Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006710.1 Hibiscus syriacus cultivar Beakdansim tig00016725_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: 2941931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:275699 original size:22 final size:22
Alignment explanation
Indices: 275650--275698 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
275640 ATAGATTATT
**
275650 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
275672 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
275695 TAAA
1 TAAA
275699 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:275759 original size:80 final size:80
Alignment explanation
Indices: 275653--276128 Score: 499
Period size: 80 Copynumber: 5.9 Consensus size: 80
275643 GATTATTTAA
275653 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
275718 CCATACAACTACAAT
66 CCATACAACTACAAT
* *
275733 AATATATCAATCCATATTTTAAAATAAATCAATCCATAGTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
275798 CCATACAACTACAAT
66 CCATACAACTACAAT
** * ** * ** **
275813 AATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATTCA-TATTTTAAAATAAATC
1 AATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATACTAATAAATTA-TTTAAAATAAATC
*
275875 AATCCATACTAA-TAAATTATTT
63 AATCCATAC-AACTACA--A--T
*** * * * *
275897 AAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATC
1 --AATAAATCAATCCATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATC
*
275955 AATCCATACTAA-TAAATTATAT
63 AATCCATAC-AACT--A-CA-AT
* *
275977 AAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACCAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
276042 ATCCATACAACTACAAT
64 ATCCATACAACTACAAT
276059 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
276124 CCATA
66 CCATA
276129 TTTTAAAATA
Statistics
Matches: 340, Mismatches: 35, Indels: 42
0.82 0.08 0.10
Matches are distributed among these distances:
79 7 0.02
80 243 0.71
81 11 0.03
82 15 0.04
83 2 0.01
84 13 0.04
85 4 0.01
86 45 0.13
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:275779 original size:22 final size:21
Alignment explanation
Indices: 275706--275779 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 21
275696 AAATTATTTA
*
275706 AAATAAATCAATCCATACAACT
1 AAATAAATCAATCCATATAA-T
**
275728 ACAATAATATATCAATCCATATTTT
1 A-AAT-A-A-ATCAATCCATATAAT
275753 AAAATAAATCAATCCATAGTAAT
1 -AAATAAATCAATCCATA-TAAT
275776 AAAT
1 AAAT
275780 TATTTAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
22 16 0.39
23 6 0.15
24 2 0.05
25 5 0.12
26 12 0.29
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.30
Consensus pattern (21 bp):
AAATAAATCAATCCATATAAT
Found at i:275866 original size:22 final size:22
Alignment explanation
Indices: 275840--275882 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
275830 TAATAAATTA
*
275840 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
275862 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
275883 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:275876 original size:134 final size:131
Alignment explanation
Indices: 275497--276183 Score: 704
Period size: 134 Copynumber: 5.0 Consensus size: 131
275487 TATAACTACA
*
275497 ATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTGATAAATTA
1 ATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
275562 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATA-T-TTTAAAATA
66 TTTAAAATAAATCAA-T--T-C--AT--A-T-TTTAAAATAAATCAATCCATATTATTTAAAATA
275625 AATCAATCCAT
121 AATCAATCCAT
*
275636 ACTAATAGATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATT
1 A-TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATT
* * ** *
275701 ATTTAAAATAAATCAATCCATACAACTACAATAATATATCAATCCATA-T-TTTAAAATAAATCA
65 ATTTAAAATAAATCAATTCAT---ATTTTAA-AATAAATCAATCCATATTATTTAAAATAAATCA
275764 ATCCAT
126 ATCCAT
* **
275770 AGTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTAATA
1 A-TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATACTAATA
275835 AATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAA
61 AATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAAT-C---C--AT--ATTATTTAAA
275900 ATAAATCAATCCAT
118 ATAAATCAATCCAT
* *
275914 ACAACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATT
1 ATAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATT
*
275973 ATATAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACCAATAAATTATTTAAAATAA
65 ATTTAAAATAAATCAATTCATATTTTAAAATAAATC-A---AT-CC-AT--ATTATTTAAAATAA
276038 ATCAATCCAT
122 ATCAATCCAT
* *
276048 ACAACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATT
1 ATAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATT
*
276107 ATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAA
65 ATTTAAAATAAATCAATTCATATTTTAAAATAAATCAA-TC---C--AT--ATTATTTAAAATAA
276172 ATCAATCCAT
122 ATCAATCCAT
276182 AT
1 AT
276184 TTTAAAATAA
Statistics
Matches: 493, Mismatches: 28, Indels: 59
0.85 0.05 0.10
Matches are distributed among these distances:
130 2 0.00
131 1 0.00
133 5 0.01
134 291 0.59
135 13 0.03
136 1 0.00
137 4 0.01
138 65 0.13
139 2 0.00
140 80 0.16
142 2 0.00
143 3 0.01
144 24 0.05
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (131 bp):
ATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
TTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTATTTAAAATAAATCAATCCA
T
Found at i:275891 original size:22 final size:22
Alignment explanation
Indices: 275842--275890 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
275832 ATAAATTATT
* **
275842 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
275864 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
275887 TAAA
1 TAAA
275891 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:275971 original size:22 final size:23
Alignment explanation
Indices: 275896--275970 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
275886 ATAAATTATT
275896 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
275918 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
275944 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
275967 TAAA
1 TAAA
275971 TTATATAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:276105 original size:22 final size:23
Alignment explanation
Indices: 276030--276104 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
276020 ATAAATTATT
276030 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
276052 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
276078 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
276101 TAAA
1 TAAA
276105 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:276134 original size:22 final size:22
Alignment explanation
Indices: 276108--276150 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
276098 TAATAAATTA
276108 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
276130 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
276151 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:276159 original size:22 final size:22
Alignment explanation
Indices: 276110--276158 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
276100 ATAAATTATT
**
276110 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
276132 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
276155 TAAA
1 TAAA
276159 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:276188 original size:22 final size:22
Alignment explanation
Indices: 276162--276204 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
276152 TAATAAATTA
276162 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
276184 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
276205 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:276213 original size:22 final size:22
Alignment explanation
Indices: 276164--276212 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
276154 ATAAATTATT
**
276164 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
276186 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
276209 TAAA
1 TAAA
276213 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:276242 original size:22 final size:22
Alignment explanation
Indices: 276216--276271 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
276206 TAATAAATTA
*
276216 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
276238 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
276260 TTTATAATAAAT
1 TTTAAAATAAAT
276272 TATTTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:276277 original size:15 final size:15
Alignment explanation
Indices: 276257--276286 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
276247 AATCAATCCA
*
276257 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
276272 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
276287 AACCTTATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:276278 original size:37 final size:36
Alignment explanation
Indices: 276235--276338 Score: 117
Period size: 37 Copynumber: 2.9 Consensus size: 36
276225 AATCAATTCA
276235 TATTTTAAAATAAATCAATCCATATTTTATAATAAA-T
1 TATTTTAAAATAAAT-AA-CCATATTTTATAATAAACT
* *
276272 TATTTTAAAATAAATAACCTTATTAAATTAT-TTAAACT
1 TATTTTAAAATAAATAACCATATT---TTATAATAAACT
276310 TATTTT--AATAAATAACCATATTTTATAAT
1 TATTTTAAAATAAATAACCATATTTTATAAT
276339 TGTTCTTGAA
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
33 4 0.07
34 1 0.02
35 6 0.10
36 17 0.29
37 19 0.33
38 11 0.19
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (36 bp):
