Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006094.1 Hibiscus syriacus cultivar Beakdansim tig00014445_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 761529
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 5
Found at i:165910 original size:6 final size:6
Alignment explanation
Indices: 165899--168573 Score: 5116
Period size: 6 Copynumber: 447.2 Consensus size: 6
165889 GGCAAAAGTA
165899 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
165947 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
165995 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166043 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166091 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166139 ACATAC ACATAC ACATAC ACATACAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACAT--AC ACATAC ACATAC ACATAC ACATAC
166189 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
*
166237 ACATAC ACATAC ACATAC ACATAC ACATAC ACAT-- ACATAT ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166283 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166331 ACATACAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACAT--AC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166381 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166429 ACATAC ACATACAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACAT--AC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166479 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166527 ACATAC ACATACAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACAT--AC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166577 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166625 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166673 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166721 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166769 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166817 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166865 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166913 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
166961 ACATAC ACATAC ACATAC ACATAC ACATAC ACATACAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACAT--AC ACATAC ACATAC
167011 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167059 ACAT-- ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167105 ACAT-- ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167151 ACAT-- ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167197 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167245 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167293 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167341 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167389 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167437 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167485 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167533 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167581 ACATAC ACATAC ACATAC AC--AC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167627 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167675 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167723 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167771 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
*
167819 ACAT-- ACATAT ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167865 ACATAC ACATAC ACATAC ACATAC ACAT-- ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167911 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
167959 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
168007 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
168055 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACAT--
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
168101 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
168149 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACAT--
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
168195 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
168243 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
168291 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
168339 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
168387 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
168435 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
168483 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
168531 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC A
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC A
168574 TAAAAGAAAA
Statistics
Matches: 2639, Mismatches: 2, Indels: 56
0.98 0.00 0.02
Matches are distributed among these distances:
4 36 0.01
6 2573 0.97
8 30 0.01
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (6 bp):
ACATAC
Found at i:171627 original size:17 final size:17
Alignment explanation
Indices: 171597--171629 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
171587 ACCCCACGTC
171597 ATATAAAAATTAAAAAA
1 ATATAAAAATTAAAAAA
171614 ATATATAAAA-TAAAAA
1 ATATA-AAAATTAAAAA
171630 GTTATTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
ATATAAAAATTAAAAAA
Found at i:183054 original size:44 final size:43
Alignment explanation
Indices: 183012--183414 Score: 234
Period size: 43 Copynumber: 9.3 Consensus size: 43
183002 GGCTTTAATA
*
183012 ATAAAGGTAGAAATTGAGATTGAAAAAATATAGGGGCCTTAATT
1 ATAAAGGTAGAAATTGAGATTGAAAAAA-ATAGGGGCCTCAATT
* * * *
183056 CTAAAGGTA-TAATTGAGATTGAAAAAAATAGGGACATCAATT
1 ATAAAGGTAGAAATTGAGATTGAAAAAAATAGGGGCCTCAATT
* * * *
183098 ATAAAGGCAGAAAATGAGATTGAAAAAAAACTTAAGAGCCTCAATT
1 ATAAAGGTAGAAATTGAGATTG-AAAAAAA--TAGGGGCCTCAATT
* * * * * *
183144 ATAAAGTTAAAAAAGTGGGATTG-AAAAACTAGGGGACTCAATT
1 ATAAAGGT-AGAAATTGAGATTGAAAAAAATAGGGGCCTCAATT
* ** * *
183187 ATAAAGGTAGAAATTGAGATTAGAGAAAGTTTGGGGCATCAATT
1 ATAAAGGTAGAAATTGAGATT-GAAAAAAATAGGGGCCTCAATT
* * ** *
183231 GTAAAGGTAGTAAAGGTGGAGATTGAAAAACTTAAGGGCCTCAATT
1 ATAAAGGTAG-AAA--TTGAGATTGAAAAAAATAGGGGCCTCAATT
* * * *
183277 ATAAA-GT--TAAGTGGGATT-AAAAAATTAGGGGTCCT-AATT
1 ATAAAGGTAGAAATTGAGATTGAAAAAAATAGGGG-CCTCAATT
** * * * * *
183316 ATAAAGGTA-AAA-AAAGATGGAAAAAAATTAGAGACTTCAGTT
1 ATAAAGGTAGAAATTGAGATTGAAAAAAA-TAGGGGCCTCAATT
* * * * *
183358 ATAAAGATAAAAAGTGAGATT-AAATAAAATTA-GGACCTCAATA
1 ATAAAGGTAGAAATTGAGATTGAAA-AAAA-TAGGGGCCTCAATT
*
183401 ATAAAGGTAAAAAT
1 ATAAAGGTAGAAAT
183415 AAGATTAAAA
Statistics
Matches: 274, Mismatches: 66, Indels: 39
0.72 0.17 0.10
Matches are distributed among these distances:
39 20 0.07
40 13 0.05
41 10 0.04
42 46 0.17
43 71 0.26
44 49 0.18
45 10 0.04
46 37 0.14
47 18 0.07
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.25
Consensus pattern (43 bp):
ATAAAGGTAGAAATTGAGATTGAAAAAAATAGGGGCCTCAATT
Found at i:183236 original size:133 final size:127
Alignment explanation
Indices: 183042--183363 Score: 312
Period size: 133 Copynumber: 2.5 Consensus size: 127
183032 TGAAAAAATA
* * * *
183042 TAGGGGCCTTAATTCTAAAGGTATAATTGAGATTGAAAAAAATAGGGACATCAATTATAAAGGCA
1 TAGGGGACTCAATTATAAAGGTAAAATTGAGATTGAAAAAAATAGGGACATCAATTATAAAGGCA
*
183107 G-AAA-AT-GAGATTGAAAAAAAACTTAAGAGCCTCAATTATAAAGTTAAAAAAGTGGGATTGAA
66 GTAAAGATGGAGATTG---AAAAACTTAAGAGCCTCAATTATAAAGTT----AAGTGGGATTAAA
183169 AAAC
124 AAAC
* ** * * *
183173 TAGGGGACTCAATTATAAAGGTAGAAATTGAGATTAGAGAAAGTTTGGGGCATCAATTGTAAAGG
1 TAGGGGACTCAATTATAAAGGTA-AAATTGAGATT-GAAAAAAATAGGGACATCAATTATAAAGG
* * * *
183238 TAGTAAAGGTGGAGATTGAAAAACTTAAGGGCCTCAATTATAAAGTTAAGTGGGATTAAAAAAT
64 CAGTAAAGATGGAGATTGAAAAACTTAAGAGCCTCAATTATAAAGTTAAGTGGGATTAAAAAAC
* ** * * * *
183302 TAGGGGTC-CTAATTATAAAGGTAAAA-AAAGATGGAAAAAAATTAGAGACTTCAGTTATAAAG
1 TAGGGGACTC-AATTATAAAGGTAAAATTGAGATTGAAAAAAA-TAGGGACATCAATTATAAAG
183364 ATAAAAAGTG
Statistics
Matches: 156, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
126 5 0.03
127 18 0.12
128 4 0.03
129 35 0.22
131 20 0.13
132 10 0.06
133 53 0.34
134 3 0.02
135 1 0.01
136 7 0.04
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (127 bp):
TAGGGGACTCAATTATAAAGGTAAAATTGAGATTGAAAAAAATAGGGACATCAATTATAAAGGCA
GTAAAGATGGAGATTGAAAAACTTAAGAGCCTCAATTATAAAGTTAAGTGGGATTAAAAAAC
Found at i:183468 original size:29 final size:29
Alignment explanation
Indices: 183460--183534 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
183450 AAAAAATGGA
183460 GACTCTAATTACAAAGATAAAAAAGAGGG
1 GACTCTAATTACAAAGATAAAAAAGAGGG
*
183489 GACTCTAATTACAAAGATAAAAAAGCGGG
1 GACTCTAATTACAAAGATAAAAAAGAGGG
183518 GACTCTAATTACAAAGA
1 GACTCTAATTACAAAGA
183535 CGTCATAACC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (29 bp):
GACTCTAATTACAAAGATAAAAAAGAGGG
Found at i:185733 original size:40 final size:40
Alignment explanation
Indices: 185620--185733 Score: 104
Period size: 40 Copynumber: 2.8 Consensus size: 40
185610 TGTTGAGGAC
* *
185620 GACACTGCTCATACATGATGAAGAGTTCTGGTCGTTTAAGGGT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGTCG--T-AGGGT
* * * * ** *
185663 GACATGGTTCCTACGTGATGAGGAAATCTGGTCG-GGGGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGTCGTAGGG-T
185703 GACACGGCTCATACGTGATGAAGAGTTCTGG
1 GACACGGCTCATACGTGATGAAGAGTTCTGG
185734 CCATCTAGAG
Statistics
Matches: 55, Mismatches: 15, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
39 3 0.05
40 26 0.47
43 26 0.47
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (40 bp):
GACACGGCTCATACGTGATGAAGAGTTCTGGTCGTAGGGT
Found at i:185826 original size:93 final size:87
Alignment explanation
Indices: 185697--186098 Score: 223
Period size: 93 Copynumber: 4.5 Consensus size: 87
185687 AATCTGGTCG
* * * * *
185697 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAGAGGTGGATGATAACTCGGTT
1 GGGG-TGACACGGCTCCTACGTGATGAGGAGGTCTGGCCATCTA-AGG-GGATG---ACACGGCT
185762 CTTACGCGATGAGGATGGCTGGTTATCTA
60 CTTACGCGATGAGGA-GGCTGGTTATCTA
*
185791 GGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGG---TC-AA-GGGATGACACGGCTCATACG
1 GGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGCCATCTAAGGGGATGACACGGCTCTTACG
** * * * **
185851 TAATGAAGAGTTCTAGCCATCTA
66 CGATGAGGAG-GCTGGTTATCTA
* * ** **
185874 GGGGTGGATGATAACTCGGTTCCTACACGATGAGGACGG-CTGGTTATCT-AGGGG-TGACACGG
1 --GG-GG-TG---ACACGGCTCCTACGTGATGAGGA-GGTCTGGCCATCTAAGGGGATGACACGG
* * *
185936 CTCCTACGTGATGAGGAGGTCTGG---TCGA
58 CTCTTACGCGATGAGGAGG-CTGGTTATCTA
* * * * * * * *
185964 GGGATGACACGGCTCATACGTGATGAAGAGTTCTGTCCATCTAGGGGTGGATGATAACTCGGTTC
1 GGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGCCATCTA-AGG-GGATG---ACACGGCTC
* *
186029 TTACACGATGAGGACGGTTGGTTATCTA
61 TTACGCGATGAGGA-GGCTGGTTATCTA
*
186057 GGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCATCT
1 GGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGCCATCT
186099 TTAGGGATAA
Statistics
Matches: 233, Mismatches: 48, Indels: 55
0.69 0.14 0.16
Matches are distributed among these distances:
82 2 0.01
83 49 0.21
85 4 0.02
86 11 0.05
87 6 0.03
88 3 0.01
89 1 0.00
90 49 0.21
91 4 0.02
93 97 0.42
94 7 0.03
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.25
Consensus pattern (87 bp):
GGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGCCATCTAAGGGGATGACACGGCTCTTACG
CGATGAGGAGGCTGGTTATCTA
Found at i:185851 original size:40 final size:40
Alignment explanation
Indices: 185790--185998 Score: 132
Period size: 40 Copynumber: 4.9 Consensus size: 40
185780 CTGGTTATCT
*
185790 AGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCA
1 AGGGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCA
* * * * *
185830 AGGGATGACACGGCTCATACGTAATGAAGAGTTCTAGCCATCTA
1 AGGGATGACACGGCTCCTACGTGATGAGGAGGTCT-G--GTC-A
* * * ** *
185874 GGGGTGGATGATAACTCGGTTCCTACACGATGAGGACGG-CTGGTTATCT
