Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 26 of 31
Found at i:12388921 original size:42 final size:42
Alignment explanation
Indices: 12388866--12388950 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
12388856 TGCTAAGCTG
*
12388866 TTTATGTTTATGACAATATGGTACTTTAACTACTAATGGATT
1 TTTATGTTAATGACAATATGGTACTTTAACTACTAATGGATT
* * *
12388908 TTTATGTTAATGACAATATGTTACTTTAATTGCTAATGGATT
1 TTTATGTTAATGACAATATGGTACTTTAACTACTAATGGATT
12388950 T
1 T
12388951 ATTTCAATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (42 bp):
TTTATGTTAATGACAATATGGTACTTTAACTACTAATGGATT
Found at i:12389741 original size:73 final size:73
Alignment explanation
Indices: 12389664--12389799 Score: 166
Period size: 74 Copynumber: 1.9 Consensus size: 73
12389654 GCTTAGTCTA
* * * * * *
12389664 AGAAACTAAGTTC-AGAGATAGAAACGACTTAATCGACTGAGAAGCATTATTAGTCGACTAAGAC
1 AGAAACTAAGATCAAAAGACAGAAACGACTTAATCGACTAAGAAGC-GTATTAGTCAACTAAGAC
12389728 CTCACTGCC
65 CTCACTGCC
** * *
12389737 AGAAACTGGGATCAAAAGACAGAAATGACTTAATTGACTAAGAAGCGTATTAGTCAACTAAGA
1 AGAAACTAAGATCAAAAGACAGAAACGACTTAATCGACTAAGAAGCGTATTAGTCAACTAAGA
12389800 GCATTTTGTC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
73 25 0.48
74 27 0.52
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (73 bp):
AGAAACTAAGATCAAAAGACAGAAACGACTTAATCGACTAAGAAGCGTATTAGTCAACTAAGACC
TCACTGCC
Found at i:12391100 original size:19 final size:19
Alignment explanation
Indices: 12391076--12391123 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
12391066 TTTGGTTATG
12391076 TTTGCTGGTGCACTAATTA
1 TTTGCTGGTGCACTAATTA
*
12391095 TTTGCTGGTGCACTAATTG
1 TTTGCTGGTGCACTAATTA
12391114 TTTGCTGGTG
1 TTTGCTGGTG
12391124 TATTGCATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.44
Consensus pattern (19 bp):
TTTGCTGGTGCACTAATTA
Found at i:12392044 original size:115 final size:114
Alignment explanation
Indices: 12391823--12392138 Score: 386
Period size: 111 Copynumber: 2.9 Consensus size: 114
12391813 TAGATAAAAT
* * ** * *
12391823 TTAATTAAATAAGTAATATTATTTAGTTTTTGAAAT-TTTAAA-T--TAATTAATGTACTAATAA
1 TTAATTAAATAAGTAATAATATTTA-ATTTAAAAATAATTAAATTAGTAATTAATGTAATAATAA
* * *
12391884 CTTA--AAAATAGTGTAATT-AATATAAT-AAATAATGTAGTAGTAAACAA
65 CTTACTTAAATAGTTTAATTGATTA-AATAAAATAATGTAGTAGTAAACAA
*
12391931 TTAATTAAATAAGTAATAATATTTAATTTAAAAAATAATTAAATTAGTAATTAATGTATTAATAA
1 TTAATTAAATAAGTAATAATATTTAATTT-AAAAATAATTAAATTAGTAATTAATGTAATAATAA
* *
12391996 CTTACTTAAGTAGTTTAATTGATTAAATAAAATAATGTATTAGTAAACAA
65 CTTACTTAAATAGTTTAATTGATTAAATAAAATAATGTAGTAGTAAACAA
* *
12392046 TTAATTAAAT-A--AATAATATTTAATTTAAAAACAATTAAATTAGTAAGTAATGTAATAATAAC
1 TTAATTAAATAAGTAATAATATTTAATTTAAAAATAATTAAATTAGTAATTAATGTAATAATAAC
*
12392108 TTACTTAAAT-TTTTAATTGATTAAATAAAAT
66 TTACTTAAATAGTTTAATTGATTAAATAAAAT
12392139 TTAATTAAAT
Statistics
Matches: 183, Mismatches: 16, Indels: 16
0.85 0.07 0.07
Matches are distributed among these distances:
107 3 0.02
108 28 0.15
109 5 0.03
110 21 0.11
111 42 0.23
112 36 0.20
114 15 0.08
115 33 0.18
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.41
Consensus pattern (114 bp):
TTAATTAAATAAGTAATAATATTTAATTTAAAAATAATTAAATTAGTAATTAATGTAATAATAAC
TTACTTAAATAGTTTAATTGATTAAATAAAATAATGTAGTAGTAAACAA
Found at i:12392840 original size:16 final size:17
Alignment explanation
Indices: 12392799--12392845 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
12392789 GCAACCAAAA
12392799 TTTAGAT-TTTGATTCT
1 TTTAGATATTTGATTCT
*
12392815 TTT-GAAATTTGATT-T
1 TTTAGATATTTGATTCT
12392830 TTTAGATATTTTGATT
1 TTTAGATA-TTTGATT
12392846 GAATGGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.23
16 13 0.50
17 7 0.27
ACGTcount: A:0.23, C:0.02, G:0.13, T:0.62
Consensus pattern (17 bp):
TTTAGATATTTGATTCT
Found at i:12394847 original size:40 final size:40
Alignment explanation
Indices: 12394798--12394874 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
12394788 TAAAAAAATG
*
12394798 ATTTCATTATGATTGGGAAGCAAACTTTGGAAATCTTAAA
1 ATTTCATTATGATTGGGAAGCAAACTTTGAAAATCTTAAA
* *
12394838 ATTTGATTATGGTTGGGAAGCAAACTTTGAAAATCTT
1 ATTTCATTATGATTGGGAAGCAAACTTTGAAAATCTT
12394875 TAGAAGTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.36
Consensus pattern (40 bp):
ATTTCATTATGATTGGGAAGCAAACTTTGAAAATCTTAAA
Found at i:12400935 original size:14 final size:14
Alignment explanation
Indices: 12400916--12400960 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
12400906 ACTAGAAGAT
12400916 TAAATTAACTTACC
1 TAAATTAACTTACC
*
12400930 TAAATTAACTAACC
1 TAAATTAACTTACC
* *
12400944 TAAAATAA-TTAAC
1 TAAATTAACTTACC
12400957 TAAA
1 TAAA
12400961 ACATATCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 7 0.26
14 20 0.74
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATTAACTTACC
Found at i:12406985 original size:15 final size:15
Alignment explanation
Indices: 12406962--12407028 Score: 54
Period size: 15 Copynumber: 4.6 Consensus size: 15
12406952 TTTATTTACA
12406962 TTTAT-TATTATAAT
1 TTTATATATTATAAT
* *
12406976 TTTATATATTTTATT
1 TTTATATATTATAAT
12406991 TTTAATATATT-TATAT
1 TTT-ATATATTATA-AT
12407007 TTT-T-TATTATTAAT
1 TTTATATATTA-TAAT
12407021 TTT-TATAT
1 TTTATATAT
12407029 AATATCATCT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
13 4 0.09
14 12 0.27
15 17 0.39
16 11 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATATATTATAAT
Found at i:12407000 original size:16 final size:16
Alignment explanation
Indices: 12406969--12407141 Score: 72
Period size: 15 Copynumber: 10.6 Consensus size: 16
12406959 ACATTTATTA
*
12406969 TTATAATTTTATATAT
1 TTATATTTTTATATAT
12406985 TT-TATTTTTAATATAT
1 TTATATTTTT-ATATAT
12407001 TTATATTTTT-TAT-T
1 TTATATTTTTATATAT
12407015 ATTA-ATTTTTATATA-
1 -TTATATTTTTATATAT
* *
12407030 ATATCATCTCTTAAATATAT
1 TTAT-AT-T-TT-TATATAT
* * * *
12407050 TTTTAATGTCATATAT
1 TTATATTTTTATATAT
* *
12407066 TT-TATTTTCATTTATT
1 TTATATTTTTATATA-T
* *
12407082 ATTATAATCTTATATAT
1 -TTATATTTTTATATAT
* *
12407099 TT-TATTTTTATTTCT
1 TTATATTTTTATATAT
*
12407114 TTAATATATTTTTTATAT
1 TT-ATAT-TTTTATATAT
12407132 TATATATTTT
1 T-TATATTTT
12407142 ATTTTAATTT
Statistics
Matches: 117, Mismatches: 22, Indels: 35
0.67 0.13 0.20
Matches are distributed among these distances:
14 9 0.08
15 35 0.30
16 23 0.20
17 18 0.15
18 23 0.20
19 7 0.06
20 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (16 bp):
TTATATTTTTATATAT
Found at i:12407029 original size:24 final size:22
Alignment explanation
Indices: 12406962--12407029 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 22
12406952 TTTATTTACA
*
12406962 TTTATTATTATAATTTTATATAT
1 TTTATTATTA-ATTTTTATATAT
* *
12406985 TTTATTTTTAATATATTTATATTT
1 TTTATTATTAAT-T-TTTATATAT
12407009 TTTATTATTAATTTTTATATA
1 TTTATTATTAATTTTTATATA
12407030 ATATCATCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
22 8 0.21
23 11 0.29
24 19 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTATTATTAATTTTTATATAT
Found at i:12407078 original size:114 final size:114
Alignment explanation
Indices: 12406877--12407108 Score: 446
Period size: 114 Copynumber: 2.0 Consensus size: 114
12406867 AAAATACAAG
12406877 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
*
12406942 TGTCATATATTTTATTTACATTTATTATTATAATTTTATATATTTTATT
66 TGTCATATATTTTATTTACATTTATTATTATAATCTTATATATTTTATT
12406991 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
*
12407056 TGTCATATATTTTATTTTCATTTATTATTATAATCTTATATATTTTATT
66 TGTCATATATTTTATTTACATTTATTATTATAATCTTATATATTTTATT
12407105 TTTA
1 TTTA
12407109 TTTCTTTAAT
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 116 1.00
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.62
Consensus pattern (114 bp):
TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
TGTCATATATTTTATTTACATTTATTATTATAATCTTATATATTTTATT
Found at i:12407131 original size:33 final size:33
Alignment explanation
Indices: 12407060--12407145 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 33
12407050 TTTTAATGTC
* *
12407060 ATATATTTTATTTTCATTTATTATTATAATCTT
1 ATATATTTTATTTTTATTTATTAATATAATCTT
* *
12407093 ATATATTTTATTTTTATTTCTTTAATAT-ATTTT
1 ATATATTTTATTTTTATTT-ATTAATATAATCTT
* *
12407126 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
12407146 TAATTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 31 0.69
34 14 0.31
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.67
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTATTAATATAATCTT
Found at i:12407156 original size:87 final size:87
Alignment explanation
Indices: 12407060--12407255 Score: 213
Period size: 87 Copynumber: 2.2 Consensus size: 87
12407050 TTTTAATGTC
* *
12407060 ATATATTTTATTTTCATT-TAT-TATTATAATCTTATATATTTTATTTTTATTTCTTTAATATAT
1 ATATTTTTTATTTT-ATTATATAAATTATAATCTTATATATTTTA-TTTTA--T-TTTAATATAT
12407123 T-TT-TTATATTATATATTTTATTTTA
61 TATTCTTATATTATATATTTTATTTTA
* * * * * * *
12407148 AT-TTTTTTACCTATATTATATAAATTTTAATTTTTTATATTTTATTTTATTTTAATTTTTTATT
1 ATATTTTTTA-TTTTATTATATAAATTATAATCTTATATATTTTATTTTATTTTAATATATTATT
12407212 CTTATATTATATATTTTATTTTA
65 CTTATATTATATATTTTATTTTA
12407235 ATATTTTTTATTTTAATTATA
1 ATATTTTTTATTTT-ATTATA
