Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004862.1 Hibiscus syriacus cultivar Beakdansim tig00010968_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: 2846896
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 13
Found at i:446744 original size:16 final size:16
Alignment explanation
Indices: 446723--446842 Score: 74
Period size: 16 Copynumber: 7.4 Consensus size: 16
446713 CATATTACTA
446723 AATATAACT-TAATAAT
1 AATATAA-TATAATAAT
446739 AATATAATATAATAAT
1 AATATAATATAATAAT
* *
446755 ACTATAATAATAGT-AT
1 AATATAAT-ATAATAAT
446771 AATATACATTCTATAATAAT
1 AATATA-A---TATAATAAT
**
446791 -ATATGCTATAATAAT
1 AATATAATATAATAAT
446806 -ATATAA-AT-ATAAT
1 AATATAATATAATAAT
*
446819 ATATATACTAT-ATAAT
1 A-ATATAATATAATAAT
446835 ATATATAA
1 A-ATATAA
446843 CACACATTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 20
0.74 0.09 0.18
Matches are distributed among these distances:
13 5 0.06
14 2 0.02
15 19 0.23
16 42 0.50
17 5 0.06
19 8 0.10
20 3 0.04
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (16 bp):
AATATAATATAATAAT
Found at i:446747 original size:5 final size:5
Alignment explanation
Indices: 446723--446842 Score: 56
Period size: 5 Copynumber: 23.4 Consensus size: 5
446713 CATATTACTA
* *
446723 AATAT AACT-T AATAAT AATAT AATAT AATAAT ACTAT AATAAT AGTAT
1 AATAT AA-TAT AAT-AT AATAT AATAT AAT-AT AATAT AAT-AT AATAT
* **
446771 AATAT ACAT-T -CTAT AATA- ATATAT GCTAT AATA- ATATAT AAATAT
1 AATAT A-ATAT AATAT AATAT A-ATAT AATAT AATAT A-ATAT -AATAT
446816 AATAT -ATAT ACTATAT AATAT -ATAT AA
1 AATAT AATAT A--ATAT AATAT AATAT AA
446843 CACACATTTC
Statistics
Matches: 88, Mismatches: 10, Indels: 34
0.67 0.08 0.26
Matches are distributed among these distances:
3 1 0.01
4 12 0.14
5 50 0.57
6 19 0.22
7 6 0.07
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:446801 original size:15 final size:15
Alignment explanation
Indices: 446723--446839 Score: 89
Period size: 15 Copynumber: 7.5 Consensus size: 15
446713 CATATTACTA
446723 AATATA-ACT-TAAT
1 AATATATACTATAAT
*
446736 AATAATATAATATAAT
1 AAT-ATATACTATAAT
*
446752 AATACTATAATAATAGTAT
1 AATA-TATACT-ATA--AT
*
446771 AATATACATTCTATAAT
1 AATAT--ATACTATAAT
*
446788 AATATATGCTATAAT
1 AATATATACTATAAT
*
446803 AATATATAAATATAAT
1 AATATAT-ACTATAAT
446819 -ATATATACTAT-AT
1 AATATATACTATAAT
446832 AATATATA
1 AATATATA
446840 TAACACACAT
Statistics
Matches: 86, Mismatches: 7, Indels: 21
0.75 0.06 0.18
Matches are distributed among these distances:
13 5 0.06
14 14 0.16
15 25 0.29
16 19 0.22
17 10 0.12
18 1 0.01
19 9 0.10
20 3 0.03
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (15 bp):
AATATATACTATAAT
Found at i:447538 original size:54 final size:54
Alignment explanation
Indices: 447466--447849 Score: 531
Period size: 54 Copynumber: 7.1 Consensus size: 54
447456 ATTGCACCTA
* * * *
447466 AGTGTCGATATGGAAATTCACAAACTCATTACGAATTCCATGGGTTGCACACAT
1 AGTGTCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
* * * *
447520 AGTGCCGATACGGTAATTCATAAACTCATTATG-ATTCTGTGGATTGCACACAT
1 AGTGTCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
* * * * **
447573 AATGTTGATACGGTAATTTACAAACTCATTATGAATTTCGTGGGTTTTACACAT
1 AGTGTCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
* *
447627 AGTGTCGATACGGTAATTCATAAACTCATTATGAATTTCGTGGGTTGCACACAT
1 AGTGTCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
* **
447681 AGT-TCTGATACGGTAATTCACAAAATCATTATGAATTTTGTGGGTTGCACACAT
1 AGTGTC-GATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
*
447735 AGTG-CTGATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTTGCACACAT
1 AGTGTC-GATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
**
447789 AGTGTCGATACGGTAATTCACAAACTCATTATGAATTCATTGGGTTGCACACAT
1 AGTGTCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
447843 AGTGTCG
1 AGTGTCG
447850 GTAGTACACA
Statistics
Matches: 295, Mismatches: 31, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
53 47 0.16
54 247 0.84
55 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (54 bp):
AGTGTCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
Found at i:450646 original size:21 final size:21
Alignment explanation
Indices: 450620--450664 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
450610 TTTATATCCT
450620 GATACATCTTATTTCCACCTA
1 GATACATCTTATTTCCACCTA
450641 GATACATCTTATTTCCACCTA
1 GATACATCTTATTTCCACCTA
450662 GAT
1 GAT
450665 GCATGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.38
Consensus pattern (21 bp):
GATACATCTTATTTCCACCTA
Found at i:454199 original size:54 final size:54
Alignment explanation
Indices: 454088--454460 Score: 543
Period size: 54 Copynumber: 6.9 Consensus size: 54
454078 GCGATATGAA
* ** **
454088 AATTCAAAAACTCATTATGAATTCCAT-GACTGCACACATAGTGTCGATACGGT
1 AATTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGT
* *
454141 AATTCACAAACTCATTATGAATTCTGTGGGTTGCAAACATAGTGTCGATATGGT
1 AATTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGT
* * * * *
454195 AATTCACAAACTCATTATCAATTCTGTGGGTTGCACACATAGTGCCAATATGAT
1 AATTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGT
* ** *
454249 AATTCACAAACTCATTATGAATTTTGTGGGTTGCACATGTAGTGTCGATACAGT
1 AATTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGT
454303 AATTCACAAACTCATTATGAATT-TCGTGGGTTGCACACATAGTGTCGATACGGT
1 AATTCACAAACTCATTATGAATTCT-GTGGGTTGCACACATAGTGTCGATACGGT
* * *
454357 AATTCACAAACTCATTATGAATTCTGTGGGTTGTACACATAGTGCCGATACGAT
1 AATTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGT
*
454411 AATTCACAAACTCATTATGAATTCTGTGGGCTGCACACATAGTGTCGATA
1 AATTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATA
454461 GTACTAATAA
Statistics
Matches: 287, Mismatches: 30, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
53 25 0.09
54 261 0.91
55 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (54 bp):
AATTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGT
Found at i:455966 original size:2 final size:2
Alignment explanation
Indices: 455946--456123 Score: 97
Period size: 2 Copynumber: 97.0 Consensus size: 2
455936 CGGTATTACA
* * * *
455946 AT AT AA AT AT AT A- AA AT AT AT A- AT AT AA AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
455986 AT A- ACT AA AT ACT AT A- AT AT AT A- AT AT A- AT AT AT AT A- AC
1 AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
456025 AT AT A- AT GT A- AT AT AT AT AT A- AT AT AT AT A- AT AT GT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
456062 AT AT AT A- AT AT AA AT AT AT ACC AT A- AT AT AT A- AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
456101 AA AT AT A- AT AT -T AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
456124 GCTAATAACA
Statistics
Matches: 135, Mismatches: 19, Indels: 44
0.68 0.10 0.22
Matches are distributed among these distances:
1 19 0.14
2 112 0.83
3 4 0.03
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (2 bp):
AT
Found at i:456006 original size:41 final size:39
Alignment explanation
Indices: 455946--456122 Score: 164
Period size: 41 Copynumber: 4.3 Consensus size: 39
455936 CGGTATTACA
*
455946 ATATAA-ATATA-TAAAATATATAATATAAATATATAAAT
1 ATATAATATATACTATAATATATAATATAAATATAT-AAT
*
455984 ATATAACTAAATACTATAATATATAATATAATATATATAACAT
1 ATATAA-TATATACTATAATATATAATATAA-ATATAT-A-AT
*
456027 ATAATGTAATATATA-TATAATATATATAATATGTAATATATAAT
1 AT-A--TAATATATACTAT-A-ATATATAATAT-AAATATATAAT
* *
456071 ATA-AATATATACCATAATATATAATATATAAAATATAAT
1 ATATAATATATACTATAATATATAATATA-AATATATAAT
456110 ATTATAATATATA
1 A-TATAATATATA
456123 TGCTAATAAC
Statistics
Matches: 117, Mismatches: 7, Indels: 27
0.77 0.05 0.18
Matches are distributed among these distances:
38 6 0.05
39 21 0.18
40 15 0.13
41 26 0.22
42 8 0.07
43 5 0.04
44 8 0.07
45 7 0.06
46 20 0.17
47 1 0.01
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (39 bp):
ATATAATATATACTATAATATATAATATAAATATATAAT
Found at i:456068 original size:39 final size:39
Alignment explanation
Indices: 455960--456153 Score: 95
Period size: 41 Copynumber: 4.9 Consensus size: 39
455950 AAATATATAA
*
455960 AATATATAATATAA-ATATATAAATATATAACTAA-ATACTAT
1 AATATAT-ATATAATATATAT-AATATATAA--AATATAATAT
* *
456001 AATATATAATATAATATATATAACATAT-A-ATGTAATAT
1 AATATAT-ATATAATATATATAATATATAAAATATAATAT
* *
456039 -ATATATAATATATATAATATGTAATATATAATATA-AATAT
1 AATATAT-ATATA-AT-ATATATAATATATAAAATATAATAT
* *
456079 ATACCATAATATATAATATATA-AA-ATATAATATTATAATAT
1 A-A-TAT-ATATATAATATATATAATATATAA-AATATAATAT
* * * *
456120 -ATATGCTA-ATAACATA-ATACTATATATAATATAA
1 AATAT-ATATATAATATATATAATATATAAAATATAA
456154 GTTATATAAT
Statistics
Matches: 122, Mismatches: 17, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
36 1 0.01
37 27 0.22
38 16 0.13
39 18 0.15
40 11 0.09
41 31 0.25
42 9 0.07
43 7 0.06
44 2 0.02
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (39 bp):
AATATATATATAATATATATAATATATAAAATATAATAT
Found at i:456149 original size:20 final size:19
Alignment explanation
Indices: 455961--456150 Score: 84
Period size: 20 Copynumber: 9.5 Consensus size: 19
455951 AATATATAAA
* *
455961 ATATATAATATAAATATATAA
1 ATATATAATA-ACATA-ATAT
*
455982 ATATATAACTAA-ATACTAT
1 ATATATAA-TAACATAATAT
*
456001 A-ATAT-ATAATATAATAT
1 ATATATAATAACATAATAT
* **
456018 ATATAACATATAATGTAATAT
1 ATAT-ATA-ATAACATAATAT
*
456039 ATATATAATATATATAATAT
1 ATATATAATA-ACATAATAT
* *
456059 GTA-ATATATAATATAAATAT
1 ATATATA-ATAACAT-AATAT
* *
456079 ATACCATAAT-ATATAATAT
1 ATA-TATAATAACATAATAT
**
456098 ATAAAATATAATATTATAATAT
1 AT---ATATAATAACATAATAT
*
456120 ATATGCTAATAACATAATACT
1 ATAT-ATAATAACATAATA-T
456141 ATATATAATA
1 ATATATAATA
456151 TAAGTTATAT
Statistics
Matches: 137, Mismatches: 15, Indels: 35
0.73 0.08 0.19
Matches are distributed among these distances:
16 3 0.02
17 8 0.06
18 6 0.04
19 23 0.17
20 45 0.33
21 36 0.26
22 16 0.12
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (19 bp):
ATATATAATAACATAATAT
Found at i:456166 original size:7 final size:7
Alignment explanation
Indices: 455945--456122 Score: 147
Period size: 7 Copynumber: 25.1 Consensus size: 7
455935 ACGGTATTAC
455945 AATATA-
1 AATATAT
455951 AATATAT
1 AATATAT
455958 AAAATATAT
1 --AATATAT
455967 AATATA-
1 AATATAT
455973 AATATAT
1 AATATAT
455980 AAATATAT
1 -AATATAT
*
455988 AA-CTA-
1 AATATAT
455993 AATACTAT
1 AATA-TAT
456001 AATATAT
1 AATATAT
456008 AATATA-
1 AATATAT
456014 ATATATAT
1 A-ATATAT
*
456022 AACATAT
1 AATATAT
*
456029 AATGTAAT
1 AATAT-AT
456037 ATATATAT
1 A-ATATAT
456045 AATATATAT
1 -A-ATATAT
*
456054 AATATGT
1 AATATAT
456061 AATATAT
1 AATATAT
