Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 24
Found at i:3769677 original size:20 final size:20
Alignment explanation
Indices: 3769652--3769704 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
3769642 TATTCTCTGG
3769652 TAATCTTACATTCCCACTGA
1 TAATCTTACATTCCCACTGA
*
3769672 TAATCTTACATTCTCACTGA
1 TAATCTTACATTCCCACTGA
3769692 TAATCTTACATTC
1 TAATCTTACATTC
3769705 AGTGAACCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (20 bp):
TAATCTTACATTCCCACTGA
Found at i:3771154 original size:22 final size:22
Alignment explanation
Indices: 3771129--3771175 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
3771119 ATCCTTTCCC
3771129 AAAAAGACATGTATAAATTTTA
1 AAAAAGACATGTATAAATTTTA
3771151 AAAAAGACATGTATAAATTTTA
1 AAAAAGACATGTATAAATTTTA
3771173 AAA
1 AAA
3771176 CATCTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (22 bp):
AAAAAGACATGTATAAATTTTA
Found at i:3773775 original size:44 final size:45
Alignment explanation
Indices: 3773664--3773851 Score: 229
Period size: 45 Copynumber: 4.2 Consensus size: 45
3773654 TTAGGCTGTC
* * * *
3773664 AAAAGTAAAATCAAAGTATTAGTTTCTTTTTATTATTGAGTTGTC-
1 AAAATTAAAATCAAAGGATTAGTTCCTTTTGATTATTGAGTTG-CG
* * *
3773709 AAAAGTAAAATCAAAGGATTAGTTCCTTGTGTTTATTGAGTTGC-
1 AAAATTAAAATCAAAGGATTAGTTCCTTTTGATTATTGAGTTGCG
* *
3773753 CAAATTAAAATCAAAGGATTAGTTCATTTTGATTATTG-GATTGCG
1 AAAATTAAAATCAAAGGATTAGTTCCTTTTGATTATTGAG-TTGCG
* * *
3773798 AAAATTAAAATCAAATGATTAGTTCCTTTTGATTATTGCGTTGCT
1 AAAATTAAAATCAAAGGATTAGTTCCTTTTGATTATTGAGTTGCG
3773843 AAAATTAAA
1 AAAATTAAA
3773852 GGATTAATTC
Statistics
Matches: 126, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 1 0.01
44 38 0.30
45 86 0.68
46 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (45 bp):
AAAATTAAAATCAAAGGATTAGTTCCTTTTGATTATTGAGTTGCG
Found at i:3773820 original size:89 final size:90
Alignment explanation
Indices: 3773664--3773851 Score: 240
Period size: 89 Copynumber: 2.1 Consensus size: 90
3773654 TTAGGCTGTC
* * *
3773664 AAAAGTAAAATCAAAGTATTAGTTTCTTTTTATTATTGAGTTGTCAAAAGTAAAATCAAAGGATT
1 AAAATTAAAATCAAAGGATTAGTTTCTTTTGATTATTGAGTTGTCAAAAGTAAAATCAAAGGATT
*
3773729 AGTTCCTTGTGTTTATTGAGTTGC-
66 AGTTCCTTGTGATTATTGAGTTGCT
* * *
3773753 CAAATTAAAATCAAAGGATTAG-TTCATTTTGATTATTG-GATTG-CGAAAATTAAAATCAAATG
1 AAAATTAAAATCAAAGGATTAGTTTC-TTTTGATTATTGAG-TTGTC-AAAAGTAAAATCAAAGG
* *
3773815 ATTAGTTCCTTTTGATTATTGCGTTGCT
63 ATTAGTTCCTTGTGATTATTGAGTTGCT
3773843 AAAATTAAA
1 AAAATTAAA
3773852 GGATTAATTC
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
88 5 0.06
89 72 0.85
90 8 0.09
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (90 bp):
AAAATTAAAATCAAAGGATTAGTTTCTTTTGATTATTGAGTTGTCAAAAGTAAAATCAAAGGATT
AGTTCCTTGTGATTATTGAGTTGCT
Found at i:3774167 original size:58 final size:57
Alignment explanation
Indices: 3774018--3774308 Score: 265
Period size: 58 Copynumber: 5.1 Consensus size: 57
3774008 TCTCAAGTTA
* * * *
3774018 ATTCTAACTTTGTAAGGAAAATAAATTATTGAATTTATTTCCTTGAGAATCTT---T-
1 ATTCTAACTTTATAA-GAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
* * * * *
3774072 ATTTTAACTTTATAAGGAAAATGAATTGTTAGATTTATTTCCTTGAGAATCTTGAATG
1 ATTCTAACTTTATAA-GAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
* * * * ** *
3774130 ATTCTAAATTTATAAGAAAATTAAATTGTTGAATTTATTTTCTTAAGAATCATGTATA
1 ATTCTAACTTTATAAGAAAA-TAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
* * *
3774188 ATTCTATCTTTTAAAAAAGAAATAAATTGTTAAATTTATTTTCTT--GAATCTTAAATG
1 ATTCTAAC-TTTATAAGA-AAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
* *
3774245 ATT-TTATTTTGA-AAGAGGAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
1 ATTCTAACTTT-ATAAGA--AAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
3774303 ATTCTA
1 ATTCTA
3774309 TTTTGTTAAA
Statistics
Matches: 195, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
54 47 0.24
55 6 0.03
56 29 0.15
57 17 0.09
58 63 0.32
59 30 0.15
60 3 0.02
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.45
Consensus pattern (57 bp):
ATTCTAACTTTATAAGAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
Found at i:3774179 original size:112 final size:112
Alignment explanation
Indices: 3774018--3774298 Score: 286
Period size: 115 Copynumber: 2.5 Consensus size: 112
3774008 TCTCAAGTTA
* * * * *
3774018 ATTCTAACTTTGTAAGGAAAATAAATTATTGAATTTATTTCCTTGAGAATCTT-T-ATTTTAAC-
1 ATTCTAAATTTATAA-GAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTATAATTCTAACT
* * * * *
3774080 TTT-ATAAGGAAAATGAATTGTTAGATTTATTTCCTTGAGAATCTTGAATG
65 TTTAAAAAAG-AAATAAATTGTTAAATTTATTTCCTT--GAATCTTAAATG
* *
3774130 ATTCTAAATTTATAAGAAAATTAAATTGTTGAATTTATTTTCTTAAGAATCATGTATAATTCTAT
1 ATTCTAAATTTATAAGAAAA-TAAATTGTTGAATTTATTTTCTTGAGAATC-T-TATAATTCTAA
*
3774195 CTTTTAAAAAAGAAATAAATTGTTAAATTTATTTTCTTGAATCTTAAATG
63 CTTTTAAAAAAGAAATAAATTGTTAAATTTATTTCCTTGAATCTTAAATG
* * *
3774245 ATT-TTATTTTGA-AAGAGGAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTA
1 ATTCTAAATTT-ATAAGA--AAATAAATTGTTGAATTTATTTTCTTGAGAATCTTA
3774299 AATGATTCTA
Statistics
Matches: 142, Mismatches: 17, Indels: 19
0.80 0.10 0.11
Matches are distributed among these distances:
111 5 0.04
112 40 0.28
113 3 0.02
114 11 0.08
115 44 0.31
116 9 0.06
117 26 0.18
118 4 0.03
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (112 bp):
ATTCTAAATTTATAAGAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTATAATTCTAACTT
TTAAAAAAGAAATAAATTGTTAAATTTATTTCCTTGAATCTTAAATG
Found at i:3774272 original size:115 final size:115
Alignment explanation
Indices: 3774090--3774345 Score: 279
Period size: 115 Copynumber: 2.2 Consensus size: 115
3774080 TTTATAAGGA
* * * *
3774090 AAATGAATTGTTAGATTTATTTCCTTGAGAATCTTGAATGATTCTAAATTTATAAGAAAATTAAA
1 AAATAAATTGTTAAATTTATTTTCTT-AGAATCTTAAATGATTCTAAATTTATAAGAAAATTAAA
* **
3774155 TTGTTGAATTTATTTTCTTAAGAATCATGTATAATTCTATCTTT-TAAAAAAG
65 TTGTTAAATTTATTTTCTTAAGAATCATAAATAATTCTAT-TTTGT-AAAAAG
* *
3774207 AAATAAATTGTTAAATTTATTTTCTT-GAATCTTAAATGATT-TTATTTTGA-AAGAGGAAA-TA
1 AAATAAATTGTTAAATTTATTTTCTTAGAATCTTAAATGATTCTAAATTT-ATAAGA--AAATTA
* * * *
3774268 AATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTGTTAAAAG
63 AATTGTTAAATTTATTTTCTTAAGAATCATAAATAATTCTATTTTGTAAAAAG
* * *
3774321 AGATAAGTTATTAAATTTATTTTCT
1 AAATAAATTGTTAAATTTATTTTCT
3774346 CGAAAATCTT
Statistics
Matches: 119, Mismatches: 16, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
114 39 0.33
115 54 0.45
116 3 0.03
117 23 0.19
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (115 bp):
AAATAAATTGTTAAATTTATTTTCTTAGAATCTTAAATGATTCTAAATTTATAAGAAAATTAAAT
TGTTAAATTTATTTTCTTAAGAATCATAAATAATTCTATTTTGTAAAAAG
Found at i:3774335 original size:58 final size:57
Alignment explanation
Indices: 3774090--3774355 Score: 252
Period size: 58 Copynumber: 4.6 Consensus size: 57
3774080 TTTATAAGGA
* * * * * *
3774090 AAATGAATTGTTAGATTTATTTCCTTGAGAATCTTGAATGATTCTAAATTTATAAGAA-
1 AAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCT-ATTTTTTAA-AAG
* * * * ** * *
3774148 AATTAAATTGTTGAATTTATTTTCTTAAGAATCATGTATAATTCTATCTTTTAAAAAAG
1 AAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTAT-TTTT-TAAAAG
* *
3774207 AAATAAATTGTTAAATTTATTTTCTT--GAATCTTAAATGATTTTA-TTTTGAAAGAGG
1 AAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTTTAAA-A-G
3774263 AAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTGTTAAAAG
1 AAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTT-TTAAAAG
* * * * *
3774321 AGATAAGTTATTAAATTTATTTTCTCGAAAATCTT
1 AAATAAATTGTTAAATTTATTTTCTTGAGAATCTT
3774356 CTATAAAGAA
Statistics
Matches: 172, Mismatches: 27, Indels: 18
0.79 0.12 0.08
Matches are distributed among these distances:
54 3 0.02
55 5 0.03
56 27 0.16
57 14 0.08
58 89 0.52
59 30 0.17
60 4 0.02
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (57 bp):
AAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTTTAAAAG
Found at i:3774644 original size:39 final size:38
Alignment explanation
Indices: 3774601--3774793 Score: 175
Period size: 39 Copynumber: 5.1 Consensus size: 38
3774591 AAAAAATACA
* * *
3774601 ATTTATTTTGCAATTTTATAAAATGAAATAAATCGTTTG
1 ATTTATTTT-CTATTTTATAAAAGGAAATAAATCGTTGG
* ** *
3774640 ATTTATTTTCTTATTTTGTACTAGGAAATAAATTGTTGG
1 ATTTATTTTC-TATTTTATAAAAGGAAATAAATCGTTGG
*
3774679 ATTTATTTTTCTATTTCT-TAAAAGGAAATAATTCGTTGG
1 ATTTA-TTTTCTATTT-TATAAAAGGAAATAAATCGTTGG
3774718 ATTTATTTTCCTA-TTT-T---AGGAAATAAATCGTTGG
1 ATTTATTTT-CTATTTTATAAAAGGAAATAAATCGTTGG
* * * *
3774752 ATTTATTTTCTTATTTTGTAAAA-AAAATAAATCATTGA
1 ATTTATTTTC-TATTTTATAAAAGGAAATAAATCGTTGG
3774790 ATTT
1 ATTT
3774794 TTTAATCTTA
Statistics
Matches: 129, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
33 1 0.01
34 27 0.21
35 3 0.02
36 1 0.01
37 2 0.02
38 23 0.18
39 66 0.51
40 6 0.05
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (38 bp):
ATTTATTTTCTATTTTATAAAAGGAAATAAATCGTTGG
Found at i:3774774 original size:73 final size:75
Alignment explanation
Indices: 3774601--3774793 Score: 207
Period size: 78 Copynumber: 2.6 Consensus size: 75
3774591 AAAAAATACA
* * * * *
3774601 ATTTATTTTGCAATTTTATAAAATGAAATAAATCGTTTGATTTATTTTCTTATTTTGTACTAGGA
1 ATTTATTTTTCTATTTT-TAAAAGGAAATAAATCGTTGGATTTATTTTCCTA-TTTGTA-TAGGA
*
3774666 AATAAATTGTTGG
63 AATAAATCGTTGG
*
3774679 ATTTATTTTTCTATTTCTTAAAAGGAAATAATTCGTTGGATTTATTTTCCTA-TT-T-TAGGAAA
1 ATTTATTTTTCTATTT-TTAAAAGGAAATAAATCGTTGGATTTATTTTCCTATTTGTATAGGAAA
3774741 TAAATCGTTGG
65 TAAATCGTTGG
* * *
3774752 ATTTA-TTTTCTTATTTTGTAAAA-AAAATAAATCATTGAATTT
1 ATTTATTTTTC-TATTTT-TAAAAGGAAATAAATCGTTGGATTT
3774794 TTTAATCTTA
Statistics
Matches: 101, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
72 21 0.21