1 --AG-GGATG---ACACGGCTCCTACGTGATGAGGA-GGTCTGG---TCA
* *
185923 AGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCG
1 AGGGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCA
* * *
185963 AGGGATGACACGGCTCATACGTGATGAAGAGTTCTG
1 AGGGATGACACGGCTCCTACGTGATGAGGAGGTCTG
185999 TCCATCTAGG
Statistics
Matches: 126, Mismatches: 28, Indels: 30
0.68 0.15 0.16
Matches are distributed among these distances:
40 64 0.51
41 1 0.01
42 2 0.02
43 25 0.20
44 1 0.01
46 5 0.04
47 6 0.05
49 1 0.01
50 20 0.16
51 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.22
Consensus pattern (40 bp):
AGGGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCA
Found at i:185874 original size:133 final size:132
Alignment explanation
Indices: 185659--186095 Score: 730
Period size: 133 Copynumber: 3.3 Consensus size: 132
185649 GGTCGTTTAA
* * ** **
185659 GGGTGACATGGTTCCTACGTGATGAGGAAATCTGGTCGGGGGATGACACGGCTCATACGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGCTCATACGTGATGA
* * *
185724 AGAGTTCTGGCCATCTAGAGGTGGATGATAACTCGGTTCTTACGCGATGAGGATGGCTGGTTATC
66 AGAGTTCT-GCCATCTAGGGGTGGATGATAACTCGGTTCTTACACGATGAGGACGGCTGGTTATC
185789 TAG
130 TAG
*
185792 GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGCTCATACGTAATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGCTCATACGTGATGA
*
185857 AGAGTTCTAGCCATCTAGGGGTGGATGATAACTCGGTTCCTACACGATGAGGACGGCTGGTTATC
66 AGAGTTCT-GCCATCTAGGGGTGGATGATAACTCGGTTCTTACACGATGAGGACGGCTGGTTATC
185922 TAG
130 TAG
*
185925 GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGGCTCATACGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGCTCATACGTGATGA
*
185990 AGAGTTCTGTCCATCTAGGGGTGGATGATAACTCGGTTCTTACACGATGAGGACGGTTGGTTATC
66 AGAGTTCTG-CCATCTAGGGGTGGATGATAACTCGGTTCTTACACGATGAGGACGGCTGGTTATC
186055 TAG
130 TAG
186058 GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCA
1 GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCA
186096 TCTTTAGGGA
Statistics
Matches: 286, Mismatches: 17, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
132 1 0.00
133 285 1.00
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (132 bp):
GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGCTCATACGTGATGA
AGAGTTCTGCCATCTAGGGGTGGATGATAACTCGGTTCTTACACGATGAGGACGGCTGGTTATCT
AG
Found at i:185960 original size:43 final size:43
Alignment explanation
Indices: 185902--186098 Score: 154
Period size: 43 Copynumber: 4.5 Consensus size: 43
185892 GTTCCTACAC
*
185902 GATGAGGACGG-CTGGTTATCTAGGGGTGACACGGCTCCTACGT
1 GATGAGGA-GGTCTGGTCATCTAGGGGTGACACGGCTCCTACGT
* * *
185945 GATGAGGAGGTCTGG---TCGAGGGATGACACGGCTCATACGT
1 GATGAGGAGGTCTGGTCATCTAGGGGTGACACGGCTCCTACGT
* * * * * **
185985 GATGAAGAGTTCT-GTCCATCTAGGGGTGGATGATAACTCGGTTCTTACAC
1 GATGAGGAGGTCTGGT-CATCTA--GG-GG-TG---ACACGGCTCCTACGT
*
186035 GATGAGGACGGT-TGGTTATCTAGGGGTGACACGGCTCCTACGT
1 GATGAGGA-GGTCTGGTCATCTAGGGGTGACACGGCTCCTACGT
186078 GATGAGGAGGTCTGGTCATCT
1 GATGAGGAGGTCTGGTCATCT
186099 TTAGGGATAA
Statistics
Matches: 118, Mismatches: 21, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
39 1 0.01
40 33 0.28
42 5 0.04
43 41 0.35
45 2 0.02
46 3 0.03
47 4 0.03
48 2 0.02
50 23 0.19
51 4 0.03
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.25
Consensus pattern (43 bp):
GATGAGGAGGTCTGGTCATCTAGGGGTGACACGGCTCCTACGT
Found at i:187054 original size:120 final size:120
Alignment explanation
Indices: 186836--187056 Score: 279
Period size: 120 Copynumber: 1.8 Consensus size: 120
186826 ACTGTCTCGA
* *
186836 GAGACAAAAGTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTGTCATTAA
1 GAGACAAAAGTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAACTGTCATGAA
*
186901 GATATAAAATTTTGTTTTAAAAGAAACAAACTCAAAGATGGATTACATCTTAAGT
66 GATACAAAATTTTGTTTTAAAAGAAACAAACTCAAAGATGGATTACATCTTAAGT
* * * **
186956 GAGACGAAA-TTTGTTTCAAAGGAAACAATCTCAAAGGTTGGTTTT-TCATTAGAAACTGTC-TC
1 GAGACAAAAGTTTGTTTCAAAGGAAACAAACTCAAAGATT--TTTTCTCAAAAGAAACTGTCAT-
* * *
187018 GAGAGATACAAAA-TTTGTTTTAACAGAAATAGACTCAAA
63 GA-AGATACAAAATTTTGTTTTAAAAGAAACAAACTCAAA
187057 TATGATTTTG
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
119 29 0.34
120 44 0.51
121 13 0.15
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (120 bp):
GAGACAAAAGTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAACTGTCATGAA
GATACAAAATTTTGTTTTAAAAGAAACAAACTCAAAGATGGATTACATCTTAAGT
Found at i:187445 original size:30 final size:31
Alignment explanation
Indices: 187391--187449 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
187381 GAGACAAAGT
187391 TTTGTTTCAAAAGAAATAGACTCAAAGATCA
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCA
187422 TTTGTTTCAAAAGAAAT-GACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
187450 GATGTTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCA
Found at i:187527 original size:36 final size:36
Alignment explanation
Indices: 187487--187624 Score: 181
Period size: 36 Copynumber: 3.8 Consensus size: 36
187477 ATAATTTGGA
*
187487 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * * *
187523 AAATTGTCTCAAACGACACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
187559 AAATTGTCTCAAGCGAGACAACATTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* *
187594 AAAATGATCTCAAGTGAGATCAAC-TTTGTTT
1 AAATTG-TCTCAAGCGAGA-CAACATTTGTTT
187625 AATATGAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
35 8 0.09
36 77 0.87
37 4 0.04
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:187754 original size:107 final size:103
Alignment explanation
Indices: 187563--187912 Score: 406
Period size: 104 Copynumber: 3.3 Consensus size: 103
187553 TTAGAGAAAT
* * *
187563 TGTCTCAAGCGAGAC-AACATTTGTTTTTGAGAAAAT--GATCTCAAGTGAGATCAACTTTGTTT
1 TGTCTCAAACGAGACGAA-ATTTG-TTTTGAAAAAATACGATCTCAAATGAGATCAACTTTGTTT
* **
187625 AATATGAAAACAAATTTGAAATTTGTATTCTCAAAGGAAAAA
64 AATGTG-AAACAAATTCAAAATTTGTA-TCTCAAAGGAAAAA
* * *
187667 TGTCTCAAACGAGACGAAATTTGTTTTGAAAAGAATAAC-AGTCTCAAGTGAGATTAATTTTTGT
1 TGTCTCAAACGAGACGAAATTTGTTTTGAAAA-AAT-ACGA-TCTCAAATGAGATCAA-CTTTGT
* *
187731 TTCAA-GTGAATCAAATTCAAAATTTGTATATCAAAGGAAAAAA
62 TT-AATGTGAAACAAATTCAAAATTTGTATCTCAAAGG-AAAAA
* * *
187774 TGTCTCAAGCAAGACGAAGTTTGTTTT-AAGAAAATACGATCTCAAATGAGATCAACTTTGTTTA
1 TGTCTCAAACGAGACGAAATTTGTTTTGAA-AAAATACGATCTCAAATGAGATCAACTTTGTTTA
*
187838 ATGTGAAACAAATTCAAATTTTGTATCTCAAAGGAAAAA
65 ATGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAA
*
187877 TGTCTCAAATGAGACGAAATTTGTTTTGAAAGAAAT
1 TGTCTCAAACGAGACGAAATTTGTTTTGAAA-AAAT
187913 TGTCTCAAGC
Statistics
Matches: 210, Mismatches: 22, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
103 39 0.19
104 64 0.30
105 18 0.09
106 15 0.07
107 63 0.30
108 9 0.04
109 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (103 bp):
TGTCTCAAACGAGACGAAATTTGTTTTGAAAAAATACGATCTCAAATGAGATCAACTTTGTTTAA
TGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAA
Found at i:187869 original size:104 final size:102
Alignment explanation
Indices: 187563--187903 Score: 397
Period size: 107 Copynumber: 3.3 Consensus size: 102
187553 TTAGAGAAAT
* *
187563 TGTCTCAAGCGAGAC-AACATTTGTTTTTGAGAAAAT--GATCTCAAGTGAGATCAACTTTGTTT
1 TGTCTCAAACGAGACGAA-ATTTG-TTTTAAGAAAATACGATCTCAAGTGAGATCAACTTTGTTT
* *
187625 AATATGAAAACAAATTTGAAATTTGTATTCTCAAAGGAAAAA
64 AATGTG-AAACAAA-TTCAAATTTGTA-TCTCAAAGGAAAAA
* *
187667 TGTCTCAAACGAGACGAAATTTGTTTTGAA-AAGAATAAC-AGTCTCAAGTGAGATTAATTTTTG
1 TGTCTCAAACGAGACGAAATTTGTTTT-AAGAA-AAT-ACGA-TCTCAAGTGAGATCAA-CTTTG
* *
187730 TTTCAA-GTGAATCAAATTCAAAATTTGTATATCAAAGGAAAAAA
61 TTT-AATGTGAAACAAATTC-AAATTTGTATCTCAAAGG-AAAAA
* * * *
187774 TGTCTCAAGCAAGACGAAGTTTGTTTTAAGAAAATACGATCTCAAATGAGATCAACTTTGTTTAA
1 TGTCTCAAACGAGACGAAATTTGTTTTAAGAAAATACGATCTCAAGTGAGATCAACTTTGTTTAA
187839 TGTGAAACAAATTCAAATTTTGTATCTCAAAGGAAAAA
66 TGTGAAACAAATTCAAA-TTTGTATCTCAAAGGAAAAA
*
187877 TGTCTCAAATGAGACGAAATTTGTTTT
1 TGTCTCAAACGAGACGAAATTTGTTTT
187904 GAAAGAAATT
Statistics
Matches: 202, Mismatches: 20, Indels: 31
0.80 0.08 0.12
Matches are distributed among these distances:
103 39 0.19
104 56 0.28
105 18 0.09
106 17 0.08
107 61 0.30
108 9 0.04
109 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (102 bp):
TGTCTCAAACGAGACGAAATTTGTTTTAAGAAAATACGATCTCAAGTGAGATCAACTTTGTTTAA
TGTGAAACAAATTCAAATTTGTATCTCAAAGGAAAAA
Found at i:190156 original size:20 final size:20
Alignment explanation
Indices: 190133--190173 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
190123 GGATAAATGC
190133 AATGTTTCAAGGTCTCAAAG
1 AATGTTTCAAGGTCTCAAAG
190153 AATGTTTCAAGGTCTCAAAG
1 AATGTTTCAAGGTCTCAAAG
190173 A
1 A
190174 GAGGGAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (20 bp):
AATGTTTCAAGGTCTCAAAG
Found at i:194212 original size:3 final size:3
Alignment explanation
Indices: 194204--194247 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
194194 ACATGTAAAT
*
194204 TAA TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA CT-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
194248 ATATTAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 3 0.08
3 32 0.89
4 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:194371 original size:42 final size:42
Alignment explanation
Indices: 194323--194430 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 42
194313 TAGGGGTCCT
* * *
194323 AATTATAAAGGTAAAAAAAAGATGGAA-AAAATTAGAGACTTC
1 AATTATAAAGGTAAAAATAAGATGAAATAAAATTAG-GACCTC
* * * *
194365 AGTTATAAAGATAAAAAGTGAGATTAAATAAAATTAGGACCTC
1 AATTATAAAGGTAAAAA-TAAGATGAAATAAAATTAGGACCTC
*
194408 AATAATAAAGGTAAAAATAAGAT
1 AATTATAAAGGTAAAAATAAGAT
194431 TAAAAACTAA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
42 20 0.38
43 25 0.47
44 8 0.15
ACGTcount: A:0.56, C:0.05, G:0.16, T:0.23
Consensus pattern (42 bp):
AATTATAAAGGTAAAAATAAGATGAAATAAAATTAGGACCTC
Found at i:194507 original size:29 final size:29
Alignment explanation
Indices: 194475--194536 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
194465 AATGGAGACT
194475 CTAATTACAAAGATAAAAAAGCGGGGACA
1 CTAATTACAAAGATAAAAAAGCGGGGACA
*
194504 CTAATTACAAAGATAAAAAAGCGGGGACT
1 CTAATTACAAAGATAAAAAAGCGGGGACA
194533 CTAA
1 CTAA
194537 ACATCGCTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.16
Consensus pattern (29 bp):
CTAATTACAAAGATAAAAAAGCGGGGACA
Found at i:199156 original size:41 final size:41
Alignment explanation
Indices: 199110--199352 Score: 120
Period size: 41 Copynumber: 6.2 Consensus size: 41
199100 AAATTCGCGT
199110 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
* * * **
199151 CGCGATTATT--T-A-----AAT-CGTA-ACGT-ATTCGCGT
1 TGCGATT-TTCCTAATTCGCAATGCGAATACGTAAATCGCAA
* * * * **
199182 TGCGGTTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATACGTAAATCGCAA
* *
199223 TGCGATTTTCTTAATTCGTAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
** * * * * *
199264 CACGA-TTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TACGTAAATCGCAA
* * * * *
199305 TGCGA-ATTCGTAAATCGCAATGCGAATATG-ACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTA-AATCGCAA
199345 TGCGATTT
1 TGCGATTT
199353 ACATAGCACC
Statistics
Matches: 153, Mismatches: 33, Indels: 32
0.70 0.15 0.15
Matches are distributed among these distances:
30 2 0.01
31 10 0.07
32 5 0.03
33 4 0.03
34 3 0.02
38 2 0.01
39 4 0.03
40 38 0.25
41 83 0.54
42 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
Found at i:199200 original size:21 final size:21
Alignment explanation
Indices: 199174--199240 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
199164 ATCGTAACGT
*
199174 ATTCGCGTTGCGGTTTTCCTA
1 ATTCGCGTTGCGATTTTCCTA
* * *
199195 ATTCGCATTGCGATTTACGT-
1 ATTCGCGTTGCGATTTTCCTA
*
199215 ATTCGCGTTGCGATTTTCTTA
1 ATTCGCGTTGCGATTTTCCTA
