Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017017.1 Corchorus olitorius cultivar O-4 contig17050, 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: 46303
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:691 original size:8 final size:7
Alignment explanation
Indices: 674--719 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
664 TATCCTAGCC
674 AAAAGAA
1 AAAAGAA
*
681 AAAAGGA
1 AAAAGAA
688 AAAAGAA
1 AAAAGAA
695 CAAAAGAA
1 -AAAAGAA
703 AAAAGAA
1 AAAAGAA
*
710 AAAATAA
1 AAAAGAA
717 AAA
1 AAA
720 GGTTATCTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
7 28 0.80
8 7 0.20
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:2124 original size:18 final size:16
Alignment explanation
Indices: 2081--2112 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2071 TCTTGATTTT
*
2081 TTCAGGGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
2097 TTCAGAGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
2113 CTTGTAGAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.25, G:0.22, T:0.44
Consensus pattern (16 bp):
TTCAGAGCTTTTCTGC
Found at i:2724 original size:31 final size:31
Alignment explanation
Indices: 2653--2724 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
2643 GTCTATAAGC
*
2653 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
* *
2684 TAATT-ATTTGTTTAATTTAATAC-TTAATTT
1 T-TTTAATTTGTTTAATTTAAGACTTTAATTT
2714 GTTTTAATTTG
1 -TTTTAATTTG
2725 CAATAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 8 0.24
31 24 0.71
32 2 0.06
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:3495 original size:16 final size:16
Alignment explanation
Indices: 3474--3559 Score: 88
Period size: 16 Copynumber: 5.4 Consensus size: 16
3464 CTACCAGAGA
*
3474 CCGAACCCGAAGATAC
1 CCGAACCCGAAAATAC
*
3490 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
3506 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
**
3522 CCGAACCCG-ACTTAAC
1 CCGAACCCGAAAAT-AC
3538 CCGAACCCGAAAA-AGC
1 CCGAACCCGAAAATA-C
3554 CCGAAC
1 CCGAAC
3560 TCGATGGATT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
15 6 0.10
16 49 0.83
17 4 0.07
ACGTcount: A:0.38, C:0.41, G:0.15, T:0.06
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:3515 original size:32 final size:32
Alignment explanation
Indices: 3474--3559 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
3464 CTACCAGAGA
*
3474 CCGAACCCGAAGATACCCGAACCCGACATAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
*
3506 CCGAACCCGAAAATACCCGAACCCGACTTAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
3538 CCGAACCCGAAAA-AGCCCGAAC
1 CCGAACCCGAAAATA-CCCGAAC
3560 TCGATGGATT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
31 1 0.02
32 50 0.98
ACGTcount: A:0.38, C:0.41, G:0.15, T:0.06
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCGAACCCGACATAAC
Found at i:5077 original size:44 final size:44
Alignment explanation
Indices: 5027--5116 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
5017 TCCTACTTGG
* *
5027 ATTTTCTTTGATAATGATTCTCCACATACCTGGATCTTCTTTCA
1 ATTTTCTTTGATAATAATCCTCCACATACCTGGATCTTCTTTCA
*
5071 ATTTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
1 ATTTTCTTTGATAATAATCCTCCACATACCTGGATCTTCTTTCA
