Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 3 of 195
Found at i:500274 original size:2 final size:2
Alignment explanation
Indices: 500255--500302 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
500245 GTGGAACTAG
* *
500255 AT AT AT AA AT AT AA 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
500297 AT AT AT
1 AT AT AT
500303 TAGGCTTATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:501666 original size:3 final size:3
Alignment explanation
Indices: 501658--501684 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
501648 ACAATCTCAA
501658 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
501685 TTTTTTCGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:502105 original size:21 final size:22
Alignment explanation
Indices: 502073--502119 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
502063 ATATTTTTTT
502073 ATTTGAAGTTATT-AGAATTAAA
1 ATTTGAAGTTATTGA-AATTAAA
502095 ATTTG-AGTTATTGAAATTAAA
1 ATTTGAAGTTATTGAAATTAAA
502116 ATTT
1 ATTT
502120 TAATATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.45
Consensus pattern (22 bp):
ATTTGAAGTTATTGAAATTAAA
Found at i:502168 original size:14 final size:13
Alignment explanation
Indices: 502146--502180 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
502136 AATAATACGA
502146 TTATTAATATTATT
1 TTATTAATATT-TT
*
502160 TTTTTAATATTTT
1 TTATTAATATTTT
502173 TTATTAAT
1 TTATTAAT
502181 TACTTTCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTAATATTTT
Found at i:506776 original size:2 final size:2
Alignment explanation
Indices: 506769--506835 Score: 102
Period size: 2 Copynumber: 34.5 Consensus size: 2
506759 TAGCTATCCA
506769 AT AT AT AT AT AT AT AT AT AT A- 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
* *
506810 AT AT AT AT AT AT A- AA AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
506836 AAAAATGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
1 2 0.03
2 58 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:506963 original size:15 final size:15
Alignment explanation
Indices: 506945--506996 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
506935 AAACTAAATT
506945 AATTTAAATAAACTA
1 AATTTAAATAAACTA
*
506960 AA-TT-AATAATA-TT
1 AATTTAAATAA-ACTA
506973 AATTTAAATAAACTA
1 AATTTAAATAAACTA
*
506988 GATTTAAAT
1 AATTTAAAT
506997 CAATAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
13 8 0.27
14 6 0.20
15 16 0.53
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (15 bp):
AATTTAAATAAACTA
Found at i:506982 original size:28 final size:31
Alignment explanation
Indices: 506942--507014 Score: 100
Period size: 28 Copynumber: 2.5 Consensus size: 31
506932 GATAAACTAA
506942 ATTAATTTAAATAAACTA-AATT-AAT-AAT
1 ATTAATTTAAATAAACTAGAATTAAATCAAT
*
506970 ATTAATTTAAATAAACTAGATTTAAATCAAT
1 ATTAATTTAAATAAACTAGAATTAAATCAAT
*
507001 AATAATTT-AATAAA
1 ATTAATTTAAATAAA
507015 AAATATTCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 18 0.45
29 3 0.08
30 9 0.22
31 10 0.25
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (31 bp):
ATTAATTTAAATAAACTAGAATTAAATCAAT
Found at i:507010 original size:16 final size:15
Alignment explanation
Indices: 506944--507010 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 15
506934 TAAACTAAAT
*
506944 TAATTTAAATAA-AC
1 TAATTTAAATAATAA
* *
506958 TAAATT-AATAATAT
1 TAATTTAAATAATAA
*
506972 TAATTTAAATAA-AC
1 TAATTTAAATAATAA
506986 TAGATTTAAATCAATAA
1 TA-ATTTAAAT-AATAA
507003 TAATTTAA
1 TAATTTAA
507011 TAAAAAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
13 5 0.12
14 14 0.33
15 13 0.30
16 8 0.19
17 3 0.07
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (15 bp):
TAATTTAAATAATAA
Found at i:507081 original size:11 final size:11
Alignment explanation
Indices: 506992--507105 Score: 50
Period size: 11 Copynumber: 10.5 Consensus size: 11
506982 AAACTAGATT
*
506992 TAAATCAATAA
1 TAAATTAATAA
*
507003 TAATTTAATAA
1 TAAATTAATAA
* * *
507014 -AAAATATTCA
1 TAAATTAATAA
* *
507024 TAATTTAATGA
1 TAAATTAATAA
* * *
507035 TAAATCATTCA
1 TAAATTAATAA
* **
507046 TAACTTAATGG
1 TAAATTAATAA
* *
507057 TAAATTATTCA
1 TAAATTAATAA
507068 TAAATTAATAA
1 TAAATTAATAA
* *
507079 TAAATCATTAA
1 TAAATTAATAA
* *
507090 TAATTTAATAG
1 TAAATTAATAA
507101 TAAAT
1 TAAAT
507106 CATTGATAAT
Statistics
Matches: 70, Mismatches: 32, Indels: 2
0.67 0.31 0.02
Matches are distributed among these distances:
10 6 0.09
11 64 0.91
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.39
Consensus pattern (11 bp):
TAAATTAATAA
Found at i:507142 original size:66 final size:66
Alignment explanation
Indices: 506992--507158 Score: 176
Period size: 66 Copynumber: 2.5 Consensus size: 66
506982 AAACTAGATT
* * *
506992 TAAATCAATAATAATTTAATAAAAAAT-ATTCATAATTTAATGATAAATCATTCATAACTTAATG
1 TAAATCAATAATAATTTAATAATAAATCATTAATAATTTAATGATAAATCATTCATAACTTAATA
507056 G
66 G
* * * * * * *
507057 TAAATTATTCATAAATTAATAATAAATCATTAATAATTTAAT-AGTAAATCATTGATAATTTAGT
1 TAAATCAATAATAATTTAATAATAAATCATTAATAATTTAATGA-TAAATCATTCATAACTTAAT
507121 AG
65 AG
* * ** *
507123 TAAATCACTGATAATTTAATTGTCAATCATTAATAA
1 TAAATCAATAATAATTTAATAATAAATCATTAATAA
507159 ATTTTTTTAT
Statistics
Matches: 83, Mismatches: 17, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
65 23 0.28
66 60 0.72
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (66 bp):
TAAATCAATAATAATTTAATAATAAATCATTAATAATTTAATGATAAATCATTCATAACTTAATA
G
Found at i:507158 original size:22 final size:22
Alignment explanation
Indices: 506992--507158 Score: 158
Period size: 22 Copynumber: 7.6 Consensus size: 22
506982 AAACTAGATT
* *
506992 TAAATCAATAATAATTTAATAA
1 TAAATCATTAATAATTTAATAG
* *
507014 AAAAT-ATTCATAATTTAAT-G
1 TAAATCATTAATAATTTAATAG
* * *
507034 ATAAATCATTCATAACTTAATGG
1 -TAAATCATTAATAATTTAATAG
* * * *
507057 TAAATTATTCATAAATTAATAA
1 TAAATCATTAATAATTTAATAG
507079 TAAATCATTAATAATTTAATAG
1 TAAATCATTAATAATTTAATAG
* *
507101 TAAATCATTGATAATTTAGTAG
1 TAAATCATTAATAATTTAATAG
* * *
507123 TAAATCACTGATAATTTAATTG
1 TAAATCATTAATAATTTAATAG
*
507145 TCAATCATTAATAA
1 TAAATCATTAATAA
507159 ATTTTTTTAT
Statistics
Matches: 120, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
21 16 0.13
22 103 0.86
23 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATAATTTAATAG
Found at i:507500 original size:22 final size:22
Alignment explanation
Indices: 507401--507502 Score: 89
Period size: 22 Copynumber: 4.6 Consensus size: 22
507391 TATATATTAG
**
507401 TAAATCAATGATAGGTTAATAA
1 TAAATCAATGATAATTTAATAA
* * *
507423 -AAAACAAGTGATAACTTAATAG
1 TAAATCAA-TGATAATTTAATAA
* * *
507445 TTAATCATTAATAATTTAATAA
1 TAAATCAATGATAATTTAATAA
*
507467 TAAATCAATGATAATTTAATTA
1 TAAATCAATGATAATTTAATAA
* *
507489 TAAATTAGTGATAA
1 TAAATCAATGATAA
507503 CTTAGTAGGA
Statistics
Matches: 62, Mismatches: 16, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
21 6 0.10
22 52 0.84
23 4 0.06
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (22 bp):
TAAATCAATGATAATTTAATAA
Found at i:507517 original size:66 final size:66
Alignment explanation
Indices: 507401--507626 Score: 174
Period size: 66 Copynumber: 3.4 Consensus size: 66
507391 TATATATTAG
** * * * *
507401 TAAATCAATGATAGGTTAATAAAAAACAAGTGATAACTTAATAGTTAATCATTAATAATTTAATA
1 TAAATCAATGATAACTTAATAATAAATAAGTGATAACTTAGTAGTAAATCATTAATAATTTAATA
507466 A
66 A
* * * *
507467 TAAATCAATGATAATTTAATTATAAATTAGTGATAACTTAGTAGGAAATCAGTT--TCAATTTAA
1 TAAATCAATGATAACTTAATAATAAATAAGTGATAACTTAGTAGTAAATCA-TTAAT-AATTTAA
*
507530 TAG
64 TAA
* ** * * *
507533 T-AATTAATTGATAAACTCCATAATAAATCA-TGAAGAACTTAGTAGTAAATCAATAATAATTTA
1 TAAATCAA-TGAT-AACTTAATAATAAATAAGTG-ATAACTTAGTAGTAAATCATTAATAATTTA
507596 ATAA
63 ATAA
* * * *
507600 TTAATTATTGAAAACTTAA-AAGTAAAT
1 TAAATCAATGATAACTTAATAA-TAAAT
507627 TAATATAATT
Statistics
Matches: 127, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
65 8 0.06
66 69 0.54
67 44 0.35
68 6 0.05
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (66 bp):
TAAATCAATGATAACTTAATAATAAATAAGTGATAACTTAGTAGTAAATCATTAATAATTTAATA
A
Found at i:507839 original size:21 final size:20
Alignment explanation
Indices: 507731--507861 Score: 84
Period size: 21 Copynumber: 6.3 Consensus size: 20
507721 AAAAATTACT
507731 AATTTTGATAACTTTTGAT-A
1 AATTTTGATAAC-TTTGATAA
** * *
507751 TGTTTTGGTAATCTTTGTTAA
1 AATTTTGATAA-CTTTGATAA
* * *
507772 AAGTTTCATAACCTTTAATAA
1 AATTTTGATAA-CTTTGATAA
*
507793 AATTTTGATAACTTTCGATAC
1 AATTTTGATAACTTT-GATAA
*
507814 AATTTTGATAATCTTTGATAT
1 AATTTTGATAA-CTTTGATAA
* * * *
507835 TATTTAGGTAACTTATGATAT
1 AATTTTGATAACTT-TGATAA
507856 AATTTT
1 AATTTT
507862 TTTTAACAAT
Statistics
Matches: 84, Mismatches: 22, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
20 20 0.24
21 60 0.71
22 4 0.05
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.49
Consensus pattern (20 bp):
AATTTTGATAACTTTGATAA
Found at i:508647 original size:17 final size:17
Alignment explanation
Indices: 508602--508647 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
508592 GTATTTTACT
508602 ATTTTTATATAATAAAA
1 ATTTTTATATAATAAAA
* *
508619 ATTTATGTATAATAAAA
1 ATTTTTATATAATAAAA
* *
508636 TTTTTTAAATAA
1 ATTTTTATATAA
508648 AGAAAAATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
ATTTTTATATAATAAAA
Found at i:510622 original size:121 final size:121
Alignment explanation
Indices: 510407--510653 Score: 404
Period size: 121 Copynumber: 2.0 Consensus size: 121
510397 CTTTATATTT
* * *
510407 TTTAATCTTTTATATGCAATTATACATCAATAATAGGTATGAAAACATATATACTAATATTTTAA
1 TTTAATCTTTTATATACAATTATACATCAATAACAGGTATGAAAACATATATACTAATAATTTAA
* *
510472 TTAAATTATTAATAAAACTTATCTCAATATGTACTATTTTATCATGAACTAAAAAA
66 TTAAATTATTAATAAAACTTATCTCAATATGTACTACTTTATCATAAACTAAAAAA
**
510528 TTTAATCTTTTATATACAATTATACATTGATAACAGGTATGAAAACATATATACTAATAATTTAA
1 TTTAATCTTTTATATACAATTATACATCAATAACAGGTATGAAAACATATATACTAATAATTTAA
* * *
510593 TTAAATTATTAATAAAACTTTTCTTAATATGTATTACTTTATCATAAACTAAAAAA
66 TTAAATTATTAATAAAACTTATCTCAATATGTACTACTTTATCATAAACTAAAAAA
510649 TTTAA
1 TTTAA
510654 GAATATCTTA
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 116 1.00