199236 ATTCG
1 ATTCG
199241 TAATGCGAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.45
21 21 0.55
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (21 bp):
ATTCGCGTTGCGATTTTCCTA
Found at i:199220 original size:20 final size:20
Alignment explanation
Indices: 199170--199230 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
199160 TTAAATCGTA
*
199170 ACGTATTCGCGTTGCGGTTT
1 ACGTATTCGCGTTGCGATTT
* * *
199190 TCCTAATTCGCATTGCGATTT
1 ACGT-ATTCGCGTTGCGATTT
199211 ACGTATTCGCGTTGCGATTT
1 ACGTATTCGCGTTGCGATTT
199231 TCTTAATTCG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (20 bp):
ACGTATTCGCGTTGCGATTT
Found at i:199275 original size:20 final size:21
Alignment explanation
Indices: 199242--199331 Score: 123
Period size: 20 Copynumber: 4.4 Consensus size: 21
199232 CTTAATTCGT
199242 AATGCGAA-TACGTAAATCGC
1 AATGCGAATTACGTAAATCGC
**
199262 AACACG-ATTACGTAAATCGC
1 AATGCGAATTACGTAAATCGC
* *
199282 AATGCGAATTAGGAAAATCGC
1 AATGCGAATTACGTAAATCGC
199303 AATGCGAATT-CGTAAATCGC
1 AATGCGAATTACGTAAATCGC
199323 AATGCGAAT
1 AATGCGAAT
199332 ATGACTATCG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.02
20 37 0.62
21 22 0.37
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (21 bp):
AATGCGAATTACGTAAATCGC
Found at i:199299 original size:21 final size:21
Alignment explanation
Indices: 199242--199354 Score: 108
Period size: 20 Copynumber: 5.6 Consensus size: 21
199232 CTTAATTCGT
*
199242 AATGCGAA-TACGTAAATCGC
1 AATGCGAATTACGAAAATCGC
** *
199262 AACACG-ATTACGTAAATCGC
1 AATGCGAATTACGAAAATCGC
*
199282 AATGCGAATTAGGAAAATCGC
1 AATGCGAATTACGAAAATCGC
*
199303 AATGCGAATT-CGTAAATCGC
1 AATGCGAATTACGAAAATCGC
* **
199323 AATGCGAA-TATGACTATCGC
1 AATGCGAATTACGAAAATCGC
*
199343 AATGCGATTTAC
1 AATGCGAATTAC
199355 ATAGCACCAT
Statistics
Matches: 75, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
19 2 0.03
20 49 0.65
21 24 0.32
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (21 bp):
AATGCGAATTACGAAAATCGC
Found at i:199919 original size:19 final size:20
Alignment explanation
Indices: 199870--199920 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
199860 TAGTTTCGAG
199870 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGCGGA
**
199890 AATGACTATCGCAACGC-GA
1 AATGAAAATCGCAACGCGGA
199909 AATGAAAATCGC
1 AATGAAAATCGC
199921 TACGAGAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.14
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGGA
Found at i:200021 original size:20 final size:19
Alignment explanation
Indices: 199950--200029 Score: 106
Period size: 20 Copynumber: 4.1 Consensus size: 19
199940 GAAACCAAAA
*
199950 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
199969 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
199988 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
200008 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
200028 TC
1 TC
200030 AACCAAAAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
19 19 0.36
20 33 0.62
21 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:201344 original size:23 final size:22
Alignment explanation
Indices: 201300--201344 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
201290 AATGTCAAGT
*
201300 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
201322 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
201345 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:202223 original size:103 final size:103
Alignment explanation
Indices: 202039--202256 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
202029 GTTGAGGGTC
202039 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
202104 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
202142 TATGTGGTCTTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
202207 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
202245 TATGTGGTCCTT
1 TATGTGGTCCTT
202257 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:202317 original size:47 final size:47
Alignment explanation
Indices: 202263--202382 Score: 206
Period size: 47 Copynumber: 2.6 Consensus size: 47
202253 CCTTATGGAC
202263 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
*
202310 ATTATTATATGGCACTACGGTGCAATTCTACGCGGTACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
* *
202357 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
202383 ATATGAGCTG
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
46 20 0.29
47 50 0.71
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
Found at i:202383 original size:23 final size:23
Alignment explanation
Indices: 202263--202387 Score: 124
Period size: 23 Copynumber: 5.3 Consensus size: 23
202253 CCTTATGGAC
*
202263 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
202287 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
202310 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * * *
202334 ATTCTACGCGGTACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
202357 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
202380 ATTATATG
1 ATTATATG
202388 AGCTGTGGTG
Statistics
Matches: 79, Mismatches: 21, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
23 58 0.73
24 21 0.27
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:204673 original size:94 final size:93
Alignment explanation
Indices: 204483--204858 Score: 607
Period size: 94 Copynumber: 4.1 Consensus size: 93
204473 TAGATTCCTT
* * *
204483 AGTAAATTTATTCAGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
204544 ATTTGTCTTTTGTTTTGTTTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
204573 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
204638 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
204667 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
204732 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
204761 AGTAAATTTGTTCGTTTGTTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
204826 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
204854 AGTAA
1 AGTAA
204859 TGCAATCCAT
Statistics
Matches: 272, Mismatches: 9, Indels: 7
0.94 0.03 0.02
Matches are distributed among these distances:
90 34 0.12
92 3 0.01
93 27 0.10
94 208 0.76
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.48
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:204976 original size:20 final size:20
Alignment explanation
Indices: 204951--205012 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
204941 TTTTGGTTGA
204951 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
204971 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
204990 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
205010 AAT
1 AAT
205013 CGCAACACGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 17 0.46
20 20 0.54
ACGTcount: A:0.50, C:0.18, G:0.23, T:0.10
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:205024 original size:33 final size:33
Alignment explanation
Indices: 204975--205058 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
204965 CGAGAGAATG
*
204975 AAAATCGCAACGCGAAACGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
* * *
205008 AGAATCGCAACACGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
205041 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
205059 TATAATAGCG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.49, C:0.25, G:0.19, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACGAAAATCGCAACGAC
Found at i:205147 original size:39 final size:36
Alignment explanation
Indices: 205067--205166 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 36
205057 ACTATAATAG
205067 CGTTGCGATTTTAATTTCGCATTGCGA-TTCTCTCT
1 CGTTGCGATTTTAATTTCGCATTGCGATTTCTCTCT
* *
205102 --TTGCGATTTTTATTTCGCTTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTAATTTCGCATTGCGA-TTTC--TCTCT
* *
205139 CGTTGCGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTAATTTCGCATTGCGAT
205167 AGTTATTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
33 23 0.42
35 3 0.05
37 5 0.09
38 1 0.02
39 23 0.42
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.49
Consensus pattern (36 bp):
CGTTGCGATTTTAATTTCGCATTGCGATTTCTCTCT
Found at i:205174 original size:19 final size:19
Alignment explanation
Indices: 205066--205166 Score: 95
Period size: 19 Copynumber: 5.5 Consensus size: 19
205056 AACTATAATA
*
205066 GCGTTGCGATTTTAATTTC
1 GCGTTGCGATTTTCATTTC
*
205085 GCATTGCGA--TTC---TC
1 GCGTTGCGATTTTCATTTC
* * *
205099 TCTTTGCGATTTTTATTTC
1 GCGTTGCGATTTTCATTTC
*
205118 GCTTTGCGATTTTCATTCTC
1 GCGTTGCGATTTTCATT-TC
*
205138 TCGTTGCGATTTTCATTTC
1 GCGTTGCGATTTTCATTTC
205157 GCGTTGCGAT
1 GCGTTGCGAT
205167 AGTTATTTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
14 9 0.14
16 2 0.03
17 2 0.03
19 36 0.55
20 17 0.26
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.49
Consensus pattern (19 bp):
GCGTTGCGATTTTCATTTC
Found at i:205660 original size:21 final size:21
Alignment explanation
Indices: 205636--205705 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
205626 CTATCATTCC
205636 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* * ** *
205657 TCAAGAGGCCACTGTCATCGT
1 TCAAGAGTCCCCTCCCACCGT
* *
205678 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCACCGT
205699 TCAAGAG
1 TCAAGAG
205706 CCCGATTCAC
Statistics
Matches: 35, Mismatches: 13, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:205663 original size:42 final size:42
Alignment explanation
Indices: 205587--205705 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
205577 GACTCGCCTG
* * * * * *
205587 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
205629 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
205671 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTC-CTCAAGA-GTCCCCTCCCACCGTTCAAGAG
205706 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.03
42 61 0.94
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:207075 original size:14 final size:14
Alignment explanation
Indices: 207056--207091 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
207046 ATTGTTTAAT
207056 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
207070 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
207084 TGATTTGT
1 TGATTTGT
207092 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:207214 original size:19 final size:19
Alignment explanation
Indices: 207198--207244 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
207188 AAAAATGACT
*
207198 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
207217 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
207236 ATCGCAACG
1 ATCGCAACG
207245 ACAAAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:207317 original size:33 final size:33
Alignment explanation
Indices: 207273--207399 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
207263 ACTAAATTCG
* * *
207273 CGTTGCAATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
207306 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
207339 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
207372 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
207400 AGTCATTTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:207365 original size:19 final size:19
Alignment explanation
Indices: 207308--207419 Score: 91
Period size: 19 Copynumber: 6.4 Consensus size: 19
207298 GATTCCCTCG
207308 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
207327 TTGTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
207341 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
207360 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
207374 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
207393 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
