Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 163 of 186
Found at i:54207552 original size:21 final size:21
Alignment explanation
Indices: 54207527--54207574 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
54207517 TATCGAGAAG
*
54207527 TTTTTCAAATTAA-GAATTAT
1 TTTTTTAAATTAATGAATTAT
* *
54207547 TTTTTTAATTTAATGTATTAT
1 TTTTTTAAATTAATGAATTAT
*
54207568 TTATTTA
1 TTTTTTA
54207575 TTTTATTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTTTTAAATTAATGAATTAT
Found at i:54209903 original size:20 final size:20
Alignment explanation
Indices: 54209878--54209927 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
54209868 TGGCTTAAAA
54209878 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
54209898 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
54209915 GTGGTAGTGGATT
1 TTGGTAGTGGATT
54209928 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:54214999 original size:48 final size:48
Alignment explanation
Indices: 54214917--54215059 Score: 171
Period size: 48 Copynumber: 3.0 Consensus size: 48
54214907 ATTCGAGAGT
* * *
54214917 CTCGCACCCT-AAGTGCCTATCTCATGGCCCGAAGCCAAATCTATGTAA
1 CTCGCA-CCTGAAGTGCCGATATCATGGCCCGAAGCCAAATCAATGTAA
* * *
54214965 CTCGCACCTGAAGTGCCGATATCATTGCCTGAAGCGAAATCAATGTAA
1 CTCGCACCTGAAGTGCCGATATCATGGCCCGAAGCCAAATCAATGTAA
* * * * *
54215013 CTTGCACCCGAAGTGTCGGTATCATGGCCCGAAGCTAAATCAATGTA
1 CTCGCACCTGAAGTGCCGATATCATGGCCCGAAGCCAAATCAATGTA
54215060 TTCCCTAATG
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
47 3 0.04
48 78 0.96
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (48 bp):
CTCGCACCTGAAGTGCCGATATCATGGCCCGAAGCCAAATCAATGTAA
Found at i:54218201 original size:155 final size:154
Alignment explanation
Indices: 54217914--54218528 Score: 739
Period size: 155 Copynumber: 4.0 Consensus size: 154
54217904 GATTGAGTAT
* * *
54217914 TAGCGGCGCTTTATCAAAAACGCCGCTATAGG-TTGAGTATT-GGAGGTGTTTTTAAGAAAGGGC
1 TAGCGGCACTTTATCAAAAACGCCGCTATAGGTTTGAGTATTAGCA-GTGTTTTTAAGAAAGCGC
* * * *
54217977 CGCTATAGGTCGACCTATAGCGGCGTTTTTATAAAAATGCCACTAAAAGATTAAGTCGAACGACG
65 CGCTATAGGTCGACCTATAGCGGCG-TTTTATAAAAACGCCACTAAAAGATTAAGCCGAACGGCA
54218042 TCGTTTATTGTGAGCTTCAGTGTCAA
129 TCGTTTATTGTGAGCTTCAGTGTCAA
* * * * *** * * * *
54218068 TAGTGGCGCTTTATTAAAAACGCCGCTA-ATGCTCAAACCTA-TAGCGGTGTTTTTGATAAAGCG
1 TAGCGGCACTTTATCAAAAACGCCGCTATA-GGTTTGA-GTATTAGCAGTGTTTTTAAGAAAGCG
* * * * * *
54218131 CCACTATAGGTCGACCTATAGTGGCGTTTTCATAAAAACACCATTAAAAAATTAAGCCAAACGGC
64 CCGCTATAGGTCGACCTATAGCGGCGTTTT-ATAAAAACGCCACTAAAAGATTAAGCCGAACGGC
54218196 ATCGTTTATTGTGAGCTTCAGTGTCAA
128 ATCGTTTATTGTGAGCTTCAGTGTCAA
* * * *
54218223 TAGCGGCACTTTATCAAAAACACCACTATAGGTTTGAGTATTAGCAATATTTTTAAGAAAGCGCC
1 TAGCGGCACTTTATCAAAAACGCCGCTATAGGTTTGAGTATTAGCAGTGTTTTTAAGAAAGCGCC
* * * *
54218288 GTTATAGGTCTACCTCAT-------TTTTGTAAAAACGCCACTAATAGATTAAGCCGAACGGCAT
66 GCTATAGGTCGACCT-ATAGCGGCGTTTTATAAAAACGCCACTAAAAGATTAAGCCGAACGGCAT
54218346 CGTTTATTGTGAGCTTCAGTGTCAA
130 CGTTTATTGTGAGCTTCAGTGTCAA
*
54218371 TAGCGGCACTTTATCAAAAACGCCGCTATAGGTTTGAGTATTAGCAGCGTTTTTAAGAAAGCGCC
1 TAGCGGCACTTTATCAAAAACGCCGCTATAGGTTTGAGTATTAGCAGTGTTTTTAAGAAAGCGCC
* * **
54218436 GCTATAGGTCGACCTATTGCGGCGTTTGTATAAAAACGCCGCTAAAAGATTAAGCCGAACGGTGT
66 GCTATAGGTCGACCTATAGCGGCGTTT-TATAAAAACGCCACTAAAAGATTAAGCCGAACGGCAT
* *
54218501 CGTTTATTTTGAGCTTCAGTGGCAA
130 CGTTTATTGTGAGCTTCAGTGTCAA
54218526 TAG
1 TAG
54218529 ATCTAAACTA
Statistics
Matches: 385, Mismatches: 60, Indels: 31
0.81 0.13 0.07
Matches are distributed among these distances:
147 2 0.01
148 128 0.33
149 4 0.01
153 1 0.00
154 36 0.09
155 208 0.54
156 6 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (154 bp):
TAGCGGCACTTTATCAAAAACGCCGCTATAGGTTTGAGTATTAGCAGTGTTTTTAAGAAAGCGCC
GCTATAGGTCGACCTATAGCGGCGTTTTATAAAAACGCCACTAAAAGATTAAGCCGAACGGCATC
GTTTATTGTGAGCTTCAGTGTCAA
Found at i:54218476 original size:40 final size:39
Alignment explanation
Indices: 54218386--54218479 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 39
54218376 GCACTTTATC
* *
54218386 AAAAACGCCGCTATAGGTTTGAGTATTAGCAGCGTTTTT
1 AAAAACGCCGCTATAGGTTCGACTATTAGCAGCGTTTTT
*
54218425 AAGAAAGCGCCGCTATAGG-TCGACCTATT-GCGGCGTTTGTAT
1 AA-AAA-CGCCGCTATAGGTTCGA-CTATTAGCAGCGTTT-T-T
54218467 AAAAACGCCGCTA
1 AAAAACGCCGCTA
54218480 AAAGATTAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
39 2 0.04
40 22 0.47
41 20 0.43
42 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (39 bp):
AAAAACGCCGCTATAGGTTCGACTATTAGCAGCGTTTTT
Found at i:54218982 original size:21 final size:21
Alignment explanation
Indices: 54218956--54219008 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
54218946 ACCAAAATTT
54218956 TAAACCTTAAGTCTCAAACCA
1 TAAACCTTAAGTCTCAAACCA
*
54218977 TAAACCCTAAGTCTCAAACCA
1 TAAACCTTAAGTCTCAAACCA
54218998 TAAACCCTTAA
1 TAAA-CCTTAA
54219009 AACTCTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.43, C:0.30, G:0.04, T:0.23
Consensus pattern (21 bp):
TAAACCTTAAGTCTCAAACCA
Found at i:54219402 original size:8 final size:7
Alignment explanation
Indices: 54219355--54219402 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
54219345 AGGTTTATGC
54219355 ATGGTTT
1 ATGGTTT
*
54219362 AGGGTATAT
1 ATGGT-T-T
54219371 ATGGTTT
1 ATGGTTT
*
54219378 AAGGTTT
1 ATGGTTT
54219385 ATGGTTT
1 ATGGTTT
54219392 ATGGATTT
1 ATGG-TTT
54219400 ATG
1 ATG
54219403 ACGAGTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
7 21 0.62
8 8 0.24
9 5 0.15
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (7 bp):
ATGGTTT
Found at i:54219480 original size:15 final size:14
Alignment explanation
Indices: 54219454--54219488 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
54219444 ATGGATTATG
54219454 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
*
54219468 GGTTTAGGGGTTTAT
1 GGTTTA-GGGTTTAA
54219483 GGTTTA
1 GGTTTA
54219489 TGAGTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:54219620 original size:7 final size:7
Alignment explanation
Indices: 54219610--54219715 Score: 50
Period size: 7 Copynumber: 14.9 Consensus size: 7
54219600 AAGGGGACAT
54219610 GGTTTAG
1 GGTTTAG
54219617 GGTTTAG
1 GGTTTAG
* *
54219624 TGTTTAA
1 GGTTTAG
*
54219631 AGTTTAG
1 GGTTTAG
* *
54219638 GGATTAAT
1 GG-TTTAG
*
54219646 GGTTTAT
1 GGTTTAG
*
54219653 GGTTTAA
1 GGTTTAG
*
54219660 GGTTGAG
1 GGTTTAG
*
54219667 GGGTTAGG
1 GGTTTA-G
*
54219675 GGTTAAG
1 GGTTTAG
*** *
54219682 GGGACAT
1 GGTTTAG
54219689 GGTTTAG
1 GGTTTAG
54219696 GGTTTAG
1 GGTTTAG
*
54219703 TGTTTAG
1 GGTTTAG
*
54219710 TGTTTA
1 GGTTTA
54219716 AATTTTAAGG
Statistics
Matches: 73, Mismatches: 24, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
7 63 0.86
8 10 0.14
ACGTcount: A:0.21, C:0.01, G:0.37, T:0.42
Consensus pattern (7 bp):
GGTTTAG
Found at i:54219829 original size:14 final size:14
Alignment explanation
Indices: 54219777--54219829 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
54219767 AGAGAATATG
*
54219777 GTTTAGGGTTTAGT
1 GTTTAAGGTTTAGT
* *
54219791 GTTTAAAGTTTAGG
1 GTTTAAGGTTTAGT
* *
54219805 GATTAATGGTTTATT
1 GTTTAA-GGTTTAGT
54219820 GTTTAAGGTT
1 GTTTAAGGTT
54219830 GATAGGTTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
14 20 0.67
15 10 0.33
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
GTTTAAGGTTTAGT
Found at i:54219873 original size:29 final size:30
Alignment explanation
Indices: 54219834--54219896 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
54219824 AAGGTTGATA
* *
54219834 GGTTTAGGGGTT-AAGGGGACAT-GGTTTAG
1 GGTTGAGGGGTTGAA-GGGACATGGGTTAAG
54219863 GGTTGAGGGGTTGAAGGGACATGGGTTAAG
1 GGTTGAGGGGTTGAAGGGACATGGGTTAAG
54219893 GGTT
1 GGTT
54219897 TAGGATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.21, C:0.03, G:0.48, T:0.29
Consensus pattern (30 bp):
GGTTGAGGGGTTGAAGGGACATGGGTTAAG
Found at i:54220049 original size:26 final size:24
Alignment explanation
Indices: 54220013--54220063 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 24
54220003 TATATTAAAT
54220013 AATTTCAAATTTT-AATGATTTCAA
1 AATTTCAAATTTTCAA-GATTTCAA
54220037 AATTTCAATAATTTTCAAGATTTCAA
1 AATTTC-A-AATTTTCAAGATTTCAA
54220063 A
1 A
54220064 TTTTATGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 6 0.25
25 1 0.04
26 15 0.62
27 2 0.08
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (24 bp):
AATTTCAAATTTTCAAGATTTCAA
Found at i:54220054 original size:18 final size:17
Alignment explanation
Indices: 54220010--54220062 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
54220000 ATATATATTA
*
54220010 AATAATTTC-AAATTTT
1 AATAATTTCAAAATTTC
*
54220026 AATGATTTCAAAATTTC
1 AATAATTTCAAAATTTC
*
54220043 AATAATTTTCAAGATTTC
1 AATAA-TTTCAAAATTTC
54220061 AA
1 AA
54220063 ATTTTATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 8 0.26
17 10 0.32
18 13 0.42
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (17 bp):
AATAATTTCAAAATTTC
Found at i:54220215 original size:18 final size:17
Alignment explanation
Indices: 54220177--54220212 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
54220167 CTATATAACG
54220177 TATTGTTTTTTAATTTA
1 TATTGTTTTTTAATTTA
54220194 TATTGTTTTTT-ATTTA
1 TATTGTTTTTTAATTTA
54220210 TAT
1 TAT
54220213 ATTAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (17 bp):
TATTGTTTTTTAATTTA
Found at i:54221227 original size:10 final size:10
Alignment explanation
Indices: 54221195--54221233 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
54221185 GCTGCACTTT
*
54221195 TTTTTTTCCA
1 TTTTTTTCAA
54221205 TTTTTGTTCCAA
1 TTTTT-TT-CAA
54221217 TTTTTTTCAA
1 TTTTTTTCAA
54221227 TTTTTTT
1 TTTTTTT
54221234 GAAGTTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 15 0.58
11 4 0.15
12 7 0.27
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.72
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:54221330 original size:13 final size:14
Alignment explanation
Indices: 54221308--54221337 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
54221298 GGAAATATTC
54221308 AAAAACAAAAACTT
1 AAAAACAAAAACTT
54221322 AAAAA-AAAAACTT
1 AAAAACAAAAACTT
54221335 AAA
1 AAA
54221338 TTTCCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAACAAAAACTT
Found at i:54221606 original size:84 final size:85
Alignment explanation
Indices: 54221509--54221666 Score: 255
Period size: 85 Copynumber: 1.9 Consensus size: 85
54221499 TGTAGTATTT
* * *
54221509 TAGTATTTCAGTATTTCAATTCATT-AACTCTTTCTGATTAACATGCCGTATGAACTCATACTTC
1 TAGTATTTCAGTATTTCAATTCATTAAACTCTCTCTGATGAACATGCCGTATGAACTAATACTTC
54221573 TCCATTTGCTTTTTTTTTGG
66 TCCATTTGCTTTTTTTTTGG
* *
54221593 TAGTATTTTAGTATTTCAATTCATTAAACTCTCTCTGATGAACATGCTGTATGAACTAATACTTC
1 TAGTATTTCAGTATTTCAATTCATTAAACTCTCTCTGATGAACATGCCGTATGAACTAATACTTC
*
54221658 TCGATTTGC
66 TCCATTTGC
54221667 ATTTGAAGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
