Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 171 of 208
Found at i:52119381 original size:2 final size:2
Alignment explanation
Indices: 52119374--52119412 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
52119364 GTAAGGCAGT
*
52119374 GA GA GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
52119413 TTGTTTTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52126549 original size:21 final size:21
Alignment explanation
Indices: 52126523--52126563 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52126513 TTTTATCATA
* * *
52126523 AAAATTTTAAACAATTTAAAT
1 AAAATTATAAAAAATATAAAT
52126544 AAAATTATAAAAAATATAAA
1 AAAATTATAAAAAATATAAA
52126564 ATCATTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATTATAAAAAATATAAAT
Found at i:52131095 original size:43 final size:43
Alignment explanation
Indices: 52131011--52131096 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
52131001 CTTTTTTTCT
**
52131011 TTTTTATTCCAATTCATATGTTTAAATACAAAGTATGCATTTA
1 TTTTTATTCCAATTCATATGTTTAAATACAAAGTAAACATTTA
* * *
52131054 TTTTTATTTCAATTTATATGTTTACATACAAAGTAAACATTTA
1 TTTTTATTCCAATTCATATGTTTAAATACAAAGTAAACATTTA
52131097 AATAGGAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (43 bp):
TTTTTATTCCAATTCATATGTTTAAATACAAAGTAAACATTTA
Found at i:52133852 original size:40 final size:40
Alignment explanation
Indices: 52133756--52133873 Score: 127
Period size: 40 Copynumber: 3.0 Consensus size: 40
52133746 GGCATTTGGA
* *
52133756 TAAAAAACGCCGCTAAAAATCA-AGCATTAGCGGCAC-TTT
1 TAAAAAAAGCCGCTAAAAAT-AGAGCATTAGCGGCGCTTTT
* * * *
52133795 TAAAAAGATGCCACTAAAGATAGAGTATTAGCGGCGCTTTT
1 TAAAAA-AAGCCGCTAAAAATAGAGCATTAGCGGCGCTTTT
*
52133836 TAAAAAAAGCCGCTAAAAAT-GAGCATTAGCAGCG-TTTT
1 TAAAAAAAGCCGCTAAAAATAGAGCATTAGCGGCGCTTTT
52133874 CCAAAAAGTG
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
38 4 0.06
39 19 0.29
40 34 0.52
41 9 0.14
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.24
Consensus pattern (40 bp):
TAAAAAAAGCCGCTAAAAATAGAGCATTAGCGGCGCTTTT
Found at i:52133912 original size:41 final size:40
Alignment explanation
Indices: 52133861--52133979 Score: 157
Period size: 41 Copynumber: 2.9 Consensus size: 40
52133851 AAAATGAGCA
* * *
52133861 TTAGCAGCGTTTTCCAAAAAGTGCCACTAATGCTCAGGGCT
1 TTAGCGGCGTTTT-CAAAAAGCGCCGCTAATGCTCAGGGCT
*
52133902 TTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTCAGGGCT
1 TTAGCGGCGTTTTCAAA-AAGCGCCGCTAATGCTCAGGGCT
* *
52133943 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAG
1 TTAGCGGCG-TTTTCAAAAAGCGCCGCTAATGCTCAG
52133980 ATTTATCATA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
40 3 0.04
41 61 0.87
42 6 0.09
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
TTAGCGGCGTTTTCAAAAAGCGCCGCTAATGCTCAGGGCT
Found at i:52133928 original size:80 final size:80
Alignment explanation
Indices: 52133756--52133931 Score: 200
Period size: 80 Copynumber: 2.2 Consensus size: 80
52133746 GGCATTTGGA
*
52133756 TAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCACTTTTAAAAAGATGCCACTAAAGATAGAGT
1 TAAAAAACGCCGCTAAAAATCAAGCATTAGCAGCACTTTTAAAAAGATGCCACTAAAGATAGAGT
52133821 ATTAGCGGCGCTTTT
66 ATTAGCGGCGCTTTT
* * * * *
52133836 TAAAAAAAGCCGCTAAAAAT-GAGCATTAGCAGC-GTTTTCCAAAAAG-TGCCACTAATGCTCAG
1 TAAAAAACGCCGCTAAAAATCAAGCATTAGCAGCACTTTT--AAAAAGATGCCACTAAAGAT-AG
*
52133898 GGCT-TTAGCGGCG-TTTT
63 AG-TATTAGCGGCGCTTTT
*
52133915 TAAAGAAGCGCCGCTAA
1 TAAA-AAACGCCGCTAA
52133932 TGCTCAGGGC
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
78 4 0.05
79 30 0.37
80 47 0.57
81 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (80 bp):
TAAAAAACGCCGCTAAAAATCAAGCATTAGCAGCACTTTTAAAAAGATGCCACTAAAGATAGAGT
ATTAGCGGCGCTTTT
Found at i:52134651 original size:15 final size:15
Alignment explanation
Indices: 52134631--52134679 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
52134621 TCTAAGGTAA
52134631 TTTAGGGATTATGTG
1 TTTAGGGATTATGTG
52134646 TTTAGGGATTATG-G
1 TTTAGGGATTATGTG
* *
52134660 ATTATGGATTATGTGG
1 TTTAGGGATTATGT-G
52134676 TTTA
1 TTTA
52134680 AGGGTTAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 12 0.41
15 13 0.45
16 4 0.14
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (15 bp):
TTTAGGGATTATGTG
Found at i:52134691 original size:14 final size:14
Alignment explanation
Indices: 52134674--52134703 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52134664 TGGATTATGT
52134674 GGTTTAAGGGTTAG
1 GGTTTAAGGGTTAG
*
52134688 GGTTTAAGGTTTAG
1 GGTTTAAGGGTTAG
52134702 GG
1 GG
52134704 AGTTACTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.43, T:0.37
Consensus pattern (14 bp):
GGTTTAAGGGTTAG
Found at i:52139661 original size:43 final size:43
Alignment explanation
Indices: 52139585--52139836 Score: 283
Period size: 43 Copynumber: 5.9 Consensus size: 43
52139575 TTTTTACTAG
* * *
52139585 AAGCGCCACTAAAGGT-TTGTTCTTTAGCGGCGTTTGTGATAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAA
* * * * *
52139627 AAGTGCTGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGATAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAA
* *
52139670 AAGCGCAGCTAAAGGTCTTGGTCTTTAGTGGCGTTTGTG-GAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAA
* ** ** ** * *
52139712 GAAGTGCCGCTAAAGACCAAGACCTTTAGCAGCGTTTGTGGGAA
1 -AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAA
* *
52139756 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGGA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAA
*
52139799 AAGCGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTGT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT
52139837 TTCTAAAAAC
Statistics
Matches: 175, Mismatches: 32, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
42 15 0.09
43 157 0.90
44 3 0.02
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.29
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAA
Found at i:52139956 original size:22 final size:22
Alignment explanation
Indices: 52139928--52139970 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
52139918 TAGCGGCGCT
*
52139928 AAAAAGCGCAGCTAAAGGCCTA
1 AAAAAGCGCAGCTAAAAGCCTA
*
52139950 AAAAAGCGCTGCTAAAAGCCT
1 AAAAAGCGCAGCTAAAAGCCT
52139971 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAAGCGCAGCTAAAAGCCTA
Found at i:52150655 original size:44 final size:44
Alignment explanation
Indices: 52150605--52150692 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
52150595 ATTAACATAA
** **
52150605 AATAGAAGTTGTGATAATTATGCATTTAAAAATAATTATAATTT
1 AATAGAAGTTGCAATAATTACACATTTAAAAATAATTATAATTT
* *
52150649 AATAGAATTTGCAATAATTACACATTTAAAAATGATTATAATTT
1 AATAGAAGTTGCAATAATTACACATTTAAAAATAATTATAATTT
52150693 CATTTACATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (44 bp):
AATAGAAGTTGCAATAATTACACATTTAAAAATAATTATAATTT
Found at i:52151665 original size:19 final size:20
Alignment explanation
Indices: 52151640--52151687 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
52151630 AATGATAAAA
52151640 AATAAAAATCAATAAAATTT
1 AATAAAAATCAATAAAATTT
* *
52151660 -ATAAAACA-CATTAAATTTT
1 AATAAAA-ATCAATAAAATTT
52151679 AATAAAAAT
1 AATAAAAAT
52151688 ATAAGAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAAAAATCAATAAAATTT
Found at i:52151704 original size:28 final size:28
Alignment explanation
Indices: 52151652--52151727 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
52151642 TAAAAATCAA
* * *
52151652 TAAAATTTATAAAACACATTAAATTTTAA-
1 TAAAAATTATAAAA-ATATTTAA-TTTAAT
52151681 TAAAAA-TATAAGAAATATTTAATTTAAT
1 TAAAAATTATAA-AAATATTTAATTTAAT
52151709 TAAAAATTATAAAAATATT
1 TAAAAATTATAAAAATATT
52151728 ATAAAAATTG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 5 0.12
28 24 0.59
29 12 0.29
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (28 bp):
TAAAAATTATAAAAATATTTAATTTAAT
Found at i:52152033 original size:10 final size:9
Alignment explanation
Indices: 52152020--52152118 Score: 51
Period size: 9 Copynumber: 10.4 Consensus size: 9
52152010 TTTTTAAGTA
52152020 TTTTATAATT
1 TTTTATAA-T
*
52152030 TTTTATGAT
1 TTTTATAAT
*
52152039 TTTTATAAAA
1 TTTTAT-AAT
52152049 TTTTAT-AT
1 TTTTATAAT
*
52152057 ATTTTATTAAAG
1 -TTTTA-T-AAT
* *
52152069 TTTAATCAT
1 TTTTATAAT
52152078 TTTTATAAT
1 TTTTATAAT
52152087 TTTT-T-AT
1 TTTTATAAT
*
52152094 TGATTTTTAAT
1 T--TTTATAAT
52152105 TTTTATAACT
1 TTTTATAA-T
52152115 TTTT
1 TTTT
52152119 TTTCACATTT
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
7 3 0.04
8 2 0.03
9 33 0.49
10 22 0.32
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:52152052 original size:20 final size:19
Alignment explanation
Indices: 52152020--52152102 Score: 78
Period size: 19 Copynumber: 4.3 Consensus size: 19
52152010 TTTTTAAGTA
*
52152020 TTTTATAATTTTTTATGAT
1 TTTTATAAATTTTTATGAT
*
52152039 TTTTATAAAATTTTAT-AT
1 TTTTATAAATTTTTATGAT
* * *
52152057 ATTTTATTAAAGTTTAATCAT
1 -TTTTA-TAAATTTTTATGAT
*
52152078 TTTTATAATTTTTTATTGAT
1 TTTTATAAATTTTTA-TGAT
52152098 TTTTA
1 TTTTA
52152103 ATTTTTATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
18 2 0.04
19 26 0.50
20 22 0.42
21 2 0.04
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTATAAATTTTTATGAT
Found at i:52152483 original size:91 final size:91
Alignment explanation
Indices: 52152292--52152483 Score: 221
Period size: 94 Copynumber: 2.1 Consensus size: 91
52152282 TTTTGAGGGC
*
52152292 CTTTGTTT-ATGCATTTTGATAATTCAATTACTCAATTGAGTGCAAAAAAAAAAAAAGTAAGGGC
1 CTTT-TTTGATGCATTTTGATAATTCAAATACTCAATTGAGTGCAAAAAAAAAAAAAG-AA--GC
* *
52152356 TTAATTGCTTTTCTTAAAAAGATTTAAAGG
62 TTAATTACTTTTCTGAAAAAGATTTAAAGG
* * *
52152386 CTTTTTTGATGCATTTTGA-AAGTTTAAATACTCAATTGAGTAGCAAACAAAAAATAAA-AA-TT
1 CTTTTTTGATGCATTTTGATAA-TTCAAATACTCAATTGAGT-GCAAA-AAAAAAAAAAGAAGCT
*
52152448 TAATTACTTTTCTGAAAAAGAATTTGAAGG
63 TAATTACTTTTCTGAAAAAG-ATTTAAAGG
52152478 CTTTTT
1 CTTTTT
52152484 ATACCCTTAA
Statistics
Matches: 86, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
91 19 0.22
92 14 0.16
93 5 0.06
94 34 0.40
95 5 0.06
96 9 0.10
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (91 bp):
CTTTTTTGATGCATTTTGATAATTCAAATACTCAATTGAGTGCAAAAAAAAAAAAAGAAGCTTAA
TTACTTTTCTGAAAAAGATTTAAAGG
Found at i:52170600 original size:19 final size:19
Alignment explanation
Indices: 52170578--52170648 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
52170568 AGAAATTACT
*
52170578 AAAATTTTATAAATTTATA
1 AAAATTATATAAATTTATA
*
52170597 AAAATTATATAAA-CTATTA
1 AAAATTATATAAATTTA-TA
*
52170616 AAAACTAT-TAAATGTTATA