207413 TTGCGAT
1 TTGCGAT
207420 AGACATTAAG
Statistics
Matches: 73, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
14 11 0.15
16 14 0.19
17 14 0.19
19 24 0.33
20 10 0.14
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:207379 original size:14 final size:14
Alignment explanation
Indices: 207294--207381 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
207284 TCATTTCGCT
*
207294 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
207308 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
207325 CATTGTGATTCTCTCG
1 --TTGCGATTCTCTCG
*
207341 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
207358 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
207374 TTGCGATT
1 TTGCGATT
207382 TTCATTTCGC
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 19 0.33
16 14 0.25
17 13 0.23
19 11 0.19
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:207418 original size:20 final size:19
Alignment explanation
Indices: 207372--207426 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
207362 GCGATTCTCT
**
207372 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
207391 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
207411 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
207427 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:210913 original size:41 final size:41
Alignment explanation
Indices: 210866--210980 Score: 160
Period size: 41 Copynumber: 2.8 Consensus size: 41
210856 GAATTAGGAA
*
210866 AATCGCGTTGCGATTTTCCTAATTTGCATTGCGATTTACGT
1 AATCGCGTTGCGATTTTCCTAATTCGCATTGCGATTTACGT
* *
210907 ATTCGCGTTGCGATTTTCCTAATTCGCATTGCGATTTATGT
1 AATCGCGTTGCGATTTTCCTAATTCGCATTGCGATTTACGT
* * * *
210948 AATCGCATTGCAATTTACGT-ATTCGCATTGCGA
1 AATCGCGTTGCGATTTTCCTAATTCGCATTGCGA
210981 ATTAGGAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 13 0.20
41 53 0.80
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (41 bp):
AATCGCGTTGCGATTTTCCTAATTCGCATTGCGATTTACGT
Found at i:210919 original size:20 final size:20
Alignment explanation
Indices: 210868--210980 Score: 118
Period size: 20 Copynumber: 5.5 Consensus size: 20
210858 ATTAGGAAAA
* * *
210868 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
*
210889 TTGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * *
210909 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
210930 TCGCATTGCGATTTATGTAA
1 TCGCATTGCGATTTACGTAT
*
210950 TCGCATTGCAATTTACGTAT
1 TCGCATTGCGATTTACGTAT
210970 TCGCATTGCGA
1 TCGCATTGCGA
210981 ATTAGGAAAA
Statistics
Matches: 74, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
20 44 0.59
21 30 0.41
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:210994 original size:21 final size:21
Alignment explanation
Indices: 210970--211022 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
210960 ATTTACGTAT
*
210970 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
210991 TCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
211012 TCGCAATGCGA
1 TCGCAATGCGA
211023 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:212014 original size:16 final size:17
Alignment explanation
Indices: 211993--212024 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
211983 ATTCGACATA
211993 ATTTTAATTTA-ATAAT
1 ATTTTAATTTATATAAT
212009 ATTTTAATTTATATAA
1 ATTTTAATTTATATAA
212025 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAATTTATATAAT
Found at i:212037 original size:22 final size:22
Alignment explanation
Indices: 212003--212050 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
211993 ATTTTAATTT
* **
212003 AATAATATTTTAATTTATATAAA
1 AATAATATATTAAAATAT-TAAA
212026 AATAA-ATATTAAAATATTAAA
1 AATAATATATTAAAATATTAAA
212047 AATA
1 AATA
212051 TAAAATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
22 9 0.41
23 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAATATATTAAAATATTAAA
Found at i:212206 original size:17 final size:19
Alignment explanation
Indices: 212166--212206 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
212156 AGATAAATGA
*
212166 AAAGTTATCTTTTGAGTTT
1 AAAGTTATCTTTTGAATTT
*
212185 TAAGTTAT-TTTT-AATTT
1 AAAGTTATCTTTTGAATTT
212202 AAAGT
1 AAAGT
212207 AAATACAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (19 bp):
AAAGTTATCTTTTGAATTT
Found at i:213248 original size:18 final size:19
Alignment explanation
Indices: 213206--213250 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
213196 ACATTCTCAG
213206 TAATTTTATTTCTTGATAA
1 TAATTTTATTTCTTGATAA
*
213225 T-TTTTTATTT-TT-ATTAA
1 TAATTTTATTTCTTGA-TAA
213242 TAATTTTAT
1 TAATTTTAT
213251 ATCTCGTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 1 0.05
17 6 0.27
18 14 0.64
19 1 0.05
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TAATTTTATTTCTTGATAA
Found at i:215041 original size:15 final size:15
Alignment explanation
Indices: 215021--215049 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
215011 GGAGTTATTC
215021 GACTGACGTTATCCG
1 GACTGACGTTATCCG
215036 GACTGACGTTATCC
1 GACTGACGTTATCC
215050 CACAATGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.28
Consensus pattern (15 bp):
GACTGACGTTATCCG
Found at i:219544 original size:30 final size:31
Alignment explanation
Indices: 219510--219576 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
219500 TAAAAAAACA
**
219510 TAAGATA-TGATCACTTTTGTTTTT-TTTAAT
1 TAAGATATTG-TCACTTTCATTTTTATTTAAT
219540 TAAGATATTGTCACTTTCATTTTTATTTAAT
1 TAAGATATTGTCACTTTCATTTTTATTTAAT
219571 TAAGAT
1 TAAGAT
219577 GTGGTCATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 19 0.58
31 14 0.42
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (31 bp):
TAAGATATTGTCACTTTCATTTTTATTTAAT
Found at i:219693 original size:25 final size:23
Alignment explanation
Indices: 219664--219723 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 23
219654 TTAAATGAAA
219664 ATAAAAAT-TCTAAATTAAGTTAAT
1 ATAAAAATAT-TAAA-TAAGTTAAT
*
219688 ACTAAAATATATTTAATAAGTTAAT
1 A-TAAAA-ATATTAAATAAGTTAAT
219713 ATAAAAATATT
1 ATAAAAATATT
219724 TTGAAGTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
23 5 0.16
24 6 0.19
25 15 0.47
26 5 0.16
27 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (23 bp):
ATAAAAATATTAAATAAGTTAAT
Found at i:219703 original size:22 final size:21
Alignment explanation
Indices: 219678--219737 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 21
219668 AAATTCTAAA
219678 TTAAGTTAATACTAAAATATATT
1 TTAAGTTAATA-TAAAA-ATATT
219701 TAATAAGTTAATATAAAAATATT
1 T--TAAGTTAATATAAAAATATT
219724 TTGAAGTTAATATA
1 TT-AAGTTAATATA
219738 TATATAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.03
22 11 0.32
23 7 0.21
24 5 0.15
25 10 0.29
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.42
Consensus pattern (21 bp):
TTAAGTTAATATAAAAATATT
Found at i:219749 original size:28 final size:29
Alignment explanation
Indices: 219704--219770 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
219694 ATATATTTAA
*
219704 TAAGT-TA-ATATAAAAATATTTTGAAGT
1 TAAGTATATATATAAAAATATTATGAAGT
* *
219731 TAA-TATATATATAATAATATTATGAATT
1 TAAGTATATATATAAAAATATTATGAAGT
*
219759 TAAGTATTTATA
1 TAAGTATATATA
219771 CTAAGATACA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 5 0.15
28 20 0.61
29 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (29 bp):
TAAGTATATATATAAAAATATTATGAAGT
Found at i:220532 original size:12 final size:12
Alignment explanation
Indices: 220494--220536 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
220484 AAAAAAATAT
*
220494 TATTATTATTAT
1 TATTATTATTAG
220506 TATTATTATTAG
1 TATTATTATTAG
*
220518 TATTATTATTGG
1 TATTATTATTAG
220530 TATTATT
1 TATTATT
220537 GGTAACAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (12 bp):
TATTATTATTAG
Found at i:220536 original size:3 final size:3
Alignment explanation
Indices: 220491--220527 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
220481 AAAAAAAAAA
*
220491 TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
220528 GGTATTATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:221041 original size:80 final size:77
Alignment explanation
Indices: 220905--221132 Score: 353
Period size: 80 Copynumber: 3.0 Consensus size: 77
220895 TGTTCGTTAA
*
220905 TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAGTCAAGTCT
1 TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAGTAAAGTCT
220970 TCTTCTTCTTCT
66 TCTTCTTCTTCT
220982 TCTTCTATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAGTAAAG
1 TC--C-ATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAGTAAAG
221047 ------TCTTCTTCT
63 TCTTCTTCTTCTTCT
* *
221056 TCCATTAACGG-AATATTATGTGACAATTAAAAATAAAAAATTCATGTGTAAAATAGTAAAGTCT
1 TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAGTAAAGTCT
221120 TCTTCTTCTTCT
66 TCTTCTTCTTCT
221132 T
1 T
221133 TTTATTCTTC
Statistics
Matches: 139, Mismatches: 3, Indels: 19
0.86 0.02 0.12
Matches are distributed among these distances:
70 48 0.35
71 8 0.06
72 1 0.01
74 11 0.08
76 10 0.07
77 2 0.01
79 1 0.01
80 58 0.42
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (77 bp):
TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAGTAAAGTCT
TCTTCTTCTTCT
Found at i:221087 original size:70 final size:71
Alignment explanation
Indices: 220976--221127 Score: 270
Period size: 70 Copynumber: 2.2 Consensus size: 71
220966 GTCTTCTTCT
*
220976 TCTTCTTCTTCTATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACA
1 TCTTCTTCTTCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACA
221041 GTAAAG
66 GTAAAG
* *
221047 TCTTCTTCTTCCATTAACGG-AATATTATGTGACAATTAAAAATAAAAAATTCATGTGTAAAATA
1 TCTTCTTCTTCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACA
221111 GTAAAG
66 GTAAAG
221117 TCTTCTTCTTC
1 TCTTCTTCTTC
221128 TTCTTTTTAT
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
70 59 0.76
71 19 0.24
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (71 bp):
TCTTCTTCTTCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACA
GTAAAG
Found at i:221396 original size:3 final size:3
Alignment explanation
Indices: 221388--221475 Score: 167
Period size: 3 Copynumber: 29.3 Consensus size: 3
221378 AACAGTCAAG
*
221388 TCT TCT TCT TCT TCG TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
221436 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
221476 ACGTTATCGA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.00, C:0.33, G:0.01, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:221423 original size:131 final size:135
Alignment explanation
Indices: 221056--221412 Score: 521
Period size: 131 Copynumber: 2.6 Consensus size: 135
221046 GTCTTCTTCT
* * *
221056 TCCATTAACGG-AATATTATGTGACAATTAAAAATAAAAAATTCATGTGTAAAATAGTAAAGTCT
1 TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAGTCAAGTCT
*
221120 TCTTCTTCTTCTTTTTATTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCGTTAA
66 TCTTCTTCTTC---TTATTCTTCTTACG-TATC-ATCCTTCTGGTTTAAGTACCTTAGGCATTAA
*
221185 TGTTCGTTAA
126 CGTTCGTTAA
221195 TCCATTAACGGAAATATTATGTGACAA-T-----TAAAAAATCCATGTGTAAAACAGTCAAGTCT
1 TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAGTCAAGTCT
*
221254 TCTTCTTCTTCTTATTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTATCTTAGGCATTAACGT
66 TCTTCTTCTTCTTATTCTTCTTACG-TATC-ATCCTTCTGGTTTAAGTACCTTAGGCATTAACGT
221319 TCGTTAA
129 TCGTTAA
*
221326 TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAAACCATGTGTAAAACAGTCAAGTCT
1 TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAGTCAAGTCT
* *
221391 TCTTCTTCTTCGTCTTCTTCTT
66 TCTTCTTCTTCTTATTCTTCTT
221413 CTTCTTCTTC
Statistics
Matches: 202, Mismatches: 9, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
131 85 0.42
132 1 0.00
134 39 0.19