84 24 0.36
85 43 0.64
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.45
Consensus pattern (85 bp):
TAGTATTTCAGTATTTCAATTCATTAAACTCTCTCTGATGAACATGCCGTATGAACTAATACTTC
TCCATTTGCTTTTTTTTTGG
Found at i:54224557 original size:64 final size:64
Alignment explanation
Indices: 54223643--54224543 Score: 1793
Period size: 64 Copynumber: 14.1 Consensus size: 64
54223633 TAATATTTCT
54223643 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
54223707 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
54223771 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
54223835 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
54223899 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
54223963 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
54224027 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
54224091 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
54224155 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
54224219 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
54224283 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
54224347 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
54224411 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
*
54224475 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
54224539 ATATT
1 ATATT
54224544 AAATAAAATA
Statistics
Matches: 836, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 836 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (64 bp):
ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
Found at i:54224619 original size:24 final size:24
Alignment explanation
Indices: 54224592--54224662 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
54224582 ATTATTATTG
*
54224592 AAATATTCTCGTCCGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
*
54224616 AAATATTATTGTCCGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
*
54224640 AAATATTATCATCCGTTTTATCA
1 AAATATTATCGTCCGTTTTATCA
54224663 TTTAAGTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.44
Consensus pattern (24 bp):
AAATATTATCGTCCGTTTTATCAC
Found at i:54224868 original size:29 final size:29
Alignment explanation
Indices: 54224836--54224909 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
54224826 AACGACATGT
*
54224836 ATATTATTTAATTAAAATAAATTTTT-TCA
1 ATATTATTTAATTAAAAT-AATTTTTATAA
54224865 ATATTATTTAATTAAAATAATTTTTATAA
1 ATATTATTTAATTAAAATAATTTTTATAA
54224894 ATATTATTTAATTAAA
1 ATATTATTTAATTAAA
54224910 TATTATTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
28 7 0.16
29 36 0.84
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
ATATTATTTAATTAAAATAATTTTTATAA
Found at i:54224909 original size:15 final size:15
Alignment explanation
Indices: 54224836--54224920 Score: 81
Period size: 15 Copynumber: 5.8 Consensus size: 15
54224826 AACGACATGT
54224836 ATATTATTTAATTAA
1 ATATTATTTAATTAA
* * *
54224851 A-ATAAATTT-TTTCA
1 ATAT-TATTTAATTAA
54224865 ATATTATTTAATTAAA
1 ATATTATTTAATT-AA
54224881 ATAATT-TTT-A-TAA
1 AT-ATTATTTAATTAA
54224894 ATATTATTTAATTAA
1 ATATTATTTAATTAA
54224909 ATATTATTTAAT
1 ATATTATTTAAT
54224921 CCCGAAACTT
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
12 3 0.05
13 7 0.12
14 12 0.21
15 25 0.45
16 6 0.11
17 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:54225037 original size:9 final size:9
Alignment explanation
Indices: 54225025--54225452 Score: 149
Period size: 9 Copynumber: 47.6 Consensus size: 9
54225015 TATTTGATAT
*
54225025 CATAATTTA
1 CATAACTTA
54225034 CATAACTTA
1 CATAACTTA
* *
54225043 CAAAACGTA
1 CATAACTTA
54225052 CATAACTTA
1 CATAACTTA
*
54225061 TATAACTTA
1 CATAACTTA
* *
54225070 GATAA-ATA
1 CATAACTTA
**
54225078 TTTAACTTA
1 CATAACTTA
*
54225087 TATAACTTA
1 CATAACTTA
54225096 CATAACTTA
1 CATAACTTA
54225105 CATAACTTA
1 CATAACTTA
*
54225114 TATAACTTA
1 CATAACTTA
*
54225123 CAT-A-TAAA
1 CATAACT-TA
*
54225131 TATAACTTA
1 CATAACTTA
*
54225140 CATAA-ATA
1 CATAACTTA
* * *
54225148 TATATCATA
1 CATAACTTA
54225157 TCATAACTTA
1 -CATAACTTA
54225167 CATAACTTA
1 CATAACTTA
54225176 CATAA--TA
1 CATAACTTA
*
54225183 CTTAGA-TATA
1 CATA-ACT-TA
54225193 CATAACTTA
1 CATAACTTA
54225202 CATAATACTTAGA
1 CAT-A-ACTT--A
* *
54225215 TATATATCATA
1 CATA-A-CTTA
*
54225226 TCATATCTTA
1 -CATAACTTA
54225236 CATAACTAGCTTA
1 CAT-A--A-CTTA
54225249 CGA-AACTTA
1 C-ATAACTTA
*
54225258 CTTAACTTA
1 CATAACTTA
54225267 CAT-ACTTA
1 CATAACTTA
* *
54225275 AATATA-TTT
1 CATA-ACTTA
*
54225284 TAT-A--TA
1 CATAACTTA
*
54225290 -ATAATTTA
1 CATAACTTA
54225298 CATAACTTA
1 CATAACTTA
*
54225307 CAAAACTTA
1 CATAACTTA
*
54225316 CATGACTTA
1 CATAACTTA
*
54225325 TATAACTTA
1 CATAACTTA
* *
54225334 GATAA-ATA
1 CATAACTTA
*
54225342 TATAACTTA
1 CATAACTTA
* *
54225351 TATAACTCA
1 CATAACTTA
*
54225360 TATAACTTA
1 CATAACTTA
* *
54225369 GATAA-ATA
1 CATAACTTA
* *
54225377 TATAATTTA
1 CATAACTTA
*
54225386 CATAA-ATA
1 CATAACTTA
* * *
54225394 TATATCATA
1 CATAACTTA
54225403 TCATAACTTA
1 -CATAACTTA
54225413 CATAACTTA
1 CATAACTTA
54225422 CATAA--TA
1 CATAACTTA
*
54225429 CTTAGA-TATA
1 CATA-ACT-TA
54225439 CATAACTTA
1 CATAACTTA
54225448 CATAA
1 CATAA
54225453 TACTTAGATA
Statistics
Matches: 319, Mismatches: 64, Indels: 72
0.70 0.14 0.16
Matches are distributed among these distances:
5 2 0.01
6 2 0.01
7 12 0.04
8 42 0.13
9 206 0.65
10 32 0.10
11 5 0.02
12 7 0.02
13 10 0.03
14 1 0.00
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (9 bp):
CATAACTTA
Found at i:54225074 original size:18 final size:18
Alignment explanation
Indices: 54225026--54225426 Score: 171
Period size: 18 Copynumber: 21.7 Consensus size: 18
54225016 ATTTGATATC
* *
54225026 ATAATTTACATAACTTAC
1 ATAACTTACATAACTTAT
* *
54225044 AAAACGTACATAACTTAT
1 ATAACTTACATAACTTAT
* *
54225062 ATAACTTAGATAA-ATAT
1 ATAACTTACATAACTTAT
* * *
54225079 TTAACTTATATAACTTAC
1 ATAACTTACATAACTTAT
54225097 ATAACTTACATAACTTAT
1 ATAACTTACATAACTTAT
*
54225115 ATAACTTACAT-A-TAAAT
1 ATAACTTACATAACT-TAT
*
54225132 ATAACTTACATAA-ATAT
1 ATAACTTACATAACTTAT
* * *
54225149 ATATCATATCATAACTTAC
1 ATAACTTA-CATAACTTAT
*
54225168 ATAACTTACATAATACTTAG
1 ATAACTTACAT-A-ACTTAT
*
54225188 AT-A--TACATAACTTAC
1 ATAACTTACATAACTTAT
*
54225203 ATAATACTTAGATATA-TATCAT
1 AT-A-ACTTACATA-ACT-T-AT
54225225 ATCATATCTTACATAAC-TAGCTT
1 AT-A-A-CTTACATAACTTA---T
* * *
54225248 ACGAAACTTACTTAACTTAC
1 A--TAACTTACATAACTTAT
* *
54225268 AT-ACTTAAATATATTTTATAT
1 ATAACTTACATA-A--CT-TAT
* *
54225289 AATAATTTACATAACTTAC
1 -ATAACTTACATAACTTAT
* *
54225308 AAAACTTACATGACTTAT
1 ATAACTTACATAACTTAT
* *
54225326 ATAACTTAGATAA-ATAT
1 ATAACTTACATAACTTAT
* *
54225343 ATAACTTATATAACTCAT
1 ATAACTTACATAACTTAT
* *
54225361 ATAACTTAGATAA-ATAT
1 ATAACTTACATAACTTAT
* *
54225378 ATAATTTACATAA-ATAT
1 ATAACTTACATAACTTAT
* * *
54225395 ATATCATATCATAACTTAC
1 ATAACTTA-CATAACTTAT
54225414 ATAACTTACATAA
1 ATAACTTACATAA
54225427 TACTTAGATA
Statistics
Matches: 286, Mismatches: 65, Indels: 64
0.69 0.16 0.15
Matches are distributed among these distances:
15 7 0.02
16 2 0.01
17 85 0.30
18 111 0.39
19 20 0.07
20 17 0.06
21 5 0.02
22 19 0.07
23 19 0.07
24 1 0.00
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.37
Consensus pattern (18 bp):
ATAACTTACATAACTTAT
Found at i:54225104 original size:62 final size:63
Alignment explanation
Indices: 54225021--54225432 Score: 236
Period size: 62 Copynumber: 6.5 Consensus size: 63
54225011 AATATATTTG
* * *
54225021 ATATCATAATTTACATAACTTACAAAACGTACATAACTTATATAACTTAGATAAATATTTAAC
1 ATATCATAACTTACATAACTTACAAAACTTACATAACTTATATAACTTAGATAAATATATAAC
* * * *
54225084 TTAT-ATAACTTACATAACTTACATAACTTATATAACTTACATATAAATATAACTTACATAAATA
1 ATATCATAACTTACATAACTTACAAAACTTACAT-A---AC-T-T--ATATAACTTAGATAAATA
*
54225148 TATATC
58 TATAAC
*
54225154 ATATCATAACTTACATAACTTACATAATACTTAGATATACATAACTTACATAATACTTAGAT--A
1 ATATCATAACTTACATAACTTACA-AA-AC-----T-TACATAACTTATAT-A-ACTTAGATAAA
54225217 TATAT--C
56 TATATAAC
* * * * *
54225223 ATATCATATCTTACATAACTAGCTTACGAAACTTACTTAACTTACAT-AC-T---TAAATATATT
1 ATATCATAACTTACAT-A--A-CTTACAAAACTTACATAACTTATATAACTTAGATAAATATATA
**
54225283 TT
62 AC
* * *
54225285 ATATAATAATTTACATAACTTACAAAACTTACATGACTTATATAACTTAGATAAATATATAAC
1 ATATCATAACTTACATAACTTACAAAACTTACATAACTTATATAACTTAGATAAATATATAAC
* * * * * *
54225348 TTAT-ATAAC-T-CAT-A--T----AACTTAGATAA-ATATATAATTTACATAAATATATATC
1 ATATCATAACTTACATAACTTACAAAACTTACATAACTTATATAACTTAGATAAATATATAAC
54225400 ATATCATAACTTACATAACTTACATAATACTTA
1 ATATCATAACTTACATAACTTACA-AA-ACTTA
54225433 GATATACATA
Statistics
Matches: 269, Mismatches: 36, Indels: 87
0.69 0.09 0.22
Matches are distributed among these distances:
52 25 0.09
53 14 0.05
54 1 0.00
55 3 0.01
56 1 0.00
57 1 0.00
58 23 0.09
59 4 0.01
60 10 0.04
61 3 0.01
62 44 0.16
63 17 0.06
64 5 0.02
65 13 0.05
66 3 0.01
67 1 0.00
68 1 0.00
69 16 0.06
70 25 0.09
71 30 0.11
72 5 0.02
73 15 0.06
74 1 0.00
75 2 0.01
78 2 0.01
79 4 0.01
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (63 bp):
ATATCATAACTTACATAACTTACAAAACTTACATAACTTATATAACTTAGATAAATATATAAC
Found at i:54225134 original size:44 final size:44
Alignment explanation
Indices: 54225086--54225170 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
54225076 TATTTAACTT
* *
54225086 ATATAACTTACATAACTTACATAACTTAT-ATAACTTACATATAA
1 ATATAACTTACATAA-ATACATAACATATCATAACTTACATATAA
* *
54225130 ATATAACTTACATAAATATATATCATATCATAACTTACATA
1 ATATAACTTACATAAATACATAACATATCATAACTTACATA
54225171 ACTTACATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 9 0.25
44 27 0.75
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (44 bp):
ATATAACTTACATAAATACATAACATATCATAACTTACATATAA
Found at i:54225194 original size:26 final size:26
Alignment explanation
Indices: 54225165--54225218 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
54225155 TATCATAACT
54225165 TACATAACTTACATAATACTTAGATA
1 TACATAACTTACATAATACTTAGATA
54225191 TACATAACTTACATAATACTTAGATA
1 TACATAACTTACATAATACTTAGATA
54225217 TA
1 TA
54225219 TATCATATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (26 bp):
TACATAACTTACATAATACTTAGATA
Found at i:54225345 original size:17 final size:17
Alignment explanation
Indices: 54225323--54225397 Score: 105
Period size: 17 Copynumber: 4.4 Consensus size: 17
54225313 TTACATGACT
54225323 TATATAACTTAGATAAA
1 TATATAACTTAGATAAA
* *
54225340 TATATAACTTATATAAC
1 TATATAACTTAGATAAA
54225357 TCATATAACTTAGATAAA
1 T-ATATAACTTAGATAAA
* *
54225375 TATATAATTTACATAAA
1 TATATAACTTAGATAAA
54225392 TATATA
1 TATATA
54225398 TCATATCATA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
17 36 0.71
18 15 0.29
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.39
Consensus pattern (17 bp):
TATATAACTTAGATAAA
Found at i:54225363 original size:35 final size:35