456068 AATATA-
1 AATATAT
456074 AATATAT
1 AATATAT
**
456081 -A-CCAT
1 AATATAT
456086 AATATAT
1 AATATAT
456093 AATATAT
1 AATATAT
*
456100 AAAATAT
1 AATATAT
456107 AATATTAT
1 AATA-TAT
456115 AATATAT
1 AATATAT
456122 A
1 A
456123 TGCTAATAAC
Statistics
Matches: 141, Mismatches: 14, Indels: 33
0.75 0.07 0.18
Matches are distributed among these distances:
5 4 0.03
6 23 0.16
7 71 0.50
8 25 0.18
9 18 0.13
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (7 bp):
AATATAT
Found at i:456179 original size:93 final size:91
Alignment explanation
Indices: 455952--456167 Score: 236
Period size: 93 Copynumber: 2.4 Consensus size: 91
455942 TACAATATAA
* *
455952 ATATATAAAATATATAATA--TA-A-AT-ATATAAATATATAAC-TAAATACTATAATATATAAT
1 ATATATAATATATATAATATGTATATATAATATAAATATATACCAT-AATA-TATAATATATAAT
*
456011 ATAATATATATAACATATAATGTAATAT
64 ATAATATATATAACATATAATGTAATAC
456039 ATATATAATATATATAATATGTAATATATAATATAAATATATACCATAATATATAATATATAAAA
1 ATATATAATATATATAATATGT-ATATATAATATAAATATATACCATAATATATAATATAT--AA
*
456104 TATAATAT-TATAATATAT-ATGCTAATAAC
63 TATAATATATATAACATATAATG-TAAT-AC
*
456133 ATA-ATACTATATATAATATAAGT-TATATAATATAA
1 ATATATAATATATATAATAT--GTATATATAATATAA
456168 CATAGTACCA
Statistics
Matches: 111, Mismatches: 5, Indels: 20
0.82 0.04 0.15
Matches are distributed among these distances:
87 18 0.16
89 1 0.01
90 1 0.01
91 1 0.01
92 15 0.14
93 58 0.52
94 15 0.14
95 2 0.02
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (91 bp):
ATATATAATATATATAATATGTATATATAATATAAATATATACCATAATATATAATATATAATAT
AATATATATAACATATAATGTAATAC
Found at i:458508 original size:12 final size:12
Alignment explanation
Indices: 458488--458527 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
458478 AAAAATAATA
458488 TTTTAATTTTTT
1 TTTTAATTTTTT
*
458500 TTTTGATTTTTT
1 TTTTAATTTTTT
* *
458512 ATTTCATTTTTT
1 TTTTAATTTTTT
458524 TTTT
1 TTTT
458528 TGCAAAACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTAATTTTTT
Found at i:461578 original size:15 final size:15
Alignment explanation
Indices: 461499--461699 Score: 229
Period size: 15 Copynumber: 13.7 Consensus size: 15
461489 TTCAAGAACA
461499 ATTATAAAATATATTT
1 ATTATAAAATA-ATTT
461515 ATTTATTAAAATAA--T
1 A-TTA-TAAAATAATTT
461530 -TT-T-AAATAATTT
1 ATTATAAAATAATTT
** *
461542 A--ATAAGGTTATTT
1 ATTATAAAATAATTT
461555 ATT-TAAAATAATTT
1 ATTATAAAATAATTT
*
461569 ATTATAAAATTATTT
1 ATTATAAAATAATTT
461584 ATTATAAAATAATTT
1 ATTATAAAATAATTT
*
461599 ATTTTAAAATAATTT
1 ATTATAAAATAATTT
461614 ATTATAAAATAATTT
1 ATTATAAAATAATTT
* *
461629 ATTTTAATATAATTT
1 ATTATAAAATAATTT
461644 ATTATAAAATAATTT
1 ATTATAAAATAATTT
*
461659 ATTATAAAATAAATT
1 ATTATAAAATAATTT
* *
461674 ATTTTAAAATAAATT
1 ATTATAAAATAATTT
461689 ATTATAAAATA
1 ATTATAAAATA
461700 TGGATTGATT
Statistics
Matches: 158, Mismatches: 17, Indels: 21
0.81 0.09 0.11
Matches are distributed among these distances:
10 6 0.04
11 1 0.01
12 2 0.01
13 9 0.06
14 11 0.07
15 117 0.74
16 1 0.01
17 4 0.03
18 7 0.04
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (15 bp):
ATTATAAAATAATTT
Found at i:461594 original size:30 final size:30
Alignment explanation
Indices: 461499--461743 Score: 229
Period size: 30 Copynumber: 8.1 Consensus size: 30
461489 TTCAAGAACA
461499 ATTATAAAATATATTTATTTATTAAAATAA--T
1 ATTATAAAATA-ATTTA-TTA-TAAAATAATTT
** *
461530 -TT-T-AAATAATTTA--ATAAGGTTATTT
1 ATTATAAAATAATTTATTATAAAATAATTT
*
461555 ATT-TAAAATAATTTATTATAAAATTATTT
1 ATTATAAAATAATTTATTATAAAATAATTT
*
461584 ATTATAAAATAATTTATTTTAAAATAATTT
1 ATTATAAAATAATTTATTATAAAATAATTT
* *
461614 ATTATAAAATAATTTATTTTAATATAATTT
1 ATTATAAAATAATTTATTATAAAATAATTT
*
461644 ATTATAAAATAATTTATTATAAAATAAATT
1 ATTATAAAATAATTTATTATAAAATAATTT
* *
461674 ATTTTAAAATAAATTATTATAAAATATGGATTGATTT
1 ATTATAAAATAATTTATTAT-AAA-AT--A---ATTT
* *
461711 ATTTTAAAATAATTTATT-TTAAATAATTT
1 ATTATAAAATAATTTATTATAAAATAATTT
461740 ATTA
1 ATTA
461744 GTATGGATTG
Statistics
Matches: 183, Mismatches: 17, Indels: 30
0.80 0.07 0.13
Matches are distributed among these distances:
23 5 0.03
24 1 0.01
25 1 0.01
26 3 0.02
27 15 0.08
28 5 0.03
29 21 0.11
30 100 0.55
31 3 0.02
32 3 0.02
34 3 0.02
35 2 0.01
36 1 0.01
37 20 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
ATTATAAAATAATTTATTATAAAATAATTT
Found at i:461608 original size:45 final size:45
Alignment explanation
Indices: 461551--461743 Score: 246
Period size: 45 Copynumber: 4.2 Consensus size: 45
461541 TAATAAGGTT
* *
461551 ATTTATT-TAAAATAATTTATTATAAAATTATTTATTATAAAATA
1 ATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATA
* *
461595 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAATATA
1 ATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATA
*
461640 ATTTATTATAAAATAATTTATTATAAAATAAATTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATA
* *
461685 AATTATTATAAAATATGGATTGATTTATTTTAAAATAATTTATTTT-AAATA
1 ATTTATTAT-AAA-AT--A---ATTTATTATAAAATAATTTATTTTAAAATA
461736 ATTTATTA
1 ATTTATTA
461744 GTATGGATTG
Statistics
Matches: 131, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
44 7 0.05
45 84 0.64
46 3 0.02
47 2 0.02
49 1 0.01
51 12 0.09
52 22 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (45 bp):
ATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATA
Found at i:461727 original size:15 final size:14
Alignment explanation
Indices: 461707--461742 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
461697 ATATGGATTG
461707 ATTTATTTTAAAATA
1 ATTTATTTT-AAATA
461722 ATTTATTTTAAATA
1 ATTTATTTTAAATA
461736 ATTTATT
1 ATTTATT
461743 AGTATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:461760 original size:32 final size:32
Alignment explanation
Indices: 461722--461873 Score: 146
Period size: 32 Copynumber: 5.4 Consensus size: 32
461712 TTTTAAAATA
461722 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
461754 ATTTA-TTT---T-A---A-GA-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
461776 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
461808 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
461830 ATTTATTTTAAATAATTTATTAGTATGTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
461862 ATTTATTTTAAA
1 ATTTATTTTAAA
461874 ATATGGATTG
Statistics
Matches: 97, Mismatches: 3, Indels: 40
0.69 0.02 0.29
Matches are distributed among these distances:
22 28 0.29
23 8 0.08
24 1 0.01
25 1 0.01
26 4 0.04
27 2 0.02
28 4 0.04
29 1 0.01
30 1 0.01
31 8 0.08
32 39 0.40
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:461761 original size:22 final size:22
Alignment explanation
Indices: 461745--461786 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
461735 AATTTATTAG
461745 TATGGATTGATTTATTTTAAGA
1 TATGGATTGATTTATTTTAAGA
461767 TATGGATTGATTTATTTTAA
1 TATGGATTGATTTATTTTAA
461787 ATAATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAGA
Found at i:461787 original size:54 final size:53
Alignment explanation
Indices: 461698--462334 Score: 428
Period size: 54 Copynumber: 12.0 Consensus size: 53
461688 TATTATAAAA
461698 TATGGATTGATTTATTTTAAA-AT--A---ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATATGGATTGATTTATTTTAAATAATTTATTAG
461745 TATGGATTGATTTATTTTAAGATATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAA-ATATGGATTGATTTATTTTAAATAATTTATTAG
461799 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTT-AAATATGGATTGATTTATTTTAAATAATTTATTAG
* *
461853 TATGTATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-G
1 TATGGATTGATTTATTTT-AAATATGGATTGATTTATTTTAAATAATTTA-TTAG
** ** * ** * * *
461901 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGA-TTGATTTATTTTA-AAA
1 TATGGATTGATTTATTTTAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAG
* * * ** * * *
461955 TATGGATTGATTTATTTTAAATA---ATTTATTTGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATATGGATTGATTTATTTTAAATAATTTA--TT--AG
** * * ** * * *
462009 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTA-TTGATTTATTTTA-AAA
1 TATGGATTGATTTATTTTAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAG
**
462063 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAAT-ATTT-TTAG
1 TATGGATTGATTTA-T-TT-TA--AATATGGATTGATTTATTTTAAATAATTTATTAG
462119 TATGGATTGATTTATTTTAAATATGGATTGA-TTATTTTAAATAA-TTATTAG
1 TATGGATTGATTTATTTTAAATATGGATTGATTTATTTTAAATAATTTATTAG
* * * ** * * *
462170 TATGGATTGATTTATTTTAAATA---ATTTATTTGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATATGGATTGATTTATTTTAAATAATTTA--TT--AG
** *
462224 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATCTATTTTAAATAATTTATTAG
1 TATGGATTGATTTA-T-TT-TA--AATATGGATTGATTTATTTTAAATAATTTATTAG
* *
462282 AATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTT-AAATATGGATTGATTTATTTTAAATAATTTATTA
462335 TTGTAGTTGT
Statistics
Matches: 468, Mismatches: 68, Indels: 101
0.73 0.11 0.16
Matches are distributed among these distances:
47 24 0.05
48 33 0.07
49 20 0.04
50 24 0.05
51 40 0.09
52 4 0.01
53 4 0.01
54 218 0.47
55 10 0.02
56 29 0.06
57 10 0.02
58 21 0.04
59 11 0.02
60 5 0.01
62 15 0.03
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (53 bp):
TATGGATTGATTTATTTTAAATATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:461824 original size:22 final size:22
Alignment explanation
Indices: 461799--461841 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
461789 AATTTATTAG
461799 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
461821 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
461842 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:461869 original size:22 final size:22
Alignment explanation
Indices: 461844--461916 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 22
461834 ATTTTAAATA
461844 ATTTATTAGTATGTATTGATTT
1 ATTTATTAGTATGTATTGATTT
* * *
461866 ATTT-TAAAATATGGATTGATTT
1 ATTTAT-TAGTATGTATTGATTT
* *
461888 A-TTATT-GTAGTTGTATGGATTG
1 ATTTATTAGTA--TGTATTGATTT
461910 ATTTATT
1 ATTTATT
461917 TTAAATAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
20 2 0.05
21 3 0.08
22 28 0.74
23 5 0.13
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (22 bp):
ATTTATTAGTATGTATTGATTT
Found at i:461916 original size:80 final size:83
Alignment explanation
Indices: 461821--462007 Score: 299
Period size: 80 Copynumber: 2.3 Consensus size: 83
461811 TATTTTAAAA
*
461821 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
461886 TTA-TT-AT-TGTAGTTG
66 TTATTTAATATGTAGTTG
461901 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
* *
461966 TTATTTTAAATAATTTATTTG
66 TTA-TTT-AAT-ATGTAGTTG
461987 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
