Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008933.1 Hibiscus syriacus cultivar Beakdansim tig00112249_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: 2862162
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2683635 original size:2 final size:2
Alignment explanation
Indices: 2683630--2683665 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2683620 TAACGTTAAC
2683630 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
2683666 CATTAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2703710 original size:21 final size:21
Alignment explanation
Indices: 2703685--2703732 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2703675 CCTAATATTG
2703685 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
2703706 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
2703727 TAATGT
1 CAATGT
2703733 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:2708370 original size:21 final size:21
Alignment explanation
Indices: 2708345--2708392 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
2708335 CCTAATATTG
*
2708345 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGAAA
2708366 CAATGTCAAAATTAGGTGAAA
1 CAATGTCAAAATTAGGTGAAA
*
2708387 TAATGT
1 CAATGT
2708393 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGAAA
Found at i:2712621 original size:16 final size:17
Alignment explanation
Indices: 2712600--2712636 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2712590 TTTTTTTTAC
*
2712600 AAAAACATT-ATAATAT
1 AAAAACATTAATAAAAT
2712616 AAAAACATTAATAAAAT
1 AAAAACATTAATAAAAT
2712633 AAAA
1 AAAA
2712637 TATGTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAACATTAATAAAAT
Found at i:2716988 original size:11 final size:14
Alignment explanation
Indices: 2716954--2716984 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2716944 AAACACTTGG
2716954 TTTGTCCACTCTTC
1 TTTGTCCACTCTTC
2716968 TTTGTCCACTCTTC
1 TTTGTCCACTCTTC
2716982 TTT
1 TTT
2716985 CACTACAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.32, G:0.06, T:0.55
Consensus pattern (14 bp):
TTTGTCCACTCTTC
Found at i:2719817 original size:10 final size:10
Alignment explanation
Indices: 2719804--2719839 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
2719794 TTTTTTGTAA
2719804 TTTTTCTGAT
1 TTTTTCTGAT
*
2719814 TTTTTTTGTAT
1 TTTTTCTG-AT
2719825 TTTTTCTGAT
1 TTTTTCTGAT
2719835 TTTTT
1 TTTTT
2719840 TTAAATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.08, C:0.06, G:0.08, T:0.78
Consensus pattern (10 bp):
TTTTTCTGAT
Found at i:2719817 original size:21 final size:21
Alignment explanation
Indices: 2719791--2719841 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
2719781 AAACATACTA
2719791 ATTTTTTTTGTAATTTTTCTG
1 ATTTTTTTTGTAATTTTTCTG
*
2719812 ATTTTTTTTGTATTTTTTCTG
1 ATTTTTTTTGTAATTTTTCTG
2719833 ATTTTTTTT
1 ATTTTTTTT
2719842 AAATTCAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.12, C:0.04, G:0.08, T:0.76
Consensus pattern (21 bp):
ATTTTTTTTGTAATTTTTCTG
Found at i:2719818 original size:11 final size:11
Alignment explanation
Indices: 2719804--2719840 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2719794 TTTTTTGTAA
2719804 TTTTTCTGATT
1 TTTTTCTGATT
2719815 TTTTT-TG-TAT
1 TTTTTCTGAT-T
2719825 TTTTTCTGATT
1 TTTTTCTGATT
2719836 TTTTT
1 TTTTT
2719841 TAAATTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.04
10 8 0.35
11 13 0.57
12 1 0.04
ACGTcount: A:0.08, C:0.05, G:0.08, T:0.78
Consensus pattern (11 bp):
TTTTTCTGATT
Found at i:2719858 original size:117 final size:114
Alignment explanation
Indices: 2719710--2719968 Score: 371
Period size: 117 Copynumber: 2.3 Consensus size: 114
2719700 TACGCTACAA
* * *
2719710 TTTTCTG-TTTTTTTTTAATTCAAATAGATTAAATTAAAATATAGATATAAATACATTGAAATTA
1 TTTTCTGATTTTTTTTAAATTCAAATAGATTAAATTAAAAGATAGATAAAAATACATTGAAATTA
*
2719774 GATATATAAACATACTAATTTTTTTTGTAATTTTTCTGATTTTTTTTGTA-TT
66 GATAAATAAACATACTAA--TTTTTTGTAATTTTTCTGA--TTTTTTGTATTT
* * ** *
2719826 TTTTCTGATTTTTTTTAAATTCAAGTAGATTAATTTGCAAGATAGATAAAAATATATTGAAATTA
1 TTTTCTGATTTTTTTTAAATTCAAATAGATTAAATTAAAAGATAGATAAAAATACATTGAAATTA
*
2719891 GATAAATAAACATACTGATTTTTTGTAATTTTTCTGATTTTTTGTATTT
66 GATAAATAAACATACTAATTTTTTGTAATTTTTCTGATTTTTTGTATTT
2719940 TTTTCTGA-TTTTTTTAAATTCAAATAGAT
1 TTTTCTGATTTTTTTTAAATTCAAATAGAT
2719969 ATTTATAGAA
Statistics
Matches: 130, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
113 29 0.22
114 10 0.08
115 19 0.15
116 7 0.05
117 65 0.50
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.51
Consensus pattern (114 bp):
TTTTCTGATTTTTTTTAAATTCAAATAGATTAAATTAAAAGATAGATAAAAATACATTGAAATTA
GATAAATAAACATACTAATTTTTTGTAATTTTTCTGATTTTTTGTATTT
Found at i:2719929 original size:19 final size:20
Alignment explanation
Indices: 2719905--2719953 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
2719895 AATAAACATA
2719905 CTGATTTTTTGTA-ATTTTT
1 CTGATTTTTTGTATATTTTT
*
2719924 CTGATTTTTTGTATTTTTTT
1 CTGATTTTTTGTATATTTTT
2719944 CTGATTTTTT
1 CTGATTTTTT
2719954 TAAATTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.12, C:0.06, G:0.10, T:0.71
Consensus pattern (20 bp):
CTGATTTTTTGTATATTTTT
Found at i:2722897 original size:61 final size:61
Alignment explanation
Indices: 2722825--2722950 Score: 252
Period size: 61 Copynumber: 2.1 Consensus size: 61
2722815 AGGGGATGAG
2722825 ATAGGAGAGAGAAAGCGAGTACAACTGCGAGTAGAGTCATGTAATTGAATTTGAAGTAAGA
1 ATAGGAGAGAGAAAGCGAGTACAACTGCGAGTAGAGTCATGTAATTGAATTTGAAGTAAGA
2722886 ATAGGAGAGAGAAAGCGAGTACAACTGCGAGTAGAGTCATGTAATTGAATTTGAAGTAAGA
1 ATAGGAGAGAGAAAGCGAGTACAACTGCGAGTAGAGTCATGTAATTGAATTTGAAGTAAGA
2722947 ATAG
1 ATAG
2722951 TTTCTTCGGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.41, C:0.08, G:0.29, T:0.21
Consensus pattern (61 bp):
ATAGGAGAGAGAAAGCGAGTACAACTGCGAGTAGAGTCATGTAATTGAATTTGAAGTAAGA
Found at i:2723983 original size:60 final size:59
Alignment explanation
Indices: 2723874--2724037 Score: 188
Period size: 60 Copynumber: 2.7 Consensus size: 59
2723864 TGAATTTGGT
* * * * * *
2723874 GATGAATTTGGAAAATTCAAAAGTTTGAGGACCAATTTAGAATGAGAGTCATAGTTTAGG
1 GATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAAT-AGAGTCATAGTTTAAG
* * *
2723934 GATGGAATT-GAA-ATGGTCAAAAGTTTAAGGACTAATTCAAAATATGAGTCATAGTTTAAG
1 GATGAAATTAGAATAT--TCAAAAGTTTAAGGACCAATTTAAAATA-GAGTCATAGTTTAAG
*
2723994 GATGAAATTAGAATATTCAAAAGTTTAAAGACCAATTTAAAATA
1 GATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAATA
2724038 AAAGAATAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
58 2 0.02
59 4 0.05
60 77 0.88
61 3 0.03
62 2 0.02
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (59 bp):
GATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAATAGAGTCATAGTTTAAG
Found at i:2724009 original size:31 final size:30
Alignment explanation
Indices: 2723910--2724009 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 30
2723900 GAGGACCAAT
*
2723910 TTAGAATGA-GAGTCATAGTTTAGGGATGGAA
1 TTAGAAT-ATGAGTCATAGTTTAAGGAT-GAA
*
2723941 TT-GAA-ATG-GTCAAAAGTTTAAGGACT-AA
1 TTAGAATATGAGTC-ATAGTTTAAGGA-TGAA
*
2723969 TTCAAAATATGAGTCATAGTTTAAGGATGAAA
1 TT-AGAATATGAGTCATAGTTTAAGGATG-AA
2724001 TTAGAATAT
1 TTAGAATAT
2724010 TCAAAAGTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
28 8 0.15
29 11 0.20
30 7 0.13
31 22 0.40
32 7 0.13
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
TTAGAATATGAGTCATAGTTTAAGGATGAA
Found at i:2724280 original size:10 final size:10
Alignment explanation
Indices: 2724267--2724311 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
2724257 TTTTTTTTTA
2724267 ATTAAAATAT
1 ATTAAAATAT
2724277 ATT-AAAT-T
1 ATTAAAATAT
*
2724285 A-TAAAATAG
1 ATTAAAATAT
*
2724294 ATAAAAATAT
1 ATTAAAATAT
2724304 ATTAAAAT
1 ATTAAAAT
2724312 TAGATAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
7 1 0.04
8 6 0.21
9 5 0.18
10 16 0.57
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:2724311 original size:20 final size:23
Alignment explanation
Indices: 2724286--2724330 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
2724276 TATTAAATTA
2724286 TAAAA-TAGATAAA-AAT-ATAT
1 TAAAATTAGATAAATAATCATAT
2724306 TAAAATTAGATAAATAATCATAT
1 TAAAATTAGATAAATAATCATAT
2724329 TA
1 TA
2724331 TTTTTTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.23
21 8 0.36
22 3 0.14
23 6 0.27
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (23 bp):
TAAAATTAGATAAATAATCATAT
Found at i:2724355 original size:20 final size:20
Alignment explanation
Indices: 2724330--2724383 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
2724320 TAATCATATT
*
2724330 ATTTTTTTGTAATTTTTT-GG
1 ATTTTTTTAT-ATTTTTTCGG
2724350 ATTTTTTTATATTTTTTCGG
1 ATTTTTTTATATTTTTTCGG
2724370 ATTTTTTTATATTT
1 ATTTTTTTATATTT
2724384 GTAAAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 7 0.22
20 25 0.78
ACGTcount: A:0.17, C:0.02, G:0.09, T:0.72
Consensus pattern (20 bp):
ATTTTTTTATATTTTTTCGG
