC
39333 AAAAAATATAA
1 AAAAAATA-AA
39344 AAAAAATAAA
1 AAAAAATAAA
39354 AAAAAATAAA
1 AAAAAATAAA
39364 AAA
1 AAA
39367 TAATGTCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:40725 original size:18 final size:19
Alignment explanation
Indices: 40704--40743 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
40694 GATGTCAAAC
40704 GAACGTTTTAC-ATCAATT
1 GAACGTTTTACGATCAATT
*
40722 GAACGTTTTACGCTCAATT
1 GAACGTTTTACGATCAATT
40741 GAA
1 GAA
40744 GAAGGAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (19 bp):
GAACGTTTTACGATCAATT
Found at i:41080 original size:33 final size:31
Alignment explanation
Indices: 41030--41145 Score: 101
Period size: 33 Copynumber: 3.6 Consensus size: 31
41020 AAAGGCACGT
*
41030 GCCGCCC-CCTGGAGCGGCTTACCATGGCTCAA
1 GCCGCCCTCCTGGGGCGGCTTACCATGG-T-AA
* ** *
41062 GCTGCCCTCCTGGGGCGGCTCTGTCA-CGTGAA
1 GCCGCCCTCCTGGGGCGGCT-TACCATGGT-AA
*
41094 GCCACCCTCCTGGGGCGGCTTGAGCCATGGTAA
1 GCCGCCCTCCTGGGGCGGCTT-A-CCATGGTAA
*
41127 GCCGCCCTCCTAGGGCGGC
1 GCCGCCCTCCTGGGGCGGC
41146 ACGGGTCATC
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
31 1 0.02
32 27 0.41
33 33 0.50
34 5 0.08
ACGTcount: A:0.12, C:0.38, G:0.33, T:0.17
Consensus pattern (31 bp):
GCCGCCCTCCTGGGGCGGCTTACCATGGTAA
Found at i:48454 original size:6 final size:6
Alignment explanation
Indices: 48443--48472 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
48433 CGCTACTACC
48443 CATATT CATATT CATATT CATATT CATATT
1 CATATT CATATT CATATT CATATT CATATT
48473 GAGAGCTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
CATATT
Found at i:49383 original size:13 final size:13
Alignment explanation
Indices: 49365--49401 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
49355 GTTGGAAGAA
49365 AATAAAAATATAT
1 AATAAAAATATAT
49378 AATAAAAATATAT
1 AATAAAAATATAT
*
49391 ATATAATAATA
1 A-ATAAAAATA
49402 AAAATCTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAAAAATATAT
Found at i:49401 original size:20 final size:19
Alignment explanation
Indices: 49372--49417 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
49362 GAAAATAAAA
49372 ATATATAATAAAAATATAT
1 ATATATAATAAAAATATAT
*
49391 ATATAATAATAAAAATCTAT
1 ATAT-ATAATAAAAATATAT
*
49411 AAATATA
1 ATATATA
49418 TGAAAAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATATAATAAAAATATAT
Found at i:50223 original size:21 final size:21
Alignment explanation
Indices: 50199--50241 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
50189 GTAAGGTTTA
50199 CTGCAAGTCTGGTCATGGGTT
1 CTGCAAGTCTGGTCATGGGTT
50220 CTGCAAGTCTGGTCATGGGTT
1 CTGCAAGTCTGGTCATGGGTT
50241 C
1 C
50242 GAGTCTGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.21, G:0.33, T:0.33
Consensus pattern (21 bp):
CTGCAAGTCTGGTCATGGGTT
Found at i:51989 original size:11 final size:11
Alignment explanation
Indices: 51973--52001 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
51963 TTATTTTACT
51973 AAATTTATACA
1 AAATTTATACA
51984 AAATTTATACA
1 AAATTTATACA
51995 AAATTTA
1 AAATTTA
52002 ATTCACTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (11 bp):
AAATTTATACA
Found at i:57301 original size:35 final size:35
Alignment explanation
Indices: 57234--57432 Score: 344
Period size: 35 Copynumber: 5.7 Consensus size: 35
57224 AGTAAGTAGT
*
57234 TTAATTCAGGGTAATTAAGCAAAGTCAGTAATCAAC
1 TTAATTCAGGGTAATTAAG-TAAGTCAGTAATCAAC
57270 TTAATTCAGGGTAATTAAGTAAGTCAGTAATCAAC
1 TTAATTCAGGGTAATTAAGTAAGTCAGTAATCAAC
57305 TTAATTCAGGGTAATTAAGTAAGTCAGTAATCAAC
1 TTAATTCAGGGTAATTAAGTAAGTCAGTAATCAAC
*
57340 TTAATTCATGGTAATTAAGTAAGTCAGTAATCAAC
1 TTAATTCAGGGTAATTAAGTAAGTCAGTAATCAAC
* * *
57375 TTAATTCAGGGTAATTAAGTGAGTAAGTAATCGAC
1 TTAATTCAGGGTAATTAAGTAAGTCAGTAATCAAC
57410 TTAATTCAGGGTAATTAAGTAAG
1 TTAATTCAGGGTAATTAAGTAAG
57433 AAGCAGAGAT
Statistics
Matches: 156, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 137 0.88
36 19 0.12
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (35 bp):
TTAATTCAGGGTAATTAAGTAAGTCAGTAATCAAC
Done.