73 32 0.32
75 1 0.01
76 2 0.02
78 44 0.44
79 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (75 bp):
ATTTATTTTTCTATTTTTAAAAGGAAATAAATCGTTGGATTTATTTTCCTATTTGTATAGGAAAT
AAATCGTTGG
Found at i:3781054 original size:23 final size:24
Alignment explanation
Indices: 3781004--3781061 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
3780994 ATTTAAATAA
* *
3781004 ATAAACGAACACGAACGAATGAAC
1 ATAAACGAACACGAACAAACGAAC
*
3781028 ATAAACGAACAC-AATAAACGAAC
1 ATAAACGAACACGAACAAACGAAC
3781051 ATAAACGAACA
1 ATAAACGAACA
3781062 ACACAAACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 19 0.61
24 12 0.39
ACGTcount: A:0.59, C:0.21, G:0.12, T:0.09
Consensus pattern (24 bp):
ATAAACGAACACGAACAAACGAAC
Found at i:3781069 original size:23 final size:23
Alignment explanation
Indices: 3781004--3781074 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
3780994 ATTTAAATAA
* *
3781004 ATAAACGAACACGAACGAATGAAC
1 ATAAACGAACAC-AACAAACGAAC
*
3781028 ATAAACGAACACAATAAACGAAC
1 ATAAACGAACACAACAAACGAAC
*
3781051 ATAAACGAACA-ACACAAACAAAC
1 ATAAACGAACACA-ACAAACGAAC
3781074 A
1 A
3781075 AAAAACTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 1 0.02
23 28 0.68
24 12 0.29
ACGTcount: A:0.61, C:0.23, G:0.10, T:0.07
Consensus pattern (23 bp):
ATAAACGAACACAACAAACGAAC
Found at i:3781338 original size:24 final size:24
Alignment explanation
Indices: 3781311--3781356 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3781301 GTCCTCTGTT
*
3781311 CGAACAAAAATGAACGAACATAAA
1 CGAACAAAAATAAACGAACATAAA
*
3781335 CGAACATAAATAAACGAACATA
1 CGAACAAAAATAAACGAACATA
3781357 TAATCAAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.61, C:0.17, G:0.11, T:0.11
Consensus pattern (24 bp):
CGAACAAAAATAAACGAACATAAA
Found at i:3781354 original size:14 final size:15
Alignment explanation
Indices: 3781330--3781366 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
3781320 ATGAACGAAC
3781330 ATAAACGAACATA-A
1 ATAAACGAACATATA
3781344 ATAAACGAACATATA
1 ATAAACGAACATATA
3781359 ATCAAACG
1 AT-AAACG
3781367 TTCACGAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 13 0.62
15 3 0.14
16 5 0.24
ACGTcount: A:0.59, C:0.16, G:0.08, T:0.16
Consensus pattern (15 bp):
ATAAACGAACATATA
Found at i:3792414 original size:24 final size:25
Alignment explanation
Indices: 3792374--3792421 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
3792364 AACTAAGTGT
3792374 CGCGTAGAGATTTGTCCCGAAGGAC
1 CGCGTAGAGATTTGTCCCGAAGGAC
3792399 CGCGTAGA-ATTTGTCCCGAAGGA
1 CGCGTAGAGATTTGTCCCGAAGGA
3792422 TCACATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (25 bp):
CGCGTAGAGATTTGTCCCGAAGGAC
Found at i:3793630 original size:2 final size:2
Alignment explanation
Indices: 3793614--3793655 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
3793604 TTTCAAAACC
3793614 TA TA TGA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3793656 ATTCTGGACA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3802236 original size:24 final size:25
Alignment explanation
Indices: 3802191--3802238 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3802181 ACCTAAGTGC
* *
3802191 CGCGTAGAGATTTGTCCTGAAGGAT
1 CGCGTAGAGATTTATCCCGAAGGAT
*
3802216 CGCGTATA-ATTTATCCCGAAGGA
1 CGCGTAGAGATTTATCCCGAAGGA
3802239 CCACATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (25 bp):
CGCGTAGAGATTTATCCCGAAGGAT
Found at i:3802479 original size:29 final size:28
Alignment explanation
Indices: 3802437--3802504 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 28
3802427 ACATAATTTA
*
3802437 TATCGCATAGACATAACA-TTCCATACCTT
1 TATC-CATAAACATAACATTTCCATA-CTT
**
3802466 TATCACATAAACATTTCATTTTCCATACTT
1 TATC-CATAAACATAACA-TTTCCATACTT
3802496 TATCCATAA
1 TATCCATAA
3802505 TTCATATAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 19 0.58
30 7 0.21
31 7 0.21
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (28 bp):
TATCCATAAACATAACATTTCCATACTT
Found at i:3803867 original size:2 final size:2
Alignment explanation
Indices: 3803860--3803922 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
3803850 TCAAGTCAGT
3803860 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3803902 TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
3803923 CGATTTAATT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3809997 original size:2 final size:2
Alignment explanation
Indices: 3809990--3810014 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3809980 AACATGCAAG
3809990 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3810015 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3819602 original size:3 final size:3
Alignment explanation
Indices: 3819596--3819628 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3819586 ATTTATAAAA
3819596 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3819629 TCATGTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3821563 original size:64 final size:64
Alignment explanation
Indices: 3821484--3821617 Score: 259
Period size: 64 Copynumber: 2.1 Consensus size: 64
3821474 CGGGTTTTTT
*
3821484 ATCCGCACCTCTAGTTGAGTTAACTTTTTTTTTCACTTATTTTTAAGGGTAAAGTACTCAAATG
1 ATCCCCACCTCTAGTTGAGTTAACTTTTTTTTTCACTTATTTTTAAGGGTAAAGTACTCAAATG
3821548 ATCCCCACCTCTAGTTGAGTTAACTTTTTTTTTCACTTATTTTTAAGGGTAAAGTACTCAAATG
1 ATCCCCACCTCTAGTTGAGTTAACTTTTTTTTTCACTTATTTTTAAGGGTAAAGTACTCAAATG
3821612 ATCCCC
1 ATCCCC
3821618 CGATGATGTG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 69 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (64 bp):
ATCCCCACCTCTAGTTGAGTTAACTTTTTTTTTCACTTATTTTTAAGGGTAAAGTACTCAAATG
Found at i:3822408 original size:23 final size:23
Alignment explanation
Indices: 3822378--3822446 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 23
3822368 TAACTAACAT
3822378 TTCTTCTTCTTCAACCCAACCTCTTC
1 TTCTTCTTCTTCAACCCAACC-C--C
*
3822404 TTCTTATTCTTCAACCCAACCCC
1 TTCTTCTTCTTCAACCCAACCCC
*
3822427 TTCTTCTTCTTTAACCCAAC
1 TTCTTCTTCTTCAACCCAAC
3822447 TAAACTTGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
23 19 0.47
25 1 0.03
26 20 0.50
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (23 bp):
TTCTTCTTCTTCAACCCAACCCC
Found at i:3822413 original size:26 final size:26
Alignment explanation
Indices: 3822378--3822434 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
3822368 TAACTAACAT
* *
3822378 TTCTTCTTCTTCAACCCAACCTCTTC
1 TTCTTATTCTTCAACCCAACCCCTTC
3822404 TTCTTATTCTTCAACCCAACCCCTTC
1 TTCTTATTCTTCAACCCAACCCCTTC
3822430 TTCTT
1 TTCTT
3822435 CTTTAACCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.16, C:0.40, G:0.00, T:0.44
Consensus pattern (26 bp):
TTCTTATTCTTCAACCCAACCCCTTC
Found at i:3824136 original size:173 final size:173
Alignment explanation
Indices: 3823838--3824188 Score: 517
Period size: 173 Copynumber: 2.0 Consensus size: 173
3823828 TTAACTCACC
* *
3823838 AATTCACTCAAGCACGTCTCAACTCTCTCAAAGCTTTCTAATCTTCTGATTCTTTTCGACGAGGA
1 AATTCACTCAAACACGTCTCAACTCTCTCAAAGCTTTCTAAGCTTCTGATTCTTTTCGACGAGGA
* * ** *
3823903 GCAATACCACTAGCAGTCCACTCCGGTTCTAGGTGTACGGAATTTGGAGTGACTGTGTTAACCTC
66 GCAATACCACCAGCAGTCCACTCCGGTTCCAGGTGTACAAAATTTGAAGTGACTGTGTTAACCTC
* * *
3823968 AGGGGACAATCCACCTATTGGGGCGATTACACACATCGGGGTA
131 AGGGGACAATCCACCTATTGGAGAGATTACACACATCCGGGTA
*
3824011 AATTCACTCAAACATC-TCTTAACTCTCTCAAAGCTTTCTAAGCTTCTGATTCTTTTCGACGAGG
1 AATTCACTCAAACA-CGTCTCAACTCTCTCAAAGCTTTCTAAGCTTCTGATTCTTTTCGACGAGG
* *
3824075 AGCAATACCACCAGCAGTCCACTCTGGTTCCGGGTGTACAAAATTTGAAGTGA-TCGTGTTAACC
65 AGCAATACCACCAGCAGTCCACTCCGGTTCCAGGTGTACAAAATTTGAAGTGACT-GTGTTAACC
* * * *
3824139 TCGGGGGATAATCCACCTATTGGAGAGATTATACACATCCGGGTG
129 TCAGGGGACAATCCACCTATTGGAGAGATTACACACATCCGGGTA
3824184 AATTC
1 AATTC
3824189 GTTTATAAGG
Statistics
Matches: 159, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
172 1 0.01
173 157 0.99
174 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (173 bp):
AATTCACTCAAACACGTCTCAACTCTCTCAAAGCTTTCTAAGCTTCTGATTCTTTTCGACGAGGA
GCAATACCACCAGCAGTCCACTCCGGTTCCAGGTGTACAAAATTTGAAGTGACTGTGTTAACCTC
AGGGGACAATCCACCTATTGGAGAGATTACACACATCCGGGTA
Found at i:3828321 original size:21 final size:21
Alignment explanation
Indices: 3828279--3828321 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3828269 TTTCTGGGCT
*
3828279 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
3828300 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
3828321 A
1 A
3828322 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:3829092 original size:103 final size:103
Alignment explanation
Indices: 3828867--3829084 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
3828857 GTAGAGGGTC
*
3828867 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
3828932 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
3828970 TATATGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
3829035 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
3829073 TATGTGGTCCTT
1 TATGTGGTCCTT
3829085 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:3829134 original size:23 final size:23
Alignment explanation
Indices: 3829101--3829163 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
3829091 ATTATTATAT
3829101 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
3829124 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
3829147 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
3829164 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:3835245 original size:21 final size:21
Alignment explanation
Indices: 3835203--3835245 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3835193 TTTCTGGGCT
* *
3835203 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
