Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015087.1 Corchorus capsularis cultivar CVL-1 contig15108, 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: 58784
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2784 original size:30 final size:31
Alignment explanation
Indices: 2750--2826 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
2740 TTCTCGTCAC
* *
2750 CCAAAATAGATTTATTTTCAATGC-CATCAA
1 CCAAAACAGATTTATTTGCAATGCTCATCAA
*
2780 CCAAAACAGGA-TTATTTGCAATGCTATGATCAA
1 CCAAAACA-GATTTATTTGCAATGC--TCATCAA
2813 CCAAAACAGATTTA
1 CCAAAACAGATTTA
2827 GTATCATCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 19 0.49
31 2 0.05
32 2 0.05
33 16 0.41
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (31 bp):
CCAAAACAGATTTATTTGCAATGCTCATCAA
Found at i:2852 original size:33 final size:33
Alignment explanation
Indices: 2814--2907 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
2804 TATGATCAAC
2814 CAAAACAGATTTAGTATCATCACAAACAACACT
1 CAAAACAGATTTAGTATCATCACAAACAACACT
* * **
2847 TAAAACAGATTTAGTGTCATTGCAAACAACACT
1 CAAAACAGATTTAGTATCATCACAAACAACACT
** *
2880 CAAATTAGGTTTAGTATCATCACAAACA
1 CAAAACAGATTTAGTATCATCACAAACA
2908 TCATCTAAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.26
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCACAAACAACACT
Found at i:4418 original size:8 final size:8
Alignment explanation
Indices: 4390--4423 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
4380 AAATCGGCTA
4390 TGAATTTT
1 TGAATTTT
*
4398 TGAAGTTTC
1 TGAA-TTTT
4407 TGAATTTT
1 TGAATTTT
4415 TGAATTTT
1 TGAATTTT
4423 T
1 T
4424 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:5775 original size:21 final size:21
Alignment explanation
Indices: 5726--5775 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
5716 AGCACTGGAG
*
5726 CACATGGGGCGCGAGGCAAAC
1 CACATGGGGCGCCAGGCAAAC
** **
5747 CAGGTGGGGCGCCAGGCTTAC
1 CACATGGGGCGCCAGGCAAAC
5768 CACATGGG
1 CACATGGG
5776 TGCCCAACGC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.28, G:0.40, T:0.10
Consensus pattern (21 bp):
CACATGGGGCGCCAGGCAAAC
Found at i:9337 original size:36 final size:34
Alignment explanation
Indices: 9288--9406 Score: 104
Period size: 36 Copynumber: 3.4 Consensus size: 34
9278 CTCTTTTTAG
*
9288 ATTAAGTTCTTTATTGATTTCACTCAATTACCTTGA
1 ATTAAGTTCTTTATTGATCTCACT-AATTACC-TGA
*
9324 ATTAAGTTTTTTA-T--TCT-ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGATCTCAC-TAATTA-CCTGA
* *
9356 ATTAAG-CCTTTTATTGACCTCACGTAATTACACTGA
1 ATTAAGTTC-TTTATTGATCTCAC-TAATTAC-CTGA
9392 ATTAAGTTCTTTATT
1 ATTAAGTTCTTTATT
9407 TTACTTAATT
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
32 20 0.30
33 6 0.09
35 4 0.06
36 36 0.54
37 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (34 bp):
ATTAAGTTCTTTATTGATCTCACTAATTACCTGA
Found at i:9357 original size:32 final size:32
Alignment explanation
Indices: 9313--9416 Score: 109
Period size: 32 Copynumber: 3.1 Consensus size: 32
9303 GATTTCACTC
*
9313 AATTACCTTGAATTAAGTTTTTTATTCTACTT
1 AATTACCCTGAATTAAGTTTTTTATTCTACTT
** *
9345 AATTACCCTGAATTAAGCCTTTTATTGACCTCACGT