12407256 ATAATATAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
85 9 0.10
86 3 0.03
87 35 0.39
88 25 0.28
89 18 0.20
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (87 bp):
ATATTTTTTATTTTATTATATAAATTATAATCTTATATATTTTATTTTATTTTAATATATTATTC
TTATATTATATATTTTATTTTA
Found at i:12407227 original size:33 final size:34
Alignment explanation
Indices: 12407180--12407255 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
12407170 AATTTTAATT
12407180 TTTTATATT-T-TATTTTATTTT-A-ATTTTTTA
1 TTTTATATTATATATTTTATTTTAATATTTTTTA
12407210 TTCTTATATTATATATTTTATTTTAATATTTTTTA
1 TT-TTATATTATATATTTTATTTTAATATTTTTTA
12407245 TTTTA-ATTATA
1 TTTTATATTATA
12407256 ATAATATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
30 2 0.05
31 7 0.17
32 1 0.02
33 17 0.41
34 4 0.10
35 10 0.24
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (34 bp):
TTTTATATTATATATTTTATTTTAATATTTTTTA
Found at i:12407244 original size:53 final size:53
Alignment explanation
Indices: 12407121--12407249 Score: 154
Period size: 54 Copynumber: 2.4 Consensus size: 53
12407111 TCTTTAATAT
*
12407121 ATTTTTTATATTATATATTTTATTTTAATTTTTTTACCTATATTATATAAATTTTA
1 ATTTTATATATT-T-TATTTTATTTTAATTTTTTTACCTATATTATAT-AATTTTA
* * *
12407177 ATTTTTTATATTTTATTTTATTTTAATTTTTTATTCTTATATTATAT-ATTTT-
1 ATTTTATATATTTTATTTTATTTTAATTTTTT-TACCTATATTATATAATTTTA
*
12407229 ATTTTAATATTTTTTATTTTA
1 ATTTT-ATATATTTTATTTTA
12407250 ATTATAATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
52 5 0.07
53 18 0.27
54 19 0.28
55 13 0.19
56 12 0.18
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (53 bp):
ATTTTATATATTTTATTTTATTTTAATTTTTTTACCTATATTATATAATTTTA
Found at i:12407249 original size:15 final size:15
Alignment explanation
Indices: 12407192--12407251 Score: 61
Period size: 15 Copynumber: 3.8 Consensus size: 15
12407182 TTATATTTTA
12407192 TTTTATTTT-A-ATT
1 TTTTATTTTAATATT
12407205 TTTTATTCTTATATTATAT
1 TTTTATT-TTA-A-TAT-T
12407224 ATTTTATTTTAATATT
1 -TTTTATTTTAATATT
12407240 TTTTATTTTAAT
1 TTTTATTTTAAT
12407252 TATAATAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 7 0.17
14 2 0.05
15 12 0.30
16 2 0.05
17 3 0.08
18 3 0.08
19 4 0.10
20 7 0.17
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTTTAATATT
Found at i:12407916 original size:31 final size:32
Alignment explanation
Indices: 12407855--12407921 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
12407845 TTTTTACCTT
12407855 TTTTCAATTTGATCCTCCAAACTTTTTCATTC
1 TTTTCAATTTGATCCTCCAAACTTTTTCATTC
*
12407887 TTTTCAATTTGATCTTCCAAAC-TTTTCATTC
1 TTTTCAATTTGATCCTCCAAACTTTTTCATTC
12407918 TTTT
1 TTTT
12407922 AACTGCGGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.38
32 21 0.62
ACGTcount: A:0.21, C:0.22, G:0.03, T:0.54
Consensus pattern (32 bp):
TTTTCAATTTGATCCTCCAAACTTTTTCATTC
Found at i:12408250 original size:44 final size:44
Alignment explanation
Indices: 12408191--12408309 Score: 143
Period size: 44 Copynumber: 2.7 Consensus size: 44
12408181 CACAAATTCT
*
12408191 AGGATTTTGCTTATTATCTTTGAAAGCTTAAAATCACAATTCCCA
1 AGGATTCTGCTTATTATCTTTGAAAGCTTAAAATCACAATT-CCA
* * * * *
12408236 A-GATTCTGCATATTATCCTTGGAAGCTTAAAATCATAGTTCCA
1 AGGATTCTGCTTATTATCTTTGAAAGCTTAAAATCACAATTCCA
*
12408279 AGGATTCTACTTATTATCTTTGGAAA-CTTAA
1 AGGATTCTGCTTATTATCTTT-GAAAGCTTAA
12408310 CATTATAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
43 4 0.06
44 54 0.87
45 4 0.06
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.38
Consensus pattern (44 bp):
AGGATTCTGCTTATTATCTTTGAAAGCTTAAAATCACAATTCCA
Found at i:12422985 original size:3 final size:3
Alignment explanation
Indices: 12422977--12423002 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12422967 TGGTCACCCC
12422977 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
12423003 TCCAATGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:12423159 original size:6 final size:6
Alignment explanation
Indices: 12423154--12423210 Score: 69
Period size: 6 Copynumber: 9.5 Consensus size: 6
12423144 TCTTATGCAG
* * * *
12423154 CAGCAG CAGCAC CAGCAC CAGCAA CAGCCA CAGCAA CAGCAA CAGCAA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA
*
12423202 CAGAAA CAG
1 CAGCAA CAG
12423211 TTTGCTGCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.44, C:0.37, G:0.19, T:0.00
Consensus pattern (6 bp):
CAGCAA
Found at i:12436717 original size:34 final size:35
Alignment explanation
Indices: 12436668--12436740 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
12436658 NNNNNNNNNN
* * *
12436668 TTAAGTTGTTGTTTG-AATATTTGTTTATAATTAT
1 TTAAGTTGATATTTGAAATATTTATTTATAATTAT
* *
12436702 TTAAGTTGATATTTGAAATATTTATTTTTGATTAT
1 TTAAGTTGATATTTGAAATATTTATTTATAATTAT
12436737 TTAA
1 TTAA
12436741 ATTTTGTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 13 0.39
35 20 0.61
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (35 bp):
TTAAGTTGATATTTGAAATATTTATTTATAATTAT
Found at i:12436951 original size:19 final size:19
Alignment explanation
Indices: 12436929--12436966 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12436919 AATCTTCTTA
*
12436929 TTCCCTCTAAATATTTTCT
1 TTCCCTCTAAATACTTTCT
12436948 TTCCCTCTAAATACTTTCT
1 TTCCCTCTAAATACTTTCT
12436967 CTTATATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (19 bp):
TTCCCTCTAAATACTTTCT
Found at i:12437093 original size:40 final size:40
Alignment explanation
Indices: 12437038--12437117 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
12437028 CTCTTTGATC
12437038 TCTCAAGTTTTAGAATTATTTTATTTTCATCATCTTCAAG
1 TCTCAAGTTTTAGAATTATTTTATTTTCATCATCTTCAAG
12437078 TCTCAAGTTTTAGAATTATTTTATTTTCATCATCTTCAAG
1 TCTCAAGTTTTAGAATTATTTTATTTTCATCATCTTCAAG
12437118 CTTCCAAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (40 bp):
TCTCAAGTTTTAGAATTATTTTATTTTCATCATCTTCAAG
Found at i:12438621 original size:91 final size:90
Alignment explanation
Indices: 12438514--12438684 Score: 315
Period size: 91 Copynumber: 1.9 Consensus size: 90
12438504 ATATTGAGAT
12438514 AATAAAGAAAGAGACACTTAATACCTCTATATTACATCTATTATCTCAAGTAGAAAGTATATGTT
1 AATAAAGAAAGAGACACTTAATACCTCTATATTACATCTATTATCTCAAGTAGAAAGTATATGTT
12438579 GAAAAAAAAAATTACTTGCTCTGTAC
66 G-AAAAAAAAATTACTTGCTCTGTAC
* *
12438605 AATAAAGAAAGAGACACTTAATACCTTTATATTACATCTATTATCTCAAGTAGAAAGTATGTGTT
1 AATAAAGAAAGAGACACTTAATACCTCTATATTACATCTATTATCTCAAGTAGAAAGTATATGTT
12438670 GAAAAAAAAATTACT
66 GAAAAAAAAATTACT
12438685 CGTTCTGTTC
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
90 14 0.18
91 64 0.82
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (90 bp):
AATAAAGAAAGAGACACTTAATACCTCTATATTACATCTATTATCTCAAGTAGAAAGTATATGTT
GAAAAAAAAATTACTTGCTCTGTAC
Found at i:12442908 original size:19 final size:20
Alignment explanation
Indices: 12442884--12442921 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
12442874 AATGTAGCAA
*
12442884 AATTTAAATAT-TTTTAAAT
1 AATTTAAAAATATTTTAAAT
12442903 AATTTAAAAATATTTTAAA
1 AATTTAAAAATATTTTAAA
12442922 GTGTTATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTTAAAAATATTTTAAAT
Found at i:12463184 original size:13 final size:13
Alignment explanation
Indices: 12463166--12463190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12463156 TTATTTAATT
12463166 TAAAATAAAAATA
1 TAAAATAAAAATA
12463179 TAAAATAAAAAT
1 TAAAATAAAAAT
12463191 TTGTAAAAAT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATAAAAATA
Found at i:12466579 original size:21 final size:22
Alignment explanation
Indices: 12466555--12466627 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 22
12466545 ACATACATTA
12466555 TCTT-AATTAAGACAAGAGTTG
1 TCTTAAATTAAGACAAGAGTTG
*
12466576 TCTTAAATT-AGACAATAGCATATG
1 TCTTAAATTAAGACAAGAG--T-TG
* * * *
12466600 TGTTGATTTAAGACAAGAGATG
1 TCTTAAATTAAGACAAGAGTTG
12466622 TCTTAA
1 TCTTAA
12466628 TTATATTATT
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 12 0.31
22 10 0.26
23 1 0.03
24 8 0.21
25 8 0.21
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (22 bp):
TCTTAAATTAAGACAAGAGTTG
Found at i:12467143 original size:20 final size:20
Alignment explanation
Indices: 12467123--12467159 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12467113 TTATTATTAT
12467123 TTTTCAA-AAATTAAAAATA
1 TTTTCAATAAATTAAAAATA
*
12467142 TTTTCAATAATTTAAAAA
1 TTTTCAATAAATTAAAAA
12467160 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTTCAATAAATTAAAAATA
Found at i:12467928 original size:20 final size:20
Alignment explanation
Indices: 12467899--12467942 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
12467889 TACAGAAACA
12467899 TAAT-GAATATAGGAAAATT
1 TAATCGAATATAGGAAAATT
*
12467918 TAATCGAATATAGGAAAGTT
1 TAATCGAATATAGGAAAATT
12467938 TAATC
1 TAATC
12467943 ACATCTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.32
Consensus pattern (20 bp):
TAATCGAATATAGGAAAATT
Found at i:12491573 original size:23 final size:22
Alignment explanation
Indices: 12491538--12491693 Score: 122
Period size: 23 Copynumber: 7.0 Consensus size: 22
12491528 TTAAAGAAAA
*
12491538 GATTTAGG-GAATTCAATAAGGG
1 GATTT-GGAGAATTGAATAAGGG
12491560 GATTTGAGAGAATTGAATAAGGG
1 GATTTG-GAGAATTGAATAAGGG
* *
12491583 GATTTGG-GAATTGAAGGAA-GA
