Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 21 of 120
Found at i:6145861 original size:19 final size:19
Alignment explanation
Indices: 6145833--6145869 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6145823 AAAACCCTAA
6145833 AAACTAAAACCCTAAATAT
1 AAACTAAAACCCTAAATAT
*
6145852 AAACTCAAACCCTAAATA
1 AAACTAAAACCCTAAATA
6145870 CAAATCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.19
Consensus pattern (19 bp):
AAACTAAAACCCTAAATAT
Found at i:6146030 original size:21 final size:21
Alignment explanation
Indices: 6145973--6146032 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
6145963 CACAAATAAT
*
6145973 AAACTATACACATAAA-CCCTA
1 AAACTAGA-ACATAAACCCCTA
*
6145994 AAACTAGAA-TTAAAACCCCTA
1 AAACTAGAACAT-AAACCCCTA
6146015 AAACCTA-AACATAAACCC
1 AAA-CTAGAACATAAACCC
6146033 TCATTATATC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.03
20 4 0.12
21 23 0.72
22 4 0.12
ACGTcount: A:0.53, C:0.28, G:0.02, T:0.17
Consensus pattern (21 bp):
AAACTAGAACATAAACCCCTA
Found at i:6146154 original size:7 final size:7
Alignment explanation
Indices: 6146144--6146183 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
6146134 CCTAAACTCG
6146144 AACACTA
1 AACACTA
6146151 AACACTA
1 AACACTA
*
6146158 AACCCTA
1 AACACTA
6146165 AACAC-A
1 AACACTA
*
6146171 AACCCTA
1 AACACTA
6146178 AACACT
1 AACACT
6146184 CTAATTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.53, C:0.35, G:0.00, T:0.12
Consensus pattern (7 bp):
AACACTA
Found at i:6146167 original size:14 final size:14
Alignment explanation
Indices: 6146148--6146183 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
6146138 AACTCGAACA
6146148 CTAAACACTAAACC
1 CTAAACACTAAACC
6146162 CTAAACAC-AAACC
1 CTAAACACTAAACC
6146175 CTAAACACT
1 CTAAACACT
6146184 CTAATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (14 bp):
CTAAACACTAAACC
Found at i:6146175 original size:13 final size:13
Alignment explanation
Indices: 6146134--6146182 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
6146124 AAACCATAAA
* *
6146134 CCTAAACTCGAAC
1 CCTAAACACAAAC
*
6146147 ACTAAACACTAAAC
1 CCTAAACAC-AAAC
6146161 CCTAAACACAAAC
1 CCTAAACACAAAC
6146174 CCTAAACAC
1 CCTAAACAC
6146183 TCTAATTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 20 0.65
14 11 0.35
ACGTcount: A:0.49, C:0.37, G:0.02, T:0.12
Consensus pattern (13 bp):
CCTAAACACAAAC
Found at i:6146178 original size:27 final size:26
Alignment explanation
Indices: 6146130--6146183 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
6146120 ATATAAACCA
* *
6146130 TAAACCTAAACTCGAACACTAAACAC
1 TAAACCTAAACACAAACACTAAACAC
*
6146156 TAAACCCTAAACACAAACCCTAAACAC
1 TAAA-CCTAAACACAAACACTAAACAC
6146183 T
1 T
6146184 CTAATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.50, C:0.33, G:0.02, T:0.15
Consensus pattern (26 bp):
TAAACCTAAACACAAACACTAAACAC
Found at i:6146290 original size:20 final size:21
Alignment explanation
Indices: 6146267--6146310 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
6146257 CCTTAAACTC
*
6146267 AAACCATCAACCCTAAA-TAT
1 AAACCATAAACCCTAAATTAT
* *
6146287 AAACCGTAAATCCTAAATTAT
1 AAACCATAAACCCTAAATTAT
6146308 AAA
1 AAA
6146311 TACTAAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.52, C:0.23, G:0.02, T:0.23
Consensus pattern (21 bp):
AAACCATAAACCCTAAATTAT
Found at i:6146387 original size:7 final size:7
Alignment explanation
Indices: 6146368--6146436 Score: 61
Period size: 7 Copynumber: 10.1 Consensus size: 7
6146358 CAATTAAATT
*
6146368 CTAAATC
1 CTAAACC
6146375 CTAAACC
1 CTAAACC
*
6146382 CTAAACA
1 CTAAACC
*
6146389 TTAAACC
1 CTAAACC
*
6146396 TTAAACC
1 CTAAACC
6146403 CTAAA-C
1 CTAAACC
*
6146409 CTAAACT
1 CTAAACC
*
6146416 C-AAACA
1 CTAAACC
*
6146422 CTAAACA
1 CTAAACC
6146429 CTAAACC
1 CTAAACC
6146436 C
1 C
6146437 AAAATGTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
6 11 0.21
7 41 0.79
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:6146393 original size:21 final size:21
Alignment explanation
Indices: 6146376--6146435 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
6146366 TTCTAAATCC
6146376 TAAACCCTAAACATTAAACCT
1 TAAACCCTAAACATTAAACCT
*
6146397 TAAACCCTAAAC-CTAAA-CT
1 TAAACCCTAAACATTAAACCT
* * *
6146416 CAAACACTAAACACTAAACC
1 TAAACCCTAAACATTAAACC
6146436 CAAAATGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.35
20 9 0.26
21 13 0.38
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (21 bp):
TAAACCCTAAACATTAAACCT
Found at i:6155849 original size:19 final size:19
Alignment explanation
Indices: 6155801--6155851 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
6155791 NNNACCCTAA
* *
6155801 AAACTCAAACCCTAAATAT
1 AAACTCAAACCCTAAACAC
6155820 AAACTCAAACCCTAAACAC
1 AAACTCAAACCCTAAACAC
6155839 AAA-TCATAACCCT
1 AAACTCA-AACCCT
6155852 TAATCCCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 3 0.10
19 26 0.90
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (19 bp):
AAACTCAAACCCTAAACAC
Found at i:6156124 original size:7 final size:7
Alignment explanation
Indices: 6156112--6156151 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
6156102 TCTAAACTCG
6156112 AACACTA
1 AACACTA
6156119 AACACTA
1 AACACTA
*
6156126 AACCCTA
1 AACACTA
6156133 AACAC-A
1 AACACTA
*
6156139 AACCCTA
1 AACACTA
6156146 AACACT
1 AACACT
6156152 CTAATTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.53, C:0.35, G:0.00, T:0.12
Consensus pattern (7 bp):
AACACTA
Found at i:6156143 original size:13 final size:14
Alignment explanation
Indices: 6156116--6156151 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
6156106 AACTCGAACA
6156116 CTAAACACTAAACC
1 CTAAACACTAAACC
6156130 CTAAACAC-AAACC
1 CTAAACACTAAACC
6156143 CTAAACACT
1 CTAAACACT
6156152 CTAATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (14 bp):
CTAAACACTAAACC
Found at i:6156446 original size:40 final size:40
Alignment explanation
Indices: 6156402--6156520 Score: 116
Period size: 40 Copynumber: 3.0 Consensus size: 40
6156392 CACTAAACAC
6156402 TAAAC-CCAAAATGTAAATCATAAA-AAGTAAATATAAACCT
1 TAAACACCAAAAT-TAAATCATAAACAA-TAAATATAAACCT
* * * *
6156442 TAAACACTATAATTATATCATAAACCATAAATATAAACCT
1 TAAACACCAAAATTAAATCATAAACAATAAATATAAACCT
* * * ** *
6156482 TAAACACTATAATCATTTCATAAACCATAAATATAAACC
1 TAAACACCAAAATTAAATCATAAACAATAAATATAAACC
6156521 CTACACCCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
40 65 0.92
41 6 0.08
ACGTcount: A:0.54, C:0.18, G:0.02, T:0.27
Consensus pattern (40 bp):
TAAACACCAAAATTAAATCATAAACAATAAATATAAACCT
Found at i:6156485 original size:20 final size:20
Alignment explanation
Indices: 6156429--6156578 Score: 73
Period size: 20 Copynumber: 7.6 Consensus size: 20
6156419 TCATAAAAAG
6156429 TAAATATAAACCTTAAA-CA
1 TAAATATAAACCTTAAACCA
* * *
6156448 CTATAAT-TATATCATAAACCA
1 -TA-AATATAAACCTTAAACCA
6156469 TAAATATAAACCTTAAA-CA
1 TAAATATAAACCTTAAACCA
** *
6156488 CTATAATCAT--TTCATAAACCA
1 -TA-AAT-ATAAACCTTAAACCA
* * *
6156509 TAAATATAAACCCTACACCC
1 TAAATATAAACCTTAAACCA
**
6156529 T-AATA-AAAAATTAAACCA
1 TAAATATAAACCTTAAACCA
*
6156547 TAAACATAAACCCTTAAA-CA
1 TAAATATAAA-CCTTAAACCA
*
6156567 TAAGTATAAACC
1 TAAATATAAACC
6156579 CTAATTCTAT
Statistics
Matches: 94, Mismatches: 24, Indels: 25
0.66 0.17 0.17
Matches are distributed among these distances:
18 11 0.12
19 17 0.18
20 49 0.52
21 15 0.16
22 2 0.02
ACGTcount: A:0.53, C:0.21, G:0.01, T:0.26
Consensus pattern (20 bp):
TAAATATAAACCTTAAACCA
Found at i:6156615 original size:7 final size:7
Alignment explanation
Indices: 6156605--6156629 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6156595 CTATAACCTC
6156605 AAACACT
1 AAACACT
6156612 AAACACT
1 AAACACT
6156619 AAACACT
1 AAACACT
6156626 AAAC
1 AAAC
6156630 CTTAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACACT
Found at i:6156635 original size:14 final size:14
Alignment explanation
Indices: 6156599--6156663 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
6156589 CCTAACCTAT
*
6156599 AACCTCAAACACTA
1 AACCTTAAACACTA
6156613 AACAC-TAAACACTA
1 AAC-CTTAAACACTA
*
6156627 AACCTTAAATTA-TA
1 AACCTTAAA-CACTA
* *
6156641 AACCATAAACCCTA
1 AACCTTAAACACTA
6156655 AACCTTAAA
1 AACCTTAAA
6156664 ACCATAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 1 0.02
14 38 0.93
15 2 0.05
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (14 bp):
AACCTTAAACACTA
Found at i:6156732 original size:20 final size:20
Alignment explanation
Indices: 6156696--6156793 Score: 60
Period size: 20 Copynumber: 4.8 Consensus size: 20
6156686 CTTACAATTA