1 AATTACCCTGAATTAAGTTTTTTATT---CT-ACTT
* * *
9381 AATTACACTGAATTAAGTTCTTTATTTTACTT
1 AATTACCCTGAATTAAGTTTTTTATTCTACTT
9413 AATT
1 AATT
9417 TCCTTTCCTG
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
32 30 0.52
33 1 0.02
35 2 0.03
36 25 0.43
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (32 bp):
AATTACCCTGAATTAAGTTTTTTATTCTACTT
Found at i:9987 original size:11 final size:11
Alignment explanation
Indices: 9971--10048 Score: 93
Period size: 11 Copynumber: 6.7 Consensus size: 11
9961 ATTAAGTCAA
9971 TCTTCTTTCAG
1 TCTTCTTTCAG
9982 TCTTCTCTTTCAG
1 TC-T-TCTTTCAG
*
9995 TCTTTTTTCAG
1 TCTTCTTTCAG
*
10006 TCTTTTTTTCAG
1 TC-TTCTTTCAG
10018 TCTTCTTTTCAG
1 TCTTC-TTTCAG
10030 TCTTCTTTCAG
1 TCTTCTTTCAG
*
10041 ACTTCTTT
1 TCTTCTTT
10049 TGCCTAATTT
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
11 26 0.43
12 24 0.40
13 10 0.17
ACGTcount: A:0.09, C:0.24, G:0.08, T:0.59
Consensus pattern (11 bp):
TCTTCTTTCAG
Found at i:9998 original size:24 final size:23
Alignment explanation
Indices: 9971--10048 Score: 104
Period size: 23 Copynumber: 3.3 Consensus size: 23
9961 ATTAAGTCAA
9971 TCTTCTTTCAGTCTTCTCTTTCAG
1 TCTTCTTTCAGTCTT-TCTTTCAG
* *
9995 TCTTTTTTCAGTCTTTTTTTCAG
1 TCTTCTTTCAGTCTTTCTTTCAG
10018 TCTTCTTTTCAGTC-TTCTTTCAG
1 TCTTC-TTTCAGTCTTTCTTTCAG
*
10041 ACTTCTTT
1 TCTTCTTT
10049 TGCCTAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 3 0.06
23 23 0.48
24 22 0.46
ACGTcount: A:0.09, C:0.24, G:0.08, T:0.59
Consensus pattern (23 bp):
TCTTCTTTCAGTCTTTCTTTCAG
Found at i:10034 original size:12 final size:12
Alignment explanation
Indices: 9971--10049 Score: 110
Period size: 12 Copynumber: 6.8 Consensus size: 12
9961 ATTAAGTCAA
9971 TCTTC-TTTCAG
1 TCTTCTTTTCAG
9982 TCTTCTCTTTCAG
1 TCTTCT-TTTCAG
9995 TCTT-TTTTCAG
1 TCTTCTTTTCAG
*
10006 TCTTTTTTTCAG
1 TCTTCTTTTCAG
10018 TCTTCTTTTCAG
1 TCTTCTTTTCAG
10030 TCTTC-TTTCAG
1 TCTTCTTTTCAG
*
10041 ACTTCTTTT
1 TCTTCTTTT
10050 GCCTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
11 25 0.40
12 27 0.44
13 10 0.16
ACGTcount: A:0.09, C:0.24, G:0.08, T:0.59
Consensus pattern (12 bp):
TCTTCTTTTCAG
Found at i:10441 original size:35 final size:34
Alignment explanation
Indices: 9420--10448 Score: 861
Period size: 35 Copynumber: 29.1 Consensus size: 34
9410 CTTAATTTCC
*
9420 TTTCC-TGAAATTAAGCCTATGT-TTTTTTACTTAA
1 TTTCCTTGAAATTAAGCC-A-GTCTTTTTTACCTAA
* *
9454 TTTCCTTGAAATTAAGACAGTCTATCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCT-TTTTTACCTAA
*
9489 TTTCATTGAAATTAAGCCAGTCTTGTCTTTACCTAGA
1 TTTCCTTGAAATTAAGCCAGTCTT-T-TTTACCTA-A
* *
9526 -TTCCTTGAAACTAAGCCAGTCCTTTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGT-C-TTTTTTACCTAA
* * * *
9561 TTCCCTTGAAATTAAGCCAGTCAATCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTC-TTTTTTACCTAA
* * *
9596 TTTCCTGGAAACTAAGCCAGTCTCTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCT-TTTTTACCTAA
* *
9631 TTTCCTTGAAATTAAGCCAGTCCTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGT-CTTTTTTACCTAA
* *
9666 TTTCCTTGAAACTAAGCCAGTCCTTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGT-CTTTTTTACCTAA
