Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 52 of 318
Found at i:19092467 original size:54 final size:55
Alignment explanation
Indices: 19092282--19092499 Score: 306
Period size: 54 Copynumber: 4.1 Consensus size: 55
19092272 CACGTGAGCC
* *
19092282 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
* *
19092337 AAGGCTCAACTCACCTCTCGCAATATGATTTGATTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAA
* *
19092388 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
*
19092442 AAGGCTCAACTCACCTCTCGGAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
19092497 AAG
1 AAG
19092500 TAGAAATTGA
Statistics
Matches: 147, Mismatches: 9, Indels: 14
0.86 0.05 0.08
Matches are distributed among these distances:
50 14 0.10
51 33 0.22
52 1 0.01
54 51 0.35
55 36 0.24
56 6 0.04
57 6 0.04
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:19092497 original size:14 final size:14
Alignment explanation
Indices: 19092478--19092512 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
19092468 GAGTTGATTT
19092478 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
19092492 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
19092506 TTGAAAA
1 TTGAAAA
19092513 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:19092745 original size:85 final size:87
Alignment explanation
Indices: 19092601--19092848 Score: 299
Period size: 85 Copynumber: 2.8 Consensus size: 87
19092591 AATAGAAATT
* * * *
19092601 AAAAATAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
19092666 TTGATTTGAAAAG-TAGAATT-AG
65 TTGATTTGAAAAGATAG-ATTGAA
* * * *
19092688 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
19092751 TTGATTTTTGAAAAGCATAGATTGAA
65 TTGA--TTTGAAAAG-ATAGATTGAA
*
19092777 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
19092841 GTTGATTT
64 GTTGATTT
19092849 TTGAAAAACA
Statistics
Matches: 137, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 31 0.23
88 3 0.02
89 31 0.23
91 33 0.24
93 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTGAAAAGATAGATTGAA
Found at i:19092794 original size:15 final size:16
Alignment explanation
Indices: 19092761--19092794 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19092751 TTGATTTTTG
* *
19092761 AAAAGCATAGATTGAA
1 AAAAACATAAATTGAA
19092777 AAAAACATAAATTGAA
1 AAAAACATAAATTGAA
19092793 AA
1 AA
19092795 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAACATAAATTGAA
Found at i:19092836 original size:91 final size:88
Alignment explanation
Indices: 19092601--19092855 Score: 315
Period size: 91 Copynumber: 2.9 Consensus size: 88
19092591 AATAGAAATT
* * * *
19092601 AAAAATAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
19092666 TTGA--TTTGAAAAGTAGAATTAG
65 TTGATTTTTGAAAAGTAGAATTAA
* * * *
19092688 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
19092751 TTGATTTTTGAAAAGCATAG-ATTGAA
65 TTGATTTTTGAAAAG--TAGAATT-AA
*
19092777 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
19092841 GTTGATTTTTGAAAA
64 GTTGATTTTTGAAAA
19092856 ACAAAAATTA
Statistics
Matches: 144, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
84 3 0.02
85 33 0.23
87 31 0.22
88 3 0.02
89 28 0.19
91 43 0.30
93 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (88 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTTTGAAAAGTAGAATTAA
Found at i:19093013 original size:73 final size:73
Alignment explanation
Indices: 19092900--19093045 Score: 220
Period size: 73 Copynumber: 2.0 Consensus size: 73
19092890 TATGAGTCAA
* * **
19092900 TTTAAAACATAATCTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAG
1 TTTAAAAAAAAATCTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAG
19092965 TTGATTTT
66 TTGATTTT
* * **
19092973 TTTAAAAAAAAATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
1 TTTAAAAAAAAATCTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAG
19093038 TTGATTTT
66 TTGATTTT
19093046 GAAAAACAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.34
Consensus pattern (73 bp):
TTTAAAAAAAAATCTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAG
TTGATTTT
Found at i:19093057 original size:73 final size:71
Alignment explanation
Indices: 19092868--19093063 Score: 211
Period size: 73 Copynumber: 2.7 Consensus size: 71
19092858 AAAAATTAAA
* ** * * * * **
19092868 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAAC-ATAATCTAAAAATACCTCGGCGT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTAAAACAAAAATTTAAAAATACCTCAACGT
19092931 GCCCCG
66 GCCCCG
19092937 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTAAAA-AAAAATTTAAAAATACCTCAA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGA---TTTTAAAACAAAAATTTAAAAATACCTCAA
* **
19093001 CGTGTCTTG
63 CGTGCCCCG
19093010 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAA-TTAAAA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT--AAAACAAAAATTTAAAA
19093064 GGCTTAACTC
Statistics
Matches: 107, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
69 25 0.23
70 6 0.06
72 10 0.09
73 66 0.62
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (71 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTAAAACAAAAATTTAAAAATACCTCAACGT
GCCCCG
Found at i:19093451 original size:122 final size:122
Alignment explanation
Indices: 19093325--19093551 Score: 305
Period size: 122 Copynumber: 1.9 Consensus size: 122
19093315 GCGTGCCCCG
* * * * **
19093325 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTAAA-A-AATTTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAG-TCA-ATTTAAAACATAAACTAAAAATACCTCAACGT
* ** *
19093388 GTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
64 GCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
* **
19093447 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAACGTGC
19093512 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
66 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
19093552 TTTAAAAAAT
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
120 6 0.07
121 3 0.03
122 81 0.90
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (122 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAACGTGC
CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
Found at i:19093464 original size:191 final size:193
Alignment explanation
Indices: 19092813--19093621 Score: 1516
Period size: 191 Copynumber: 4.2 Consensus size: 193
19092803 CATGTGAGCC
** *
19092813 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
*
19092878 CACCTCTCGCAATATGAGTCAATTTAAAACATAATCTAAAAATACCTCGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
*
19092943 AACTCATTTCTCGCAATATGAGTTGATTTTTTTAAAAAAAAATTTAAAAATACCTCAACGTGTCT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTT--AAAAAAATTTAAAAATACCTCAACGTGTCT
19093008 T
193 T
19093009 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
*
19093074 ACCTCCCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
19093139 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
19093202 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
19093267 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
19093332 ACTCACTTCTCGCAATATGAGTTGA-TTTTTT-AAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
19093393 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
19093458 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
19093523 ACTCACTTCTCGCAATATGAGTTGATTTTTTT-AAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
19093585 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
19093622 CCTTGGAAAG
Statistics
Matches: 605, Mismatches: 7, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
191 185 0.31
192 79 0.13
193 185 0.31
195 126 0.21
196 30 0.05
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (193 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:19093560 original size:384 final size:385
Alignment explanation
Indices: 19092813--19093621 Score: 1514
Period size: 384 Copynumber: 2.1 Consensus size: 385
19092803 CATGTGAGCC
** *
19092813 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
*
19092878 CACCTCTCGCAATATGAGTCAATTTAAAACATAATCTAAAAATACCTCGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
*
19092943 AACTCATTTCTCGCAATATGAGTTGATTTTTTTAAAAAAAAATTTAAAAATACCTCAACGTGTCT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTT--AAAAAAATTTAAAAATACCTCAACGTGTCT
19093008 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACT
193 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACT
19093073 CACCTCCCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
258 CACCTCCCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
19093138 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
323 AACTCACTTCTCGCAATATGAGTTGATTTTTTT-AAAAAATTTAAAAATACCTCAACGTGTCTT
19093202 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
19093267 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
19093332 ACTCACTTCTCGCAATATGAGTTGA-TTTTTT-AAAAAATTTAAAAATACCTCAACGTGTCTTGA
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTTGA
19093395 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
196 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
*
19093460 CTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAAC
261 CTCCCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAAC
19093525 TCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
326 TCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
19093585 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
19093622 CCTTGGAAAG
Statistics
Matches: 414, Mismatches: 6, Indels: 6
0.97 0.01 0.01
Matches are distributed among these distances:
383 67 0.16
384 191 0.46
387 6 0.01
388 120 0.29
389 30 0.07
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (385 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTTGA
GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
CTCCCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAAC
TCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:19101612 original size:56 final size:57
Alignment explanation
Indices: 19101540--19101646 Score: 162
Period size: 56 Copynumber: 1.9 Consensus size: 57
19101530 GATCCGATTG
* * *
19101540 AAAAATGAAAACTTTTTTTTAAGACACGAGAATTTTGAAGCACGGAAATTTTTTTTA
1 AAAAATGAAAACTTTTTTTAAAAACACGAGAATTTTGAAACACGGAAATTTTTTTTA
* *
19101597 AAAAATG-AAATTTTTTTTAAAAACACGAGAATTTTTAAACACGGAAATTT
1 AAAAATGAAAACTTTTTTTAAAAACACGAGAATTTTGAAACACGGAAATTT
19101647 CAGAAACACG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
56 38 0.84
57 7 0.16
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (57 bp):
AAAAATGAAAACTTTTTTTAAAAACACGAGAATTTTGAAACACGGAAATTTTTTTTA
Found at i:19101631 original size:17 final size:17
Alignment explanation
Indices: 19101610--19101705 Score: 97
Period size: 17 Copynumber: 5.6 Consensus size: 17
19101600 AATGAAATTT
19101610 TTTTTAAAAACACGAGAA
1 TTTTT-AAAACACGAGAA
19101628 TTTTT-AAACACG-GAA
1 TTTTTAAAACACGAGAA
* * *
19101643 ATTTCAGAAACACGAAAA
1 TTTTTA-AAACACGAGAA
***
19101661 TTTTTAAAACACGACCT
1 TTTTTAAAACACGAGAA
*
19101678 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGAGAA
19101695 TTTTTAAAACA
1 TTTTTAAAACA
19101706 AGACATTTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 7
0.76 0.16 0.09
Matches are distributed among these distances:
15 6 0.10
16 7 0.11
17 38 0.61
18 11 0.18
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (17 bp):
TTTTTAAAACACGAGAA
Found at i:19101638 original size:16 final size:16
Alignment explanation
Indices: 19101617--19101715 Score: 76
Period size: 17 Copynumber: 6.0 Consensus size: 16
19101607 TTTTTTTTAA
19101617 AAACACGAGAATTTTT
1 AAACACGAGAATTTTT
**
19101633 AAACACG-GAAATTTCAG
1 AAACACGAG-AATTT-TT
*
19101650 AAACACGAAAATTTTT
1 AAACACGAGAATTTTT
***
19101666 AAAACACGACCTTTTTT
1 -AAACACGAGAATTTTT
19101683 GAAACACGAGAATTTTT
1 -AAACACGAGAATTTTT
*
19101700 AAA-ACAAGACATTTTT
1 AAACACGAGA-ATTTTT
19101716 TGAAACACAA
Statistics
Matches: 65, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
15 6 0.09
16 21 0.32
17 38 0.58
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.29
Consensus pattern (16 bp):
AAACACGAGAATTTTT
Found at i:19101687 original size:34 final size:34
Alignment explanation
Indices: 19101649--19101723 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
19101639 GGAAATTTCA
* *
19101649 GAAACACGAAAATTTTTAAAACACGACCTTTTTT
1 GAAACACGAAAATTTTTAAAACAAGACATTTTTT
*
19101683 GAAACACGAGAATTTTTAAAACAAGACATTTTTT
1 GAAACACGAAAATTTTTAAAACAAGACATTTTTT
19101717 GAAACAC
1 GAAACAC
19101724 AATTTTTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (34 bp):
GAAACACGAAAATTTTTAAAACAAGACATTTTTT
Found at i:19101705 original size:51 final size:50
Alignment explanation
Indices: 19101610--19101723 Score: 113
Period size: 51 Copynumber: 2.2 Consensus size: 50
19101600 AATGAAATTT
* *
19101610 TTTTTAAAAACACGAGAATTTTTAAACACGGAAATTTCAGAAACACGAAAA
1 TTTTT-AAAACACGACAATTTTTAAACACGGAAATTTCAGAAACAAGAAAA
** * * * *
19101661 TTTTTAAAACACGACCTTTTTTGAAACACGAGAATTTTTA-AAACAAGACAT
1 TTTTTAAAACACGACAATTTTT-AAACACG-GAAATTTCAGAAACAAGAAAA
*
19101712 TTTTTGAAACAC
1 TTTTTAAAACAC
19101724 AATTTTTTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
50 14 0.27
51 31 0.60
52 7 0.13
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (50 bp):
TTTTTAAAACACGACAATTTTTAAACACGGAAATTTCAGAAACAAGAAAA
Found at i:19101715 original size:17 final size:17
Alignment explanation
Indices: 19101650--19101731 Score: 78
Period size: 17 Copynumber: 4.9 Consensus size: 17
19101640 GAAATTTCAG
* *
19101650 AAACACGAAAATTTTTA
1 AAACACGACATTTTTTA
* *
19101667 AAACACGACCTTTTTTG
1 AAACACGACATTTTTTA
* *
19101684 AAACACGAGAATTTTTA
1 AAACACGACATTTTTTA
* *
19101701 AAACAAGACATTTTTTG
1 AAACACGACATTTTTTA
19101718 AAACAC-A-ATTTTTT
1 AAACACGACATTTTTT
19101732 TCTTAAAAAA
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
15 7 0.13
16 1 0.02
17 44 0.85
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (17 bp):
AAACACGACATTTTTTA
Found at i:19101766 original size:17 final size:17
Alignment explanation
Indices: 19101744--19102118 Score: 90
Period size: 17 Copynumber: 20.6 Consensus size: 17
19101734 TTAAAAAAAA
* *
19101744 TTAAAATACGAGAATTT
1 TTAAAACACGAAAATTT
19101761 TTAAAACACGAAAATTT
1 TTAAAACACGAAAATTT
* *
19101778 TTGAAACACGGAAATTTT
1 TTAAAACAC-GAAAATTT
* ***
19101796 TTAGAAA-ATGATTTTGTT
1 TTA-AAACACGAAAAT-TT
* *
19101814 TTAAAAATCACCG-GAGTTT
1 TT-AAAA-CA-CGAAAATTT
* *
19101833 TTGAAAACATGAAAATCT
1 TT-AAAACACGAAAATTT
*
19101851 TTGAAACACCG-AAATTT
1 TTAAAACA-CGAAAATTT
*
19101868 TTGAAAACACGAAGATTT
1 TT-AAAACACGAAAATTT
* **
19101886 TTGAAACACCGAATTTTTT
1 TTAAAACA-CGAA-AATTT
* *
19101905 TTGAAAATACGAATATTTT
1 TT-AAAACACGAA-AATTT
** *
19101924 TTTTAACACGGAAATTT
1 TTAAAACACGAAAATTT
* ****
19101941 TTGAAACACGGTCTTTTTTTT
1 TTAAAACAC-G---AAAATTT
19101962 TTGAAAACACGAAAATTT
1 TT-AAAACACGAAAATTT
* ***
19101980 TTGAAAGACATGATTTTTTT
1 TT-AAA-ACACGA-AAATTT
* *
19102000 TTGAAAATACGGAAATTT
1 TT-AAAACACGAAAATTT
*
19102018 ATAAAACACGAAAATTTTT
1 TTAAAACACGAAAA--TTT
*
19102037 TCTGAAAACAAGAAAATTT
1 T-T-AAAACACGAAAATTT
* * *
19102056 TTGAAACACTAGAATTT
1 TTAAAACACGAAAATTT
* *
19102073 TGAAAACACGAAGATTT
1 TTAAAACACGAAAATTT
** * *
19102090 TTGGAACATGAGAATTT
1 TTAAAACACGAAAATTT
19102107 TTAAAAGCACGA
1 TTAAAA-CACGA
19102119 GGATTATTGA
Statistics
Matches: 255, Mismatches: 77, Indels: 51
0.67 0.20 0.13
Matches are distributed among these distances:
17 106 0.42
18 66 0.26
19 43 0.17
20 16 0.06
21 18 0.07
22 6 0.02
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (17 bp):
TTAAAACACGAAAATTT
Found at i:19101917 original size:19 final size:18
Alignment explanation
Indices: 19101865--19101926 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
19101855 AACACCGAAA
**
19101865 TTTTTGAAAACACGAA-GA
1 TTTTTGAAAA-ACGAATTT
*
19101883 TTTTTGAAACACCGAATTT
1 TTTTTGAAA-AACGAATTT
19101902 TTTTTGAAAATACGAATATT
1 TTTTTGAAAA-ACGAAT-TT
19101922 TTTTT
1 TTTTT
19101927 TAACACGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 14 0.39
19 15 0.42
20 7 0.19
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (18 bp):
TTTTTGAAAAACGAATTT
Found at i:19101932 original size:55 final size:56
Alignment explanation
Indices: 19101873--19101981 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 56
19101863 AATTTTTGAA
* *
19101873 AACAC-GAAGATTTTTGAAACACCG-AATTTTTTTTGAAAATACGAATATTTTTTTT
1 AACACGGAA-ATTTTTGAAACACCGCAATTTTTTTTGAAAACACGAAAATTTTTTTT
* **
19101928 AACACGGAAATTTTTGAAACACGGTCTTTTTTTTTTGAAAACACGAAAATTTTT
1 AACACGGAAATTTTTGAAACACCG-CAATTTTTTTTGAAAACACGAAAATTTTT
19101982 GAAAGACATG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
55 19 0.41
56 3 0.07
57 24 0.52
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (56 bp):
AACACGGAAATTTTTGAAACACCGCAATTTTTTTTGAAAACACGAAAATTTTTTTT
Found at i:19101942 original size:37 final size:35
Alignment explanation
Indices: 19101756--19101950 Score: 135
Period size: 35 Copynumber: 5.5 Consensus size: 35
19101746 AAAATACGAG
* *
19101756 AATTTTT-AAAACACGAAAATTTTTGAAACACGGA
1 AATTTTTGAAAACACGAAGATTTTTGAAACACCGA
* * *** * *
19101790 AATTTTTTAGAAA-ATGATTTTGTTTTAAAAATCACCGG
1 AATTTTTGA-AAACACGAAGAT-TTTT-GAAA-CACCGA
* * * *
19101828 AGTTTTTGAAAACATGAAAATCTTTGAAACACCGA
1 AATTTTTGAAAACACGAAGATTTTTGAAACACCGA
19101863 AATTTTTGAAAACACGAAGATTTTTGAAACACCGA
1 AATTTTTGAAAACACGAAGATTTTTGAAACACCGA
* * * ** *
19101898 ATTTTTTTTGAAAATACGAATATTTTTTTTAACACGGA
1 A--ATTTTTGAAAACACGAAGA-TTTTTGAAACACCGA
19101936 AATTTTTG-AAACACG
1 AATTTTTGAAAACACG
19101951 GTCTTTTTTT
Statistics
Matches: 125, Mismatches: 27, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
34 7 0.06
35 48 0.38
36 16 0.13
37 25 0.20
38 29 0.23
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (35 bp):
AATTTTTGAAAACACGAAGATTTTTGAAACACCGA
Found at i:19101997 original size:39 final size:38
Alignment explanation
Indices: 19101850--19102061 Score: 140
Period size: 38 Copynumber: 5.7 Consensus size: 38
19101840 CATGAAAATC
**
19101850 TTTG-AAACACCG-AAATTTTTGAAAACACGAA--GATT