462008 ATATGGATTG
Statistics
Matches: 98, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
80 67 0.68
82 2 0.02
84 2 0.02
86 27 0.28
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (83 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTTAATATGTAGTTG
Found at i:461929 original size:188 final size:187
Alignment explanation
Indices: 461722--462190 Score: 883
Period size: 188 Copynumber: 2.5 Consensus size: 187
461712 TTTTAAAATA
461722 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAGATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA-ATATGGATTGATTTATTTTAA
461787 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
65 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
461852 GTATGTATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
130 GTATGTATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
461910 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATATGGATTGATTTATTTTAA
*
461975 ATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
65 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
462040 GTATGTATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
130 GTATGTATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
462098 ATTTATTTTAAAT-ATTT-TTAGTATGGATTGATTTATTTTAAATATGGATTGA-TTATTTTAAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATATGGATTGATTTATTTTAAA
462160 TAA-TTATTAGTATGGATTGATTTATTTTAAA
66 TAATTTATTAGTATGGATTGATTTATTTTAAA
462191 TAATTTATTT
Statistics
Matches: 278, Mismatches: 2, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
183 27 0.10
184 13 0.05
185 13 0.05
186 22 0.08
187 4 0.01
188 197 0.71
189 2 0.01
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (187 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATATGGATTGATTTATTTTAAA
TAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
TATGTATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
Found at i:461941 original size:32 final size:32
Alignment explanation
Indices: 461900--462061 Score: 166
Period size: 32 Copynumber: 5.7 Consensus size: 32
461890 TATTGTAGTT
461900 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
461932 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
461955 -TATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
461986 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
462009 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
462040 GTATGTATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
462062 ATATGGATTG
Statistics
Matches: 107, Mismatches: 3, Indels: 40
0.71 0.02 0.27
Matches are distributed among these distances:
22 28 0.26
23 7 0.07
25 2 0.02
26 6 0.06
28 6 0.06
29 2 0.02
31 7 0.07
32 49 0.46
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:461958 original size:22 final size:22
Alignment explanation
Indices: 461933--461975 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
461923 AATTTATTAG
461933 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
461955 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
461976 TAATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:462012 original size:22 final size:22
Alignment explanation
Indices: 461987--462029 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
461977 AATTTATTTG
461987 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
462009 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
462030 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:462057 original size:22 final size:22
Alignment explanation
Indices: 462032--462104 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 22
462022 ATTTTAAATA
462032 ATTTATTAGTATGTATTGATTT
1 ATTTATTAGTATGTATTGATTT
* * *
462054 ATTT-TAAAATATGGATTGATTT
1 ATTTAT-TAGTATGTATTGATTT
* *
462076 A-TTATT-GTAGTTGTATGGATTG
1 ATTTATTAGTA--TGTATTGATTT
462098 ATTTATT
1 ATTTATT
462105 TTAAATATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
20 2 0.05
21 3 0.08
22 28 0.74
23 5 0.13
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (22 bp):
ATTTATTAGTATGTATTGATTT
Found at i:462136 original size:21 final size:20
Alignment explanation
Indices: 462119--462161 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
462109 ATATTTTTAG
462119 TATGGATTGATTTATTTTAAA
1 TATGGATTGA-TTATTTTAAA
462140 TATGGATTGATTATTTTAAA
1 TATGGATTGATTATTTTAAA
462160 TA
1 TA
462162 ATTATTAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (20 bp):
TATGGATTGATTATTTTAAA
Found at i:462153 original size:20 final size:21
Alignment explanation
Indices: 462110--462161 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
462100 TTATTTTAAA
* *
462110 TATTTTTAGTATGGATTGATT
1 TATTTTAAATATGGATTGATT
462131 TATTTTAAATATGGATTGA-T
1 TATTTTAAATATGGATTGATT
462151 TATTTTAAATA
1 TATTTTAAATA
462162 ATTATTAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (21 bp):
TATTTTAAATATGGATTGATT
Found at i:462192 original size:161 final size:166
Alignment explanation
Indices: 461767--462334 Score: 605
Period size: 161 Copynumber: 3.5 Consensus size: 166
461757 TATTTTAAGA
* * *
461767 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATCTATTTTAAATAATTTATTAGAATGAATTGATTTATTTTAAAATATGGATTGAT
* * * *
461832 TTATTTTAAATAATTTATTAGTATGTATTGATTTATTTT-AA-AA--TA-T-GGATTGATTTA-T
66 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
* *** *
461890 TATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTA-TTAG
131 TATTTTA-AAATATGGATTGATTTA--TT--AT--TGTAGTT-G
* *
461933 TATGGATTGATTTATTTT-AA-AA--TA-T-G---G-ATTGATTTATTTT-AAATA---ATTTAT
1 TATGGATTGATCTATTTTAAATAATTTATTAGAATGAATTGATTTATTTTAAAATATGGATTGAT
* * ** * * * *
461984 TTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGTATT
66 TTATTTTAAATAATTTA--TT--AGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATT
462049 GATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
127 GATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
* * *
462089 TATGGATTGATTTATTTTAAAT-ATTT-TTAGTATGGATTGATTTATTTT-AAATATGGATTGA-
1 TATGGATTGATCTATTTTAAATAATTTATTAGAATGAATTGATTTATTTTAAAATATGGATTGAT
*
462150 TTATTTTAAATAA-TTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATT
66 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
462214 TATTTTAAAATATGGATTGATTTATTATTGTAGTTG
131 TATTTTAAAATATGGATTGATTTATTATTGTAGTTG
462250 TATGGATTGATCTATTTTAAATAATTTATTAGAATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATCTATTTTAAATAATTTATTAGAATGAATTGATTTATTTTAAAATATGGATTGAT
462315 TTATTTTAAATAATTTATTA
66 TTATTTTAAATAATTTATTA
462335 TTGTAGTTGT
Statistics
Matches: 341, Mismatches: 31, Indels: 60
0.79 0.07 0.14
Matches are distributed among these distances:
152 16 0.05
154 2 0.01
155 5 0.01
156 53 0.16
157 8 0.02
158 4 0.01
159 2 0.01
160 6 0.02
161 102 0.30
162 27 0.08
163 30 0.09
164 33 0.10
165 18 0.05
166 31 0.09
167 4 0.01
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (166 bp):
TATGGATTGATCTATTTTAAATAATTTATTAGAATGAATTGATTTATTTTAAAATATGGATTGAT
TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
TATTTTAAAATATGGATTGATTTATTATTGTAGTTG
Found at i:462205 original size:32 final size:31
Alignment explanation
Indices: 462140--462222 Score: 141
Period size: 32 Copynumber: 2.7 Consensus size: 31
462130 TTATTTTAAA
462140 TATGGATTGA-TTATTTTAAATAATTATTAG
1 TATGGATTGATTTATTTTAAATAATTATTAG
*
462170 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAA-TTATTAG
462202 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
462223 ATATGGATTG
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 10 0.20
31 13 0.26
32 27 0.54
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (31 bp):
TATGGATTGATTTATTTTAAATAATTATTAG
Found at i:462214 original size:18 final size:18
Alignment explanation
Indices: 462163--462218 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
462153 TTTTAAATAA
*
462163 TTATTAGTATGGATTGAT
1 TTATTTGTATGGATTGAT
* *
462181 TTATTT-TA---AATAAT
1 TTATTTGTATGGATTGAT
462195 TTATTTGTATGGATTGAT
1 TTATTTGTATGGATTGAT
462213 TTATTT
1 TTATTT
462219 TAAAATATGG
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
14 10 0.34
15 2 0.07
17 2 0.07
18 15 0.52
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (18 bp):
TTATTTGTATGGATTGAT
Found at i:462273 original size:80 final size:80
Alignment explanation
Indices: 462009--462319 Score: 479
Period size: 80 Copynumber: 3.9 Consensus size: 80
461999 TATTTTAAAA
*
462009 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
462074 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
462089 TATGGATTGATTTATTTTAAAT-ATTT-TTAGTATGGATTGATTTATTTT-AAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
462151 TATTTTAAATAAT-TA-TTAG
66 T-TATT--AT--TGTAGTT-G
*
462170 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
462235 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
* * *
462250 TATGGATTGATCTATTTTAAATAATTTATTAGAATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
462315 TTATT
66 TTATT
462320 TTAAATAATT
Statistics
Matches: 212, Mismatches: 8, Indels: 22
0.88 0.03 0.09
Matches are distributed among these distances:
77 15 0.07
78 24 0.11
79 5 0.02
80 95 0.45
81 29 0.14
82 5 0.02
83 24 0.11
84 15 0.07
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:467808 original size:29 final size:29
Alignment explanation
Indices: 467773--467848 Score: 143
Period size: 29 Copynumber: 2.6 Consensus size: 29
467763 TCCCCAAGCA
*
467773 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
467802 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
467831 TAGGTCGCCATGCACTCC
1 TAGGTCGCCATGCACTCC
467849 CTCCTACTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.37, G:0.29, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:468584 original size:19 final size:19
Alignment explanation
Indices: 468560--468605 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
468550 TGATTGCGGC
468560 CGCGGGCTATTACGG-CTGT
1 CGCGGGCTATTACGGTC-GT
468579 CGCGGGCGCTATTACGGTCGT
1 CGC-GG-GCTATTACGGTCGT
468600 CGCGGG
1 CGCGGG
468606 TAACTCGGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 15 0.62
22 1 0.04
ACGTcount: A:0.09, C:0.28, G:0.41, T:0.22
Consensus pattern (19 bp):
CGCGGGCTATTACGGTCGT
Found at i:468591 original size:21 final size:21
Alignment explanation
Indices: 468565--468605 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
468555 GCGGCCGCGG
468565 GCTATTACGG-CTGTCGCGGGC
1 GCTATTACGGTC-GTCGCGGGC
468586 GCTATTACGGTCGTCGCGGG
1 GCTATTACGGTCGTCGCGGG
468606 TAACTCGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.10, C:0.27, G:0.39, T:0.24