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.41
Consensus pattern (121 bp):
TTTAATCTTTTATATACAATTATACATCAATAACAGGTATGAAAACATATATACTAATAATTTAA
TTAAATTATTAATAAAACTTATCTCAATATGTACTACTTTATCATAAACTAAAAAA
Found at i:511034 original size:22 final size:22
Alignment explanation
Indices: 510995--511056 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
510985 AATAATCATA
** * *
510995 AATAATTTAATAACAAATTACT
1 AATAATTTAATAGTAAATGAAT
511017 AATAATTTAATAGTAAATGAAT
1 AATAATTTAATAGTAAATGAAT
* *
511039 GATAATTTAATGGTAAAT
1 AATAATTTAATAGTAAAT
511057 AGTTGATAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (22 bp):
AATAATTTAATAGTAAATGAAT
Found at i:511208 original size:22 final size:22
Alignment explanation
Indices: 511183--511267 Score: 98
Period size: 22 Copynumber: 3.9 Consensus size: 22
511173 AAAAAAAGAG
* *
511183 TGATAACTTAATAATTAATTAC
1 TGATAACTTAATAATAAATTAA
*
511205 TGATAACTTAGTAATAAATTAA
1 TGATAACTTAATAATAAATTAA
* * *
511227 TGATAATTTAATAGTAAATTAG
1 TGATAACTTAATAATAAATTAA
* *
511249 TGATAATTTAATAGTAAAT
1 TGATAACTTAATAATAAAT
511268 CAACTTTAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (22 bp):
TGATAACTTAATAATAAATTAA
Found at i:511232 original size:11 final size:11
Alignment explanation
Indices: 511183--511260 Score: 50
Period size: 11 Copynumber: 7.1 Consensus size: 11
511173 AAAAAAAGAG
*
511183 TGATAACTTAA
1 TGATAAATTAA
* * *
511194 TAATTAATTAC
1 TGATAAATTAA
* *
511205 TGATAACTTAG
1 TGATAAATTAA
*
511216 TAATAAATTAA
1 TGATAAATTAA
*
511227 TGATAATTTAA
1 TGATAAATTAA
*
511238 T-AGTAAATTAG
1 TGA-TAAATTAA
*
511249 TGATAATTTAA
1 TGATAAATTAA
511260 T
1 T
511261 AGTAAATCAA
Statistics
Matches: 48, Mismatches: 17, Indels: 4
0.70 0.25 0.06
Matches are distributed among these distances:
10 1 0.02
11 46 0.96
12 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (11 bp):
TGATAAATTAA
Found at i:511267 original size:44 final size:43
Alignment explanation
Indices: 511183--512108 Score: 155
Period size: 44 Copynumber: 21.5 Consensus size: 43
511173 AAAAAAAGAG
* * * * * *
511183 TGATAACTTAATAATTAATTACTGATAACTTAGTAATAAATTAA
1 TGATAATTTAATAGTAAATTA-TGATAATTTAATAGTAAATTAA
*
511227 TGATAATTTAATAGTAAATTAGTGATAATTTAATAGTAAATCAA
1 TGATAATTTAATAGTAAATTA-TGATAATTTAATAGTAAATTAA
* * * *
511271 CT-TTAGTTTAATAGT-AATTA--AT--TTATAGTAGTAAA-CAA
1 -TGATAATTTAATAGTAAATTATGATAATT-TAATAGTAAATTAA
* * * * * * * * *
511309 TAAACAACTTAATCGTAAATCAATTATAAATTAGTAATAAA-TAA
1 T-GATAATTTAATAGTAAAT-TATGATAATTTAATAGTAAATTAA
* *
511353 TTGATAATTTAGTAGTAAATTAGTGATAATTTAATAGTAAATCAAA
1 -TGATAATTTAATAGTAAATTA-TGATAATTTAATAGTAAAT-TAA
* * * *
511399 T-TTAGTTTAATAGT-AATTA--AT--TTATAGTAGTAAA-CAA
1 TGATAATTTAATAGTAAATTATGATAATT-TAATAGTAAATTAA
* * * * * * * *
511436 TAAATAACTTAATCGTAAATCAATTATAAATTAGTAATAAA-TAA
1 T-GATAATTTAATAGTAAAT-TATGATAATTTAATAGTAAATTAA
* * * * * *
511480 TTGATAATTTAGTAGT-TATTCATTGAAAACTTAAAAGT-AATTAG
1 -TGATAATTTAATAGTAAATT-A-TGATAATTTAATAGTAAATTAA
* * * * * * *
511524 T-ATAACTTAGTAGTAAATTATCGGTAATATAATAGTTAATCAT
1 TGATAATTTAATAGTAAATTAT-GATAATTTAATAGTAAATTAA
* * * *
511567 TGATGACTTAATAGTAAATTATACATAATTTAATA-TAAAATAA
1 TGATAATTTAATAGTAAATTAT-GATAATTTAATAGTAAATTAA
* * * *
511610 TAATAATTTAATAGCT-AATCATTGATAACTTAATAGTAAA-TCA
1 TGATAATTTAATAG-TAAATTA-TGATAATTTAATAGTAAATTAA
* * * * * *
511653 TACATAATTTAATA-TAAAGTAGTAAATCAACTTTAGT-TTAATAGTAA
1 T-GATAATTTAATAGTAAATTA-T-GAT-AA-TTTAATAGTAA-ATTAA
** * * * *
511700 T--TAATTTATAGTAGTAAACAATAAATAACTTAATCGTAAATCAA
1 TGATAATTTA-A-TAGTAAATTAT-GATAATTTAATAGTAAATTAA
* * * * * * * *
511744 TTATAAATTAGTTGTAAATAATTGATAATTTAGTAGT-TATTCAT
1 TGATAATTTAATAGTAAATTA-TGATAATTTAATAGTAAATT-AA
* * * * *
511788 TGAAAACTTAAAAGT-AATTA-GTATAACTTAGTAGTAAATT-A
1 TGATAATTTAATAGTAAATTATG-ATAATTTAATAGTAAATTAA
* * * * *
511829 TCGGTAATATAATAGTTAATCATTGATAACTTAATAGTAAATT-A
1 T-GATAATTTAATAGTAAATTA-TGATAATTTAATAGTAAATTAA
* * * * * *
511873 TACATAATTTAATAATGAATCATAGATAATTTAGT-GATAAATTAG
1 T-GATAATTTAATAGTAAATTAT-GATAATTTAATAG-TAAATTAA
* ** * * * * *
511918 TGACAATTTTGT-GATAAATAATTAAAAATTAAGTAGTAAATCAA
1 TGATAATTTAATAG-TAAATTATGATAATTTAA-TAGTAAATTAA
** * * * * * * * *
511962 TGATAACATAATAATAAATATATAAAAATATAACAATAAATCAT
1 TGATAATTTAATAGTAAAT-TATGATAATTTAATAGTAAATTAA
* * *
512006 TGATAATTTAATAGTAAA-T-TGATAA-CT--TAGTAATTTAC
1 TGATAATTTAATAGTAAATTATGATAATTTAATAGTAAATTAA
* * * * * * *
512044 TAATAATATAATAGTAAATTACTAACAACTTAATTGTAAATCAA
1 TGATAATTTAATAGTAAATTA-TGATAATTTAATAGTAAATTAA
512088 TGATAATTTAATAGTAAATTA
1 TGATAATTTAATAGTAAATTA
512109 GTTAATCATT
Statistics
Matches: 629, Mismatches: 184, Indels: 138
0.66 0.19 0.15
Matches are distributed among these distances:
37 4 0.01
38 29 0.05
39 36 0.06
40 11 0.02
41 13 0.02
42 46 0.07
43 86 0.14
44 346 0.55
45 30 0.05
46 20 0.03
47 8 0.01
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.38
Consensus pattern (43 bp):
TGATAATTTAATAGTAAATTATGATAATTTAATAGTAAATTAA
Found at i:511299 original size:22 final size:23
Alignment explanation
Indices: 511219--511299 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 23
511209 AACTTAGTAA
* *
511219 TAAATTAA-TGATAATTTAATAG
1 TAAATTAACTTATAGTTTAATAG
* * *
511241 TAAATT-AGTGATAATTTAATAG
1 TAAATTAACTTATAGTTTAATAG
*
511263 TAAATCAACTT-TAGTTTAATAG
1 TAAATTAACTTATAGTTTAATAG
*
511285 T-AATTAATTTATAGT
1 TAAATTAACTTATAGT
511300 AGTAAACAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 8 0.16
22 40 0.80
23 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.43
Consensus pattern (23 bp):
TAAATTAACTTATAGTTTAATAG
Found at i:511321 original size:61 final size:60
Alignment explanation
Indices: 511251--511460 Score: 217
Period size: 61 Copynumber: 3.4 Consensus size: 60
511241 TAAATTAGTG
*
511251 ATAATTTAATAGTAAATCAACTTTAGTTTAATAGTAATTAATTTATAGTAGTAAACAATAA
1 ATAACTTAATAGTAAATCAA-TTTAGTTTAATAGTAATTAATTTATAGTAGTAAACAATAA
* * * * * * *
511312 ACAACTTAATCGTAAATCAATTATAAATTAGTAATAAATAATTGATAATT-TAGTAGTAAATTAG
1 ATAACTTAATAGTAAATCAATT-T-AGTT--TAAT-AGTAATT-A-ATTTATAGTAGTAAA-CAA
*
511376 T-G
58 TAA
*
511378 ATAATTTAATAGTAAATCAAATTTAGTTTAATAGTAATTAATTTATAGTAGTAAACAATAA
1 ATAACTTAATAGTAAATC-AATTTAGTTTAATAGTAATTAATTTATAGTAGTAAACAATAA
*
511439 ATAACTTAATCGTAAATCAATT
1 ATAACTTAATAGTAAATCAATT
511461 ATAAATTAGT
Statistics
Matches: 118, Mismatches: 20, Indels: 23
0.73 0.12 0.14
Matches are distributed among these distances:
60 11 0.09
61 45 0.38
62 9 0.08
63 4 0.03
64 4 0.03
65 9 0.08
66 27 0.23
67 9 0.08
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.38
Consensus pattern (60 bp):
ATAACTTAATAGTAAATCAATTTAGTTTAATAGTAATTAATTTATAGTAGTAAACAATAA
Found at i:511349 original size:22 final size:22
Alignment explanation
Indices: 511324--511381 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
511314 AACTTAATCG
511324 TAAATCAATT-ATAAATTAGTAA
1 TAAAT-AATTGATAAATTAGTAA
* *
511346 TAAATAATTGATAATTTAGTAG
1 TAAATAATTGATAAATTAGTAA
* *
511368 TAAATTAGTGATAA
1 TAAATAATTGATAA
511382 TTTAATAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (22 bp):
TAAATAATTGATAAATTAGTAA
Found at i:511382 original size:22 final size:22
Alignment explanation
Indices: 511334--511394 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
511324 TAAATCAATT
* * *
511334 ATAAATTAGTAATAAATAATTG
1 ATAATTTAGTAGTAAATAAGTG
*
511356 ATAATTTAGTAGTAAATTAGTG
1 ATAATTTAGTAGTAAATAAGTG
*
511378 ATAATTTAATAGTAAAT
1 ATAATTTAGTAGTAAAT
511395 CAAATTTAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.39
Consensus pattern (22 bp):
ATAATTTAGTAGTAAATAAGTG
Found at i:511476 original size:22 final size:22
Alignment explanation
Indices: 511451--511493 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
511441 AACTTAATCG
511451 TAAATCAATT-ATAAATTAGTAA
1 TAAAT-AATTGATAAATTAGTAA
*
511473 TAAATAATTGATAATTTAGTA
1 TAAATAATTGATAAATTAGTA
511494 GTTATTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (22 bp):
TAAATAATTGATAAATTAGTAA
Found at i:511519 original size:127 final size:127
Alignment explanation
Indices: 511207--511495 Score: 526
Period size: 127 Copynumber: 2.3 Consensus size: 127
511197 TTAATTACTG
* *
511207 ATAACTTAGTAATAAATTAA-TGATAATTTAATAGTAAATTAGTGATAATTTAATAGTAAATCAA
1 ATAAATTAGTAATAAA-TAATTGATAATTTAGTAGTAAATTAGTGATAATTTAATAGTAAATCAA
*
511271 CTTTAGTTTAATAGTAATTAATTTATAGTAGTAAACAATAAACAACTTAATCGTAAATCAATT
65 ATTTAGTTTAATAGTAATTAATTTATAGTAGTAAACAATAAACAACTTAATCGTAAATCAATT
511334 ATAAATTAGTAATAAATAATTGATAATTTAGTAGTAAATTAGTGATAATTTAATAGTAAATCAAA
1 ATAAATTAGTAATAAATAATTGATAATTTAGTAGTAAATTAGTGATAATTTAATAGTAAATCAAA
*
511399 TTTAGTTTAATAGTAATTAATTTATAGTAGTAAACAATAAATAACTTAATCGTAAATCAATT
66 TTTAGTTTAATAGTAATTAATTTATAGTAGTAAACAATAAACAACTTAATCGTAAATCAATT
511461 ATAAATTAGTAATAAATAATTGATAATTTAGTAGT
1 ATAAATTAGTAATAAATAATTGATAATTTAGTAGT
511496 TATTCATTGA
Statistics
Matches: 157, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
126 3 0.02
127 154 0.98
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.38
Consensus pattern (127 bp):
ATAAATTAGTAATAAATAATTGATAATTTAGTAGTAAATTAGTGATAATTTAATAGTAAATCAAA
TTTAGTTTAATAGTAATTAATTTATAGTAGTAAACAATAAACAACTTAATCGTAAATCAATT
Found at i:511599 original size:22 final size:22
Alignment explanation
Indices: 511574--511670 Score: 103
Period size: 22 Copynumber: 4.5 Consensus size: 22
511564 CATTGATGAC
*
511574 TTAATAGTAAATTATACATAAT
1 TTAATAGTAAATCATACATAAT
*
511596 TTAATA-TAAAATAATA-ATAAT
1 TTAATAGT-AAATCATACATAAT
** *
511617 TTAATAGCT-AATCATTGATAAC
1 TTAATAG-TAAATCATACATAAT
511639 TTAATAGTAAATCATACATAAT
1 TTAATAGTAAATCATACATAAT
511661 TTAATA-TAAA
1 TTAATAGTAAA
511671 GTAGTAAATC
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
21 22 0.35
22 40 0.63
23 1 0.02
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (22 bp):
TTAATAGTAAATCATACATAAT
Found at i:511622 original size:43 final size:44
Alignment explanation
Indices: 511574--511670 Score: 103
Period size: 43 Copynumber: 2.2 Consensus size: 44
511564 CATTGATGAC
* *
511574 TTAATAGTAAATTATACATAATTTAATA-TAAAATAATA-ATAAT
1 TTAATAGTAAATCATACATAACTTAATAGT-AAATAATACATAAT