TATTTTAAAATAAATAACCATATTTTATAATAAACT
Found at i:301408 original size:21 final size:21
Alignment explanation
Indices: 301365--301410 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
301355 TTTCAGAGAC
*
301365 ACTTACCAAGGTACTTCATCT
1 ACTTACCAAGGTACTTCACCT
* *
301386 ACTTACCAAGGTATTTTACCT
1 ACTTACCAAGGTACTTCACCT
301407 ACTT
1 ACTT
301411 CCACTTCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.37
Consensus pattern (21 bp):
ACTTACCAAGGTACTTCACCT
Found at i:301615 original size:114 final size:110
Alignment explanation
Indices: 301405--301615 Score: 289
Period size: 114 Copynumber: 1.9 Consensus size: 110
301395 GGTATTTTAC
* * *
301405 CTACTTCCACTTCTTCTTCTACTGCACCTTCTACCATAGATACTCGGATAATAAAATCAATGAAT
1 CTACTTCCACTTCTTCTTCTACTCCACCTTCTACCATAGATACTCGAACAATAAAATCAATGAAT
* *
301470 ATGATGCTAGTAGCATTGTAATAGAAGATACCCAATGTAGTTCAT
66 ACGATGCTAGTAGCATTATAATAGAAGATACCCAATGTAGTTCAT
* * *
301515 CTACTTCCACTTCTTCTTCTACTCCACCTTCTACCA-AGGATATTCAATCGAACAATGACATCGA
1 CTACTTCCACTTCTTCTTCTACTCCACCTTCTACCATA-GATA--C--TCGAACAATAAAATCAA
*
301579 TGAATACGATGCTAGTAGCATTATAATAGAATATACC
61 TGAATACGATGCTAGTAGCATTATAATAGAAGATACC
301616 AATATTCAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
109 1 0.01
110 39 0.45
112 1 0.01
114 46 0.53
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.32
Consensus pattern (110 bp):
CTACTTCCACTTCTTCTTCTACTCCACCTTCTACCATAGATACTCGAACAATAAAATCAATGAAT
ACGATGCTAGTAGCATTATAATAGAAGATACCCAATGTAGTTCAT
Found at i:316942 original size:7 final size:7
Alignment explanation
Indices: 316930--316955 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
316920 ATTAATCAAA
316930 AATATTT
1 AATATTT
316937 AATATTT
1 AATATTT
316944 AATATTT
1 AATATTT
316951 AATAT
1 AATAT
316956 ACTATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AATATTT
Found at i:324004 original size:20 final size:20
Alignment explanation
Indices: 323979--324016 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
323969 TATTTATTAT
323979 TTAATAATAATAATAAAATA
1 TTAATAATAATAATAAAATA
*
323999 TTAATATTAATAATAAAA
1 TTAATAATAATAATAAAA
324017 ATAAATAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAATAATAATAATAAAATA
Found at i:324538 original size:73 final size:73
Alignment explanation
Indices: 324234--324519 Score: 457
Period size: 73 Copynumber: 3.9 Consensus size: 73
324224 CTTCTGGAAA
* *
324234 TGTTTTAAGAAAAACAATCTCAAGTGAGATAGATTGCTATTTCGAGTTAAACTTT-TGCAAGCAA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCT-CAAGCAA
324298 GAAAAAGTT
65 GAAAAAGTT
* *
324307 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCGAGTGAAACTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCAAG
324372 AAAAAGTT
66 AAAAAGTT
* * * * *
324380 TGTTTTAAGAAAAACAATCTCATGTAAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCAAG
324445 AAAAAGTT
66 AAAAAGTT
*
324453 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAGTTGCTATTTCGAGTGAAACTTGTCTCAAGCAA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTT-TCTCAAGCAA
324518 GA
65 GA
324520 CAAATCTTTG
Statistics
Matches: 196, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
73 185 0.94
74 11 0.06
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.31
Consensus pattern (73 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCAAG
AAAAAGTT
Found at i:325462 original size:54 final size:53
Alignment explanation
Indices: 325372--325524 Score: 207
Period size: 53 Copynumber: 2.9 Consensus size: 53
325362 ATAATCACTG
*
325372 GTTCATAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTACACAGAT
1 GTTCATAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTAC-CAGAT
* * * * *
325426 GTTCGTAGAACATTTGACAACACGTTCATTCTTTCCTGTGGCTTCTTCCAGAT
1 GTTCATAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTACCAGAT
* * * *
325479 GTTCATAAAACATTTGACAATACATTCATCATTTCTTATGGCTTCT
1 GTTCATAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCT
325525 GCCCAGATTT
Statistics
Matches: 85, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
53 43 0.51
54 42 0.49
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (53 bp):
GTTCATAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTACCAGAT
Found at i:327156 original size:18 final size:18
Alignment explanation
Indices: 327116--327260 Score: 110
Period size: 16 Copynumber: 8.1 Consensus size: 18
327106 CTCGATTCAA
*
327116 TTTCTTTTTTCTTCTTTCAT
1 TTTCTTTTTTC-TCTTT-TT
327136 TTTCTTTTTTCTCTTTTT
1 TTTCTTTTTTCTCTTTTT
*
327154 TTT-TCTTTTTCTTATTTTT
1 TTTCT-TTTTTC-TCTTTTT
* *
327173 CTTTCTCTTTAT-T-TTTCT
1 -TTTCT-TTTTTCTCTTTTT
327191 TTTCTTTTTT-TC-TTTT
1 TTTCTTTTTTCTCTTTTT
327207 TTTCTTTTTTCT-TTTTT
1 TTTCTTTTTTCTCTTTTT
327224 CTTTC--TTTTCTC-TTTT
1 -TTTCTTTTTTCTCTTTTT
*
327240 TTCCTTCTTTTCTCTTTTT
1 TTTCTT-TTTTCTCTTTTT
327259 TT
1 TT
327261 CTCTAATGGA
Statistics
Matches: 105, Mismatches: 7, Indels: 27
0.76 0.05 0.19
Matches are distributed among these distances:
15 3 0.03
16 28 0.27
17 11 0.10
18 25 0.24
19 18 0.17
20 14 0.13
21 6 0.06
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTCTTTTTTCTCTTTTT
Found at i:327164 original size:25 final size:25
Alignment explanation
Indices: 327116--327258 Score: 111
Period size: 25 Copynumber: 5.8 Consensus size: 25
327106 CTCGATTCAA
* *
327116 TTTCTTTTTTCTTCTTTCATTTTCTTT
1 TTTCTCTTTT-TT-TTTCTTTTTCTTT
327143 TTTCTCTTTTTTTTTCTTTTTCTTAT
1 TTTCTCTTTTTTTTTCTTTTTCTT-T
* * *
327169 TTT-TCTTTCTCTTTATTTTTC--T
1 TTTCTCTTTTTTTTTCTTTTTCTTT
*
327191 TTTCT-TTTTTTCTT-TTTTTCTTT
1 TTTCTCTTTTTTTTTCTTTTTCTTT
* *
327214 TTTCTTTTTT-CTTTCTTTTCTCTTT
1 TTTCTCTTTTTTTTTCTTTT-TCTTT
* *
327239 TTTC-CTTCTTTTCTCTTTTT
1 TTTCTCTTTTTTTTTCTTTTT
327259 TTCTCTAATG
Statistics
Matches: 94, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
21 6 0.06
22 10 0.11
23 9 0.10
24 12 0.13
25 42 0.45
26 6 0.06
27 9 0.10
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTCTCTTTTTTTTTCTTTTTCTTT
Found at i:327188 original size:44 final size:42
Alignment explanation
Indices: 327116--327260 Score: 150
Period size: 44 Copynumber: 3.3 Consensus size: 42
327106 CTCGATTCAA
327116 TTTCTTTTTTCTTCTTTCATTTTCTTTTTTCTCTTTTTTTTTCTT
1 TTTCTTTTTT-TTCTTTC-TTTT-TTTTTTCTCTTTTTTTTTCTT
* * *
327161 TTTCTTATTTTTCTTTCTCTTTATTTTTCTTTTCTTTTTTTCTT
1 TTTCTTTTTTTTCTTTCT-TTTTTTTTTCTCTT-TTTTTTTCTT
*
327205 TTT-TTCTTTTTTCTTT-TTTCTTTCTTTTCTCTTTTTTCCTTCTT
1 TTTCTT-TTTTTTCTTTCTTT-TTT-TTTTCTCTTTTTT-TTTCTT
327249 TTCTCTTTTTTT
1 TT-TCTTTTTTT
327261 CTCTAATGGA
Statistics
Matches: 85, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
42 2 0.02
43 19 0.22
44 47 0.55
45 15 0.18
46 2 0.02
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (42 bp):
TTTCTTTTTTTTCTTTCTTTTTTTTTTCTCTTTTTTTTTCTT
Found at i:327261 original size:10 final size:10
Alignment explanation
Indices: 327140--327264 Score: 94
Period size: 10 Copynumber: 12.0 Consensus size: 10
327130 TTTCATTTTC
327140 TTTTTTCTCT
1 TTTTTTCTCT
*
327150 TTTTTTTTCT
1 TTTTTTCTCT
*
327160 TTTTCTTAT-T
1 TTTT-TTCTCT
327170 TTTCTTTCTCTT
1 TTT-TTTCTC-T
*
327182 TATTTTTCTTT
1 T-TTTTTCTCT
*
327193 TCTTTTTTTCT
1 T-TTTTTCTCT
*
327204 TTTTTTCTTTT
1 TTTTTTC-TCT
*
327215 TTCTTTTTTCT
1 TT-TTTTCTCT
327226 TTCTTTTCTC-
1 TT-TTTTCTCT
327236 TTTTTTC-CT
1 TTTTTTCTCT
*
327245 TCTTTTCTCT
1 TTTTTTCTCT
327255 TTTTTTCTCT
1 TTTTTTCTCT
327265 AATGGATGAG
Statistics
Matches: 92, Mismatches: 14, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
8 1 0.01
9 11 0.12
10 38 0.41
11 29 0.32
12 11 0.12
13 2 0.02
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTCTCT
Found at i:327262 original size:44 final size:40
Alignment explanation
Indices: 327118--327259 Score: 143
Period size: 38 Copynumber: 3.6 Consensus size: 40
327108 CGATTCAATT
* * * *
327118 TCTTTTTTC-TTCTTTC-ATTTTCTTTTTTCTCTTTTTTTT
1 TCTTTTTTCTTTTTTTCTTTTTTCTTTTTTCT-TTCTTTTC
* *
327157 TC-TTTTTCTTATTTTTC-TTTCTCTTTATT-TTTCTTTTC
1 TCTTTTTTCTT-TTTTTCTTTTTTCTTTTTTCTTTCTTTTC
327195 T-TTTTTTCTTTTTTTCTTTTTTCTTTTTTCTTTCTTTTC
1 TCTTTTTTCTTTTTTTCTTTTTTCTTTTTTCTTTCTTTTC
327234 TCTTTTTTCCTTCTTTTCTCTTTTTT
1 TCTTTTTT-CTT-TTTT-TCTTTTTT
327260 TCTCTAATGG
Statistics
Matches: 86, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
37 6 0.07
38 31 0.36
39 14 0.16
40 20 0.23
41 3 0.03
42 4 0.05
43 8 0.09
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (40 bp):
TCTTTTTTCTTTTTTTCTTTTTTCTTTTTTCTTTCTTTTC
Found at i:330653 original size:18 final size:17
Alignment explanation
Indices: 330615--330655 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
330605 TTTAAAAGAG
330615 TTTTTAAGAAAACATCA
1 TTTTTAAGAAAACATCA
330632 TTTTTAAGAAAACATCA
1 TTTTTAAGAAAACATCA
330649 TTTTTAA
1 TTTTTAA
330656 AAGATAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (17 bp):
TTTTTAAGAAAACATCA
Found at i:331067 original size:2 final size:2
Alignment explanation
Indices: 331060--331093 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
331050 CTTAAAACAA
331060 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
331094 TTGTTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:332664 original size:3 final size:3
Alignment explanation
Indices: 332658--332701 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
332648 ATTTATTATT
* *
332658 TAA TAA TAA TAA TAA -AA TAA TAT TAA TAC TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
332702 ATAACAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:339414 original size:16 final size:16