5115 AT
1 AT
5117 AATAATCCTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.44
Consensus pattern (44 bp):
ATTTTCTTTGATAATAATCCTCCACATACCTGGATCTTCTTTCA
Found at i:6286 original size:178 final size:178
Alignment explanation
Indices: 6017--6346 Score: 502
Period size: 178 Copynumber: 1.9 Consensus size: 178
6007 CCAATAAAGG
* * *
6017 TGATTTAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATTAAGGACTTGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* * * * *
6082 AATTTAATGTTTCAAGTATCAAAAATGCTTCTGAAA-AATTTGTTGTTTCGGTTAATGGGAATAG
66 AATTTAATGTTTCAAGTATAAAAAATGCTTC-CAAACAATTAGTTGTTTCGGTTAACGGAAATAG
*
6146 ACGGTCCACTTAATATTATATAACTTTTGCTCTAGATGTCTGATTATGA
130 ACGGTCCACTTAATATTACATAACTTTTGCTCTAGATGTCTGATTATGA
* * * *
6195 TGATTCAAGTGTCTCTTGAAAGGTTGTTGCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
6260 AATTTAATG-TTCAAGGTATAAAAAATGCTTCCAAACAATTAGTTGTTTCGGTTAACGGAAATAG
66 AATTTAATGTTTCAA-GTATAAAAAATGCTTCCAAACAATTAGTTGTTTCGGTTAACGGAAATAG
*
6324 ACGGTCTACTTAATATTACATAA
130 ACGGTCCACTTAATATTACATAA
6347 TTTGAACTTA
Statistics
Matches: 136, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
177 8 0.06
178 128 0.94
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAACAATTAGTTGTTTCGGTTAACGGAAATAGA
CGGTCCACTTAATATTACATAACTTTTGCTCTAGATGTCTGATTATGA
Found at i:14794 original size:33 final size:33
Alignment explanation
Indices: 14758--14821 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
14748 AATGTTTTTT
*
14758 TTTTTTTTTG-CAGT-AATCATGAGAATAGTTTC
1 TTTTTTTTTGACA-TCAATCATAAGAATAGTTTC
14790 TTTTTTTTTGACATCAATCATAAGAATAGTTT
1 TTTTTTTTTGACATCAATCATAAGAATAGTTT
14822 AGGAAGCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 11 0.38
33 18 0.62
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.50
Consensus pattern (33 bp):
TTTTTTTTTGACATCAATCATAAGAATAGTTTC
Found at i:19490 original size:14 final size:13
Alignment explanation
Indices: 19473--19506 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
19463 CAAAATAACT
19473 GAATTAAAAAAGCA
1 GAATTAAAAAA-CA
19487 GAATTGAAAAAACA
1 GAATT-AAAAAACA
19501 GAATTA
1 GAATTA
19507 CTAAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 12 0.63
15 6 0.32
ACGTcount: A:0.62, C:0.06, G:0.15, T:0.18
Consensus pattern (13 bp):
GAATTAAAAAACA
Found at i:19498 original size:36 final size:37
Alignment explanation
Indices: 19458--19531 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
19448 ACATAATTTC
* *
19458 AAAAACAAAATAACTGAA-TTAAAAAAGCAGAATTGA
1 AAAAACAAAATAACTAAATTTAAAAAAACAGAATTGA
* *
19494 AAAAACAGAATTACTAAATTTAAAAAAACAGAATTGA
1 AAAAACAAAATAACTAAATTTAAAAAAACAGAATTGA
19531 A
1 A
19532 TTCACAGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 15 0.45
37 18 0.55
ACGTcount: A:0.64, C:0.08, G:0.09, T:0.19
Consensus pattern (37 bp):
AAAAACAAAATAACTAAATTTAAAAAAACAGAATTGA
Found at i:19540 original size:51 final size:50
Alignment explanation
Indices: 19485--19581 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 50
19475 ATTAAAAAAG
*
19485 CAGAATTGAAAAAACAGAATTACTAAATTTAAAAAAACAGAATTGAATTCA
1 CAGAATTGAAAAAACAGAATAACTAAA-TTAAAAAAACAGAATTGAATTCA
** * *
19536 CAGAATTTCAAAAACAGAATAACTAAATTAAATAAGCAGAATTGAA