6156696 AATA-TAAACCCTAAAACTAT
1 AATACTAAACCCT-AAACTAT
**
6156716 AATACTAAACCCTAAACCCT
1 AATACTAAACCCTAAACTAT
* **
6156736 AA-CCATAAACAATAAACTAT
1 AATAC-TAAACCCTAAACTAT
*
6156756 AA-ACATAAACCCTAAAACTAG
1 AATAC-TAAACCCT-AAACTAT
*
6156777 AATTA-AAAACCCTAAAC
1 AA-TACTAAACCCTAAAC
6156794 CTAAACCCTA
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
19 1 0.02
20 36 0.59
21 23 0.38
23 1 0.02
ACGTcount: A:0.55, C:0.24, G:0.01, T:0.19
Consensus pattern (20 bp):
AATACTAAACCCTAAACTAT
Found at i:6157509 original size:7 final size:7
Alignment explanation
Indices: 6157484--6157572 Score: 81
Period size: 7 Copynumber: 12.4 Consensus size: 7
6157474 ATAATCCCTA
6157484 AAACCTT
1 AAACCTT
*
6157491 AAATCCTA
1 AAA-CCTT
6157499 AAACCTT
1 AAACCTT
*
6157506 AAACCCT
1 AAACCTT
*
6157513 AAACCCT
1 AAACCTT
*
6157520 AAACCCTA
1 AAA-CCTT
6157528 AAACC-T
1 AAACCTT
*
6157534 AAACCCTA
1 AAA-CCTT
*
6157542 AAACCCT
1 AAACCTT
6157549 AAACCTT
1 AAACCTT
6157556 AAACCTT
1 AAACCTT
*
6157563 AAACCCT
1 AAACCTT
6157570 AAA
1 AAA
6157573 ATAAAAACCT
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
6 3 0.04
7 50 0.75
8 14 0.21
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (7 bp):
AAACCTT
Found at i:6157522 original size:14 final size:14
Alignment explanation
Indices: 6157479--6157572 Score: 107
Period size: 14 Copynumber: 6.5 Consensus size: 14
6157469 NNNNNATAAT
*
6157479 CCCTAAAACCTTAAA
1 CCCT-AAACCCTAAA
* *
6157494 TCCTAAAACCTTAAA
1 CCCT-AAACCCTAAA
6157509 CCCTAAACCCTAAA
1 CCCTAAACCCTAAA
*
6157523 CCCTAAAACCTAAA
1 CCCTAAACCCTAAA
6157537 CCCTAAAACCCTAAA
1 CCCT-AAACCCTAAA
* *
6157552 CCTTAAACCTTAAA
1 CCCTAAACCCTAAA
6157566 CCCTAAA
1 CCCTAAA
6157573 ATAAAAACCT
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
14 41 0.59
15 29 0.41
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (14 bp):
CCCTAAACCCTAAA
Found at i:6157522 original size:29 final size:29
Alignment explanation
Indices: 6157479--6157573 Score: 140
Period size: 29 Copynumber: 3.3 Consensus size: 29
6157469 NNNNNATAAT
*
6157479 CCCTAAAACCTTAAATCCTAAAACCTTAAA
1 CCCTAAAACCCTAAA-CCTAAAACCTTAAA
6157509 CCCT-AAACCCTAAACCCTAAAACC-TAAA
1 CCCTAAAACCCTAAA-CCTAAAACCTTAAA
*
6157537 CCCTAAAACCCTAAACCTTAAACCTTAAA
1 CCCTAAAACCCTAAACCTAAAACCTTAAA
6157566 CCCTAAAA
1 CCCTAAAA
6157574 TAAAAACCTA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
28 16 0.27
29 40 0.67
30 4 0.07
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (29 bp):
CCCTAAAACCCTAAACCTAAAACCTTAAA
Found at i:6157768 original size:20 final size:21
Alignment explanation
Indices: 6157745--6157794 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
6157735 CCTTAAACTC
*
6157745 AAACCATCAACCCTAAA-TAT
1 AAACCATAAACCCTAAATTAT
* *
6157765 AAACCGTAAATCCTAAATTAT
1 AAACCATAAACCCTAAATTAT
6157786 AAACC-TAAA
1 AAACCATAAA
6157795 ACCGTAAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.22
Consensus pattern (21 bp):
AAACCATAAACCCTAAATTAT
Found at i:6157802 original size:21 final size:20
Alignment explanation
Indices: 6157756--6157802 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
6157746 AACCATCAAC
*
6157756 CCTAAATATAAACCGTAAAT
1 CCTAAATATAAACCGTAAAA
6157776 CCTAAATTATAAACC-TAAAA
1 CCTAAA-TATAAACCGTAAAA
6157796 CCGTAAA
1 CC-TAAA
6157803 CCCTAAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.23
Consensus pattern (20 bp):
CCTAAATATAAACCGTAAAA
Found at i:6157944 original size:20 final size:20
Alignment explanation
Indices: 6157901--6157944 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
6157891 GCATCAAACC
*
6157901 TAAACACTAAATCTAAACTT
1 TAAACACTAAATCTAAAATT
*
6157921 TAAACCCTAAAT-TAAAATT
1 TAAACACTAAATCTAAAATT
6157940 ATAAA
1 -TAAA
6157945 TTATAAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAACACTAAATCTAAAATT
Found at i:6158128 original size:20 final size:20
Alignment explanation
Indices: 6158100--6158142 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
6158090 TAAACCTTTT
*
6158100 AACCCTAAA-ATTAAACATTA
1 AACCATAAACATTAAAC-TTA
*
6158120 AACCATAAACCTTAAACTTA
1 AACCATAAACATTAAACTTA
6158140 AAC
1 AAC
6158143 ACTAAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (20 bp):
AACCATAAACATTAAACTTA
Found at i:6158176 original size:48 final size:48
Alignment explanation
Indices: 6158118--6158210 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
6158108 AATTAAACAT
* * * *
6158118 TAAACCATAAACCTTAAACTTAAACACTAAAAACTAGACTCTAAATGA
1 TAAACCATAAACCCTAAACTTAAACAATAAAAACTAAACCCTAAATGA
* *
6158166 TAAACTATAAACCCTAAACTTAAACAATAAATACTAAACCCTAAA
1 TAAACCATAAACCCTAAACTTAAACAATAAAAACTAAACCCTAAA
6158211 AACTAAACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.54, C:0.22, G:0.02, T:0.23
Consensus pattern (48 bp):
TAAACCATAAACCCTAAACTTAAACAATAAAAACTAAACCCTAAATGA
Found at i:6158592 original size:7 final size:7
Alignment explanation
Indices: 6158580--6158619 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
6158570 TCTAAACTCG
6158580 AACACTA
1 AACACTA
6158587 AACACTA
1 AACACTA
*
6158594 AACCCTA
1 AACACTA
6158601 AACAC-A
1 AACACTA
*
6158607 AACCCTA
1 AACACTA
6158614 AACACT
1 AACACT
6158620 CTAATTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.53, C:0.35, G:0.00, T:0.12
Consensus pattern (7 bp):
AACACTA
Found at i:6158611 original size:13 final size:14
Alignment explanation
Indices: 6158584--6158619 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
6158574 AACTCGAACA
6158584 CTAAACACTAAACC
1 CTAAACACTAAACC
6158598 CTAAACAC-AAACC
1 CTAAACACTAAACC
6158611 CTAAACACT
1 CTAAACACT
6158620 CTAATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (14 bp):
CTAAACACTAAACC
Found at i:6158774 original size:28 final size:26
Alignment explanation
Indices: 6158715--6158774 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
6158705 CCATCAACCC
* *
6158715 AAAATATAAACCGTAAATCCTAAATT
1 AAAATATAAACCGTAAACCCTAAACT
*
6158741 ATAAATACTAAACCTTAAACCCTAAAACT
1 A-AAATA-TAAACCGTAAACCCT-AAACT
6158770 AAAAT
1 AAAAT
6158775 CACAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.04
27 5 0.18
28 17 0.61
29 5 0.18
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (26 bp):
AAAATATAAACCGTAAACCCTAAACT
Found at i:6158820 original size:21 final size:21
Alignment explanation
Indices: 6158810--6158869 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
6158800 TTCTAAATCC
6158810 TAAACCCTAAACATTAAACCT
1 TAAACCCTAAACATTAAACCT
*
6158831 TAAACCCTAAAC-CTAAA-CT
1 TAAACCCTAAACATTAAACCT
* * *
6158850 CAAACACTAAACACTAAACC
1 TAAACCCTAAACATTAAACC
6158870 CAAAATGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.35
20 9 0.26
21 13 0.38
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (21 bp):
TAAACCCTAAACATTAAACCT
Found at i:6158821 original size:7 final size:7
Alignment explanation
Indices: 6158802--6158870 Score: 61
Period size: 7 Copynumber: 10.1 Consensus size: 7
6158792 CAATTAAATT
*
6158802 CTAAATC
1 CTAAACC
6158809 CTAAACC
1 CTAAACC
*
6158816 CTAAACA
1 CTAAACC
*
6158823 TTAAACC
1 CTAAACC
*
6158830 TTAAACC
1 CTAAACC
6158837 CTAAA-C
1 CTAAACC
*
6158843 CTAAACT
1 CTAAACC
*
6158850 C-AAACA
1 CTAAACC
*
6158856 CTAAACA
1 CTAAACC
6158863 CTAAACC
1 CTAAACC
6158870 C
1 C
6158871 AAAATGTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
6 11 0.21
7 41 0.79
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:6159854 original size:13 final size:13
Alignment explanation
Indices: 6159836--6159860 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6159826 AAACTTAACA
6159836 ATAAACCATAAAT
1 ATAAACCATAAAT
6159849 ATAAACCATAAA
1 ATAAACCATAAA
6159861 CCCTAAATCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (13 bp):
ATAAACCATAAAT
Found at i:6159872 original size:7 final size:7
Alignment explanation
Indices: 6159850--6159901 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
6159840 ACCATAAATA
*
6159850 TAAACCA
1 TAAACCC
6159857 TAAACCC
1 TAAACCC
*
6159864 TAAATCC
1 TAAACCC
**
6159871 TAAAAAC
1 TAAACCC
*
6159878 TAAACCT
1 TAAACCC
*
6159885 TAAACAC
1 TAAACCC
6159892 TAAACCC
1 TAAACCC
6159899 TAA
1 TAA
6159902 TCACAAATAA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:6159874 original size:14 final size:13
Alignment explanation
Indices: 6159818--6159897 Score: 56
Period size: 14 Copynumber: 6.0 Consensus size: 13
6159808 CGATAAACTA
*
6159818 TAAACCCTAAA-C
1 TAAACACTAAACC
* *
6159830 TTAACAATAAACC
1 TAAACACTAAACC
*
6159843 ATAAATA-TAAACC
1 -TAAACACTAAACC
*
6159856 ATAAACCCTAAATCC
1 -TAAACACTAAA-CC
*
6159871 TAAAAACTAAACC
1 TAAACACTAAACC
6159884 TTAAACACTAAACC