Alignment explanation
Indices: 339393--339451 Score: 100
Period size: 16 Copynumber: 3.7 Consensus size: 16
339383 ATAAATGAAT
339393 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
339409 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
339425 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
*
339441 ATAAATGAACA
1 ATAAACGAACA
339452 TAAACGTTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:340382 original size:14 final size:14
Alignment explanation
Indices: 340365--340440 Score: 78
Period size: 14 Copynumber: 6.0 Consensus size: 14
340355 GATTGGGTTA
340365 AACATAACCGAACG
1 AACATAACCGAACG
*
340379 AACAT-A---AACA
1 AACATAACCGAACG
340389 AACATAACCGAACG
1 AACATAACCGAACG
340403 AACAT-A---AACG
1 AACATAACCGAACG
*
340413 AACATAACAGAACG
1 AACATAACCGAACG
340427 AACATAACCGAACG
1 AACATAACCGAACG
340441 TTCACAAACG
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
10 17 0.33
11 2 0.04
13 2 0.04
14 30 0.59
ACGTcount: A:0.55, C:0.25, G:0.12, T:0.08
Consensus pattern (14 bp):
AACATAACCGAACG
Found at i:340438 original size:24 final size:24
Alignment explanation
Indices: 340365--340439 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
340355 GATTGGGTTA
*
340365 AACATAACCGAACGAACATAAACA
1 AACATAACCGAACGAACATAAACG
340389 AACATAACCGAACGAACATAAACG
1 AACATAACCGAACGAACATAAACG
* *
340413 AACATAACAGAACGAACATAACCG
1 AACATAACCGAACGAACATAAACG
340437 AAC
1 AAC
340440 GTTCACAAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.56, C:0.25, G:0.11, T:0.08
Consensus pattern (24 bp):
AACATAACCGAACGAACATAAACG
Found at i:341696 original size:27 final size:28
Alignment explanation
Indices: 341650--341702 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
341640 GTTATGTTTA
341650 AAATTAGTTACTTAAATTTAAATTAATT
1 AAATTAGTTACTTAAATTTAAATTAATT
* * *
341678 AAATTATTTA-TTAACTTTAATTTAA
1 AAATTAGTTACTTAAATTTAAATTAA
341703 AATTAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (28 bp):
AAATTAGTTACTTAAATTTAAATTAATT
Found at i:342485 original size:15 final size:15
Alignment explanation
Indices: 342467--342505 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
342457 ATGACGACGA
* *
342467 TGATGATGGTGGTTG
1 TGATGATGATGGTGG
342482 TGATGATGATGGTGG
1 TGATGATGATGGTGG
*
342497 TGATAATGA
1 TGATGATGA
342506 AGGTACGTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (15 bp):
TGATGATGATGGTGG
Found at i:346414 original size:21 final size:21
Alignment explanation
Indices: 346388--346440 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
346378 AATGATGAAT
* *
346388 AAGAAAAAGAAAAAGAAGATG
1 AAGAAAAAGAAAAACAAGAAG
346409 AAG-AAAAGAAAAAACAAGAAG
1 AAGAAAAAG-AAAAACAAGAAG
*
346430 AAGAAGAAGAA
1 AAGAAAAAGAA
346441 GAAGGTAGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 5 0.19
21 18 0.67
22 4 0.15
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (21 bp):
AAGAAAAAGAAAAACAAGAAG
Found at i:346432 original size:3 final size:3
Alignment explanation
Indices: 346388--346444 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
346378 AATGATGAAT
* * * *
346388 AAG AAA AAG AAA AAG AAG ATG AAG AA- AAG AA- AA- AAC AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
346433 AAG AAG AAG AAG
1 AAG AAG AAG AAG
346445 GTAGGCATTG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
2 6 0.13
3 39 0.87
ACGTcount: A:0.72, C:0.02, G:0.25, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:346926 original size:20 final size:20
Alignment explanation
Indices: 346898--346940 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
346888 TTTTCTCTTG
* *
346898 AAAGCAAAATTAGATTTTGA
1 AAAGCAAAATGAAATTTTGA
*
346918 AAAGTAAAATGAAATTTTGA
1 AAAGCAAAATGAAATTTTGA
346938 AAA
1 AAA
346941 ATGATTTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.02, G:0.14, T:0.28
Consensus pattern (20 bp):
AAAGCAAAATGAAATTTTGA
Found at i:351806 original size:3 final size:3
Alignment explanation
Indices: 351798--351873 Score: 86
Period size: 3 Copynumber: 25.7 Consensus size: 3
351788 TAAAATTATT
* *
351798 TAA TAA TAA TCA TAA TAAA TAA TAA T-A TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
351843 TAA TAA TTA TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
351874 TTCAAATAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
2 6 0.10
3 51 0.82
4 5 0.08
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:351865 original size:32 final size:34
Alignment explanation
Indices: 351784--351873 Score: 103
Period size: 36 Copynumber: 2.6 Consensus size: 34
351774 GGCCTGTTTG
*
351784 TAAATAAAATTATTTAATAATAATCATAATAAATAA
1 TAAATAAAA-TA-TTAATAATAATAATAATAAATAA
*
351820 TAATATAATAATATTAATAATAATAATAAT-TATAA
1 TAA-ATAA-AATATTAATAATAATAATAATAAATAA
*
351855 T-AATAAAATATAAATAATA
1 TAAATAAAATATTAATAATA
351874 TTCAAATAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
32 12 0.24
33 4 0.08
34 1 0.02
35 5 0.10
36 19 0.39
37 6 0.12
38 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (34 bp):
TAAATAAAATATTAATAATAATAATAATAAATAA
Found at i:352350 original size:119 final size:121
Alignment explanation
Indices: 352078--352422 Score: 430
Period size: 120 Copynumber: 2.9 Consensus size: 121
352068 ATCTTCTTTT
* * ** * * *
352078 GTGATATAATCATGCAAAA-GTTGAACAAATTCTTCTCATTATGAATTTTTTTCCTTCTTTAGAT
1 GTGATAGAGTCATG-AAAAGGTTGAACAAGCTCTTCTCATTATGAATCTTCTTCCTTCTTCAGAT
** * * *
352142 GAGTTCTTCTCATTATGAACACT-TCTGGAAATA-TTGATGTTGATCTATCTCCTTAT
65 GAGTTCTTCTCATTATGAACTTTCTCTGGAAA-AGTTGATGCTGATCTATCTCATTAC
* * *
352198 ATGATTGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA-CTTCTTCC-TCTTCAAAT
1 GTGATAGAGTCATG-AAAAGGTTGAACAAGCTCTTCTCATTATGAATCTTCTTCCTTCTTCAGAT
* * *
352261 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTTATTCC
65 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCATTAC
* *
352318 GTGATAGAGTCATGTAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGA
1 GTGATAGAGTCATGAAAAGGTTGAACAAGCTCTTCTCATTATGAA--TCTTCTTCCTTCTTCAGA
352383 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT
64 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT
352423 CAATCGAGTG
Statistics
Matches: 194, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
119 57 0.29
120 59 0.30
121 24 0.12
122 8 0.04
123 46 0.24
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (121 bp):
GTGATAGAGTCATGAAAAGGTTGAACAAGCTCTTCTCATTATGAATCTTCTTCCTTCTTCAGATG
AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCATTAC
Found at i:352472 original size:113 final size:113
Alignment explanation
Indices: 352333--352668 Score: 548
Period size: 113 Copynumber: 3.0 Consensus size: 113
352323 AGAGTCATGT
** * *
352333 AAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATAAGTTCTTCTCATT
*
352398 ATGAACTTTCTCTGGAAAAGTTGATCAATCGAGTGATGAATTCAAGCG
66 ATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCG
* * *
352446 AAAGGTTGAACAAATTCTTCTTATTATGAACTTGTTCTTCTTTCTTCAAATAAATTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATAAGTTCTTCTCATT
* *
352511 ATGAACTTTCTCTGGAAAAATTGATCCATCGAGTGATGAATTCGAGCG
66 ATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCG
*
352559 AAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCTTTCTTTAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATAAGTTCTTCTCATT
*
352624 ATGAACTTTCTCTGG-AAAGATTGATCCATCGAGTGATGGATTCAA
66 ATGAACTTTCTCTGGAAAAG-TTGATCCATCGAGTGATGAATTCAA
352669 ATCTTGCTAA
Statistics
Matches: 205, Mismatches: 17, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
112 3 0.01
113 202 0.99
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (113 bp):
AAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATAAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCG
Found at i:353833 original size:18 final size:18
Alignment explanation
Indices: 353810--353844 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
353800 TATATGAAAC
353810 AAATTGAATTTCAAAAAT
1 AAATTGAATTTCAAAAAT
353828 AAATTGAATTTCAAAAA
1 AAATTGAATTTCAAAAA
353845 GATAAACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATTGAATTTCAAAAAT
Found at i:364878 original size:23 final size:23
Alignment explanation
Indices: 364852--364905 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
364842 TTAATACATG
364852 AAAATAA-A-ATAAAGATATTAATA
1 AAAATAATATATAAA-ATATT-ATA
*
364875 AAAA-AATATATAAAATATTATG
1 AAAATAATATATAAAATATTATA
364897 AAAATAATA
1 AAAATAATA
364906 AAAGTATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 8 0.30
23 14 0.52
24 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (23 bp):
AAAATAATATATAAAATATTATA
Found at i:367157 original size:3 final size:3
Alignment explanation
Indices: 367149--367224 Score: 68
Period size: 3 Copynumber: 25.7 Consensus size: 3
367139 TAAAATTATT
* *
367149 TAA TAA TAA TCA TAA TAAA TAA TAA T-A TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
367194 TTA TTA TTA TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
367225 TTCAAATGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
2 6 0.10
3 51 0.82
4 5 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:367190 original size:27 final size:26
Alignment explanation
Indices: 367149--367224 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 26
367139 TAAAATTATT
*
367149 TAATAATAATCATAATAAATAATAATA
1 TAATAAT-ATAATAATAAATAATAATA
* * *
367176 TAATAATATTAATAATAATTATTATTA
1 TAATAATA-TAATAATAAATAATAATA
*
367203 TAATAATAAAAT-ATAAATAATA
1 TAATAATATAATAATAAATAATA