1 AAAATTATATAAAT-TTATA
52170635 AAAATT-TA-AAATTT
1 AAAATTATATAAATTT
52170649 TATTATTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
17 2 0.05
18 11 0.26
19 28 0.65
20 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (19 bp):
AAAATTATATAAATTTATA
Found at i:52170736 original size:29 final size:30
Alignment explanation
Indices: 52170689--52170761 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
52170679 TATAATCTAA
**
52170689 AAAAATCAATTAAGCCCTCTTAAAATAATT
1 AAAAATCAATTAAGCCCTCGAAAAATAATT
**
52170719 AAAAA-CAATTAATTCCTCGAAAAATAATT
1 AAAAATCAATTAAGCCCTCGAAAAATAATT
*
52170748 AAAATATAAATTAA
1 AAAA-ATCAATTAA
52170762 CTTTTCACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 24 0.67
30 6 0.17
31 6 0.17
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (30 bp):
AAAAATCAATTAAGCCCTCGAAAAATAATT
Found at i:52170978 original size:59 final size:59
Alignment explanation
Indices: 52170886--52171017 Score: 228
Period size: 59 Copynumber: 2.2 Consensus size: 59
52170876 ACCATATTAC
*
52170886 AGGGGCTCAATTAACTGCTAACTTTCGATTAAAGGTTTAATTGATTGCACTTTTTGACA
1 AGGGGCTCAATTAACTACTAACTTTCGATTAAAGGTTTAATTGATTGCACTTTTTGACA
* * *
52170945 AGGGGCTCAATTAATTACTAATTTTCGATTAAAGGTTTAATTGATTGCATTTTTTGACA
1 AGGGGCTCAATTAACTACTAACTTTCGATTAAAGGTTTAATTGATTGCACTTTTTGACA
52171004 AGGGGCTCAATTAA
1 AGGGGCTCAATTAA
52171018 ATTTACAATT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 69 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (59 bp):
AGGGGCTCAATTAACTACTAACTTTCGATTAAAGGTTTAATTGATTGCACTTTTTGACA
Found at i:52171015 original size:29 final size:29
Alignment explanation
Indices: 52170924--52171015 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
52170914 TTAAAGGTTT
*
52170924 AATTGATTGCACTTTTTGACAAGGGGCTC
1 AATTGATTGCAATTTTTGACAAGGGGCTC
* * * * * * *
52170953 AATTAATTACTAATTTTCGATTAA-AGGTTT
1 AATTGATTGC-AATTTTTGA-CAAGGGGCTC
*
52170983 AATTGATTGCATTTTTTGACAAGGGGCTC
1 AATTGATTGCAATTTTTGACAAGGGGCTC
52171012 AATT
1 AATT
52171016 AAATTTACAA
Statistics
Matches: 44, Mismatches: 16, Indels: 6
0.67 0.24 0.09
Matches are distributed among these distances:
28 2 0.05
29 22 0.50
30 18 0.41
31 2 0.05
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.40
Consensus pattern (29 bp):
AATTGATTGCAATTTTTGACAAGGGGCTC
Found at i:52182822 original size:11 final size:11
Alignment explanation
Indices: 52182806--52182837 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
52182796 GAAGACATAC
52182806 GAACCAAAGAA
1 GAACCAAAGAA
52182817 GAACCAAAGAA
1 GAACCAAAGAA
52182828 GAACCAAAGA
1 GAACCAAAGA
52182838 TATGGATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.62, C:0.19, G:0.19, T:0.00
Consensus pattern (11 bp):
GAACCAAAGAA
Found at i:52188977 original size:16 final size:16
Alignment explanation
Indices: 52188956--52189011 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
52188946 CATTTGGTTC
52188956 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
52188972 GCTGTAATTGAATAGA
1 GCTGTAATGGAATAGA
*
52188988 GCTATAATGGAATAGA
1 GCTGTAATGGAATAGA
52189004 GCTGTAAT
1 GCTGTAAT
52189012 AGTAATTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:52189047 original size:45 final size:44
Alignment explanation
Indices: 52188993--52189085 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
52188983 ATAGAGCTAT
*
52188993 AATGGAATAGAGCTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
52189038 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
52189082 AATG
1 AATG
52189086 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:52189094 original size:39 final size:41
Alignment explanation
Indices: 52188993--52189097 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 41
52188983 ATAGAGCTAT
52188993 AATGGAATAGA-GCTGTAATAGTAATTCAATTGTTTGGTTG
1 AATGGAATAGATGCTGTAATAGTAATTCAATTGTTTGGTTG
* *
52189033 AATGGAATGGAATAGAACTGTAATAGT-ATTC-TTGTGTTTGGTTG
1 AATGGAATAG-AT-G--CTGTAATAGTAATTCAAT-TGTTTGGTTG
*
52189077 AATGGAAT-GATGTTGTAATAG
1 AATGGAATAGATGCTGTAATAG
52189098 CATAAGGAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 8 0.14
40 9 0.16
41 2 0.04
42 2 0.04
43 3 0.05
44 22 0.39
45 10 0.18
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (41 bp):
AATGGAATAGATGCTGTAATAGTAATTCAATTGTTTGGTTG
Found at i:52189264 original size:18 final size:18
Alignment explanation
Indices: 52189241--52189276 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
52189231 AATTATTATT
52189241 AAATATAATTTAATAAAA
1 AAATATAATTTAATAAAA
52189259 AAATATAATTTAATAAAA
1 AAATATAATTTAATAAAA
52189277 TTCTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATAATTTAATAAAA
Found at i:52189306 original size:55 final size:54
Alignment explanation
Indices: 52189208--52189313 Score: 133
Period size: 55 Copynumber: 1.9 Consensus size: 54
52189198 TAAATAATAA
* * *
52189208 ATAATTTAATCATATTTTAACATAATTATTATTAAATATAATTTAATAAAAAAAT
1 ATAATTTAATAAAATTTTAAAATAATTATTATT-AATATAATTTAATAAAAAAAT
* *
52189263 ATAATTTAATAAAATTCTTAAAATAATTATTCTT-ATATGAATTTACTAAAA
1 ATAATTTAATAAAATT-TTAAAATAATTATTATTAATAT-AATTTAATAAAA
52189314 TCATAATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
54 4 0.09
55 25 0.57
56 15 0.34
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (54 bp):
ATAATTTAATAAAATTTTAAAATAATTATTATTAATATAATTTAATAAAAAAAT
Found at i:52201630 original size:34 final size:35
Alignment explanation
Indices: 52201592--52201662 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 35
52201582 ATGAGTATAG
52201592 TTGAATTATGAAGTCTTATAGTAGAAAAT-AAATT
1 TTGAATTATGAAGTCTTATAGTAGAAAATGAAATT
52201626 TTGAATTATGAAGTCTTATAGTAGAAAATGAAATT
1 TTGAATTATGAAGTCTTATAGTAGAAAATGAAATT
52201661 TT
1 TT
52201663 TTTGATAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 29 0.81
35 7 0.19
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (35 bp):
TTGAATTATGAAGTCTTATAGTAGAAAATGAAATT
Found at i:52203779 original size:11 final size:11
Alignment explanation
Indices: 52203763--52203818 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
52203753 TTTTATGATC
52203763 CATTTCAATTT
1 CATTTCAATTT
52203774 CATTTC-ATTT
1 CATTTCAATTT
* *
52203784 CATATC-ATCCT
1 CATTTCAAT-TT
*
52203795 CATTTCAGTTT
1 CATTTCAATTT
*
52203806 CATTTCAAGTT
1 CATTTCAATTT
52203817 CA
1 CA
52203819 AATCATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
10 11 0.31
11 24 0.67
12 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.04, T:0.48
Consensus pattern (11 bp):
CATTTCAATTT
Found at i:52203780 original size:5 final size:5
Alignment explanation
Indices: 52203763--52203812 Score: 55
Period size: 5 Copynumber: 9.4 Consensus size: 5
52203753 TTTTATGATC
* *
52203763 CATTT CAATTT CATTT CATTT CATAT CATCCT CATTT CAGTTT CATTT
1 CATTT C-ATTT CATTT CATTT CATTT CAT-TT CATTT CA-TTT CATTT
52203811 CA
1 CA
52203813 AGTTCAAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
5 25 0.64
6 14 0.36
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.50
Consensus pattern (5 bp):
CATTT
Found at i:52215057 original size:19 final size:19
Alignment explanation
Indices: 52215033--52215070 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
52215023 TGGGCCACTC
52215033 TGGGCCAAAATGGGC-CGTG
1 TGGGCC-AAATGGGCTCGTG
*
52215052 TGGGCCCAATGGGCTCGTG
1 TGGGCCAAATGGGCTCGTG
52215071 GGCCCCACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.16, C:0.24, G:0.42, T:0.18
Consensus pattern (19 bp):
TGGGCCAAATGGGCTCGTG
Found at i:52215404 original size:27 final size:27
Alignment explanation
Indices: 52215301--52215409 Score: 132
Period size: 27 Copynumber: 4.0 Consensus size: 27
52215291 AAATAATCTC
*
52215301 ATAGGGTAAAATGATCGAAATACTCCC-
1 ATAGGGTAAAATGACCGAAATAC-CCCT
52215328 ATAGGGTAAAATGACCGAAATA-CCCT
1 ATAGGGTAAAATGACCGAAATACCCCT
**
52215354 CATAGGGTAAAATGACTAAAATACCCCT
1 -ATAGGGTAAAATGACCGAAATACCCCT
* **
52215382 ATAGGGTAAAATGTCCGTTATACCCCT
1 ATAGGGTAAAATGACCGAAATACCCCT
52215409 A
1 A
52215410 GGAGATAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
25 3 0.04
27 64 0.90
28 4 0.06
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.23
Consensus pattern (27 bp):
ATAGGGTAAAATGACCGAAATACCCCT
Found at i:52215405 original size:54 final size:54
Alignment explanation
Indices: 52215286--52215425 Score: 162
Period size: 54 Copynumber: 2.6 Consensus size: 54
52215276 GTCGATATAC
** *
52215286 GACCGAAATAATCTCATAGGGTAAAATGA-TCGAAATACTCCCATAGGGTAAAAT
1 GACCGAAATACCCTCATAGGGTAAAATGACT-AAAATACTCCCATAGGGTAAAAT
52215340 GACCGAAATACCCTCATAGGGTAAAATGACTAAAATAC-CCCTATAGGGTAAAAT
1 GACCGAAATACCCTCATAGGGTAAAATGACTAAAATACTCCC-ATAGGGTAAAAT
* **
52215394 GTCCGTTATACCC-C-TAGGAGATAAAATGACTA
1 GACCGAAATACCCTCATAGG-G-TAAAATGACTA
52215426 TTATGGCCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
52 4 0.05
53 5 0.07
54 66 0.87
55 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (54 bp):
GACCGAAATACCCTCATAGGGTAAAATGACTAAAATACTCCCATAGGGTAAAAT
Found at i:52215808 original size:28 final size:28
Alignment explanation
Indices: 52215774--52215844 Score: 133
Period size: 28 Copynumber: 2.5 Consensus size: 28
52215764 ATGTTACTAT
52215774 ATTGGGCTAAGGCCCACACTGATACTGA
1 ATTGGGCTAAGGCCCACACTGATACTGA
*
52215802 ATTGGGCTAAGGCCCACACTGCTACTGA
1 ATTGGGCTAAGGCCCACACTGATACTGA
52215830 ATTGGGCTAAGGCCC
1 ATTGGGCTAAGGCCC
52215845 TCATTGTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (28 bp):
ATTGGGCTAAGGCCCACACTGATACTGA
Found at i:52218370 original size:6 final size:6
Alignment explanation
Indices: 52218349--52218392 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
52218339 ACCCTTCTTC
* *
52218349 TCCCCTT TCTCCT TCCCCT TCCCCT TCCCTT TCCCCT TCCCCT T
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
52218393 GGGTTGCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
6 29 0.88
7 4 0.12
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (6 bp):
TCCCCT
Found at i:52221149 original size:12 final size:12
Alignment explanation
Indices: 52221123--52221155 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
52221113 ATGCAACAGG
52221123 AAACCAGCA-GC
1 AAACCAGCATGC
52221134 AAACCAGCATGC
1 AAACCAGCATGC
52221146 AAACCAGCAT
1 AAACCAGCAT
52221156 CCAAGCTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.45, C:0.33, G:0.15, T:0.06
Consensus pattern (12 bp):
AAACCAGCATGC
Found at i:52222176 original size:16 final size:18
Alignment explanation
Indices: 52222152--52222204 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