Alignment explanation
Indices: 54225310--54225390 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
54225300 TAACTTACAA
* *
54225310 AACTTACATGACTTATATAACTTAGATAAATATAT
1 AACTTACATAACTCATATAACTTAGATAAATATAT
*
54225345 AACTTATATAACTCATATAACTTAGATAAATATAT
1 AACTTACATAACTCATATAACTTAGATAAATATAT
*
54225380 AATTTACATAA
1 AACTTACATAA
54225391 ATATATATCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (35 bp):
AACTTACATAACTCATATAACTTAGATAAATATAT
Found at i:54225440 original size:26 final size:26
Alignment explanation
Indices: 54225411--54225464 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
54225401 TATCATAACT
54225411 TACATAACTTACATAATACTTAGATA
1 TACATAACTTACATAATACTTAGATA
54225437 TACATAACTTACATAATACTTAGATA
1 TACATAACTTACATAATACTTAGATA
54225463 TA
1 TA
54225465 TATCATATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (26 bp):
TACATAACTTACATAATACTTAGATA
Found at i:54225449 original size:62 final size:61
Alignment explanation
Indices: 54225096--54225488 Score: 256
Period size: 62 Copynumber: 6.3 Consensus size: 61
54225086 ATATAACTTA
* * *
54225096 CATAACTTACATAACTTATAT-AACTTACATATAAATATAACTTACATAAATATATATCATAT
1 CATAACTTACATAACTTACATAAACTTAGATAT--ACATAACTTACATAAATATATATCATAT
54225158 CATAACTTACATAACTTACATAATACTTAGATATACATAACTTACATAATACTTAGATATATATC
1 CATAACTTACATAACTTACATAA-ACTTAGATATACATAACTTAC---ATA---A-ATATATATC
54225223 ATAT
58 ATAT
* * ** * * * * *
54225227 CATATCTTACATAAC-TAGCTTACGAAACTTACTTA-AC-TTACATACTTAAATATATTTTATAT
1 CATAACTTACATAACTTA-C--A-TAAACTTAGATATACATAACTTACATAAATATATATCATAT
* * * * * * *
54225289 AATAATTTACATAACTTACA-AAACTTACATGACTTATATAACTTAGATAAATATATAACTTAT
1 CATAACTTACATAACTTACATAAACTTAGAT-A--TACATAACTTACATAAATATATATCATAT
* * *
54225352 -ATAACTCATATAACTTAGATAAA--T--ATATA-AT---TTACATAAATATATATCATAT
1 CATAACTTACATAACTTACATAAACTTAGATATACATAACTTACATAAATATATATCATAT
54225404 CATAACTTACATAACTTACATAATACTTAGATATACATAACTTACATAATACTTAGATATATATC
1 CATAACTTACATAACTTACATAA-ACTTAGATATACATAACTTAC---ATA---A-ATATATATC
54225469 ATAT
58 ATAT
*
54225473 CATATCTTACATAACT
1 CATAACTTACATAACT
54225489 AGCTTACGAA
Statistics
Matches: 258, Mismatches: 36, Indels: 67
0.71 0.10 0.19
Matches are distributed among these distances:
52 18 0.07
53 19 0.07
54 1 0.00
55 2 0.01
56 3 0.01
58 15 0.06
59 5 0.02
60 1 0.00
61 1 0.00
62 74 0.29
63 24 0.09
64 9 0.03
65 6 0.02
66 2 0.01
68 4 0.02
69 62 0.24
70 2 0.01
71 8 0.03
72 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.37
Consensus pattern (61 bp):
CATAACTTACATAACTTACATAAACTTAGATATACATAACTTACATAAATATATATCATAT
Found at i:54228648 original size:54 final size:53
Alignment explanation
Indices: 54228520--54228650 Score: 145
Period size: 54 Copynumber: 2.4 Consensus size: 53
54228510 GGCATTTTGT
* **
54228520 TAGCCTTTGTGATGAACTCTGAAAGAATAGCCTTTGTGGTGAACTTTGAAAAAA
1 TAGCCTTTGTGA-GAACTCTGAAAGAATAGCCTTTATGGAAAACTTTGAAAAAA
** * * **
54228574 TAGTATTTGTAGCGAGCTCTGAAAGAATAGCCTTTATGGAAAACTTTGAATGAA
1 TAGCCTTTGT-GAGAACTCTGAAAGAATAGCCTTTATGGAAAACTTTGAAAAAA
*
54228628 TAGCCTTTGTGGAAAACTCTGAA
1 TAGCCTTTGT-GAGAACTCTGAA
54228651 TGGACTGACT
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
54 60 0.98
55 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (53 bp):
TAGCCTTTGTGAGAACTCTGAAAGAATAGCCTTTATGGAAAACTTTGAAAAAA
Found at i:54228652 original size:27 final size:27
Alignment explanation
Indices: 54228520--54228650 Score: 129
Period size: 27 Copynumber: 4.9 Consensus size: 27
54228510 GGCATTTTGT
54228520 TAGCCTTTGT-GATGAACTCTGAAAGAA
1 TAGCCTTTGTGGA-GAACTCTGAAAGAA
* * *
54228547 TAGCCTTTGTGGTGAACTTTGAAAAAA
1 TAGCCTTTGTGGAGAACTCTGAAAGAA
** * * *
54228574 TAGTATTTGTAGCGAGCTCTGAAAGAA
1 TAGCCTTTGTGGAGAACTCTGAAAGAA
* * * *
54228601 TAGCCTTTATGGAAAACTTTGAATGAA
1 TAGCCTTTGTGGAGAACTCTGAAAGAA
*
54228628 TAGCCTTTGTGGAAAACTCTGAA
1 TAGCCTTTGTGGAGAACTCTGAA
54228651 TGGACTGACT
Statistics
Matches: 82, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
27 81 0.99
28 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (27 bp):
TAGCCTTTGTGGAGAACTCTGAAAGAA
Found at i:54228662 original size:27 final size:27
Alignment explanation
Indices: 54228590--54228666 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 27
54228580 TTGTAGCGAG
* * *
54228590 CTCTGAAAGAATAGCCTTTATGGAAAA
1 CTCTGAATGAATAGACTTTGTGGAAAA
* *
54228617 CTTTGAATGAATAGCCTTTGTGGAAAA
1 CTCTGAATGAATAGACTTTGTGGAAAA
*
54228644 CTCTGAATGGACT-GACTTTGTGG
1 CTCTGAAT-GAATAGACTTTGTGG
54228667 CATACCCTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 40 0.93
28 3 0.07
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (27 bp):
CTCTGAATGAATAGACTTTGTGGAAAA
Found at i:54231996 original size:72 final size:72
Alignment explanation
Indices: 54231887--54232031 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
54231877 GCTGAATACT
54231887 ATTATGGTATAATATTAAATTGTGTGTTGACGAAAAAATCCAACGGCGTAACGGGGATCATCGAT
1 ATTATGGTATAATATTAAATTGTGTGTTGACGAAAAAATCCAACGGCGTAACGGGGATCATCGAT
54231952 GAATGAA
66 GAATGAA
*
54231959 ATTATGGTATAATATTAAATTGTGTGTTGACGAAAAAATCCAACGGCGTAACGGTGATCATCGAT
1 ATTATGGTATAATATTAAATTGTGTGTTGACGAAAAAATCCAACGGCGTAACGGGGATCATCGAT
54232024 GAATGAA
66 GAATGAA
54232031 A
1 A
54232032 AGGAATAGCT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (72 bp):
ATTATGGTATAATATTAAATTGTGTGTTGACGAAAAAATCCAACGGCGTAACGGGGATCATCGAT
GAATGAA
Found at i:54232139 original size:30 final size:29
Alignment explanation
Indices: 54232077--54232156 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
54232067 GGTGATGACC
* **
54232077 ATCAGACTATGGAAAGGGATGGCTTCGGCT
1 ATCA-ACTATGAAAAGGGATGGCTTCAACT
*
54232107 ATCGAACTATGAAAATGGATGGCTTCAACT
1 ATC-AACTATGAAAAGGGATGGCTTCAACT
*
54232137 ATCAATCTAAGAAAAGGGAT
1 ATCAA-CTATGAAAAGGGAT
54232157 AACTTCAGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
29 2 0.05
30 39 0.93
31 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (29 bp):
ATCAACTATGAAAAGGGATGGCTTCAACT
Found at i:54232238 original size:30 final size:30
Alignment explanation
Indices: 54232197--54232276 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 30
54232187 AGTTTTGGCA
* *
54232197 ATCAAATTATGAAAAGGGATGGTGATGACC
1 ATCAAACTATGAAAAGGGATGGTGACGACC
* * *
54232227 ATCGAACTATGAAAAAGAATGGTGACGACC
1 ATCAAACTATGAAAAGGGATGGTGACGACC
*
54232257 ATCAAATTATGAAAAGGGAT
1 ATCAAACTATGAAAAGGGAT
54232277 AGTTTCGGCT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (30 bp):
ATCAAACTATGAAAAGGGATGGTGACGACC
Found at i:54239755 original size:29 final size:28
Alignment explanation
Indices: 54239582--54239757 Score: 239
Period size: 28 Copynumber: 6.3 Consensus size: 28
54239572 TTAAGTCCGT
* *
54239582 ACACTCAGTGCTATATAATC-AACTCGC
1 ACACTTAGTGCTACATAATCAAACTCGC
* *
54239609 ACACTTAGTGATATATAATCAAACTCGC
1 ACACTTAGTGCTACATAATCAAACTCGC
*
54239637 ACACTTAGTGCTACGTAATCAAACTCGC
1 ACACTTAGTGCTACATAATCAAACTCGC
*
54239665 ACACTTAGTGCTACGTAATCAAACTCGC
1 ACACTTAGTGCTACATAATCAAACTCGC
54239693 ACACTTAGTGCTACATAATCAAACTCGC
1 ACACTTAGTGCTACATAATCAAACTCGC
* * *
54239721 ACACTTAGTGCCGTACA-ATTTAAACCCGC
1 ACACTTAGTG-C-TACATAATCAAACTCGC
54239750 ACACTTAG
1 ACACTTAG
54239758 CGCCAATCTC
Statistics
Matches: 137, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
27 18 0.13
28 97 0.71
29 18 0.13
30 4 0.03
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
ACACTTAGTGCTACATAATCAAACTCGC
Found at i:54243881 original size:40 final size:40
Alignment explanation
Indices: 54243825--54244017 Score: 239
Period size: 40 Copynumber: 4.8 Consensus size: 40
54243815 TCGGATAATA
* *
54243825 ACCGGGCTAAGTCCCGAAAGCATTTGTGCTAGTGACTAAT-
1 ACCGGGCTAAGTCCCGAAAGCATTTGTGCGAGTTACT-ATG
* * * *
54243865 TCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATA
1 ACCGGGCTAAGTCCCGAAAGCATTTGTGCGAGTTACTATG
* *
54243905 ACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATG
1 ACCGGGCTAAGTCCCGAAAGCATTTGTGCGAGTTACTATG
* *
54243945 ACCGGGTTAAGTTCC-AAAGGCATTTGTGCGAGTTACTATG
1 ACCGGGCTAAGTCCCGAAA-GCATTTGTGCGAGTTACTATG
*
54243985 ACCGGGCTAAGTCCC-AAAGGCATTTGGGCGAGT
1 ACCGGGCTAAGTCCCGAAA-GCATTTGTGCGAGT
54244018 AGCTATATCC
Statistics
Matches: 137, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 4 0.03
40 133 0.97
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
ACCGGGCTAAGTCCCGAAAGCATTTGTGCGAGTTACTATG
Found at i:54243956 original size:80 final size:80
Alignment explanation
Indices: 54243822--54244017 Score: 268
Period size: 80 Copynumber: 2.5 Consensus size: 80
54243812 TATTCGGATA
* * * *
54243822 ATAACCGGGCTAAGTCCCGAAAGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCAAAGGCA
54243887 ATTGTGCGAGTTACT
66 ATTGTGCGAGTTACT
* * * *
54243902 ATAACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATGACCGGGTTAAGTTCCAAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAGTCCCAAAGGC
*
54243966 ATTTGTGCGAGTTACT
65 AATTGTGCGAGTTACT
* * *
54243982 ATGACCGGGCTAAGTCCCAAAGGCATTTGGGCGAGT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
54244018 AGCTATATCC
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
79 2 0.02
80 100 0.98
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCAAAGGCA
ATTGTGCGAGTTACT
Found at i:54256056 original size:46 final size:44
Alignment explanation
Indices: 54255991--54256210 Score: 176
Period size: 46 Copynumber: 4.8 Consensus size: 44
54255981 ATTATAAAAT
**
54255991 GCTAGTGTAAGACATGTCTGGGACATGCATCAACATTGAGACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGC-TTGAGA-GAGA
* *
54256037 GCTAGTGTAAGACATGTCTGGGACATGTATCGGCCTCGAGATGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG-CTTGAGA-G-AGA
* * * *
54256083 GCCAATGTAAGACATGTCTAGGACATGCATCGGC-T-ACGAGATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTTGA-GAGA-GA
* ** *
54256127 GCTAGTGTAAGACATGTCTGGGACATGCATTGGCACAGATATATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGC-TTG--AGA-GAGA
* *
54256175 GCTAGTGTAAGACCATATCTGGGATATGGCATCGGC
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
54256211 ATAGATATGT
Statistics
Matches: 140, Mismatches: 21, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 32 0.23
45 1 0.01
46 66 0.47
47 2 0.01
48 14 0.10
49 15 0.11
50 7 0.05
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (44 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTTGAGAGAGA
Found at i:54256184 original size:92 final size:90
Alignment explanation
Indices: 54255942--54256212 Score: 251
Period size: 93 Copynumber: 2.9 Consensus size: 90
54255932 GCTGTTATGT
* ** * * *
54255942 GAGCCAGTGTAAGACATGTCTAAGACATGCATCGACCATATTATAAAATGCTAGTGTAAGACATG
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAGA-TATATAA-GCTAGTGTAAGACATG
**
54256007 TCTGGGACATGCATCAACATTGAGACGA
64 TCTGGGACATGCATCGGCA-TGAGACGA
* * * * * *
