Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 99 of 133
Found at i:19244602 original size:210 final size:211
Alignment explanation
Indices: 19243982--19244606 Score: 774
Period size: 210 Copynumber: 3.0 Consensus size: 211
19243972 GAGCCGTAAA
* * * * *
19243982 TCAAAAGATAGAGATAACCAGGATTGAATCATAAGTCAAAGAAATGAATATGATCGGGACTGAAT
1 TCAAAAGATAGAGATGACCAAGATTGAATCATAAGTCAAAGAAATAAATATGATCGGGACTAAAC
* * *
19244047 CGCAAGTCAAAAAATAAAAATGATCGAGATTGAACCATGAGTCAAGTTAATAAATATGATTGGGA
66 CGCAAGTCAAAAAATAAAAATGATCGAGATTGAATCATGAGTCAAG-AAATAAATATGATTAGGA
* * * *
19244112 CTAAGCCACAAGTTAAAAGATAGAGATAATTGAGATTGAACCATAAGTTAAAGAATAACGATGAC
130 CTAAGCCATAAGTTAAAAGATAGAGATGATTGAGATTGAACCATAAGTTGAAGAATAATGATGAC
*
19244177 TGGGACTGAGCTACATG
195 TAGGACTGAGCTACATG
* *
19244194 TCAAAAGATAGAGATGACCAAGATTGAA-CTTCAAGTCAAAGAAATAAATATTATCGGGACTAAA
1 TCAAAAGATAGAGATGACCAAGATTGAATCAT-AAGTCAAAGAAATAAATATGATCGGGACTAAA
* * ** * **
19244258 CTGCAAGTCAAAAAATAAAAATGA-CTGGGATTGAATCACAAGTTAAGAAATAAATATGACAAGG
65 CCGCAAGTCAAAAAATAAAAATGATC-GAGATTGAATCATGAGTCAAGAAATAAATATGATTAGG
* *** * *
19244322 ACTAAGCCATAAGTTAGAAGATAGAGATGACCAAGATTGAA-TAGTAAGTCGAAGAATAATGATG
129 ACTAAGCCATAAGTTAAAAGATAGAGATGATTGAGATTGAACCA-TAAGTTGAAGAATAATGATG
19244386 ACTAGGA-TGAGCTACATG
193 ACTAGGACTGAGCTACATG
* * * * * *
19244404 TCAAATGATAGGGATGACCAAGATTGAATCGTAAGTCAAAGGAATAAATATGATCAGGACTTAAC
1 TCAAAAGATAGAGATGACCAAGATTGAATCATAAGTCAAAGAAATAAATATGATCGGGACTAAAC
* * *
19244469 CGCAAGTCAAAAAATAAAAATGATCGAGATTGAATCGTGAGTCGAGAAATAAATATGATTAGGAT
66 CGCAAGTCAAAAAATAAAAATGATCGAGATTGAATCATGAGTCAAGAAATAAATATGATTAGGAC
* * * * * **
19244534 TGAGCCATAAGTCAAAAGATAGAGATGATTGAGATT-ACACCATGAGTTGAATAATAATAACAAC
131 TAAGCCATAAGTTAAAAGATAGAGATGATTGAGATTGA-ACCATAAGTTGAAGAATAATGATGAC
19244598 TAGGACTGA
195 TAGGACTGA
19244607 ATCGCAAGTT
Statistics
Matches: 347, Mismatches: 58, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
209 1 0.00
210 172 0.50
211 81 0.23
212 93 0.27
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (211 bp):
TCAAAAGATAGAGATGACCAAGATTGAATCATAAGTCAAAGAAATAAATATGATCGGGACTAAAC
CGCAAGTCAAAAAATAAAAATGATCGAGATTGAATCATGAGTCAAGAAATAAATATGATTAGGAC
TAAGCCATAAGTTAAAAGATAGAGATGATTGAGATTGAACCATAAGTTGAAGAATAATGATGACT
AGGACTGAGCTACATG
Found at i:19245257 original size:36 final size:35
Alignment explanation
Indices: 19245165--19245266 Score: 132
Period size: 35 Copynumber: 2.9 Consensus size: 35
19245155 AAAAAAATGG
* * * *
19245165 GGATTGAACCGTGAGCCAAAAAATAAAGACAATTG
1 GGATTGAACCGTGAGTCAAAAAATAAAAACAACTA
* *
19245200 GGATTGAACTGTGAGTCAAAAAATAAAAATAACTA
1 GGATTGAACCGTGAGTCAAAAAATAAAAACAACTA
*
19245235 GGATTAAACCGTGAGTCAAAAAAATAAAAACA
1 GGATTGAACCGTGAGTC-AAAAAATAAAAACA
19245267 TAATTGGGAC
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
35 44 0.77
36 13 0.23
ACGTcount: A:0.51, C:0.12, G:0.19, T:0.19
Consensus pattern (35 bp):
GGATTGAACCGTGAGTCAAAAAATAAAAACAACTA
Found at i:19245290 original size:73 final size:70
Alignment explanation
Indices: 19245165--19245299 Score: 164
Period size: 73 Copynumber: 1.9 Consensus size: 70
19245155 AAAAAAATGG
* * * ** *
19245165 GGATTGAACCGTGAGCCAAAAAATAAAGACAATTGGGATTGAACTGTGAGTCAAAAAATAAAAAT
1 GGATTAAACCGTGAGCAAAAAAATAAAAACAATTGGGATCAAACTGTAAGTCAAAAAATAAAAAT
19245230 AACTA
66 AACTA
*
19245235 GGATTAAACCGTGAGTCAAAAAAATAAAAACATAATTGGGA-CAACACTGTAAGTCAGAAAATAA
1 GGATTAAACCGTGAG-CAAAAAAATAAAAAC--AATTGGGATCAA-ACTGTAAGTCAAAAAATAA
19245299 A
62 A
19245300 GAAACAACAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
70 14 0.26
71 13 0.24
72 1 0.02
73 26 0.48
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (70 bp):
GGATTAAACCGTGAGCAAAAAAATAAAAACAATTGGGATCAAACTGTAAGTCAAAAAATAAAAAT
AACTA
Found at i:19245307 original size:28 final size:28
Alignment explanation
Indices: 19245275--19245330 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
19245265 CATAATTGGG
*
19245275 ACAACA-CTGTAAGTCAGAAAATAAAGAA
1 ACAACATC-GTAAGTCAAAAAATAAAGAA
*
19245303 ACAACATCGTAAGTTAAAAAATAAAGAA
1 ACAACATCGTAAGTCAAAAAATAAAGAA
19245331 TGACAGAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.16
Consensus pattern (28 bp):
ACAACATCGTAAGTCAAAAAATAAAGAA
Found at i:19246096 original size:10 final size:10
Alignment explanation
Indices: 19246081--19246117 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
19246071 TAAATTTCCC
19246081 TTTTTTTGTT
1 TTTTTTTGTT
19246091 TTTTTTTGTT
1 TTTTTTTGTT
* *
19246101 ATTTTTTATT
1 TTTTTTTGTT
19246111 TTTTTTT
1 TTTTTTT
19246118 TACAAATCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.05, C:0.00, G:0.05, T:0.89
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:19247493 original size:24 final size:23
Alignment explanation
Indices: 19247466--19247512 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
19247456 CCCATTCATT
*
19247466 TTTTTTTTTTTATTCTTCCTTTCA
1 TTTTTTTTTTTAGTC-TCCTTTCA
19247490 TTTTTTTTTTTAGTCTCCTTTCA
1 TTTTTTTTTTTAGTCTCCTTTCA
19247513 CTGAATGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTTTTTTTTAGTCTCCTTTCA
Found at i:19255111 original size:4 final size:4
Alignment explanation
Indices: 19255102--19255132 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
19255092 ACAAAATGAA
19255102 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
19255133 AACTGTGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:19255436 original size:3 final size:3
Alignment explanation
Indices: 19255428--19255465 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
19255418 TTTCATTAAA
19255428 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
19255466 TATTATAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:19257593 original size:145 final size:144
Alignment explanation
Indices: 19257175--19257598 Score: 521
Period size: 144 Copynumber: 2.9 Consensus size: 144
19257165 TCATTTTTAG
* * * **
19257175 GATTTTAAAT-CATCAAAAATCATGAAATATTATAAAATTGATATCTGAAAAGTTTCATGAAAA-
1 GATTTCAAATGCACCAAAAATTATGAAATATTATAAAATTGATATCTGAAAAGTTTCACAAAAAT
* * * *
19257238 TCTGAGCTCTGAAAAGCCAAATTACGAAAATACCCTTATAAGGGTATTTTGGTAATTTCATACTC
66 TC-GAGCT-TGAAAAGCCAAATTACAAAAATACCCCTATAAGGGTATTTTGGTAATTTCACACTT
* * *
19257303 CCCAGGGTACTGCTAT
129 CTCGGGGGACTGCTAT
* * *
19257319 GATTTCAAATGCACCAAAAA-TATGAAATATCATAAAATTAAGATCTGAAAAGTTTCACAAAAAT
1 GATTTCAAATGCACCAAAAATTATGAAATATTATAAAATTGATATCTGAAAAGTTTCACAAAAAT
* * *
19257383 CCGAGCTTGTGAAGGCCAAATTACAAAAATACCCCTATAAGGGTATTTTGGTAATTTCACACTTC
66 TCGAGCTTG-AAAAGCCAAATTACAAAAATACCCCTATAAGGGTATTTTGGTAATTTCACACTTC
*
19257448 TTGGGGGACTGCTAT
130 TCGGGGGACTGCTAT
* *
19257463 GATTTCAAATGCACCAAAAATTATGAAATGTTATAAAATTGATATCTAAAAAGTTTCACAAAAAT
1 GATTTCAAATGCACCAAAAATTATGAAATATTATAAAATTGATATCTGAAAAGTTTCACAAAAAT
* * ** * * ** *
19257528 TCGACCTTGAAAAGATCAAATTACTTAAATACCCCTAGAAGGGTATTTTAGTAATTTTGCCCTTC
66 TCGAGCTTGAAAAG-CCAAATTACAAAAATACCCCTATAAGGGTATTTTGGTAATTTCACACTTC
19257593 TCGGGG
130 TCGGGG
19257599 TACAATGAAA
Statistics
Matches: 238, Mismatches: 37, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
143 2 0.01
144 134 0.56
145 102 0.43
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (144 bp):
GATTTCAAATGCACCAAAAATTATGAAATATTATAAAATTGATATCTGAAAAGTTTCACAAAAAT
TCGAGCTTGAAAAGCCAAATTACAAAAATACCCCTATAAGGGTATTTTGGTAATTTCACACTTCT
CGGGGGACTGCTAT
Found at i:19264214 original size:23 final size:23
Alignment explanation
Indices: 19264153--19264215 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
19264143 ATAAGATTAT
19264153 AAAAAAATTAATTATTTTTTCGAAA
1 AAAAAAATTAA--ATTTTTTCGAAA
* *
19264178 AAAAAAAATCAATTTTTTC-AAA
1 AAAAAAATTAAATTTTTTCGAAA
*
19264200 ATTAAAAATTAAATTT
1 A-AAAAAATTAAATTT
19264216 ATATACCTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 4 0.12
23 19 0.59
25 9 0.28
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAAAAATTAAATTTTTTCGAAA
Found at i:19264298 original size:17 final size:17
Alignment explanation
Indices: 19264269--19264331 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
19264259 TTATATAAAC
*
19264269 TTTAA-CAAAAAATAAT
1 TTTAATCAATAAATAAT
19264285 TTTAATCAATAAATAA-
1 TTTAATCAATAAATAAT
* *
19264301 ATT-ATC-TTAAATAAT
1 TTTAATCAATAAATAAT
19264316 TTTAATCAATAAATAA
1 TTTAATCAATAAATAA
19264332 ATTATCTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 7 0.18
15 5 0.13
16 10 0.26
17 16 0.42
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTAATCAATAAATAAT
Found at i:19264365 original size:35 final size:31
Alignment explanation
Indices: 19264278--19264340 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
19264268 CTTTAACAAA
19264278 AAATAATTTTAATCAATAAATAAATTATCTT
1 AAATAATTTTAATCAATAAATAAATTATCTT
19264309 AAATAATTTTAATCAATAAATAAATTATCTT
1 AAATAATTTTAATCAATAAATAAATTATCTT
19264340 A
1 A
19264341 TCATAAGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (31 bp):
AAATAATTTTAATCAATAAATAAATTATCTT
Found at i:19265011 original size:2 final size:2
Alignment explanation
Indices: 19265004--19265029 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19264994 ATACATCTAC
19265004 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
19265030 TCCATTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19265466 original size:2 final size:2
Alignment explanation
Indices: 19265459--19265488 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19265449 CACTATTCAG
*