3835224 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
3835245 A
1 A
3835246 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:3835298 original size:20 final size:20
Alignment explanation
Indices: 3835273--3835310 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3835263 GAATGCTAGA
*
3835273 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
3835293 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
3835311 TAATGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:3836007 original size:103 final size:103
Alignment explanation
Indices: 3835782--3835999 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
3835772 GTAGAGGGTC
* *
3835782 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
3835847 TTGATCCTTGGTATATGTATTTGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
3835885 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
3835950 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
3835988 TATGTGGTCCTT
1 TATGTGGTCCTT
3836000 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:3836049 original size:23 final size:23
Alignment explanation
Indices: 3836016--3836078 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
3836006 ATTATTATAT
3836016 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
3836039 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
3836062 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
3836079 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:3838042 original size:2 final size:2
Alignment explanation
Indices: 3838037--3838079 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3838027 TAATTTTGTG
3838037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3838079 T
1 T
3838080 CTTACACATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3838816 original size:21 final size:21
Alignment explanation
Indices: 3838790--3838847 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
3838780 AGGATTGTTT
* *
3838790 ATTACACCAGTTACAAGTGTA
1 ATTACACAAGTTACAAGAGTA
3838811 ATTACACAAGTTACAAGAGTA
1 ATTACACAAGTTACAAGAGTA
3838832 ATTACA-AACGTTACAA
1 ATTACACAA-GTTACAA
3838848 ACAGCTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.06
21 32 0.94
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (21 bp):
ATTACACAAGTTACAAGAGTA
Found at i:3842916 original size:17 final size:18
Alignment explanation
Indices: 3842894--3842936 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
3842884 CCTATGTATT
3842894 TTGAGAATATAGA-GAAA
1 TTGAGAATATAGAGGAAA
*
3842911 TTGAGAATTTAGAGGGAAA
1 TTGAGAATATAGA-GGAAA
3842930 TTGAGAA
1 TTGAGAA
3842937 ATTTAGAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.52
19 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.26
Consensus pattern (18 bp):
TTGAGAATATAGAGGAAA
Found at i:3842931 original size:19 final size:19
Alignment explanation
Indices: 3842894--3842977 Score: 93
Period size: 19 Copynumber: 4.5 Consensus size: 19
3842884 CCTATGTATT
*
3842894 TTGAGAATATAGA--GAAA
1 TTGAGAATTTAGAGGGAAA
3842911 TTGAGAATTTAGAGGGAAA
1 TTGAGAATTTAGAGGGAAA
3842930 TTGAGAAATTTAGAGGG-AA
1 TTGAG-AATTTAGAGGGAAA
* * *
3842949 TAGAAAAATTTGGAGGGAAA
1 TTG-AGAATTTAGAGGGAAA
3842969 TTGAGAATT
1 TTGAGAATT
3842978 GAGATTTTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
17 12 0.21
19 28 0.50
20 16 0.29
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (19 bp):
TTGAGAATTTAGAGGGAAA
Found at i:3842941 original size:20 final size:20
Alignment explanation
Indices: 3842907--3842975 Score: 97
Period size: 19 Copynumber: 3.5 Consensus size: 20
3842897 AGAATATAGA
3842907 GAAATTGAG-AATTTAGAGG
1 GAAATTGAGAAATTTAGAGG
3842926 GAAATTGAGAAATTTAGAGG
1 GAAATTGAGAAATTTAGAGG
* * *
3842946 G-AATAGAAAAATTTGGAGG
1 GAAATTGAGAAATTTAGAGG
3842965 GAAATTGAGAA
1 GAAATTGAGAA
3842976 TTGAGATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 25 0.58
20 18 0.42
ACGTcount: A:0.46, C:0.00, G:0.30, T:0.23
Consensus pattern (20 bp):
GAAATTGAGAAATTTAGAGG
Found at i:3843442 original size:2 final size:2
Alignment explanation
Indices: 3843431--3843475 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
3843421 ATAAACCATG
*
3843431 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3843472 TA TA
1 TA TA
3843476 AAGTAAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3844082 original size:16 final size:16
Alignment explanation
Indices: 3844061--3844091 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3844051 TCATTTACAG
3844061 GTCAGGTTGAAAACAT
1 GTCAGGTTGAAAACAT
3844077 GTCAGGTTGAAAACA
1 GTCAGGTTGAAAACA
3844092 GGTCGGGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (16 bp):
GTCAGGTTGAAAACAT
Found at i:3847746 original size:33 final size:33
Alignment explanation
Indices: 3847698--3847773 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 33
3847688 GTTTGAATGG
*
3847698 TAAAAGAAATTTTATCT-TTTGAATATTCAA-AT
1 TAAAAGATATTTTATCTGTTTG-ATATTCAATAT
* *
3847730 TAAAAGATATTCTTATCTGTTTGATGTTGAATAT
1 TAAAAGATATT-TTATCTGTTTGATATTCAATAT
3847764 TAAAAGATAT
1 TAAAAGATAT
3847774 CTAGTTAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 10 0.26
33 12 0.32
34 16 0.42
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (33 bp):
TAAAAGATATTTTATCTGTTTGATATTCAATAT
Found at i:3850872 original size:20 final size:20
Alignment explanation
Indices: 3850847--3850896 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3850837 ATTCAAGAAC
3850847 TTTTCTTTTCTT-GAAAAATA
1 TTTTCTTTTCTTAG-AAAATA
*
3850867 TTTTCTTTCCTTAGAAAATA
1 TTTTCTTTTCTTAGAAAATA
3850887 --TTCTTTTCTT
1 TTTTCTTTTCTT
3850897 CCACTAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.33
20 17 0.63
21 1 0.04
ACGTcount: A:0.24, C:0.14, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTCTTTTCTTAGAAAATA
Found at i:3853478 original size:15 final size:15
Alignment explanation
Indices: 3853435--3853478 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3853425 ATTATAATTA
3853435 TTTAATAATTTATTAT
1 TTTAATAATTT-TTAT
* *
3853451 TTTATTAAATTTTAT
1 TTTAATAATTTTTAT
*
3853466 TTTACTAATTTTT
1 TTTAATAATTTTT
3853479 TAATTACTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTAATAATTTTTAT
Found at i:3857729 original size:76 final size:77
Alignment explanation
Indices: 3857601--3857793 Score: 286
Period size: 76 Copynumber: 2.5 Consensus size: 77
3857591 CCGTTGTACA
* * *
3857601 AGGGGGGAATCGGTACCCCCT-TGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
**
3857664 -CAAAACTGTTT
66 CCAAAACCATTT
* *
3857675 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
3857740 CCAAAACCATTT
66 CCAAAACCATTT
3857752 A-GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTC
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTC
3857794 TAAGCAATCT
Statistics
Matches: 108, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
74 19 0.18
75 7 0.06
76 53 0.49
77 29 0.27
ACGTcount: A:0.19, C:0.24, G:0.33, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
CCAAAACCATTT
Found at i:3866040 original size:77 final size:77
Alignment explanation
Indices: 3865849--3866048 Score: 282
Period size: 76 Copynumber: 2.6 Consensus size: 77
3865839 CCGTTGTATA
* * * *
3865849 AGGGGGGAATCGGTACCCCCT-TGGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCATACTGGAAATCTCGGA
**
3865912 GCAAAACTGTTT
66 GCAAAACCATTT
* * *
3865924 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCTGAGTATTCTGGAAATCTCGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCATACTGGAAATCTCGGA
3865988 GCCAAAACCATTT
66 G-CAAAACCATTT
3866001 A-GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
3866049 ATCTGTAATT
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
75 25 0.23
76 52 0.47
77 34 0.31
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.24
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCATACTGGAAATCTCGGA
GCAAAACCATTT
Found at i:3869307 original size:39 final size:39
Alignment explanation
Indices: 3869253--3869337 Score: 170
Period size: 39 Copynumber: 2.2 Consensus size: 39
3869243 AAATAATATT
3869253 TGGGAGCGCCTCAATCGTGGGGTTACACATCCAAGCTGG
1 TGGGAGCGCCTCAATCGTGGGGTTACACATCCAAGCTGG
3869292 TGGGAGCGCCTCAATCGTGGGGTTACACATCCAAGCTGG
1 TGGGAGCGCCTCAATCGTGGGGTTACACATCCAAGCTGG
3869331 TGGGAGC
1 TGGGAGC
3869338 TTTTTCCTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.20, C:0.25, G:0.35, T:0.20
Consensus pattern (39 bp):
TGGGAGCGCCTCAATCGTGGGGTTACACATCCAAGCTGG
Found at i:3876257 original size:151 final size:151
Alignment explanation
Indices: 3875983--3876285 Score: 597
Period size: 151 Copynumber: 2.0 Consensus size: 151
3875973 ATTTCGAAAA
3875983 CAAAGAAACACTTGTTTGTAGTTTGATAGTCATTGAATATGATTTTATCTTTAAATGCCAGACTC
1 CAAAGAAACACTTGTTTGTAGTTTGATAGTCATTGAATATGATTTTATCTTTAAATGCCAGACTC
*
3876048 CTTTGATTAATTAATTGGCTTGAGAACACTACTTTCCATGGTTATTGCTTAAACCTGTGAGTTAT
66 CTGTGATTAATTAATTGGCTTGAGAACACTACTTTCCATGGTTATTGCTTAAACCTGTGAGTTAT
3876113 TGGGGGGGGGGGGAATATGAG
131 TGGGGGGGGGGGGAATATGAG
3876134 CAAAGAAACACTTGTTTGTAGTTTGATAGTCATTGAATATGATTTTATCTTTAAATGCCAGACTC
1 CAAAGAAACACTTGTTTGTAGTTTGATAGTCATTGAATATGATTTTATCTTTAAATGCCAGACTC
3876199 CTGTGATTAATTAATTGGCTTGAGAACACTACTTTCCATGGTTATTGCTTAAACCTGTGAGTTAT
66 CTGTGATTAATTAATTGGCTTGAGAACACTACTTTCCATGGTTATTGCTTAAACCTGTGAGTTAT
3876264 TGGGGGGGGGGGGAATATGAG
131 TGGGGGGGGGGGGAATATGAG
3876285 C
1 C
3876286 TTTACAATTG
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 151 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (151 bp):
CAAAGAAACACTTGTTTGTAGTTTGATAGTCATTGAATATGATTTTATCTTTAAATGCCAGACTC
CTGTGATTAATTAATTGGCTTGAGAACACTACTTTCCATGGTTATTGCTTAAACCTGTGAGTTAT
TGGGGGGGGGGGGAATATGAG
Found at i:3877030 original size:2 final size:2