367225 TTCAAATGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 8 0.20
26 4 0.10
27 29 0.71
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (26 bp):
TAATAATATAATAATAAATAATAATA
Found at i:369913 original size:15 final size:15
Alignment explanation
Indices: 369895--369923 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
369885 TTCATTTCAA
369895 AATTTTATAAAATAC
1 AATTTTATAAAATAC
369910 AATTTTATAAAATA
1 AATTTTATAAAATA
369924 ACTTAAAAAA
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:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTTATAAAATAC
Found at i:370426 original size:21 final size:21
Alignment explanation
Indices: 370401--370445 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
370391 ATTTCATTAT
*
370401 ATCTAGTAGTATTTTATAATA
1 ATCTAGTAGTAATTTATAATA
370422 ATCTAGTAGTAATTTATAATA
1 ATCTAGTAGTAATTTATAATA
370443 ATC
1 ATC
370446 ACTGCGGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (21 bp):
ATCTAGTAGTAATTTATAATA
Found at i:375476 original size:15 final size:15
Alignment explanation
Indices: 375456--375495 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
375446 AATTTCTCTT
375456 TCATTATCTAAGTCA
1 TCATTATCTAAGTCA
*
375471 TCATTATCTAAGTCG
1 TCATTATCTAAGTCA
*
375486 TCAATATCTA
1 TCATTATCTA
375496 GACCAAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
TCATTATCTAAGTCA
Found at i:376141 original size:19 final size:20
Alignment explanation
Indices: 376107--376151 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
376097 TATAGTTTTT
376107 AAAACAACATAATTAAATAA-
1 AAAACAACATAATTAAA-AAC
*
376127 AAAACAACA-ATTTAAAAAC
1 AAAACAACATAATTAAAAAC
376146 AAAACA
1 AAAACA
376152 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 12 0.52
20 9 0.39
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAACAACATAATTAAAAAC
Found at i:376603 original size:21 final size:23
Alignment explanation
Indices: 376562--376610 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
376552 AGGGGTATTG
376562 ATACACATTCAAGGAATGTATCA
1 ATACACATTCAAGGAATGTATCA
*
376585 ATACACATTCAA-G-ATGTATCG
1 ATACACATTCAAGGAATGTATCA
376606 ATACA
1 ATACA
376611 TAGCAAGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.48
22 1 0.04
23 12 0.48
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (23 bp):
ATACACATTCAAGGAATGTATCA
Found at i:383492 original size:31 final size:30
Alignment explanation
Indices: 383449--383596 Score: 130
Period size: 30 Copynumber: 5.0 Consensus size: 30
383439 TTTATATATT
383449 TTAACATTAAAAATATACATTTTATTCTTATA
1 TTAAC-TTAAAAATATA-ATTTTATTCTTATA
* *
383481 ATAACTTAAAAATAT-ATTTTATTCTTATT
1 TTAACTTAAAAATATAATTTTATTCTTATA
* *
383510 TTAATTTTAAAAATAT-ATTTTAATT-TTTTA
1 TTAA-CTTAAAAATATAATTTT-ATTCTTATA
**
383540 TTAACTT-AAAA-A-AA-TTTATTCTTACC
1 TTAACTTAAAAATATAATTTTATTCTTATA
* *
383566 TTAACTTAAACATTTATATTTTATTCTTATA
1 TTAACTTAAAAATATA-ATTTTATTCTTATA
383597 ATATTTTAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
25 3 0.03
26 12 0.13
27 5 0.05
28 4 0.04
29 19 0.20
30 23 0.25
31 23 0.25
32 4 0.04
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (30 bp):
TTAACTTAAAAATATAATTTTATTCTTATA
Found at i:383506 original size:29 final size:29
Alignment explanation
Indices: 383449--383596 Score: 142
Period size: 29 Copynumber: 5.0 Consensus size: 29
383439 TTTATATATT
383449 TTAACATTAAAAATATACATTTTATTCTTATA
1 TTAAC-TTAAAAATAT--ATTTTATTCTTATA
* *
383481 ATAACTTAAAAATATATTTTATTCTTATT
1 TTAACTTAAAAATATATTTTATTCTTATA
* *
383510 TTAATTTTAAAAATATATTTTAATT-TTTTA
1 TTAA-CTTAAAAATATATTTT-ATTCTTATA
**
383540 TTAACTTAAAAA-A-A-TTTATTCTTACC
1 TTAACTTAAAAATATATTTTATTCTTATA
*
383566 TTAACTTAAACATTTATATTTTATTCTTATA
1 TTAACTTAAA-A-ATATATTTTATTCTTATA
383597 ATATTTTAAA
Statistics
Matches: 95, Mismatches: 13, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
25 3 0.03
26 15 0.16
27 2 0.02
28 1 0.01
29 24 0.25
30 23 0.24
31 23 0.24
32 4 0.04
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTATTCTTATA
Found at i:383545 original size:59 final size:57
Alignment explanation
Indices: 383445--383599 Score: 163
Period size: 59 Copynumber: 2.7 Consensus size: 57
383435 TTATTTTATA
383445 TATTTTAACATTAAAAATATACATTTTATTCTTATAATAACTTAAAAATATATTTTATTCT
1 TATTTTAACATTAAAAATATA-ATTTTATTCTTATAATAACTTAAAAA-A-A-TTTATTCT
** * *
383506 TATTTTAATTTTAAAAATAT-ATTTTAATT-TTTTATTAACTTAAAAAAATTTATTCT
1 TATTTTAACATTAAAAATATAATTTT-ATTCTTATAATAACTTAAAAAAATTTATTCT
** * *
383562 TACCTTAAC-TTAAACATTTATATTTTATTCTTATAATA
1 TATTTTAACATTAAAAATATA-ATTTTATTCTTATAATA
383600 TTTTAAAATT
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
55 8 0.10
56 17 0.22
57 12 0.15
58 1 0.01
59 20 0.25
60 3 0.04
61 18 0.23
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.52
Consensus pattern (57 bp):
TATTTTAACATTAAAAATATAATTTTATTCTTATAATAACTTAAAAAAATTTATTCT
Found at i:383636 original size:25 final size:23
Alignment explanation
Indices: 383608--383716 Score: 87
Period size: 25 Copynumber: 4.5 Consensus size: 23
383598 TATTTTAAAA
383608 TTAAGATAAGAATAAAATATATATT
1 TTAA-ATAA-AATAAAATATATATT
* *
383633 TTAAATAAAA-AATATACAT-TT
1 TTAAATAAAATAAAATATATATT
*
383654 TTAAATCAAAATAAAATATACATT
1 TTAAAT-AAAATAAAATATATATT
* *
383678 TTAAGTTAAAAATAAGAATAAATATT
1 TTAA-AT-AAAATAA-AATATATATT
*
383704 TAAAAATAAAATA
1 T-TAAATAAAATA
383717 TAGGAATTAA
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
21 8 0.12
22 11 0.16
23 8 0.12
24 10 0.15
25 18 0.27
26 10 0.15
27 2 0.03
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.34
Consensus pattern (23 bp):
TTAAATAAAATAAAATATATATT
Found at i:383727 original size:14 final size:14
Alignment explanation
Indices: 383710--383738 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
383700 TATTTAAAAA
383710 TAAAATATAGGAAT
1 TAAAATATAGGAAT
383724 TAAAATATAGGAAT
1 TAAAATATAGGAAT
383738 T
1 T
383739 TAAGTTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (14 bp):
TAAAATATAGGAAT
Found at i:400065 original size:17 final size:16
Alignment explanation
Indices: 400024--400065 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
400014 AAATATCTTT
400024 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
400040 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
400057 TAAAA-AATT
1 TAAAATAATT
400066 GATCTGCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:402166 original size:3 final size:3
Alignment explanation
Indices: 402160--402197 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
402150 TTTATTATTC
*
402160 AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
402198 TATCGGGTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:402780 original size:20 final size:20
Alignment explanation
Indices: 402755--402807 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
402745 CTAATACATT
*
402755 AGTATCAATATCCTATTGGA
1 AGTATCGATATCCTATTGGA
*
402775 AGTATCGATA-CACTATTGGG
1 AGTATCGATATC-CTATTGGA
*
402795 ACTATCGATATCC
1 AGTATCGATATCC
402808 ATATGAGTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (20 bp):
AGTATCGATATCCTATTGGA
Found at i:403775 original size:31 final size:31
Alignment explanation
Indices: 403731--403792 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
403721 ATTGGTATTA
* * *
403731 TATCTAAAGTTTAA-AAGTCAAATTAATAATT
1 TATCAAAAATTTAAGAA-TCAAATTAAAAATT
403762 TATCAAAAATTTAAGAATCAAATTAAAAATT
1 TATCAAAAATTTAAGAATCAAATTAAAAATT
403793 AACTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.35
Consensus pattern (31 bp):
TATCAAAAATTTAAGAATCAAATTAAAAATT
Found at i:418746 original size:43 final size:44
Alignment explanation
Indices: 418681--418798 Score: 150
Period size: 43 Copynumber: 2.7 Consensus size: 44
418671 CAGAAGTATT
* * *
418681 AATGTTGGGGCACTTTTGAAGGCCTATATCAACATGAAATAATA
1 AATGTTGGGGTACTTTTGAAGGCCAATATCAACAAGAAATAATA
418725 AATGTTGGGGTA-TTTTGAAGGCCAATATCAACAAGAAATAATA
1 AATGTTGGGGTACTTTTGAAGGCCAATATCAACAAGAAATAATA
* * * *
418768 AGTG-TGGGGATATTTTTTAAGGCCCATATCA
1 AATGTTGGGG-TACTTTTGAAGGCCAATATCA
418799 TCCGGGAATA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
42 5 0.08
43 34 0.52
44 27 0.41
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (44 bp):
AATGTTGGGGTACTTTTGAAGGCCAATATCAACAAGAAATAATA
Found at i:420725 original size:135 final size:135
Alignment explanation
Indices: 420343--420816 Score: 550
Period size: 135 Copynumber: 3.5 Consensus size: 135
420333 ATCTTATCAC
** **
420343 TTCAGATTTGGTCTTCCTGAAGAGCAGCAAAGCAAATCAAGTTCAATTCAATCTTCCCTGAAGAG
1 TTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTTGATTCAATCTTCCCTGAAGAG
* * * * *
420408 CAGCGAAGTGGATCAAAATGTTTCTCGAGTATGATCTCTCCTAAAGAGAAGCGGAGAAGATTCTT
66 CAGCGAAGTGGATCAAAATATTTCTCGATTCTGATCTCCCCTAAAGAGTAGCGGAGAAGA-T-TT
*
420473 CTTCTACT
129 -TTCTTCT
* * * * *
420481 TTCAGATTTAGTCTTCCTGAAGAGCAGCGAAGATAAGTAAATCAAGTTTGAGTCAATCTTACCTG
1 TTCAGATTTGGTCTTCCTGAAGAGCA--G-TG--AAGCAAATCAAGTTTGATTCAATCTTCCCTG
420546 AAGAGCAGC------GATCAAAATATTTCTCGATTCTGATCTCCCCTAAAGAGTAGCGGATG-AG
61 AAGAGCAGCGAAGTGGATCAAAATATTTCTCGATTCTGATCTCCCCTAAAGAGTAGCGGA-GAAG
420604 ATTTTTCTTCT
125 ATTTTTCTTCT
* *
420615 TTCAGATTTGGTCTTCTTGAAGAGCAGTGAAGCAAATCAATTTTGATTCAATCTTCCCTGAAGAG
1 TTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTTGATTCAATCTTCCCTGAAGAG
* * *
420680 CAGCGAAGTGGATCAAAATATTTCTCGATTCTGATATCCCCTAAAGAGTAGCGGAGTAGATTCTT
66 CAGCGAAGTGGATCAAAATATTTCTCGATTCTGATCTCCCCTAAAGAGTAGCGGAGAAGATTTTT
420745 CTTCT
131 CTTCT
* * * * * * * *