52222142 TATGAAAAAA
* *
52222152 ATTAAAATATAAAAATTT
1 ATTAATATATATAAATTT
52222170 ATTAATATGTATATAAATTT
1 ATTAATA--TATATAAATTT
*
52222190 ATTAATATATGTAAA
1 ATTAATATATATAAA
52222205 AATAACTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 13 0.43
20 17 0.57
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (18 bp):
ATTAATATATATAAATTT
Found at i:52222199 original size:22 final size:20
Alignment explanation
Indices: 52222159--52222207 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
52222149 AAAATTAAAA
52222159 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
52222179 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
52222199 TGTAAAAAT
1 TATAAAAAT
52222208 AACTTTTTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:52222755 original size:21 final size:21
Alignment explanation
Indices: 52222731--52222783 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
52222721 CGCTGTTTCT
*
52222731 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTATCC
*
52222752 AATCTCACCGCTACAGTATCT
1 AATCTCACCGCTACAGTATCC
52222773 AATCTCACCGC
1 AATCTCACCGC
52222784 CACCACTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.36, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTATCC
Found at i:52224756 original size:2 final size:2
Alignment explanation
Indices: 52224749--52224774 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52224739 AAGAACCCAT
52224749 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
52224775 TATGACTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:52228539 original size:21 final size:21
Alignment explanation
Indices: 52228515--52228624 Score: 69
Period size: 21 Copynumber: 5.2 Consensus size: 21
52228505 AAAGCCCGAA
52228515 GGTTGAACAGAAACCCATAAG
1 GGTTGAACAGAAACCCATAAG
* * * *
52228536 GGTTGAACGGAAGCTCGTAAG
1 GGTTGAACAGAAACCCATAAG
* *
52228557 AGCTGAAC-GAAAACCCATAAGG
1 GGTTGAACAG-AAACCCATAA-G
* * * * *
52228579 GGTTAAACTGAAGCTCAAAAG
1 GGTTGAACAGAAACCCATAAG
* * *
52228600 AGCTGAACAGAAACCCATTAG
1 GGTTGAACAGAAACCCATAAG
52228621 GGTT
1 GGTT
52228625 AAACTGAAGC
Statistics
Matches: 61, Mismatches: 25, Indels: 6
0.66 0.27 0.07
Matches are distributed among these distances:
20 1 0.02
21 46 0.75
22 13 0.21
23 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.16
Consensus pattern (21 bp):
GGTTGAACAGAAACCCATAAG
Found at i:52228601 original size:43 final size:42
Alignment explanation
Indices: 52228518--52228679 Score: 182
Period size: 42 Copynumber: 3.8 Consensus size: 42
52228508 GCCCGAAGGT
* * **
52228518 TGAACAGAAACCCATAAGGGTTGAACGGAAGCTCGTAAGAGC
1 TGAACAGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGC
52228560 TGAAC-GAAAACCCATAAGGGGTTAAACTGAAGCTCAAAAGAGC
1 TGAACAG-AAACCCATAA-GGGTTAAACTGAAGCTCAAAAGAGC
* *
52228603 TGAACAGAAACCCATTAGGGTTAAACTGAAGCTAAAAAGAGC
1 TGAACAGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGC
* ** * * * *
52228645 TTAATGGAGACCCATTAGGGTTAAACGGAAACTCA
1 TGAACAGAAACCCATAAGGGTTAAACTGAAGCTCA
52228680 TATGACTTAA
Statistics
Matches: 104, Mismatches: 13, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 67 0.64
43 35 0.34
44 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (42 bp):
TGAACAGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGC
Found at i:52231071 original size:3 final size:3
Alignment explanation
Indices: 52231063--52231105 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
52231053 TATACTAAAT
52231063 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
52231106 TAAAAAATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:52232303 original size:9 final size:9
Alignment explanation
Indices: 52232286--52232322 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52232276 TGAGTTTTCG
52232286 AATTCGAAT
1 AATTCGAAT
*
52232295 AACTCGAAT
1 AATTCGAAT
52232304 AATTCGAAT
1 AATTCGAAT
52232313 AATTCGAAT
1 AATTCGAAT
52232322 A
1 A
52232323 TCAAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:52232712 original size:17 final size:17
Alignment explanation
Indices: 52232673--52232718 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
52232663 ACTCCCCCTA
52232673 TTTACTTTCCCTC-AAACT
1 TTTA-TTTCCC-CAAAACT
52232691 TTTA-TTCCCCAAAACTT
1 TTTATTTCCCCAAAAC-T
52232708 TTTATTTCCCC
1 TTTATTTCCCC
52232719 CCTAAACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 9 0.36
17 5 0.20
18 10 0.40
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTATTTCCCCAAAACT
Found at i:52235198 original size:50 final size:50
Alignment explanation
Indices: 52235131--52235420 Score: 296
Period size: 50 Copynumber: 5.7 Consensus size: 50
52235121 TTTCTTGTAC
* * * * ** * * *
52235131 TGCCAATGCCATATCCCATATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATCTTGA
* * * * * *
52235181 TGCCCATGCCATGTCCCAAACATGGTCTTAAAGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATCTTGA
52235231 TGCCAACGCCATGTCCCAAACATGGTCTTACAT-AGGACCTCTCATCTTGA
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGA-GACCTCTCATCTTGA
* *
52235281 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGA
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATCTTGA
* *
52235331 TGCCAACGCCATGTCCCACACATGGTCTTATAT-AGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGA-GACCTCTC---ATCT---TGA
** *
52235387 TGCCAATACCATGTCTCAAACATGGTCTTACATG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATG
52235421 GAATCTCTTT
Statistics
Matches: 202, Mismatches: 28, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
50 168 0.83
53 4 0.02
56 30 0.15
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATCTTGA
Found at i:52237133 original size:43 final size:43
Alignment explanation
Indices: 52237085--52237843 Score: 692
Period size: 43 Copynumber: 17.6 Consensus size: 43
52237075 CCGGTACGTA
* * *
52237085 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
** * * *
52237128 AGTGCATCATCAAATATATCGAAGCAAATATACTAGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * * * * * *
52237171 AGTGCATCATCAGATGAAACTGAAACTACTATATTGGCACACAT
1 AGTGCATCATCGGAT-AAACCGAAGCAAATATACTGGCACACAC
* * * *
52237215 AGGGCATCATTGGATCAACCGAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
** * * *
52237258 AGTGCATCATCAAATATATCGAAGCAAATATACTAGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * * * * ** *
52237301 AGTGCATCATCAGATGAAACTGAAACTACTATTTTGGCACACAT
1 AGTGCATCATCGGAT-AAACCGAAGCAAATATACTGGCACACAC
* * *
52237345 AGTGCATCATTGGATCAACCGAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* *
52237388 AGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACAC
1 AGTGCATCATCGGAT-AAACCGAAGCAAATATACTGGCACACAC
* * * * * *
52237432 AGTGCATCATTGTATAAATCAAAGAAAATATACTGGCACACAT
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * * *
52237475 AATGCATCATCGAATATATCGAAGCAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * * * *
52237518 AGTGCATTATCGGATATACCGAAGCAAGTATACTGGTACACAT
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * * * * *
52237561 AGTGCATCATCAGATGAAATCAAAGCTACTGA-ATTGGCACACAC
1 AGTGCATCATCGGAT-AAACCGAAGCAAAT-ATACTGGCACACAC
* * *
52237605 AGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * *
52237648 AGTGCATCATCGGATATACCGAAGCAAATATACTAGCACATAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * * * **
52237691 AGTGCATCATCAGATATACCAAAGCAAATATACTAGCGTACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * ** ** *
52237734 AGTGCTTAATCAAATTTACTGAAGCAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * * ***
52237777 AATGCATCATCGGATATACCGAAGCAAATATACAGGCACATGT
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * *
52237820 AGTGCATCGTTGGATATACCGAAG
1 AGTGCATCATCGGATAAACCGAAG
52237844 TATAACCTGT
Statistics
Matches: 576, Mismatches: 134, Indels: 12
0.80 0.19 0.02
Matches are distributed among these distances:
42 1 0.00
43 443 0.77
44 131 0.23
45 1 0.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (43 bp):
AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
Found at i:52237244 original size:130 final size:130
Alignment explanation
Indices: 52237085--52237809 Score: 852
Period size: 130 Copynumber: 5.6 Consensus size: 130
52237075 CCGGTACGTA
** *
52237085 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGA
1 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACACAGTGCATCATCGGATATACCGA
*
52237150 AGCAAATATACTAGCACACACAGTGCATCATCAGATGAAACTGAAA-CTACTATATTGGCACACA
66 AGCAAATATACTAGCACACACAGTGCATCATCAGATGAAA-TCAAAGCTACTATATTGGCACACA
52237214 T
130 T
* * * ** *
52237215 AGGGCATCATTGGATCAACCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGA
1 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACACAGTGCATCATCGGATATACCGA
* *
52237280 AGCAAATATACTAGCACACACAGTGCATCATCAGATGAAACTGAAA-CTACTATTTTGGCACACA
66 AGCAAATATACTAGCACACACAGTGCATCATCAGATGAAA-TCAAAGCTACTATATTGGCACACA
52237344 T
130 T
* * *
52237345 AGTGCATCATTGGATCAACCGAAGAAAATATACTGGCACACACAGTGCATCATCGGATGAAACCG
1 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACACAGTGCATCATCGGAT-ATACCG
* * * * ** * *
52237410 AAGCTACTATACTGGCACACACAGTGCATCAT-TGTAT-AAATCAAAGAAAATATACTGGCACAC
65 AAGCAAATATACTAGCACACACAGTGCATCATCAG-ATGAAATCAAAGCTACTATATTGGCACAC
52237473 AT
129 AT
* * * * * *
52237475 AATGCATCATCGAATATATCGAAGCAAATATACTGGCACACACAGTGCATTATCGGATATACCGA
1 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACACAGTGCATCATCGGATATACCGA
* * * *
52237540 AGCAAGTATACTGGTACACATAGTGCATCATCAGATGAAATCAAAGCTACTGA-ATTGGCACACA
66 AGCAAATATACTAGCACACACAGTGCATCATCAGATGAAATCAAAGCTACT-ATATTGGCACACA
*
52237604 C
130 T
* *
52237605 AGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACACACAGTGCATCATCGGATATACCGA
1 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACACAGTGCATCATCGGATATACCGA
* * * * * * * ** *
52237670 AGCAAATATACTAGCACATACAGTGCATCATCAGAT-ATACCAAAGCAAATATACTAGCGTACAC
66 AGCAAATATACTAGCACACACAGTGCATCATCAGATGAAATCAAAGCTACTATATTGGCACACAT
* * *** ** * *
52237734 AGTGCTTAATCAAATTTA-CTGAAGCAAATATACTGGCACACACAATGCATCATCGGATATACCG
1 AGTGCATCATTGGATAAATC-GAAGAAAATATACTGGCACACACAGTGCATCATCGGATATACCG
52237798 AAGCAAATATAC
65 AAGCAAATATAC
52237810 AGGCACATGT
Statistics
Matches: 521, Mismatches: 66, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
128 2 0.00
129 122 0.23
130 361 0.69
131 36 0.07
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (130 bp):
AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACACAGTGCATCATCGGATATACCGA
AGCAAATATACTAGCACACACAGTGCATCATCAGATGAAATCAAAGCTACTATATTGGCACACAT
Found at i:52237709 original size:173 final size:174
Alignment explanation
Indices: 52237085--52237816 Score: 738
Period size: 173 Copynumber: 4.2 Consensus size: 174
52237075 CCGGTACGTA
* * *
52237085 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGA
1 AGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACACACAGTGCATCATCAAATATACCGA
* * * * * * *
52237150 AGCAAATATACTAGCACACACAGTGCATCATCAGATGAAACTGAAACTACTATATTGGCACACAT
66 AGCAAATATACTAGCACACACAGTGCATCATCAGATCATACCGAAGCAAATATACTGGCACACAT
* * * ** *
52237215 AGGGCATCATTGGAT-CAACCGAAGAAAATATACTGGCACACAC
131 AGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACAC
** * * * * * * *
52237258 AGTGCATCATCAAATATATCGAAGCAAATATACTAGCACACACAGTGCATCATCAGATGAAACTG
1 AGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACACACAGTGCATCATCAAAT-ATACCG
* * * ** * * ** *
52237323 AAACTACTATTTTGGCACACATAGTGCATCATTGGATCA-ACCGAAGAAAATATACTGGCACACA
65 AAGCAAATATACTAGCACACACAGTGCATCATCAGATCATACCGAAGCAAATATACTGGCACACA
*
52237387 CAGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACAC
130 TAGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACAC
* * * * * *
52237432 AGTGCATCATTGTATAAATCAAAGAAAATATACTGGCACACATAATGCATCATCGAATATATCGA
1 AGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACACACAGTGCATCATCAAATATACCGA
* * * * *
52237497 AGCAAATATACTGGCACACACAGTGCATTATCGGAT-ATACCGAAGCAAGTATACTGGTACACAT
66 AGCAAATATACTAGCACACACAGTGCATCATCAGATCATACCGAAGCAAATATACTGGCACACAT
* * * *
52237561 AGTGCATCATCAGATGAAATCAAAGCTACTGA-ATTGGCACACAC
131 AGTGCATCATCGGATGAAACCGAAGCTACT-ATACTGGCACACAC
**
52237605 AGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACACACAGTGCATCATCGGATATACCGA
1 AGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACACACAGTGCATCATCAAATATACCGA
* * * ** *
52237670 AGCAAATATACTAGCACATACAGTGCATCATCAGAT-ATACCAAAGCAAATATACTAGCGTACAC
66 AGCAAATATACTAGCACACACAGTGCATCATCAGATCATACCGAAGCAAATATACTGGCACACAT
* * ** ** * * *
52237734 AGTGCTTAATCAAAT-TTACTGAAGCAAATATACTGGCACACAC
131 AGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACAC
* * * * * *
52237777 AATGCATCATCGGATATACCGAAGCAAATATACAGGCACA
1 AGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACA
52237817 TGTAGTGCAT
Statistics
Matches: 457, Mismatches: 97, Indels: 11
0.81 0.17 0.02
Matches are distributed among these distances:
171 1 0.00
172 53 0.12
173 299 0.65
174 104 0.23
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.21
Consensus pattern (174 bp):
AGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACACACAGTGCATCATCAAATATACCGA
AGCAAATATACTAGCACACACAGTGCATCATCAGATCATACCGAAGCAAATATACTGGCACACAT
AGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACAC
Found at i:52237824 original size:86 final size:87
Alignment explanation
Indices: 52237085--52237827 Score: 619
Period size: 87 Copynumber: 8.6 Consensus size: 87
52237075 CCGGTACGTA
* * * * * *
52237085 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATA-TCG
1 AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACATAGTGCATCATCAAATATACTCG
*
52237149 AAGCAAATATACTAGCACACAC
66 AAGCAAATATACTGGCACACAC
* * * * * * * ***
52237171 AGTGCATCATCAGATGAAACTGAAA-CTACTATATTGGCACACATAGGGCATCATTGGATCA-AC
1 AGTGCATCATCGGAT-ATAC-CAAAGCAAATATACTGGCACACATAGTGCATCATCAAAT-ATAC
*
52237234 -CGAAGAAAATATACTGGCACACAC
63 TCGAAGCAAATATACTGGCACACAC
** * * * * * *
52237258 AGTGCATCATCAAATATATCGAAGCAAATATACTAGCACACACAGTGCATCATCAGATGAAACT-
1 AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACATAGTGCATCATCAAAT-ATACTC
* * * ** *
52237322 GAAACTACTATTTTGGCACACAT
65 GAAGCAAATATACTGGCACACAC
* * * * ** *
52237345 AGTGCATCATTGGATCA-ACCGAAGAAAATATACTGGCACACACAGTGCATCATCGGATGAAAC-
1 AGTGCATCATCGGAT-ATACCAAAGCAAATATACTGGCACACATAGTGCATCATCAAAT-ATACT
* *
52237408 CGAAGCTACTATACTGGCACACAC
64 CGAAGCAAATATACTGGCACACAC
* * * * * * *
52237432 AGTGCATCATTGTATAAATCAAAGAAAATATACTGGCACACATAATGCATCATCGAATATA-TCG
1 AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACATAGTGCATCATCAAATATACTCG
52237496 AAGCAAATATACTGGCACACAC
66 AAGCAAATATACTGGCACACAC
* * * * * *
52237518 AGTGCATTATCGGATATACCGAAGCAAGTATACTGGTACACATAGTGCATCATCAGATGA-AATC
1 AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACATAGTGCATCATCAAAT-ATACTC
* * * *
52237582 AAAGCTACTGA-ATTGGCACACAC
65 GAAGCAAAT-ATACTGGCACACAC
* * * * **
52237605 AGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACACACAGTGCATCATCGGATATAC-CG
1 AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACATAGTGCATCATCAAATATACTCG
* *
52237669 AAGCAAATATACTAGCACATAC
66 AAGCAAATATACTGGCACACAC
* * ** * * * *
52237691 AGTGCATCATCAGATATACCAAAGCAAATATACTAGCGTACACAGTGCTTAATCAAATTTACT-G
1 AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACATAGTGCATCATCAAATATACTCG
52237755 AAGCAAATATACTGGCACACAC
66 AAGCAAATATACTGGCACACAC
* * * **
52237777 AATGCATCATCGGATATACCGAAGCAAATATACAGGCACATGTAGTGCATC
1 AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACATAGTGCATC
52237828 GTTGGATATA
Statistics
Matches: 525, Mismatches: 115, Indels: 34
0.78 0.17 0.05
Matches are distributed among these distances:
85 3 0.01
86 241 0.46
87 276 0.53
88 5 0.01
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (87 bp):
AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACATAGTGCATCATCAAATATACTCG
AAGCAAATATACTGGCACACAC
Found at i:52240184 original size:12 final size:12
Alignment explanation
Indices: 52240147--52240189 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
52240137 AATATTAATC
52240147 AAAA-TAATTAA
1 AAAATTAATTAA
*
52240158 AAATATT-ATTTA
1 AAA-ATTAATTAA
52240170 AAAATTAATTAA
1 AAAATTAATTAA
52240182 AAAATTAA
1 AAAATTAA
52240190 ATGTGTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 6 0.22
12 20 0.74
13 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAAATTAATTAA
Found at i:52248718 original size:33 final size:33
Alignment explanation
Indices: 52248672--52248829 Score: 158
Period size: 33 Copynumber: 4.8 Consensus size: 33
52248662 GAACATTGAA
* *
52248672 AGTCCATTAGGACAGTAAGCACATAATAGAGAT
1 AGTCCACTAGGACAGTAAACACATAATAGAGAT
* * * * *
52248705 AGTCCACTGGGACAGTAAACACAAAACAGAAAC
1 AGTCCACTAGGACAGTAAACACATAATAGAGAT
** *
52248738 AGTCTGCTAGGACAGTAAACACATAATAAAGAT
1 AGTCCACTAGGACAGTAAACACATAATAGAGAT
* * *
52248771 AGTCCGCTAGGACATTAAACACGTAATAGAGAT
1 AGTCCACTAGGACAGTAAACACATAATAGAGAT
* * *
52248804 AGTCCGCCA-GAGAGTAAACACA-AATA
1 AGTCCACTAGGACAGTAAACACATAATA
52248830 AAGTTTGTCG
Statistics
Matches: 102, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
31 4 0.04
32 10 0.10
33 88 0.86
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (33 bp):
AGTCCACTAGGACAGTAAACACATAATAGAGAT
Found at i:52250150 original size:36 final size:36
Alignment explanation
Indices: 52250106--52250175 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
52250096 AGAATATATT
52250106 AAAATACATATAAACATACCATATGAACTTACCTTA
1 AAAATACATATAAACATACCATATGAACTTACCTTA
52250142 AAAATACATATAAACATACCATATGAACTTACCT
1 AAAATACATATAAACATACCATATGAACTTACCT
52250176 GAAATAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.50, C:0.20, G:0.03, T:0.27
Consensus pattern (36 bp):
AAAATACATATAAACATACCATATGAACTTACCTTA
Found at i:52250161 original size:23 final size:24
Alignment explanation
Indices: 52250116--52250161 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
52250106 AAAATACATA
* * *
52250116 TAAACATACCATATGAACTTACCT
1 TAAAAATACCATATAAACATACCT
52250140 TAAAAATA-CATATAAACATACC
1 TAAAAATACCATATAAACATACC
52250162 ATATGAACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.50, C:0.22, G:0.02, T:0.26
Consensus pattern (24 bp):
TAAAAATACCATATAAACATACCT
Found at i:52250174 original size:13 final size:13
Alignment explanation
Indices: 52250112--52250165 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 13
52250102 TATTAAAATA
52250112 CATATAAACATAC
1 CATATAAACATAC
* *
52250125 CATATGAACTTAC
1 CATATAAACATAC
*
52250138 C-T-TAAAAATA-
1 CATATAAACATAC
52250148 CATATAAACATAC
1 CATATAAACATAC
52250161 CATAT
1 CATAT
52250166 GAACTTACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
10 1 0.03
11 6 0.19
12 8 0.25
13 17 0.53
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.28
Consensus pattern (13 bp):
CATATAAACATAC
Found at i:52263997 original size:22 final size:22
Alignment explanation
Indices: 52263966--52264013 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
52263956 TGTCTTAAGG
52263966 CAAAAACTTGCATATCTCGAGA
1 CAAAAACTTGCATATCTCGAGA
* ** *
52263988 CAAAAGCTTGTTTGTCTCGAGA
1 CAAAAACTTGCATATCTCGAGA
52264010 CAAA
1 CAAA
52264014 GTTTGCCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (22 bp):
CAAAAACTTGCATATCTCGAGA
Found at i:52275631 original size:12 final size:12
Alignment explanation
Indices: 52275599--52275632 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
52275589 AGTTGTTAAA
52275599 TTGTTAG-TAGT
1 TTGTTAGTTAGT
52275610 TTGGTTAGTTAGT
1 TT-GTTAGTTAGT
52275623 TTGTTAGTTA
1 TTGTTAGTTA
52275633 TTTAAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 13 0.62
13 6 0.29
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (12 bp):
TTGTTAGTTAGT
Found at i:52284120 original size:46 final size:45
Alignment explanation
Indices: 52283999--52284137 Score: 179
Period size: 46 Copynumber: 3.0 Consensus size: 45
52283989 ACAAGGCTAT
*
52283999 AACTCAGTATGGCTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACGG-AATACCATACCTACTTTTCAC
* * **
52284045 AACTCAGTATGGTTTCCTTTACCAAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCA-CGGAATACCATACCTACTTTTCAC
* * *
52284091 AACTCAGTATGGTTTTCTTCATTGGAATACCATACCTGCGTTTCAC
1 AACTCAGTATGGTTTTCTTCA-CGGAATACCATACCTACTTTTCAC
52284137 A
1 A
52284138 CTTTGCCATG
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
46 78 0.99
47 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.35
Consensus pattern (45 bp):
AACTCAGTATGGTTTTCTTCACGGAATACCATACCTACTTTTCAC
Found at i:52286620 original size:27 final size:27
Alignment explanation
Indices: 52286585--52286649 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
52286575 AAGTTTTGAG
* *
52286585 AGTTCTTATTTTCGGGTTTTGGGGGCT
1 AGTTTTTATCTTCGGGTTTTGGGGGCT
52286612 AGTTTTTATCTTCGGGTTTTGGGGGCT
1 AGTTTTTATCTTCGGGTTTTGGGGGCT
52286639 AGTTTTTATCT
1 AGTTTTTATCT
52286650 CCATCTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.09, C:0.11, G:0.29, T:0.51
Consensus pattern (27 bp):
