Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 175 of 182
Found at i:53208906 original size:20 final size:19
Alignment explanation
Indices: 53208853--53208906 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
53208843 TATTTCTAAT
* * *
53208853 TTTTAATAATTTTTTATAT
1 TTTTATTAATTTTTAATAC
**
53208872 TTTTATTAAAGTTTAATCAC
1 TTTTATTAATTTTTAAT-AC
53208892 TTTTATTAATTTTTA
1 TTTTATTAATTTTTA
53208907 TTTTTCATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTATTAATTTTTAATAC
Found at i:53209154 original size:81 final size:81
Alignment explanation
Indices: 53209066--53209224 Score: 187
Period size: 81 Copynumber: 2.0 Consensus size: 81
53209056 ATTGCTCTCT
* * * *
53209066 TTTTTTTTTGAAAACTTTTGAGGGT-CTTTTTAATGTATTTCGACAGT-TCAAGTACTCAATTGA
1 TTTTTTTTTGAAAA-GTTTGA-GGTCCTTTTTAATGCATTTCGA-AATATCAAGTACCCAATTGA
*
53209129 GTGTAAAAAAAAAGGTTAA
63 GTGCAAAAAAAAAGGTTAA
*** * *
53209148 TTTTTTTTTTTTAAGTTTGAGTTCCTTTTTAATGCATTTTGAAATATCAAGTACCCAATTGAGTG
1 TTTTTTTTTGAAAAGTTTGAGGTCCTTTTTAATGCATTTCGAAATATCAAGTACCCAATTGAGTG
53209213 CAAAAAAAAAGG
66 CAAAAAAAAAGG
53209225 AGTTTAATTG
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
80 4 0.06
81 50 0.77
82 11 0.17
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (81 bp):
TTTTTTTTTGAAAAGTTTGAGGTCCTTTTTAATGCATTTCGAAATATCAAGTACCCAATTGAGTG
CAAAAAAAAAGGTTAA
Found at i:53215015 original size:20 final size:20
Alignment explanation
Indices: 53214979--53215017 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
53214969 ATTTTTTAAA
*
53214979 ATTAAAAAATTTTAAAAATT
1 ATTAAAAAATTTAAAAAATT
53214999 ATTAAAATAA-TTAAAAAAT
1 ATTAAAA-AATTTAAAAAAT
53215018 GTAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTAAAAAATTTAAAAAATT
Found at i:53217540 original size:25 final size:23
Alignment explanation
Indices: 53217512--53217589 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 23
53217502 CATATAAACA
53217512 GGAAGCTCATGCGAGCCATGTAACG
1 GGAAGCTCAT-CGAGCCAT-TAACG
*
53217537 GGAAGCTCCA-CAAAGCCATTAACG
1 GGAAGCT-CATC-GAGCCATTAACG
* *
53217561 GGAAGCTCATAAGAGCCAATAACG
1 GGAAGCTCAT-CGAGCCATTAACG
53217585 GGAAG
1 GGAAG
53217590 GTTCAAGCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
23 2 0.04
24 28 0.62
25 13 0.29
26 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.28, T:0.13
Consensus pattern (23 bp):
GGAAGCTCATCGAGCCATTAACG
Found at i:53217564 original size:24 final size:24
Alignment explanation
Indices: 53217524--53217589 Score: 89
Period size: 24 Copynumber: 2.7 Consensus size: 24
53217514 AAGCTCATGC
53217524 GAGCCATGTAACGGGAAGCTCCACAA
1 GAGCCAT-TAACGGGAAGCT-CACAA
*
53217550 -AGCCATTAACGGGAAGCTCATAA
1 GAGCCATTAACGGGAAGCTCACAA
*
53217573 GAGCCAATAACGGGAAG
1 GAGCCATTAACGGGAAG
53217590 GTTCAAGCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 4 0.11
24 27 0.73
25 6 0.16
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.12
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCACAA
Found at i:53217659 original size:27 final size:27
Alignment explanation
Indices: 53217636--53217697 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
53217626 AAATTAATTA
53217636 GGAAGCTCATGAAAGAGCCTTTAATCG
1 GGAAGCTCATGAAAGAGCCTTTAATCG
53217663 GGAAGCTCATGAAAGAGCCTTTAATCG
1 GGAAGCTCATGAAAGAGCCTTTAATCG
53217690 GGAAGCTC
1 GGAAGCTC
53217698 CGGAGATCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.21
Consensus pattern (27 bp):
GGAAGCTCATGAAAGAGCCTTTAATCG
Found at i:53218202 original size:11 final size:11
Alignment explanation
Indices: 53218186--53218213 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
53218176 TATTCGAATG
53218186 AATTTAACATA
1 AATTTAACATA
53218197 AATTTAACATA
1 AATTTAACATA
53218208 AATTTA
1 AATTTA
53218214 TATTCAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (11 bp):
AATTTAACATA
Found at i:53218405 original size:18 final size:19
Alignment explanation
Indices: 53218378--53218413 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
53218368 CATGTATTTC
53218378 ATAAAATTTA-ATTTTTTT
1 ATAAAATTTACATTTTTTT
*
53218396 ATAAAGTTTACATTTTTT
1 ATAAAATTTACATTTTTT
53218414 CAATTTAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (19 bp):
ATAAAATTTACATTTTTTT
Found at i:53220204 original size:27 final size:27
Alignment explanation
Indices: 53220166--53220219 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
53220156 AATAAAATAT
*
53220166 TGGTCTTGCCTCTGTCAGAGGCGGCAC
1 TGGTCTTGCCTCTGCCAGAGGCGGCAC
53220193 TGGTCTTGCCTCTGCCAGAGGCGGCAC
1 TGGTCTTGCCTCTGCCAGAGGCGGCAC
53220220 CAGTTGGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.11, C:0.31, G:0.33, T:0.24
Consensus pattern (27 bp):
TGGTCTTGCCTCTGCCAGAGGCGGCAC
Found at i:53220885 original size:22 final size:22
Alignment explanation
Indices: 53220844--53220885 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53220834 GATTCAAAAA
* *
53220844 TTTTTTTATTACTTTCAACTAT
1 TTTTTTTACTAATTTCAACTAT
*
53220866 TTTTTTTACTAATTTTAACT
1 TTTTTTTACTAATTTCAACT
53220886 GTTTGTGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTTTTACTAATTTCAACTAT
Found at i:53222034 original size:17 final size:18
Alignment explanation
Indices: 53222002--53222041 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 18
53221992 ATTATGTCAT
53222002 ATTTAATTAATTTTTTATA
1 ATTTAATT-ATTTTTTATA
53222021 ATTTAATT-TTTTTTATA
1 ATTTAATTATTTTTTATA
53222038 ATTT
1 ATTT
53222042 TAATACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.62
19 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTAATTATTTTTTATA
Found at i:53222051 original size:18 final size:17
Alignment explanation
Indices: 53222013--53222051 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
53222003 TTTAATTAAT
**
53222013 TTTTTATAATTTAATTT
1 TTTTTATAATTTAATAC
53222030 TTTTTATAATTTTAATAC
1 TTTTTATAA-TTTAATAC
53222048 TTTT
1 TTTT
53222052 ATTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTATAATTTAATAC
Found at i:53222068 original size:26 final size:27
Alignment explanation
Indices: 53222009--53222070 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
53221999 CATATTTAAT
* *
53222009 TAATTTTTTATAATTTAATTTTTTTTA
1 TAATTTTTAATAATTTAATTTATTTTA
* *
53222036 TAA-TTTTAATACTTTTATTTATTTTA
1 TAATTTTTAATAATTTAATTTATTTTA
53222062 -AATTTTTAA
1 TAATTTTTAA
53222071 AAGTATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 2 0.07
26 25 0.83
27 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (27 bp):
TAATTTTTAATAATTTAATTTATTTTA
Found at i:53222097 original size:17 final size:17
Alignment explanation
Indices: 53222075--53222107 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53222065 TTTTAAAAGT
*
53222075 ATTTTTTAAAATTTTAA
1 ATTTTTTAAAAATTTAA
53222092 ATTTTTTAAAAATTTA
1 ATTTTTTAAAAATTTA
53222108 TTTATTGCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTTTAAAAATTTAA
Found at i:53222111 original size:29 final size:28
Alignment explanation
Indices: 53222056--53222111 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 28
53222046 ACTTTTATTT
53222056 ATTTTAAATTTTTAAAAGTATTTTTTAAA
1 ATTTTAAATTTTTAAAAG-ATTTTTTAAA
53222085 ATTTTAAATTTTTTAAAA-ATTTATTTA
1 ATTTTAAA-TTTTTAAAAGATTT-TTTA
53222112 TTGCCACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 4 0.16
29 12 0.48
30 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
ATTTTAAATTTTTAAAAGATTTTTTAAA
Found at i:53226213 original size:32 final size:31
Alignment explanation
Indices: 53226177--53226239 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 31
53226167 CCAAATGTAA
53226177 GAGCGGTTAGAAAAAATTTAGCAAGATTTGG
1 GAGCGGTTAGAAAAAATTTAGCAAGATTTGG
53226208 NGAGCGGTTAGAAAAAATTTAGCAAGATTTGG
1 -GAGCGGTTAGAAAAAATTTAGCAAGATTTGG
53226240 CGGAAAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.06, G:0.29, T:0.25
Consensus pattern (31 bp):
GAGCGGTTAGAAAAAATTTAGCAAGATTTGG
Found at i:53232600 original size:46 final size:46
Alignment explanation
Indices: 53232523--53232707 Score: 273
Period size: 46 Copynumber: 4.0 Consensus size: 46
53232513 ACAAGGCTAT
53232523 AACTCAGTATGGTTTTCTTCA-CGAAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCG-AAATACCATACCTACTTTTCAC
* *
53232569 AACTCAGTATGGTTTTCTTTACCGAATTACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
** * *
53232615 AACTCAGTATGGTTTTCTTCATTGAAATATCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* * *
53232661 AACTCAGTATGGTTTTCTTCACTGGAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
53232707 A
1 A
53232708 CTTTGCCATG
Statistics
Matches: 125, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
46 123 0.98
47 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
Found at i:53233953 original size:17 final size:17
Alignment explanation
Indices: 53233931--53233979 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
53233921 TAAATTCTTT