1 CAGAATTGAAAAAACAGAATAACTAAATTAAAAAAACAGAATTGAA
19582 AAAACAGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 17 0.41
51 24 0.59
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (50 bp):
CAGAATTGAAAAAACAGAATAACTAAATTAAAAAAACAGAATTGAATTCA
Found at i:19626 original size:50 final size:50
Alignment explanation
Indices: 19572--19667 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
19562 ATTAAATAAG
*
19572 CAGAATTGAAAAAACAGAATTACTAAATTACAA-AAACAGAATTGAATTCA
1 CAGAATTGAAAAAACAGAATAACTAAATTA-AATAAACAGAATTGAATTCA
** * *
19622 CAGAATTTCAAAAACAGAATAACTGAATTAAATAAGCAGAATTGAA
1 CAGAATTGAAAAAACAGAATAACTAAATTAAATAAACAGAATTGAA
19668 AAAACAGAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 2 0.05
50 38 0.95
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.22
Consensus pattern (50 bp):
CAGAATTGAAAAAACAGAATAACTAAATTAAATAAACAGAATTGAATTCA
Found at i:19628 original size:36 final size:36
Alignment explanation
Indices: 19535--19617 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
19525 AATTGAATTC
** *
19535 ACAGAATTTCAAAAACAGAATAACTAAATTAAATAA
1 ACAGAATTGAAAAAACAGAATTACTAAATTAAATAA
*
19571 GCAGAATTGAAAAAACAGAATTACTAAATTACAA-AA
1 ACAGAATTGAAAAAACAGAATTACTAAATTA-AATAA
19607 ACAGAATTGAA
1 ACAGAATTGAA
19618 TTCACAGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
36 39 0.95
37 2 0.05
ACGTcount: A:0.59, C:0.11, G:0.10, T:0.20
Consensus pattern (36 bp):
ACAGAATTGAAAAAACAGAATTACTAAATTAAATAA
Found at i:19639 original size:86 final size:86
Alignment explanation
Indices: 19409--19680 Score: 490
Period size: 86 Copynumber: 3.2 Consensus size: 86
19399 ACCTGAAATG
* *
19409 AAAACAGAATTACTAAATTACAAAAACAGAATTGAATTCACATAATTTCAAAAACAAAATAACTG
1 AAAACAGAATTACTAAATTACAAAAACAGAATTGAATTCACAGAATTTCAAAAACAGAATAACTG
*
19474 AATTAAAAAAGCAGAATTGAA
66 AATTAAATAAGCAGAATTGAA
*
19495 AAAACAGAATTACTAAATTTAAAAAAACAGAATTGAATTCACAGAATTTCAAAAACAGAATAACT
1 AAAACAGAATTACTAAA-TTACAAAAACAGAATTGAATTCACAGAATTTCAAAAACAGAATAACT
*
19560 AAATTAAATAAGCAGAATTGAA
65 GAATTAAATAAGCAGAATTGAA
19582 AAAACAGAATTACTAAATTACAAAAACAGAATTGAATTCACAGAATTTCAAAAACAGAATAACTG
1 AAAACAGAATTACTAAATTACAAAAACAGAATTGAATTCACAGAATTTCAAAAACAGAATAACTG
19647 AATTAAATAAGCAGAATTGAA
66 AATTAAATAAGCAGAATTGAA
19668 AAAACAGAATTAC
1 AAAACAGAATTAC
19681 AGAAATTGAG
Statistics
Matches: 178, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
86 97 0.54
87 81 0.46
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.22
Consensus pattern (86 bp):
AAAACAGAATTACTAAATTACAAAAACAGAATTGAATTCACAGAATTTCAAAAACAGAATAACTG
AATTAAATAAGCAGAATTGAA
Found at i:19675 original size:50 final size:50
Alignment explanation
Indices: 19572--19678 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
19562 ATTAAATAAG
* ***
19572 CAGAATTGAAAAAACAGAATTACTAAATTACAAAAACAGAATTGAATTCA
1 CAGAATTGAAAAAACAGAATAACTAAATTACAAAAACAGAATTGAAAAAA
** * *
19622 CAGAATTTCAAAAACAGAATAACTGAATTA-AATAAGCAGAATTGAAAAAA
1 CAGAATTGAAAAAACAGAATAACTAAATTACAA-AAACAGAATTGAAAAAA
19672 CAGAATT
1 CAGAATT
19679 ACAGAAATTG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 2 0.04
50 46 0.96
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.21
Consensus pattern (50 bp):