* *
9701 TTTCCTTGAAATTAAGCCAGTCCACTTTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGT-C-TTTTTTACCTAA
* * *
9737 TTTCCTTGAAACTAAGCCAGCCTTTGTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTC-TT-TTTTACCTAA
* * *
9773 TTTCCTTGAAATTAAGCCAGTCTATCTCTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCT-TTTTTACCTAA
* *
9808 TTTCCTTGAAACTAAGCCAATCTCTTTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCT-TTTTTACCTAA
9843 TTTCCTTGAAATTAAGCCAGTCTTGTCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCTT-T-TTTACCTAA
* *
9879 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTATCTAG
1 TTTCCTTGAAATTAAGCCAGTC-TTT-TTTACCTAA
* * *
9915 TTTCCTTGAAACTAAGCCAGTTCTTTCTTTATCTAG
1 TTTCCTTGAAATTAAGCCAG-TCTTT-TTTACCTAA
* * * *
9951 TTTCCTTGAAATTAAGTCAATCTTCTTT--C-AG
1 TTTCCTTGAAATTAAGCCAGTCTTTTTTACCTAA
* ** **** * *
9982 TCTTCTCTTTCAGTCTTTTTTCAGTCTTTTTT-TC-AG
1 T-TTC-C-TTGA-AATTAAGCCAGTCTTTTTTACCTAA
* * ** **** * *
10018 TCTTCTTTTCAGTCTTCTTTCAGACTTCTTTTGCCTAA
1 T-TTC-CTTGA-AATTAAGCCAGTCTT-TTTTACCTAA
*
10056 TTTCCTTGAAATTAAGCC-GTCATTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTC-TTT-TTTACCTAA
* * * *
10091 TTTCCTTGAAACTAGGCCAGTCTTCTCTTTACTTAG
1 TTTCCTTGAAATTAAGCCAGTCTT-T-TTTACCTAA
* *
10127 TTTCCTTGAAACTAAGCCAGTCATTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTC-TTTTTTACCTAA
*
10162 TTTCCTTGAAATTAAGCCAGTCTACTTTTTCACCTAG
1 TTTCCTTGAAATTAAGCCAGTCT--TTTTT-ACCTAA
* *
10199 TTTCCTTGAAACTAAGCCAGTCTTGTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTT-TTTTACCTAA
* *
10234 TTTCCTTGAAATTAAGTCAGTCTTCTTTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTC-T-TTTTTACCTAA
** *
10270 TTTCCTTGAAACGAAGCCAGTCTATCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCT-TTTTTACCTAA
*
10305 TTTCCTTGAAATTAAGCCTGTCTTTTCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTC-TTT-TTTACCTAA
* *
10341 TTTCCTTGAAACTAAGCCAGTCATTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTC-TTTTTTACCTAA
*
10376 TTTCCTTGAAATTAAGCCAGTCTACTTTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCT--TTTTTACCTAA
* *
10412 TTTCCTTGAAACTAAGCCAGTCTTGTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTT-TTTTACCTAA
10447 TT
1 TT
10449 ACTATGAATT
Statistics
Matches: 831, Mismatches: 122, Indels: 83
0.80 0.12 0.08
Matches are distributed among these distances:
31 3 0.00
32 4 0.00
33 3 0.00
34 21 0.03
35 405 0.49
36 351 0.42
37 40 0.05
38 4 0.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.43
Consensus pattern (34 bp):
TTTCCTTGAAATTAAGCCAGTCTTTTTTACCTAA
Found at i:10441 original size:71 final size:69
Alignment explanation
Indices: 9420--10448 Score: 885
Period size: 71 Copynumber: 14.5 Consensus size: 69
9410 CTTAATTTCC
* * * *
9420 TTTCC-TGAAATTAAGCCTATGT-TTTTTTACTTAATTTCCTTGAAATTAAGACAGTCTATCTTT
1 TTTCCTTGAAATTAAGCC-A-GTCTTTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTCTTTTT
9483 ACCTAA
64 ACCTAA
* * *
9489 TTTCATTGAAATTAAGCCAGTCTTGTCTTTACCTAGA-TTCCTTGAAACTAAGCCAGTCCTTTTT
1 TTTCCTTGAAATTAAGCCAGTCTT-T-TTTACCTA-ATTTCCTTGAAATTAAGCCAGT-CTCTTT