Found at i:2724383 original size:10 final size:10
Alignment explanation
Indices: 2724329--2724383 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
2724319 ATAATCATAT
2724329 TATTTTTTTG
1 TATTTTTTTG
*
2724339 TAATTTTTTG
1 TATTTTTTTG
* *
2724349 GATTTTTTTA
1 TATTTTTTTG
*
2724359 TATTTTTTCG
1 TATTTTTTTG
* *
2724369 GATTTTTTTA
1 TATTTTTTTG
2724379 TATTT
1 TATTT
2724384 GTAAAATTAA
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.73
Consensus pattern (10 bp):
TATTTTTTTG
Found at i:2724994 original size:36 final size:37
Alignment explanation
Indices: 2724920--2724994 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 37
2724910 TATAATTTTT
* * *
2724920 AGATCAAATAGATGATATATAATTTTTTAATTGCATC
1 AGATCAAATAGAGGATACATAATTTTTTAATTGAATC
*
2724957 AGATCAGATAGAGGATACAT-A-TTTTTATATTGAATC
1 AGATCAAATAGAGGATACATAATTTTTTA-ATTGAATC
2724993 AG
1 AG
2724995 GTTGACCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 6 0.18
36 10 0.30
37 17 0.52
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (37 bp):
AGATCAAATAGAGGATACATAATTTTTTAATTGAATC
Found at i:2730318 original size:12 final size:12
Alignment explanation
Indices: 2730301--2730330 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2730291 GGAGAAGAAA
2730301 GAAAATTAAGAG
1 GAAAATTAAGAG
2730313 GAAAATTAAGAG
1 GAAAATTAAGAG
2730325 GAAAAT
1 GAAAAT
2730331 GAAAAGCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (12 bp):
GAAAATTAAGAG
Found at i:2730668 original size:21 final size:21
Alignment explanation
Indices: 2730628--2730687 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 21
2730618 AATTACTGTT
2730628 TAATTAAATATTAAAAATAAAA
1 TAATTAAA-ATTAAAAATAAAA
**
2730650 TAATTAAAATTTCAAATAAAA
1 TAATTAAAATTAAAAATAAAA
2730671 TAATCTTAAAATTAAAA
1 TAA--TTAAAATTAAAA
2730688 GTTTGGCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 14 0.44
22 8 0.25
23 10 0.31
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATTAAAATTAAAAATAAAA
Found at i:2731288 original size:37 final size:37
Alignment explanation
Indices: 2731230--2731326 Score: 135
Period size: 37 Copynumber: 2.6 Consensus size: 37
2731220 TCTTTTCGTC
2731230 CTACTA-GAATTCAAACTCCTAAAAATAGGATATAA-TT
1 CTACTATG-ATTCAAACTCCTAAAAATAGGATA-AAGTT
* *
2731267 TTGCTATGATTCAAACTCCTAAAAATAGGATAAAGTT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAAAGTT
*
2731304 CTACTATGATTTAAACTCCTAAA
1 CTACTATGATTCAAACTCCTAAA
2731327 GATAAGATCC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
36 2 0.04
37 50 0.94
38 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.32
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATAGGATAAAGTT
Found at i:2731936 original size:2 final size:2
Alignment explanation
Indices: 2731929--2731967 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2731919 AGCGTATTAT
2731929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2731968 TGTAATTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2732119 original size:17 final size:17
Alignment explanation
Indices: 2732062--2732120 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
2732052 TATGTATACT
2732062 TTATATTTGGTTTATATA
1 TTATATTT-GTTTATATA
* * * *
2732080 TT-TATTTATTTTTTTT
1 TTATATTTGTTTATATA
*
2732096 TTTTATTTGTTTATATA
1 TTATATTTGTTTATATA
2732113 TTATATTT
1 TTATATTT
2732121 CATATTCCTA
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
16 7 0.23
17 22 0.71
18 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (17 bp):
TTATATTTGTTTATATA
Found at i:2732216 original size:12 final size:11
Alignment explanation
Indices: 2732202--2732250 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
2732192 TAATATTTCA
2732202 TTTATTTATTT
1 TTTATTTATTT
*
2732213 ATTTATTTATCCT
1 -TTTATTTAT-TT
2732226 TTTATTTTATTT
1 TTTA-TTTATTT
*
2732238 TTTACTTATTT
1 TTTATTTATTT
2732249 TT
1 TT
2732251 ATTCCTCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
11 8 0.25
12 18 0.56
13 6 0.19
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTATTT
Found at i:2736720 original size:22 final size:23
Alignment explanation
Indices: 2736695--2736745 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2736685 AACAAAAAGG
*
2736695 GCAAAAA-GAAAAAAGAAAAGAA
1 GCAAAAAGGAAAAAAGAAAAAAA
*
2736717 GCAAAAAGGAAAAAGGAAAAAAA
1 GCAAAAAGGAAAAAAGAAAAAAA
*
2736740 ACAAAA
1 GCAAAA
2736746 TAACAAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (23 bp):
GCAAAAAGGAAAAAAGAAAAAAA
Found at i:2736753 original size:14 final size:13
Alignment explanation
Indices: 2736736--2736767 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
2736726 AAAAAGGAAA
2736736 AAAAACAAAATAAC
1 AAAAAC-AAATAAC
2736750 AAAAACAAATAAC
1 AAAAACAAATAAC
2736763 AAAAA
1 AAAAA
2736768 TCGAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.81, C:0.12, G:0.00, T:0.06
Consensus pattern (13 bp):
AAAAACAAATAAC
Found at i:2737426 original size:22 final size:23
Alignment explanation
Indices: 2737384--2737439 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
2737374 GCTACCCCAT
*
2737384 CAAAACTTTGAGCATCAAAATGC
1 CAAACCTTTGAGCATCAAAATGC
* *
2737407 CAAACCTTTTAGCATC-AAATGT
1 CAAACCTTTGAGCATCAAAATGC
2737429 CAAACCTTTGA
1 CAAACCTTTGA
2737440 CCAAACACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (23 bp):
CAAACCTTTGAGCATCAAAATGC
Found at i:2737826 original size:20 final size:19
Alignment explanation
Indices: 2737782--2737835 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2737772 AGTTTCCAGA
*
2737782 TTCGCAACGCGATTATGACT
1 TTCGCAACGCGA-TATAACT
*
2737802 ATCGCAACGCGATACTAACT
1 TTCGCAACGCGATA-TAACT
*
2737822 TTCGCAACGAGATA
1 TTCGCAACGCGATA
2737836 ATACATAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (19 bp):
TTCGCAACGCGATATAACT
Found at i:2738050 original size:22 final size:22
Alignment explanation
Indices: 2738022--2738065 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2738012 CACTCTCTCA
2738022 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
**
2738044 CCCATCTCCGGTGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2738066 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2738353 original size:20 final size:20
Alignment explanation
Indices: 2738324--2738367 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2738314 GCGATTTTAG
2738324 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
2738344 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
2738364 TTTC
1 TTTC
2738368 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:2738558 original size:25 final size:24
Alignment explanation
Indices: 2738504--2738558 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2738494 TGTTTATTAT
* *
2738504 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
2738528 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
2738554 TGTTT
1 TGTTT
2738559 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2739708 original size:18 final size:18
Alignment explanation
Indices: 2739687--2739734 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2739677 TCCACTTCGG
2739687 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
2739705 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2739723 GAGCCATCACCT
1 GAGCCATCACCT
2739735 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2740294 original size:20 final size:20
Alignment explanation
Indices: 2740269--2740314 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2740259 TAGTTTACTT
2740269 TCGCAACACGAAAAT-GACTA
1 TCGCAACACGAAAATAG-CTA
* *
2740289 TCGCAACGCGGAAATAGCTA
1 TCGCAACACGAAAATAGCTA
2740309 TCGCAA
1 TCGCAA
2740315 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATAGCTA
Found at i:2740323 original size:19 final size:20
Alignment explanation
Indices: 2740286--2740323 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2740276 ACGAAAATGA
2740286 CTATCGCAACGCGGAAATAG
1 CTATCGCAACGCGGAAATAG
*
2740306 CTATCGCAATGC-GAAATA
1 CTATCGCAACGCGGAAATA
2740324 AAAATCGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGGAAATAG
Found at i:2740330 original size:19 final size:19
Alignment explanation
Indices: 2740308--2740404 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
2740298 GGAAATAGCT
*
2740308 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATCAAA
2740327 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATCAAA
*
2740341 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
2740360 ATCGCAAT--G--A-CAAA
1 ATCGCAATGCGAAATCAAA
* *
2740374 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
2740393 ATCGCAATGCGA
1 ATCGCAATGCGA
2740405 TTTGTGTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATCAAA
Found at i:2740343 original size:14 final size:14
Alignment explanation
Indices: 2740324--2740382 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
2740314 ATGCGAAATA
2740324 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2740338 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
2740357 AAAATCGCAATGAC
