Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008341.1 Hibiscus syriacus cultivar Beakdansim tig00111067_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: 1248125
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:293442 original size:140 final size:140
Alignment explanation
Indices: 293101--293539 Score: 585
Period size: 140 Copynumber: 3.1 Consensus size: 140
293091 AATCCATGAT
* *
293101 TTAAACTGCATTAAAGGATGCATTAAGGCATGAAATGATGCCATAATTTAAAATGCATGAAAGGA
1 TTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATAATTTAAAATGCATGAAAGGA
* * *
293166 TGCCATAATTTAAAATGCGTGAAAGGATGCCATAATTTAAAATGCATGAAA-GAATGCATTAAGA
66 TG-C---A-TT--AAGGCATGAAAGGATGCCATAATTTAAAATGCATGAAATG-ATGCATTAAGG
* * ***
293230 TATGAAATGATTTAATAA
123 CATGAAAGGATGCCATAA
* * * * * *
293248 ATGATATGCATGAAAGGATTCATTAAGGCATGAAAGGATGTCATAATTTAAAATGCATGAAAGGA
1 TTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATAATTTAAAATGCATGAAAGGA
* *
293313 TGCATTAAGGCATGAAAGGATGCCATGATTTAAAATGCATGAAATGATTCATTAAGGCATGAAAG
66 TGCATTAAGGCATGAAAGGATGCCATAATTTAAAATGCATGAAATGATGCATTAAGGCATGAAAG
293378 GATGCCATAA
131 GATGCCATAA
293388 TTTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATAATTT-AAATGCATGAAAGG
1 -TTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATAATTTAAAATGCATGAAAGG
* *
293452 ATGCATTAAGGCATGAAAGGATGCCAAAATTTTAAAATGCATGAAATGATGCATTAAGGCATAAA
65 ATGCATTAAGGCATGAAAGGATGCCATAA-TTTAAAATGCATGAAATGATGCATTAAGGCATGAA
*
293517 AGGATGACATAA
129 AGGATGCCATAA
293529 TTAAAATGCAT
1 TTAAAATGCAT
293540 AAATAAATGG
Statistics
Matches: 260, Mismatches: 29, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
140 109 0.42
141 88 0.34
142 2 0.01
143 1 0.00
146 1 0.00
147 59 0.23
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (140 bp):
TTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATAATTTAAAATGCATGAAAGGA
TGCATTAAGGCATGAAAGGATGCCATAATTTAAAATGCATGAAATGATGCATTAAGGCATGAAAG
GATGCCATAA
Found at i:293474 original size:20 final size:20
Alignment explanation
Indices: 293255--293475 Score: 127
Period size: 20 Copynumber: 9.7 Consensus size: 20
293245 TAAATGATAT
*
293255 GCATGAAAGGATTCATTAAG
1 GCATGAAAGGATGCATTAAG
*
293275 GCATGAAAGGATGTCATAATTTAAAAT
1 GCATGAAAGGATG-C---A-TT--AAG
293302 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
293322 GCATGAAAGGATGCCATGATTTAAAAT
1 GCATGAAAGGATG-C---A-TT--AAG
* *
293349 GCATGAAATGATTCATTAAG
1 GCATGAAAGGATGCATTAAG
*
293369 GCATGAAAGGATGCCATAATTTAAAAT
1 GCATGAAAGGATG-C---A-TT--AAG
293396 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
293416 GCATGAAATGATGCCATAATTTAAAT
1 GCATGAAAGGATG-C---A-TT-AAG
293442 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
293462 GCATGAAAGGATGC
1 GCATGAAAGGATGC
293476 CAAAATTTTA
Statistics
Matches: 159, Mismatches: 15, Indels: 54
0.70 0.07 0.24
Matches are distributed among these distances:
20 70 0.44
21 6 0.04
22 7 0.04
23 3 0.02
24 4 0.03
25 9 0.06
26 17 0.11
27 43 0.27
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.25
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:306005 original size:19 final size:19
Alignment explanation
Indices: 305981--306051 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 19
305971 TGCAAAAATG
305981 GTATCGATACCATAATAGA
1 GTATCGATACCATAATAGA
* *
306000 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATA--ATAG-A
* *
306022 GTATCGATACCATGATAGGG
1 GTATCGATACCATAATA-GA
306042 GTATCGATAC
1 GTATCGATAC
306052 TGAGGAGCCA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
19 13 0.31
20 12 0.29
21 4 0.10
22 13 0.31
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (19 bp):
GTATCGATACCATAATAGA
Found at i:307885 original size:20 final size:20
Alignment explanation
Indices: 307860--307941 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 20
307850 AATTTAAGAT
307860 GCATGAAAGAATGCATTAAG
1 GCATGAAAGAATGCATTAAG
*
307880 GCATGAAAGGATAT-CATAATTTAAAAT
1 GCATGAAA-GA-ATGC---A-TT--AAG
*
307907 GCATGAAAGGATGCATTAAG
1 GCATGAAAGAATGCATTAAG
307927 GCATGAAAGAATGCA
1 GCATGAAAGAATGCA
307942 ATAATTTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
20 24 0.49
21 3 0.06
22 4 0.08
23 1 0.02
24 1 0.02
25 4 0.08
26 2 0.04
27 10 0.20
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22
Consensus pattern (20 bp):
GCATGAAAGAATGCATTAAG
Found at i:307921 original size:47 final size:46
Alignment explanation
Indices: 307842--307966 Score: 171
Period size: 47 Copynumber: 2.7 Consensus size: 46
307832 TTTATAAATC
* * *
307842 GAATCCATAATTTAAGATGCATGAAAGAATGCATTAAGGCATGAAA
1 GAATGCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
307888 GGATAT-CATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
1 -GA-ATGCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
* *
307935 GAATGCAATAATTTAAAATTCATAAAAGGATG
1 GAATGC-ATAATTTAAAATGCATGAAAGGATG
307967 TCATAATTTA
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
45 2 0.03
46 3 0.04
47 64 0.90
48 2 0.03
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.26
Consensus pattern (46 bp):
GAATGCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
Found at i:307993 original size:27 final size:25
Alignment explanation
Indices: 307880--308115 Score: 153
Period size: 27 Copynumber: 9.6 Consensus size: 25
307870 ATGCATTAAG
*
307880 GCATGAAAGGATATCATAATTTAAAAT
1 GCATGAAAGGAT-GCAT-ATTTAAAAT
*
307907 GCATGAAAGGATGC--A-TT--AAG
1 GCATGAAAGGATGCATATTTAAAAT
*
307927 GCATGAAAGAATGCAATAATTTAAAAT
1 GCATGAAAGGATGC-AT-ATTTAAAAT
* *
307954 TCATAAAAGGATGTCATAATTTAAAAT
1 GCATGAAAGGATG-CAT-ATTTAAAAT
*
307981 GCATGAAAGGATGC--A-TT--AAG
1 GCATGAAAGGATGCATATTTAAAAT
* *
308001 GCATGGAATGATGCCATGATTTAAAAT
1 GCATGAAAGGATG-CAT-ATTTAAAAT
* *
308028 GTATGAAAGGATGC--A-TT--AAG
1 GCATGAAAGGATGCATATTTAAAAT
*
308048 GAATGAAAGGATGCCATATTTAAAAT
1 GCATGAAAGGATG-CATATTTAAAAT
*
308074 ACATGAAAGGATGCCATAATTT-AAAT
1 GCATGAAAGGATG-CAT-ATTTAAAAT
308100 GCATGAAAGGATGCAT
1 GCATGAAAGGATGCAT
308116 TAAGGCATGA
Statistics
Matches: 165, Mismatches: 22, Indels: 46
0.71 0.09 0.20
Matches are distributed among these distances:
20 42 0.25
21 2 0.01
22 6 0.04
23 4 0.02
24 4 0.02
25 7 0.04
26 36 0.22
27 63 0.38
28 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (25 bp):
GCATGAAAGGATGCATATTTAAAAT
Found at i:308023 original size:74 final size:74
Alignment explanation
Indices: 307885--308040 Score: 235
Period size: 74 Copynumber: 2.1 Consensus size: 74
307875 TTAAGGCATG
*
307885 AAAGGATATCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGCAATAATTTA
1 AAAGGATGTCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGCAATAATTTA
307950 AAAT-TCATA
66 AAATGT-ATA
* * *
307959 AAAGGATGTCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGGAATG-ATGCCATGATTT
1 AAAGGATGTCATAATTTAAAATGCATGAAAGGATGCATTAAGGCAT-GAAAGAATGCAATAATTT
*
308023 AAAATGTATG
65 AAAATGTATA
308033 AAAGGATG
1 AAAGGATG
308041 CATTAAGGAA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
74 70 0.93
75 5 0.07
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.27
Consensus pattern (74 bp):
AAAGGATGTCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGCAATAATTTA
AAATGTATA
Found at i:308054 original size:121 final size:120
Alignment explanation
Indices: 307846--308181 Score: 469
Period size: 121 Copynumber: 2.8 Consensus size: 120
307836 TAAATCGAAT
* * * **
307846 CCATAATTTAAGATGCATGAAAGAATGCATTAAGGCATGAAAGGATATCATAATTTAAAATGCAT
1 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATAATTTAAAATGCAT
* * *
307911 GAAAGGATGCATTAAGGCATGAAAGAATGCAATAATTTAAAATTCATAAAAGGATG
66 GAAAGGATGCATTAAGGAATGAAAGGATGCAAT-ATTTAAAATACATAAAAGGATG
* * * *
307967 TCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGGAATGATGCCATGATTTAAAATGTAT
1 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATAATTTAAAATGCAT
* *
308032 GAAAGGATGCATTAAGGAATGAAAGGATGCCATATTTAAAATACATGAAAGGATG
66 GAAAGGATGCATTAAGGAATGAAAGGATGCAATATTTAAAATACATAAAAGGATG
*
308087 CCATAATTT-AAATGCATGAAAGGATGCATTAAGGCATGAAAAT-ATGCCAAAATTTTAAAATGC
1 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATG-AAATGATGCCATAA-TTTAAAATGC
* * *
308150 ATAAAAGGATGCATTAATGAATAAAAGGATGC
64 ATGAAAGGATGCATTAAGGAATGAAAGGATGC
308182 CAGAATTAAA
Statistics
Matches: 191, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
119 36 0.19
120 69 0.36
121 86 0.45
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.26
Consensus pattern (120 bp):
CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATAATTTAAAATGCAT
GAAAGGATGCATTAAGGAATGAAAGGATGCAATATTTAAAATACATAAAAGGATG
Found at i:308079 original size:26 final size:27
Alignment explanation
Indices: 308050--308113 Score: 105
Period size: 26 Copynumber: 2.4 Consensus size: 27
308040 GCATTAAGGA
*
308050 ATGAAAGGATGCCAT-ATTTAAAATAC
1 ATGAAAGGATGCCATAATTTAAAATGC
308076 ATGAAAGGATGCCATAATTT-AAATGC
1 ATGAAAGGATGCCATAATTTAAAATGC
308102 ATGAAAGGATGC
1 ATGAAAGGATGC
308114 ATTAAGGCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 32 0.89
27 4 0.11
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (27 bp):
ATGAAAGGATGCCATAATTTAAAATGC
Found at i:308086 original size:46 final size:47
Alignment explanation
Indices: 307959--308087 Score: 188
Period size: 47 Copynumber: 2.8 Consensus size: 47
307949 AAAATTCATA
* *
307959 AAAGGATGTCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATG
1 AAAGGATGCCATAATTTAAAATGCATGAAAGGATGCATTAAGGAATG
* * * *
308006 GAATGATGCCATGATTTAAAATGTATGAAAGGATGCATTAAGGAATG
1 AAAGGATGCCATAATTTAAAATGCATGAAAGGATGCATTAAGGAATG
*
308053 AAAGGATGCCAT-ATTTAAAATACATGAAAGGATGC
1 AAAGGATGCCATAATTTAAAATGCATGAAAGGATGC
308088 CATAATTTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 21 0.29
47 51 0.71
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.26
Consensus pattern (47 bp):
AAAGGATGCCATAATTTAAAATGCATGAAAGGATGCATTAAGGAATG
Found at i:308111 original size:72 final size:75
Alignment explanation
Indices: 308010--308161 Score: 211
Period size: 72 Copynumber: 2.1 Consensus size: 75
308000 GGCATGGAAT
* * * *
308010 GATGCCATGATTTAAAATGTATGAAAGGATGCATTAAGGAATGAAAGGATGCC-ATA-TTTAAAA
1 GATGCCATAATTTAAAATGCATGAAAGGATGCATTAAGGAATGAAAAGATGCCAAAATTTTAAAA
*
308073 TACATGAAAG
66 TACATAAAAG
* *
308083 GATGCCATAATTT-AAATGCATGAAAGGATGCATTAAGGCATGAAAATATGCCAAAATTTTAAAA
1 GATGCCATAATTTAAAATGCATGAAAGGATGCATTAAGGAATGAAAAGATGCCAAAATTTTAAAA
*
308147 TGCATAAAAG
66 TACATAAAAG
308157 GATGC
1 GATGC
308162 ATTAATGAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
72 35 0.51
73 14 0.20
74 20 0.29
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (75 bp):
GATGCCATAATTTAAAATGCATGAAAGGATGCATTAAGGAATGAAAAGATGCCAAAATTTTAAAA
TACATAAAAG
Found at i:308162 original size:48 final size:46
Alignment explanation
Indices: 308075--308204 Score: 147
Period size: 48 Copynumber: 2.8 Consensus size: 46
308065 ATTTAAAATA
* * *
308075 CATGAAAGGATGCCATAATTTAAATGCATGAAAGGATGCATTAAGG
1 CATGAAAAGATGCCAAAATTTAAATGCATAAAAGGATGCATTAAGG
* *
308121 CATGAAAATATGCCAAAATTTTAAAATGCATAAAAGGATGCATTAATG
1 CATGAAAAGATGCCAAAA-TTT-AAATGCATAAAAGGATGCATTAAGG
* * *
308169 AAT-AAAAGGATGCCAGAA-TTAAATGCATAAATGGAT
1 CATGAAAA-GATGCCAAAATTTAAATGCATAAAAGGAT
308205 AAGTTAATAT
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
45 15 0.21
46 17 0.24
47 7 0.10
48 33 0.46
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (46 bp):
CATGAAAAGATGCCAAAATTTAAATGCATAAAAGGATGCATTAAGG
Found at i:316115 original size:20 final size:20
Alignment explanation
Indices: 316075--316113 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
316065 CATTGCAAGA
*
316075 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
316095 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
316114 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:329122 original size:6 final size:6
Alignment explanation
Indices: 329091--329151 Score: 60
Period size: 6 Copynumber: 10.7 Consensus size: 6
329081 TTGATATAAC
*