*
9553 TTACTTAA
62 TTACCTAA
* * * * * *
9561 TTCCCTTGAAATTAAGCCAGTCAATCTTTACCTAGTTTCCTGGAAACTAAGCCAGTCTCTTTTTA
1 TTTCCTTGAAATTAAGCCAGTC-TTTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTCTTTTTA
*
9626 CTTAA
65 CCTAA
* * *
9631 TTTCCTTGAAATTAAGCCAGTCCTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTC-CTTTTTT
1 TTTCCTTGAAATTAAGCCAGT-CTTTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTC-TTTTT
*
9695 ACTTAA
64 ACCTAA
* * * * *
9701 TTTCCTTGAAATTAAGCCAGTCCACTTTTTACCTAGTTTCCTTGAAACTAAGCCAGCCTTTGTTT
1 TTTCCTTGAAATTAAGCCAGT-C-TTTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTCT-TTT
*
9766 TACTTAA
63 TACCTAA
* * * * *
9773 TTTCCTTGAAATTAAGCCAGTCTATCTCTACCTAGTTTCCTTGAAACTAAGCCAATCTCTTTTTA
1 TTTCCTTGAAATTAAGCCAGTCT-TTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTCTTTTTA
9838 CCTAA
65 CCTAA
*
9843 TTTCCTTGAAATTAAGCCAGTCTTGTCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTT
1 TTTCCTTGAAATTAAGCCAGTCTT-T-TTTACCTAATTTCCTTGAAATTAAGCCAGTCTCTT-TT
* *
9908 TATCTAG
63 TACCTAA
* * * * * *
9915 TTTCCTTGAAACTAAGCCAGTTCTTTCTTTATCTAGTTTCCTTGAAATTAAGTCAATCT-TCTTT
1 TTTCCTTGAAATTAAGCCAG-TCTTT-TTTACCTAATTTCCTTGAAATTAAGCCAGTCTCTTTTT
*
9979 --C-AG
64 ACCTAA
* ** **** * * * * ** **** *
9982 TCTTCTCTTTCAGTCTTTTTTCAGTCTTTTTT-TC-AGTCTTCTTTTCAGTCTTCTTTCAGACT-
1 T-TTC-C-TTGA-AATTAAGCCAGTCTTTTTTACCTAAT-TTC-CTTGA-AATTAAGCCAGTCTC
*
10044 TCTTTTGCCTAA
59 T-TTTTACCTAA
* * * *
10056 TTTCCTTGAAATTAAGCC-GTCATTTCTTTACCTAGTTTCCTTGAAACTAGGCCAGTCTTCTCTT
1 TTTCCTTGAAATTAAGCCAGTC-TTT-TTTACCTAATTTCCTTGAAATTAAGCCAGTC-TCTTTT
* *
10120 TACTTAG
63 TACCTAA
* *
10127 TTTCCTTGAAACTAAGCCAGTCATTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTACTTTTT
1 TTTCCTTGAAATTAAGCCAGTC-TTTTTTACCTAATTTCCTTGAAATTAAGCCAGTCT-CTTTTT
*
10192 CACCTAG
64 -ACCTAA
* * *
10199 TTTCCTTGAAACTAAGCCAGTCTTGTTTTACTTAATTTCCTTGAAATTAAGTCAGTCTTCTTTTT
1 TTTCCTTGAAATTAAGCCAGTCTT-TTTTACCTAATTTCCTTGAAATTAAGCCAGTC-TCTTTTT
*
10264 ACCTAG
64 ACCTAA
** * * *
10270 TTTCCTTGAAACGAAGCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGCCTGTCTTTTCTTT
1 TTTCCTTGAAATTAAGCCAGTCT-TTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTCTT-TTT
10335 ACCTAA
64 ACCTAA
* *
10341 TTTCCTTGAAACTAAGCCAGTCATTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTACTTTTT
1 TTTCCTTGAAATTAAGCCAGTC-TTTTTTACCTAATTTCCTTGAAATTAAGCCAGTCT-CTTTTT
*
10406 ACCTAG
64 ACCTAA
* *
10412 TTTCCTTGAAACTAAGCCAGTCTTGTTTTACTTAATT
1 TTTCCTTGAAATTAAGCCAGTCTT-TTTTACCTAATT
10449 ACTATGAATT
Statistics
Matches: 811, Mismatches: 104, Indels: 88
0.81 0.10 0.09
Matches are distributed among these distances:
67 6 0.01
68 11 0.01
69 19 0.02
70 180 0.22
71 380 0.47
72 200 0.25
73 13 0.02
74 2 0.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.43
Consensus pattern (69 bp):
TTTCCTTGAAATTAAGCCAGTCTTTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTCTTTTTAC
CTAA
Found at i:10525 original size:40 final size:40
Alignment explanation
Indices: 10437--10530 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 40
10427 GCCAGTCTTG
* * *