1 GATTTGGAGAATTGAA-TAAGGG
* *
12491604 TATATGGAAGAATTGAATAAGGG
1 GATTTGG-AGAATTGAATAAGGG
* *
12491627 GATTT-AAGGAATTGAAGAAGGG
1 GATTTGGA-GAATTGAATAAGGG
* * **
12491649 GATTTGGGAGAATTAAAGAAAAG
1 GATTT-GGAGAATTGAATAAGGG
*
12491672 GATTTGGGGAATTGAATAAGGG
1 GATTTGGAGAATTGAATAAGGG
12491694 AATTGAAGAA
Statistics
Matches: 105, Mismatches: 20, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
21 16 0.15
22 41 0.39
23 47 0.45
24 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.35, T:0.25
Consensus pattern (22 bp):
GATTTGGAGAATTGAATAAGGG
Found at i:12491675 original size:45 final size:45
Alignment explanation
Indices: 12491525--12491693 Score: 146
Period size: 45 Copynumber: 3.8 Consensus size: 45
12491515 AAATTTAGAG
* * *
12491525 GAATTAAAGAAAA-GATTTAGGGAATTCAATAAGGGGATTTGAGA
1 GAATTAAAGAAAAGGATTTAGGGAATTGAAGAAGGGGATTTGGGA
* * ** ** * *
12491569 GAATTGAATAAGGGGATTT-GGGAATTGAAGGAA-GATATATGGAA
1 GAATTAAAGAAAAGGATTTAGGGAATTGAA-GAAGGGGATTTGGGA
* * ** *
12491613 GAATTGAATAAGGGGATTTAAGGAATTGAAGAAGGGGATTTGGGA
1 GAATTAAAGAAAAGGATTTAGGGAATTGAAGAAGGGGATTTGGGA
* *
12491658 GAATTAAAGAAAAGGATTTGGGGAATTGAATAAGGG
1 GAATTAAAGAAAAGGATTTAGGGAATTGAAGAAGGG
12491694 AATTGAAGAA
Statistics
Matches: 98, Mismatches: 23, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
44 46 0.47
45 52 0.53
ACGTcount: A:0.42, C:0.01, G:0.33, T:0.24
Consensus pattern (45 bp):
GAATTAAAGAAAAGGATTTAGGGAATTGAAGAAGGGGATTTGGGA
Found at i:12491712 original size:89 final size:89
Alignment explanation
Indices: 12491538--12491712 Score: 192
Period size: 89 Copynumber: 2.0 Consensus size: 89
12491528 TTAAAGAAAA
* * * * **
12491538 GATTTAGGGAATTCAATAAGGGGATTTGAGAGAATTGAATAAGGGGATTTGGGAATTGAAGGAAG
1 GATTTAAGGAATTCAAGAAGGGGATTTGAGAGAATTAAAGAAAAGGATTTGGGAATTGAAGGAAG
* * *
12491603 ATATATGGAAGAATTGAATAAGGG
66 AGATATGGAAGAAATAAATAAGGG
* * *
12491627 GATTTAAGGAATTGAAGAAGGGGATTTGGGAGAATTAAAGAAAAGGATTTGGGGAATTGAA-TAA
1 GATTTAAGGAATTCAAGAAGGGGATTTGAGAGAATTAAAGAAAAGGATTT-GGGAATTGAAGGAA
* *
12491691 GGGA-ATTGAAGAAAATAAATAA
65 GAGATATGGAAG-AAATAAATAA
12491713 AGCGATGTTC
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
88 6 0.09
89 54 0.77
90 10 0.14
ACGTcount: A:0.43, C:0.01, G:0.32, T:0.25
Consensus pattern (89 bp):
GATTTAAGGAATTCAAGAAGGGGATTTGAGAGAATTAAAGAAAAGGATTTGGGAATTGAAGGAAG
AGATATGGAAGAAATAAATAAGGG
Found at i:12495673 original size:21 final size:21
Alignment explanation
Indices: 12495649--12495693 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12495639 AACCTTGCTG
*
12495649 CTTAAAAAAAAAGTCTCGAGA
1 CTTAAAAAAAAAGTCTAGAGA
* * *
12495670 CTTACACAAGAAGTCTAGAGA
1 CTTAAAAAAAAAGTCTAGAGA
12495691 CTT
1 CTT
12495694 GAGTTGAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (21 bp):
CTTAAAAAAAAAGTCTAGAGA
Found at i:12496869 original size:22 final size:21
Alignment explanation
Indices: 12496844--12496891 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
12496834 TCGTGCAAGT
12496844 TTAGAATTCCAAGAA-TCGATTC
1 TTAGAA-T-CAAGAAGTCGATTC
12496866 TTAGGAATCAAGAAGTCGATTC
1 TTA-GAATCAAGAAGTCGATTC
12496888 TTAG
1 TTAG
12496892 GCTCTAGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.29
22 14 0.58
23 3 0.12
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (21 bp):
TTAGAATCAAGAAGTCGATTC
Found at i:12498600 original size:20 final size:21
Alignment explanation
Indices: 12498562--12498603 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12498552 AAGTGATTAA
12498562 TTTAAGTTATTTTAGTTAAAT
1 TTTAAGTTATTTTAGTTAAAT
*
12498583 TTTAAGTTATTTT-TTTAAAT
1 TTTAAGTTATTTTAGTTAAAT
12498603 T
1 T
12498604 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (21 bp):
TTTAAGTTATTTTAGTTAAAT
Found at i:12516701 original size:2 final size:2
Alignment explanation
Indices: 12516689--12516726 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
12516679 AATCAATGGA
* *
12516689 TC TC TC CC TC TC T- TC TC TT TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12516727 ATCAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:12534157 original size:21 final size:24
Alignment explanation
Indices: 12534111--12534161 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 24
12534101 TTTTGCAAAC
*
12534111 AGAAA-ATAAATAAAGATTAAAGT
1 AGAAATATAAATAAAGATTAAAAT
12534134 AGAAATATAAAT-AA-A-TAAAAT
1 AGAAATATAAATAAAGATTAAAAT
12534155 AGAAATA
1 AGAAATA
12534162 ACTGAACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 12 0.46
22 1 0.04
23 7 0.27
24 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.22
Consensus pattern (24 bp):
AGAAATATAAATAAAGATTAAAAT
Found at i:12537093 original size:6 final size:6
Alignment explanation
Indices: 12537082--12537108 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12537072 AAAATTAAAG
12537082 AAACTA AAACTA AAACTA AAACTA AAA
1 AAACTA AAACTA AAACTA AAACTA AAA
12537109 AAAAGAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAACTA
Found at i:12558294 original size:34 final size:34
Alignment explanation
Indices: 12558256--12558345 Score: 146
Period size: 33 Copynumber: 2.7 Consensus size: 34
12558246 AAAGCTGGGC
*
12558256 AATTCGCAGGATTAGGAACATTAAATGTATTGGT
1 AATTCACAGGATTAGGAACATTAAATGTATTGGT
12558290 AATTCACAGGATTAGGAACATT-AATGTATTGGT
1 AATTCACAGGATTAGGAACATTAAATGTATTGGT
* *
12558323 AATTCATAGGAATAGGAACATTA
1 AATTCACAGGATTAGGAACATTA
12558346 CTGTTACCTC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
33 31 0.60
34 21 0.40
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (34 bp):
AATTCACAGGATTAGGAACATTAAATGTATTGGT
Found at i:12566272 original size:21 final size:21
Alignment explanation
Indices: 12566246--12566285 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
12566236 AAATGTAAAC
12566246 TTTGGTGTTGTGTGAGTGAAT
1 TTTGGTGTTGTGTGAGTGAAT
12566267 TTTGGTGTTGTGTGAGTGA
1 TTTGGTGTTGTGTGAGTGA
12566286 CGGTGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.47
Consensus pattern (21 bp):
TTTGGTGTTGTGTGAGTGAAT
Found at i:12569272 original size:61 final size:60
Alignment explanation
Indices: 12569207--12569327 Score: 161
Period size: 61 Copynumber: 2.0 Consensus size: 60
12569197 CAACGAAAAC
* * * * *
12569207 CTCACTATCTCAAAAGTATTGATATATTAATCAAGTGTATCAATACATTTTCAATAAAATG
1 CTCACTACCTCAAAAGTATTGATAAATTAA-CAAATGTACCAATACATTTCCAATAAAATG
* * *
12569268 CTCACTGCCTCAAAAGTATTGATAAATTAACAAATGTACCGATACATTTCCAATAGAATG
1 CTCACTACCTCAAAAGTATTGATAAATTAACAAATGTACCAATACATTTCCAATAAAATG
12569328 TTCAAACCCT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 25 0.48
61 27 0.52
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.32
Consensus pattern (60 bp):
CTCACTACCTCAAAAGTATTGATAAATTAACAAATGTACCAATACATTTCCAATAAAATG
Found at i:12569377 original size:18 final size:19
Alignment explanation
Indices: 12569351--12569405 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
12569341 AACCAAGTTG
*
12569351 AAAAATATCAATACATTC-
1 AAAAGTATCAATACATTCT
* *
12569369 AAAAGTATCAATAAATCCT
1 AAAAGTATCAATACATTCT
*
12569388 AAAATGTATCGATACATT
1 AAAA-GTATCAATACATT
12569406 TAACAGGAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 15 0.52
19 4 0.14
20 10 0.34
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAAGTATCAATACATTCT
Found at i:12569880 original size:37 final size:36
Alignment explanation
Indices: 12569838--12569907 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
12569828 GGTATTGTGA
*
12569838 TTGTGCTTTAAT-CATAAAAAGGCATTGTATTGAAAGG
1 TTGTGC-TTAATCCACAAAAA-GCATTGTATTGAAAGG
*
12569875 TTGTGCTTGATCCACAAAAAGCATTGTATTGAA
1 TTGTGCTTAATCCACAAAAAGCATTGTATTGAA
12569908 TCTTTTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 17 0.57
37 13 0.43
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (36 bp):
TTGTGCTTAATCCACAAAAAGCATTGTATTGAAAGG
Found at i:12575532 original size:15 final size:15
Alignment explanation
Indices: 12575501--12575555 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
12575491 TTTACAATGC
* *
12575501 AATGTGATTACAGGT
1 AATGTGATTGCAAGT
12575516 AATGTGATTGCAAGT
1 AATGTGATTGCAAGT
* * *
12575531 AATATAATTGCAAGC
1 AATGTGATTGCAAGT
12575546 AATGTGATTG
1 AATGTGATTG
12575556 TTGGGAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:12575845 original size:34 final size:33
Alignment explanation
Indices: 12575777--12575859 Score: 103
Period size: 34 Copynumber: 2.5 Consensus size: 33
12575767 AATGTCATAC
*
12575777 ATTTTATTTTTATTTATTATTATAATCTTATAT
1 ATTTTATTTTTATTTATTAATATAATCTTATAT
* * *
12575810 ATTTTATTTTTATTTCTTTAATATAATTTTTTAT
1 ATTTTATTTTTATTT-ATTAATATAATCTTATAT
*
12575844 ATTATATATTTTATTT
1 ATTTTAT-TTTTATTT
12575860 TAATTTCTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 15 0.35
34 20 0.47
35 8 0.19
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (33 bp):
ATTTTATTTTTATTTATTAATATAATCTTATAT
Found at i:12575893 original size:7 final size:7
Alignment explanation
Indices: 12575883--12575916 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
12575873 CTATATGATA
12575883 TAAATTT
1 TAAATTT
12575890 TAAATTT
1 TAAATTT
12575897 TAAATTT
1 TAAATTT
12575904 T--ATTT
1 TAAATTT
12575909 TAAATTT
1 TAAATTT
12575916 T
1 T