329091 ATAAAT -TAAAT ACAAAT AT--AT A-AAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
329135 ATTATAAT AT-AAT ATAA
1 A-TA-AAT ATAAAT ATAA
329152 GAATTAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
4 3 0.07
5 13 0.28
6 23 0.50
7 3 0.07
8 4 0.09
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAAAT
Found at i:329123 original size:21 final size:20
Alignment explanation
Indices: 329093--329131 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
329083 GATATAACAT
329093 AAATTAAATACAAATATATA
1 AAATTAAATACAAATATATA
*
329113 AAATATAAATATAAATATA
1 AAAT-TAAATACAAATATA
329132 AATATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATTAAATACAAATATATA
Found at i:329140 original size:21 final size:20
Alignment explanation
Indices: 329093--329151 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
329083 GATATAACAT
*
329093 AAAT-TAAATACAAATATATA
1 AAATATAAATATAAATATA-A
329113 AAATATAAATATAAATATAA
1 AAATATAAATATAAATATAA
*
329133 ATAT-TATAATAT-AATATAA
1 AAATATA-AATATAAATATAA
329152 GAATTAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 9 0.26
20 13 0.37
21 13 0.37
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATATAAATATAAATATAA
Found at i:329157 original size:19 final size:19
Alignment explanation
Indices: 329093--329162 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
329083 GATATAACAT
*
329093 AAATTA-AATACAAATATA
1 AAATTATAATATAAATATA
*
329111 TAAAATATAAATATAAATATA
1 -AAATTAT-AATATAAATATA
329132 AATATTATAATAT-AATATA
1 AA-ATTATAATATAAATATA
*
329151 AGAATTAAAATA
1 A-AATTATAATA
329163 GGATACTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 20 0.47
20 8 0.19
21 15 0.35
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (19 bp):
AAATTATAATATAAATATA
Found at i:330865 original size:98 final size:98
Alignment explanation
Indices: 330730--330934 Score: 365
Period size: 98 Copynumber: 2.1 Consensus size: 98
330720 GAAGGCTGAT
* *
330730 TTGACTTGAAAAGAACAAAATATGTTTCACTACTCTTCCGTGAATATCAGATTCGAGGTTGGAAT
1 TTGACTTCAAAAGAACAAAATATATTTCACTACTCTTCCGTGAATATCAGATTCGAGGTTGGAAT
330795 ACTTCACTACTCTTCTGTGAAGGTTGAAAATGA
66 ACTTCACTACTCTTCTGTGAAGGTTGAAAATGA
* * *
330828 TTGACTTCAGAAGAACAGAATCTATTTCACTACTCTTCCGTGAATATCAGATTCGAGGTTGGAAT
1 TTGACTTCAAAAGAACAAAATATATTTCACTACTCTTCCGTGAATATCAGATTCGAGGTTGGAAT
330893 ACTTCACTACTCTTCTGTGAAGGTTGAAAATGA
66 ACTTCACTACTCTTCTGTGAAGGTTGAAAATGA
330926 TTGACTTCA
1 TTGACTTCA
330935 CTACTCTTCA
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 102 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (98 bp):
TTGACTTCAAAAGAACAAAATATATTTCACTACTCTTCCGTGAATATCAGATTCGAGGTTGGAAT
ACTTCACTACTCTTCTGTGAAGGTTGAAAATGA
Found at i:331088 original size:40 final size:40
Alignment explanation
Indices: 331044--331128 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
331034 AGACTGACAG
331044 ATGACCCAAAGGATTTACAAATTA-CTAGAAGGTTTTACAA
1 ATGACCCAAAGGATTTACAAATTACCT-GAAGGTTTTACAA
**
331084 ATGACCCGGAGGATTTACAAATTACCTGAAGGTTTTACAA
1 ATGACCCAAAGGATTTACAAATTACCTGAAGGTTTTACAA
331124 ATGAC
1 ATGAC
331129 AAATGACCCG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 40 0.95
41 2 0.05
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (40 bp):
ATGACCCAAAGGATTTACAAATTACCTGAAGGTTTTACAA
Found at i:331130 original size:27 final size:27
Alignment explanation
Indices: 331100--331153 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
331090 CGGAGGATTT
* *
331100 ACAAATTACCTGAAGGTTTTACAAATG
1 ACAAATGACCCGAAGGTTTTACAAATG
*
331127 ACAAATGACCCGGAGGTTTTACAAATG
1 ACAAATGACCCGAAGGTTTTACAAATG
331154 TGTGGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.26
Consensus pattern (27 bp):
ACAAATGACCCGAAGGTTTTACAAATG
Found at i:331153 original size:20 final size:20
Alignment explanation
Indices: 331044--331128 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
331034 AGACTGACAG
* *
331044 ATGACCCAAAGGATTTACAA
1 ATGACCCGAAGGTTTTACAA
* **
331064 ATTACTAGAAGGTTTTACAA
1 ATGACCCGAAGGTTTTACAA
* *
331084 ATGACCCGGAGGATTTACAA
1 ATGACCCGAAGGTTTTACAA
* *
331104 ATTACCTGAAGGTTTTACAA
1 ATGACCCGAAGGTTTTACAA
331124 ATGAC
1 ATGAC
331129 AAATGACCCG
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (20 bp):
ATGACCCGAAGGTTTTACAA
Found at i:338151 original size:6 final size:6
Alignment explanation
Indices: 338120--338180 Score: 60
Period size: 6 Copynumber: 10.7 Consensus size: 6
338110 ATGAAATAAC
*
338120 ATAAAT -TAAAT ACAAAT AT--AT A-AAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
338164 ATTATAAT AT-AAT ATAA
1 A-TA-AAT ATAAAT ATAA
338181 GAATTAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
4 3 0.07
5 13 0.28
6 23 0.50
7 3 0.07
8 4 0.09
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAAAT
Found at i:338152 original size:21 final size:20
Alignment explanation
Indices: 338122--338160 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
338112 GAAATAACAT
338122 AAATTAAATACAAATATATA
1 AAATTAAATACAAATATATA
*
338142 AAATATAAATATAAATATA
1 AAAT-TAAATACAAATATA
338161 AATATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATTAAATACAAATATATA
Found at i:338169 original size:21 final size:20
Alignment explanation
Indices: 338122--338180 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
338112 GAAATAACAT
*
338122 AAAT-TAAATACAAATATATA
1 AAATATAAATATAAATATA-A
338142 AAATATAAATATAAATATAA
1 AAATATAAATATAAATATAA
*
338162 ATAT-TATAATAT-AATATAA
1 AAATATA-AATATAAATATAA
338181 GAATTAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 9 0.26
20 13 0.37
21 13 0.37
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATATAAATATAAATATAA
Found at i:338186 original size:19 final size:19
Alignment explanation
Indices: 338122--338191 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
338112 GAAATAACAT
*
338122 AAATTA-AATACAAATATA
1 AAATTATAATATAAATATA
*
338140 TAAAATATAAATATAAATATA
1 -AAATTAT-AATATAAATATA
338161 AATATTATAATAT-AATATA
1 AA-ATTATAATATAAATATA
*
338180 AGAATTAAAATA
1 A-AATTATAATA
338192 GGATGACTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 20 0.47
20 8 0.19
21 15 0.35
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (19 bp):
AAATTATAATATAAATATA
Found at i:341188 original size:27 final size:24
Alignment explanation
Indices: 341142--341198 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 24
341132 AAATTTAATT
341142 TTACAAATAAATTAATATAAATAA
1 TTACAAATAAATTAATATAAATAA
341166 TTACTAAATAATATTTAATATAAATAA
1 TTAC-AAATAA-A-TTAATATAAATAA
*
341193 TAACAA
1 TTACAA
341199 TACTACTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 4 0.14
25 6 0.21
26 3 0.10
27 16 0.55
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (24 bp):
TTACAAATAAATTAATATAAATAA
Found at i:341328 original size:35 final size:35
Alignment explanation
Indices: 341245--341328 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 35
341235 TTGTCCTAAT
* **
341245 ATAAATTATAA-ATAATAATATTGTAATTAATAAC
1 ATAAATTATAATATAATAATACTAAAATTAATAAC
*
341279 -TAATGATTAAAATATAA-AATACTAAAATTAATTAAC
1 ATAA--ATTATAATATAATAATACTAAAATTAA-TAAC
341315 ATAAATTATAATAT
1 ATAAATTATAATAT
341329 TACTAAAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
33 3 0.08
35 26 0.65
36 8 0.20
37 3 0.08
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (35 bp):
ATAAATTATAATATAATAATACTAAAATTAATAAC
Found at i:342972 original size:185 final size:186
Alignment explanation
Indices: 342737--343092 Score: 615
Period size: 185 Copynumber: 1.9 Consensus size: 186
342727 ACTTTTGTGA
* *
342737 AGACTTCATACTCTGCTGAAAAATCTGTTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCGTG
1 AGACTTCATACTCTGCTGAAAAATCTATTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCCTG
*
342802 CTCCTGCTTCACTACTCTTCTGTGAAGGCTTGATTTGAATGACTTGAACAAAAGGAATTTGTTTC
66 CTCCTGCTTCACTACTCTTCTGTGAAGGCTTGATTTGAATGACTTGAACAAAAGGAATCTGTTTC
* * *
342867 ATTACTCTTTCGTGAAGATCAGACTCGAGGTTGGATTACTTCATTACTCTTCCATG
131 ACTACTCTTTCGTGAAGATCAGACTCGAGATTGAATTACTTCATTACTCTTCCATG
*
342923 AGACTTCATACTTTGCTG-AAAATCTATTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCCTG
1 AGACTTCATACTCTGCTGAAAAATCTATTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCCTG
* *
342987 CTCCTGCTTCACTACTCTTCTGTGAAGGCTTGATTTGAATGACTTGAATAGAAGGAATCTGTTTC
66 CTCCTGCTTCACTACTCTTCTGTGAAGGCTTGATTTGAATGACTTGAACAAAAGGAATCTGTTTC
*
343052 ACTACTCTTTCGTGAAGATCCGACTCGAGATTGAATTACTT
131 ACTACTCTTTCGTGAAGATCAGACTCGAGATTGAATTACTT
343093 GACTATTCTT
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
185 143 0.89
186 17 0.11
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (186 bp):
AGACTTCATACTCTGCTGAAAAATCTATTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCCTG
CTCCTGCTTCACTACTCTTCTGTGAAGGCTTGATTTGAATGACTTGAACAAAAGGAATCTGTTTC
ACTACTCTTTCGTGAAGATCAGACTCGAGATTGAATTACTTCATTACTCTTCCATG
Found at i:343275 original size:20 final size:20
Alignment explanation
Indices: 343250--343427 Score: 204
Period size: 20 Copynumber: 9.1 Consensus size: 20
343240 AAACTGATAG
* *
343250 ATGACCCAAAGGATTTACAA
1 ATGACCCGAAGGCTTTACAA
*
343270 ATGACCC--AGAG-TCTA-A-
1 ATGACCCGAAG-GCTTTACAA
*
343286 ATGACCCAAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
* * *
343306 ATGACCTGGAGTCTTTACAA
1 ATGACCCGAAGGCTTTACAA
343326 ATGACCCGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
343346 ATGACCCGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
* *
343366 ATGACCCGGAGGTTTTACAA
1 ATGACCCGAAGGCTTTACAA
* *
343386 ATAACCTGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
*
343406 ATGACACGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
343426 AT
1 AT
343428 TCATGAGAAA
Statistics
Matches: 134, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
16 7 0.05
17 2 0.01
18 10 0.07
19 2 0.01
20 113 0.84
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
ATGACCCGAAGGCTTTACAA
Found at i:343364 original size:60 final size:60
Alignment explanation
Indices: 343284--343427 Score: 227
Period size: 60 Copynumber: 2.4 Consensus size: 60
343274 CCCAGAGTCT
* * *
343284 AAATGACCCAAAGGCTTTACAAATGACCTGGA-GTCTTTACAAATGACCCGAAGGCTTTAC
1 AAATGACCCGAAGGCTTTACAAATGACCCGGAGGT-TTTACAAATAACCCGAAGGCTTTAC
*
343344 AAATGACCCGAAGGCTTTACAAATGACCCGGAGGTTTTACAAATAACCTGAAGGCTTTAC
1 AAATGACCCGAAGGCTTTACAAATGACCCGGAGGTTTTACAAATAACCCGAAGGCTTTAC
*
343404 AAATGACACGAAGGCTTTACAAAT
1 AAATGACCCGAAGGCTTTACAAAT
343428 TCATGAGAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
60 76 0.97
61 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (60 bp):
AAATGACCCGAAGGCTTTACAAATGACCCGGAGGTTTTACAAATAACCCGAAGGCTTTAC
Found at i:350515 original size:35 final size:35
Alignment explanation
Indices: 350432--350515 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 35
350422 TTGTCCTAAT
* **
350432 ATAAATTATAA-ATAATAATATTGTAATTAATAAC
1 ATAAATTATAATATAATAATACTAAAATTAATAAC
*
350466 -TAATGATTAAAATATAA-AATACTAAAATTAATTAAC
1 ATAA--ATTATAATATAATAATACTAAAATTAA-TAAC
350502 ATAAATTATAATAT
1 ATAAATTATAATAT
350516 TATTAAAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
33 3 0.08
35 26 0.65
36 8 0.20
37 3 0.08
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (35 bp):
ATAAATTATAATATAATAATACTAAAATTAATAAC
Found at i:351694 original size:3 final size:3
Alignment explanation
Indices: 351683--351728 Score: 67
Period size: 3 Copynumber: 15.0 Consensus size: 3
351673 ATAATAATAA
351683 TAT TA- TAT TAT TATT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
351729 ATATAATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.05
3 32 0.80
4 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:351703 original size:10 final size:10
Alignment explanation
Indices: 351683--351726 Score: 72
Period size: 10 Copynumber: 4.4 Consensus size: 10
351673 ATAATAATAA
351683 TATTATATTAT
1 TATT-TATTAT
351694 TATTTATTAT
1 TATTTATTAT
351704 TATTTATTAT
1 TATTTATTAT
351714 TA-TTATTAT
1 TATTTATTAT
351723 TATT
1 TATT
351727 ATATATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.28
10 19 0.59