CAGAATTGAAAAAACAGAATAACTAAATTACAAAAACAGAATTGAAAAAA
Found at i:21908 original size:13 final size:13
Alignment explanation
Indices: 21890--21920 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
21880 CTCATTTCTC
21890 AAGCACTACAGGT
1 AAGCACTACAGGT
21903 AAGCACTACAGGT
1 AAGCACTACAGGT
21916 AAGCA
1 AAGCA
21921 GTAAGCACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.13
Consensus pattern (13 bp):
AAGCACTACAGGT
Found at i:22797 original size:2 final size:2
Alignment explanation
Indices: 22790--22828 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
22780 AATAACTTAA
22790 AT AT AT AT AT AT A- 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 AT AT
22829 TACACAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22803 original size:19 final size:19
Alignment explanation
Indices: 22787--22827 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
22777 AGAAATAACT
22787 TAAATATATATATATAATA
1 TAAATATATATATATAATA
*
22806 TATATATATATATATATATA
1 TAAATATATATATATA-ATA
22826 TA
1 TA
22828 TTACACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATATATATATATAATA
Found at i:22998 original size:13 final size:13
Alignment explanation
Indices: 22980--23012 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
22970 ATTAATTCGG
22980 TTTCGGTCGGTTT
1 TTTCGGTCGGTTT
22993 TTTCGGTCGGTTT
1 TTTCGGTCGGTTT
23006 TTTCGGT
1 TTTCGGT
23013 TAAACCGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.30, T:0.55
Consensus pattern (13 bp):
TTTCGGTCGGTTT
Found at i:24521 original size:21 final size:20
Alignment explanation
Indices: 24479--24525 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
24469 TTACTCTCCT
*
24479 TTTTTAATTACCGAATTCCA
1 TTTTTAATTACCAAATTCCA
* *
24499 TTTTTAATTTCCAAGATTTCA
1 TTTTTAATTACCAA-ATTCCA
24520 TTTTTA
1 TTTTTA
24526 CCTCTTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTTTAATTACCAAATTCCA
Found at i:24618 original size:32 final size:32
Alignment explanation
Indices: 24557--24618 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
24547 ATATTCCATA
*
24557 TTACCAAATTCCATTTCTTTACTCCCTTTTAC
1 TTACCAAATTCCATTTCTTTAATCCCTTTTAC
* *
24589 TTACCAATTTTCATTTC-TTAATCCTCTTTT
1 TTACCAAATTCCATTTCTTTAATCC-CTTTT
24619 TTTATTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.21, C:0.27, G:0.00, T:0.52
Consensus pattern (32 bp):
TTACCAAATTCCATTTCTTTAATCCCTTTTAC
Found at i:24737 original size:26 final size:26
Alignment explanation
Indices: 24708--24803 Score: 81
Period size: 26 Copynumber: 3.6 Consensus size: 26
24698 AAATTATACC
24708 CTTTAATTACCAAATTTTCTCTTACT
1 CTTTAATTACCAAATTTTCTCTTACT
*
24734 CTTTAATTGTCC-AATTTTAC-CAATTACT
1 CTTTAATT-ACCAAATTTT-CTC--TTACT
* * *
24762 CTTTAATCACCCAA-TTTCATTTTACT
1 CTTTAATTACCAAATTTTC-TCTTACT
*
24788 TTTTAATTACCAAATT
1 CTTTAATTACCAAATT
24804 AACCAATTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
26 32 0.58
27 9 0.16
28 14 0.25
ACGTcount: A:0.29, C:0.22, G:0.01, T:0.48
Consensus pattern (26 bp):
CTTTAATTACCAAATTTTCTCTTACT
Found at i:24812 original size:34 final size:34
Alignment explanation
Indices: 24772--24896 Score: 115
Period size: 34 Copynumber: 3.9 Consensus size: 34
24762 CTTTAATCAC