19265459 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19265489 GTAATGCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19266911 original size:2 final size:2
Alignment explanation
Indices: 19266904--19266930 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19266894 AGAACTTCCT
19266904 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
19266931 TTTAGAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:19267907 original size:16 final size:15
Alignment explanation
Indices: 19267890--19267939 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
19267880 TAATTTTTTA
*
19267890 TTTATATAATTATAT
1 TTTAAATAATTATAT
*
19267905 ATTTAAATATTTATAT
1 -TTTAAATAATTATAT
* *
19267921 TTTAAAAAATAATAT
1 TTTAAATAATTATAT
19267936 TTTA
1 TTTA
19267940 TTAATTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAAATAATTATAT
Found at i:19268802 original size:85 final size:86
Alignment explanation
Indices: 19268705--19268878 Score: 271
Period size: 85 Copynumber: 2.0 Consensus size: 86
19268695 AAAAAAAAAA
* * *
19268705 AACTATAACTTTTAATCTCAAAGGTTTATTTTATTATTTCAATTA-TATATTTATTTTCTTTCTT
1 AACTATAACTTTTAATCTCAAAGGTTAATTTTATTATTTCAA-AAGTATATTTATTTTCTTGCTT
*
19268769 TGTT-AAAAAAATTTGTTTCTT
65 TGTTAAAAAAAATATGTTTCTT
* *
19268790 AACTATAGCTTTTAATCTCAAAGGTTAATTTTATTATTTTAAAAGTATATTTATTTTCTTGCTTT
1 AACTATAACTTTTAATCTCAAAGGTTAATTTTATTATTTCAAAAGTATATTTATTTTCTTGCTTT
19268855 GTTAAAAAAAATATGTTTCTT
66 GTTAAAAAAAATATGTTTCTT
19268876 AAC
1 AAC
19268879 CATTGATTTG
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
84 1 0.01
85 61 0.75
86 19 0.23
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (86 bp):
AACTATAACTTTTAATCTCAAAGGTTAATTTTATTATTTCAAAAGTATATTTATTTTCTTGCTTT
GTTAAAAAAAATATGTTTCTT
Found at i:19269074 original size:2 final size:2
Alignment explanation
Indices: 19269067--19269094 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19269057 TATTGTTTTC
19269067 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
19269095 GGATTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19269329 original size:2 final size:2
Alignment explanation
Indices: 19269322--19269360 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19269312 TTTGAAACCA
19269322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19269361 ATAATTTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19273785 original size:30 final size:30
Alignment explanation
Indices: 19273716--19273798 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
19273706 TCTTTATTAA
*
19273716 AATTTTTTTAAAGATTTAATTGATAAAAAT
1 AATTTTTTAAAAGATTTAATTGATAAAAAT
* *
19273746 AAATATTTAAAAG-TTTAATTTGATAAAAAT
1 AATTTTTTAAAAGATTTAA-TTGATAAAAAT
* *
19273776 AATTTTTTAAGA-ATTCAATTGAT
1 AATTTTTTAAAAGATTTAATTGAT
19273799 TTGAAATAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 10 0.23
30 34 0.77
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (30 bp):
AATTTTTTAAAAGATTTAATTGATAAAAAT
Found at i:19274145 original size:22 final size:23
Alignment explanation
Indices: 19274117--19274170 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
19274107 AATTTTACAT
*
19274117 ATAAATAATATTATATTA-ATAA
1 ATAAATAATATTATAATATATAA
* *
19274139 ATAAATAGTATTATAATATATTA
1 ATAAATAATATTATAATATATAA
19274162 ATAAATAAT
1 ATAAATAAT
19274171 TTCAATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAAATAATATTATAATATATAA
Found at i:19274211 original size:25 final size:26
Alignment explanation
Indices: 19274160--19274214 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
19274150 TATAATATAT
19274160 TAATAAATAATTTCAATATATTTTAA
1 TAATAAATAATTTCAATATATTTTAA
**
19274186 TAATAAATAATTTTTA-ATATTTTAA
1 TAATAAATAATTTCAATATATTTTAA
19274211 TAAT
1 TAAT
19274215 TATATTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
TAATAAATAATTTCAATATATTTTAA
Found at i:19274211 original size:48 final size:49
Alignment explanation
Indices: 19274122--19274241 Score: 138
Period size: 48 Copynumber: 2.4 Consensus size: 49
19274112 TACATATAAA
* *
19274122 TAATATTATATTAATAAATAAATAGTATTATAATATATTAATAAATAAT-T
1 TAATATTATTTTAAT-AATAAATAATATTATAATATATTAAT-AATAATAT
* * *
19274172 TCAATA-TATTTTAATAATAAATAAT-TTTTAATATTTTAATAATTATAT
1 T-AATATTATTTTAATAATAAATAATATTATAATATATTAATAATAATAT
*
19274220 TAATATTATTTTAAAAATAAAT
1 TAATATTATTTTAATAATAAAT
19274242 TTTTCAAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
47 9 0.15
48 30 0.49
49 9 0.15
50 9 0.15
51 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (49 bp):
TAATATTATTTTAATAATAAATAATATTATAATATATTAATAATAATAT
Found at i:19277097 original size:26 final size:26
Alignment explanation
Indices: 19277061--19277115 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
19277051 TTATGTCAAC
* *
19277061 AATTTCTATATTCTATTGAAATTTAA
1 AATTTCTATATGCTATTAAAATTTAA
*
19277087 AATTTTTATATGCTATTAAAATTTAA
1 AATTTCTATATGCTATTAAAATTTAA
19277113 AAT
1 AAT
19277116 CTAATCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (26 bp):
AATTTCTATATGCTATTAAAATTTAA
Found at i:19277175 original size:14 final size:15
Alignment explanation
Indices: 19277151--19277181 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
19277141 AAATAAAATT
19277151 TTTATATTATTTTAA
1 TTTATATTATTTTAA
19277166 TTTA-ATTATTTTAA
1 TTTATATTATTTTAA
19277180 TT
1 TT
19277182 CAATCATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATATTATTTTAA
Found at i:19279267 original size:37 final size:38
Alignment explanation
Indices: 19279221--19279295 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 38
19279211 AAATATTTGA
* * *
19279221 TATTTATAGC-ATTAAGAGTTTGATTCTTCACCTTCAT
1 TATTAATAGCTATTAAGAGTTCGATTCTTCAACTTCAT
19279258 TATTAATAGCATTATTAAGAGTTCGATTCTTCAACTTC
1 TATTAATAGC--TATTAAGAGTTCGATTCTTCAACTTC
19279296 CCCTTGAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 9 0.28
40 23 0.72
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (38 bp):
TATTAATAGCTATTAAGAGTTCGATTCTTCAACTTCAT
Found at i:19281136 original size:67 final size:65
Alignment explanation
Indices: 19281019--19281183 Score: 222
Period size: 67 Copynumber: 2.5 Consensus size: 65
19281009 AAGGAACCAG
* * *
19281019 AAATTGGACAATGAACAGAAAAGCCATCATGCAGCATCAATTTGAAGTAATAAGAACACGGATAA
1 AAATTGGAAAATGAACAGAAAA-CCATCATGCAGCATCAATTCGAAGTAATAAGAACACGAATAA
19281084 A
65 A
* * * * *
19281085 AAATTGAGGAAAATGAACAGAAAACAATCATGCAGCATCCATTCGAGGTAATAAGAACATGAATC
1 AAATT--GGAAAATGAACAGAAAACCATCATGCAGCATCAATTCGAAGTAATAAGAACACGAATA
19281150 AA
64 AA
*
19281152 AAATTGGAAAATGAACCGAAAACCATCATGCA
1 AAATTGGAAAATGAACAGAAAACCATCATGCA
19281184 ACCACTTGAT
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 25 0.29
66 5 0.06
67 41 0.47
68 16 0.18
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (65 bp):
AAATTGGAAAATGAACAGAAAACCATCATGCAGCATCAATTCGAAGTAATAAGAACACGAATAAA
Found at i:19285508 original size:33 final size:33
Alignment explanation
Indices: 19285425--19285508 Score: 84
Period size: 33 Copynumber: 2.5 Consensus size: 33
19285415 TGAAATCATG
*
19285425 TAAAATATTTAATTTAAATTAATTAATAATAAA
1 TAAAATATTTAATTTTAATTAATTAATAATAAA
* * *
19285458 TAAAAGAGTTT-ACTTTAATTAATATAA-AAT-CA
1 TAAAATA-TTTAATTTTAATTAAT-TAATAATAAA
19285490 TAAAATATTTAATATTTAA
1 TAAAATATTTAAT-TTTAA
19285509 CACAAACATT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
31 3 0.07
32 8 0.20
33 24 0.59
34 6 0.15
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (33 bp):
TAAAATATTTAATTTTAATTAATTAATAATAAA
Found at i:19286742 original size:19 final size:19
Alignment explanation
Indices: 19286694--19286742 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
19286684 GTAAATTAAA
*
19286694 TAAATAAAATTTAAAAAAT
1 TAAATAAAAATTAAAAAAT
**
19286713 TAAA-AATAAATTAAAACTT
1 TAAATAA-AAATTAAAAAAT
19286732 TAAATAAAAAT
1 TAAATAAAAAT
19286743 AATTATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 21 0.84
20 2 0.08
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAATAAAAATTAAAAAAT
Found at i:19287243 original size:19 final size:20
Alignment explanation
Indices: 19287219--19287257 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
19287209 AATGTAACAT
19287219 AAAAT-AATTATTTTATATA
1 AAAATAAATTATTTTATATA
19287238 AAAATAAAATTATTTTATAT
1 AAAAT-AAATTATTTTATAT
19287258 TTTATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATAAATTATTTTATATA
Found at i:19288165 original size:21 final size:21
Alignment explanation
Indices: 19288103--19288167 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
19288093 CATCGCAAGT
* *
19288103 TTAATTTTATTGTTATAATAT
1 TTAATTTTATCGTTATAATAA
* *
19288124 TTAATTTCATCATTATAATAA
1 TTAATTTTATCGTTATAATAA
* *
19288145 TTAATTTTATGGTTATCATAA
1 TTAATTTTATCGTTATAATAA
19288166 TT
1 TT
19288168 TTAAAATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (21 bp):
TTAATTTTATCGTTATAATAA
Found at i:19289621 original size:29 final size:29
Alignment explanation
Indices: 19289588--19289649 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
19289578 TATAGATAAT
*
19289588 TAAAATTATAC-AAAAATGTAATAAACTAA
1 TAAAATTATACAAAAAATAT-ATAAACTAA
* *
19289617 TAAAATTATATAAAAAATATATAAAGTAA
1 TAAAATTATACAAAAAATATATAAACTAA
19289646 TAAA
1 TAAA
19289650 TATGGAATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (29 bp):
TAAAATTATACAAAAAATATATAAACTAA
Found at i:19299498 original size:195 final size:194
Alignment explanation
Indices: 19299144--19299498 Score: 465
Period size: 195 Copynumber: 1.8 Consensus size: 194