53233931 TTAAATCACAAAATTCA
1 TTAAATCACAAAATTCA
53233948 TTAAATCACAAAATTCA
1 TTAAATCACAAAATTCA
* *
53233965 CTAATTCA-AAAATTC
1 TTAAATCACAAAATTC
53233980 TTCTAAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.23
17 23 0.77
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAATCACAAAATTCA
Found at i:53245895 original size:102 final size:102
Alignment explanation
Indices: 53245769--53245972 Score: 277
Period size: 102 Copynumber: 2.0 Consensus size: 102
53245759 TAGGGATAAG
* *
53245769 GTAACTTTTGACCCTGCACTTTTTTTTAGCCACTTTAACCTTTGAA-CTTAAAAACCGTTATTCA
1 GTAACTTTTGACCCTGAACTTTTTTTTAGCCACTTTAACCCTT-AAGCTTAAAAACCGTTATTCA
* *
53245833 TTTAAGCTCATTTGCAATGACTGTGAAAAAAATGGGGA
65 TTTAAGCTCATTTACAATGACTGTGAAAAAAATAGGGA
* * * * *
53245871 GTAACTTTTGACCCCTGAAC-TTTTTTTATCCACTTTGACCCTTAAGCTTGAAAAGCTTTATTCA
1 GTAACTTTTGA-CCCTGAACTTTTTTTTAGCCACTTTAACCCTTAAGCTTAAAAACCGTTATTCA
* *
53245935 TTTAAGCTCATTTATAATGATTGTGAAAAAAATAGGGA
65 TTTAAGCTCATTTACAATGACTGTGAAAAAAATAGGGA
53245973 TAATATAAAT
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
101 2 0.02
102 80 0.90
103 7 0.08
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (102 bp):
GTAACTTTTGACCCTGAACTTTTTTTTAGCCACTTTAACCCTTAAGCTTAAAAACCGTTATTCAT
TTAAGCTCATTTACAATGACTGTGAAAAAAATAGGGA
Found at i:53246515 original size:138 final size:138
Alignment explanation
Indices: 53246360--53246774 Score: 830
Period size: 138 Copynumber: 3.0 Consensus size: 138
53246350 CTTGGCTTTT
53246360 TAGATTTTTATGATTTTTAATAATTAAAAAAAGTAACATTTTAGATTTTTCAAGTTTAGGGATCA
1 TAGATTTTTATGATTTTTAATAATTAAAAAAAGTAACATTTTAGATTTTTCAAGTTTAGGGATCA
53246425 AAATGGACTTAGTTGTCAATTTTAAGTGCCACAATGAATAAAAAATGTACAGGTACTAAAGCGAA
66 AAATGGACTTAGTTGTCAATTTTAAGTGCCACAATGAATAAAAAATGTACAGGTACTAAAGCGAA
53246490 CCTAGTTG
131 CCTAGTTG
53246498 TAGATTTTTATGATTTTTAATAATTAAAAAAAGTAACATTTTAGATTTTTCAAGTTTAGGGATCA
1 TAGATTTTTATGATTTTTAATAATTAAAAAAAGTAACATTTTAGATTTTTCAAGTTTAGGGATCA
53246563 AAATGGACTTAGTTGTCAATTTTAAGTGCCACAATGAATAAAAAATGTACAGGTACTAAAGCGAA
66 AAATGGACTTAGTTGTCAATTTTAAGTGCCACAATGAATAAAAAATGTACAGGTACTAAAGCGAA
53246628 CCTAGTTG
131 CCTAGTTG
53246636 TAGATTTTTATGATTTTTAATAATTAAAAAAAGTAACATTTTAGATTTTTCAAGTTTAGGGATCA
1 TAGATTTTTATGATTTTTAATAATTAAAAAAAGTAACATTTTAGATTTTTCAAGTTTAGGGATCA
53246701 AAATGGACTTAGTTGTCAATTTTAAGTGCCACAATGAATAAAAAATGTACAGGTACTAAAGCGAA
66 AAATGGACTTAGTTGTCAATTTTAAGTGCCACAATGAATAAAAAATGTACAGGTACTAAAGCGAA
53246766 CCTAGTTG
131 CCTAGTTG
53246774 T
1 T
53246775 CAAGTTTAGT
Statistics
Matches: 277, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 277 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (138 bp):
TAGATTTTTATGATTTTTAATAATTAAAAAAAGTAACATTTTAGATTTTTCAAGTTTAGGGATCA
AAATGGACTTAGTTGTCAATTTTAAGTGCCACAATGAATAAAAAATGTACAGGTACTAAAGCGAA
CCTAGTTG
Found at i:53249820 original size:17 final size:16
Alignment explanation
Indices: 53249800--53249864 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 16
53249790 TTTCTCATAA
53249800 AAATAATAAAAAATTAT
1 AAAT-ATAAAAAATTAT
*
53249817 AAATATCAGAAAA-TAT
1 AAATAT-AAAAAATTAT
* *
53249833 CAAAAATATAAAAATGATT
1 -AAATATA-AAAAATTA-T
53249852 AAATATAAAAAAT
1 AAATATAAAAAAT
53249865 ATATGAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 6 0.16
17 24 0.63
18 7 0.18
19 1 0.03
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATATAAAAAATTAT
Found at i:53249843 original size:25 final size:25
Alignment explanation
Indices: 53249799--53249867 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
53249789 TTTTCTCATA
*
53249799 AAAATAATAAAAAATTATAAATATCAG
1 AAAAT-ATAAAAAA-TATAAAAATCAG
* * *
53249826 AAAATATCAAAAATATAAAAATGAT
1 AAAATATAAAAAATATAAAAATCAG
*
53249851 TAAATATAAAAAATATA
1 AAAATATAAAAAATATA
53249868 TGAAAATTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 24 0.67
26 7 0.19
27 5 0.14
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (25 bp):
AAAATATAAAAAATATAAAAATCAG
Found at i:53249868 original size:27 final size:27
Alignment explanation
Indices: 53249800--53249883 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 27
53249790 TTTCTCATAA
* * **
53249800 AAATAATAAAAAAT-TATAAATATCAGA
1 AAAT-ATAAAAAATATATAAAAATGATT
*
53249827 AAATAT-CAAAA-ATATAAAAATGATT
1 AAATATAAAAAATATATAAAAATGATT
*
53249852 AAATATAAAAAATATATGAAAATTGATAT
1 AAATATAAAAAATATAT-AAAAATGAT-T
53249881 AAA
1 AAA
53249884 CTTATAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
25 19 0.42
26 6 0.13
27 8 0.18
28 8 0.18
29 4 0.09
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.27
Consensus pattern (27 bp):
AAATATAAAAAATATATAAAAATGATT
Found at i:53249914 original size:23 final size:24
Alignment explanation
Indices: 53249879--53249928 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
53249869 GAAAATTGAT
*
53249879 ATAAACTTAT-AAATATTATAAAA
1 ATAAACTTATAAAAAATTATAAAA
* * *
53249902 ATAAATTTCTAAAAAATTCTAAAA
1 ATAAACTTATAAAAAATTATAAAA
53249926 ATA
1 ATA
53249929 TATAAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (24 bp):
ATAAACTTATAAAAAATTATAAAA
Found at i:53256608 original size:15 final size:15
Alignment explanation
Indices: 53256588--53256617 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53256578 AATAATTAAA
53256588 GTTACATTTGGTTTC
1 GTTACATTTGGTTTC
53256603 GTTACATTTGGTTTC
1 GTTACATTTGGTTTC
53256618 AAGGAACAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.20, T:0.53
Consensus pattern (15 bp):
GTTACATTTGGTTTC
Found at i:53262036 original size:27 final size:27
Alignment explanation
Indices: 53262006--53262060 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
53261996 TTCCACCCAC
53262006 ACTCTTACCTTCAGAATCTGTGTCATG
1 ACTCTTACCTTCAGAATCTGTGTCATG
*
53262033 ACTCTTTCCTTCAGAATCTGTGTCATG
1 ACTCTTACCTTCAGAATCTGTGTCATG
53262060 A
1 A
53262061 AGCCAGTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (27 bp):
ACTCTTACCTTCAGAATCTGTGTCATG
Found at i:53265889 original size:3 final size:3
Alignment explanation
Indices: 53265881--53265912 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53265871 TATCAAAATG
53265881 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53265913 AAAATTAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:53273146 original size:11 final size:12
Alignment explanation
Indices: 53273132--53273169 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
53273122 ACAAAGCGAA
53273132 GAAAAAGAAA-T
1 GAAAAAGAAATT
*
53273143 GAAAAAAAAATT
1 GAAAAAGAAATT
*
53273155 GAAAAAGAACTT
1 GAAAAAGAAATT
53273167 GAA
1 GAA
53273170 TAGAAGAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.68, C:0.03, G:0.16, T:0.13
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:53274067 original size:88 final size:88
Alignment explanation
Indices: 53273918--53274093 Score: 334
Period size: 88 Copynumber: 2.0 Consensus size: 88
53273908 TTACTTACAT
**
53273918 GCGGGTGTTGCAGGTAATTAGAGCAAAGGACTTGAACCTGGTCATGCAGGAACCTGATATAACCC
1 GCGGGTGTTGCAGGTAAGGAGAGCAAAGGACTTGAACCTGGTCATGCAGGAACCTGATATAACCC
53273983 ATTGCTTCATGGAGTACTGATGC
66 ATTGCTTCATGGAGTACTGATGC
53274006 GCGGGTGTTGCAGGTAAGGAGAGCAAAGGACTTGAACCTGGTCATGCAGGAACCTGATATAACCC
1 GCGGGTGTTGCAGGTAAGGAGAGCAAAGGACTTGAACCTGGTCATGCAGGAACCTGATATAACCC
53274071 ATTGCTTCATGGAGTACTGATGC
66 ATTGCTTCATGGAGTACTGATGC
53274094 CGTATCTGTC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (88 bp):
GCGGGTGTTGCAGGTAAGGAGAGCAAAGGACTTGAACCTGGTCATGCAGGAACCTGATATAACCC
ATTGCTTCATGGAGTACTGATGC
Found at i:53276321 original size:24 final size:23
Alignment explanation
Indices: 53276260--53276326 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
53276250 GATGAAATCG
53276260 AGGGTGGAGATGAAAATGAAGACA
1 AGGGTGGAGATGAAAATG-AGACA
** *
53276284 ATTGTAGAGATGAAAATGAGTACA
1 AGGGTGGAGATGAAAATGAG-ACA
* *
53276308 AGGGTGGAGGTGAAGATGA
1 AGGGTGGAGATGAAAATGA
53276327 AGAAGATGAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
23 2 0.06
24 32 0.94
ACGTcount: A:0.42, C:0.03, G:0.37, T:0.18
Consensus pattern (23 bp):
AGGGTGGAGATGAAAATGAGACA
Found at i:53277470 original size:31 final size:31
Alignment explanation
Indices: 53277427--53277495 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
53277417 AAACCCTAAA
* *
53277427 AACCC-AACCCTAACAAAAATGAAAAACCCT
1 AACCCTAACCCTAACAAAAATAAAAAACCAT
*
53277457 AACTCTAACCCTAACAAAAATAAAAAACCAT
1 AACCCTAACCCTAACAAAAATAAAAAACCAT
53277488 AACCCTAA
1 AACCCTAA
53277496 TTGAGAGTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.55, C:0.30, G:0.01, T:0.13
Consensus pattern (31 bp):
AACCCTAACCCTAACAAAAATAAAAAACCAT
Found at i:53278433 original size:103 final size:103
Alignment explanation
Indices: 53278249--53278454 Score: 403
Period size: 103 Copynumber: 2.0 Consensus size: 103
53278239 CCAGTCTAAT
53278249 TGGGACAAATGACCTCATTTGAACACGATGGATCACACAAGCTCATCATGGTTGCGGGATCCCAT