24772 CCAATTTCATTTTACTTTTTAATTACCAAATTAA
1 CCAATTTCATTTTACTTTTTAATTACCAAATTAA
* * * *
24806 CCAATTTCCTTTTAC--TCT--TT----GATT-G
1 CCAATTTCATTTTACTTTTTAATTACCAAATTAA
*
24831 CCAAGTTCATTTTACTTTTTAATTACCAAATTAA
1 CCAATTTCATTTTACTTTTTAATTACCAAATTAA
* * *
24865 CCAGTTTCCTTTTACTCTTTAATTACCAAATT
1 CCAATTTCATTTTACTTTTTAATTACCAAATT
24897 CTTTTTAATT
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
25 13 0.19
26 3 0.04
27 2 0.03
29 2 0.03
30 2 0.03
32 2 0.03
33 3 0.04
34 42 0.61
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47
Consensus pattern (34 bp):
CCAATTTCATTTTACTTTTTAATTACCAAATTAA
Found at i:24859 original size:25 final size:25
Alignment explanation
Indices: 24800--24859 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
24790 TTAATTACCA
* *
24800 AATTAACCAATTTCCTTTTACTCTTT
1 AATT-ACCAAGTTCATTTTACTCTTT
* * *
24826 GATTGCCAAGTTCATTTTACTTTTT
1 AATTACCAAGTTCATTTTACTCTTT
24851 AATTACCAA
1 AATTACCAA
24860 ATTAACCAGT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
25 24 0.89
26 3 0.11
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (25 bp):
AATTACCAAGTTCATTTTACTCTTT
Found at i:24889 original size:26 final size:26
Alignment explanation
Indices: 24859--25153 Score: 135
Period size: 25 Copynumber: 11.4 Consensus size: 26
24849 TTAATTACCA
*
24859 AATTAACCAGTTTCCTTTTACTCTTT
1 AATTAACCAATTTCCTTTTACTCTTT
* * * **
24885 AATT-ACCAAATTCTTTTTAAT-TACCA
1 AATTAACCAATTTCCTTTTACTCT--TT
*
24911 AATTAACCAATTTACTTTTACTCTTT
1 AATTAACCAATTTCCTTTTACTCTTT
* * * **
24937 AATT-ACCAAATTCTTTTTAAT-TACCA
1 AATTAACCAATTTCCTTTTACTCT--TT
*
24963 AATTAACCAATTTACTTTTACTCTTT
1 AATTAACCAATTTCCTTTTACTCTTT
* * * **
24989 AATT-ACCAAATTCTTTTTAAT-TACCA
1 AATTAACCAATTTCCTTTTACTCT--TT
* *
25015 AATTAACCAATTTACTTTTACTCCTT
1 AATTAACCAATTTCCTTTTACTCTTT
* * * **
25041 AATT-ACCAAATTCTTTTTAAT-TACCA
1 AATTAACCAATTTCCTTTTACTCT--TT
*
25067 AATTAACCAATTTACTTTTACTCTTT
1 AATTAACCAATTTCCTTTTACTCTTT
* * * **
25093 AATT-ACCAAATTCTTTTTAAT-TACCA
1 AATTAACCAATTTCCTTTTACTCT--TT
*
25119 AATTAACCAATTTACTTTTACTCTTT
1 AATTAACCAATTTCCTTTTACTCTTT
25145 AATT-ACCAA
1 AATTAACCAA
25154 ATCAACCAAT
Statistics
Matches: 187, Mismatches: 62, Indels: 41
0.64 0.21 0.14
Matches are distributed among these distances:
24 4 0.02
25 70 0.37
26 44 0.24
27 65 0.35
28 4 0.02
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.45
Consensus pattern (26 bp):
AATTAACCAATTTCCTTTTACTCTTT
Found at i:24902 original size:52 final size:52
Alignment explanation
Indices: 24845--25155 Score: 595
Period size: 52 Copynumber: 6.0 Consensus size: 52
24835 GTTCATTTTA
* *
24845 CTTTTTAATTACCAAATTAACCAGTTTCCTTTTACTCTTTAATTACCAAATT
1 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
24897 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
1 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
24949 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
1 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
*
25001 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCCTTAATTACCAAATT
1 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
25053 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
1 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