11 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTTATTAT
Found at i:353473 original size:17 final size:15
Alignment explanation
Indices: 353422--353476 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
353412 AGCATCATCG
*
353422 TATAAAA-ACAACAT
1 TATAAAATAAAACAT
353436 TATTAAAATAAAACAT
1 TA-TAAAATAAAACAT
353452 GTATAAAATAGAAACAAT
1 -TATAAAATA-AAAC-AT
353470 TATAAAA
1 TATAAAA
353477 ATTCCTTAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
14 2 0.06
15 5 0.14
16 13 0.37
17 13 0.37
18 2 0.06
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.25
Consensus pattern (15 bp):
TATAAAATAAAACAT
Found at i:361549 original size:20 final size:20
Alignment explanation
Indices: 361524--361561 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
361514 TCAAAATTGG
361524 AGAATAATTCAATAAACTGA
1 AGAATAATTCAATAAACTGA
*
361544 AGAATAATTCCATAAACT
1 AGAATAATTCAATAAACT
361562 TATGCCAATG
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:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (20 bp):
AGAATAATTCAATAAACTGA
Found at i:364709 original size:23 final size:23
Alignment explanation
Indices: 364676--364733 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
364666 ATATTTATTA
*
364676 ATAATTT-TAATGA-TATAATATT
1 ATAATTTATAAT-ACTATAATAAT
* *
364698 ATATTTTATAATACTTTAATAAT
1 ATAATTTATAATACTATAATAAT
364721 ATAATTTATAATA
1 ATAATTTATAATA
364734 TTTGTATTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 7 0.23
23 23 0.77
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
ATAATTTATAATACTATAATAAT
Found at i:369911 original size:13 final size:13
Alignment explanation
Indices: 369893--369931 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
369883 ATGGGCAAAT
369893 TTTGAAAA-ATATG
1 TTTGAAAACA-ATG
369906 TTTGAAAACAATG
1 TTTGAAAACAATG
369919 TTTGAAAATCAAT
1 TTTGAAAA-CAAT
369932 ATGTAGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:376528 original size:19 final size:20
Alignment explanation
Indices: 376488--376525 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
376478 TAAATGATTA
376488 GGGGTATCGGTACCCATAAG
1 GGGGTATCGGTACCCATAAG
*
376508 GGGGTATTGGTACCCATA
1 GGGGTATCGGTACCCATA
376526 GGGCATTCTA
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:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (20 bp):
GGGGTATCGGTACCCATAAG
Found at i:380578 original size:46 final size:46
Alignment explanation
Indices: 380508--380631 Score: 176
Period size: 46 Copynumber: 2.7 Consensus size: 46
380498 TATTCACTGC
* ***
380508 TTCAACTACTTTTCAAAGGTCATTTATTGCATCAATAATGCATCGT
1 TTCAACTACTTTTCAGAGGTCATTTATTGCATCAATAATGCAAAAT
* *
380554 TTGAACTACTTTTCAGAGGTCATTTATTGCAGCAATAATGCAAAAT
1 TTCAACTACTTTTCAGAGGTCATTTATTGCATCAATAATGCAAAAT
* *
380600 TTCAGCTACTTTTCAGAGGTCATTTAATGCAT
1 TTCAACTACTTTTCAGAGGTCATTTATTGCAT
380632 AATTCAAGCA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 68 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (46 bp):
TTCAACTACTTTTCAGAGGTCATTTATTGCATCAATAATGCAAAAT
Found at i:380650 original size:46 final size:45
Alignment explanation
Indices: 380508--380649 Score: 146
Period size: 46 Copynumber: 3.1 Consensus size: 45
380498 TATTCACTGC
* *
380508 TTCAACTACTTTTCAAAGGTCATTTATTGCATCAATAATGC-ATCG
1 TTCAACTACTTTTCAGAGGTCATTTATTGCAT-AATAATGCAATTG
* * *
380553 TTTGAACTACTTTTCAGAGGTCATTTATTGCAGCAATAATGCAAAAT-
1 -TTCAACTACTTTTCAGAGGTCATTTATTGCA-TAATAATGC-AATTG
* *
380600 TTCAGCTACTTTTCAGAGGTCATTTAATGCATAATTCAA-GCAATTG
1 TTCAACTACTTTTCAGAGGTCATTTATTGCATAA-T-AATGCAATTG
380646 TTCA
1 TTCA
380650 GAAACGGGTG
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
45 5 0.06
46 72 0.90
47 2 0.03
48 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (45 bp):
TTCAACTACTTTTCAGAGGTCATTTATTGCATAATAATGCAATTG
Found at i:381993 original size:120 final size:119
Alignment explanation
Indices: 381780--382018 Score: 469
Period size: 120 Copynumber: 2.0 Consensus size: 119
381770 CCATGCTTGG
381780 CCTCCCTCTGAATTTGACCTAATTGATCATCGGCCCATATATTTGGTCTGAACTTGAACATTCAA
1 CCTCCCTCTGAATTTGACCTAATTGATCATCGGCCCATATATTTGGTCTGAACTTGAACATTCAA
381845 AGTCAACTGCCAATCGTTGAAAGTTGAATTCCTAGGTGGCAACAGTTTTCGGTCA
66 AGTCAACTGCCAATCGTTGAAAGTTGAATTCCTAGGTGGCAACAG-TTTCGGTCA
381900 CCTCCCTCTGAATTTGACCTAATTGATCATCGGCCCATATATTTGGTCTGAACTTGAACATTCAA
1 CCTCCCTCTGAATTTGACCTAATTGATCATCGGCCCATATATTTGGTCTGAACTTGAACATTCAA
381965 AGTCAACTGCCAATCGTTGAAAGTTGAATTCCTAGGTGGCAACAGTTTCGGTCA
66 AGTCAACTGCCAATCGTTGAAAGTTGAATTCCTAGGTGGCAACAGTTTCGGTCA
382019 AAACGAGTCC
Statistics
Matches: 119, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
119 9 0.08
120 110 0.92
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (119 bp):
CCTCCCTCTGAATTTGACCTAATTGATCATCGGCCCATATATTTGGTCTGAACTTGAACATTCAA
AGTCAACTGCCAATCGTTGAAAGTTGAATTCCTAGGTGGCAACAGTTTCGGTCA
Found at i:384777 original size:70 final size:70
Alignment explanation
Indices: 384664--384803 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
384654 ACTCAAGTCC
384664 CAGACCCAAACTTACATCCCTTCCACTCAATTACTTCTGCTTCCCAAAGCTGTTGCAATGGACTC
1 CAGACCCAAACTTACATCCCTTCCACTCAATTACTTCTGCTTCCCAAAGCTGTTGCAATGGACTC
384729 CTAGT
66 CTAGT
384734 CAGACCCAAACTTACATCCCTTCCACTCAATTACTTCTGCTTCCCAAAGCTGTTGCAATGGACTC
1 CAGACCCAAACTTACATCCCTTCCACTCAATTACTTCTGCTTCCCAAAGCTGTTGCAATGGACTC
384799 CTAGT
66 CTAGT
384804 TTTCCCATCA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.26, C:0.34, G:0.11, T:0.29
Consensus pattern (70 bp):
CAGACCCAAACTTACATCCCTTCCACTCAATTACTTCTGCTTCCCAAAGCTGTTGCAATGGACTC
CTAGT
Found at i:386252 original size:21 final size:21
Alignment explanation
Indices: 386228--386274 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
386218 AGTATGGGTC
* *
386228 AATTTTAAAATGTTAAGTTGA
1 AATTATAAAATGTTAAGTTAA
386249 AATTATAAAATGTTAAGTTAA
1 AATTATAAAATGTTAAGTTAA
386270 AATTA
1 AATTA
386275 ATATAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (21 bp):
AATTATAAAATGTTAAGTTAA
Found at i:386821 original size:2 final size:2
Alignment explanation
Indices: 386814--386886 Score: 112
Period size: 2 Copynumber: 36.5 Consensus size: 2
386804 TATACTTGTA
386814 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
* *
386856 AGT AT AT A- AT TT AT AT AT AT AC AT AT AT AT A
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
386887 AGGATATACA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.02
2 62 0.95
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:391975 original size:18 final size:18
Alignment explanation
Indices: 391948--391983 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
391938 AAAAAAAAGG
*
391948 ATATACATAAGTTTATAT
1 ATATACATAAGTATATAT
*
391966 ATATATATAAGTATATAT
1 ATATACATAAGTATATAT
391984 GTATGATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATACATAAGTATATAT
Found at i:392025 original size:8 final size:8
Alignment explanation
Indices: 391961--392028 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
391951 TACATAAGTT
*
391961 TATATATA
1 TATATATG
*
391969 TATATAAG
1 TATATATG
391977 TATATATG
1 TATATATG
391985 TATGATGTATG
1 TAT-A--TATG
* *
391996 TACATAAG
1 TATATATG
*
392004 T-T-TATA
1 TATATATG
392010 TATATATG
1 TATATATG
392018 TATATATG
1 TATATATG
392026 TAT
1 TAT
392029 CATGCGCATG
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
6 3 0.07
7 1 0.02
8 34 0.74
9 1 0.02
10 1 0.02
11 6 0.13
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (8 bp):
TATATATG
Found at i:392530 original size:22 final size:22
Alignment explanation
Indices: 392487--392546 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
392477 ATATGCATAA
*
392487 GTATATATGTATGATGCGTGTGT
1 GTATATATATAT-ATGCGTGTGT
*
392510 GTATATATATATATGCTTGTGT
1 GTATATATATATATGCGTGTGT
392532 GTATATATATATATG
1 GTATATATATATATG
392547 TATGTATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 24 0.69
23 11 0.31
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.47
Consensus pattern (22 bp):
GTATATATATATATGCGTGTGT
Found at i:392556 original size:22 final size:22
Alignment explanation
Indices: 392487--392557 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
392477 ATATGCATAA
* * *
392487 GTATATATGTATGATGCGTGTGT
1 GTATATATATAT-ATGCTTGTAT
*
392510 GTATATATATATATGCTTGTGT
1 GTATATATATATATGCTTGTAT
392532 GTATATATATATATG-TATGTAT
1 GTATATATATATATGCT-TGTAT
392554 GTAT
1 GTAT
392558 GTATGTATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 1 0.02
22 32 0.73
23 11 0.25
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (22 bp):
GTATATATATATATGCTTGTAT
Found at i:392608 original size:31 final size:30
Alignment explanation
Indices: 392570--392658 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 30
392560 ATGTATGATG
* **
392570 CGTTAGTGACCAATTCGTTATAAATCATTAA
1 CGTTAGTGAACAATTTATTATAAATCA-TAA
*
392601 CGTTAGTGATCAATTTATTATAAATCGATAA
1 CGTTAGTGAACAATTTATTATAAATC-ATAA
*
392632 CTTTAGTGAACAATTTATTATAAATCA
1 CGTTAGTGAACAATTTATTATAAATCA
392659 ATAATATTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
30 1 0.02
31 50 0.96
32 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.38
Consensus pattern (30 bp):
CGTTAGTGAACAATTTATTATAAATCATAA
Found at i:393592 original size:2 final size:2
Alignment explanation
Indices: 393587--393618 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
393577 ACACACACAC
393587 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
393619 TAAACACATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:394481 original size:54 final size:54
Alignment explanation
Indices: 394170--394479 Score: 399
Period size: 54 Copynumber: 5.8 Consensus size: 54
394160 TAAAATGCAA
* * * * * * *
394170 ATTCACAAACTTATTATGAATTCCATGGATTGCTCAC--AGTGCAGATATGGTT
1 ATTCATAAACTCATTATGAATTCCATGGGTTGCACACATAGTGCTGATACGGTC
*** * * *
394222 ATTCATAAACTCATTATGAATTTTGTGGGTTGCACACATAATGCCGATAAGGTC
1 ATTCATAAACTCATTATGAATTCCATGGGTTGCACACATAGTGCTGATACGGTC
*
394276 ATTCATAAACTCATTATGAATTCCATGGGTTGTACACATAGTGCTGATACGGTC
1 ATTCATAAACTCATTATGAATTCCATGGGTTGCACACATAGTGCTGATACGGTC
* **
394330 ATTCATAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCTGATACAATC
1 ATTCATAAACTCATTATGAATTCCATGGGTTGCACACATAGTGCTGATACGGTC
* * *
394384 ATTCATAAACTCATTATGAATTCCGTGGGTTACACACATAGTACTGATACGGTC
1 ATTCATAAACTCATTATGAATTCCATGGGTTGCACACATAGTGCTGATACGGTC
* * *
394438 ATTCATAAAATTATTATGAATTCCATGGGCTGCACACATAGT
1 ATTCATAAACTCATTATGAATTCCATGGGTTGCACACATAGT
394480 ACCAAAAGTA
Statistics
Matches: 225, Mismatches: 31, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
52 30 0.13
54 195 0.87
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (54 bp):
ATTCATAAACTCATTATGAATTCCATGGGTTGCACACATAGTGCTGATACGGTC
Found at i:400491 original size:54 final size:54
Alignment explanation
Indices: 400433--400631 Score: 272
Period size: 54 Copynumber: 3.7 Consensus size: 54
400423 CGAAATGTAA
* * ** *
400433 ATTCACAAACTTATTATGAATTCCATGGATTGCACACATAGTGCCAATACGGTC
1 ATTCATAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGCCAATACGGTC
* * * * * *
400487 ATTCATAAACTCATTATGAATTATGTGGGTTGCATAGATAGTGCCGATATGATC
1 ATTCATAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGCCAATACGGTC
* *
400541 ATTCATAAACTCAATATGAATTCTGTGGGTTGTACACATAGTGCCAATACGGTC
1 ATTCATAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGCCAATACGGTC
400595 ATTCATAAACTCATTATGAATTCTGTGGGTTGGCACA
1 ATTCATAAACTCATTATGAATTCTGTGGGTT-GCACA
400632 TTGTGTCGAT
Statistics
Matches: 123, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
54 119 0.97
55 4 0.03
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (54 bp):
ATTCATAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGCCAATACGGTC
Found at i:402072 original size:16 final size:18
Alignment explanation
Indices: 402051--402084 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
402041 TTGAACTTTT
402051 CTTAA-GCTTT-AAACCA
1 CTTAAGGCTTTGAAACCA
402067 CTTAAGGCTTTGAAACCA
1 CTTAAGGCTTTGAAACCA
402085 ACCCAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (18 bp):
