Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 126 of 325
Found at i:40429632 original size:48 final size:46
Alignment explanation
Indices: 40429483--40429665 Score: 162
Period size: 48 Copynumber: 4.0 Consensus size: 46
40429473 TAGGGTTATG
* *
40429483 TACGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGGATCGA
1 TACGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGA
** * * *
40429529 TACGTAATATCATGTAAGACCATAG-CTAGG-C-T---ATCGGAATCGA
1 TACG--ATCCCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGA
**
40429572 TGTGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGA
1 --TACGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGA
* *
40429620 CCTACGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATC
1 --TACGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
40429666 CTACTATGTG
Statistics
Matches: 107, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
42 1 0.01
43 27 0.25
44 1 0.01
45 3 0.03
46 5 0.05
47 1 0.01
48 68 0.64
49 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (46 bp):
TACGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGA
Found at i:40431013 original size:18 final size:18
Alignment explanation
Indices: 40430990--40431076 Score: 174
Period size: 18 Copynumber: 4.8 Consensus size: 18
40430980 GTGTCCCAAG
40430990 CCACACGGGCGTGTGTGA
1 CCACACGGGCGTGTGTGA
40431008 CCACACGGGCGTGTGTGA
1 CCACACGGGCGTGTGTGA
40431026 CCACACGGGCGTGTGTGA
1 CCACACGGGCGTGTGTGA
40431044 CCACACGGGCGTGTGTGA
1 CCACACGGGCGTGTGTGA
40431062 CCACACGGGCGTGTG
1 CCACACGGGCGTGTG
40431077 ACTCTGTTTC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 69 1.00
ACGTcount: A:0.16, C:0.29, G:0.39, T:0.16
Consensus pattern (18 bp):
CCACACGGGCGTGTGTGA
Found at i:40431797 original size:30 final size:29
Alignment explanation
Indices: 40431712--40431873 Score: 209
Period size: 29 Copynumber: 5.5 Consensus size: 29
40431702 AGTCATCACC
* * *
40431712 ATCCATTTTCATAATCGATAGCTGAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
* * *
40431741 ATCCCTTTTCATAATCGACAGTCGAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
*
40431770 ATCCCCTTTCCATATTCGATAGCCGAAGCT
1 AT-CCCTTTTCATATTCGATAGCCGAAGCT
40431800 ATCCCCTTTTCATATTCGATA-CTCGAAGCT
1 AT-CCCTTTTCATATTCGATAGC-CGAAGCT
* *
40431830 ATCCCTTTTCATATTTGATAGCCTAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
40431859 ATCCCTTTTCATATT
1 ATCCCTTTTCATATT
40431874 ACATAGCTTG
Statistics
Matches: 119, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
29 66 0.55
30 53 0.45
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.36
Consensus pattern (29 bp):
ATCCCTTTTCATATTCGATAGCCGAAGCT
Found at i:40431836 original size:59 final size:58
Alignment explanation
Indices: 40431712--40431873 Score: 225
Period size: 59 Copynumber: 2.8 Consensus size: 58
40431702 AGTCATCACC
* * * * *
40431712 ATCCATTTTCATAATCGATAGCTGAAGCTATCCCTTTTCATAATCGACAGTCGAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCATATTCGACACTCGAAGCT
* *
40431770 ATCCCCTTTCCATATTCGATAGCCGAAGCTATCCCCTTTTCATATTCGATACTCGAAGCT
1 AT-CCCTTTTCATATTCGATAGCCGAAGCTAT-CCCTTTTCATATTCGACACTCGAAGCT
* *
40431830 ATCCCTTTTCATATTTGATAGCCTAAGCTATCCCTTTTCATATT
1 ATCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCATATT
40431874 ACATAGCTTG
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 15 0.16
59 51 0.55
60 26 0.28
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.36
Consensus pattern (58 bp):
ATCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCATATTCGACACTCGAAGCT
Found at i:40432075 original size:23 final size:22
Alignment explanation
Indices: 40432043--40432086 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
40432033 AACCAATCCA
40432043 ATTCAACATATTT-TCAAGATAG
1 ATTCAACATATTTAT-AAGATAG
40432065 ATTCATACATATTTATAAGATA
1 ATTCA-ACATATTTATAAGATA
40432087 ACCTCATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 14 0.70
24 1 0.05
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (22 bp):
ATTCAACATATTTATAAGATAG
Found at i:40439003 original size:40 final size:40
Alignment explanation
Indices: 40438908--40439125 Score: 282
Period size: 40 Copynumber: 5.5 Consensus size: 40
40438898 TGGATGATAA
* *
40438908 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTATAT
* *
40438949 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
40438989 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
40439029 CCGGGCTAAGTCCCGAAGGCAATGGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
40439069 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
40439108 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
40439126 TACTTGGCTT
Statistics
Matches: 159, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
38 15 0.09
39 14 0.09
40 102 0.64
41 24 0.15
42 4 0.03
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:40447081 original size:40 final size:40
Alignment explanation
Indices: 40446983--40447200 Score: 230
Period size: 40 Copynumber: 5.5 Consensus size: 40
40446973 TGGATGATAA
** * *
40446983 CCGGGCTAAGTCCTAAAGGCATTT-TGCGCTAGTGACT-TGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTAT-AT
* * * *
40447024 CCGGGCTAAGTCTCGAAGGCATTTGTGTGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
40447064 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
40447104 CCGGGCTAAGTCCCGAAGGCAATGGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
40447144 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
40447183 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
40447201 TACTTGGCTT
Statistics
Matches: 152, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
38 15 0.10
39 14 0.09
40 99 0.65
41 21 0.14
42 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:40449788 original size:17 final size:17
Alignment explanation
Indices: 40449762--40449807 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
40449752 TGGGCCATGT
*
40449762 GGGCCTATTGGGCCTAC
1 GGGCCCATTGGGCCTAC
40449779 GGGCCCATTGGGCCTAC
1 GGGCCCATTGGGCCTAC
40449796 GGGCCCAATTGG
1 GGGCCC-ATTGG
40449808 ATAAGTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 22 0.81
18 5 0.19
ACGTcount: A:0.13, C:0.30, G:0.37, T:0.20
Consensus pattern (17 bp):
GGGCCCATTGGGCCTAC
Found at i:40450043 original size:54 final size:54
Alignment explanation
Indices: 40449970--40450092 Score: 142
Period size: 54 Copynumber: 2.3 Consensus size: 54
40449960 AATACTTTAG
* * *
40449970 TTTACTAAAATTACCGAAATACCCTTAG-TTTGTAAAAATACTGAAA-TACCCTCGA
1 TTTA-TAAAATTACTGAAATA-CCTTAGACTTGTAAAAATAC-CAAAGTACCCTCGA
* * *
40450025 TTTGTAAAATTACTGAAATACCTTCGACTTGTAAAATTACCAAAGTACCCTCGA
1 TTTATAAAATTACTGAAATACCTTAGACTTGTAAAAATACCAAAGTACCCTCGA
*
40450079 TTTACAAAATTACT
1 TTTATAAAATTACT
40450093 ATTTTACCCC
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
53 8 0.14
54 47 0.81
55 3 0.05
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (54 bp):
TTTATAAAATTACTGAAATACCTTAGACTTGTAAAAATACCAAAGTACCCTCGA
Found at i:40450078 original size:27 final size:27
Alignment explanation
Indices: 40449975--40450092 Score: 114
Period size: 27 Copynumber: 4.4 Consensus size: 27
40449965 TTTAGTTTAC
* * *
40449975 TAAAATTACCGAAATACCCT-TAGTTTG
1 TAAAATTACTGAAATACCCTCGA-CTTG
* *
40450002 TAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACTGAAATACCCTCGACTTG
*
40450029 TAAAATTACTGAAATACCTTCGACTTG
1 TAAAATTACTGAAATACCCTCGACTTG
* * *
40450056 TAAAATTAC-CAAAGTACCCTCGATTTA
1 TAAAATTACTGAAA-TACCCTCGACTTG
*
40450083 CAAAATTACT
1 TAAAATTACT
40450093 ATTTTACCCC
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
26 3 0.04
27 73 0.95
28 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
TAAAATTACTGAAATACCCTCGACTTG
Found at i:40450100 original size:27 final size:27
Alignment explanation
Indices: 40450070--40450246 Score: 174
Period size: 27 Copynumber: 6.9 Consensus size: 27
40450060 ATTACCAAAG
*
40450070 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
40450097 TACCCCCGATTTACATAATTA-TCGTTT
1 TACCCTCGATTTACAAAATTACT-GTTT
* *
40450124 TACCCTCGACTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
40450151 TACCCTCGATTT-----A-TA--GATT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
40450170 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
40450197 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
40450224 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAAAATTACT
40450247 AAAATACCCT
Statistics
Matches: 126, Mismatches: 14, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
19 15 0.12
21 2 0.02
22 1 0.01
24 1 0.01
25 2 0.02
26 1 0.01
27 103 0.82
28 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTGTTT
Found at i:40450117 original size:54 final size:54
Alignment explanation
Indices: 40450070--40450247 Score: 192
Period size: 54 Copynumber: 3.4 Consensus size: 54
40450060 ATTACCAAAG
* * *
40450070 TACCCTCGATTTACAAAATTACTATTTTACCCCCGATTTACATAATTATCGTTT
1 TACCCTCGATTTACAAAATTACTATTTTACCCTCGATTTACATAATTACCATTT
* * * *
40450124 TACCCTCGACTTACAGAATTACTGTTTTACCCTCGA-TT---T-A-TA-GA-TT
1 TACCCTCGATTTACAAAATTACTATTTTACCCTCGATTTACATAATTACCATTT
* * * * *
40450170 TACCCTCGATTTATAGAATTACTATTTTACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTATTTTACCCTCGATTTACATAATTACCATTT
40450224 TACCCTCGATTTACAAAATTACTA
1 TACCCTCGATTTACAAAATTACTA
40450248 AAATACCCTT
Statistics
Matches: 102, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
46 34 0.33
47 2 0.02
48 2 0.02
49 1 0.01
50 1 0.01
51 1 0.01
52 2 0.02
53 3 0.03
54 56 0.55
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.40
Consensus pattern (54 bp):
TACCCTCGATTTACAAAATTACTATTTTACCCTCGATTTACATAATTACCATTT
Found at i:40450173 original size:19 final size:19
Alignment explanation
Indices: 40450149--40450191 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
40450139 GAATTACTGT
40450149 TTTACCCTCGATTTATAGA
1 TTTACCCTCGATTTATAGA
40450168 TTTACCCTCGATTTATAGA
1 TTTACCCTCGATTTATAGA
*
40450187 ATTAC
1 TTTAC
40450192 TATTTTACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (19 bp):
TTTACCCTCGATTTATAGA
Found at i:40450175 original size:46 final size:46
Alignment explanation
Indices: 40450122--40450218 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
40450112 TAATTATCGT
* *
40450122 TTTACCCTCGACTTACAGAATTACTGTTTTACCCTCGATTTATAGA
1 TTTACCCTCGACTTACAGAATTACTATTTTACCCTCGATTTACAGA
* * *
40450168 TTTACCCTCGATTTATAGAATTACTATTTTACCCTTGATTTACAGA
1 TTTACCCTCGACTTACAGAATTACTATTTTACCCTCGATTTACAGA
*
40450214 ATTAC
1 TTTAC
40450219 TATTTTACCC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (46 bp):
TTTACCCTCGACTTACAGAATTACTATTTTACCCTCGATTTACAGA
Found at i:40450214 original size:73 final size:73
Alignment explanation
Indices: 40450095--40450236 Score: 205
Period size: 73 Copynumber: 1.9 Consensus size: 73
40450085 AAATTACTAT
* * *
40450095 TTTACCCCCGATTTACATAATTATCGTTTTACCCTCGACTTACAGAATTACTGTTTTACCCTCGA
1 TTTACCCCCGATTTACAGAATTATCATTTTACCCTCGACTTACAGAATTACTATTTTACCCTCGA
40450160 TTTATAGA
66 TTTATAGA
* * * *
40450168 TTTACCCTCGATTTATAGAATTA-CTATTTTACCCTTGATTTACAGAATTACTATTTTACCCTCG
1 TTTACCCCCGATTTACAGAATTATC-ATTTTACCCTCGACTTACAGAATTACTATTTTACCCTCG
40450232 ATTTA
65 ATTTA
40450237 CAAAATTACT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
72 1 0.02