54256035 GAGCTAGTGTAAGACATGTCTGGGACATGTATCGGCCTCGAGATGTAAGCCAATGTAAGACATGT
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-AGATATATAAGCTAGTGTAAGACATGT
*
54256100 CTAGGACATGCATCGGC-T-ACGA-GA
65 CTGGGACATGCATCGGCATGA-GACGA
* *
54256124 TGTGCTAGTGTAAGACATGTCTGGGACATGCATTGGCACAGATATATGAGAGCTAGTGTAAGACC
1 -GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGC-CAGATATAT-A-AGCTAGTGTAAGA-C
* *
54256189 ATATCTGGGATATGGCATCGGCAT
61 ATGTCTGGGACAT-GCATCGGCAT
54256213 AGATATGTGT
Statistics
Matches: 143, Mismatches: 26, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
89 3 0.02
90 41 0.29
91 2 0.01
92 40 0.28
93 47 0.33
94 9 0.06
95 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (90 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAGATATATAAGCTAGTGTAAGACATGTC
TGGGACATGCATCGGCATGAGACGA
Found at i:54265132 original size:38 final size:38
Alignment explanation
Indices: 54265089--54265231 Score: 171
Period size: 38 Copynumber: 3.7 Consensus size: 38
54265079 GTATTGGGCC
*
54265089 TTGAGCCTAGCAGGCATCGTGCTGGTGTTTATCGAGCT
1 TTGAGCCTAGCAGGCTTCGTGCTGGTGTTTATCGAGCT
* * * * *
54265127 TTGAGCCTAGCAAGCTTCATGCTGATGACTTATAGAGCT
1 TTGAGCCTAGCAGGCTTCGTGCTGGTG-TTTATCGAGCT
** * *
54265166 TTGAGCCTAATAGGCTTCGTGCCGGTGTTTATCGGGC-
1 TTGAGCCTAGCAGGCTTCGTGCTGGTGTTTATCGAGCT
54265203 TTGATGCCTAGCAGGCTTCGTGCTGGTGT
1 TTGA-GCCTAGCAGGCTTCGTGCTGGTGT
54265232 AACAATTCAT
Statistics
Matches: 85, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
37 4 0.05
38 51 0.60
39 30 0.35
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.32
Consensus pattern (38 bp):
TTGAGCCTAGCAGGCTTCGTGCTGGTGTTTATCGAGCT
Found at i:54276114 original size:322 final size:322
Alignment explanation
Indices: 54275522--54276165 Score: 1234
Period size: 322 Copynumber: 2.0 Consensus size: 322
54275512 CTGACTTGAG
54275522 CTATGAAGAAGAACCGATTCGTATCCTAGCTCGTGAAGTGAAAGAGTTGCGAAATAAAAGGGTTC
1 CTATGAAGAAGAACCGATTCGTATCCTAGCTCGTGAAGTGAAAGAGTTGCGAAATAAAAGGGTTC
54275587 CGTTGGTTAAGGTGTTGTGGCTCAAACACGGGATCGAGGAAGCAACCTGGGAACCCGAGAGCTCG
66 CGTTGGTTAAGGTGTTGTGGCTCAAACACGGGATCGAGGAAGCAACCTGGGAACCCGAGAGCTCG
54275652 ATGAAAGAACGATATCCAAACCTATTTACCGGTAAGATTTTCGAGGACGAAAATTTCTTAAGTGA
131 ATGAAAGAACGATATCCAAACCTATTTACCGGTAAGATTTTCGAGGACGAAAATTTCTTAAGTGA
54275717 GGGAGAGTTGAGACAGCCCAAAATTAACCCTAGTCAGGAAGTGGTTTCGGGACCGCTAAACCGAG
196 GGGAGAGTTGAGACAGCCCAAAATTAACCCTAGTCAGGAAGTGGTTTCGGGACCGCTAAACCGAG
54275782 TCACCGAAAGGTTTGAATGTGATGTTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAA
261 TCACCGAAAGGTTTGAATGTGATGTTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAA
*
54275844 CTATGATGAAGAACCGATTCGTATCCTAGCTCGTGAAGTGAAAGAGTTGCGAAATAAAAGGGTTC
1 CTATGAAGAAGAACCGATTCGTATCCTAGCTCGTGAAGTGAAAGAGTTGCGAAATAAAAGGGTTC
54275909 CGTTGGTTAAGGTGTTGTGGCTCAAACACGGGATCGAGGAAGCAACCTGGGAACCCGAGAGCTCG
66 CGTTGGTTAAGGTGTTGTGGCTCAAACACGGGATCGAGGAAGCAACCTGGGAACCCGAGAGCTCG
* *
54275974 ATGAAAGAACGATATCCAAACCTATTTACTGTTAAGATTTTCGAGGACGAAAATTTCTTAAGTGA
131 ATGAAAGAACGATATCCAAACCTATTTACCGGTAAGATTTTCGAGGACGAAAATTTCTTAAGTGA
* * *
54276039 GGGAGAGTTGTGACAGCCCAAAATTGACCCTAGTCGGGAAGTGGTTTCGGGACCGCTAAACCGAG
196 GGGAGAGTTGAGACAGCCCAAAATTAACCCTAGTCAGGAAGTGGTTTCGGGACCGCTAAACCGAG
54276104 TCACCGAAAGGTTTGAATGTGATGTTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAA
261 TCACCGAAAGGTTTGAATGTGATGTTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAA
54276166 TTTCAAGCTT
Statistics
Matches: 316, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
322 316 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (322 bp):
CTATGAAGAAGAACCGATTCGTATCCTAGCTCGTGAAGTGAAAGAGTTGCGAAATAAAAGGGTTC
CGTTGGTTAAGGTGTTGTGGCTCAAACACGGGATCGAGGAAGCAACCTGGGAACCCGAGAGCTCG
ATGAAAGAACGATATCCAAACCTATTTACCGGTAAGATTTTCGAGGACGAAAATTTCTTAAGTGA
GGGAGAGTTGAGACAGCCCAAAATTAACCCTAGTCAGGAAGTGGTTTCGGGACCGCTAAACCGAG
TCACCGAAAGGTTTGAATGTGATGTTTATTGTCTAGAATATGTAATCATGAATGTGTGAAAA
Found at i:54277792 original size:27 final size:27
Alignment explanation
Indices: 54277761--54277938 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54277751 TAAATTGTAC
54277761 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
54277788 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54277814 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
54277842 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
54277870 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54277897 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54277924 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54277939 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:54277876 original size:82 final size:81
Alignment explanation
Indices: 54277762--54277917 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54277752 AAATTGTACA
* *
54277762 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
54277826 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
54277843 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
54277908 TGCGAGTTGA
65 TGCGAATTGA
54277918 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:54277929 original size:82 final size:81
Alignment explanation
Indices: 54277758--54277938 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
54277748 GATTAAATTG
* *
54277758 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
54277823 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
54277839 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
54277903 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
54277921 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
54277939 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:54282834 original size:13 final size:13
Alignment explanation
Indices: 54282816--54282840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54282806 AGAAACCATA
54282816 AAATTTTCACACG
1 AAATTTTCACACG
54282829 AAATTTTCACAC
1 AAATTTTCACAC
54282841 ATATCACATA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:54296726 original size:25 final size:24
Alignment explanation
Indices: 54296676--54296726 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
54296666 AACATCACAA
* ** *
54296676 AACTCAACTATTCATCAATTTTAT
1 AACTCAAATATTCATCAAAATCAT
54296700 AACTCAAAATATTCATCAAAATCAT
1 AACTC-AAATATTCATCAAAATCAT
54296725 AA
1 AA
54296727 ATTCAAGCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (24 bp):
AACTCAAATATTCATCAAAATCAT
Found at i:54311212 original size:27 final size:27
Alignment explanation
Indices: 54311182--54311359 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54311172 ATATTGAGTC
* * * *
54311182 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54311209 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54311236 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54311264 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54311291 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54311318 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54311345 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54311360 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54311321 original size:82 final size:81
Alignment explanation
Indices: 54311203--54311358 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54311193 TGCTATATAA
* *
54311203 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54311268 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54311285 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54311349 CACTTAGTGC
65 CACTTAGTGC
54311359 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54319275 original size:27 final size:27
Alignment explanation
Indices: 54319245--54319422 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54319235 ATATTGAGTC
* * * *
54319245 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54319272 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54319299 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54319327 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54319354 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54319381 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54319408 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54319423 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54319384 original size:82 final size:81
Alignment explanation
Indices: 54319266--54319421 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54319256 TGCTATATAA
* *
54319266 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54319331 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54319348 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54319412 CACTTAGTGC
65 CACTTAGTGC
54319422 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54330920 original size:27 final size:27
Alignment explanation
Indices: 54330877--54331246 Score: 472
Period size: 27 Copynumber: 13.7 Consensus size: 27
54330867 CGTACCTGAA
* *
54330877 CCCTCATGTGATAAAATTATGATTTTT
1 CCCTTATGTGATAAAATGATGATTTTT
*
54330904 CCCATATGTGATAAAATGATGATTTTT
1 CCCTTATGTGATAAAATGATGATTTTT
* *
54330931 CCCTTATGTGATCAAATGATGATTTTG
1 CCCTTATGTGATAAAATGATGATTTTT
* *
54330958 CCCTCATGTGATAAAATGATGATTTTG
1 CCCTTATGTGATAAAATGATGATTTTT
* * *
54330985 CCCTCATGTGATCAAATGACT-ATTTTG
1 CCCTTATGTGATAAAATGA-TGATTTTT
*
54331012 CCCTCATGTGATAAAATGATGATTTTT
1 CCCTTATGTGATAAAATGATGATTTTT
* * *
54331039 CCCTTAGGTGATAAAATGACGATTTTG
1 CCCTTATGTGATAAAATGATGATTTTT
* * **
54331066 CCCTTAAGTGAGAAAATGACAATTTTT
1 CCCTTATGTGATAAAATGATGATTTTT
* * *
54331093 CCCTTATGTGATAAAATAACGATTTTG
1 CCCTTATGTGATAAAATGATGATTTTT
*
54331120 CCCTTAGGTGATAAAATGATGATTTTT
1 CCCTTATGTGATAAAATGATGATTTTT
*
54331147 CCCTTATGTGGTAAAATGATGATTTTT
1 CCCTTATGTGATAAAATGATGATTTTT
* *
54331174 CCCTTATGTGATAAAATAACGATTTTT
1 CCCTTATGTGATAAAATGATGATTTTT
* *
54331201 CCCTTATGTGATAAAATGAAGATTTTG
1 CCCTTATGTGATAAAATGATGATTTTT
*
54331228 CCCTTAGGTGATAAAATGA
1 CCCTTATGTGATAAAATGA
54331247 CCGAAATACC
Statistics
Matches: 304, Mismatches: 37, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
26 1 0.00
27 302 0.99
28 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.38
Consensus pattern (27 bp):
CCCTTATGTGATAAAATGATGATTTTT
Found at i:54331269 original size:27 final size:27
Alignment explanation
Indices: 54331239--54331301 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
54331229 CCTTAGGTGA
*
54331239 TAAAATGACCGAAATACCCCTA-TAGGG
1 TAAAATGACCGAAATA-CCCTAGTAAGG
* * *
54331266 TAAAATGACTGTAATACCTTAGTAAGG
1 TAAAATGACCGAAATACCCTAGTAAGG
54331293 TAAAATGAC
1 TAAAATGAC
54331302 AGATTTGTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTAGTAAGG
Found at i:54331379 original size:23 final size:23
Alignment explanation
Indices: 54331336--54331385 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