CTTAAGGCTTTGAAACCA
Found at i:402747 original size:16 final size:16
Alignment explanation
Indices: 402723--402761 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
402713 TTACAGGTCT
402723 GGTTAATAACATGTCA
1 GGTTAATAACATGTCA
* *
402739 GGTTTATAACATGTTA
1 GGTTAATAACATGTCA
402755 GG-TAATA
1 GGTTAATA
402762 CCAATTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (16 bp):
GGTTAATAACATGTCA
Found at i:406399 original size:65 final size:61
Alignment explanation
Indices: 406317--406455 Score: 170
Period size: 61 Copynumber: 2.2 Consensus size: 61
406307 GTAGGGTTAT
* * *
406317 ATTAGCACTAGTGTGTAAGGACACTAAGTGCAGGTGGAGGGTACAACCATATGTGTCATATCCGA
1 ATTAGCACTAGAGTGTAA--AC-CTAA-TACAGGTGGAGGGCACAACCATATGTGTCATATCCGA
* * * * *
406382 ATTAGCTCTAGAGTGTAAACCTAATATAGGTGGTGGGCACAACCTTATGTGTCATATCCGG
1 ATTAGCACTAGAGTGTAAACCTAATACAGGTGGAGGGCACAACCATATGTGTCATATCCGA
406443 ATTAGCACTAGAG
1 ATTAGCACTAGAG
406456 CATAAGCTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
61 43 0.66
62 4 0.06
63 2 0.03
65 16 0.25
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (61 bp):
ATTAGCACTAGAGTGTAAACCTAATACAGGTGGAGGGCACAACCATATGTGTCATATCCGA
Found at i:407952 original size:2 final size:2
Alignment explanation
Indices: 407941--408267 Score: 152
Period size: 2 Copynumber: 177.5 Consensus size: 2
407931 ATTCTTTTAG
*
407941 TA TA TA -A TA TA T- TA TA TA GTA TA TA T- TG T- TA TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
407978 TG T- TA TA TA -A TA TA TA TA T- TA TA TA TG TA T- TA TA TA GT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
**
408016 TA TA TA TA T- TA GC TA TA T- TA TA TA TA TA GT- 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
* * * *
408056 T- TA TA T- TA T- TA TA TA GTT TG T- TA TG TC TA T- TA TA TA T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
*
408093 TA TA TA TA CTA T- TA TA TA GT- TA TA TG T- TA TA TA GT- TA TA
1 TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA
*
408132 TA T- TA CA TA T- TA T- TA TA TA TA TA TA TA TA -A TA TA GT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
408170 TA TA TT TA TA TA TA TA TA TA TA TC TA TA TA T- TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
408211 TA T- TA TA -A TA -A T- TA TG TA GTA TA TA TA T- TA TT TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
408248 TA TC TA TA TT TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
408268 TAATTTTTAT
Statistics
Matches: 250, Mismatches: 29, Indels: 92
0.67 0.08 0.25
Matches are distributed among these distances:
1 37 0.15
2 201 0.80
3 12 0.05
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.54
Consensus pattern (2 bp):
TA
Found at i:407992 original size:35 final size:35
Alignment explanation
Indices: 407947--408238 Score: 109
Period size: 35 Copynumber: 8.6 Consensus size: 35
407937 TTAGTATATA
*
407947 ATATATTATATAGTATATAT-TGTTATAAT-TATGTT
1 ATATAATATATAGTATATATATG-TATAATATA-GTT
*
407982 ATATAATATATA-TATTATATATGTATTATATAGTT
1 ATATAATATATAGTA-TATATATGTATAATATAGTT
408017 ATAT-ATAT-TAGCTATAT-TA--TAT-ATATAGTT
1 ATATAATATATAG-TATATATATGTATAATATAGTT
*
408047 ATAT-ATATAT--TATAT-TAT-TAT-ATAGTTTGTT
1 ATATAATATATAGTATATATATGTATAATA--TAGTT
* * * * *
408078 ATGTCTATTATATATTATATATA-CTATTATATAGTT
1 A--TATAATATATAGTATATATATGTATAATATAGTT
** *
408114 ATATGTTATATAGT-TATATAT-TA-CATATTA-TT
1 ATATAATATATAGTATATATATGTATAATA-TAGTT
*
408146 ATAT-ATATATA-TATA-ATATAGT-T-ATATATTT
1 ATATAATATATAGTATATATAT-GTATAATATAGTT
408177 ATATATATATATA-TATCTATATAT-TATATTTATATA-TT
1 ATATA-ATATATAGTA--TATATATGTATA---ATATAGTT
*
408215 ATAATAATTATGTAGTATATATAT
1 AT-ATAA-TATATAGTATATATAT
408239 TATTTATTAT
Statistics
Matches: 208, Mismatches: 12, Indels: 71
0.71 0.04 0.24
Matches are distributed among these distances:
28 7 0.03
29 6 0.03
30 23 0.11
31 26 0.12
32 10 0.05
33 25 0.12
34 25 0.12
35 33 0.16
36 18 0.09
37 5 0.02
38 15 0.07
39 13 0.06
40 2 0.01
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (35 bp):
ATATAATATATAGTATATATATGTATAATATAGTT
Found at i:408066 original size:40 final size:38
Alignment explanation
Indices: 407948--408309 Score: 162
Period size: 39 Copynumber: 9.5 Consensus size: 38
407938 TAGTATATAA
* * *
407948 TATATTATATAGTATA-TAT-TGT-TATAAT-TA-TGT
1 TATATTATATAGTATATTATATATATATTATATATTAT
* *
407981 TATATAATATA-TATATTATATATGTATTATATAGTTA-
1 TATATTATATAGTATATTATATATATATTATATA-TTAT
408018 TATA-TAT-TAGCTATATTATATATATAGTTATATATATAT
1 TATATTATATAG-TATATTATATATATA-TTATATAT-TAT
* * *
408057 TATATTAT-TA-TATAGTTTGTTATGTCTATTATATATTATAT
1 TATATTATATAGTATA--TT-ATATATATATTATATA-T-TAT
*
408098 ATACTATTATATAGTTATATGT-TATATA-GTTATATATTA-
1 -TA-TATTATATAG-TATAT-TATATATATATTATATATTAT
*
408137 CATATTATTATA-TATATATATATAATATAGTTATATA-T-T
1 TATATTA-TATAGTATAT-TATAT-ATATA-TTATATATTAT
408176 TATATATATATA-TATATCTATATATTATATTTATATATTAT
1 TATAT-TATATAGTATAT-TATATA-TATA-TTATATATTAT
* * * *
408217 AATAATTATGTAGTATA-TATATTATTTATTATATCTATAT
1 TAT-ATTATATAGTATATTATA-TATATATTATATAT-TAT
* *
408257 T-TATTATATATTA-ATT-TTTATTATATTAT-TA-TAT
1 TATATTATATAGTATATTATATA-TATATTATATATTAT
* *
408291 T-TATTATTTATTATATTAT
1 TATATTATATAGTATATTAT
408310 TACTTATTTA
Statistics
Matches: 260, Mismatches: 29, Indels: 77
0.71 0.08 0.21
Matches are distributed among these distances:
32 4 0.02
33 13 0.05
34 17 0.07
35 10 0.04
36 14 0.05
37 36 0.14
38 33 0.13
39 42 0.16
40 36 0.14
41 22 0.08
42 15 0.06
43 10 0.04
44 3 0.01
45 1 0.00
46 4 0.02
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (38 bp):
TATATTATATAGTATATTATATATATATTATATATTAT
Found at i:408184 original size:52 final size:50
Alignment explanation
Indices: 407941--408287 Score: 172
Period size: 52 Copynumber: 6.8 Consensus size: 50
407931 ATTCTTTTAG
* * * *
407941 TATATA-ATATATTATATAGTATATA-TTGT-TATA-ATT--ATGTTATA
1 TATATATATATATAATATATTATATATTTATATATATATTACATATTATA
* *
407985 TA-ATATATATATTATATATGTAT-TATATAGTTATATATATTAGCTATATTATA
1 TATATATATATATAATATAT-TATATATTTA--TATATATATTA-C-ATATTATA
* *
408038 TATATAGT-TATAT-ATATATTATAT-TATTATATAGTTTGTTATGTC-TATTATA
1 TATATA-TATATATAATATATTATATAT-TTATATA-TATATTA---CATATTATA
* *
408090 TATTATATATACTATTATATAGTTATATGTTATATAGTTATATATTACATATTATTA
1 TA-TATATATA-TATAATATA-TTATATATT-TATA--TATATATTACATATTA-TA
*
408147 TATATATATATATAATATAGTTATATATTTATATATATA-TATATATCTATA
1 TATATATATATATAATATA-TTATATATTTATATATATATTACATAT-TATA
* * * * **
408198 TATTATATTTATATATTATAATA-ATTATGTAGTATATATATTATTTATTATA
1 TA-TATATATATATAATATATTATA-TATTTA-TATATATATTACATATTATA
* * *
408250 TCTATAT-T-TATTATATATTA-ATTTTTAT-TATATTATTA
1 TATATATATATATAATATATTATATATTTATATATA-TATTA
408288 TATTTATTAT
Statistics
Matches: 244, Mismatches: 24, Indels: 67
0.73 0.07 0.20
Matches are distributed among these distances:
43 3 0.01
44 16 0.07
45 4 0.02
46 4 0.02
47 7 0.03
48 8 0.03
49 13 0.05
50 2 0.01
51 26 0.11
52 55 0.23
53 30 0.12
54 16 0.07
55 24 0.10
56 20 0.08
57 9 0.04
58 5 0.02
59 2 0.01
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (50 bp):
TATATATATATATAATATATTATATATTTATATATATATTACATATTATA
Found at i:408213 original size:152 final size:151
Alignment explanation
Indices: 407941--408217 Score: 360
Period size: 152 Copynumber: 1.8 Consensus size: 151
407931 ATTCTTTTAG
* *
407941 TATATAATATATTATATAGTATATATTGTTATAATTATGTTATATAATATATATATTATATATGT
1 TATATAATATATTATATAGTATATATTGTTATAATTATGATATATAATATATATATTATATATAT
*
408006 ATTATATAGTTATATATATTAGCTATATTATATATATAGTTATATATATATTATATTATTATATA
66 ATAATATAGTTATATATATTA-CTATATTATATATATAGTTATATATATATTATATTATTATATA
408071 GTTTGTTATGTCTATTATATAT
130 GTTTGTTATGTCTATTATATAT
408093 TATAT-ATACTATTATATAGT-TATA-TGTTATATAGTTAT-ATAT-TACATAT-TATTATATAT
1 TATATAATA-TATTATATAGTATATATTGTTATA-A-TTATGATATATA-ATATATA-TAT-TAT
408152 ATATATATAATATAGTTATATAT-TTA-TATA-TATATATATA-TCTATATATTATATT-TATAT
60 ATATATATAATATAGTTATATATATTACTATATTATATATATAGT-TATATA-TATATTATAT-T
408212 ATTATA
122 ATTATA
408218 ATAATTATGT
Statistics
Matches: 113, Mismatches: 3, Indels: 21
0.82 0.02 0.15
Matches are distributed among these distances:
147 1 0.01
148 19 0.17
149 17 0.15
150 11 0.10
151 21 0.19
152 44 0.39
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (151 bp):
TATATAATATATTATATAGTATATATTGTTATAATTATGATATATAATATATATATTATATATAT
ATAATATAGTTATATATATTACTATATTATATATATAGTTATATATATATTATATTATTATATAG
TTTGTTATGTCTATTATATAT
Found at i:408247 original size:101 final size:97
Alignment explanation
Indices: 407947--408256 Score: 261
Period size: 97 Copynumber: 3.2 Consensus size: 97
407937 TTAGTATATA
* *
407947 ATATAT-TATATAGTAT-ATATTGTTATAATTATGTTATATA-ATATATATATTATATATGTA-T
1 ATATATATATATA-TATAATATAGTTATAA-TATGTTATATATATATATATATTATATATATATT
408008 TATATAGTTATATATATTA-GCTATATTATATATATAGTT
64 TATATA-TTATATA-ATTATG-TATA-TATATAT-TA-TT
* ** *
408047 ATATATATATTATATTATTATATAGTT-TGTTATGTCTATTATATATTATATATACTAT-TATAT
1 ATATATATA-TATA-TATAATATAGTTATAATATGT-TA-TATATA-TATATATATTATATATAT
* * * * *
408110 AGTTATATGTTATATAGTTATATAT-TACATATTA-T
61 ATTTATATATTATATAATTATGTATATATATATTATT
408145 -TATATATATATATATAATATAGTTAT-ATAT-TTATATATATATATATATCTATATATTATATT
1 ATATATATATATATATAATATAGTTATAATATGTTATATATATATATATAT-TATATA-TATATT
408207 TATATATTATAATAATTATGTAGTATATATATTATT
64 TATATATTAT-ATAATTATGTA-TATATATATTATT
*
408243 -TAT-TATATCTATAT
1 ATATATATATATATAT
408257 TTATTATATA
Statistics
Matches: 174, Mismatches: 19, Indels: 37
0.76 0.08 0.16
Matches are distributed among these distances:
91 8 0.05
92 9 0.05
93 4 0.02
94 15 0.09
95 23 0.13
96 6 0.03
97 26 0.15
98 5 0.03
100 8 0.05
101 13 0.07
102 10 0.06
103 17 0.10
104 13 0.07
105 17 0.10
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (97 bp):
ATATATATATATATATAATATAGTTATAATATGTTATATATATATATATATTATATATATATTTA
TATATTATATAATTATGTATATATATATTATT
Found at i:408266 original size:101 final size:98
Alignment explanation
Indices: 407948--408266 Score: 268
Period size: 95 Copynumber: 3.2 Consensus size: 98
407938 TAGTATATAA
* * *
407948 TATATTATATAGTA-TATATTGTTATAATTATGTTATATA-ATATATATATTATATATGTA-TTA
1 TATATTATAT-TTATTATATAGTTATAA-TATGTTATATATATATATATATTATATATATATTTA
408010 TATAGTTATATATATTA-GCTATATTATATATATAGTTATAT
64 TATA-TTATATA-ATTATG-TATA-TATATAT-TA-TT-TAT
** * *
408051 ATATATTATA-TTATTATATAGTT-TGTTATGTCTATTATATATTATATATACTAT-TATATAGT
1 -TATATTATATTTATTATATAGTTATAATATGT-TA-TATATA-TATATATATTATATATATATT
* * * *
408113 TATATGTTATATAGTTATATAT-TACATATTA-TTA-
62 TATATATTATATAATTATGTATATATATATTATTTAT
* *
408147 TATA-TATATATATAATATAGTTAT-ATAT-TTATATATATATATATATCTATATATTATATTTA
1 TATATTATATTTATTATATAGTTATAATATGTTATATATATATATATAT-TATATA-TATATTTA
408209 TATATTATAATAATTATGTAGTATATATATTATTTAT
64 TATATTAT-ATAATTATGTA-TATATATATTATTTAT
408246 TATATCTATATTTATTATATA
1 TATAT-TATATTTATTATATA
408267 TTAATTTTTA
Statistics
Matches: 175, Mismatches: 21, Indels: 41
0.74 0.09 0.17
Matches are distributed among these distances:
91 8 0.05
92 9 0.05
93 4 0.02
94 19 0.11
95 27 0.15
96 2 0.01
97 10 0.06
98 4 0.02
99 4 0.02
100 2 0.01
101 24 0.14
102 5 0.03
103 18 0.10
104 22 0.13
105 17 0.10
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (98 bp):
TATATTATATTTATTATATAGTTATAATATGTTATATATATATATATATTATATATATATTTATA
TATTATATAATTATGTATATATATATTATTTAT
Found at i:408297 original size:56 final size:60
Alignment explanation
Indices: 407980--408306 Score: 203
Period size: 58 Copynumber: 5.5 Consensus size: 60
407970 TATAATTATG
* * * *
407980 TTATATAATATATATATTATATATGTATTATATAGTTATATATATTAGCTATATTATATATA-TA
1 TTATATTAT-TATATATTATATATTTATTATAT--CTATATTTATTA--TATATTATATATATTA
* * * * *
408044 GTTATA-TATATATTATATTAT-TATATAGTT-TGT-TATGTCTATTATATATTATATATACTA
1 -TTATATTAT-TA-TATATTATATATTTA-TTATATCTATATTTATTATATATTATATATATTA
* * *
408104 TTATA-TAGTTATATGTTATATAGTTA-TATAT-TACATATTATTATATA-TATATATA-TA
1 TTATATTA-TTATATATTATATATTTATTATATCTATAT-TTATTATATATTATATATATTA
* *
408161 ATATAGTTA-TATAT-TTATATATATATATATATCTATA--TA-T-TATATT-TATATATTA