19299134 TTTGGAAAAG
* * *
19299144 AATACAATTACTTTTATTGAAATTTTATCTAAATTATTTCACAATTTGGCACAAATTTAGAGAAA
1 AATACAATTACTTTTATTGAAACTTTAACTAAATTATTCCACAATTTGGCACAAATTTAGAGAAA
* *
19299209 ATTTCTCACCTAGAGATTTCTTAGAAATTTACCATTTGAAATTTCTAAGAATCTCATCCTTGGGT
66 ATTTCTCACCTAGAGATTTCTTAAAAATTTACCATTTGAAATTTCTAAGAATCTCATCCTTGGAT
**
19299274 AATTTGTATTTAATTCCAAAAATTTTTATTAATTTTTATATTTTTTCTTTTTTTATTGAAAATA
131 AATTAATATTTAATTCCAAAAATTTTTATTAATTTTTATATTTTTTCTTTTTTTATTGAAAATA
* * *
19299338 AATATCAATTA-TTGTTGTTGAAACTTTAACTAAATTATTCCACCATTTAGG-ACAAATTTAGAT
1 AATA-CAATTACTT-TTATTGAAACTTTAACTAAATTATTCCACAATTT-GGCACAAATTTAGAG
*
19299401 AAAATTTTTCACCTA-AGAATTT-TATAAAAATTTACCATTTGAAATTTCTATA-AAT-TCCATC
63 AAAATTTCTCACCTAGAG-ATTTCT-TAAAAATTTACCATTTGAAATTTCTA-AGAATCT-CATC
*
19299462 TTTGGATAATTAATATTT-ATT-CACAAAATGTTTTATT
124 CTTGGATAATTAATATTTAATTCCA-AAAAT-TTTTATT
19299499 TTTATTTTTT
Statistics
Matches: 140, Mismatches: 12, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
193 2 0.01
194 18 0.13
195 117 0.84
196 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (194 bp):
AATACAATTACTTTTATTGAAACTTTAACTAAATTATTCCACAATTTGGCACAAATTTAGAGAAA
ATTTCTCACCTAGAGATTTCTTAAAAATTTACCATTTGAAATTTCTAAGAATCTCATCCTTGGAT
AATTAATATTTAATTCCAAAAATTTTTATTAATTTTTATATTTTTTCTTTTTTTATTGAAAATA
Found at i:19299599 original size:18 final size:19
Alignment explanation
Indices: 19299561--19299600 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
19299551 ACACATAAAT
*
19299561 AAATAAATAAAATAACAAA
1 AAATAAAGAAAATAACAAA
*
19299580 AAATAAAGAAAA-ACCAAA
1 AAATAAAGAAAATAACAAA
19299598 AAA
1 AAA
19299601 AAGAAACTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (19 bp):
AAATAAAGAAAATAACAAA
Found at i:19300128 original size:21 final size:21
Alignment explanation
Indices: 19300102--19300143 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
19300092 AACAATTTCA
19300102 GAAAAAAATAGCC-AAAAATTT
1 GAAAAAAA-AGCCTAAAAATTT
*
19300123 GAAAAAAAATCCTAAAAATTT
1 GAAAAAAAAGCCTAAAAATTT
19300144 TAGAATTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (21 bp):
GAAAAAAAAGCCTAAAAATTT
Found at i:19300737 original size:40 final size:41
Alignment explanation
Indices: 19300645--19301001 Score: 200
Period size: 41 Copynumber: 9.1 Consensus size: 41
19300635 GATAAATTAA
* *
19300645 GCTCCTTTAAATAGAGGCACCACAACTTTGAAAAGTAAAAAT
1 GCTCCTCTAAATAGAGGTACCACAACTTTGAAAAGT-AAAAT
* * * **
19300687 ACTCTTCTAAATAGAGGTACCATAACTAGGAAAA-TAAAAT
1 GCTCCTCTAAATAGAGGTACCACAACTTTGAAAAGTAAAAT
*
19300727 GCTCCTCTAAACAGAGGTACCACAACTTTGAAAAGTAAAAT
1 GCTCCTCTAAATAGAGGTACCACAACTTTGAAAAGTAAAAT
* * *
19300768 G-T--TC---CT--A-GCACCAAAACTTTGAAAAGTAAAAT
1 GCTCCTCTAAATAGAGGTACCACAACTTTGAAAAGTAAAAT
* *
19300800 GCT-C-C----T--A-GCACCATAACTTTGAAAAGTAAAAT
1 GCTCCTCTAAATAGAGGTACCACAACTTTGAAAAGTAAAAT
* * ** *
19300832 GCTCTTCTAAATAAAGACACCACAATTTTGGAAAA-TAAAAT
1 GCTCCTCTAAATAGAGGTACCACAACTTT-GAAAAGTAAAAT
* *** * *
19300873 GCTCATCTAAATAGAAACACCCCAACTTTGAAAAATAAAAT
1 GCTCCTCTAAATAGAGGTACCACAACTTTGAAAAGTAAAAT
** * * * * *
19300914 GCTTTTTTAAACAAAGGCACC-CTAACTTTGTAAAA-CAAAAT
1 GCTCCTCTAAATAGAGGTACCAC-AACTTTG-AAAAGTAAAAT
* * * * *
19300955 GCTCCTCTAAACAGAGGCACCGCAACTTTGAAAAATAAAAG
1 GCTCCTCTAAATAGAGGTACCACAACTTTGAAAAGTAAAAT
19300996 GCTCCT
1 GCTCCT
19301002 TGACAATCAT
Statistics
Matches: 256, Mismatches: 41, Indels: 37
0.77 0.12 0.11
Matches are distributed among these distances:
32 53 0.21
33 3 0.01
34 1 0.00
38 3 0.01
40 45 0.18
41 114 0.45
42 37 0.14
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAATAGAGGTACCACAACTTTGAAAAGTAAAAT
Found at i:19300786 original size:32 final size:32
Alignment explanation
Indices: 19300745--19300835 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 32
19300735 AAACAGAGGT
* *
19300745 ACCACAACTTTGAAAAGTAAAATGTTCCTAGC
1 ACCAAAACTTTGAAAAGTAAAATGCTCCTAGC
19300777 ACCAAAACTTTGAAAAGTAAAATGCTCCTAGC
1 ACCAAAACTTTGAAAAGTAAAATGCTCCTAGC
*
19300809 ACCATAACTTTGAAAAGTAAAATGCTC
1 ACCAAAACTTTGAAAAGTAAAATGCTC
19300836 TTCTAAATAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (32 bp):
ACCAAAACTTTGAAAAGTAAAATGCTCCTAGC
Found at i:19300954 original size:82 final size:82
Alignment explanation
Indices: 19300814--19300999 Score: 230
Period size: 82 Copynumber: 2.3 Consensus size: 82
19300804 CTAGCACCAT
* * * *
19300814 AACTTTGAAAAGTAAAATGCTCTTCTAAATAAAGACACCACAATTTTGGAAAATAAAATGCTCAT
1 AACTTTGAAAAATAAAATGCTCTTCTAAACAAAGACACCACAACTTTGGAAAACAAAATGCTCAT
*
19300879 CTAAATAGAAACACCCC
66 CTAAACAGAAACACCCC
* * * * *
19300896 AACTTTGAAAAATAAAATGCTTTTTTAAACAAAGGCACC-CTAACTTTGTAAAACAAAATGCTCC
1 AACTTTGAAAAATAAAATGCTCTTCTAAACAAAGACACCAC-AACTTTGGAAAACAAAATGCTCA
** *
19300960 TCTAAACAGAGGCACCGC
65 TCTAAACAGAAACACCCC
*
19300978 AACTTTGAAAAATAAAAGGCTC
1 AACTTTGAAAAATAAAATGCTC
19301000 CTTGACAATC
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 1 0.01
82 87 0.99
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (82 bp):
AACTTTGAAAAATAAAATGCTCTTCTAAACAAAGACACCACAACTTTGGAAAACAAAATGCTCAT
CTAAACAGAAACACCCC
Found at i:19312980 original size:26 final size:25
Alignment explanation
Indices: 19312926--19312980 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
19312916 CTTACCTATG
*
19312926 AATTTTATAGAAATTTACCATTTGA
1 AATTTTATAGAAATTTACCATTAGA
* *
19312951 AATTTT-TATAAATTCTATCATTAGA
1 AATTTTATAGAAATT-TACCATTAGA
19312976 TAATT
1 -AATT
19312981 AATATTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 7 0.28
25 14 0.56
26 4 0.16
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (25 bp):
AATTTTATAGAAATTTACCATTAGA
Found at i:19313108 original size:21 final size:21
Alignment explanation
Indices: 19313074--19313114 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19313064 ATAAATAAAT
*
19313074 AAATAAATAAAATA-CAAAAC
1 AAATAAAAAAAATACCAAAAC
19313094 AAATAAAAAAAAATACCAAAA
1 AAAT-AAAAAAAATACCAAAA
19313115 ACATGAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (21 bp):
AAATAAAAAAAATACCAAAAC
Found at i:19326539 original size:18 final size:18
Alignment explanation
Indices: 19326463--19326539 Score: 54
Period size: 18 Copynumber: 4.3 Consensus size: 18
19326453 AAAAATTGTT
*
19326463 TGATATTTAATTTTATTA
1 TGATTTTTAATTTTATTA
* *
19326481 TGATTATT--GTTTATTGTA
1 TGATTTTTAATTTTA-T-TA
* *
19326499 TG-TTTTAAATTTTATCA
1 TGATTTTTAATTTTATTA
19326516 -GAATTTTTAATTTTATTA
1 TG-ATTTTTAATTTTATTA
19326534 TGATTT
1 TGATTT
19326540 GATGTTTTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 14
0.65 0.14 0.21
Matches are distributed among these distances:
16 5 0.12
17 5 0.12
18 28 0.65
19 5 0.12
ACGTcount: A:0.29, C:0.01, G:0.09, T:0.61
Consensus pattern (18 bp):
TGATTTTTAATTTTATTA
Found at i:19328285 original size:26 final size:27
Alignment explanation
Indices: 19328256--19328409 Score: 145
Period size: 29 Copynumber: 5.4 Consensus size: 27
19328246 ATTAAGAAAA
19328256 AGATAA-AATAAAAAATATATATTAAT
1 AGATAATAATAAAAAATATATATTAAT
19328282 AGATAAATAATAAAATATAATAAAATATATTAAT
1 AGAT-AATAAT-AAA-A-AAT---ATATATTAAT
19328316 AGATAAATAATAATAAAATATATATTAAT
1 AGAT-AATAATAA-AAAATATATATTAAT
* *
19328345 AGAT-A-AATAATAAA-ATATGTTAAT
1 AGATAATAATAAAAAATATATATTAAT
19328369 AGATAAATAATTAAAAATATATATATTAAT
1 AGAT-AATAA-TAAAAA-ATATATATTAAT
*
19328399 AAATAATAATA
1 AGATAATAATA
19328410 GTAATAATAA
Statistics
Matches: 108, Mismatches: 5, Indels: 28
0.77 0.04 0.20
Matches are distributed among these distances:
24 13 0.12
25 3 0.03
26 10 0.09
27 5 0.05
28 10 0.09
29 23 0.21
30 13 0.12
31 3 0.03
32 3 0.03
33 3 0.03
34 22 0.20
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (27 bp):
AGATAATAATAAAAAATATATATTAAT
Found at i:19328314 original size:34 final size:33
Alignment explanation
Indices: 19328258--19328362 Score: 148
Period size: 29 Copynumber: 3.3 Consensus size: 33
19328248 TAAGAAAAAG
19328258 ATAAAATA-AAAAATATATATTAATAGATAAATA
1 ATAAAATATAAAAA-ATATATTAATAGATAAATA
19328291 ATAAAATATAATAAAATATATTAATAGATAAATA
1 ATAAAATATAA-AAAATATATTAATAGATAAATA
*
19328325 AT---A-ATAAAATATATATTAATAGATAAATA
1 ATAAAATATAAAAAATATATTAATAGATAAATA
19328354 ATAAAATAT
1 ATAAAATAT
19328363 GTTAATAGAT
Statistics
Matches: 65, Mismatches: 1, Indels: 12
0.83 0.01 0.15
Matches are distributed among these distances:
29 23 0.35
30 4 0.06
31 1 0.02
32 1 0.02
33 10 0.15
34 23 0.35
35 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (33 bp):
ATAAAATATAAAAAATATATTAATAGATAAATA
Found at i:19328360 original size:53 final size:51
Alignment explanation
Indices: 19328288--19328438 Score: 175
Period size: 53 Copynumber: 2.9 Consensus size: 51
19328278 TAATAGATAA
19328288 ATAATAA-AATATAATAAAATATATTAATAGATAAATAATAATAAAATATAT
1 ATAATAATAA-ATAATAAAATATATTAATAGATAAATAATAATAAAATATAT
* *
19328339 ATTAATAGATAAATAATAAAATATGTTAATAGATAAATAATTA-AAAATATAT
1 A-TAATA-ATAAATAATAAAATATATTAATAGATAAATAATAATAAAATATAT
* * * *
19328391 ATATTAATAAATAAT--AATAGTAATAATAAATAAATAAAAATACAAATA
1 ATAATAATAAATAATAAAATA-TATTAATAGATAAATAATAATA-AAATA
19328439 CAAATGGGCT
Statistics
Matches: 86, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
48 4 0.05
49 15 0.17
50 10 0.12
51 10 0.12
52 15 0.17
53 30 0.35
54 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (51 bp):
ATAATAATAAATAATAAAATATATTAATAGATAAATAATAATAAAATATAT
Found at i:19328361 original size:37 final size:37
Alignment explanation
Indices: 19328287--19328358 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