1 TTTGAAAACA-CGAAAATTTTTGAAAACACGAATTTTTT
** *
19101885 TTTG-AAACACCGAATTTTTTTTGAAAATACGAATATTTTT
1 TTTGAAAACA-CGAA-AATTTTTGAAAACACGAAT-TTTTT
* **
19101925 TTT---AACACGGAAATTTTTG-AAACACGGTCTTTTTTT
1 TTTGAAAACACGAAAATTTTTGAAAACAC-G-AATTTTTT
*
19101961 TTTGAAAACACGAAAATTTTTGAAAGACATG-ATTTTTT
1 TTTGAAAACACGAAAATTTTTGAAA-ACACGAATTTTTT
* * * *
19101999 TTTGAAAATACGGAAATTTAT-AAAACACGAAAATTTTT
1 TTTGAAAACACGAAAATTTTTGAAAACACG-AATTTTTT
* *
19102037 TCTGAAAACAAGAAAATTTTTGAAA
1 TTTGAAAACACGAAAATTTTTGAAA
19102062 CACTAGAATT
Statistics
Matches: 138, Mismatches: 24, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
35 17 0.12
36 20 0.14
37 22 0.16
38 50 0.36
39 18 0.13
40 8 0.06
41 3 0.02
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (38 bp):
TTTGAAAACACGAAAATTTTTGAAAACACGAATTTTTT
Found at i:19102026 original size:94 final size:94
Alignment explanation
Indices: 19101865--19102036 Score: 240
Period size: 94 Copynumber: 1.8 Consensus size: 94
19101855 AACACCGAAA
* * **
19101865 TTTTTGAAAACACGAAGATTTTTGAAACACCGAATTTTTTTTGAAAATACGAATATTTTTTTTAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAATTTTTTTTGAAAATACGAATATTTTATAAAA
*
19101930 CACGGAAATTTTTGAAACACGGTCTTTTT
66 CACGAAAATTTTTGAAACACGGTCTTTTT
* * *
19101959 TTTTTGAAAACACGAAAATTTTTGAAAGACATGATTTTTTTTTGAAAATACGGAA-A-TTTATAA
1 TTTTTGAAAACACGAAAATTTTTGAAACAC-CGAATTTTTTTTGAAAATAC-GAATATTTTATAA
19102022 AACACGAAAATTTTT
64 AACACGAAAATTTTT
19102037 TCTGAAAACA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
94 46 0.68
95 19 0.28
96 3 0.04
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (94 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACCGAATTTTTTTTGAAAATACGAATATTTTATAAAA
CACGAAAATTTTTGAAACACGGTCTTTTT
Found at i:19102063 original size:38 final size:37
Alignment explanation
Indices: 19101928--19102108 Score: 136
Period size: 38 Copynumber: 4.8 Consensus size: 37
19101918 TATTTTTTTT
* * **
19101928 AACACGGAAATTTTTGAAACACGGTCTTTTTTTTTTGAA
1 AACACGAAAATTTTTGAAACACAG--AATTTTTTTTGAA
* *
19101967 AACACGAAAATTTTTGAAAGACATGATTTTTTTTTGAA
1 AACACGAAAATTTTTGAAACACA-GAATTTTTTTTGAA
* * * * * *
19102005 AATACGGAAATTTATAAAACACGAAAATTTTTTCTGAA
1 AACACGAAAATTTTTGAAACAC-AGAATTTTTTTTGAA
*
19102043 AACAAGAAAATTTTTGAAACACTAGAA----TTTTGAA
1 AACACGAAAATTTTTGAAACAC-AGAATTTTTTTTGAA
* * *
19102077 AACACGAAGATTTTTGGAACATGAGAATTTTT
1 AACACGAAAATTTTTGAAACA-CAGAATTTTT
19102109 AAAAGCACGA
Statistics
Matches: 111, Mismatches: 24, Indels: 15
0.74 0.16 0.10
Matches are distributed among these distances:
34 28 0.25
38 61 0.55
39 21 0.19
40 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (37 bp):
AACACGAAAATTTTTGAAACACAGAATTTTTTTTGAA
Found at i:19102090 original size:34 final size:34
Alignment explanation
Indices: 19102039--19102130 Score: 105
Period size: 34 Copynumber: 2.7 Consensus size: 34
19102029 AAATTTTTTC
* *
19102039 TGAAAACAAGAAAATTTTTGAAACACT-AGAATTT
1 TGAAAACACGAAGATTTTTGAAACA-TGAGAATTT
*
19102073 TGAAAACACGAAGATTTTTGGAACATGAGAATTT
1 TGAAAACACGAAGATTTTTGAAACATGAGAATTT
* * *
19102107 TTAAAAGCACGAGGATTATTGAAA
1 TGAAAA-CACGAAGATTTTTGAAA
19102131 TTACAATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
33 1 0.02
34 34 0.69
35 14 0.29
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (34 bp):
TGAAAACACGAAGATTTTTGAAACATGAGAATTT
Found at i:19102295 original size:16 final size:17
Alignment explanation
Indices: 19102270--19102319 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
19102260 AAAATTATTT
19102270 AAAATAAAA-TAAATTA
1 AAAATAAAATTAAATTA
*
19102286 AAAATCAAATTAAATTA
1 AAAATAAAATTAAATTA
19102303 AAAATATAAATATAAAT
1 AAAATA-AAAT-TAAAT
19102320 ATGCATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 8 0.28
17 12 0.41
18 4 0.14
19 5 0.17
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATAAAATTAAATTA
Found at i:19102473 original size:11 final size:11
Alignment explanation
Indices: 19102447--19102520 Score: 66
Period size: 11 Copynumber: 6.8 Consensus size: 11
19102437 GAATTGAACC
19102447 TCTTTTTT--T
1 TCTTTTTTCCT
19102456 TCTTTTTTTCCT
1 TC-TTTTTTCCT
19102468 TCTTTTTTCCT
1 TCTTTTTTCCT
19102479 TCTCTTTTT-CT
1 TCT-TTTTTCCT
*
19102490 TC-TTTTTCTTT
1 TCTTTTTTC-CT
*
19102501 TCTTTTTTTCT
1 TCTTTTTTCCT
*
19102512 TTTTTTTTC
1 TCTTTTTTC
19102521 TCTGCTGGGC
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
9 7 0.13
10 6 0.11
11 27 0.51
12 13 0.25
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TCTTTTTTCCT
Found at i:19102486 original size:22 final size:20
Alignment explanation
Indices: 19102447--19102523 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
19102437 GAATTGAACC
19102447 TCTT-TTTTTTCTT-T-TTT
1 TCTTCTTTTTTCTTCTCTTT
19102464 TCCTTCTTTTTTCCTTCTCTTTT
1 T-CTTCTTTTTT-CTTCTC-TTT
*
19102487 TCTTC-TTTTTCTTTTCTTT
1 TCTTCTTTTTTCTTCTCTTT
* *
19102506 TTTTCTTTTTTTTTCTCT
1 TCTTCTTTTTTCTTCTCT
19102524 GCTGGGCCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
17 1 0.02
18 3 0.06
19 13 0.27
20 18 0.37
21 6 0.12
22 4 0.08
23 4 0.08
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTCTTTTTTCTTCTCTTT
Found at i:19102816 original size:24 final size:24
Alignment explanation
Indices: 19102796--19102855 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
19102786 CTTTTCTTTT
*
19102796 TCTTTT-TTCTTTCTTTCTTCTTCC
1 TCTTTTCTTC-TTCCTTCTTCTTCC
19102820 TCTTTTCTTCTTCCTTCTTCTTCC
1 TCTTTTCTTCTTCCTTCTTCTTCC
*
19102844 T-TCTTCTTCTTC
1 TCTTTTCTTCTTC
19102856 AAAGTCTAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 10 0.30
24 20 0.61
25 3 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (24 bp):
TCTTTTCTTCTTCCTTCTTCTTCC
Found at i:19102818 original size:3 final size:3
Alignment explanation
Indices: 19102784--19102855 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
19102774 TTTTTATTAT
* *
19102784 TTC TT- TTC TTT TTC TT- TT- TTC TTTC TTTC TTC TTC CTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC TTC TTC
19102827 TTC TTCC TTC TTC TTCC TTC TTC TTC TTC
1 TTC TT-C TTC TTC TT-C TTC TTC TTC TTC
19102856 AAAGTCTAGC
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.14
3 38 0.64
4 13 0.22
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:19102823 original size:13 final size:13
Alignment explanation
Indices: 19102807--19102855 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
19102797 CTTTTTTCTT
19102807 TCTTTCTTCTTCC
1 TCTTTCTTCTTCC
19102820 TCTTTTCTTCTT-C
1 TC-TTTCTTCTTCC
19102833 -C-TTCTTCTTCC
1 TCTTTCTTCTTCC
19102844 T-TCTTCTTCTTC
1 TCT-TTCTTCTTC
19102856 AAAGTCTAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
10 8 0.26
11 1 0.03
12 1 0.03
13 12 0.39
14 9 0.29
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTTTCTTCTTCC
Found at i:19102839 original size:10 final size:10
Alignment explanation
Indices: 19102824--19102852 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
19102814 TCTTCCTCTT
19102824 TTCTTCTTCC
1 TTCTTCTTCC
19102834 TTCTTCTTCC
1 TTCTTCTTCC
19102844 TTCTTCTTC
1 TTCTTCTTC
19102853 TTCAAAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:19103260 original size:29 final size:29
Alignment explanation
Indices: 19103227--19103343 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
19103217 TGTAATTTTT
*
19103227 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
19103256 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
19103286 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
19103315 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
19103344 TTATTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:19103282 original size:30 final size:30
Alignment explanation
Indices: 19103242--19103343 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
19103232 ATTTAGGATT
*
19103242 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
19103272 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
19103302 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
19103332 AAAATGCAATTT
1 AAAATGAAATTT
19103344 TTATTTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:19109966 original size:37 final size:37
Alignment explanation
Indices: 19109925--19110006 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
19109915 AAATATTTAT
* * *
19109925 TAATCAATGTTCAAACTTTGAACATGCTTTATTAAAC
1 TAATCAATGCTAAAACTTTGAACATGCTTTAATAAAC
*
19109962 TAATCAATGCTAAAACTTTGAACATGCTTTAATGAAC
1 TAATCAATGCTAAAACTTTGAACATGCTTTAATAAAC
19109999 TAATCAAT
1 TAATCAAT
19110007 ATATTTATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (37 bp):
TAATCAATGCTAAAACTTTGAACATGCTTTAATAAAC
Found at i:19110086 original size:33 final size:33
Alignment explanation
Indices: 19110049--19110124 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
19110039 TTAAAACTTG
*
19110049 AATTATACATATACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
19110082 AATTATACATACACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
19110115 AATTATACAT
1 AATTATACAT
19110125 GCTTTATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (33 bp):