Consensus pattern (21 bp):
GCTATTACGGTCGTCGCGGGC
Found at i:469921 original size:22 final size:22
Alignment explanation
Indices: 469891--469968 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
469881 TTTATTAAAA
* *
469891 TAAAGTATTATACT-ATATTTTT
1 TAAATTATTA-ACTAATATATTT
*
469913 TAAATTATTAATTAATATATTT
1 TAAATTATTAACTAATATATTT
*** *
469935 TAAATATATTTTTTAAAATATTAT
1 TAAAT-TATTAACTAATATATT-T
469959 TAAATTATTA
1 TAAATTATTA
469969 TATTAATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.04
22 21 0.46
23 17 0.37
24 6 0.13
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (22 bp):
TAAATTATTAACTAATATATTT
Found at i:469921 original size:35 final size:36
Alignment explanation
Indices: 469882--469957 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 36
469872 ATTATATTAT
*
469882 TTATTAAAATAA-AGTATTAT-ACTATATTTTTTAAA
1 TTATTAAAATAATA-TATTATAAATATATTTTTTAAA
* *
469917 TTATT-AATTAATATATTTTAAATATATTTTTTAAA
1 TTATTAAAATAATATATTATAAATATATTTTTTAAA
*
469952 ATATTA
1 TTATTA
469958 TTAAATTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (36 bp):
TTATTAAAATAATATATTATAAATATATTTTTTAAA
Found at i:469944 original size:23 final size:22
Alignment explanation
Indices: 469905--469976 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 22
469895 GTATTATACT
*
469905 ATATTTTTTAAATTATTAATTA
1 ATATATTTTAAATTATTAATTA
**
469927 ATATATTTTAAATATATTTTTTA
1 ATATATTTTAAAT-TATTAATTA
*
469950 AAATATTATTAAATTATTATATTA
1 ATATATT-TTAAATTATTA-ATTA
469974 ATA
1 ATA
469977 ATAAATTCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 12 0.30
23 17 0.43
24 11 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATATTTTAAATTATTAATTA
Found at i:470124 original size:23 final size:24
Alignment explanation
Indices: 470098--470160 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
470088 TATAATTGAG
470098 TATATAATTATAATATTAAAAA-A
1 TATATAATTATAATATTAAAAATA
* *
470121 TATA-ATATTATATTGTTAAAAATA
1 TATATA-ATTATAATATTAAAAATA
* *
470145 TAAATAAATAT-ATATT
1 TATATAATTATAATATT
470161 TTTTAAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
22 1 0.03
23 21 0.68
24 8 0.26
25 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TATATAATTATAATATTAAAAATA
Found at i:470155 original size:27 final size:27
Alignment explanation
Indices: 470118--470171 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
470108 TAATATTAAA
470118 AAATATAATATTATATTGTTAAAAATAT
1 AAATATAATA-TATATTGTTAAAAATAT
* *
470146 AAATA-AATATATATTTTTTAAAATAT
1 AAATATAATATATATTGTTAAAAATAT
470172 TTTAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.62
27 4 0.17
28 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
AAATATAATATATATTGTTAAAAATAT
Found at i:470214 original size:28 final size:27
Alignment explanation
Indices: 470124--470224 Score: 91
Period size: 27 Copynumber: 3.7 Consensus size: 27
470114 TAAAAAATAT
* * *
470124 AATATTATATTGTTAAAAATATA-AATA
1 AATATTATATTTTTTAAAATATATTA-A
*
470151 AATA-TATATTTTTTAAAATATTTTAA
1 AATATTATATTTTTTAAAATATATTAA
*
470177 TAAT-TAATATTTTTTAAAATGATATTAA
1 -AATATTATATTTTTTAAAAT-ATATTAA
470205 AATATTATATTATTATTAAA
1 AATATTATATT-TT-TTAAA
470225 TACATCAAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
26 16 0.27
27 25 0.42
28 12 0.20
29 2 0.03
30 5 0.08
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
AATATTATATTTTTTAAAATATATTAA
Found at i:470442 original size:24 final size:24
Alignment explanation
Indices: 470391--470442 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
470381 ACCAAACACT
* * *
470391 AAAAATGAGGAAAACGTTTTTTTG
1 AAAAACGAGGAAAACGATTTTTCG
470415 AAAAACGAGGAAAAC-ATTTTTCG
1 AAAAACGAGGAAAACGATTTTTCG
470438 AAAAA
1 AAAAA
470443 TGTTTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (24 bp):
AAAAACGAGGAAAACGATTTTTCG
Found at i:473919 original size:21 final size:21
Alignment explanation
Indices: 473895--473952 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
473885 TAAATAAGTA
473895 AATAATATATAACATATAT-AG
1 AATAATATATAA-ATATATAAG
* *
473916 AATAATGTAATAAATATATAAT
1 AATAATAT-ATAAATATATAAG
473938 AATAATATATAAATA
1 AATAATATATAAATA
473953 ATACTATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (21 bp):
AATAATATATAAATATATAAG
Found at i:473930 original size:33 final size:34
Alignment explanation
Indices: 473883--474012 Score: 92
Period size: 33 Copynumber: 3.9 Consensus size: 34
473873 TTGGACATGA
473883 AATAA-ATAAGTA-AATAATATATAACATATATAG
1 AATAATATAA-TACAATAATATATAACATATATAG
* *
473916 AATAATGTAATA-AAT-ATATAATAATAATATATA-
1 AATAATATAATACAATAATAT-ATAA-CATATATAG
* * * *
473949 AATAATACTATATACTATAATAAAGAATATATATAG
1 AATAATA-TA-ATACAATAATATATAACATATATAG
** *
473985 -ATAATATAATATTATAATACATAACATA
1 AATAATATAATACAATAATATATAACATA
474013 CCATATTATA
Statistics
Matches: 78, Mismatches: 11, Indels: 16
0.74 0.10 0.15
Matches are distributed among these distances:
32 4 0.05
33 36 0.46
34 14 0.18
35 16 0.21
36 5 0.06
37 3 0.04
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (34 bp):
AATAATATAATACAATAATATATAACATATATAG
Found at i:473949 original size:7 final size:7
Alignment explanation
Indices: 473896--474038 Score: 55
Period size: 7 Copynumber: 19.9 Consensus size: 7
473886 AAATAAGTAA
473896 ATAATAT
1 ATAATAT
*
473903 ATAACAT
1 ATAATAT
*
473910 AT-ATAGA
1 ATAATA-T
*
473917 ATAATGT
1 ATAATAT
473924 AATAAATAT
1 -AT-AATAT
473933 ATAATA-
1 ATAATAT
473939 ATAATAT
1 ATAATAT
473946 ATAA-AT
1 ATAATAT
*
473952 AATACTAT
1 -ATAATAT
*
473960 ATACTAT
1 ATAATAT
*
473967 AATAA-AG
1 -ATAATAT
473974 A-ATATAT
1 ATA-ATAT
473981 ATAGATAAT
1 ATA-AT-AT
473990 ATAATATT
1 ATAATA-T
*
473998 ATAATAC
1 ATAATAT
*
474005 ATAACAT
1 ATAATAT
**
474012 ACCATAT
1 ATAATAT
474019 -TATATAT
1 ATA-ATAT
*
474026 ATACTAT
1 ATAATAT
474033 ATAATA
1 ATAATA
474039 CCCTATATAT
Statistics
Matches: 100, Mismatches: 21, Indels: 30
0.66 0.14 0.20
Matches are distributed among these distances:
5 1 0.01
6 12 0.12
7 53 0.53
8 25 0.25
9 9 0.09
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (7 bp):
ATAATAT
Found at i:473967 original size:21 final size:21
Alignment explanation
Indices: 473883--474407 Score: 192
Period size: 20 Copynumber: 25.2 Consensus size: 21
473873 TTGGACATGA
473883 AATAAATAAGTA-A-ATAATAT
1 AATAAATAA-TATATATAATAT
* *
473903 -ATAACAT-ATATAGAATAATGT
1 AATAA-ATAATATA-TATAATAT
473924 AATAAAT-ATATA-ATAATAAT
1 AATAAATAATATATATAAT-AT
*
473944 ATATAAATAATACTATATACTAT
1 A-ATAAATAATA-TATATAATAT
* *
473967 AATAAAGAATATATAT-AGAT
1 AATAAATAATATATATAATAT
473987 AAT--ATAATAT-TATAATA-
1 AATAAATAATATATATAATAT
*
474004 CATAACATACCATAT-TATATATAT
1 AATAA-ATA--ATATATATA-ATAT
* * **
474028 ACTATATAATACCCTAT-ATAT
1 AATAAATAATA-TATATAATAT
* * * * *
474049 ACTATATAATAGAATAGAATAG
1 AATAAATAATA-TATATAATAT
* * *
474071 AATAGAAT-AGA-ATAGAATAG
1 AATA-AATAATATATATAATAT
* * *
474091 AATAGAAT-AGA-ATAGAATAG
1 AATA-AATAATATATATAATAT
* * *
474111 AATAGAAT-AGA-ATAGAATAG
1 AATA-AATAATATATATAATAT
* * *
474131 AATAGAAT-AGA-ATAGAATAG
1 AATA-AATAATATATATAATAT
474151 AATATAAT-ATA-ATATAATAT
1 AATA-AATAATATATATAATAT
474171 AAT--ATAATATAATATAATAT
1 AATAAATAATAT-ATATAATAT
474191 AATATAATAA-ATATATAATAT
1 AATA-AATAATATATATAATAT
474212 AAT--ATAATATAATATAATAT
1 AATAAATAATAT-ATATAATAT
474232 AAT--ATAATATAATATAATAT
1 AATAAATAATAT-ATATAATAT
*
474252 -ATAAATAGA-ATAAATAA-AT
1 AATAAATA-ATATATATAATAT
474271 AGATATAATAATATAATATAATAT
1 A-ATA-AATAATAT-ATATAATAT
*
474295 AATAGAATAA-ATAAATAA-AT
1 AATA-AATAATATATATAATAT
* *
474315 AAATAAATAAATAGAATAATAAATAG
1 -AATAAAT-AATA-TAT-AT-AATAT
474341 AATAAATAATATAATATAATAT
1 AATAAATAATAT-ATATAATAT
474363 AAT--ATAATATAATATAATAT
1 AATAAATAATAT-ATATAATAT
474383 AAT--ATAATATAATATAATAT
1 AATAAATAATAT-ATATAATAT
474403 AATAA
1 AATAA
474408 TCCCGGACGA
Statistics
Matches: 422, Mismatches: 34, Indels: 96
0.76 0.06 0.17
Matches are distributed among these distances:
17 7 0.02
18 17 0.04
19 17 0.04
20 191 0.45
21 76 0.18
22 51 0.12
23 36 0.09
24 17 0.04
25 9 0.02
26 1 0.00
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.33
Consensus pattern (21 bp):
AATAAATAATATATATAATAT
Found at i:474064 original size:5 final size:5
Alignment explanation
Indices: 474052--474406 Score: 358
Period size: 5 Copynumber: 72.6 Consensus size: 5
474042 TATATATACT
* * * * * * * * *
474052 ATATA ATAGA ATAGA ATAGA ATAGA ATAGA ATAGA ATAGA ATAGA ATAGA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * * * * * * * *
474102 ATAGA ATAGA ATAGA ATAGA ATAGA ATAGA ATAGA ATAGA ATAGA ATAGA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
*
474152 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAAA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
474202 TATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT-
1 -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * *
474252 ATA-A ATAGA ATA-A ATA-A ATAGA TATAATA ATATA ATATA ATATA ATAGA
1 ATATA ATATA ATATA ATATA ATATA -AT-ATA ATATA ATATA ATATA ATATA
*
474301 ATA-A ATA-A ATA-A ATA-A ATA-A ATA-A ATAGA ATAATA A-ATA GA-ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA -ATATA
474345 A-ATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
474394 ATATA ATATA ATA
1 ATATA ATATA ATA
474407 ATCCCGGACG
Statistics
Matches: 333, Mismatches: 7, Indels: 20
0.93 0.02 0.06
Matches are distributed among these distances:
4 46 0.14
5 274 0.82
6 11 0.03
7 2 0.01
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (5 bp):
ATATA
Found at i:474064 original size:26 final size:25
Alignment explanation
Indices: 473997--474064 Score: 61
Period size: 26 Copynumber: 2.7 Consensus size: 25
473987 AATATAATAT
473997 TATA-ATACATA-ACATACCATATTA
1 TATATATACATAGA-ATACCATATTA
* *
474021 TATATATACTATATAATACCCTATATA
1 TATATATAC-ATAGAATACCATAT-TA
474048 TACTATATA-ATAGAATA
1 TA-TATATACATAGAATA
474065 GAATAGAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
24 4 0.11
25 4 0.11
26 18 0.49
27 5 0.14
28 6 0.16
ACGTcount: A:0.49, C:0.13, G:0.01, T:0.37
Consensus pattern (25 bp):
TATATATACATAGAATACCATATTA
Found at i:477242 original size:18 final size:19
Alignment explanation
Indices: 477200--477243 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
477190 ATATTTGATT
* *
477200 TTATTTATAATTTTTTACA
1 TTATTTATAATTTTTAAAA
477219 TCTATTTATAA-TTTTAAAA
1 T-TATTTATAATTTTTAAAA
477238 TTATTT
1 TTATTT
477244 TATATGACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTTATAATTTTTAAAA
Found at i:485565 original size:30 final size:30
Alignment explanation