25105 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAAT
1 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAAT
25156 CAACCAATTT
Statistics
Matches: 255, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 255 1.00
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (52 bp):
CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
Found at i:24997 original size:104 final size:104
Alignment explanation
Indices: 24786--25155 Score: 623
Period size: 104 Copynumber: 3.5 Consensus size: 104
24776 TTTCATTTTA
* * *
24786 CTTTTTAATTACCAAATTAACCAATTTCCTTTTACTCTTTGATTGCCAAGTTCATTTTACTTTTT
1 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAA----A--TT-CTTTTT
* *
24851 AATTACCAAATTAACCAGTTTCCTTTTACTCTTTAATTACCAAATT
59 AATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
24897 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATTCTTTTTAATTACC
1 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATTCTTTTTAATTACC
24962 AAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
66 AAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
*
25001 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCCTTAATTACCAAATTCTTTTTAATTACC
1 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATTCTTTTTAATTACC
25066 AAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
66 AAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
25105 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAAT
1 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAAT
25156 CAACCAATTT
Statistics
Matches: 252, Mismatches: 7, Indels: 7
0.95 0.03 0.03
Matches are distributed among these distances:
104 203 0.81
105 2 0.01
107 1 0.00
111 46 0.18
ACGTcount: A:0.33, C:0.20, G:0.01, T:0.46
Consensus pattern (104 bp):
CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATTCTTTTTAATTACC
AAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
Found at i:25043 original size:156 final size:157
Alignment explanation
Indices: 24786--25155 Score: 625
Period size: 156 Copynumber: 2.3 Consensus size: 157
24776 TTTCATTTTA
* * *
24786 CTTTTTAATTACCAAATTAACCAATTTCCTTTTACTCTTTGATTGCCAAGTTCATTTTACTTTTT
1 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAA----A--TTACTTTTT
* * *
24851 AATTACCAAATTAACCAGTTTCCTTTTACTCTTTAATTACCAAATTCTTTTTAATTACCAAATTA
60 AATTACCAAATTAACCAATTTACTTTTACTCCTTAATTACCAAATTCTTTTTAATTACCAAATTA
24916 ACCAATTTACTTTTACTCTTTAATTACCAAATT
125 ACCAATTTACTTTTACTCTTTAATTACCAAATT
24949 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT-CTTTTTAATTAC
1 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATTACTTTTTAATTAC
25013 CAAATTAACCAATTTACTTTTACTCCTTAATTACCAAATTCTTTTTAATTACCAAATTAACCAAT
66 CAAATTAACCAATTTACTTTTACTCCTTAATTACCAAATTCTTTTTAATTACCAAATTAACCAAT
25078 TTACTTTTACTCTTTAATTACCAAATT
131 TTACTTTTACTCTTTAATTACCAAATT
25105 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAAT
1 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAAT
25156 CAACCAATTT
Statistics
Matches: 201, Mismatches: 6, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
156 152 0.76
157 2 0.01
159 1 0.00
163 46 0.23
ACGTcount: A:0.33, C:0.20, G:0.01, T:0.46
Consensus pattern (157 bp):
CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATTACTTTTTAATTAC
CAAATTAACCAATTTACTTTTACTCCTTAATTACCAAATTCTTTTTAATTACCAAATTAACCAAT
TTACTTTTACTCTTTAATTACCAAATT
Found at i:25149 original size:34 final size:34
Alignment explanation
Indices: 25108--25247 Score: 207
Period size: 34 Copynumber: 4.2 Consensus size: 34
25098 CCAAATTCTT
25108 TTTAATTACCAAATTAACCAATTTACTTTTACTC
1 TTTAATTACCAAATTAACCAATTTACTTTTACTC
*
25142 TTTAATTACCAAATCAACCAATTTACTTTTACTC
1 TTTAATTACCAAATTAACCAATTTACTTTTACTC
25176 TTTAATTACCAAATTAACCAATTTACTTTTACTC
1 TTTAATTACCAAATTAACCAATTTACTTTTACTC
* * * *
25210 TTTCATTGCCAAGTT---CATTTTAC-TTTACTC
1 TTTAATTACCAAATTAACCAATTTACTTTTACTC
25240 TTTAATTA
1 TTTAATTA
25248 GCAAGTTCAT
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
30 13 0.13
31 7 0.07
34 78 0.80
ACGTcount: A:0.32, C:0.21, G:0.01, T:0.46
Consensus pattern (34 bp):
TTTAATTACCAAATTAACCAATTTACTTTTACTC
Found at i:25239 original size:30 final size:30
Alignment explanation
Indices: 25163--25264 Score: 107
Period size: 30 Copynumber: 3.2 Consensus size: 30
25153 AATCAACCAA
* * *
25163 TTTACTTTTACTCTTTAATTACCAAATTAACCAA
1 TTTAC-TTTACTCTTTAATTAGCAAGTT---CAT
*
25197 TTTACTTTTACTCTTTCATT-GCCAAGTTCAT
1 TTTAC-TTTACTCTTTAATTAG-CAAGTTCAT
25228 TTTACTTTACTCTTTAATTAGCAAGTTCAT
1 TTTACTTTACTCTTTAATTAGCAAGTTCAT
25258 TTTACTT
1 TTTACTT
25265 CTTAATTTCC
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
30 29 0.48
31 8 0.13
34 24 0.39
ACGTcount: A:0.26, C:0.20, G:0.04, T:0.50
Consensus pattern (30 bp):
TTTACTTTACTCTTTAATTAGCAAGTTCAT
Found at i:28137 original size:9 final size:9
Alignment explanation
Indices: 28123--28155 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
28113 TTAAGGATAG
28123 AAAAGAAGA
1 AAAAGAAGA
28132 AAAAGAAGA
1 AAAAGAAGA
28141 AAAAGAAGA
1 AAAAGAAGA
28150 AAAAGA
1 AAAAGA
28156 GATTGTACCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAGAAGA
Found at i:30181 original size:28 final size:27
Alignment explanation
Indices: 30128--30181 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
30118 GTTCGAAATG
* * *
30128 GTTGGACCCTTATTTGACATTTTTTTA
1 GTTGGACCCTTAATTGACAATATTTTA
*
30155 GTTGGTACCCTTAATTGAGAATATTTT
1 GTTGG-ACCCTTAATTGACAATATTTT
30182 GAAAGGTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (27 bp):
GTTGGACCCTTAATTGACAATATTTTA
Found at i:32204 original size:13 final size:13
Alignment explanation
Indices: 32174--32215 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
32164 TCTGACTATC
*
32174 TTGGTTTATT-GT
1 TTGGTTTATTACT
32186 TCTGGTTTATTACT
1 T-TGGTTTATTACT
*
32200 TTGGTTTATGACT
1 TTGGTTTATTACT
32213 TTG
1 TTG
32216 ATTATGATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 1 0.04
13 23 0.88
14 2 0.08
ACGTcount: A:0.12, C:0.07, G:0.21, T:0.60
Consensus pattern (13 bp):
TTGGTTTATTACT
Found at i:39840 original size:15 final size:15
Alignment explanation
Indices: 39820--39850 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
39810 ACAGAGGTTG
39820 AAAGAAAGCAATTAT
1 AAAGAAAGCAATTAT
39835 AAAGAAAGCAATTAT
1 AAAGAAAGCAATTAT
39850 A
1 A
39851 CTAGAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.13, T:0.19
Consensus pattern (15 bp):
AAAGAAAGCAATTAT
Done.