54331326 CTGTATTTGA
54331336 GCATGCCATGTTATATGTATGTC
1 GCATGCCATGTTATATGTATGTC
*
54331359 GCAT-CCATGTATAATAT-TATGTT
1 GCATGCCATGT-T-ATATGTATGTC
54331382 GCAT
1 GCAT
54331386 TGCATGGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 6 0.25
23 14 0.58
24 4 0.17
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (23 bp):
GCATGCCATGTTATATGTATGTC
Found at i:54331730 original size:35 final size:35
Alignment explanation
Indices: 54331690--54331782 Score: 143
Period size: 35 Copynumber: 2.7 Consensus size: 35
54331680 TACTGCACTA
54331690 ATTACTATTACTGAAATGGGCTAAAACCCAGACTG
1 ATTACTATTACTGAAATGGGCTAAAACCCAGACTG
* *
54331725 ATTACTATTACTAAAATGGGATAAAACCCAGACTG
1 ATTACTATTACTGAAATGGGCTAAAACCCAGACTG
* *
54331760 -CTACTGTTACTGAAATGGGCTAA
1 ATTACTATTACTGAAATGGGCTAA
54331783 GGCCCAGATT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 19 0.37
35 33 0.63
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (35 bp):
ATTACTATTACTGAAATGGGCTAAAACCCAGACTG
Found at i:54331813 original size:34 final size:34
Alignment explanation
Indices: 54331692--54331814 Score: 149
Period size: 34 Copynumber: 3.6 Consensus size: 34
54331682 CTGCACTAAT
*
54331692 TACTATTACTGAAATGGGCTAAAACCCAGACTGAT
1 TACTATTACTGAAATGGGCTAAAACCCAGACTG-C
* *
54331727 TACTATTACTAAAATGGGATAAAACCCAGACTGC
1 TACTATTACTGAAATGGGCTAAAACCCAGACTGC
* ** *
54331761 TACTGTTACTGAAATGGGCTAAGGCCCAGATTGC
1 TACTATTACTGAAATGGGCTAAAACCCAGACTGC
*
54331795 CACTATTACT-AATATGGGCT
1 TACTATTACTGAA-ATGGGCT
54331815 TAGGCCCCAC
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
33 2 0.03
34 43 0.57
35 31 0.41
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (34 bp):
TACTATTACTGAAATGGGCTAAAACCCAGACTGC
Found at i:54340880 original size:26 final size:26
Alignment explanation
Indices: 54340814--54340880 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 26
54340804 GGCATAGCAG
* * * *
54340814 GCTTTTTGCTGGTGTATTTTTAGCAG
1 GCTTTGTGCTGGTGTATATTTAGAAA
* * *
54340840 GCTTCGAGCTAGTGTATATTTAGAAA
1 GCTTTGTGCTGGTGTATATTTAGAAA
54340866 GCTTTGTGCTGGTGT
1 GCTTTGTGCTGGTGT
54340881 TGTATTAGCA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.16, C:0.12, G:0.28, T:0.43
Consensus pattern (26 bp):
GCTTTGTGCTGGTGTATATTTAGAAA
Found at i:54340937 original size:34 final size:34
Alignment explanation
Indices: 54340893--54340960 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
54340883 TATTAGCAGG
54340893 CACTACGTGTTAGTGTTTTATTTAGAATGTACTA
1 CACTACGTGTTAGTGTTTTATTTAGAATGTACTA
* *
54340927 CACTATGTGTTAGTGTTTTATTTAGCATGTACTA
1 CACTACGTGTTAGTGTTTTATTTAGAATGTACTA
54340961 TGTACCGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.46
Consensus pattern (34 bp):
CACTACGTGTTAGTGTTTTATTTAGAATGTACTA
Found at i:54340961 original size:29 final size:29
Alignment explanation
Indices: 54340877--54340963 Score: 77
Period size: 34 Copynumber: 2.9 Consensus size: 29
54340867 CTTTGTGCTG
* * * *
54340877 GTGTTGTA-TTAGCAGGCACTACGTGTTA
1 GTGTTTTATTTAGCATGTACTATGTGTTA
*
54340905 GTGTTTTATTTAGAATGTACTACACTATGTGTTA
1 GTGTTTTATTTAGCATG---T--ACTATGTGTTA
54340939 GTGTTTTATTTAGCATGTACTATGT
1 GTGTTTTATTTAGCATGTACTATGT
54340964 ACCGATGATG
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
28 7 0.15
29 13 0.28
31 1 0.02
34 26 0.55
ACGTcount: A:0.23, C:0.10, G:0.22, T:0.45
Consensus pattern (29 bp):
GTGTTTTATTTAGCATGTACTATGTGTTA
Found at i:54345150 original size:20 final size:20
Alignment explanation
Indices: 54345125--54345169 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
54345115 CTAATGGTAC
54345125 AGGCAATTAACCAAGTCTAA
1 AGGCAATTAACCAAGTCTAA
54345145 AGGCAATTAACCAAGTCTAA
1 AGGCAATTAACCAAGTCTAA
54345165 AGGCA
1 AGGCA
54345170 TAAAGTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (20 bp):
AGGCAATTAACCAAGTCTAA
Found at i:54351032 original size:29 final size:29
Alignment explanation
Indices: 54350990--54351054 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
54350980 GTGTCTCAGC
*
54350990 CGTGTGTGCCACACGGCCTAGAACACAGG
1 CGTGTGTGCCACACGACCTAGAACACAGG
54351019 CGTGTGTGCCACACGACCTAGAACACAGG
1 CGTGTGTGCCACACGACCTAGAACACAGG
54351048 CGTGTGT
1 CGTGTGT
54351055 CTTGGCTGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.23, C:0.29, G:0.31, T:0.17
Consensus pattern (29 bp):
CGTGTGTGCCACACGACCTAGAACACAGG
Found at i:54361151 original size:13 final size:13
Alignment explanation
Indices: 54361133--54361161 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54361123 AATTTTAGGT
54361133 CATACCACACGCC
1 CATACCACACGCC
54361146 CATACCACACGCC
1 CATACCACACGCC
54361159 CAT
1 CAT
54361162 GGGGGTGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.52, G:0.07, T:0.10
Consensus pattern (13 bp):
CATACCACACGCC
Found at i:54365739 original size:189 final size:189
Alignment explanation
Indices: 54365419--54365784 Score: 732
Period size: 189 Copynumber: 1.9 Consensus size: 189
54365409 AATTTCACCC
54365419 TCAGACAAAATGACCATTTTTCCTCTAACCTTTCTCATTATTTACGATTTAGTCCCTAGGCTCGT
1 TCAGACAAAATGACCATTTTTCCTCTAACCTTTCTCATTATTTACGATTTAGTCCCTAGGCTCGT
54365484 ATGATGAAATACATGAATTTTCTACATTACCCAAGTCTATCTGAATGTTCTTTTCTCTTATGGCA
66 ATGATGAAATACATGAATTTTCTACATTACCCAAGTCTATCTGAATGTTCTTTTCTCTTATGGCA
54365549 GCCAAAAATTTTCCATTATTTCACATTTCTACCACATATTTTACACCTTTTGCAAAAAG
131 GCCAAAAATTTTCCATTATTTCACATTTCTACCACATATTTTACACCTTTTGCAAAAAG
54365608 TCAGACAAAATGACCATTTTTCCTCTAACCTTTCTCATTATTTACGATTTAGTCCCTAGGCTCGT
1 TCAGACAAAATGACCATTTTTCCTCTAACCTTTCTCATTATTTACGATTTAGTCCCTAGGCTCGT
54365673 ATGATGAAATACATGAATTTTCTACATTACCCAAGTCTATCTGAATGTTCTTTTCTCTTATGGCA
66 ATGATGAAATACATGAATTTTCTACATTACCCAAGTCTATCTGAATGTTCTTTTCTCTTATGGCA
54365738 GCCAAAAATTTTCCATTATTTCACATTTCTACCACATATTTTACACC
131 GCCAAAAATTTTCCATTATTTCACATTTCTACCACATATTTTACACC
54365785 GTAAGTTATT
Statistics
Matches: 177, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 177 1.00
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (189 bp):
TCAGACAAAATGACCATTTTTCCTCTAACCTTTCTCATTATTTACGATTTAGTCCCTAGGCTCGT
ATGATGAAATACATGAATTTTCTACATTACCCAAGTCTATCTGAATGTTCTTTTCTCTTATGGCA
GCCAAAAATTTTCCATTATTTCACATTTCTACCACATATTTTACACCTTTTGCAAAAAG
Found at i:54369894 original size:26 final size:26
Alignment explanation
Indices: 54369865--54369921 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
54369855 GCACTCTCTC
54369865 GAGCCATATAA-CAGGAAACTCACAAA
1 GAGCCAT-TAATCAGGAAACTCACAAA
*
54369891 GAGCCATTAATCAGGAAGCTCACAAA
1 GAGCCATTAATCAGGAAACTCACAAA
54369917 GAGCC
1 GAGCC
54369922 TATCAAGAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 3 0.10
26 26 0.90
ACGTcount: A:0.44, C:0.25, G:0.19, T:0.12
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAACTCACAAA
Found at i:54369931 original size:23 final size:25
Alignment explanation
Indices: 54369865--54369933 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 25
54369855 GCACTCTCTC
* * *
54369865 GAGCCATATAACAGGAAACTCACAAA
1 GAGCCATA-ATCAAGAAGCTCACAAA
*
54369891 GAGCCATTAATCAGGAAGCTCACAAA
1 GAGCCA-TAATCAAGAAGCTCACAAA
54369917 GAGCC-T-ATCAAGAAGCT
1 GAGCCATAATCAAGAAGCT
54369934 TGTCCAACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 10 0.26
24 1 0.03
26 26 0.67
27 2 0.05
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.14
Consensus pattern (25 bp):
GAGCCATAATCAAGAAGCTCACAAA
Found at i:54371858 original size:21 final size:21
Alignment explanation
Indices: 54371822--54371863 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
54371812 TGTATGGAAT
*
54371822 GTTAATTTAATGGTATCAAAG
1 GTTAATTTAATAGTATCAAAG
*
54371843 GTTAATTTACTAGTATCAAAG
1 GTTAATTTAATAGTATCAAAG
54371864 CTACAAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (21 bp):
GTTAATTTAATAGTATCAAAG
Found at i:54380718 original size:13 final size:13
Alignment explanation
Indices: 54380700--54380724 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54380690 CACTATCAAC
54380700 AGGATCAAGGATT
1 AGGATCAAGGATT
54380713 AGGATCAAGGAT
1 AGGATCAAGGAT
54380725 ACTTCCAGCA
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:0.40, C:0.08, G:0.32, T:0.20
Consensus pattern (13 bp):
AGGATCAAGGATT
Found at i:54383676 original size:30 final size:29
Alignment explanation
Indices: 54383629--54383709 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
54383619 AATGATAAAA
*
54383629 AATAACAATTATA-AAATATATTAAATTTT
1 AATAAAAATTA-AGAAATATATTAAATTTT
**
54383658 AATAAAAATATAAGAAATAT-TTATTTTTT
1 AATAAAAAT-TAAGAAATATATTAAATTTT
* * *
54383687 ATTAAAAATTAGGAAAAATATTA
1 AATAAAAATTAAGAAATATATTA
54383710 TAAATTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 8 0.19
29 27 0.63
30 8 0.19
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.40
Consensus pattern (29 bp):
AATAAAAATTAAGAAATATATTAAATTTT
Found at i:54383727 original size:20 final size:20
Alignment explanation
Indices: 54383702--54383756 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
54383692 AAATTAGGAA
*
54383702 AAATATTATAAATTATATAG
1 AAATATTATAAAATATATAG
* *
54383722 AAATATAGAAAAAAATATATAG
1 AAATAT--TATAAAATATATAG
*
54383744 AAATTTTATAAAA
1 AAATATTATAAAA
54383757 CTGTAAGAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
20 11 0.41
22 16 0.59
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AAATATTATAAAATATATAG
Found at i:54384112 original size:26 final size:26
Alignment explanation
Indices: 54384083--54384132 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
54384073 TTTTTATATT
54384083 TTTATTAAAGTTTAATTTTTATAACA
1 TTTATTAAAGTTTAATTTTTATAACA
* ** *
54384109 TTTATTGATTTTTATTTTTTATAA
1 TTTATTAAAGTTTAATTTTTATAA
54384133 TTTTTTTGTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTATTAAAGTTTAATTTTTATAACA
Found at i:54384719 original size:26 final size:25
Alignment explanation
Indices: 54384668--54384717 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
54384658 TACAACCAAA
* *
54384668 AAATTTTTTTAAAAGTTTATTTTTT
1 AAATCTTTTTAAAAGATTATTTTTT
54384693 AAATCTTTTTAAAAGATTATTTTTT
1 AAATCTTTTTAAAAGATTATTTTTT
54384718 TACTTTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (25 bp):
AAATCTTTTTAAAAGATTATTTTTT
Found at i:54384778 original size:26 final size:26
Alignment explanation
Indices: 54384750--54384800 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
54384740 AATTTGTGAG
* *
54384750 AAATTTAAAATAATTTAAAATATATGA
1 AAATTTAAAA-AATTAAAAAAATATGA
*
54384777 AAATTTTAAAAATTAAAAAAATAT
1 AAATTTAAAAAATTAAAAAAATAT
54384801 TATTTTCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
AAATTTAAAAAATTAAAAAAATATGA
Found at i:54385863 original size:187 final size:187
Alignment explanation
Indices: 54385548--54385922 Score: 741
Period size: 187 Copynumber: 2.0 Consensus size: 187
54385538 TATTGCATTC
54385548 TCCAAAATAAACGCAAATATAAAGAAAATAAAAGATATAATCATGGACCACTAAAAGTGGGAACA