12575917 GATTCTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
7 20 0.80
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TAAATTT
Found at i:12575910 original size:12 final size:13
Alignment explanation
Indices: 12575883--12575916 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
12575873 CTATATGATA
12575883 TAAATTTTAAATTT
1 TAAATTTT-AATTT
12575897 TAAATTTT-ATTT
1 TAAATTTTAATTT
12575909 TAAATTTT
1 TAAATTTT
12575917 GATTCTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
14 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TAAATTTTAATTT
Found at i:12575952 original size:15 final size:15
Alignment explanation
Indices: 12575929--12575960 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12575919 TTCTTATATT
12575929 ATATATTTTATTTTA
1 ATATATTTTATTTTA
*
12575944 ATATTTTTTATTTTA
1 ATATATTTTATTTTA
12575959 AT
1 AT
12575961 TATAACATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:12575963 original size:33 final size:31
Alignment explanation
Indices: 12575886--12575965 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 31
12575876 TATGATATAA
*
12575886 ATTTTAAATTTTAAATTTTATTTTAAATTTTG
1 ATTTT-AATTATAAATTTTATTTTAAATTTTG
* *
12575918 ATTCTTATATTATATATTTTATTTTAATATTTTTT
1 ATT-TTA-ATTATAAATTTTATTTTAA-A-TTTTG
12575953 ATTTTAATTATAA
1 ATTTTAATTATAA
12575966 CATTATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
32 4 0.10
33 25 0.62
34 4 0.10
35 7 0.17
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (31 bp):
ATTTTAATTATAAATTTTATTTTAAATTTTG
Found at i:12577059 original size:6 final size:6
Alignment explanation
Indices: 12577048--12577080 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
12577038 CTTTCTCTAT
*
12577048 AAGGAA AAGGAA AAGGAA AAGGAA AAAGAA AAG
1 AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAG
12577081 CTACTTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (6 bp):
AAGGAA
Found at i:12585521 original size:209 final size:208
Alignment explanation
Indices: 12585175--12585588 Score: 747
Period size: 209 Copynumber: 2.0 Consensus size: 208
12585165 TGTGATTCAA
*
12585175 AAATATAAGTTGTAGGTTTGTATTATTGGTTATTGCTTAAAATTTCACCAACATATTATTTTTTA
1 AAATATAAGTTGTAGGGTTGTATTATTGGTTATTGCTTAAAATTTCACCAACATATTATTTTTTA
* *
12585240 TTAATCGTGATTATATTAGAAGAAATTATCTTAAGTATATCGTTTTTATGTGCTTTATGTTTTAT
66 TTAATCGTGATTATATAAGAAGAAATTATCTTAAGTATATCATTTTTATGTGCTTTATGTTTTAT
* *
12585305 ATTTAGTTGAAAAGAAATTATCTTGAATATTTAGTCTCTAAACAATCTTGATTATATAAGAGAAA
131 ATTTAGTTAAAAAGAAATTATCTTGAATATTTAGTCTCTAAACAATCCTGATTATATAAGAGAAA
12585370 ATTATGTAATTTTC
196 ATTAT-TAATTTTC
*
12585384 AAATATAAGTTGTAGGGTTGTATTATTGGTTGTTGCTTAAAATTTCACCAACATATTATTTTTTA
1 AAATATAAGTTGTAGGGTTGTATTATTGGTTATTGCTTAAAATTTCACCAACATATTATTTTTTA
*
12585449 TTAATCGTGATTATATAAGAAGAAATTATCTTAAGTATATTATTTTTATGTGCTTTATGTTTTAT
66 TTAATCGTGATTATATAAGAAGAAATTATCTTAAGTATATCATTTTTATGTGCTTTATGTTTTAT
*
12585514 ATTTAGTTAAAAAGAAATTATCTTGAATATTTAGTCTTTAAACAATCCTGATTATATAAGAGAAA
131 ATTTAGTTAAAAAGAAATTATCTTGAATATTTAGTCTCTAAACAATCCTGATTATATAAGAGAAA
12585579 ATTATTAATT
196 ATTATTAATT
12585589 CTATATATTG
Statistics
Matches: 197, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
208 5 0.03
209 192 0.97
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (208 bp):
AAATATAAGTTGTAGGGTTGTATTATTGGTTATTGCTTAAAATTTCACCAACATATTATTTTTTA
TTAATCGTGATTATATAAGAAGAAATTATCTTAAGTATATCATTTTTATGTGCTTTATGTTTTAT
ATTTAGTTAAAAAGAAATTATCTTGAATATTTAGTCTCTAAACAATCCTGATTATATAAGAGAAA
ATTATTAATTTTC
Found at i:12585571 original size:106 final size:106
Alignment explanation
Indices: 12585242--12585583 Score: 292
Period size: 106 Copynumber: 3.3 Consensus size: 106
12585232 ATTTTTTATT
* **
12585242 AATCGTGATTATATTAGA-AGAAATTATCTTAAGTATATCGTTTTTATGTGCTTTATGTTTTATA
1 AATCGTGATTATATAAGAGA-AAATTATCTTAAGTATATTATTTTTATGTGCTTTATGTTTTATA
*
12585306 TTTAGTTGAAAAGAAATTATCTTGAATATTTAGTCTCTAAAC
65 TTTAGTTGAAAAGAAATTATCTTGAATATTTAGTCTTTAAAC
* * ** * * * * *
12585348 AATCTTGATTATATAAGAGAAAATTAT-GTAA-T-T-TTCAAATATAAGT--TGTAGGGTTGTAT
1 AATCGTGATTATATAAGAGAAAATTATCTTAAGTATATT-ATTTTTATGTGCTTTA-TGTTTTA-
* *** *** * * * **
12585407 TATTGGTTGTTGCTTA-AAATT-TCACCAACATATTA-TTTTTTATT
63 TATT--TAGTTGAAAAGAAATTATCTTGAATAT-TTAGTCTTTAAAC
12585451 AATCGTGATTATATAAGA-AGAAATTATCTTAAGTATATTATTTTTATGTGCTTTATGTTTTATA
1 AATCGTGATTATATAAGAGA-AAATTATCTTAAGTATATTATTTTTATGTGCTTTATGTTTTATA
*
12585515 TTTAGTTAAAAAGAAATTATCTTGAATATTTAGTCTTTAAAC
65 TTTAGTTGAAAAGAAATTATCTTGAATATTTAGTCTTTAAAC
*
12585557 AATCCTGATTATATAAGAGAAAATTAT
1 AATCGTGATTATATAAGAGAAAATTAT
12585584 TAATTCTATA
Statistics
Matches: 170, Mismatches: 48, Indels: 36
0.67 0.19 0.14
Matches are distributed among these distances:
101 3 0.02
102 7 0.04
103 44 0.26
104 17 0.10
105 18 0.11
106 69 0.41
107 9 0.05
108 3 0.02
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.45
Consensus pattern (106 bp):
AATCGTGATTATATAAGAGAAAATTATCTTAAGTATATTATTTTTATGTGCTTTATGTTTTATAT
TTAGTTGAAAAGAAATTATCTTGAATATTTAGTCTTTAAAC
Found at i:12603349 original size:19 final size:18
Alignment explanation
Indices: 12603282--12603349 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 18
12603272 AAAATTTTAA
12603282 ATTTTTAAAAAATAAAAAT
1 ATTTTT-AAAAATAAAAAT
* *
12603301 ATATTATAAAAATTTTAAAAT
1 AT-TTTTAAAAA--TAAAAAT
*
12603322 -TTTTAAAAAATAAAAAT
1 ATTTTTAAAAATAAAAAT
12603339 ATGTTTTAAAA
1 AT-TTTTAAAA
12603350 TTCTTTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
17 6 0.16
18 1 0.03
19 21 0.55
20 4 0.11
21 6 0.16
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (18 bp):
ATTTTTAAAAATAAAAAT
Found at i:12603357 original size:39 final size:37
Alignment explanation
Indices: 12603272--12603364 Score: 141
Period size: 38 Copynumber: 2.5 Consensus size: 37
12603262 TTGTAAAAAT
12603272 AAAATTTTAAATTTTTAAAAAATAAAAATATATTATA
1 AAAATTTTAAATTTTTAAAAAATAAAAATATATTATA
* *
12603309 AAAATTTTAAAATTTTTAAAAAATAAAAATATGTTTTA
1 AAAATTTT-AAATTTTTAAAAAATAAAAATATATTATA
*
12603347 AAATTCTTTAAATTTTTA
1 AAAAT-TTTAAATTTTTA
12603365 GAGGGACGGC
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
37 8 0.16
38 40 0.78
39 3 0.06
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (37 bp):
AAAATTTTAAATTTTTAAAAAATAAAAATATATTATA
Found at i:12603475 original size:3 final size:3
Alignment explanation
Indices: 12603467--12603500 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
12603457 TTTATTTATT
* *
12603467 TAA TAA TAA TAA TAA TAA TAA TGA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
12603501 TATATCATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12603683 original size:20 final size:22
Alignment explanation
Indices: 12603643--12603684 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12603633 AGTTTTGAAT
*
12603643 ATATTTTAATAAAATGTAAAAA
1 ATATTTTAATAAAAAGTAAAAA
12603665 ATATTTTAA-AAAAAG-AAAAA
1 ATATTTTAATAAAAAGTAAAAA
12603685 TAAAGAGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 5 0.26
22 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
ATATTTTAATAAAAAGTAAAAA
Found at i:12605883 original size:133 final size:132
Alignment explanation
Indices: 12605643--12606043 Score: 507
Period size: 133 Copynumber: 3.0 Consensus size: 132
12605633 TGAATAACTC
* * * * ** *
12605643 TACAAATTAAAGGATTTAGTAAATAAACAAATTGAACATCCCTTGGCAGGTACAGATAAGAAGCA
1 TACAAATTAAAGGATTTAGTGAATAAACAGATAGAACATCCATCAGCAGGTACAGTTAAGAAGCA
* * * *
12605708 TATATTGTCACATGTAATCTAGTGAACAACTTAAATCGATAAACTAATTGCTAATTCAGGAAGAA
66 TATATTGTCA-GTGTAAACTAGTGAACAACTTAAATCAATAAACTAATTGCTAATACAGGAAGAA
12605773 ACA
130 ACA
* ** *
12605776 TACAAATCAAAGGATTTAGTGAATAAACAGATAGATTATCCATCAGCAGGCACAGTTAAGAAGCA
1 TACAAATTAAAGGATTTAGTGAATAAACAGATAGAACATCCATCAGCAGGTACAGTTAAGAAGCA
* * *
12605841 TTTATTGCTCAGTGTAAACTAATGAACAACTTAAATCAATAAACTGATTGCTAATACAGGAAGAA
66 TATATTG-TCAGTGTAAACTAGTGAACAACTTAAATCAATAAACTAATTGCTAATACAGGAAGAA
12605906 ACA
130 ACA
* * *
12605909 TACAAATTAAAGGATTTAGTGAATAAACAGTTAGAACATCCATCAGCAGATACAGTTAA-ACGGC
1 TACAAATTAAAGGATTTAGTGAATAAACAGATAGAACATCCATCAGCAGGTACAGTTAAGA-AGC
** * * * * *
12605973 ATATATTGGAAAGTGTCAACTAGTGAACAACTTAAACCAATAAGCTAGTTGCTAATACCGGAAGA
65 ATATATT-GTCAGTGTAAACTAGTGAACAACTTAAATCAATAAACTAATTGCTAATACAGGAAGA
12606038 AACA
129 AACA
12606042 TA
1 TA
12606044 TTTCTTGTAC
Statistics
Matches: 230, Mismatches: 35, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
132 1 0.00
133 225 0.98
134 4 0.02
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (132 bp):
TACAAATTAAAGGATTTAGTGAATAAACAGATAGAACATCCATCAGCAGGTACAGTTAAGAAGCA
TATATTGTCAGTGTAAACTAGTGAACAACTTAAATCAATAAACTAATTGCTAATACAGGAAGAAA
CA
Found at i:12616864 original size:25 final size:25
Alignment explanation
Indices: 12616829--12616974 Score: 139
Period size: 25 Copynumber: 5.8 Consensus size: 25
12616819 TTATTTTAAT
12616829 TCTAAGGATAATTTTACTATCAGAA
1 TCTAAGGATAATTTTACTATCAGAA
* * * *
12616854 TTTAAGAATAATTTTATTACCAGAA
1 TCTAAGGATAATTTTACTATCAGAA
** * *
12616879 GTGGATGGATAATTTTATTATCAGAA
1 -TCTAAGGATAATTTTACTATCAGAA
* *
12616905 TCTAAGAATAATTTTACTATAAGAA
1 TCTAAGGATAATTTTACTATCAGAA
** * *
12616930 GTGGATGGGTAATTTTACTATCAGAA
1 -TCTAAGGATAATTTTACTATCAGAA
*