Indices: 485529--485602 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
485519 TTATTAATAT
485529 GTGAATGTGTTCTATGTAAAAATGCTTTAC
1 GTGAATGTGTTCTATGTAAAAATGCTTTAC
* * * * *
485559 GTGAATGTGTTTTATGTGAAGATGTTTTAT
1 GTGAATGTGTTCTATGTAAAAATGCTTTAC
*
485589 ATGAATGTGTTCTA
1 GTGAATGTGTTCTA
485603 CGTGGATAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.45
Consensus pattern (30 bp):
GTGAATGTGTTCTATGTAAAAATGCTTTAC
Found at i:485577 original size:15 final size:15
Alignment explanation
Indices: 485526--485599 Score: 69
Period size: 15 Copynumber: 4.9 Consensus size: 15
485516 ATTTTATTAA
*
485526 TATGTGAATGTGTTC
1 TATGTGAATGTGTTT
* ** *
485541 TATGTAAAAATGCTT
1 TATGTGAATGTGTTT
*
485556 TACGTGAATGTGTTT
1 TATGTGAATGTGTTT
485571 TATGTGAA-GATGTTT
1 TATGTGAATG-TGTTT
*
485586 TATATGAATGTGTT
1 TATGTGAATGTGTT
485600 CTACGTGGAT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
14 1 0.02
15 43 0.96
16 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.23, T:0.46
Consensus pattern (15 bp):
TATGTGAATGTGTTT
Found at i:485810 original size:24 final size:25
Alignment explanation
Indices: 485715--485802 Score: 133
Period size: 25 Copynumber: 3.6 Consensus size: 25
485705 TCGAGGGTAA
485715 TACGCGGTCCTTCGGGACAAATTTC
1 TACGCGGTCCTTCGGGACAAATTTC
*
485740 TACGTGGTCCTTCGGGACAAATTTC
1 TACGCGGTCCTTCGGGACAAATTTC
* *
485765 TACGTGGTTCTTCGGGACAAA-TTC
1 TACGCGGTCCTTCGGGACAAATTTC
*
485789 TACGCGGTCTTTCG
1 TACGCGGTCCTTCG
485803 AGATAAATCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
24 14 0.24
25 44 0.76
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (25 bp):
TACGCGGTCCTTCGGGACAAATTTC
Found at i:491802 original size:33 final size:32
Alignment explanation
Indices: 491744--491902 Score: 107
Period size: 33 Copynumber: 4.9 Consensus size: 32
491734 CTTTTGGTAT
**
491744 TCGGGTCAGATTTTTTTTTTA-AAAATTCGGGA
1 TCGGGTCA-ATTTTTTTTAAATAAAATTCGGGA
*
491776 TCGGGTCTAATTTTTTTTAAATAAAATTCAGGTTCGG
1 TCGGGTC-AATTTTTTTTAAATAAAATTC-GG---GA
** **
491813 TCGGGTC-AGGTTTTTTAAAGT----TT-GATA
1 TCGGGTCAATTTTTTTTAAA-TAAAATTCGGGA
*
491840 TTCGGGTCAGATTTTTTTTAAAAAAAATTCGGGA
1 -TCGGGTCA-ATTTTTTTTAAATAAAATTCGGGA
491874 TCGGGTCTAATTTTTTTTAAATAAAATTC
1 TCGGGTC-AATTTTTTTTAAATAAAATTC
491903 AGGTTCGGTC
Statistics
Matches: 97, Mismatches: 14, Indels: 31
0.68 0.10 0.22
Matches are distributed among these distances:
28 7 0.07
30 11 0.11
32 19 0.20
33 36 0.37
34 5 0.05
35 10 0.10
36 1 0.01
37 8 0.08
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.43
Consensus pattern (32 bp):
TCGGGTCAATTTTTTTTAAATAAAATTCGGGA
Found at i:491909 original size:98 final size:98
Alignment explanation
Indices: 491736--491958 Score: 398
Period size: 98 Copynumber: 2.3 Consensus size: 98
491726 TCATCAATCT
* **
491736 TTTGGTATTCGGGTCAGATTTTTTTT-TTAAAAATTCGGGATCGGGTCTAATTTTTTTTAAATAA
1 TTTGATATTCGGGTCAGATTTTTTTTAAAAAAAATTCGGGATCGGGTCTAATTTTTTTTAAATAA
491800 AATTCAGGTTCGGTCGGGTCAGGTTTTTTAAAG
66 AATTCAGGTTCGGTCGGGTCAGGTTTTTTAAAG
491833 TTTGATATTCGGGTCAGATTTTTTTTAAAAAAAATTCGGGATCGGGTCTAATTTTTTTTAAATAA
1 TTTGATATTCGGGTCAGATTTTTTTTAAAAAAAATTCGGGATCGGGTCTAATTTTTTTTAAATAA
491898 AATTCAGGTTCGGTCGGGTCAGGTTTTTTAAAG
66 AATTCAGGTTCGGTCGGGTCAGGTTTTTTAAAG
491931 TTTGATATTCGGGTCAG--TTTTTTTAAAA
1 TTTGATATTCGGGTCAGATTTTTTTTAAAA
491959 GTTTTCGGGT
Statistics
Matches: 122, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
96 11 0.09
97 25 0.20
98 86 0.70
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.44
Consensus pattern (98 bp):
TTTGATATTCGGGTCAGATTTTTTTTAAAAAAAATTCGGGATCGGGTCTAATTTTTTTTAAATAA
AATTCAGGTTCGGTCGGGTCAGGTTTTTTAAAG
Found at i:492042 original size:28 final size:28
Alignment explanation
Indices: 492010--492111 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 28
492000 AGTGTTTGGG
492010 TCGGGTCGGGTTTTTTTAAGTTTGATAT
1 TCGGGTCGGGTTTTTTTAAGTTTGATAT
* *
492038 TCGGGTTGGGTCAGGTTTTTTTAAATGTT-ATAT
1 TC-----GGGTCGGGTTTTTTTAAGT-TTGATAT
** *
492071 TCGGGTCTTGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTTTGATAT
* *
492099 TTGGGTCGAGTTT
1 TCGGGTCGGGTTT
492112 GGGTTTAGGG
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
27 1 0.02
28 32 0.55
33 23 0.40
34 2 0.03
ACGTcount: A:0.15, C:0.07, G:0.28, T:0.50
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTTTGATAT
Found at i:492055 original size:33 final size:33
Alignment explanation
Indices: 492007--492077 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
491997 GTTAGTGTTT
* *
492007 GGGTCGGGTCGGGTTTTTTTAAGT-TTGATATTC
1 GGGTCGGGTCAGGTTTTTTTAAATGTT-ATATTC
*
492040 GGGTTGGGTCAGGTTTTTTTAAATGTTATATTC
1 GGGTCGGGTCAGGTTTTTTTAAATGTTATATTC
492073 GGGTC
1 GGGTC
492078 TTGTTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.14, C:0.08, G:0.32, T:0.45
Consensus pattern (33 bp):
GGGTCGGGTCAGGTTTTTTTAAATGTTATATTC
Found at i:493297 original size:14 final size:14
Alignment explanation
Indices: 493278--493312 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
493268 AGAGAAGTAT
493278 CGGTACTGTAGGAA
1 CGGTACTGTAGGAA
493292 CGGTACTGTAGGAA
1 CGGTACTGTAGGAA
*
493306 TGGTACT
1 CGGTACT
493313 ATACTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.26
Consensus pattern (14 bp):
CGGTACTGTAGGAA
Found at i:493698 original size:15 final size:15
Alignment explanation
Indices: 493678--493761 Score: 66
Period size: 15 Copynumber: 5.6 Consensus size: 15
493668 ATTTCATTAA
493678 TATGTGAATGTGTTC
1 TATGTGAATGTGTTC
**
493693 TATGTGAAAATGATT-
1 TATGTGAATGTG-TTC
**
493708 TACATGAATGTGTTC
1 TATGTGAATGTGTTC
493723 TATGTGAA-GATGCTT-
1 TATGTGAATG-TG-TTC
*
493738 TATATGAATGTGTTC
1 TATGTGAATGTGTTC
*
493753 TACGTGAAT
1 TATGTGAAT
493762 AAAGGATACC
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
14 5 0.10
15 42 0.81
16 5 0.10
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.42
Consensus pattern (15 bp):
TATGTGAATGTGTTC
Found at i:493716 original size:30 final size:30
Alignment explanation
Indices: 493682--493760 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
493672 CATTAATATG
493682 TGAATGTGTTCTATGTGAAAATGATTTACA
1 TGAATGTGTTCTATGTGAAAATGATTTACA
* * *
493712 TGAATGTGTTCTATGTGAAGATGCTTTATA
1 TGAATGTGTTCTATGTGAAAATGATTTACA
*
493742 TGAATGTGTTCTACGTGAA
1 TGAATGTGTTCTATGTGAA
493761 TAAAGGATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.41
Consensus pattern (30 bp):
TGAATGTGTTCTATGTGAAAATGATTTACA
Found at i:493904 original size:25 final size:25
Alignment explanation
Indices: 493864--493937 Score: 89
Period size: 24 Copynumber: 3.0 Consensus size: 25
493854 GAGGCGAAGG
* *
493864 TTCTACGCGGTACTTCGGGACTAAT
1 TTCTACGCGGTCCTTCGGGACTAAA
* *
493889 TTCTACGTGGTCCTTCAGGA-TAAA
1 TTCTACGCGGTCCTTCGGGACTAAA
*
493913 TTCTACGCAGTCCTTCGGGAC-AAA
1 TTCTACGCGGTCCTTCGGGACTAAA
493937 T
1 T
493938 CTATGTGGCA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
24 24 0.59
25 17 0.41
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (25 bp):
TTCTACGCGGTCCTTCGGGACTAAA
Found at i:493990 original size:24 final size:24
Alignment explanation
Indices: 493939--493990 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
493929 GGGACAAATC
* * ** *
493939 TATGTGGCACTTCGGTGCATGTTC
1 TATGTGGCACATCGGTGAAAATTA
493963 TATGTGGCACATCGGTGAAAATTA
1 TATGTGGCACATCGGTGAAAATTA
493987 TATG
1 TATG
493991 AGCTGTGGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (24 bp):
TATGTGGCACATCGGTGAAAATTA
Found at i:496170 original size:22 final size:22
Alignment explanation
Indices: 496145--496195 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
496135 ACTCTAATTT
496145 GTGGTTTATCGATAATCTTTTA
1 GTGGTTTATCGATAATCTTTTA
*
496167 GTGGTTTGTCGATAATCTTTTA
1 GTGGTTTATCGATAATCTTTTA
*
496189 GTAGTTT
1 GTGGTTT
496196 GATCCTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.51
Consensus pattern (22 bp):
GTGGTTTATCGATAATCTTTTA
Found at i:497004 original size:20 final size:21
Alignment explanation
Indices: 496973--497011 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
496963 ACAAGCTTTG
496973 ACAATAAGTTTCGAAACTTCT
1 ACAATAAGTTTCGAAACTTCT
496994 ACAAT-AGTTTCGAAACTT
1 ACAATAAGTTTCGAAACTT
497012 TCCCTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (21 bp):
ACAATAAGTTTCGAAACTTCT
Found at i:497022 original size:20 final size:20
Alignment explanation
Indices: 496978--497032 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
496968 CTTTGACAAT
496978 AAGTTTCGAAAC-TTCTACA
1 AAGTTTCGAAACTTTCTACA
*
496997 ATAGTTTCGAAACTTTC-CCTA
1 A-AGTTTCGAAACTTTCTAC-A
*
497018 AAGTTTCGATACTTT
1 AAGTTTCGAAACTTT
497033 GGCTCCAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 25 0.81
21 5 0.16
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (20 bp):
AAGTTTCGAAACTTTCTACA
Found at i:500038 original size:17 final size:17
Alignment explanation
Indices: 500016--500049 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
500006 AATGCTGAAA
* *
500016 TGGTATTGATACTAAAG
1 TGGTATAGATACCAAAG
500033 TGGTATAGATACCAAAG
1 TGGTATAGATACCAAAG
500050 AAGAGAAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (17 bp):
TGGTATAGATACCAAAG
Found at i:500482 original size:15 final size:15
Alignment explanation
Indices: 500464--500522 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
500454 ATGAATGTGT
500464 TCTATGTGAAAGTGC
1 TCTATGTGAAAGTGC
* *
500479 TCTATGTGAATGTGT
1 TCTATGTGAAAGTGC
* *
500494 TCTACGTGAAAATGC
1 TCTATGTGAAAGTGC
* *
500509 TTTATGCGAAAGTG
1 TCTATGTGAAAGTG
500523 TTATATGTGG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (15 bp):
TCTATGTGAAAGTGC
Found at i:500489 original size:30 final size:30
Alignment explanation
Indices: 500455--500531 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
500445 TATTAACATA
*
500455 TGAATGTGTTCTATGTGAAAGTGCTCTATG
1 TGAATGTGTTCTATGTGAAAATGCTCTATG
* *
500485 TGAATGTGTTCTACGTGAAAATGCTTTATG
1 TGAATGTGTTCTATGTGAAAATGCTCTATG
* * *
500515 CGAAAGTGTTATATGTG
1 TGAATGTGTTCTATGTG
500532 GATAAAAACA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (30 bp):
TGAATGTGTTCTATGTGAAAATGCTCTATG
Found at i:507295 original size:15 final size:15
Alignment explanation
Indices: 507277--507333 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
507267 GGATGTGTTC
507277 TATGTGAATGTGCTT
1 TATGTGAATGTGCTT
507292 TATGTGAATGTG-TT
1 TATGTGAATGTGCTT
* *
507306 ATACGTGAAAGTGCTT
1 -TATGTGAATGTGCTT
*
507322 TTTGTGAATGTG
1 TATGTGAATGTG
507334 TTCTACATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 2 0.06
15 31 0.89
16 2 0.06
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.44
Consensus pattern (15 bp):