AATTATACATACACCAACAATTAATTTTAGGTC
Found at i:19113279 original size:121 final size:121
Alignment explanation
Indices: 19113146--19114134 Score: 1722
Period size: 121 Copynumber: 8.2 Consensus size: 121
19113136 TTTTCAAGTT
19113146 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
19113211 TAATATAAGAATATTATCCAACTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
19113267 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
19113332 TAATATAAGAATATTATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
*
19113388 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* *
19113453 TAATATAAGAATATTAAT--TATTAAGAATTTCATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
*
19113508 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* * *
19113573 TAATATAAGAATATTAAT--TATTAAGAATTT-TTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
* **
19113627 ATAAAGTAACAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAA
1 ATATA-T-TTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAA
****
19113692 ATTAATATTCTTATATTATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
64 ATTAATATAAGAATATTATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
19113750 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
19113815 TAATATAAGAATATTATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
19113871 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
19113936 TAATATAAGAATATTATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
*
19113992 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* *
19114057 TAATATAAGAATATTAAT--TATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
19114112 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
19114135 TAAATATGAT
Statistics
Matches: 835, Mismatches: 26, Indels: 15
0.95 0.03 0.02
Matches are distributed among these distances:
119 27 0.03
120 191 0.23
121 575 0.69
122 16 0.02
123 26 0.03
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (121 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
TAATATAAGAATATTATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
Found at i:19114111 original size:18 final size:17
Alignment explanation
Indices: 19114083--19114117 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19114073 ATTATTAAGA
*
19114083 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
19114100 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
19114118 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:19114347 original size:44 final size:45
Alignment explanation
Indices: 19114282--19114372 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
19114272 ACCTCTATTC
* * *
19114282 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
19114326 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
19114371 CA
1 CA
19114373 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:19114374 original size:16 final size:16
Alignment explanation
Indices: 19114353--19114421 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
19114343 GATTAGCTAT
19114353 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19114369 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
19114386 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
19114402 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
19114418 TACA
1 TACA
19114422 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:19114395 original size:33 final size:32
Alignment explanation
Indices: 19114353--19114421 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
19114343 GATTAGCTAT
19114353 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
19114386 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
19114418 TACA
1 TACA
19114422 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:19123246 original size:6 final size:6
Alignment explanation
Indices: 19123213--19123243 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
19123203 GAATGAAAGC
*
19123213 GGCGTT GGCGTT GGCGTT GGCGTT GACGTT G
1 GGCGTT GGCGTT GGCGTT GGCGTT GGCGTT G
19123244 ACGATGGGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.16, G:0.48, T:0.32
Consensus pattern (6 bp):
GGCGTT
Found at i:19124216 original size:27 final size:27
Alignment explanation
Indices: 19124186--19124246 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
19124176 TAACTCATTC
19124186 ATACGAAAGTGCTTTGCCTTGAACAAA
1 ATACGAAAGTGCTTTGCCTTGAACAAA
19124213 ATACGAAAGTGCTTTGCCTTGAACAAA
1 ATACGAAAGTGCTTTGCCTTGAACAAA
19124240 A-ACGAAA
1 ATACGAAA
19124247 CAAACACTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 6 0.18
27 28 0.82
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (27 bp):
ATACGAAAGTGCTTTGCCTTGAACAAA
Found at i:19127148 original size:28 final size:28
Alignment explanation
Indices: 19127115--19127175 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
19127105 AAAAATATAA
*
19127115 ACTATTAAAATGATAAACTTGTATTTTT
1 ACTATTAAAATAATAAACTTGTATTTTT
19127143 ACTATTAAAATAATAAACTTGTATTTTT
1 ACTATTAAAATAATAAACTTGTATTTTT
19127171 ACTAT
1 ACTAT
19127176 CATCAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (28 bp):
ACTATTAAAATAATAAACTTGTATTTTT
Found at i:19128014 original size:17 final size:17
Alignment explanation
Indices: 19127981--19128021 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
19127971 CCTTAAAAAA
*
19127981 TTAATATTTCTCTTTTT
1 TTAATATTTATCTTTTT
*
19127998 TTAATATTTA--TTATT
1 TTAATATTTATCTTTTT
19128013 TTAATATTT
1 TTAATATTT
19128022 TACTGTGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.59
17 9 0.41
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
TTAATATTTATCTTTTT
Found at i:19130112 original size:26 final size:25
Alignment explanation
Indices: 19130079--19130130 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
19130069 TGTGAAAATT
*
19130079 AAACC-AAATCAAAATTCCATATATA
1 AAACCAAAATCAAAACT-CATATATA
*
19130104 AAACACAAAATTAAAACTCATATATA
1 AAAC-CAAAATCAAAACTCATATATA
19130130 A
1 A
19130131 TATTAACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 4 0.17
26 10 0.43
27 9 0.39
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (25 bp):
AAACCAAAATCAAAACTCATATATA
Found at i:19131265 original size:36 final size:36
Alignment explanation
Indices: 19131199--19131268 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
19131189 AAATAAAAAA
* *
19131199 ATAAAAAAATAAAAGTATATACAATTTTTTTAAATC
1 ATAAAAAAATAAAAATATATACAATGTTTTTAAATC
* *
19131235 ATAAAAAACTAAAAATATATTAGAA-GTTTTTAAA
1 ATAAAAAAATAAAAATATA-TACAATGTTTTTAAA
19131269 AACTACAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 25 0.86
37 4 0.14
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (36 bp):
ATAAAAAAATAAAAATATATACAATGTTTTTAAATC
Found at i:19135335 original size:18 final size:18
Alignment explanation
Indices: 19135298--19135336 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19135288 TTAGAAATCA
*
19135298 AAATTATTAAAAGATGAT
1 AAATTATTAAAAGATAAT
19135316 AAATTATTAAATAGA-AAT
1 AAATTATTAAA-AGATAAT
19135334 AAA
1 AAA
19135337 AATAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATTATTAAAAGATAAT
Found at i:19137252 original size:46 final size:45
Alignment explanation
Indices: 19137202--19137377 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
19137192 TGGTTGAACA
19137202 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
19137248 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
19137295 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
19137341 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
19137378 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 68 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:19137359 original size:93 final size:93
Alignment explanation
Indices: 19137200--19137370 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
19137190 GATGGTTGAA
* *
19137200 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
19137265 GAGTCCGAGTTCGAGAGATGTAACTAGG
66 GAGTCCGAGTTCGAGAGATGTAACTAGG
* *
19137293 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
19137358 GAGTCCGAGTTCG
66 GAGTCCGAGTTCG
19137371 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGAGAGATGTAACTAGG
Found at i:19139805 original size:57 final size:57
Alignment explanation
Indices: 19139717--19139835 Score: 238
Period size: 57 Copynumber: 2.1 Consensus size: 57
19139707 AAGTTCTAAT
19139717 ATGAAATGATCTGAACATTGAAATGAACTAGTATCAAATTATACTTGTAATAATGAG
1 ATGAAATGATCTGAACATTGAAATGAACTAGTATCAAATTATACTTGTAATAATGAG
19139774 ATGAAATGATCTGAACATTGAAATGAACTAGTATCAAATTATACTTGTAATAATGAG
1 ATGAAATGATCTGAACATTGAAATGAACTAGTATCAAATTATACTTGTAATAATGAG
19139831 ATGAA
1 ATGAA
19139836 TTATGCATGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (57 bp):
ATGAAATGATCTGAACATTGAAATGAACTAGTATCAAATTATACTTGTAATAATGAG
Found at i:19153154 original size:42 final size:42
Alignment explanation
Indices: 19153095--19153202 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 42
19153085 GATGTCACTA
* *
19153095 TCCCAGACAGGGTCTTACACGAAATC-AAGTGCGATGCCAACG