Alignment explanation
Indices: 3877023--3877049 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3877013 TTCCTAACGT
3877023 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3877050 TCTTACTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3877176 original size:21 final size:20
Alignment explanation
Indices: 3877152--3877207 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
3877142 ACTATTTAGT
3877152 ATTTTATTTTATTATACATAC
1 ATTTTATTTT-TTATACATAC
* *
3877173 ATTTTATATTTTTATATATAT
1 ATTTTAT-TTTTTATACATAC
*
3877194 TTTTTATTTTTTAT
1 ATTTTATTTTTTAT
3877208 TTATTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 21 0.68
22 3 0.10
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTTATTTTTTATACATAC
Found at i:3877210 original size:4 final size:4
Alignment explanation
Indices: 3877191--3877240 Score: 59
Period size: 4 Copynumber: 12.2 Consensus size: 4
3877181 TTTTTATATA
3877191 TATT T-TT TATT T-TT TATT TATTT TATTT TATT TATAT TATT TATT TATT
1 TATT TATT TATT TATT TATT TA-TT TA-TT TATT TAT-T TATT TATT TATT
3877240 T
1 T
3877241 TCATTATGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 6 0.14
4 23 0.55
5 13 0.31
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TATT
Found at i:3877212 original size:18 final size:18
Alignment explanation
Indices: 3877173--3877241 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
3877163 TTATACATAC
* *
3877173 ATTTTATATTTTTATATAT
1 ATTTTTTATTTTT-TATTT
3877192 ATTTTTTATTTTTTATTT
1 ATTTTTTATTTTTTATTT
*
3877210 ATTTTATT-TTATTTATATT
1 ATTTT-TTATTTTTTAT-TT
3877229 ATTTATTTATTTT
1 ATTT-TTTATTTT
3877242 CATTATGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 16 0.38
19 22 0.52
20 4 0.10
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTTTTTATTTTTTATTT
Found at i:3877254 original size:17 final size:16
Alignment explanation
Indices: 3877197--3877259 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 16
3877187 TATATATTTT
3877197 TTATTTTTTA-TTT-A
1 TTATTTTTTATTTTCA
3877211 TT-TTATTTTATTTAT-A
1 TTATT-TTTTATTT-TCA
3877227 TTATTTATTTATTTTCA
1 TTATTT-TTTATTTTCA
*
3877244 TTATGTTTTTAGTTTC
1 TTAT-TTTTTATTTTC
3877260 TTTGCTCTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
13 2 0.05
14 7 0.17
15 2 0.05
16 6 0.15
17 22 0.54
18 2 0.05
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (16 bp):
TTATTTTTTATTTTCA
Found at i:3877254 original size:34 final size:34
Alignment explanation
Indices: 3877176--3877254 Score: 81
Period size: 34 Copynumber: 2.3 Consensus size: 34
3877166 TACATACATT
* * *
3877176 TTATATTTTTATATATATTTTTTATTTTTTATTTA
1 TTAT-TTTTTATATATATTATTTATTTATTATTCA
*
3877211 TT-TTATTTTATTTATATTATTTATTTATT-TTCA
1 TTATT-TTTTATATATATTATTTATTTATTATTCA
3877244 TTATGTTTTTA
1 TTAT-TTTTTA
3877255 GTTTCTTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
33 6 0.16
34 28 0.76
35 3 0.08
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.73
Consensus pattern (34 bp):
TTATTTTTTATATATATTATTTATTTATTATTCA
Found at i:3882024 original size:7 final size:7
Alignment explanation
Indices: 3881998--3882038 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
3881988 AATCAAGAAC
3881998 AAAAAAG
1 AAAAAAG
3882005 AAAAGAAG
1 AAAA-AAG
3882013 CAAAAAA-
1 -AAAAAAG
3882020 AAAAAAG
1 AAAAAAG
3882027 AAAAAAG
1 AAAAAAG
3882034 AAAAA
1 AAAAA
3882039 CAAGAACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 6 0.19
7 16 0.52
8 5 0.16
9 4 0.13
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:3882037 original size:17 final size:18
Alignment explanation
Indices: 3881992--3882038 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
3881982 AGATCCAATC
*
3881992 AAGAACAAAAAAGAAAAG
1 AAGAAAAAAAAAGAAAAG
*
3882010 AAGCAAAAAAAA-AAAAG
1 AAGAAAAAAAAAGAAAAG
3882027 AA-AAAAGAAAAA
1 AAGAAAA-AAAAA
3882039 CAAGAACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 3 0.12
17 12 0.48
18 10 0.40
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAAAAGAAAAG
Found at i:3882906 original size:22 final size:22
Alignment explanation
Indices: 3882832--3882908 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
3882822 GCTACCCCAT
*
3882832 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
3882854 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
3882876 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
3882898 CAAACCTTTGA
1 CAAACCTTTGA
3882909 CCAAACATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:3884776 original size:106 final size:106
Alignment explanation
Indices: 3883712--3884775 Score: 1646
Period size: 106 Copynumber: 10.0 Consensus size: 106
3883702 ATATCGTGCC
* * * * *
3883712 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
3883777 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
3883818 ACACCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
3883883 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
3883924 ACTCCATACAACGCAAGTTCAACTTCACAATGAAGGGACCGCTGGTTGTCAGCAAACGACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
3883989 AATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
3884030 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
3884095 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
3884136 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
3884201 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
3884242 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
3884307 AATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
3884348 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
3884413 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
3884454 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
3884519 AATTTCAAAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
3884560 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
3884625 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
3884666 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGA-CGACTGGTCGTCAACAAATAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
* * *
3884730 CGATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
3884772 ACTC
1 ACTC
3884776 GGAACAATGC
Statistics
Matches: 882, Mismatches: 74, Indels: 4
0.92 0.08 0.00
Matches are distributed among these distances:
105 2 0.00
106 880 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:3885577 original size:37 final size:37
Alignment explanation
Indices: 3885524--3885628 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
3885514 CATTTTCGTC
3885524 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
3885561 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
3885598 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
3885629 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:3886335 original size:36 final size:34
Alignment explanation
Indices: 3886208--3886335 Score: 84
Period size: 36 Copynumber: 3.6 Consensus size: 34
3886198 TAACGTTATA
* * * * * *
3886208 TATATATATATTCTTACTTCATTTTATTTTATATT
1 TATATTTATATT-TTATTTTATTTAATATTATATG
*
3886243 TATATGATTACTATTTT-TTTTAGTTAATATTATATG
1 TATAT--TTA-TATTTTATTTTATTTAATATTATATG
*
3886279 TATATTTAT-TTTTCA-TTTATTTATTATTAT-TG
1 TATATTTATATTTT-ATTTTATTTAATATTATATG
3886311 TTACTATTTAGTATTTTATTTTATT
1 -TA-TATTTA-TATTTTATTTTATT
3886336 ATACATACAT
Statistics
Matches: 74, Mismatches: 9, Indels: 19
0.73 0.09 0.19
Matches are distributed among these distances:
32 6 0.08
33 16 0.22
34 9 0.12
35 7 0.09
36 28 0.38
37 4 0.05
38 4 0.05
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (34 bp):
TATATTTATATTTTATTTTATTTAATATTATATG
Found at i:3886376 original size:25 final size:29
Alignment explanation
Indices: 3886348--3886408 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
3886338 ACATACATTG
3886348 TTATATTTT-TATATA-T-TTTA-TTATT
1 TTATATTTTATATATACTATTTATTTATT
*
3886373 TTATTATTTTATTTATACTATTTATTTATT
1 TTA-TATTTTATATATACTATTTATTTATT
3886403 TT-TATT
1 TTATATT
3886409 ATGTTTTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 3 0.10
26 6 0.20
27 5 0.17
28 5 0.17
29 4 0.13
30 7 0.23
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (29 bp):
TTATATTTTATATATACTATTTATTTATT
Found at i:3886388 original size:17 final size:17
Alignment explanation
Indices: 3886354--3886385 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3886344 ATTGTTATAT
3886354 TTTTATATATTTTATTA
1 TTTTATATATTTTATTA
3886371 TTTTAT-TATTTTATT
1 TTTTATATATTTTATT
3886386 TATACTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATATATTTTATTA
Found at i:3886417 original size:17 final size:16
Alignment explanation
Indices: 3886351--3886417 Score: 59
Period size: 17 Copynumber: 4.1 Consensus size: 16
3886341 TACATTGTTA
3886351 TATTTTTATATATTTTAT
1 TATTTTTAT-TATTTT-T
3886369 TA-TTTTATTA--TTT
1 TATTTTTATTATTTTT
* *
3886382 TATTTATACTATTTATT
1 TATTTTTATTATTT-TT
3886399 TATTTTTATTATGTTTT
1 TATTTTTATTAT-TTTT
3886416 TA
1 TA
3886418 GTTTCTTTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
13 3 0.08
14 8 0.20
16 3 0.08
17 22 0.55
18 4 0.10
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (16 bp):
TATTTTTATTATTTTT
Found at i:3886533 original size:18 final size:17
Alignment explanation
Indices: 3886490--3886534 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
3886480 TTGTATATAT
*
3886490 ATTTTTTTCTTCATTTA
1 ATTTTTTTATTCATTTA
*
3886507 TTTTATTTTATTCAATTTA
1 ATTT-TTTTATTC-ATTTA
3886526 ATTTTTTTA
1 ATTTTTTTA
3886535 AAATATTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
19 8 0.35
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTATTCATTTA
Found at i:3891734 original size:492 final size:492
Alignment explanation