TATGTGAATGTGCTT
Found at i:507303 original size:30 final size:30
Alignment explanation
Indices: 507269--507368 Score: 121
Period size: 30 Copynumber: 3.3 Consensus size: 30
507259 TAACATATGG
* *
507269 ATGTGTTCTATGTGAATGTGCTTTATGTGA
1 ATGTGTTCTACGTGAAAGTGCTTTATGTGA
* *
507299 ATGTGTTATACGTGAAAGTGCTTTTTGTGA
1 ATGTGTTCTACGTGAAAGTGCTTTATGTGA
* *
507329 ATGTGTTCTACATGAAAATGCTTTAT-TCGA
1 ATGTGTTCTACGTGAAAGTGCTTTATGT-GA
*
507359 AAGTGTTCTA
1 ATGTGTTCTA
507369 TGTGGATAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
29 1 0.02
30 59 0.98
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (30 bp):
ATGTGTTCTACGTGAAAGTGCTTTATGTGA
Found at i:507537 original size:24 final size:25
Alignment explanation
Indices: 507477--507540 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
507467 GAGTCGAGGG
* *
507477 TTCTACGCGGTCTTTCTGGACAAAT
1 TTCTACGCGGTCCTTCGGGACAAAT
* *
507502 TTCTATGTGGTCCTTCGGGACAAA-
1 TTCTACGCGGTCCTTCGGGACAAAT
507526 TTCTACGCGGTCCTT
1 TTCTACGCGGTCCTT
507541 TTGGGACATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (25 bp):
TTCTACGCGGTCCTTCGGGACAAAT
Found at i:507546 original size:25 final size:26
Alignment explanation
Indices: 507477--507548 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 26
507467 GAGTCGAGGG
507477 TTCTACGCGGT-CTTTCT-GGACAAAT
1 TTCTACGCGGTCCTTT-TGGGACAAAT
* * *
507502 TTCTATGTGGTCC-TTCGGGACAAA-
1 TTCTACGCGGTCCTTTTGGGACAAAT
507526 TTCTACGCGGTCCTTTTGGGACA
1 TTCTACGCGGTCCTTTTGGGACA
507549 TATCTAAGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 11 0.29
25 26 0.68
26 1 0.03
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (26 bp):
TTCTACGCGGTCCTTTTGGGACAAAT
Found at i:517758 original size:29 final size:30
Alignment explanation
Indices: 517679--517765 Score: 81
Period size: 29 Copynumber: 2.9 Consensus size: 30
517669 AACTATATAG
*
517679 CTTTT-AAAAATTAAAATTTTAGTCC-CTAAA
1 CTTTTCAAAACTT-AAATTTTAG-CCACTAAA
** * *
517709 CTTTTCAAAGTTTATACTTTAGCCACTAAA
1 CTTTTCAAAACTTAAATTTTAGCCACTAAA
*
517739 C-TTTCAAAACTTAAATTTTAGTCACTA
1 CTTTTCAAAACTTAAATTTTAGCCACTA
517766 GTCAAAATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 23 0.50
30 18 0.39
31 5 0.11
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (30 bp):
CTTTTCAAAACTTAAATTTTAGCCACTAAA
Found at i:518712 original size:23 final size:24
Alignment explanation
Indices: 518663--518727 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
518653 CATAAGGAAC
** *
518663 GTGCCACAAGAACAAAGAAAAAGT
1 GTGCCACAAGAGTAGAGAAAAAGT
518687 GTGCCACAAGAGTAGAGAAAAA-T
1 GTGCCACAAGAGTAGAGAAAAAGT
*
518710 GTGTCACAA-AGATAGAGA
1 GTGCCACAAGAG-TAGAGA
518728 TTCTTATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 2 0.06
23 15 0.42
24 19 0.53
ACGTcount: A:0.49, C:0.14, G:0.25, T:0.12
Consensus pattern (24 bp):
GTGCCACAAGAGTAGAGAAAAAGT
Found at i:520082 original size:13 final size:13
Alignment explanation
Indices: 520064--520091 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
520054 CTTATACTTC
520064 CCTTAGTCCTCTG
1 CCTTAGTCCTCTG
520077 CCTTAGTCCTCTG
1 CCTTAGTCCTCTG
520090 CC
1 CC
520092 AAAGGCCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.43, G:0.14, T:0.36
Consensus pattern (13 bp):
CCTTAGTCCTCTG
Found at i:520242 original size:32 final size:32
Alignment explanation
Indices: 520206--520327 Score: 95
Period size: 32 Copynumber: 3.8 Consensus size: 32
520196 TATAACCCTA
* *
520206 AACATATTATGCAATATCTACATGCAAACCTG
1 AACATACTATGCAATATCTAAATGCAAACCTG
* * * * *
520238 AACATACGATG-AATTATTTGAATG-TAACCTTA
1 AACATACTATGCAA-TATCTAAATGCAAACC-TG
* *
520270 AACATACTATGCATTATCTAAATTCAAACCTG
1 AACATACTATGCAATATCTAAATGCAAACCTG
* * * *
520302 AACATATTGTGTATTATCTAAATGCA
1 AACATACTATGCAATATCTAAATGCA
520328 CCCTGACTAG
Statistics
Matches: 68, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
31 6 0.09
32 57 0.84
33 5 0.07
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (32 bp):
AACATACTATGCAATATCTAAATGCAAACCTG
Found at i:520659 original size:21 final size:23
Alignment explanation
Indices: 520616--520712 Score: 57
Period size: 22 Copynumber: 4.3 Consensus size: 23
520606 CTGATAATAT
* *
520616 ATAATATATAGTTTTGTTTAAAA
1 ATAATATATAGATTTGTTGAAAA
520639 ATAATATAT-GATTT-TTG-AAA
1 ATAATATATAGATTTGTTGAAAA
520659 ATATATAGTATAG-TTT-TT-AAAA
1 ATA-ATA-TATAGATTTGTTGAAAA
*
520681 ACATATAGTATAG-TTT-TTGAAAA
1 ATA-ATA-TATAGATTTGTTGAAAA
*
520704 CATATTATA
1 -ATAATATA
520713 AGAACATGAT
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
20 6 0.10
21 5 0.08
22 34 0.54
23 16 0.25
24 2 0.03
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (23 bp):
ATAATATATAGATTTGTTGAAAA
Found at i:520681 original size:22 final size:22
Alignment explanation
Indices: 520650--520708 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
520640 TAATATATGA
* *
520650 TTTTTGAAAATATATAGTATAG
1 TTTTTAAAAACATATAGTATAG
520672 TTTTTAAAAACATATAGTATAG
1 TTTTTAAAAACATATAGTATAG
*
520694 TTTTTGAAAACATAT
1 TTTTTAAAAACATAT
520709 TATAAGAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.44
Consensus pattern (22 bp):
TTTTTAAAAACATATAGTATAG
Found at i:523320 original size:33 final size:34
Alignment explanation
Indices: 523250--523321 Score: 85
Period size: 33 Copynumber: 2.1 Consensus size: 34
523240 TTTTCAATAC
* *
523250 TTTCAAATTTCATTTTTGAGAGTTCTAAATCCTT
1 TTTCAAATTTCATTTTTGAGAGTTCAAAATCCAT
**
523284 TTTCAAGATTTCA-TTTTGA-TTTTCAAAATCCAT
1 TTTCAA-ATTTCATTTTTGAGAGTTCAAAATCCAT
523317 TTTCA
1 TTTCA
523322 TTTCTAGAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 15 0.45
34 12 0.36
35 6 0.18
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (34 bp):
TTTCAAATTTCATTTTTGAGAGTTCAAAATCCAT
Found at i:529626 original size:104 final size:103
Alignment explanation
Indices: 529275--529616 Score: 300
Period size: 104 Copynumber: 3.3 Consensus size: 103
529265 GTTATCTTTA
* ** ** * * *
529275 AAATTATC-CCGATTGACCCGACTTCCTCAATGAAAAGGAATAACATCATATGAAAGCAGCTAGA
1 AAATTATCTCCGATTTAATCGACTTCCTCAAAAAAAAGGAACAACATCATCTGAAAGTAGCTAGA
* **
529339 ACTCTTCAACATAT-AT-GAGCAATGTTCCCTTCAAAACC
66 ACTCTTCAACA-ATGATGGA-CAGTGTTGTCTTCAAAACC
* * ** * * * * * *
529377 AAATTATCTCCAGCTTGACCCGACTTCCTCAACAAAAAGAAAGAACGTCATCTGAAAGTGGCCAG
1 AAATTATCTCC-GATTTAATCGACTTCCTCAAAAAAAAGGAACAACATCATCTGAAAGTAGCTAG
* * * *
529442 AACTCTTCAAC-ATGGATGGGCAGTATCGTCTTCAAAATC
65 AACTCTTCAACAAT-GATGGACAGTGTTGTCTTCAAAACC
* * *
529481 AAATTATCTCC-ATCTTAACTCGA-TATTCTCAAAAATAAGGAACAACTTCATCTGAAAGTAGCT
1 AAATTATCTCCGAT-TTAA-TCGACT-TCCTCAAAAAAAAGGAACAACATCATCTGAAAGTAGCT
*
529544 AGAACTCTTCAACAATGATGGACAGTGTTGTCTTCAACACC
63 AGAACTCTTCAACAATGATGGACAGTGTTGTCTTCAAAACC
*
529585 ATATTATCTCCGGATTTAATCGACTTCCTCAA
1 AAATTATCTCC-GATTTAATCGACTTCCTCAA
529617 GGAGAAGGAA
Statistics
Matches: 192, Mismatches: 36, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
102 11 0.06
103 5 0.03
104 166 0.86
105 8 0.04
106 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (103 bp):
AAATTATCTCCGATTTAATCGACTTCCTCAAAAAAAAGGAACAACATCATCTGAAAGTAGCTAGA
ACTCTTCAACAATGATGGACAGTGTTGTCTTCAAAACC
Found at i:529830 original size:3 final size:3
Alignment explanation
Indices: 529822--529851 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
529812 TTAATTGTTC
529822 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
529852 ATAAACTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:530837 original size:20 final size:19
Alignment explanation
Indices: 530803--530842 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
530793 ATTCATTTAT
*
530803 TAGCTCATGTAATGTTATTC
1 TAGCTCATATAATGTT-TTC
*
530823 TAGCTCATATTATGTTTTC
1 TAGCTCATATAATGTTTTC
530842 T
1 T
530843 TTTATAGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (19 bp):
TAGCTCATATAATGTTTTC
Found at i:534907 original size:20 final size:19
Alignment explanation
Indices: 534873--534912 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
534863 ATTCATTTAT
*
534873 TAGCTCATGTCATGTTATTC
1 TAGCTCATATCATGTT-TTC
*
534893 TAGCTCATATTATGTTTTC
1 TAGCTCATATCATGTTTTC
534912 T
1 T
534913 TTTATAGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.50
Consensus pattern (19 bp):
TAGCTCATATCATGTTTTC
Found at i:538482 original size:14 final size:14
Alignment explanation
Indices: 538463--538491 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
538453 AATTAGAACC
538463 ATTATAATATTACA
1 ATTATAATATTACA
538477 ATTATAATATTACA
1 ATTATAATATTACA
538491 A
1 A
538492 ATAATGAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTATAATATTACA
Found at i:540160 original size:20 final size:20
Alignment explanation
Indices: 540131--540169 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
540121 ATTTCACCAC
*
540131 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
540151 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
540170 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:541232 original size:11 final size:11
Alignment explanation
Indices: 541216--541241 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
541206 GCTTGTGGTA
541216 GTGCAGCGGTC
1 GTGCAGCGGTC
541227 GTGCAGCGGTC
1 GTGCAGCGGTC
541238 GTGC
1 GTGC
541242 GACGTGTGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.27, G:0.46, T:0.19
Consensus pattern (11 bp):
GTGCAGCGGTC
Found at i:555954 original size:43 final size:42
Alignment explanation
Indices: 555899--556003 Score: 129
Period size: 43 Copynumber: 2.5 Consensus size: 42
555889 GTCTTGTTTA
* * *
555899 ATTCTCATTTCCATAATTTGATTGTTCATTGCAGTCTTCTTTC
1 ATTCTCACTTCCATAATTTGATTGTTCATTGCACTATT-TTTC
* ** * *
555942 GTTCTCACTTCCATAAACTAATTGTTCATTGCACTATTTTTT
1 ATTCTCACTTCCATAATTTGATTGTTCATTGCACTATTTTTC
555984 ATTCTCACTTCCATAATTTG
1 ATTCTCACTTCCATAATTTG
556004 TATCGATAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
42 19 0.38
43 31 0.62
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.49
Consensus pattern (42 bp):
ATTCTCACTTCCATAATTTGATTGTTCATTGCACTATTTTTC
Found at i:557261 original size:13 final size:14
Alignment explanation
Indices: 557243--557279 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
557233 AATATTATAT
557243 ATAATT-ATAAATG
1 ATAATTAATAAATG
557256 ATAATTAATAAAT-
1 ATAATTAATAAATG
*
557269 AAAATTAATAA
1 ATAATTAATAA
557280 TTAATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
ATAATTAATAAATG
Found at i:557515 original size:144 final size:146
Alignment explanation
Indices: 557260--557527 Score: 341
Period size: 143 Copynumber: 1.8 Consensus size: 146
557250 TAAATGATAA
* * *