1 TGGGACAAATGACCTCATTTGAACACGATGGATCACACAAGCTCATCATGGTTGCGGGATCCCAT
53278314 GACATTATCCATCACTTGTTCTAGCGACGACCTCGTCA
66 GACATTATCCATCACTTGTTCTAGCGACGACCTCGTCA
*
53278352 TGGGCCAAATGACCTCATTTGAACACGATGGATCACACAAGCTCATCATGGTTGCGGGATCCCAT
1 TGGGACAAATGACCTCATTTGAACACGATGGATCACACAAGCTCATCATGGTTGCGGGATCCCAT
53278417 GACATTATCCATCACTTGTTCTAGCGACGACCTCGTCA
66 GACATTATCCATCACTTGTTCTAGCGACGACCTCGTCA
53278455 CGTCCTCCTC
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (103 bp):
TGGGACAAATGACCTCATTTGAACACGATGGATCACACAAGCTCATCATGGTTGCGGGATCCCAT
GACATTATCCATCACTTGTTCTAGCGACGACCTCGTCA
Found at i:53287680 original size:29 final size:28
Alignment explanation
Indices: 53287636--53287726 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
53287626 ATAATTTTGC
* * *
53287636 ATAAATTAAATTAAATTAATATTTCATGT
1 ATAAATTAAATAAAATCAA-AATTCATGT
*
53287665 ATAAATTATATAAAATCAAAATTCATGT
1 ATAAATTAAATAAAATCAAAATTCATGT
** *
53287693 ATAACATTACACATTGAACCAAAATTCATGT
1 ATAA-ATTA-A-ATAAAATCAAAATTCATGT
53287724 ATA
1 ATA
53287727 GATGAAATCT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 12 0.24
29 20 0.39
31 19 0.37
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.36
Consensus pattern (28 bp):
ATAAATTAAATAAAATCAAAATTCATGT
Found at i:53288924 original size:90 final size:89
Alignment explanation
Indices: 53288795--53288978 Score: 235
Period size: 90 Copynumber: 2.1 Consensus size: 89
53288785 AATTTTTTAT
* * * * *
53288795 AAAAAAGCAATTAAGCCCCTCCTTTTTTTTTCACTCAATTA-AGTATTTGAACTTTTAAAATGCA
1 AAAAAAGCAATTAAGCCCCTCCTTTTCTTTCCACTCAATTAGA-TACTTGAACTTTCAAAATGAA
* * *
53288859 CCAAAAAGGCCCTTAAACTTCTTCA
65 CCAAAAAGACCCTCAAAATTCTTCA
*
53288884 AAAAAAGCAATTAAGCCCCTACCTTTTCTTTCCACTCAATTGGATACTTGAACTTTCAAAATGAA
1 AAAAAAGCAATTAAGCCCCT-CCTTTTCTTTCCACTCAATTAGATACTTGAACTTTCAAAATGAA
** *
53288949 TTAAAAAGACCCTCAAAATTTTTCA
65 CCAAAAAGACCCTCAAAATTCTTCA
53288974 AAAAA
1 AAAAA
53288979 GACCCTCAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
89 20 0.25
90 60 0.74
91 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.32
Consensus pattern (89 bp):
AAAAAAGCAATTAAGCCCCTCCTTTTCTTTCCACTCAATTAGATACTTGAACTTTCAAAATGAAC
CAAAAAGACCCTCAAAATTCTTCA
Found at i:53288967 original size:22 final size:22
Alignment explanation
Indices: 53288939--53288990 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
53288929 ACTTGAACTT
53288939 TCAAAATGAATT-AAAAAGACCC
1 TCAAAAT-AATTAAAAAAGACCC
**
53288961 TCAAAATTTTTCAAAAAAGACCC
1 TCAAAATAATT-AAAAAAGACCC
53288984 TCAAAAT
1 TCAAAAT
53288991 TTTTCAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.08
22 7 0.27
23 17 0.65
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (22 bp):
TCAAAATAATTAAAAAAGACCC
Found at i:53288993 original size:22 final size:23
Alignment explanation
Indices: 53288951--53289001 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
53288941 AAAATGAATT
53288951 AAAAAGACCCTCAAAATTTTTCA
1 AAAAAGACCCTCAAAATTTTTCA
53288974 AAAAAGACCCTCAAAATTTTTCA
1 AAAAAGACCCTCAAAATTTTTCA
53288997 AAAAA
1 AAAAA
53289002 TCAATAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.24
Consensus pattern (23 bp):
AAAAAGACCCTCAAAATTTTTCA
Found at i:53289171 original size:18 final size:17
Alignment explanation
Indices: 53289146--53289184 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
53289136 ATTTTGCAAC
53289146 TTTTTATTTTTT-TACAT
1 TTTTTATTTTTTCTA-AT
53289163 TTTTCTATTTTTTCTAAT
1 TTTT-TATTTTTTCTAAT
53289181 TTTT
1 TTTT
53289185 AATATTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 14 0.70
19 2 0.10
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTATTTTTTCTAAT
Found at i:53292389 original size:8 final size:8
Alignment explanation
Indices: 53292376--53292404 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
53292366 AACATTTAAA
53292376 AAATTATT
1 AAATTATT
53292384 AAATTATT
1 AAATTATT
53292392 AAATTATT
1 AAATTATT
53292400 AAATT
1 AAATT
53292405 TTATTACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AAATTATT
Found at i:53297371 original size:14 final size:14
Alignment explanation
Indices: 53297326--53297372 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
53297316 GATATTACTG
53297326 CACTTCGATGGCTT
1 CACTTCGATGGCTT
*
53297340 CACTTTCAGA-GG-TG
1 CAC-TTC-GATGGCTT
53297354 CACTTCGATGGCTT
1 CACTTCGATGGCTT
53297368 CACTT
1 CACTT
53297373 TGCTCGTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
12 2 0.07
13 5 0.19
14 13 0.48
15 5 0.19
16 2 0.07
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (14 bp):
CACTTCGATGGCTT
Found at i:53299515 original size:11 final size:11
Alignment explanation
Indices: 53299501--53299532 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
53299491 TATGTTTGAC
53299501 ATAATAGTTTT
1 ATAATAGTTTT
53299512 ATAATAG-TTT
1 ATAATAGTTTT
53299522 ATAATAGTTTT
1 ATAATAGTTTT
53299533 CTTTTGCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (11 bp):
ATAATAGTTTT
Found at i:53300058 original size:28 final size:27
Alignment explanation
Indices: 53300013--53300065 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
53300003 CAAATGCCTA
*
53300013 TTTTTGTAATTATTTTATTTTCTATACC
1 TTTTTGTAATTATATTATTTT-TATACC
53300041 TTTTTCGTAATTA-ATTATTTTTATA
1 TTTTT-GTAATTATATTATTTTTATA
53300066 TTATTTGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 12 0.52
29 7 0.30
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.64
Consensus pattern (27 bp):
TTTTTGTAATTATATTATTTTTATACC
Found at i:53302317 original size:28 final size:27
Alignment explanation
Indices: 53302234--53302318 Score: 66
Period size: 28 Copynumber: 3.0 Consensus size: 27
53302224 TATTAAGTTA
*
53302234 TTTAAATATGATTTATTATTATATTTTAAAT
1 TTTAAATA--ATTTATTAAT-TA-TTTAAAT
* *
53302265 TTTAAATTATTTCATGT-A-TAATTAAAT
1 TTTAAATAATTT-AT-TAATTATTTAAAT
53302292 TTATAAATAATTTATTAATTATTTAAA
1 TT-TAAATAATTTATTAATTATTTAAA
53302319 ATGTATATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
26 1 0.02
27 11 0.25
28 18 0.41
29 4 0.09
30 2 0.05
31 8 0.18
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTAAATAATTTATTAATTATTTAAAT
Found at i:53327129 original size:16 final size:16
Alignment explanation
Indices: 53327108--53327141 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
53327098 AACTTAAAAG
53327108 TTAAAACTAATTGTTA
1 TTAAAACTAATTGTTA
*
53327124 TTAAAATTAATTGTTA
1 TTAAAACTAATTGTTA
53327140 TT
1 TT
53327142 GAATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
TTAAAACTAATTGTTA
Found at i:53332365 original size:30 final size:29
Alignment explanation
Indices: 53332303--53332365 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
53332293 TCTAATATGT
* * *
53332303 AATTTTATACGTAAACTTTGATTTTGTAC
1 AATTTTATACATAAAATTTGATTTTATAC
*
53332332 AATTTTATACATGAAAATTTGATTTTATCC
1 AATTTTATACAT-AAAATTTGATTTTATAC
53332362 AATT
1 AATT
53332366 CTCACAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.48
Consensus pattern (29 bp):
AATTTTATACATAAAATTTGATTTTATAC
Found at i:53332803 original size:21 final size:21
Alignment explanation
Indices: 53332777--53332843 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
53332767 GATGCCTAGG
*
53332777 GAAAGATAGAAGAGGAGAGGA
1 GAAAGATAGAAGAGGTGAGGA
* **
53332798 GAAAGAGAGTTGAGAGTGTANGG-
1 GAAAGATAGAAGAG-GTG-A-GGA
53332821 GAAAGATAGAAGAGGTGAGGA
1 GAAAGATAGAAGAGGTGAGGA
53332842 GA
1 GA
53332844 GAGAGTTGAG
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
20 2 0.06
21 14 0.40
22 5 0.14
23 12 0.34
24 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.43, T:0.10
Consensus pattern (21 bp):
GAAAGATAGAAGAGGTGAGGA
Found at i:53332825 original size:44 final size:41
Alignment explanation
Indices: 53332773--53332859 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 41
53332763 TTTGGATGCC
53332773 TAGGGAAAGATAGAAGAGGAGAGGAGAAAGAGAGTTGAGAGTG
1 TAGGGAAAGATAGAAGAGGAGAGGAG--AGAGAGTTGAGAGTG
*
53332816 TANGGGAAAGATAGAAGAGGTGAGGAGAGAGAGTTGAGAGTG
1 TA-GGGAAAGATAGAAGAGGAGAGGAGAGAGAGTTGAGAGTG
53332858 TA
1 TA
53332860 AGAGGAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 17 0.40
43 2 0.05
44 23 0.55
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.14
Consensus pattern (41 bp):
TAGGGAAAGATAGAAGAGGAGAGGAGAGAGAGTTGAGAGTG
Found at i:53333817 original size:124 final size:126
Alignment explanation
Indices: 53333633--53333881 Score: 394
Period size: 124 Copynumber: 2.0 Consensus size: 126
53333623 AGGGTTTTTA
* * *
53333633 GGTCTTGGAAGAAATAATTTTGAGTTGACGTTTCTGATCAAATAGTATAAAATCGTTTCTAGCAG
1 GGTCATGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAG
* *
53333698 GATGCTATTTGAGAAGAATTTTTG-AAATCGCGCCCTCGTGGACGTGCTTTTGCTACAGTC
66 GATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTC
* ** *
53333758 GGTCATGGAAGAAATACTTTT-TTTTGACGTTTCTGAGCAAATAGTATAAAATTGCTTCTAGCAG