1 -TAAACACTAAACC
6159898 CTAATCACAA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
12 8 0.15
13 14 0.26
14 29 0.55
15 2 0.04
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAACACTAAACC
Found at i:6159951 original size:15 final size:15
Alignment explanation
Indices: 6159931--6160037 Score: 148
Period size: 15 Copynumber: 7.3 Consensus size: 15
6159921 CACATAACTT
* *
6159931 TAAAACCATAATCCC
1 TAAAACCTTAAACCC
*
6159946 TAAAACCTTAAATCC
1 TAAAACCTTAAACCC
6159961 TAAAACCTTAAACCC
1 TAAAACCTTAAACCC
*
6159976 T-AAACCCTAAACCC
1 TAAAACCTTAAACCC
6159990 TAAAACC-TAAACCC
1 TAAAACCTTAAACCC
6160004 TAAAACCTTAAA-CC
1 TAAAACCTTAAACCC
*
6160018 TTAAACCTTAAACCC
1 TAAAACCTTAAACCC
6160033 TAAAA
1 TAAAA
6160038 TAAAAACCTA
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
14 40 0.49
15 42 0.51
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAAACCTTAAACCC
Found at i:6159973 original size:7 final size:7
Alignment explanation
Indices: 6159948--6160036 Score: 90
Period size: 7 Copynumber: 12.4 Consensus size: 7
6159938 ATAATCCCTA
6159948 AAACCTT
1 AAACCTT
*
6159955 AAATCCTA
1 AAA-CCTT
6159963 AAACCTT
1 AAACCTT
*
6159970 AAACCCT
1 AAACCTT
*
6159977 AAACCCT
1 AAACCTT
*
6159984 AAACCCTA
1 AAA-CCTT
6159992 AAACC-T
1 AAACCTT
*
6159998 AAACCCTA
1 AAA-CCTT
6160006 AAACCTT
1 AAACCTT
6160013 AAACCTT
1 AAACCTT
6160020 AAACCTT
1 AAACCTT
*
6160027 AAACCCT
1 AAACCTT
6160034 AAA
1 AAA
6160037 ATAAAAACCT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
6 3 0.04
7 52 0.75
8 14 0.20
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCTT
Found at i:6159986 original size:14 final size:14
Alignment explanation
Indices: 6159933--6160036 Score: 120
Period size: 14 Copynumber: 7.2 Consensus size: 14
6159923 CATAACTTTA
* *
6159933 AAACCATAATCCCT
1 AAACCTTAAACCCT
*
6159947 AAAACCTTAAATCCT
1 -AAACCTTAAACCCT
6159962 AAAACCTTAAACCCT
1 -AAACCTTAAACCCT
*
6159977 AAACCCTAAACCCT
1 AAACCTTAAACCCT
6159991 AAAACC-TAAACCCT
1 -AAACCTTAAACCCT
*
6160005 AAAACCTTAAACCTT
1 -AAACCTTAAACCCT
6160020 AAACCTTAAACCCT
1 AAACCTTAAACCCT
6160034 AAA
1 AAA
6160037 ATAAAAACCT
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
14 43 0.54
15 37 0.46
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACCTTAAACCCT
Found at i:6160340 original size:14 final size:15
Alignment explanation
Indices: 6160303--6160349 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
6160293 CCCTAAATAT
*
6160303 AAACCGTAAATCCTA
1 AAACCGTAAACCCTA
**
6160318 AATTC-TAAA-CCTA
1 AAACCGTAAACCCTA
6160331 AAACCGTAAACCCTA
1 AAACCGTAAACCCTA
6160346 AAAC
1 AAAC
6160350 TAAACTCACA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 7 0.27
14 8 0.31
15 11 0.42
ACGTcount: A:0.49, C:0.28, G:0.04, T:0.19
Consensus pattern (15 bp):
AAACCGTAAACCCTA
Found at i:6160482 original size:20 final size:20
Alignment explanation
Indices: 6160439--6160482 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
6160429 GCATCAAACC
*
6160439 TAAACACTAAATCTAAACTT
1 TAAACACTAAATCTAAAATT
*
6160459 TAAACCCTAAAT-TAAAATT
1 TAAACACTAAATCTAAAATT
6160478 ATAAA
1 -TAAA
6160483 TTATAAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAACACTAAATCTAAAATT
Found at i:6160666 original size:20 final size:20
Alignment explanation
Indices: 6160638--6160680 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
6160628 TAAACCTTTT
*
6160638 AACCCTAAA-ATTAAACATTA
1 AACCATAAACATTAAAC-TTA
*
6160658 AACCATAAACCTTAAACTTA
1 AACCATAAACATTAAACTTA
6160678 AAC
1 AAC
6160681 ACTAAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (20 bp):
AACCATAAACATTAAACTTA
Found at i:6160714 original size:48 final size:48
Alignment explanation
Indices: 6160656--6160770 Score: 142
Period size: 48 Copynumber: 2.4 Consensus size: 48
6160646 AATTAAACAT
* * * * *
6160656 TAAACCATAAACCTTAAACTTAAACACTAAAAACTAGACTCTAAATGA-
1 TAAACTATAAACCTTAAACTTAAACAATAAAAACTAAACCCTAAA-AAC
* *
6160704 TAAACTATAAACCCTAAACTTAAACAATAAATACTAAACCCTAAAAAC
1 TAAACTATAAACCTTAAACTTAAACAATAAAAACTAAACCCTAAAAAC
*
6160752 TAAACTTTAAACCTTAAAC
1 TAAACTATAAACCTTAAAC
6160771 CCTAATTACA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 1 0.02
48 56 0.98
ACGTcount: A:0.53, C:0.22, G:0.02, T:0.23
Consensus pattern (48 bp):
TAAACTATAAACCTTAAACTTAAACAATAAAAACTAAACCCTAAAAAC
Found at i:6161335 original size:28 final size:26
Alignment explanation
Indices: 6161276--6161335 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
6161266 CCATCAACCC
* *
6161276 AAAATATAAACCGTAAATCCTAAATT
1 AAAATATAAACCGTAAACCCTAAACT
*
6161302 ATAAATACTAAACCTTAAACCCTAAAACT
1 A-AAATA-TAAACCGTAAACCCT-AAACT
6161331 AAAAT
1 AAAAT
6161336 CACAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.04
27 5 0.18
28 17 0.61
29 5 0.18
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (26 bp):
AAAATATAAACCGTAAACCCTAAACT
Found at i:6161381 original size:21 final size:21
Alignment explanation
Indices: 6161371--6161430 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
6161361 TTCTAAATCC
6161371 TAAACCCTAAACATTAAACCT
1 TAAACCCTAAACATTAAACCT
*
6161392 TAAACCCTAAAC-CTAAA-CT
1 TAAACCCTAAACATTAAACCT
* * *
6161411 CAAACACTAAACACTAAACC
1 TAAACCCTAAACATTAAACC
6161431 CAAAATGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.35
20 9 0.26
21 13 0.38
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (21 bp):
TAAACCCTAAACATTAAACCT
Found at i:6161382 original size:7 final size:7
Alignment explanation
Indices: 6161363--6161431 Score: 61
Period size: 7 Copynumber: 10.1 Consensus size: 7
6161353 CAATTAAATT
*
6161363 CTAAATC
1 CTAAACC
6161370 CTAAACC
1 CTAAACC
*
6161377 CTAAACA
1 CTAAACC
*
6161384 TTAAACC
1 CTAAACC
*
6161391 TTAAACC
1 CTAAACC
6161398 CTAAA-C
1 CTAAACC
*
6161404 CTAAACT
1 CTAAACC
*
6161411 C-AAACA
1 CTAAACC
*
6161417 CTAAACA
1 CTAAACC
6161424 CTAAACC
1 CTAAACC
6161431 C
1 C
6161432 AAAATGTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
6 11 0.21
7 41 0.79
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:6161469 original size:40 final size:40
Alignment explanation
Indices: 6161425--6161543 Score: 125
Period size: 40 Copynumber: 3.0 Consensus size: 40
6161415 CACTAAACAC
6161425 TAAAC-CCAAAATGTAAATCATAAA-AAGTAAATATAAACCT
1 TAAACACCAAAAT-TAAATCATAAACAA-TAAATATAAACCT
* * * *
6161465 TAAACACTATAATTATATCATAAACCATAAATATAAACCT
1 TAAACACCAAAATTAAATCATAAACAATAAATATAAACCT
* * * * *
6161505 TAAACACTATAATCATATCATAAACCATAAATATAAACC
1 TAAACACCAAAATTAAATCATAAACAATAAATATAAACC
6161544 CTACACCCTA
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
40 66 0.92
41 6 0.08
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.26
Consensus pattern (40 bp):
TAAACACCAAAATTAAATCATAAACAATAAATATAAACCT
Found at i:6161508 original size:20 final size:20
Alignment explanation
Indices: 6161452--6161601 Score: 82
Period size: 20 Copynumber: 7.6 Consensus size: 20
6161442 TCATAAAAAG
6161452 TAAATATAAACCTTAAA-CA
1 TAAATATAAACCTTAAACCA
* * *
6161471 CTATAAT-TATATCATAAACCA
1 -TA-AATATAAACCTTAAACCA
6161492 TAAATATAAACCTTAAA-CA
1 TAAATATAAACCTTAAACCA
* *
6161511 CTATAATCAT--ATCATAAACCA
1 -TA-AAT-ATAAACCTTAAACCA
* * *
6161532 TAAATATAAACCCTACACCC
1 TAAATATAAACCTTAAACCA
**
6161552 T-AATA-AAAAATTAAACCA
1 TAAATATAAACCTTAAACCA
*
6161570 TAAACATAAACCCTTAAA-CA
1 TAAATATAAA-CCTTAAACCA
*
6161590 TAAGTATAAACC
1 TAAATATAAACC
6161602 CTAATTCTAT
Statistics
Matches: 96, Mismatches: 22, Indels: 25
0.67 0.15 0.17
Matches are distributed among these distances:
18 11 0.11
19 17 0.18
20 51 0.53
21 15 0.16
22 2 0.02
ACGTcount: A:0.53, C:0.21, G:0.01, T:0.25
Consensus pattern (20 bp):
TAAATATAAACCTTAAACCA
Found at i:6161542 original size:13 final size:13
Alignment explanation
Indices: 6161484--6161543 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
6161474 TAATTATATC
6161484 ATAAACCATAAAT
1 ATAAACCATAAAT
* *
6161497 ATAAACCTTAAAC
1 ATAAACCATAAAT
*
6161510 ACTATAATCAT--AT
1 A-TA-AACCATAAAT
6161523 CATAAACCATAAAT
1 -ATAAACCATAAAT
6161537 ATAAACC
1 ATAAACC
6161544 CTACACCCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
12 5 0.14
13 22 0.61
14 5 0.14
15 4 0.11
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (13 bp):
ATAAACCATAAAT
Found at i:6161638 original size:7 final size:7
Alignment explanation
Indices: 6161628--6161652 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6161618 CTATAACCTC
6161628 AAACACT
1 AAACACT
6161635 AAACACT
1 AAACACT
6161642 AAACACT
1 AAACACT
6161649 AAAC
1 AAAC
6161653 CTTAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACACT
Found at i:6161658 original size:14 final size:14