557260 TTAATAAATAAAATTAATAATTAATTTTTCCATTAATAAAAATAAAAAATATACAAAAATACTGT
1 TTAATAAATAAAAATAAAAATTAATTTTTCCATTAATAAAAATAAAAAATATACAAAAATACGGT
557325 AAATTATAATTAAATAATAAATCAAGAACTATTTATGTCATTAAAAA-TTAAAA-ATATGTCAAT
66 AAATTATAATTAAATAATAAATCAAGAACTATTTATGTCATTAAAAACTTAAAATATATGTCAAT
557388 ATTTTTGAAATTATTG
131 ATTTTTGAAATTATTG
* * * *
557404 TTAATAAATAAAAATAAAAATT-ATTTCTTTCATTAATAAAAAT-AAAGATATATAAAACTACGG
1 TTAATAAATAAAAATAAAAATTAATTT-TTCCATTAATAAAAATAAAAAATATACAAAAATACGG
* * * * * *
557467 TAATTTATAGTTAATATAA-AAATTAGGAATTATTTCT-TCCATTAAAAAACTTAAAATATAT
65 TAAATTATAATTAA-ATAATAAATCAAGAACTATTTATGT-CATT-AAAAACTTAAAATATAT
557528 AAAAATGTTA
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
142 1 0.01
143 50 0.48
144 44 0.42
145 6 0.06
146 4 0.04
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.37
Consensus pattern (146 bp):
TTAATAAATAAAAATAAAAATTAATTTTTCCATTAATAAAAATAAAAAATATACAAAAATACGGT
AAATTATAATTAAATAATAAATCAAGAACTATTTATGTCATTAAAAACTTAAAATATATGTCAAT
ATTTTTGAAATTATTG
Found at i:557543 original size:144 final size:144
Alignment explanation
Indices: 557260--557545 Score: 323
Period size: 144 Copynumber: 2.0 Consensus size: 144
557250 TAAATGATAA
* * *
557260 TTAATAAATAAAATTAATAATTAATTTTTCCATTAATAAAAATAAAAAATATACAAAAATACTGT
1 TTAATAAATAAAAATAAAAATTAATTTTTCCATTAATAAAAATAAAAAATATACAAAAATACGGT
* * *
557325 AAATTATAATTAAATAATAAATCAAGAACTATTTATGTCATTAAAAATTAAAAATATGTCAATAT
66 AAATTATAATTAAATAATAAATCAAGAACTATTTATGTCATTAAAAATTAAAAATATATAAAAAT
*
557390 TTTTGAAATTATTG
131 TTATGAAATTATTG
* * * *
557404 TTAATAAATAAAAATAAAAATT-ATTTCTTTCATTAATAAAAAT-AAAGATATATAAAACTACGG
1 TTAATAAATAAAAATAAAAATTAATTT-TTCCATTAATAAAAATAAAAAATATACAAAAATACGG
* * * * * *
557467 TAATTTATAGTTAATATAA-AAATTAGGAATTATTTCT-TCCATTAAAAAACTT-AAAATATATA
65 TAAATTATAATTAA-ATAATAAATCAAGAACTATTTATGT-CATT-AAAAA-TTAAAAATATATA
557529 AAAATGTTAT-AAATTAT
126 AAAAT-TTATGAAATTAT
557546 ATTCAAATAT
Statistics
Matches: 119, Mismatches: 17, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
142 1 0.01
143 50 0.42
144 63 0.53
145 5 0.04
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (144 bp):
TTAATAAATAAAAATAAAAATTAATTTTTCCATTAATAAAAATAAAAAATATACAAAAATACGGT
AAATTATAATTAAATAATAAATCAAGAACTATTTATGTCATTAAAAATTAAAAATATATAAAAAT
TTATGAAATTATTG
Found at i:557546 original size:71 final size:71
Alignment explanation
Indices: 557206--557546 Score: 198
Period size: 72 Copynumber: 4.7 Consensus size: 71
557196 TAATATTACA
* * * * * * *
557206 AATTATTTCTTCTATTAACTACAATT-TAATAT-TATATATAATTATAAATGATAATTAATAAAT
1 AATTATTTCTTCCATTAA-TAAAATTAAAATATATAAAAAT-ATTATAAATTATAATTAATATA-
*
557269 AAAATTAAT
63 AAAATTAAG
* * * *
557278 AATTAATTT-TTCCATTAATAAAAATAAAAAATATACAAAAATACTGTAAATTATAATTAA-ATA
1 AATT-ATTTCTTCCATTAAT-AAAAT-TAAAATATATAAAAATATTATAAATTATAATTAATATA
*
557341 ATAAATCAAG
63 A-AAATTAAG
* * *** * **
557351 AACTATTTATGT-CATT-A-AAAATTAAAA-ATATGTCAATATTTTTGAAATTATTGTTAATAAA
1 AATTATTTCT-TCCATTAATAAAATTAAAATATATAAAAATA-TTAT-AAATTATAATTAAT--A
*
557412 TAAAAA-TAAA
61 TAAAAATTAAG
* * * *** * *
557422 AATTATTTCTTTCATTAATAAAAATAAAGATATATAAAACTACGGTAATTTATAGTTAATATAAA
1 AATTATTTCTTCCATTAATAAAATTAAA-ATATATAAAAATATTATAAATTATAATTAATATAAA
*
557487 AATTAGG
65 AATTAAG
*
557494 AATTATTTCTTCCATTAA-AAAACTTAAAATATATAAAAATGTTATAAATTATA
1 AATTATTTCTTCCATTAATAAAA-TTAAAATATATAAAAATATTATAAATTATA
557547 TTCAAATATG
Statistics
Matches: 202, Mismatches: 47, Indels: 41
0.70 0.16 0.14
Matches are distributed among these distances:
68 7 0.03
69 6 0.03
70 17 0.08
71 45 0.22
72 49 0.24
73 44 0.22
74 23 0.11
75 11 0.05
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (71 bp):
AATTATTTCTTCCATTAATAAAATTAAAATATATAAAAATATTATAAATTATAATTAATATAAAA
ATTAAG
Found at i:558095 original size:29 final size:30
Alignment explanation
Indices: 558039--558104 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
558029 CCCAAATTTG
*
558039 AAAGTTTAGTGGCCAAAATATAAATTTTGGA
1 AAAGTTTAGTGGCCAAAATAT-AATTTTGAA
* *
558070 AAAGTTTAG-GGACCAAAGTAT-ATTTTTAA
1 AAAGTTTAGTGG-CCAAAATATAATTTTGAA
558099 AAAGTT
1 AAAGTT
558105 AGGTATTCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 12 0.39
30 2 0.06
31 17 0.55
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (30 bp):
AAAGTTTAGTGGCCAAAATATAATTTTGAA
Found at i:560326 original size:29 final size:30
Alignment explanation
Indices: 560294--560354 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
560284 AATTTTGTAA
**
560294 TAGTGACCAAAATATATGTTTTG-AAAGTT
1 TAGTGACCAAAATATAAATTTTGAAAAGTT
** *
560323 TAGTGGTCAAAGTATAAATTTTGAAAAGTT
1 TAGTGACCAAAATATAAATTTTGAAAAGTT
560353 TA
1 TA
560355 AGGACTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.38
Consensus pattern (30 bp):
TAGTGACCAAAATATAAATTTTGAAAAGTT
Found at i:562324 original size:26 final size:26
Alignment explanation
Indices: 562290--562355 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
562280 ATACCTTAAT
*
562290 GCATCCTTTCATGCATTTCATTTATG
1 GCATTCTTTCATGCATTTCATTTATG
562316 GCATTCTTTCATGCATTTCATTTATG
1 GCATTCTTTCATGCATTTCATTTATG
562342 GCATTCTTTCATGC
1 GCATTCTTTCATGC
562356 CTTAATGCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.18, C:0.23, G:0.12, T:0.47
Consensus pattern (26 bp):
GCATTCTTTCATGCATTTCATTTATG
Found at i:562336 original size:72 final size:73
Alignment explanation
Indices: 562260--562483 Score: 215
Period size: 72 Copynumber: 2.9 Consensus size: 73
562250 ATTCATTAAA
* * *
562260 TTCATTTATGACA-TCATTTCATACCTTAATGCATCCTTTCATGCA-TTTCATTTATGGCATTCT
1 TTCATTTATGACATTC-TTTCATACCTTAATGCATCATTTCATGCATTTTCAGTTATGGCATCCT
562323 TTCATGCAT
65 TTCATGCAT
* * *
562332 TTCATTTATGGCATTCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGGCATCCTT
1 TTCATTTATGACATTCTTTCATACCTTAATGCATCATTTCATGCATTTTCAGTTATGGCATCCTT
562397 TCATGCGTCAAT
66 TCAT--G-C-AT
* *
562409 GTATCCTTTCATG-CATTTAAATTATGGCAT-CCTTAATGCATCATTTCATGCATTTT-AGTTAT
1 -T-TCATTT-ATGACA-TT--CTT-T--CATACCTTAATGCATCATTTCATGCATTTTCAGTTAT
562471 GGCATCCTTTCAT
57 GGCATCCTTTCAT
562484 ACCTTAATGC
Statistics
Matches: 129, Mismatches: 8, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
72 39 0.30
73 22 0.17
75 1 0.01
76 1 0.01
77 2 0.02
78 1 0.01
79 7 0.05
80 5 0.04
82 2 0.02
83 20 0.16
84 26 0.20
85 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (73 bp):
TTCATTTATGACATTCTTTCATACCTTAATGCATCATTTCATGCATTTTCAGTTATGGCATCCTT
TCATGCAT
Found at i:562372 original size:46 final size:46
Alignment explanation
Indices: 562322--562699 Score: 506
Period size: 46 Copynumber: 8.4 Consensus size: 46
562312 TATGGCATTC
* * *
562322 TTTCATGCATTTCATTTATGGCATTCTTTCATGCCTTAATGCATCA
1 TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCA
* * * * *
562368 TTTCATGCATTTTTAGTTATGGCATCCTTTCATGCGTCAATGTATCC
1 TTTCATGCA-TTTTAATTATGGCATCCTTTCATGCCTTAATGCATCA
*
562415 TTTCATGCATTTAAATTATGG--------CAT-CCTTAATGCATCA
1 TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCA
* * **
562452 TTTCATGCATTTTAGTTATGGCATCCTTTCATACCTTAATGCATTT
1 TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCA
** *
562498 TTTCATGCA-TTTAATTATGGCATCCTTTCATGCCTTAATGTTTCC
1 TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCA
*
562543 TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATACATCA
1 TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCA
*
562589 TTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCA
1 TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCA
562635 TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCA
1 TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCA
*
562681 TTTCATGCATTTTAGTTAT
1 TTTCATGCATTTTAATTAT
562700 TAATTTGTTT
Statistics
Matches: 290, Mismatches: 31, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
37 28 0.10
38 3 0.01
45 42 0.14
46 178 0.61
47 39 0.13
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (46 bp):
TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCA
Found at i:562471 original size:37 final size:37
Alignment explanation
Indices: 562406--562479 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
562396 TTCATGCGTC
* *
562406 AATGTATCCTTTCATGCATTTAAATTATGGCATCCTT
1 AATGCATCATTTCATGCATTTAAATTATGGCATCCTT
* *
562443 AATGCATCATTTCATGCATTTTAGTTATGGCATCCTT
1 AATGCATCATTTCATGCATTTAAATTATGGCATCCTT
562480 TCATACCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (37 bp):
AATGCATCATTTCATGCATTTAAATTATGGCATCCTT
Found at i:562592 original size:20 final size:20
Alignment explanation
Indices: 562564--562688 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
562554 TTAATTATGG
*
562564 CATCCTTTCATGCCTTAATA
1 CATCATTTCATGCCTTAATA
*
562584 CATCATTTCATGCATTTTAATTATGA
1 CATCATTTCATGC--CTT-A--AT-A
* *
562610 CATCCTTTCATGCCTTAATG
1 CATCATTTCATGCCTTAATA
*
562630 CATCATTTCATGCATTTTAATTA
1 CATCATTTCATGC--CTTAA-TA
* *
562653 TGGCATCCTTTCATGCCTTAATG
1 ---CATCATTTCATGCCTTAATA
562676 CATCATTTCATGC
1 CATCATTTCATGC
562689 ATTTTAGTTA
Statistics
Matches: 81, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
20 36 0.44
21 2 0.02
22 6 0.07
23 4 0.05
24 6 0.07
25 2 0.02
26 25 0.31
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.42
Consensus pattern (20 bp):
CATCATTTCATGCCTTAATA
Found at i:562674 original size:183 final size:176
Alignment explanation
Indices: 562316--562692 Score: 497
Period size: 183 Copynumber: 2.1 Consensus size: 176
562306 TTCATTTATG
* * *
562316 GCATTCTTTCATGCATTTCATTTATGGCATTCTTTCATGCCTTAATGCATCATTTCATGCATTTT
1 GCATTATTTCATGCATTTCAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
* * ** *
562381 TAGTTATGGCATCCTTTCATGCGTCAATGTATCCTTTCATGCATTTAAATTATGGCATCCTTAAT
66 TAATTATGGCATCCTTTCATGCCTCAATACATCATTTCATGCATTTAAATTATGGCATCCTTAAT
*
562446 GCATCATTTCATGCATTTTAGTTATGGCATCCTTTCATACCTTAAT
131 GCATCATTTCATGCATTTTAATTATGGCATCCTTTCATACCTTAAT
* ** *
562492 GCATTTTTTCATGCATTT-AATTATGGCATCCTTTCATGCCTTAATGTTTCCTTTCATGCA-TTT
1 GCATTATTTCATGCATTTCAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
* * *
562555 TAATTATGGCATCCTTTCATGCCTTAATACATCATTTCATGCATTTTAATTATGACATCCTTTCA
66 TAATTATGGCATCCTTTCATGCCTCAATACATCATTTCATGCATTTAAATTATG--------GCA
*
562620 TGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
123 T-CCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATACCTTAAT
*
562675 GCATCATTTCATGCATTT
1 GCATTATTTCATGCATTT
562693 TAGTTATTAA
Statistics
Matches: 174, Mismatches: 18, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
174 50 0.29
175 37 0.21
176 17 0.10
182 3 0.02
183 67 0.39
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (176 bp):
GCATTATTTCATGCATTTCAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
TAATTATGGCATCCTTTCATGCCTCAATACATCATTTCATGCATTTAAATTATGGCATCCTTAAT
GCATCATTTCATGCATTTTAATTATGGCATCCTTTCATACCTTAAT
Found at i:569406 original size:20 final size:20
Alignment explanation
Indices: 569381--569592 Score: 126
Period size: 20 Copynumber: 9.7 Consensus size: 20
569371 TCATTTATGA
569381 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
569401 CATCCTTTCATGCATTTCATTTATGG
1 CATCCTTTCATGC----C-TTAAT-G
*
569427 CATTCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* *
569447 CATCCTTTCTTGCATTTTAGTTATGG
1 CATCCTTTCATGC--CTTA---AT-G
569473 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
569493 CATCCTTT--TGCATTTTAATTACGG
1 CATCCTTTCATGC--CTTAA-T---G
*
569517 TATCCTTTCATGCCTTAAT-
1 CATCCTTTCATGCCTTAATG
*
569536 -ATCCTTTCATGCATTTTATTATG
1 CATCCTTTCATGC--CTTA--ATG
569559 ACATCCTTTCATGCCTTAATG
1 -CATCCTTTCATGCCTTAATG
569580 CATCCTTTCATGC
1 CATCCTTTCATGC
569593 ATTTTAGTTA
Statistics
Matches: 152, Mismatches: 13, Indels: 54
0.69 0.06 0.25
Matches are distributed among these distances:
18 15 0.10
20 54 0.36
21 10 0.07
22 6 0.04
23 4 0.03
24 16 0.11
25 18 0.12
26 29 0.19
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:569418 original size:46 final size:46
Alignment explanation
Indices: 569368--569603 Score: 338
Period size: 46 Copynumber: 5.2 Consensus size: 46
569358 TTATTCATTA
* *
569368 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
569414 ATTTCATTTATGGCATTCTTTCATGCCTTAATGCATCCTTTCTTGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
569460 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTT--TGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
569504 ATTTTAATTACGGTATCCTTTCATGCCTTAAT--ATCCTTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
569548 ATTTTA-TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
569593 ATTTTAGTTAT
1 ATTTTATTTAT
569604 AAATTCATTT
Statistics
Matches: 173, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
42 7 0.04
43 22 0.13
44 41 0.24
45 18 0.10
46 85 0.49
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (46 bp):
ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:570699 original size:31 final size:31
Alignment explanation
Indices: 570643--570719 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 31
570633 CGTCTATGTT
*
570643 CGTTCGTTTATGTTTTTTTACGTTTGATAATC
1 CGTTCG-TTATGTTTGTTTACGTTTGATAATC
* * *
570675 CGTTCGTTCTGTTTGTTTATGTTTGATAATT
1 CGTTCGTTATGTTTGTTTACGTTTGATAATC
570706 CGTTCGTTTATGTT
1 CGTTCG-TTATGTT
570720 CGTACGTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 27 0.69
32 12 0.31
ACGTcount: A:0.13, C:0.12, G:0.18, T:0.57
Consensus pattern (31 bp):
CGTTCGTTATGTTTGTTTACGTTTGATAATC
Found at i:572515 original size:13 final size:13
Alignment explanation
Indices: 572497--572522 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
572487 TACAGATCGC
572497 ATATGAAGACTGT
1 ATATGAAGACTGT
572510 ATATGAAGACTGT
1 ATATGAAGACTGT
572523 TCAACTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
ATATGAAGACTGT
Found at i:580683 original size:16 final size:17
Alignment explanation
Indices: 580640--580706 Score: 100
Period size: 17 Copynumber: 3.9 Consensus size: 17
580630 ACATTGTTTA
580640 TAACTTAAAAATACTTT
1 TAACTTAAAAATACTTT
580657 TAACTTAAAAATACTTT
1 TAACTTAAAAATACTTT
*
580674 TAACTT-AAAATAGTTT
1 TAACTTAAAAATACTTT
*
580690 TAACTCCAAAAATACTT
1 TAACT-TAAAAATACTT
580707 AAAAATACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
16 14 0.31
17 23 0.51
18 8 0.18
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.39
Consensus pattern (17 bp):
TAACTTAAAAATACTTT
Found at i:581648 original size:39 final size:39
Alignment explanation
Indices: 581548--581650 Score: 113
Period size: 39 Copynumber: 2.6 Consensus size: 39
581538 ATTATCAAAT
*
581548 TATTTCACTTTAACATTCTAAATTACTAATATCTTAAAA
1 TATTTCACATTAACATTCTAAATTACTAATATCTTAAAA
* * * *
581587 T-TTTCCACCA-TAATATTTTAAATT-CTTAATTTCTTAAAC
1 TATTT-CA-CATTAACATTCTAAATTAC-TAATATCTTAAAA
581626 TATTTCACATTAACATTCTAAATTA
1 TATTTCACATTAACATTCTAAATTA
581651 TTCTTTAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
38 6 0.12
39 41 0.80
40 4 0.08
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.46
Consensus pattern (39 bp):
TATTTCACATTAACATTCTAAATTACTAATATCTTAAAA
Found at i:585677 original size:46 final size:46
Alignment explanation
Indices: 585606--585699 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
585596 CTTTACACCC
* *
585606 CCGGAGTAATCAACTACGATTGACAGAGACTGATCTTTGTTTCGGT
1 CCGGAGTAATCAACTACGATCGACAGAGACTGATCTTTGTTTCAGT
* * *
585652 CCGGAGTAGTCGACTATGATCGACAGAGACTGATCTTTGTTTCAGT
1 CCGGAGTAATCAACTACGATCGACAGAGACTGATCTTTGTTTCAGT
585698 CC
1 CC
585700 AGCTGCTTCG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (46 bp):
CCGGAGTAATCAACTACGATCGACAGAGACTGATCTTTGTTTCAGT
Found at i:594550 original size:13 final size:14
Alignment explanation
Indices: 594523--594552 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
594513 TAGCATATTT
594523 AAAAATAAAACTAA
1 AAAAATAAAACTAA
594537 AAAAATAAAA-TAA
1 AAAAATAAAACTAA
594550 AAA
1 AAA
594553 TGAAAACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAATAAAACTAA
Found at i:594833 original size:27 final size:27
Alignment explanation
Indices: 594795--594868 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
594785 CTAGTATGCG
*
594795 CTGACTAAATCTTCTAGAAAACTGTTA
1 CTGACTAGATCTTCTAGAAAACTGTTA
594822 CTGACTAGATCTTCTAGAAAACTGTTA
1 CTGACTAGATCTTCTAGAAAACTGTTA
* * *
594849 CTGACTGGACCTTTTAGAAA
1 CTGACTAGATCTTCTAGAAA
594869 CTTCCACGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (27 bp):
CTGACTAGATCTTCTAGAAAACTGTTA
Found at i:600517 original size:40 final size:40
Alignment explanation
Indices: 600452--600535 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 40
600442 TTGGGAAATA
* *
600452 AATTGAAATTGAAGATGACAGCTTGTGATTTTGATGTGTT
1 AATTAAAATTGAAGATGACAACTTGTGATTTTGATGTGTT
*
600492 AATTAAAATTGAAGATGGCAACTTGTGATTTTGATGTGTT
1 AATTAAAATTGAAGATGACAACTTGTGATTTTGATGTGTT
600532 AATT
1 AATT
600536 GAGGAATGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (40 bp):
AATTAAAATTGAAGATGACAACTTGTGATTTTGATGTGTT
Found at i:601087 original size:11 final size:11
Alignment explanation
Indices: 601068--601105 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
601058 AACACATCTT
601068 CATTCAGAAAA
1 CATTCAGAAAA
*
601079 CATTTAGAAAA
1 CATTCAGAAAA
*
601090 CATTCAGAAAT
1 CATTCAGAAAA
601101 CATTC
1 CATTC
601106 TTCTTCTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.26
Consensus pattern (11 bp):
CATTCAGAAAA
Found at i:601172 original size:29 final size:30
Alignment explanation
Indices: 601135--601192 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
601125 TAATAAAAGC
601135 TTTTCTTTTC-TTTTTCAAAGTTATTCTTTG
1 TTTTCTTTTCTTTTTTCAAAGTT-TTCTTTG
*
601165 TTTT-TTTTCTTTTTTCTAAGTTTTCTTT
1 TTTTCTTTTCTTTTTTCAAAGTTTTCTTT
601193 TAAGCCGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.72
Consensus pattern (30 bp):
TTTTCTTTTCTTTTTTCAAAGTTTTCTTTG
Found at i:603672 original size:15 final size:15
Alignment explanation
Indices: 603649--603678 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
603639 ATTCAATTTA
*
603649 TTTATTATATATAAT
1 TTTACTATATATAAT
603664 TTTACTATATATAAT
1 TTTACTATATATAAT
603679 AAACATAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTACTATATATAAT
Found at i:604954 original size:16 final size:16
Alignment explanation
Indices: 604935--604965 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
604925 CCAATATCCT
604935 TAAATAATATTACACA
1 TAAATAATATTACACA
*
604951 TAAATGATATTACAC
1 TAAATAATATTACAC
604966 CCACAAGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (16 bp):
TAAATAATATTACACA
Found at i:611108 original size:16 final size:18
Alignment explanation
Indices: 611075--611116 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
611065 TTGTTTTCCA
611075 TTTTTTCTTTCATGTCTTT
1 TTTTTTCTTT-ATGTCTTT
611094 TTTTTTCTTT-T-TCTTT
1 TTTTTTCTTTATGTCTTT
*
611110 TTCTTTC
1 TTTTTTC
611117 GAACAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 11 0.50
17 1 0.05
19 10 0.45
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTTCTTTATGTCTTT
Found at i:614018 original size:14 final size:14
Alignment explanation
Indices: 613999--614034 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
613989 CGGTTTCTGC
*
613999 AAAATAAAAATAAA
1 AAAATAAAAAGAAA
614013 AAAATAAAAAGAAA
1 AAAATAAAAAGAAA
614027 AAAATAAA
1 AAAATAAA
614035 TTAAACACGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (14 bp):
AAAATAAAAAGAAA
Found at i:627480 original size:12 final size:12
Alignment explanation
Indices: 627459--627501 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
627449 GAAAGGAAAC
*
627459 AATAATAAGAAG
1 AATAAGAAGAAG
627471 AATAAGAAGAAG
1 AATAAGAAGAAG
627483 AATAAG-AGAATG
1 AATAAGAAGAA-G
627495 AA-AAGAA
1 AATAAGAA
627502 TAAGGAGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 7 0.25
12 21 0.75
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (12 bp):
AATAAGAAGAAG
Found at i:628066 original size:42 final size:41
Alignment explanation
Indices: 627991--628094 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 41
627981 TTTTCCTTTC
* * *
627991 AAAGAAAAATTAGATTTTGAAAAATAAAATGAAGATTT-GA
1 AAAGAAAATTTTGATTTTAAAAAATAAAATGAAGATTTGGA
*
628031 AAA-AAGATTTTGAGTTTTAAAAAATAAAAATTGAAGATTTGGA
1 AAAGAAAATTTTGA-TTTTAAAAAAT-AAAA-TGAAGATTTGGA
628074 AAAGAAAATTTTGA-TTTAAAA
1 AAAGAAAATTTTGATTTTAAAA
628095 GTTAAGCTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
39 7 0.13
40 13 0.24
41 4 0.07
42 16 0.30
43 5 0.09
44 9 0.17
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (41 bp):
AAAGAAAATTTTGATTTTAAAAAATAAAATGAAGATTTGGA
Found at i:629508 original size:21 final size:21
Alignment explanation
Indices: 629470--629509 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
629460 TAAATATTAT
*
629470 AAAGGAAGTATTGATACTCCA
1 AAAGGAAGTATAGATACTCCA
* *
629491 AAAGGTAGTATAGGTACTC
1 AAAGGAAGTATAGATACTC
629510 ATTGTTCTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (21 bp):
AAAGGAAGTATAGATACTCCA
Found at i:632271 original size:13 final size:13
Alignment explanation
Indices: 632253--632278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
632243 CCGCGAAGGT
632253 CAATGGAATTTGC
1 CAATGGAATTTGC
632266 CAATGGAATTTGC
1 CAATGGAATTTGC
632279 ACTAAGTCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
CAATGGAATTTGC
Done.