137 50 0.25
139 12 0.06
140 15 0.07
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.39
Consensus pattern (135 bp):
TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAGTCAAGTCT
TCTTCTTCTTCTTATTCTTCTTACGTATCATCCTTCTGGTTTAAGTACCTTAGGCATTAACGTTC
GTTAA
Found at i:221522 original size:331 final size:321
Alignment explanation
Indices: 221117--221740 Score: 1000
Period size: 331 Copynumber: 1.9 Consensus size: 321
221107 AATAGTAAAG
* *
221117 TCTTCTTCTTCTTCTTTTTATTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCGT
1 TCTTCTTCTTCTTCTTCTTATTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCAT
221182 TAATGTTCGTTAATCCATTAACGGAAATATTATGTGACAA-T-TAAAAAATCCATGTGTAAAACA
66 TAATGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTATAAAAAATCCATGTGTAAAACA
* *
221245 GTCAAGTCTTCTTCTTCTTCTTATTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTATCTTAGG
131 ATCAAG---TCTTCTTCTTC---TTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGG
221310 CATTAACGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAAACCATGTG
190 CATTAACGTTCGTTAATCCATTAACGGAAATATTATGTGACAA-T-----TAAAAAAACCATGTG
221375 TAAAACAGTCAAGTCTTCTTCTTCTTCGTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT
249 TAAAACAGTCAAGTCTTCTTCTTCTTCGTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT
221440 CTTCTTCT
314 CTTCTTCT
* * *
221448 TCTTCTTCTTCTTCTTCTTCTTCTTCTTACGTTATCGATCTTTCTGGTTTTAGTACCTTAGGCAT
1 TCTTCTTCTTCTTCTTCTTATTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCAT
221513 TAATGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAA
66 TAATGTTCGTTAATCCATTAACGGAAATATTATGTGACAATT----ATAAAAAATCCATGTGTAA
221578 AACAATCAAGTCTTCTTCTTCTTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCA
127 AACAATCAAGTCTTCTTCTTCTTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCA
* *
221643 TTAATGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAAATCCATGTGTAAAACAG
192 TTAACGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAAAACCATGTGTAAAACAG
*
221708 TCAAGTCTTCTTCTTCTTCTTCTTCTTCTTCTT
257 TCAAGTCTTCTTCTTCTTCGTCTTCTTCTTCTT
221741 ACGTTTTGAT
Statistics
Matches: 277, Mismatches: 10, Indels: 18
0.91 0.03 0.06
Matches are distributed among these distances:
325 54 0.19
330 1 0.00
331 183 0.66
332 1 0.00
334 11 0.04
337 27 0.10
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (321 bp):
TCTTCTTCTTCTTCTTCTTATTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCAT
TAATGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTATAAAAAATCCATGTGTAAAACA
ATCAAGTCTTCTTCTTCTTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCATTAA
CGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAAAACCATGTGTAAAACAGTCAA
GTCTTCTTCTTCTTCGTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
Found at i:221721 original size:3 final size:3
Alignment explanation
Indices: 221713--221740 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
221703 AACAGTCAAG
221713 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
221741 ACGTTTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:221821 original size:133 final size:136
Alignment explanation
Indices: 221448--221879 Score: 645
Period size: 131 Copynumber: 3.2 Consensus size: 136
221438 TTCTTCTTCT
* *
221448 TCTTCTTCTTCTTCTTCTTCTTCTTCTTACGTTATCGATCTTTCTGGTTTTAGTACCTTAGGCAT
1 TCTTCTTCTTCTTCTTCTTCTTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCAT
221513 TAATGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAA
66 TAATGTTCGTTAATCCATTAACGGAAATATTATGTGACAATT----ATAAAAAATCCATGTGTAA
*
221578 AACAATCAAG
127 AACAGTCAAG
221588 ---------TCTTCTTCTTCTTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCAT
1 TCTTCTTCTTCTTCTTCTTCTTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCAT
221644 TAATGTTCGTTAATCCATTAACGGAAATATTATGTGACAA-T-TAAAAAATCCATGTGTAAAACA
66 TAATGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTATAAAAAATCCATGTGTAAAACA
221707 GTCAAG
131 GTCAAG
*
221713 TCTTCTTCTTCTTCTTCTTCTTCTTCTTACGTT-TTGATCCTTCTGGTTTAAGTACCTTAGGCAT
1 TCTTCTTCTTCTTCTTCTTCTTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCAT
* *
221777 TAATGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAAACCATGCGTAA
66 TAATGTTCGTTAATCCATTAACGGAAATATTATGTGACAATT----ATAAAAAATCCATGTGTAA
221842 AACAGTCAAG
127 AACAGTCAAG
*
221852 TCTTCTTCTTCTTCTTCGTCTTCTTCTT
1 TCTTCTTCTTCTTCTTCTTCTTCTTCTT
221880 CTTCTTCTTC
Statistics
Matches: 270, Mismatches: 7, Indels: 31
0.88 0.02 0.10
Matches are distributed among these distances:
125 27 0.10
130 1 0.00
131 94 0.35
133 70 0.26
134 25 0.09
139 53 0.20
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (136 bp):
TCTTCTTCTTCTTCTTCTTCTTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCAT
TAATGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTATAAAAAATCCATGTGTAAAACA
GTCAAG
Found at i:221860 original size:3 final size:3
Alignment explanation
Indices: 221852--221927 Score: 134
Period size: 3 Copynumber: 25.3 Consensus size: 3
221842 AACAGTCAAG
*
221852 TCT TCT TCT TCT TCT TCG TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
221900 TTT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
221928 ACGTTATCGA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:222032 original size:188 final size:187
Alignment explanation
Indices: 221715--222062 Score: 624
Period size: 188 Copynumber: 1.9 Consensus size: 187
221705 CAGTCAAGTC
* *
221715 TTCTTCTTCTTCTTCTTCTTCTTCTTACGTTTTGATCCTTCTGGTTTAAGTACCTTAGGCATTAA
1 TTCTTCTTCTTCTTCTTCTTCTTCTTACGTTTCGATCCTACTGGTTTAAGTACCTTAGGCATTAA
221780 TGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAAACCATGCGTAAAAC
66 TGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAAACCATGCGTAAAAC
* *
221845 AGTCAAGTCTTCTTCTTCTTCTTCGTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTT
131 AGTCAAGTCTTCTTCTTCTTCCTCCTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTT
221902 TTCTTCTTCTTCTTCTTCTTCTTCTTACGTTATCGATCCTACTGGTTTAAGTACCTTAGGCATTA
1 TTCTTCTTCTTCTTCTTCTTCTTCTTACGTT-TCGATCCTACTGGTTTAAGTACCTTAGGCATTA
* * *
221967 ATGTTTGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAA
65 ATGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAAACCATGCGTAAAA
222032 CAGTCAAGTCTTCTTCTTCTTCCTCCTCTTC
130 CAGTCAAGTCTTCTTCTTCTTCCTCCTCTTC
222063 CATAAACTTG
Statistics
Matches: 153, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
187 31 0.20
188 122 0.80
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (187 bp):
TTCTTCTTCTTCTTCTTCTTCTTCTTACGTTTCGATCCTACTGGTTTAAGTACCTTAGGCATTAA
TGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAAACCATGCGTAAAAC
AGTCAAGTCTTCTTCTTCTTCCTCCTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTT
Found at i:222099 original size:16 final size:16
Alignment explanation
Indices: 222078--222111 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
222068 ACTTGCTTCA
222078 TCGGTTCTACTATAAC
1 TCGGTTCTACTATAAC
222094 TCGGTTCTACTATAAC
1 TCGGTTCTACTATAAC
222110 TC
1 TC
222112 CGATCTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (16 bp):
TCGGTTCTACTATAAC
Found at i:222166 original size:3 final size:3
Alignment explanation
Indices: 222158--222196 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
222148 TATGTAGTTT
* *
222158 TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC CTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
222197 CATAAACTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:222183 original size:452 final size:454
Alignment explanation
Indices: 221056--222053 Score: 1388
Period size: 452 Copynumber: 2.2 Consensus size: 454
221046 GTCTTCTTCT
* * * *
221056 TCCATTAACGG-AATATTATGTGACAATTAAAAATAAAAAATTCATGTGTAAAATAGTAAAGTCT
1 TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAATCAAG---
* * * * *
221120 TCTTCTTCTTCTTTTTATTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCGTTAA
63 TCTTCTTCTTC------TTCTTCTTACATAAACGATCCTTCTGGTTTAAGTAACTTAGGCATTAA
* * * * *
221185 TGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAAATCCATGTGTAAAACAGTCAA
122 TCTCCG-T-ATCCATGAACGGAAATATTATATCACAA-TAAAAAAT-CATGTGTAAAACAGTC-A
*
221250 G---TCTTCTTCTTCTTCTTATTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTATCTTAGGCA
182 GTCTTCTTCTTCTTCTTCTTATTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCA
*
221312 TTAACGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAAACCATGTGTA
247 TTAACGTTCGTTAATCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAAACCATGCGTA
*
221377 AAACAGTCAAGTCTTCTTCTTCTTCGTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
312 AAACAGTCAAG-----TTCTTCTTC-TCTTCTTCTTCGTCTTCTTCTTCTTCTTCTTCTTCTTCT
* * *
221442 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTACGTTATCGATCTTTCTGGTTTTAGTACCTT
371 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTACGTTATCGATCCTACTGGTTTAAGTACCTT
221507 AGGCATTAATGTTCGTTAA
436 AGGCATTAATGTTCGTTAA
221526 TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAATCAAGTCT
1 TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAATCAAGTCT
* * * * * *
221591 TCTTCTTCTTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCATTAATGTTCGTTA
66 TCTTCTTCTTCTTCTTACATAAACGATCCTTCTGGTTTAAGTAACTTAGGCATTAATCTCCG-T-
* * *
221656 ATCCATTAACGGAAATATTATGTGACAATTAAAAAATCCATGTGTAAAACAGTCAAGTCTTCTTC
129 ATCCATGAACGGAAATATTATATCACAA-TAAAAAAT-CATGTGTAAAACAGTC-AGTCTTCTTC
* * *
221721 TTCTTCTTCTTCTTCTTCTTACGTT-TTGATCCTTCTGGTTTAAGTACCTTAGGCATTAATGTTC
191 TTCTTCTTCTTATTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCATTAACGTTC
221785 GTTAATCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAAACCATGCGTAAAACAGTCA
256 GTTAATCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAAACCATGCGTAAAACAGTCA
221850 AG-TCTTC-T-TCTTCTTCTTCGTCTTCTTCTTCTTCTTCTTCTTCTTCTTC-T-TT-TTCTTCT
321 AGTTCTTCTTCTCTTCTTCTTCGTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
*
221909 TCTTCTTCTTCTTCTTCTTACGTTATCGATCCTACTGGTTTAAGTACCTTAGGCATTAATGTTTG
386 TCTTCTTCTTCTTCTTCTTACGTTATCGATCCTACTGGTTTAAGTACCTTAGGCATTAATGTTCG
221974 TTAA
451 TTAA
*
221978 TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAGTCAAGTCT
1 TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAATCAAGTCT
222043 TCTTCTTCTTC
66 TCTTCTTCTTC
222054 CTCCTCTTCC
Statistics
Matches: 508, Mismatches: 16, Indels: 26
0.92 0.03 0.05
Matches are distributed among these distances:
452 147 0.29
453 2 0.00
454 1 0.00
455 40 0.08
457 1 0.00
458 5 0.01
462 113 0.22
464 102 0.20
465 29 0.06
468 11 0.02
470 11 0.02
471 46 0.09
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (454 bp):
TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAATCCATGTGTAAAACAATCAAGTCT
TCTTCTTCTTCTTCTTACATAAACGATCCTTCTGGTTTAAGTAACTTAGGCATTAATCTCCGTAT
CCATGAACGGAAATATTATATCACAATAAAAAATCATGTGTAAAACAGTCAGTCTTCTTCTTCTT
CTTCTTATTCTTCTTACGTTATCGATCCTTCTGGTTTAAGTACCTTAGGCATTAACGTTCGTTAA
TCCATTAACGGAAATATTATGTGACAATTAAAAATAAAAAAACCATGCGTAAAACAGTCAAGTTC
TTCTTCTCTTCTTCTTCGTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC
TTCTTCTTCTTCTTACGTTATCGATCCTACTGGTTTAAGTACCTTAGGCATTAATGTTCGTTAA
Found at i:224235 original size:2 final size:2
Alignment explanation
Indices: 224223--224295 Score: 93
Period size: 2 Copynumber: 39.0 Consensus size: 2
224213 AATCACTTAA
* *
224223 AT AT AT A- AT AT AT A- AA AT A- AT A- AA AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
224260 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
224296 CGGATCGGGG
Statistics
Matches: 64, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
1 5 0.08
2 59 0.92
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:232749 original size:14 final size:14
Alignment explanation
Indices: 232732--232782 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