Alignment explanation
Indices: 6161622--6161686 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
6161612 CCTAACCTAT
*
6161622 AACCTCAAACACTA
1 AACCTTAAACACTA
6161636 AACAC-TAAACACTA
1 AAC-CTTAAACACTA
*
6161650 AACCTTAAATTA-TA
1 AACCTTAAA-CACTA
* *
6161664 AACCATAAACCCTA
1 AACCTTAAACACTA
6161678 AACCTTAAA
1 AACCTTAAA
6161687 ACCATAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 1 0.02
14 38 0.93
15 2 0.05
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (14 bp):
AACCTTAAACACTA
Found at i:6161781 original size:27 final size:28
Alignment explanation
Indices: 6161717--6161782 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
6161707 ACCTTACAAT
*
6161717 TAAA-TATAAACCCTAAAACTATAATAC
1 TAAACTATAAACCCTAAAACTATAATAA
** *
6161744 TAAACCCTAAACCCT--AACCATAAATAA
1 TAAACTATAAACCCTAAAACTAT-AATAA
6161771 TAAACTATAAAC
1 TAAACTATAAAC
6161783 ATAAACCCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
26 5 0.16
27 18 0.58
28 8 0.26
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (28 bp):
TAAACTATAAACCCTAAAACTATAATAA
Found at i:6161794 original size:20 final size:20
Alignment explanation
Indices: 6161717--6161794 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
6161707 ACCTTACAAT
*
6161717 TAAATATAAACCCTAAAACTA
1 TAAACATAAACCCT-AAACTA
**
6161738 TAATAC-TAAACCCTAAACCC
1 TAA-ACATAAACCCTAAACTA
* ***
6161758 TAACCATAAATAATAAACTA
1 TAAACATAAACCCTAAACTA
6161778 TAAACATAAACCCTAAA
1 TAAACATAAACCCTAAA
6161795 ACTAGAATTA
Statistics
Matches: 42, Mismatches: 13, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
19 1 0.02
20 29 0.69
21 11 0.26
22 1 0.02
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAACATAAACCCTAAACTA
Found at i:6161962 original size:7 final size:7
Alignment explanation
Indices: 6161950--6162122 Score: 63
Period size: 7 Copynumber: 25.4 Consensus size: 7
6161940 ATCGAACACA
6161950 AAACCCT
1 AAACCCT
6161957 AAACCCT
1 AAACCCT
* *
6161964 ACACAC-
1 AAACCCT
**
6161970 AAACTTT
1 AAACCCT
6161977 AAACCCT
1 AAACCCT
* *
6161984 AAATCAT
1 AAACCCT
*
6161991 AAACACT
1 AAACCCT
**
6161998 AAATACT
1 AAACCCT
6162005 AAACCCT
1 AAACCCT
6162012 AAAACCCT
1 -AAACCCT
*
6162020 AAAACCT
1 AAACCCT
*
6162027 AAA-CAT
1 AAACCCT
6162033 AAACCCT
1 AAACCCT
6162040 -AA--CT
1 AAACCCT
* *
6162044 ATATCCT
1 AAACCCT
*
6162051 AAACCAT
1 AAACCCT
6162058 -AA-CCT
1 AAACCCT
*
6162063 CAAACACT
1 -AAACCCT
* *
6162071 AAACACA
1 AAACCCT
*
6162078 AAACACT
1 AAACCCT
*
6162085 AAACCTT
1 AAACCCT
***
6162092 AAATTAT
1 AAACCCT
*
6162099 AAACCAT
1 AAACCCT
6162106 AAACCCT
1 AAACCCT
*
6162113 AAACCTT
1 AAACCCT
6162120 AAA
1 AAA
6162123 ACCATAAAAA
Statistics
Matches: 122, Mismatches: 35, Indels: 18
0.70 0.20 0.10
Matches are distributed among these distances:
4 2 0.02
5 3 0.02
6 12 0.10
7 96 0.79
8 9 0.07
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:6161973 original size:20 final size:19
Alignment explanation
Indices: 6161945--6161984 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
6161935 CTAAAATCGA
6161945 ACACAAAACCCTAAACCCT
1 ACACAAAACCCTAAACCCT
**
6161964 ACACACAAACTTTAAACCCT
1 ACACA-AAACCCTAAACCCT
6161984 A
1 A
6161985 AATCATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (19 bp):
ACACAAAACCCTAAACCCT
Found at i:6161996 original size:27 final size:28
Alignment explanation
Indices: 6161950--6162041 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 28
6161940 ATCGAACACA
* * *
6161950 AAACCCTAAACCCTACACAC-AAACT-TT
1 AAACCCTAAACCATAAACACTAAA-TACT
*
6161977 AAACCCTAAATCATAAACACTAAATACT
1 AAACCCTAAACCATAAACACTAAATACT
* *
6162005 AAACCCTAAAACCCTAAA-ACCTAAACA-T
1 AAACCCT-AAACCATAAACA-CTAAATACT
6162033 AAACCCTAA
1 AAACCCTAA
6162042 CTATATCCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
27 20 0.37
28 20 0.37
29 14 0.26
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (28 bp):
AAACCCTAAACCATAAACACTAAATACT
Found at i:6162135 original size:28 final size:28
Alignment explanation
Indices: 6162070--6162138 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
6162060 CCTCAAACAC
* **
6162070 TAAACACA-AAACACTAAACCTTAAATTA
1 TAAACA-ATAAACCCTAAACCTTAAACCA
*
6162098 TAAACCATAAACCCTAAACCTTAAAACCA
1 TAAACAATAAACCCTAAACCTT-AAACCA
6162127 TAAA-AATAAACC
1 TAAACAATAAACC
6162139 TTTAACCCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.03
28 25 0.74
29 8 0.24
ACGTcount: A:0.57, C:0.25, G:0.00, T:0.19
Consensus pattern (28 bp):
TAAACAATAAACCCTAAACCTTAAACCA
Found at i:6162170 original size:47 final size:48
Alignment explanation
Indices: 6162112--6162237 Score: 123
Period size: 47 Copynumber: 2.7 Consensus size: 48
6162102 CCATAAACCC
* * *
6162112 TAAACCTTAAAACCATAAAAATAAACCTTTAACCCTATAAT-TAAAC-A
1 TAAACCCTAAAACCATAAAAATAAACCCTAAACCCTA-AATGTAAACAA
* ** *
6162159 TAAACCCTAAAACTATAATCATTAACCCTAAACCCTAAATGTAAACAA
1 TAAACCCTAAAACCATAAAAATAAACCCTAAACCCTAAATGTAAACAA
* * * *
6162207 TAAACACTATAACTAT-ACAATAAACCCTAAA
1 TAAACCCTAAAACCATAAAAATAAACCCTAAA
6162238 TATCAAAACC
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
46 3 0.05
47 47 0.72
48 15 0.23
ACGTcount: A:0.52, C:0.23, G:0.01, T:0.24
Consensus pattern (48 bp):
TAAACCCTAAAACCATAAAAATAAACCCTAAACCCTAAATGTAAACAA
Found at i:6162187 original size:21 final size:19
Alignment explanation
Indices: 6162140--6162190 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
6162130 AAATAAACCT
*
6162140 TTAACCCTATAATTAAACA
1 TTAACCCTAAAATTAAACA
* *
6162159 TAAACCCTAAAACTATAATCA
1 TTAACCCTAAAA-T-TAAACA
6162180 TTAACCCTAAA
1 TTAACCCTAAA
6162191 CCCTAAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 10 0.38
20 1 0.04
21 15 0.58
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (19 bp):
TTAACCCTAAAATTAAACA
Found at i:6162210 original size:20 final size:20
Alignment explanation
Indices: 6162187--6162238 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
6162177 TCATTAACCC
*
6162187 TAAACCCTAAATGTAAACAA
1 TAAACCCTAAATCTAAACAA
* *
6162207 TAAACACTATAA-CTATACAA
1 TAAACCCTA-AATCTAAACAA
6162227 TAAACCCTAAAT
1 TAAACCCTAAAT
6162239 ATCAAAACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.54, C:0.21, G:0.02, T:0.23
Consensus pattern (20 bp):
TAAACCCTAAATCTAAACAA
Found at i:6162510 original size:15 final size:15
Alignment explanation
Indices: 6162490--6162610 Score: 151
Period size: 15 Copynumber: 8.3 Consensus size: 15
6162480 CACATAACTT
* *
6162490 TAAAACCATAATCCC
1 TAAAACCTTAAACCC
6162505 TAAAACCTTAAACCC
1 TAAAACCTTAAACCC
6162520 TAAAACCTTAAACCC
1 TAAAACCTTAAACCC
* *
6162535 T-AAACCCTAAAACC
1 TAAAACCTTAAACCC
6162549 TAAAACC-TAAACCC
1 TAAAACCTTAAACCC
* *
6162563 TAAACCCTAAAACCC
1 TAAAACCTTAAACCC
6162578 T-AAACCTTAAA-CC
1 TAAAACCTTAAACCC
*
6162591 TTAAACCTTAAACCC
1 TAAAACCTTAAACCC
6162606 TAAAA
1 TAAAA
6162611 TAAAAACCTA
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
13 3 0.03
14 42 0.46
15 47 0.51
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAAACCTTAAACCC
Found at i:6162523 original size:7 final size:7
Alignment explanation
Indices: 6162492--6162609 Score: 128
Period size: 7 Copynumber: 16.4 Consensus size: 7
6162482 CATAACTTTA
*
6162492 AAACCAT
1 AAACCCT
*
6162499 AATCCCT
1 AAACCCT
*
6162506 AAAACCTT
1 -AAACCCT
6162514 AAACCCT
1 AAACCCT
*
6162521 AAAACCTT
1 -AAACCCT
6162529 AAACCCT
1 AAACCCT
6162536 AAACCCT
1 AAACCCT
*
6162543 AAAACCT
1 AAACCCT
*
6162550 AAAACCT
1 AAACCCT
6162557 AAACCCT
1 AAACCCT
6162564 AAACCCT
1 AAACCCT
6162571 AAAACCCT
1 -AAACCCT
*
6162579 AAACCTT
1 AAACCCT
*
6162586 AAACCTT
1 AAACCCT
*
6162593 AAACCTT
1 AAACCCT
6162600 AAACCCT
1 AAACCCT
6162607 AAA
1 AAA
6162610 ATAAAAACCT
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
7 79 0.81
8 18 0.19
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:6162805 original size:20 final size:21
Alignment explanation
Indices: 6162782--6162825 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
6162772 CCTTAAACTC
*
6162782 AAACCATCAACCCTAAA-TAT
1 AAACCATAAACCCTAAATTAT
* *
6162802 AAACCGTAAATCCTAAATTAT
1 AAACCATAAACCCTAAATTAT
6162823 AAA
1 AAA
6162826 TACTAAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.52, C:0.23, G:0.02, T:0.23
Consensus pattern (21 bp):
AAACCATAAACCCTAAATTAT
Found at i:6162981 original size:20 final size:20
Alignment explanation
Indices: 6162938--6162981 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
6162928 GCATCAAACC
*
6162938 TAAACACTAAATCTAAACTT
1 TAAACACTAAATCTAAAATT
*
6162958 TAAACCCTAAAT-TAAAATT
1 TAAACACTAAATCTAAAATT
6162977 ATAAA
1 -TAAA