** *
511617 TTAATAGCT-AATCATTGATAACTTAATAGTAAATCATACATAAT
1 TTAATAG-TAAATCATACATAACTTAATAGTAAATAATACATAAT
511661 TTAATA-TAAA
1 TTAATAGTAAA
511671 GTAGTAAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
42 1 0.02
43 31 0.69
44 13 0.29
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (44 bp):
TTAATAGTAAATCATACATAACTTAATAGTAAATAATACATAAT
Found at i:511631 original size:65 final size:65
Alignment explanation
Indices: 511548--511670 Score: 210
Period size: 65 Copynumber: 1.9 Consensus size: 65
511538 AAATTATCGG
* * *
511548 TAATATAATAGTTAATCATTGATGACTTAATAGTAAATTATACATAATTTAATATAAAATAATAA
1 TAATATAATAGCTAATCATTGATAACTTAATAGTAAATCATACATAATTTAATATAAAATAATAA
*
511613 TAATTTAATAGCTAATCATTGATAACTTAATAGTAAATCATACATAATTTAATATAAA
1 TAATATAATAGCTAATCATTGATAACTTAATAGTAAATCATACATAATTTAATATAAA
511671 GTAGTAAATC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.38
Consensus pattern (65 bp):
TAATATAATAGCTAATCATTGATAACTTAATAGTAAATCATACATAATTTAATATAAAATAATAA
Found at i:511825 original size:64 final size:64
Alignment explanation
Indices: 511745--511868 Score: 158
Period size: 64 Copynumber: 1.9 Consensus size: 64
511735 GTAAATCAAT
* * * * *
511745 TATAAATTAGTTGTAAATAATTGATAATTTAGTAGTTATTCATTGAAAACTTAAAAGTAATTAG
1 TATAAATTAGTAGTAAATAATCGATAATATAATAGTTAATCATTGAAAACTTAAAAGTAATTAG
* * * * *
511809 TATAACTTAGTAGTAAATTATCGGTAATATAATAGTTAATCATTGATAACTTAATAGTAA
1 TATAAATTAGTAGTAAATAATCGATAATATAATAGTTAATCATTGAAAACTTAAAAGTAA
511869 ATTATACATA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.40
Consensus pattern (64 bp):
TATAAATTAGTAGTAAATAATCGATAATATAATAGTTAATCATTGAAAACTTAAAAGTAATTAG
Found at i:511863 original size:22 final size:22
Alignment explanation
Indices: 511724--512106 Score: 87
Period size: 22 Copynumber: 17.8 Consensus size: 22
511714 TAAACAATAA
*
511724 ATAACTTAATCGTAAATCAATT-
1 ATAACTTAATAGTAAATC-ATTG
* * * *
511746 ATAAATTAGTTGTAAATAATTG
1 ATAACTTAATAGTAAATCATTG
* * * *
511768 ATAATTTAGTAGTTATTCATTG
1 ATAACTTAATAGTAAATCATTG
* * * *
511790 AAAACTTAAAAGT-AATTAGT-
1 ATAACTTAATAGTAAATCATTG
* * *
511810 ATAACTTAGTAGTAAATTATCG
1 ATAACTTAATAGTAAATCATTG
* *
511832 GTAA-TATAATAGTTAATCATTG
1 ATAACT-TAATAGTAAATCATTG
* **
511854 ATAACTTAATAGTAAATTATAC
1 ATAACTTAATAGTAAATCATTG
* * * *
511876 ATAATTTAATAATGAATCATAG
1 ATAACTTAATAGTAAATCATTG
* * * *
511898 ATAATTTAGT-GATAAATTAGTG
1 ATAACTTAATAG-TAAATCATTG
* * ** *
511920 ACAATTTTGT-GATAAATAATT-
1 ATAACTTAATAG-TAAATCATTG
* * *
511941 AAAAATTAAGTAGTAAATCAATG
1 ATAACTTAA-TAGTAAATCATTG
* *
511964 ATAACATAATAATAAAT-ATAT-
1 ATAACTTAATAGTAAATCAT-TG
* * * *
511985 AAAAATATAACAATAAATCATTG
1 ATAACT-TAATAGTAAATCATTG
*
512008 ATAATTTAATAGT-AA--ATTG
1 ATAACTTAATAGTAAATCATTG
* * * *
512027 ATAAC-T--TAGTAATTTACTA
1 ATAACTTAATAGTAAATCATTG
* * *
512046 ATAA-TATAATAGTAAATTACTA
1 ATAACT-TAATAGTAAATCATTG
* * *
512068 ACAACTTAATTGTAAATCAATG
1 ATAACTTAATAGTAAATCATTG
*
512090 ATAATTTAATAGTAAAT
1 ATAACTTAATAGTAAAT
512107 TAGTTAATCA
Statistics
Matches: 262, Mismatches: 78, Indels: 42
0.69 0.20 0.11
Matches are distributed among these distances:
16 4 0.02
17 1 0.00
18 1 0.00
19 14 0.05
20 11 0.04
21 24 0.09
22 192 0.73
23 15 0.06
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (22 bp):
ATAACTTAATAGTAAATCATTG
Found at i:512160 original size:44 final size:43
Alignment explanation
Indices: 512107--512204 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 43
512097 AATAGTAAAT
* * * * *
512107 TAGTTAATCATTAATAATTTTTTAGTAAATCATCAATAAAGTAG
1 TAGTAAATCATT-ATAACTTTATAATAAATCATCAATAAAGTAA
* **
512151 TAGTAAATCAATTATAACTTTATAATAAATTATCAATAATTTAA
1 TAGTAAATC-ATTATAACTTTATAATAAATCATCAATAAAGTAA
512195 TAGTAAATCA
1 TAGTAAATCA
512205 CTAACAATGG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
43 1 0.02
44 41 0.91
45 3 0.07
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (43 bp):
TAGTAAATCATTATAACTTTATAATAAATCATCAATAAAGTAA
Found at i:512700 original size:19 final size:19
Alignment explanation
Indices: 512676--512737 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
512666 TAATTAATTA
512676 ATAAATTTAGTAGTAAATC
1 ATAAATTTAGTAGTAAATC
* *
512695 ATAAA-TAACTTAGTAAATC
1 ATAAATTTA-GTAGTAAATC
*
512714 AATGATAATTTAGTAGTTAATC
1 -AT-A-AATTTAGTAGTAAATC
512736 AT
1 AT
512738 TGGAAACTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 2 0.06
19 14 0.42
20 2 0.06
21 3 0.09
22 10 0.30
23 2 0.06
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (19 bp):
ATAAATTTAGTAGTAAATC
Found at i:512730 original size:22 final size:22
Alignment explanation
Indices: 512553--513351 Score: 120
Period size: 22 Copynumber: 35.9 Consensus size: 22
512543 AACAACATAT
**
512553 TAGTAAATCAATGATAGGTTAA
1 TAGTAAATCAATGATAATTTAA
** * *
512575 TAAAAAAT-AAGTAATAACTTAA
1 TAGTAAATCAA-TGATAATTTAA
* *
512597 TAGTTAAT-AATTGATAACTTAA
1 TAGTAAATCAA-TGATAATTTAA
* * * *
512619 TATTAAATTAGTGATAACTTAA
1 TAGTAAATCAATGATAATTTAA
*
512641 TAGTAAATCAAT-TTCAATTTAA
1 TAGTAAATCAATGAT-AATTTAA
* * * *
512663 AAGT-AATTAATTAATAAATTTAG
1 TAGTAAATCAA-TGAT-AATTTAA
512686 TAGTAAATC-AT-A-AA--TAA
1 TAGTAAATCAATGATAATTTAA
*
512703 CTTAGTAAATCAATGATAATTTAG
1 --TAGTAAATCAATGATAATTTAA
* * *
512727 TAGTTAATCATTGGA-AACTTAA
1 TAGTAAATCAAT-GATAATTTAA
* * *
512749 AAGTAAACCAAT-ATAACTTAA
1 TAGTAAATCAATGATAATTTAA
*
512770 TAGTAGTTAATC-ATCAATAATTTAA
1 TAGTA---AATCAAT-GATAATTTAA
* * * **
512795 TAATTAATCAATAATAGCTTAA
1 TAGTAAATCAATGATAATTTAA
*
512817 GAGTAAATC-ATGAATAATTTAA
1 TAGTAAATCAATG-ATAATTTAA
* *
512839 TA-TAAATTAATGATAATTGACA
1 TAGTAAATCAATGATAATTTA-A
* * * **
512861 -A-CAAAT-TATGGTTAATTTTG
1 TAGTAAATCAAT-GATAATTTAA
* * *** * *
512881 TAATAAGTTTGTGATGATTTTA
1 TAGTAAATCAATGATAATTTAA
* * *
512903 TAGTAAAT-AATCAAAAATTAAA
1 TAGTAAATCAAT-GATAATTTAA
* * *
512925 TAGTAAATCAAAGATAATATAG
1 TAGTAAATCAATGATAATTTAA
*
512947 TAGTAAATGC-AT-ATTAATATAA
1 TAGTAAAT-CAATGA-TAATTTAA
* * * *
512969 TAATAAATTATTAATAATTT-A
1 TAGTAAATCAATGATAATTTAA
* * * *
512990 TATGTAAATTATTAATAATTTAG
1 TA-GTAAATCAATGATAATTTAA
* * * * *
513013 TAATAAATCACTAATAATCTAG
1 TAGTAAATCAATGATAATTTAA
* *
513035 TTGTAAAT-AAGTGATAATTTAG
1 TAGTAAATCAA-TGATAATTTAA
* * * * *
513057 TAGCAAATTAGTTAACAATTGATAA
1 TAGTAAATCA-ATGATAATT--TAA
* * * *
513082 CTTTGTAATAAATCATTAATAAATTAA
1 --TAGT---AAATCAATGATAATTTAA
* * * *
513109 TAGTAAATTAGTTATAATTTTA
1 TAGTAAATCAATGATAATTTAA
* * * *
513131 TAATAAATCATTAATAACTTAA
1 TAGTAAATCAATGATAATTTAA
* *
513153 TAGTAAATC-ATCAATAATTTGA
1 TAGTAAATCAAT-GATAATTTAA
* *
513175 TAGTAAATCAATCATAATTTAG
1 TAGTAAATCAATGATAATTTAA
* * * * * *
513197 CAATAAATTATTCATAAATTAA
1 TAGTAAATCAATGATAATTTAA
* *
513219 TAGTAAATTAAT-ACTAATTAAA
1 TAGTAAATCAATGA-TAATTTAA
*
513241 TAGTAAATTAATATTGATAA-TTAA
1 TAGTAAA-TCA-A-TGATAATTTAA
* * * *
513265 -ACGATATATCATTGATGATTTAG
1 TA-G-TAAATCAATGATAATTTAA
* *
513288 TAGTAAATCACTGATAATATAA
1 TAGTAAATCAATGATAATTTAA
* *
513310 TAGTAAATCAATAATAATTAAA
1 TAGTAAATCAATGATAATTTAA
* * * *
513332 TTGTCACTCATTGATAATTT
1 TAGTAAATCAATGATAATTT
513352 TTTTAAACTT
Statistics
Matches: 562, Mismatches: 158, Indels: 114
0.67 0.19 0.14
Matches are distributed among these distances:
17 2 0.00
19 11 0.02
20 5 0.01
21 55 0.10
22 390 0.69
23 42 0.07
24 16 0.03
25 23 0.04
26 1 0.00
27 5 0.01
29 7 0.01
30 5 0.01
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (22 bp):
TAGTAAATCAATGATAATTTAA
Found at i:512746 original size:41 final size:42
Alignment explanation
Indices: 512675--512783 Score: 100
Period size: 41 Copynumber: 2.5 Consensus size: 42
512665 GTAATTAATT
* *
512675 AATA-AATTTAGTAGTAAATCA-TAAATAACTT-AGTAAATC
1 AATATAATTTAGTAGTTAATCATTAAATAACTTAAGTAAACC
**
512714 AATGATAATTTAGTAGTTAATCATTGGA-AACTTAAAAGTAAACC
1 AAT-ATAATTTAGTAGTTAATCATTAAATAACTT--AAGTAAACC
512758 AATATAACTTAATAGTAGTTAATCAT
1 AATATAA-TT--TAGTAGTTAATCAT
512784 CAATAATTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
39 3 0.05
40 1 0.02
41 21 0.37
42 2 0.04
43 4 0.07
44 12 0.21
46 14 0.25
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (42 bp):
AATATAATTTAGTAGTTAATCATTAAATAACTTAAGTAAACC
Found at i:512985 original size:11 final size:11
Alignment explanation
Indices: 512969--513020 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
512959 ATTAATATAA
512969 TAATAAATTAT
1 TAATAAATTAT
*
512980 TAATAATTTA-
1 TAATAAATTAT
*
512990 TATGTAAATTAT
1 TA-ATAAATTAT
* *
513002 TAATAATTTAG
1 TAATAAATTAT
513013 TAATAAAT
1 TAATAAAT
513021 CACTAATAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
10 2 0.06
11 28 0.88
12 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (11 bp):
TAATAAATTAT
Found at i:513017 original size:44 final size:44
Alignment explanation
Indices: 512969--513226 Score: 139
Period size: 44 Copynumber: 5.7 Consensus size: 44
512959 ATTAATATAA
*
512969 TAATAAATTATTAATAATTTATATGTAAATTATTAATAATTTAG
1 TAATAAATTATTAATAATTTATATGTAAATCATTAATAATTTAG
* * * * * *
513013 TAATAAATCACTAATAATCTAGT-TGTAAATAAGTGATAATTTAG
1 TAATAAATTATTAATAATTTA-TATGTAAATCATTAATAATTTAG
** * * * *
513057 TAGCAAATTAGTTAACAATTGATAACTTTGTAATAAATCATTAATAAATTAA
1 TAATAAATTA-TTAATAATT--T-A-TATG---TAAATCATTAATAATTTAG
* * * *
513109 TAGTAAATTAGTT-ATAATTT-TATAATAAATCATTAATAACTTAA
1 TAATAAATTA-TTAATAATTTATAT-GTAAATCATTAATAATTTAG
* * * * *
513153 TAGTAAATCATCAATAATTTGATA-GTAAATCAATCATAATTTAG
1 TAATAAATTATTAATAATTT-ATATGTAAATCATTAATAATTTAG
* * *
513197 CAATAAATTATTCATAAATTA-ATAGTAAAT
1 TAATAAATTATTAATAATTTATAT-GTAAAT
513227 TAATACTAAT
Statistics
Matches: 163, Mismatches: 36, Indels: 30
0.71 0.16 0.13
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 112 0.69
45 7 0.04
46 4 0.02
47 1 0.01
48 2 0.01
49 3 0.02
51 5 0.03
52 26 0.16
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.40
Consensus pattern (44 bp):
TAATAAATTATTAATAATTTATATGTAAATCATTAATAATTTAG
Found at i:513163 original size:66 final size:66
Alignment explanation
Indices: 513090--513252 Score: 177
Period size: 66 Copynumber: 2.5 Consensus size: 66
513080 AACTTTGTAA
* * * *
513090 TAAATCATTAATAAATTAATAGTAAATTAGTTATAATTTTA-TAATAAATCATTAATAACTTAAT