10437 TTTTACTTAATTACTATGAATTAAGTCTTTTAACTGCTGC
1 TTTTACTTAATTTCTATGAAATAAGTCTTTTAACTGCTAC
*** * *
10477 TCCCACTTAATTTCTATGAAA-ATAGTCTTTTGACTGCTAT
1 TTTTACTTAATTTCTATGAAATA-AGTCTTTTAACTGCTAC
10517 TTTTACTTAATTTC
1 TTTTACTTAATTTC
10531 GTTGAATTAA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
39 1 0.02
40 41 0.98
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.48
Consensus pattern (40 bp):
TTTTACTTAATTTCTATGAAATAAGTCTTTTAACTGCTAC
Found at i:11784 original size:43 final size:44
Alignment explanation
Indices: 11718--12063 Score: 479
Period size: 44 Copynumber: 7.9 Consensus size: 44
11708 TAAAATGCCC
* *
11718 CCTTGTGAGCAACTGGAAAACTGAAAAGTTGTCGGAATGCCTCCT
1 CCTTG-GAGCAACTGAAAAACTGAAAAGTTGTTGGAATGCCTCCT
* * *
11763 CTTTGGAGCAACTG-AAAACTGAAAAGATGTTGTAATG-CTCCCT
1 CCTTGGAGCAACTGAAAAACTGAAAAGTTGTTGGAATGCCT-CCT
* *
11806 CCTTGGAGCAACTGAAAAACTGAAAAGTGGTTGGGATGCC-CCT
1 CCTTGGAGCAACTGAAAAACTGAAAAGTTGTTGGAATGCCTCCT
* * *
11849 CCTTGGAGCAACAGAAAAATTGAAAAGTTGTT-GACATGCCCCCT
1 CCTTGGAGCAACTGAAAAACTGAAAAGTTGTTGGA-ATGCCTCCT
*
11893 CCTTGGAGCAACTGAAAAACTAAAAAGTTGTTGGAATGCCTCCT
1 CCTTGGAGCAACTGAAAAACTGAAAAGTTGTTGGAATGCCTCCT
* * *
11937 CCTTGGAGCAACAGAAAAATTGAAAAGTTGTT-GACATGCCCCCT
1 CCTTGGAGCAACTGAAAAACTGAAAAGTTGTTGGA-ATGCCTCCT
*
11981 CCTTGGAGCAACTGAAAAACTAAAAAGTTGTTGGAATGCCTCCT
1 CCTTGGAGCAACTGAAAAACTGAAAAGTTGTTGGAATGCCTCCT
12025 CCTTGGAGCAACTG-AAAACTGAAAAGTTGTTGGAATGCC
1 CCTTGGAGCAACTGAAAAACTGAAAAGTTGTTGGAATGCC
12064 CCCTGTTTCC
Statistics
Matches: 267, Mismatches: 26, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
42 3 0.01
43 99 0.37
44 156 0.58
45 9 0.03
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (44 bp):
CCTTGGAGCAACTGAAAAACTGAAAAGTTGTTGGAATGCCTCCT
Found at i:11873 original size:87 final size:87
Alignment explanation
Indices: 11718--12067 Score: 517
Period size: 87 Copynumber: 4.0 Consensus size: 87
11708 TAAAATGCCC
* * * * *
11718 CCTTGTGAGCAACTGGAAAACTGAAAAGTTGTCGGAATGCCTCCTCTTTGGAGCAACTGAAAACT
1 CCTTG-GAGCAACTGAAAAACTAAAAAGTTGTTGGAATGCCTCCTCCTTGGAGCAACAGAAAACT
* *
11783 GAAAAGATGTTGTA-ATGCTCCCT
65 GAAAAGTTGTTG-ACATGCCCCCT
* * * *
11806 CCTTGGAGCAACTGAAAAACTGAAAAGTGGTTGGGATGCC-CCTCCTTGGAGCAACAGAAAAATT
1 CCTTGGAGCAACTGAAAAACTAAAAAGTTGTTGGAATGCCTCCTCCTTGGAGCAACAG-AAAACT
11870 GAAAAGTTGTTGACATGCCCCCT
65 GAAAAGTTGTTGACATGCCCCCT
*
11893 CCTTGGAGCAACTGAAAAACTAAAAAGTTGTTGGAATGCCTCCTCCTTGGAGCAACAGAAAAATT
1 CCTTGGAGCAACTGAAAAACTAAAAAGTTGTTGGAATGCCTCCTCCTTGGAGCAACAG-AAAACT
11958 GAAAAGTTGTTGACATGCCCCCT
65 GAAAAGTTGTTGACATGCCCCCT
*
11981 CCTTGGAGCAACTGAAAAACTAAAAAGTTGTTGGAATGCCTCCTCCTTGGAGCAACTGAAAACTG
1 CCTTGGAGCAACTGAAAAACTAAAAAGTTGTTGGAATGCCTCCTCCTTGGAGCAACAGAAAACTG
12046 AAAAGTTGTTGGA-ATGCCCCCT
66 AAAAGTTGTT-GACATGCCCCCT
12068 GTTTCCAGTC
Statistics
Matches: 244, Mismatches: 14, Indels: 9
0.91 0.05 0.03
Matches are distributed among these distances:
86 16 0.07
87 117 0.48
88 111 0.45
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (87 bp):
CCTTGGAGCAACTGAAAAACTAAAAAGTTGTTGGAATGCCTCCTCCTTGGAGCAACAGAAAACTG
AAAAGTTGTTGACATGCCCCCT
Found at i:15816 original size:120 final size:124