Indices: 3890810--3891794 Score: 1898
Period size: 492 Copynumber: 2.0 Consensus size: 492
3890800 GATCTCTCAT
*
3890810 CAGCAGGTACATGCATATAAGCAGGACAACCAAAAATCCGTAAGTTATCAAAACTAACATCATGA
1 CAGCAGGTACATGCACATAAGCAGGACAACCAAAAATCCGTAAGTTATCAAAACTAACATCATGA
3890875 CCAGTCCATACCTCTTCTGCAACTTTCCCAGCCAATGATGCCATTGGCGATCTGTTGATAAGATA
66 CCAGTCCATACCTCTTCTGCAACTTTCCCAGCCAATGATGCCATTGGCGATCTGTTGATAAGATA
*
3890940 ACACGCCATGTTAATAGCCTCGACCCAGAAGTGTTTGGGAAGCCCCACATTCAATCGCAAACATC
131 ACACGCCATGTTAATAGCCTCGACCCAGAAGTGTTTGGGAAGCCCCACATTCAATCACAAACATC
3891005 TGACTCTTTCATTCAACGACCTGTTCATCCGTTCCGCAACACCATTCTGTTGTGGTGTCTTGCGC
196 TGACTCTTTCATTCAACGACCTGTTCATCCGTTCCGCAACACCATTCTGTTGTGGTGTCTTGCGC
3891070 ACTGTAAAATGTCTCTTAATCCTGTGCTCCTTACAGAAGTGTAAGAACTGTGAATCTGTGTACTC
261 ACTGTAAAATGTCTCTTAATCCTGTGCTCCTTACAGAAGTGTAAGAACTGTGAATCTGTGTACTC
3891135 CGTACCATTGTCAGACCGCAAACACTTGATTTTTCGTCCTGTTTGGTTTTCTACCTCAGCTTTCC
326 CGTACCATTGTCAGACCGCAAACACTTGATTTTTCGTCCTGTTTGGTTTTCTACCTCAGCTTTCC
*
3891200 ACAGCTTGAACTTCTCAAAAACTTCAGATTTCTGTTTCAAAAAATACACCCAAACTTTCTGTGAA
391 ACAGCTTGAACTTCTCAAAAACTTCAGATTTCTGTTTCAAAAAATACACCCAAACTTTCCGTGAA
*
3891265 AATTCATCAATAAAAGTAACATAATACCTAGATCCAC
456 AAATCATCAATAAAAGTAACATAATACCTAGATCCAC
3891302 CAGCAGGTACATGCACATAAGCAGGACAACCAAAAATCCGTAAGTTATCAAAACTAACATCATGA
1 CAGCAGGTACATGCACATAAGCAGGACAACCAAAAATCCGTAAGTTATCAAAACTAACATCATGA
*
3891367 CCAGTCCATACCTCTTCTGCAACTTTCCCAGCCAATGATGCCCTTGGCGATCTGTTGATAAGATA
66 CCAGTCCATACCTCTTCTGCAACTTTCCCAGCCAATGATGCCATTGGCGATCTGTTGATAAGATA
* *
3891432 ACACGCCATGTTAATAGCCTCGGCCCAGAAGTGTTTGGGAAGCCCCGCATTCAATCACAAACATC
131 ACACGCCATGTTAATAGCCTCGACCCAGAAGTGTTTGGGAAGCCCCACATTCAATCACAAACATC
3891497 TGACTCTTTCATTCAACGACCTGTTCATCCGTTCCGCAACACCATTCTGTTGTGGTGTCTTGCGC
196 TGACTCTTTCATTCAACGACCTGTTCATCCGTTCCGCAACACCATTCTGTTGTGGTGTCTTGCGC
3891562 ACTGTAAAATGTCTCTTAATCCTGTGCTCCTTACAGAAGTGTAAGAACTGTGAATCTGTGTACTC
261 ACTGTAAAATGTCTCTTAATCCTGTGCTCCTTACAGAAGTGTAAGAACTGTGAATCTGTGTACTC
*
3891627 CGTACTATTGTCAGACCGCAAACACTTGATTTTTCGTCCTGTTTGGTTTTCTACCTCAGCTTTCC
326 CGTACCATTGTCAGACCGCAAACACTTGATTTTTCGTCCTGTTTGGTTTTCTACCTCAGCTTTCC
3891692 ACAGCTTGAACTTCTCAAAAACTTCAGATTTCTGTTTCAAAAAATACACCCAAACTTTCCGTGAA
391 ACAGCTTGAACTTCTCAAAAACTTCAGATTTCTGTTTCAAAAAATACACCCAAACTTTCCGTGAA
3891757 AAATCATCAATAAAAGTAACATAATACCTAGATCCAC
456 AAATCATCAATAAAAGTAACATAATACCTAGATCCAC
3891794 C
1 C
3891795 CAAAGACGAT
Statistics
Matches: 485, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
492 485 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (492 bp):
CAGCAGGTACATGCACATAAGCAGGACAACCAAAAATCCGTAAGTTATCAAAACTAACATCATGA
CCAGTCCATACCTCTTCTGCAACTTTCCCAGCCAATGATGCCATTGGCGATCTGTTGATAAGATA
ACACGCCATGTTAATAGCCTCGACCCAGAAGTGTTTGGGAAGCCCCACATTCAATCACAAACATC
TGACTCTTTCATTCAACGACCTGTTCATCCGTTCCGCAACACCATTCTGTTGTGGTGTCTTGCGC
ACTGTAAAATGTCTCTTAATCCTGTGCTCCTTACAGAAGTGTAAGAACTGTGAATCTGTGTACTC
CGTACCATTGTCAGACCGCAAACACTTGATTTTTCGTCCTGTTTGGTTTTCTACCTCAGCTTTCC
ACAGCTTGAACTTCTCAAAAACTTCAGATTTCTGTTTCAAAAAATACACCCAAACTTTCCGTGAA
AAATCATCAATAAAAGTAACATAATACCTAGATCCAC
Found at i:3895929 original size:2 final size:2
Alignment explanation
Indices: 3895924--3895963 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3895914 ATATTGTGTG
3895924 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3895964 CGTGGAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3902609 original size:19 final size:20
Alignment explanation
Indices: 3902576--3902625 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
3902566 TCATTTTACG
3902576 AATATAA-AT-TA-CAAATAC
1 AATATAATATATATCAAAT-C
3902594 AA-ATAAT-TATATCAAATC
1 AATATAATATATATCAAATC
3902612 AATATAATATATAT
1 AATATAATATATAT
3902626 ATATATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 5 0.19
18 7 0.26
19 10 0.37
20 5 0.19
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
AATATAATATATATCAAATC
Found at i:3906317 original size:14 final size:14
Alignment explanation
Indices: 3906298--3906324 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3906288 ATACTTTAAA
3906298 CCACCGTTGTTATG
1 CCACCGTTGTTATG
3906312 CCACCGTTGTTAT
1 CCACCGTTGTTAT
3906325 ACTTGAGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.30, G:0.19, T:0.37
Consensus pattern (14 bp):
CCACCGTTGTTATG
Found at i:3907541 original size:16 final size:17
Alignment explanation
Indices: 3907522--3907558 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3907512 TAAAATATTA
3907522 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
3907538 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
3907555 TTTT
1 TTTT
3907559 TCATCCCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:3908459 original size:34 final size:34
Alignment explanation
Indices: 3908419--3908500 Score: 155
Period size: 34 Copynumber: 2.4 Consensus size: 34
3908409 CCGGGCTAAA
*
3908419 CTAGAACCTTTCCCTAGCTTTTACACGTGATTAG
1 CTAGAACCTTTCCCTAGCTTTTACACGGGATTAG
3908453 CTAGAACCTTTCCCTAGCTTTTACACGGGATTAG
1 CTAGAACCTTTCCCTAGCTTTTACACGGGATTAG
3908487 CTAGAACCTTTCCC
1 CTAGAACCTTTCCC
3908501 CTTTACAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (34 bp):
CTAGAACCTTTCCCTAGCTTTTACACGGGATTAG
Found at i:3908874 original size:20 final size:20
Alignment explanation
Indices: 3908849--3908912 Score: 101
Period size: 20 Copynumber: 3.1 Consensus size: 20
3908839 CCGTTAGACA
*
3908849 GGGGGGAATCGGTACCCCTT
1 GGGGGGAATCTGTACCCCTT
3908869 GGGGGGAATCTGTACCCCTT
1 GGGGGGAATCTGTACCCCTT
*
3908889 GGGGGGGAATCTGTACCCCCT
1 -GGGGGGAATCTGTACCCCTT
3908910 GGG
1 GGG
3908913 CAATCTGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 22 0.54
21 19 0.46
ACGTcount: A:0.14, C:0.25, G:0.41, T:0.20
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCTT
Found at i:3908893 original size:21 final size:21
Alignment explanation
Indices: 3908849--3908912 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
3908839 CCGTTAGACA
*
3908849 GGGGGGAATCGGTACCCCTT-
1 GGGGGGAATCTGTACCCCTTG
3908869 GGGGGGAATCTGTACCCCTTG
1 GGGGGGAATCTGTACCCCTTG
*
3908890 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCTTG
3908911 GG
1 GG
3908913 CAATCTGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 19 0.46
21 22 0.54
ACGTcount: A:0.14, C:0.25, G:0.41, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCTTG
Found at i:3912636 original size:16 final size:16
Alignment explanation
Indices: 3912610--3912647 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
3912600 TCTACTAAAG
3912610 CATGATTGGGTAGATAT
1 CATG-TTGGGTAGATAT
3912627 CATGTTGGGTAGATAT
1 CATGTTGGGTAGATAT
3912643 CATGT
1 CATGT
3912648 GAATAAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (16 bp):
CATGTTGGGTAGATAT
Found at i:3922647 original size:7 final size:8
Alignment explanation
Indices: 3922627--3922692 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
3922617 AAAAAATGAG
3922627 TGAAAAAA
1 TGAAAAAA
3922635 TGAAAAAA
1 TGAAAAAA
3922643 T--AAAAA
1 TGAAAAAA
*
3922649 --AAATAA
1 TGAAAAAA
*
3922655 TAAAAATAA
1 TGAAAA-AA
*
3922664 TAAAAATGAA
1 TGAAAA--AA
3922674 TGAAAAAA
1 TGAAAAAA
3922682 TGAAAAAA
1 TGAAAAAA
3922690 TGA
1 TGA
3922693 GGGTTCAAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
6 9 0.18
8 25 0.51
9 8 0.16
10 7 0.14
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (8 bp):
TGAAAAAA
Found at i:3922649 original size:9 final size:9
Alignment explanation
Indices: 3922637--3922689 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
3922627 TGAAAAAATG
3922637 AAAAAATAA
1 AAAAAATAA
3922646 AAAAAATAA
1 AAAAAATAA
*
3922655 TAAAAATAA
1 AAAAAATAA
*
3922664 TAAAAATGAA
1 AAAAAAT-AA
*
3922674 TGAAAAAATGA
1 --AAAAAATAA
3922685 AAAAA
1 AAAAA
3922690 TGAGGGTTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
9 29 0.76
10 2 0.05
11 1 0.03
12 6 0.16
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (9 bp):
AAAAAATAA
Found at i:3922680 original size:12 final size:10
Alignment explanation
Indices: 3922637--3922682 Score: 53
Period size: 9 Copynumber: 4.7 Consensus size: 10
3922627 TGAAAAAATG
3922637 AAAAAATAA-
1 AAAAAATAAT
3922646 AAAAAATAAT
1 AAAAAATAAT
3922656 -AAAAATAAT
1 AAAAAATAAT
3922665 -AAAAATGAAT
1 AAAAAAT-AAT
3922675 GAAAAAAT
1 -AAAAAAT
3922683 GAAAAAATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 24 0.73
10 3 0.09
12 6 0.18
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.17
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:3923864 original size:110 final size:109
Alignment explanation
Indices: 3923671--3924039 Score: 504
Period size: 110 Copynumber: 3.4 Consensus size: 109
3923661 AGGTTCCCTA
* *
3923671 CGATCGTTGAAGATTGTTCAAGTCTTATACTCTCTGAGGAAATAGGGGGCGGACATGATTGTTGA
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGACATGATTGTTGA
3923736 AGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGAGGGCAGACG
66 AGATTGTTCGGGTCTTATACTCTCTGAAGAAATAG-GGGCAGACG
*
3923781 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGACACGATTGTTGA
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGACATGATTGTTGA
3923846 AGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
66 AGATTGTTCGGGTCTTATACTCTCTGAAGAAATA-GGGGCAGACG
* * * ** * *
3923891 CGATTGATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGAAGACGTGATTGATGA
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGACATGATTGTTGA
* *
3923954 AGATTG-T-GGGTTTTATACTCTCTGAAGAAATAGGGAGCAGACA
66 AGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGG-GCAGACG
* * *
3923997 CG-T--TTGAAGATT-TTCGAGT-TCTATACTCCCTAAAGAAAGAGGG
1 CGATCGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGG
3924040 AGCGAACCTG
Statistics