1 TAAATCATTAATAAATTAATAGTAAATTAATCATAA-TTTAGCAATAAATCATTAATAAATTAAT
513154 AG
65 AG
* * * * * *
513156 TAAATCATCAATAATTTGATAGTAAATCAATCATAATTTAGCAATAAATTATTCATAAATTAATA
1 TAAATCATTAATAAATTAATAGTAAATTAATCATAATTTAGCAATAAATCATTAATAAATTAATA
513221 G
66 G
* * *
513222 TAAATTAATACT-AATTAAATAGTAAATTAAT
1 TAAATCATTAATAAATT-AATAGTAAATTAAT
513253 ATTGATAATT
Statistics
Matches: 78, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
65 7 0.09
66 71 0.91
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (66 bp):
TAAATCATTAATAAATTAATAGTAAATTAATCATAATTTAGCAATAAATCATTAATAAATTAATA
G
Found at i:513225 original size:11 final size:11
Alignment explanation
Indices: 513211--513253 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
513201 AAATTATTCA
513211 TAAATTAATAG
1 TAAATTAATAG
*
513222 TAAATTAATAC
1 TAAATTAATAG
513233 T-AATTAAATAG
1 TAAATT-AATAG
513244 TAAATTAATA
1 TAAATTAATA
513254 TTGATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 4 0.14
11 20 0.71
12 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (11 bp):
TAAATTAATAG
Found at i:513653 original size:21 final size:21
Alignment explanation
Indices: 513625--513735 Score: 97
Period size: 21 Copynumber: 5.3 Consensus size: 21
513615 TTATCATAAG
*
513625 TTAT-TAAAAGATTACTAAAA
1 TTATATAAAAGATTACCAAAA
**
513645 TTATATAAAGAGATTATTAAAA
1 TTATATAAA-AGATTACCAAAA
*
513667 TTTTATCAAAA-ATTACCAAAA
1 TTATAT-AAAAGATTACCAAAA
* *
513688 TTGTATACATAG-TTACCAAAA
1 TTATATA-AAAGATTACCAAAA
513709 TTATATAATAAG-TTACCAAAA
1 TTATATAA-AAGATTACCAAAA
513730 -TATATA
1 TTATATA
513736 GAAGGTTTTA
Statistics
Matches: 77, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
20 12 0.16
21 45 0.58
22 17 0.22
23 3 0.04
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (21 bp):
TTATATAAAAGATTACCAAAA
Found at i:513665 original size:22 final size:20
Alignment explanation
Indices: 513625--513668 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
513615 TTATCATAAG
513625 TTATTAAAAGATTACTAAAA
1 TTATTAAAAGATTACTAAAA
*
513645 TTATATAAAGAGATTATTAAAA
1 TTAT-TAAA-AGATTACTAAAA
513667 TT
1 TT
513669 TTATCAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 4 0.19
22 13 0.62
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (20 bp):
TTATTAAAAGATTACTAAAA
Found at i:519668 original size:67 final size:67
Alignment explanation
Indices: 519560--519693 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
519550 TATTACAATA
519560 AATTAACGCCAATTTAGAAATGCTTGAAATTTATTAAAAATTTTATATAAAACTTACATTTATAA
1 AATTAACGCCAATTTAGAAATGCTTGAAATTTATTAAAAATTTTATATAAAACTTACATTTATAA
519625 AT
66 AT
*
519627 AATTAACGCCAATTTAGAAATGCTTGAAATTTATTAAAAATTTTATATAAAACTTTCATTTATAA
1 AATTAACGCCAATTTAGAAATGCTTGAAATTTATTAAAAATTTTATATAAAACTTACATTTATAA
519692 AT
66 AT
519694 GATAAATTTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (67 bp):
AATTAACGCCAATTTAGAAATGCTTGAAATTTATTAAAAATTTTATATAAAACTTACATTTATAA
AT
Found at i:527752 original size:23 final size:22
Alignment explanation
Indices: 527713--527757 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
527703 CAAACTCAAA
*
527713 TTAATATATATATATATATATAT
1 TTAATATATATAGATATA-ATAT
527736 TTAATATAT-TAAGATATAATAT
1 TTAATATATAT-AGATATAATAT
527758 CATATTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATATATATAGATATAATAT
Found at i:553294 original size:14 final size:14
Alignment explanation
Indices: 553261--553302 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
553251 ATCAAGTAAT
*
553261 ATTAAT-TTTTAAA
1 ATTAATATTTAAAA
*
553274 ATAAATATTTAAAA
1 ATTAATATTTAAAA
553288 ATTAATATTTAAAA
1 ATTAATATTTAAAA
553302 A
1 A
553303 AAAAATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTAATATTTAAAA
Found at i:555363 original size:2 final size:2
Alignment explanation
Indices: 555352--555384 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
555342 CATGTTTTTC
555352 AT AT -T 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
555385 TGCAGCAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:563347 original size:133 final size:132
Alignment explanation
Indices: 563082--563321 Score: 313
Period size: 133 Copynumber: 1.8 Consensus size: 132
563072 TATCTTTGAG
* * * *
563082 ATGTAGCTACTTTAGAGGCATTTGAATATGAAAATGGCTCAATATTGGCGGCATTTGTATCTTTT
1 ATGTAGCTACTTTAGAGGCATTTGAATATAAAAACGCCTCAATATTGGCAGCATTTGTATCTTTT
*
563147 AGTCGCCACTAATTCAATGACATTTTTATGAGAAAAACGTCGTGTATTGACGGTATTTACAACAA
66 AG-CGCCACTAATTCAATGACATTGTTATGAGAAAAACGTCGTGTATTGACGGTATTTACAACAA
563212 AAA
130 AAA
* * * * *
563215 ATGTCGCTACTTTATAGGCATTTGAATTTAAAAACGCCTCAATATTTGTAGCATTTGTATCTTTT
1 ATGTAGCTACTTTAGAGGCATTTGAATATAAAAACGCCTCAATATTGGCAGCATTTGTATCTTTT
* * * *
563280 AG-GCTTACTATTTTAAT-AGCGTTGTTATGAGAAAAACGTCGT
66 AGCGC-CACTAATTCAATGA-CATTGTTATGAGAAAAACGTCGT
563322 TGCTTTAGTG
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
131 3 0.03
132 30 0.33
133 58 0.64
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (132 bp):
ATGTAGCTACTTTAGAGGCATTTGAATATAAAAACGCCTCAATATTGGCAGCATTTGTATCTTTT
AGCGCCACTAATTCAATGACATTGTTATGAGAAAAACGTCGTGTATTGACGGTATTTACAACAAA
AA
Found at i:571718 original size:357 final size:356
Alignment explanation
Indices: 570730--572280 Score: 1852
Period size: 357 Copynumber: 4.4 Consensus size: 356
570720 CGCTTTGAAC
* * * *
570730 ATATCACCACACAAAATT-TAATACGGTTATTGAAGGCATATATCCAAAAAAGATGCCTTTAATA
1 ATATCGCCACAC-AAATTCTAACACGGTTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATA
** * ** * * *
570794 ATTCCTATCATAATTTGTAGATAATTAGTGAAG-GTGTTTGCAGATAACAACGCTTTCAATAATT
65 ATTTTTATCACAATTTGTAGATAATTAGTGAAGACAG-TTACAGATAACAATGCCTTCAATAATT
** * * *
570858 TTTTTAAAAAAAA-TTTTTGAATTATTAAAGGTGTCTTTTTTTATGAAACGCCTTCAATATATCA
129 TTTTTAAAAAAAATTTTTTG-ATTATTAAAGGCATCTTTTATTATGACACGCCTTCAATATACCA
* * * *
570922 CGATGGTTATGAAAGGCGTTTATTAGAAAAAAGGCCTTCAGTATACCTTTAAACTTAGTAATCCA
193 CGATGGTTATGAAAGGCGTTTATTCGAAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCA
* * * *
570987 TTACTGAAGGCATTTGTTAATAACAGATGCCTTCAAAATTTTCGTACTTAAAATTTTGAGAATCA
258 TTACTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTTGCACTAAAAATTTTGAGAATCA
* * *
571052 -TAAAAGCTATCTTCTACTGTAAAATATCTT-TAT
323 TTAAAGGC-GTCTTCTACTGTAAAATACCTTCTAT
* * * *
571085 ATATCGTCACACAAATTTTAACACAGTTATTGAAGGCGTATATCCAAGAAAGACGCCTTTAATAA
1 ATATCGCCACACAAATTCTAACACGGTTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAA
* * *
571150 TTTTTATCATAGTTTGTAGATAATTAGTGAAGACAGTTACAGATAACAA-G-TTTCAATAATTTT
66 TTTTTATCACAATTTGTAGATAATTAGTGAAGACAGTTACAGATAACAATGCCTTCAATAA-TTT
* * * * * *
571213 TTTTAAAAAAAAATTTTAGATTATTAAAGGCATATTTTATTATGGCACACCTTCAATATACCACA
130 TTTTAAAAAAAATTTTTTGATTATTAAAGGCATCTTTTATTATGACACGCCTTCAATATACCACG
* * * * * *
571278 ATAGTTATGGAAGGTGTTTATTCAAAAAGGCACCTTCAATATACCTTTAAACTTAGTAATCCATT
195 ATGGTTATGAAAGGCGTTTATTCGAAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCATT
* * * *
571343 A-TCGAAGGCGTTTGTTAATAACAGACGCCTTTAAAATTTTTGCATTAAAAATTTTGGGAATCAT
260 ACT-GAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTTGCACTAAAAATTTTGAGAATCAT
* *
571407 TAAAGACGTCTTCTACTATAAAATACCTTCTAT
324 TAAAGGCGTCTTCTACTGTAAAATACCTTCTAT
* * * * *
571440 ATACCACCATACAAATTCTAACATGGTTATTGAATGCGTATATCCAAGAAAGATGCCTTTAATAA
1 ATATCGCCACACAAATTCTAACACGGTTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAA
* * * * *
571505 TTTCTATCACAATTTGTAGATAATTAGTAAAAATAATTACAGATAACAATGCCTTCAATAATTTT
66 TTTTTATCACAATTTGTAGATAATTAGTGAAGACAGTTACAGATAACAATGCCTTCAATAATTTT
* * * *
571570 TTTAAAAAAATATTTTTTGATTATTAAAGGCGTCTTTTATTATGACATGCCTTTAATATATCACG
131 TTTAAAAAAA-ATTTTTTGATTATTAAAGGCATCTTTTATTATGACACGCCTTCAATATACCACG
* *
571635 ATGGTTAT-AGAAGGCGTTTATTCGAAAAGACGCCTTCAATATAGCTTTAAACTTAGTAATCAAT
195 ATGGTTATGA-AAGGCGTTTATTCGAAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCAT
**
571699 TACTGAAGGTGTTTGTTAATAACAGACGCCTTCAAAATTTTTGCACTAAAAATTTTGAGAATCAT
259 TACTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTTGCACTAAAAATTTTGAGAATCAT
* * *
571764 TAAAGGTGTCTTCTACTGTAAAATACTTTTTAT
324 TAAAGGCGTCTTCTACTGTAAAATACCTTCTAT
* * * * * *
571797 ATAGCGCCACATAAATTTTAACAAGGTTATTGAAGACGTATATCAAAGAAAGATGCCTTTAATAA
1 ATATCGCCACACAAATTCTAACACGGTTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAA
* * *
571862 TTTTTATCACAGTTTGTATATAATTAGTGAACG-CGGTTACAGATAACAATGCCTTCAATAATTT
66 TTTTTATCACAATTTGTAGATAATTAGTGAA-GACAGTTACAGATAACAATGCCTTCAATAATTT
* * * *
571926 TTCTAAAAAAAATTTTTGGATTATTAAAGGCATCTTTTATTATGACATGCTTTCAATATACCACG
130 TTTTAAAAAAAATTTTTTGATTATTAAAGGCATCTTTTATTATGACACGCCTTCAATATACCACG
* * *
571991 ATGGTTATGAAAGGTGTTTATTCGAAAATG-TGCCTTCAATATA-TTTTAAACTTAGTAATCCAT
195 ATGGTTATGAAAGGCGTTTATTCGAAAA-GACGCCTTCAATATACCTTTAAACTTAGTAATCCAT
* * * * * * * *
572054 TACTGAAGGCATTTCTTAATAATAAATGCCTTTAAAA-TTTT-CTACTAAAAATTTTAAAAATTA
259 TACTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTTGC-ACTAAAAATTTTGAGAATCA
*
572117 TTAAAGGCGACTTCTACTGTAAAATACCTTCTAT
323 TTAAAGGCGTCTTCTACTGTAAAATACCTTCTAT
* * ** * **
572151 ATATCGTCACACTAATTCTAACACGGTTATAAAAGGCGTATATCTAAGAAAGACACCTTTAATAA
1 ATATCGCCACACAAATTCTAACACGGTTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAA
* * * * * * * * **
572216 TTTTTCTTACAGTTTTGTAGATAATTAGTAAAGGCGGTTGCATATAACAACCCCTTCAATAATTT
66 TTTTTATCACA-ATTTGTAGATAATTAGTGAAGACAGTTACAGATAACAATGCCTTCAATAATTT
572281 ATTATAAATT
Statistics
Matches: 1026, Mismatches: 152, Indels: 36
0.85 0.13 0.03
Matches are distributed among these distances:
353 11 0.01
354 299 0.29
355 296 0.29
356 102 0.10
357 317 0.31
358 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (356 bp):
ATATCGCCACACAAATTCTAACACGGTTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAA
TTTTTATCACAATTTGTAGATAATTAGTGAAGACAGTTACAGATAACAATGCCTTCAATAATTTT
TTTAAAAAAAATTTTTTGATTATTAAAGGCATCTTTTATTATGACACGCCTTCAATATACCACGA
TGGTTATGAAAGGCGTTTATTCGAAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCATTA
CTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTTGCACTAAAAATTTTGAGAATCATTA
AAGGCGTCTTCTACTGTAAAATACCTTCTAT
Found at i:572122 original size:711 final size:709
Alignment explanation
Indices: 570734--572247 Score: 2047