Alignment explanation
Indices: 15596--15935 Score: 508
Period size: 129 Copynumber: 2.7 Consensus size: 124
15586 TCAAAGGTGT
* *
15596 GGAGTCCCTCCCCAATTTGGTAGGAACTTTTCCACTAGCCAAAAGCCGTGACCATTTACAATTTT
1 GGAGTCCCTCCACAATTTGGTAGGAAC--TTCCACAAGCCAAAAGCCGTGACCATTTACAATTTT
*
15661 GTGAATAATCAGGGTTCTAGCCTTTATGCAATTGA-TG-CG-A-ATGACAAGTTATAACAC
64 GTGAATAATCAGGGTTCTTGCCTTTATGCAATTGAGTGACGAATATGACAAGTTATAACAC
* *
15718 GGGGTCCCTCCACAATTTGGTAGGAACTTCCACAAGTCAAAAGCCGTGACCATTTACAATTTTGT
1 GGAGTCCCTCCACAATTTGGTAGGAACTTCCACAAGCCAAAAGCCGTGACCATTTACAATTTTGT
* * *
15783 GAATAATCAGGGTTCTTGCCTTTATGCAGTTGATGTGAATGAATGCTATGACAAGTTATAACAT
66 GAATAATCAGGGTTCTTGCCTTTATGCAATTGA-GTG-ACGAA---TATGACAAGTTATAACAC
*
15847 GGAGTCCCTCCACAATTTGGTAGGAACTTCCACAAGCCAAAAGCCGTGACCATTTACAATTCTGT
1 GGAGTCCCTCCACAATTTGGTAGGAACTTCCACAAGCCAAAAGCCGTGACCATTTACAATTTTGT
15912 GAATAATCAGGGTTCTTGCCTTTA
66 GAATAATCAGGGTTCTTGCCTTTA
15936 ATGAGGTATG
Statistics
Matches: 198, Mismatches: 11, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
120 67 0.34
122 27 0.14
124 1 0.01
125 1 0.01
129 102 0.52
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (124 bp):
GGAGTCCCTCCACAATTTGGTAGGAACTTCCACAAGCCAAAAGCCGTGACCATTTACAATTTTGT
GAATAATCAGGGTTCTTGCCTTTATGCAATTGAGTGACGAATATGACAAGTTATAACAC
Found at i:19344 original size:9 final size:9
Alignment explanation
Indices: 19330--19427 Score: 50
Period size: 9 Copynumber: 11.4 Consensus size: 9
19320 TATAATATTC
19330 TCGGGTCAT
1 TCGGGTCAT
*
19339 TCGGGTTAACT
1 TCGGG-TCA-T
*
19350 CTCGGGTTAT
1 -TCGGGTCAT
19360 TCGGGT--T
1 TCGGGTCAT
19367 TCGGGTCAT
1 TCGGGTCAT
*
19376 ACGGGTC--
1 TCGGGTCAT
*
19383 TCGGGTCAC
1 TCGGGTCAT
19392 TCGGGT--T
1 TCGGGTCAT
* *
19399 ACGGGTCAC
1 TCGGGTCAT
19408 TCGGGT--T
1 TCGGGTCAT
*
19415 ACGGGTCAT
1 TCGGGTCAT
19424 TCGG
1 TCGG
19428 ATCTTGAGTC
Statistics
Matches: 67, Mismatches: 11, Indels: 22
0.67 0.11 0.22
Matches are distributed among these distances:
7 23 0.34
9 33 0.49
10 3 0.04
11 3 0.04
12 5 0.07
ACGTcount: A:0.11, C:0.22, G:0.36, T:0.31
Consensus pattern (9 bp):
TCGGGTCAT
Found at i:19372 original size:16 final size:16
Alignment explanation
Indices: 19351--19427 Score: 91
Period size: 16 Copynumber: 4.8 Consensus size: 16
19341 GGGTTAACTC
*
19351 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
19367 TCGGGTCATACGGGTC
1 TCGGGTCATTCGGGTT
*
19383 TCGGGTCACTCGGGTT
1 TCGGGTCATTCGGGTT
* *
19399 ACGGGTCACTCGGGTT
1 TCGGGTCATTCGGGTT
*
19415 ACGGGTCATTCGG
1 TCGGGTCATTCGG
19428 ATCTTGAGTC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 53 1.00
ACGTcount: A:0.10, C:0.22, G:0.38, T:0.30
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:19927 original size:31 final size:29
Alignment explanation
Indices: 19883--19961 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
19873 GCTTAATATC
*
19883 CAAATTAGCCCCTTAACTATCCATTTTAGGA
1 CAAATTGGCCCCTTAACT-T-CATTTTAGGA
* **
19914 CAAATTGGACCCTTAACTTTTTTTTAGGA
1 CAAATTGGCCCCTTAACTTCATTTTAGGA
19943 CAAATTGGCCCCTTAACTT
1 CAAATTGGCCCCTTAACTT