1 TCCCAGACATGATCTTACACGAAATCAAAGT-CGATGCCAACG
* *
19153137 TCCCAGACATGCTCTTACACATAAATCATAAGTCGATGCCAACG
1 TCCCAGACATGATCTTACAC-GAAATCA-AAGTCGATGCCAACG
*
19153181 TCCCAGACGTGATCTTACACGA
1 TCCCAGACATGATCTTACACGA
19153203 TAACACATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 18 0.32
43 6 0.11
44 29 0.51
45 4 0.07
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (42 bp):
TCCCAGACATGATCTTACACGAAATCAAAGTCGATGCCAACG
Found at i:19154402 original size:16 final size:13
Alignment explanation
Indices: 19154371--19154433 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
19154361 AAATAGATAT
19154371 TTATTATTTATCA
1 TTATTATTTATCA
19154384 TTATTATTCTATCAAA
1 TTATTATT-TATC--A
*
19154400 TTATAATTTAT-A
1 TTATTATTTATCA
* *
19154412 TTATTAAATTATTA
1 TTATT-ATTTATCA
19154426 TTATTATT
1 TTATTATT
19154434 ATTAAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
12 5 0.12
13 15 0.37
14 10 0.24
15 3 0.07
16 8 0.20
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (13 bp):
TTATTATTTATCA
Found at i:19154433 original size:20 final size:20
Alignment explanation
Indices: 19154383--19154439 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
19154373 ATTATTTATC
* *
19154383 ATTATTATT-CTATCAAATT
1 ATTATTATTATTATTAAATT
*
19154402 ATAATT-TATATTATTAAATT
1 ATTATTAT-TATTATTAAATT
19154422 ATTATTATTATTATTAAA
1 ATTATTATTATTATTAAA
19154440 AATAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 1 0.03
19 6 0.19
20 23 0.74
21 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTATTATTATTATTAAATT
Found at i:19154745 original size:13 final size:13
Alignment explanation
Indices: 19154744--19154768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19154734 TAAAAGAATA
19154744 AAATAAATAAAAT
1 AAATAAATAAAAT
19154757 AAATAAATAAAA
1 AAATAAATAAAA
19154769 CAAAAGAAAG
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:19154754 original size:9 final size:9
Alignment explanation
Indices: 19154727--19154767 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
19154717 TTATTAATTT
19154727 AATAAAGTAA
1 AATAAA-TAA
*
19154737 AA-GAATAA
1 AATAAATAA
19154745 AATAAATAA
1 AATAAATAA
19154754 AATAAAT-A
1 AATAAATAA
19154762 AATAAA
1 AATAAA
19154768 ACAAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 12 0.43
9 14 0.50
10 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (9 bp):
AATAAATAA
Found at i:19157470 original size:23 final size:23
Alignment explanation
Indices: 19157426--19157470 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
19157416 CAAAGGAATC
*
19157426 AGTAAAAAGCTGATATGAATATA
1 AGTAAAAAGCTGATAGGAATATA
* * *
19157449 AGTACAAAGTTGATAGGTATAT
1 AGTAAAAAGCTGATAGGAATAT
19157471 TCAACTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (23 bp):
AGTAAAAAGCTGATAGGAATATA
Found at i:19158981 original size:17 final size:18
Alignment explanation
Indices: 19158944--19158985 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
19158934 TATATATATT
* *
19158944 TAAAAATATCAATTACTA
1 TAAAAATATCAAGTACAA
19158962 TAAAAATATC-AGTACAA
1 TAAAAATATCAAGTACAA
19158979 TAAAAAT
1 TAAAAAT
19158986 TTTCTAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAAATATCAAGTACAA
Found at i:19161290 original size:14 final size:14
Alignment explanation
Indices: 19161271--19161300 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
19161261 TCAAATCACC
19161271 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
19161285 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
19161299 GG
1 GG
19161301 CCTAAATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.13, G:0.47, T:0.33
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:19166416 original size:14 final size:14
Alignment explanation
Indices: 19166397--19166426 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
19166387 TCAAATCACC
19166397 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
19166411 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
19166425 GG
1 GG
19166427 CCTAAATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.13, G:0.47, T:0.33
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:19175612 original size:4 final size:4
Alignment explanation
Indices: 19175603--19175631 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
19175593 AGCAAACGTG
19175603 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
19175632 TAGAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:19176458 original size:47 final size:47
Alignment explanation
Indices: 19176394--19176504 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
19176384 GACATTGAGT
* *
19176394 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTATTC
* * *
19176441 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTATTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATTC
19176488 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
19176505 CTTATCCCGG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 51 0.93
48 4 0.07
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATTC
Found at i:19184230 original size:32 final size:32
Alignment explanation
Indices: 19184170--19184232 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
19184160 AACACCTTTT
*
19184170 TTTTTTAATATATTATTTAATATTTAAATTTA
1 TTTTTTAATATATTATTTAATATCTAAATTTA
* *
19184202 TTTTTTAATCT-TTAATTTGATATCTAAATTT
1 TTTTTTAATATATT-ATTTAATATCTAAATTT
19184233 TTTCAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (32 bp):
TTTTTTAATATATTATTTAATATCTAAATTTA
Found at i:19184377 original size:33 final size:33
Alignment explanation
Indices: 19184338--19184403 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
19184328 TAAATACTTT
*
19184338 TACTTAAAAACATGTATTAAATAAATATTAATC
1 TACTTAAAAACATATATTAAATAAATATTAATC
*
19184371 TACTTAAATACATATATTAAATAAATATTAATC
1 TACTTAAAAACATATATTAAATAAATATTAATC
19184404 AACGTATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (33 bp):
TACTTAAAAACATATATTAAATAAATATTAATC
Found at i:19184420 original size:31 final size:33
Alignment explanation
Indices: 19184347--19184428 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
19184337 TTACTTAAAA
* *
19184347 ACAT-GTATTAAATAAATATTAATCTACTTAAAT
1 ACATAGTATTAAATAAATATTAATCAACGT-AAT
19184380 ACATA-TATTAAATAAATATTAATCAACGT-AT
1 ACATAGTATTAAATAAATATTAATCAACGTAAT
19184411 ACA-AGTATTAAATTAAAT
1 ACATAGTATTAAA-TAAAT
19184429 TTTGAAACCA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
30 1 0.02
31 12 0.27
32 5 0.11
33 26 0.59
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (33 bp):
ACATAGTATTAAATAAATATTAATCAACGTAAT
Found at i:19185322 original size:36 final size:38
Alignment explanation
Indices: 19185275--19185355 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
19185265 ATATTATTGT
* *
19185275 TGGTATATTGTTGGTT-ATAT-TGGTATACATGGCTGC
1 TGGTATATTGTTGCTTAACATATGGTATACATGGCTGC
*
19185311 TGGTATATTGTTGCTTAACATATGTTATACATGGCTGC
1 TGGTATATTGTTGCTTAACATATGGTATACATGGCTGC
19185349 TGGTATA
1 TGGTATA
19185356 CATGGCTAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 15 0.38
37 3 0.08
38 22 0.55
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.43
Consensus pattern (38 bp):
TGGTATATTGTTGCTTAACATATGGTATACATGGCTGC
Found at i:19186105 original size:17 final size:17
Alignment explanation
Indices: 19186083--19186118 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
19186073 GCTGATTTGG
19186083 TACACATTTTCAAAATT
1 TACACATTTTCAAAATT
19186100 TACACATTTTCAAAATT
1 TACACATTTTCAAAATT
19186117 TA
1 TA
19186119 ACAAAATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (17 bp):
TACACATTTTCAAAATT
Found at i:19186412 original size:188 final size:188
Alignment explanation
Indices: 19186095--19186451 Score: 696
Period size: 188 Copynumber: 1.9 Consensus size: 188
19186085 CACATTTTCA
19186095 AAATTTACACATTTTCAAAATTTAACAAAATAAGTTTTGTTCACATCATTATCAATGGTCTGTCA
1 AAATTTACACATTTTCAAAATTTAACAAAATAAGTTTTGTTCACATCATTATCAATGGTCTGTCA
*
19186160 TGGATGCCTCCTATGGATGACCTTTGAGTAGGAGGCATCCATCTAACAATGGTTGGTCTTCTCTT
66 TGGATGCCTCCTATAGATGACCTTTGAGTAGGAGGCATCCATCTAACAATGGTTGGTCTTCTCTT
*
19186225 GAATGAGCGTTTTTCTCTTAGGGCGGCTTGTTGATAAGTTGATAGATCAATAGCGAGC
131 GAATGAGAGTTTTTCTCTTAGGGCGGCTTGTTGATAAGTTGATAGATCAATAGCGAGC
19186283 AAATTTACACATTTTCAAAATTTAACAAAATAAGTTTTGTTCACATCATTATCAATGGTCTGTCA
1 AAATTTACACATTTTCAAAATTTAACAAAATAAGTTTTGTTCACATCATTATCAATGGTCTGTCA
19186348 TGGATGCCTCCTATAGATGACCTTTGAGTAGGAGGCATCCATCTAACAATGGTTGGTCTTCTCTT
66 TGGATGCCTCCTATAGATGACCTTTGAGTAGGAGGCATCCATCTAACAATGGTTGGTCTTCTCTT
19186413 GAATGAGAGTTTTTCTCTTAGGGCGGCTTGTTGATAAGT
131 GAATGAGAGTTTTTCTCTTAGGGCGGCTTGTTGATAAGT
19186452 CACACACACA
Statistics
Matches: 167, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
188 167 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (188 bp):
AAATTTACACATTTTCAAAATTTAACAAAATAAGTTTTGTTCACATCATTATCAATGGTCTGTCA
TGGATGCCTCCTATAGATGACCTTTGAGTAGGAGGCATCCATCTAACAATGGTTGGTCTTCTCTT
GAATGAGAGTTTTTCTCTTAGGGCGGCTTGTTGATAAGTTGATAGATCAATAGCGAGC