Period size: 711 Copynumber: 2.1 Consensus size: 709
570724 TTGAACATAT
* * * *
570734 CACCACACAAAATT-TAATACGGTTATTGAAGGCATATATCCAAAAAAGATGCCTTTAATAATTC
1 CACCACAC-AAATTCTAACACGGTTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAATTT
* * ** ** * *
570798 CTATCATAATTTGTAGATAATTAGTGAAGGTGTTTGCAGATAACAACGCTTTCAATAATTTTTTT
65 CTATCACAATTTGTAGATAATTAGTAAAAATAATTACAGATAACAACGCCTTCAATAATTTTTTT
* *
570863 AAAAAAAATTTTTGAATTATTAAAGGTGTCTTTTTTTATGAAACGCCTTCAATATATCACGATGG
130 AAAAAAAATTTTTGAATTATTAAAGGCGTCTTTTATTATGAAACGCCTTCAATATATCACGATGG
* * *
570928 TTATGAAAGGCGTTTATTAGAAAAAAGGCCTTCAGTATACCTTTAAACTTAGTAATCCATTACTG
195 TTATGAAAGGCGTTTATTAGAAAAAACGCCTTCAATATACCTTTAAACTTAGTAATCAATTACTG
* * *
570993 AAGGCATTTGTTAATAACAGATGCCTTCAAAATTTTCGTACTTAAAATTTTGAGAATCATAAAAG
260 AAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTCGCACTAAAAATTTTGAGAATCATAAAAG
* * *
571058 CTATCTTCTACTGTAAAATATCTTTATATATCGTCACACAAATTTTAACACAGTTATTGAAGGCG
325 CTATCTTCTACTGTAAAATATCTTTATATAGCGCCACACAAATTTTAACACAGTTATTGAAGACG
* *
571123 TATATCCAAGAAAGACGCCTTTAATAATTTTTATCATAGTTTGTAGATAATTAGTGAAGACAGTT
390 TATATCAAAGAAAGACGCCTTTAATAATTTTTATCACAGTTTGTAGATAATTAGTGAAGACAGTT
* *
571188 ACAGATAACAAGTTTCAATAATTTTTTTTAAAAAAAAATTTTAGATTATTAAAGGCATATTTTAT
455 ACAGATAACAAGCTTCAATAATTTTTTCTAAAAAAAAATTTTAGATTATTAAAGGCATATTTTAT
* *
571253 TATGGCACACCTTCAATATACCACAATAGTTATGGAAGGTGTTTATTCAAAAAGGCACCTTCAAT
520 TATGACACACCTTCAATATACCACAATAGTTATGAAAGGTGTTTATTCAAAAAGGCACCTTCAAT
* * *
571318 ATACCTTTAAACTTAGTAATCCATTATCGAAGGCGTTTGTTAATAACAGACGCCTTTAAAATTTT
585 ATACCTTTAAACTTAGTAATCCATTATCGAAGGCATTTCTTAATAACAAACGCCTTTAAAATTTT
* *** *
571383 TGCATTAAAAATTTTGGGAATCATTAAAGACGTCTTCTACTATAAAATACCTTCTATATAC
650 T-CACTAAAAATTTTAAAAATCATTAAAGACGACTTCTACTATAAAATACCTTCTATATAC
* * *
571444 CACCATACAAATTCTAACATGGTTATTGAATGCGTATATCCAAGAAAGATGCCTTTAATAATTTC
1 CACCACACAAATTCTAACACGGTTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAATTTC
*
571509 TATCACAATTTGTAGATAATTAGTAAAAATAATTACAGATAACAATGCCTTCAATAATTTTTTTA
66 TATCACAATTTGTAGATAATTAGTAAAAATAATTACAGATAACAACGCCTTCAATAATTTTTTTA
* * *
571574 AAAAAATATTTTTTG-ATTATTAAAGGCGTCTTTTATTATGACATGCCTTTAATATATCACGATG
131 AAAAAA-A-TTTTTGAATTATTAAAGGCGTCTTTTATTATGAAACGCCTTCAATATATCACGATG
* * *
571638 GTTAT-AGAAGGCGTTTATTCGAAAAGACGCCTTCAATATAGCTTTAAACTTAGTAATCAATTAC
194 GTTATGA-AAGGCGTTTATTAGAAAAAACGCCTTCAATATACCTTTAAACTTAGTAATCAATTAC
** * *
571702 TGAAGGTGTTTGTTAATAACAGACGCCTTCAAAATTTTTGCACTAAAAATTTTGAGAATCATTAA
258 TGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTCGCACTAAAAATTTTGAGAATCATAAA
* * * *
571767 AGGTGTCTTCTACTGTAAAATACTTTTTATATAGCGCCACATAAATTTTAACA-AGGTTATTGAA
323 AGCTATCTTCTACTGTAAAATA-TCTTTATATAGCGCCACACAAATTTTAACACA-GTTATTGAA
* *
571831 GACGTATATCAAAGAAAGATGCCTTTAATAATTTTTATCACAGTTTGTATATAATTAGTGAACG-
386 GACGTATATCAAAGAAAGACGCCTTTAATAATTTTTATCACAGTTTGTAGATAATTAGTGAA-GA
* * *
571895 CGGTTACAGATAACAATGCCTTCAATAA-TTTTTCTAAAAAAAATTTTTGGATTATTAAAGGCAT
450 CAGTTACAGATAACAA-G-CTTCAATAATTTTTTCTAAAAAAAAATTTTAGATTATTAAAGGCAT
* ** * * * * * **
571959 CTTTTATTATGACATGCTTTCAATATACCACGATGGTTATGAAAGGTGTTTATTCGAAAATGTGC
513 ATTTTATTATGACACACCTTCAATATACCACAATAGTTATGAAAGGTGTTTATTCAAAAAGGCAC
* * *
572024 CTTCAATATA-TTTTAAACTTAGTAATCCATTA-CTGAAGGCATTTCTTAATAATAAATGCCTTT
578 CTTCAATATACCTTTAAACTTAGTAATCCATTATC-GAAGGCATTTCTTAATAACAAACGCCTTT
* * *
572087 AAAA-TTTTCTACTAAAAATTTTAAAAATTATTAAAGGCGACTTCTACTGTAAAATACCTTCTAT
642 AAAATTTTTC-ACTAAAAATTTTAAAAATCATTAAAGACGACTTCTACTATAAAATACCTTCTAT
*
572151 ATAT
706 ATAC
** * ** * ** *
572155 CGTCACACTAATTCTAACACGGTTATAAAAGGCGTATATCTAAGAAAGACACCTTTAATAATTTT
1 CACCACACAAATTCTAACACGGTTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAATTTC
* * *
572220 TCTTACAGTTTTGTAGATAATTAGTAAA
66 TATCACA-ATTTGTAGATAATTAGTAAA
572248 GGCGGTTGCA
Statistics
Matches: 700, Mismatches: 92, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
709 5 0.01
710 116 0.17
711 292 0.42
712 181 0.26
713 98 0.14
714 8 0.01
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (709 bp):
CACCACACAAATTCTAACACGGTTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAATTTC
TATCACAATTTGTAGATAATTAGTAAAAATAATTACAGATAACAACGCCTTCAATAATTTTTTTA
AAAAAAATTTTTGAATTATTAAAGGCGTCTTTTATTATGAAACGCCTTCAATATATCACGATGGT
TATGAAAGGCGTTTATTAGAAAAAACGCCTTCAATATACCTTTAAACTTAGTAATCAATTACTGA
AGGCATTTGTTAATAACAGACGCCTTCAAAATTTTCGCACTAAAAATTTTGAGAATCATAAAAGC
TATCTTCTACTGTAAAATATCTTTATATAGCGCCACACAAATTTTAACACAGTTATTGAAGACGT
ATATCAAAGAAAGACGCCTTTAATAATTTTTATCACAGTTTGTAGATAATTAGTGAAGACAGTTA
CAGATAACAAGCTTCAATAATTTTTTCTAAAAAAAAATTTTAGATTATTAAAGGCATATTTTATT
ATGACACACCTTCAATATACCACAATAGTTATGAAAGGTGTTTATTCAAAAAGGCACCTTCAATA
TACCTTTAAACTTAGTAATCCATTATCGAAGGCATTTCTTAATAACAAACGCCTTTAAAATTTTT
CACTAAAAATTTTAAAAATCATTAAAGACGACTTCTACTATAAAATACCTTCTATATAC
Found at i:573515 original size:22 final size:22
Alignment explanation
Indices: 573487--573531 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
573477 AGATATGGCA
573487 ATCCGTTGTAGTATGTTTATTC
1 ATCCGTTGTAGTATGTTTATTC
573509 ATCCGTTGTAGTATGTTTATTC
1 ATCCGTTGTAGTATGTTTATTC
573531 A
1 A
573532 ACTATTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (22 bp):
ATCCGTTGTAGTATGTTTATTC
Found at i:576853 original size:123 final size:124
Alignment explanation
Indices: 576720--576981 Score: 388
Period size: 123 Copynumber: 2.1 Consensus size: 124
576710 ATTTTAAGCT
* *
576720 AAAAACGCCTTCAAGCATCCCATCCAAGTTTTGTTTATGAAATATTGAAGACGTTTTTTATAAAA
1 AAAAACGCCTTCAAACATCCCATCCAAGTTTTGTTTATGAAATATTGAAGACGTTTTCTATAAAA
*
576785 -CTGCCTTTAAAAATCAT-AAAAAAATTTACTGATTAGATTATAGAAGGTGAGTTCAGTA
66 TC-GCCTTTAAAAATCATAAAAAAAATTTACTGATTAGATTATAGAAGGCGAGTTCAGTA
* * * *
576843 AAAAATGCCTTCAAACATCCCATCTAAGTTTTGTTTATGAAATATTGACGGCGTTTTCTATAAAA
1 AAAAACGCCTTCAAACATCCCATCCAAGTTTTGTTTATGAAATATTGAAGACGTTTTCTATAAAA
*
576908 TCGCCTTTAAAAATCATAAAAAAAAATTTACTGATTGGATTATAGAAGGCGAGTTC-G-A
66 TCGCCTTTAAAAATCAT-AAAAAAAATTTACTGATTAGATTATAGAAGGCGAGTTCAGTA
576966 CCAAAAACGCCTTCAA
1 --AAAAACGCCTTCAA
576982 GAATCGACTC
Statistics
Matches: 125, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
123 75 0.60
124 2 0.02
125 48 0.38
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (124 bp):
AAAAACGCCTTCAAACATCCCATCCAAGTTTTGTTTATGAAATATTGAAGACGTTTTCTATAAAA
TCGCCTTTAAAAATCATAAAAAAAATTTACTGATTAGATTATAGAAGGCGAGTTCAGTA
Found at i:577670 original size:16 final size:16
Alignment explanation
Indices: 577649--577685 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
577639 GTCTATGTTC
577649 TTTTTTTTC-TTTATA
1 TTTTTTTTCATTTATA
*
577664 TTTTTTTTCATTTTTA
1 TTTTTTTTCATTTATA
577680 TTTTTT
1 TTTTTT
577686 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTCATTTATA
Found at i:577682 original size:6 final size:6
Alignment explanation
Indices: 577658--577776 Score: 91
Period size: 6 Copynumber: 18.8 Consensus size: 6
577648 CTTTTTTTTC
*
577658 TTTATAT TTT-TT TTCATT TTTATTT TTTATT TTTATTT TATTATT TTTATT
1 TTTAT-T TTTATT TTTATT TTTA-TT TTTATT TTTA-TT T-TTATT TTTATT
* * *
577709 ATTT-TAT TCTATT TTTATT TTTATT TTTATT TTTATTAT TTTATA TATATT
1 -TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTA-T-T TTTATT TTTATT
*
577760 TTT-TCC TTTATT TTTAT
1 TTTAT-T TTTATT TTTAT
577777 CTTAGCTATT
Statistics
Matches: 91, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
5 4 0.04
6 56 0.62
7 23 0.25
8 8 0.09
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:577723 original size:46 final size:45
Alignment explanation
Indices: 577658--577776 Score: 158
Period size: 46 Copynumber: 2.7 Consensus size: 45
577648 CTTTTTTTTC
577658 TTTATATT-TTTTTTCATTTTTATTTTTTATTTTTA-TTTTATTAT
1 TTTATATTATTTTTTCATTTTTA-TTTTTATTTTTATTTTTATTAT
577702 TTT-TATTATTTTATTCTATTTTTATTTTTATTTTTATTTTTATTAT
1 TTTATATTATTTT-TTC-ATTTTTATTTTTATTTTTATTTTTATTAT
*
577748 TTTATATATATTTTTTC--CTTTATTTTTAT
1 TTTATAT-TATTTTTTCATTTTTATTTTTAT
577777 CTTAGCTATT
Statistics
Matches: 68, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
43 4 0.06
44 18 0.26
45 15 0.22
46 19 0.28
47 6 0.09
48 6 0.09
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (45 bp):
TTTATATTATTTTTTCATTTTTATTTTTATTTTTATTTTTATTAT
Found at i:577948 original size:13 final size:13
Alignment explanation
Indices: 577907--577949 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
577897 GATTTATCTG
577907 ATTTATTTTCATTT
1 ATTT-TTTTCATTT
*
577921 GATTTTTTTCTTTT
1 -ATTTTTTTCATTT
*
577935 ATTTTTTTGATTT
1 ATTTTTTTCATTT
577948 AT
1 AT
577950 CTGGTTGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.52
14 8 0.32
15 4 0.16
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (13 bp):
ATTTTTTTCATTT
Found at i:578783 original size:4 final size:4
Alignment explanation
Indices: 578770--578807 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
578760 CAATTTTTTT
*
578770 TTTA TATA TTTA TTTA TTTA TTTA -TTA TTTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TT
578808 AAATTAGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 24 0.80
5 3 0.10
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:578848 original size:5 final size:5
Alignment explanation
Indices: 578830--578907 Score: 72
Period size: 5 Copynumber: 14.8 Consensus size: 5
578820 TTTAATGTTC
578830 TTTTA TTTTCA TTTTA TTTTTA TTTTTA TTTTA CTCTTT- TTTTA TTTTCA
1 TTTTA TTTT-A TTTTA -TTTTA -TTTTA TTTTA -T-TTTA TTTTA TTTT-A
578880 CTTTTA TTTTA TTTTA --TTA TTTTA TTTT
1 -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
578908 CTTTAAATAA
Statistics
Matches: 64, Mismatches: 0, Indels: 18
0.78 0.00 0.22
Matches are distributed among these distances:
3 3 0.05
4 3 0.05
5 32 0.50
6 19 0.30
7 7 0.11
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:578852 original size:17 final size:17
Alignment explanation
Indices: 578830--578907 Score: 81
Period size: 17 Copynumber: 4.5 Consensus size: 17
578820 TTTAATGTTC
578830 TTTTATTTTCATTTTA-T
1 TTTTATTTT-ATTTTACT
578847 TTTTATTTTTATTTTACT
1 TTTTA-TTTTATTTTACT
*
578865 CTTT-TTTTATTTTCAC-
1 TTTTATTTTATTTT-ACT
*
578881 TTTTATTTTATTTTATT