19962 TTAAAAACAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 26 0.60
30 1 0.02
31 16 0.37
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (29 bp):
CAAATTGGCCCCTTAACTTCATTTTAGGA
Found at i:19948 original size:29 final size:29
Alignment explanation
Indices: 19906--19963 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
19896 TAACTATCCA
19906 TTTTAGGACAAATTGGACCCTTAACTTTT
1 TTTTAGGACAAATTGGACCCTTAACTTTT
*
19935 TTTTAGGACAAATTGGCCCCTTAACTTTT
1 TTTTAGGACAAATTGGACCCTTAACTTTT
19964 AAAAACAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (29 bp):
TTTTAGGACAAATTGGACCCTTAACTTTT
Found at i:21392 original size:15 final size:15
Alignment explanation
Indices: 21372--21400 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21362 TTGTAATTAA
21372 AAATAATTAATAATT
1 AAATAATTAATAATT
21387 AAATAATTAATAAT
1 AAATAATTAATAAT
21401 AATCAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATAATTAATAATT
Found at i:21393 original size:25 final size:25
Alignment explanation
Indices: 21365--21414 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
21355 TTCAAAATTG
*
21365 TAATTAAAAATAATTAATAATTAAA
1 TAATTAAAAATAATCAATAATTAAA
*
21390 TAATTAATAATAATCAATAATTAAA
1 TAATTAAAAATAATCAATAATTAAA
21415 AAAAATGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
TAATTAAAAATAATCAATAATTAAA
Found at i:30723 original size:30 final size:30
Alignment explanation
Indices: 30687--30751 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
30677 TTGAGAGCAA
*
30687 CGCCCTGGGCGCACAAGTCATTCACATGGG
1 CGCCCTGGGCGCACAAGCCATTCACATGGG
30717 CGCCCTGGGCGCACAAGCCATTCACATGGG
1 CGCCCTGGGCGCACAAGCCATTCACATGGG
30747 CGCCC
1 CGCCC
30752 AGGGGGAGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.18, C:0.38, G:0.29, T:0.14
Consensus pattern (30 bp):
CGCCCTGGGCGCACAAGCCATTCACATGGG
Found at i:34523 original size:29 final size:29
Alignment explanation
Indices: 34457--34568 Score: 109
Period size: 31 Copynumber: 3.8 Consensus size: 29
34447 TATGAAAAGT
* * *
34457 TACTAAATTGAACAAATTTGATAGGGTTTAG
1 TACTAAATTGAGCAACTTT-A-AAGGTTTAG
* *
34488 TAATAAATTGAGCAACTTTAAAGGTTTGG
1 TACTAAATTGAGCAACTTTAAAGGTTTAG
**
34517 TACTAAATTGAGCAATTCTTTAAACATTTAG
1 TACTAAATTGAGCAA--CTTTAAAGGTTTAG
*
34548 TACTAAATTGAGTAA-TTTAAA
1 TACTAAATTGAGCAACTTTAAA
34569 TCCAGGTAGG
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
28 6 0.09
29 21 0.30
30 1 0.01
31 41 0.59
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (29 bp):
TACTAAATTGAGCAACTTTAAAGGTTTAG
Found at i:39267 original size:35 final size:35
Alignment explanation
Indices: 39216--39449 Score: 294
Period size: 35 Copynumber: 6.7 Consensus size: 35
39206 TTCTTACTAA
* * *
39216 ACTTAATTACCTTGAATTAAGTTAATTATTGAACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACT
** *
39251 ACTTAATTACCCTGAATTAAGTT-ATTTGTTAACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACT
*
39285 CACTTAATTACCCTGAATTAAGTTGATTACCG-ACT
1 -ACTTAATTACCCTGAATTAAGTTGATTACTGAACT
*
39320 CACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 -ACTTAATTACCCTGAATTAAGTTGATTACTGAACT
* * * *