1 TTATA-TTATTATATATTATATATTTAT-TATATCTATATTTATTATATATTATATATATTA
* *
408216 TAATAATTATGTAGTATA-TATATTATTTATTATATCTATATTTATTATATATTA-AT-TTTTA
1 TTAT-ATTAT-TA-TATATTATA-TATTTATTATATCTATATTTATTATATATTATATATATTA
408277 TTATATTATTATAT-TTAT-TATTTATTATAT
1 TTATATTATTATATATTATATATTTATTATAT
408307 TATTACTTAT
Statistics
Matches: 215, Mismatches: 21, Indels: 61
0.72 0.07 0.21
Matches are distributed among these distances:
54 10 0.05
55 9 0.04
56 24 0.11
57 14 0.07
58 48 0.22
59 48 0.22
60 10 0.05
61 17 0.08
62 8 0.04
64 12 0.06
65 15 0.07
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (60 bp):
TTATATTATTATATATTATATATTTATTATATCTATATTTATTATATATTATATATATTA
Found at i:408316 original size:15 final size:15
Alignment explanation
Indices: 407992--408321 Score: 104
Period size: 15 Copynumber: 21.4 Consensus size: 15
407982 ATATAATATA
*
407992 TATATTATATATGTAT
1 TATATTAT-TATTTAT
408008 TATA-TAGTTATATATAT
1 TATATTA-TTAT-T-TAT
*
408025 TAGCTA-TATTATATA-
1 TA--TATTATTATTTAT
*
408040 TATAGTTATATATATAT
1 TATA-TTAT-TATTTAT
*
408057 TATATTATTATATAGT
1 TATATTATTATTTA-T
* * *
408073 T-TGTTA-TGTCTAT
1 TATATTATTATTTAT
*
408086 TATA-TATTATATA-
1 TATATTATTATTTAT
*
408099 TACTATTATATAGTTA-
1 TA-TATTAT-TATTTAT
* *
408115 TATGTTATATAGTTA-
1 TATATTAT-TATTTAT
*
408130 TATATTA-CATATTAT
1 TATATTATTAT-TTAT
* *
408145 TATATATATATATATAA
1 TATAT-TAT-TATTTAT
408162 TATAGTTATATATTTAT
1 TATA-TTAT-TATTTAT
*
408179 ATATATATATATATCTA-
1 -TATAT-TAT-TATTTAT
408196 TATATTA-TATTTAT
1 TATATTATTATTTAT
* *
408210 ATATTATAATAATTATGTAG
1 -TA-TAT--T-ATTATTTAT
408230 TATATATATTATTTAT
1 TATAT-TATTATTTAT
408246 TATATCTA-TATTTAT
1 TATAT-TATTATTTAT
*
408261 TATA-TATTAATT-T
1 TATATTATTATTTAT
408274 T-TATTA-TA-TTAT
1 TATATTATTATTTAT
408286 TATATTTATTATTTAT
1 TATA-TTATTATTTAT
*
408302 TATATTATTACTTAT
1 TATATTATTATTTAT
408317 T-TATT
1 TATATT
408322 CGTTTATTTT
Statistics
Matches: 249, Mismatches: 28, Indels: 76
0.71 0.08 0.22
Matches are distributed among these distances:
11 2 0.01
12 6 0.02
13 22 0.09
14 25 0.10
15 74 0.30
16 57 0.23
17 27 0.11
18 24 0.10
19 7 0.03
20 5 0.02
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (15 bp):
TATATTATTATTTAT
Found at i:408320 original size:16 final size:16
Alignment explanation
Indices: 408198--408321 Score: 71
Period size: 16 Copynumber: 7.6 Consensus size: 16
408188 TATATCTATA
408198 TATTATATTTATATA-T
1 TATTATATTTAT-TACT
* * *
408214 TATAATAATTATGTAGT
1 TATTATATTTAT-TACT
408231 ATATATATTATTTATTA--
1 -TAT-TA-TATTTATTACT
408248 TATCTATATTTATTA-T
1 TAT-TATATTTATTACT
* *
408264 ATATTAATTTTTATTATAT
1 -TATT-ATATTTATTA-CT
*
408283 TATTATATTTATTATT
1 TATTATATTTATTACT
408299 TATTATA-TTATTACT
1 TATTATATTTATTACT
408314 TATT-TATT
1 TATTATATT
408322 CGTTTATTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
14 2 0.02
15 21 0.24
16 26 0.30
17 22 0.25
18 7 0.08
19 4 0.05
20 6 0.07
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (16 bp):
TATTATATTTATTACT
Found at i:408328 original size:34 final size:34
Alignment explanation
Indices: 408255--408329 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
408245 TTATATCTAT
* *
408255 ATTTATTATATATTAATTTTTATTATATTATTAT
1 ATTTATTATATATTAATTATTATTATATTATTAC
*
408289 ATTTATTATTTATTATATTATTACTTAT-TTATT-C
1 ATTTATTATATATTA-ATTATTA-TTATATTATTAC
*
408323 GTTTATT
1 ATTTATT
408330 TTTTGCAGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 20 0.57
35 11 0.31
36 4 0.11
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (34 bp):
ATTTATTATATATTAATTATTATTATATTATTAC
Found at i:409998 original size:15 final size:15
Alignment explanation
Indices: 409978--410007 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
409968 TATTAACTAA
409978 CAAAAAATGTCTCAT
1 CAAAAAATGTCTCAT
409993 CAAAAAATGTCTCAT
1 CAAAAAATGTCTCAT
410008 TTCTTTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (15 bp):
CAAAAAATGTCTCAT
Found at i:416895 original size:2 final size:2
Alignment explanation
Indices: 416884--417320 Score: 189
Period size: 2 Copynumber: 236.0 Consensus size: 2
416874 TTAGTATACA
* *
416884 AT AT AT -T AT AT AGT AT AT AT AT GT -T AT A- AT -T AT GT -T AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
416922 AT AGT AT AT AT AT -T TT AT AT CT AT -T AT AT AGT -T AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* *
416963 -T AG CT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
417002 AT AT AGT -T AT AT AT -T AT AC AT AT -T AT AT AT -T AT -T AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
417040 -T GT -T AT AT AT -T AT GT AT AT -T AT -T AT AT AT -T AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* *
417077 -T AT AT AT -T AT AT AT -T AT -T AT -T AT GT AG AT -T 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
* *
417113 -T AT AT AT ACT TT GT AT AT -T AT AT AT ACT AT CAT AT AGT A- AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT -AT AT A-T AT AT
* *
417154 AT GT -T AT AT ACT AT AA AT -T AT AT AGT -T AT AT AT -T AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
417194 -T AT -T AT AT A- AT -T AT AT AT CAT AT AT -T AT AT AGT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT A-T AT AT AT
* * * * *
417232 AT TT AT TT AT -T AT AT CT AT AT AT -T AT TT TT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
417271 A- AT -T AT GT AGT AT AT AT AT AT -T AT TT AT -T AT AT CT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
417310 TT AT -T AT AT AT
1 AT AT AT AT AT AT
417321 TAGTTTTTAT
Statistics
Matches: 333, Mismatches: 39, Indels: 126
0.67 0.08 0.25
Matches are distributed among these distances:
1 49 0.15
2 262 0.79
3 22 0.07
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (2 bp):
AT
Found at i:416986 original size:81 final size:78
Alignment explanation
Indices: 416885--417368 Score: 291
Period size: 81 Copynumber: 6.1 Consensus size: 78
416875 TAGTATACAA
* *
416885 TATATTATATAGTATATATATGTTATAATTATGTTATATAGTATATATATTTTATATCTATTATA
1 TATATTATATA-TATATATAT-TTATAATTATGTTATATACTATATATATTTTATATATATTATA
416950 TAGTTATATATATTAG
64 TA-TTATATATATTAG
* * * *
416966 CTATATTATATATATATATATATATATATATATATTATATAGT-TATATA--TTATACATATTAT
1 -TATATTATATATATATATATTTATA-AT-TATGTTATATACTATATATATTTTATATATATTAT
417028 ATATTAT-TATATT-G
63 ATATTATATATATTAG
* * * * *
417042 T-TA-TATATTATGTATATTATTATATATTATATAGTTATATATTATATATTATTATTATGTAGA
1 TATATTATA-TATATATA-TATT-TATAAT-TAT-GTTATATACTATATA-TATT-TTATATATA
*
417105 TTATATATTATATATACTTTG
59 TTATATATTATATATA-TTAG
417126 TATATTATATATACTATCATA--TAGTAA-TATGTTATATACTATA-A-ATTATATAGTTATATA
1 TATATTATATATA-TAT-ATATTTA-TAATTATGTTATATACTATATATATT-T-TA--TATATA
417186 TTATATATTATTATATAATTA-
59 TTATATATTA-TATAT-ATTAG
* *
417207 TATATCATATAT-TATATAGTTATATATTTAT-TTATTATATCTATATATTATTTT-TATATATT
1 TATATTATATATATATATA-TT-TATAATTATGTTA-TATA-CTATATA-TATTTTATATATATT
*
417269 ATA-ATTATGTAGTATATA-
61 ATATATTATATA-TAT-TAG
* * * **
417287 TATATTATTTATTATATCTATATTTATTA-TATATTAGT-TTTTAT-TATATTTT-TATAT-TTA
1 TATATTA--TA-TATATATATATTTATAATTATGTTA-TATACTATATATATTTTATATATATTA
*
417347 T-TATT-TAT-TATTAT
62 TATATTATATATATTAG
417361 TATATTAT
1 TATATTAT
417369 TACATATTTA
Statistics
Matches: 330, Mismatches: 29, Indels: 96
0.73 0.06 0.21
Matches are distributed among these distances:
72 1 0.00
73 6 0.02
74 19 0.06
75 9 0.03
76 15 0.05
77 17 0.05
78 25 0.08
79 26 0.08
80 21 0.06
81 91 0.28
82 55 0.17
83 15 0.05
84 11 0.03
85 6 0.02
86 12 0.04
87 1 0.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (78 bp):
TATATTATATATATATATATTTATAATTATGTTATATACTATATATATTTTATATATATTATATA
TTATATATATTAG
Found at i:416992 original size:34 final size:32
Alignment explanation
Indices: 416885--417365 Score: 271
Period size: 31 Copynumber: 15.3 Consensus size: 32
416875 TAGTATACAA
*
416885 TATAT-TATATAGTATATATATGTTATA-ATTA
1 TATATATATATA-TATATATATATTATATATTA
*
416916 TGT-TATATAGTATATATAT-T-TTATATCTATTA
1 TATATATATA-TATATATATATATTATA--TATTA
416948 TATAGT-TATATATAT-TAGCTATA-T-TATA-TA
1 TATA-TATATATATATATA--TATATTATATATTA
416978 TATATATATATATATATATATATTATATAGTTA
1 TATATATATATATATATATATATTATATA-TTA
* *
417011 TATAT-TATACATAT-TATATATTATTATATTG
1 TATATATATATATATATATATATTA-TATATTA
*
417042 T-TATATAT-TATGTATAT-TATTATATATTA
1 TATATATATATATATATATATATTATATATTA
417071 TATAGT-TATATAT-TATATATTATTAT-TATGTA
1 TATA-TATATATATATATATA-TATTATATAT-TA
* *
417103 GAT-TATATAT-TATATATACT-TTGTATATTA
1 TATATATATATATATATATA-TATTATATATTA
* *
417133 TATATACTATCATATAGTA-ATATGTTATATACTA
1 TATATA-TAT-ATATA-TATATATATTATATATTA
417167 TA-A-AT-TATATAGT-TATATATTATATATTA
1 TATATATATATATA-TATATATATTATATATTA
417196 T-TATATA-ATTATATATCATATATTATATAGTTA
1 TATATATATA-TATATAT-ATATATTATATA-TTA
* * *
417229 TATATTTATTTATTATATCTATATATTAT-TTTTA
1 TATA--TATATA-TATATATATATATTATATATTA
*
417263 TATAT-TATA-AT-TATGTAGTATATATATATTA
1 TATATATATATATATATATA-TAT-TATATATTA
* *
417294 T-T-TAT-TATATCTATATTTATTATATATTA
1 TATATATATATATATATATATATTATATATTA
* * * * * *
417323 GTTTTTATTATATTTTTATATTTATTATTTATTA
1 -TATATA-TATATATATATATATATTATATATTA
417357 T-TAT-TATAT
1 TATATATATAT
417366 TATTACATAT
Statistics
Matches: 364, Mismatches: 28, Indels: 117
0.72 0.06 0.23
Matches are distributed among these distances:
28 4 0.01
29 56 0.15
30 69 0.19
31 84 0.23
32 56 0.15
33 24 0.07
34 48 0.13
35 3 0.01
36 12 0.03
37 8 0.02
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (32 bp):
TATATATATATATATATATATATTATATATTA
Found at i:417265 original size:47 final size:47
Alignment explanation
Indices: 416884--417335 Score: 241
Period size: 47 Copynumber: 9.4 Consensus size: 47
416874 TTAGTATACA
* * *
416884 ATATATTATATAGTA-TATATATGTTATA-AT--TATGTTATATAGTAT
1 ATATATTATATATTATTATATA-ATTATATATCATATATTATATAGT-T
* * **
416929 ATATATTTTATATCTATTATATAGTTATATAT-AT-TA-GCTATA-TT
1 ATATATTATATAT-TATTATATAATTATATATCATATATTATATAGTT
*
416973 ATATATATATATATATATATATATATATTATATAGTTATATATTATACATA-TT
1 ATATAT-TATATAT-TAT-TATATA-ATTATATA-TCATATATTAT--ATAGTT
* *
417026 ATATATTATTATATTGTTATATATTATGTATATTATTATATATTATATAGTT
1 ATATATTA-TATATTATTATATA--AT-TATA-TATCATATATTATATAGTT
417078 ATATATTATATATTATTATTATGTAGATTATATAT--TATA-TATACT--TT
1 ATATATTATATATTATTA-TA--TA-ATTATATATCATATATTATA-TAGTT
* * *
417125 GTATATTATATATACTATCATATAGTAATATGTTATATACTATAAATTATATAGTT
1 ATATATTATATAT--TAT--TATA-TAAT-T-ATATAT-C-ATATATTATATAGTT
417181 ATATATTATATATTATTATATAATTATATATCATATATTATATAGTT
1 ATATATTATATATTATTATATAATTATATATCATATATTATATAGTT
* * *
417228 ATATATT-TAT-TTATTATAT--CTATATATTAT-TTTTATATA-TT
1 ATATATTATATATTATTATATAATTATATATCATATATTATATAGTT
* * * * * *
417269 ATA-ATTATGTAGTA-TATATATATTATTTATTATATCTATATTTA-TT
1 ATATATTATATATTATTATATA-ATTATATATCATATAT-TATATAGTT
*
417315 ATATATTAGT-TTTTATTATAT
1 ATATATTA-TATATTATTATAT
417336 TTTTATATTT
Statistics
Matches: 332, Mismatches: 30, Indels: 87
0.74 0.07 0.19
Matches are distributed among these distances:
40 3 0.01
41 12 0.04
42 10 0.03
43 9 0.03
44 16 0.05
45 32 0.10
46 31 0.09
47 58 0.17
48 15 0.05
49 19 0.06
50 10 0.03
51 28 0.08
52 27 0.08
53 33 0.10
54 11 0.03
55 4 0.01
56 14 0.04
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (47 bp):
ATATATTATATATTATTATATAATTATATATCATATATTATATAGTT
Found at i:417298 original size:22 final size:20
Alignment explanation
Indices: 416884--417369 Score: 201
Period size: 22 Copynumber: 23.5 Consensus size: 20
416874 TTAGTATACA
*
416884 ATATATTATATAGTATATATAT
1 ATATATTATTTA-T-TATATAT
*
416906 GTTATAATTATGTTATATAGTATAT
1 -ATAT-ATTAT-TTAT-TA-TATAT
*
416931 ATATTTTATATCTATTATATAGT
1 ATATATTAT-T-TATTATATA-T
*
416954 -TATA-TATATTAGCTATAT-T
1 ATATATTAT-TTA-TTATATAT
*
416973 ATATATATATATATATATATAT
1 ATATAT-TATTTAT-TATATAT
*
416995 ATATATTATATAGTTATATATT
1 ATATATTATTTA-TTATATA-T
*
417017 ATACATATTATATATTAT-TAT
1 AT--ATATTATTTATTATATAT
* * *
417038 AT-TGTTATATATTATGTAT
1 ATATATTATTTATTATATAT
*
417057 AT-TATTATATATTATATAGTT
1 ATATATTATTTATTATATA--T
*
417078 ATATATTATATATTATTATTAT
1 ATATATTATTTATTA-TA-TAT
* * *
417100 GTAGATTATATATTATATAT