232722 CATTCCTATT
232732 TTTGCATCTTTGCA
1 TTTGCATCTTTGCA
*
232746 TTTGCA--TGTGCA
1 TTTGCATCTTTGCA
232758 TCTTCGCATCTTTGCA
1 T-TT-GCATCTTTGCA
*
232774 TTAGCATCT
1 TTTGCATCT
232783 ATATATAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
12 6 0.20
13 2 0.07
14 15 0.50
15 1 0.03
16 6 0.20
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.45
Consensus pattern (14 bp):
TTTGCATCTTTGCA
Found at i:233815 original size:2 final size:2
Alignment explanation
Indices: 233808--233837 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
233798 AGCCTTTCAA
233808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
233838 CCCTTGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:234122 original size:23 final size:21
Alignment explanation
Indices: 234096--234157 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 21
234086 GATATATCAT
234096 AAAAAATAAAAGAAATAGAGAAA
1 AAAAAATAAAAGAAA-A-AGAAA
234119 AAAAAGA-AAAAGCATAAAAGAAA
1 AAAAA-ATAAAAG-A-AAAAGAAA
234142 AGAAAGAATAAAAGAA
1 A-AAA-AATAAAAGAA
234158 GAAAAAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
23 17 0.52
24 8 0.24
25 8 0.24
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (21 bp):
AAAAAATAAAAGAAAAAGAAA
Found at i:234126 original size:9 final size:9
Alignment explanation
Indices: 234114--234251 Score: 53
Period size: 9 Copynumber: 13.7 Consensus size: 9
234104 AAAGAAATAG
234114 AGAAAAAAA
1 AGAAAAAAA
234123 AGAAAAAGCATAA
1 AG-AAAA--A-AA
*
234136 AAGAAAAGAA
1 -AGAAAAAAA
234146 AGAATAAAAGA
1 AGAA-AAAA-A
*
234157 AGAAAAAAG
1 AGAAAAAAA
**
234166 AGCTAAAAA
1 AGAAAAAAA
* *
234175 AGAGAGAAA
1 AGAAAAAAA
234184 AGAAAGAAAGA
1 AGAAA-AAA-A
*
234195 AGGAAAAGAA
1 A-GAAAAAAA
234205 AGAAAAATGAGAA
1 AG-AAAA--A-AA
234218 AGAAAAAAA
1 AGAAAAAAA
*
234227 A-AGACAAAA
1 AGA-AAAAAA
234236 AGAAAAAGAA
1 AGAAAAA-AA
234246 AGAAAA
1 AGAAAA
234252 TACTTCAAGA
Statistics
Matches: 97, Mismatches: 15, Indels: 33
0.67 0.10 0.23
Matches are distributed among these distances:
8 1 0.01
9 35 0.36
10 31 0.32
11 9 0.09
12 9 0.09
13 10 0.10
14 2 0.02
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.03
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:234138 original size:31 final size:33
Alignment explanation
Indices: 234101--234163 Score: 87
Period size: 31 Copynumber: 1.9 Consensus size: 33
234091 ATCATAAAAA
234101 ATAAAAGAAATAG-AGAA-AAAA-AAGAAAAAGC
1 ATAAAAGAAA-AGAAGAATAAAAGAAGAAAAAGC
234132 ATAAAAGAAAAGAAAGAATAAAAGAAGAAAAA
1 ATAAAAGAAAAG-AAGAATAAAAGAAGAAAAA
234164 AGAGCTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 2 0.07
31 10 0.36
32 4 0.14
33 4 0.14
34 8 0.29
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.06
Consensus pattern (33 bp):
ATAAAAGAAAAGAAGAATAAAAGAAGAAAAAGC
Found at i:234144 original size:19 final size:17
Alignment explanation
Indices: 234098--234251 Score: 79
Period size: 17 Copynumber: 8.8 Consensus size: 17
234088 TATATCATAA
*
234098 AAAATAAAAGAAATAGAG
1 AAAA-AAAAGAAAAAGAG
*
234116 AAAAAAAAGAAAAAGCAT
1 AAAAAAAAGAAAAAG-AG
234134 AAAAGAAAAG--AAAGA-
1 AAAA-AAAAGAAAAAGAG
*
234149 ATAAAAGAAGAAAAAAGAG
1 A-AAAAAAAG-AAAAAGAG
*
234168 CTAAAAAAGAGAGAAAAGA-
1 --AAAAAAAAGA-AAAAGAG
* *
234187 AAGAAAGAAGGAAAAGA-
1 AA-AAAAAAGAAAAAGAG
* *
234204 AAGAAAAATGAGAAAGA-
1 AA-AAAAAAGAAAAAGAG
234221 AAAAAAAAGACAAAA-AG
1 AAAAAAAAGA-AAAAGAG
234238 AAAAAGAAAGAAAA
1 AAAAA-AAAGAAAA
234252 TACTTCAAGA
Statistics
Matches: 108, Mismatches: 14, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
15 5 0.05
16 12 0.11
17 48 0.44
18 24 0.22
19 6 0.06
20 12 0.11
21 1 0.01
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (17 bp):
AAAAAAAAGAAAAAGAG
Found at i:234240 original size:22 final size:23
Alignment explanation
Indices: 234139--234250 Score: 83
Period size: 22 Copynumber: 4.9 Consensus size: 23
234129 AGCATAAAAG
*
234139 AAAAGAAAGAATAAAAG-AAGAA
1 AAAAGAAAGAAGAAAAGAAAGAA
*** *
234161 AAAAGAGCTAA-AAAAGAGAGAAA
1 AAAAGAAAGAAGAAAAGAAAG-AA
234184 AGAAAGAAAGAAGGAAAAGAAAGAA
1 A-AAAGAAAGAA-GAAAAGAAAGAA
234209 AAATGAGAAAGAA-AAAA-AAAGACA
1 AAA--AGAAAGAAGAAAAGAAAGA-A
234233 AAAAGAAA-AAG-AAAGAAA
1 AAAAGAAAGAAGAAAAGAAA
234251 ATACTTCAAG
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
21 10 0.14
22 18 0.25
23 8 0.11
24 17 0.24
25 3 0.04
26 16 0.22
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.03
Consensus pattern (23 bp):
AAAAGAAAGAAGAAAAGAAAGAA
Found at i:236934 original size:55 final size:54
Alignment explanation
Indices: 236742--236934 Score: 193
Period size: 55 Copynumber: 3.6 Consensus size: 54
236732 CGTTTTTTTT
* * * **
236742 AGAAACTAAGTC-CATTTTTAGAAGTTTCTTGATTATTTTTAAATGAGTTTTCAA
1 AGAAACTAAATCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGTTTT-AA
* *
236796 AGAAACTAAATATGATTTTCAGAAGTTAC-T--CGA---TTAACATGAGTTTTTAA
1 AGAAACTAAATCTGATTTTCAGAAGTTTCTTGACGATTTTTAA-ATGAG-TTTTAA
* *
236846 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTTAAATGAGCTTTTAA
1 AGAAACTAAATCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAG-TTTTAA
* * *
236901 AGAAATTAACTCTGATTTTCAGAAATTTCTTGAC
1 AGAAACTAAATCTGATTTTCAGAAGTTTCTTGAC
236935 AAAATAAATT
Statistics
Matches: 114, Mismatches: 16, Indels: 17
0.78 0.11 0.12
Matches are distributed among these distances:
49 4 0.04
50 32 0.28
51 5 0.04
52 1 0.01
53 3 0.03
54 11 0.10
55 54 0.47
56 4 0.04
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.40
Consensus pattern (54 bp):
AGAAACTAAATCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGTTTTAA
Found at i:237044 original size:54 final size:54
Alignment explanation
Indices: 236936--237090 Score: 215
Period size: 54 Copynumber: 2.9 Consensus size: 54
236926 TTTCTTGACA
* * * * * *
236936 AAATAAATTTTAAAGAAGCTAAGCTTGA-TTTTCAAGAGTTTCTGGATGTTTTC
1 AAATGAATTTTAAAGAAGCTAAGCCTAATTTTTCAGGGGTTTCTTGATGTTTTC
*
236989 AAATGAATTTGAAAGAAGCTAAGCCTAATTTTTCAGGGGTTTCTTGATGTTTTC
1 AAATGAATTTTAAAGAAGCTAAGCCTAATTTTTCAGGGGTTTCTTGATGTTTTC
* *
237043 AAATGAATTTTATAGAAGCTAACCCTAATTTTT-AGGGGTTTCTTGATG
1 AAATGAATTTTAAAGAAGCTAAGCCTAATTTTTCAGGGGTTTCTTGATG
237091 ATAAATGTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 39 0.43
54 52 0.57
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (54 bp):
AAATGAATTTTAAAGAAGCTAAGCCTAATTTTTCAGGGGTTTCTTGATGTTTTC
Found at i:237628 original size:104 final size:103
Alignment explanation
Indices: 237440--237629 Score: 294
Period size: 104 Copynumber: 1.8 Consensus size: 103
237430 TTTTTACTCA
* *
237440 AAACAAGAAATTTTATCTCACTCGGGATTGTTTTCTTAAAACAAATTTCATCTCGCTTGAGAAAG
1 AAACAAGAAATTTTATCTCACTCGAGATTGTTTTCTTAAAACAAACTTCATCTCGCTTGAGAAAG
* * *
237505 TTTCCCTTGAAATATAAATTTTGAAAGTGTTTCACTTG
66 TTTCACTCGAAATAAAAATTTTGAAAGTGTTTCACTTG
237543 AAACAAGAAATTTTATCTCACTCGAGATTGTTTTTCTTAAAACAAACTTC-TACTCGCTTGAGAC
1 AAACAAGAAATTTTATCTCACTCGAGATTG-TTTTCTTAAAACAAACTTCAT-CTCGCTTGAGA-
237607 AA-TTTCACTCGAAATAAAAATTT
63 AAGTTTCACTCGAAATAAAAATTT
237630 ATCTCACTTG
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
103 30 0.38
104 47 0.59
105 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (103 bp):
AAACAAGAAATTTTATCTCACTCGAGATTGTTTTCTTAAAACAAACTTCATCTCGCTTGAGAAAG
TTTCACTCGAAATAAAAATTTTGAAAGTGTTTCACTTG
Found at i:237677 original size:36 final size:36
Alignment explanation
Indices: 237557--237753 Score: 128
Period size: 36 Copynumber: 5.4 Consensus size: 36
237547 AAGAAATTTT
* *
237557 ATCTCACTCGAGATTGTTTTTCTTAAAACAAACTTC
1 ATCTCGCTTGAGATTGTTTTTCTTAAAACAAACTTC
*** ** * * *
237593 -TACTCGCTTGAGACAATTTCACTCGAAATA-AAAATTT
1 AT-CTCGCTTGAGATTGTTTTTCT-TAAA-ACAAACTTC
*
237630 ATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTC
1 ATCTCGCTTGAGATTGTTTTTCTTAAAACAAACTTC
* ** * ** * *
237666 ATCTCGTTTGAGACAGTTTTCACTCGAAACAAAAATTT
1 ATCTCGCTTGAGATTGTTTT-TCTTAAAAC-AAACTTC
* *
237704 ATCTCACTTGAGATTGTTTTTCTTAAAAAAAACTTC
1 ATCTCGCTTGAGATTGTTTTTCTTAAAACAAACTTC
* *
237740 GTTTCGCTTGAGAT
1 ATCTCGCTTGAGAT
237754 AATTCTTACT
Statistics
Matches: 113, Mismatches: 41, Indels: 14
0.67 0.24 0.08
Matches are distributed among these distances:
35 2 0.02
36 54 0.48
37 34 0.30
38 23 0.20
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (36 bp):
ATCTCGCTTGAGATTGTTTTTCTTAAAACAAACTTC
Found at i:237677 original size:73 final size:72
Alignment explanation
Indices: 237534--237813 Score: 355
Period size: 73 Copynumber: 3.8 Consensus size: 72
237524 TTTGAAAGTG
* *
237534 TTTCACTTGAAACAAGAAATTTTATCTCACTCGAGATTGTTTTTCTTAAAACAAACTTCTACTCG
1 TTTCACTCGAAACAA-AAA-TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCT-CTCG
237599 CTTGAGACAA
63 CTTGAGACAA
* *
237609 TTTCACTCGAAATAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCATCTCGTT
1 TTTCACTCGAAACAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTC-TCTCGCT
*
237674 TGAGACAGT
65 TGAGACA-A
* *
237683 TTTCACTCGAAACAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAAAAAACTTCGTTTCGCT
1 TTTCACTCGAAACAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTC-TCTCGCT
*
237748 TGAGATAA
65 TGAGACAA
* * * * * * *
237756 TTCTTACTCGAAAC-AAATTTTATCTCACCTGAGATAGTTTCTCTTCAAACAAATTTCT
1 TT-TCACTCGAAACAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCT
237814 TTTGATTCAT
Statistics
Matches: 182, Mismatches: 20, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
72 1 0.01
73 88 0.48
74 80 0.44
75 13 0.07
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (72 bp):
TTTCACTCGAAACAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCTCTCGCTT
GAGACAA
Found at i:237717 original size:147 final size:149
Alignment explanation
Indices: 237534--237808 Score: 396
Period size: 147 Copynumber: 1.9 Consensus size: 149
237524 TTTGAAAGTG
* *
237534 TTTCACTTGAAACAAGAAATTTTATCTCACTCGAGATTGTTTTTCTTAAAACAAACTTC-TACTC
1 TTTCACTCGAAACAAGAAATTTTATCTCACTCGAGATTGTTTTTCTTAAAAAAAACTTCGT-CTC
* * *
237598 GCTTGAGACAATT-TCACTCGAAATAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA
65 GCTTGAGACAATTCTCACTCGAAA-AAAAATTTATCTCACCTGAGATAGTTTCTCTTAAAACAAA
237662 CTTCATCTCGTTTGAGACAGT
129 CTTCATCTCGTTTGAGACAGT
* *
237683 TTTCACTCGAAACAA-AAA-TTTATCTCACTTGAGATTGTTTTTCTTAAAAAAAACTTCGTTTCG
1 TTTCACTCGAAACAAGAAATTTTATCTCACTCGAGATTGTTTTTCTTAAAAAAAACTTCGTCTCG
* * * * *
237746 CTTGAGATAATTCTTACTCGAAACAAATTTTATCTCACCTGAGATAGTTTCTCTTCAAACAAA
66 CTTGAGACAATTCTCACTCGAAAAAAAATTTATCTCACCTGAGATAGTTTCTCTTAAAACAAA
237809 TTTCTTTTGA
Statistics
Matches: 112, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
147 85 0.76
148 13 0.12
149 14 0.12
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.37
Consensus pattern (149 bp):
TTTCACTCGAAACAAGAAATTTTATCTCACTCGAGATTGTTTTTCTTAAAAAAAACTTCGTCTCG
CTTGAGACAATTCTCACTCGAAAAAAAATTTATCTCACCTGAGATAGTTTCTCTTAAAACAAACT
TCATCTCGTTTGAGACAGT
Found at i:238576 original size:273 final size:272
Alignment explanation
Indices: 238083--238733 Score: 856
Period size: 273 Copynumber: 2.4 Consensus size: 272
238073 GAAGATAAAC
* * *
238083 CGATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAATAAGTT
1 CGATCAACATTTCCAATGGAGAGTTCATTATGAGAAGAACTCATCCGATAAAGGGAG---AAGTT
* *
238148 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGTATTTCAAATCAGTGACGCCTCG
63 CATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGGTATTTCAAATCAGTGACACCTCG
*
238213 CTTGAGGAATTAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAG
128 CTTGAGGAATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAG
* * * * * * * *
238278 AAGTTCATAATGAGAAGAGCTTGTTCGACCTATCA-CTCGATTAATCGCATTTGGATTTGAATTA
193 AAGTTCATAATAAGAAGAACTTGTTCAACCT-T-AGCTCAATTAATCACATATGGAGTTGAATCA
*
238342 GCAACACCTCACTCAAG
256 GAAACACCTCACTCAAG
* *
238359 GGATCAACATTTCCAATGGAGAGTTCATTATGAGAAGAACTCATCCGACAAAGGGAGAAGTTCAT