73 60 0.98
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (73 bp):
TTTACCCCCGATTTACAGAATTATCATTTTACCCTCGACTTACAGAATTACTATTTTACCCTCGA
TTTATAGA
Found at i:40450255 original size:100 final size:100
Alignment explanation
Indices: 40450070--40450256 Score: 250
Period size: 100 Copynumber: 1.9 Consensus size: 100
40450060 ATTACCAAAG
* *
40450070 TACCCTCGATTTACAAAATTACTATTTTACCCCCGATTTACATAATTATCGTTTTACCCTCGACT
1 TACCCTCGATTTACAAAATTACTATTTTACCCCCGATTTACAGAATTATCATTTTACCCTCGACT
* ****
40450135 TACAGAATTACTGTTTTACCCTCGATTTATAGATT
66 TACAAAATTACTAAAATACCCTCGATTTATAGATT
* * ** *
40450170 TACCCTCGATTTATAGAATTACTATTTTACCCTTGATTTACAGAATTA-CTATTTTACCCTCGAT
1 TACCCTCGATTTACAAAATTACTATTTTACCCCCGATTTACAGAATTATC-ATTTTACCCTCGAC
40450234 TTACAAAATTACTAAAATACCCT
65 TTACAAAATTACTAAAATACCCT
40450257 TGGTTTGTAA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 1 0.01
100 73 0.99
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (100 bp):
TACCCTCGATTTACAAAATTACTATTTTACCCCCGATTTACAGAATTATCATTTTACCCTCGACT
TACAAAATTACTAAAATACCCTCGATTTATAGATT
Found at i:40450271 original size:54 final size:54
Alignment explanation
Indices: 40450167--40450363 Score: 173
Period size: 54 Copynumber: 3.6 Consensus size: 54
40450157 CGATTTATAG
* *** * ** * *
40450167 ATTTACCCTCGATTTATAGAATTACTATTTTACCCTTGATTTACAGAATTACTA
1 ATTTACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCA
* *
40450221 TTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCA
1 ATTTACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCA
** * * * *
40450275 AAATACCCT-TAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTGAAATTACCGA
1 ATTTACCCTCGA-TTTATAAAATTACTAAAATACCCTTGGTTTGTAAAATTACC-A
* * * *
40450330 A-ATACCCTCAATTTGTAAAATTACCAAAATACCC
1 ATTTACCCTCGATTTATAAAATTACTAAAATACCC
40450364 CTAATTTACA
Statistics
Matches: 120, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
53 1 0.01
54 116 0.97
55 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (54 bp):
ATTTACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCA
Found at i:40450309 original size:81 final size:80
Alignment explanation
Indices: 40450224--40450476 Score: 215
Period size: 81 Copynumber: 3.1 Consensus size: 80
40450214 ATTACTATTT
*
40450224 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTTAGTT
1 TACCCTTGATTT-CAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTTAGTT
40450289 TGTAAAATTACCAAAA
65 TGTAAAATTACCAAAA
* ** ** *** * *
40450305 TACCCTTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAATT
1 TACCCTTGATTT-CAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTTAGTT
** *
40450370 TACAAAGTTA-CAGAAA
65 TGTAAAATTACCA-AAA
** **
40450386 TACCCTTGACTTTCTAAAAATTA-TAGAAATACCAC-TGGTTTACAAAATTACTGAAATACCCTT
1 TACCCTTGA-TTTC--AAAATTACTA-AAATACC-CTTGGTTTGTAAAATTACCAAAATACCCTT
* * *
40450449 GGTTTGTAGATTTACCAAAA
61 AGTTTGTAAAATTACCAAAA
*
40450469 CACCCTTG
1 TACCCTTG
40450477 TAGGATGAAA
Statistics
Matches: 130, Mismatches: 35, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
80 2 0.02
81 71 0.55
82 3 0.02
83 51 0.39
84 3 0.02
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (80 bp):
TACCCTTGATTTCAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTTAGTTT
GTAAAATTACCAAAA
Found at i:40450451 original size:27 final size:27
Alignment explanation
Indices: 40450197--40450476 Score: 154
Period size: 27 Copynumber: 10.3 Consensus size: 27
40450187 ATTACTATTT
* * * ***
40450197 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTTGGTTTACAAAATTACCAAAA
* * *
40450224 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
**
40450251 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
* **
40450278 TACCCTTAGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
*** *
40450305 TACCCTTGGTTTGTGAAATTACCGAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
*** **
40450332 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
* ** *
40450359 TACCCCTAATTTACAAAGTTA-CAGAAA
1 TACCCTTGGTTTACAAAATTACCA-AAA
* *
40450386 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTG-GTTTAC--AAAATTACCA-AAA
**
40450415 TACCAC-TGGTTTACAAAATTACTGAAA
1 TACC-CTTGGTTTACAAAATTACCAAAA
** * *
40450442 TACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
*
40450469 CACCCTTG
1 TACCCTTG
40450477 TAGGATGAAA
Statistics
Matches: 207, Mismatches: 38, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
26 3 0.01
27 178 0.86
28 7 0.03
29 18 0.09
30 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (27 bp):
TACCCTTGGTTTACAAAATTACCAAAA
Found at i:40450530 original size:27 final size:27
Alignment explanation
Indices: 40450498--40450598 Score: 134
Period size: 27 Copynumber: 3.7 Consensus size: 27
40450488 GACTAAAATA
*
40450498 CCCCTGTTA-GGTAAAAAGACCGTAAAG
1 CCCCTG-TAGGGTAAAATGACCGTAAAG
*
40450525 CCCCTGTAGGGTAAAGTGACCGTAAAG
1 CCCCTGTAGGGTAAAATGACCGTAAAG
*
40450552 CCCCTGTAGGGTAAAGTGACCGTAATA-
1 CCCCTGTAGGGTAAAATGACCGTAA-AG
*
40450579 CCCCTGTATGGTAAAATGAC
1 CCCCTGTAGGGTAAAATGAC
40450599 GAATATGCCA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
26 2 0.03
27 65 0.96
28 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.21
Consensus pattern (27 bp):
CCCCTGTAGGGTAAAATGACCGTAAAG
Found at i:40451451 original size:37 final size:37
Alignment explanation
Indices: 40451401--40451471 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
40451391 GAGGAAGTGC
40451401 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCATA
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCATA
**
40451438 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGC
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGC
40451472 TTATGCCCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (37 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCATA
Found at i:40451474 original size:26 final size:26
Alignment explanation
Indices: 40451438--40451561 Score: 196
Period size: 26 Copynumber: 4.8 Consensus size: 26
40451428 AAAGGGCATA
*
40451438 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
40451464 AAAAGGGCTTATGCCCCAATTTACTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
* *
40451490 AAAAGGGCTTATGCACCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
40451516 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACTG
40451542 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
40451562 ATTAAAGAGG
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
25 10 0.11
26 80 0.89
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACTG
Found at i:40451765 original size:42 final size:42
Alignment explanation
Indices: 40451706--40451794 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
40451696 TAGTCTCCCC
* * ** * * *
40451706 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGAGCTTGCATACATCCATTGACATTACATATAATATTG
40451748 AAATGAGCTTGCATACATCCATTGACATTACATATAATATTG
1 AAATGAGCTTGCATACATCCATTGACATTACATATAATATTG
40451790 AAATG
1 AAATG
40451795 GGCCTATGGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (42 bp):
AAATGAGCTTGCATACATCCATTGACATTACATATAATATTG
Found at i:40451857 original size:31 final size:31
Alignment explanation
Indices: 40451821--40451899 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
40451811 CGTTTACAGT
40451821 AAAGGCTTTGGCCTAGTGAAATGATTTATGA
1 AAAGGCTTTGGCCTAGTGAAATGATTTATGA
* *
40451852 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTTGGCCTAGTGAAATGATTTATGA
*
40451883 AAAGGCTTCGGCCTAGT
1 AAAGGCTTTGGCCTAGT
40451900 AATCGTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (31 bp):
AAAGGCTTTGGCCTAGTGAAATGATTTATGA
Found at i:40457729 original size:29 final size:29
Alignment explanation
Indices: 40457692--40457831 Score: 151
Period size: 29 Copynumber: 4.8 Consensus size: 29
40457682 AGGCCATTAC
40457692 ATAGCTGAAGCTATCCCTTTTCAT-ATTAG
1 ATAGCTGAAGCTATCCCTTTTCATAATT-G
* **
40457721 ATAGCTGAAACTATCCCTTTTCATGTTTG
1 ATAGCTGAAGCTATCCCTTTTCATAATTG
* * *
40457750 ATGATCAT-CA-CCATCCCTTTTCATAATTG
1 AT-AGC-TGAAGCTATCCCTTTTCATAATTG
* *
40457779 ATAGCCGGAGCTATCCCTTTTCATAATTG
1 ATAGCTGAAGCTATCCCTTTTCATAATTG
*
40457808 ATAGCTAAAGCTATCCCTTTTCAT
1 ATAGCTGAAGCTATCCCTTTTCAT
40457832 TGGTCGATGA
Statistics
Matches: 92, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
28 3 0.03
29 83 0.90
30 5 0.05
31 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (29 bp):
ATAGCTGAAGCTATCCCTTTTCATAATTG
Found at i:40458391 original size:26 final size:26
Alignment explanation
Indices: 40458361--40458413 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
40458351 TAACATACTC
40458361 AAAAGCATTGAAAAATCATACAAACT
1 AAAAGCATTGAAAAATCATACAAACT
40458387 AAAAGCATTGAAAAATCATACAAACT
1 AAAAGCATTGAAAAATCATACAAACT
40458413 A
1 A
40458414 GACCAAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (26 bp):
AAAAGCATTGAAAAATCATACAAACT
Found at i:40460645 original size:14 final size:14
Alignment explanation
Indices: 40460626--40460653 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40460616 AGAAATATTC
40460626 TACAAAGAAACAAA
1 TACAAAGAAACAAA
40460640 TACAAAGAAACAAA
1 TACAAAGAAACAAA
40460654 CTCATAGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.14, G:0.07, T:0.07
Consensus pattern (14 bp):
TACAAAGAAACAAA
Found at i:40461280 original size:13 final size:13
Alignment explanation
Indices: 40461264--40461289 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40461254 GGAATGATTT
40461264 TTTGAAAATTTTG
1 TTTGAAAATTTTG
40461277 TTTGAAAATTTTG
1 TTTGAAAATTTTG
40461290 ACGTTTGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTTGAAAATTTTG
Found at i:40462509 original size:45 final size:44
Alignment explanation
Indices: 40462446--40462533 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 44
40462436 AAATATGTGA
40462446 CTGAACTCATGAGTTGTGGTCTGAGTTCATGATATATGTGACAT
1 CTGAACTCATGAGTTGTGGTCTGAGTTCATGATATATGTGACAT
*
40462490 CTGAACTCATTGAGTTGTGGTCTGAGTTCATGATGTATGTGACA
1 CTGAACTCA-TGAGTTGTGGTCTGAGTTCATGATATATGTGACA
40462534 CATGTTTTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 9 0.21
45 33 0.79
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (44 bp):
CTGAACTCATGAGTTGTGGTCTGAGTTCATGATATATGTGACAT
Found at i:40470653 original size:18 final size:17
Alignment explanation
Indices: 40470630--40470688 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
40470620 ATCTCATGTA
40470630 TCATATTATCCATGTAAT
1 TCATA-TATCCATGTAAT
*
40470648 TCATATAAACCATGTAAT
1 TCATAT-ATCCATGTAAT
* *
40470666 TCATA-ATTCATGTAAA
1 TCATATATCCATGTAAT
40470682 TCATATA
1 TCATATA
40470689 GCTTTTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 13 0.37
17 2 0.06
18 20 0.57
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (17 bp):
TCATATATCCATGTAAT
Found at i:40474505 original size:23 final size:23
Alignment explanation
Indices: 40474436--40474512 Score: 102
Period size: 23 Copynumber: 3.4 Consensus size: 23
40474426 CTGAGCTGAT
40474436 AAACGGTAAGCCCCGAAGAGCTG
1 AAACGGTAAGCCCCGAAGAGCTG
* * **
40474459 -AACGGTAAGCTCCGTAGATTTG
1 AAACGGTAAGCCCCGAAGAGCTG
*
40474481 AAACGATAAGCCCCGAAGAGCTG
1 AAACGGTAAGCCCCGAAGAGCTG
40474504 AAACGGTAA
1 AAACGGTAA
40474513 ACTCATATGA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
22 18 0.42
23 25 0.58
ACGTcount: A:0.36, C:0.22, G:0.27, T:0.14