1 TTTTATTTTATTTTACT
578898 ATTTTATTTT
1 -TTTTATTTT
578908 CTTTAAATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
16 13 0.25
17 22 0.42
18 17 0.33
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTTTATTTTACT
Found at i:578903 original size:13 final size:13
Alignment explanation
Indices: 578883--578907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
578873 ATTTTCACTT
578883 TTATTTTATTTTA
1 TTATTTTATTTTA
578896 TTATTTTATTTT
1 TTATTTTATTTT
578908 CTTTAAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:578975 original size:59 final size:58
Alignment explanation
Indices: 578924--579500 Score: 611
Period size: 59 Copynumber: 9.7 Consensus size: 58
578914 ATAAAATCCA
* * *
578924 AAAAAAATATTTTTTGGGGAAAAGTTGAAAGTACCAATTTTCCTTAAAAATAAAATTTC
1 AAAAAAATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
** * *
578983 AAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC
* * *
579042 CAAAAAATATTTTTG-GGAAAAAGTTAAAAGTATCAATTTTCCTTTAAAAATAAATTTTT
1 AAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCC-TTAAAAATAAATTTTC
* * * * ** ** *
579101 AAAAAAGTTTTTTTTGAGGAAAAATTGAAAATATCAATTTTCCTCGAAAATCAAAGAATCC
1 AAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTTC
* * *
579162 AAAAAAAATATTTTTGAAGAAAAGTTGAAAATATCAATTTTTCTTAAAAATAAATTTTC
1 -AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * * * ** *
579221 AAAAGAAGGTTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAAATCAAAGTTTC
1 AAAA-AA---ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC
* * *
579284 CAAAAAATATTTTTGGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * * **
579342 AAAAAAGTTTTTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTCGAAAATCAAAGTTTTC
1 AAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTTC
* *
579403 -AAAAAATATTTTTG-GTAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
579460 AAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
579501 TCCTACACAA
Statistics
Matches: 428, Mismatches: 70, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
57 5 0.01
58 65 0.15
59 208 0.49
60 50 0.12
61 45 0.11
62 45 0.11
63 10 0.02
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.36
Consensus pattern (58 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:579411 original size:118 final size:118
Alignment explanation
Indices: 578925--579500 Score: 818
Period size: 118 Copynumber: 4.8 Consensus size: 118
578915 TAAAATCCAA
* * *
578925 AAAAAATATTTTTTGGGGAAAAGTTGAAAGTACCAATTTTCCTTAAAAATAAAATTTCAAAAAAA
1 AAAAAATA-TTTTTGGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTC-AAAAAA
* *
578990 G--GTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCC
64 GTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGTTTCC
* *
579043 AAAAAATATTTTTGGGAAAAAGTTAAAAGTATCAATTTTCCTTTAAAAATAAATTTTTAAAAAAG
1 AAAAAATATTTTTGGGGAAAAGTTAAAAGTATCAATTTTCC-TTAAAAATAAATTTTCAAAAAAG
* * **
579108 TTTTTTTTGAGGAAAAATTGAAAATATCAATTTTCCTCGAAAATCAAAGAATCC
65 TTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGTTTCC
** *
579162 AAAAAAAATATTTTTGAAGAAAAGTTGAAAA-TATCAATTTTTCTTAAAAATAAATTTTCAAAAG
1 --AAAAAATATTTTTGGGGAAAAGTT-AAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAA-
* *
579226 AAGGTTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAAATCAAAGTTTCC
62 AA-G-TTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGTTTCC
579285 AAAAAATATTTTTGGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGT
1 AAAAAATATTTTTGGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGT
* *
579350 TTTTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTCGAAAATCAAAGTTTTC
66 TTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGTTTCC
** * *
579403 AAAAAATATTTTTGGTAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAA-T
1 AAAAAATATTTTTGGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGT
**
579467 AAATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
66 -TTTTTTTGAGGAAAAGTTGAAAGTATCAATTTT
579501 TCCTACACAA
Statistics
Matches: 411, Mismatches: 36, Indels: 22
0.88 0.08 0.05
Matches are distributed among these distances:
117 38 0.09
118 161 0.39
119 47 0.11
120 25 0.06
121 87 0.21
122 5 0.01
123 48 0.12
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.36
Consensus pattern (118 bp):
AAAAAATATTTTTGGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGT
TTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGTTTCC
Found at i:579474 original size:16 final size:17
Alignment explanation
Indices: 579436--579474 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
579426 TGAAAGTATC
*
579436 AATTTTTCTTAAAAATA
1 AATTTTTCTAAAAAATA
579453 AA-TTTTC-AAAAAATA
1 AATTTTTCTAAAAAATA
579468 AATTTTT
1 AATTTTT
579475 GAGGAAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 9 0.45
16 9 0.45
17 2 0.10
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTTTCTAAAAAATA
Found at i:580136 original size:2 final size:2
Alignment explanation
Indices: 580129--580171 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
580119 ATTGTGGGTT
580129 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
580171 T
1 T
580172 TAAGTAAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:580426 original size:29 final size:30
Alignment explanation
Indices: 580392--580466 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
580382 AAATTGTTAG
**
580392 TTTAATTAAATAAAAATAATA-TTTAAGGA
1 TTTAATTAAATAAAAATAATATTTTAAAAA
* *
580421 TTTAATTAGACAAAAATAATATTTTAAAAA
1 TTTAATTAAATAAAAATAATATTTTAAAAA
*
580451 CTTAATTAAATAAAAA
1 TTTAATTAAATAAAAA
580467 AAGTACTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 19 0.50
30 19 0.50
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (30 bp):
TTTAATTAAATAAAAATAATATTTTAAAAA
Found at i:580477 original size:30 final size:29
Alignment explanation
Indices: 580393--580466 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 29
580383 AATTGTTAGT
** *
580393 TTAATTAAATAAAAATAATATTTAAGGAT
1 TTAATTAAATAAAAATAATATTTAAAAAC
* *
580422 TTAATTAGACAAAAATAATATTTTAAAAAC
1 TTAATTAAATAAAAATAATA-TTTAAAAAC
580452 TTAATTAAATAAAAA
1 TTAATTAAATAAAAA
580467 AAGTACTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (29 bp):
TTAATTAAATAAAAATAATATTTAAAAAC
Found at i:590538 original size:3 final size:3
Alignment explanation
Indices: 590530--590568 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
590520 AGCTGCTCGT
*
590530 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
590569 GGGCATGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:592355 original size:16 final size:16
Alignment explanation
Indices: 592334--592366 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
592324 GCAGATGGCG
*
592334 TTTTATGTACTTGGGC
1 TTTTATGGACTTGGGC
592350 TTTTATGGACTTGGGC
1 TTTTATGGACTTGGGC
592366 T
1 T
592367 CAATCCGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.27, T:0.48
Consensus pattern (16 bp):
TTTTATGGACTTGGGC
Found at i:593955 original size:75 final size:75
Alignment explanation
Indices: 593802--593954 Score: 263
Period size: 75 Copynumber: 2.1 Consensus size: 75
593792 TGTTTATCAT
593802 AAAAGTGTTTAATAATATAATGTTATCCTCAAGTAAAATTAAAAAAAAAAATTAGAAAGAGAAGA
1 AAAAGTGTTTAATAATATAATGTTATCCTCAAGTAAAATTAAAAAAAAAAATTAGAAAGAGAAGA
*
593867 CGATATGAAA
66 CGAGATGAAA
* **
593877 AAAAGTGTTTAATAATATAATGTTATTCTCAAGTAAAATT-TTAAAAAAAATTAGAAAGAGAAGA
1 AAAAGTGTTTAATAATATAATGTTATCCTCAAGTAAAATTAAAAAAAAAAATTAGAAAGAGAAGA
593941 CGAGATGAAA
66 CGAGATGAAA
593951 AAAA
1 AAAA
593955 AAAAAAAAAT
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
74 35 0.47
75 39 0.53
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.26
Consensus pattern (75 bp):
AAAAGTGTTTAATAATATAATGTTATCCTCAAGTAAAATTAAAAAAAAAAATTAGAAAGAGAAGA
CGAGATGAAA
Found at i:594264 original size:20 final size:21
Alignment explanation
Indices: 594233--594272 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
594223 TTCGTAAGTG
*
594233 AATTTGATTTAATTTTATATA
1 AATTTGATTTAATTATATATA
594254 AATTT-ATTTAATTATATAT
1 AATTTGATTTAATTATATAT
594273 TGATCGTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
AATTTGATTTAATTATATATA
Found at i:594734 original size:4 final size:4
Alignment explanation
Indices: 594725--594766 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
594715 TTTTTTATAA
594725 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
594767 TTATATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:598715 original size:29 final size:30
Alignment explanation
Indices: 598652--598732 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 30
598642 AAATTAAGAT
598652 GAAAAAATCCAACAAAAATAAAAATCAACC
1 GAAAAAATCCAACAAAAATAAAAATCAACC
* * **
598682 CAAAAAAT-C-ACTAAAAATAAAACTCAGTC
1 GAAAAAATCCAAC-AAAAATAAAAATCAACC
*
598711 G-AAAAATCCATCGAAAAATAAA
1 GAAAAAATCCAAC-AAAAATAAA
598733 CTAATCAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
28 8 0.20
29 16 0.39
30 17 0.41
ACGTcount: A:0.63, C:0.19, G:0.05, T:0.14
Consensus pattern (30 bp):
GAAAAAATCCAACAAAAATAAAAATCAACC
Found at i:599125 original size:3 final size:3
Alignment explanation
Indices: 599117--599172 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
599107 ATAATTACCT
599117 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
599165 TTA TTA TT
1 TTA TTA TT
599173 TAATTTAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:599749 original size:14 final size:14
Alignment explanation
Indices: 599730--599762 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
599720 TTCACATACC
*
599730 ATATAAATATAAAT
1 ATATAAAAATAAAT
599744 ATATAAAAATAAAT
1 ATATAAAAATAAAT
599758 ATATA
1 ATATA
599763 TTGATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATAAAAATAAAT
Found at i:600084 original size:5 final size:5
Alignment explanation
Indices: 600066--600100 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
600056 CTTTTGAACC
600066 AAAT- AAAT- AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA
600101 TAGGCAGCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:601244 original size:10 final size:11
Alignment explanation