1 GGTCATGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAG
*
53333822 GATGCTATTTGAGAAGAATTTGTGAAAATCGCGCTCTCGTGGACGCGCTTTTGCTACAGT
66 GATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
53333882 AGCATGTTTA
Statistics
Matches: 113, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
124 61 0.54
125 52 0.46
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (126 bp):
GGTCATGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAG
GATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTC
Found at i:53335597 original size:11 final size:11
Alignment explanation
Indices: 53335581--53335609 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
53335571 AAAAAGGGAG
53335581 TTAAGAGGAAC
1 TTAAGAGGAAC
53335592 TTAAGAGGAAC
1 TTAAGAGGAAC
53335603 TTAAGAG
1 TTAAGAG
53335610 AATTTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.07, G:0.28, T:0.21
Consensus pattern (11 bp):
TTAAGAGGAAC
Found at i:53340082 original size:16 final size:15
Alignment explanation
Indices: 53340052--53340086 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
53340042 TTCTATTGTT
53340052 TATATTTTTTATAGA
1 TATATTTTTTATAGA
*
53340067 TATATTTTTATCTAGA
1 TATATTTTT-TATAGA
53340083 TATA
1 TATA
53340087 CAAGATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (15 bp):
TATATTTTTTATAGA
Found at i:53341606 original size:23 final size:23
Alignment explanation
Indices: 53341571--53341692 Score: 154
Period size: 23 Copynumber: 5.3 Consensus size: 23
53341561 AGTGTTATTG
*
53341571 ATCAATGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTTGGCTACAT
* *
53341594 TTCAGTGGTAGCTATGGCTACAT
1 ATCAGTGGTAGCTTTGGCTACAT
53341617 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTTGGCTACAT
* ** * *
53341640 TTCAGTGGTAGCTACGTCTACGT
1 ATCAGTGGTAGCTTTGGCTACAT
* *
53341663 ATCAGTAGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTTGGCTACAT
53341686 ATCAGTG
1 ATCAGTG
53341693 TGGCACTTAT
Statistics
Matches: 83, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (23 bp):
ATCAGTGGTAGCTTTGGCTACAT
Found at i:53341628 original size:46 final size:46
Alignment explanation
Indices: 53341571--53341692 Score: 181
Period size: 46 Copynumber: 2.7 Consensus size: 46
53341561 AGTGTTATTG
* *
53341571 ATCAATGGTAGCTTTGGCTACATTTCAGTGGTAGCTATGGCTACAT
1 ATCAGTGGTAGCTTTGGCTACATTTCAGTGGTAGCTACGGCTACAT
* *
53341617 ATCAGTGGTAGCTTTGGCTACATTTCAGTGGTAGCTACGTCTACGT
1 ATCAGTGGTAGCTTTGGCTACATTTCAGTGGTAGCTACGGCTACAT
* * *
53341663 ATCAGTAGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTTGGCTACATTTCAGTG
53341693 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (46 bp):
ATCAGTGGTAGCTTTGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:53343453 original size:46 final size:46
Alignment explanation
Indices: 53343355--53343533 Score: 310
Period size: 46 Copynumber: 4.0 Consensus size: 46
53343345 TACGTATGAT
* * *
53343355 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTCGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
53343398 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
53343444 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
53343490 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
53343534 TGATCAGATA
Statistics
Matches: 130, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
43 10 0.08
44 5 0.04
45 19 0.15
46 96 0.74
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:53343541 original size:25 final size:25
Alignment explanation
Indices: 53343507--53343558 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
53343497 CACTTTGTCA
53343507 CTTGATCAGATAAGTGTAGCTAAAG
1 CTTGATCAGATAAGTGTAGCTAAAG
53343532 CTTGATCAGATAAGTGTAGCTAAAG
1 CTTGATCAGATAAGTGTAGCTAAAG
53343557 CT
1 CT
53343559 ATCACTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (25 bp):
CTTGATCAGATAAGTGTAGCTAAAG
Found at i:53343565 original size:71 final size:71
Alignment explanation
Indices: 53343461--53343604 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 71
53343451 CACTTTGTCA
53343461 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
53343526 CTAAAG
66 CTAAAG
*
53343532 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
53343597 CTAAAG
66 CTAAAG
53343603 CT
1 CT
53343605 ACCAATTATC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (71 bp):
CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
CTAAAG
Found at i:53343599 original size:46 final size:46
Alignment explanation
Indices: 53343532--53343676 Score: 256
Period size: 46 Copynumber: 3.2 Consensus size: 46
53343522 GTAGCTAAAG
*
53343532 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCA
1 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCA
* *
53343578 CTTGATCAGATAAGTGTAGCTAAAGCTACCAATTATCACTTTGTCT
1 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCA
53343624 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCA
1 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCA
53343670 C-TGATCA
1 CTTGATCA
53343677 TAAGTATTCA
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 6 0.06
46 88 0.94
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (46 bp):
CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCA
Found at i:53343621 original size:117 final size:117
Alignment explanation
Indices: 53343415--53343650 Score: 445
Period size: 117 Copynumber: 2.0 Consensus size: 117
53343405 CACTTTGTCA
53343415 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
*
53343480 CTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAG
66 CTAAAGCTACCAATTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAG
*
53343532 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
*
53343597 CTAAAGCTACCAATTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAG
66 CTAAAGCTACCAATTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAG
53343649 CT
1 CT
53343651 ACCACTTATC
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 116 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (117 bp):
CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
CTAAAGCTACCAATTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAG
Found at i:53343641 original size:163 final size:161
Alignment explanation
Indices: 53343372--53343676 Score: 547
Period size: 163 Copynumber: 1.9 Consensus size: 161
53343362 CACTTGTCCC
* *
53343372 TGATCAGATAAGTGTCGCTAGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTA
1 TGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTA
*
53343437 AAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTT
66 AAGCTACCAATTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTT
53343502 TGTCACTTGATCAGATAAGTGTAGCTAAAGCT
131 TGTCAC-TGATCAGATAAGTGTAGCTAAAGCT
*
53343534 TGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT
1 TGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT
*
53343599 AAAGCTACCAATTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACT
65 AAAGCTACCAATTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACT
53343664 TTGTCACTGATCA
130 TTGTCACTGATCA
53343677 TAAGTATTCA
Statistics
Matches: 137, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
162 24 0.18
163 113 0.82
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (161 bp):
TGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTA
AAGCTACCAATTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTT
TGTCACTGATCAGATAAGTGTAGCTAAAGCT
Found at i:53356069 original size:17 final size:17
Alignment explanation
Indices: 53356047--53356082 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
53356037 TCTTAAATTG
53356047 AAGCAAAATTAACAATA
1 AAGCAAAATTAACAATA
53356064 AAGCAAAATTAACAATA
1 AAGCAAAATTAACAATA
53356081 AA
1 AA
53356083 ACAAGAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.11, G:0.06, T:0.17
Consensus pattern (17 bp):
AAGCAAAATTAACAATA
Found at i:53358267 original size:30 final size:30
Alignment explanation
Indices: 53358221--53358287 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
53358211 CGTTTAAGAA
* *
53358221 CTTGAGAAGACCCAATAT-CTTGTTCAGGAT
1 CTTGGGAAGACCCAATATGC-CGTTCAGGAT
*
53358251 CTTGGGAAGACTCAATATGCCGTTCAGGAT
1 CTTGGGAAGACCCAATATGCCGTTCAGGAT
*
53358281 TTTGGGA
1 CTTGGGA
53358288 TTAAGAAGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (30 bp):
CTTGGGAAGACCCAATATGCCGTTCAGGAT
Found at i:53358331 original size:66 final size:66
Alignment explanation
Indices: 53358225--53358386 Score: 182
Period size: 66 Copynumber: 2.5 Consensus size: 66
53358215 TAAGAACTTG
** * * * ** *
53358225 AGAAGACCCAATATCTTGTTCAGGATCTTGGGAAGACTCAATA-TGCCGTTCAGGATTTTGGGAT
1 AGAAGACCTGATATCTCGTTCAGGAGCTTGAGAAGACTCAATATTG-CGTTCAGGAGCTTAGGAT
53358289 TA
65 TA
* **
53358291 AGAAGACTTGATATCTCGTTCAGGAGCTTGAGAAGACTCAATATTGCGTTTTGGAGCTTAGGATT
1 AGAAGACCTGATATCTCGTTCAGGAGCTTGAGAAGACTCAATATTGCGTTCAGGAGCTTAGGATT