19328277 TTAATAGATA
* *
19328287 AATAATAAAATATAATAAAATATATTAATAGATAAAT
1 AATAATAAAATATAATAAAATAGATAAATAGATAAAT
*
19328324 AATAATAAAATAT-ATATTAATAGATAAATA-ATAAA
1 AATAATAAAATATAATA-AAATAGATAAATAGATAAA
19328359 ATATGTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 8 0.26
37 23 0.74
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (37 bp):
AATAATAAAATATAATAAAATAGATAAATAGATAAAT
Found at i:19328406 original size:19 final size:19
Alignment explanation
Indices: 19328262--19328423 Score: 67
Period size: 19 Copynumber: 8.5 Consensus size: 19
19328252 AAAAAGATAA
* *
19328262 AATAAAAAATATATATTAAT
1 AATAAATAATA-ATAGTAAT
*
19328282 AGATAAATAATAA-AAT-AT
1 A-ATAAATAATAATAGTAAT
*
19328300 AAT-AA-AAT-ATATTAAT
1 AATAAATAATAATAGTAAT
*
19328316 AGATAAATAATAATA-AAAT
1 A-ATAAATAATAATAGTAAT
19328335 ATATATTAATAGATAA-A-TAAT
1 A-ATA--AATA-ATAATAGTAAT
**
19328356 AA-AATATGTTAATAGATAAAT
1 AATAA-ATAATAATAG-T-AAT
*
19328377 AATTAAA-AATATATA-TATT
1 AA-TAAATAATA-ATAGTAAT
19328396 AATAAATAATAATAGTAAT
1 AATAAATAATAATAGTAAT
19328415 AATAAATAA
1 AATAAATAA
19328424 ATAAAAATAC
Statistics
Matches: 110, Mismatches: 12, Indels: 41
0.67 0.07 0.25
Matches are distributed among these distances:
14 1 0.01
15 5 0.05
16 5 0.05
17 8 0.07
18 15 0.14
19 33 0.30
20 8 0.07
21 25 0.23
22 8 0.07
23 2 0.02
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
AATAAATAATAATAGTAAT
Found at i:19328682 original size:26 final size:26
Alignment explanation
Indices: 19328652--19328704 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
19328642 GCTCAACGAT
*
19328652 TTTGAGAAAAATAAACAAATCTCATC
1 TTTGAGAAAAATAAACAAAGCTCATC
*
19328678 TTTGAGAAAAATAAATAAAGCTCATC
1 TTTGAGAAAAATAAACAAAGCTCATC
19328704 T
1 T
19328705 AATCGTAGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.28
Consensus pattern (26 bp):
TTTGAGAAAAATAAACAAAGCTCATC
Found at i:19328898 original size:41 final size:41
Alignment explanation
Indices: 19328801--19329012 Score: 216
Period size: 41 Copynumber: 5.2 Consensus size: 41
19328791 AATAAACAAA
* * *
19328801 GCTCCTCTAAATAGAGGCATCACAACTTTTGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCATCACAACTTTGGAAAATAAATT
** * *
19328842 GCTTTTGTAAGCAGAGGCATCACAACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCATCACAACTTTGGAAAATAAATT
* * *
19328883 GTTCCTCTAAACAGAGGC-TCAACAACTTTGAAAAAATAAATA
1 GCTCCTCTAAACAGAGGCATC-ACAACTTTG-GAAAATAAATT
* *
19328925 ACACCTCTAAACAGAGGCA--ACGAACTTT-GAGAAATAAATT
1 GCTCCTCTAAACAGAGGCATCAC-AACTTTGGA-AAATAAATT
* * * *
19328965 GCTCCTCTAAATAGAGGCACCACAACTTTGAAAAATAAATG
1 GCTCCTCTAAACAGAGGCATCACAACTTTGGAAAATAAATT
19329006 GCTCCTC
1 GCTCCTC
19329013 GACAATCACG
Statistics
Matches: 139, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
39 1 0.01
40 28 0.20
41 83 0.60
42 27 0.19
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCATCACAACTTTGGAAAATAAATT
Found at i:19328981 original size:123 final size:126
Alignment explanation
Indices: 19328770--19329004 Score: 300
Period size: 123 Copynumber: 1.9 Consensus size: 126
19328760 TTTTAATCAA
* * *
19328770 AGGCTCAACGACTTTGGAAAAAATAAACAAAGCTCCTCTAAATAGAGGCATCACAACTTTTGAAA
1 AGGCTCAACAACTTTGGAAAAAATAAACAAAGCACCTCTAAACAGAGGCA-CACAACTTTTGAAA
* ** * * * *
19328835 GTAAATTGCTTTTGTAAGCAGAGGCATCACAACTTTGGAAAATAAATTGTTCCTCTAAACAG
65 ATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATTGTTCCTCTAAACAG
*
19328897 AGGCTCAACAACTTT-GAAAAAATAAA-TAA-CACCTCTAAACAGAGGCA-ACGAAC-TTTGAGA
1 AGGCTCAACAACTTTGGAAAAAATAAACAAAGCACCTCTAAACAGAGGCACAC-AACTTTTGA-A
*
19328957 AATAAATTGCTCCTCTAAATAGAGGCACCACAACTTTGAAAAATAAAT
64 AATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAAT
19329005 GGCTCCTCGA
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
122 7 0.07
123 44 0.47
124 16 0.17
125 2 0.02
126 11 0.12
127 14 0.15
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (126 bp):
AGGCTCAACAACTTTGGAAAAAATAAACAAAGCACCTCTAAACAGAGGCACACAACTTTTGAAAA
TAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATTGTTCCTCTAAACAG
Found at i:19340887 original size:3 final size:3
Alignment explanation
Indices: 19340879--19340916 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
19340869 CTAATCAATA
19340879 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19340917 AAATGAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19341787 original size:32 final size:31
Alignment explanation
Indices: 19341749--19341846 Score: 109
Period size: 32 Copynumber: 3.3 Consensus size: 31
19341739 AAAGAAAAAG
19341749 ATAAAATCAATATATATATTAATAGATAAATA
1 ATAAAAT-AATATATATATTAATAGATAAATA
* *
19341781 ATAAAAT-ATAT-TA-A--AATATATTAATA
1 ATAAAATAATATATATATTAATAGATAAATA
19341807 AT-AAATAAATAATATATATTAATAGATAAATA
1 ATAAAAT-AAT-ATATATATTAATAGATAAATA
19341839 ATAAAATA
1 ATAAAATA
19341847 TGTTAATAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
25 4 0.07
26 12 0.22
27 2 0.04
28 3 0.06
29 4 0.07
30 5 0.09
32 20 0.37
33 4 0.07
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (31 bp):
ATAAAATAATATATATATTAATAGATAAATA
Found at i:19341797 original size:10 final size:11
Alignment explanation
Indices: 19341757--19341841 Score: 59
Period size: 11 Copynumber: 7.6 Consensus size: 11
19341747 AGATAAAATC
19341757 AATATATATATT
1 AATA-ATATATT
*
19341769 AATAGATA-AAT
1 AATA-ATATATT
19341780 AATAAAATATATT
1 AAT--AATATATT
19341793 AA-AATATATT
1 AATAATATATT
* *
19341803 AATAATAAATA
1 AATAATATATT
19341814 AATAATATA-T
1 AATAATATATT
* * *
19341824 ATTAATAGATA
1 AATAATATATT
19341835 AATAATA
1 AATAATA
19341842 AAATATGTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
10 17 0.30
11 25 0.44
12 10 0.18
13 5 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
AATAATATATT
Found at i:19341802 original size:34 final size:34
Alignment explanation
Indices: 19341762--19341828 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
19341752 AAATCAATAT
19341762 ATATATTAATAGATAAAT-AATAAAATATATTAAA
1 ATATATTAATA-ATAAATAAATAAAATATATTAAA
*
19341796 ATATATTAATAATAAATAAATAATATATATTAA
1 ATATATTAATAATAAATAAATAAAATATATTAA
19341829 TAGATAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 6 0.19
34 25 0.81
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (34 bp):
ATATATTAATAATAAATAAATAAAATATATTAAA
Found at i:19341822 original size:58 final size:56
Alignment explanation
Indices: 19341752--19341930 Score: 192
Period size: 58 Copynumber: 3.2 Consensus size: 56
19341742 GAAAAAGATA
* * *
19341752 AAATCAAT-ATATATATTAATAGATAAATAATAAAATATATTAAAATATATTAATAAT
1 AAATAAATAATATATATTAATAGATAAATAATAAAATATATT--AATAGATAAATAAT
*
19341809 AAATAAATAATATATATTAATAGATAAATAATAAAATATGTTAATAGATAAATAAT
1 AAATAAATAATATATATTAATAGATAAATAATAAAATATATTAATAGATAAATAAT
* * * * *
19341865 TAA-AAA-AATATATATTAATAAAT-AATAATAGTAATA-ATAAATAAATAAAT-AT
1 AAATAAATAATATATATTAATAGATAAATAATA-AAATATATTAATAGATAAATAAT
19341917 CAAATAAA-AATATA
1 -AAATAAATAATATA
19341931 AAATGTGCTT
Statistics
Matches: 107, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
52 2 0.02
53 20 0.19
54 29 0.27
55 3 0.03
56 14 0.13
57 7 0.07
58 32 0.30
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.34
Consensus pattern (56 bp):
AAATAAATAATATATATTAATAGATAAATAATAAAATATATTAATAGATAAATAAT
Found at i:19341854 original size:16 final size:15
Alignment explanation
Indices: 19341792--19341905 Score: 58
Period size: 15 Copynumber: 7.3 Consensus size: 15
19341782 TAAAATATAT
19341792 TAAAATATATTAATAA
1 TAAAATA-ATTAATAA
*
19341808 T-AAATAAATAATATA
1 TAAAATAATTAATA-A
* *
19341823 TATTAATAGATAAATAA
1 TA-AAATA-ATTAATAA
*
19341840 TAAAATATGTTAATAGA
1 TAAAATA-ATTAATA-A
19341857 T-AAATAATTAA-AA
1 TAAAATAATTAATAA
19341870 -AAATATATATTAATAAA
1 TAAA-ATA-ATTAAT-AA
*
19341887 TAATAAT-AGTAATAA
1 TAA-AATAATTAATAA
19341902 TAAA
1 TAAA
19341906 TAAATAAATA
Statistics
Matches: 76, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
13 3 0.04
14 11 0.14
15 21 0.28
16 20 0.26
17 11 0.14
18 9 0.12
19 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (15 bp):
TAAAATAATTAATAA
Found at i:19342467 original size:8 final size:8
Alignment explanation
Indices: 19342442--19342506 Score: 53
Period size: 8 Copynumber: 8.0 Consensus size: 8
19342432 TATATATAAA
19342442 AATAATTT
1 AATAATTT
*
19342450 AAT-ATAT
1 AATAATTT
19342457 AATAATTT
1 AATAATTT
*
19342465 AATTATTT
1 AATAATTT
*
19342473 ATTAATTT
1 AATAATTT
*
19342481 TATAAATATT
1 AAT-AAT-TT
19342491 AAATAATTT
1 -AATAATTT
19342500 AA-AATTT
1 AATAATTT
19342507 TCATTATATA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
7 11 0.24
8 22 0.49
9 5 0.11
10 5 0.11
11 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
AATAATTT
Found at i:19342570 original size:18 final size:16
Alignment explanation
Indices: 19342543--19342576 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
19342533 TCTATTTTTA
19342543 TTTTTTATAATTTATTT
1 TTTTTTATAA-TTATTT
19342560 TTTTATTATAATTATTT
1 TTTT-TTATAATTATTT
19342577 ATATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTATAATTATTT
Found at i:19343339 original size:5 final size:5
Alignment explanation
Indices: 19343322--19343365 Score: 72
Period size: 5 Copynumber: 9.0 Consensus size: 5
19343312 CTGTATGTGG
*
19343322 TATAA TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
19343366 GCCAATAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 34 0.89