1 CGATCAACATTTCCAATGGAGAGTTCATTATGAGAAGAACTCATCCGATAAAGGGAGAAGTTCAT
* * * *
238424 AACGAGAAGATCTTGTTCGACCTATCACTCGATTCACTGTATTTCAAATTAGTGACACCTCGCTT
66 AATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGGTATTTCAAATCAGTGACACCTCGCTT
* * ** * *
238489 GAGGGATCAACGTTTCCGATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAG
131 GAGGAATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAAG
* *
238554 TTCATAATAAGAAGAACTTGTTCAACCTTAGCTCAATTCATCATATATGGAGTTGAATCAGAAAC
196 TTCATAATAAGAAGAACTTGTTCAACCTTAGCTCAATTAATCACATATGGAGTTGAATCAGAAAC
* * **
238619 TCCTCGCTTGAG
261 ACCTCACTCAAG
* * * * *
238631 CGATCAACATTTCCAGTGGAGAGTTCATTATGAGAAAAACTCACCCGATGAGGGAGAAGAAGTTC
1 CGATCAACATTTCCAATGGAGAGTTCATTATGAGAAGAACTCATCCGATAAAGG-G-AGAAGTTC
* *
238696 ATAATGAGAAGAACTTGTTCAACCT-TAACTCGAATTCA
64 ATAATGAGAAGAACTTGTTCGACCTATCACTCG-ATTCA
238734 TCACATATGG
Statistics
Matches: 328, Mismatches: 43, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
271 1 0.00
272 82 0.25
273 158 0.48
274 35 0.11
276 52 0.16
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (272 bp):
CGATCAACATTTCCAATGGAGAGTTCATTATGAGAAGAACTCATCCGATAAAGGGAGAAGTTCAT
AATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGGTATTTCAAATCAGTGACACCTCGCTT
GAGGAATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAAG
TTCATAATAAGAAGAACTTGTTCAACCTTAGCTCAATTAATCACATATGGAGTTGAATCAGAAAC
ACCTCACTCAAG
Found at i:238652 original size:139 final size:138
Alignment explanation
Indices: 238083--238763 Score: 724
Period size: 139 Copynumber: 4.9 Consensus size: 138
238073 GAAGATAAAC
* *
238083 CGATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAATAAGTT
1 CGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAT-GAGGGAGAAGAAGTT
* * ** * *
238148 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCA-CGGTAT-T--TCAAATCAGTGACGC
65 CATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATC-ATATATGGTTGAATCAGTAACAC
238209 CTCGCTTGAG
129 CTCGCTTGAG
* * * *
238219 -GAATTAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAAGTT
1 CG-ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTT
* * ** * * *
238283 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTAATCGCATTTGGATTTGAATTAGCAACA
65 CATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATCATATATGG--TTGAATCAGTAACA
* **
238348 CCTCACTCAAG
128 CCTCGCTTGAG
* * ** *
238359 GGATCAACATTTCCAATGGAGAGTTCATTATGAGAAGAACTCATCCGACAAAGG-G-AGAAGTTC
1 CGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
* * * * * *
238422 ATAACGAGAAGATCTTGTTCGACCTATCACTCGATTCA-C-TGTAT--TTCAAATTAGTGACACC
66 ATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATCATATATGGTT-GAATCAGTAACACC
238483 TCGCTTGAG
130 TCGCTTGAG
* * *
238492 GGATCAACGTTTCCGATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
1 CGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
* * * * *
238557 ATAATAAGAAGAACTTGTTCAACCT-T-AGCTCAATTCATCATATATGGAGTTGAATCAGAAACT
66 ATAATGAGAAGAACTTGTTCGACCTATCA-CTCGATTCATCATATAT-G-GTTGAATCAGTAACA
238620 CCTCGCTTGAG
128 CCTCGCTTGAG
* * * *
238631 CGATCAACATTTCCAGTGGAGAGTTCATTATGAGAAAAACTCACCCGATGAGGGAGAAGAAGTTC
1 CGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
* * *
238696 ATAATGAGAAGAACTTGTTCAACCT-TAACTCGAATTCATCACATATGGTGTTGAATCAGTAACA
66 ATAATGAGAAGAACTTGTTCGACCTATCACTCG-ATTCATCATATAT-G-GTTGAATCAGTAACA
238760 CCTC
128 CCTC
238764 ACTAGAGAGA
Statistics
Matches: 462, Mismatches: 63, Indels: 36
0.82 0.11 0.06
Matches are distributed among these distances:
132 2 0.00
133 66 0.14
134 10 0.02
135 85 0.18
136 53 0.11
137 1 0.00
138 43 0.09
139 105 0.23
140 96 0.21
141 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (138 bp):
CGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATCATATATGGTTGAATCAGTAACACCT
CGCTTGAG
Found at i:240132 original size:22 final size:22
Alignment explanation
Indices: 240101--240149 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
240091 TTGCTATTTT
* *
240101 TGTTTGATTATATTTTGGTCAC
1 TGTTTAATTATAATTTGGTCAC
*
240123 TGTTTAATTATAATTTGGTTAC
1 TGTTTAATTATAATTTGGTCAC
240145 TGTTT
1 TGTTT
240150 TTATTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.06, G:0.16, T:0.57
Consensus pattern (22 bp):
TGTTTAATTATAATTTGGTCAC
Found at i:243888 original size:17 final size:17
Alignment explanation
Indices: 243866--243898 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
243856 CTCACTCAAC
243866 TACATGACAC-ATGCAAA
1 TACATGA-ACTATGCAAA
243883 TACATGAACTATGCAA
1 TACATGAACTATGCAA
243899 GTTCTACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.21
Consensus pattern (17 bp):
TACATGAACTATGCAAA
Found at i:244074 original size:3 final size:3
Alignment explanation
Indices: 244066--244123 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
244056 AGGGACCATT
244066 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
244114 AAG AAG AAG A
1 AAG AAG AAG A
244124 TTCAAACTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:244268 original size:3 final size:3
Alignment explanation
Indices: 244260--244332 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
244250 AGGGACCATT
244260 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
244308 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
244333 TTCAAACTTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:244790 original size:30 final size:30
Alignment explanation
Indices: 244738--244801 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
244728 TAATGCTTTC
* *
244738 TTAATCTACTCAAACAAAAATAAAATATTT
1 TTAATCTACTCAAACAAAAATAAAAAATTA
* * * *
244768 TTAATCTATTCATATAATAATAAAAAATTA
1 TTAATCTACTCAAACAAAAATAAAAAATTA
244798 TTAA
1 TTAA
244802 AAGATTAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (30 bp):
TTAATCTACTCAAACAAAAATAAAAAATTA
Found at i:247384 original size:21 final size:21
Alignment explanation
Indices: 247358--247397 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
247348 TGATTCTACT
247358 CCTTTTCCATTTATCTTTTCC
1 CCTTTTCCATTTATCTTTTCC
* *
247379 CCTTTTGCATTTGTCTTTT
1 CCTTTTCCATTTATCTTTT
247398 GGAGGAGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.28, G:0.05, T:0.60
Consensus pattern (21 bp):
CCTTTTCCATTTATCTTTTCC
Found at i:266220 original size:17 final size:17
Alignment explanation
Indices: 266198--266230 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
266188 ATAAATATAA
*
266198 AACATCTTATAACTATT
1 AACATCTGATAACTATT
266215 AACATCTGATAACTAT
1 AACATCTGATAACTAT
266231 GAAATGTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.36
Consensus pattern (17 bp):
AACATCTGATAACTATT
Found at i:270706 original size:28 final size:28
Alignment explanation
Indices: 270674--270738 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
270664 AAAAAATGTT
270674 TTAAATATATGTATGAATTTGATTTTAG
1 TTAAATATATGTATGAATTTGATTTTAG
*
270702 TTAAATACATGTATGAATTTGATTTTAG
1 TTAAATATATGTATGAATTTGATTTTAG
270730 TTAAATATA
1 TTAAATATA
270739 AGGTTAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (28 bp):
TTAAATATATGTATGAATTTGATTTTAG
Found at i:271968 original size:21 final size:21
Alignment explanation
Indices: 271942--271994 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
271932 TAAGTAGGGG
271942 TGTACCGATACACTATTCAGA
1 TGTACCGATACACTATTCAGA
* *
271963 TGTACCGATAAACTCTTCAGA
1 TGTACCGATACACTATTCAGA
*
271984 TATACCGATAC
1 TGTACCGATAC
271995 CCCTGAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (21 bp):
TGTACCGATACACTATTCAGA
Found at i:272069 original size:20 final size:20
Alignment explanation
Indices: 272019--272070 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
272009 TGTAATAAAG
*
272019 GTACCGATACACAGCCGAAT
1 GTACCGATACCCAGCCGAAT
272039 GTACCGATACCCAGCCGAAT
1 GTACCGATACCCAGCCGAAT
*
272059 GTACTGATACCC
1 GTACCGATACCC
272071 CTCTGGCTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (20 bp):
GTACCGATACCCAGCCGAAT
Found at i:277930 original size:23 final size:23
Alignment explanation
Indices: 277899--277955 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
277889 CCCCTTGCTA
277899 TGTATCGATACATTCCTTGAATG
1 TGTATCGATACATTCCTTGAATG
*
277922 TGTACCGATACATTCCTTGAATG
1 TGTATCGATACATTCCTTGAATG
277945 TGTATCGATAC
1 TGTATCGATAC
277956 CCCTATAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (23 bp):
TGTATCGATACATTCCTTGAATG
Found at i:278398 original size:18 final size:20
Alignment explanation
Indices: 278377--278421 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
278367 AATAAAAAAA
278377 TGTTTTGT-TTTAAAT-TGT
1 TGTTTTGTATTTAAATATGT
* *
278395 TGTTTTTTATTTAATTATGT
1 TGTTTTGTATTTAAATATGT
278415 TGTTTTG
1 TGTTTTG
278422 AAAACTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 6 0.27
20 9 0.41
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.69
Consensus pattern (20 bp):
TGTTTTGTATTTAAATATGT
Found at i:280209 original size:14 final size:13
Alignment explanation
Indices: 280190--280229 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
280180 AGAATAAAGT
280190 ATTAATTTTTCAAA
1 ATTAA-TTTTCAAA
280204 ATTAA-TTTCAAA
1 ATTAATTTTCAAA
*
280216 AATAATTTTCAAA
1 ATTAATTTTCAAA
280229 A
1 A
280230 AGAAAATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 11 0.46
13 8 0.33
14 5 0.21
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTAATTTTCAAA
Found at i:280749 original size:21 final size:21
Alignment explanation
Indices: 280723--280779 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
280713 TTTTACACTG
280723 GGTGTACCGATACCCTTTGCA
1 GGTGTACCGATACCCTTTGCA
280744 GGTGTACCGATACCCTTTGCA
1 GGTGTACCGATACCCTTTGCA
*
280765 GATGTACCGATACCC
1 GGTGTACCGATACCC
280780 CTACACTCCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (21 bp):
GGTGTACCGATACCCTTTGCA
Found at i:284296 original size:126 final size:126
Alignment explanation
Indices: 284070--284333 Score: 377
Period size: 126 Copynumber: 2.1 Consensus size: 126
284060 TTCAGAATGC
* * * *
284070 GCCATTAATAATGTAGGATTCCAGAAAATGTCAGCAACTCTTTAGTGCCCCATCAATCATCTTCA
1 GCCATTAATAATGCAGGATGCCAGAAAATGCCAACAACTCTTTAGTGCCCCATCAATCATCTTCA
* * **
284135 GTAACTTTTCAATTAAATGTCATCTCTAATAATGCACCATGCCCGAAAAATATCAAAACG-
66 GCAACTTTTCAATGAAATGTCATCTCTAATAATGCACCATGCCAAAAAAATATCAAAACGA
* * * *
284195 GACCATTAATAATGCAGGATGCCAGAAAATGCCAACATCTTTTTAGTGTCCCATCACTCATCTTC
1 G-CCATTAATAATGCAGGATGCCAGAAAATGCCAACAACTCTTTAGTGCCCCATCAATCATCTTC
* *
284260 AGCAACTTTTCAGTGAAATGTCATCTCTAATAATGCACCATGCCAAAAAAATGTCAAAACGA
65 AGCAACTTTTCAATGAAATGTCATCTCTAATAATGCACCATGCCAAAAAAATATCAAAACGA
*
284322 GCAATTAATAAT
1 GCCATTAATAAT
284334 CTTCAAAACA
Statistics
Matches: 122, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
125 1 0.01
126 120 0.98
127 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (126 bp):
GCCATTAATAATGCAGGATGCCAGAAAATGCCAACAACTCTTTAGTGCCCCATCAATCATCTTCA
GCAACTTTTCAATGAAATGTCATCTCTAATAATGCACCATGCCAAAAAAATATCAAAACGA
Found at i:284351 original size:23 final size:23
Alignment explanation
Indices: 284313--284356 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
284303 CAAAAAAATG
*
284313 TCAAAACGAGCAATTAATAATCT
1 TCAAAACAAGCAATTAATAATCT
*
284336 TCAAAACAAGCCATTAATAAT
1 TCAAAACAAGCAATTAATAAT
284357 GCAGGATGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.18, G:0.07, T:0.25
Consensus pattern (23 bp):
TCAAAACAAGCAATTAATAATCT
Found at i:284430 original size:275 final size:272
Alignment explanation
Indices: 283923--284543 Score: 850
Period size: 275 Copynumber: 2.3 Consensus size: 272
283913 TTCAGAAAAT
* *
283923 ACCATTAATAATGCAAGATGCCATAAAATGTCAGCAACTTTTCAGTGCCCCATCAATCATCTTCA
1 ACCATTAATAATGCAGGATGCCAGAAAATGTCAGCAACTTTTCAGTGCCCCATCAATCATCTTCA