53358356 A
66 A
* * *
53358357 AGAAGGCCTGATATCTCATTCAGAAGCTTG
1 AGAAGACCTGATATCTCGTTCAGGAGCTTG
53358387 GAAAGATCTA
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
66 78 0.98
67 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (66 bp):
AGAAGACCTGATATCTCGTTCAGGAGCTTGAGAAGACTCAATATTGCGTTCAGGAGCTTAGGATT
A
Found at i:53361133 original size:19 final size:19
Alignment explanation
Indices: 53361096--53361134 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53361086 TTTTGCTACA
*
53361096 TAGACTAAATCGTAAAAAC
1 TAGACTAAATCGAAAAAAC
53361115 TAGACTAAATC-AAATAAAC
1 TAGACTAAATCGAAA-AAAC
53361134 T
1 T
53361135 TCAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (19 bp):
TAGACTAAATCGAAAAAAC
Found at i:53371164 original size:20 final size:22
Alignment explanation
Indices: 53371116--53371165 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
53371106 AAATAAAATT
*
53371116 ACGTAACAAATATATTTATAAA
1 ACGTAAAAAATATATTTATAAA
**
53371138 AATTAAAAAATA-ATTT-TAAA
1 ACGTAAAAAATATATTTATAAA
53371158 ACGTAAAA
1 ACGTAAAA
53371166 GGTTAGACTC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 10 0.43
21 4 0.17
22 9 0.39
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (22 bp):
ACGTAAAAAATATATTTATAAA
Found at i:53373224 original size:16 final size:16
Alignment explanation
Indices: 53373203--53373254 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
53373193 CGGCCAAATT
53373203 TTTATTTAAAGGTAAA
1 TTTATTTAAAGGTAAA
***
53373219 TTTATTT-TTTGT-AA
1 TTTATTTAAAGGTAAA
53373233 -TTATTTAAAGGTAAA
1 TTTATTTAAAGGTAAA
53373248 TTTATTT
1 TTTATTT
53373255 TTAGTTTTGG
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 6 0.22
14 4 0.15
15 4 0.15
16 13 0.48
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.56
Consensus pattern (16 bp):
TTTATTTAAAGGTAAA
Found at i:53374252 original size:12 final size:12
Alignment explanation
Indices: 53374235--53374262 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53374225 CATGTTTGAT
53374235 TTGAAATACAAC
1 TTGAAATACAAC
53374247 TTGAAATACAAC
1 TTGAAATACAAC
53374259 TTGA
1 TTGA
53374263 TATTCACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (12 bp):
TTGAAATACAAC
Found at i:53374572 original size:22 final size:24
Alignment explanation
Indices: 53374541--53374585 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
53374531 TTATAGTAAA
53374541 TTAATGTTTT-A-AAACTTTTGAC
1 TTAATGTTTTAACAAACTTTTGAC
*
53374563 TTAATTTTTTAACAAACTTTTGA
1 TTAATGTTTTAACAAACTTTTGA
53374586 TTTTTTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
24 10 0.50
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (24 bp):
TTAATGTTTTAACAAACTTTTGAC
Found at i:53385002 original size:26 final size:23
Alignment explanation
Indices: 53384968--53385022 Score: 58
Period size: 26 Copynumber: 2.3 Consensus size: 23
53384958 GATCAAAAGA
53384968 TGTCAACCAATATGATAAGTTACAAT
1 TGTCAACCAA-ATG-TAAGTTA-AAT
* *
53384994 TGTCTACCAAATGTACGTTAAAT
1 TGTCAACCAAATGTAAGTTAAAT
53385017 TG-CAAC
1 TGTCAAC
53385023 TGGAGTTGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 3 0.12
23 5 0.19
24 6 0.23
25 3 0.12
26 9 0.35
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (23 bp):
TGTCAACCAAATGTAAGTTAAAT
Found at i:53392296 original size:15 final size:15
Alignment explanation
Indices: 53392278--53392430 Score: 62
Period size: 15 Copynumber: 10.3 Consensus size: 15
53392268 AAGCCAAAGG
53392278 AGCTGGTGGTGGGGT
1 AGCTGGTGGTGGGGT
* * *
53392293 AGCTGGAGGAGGAGT
1 AGCTGGTGGTGGGGT
* * *
53392308 AGCAGGAGG-GGGAGA
1 AGCTGGTGGTGGG-GT
*
53392323 AGCAGGTGGTGGGGT
1 AGCTGGTGGTGGGGT
* * *
53392338 AGCCT-GCGGTGGAGA
1 AG-CTGGTGGTGGGGT
*
53392353 AGCCGGTGG-GGGAGT
1 AGCTGGTGGTGGG-GT
* * *
53392368 TGCGGGAGGTGGGGT
1 AGCTGGTGGTGGGGT
* * *
53392383 AGCTGGGGGAGGAGT
1 AGCTGGTGGTGGGGT
* * * *
53392398 AGCCGGTGGAGGAGA
1 AGCTGGTGGTGGGGT
53392413 AGCTGGTGGTGGGG-
1 AGCTGGTGGTGGGGT
53392427 AGCT
1 AGCT
53392431 AACGGGCGGG
Statistics
Matches: 102, Mismatches: 30, Indels: 13
0.70 0.21 0.09
Matches are distributed among these distances:
14 9 0.09
15 86 0.84
16 7 0.07
ACGTcount: A:0.18, C:0.10, G:0.58, T:0.15
Consensus pattern (15 bp):
AGCTGGTGGTGGGGT
Found at i:53392364 original size:45 final size:45
Alignment explanation
Indices: 53392282--53392430 Score: 167
Period size: 45 Copynumber: 3.3 Consensus size: 45
53392272 CAAAGGAGCT
* *
53392282 GGTGGTGGGGTAGCTGGAGGAGGAGTAGCAGGAGGGGGAGAAGCA
1 GGTGGTGGGGTAGCTGGAGGAGGAGTAGCCGGTGGGGGAGAAGCA
* * * ** *
53392327 GGTGGTGGGGTAGCCT-GCGGTGGAGAAGCCGGTGGGGGAGTTGCG
1 GGTGGTGGGGTAG-CTGGAGGAGGAGTAGCCGGTGGGGGAGAAGCA
* * * *
53392372 GGAGGTGGGGTAGCTGGGGGAGGAGTAGCCGGTGGAGGAGAAGCT
1 GGTGGTGGGGTAGCTGGAGGAGGAGTAGCCGGTGGGGGAGAAGCA
53392417 GGTGGTGGGG-AGCT
1 GGTGGTGGGGTAGCT
53392431 AACGGGCGGG
Statistics
Matches: 85, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
44 6 0.07
45 77 0.91
46 2 0.02
ACGTcount: A:0.17, C:0.09, G:0.58, T:0.15
Consensus pattern (45 bp):
GGTGGTGGGGTAGCTGGAGGAGGAGTAGCCGGTGGGGGAGAAGCA
Found at i:53392417 original size:30 final size:30
Alignment explanation
Indices: 53392293--53392418 Score: 92
Period size: 30 Copynumber: 4.2 Consensus size: 30
53392283 GTGGTGGGGT
* * *
53392293 AGCTGGAGGAGGAGTAGCAGGAGGGGGAGA
1 AGCTGGGGGAGGAGTAGCCGGAGGTGGAGA
* * * * * *
53392323 AGCAGGTGGTGGGGTAGCCTGCGGTGGAGA
1 AGCTGGGGGAGGAGTAGCCGGAGGTGGAGA
* * * * *
53392353 AGCCGGTGGG-GGAGTTGCGGGAGGTGGGGT
1 AGCTGG-GGGAGGAGTAGCCGGAGGTGGAGA
* *
53392383 AGCTGGGGGAGGAGTAGCCGGTGGAGGAGA
1 AGCTGGGGGAGGAGTAGCCGGAGGTGGAGA
53392413 AGCTGG
1 AGCTGG
53392419 TGGTGGGGAG
Statistics
Matches: 70, Mismatches: 24, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
29 3 0.04
30 65 0.93
31 2 0.03
ACGTcount: A:0.20, C:0.10, G:0.57, T:0.13
Consensus pattern (30 bp):
AGCTGGGGGAGGAGTAGCCGGAGGTGGAGA
Found at i:53393830 original size:22 final size:22
Alignment explanation
Indices: 53393782--53393833 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
53393772 ATATCCAAAC
* *
53393782 AATAACAGCAAAATAGTAGTAA
1 AATAACAGCAAAATAGCAGCAA
* * *
53393804 TATAATAGCAAAATGGCAGCAA
1 AATAACAGCAAAATAGCAGCAA
53393826 AATAACAG
1 AATAACAG
53393834 TAGAAAAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (22 bp):
AATAACAGCAAAATAGCAGCAA
Found at i:53408600 original size:28 final size:28
Alignment explanation
Indices: 53408569--53408622 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
53408559 GCTCTTTCAA
* *
53408569 CATTGTTATTTAATATAAATATGATTTT
1 CATTATTATTTAATACAAATATGATTTT
53408597 CATTATTATTTAATACAAATATGATT
1 CATTATTATTTAATACAAATATGATT
53408623 ATAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (28 bp):
CATTATTATTTAATACAAATATGATTTT
Found at i:53417972 original size:12 final size:12
Alignment explanation
Indices: 53417955--53417981 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53417945 TTTGTTTACC
53417955 TTAAGTTACATT
1 TTAAGTTACATT
53417967 TTAAGTTACATT
1 TTAAGTTACATT
53417979 TTA
1 TTA
53417982 GTCACTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (12 bp):
TTAAGTTACATT
Found at i:53418233 original size:20 final size:20
Alignment explanation
Indices: 53418195--53418233 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53418185 CCATTCTCTT
* *
53418195 CTCCTTCTCCCTTTGTTTTC
1 CTCCTTCTCCATTTCTTTTC
53418215 CTCCTTCTCCATTTCTTTT
1 CTCCTTCTCCATTTCTTTT
53418234 AACATAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.38, G:0.03, T:0.56
Consensus pattern (20 bp):
CTCCTTCTCCATTTCTTTTC
Found at i:53421721 original size:18 final size:18
Alignment explanation
Indices: 53421700--53421739 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
53421690 TGTAGAGGCT
* *
53421700 AAATATTAATAACTAATA
1 AAATATTAAGAAATAATA
*
53421718 AAATATTACGAAATAATA
1 AAATATTAAGAAATAATA
53421736 AAAT
1 AAAT
53421740 TGATATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (18 bp):
AAATATTAAGAAATAATA
Found at i:53422347 original size:16 final size:16
Alignment explanation
Indices: 53422289--53422353 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
53422279 CTTTGCTAGG
*
53422289 TAGAATGGAAAGAAAAC
1 TAGAAT-GATAGAAAAC
* *
53422306 TAGAAAGAT-GAAAAA
1 TAGAATGATAGAAAAC
* *
53422321 TTGAAGGGATAGAAAAC
1 TAGAA-TGATAGAAAAC
53422338 TAGAATGATAGAAAAC
1 TAGAATGATAGAAAAC
53422354 ATATACTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
15 9 0.24
16 15 0.39
17 14 0.37
ACGTcount: A:0.57, C:0.05, G:0.23, T:0.15
Consensus pattern (16 bp):
TAGAATGATAGAAAAC
Found at i:53429811 original size:13 final size:13
Alignment explanation
Indices: 53429793--53429817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53429783 GAGATATTGG
53429793 ATAAATTAACTCC
1 ATAAATTAACTCC
53429806 ATAAATTAACTC
1 ATAAATTAACTC
53429818 ACATGCAGTC