1 AAAATCGCAACGAC
2740371 AAAATCGCAACG
1 AAAATCGCAACG
2740383 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.28
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2740400 original size:33 final size:33
Alignment explanation
Indices: 2740308--2740401 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
2740298 GGAAATAGCT
* *
2740308 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
2740341 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
2740374 ATCGCAACGCGAAATGAAAATCGCAATG
1 ATCGCAATGCGAAATGAAAATCGCAATG
2740402 CGATTTGTGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGACAAA
Found at i:2740433 original size:14 final size:13
Alignment explanation
Indices: 2740411--2740441 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
2740401 GCGATTTGTG
2740411 TTTTGCGTTGCGA
1 TTTTGCGTTGCGA
2740424 TTTTGTCGTTGCGA
1 TTTTG-CGTTGCGA
2740438 TTTT
1 TTTT
2740442 CATTTCGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.06, C:0.13, G:0.26, T:0.55
Consensus pattern (13 bp):
TTTTGCGTTGCGA
Found at i:2740476 original size:20 final size:19
Alignment explanation
Indices: 2740442--2740497 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
2740432 TTGCGATTTT
2740442 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* *
2740461 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTGCGATAGC
*
2740481 CATTTTCACATTGCGAT
1 CA-TTTCGCATTGCGAT
2740498 TTTAAGTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.36
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:2741838 original size:11 final size:11
Alignment explanation
Indices: 2741822--2741856 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2741812 ATTTATCATT
2741822 TTAAAACACAC
1 TTAAAACACAC
*
2741833 TTAAAACATAC
1 TTAAAACACAC
*
2741844 TCAAAACACAC
1 TTAAAACACAC
2741855 TT
1 TT
2741857 CTCCCCCTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (11 bp):
TTAAAACACAC
Found at i:2744094 original size:21 final size:21
Alignment explanation
Indices: 2744068--2744107 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2744058 CAGAACCCCA
*
2744068 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2744089 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2744108 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2744138 original size:22 final size:21
Alignment explanation
Indices: 2744089--2744152 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
2744079 ATTCCCCTGT
2744089 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* *
2744112 AGGGGGAATCGGTTCCCTCAGG
1 GGGGGGAATCGGTTCCCTCA-A
* *
2744134 GGGGGGGATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
2744153 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 3 0.09
22 19 0.54
23 13 0.37
ACGTcount: A:0.16, C:0.25, G:0.39, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:2746237 original size:30 final size:30
Alignment explanation
Indices: 2746201--2746264 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
2746191 GAAGGACCTG
* *
2746201 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
2746231 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
2746261 TCCA
1 TCCA
2746265 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:2747044 original size:64 final size:64
Alignment explanation
Indices: 2746931--2747096 Score: 194
Period size: 64 Copynumber: 2.6 Consensus size: 64
2746921 CTCTTCAATG
* * * *
2746931 AATGTATGCATCGATGCACTACTTGTGCATTGGTGCATAAAATGCATTCGATGTTTT-TATTT-
1 AATGCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTA
* * *
2746993 AATGGGGATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATT
1 AAT--GCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATT
2747057 TA
63 TA
* * *
2747059 AATTCATGCATCGATGCACTGCATGTGCATCGATGCAT
1 AATGCATGCATCGATGCACTACTTGTGCATCGATGCAT
2747097 CTTAAACAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
62 3 0.03
63 5 0.06
64 72 0.82
65 5 0.06
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (64 bp):
AATGCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTA
Found at i:2747306 original size:208 final size:208
Alignment explanation
Indices: 2747061--2747482 Score: 821
Period size: 208 Copynumber: 2.0 Consensus size: 208
2747051 TCTATTTAAA
2747061 TTCATGCATCGATGCACTGCATGTGCATCGATGCATCTTAAACAATTTCTGGTATTTATCATCGA
1 TTCATGCATCGATGCACTGCATGTGCATCGATGCATCTTAAACAATTTCTGGTATTTATCATCGA
2747126 TGCATCGGTGCACAATGAATGTGCATCGATGCACATTGCCCAGAACTGACATTTTAA-ACAGTAA
66 TGCATCGGTGCACAATGAATGTGCATCGATGCACATTGCCCAGAACTGACATTTTAACAC-GTAA
2747190 ATCATCAACTCTTCCCTTAATTCTTCTATTTTGATCCCCTATTATGACTTTAAACTCAACTATCA
130 ATCATCAACTCTTCCCTTAATTCTTCTATTTTGATCCCCTATTATGACTTTAAACTCAACTATCA
2747255 TTATTGAAACCAAC
195 TTATTGAAACCAAC
2747269 TTCATGCATCGATGCACTGCATGTGCATCGATGCATCTTAAACAATTTCTGGTATTTATCATCGA
1 TTCATGCATCGATGCACTGCATGTGCATCGATGCATCTTAAACAATTTCTGGTATTTATCATCGA
2747334 TGCATCGGTGCACAATGAATGTGCATCGATGCACATTGCCCAGAACTGACATTTTAACACGTAAA
66 TGCATCGGTGCACAATGAATGTGCATCGATGCACATTGCCCAGAACTGACATTTTAACACGTAAA
2747399 TCATCAACTCTTCCCTTAATTCTTCTATTTTGATCCCCTATTATGACTTTAAACTCAACTATCAT
131 TCATCAACTCTTCCCTTAATTCTTCTATTTTGATCCCCTATTATGACTTTAAACTCAACTATCAT
2747464 TATTGAAACCAAC
196 TATTGAAACCAAC
2747477 TT-ATGC
1 TTCATGC
2747483 CCATATAAAT
Statistics
Matches: 213, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
207 4 0.02
208 207 0.97
209 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (208 bp):
TTCATGCATCGATGCACTGCATGTGCATCGATGCATCTTAAACAATTTCTGGTATTTATCATCGA
TGCATCGGTGCACAATGAATGTGCATCGATGCACATTGCCCAGAACTGACATTTTAACACGTAAA
TCATCAACTCTTCCCTTAATTCTTCTATTTTGATCCCCTATTATGACTTTAAACTCAACTATCAT
TATTGAAACCAAC
Found at i:2750690 original size:30 final size:30
Alignment explanation
Indices: 2750654--2750717 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
2750644 GAAGGACCTG
* *
2750654 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
2750684 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
2750714 TCCA
1 TCCA
2750718 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:2750906 original size:17 final size:19
Alignment explanation
Indices: 2750874--2750909 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2750864 CATATATCTC
2750874 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
2750893 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
2750910 CACGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:2751512 original size:64 final size:64
Alignment explanation
Indices: 2751394--2751559 Score: 194
Period size: 64 Copynumber: 2.6 Consensus size: 64
2751384 TCTTTCAATG
* * *
2751394 AATGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCAATGTTTT-TATTT-
1 AATGCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCAATGTTTTCTATTTA
* * * *
2751456 AATGGGGATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATT
1 AAT--GCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCAATGTTTTCTATT
2751520 TA
63 TA
* * *
2751522 AATTCATGCATCGATGCACTGCATGTGCATCGATGCAT
1 AATGCATGCATCGATGCACTACTTGTGCATCGATGCAT
2751560 CTTAAACAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
62 3 0.03
63 5 0.06
64 72 0.82
65 5 0.06
66 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (64 bp):
AATGCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCAATGTTTTCTATTTA
Found at i:2756968 original size:41 final size:42
Alignment explanation
Indices: 2756872--2756959 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
2756862 GACTCACCTG
* * *
2756872 TCATCCCTCAAGAGTCCCCTCCAATCGTTTAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* *
2756914 TCCTCCCTCAAGAGTCCCC-CCTACCGTTCAAGAGGCCACTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
2756955 TCATC
1 TCATC
2756960 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.23, C:0.41, G:0.14, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:2758323 original size:14 final size:14
Alignment explanation
Indices: 2758304--2758339 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2758294 ATTGTTTAAT
2758304 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2758318 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2758332 TGATTTGT
1 TGATTTGT
2758340 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2758568 original size:20 final size:20
Alignment explanation
Indices: 2758543--2758598 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
2758533 TCGCATTGCG
*
2758543 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2758563 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2758583 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
2758599 TTCCCCGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:2760846 original size:12 final size:12
Alignment explanation
Indices: 2760829--2760853 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2760819 TCTTCGGGGA
2760829 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2760841 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2760853 C