Consensus pattern (23 bp):
AAACGGTAAGCCCCGAAGAGCTG
Found at i:40475883 original size:31 final size:31
Alignment explanation
Indices: 40475841--40475904 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
40475831 CCTTTTCATA
*
40475841 TTTCATTTTTCATAACACTAGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
** *
40475872 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
40475903 TT
1 TT
40475905 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTAGGCCGAAGCCT
Found at i:40476150 original size:24 final size:24
Alignment explanation
Indices: 40476098--40476263 Score: 212
Period size: 24 Copynumber: 7.0 Consensus size: 24
40476088 ACTTTATCAT
*
40476098 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* * *
40476123 ATAACTGGGGTAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
40476147 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
40476170 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
40476194 ATAACTGGGGCATAAGCCTTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
40476218 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
40476241 ATAACTAGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40476264 TCACTTCCTC
Statistics
Matches: 123, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
23 42 0.34
24 69 0.56
25 12 0.10
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:40476198 original size:71 final size:71
Alignment explanation
Indices: 40476098--40476263 Score: 244
Period size: 71 Copynumber: 2.3 Consensus size: 71
40476088 ACTTTATCAT
* *
40476098 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGTAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAA
40476162 GCCCTTTA
64 GCCCTTTA
* * * *
40476170 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCTTTTTTATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAAGC
40476235 CCTTTA
66 CCTTTA
*
40476241 ATAACTAGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40476264 TCACTTCCTC
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
71 74 0.86
72 12 0.14
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (71 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAAGC
CCTTTA
Found at i:40476264 original size:47 final size:48
Alignment explanation
Indices: 40476098--40476263 Score: 212
Period size: 47 Copynumber: 3.5 Consensus size: 48
40476088 ACTTTATCAT
* * * *
40476098 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGTAAAAGCCCTTTTT
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTA
* *
40476147 ATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTA
* *
40476194 ATAACTGGGGCATAAGCCTTTTTTATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTA
*
40476241 ATAACTAGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40476264 TCACTTCCTC
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
47 66 0.63
48 26 0.25
49 12 0.12
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTA
Found at i:40476339 original size:20 final size:20
Alignment explanation
Indices: 40476314--40476352 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
40476304 TATGATTACA
40476314 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
40476334 TCATGTGCATATCATACAT
1 TCATGTGCATATCATACAT
40476353 ACCATGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:40476358 original size:20 final size:20
Alignment explanation
Indices: 40476315--40476359 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
40476305 ATGATTACAT
**
40476315 CATGTGCATATCATACATGT
1 CATGTGCATATCATACATAC
40476335 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAC
40476355 CATGT
1 CATGT
40476360 TTATCAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTGCATATCATACATAC
Found at i:40476428 original size:25 final size:25
Alignment explanation
Indices: 40476396--40476443 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
40476386 ATACATAAAC
* *
40476396 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
40476421 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
40476444 CATGTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:40477634 original size:27 final size:27
Alignment explanation
Indices: 40477600--40477702 Score: 100
Period size: 27 Copynumber: 3.8 Consensus size: 27
40477590 GGGCATATTC
* *
40477600 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACA
40477627 GTCATTTTACCCTACAGGGGCT-TTACA
1 GTCATTTTACCCTACAGGGG-TATTACA
* * **
40477654 GTCACTTTACCCTAATAGGGGTATTTTA
1 GTCATTTTACCCT-ACAGGGGTATTACA
* * *
40477682 GTCATTTCATCCTACAAGGGT
1 GTCATTTTACCCTACAGGGGT
40477703 GTTTTGGTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
27 42 0.68
28 20 0.32
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTACA
Found at i:40477832 original size:27 final size:27
Alignment explanation
Indices: 40477809--40477934 Score: 171
Period size: 27 Copynumber: 4.7 Consensus size: 27
40477799 TGTAAATCAG
***
40477809 GGGTATTTTGGTAATTTTACAAATTGA
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
40477836 GGGTATTTCGGTAATTTCACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
40477863 GGGTATTTTGGTAATTTTATAAACTAA
1 GGGTATTTTGGTAATTTTACAAACCAA
40477890 GGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
40477917 AGGTATTTTAGTAATTTT
1 GGGTATTTTGGTAATTTT
40477935 GTAAATCGAG
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 86 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:40477867 original size:54 final size:54
Alignment explanation
Indices: 40477809--40477948 Score: 199
Period size: 54 Copynumber: 2.6 Consensus size: 54
40477799 TGTAAATCAG
*
40477809 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
1 GGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
* * * *
40477863 GGGTATTTTGGTAATTTTATAAACTAAGGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
* * * *
40477917 AGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTATAAATTGAGGGTA
40477949 AAATAGTAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
Found at i:40477948 original size:27 final size:27
Alignment explanation
Indices: 40477727--40477948 Score: 162
Period size: 27 Copynumber: 8.1 Consensus size: 27
40477717 ACAAACCATA
* * * *
40477727 GGTATTTCAGTAATTTTGTAAACCAAT
1 GGTATTTTAGTAATTTTATAAATCAAG
*
40477754 GGTATTTCTA-TAATTTTTAGAAAGTCAAG
1 GGTATTT-TAGTAA-TTTTATAAA-TCAAG
* * *
40477783 GGTATTTCTA-TAACTTTGTAAATCAGG
1 GGTATTT-TAGTAATTTTATAAATCAAG
* * **
40477810 GGTATTTTGGTAATTTTACAAATTGAG
1 GGTATTTTAGTAATTTTATAAATCAAG
** * * *
40477837 GGTATTTCGGTAATTTCACAAACCAAG
1 GGTATTTTAGTAATTTTATAAATCAAG
*
40477864 GGTATTTTGGTAATTTTATAAA-CTAAG
1 GGTATTTTAGTAATTTTATAAATC-AAG
* * * *
40477891 GGTATTTTGGTAATTTTACAAACCAAA
1 GGTATTTTAGTAATTTTATAAATCAAG
* *
40477918 GGTATTTTAGTAATTTTGTAAATCGAG
1 GGTATTTTAGTAATTTTATAAATCAAG
40477945 GGTA
1 GGTA
40477949 AAATAGTAAT
Statistics
Matches: 157, Mismatches: 32, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.01
27 124 0.79
28 15 0.10
29 16 0.10
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
GGTATTTTAGTAATTTTATAAATCAAG
Found at i:40477955 original size:27 final size:27
Alignment explanation
Indices: 40477925--40478050 Score: 117
Period size: 27 Copynumber: 5.0 Consensus size: 27
40477915 AAAGGTATTT
*
40477925 TAGTAATTTTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
*
40477952 TAGTAATTCTGTAAATTGAGGG-----
1 TAGTAATTCTGTAAATCGAGGGTAAAA
40477974 TA--AA-TCTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
** *
40477998 CGGTAATTCTGTAAGTCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* *
40478025 -CGATAATTCTGTAAGTCGAGGGTAAA
1 TAG-TAATTCTGTAAATCGAGGGTAAA
40478051 TCAAGGGTAA
Statistics
Matches: 83, Mismatches: 7, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
19 14 0.17
20 2 0.02
22 2 0.02
26 3 0.04
27 62 0.75
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.29
Consensus pattern (27 bp):
TAGTAATTCTGTAAATCGAGGGTAAAA
Found at i:40477976 original size:19 final size:19
Alignment explanation
Indices: 40477954--40477996 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
40477944 GGGTAAAATA
* *
40477954 GTAATTCTGTAAATTGAGG
1 GTAAATCTGTAAATCGAGG
40477973 GTAAATCTGTAAATCGAGG
1 GTAAATCTGTAAATCGAGG
40477992 GTAAA
1 GTAAA
40477997 ACGGTAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (19 bp):
GTAAATCTGTAAATCGAGG
Found at i:40477987 original size:46 final size:46
Alignment explanation
Indices: 40477934--40478023 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
40477924 TTAGTAATTT
* *
40477934 TGTAAATCGAGGGTAAAATAGTAATTCTGTAAATTGAGGGTAAATC
1 TGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAATC
* *
40477980 TGTAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAA
1 TGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAA
40478024 ACGATAATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.28
Consensus pattern (46 bp):
TGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAATC
Found at i:40478003 original size:19 final size:19
Alignment explanation
Indices: 40477962--40478003 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40477952 TAGTAATTCT
* * *
40477962 GTAAATTGAGGGTAAATCT
1 GTAAATCGAGGGTAAAACG
40477981 GTAAATCGAGGGTAAAACG
1 GTAAATCGAGGGTAAAACG
40478000 GTAA
1 GTAA
40478004 TTCTGTAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.29, T:0.24
Consensus pattern (19 bp):
GTAAATCGAGGGTAAAACG
Found at i:40478058 original size:38 final size:38
Alignment explanation
Indices: 40478016--40478088 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
40478006 CTGTAAGTCG
* *
40478016 AGGGTAAAACGATAATTCTGTAAGTCGAGGGTAAATCA
1 AGGGTAAAACGATAATTATGTAAATCGAGGGTAAATCA
* * *
40478054 AGGGTAAAATGGTAATTATGTAAATCGGGGGTAAA
1 AGGGTAAAACGATAATTATGTAAATCGAGGGTAAA
40478089 ATGGTAATTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.40, C:0.07, G:0.29, T:0.25
Consensus pattern (38 bp):
AGGGTAAAACGATAATTATGTAAATCGAGGGTAAATCA
Found at i:40478068 original size:73 final size:71
Alignment explanation
Indices: 40477927--40478110 Score: 179
Period size: 73 Copynumber: 2.7 Consensus size: 71
40477917 AGGTATTTTA
* * * *
40477927 GTAATTTTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATTGAGGGTAAATCTGTAAATCGAGG
1 GTAATTCTGTAAATCGAGGGTAAAAGAGTAATTCTGTAAATCGAGGGTAAATCGGTAAA-C-AGG
40477992 GTAAAACG
64 GTAAAACG
* *
40478000 GTAATTCTGTAAGTCGAGGGTAAAACGA-TAATTCTGTAAGTCGAGGGTAAATC-----A-AGGG
1 GTAATTCTGTAAATCGAGGGTAAAA-GAGTAATTCTGTAAATCGAGGGTAAATCGGTAAACAGGG
*
40478058 TAAAATG
65 TAAAACG
* * *
40478065 GTAATTATGTAAATCGGGGGTAAAATG-GTAATTCTATAAATC-AGGG
1 GTAATTCTGTAAATCGAGGGTAAAA-GAGTAATTCTGTAAATCGAGGG
40478111 GTACTTTGGT
Statistics
Matches: 97, Mismatches: 12, Indels: 13
0.80 0.10 0.11
Matches are distributed among these distances:
64 4 0.04
65 45 0.46
68 1 0.01
73 46 0.47
74 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.29
Consensus pattern (71 bp):
GTAATTCTGTAAATCGAGGGTAAAAGAGTAATTCTGTAAATCGAGGGTAAATCGGTAAACAGGGT
AAAACG
Found at i:40478076 original size:27 final size:27
Alignment explanation
Indices: 40478046--40478113 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
40478036 TAAGTCGAGG
*
40478046 GTAAATCAAGGGTAAAATGGTAATTAT
1 GTAAATCAGGGGTAAAATGGTAATTAT
* *
40478073 GTAAATCGGGGGTAAAATGGTAATTCT
1 GTAAATCAGGGGTAAAATGGTAATTAT
*