Found at i:19186459 original size:2 final size:2
Alignment explanation
Indices: 19186452--19186478 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19186442 GTTGATAAGT
19186452 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
19186479 CCTAAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:19186537 original size:26 final size:28
Alignment explanation
Indices: 19186482--19186540 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
19186472 CACACACCCT
* *
19186482 AAAAAACAGTCACTATATGCATATTATA
1 AAAAAACACTCACTACATGCATATTATA
*
19186510 AAAAAATACTCACTACATGCATATTA-A
1 AAAAAACACTCACTACATGCATATTATA
19186537 AAAA
1 AAAA
19186541 TAGTCAACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.25
Consensus pattern (28 bp):
AAAAAACACTCACTACATGCATATTATA
Found at i:19187507 original size:39 final size:39
Alignment explanation
Indices: 19187453--19187557 Score: 140
Period size: 39 Copynumber: 2.7 Consensus size: 39
19187443 AGTCATTTAG
* *
19187453 TAACTATCAAATATTCAGTGCAGTAGTTTAGTTATTCAA
1 TAACTATCAATTATTCAGTACAGTAGTTTAGTTATTCAA
* * *
19187492 TAACTATTAATTATTCTA-TACAGTAATTTAGTTATTCAG
1 TAACTATCAATTATTC-AGTACAGTAGTTTAGTTATTCAA
*
19187531 TATCTATCAATTATTCAGTACAGTAGT
1 TAACTATCAATTATTCAGTACAGTAGT
19187558 CATCGACTCG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.02
39 54 0.96
40 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (39 bp):
TAACTATCAATTATTCAGTACAGTAGTTTAGTTATTCAA
Found at i:19187995 original size:8 final size:9
Alignment explanation
Indices: 19187980--19188015 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
19187970 TCTATTTCCC
19187980 CTTTTTTTT
1 CTTTTTTTT
19187989 CTTTTTTTT
1 CTTTTTTTT
19187998 CTTCTTTCTTT
1 CTT-TTT-TTT
19188009 CTTTTTT
1 CTTTTTT
19188016 CCTGCTCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 13 0.52
10 6 0.24
11 6 0.24
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:19190519 original size:20 final size:20
Alignment explanation
Indices: 19190496--19190557 Score: 124
Period size: 20 Copynumber: 3.1 Consensus size: 20
19190486 ATATTAGGTA
19190496 AGTATAATTCTTGTTACATG
1 AGTATAATTCTTGTTACATG
19190516 AGTATAATTCTTGTTACATG
1 AGTATAATTCTTGTTACATG
19190536 AGTATAATTCTTGTTACATG
1 AGTATAATTCTTGTTACATG
19190556 AG
1 AG
19190558 CTTACTAAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.44
Consensus pattern (20 bp):
AGTATAATTCTTGTTACATG
Found at i:19192606 original size:15 final size:15
Alignment explanation
Indices: 19192574--19192623 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
19192564 CTATCCTATT
**
19192574 AGACACATCACTTTC
1 AGACACATCACTACC
**
19192589 AGATGCATCACTACC
1 AGACACATCACTACC
19192604 AGACACATCACTACC
1 AGACACATCACTACC
19192619 AGACA
1 AGACA
19192624 TGTCTTCTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.18
Consensus pattern (15 bp):
AGACACATCACTACC
Found at i:19192940 original size:89 final size:89
Alignment explanation
Indices: 19192838--19193004 Score: 307
Period size: 89 Copynumber: 1.9 Consensus size: 89
19192828 ACACAACCAT
* *
19192838 TTTTGTCATATACAATATAGCAGCTTGGATACAAACAATGGCAGATATACACAATAAACATTAGT
1 TTTTGCCACATACAATATAGCAGCTTGGATACAAACAATGGCAGATATACACAATAAACATTAGT
19192903 TTGATAATGGCATTCAAATTTTGA
66 TTGATAATGGCATTCAAATTTTGA
*
19192927 TTTTGCCACATACAATATAGTAGCTTGGATACAAACAATGGCAGATATACACAATAAACATTAGT
1 TTTTGCCACATACAATATAGCAGCTTGGATACAAACAATGGCAGATATACACAATAAACATTAGT
19192992 TTGATAATGGCAT
66 TTGATAATGGCAT
19193005 CCATACAATG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 75 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (89 bp):
TTTTGCCACATACAATATAGCAGCTTGGATACAAACAATGGCAGATATACACAATAAACATTAGT
TTGATAATGGCATTCAAATTTTGA
Found at i:19193030 original size:48 final size:48
Alignment explanation
Indices: 19192961--19193085 Score: 205
Period size: 48 Copynumber: 2.6 Consensus size: 48
19192951 TTGGATACAA
* * *
19192961 ACAATGGCAGATATACACAATAAACATTAGTTTGATAATGGCATCCAT
1 ACAATGGCAGATACAAACAATAAACATCAGTTTGATAATGGCATCCAT
19193009 ACAATGGCAGATACAAACAATAAACATCAGTTTGATAATGGCATCCAT
1 ACAATGGCAGATACAAACAATAAACATCAGTTTGATAATGGCATCCAT
* *
19193057 ACGATGGCAGATACAAACAGTAAACATCA
1 ACAATGGCAGATACAAACAATAAACATCA
19193086 TGCACATGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.22
Consensus pattern (48 bp):
ACAATGGCAGATACAAACAATAAACATCAGTTTGATAATGGCATCCAT
Found at i:19193164 original size:6 final size:6
Alignment explanation
Indices: 19193155--19193214 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
19193145 ATCCAAATTG
* * * * * * *
19193155 AAATCA AAATCA AAATCT AAAGCT AAATCG AGATCG AAATTA AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
19193203 AAATCA AAATCA
1 AAATCA AAATCA
19193215 GTTTAGTGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.58, C:0.15, G:0.07, T:0.20
Consensus pattern (6 bp):
AAATCA
Found at i:19193243 original size:6 final size:6
Alignment explanation
Indices: 19193234--19193353 Score: 84
Period size: 6 Copynumber: 19.7 Consensus size: 6
19193224 TTCAAAATTG
* *
19193234 AAATCA AAATCA AAAT-A GAAATCA AAATCA AAATCA GAATCG AAATCA
1 AAATCA AAATCA AAATCA -AAATCA AAATCA AAATCA AAATCA AAATCA
** * ** * * *
19193282 AAATCA AAATTG AAATCG AAAT-A ACCCTAA ATAACCCT AAATCA AAAT-A
1 AAATCA AAATCA AAATCA AAATCA A-AATCA A-AA-TCA AAATCA AAATCA
19193331 ACAATCA AAATCA AAATCA AAAT
1 A-AATCA AAATCA AAATCA AAAT
19193354 TGAAATCGAA
Statistics
Matches: 89, Mismatches: 18, Indels: 14
0.74 0.15 0.12
Matches are distributed among these distances:
5 4 0.04
6 77 0.87
7 7 0.08
8 1 0.01
ACGTcount: A:0.61, C:0.17, G:0.04, T:0.18
Consensus pattern (6 bp):
AAATCA
Found at i:19193248 original size:18 final size:18
Alignment explanation
Indices: 19193225--19193303 Score: 86
Period size: 18 Copynumber: 4.1 Consensus size: 18
19193215 GTTTAGTGTT
19193225 TCAAAATTGAAATCAAAA
1 TCAAAATTGAAATCAAAA
*
19193243 TCAAAATAGAAATCAAAA
1 TCAAAATTGAAATCAAAA
19193261 TCAAAATCAGAATCGAAATCAAAA
1 TCAAAAT-----T-GAAATCAAAA
*
19193285 TCAAAATTGAAATCGAAA
1 TCAAAATTGAAATCAAAA
19193303 T
1 T
19193304 AACCCTAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
18 34 0.65
19 1 0.02
24 17 0.33
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.20
Consensus pattern (18 bp):
TCAAAATTGAAATCAAAA
Found at i:19193261 original size:24 final size:24
Alignment explanation
Indices: 19193234--19193291 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
19193224 TTCAAAATTG
19193234 AAATCAAAATCAAAATAGAAATCA
1 AAATCAAAATCAAAATAGAAATCA
* *
19193258 AAATCAAAATCAGAATCGAAATCA
1 AAATCAAAATCAAAATAGAAATCA
19193282 AAATCAAAAT
1 AAATCAAAAT
19193292 TGAAATCGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.64, C:0.14, G:0.05, T:0.17
Consensus pattern (24 bp):
AAATCAAAATCAAAATAGAAATCA
Found at i:19193298 original size:24 final size:24
Alignment explanation
Indices: 19193234--19193303 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
19193224 TTCAAAATTG
* *
19193234 AAATCAAAATCAAAATAGAAATCA
1 AAATCAAAATTAAAATCGAAATCA
* *
19193258 AAATCAAAATCAGAATCGAAATCA
1 AAATCAAAATTAAAATCGAAATCA
*
19193282 AAATCAAAATTGAAATCGAAAT
1 AAATCAAAATTAAAATCGAAAT
19193304 AACCCTAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.61, C:0.13, G:0.07, T:0.19
Consensus pattern (24 bp):
AAATCAAAATTAAAATCGAAATCA
Found at i:19193342 original size:62 final size:62
Alignment explanation
Indices: 19193258--19193375 Score: 209
Period size: 62 Copynumber: 1.9 Consensus size: 62
19193248 ATAGAAATCA
* * *
19193258 AAATCAAAATCAGAATCGAAATCAAAATCAAAATTGAAATCGAAATAACCCTAAATAACCCT
1 AAATCAAAATAACAATCAAAATCAAAATCAAAATTGAAATCGAAATAACCCTAAATAACCCT
19193320 AAATCAAAATAACAATCAAAATCAAAATCAAAATTGAAATCGAAATAACCCTAAAT
1 AAATCAAAATAACAATCAAAATCAAAATCAAAATTGAAATCGAAATAACCCTAAAT
19193376 CAAAATAACA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.58, C:0.18, G:0.05, T:0.19
Consensus pattern (62 bp):
AAATCAAAATAACAATCAAAATCAAAATCAAAATTGAAATCGAAATAACCCTAAATAACCCT
Found at i:19200839 original size:29 final size:29
Alignment explanation
Indices: 19200759--19200845 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 29
19200749 TTGAGTTCAA
*
19200759 AAAGGTCTGGCTCTTATTTGAGCACTTCCC
1 AAAGGTTTGGCT-TTATTTGAGCACTTCCC
* * * *
19200789 AAATGTTTTGGCCATTACTTGAGCACTT-CG
1 AAA-GGTTTGG-CTTTATTTGAGCACTTCCC
19200819 AAAGGTTTGGCTTTCATTTGAGCACTT
1 AAAGGTTTGGCTTT-ATTTGAGCACTT
19200846 TTGCAAAGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
28 3 0.07
29 17 0.37
30 7 0.15
31 18 0.39
32 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (29 bp):
AAAGGTTTGGCTTTATTTGAGCACTTCCC
Found at i:19201959 original size:30 final size:31
Alignment explanation
Indices: 19201899--19201961 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
19201889 AAAAAGTGAC
*
19201899 ATCAAAAGTGAAAAAGTTATAGTCATTCAGA
1 ATCAAAAGTGAAAAAGTTATAGTAATTCAGA
19201930 ATCAAAAGTGAAAAAGTTA-AGTAATTCAGA
1 ATCAAAAGTGAAAAAGTTATAGTAATTCAGA
19201960 AT
1 AT
19201962 TATATCAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.25
Consensus pattern (31 bp):