1 ATATATTATTTATTATATAT
417120 ACT-T-TGTATATTATATATACTAT
1 A-TATAT-TAT-TTAT-TATA-TAT
* * *
417143 CATATAGTAATATGTTATATACT
1 -ATATA-TTATTTATTATATA-T
* *
417166 ATAAATTATATAGTTATATAT
1 ATATATTATTTA-TTATATAT
417187 -TATA-TA-TTATTATATAATT
1 ATATATTATTTATTATAT-A-T
* *
417206 ATATATCATATATTATATAGTT
1 ATATATTATTTATTATATA--T
*
417228 ATATATTTATTTATTATATCT
1 ATATA-TTATTTATTATATAT
417249 ATATATTATTT-TTATATAT
1 ATATATTATTTATTATATAT
417268 -TATA--A-TTATGTAGTATAT
1 ATATATTATTTAT-TA-TATAT
*
417286 ATATATTATTTATTATATCT
1 ATATATTATTTATTATATAT
417306 ATAT-TTA-TTA-TATAT-T
1 ATATATTATTTATTATATAT
* *
417322 AGT-TTTTATTATATT-TTTAT
1 A-TATATTATT-TATTATATAT
*
417342 ATTTATTATTTATTAT-TAT
1 ATATATTATTTATTATATAT
417361 -TATATTATT
1 ATATATTATT
417370 ACATATTTAT
Statistics
Matches: 374, Mismatches: 35, Indels: 113
0.72 0.07 0.22
Matches are distributed among these distances:
15 2 0.01
16 5 0.01
17 17 0.05
18 36 0.10
19 50 0.13
20 43 0.11
21 58 0.16
22 85 0.23
23 37 0.10
24 31 0.08
25 9 0.02
26 1 0.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
ATATATTATTTATTATATAT
Found at i:417343 original size:8 final size:9
Alignment explanation
Indices: 417184--417380 Score: 86
Period size: 11 Copynumber: 20.4 Consensus size: 9
417174 TATAGTTATA
417184 TATTATATAT
1 TATTATAT-T
417194 TATTATATAAT
1 TATTATAT--T
*
417205 TATATATCATA
1 TAT-TAT-ATT
417216 TATTATATAGT
1 TATTATAT--T
417227 TA-TATATT
1 TATTATATT
417235 TATT-TATT
1 TATTATATT
417243 ATATCTATATAT
1 -TAT-TATAT-T
* *
417255 TATTTTTATA
1 TA-TTATATT
*
417265 TATTATAAT
1 TATTATATT
*
417274 TATGTAGTATA
1 TAT-TA-TATT
417285 TA-TATA-T
1 TATTATATT
417292 TATT-TATT
1 TATTATATT
417300 ATATCTATATT
1 -TAT-TATATT
417311 TATTATA--
1 TATTATATT
*
417318 TATTAGTTTT
1 TATTA-TATT
417328 TATTATATT
1 TATTATATT
417337 T-TTATATT
1 TATTATATT
*
417345 TATTATTTAT
1 TATTATAT-T
417355 TATTATTATAT
1 TATTA-TAT-T
417366 TATTACATATT
1 TATT--ATATT
417377 TATT
1 TATT
417381 CATTTATTTT
Statistics
Matches: 147, Mismatches: 14, Indels: 51
0.69 0.07 0.24
Matches are distributed among these distances:
7 9 0.06
8 20 0.14
9 31 0.21
10 36 0.24
11 40 0.27
12 8 0.05
13 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (9 bp):
TATTATATT
Found at i:418645 original size:19 final size:18
Alignment explanation
Indices: 418621--418666 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
418611 TTTTAACATA
*
418621 TTTTTAATTTATTATTCTT
1 TTTTTAATTTATT-TTATT
418640 TTTTT-ATTT-TTTTATT
1 TTTTTAATTTATTTTATT
*
418656 TTCTTAATTTA
1 TTTTTAATTTA
418667 AACTTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 8 0.35
17 6 0.26
18 4 0.17
19 5 0.22
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTAATTTATTTTATT
Found at i:426938 original size:27 final size:25
Alignment explanation
Indices: 426907--426956 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
426897 TAATTTCAGC
426907 ATTATCACTATATTTTAGAAATAGAGA
1 ATTATCA-TATATTTTAG-AATAGAGA
* *
426934 ATTATGATCTATTTTAGAATAGA
1 ATTATCATATATTTTAGAATAGA
426957 TTGTAATGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 9 0.43
27 6 0.29
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (25 bp):
ATTATCATATATTTTAGAATAGAGA
Found at i:430721 original size:2 final size:2
Alignment explanation
Indices: 430714--430745 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
430704 TATGCGAATA
430714 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
430746 GGTTTATAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:432979 original size:19 final size:19
Alignment explanation
Indices: 432955--432996 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
432945 GATAATAGAT
* *
432955 ATCAGAGTAGAGATCAGAG
1 ATCAGAATAGAAATCAGAG
*
432974 ATCAGAATAGAAATCAGTG
1 ATCAGAATAGAAATCAGAG
432993 ATCA
1 ATCA
432997 AAACATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.19
Consensus pattern (19 bp):
ATCAGAATAGAAATCAGAG
Found at i:434917 original size:22 final size:22
Alignment explanation
Indices: 434869--434928 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
434859 TTTGTTCCAA
*
434869 GTCAAAGTCAACGGTCGGACCG
1 GTCAAAGTCAACGGTCGGACAG
* * *
434891 ATCAAAGTCAATGGTCTGACAG
1 GTCAAAGTCAACGGTCGGACAG
*
434913 GTCAATCGTCAACGGT
1 GTCAA-AGTCAACGGT
434929 TCAGTTCATT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 22 0.73
23 8 0.27
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (22 bp):
GTCAAAGTCAACGGTCGGACAG
Found at i:437259 original size:17 final size:17
Alignment explanation
Indices: 437237--437276 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
437227 CTGAAGCATA
437237 GGTGCCCACCTGAGGGG
1 GGTGCCCACCTGAGGGG
437254 GGTG-CCACCTGAGGGG
1 GGTGCCCACCTGAGGGG
*
437270 AGTGCCC
1 GGTGCCC
437277 TTAGGTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.12, C:0.30, G:0.45, T:0.12
Consensus pattern (17 bp):
GGTGCCCACCTGAGGGG
Found at i:438083 original size:19 final size:20
Alignment explanation
Indices: 438047--438085 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
438037 ATGGAAGTTA
438047 ATGTTAGAGTGTTGAAATTG
1 ATGTTAGAGTGTTGAAATTG
438067 ATGTTAGAGTG-TGAAATTG
1 ATGTTAGAGTGTTGAAATTG
438086 GGCAATTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (20 bp):
ATGTTAGAGTGTTGAAATTG
Found at i:439223 original size:22 final size:22
Alignment explanation
Indices: 439195--439239 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
439185 CACTAGTTAT
439195 TATATATGATGTTTATCATGAA
1 TATATATGATGTTTATCATGAA
*
439217 TATATATGATGTTTATTATGAA
1 TATATATGATGTTTATCATGAA
439239 T
1 T
439240 GTTATTTCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (22 bp):
TATATATGATGTTTATCATGAA
Found at i:439470 original size:39 final size:39
Alignment explanation
Indices: 439409--439502 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 39
439399 AGGATACTCA
* * **
439409 GTGCATACGGTGGGGATGACCTTATGTGTAAGCACTTCG
1 GTGCATATGGTGGGCACAACCTTATGTGTAAGCACTTCG
* *
439448 GTGCATATGGTGGGCACAACCTTATGTGTATGCACTTTG
1 GTGCATATGGTGGGCACAACCTTATGTGTAAGCACTTCG
439487 GTGCATATGGTGGGCA
1 GTGCATATGGTGGGCA
439503 TGAAATTATG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (39 bp):
GTGCATATGGTGGGCACAACCTTATGTGTAAGCACTTCG
Found at i:459233 original size:35 final size:35
Alignment explanation
Indices: 459183--459253 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
459173 GATAAATTCT
* *
459183 AAATATTTATAGTTATCAGA-TGATTTTTAGCTATC
1 AAATATATATAGTTATCA-ATTGATTTTCAGCTATC
* *
459218 AAATATATATTGTTATCAATTGATTTTCAGTTATC
1 AAATATATATAGTTATCAATTGATTTTCAGCTATC
459253 A
1 A
459254 TATGTTTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 1 0.03
35 30 0.97
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.46
Consensus pattern (35 bp):
AAATATATATAGTTATCAATTGATTTTCAGCTATC
Found at i:462503 original size:36 final size:37
Alignment explanation
Indices: 462463--462568 Score: 115
Period size: 46 Copynumber: 2.6 Consensus size: 37
462453 AAAGAGAATT
*
462463 CATAACTAAAATGCATGAAATGAT-ATGAAAGGATGC
1 CATAACTAAAATGCATGAAATGATAATGAAAAGATGC
462499 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGC
1 CATAACTAAAATGCATG-AA--ATG-A-T-A---ATGAAAAGATGC
462545 CATAACTAAAATGCATGAAATGAT
1 CATAACTAAAATGCATGAAATGAT
462569 GCATTAAAGC
Statistics
Matches: 59, Mismatches: 1, Indels: 15
0.79 0.01 0.20
Matches are distributed among these distances:
36 17 0.29
37 2 0.03
39 3 0.05
40 1 0.02
41 2 0.03
42 1 0.02
43 3 0.05
45 2 0.03
46 28 0.47
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (37 bp):
CATAACTAAAATGCATGAAATGATAATGAAAAGATGC
Found at i:462517 original size:26 final size:26
Alignment explanation
Indices: 462487--462856 Score: 262
Period size: 26 Copynumber: 14.4 Consensus size: 26
462477 ATGAAATGAT
462487 ATGAAAGGATGCCATAACTAAAATGC
1 ATGAAAGGATGCCATAACTAAAATGC
*
462513 ATGAAAGGATG-CAT---T--AAGGC
1 ATGAAAGGATGCCATAACTAAAATGC
*
462533 ATGAAAAGATGCCATAACTAAAATGC
1 ATGAAAGGATGCCATAACTAAAATGC
*
462559 ATGAAATGATG-CAT---T-AAA-GC
1 ATGAAAGGATGCCATAACTAAAATGC
462579 ATGAAAGGATGCCATAACTAAAATGC
1 ATGAAAGGATGCCATAACTAAAATGC
*
462605 ATGAAAAGATGCCATAACTAAAATGC
1 ATGAAAGGATGCCATAACTAAAATGC
*
462631 ATGAAATGATG-CATTAAGGCATTAAAGGATGCC
1 ATGAAAGGATGCCA-TAA--C--TAAA--ATG-C
** * * * *
462664 AT-AACTAAAATG-CATGAAAGGATGCATTAAGGA
1 ATGAA--AGGATGCCAT--AA--CT--A-AAATGC
*
462697 ATCAAAGGATGCCATAACTAAAATGC
1 ATGAAAGGATGCCATAACTAAAATGC
*
462723 ATGAAAAGATGCCATAACTAAAATGC
1 ATGAAAGGATGCCATAACTAAAATGC
*
462749 ATGAAAGGATACCATAACTAAAATGC
1 ATGAAAGGATGCCATAACTAAAATGC
*
462775 ATGAAATGATG-CAT---T---ATGGC
1 ATGAAAGGATGCCATAACTAAAAT-GC
*
462795 ATGAAAGGATGTCATAACTAAAATGC
1 ATGAAAGGATGCCATAACTAAAATGC
* *
462821 ATGAAAGGATGACATAAATAAAATGC
1 ATGAAAGGATGCCATAACTAAAATGC
462847 ATGAAAGGAT
1 ATGAAAGGAT
462857 TCATTAAGGC
Statistics
Matches: 279, Mismatches: 28, Indels: 74
0.73 0.07 0.19
Matches are distributed among these distances:
19 2 0.01
20 38 0.14
21 12 0.04
22 3 0.01
24 3 0.01
25 14 0.05
26 161 0.58
27 3 0.01
28 1 0.00
29 1 0.00
30 4 0.01
31 2 0.01
32 9 0.03
33 10 0.04
34 10 0.04
35 5 0.02
36 1 0.00
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (26 bp):
ATGAAAGGATGCCATAACTAAAATGC
Found at i:462537 original size:46 final size:48
Alignment explanation
Indices: 462487--462936 Score: 315
Period size: 46 Copynumber: 9.5 Consensus size: 48
462477 ATGAAATGAT
*
462487 ATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCAT-T-AAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATATAAATGC
* *
462533 ATGAAAAGATGCCATAACTAAAATGCATGAAATGATGCAT-TAAA-GC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATATAAATGC
*
462579 ATGAAAGGATGCCATAACTAAAATGCATGAAAAGATGCCATAACTAAAATGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAAGGATG-CAT-A-T-AAATGC
* * *
462631 ATGAAATGATG-CAT---T--AAGGCATTAAAGGATGCCATAACTAAAATGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAAGGATG-CAT-A-T-AAATGC
* * *
462677 ATGAAAGGATG-CAT---T--AAGGAATCAAAGGATGCCATAACTAAAATGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAAGGATG-CAT-A-T-AAATGC
* *
462723 ATGAAAAGATGCCATAACTAAAATGCATGAAAGGATACCATAACTAAAATGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAAGGAT-GCAT-A-T-AAATGC
*
462775 ATGAAATGATG-CAT---T---ATGGCATGAAAGGATGTCATAACTAAAATGC
1 ATGAAAGGATGCCATAACTAAAAT-GCATGAAAGGATG-CAT-A-T-AAATGC
* * * *
462821 ATGAAAGGATGACATAAATAAAATGCATGAAAGGATTCAT-T-AAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATATAAATGC
* * * *
462867 ATAAAAGGATGCCATAGCTAAAATGCATGAAATGATGCAT-T-AAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATATAAATGC
* *
462913 ATGAAAGGATGTCAAAACTAAAAT
1 ATGAAAGGATGCCATAACTAAAAT
462937 TTTCGAATAA
Statistics
Matches: 350, Mismatches: 31, Indels: 46
0.82 0.07 0.11
Matches are distributed among these distances:
45 2 0.01
46 257 0.73
47 11 0.03
48 3 0.01
50 3 0.01
51 12 0.03
52 60 0.17
53 2 0.01
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (48 bp):
ATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATATAAATGC
Found at i:462649 original size:118 final size:118
Alignment explanation
Indices: 462487--462758 Score: 472
Period size: 118 Copynumber: 2.3 Consensus size: 118
462477 ATGAAATGAT
*
462487 ATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAACT
1 ATGAAAAGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAACT
* * *
462552 AAAATGCATGAAATGATGCATTAAAGCATGAAAGGATGCCATAACTAAAATGC
66 AAAATGCATGAAAGGATGCATTAAAGAATCAAAGGATGCCATAACTAAAATGC
* * *
462605 ATGAAAAGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGCATTAAAGGATGCCATAACT
1 ATGAAAAGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAACT
*
462670 AAAATGCATGAAAGGATGCATTAAGGAATCAAAGGATGCCATAACTAAAATGC
66 AAAATGCATGAAAGGATGCATTAAAGAATCAAAGGATGCCATAACTAAAATGC
462723 ATGAAAAGATGCCATAACTAAAATGCATGAAAGGAT
1 ATGAAAAGATGCCATAACTAAAATGCATGAAAGGAT
462759 ACCATAACTA
Statistics
Matches: 145, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 145 1.00
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (118 bp):
ATGAAAAGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAACT
AAAATGCATGAAAGGATGCATTAAAGAATCAAAGGATGCCATAACTAAAATGC
Found at i:462797 original size:118 final size:116
Alignment explanation
Indices: 462487--462923 Score: 366
Period size: 118 Copynumber: 3.7 Consensus size: 116
462477 ATGAAATGAT
* * * *
462487 ATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCAT--T--AAGGCATGAAAAGATGCCAT
1 ATGAAAAGATGCCATAACTAAAATGCATGAAAGGATCCATACTAAAATGCATGAAATGATG-CAT
*
462548 AACTAAAAT-GCATGAAATGATGCATTAAAGCATGAAAGGATGCCATAACTAAAATGC
65 ---T---ATGGCATGAAAGGATGCATTAAAGCATGAAAGGATGCCATAACTAAAATGC
* * * * *
462605 ATGAAAAGATGCCATAACTAAAATGCATGAAATGATGCAT--T--AAGGCATTAAAGGATGCCAT
1 ATGAAAAGATGCCATAACTAAAATGCATGAAAGGATCCATACTAAAATGCATGAAATGATG-CAT
* * *
462666 AACTAAAAT-GCATGAAAGGATGCATTAAGGAATCAAAGGATGCCATAACTAAAATGC
65 ---T---ATGGCATGAAAGGATGCATTAAAGCATGAAAGGATGCCATAACTAAAATGC
462723 ATGAAAAGATGCCATAACTAAAATGCATGAAAGGATACCATAACTAAAATGCATGAAATGATGCA
1 ATGAAAAGATGCCATAACTAAAATGCATGAAAGGAT-CCAT-ACTAAAATGCATGAAATGATGCA
* *
462788 TTATGGCATGAAAGGATGTCATAACTAAAATGCATGAAAGGATGACATAAATAAAATGC
64 TTATGGCATGAAAGGATG-CAT---T-AAA-GCATGAAAGGATGCCATAACTAAAATGC
* * * *
462847 ATGAAAGGAT-TCAT---T--AAGGCATAAAAGGATGCCATAGCTAAAATGCATGAAATGATGCA
1 ATGAAAAGATGCCATAACTAAAATGCATGAAAGGAT-CCATA-CTAAAATGCATGAAATGATGCA
*
462906 TTAAGGCATGAAAGGATG
64 TTATGGCATGAAAGGATG
462924 TCAAAACTAA
Statistics
Matches: 281, Mismatches: 24, Indels: 28
0.84 0.07 0.08
Matches are distributed among these distances:
117 3 0.01
118 214 0.76
119 6 0.02
120 2 0.01
122 2 0.01
123 8 0.03
124 46 0.16
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (116 bp):
ATGAAAAGATGCCATAACTAAAATGCATGAAAGGATCCATACTAAAATGCATGAAATGATGCATT
ATGGCATGAAAGGATGCATTAAAGCATGAAAGGATGCCATAACTAAAATGC
Found at i:462888 original size:72 final size:72
Alignment explanation
Indices: 462531--462903 Score: 438
Period size: 72 Copynumber: 5.2 Consensus size: 72
462521 ATGCATTAAG
* * * *
462531 GCATGAAAAGATGCCATAACTAAAATGCATGAAATGATGCATTAAAGCATGAAAGGATGCCATAA
1 GCATGAAAGGATGACATAACTAAAATGCATGAAATGATGCATTAAGGCATAAAAGGATGCCATAA
462596 CTAAAAT
66 CTAAAAT
* * *
462603 GCATGAAAAGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGCATTAAAGGATGCCATAA
1 GCATGAAAGGATGACATAACTAAAATGCATGAAATGATGCATTAAGGCATAAAAGGATGCCATAA
462668 CTAAAAT
66 CTAAAAT
* * * * *
462675 GCATGAAAGGATG-CAT---T--AAGGAATCAAAGGATGCCATAACTAAAATGCATGAAAA-GAT
1 GCATGAAAGGATGACATAACTAAAATGCATGAAATGATG-CAT---T--AAGGCAT-AAAAGGAT
462733 GCCATAACTAAAAT
59 GCCATAACTAAAAT
* * *
462747 GCATGAAAGGAT-ACCATAACTAAAATGCATGAAATGATGCATTATGGCATGAAAGGATGTCATA
1 GCATGAAAGGATGA-CATAACTAAAATGCATGAAATGATGCATTAAGGCATAAAAGGATGCCATA
462811 ACTAAAAT
65 ACTAAAAT
* * * *
462819 GCATGAAAGGATGACATAAATAAAATGCATGAAAGGATTCATTAAGGCATAAAAGGATGCCATAG
1 GCATGAAAGGATGACATAACTAAAATGCATGAAATGATGCATTAAGGCATAAAAGGATGCCATAA
462884 CTAAAAT
66 CTAAAAT
*
462891 GCATGAAATGATG
1 GCATGAAAGGATG
462904 CATTAAGGCA
Statistics
Matches: 260, Mismatches: 25, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
66 12 0.05
67 3 0.01
68 1 0.00
70 1 0.00
71 6 0.02
72 213 0.82
73 7 0.03
74 1 0.00
76 1 0.00
77 3 0.01
78 12 0.05
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (72 bp):
GCATGAAAGGATGACATAACTAAAATGCATGAAATGATGCATTAAGGCATAAAAGGATGCCATAA
CTAAAAT
Found at i:469655 original size:33 final size:33
Alignment explanation
Indices: 469613--469675 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
469603 AAAATGAATT
*
469613 CATAACTAAAATGCATGAAATGATGCATTATGA
1 CATAACTAAAATGCATGAAAGGATGCATTATGA
* *
469646 CATACCTAAAATGGATGAAAGGATGCATTA
1 CATAACTAAAATGCATGAAAGGATGCATTA
469676 AGGCATGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.25
Consensus pattern (33 bp):
CATAACTAAAATGCATGAAAGGATGCATTATGA
Found at i:469708 original size:26 final size:25
Alignment explanation
Indices: 469646--469795 Score: 114
Period size: 20 Copynumber: 6.5 Consensus size: 25
469636 TGCATTATGA
* *
469646 CATACCTAAAATGGATGAAAGGATG
1 CATAACTAAAATGCATGAAAGGATG
*
469671 CAT---T--AAGGCATGAAAGGATG
1 CATAACTAAAATGCATGAAAGGATG
469691 CCATAACTAAAATGCATGAAAGGATG
1 -CATAACTAAAATGCATGAAAGGATG
* *
469717 CAT---T-AAA-GGATGAAAGTATG
1 CATAACTAAAATGCATGAAAGGATG
469737 TCATAACTAAAATGCATGAAAGGATG
1 -CATAACTAAAATGCATGAAAGGATG
*
469763 CAT---T--AAGGCATGAAAGGATG
1 CATAACTAAAATGCATGAAAGGATG
469783 CCATAACTAAAAT
1 -CATAACTAAAAT
469796 TTATGAATAA
Statistics
Matches: 98, Mismatches: 9, Indels: 35
0.69 0.06 0.25
Matches are distributed among these distances:
20 40 0.41
21 12 0.12
22 3 0.03
24 3 0.03
25 12 0.12
26 28 0.29
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (25 bp):
CATAACTAAAATGCATGAAAGGATG
Found at i:469802 original size:46 final size:46
Alignment explanation
Indices: 469646--469795 Score: 248
Period size: 46 Copynumber: 3.3 Consensus size: 46
469636 TGCATTATGA
* *
469646 CATACCTAAAATGGATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
469692 CATAACTAAAATGCATGAAAGGATGCATTAAAGG-ATGAAAGTATGT
1 CATAACTAAAATGCATGAAAGGATGCATT-AAGGCATGAAAGGATGC
469738 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
469784 CATAACTAAAAT
1 CATAACTAAAAT
469796 TTATGAATAA
Statistics
Matches: 96, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
45 4 0.04
46 88 0.92
47 4 0.04
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (46 bp):
CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:471750 original size:20 final size:20
Alignment explanation
Indices: 471725--471786 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
471715 ATGTTTTACA
471725 TATGTTTTAGATTCATTTAT
1 TATGTTTTAGATTCATTTAT
471745 TATG-TTT-GCATGTCATTTAT
1 TATGTTTTAG-AT-TCATTTAT
*
471765 TATGTTTTAGATTCATTCAT
1 TATGTTTTAGATTCATTTAT
471785 TA
1 TA
471787 GCTCATGTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
18 1 0.03
19 5 0.14
20 25 0.68
21 5 0.14
22 1 0.03
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.56
Consensus pattern (20 bp):
TATGTTTTAGATTCATTTAT
Found at i:472692 original size:19 final size:19
Alignment explanation
Indices: 472666--472718 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
472656 TTCGGCCAAG
472666 AGCATGTATTTTCATT-AA
1 AGCATGTATTTTCATTAAA
*
472684 AGTCATGTATTTTTATTAAAA
1 AG-CATGTATTTTCATT-AAA
472705 AGCATGTATTTTCA
1 AGCATGTATTTTCA
472719 AAGGGATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 2 0.07
19 13 0.43
20 11 0.37
21 4 0.13
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (19 bp):
AGCATGTATTTTCATTAAA
Found at i:479001 original size:19 final size:16
Alignment explanation
Indices: 478964--478999 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
478954 TATCAAAGTC
478964 AATTTTTTATTTTGAA
1 AATTTTTTATTTTGAA
478980 AATTATTTTGATTTTGAA
1 AATT-TTTT-ATTTTGAA
478998 AA
1 AA
479000 ATAAGCACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 4 0.22
18 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (16 bp):
AATTTTTTATTTTGAA
Found at i:485153 original size:52 final size:53
Alignment explanation
Indices: 485091--485196 Score: 187
Period size: 52 Copynumber: 2.0 Consensus size: 53
485081 CAGTAAAGTC
*
485091 ATCCATGAAGACTTCAATACCTTTCTCAAATAATCA-AAAAAATATTAATCAT
1 ATCCATGAAGACTTCAATACCTTTCTCAAATAATCAGAAAAAATACTAATCAT
*
485143 ATCCATGAAGACTTCGATACCTTTCTCAAATAATCAGAAAAAATACTAATCAT
1 ATCCATGAAGACTTCAATACCTTTCTCAAATAATCAGAAAAAATACTAATCAT
485196 A
1 A
485197 CACCATAGGA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 35 0.69
53 16 0.31
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (53 bp):
ATCCATGAAGACTTCAATACCTTTCTCAAATAATCAGAAAAAATACTAATCAT
Found at i:494252 original size:25 final size:24
Alignment explanation
Indices: 494202--494263 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
494192 TTCGAATTAT
* *
494202 TTATAT-TATAT-TATATTTTTTC
1 TTATATATATATATATATTATGTC
494224 TTATATATATATATATATTATGTC
1 TTATATATATATATATATTATGTC
* *
494248 ATTATTTATATGTATA
1 -TTATATATATATATA
494264 AGTAGAGATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 6 0.18
23 5 0.15
24 9 0.27
25 13 0.39
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (24 bp):
TTATATATATATATATATTATGTC
Found at i:498693 original size:183 final size:183
Alignment explanation
Indices: 498385--498734 Score: 646
Period size: 183 Copynumber: 1.9 Consensus size: 183
498375 ATTAAATCCG
498385 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
498450 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTATTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTATTTGCTCCACTGCTT
498515 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
498568 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
498633 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTATTTGCTCCACTGCTT
*
498698 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTT
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTT
498735 TAGTTAAACT
Statistics
Matches: 161, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 161 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTATTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
Found at i:499600 original size:12 final size:12
Alignment explanation
Indices: 499583--499607 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
499573 CCCTCACATC
499583 TCAACATATACA
1 TCAACATATACA
499595 TCAACATATACA
1 TCAACATATACA
499607 T
1 T
499608 ACATGATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (12 bp):
TCAACATATACA
Found at i:500091 original size:37 final size:37
Alignment explanation
Indices: 500023--500110 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
500013 CATTGAAAAC
** * *
500023 ATTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
*
500059 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
*
500096 ATTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
500111 TAAACATTGA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 12 0.27
37 32 0.73
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.40
Consensus pattern (37 bp):
ATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
Found at i:500113 original size:102 final size:105
Alignment explanation
Indices: 499929--500176 Score: 360
Period size: 102 Copynumber: 2.4 Consensus size: 105
499919 TTTTTCTTAA
* * * *
499929 AACAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACA
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGACA
* *
499994 GTTTCTCTTTAAACATAAACATTGAAAACATTTCCCTT-G
66 ATTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
* * *
500033 AA-ATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAA-TTTTGTCTCCCTTGAGAC
1 AACA-AAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGAC
500095 AATTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
65 AATTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
* *
500136 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
500177 TAAACATTGA
Statistics
Matches: 129, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
102 54 0.42
103 40 0.31
104 35 0.27
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (105 bp):
AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGACA
ATTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
Found at i:500167 original size:66 final size:66
Alignment explanation
Indices: 500060--500239 Score: 269
Period size: 66 Copynumber: 2.8 Consensus size: 66
500050 CTTGAGATAG
* *
500060 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
500125 A
66 A
*
500126 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
500191 A
66 A
* * *
500192 TTTCCCTT-GAA-ATAAA--TTGTCTCTCTTGAGATAGTTTCACTTGAAACA
1 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
500240 AAATTTTGTC
Statistics
Matches: 107, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
63 29 0.27
64 1 0.01
65 6 0.06
66 71 0.66
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (66 bp):
TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
A