40478100 ATAAATCAGGGGTA
1 GTAAATCAGGGGTA
40478114 CTTTGGTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.28
Consensus pattern (27 bp):
GTAAATCAGGGGTAAAATGGTAATTAT
Found at i:40478113 original size:65 final size:65
Alignment explanation
Indices: 40477981--40478110 Score: 172
Period size: 65 Copynumber: 2.0 Consensus size: 65
40477971 GGGTAAATCT
* * * * *
40477981 GTAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAACGATAATTCTGTAAGTCGAGG
1 GTAAATCAAGGGTAAAACGGTAATTATGTAAATCGAGGGTAAAACGATAATTCTATAAATCGAGG
* * * *
40478046 GTAAATCAAGGGTAAAATGGTAATTATGTAAATCGGGGGTAAAATGGTAATTCTATAAATC-AGG
1 GTAAATCAAGGGTAAAACGGTAATTATGTAAATCGAGGGTAAAACGATAATTCTATAAATCGAGG
40478110 G
1 G
40478111 GTACTTTGGT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
64 4 0.07
65 52 0.93
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.26
Consensus pattern (65 bp):
GTAAATCAAGGGTAAAACGGTAATTATGTAAATCGAGGGTAAAACGATAATTCTATAAATCGAGG
Found at i:40478181 original size:26 final size:27
Alignment explanation
Indices: 40478119--40478207 Score: 110
Period size: 27 Copynumber: 3.3 Consensus size: 27
40478109 GGGTACTTTG
*
40478119 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
* *
40478146 GTAATTTTACAAATCGAGGGT-TTTTA
1 GTAATTTTACAAATCGAAGGTATTTCA
* *
40478172 GTATTTTTACAAA-CTAAGCGTATTTCA
1 GTAATTTTACAAATCGAAG-GTATTTCA
40478199 GTAATTTTA
1 GTAATTTTA
40478208 GTAAACTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
25 3 0.06
26 18 0.35
27 31 0.60
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.42
Consensus pattern (27 bp):
GTAATTTTACAAATCGAAGGTATTTCA
Found at i:40485987 original size:18 final size:18
Alignment explanation
Indices: 40485963--40486003 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
40485953 TATCTCATGT
*
40485963 ATCATATTATCCATGTAA
1 ATCATATAATCCATGTAA
* *
40485981 CTCATATAATTCATGTAA
1 ATCATATAATCCATGTAA
40485999 ATCAT
1 ATCAT
40486004 GTAACTCATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (18 bp):
ATCATATAATCCATGTAA
Found at i:40486012 original size:18 final size:18
Alignment explanation
Indices: 40485974--40486012 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40485964 TCATATTATC
* *
40485974 CATGTAACTCATATAATT
1 CATGTAAATCATATAACT
*
40485992 CATGTAAATCATGTAACT
1 CATGTAAATCATATAACT
40486010 CAT
1 CAT
40486013 AATTCATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (18 bp):
CATGTAAATCATATAACT
Found at i:40486020 original size:25 final size:26
Alignment explanation
Indices: 40485974--40486024 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
40485964 TCATATTATC
40485974 CATGTAACTCATATAATTCATGTAAAT
1 CATGTAACTCA-ATAATTCATGTAAAT
40486001 CATGTAACTC-ATAATTCATGTAAA
1 CATGTAACTCAATAATTCATGTAAA
40486025 ACATATAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 14 0.58
27 10 0.42
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (26 bp):
CATGTAACTCAATAATTCATGTAAAT
Found at i:40486259 original size:23 final size:23
Alignment explanation
Indices: 40486205--40486285 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
40486195 CTGAGCTGAT
**
40486205 AAACGGTAAGCTCTAAAGAGCTG
1 AAACGGTAAGCTCCGAAGAGCTG
* *
40486228 -AACGATAAGCTCCGTAGAGCTG
1 AAACGGTAAGCTCCGAAGAGCTG
*
40486250 AAACGGTAAG-TCCTGAAGAGCTA
1 AAACGGTAAGCTCC-GAAGAGCTG
*
40486273 AAATGGTAAGCTC
1 AAACGGTAAGCTC
40486286 ATATGAACTA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
22 21 0.45
23 24 0.51
24 2 0.04
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.19
Consensus pattern (23 bp):
AAACGGTAAGCTCCGAAGAGCTG
Found at i:40491748 original size:19 final size:19
Alignment explanation
Indices: 40491724--40491762 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40491714 AACAAAACAT
40491724 AACTAAAAATCTACTATTA
1 AACTAAAAATCTACTATTA
40491743 AACTAAAAATCTACTATTA
1 AACTAAAAATCTACTATTA
40491762 A
1 A
40491763 TCCTACTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (19 bp):
AACTAAAAATCTACTATTA
Found at i:40493436 original size:48 final size:49
Alignment explanation
Indices: 40493384--40493512 Score: 156
Period size: 48 Copynumber: 2.7 Consensus size: 49
40493374 TTGGCTTCAG
* *
40493384 GCCATGATACTGGCACTTCGGGTGCGAGCTTCACA-GATTTAGCTTCGA
1 GCCATGATATTGGCACTTCGGGTGCGAGCTTCACATGAGTTAGCTTCGA
* * *
40493432 GCCATGATATTAGCACTTCGGGTGCGAG-TT-ATATTGAGTTGGCTTCGA
1 GCCATGATATTGGCACTTCGGGTGCGAGCTTCACA-TGAGTTAGCTTCGA
* *
40493480 GCCATGATATTGGCACTTAGTGTGCGAGACTTC
1 GCCATGATATTGGCACTTCGGGTGCGAG-CTTC
40493513 TGAGTATCCG
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
46 2 0.03
47 2 0.03
48 62 0.91
50 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (49 bp):
GCCATGATATTGGCACTTCGGGTGCGAGCTTCACATGAGTTAGCTTCGA
Found at i:40500287 original size:13 final size:13
Alignment explanation
Indices: 40500269--40500293 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40500259 TTAAACGATA
40500269 AAATTTTCACACG
1 AAATTTTCACACG
40500282 AAATTTTCACAC
1 AAATTTTCACAC
40500294 ATGTCTCATA
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:40508811 original size:43 final size:42
Alignment explanation
Indices: 40508763--40508868 Score: 99
Period size: 42 Copynumber: 2.5 Consensus size: 42
40508753 CAATGCTGAC
* * * **
40508763 GTCCCAGACGTGGTCTTACATGTAATTCAG-TATCGATGCCTCT
1 GTCCCAGACGTGGTCTTACACGAAAAT-AGATA-CGATGCCGAT
* *
40508806 GTCCCATACAG-GGTCTTATACGAAAATAGATACGATGCCGAT
1 GTCCCAGAC-GTGGTCTTACACGAAAATAGATACGATGCCGAT
*
40508848 GTCCCAGACATGGTCTTACAC
1 GTCCCAGACGTGGTCTTACAC
40508869 TTAAATTTCA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
42 27 0.54
43 22 0.44
44 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (42 bp):
GTCCCAGACGTGGTCTTACACGAAAATAGATACGATGCCGAT
Found at i:40510123 original size:32 final size:32
Alignment explanation
Indices: 40510081--40510184 Score: 190
Period size: 32 Copynumber: 3.2 Consensus size: 32
40510071 CTTTCTATAT
* *
40510081 CATGGATTCATATAACATGTGCAAAACATTTC
1 CATGTATTCATATAACATGTACAAAACATTTC
40510113 CATGTATTCATATAACATGTACAAAACATTTC
1 CATGTATTCATATAACATGTACAAAACATTTC
40510145 CATGTATTCATATAACATGTACAAAACATTTC
1 CATGTATTCATATAACATGTACAAAACATTTC
40510177 CATGTATT
1 CATGTATT
40510185 TCAAAAATAC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (32 bp):
CATGTATTCATATAACATGTACAAAACATTTC
Found at i:40510598 original size:26 final size:26
Alignment explanation
Indices: 40510487--40510621 Score: 104
Period size: 25 Copynumber: 5.4 Consensus size: 26
40510477 GGGTAGTTCT
* *
40510487 GAAGAGCCAGTAATCAGGAAGCTC-C
1 GAAGAGCCATTAATCAGGAAGCTCAA
* * *
40510512 GAATAGCCA-TATATCAGGAAGTTTAA
1 GAAGAGCCATTA-ATCAGGAAGCTCAA
* * *
40510538 G-CGAGCCA-T-ATCGGGAAGCTC-T
1 GAAGAGCCATTAATCAGGAAGCTCAA
*
40510560 GGAGAGCCATTAATCAGGAAGCTCACA
1 GAAGAGCCATTAATCAGGAAGCTCA-A
* *
40510587 -AAGAGCCTTTAATCGGGAAGCTCAA
1 GAAGAGCCATTAATCAGGAAGCTCAA
40510612 GAAGAGCCAT
1 GAAGAGCCAT
40510622 ATAGCAGGAT
Statistics
Matches: 85, Mismatches: 17, Indels: 15
0.73 0.15 0.13
Matches are distributed among these distances:
22 1 0.01
23 15 0.18
24 3 0.04
25 36 0.42
26 30 0.35
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.18
Consensus pattern (26 bp):
GAAGAGCCATTAATCAGGAAGCTCAA
Found at i:40513007 original size:26 final size:25
Alignment explanation
Indices: 40512971--40513045 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
40512961 GAAGCTCTGG
40512971 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCC-TTAATCAGGAAGCTCACAA
* *
40512997 AGAGCCTTTAATCAGAAAGCTCACGA
1 AGAGCC-TTAATCAGGAAGCTCACAA
* *
40513023 AGAGCCATATATCAGGATGCTCA
1 AGAGCCTTA-ATCAGGAAGCTCA
40513046 TAAGAGCTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 2 0.05
26 40 0.95
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.19
Consensus pattern (25 bp):
AGAGCCTTAATCAGGAAGCTCACAA
Found at i:40513037 original size:52 final size:48
Alignment explanation
Indices: 40512925--40513052 Score: 123
Period size: 52 Copynumber: 2.6 Consensus size: 48
40512915 AGCTTAGGAT
* * * * * *
40512925 AGCCATATATCAGGAAGTTTAAAAGAGCCATATCGGGAAGCTCTGGAG
1 AGCCATATATCAGGAAGCTCAAAAGAGCCATATCAGAAAGCTCCGAAG
*
40512973 AGCCAT-TAATCAGGAAGCTCACAAAGAGCCTTTAATCAGAAAGCTCACGAAG
1 AGCCATAT-ATCAGGAAGCTCA-AAAGAGCC-AT-ATCAGAAAGCTC-CGAAG
* *
40513025 AGCCATATATCAGGATGCTCATAAGAGC
1 AGCCATATATCAGGAAGCTCAAAAGAGC
40513053 TGTGGTGTGT
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
47 1 0.02
48 17 0.26
49 8 0.12
50 1 0.02
51 16 0.25
52 21 0.32
53 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (48 bp):
AGCCATATATCAGGAAGCTCAAAAGAGCCATATCAGAAAGCTCCGAAG
Found at i:40520005 original size:23 final size:23
Alignment explanation
Indices: 40519979--40520022 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
40519969 AACCTATAAA
40519979 TACTATTATA-ACCAAAATAAGTT
1 TACTATT-TACACCAAAATAAGTT
*
40520002 TACTATTTACATCAAAATAAG
1 TACTATTTACACCAAAATAAG
40520023 CCGAGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (23 bp):
TACTATTTACACCAAAATAAGTT
Found at i:40520743 original size:26 final size:26
Alignment explanation
Indices: 40520712--40520771 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
40520702 CAAGCTCTGG
40520712 AGAGCCATTAATCAAGAAGCTCACAA
1 AGAGCCATTAATCAAGAAGCTCACAA
* * ** *
40520738 AGAGCCTTTATTCGGGAAGCTCACGA
1 AGAGCCATTAATCAAGAAGCTCACAA
40520764 AGAGCCAT
1 AGAGCCAT
40520772 ATATCGGGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCAAGAAGCTCACAA
Found at i:40520778 original size:26 final size:26
Alignment explanation
Indices: 40520727--40520786 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
40520717 CATTAATCAA
*
40520727 GAAGCTCACAAAGAGCCTTTATTCGG
1 GAAGCTCACAAAGAGCCTATATTCGG
*
40520753 GAAGCTCACGAAGAGCC-ATATATCGG
1 GAAGCTCACAAAGAGCCTATAT-TCGG
*
40520779 GATGCTCA
1 GAAGCTCA
40520787 TAAGAGCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (26 bp):
GAAGCTCACAAAGAGCCTATATTCGG
Found at i:40521475 original size:19 final size:19
Alignment explanation
Indices: 40521435--40521477 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
40521425 TGCCCATGTA
*
40521435 TTTCATAAAATTTAATTTT
1 TTTCATAAAATTTAATTCT
*
40521454 TTTCATAAATTTTACA-TCT
1 TTTCATAAAATTTA-ATTCT
40521473 TTTCA
1 TTTCA
40521478 ATTTTGTCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTCATAAAATTTAATTCT
Found at i:40524134 original size:7 final size:7
Alignment explanation
Indices: 40524122--40524150 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
40524112 TCTTACACTG
40524122 TATACCT
1 TATACCT
40524129 TATACCT
1 TATACCT
40524136 TATACCT
1 TATACCT
40524143 TATACCT
1 TATACCT
40524150 T
1 T
40524151 GTGATCTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.45
Consensus pattern (7 bp):
TATACCT
Found at i:40538268 original size:25 final size:25
Alignment explanation
Indices: 40538183--40538268 Score: 120
Period size: 26 Copynumber: 3.4 Consensus size: 25
40538173 GAGGAAGTGC
40538183 AAAAGGGCTTATGCCCCAGTTTATT
1 AAAAGGGCTTATGCCCCAGTTTATT
* *
40538208 AGAAAGGGCTTATGCCCTAGTTTATCG
1 A-AAAGGGCTTATGCCCCAGTTTAT-T
40538235 AAAAGGGCTTATGCCCCAG-TTATT
1 AAAAGGGCTTATGCCCCAGTTTATT
40538259 AAAAGAGGCT
1 AAAAG-GGCT
40538269 AGGCCTCCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
24 5 0.09
25 9 0.17
26 39 0.72
27 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTATGCCCCAGTTTATT
Found at i:40538512 original size:31 final size:31
Alignment explanation
Indices: 40538477--40538540 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
40538467 CGTTTACAAT
* *
40538477 AAAGGGGTCGACCGAGTAATATGAAATATGA
1 AAAGGCGTCGACCAAGTAATATGAAATATGA
* * **
40538508 AAAGGCTTCGGCCAAGTGTTATGAAATATGA
1 AAAGGCGTCGACCAAGTAATATGAAATATGA
40538539 AA
1 AA
40538541 TATGAAAAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.27, T:0.22
Consensus pattern (31 bp):
AAAGGCGTCGACCAAGTAATATGAAATATGA
Found at i:40544511 original size:31 final size:33
Alignment explanation
Indices: 40544473--40544536 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
40544463 CTAGCACGTA
*
40544473 GCCTGCGGA-CTTAAGTCCGGTTAT-ATTCCAG
1 GCCTGCGGACCTTAAGTCCGGGTATAATTCCAG
*
40544504 GCCTGCGGACCTTAAGTCTGGGTATAATTCCAG
1 GCCTGCGGACCTTAAGTCCGGGTATAATTCCAG
40544537 CATAATAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 9 0.31
32 13 0.45
33 7 0.24
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.28
Consensus pattern (33 bp):
GCCTGCGGACCTTAAGTCCGGGTATAATTCCAG
Found at i:40548205 original size:39 final size:40
Alignment explanation
Indices: 40548162--40548246 Score: 118
Period size: 39 Copynumber: 2.1 Consensus size: 40
40548152 TCCTCGTTCA
* * *
40548162 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCACACG
* *
40548201 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCACACG
40548241 AATGCC
1 AATGCC
40548247 GCTTAACGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 34 0.85
40 6 0.15
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCACACG
Found at i:40548320 original size:40 final size:39
Alignment explanation
Indices: 40548265--40548351 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
40548255 CTCGACGAAT
*
40548265 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAG
1 GCCTTCGGGACTTAACCCGGAATT-GTATCTCGCACAAAG
* *
40548305 GCCTTCGGGGCTTAACCCGGAATTGTATCTCGCACAAAT
1 GCCTTCGGGACTTAACCCGGAATTGTATCTCGCACAAAG
40548344 GCCTTCGG
1 GCCTTCGG
40548352 ATCTTAGTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 22 0.50
40 22 0.50
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (39 bp):
GCCTTCGGGACTTAACCCGGAATTGTATCTCGCACAAAG
Found at i:40548337 original size:100 final size:100
Alignment explanation
Indices: 40548162--40548346 Score: 255
Period size: 100 Copynumber: 1.9 Consensus size: 100
40548152 TCCTCGTTCA
* * * *
40548162 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGAAT
*
40548227 TAATAACTCGCACGAATGCCGCTTAACGCTCGACG
66 TAATAACTCGCACAAATGCCGCTTAACGCTCGACG
* * * *
40548262 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACTTAACCCGGAA
* *
40548327 TT-GTATCTCGCACAAATGCC
65 TTAATAACTCGCACAAATGCC
40548347 TTCGGATCTT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
100 49 0.67
101 24 0.33
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (100 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGAAT
TAATAACTCGCACAAATGCCGCTTAACGCTCGACG
Found at i:40548348 original size:39 final size:40
Alignment explanation
Indices: 40548262--40548351 Score: 146
Period size: 40 Copynumber: 2.3 Consensus size: 40
40548252 ACGCTCGACG
*
40548262 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
* *
40548302 AAGGCCTTCGGGGCTTAACCCGGAATT-GTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
40548341 AATGCCTTCGG
1 AATGCCTTCGG
40548352 ATCTTAGTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 22 0.48
40 24 0.52
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
Found at i:40548413 original size:41 final size:41
Alignment explanation
Indices: 40548336--40548413 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
40548326 ATTGTATCTC
* * *
40548336 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
40548377 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
40548414 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:40551710 original size:39 final size:40
Alignment explanation
Indices: 40551639--40551818 Score: 242
Period size: 39 Copynumber: 4.6 Consensus size: 40
40551629 TCCTCGTTCA
* * * *
40551639 AATGCCTTCGGGAC-TAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
40551677 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
40551717 AATGCCTTCGAGAC-TAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
40551756 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
40551795 AAAGGCTTCGGGGCTTAACCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
40551819 ACTTGTATCT
Statistics
Matches: 128, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
38 14 0.11
39 79 0.62
40 35 0.27
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:40551781 original size:79 final size:78
Alignment explanation
Indices: 40551639--40551794 Score: 240
Period size: 79 Copynumber: 2.0 Consensus size: 78
40551629 TCCTCGTTCA
* * * *
40551639 AATGCCTTCGGGACTAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATTT
1 AATGCCTTCGAGACTAACCCGGATTTAATAACTCACACAATGCCTTCGGGACTTAACCCGGATTT
40551704 AATAACTCGCACG
66 AATAACTCGCACG
*
40551717 AATGCCTTCGAGACTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGAGACTAACCCGGATTTAATAACTCACAC-AATGCCTTCGGGACTTAACCCGGATT
* *
40551782 TAGTATCTCGCAC
65 TAATAACTCGCAC
40551795 AAAGGCTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
78 33 0.47
79 37 0.53
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (78 bp):
AATGCCTTCGAGACTAACCCGGATTTAATAACTCACACAATGCCTTCGGGACTTAACCCGGATTT
AATAACTCGCACG
Found at i:40551814 original size:79 final size:78
Alignment explanation
Indices: 40551642--40551818 Score: 230
Period size: 79 Copynumber: 2.3 Consensus size: 78
40551632 TCGTTCAAAT
* * * *
40551642 GCCTTCGGGACTAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATTTAAT
1 GCCTTCGAGACTAACCCGGATTTAATAACTCACACAATGCCTTCGGGACTTAACCCGGATTTAAT
*
40551707 AACTCGCACGAAT
66 AACTCGCACGAAA
* *
40551720 GCCTTCGAGACTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAG
1 GCCTTCGAGACTAACCCGGATTTAATAACTCACAC-AATGCCTTCGGGACTTAACCCGGATTTAA
*
40551785 TATCTCGCAC-AAA
65 TAACTCGCACGAAA
* * *
40551798 GGCTTCGGGGCTTAACCCGGA
1 GCCTTCGAGAC-TAACCCGGA
40551819 ACTTGTATCT
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
78 40 0.47
79 46 0.53
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (78 bp):
GCCTTCGAGACTAACCCGGATTTAATAACTCACACAATGCCTTCGGGACTTAACCCGGATTTAAT
AACTCGCACGAAA
Found at i:40551827 original size:39 final size:39
Alignment explanation
Indices: 40551644--40551844 Score: 165
Period size: 39 Copynumber: 5.2 Consensus size: 39
40551634 GTTCAAATGC
* ** * * * *
40551644 CTTCGGGAC-TAGCCCGGTTTTAGTAACTCACACAATGC
1 CTTCGGGACTTAACCCGGACTTAGTATCTCGCACAAAGG
* * * * *
40551682 CTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGC
1 CTTCGGGACTTAACCCGGACTTAGTATCTCGCAC-AAAGG
* * * * * *
40551722 CTTCGAGAC-TAACCCGGATTTAATAACTCGCACGAATGC
1 CTTCGGGACTTAACCCGGACTTAGTATCTCGCAC-AAAGG
*
40551761 CTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CTTCGGGACTTAACCCGGACTTAGTATCTCGCACAAAGG
* *
40551800 CTTCGGGGCTTAACCCGGAACTT-GTATCTCGCACAAATG
1 CTTCGGGACTTAACCCGG-ACTTAGTATCTCGCACAAAGG
40551839 CTTCGG
1 CTTCGG
40551845 ATCTTAGTCC
Statistics
Matches: 146, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
38 9 0.06
39 99 0.68
40 38 0.26
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
CTTCGGGACTTAACCCGGACTTAGTATCTCGCACAAAGG
Found at i:40551831 original size:79 final size:79
Alignment explanation
Indices: 40551642--40551844 Score: 216
Period size: 79 Copynumber: 2.6 Consensus size: 79
40551632 TCGTTCAAAT
* * ** * *
40551642 GCCTTCGGGACTAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGGATTTAA
1 GCCTTCGAGACTAACCCGGACTTAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAA
*
40551706 TAACTCGCACGAAT
66 TAACTCGCACGAAA
* * *
40551720 GCCTTCGAGACTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAG
1 GCCTTCGAGACTAACCCGGACTTAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAA
*
40551785 TATCTCGCAC-AAA
66 TAACTCGCACGAAA
* * * * *
40551798 GGCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCACAAATG-CTTCGG
1 GCCTTCGAGAC-TAACCCGG-ACTTAATAACTCGCACAAATGCCTTCGG
40551845 ATCTTAGTCC
Statistics
Matches: 107, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
78 46 0.43
79 58 0.54
80 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
GCCTTCGAGACTAACCCGGACTTAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAA
TAACTCGCACGAAA
Found at i:40551881 original size:118 final size:117
Alignment explanation
Indices: 40551637--40551896 Score: 269
Period size: 118 Copynumber: 2.2 Consensus size: 117
40551627 GCTCCTCGTT
* *
40551637 CAAATGCCTTCGGGAC-TAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA
* * * *
40551701 TTTAATAACTCGCACGAATGCCTTCGAGACTAACCCGGATTTAATAACTCGCA
65 CTTAATAACTCGCACAAATGCCTTCGAGACTAACCCGGATATAATAACTAGCA
* * * * * *
40551754 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCTTCGGGGCTTAACCCGGA
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGG-
* * ** * *
40551819 ACTT-GTATCTCGCACAAATG-CTTCG-GATCTTAGTCCGGATATATTCACTTAGCA
64 ACTTAATAACTCGCACAAATGCCTTCGAGA-C-TAACCCGGATATAATAAC-TAGCA
40551873 CAAAGCCTTC-GGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
40551897 CAGCATTCAA
Statistics
Matches: 117, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
116 2 0.02
117 31 0.26
118 76 0.65
119 8 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (117 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGAC
TTAATAACTCGCACAAATGCCTTCGAGACTAACCCGGATATAATAACTAGCA
Found at i:40551905 original size:40 final size:40
Alignment explanation
Indices: 40551830--40551905 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
40551820 CTTGTATCTC
* * *
40551830 GCACAAATGCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCTTCGGATCTTAGCCCGGACACATTCACTTA
40551870 GCACAAA-GCCTTCGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATG-CTTCGGATCTTAGCCCGGACA-CATTCA
40551906 ATTAATCATG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
39 12 0.39
40 19 0.61
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
GCACAAATGCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:40558979 original size:39 final size:39
Alignment explanation
Indices: 40558936--40559073 Score: 177
Period size: 39 Copynumber: 3.5 Consensus size: 39
40558926 CCAGACATAT
* * *
40558936 TTCCAGCACGTAGCCGGCGGACCTTAAGTCCGGTTATAA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
*
40558975 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGGTATAA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
* * * * *
40559014 TTCCAACATATAGCCTGCGGGTCTTTAAGCCCGGATATAA
1 TTCCAGCACATAGCCTGC-GGACCTTAAGTCCGGATATAA
*
40559054 TTCCAGCATATAGCCTGCGG
1 TTCCAGCACATAGCCTGCGG
40559074 GTCTTTAAGC
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 54 0.61
40 34 0.39
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
Found at i:40559053 original size:40 final size:40
Alignment explanation
Indices: 40558959--40559090 Score: 185
Period size: 40 Copynumber: 3.3 Consensus size: 40
40558949 CCGGCGGACC
* * * * *
40558959 TTAAGTCCGGTTATAATTCCAGCACATAGCCTGC-GGACC
1 TTAAGCCCGGATATAATTCCAGCATATAGCCTGCGGGTCT
* * *