ATCAAAAGTGAAAAAGTTATAGTAATTCAGA
Found at i:19204248 original size:3 final size:3
Alignment explanation
Indices: 19204240--19204274 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
19204230 ATATGTAGTA
*
19204240 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG CAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
19204275 AAAAATGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19205621 original size:11 final size:11
Alignment explanation
Indices: 19205599--19205631 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
19205589 TAAACCAAGA
19205599 TTTTTG-AATT
1 TTTTTGAAATT
19205609 TTTTT-AAATT
1 TTTTTGAAATT
19205619 TTTTTGAAATT
1 TTTTTGAAATT
19205630 TT
1 TT
19205632 AATTTAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (11 bp):
TTTTTGAAATT
Found at i:19213001 original size:17 final size:19
Alignment explanation
Indices: 19212958--19213004 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
19212948 GTTTTATCAA
19212958 ATAAATT-ATTAAAAATTC
1 ATAAATTAATTAAAAATTC
19212976 ATAAA--AATTAAAAATT-
1 ATAAATTAATTAAAAATTC
19212992 A-AAATTAATTAAA
1 ATAAATTAATTAAA
19213005 CTGATTCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.12
16 1 0.04
17 17 0.65
18 5 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAATTAATTAAAAATTC
Found at i:19213120 original size:41 final size:41
Alignment explanation
Indices: 19213063--19213146 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
19213053 AGGTCAACCG
19213063 ATTCAATCTCTCTCTCTACATTGATTCCTAATCAATTTTTT
1 ATTCAATCTCTCTCTCTACATTGATTCCTAATCAATTTTTT
19213104 ATTCAATCTCTCTCTCTACATTGATTCCTAATCAATTTTTT
1 ATTCAATCTCTCTCTCTACATTGATTCCTAATCAATTTTTT
19213145 AT
1 AT
19213147 CCGATTGATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.25, C:0.24, G:0.02, T:0.49
Consensus pattern (41 bp):
ATTCAATCTCTCTCTCTACATTGATTCCTAATCAATTTTTT
Found at i:19214012 original size:32 final size:32
Alignment explanation
Indices: 19213974--19214034 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
19213964 TAATCATTAT
*
19213974 GAGTTATCAAATTAAAATAATTAATTTATCAC
1 GAGTTATCAAATTAAAATAATCAATTTATCAC
* *
19214006 GAGTTATTAAATTAAAGTAATCAATTTAT
1 GAGTTATCAAATTAAAATAATCAATTTAT
19214035 AAATTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (32 bp):
GAGTTATCAAATTAAAATAATCAATTTATCAC
Found at i:19217638 original size:22 final size:24
Alignment explanation
Indices: 19217599--19217649 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
19217589 TATTATTTTG
19217599 AAATAAAAAATATAT-AAAATTA-
1 AAATAAAAAATATATAAAAATTAT
* * *
19217621 AAATAAATAATTTTTAAAAATTAT
1 AAATAAAAAATATATAAAAATTAT
19217645 AAATA
1 AAATA
19217650 TTTGGAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.50
23 7 0.29
24 5 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATAAAAAATATATAAAAATTAT
Found at i:19218756 original size:29 final size:29
Alignment explanation
Indices: 19218714--19218806 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 29
19218704 GTCTTTATAT
19218714 TTTTTATAAATTTAAATATTTAATTTTACA
1 TTTTT-TAAATTTAAATATTTAATTTTACA
* *
19218744 TTTTTTAAATTTAAAAATTTAAGTTTA-A
1 TTTTTTAAATTTAAATATTTAATTTTACA
* * * * *
19218772 TTGTTAAAATATTAAATTTATTAATGTAACA
1 TTTTTTAAAT-TTAAATAT-TTAATTTTACA
19218803 TTTT
1 TTTT
19218807 GAATTAAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 9 0.18
29 26 0.52
30 11 0.22
31 4 0.08
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (29 bp):
TTTTTTAAATTTAAATATTTAATTTTACA
Found at i:19219596 original size:16 final size:15
Alignment explanation
Indices: 19219567--19219610 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
19219557 TTAAAATACA
19219567 ATTATAAAAT-AATATT
1 ATTA-AAAATAAATA-T
19219583 ATTAAAAATAAATAT
1 ATTAAAAATAAATAT
19219598 ATGTAAAAATAAA
1 AT-TAAAAATAAA
19219611 CACTATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
ATTAAAAATAAATAT
Found at i:19231851 original size:44 final size:43
Alignment explanation
Indices: 19231754--19231881 Score: 143
Period size: 43 Copynumber: 3.0 Consensus size: 43
19231744 CTCGTACAAC
* *
19231754 GCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGAT
1 GCCAACGTCCCAGACGTGGTCTTACACGTAATCACAAATCGAT
* *
19231797 GTC-ACTGTCCCAGGCAG-GGTCTTACACGTAAATCACAAATCGAT
1 GCCAAC-GTCCCAGAC-GTGGTCTTACACGT-AATCACAAATCGAT
* ** *
19231841 GCCAACGTCCCAAACGTGGTCTTACACAAAATCACATATCG
1 GCCAACGTCCCAGACGTGGTCTTACACGTAATCACAAATCG
19231882 GAACCCTATG
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
42 2 0.03
43 33 0.47
44 33 0.47
45 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (43 bp):
GCCAACGTCCCAGACGTGGTCTTACACGTAATCACAAATCGAT
Found at i:19236715 original size:14 final size:14
Alignment explanation
Indices: 19236692--19236721 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19236682 TTGAAAATAT
19236692 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
19236706 GTTGATTTGGATTG
1 GTTGAATTGGATTG
19236720 GT
1 GT
19236722 CTCGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:19240083 original size:14 final size:15
Alignment explanation
Indices: 19240064--19240093 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19240054 TTTCCGAAGT
19240064 AAAAT-AAAAAATAA
1 AAAATAAAAAAATAA
19240078 AAAATAAAAAAATAA
1 AAAATAAAAAAATAA
19240093 A
1 A
19240094 GATTTGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAATAAAAAAATAA
Found at i:19240087 original size:8 final size:7
Alignment explanation
Indices: 19240064--19240093 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
19240054 TTTCCGAAGT
19240064 AAAATAA
1 AAAATAA
19240071 AAAATAA
1 AAAATAA
19240078 AAAATAAA
1 AAAAT-AA
19240086 AAAATAA
1 AAAATAA
19240093 A
1 A
19240094 GATTTGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:19244673 original size:17 final size:17
Alignment explanation
Indices: 19244651--19244685 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19244641 TTTTTGAAAC
19244651 TTTATAT-ATATTATTTT
1 TTTATATCATATT-TTTT
19244668 TTTATATCATATTTTTT
1 TTTATATCATATTTTTT
19244685 T
1 T
19244686 ACGTTACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATATCATATTTTTT
Found at i:19245248 original size:15 final size:15
Alignment explanation
Indices: 19245210--19245263 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
19245200 AAAAAAATTG
*
19245210 TAAGTGTTGAAAAA-
1 TAAGTATTGAAAAAT
* *
19245224 TAAATGTTGAAAAAT
1 TAAGTATTGAAAAAT
*
19245239 TAAGTATTGAAAATT
1 TAAGTATTGAAAAAT
*
19245254 TAACTATTGA
1 TAAGTATTGA
19245264 GTTTAAGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 13 0.38
15 21 0.62
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (15 bp):
TAAGTATTGAAAAAT
Found at i:19246414 original size:34 final size:34
Alignment explanation
Indices: 19246371--19246438 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
19246361 AATAAAGATA
19246371 GTGTGAAAGAGTGGCAAGATAGATACCTTTCTTT
1 GTGTGAAAGAGTGGCAAGATAGATACCTTTCTTT
19246405 GTGTGAAAGAGTGGCAAGATAGATACCTTTCTTT
1 GTGTGAAAGAGTGGCAAGATAGATACCTTTCTTT
19246439 TCCCTTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (34 bp):
GTGTGAAAGAGTGGCAAGATAGATACCTTTCTTT
Found at i:19246651 original size:6 final size:6
Alignment explanation
Indices: 19246640--19246664 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19246630 TGCTTGTATT
19246640 ATAATC ATAATC ATAATC ATAATC A
1 ATAATC ATAATC ATAATC ATAATC A
19246665 GAGTCGGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATAATC
Found at i:19251949 original size:14 final size:14
Alignment explanation
Indices: 19251907--19251949 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
19251897 AAAGATAAAA
*
19251907 AATTAAATTCCTAAA
1 AATTAAATT-CTAAT
* *
19251922 AATAAAATTATAAT
1 AATTAAATTCTAAT
19251936 AATTAAATTCTAAT
1 AATTAAATTCTAAT
19251950 TTTACGAAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTAAATTCTAAT
Found at i:19252442 original size:61 final size:62
Alignment explanation
Indices: 19252364--19252481 Score: 177
Period size: 61 Copynumber: 1.9 Consensus size: 62
19252354 ATTGAAGTAA
*
19252364 TATAAAGTAGTATTTAAATATTAAGTT-GAAAAAAATAAAATTTAATAATTACAATATTTAAG
1 TATAAAGTAGTATTTAAATATTAA-TTAGAAAAAAATAAAATTAAATAATTACAATATTTAAG
* * *
19252426 TATAAA-TAGTATTTAAATATTAATTAGATAAAAATAAACTTAAATAATTATAATAT
1 TATAAAGTAGTATTTAAATATTAATTAGAAAAAAATAAAATTAAATAATTACAATAT
19252482 ATAATACAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
60 2 0.04
61 43 0.84
62 6 0.12
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (62 bp):
TATAAAGTAGTATTTAAATATTAATTAGAAAAAAATAAAATTAAATAATTACAATATTTAAG
Found at i:19252918 original size:21 final size:20
Alignment explanation
Indices: 19252878--19252915 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19252868 AGTTTAATTT
*
19252878 TTTTTTAAATTTAATCAATA
1 TTTTTTAAATATAATCAATA
19252898 TTTTTT-AATATATATCAA
1 TTTTTTAAATATA-ATCAA
19252916 ATAGAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTTAAATATAATCAATA
Found at i:19255264 original size:12 final size:12
Alignment explanation