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:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAATTAACTCC
Found at i:53432118 original size:16 final size:16
Alignment explanation
Indices: 53432086--53432129 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
53432076 GCTAATATTA
53432086 AATTTTAGGTTTAAGGT
1 AATTTTA-GTTTAAGGT
*
53432103 AATTTTAGTTTCAGGT
1 AATTTTAGTTTAAGGT
*
53432119 TATTTTGAGTT
1 AATTTT-AGTT
53432130 GAAGTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.25, C:0.02, G:0.20, T:0.52
Consensus pattern (16 bp):
AATTTTAGTTTAAGGT
Found at i:53437904 original size:16 final size:16
Alignment explanation
Indices: 53437885--53437915 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53437875 TAATTAAGAT
*
53437885 CATAAATTCATTCATC
1 CATAAATTCAATCATC
53437901 CATAAATTCAATCAT
1 CATAAATTCAATCAT
53437916 TCTAATCCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (16 bp):
CATAAATTCAATCATC
Found at i:53438497 original size:15 final size:15
Alignment explanation
Indices: 53438474--53438507 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
53438464 AAACGTATTT
*
53438474 TAAATTATTAAAAAA
1 TAAAATATTAAAAAA
*
53438489 TAAAATATTAAGAAA
1 TAAAATATTAAAAAA
53438504 TAAA
1 TAAA
53438508 TAAACTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (15 bp):
TAAAATATTAAAAAA
Found at i:53439184 original size:18 final size:18
Alignment explanation
Indices: 53439148--53439185 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
53439138 ATATTGAAAT
*
53439148 TATGCTTAGTTAAATAAA
1 TATGCTTAGCTAAATAAA
53439166 TATGCTTAGACTAAA-AAA
1 TATGCTTAG-CTAAATAAA
53439184 TA
1 TA
53439186 AAGCTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (18 bp):
TATGCTTAGCTAAATAAA
Found at i:53441799 original size:46 final size:44
Alignment explanation
Indices: 53441695--53441802 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
53441685 TGTCTTTGAC
** * * *
53441695 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
53441739 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
53441785 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
53441803 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:53447677 original size:18 final size:17
Alignment explanation
Indices: 53447656--53447717 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 17
53447646 TTTTATGATT
53447656 TTTTTATAATTTCTTAAA
1 TTTTTATAATTT-TTAAA
* *
53447674 TTTTGAGT-TTTGTTTAATA
1 TTTTTA-TAATT-TTTAA-A
53447693 TTTTTATAATTTTTAAA
1 TTTTTATAATTTTTAAA
53447710 TTATTTAT
1 TT-TTTAT
53447718 TGACGAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 3 0.09
18 22 0.63
19 10 0.29
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65
Consensus pattern (17 bp):
TTTTTATAATTTTTAAA
Found at i:53449161 original size:6 final size:6
Alignment explanation
Indices: 53449150--53449180 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
53449140 GACTTCGAGG
53449150 AGCCCC AGCCCC AGCCCC AGCCCC AGCCCC A
1 AGCCCC AGCCCC AGCCCC AGCCCC AGCCCC A
53449181 ACCAGTGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.65, G:0.16, T:0.00
Consensus pattern (6 bp):
AGCCCC
Found at i:53449862 original size:20 final size:20
Alignment explanation
Indices: 53449814--53449865 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
53449804 TTTTCTAATT
*
53449814 TATGCATTTTTATAATTCTTG
1 TATG-ATTTTTATAATTCTTA
* * *
53449835 TATAATTTTTATACTTTTTA
1 TATGATTTTTATAATTCTTA
53449855 TATGATTTTTA
1 TATGATTTTTA
53449866 ATAAAAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.62
Consensus pattern (20 bp):
TATGATTTTTATAATTCTTA
Found at i:53454212 original size:30 final size:30
Alignment explanation
Indices: 53454169--53454292 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
53454159 TCCATATTTA
* * *
53454169 TGGAAAATCAAAGATATGTGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
53454199 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
53454229 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
53454259 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
53454290 TGG
1 TGG
53454293 CATAATAAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 79 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:53454224 original size:15 final size:15
Alignment explanation
Indices: 53454175--53454282 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
53454165 TTTATGGAAA
*
53454175 ATCAAAGATATGTGT
1 ATCAAAGATATGGGT
* * **
53454190 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
53454204 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
53454220 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
53454234 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
53454250 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
53454264 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
53454280 ATC
1 ATC
53454283 GAGATATTGG
Statistics
Matches: 66, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
14 11 0.17
15 43 0.65
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.27
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:53458886 original size:15 final size:15
Alignment explanation
Indices: 53458866--53458973 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
53458856 TCTATGGAAA
*
53458866 ATCAAAGATATGGGT
1 ATCAAATATATGGGT
* **
53458881 ATCAAATA-ATAGAA
1 ATCAAATATATGGGT
53458895 AGTCAAATATATGGGT
1 A-TCAAATATATGGGT
**
53458911 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
*
53458925 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
**
53458941 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
*
53458955 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
53458971 ATC
1 ATC
53458974 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 12 0.17
15 45 0.65
16 12 0.17
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.27
Consensus pattern (15 bp):
ATCAAATATATGGGT
Found at i:53458907 original size:30 final size:30
Alignment explanation
Indices: 53458860--53458983 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
53458850 TCCATATCTA
* *
53458860 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
* *
53458890 TAGAAAGTCAAATATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
53458920 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
53458950 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
53458981 TGG
1 TGG
53458984 CATAATAAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 78 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:53470627 original size:19 final size:19
Alignment explanation
Indices: 53470605--53470647 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
53470595 GTCAATTCAA
*
53470605 TTTAACATGAAGAATTTTT
1 TTTAACATGAAGAATATTT
* *
53470624 TTTAATATTAAGAATATTT
1 TTTAACATGAAGAATATTT
53470643 TTTAA
1 TTTAA
53470648 ATTTTATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (19 bp):
TTTAACATGAAGAATATTT
Found at i:53475504 original size:21 final size:21
Alignment explanation
Indices: 53475452--53475508 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
53475442 TATTTATTAA
*
53475452 ATATAATTAGAATATATAAACT
1 ATATAATTA-AATATTTAAACT
53475474 ATAT--TTAAATATTTAAA-T
1 ATATAATTAAATATTTAAACT
53475492 ATAATAATTAAATATTT
1 AT-ATAATTAAATATTT
53475509 GTAATTAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.10
19 11 0.35
20 3 0.10
21 10 0.32
22 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATAATTAAATATTTAAACT
Found at i:53475880 original size:12 final size:12
Alignment explanation
Indices: 53475842--53475874 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
53475832 TTGATTCAGT
53475842 GTCATCATCACC
1 GTCATCATCACC
53475854 GTCATCATCACC
1 GTCATCATCACC
53475866 GTCATCATC
1 GTCATCATC
53475875 GTCGTCGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.39, G:0.09, T:0.27
Consensus pattern (12 bp):
GTCATCATCACC
Found at i:53476619 original size:43 final size:43
Alignment explanation
Indices: 53476555--53476704 Score: 174
Period size: 43 Copynumber: 3.5 Consensus size: 43
53476545 AGAATAGNCA
* * ** *
53476555 CTTCTATCACAAACGCCGCTAAAGATTATGATGTTTAGCGACG
1 CTTCTACCACAAACGCCGCTAAAGATCATGACCTTTAGCGAAG
*
53476598 CTTCTACCACAAACGCTGCTAAAGATCATGACCTTTAGCGAAG
1 CTTCTACCACAAACGCCGCTAAAGATCATGACCTTTAGCGAAG
* * * * * **
53476641 CTTATACCAAAAATGCCGCTAAAGACCATGACCTTTAACGGTG
1 CTTCTACCACAAACGCCGCTAAAGATCATGACCTTTAGCGAAG
*
53476684 CTTCTACCACAAACGTCGCTA
1 CTTCTACCACAAACGCCGCTA
53476705 TAAAGAATGA
Statistics
Matches: 89, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 89 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (43 bp):
CTTCTACCACAAACGCCGCTAAAGATCATGACCTTTAGCGAAG
Found at i:53476774 original size:14 final size:15
Alignment explanation
Indices: 53476745--53476777 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