6162982 TTATAAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAACACTAAATCTAAAATT
Found at i:6163652 original size:7 final size:7
Alignment explanation
Indices: 6163640--6163679 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
6163630 NNNNNNNNCG
6163640 AACACTA
1 AACACTA
6163647 AACACTA
1 AACACTA
*
6163654 AACCCTA
1 AACACTA
6163661 AACAC-A
1 AACACTA
*
6163667 AACCCTA
1 AACACTA
6163674 AACACT
1 AACACT
6163680 CTAATTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.53, C:0.35, G:0.00, T:0.12
Consensus pattern (7 bp):
AACACTA
Found at i:6163671 original size:13 final size:14
Alignment explanation
Indices: 6163644--6163679 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
6163634 NNNNCGAACA
6163644 CTAAACACTAAACC
1 CTAAACACTAAACC
6163658 CTAAACAC-AAACC
1 CTAAACACTAAACC
6163671 CTAAACACT
1 CTAAACACT
6163680 CTAATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (14 bp):
CTAAACACTAAACC
Found at i:6163834 original size:28 final size:26
Alignment explanation
Indices: 6163775--6163834 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
6163765 CCATCAACCC
* *
6163775 AAAATATAAACCGTAAATCCTAAATT
1 AAAATATAAACCGTAAACCCTAAACT
*
6163801 ATAAATACTAAACCTTAAACCCTAAAACT
1 A-AAATA-TAAACCGTAAACCCT-AAACT
6163830 AAAAT
1 AAAAT
6163835 CACAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.04
27 5 0.18
28 17 0.61
29 5 0.18
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (26 bp):
AAAATATAAACCGTAAACCCTAAACT
Found at i:6163880 original size:21 final size:21
Alignment explanation
Indices: 6163870--6163929 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
6163860 TTCTAAATCC
6163870 TAAACCCTAAACATTAAACCT
1 TAAACCCTAAACATTAAACCT
*
6163891 TAAACCCTAAAC-CTAAA-CT
1 TAAACCCTAAACATTAAACCT
* * *
6163910 CAAACACTAAACACTAAACC
1 TAAACCCTAAACATTAAACC
6163930 CAAAATGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.35
20 9 0.26
21 13 0.38
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (21 bp):
TAAACCCTAAACATTAAACCT
Found at i:6163881 original size:7 final size:7
Alignment explanation
Indices: 6163862--6163930 Score: 61
Period size: 7 Copynumber: 10.1 Consensus size: 7
6163852 CAATTAAATT
*
6163862 CTAAATC
1 CTAAACC
6163869 CTAAACC
1 CTAAACC
*
6163876 CTAAACA
1 CTAAACC
*
6163883 TTAAACC
1 CTAAACC
*
6163890 TTAAACC
1 CTAAACC
6163897 CTAAA-C
1 CTAAACC
*
6163903 CTAAACT
1 CTAAACC
*
6163910 C-AAACA
1 CTAAACC
*
6163916 CTAAACA
1 CTAAACC
6163923 CTAAACC
1 CTAAACC
6163930 C
1 C
6163931 AAAATGTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
6 11 0.21
7 41 0.79
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:6163968 original size:40 final size:40
Alignment explanation
Indices: 6163924--6164042 Score: 125
Period size: 40 Copynumber: 3.0 Consensus size: 40
6163914 CACTAAACAC
6163924 TAAAC-CCAAAATGTAAATCATAAA-AAGTAAATATAAACCT
1 TAAACACCAAAAT-TAAATCATAAACAA-TAAATATAAACCT
* * * *
6163964 TAAACACTATAATTATATCATAAACCATAAATATAAACCT
1 TAAACACCAAAATTAAATCATAAACAATAAATATAAACCT
* * * * *
6164004 TAAACACTATAATCATATCATAAACCATAAATATAAACC
1 TAAACACCAAAATTAAATCATAAACAATAAATATAAACC
6164043 CTACACCCTA
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
40 66 0.92
41 6 0.08
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.26
Consensus pattern (40 bp):
TAAACACCAAAATTAAATCATAAACAATAAATATAAACCT
Found at i:6164007 original size:20 final size:20
Alignment explanation
Indices: 6163951--6164100 Score: 82
Period size: 20 Copynumber: 7.6 Consensus size: 20
6163941 TCATAAAAAG
6163951 TAAATATAAACCTTAAA-CA
1 TAAATATAAACCTTAAACCA
* * *
6163970 CTATAAT-TATATCATAAACCA
1 -TA-AATATAAACCTTAAACCA
6163991 TAAATATAAACCTTAAA-CA
1 TAAATATAAACCTTAAACCA
* *
6164010 CTATAATCAT--ATCATAAACCA
1 -TA-AAT-ATAAACCTTAAACCA
* * *
6164031 TAAATATAAACCCTACACCC
1 TAAATATAAACCTTAAACCA
**
6164051 T-AATA-AAAAATTAAACCA
1 TAAATATAAACCTTAAACCA
*
6164069 TAAACATAAACCCTTAAA-CA
1 TAAATATAAA-CCTTAAACCA
*
6164089 TAAGTATAAACC
1 TAAATATAAACC
6164101 CTAATTCTAT
Statistics
Matches: 96, Mismatches: 22, Indels: 25
0.67 0.15 0.17
Matches are distributed among these distances:
18 11 0.11
19 17 0.18
20 51 0.53
21 15 0.16
22 2 0.02
ACGTcount: A:0.53, C:0.21, G:0.01, T:0.25
Consensus pattern (20 bp):
TAAATATAAACCTTAAACCA
Found at i:6164041 original size:13 final size:13
Alignment explanation
Indices: 6163983--6164042 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
6163973 TAATTATATC
6163983 ATAAACCATAAAT
1 ATAAACCATAAAT
* *
6163996 ATAAACCTTAAAC
1 ATAAACCATAAAT
*
6164009 ACTATAATCAT--AT
1 A-TA-AACCATAAAT
6164022 CATAAACCATAAAT
1 -ATAAACCATAAAT
6164036 ATAAACC
1 ATAAACC
6164043 CTACACCCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
12 5 0.14
13 22 0.61
14 5 0.14
15 4 0.11
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (13 bp):
ATAAACCATAAAT
Found at i:6164137 original size:7 final size:7
Alignment explanation
Indices: 6164127--6164151 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6164117 CTATAACCTC
6164127 AAACACT
1 AAACACT
6164134 AAACACT
1 AAACACT
6164141 AAACACT
1 AAACACT
6164148 AAAC
1 AAAC
6164152 CTTAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACACT
Found at i:6164157 original size:14 final size:14
Alignment explanation
Indices: 6164121--6164185 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
6164111 CCTAACCTAT
*
6164121 AACCTCAAACACTA
1 AACCTTAAACACTA
6164135 AACAC-TAAACACTA
1 AAC-CTTAAACACTA
*
6164149 AACCTTAAATTA-TA
1 AACCTTAAA-CACTA
* *
6164163 AACCATAAACCCTA
1 AACCTTAAACACTA
6164177 AACCTTAAA
1 AACCTTAAA
6164186 ACCATAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 1 0.02
14 38 0.93
15 2 0.05
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (14 bp):
AACCTTAAACACTA
Found at i:6164280 original size:27 final size:28
Alignment explanation
Indices: 6164216--6164281 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
6164206 ACCTTACAAT
*
6164216 TAAA-TATAAACCCTAAAACTATAATAC
1 TAAACTATAAACCCTAAAACTATAATAA
** *
6164243 TAAACCCTAAACCCT--AACCATAAATAA
1 TAAACTATAAACCCTAAAACTAT-AATAA
6164270 TAAACTATAAAC
1 TAAACTATAAAC
6164282 ATAAACCCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
26 5 0.16
27 18 0.58
28 8 0.26
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (28 bp):
TAAACTATAAACCCTAAAACTATAATAA
Found at i:6164293 original size:20 final size:20
Alignment explanation
Indices: 6164216--6164293 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
6164206 ACCTTACAAT
*
6164216 TAAATATAAACCCTAAAACTA
1 TAAACATAAACCCT-AAACTA
**
6164237 TAATAC-TAAACCCTAAACCC
1 TAA-ACATAAACCCTAAACTA
* ***
6164257 TAACCATAAATAATAAACTA
1 TAAACATAAACCCTAAACTA
6164277 TAAACATAAACCCTAAA
1 TAAACATAAACCCTAAA
6164294 ACTAGAATTA
Statistics
Matches: 42, Mismatches: 13, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
19 1 0.02
20 29 0.69
21 11 0.26
22 1 0.02
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAACATAAACCCTAAACTA
Found at i:6164461 original size:7 final size:7
Alignment explanation
Indices: 6164449--6164621 Score: 63
Period size: 7 Copynumber: 25.4 Consensus size: 7
6164439 ATCGAACACA
6164449 AAACCCT
1 AAACCCT
6164456 AAACCCT
1 AAACCCT
* *
6164463 ACACAC-
1 AAACCCT
**
6164469 AAACTTT
1 AAACCCT
6164476 AAACCCT
1 AAACCCT
* *
6164483 AAATCAT
1 AAACCCT
*
6164490 AAACACT
1 AAACCCT
**
6164497 AAATACT
1 AAACCCT
6164504 AAACCCT
1 AAACCCT
6164511 AAAACCCT
1 -AAACCCT
*
6164519 AAAACCT
1 AAACCCT
*
6164526 AAA-CAT
1 AAACCCT
6164532 AAACCCT
1 AAACCCT
6164539 -AA--CT
1 AAACCCT
* *
6164543 ATATCCT
1 AAACCCT
*
6164550 AAACCAT
1 AAACCCT
6164557 -AA-CCT
1 AAACCCT
*
6164562 CAAACACT
1 -AAACCCT
* *
6164570 AAACACA
1 AAACCCT
*
6164577 AAACACT
1 AAACCCT
*
6164584 AAACCTT
1 AAACCCT
***
6164591 AAATTAT
1 AAACCCT
*
6164598 AAACCAT
1 AAACCCT
6164605 AAACCCT
1 AAACCCT
*
6164612 AAACCTT
1 AAACCCT
6164619 AAA
1 AAA
6164622 ACCATAAAAA
Statistics
Matches: 122, Mismatches: 35, Indels: 18
0.70 0.20 0.10
Matches are distributed among these distances:
4 2 0.02
5 3 0.02
6 12 0.10
7 96 0.79
8 9 0.07
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:6164472 original size:20 final size:19
Alignment explanation
Indices: 6164444--6164483 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
6164434 CTAAAATCGA
6164444 ACACAAAACCCTAAACCCT
1 ACACAAAACCCTAAACCCT
**
6164463 ACACACAAACTTTAAACCCT
1 ACACA-AAACCCTAAACCCT
6164483 A
1 A
6164484 AATCATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (19 bp):
ACACAAAACCCTAAACCCT
Found at i:6164495 original size:27 final size:28
Alignment explanation