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:19347456 original size:22 final size:22
Alignment explanation
Indices: 19347431--19347475 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
19347421 AACAGAGAGA
*
19347431 GAAAGACAAGAGGGAGGTCGAT
1 GAAAGACAAAAGGGAGGTCGAT
*
19347453 GAAAGACAAAAGGGAGGTTGAT
1 GAAAGACAAAAGGGAGGTCGAT
19347475 G
1 G
19347476 TTAGATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.40, T:0.11
Consensus pattern (22 bp):
GAAAGACAAAAGGGAGGTCGAT
Found at i:19347932 original size:13 final size:14
Alignment explanation
Indices: 19347915--19347952 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
19347905 TTTTTAATTA
19347915 GATTAATTTATAAT
1 GATTAATTTATAAT
19347929 -ATTAATTTCATAAT
1 GATTAATTT-ATAAT
19347943 GA-TAATTTAT
1 GATTAATTTAT
19347953 CATCAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 10 0.45
14 11 0.50
15 1 0.05
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (14 bp):
GATTAATTTATAAT
Found at i:19348120 original size:19 final size:21
Alignment explanation
Indices: 19348096--19348144 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
19348086 TAAAGAATTA
19348096 AAATATTATAAAT-TATTT-T
1 AAATATTATAAATGTATTTAT
*
19348115 AAATATAATAAATGTATTTAT
1 AAATATTATAAATGTATTTAT
*
19348136 AATTATTAT
1 AAATATTAT
19348145 TTATTTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 12 0.48
20 5 0.20
21 8 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATATTATAAATGTATTTAT
Found at i:19360862 original size:52 final size:53
Alignment explanation
Indices: 19360754--19360864 Score: 161
Period size: 53 Copynumber: 2.1 Consensus size: 53
19360744 AATTTTAGGA
* *
19360754 AAAATATTTCTAAATTTGGCCAAAACGGTAAAAAATTTAGAAATGAAACTTAT
1 AAAATATTTCTAAATTAGGCCAAAACGGTAAAAAATTTAGAAATAAAACTTAT
* * * *
19360807 AAAATATTTCTAAATTAGGCCCAAATGGTAAAAATTTTA-AAATAAAACTTGT
1 AAAATATTTCTAAATTAGGCCAAAACGGTAAAAAATTTAGAAATAAAACTTAT
19360859 AAAATA
1 AAAATA
19360865 AATAAAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 17 0.33
53 35 0.67
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (53 bp):
AAAATATTTCTAAATTAGGCCAAAACGGTAAAAAATTTAGAAATAAAACTTAT
Found at i:19366898 original size:13 final size:13
Alignment explanation
Indices: 19366880--19366906 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19366870 TTCCCTACAA
19366880 ACATTAAATGTTG
1 ACATTAAATGTTG
19366893 ACATTAAATGTTG
1 ACATTAAATGTTG
19366906 A
1 A
19366907 TTACACATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ACATTAAATGTTG
Found at i:19367943 original size:32 final size:32
Alignment explanation
Indices: 19367907--19367991 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 32
19367897 TCATCATTGT
* *
19367907 ATTTATCATTATTTTATTTTGTTTTATTT-TAC
1 ATTTATCTTTATTTTATTTT-ATTTATTTATAC
**
19367939 ATTTATCTTTATCTTTATTTTATTTATTTATTT
1 ATTTATCTTTAT-TTTATTTTATTTATTTATAC
19367972 ATTTATCTTTATTTTGATTT
1 ATTTATCTTTATTTT-ATTT
19367992 ACTTTTCATG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
32 21 0.46
33 25 0.54
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (32 bp):
ATTTATCTTTATTTTATTTTATTTATTTATAC
Found at i:19367949 original size:6 final size:5
Alignment explanation
Indices: 19367860--19367991 Score: 80
Period size: 5 Copynumber: 25.6 Consensus size: 5
19367850 AATGTCTAAT
*
19367860 TTTTA TTTTA TTTTA TTTTA --TTA TTTTAA TTTTA TCTTCATCA TTGTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA T-TT--T-A TTTTA
* * *
19367908 -TTTA TCATTA TTTTA TTTTG TTTTA TTTTA CATTTA TCTTTA TCTTTA
1 TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA -TTTTA T-TTTA T-TTTA
19367956 TTTTA -TTTA -TTTA -TTTA -TTTA TCTTTA TTTTGA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTT-A TTT
19367992 ACTTTTCATG
Statistics
Matches: 105, Mismatches: 8, Indels: 27
0.75 0.06 0.19
Matches are distributed among these distances:
3 3 0.03
4 19 0.18
5 43 0.41
6 36 0.34
8 2 0.02
9 2 0.02
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.70
Consensus pattern (5 bp):
TTTTA
Found at i:19367958 original size:33 final size:32
Alignment explanation
Indices: 19367907--19368005 Score: 111
Period size: 32 Copynumber: 3.2 Consensus size: 32
19367897 TCATCATTGT
* *
19367907 ATTTATCATTAT-TTTATTTTGTTTTATTTTAC
1 ATTTATCTTTATCTTTATTTTGATTTATTTT-C
19367939 ATTTATCTTTATCTTTATTTT-ATTTA-TTT-
1 ATTTATCTTTATCTTTATTTTGATTTATTTTC
19367968 ATTTA--TTTATCTTTATTTTGATTTACTTTTC
1 ATTTATCTTTATCTTTATTTTGATTTA-TTTTC
*
19367999 ATGTATC
1 ATTTATC
19368006 ATATTCATAT
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
27 14 0.25
28 5 0.09
29 5 0.09
30 3 0.05
31 7 0.12
32 15 0.26
33 8 0.14
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (32 bp):
ATTTATCTTTATCTTTATTTTGATTTATTTTC
Found at i:19368005 original size:27 final size:27
Alignment explanation
Indices: 19367948--19368005 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
19367938 CATTTATCTT
* * *
19367948 TATCTTTATTTTATTTATTTATTTATT
1 TATCTTTATTTTATTTACTTATTCATG
19367975 TATCTTTATTTTGATTTACTT-TTCATG
1 TATCTTTATTTT-ATTTACTTATTCATG
19368002 TATC
1 TATC
19368006 ATATTCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.67
Consensus pattern (27 bp):
TATCTTTATTTTATTTACTTATTCATG
Found at i:19368021 original size:3 final size:3
Alignment explanation
Indices: 19368013--19368039 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
19368003 ATCATATTCA
19368013 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
19368040 CTTTTTGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:19368735 original size:20 final size:20
Alignment explanation
Indices: 19368694--19368731 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19368684 AATTTTGATT
*
19368694 AATTTTTTGACTAATGTTTG
1 AATTTTTTGACCAATGTTTG
19368714 AATTTTTTGACCAA-GTTT
1 AATTTTTTGACCAATGTTT
19368732 TGAAGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (20 bp):
AATTTTTTGACCAATGTTTG
Found at i:19368740 original size:20 final size:20
Alignment explanation
Indices: 19368697--19368740 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
19368687 TTTGATTAAT
* *
19368697 TTTTTGACTAATGTTTGAAT
1 TTTTTGACCAATGTTTGAAG
19368717 TTTTTGACCAA-GTTTTGAAG
1 TTTTTGACCAATG-TTTGAAG
19368737 TTTT
1 TTTT
19368741 CTTTCACTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.55
Consensus pattern (20 bp):
TTTTTGACCAATGTTTGAAG
Found at i:19369205 original size:59 final size:56
Alignment explanation
Indices: 19369132--19369276 Score: 152
Period size: 59 Copynumber: 2.5 Consensus size: 56
19369122 TGAAATTAAA
* *
19369132 AAATAAAAAAATCTTACCAATATATTGGA-GGATTTTAAAGTTTTAAAAAAAATTTTTTAG
1 AAATAAAAAAATCTTACCAATATATTGAAGGGATTTTAAAATTTT-AAAAAAA----TTAG
* * *
19369192 AAAT-AAAAAATCTTATCC-ACACATTGAAGGGTTTTTAAAATTTTAAAAAAATTAG
1 AAATAAAAAAATCTTA-CCAATATATTGAAGGGATTTTAAAATTTTAAAAAAATTAG
*
19369247 AAATAAAAAAAAACTTACCAATATATTGAA
1 AAAT-AAAAAAATCTTACCAATATATTGAA
19369277 AGGTTCTTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
55 8 0.11
56 2 0.03
57 18 0.25
59 25 0.35
60 19 0.26
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (56 bp):
AAATAAAAAAATCTTACCAATATATTGAAGGGATTTTAAAATTTTAAAAAAATTAG
Found at i:19407902 original size:14 final size:13
Alignment explanation
Indices: 19407879--19407984 Score: 69
Period size: 12 Copynumber: 8.2 Consensus size: 13
19407869 TCAGTTATTT
*
19407879 AATAAGAATAAATA
1 AATAAAAATAAA-A
19407893 AATAAAAATAGAAA
1 AATAAAAATA-AAA
*
19407907 AACAAAAATAAAA
1 AATAAAAATAAAA
* *
19407920 CAT-AAACTAAAA
1 AATAAAAATAAAA
19407932 AATAAAAA-AAAA
1 AATAAAAATAAAA
*
19407944 CAA-AAAAATTAGAA
1 -AATAAAAA-TAAAA
*
19407958 ACT-AAAAT-AAA
1 AATAAAAATAAAA
* *
19407969 AATCAAAATAGAA
1 AATAAAAATAAAA
19407982 AAT
1 AAT
19407985 CAAACGAAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
11 4 0.06
12 25 0.35
13 19 0.26
14 22 0.31
15 2 0.03
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (13 bp):
AATAAAAATAAAA
Found at i:19407932 original size:19 final size:19
Alignment explanation
Indices: 19407910--19407970 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
19407900 ATAGAAAAAC
19407910 AAAAATAAAACATAAACTA
1 AAAAATAAAACATAAACTA
* *
19407929 AAAAATAAAA-AAAAACAA
1 AAAAATAAAACATAAACTA
*
19407947 AAAAATTAGAAAC-TAAAATA
1 AAAAA-TA-AAACATAAACTA
19407967 AAAA
1 AAAA
19407971 TCAAAATAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
18 11 0.32
19 12 0.35
20 11 0.32
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.13
Consensus pattern (19 bp):
AAAAATAAAACATAAACTA
Found at i:19407944 original size:18 final size:19
Alignment explanation
Indices: 19407910--19407952 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
19407900 ATAGAAAAAC
* *
19407910 AAAAATAAAACATAAACTA
1 AAAAATAAAACAAAAACAA
19407929 AAAAATAAAA-AAAAACAA
1 AAAAATAAAACAAAAACAA
19407947 AAAAAT
1 AAAAAT
19407953 TAGAAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (19 bp):
AAAAATAAAACAAAAACAA
Found at i:19407965 original size:50 final size:51
Alignment explanation
Indices: 19407906--19408003 Score: 121
Period size: 50 Copynumber: 1.9 Consensus size: 51
19407896 AAAAATAGAA
*
19407906 AAACAAAAATAAAACAT-AAACTAAAAAAT-AAA-AAAAAACAAAAAAATTAG
1 AAACAAAAATAAAA-ATCAAAATAAAAAATCAAACAAAAAA-AAAAAAATTAG
* *
19407956 AAACTAAAATAAAAATCAAAATAGAAAATCAAACGAAAAAAAAAAAAA
1 AAACAAAAATAAAAATCAAAATAAAAAATCAAAC-AAAAAAAAAAAAA
19408004 GGGCGATTCG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