53476735 CAAACACCGC
53476745 TAAAAAATATGAATTT
1 TAAAAAATAT-AATTT
53476761 TAAAAAATAT-ATTT
1 TAAAAAATATAATTT
53476775 TAA
1 TAA
53476778 TTAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
16 10 0.59
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
TAAAAAATATAATTT
Found at i:53482737 original size:14 final size:14
Alignment explanation
Indices: 53482718--53482749 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
53482708 TTCAACATGC
53482718 TTACTATAAAAGTT
1 TTACTATAAAAGTT
53482732 TTACTATAAAAGTT
1 TTACTATAAAAGTT
53482746 TTAC
1 TTAC
53482750 AGATTTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (14 bp):
TTACTATAAAAGTT
Found at i:53487075 original size:14 final size:14
Alignment explanation
Indices: 53487056--53487089 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
53487046 ACCCTTGAAT
53487056 CCCTAAC-TCTTAAC
1 CCCTAACGTC-TAAC
53487070 CCCTAACGTCTAAC
1 CCCTAACGTCTAAC
53487084 CCCTAA
1 CCCTAA
53487090 ACCCCTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.29, C:0.44, G:0.03, T:0.24
Consensus pattern (14 bp):
CCCTAACGTCTAAC
Found at i:53487102 original size:15 final size:15
Alignment explanation
Indices: 53487066--53487107 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
53487056 CCCTAACTCT
**
53487066 TAACCCCT-AACGTC
1 TAACCCCTAAACCCC
53487080 TAACCCCTAAACCCC
1 TAACCCCTAAACCCC
*
53487095 TAATCCCTAAACC
1 TAACCCCTAAACC
53487108 TTAAATCCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.33, C:0.45, G:0.02, T:0.19
Consensus pattern (15 bp):
TAACCCCTAAACCCC
Found at i:53487104 original size:22 final size:21
Alignment explanation
Indices: 53487053--53487120 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
53487043 TCGACCCTTG
* *
53487053 AATCCCTAACTCTTAACCCCT
1 AATCCCTAACCCTAAACCCCT
*
53487074 AA-CGTCTAACCCCTAAACCCCT
1 AATC-CCTAA-CCCTAAACCCCT
* *
53487096 AATCCCTAAACCTTAAATCCCT
1 AATCCCT-AACCCTAAACCCCT
53487118 AAT
1 AAT
53487121 TCGTAATCTC
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.03
21 6 0.16
22 27 0.73
23 3 0.08
ACGTcount: A:0.34, C:0.40, G:0.01, T:0.25
Consensus pattern (21 bp):
AATCCCTAACCCTAAACCCCT
Found at i:53487411 original size:44 final size:43
Alignment explanation
Indices: 53487319--53487414 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 43
53487309 GCCCCTAAAT
* *
53487319 CCCTAAACCTTAAATTCTTAACTCCCAACCCCTAACGTCTAAC
1 CCCTAAACCTTAAATTCCTAACTCCCAACCCCTAACGTCCAAC
* *
53487362 TCCTAAACCTCTAAATTCCTAAC-CCCAACACCTTAAAC-TCCAAC
1 CCCTAAACCT-TAAATTCCTAACTCCCAAC-CCCT-AACGTCCAAC
53487406 CCCTAAACC
1 CCCTAAACC
53487415 ATAATCTCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
43 15 0.33
44 27 0.60
45 3 0.07
ACGTcount: A:0.34, C:0.42, G:0.01, T:0.23
Consensus pattern (43 bp):
CCCTAAACCTTAAATTCCTAACTCCCAACCCCTAACGTCCAAC
Found at i:53487453 original size:15 final size:15
Alignment explanation
Indices: 53487406--53487455 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
53487396 AAACTCCAAC
53487406 CCCTAAA-CCATAAT
1 CCCTAAATCCATAAT
*
53487420 CTCT-AATCCATAAT
1 CCCTAAATCCATAAT
* *
53487434 TCCTAAATCCATACT
1 CCCTAAATCCATAAT
53487449 CCCTAAA
1 CCCTAAA
53487456 CCTTAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 2 0.07
14 12 0.41
15 15 0.52
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (15 bp):
CCCTAAATCCATAAT
Found at i:53487884 original size:40 final size:40
Alignment explanation
Indices: 53487814--53487889 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
53487804 AGCCGCGCTT
* * *
53487814 TTTTAAAAACGCCGCTAAAGCCCCCTAGCATTAACGACGC
1 TTTTAAAAACGCCGCTAAAGACACCGAGCATTAACGACGC
*
53487854 TTTTAAAAAGCTCCGCTAAA-ACACCGAGCATTAACG
1 TTTTAAAAA-CGCCGCTAAAGACACCGAGCATTAACG
53487890 GTGCATTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 22 0.71
41 9 0.29
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (40 bp):
TTTTAAAAACGCCGCTAAAGACACCGAGCATTAACGACGC
Found at i:53488446 original size:72 final size:71
Alignment explanation
Indices: 53488325--53488563 Score: 365
Period size: 72 Copynumber: 3.3 Consensus size: 71
53488315 AAAATCATAT
*
53488325 ATAAACAACTATTGACAAAACTA-ATTCAGT-ATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTAGATT-A-TAATAAATAAGTAGAACATAAATTCAATATCCAAA
*
53488388 GACCAAAC
64 AACCAAAC
*
53488396 ATAAACAACTATTAATAAAACTAGATTATACATAAATAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTATA-ATAAATAAGTAGAACATAAATTCAATATCCAAAA
53488461 ACCAAAC
65 ACCAAAC
* * *
53488468 ATAAACGACCATTGATAAAACTAGATTACATATAAATAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTATA-ATAAATAAGTAGAACATAAATTCAATATCCAAAA
53488533 ACCAAAC
65 ACCAAAC
*
53488540 ATAAATAACTATTGATAAAACTAG
1 ATAAACAACTATTGATAAAACTAG
53488564 TTTAGCATTG
Statistics
Matches: 154, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
70 1 0.01
71 22 0.14
72 131 0.85
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.23
Consensus pattern (71 bp):
ATAAACAACTATTGATAAAACTAGATTATAATAAATAAGTAGAACATAAATTCAATATCCAAAAA
CCAAAC
Found at i:53493615 original size:5 final size:5
Alignment explanation
Indices: 53493595--53493650 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
53493585 AAAGAATGTT
* *
53493595 AAAA- AAAAG -AAA- AAAAG AAAAA AAATAG AAAGAA AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA-AG AAA-AG AAAAG AAAAG AAAAG
53493644 AAAAG AA
1 AAAAG AA
53493651 GAAGGAGAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
4 10 0.23
5 25 0.58
6 8 0.19
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:53493648 original size:22 final size:20
Alignment explanation
Indices: 53493595--53493650 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 20
53493585 AAAGAATGTT
53493595 AAAAAAAAGAAAAAAAGAAAA
1 AAAAAAAAG-AAAAAAGAAAA
53493616 AAAATAGAAAGAAAAAAGAAAA
1 AAAA-A-AAAGAAAAAAGAAAA
53493638 GAAAAGAAAAGAA
1 -AAAA-AAAAGAA
53493651 GAAGGAGAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 4 0.13
22 18 0.58
23 9 0.29
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAGAAAA
Found at i:53494133 original size:107 final size:107
Alignment explanation
Indices: 53493916--53494136 Score: 302
Period size: 108 Copynumber: 2.1 Consensus size: 107
53493906 GGGGCACCTA
* * *
53493916 TTTTCATCTTATTCATTTCGTATCTTAGAAAAATTTGCTATCTTGATTATTTATTTATTTCGAGC
1 TTTTCATCTTATTCATTTCGAATCTTAGAAAAATTTGCTATCCTGATTATTTATTTATTTAGAGC
**
53493981 TTTGTTCTCAATAAAATTCCATCTTATCCATTGTGATAATCC
66 TTTACTCTCAATAAAATTCCATCTTATCCATTGTGATAATCC
* * * *
53494023 TTTTCATCTTATTCATTTTGAATCTTAGCAAAATTTTCTATCCTGATTAATTTATTTGTTTAGAG
1 TTTTCATCTTATTCATTTCGAATCTTAGAAAAATTTGCTATCCTGATT-ATTTATTTATTTAGAG
* *
53494088 -TTCTACTCTCAATAAAATTTCATCTT-TCCCATTGTGATAATCT
65 CTT-TACTCTCAATAAAATTCCATCTTAT-CCATTGTGATAATCC
53494131 TTTTCA
1 TTTTCA
53494137 AGCATTTTCC
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
107 46 0.46
108 54 0.54
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (107 bp):
TTTTCATCTTATTCATTTCGAATCTTAGAAAAATTTGCTATCCTGATTATTTATTTATTTAGAGC
TTTACTCTCAATAAAATTCCATCTTATCCATTGTGATAATCC
Found at i:53495225 original size:89 final size:88
Alignment explanation
Indices: 53495005--53495256 Score: 317
Period size: 88 Copynumber: 2.9 Consensus size: 88
53494995 CAGAGGAATG
* * *
53495005 GACTAAAAGCAGCAGATCTCGTCTTTCTGTA-TCGACAACGAAGTAGATCGAAAACACAAGCCTA
1 GACTAAAAGCAGCAGATCTCGTCTTCCTGTACT-GACAGCGAAGCAGATCGAAAACACAAGCCTA
53495069 ACCTCCCTGAGTTTGCAGCAAACA
65 ACCTCCCTGAGTTTGCAGCAAACA
* * * *
53495093 AACTAAAAGCAGCAGATCTCGTCTTCTTGTACTGACAGCGAAGCAGATTGAAGACACAAGCCTAA
1 GACTAAAAGCAGCAGATCTCGTCTTCCTGTACTGACAGCGAAGCAGATCGAAAACACAAGCCTAA
** * *
53495158 CCTTTCTGAGTTTGCAGCGGAGCA
66 CCTCCCTGAGTTTGCAGC-AAACA
* * * * * *
53495182 GACTAAAAGCAACAGATCTCGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAAGCACTAGCCTTA
1 GACTAAAAGCAGCAGATCTCGTCTTCCTGTACTGACAGCGAAGCAGATCGAAAACACAAGCCTAA
*
53495247 TCTCCCTGAG
66 CCTCCCTGAG
53495257 CAGTAGCAAG
Statistics
Matches: 138, Mismatches: 24, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
88 72 0.52
89 66 0.48
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (88 bp):
GACTAAAAGCAGCAGATCTCGTCTTCCTGTACTGACAGCGAAGCAGATCGAAAACACAAGCCTAA
CCTCCCTGAGTTTGCAGCAAACA
Found at i:53495768 original size:44 final size:44
Alignment explanation
Indices: 53495709--53495816 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 44
53495699 ACAAACCCTG
* *
53495709 TCTCTCTGAAGTTGCAGTAGAGTAGGTTGAAATAACAAACATTA
1 TCTCTCTAAAGTTGCAGTAGAGCAGGTTGAAATAACAAACATTA
* * * *
53495753 TCTCTCTAAAATTGCAGTAGAGCAGGTTGAAGTTACTAACATTA
1 TCTCTCTAAAGTTGCAGTAGAGCAGGTTGAAATAACAAACATTA
* * *
53495797 TCCCCCTAAAGTTCCAGTAG
1 TCTCTCTAAAGTTGCAGTAG
53495817 GGCAAGTCGA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (44 bp):
TCTCTCTAAAGTTGCAGTAGAGCAGGTTGAAATAACAAACATTA