420750 TTCAGATTTGGTCTTCTTAAATAGCAGTGAAGCGAATC-GGATCTGATTCAGTTTTCCCTGAAGA
1 TTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCAAG-TTTGATTCAATCTTCCCTGAAGA
420814 GCA
65 GCA
420817 ATGAGATGAG
Statistics
Matches: 291, Mismatches: 31, Indels: 31
0.82 0.09 0.09
Matches are distributed among these distances:
129 36 0.12
131 1 0.00
132 1 0.00
134 31 0.11
135 116 0.40
136 1 0.00
137 43 0.15
138 26 0.09
140 1 0.00
143 35 0.12
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (135 bp):
TTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTTGATTCAATCTTCCCTGAAGAG
CAGCGAAGTGGATCAAAATATTTCTCGATTCTGATCTCCCCTAAAGAGTAGCGGAGAAGATTTTT
CTTCT
Found at i:421010 original size:3 final size:3
Alignment explanation
Indices: 421002--421045 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
420992 TCTTCCCATG
*
421002 TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
421046 AATAATTACA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:434614 original size:4 final size:4
Alignment explanation
Indices: 434605--434631 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
434595 TCTTTTATCC
434605 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
434632 TTGTCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:444254 original size:55 final size:55
Alignment explanation
Indices: 444193--444660 Score: 482
Period size: 55 Copynumber: 8.5 Consensus size: 55
444183 GGTCCACTCC
* * * *
444193 CTATTCATTCAGGGAGTATAAGACTC-AACCAATCTTCAGCAAACGTGTCTGGTCT
1 CTATTCATTCAGAGAGTATAAGACTCGAA-CAATCTTCAACAAACGGGTCTGCTCT
* * ** *
444248 CTATTCATTCAGAGAGTATAAGACTCAAACAATCTTCAGCAAACGCATCTGCTCC
1 CTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCTGCTCT
* * * *
444303 CTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGGGT-TCGCTCC
1 CTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCT-GCTCT
* * * * * *
444358 CTATTCGTTCAGGGAGTATAAAATTCGAACAATCTTCAACAAACGTGTCCGCTCT
1 CTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCTGCTCT
* * * *
444413 CTATTCTTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACAAATGGGTCCGCTTT
1 CTATTCATTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCTGCTCT
* * *
444468 CTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACAAACGGGTCCGCTCC
1 CTATTCATTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCTGCTCT
* * * ** *
444523 CTACTCCTTCAGAGAGTAT-AGAGCCCGAACAATCTTCAACAAACGGGTCCACTAT
1 CTATTCATTCAGAGAGTATAAGA-CTCGAACAATCTTCAACAAACGGGTCTGCTCT
* * * * *
444578 CTACTCCTTCAGAAAGTAT-AGAACTCGAACAATCTTCAACAAACGGGTATGCTCC
1 CTATTCATTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCTGCTCT
*
444633 CTATTCTATT-AGAGAGTATAGGACTCGA
1 CTATTC-ATTCAGAGAGTATAAGACTCGA
444661 TCTTCATAAA
Statistics
Matches: 360, Mismatches: 45, Indels: 16
0.86 0.11 0.04
Matches are distributed among these distances:
54 3 0.01
55 351 0.98
56 6 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (55 bp):
CTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCTGCTCT
Found at i:444362 original size:110 final size:109
Alignment explanation
Indices: 444180--444660 Score: 547
Period size: 110 Copynumber: 4.4 Consensus size: 109
444170 TCTTCGAATG
* * * * *
444180 ACGGGTCCACTCCCTATTCATTCAGGGAGTATAAGACTC-AACCAATCTTCAGCAAACGTGTCTG
1 ACGGGTCCGCTCCCTATTC-TTCAGAGAGTATAAGACTCGAA-CAATCTTCAACAAACGGGTCCG
* * * *
444244 GTCTCTATTCATTCAGAGAGTATA-AGACTCAAACAATCTTCAGCAA
64 CTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAA
** * * * *
444290 ACGCATCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGGGTTCGC
1 ACGGGTCCGCTCCCTATTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGC
* * * * *
444355 TCCCTATTCGTTCAGGGAGTATAAAATTCGAACAATCTTCAACAA
65 TCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * *
444400 ACGTGTCCGCTCTCTATTCTTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACAAATGGGTCCG
1 ACGGGTCCGCTCCCTATTC-TTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCCG
*
444464 CTTTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
64 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * *
444510 ACGGGTCCGCTCCCTACTCCTTCAGAGAGTAT-AGAGCCCGAACAATCTTCAACAAACGGGTCCA
1 ACGGGTCCGCTCCCTA-TTCTTCAGAGAGTATAAGA-CTCGAACAATCTTCAACAAACGGGTCCG
* * *
444574 CTATCTACTCCTTCAGAAAGTATAGAACTCGAACAATCTTCAACAA
64 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
** * *
444620 ACGGGTATGCTCCCTATTCTATTAGAGAGTATAGGACTCGA
1 ACGGGTCCGCTCCCTATTCT-TCAGAGAGTATAAGACTCGA
444661 TCTTCATAAA
Statistics
Matches: 317, Mismatches: 47, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
109 6 0.02
110 304 0.96
111 7 0.02
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (109 bp):
ACGGGTCCGCTCCCTATTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGCT
CTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
Found at i:444446 original size:165 final size:164
Alignment explanation
Indices: 444180--444660 Score: 581
Period size: 165 Copynumber: 2.9 Consensus size: 164
444170 TCTTCGAATG
* * * *
444180 ACGGGTCCACTCCCTATTCATTCAGGGAGTATAAGACTC-AACCAATCTTCAGCAAACGTGTCTG
1 ACGGGTCCGCTCCCTATTCATTCAGGGAGTATAAAACTCGAA-CAATCTTCAACAAACGTGTCCG
* * * **
444244 GTCTCTATTCATTCAGAGAGTATA-AGACTCAAACAATCTTCAGCAAACGCATCTGCTCCCTATT
65 CTCTCTATTCATTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATT
* *
444308 CGTTCAGGGAGTATAAGACTCGAACAATCTTCAATAA
129 C-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
* * *
444345 ACGGGTTCGCTCCCTATTCGTTCAGGGAGTATAAAATTCGAACAATCTTCAACAAACGTGTCCGC
1 ACGGGTCCGCTCCCTATTCATTCAGGGAGTATAAAACTCGAACAATCTTCAACAAACGTGTCCGC
* * * **
444410 TCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAATGGGTCCGCTTTCTATTCC
66 TCTCTATTCATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATT-C
444475 TTCAGAGAGTAT-AGAACTCGAACAATCTTCAACAA
130 TTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAA
* * * * * * * *
444510 ACGGGTCCGCTCCCTACTCCTTCAGAGAGTATAGAGCCCGAACAATCTTCAACAAACGGGTCCAC
1 ACGGGTCCGCTCCCTATTCATTCAGGGAGTATAAAACTCGAACAATCTTCAACAAACGTGTCCGC
* * * * *
444575 TATCTACTCCTTCAGAAAGTATAGAACTCGAACAATCTTCAACAAACGGGTATGCTCCCTATTCT
66 TCTCTATTCATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTCT
* *
444640 ATTAGAGAGTATAGGACTCGA
131 -TCAGAGAGTATAAGACTCGA
444661 TCTTCATAAA
Statistics
Matches: 270, Mismatches: 40, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
164 4 0.01
165 261 0.97
166 5 0.02
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (164 bp):
ACGGGTCCGCTCCCTATTCATTCAGGGAGTATAAAACTCGAACAATCTTCAACAAACGTGTCCGC
TCTCTATTCATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTCT
TCAGAGAGTATAAGACTCGAACAATCTTCAACAA
Found at i:446193 original size:94 final size:95
Alignment explanation
Indices: 446033--446204 Score: 224
Period size: 93 Copynumber: 1.8 Consensus size: 95
446023 CCCCCTTTTA
** * * *
446033 TTTTTCTCTATTTTTTCATTTTTCATTTTTCATTTTTCATTTTTCTCTTTGTTCTTTTTTCGTTT
1 TTTTTCTCTATTTTCCCATTTTTAATTTTTCATTTTTCATTTTTCTATTTGTTATTTTTTCGTTT
*
446098 TTTCATTTTTTTTCTTTCACCATTTTTCATT
66 TTTC-TCTTTTTTCTTTCACCATTTTTCATT
* * *
446129 TTTTTCT-TATTTTCCCTTTTTTAATTTTT-ATTTTTCATTTTT-TATTTTTTATTTTTTCATTT
1 TTTTTCTCTATTTTCCCATTTTTAATTTTTCATTTTTCATTTTTCTATTTGTTATTTTTTC-GTT
446191 TTTTCTCTTTTTTC
65 TTTTCTCTTTTTTC
446205 ATTTTTTTCA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
93 21 0.32
94 20 0.30
95 18 0.27
96 7 0.11
ACGTcount: A:0.10, C:0.15, G:0.01, T:0.74
Consensus pattern (95 bp):
TTTTTCTCTATTTTCCCATTTTTAATTTTTCATTTTTCATTTTTCTATTTGTTATTTTTTCGTTT
TTTCTCTTTTTTCTTTCACCATTTTTCATT
Found at i:446210 original size:7 final size:7
Alignment explanation
Indices: 446044--446192 Score: 92
Period size: 7 Copynumber: 20.7 Consensus size: 7
446034 TTTTCTCTAT
446044 TTTTTCA
1 TTTTTCA
446051 TTTTTCA
1 TTTTTCA
446058 TTTTTCA
1 TTTTTCA
446065 TTTTTCA
1 TTTTTCA
*
446072 TTTTTCTC
1 TTTTTC-A
*
446080 TTTGTTCT
1 TTT-TTCA
*
446088 TTTTTCGT
1 TTTTTC-A
446096 TTTTTCA
1 TTTTTCA
*
446103 TTTTT-T
1 TTTTTCA
446109 TTCTTTCACCA
1 TT-TTT---CA
446120 TTTTTCA
1 TTTTTCA
446127 TTTTT--
1 TTTTTCA
*
446132 TTCTT-A
1 TTTTTCA
* *
446138 TTTTCCCT
1 TTTT-TCA
*
446146 TTTTTAA
1 TTTTTCA
446153 TTTTT-A
1 TTTTTCA
446159 TTTTTCA
1 TTTTTCA
*
446166 TTTTTTA
1 TTTTTCA
*
446173 TTTTTTA
1 TTTTTCA
446180 TTTTTTCA
1 -TTTTTCA
446188 TTTTT
1 TTTTT
446193 TTCTCTTTTT
Statistics
Matches: 115, Mismatches: 14, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
5 4 0.03
6 11 0.10
7 69 0.60
8 23 0.20
9 3 0.03
10 3 0.03
11 2 0.02
ACGTcount: A:0.11, C:0.13, G:0.01, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:446220 original size:21 final size:21
Alignment explanation
Indices: 446131--446220 Score: 69
Period size: 22 Copynumber: 4.3 Consensus size: 21
446121 TTTTCATTTT
** *
446131 TTTCTTATTTTCCCTTTTTTAA
1 TTTCTT-TTTTCATTTTTTTCA
* **
446153 TTTTTATTTTTCATTTTTTATTT
1 TTTCT-TTTTTCATTTTTT-TCA
*
446176 TTTATTTTTTCATTTTTTTC-
1 TTTCTTTTTTCATTTTTTTCA
446196 --TCTTTTTTCATTTTTTTCA
1 TTTCTTTTTTCATTTTTTTCA
446215 TTTCTT
1 TTTCTT
446221 CTTCAAGAGA
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
18 17 0.31
21 5 0.09
22 27 0.49
23 6 0.11
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTCTTTTTTCATTTTTTTCA
Found at i:449707 original size:2 final size:2
Alignment explanation
Indices: 449694--449727 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
449684 ATGAAAGAAG
*
449694 AT AT AC 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