49 2 0.05
50 23 0.56
51 3 0.07
52 7 0.17
53 6 0.15
ACGTcount: A:0.78, C:0.08, G:0.03, T:0.11
Consensus pattern (51 bp):
AAACAAAAATAAAAATCAAAATAAAAAATCAAACAAAAAAAAAAAAATTAG
Found at i:19408859 original size:5 final size:5
Alignment explanation
Indices: 19408849--19408874 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19408839 TTCTTCATTA
19408849 TGATT TGATT TGATT TGATT TGATT T
1 TGATT TGATT TGATT TGATT TGATT T
19408875 TCATAGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (5 bp):
TGATT
Found at i:19409043 original size:6 final size:6
Alignment explanation
Indices: 19409042--19409138 Score: 70
Period size: 6 Copynumber: 16.2 Consensus size: 6
19409032 ACCAAAATCA
* * * * *
19409042 AAAAAT AAAA-T AAAATC ACAATT AAAATCC AAAATT AAAATT AAACTT
1 AAAATT AAAATT AAAATT AAAATT AAAAT-T AAAATT AAAATT AAAATT
* * * * * * *
19409090 AAAATC AAAGTT ACAATT AAAATT AACATC AACATT ATAATT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
19409138 A
1 A
19409139 TGGGCCTTTA
Statistics
Matches: 69, Mismatches: 20, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
5 5 0.07
6 59 0.86
7 5 0.07
ACGTcount: A:0.61, C:0.10, G:0.01, T:0.28
Consensus pattern (6 bp):
AAAATT
Found at i:19409135 original size:24 final size:23
Alignment explanation
Indices: 19409043--19409138 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 23
19409033 CCAAAATCAA
* * *
19409043 AAAAT-AAAATAAAATCACAATT
1 AAAATCAAATTAAAATTAAAATT
*
19409065 AAAATCCAAAATTAAAATTAAACTT
1 AAAAT-C-AAATTAAAATTAAAATT
*
19409090 AAAATCAAAGTTACAATTAAAATT
1 AAAATCAAA-TTAAAATTAAAATT
* *
19409114 AACATCAACATTATAATTAAAATT
1 AAAATCAA-ATTAAAATTAAAATT
19409138 A
1 A
19409139 TGGGCCTTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
22 5 0.08
23 3 0.05
24 34 0.56
25 19 0.31
ACGTcount: A:0.60, C:0.10, G:0.01, T:0.28
Consensus pattern (23 bp):
AAAATCAAATTAAAATTAAAATT
Found at i:19411755 original size:3 final size:3
Alignment explanation
Indices: 19411747--19411780 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
19411737 ATTTATTTAT
19411747 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19411781 ATTTTTGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19416742 original size:20 final size:20
Alignment explanation
Indices: 19416695--19416744 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
19416685 TTAATTTATT
* *
19416695 TTTAAAAATTTTAATATGAA
1 TTTAAATATTTTAATATAAA
*
19416715 TTTTAATATATTTAA-ATAAA
1 TTTAAATAT-TTTAATATAAA
19416735 TTTAAATATT
1 TTTAAATATT
19416745 AAATAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 19 0.76
21 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTAAATATTTTAATATAAA
Found at i:19416748 original size:17 final size:19
Alignment explanation
Indices: 19416716--19416750 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
19416706 TAATATGAAT
19416716 TTTAATATATTTAAATAAA
1 TTTAATATATTTAAATAAA
19416735 TTTAA-ATA-TTAAATAA
1 TTTAATATATTTAAATAA
19416751 TTATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTAATATATTTAAATAAA
Found at i:19417441 original size:30 final size:30
Alignment explanation
Indices: 19417396--19417478 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 30
19417386 TTAATCATCA
19417396 AATTTATAATAAAATTATATTTTTTAA-TATTT
1 AATTTAT-A-AAAATTATATTTTTTAATTA-TT
19417428 AA-TTACTAAAAATT-T-TTGTTTTAATTATT
1 AATTTA-TAAAAATTATATT-TTTTAATTATT
*
19417457 AATTTATAAAAGATAATATTTT
1 AATTTATAAAA-ATTATATTTT
19417479 GATCACGACA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
28 2 0.05
29 16 0.37
30 13 0.30
31 7 0.16
32 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (30 bp):
AATTTATAAAAATTATATTTTTTAATTATT
Found at i:19418964 original size:24 final size:23
Alignment explanation
Indices: 19418936--19418994 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
19418926 TTTTATTAGA
*
19418936 ATTTTAAATTATATTATTA-TATT
1 ATTTTAAATTATATCATTATTA-T
* *
19418959 ATTTTTATATTATATCATTCTTAT
1 A-TTTTAAATTATATCATTATTAT
19418983 ATTTTAAATTAT
1 ATTTTAAATTAT
19418995 TAGAGATACC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 11 0.37
24 17 0.57
25 2 0.07
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTAAATTATATCATTATTAT
Found at i:19418971 original size:16 final size:16
Alignment explanation
Indices: 19418950--19418985 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19418940 TAAATTATAT
* *
19418950 TATTATATTATTTTTA
1 TATTATATCATTCTTA
19418966 TATTATATCATTCTTA
1 TATTATATCATTCTTA
19418982 TATT
1 TATT
19418986 TTAAATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTATATCATTCTTA
Found at i:19420190 original size:18 final size:18
Alignment explanation
Indices: 19420164--19420291 Score: 102
Period size: 18 Copynumber: 7.7 Consensus size: 18
19420154 AGTATAATTT
*
19420164 TATTTATAAATAATATTA
1 TATTAATAAATAATATTA
19420182 TATTAATAAAT-A-A-TA
1 TATTAATAAATAATATTA
*
19420197 TATTAATAAATATTATTA
1 TATTAATAAATAATATTA
19420215 TA--AAT--A-AATATTA
1 TATTAATAAATAATATTA
* *
19420228 TACTAAT--AT-AT-TAA
1 TATTAATAAATAATATTA
*
19420242 TTTTAATAAATAATATTA
1 TATTAATAAATAATATTA
19420260 TATTAATAAATAATA-TA
1 TATTAATAAATAATATTA
19420277 CTATTAATATAATAA
1 -TATTAATA-AATAA
19420292 AATAAATAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
13 8 0.09
14 8 0.09
15 19 0.21
16 6 0.07
17 6 0.07
18 38 0.42
19 5 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTAATAAATAATATTA
Found at i:19420198 original size:15 final size:15
Alignment explanation
Indices: 19420175--19420304 Score: 99
Period size: 15 Copynumber: 8.6 Consensus size: 15
19420165 ATTTATAAAT
*
19420175 AATATTATATTAATA
1 AATAATATATTAATA
19420190 AATAATATATTAATA
1 AATAATATATTAATA
* *
19420205 AATATTATTATAAATA
1 AATAATA-TATTAATA
* *
19420221 AATATTATACTAATA
1 AATAATATATTAATA
*
19420236 TATTAAT-T-TTAATA
1 -AATAATATATTAATA
19420250 AATAATATTATATTAATA
1 AAT-A-A-TATATTAATA
* *
19420268 AATAATATACTATTA
1 AATAATATATTAATA
19420283 ATATAATA-A--AATA
1 A-ATAATATATTAATA
19420296 AATAATATA
1 AATAATATA
19420305 AAGAATAATA
Statistics
Matches: 94, Mismatches: 12, Indels: 20
0.75 0.10 0.16
Matches are distributed among these distances:
12 6 0.06
13 7 0.07
14 6 0.06
15 38 0.40
16 26 0.28
17 2 0.02
18 9 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAATATATTAATA
Found at i:19420324 original size:78 final size:77
Alignment explanation
Indices: 19420159--19420324 Score: 192
Period size: 78 Copynumber: 2.1 Consensus size: 77
19420149 TTTAGAGTAT
* * **
19420159 AATTTTATTT-ATAAATAATATTATATTAATAAATAATATATTAATAAATATTATTATAAATAAA
1 AATTTT-TTTAATAAATAATATTATATTAATAAATAATATACTAATAAATAATAAAATAAATAAA
* * *
19420223 TATTATACTAATA
65 TATAAGAATAATA
* * *
19420236 TATTAATTTTAATAAATAATATTATATTAATAAATAATATACTATTAATATAATAAAATAAAT-A
1 AATT-TTTTTAATAAATAATATTATATTAATAAATAATATACTAATAA-ATAATAAAATAAATAA
19420300 ATATAAAGAATAATA
64 ATAT-AAGAATAATA
19420315 AATTTTTTTA
1 AATTTTTTTA
19420325 TTTTAATAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
77 6 0.08
78 46 0.63
79 21 0.29
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (77 bp):
AATTTTTTTAATAAATAATATTATATTAATAAATAATATACTAATAAATAATAAAATAAATAAAT
ATAAGAATAATA
Found at i:19420453 original size:27 final size:26
Alignment explanation
Indices: 19420396--19420454 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
19420386 TTTTTTAATA
*
19420396 TTAATA-ATTCTAACAATAAATATTT
1 TTAATATATTCTAACAATAAAAATTT
* * *
19420421 TCAATATATTTTAATAATAAAAAATTT
1 TTAATATATTCTAACAAT-AAAAATTT
19420448 TTAATAT
1 TTAATAT
19420455 TTTAGTAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 5 0.19
26 9 0.33
27 13 0.48
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (26 bp):
TTAATATATTCTAACAATAAAAATTT
Found at i:19420610 original size:13 final size:14
Alignment explanation
Indices: 19420580--19420609 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19420570 TATAAATATA
19420580 TTTCAAAAAGCATT
1 TTTCAAAAAGCATT
*
19420594 TTTCAAAAATCATT
1 TTTCAAAAAGCATT
19420608 TT
1 TT
19420610 CTATGAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.43
Consensus pattern (14 bp):
TTTCAAAAAGCATT
Found at i:19421352 original size:2 final size:2
Alignment explanation
Indices: 19421345--19421396 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
19421335 TCTTTTACTC
* * *
19421345 TA TA TA TA TG TG TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19421387 TA TA TA TA TA
1 TA TA TA TA TA
19421397 ATGATCCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19424307 original size:15 final size:16
Alignment explanation
Indices: 19424287--19424328 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
19424277 ATTTTCAGAA
19424287 TTTTGGATTTTAAA-G
1 TTTTGGATTTTAAAGG
19424302 TTTTGGA-TTTAAAGG
1 TTTTGGATTTTAAAGG
*
19424317 TTTAGGATTTTA
1 TTTTGGATTTTA
19424329 GATTTTAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 14 0.58
16 4 0.17
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.52
Consensus pattern (16 bp):
TTTTGGATTTTAAAGG
Found at i:19424500 original size:3 final size:3
Alignment explanation
Indices: 19424474--19424553 Score: 92
Period size: 3 Copynumber: 27.3 Consensus size: 3
19424464 TTATGAAAAC
* * * * *
19424474 TTA TTG TTA TTA TTG TTA AT- TTA TTA TTG TT- TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
19424520 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19424554 CTTTTTTTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