Indices: 6164449--6164540 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 28
6164439 ATCGAACACA
* * *
6164449 AAACCCTAAACCCTACACAC-AAACT-TT
1 AAACCCTAAACCATAAACACTAAA-TACT
*
6164476 AAACCCTAAATCATAAACACTAAATACT
1 AAACCCTAAACCATAAACACTAAATACT
* *
6164504 AAACCCTAAAACCCTAAA-ACCTAAACA-T
1 AAACCCT-AAACCATAAACA-CTAAATACT
6164532 AAACCCTAA
1 AAACCCTAA
6164541 CTATATCCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
27 20 0.37
28 20 0.37
29 14 0.26
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (28 bp):
AAACCCTAAACCATAAACACTAAATACT
Found at i:6164634 original size:28 final size:28
Alignment explanation
Indices: 6164569--6164637 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
6164559 CCTCAAACAC
* **
6164569 TAAACACA-AAACACTAAACCTTAAATTA
1 TAAACA-ATAAACCCTAAACCTTAAACCA
*
6164597 TAAACCATAAACCCTAAACCTTAAAACCA
1 TAAACAATAAACCCTAAACCTT-AAACCA
6164626 TAAA-AATAAACC
1 TAAACAATAAACC
6164638 TTTAACCCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.03
28 25 0.74
29 8 0.24
ACGTcount: A:0.57, C:0.25, G:0.00, T:0.19
Consensus pattern (28 bp):
TAAACAATAAACCCTAAACCTTAAACCA
Found at i:6164669 original size:47 final size:48
Alignment explanation
Indices: 6164611--6164710 Score: 114
Period size: 47 Copynumber: 2.1 Consensus size: 48
6164601 CCATAAACCC
* * *
6164611 TAAACCTTAAAACCATAAAAATAAACCTTTAACCCTATAAT-TAAAC-A
1 TAAACCCTAAAACCATAAAAATAAACCCTAAACCCTA-AATGTAAACAA
* ** *
6164658 TAAACCCTAAAACTATAATCATTAACCCTAAACCCTAAATGTAAACAA
1 TAAACCCTAAAACCATAAAAATAAACCCTAAACCCTAAATGTAAACAA
6164706 TAAAC
1 TAAAC
6164711 ACTATAATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
46 3 0.07
47 35 0.80
48 6 0.14
ACGTcount: A:0.52, C:0.23, G:0.01, T:0.24
Consensus pattern (48 bp):
TAAACCCTAAAACCATAAAAATAAACCCTAAACCCTAAATGTAAACAA
Found at i:6164686 original size:21 final size:19
Alignment explanation
Indices: 6164639--6164689 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
6164629 AAATAAACCT
*
6164639 TTAACCCTATAATTAAACA
1 TTAACCCTAAAATTAAACA
* *
6164658 TAAACCCTAAAACTATAATCA
1 TTAACCCTAAAA-T-TAAACA
6164679 TTAACCCTAAA
1 TTAACCCTAAA
6164690 CCCTAAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 10 0.38
20 1 0.04
21 15 0.58
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (19 bp):
TTAACCCTAAAATTAAACA
Found at i:6164956 original size:13 final size:13
Alignment explanation
Indices: 6164938--6164962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6164928 AAACTTAACA
6164938 ATAAACCATAAAT
1 ATAAACCATAAAT
6164951 ATAAACCATAAA
1 ATAAACCATAAA
6164963 CCCTAAATCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (13 bp):
ATAAACCATAAAT
Found at i:6164974 original size:7 final size:7
Alignment explanation
Indices: 6164952--6165003 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
6164942 ACCATAAATA
*
6164952 TAAACCA
1 TAAACCC
6164959 TAAACCC
1 TAAACCC
*
6164966 TAAATCC
1 TAAACCC
**
6164973 TAAAAAC
1 TAAACCC
*
6164980 TAAACCT
1 TAAACCC
*
6164987 TAAACAC
1 TAAACCC
6164994 TAAACCC
1 TAAACCC
6165001 TAA
1 TAA
6165004 TCACAAATAA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:6164976 original size:14 final size:13
Alignment explanation
Indices: 6164920--6164999 Score: 56
Period size: 14 Copynumber: 6.0 Consensus size: 13
6164910 TGATAAACTA
*
6164920 TAAACCCTAAA-C
1 TAAACACTAAACC
* *
6164932 TTAACAATAAACC
1 TAAACACTAAACC
*
6164945 ATAAATA-TAAACC
1 -TAAACACTAAACC
*
6164958 ATAAACCCTAAATCC
1 -TAAACACTAAA-CC
*
6164973 TAAAAACTAAACC
1 TAAACACTAAACC
6164986 TTAAACACTAAACC
1 -TAAACACTAAACC
6165000 CTAATCACAA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
12 8 0.15
13 14 0.26
14 29 0.55
15 2 0.04
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAACACTAAACC
Found at i:6165053 original size:15 final size:15
Alignment explanation
Indices: 6165033--6165139 Score: 139
Period size: 15 Copynumber: 7.3 Consensus size: 15
6165023 CACATAACTT
* *
6165033 TAAAACCATAATCCC
1 TAAAACCTTAAACCC
6165048 TAAAACCTTAAACCC
1 TAAAACCTTAAACCC
6165063 TAAAACCTTAAACCC
1 TAAAACCTTAAACCC
* *
6165078 T-AAACCCTAAAACC
1 TAAAACCTTAAACCC
6165092 TAAAACC-TAAACCC
1 TAAAACCTTAAACCC
*
6165106 TAAAACCCTAAA-CC
1 TAAAACCTTAAACCC
*
6165120 TTAAACCTTAAACCC
1 TAAAACCTTAAACCC
6165135 TAAAA
1 TAAAA
6165140 TAAAAACCTA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
14 37 0.46
15 44 0.54
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAAACCTTAAACCC
Found at i:6165061 original size:22 final size:22
Alignment explanation
Indices: 6165035--6165139 Score: 124
Period size: 22 Copynumber: 4.8 Consensus size: 22
6165025 CATAACTTTA
* *
6165035 AAACCATAATCCCTAAAACCTT
1 AAACCCTAAACCCTAAAACCTT
* * *
6165057 AAACCCTAAAACCTTAAACCCT
1 AAACCCTAAACCCTAAAACCTT
*
6165079 AAACCCTAAAACCTAAAACC-T
1 AAACCCTAAACCCTAAAACCTT
6165100 AAACCCTAAAACCCT-AAACCTT
1 AAACCCT-AAACCCTAAAACCTT
*
6165122 AAACCTTAAACCCTAAAA
1 AAACCCTAAACCCTAAAA
6165140 TAAAAACCTA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
21 20 0.28
22 52 0.72
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (22 bp):
AAACCCTAAACCCTAAAACCTT
Found at i:6165066 original size:7 final size:7
Alignment explanation
Indices: 6165035--6165138 Score: 109
Period size: 7 Copynumber: 14.4 Consensus size: 7
6165025 CATAACTTTA
*
6165035 AAACCAT
1 AAACCCT
*
6165042 AATCCCT
1 AAACCCT
*
6165049 AAAACCTT
1 -AAACCCT
6165057 AAACCCT
1 AAACCCT
*
6165064 AAAACCTT
1 -AAACCCT
6165072 AAACCCT
1 AAACCCT
6165079 AAACCCT
1 AAACCCT
*
6165086 AAAACCT
1 AAACCCT
*
6165093 AAAACCT
1 AAACCCT
6165100 AAACCCT
1 AAACCCT
6165107 AAAACCCT
1 -AAACCCT
*
6165115 AAACCTT
1 AAACCCT
*
6165122 AAACCTT
1 AAACCCT
6165129 AAACCCT
1 AAACCCT
6165136 AAA
1 AAA
6165139 ATAAAAACCT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
7 65 0.78
8 18 0.22
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:6165354 original size:14 final size:14
Alignment explanation
Indices: 6165335--6165376 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
6165325 AAATATAAAC
*
6165335 CGTAAATCCTAAATT
1 CGTAAA-CCTAAAAT
6165350 C-TAAACCTAAAAT
1 CGTAAACCTAAAAT
6165363 CGTAAACCCTAAAA
1 CGTAAA-CCTAAAA
6165377 CTAAACTCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 8 0.33
14 8 0.33
15 8 0.33
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.24
Consensus pattern (14 bp):
CGTAAACCTAAAAT
Found at i:6165726 original size:20 final size:20
Alignment explanation
Indices: 6165698--6165740 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
6165688 TAAACCTTTT
*
6165698 AACCCTAAA-ATTAAACATTA
1 AACCATAAACATTAAAC-TTA
*
6165718 AACCATAAACCTTAAACTTA
1 AACCATAAACATTAAACTTA
6165738 AAC
1 AAC
6165741 ACTAAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (20 bp):
AACCATAAACATTAAACTTA
Found at i:6165774 original size:48 final size:48
Alignment explanation
Indices: 6165716--6165830 Score: 142
Period size: 48 Copynumber: 2.4 Consensus size: 48
6165706 AATTAAACAT
* * * * *
6165716 TAAACCATAAACCTTAAACTTAAACACTAAAAACTAGACTCTAAATGA-
1 TAAACTATAAACCTTAAACTTAAACAATAAAAACTAAACCCTAAA-AAC
* *
6165764 TAAACTATAAACCCTAAACTTAAACAATAAATACTAAACCCTAAAAAC
1 TAAACTATAAACCTTAAACTTAAACAATAAAAACTAAACCCTAAAAAC
*
6165812 TAAACTTTAAACCTTAAAC
1 TAAACTATAAACCTTAAAC
6165831 CCTAATTACA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 1 0.02
48 56 0.98
ACGTcount: A:0.53, C:0.22, G:0.02, T:0.23
Consensus pattern (48 bp):
TAAACTATAAACCTTAAACTTAAACAATAAAAACTAAACCCTAAAAAC
Found at i:6166698 original size:7 final size:7
Alignment explanation
Indices: 6166688--6166712 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6166678 CTATAACCTC
6166688 AAACACT
1 AAACACT
6166695 AAACACT
1 AAACACT
6166702 AAACACT
1 AAACACT
6166709 AAAC
1 AAAC
6166713 CTTAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACACT
Found at i:6166718 original size:14 final size:14
Alignment explanation
Indices: 6166682--6166746 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
6166672 CCTAACCTAT
*
6166682 AACCTCAAACACTA
1 AACCTTAAACACTA
6166696 AACAC-TAAACACTA
1 AAC-CTTAAACACTA
*
6166710 AACCTTAAATTA-TA
1 AACCTTAAA-CACTA
* *
6166724 AACCATAAACCCTA
1 AACCTTAAACACTA
6166738 AACCTTAAA
1 AACCTTAAA
6166747 ACCATAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 1 0.02
14 38 0.93
15 2 0.05
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (14 bp):
AACCTTAAACACTA
Found at i:6166841 original size:27 final size:28
Alignment explanation
Indices: 6166777--6166842 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
6166767 ACCTTACAAT
*
6166777 TAAA-TATAAACCCTAAAACTATAATAC