449728 GCGAGGATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:455574 original size:45 final size:47
Alignment explanation
Indices: 455507--455596 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 47
455497 CCATGCTTTG
*
455507 TTATTCACAAAAAGAAATCCTAACTACATGATATCTAATTCGCATGC
1 TTATTCACAAAAAGAAATCCTAACCACATGATATCTAATTCGCATGC
* * *
455554 TTATTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCAT
1 TTATTCACAAAAAGAAATCCTAACCACATGATATCTAATTCGCAT
455597 ACATTTATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 24 0.62
46 8 0.21
47 7 0.18
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (47 bp):
TTATTCACAAAAAGAAATCCTAACCACATGATATCTAATTCGCATGC
Found at i:455606 original size:47 final size:46
Alignment explanation
Indices: 455507--455617 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 46
455497 CCATGCTTTG
* *
455507 TTATTCACAAAAAGAAATCCTAACTACATGATATCTAATTCGCATGC
1 TTATTCA-AAAAAGAAATCCTAACCACATGATATCTAATTCGCATAC
* * *
455554 TTATTCAAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATAC
1 TTATTCAAAAAAGAAATCCTAACCACATGATATCTAATTCGCATAC
*
455599 ATTTATTCGAAAAACGAAA
1 --TTATTC-AAAAAAGAAA
455618 ATAAATTACT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
45 25 0.46
46 8 0.15
47 13 0.24
48 8 0.15
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (46 bp):
TTATTCAAAAAAGAAATCCTAACCACATGATATCTAATTCGCATAC
Found at i:461281 original size:21 final size:21
Alignment explanation
Indices: 461239--461287 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
461229 TGACCATCAT
**
461239 ATTGCGATTTTCGAAATCCGC
1 ATTGCGATTTTAAAAATCCGC
461260 ATTGCGATTTTAAATAAT-CGC
1 ATTGCGATTTTAAA-AATCCGC
*
461281 AATGCGA
1 ATTGCGA
461288 ATATGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (21 bp):
ATTGCGATTTTAAAAATCCGC
Found at i:461342 original size:20 final size:20
Alignment explanation
Indices: 461317--461361 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
461307 ATAACACGTG
*
461317 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
461337 ATCGCAATGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
461357 ATCGC
1 ATCGC
461362 GTTACGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:461560 original size:22 final size:22
Alignment explanation
Indices: 461535--461603 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
461525 AGCGACATCT
461535 GTCCCCATCTCCGACGAAATCC
1 GTCCCCATCTCCGACGAAATCC
* *
461557 GTCCCCATTTCCGGCGAAATCC
1 GTCCCCATCTCCGACGAAATCC
*
461579 GTCCCCATCTCCGACAAAATCC
1 GTCCCCATCTCCGACGAAATCC
461601 GTC
1 GTC
461604 TATCTCCATC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.20
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCC
Found at i:462006 original size:20 final size:20
Alignment explanation
Indices: 461941--462029 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 20
461931 CGCAACGAAA
461941 AAATTCGCGTTGCGATAG-C
1 AAATTCGCGTTGCGATAGTC
* *
461960 CATTTCGCGTTGCGAT--T-
1 AAATTCGCGTTGCGATAGTC
*
461977 --A-TCTCGTTGCGATAGTC
1 AAATTCGCGTTGCGATAGTC
*
461994 AAATTCGCGTTGCGATAATC
1 AAATTCGCGTTGCGATAGTC
** *
462014 ATTTTCGTGTTGCGAT
1 AAATTCGCGTTGCGAT
462030 TTTAAGTTTC
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
14 11 0.20
16 1 0.02
19 15 0.28
20 27 0.50
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
AAATTCGCGTTGCGATAGTC
Found at i:463505 original size:36 final size:30
Alignment explanation
Indices: 463425--463490 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
463415 ATAAGAGTTG
463425 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
463455 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
463485 ATTTGT
1 ATTTGT
463491 GCTTGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:463668 original size:20 final size:20
Alignment explanation
Indices: 463640--463917 Score: 216
Period size: 20 Copynumber: 14.8 Consensus size: 20
463630 GCGATTTTCT
* * *
463640 CGTTACGATAGTTAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
463660 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
463680 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
463699 CGTTGCGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
*
463713 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
463733 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
463753 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
463773 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
463787 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
463807 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
463827 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* * *
463841 CGTTGCGATATTTAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
463861 TGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
463881 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
463901 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
463918 GAATGTGTAA
Statistics
Matches: 204, Mismatches: 36, Indels: 36
0.74 0.13 0.13
Matches are distributed among these distances:
14 30 0.15
16 3 0.01
17 1 0.00
18 2 0.01
19 17 0.08
20 151 0.74
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:463738 original size:34 final size:34
Alignment explanation
Indices: 463607--463815 Score: 152
Period size: 34 Copynumber: 5.8 Consensus size: 34
463597 TCATATTCGT
* * * * *
463607 GTTGCGATAGTCTAATACACTTTGCGATTTTCTC
1 GTTGCGATAGTCAAATTCGCGTTGCGATTATCTC
* * * *
463641 GTTACGATAGTTAAATTCCCGTTGCGATAATCAAATTCGC
1 GTTGCGATAGTCAAATTCGCGTTGCGAT--T---A-TCTC
*
463681 GTTGCGATAGTC-ATTTCGCGTTGCGATTATCTC
1 GTTGCGATAGTCAAATTCGCGTTGCGATTATCTC
*
463714 ATTGCGATAGTCAAATTCGCGTTGCGATAGTTAAAT-TC
1 GTTGCGATAGTCAAATTCGCGTTGCG--A-TT--ATCTC
** * *
463752 GTGTTGCGATAGTCATTTTCGCATTGCGATTATCCC
1 --GTTGCGATAGTCAAATTCGCGTTGCGATTATCTC
463788 GTTGCGATAGTCAAATTCGCGTTGCGAT
1 GTTGCGATAGTCAAATTCGCGTTGCGAT
463816 AGTCATTTTC
Statistics
Matches: 137, Mismatches: 23, Indels: 30
0.72 0.12 0.16
Matches are distributed among these distances:
33 14 0.10
34 60 0.44
35 2 0.01
36 3 0.02
37 5 0.04
38 3 0.02
39 15 0.11
40 35 0.26
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (34 bp):
GTTGCGATAGTCAAATTCGCGTTGCGATTATCTC
Found at i:463794 original size:54 final size:54
Alignment explanation
Indices: 463733--463889 Score: 260
Period size: 54 Copynumber: 2.9 Consensus size: 54
463723 GTCAAATTCG
463733 CGTTGCGATAGTTAAATTCGTGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTTAAATTCGTGTTGCGATAGTCATTTTCGCATTGCGATTATCC
* *
463787 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTTAAATTCGTGTTGCGATAGTCATTTTCGCATTGCGATTATCC
* * * *
463841 CGTTGCGATATTTAAATTCATGTTGCGATAGTCATATTCGCGTTGCGAT
1 CGTTGCGATAGTTAAATTCGTGTTGCGATAGTCATTTTCGCATTGCGAT
463890 AGTCATATTC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 95 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (54 bp):
CGTTGCGATAGTTAAATTCGTGTTGCGATAGTCATTTTCGCATTGCGATTATCC
Found at i:463833 original size:74 final size:73
Alignment explanation
Indices: 463601--463914 Score: 307
Period size: 74 Copynumber: 4.3 Consensus size: 73
463591 TCTGCATCAT
* * * * * * * * *
463601 ATTCGTGTTGCGATAGTCTAATACACTTTGCGATTTTCTCGTTACGATAGTTAAATTCCCGTTGC
1 ATTCGCGTTGCGATAGTC-ATTTCGCATTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGC
*
463666 GATAATCAA
65 GATAGTCAA
* *
463675 ATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCTCATTGCGATAGTCAAATTCGCGTTGCG
1 ATTCGCGTTGCGATAGTCATTTCGCATTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCG
*
463740 ATAGTTAA
66 ATAGTCAA
* *
463748 ATTCGTGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGC
1 ATTCGCGTTGCGATAGTCA-TTTCGCATTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGC
*
463813 GATAGTCAT
65 GATAGTCAA
* * * * *
463822 TTTCGCATTGCGAT--T-A--TCCCGTTGCGATATTTAAAT-TCATGTTGCGATAGTCATATTCG
1 ATTCGCGTTGCGATAGTCATTTCGCATTGCG--A-TT--ATCTC--GTTGCGATAGTCAAATTCG
*
463881 CGTTGCGATAGTCAT
59 CGTTGCGATAGTCAA
463896 ATTCGCGTTGCGATAGTCA
1 ATTCGCGTTGCGATAGTCA
463915 AATGAATGTG
Statistics
Matches: 202, Mismatches: 27, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
68 8 0.04
70 1 0.00
71 3 0.01
72 2 0.01
73 64 0.32
74 122 0.60
76 1 0.00
77 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (73 bp):
ATTCGCGTTGCGATAGTCATTTCGCATTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCG
ATAGTCAA
Found at i:467254 original size:20 final size:20
Alignment explanation
Indices: 467226--467331 Score: 178
Period size: 20 Copynumber: 5.3 Consensus size: 20
467216 AATTCAGTGA
*
467226 TGCGTTAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
467246 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
*
467266 TGCGATAGTCAGAATCTCGT
1 TGCGATAGTCAGAATCGCGT
467286 TGCGATAGTTC-GAATCGCGT
1 TGCGATAG-TCAGAATCGCGT
467306 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
467326 TGCGAT
1 TGCGAT
467332 CACGTGTTAT
Statistics
Matches: 81, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
19 2 0.02
20 77 0.95
21 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:467424 original size:20 final size:21
Alignment explanation
Indices: 467378--467426 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
467368 ACGATTATCT
*
467378 AAAATCGCAATGCGGATTTCG
1 AAAATCGCAATGCGGATGTCG
467399 AAAATCGCAATGC-GATGGTC-
1 AAAATCGCAATGCGGAT-GTCG
467419 AAAATCGC
1 AAAATCGC
467427 GTTGCAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (21 bp):
AAAATCGCAATGCGGATGTCG
Found at i:467483 original size:19 final size:19