1 C
2760854 AGGATTATAA
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2761058 original size:24 final size:24
Alignment explanation
Indices: 2761024--2761077 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2761014 CTGAAACATC
*
2761024 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
2761048 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2761072 ATCAAA
1 ATCAAA
2761078 TTTCGAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2761833 original size:40 final size:40
Alignment explanation
Indices: 2761787--2761958 Score: 152
Period size: 41 Copynumber: 4.2 Consensus size: 40
2761777 TGTATTATCT
* *
2761787 CGTTGCGATTGTCAGAATCTCGTTGCGAAAGTCAGAATCG
1 CGTTGCGATTGTCAGTATCGCGTTGCGAAAGTCAGAATCG
** *
2761827 CGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCA-ATATCA
1 CGTTGCGATTGTCAGTATCGCGTTGCGAAAGTCAGA-ATCG
* * *
2761867 CGTTGCGATTTTGT-ATTATCGCGTTGCGATAGTCAGTATCG
1 CGTTGCGA--TTGTCAGTATCGCGTTGCGAAAGTCAGAATCG
* * * * *
2761908 CATTGCGATTTTGT-ATTATCGAGTTGCGATAGTCAGTATCG
1 CGTTGCGA--TTGTCAGTATCGCGTTGCGAAAGTCAGAATCG
*
2761949 CATTGCGATT
1 CGTTGCGATT
2761959 TACTTATTCG
Statistics
Matches: 115, Mismatches: 13, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
39 3 0.03
40 41 0.36
41 69 0.60
42 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (40 bp):
CGTTGCGATTGTCAGTATCGCGTTGCGAAAGTCAGAATCG
Found at i:2761891 original size:21 final size:21
Alignment explanation
Indices: 2761862--2761937 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
2761852 CGAAAGTCAA
*
2761862 TATCACGTTGCGATTTTGTAT
1 TATCGCGTTGCGATTTTGTAT
* *
2761883 TATCGCGTTGCGA--TAGTCAG
1 TATCGCGTTGCGATTTTGT-AT
*
2761903 TATCGCATTGCGATTTTGTAT
1 TATCGCGTTGCGATTTTGTAT
*
2761924 TATCGAGTTGCGAT
1 TATCGCGTTGCGAT
2761938 AGTCAGTATC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.07
20 13 0.30
21 25 0.57
22 3 0.07
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.41
Consensus pattern (21 bp):
TATCGCGTTGCGATTTTGTAT
Found at i:2761901 original size:41 final size:41
Alignment explanation
Indices: 2761842--2761959 Score: 191
Period size: 41 Copynumber: 2.9 Consensus size: 41
2761832 CGAAAGTCAG
* * * *
2761842 TATCGCGTTGCGAAAGTCAATATCACGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTGTAT
2761883 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTGTAT
*
2761924 TATCGAGTTGCGATAGTCAGTATCGCATTGCGATTT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTT
2761960 ACTTATTCGC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTGTAT
Found at i:2761908 original size:20 final size:20
Alignment explanation
Indices: 2761782--2761957 Score: 149
Period size: 20 Copynumber: 8.7 Consensus size: 20
2761772 GATTCTGTAT
* *
2761782 TATCTCGTTGCGATTGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
2761802 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
2761822 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
2761842 TATCGCGTTGCGAAAGTCAA
1 TATCGCGTTGCGATAGTCAG
* * *
2761862 TATCACGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
2761883 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
2761903 TATCGCATTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
*
2761924 TATCGAGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
2761944 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
2761958 TTACTTATTC
Statistics
Matches: 128, Mismatches: 22, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
19 6 0.05
20 92 0.72
21 25 0.20
22 5 0.04
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:2761948 original size:61 final size:60
Alignment explanation
Indices: 2761807--2761957 Score: 146
Period size: 61 Copynumber: 2.5 Consensus size: 60
2761797 GTCAGAATCT
* * * *
2761807 CGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAATATCA
1 CGTTGCGATAGTCAGTATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTCAATATCA
* * ** *
2761867 CGTTGCGATTTTGT-ATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTGT-ATTATCGA
1 CGTTGCGA--TAGTCAGTATCGCGTTGCGATAGTCAGTATCGCATTGCGA--AAGTCAATATC-A
*
2761930 -GTTGCGATAGTCAGTATCGCATTGCGAT
1 CGTTGCGATAGTCAGTATCGCGTTGCGAT
2761958 TTACTTATTC
Statistics
Matches: 73, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
60 11 0.15
61 45 0.62
62 14 0.19
63 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (60 bp):
CGTTGCGATAGTCAGTATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTCAATATCA
Found at i:2762018 original size:21 final size:22
Alignment explanation
Indices: 2761966--2762018 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2761956 ATTTACTTAT
2761966 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
* **
2761987 TCGTAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
2762008 TCGCATTGCGA
1 TCGCATTGCGA
2762019 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:2762869 original size:106 final size:106
Alignment explanation
Indices: 2762684--2763589 Score: 1290
Period size: 106 Copynumber: 8.6 Consensus size: 106
2762674 AACTCGCAGA
* * * *
2762684 TTGTCAACAAACAATTTCCTAATTTCATAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 TTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
** *
2762749 CAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTAG
66 CAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGG
*
2762790 TTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTC
1 TTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* *
2762855 CAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGA
66 CAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGG
* *
2762896 TTGTCAATAAACAACTTCCCAATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
1 TTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
2762961 CAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGG
66 CAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGG
* * * *
2763002 TTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGATTC
1 TTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* * *
2763067 AAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGG
66 CAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGG
* * * * * *
2763108 TTATCAA-CAATAGTTTCCCAATTTCAGAGCCAGTTTCAACTTCACATCGAAGGATATTGGACTC
1 TTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
*
2763172 CAGACAACACAAGTTCAACTTCACGACGAAGGGACCACTGG
66 CAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGG
*
2763213 TTGTCAATAAACAATTTCCTAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
1 TTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* *
2763278 CAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGG
66 CAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGG
* * * *
2763319 TTGTCAATAAACAACTTCCCAATTTCAGAGCTAATTTCAACTTCTCAGCGAAGGATCTTGGAC-C
1 TTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
** * * * *
2763383 CAAGACAACACAAGCCCAACTTCACGAGGAAGGGGCGGCTGA
66 C-AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGG
* *
2763425 TTGTCAAT-AA-AATTT--C-A-TTCAGAGTCAATTTCAACTTCACAGCGAATGATATTGGACTC
1 TTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* * *
2763484 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGG
66 CAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGG
* ** * *
2763525 TTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACT
1 TTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACT
2763589 C
65 C
2763590 GGAACAATGC
Statistics
Matches: 714, Mismatches: 76, Indels: 20
0.88 0.09 0.02
Matches are distributed among these distances:
100 76 0.11
101 4 0.01
102 6 0.01
104 5 0.01
105 96 0.13
106 527 0.74
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (106 bp):
TTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
CAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGG
Found at i:2763260 original size:317 final size:315
Alignment explanation
Indices: 2762684--2763589 Score: 1309
Period size: 317 Copynumber: 2.9 Consensus size: 315
2762674 AACTCGCAGA
* * * *
2762684 TTGTCAACAAACAATTTCCTAATTTCATAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 TTGTCAATAAACAACTTCC-AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* ** * *
2762749 CAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATAAACAATTTCCCAATT
65 AAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAA-AAA-AATTTCCCAATT
*
2762814 TCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
128 TCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACACAAGTTCAACTTCAC
* * *
2762879 GACGAAGGGACCGCTGATTGTCAATAAACAACTTCCCAATTTCATAGCCAATTTCAACTTCACAG
193 GACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
*
2762944 CGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGG
258 CGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGG
* *
2763002 TTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGATTC
1 TTGTCAATAAACAACTTC-CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* * * *
2763067 AAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTATCAACAATAGTTTCCCAATTT
65 AAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAA-AAAAATTTCCCAATTT
* * *
2763132 CAGAGCCAGTTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
129 CAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
* *
2763197 ACGAAGGGACCACTGGTTGTCAATAAACAATTTCCTAATTTCAGAGCCAATTTCAACTTCACAGC
194 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
*
2763262 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGG
259 GAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGG
* * * *
2763319 TTGTCAATAAACAACTTCCCAATTTCAGAGCTAATTTCAACTTCTCAGCGAAGGATCTTGGACCC
1 TTGTCAATAAACAACTT-CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
** * * * *
2763384 AAGACAACACAAGCCCAACTTCACGAGGAAGGGGCGGCTGATTGTCAATAAAATTT--C-A-TTC
65 AAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAAAAAAATTTCCCAATTTC
* * *
2763445 AGAGTCAATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
130 AGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
* * ** *
2763510 CGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCAC-GAC
195 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAG-C
*
2763574 GGAGGATATTGGACTC
259 GAAGGATATTGGACTC
2763590 GGAACAATGC
Statistics
Matches: 528, Mismatches: 57, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
311 1 0.00
312 132 0.25
313 1 0.00
314 1 0.00
316 5 0.01
317 286 0.54
318 101 0.19
319 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (315 bp):
TTGTCAATAAACAACTTCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
AGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAAAAAAATTTCCCAATTTCA
GAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACACAAGTTCAACTTCACGAC
GAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGA
AGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGG
Found at i:2763431 original size:423 final size:417
Alignment explanation
Indices: 2762687--2763589 Score: 1405
Period size: 423 Copynumber: 2.1 Consensus size: 417
2762677 TCGCAGATTG
* *
2762687 TCAACAAACAATTTCCTAATTTCATAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
1 TCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAG
** *
2762752 ACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATAAACAATTTCCCAATTTCA
65 ACAACACAAGTTCAACTTCACGACGAAGGGACCACTAGTTGTCAATAAACAATTTCCCAATTTCA
* *
2762817 GAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
130 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAAC
*
2762882 GAAGGGACCGCTGATTGTCAATAAACAACTTCCCAATTTCATAGCCAATTTCAACTTCACAGCGA
195 GAAGGGACCGCTGATTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGA
** *
2762947 AGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
260 AGGATATTGGACTCCAGACAACACAAGCCCAACTTCACGACGAAGGGACCGCTGATTGTCAAT-A
*
2763012 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGATTCAAGACAACAC
324 A-AA-TT-TC-A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACAC
2763077 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTA
384 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTA
* * *
2763111 TCAAC-AATAGTTTCCCAATTTCAGAGCCAGTTTCAACTTCACATCGAAGGATATTGGACTCCAG
1 TCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA-CGAAGGATATTGGACTCCAG
* *
2763175 ACAACACAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCTAATTTCA
65 ACAACACAAGTTCAACTTCACGACGAAGGGACCACTAGTTGTCAATAAACAATTTCCCAATTTCA
2763240 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAAC
130 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAAC
* * *
2763305 GAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCTAATTTCAACTTCTCAGCGA
195 GAAGGGACCGCTGATTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGA
* * * *
2763370 AGGATCTTGGAC-CCAAGACAACACAAGCCCAACTTCACGAGGAAGGGGCGGCTGATTGTCAATA
260 AGGATATTGGACTCC-AGACAACACAAGCCCAACTTCACGACGAAGGGACCGCTGATTGTCAATA
* * * *
2763434 AAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACACAAGTT
324 AAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGTT
*
2763499 CAACTTCACAACGAAGGGACGGCTGGTTG
389 CAACTTCACAACGAAGGGACGGCTGGTTA
** * *
2763528 TCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTC
1 TCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCAC-ACGAAGGATATTGGACTC
2763590 GGAACAATGC
Statistics
Matches: 439, Mismatches: 36, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
417 85 0.19
418 48 0.11
419 3 0.01
420 2 0.00
421 2 0.00
422 5 0.01
423 289 0.66
424 5 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (417 bp):
TCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACACGAAGGATATTGGACTCCAGA
CAACACAAGTTCAACTTCACGACGAAGGGACCACTAGTTGTCAATAAACAATTTCCCAATTTCAG
AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACG
AAGGGACCGCTGATTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
GGATATTGGACTCCAGACAACACAAGCCCAACTTCACGACGAAGGGACCGCTGATTGTCAATAAA
ATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGTTCA
ACTTCACAACGAAGGGACGGCTGGTTA
Found at i:2764349 original size:37 final size:37
Alignment explanation
Indices: 2764296--2764392 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
2764286 TCTTACTAGA
* * * *
2764296 ATTCAAACTCCCAAAAATAGGATATAATTTTTCTATG
1 ATTCAAACTCCTAAAAATAGGATAGAATTCTACTATG
*
2764333 ATTCAAACTCCTAAAAATAGGATAGAGTTCTACTATG
1 ATTCAAACTCCTAAAAATAGGATAGAATTCTACTATG
* *
2764370 ATTTAAACTCCTAAAGATAGGAT
1 ATTCAAACTCCTAAAAATAGGAT
2764393 CCACAAGCAC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (37 bp):
ATTCAAACTCCTAAAAATAGGATAGAATTCTACTATG
Found at i:2764950 original size:2 final size:2
Alignment explanation
Indices: 2764930--2764972 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
2764920 TTTTTAATAC
* *
2764930 TA TA TT TA T- TA TT 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
2764971 TA
1 TA
2764973 CTTTTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:2765158 original size:11 final size:11
Alignment explanation
Indices: 2765144--2765172 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2765134 GGTTTATATA
2765144 TTTGTTTTTTT
1 TTTGTTTTTTT
2765155 TTTGTTTTTTT
1 TTTGTTTTTTT
2765166 TTTGTTT
1 TTTGTTT
2765173 ATATTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTTGTTTTTTT
Found at i:2766131 original size:65 final size:65
Alignment explanation
Indices: 2765973--2766131 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 65
2765963 GTTTAAGGTA
* * * **
2765973 CATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTTAT
1 CATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTTAT
2766036 G
65 G
*
2766037 CATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTATG
1 CATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTATG
*
2766101 CATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 CATCGATGCATAAG-G-AGTGCATCGATGCAT
2766132 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 60 0.71
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (65 bp):
CATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTATG
Found at i:2766646 original size:18 final size:18
Alignment explanation
Indices: 2766623--2766657 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2766613 CTAGGAGATT
2766623 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
2766641 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
2766658 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:2767730 original size:149 final size:149
Alignment explanation
Indices: 2767557--2767863 Score: 544
Period size: 149 Copynumber: 2.1 Consensus size: 149
2767547 GAGTCGAGGG
* * **
2767557 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCAGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
2767622 A-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 ACT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
2767686 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
*
2767706 TCTACGCGGTCCTTCAGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCAGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
2767771 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
2767836 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2767855 TCTACGCGG
1 TCTACGCGG
2767864 CACTTCGGTG
Statistics
Matches: 151, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
149 150 0.99
150 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCAGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:2767872 original size:23 final size:23
Alignment explanation
Indices: 2767839--2767883 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2767829 ATTATTATAT
*
2767839 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
2767862 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
2767884 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:2771344 original size:64 final size:63
Alignment explanation