40558998 TTAAGTCCGGGTATAATTCCAACATATAGCCTGCGGGTCT
1 TTAAGCCCGGATATAATTCCAGCATATAGCCTGCGGGTCT
40559038 TTAAGCCCGGATATAATTCCAGCATATAGCCTGCGGGTCT
1 TTAAGCCCGGATATAATTCCAGCATATAGCCTGCGGGTCT
40559078 TTAAGCCCGGATA
1 TTAAGCCCGGATA
40559091 CACATCAAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 31 0.37
40 53 0.63
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (40 bp):
TTAAGCCCGGATATAATTCCAGCATATAGCCTGCGGGTCT
Found at i:40564334 original size:40 final size:40
Alignment explanation
Indices: 40564279--40564500 Score: 331
Period size: 40 Copynumber: 5.6 Consensus size: 40
40564269 TATTCGAATG
* *
40564279 ATATCTGGGCTAAGTCCCAAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* *
40564319 ATATCCGGGCTAAGTCCCGAAGGGATTTGTGCTATTGGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
40564359 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* *
40564399 ATATCCGGGCTAAGTGCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* *
40564439 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-TTGACT
*
40564479 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
40564501 TACTTGGCTT
Statistics
Matches: 165, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
39 14 0.08
40 148 0.90
41 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
Found at i:40566528 original size:22 final size:22
Alignment explanation
Indices: 40566477--40566542 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
40566467 GGTATTTTGG
* *
40566477 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
40566498 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
40566520 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
40566543 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:40580022 original size:42 final size:42
Alignment explanation
Indices: 40579975--40580081 Score: 117
Period size: 43 Copynumber: 2.5 Consensus size: 42
40579965 ATAATTTATG
* *
40579975 TGTAAGACCATGTCTCGGACATCAGCATCG-TATTTGATTTCA
1 TGTAAGACCATGTCTGGGACAT-AGCATCGATATTTGATTACA
* * * * *
40580017 TGTAAGACCCTATTTGGGGCAGTGGCATCGATATTTGATTACA
1 TGTAAGACCATGTCTGGGACA-TAGCATCGATATTTGATTACA
*
40580060 TGTAAGACCACGTCTGGGACAT
1 TGTAAGACCATGTCTGGGACAT
40580082 TGGTATTGTA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 23 0.45
43 28 0.55
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATAGCATCGATATTTGATTACA
Found at i:40581656 original size:25 final size:25
Alignment explanation
Indices: 40581628--40581697 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
40581618 CTCTTTTAAT
*
40581628 AACTGGGGCAAAGCCCTTTTTGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
40581653 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
* *
40581678 AACTAGGGCAAAACCCTTTT
1 AACTGGGGCAAAGCCCTTTT
40581698 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:40581988 original size:27 final size:27
Alignment explanation
Indices: 40581957--40582234 Score: 288
Period size: 27 Copynumber: 10.3 Consensus size: 27
40581947 CGATGTTTCA
* **
40581957 GTAATTTCACAAATTAGGGGTATTTTG
1 GTAATTTTACAAACCAGGGGTATTTTG
** *
40581984 GTAATTTTGTAAACCAAGGGTATTTTG
1 GTAATTTTACAAACCAGGGGTATTTTG
*
40582011 GTAATTTTACAAACTAGGGGTATTTTG
1 GTAATTTTACAAACCAGGGGTATTTTG
** *
40582038 GTAATTTTTTAAACCAAGGGTATTTTG
1 GTAATTTTACAAACCAGGGGTATTTTG
*
40582065 GTAATTTTACAAACTAGGGGTATTTTG
1 GTAATTTTACAAACCAGGGGTATTTTG
* * * * * *
40582092 GTAATTGTATAAACCAAGGGTACTCTA
1 GTAATTTTACAAACCAGGGGTATTTTG
* *
40582119 CTAATTTTACAAACCAGGGGTATTTTA
1 GTAATTTTACAAACCAGGGGTATTTTG
*
40582146 GTAATTTTACAAACCAGGAGTATTTTG
1 GTAATTTTACAAACCAGGGGTATTTTG
* *
40582173 GTAATTTTACTAATC-GAGGGTATTTTG
1 GTAATTTTACAAACCAG-GGGTATTTTG
** * * * *
40582200 GTAATTTTGTAAATCAAGGGCATTTTA
1 GTAATTTTACAAACCAGGGGTATTTTG
40582227 GTAATTTT
1 GTAATTTT
40582235 GTAAATCGAG
Statistics
Matches: 206, Mismatches: 43, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
26 1 0.00
27 205 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAACCAGGGGTATTTTG
Found at i:40582015 original size:54 final size:54
Alignment explanation
Indices: 40581957--40582234 Score: 362
Period size: 54 Copynumber: 5.1 Consensus size: 54
40581947 CGATGTTTCA
* * *
40581957 GTAATTTCACAAATTAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTG
1 GTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTG
*
40582011 GTAATTTTACAAACTAGGGGTATTTTGGTAATTTTTTAAACCAAGGGTATTTTG
1 GTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTG
* * * *
40582065 GTAATTTTACAAACTAGGGGTATTTTGGTAATTGTATAAACCAAGGGTACTCTA
1 GTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTG
* * * *
40582119 CTAATTTTACAAACCAGGGGTATTTTAGTAATTTTACAAACC-AGGAGTATTTTG
1 GTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGG-GTATTTTG
* * * * * *
40582173 GTAATTTTACTAA-TCGAGGGTATTTTGGTAATTTTGTAAATCAAGGGCATTTTA
1 GTAATTTTACAAACTAG-GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTG
40582227 GTAATTTT
1 GTAATTTT
40582235 GTAAATCGAG
Statistics
Matches: 195, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
53 4 0.02
54 188 0.96
55 3 0.02
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (54 bp):
GTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTG
Found at i:40582257 original size:27 final size:27
Alignment explanation
Indices: 40582227--40582633 Score: 541
Period size: 27 Copynumber: 15.1 Consensus size: 27
40582217 GGGCATTTTA
* *
40582227 GTAATTTTGTAAATCGAGGATAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* **
40582254 GTAATTCTGTAAATTGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40582281 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
40582308 GTAA-T-TGATAAATCGAGGGTAAAACT-
1 GTAATTCTG-TAAATCGAGGGTAAAA-TG
* * * *
40582334 ATAATTCTATAAATCGAAGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40582361 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
40582388 GTTATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* **
40582415 GTAATTCTGTCAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40582442 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40582469 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
40582496 GTAATTCTATAAATTGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40582523 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* * *
40582550 ATAATTATGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40582577 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40582604 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
40582631 GTA
1 GTA
40582634 TGTAACAGCC
Statistics
Matches: 343, Mismatches: 32, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
25 2 0.01
26 21 0.06
27 319 0.93
28 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATG
Found at i:40584155 original size:28 final size:28
Alignment explanation
Indices: 40584115--40584193 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
40584105 GCAATCAAAT
* * *
40584115 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
40584143 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* * *
40584171 ATGACACATAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
40584194 CTAATGATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.28
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:40585938 original size:80 final size:81
Alignment explanation
Indices: 40585803--40585955 Score: 245
Period size: 80 Copynumber: 1.9 Consensus size: 81
40585793 TGTTACACGA
*
40585803 TAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAA
1 TAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAA
40585868 ATTGAGGGTAAAATGG
66 ATTGAGGGTAAAATGG
* ** *
40585884 TAATTCTGTAAATCAAGGGTAAAA-TGTAATTCTATAAATCGAGGGTAATTTGGTAATTTTATAA
1 TAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAA
*
40585948 TTTGAGGG
66 ATTGAGGG
40585956 CATTTCAGTA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
80 43 0.65
81 23 0.35
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (81 bp):
TAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAA
ATTGAGGGTAAAATGG
Found at i:40585955 original size:27 final size:27
Alignment explanation
Indices: 40585803--40585947 Score: 211
Period size: 27 Copynumber: 5.4 Consensus size: 27
40585793 TGTTACACGA
* *
40585803 TAATTCTGTAAATCGAGGGTAAAACGG
1 TAATTCTATAAATCGAGGGTAAAATGG
40585830 TAATTCTATAAATCGAGGGTAAAATGG
1 TAATTCTATAAATCGAGGGTAAAATGG
*
40585857 TAATTCTATAAATTGAGGGTAAAATGG
1 TAATTCTATAAATCGAGGGTAAAATGG
* *
40585884 TAATTCTGTAAATCAAGGGTAAAAT-G
1 TAATTCTATAAATCGAGGGTAAAATGG
**
40585910 TAATTCTATAAATCGAGGGTAATTTGG
1 TAATTCTATAAATCGAGGGTAAAATGG
*
40585937 TAATTTTATAA
1 TAATTCTATAA
40585948 TTTGAGGGCA
Statistics
Matches: 106, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
26 22 0.21
27 84 0.79
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (27 bp):
TAATTCTATAAATCGAGGGTAAAATGG
Found at i:40588448 original size:27 final size:27
Alignment explanation
Indices: 40588413--40588473 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
40588403 GGGGCAAAAT
40588413 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
40588440 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
40588467 AGTAATT
1 GGTAATT
40588474 TATCAAATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:40588513 original size:27 final size:27
Alignment explanation
Indices: 40588458--40588696 Score: 239
Period size: 27 Copynumber: 8.9 Consensus size: 27
40588448 TACCCTACAA
** *
40588458 GGGTATTTCAGTAA-TTTATCAAATCAG
1 GGGTATTTTGGTAATTTTAT-AAACCAG
* *
40588485 GGGTATTTTGGTAATTTTGTAAACTAG
1 GGGTATTTTGGTAATTTTATAAACCAG
* *
40588512 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAG
* * *
40588539 GGGTATTTTGGTAATTTTACAGACCAA
1 GGGTATTTTGGTAATTTTATAAACCAG
*
40588566 GGGTATTTTGGTAATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAG
** **
40588593 GGGTATTTTATTAATTTTACGAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAG
* *
40588620 GGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAG
* * * *
40588647 GGATATTTTGGTAATTTTACTGATCGA-
1 GGGTATTTTGGTAATTTTA-TAAACCAG
* *
40588674 GGGCATTTTGGTAATTTTGTAAA
1 GGGTATTTTGGTAATTTTATAAA
40588697 TCGATGGTAT
Statistics
Matches: 180, Mismatches: 30, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
26 2 0.01
27 171 0.95
28 7 0.04
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAACCAG
Found at i:40588516 original size:81 final size:81
Alignment explanation
Indices: 40588428--40588718 Score: 243
Period size: 81 Copynumber: 3.6 Consensus size: 81
40588418 TTCTACCCTA
** * *
40588428 CAAGGGTATTTCGGT-A-TTTCTACCCTACAAGGGTATTTCAGTAA-TTTATCAAATCAGGGGTA
1 CAAGGGTATTTCGGTAATTTTCTAAAC--CAAGGGTATTTCAGTAATTTTA-CAAACCAAGGGTA
*
40588490 TTTTGGTAATTTTGTAAAC
63 TTTTGGTAATTTTATAAAC
* * * * ** *
40588509 TAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACAGACCAAGGGTATTT
1 CAAGGGTATTTCGGTAATTTTCTAAACCAAGGGTATTTCAGTAATTTTACAAACCAAGGGTATTT
40588574 TGGTAATTTTATAAAC
66 TGGTAATTTTATAAAC
*** * * *
40588590 CAAGGGTATTTTATTAATTTTAC-GAACCAGGGGTATTTTAGTAATTTTACAAACC-AGGGATAT
1 CAAGGGTATTTCGGTAATTTT-CTAAACCAAGGGTATTTCAGTAATTTTACAAACCAAGGG-TAT
* *
40588653 TTTGGTAATTTTACT-GAT
64 TTTGGTAATTTTA-TAAAC
* * * * * * *
40588671 CGAGGGCATTTTGGTAATTTTGTAAATCGATGGTATTTCAGTAATTTT
1 CAAGGGTATTTCGGTAATTTTCTAAACCAAGGGTATTTCAGTAATTTT