12616956 TCTGAGGATAATTTTACTA
1 TCTAAGGATAATTTTACTA
12616975 CTAGAAGCGG
Statistics
Matches: 93, Mismatches: 26, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
25 54 0.58
26 39 0.42
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (25 bp):
TCTAAGGATAATTTTACTATCAGAA
Found at i:12616890 original size:51 final size:51
Alignment explanation
Indices: 12616834--12616995 Score: 216
Period size: 51 Copynumber: 3.2 Consensus size: 51
12616824 TTAATTCTAA
* * *
12616834 GGATAATTTTACTATCAGAATTTAAGAATAATTTTATTACCAGAAGTGGAT
1 GGATAATTTTACTATCAGAATCTAAGAATAATTTTACTACAAGAAGTGGAT
* *
12616885 GGATAATTTTATTATCAGAATCTAAGAATAATTTTACTATAAGAAGTGGAT
1 GGATAATTTTACTATCAGAATCTAAGAATAATTTTACTACAAGAAGTGGAT
* * * * *
12616936 GGGTAATTTTACTATCAGAATCTGAGGATAATTTTACTACTAGAAGCGGAT
1 GGATAATTTTACTATCAGAATCTAAGAATAATTTTACTACAAGAAGTGGAT
**
12616987 AAATAATTT
1 GGATAATTT
12616996 AACCATCAAA
Statistics
Matches: 96, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 96 1.00
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (51 bp):
GGATAATTTTACTATCAGAATCTAAGAATAATTTTACTACAAGAAGTGGAT
Found at i:12617281 original size:24 final size:24
Alignment explanation
Indices: 12617248--12617374 Score: 109
Period size: 24 Copynumber: 5.4 Consensus size: 24
12617238 ATAGGTTGTT
* *
12617248 ACACGTCATGTACAAAAATGTGTG
1 ACACGCCATGTACAAAAACGTGTG
* * *
12617272 ACACGCCATGTATAAAAACATGTT
1 ACACGCCATGTACAAAAACGTGTG
* ** * *
12617296 ACACGTCATG----ATTAGGTTGTT
1 ACACGCCATGTACAAAAACG-TGTG
*
12617317 ACACGTCATGTACAAAAACGTGTG
1 ACACGCCATGTACAAAAACGTGTG
12617341 ACACGCCATGTACAAAAACGTGTG
1 ACACGCCATGTACAAAAACGTGTG
*
12617365 ACATGCCATG
1 ACACGCCATG
12617375 GTTAAGTTAT
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
20 2 0.02
21 14 0.17
24 63 0.77
25 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (24 bp):
ACACGCCATGTACAAAAACGTGTG
Found at i:12617304 original size:69 final size:69
Alignment explanation
Indices: 12617211--12617416 Score: 265
Period size: 69 Copynumber: 3.0 Consensus size: 69
12617201 TTACACACTG
*
12617211 TGTACAGAAACATGTTACACGTCATGGATAGGTTGTTACACGTCATGTACAAAAATGTGTGACAC
1 TGTACAAAAACATGTTACACGTCATGGATAGGTTGTTACACGTCATGTACAAAAATGTGTGACAC
12617276 GCCA
66 GCCA
* *
12617280 TGTATAAAAACATGTTACACGTCAT-GATTAGGTTGTTACACGTCATGTACAAAAACGTGTGACA
1 TGTACAAAAACATGTTACACGTCATGGA-TAGGTTGTTACACGTCATGTACAAAAATGTGTGACA
12617344 CGCCA
65 CGCCA
* * * * * * * * * *
12617349 TGTACAAAAACGTGTGACATGCCATGGTTAAGTTATTACACGCCATGTATAAACATGT-T-ACAC
1 TGTACAAAAACATGTTACACGTCATGGATAGGTTGTTACACGTCATGTACAAAAATGTGTGACAC
12617412 GCCA
66 GCCA
12617416 T
1 T
12617417 TGTTAAGTTG
Statistics
Matches: 120, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
67 9 0.08
68 3 0.03
69 107 0.89
70 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (69 bp):
TGTACAAAAACATGTTACACGTCATGGATAGGTTGTTACACGTCATGTACAAAAATGTGTGACAC
GCCA
Found at i:12617395 original size:21 final size:20
Alignment explanation
Indices: 12617369--12617442 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
12617359 CGTGTGACAT
*
12617369 GCCATGGTTAAGTTATTACAC
1 GCCAT-GTTAAGTTGTTACAC
**
12617390 GCCATGTATAAACATGTTACAC
1 GCCATGT-T-AAGTTGTTACAC
12617412 GCCATTGTTAAGTTGTTACAC
1 GCCA-TGTTAAGTTGTTACAC
*
12617433 GCCATATTAA
1 GCCATGTTAA
12617443 AAAAAATACT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
20 7 0.16
21 20 0.45
22 14 0.32
23 3 0.07
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (20 bp):
GCCATGTTAAGTTGTTACAC
Found at i:12617424 original size:43 final size:44
Alignment explanation
Indices: 12617341--12617446 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 44
12617331 AAAACGTGTG
* *
12617341 ACACGCCATGTACAAAAACGTGTGACATGCCATGGTTAAGTTATT
1 ACACGCCATGTA-AAAAACATGTGACACGCCATGGTTAAGTTATT
* * * *
12617386 ACACGCCATGT-ATAAACATGTTACACGCCATTGTTAAGTTGTT
1 ACACGCCATGTAAAAAACATGTGACACGCCATGGTTAAGTTATT
*
12617429 ACACGCCATATTAAAAAA
1 ACACGCCAT-GTAAAAAA
12617447 AATACTGTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
43 35 0.69
44 1 0.02
45 15 0.29
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (44 bp):
ACACGCCATGTAAAAAACATGTGACACGCCATGGTTAAGTTATT
Found at i:12619084 original size:20 final size:20
Alignment explanation
Indices: 12619043--12619085 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
12619033 TATTATTTTC
*
12619043 TATTAAGTCTTAAAGAAGTT
1 TATTAAGTCTTAAAGAAATT
*
12619063 TATTAAGTTTTAAA-AATATT
1 TATTAAGTCTTAAAGAA-ATT
12619083 TAT
1 TAT
12619086 CTGATAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (20 bp):
TATTAAGTCTTAAAGAAATT
Found at i:12622858 original size:30 final size:28
Alignment explanation
Indices: 12622824--12622880 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
12622814 TGTAAAGAAT
* *
12622824 TAAATTAGTTAATTTAAATTATTTTATAAA
1 TAAATTAGTCAA-TT-AATTAATTTATAAA
12622854 TAAATTAGTCAATTAATTAATTTATAA
1 TAAATTAGTCAATTAATTAATTTATAA
12622881 TCTTTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.48
29 2 0.08
30 11 0.44
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (28 bp):
TAAATTAGTCAATTAATTAATTTATAAA
Found at i:12628568 original size:21 final size:21
Alignment explanation
Indices: 12628543--12628593 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
12628533 ATGGTGAAAT
*
12628543 ATGTCATATAATCATGTCATA
1 ATGTCACATAATCATGTCATA
*
12628564 ATGTCACATGATCATGTCATA
1 ATGTCACATAATCATGTCATA
*
12628585 ATGCCACAT
1 ATGTCACAT
12628594 TAGCATACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (21 bp):
ATGTCACATAATCATGTCATA
Found at i:12634829 original size:30 final size:31
Alignment explanation
Indices: 12634793--12634908 Score: 102
Period size: 30 Copynumber: 3.9 Consensus size: 31
12634783 ACAGTTTTAC
*
12634793 CATGTTT-ATCTTAATTTAGATAAAAAAAAG
1 CATGTTTGATCTTAATTTAGACAAAAAAAAG
*
12634823 CATGTTTGGTCTTAATTTAGAC--AAAAAA-
1 CATGTTTGATCTTAATTTAGACAAAAAAAAG
*
12634851 TATGTTTG-TCTTAATTTA-ACACAAAAAAA-
1 CATGTTTGATCTTAATTTAGACA-AAAAAAAG
* * * * *
12634880 TATTTTTTATCTTAATCTAGACAAGAAAA
1 CATGTTTGATCTTAATTTAGACAAAAAAA
12634909 CATATTTGTC
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
26 2 0.03
27 10 0.14
28 7 0.10
29 18 0.25
30 21 0.29
31 15 0.21
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.38
Consensus pattern (31 bp):
CATGTTTGATCTTAATTTAGACAAAAAAAAG
Found at i:12634857 original size:28 final size:27
Alignment explanation
Indices: 12634793--12634931 Score: 107
Period size: 28 Copynumber: 4.9 Consensus size: 27
12634783 ACAGTTTTAC
* *
12634793 CATGTTTATCTTAATTTAGATAAAAAAAA
1 CATGTTTGTCTTAATTTAG--ACAAAAAA
12634822 GCATGTTTGGTCTTAATTTAGACAAAAAA
1 -CATGTTT-GTCTTAATTTAGACAAAAAA
* *
12634851 TATGTTTGTCTTAATTTAACACAAAAAAA
1 CATGTTTGTCTTAATTT-AGAC-AAAAAA
* * * *
12634880 TATTTTTTATCTTAATCTAGACAAGAAAA
1 CA-TGTTTGTCTTAATTTAGACAA-AAAA
* * *
12634909 CATATTTGTCTCAATGTAGACAA
1 CATGTTTGTCTTAATTTAGACAA
12634932 GATAAAATAT
Statistics
Matches: 91, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
27 10 0.11
28 28 0.31
29 23 0.25
30 19 0.21
31 11 0.12
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (27 bp):
CATGTTTGTCTTAATTTAGACAAAAAA
Found at i:12634903 original size:29 final size:29
Alignment explanation
Indices: 12634797--12634954 Score: 99
Period size: 30 Copynumber: 5.4 Consensus size: 29
12634787 TTTTACCATG
* * *
12634797 TTTATCTTAATTTAGATAAAAAAAAGCATGT
1 TTTATCTTAATTTAGA-CAAAAAAA-TATTT
** *
12634828 TTGGTCTTAATTTAGAC-AAAAAATA-TG
1 TTTATCTTAATTTAGACAAAAAAATATTT
* *
12634855 TTTGTCTTAATTTAACACAAAAAAATATTT
1 TTTATCTTAATTT-AGACAAAAAAATATTT
* * * *
12634885 TTTATCTTAATCTAGACAAGAAAACA-TA
1 TTTATCTTAATTTAGACAAAAAAATATTT
* * *
12634913 TTTGTCTCAATGTAGACAAGATAAAATA-TT
1 TTTATCTTAATTTAGACAA-A-AAAATATTT
*
12634943 TTTATTTTAATT
1 TTTATCTTAATT
12634955 AAAGACAAGA
Statistics
Matches: 97, Mismatches: 25, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
27 12 0.12
28 21 0.22
29 24 0.25
30 26 0.27
31 14 0.14
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.41
Consensus pattern (29 bp):
TTTATCTTAATTTAGACAAAAAAATATTT
Found at i:12634917 original size:58 final size:57
Alignment explanation
Indices: 12634832--12634953 Score: 140
Period size: 58 Copynumber: 2.1 Consensus size: 57
12634822 GCATGTTTGG
* * * * *
12634832 TCTTAATTTAGACAAAAAATATGTTTGTCTTAATTTA-ACACA-AAAAAATATTTTTTA
1 TCTTAATCTAGACAAAAAACATATTTGTCTCAATGTAGACA-AGAAAAAATA-TTTTTA
*
12634889 TCTTAATCTAGACAAGAAAACATATTTGTCTCAATGTAGACAAGATAAAATATTTTTA
1 TCTTAATCTAGACAA-AAAACATATTTGTCTCAATGTAGACAAGAAAAAATATTTTTA
*
12634947 TTTTAAT
1 TCTTAAT
12634954 TAAAGACAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
57 14 0.25
58 31 0.56
59 10 0.18
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (57 bp):
TCTTAATCTAGACAAAAAACATATTTGTCTCAATGTAGACAAGAAAAAATATTTTTA
Found at i:12636430 original size:2 final size:2
Alignment explanation
Indices: 12636423--12636447 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12636413 AAAATTAAAT
12636423 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12636448 GATTATGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12637040 original size:36 final size:36