Indices: 2771259--2771399 Score: 185
Period size: 64 Copynumber: 2.2 Consensus size: 63
2771249 TTGTTTAAGG
* * *
2771259 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTTA
* * *
2771323 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTA
*
2771387 TGCATAGATGCAT
1 TGCATCGATGCAT
2771400 GGTGTAGTTC
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 60 0.88
65 7 0.10
66 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAAGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTA
Found at i:2771934 original size:18 final size:18
Alignment explanation
Indices: 2771911--2771945 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2771901 CTAGGAGATT
2771911 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
2771929 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
2771946 CTAGATGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:2772284 original size:2 final size:2
Alignment explanation
Indices: 2772277--2772304 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2772267 GAACATGTGA
2772277 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
2772305 GTCTAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2773020 original size:147 final size:148
Alignment explanation
Indices: 2772849--2773153 Score: 506
Period size: 149 Copynumber: 2.1 Consensus size: 148
2772839 GAGTCGAGGG
* * **
2772849 TCTACGCGGTCCTTC-GGGATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 TCTACGCGGTCCTTCAGGAATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATA
*
2772913 -TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 CT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATCATTA
2772977 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
*
2772996 TCTACGCGGTCCTTCAGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCAGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
2773061 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATTATTT
65 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATCATTA
2773126 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
2773145 TCTACGCGG
1 TCTACGCGG
2773154 CACTTCGGTG
Statistics
Matches: 147, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
147 15 0.10
148 2 0.01
149 129 0.88
150 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (148 bp):
TCTACGCGGTCCTTCAGGAATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATA
CTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATCATTAT
ATGGCACTACGGTGCAAT
Found at i:2773162 original size:23 final size:23
Alignment explanation
Indices: 2773129--2773173 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2773119 ATTATTTTAT
*
2773129 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
2773152 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
2773174 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:2773937 original size:20 final size:19
Alignment explanation
Indices: 2773912--2773960 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
2773902 AATTCATTTA
*
2773912 TTTATTTTATTATTTTTCCT
1 TTTATTTTATT-TTTTTACT
2773932 TTTATTTTATTTTTTTACT
1 TTTATTTTATTTTTTTACT
*
2773951 TAT-TTTTATT
1 TTTATTTTATT
2773961 CTTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 7 0.26
19 9 0.33
20 11 0.41
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTATTTTATTTTTTTACT
Found at i:2773940 original size:29 final size:30
Alignment explanation
Indices: 2773904--2773987 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 30
2773894 TTTTTAATAA
*
2773904 TTCA-TTTATTTATTTTATTATTTTTCCTT-
1 TTCATTTTATTTATTTTATTATTTTT-ATTC
2773933 TT-ATTTTATTT-TTTTACTTATTTTTATTC
1 TTCATTTTATTTATTTTA-TTATTTTTATTC
*
2773962 TTCATTTTTTTTA-TTTATTCATTTTT
1 TTCATTTTATTTATTTTATT-ATTTTT
2773988 TCCCTCTAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
28 8 0.17
29 21 0.45
30 18 0.38
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (30 bp):
TTCATTTTATTTATTTTATTATTTTTATTC
Found at i:2773974 original size:16 final size:17
Alignment explanation
Indices: 2773907--2773988 Score: 62
Period size: 17 Copynumber: 4.9 Consensus size: 17
2773897 TTAATAATTC
* *
2773907 ATTTATTTA-TTTTATT
1 ATTTATTCATTTTTTTT
*
2773923 ATTT-TTCCTTTTATTTT
1 ATTTATTCATTTT-TTTT
* * *
2773940 ATTTTTTTACTTATTTTT
1 ATTTATTCA-TTTTTTTT
*
2773958 A-TTCTTCATTTTTTTT
1 ATTTATTCATTTTTTTT
2773974 ATTTATTCATTTTTT
1 ATTTATTCATTTTTT
2773989 CCCTCTAACA
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
15 2 0.04
16 15 0.29
17 24 0.47
18 7 0.14
19 3 0.06
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTATTCATTTTTTTT
Found at i:2775312 original size:11 final size:11
Alignment explanation
Indices: 2775296--2775350 Score: 58
Period size: 11 Copynumber: 4.8 Consensus size: 11
2775286 TCGGTTGTGA
2775296 GAAGAAGGAAG
1 GAAGAAGGAAG
2775307 GAAGAAGGAAG
1 GAAGAAGGAAG
* *
2775318 AAGGAGAAGGAGAA
1 --GAAGAAGGA-AG
2775332 GAA-AAGGAAG
1 GAAGAAGGAAG
2775342 GAAGAAGGA
1 GAAGAAGGA
2775351 TAAGGACAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
10 4 0.11
11 21 0.58
12 2 0.06
13 8 0.22
14 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (11 bp):
GAAGAAGGAAG
Found at i:2775313 original size:3 final size:3
Alignment explanation
Indices: 2775295--2775391 Score: 61
Period size: 3 Copynumber: 30.3 Consensus size: 3
2775285 TTCGGTTGTG
* *
2775295 AGA AGA AGGA AGGA AGA AGGA AGA AGG AGA AGG AGA AGA A-A AGGA AGGA
1 AGA AGA A-GA A-GA AGA A-GA AGA AGA AGA AGA AGA AGA AGA A-GA A-GA
* * * * *
2775344 AGA AGG ATA AGG ACA AGA AGA AAA AGAA AGA AGGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA A-GA AGA AGA AGA AGA
2775391 A
1 A
2775392 ACTATTGGTG
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
2 2 0.03
3 50 0.68
4 22 0.30
ACGTcount: A:0.61, C:0.01, G:0.37, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:2775327 original size:6 final size:7
Alignment explanation
Indices: 2775303--2775389 Score: 67
Period size: 7 Copynumber: 12.6 Consensus size: 7
2775293 TGAGAAGAAG
2775303 GAAGGAA
1 GAAGGAA
2775310 GAAGGAA
1 GAAGGAA
2775317 GAAGG-A
1 GAAGGAA
2775323 GAAGG-A
1 GAAGGAA
*
2775329 GAAGAAAA
1 GAAG-GAA
2775337 GGAAGGAA
1 -GAAGGAA
2775345 GAAGG-A
1 GAAGGAA
*
2775351 TAAGGACAA
1 GAAGG--AA
2775360 GAA-GAA
1 GAAGGAA
* *
2775366 AAAGAAA
1 GAAGGAA
2775373 GAAGGAA
1 GAAGGAA
2775380 GAA-GAA
1 GAAGGAA
2775386 GAAG
1 GAAG
2775390 AAACTATTGG
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
6 26 0.41
7 27 0.42
8 4 0.06
9 7 0.11
ACGTcount: A:0.60, C:0.01, G:0.38, T:0.01
Consensus pattern (7 bp):
GAAGGAA
Found at i:2775342 original size:35 final size:36
Alignment explanation
Indices: 2775295--2775389 Score: 124
Period size: 35 Copynumber: 2.7 Consensus size: 36
2775285 TTCGGTTGTG
* *
2775295 AGAAGAAGGAAGGAAGAAGGAAGAAGGAGAAGGAGA
1 AGAAGAAGGAAGGAAGAAGGAAGAAGGACAAGAAGA
*
2775331 AGAA-AAGGAAGGAAGAAGG-ATAAGGACAAGAAGA
1 AGAAGAAGGAAGGAAGAAGGAAGAAGGACAAGAAGA
* *
2775365 AAAAGAAAGAAGGAAGAA-GAAGAAG
1 AGAAGAAGGAAGGAAGAAGGAAGAAG
2775390 AAACTATTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
34 16 0.31
35 31 0.61
36 4 0.08
ACGTcount: A:0.60, C:0.01, G:0.38, T:0.01
Consensus pattern (36 bp):
AGAAGAAGGAAGGAAGAAGGAAGAAGGACAAGAAGA
Found at i:2775363 original size:31 final size:28
Alignment explanation
Indices: 2775308--2775392 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
2775298 AGAAGGAAGG
2775308 AAGAAGGAAGAAGGAGAAGGAGAAGAAA
1 AAGAAGGAAGAAGGAGAAGGAGAAGAAA
* * *
2775336 AGGAAGGAAGAAGGATAAGGACAAGAAGA
1 AAGAAGGAAGAAGGAGAAGGAGAAGAA-A
* *
2775365 AA-AAGAAAGAAGGAAGAAGAAGAAGAAA
1 AAGAAGGAAGAAGG-AGAAGGAGAAGAAA
2775393 CTATTGGTGC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
28 35 0.74
29 12 0.26
ACGTcount: A:0.62, C:0.01, G:0.35, T:0.01
Consensus pattern (28 bp):
AAGAAGGAAGAAGGAGAAGGAGAAGAAA
Found at i:2782625 original size:29 final size:29
Alignment explanation
Indices: 2782592--2782652 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
2782582 CATTTGTTGA
2782592 GTTCGAATAAGTTTGTTTTTTGTGTTTGT
1 GTTCGAATAAGTTTGTTTTTTGTGTTTGT
2782621 GTTCGAATAAGTTTGTTTTTTGTGTTTGT
1 GTTCGAATAAGTTTGTTTTTTGTGTTTGT
2782650 GTT
1 GTT
2782653 GTTCATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.13, C:0.03, G:0.25, T:0.59
Consensus pattern (29 bp):
GTTCGAATAAGTTTGTTTTTTGTGTTTGT
Found at i:2782698 original size:10 final size:10
Alignment explanation
Indices: 2782683--2782712 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2782673 TATTATGTTC
*
2782683 GTTCGTTTGT
1 GTTCGTTTAT
2782693 GTTCGTTTAT
1 GTTCGTTTAT
2782703 GTTCGTTTAT
1 GTTCGTTTAT
2782713 CATTTAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.10, G:0.23, T:0.60
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:2786000 original size:21 final size:21
Alignment explanation
Indices: 2785949--2786001 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
2785939 ATTATGACTA
2785949 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