Indices: 19255249--19255274 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19255239 GGGGAAAAGG
19255249 GAGAAAGAAAAA
1 GAGAAAGAAAAA
19255261 GAGAAAGAAAAA
1 GAGAAAGAAAAA
19255273 GA
1 GA
19255275 AGTAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAGAAAGAAAAA
Found at i:19258815 original size:30 final size:30
Alignment explanation
Indices: 19258779--19258837 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
19258769 TTCGTGATAA
*
19258779 TTTTTTTT-TTATTAATGGAATAAAAAAAC
1 TTTTTTTTGGTATTAATGGAATAAAAAAAC
*
19258808 TTTTTTTTGGTATTAATGGAGTAAAAAAAC
1 TTTTTTTTGGTATTAATGGAATAAAAAAAC
19258838 CTAAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (30 bp):
TTTTTTTTGGTATTAATGGAATAAAAAAAC
Found at i:19264624 original size:19 final size:20
Alignment explanation
Indices: 19264586--19264624 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19264576 TTTATAATTA
19264586 AAAAAATTAAATTTATTTTT
1 AAAAAATTAAATTTATTTTT
**
19264606 AAAAAATTATTTTTATTTT
1 AAAAAATTAAATTTATTTT
19264625 GATTTCGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AAAAAATTAAATTTATTTTT
Found at i:19282140 original size:17 final size:17
Alignment explanation
Indices: 19282118--19282152 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19282108 ATAATAAATA
19282118 TATATTT-TATTTTTAAT
1 TATATTTATA-TTTTAAT
19282135 TATATTTATATTTTAAT
1 TATATTTATATTTTAAT
19282152 T
1 T
19282153 TTAATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATATTTATATTTTAAT
Found at i:19282215 original size:12 final size:12
Alignment explanation
Indices: 19282198--19282231 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19282188 CAAATTGTGT
19282198 ATTGTTTTAAGA
1 ATTGTTTTAAGA
*
19282210 ATTGTTTTAATA
1 ATTGTTTTAAGA
*
19282222 TTTGTTTTAA
1 ATTGTTTTAA
19282232 ATGTATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (12 bp):
ATTGTTTTAAGA
Found at i:19289244 original size:13 final size:14
Alignment explanation
Indices: 19289218--19289247 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
19289208 TCATTTAGTA
19289218 AATTAAGCTTGATT
1 AATTAAGCTTGATT
19289232 AATTAAG-TTGATT
1 AATTAAGCTTGATT
19289245 AAT
1 AAT
19289248 CTTAGTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.43
Consensus pattern (14 bp):
AATTAAGCTTGATT
Found at i:19292206 original size:20 final size:20
Alignment explanation
Indices: 19292157--19292208 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
19292147 CGGACAAGGG
19292157 ACACGGGCGTGTCCCAAGCC
1 ACACGGGCGTGTCCCAAGCC
* * *
19292177 ACATGAGCGTGTCTCAAGCC
1 ACACGGGCGTGTCCCAAGCC
19292197 ACACGGGCGTGT
1 ACACGGGCGTGT
19292209 GGAATCCACA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (20 bp):
ACACGGGCGTGTCCCAAGCC
Found at i:19293917 original size:56 final size:56
Alignment explanation
Indices: 19293855--19293990 Score: 227
Period size: 56 Copynumber: 2.4 Consensus size: 56
19293845 ACCATGGCAT
* *
19293855 CGATATATATGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCACCGATATGTGATTC
*
19293911 CGATATATGTGTGCGAGTAAGAGCACGTTTAATACGTTGGCACCGATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCACCGATATGTGATTC
* *
19293967 TGATTTATGTGTGCGAGTAAGACC
1 CGATATATGTGTGCGAGTAAGACC
19293991 CTGTCTGGGA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (56 bp):
CGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCACCGATATGTGATTC
Found at i:19295218 original size:39 final size:39
Alignment explanation
Indices: 19295159--19295259 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
19295149 ATCATGATTT
* * * *
19295159 GAAGCCCGAAGTCTAGCTGAAGCATATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
*
19295198 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAATG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
*
19295237 GAAGCCCAAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
19295260 TCATCAGAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
Found at i:19295241 original size:21 final size:21
Alignment explanation
Indices: 19295177--19295241 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
19295167 AAGTCTAGCT
* * *
19295177 GAAGCATATAAGTGCTAAACG
1 GAAGCACACAAGTGCTAAATG
*
19295198 GAAGC-C-CGAAG-GCTAACT-
1 GAAGCACAC-AAGTGCTAAATG
19295216 GAAGCACACAAGTGCTAAATG
1 GAAGCACACAAGTGCTAAATG
19295237 GAAGC
1 GAAGC
19295242 CCAAAGGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
18 5 0.15
19 9 0.26
20 10 0.29
21 10 0.29
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (21 bp):
GAAGCACACAAGTGCTAAATG
Found at i:19296901 original size:18 final size:19
Alignment explanation
Indices: 19296867--19296902 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19296857 AATGCAATTT
19296867 ATATATGATGTAAGTGAAA
1 ATATATGATGTAAGTGAAA
*
19296886 ATATATG-TGTATGTGAA
1 ATATATGATGTAAGTGAA
19296903 TAGTACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (19 bp):
ATATATGATGTAAGTGAAA
Found at i:19298803 original size:23 final size:23
Alignment explanation
Indices: 19298774--19298820 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
19298764 GTATATATAT
*
19298774 AAAAAAAGGAATA-AAAGAAAGA
1 AAAAAAAAGAATAGAAAGAAAGA
*
19298796 AAAAAAAAGAATAGAAAGGAAGA
1 AAAAAAAAGAATAGAAAGAAAGA
19298819 AA
1 AA
19298821 CAAAGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (23 bp):
AAAAAAAAGAATAGAAAGAAAGA
Found at i:19300849 original size:46 final size:46
Alignment explanation
Indices: 19300797--19301011 Score: 324
Period size: 46 Copynumber: 4.7 Consensus size: 46
19300787 GCTCTTTGAA
*
19300797 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
* *
19300843 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
* *
19300889 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
**
19300935 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
* * *
19300981 A-GAAAGTGAGTAAAACCATAGTTGAAAGATA
1 ATGAAA-TGTGTAAGACCATGGTTGAAAGATA
19301012 TTATGGCATC
Statistics
Matches: 157, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
45 4 0.03
46 153 0.97
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
Found at i:19302926 original size:24 final size:24
Alignment explanation
Indices: 19302894--19302942 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
19302884 CATATCGACG
19302894 ATTCAAATCCGCACACATAGTGCC
1 ATTCAAATCCGCACACATAGTGCC
19302918 ATTCAAATCCGCACACATAGTGCC
1 ATTCAAATCCGCACACATAGTGCC
19302942 A
1 A
19302943 AGGTCATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.33, G:0.12, T:0.20
Consensus pattern (24 bp):
ATTCAAATCCGCACACATAGTGCC
Found at i:19308515 original size:24 final size:24
Alignment explanation
Indices: 19308487--19308533 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
19308477 TTTAATGCTA
*
19308487 TGCTGTCAG-ATTTATGAATCAAAT
1 TGCTGTCAGCATTTA-AAATCAAAT
19308511 TGCTGTCAGCATTTAAAATCAAA
1 TGCTGTCAGCATTTAAAATCAAA
19308534 GTTCCATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (24 bp):
TGCTGTCAGCATTTAAAATCAAAT
Found at i:19316428 original size:66 final size:66
Alignment explanation
Indices: 19316309--19316441 Score: 185
Period size: 66 Copynumber: 2.0 Consensus size: 66
19316299 TCCAAGCTCT
* * * * *
19316309 AGACCTGCTTCCATCGATCCTAATTATAGAGCGGATCCAAGCTCCAGATCTGCTTCCATTGATCC
1 AGACCCGCTTCCATCGATCCCAACTATAGAGCGGATCCAAGCTCCAGAGCTGCTCCCATTGATCC
19316374 C
66 C
* ** *
19316375 AGACCCGCTTCCATTGATCCCAACTATAGAGCGGATCCGGGCTCTAGAGCTGCTCCCATTGATCC
1 AGACCCGCTTCCATCGATCCCAACTATAGAGCGGATCCAAGCTCCAGAGCTGCTCCCATTGATCC
19316440 C
66 C
19316441 A
1 A
19316442 ATTATAGAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (66 bp):
AGACCCGCTTCCATCGATCCCAACTATAGAGCGGATCCAAGCTCCAGAGCTGCTCCCATTGATCC
C
Found at i:19316436 original size:45 final size:45
Alignment explanation
Indices: 19316385--19316586 Score: 289
Period size: 45 Copynumber: 4.5 Consensus size: 45
19316375 AGACCCGCTT
* * *
19316385 CCATTGATCCCAACTATAGAGCGGATCCGGGCTCTAGAGCTGCTC
1 CCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAGGTGCTC
* * *
19316430 CCATTGATCCCAATTATAGAGTGGATCCGAGCTCTAGAGTTGCTT
1 CCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAGGTGCTC
* * *
19316475 CCATTGATCCCAATTATAGAGCGGATCCAAGCGCTAGAGGTGCTT
1 CCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAGGTGCTC
*
19316520 CCATTGAGCCCAATTATAGAGCGGATCCGAG-TGCTAGAGGTGCTC
1 CCATTGATCCCAATTATAGAGCGGATCCGAGCT-CTAGAGGTGCTC
*
19316565 CGATTGATCCCAATTATAGAGC
1 CCATTGATCCCAATTATAGAGC
19316587 TGCTCCAGAG
Statistics
Matches: 141, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
45 141 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (45 bp):
CCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAGGTGCTC
Found at i:19318886 original size:18 final size:18
Alignment explanation
Indices: 19318865--19318901 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
19318855 TATCTTATCC
19318865 TTTTCTTGAGTCTCTGAT
1 TTTTCTTGAGTCTCTGAT
19318883 TTTTCTTGAGTCTCTGAT
1 TTTTCTTGAGTCTCTGAT
19318901 T
1 T
19318902 ACCTTTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (18 bp):
TTTTCTTGAGTCTCTGAT
Done.