1 TCCAAAATAAACGCAAATATAAAGAAAATAAAAGATATAATCATGGACCACTAAAAGTGGGAACA
54385613 TACTAAAAAATAAGAGAACAATGAGAGTTCTCAAGATAACTCTTTAAAGAGTAAATATAACTTAT
66 TACTAAAAAATAAGAGAACAATGAGAGTTCTCAAGATAACTCTTTAAAGAGTAAATATAACTTAT
54385678 GCTATTAATGTGATATGAAAGATTATTGGCCACATATGTGGCATATGCCTAAATATT
131 GCTATTAATGTGATATGAAAGATTATTGGCCACATATGTGGCATATGCCTAAATATT
54385735 TCCAAAATAAACGCAAATATAAAGAAAATAAAAGATATAATCATGGACCACTAAAAGTGGGAACA
1 TCCAAAATAAACGCAAATATAAAGAAAATAAAAGATATAATCATGGACCACTAAAAGTGGGAACA
54385800 TACTAAAAAATAAGAGAACAATGAGAGTTCTCAAGATAACTCTTTAAAGAGTAAATATAACTTAT
66 TACTAAAAAATAAGAGAACAATGAGAGTTCTCAAGATAACTCTTTAAAGAGTAAATATAACTTAT
*
54385865 GCTATTAATGTGATATGAAAGATTATTGGCCACATATGTGGCATATGCCTAACTATT
131 GCTATTAATGTGATATGAAAGATTATTGGCCACATATGTGGCATATGCCTAAATATT
54385922 T
1 T
54385923 TGTCTCTGTT
Statistics
Matches: 187, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
187 187 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (187 bp):
TCCAAAATAAACGCAAATATAAAGAAAATAAAAGATATAATCATGGACCACTAAAAGTGGGAACA
TACTAAAAAATAAGAGAACAATGAGAGTTCTCAAGATAACTCTTTAAAGAGTAAATATAACTTAT
GCTATTAATGTGATATGAAAGATTATTGGCCACATATGTGGCATATGCCTAAATATT
Found at i:54391025 original size:39 final size:39
Alignment explanation
Indices: 54390974--54391091 Score: 236
Period size: 39 Copynumber: 3.0 Consensus size: 39
54390964 ACCTGAAGAG
54390974 TGCTTGAAGTGTGCTATATCATTGCTGAGGGATTCGGCT
1 TGCTTGAAGTGTGCTATATCATTGCTGAGGGATTCGGCT
54391013 TGCTTGAAGTGTGCTATATCATTGCTGAGGGATTCGGCT
1 TGCTTGAAGTGTGCTATATCATTGCTGAGGGATTCGGCT
54391052 TGCTTGAAGTGTGCTATATCATTGCTGAGGGATTCGGCT
1 TGCTTGAAGTGTGCTATATCATTGCTGAGGGATTCGGCT
54391091 T
1 T
54391092 ATCATTGGTG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (39 bp):
TGCTTGAAGTGTGCTATATCATTGCTGAGGGATTCGGCT
Found at i:54394724 original size:12 final size:12
Alignment explanation
Indices: 54394707--54394732 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54394697 CATTCCGAAG
54394707 TATATATATACA
1 TATATATATACA
54394719 TATATATATACA
1 TATATATATACA
54394731 TA
1 TA
54394733 AGTATGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:54395248 original size:27 final size:27
Alignment explanation
Indices: 54395214--54395391 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54395204 TTTATTGTAC
54395214 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
54395241 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54395267 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
54395295 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
54395323 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54395350 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54395377 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54395392 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:54395328 original size:82 final size:81
Alignment explanation
Indices: 54395215--54395370 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54395205 TTATTGTACA
* *
54395215 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
54395279 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
54395296 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
54395361 TGCGAGTTGA
65 TGCGAATTGA
54395371 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:54395382 original size:82 final size:81
Alignment explanation
Indices: 54395211--54395391 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
54395201 GTTTTTATTG
* *
54395211 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
54395276 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
54395292 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
54395356 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
54395374 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
54395392 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:54397030 original size:43 final size:43
Alignment explanation
Indices: 54396965--54397260 Score: 463
Period size: 43 Copynumber: 6.9 Consensus size: 43
54396955 GTCTAAACTC
* *
54396965 ACTCACCAGCATTACT--CCTGCTAGGCTCGAAGCCCAATATTA
1 ACTCACCGGCATTA-TAGCCTGCTAGGCTCGAAGCCCGATATTA
* ** *
54397007 AATCACTAGCATTATAGCCTGCTAGGTTCGAAGCCCGATATTA
1 ACTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTA
*
54397050 ACTCATCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTA
1 ACTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTA
54397093 ACTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTA
1 ACTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTA
*
54397136 ACTCACCGGCATTATAGCATGCTAGGCTCGAAGCCCGATATTA
1 ACTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTA
*
54397179 ACTCACCGGCATTATAGACAT-CTAGGCTCGAAGCCCGATATTA
1 ACTCACCGGCATTATAG-CCTGCTAGGCTCGAAGCCCGATATTA
54397222 ACTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGA
1 ACTCACCGGCATTATAGCCTGCTAGGCTCGAA-GCCCGA
54397261 ATAGTACCGT
Statistics
Matches: 237, Mismatches: 12, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
41 1 0.00
42 14 0.06
43 213 0.90
44 9 0.04
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (43 bp):
ACTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTA
Found at i:54409801 original size:43 final size:43
Alignment explanation
Indices: 54409733--54409854 Score: 185
Period size: 43 Copynumber: 2.8 Consensus size: 43
54409723 CTAAACTCAT
*
54409733 TCACCGGCATTACT-G-CTGCTAGGCTCGAAGCCTGATATTAAC
1 TCACCGGCATT-CTAGCCTGCTAGGCTCGAAGCCCGATATTAAC
54409775 TCACCGGCATTCTAGCCTGCTAGGCTCGAAGCCCGATATTAAC
1 TCACCGGCATTCTAGCCTGCTAGGCTCGAAGCCCGATATTAAC
* *
54409818 TCACCGACATTATAGCCTGCTAGGCTCGAAGGCCCGA
1 TCACCGGCATTCTAGCCTGCTAGGCTCGAA-GCCCGA
54409855 ATAGTTCCAT
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
41 2 0.03
42 12 0.16
43 54 0.73
44 6 0.08
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.23
Consensus pattern (43 bp):
TCACCGGCATTCTAGCCTGCTAGGCTCGAAGCCCGATATTAAC
Found at i:54410259 original size:73 final size:73
Alignment explanation
Indices: 54410135--54410280 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
54410125 TCTTTAACAT
*
54410135 TCGGCTAAATCCATACCTTACAAGGAATACCTAATTCACATAATATATCAGATTATAATCAATTG
1 TCGGCTAAATCCATACCTTACAAGGAATACCTAATCCACATAATATATCAGATTATAATCAATTG
54410200 TTATTTAC
66 TTATTTAC
*
54410208 TCGGTTAAATCCATACCTTACAAGGAATACCTAATCCACATAATATATCAGATTATAATCAATTG
1 TCGGCTAAATCCATACCTTACAAGGAATACCTAATCCACATAATATATCAGATTATAATCAATTG
54410273 TTATTTAC
66 TTATTTAC
54410281 ATTTGATTAC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.34
Consensus pattern (73 bp):
TCGGCTAAATCCATACCTTACAAGGAATACCTAATCCACATAATATATCAGATTATAATCAATTG
TTATTTAC
Found at i:54411996 original size:46 final size:46
Alignment explanation
Indices: 54411924--54412186 Score: 273
Period size: 46 Copynumber: 5.7 Consensus size: 46
54411914 GATATTTGGG
*
54411924 CATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * * * * * *
54411970 CAACCGAACTCATTGAGTTGAGTCCGAGTTCA-TGAAATGTA-ACTAGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGA-A
*
54412017 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * * * * * * * *
54412063 CGTCTGAACTCATTGAGTTGAGTCTGAGTTC-GTGAAATGTA-ACTAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGAA
54412109 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 -CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
*
54412156 CGTCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTC
54412187 GTGAGATGTA
Statistics
Matches: 171, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
45 2 0.01
46 98 0.57
47 69 0.40
48 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:54412081 original size:93 final size:93
Alignment explanation
Indices: 54411922--54412218 Score: 504
Period size: 93 Copynumber: 3.2 Consensus size: 93
54411912 CAGATATTTG
* **
54411922 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACAACCGAACTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
*
54411987 TTGAGTCCGAGTTCATGAAATGTAACTA
66 TTGAGTCCGAGTTCGTGAAATGTAACTA
* *
54412015 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGTCTGAACTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
*
54412080 TTGAGTCTGAGTTCGTGAAATGTAACTA
66 TTGAGTCCGAGTTCGTGAAATGTAACTA
* *
54412108 AGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
*
54412173 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAAATGTAACTA
54412201 GGCATCCGAACTCGTTGA
1 GGCATCCGAACTCGTTGA
54412219 ATGATGAATA
Statistics
Matches: 190, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 190 1.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
TTGAGTCCGAGTTCGTGAAATGTAACTA
Found at i:54414322 original size:174 final size:174
Alignment explanation
Indices: 54414032--54414379 Score: 696
Period size: 174 Copynumber: 2.0 Consensus size: 174
54414022 TATAGATTGT
54414032 ATACTCTTTTTCCTTAATTAGGTTTTTATCCCACAGAGTTTTTCCTAGTAAGGTTTTAACGAAGC
1 ATACTCTTTTTCCTTAATTAGGTTTTTATCCCACAGAGTTTTTCCTAGTAAGGTTTTAACGAAGC
54414097 ACATTATCTACCAATGGACATCCAATGGGGAGTGTTATGAATATCTTATTAAGTGGATGTCCATC
66 ACATTATCTACCAATGGACATCCAATGGGGAGTGTTATGAATATCTTATTAAGTGGATGTCCATC
54414162 ATGATCAAGATAAAGTTTTAATATACTTTAAACTCTAATTGTTA
131 ATGATCAAGATAAAGTTTTAATATACTTTAAACTCTAATTGTTA
54414206 ATACTCTTTTTCCTTAATTAGGTTTTTATCCCACAGAGTTTTTCCTAGTAAGGTTTTAACGAAGC
1 ATACTCTTTTTCCTTAATTAGGTTTTTATCCCACAGAGTTTTTCCTAGTAAGGTTTTAACGAAGC
54414271 ACATTATCTACCAATGGACATCCAATGGGGAGTGTTATGAATATCTTATTAAGTGGATGTCCATC
66 ACATTATCTACCAATGGACATCCAATGGGGAGTGTTATGAATATCTTATTAAGTGGATGTCCATC
54414336 ATGATCAAGATAAAGTTTTAATATACTTTAAACTCTAATTGTTA
131 ATGATCAAGATAAAGTTTTAATATACTTTAAACTCTAATTGTTA
54414380 TTAGAAATAG
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (174 bp):
ATACTCTTTTTCCTTAATTAGGTTTTTATCCCACAGAGTTTTTCCTAGTAAGGTTTTAACGAAGC
ACATTATCTACCAATGGACATCCAATGGGGAGTGTTATGAATATCTTATTAAGTGGATGTCCATC
ATGATCAAGATAAAGTTTTAATATACTTTAAACTCTAATTGTTA
Found at i:54415348 original size:26 final size:26
Alignment explanation
Indices: 54415319--54415383 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
54415309 TTTTGAGAAA
54415319 TTAAAAAAATTAAAAAT-TAAAATATT
1 TTAAAAAAATTAAAAATATAAAA-ATT
* *
54415345 TT-AAAATATATGAAAATATAAAAATT
1 TTAAAAAAAT-TAAAAATATAAAAATT
54415371 TTAAAAAATATTA
1 TTAAAAAA-ATTA
54415384 TTTTCTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
25 6 0.19
26 13 0.42
27 10 0.32
28 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
TTAAAAAAATTAAAAATATAAAAATT
Found at i:54426702 original size:27 final size:27
Alignment explanation
Indices: 54426671--54426726 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 27
54426661 TTTTTTGATG
54426671 AAATGAGATATTTG-GG-CTAATTTGTGA
1 AAATGAG-T-TTTGAGGACTAATTTGTGA
54426698 AAATGAGTTTTGAAGGACTAATTTGTGA
1 AAATGAGTTTTG-AGGACTAATTTGTGA
54426726 A
1 A