AGTTTTTATCTTCGGGTTTTGGGGGCT
Found at i:52289808 original size:17 final size:18
Alignment explanation
Indices: 52289777--52289814 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
52289767 TAATGTGTTG
*
52289777 TTTTTAATTTATTTTCTA
1 TTTTTAATTTATTTTATA
*
52289795 TTTTTTATTT-TTTTATA
1 TTTTTAATTTATTTTATA
52289812 TTT
1 TTT
52289815 CAAATTTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTAATTTATTTTATA
Found at i:52294012 original size:31 final size:31
Alignment explanation
Indices: 52293976--52294040 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
52293966 TTGATTTGAC
52293976 CCTCCCCATGACTAGTCAACAGTAAGGTAAA
1 CCTCCCCATGACTAGTCAACAGTAAGGTAAA
* *
52294007 CCTCCCTATGACTGGTCAACAGTAAGGTAAA
1 CCTCCCCATGACTAGTCAACAGTAAGGTAAA
52294038 CCT
1 CCT
52294041 TCATCGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (31 bp):
CCTCCCCATGACTAGTCAACAGTAAGGTAAA
Found at i:52295123 original size:25 final size:25
Alignment explanation
Indices: 52295095--52295233 Score: 161
Period size: 25 Copynumber: 5.6 Consensus size: 25
52295085 GTAAACTTGA
* *
52295095 GAATTCTCTGGAAAGCCTTTGTGGT
1 GAATTATCTGGAAAGCCTTTGTGGC
* * *
52295120 GAATTCTCTAGAAAGCTTTTGTGGC
1 GAATTATCTGGAAAGCCTTTGTGGC
* * * *
52295145 GTATCATTTGGAAAGCCTTTGTGGA
1 GAATTATCTGGAAAGCCTTTGTGGC
* *
52295170 GAATTATTTGGAAAGCCCTTGTGGC
1 GAATTATCTGGAAAGCCTTTGTGGC
* *
52295195 GTATTATTTGGAAAGCCTTTGTGGC
1 GAATTATCTGGAAAGCCTTTGTGGC
52295220 GAATTATCTGGAAA
1 GAATTATCTGGAAA
52295234 TTCATTATGG
Statistics
Matches: 96, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 96 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (25 bp):
GAATTATCTGGAAAGCCTTTGTGGC
Found at i:52295184 original size:50 final size:50
Alignment explanation
Indices: 52295103--52295233 Score: 190
Period size: 50 Copynumber: 2.6 Consensus size: 50
52295093 GAGAATTCTC
* * * **
52295103 TGGAAAGCCTTTGTGGTGAATTCTCTAGAAAGCTTTTGTGGCGTATCATT
1 TGGAAAGCCTTTGTGGAGAATTATCTGGAAAGCCCTTGTGGCGTATCATT
* *
52295153 TGGAAAGCCTTTGTGGAGAATTATTTGGAAAGCCCTTGTGGCGTATTATT
1 TGGAAAGCCTTTGTGGAGAATTATCTGGAAAGCCCTTGTGGCGTATCATT
*
52295203 TGGAAAGCCTTTGTGGCGAATTATCTGGAAA
1 TGGAAAGCCTTTGTGGAGAATTATCTGGAAA
52295234 TTCATTATGG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.35
Consensus pattern (50 bp):
TGGAAAGCCTTTGTGGAGAATTATCTGGAAAGCCCTTGTGGCGTATCATT
Found at i:52307701 original size:16 final size:16
Alignment explanation
Indices: 52307682--52307712 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52307672 ATTTCTTGGG
52307682 TTTAGGGTCATTTTGA
1 TTTAGGGTCATTTTGA
*
52307698 TTTAGGGTTATTTTG
1 TTTAGGGTCATTTTG
52307713 GGTTATTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.03, G:0.26, T:0.55
Consensus pattern (16 bp):
TTTAGGGTCATTTTGA
Found at i:52307732 original size:6 final size:6
Alignment explanation
Indices: 52307717--52307751 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
52307707 ATTTTGGGTT
*
52307717 ATTTTG ATTTTA ATTTTG ATTTTG ATTTTGG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT-G ATTT
52307752 AGGGTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (6 bp):
ATTTTG
Found at i:52310016 original size:77 final size:77
Alignment explanation
Indices: 52309930--52310103 Score: 267
Period size: 77 Copynumber: 2.3 Consensus size: 77
52309920 TTAGTGAGTG
* * * *
52309930 TTTTTTAATATGCATGCAGTTTTTTTTAATTTATCTGTGTATGATTGTTGGTGGGGTTGGTCGCA
1 TTTTTTAATATGCATGCAGTGTTTTTTAATTTATCTGTGTATGATTGTTGGTGGGGATAGTCACA
52309995 TGCTATTGACTA
66 TGCTATTGACTA
* * * *
52310007 TTTTTTAATATGCATGTAGTGTTTTTTAATTTGTCTGTGTATGATTGTTGGTGGGGATAGTTATA
1 TTTTTTAATATGCATGCAGTGTTTTTTAATTTATCTGTGTATGATTGTTGGTGGGGATAGTCACA
*
52310072 TGCTGTTGACTA
66 TGCTATTGACTA
52310084 TTTTTTAATATGCATGCAGT
1 TTTTTTAATATGCATGCAGT
52310104 AACGTTTTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 87 1.00
ACGTcount: A:0.20, C:0.07, G:0.23, T:0.50
Consensus pattern (77 bp):
TTTTTTAATATGCATGCAGTGTTTTTTAATTTATCTGTGTATGATTGTTGGTGGGGATAGTCACA
TGCTATTGACTA
Found at i:52310875 original size:21 final size:21
Alignment explanation
Indices: 52310807--52310881 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
52310797 AAGAACAGGC
* **
52310807 TACCCCAAATCAGTAAGAGAG
1 TACCCCAACTCAACAAGAGAG
*
52310828 TACCCCAACTCAGCAAGAGAG
1 TACCCCAACTCAACAAGAGAG
52310849 TACCCCAACTCAACAAGAG-G
1 TACCCCAACTCAACAAGAGAG
*
52310869 CTGCCCCAACTCA
1 -TACCCCAACTCA
52310882 GTTACGAACT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 1 0.02
21 48 0.98
ACGTcount: A:0.37, C:0.35, G:0.16, T:0.12
Consensus pattern (21 bp):
TACCCCAACTCAACAAGAGAG
Found at i:52311699 original size:36 final size:36
Alignment explanation
Indices: 52311659--52311782 Score: 97
Period size: 36 Copynumber: 3.2 Consensus size: 36
52311649 CATGTATAAC
52311659 AACATAAGCAACAATATACCAACAACAATATTACAA
1 AACATAAGCAACAATATACCAACAACAATATTACAA
** * * * * *
52311695 AACATAAACTGGTTCTCCATGTATACCAACAGCCATGTATA-AC
1 AACAT-AA---G--CAACA-ATATACCAACAACAATAT-TACAA
*
52311738 AACATAAGCAACAATATACCAGCAACAATATTACAA
1 AACATAAGCAACAATATACCAACAACAATATTACAA
52311774 AACATAAGC
1 AACATAAGC
52311783 TGGTTAGCCA
Statistics
Matches: 64, Mismatches: 15, Indels: 18
0.66 0.15 0.19
Matches are distributed among these distances:
35 2 0.03
36 28 0.44
37 5 0.08
39 1 0.02
40 1 0.02
42 5 0.08
43 20 0.31
44 2 0.03
ACGTcount: A:0.50, C:0.23, G:0.07, T:0.19
Consensus pattern (36 bp):
AACATAAGCAACAATATACCAACAACAATATTACAA
Found at i:52311732 original size:16 final size:16
Alignment explanation
Indices: 52311711--52311741 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52311701 AACTGGTTCT
*
52311711 CCATGTATACCAACAG
1 CCATGTATAACAACAG
52311727 CCATGTATAACAACA
1 CCATGTATAACAACA
52311742 TAAGCAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (16 bp):
CCATGTATAACAACAG
Found at i:52311747 original size:79 final size:79
Alignment explanation
Indices: 52311616--52311866 Score: 430
Period size: 79 Copynumber: 3.2 Consensus size: 79
52311606 TGTAAGCAAC
* *
52311616 AACATAAGCTAGTTAGCCATGTATACCAGCAGCCATGTATAACAACATAAGCAACAATATACCAA
1 AACATAAGCTGGTTAGCCATGTATACCAGCAGCCATGTATAACAACATAAGCAACAATATACCAG
52311681 CAACAATATTACAA
66 CAACAATATTACAA
* ** *
52311695 AACATAAACTGGTTCTCCATGTATACCAACAGCCATGTATAACAACATAAGCAACAATATACCAG
1 AACATAAGCTGGTTAGCCATGTATACCAGCAGCCATGTATAACAACATAAGCAACAATATACCAG
52311760 CAACAATATTACAA
66 CAACAATATTACAA
* *
52311774 AACATAAGCTGGTTAGCCATGTATACCAGCAGCCATGTATAATAACATAAGAAACAATATACCAG
1 AACATAAGCTGGTTAGCCATGTATACCAGCAGCCATGTATAACAACATAAGCAACAATATACCAG
52311839 CAACAATATTACAA
66 CAACAATATTACAA
52311853 AACATAAGCTGGTT
1 AACATAAGCTGGTT
52311867 TTCAGTGCTA
Statistics
Matches: 160, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 160 1.00
ACGTcount: A:0.45, C:0.22, G:0.11, T:0.22
Consensus pattern (79 bp):
AACATAAGCTGGTTAGCCATGTATACCAGCAGCCATGTATAACAACATAAGCAACAATATACCAG
CAACAATATTACAA
Found at i:52313559 original size:25 final size:26
Alignment explanation
Indices: 52313524--52313582 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
52313514 GAAGCTCCGG
52313524 AGAGCCATTAA-TGGGAAGCTCACAA
1 AGAGCCATTAATTGGGAAGCTCACAA
* * *
52313549 AGAGCCTTTAATTGGGAAGCTTACGA
1 AGAGCCATTAATTGGGAAGCTCACAA
52313575 AGAGCCAT
1 AGAGCCAT
52313583 ATAACGGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (26 bp):
AGAGCCATTAATTGGGAAGCTCACAA
Found at i:52329826 original size:14 final size:15
Alignment explanation
Indices: 52329796--52329832 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
52329786 ATGAGAAGAG
52329796 AGAAAAATAAAAGGGA
1 AGAAAAA-AAAAGGGA
52329812 AGAAAAAAAAA-GGA
1 AGAAAAAAAAAGGGA
52329826 A-AAAAAA
1 AGAAAAAA
52329833 GAACAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.29
14 4 0.19
15 4 0.19
16 7 0.33
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (15 bp):
AGAAAAAAAAAGGGA
Found at i:52329977 original size:9 final size:10
Alignment explanation
Indices: 52329965--52330008 Score: 56
Period size: 9 Copynumber: 4.5 Consensus size: 10
52329955 TAAGAGAATG
52329965 GAAAAT-AAA
1 GAAAATAAAA
52329974 GAAAA-AAAA
1 GAAAATAAAA
52329983 GAAAATTAAAA
1 GAAAA-TAAAA
*
52329994 GAATATAAAA
1 GAAAATAAAA
52330004 GAAAA
1 GAAAA
52330009 AAATTAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 13 0.43
10 9 0.30
11 8 0.27
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (10 bp):
GAAAATAAAA
Found at i:52330531 original size:35 final size:36
Alignment explanation
Indices: 52330463--52330546 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 36
52330453 CACCTTTTTA
52330463 AAATATTAAATTTTTCAAAATGTAAAATTTATATATG
1 AAATATT-AATTTTTCAAAATGTAAAATTTATATATG
52330500 AAATATT-ATTTTT-AAAAT-TAAAATTTATATAT-
1 AAATATTAATTTTTCAAAATGTAAAATTTATATATG
52330532 AATATATTATATTTT
1 AA-ATATTA-ATTTT
52330547 CATGTGTGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
32 2 0.05
33 19 0.43
34 5 0.11
35 11 0.25
37 7 0.16
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (36 bp):
AAATATTAATTTTTCAAAATGTAAAATTTATATATG
Found at i:52332105 original size:33 final size:33
Alignment explanation
Indices: 52332003--52332106 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
52331993 GGTTTGAATT
* * *
52332003 AAAAAAAGATAAAAGGGTTTTGATTAGGGTCT-
1 AAAAAAAGATTAGAGGGTTTTGTTTAGGGTCTA
******
52332035 AAAAAAAGAATTATG-GGGTTTTGTTTAAAAAAAA
1 AAAAAAAG-ATTA-GAGGGTTTTGTTTAGGGTCTA
52332069 AAAAAAAGATTAGAGGGTTTTGTTTAGGGTCTA
1 AAAAAAAGATTAGAGGGTTTTGTTTAGGGTCTA
52332102 AAAAA
1 AAAAA
52332107 GGGTTAAAAA
Statistics
Matches: 53, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
32 9 0.17
33 36 0.68
34 8 0.15
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (33 bp):
AAAAAAAGATTAGAGGGTTTTGTTTAGGGTCTA
Found at i:52332671 original size:14 final size:14
Alignment explanation
Indices: 52332642--52332672 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
52332632 TGTAATGATA
52332642 TTATTGTACTATAT
1 TTATTGTACTATAT
*
52332656 TTATTGTATTATAT
1 TTATTGTACTATAT
52332670 TTA
1 TTA
52332673 GGTGATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTGTACTATAT
Found at i:52334428 original size:7 final size:7
Alignment explanation
Indices: 52334407--52334470 Score: 51
Period size: 7 Copynumber: 9.3 Consensus size: 7
52334397 TGTCTCTGCA
52334407 TTAGGG-
1 TTAGGGT
52334413 TTAGGGT
1 TTAGGGT
*
52334420 TTGGGGT
1 TTAGGGT
*
52334427 TTTGGGT
1 TTAGGGT
52334434 TTAGGG-
1 TTAGGGT
*
52334440 TTAGAGT
1 TTAGGGT
*
52334447 TTGGAGGT