40588719 GTAAATCGAG
Statistics
Matches: 169, Mismatches: 34, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
80 4 0.02
81 153 0.91
82 6 0.04
83 6 0.04
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.41
Consensus pattern (81 bp):
CAAGGGTATTTCGGTAATTTTCTAAACCAAGGGTATTTCAGTAATTTTACAAACCAAGGGTATTT
TGGTAATTTTATAAAC
Found at i:40588682 original size:54 final size:54
Alignment explanation
Indices: 40588428--40588691 Score: 241
Period size: 54 Copynumber: 4.9 Consensus size: 54
40588418 TTCTACCCTA
* *** ** *
40588428 CAAGGGTATTTCGGT-ATTTCTACCCTACAAGGGTATTTCAGTAA-TTTATCAAAT
1 CAAGGGTATTTTGGTAATTT-TACTGAACAAGGGTATTTTGGTAATTTTA-CAAAC
* * * * **
40588482 CAGGGGTATTTTGGTAATTTT-GTAAACTAGGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACTGAAC-AAGGGTATTTTGGTAATTTTACAAAC
* * *
40588536 CAAGGGTATTTTGGTAATTTTACAGACCAAGGGTATTTTGGTAATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTACTGAACAAGGGTATTTTGGTAATTTTACAAAC
** * *
40588590 CAAGGGTATTTTATTAATTTTAC-GAACCAGGGGTATTTTAGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACTGAA-CAAGGGTATTTTGGTAATTTTACAAAC
* * *
40588644 C-AGGGATATTTTGGTAATTTTACTGATCGAGGGCATTTTGGTAATTTT
1 CAAGGG-TATTTTGGTAATTTTACTGAACAAGGGTATTTTGGTAATTTT
40588692 GTAAATCGAT
Statistics
Matches: 171, Mismatches: 32, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
53 8 0.05
54 152 0.89
55 11 0.06
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (54 bp):
CAAGGGTATTTTGGTAATTTTACTGAACAAGGGTATTTTGGTAATTTTACAAAC
Found at i:40588699 original size:27 final size:26
Alignment explanation
Indices: 40588454--40588732 Score: 209
Period size: 27 Copynumber: 10.3 Consensus size: 26
40588444 TTTCTACCCT
**
40588454 ACAAGGGTATTTCAGTAA-TTTATCAA
1 ACAAGGGTATTTTGGTAATTTTAT-AA
* *
40588480 ATCAGGGGTATTTTGGTAATTTTGTAA
1 A-CAAGGGTATTTTGGTAATTTTATAA
* *
40588507 ACTAGGGGTATTTTGGTAATTTTGTAA
1 AC-AAGGGTATTTTGGTAATTTTATAA
*
40588534 ACCAAGGGTATTTTGGTAATTTTACAGA
1 A-CAAGGGTATTTTGGTAATTTTATA-A
*
40588562 CCAAGGGTATTTTGGTAATTTTATAA
1 ACAAGGGTATTTTGGTAATTTTATAA
** *
40588588 ACCAAGGGTATTTTATTAATTTTACGAA
1 A-CAAGGGTATTTTGGTAATTTTA-TAA
* * * *
40588616 CCAGGGGTATTTTAGTAATTTTACAA
1 ACAAGGGTATTTTGGTAATTTTATAA
* *
40588642 ACCAGGGATATTTTGGTAATTTTACTGA
1 ACAAGGG-TATTTTGGTAATTTTA-TAA
* * * *
40588670 TCGAGGGCATTTTGGTAATTTTGTAA
1 ACAAGGGTATTTTGGTAATTTTATAA
* * ** *
40588696 ATCGATGGTATTTCAGTAATTTTGTAA
1 A-CAAGGGTATTTTGGTAATTTTATAA
*
40588723 ATCGAGGGTA
1 A-CAAGGGTA
40588733 AAATAGTAAT
Statistics
Matches: 209, Mismatches: 34, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
26 11 0.05
27 184 0.88
28 14 0.07
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.40
Consensus pattern (26 bp):
ACAAGGGTATTTTGGTAATTTTATAA
Found at i:40589202 original size:27 final size:27
Alignment explanation
Indices: 40588711--40589190 Score: 620
Period size: 27 Copynumber: 17.8 Consensus size: 27
40588701 TGGTATTTCA
* * *
40588711 GTAATTTTGTAAATCGAGGGTAAAATA
1 GTAATTCTATAAATCGAGGGTAAAATG
* ** * *
40588738 GTAATTCTGTAAATTAAGGGTGAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
40588765 GTAATTCTGTAAGTCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
40588792 GTAATTCTATAAATCGCGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
**
40588819 GTAATTCTATAAATCGAGGGTAAAACA
1 GTAATTCTATAAATCGAGGGTAAAATG
*
40588846 GTAATTCTATCAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
40588873 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
* * *
40588900 GTAATTTTGTAAATTGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
40588927 GTAATTCTGTAAATCGAGGGTAAAACT-
1 GTAATTCTATAAATCGAGGGTAAAA-TG
* * *
40588954 GTAATTTTATAAATTGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
* **
40588981 ATAATTCTATAAATCGAGGGTAAAACA
1 GTAATTCTATAAATCGAGGGTAAAATG
* * *
40589008 ATAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
* * *
40589035 ATAATTCTATAAATTGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
40589062 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
40589089 GTAATTCTATAAATCGAGGGTAAGATG
1 GTAATTCTATAAATCGAGGGTAAAATG
* * *
40589116 GTAATTCTGTAAATTGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
40589143 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
40589170 GTAATTCTGTAAATCGAGGGT
1 GTAATTCTATAAATCGAGGGT
40589191 GCTTTGGTAA
Statistics
Matches: 401, Mismatches: 50, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
27 400 1.00
28 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (27 bp):
GTAATTCTATAAATCGAGGGTAAAATG
Found at i:40591416 original size:25 final size:24
Alignment explanation
Indices: 40591388--40591464 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 24
40591378 GCCTAGCCTC
*
40591388 TTTTAATAATTGGGGCAAAGCCCT
1 TTTTTATAATTGGGGCAAAGCCCT
* * *
40591412 TTTTTGTAAACTGGAGCAAAGCCCT
1 TTTTTAT-AATTGGGGCAAAGCCCT
*
40591437 TTTCGGTA-AATTGGGGCAAAGCCCT
1 TTT--TTATAATTGGGGCAAAGCCCT
40591462 TTT
1 TTT
40591465 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
24 5 0.12
25 36 0.86
27 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (24 bp):
TTTTTATAATTGGGGCAAAGCCCT
Found at i:40591704 original size:27 final size:27
Alignment explanation
Indices: 40591669--40591722 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
40591659 CGGGCAAAAT
*
40591669 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
40591696 GGTATTTCTACCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
40591723 ATTAATTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:40591772 original size:54 final size:54
Alignment explanation
Indices: 40591725--40591961 Score: 289
Period size: 54 Copynumber: 4.4 Consensus size: 54
40591715 GGTATTTCAT
*
40591725 TAATTTCACAAATCAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
1 TAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
**
40591779 TAATTTTGTAAA-CTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
1 TAATTTTACAAATC-AAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
* * * *
40591833 TAATTTTATAAACCAAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGG
1 TAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
** * ** * *
40591887 TAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAA-TCAAGGGTATTTTAG
1 TAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTGG
** *
40591941 TAATTTTGTAAATCGAGGGTA
1 TAATTTTACAAATCAAGGGTA
40591962 AAATGGTAAT
Statistics
Matches: 159, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 157 0.99
55 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (54 bp):
TAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
Found at i:40591796 original size:81 final size:81
Alignment explanation
Indices: 40591711--40591952 Score: 299
Period size: 81 Copynumber: 3.0 Consensus size: 81
40591701 TTCTACCCTA
*** * * *
40591711 TAAGGGTATTTCATTAATTTCACAAATCAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTT
1 TAAGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTATAAACTAAGGGTATTT
*
40591776 TGGTAATTTTGTAAAC
66 TAGTAATTTTGTAAAC
* *
40591792 TAAGGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATT
1 TAAGGGTATTTTGGTAATTTTACAAATC-AAGGGTATTTTGGTAATTTTATAAACTAAGGGTATT
**
40591856 TTAGTAATTTTACAAAC
65 TTAGTAATTTTGTAAAC
* * ** * *
40591873 CAGGGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAA-TCAAGGGTATT
1 TAAGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTATAAACT-AAGGGTATT
40591937 TTAGTAATTTTGTAAA
65 TTAGTAATTTTGTAAA
40591953 TCGAGGGTAA
Statistics
Matches: 137, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
80 1 0.01
81 135 0.99
82 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (81 bp):
TAAGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTATAAACTAAGGGTATTT
TAGTAATTTTGTAAAC
Found at i:40591948 original size:27 final size:27
Alignment explanation
Indices: 40591725--40592353 Score: 258
Period size: 27 Copynumber: 23.3 Consensus size: 27
40591715 GGTATTTCAT
* *
40591725 TAATTTCACAAATCAAGGGTATTTTGG
1 TAATTTTATAAATCAAGGGTATTTTGG
* *
40591752 TAATTTTACAAA-CTAGGGGTATTTTGG
1 TAATTTTATAAATC-AAGGGTATTTTGG
*
40591779 TAATTTTGTAAA-CTAAGGGTATTTTGG
1 TAATTTTATAAATC-AAGGGTATTTTGG
* *
40591806 TAATTTTACAAA-CTAGGGGTATTTTGG
1 TAATTTTATAAATC-AAGGGTATTTTGG
* *
40591833 TAATTTTATAAACCAAGGGTATTTTAG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * *
40591860 TAATTTTACAAACCAGGGGTATTTTGG
1 TAATTTTATAAATCAAGGGTATTTTGG
* *
40591887 TAATTTTACT-GATCGAGGGTATTTTGG
1 TAATTTTA-TAAATCAAGGGTATTTTGG
* *
40591914 TAATTTTGTAAATCAAGGGTATTTTAG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * ***
40591941 TAATTTTGTAAATCGAGGGTAAAATGG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * *****
40591968 TAATTTTGTAAATCGAGGGTAAAACAG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * * * ****
40591995 TAATTCTGTAAGTCGAGGGTAAAACGG
1 TAATTTTATAAATCAAGGGTATTTTGG
* ***
40592022 TAATTCTATAAATCAAGGGTAAAATGG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * *****
40592049 TAATTTTGTAAATCGAGGGTAAAACAG
1 TAATTTTATAAATCAAGGGTATTTTGG
* ***
40592076 TAATTTTATAAATCTAGGGTAAAATGG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * * * *** *
40592103 TAATTCTGTAAATCGATGGTAAAATAG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * * ****
40592130 TAATTCTGTAAATCGAGGGTAAAACGG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * ***
40592157 TAATTCTATAAATCTAGGGTAAAATGG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * * ****
40592184 TAATTCTGTAAATCGAGGGTAAAACGG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * ***
40592211 TAATTCTATAAATCGAGGGTAAAATGG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * ***
40592238 TAATTCTATAAATCGAGGGTAAAATGG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * ****
40592265 TAATTCTATAAATCGAGGGTAAAACGG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * ***
40592292 TAATTCTATAAATCGAGGGTAAAATGG
1 TAATTTTATAAATCAAGGGTATTTTGG
* * ** *
40592319 TAATTCTGTAAATCGCGGGTACTTTGG
1 TAATTTTATAAATCAAGGGTATTTTGG
40592346 TAATTTTA
1 TAATTTTA
40592354 CAATTTGAGG
Statistics
Matches: 527, Mismatches: 71, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
26 2 0.00
27 524 0.99
28 1 0.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (27 bp):
TAATTTTATAAATCAAGGGTATTTTGG
Found at i:40592350 original size:54 final size:54
Alignment explanation
Indices: 40591940--40592339 Score: 575
Period size: 54 Copynumber: 7.4 Consensus size: 54
40591930 GGGTATTTTA
* * * **
40591940 GTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATG
* * *
40591994 GTAATTCTGTAAGTCGAGGGTAAAACGGTAATTCTATAAATCAAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATG
* ** * *
40592048 GTAATTTTGTAAATCGAGGGTAAAACAGTAATTTTATAAATCTAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATG
* * * *
40592102 GTAATTCTGTAAATCGATGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATG
* * * *
40592156 GTAATTCTATAAATCTAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATG
*
40592210 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATG
* *
40592264 GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATG
*
40592318 GTAATTCTGTAAATCGCGGGTA
1 GTAATTCTGTAAATCGAGGGTA
40592340 CTTTGGTAAT
Statistics
Matches: 316, Mismatches: 30, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 316 1.00