39356 ACTTAATTACCATGAATTAAGTTGCTTACTTAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACT
*
39391 ACTTAATTACCCTGAATTAAGTTGATTACCG-ACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAAC-T
*
39426 GCTTAATTACCCTGAATTAAGTTG
1 ACTTAATTACCCTGAATTAAGTTG
39450 CTTATTACTG
Statistics
Matches: 176, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
34 9 0.05
35 162 0.92
36 5 0.03
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.40
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGAACT
Found at i:39398 original size:105 final size:105
Alignment explanation
Indices: 39216--39449 Score: 353
Period size: 105 Copynumber: 2.2 Consensus size: 105
39206 TTCTTACTAA
* * * * **
39216 ACTTAATTACCTTGAATTAAGTTAATTATTGAACTACTTAATTACCCTGAATTAAGTTATTTGTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACTACTTAATTACCATGAATTAAGTTATTACTT
39281 AACTCACTTAATTACCCTGAATTAAGTTGATTACCGACTC
66 AACTCACTTAATTACCCTGAATTAAGTTGATTACCGACTC
* *
39321 ACTTAATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCATGAATTAAGTTGCTTACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACTACTTAATTACCATGAATTAAGTT-ATTACT
* *
39386 TAA-TTACTTAATTACCCTGAATTAAGTTGATTACCGACTT
65 TAACTCACTTAATTACCCTGAATTAAGTTGATTACCGACTC
*
39426 GCTTAATTACCCTGAATTAAGTTG
1 ACTTAATTACCCTGAATTAAGTTG
39450 CTTATTACTG
Statistics
Matches: 117, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
105 111 0.95
106 6 0.05
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.40
Consensus pattern (105 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGAACTACTTAATTACCATGAATTAAGTTATTACTT
AACTCACTTAATTACCCTGAATTAAGTTGATTACCGACTC
Found at i:40087 original size:25 final size:27
Alignment explanation
Indices: 40050--40101 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
40040 GTAAGCAAAC
40050 AAAGTAAAACCCA-ATA-TATATAAAAA
1 AAAGTAAAACCCACATACTA-ATAAAAA
*
40076 AAAG-AAAGCCCACATACTAATAAAAA
1 AAAGTAAAACCCACATACTAATAAAAA
40102 GACCAAGCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 7 0.30
26 14 0.61
27 2 0.09
ACGTcount: A:0.63, C:0.15, G:0.06, T:0.15
Consensus pattern (27 bp):
AAAGTAAAACCCACATACTAATAAAAA
Found at i:55920 original size:38 final size:39
Alignment explanation
Indices: 55832--55927 Score: 149
Period size: 39 Copynumber: 2.5 Consensus size: 39
55822 ATTAAACAGA
*
55832 CTAATTACATTTAAGAGATTCACTAGCCACAAAATTATG
1 CTAATTAAATTTAAGAGATTCACTAGCCACAAAATTATG
* * *
55871 CTAATTAAATTTAAGAGATTTATTAGCCACAAAA-TCTG
1 CTAATTAAATTTAAGAGATTCACTAGCCACAAAATTATG
55909 CTAATTAAATTTAAGAGAT
1 CTAATTAAATTTAAGAGAT
55928 AATAATTAGC
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 22 0.42
39 31 0.58
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (39 bp):
CTAATTAAATTTAAGAGATTCACTAGCCACAAAATTATG
Found at i:58396 original size:19 final size:20
Alignment explanation
Indices: 58371--58416 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
58361 TATTTATTTG
58371 TTTATTTATTTATGAAATAA
1 TTTATTTATTTATGAAATAA
58391 -TTATTTATTTATGAAATAA
1 TTTATTTATTTATGAAATAA
58410 TTTATTT
1 TTTATTT
58417 TTTTGAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTATTTATTTATGAAATAA
Done.