2 3 0.05
3 61 0.95
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19424696 original size:3 final size:3
Alignment explanation
Indices: 19424688--19424719 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19424678 TATTTTTTAG
19424688 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
19424720 CTTTTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:19424710 original size:166 final size:166
Alignment explanation
Indices: 19424522--19424885 Score: 608
Period size: 166 Copynumber: 2.2 Consensus size: 166
19424512 TATTATTATT
*
19424522 ATTATTATTATTATTATTATTATTATTTTTATCTTTTTTTAATATTTTTT-ATATAATTTTTCAA
1 ATTATTATTATTATTATTATTATTATTATTATCTTTTTTTAATATTTTTTAATATAATTTTTCAA
*
19424586 CATCTAGGC-AGAATTACATTTTAAGGTTTAAAGTTTTT-TTTCCCTCCAACATCTAGGTAGGAA
66 CATCTAGGCGA-AATTACATTTTAAGGTTTAAAGTTTTTATTT-ACTCCAACATCTAGGTAGGAA
19424649 AAATTAAAAAAATATATTTTATTCTTGTTTATTTTTTAG
129 AAATTAAAAAAA-ATATTTTATTCTTGTTTATTTTTTAG
19424688 ATTATTATTATTATTATTATTATTATTATTATCTTTTTTTAATATTTTTTAATATAATTTTTCAA
1 ATTATTATTATTATTATTATTATTATTATTATCTTTTTTTAATATTTTTTAATATAATTTTTCAA
* * * *
19424753 CCTCTAGGCGAAATTATATTTTAAGGTTTGAAGTTTTTATTTATTCCAACATCTAGGTAGGAAAA
66 CATCTAGGCGAAATTACATTTTAAGGTTTAAAGTTTTTATTTACTCCAACATCTAGGTAGGAAAA
*
19424818 ATTAAAAAAAATATTTTATTCTTTTTTATTTTTTAG
131 ATTAAAAAAAATATTTTATTCTTGTTTATTTTTTAG
*
19424854 ATTATTATTATTATTATTATTATTGTTATTAT
1 ATTATTATTATTATTATTATTATTATTATTAT
19424886 TATTATTATT
Statistics
Matches: 187, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
166 105 0.56
167 78 0.42
168 4 0.02
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (166 bp):
ATTATTATTATTATTATTATTATTATTATTATCTTTTTTTAATATTTTTTAATATAATTTTTCAA
CATCTAGGCGAAATTACATTTTAAGGTTTAAAGTTTTTATTTACTCCAACATCTAGGTAGGAAAA
ATTAAAAAAAATATTTTATTCTTGTTTATTTTTTAG
Found at i:19424862 original size:3 final size:3
Alignment explanation
Indices: 19424854--19424901 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
19424844 TATTTTTTAG
*
19424854 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19424902 TTAGCATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19426507 original size:37 final size:37
Alignment explanation
Indices: 19426467--19426702 Score: 205
Period size: 37 Copynumber: 6.4 Consensus size: 37
19426457 ACAGATAAAT
*
19426467 GGGATAACACTGTGAGTCGAAAAGTAAAAAATCGATT
1 GGGATAACACTGTGAGTCGAAAAGTAAAAAATCGATC
* * *
19426504 GGGATAACACCGTAAGTCAAAAAGTAAGAAAA-CGATC
1 GGGATAACACTGTGAGTCGAAAAGTAA-AAAATCGATC
* * *
19426541 GAGACAACACTGCGAGTC-AAGAAGTAAAAAATCGATC
1 GGGATAACACTGTGAGTCGAA-AAGTAAAAAATCGATC
** *
19426578 GGGATAACA-TCACGAGTCAAAAAGTAAGAAAAT-GATC
1 GGGATAACACT-GTGAGTCGAAAAGTAA-AAAATCGATC
* * * *
19426615 GGGACAACACAGTGAGTCGAAAAGTAAAGAATC-AAC
1 GGGATAACACTGTGAGTCGAAAAGTAAAAAATCGATC
* * ** *
19426651 GAGATAACACCGCAAGTCGAGAAA-TAAAGAATCGATC
1 GGGATAACACTGTGAGTCGA-AAAGTAAAAAATCGATC
*
19426688 GAGATAACACTGTGA
1 GGGATAACACTGTGA
19426703 ATCAAAATTA
Statistics
Matches: 161, Mismatches: 28, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
36 37 0.23
37 113 0.70
38 11 0.07
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.15
Consensus pattern (37 bp):
GGGATAACACTGTGAGTCGAAAAGTAAAAAATCGATC
Found at i:19426570 original size:74 final size:73
Alignment explanation
Indices: 19426472--19426702 Score: 265
Period size: 74 Copynumber: 3.1 Consensus size: 73
19426462 TAAATGGGAT
*
19426472 AACACTGTGAGTCGAAAAGTAAAAAATCGATTGGGATAACACCGTAAGTCAAAAAGTAAGAAAAC
1 AACACTGTGAGTCGAAAAGTAAAAAATCGATCGGGATAACACCG-AAGTCAAAAAGTAAGAAAAC
19426537 GATCGAGAC
65 GATCGAGAC
*
19426546 AACACTGCGAGTC-AAGAAGTAAAAAATCGATCGGGATAACATCACG-AGTCAAAAAGTAAGAAA
1 AACACTGTGAGTCGAA-AAGTAAAAAATCGATCGGGATAACA-C-CGAAGTCAAAAAGTAAGAAA
* *
19426609 ATGATCGGGAC
63 ACGATCGAGAC
* * * * *
19426620 AACACAGTGAGTCGAAAAGTAAAGAATC-AACGAGATAACACCGCAAGTCGAGAAA-TAA-AGAA
1 AACACTGTGAGTCGAAAAGTAAAAAATCGATCGGGATAACACCG-AAGTC-AAAAAGTAAGA-AA
* *
19426682 TCGATCGAGAT
63 ACGATCGAGAC
19426693 AACACTGTGA
1 AACACTGTGA
19426703 ATCAAAATTA
Statistics
Matches: 134, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
71 2 0.01
72 2 0.01
73 37 0.28
74 88 0.66
75 3 0.02
76 2 0.01
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (73 bp):
AACACTGTGAGTCGAAAAGTAAAAAATCGATCGGGATAACACCGAAGTCAAAAAGTAAGAAAACG
ATCGAGAC
Found at i:19426708 original size:110 final size:111
Alignment explanation
Indices: 19426469--19426709 Score: 265
Period size: 110 Copynumber: 2.2 Consensus size: 111
19426459 AGATAAATGG
* * * *
19426469 GATAACACTGTGAGTCGAAAAGTAAAAAATCGATTGGGATAACACCGTAAGTCAAAAAGTAAGAA
1 GATAACACTGTGAGTCAAAAAGTAAAAAATCGATCGGGACAACACAGTAAGTCAAAAAGTAAGAA
* * * * *
19426534 AACGATCGAGACAACACTGCGAGTCAAGAAGTAAAAAATCGATCGG
66 AACGAACGAGACAACACCGCAAGTCAAGAAATAAAAAATCGATCGA
** * *
19426580 GATAACA-TCACGAGTCAAAAAGTAAGAAAAT-GATCGGGACAACACAGTGAGTCGAAAAGTAA-
1 GATAACACT-GTGAGTCAAAAAGTAA-AAAATCGATCGGGACAACACAGTAAGTCAAAAAGTAAG
* * * *
19426642 AGAATC-AACGAGATAACACCGCAAGTCGAGAAATAAAGAATCGATCGA
64 A-AAACGAACGAGACAACACCGCAAGTCAAGAAATAAAAAATCGATCGA
*
19426690 GATAACACTGTGAATCAAAA
1 GATAACACTGTGAGTCAAAA
19426710 TTATGCCCGC
Statistics
Matches: 106, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
110 51 0.48
111 50 0.47
112 5 0.05
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (111 bp):
GATAACACTGTGAGTCAAAAAGTAAAAAATCGATCGGGACAACACAGTAAGTCAAAAAGTAAGAA
AACGAACGAGACAACACCGCAAGTCAAGAAATAAAAAATCGATCGA
Found at i:19427081 original size:130 final size:131
Alignment explanation
Indices: 19426910--19427164 Score: 334
Period size: 130 Copynumber: 1.9 Consensus size: 131
19426900 ACCGTAAGTC
* *
19426910 AAAATTAAAGAATCGATCGAGATAATATCGCGAATCAAAATTATGC-CTGGAGATCTTAAAGATT
1 AAAAATAAAGAATCGATCGAGATAACATCGCGAATCAAAATTATGCTC-GGAGATCTTAAAGATT
** * * * * *
19426974 ATGCCT-AGGTCTTAGAAATCATGTCCGGAGGTTTTACAGAATCGATTAGGACAACATCGCAAGT
65 ATGCCTAAAATCTTACAAATCATGCCCAGAGGTTTTACAAAATCGATCAGGACAACATCGCAAGT
19427038 TA
130 TA
* * * *
19427040 AAAAATAAAGAATCGATCGGGATAACATCGTGAATCGAAATTATGCTCGGAGGTCTTAAAGATTA
1 AAAAATAAAGAATCGATCGAGATAACATCGCGAATCAAAATTATGCTCGGAGATCTTAAAGATTA
* * *
19427105 TGTCTGAAAATCTTACAAATCATGCCCAGAGGTTTTACAAAATTGATCAGGATAACATCG
66 TGCCT-AAAATCTTACAAATCATGCCCAGAGGTTTTACAAAATCGATCAGGACAACATCG
19427165 TGAATCGAAA
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
130 61 0.58
131 1 0.01
132 44 0.42
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (131 bp):
AAAAATAAAGAATCGATCGAGATAACATCGCGAATCAAAATTATGCTCGGAGATCTTAAAGATTA
TGCCTAAAATCTTACAAATCATGCCCAGAGGTTTTACAAAATCGATCAGGACAACATCGCAAGTT
A
Found at i:19427095 original size:239 final size:240
Alignment explanation
Indices: 19426653--19427097 Score: 619
Period size: 239 Copynumber: 1.9 Consensus size: 240
19426643 GAATCAACGA
*
19426653 GATAACACCGCAAGTCGAGAAATAAAGAATCGATCGAGATAACACTGTGAATCAAAATTATGCCC
1 GATAACACCGCAAGTCGAGAAATAAAGAATCGATCGAGATAACACTGCGAATCAAAATTATGCCC
* * * *
19426718 GCAGTTCTTAAAGATTATGCTTGGAGGTTTTAAAATCATACCCGGAGGTCTTACAGAATTGACTA
66 GCAGATCTTAAAGATTATGCCT-GAGGTCTTAAAATCATACCCGGAGGTCTTACAGAATCGACTA
* *
19426783 GGACAACATCACAAGTCGAAAAATAAAGAATAGATCAGGATAATATCACGAATCAAAATTATGCT
130 GGACAACATCACAAGTCAAAAAATAAAGAATAGATCAGGATAACATCACGAATCAAAATTATGCT
19426848 CGGAGGTCTTACAAATCATACTTGGAGGTCTTACAAAATAGATCGG
195 CGGAGGTCTTACAAATCATACTTGGAGGTCTTACAAAATAGATCGG
* * *
19426894 GATAATACCGTAAGTC-A-AAATTAAAGAATCGATCGAGATAATA-TCGCGAATCAAAATTATGC
1 GATAACACCGCAAGTCGAGAAA-TAAAGAATCGATCGAGATAACACT-GCGAATCAAAATTATGC
* * ** * *
19426956 CTGGAGATCTTAAAGATTATGCCT-AGGTCTTAGAAATCATGTCCGGAGGTTTTACAGAATCGAT
64 CCGCAGATCTTAAAGATTATGCCTGAGGTCTTA-AAATCATACCCGGAGGTCTTACAGAATCGAC
* * * * ** *
19427020 TAGGACAACATCGCAAGTTAAAAAATAAAGAATCGATCGGGATAACATCGTGAATCGAAATTATG
128 TAGGACAACATCACAAGTCAAAAAATAAAGAATAGATCAGGATAACATCACGAATCAAAATTATG
19427085 CTCGGAGGTCTTA
193 CTCGGAGGTCTTA
19427098 AAGATTATGT
Statistics
Matches: 178, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
238 7 0.04
239 99 0.56
240 58 0.33
241 14 0.08
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (240 bp):
GATAACACCGCAAGTCGAGAAATAAAGAATCGATCGAGATAACACTGCGAATCAAAATTATGCCC
GCAGATCTTAAAGATTATGCCTGAGGTCTTAAAATCATACCCGGAGGTCTTACAGAATCGACTAG
GACAACATCACAAGTCAAAAAATAAAGAATAGATCAGGATAACATCACGAATCAAAATTATGCTC
GGAGGTCTTACAAATCATACTTGGAGGTCTTACAAAATAGATCGG
Found at i:19427387 original size:110 final size:110
Alignment explanation
Indices: 19427183--19427388 Score: 279
Period size: 110 Copynumber: 1.9 Consensus size: 110
19427173 AATTATGCCC
* * * * *
19427183 GGAGGTCTTACATAATTGACTAGGCCAACACCGTAAGTTGAAAAAAAAAGAATCGATCGGGATAA
1 GGAGGTCTTACAAAATTGACTAGGACAACACCGCAAGTTCAAAAAAAAAGAATCGATCGAGATAA
* **
19427248 CATCGTAAATCAAAATTATACCCGGAGGTCTAAGAAATCATGTCT
66 CATCGCAAATCAAAATTATACCCAAAGGTCTAAGAAATCATGTCT
* *
19427293 GGAGGTCTTACAAAATTGATTGGGACAACACCGCAAG-TCAAAAAATAAAGAATCGATCGAGATA
1 GGAGGTCTTACAAAATTGACTAGGACAACACCGCAAGTTCAAAAAA-AAAGAATCGATCGAGATA
* **
19427357 ACATCGCGAATCAAAATTATGTCCAAAGGTCT
65 ACATCGCAAATCAAAATTATACCCAAAGGTCT
19427389 TATAGAATTC
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
109 7 0.09
110 75 0.91
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (110 bp):
GGAGGTCTTACAAAATTGACTAGGACAACACCGCAAGTTCAAAAAAAAAGAATCGATCGAGATAA
CATCGCAAATCAAAATTATACCCAAAGGTCTAAGAAATCATGTCT
Found at i:19427478 original size:88 final size:88