1 TAAACTATAAACCCTAAAACTATAATAA
** *
6166804 TAAACCCTAAACCCT--AACCATAAATAA
1 TAAACTATAAACCCTAAAACTAT-AATAA
6166831 TAAACTATAAAC
1 TAAACTATAAAC
6166843 ATAAACCCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
26 5 0.16
27 18 0.58
28 8 0.26
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (28 bp):
TAAACTATAAACCCTAAAACTATAATAA
Found at i:6166854 original size:20 final size:20
Alignment explanation
Indices: 6166777--6166854 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
6166767 ACCTTACAAT
*
6166777 TAAATATAAACCCTAAAACTA
1 TAAACATAAACCCT-AAACTA
**
6166798 TAATAC-TAAACCCTAAACCC
1 TAA-ACATAAACCCTAAACTA
* ***
6166818 TAACCATAAATAATAAACTA
1 TAAACATAAACCCTAAACTA
6166838 TAAACATAAACCCTAAA
1 TAAACATAAACCCTAAA
6166855 ACTAGAATTA
Statistics
Matches: 42, Mismatches: 13, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
19 1 0.02
20 29 0.69
21 11 0.26
22 1 0.02
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAACATAAACCCTAAACTA
Found at i:6167021 original size:7 final size:7
Alignment explanation
Indices: 6167009--6167181 Score: 63
Period size: 7 Copynumber: 25.4 Consensus size: 7
6166999 ATCGAACACA
6167009 AAACCCT
1 AAACCCT
6167016 AAACCCT
1 AAACCCT
* *
6167023 ACACAC-
1 AAACCCT
**
6167029 AAACTTT
1 AAACCCT
6167036 AAACCCT
1 AAACCCT
* *
6167043 AAATCAT
1 AAACCCT
*
6167050 AAACACT
1 AAACCCT
**
6167057 AAATACT
1 AAACCCT
6167064 AAACCCT
1 AAACCCT
6167071 AAAACCCT
1 -AAACCCT
*
6167079 AAAACCT
1 AAACCCT
*
6167086 AAA-CAT
1 AAACCCT
6167092 AAACCCT
1 AAACCCT
6167099 -AA--CT
1 AAACCCT
* *
6167103 ATATCCT
1 AAACCCT
*
6167110 AAACCAT
1 AAACCCT
6167117 -AA-CCT
1 AAACCCT
*
6167122 CAAACACT
1 -AAACCCT
* *
6167130 AAACACA
1 AAACCCT
*
6167137 AAACACT
1 AAACCCT
*
6167144 AAACCTT
1 AAACCCT
***
6167151 AAATTAT
1 AAACCCT
*
6167158 AAACCAT
1 AAACCCT
6167165 AAACCCT
1 AAACCCT
*
6167172 AAACCTT
1 AAACCCT
6167179 AAA
1 AAA
6167182 ACCATAAAAA
Statistics
Matches: 122, Mismatches: 35, Indels: 18
0.70 0.20 0.10
Matches are distributed among these distances:
4 2 0.02
5 3 0.02
6 12 0.10
7 96 0.79
8 9 0.07
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:6167032 original size:20 final size:19
Alignment explanation
Indices: 6167004--6167043 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
6166994 CTAAAATCGA
6167004 ACACAAAACCCTAAACCCT
1 ACACAAAACCCTAAACCCT
**
6167023 ACACACAAACTTTAAACCCT
1 ACACA-AAACCCTAAACCCT
6167043 A
1 A
6167044 AATCATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (19 bp):
ACACAAAACCCTAAACCCT
Found at i:6167055 original size:27 final size:28
Alignment explanation
Indices: 6167009--6167100 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 28
6166999 ATCGAACACA
* * *
6167009 AAACCCTAAACCCTACACAC-AAACT-TT
1 AAACCCTAAACCATAAACACTAAA-TACT
*
6167036 AAACCCTAAATCATAAACACTAAATACT
1 AAACCCTAAACCATAAACACTAAATACT
* *
6167064 AAACCCTAAAACCCTAAA-ACCTAAACA-T
1 AAACCCT-AAACCATAAACA-CTAAATACT
6167092 AAACCCTAA
1 AAACCCTAA
6167101 CTATATCCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
27 20 0.37
28 20 0.37
29 14 0.26
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (28 bp):
AAACCCTAAACCATAAACACTAAATACT
Found at i:6167194 original size:28 final size:28
Alignment explanation
Indices: 6167129--6167197 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
6167119 CCTCAAACAC
* **
6167129 TAAACACA-AAACACTAAACCTTAAATTA
1 TAAACA-ATAAACCCTAAACCTTAAACCA
*
6167157 TAAACCATAAACCCTAAACCTTAAAACCA
1 TAAACAATAAACCCTAAACCTT-AAACCA
6167186 TAAA-AATAAACC
1 TAAACAATAAACC
6167198 TTTAACCCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.03
28 25 0.74
29 8 0.24
ACGTcount: A:0.57, C:0.25, G:0.00, T:0.19
Consensus pattern (28 bp):
TAAACAATAAACCCTAAACCTTAAACCA
Found at i:6167229 original size:47 final size:48
Alignment explanation
Indices: 6167171--6167296 Score: 123
Period size: 47 Copynumber: 2.7 Consensus size: 48
6167161 CCATAAACCC
* * *
6167171 TAAACCTTAAAACCATAAAAATAAACCTTTAACCCTATAAT-TAAAC-A
1 TAAACCCTAAAACCATAAAAATAAACCCTAAACCCTA-AATGTAAACAA
* ** *
6167218 TAAACCCTAAAACTATAATCATTAACCCTAAACCCTAAATGTAAACAA
1 TAAACCCTAAAACCATAAAAATAAACCCTAAACCCTAAATGTAAACAA
* * * *
6167266 TAAACACTATAACTAT-ACAATAAACCCTAAA
1 TAAACCCTAAAACCATAAAAATAAACCCTAAA
6167297 TATCAAAACC
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
46 3 0.05
47 47 0.72
48 15 0.23
ACGTcount: A:0.52, C:0.23, G:0.01, T:0.24
Consensus pattern (48 bp):
TAAACCCTAAAACCATAAAAATAAACCCTAAACCCTAAATGTAAACAA
Found at i:6167246 original size:21 final size:19
Alignment explanation
Indices: 6167199--6167249 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
6167189 AAATAAACCT
*
6167199 TTAACCCTATAATTAAACA
1 TTAACCCTAAAATTAAACA
* *
6167218 TAAACCCTAAAACTATAATCA
1 TTAACCCTAAAA-T-TAAACA
6167239 TTAACCCTAAA
1 TTAACCCTAAA
6167250 CCCTAAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 10 0.38
20 1 0.04
21 15 0.58
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (19 bp):
TTAACCCTAAAATTAAACA
Found at i:6167269 original size:20 final size:20
Alignment explanation
Indices: 6167246--6167297 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
6167236 TCATTAACCC
*
6167246 TAAACCCTAAATGTAAACAA
1 TAAACCCTAAATCTAAACAA
* *
6167266 TAAACACTATAA-CTATACAA
1 TAAACCCTA-AATCTAAACAA
6167286 TAAACCCTAAAT
1 TAAACCCTAAAT
6167298 ATCAAAACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.54, C:0.21, G:0.02, T:0.23
Consensus pattern (20 bp):
TAAACCCTAAATCTAAACAA
Found at i:6167472 original size:13 final size:13
Alignment explanation
Indices: 6167454--6167478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6167444 AAACTTAACA
6167454 ATAAACCATAAAT
1 ATAAACCATAAAT
6167467 ATAAACCATAAA
1 ATAAACCATAAA
6167479 CCCTAAATCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (13 bp):
ATAAACCATAAAT
Found at i:6167490 original size:7 final size:7
Alignment explanation
Indices: 6167468--6167519 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
6167458 ACCATAAATA
*
6167468 TAAACCA
1 TAAACCC
6167475 TAAACCC
1 TAAACCC
*
6167482 TAAATCC
1 TAAACCC
**
6167489 TAAAAAC
1 TAAACCC
*
6167496 TAAACCT
1 TAAACCC
*
6167503 TAAACAC
1 TAAACCC
6167510 TAAACCC
1 TAAACCC
6167517 TAA
1 TAA
6167520 TCACAAATAA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:6167492 original size:14 final size:13
Alignment explanation
Indices: 6167436--6167515 Score: 56
Period size: 14 Copynumber: 6.0 Consensus size: 13
6167426 TGATAAACTA
*
6167436 TAAACCCTAAA-C
1 TAAACACTAAACC
* *
6167448 TTAACAATAAACC
1 TAAACACTAAACC
*
6167461 ATAAATA-TAAACC
1 -TAAACACTAAACC
*
6167474 ATAAACCCTAAATCC
1 -TAAACACTAAA-CC
*
6167489 TAAAAACTAAACC
1 TAAACACTAAACC
6167502 TTAAACACTAAACC
1 -TAAACACTAAACC
6167516 CTAATCACAA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
12 8 0.15
13 14 0.26
14 29 0.55
15 2 0.04
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAACACTAAACC
Found at i:6167569 original size:15 final size:15
Alignment explanation
Indices: 6167549--6167654 Score: 128
Period size: 15 Copynumber: 7.3 Consensus size: 15
6167539 CACATAACTT
* *
6167549 TAAAACCATAATCCC
1 TAAAACCTTAAACCC
6167564 TAAAACCTTAAACCC
1 TAAAACCTTAAACCC
6167579 TAAAACCTTAAA-CC
1 TAAAACCTTAAACCC
*
6167593 TTAAACCTTAAACCC
1 TAAAACCTTAAACCC
*
6167608 TAAAACC-TAAAACC
1 TAAAACCTTAAACCC
* *
6167622 TAAACCCTAAAACCC
1 TAAAACCTTAAACCC
*
6167637 T-AAACCCTAAACCC
1 TAAAACCTTAAACCC
6167651 TAAA
1 TAAA
6167655 CCCTAAAATA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
14 36 0.47
15 41 0.53
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAAACCTTAAACCC
Found at i:6167577 original size:22 final size:22
Alignment explanation
Indices: 6167551--6167654 Score: 138
Period size: 22 Copynumber: 4.8 Consensus size: 22
6167541 CATAACTTTA
* *
6167551 AAACCATAATCCCTAAAACCTT
1 AAACCCTAAACCCTAAAACCTT
* *
6167573 AAACCCTAAAACCTTAAACCTT
1 AAACCCTAAACCCTAAAACCTT
*
6167595 AAACCTTAAACCCTAAAACC-T
1 AAACCCTAAACCCTAAAACCTT
* *
6167616 AAAACCTAAACCCTAAAACCCT
1 AAACCCTAAACCCTAAAACCTT
6167638 AAACCCTAAACCCTAAA
1 AAACCCTAAACCCTAAA
6167655 CCCTAAAATA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
21 19 0.27
22 52 0.73
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.18
Consensus pattern (22 bp):
AAACCCTAAACCCTAAAACCTT
Found at i:6167582 original size:7 final size:7
Alignment explanation
Indices: 6167551--6167661 Score: 123
Period size: 7 Copynumber: 15.4 Consensus size: 7
6167541 CATAACTTTA
*
6167551 AAACCAT
1 AAACCCT
*
6167558 AATCCCT
1 AAACCCT
*
6167565 AAAACCTT
1 -AAACCCT
6167573 AAACCCT
1 AAACCCT
*