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (54 bp):
GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATG
Found at i:40592350 original size:81 final size:81
Alignment explanation
Indices: 40591940--40592339 Score: 584
Period size: 81 Copynumber: 4.9 Consensus size: 81
40591930 GGGTATTTTA
* * * *
40591940 GTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTA
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATA
* *
40592005 AGTCGAGGGTAAAACG
66 AATCGAGGGTAAAATG
* * * * *
40592021 GTAATTCTATAAATCAAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACAGTAATTTTATA
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATA
*
40592086 AATCTAGGGTAAAATG
66 AATCGAGGGTAAAATG
* *
40592102 GTAATTCTGTAAATCGATGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATA
*
40592167 AATCTAGGGTAAAATG
66 AATCGAGGGTAAAATG
* * *
40592183 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATA
40592248 AATCGAGGGTAAAATG
66 AATCGAGGGTAAAATG
* * * * *
40592264 GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTA
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATA
*
40592329 AATCGCGGGTA
66 AATCGAGGGTA
40592340 CTTTGGTAAT
Statistics
Matches: 295, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 295 1.00
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (81 bp):
GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATA
AATCGAGGGTAAAATG
Found at i:40594575 original size:70 final size:69
Alignment explanation
Indices: 40594477--40594611 Score: 207
Period size: 70 Copynumber: 1.9 Consensus size: 69
40594467 CTCCGGAAGA
* * * *
40594477 ATGCATAAAATGTTTCTTTCACTTTTGAGGGATATGACGCATCATTGGTGGAAGACATTGATATT
1 ATGCATAAAATGTGTCTTTCACTTTTGAGAGATACGACACATCATTGGTGGAAGACATTGATATT
40594542 AAGG
66 AAGG
* *
40594546 ATGCATAAAATGTGTCGTTTCACTTTTGAGAGATACGACATATTATTGGTGGAAGACATTGATAT
1 ATGCATAAAATGTGTC-TTTCACTTTTGAGAGATACGACACATCATTGGTGGAAGACATTGATAT
40594611 T
65 T
40594612 TGTGGTTCCG
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
69 15 0.25
70 44 0.75
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (69 bp):
ATGCATAAAATGTGTCTTTCACTTTTGAGAGATACGACACATCATTGGTGGAAGACATTGATATT
AAGG
Found at i:40609048 original size:50 final size:49
Alignment explanation
Indices: 40608926--40609163 Score: 282
Period size: 49 Copynumber: 4.8 Consensus size: 49
40608916 TGAGGTCGCA
* * * *
40608926 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCA-AAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGATAA-T-TGGTCACG
* **
40608977 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACG
* *
40609027 TGTGTAGTACTAAGTGTAGGCTACTACGTGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* * *
40609076 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GAATAAGTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATAATTGGTCACG
* * *
40609125 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
40609164 GCTTTGGCTA
Statistics
Matches: 164, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
48 1 0.01
49 85 0.52
50 47 0.29
51 31 0.19
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Found at i:40609105 original size:99 final size:101
Alignment explanation
Indices: 40608926--40609158 Score: 296
Period size: 99 Copynumber: 2.3 Consensus size: 101
40608916 TGAGGTCGCA
*
40608926 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAAAAACTGTGATCACGTGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCAAAAACTGTGATCACGTGTGTAGTACTAAG
40608991 TGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
66 TGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
* * ** * *
40609027 TGTGTAGTACTAAGTGTAGGCTACTACGTGTACCGGATAA-T-TGGTCACGTGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCAAAAACTGTGATCACGTGTGTAGTACTAAG
* * * *
40609090 TGCAGGCTACTACGTGTA-CCGAATAAG-T-GGTCGCA
66 TGCAGGCTACTACGTGTATCAG-AT-GGTTAGGTCACG
* *
40609125 TGTGTAGTACTATGTGCAGGCTACTATGCGTACC
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACC
40609159 AGATAGCTTT
Statistics
Matches: 115, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
98 37 0.32
99 42 0.37
100 2 0.02
101 34 0.30
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (101 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCAAAAACTGTGATCACGTGTGTAGTACTAAG
TGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
Found at i:40614124 original size:38 final size:38
Alignment explanation
Indices: 40614064--40614138 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
40614054 GGACGTTAGC
*
40614064 ATCGACTTATGATTTACATGTAAGACCATGTCTGGGAT
1 ATCGACTTATGATTTACATGTAAGACCATGCCTGGGAT
* * *
40614102 ATCGACATTTTGATTT-CGTGTAAGACCCTGCCTGGGA
1 ATCGAC-TTATGATTTACATGTAAGACCATGCCTGGGA
40614139 CAATGGCATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 24 0.75
39 8 0.25
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (38 bp):
ATCGACTTATGATTTACATGTAAGACCATGCCTGGGAT
Found at i:40614189 original size:43 final size:42
Alignment explanation
Indices: 40614038--40614190 Score: 113
Period size: 43 Copynumber: 3.7 Consensus size: 42
40614028 CGTGTTTTTG
* * *
40614038 TGTAAGACCACATCTGGGACGTTAGCATCGACTTATGATTTACA
1 TGTAAGACCACATCTGGGACGTTGGCATC-AATTTTGA-TTACA
** * * *
40614082 TGTAAGACCATGTCTGGGA--TATCG-A-C-ATTTTGATTTCG
1 TGTAAGACCACATCTGGGACGT-TGGCATCAATTTTGATTACA
**
40614120 TGTAAGACC-C-TGCCTGGGACAATGGCATCAATATTTGATTACA
1 TGTAAGACCACAT--CTGGGACGTTGGCATCAAT-TTTGATTACA
40614163 TGTAAGACCACATCTGGGACGTTGGCAT
1 TGTAAGACCACATCTGGGACGTTGGCAT
40614191 TGTACGATCT
Statistics
Matches: 84, Mismatches: 14, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
36 1 0.01
38 18 0.21
39 7 0.08
40 1 0.01
41 2 0.02
42 4 0.05
43 32 0.38
44 18 0.21
45 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (42 bp):
TGTAAGACCACATCTGGGACGTTGGCATCAATTTTGATTACA
Found at i:40624585 original size:40 final size:41
Alignment explanation
Indices: 40624541--40624685 Score: 226
Period size: 40 Copynumber: 3.6 Consensus size: 41
40624531 CTTGCTCAAT
40624541 TGCCTTCGGGACTTAGCCC-GATTATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAA
40624581 TGCCTTCGGGACTTAGCCCGGA-TATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAA
* * *
40624621 TGCCTTCGGGACTTAGCCCGGAAT-TAGTCACTAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAA
*
40624661 CGCCTTCGGGACTTAGCCC-GATTAT
1 TGCCTTCGGGACTTAGCCCGGATTAT
40624686 CATCCGAATA
Statistics
Matches: 98, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
39 3 0.03
40 92 0.94
41 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (41 bp):
TGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAA
Found at i:40624636 original size:80 final size:80
Alignment explanation
Indices: 40624504--40624680 Score: 234
Period size: 80 Copynumber: 2.2 Consensus size: 80
40624494 AAACCAAGTA
* * * * * *
40624504 CCTTCGGAATTTAG-CCGGATATAGCTACTTGCTCAATTGCCTTCGGGACTTAGCCC-GATTATA
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TA
* *
40624567 GTAACTCGCACAAATG
65 GTAACTAGCACAAACG
40624583 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
1 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
*
40624647 GTCACTAGCACAAACG
65 GTAACTAGCACAAACG
40624663 CCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
40624681 ATTATCATCC
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
79 13 0.15
80 70 0.81
81 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAG
TAACTAGCACAAACG
Found at i:40628178 original size:29 final size:27
Alignment explanation
Indices: 40628160--40628229 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
40628150 ATATTAAGTC
40628160 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
40628187 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
40628215 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
40628230 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:40628223 original size:28 final size:28
Alignment explanation
Indices: 40628160--40628257 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
40628150 ATATTAAGTC
*
40628160 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
40628187 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
40628215 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
40628244 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40628258 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:40647208 original size:40 final size:40
Alignment explanation
Indices: 40647131--40647308 Score: 288
Period size: 40 Copynumber: 4.5 Consensus size: 40
40647121 AACCCAAGTA
* *
40647131 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
40647170 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40647210 CCTTCGGGACTTAGCCCGGATATCGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40647250 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40647290 CCTTCTGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40647309 TTATCATCCG
Statistics
Matches: 130, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 14 0.11
40 116 0.89
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40648635 original size:37 final size:37
Alignment explanation
Indices: 40648577--40648758 Score: 319
Period size: 37 Copynumber: 4.9 Consensus size: 37
40648567 GCTCAGACGA
* * * *
40648577 AATCTCCACATGAAGTTATCGGGTCTTACCCGGACAA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
40648614 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
40648651 AATCTCCACACGTAGTCATCGGGTCTTACCCAGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
40648688 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
40648725 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
40648759 ATATATTTCC
Statistics
Matches: 139, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 139 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:40649029 original size:47 final size:47
Alignment explanation
Indices: 40648967--40649600 Score: 845
Period size: 47 Copynumber: 13.1 Consensus size: 47
40648957 ACACGTTTCG
* * * **
40648967 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * *
40649014 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
40649061 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* ** *
40649108 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C----ACATACGCATGTTCACATTCATCA
40649161 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
40649208 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
40649255 CATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* ** *
40649302 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C----ACATACGCATGTTCACATTCATCA
***
40649355 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCA
*
40649406 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
40649453 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
***
40649500 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCA
* *
40649551 CATTGGTCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
40649598 CAT
1 CAT
40649601 AAAATCCTAA
Statistics
Matches: 530, Mismatches: 37, Indels: 40
0.87 0.06 0.07
Matches are distributed among these distances:
47 354 0.67
49 2 0.00
51 89 0.17
53 85 0.16
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.31
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Done.