1 TTAG-GGT
* *
52334455 TTTGAGT
1 TTAGGGT
52334462 TTAGGGT
1 TTAGGGT
52334469 TT
1 TT
52334471 TTAAAAAATT
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
6 11 0.24
7 29 0.64
8 5 0.11
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.45
Consensus pattern (7 bp):
TTAGGGT
Found at i:52334448 original size:27 final size:28
Alignment explanation
Indices: 52334407--52334469 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
52334397 TGTCTCTGCA
* *
52334407 TTAGGGTTAGGGTTTGG-GGTTTTGGGT
1 TTAGGGTTAGAGTTTGGAGGTTTTGAGT
52334434 TTAGGGTTAGAGTTTGGAGGTTTTGAGT
1 TTAGGGTTAGAGTTTGGAGGTTTTGAGT
52334462 TTAGGGTT
1 TTAGGGTT
52334470 TTTAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 16 0.48
28 17 0.52
ACGTcount: A:0.13, C:0.00, G:0.43, T:0.44
Consensus pattern (28 bp):
TTAGGGTTAGAGTTTGGAGGTTTTGAGT
Found at i:52334624 original size:96 final size:95
Alignment explanation
Indices: 52334494--52334797 Score: 396
Period size: 96 Copynumber: 3.2 Consensus size: 95
52334484 TAAACAAAGG
* * * * * *
52334494 ATTAGGGTTTAGGGTT-TCTTAATTAAATTGATTATAAAATTTTCAAAATTAGATTAGGGTTTCG
1 ATTAGGGTTTAGGGTTAT-TTGAGTAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAG
* * *
52334558 TGTTTATAGTTTTTAAGGAAAAAGTCAATTAA
65 TGTTTA-GGTTTTTAAGGAAAAAATCAAATAA
* * *
52334590 ATTAAGGTTTAGGGTTATTTGAGTAAATTAATTATAAATTTTTAAGAAATCAGATTAGAGTTTAG
1 ATTAGGGTTTAGGGTTATTTGAGTAAATTAATTATAAATTTTTAA-AAATTAGATTAGGGTTTAG
*
52334655 TGTTAAGGGTTTTTAA-GAAAAAATCAAATAA
65 TGTTTA-GGTTTTTAAGGAAAAAATCAAATAA
*
52334686 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAG
1 ATTAGGGTTTAGGGTTATTTGAGTAAATTAATTATAAATTTTT-AAAAATTAGATTAGGGTTTAG
* *
52334751 TGTTTAGGGTTTTAAGGAAAAACTCAAATAA
65 TGTTTAGGTTTTTAAGGAAAAAATCAAATAA
*
52334782 ATTAGGGTTTGGGGTT
1 ATTAGGGTTTAGGGTT
52334798 TAGGGTTACT
Statistics
Matches: 182, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
95 8 0.04
96 142 0.78
97 32 0.18
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (95 bp):
ATTAGGGTTTAGGGTTATTTGAGTAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGT
GTTTAGGTTTTTAAGGAAAAAATCAAATAA
Found at i:52336493 original size:61 final size:60
Alignment explanation
Indices: 52336303--52336496 Score: 199
Period size: 61 Copynumber: 3.3 Consensus size: 60
52336293 ATATTGTATT
*
52336303 ATTTATATTTT-TTAAAATGAAATAATATAGAAATATTCAAAATATTGTCTTATTTAAAAGA
1 ATTTCTATTTTATT-AAATGAAATAATATAGAAATATTCAAAATATTGTCTTA-TTAAAAGA
* * * * ** *
52336364 ATTTCTATTTTATT-AA--AAATATTAAAGTAA-ATT-ACAAT-TACT-TTATTCAAAACA
1 ATTTCTATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGTCTTATT-AAAAGA
52336418 ACGTTT-TATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGTCTTATGTAAAAGA
1 A--TTTCTATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGTCTTAT-TAAAAGA
52336480 ATTTCTATTTTATTAAA
1 ATTTCTATTTTATTAAA
52336497 AATATAAAAG
Statistics
Matches: 105, Mismatches: 15, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
53 2 0.02
54 9 0.09
55 11 0.10
56 9 0.09
57 3 0.03
58 22 0.21
59 3 0.03
60 9 0.09
61 24 0.23
62 12 0.11
63 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (60 bp):
ATTTCTATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGTCTTATTAAAAGA
Found at i:52336511 original size:29 final size:28
Alignment explanation
Indices: 52336473--52336587 Score: 149
Period size: 30 Copynumber: 3.8 Consensus size: 28
52336463 TTGTCTTATG
52336473 TAAAAGAATTTCTATTTTATTAAAAATA
1 TAAAAGAATTTCTATTTTATTAAAAATA
52336501 TAAAAGTAATTTCTATTTTATTACATGAAATAATA
1 TAAAAG-AATTTCTATTTTA-T---T-AAA-AATA
52336536 TAAAAGAATTTCTATTTTATTAAAAATA
1 TAAAAGAATTTCTATTTTATTAAAAATA
52336564 TAAAAGTAAATTTCTATTTTATTA
1 TAAAAG--AATTTCTATTTTATTA
52336588 CATGAAATAA
Statistics
Matches: 78, Mismatches: 0, Indels: 16
0.83 0.00 0.17
Matches are distributed among these distances:
28 16 0.21
29 16 0.21
30 18 0.23
33 2 0.03
34 16 0.21
35 10 0.13
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (28 bp):
TAAAAGAATTTCTATTTTATTAAAAATA
Found at i:52336547 original size:63 final size:64
Alignment explanation
Indices: 52336473--52336621 Score: 273
Period size: 64 Copynumber: 2.3 Consensus size: 64
52336463 TTGTCTTATG
52336473 TAAAAGAATTTCTATTTTATTAAAAATATAAAAGT-AATTTCTATTTTATTACATGAAATAATA
1 TAAAAGAATTTCTATTTTATTAAAAATATAAAAGTAAATTTCTATTTTATTACATGAAATAATA
52336536 TAAAAGAATTTCTATTTTATTAAAAATATAAAAGTAAATTTCTATTTTATTACATGAAATAATA
1 TAAAAGAATTTCTATTTTATTAAAAATATAAAAGTAAATTTCTATTTTATTACATGAAATAATA
* *
52336600 TAAAAGAATTTTTGTTTTATTA
1 TAAAAGAATTTCTATTTTATTA
52336622 CATGTAATAG
Statistics
Matches: 83, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
63 35 0.42
64 48 0.58
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.44
Consensus pattern (64 bp):
TAAAAGAATTTCTATTTTATTAAAAATATAAAAGTAAATTTCTATTTTATTACATGAAATAATA
Found at i:52336551 original size:34 final size:34
Alignment explanation
Indices: 52336473--52336630 Score: 178
Period size: 34 Copynumber: 4.9 Consensus size: 34
52336463 TTGTCTTATG
52336473 TAAAAGAATTTCTATTTTA-T---T-AAA-AATA
1 TAAAAGAATTTCTATTTTATTACATGAAATAATA
52336501 TAAAAGTAATTTCTATTTTATTACATGAAATAATA
1 TAAAAG-AATTTCTATTTTATTACATGAAATAATA
52336536 TAAAAGAATTTCTATTTTA-T---T-AAA-AATA
1 TAAAAGAATTTCTATTTTATTACATGAAATAATA
52336564 TAAAAGTAAATTTCTATTTTATTACATGAAATAATA
1 TAAAAG--AATTTCTATTTTATTACATGAAATAATA
* * *
52336600 TAAAAGAATTTTTGTTTTATTACATGTAATA
1 TAAAAGAATTTCTATTTTATTACATGAAATA
52336631 GGCATCAATA
Statistics
Matches: 112, Mismatches: 3, Indels: 24
0.81 0.02 0.17
Matches are distributed among these distances:
28 16 0.14
29 16 0.14
30 15 0.13
31 1 0.01
33 2 0.02
34 39 0.35
35 13 0.12
36 10 0.09
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (34 bp):
TAAAAGAATTTCTATTTTATTACATGAAATAATA
Found at i:52337097 original size:18 final size:18
Alignment explanation
Indices: 52337056--52337098 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
52337046 GACTAGAAAA
* * *
52337056 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
*
52337074 ATGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
52337092 AGGATAC
1 AGGATAC
52337099 GCACCTGGCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:52337726 original size:7 final size:7
Alignment explanation
Indices: 52337716--52337783 Score: 136
Period size: 7 Copynumber: 9.7 Consensus size: 7
52337706 TTATATACAT
52337716 AATACTA
1 AATACTA
52337723 AATACTA
1 AATACTA
52337730 AATACTA
1 AATACTA
52337737 AATACTA
1 AATACTA
52337744 AATACTA
1 AATACTA
52337751 AATACTA
1 AATACTA
52337758 AATACTA
1 AATACTA
52337765 AATACTA
1 AATACTA
52337772 AATACTA
1 AATACTA
52337779 AATAC
1 AATAC
52337784 GAATCGAGTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 61 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:52338961 original size:10 final size:11
Alignment explanation
Indices: 52338936--52339007 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
52338926 TAAAGAGAGC
52338936 TTTGAGAGGAA
1 TTTGAGAGGAA
52338947 TTTGAGAGG-A
1 TTTGAGAGGAA
**
52338957 TTTGAGATAAA
1 TTTGAGAGGAA
*
52338968 TATGAGA-GAA
1 TTTGAGAGGAA
*
52338978 TATTGGAGAGAAA
1 T-TT-GAGAGGAA
*
52338991 TATGAGA-GAA
1 TTTGAGAGGAA
52339001 TTTGAGA
1 TTTGAGA
52339008 AAAAGGATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
10 19 0.40
11 21 0.44
12 5 0.10
13 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.28
Consensus pattern (11 bp):
TTTGAGAGGAA
Found at i:52338962 original size:21 final size:21
Alignment explanation
Indices: 52338936--52339007 Score: 90
Period size: 21 Copynumber: 3.3 Consensus size: 21
52338926 TAAAGAGAGC
* * *
52338936 TTTGAGAGGAATTTGAGAGGA
1 TTTGAGAGAAATATGAGAGAA
*
52338957 TTTGAGATAAATATGAGAGAA
1 TTTGAGAGAAATATGAGAGAA
52338978 TATTGGAGAGAAATATGAGAGAA
1 T-TT-GAGAGAAATATGAGAGAA
52339001 TTTGAGA
1 TTTGAGA
52339008 AAAAGGATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
21 22 0.50
22 4 0.09
23 18 0.41
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.28
Consensus pattern (21 bp):
TTTGAGAGAAATATGAGAGAA
Found at i:52340565 original size:5 final size:5
Alignment explanation
Indices: 52340555--52340589 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
52340545 AAATCCAAAG
52340555 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
52340590 ATAACTAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:52349939 original size:20 final size:22
Alignment explanation
Indices: 52349906--52349980 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 22
52349896 CTTGAAACCA
*
52349906 AACTCCAAACCCTTGAACCTTG
1 AACTCCAAACCCTTCAACCTTG
52349928 AACT-CAAA-CCTTCAACCTTG
1 AACTCCAAACCCTTCAACCTTG
52349948 AA-TCCTTAAACCC-TCAACC-TG
1 AACTCC--AAACCCTTCAACCTTG
*
52349969 AACTCCGAACCC
1 AACTCCAAACCC
52349981 AAAATCCAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.02
20 19 0.41
21 8 0.17
22 16 0.35
23 2 0.04
ACGTcount: A:0.33, C:0.39, G:0.07, T:0.21
Consensus pattern (22 bp):
AACTCCAAACCCTTCAACCTTG
Found at i:52351518 original size:13 final size:13
Alignment explanation
Indices: 52351500--52351526 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52351490 TCGCCATGGT
52351500 AGAAACACAAAGA
1 AGAAACACAAAGA
52351513 AGAAACACAAAGA
1 AGAAACACAAAGA
52351526 A
1 A
52351527 AACTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.15, G:0.15, T:0.00
Consensus pattern (13 bp):
AGAAACACAAAGA
Found at i:52363166 original size:116 final size:115
Alignment explanation
Indices: 52362934--52363187 Score: 278
Period size: 116 Copynumber: 2.2 Consensus size: 115
52362924 TCGACCAAAA
* ** * * * *
52362934 AAAAAGGATAGCTTCAGCTATCAATTATGAAAAGGGATAGCTTCGGCTATAGATTATGAAAAGGG
1 AAAAGGGATAGCTTTGGCTATCAATGATGAAAAGAGATAGATTCAGCTATAGATTATGAAAAGGG
*** * * * *
52362999 ATGGTGGCGACCATCTACTATGAAAAGGAATGGTGACGACCATCGAATATG
66 ATGGCAACGACCATCGAATACGAAAAGGAATGGTGA-GACCAACGAATATG
*
52363050 AAAAGGGATAGCTTTGGCTATCAATGATGAAAAGAGATAGATTCAGCTATCGATTATGAAAAGGG
1 AAAAGGGATAGCTTTGGCTATCAATGATGAAAAGAGATAGATTCAGCTATAGATTATGAAAAGGG
** * *
52363115 ATGGCAACGACCATCGAATACGAAAAGGGATATCTTTG-G-CTAACGATTATG
66 ATGGCAACGACCATCGAATACGAAAA-GGA-AT-GGTGAGACCAACGAATATG
*
52363166 AAAAGGGATAGTTTTGGCTATC
1 AAAAGGGATAGCTTTGGCTATC
52363188 GATTAAAGAA
Statistics
Matches: 115, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
116 107 0.93
117 4 0.03
118 2 0.02
119 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (115 bp):
AAAAGGGATAGCTTTGGCTATCAATGATGAAAAGAGATAGATTCAGCTATAGATTATGAAAAGGG