Alignment explanation
Indices: 467459--467497 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
467449 TACGATAATG
*
467459 GAGATCACGTTGCGATTTA
1 GAGATCACATTGCGATTTA
*
467478 GAGATCCCATTGCGATTTA
1 GAGATCACATTGCGATTTA
467497 G
1 G
467498 TTGGTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (19 bp):
GAGATCACATTGCGATTTA
Found at i:469516 original size:30 final size:30
Alignment explanation
Indices: 469309--469560 Score: 175
Period size: 30 Copynumber: 8.4 Consensus size: 30
469299 ATAGTCCCCG
* * * *
469309 TTCTGATTATGTATGGGACCACGTTCCCCA
1 TTCTGATTCTGTATGGGACTATGTTCCCTA
* * *
469339 TTCTAATTCTGCATGGGACTATGTTACCTA
1 TTCTGATTCTGTATGGGACTATGTTCCCTA
* * * *
469369 TTTTGATTCTGTATGGGTCTACGTT-CTTCA
1 TTCTGATTCTGTATGGGACTATGTTCCCT-A
* * *
469399 TTTTGATTCTGAAAGGGACTATGTTCCCTA
1 TTCTGATTCTGTATGGGACTATGTTCCCTA
* ** * *
469429 TTCTGATTTTGTATGGGACTACATTCCATG
1 TTCTGATTCTGTATGGGACTATGTTCCCTA
* * * *
469459 TTCTGGTTTTGTATAGGACCATGTTCCCTA
1 TTCTGATTCTGTATGGGACTATGTTCCCTA
* * * **
469489 TTTTGATTATGTATGGGAATATGTTCCCCG
1 TTCTGATTCTGTATGGGACTATGTTCCCTA
* * * *
469519 TTCTGATTCTGCATAGGATTACGTT-CCTCA
1 TTCTGATTCTGTATGGGACTATGTTCCCT-A
*
469549 TTCTGTTTCTGT
1 TTCTGATTCTGT
469561 TTGGAATCCT
Statistics
Matches: 168, Mismatches: 51, Indels: 6
0.75 0.23 0.03
Matches are distributed among these distances:
29 4 0.02
30 162 0.96
31 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (30 bp):
TTCTGATTCTGTATGGGACTATGTTCCCTA
Found at i:469535 original size:60 final size:60
Alignment explanation
Indices: 469312--469545 Score: 227
Period size: 60 Copynumber: 3.9 Consensus size: 60
469302 GTCCCCGTTC
* * * *
469312 TGATTATGTATGGGACCACGTTCCCCATTCTAATTCTGCATGGGACTATGTTACCTATTT
1 TGATTATGTATGGGACTACGTTCCCCATTCTGATTCTGCATAGGACTATGTTCCCTATTT
* * ** * * *
469372 TGATTCTGTATGGGTCTACGTTCTTCATTTTGATTCTG-AAAGGGACTATGTTCCCTATTC
1 TGATTATGTATGGGACTACGTTCCCCATTCTGATTCTGCATA-GGACTATGTTCCCTATTT
* * *** * * * *
469432 TGATTTTGTATGGGACTACATTCCATGTTCTGGTTTTGTATAGGACCATGTTCCCTATTT
1 TGATTATGTATGGGACTACGTTCCCCATTCTGATTCTGCATAGGACTATGTTCCCTATTT
* * * * *
469492 TGATTATGTATGGGAATATGTTCCCCGTTCTGATTCTGCATAGGATTACGTTCC
1 TGATTATGTATGGGACTACGTTCCCCATTCTGATTCTGCATAGGACTATGTTCC
469546 TCATTCTGTT
Statistics
Matches: 136, Mismatches: 36, Indels: 4
0.77 0.20 0.02
Matches are distributed among these distances:
59 1 0.01
60 133 0.98
61 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (60 bp):
TGATTATGTATGGGACTACGTTCCCCATTCTGATTCTGCATAGGACTATGTTCCCTATTT
Found at i:471954 original size:2 final size:2
Alignment explanation
Indices: 471947--472037 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
471937 TAAACAAATA
471947 AT AT AT 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 AT AT AT
471989 AT AT AT 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 AT AT AT
472031 AT AT AT A
1 AT AT AT A
472038 CACAAAGGAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:479997 original size:22 final size:22
Alignment explanation
Indices: 479960--480019 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
479950 AAACTTTTTG
* * *
479960 AATTTTTTTGATAAATTTAATAT
1 AATTTTTTTTA-AAATATAAAAT
479983 AATTTTTTTTAAAATATAAAAT
1 AATTTTTTTTAAAATATAAAAT
*
480005 AATATATTTTTAAAA
1 AAT-TTTTTTTAAAA
480020 AAAAAGGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AATTTTTTTTAAAATATAAAAT
Found at i:485612 original size:3 final size:3
Alignment explanation
Indices: 485604--485628 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
485594 ACAATTTCTA
485604 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
485629 TTACTGCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:486840 original size:3 final size:3
Alignment explanation
Indices: 486770--486823 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
486760 TAATATTAGC
486770 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
486818 ATT ATT
1 ATT ATT
486824 TTAAAGTTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:486873 original size:20 final size:17
Alignment explanation
Indices: 486832--486864 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
486822 TTTTAAAGTT
486832 GTTATTATTTGTATTTA
1 GTTATTATTTGTATTTA
*
486849 ATTATTATTTGTATTT
1 GTTATTATTTGTATTT
486865 GATGGTTATC
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:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (17 bp):
GTTATTATTTGTATTTA
Found at i:488122 original size:21 final size:21
Alignment explanation
Indices: 488071--488123 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
488061 ATTATGACTA
488071 TCGCAATGCGATTTTACAATT
1 TCGCAATGCGATTTTACAATT
** *
488092 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-ACAATT
488113 TCGCAATGCGA
1 TCGCAATGCGA
488124 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTACAATT
Found at i:488138 original size:20 final size:21
Alignment explanation
Indices: 488113--488164 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
488103 TTTTCCCAAT
*
488113 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
488133 TCGCAATACGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
488154 TCGCAATGCGA
1 TCGCAATGCGA
488165 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:488178 original size:20 final size:20
Alignment explanation
Indices: 488153--488280 Score: 141
Period size: 20 Copynumber: 6.3 Consensus size: 20
488143 AATTTGGAAA
*
488153 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
488173 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
488194 ATCGTAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
488214 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
488234 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
488254 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
488274 TTCGCAA
1 ATCGCAA
488281 TGAGATTCTG
Statistics
Matches: 96, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
19 2 0.02
20 78 0.81
21 14 0.15
22 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:488195 original size:41 final size:42
Alignment explanation
Indices: 488150--488266 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 42
488140 ACGAATTTGG
* *
488150 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAAT-AC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
* *
488191 AAAATCGTAACGCGATACTGACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
** *
488233 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGAT
488267 TCTGACTTTC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 30 0.45
41 35 0.52
42 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
Found at i:488254 original size:40 final size:40
Alignment explanation
Indices: 488154--488280 Score: 157
Period size: 40 Copynumber: 3.1 Consensus size: 40
488144 ATTTGGAAAA
* * * **
488154 TCGCAATGCGATACTGACTATCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGACTTTCGCAACGCGATACTGAC--TT
*
488195 TCGTAACGCGATACTGACTTTCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTTTCGCAACGCGATACTGACTT
* *
488235 TCGCAACGCGATTCTGACTTTCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTTTCGCAACGCGATACTGACTT
488275 TCGCAA
1 TCGCAA
488281 TGAGATTCTG
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
40 43 0.57
41 31 0.41
42 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (40 bp):
TCGCAACGCGATACTGACTTTCGCAACGCGATACTGACTT
Found at i:488287 original size:20 final size:20
Alignment explanation
Indices: 488199--488291 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
488189 ACAAAATCGT
*
488199 AACGCGATACTGACTTTCGC
1 AACGCGATTCTGACTTTCGC
*
488219 AACGCGATACTGACTTTCGC
1 AACGCGATTCTGACTTTCGC
488239 AACGCGATTCTGACTTTCGC
1 AACGCGATTCTGACTTTCGC
488259 AACGCGATTCTGACTTTCGC
1 AACGCGATTCTGACTTTCGC
* *
488279 AATGAGATTCTGA
1 AACGCGATTCTGA
488292 AAATCGCAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (20 bp):
AACGCGATTCTGACTTTCGC
Found at i:488299 original size:40 final size:40
Alignment explanation
Indices: 488215--488300 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
488205 ATACTGACTT
* ***
488215 TCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTTTCGCAACGAGATTCTGAAAA
* *
488255 TCGCAACGCGATTCTGACTTTCGCAATGAGATTCTGAAAA
1 TCGCAACGCGATACTGACTTTCGCAACGAGATTCTGAAAA
488295 TCGCAA
1 TCGCAA
488301 TCATCTTCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (40 bp):
TCGCAACGCGATACTGACTTTCGCAACGAGATTCTGAAAA
Found at i:488520 original size:20 final size:20
Alignment explanation
Indices: 488495--488575 Score: 128
Period size: 20 Copynumber: 4.0 Consensus size: 20
488485 GACATTCATT
488495 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAAAA
488515 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAAAA
*
488535 TGGCTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAAAA
*
488555 TGGA-TATCGCAACGAGAAAA
1 T-GACTATCGCAACGCGAAAA
488575 T
1 T
488576 CGCAATGCGA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 56 0.98
21 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
TGACTATCGCAACGCGAAAA
Found at i:488635 original size:19 final size:19
Alignment explanation
Indices: 488594--488658 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
488584 GAAATGAAAA
488594 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
488610 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
488627 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
488646 TCGCATTGCGATT
1 TCGCATTGCGATT