Matches: 236, Mismatches: 18, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
103 10 0.04
104 22 0.09
105 4 0.02
106 32 0.14
107 1 0.00
108 46 0.19
109 1 0.00
110 119 0.50
111 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (109 bp):
CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGACATGATTGTTGA
AGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGCAGACG
Found at i:3923935 original size:53 final size:55
Alignment explanation
Indices: 3923671--3923995 Score: 460
Period size: 55 Copynumber: 6.0 Consensus size: 55
3923661 AGGTTCCCTA
* ** * * *
3923671 CGATCGTTGAAGATTGTTCAAGTCTTATACTCTCTGAGGAAATAGGGGGCGGACA
1 CGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
3923726 TGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGAGGGCAGACG
1 CGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * *
3923781 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGACA
1 CGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
3923836 CGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
1 CGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
3923891 CGATTGATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGAAGACG
1 CGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * *
3923944 TGATTGATGAAGATTG-T-GGGTTTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 CGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
3923996 ACGTTTGAAG
Statistics
Matches: 246, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
53 83 0.34
54 1 0.00
55 162 0.66
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.29
Consensus pattern (55 bp):
CGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
Found at i:3924141 original size:54 final size:54
Alignment explanation
Indices: 3924002--3924529 Score: 560
Period size: 54 Copynumber: 9.9 Consensus size: 54
3923992 AGACACGTTT
* * * *
3924002 GAAGATTTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCTG-TT--A
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCGTTTGAA
* *
3924053 GAAGATGTTCGAGTTCCATACTCCCTAGATAAAGAGGGAACGAACCCGTTTGAA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCGTTTGAA
* * * * * *
3924107 GAAGATATTTGAGTTCTATTCTCCCT-GAAGAAAGAGGGAGCAAACCTG-TT--A
1 GAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAACGAACCCGTTTGAA
* * *
3924158 GAAGATGTTCGAGTTCCATACTCCCTAGATAAAGAGGGAATGAACCCGTTTGAA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCGTTTGAA
* * * * * *
3924212 GAAGATATTTGAGTTCTATTCTCCCT-GAAGAAAGAGAGAGCAAACCCGTTT---
1 GAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAACGAACCCGTTTGAA
* * * **
3924263 GAAGATGTTCGAGTTCCATACTCCCTAGATAAAGAGGGAACGAACCCATAAGAA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCGTTTGAA
* * *
3924317 GAAGATGTTCGAGTTCTATACTCCCTAGATAAAGAGGGAACGAACCTGTTTGCA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCGTTTGAA
* **
3924371 GAAGATGTTCGAGTTCTATACTCCCTAGATAAAGAGGGAACGAACCCGTAAGAA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCGTTTGAA
* * * * *
3924425 GAAGACGTTTGAGTTCTATACTCCCTAGAGAAAGAGGGATCAAACTCGTTTGCAA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCGTTTG-AA
* * *
3924480 -ATGATTGTTCAAGTTCTATACTCCCT-GAAGGAAGAGGGAACGAACCCGTT
1 GAAGA-TGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAACGAACCCGTT
3924530 GACTGAAGGT
Statistics
Matches: 392, Mismatches: 69, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
51 118 0.30
52 6 0.02
53 4 0.01
54 226 0.58
55 38 0.10
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (54 bp):
GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCGTTTGAA
Found at i:3924147 original size:105 final size:104
Alignment explanation
Indices: 3924002--3924529 Score: 668
Period size: 105 Copynumber: 5.0 Consensus size: 104
3923992 AGACACGTTT
*
3924002 GAAGAT-TTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCTGTTAGAAGATGTTCGAG
1 GAAGATATTT-GAGTTCTATACTCCCT-AAGAAAGAGGGAGCAAACCTGTTAGAAGATGTTCGAG
*
3924066 TTCCATACTCCCTAGATAAAGAGGGAACGAACCCGTTTGAA
64 TTCCATACTCCCTAGATAAAGAGGGAACGAACCCGTTAGAA
*
3924107 GAAGATATTTGAGTTCTATTCTCCCTGAAGAAAGAGGGAGCAAACCTGTTAGAAGATGTTCGAGT
1 GAAGATATTTGAGTTCTATACTCCCT-AAGAAAGAGGGAGCAAACCTGTTAGAAGATGTTCGAGT
* *
3924172 TCCATACTCCCTAGATAAAGAGGGAATGAACCCGTTTGAA
65 TCCATACTCCCTAGATAAAGAGGGAACGAACCCGTTAGAA
* * * *
3924212 GAAGATATTTGAGTTCTATTCTCCCTGAAGAAAGAGAGAGCAAACCCGTTTGAAGATGTTCGAGT
1 GAAGATATTTGAGTTCTATACTCCCT-AAGAAAGAGGGAGCAAACCTGTTAGAAGATGTTCGAGT
* *
3924277 TCCATACTCCCTAGATAAAGAGGGAACGAACCCATAAGAA
65 TCCATACTCCCTAGATAAAGAGGGAACGAACCCGTTAGAA
* * * * *
3924317 GAAGATGTTCGAGTTCTATACTCCCTAGATAAAGAGGGAACGAACCTGTTTGCAGAAGATGTTCG
1 GAAGATATTTGAGTTCTATACTCCCTA-AGAAAGAGGGAGCAAACCTG-TT--AGAAGATGTTCG
* *
3924382 AGTTCTATACTCCCTAGATAAAGAGGGAACGAACCCGTAAGAA
62 AGTTCCATACTCCCTAGATAAAGAGGGAACGAACCCGTTAGAA
** * *
3924425 GAAGACGTTTGAGTTCTATACTCCCTAGAGAAAGAGGGATCAAA-CTCGTTTGCAAATGATTGTT
1 GAAGATATTTGAGTTCTATACTCCCTA-AGAAAGAGGGAGCAAACCT-GTTAG--AA-GA-TGTT
* *
3924489 CAAGTTCTATACTCCCT-GA-AGGAAGAGGGAACGAACCCGTT
60 CGAGTTCCATACTCCCTAGATA--AAGAGGGAACGAACCCGTT
3924530 GACTGAAGGT
Statistics
Matches: 381, Mismatches: 30, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
104 1 0.00
105 234 0.61
106 5 0.01
107 7 0.02
108 96 0.25
109 38 0.10
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (104 bp):
GAAGATATTTGAGTTCTATACTCCCTAAGAAAGAGGGAGCAAACCTGTTAGAAGATGTTCGAGTT
CCATACTCCCTAGATAAAGAGGGAACGAACCCGTTAGAA
Found at i:3928570 original size:19 final size:20
Alignment explanation
Indices: 3928527--3928574 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3928517 TCTCAATCCT
*
3928527 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
3928547 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
3928566 TTTTCAAAA
1 TTTTCAAAA
3928575 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:3930805 original size:2 final size:2
Alignment explanation
Indices: 3930800--3930829 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3930790 ATAAAATTTC
3930800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3930830 GTTGTAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3933327 original size:21 final size:21
Alignment explanation
Indices: 3933301--3933341 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3933291 ATGTCAACAC
*
3933301 CGTGAATTGTCACGCCAGCAT
1 CGTGAACTGTCACGCCAGCAT
*
3933322 CGTGAACTGTCACGTCAGCA
1 CGTGAACTGTCACGCCAGCA
3933342 CCATAATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (21 bp):
CGTGAACTGTCACGCCAGCAT
Found at i:3936128 original size:5 final size:5
Alignment explanation
Indices: 3936120--3936168 Score: 61
Period size: 5 Copynumber: 10.4 Consensus size: 5
3936110 TAAGAATAAT
3936120 ATATA ATATA ATAT- A-ATA ATATA ATA-A TATATA ATATA ATA-A ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA -ATATA ATATA ATATA ATATA
3936167 AT
1 AT
3936169 TCTTCAACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
3 2 0.05
4 7 0.18
5 29 0.74
6 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:3936140 original size:8 final size:8
Alignment explanation
Indices: 3936127--3936168 Score: 68
Period size: 8 Copynumber: 5.2 Consensus size: 8
3936117 AATATATAAT
3936127 ATAATATA
1 ATAATATA
3936135 ATAATATA
1 ATAATATA
3936143 ATAATAT-
1 ATAATATA
3936150 ATAATATA
1 ATAATATA
3936158 ATAAATATA
1 AT-AATATA
3936167 AT
1 AT
3936169 TCTTCAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.22
8 17 0.53
9 8 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATATA
Found at i:3936143 original size:18 final size:18
Alignment explanation
Indices: 3936115--3936168 Score: 73
Period size: 16 Copynumber: 3.3 Consensus size: 18
3936105 TAGAGTAAGA
3936115 ATAAT-ATATAATATAAT
1 ATAATAATATAATATAAT
3936132 ATAATAATAT-A-ATAAT
1 ATAATAATATAATATAAT
3936148 AT-ATAATATAATA-AAT
1 ATAATAATATAATATAAT
3936164 ATAAT
1 ATAAT
3936169 TCTTCAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
15 7 0.21
16 13 0.39
17 9 0.27
18 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATAATATAATATAAT
Found at i:3937378 original size:24 final size:24
Alignment explanation
Indices: 3937324--3937393 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
3937314 ATAAACAAAT
* * * * *
3937324 ATATCAGAAATCAAAACAGAATTC
1 ATATCATATATCAGAACAAAATCC
3937348 ATATCATATATCAGAACAAAATCC
1 ATATCATATATCAGAACAAAATCC
*
3937372 ATATCATATATTAGAACAAAAT
1 ATATCATATATCAGAACAAAAT
3937394 TCAAATCGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.26
Consensus pattern (24 bp):
ATATCATATATCAGAACAAAATCC
Found at i:3937406 original size:24 final size:24
Alignment explanation
Indices: 3937326--3937410 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
3937316 AAACAAATAT
* * * * *
3937326 ATCAGAAATCAAAACAGAATTCAT
1 ATCAGATATCAGAACAAAATCCAA
* *
3937350 ATCATATATCAGAACAAAATCCAT
1 ATCAGATATCAGAACAAAATCCAA
* * *
3937374 ATCATATATTAGAACAAAATTCAA
1 ATCAGATATCAGAACAAAATCCAA
*
3937398 ATCGGATATCAGA
1 ATCAGATATCAGA
3937411 TAAAATATTC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.25
Consensus pattern (24 bp):
ATCAGATATCAGAACAAAATCCAA
Found at i:3937406 original size:26 final size:24
Alignment explanation
Indices: 3937350--3937410 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
3937340 CAGAATTCAT
*
3937350 ATCATATATCAGAACAAAATCCAT
1 ATCATATATCAGAACAAAATCCAA
* *
3937374 ATCATATATTAGAACAAAATTCAA
1 ATCATATATCAGAACAAAATCCAA
**
3937398 ATCGGATATCAGA
1 ATCATATATCAGA
3937411 TAAAATATTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.26
Consensus pattern (24 bp):
ATCATATATCAGAACAAAATCCAA
Found at i:3938019 original size:12 final size:12
Alignment explanation