ATGGCAACGACCATCGAATACGAAAAGGAATGGTGAGACCAACGAATATG
Found at i:52363181 original size:29 final size:29
Alignment explanation
Indices: 52362934--52363192 Score: 155
Period size: 29 Copynumber: 8.9 Consensus size: 29
52362924 TCGACCAAAA
* ** *
52362934 AAAAAGGATAGCTTCAGCTATCAATTATG
1 AAAAGGGATAGCTTTGGCTATCGATTATG
* *
52362963 AAAAGGGATAGCTTCGGCTATAGATTATG
1 AAAAGGGATAGCTTTGGCTATCGATTATG
* * * * *
52362992 AAAAGGGAT-G-GTGGCGACCATCTACTATG
1 AAAAGGGATAGCTTTG-G-CTATCGATTATG
* * ** * * *
52363021 AAAAGGAAT-GGTGACGACCATCGAATATG
1 AAAAGGGATAGCT-TTGGCTATCGATTATG
* *
52363050 AAAAGGGATAGCTTTGGCTATCAATGATG
1 AAAAGGGATAGCTTTGGCTATCGATTATG
* * **
52363079 AAAAGAGATAGATTCAGCTATCGATTATG
1 AAAAGGGATAGCTTTGGCTATCGATTATG
* *** * * * *
52363108 AAAAGGGATGGCAACGACCATCGAATACG
1 AAAAGGGATAGCTTTGGCTATCGATTATG
* *
52363137 AAAAGGGATATCTTTGGCTAACGATTATG
1 AAAAGGGATAGCTTTGGCTATCGATTATG
*
52363166 AAAAGGGATAGTTTTGGCTATCGATTA
1 AAAAGGGATAGCTTTGGCTATCGATTA
52363193 AAGAAAATGG
Statistics
Matches: 170, Mismatches: 55, Indels: 10
0.72 0.23 0.04
Matches are distributed among these distances:
27 2 0.01
28 2 0.01
29 163 0.96
30 2 0.01
31 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (29 bp):
AAAAGGGATAGCTTTGGCTATCGATTATG
Found at i:52363186 original size:87 final size:87
Alignment explanation
Indices: 52362962--52363232 Score: 283
Period size: 87 Copynumber: 3.1 Consensus size: 87
52362952 TATCAATTAT
* * ** * * * *
52362962 GAAAAGGGATAGCTTCGGCTATA-GATTATGAAAAGGGATGGTGGCGACCATCTACTATGAAAAG
1 GAAAAGGGATAGCTTTGGCTA-ACGATTATGAAAAGGGATAGTTTCGGCTATCGATTATGAAAAG
* * *
52363026 GAATGGTGACGACCATCGAATAT
65 GGATGGTAACGACCATCGAATAA
* * * * * *
52363049 GAAAAGGGATAGCTTTGGCTATCAATGATGAAAAGAGATAGATTCAGCTATCGATTATGAAAAGG
1 GAAAAGGGATAGCTTTGGCTAACGATTATGAAAAGGGATAGTTTCGGCTATCGATTATGAAAAGG
* *
52363114 GATGGCAACGACCATCGAATAC
66 GATGGTAACGACCATCGAATAA
* * * *
52363136 GAAAAGGGATATCTTTGGCTAACGATTATGAAAAGGGATAGTTTTGGCTATCGATTAAAGAAAAT
1 GAAAAGGGATAGCTTTGGCTAACGATTATGAAAAGGGATAGTTTCGGCTATCGATT-ATGAAAAG
** *
52363201 GGATGGTTTCGACCATCGACTAA
65 GGATGGTAACGACCATCGAATAA
52363224 GAAAAGGGA
1 GAAAAGGGA
52363233 CGGTTACGAC
Statistics
Matches: 149, Mismatches: 33, Indels: 3
0.81 0.18 0.02
Matches are distributed among these distances:
87 116 0.78
88 33 0.22
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (87 bp):
GAAAAGGGATAGCTTTGGCTAACGATTATGAAAAGGGATAGTTTCGGCTATCGATTATGAAAAGG
GATGGTAACGACCATCGAATAA
Found at i:52368617 original size:21 final size:20
Alignment explanation
Indices: 52368593--52368631 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52368583 GGACTAATTT
52368593 AAAACAAATAAAAAATTTGGG
1 AAAA-AAATAAAAAATTTGGG
**
52368614 AAAAAGTTAAAAAATTTG
1 AAAAAAATAAAAAATTTG
52368632 AAAACAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.62, C:0.03, G:0.13, T:0.23
Consensus pattern (20 bp):
AAAAAAATAAAAAATTTGGG
Found at i:52374261 original size:79 final size:79
Alignment explanation
Indices: 52374120--52374284 Score: 195
Period size: 79 Copynumber: 2.1 Consensus size: 79
52374110 TGAAATTGTA
** * * * * * *
52374120 TTCTATTTGTAAATAGAAATCAATTGAACAATTCTATTTTAGGATTTTATTCTTGATATTCAATA
1 TTCTATTTCCAAACAGAAATCAATTGAAAAATTCTATTTTAGGATTCTATTCCTGACATTCAACA
* *
52374185 GAATTTGTTTGATT
66 AAATTTATTTGATT
* * * *
52374199 TTCTATTTCCAAACAGAAATTAATTGAAAAATTCTGTTTTAGGATTCTATTCCTGCCGTTCAACA
1 TTCTATTTCCAAACAGAAATCAATTGAAAAATTCTATTTTAGGATTCTATTCCTGACATTCAACA
52374264 AAATTTATTTGATT
66 AAATTTATTTGATT
*
52374278 TTTTATT
1 TTCTATT
52374285 GTTAACGGTA
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (79 bp):
TTCTATTTCCAAACAGAAATCAATTGAAAAATTCTATTTTAGGATTCTATTCCTGACATTCAACA
AAATTTATTTGATT
Found at i:52389990 original size:9 final size:9
Alignment explanation
Indices: 52389976--52390006 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
52389966 GTTAAACGAA
52389976 TCGAGTTAT
1 TCGAGTTAT
*
52389985 TCGAGTTAA
1 TCGAGTTAT
52389994 TCGAGTTAT
1 TCGAGTTAT
52390003 TCGA
1 TCGA
52390007 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:52390076 original size:9 final size:9
Alignment explanation
Indices: 52390059--52390095 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52390049 TGAGTTTTCG
52390059 AATTCGAAT
1 AATTCGAAT
*
52390068 AACTCGAAT
1 AATTCGAAT
52390077 AATTCGAAT
1 AATTCGAAT
52390086 AATTCGAAT
1 AATTCGAAT
52390095 A
1 A
52390096 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:52391136 original size:5 final size:5
Alignment explanation
Indices: 52391126--52391151 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52391116 CTCGAAAATT
52391126 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
52391152 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:52392980 original size:2 final size:2
Alignment explanation
Indices: 52392973--52392999 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52392963 TTAAATATTA
52392973 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
52393000 CGACATTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52398059 original size:3 final size:3
Alignment explanation
Indices: 52398051--52398081 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
52398041 ATATGTATAG
52398051 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
52398082 ATGGGGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:52402322 original size:48 final size:49
Alignment explanation
Indices: 52402219--52402654 Score: 318
Period size: 48 Copynumber: 8.8 Consensus size: 49
52402209 AAAAAAAACA
**
52402219 AAAAAAAAATTTGGGTGCT-GCCTTGTCAATGGCCGGCACCA--ATATACG
1 AAAAAAATTTTTGGGTGCTGGCC-TGTCAATGGCCGGCACCAGCA-ATACG
*
52402267 AAAAAAAAAATTTTTGGGTGCTGGACTGTCAATGGCCGGCACCA-CAATACG
1 ---AAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGCAATACG
* * *
52402318 AAAAAAAATTTAT-GGTGCTGGCCTGTCAATGGCCGGCACAAGCAATATG
1 -AAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGCAATACG
** * *
52402367 AAAAAAAAATTT-GGTGCTGGCCTGTTAATGGCCGGCACCAGCAGTACGG
1 AAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGCAATAC-G
**** * * *
52402416 AAATTTTTTTTTTTGGGTGTTGGCTTGTCAATGGCCGGCACCAG-TATACG
1 AAA--AAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGCAATACG
** ** * * * *
52402466 -AAAATTTTTTTTTGTGCTGGCCTGACAATGGCCTGCACCAG-TATACA
1 AAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGCAATACG
* * * *
52402513 AAAAAAACTTTTTTGAGTGCTGGCCTGTCAATGGACGACACCAGCAGTACG
1 AAAAAAA--TTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGCAATACG
** * ** * *
52402564 AAAAAAAAAATTTAGGTGCTGGCCTGTCAATGGTTGGCACCAGTAGATGA-A
1 -AAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGCA-AT-ACG
* * *
52402615 AAAAAAAATTTT-GGTGTTGGCCTGTCAATGGCTGGCACCA
1 AAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCA
52402655 AATTTATCAA
Statistics
Matches: 313, Mismatches: 58, Indels: 30
0.78 0.14 0.07
Matches are distributed among these distances:
47 36 0.12
48 70 0.22
49 50 0.16
50 70 0.22
51 50 0.16
52 37 0.12
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (49 bp):
AAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGCAATACG
Found at i:52402323 original size:50 final size:50
Alignment explanation
Indices: 52402218--52402654 Score: 335
Period size: 50 Copynumber: 8.9 Consensus size: 50
52402208 TAAAAAAAAC
*
52402218 AAAAAAAAA-ATTTGGGTGCT-GCCTTGTCAATGGCCGGCACCA-ATATACG
1 AAAAAAAAATTTTTGGGTGCTGGCC-TGTCAATGGCCGGCACCACA-ATACG
*
52402267 AAAAAAAAAATTTTTGGGTGCTGGACTGTCAATGGCCGGCACCACAATACG
1 -AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACAATACG
* * *
52402318 -AAAAAAAATTTAT-GGTGCTGGCCTGTCAATGGCCGGCACAAGCAATATG
1 AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCA-CAATACG
* *
52402367 AAAAAAAAA--TTT-GGTGCTGGCCTGTTAATGGCCGGCACCAGCAGTACGG
1 AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCA-CAATAC-G
****** * * **
52402416 AAATTTTTTTTTTTGGGTGTTGGCTTGTCAATGGCCGGCACCAGTATACG
1 AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACAATACG
** ** * * **
52402466 ---AAAATTTTTTTTTGTGCTGGCCTGACAATGGCCTGCACCAGTATAC-
1 AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACAATACG
* * * * *
52402512 AAAAAAAACTTTTTTGAGTGCTGGCCTGTCAATGGACGACACCAGCAGTACG
1 AAAAAAAA-ATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCA-CAATACG
* * ** ** * *
52402564 AAAAAAAAA-ATTTAGGTGCTGGCCTGTCAATGGTTGGCACCAGTAGATG
1 AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACAATACG
* * *
52402613 AAAAAAAAAATTTT-GGTGTTGGCCTGTCAATGGCTGGCACCA
1 AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCA
52402655 AATTTATCAA
Statistics
Matches: 313, Mismatches: 58, Indels: 33
0.77 0.14 0.08
Matches are distributed among these distances:
47 36 0.12
48 59 0.19
49 63 0.20
50 77 0.25
51 42 0.13
52 36 0.12
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (50 bp):
AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACAATACG
Found at i:52402345 original size:99 final size:95
Alignment explanation
Indices: 52402220--52402655 Score: 346
Period size: 99 Copynumber: 4.4 Consensus size: 95
52402210 AAAAAAACAA
*
52402220 AAAAAAAATTTGGGTGCT-GCCTTGTCAATGGCCGGCACCAATATACGAAAAAAAAAATTTTTGG
1 AAAAAAAATTTTGGTGCTGGCC-TGTCAATGGCCGGCACCAATATACG-AAAAAAAAA--TTT-G
*
52402284 GTGCTGGACTGTCAATGGCCGGCACCA-CAATACG
61 GTGCTGGCCTGTCAATGGCCGGCACCAGCAATACG
52402318 AAAAAAAATTTATGGTGCTGGCCTGTCAATGGCCGGCACAAGCAATAT--GAAAAAAAAATTTGG
1 AAAAAAAATTT-TGGTGCTGGCCTGTCAATGGCCGGCAC---CAATATACGAAAAAAAAATTTGG
* *
52402381 TGCTGGCCTGTTAATGGCCGGCACCAGCAGTACGG
62 TGCTGGCCTGTCAATGGCCGGCACCAGCAATAC-G
***** * * * ***** *
52402416 AAATTTTTTTTTTTGGGTGTTGGCTTGTCAATGGCCGGCACCAGTATACGAAAATTTTTTTTTGT
1 AAA--AAAAATTTT-GGTGCTGGCCTGTCAATGGCCGGCACCAATATACGAAAAAAAAATTTGGT
* * *
52402481 GCTGGCCTGACAATGGCCTGCACCAG-TATAC-
63 GCTGGCCTGTCAATGGCCGGCACCAGCAATACG
* * **
52402512 AAAAAAAACTTTTTTGAGTGCTGGCCTGTCAATGGACGACACCAGCAGTACGAAAAAAAAAATTT
1 AAAAAAAA---TTTTG-GTGCTGGCCTGTCAATGGCCGGCACCAATA-TACG-AAAAAAAAATTT
** * *
52402577 AGGTGCTGGCCTGTCAATGGTTGGCACCAGTAGATGA-A
60 -GGTGCTGGCCTGTCAATGGCCGGCACCAGCA-AT-ACG
* *
52402615 AAAAAAAATTTTGGTGTTGGCCTGTCAATGGCTGGCACCAA
1 AAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCAA
52402656 ATTTATCAAA
Statistics
Matches: 266, Mismatches: 49, Indels: 45
0.74 0.14 0.12
Matches are distributed among these distances:
96 30 0.11
97 42 0.16
98 22 0.08
99 95 0.36
100 60 0.23
102 8 0.03
103 9 0.03
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (95 bp):
AAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCAATATACGAAAAAAAAATTTGGTGCT
GGCCTGTCAATGGCCGGCACCAGCAATACG
Found at i:52402450 original size:148 final size:147
Alignment explanation
Indices: 52402277--52402563 Score: 346
Period size: 148 Copynumber: 1.9 Consensus size: 147
52402267 AAAAAAAAAA
52402277 TTTTTGGGTGCTGGACTGTCAATGGCCGGCACCACAATACGAAAAAAAATTTATGGTGCTGGCCT
1 TTTTTGGGTGCTGGACTGTCAATGGCCGGCACCACAATACG-AAAAAAATTTATGGTGCTGGCCT
* * * * *
52402342 GTCAATGGCCGGCACAAGCAATATGAAAAAAAA-ATTTG-GTGCTGGCCTGTTAATGGCCGGCAC
65 GACAATGGCCGGCACAAG-AATA-CAAAAAAAATATTTGAGTGCTGGCCTGTCAATGGACGACAC
52402405 CAGCAGTACGGAAATTTTTT
128 CAGCAGTACGGAAATTTTTT
* ** *** * *
52402425 TTTTTGGGTGTTGG-CTTGTCAATGGCCGGCACCAGTATACGAAAATTTTTTTTTGTGCTGGCCT
1 TTTTTGGGTGCTGGAC-TGTCAATGGCCGGCACCACAATACGAAAAAAATTTATGGTGCTGGCCT
* * * *
52402489 GACAATGGCCTGCACCAGTATACAAAAAAAACTTTTTTGAGTGCTGGCCTGTCAATGGACGACAC
65 GACAATGGCCGGCACAAGAATACAAAAAAAA--TATTTGAGTGCTGGCCTGTCAATGGACGACAC
52402554 CAGCAGTACG
128 CAGCAGTACG
52402564 AAAAAAAAAA
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
145 8 0.07
146 3 0.03
147 34 0.29
148 40 0.34
149 32 0.27
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (147 bp):
TTTTTGGGTGCTGGACTGTCAATGGCCGGCACCACAATACGAAAAAAATTTATGGTGCTGGCCTG
ACAATGGCCGGCACAAGAATACAAAAAAAATATTTGAGTGCTGGCCTGTCAATGGACGACACCAG
CAGTACGGAAATTTTTT
Found at i:52403964 original size:20 final size:20
Alignment explanation
Indices: 52403939--52403976 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
52403929 ATAGTTAGAA
52403939 GGGATAAGCTTGATTGGTGC
1 GGGATAAGCTTGATTGGTGC
52403959 GGGATAAGCTTGATTGGT
1 GGGATAAGCTTGATTGGT
52403977 TCTCGAGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.08, G:0.39, T:0.32
Consensus pattern (20 bp):
GGGATAAGCTTGATTGGTGC
Found at i:52409402 original size:41 final size:41
Alignment explanation
Indices: 52409346--52409448 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
52409336 TTTTGCAGTG
* * *
52409346 TTTTCAAAAAAGCGCCACTAATGCTCGGGGTTTTAGCGGCGT
1 TTTTC-AAAAAGCGCCGCTAATACTCAGGGTTTTAGCGGCGT
52409388 TTTTCAAAAAGCGCCGCTAATACTCAGGGTTTTAGCGGCGT
1 TTTTCAAAAAGCGCCGCTAATACTCAGGGTTTTAGCGGCGT
*
52409429 TTTTGAAAAAGCGCCGCTAA
1 TTTTCAAAAAGCGCCGCTAA
52409449 AAACATTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 52 0.91
42 5 0.09
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (41 bp):
TTTTCAAAAAGCGCCGCTAATACTCAGGGTTTTAGCGGCGT
Found at i:52409861 original size:7 final size:7
Alignment explanation
Indices: 52409851--52409881 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
52409841 TAAGGTTTAA
52409851 GGGTTAG
1 GGGTTAG
52409858 GGGTTAG
1 GGGTTAG
52409865 GGGTTAG
1 GGGTTAG
52409872 GGGTTTAG
1 GGG-TTAG
52409880 GG
1 GG
52409882 ATTTAGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.74
8 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.58, T:0.29
Consensus pattern (7 bp):
GGGTTAG
Found at i:52409870 original size:14 final size:15
Alignment explanation
Indices: 52409844--52409881 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
52409834 TGAGATTTAA
*
52409844 GGTTTAAGGGTTAGG
1 GGTTTAGGGGTTAGG
52409859 GG-TTAGGGGTTAGG
1 GGTTTAGGGGTTAGG
52409873 GGTTTAGGG
1 GGTTTAGGG
52409882 ATTTAGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.16, C:0.00, G:0.53, T:0.32
Consensus pattern (15 bp):
GGTTTAGGGGTTAGG
Found at i:52409969 original size:25 final size:25
Alignment explanation
Indices: 52409937--52409984 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
52409927 AGATTAATTA
*
52409937 TTTTTTAATTTATATTTTAAATATG
1 TTTTTTAATTTATATATTAAATATG
52409962 TTTTTTAATTTATATATTAAATA
1 TTTTTTAATTTATATATTAAATA
52409985 ATTTCATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTTTAATTTATATATTAAATATG
Found at i:52410206 original size:7 final size:7
Alignment explanation
Indices: 52410196--52410235 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
52410186 GATTTAAGAT
*
52410196 TTAGGGG
1 TTAGGAG
52410203 TTAGGAG
1 TTAGGAG
52410210 TTAGGAG
1 TTAGGAG
52410217 TTAGGAG
1 TTAGGAG
52410224 TTAGGAG
1 TTAGGAG
52410231 TTAGG
1 TTAGG
52410236 GGTCAGGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.45, T:0.30
Consensus pattern (7 bp):
TTAGGAG
Found at i:52410220 original size:21 final size:21
Alignment explanation
Indices: 52410196--52410265 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
52410186 GATTTAAGAT
52410196 TTAGGGGTTAGGAGTTAGGAG
1 TTAGGGGTTAGGAGTTAGGAG
* *
52410217 TTAGGAGTTAGGAGTTAGGGG
1 TTAGGGGTTAGGAGTTAGGAG
* * * *
52410238 TCAGGGGTTAAGAGATAGAGAT
1 TTAGGGGTTAGGAGTTAG-GAG
52410260 TTAGGG
1 TTAGGG
52410266 TTTTAAGGGC
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 33 0.85
22 6 0.15
ACGTcount: A:0.27, C:0.01, G:0.44, T:0.27
Consensus pattern (21 bp):
TTAGGGGTTAGGAGTTAGGAG
Found at i:52410550 original size:12 final size:12
Alignment explanation
Indices: 52410533--52410582 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
52410523 AAATATTTAA
52410533 TAATTCTTTATG
1 TAATTCTTTATG
52410545 TAATTCTTTATG
1 TAATTCTTTATG
* *
52410557 TAAAAT-TTTA-A
1 T-AATTCTTTATG
52410568 TAATTCTTTATG
1 TAATTCTTTATG
52410580 TAA
1 TAA
52410583 AATTTATAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 3 0.10
11 5 0.16
12 20 0.65
13 3 0.10
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (12 bp):
TAATTCTTTATG
Found at i:52412356 original size:8 final size:8
Alignment explanation
Indices: 52412343--52412369 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
52412333 CCAAATTGTA
52412343 TTTGTTTT
1 TTTGTTTT
52412351 TTTGTTTT
1 TTTGTTTT
52412359 TTTGTTTT
1 TTTGTTTT
52412367 TTT
1 TTT
52412370 TTTGTCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTGTTTT
Found at i:52412597 original size:16 final size:16
Alignment explanation
Indices: 52412578--52412614 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
52412568 TTTTTAAATT
52412578 ACTTTTTAAGGCATGC
1 ACTTTTTAAGGCATGC
52412594 ACTTTTTAAGGCATGC
1 ACTTTTTAAGGCATGC
52412610 ACTTT
1 ACTTT
52412615 ATACAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (16 bp):
ACTTTTTAAGGCATGC
Found at i:52413482 original size:28 final size:28
Alignment explanation
Indices: 52413440--52413500 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
52413430 ATTCTTTTCT
*
52413440 TTTGACAAAGAACTT-GAGGTTGAACTGA
1 TTTGACAAAGAACTTGGA-GTTGAACTAA
* *
52413468 TTTGACTAAGGACTTGGAGTTGAACTAA
1 TTTGACAAAGAACTTGGAGTTGAACTAA
52413496 TTTGA
1 TTTGA
52413501 TTCTTGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.93
29 2 0.07
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.33
Consensus pattern (28 bp):
TTTGACAAAGAACTTGGAGTTGAACTAA
Found at i:52413519 original size:5 final size:5
Alignment explanation
Indices: 52413509--52413535 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
52413499 GATTCTTGTT
52413509 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
52413536 GGCAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:52414563 original size:17 final size:17
Alignment explanation
Indices: 52414541--52414573 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
52414531 ATTTTTATTT
52414541 TGTAGCATTAAGTTTTC
1 TGTAGCATTAAGTTTTC
52414558 TGTAGCATTAAGTTTT
1 TGTAGCATTAAGTTTT
52414574 TATTTTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (17 bp):
TGTAGCATTAAGTTTTC
Found at i:52414996 original size:43 final size:42
Alignment explanation
Indices: 52414946--52415150 Score: 239
Period size: 43 Copynumber: 4.8 Consensus size: 42
52414936 AGTTTATGTT
* * * * * *
52414946 TTTAGCGGCGTTTTTGCTAGAAGCGTCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAAGTCGTGGTC
* *
52414989 TATAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAAGTCGTGGTC
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAAGTCGTGGTC
* * *
52415032 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAAGTCGTGGTC
* * *
52415075 TTTAGCAGCGTTTGTGGGGAAAGCGCTGCTAAAAGTCGTGGTC
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAAGTCGTGGTC
52415118 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAA
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAA
52415151 GTTAGCAACG
Statistics
Matches: 137, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
42 1 0.01
43 134 0.98
44 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAAGTCGTGGTC
Found at i:52415086 original size:86 final size:86
Alignment explanation
Indices: 52414946--52415151 Score: 304
Period size: 86 Copynumber: 2.4 Consensus size: 86
52414936 AGTTTATGTT
* * * * *
52414946 TTTAGCGGCGTTTTTGCTAGAAGCGTCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAA
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGGTCTATAGCAGCGTTTGTGGGAAAA
*
52415011 GCGCCGTTAAAAGTCGTGGTC
66 GCGCCGCTAAAAGTCGTGGTC
* * *
52415032 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTGTGGGGAAA
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGGTCTATAGCAGCGTTTGTGGGAAAA
*
52415097 GCGCTGCTAAAAGTCGTGGTC
66 GCGCCGCTAAAAGTCGTGGTC
**
52415118 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAG
52415152 TTAGCAACGC
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 108 1.00
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.28
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGGTCTATAGCAGCGTTTGTGGGAAAA
GCGCCGCTAAAAGTCGTGGTC
Found at i:52416113 original size:16 final size:16
Alignment explanation
Indices: 52416064--52416116 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
52416054 TTGGTTCGCT
*
52416064 GTAATGGAATAGATGT
1 GTAATGGAATAGATGC
* *
52416080 GTAATGAAATATATGC
1 GTAATGGAATAGATGC
*
52416096 GTAATGGAATAGAGGC
1 GTAATGGAATAGATGC
52416112 GTAAT
1 GTAAT
52416117 AGGTAGTTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (16 bp):
GTAATGGAATAGATGC
Found at i:52416186 original size:44 final size:46
Alignment explanation
Indices: 52416103--52416191 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
52416093 TGCGTAATGG
52416103 AATAGAGGCGTAATAGGTAGTTCAATTGTTTGGTTGAATGAAATAC
1 AATAGAGGCGTAATAGGTAGTTCAATTGTTTGGTTGAATGAAATAC
* *
52416149 AATAGAGGCGTAAT-GGTA-TTC-TTGTGTTTGGTTGAATGGAATA
1 AATAGAGGCGTAATAGGTAGTTCAAT-TGTTTGGTTGAATGAAATA
52416192 GAGGTGTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 1 0.03
44 21 0.52
45 4 0.10
46 14 0.35
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.35
Consensus pattern (46 bp):
AATAGAGGCGTAATAGGTAGTTCAATTGTTTGGTTGAATGAAATAC
Done.