2785970 TCGCGTTGCGATTTTCCCAATT
1 TCGCAATGCGATTTT-CCAATT
2785992 T-GCAATGCGA
1 TCGCAATGCGA
2786002 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2786056 original size:20 final size:20
Alignment explanation
Indices: 2786031--2786165 Score: 130
Period size: 20 Copynumber: 6.7 Consensus size: 20
2786021 AATTGGGAAA
2786031 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
2786051 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
2786071 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
2786092 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
2786112 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
2786132 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
2786152 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
2786166 TTTCAAAGCG
Statistics
Matches: 98, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
19 4 0.04
20 68 0.69
21 24 0.24
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2786093 original size:61 final size:61
Alignment explanation
Indices: 2786028--2786165 Score: 204
Period size: 61 Copynumber: 2.3 Consensus size: 61
2786018 GCGAATTGGG
* *
2786028 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * *
2786089 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
2786150 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
2786166 TTTCAAAGCG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:2786361 original size:22 final size:22
Alignment explanation
Indices: 2786333--2786376 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2786323 CACTCTCTCA
2786333 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2786355 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2786377 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2786663 original size:20 final size:20
Alignment explanation
Indices: 2786634--2786677 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2786624 GCGATTTTAG
2786634 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
2786654 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
2786674 TTTC
1 TTTC
2786678 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:2786868 original size:25 final size:24
Alignment explanation
Indices: 2786814--2786868 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2786804 TGTTTATTAT
* *
2786814 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
2786838 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
2786864 TGTTT
1 TGTTT
2786869 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2788018 original size:18 final size:18
Alignment explanation
Indices: 2787997--2788044 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2787987 TCCACTTCGG
2787997 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
2788015 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2788033 GAGCCATCACCT
1 GAGCCATCACCT
2788045 GATCAACCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2788604 original size:20 final size:20
Alignment explanation
Indices: 2788579--2788621 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2788569 TAGTTTACTT
2788579 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
2788599 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
2788619 TCG
1 TCG
2788622 AAATGCGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:2788633 original size:19 final size:20
Alignment explanation
Indices: 2788590--2788634 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2788580 CGCAACACGA
*
2788590 AAATGACTATCGCAACGCGG
1 AAATGACTATCGAAACGCGG
* *
2788610 AAATGGCTATCGAAATGC-G
1 AAATGACTATCGAAACGCGG
2788629 AAATGA
1 AAATGA
2788635 AAATCGCAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGAAACGCGG
Found at i:2788640 original size:19 final size:19
Alignment explanation
Indices: 2788618--2788714 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
2788608 GGAAATGGCT
*
2788618 ATCGAAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2788637 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
2788651 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2788670 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
* *
2788684 ATCGCAACGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
2788703 ATCGCAATGCGA
1 ATCGCAATGCGA
2788715 TTTGTGTTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
14 20 0.33
15 2 0.03
16 3 0.05
17 4 0.07
18 2 0.03
19 29 0.48
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2788665 original size:33 final size:33
Alignment explanation
Indices: 2788618--2788709 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
2788608 GGAAATGGCT
*
2788618 ATCGAAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2788651 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
2788684 ATCGCAACGCAAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2788710 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.50, C:0.21, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2788698 original size:13 final size:14
Alignment explanation
Indices: 2788634--2788698 Score: 69
Period size: 14 Copynumber: 4.4 Consensus size: 14
2788624 ATGCGAAATG
2788634 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2788648 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
2788667 AAAATCGCAACGAC
1 AAAATCGCAACGAC
2788681 AAAATCGCAACG-C
1 AAAATCGCAACGAC
2788694 AAAAT
1 AAAAT
2788699 GAAAATCGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
13 6 0.14
14 22 0.50
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.23
ACGTcount: A:0.51, C:0.23, G:0.15, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2788743 original size:19 final size:19
Alignment explanation
Indices: 2788721--2788878 Score: 120
Period size: 20 Copynumber: 8.7 Consensus size: 19
2788711 GCGATTTGTG
2788721 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
2788740 TTTCGCGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
2788756 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
2788773 TTTCGCATTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
2788789 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
2788806 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
**
2788825 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
*
2788845 TTTCCGCGTTGCGATTTTAA
1 TTT-CGCGTTGCGATTTTCA
*
2788865 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
2788879 AAGTAAAATA
Statistics
Matches: 111, Mismatches: 16, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
14 15 0.14
15 6 0.05
16 4 0.04
17 4 0.04
18 6 0.05
19 33 0.30
20 40 0.36
21 3 0.03
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.44
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:2788764 original size:14 final size:14
Alignment explanation
Indices: 2788745--2788803 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2788735 TTTCATTTCG
2788745 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2788759 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
2788776 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
2788792 CGTTGCGATTTT
1 CGTTGCGATTTT
2788804 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2788768 original size:33 final size:33
Alignment explanation
Indices: 2788726--2788819 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
2788716 TTGTGTTTCG
*
2788726 CGTTGCGATTTTCATTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
2788759 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
2788792 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2788820 AGCCATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:2790940 original size:38 final size:33
Alignment explanation
Indices: 2790890--2790981 Score: 130
Period size: 38 Copynumber: 2.6 Consensus size: 33
2790880 TGACTATCGT
*
2790890 AACGAGAGAATCGCAATGCGAAATGAAAATCAC
1 AACGAGAAAATCGCAATGCGAAATGAAAATCAC
2790923 AATGCGAAATGAAAATCGCAATGCGAAATGAAAATCAC
1 AA--CG--A-GAAAATCGCAATGCGAAATGAAAATCAC
2790961 AACGAGAAAATCGCAATGCGA
1 AACGAGAAAATCGCAATGCGA
2790982 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
33 18 0.34
34 1 0.02
35 2 0.04
36 2 0.04
37 1 0.02
38 29 0.55
ACGTcount: A:0.49, C:0.17, G:0.21, T:0.13
Consensus pattern (33 bp):
AACGAGAAAATCGCAATGCGAAATGAAAATCAC
Found at i:2790969 original size:19 final size:19
Alignment explanation
Indices: 2790898--2790962 Score: 112
Period size: 19 Copynumber: 3.4 Consensus size: 19
2790888 GTAACGAGAG
*
2790898 AATCGCAATGCGAAATGAA
1 AATCACAATGCGAAATGAA
2790917 AATCACAATGCGAAATGAA
1 AATCACAATGCGAAATGAA
*
2790936 AATCGCAATGCGAAATGAA
1 AATCACAATGCGAAATGAA
2790955 AATCACAA
1 AATCACAA
2790963 CGAGAAAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.15
Consensus pattern (19 bp):
AATCACAATGCGAAATGAA
Found at i:2791025 original size:20 final size:20
Alignment explanation
Indices: 2791009--2791057 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
2790999 GATTTTCTCA