** * **
283988 ACAACTTTTCAATGAAAGTCAATTATAATAATGCACCATGCCTGAAAATGTTAAAACGAACCTTT
66 ACAACTTTTCAATGAAAGTCAATTATAATAATGCACCATGCCAAAAAATGTCAAAACGAACAATT
* *** * *
284053 AATAATCTTCAGAATGCGCCATTAATAATGTAGGATTCCAGAAAATGTCAGCAACTCTTTAGTGC
131 AATAATCTTCAAAACAAGCCATTAATAATGCAGGATGCCAGAAAATGTCAGCAACTCTTTAGTGC
** * *
284118 CCCATCAATCATCTTCAGTAACTTTTCAATTAAATGTCATCTCTAATAATGCACCATGCCCGAAA
196 CCCATCAATCATCTTCAACAACGTTTCAATGAAATGTCATCTCTAATAATGCACCATGCCCG-AA
284183 AATATCAAAACGG
260 AATATCAAAACGG
* * * * * *
284196 ACCATTAATAATGCAGGATGCCAGAAAATGCCAACATCTTTTTAGTGTCCCATCACTCATCTTCA
1 ACCATTAATAATGCAGGATGCCAGAAAATGTCAGCAACTTTTCAGTGCCCCATCAATCATCTTCA
* * * *
284261 GCAACTTTTCAGTGAAATGTC-ATCTCTAATAATGCACCATGCCAAAAAAATGTCAAAACGAGCA
66 ACAACTTTTCAATGAAA-GTCAAT-TATAATAATGCACCATGCC-AAAAAATGTCAAAACGAACA
284325 ATTAATAATCTTCAAAACAAGCCATTAATAATGCAGGATGCCAGAAAATGTCAGCAACT-TTTCA
128 ATTAATAATCTTCAAAACAAGCCATTAATAATGCAGGATGCCAGAAAATGTCAGCAACTCTTT-A
* * * **
284389 GTGCCTCATCAATCATCTTCAACAACGTTTCAGTGAAATGTCATCTCTAATAATGCATCATGTTC
192 GTGCCCCATCAATCATCTTCAACAACGTTTCAATGAAATGTCATCTCTAATAATGCACCATGCCC
*
284454 GAAAATGTCAAAACGG
257 GAAAATATCAAAACGG
* * * *
284470 GCCATTAATAATACAGGATGCCAGAAAATGTCAGTAACTTTTCATTGCCCCATCAATCATCTTCA
1 ACCATTAATAATGCAGGATGCCAGAAAATGTCAGCAACTTTTCAGTGCCCCATCAATCATCTTCA
284535 ACAACTTTT
66 ACAACTTTT
284544 TAGTTACATG
Statistics
Matches: 300, Mismatches: 44, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
273 74 0.25
274 101 0.34
275 125 0.42
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (272 bp):
ACCATTAATAATGCAGGATGCCAGAAAATGTCAGCAACTTTTCAGTGCCCCATCAATCATCTTCA
ACAACTTTTCAATGAAAGTCAATTATAATAATGCACCATGCCAAAAAATGTCAAAACGAACAATT
AATAATCTTCAAAACAAGCCATTAATAATGCAGGATGCCAGAAAATGTCAGCAACTCTTTAGTGC
CCCATCAATCATCTTCAACAACGTTTCAATGAAATGTCATCTCTAATAATGCACCATGCCCGAAA
ATATCAAAACGG
Found at i:286202 original size:88 final size:88
Alignment explanation
Indices: 286049--286292 Score: 321
Period size: 89 Copynumber: 2.8 Consensus size: 88
286039 GTATTCCCAT
* * *
286049 ATTTGAGCAATGCTGGTAGTATTGATACTACATTGTGAGTATCGATACTGCCACTACCTTTGGTA
1 ATTTGAGCAATG-TGGTAGTATCGATACTACCTTGTGAGTATCGATACTTCCACTACCTTTGGTA
*
286114 TCGGTACC-TTTTTGCATTCTAGA
65 TCAGTACCATTTTTGCATTCTAGA
* * *
286137 ATTTGAGTAATGTTGGTAGTATCGATACTACCTTGTGAGTATCGATACTTTC-GTACCTTTGGGT
1 ATTTGAGCAATG-TGGTAGTATCGATACTACCTTGTGAGTATCGATACTTCCACTACCTTT-GGT
* *
286201 ATCAGTACCATTTTTGCATTTTGGA
64 ATCAGTACCATTTTTGCATTCTAGA
* * * *
286226 ATTTGAGCAATGCGAGTAGTATCGATACTACCTTATGAGTATCGATACTTCCATTACATTTGGTA
1 ATTTGAGCAATGTG-GTAGTATCGATACTACCTTGTGAGTATCGATACTTCCACTACCTTTGGTA
286291 TC
65 TC
286293 GGTGCCCCTT
Statistics
Matches: 136, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
87 7 0.05
88 58 0.43
89 65 0.48
90 6 0.04
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39
Consensus pattern (88 bp):
ATTTGAGCAATGTGGTAGTATCGATACTACCTTGTGAGTATCGATACTTCCACTACCTTTGGTAT
CAGTACCATTTTTGCATTCTAGA
Found at i:291064 original size:159 final size:157
Alignment explanation
Indices: 290707--291068 Score: 377
Period size: 157 Copynumber: 2.3 Consensus size: 157
290697 CCAGCGCTAG
* * ** * * * *
290707 TCAAACGTTGGATTCCAGTCGGTTTTAGTCATATACAACTGTGTTGGTTCCTATGACACATTGAA
1 TCAAACGATGGAATCCAGTCATTTTTAATCAGATACAATTGTGTTGGTTCCTATGAAACATTGAA
* * * * ** * * *
290772 ATAGATGTAGTCAAAGCAGTTTCAGGTTATGAGGGTGGGGGATTGATGTGATTTAAGGAGCATTG
66 ACACATGTAATAAAAGCAGTTTCACCTTATGAGGGAGGGGAATTGATGTGATCTAAGGAGCATTG
*
290837 AAATGAAGCAATGCGTGGTCAGCAAAT
131 AAATGAAGCAATGCGCGGTCAGCAAAT
* ** *
290864 TCAAATGATGGGTTCCAGTCATTTTTAATCAGATACAATTGTGTTGGTTTCTATGAAACATTGAA
1 TCAAACGATGGAATCCAGTCATTTTTAATCAGATACAATTGTGTTGGTTCCTATGAAACATTGAA
*
290929 ACACATGTAATAAAAGCAGTTTCCCCTTATGATGAGGAGGGGAATTGATGTGATCTAAGGATG-A
66 ACACATGTAATAAAAGCAGTTTCACCTTATGA-G-GGAGGGGAATTGATGTGATCTAAGGA-GCA
* * ***
290993 TTGAAATGAAGTAATGTGCGGTCAGTGCAT
128 TTGAAATGAAGCAATGCGCGGTCAGCAAAT
* * * * *
291023 TCAAGCGTTTGGAATCCTGTCGTTTTTAATTAGATA-AATTGTGTTG
1 TCAAACG-ATGGAATCCAGTCATTTTTAATCAGATACAATTGTGTTG
291069 CATTAAAACA
Statistics
Matches: 167, Mismatches: 34, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
157 80 0.48
158 1 0.01
159 63 0.38
160 23 0.14
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (157 bp):
TCAAACGATGGAATCCAGTCATTTTTAATCAGATACAATTGTGTTGGTTCCTATGAAACATTGAA
ACACATGTAATAAAAGCAGTTTCACCTTATGAGGGAGGGGAATTGATGTGATCTAAGGAGCATTG
AAATGAAGCAATGCGCGGTCAGCAAAT
Found at i:294341 original size:18 final size:19
Alignment explanation
Indices: 294320--294356 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
294310 CTTATTTTTA
294320 TTTAATAAA-AAATTATTT
1 TTTAATAAATAAATTATTT
*
294338 TTTAATAAATATATTATTT
1 TTTAATAAATAAATTATTT
294357 CGGGTTAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAATAAATAAATTATTT
Found at i:314190 original size:19 final size:19
Alignment explanation
Indices: 314166--314205 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
314156 GCTGCCAAGA
314166 ACGCCATTAAAATAAGCAT
1 ACGCCATTAAAATAAGCAT
314185 ACGCCATTAAAATAAGCAT
1 ACGCCATTAAAATAAGCAT
314204 AC
1 AC
314206 TAGACAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.23, G:0.10, T:0.20
Consensus pattern (19 bp):
ACGCCATTAAAATAAGCAT
Found at i:314862 original size:17 final size:17
Alignment explanation
Indices: 314842--314876 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
314832 TTTCGACTAT
314842 TAAATTT-TTAAATATTA
1 TAAATTTATTAAAT-TTA
314859 TAAATTTATTAAATTTA
1 TAAATTTATTAAATTTA
314876 T
1 T
314877 CGATATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAATTTATTAAATTTA
Found at i:314871 original size:9 final size:9
Alignment explanation
Indices: 314839--314876 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
314829 TTATTTCGAC
314839 TATTAAATT
1 TATTAAATT
314848 T-TTAAATAT
1 TATTAAAT-T
314857 TA-TAAATT
1 TATTAAATT
314865 TATTAAATT
1 TATTAAATT
314874 TAT
1 TAT
314877 CGATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 9 0.35
9 17 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TATTAAATT
Found at i:316088 original size:21 final size:21
Alignment explanation
Indices: 316051--316090 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
316041 TAAATTTAAA
*
316051 TTTAATGAATATTTTATAATT
1 TTTAATGAATATATTATAATT
316072 TTTAAT-AATATAATTATAA
1 TTTAATGAATAT-ATTATAA
316091 AAATAACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTAATGAATATATTATAATT
Found at i:316239 original size:6 final size:6
Alignment explanation
Indices: 316230--316260 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
316220 CCATCTTGGT
*
316230 CTAGCC CTAGCC CTAGCC CTAACC CTAGCC C
1 CTAGCC CTAGCC CTAGCC CTAGCC CTAGCC C
316261 CTATGTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.52, G:0.13, T:0.16
Consensus pattern (6 bp):
CTAGCC
Found at i:328340 original size:3 final size:3
Alignment explanation
Indices: 328332--328376 Score: 54
Period size: 3 Copynumber: 14.0 Consensus size: 3
328322 TTGAGTTTTA
*
328332 ATT ATT ATT ATT ATT ATT ATT AATT GTT ATT AATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT -ATT -ATT ATT ATT
328377 TGTTATGGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 28 0.74
4 10 0.26
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:328363 original size:10 final size:10
Alignment explanation
Indices: 328329--328374 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
328319 TGTTTGAGTT
328329 TTAATTATTA
1 TTAATTATTA
328339 TTATTATTATTA
1 TTA--ATTATTA
*
328351 TTAATTGTTA
1 TTAATTATTA
328361 TTAATTAATTA
1 TTAATT-ATTA
328372 TTA
1 TTA
328375 TTTGTTATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 15 0.48
11 6 0.19
12 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
TTAATTATTA
Found at i:329136 original size:24 final size:23
Alignment explanation
Indices: 329076--329136 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
329066 CTAGATTTTT
329076 ACAAAAAAAA-GAGAGAAAAAGA
1 ACAAAAAAAATGAGAGAAAAAGA
* **
329098 A-TAAAAAAATAGAGAGAAGTGAGA
1 ACAAAAAAAAT-GAGAGAA-AAAGA
329122 ACAAAAAAAATGAGA
1 ACAAAAAAAATGAGA
329137 CTAAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 7 0.23
22 1 0.03
23 7 0.23
24 8 0.26
25 8 0.26
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (23 bp):
ACAAAAAAAATGAGAGAAAAAGA
Found at i:333440 original size:20 final size:20
Alignment explanation
Indices: 333415--333470 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
333405 TGCAATATTC
333415 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* **
333435 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAAAGT
333454 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
333471 TTTAATTTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:333473 original size:20 final size:20
Alignment explanation
Indices: 333313--333483 Score: 95
Period size: 20 Copynumber: 8.6 Consensus size: 20
333303 AAATGACCAA
*
333313 CAAATTCGCAACGCGAATTC
1 CAAATTCGCAACGCGAATTT
* *
333333 CAATTTCGCAATC-C-AGTTT
1 CAAATTCGCAA-CGCGAATTT
*
333352 CCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCGAAT-T-T
** **
333375 -AAA-TCGCATTGCGTTTTT
1 CAAATTCGCAACGCGAATTT
***
333393 CCAAATTCGCGTTGC-AATATT
1 -CAAATTCGCAACGCGAAT-TT
**
333414 CCAAATTCGCAACGCGAAAGT
1 -CAAATTCGCAACGCGAATTT
*
333435 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
333454 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
333474 -AATTTCGCAA
1 CAAATTCGCAA
333484 TAGGTTTTAG
Statistics
Matches: 117, Mismatches: 22, Indels: 25
0.71 0.13 0.15
Matches are distributed among these distances:
18 1 0.01
19 30 0.26
20 54 0.46
21 28 0.24
22 3 0.03
23 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:334251 original size:12 final size:12
Alignment explanation
Indices: 334230--334263 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
334220 ACCACATTTC
*
334230 CAATACCAAACA
1 CAATATCAAACA
334242 CAATATCAAACA
1 CAATATCAAACA
*
334254 CAATCTCAAA
1 CAATATCAAA
334264 ACCCACAACC
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:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:334415 original size:24 final size:24
Alignment explanation
Indices: 334388--334465 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
334378 GTATTCGAAA
334388 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
*
334412 TTTGATCTTGGTCAATACCTGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
334436 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
334460 TTTGAT
1 TTTGAT
334466 GATGTGATGG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:334648 original size:3 final size:3
Alignment explanation
Indices: 334640--334679 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
334630 ATATAACCCT
* * *
334640 GAA GAA GAA AAA GAG GAA GAA GAA AAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
334680 TCCCCGAAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:334660 original size:15 final size:15
Alignment explanation
Indices: 334640--334678 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
334630 ATATAACCCT
*
334640 GAAGAAGAAAAAGAG
1 GAAGAAGAAAAAGAA
334655 GAAGAAGAAAAAGAA
1 GAAGAAGAAAAAGAA
334670 GAAGAAGAA
1 GAAGAAGAA
334679 GTCCCCGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAAAAGAA
Found at i:336961 original size:5 final size:5
Alignment explanation
Indices: 336944--337023 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
336934 AACGGTCAAC
* * *
336944 GGTCG GGTTG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
336993 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
337024 AACCGATTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 49 0.80
7 12 0.20
ACGTcount: A:0.07, C:0.21, G:0.51, T:0.20
Consensus pattern (5 bp):
GGTCG
Done.