Indices: 3938002--3938032 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3937992 ATTATACGAT
3938002 ATGAACAGTACC
1 ATGAACAGTACC
*
3938014 ATGAACTGTACC
1 ATGAACAGTACC
3938026 ATGAACA
1 ATGAACA
3938033 TATCAGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:3938113 original size:12 final size:12
Alignment explanation
Indices: 3938079--3938141 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
3938069 ATGCACTGCT
3938079 ACAGTACCATGA
1 ACAGTACCATGA
* * *
3938091 ACTGAATCATGA
1 ACAGTACCATGA
3938103 ACAGTACCATGA
1 ACAGTACCATGA
* *
3938115 GCAGTACCGTGA
1 ACAGTACCATGA
3938127 ACAGTACCATGA
1 ACAGTACCATGA
3938139 ACA
1 ACA
3938142 ATGAAATTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (12 bp):
ACAGTACCATGA
Found at i:3938944 original size:31 final size:30
Alignment explanation
Indices: 3938906--3939001 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 30
3938896 GAACCTCGAC
* *
3938906 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCC-AAGAACATAGGTA
**
3938937 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATG-TCCCAAGAACATAGGTA
* *
3938968 TACTGTCCATATGTCCCAAAAGACATAGGTA
1 AACTGTCCATATGTCCCAAGA-ACATAGGTA
3938999 AAC
1 AAC
3939002 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 5 0.09
31 46 0.85
32 3 0.06
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (30 bp):
AACTGTCCATATGTCCCAAGAACATAGGTA
Found at i:3939210 original size:59 final size:59
Alignment explanation
Indices: 3939101--3939216 Score: 144
Period size: 59 Copynumber: 2.0 Consensus size: 59
3939091 ATATCATTTC
* * *
3939101 TCTTATAAACACATATCTCTTCTTTTCTGTCACGTATCACATATACGTGTAATCATTGA
1 TCTTATAAACACATATCTCTTCTTTTCTGTCACATACCACATATACGTGTAAACATTGA
* * * * *
3939160 TCTTATAATCACATATTTCTT-TTCTTCTGTCACATACCATATGTATGTGTAAACATT
1 TCTTATAAACACATATCTCTTCTT-TTCTGTCACATACCACATATACGTGTAAACATT
3939217 TATTTCATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 2 0.04
59 46 0.96
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (59 bp):
TCTTATAAACACATATCTCTTCTTTTCTGTCACATACCACATATACGTGTAAACATTGA
Found at i:3943214 original size:13 final size:13
Alignment explanation
Indices: 3943194--3943246 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
3943184 ACTGAAATTA
3943194 ATGATTCACGACG
1 ATGATTCACGACG
* *
3943207 ACGATTCACGACA
1 ATGATTCACGACG
*
3943220 ATGATTCACGATG
1 ATGATTCACGACG
3943233 ATGATTCACGACG
1 ATGATTCACGACG
3943246 A
1 A
3943247 AAGGTTTGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (13 bp):
ATGATTCACGACG
Found at i:3944164 original size:20 final size:20
Alignment explanation
Indices: 3944139--3944184 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3944129 TCGTGGGTTC
*
3944139 TGATACTAACCCTTTAGTAT
1 TGATACTAAACCTTTAGTAT
*
3944159 TGATACTAAACCTTTGGTAT
1 TGATACTAAACCTTTAGTAT
*
3944179 CGATAC
1 TGATAC
3944185 CCCACCTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (20 bp):
TGATACTAAACCTTTAGTAT
Found at i:3944457 original size:20 final size:20
Alignment explanation
Indices: 3944428--3944465 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3944418 CTTTACTGGA
*
3944428 GAACATTATCAATACTATTC
1 GAACAATATCAATACTATTC
*
3944448 GAACAATATCGATACTAT
1 GAACAATATCAATACTAT
3944466 CACTAATGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (20 bp):
GAACAATATCAATACTATTC
Found at i:3951845 original size:5 final size:5
Alignment explanation
Indices: 3951835--3951875 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
3951825 TTTTTATATA
*
3951835 ATTAT ATTAT ATTAT ATTAT A-TAT -TATAT ATTAT TTTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT ATTAT ATTAT AT
3951876 ACTATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 3 0.10
5 27 0.87
6 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTAT
Found at i:3951859 original size:7 final size:7
Alignment explanation
Indices: 3951828--3951884 Score: 57
Period size: 7 Copynumber: 8.1 Consensus size: 7
3951818 GAGTTTATTT
3951828 TTATATAA
1 TTATAT-A
3951836 TTATAT-
1 TTATATA
3951842 TATATTATA
1 T-TA-TATA
3951851 TTATATA
1 TTATATA
3951858 TTATATA
1 TTATATA
3951865 TTAT-T-
1 TTATATA
3951870 TTATATA
1 TTATATA
*
3951877 CTATATA
1 TTATATA
3951884 T
1 T
3951885 AGTATGGTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
5 4 0.10
6 3 0.07
7 23 0.55
8 11 0.26
9 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (7 bp):
TTATATA
Found at i:3951859 original size:17 final size:17
Alignment explanation
Indices: 3951837--3951882 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
3951827 TTTATATAAT
3951837 TATATTATATTATATTA
1 TATATTATATTATATTA
*
3951854 TATATTATATATTATTTTA
1 TATA-T-TATATTATATTA
*
3951873 TATACTATAT
1 TATATTATAT
3951883 ATAGTATGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 9 0.36
18 1 0.04
19 15 0.60
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATTATATTATATTA
Found at i:3951866 original size:19 final size:19
Alignment explanation
Indices: 3951842--3951884 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
3951832 ATAATTATAT
*
3951842 TATATTATATTATATATTA
1 TATATTATATTATATACTA
*
3951861 TATATTATTTTATATACTA
1 TATATTATATTATATACTA
3951880 TATAT
1 TATAT
3951885 AGTATGGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATACTA
Found at i:3953808 original size:168 final size:169
Alignment explanation
Indices: 3953530--3953869 Score: 673
Period size: 168 Copynumber: 2.0 Consensus size: 169
3953520 AGAAAGAAAC
3953530 CATATGTTATTCACGAAAGTAAAATGGTAAAAGCAAATAAACCTTTTACCCTCAGTCCCACACCC
1 CATATGTTATTCACGAAAGTAAAATGGTAAAAGCAAATAAACCTTTTACCCTCAGTCCCACACCC
3953595 AGAAAAAACTATATATGTAGCCTAATAGCCTTTGTTGGTTGCTGATGGACAAGTGA-TGGACCCA
66 AGAAAAAACTATATATGTAGCCTAATAGCCTTTGTTGGTTGCTGATGGACAAGTGATTGGACCCA
3953659 AAGGGCCGGGCCCGGTTCAACTCAAAATTATTTTCGTTT
131 AAGGGCCGGGCCCGGTTCAACTCAAAATTATTTTCGTTT
3953698 CATATGTTATTCACGAAAGTAAAATGGTAAAAGCAAATAAACCTTTTACCCTCAGTCCCACACCC
1 CATATGTTATTCACGAAAGTAAAATGGTAAAAGCAAATAAACCTTTTACCCTCAGTCCCACACCC
3953763 AGAAAAAACTATATATGTAGCCTAATAGCCTTTGTTGGTTGCTGATGGACAAGTGATTGGACCCA
66 AGAAAAAACTATATATGTAGCCTAATAGCCTTTGTTGGTTGCTGATGGACAAGTGATTGGACCCA
3953828 AAGGGCCGGGCCCGGTTCAACTCAAAATTATTTTCGTTT
131 AAGGGCCGGGCCCGGTTCAACTCAAAATTATTTTCGTTT
3953867 CAT
1 CAT
3953870 GATAACATAA
Statistics
Matches: 171, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
168 121 0.71
169 50 0.29
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (169 bp):
CATATGTTATTCACGAAAGTAAAATGGTAAAAGCAAATAAACCTTTTACCCTCAGTCCCACACCC
AGAAAAAACTATATATGTAGCCTAATAGCCTTTGTTGGTTGCTGATGGACAAGTGATTGGACCCA
AAGGGCCGGGCCCGGTTCAACTCAAAATTATTTTCGTTT
Found at i:3954542 original size:27 final size:28
Alignment explanation
Indices: 3954484--3954542 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
3954474 ACTTTACACG
* * *
3954484 ACCCGAAAATTATACACCCTCCACCCGT
1 ACCCAAAAACTATACACACTCCACCCGT
3954512 -CCCAAAAACTATACACACTCCACCC-T
1 ACCCAAAAACTATACACACTCCACCCGT
3954538 ACCCA
1 ACCCA
3954543 CCCTTTTGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.46, G:0.03, T:0.15
Consensus pattern (28 bp):
ACCCAAAAACTATACACACTCCACCCGT
Found at i:3955990 original size:29 final size:30
Alignment explanation
Indices: 3955957--3956015 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3955947 TACACCCAAC
*
3955957 AATTTTACAAGTTCAAATTCGCCC-CCTAA
1 AATTTTACAAGTTCAAATTCACCCTCCTAA
** *
3955986 AATTTTTTAAGTTCAAGTTCACCCTCCTAA
1 AATTTTACAAGTTCAAATTCACCCTCCTAA
3956016 CATCAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (30 bp):
AATTTTACAAGTTCAAATTCACCCTCCTAA
Found at i:3957776 original size:2 final size:2
Alignment explanation
Indices: 3957769--3957797 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3957759 TATGTATCTG
3957769 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3957798 TCATGCTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3962486 original size:25 final size:24
Alignment explanation
Indices: 3962437--3962490 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
3962427 TTAAAAAGTT
3962437 AAATT-TAAAATTTAAAGAATATA
1 AAATTATAAAATTTAAAGAATATA
*
3962460 AAATTATAAAATTTTATAAG-ATGTA
1 AAATTATAAAA-TTTA-AAGAATATA
3962485 AAATTA
1 AAATTA
3962491 AATCGTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 14 0.52
26 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATTATAAAATTTAAAGAATATA
Found at i:3965781 original size:2 final size:2
Alignment explanation
Indices: 3965776--3965806 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3965766 TCTCTCTCTC
3965776 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3965807 GGTAATAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3971479 original size:81 final size:81
Alignment explanation
Indices: 3971344--3971507 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
3971334 TAACTGAAAT
3971344 GCTTATTTGTGTTGGGGTTGTTGACGAGGGAAACACAGTTCTATTTCATTGCTAAGTTTCAAAAT
1 GCTTATTTGTGTTGGGGTTGTTGACGAGGGAAACACAGTTCTATTTCATTGCTAAGTTTCAAAAT
3971409 CTTTGTTTCTATTCAA
66 CTTTGTTTCTATTCAA
3971425 GCTTATTTGTGTTGGGGTTGTTGACGAGGGAAACACAGTTCTATTTCATTGCTAAGTTTCAAAAT
1 GCTTATTTGTGTTGGGGTTGTTGACGAGGGAAACACAGTTCTATTTCATTGCTAAGTTTCAAAAT
3971490 CTTTGTTTCTATTCAA
66 CTTTGTTTCTATTCAA
3971506 GC
1 GC
3971508 AAGAGTTACT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.41
Consensus pattern (81 bp):
GCTTATTTGTGTTGGGGTTGTTGACGAGGGAAACACAGTTCTATTTCATTGCTAAGTTTCAAAAT
CTTTGTTTCTATTCAA
Found at i:3973566 original size:25 final size:25
Alignment explanation
Indices: 3973529--3973601 Score: 112
Period size: 25 Copynumber: 2.9 Consensus size: 25
3973519 AAGTAAGAGC
3973529 AACATTTTTCAAAATTCTTTCATCA
1 AACATTTTTCAAAATTCTTTCATCA
* *