2791009 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
2791029 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
2791049 TTGCGATAG
1 TTGCGATAG
2791058 TCAAATGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Found at i:2793339 original size:12 final size:12
Alignment explanation
Indices: 2793322--2793346 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2793312 TCTTCGGGGA
2793322 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2793334 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2793346 C
1 C
2793347 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2794372 original size:40 final size:41
Alignment explanation
Indices: 2794316--2794429 Score: 149
Period size: 40 Copynumber: 2.8 Consensus size: 41
2794306 GATTCTGTAT
* *
2794316 TATCTCGTTGCGAAAGTCAGAATCGCGTTGCGAAATT-CAG
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAATTGCAG
** * *
2794356 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAATTGCAG
* *
2794397 TATCGCGTTGCGATAGTCAGTATCGCATTGCGA
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGA
2794430 TTTTCCCAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 33 0.51
41 32 0.49
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (41 bp):
TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAATTGCAG
Found at i:2794430 original size:20 final size:20
Alignment explanation
Indices: 2794316--2794429 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
2794306 GATTCTGTAT
*
2794316 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
2794336 AATCGCGTTGCGAAATTCAG
1 TATCGCGTTGCGAAAGTCAG
2794356 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
2794376 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
2794397 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2794417 TATCGCATTGCGA
1 TATCGCGTTGCGA
2794430 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.76
21 14 0.17
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:2794432 original size:41 final size:41
Alignment explanation
Indices: 2794296--2794433 Score: 179
Period size: 41 Copynumber: 3.4 Consensus size: 41
2794286 AACTTTGAAA
* * *
2794296 ATCGCATTGCGATTCTGTATTATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** * *
2794337 ATCGCGTTGCGAAATT-CAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* *
2794377 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
2794418 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
2794434 CCCAATTCGC
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 34 0.41
41 48 0.59
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:2794444 original size:41 final size:41
Alignment explanation
Indices: 2794296--2794451 Score: 145
Period size: 41 Copynumber: 3.8 Consensus size: 41
2794286 AACTTTGAAA
* ** * * * *
2794296 ATCGCATTGCGATTCTGTATTATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* ** * *
2794337 ATCGCGTTGCGAAATT-CAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* ** *
2794377 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
2794418 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
2794452 TTACTTATTC
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
40 34 0.35
41 60 0.62
42 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
Found at i:2794541 original size:21 final size:21
Alignment explanation
Indices: 2794498--2794541 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2794488 GACACTGTAG
* ** *
2794498 ACTATTGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
2794519 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
2794540 AC
1 AC
2794542 GCGAATTTGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:2794941 original size:18 final size:17
Alignment explanation
Indices: 2794908--2794941 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2794898 AATATATTAT
*
2794908 TTTTTCTCATTCTTAAC
1 TTTTTCTCATTATTAAC
2794925 TTTTTCTCATCTATTAA
1 TTTTTCTCAT-TATTAA
2794942 TTAAAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTCTCATTATTAAC
Found at i:2795008 original size:24 final size:23
Alignment explanation
Indices: 2794961--2795014 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
2794951 ATATGAAAAT
**
2794961 ATAGATTTGTGGGAAATTTTTAA
1 ATAGATTTGTGGGAAATTCATAA
*
2794984 ATAGATTTGTGCGTAAATTCATAA
1 ATAGATTTGTG-GGAAATTCATAA
2795008 ATA-ATTT
1 ATAGATTT
2795015 TATATGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.43
Consensus pattern (23 bp):
ATAGATTTGTGGGAAATTCATAA
Found at i:2795082 original size:2 final size:2
Alignment explanation
Indices: 2795075--2795100 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2795065 ATGACTTGAA
2795075 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
2795101 TAATAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2800022 original size:31 final size:31
Alignment explanation
Indices: 2799984--2800077 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
2799974 ATGGTCGAGG
2799984 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2800015 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
2800046 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
2800077 G
1 G
2800078 GTCCTTCGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 57 0.98
32 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2800814 original size:21 final size:21
Alignment explanation
Indices: 2800788--2800829 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2800778 TCGAAGTTTC
*
2800788 ATGCATCGGTGCACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
*
2800809 ATGCATCGATGTACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
2800830 CTGTAGCAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
ATGCATCGATGCACTGTAGCA
Found at i:2804175 original size:29 final size:29
Alignment explanation
Indices: 2804141--2804203 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
2804131 GGTAGTTAAG
*
2804141 GCGGACGGTTGGAGGTAATTTTGGAAGGC
1 GCGGACGATTGGAGGTAATTTTGGAAGGC
2804170 GCGGACGATTGGAGGTAATTTTGGAAGGC
1 GCGGACGATTGGAGGTAATTTTGGAAGGC
*
2804199 ACGGA
1 GCGGA
2804204 TGGTGATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.24, C:0.11, G:0.43, T:0.22
Consensus pattern (29 bp):
GCGGACGATTGGAGGTAATTTTGGAAGGC
Found at i:2806815 original size:27 final size:28
Alignment explanation
Indices: 2806770--2806827 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
2806760 AGGGGTGCAC
*
2806770 AAAAAATCCGAATATCCGATTTTGCGAA
1 AAAAAATCCGAATATCCGAATTTGCGAA
*
2806798 AAAAATATCCGAA-A-CCGAATTTGGGAA
1 AAAAA-ATCCGAATATCCGAATTTGCGAA
2806825 AAA
1 AAA
2806828 CCGATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 14 0.52
28 6 0.22
29 7 0.26
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.21
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGAATTTGCGAA
Found at i:2809268 original size:21 final size:21
Alignment explanation
Indices: 2809244--2809285 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2809234 AGTTTATTTT
2809244 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
2809265 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
2809286 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:2809321 original size:32 final size:32
Alignment explanation
Indices: 2809274--2809349 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
2809264 GTAAACTTTG
*
2809274 TTTCAATTATCGAACTTG-AAGTTTTTAAGTA
1 TTTCAATTATCGAACTTGAAAGTATTTAAGTA
*
2809305 TTTGAATTTATCGAACTTGAAAGTATTTAAGTA
1 TTTCAA-TTATCGAACTTGAAAGTATTTAAGTA
2809338 TTTCAATTATCG
1 TTTCAATTATCG
2809350 TAAACTTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 5 0.12
32 18 0.45
33 17 0.43
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (32 bp):
TTTCAATTATCGAACTTGAAAGTATTTAAGTA
Found at i:2809434 original size:21 final size:21
Alignment explanation
Indices: 2809410--2809459 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2809400 GTTTTTTTAT
2809410 AACCGGTTTTTTTAAAACCGA
1 AACCGGTTTTTTTAAAACCGA
2809431 AACCGGTTTTTTTAAAACCGA
1 AACCGGTTTTTTTAAAACCGA
2809452 AACCGGTT
1 AACCGGTT
2809460 ACACCGGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (21 bp):
AACCGGTTTTTTTAAAACCGA
Found at i:2809450 original size:15 final size:15
Alignment explanation
Indices: 2809391--2809429 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2809381 TTTAATAATA
*
2809391 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
2809406 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
2809421 TTAAAACCG
1 TTAAAACCG
2809430 AAACCGGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:2809569 original size:15 final size:17
Alignment explanation
Indices: 2809543--2809574 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2809533 TTCTATGGGA
2809543 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
2809559 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
2809575 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Done.