Found at i:53497348 original size:151 final size:150
Alignment explanation
Indices: 53497099--53497399 Score: 568
Period size: 151 Copynumber: 2.0 Consensus size: 150
53497089 AAAGCCATCA
*
53497099 CCAAGTCAATGTATTTTTTTTACTATAGACATATTAGAAAATAAAAAAAAACAAAACTTCAAAGG
1 CCAAGTCAATGTATTTTTTTTACTACAGACATATTAGAAAATAAAAAAAAACAAAACTTCAAAGG
53497164 TGATTTTCGGTTGTTATTTCTATTTATTTTGTTCTTGAGTTTTTTTTGTTTATTTATTTTTATTT
66 TGATTTTCGGTTGTTATTTCTATTTATTTTGTTCTTGAGTTTTTTTTGTTTATTTATTTTTATTT
53497229 CTACCTACAAAGATAAAAAG
131 CTACCTACAAAGATAAAAAG
53497249 CCAAGTCAATGTA-TTTTTTTACTACAGACATATTAGAAAATAAAAAAAAAAACAAAACTTCAAA
1 CCAAGTCAATGTATTTTTTTTACTACAGACATATTAGAAAAT--AAAAAAAAACAAAACTTCAAA
53497313 GGTGATTTTCGGTTGTTATTTCTATTTATTTTGTTCTTGAGTTTTTTTTGTTTATTTATTTTTAT
64 GGTGATTTTCGGTTGTTATTTCTATTTATTTTGTTCTTGAGTTTTTTTTGTTTATTTATTTTTAT
53497378 TTCTACCTACAAAGATAAAAAG
129 TTCTACCTACAAAGATAAAAAG
53497400 GAAAAATAAA
Statistics
Matches: 148, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
149 27 0.18
150 13 0.09
151 108 0.73
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.45
Consensus pattern (150 bp):
CCAAGTCAATGTATTTTTTTTACTACAGACATATTAGAAAATAAAAAAAAACAAAACTTCAAAGG
TGATTTTCGGTTGTTATTTCTATTTATTTTGTTCTTGAGTTTTTTTTGTTTATTTATTTTTATTT
CTACCTACAAAGATAAAAAG
Found at i:53498860 original size:18 final size:17
Alignment explanation
Indices: 53498835--53498868 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
53498825 CGTTTCCATC
53498835 AAATTGAACATCATTTG
1 AAATTGAACATCATTTG
53498852 AAATGTGAACATCATTT
1 AAAT-TGAACATCATTT
53498869 CTAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
AAATTGAACATCATTTG
Found at i:53501757 original size:23 final size:24
Alignment explanation
Indices: 53501716--53501777 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
53501706 ACTCTAAAAT
53501716 AGTATTTAATC-AGTAAAATAATC-
1 AGTATTTAATCTA-TAAAATAATCA
* *
53501739 AGTATTTAATCTATTAAATATTCA
1 AGTATTTAATCTATAAAATAATCA
* *
53501763 AATATTTAGTCTATA
1 AGTATTTAATCTATA
53501778 TTTCTTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 19 0.59
24 13 0.41
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (24 bp):
AGTATTTAATCTATAAAATAATCA
Found at i:53510061 original size:40 final size:39
Alignment explanation
Indices: 53509974--53510061 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 39
53509964 AGATCCAATT
* *
53509974 AAAAAAAATCAAGATCAAAATCAAAAACAAAAAGAAGAG
1 AAAAAAAATCAAAATCAAAATCAAAAACAAAAAGAAAAG
* **
53510013 AAAGAAAAATCAAAATCAAAGTCAAAGTCAAAATA-AAAATG
1 AAA-AAAAATCAAAATCAAAATCAAAAACAAAA-AGAAAA-G
53510054 AAAAAAAA
1 AAAAAAAA
53510062 GAGAAGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
39 3 0.07
40 33 0.80
41 5 0.12
ACGTcount: A:0.72, C:0.09, G:0.09, T:0.10
Consensus pattern (39 bp):
AAAAAAAATCAAAATCAAAATCAAAAACAAAAAGAAAAG
Found at i:53510953 original size:7 final size:7
Alignment explanation
Indices: 53510941--53510993 Score: 65
Period size: 7 Copynumber: 7.4 Consensus size: 7
53510931 AAATATATAT
53510941 ATGAAAA
1 ATGAAAA
53510948 ATGAAAAA
1 ATG-AAAA
53510956 ATG-AAA
1 ATGAAAA
53510962 ATGAAAA
1 ATGAAAA
53510969 ATGAAAAA
1 ATG-AAAA
53510977 ATGAAAA
1 ATGAAAA
53510984 A-GTAAAA
1 ATG-AAAA
53510991 ATG
1 ATG
53510994 GAGAGGCTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
6 7 0.17
7 19 0.46
8 15 0.37
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:53510957 original size:8 final size:8
Alignment explanation
Indices: 53510944--53510984 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
53510934 TATATATATG
53510944 AAAAATGA
1 AAAAATGA
53510952 AAAAATG-
1 AAAAATGA
53510959 -AAAATG-
1 AAAAATGA
53510965 AAAAATGA
1 AAAAATGA
53510973 AAAAATGA
1 AAAAATGA
53510981 AAAA
1 AAAA
53510985 GTAAAAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.19
7 6 0.19
8 19 0.61
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAATGA
Found at i:53510962 original size:14 final size:13
Alignment explanation
Indices: 53510945--53510975 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
53510935 ATATATATGA
53510945 AAAATGAAAAAATG
1 AAAATG-AAAAATG
53510959 AAAATGAAAAATG
1 AAAATGAAAAATG
53510972 AAAA
1 AAAA
53510976 AATGAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:53510965 original size:21 final size:21
Alignment explanation
Indices: 53510941--53510993 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
53510931 AAATATATAT
53510941 ATGAAAAATGAAAAAATGAAA
1 ATGAAAAATGAAAAAATGAAA
53510962 ATGAAAAATGAAAAAATGAAA
1 ATGAAAAATGAAAAAATGAAA
*
53510983 AAGTAAAAATG
1 ATG-AAAAATG
53510994 GAGAGGCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (21 bp):
ATGAAAAATGAAAAAATGAAA
Found at i:53512363 original size:50 final size:50
Alignment explanation
Indices: 53512298--53512553 Score: 169
Period size: 50 Copynumber: 5.1 Consensus size: 50
53512288 TCCCAGGTGA
* * * *
53512298 TGCAGTGGAACAGATTAAAGCCACATCGATGAATCTTGCTTCCCCGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACGACGAATCTTGCTTCCCCGACAT
* * * * *
53512348 TACAGTTAAAAAGATTAAAGCTACAAC-AGCGAATCTTAC-TCCCCAGGCGA-
1 TGCAGTGAAAAAGATTAAAGCCACAACGA-CGAATCTTGCTTCCCC-GAC-AT
* * * ** ***
53512398 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTTTGCGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACGACGAATCTTGCTTCCCCGACAT
* * * * * * **
53512448 TGCAGTTAAAAAGATAAAAGCTACAACCG-CGAATCTTACTTCCCTGGCGG
1 TGCAGTGAAAAAGATTAAAGCCACAA-CGACGAATCTTGCTTCCCCGACAT
* * ** * *
53512498 TACAGTGGAGTAGATTAAAGCCACAACGGCGAATCTTGTTTCCCCGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACGACGAATCTTGCTTCCCCGACAT
53512548 TGCAGT
1 TGCAGT
53512554 CAGACAGAAG
Statistics
Matches: 147, Mismatches: 51, Indels: 16
0.69 0.24 0.07
Matches are distributed among these distances:
49 9 0.06
50 133 0.90
51 5 0.03
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (50 bp):
TGCAGTGAAAAAGATTAAAGCCACAACGACGAATCTTGCTTCCCCGACAT
Found at i:53512456 original size:100 final size:100
Alignment explanation
Indices: 53512283--53512553 Score: 382
Period size: 100 Copynumber: 2.7 Consensus size: 100
53512273 AATATCAGTT
* * *
53512283 TTACTTCCCAGGTGATGCAGTGGAACAGATTAAAGCCACATCGATGAATCTTGCTTCCCCGACAT
1 TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTTCCCGACAT
* *
53512348 TACAGTTAAAAAGATTAAAGCTACAACAGCGAATC
66 TGCAGTTAAAAAGATAAAAGCTACAACAGCGAATC
* **
53512383 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTTTGCGACAT
1 TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTTCCCGACAT
*
53512448 TGCAGTTAAAAAGATAAAAGCTACAACCGCGAATC
66 TGCAGTTAAAAAGATAAAAGCTACAACAGCGAATC
* * * ** * *
53512483 TTACTTCCCTGGCGGTACAGTGGAGTAGATTAAAGCCACAACGGCGAATCTTG-TTTCCCCGACA
1 TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTT-CCCGACA
53512547 TTGCAGT
65 TTGCAGT
53512554 CAGACAGAAG
Statistics
Matches: 151, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
99 3 0.02
100 148 0.98
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (100 bp):
TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTTCCCGACAT
TGCAGTTAAAAAGATAAAAGCTACAACAGCGAATC
Found at i:53514019 original size:17 final size:17
Alignment explanation
Indices: 53513997--53514038 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
53513987 TATTCAGTAA
53513997 TATTATTAATCTATTAT
1 TATTATTAATCTATTAT
* *
53514014 TATTATCAATTTATTAT
1 TATTATTAATCTATTAT
53514031 TATTATTA
1 TATTATTA
53514039 TCACCGTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATTAATCTATTAT
Found at i:53530278 original size:24 final size:24
Alignment explanation
Indices: 53530250--53530301 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
53530240 TTACTAAGTC
*
53530250 AAATAAACTATGCTAATAAATACT
1 AAATAAACTATACTAATAAATACT
* *
53530274 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
53530298 AAAT
1 AAAT
53530302 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:53530495 original size:14 final size:14
Alignment explanation
Indices: 53530476--53530506 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
53530466 CAAAATACAA
53530476 TATCATCCACATTT
1 TATCATCCACATTT
53530490 TATCATCCACATTT
1 TATCATCCACATTT
53530504 TAT
1 TAT
53530507 TATATATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (14 bp):
TATCATCCACATTT
Found at i:53536514 original size:36 final size:35
Alignment explanation
Indices: 53536474--53536546 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 35
53536464 AAGCATGAGA
53536474 ATTTTTTTAAAAAAAACACGAGAA-TTTTGAAACACG
1 ATTTTTTT-AAAAAAACACGA-AAGTTTTGAAACACG
*
53536510 ATTTTTTTAAAAAAACACGAAAGTTTTTGAATCACG
1 ATTTTTTTAAAAAAACACGAAAG-TTTTGAAACACG
53536546 A
1 A
53536547 GAATTTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
34 2 0.06
35 12 0.35
36 20 0.59
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (35 bp):
ATTTTTTTAAAAAAACACGAAAGTTTTGAAACACG
Done.