Alignment explanation
Indices: 12636956--12637130 Score: 192
Period size: 36 Copynumber: 4.9 Consensus size: 36
12636946 TTAATTGTTT
* * * * * *
12636956 AATTTAATCAATTAGGTCGAATAACTGAATTAAA-T
1 AATTTAATTAATTAAGCCCAATAACTTAATTAAACA
* * *
12636991 AATTTAATTAATTAAGCCTAACAATTTAATTAAACA
1 AATTTAATTAATTAAGCCCAATAACTTAATTAAACA
* * *
12637027 ATTTTAATTAATTAGGCCCAATGACTTAATTAAACA
1 AATTTAATTAATTAAGCCCAATAACTTAATTAAACA
* *
12637063 AATTTAATTAATTAGGCCTAATAACTTAATTAAA-A
1 AATTTAATTAATTAAGCCCAATAACTTAATTAAACA
* *
12637098 AATTTAATTAATTAAGCCCAATGATTTAATTAA
1 AATTTAATTAATTAAGCCCAATAACTTAATTAA
12637131 TTAGGCACAA
Statistics
Matches: 118, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
35 57 0.48
36 61 0.52
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (36 bp):
AATTTAATTAATTAAGCCCAATAACTTAATTAAACA
Found at i:12637073 original size:18 final size:18
Alignment explanation
Indices: 12637016--12637112 Score: 58
Period size: 18 Copynumber: 5.4 Consensus size: 18
12637006 GCCTAACAAT
*
12637016 TTAATTAAACAATTTTAA
1 TTAATTAAACAAATTTAA
** * * *
12637034 TTAATTAGGCCCAA-TGAC
1 TTAATTA-AACAAATTTAA
12637052 TTAATTAAACAAATTTAA
1 TTAATTAAACAAATTTAA
** *
12637070 TTAATTAGGCCTAA--TAA
1 TTAATTA-AACAAATTTAA
12637087 CTTAATTAAA-AAATTTAA
1 -TTAATTAAACAAATTTAA
12637105 TTAATTAA
1 TTAATTAA
12637113 GCCCAATGAT
Statistics
Matches: 56, Mismatches: 17, Indels: 13
0.65 0.20 0.15
Matches are distributed among these distances:
16 2 0.04
17 14 0.25
18 35 0.62
19 5 0.09
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.38
Consensus pattern (18 bp):
TTAATTAAACAAATTTAA
Found at i:12637120 original size:71 final size:71
Alignment explanation
Indices: 12636956--12637130 Score: 226
Period size: 71 Copynumber: 2.5 Consensus size: 71
12636946 TTAATTGTTT
* * * * * * *
12636956 AATTTAATCAATTAGGTCGAATAACTGAATTAAATAATTTAATTAATTAAGCCTAACAATTTAAT
1 AATTTAATTAATTAGGCCCAATGACTTAATTAAAAAATTTAATTAATTAAGCCTAACAACTTAAT
12637021 TAAACA
66 TAAACA
* * *
12637027 ATTTTAATTAATTAGGCCCAATGACTTAATTAAACAAATTTAATTAATTAGGCCTAATAACTTAA
1 AATTTAATTAATTAGGCCCAATGACTTAATTAAA-AAATTTAATTAATTAAGCCTAACAACTTAA
12637092 TTAAA-A
65 TTAAACA
* *
12637098 AATTTAATTAATTAAGCCCAATGATTTAATTAA
1 AATTTAATTAATTAGGCCCAATGACTTAATTAA
12637131 TTAGGCACAA
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
71 59 0.66
72 31 0.34
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (71 bp):
AATTTAATTAATTAGGCCCAATGACTTAATTAAAAAATTTAATTAATTAAGCCTAACAACTTAAT
TAAACA
Found at i:12638077 original size:24 final size:24
Alignment explanation
Indices: 12638029--12638078 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
12638019 AAGAATATAG
*
12638029 AATATACCAGTCTCTAAGTATATT
1 AATATACCAGTCTCTAAGTACATT
12638053 AATAT-CCAGTCTC-AATGATACATT
1 AATATACCAGTCTCTAA-G-TACATT
12638077 AA
1 AA
12638079 CCAGGAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 2 0.09
23 9 0.39
24 12 0.52
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (24 bp):
AATATACCAGTCTCTAAGTACATT
Found at i:12639031 original size:2 final size:2
Alignment explanation
Indices: 12639024--12639063 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
12639014 TTCAACATTC
* * *
12639024 AT AT AT AT AT GT AC AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12639064 TTGGTTCATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:12640897 original size:17 final size:18
Alignment explanation
Indices: 12640875--12640908 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12640865 AAAAATTTTT
*
12640875 AAAATTTATTT-TTTTAG
1 AAAATTAATTTATTTTAG
12640892 AAAATTAATTTATTTTA
1 AAAATTAATTTATTTTA
12640909 ATCTTGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
AAAATTAATTTATTTTAG
Found at i:12647029 original size:29 final size:29
Alignment explanation
Indices: 12646988--12647143 Score: 120
Period size: 29 Copynumber: 5.3 Consensus size: 29
12646978 TGACAACTTT
* *
12646988 AATATATTT-ATCTTGATTTAGACAAAAA
1 AATATTTTTGATCTTAATTTAGACAAAAA
*
12647016 AATATTTTTGATCTTAATTTAGACAAGAA
1 AATATTTTTGATCTTAATTTAGACAAAAA
* * *
12647045 AATATGTTTG-TATTAATTTAAGATAAGAAA
1 AATATTTTTGATCTTAATTT-AGACAA-AAA
** * * *
12647075 AATATTTTTTTTCTTAATCTAGATAAGAA
1 AATATTTTTGATCTTAATTTAGACAAAAA
* * * *
12647104 AACATATTTG-TCTCAATTTATACAAGATAA
1 AATATTTTTGATCTTAATTTAGACAA-A-AA
12647134 AATATTTTTG
1 AATATTTTTG
12647144 CATTAATTAA
Statistics
Matches: 100, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
28 27 0.27
29 40 0.40
30 26 0.26
31 7 0.07
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (29 bp):
AATATTTTTGATCTTAATTTAGACAAAAA
Found at i:12647079 original size:30 final size:29
Alignment explanation
Indices: 12646988--12647161 Score: 142
Period size: 28 Copynumber: 5.9 Consensus size: 29
12646978 TGACAACTTT
* * *
12646988 AATATATTTATCTTGATTTAGACAA-AAA
1 AATATTTTTGTCTTAATTTAGACAAGAAA
12647016 AATATTTTTGATCTTAATTTAGACAAG-AA
1 AATATTTTTG-TCTTAATTTAGACAAGAAA
* * *
12647045 AATATGTTTGTATTAATTTAAGATAAGAAA
1 AATATTTTTGTCTTAATTT-AGACAAGAAA
* * *
12647075 AATATTTTTTTTCTTAATCTAGATAAGAAA
1 AATA-TTTTTGTCTTAATTTAGACAAGAAA
* *
12647105 ACATA--TTTGTCTCAATTTATACAAGATAA
1 A-ATATTTTTGTCTTAATTTAGACAAGA-AA
*
12647134 AATATTTTTG-CATTAATTAAAGACAAGA
1 AATATTTTTGTC-TTAATT-TAGACAAGA
12647162 GTTGTCTTAA
Statistics
Matches: 117, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
28 35 0.30
29 35 0.30
30 26 0.22
31 21 0.18
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (29 bp):
AATATTTTTGTCTTAATTTAGACAAGAAA
Found at i:12647081 original size:59 final size:58
Alignment explanation
Indices: 12647003--12647143 Score: 167
Period size: 59 Copynumber: 2.4 Consensus size: 58
12646993 ATTTATCTTG
* * * *
12647003 ATTTAGACAA-AAAAATATTTTTGATCTTAATTTAGACAAGAAAATATGTTTGTATTA
1 ATTTAGACAAGAAAAATATTTTTGATCTTAATCTAGACAAGAAAACATATTTGTATCA
* ** * *
12647060 ATTTAAGATAAGAAAAATATTTTTTTTCTTAATCTAGATAAGAAAACATATTTGTCTCA
1 ATTT-AGACAAGAAAAATATTTTTGATCTTAATCTAGACAAGAAAACATATTTGTATCA
*
12647119 ATTTATACAAGATAAAATATTTTTG
1 ATTTAGACAAGA-AAAATATTTTTG
12647144 CATTAATTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 4 0.06
58 11 0.16
59 54 0.78
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.41
Consensus pattern (58 bp):
ATTTAGACAAGAAAAATATTTTTGATCTTAATCTAGACAAGAAAACATATTTGTATCA
Found at i:12647323 original size:17 final size:17
Alignment explanation
Indices: 12647301--12647333 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12647291 ATAATAATAA
12647301 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
12647318 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
12647334 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:12666773 original size:2 final size:2
Alignment explanation
Indices: 12666766--12666791 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12666756 CAACACAAAT
12666766 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
12666792 ATGAATCCAT
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12668829 original size:2 final size:2
Alignment explanation
Indices: 12668822--12668851 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12668812 GAAAAACATT
12668822 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12668852 CAATGTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12672347 original size:6 final size:6
Alignment explanation
Indices: 12672331--12672373 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
12672321 TGGCGATGAA
* * * *
12672331 TGATGG CGATGG TGATGG TGATGG TGGTGG TAATGG TAATGG T
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG T
12672374 AGTATAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.19, C:0.02, G:0.47, T:0.33
Consensus pattern (6 bp):
TGATGG
Found at i:12676474 original size:21 final size:21
Alignment explanation
Indices: 12676448--12676487 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12676438 ATTTGATCTA
*
12676448 AATATCGTAGTTAGAATTTAG
1 AATATCATAGTTAGAATTTAG
*
12676469 AATATCATATTTAGAATTT
1 AATATCATAGTTAGAATTT
12676488 TCATAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.42
Consensus pattern (21 bp):
AATATCATAGTTAGAATTTAG
Found at i:12678607 original size:13 final size:13
Alignment explanation
Indices: 12678585--12678618 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12678575 AATTAGGCCC
*
12678585 AATAACTTAATTA
1 AATAATTTAATTA
12678598 AATAATTTAATTA
1 AATAATTTAATTA
*
12678611 AACAATTT
1 AATAATTT
12678619 TAATCAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (13 bp):
AATAATTTAATTA
Found at i:12678730 original size:35 final size:35
Alignment explanation
Indices: 12678604--12678754 Score: 167
Period size: 35 Copynumber: 4.3 Consensus size: 35
12678594 ATTAAATAAT
*
12678604 TTAATTAAACAATTTTAATCAATTAGGCCCAATGGC
1 TTAATTAAACAA-TTTAATCAATTAGGCCCAATGAC
* *
12678640 TTAATTAAACAAATTTAATCAATTAAGCCCAATAAC
1 TTAATTAAAC-AATTTAATCAATTAGGCCCAATGAC
**** *
12678676 TTAATTGTTTAATTTAATTAATTAGGCCCAATGAC
1 TTAATTAAACAATTTAATCAATTAGGCCCAATGAC
* * * * *
12678711 TTAATTAAACAATTCAATTAATTAGACCTAATGAT
1 TTAATTAAACAATTTAATCAATTAGGCCCAATGAC
12678746 TTAATTAAA
1 TTAATTAAA
12678755 TATGCACAAC
Statistics