488659 CTCTCATTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.24
16 3 0.07
17 3 0.07
19 26 0.62
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:490297 original size:41 final size:42
Alignment explanation
Indices: 490243--490334 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
490233 CCTCTTCAAC
* *
490243 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
490284 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
490326 GATGACAGG
1 GATGACAGG
490335 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.44
42 25 0.56
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:490299 original size:21 final size:21
Alignment explanation
Indices: 490270--490330 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
490260 GAACGGTGGG
*
490270 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
490291 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
490312 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
490331 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:490697 original size:20 final size:20
Alignment explanation
Indices: 490672--490752 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
490662 GAAGAATAGT
*
490672 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
490692 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* * * *
490712 TGACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
** * *
490732 TGGCTATCGCAACACGGAAA
1 TTACTTTCGCAACACGAAAA
490752 T
1 T
490753 GGCTATCGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:490753 original size:20 final size:20
Alignment explanation
Indices: 490698--490772 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
490688 AAACTTACTT
* *
490698 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGGCTA
490718 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
*
490738 TCGCAACACGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
*
490758 TCGCAATGC-GAAATG
1 TCGCAACGCGGAAATG
490773 AAAATCGCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 6 0.12
20 44 0.88
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGGCTA
Found at i:490779 original size:19 final size:19
Alignment explanation
Indices: 490757--490817 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
490747 GGAAATGGCT
490757 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
490776 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
490790 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
490809 ATCGCAATG
1 ATCGCAATG
490818 ACAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:490792 original size:14 final size:14
Alignment explanation
Indices: 490773--490831 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
490763 ATGCGAAATG
490773 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
490787 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
490806 AAAATCGCAATGAC
1 AAAATCGCAACGAC
490820 AAAATCGCAACG
1 AAAATCGCAACG
490832 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.28
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:490847 original size:33 final size:33
Alignment explanation
Indices: 490757--490836 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
490747 GGAAATGGCT
490757 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
490790 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
490823 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
490837 CACAAATCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:490870 original size:19 final size:19
Alignment explanation
Indices: 490848--490939 Score: 69
Period size: 19 Copynumber: 5.4 Consensus size: 19
490838 ACAAATCGCA
490848 TTGCGATTTTCATTTTGCG
1 TTGCGATTTTCATTTTGCG
*
490867 TTGCGA--TT--TTGT-CG
1 TTGCGATTTTCATTTTGCG
* *
490881 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTTGCG
490900 TTGCGA--TT--TTTT-CG
1 TTGCGATTTTCATTTTGCG
* *
490914 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTTGCG
490933 TTGCGAT
1 TTGCGAT
490940 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 15 0.27
15 6 0.11
16 4 0.07
17 4 0.07
18 5 0.09
19 21 0.38
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTCATTTTGCG
Found at i:490882 original size:14 final size:14
Alignment explanation
Indices: 490859--490923 Score: 60
Period size: 14 Copynumber: 4.4 Consensus size: 14
490849 TGCGATTTTC
490859 ATTTTG-CGTTGCG
1 ATTTTGTCGTTGCG
490872 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
*
490886 ATTTTCATTTCGCATTGCG
1 A-TTT--TGTCG--TTGCG
*
490905 ATTTTTTCGTTGCG
1 ATTTTGTCGTTGCG
490919 ATTTT
1 ATTTT
490924 CATTTCGCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
13 6 0.13
14 18 0.40
15 3 0.07
16 5 0.11
17 4 0.09
18 3 0.07
19 6 0.13
ACGTcount: A:0.11, C:0.15, G:0.22, T:0.52
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:490890 original size:33 final size:33
Alignment explanation
Indices: 490848--490939 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
490838 ACAAATCGCA
* *
490848 TTGCGATTTTCATTTTGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
490881 TTGCGATTTTCATTTCGCATTGCGATTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
490914 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
490940 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.50
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:490978 original size:20 final size:20
Alignment explanation
Indices: 490924--490967 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
490914 TTGCGATTTT
490924 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
490943 CATTTCCGCATTGCGATAGT
1 CATTTCCGCATTGCGATAGC
490963 CATTT
1 CATTT
490968 TCGTGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:491498 original size:20 final size:17
Alignment explanation
Indices: 491458--491498 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
491448 GAAGAGGCTC
491458 GATGATGTGACAGAATA
1 GATGATGTGACAGAATA
491475 GATGATGTGACAGAATA
1 GATGATGTGACAGAATA
*
491492 GGTGATG
1 GATGATG
491499 GCTGTCCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.05, G:0.34, T:0.24
Consensus pattern (17 bp):
GATGATGTGACAGAATA
Found at i:491556 original size:18 final size:18
Alignment explanation
Indices: 491533--491580 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
491523 CGGGTCGATC
491533 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
491551 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
491569 AGGTGATGGCTC
1 AGGTGATGGCTC
491581 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:492908 original size:20 final size:20
Alignment explanation
Indices: 492885--492923 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
492875 AAATAGTTTC
492885 TGAAAATGAAAATCGCAACA
1 TGAAAATGAAAATCGCAACA
*
492905 TGAAAATGACAATCGCAAC
1 TGAAAATGAAAATCGCAAC
492924 GCGAATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
TGAAAATGAAAATCGCAACA
Found at i:493464 original size:20 final size:20
Alignment explanation
Indices: 493436--493506 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
493426 GATTATGTAT
*
493436 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
493456 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
493476 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
493496 TATCGCGTTGC
1 TATCGCGTTGC
493507 AATTTTGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:493543 original size:21 final size:21
Alignment explanation
Indices: 493519--493571 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
493509 TTTTGTATTA
*
493519 TCGCGTTGCGATTTTCCGAAT
1 TCGCGTTGCGATTTTACGAAT
* **
493540 TCGCATTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTACGAAT
493560 TCGCGTTGCGAT
1 TCGCGTTGCGAT
493572 GAAAATCGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (21 bp):
TCGCGTTGCGATTTTACGAAT
Found at i:494631 original size:28 final size:27
Alignment explanation
Indices: 494581--494637 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
494571 GCTTATTAAG
* * * *
494581 TTAATTAATTATATATTTTTATTCATT
1 TTAAATAATTATATATATATATTAATT
494608 TTAAATAATATATATATATATATTAATT
1 TTAAATAAT-TATATATATATATTAATT
494636 TT
1 TT
494638 TTATATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (27 bp):
TTAAATAATTATATATATATATTAATT
Found at i:494644 original size:15 final size:16
Alignment explanation
Indices: 494624--494653 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
494614 AATATATATA
494624 TATATATTA-ATTTTT
1 TATATATTACATTTTT
494639 TATATATTACATTTT
1 TATATATTACATTTT
494654 ACATAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATATTACATTTTT
Found at i:497553 original size:6 final size:6
Alignment explanation
Indices: 497537--497571 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
497527 AATCAAGAAA
*
497537 GAAGGT AAAGGT GAAGGT GAAGGT GAAGGT GAAGG
1 GAAGGT GAAGGT GAAGGT GAAGGT GAAGGT GAAGG
497572 GGTTGTATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.49, T:0.14
Consensus pattern (6 bp):
GAAGGT
Found at i:509797 original size:16 final size:15
Alignment explanation
Indices: 509765--509811 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
509755 ATAATATATA
509765 TATATATATTAACTTT
1 TATATATATT-ACTTT
*
509781 TTTATATATTACGTTT
1 TATATATATTAC-TTT
509797 TATATA-ATTA-TTT
1 TATATATATTACTTT
509810 TA
1 TA
509812 ATAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 5 0.18
15 6 0.21
16 17 0.61
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (15 bp):
TATATATATTACTTT
Done.