Indices: 601203--601244 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
601193 TGAATAATAA
601203 ATGATTATTAT
1 ATGATTATTAT
**
601214 ATGATTTAAAAT
1 ATGA-TTATTAT
601226 ATGATTATTAT
1 ATGATTATTAT
601237 AT-ATTATT
1 ATGATTATT
601245 TTTAAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 6 0.23
11 11 0.42
12 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (11 bp):
ATGATTATTAT
Found at i:601272 original size:13 final size:13
Alignment explanation
Indices: 601254--601297 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
601244 TTTTAAAAAT
601254 AAAATAATTTTAA
1 AAAATAATTTTAA
601267 AAAAT-ATTTTAA
1 AAAATAATTTTAA
* *
601279 AAAACATTTTTAA
1 AAAATAATTTTAA
*
601292 ATAATA
1 AAAATA
601298 CATAACAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAATAATTTTAA
Found at i:601275 original size:12 final size:12
Alignment explanation
Indices: 601254--601288 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
601244 TTTTAAAAAT
601254 AAAATAATTTTAA
1 AAAAT-ATTTTAA
601267 AAAATATTTTAA
1 AAAATATTTTAA
*
601279 AAAACATTTT
1 AAAATATTTT
601289 TAAATAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATATTTTAA
Found at i:605946 original size:2 final size:2
Alignment explanation
Indices: 605939--605984 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
605929 TTTGGGTAGC
605939 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
605981 AT AT
1 AT AT
605985 GCAAATGGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:608569 original size:4 final size:4
Alignment explanation
Indices: 608560--608590 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
608550 CAGAAATGCT
*
608560 ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
608591 TATTGACTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:608591 original size:8 final size:8
Alignment explanation
Indices: 608559--608593 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
608549 TCAGAAATGC
608559 TATACATA
1 TATACATA
*
608567 CATACATA
1 TATACATA
*
608575 CATACATA
1 TATACATA
608583 TATACATA
1 TATACATA
608591 TAT
1 TAT
608594 TGACTCGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (8 bp):
TATACATA
Found at i:610016 original size:24 final size:22
Alignment explanation
Indices: 609958--610017 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
609948 TATTTATAAA
*
609958 AATATTATTTTTTAATATAAATT
1 AATA-TATTTATTAATATAAATT
* *
609981 -ATATCTTAATTATATATAAATAT
1 AATATATTTATTA-ATATAAAT-T
610004 AATATATTTATTAA
1 AATATATTTATTAA
610018 GTTAATCTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
21 6 0.21
22 11 0.38
23 2 0.07
24 10 0.34
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATATTTATTAATATAAATT
Found at i:610059 original size:16 final size:16
Alignment explanation
Indices: 610038--610102 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
610028 TAAATTAAGA
610038 TATTAAATAATAAATT
1 TATTAAATAATAAATT
*
610054 TATTAATATAATATATATG
1 TATTAA-ATAATA-A-ATT
610073 TATATAAAT-ATAAAATT
1 TAT-TAAATAAT-AAATT
* *
610090 AAATAAATAATAA
1 TATTAAATAATAA
610103 TATATATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
16 13 0.33
17 11 0.28
18 4 0.10
19 8 0.21
20 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
TATTAAATAATAAATT
Found at i:616624 original size:24 final size:24
Alignment explanation
Indices: 616570--616624 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
616560 TTAAAATAGT
* *
616570 AATA-TAAAAATATTTATCTTTAA
1 AATATTAAAAATATCTATATTTAA
*
616593 AATATTAAAAATACTCTATATTTTA
1 AATATTAAAAATA-TCTATATTTAA
616618 AAT-TTAA
1 AATATTAA
616625 GAAAATTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 12 0.44
25 11 0.41
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (24 bp):
AATATTAAAAATATCTATATTTAA
Found at i:616704 original size:18 final size:18
Alignment explanation
Indices: 616670--616723 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
616660 TAACAATTTT
*
616670 ATTATTAAAATAATAATATT
1 ATTATTAAAATAAT-AT-TC
*
616690 GTTATATAAAATAATATTC
1 ATTAT-TAAAATAATATTC
616709 ATTATTAAAATAATA
1 ATTATTAAAATAATA
616724 AAATATTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 10 0.33
19 5 0.17
20 6 0.20
21 9 0.30
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTATTAAAATAATATTC
Found at i:619409 original size:2 final size:2
Alignment explanation
Indices: 619402--619444 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
619392 ACGTTTCAAC
619402 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
619444 T
1 T
619445 TTGGTTTTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:619606 original size:3 final size:3
Alignment explanation
Indices: 619598--619626 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
619588 TTGATTAATC
619598 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
619627 CAAATATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:624152 original size:89 final size:89
Alignment explanation
Indices: 624001--624173 Score: 285
Period size: 89 Copynumber: 1.9 Consensus size: 89
623991 TCAGCGTTAC
* * *
624001 GAAAGGCCTACAATATTTTGCGGGGTAAAGATTGTATAAGATGTACTTATCTCAAGTAAAGGACA
1 GAAAGGCCTACAATATTTTGCAGGGTAAAGATTCTATAAGATGTACTTATCCCAAGTAAAGGACA
* *
624066 GTACAGCAAAGGCAATGGAGTCAT
66 ATACAACAAAGGCAATGGAGTCAT
624090 GAAAGGCCTACAATATTTTGCAGGGTAAAGATTCTA-AAGGATGTACTTATCCCAAGTAAAGGAC
1 GAAAGGCCTACAATATTTTGCAGGGTAAAGATTCTATAA-GATGTACTTATCCCAAGTAAAGGAC
624154 AATACAACAAAGGCAATGGA
65 AATACAACAAAGGCAATGGA
624174 TCTCATTTTC
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
88 2 0.03
89 76 0.97
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.23
Consensus pattern (89 bp):
GAAAGGCCTACAATATTTTGCAGGGTAAAGATTCTATAAGATGTACTTATCCCAAGTAAAGGACA
ATACAACAAAGGCAATGGAGTCAT
Found at i:642533 original size:20 final size:20
Alignment explanation
Indices: 642485--642527 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
642475 TAAATGATGC
642485 AGTCAAAGTTGCTTCACTCA
1 AGTCAAAGTTGCTTCACTCA
642505 AGTCAAAGTTGCTTCACTCA
1 AGTCAAAGTTGCTTCACTCA
642525 AGT
1 AGT
642528 TCAAGTCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (20 bp):
AGTCAAAGTTGCTTCACTCA
Found at i:651569 original size:19 final size:19
Alignment explanation
Indices: 651545--651584 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
651535 ATATTTTTTA
651545 TTTAATTACA-ATTATAATT
1 TTTAATTACACA-TATAATT
*
651564 TTTAATTATACATATAATT
1 TTTAATTACACATATAATT
651583 TT
1 TT
651585 ATTAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAATTACACATATAATT
Found at i:651589 original size:21 final size:21
Alignment explanation
Indices: 651540--651589 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 21
651530 ATTTGATATT
651540 TTTTATTTAATTACAATTATAA
1 TTTTA-TTAATTACAATTATAA
*
651562 -TTT-TTAATTATACA-TATAA
1 TTTTATTAATTACA-ATTATAA
651581 TTTTATTAA
1 TTTTATTAA
651590 AATTAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
19 13 0.54
20 4 0.17
21 7 0.29
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATTAATTACAATTATAA
Found at i:653304 original size:10 final size:10
Alignment explanation
Indices: 653286--653329 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
653276 ATAATTATTT
*
653286 TATACTTAAA
1 TATATTTAAA
653296 TATATTTAAA
1 TATATTTAAA
653306 TATATTTAAAA
1 TATATTT-AAA
*
653317 TTATATTAAAA
1 -TATATTTAAA
653328 TA
1 TA
653330 ATTAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 18 0.60
11 6 0.20
12 6 0.20
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (10 bp):
TATATTTAAA
Found at i:653328 original size:22 final size:21
Alignment explanation
Indices: 653296--653338 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
653286 TATACTTAAA
* *
653296 TATATTTAAATATATTTAAAAT
1 TATATTAAAATA-ATTAAAAAT
653318 TATATTAAAATAATTAAAAAT
1 TATATTAAAATAATTAAAAAT
653339 AAATAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATATTAAAATAATTAAAAAT
Found at i:654793 original size:9 final size:9
Alignment explanation
Indices: 654779--654808 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
654769 GATATTTTAT
654779 TAATTAAAA
1 TAATTAAAA
654788 TAATTAAAA
1 TAATTAAAA
654797 TATATTAAAA
1 TA-ATTAAAA
654807 TA
1 TA
654809 TAAAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:654805 original size:10 final size:10
Alignment explanation
Indices: 654781--654810 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
654771 TATTTTATTA
654781 ATTAAAATA-
1 ATTAAAATAT
654790 ATTAAAATAT
1 ATTAAAATAT
654800 ATTAAAATAT
1 ATTAAAATAT
654810 A
1 A
654811 AAAATTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:657088 original size:21 final size:21
Alignment explanation
Indices: 657051--657101 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
657041 AGTGGTGAAG
* * *
657051 TTAATTATTATAGTGATGAGA
1 TTAAATATTATAGTGATAAAA
657072 TTAAATATTATTA-TGATAAAA
1 TTAAATATTA-TAGTGATAAAA
657093 TTAAA-ATTA
1 TTAAATATTA
657102 ATAATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 20 0.77
22 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (21 bp):
TTAAATATTATAGTGATAAAA
Found at i:657382 original size:21 final size:22
Alignment explanation
Indices: 657358--657403 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
657348 TTAAAAATTG
657358 ATATTAATTATTTATATT-AAA
1 ATATTAATTATTTATATTCAAA
*
657379 ATATTAATTATTTTTATTCAAA
1 ATATTAATTATTTATATTCAAA
657401 ATA
1 ATA
657404 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATTAATTATTTATATTCAAA
Found at i:657836 original size:59 final size:59
Alignment explanation
Indices: 657743--657855 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
657733 CAAATGCAGC
* *
657743 TTTAATTGTGAGAATAAATGACTGCATAGCCTTTATGCACTAAGAAATAAATAATCTTA
1 TTTAATTGTGAGAATAAATGACGGCATAGACTTTATGCACTAAGAAATAAATAATCTTA
* * * ** *
657802 TTTAATTGTGATAATCAATGACGGCATATACTTTATGCGTTACGAAATAAATAA
1 TTTAATTGTGAGAATAAATGACGGCATAGACTTTATGCACTAAGAAATAAATAA
657856 CCTTCAATAG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (59 bp):
TTTAATTGTGAGAATAAATGACGGCATAGACTTTATGCACTAAGAAATAAATAATCTTA
Found at i:662384 original size:126 final size:126
Alignment explanation