Matches: 96, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
35 58 0.60
36 36 0.38
37 2 0.02
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (35 bp):
TTAATTAAACAATTTAATCAATTAGGCCCAATGAC
Found at i:12686531 original size:36 final size:36
Alignment explanation
Indices: 12686450--12686604 Score: 192
Period size: 36 Copynumber: 4.4 Consensus size: 36
12686440 TTAATTGTTT
* * *
12686450 AATTTAATCAATTAGGCCGAATAA-TTGAATTAAA-T
1 AATTTAATTAATTAGGCCTAATAACTT-AATTAAACA
* * *
12686485 AA-TTAATTAATTAAGCCTAACAATTTAATTAAACA
1 AATTTAATTAATTAGGCCTAATAACTTAATTAAACA
* * *
12686520 ATTTTAATTAATTAGGCCCAATGACTTAATTAAACA
1 AATTTAATTAATTAGGCCTAATAACTTAATTAAACA
12686556 AATTTAATTAATTAGGCCTAATAACTTAATTAAA-A
1 AATTTAATTAATTAGGCCTAATAACTTAATTAAACA
12686591 AATTTAATTAATTA
1 AATTTAATTAATTA
12686605 AGCCCAATGA
Statistics
Matches: 103, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
34 24 0.23
35 20 0.19
36 59 0.57
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (36 bp):
AATTTAATTAATTAGGCCTAATAACTTAATTAAACA
Found at i:12686566 original size:18 final size:18
Alignment explanation
Indices: 12686509--12686605 Score: 58
Period size: 18 Copynumber: 5.4 Consensus size: 18
12686499 GCCTAACAAT
*
12686509 TTAATTAAACAATTTTAA
1 TTAATTAAACAAATTTAA
** * * *
12686527 TTAATTAGGCCCAA-TGAC
1 TTAATTA-AACAAATTTAA
12686545 TTAATTAAACAAATTTAA
1 TTAATTAAACAAATTTAA
** *
12686563 TTAATTAGGCCTAA--TAA
1 TTAATTA-AACAAATTTAA
12686580 CTTAATTAAA-AAATTTAA
1 -TTAATTAAACAAATTTAA
12686598 TTAATTAA
1 TTAATTAA
12686606 GCCCAATGAT
Statistics
Matches: 56, Mismatches: 17, Indels: 13
0.65 0.20 0.15
Matches are distributed among these distances:
16 2 0.04
17 14 0.25
18 35 0.62
19 5 0.09
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.38
Consensus pattern (18 bp):
TTAATTAAACAAATTTAA
Found at i:12687258 original size:12 final size:13
Alignment explanation
Indices: 12687232--12687263 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
12687222 ATAACCAAAA
12687232 GCATCTTGTTTTG
1 GCATCTTGTTTTG
12687245 GCATCTTG-TTTG
1 GCATCTTGTTTTG
12687257 GCATCTT
1 GCATCTT
12687264 TGGTTAGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.09, C:0.19, G:0.22, T:0.50
Consensus pattern (13 bp):
GCATCTTGTTTTG
Found at i:12688519 original size:2 final size:2
Alignment explanation
Indices: 12688512--12688552 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
12688502 TTCAACATTC
* *
12688512 AT AT AT AT AT -T AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12688553 TTGGTTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:12690749 original size:4 final size:4
Alignment explanation
Indices: 12690740--12690773 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
12690730 ATTAATTCCG
*
12690740 CATA CATA CATA CATA CATA CATA CATA TATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CA
12690774 ATCGTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:12706546 original size:15 final size:14
Alignment explanation
Indices: 12706526--12706566 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
12706516 GAAAACATTC
12706526 CATTAATAGCAATTA
1 CATTAATA-CAATTA
12706541 CATTAA-ACAATTA
1 CATTAATACAATTA
12706554 -ATTAATACTAATT
1 CATTAATAC-AATT
12706567 GTCCATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.21
13 8 0.33
14 5 0.21
15 6 0.25
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (14 bp):
CATTAATACAATTA
Found at i:12707130 original size:2 final size:2
Alignment explanation
Indices: 12707123--12707148 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12707113 AATTTCGGTA
12707123 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
12707149 CAATTTCTTA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:12707476 original size:15 final size:16
Alignment explanation
Indices: 12707456--12707495 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
12707446 CAACACTTCG
12707456 TTCTTTTTCTCCTTT-
1 TTCTTTTTCTCCTTTC
12707471 TTC-TTTTC-CCTTTC
1 TTCTTTTTCTCCTTTC
*
12707485 TTTTTTTTCTC
1 TTCTTTTTCTC
12707496 AATTTTCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
13 5 0.24
14 7 0.33
15 8 0.38
16 1 0.05
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (16 bp):
TTCTTTTTCTCCTTTC
Found at i:12709972 original size:12 final size:13
Alignment explanation
Indices: 12709953--12710044 Score: 124
Period size: 12 Copynumber: 7.5 Consensus size: 13
12709943 CAGAATAGTT
12709953 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
12709966 T-TTGCTGCCT-C
1 TCTTGCTGCCTCC
12709977 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
12709990 T-TTGCTGCCT-C
1 TCTTGCTGCCTCC
*
12710001 TCTTGCTGCCT-T
1 TCTTGCTGCCTCC
12710013 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
*
12710026 TTTTGCTGCCT-C
1 TCTTGCTGCCTCC
12710038 TCTTGCT
1 TCTTGCT
12710045 CTGAAAAAGT
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
11 4 0.06
12 54 0.76
13 13 0.18
ACGTcount: A:0.00, C:0.39, G:0.16, T:0.45
Consensus pattern (13 bp):
TCTTGCTGCCTCC
Found at i:12709996 original size:36 final size:38
Alignment explanation
Indices: 12709955--12710044 Score: 143
Period size: 36 Copynumber: 2.5 Consensus size: 38
12709945 GAATAGTTTC
12709955 TTGCTGCCTCCT-TTGCTGCCTCTCTTGCTGCCTCC-T
1 TTGCTGCCTCCTCTTGCTGCCTCTCTTGCTGCCTCCTT
*
12709991 TTGCTGCCT-CTCTTGCTGCCTTTCTTGCTGCCTCCTT
1 TTGCTGCCTCCTCTTGCTGCCTCTCTTGCTGCCTCCTT
12710028 TTGCTGCCT-CTCTTGCT
1 TTGCTGCCTCCTCTTGCT
12710045 CTGAAAAAGT
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
35 2 0.04
36 31 0.61
37 18 0.35
ACGTcount: A:0.00, C:0.39, G:0.17, T:0.44
Consensus pattern (38 bp):
TTGCTGCCTCCTCTTGCTGCCTCTCTTGCTGCCTCCTT
Found at i:12710722 original size:21 final size:22
Alignment explanation
Indices: 12710687--12710730 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
12710677 CTCTTAAAGT
12710687 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
12710709 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
12710730 A
1 A
12710731 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:12712956 original size:9 final size:9
Alignment explanation
Indices: 12712942--12712968 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
12712932 CACATGCAAA
12712942 CGCACATGT
1 CGCACATGT
12712951 CGCACATGT
1 CGCACATGT
12712960 CGCACATGT
1 CGCACATGT
12712969 AATACAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (9 bp):
CGCACATGT
Found at i:12713297 original size:14 final size:14
Alignment explanation
Indices: 12713278--12713307 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12713268 TTACCTATCT
12713278 TAATTAATTTTTCA
1 TAATTAATTTTTCA
12713292 TAATTAATTTTTCA
1 TAATTAATTTTTCA
12713306 TA
1 TA
12713308 TGTCTATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATTAATTTTTCA
Found at i:12713976 original size:25 final size:23
Alignment explanation
Indices: 12713948--12713997 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 23
12713938 GCGTGTTTTA
*
12713948 GCAATAGCCAAAATCAATTCTTGCT
1 GCAA-AGCCAAAAT-AAATCTTGCT
*
12713973 GC-AAGCTAAAATAAATCTTGCT
1 GCAAAGCCAAAATAAATCTTGCT
12713995 GCA
1 GCA
12713998 GTCAAAATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
22 11 0.50
23 8 0.36
24 1 0.05
25 2 0.09
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (23 bp):
GCAAAGCCAAAATAAATCTTGCT
Found at i:12721576 original size:31 final size:31
Alignment explanation
Indices: 12721472--12721568 Score: 140
Period size: 31 Copynumber: 3.1 Consensus size: 31
12721462 CATGCCAACT
* * *
12721472 TGTCAATGCCATGTGACACTGCCATGTCATCA
1 TGTCAGTGCCATATGGCA-TGCCATGTCATCA
*
12721504 TGTTAGTGCCATATGGCATGCCATGTCATCA
1 TGTCAGTGCCATATGGCATGCCATGTCATCA
*
12721535 TGTCAGTGCCATATGGCATGCTATGTCATCA
1 TGTCAGTGCCATATGGCATGCCATGTCATCA
12721566 TGT
1 TGT
12721569 GGGTGCCACA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 45 0.76
32 14 0.24
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.32
Consensus pattern (31 bp):
TGTCAGTGCCATATGGCATGCCATGTCATCA
Found at i:12734412 original size:12 final size:12
Alignment explanation
Indices: 12734391--12734427 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12734381 TATCTTAAAA
*
12734391 ATATAGTATTAT
1 ATATAATATTAT
12734403 ATATAATATTAT
1 ATATAATATTAT
12734415 ATAT-ATATT-T
1 ATATAATATTAT
12734425 ATA
1 ATA
12734428 CTTCAAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 4 0.17
11 5 0.21
12 15 0.62
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (12 bp):
ATATAATATTAT
Found at i:12741836 original size:3 final size:3
Alignment explanation
Indices: 12741828--12741852 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12741818 CGTTTAAAAG
12741828 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
12741853 ATGAGGACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12753051 original size:26 final size:26
Alignment explanation
Indices: 12752996--12753051 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
12752986 AATTTCAAAT
* * *
12752996 AAATTTTTATTTTTTTATATTTAATA
1 AAATCTTTATATTTTTATATTGAATA
* *
12753022 AAATCTTTATATTTTTATTTTGAATC
1 AAATCTTTATATTTTTATATTGAATA
12753048 AAAT
1 AAAT
12753052 AAACTCTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (26 bp):