Found at i:500268 original size:166 final size:169
Alignment explanation
Indices: 499956--500341 Score: 613
Period size: 166 Copynumber: 2.3 Consensus size: 169
499946 CTTGAGATAG
* * *
499956 TTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAGTTTCTCTTTAAACATAAACATTGAAA
1 TTTCCCTTGGAACAGAAA-TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
* *
500021 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
65 ACATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCACTTGAAACAAAATTTTGTCTC
*
500086 CCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
130 CCTTGAGAAAATTTCTCTTGAAACATAAACATTGAAAACA
* *
500126 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAG
1 TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
500190 CATTTCCCTTGAAAT-AA-ATTGTCTCTCTTGAGATAGTTTCACTTGAAACAAAATTTTGTCTCC
66 CATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCACTTGAAACAAAATTTTGTCTCC
500253 CTTGAGAAAATTTCTCTTGAAACATAAACATTGAAAACA
131 CTTGAGAAAATTTCTCTTGAAACATAAACATTGAAAACA
* * *
500292 TTTCCCTT-GAA-ATG-AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-GAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACA
500342 AATTTTGTCT
Statistics
Matches: 203, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
164 1 0.00
165 36 0.18
166 90 0.44
167 2 0.01
168 59 0.29
169 3 0.01
170 12 0.06
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (169 bp):
TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
CATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCACTTGAAACAAAATTTTGTCTCC
CTTGAGAAAATTTCTCTTGAAACATAAACATTGAAAACA
Found at i:500339 original size:36 final size:36
Alignment explanation
Indices: 500292--500377 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
500282 ATTGAAAACA
** *
500292 TTTCCCTTGAAATGAATTTTGTCTC-TCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCAT-TTGAGACAG
500328 TTTCCCTTGAAACAAATTTTGTCTCATTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCATTTGAGACAG
**
500364 TTTCTATTGAAACA
1 TTTCCCTTGAAACA
500378 TAAACTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 43 0.98
37 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCATTTGAGACAG
Found at i:500388 original size:101 final size:100
Alignment explanation
Indices: 500126--500472 Score: 442
Period size: 100 Copynumber: 3.5 Consensus size: 100
500116 ATTGAAAACA
* *
500126 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
500191 ATTTCCCTTGAAATAAATTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAATAAATTGTCTCTCTTGAGATAG
* * *
500226 TTTCACTTGAAACAAAATTTTGTCTCCCTTGAGAAAATTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
*
500291 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAAT-AA-ATTGTCTCTCTTGAGATAG
** * *
500328 TTTCCCTTGAAAC-AAATTTTGTCTCATTTGAGACAGTTTCTATTGAAACATAAACTTTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
500392 AGTTTCCCTTGAAACAAA----ATCT-TTGA-ATATG
66 A-TTTCCCTTGAAATAAATTGTCTCTCTTGAGATA-G
* * * *
500423 TTTTACATT-AAAC-AAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 -TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
500473 AATTTTGTCT
Statistics
Matches: 220, Mismatches: 22, Indels: 15
0.86 0.09 0.06
Matches are distributed among these distances:
94 3 0.01
95 42 0.19
96 9 0.04
100 74 0.34
101 50 0.23
102 42 0.19
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (100 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATAAATTGTCTCTCTTGAGATAG
Found at i:500394 original size:30 final size:30
Alignment explanation
Indices: 500360--500418 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
500350 CTCATTTGAG
*
500360 ACAGTTTCTATTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCATTGAAACA-AAATCTTTGAAA
*
500390 ACAGTTTCCCTTGAAACAAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAAATCTTTGAA
500419 TATGTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
ACAGTTTCCATTGAAACAAAATCTTTGAAA
Found at i:500514 original size:38 final size:36
Alignment explanation
Indices: 500432--500546 Score: 167
Period size: 36 Copynumber: 3.1 Consensus size: 36
500422 GTTTTACATT
*
500432 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
500468 AAACAAATTTTGTCTCTCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
*
500505 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
500542 AAACA
1 AAACA
500547 TCAATCCTTG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
36 25 0.36
37 24 0.35
38 20 0.29
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:500651 original size:34 final size:34
Alignment explanation
Indices: 500586--500701 Score: 166
Period size: 34 Copynumber: 3.4 Consensus size: 34
500576 CCTTGATACA
500586 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC-AAAA-AAACCTTTGAAATT
*
500622 GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAATT
*
500656 GTTTCTCTTGAAACAC---AAAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAATT
*
500687 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
500702 AATTTCGTCT
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 27 0.36
34 29 0.38
35 4 0.05
36 16 0.21
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (34 bp):
GTTTCTCTTGAAACACAAAAAAACCTTTGAAATT
Found at i:500748 original size:67 final size:67
Alignment explanation
Indices: 500656--500842 Score: 239
Period size: 67 Copynumber: 2.7 Consensus size: 67
500646 CTTTGAAAAT
*
500656 GTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
500721 CA
66 CA
* * * *
500723 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCCTTAAAACAAAATTTTGTCTCCCTTGAG
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-AAATTTCGTCTCCCTTGAG
* *
500788 GCC
65 ACA
* * * * *
500791 GTTTCTCATGAAACAACATATATCTTTAAGATCGTTTCCCTTGAAACGAATT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAGATTGTTTCCCTTGAAACAAATT
500843 CTGTCTTTTT
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
67 41 0.40
68 32 0.31
69 7 0.07
70 22 0.22
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
CA
Found at i:501230 original size:43 final size:43
Alignment explanation
Indices: 501165--501273 Score: 146
Period size: 43 Copynumber: 2.5 Consensus size: 43
501155 TAGCTAGAGC
*
501165 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACA
1 CAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACA
** * * *
501208 CAATTTCAACTTCACATTGAAGGGCATTGGACTCGAGACAGCA
1 CAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACA
* *
501251 CAAGTTCAACTTCACAACGAAGG
1 CAATTTCAACTTCACAGCGAAGG
501274 GACGGCTAAC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (43 bp):
CAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACA
Found at i:502599 original size:60 final size:59
Alignment explanation
Indices: 502485--502601 Score: 134
Period size: 60 Copynumber: 1.9 Consensus size: 59
502475 TTTTTTCCCT
502485 CATTTTATTTATTGTATATTTTTTATTATATTTATTTACTTTCAAGTTATTATATATACA
1 CATTTTATTTATTGTATATTTTTTATTATATTTATTTA-TTTCAAGTTATTATATATACA
* *
502545 CATTTT-TTTATGTTTACTATTATTTTATTAT-TATTATTT-TTTCATG-TATATATATAT
1 CATTTTATTTAT-TGTA-TATT-TTTTATTATAT-TTATTTATTTCAAGTTAT-TATATAT
502602 TCTTTTTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
59 8 0.16
60 22 0.44
61 5 0.10
62 15 0.30
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (59 bp):
CATTTTATTTATTGTATATTTTTTATTATATTTATTTATTTCAAGTTATTATATATACA
Found at i:505097 original size:42 final size:42
Alignment explanation
Indices: 505038--505206 Score: 295
Period size: 42 Copynumber: 4.0 Consensus size: 42
505028 AGTTATAACA
*
505038 ACCTTTTGATGAATGAATCC-AACGAAATGAGAAATAAATTAG
1 ACCTTTTGATGAATGAATCCAAAC-AAATGAGAAATGAATTAG
505080 ACCTTTTGATGAATGAATCCAAACAAATGAGAAATGAATTAG
1 ACCTTTTGATGAATGAATCCAAACAAATGAGAAATGAATTAG
*
505122 ACCTCTTGATGAATGAATCCAAACAAATGAGAAATGAATTAG
1 ACCTTTTGATGAATGAATCCAAACAAATGAGAAATGAATTAG
*
505164 ACCTTTTGATGAATGAATCCAAACAAATGAGAAATTAATTAG
1 ACCTTTTGATGAATGAATCCAAACAAATGAGAAATGAATTAG
505206 A
1 A
505207 ATGAAATGAG
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
42 119 0.98
43 3 0.02
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (42 bp):
ACCTTTTGATGAATGAATCCAAACAAATGAGAAATGAATTAG
Found at i:505115 original size:21 final size:21
Alignment explanation
Indices: 505091--505160 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
505081 CCTTTTGATG
505091 AATGAATCCAAACAAATGAGA
1 AATGAATCCAAACAAATGAGA
* * ***
505112 AATGAAT-TAGACCTCTTGATG-
1 AATGAATCCA-AACAAATGA-GA
505133 AATGAATCCAAACAAATGAGA
1 AATGAATCCAAACAAATGAGA
505154 AATGAAT
1 AATGAAT
505161 TAGACCTTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
20 2 0.06
21 31 0.89
22 2 0.06
ACGTcount: A:0.50, C:0.13, G:0.16, T:0.21
Consensus pattern (21 bp):
AATGAATCCAAACAAATGAGA
Found at i:507227 original size:22 final size:22
Alignment explanation
Indices: 507200--507250 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
507190 GAGTTGACCG
507200 TTGACCAGTCA-GACCATTGACT
1 TTGACCAGT-ATGACCATTGACT
* **
507222 TTGACCGGTATGACTGTTGACT
1 TTGACCAGTATGACCATTGACT
507244 TTGACCA
1 TTGACCA
507251 AAAAGTCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (22 bp):
TTGACCAGTATGACCATTGACT
Found at i:519247 original size:19 final size:19
Alignment explanation
Indices: 519225--519267 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
519215 ACAAAATGCG
519225 TAAAAATAATA-AAAATAAA
1 TAAAAATAA-ACAAAATAAA
*
519244 TAAAAATAAACAAAATGAA
1 TAAAAATAAACAAAATAAA
519263 TAAAA
1 TAAAA
519268 TGTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (19 bp):
TAAAAATAAACAAAATAAA
Found at i:519269 original size:9 final size:10
Alignment explanation
Indices: 519225--519267 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
519215 ACAAAATGCG
519225 TAAAAAT-AA
1 TAAAAATAAA
519234 TAAAAATAAA
1 TAAAAATAAA
519244 TAAAAATAAA
1 TAAAAATAAA
* *
519254 -CAAAATGAA
1 TAAAAATAAA
519263 TAAAA
1 TAAAA
519268 TGTTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:519344 original size:18 final size:17
Alignment explanation
Indices: 519312--519358 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
519302 TGTTAATGGA
519312 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
*
519329 GTAAAAGAAATTAAAAAG
1 GTAAAA-AAATAAAAAAG
519347 G-AATAAAAATAA
1 GTAA-AAAAATAA
519359 TGTGTACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:519490 original size:16 final size:17
Alignment explanation
Indices: 519458--519496 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
519448 TGATATTAAA
519458 AAAATAACAGAAAAAAT
1 AAAATAACAGAAAAAAT
*
519475 AAAATAA-AGTAAAAAT
1 AAAATAACAGAAAAAAT
*
519491 ATAATA
1 AAAATA
519497 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAATAACAGAAAAAAT
Found at i:519518 original size:55 final size:57
Alignment explanation
Indices: 519430--519554 Score: 136
Period size: 55 Copynumber: 2.3 Consensus size: 57
519420 TAAAACAAAT
* *
519430 AAAAAATA-AAGATATACATGATATTAAAAAAATAACAGA-AAAAATA-AA-ATAAAG
1 AAAAAATATAATATATACATGATATTAAAAAAATAA-AAACAAAAATAGAATATAAAG
* * * *
519484 TAAAAATATAATATATATAT-ATATATAAATAAATAAAAACAAAAATAGAATATTAAG
1 AAAAAATATAATATATACATGATAT-TAAAAAAATAAAAACAAAAATAGAATATAAAG
519541 AAAAAATAT-ATATA
1 AAAAAATATAATATA
519555 AAAACGTATA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
54 13 0.22
55 26 0.44
56 7 0.12
57 13 0.22
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (57 bp):
AAAAAATATAATATATACATGATATTAAAAAAATAAAAACAAAAATAGAATATAAAG
Found at i:519662 original size:25 final size:23
Alignment explanation
Indices: 519638--519705 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 23
519628 TAATGTTATA
519638 AGATATATATAATAAAAATAATAT
1 AGATATATATAATAAAAA-AATAT
* *
519662 A-ATATAAATAA-AAAAGGAATAT
1 AGATATATATAATAAAA-AAATAT
*
519684 AG-TAAATA-AATAAAAAAATAT
1 AGATATATATAATAAAAAAATAT
519705 A
1 A
519706 ATTAAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
21 8 0.22
22 18 0.50
23 9 0.25
24 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (23 bp):
AGATATATATAATAAAAAAATAT
Done.