3973554 AATATTTTTCAAAGTTCTTTCATCA
1 AACATTTTTCAAAATTCTTTCATCA
3973579 AACATTTTTCAAAACTT-TTTCAT
1 AACATTTTTCAAAA-TTCTTTCAT
3973602 TAATCTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 41 0.95
26 2 0.05
ACGTcount: A:0.34, C:0.18, G:0.01, T:0.47
Consensus pattern (25 bp):
AACATTTTTCAAAATTCTTTCATCA
Found at i:3974208 original size:101 final size:102
Alignment explanation
Indices: 3974031--3974275 Score: 336
Period size: 101 Copynumber: 2.4 Consensus size: 102
3974021 TAAGAAATCA
* * ** * * *
3974031 TTTTGTCTTTCTTAAGATTGTTTTCCTAGAGACTTCAA-CTTGTTTGTGTCGTCCAGGGGAGTCA
1 TTTTGTCTTTCTTAAGATTGTTTCCCTAGAAACTTCAACCTTGACTATCTCGTCCAGAGGAGTCA
*
3974095 ACTAGCCTTTCTTAGGATCATTTCTCTAGAAATTCGT
66 ACTAGCCTTTCTTAGAATCATTTCTCTAGAAATTCGT
* *
3974132 TTTTGTCTTTCTTAAGATTGTTTCCCTAGAAACTTAAACCTT-ACTATCTCGTGCAGAGGAGTCA
1 TTTTGTCTTTCTTAAGATTGTTTCCCTAGAAACTTCAACCTTGACTATCTCGTCCAGAGGAGTCA
*
3974196 ACTAGTCC-TTCTTAGAATCATTTCTCTAGAAATTTGT
66 ACTAG-CCTTTCTTAGAATCATTTCTCTAGAAATTCGT
*
3974233 TTTAT-TCTTTCTTAAGATTGTTTCCCTAGAAACATCAACCTTG
1 TTT-TGTCTTTCTTAAGATTGTTTCCCTAGAAACTTCAACCTTG
3974276 TCTTTCATAA
Statistics
Matches: 127, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
101 121 0.95
102 6 0.05
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (102 bp):
TTTTGTCTTTCTTAAGATTGTTTCCCTAGAAACTTCAACCTTGACTATCTCGTCCAGAGGAGTCA
ACTAGCCTTTCTTAGAATCATTTCTCTAGAAATTCGT
Found at i:3975135 original size:3 final size:3
Alignment explanation
Indices: 3975127--3975190 Score: 73
Period size: 3 Copynumber: 22.7 Consensus size: 3
3975117 TTTTGTTTAG
* *
3975127 TTA TTA TTA TTA TTA TTA -TA TTA ATA TT- TAA TTA -TA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3975171 TTC TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
3975191 TTGTAGGGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 7 0.13
3 45 0.87
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3975162 original size:16 final size:16
Alignment explanation
Indices: 3975141--3975171 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3975131 TATTATTATT
3975141 ATTATATTAATATTTA
1 ATTATATTAATATTTA
*
3975157 ATTATATTATTATTT
1 ATTATATTAATATTT
3975172 TCTTATTATT
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATATTAATATTTA
Found at i:3976093 original size:15 final size:15
Alignment explanation
Indices: 3976069--3976102 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3976059 CCGTAGGACC
*
3976069 ACTACATCCCGAAGG
1 ACTACATCCCGAAAG
*
3976084 ACTACGTCCCGAAAG
1 ACTACATCCCGAAAG
3976099 ACTA
1 ACTA
3976103 TTATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAAG
Found at i:3976700 original size:64 final size:64
Alignment explanation
Indices: 3976631--3976787 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
3976621 TAATGAAGGT
* *
3976631 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATAG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAAAAG
3976694 A
64 A
* * * * *
3976695 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTTGATCTTTTTATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
* * *
3976759 GTGCATTGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACTTGTGCATCGAT
3976788 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
63 1 0.01
64 67 0.87
65 9 0.12
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
Found at i:3976851 original size:21 final size:21
Alignment explanation
Indices: 3976825--3976877 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
3976815 ACCTTGATGA
3976825 ATCGATGCACTATGAATATGC
1 ATCGATGCACTATGAATATGC
3976846 ATCGATGCACTATGAATATGC
1 ATCGATGCACTATGAATATGC
3976867 ATCGATGCACT
1 ATCGATGCACT
3976878 CTGCCCAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (21 bp):
ATCGATGCACTATGAATATGC
Found at i:3983273 original size:94 final size:94
Alignment explanation
Indices: 3983112--3983491 Score: 674
Period size: 94 Copynumber: 4.1 Consensus size: 94
3983102 TAGATTGCTT
* * *
3983112 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTATTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3983177 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
3983206 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3983271 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
3983300 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3983365 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
3983394 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3983459 ATTTGTCTTTGTTTTGTCTTTTGGTT-AA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
3983487 AGTAA
1 AGTAA
3983492 TGCAATCCAT
Statistics
Matches: 279, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
93 27 0.10
94 252 0.90
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3983588 original size:19 final size:19
Alignment explanation
Indices: 3983548--3983694 Score: 144
Period size: 19 Copynumber: 7.9 Consensus size: 19
3983538 TGCGAAACTT
*
3983548 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
3983569 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
3983588 AAATTCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
3983607 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
3983626 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAATG
* **
3983640 AAAATCGCAACGTGAAACC
1 AAAATCGCAACGCGAAATG
3983659 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAA-TG
*
3983678 ATAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
3983695 CTATAATCGC
Statistics
Matches: 108, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 1 0.01
17 2 0.02
18 1 0.01
19 82 0.76
21 11 0.10
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:3983695 original size:19 final size:19
Alignment explanation
Indices: 3983539--3983704 Score: 141
Period size: 19 Copynumber: 8.8 Consensus size: 19
3983529 TAGTTTACTT
3983539 GCGAAACTTAAAATCGCAAC
1 GCGAAAC-TAAAATCGCAAC
* * **
3983559 GTGAAAAATGACTATCGCAAC
1 GCG-AAACT-AAAATCGCAAC
*
3983580 GCGAAA-TGAAATTCGCAAC
1 GCGAAACT-AAAATCGCAAC
3983599 GCGAAA-TGAAAATCGCAAC
1 GCGAAACT-AAAATCGCAAC
3983618 GCGAAA-TGAAAATCGCAA-
1 GCGAAACT-AAAATCGCAAC
3983636 -CG--AC-AAAATCGCAAC
1 GCGAAACTAAAATCGCAAC
* *
3983651 GTGAAACCAAAATCGCAAC
1 GCGAAACTAAAATCGCAAC
*
3983670 GCGAAACTATAATCGCAAC
1 GCGAAACTAAAATCGCAAC
*
3983689 GCGAAACTATAATCGC
1 GCGAAACTAAAATCGC
3983705 GTTGCGATTT
Statistics
Matches: 125, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.08
15 1 0.01
16 1 0.01
17 2 0.02
18 2 0.02
19 89 0.71
20 6 0.05
21 14 0.11
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (19 bp):
GCGAAACTAAAATCGCAAC
Found at i:3983723 original size:19 final size:19
Alignment explanation
Indices: 3983701--3983788 Score: 78
Period size: 19 Copynumber: 4.8 Consensus size: 19
3983691 GAAACTATAA
3983701 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3983720 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3983734 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3983753 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
3983774 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
3983789 AAGTTCCAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 9 0.17
16 3 0.06
17 3 0.06
19 24 0.45
21 14 0.26
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3985677 original size:14 final size:14
Alignment explanation
Indices: 3985658--3985693 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3985648 ATTGTTTAAT
3985658 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3985672 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3985686 TGATTTGT
1 TGATTTGT
3985694 TTAATTGATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3985847 original size:33 final size:33
Alignment explanation
Indices: 3985800--3985884 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
3985790 AAAAATGACT
* * *
3985800 ATCGTAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
*
3985833 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
*
3985866 ATCGCAACGCGAAACTAAA
1 ATCGCAATGCGAAA-TAAA
3985885 TTCGCGTTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 42 0.93
34 3 0.07
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATAAAAATCGCAACGACAAA
Found at i:3985948 original size:19 final size:19
Alignment explanation
Indices: 3985924--3986022 Score: 109
Period size: 19 Copynumber: 5.4 Consensus size: 19
3985914 GATTCCCTCG
3985924 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3985943 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3985957 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
3985976 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
*
3985996 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
3986015 TTGCGATT
1 TTGCGATT
3986023 CTCTCGTTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.11
17 7 0.11
19 29 0.45
20 16 0.25
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3986001 original size:20 final size:19
Alignment explanation
Indices: 3985955--3986057 Score: 63
Period size: 20 Copynumber: 5.6 Consensus size: 19
3985945 GCGATTCTCT
**
3985955 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
3985974 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
**
3985994 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
** *
3986013 TATTGCGAT--TC---TCT
1 CGTTGCGATAGTCATTTCG
*
3986027 CGTTGCGATAGTAATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
3986047 TGTTGCGATAG
1 CGTTGCGATAG
3986058 ATATTAAGAT
Statistics
Matches: 63, Mismatches: 14, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
14 9 0.14
16 1 0.02
17 2 0.03
19 24 0.38
20 27 0.43
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Done.