54426727 TTTAACATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 4 0.15
26 1 0.04
27 9 0.35
28 12 0.46
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (27 bp):
AAATGAGTTTTGAGGACTAATTTGTGA
Found at i:54427250 original size:42 final size:43
Alignment explanation
Indices: 54427145--54427301 Score: 142
Period size: 42 Copynumber: 3.7 Consensus size: 43
54427135 TAAATTATCG
* * * *
54427145 TATAAGATCGTGTCTGGGACA-CTGGCATCGAT-TTGAAATTTACG
1 TATAAGACCATGTCTGGGACATC-GGCATCGATACTG-AA-TTACA
* * *
54427189 TGTAAGACCATGTCTGGGACATCGGCATCG-TATCTG-TTTTCA
1 TATAAGACCATGTCTGGGACATCGGCATCGATA-CTGAATTACA
**
54427231 TATAAGACCATGTCTGGGACAGAGGCATCGATACTGAATTACA
1 TATAAGACCATGTCTGGGACATCGGCATCGATACTGAATTACA
* * *
54427274 TGTAAGACCACGTCTGGGACGTCGGCAT
1 TATAAGACCATGTCTGGGACATCGGCAT
54427302 TGTACTTGTC
Statistics
Matches: 91, Mismatches: 17, Indels: 11
0.76 0.14 0.09
Matches are distributed among these distances:
42 33 0.36
43 30 0.33
44 25 0.27
45 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (43 bp):
TATAAGACCATGTCTGGGACATCGGCATCGATACTGAATTACA
Found at i:54428047 original size:207 final size:207
Alignment explanation
Indices: 54427692--54428073 Score: 728
Period size: 207 Copynumber: 1.8 Consensus size: 207
54427682 TTATCATCAC
54427692 ACCATTAAACTCTTTTTGGTACTTTAAAAAATGTACATAATTATGTATGGCATGTATAAGCTAGA
1 ACCATTAAACTCTTTTTGGTACTTTAAAAAATGTACATAATTATGTATGGCATGTATAAGCTAGA
*
54427757 ATGAATTAGTTGATATGTATGTGCAAGTTATGCTATTTGAATTGGCTAGCAAATGATATATTTGT
66 ATGAATTAGTTGATATGTATGTGCAAGTTATGCTATTTGAATTGGCTAGCAAATGATATATTTAT
54427822 GTATTGTTTTGGTGTATGTCTTAAAATGCTATGTTCTAATGTGTTTTTGGTCATATTTGAGAAAT
131 GTATTGTTTTGGTGTATGTCTTAAAATGCTATGTTCTAATGTGTTTTTGGTCATATTTGAGAAAT
54427887 GAATTGGTTGGA
196 GAATTGGTTGGA
**
54427899 ACCATTAAACTCTTTTTGGTACTTTAAAAAATGTACATAATTATGTATGGCATGTATAAGCTTTA
1 ACCATTAAACTCTTTTTGGTACTTTAAAAAATGTACATAATTATGTATGGCATGTATAAGCTAGA
54427964 ATGAATTAGTTGATATGTATGTGCAAGTTATGCTATTTGAATTGGCTAGCAAATGATATATTTAT
66 ATGAATTAGTTGATATGTATGTGCAAGTTATGCTATTTGAATTGGCTAGCAAATGATATATTTAT
*
54428029 GTATTGTTTTGTTGTATGTCTTAAAATGCTATGTTCTAATGTGTT
131 GTATTGTTTTGGTGTATGTCTTAAAATGCTATGTTCTAATGTGTT
54428074 GGTATACTTG
Statistics
Matches: 171, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
207 171 1.00
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (207 bp):
ACCATTAAACTCTTTTTGGTACTTTAAAAAATGTACATAATTATGTATGGCATGTATAAGCTAGA
ATGAATTAGTTGATATGTATGTGCAAGTTATGCTATTTGAATTGGCTAGCAAATGATATATTTAT
GTATTGTTTTGGTGTATGTCTTAAAATGCTATGTTCTAATGTGTTTTTGGTCATATTTGAGAAAT
GAATTGGTTGGA
Found at i:54428709 original size:45 final size:45
Alignment explanation
Indices: 54428645--54428736 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
54428635 TTTAATTCCA
54428645 GATCTTTTTCGGTAACATTAGATACTTTAACCCATTAGGATTTAG
1 GATCTTTTTCGGTAACATTAGATACTTTAACCCATTAGGATTTAG
54428690 GATCTTTTTCGGTAACATTAGATACTTTAACCCATTAGGATTTAG
1 GATCTTTTTCGGTAACATTAGATACTTTAACCCATTAGGATTTAG
54428735 GA
1 GA
54428737 AGCATATGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.39
Consensus pattern (45 bp):
GATCTTTTTCGGTAACATTAGATACTTTAACCCATTAGGATTTAG
Found at i:54430807 original size:42 final size:42
Alignment explanation
Indices: 54430761--54430999 Score: 124
Period size: 42 Copynumber: 5.5 Consensus size: 42
54430751 ACGTTTACTT
* *
54430761 GATGCCATAGT-CCA-ACTATGGTCTTACACGAAGTCTCACATC
1 GATGCCAT-GTCCCAGAC-ATGGTCTTACACGAAATCACACATC
* * *
54430803 GATGCCATTTCCCAGACATGGTCTTATACGAAATCACATATC
1 GATGCCATGTCCCAGACATGGTCTTACACGAAATCACACATC
*** ** * * *
54430845 GATGCCGCATCCCAGACACAGTCTTACACGAAATCTCATACC
1 GATGCCATGTCCCAGACATGGTCTTACACGAAATCACACATC
* * * ** * * *
54430887 AAAGTCATACCCCAGATATAGTCTTACAC-ATAATCCCATATCGATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACGA-AAT--CACA-C-AT--C
* * * ** * *
54430935 GATGCCATATCCCAGATATGGTTTTACACGGGATCTCATATC
1 GATGCCATGTCCCAGACATGGTCTTACACGAAATCACACATC
54430977 GATGCCATGTCCCAGACATGGTC
1 GATGCCATGTCCCAGACATGGTC
54431000 AATTCCATAG
Statistics
Matches: 148, Mismatches: 39, Indels: 20
0.71 0.19 0.10
Matches are distributed among these distances:
41 2 0.01
42 111 0.75
43 2 0.01
44 4 0.03
46 3 0.02
48 26 0.18
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.26
Consensus pattern (42 bp):
GATGCCATGTCCCAGACATGGTCTTACACGAAATCACACATC
Found at i:54432035 original size:18 final size:20
Alignment explanation
Indices: 54432012--54432055 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
54432002 TGCGGGTAGG
54432012 CCGTGTGG-TCA-CACACGC
1 CCGTGTGGCTCAGCACACGC
*
54432030 CCGTGTGGCTCAGGACACGC
1 CCGTGTGGCTCAGCACACGC
54432050 CCGTGT
1 CCGTGT
54432056 CCTCATCCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 3 0.13
20 12 0.52
ACGTcount: A:0.14, C:0.36, G:0.32, T:0.18
Consensus pattern (20 bp):
CCGTGTGGCTCAGCACACGC
Found at i:54433856 original size:40 final size:40
Alignment explanation
Indices: 54433807--54433899 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
54433797 CCACATATAT
* *
54433807 ATATGTAGCCGATGCTATCACAAATTGCACACCAAGTGCC
1 ATATTTAGCCGATGCTATCACAAACTGCACACCAAGTGCC
* ** *
54433847 ATATTTAGCCGAAGCTATTTCAAACTGCACACTAAGTGCC
1 ATATTTAGCCGATGCTATCACAAACTGCACACCAAGTGCC
54433887 AT-TCTTAGCCGAT
1 ATAT-TTAGCCGAT
54433900 ATGTCATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 1 0.02
40 44 0.98
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (40 bp):
ATATTTAGCCGATGCTATCACAAACTGCACACCAAGTGCC
Found at i:54436435 original size:19 final size:19
Alignment explanation
Indices: 54436411--54436461 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
54436401 AAATGAGAAT
*
54436411 CAGAATTAGAATCAGGTGA
1 CAGAATCAGAATCAGGTGA
*
54436430 CAGAATCAGAATTAGGTGA
1 CAGAATCAGAATCAGGTGA
54436449 CAGAATCAGAATC
1 CAGAATCAGAATC
54436462 GATATCAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.20
Consensus pattern (19 bp):
CAGAATCAGAATCAGGTGA
Found at i:54436438 original size:25 final size:25
Alignment explanation
Indices: 54436406--54436534 Score: 128
Period size: 25 Copynumber: 5.4 Consensus size: 25
54436396 AATCAAAATG
54436406 AGAATCAGAATTAGAATCAGGTGAC
1 AGAATCAGAATTAGAATCAGGTGAC
54436431 AGAATCAGAA-T----T-AGGTGAC
1 AGAATCAGAATTAGAATCAGGTGAC
* *
54436450 AGAATCAGAA-TCGATATCAGGTAAC
1 AGAATCAGAATTAGA-ATCAGGTGAC
*
54436475 AGAATCAGAATTAGAATTAGGTGAC
1 AGAATCAGAATTAGAATCAGGTGAC
* * * * *
54436500 AGAATTAGAATCAGTATCAGGTAAT
1 AGAATCAGAATTAGAATCAGGTGAC
54436525 AGAATCAGAA
1 AGAATCAGAA
54436535 CCAGAATGTG
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
19 18 0.21
20 1 0.01
24 2 0.02
25 62 0.72
26 3 0.03
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (25 bp):
AGAATCAGAATTAGAATCAGGTGAC
Found at i:54436491 original size:50 final size:50
Alignment explanation
Indices: 54436430--54436541 Score: 172
Period size: 50 Copynumber: 2.2 Consensus size: 50
54436420 AATCAGGTGA
54436430 CAGAATCAGAATTAGGTGACAGAATCAGAATC-GATATCAGGTAACAGAAT
1 CAGAATCAGAATTAGGTGACAGAATCAGAATCAG-TATCAGGTAACAGAAT
* * *
54436480 CAGAATTAGAATTAGGTGACAGAATTAGAATCAGTATCAGGTAATAGAAT
1 CAGAATCAGAATTAGGTGACAGAATCAGAATCAGTATCAGGTAACAGAAT
*
54436530 CAGAACCAGAAT
1 CAGAATCAGAAT
54436542 GTGAATGCAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 55 0.98
51 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (50 bp):
CAGAATCAGAATTAGGTGACAGAATCAGAATCAGTATCAGGTAACAGAAT
Found at i:54436513 original size:44 final size:44
Alignment explanation
Indices: 54436406--54436534 Score: 125
Period size: 44 Copynumber: 2.8 Consensus size: 44
54436396 AATCAAAATG
* *
54436406 AGAATCAGAATTAGAATCAGGTGACAGAATCAGAATTAGGTGAC
1 AGAATCAGAATTAGAATCAGGTAACAGAATCAGAATTAGATGAC
*
54436450 AGAATCAGAA-TCGATATCAGGTAACAGAATCAGAATTAGAATTAGGTGAC
1 AGAATCAGAATTAGA-ATCAGGTAACAGAATCAGAATTAG----A--TGAC
* * * *
54436500 AGAATTAGAATCAGTATCAGGTAATAGAATCAGAA
1 AGAATCAGAATTAGAATCAGGTAACAGAATCAGAA
54436535 CCAGAATGTG
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
43 3 0.04
44 33 0.48
50 32 0.46
51 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (44 bp):
AGAATCAGAATTAGAATCAGGTAACAGAATCAGAATTAGATGAC
Found at i:54437638 original size:80 final size:80
Alignment explanation
Indices: 54437504--54437651 Score: 242
Period size: 80 Copynumber: 1.9 Consensus size: 80
54437494 GCAAACACAC
* * *
54437504 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCCTAATTGCCTTCGAGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCATAACCCGGACATATCAACTCGCATAATTGCCTTCGAGTCTTAGCCCGGATA
54437569 TATCGTCTCGCATAA
66 TATCGTCTCGCATAA
* * *
54437584 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCATAACCCGGACATATCAACTCGCATAATTGCCTTCGAGTCTTAGCCCGGATA
54437649 TAT
66 TAT
54437652 TCCAATGCTC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 62 1.00
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.31
Consensus pattern (80 bp):
TTGCCTTCGGGTCATAACCCGGACATATCAACTCGCATAATTGCCTTCGAGTCTTAGCCCGGATA
TATCGTCTCGCATAA
Found at i:54437652 original size:40 final size:40
Alignment explanation
Indices: 54437504--54437651 Score: 206
Period size: 40 Copynumber: 3.7 Consensus size: 40
54437494 GCAAACACAC
* * *
54437504 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCCTAA
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
* * **
54437544 TTGCCTTCGAGTCTTAGCCCGGATATATCGTCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
* *
54437584 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
*
54437624 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGACATAT
54437652 TCCAATGCTC
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 93 1.00
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
Found at i:54448525 original size:28 final size:28
Alignment explanation
Indices: 54448492--54448546 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
54448482 TTCGAATGGT
54448492 TTGAATGTTGATGTATGTTGAGAATTTA
1 TTGAATGTTGATGTATGTTGAGAATTTA
54448520 TTGAATGTTGATGTATGTTGAGAATTT
1 TTGAATGTTGATGTATGTTGAGAATTT
54448547 GTGGTCTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.47
Consensus pattern (28 bp):
TTGAATGTTGATGTATGTTGAGAATTTA
Found at i:54453689 original size:35 final size:33
Alignment explanation
Indices: 54453630--54453696 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 33
54453620 ATATATGTAC
*
54453630 AAATAATATATAATATGTACAAATAATTAATAAA
1 AAATAATAGATAATATGTACAAATAA-TAATAAA
54453664 AAATATATAGATAATAATGTA-AAATAATAATAA
1 AAATA-ATAGATAAT-ATGTACAAATAATAATAA
54453697 TTTCTGTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 11 0.37
35 14 0.47
36 5 0.17
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (33 bp):
AAATAATAGATAATATGTACAAATAATAATAAA
Found at i:54457277 original size:26 final size:26
Alignment explanation
Indices: 54457248--54457355 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