6167580 AAAACCTT
1 -AAACCCT
*
6167588 AAACCTT
1 AAACCCT
*
6167595 AAACCTT
1 AAACCCT
6167602 AAACCCT
1 AAACCCT
*
6167609 AAAACCT
1 AAACCCT
*
6167616 AAAACCT
1 AAACCCT
6167623 AAACCCT
1 AAACCCT
6167630 AAAACCCT
1 -AAACCCT
6167638 AAACCCT
1 AAACCCT
6167645 AAACCCT
1 AAACCCT
6167652 AAACCCT
1 AAACCCT
6167659 AAA
1 AAA
6167662 ATAGNNNNNN
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
7 74 0.80
8 18 0.20
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:6167601 original size:29 final size:28
Alignment explanation
Indices: 6167581--6167662 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 28
6167571 TTAAACCCTA
* * *
6167581 AAACCTTAAACCTTAAACCTTAAACCCTA
1 AAACC-TAAACCTTAAACCCTAAAACCTT
*
6167610 AAACCTAAAACC-TAAACCCTAAAACCCT
1 AAACCT-AAACCTTAAACCCTAAAACCTT
*
6167638 AAACCCTAAACCCTAAACCCTAAAA
1 AAA-CCTAAACCTTAAACCCTAAAA
6167663 TAGNNNNNNN
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 21 0.46
29 25 0.54
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (28 bp):
AAACCTAAACCTTAAACCCTAAAACCTT
Found at i:6167902 original size:20 final size:21
Alignment explanation
Indices: 6167879--6167922 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
6167869 CCTTAAACTC
*
6167879 AAACCATCAACCCTAAA-TAT
1 AAACCATAAACCCTAAATTAT
* *
6167899 AAACCGTAAATCCTAAATTAT
1 AAACCATAAACCCTAAATTAT
6167920 AAA
1 AAA
6167923 TACTAAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.52, C:0.23, G:0.02, T:0.23
Consensus pattern (21 bp):
AAACCATAAACCCTAAATTAT
Found at i:6168078 original size:20 final size:20
Alignment explanation
Indices: 6168035--6168078 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
6168025 GCATCAAACC
*
6168035 TAAACACTAAATCTAAACTT
1 TAAACACTAAATCTAAAATT
*
6168055 TAAACCCTAAAT-TAAAATT
1 TAAACACTAAATCTAAAATT
6168074 ATAAA
1 -TAAA
6168079 TTATAAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAACACTAAATCTAAAATT
Found at i:6168366 original size:48 final size:48
Alignment explanation
Indices: 6168252--6168366 Score: 124
Period size: 48 Copynumber: 2.4 Consensus size: 48
6168242 AATTAAACAT
* * * * *
6168252 TAAACCATAAACCTTAAACTCAAACACTAAAAACTAGACTCTAAATGA
1 TAAACTATAAACCTTAAACTCAAACAATAAAAACTAAACCCTAAATAA
* * *
6168300 TAAACTATAAACCCTAAACTTAAACAATAAATACTAAACCCTAAA-AA
1 TAAACTATAAACCTTAAACTCAAACAATAAAAACTAAACCCTAAATAA
* *
6168347 CTAAACTTTAAACATTAAAC
1 -TAAACTATAAACCTTAAAC
6168367 CCTAATTACA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.02
48 54 0.98
ACGTcount: A:0.54, C:0.22, G:0.02, T:0.23
Consensus pattern (48 bp):
TAAACTATAAACCTTAAACTCAAACAATAAAAACTAAACCCTAAATAA
Found at i:6169308 original size:20 final size:20
Alignment explanation
Indices: 6169236--6169308 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
6169226 CAGTAAAAAC
*
6169236 TAAACCCTAAATGATAAACTA
1 TAAACCCTAAAT-ATAAACAA
6169257 TAAACCCTAAACT-TAAACAA
1 TAAACCCTAAA-TATAAACAA
* *
6169277 TAAACCTTAAATATAAACCA
1 TAAACCCTAAATATAAACAA
*
6169297 TAAATCCTAAAT
1 TAAACCCTAAAT
6169309 CTGAAAAACT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.02
20 32 0.71
21 11 0.24
22 1 0.02
ACGTcount: A:0.53, C:0.21, G:0.01, T:0.25
Consensus pattern (20 bp):
TAAACCCTAAATATAAACAA
Found at i:6169539 original size:7 final size:7
Alignment explanation
Indices: 6169523--6169573 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
6169513 ACTCGAACGT
6169523 TAAACCC
1 TAAACCC
*
6169530 TAAACAC
1 TAAACCC
*
6169537 TAAACAC
1 TAAACCC
6169544 -AAACCC
1 TAAACCC
**
6169550 TAAACTT
1 TAAACCC
6169557 TAAACCC
1 TAAACCC
6169564 TAAACCC
1 TAAACCC
6169571 TAA
1 TAA
6169574 CTAAAACTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:6169547 original size:20 final size:21
Alignment explanation
Indices: 6169523--6169573 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
6169513 ACTCGAACGT
6169523 TAAACCCTAAACACTAAACAC
1 TAAACCCTAAACACTAAACAC
** *
6169544 -AAACCCTAAACTTTAAACCC
1 TAAACCCTAAACACTAAACAC
6169564 TAAACCCTAA
1 TAAACCCTAA
6169574 CTAAAACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (21 bp):
TAAACCCTAAACACTAAACAC
Found at i:6169599 original size:30 final size:31
Alignment explanation
Indices: 6169564--6169621 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
6169554 CTTTAAACCC
6169564 TAAACCCTAACTA-AAACTAAACCATAAGCA
1 TAAACCCTAACTATAAACTAAACCATAAGCA
* **
6169594 TAAACCCTAATTATATCCTAAACCATAA
1 TAAACCCTAACTATAAACTAAACCATAA
6169622 CCTCAAACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.50, C:0.26, G:0.02, T:0.22
Consensus pattern (31 bp):
TAAACCCTAACTATAAACTAAACCATAAGCA
Found at i:6169642 original size:27 final size:27
Alignment explanation
Indices: 6169611--6169676 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
6169601 TAATTATATC
* *
6169611 CTAAACCATAACCTCAAACACTAAACA
1 CTAAACCATAAACTAAAACACTAAACA
* * * *
6169638 CTAAACCTTAAAGTAAAACCCTAAACC
1 CTAAACCATAAACTAAAACACTAAACA
*
6169665 CTAAACCTTAAA
1 CTAAACCATAAA
6169677 ACCATAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.18
Consensus pattern (27 bp):
CTAAACCATAAACTAAAACACTAAACA
Found at i:6170062 original size:20 final size:21
Alignment explanation
Indices: 6170039--6170081 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
6170029 NCTAAGCTCC
*
6170039 AACCATCAACCCTAAA-TATA
1 AACCATAAACCCTAAATTATA
*
6170059 AACCATAAATCCTAAATTATA
1 AACCATAAACCCTAAATTATA
6170080 AA
1 AA
6170082 TACTAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCATAAACCCTAAATTATA
Found at i:6170189 original size:14 final size:14
Alignment explanation
Indices: 6170142--6170231 Score: 57
Period size: 13 Copynumber: 6.7 Consensus size: 14
6170132 TTAAATTTTA
*
6170142 ACTAAACCCTAAAC
1 ACTAAAACCTAAAC
*
6170156 CCT-AAA-CTAAA-
1 ACTAAAACCTAAAC
6170167 ACTACAAACCCTAAAC
1 ACTA-AAA-CCTAAAC
6170183 A-TAAAACCTAAAC
1 ACTAAAACCTAAAC
*
6170196 ACT-AAATCTAAAC
1 ACTAAAACCTAAAC
* * *
6170209 -TTTAAACCTTAAC
1 ACTAAAACCTAAAC
*
6170222 CCTAAAACCT
1 ACTAAAACCT
6170232 TAAAAATAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
11 2 0.03
12 6 0.10
13 30 0.51
14 13 0.22
15 7 0.12
16 1 0.02
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (14 bp):
ACTAAAACCTAAAC
Found at i:6170189 original size:27 final size:29
Alignment explanation
Indices: 6170145--6170199 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
6170135 AATTTTAACT
*
6170145 AAACCCTAAACCCTAAA-CTAAA-ACTAC
1 AAACCCTAAACCATAAACCTAAACACTAC
6170172 AAACCCTAAA-CATAAAACCTAAACACTA
1 AAACCCTAAACCAT-AAACCTAAACACTA
6170200 AATCTAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 2 0.08
27 13 0.54
28 5 0.21
29 4 0.17
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.15
Consensus pattern (29 bp):
AAACCCTAAACCATAAACCTAAACACTAC
Found at i:6170195 original size:20 final size:19
Alignment explanation
Indices: 6170141--6170207 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
6170131 ATTAAATTTT
*
6170141 AACTAAACCCTAAACCCTA
1 AACTAAAACCTAAACCCTA
6170160 AACTAAAA-CTACAAACCCTA
1 AACTAAAACCT--AAACCCTA
*
6170180 AACATAAAACCTAAACACTA
1 AAC-TAAAACCTAAACCCTA
6170200 AATCTAAA
1 AA-CTAAA
6170208 CTTTAAACCT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
18 2 0.05
19 7 0.17
20 24 0.59
21 6 0.15
22 2 0.05
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.16
Consensus pattern (19 bp):
AACTAAAACCTAAACCCTA
Found at i:6170216 original size:40 final size:39
Alignment explanation
Indices: 6170144--6170262 Score: 114
Period size: 40 Copynumber: 3.0 Consensus size: 39
6170134 AAATTTTAAC
* * **
6170144 TAAACCCTAAACCCTAAACTAAAACTACAAACCCTAAACA
1 TAAAACCTAAACACTAAACT-AAACTTTAAACCCTAAACA
* * *
6170184 TAAAACCTAAACACTAAATCTAAACTTTAAACCTTAACCC
1 TAAAACCTAAACACTAAA-CTAAACTTTAAACCCTAAACA
* *
6170224 TAAAACCTTAAA-AATAAACTTAAACTTTAAACCCCAAAC
1 TAAAACC-TAAACACTAAAC-TAAACTTTAAACCCTAAAC
6170263 CTTAAAACAT
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
39 1 0.02
40 58 0.89
41 6 0.09
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (39 bp):
TAAAACCTAAACACTAAACTAAACTTTAAACCCTAAACA
Found at i:6170247 original size:33 final size:34
Alignment explanation
Indices: 6170204--6170269 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
6170194 ACACTAAATC
6170204 TAAACTTTAAACCTT-AACCCTAAAACCTTAAAAA
1 TAAACTTTAAACCTTAAACCC-AAAACCTTAAAAA
* *
6170238 TAAAC-TTAAACTTTAAACCCCAAACCTTAAAA
1 TAAACTTTAAACCTTAAACCCAAAACCTTAAAA
6170270 CATTAAATCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 19 0.66
34 10 0.34
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (34 bp):
TAAACTTTAAACCTTAAACCCAAAACCTTAAAAA
Done.