Alignment explanation
Indices: 19427295--19427465 Score: 231
Period size: 88 Copynumber: 1.9 Consensus size: 88
19427285 TCATGTCTGG
* * * * *
19427295 AGGTCTTACAAAATTGATTGGGACAACACCGCAAGTCAAAAAATAAAGAATCGATCGAGATAACA
1 AGGTCTTATAGAATTCACTGGGACAACACCGCAAGTAAAAAAATAAAGAATCGATCGAGATAACA
* *
19427360 TCGCGAATCAAAATTATGTCCAA
66 TCACAAATCAAAATTATGTCCAA
19427383 AGGTCTTATAGAATTCACTGGGACAACACCGCAAG-AAGAAAAATAAAGAATCGATC-AGGATAA
1 AGGTCTTATAGAATTCACTGGGACAACACCGCAAGTAA-AAAAATAAAGAATCGATCGA-GATAA
19427446 CA-CTACAAATCAAAATTATG
64 CATC-ACAAATCAAAATTATG
19427466 CCTAGAAGTC
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
87 3 0.04
88 70 0.96
ACGTcount: A:0.46, C:0.18, G:0.17, T:0.20
Consensus pattern (88 bp):
AGGTCTTATAGAATTCACTGGGACAACACCGCAAGTAAAAAAATAAAGAATCGATCGAGATAACA
TCACAAATCAAAATTATGTCCAA
Found at i:19427621 original size:22 final size:22
Alignment explanation
Indices: 19427596--19427637 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
19427586 ATCAAAATTA
*
19427596 TGCTCGGAGGTCTTACAAATCT
1 TGCTCGAAGGTCTTACAAATCT
19427618 TGCTCGAAGGTCTTACAAAT
1 TGCTCGAAGGTCTTACAAAT
19427638 TTTAAAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (22 bp):
TGCTCGAAGGTCTTACAAATCT
Found at i:19427933 original size:41 final size:41
Alignment explanation
Indices: 19427867--19428016 Score: 203
Period size: 41 Copynumber: 3.7 Consensus size: 41
19427857 TTTGAAGAAA
* *
19427867 GGTTCCTCCTAAACAAAGGCTTTGAAATCTTGATTAAAATT
1 GGTTCCTCTTAAACAGAGGCTTTGAAATCTTGATTAAAATT
** *
19427908 GGTTTTTCTTAAACAGAGGCTTTGAAATCTTGATTGAAATT
1 GGTTCCTCTTAAACAGAGGCTTTGAAATCTTGATTAAAATT
19427949 GGTTCCTCTTAAACAGAGGCTTTGAAATCTTGATTGAAAA-T
1 GGTTCCTCTTAAACAGAGGCTTTGAAATCTTGATT-AAAATT
* * * *
19427990 GATTCCTTTTAAATAGAGGCTTAGAAA
1 GGTTCCTCTTAAACAGAGGCTTTGAAA
19428017 CTTTAAAACT
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 93 0.97
42 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (41 bp):
GGTTCCTCTTAAACAGAGGCTTTGAAATCTTGATTAAAATT
Found at i:19436275 original size:16 final size:17
Alignment explanation
Indices: 19436250--19436282 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19436240 CTTCATTTAC
*
19436250 TATTATATCTTTTTATT
1 TATTATATCTTATTATT
19436267 TATTA-ATCTTATTATT
1 TATTATATCTTATTATT
19436283 AATGTGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTATATCTTATTATT
Found at i:19436519 original size:15 final size:15
Alignment explanation
Indices: 19436499--19436539 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
19436489 ATTTTCAAAA
19436499 TTTTGGAGTTTAAG-G
1 TTTTGGA-TTTAAGAG
19436514 TTTTGGATTTAAGAG
1 TTTTGGATTTAAGAG
*
19436529 TTTAGGATTTA
1 TTTTGGATTTA
19436540 GGATTTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (15 bp):
TTTTGGATTTAAGAG
Found at i:19436523 original size:22 final size:23
Alignment explanation
Indices: 19436498--19436554 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
19436488 GATTTTCAAA
*
19436498 ATTTTGGAGTTTAAGG-TTTTGG
1 ATTTTGGAGTTTAAGGATTTAGG
**
19436520 ATTTAAGAGTTT-AGGATTTAGG
1 ATTTTGGAGTTTAAGGATTTAGG
19436542 ATTTTAGG-GTTTA
1 ATTTT-GGAGTTTA
19436555 GATTTTTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
21 3 0.11
22 23 0.85
23 1 0.04
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (23 bp):
ATTTTGGAGTTTAAGGATTTAGG
Found at i:19436555 original size:22 final size:21
Alignment explanation
Indices: 19436504--19436559 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
19436494 CAAAATTTTG
* *
19436504 GAGTTTAAGGTTTTGGATTTAA
1 GAGTTT-AGATTTAGGATTTAA
*
19436526 GAGTTTAGGATTTAGGATTTTA
1 GAGTTTA-GATTTAGGATTTAA
*
19436548 GGGTTTAGATTT
1 GAGTTTAGATTT
19436560 TTTTATCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (21 bp):
GAGTTTAGATTTAGGATTTAA
Found at i:19436561 original size:15 final size:15
Alignment explanation
Indices: 19436514--19436560 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
19436504 GAGTTTAAGG
*
19436514 TTTT-GGATTTAAGA
1 TTTTAGGATTTAGGA
*
19436528 GTTTAGGATTTAGGA
1 TTTTAGGATTTAGGA
*
19436543 TTTTAGGGTTTA-GA
1 TTTTAGGATTTAGGA
19436557 TTTT
1 TTTT
19436561 TTTATCTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 9 0.32
15 19 0.68
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (15 bp):
TTTTAGGATTTAGGA
Found at i:19436698 original size:3 final size:3
Alignment explanation
Indices: 19436686--19436753 Score: 77
Period size: 3 Copynumber: 23.3 Consensus size: 3
19436676 TTTTGAAAAC
* * * *
19436686 TTA TTG TTA TTA TTG TTA AT- TTA TTA TTG TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
19436732 TTA TTA TTA TTA TTA CTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
19436754 CTTTTTTTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 3 0.06
3 51 0.94
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:19436723 original size:14 final size:14
Alignment explanation
Indices: 19436692--19436742 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
19436682 AAACTTATTG
*
19436692 TTATTATTG-TTAA
1 TTATTATTGTTTTA
19436705 TTTATTATTGTTTTA
1 -TTATTATTGTTTTA
*
19436720 TTATTATTATTATTA
1 TTATTATTGTT-TTA
19436735 TTATTATT
1 TTATTATT
19436743 ATTACTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 19 0.58
15 14 0.42
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (14 bp):
TTATTATTGTTTTA
Found at i:19436897 original size:3 final size:3
Alignment explanation
Indices: 19436862--19436919 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
19436852 AAATAAATAA
* * *
19436862 ATT ATT -TT ATT CTT GTT ATT ATT -TT -TT A-G ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
19436906 ATT ATT ATT GTT AT
1 ATT ATT ATT ATT AT
19436920 AGCATTTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
2 7 0.16
3 38 0.84
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19438533 original size:2 final size:2
Alignment explanation
Indices: 19438526--19438550 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19438516 ATTTAGAAAC
19438526 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
19438551 CATAGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19444442 original size:18 final size:18
Alignment explanation
Indices: 19444419--19444455 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
19444409 TAATGAAATA
* *
19444419 AAACATTCATATATTTAG
1 AAACATACATATATATAG
19444437 AAACATACATATATATAG
1 AAACATACATATATATAG
19444455 A
1 A
19444456 TTCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
AAACATACATATATATAG
Found at i:19445799 original size:18 final size:17
Alignment explanation
Indices: 19445772--19445805 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
19445762 GCAAATGCAC
*
19445772 ATAATTTTTATATTTAAG
1 ATAATATTTA-ATTTAAG
19445790 ATAATATTTAATTTAA
1 ATAATATTTAATTTAA
19445806 TTCATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATAATATTTAATTTAAG
Found at i:19446463 original size:21 final size:20
Alignment explanation
Indices: 19446430--19446468 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
19446420 TTTTATCACC
*
19446430 GTAATAGAATAGAGTTTAAA
1 GTAATAGAATAGAATTTAAA
19446450 GTAATAGCAATAGAATTTA
1 GTAATAG-AATAGAATTTA
19446469 TATATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.31
Consensus pattern (20 bp):
GTAATAGAATAGAATTTAAA
Found at i:19446875 original size:26 final size:26
Alignment explanation
Indices: 19446824--19446880 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
19446814 TTGAATATGA
* *
19446824 TTTTATCTATTTATTTAAATATATAT
1 TTTTATCTACTTATTTAAATAGATAT
* *
19446850 TTTTATCTACTTATTTAATTGGATAT
1 TTTTATCTACTTATTTAAATAGATAT
19446876 TTTTA
1 TTTTA
19446881 AAAAATGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (26 bp):
TTTTATCTACTTATTTAAATAGATAT
Found at i:19456634 original size:21 final size:22
Alignment explanation
Indices: 19456608--19456658 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
19456598 TAAAGTTATT
19456608 TATAAATTTTA-AAAATAATTA
1 TATAAATTTTATAAAATAATTA
* *
19456629 TATAAATTATATAAATTAATTA
1 TATAAATTTTATAAAATAATTA
19456651 T-TAAATTT
1 TATAAATTT
19456659 ATTTTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATAAATTTTATAAAATAATTA
Found at i:19457117 original size:11 final size:11
Alignment explanation
Indices: 19457103--19457176 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
19457093 ATAATAAAAT
19457103 TAAAATAATAA
1 TAAAATAATAA
*
19457114 TAAATTAATAA
1 TAAAATAATAA
**
19457125 TATTATAATTAA
1 TAAAATAA-TAA
* *
19457137 -AAAATTATTA
1 TAAAATAATAA
19457147 TAAATATAATTAA
1 TAAA-ATAA-TAA
19457160 TAAAATAAATAA
1 TAAAAT-AATAA
19457172 -AAAAT
1 TAAAAT
19457177 TTATATTAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
10 2 0.04
11 27 0.56
12 11 0.23
13 8 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:19457173 original size:35 final size:33
Alignment explanation
Indices: 19457104--19457191 Score: 86
Period size: 35 Copynumber: 2.6 Consensus size: 33
19457094 TAATAAAATT
* ** *
19457104 AAAATAATAATAAATTAATAATATTATAATTAA
1 AAAATTATAATAAATTAATAATAAAATAAATAA
*
19457137 AAAATTATTATAAATATAATTAATAAAATAAATAA
1 AAAATTATAATAAAT-TAA-TAATAAAATAAATAA
* *
19457172 AAAATTTATATTAATTTAAT
1 AAAA-TTATAATAAATTAAT
19457192 TTTATTAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
33 13 0.30
34 4 0.09
35 19 0.43
36 8 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
AAAATTATAATAAATTAATAATAAAATAAATAA
Done.