AAATCTTTATATTTTTATATTGAATA
Found at i:12756924 original size:16 final size:17
Alignment explanation
Indices: 12756900--12756940 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
12756890 TATGTATATC
12756900 TAGATTTGAA-TATAGAT
1 TAGATTTGAATTA-AGAT
12756917 TAGA-TTGAATTAAGAT
1 TAGATTTGAATTAAGAT
12756933 TAGGATTT
1 TA-GATTT
12756941 AATCTATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 11 0.52
17 8 0.38
18 2 0.10
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (17 bp):
TAGATTTGAATTAAGAT
Found at i:12762979 original size:17 final size:19
Alignment explanation
Indices: 12762946--12762981 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
12762936 AACAGTCTCA
12762946 CCATTCGCTGAATAATCCT
1 CCATTCGCTGAATAATCCT
12762965 CCATT-GCTG-ATAATCCT
1 CCATTCGCTGAATAATCCT
12762982 TTTTACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 4 0.24
19 5 0.29
ACGTcount: A:0.25, C:0.31, G:0.11, T:0.33
Consensus pattern (19 bp):
CCATTCGCTGAATAATCCT
Found at i:12764550 original size:31 final size:31
Alignment explanation
Indices: 12764515--12764586 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
12764505 ATAGTTATAT
* *
12764515 AAATATAAATATTTTTAAAATTTATAAT-TTA
1 AAATATAAATA-ATTGAAAATTTATAATATTA
* *
12764546 AAATACAAATAATTGAAATTTTATAATATTA
1 AAATATAAATAATTGAAAATTTATAATATTA
*
12764577 ATATATAAAT
1 AAATATAAAT
12764587 TATTCAACCC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 13 0.38
31 21 0.62
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (31 bp):
AAATATAAATAATTGAAAATTTATAATATTA
Found at i:12768225 original size:29 final size:29
Alignment explanation
Indices: 12768183--12768242 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
12768173 AGCCATTGTG
12768183 TTTAGTTTTACCATTTGTAATACTTTATA
1 TTTAGTTTTACCATTTGTAATACTTTATA
12768212 TTTAGTTTTACCATTTGTAATACTTTATA
1 TTTAGTTTTACCATTTGTAATACTTTATA
12768241 TT
1 TT
12768243 CTTTTTATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.57
Consensus pattern (29 bp):
TTTAGTTTTACCATTTGTAATACTTTATA
Found at i:12781772 original size:25 final size:25
Alignment explanation
Indices: 12781705--12781846 Score: 133
Period size: 25 Copynumber: 5.6 Consensus size: 25
12781695 CTATTTTAAT
*
12781705 TCTAAGAATAATTTTACCACCAGAA
1 TCTAAGAATAATTTTACCATCAGAA
* * *
12781730 GT-AAATGAATAATATTACCATTAGAA
1 -TCTAA-GAATAATTTTACCATCAGAA
*
12781756 TCTAAGAATAATTTTACTATCAGAA
1 TCTAAGAATAATTTTACCATCAGAA
** * * *
12781781 GTGGATGGATAATTTTACCATTAGAA
1 -TCTAAGAATAATTTTACCATCAGAA
* *
12781807 TCTAAGGATAATTTTACTATCAGAA
1 TCTAAGAATAATTTTACCATCAGAA
*
12781832 TCTAAGGATAATTTT
1 TCTAAGAATAATTTT
12781847 TCTACCAAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
25 55 0.59
26 39 0.41
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (25 bp):
TCTAAGAATAATTTTACCATCAGAA
Found at i:12781781 original size:51 final size:51
Alignment explanation
Indices: 12781705--12781831 Score: 191
Period size: 51 Copynumber: 2.5 Consensus size: 51
12781695 CTATTTTAAT
* *
12781705 TCTAAGAATAATTTTACCACCAGAAGTAAATGAATAATATTACCATTAGAA
1 TCTAAGAATAATTTTACTATCAGAAGTAAATGAATAATATTACCATTAGAA
** * *
12781756 TCTAAGAATAATTTTACTATCAGAAGTGGATGGATAATTTTACCATTAGAA
1 TCTAAGAATAATTTTACTATCAGAAGTAAATGAATAATATTACCATTAGAA
*
12781807 TCTAAGGATAATTTTACTATCAGAA
1 TCTAAGAATAATTTTACTATCAGAA
12781832 TCTAAGGATA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.33
Consensus pattern (51 bp):
TCTAAGAATAATTTTACTATCAGAAGTAAATGAATAATATTACCATTAGAA
Found at i:12781967 original size:18 final size:18
Alignment explanation
Indices: 12781926--12781969 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12781916 AATCCATTAG
*
12781926 AAGTGGATAACTAATCAT
1 AAGTGGATAACTAATCAA
* *
12781944 ATGTGGATCACTAATCAA
1 AAGTGGATAACTAATCAA
12781962 AAGTGGAT
1 AAGTGGAT
12781970 GTATACTTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (18 bp):
AAGTGGATAACTAATCAA
Found at i:12795369 original size:27 final size:26
Alignment explanation
Indices: 12795338--12795394 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 26
12795328 TATCTAATTT
*
12795338 TAAATTTTAAATTATTAATATTTAAAA
1 TAAATTATAAATTATTAATA-TTAAAA
12795365 TAAATTATAAATTATTAATATTAAAA
1 TAAATTATAAATTATTAATATTAAAA
12795391 -AAAT
1 TAAAT
12795395 AAAATAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 6 0.21
27 19 0.66
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAATTATAAATTATTAATATTAAAA
Found at i:12795443 original size:118 final size:122
Alignment explanation
Indices: 12795314--12795575 Score: 306
Period size: 118 Copynumber: 2.2 Consensus size: 122
12795304 ATTAATAATT
* * * *
12795314 AATTATAAATAAAATATCTAAT-TTTAAATTTTAAATTATTAATAT-TTAAAATAAATTATAAAT
1 AATTATAAATAAAATA-ATAATAATTAAATTATAAATTACTAATATATT-AAATAAATTATAAAT
*
12795377 TATTAATA-TT-AAAA-AAA-TAAAATAACTTAAAAATAAATAAGCATAATAAAATTTC
64 TATTAATATTTAAAAATAAATTAAAATAAATTAAAAATAAATAAGCATAATAAAATTTC
* * *
12795432 AATTATCAATAAAATAATAATAATTAAATTATCAATTACTAATATATTAAATAAATTATTAATTA
1 AATTATAAATAAAATAATAATAATTAAATTATAAATTACTAATATATTAAATAAATTATAAATTA
* * * *
12795497 TTAATATTTAAAAATAAATTAAATTAAATTAAAAAT-AATTAGACATAATGATATTTC
66 TTAATATTTAAAAATAAATTAAAATAAATTAAAAATAAATAAG-CATAATAAAATTTC
* *
12795554 AACTATAAACT-AAATATTAATA
1 AATTATAAA-TAAAATAATAATA
12795576 TTTTAAAATG
Statistics
Matches: 121, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
117 4 0.03
118 56 0.46
119 4 0.03
120 4 0.03
121 8 0.07
122 44 0.36
123 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (122 bp):
AATTATAAATAAAATAATAATAATTAAATTATAAATTACTAATATATTAAATAAATTATAAATTA
TTAATATTTAAAAATAAATTAAAATAAATTAAAAATAAATAAGCATAATAAAATTTC
Found at i:12795495 original size:27 final size:27
Alignment explanation
Indices: 12795456--12795517 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
12795446 TAATAATAAT
12795456 TAAATTATCAATTACTAATATATT-AAA
1 TAAATTATCAATTACTAATAT-TTAAAA
* *
12795483 TAAATTATTAATTATTAATATTTAAAAA
1 TAAATTATCAATTACTAATATTT-AAAA
12795511 TAAATTA
1 TAAATTA
12795518 AATTAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 2 0.06
27 19 0.61
28 10 0.32
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAATTATCAATTACTAATATTTAAAA
Found at i:12795608 original size:122 final size:118
Alignment explanation
Indices: 12795353--12795584 Score: 263
Period size: 122 Copynumber: 1.9 Consensus size: 118
12795343 TTTAAATTAT
*
12795353 TAATAT-TTAAAATAAATTATAAATTATTAATATTAAAAAAATAAAATAACTTAAAAATAAATAA
1 TAATATATT-AAATAAATTATAAATTATTAATATTAAAAAAATAAAATAAATTAAAAATAAATAA
* * * *
12795417 GCATAATAAAATTTCAATTATCAATAAAATAATAATAATTAAATTATCAATTAC
65 GCATAATAAAATTTCAACTATAAATAAAATAATAATAATTAAAATATCAATGAC
* *
12795471 TAATATATTAAATAAATTATTAATTATTAATATTTAAAAATAAATTAAATTAAATTAAAAAT-AA
1 TAATATATTAAATAAATTATAAATTATTAATA-TT-AAAA-AAA-TAAAATAAATTAAAAATAAA
* * * * *
12795535 TTAGACATAATGATATTTCAACTATAAACT-AAATATTAATATTTTAAAAT
62 TAAG-CATAATAAAATTTCAACTATAAA-TAAAATAATAATA-ATTAAAAT
12795585 GTTAATGATT
Statistics
Matches: 95, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
118 28 0.29
119 4 0.04
120 4 0.04
121 8 0.08
122 44 0.46
123 7 0.07
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (118 bp):
TAATATATTAAATAAATTATAAATTATTAATATTAAAAAAATAAAATAAATTAAAAATAAATAAG
CATAATAAAATTTCAACTATAAATAAAATAATAATAATTAAAATATCAATGAC
Found at i:12795894 original size:27 final size:28
Alignment explanation
Indices: 12795862--12795920 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
12795852 TATTAATATT
* *
12795862 TAAATTATCACCTATTAATATTT-TAAA
1 TAAATTATCAACTATTAATATTTAAAAA
*
12795889 TAAATTATCAATTATTAATATTTAAAAA
1 TAAATTATCAACTATTAATATTTAAAAA
12795917 TAAA
1 TAAA
12795921 ATAAAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAATTATCAACTATTAATATTTAAAAA
Found at i:12795914 original size:22 final size:22
Alignment explanation
Indices: 12795852--12795914 Score: 63
Period size: 27 Copynumber: 2.6 Consensus size: 22
12795842 TTAAATTAAA
*
12795852 TATTAATATTTAAATTATCACC
1 TATTAATATTTAAATTATCAAC
*
12795874 TATTAATATTTTAAATAAATTATCAAT
1 TATTAATA--TT---TAAATTATCAAC
12795901 TATTAATATTTAAA
1 TATTAATATTTAAA
12795915 AATAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
22 12 0.35
24 2 0.06
25 2 0.06
27 18 0.53
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTAATATTTAAATTATCAAC
Found at i:12795932 original size:27 final size:27
Alignment explanation
Indices: 12795875--12795932 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
12795865 ATTATCACCT
* * * *
12795875 ATTAATATTTTAAATAAATTATCAATT
1 ATTAATATTTAAAATAAAATATAAATA
12795902 ATTAATATTTAAAAATAAAATA-AAATA
1 ATTAATATTT-AAAATAAAATATAAATA
12795929 ATTA
1 ATTA
12795933 CTCATAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTAATATTTAAAATAAAATATAAATA
Found at i:12795991 original size:15 final size:15
Alignment explanation
Indices: 12795971--12796006 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
12795961 TATTAGTTTT
12795971 TTTAAAATATTAATA
1 TTTAAAATATTAATA
12795986 TTTAAAATATTAATA
1 TTTAAAATATTAATA
12796001 TTTAAA
1 TTTAAA
12796007 TGATCAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAAATATTAATA
Done.