54457238 TGGTACAAAT
54457248 TGATAATGGATTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
54457274 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
54457300 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
54457326 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
54457352 TGAT
1 TGAT
54457356 GGGCATTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:54459031 original size:28 final size:26
Alignment explanation
Indices: 54458938--54459049 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
54458928 AGGAAGTGTC
* * *
54458938 CTGGTGGCTATGCCACAAATATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
54458965 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
*
54458992 CTGGTGGCTCTGCCACGATTATTTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGT-T
* *
54459020 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
54459046 CTGG
1 CTGG
54459050 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 6 0.08
27 52 0.69
28 17 0.23
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:54459042 original size:54 final size:54
Alignment explanation
Indices: 54458938--54459049 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
54458928 AGGAAGTGTC
*
54458938 CTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * * * *
54458992 CTGGTGGCTCTGCCACGATTATTTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
54459046 CTGG
1 CTGG
54459050 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:54473436 original size:16 final size:16
Alignment explanation
Indices: 54473412--54473455 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
54473402 GAATGCTCGT
54473412 GAAAAAAAA-AAGAAAA
1 GAAAAAAAATAA-AAAA
*
54473428 GAAATAAAATAAAAAA
1 GAAAAAAAATAAAAAA
54473444 GAAAAAGAAATA
1 GAAAAA-AAATA
54473456 GCATATGTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (16 bp):
GAAAAAAAATAAAAAA
Found at i:54475167 original size:32 final size:34
Alignment explanation
Indices: 54475131--54475195 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
54475121 TAACAGTGGT
*
54475131 ACTGGGCCAGAG-CCCTT-TTCAGATTACAATAA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAATAA
**
54475163 ACTGGGCCTTAGCCCCTTATTCAGATAACAATA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAATA
54475196 TGGCCCATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.36
33 5 0.18
34 13 0.46
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (34 bp):
ACTGGGCCAGAGCCCCTTATTCAGATAACAATAA
Found at i:54477067 original size:26 final size:26
Alignment explanation
Indices: 54477036--54477143 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
54477026 TGAAATGCCC
54477036 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
54477062 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
* *
54477088 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
*
54477114 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
54477140 ATCA
1 ATCA
54477144 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
25 4 0.05
26 69 0.91
27 3 0.04
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:54479251 original size:46 final size:46
Alignment explanation
Indices: 54479201--54479562 Score: 381
Period size: 46 Copynumber: 7.8 Consensus size: 46
54479191 TGATTGAGCA
54479201 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54479247 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
54479292 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54479340 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
54479385 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54479433 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54479478 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54479526 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54479563 GCGGGTTACA
Statistics
Matches: 267, Mismatches: 21, Indels: 56
0.78 0.06 0.16
Matches are distributed among these distances:
42 6 0.02
43 15 0.06
45 11 0.04
46 119 0.45
47 87 0.33
48 9 0.03
50 14 0.05
51 6 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54479357 original size:93 final size:93
Alignment explanation
Indices: 54479198--54479555 Score: 682
Period size: 93 Copynumber: 3.8 Consensus size: 93
54479188 GGATGATTGA
54479198 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
54479263 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
54479291 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
54479356 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
54479384 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
54479449 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
54479477 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-GAACTCGTTGAG
54479541 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
54479556 CTTATGGGCG
Statistics
Matches: 262, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 2 0.01
93 260 0.99
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54482801 original size:15 final size:15
Alignment explanation
Indices: 54482772--54482810 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
54482762 ACTTATTTTA
*
54482772 TTTAATTT-CATTAG
1 TTTAATTTAAATTAG
54482786 TTTAATTTAAATTAG
1 TTTAATTTAAATTAG
54482801 TTTAATTTAA
1 TTTAATTTAA
54482811 TTTCTACTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (15 bp):
TTTAATTTAAATTAG
Found at i:54491314 original size:16 final size:16
Alignment explanation
Indices: 54491293--54491324 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54491283 CCTATTTTCA
54491293 AATTGAATTAATTAAC
1 AATTGAATTAATTAAC
*
54491309 AATTGAATTAGTTAAC
1 AATTGAATTAATTAAC
54491325 CACATGGCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (16 bp):
AATTGAATTAATTAAC
Found at i:54497841 original size:57 final size:57
Alignment explanation
Indices: 54497753--54497862 Score: 134
Period size: 57 Copynumber: 1.9 Consensus size: 57
54497743 TGATATAATA
* *
54497753 CCTCTCGAGCATACATTGTAATTAGGGTTTAGCCTGGACTAGTAATCCTAGTTAAGCT
1 CCTCTCGAGCATACATTGTAATAAGGATTTAGCCTGGACTAGTAATCCT-GTTAAGCT
* * * *
54497811 CCTCT-GAGCATACGTTGT-ATAAAGGATTTAGCTTGGATTGGTAATCCTGTTA
1 CCTCTCGAGCATACATTGTAAT-AAGGATTTAGCCTGGACTAGTAATCCTGTTA
54497863 TACGATATGT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 6 0.13
57 34 0.76
58 5 0.11
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (57 bp):
CCTCTCGAGCATACATTGTAATAAGGATTTAGCCTGGACTAGTAATCCTGTTAAGCT
Found at i:54501761 original size:16 final size:16
Alignment explanation
Indices: 54501740--54501779 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
54501730 TTTGAACCTA
54501740 GTTTGATAATGACATG
1 GTTTGATAATGACATG
54501756 GTTTGATAATGACATG
1 GTTTGATAATGACATG
54501772 GTTTGATA
1 GTTTGATA
54501780 GAGAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.40
Consensus pattern (16 bp):
GTTTGATAATGACATG
Found at i:54508204 original size:31 final size:31
Alignment explanation
Indices: 54508169--54508232 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
54508159 ATATTCAAGA
54508169 ATCTATACTTACCAAAATACCATATGTACAT
1 ATCTATACTTACCAAAATACCATATGTACAT
54508200 ATCTATACTTACCAAAATACCATATGTACAT
1 ATCTATACTTACCAAAATACCATATGTACAT
54508231 AT
1 AT
54508233 AAGCATGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.22, G:0.03, T:0.33
Consensus pattern (31 bp):
ATCTATACTTACCAAAATACCATATGTACAT
Found at i:54509051 original size:25 final size:25
Alignment explanation
Indices: 54508968--54509051 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 25
54508958 GCACTCTCTC
* **
54508968 GAGCCATATAATGAGAAGCTCATGT
1 GAGCCATATAATGGGAAGCTCATAA
* * * * *
54508993 GAGTCATGTAACGGGAAGCTTATCCA
1 GAGCCATATAATGGGAAGCTCAT-AA
*
54509019 G-GCTATATAATGGGAAGCTCATAA
1 GAGCCATATAATGGGAAGCTCATAA
54509043 GAGCCATAT
1 GAGCCATAT
54509052 TCAGGAAGCT
Statistics
Matches: 43, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
24 2 0.05
25 40 0.93
26 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.24
Consensus pattern (25 bp):
GAGCCATATAATGGGAAGCTCATAA
Found at i:54509095 original size:24 final size:25
Alignment explanation
Indices: 54509068--54509226 Score: 85
Period size: 25 Copynumber: 6.4 Consensus size: 25
54509058 AGCTCGTGTA
* *
54509068 AGCCAATAA-CGGGTAGCTCCAAAG
1 AGCCAATAATCAGGAAGCTCCAAAG
** *
54509092 AGCCGTTAATCAGGAAGCTCCAAAT
1 AGCCAATAATCAGGAAGCTCCAAAG
* *
54509117 AGCCAA-ATATCAGGAAG-TTCAAGTG
1 AGCCAATA-ATCAGGAAGCTCCAA-AG
* * * *
54509142 AGCC-AT-ATCTGGAAGTTCTAGAG
1 AGCCAATAATCAGGAAGCTCCAAAG
* *
54509165 AGCCATTAATCAAGAAGCTCACAAAG
1 AGCCAATAATCAGGAAGCTC-CAAAG
** * *
54509191 AGCCTTTAATCGGGAAGCTCACGAAG
1 AGCCAATAATCAGGAAGCTC-CAAAG
54509217 AGCCATATAA
1 AGCCA-ATAA
54509227 CGAGATGCTC
Statistics
Matches: 99, Mismatches: 27, Indels: 15
0.70 0.19 0.11
Matches are distributed among these distances:
23 13 0.13
24 16 0.16
25 38 0.38
26 29 0.29
27 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (25 bp):
AGCCAATAATCAGGAAGCTCCAAAG
Found at i:54509155 original size:23 final size:23
Alignment explanation
Indices: 54509123--54509170 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
54509113 AAATAGCCAA
*
54509123 ATATCAGGAAGTTCAAGTGAGCC
1 ATATCAGGAAGTTCAAGAGAGCC
* *
54509146 ATATCTGGAAGTTCTAGAGAGCC
1 ATATCAGGAAGTTCAAGAGAGCC
54509169 AT
1 AT
54509171 TAATCAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (23 bp):
ATATCAGGAAGTTCAAGAGAGCC
Found at i:54509236 original size:26 final size:26
Alignment explanation
Indices: 54509163--54509237 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
54509153 GAAGTTCTAG
*
54509163 AGAGCCATTAATCAAGAAGCTCACAA
1 AGAGCCATTAATCGAGAAGCTCACAA
* * *
54509189 AGAGCCTTTAATCGGGAAGCTCACGA
1 AGAGCCATTAATCGAGAAGCTCACAA
*
54509215 AGAGCCATATAA-CGAGATGCTCA
1 AGAGCCAT-TAATCGAGAAGCTCA
54509238 TAAGAGCTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 38 0.93
27 3 0.07
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (26 bp):
AGAGCCATTAATCGAGAAGCTCACAA
Found at i:54512069 original size:19 final size:20
Alignment explanation
Indices: 54512045--54512094 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
54512035 CGTGTGACCC
54512045 TTTTTTTCAAAATTTTC-AA
1 TTTTTTTCAAAATTTTCTAA
* *
54512064 TTTTTTCCAAAATTTTCTGA
1 TTTTTTTCAAAATTTTCTAA
*
54512084 TTTGTTTCAAA
1 TTTTTTTCAAA
54512095 TTGATCCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTTTTCAAAATTTTCTAA
Found at i:54514397 original size:13 final size:13
Alignment explanation
Indices: 54514379--54514410 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
54514369 TTGTTAACAT
54514379 TTTAAAATATTTA
1 TTTAAAATATTTA
54514392 TTTAAAATATTTA
1 TTTAAAATATTTA
54514405 TTTAAA
1 TTTAAA
54514411 CTTTTACCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTAAAATATTTA
Done.