Indices: 662231--662470 Score: 340
Period size: 126 Copynumber: 1.9 Consensus size: 126
662221 AATTTTAAAC
* * * ** * *
662231 AAATTGAGTTTAAAAAAAAAAAATTATCTAAATAAAATAATCTATCATTATAACTAACATCAATT
1 AAATTGAGATTAAAAAAAAAAAATTATCCAAATAAAATAATCTACCAAAACAACTAACATCAATG
* * *
662296 AAAGAGTAACCGTGCGC-GATATCTAATCTTATTTTATTGACAATTGCTTGCATATGAAAAT
66 AAAGAGGAACCGTGAGCTG-TATCTAATCTTATCTTATTGACAATTGCTTGCATATGAAAAT
*
662357 AAATTGA-ATTAAAAAAAAAAGGATTATCCAAATAAAATAATCTACCAAAACAACTAACATCAAT
1 AAATTGAGATTAAAAAAAAAA-AATTATCCAAATAAAATAATCTACCAAAACAACTAACATCAAT
*
662421 GAAAGAGGAACCGTGAGCTGTATCTAATCTTGTCTTATTGACAATTGCTT
65 GAAAGAGGAACCGTGAGCTGTATCTAATCTTATCTTATTGACAATTGCTT
662471 CCATGTGAGC
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
125 12 0.12
126 87 0.87
127 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.30
Consensus pattern (126 bp):
AAATTGAGATTAAAAAAAAAAAATTATCCAAATAAAATAATCTACCAAAACAACTAACATCAATG
AAAGAGGAACCGTGAGCTGTATCTAATCTTATCTTATTGACAATTGCTTGCATATGAAAAT
Found at i:663854 original size:6 final size:6
Alignment explanation
Indices: 663843--663869 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
663833 AAGGGTTAAA
663843 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
663870 GCTACCATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:666875 original size:2 final size:2
Alignment explanation
Indices: 666868--666898 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
666858 ACTTTGCAAT
666868 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
666899 TTATGTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:669166 original size:2 final size:2
Alignment explanation
Indices: 669161--669192 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
669151 TAACATCAAC
669161 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
669193 GTTTGTATCA
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:676650 original size:14 final size:14
Alignment explanation
Indices: 676633--676659 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
676623 AATAATAATA
676633 AAATTTTATTAAAT
1 AAATTTTATTAAAT
676647 AAATTTTATTAAA
1 AAATTTTATTAAA
676660 ATTAATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTTATTAAAT
Found at i:677583 original size:25 final size:26
Alignment explanation
Indices: 677540--677605 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 26
677530 AAAATAATTT
*
677540 TTTATATA-ATTTATTTAATTTT-TA
1 TTTATATATATTTATATAATTTTATA
677564 TTTATATATATTTATATAATTTTATA
1 TTTATATATATTTATATAATTTTATA
*
677590 TTTAAATAT-TTTATAT
1 TTTATATATATTTATAT
677606 TTAAAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 8 0.21
25 20 0.53
26 10 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTATATATATTTATATAATTTTATA
Found at i:677602 original size:15 final size:16
Alignment explanation
Indices: 677570--677610 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
677560 TTTATTTATA
*
677570 TATATTTATATAATTT
1 TATATTTAAATAATTT
677586 TATATTTAAAT-ATTT
1 TATATTTAAATAATTT
677601 TATATTTAAA
1 TATATTTAAA
677611 AAATAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATTTAAATAATTT
Found at i:678964 original size:3 final size:3
Alignment explanation
Indices: 678956--678987 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
678946 ATACCCAACT
*
678956 TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
678988 ATTGGTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:682509 original size:23 final size:23
Alignment explanation
Indices: 682483--682527 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
682473 ATTTTTATAT
682483 AAATATCAAATTAAAT-TTATTTA
1 AAAT-TCAAATTAAATCTTATTTA
* *
682506 AAATTTAAATTCAATCTTATTT
1 AAATTCAAATTAAATCTTATTT
682528 TATTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (23 bp):
AAATTCAAATTAAATCTTATTTA
Found at i:682954 original size:25 final size:25
Alignment explanation
Indices: 682926--682981 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
682916 ATTTTATTAA
*
682926 AATTTTTTTTAATTAAAATTATAAT
1 AATTTTTTTTAATCAAAATTATAAT
*
682951 AATTTTTTTTAATCATAATTATAAT
1 AATTTTTTTTAATCAAAATTATAAT
682976 AATTTT
1 AATTTT
682982 ATTATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
AATTTTTTTTAATCAAAATTATAAT
Found at i:683297 original size:21 final size:21
Alignment explanation
Indices: 683251--683299 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
683241 TATAGTTTAA
* *
683251 AATTTTAATAAAATCATATAT
1 AATTTTAATAAAATAAAATAT
683272 AATTTTAATAAAATAAAA-AT
1 AATTTTAATAAAATAAAATAT
683292 ATATTTTA
1 A-ATTTTA
683300 TATTTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTTTAATAAAATAAAATAT
Found at i:684929 original size:27 final size:28
Alignment explanation
Indices: 684891--684947 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
684881 GCGATGCTTG
**
684891 TGGAACCTTATGTGTAAGACAAAA-CAT
1 TGGAACCTTATGTACAAGACAAAAGCAT
*
684918 TGGACCCTTATGTACAAGACAAAAGCAT
1 TGGAACCTTATGTACAAGACAAAAGCAT
684946 TG
1 TG
684948 TTGAATCCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (28 bp):
TGGAACCTTATGTACAAGACAAAAGCAT
Found at i:693678 original size:2 final size:2
Alignment explanation
Indices: 693671--693716 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
693661 GCAGAATTGT
*
693671 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT 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
693712 TA TA T
1 TA TA T
693717 GTATGTATGT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:728208 original size:12 final size:12
Alignment explanation
Indices: 728185--728215 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
728175 TATGATAATA
728185 TAATAT-AAAAT
1 TAATATAAAAAT
728196 TAATATAAAAAT
1 TAATATAAAAAT
728208 TAATATAA
1 TAATATAA
728216 TCATGTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TAATATAAAAAT
Found at i:728239 original size:11 final size:11
Alignment explanation
Indices: 728223--728247 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
728213 TAATCATGTT
728223 TTATATTTTAA
1 TTATATTTTAA
728234 TTATATTTTAA
1 TTATATTTTAA
728245 TTA
1 TTA
728248 AAAAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATATTTTAA
Found at i:729479 original size:30 final size:31
Alignment explanation
Indices: 729423--729483 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
729413 AAAAATTTAC
*
729423 TTATTAATAAAATAAAAATATTTTATTTATT
1 TTATTAATAAAATAAAAATATATTATTTATT
*
729454 TTATTAA-AAAAT-AATATCATATTATTTATT
1 TTATTAATAAAATAAAAAT-ATATTATTTATT
729484 AATAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 4 0.15
30 16 0.59
31 7 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (31 bp):
TTATTAATAAAATAAAAATATATTATTTATT
Found at i:730745 original size:3 final size:3
Alignment explanation
Indices: 730737--730770 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
730727 TTGGAGTCAC
*
730737 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
730771 CATATATCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:733502 original size:19 final size:18
Alignment explanation
Indices: 733480--733521 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
733470 TTAAACGAGA
*
733480 AAAAAATTATTAAATATAT
1 AAAAAATTATTAAA-AAAT
*
733499 AAAAAATTTTTAAAAAAT
1 AAAAAATTATTAAAAAAT
733517 AAAAA
1 AAAAA
733522 GTACTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAAATTATTAAAAAAT
Found at i:733551 original size:10 final size:10
Alignment explanation
Indices: 733538--733572 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
733528 AAAATGTATT
733538 AAAAAATTTA
1 AAAAAATTTA
*
733548 AAAAAATTAA
1 AAAAAATTTA
*
733558 AAAAAATTTT
1 AAAAAATTTA
733568 AAAAA
1 AAAAA
733573 CAAAATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:734280 original size:46 final size:46
Alignment explanation
Indices: 734184--734280 Score: 126
Period size: 46 Copynumber: 2.1 Consensus size: 46
734174 TTGTAAATCT
* * * *
734184 ACAAATCAGTTCATAATATCTGGTGGAAAAAAGAATTTATAGATCT
1 ACAAATCAGTCCATAATATCTGGTGGAAAAAAGAATTTATAAAGCG
734230 ACAAATCAGTCCATAATA-CATGGTGGAAAAAAGAAATTT-TAAAGCG
1 ACAAATCAGTCCATAATATC-TGGTGGAAAAAAG-AATTTATAAAGCG
734276 ACAAA
1 ACAAA
734281 AAAAATAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
45 1 0.02
46 39 0.87
47 5 0.11
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (46 bp):
ACAAATCAGTCCATAATATCTGGTGGAAAAAAGAATTTATAAAGCG
Found at i:738554 original size:2 final size:2
Alignment explanation
Indices: 738547--738579 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
738537 CTGGTTCTCT
738547 AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
738580 CTGTATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:740221 original size:84 final size:84
Alignment explanation
Indices: 740060--740222 Score: 245
Period size: 84 Copynumber: 1.9 Consensus size: 84
740050 CCATAACTTC
* **
740060 AAAACAACCATTAAAACTAAATGCATGTATCAATAGATGAACATATTGCATTTAAGAGAATTAGT
1 AAAACAACCATTAAAACTAAATGCATGTACCAATAGATGAACATATTGCATTTAAGAGAACCAGT
*
740125 ACCTATGCAATGTAATTCG
66 AACTATGCAATGTAATTCG
* * *
740144 AAAACAACCGTTAAAACTAAATGCATGTACCATTAGATGAGCATATTGCATTTAAGAGAACCAGT
1 AAAACAACCATTAAAACTAAATGCATGTACCAATAGATGAACATATTGCATTTAAGAGAACCAGT
* *
740209 AACTCTGTAATGTA
66 AACTATGCAATGTA
740223 CTTAGAGTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 70 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (84 bp):
AAAACAACCATTAAAACTAAATGCATGTACCAATAGATGAACATATTGCATTTAAGAGAACCAGT
AACTATGCAATGTAATTCG
Found at i:742605 original size:3 final size:3
Alignment explanation
Indices: 742597--742628 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
742587 GCTGGCTTTA
742597 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
742629 AAAGGAGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:744291 original size:15 final size:15
Alignment explanation
Indices: 744271--744303 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
744261 ATATTTTCAC
744271 TTTTATCTTCTCATT
1 TTTTATCTTCTCATT
*
744286 TTTTATCTTTTCATT
1 TTTTATCTTCTCATT
744301 TTT
1 TTT
744304 CTATGTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATCTTCTCATT
Done.