Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 24 of 195
Found at i:5542026 original size:22 final size:22
Alignment explanation
Indices: 5542000--5542082 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
5541990 AGTAATTATA
5542000 ATTTATTATCAAGTTATTATTG
1 ATTTATTATCAAGTTATTATTG
* * * * *
5542022 GTTTA-TATTAAATTGTTCA-TA
1 ATTTATTATCAAGTTATT-ATTG
5542043 ATTTATTATCAAGTTATTATTG
1 ATTTATTATCAAGTTATTATTG
* *
5542065 ATTAATTATTAAGTTATT
1 ATTTATTATCAAGTTATT
5542083 GATGATTAAC
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
21 15 0.33
22 31 0.67
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (22 bp):
ATTTATTATCAAGTTATTATTG
Found at i:5542088 original size:22 final size:22
Alignment explanation
Indices: 5542004--5542091 Score: 65
Period size: 22 Copynumber: 4.0 Consensus size: 22
5541994 ATTATAATTT
* *
5542004 ATTATCAAGTTATTATTGGTTT
1 ATTATCAAGTTATTATTGATTA
* * * * *
5542026 A-TATTAAATTGTTCA-TAATTT
1 ATTATCAAGTTATT-ATTGATTA
5542047 ATTATCAAGTTATTATTGATTA
1 ATTATCAAGTTATTATTGATTA
*
5542069 ATTATTAAGTTATTGA-TGATTA
1 ATTATCAAGTTATT-ATTGATTA
5542091 A
1 A
5542092 CTACTATTAA
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
21 15 0.29
22 35 0.69
23 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.51
Consensus pattern (22 bp):
ATTATCAAGTTATTATTGATTA
Found at i:5542178 original size:44 final size:44
Alignment explanation
Indices: 5542069--5542210 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 44
5542059 TTATTGATTA
* * * *
5542069 ATTATTAAGTTATTGATGATTAACTACTATTAAATTAT-GTTGATTT
1 ATTATTAAGTTTTTAATGATTAACTAC---TAAATTATCATTAATTT
* *
5542115 ATTTTTTA-TTTTTCAATGATTAACTACTAAATTATCATTAATTT
1 ATTATTAAGTTTTT-AATGATTAACTACTAAATTATCATTAATTT
* * * *
5542159 ATTATTAAGTTTTTTATGATTCACTACTTATTTATCAATTAA-TT
1 ATTATTAAGTTTTTAATGATTAACTACTAAATTATC-ATTAATTT
*
5542203 ACTATTAA
1 ATTATTAA
5542211 ATTAAAATTG
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
43 8 0.10
44 39 0.49
45 14 0.18
46 18 0.23
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.52
Consensus pattern (44 bp):
ATTATTAAGTTTTTAATGATTAACTACTAAATTATCATTAATTT
Found at i:5542223 original size:44 final size:44
Alignment explanation
Indices: 5542175--5542267 Score: 100
Period size: 44 Copynumber: 2.1 Consensus size: 44
5542165 AAGTTTTTTA
* *
5542175 TGATTCACTACTT-ATTTATCAATTAA-TTACTATTAAATTAAAAT
1 TGATTCACTA-TTAAGTTATC-ACTAATTTACTATTAAATTAAAAT
* * **
5542219 TGATTTACTATTAAGTTATCACTAATTTACTTTTAAATTATCAT
1 TGATTCACTATTAAGTTATCACTAATTTACTATTAAATTAAAAT
5542263 TGATT
1 TGATT
5542268 TCTTATTAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
43 6 0.15
44 35 0.85
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (44 bp):
TGATTCACTATTAAGTTATCACTAATTTACTATTAAATTAAAAT
Found at i:5542226 original size:22 final size:22
Alignment explanation
Indices: 5542201--5542276 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
5542191 TATCAATTAA
**
5542201 TTACTATTAAATTAAAATTGAT
1 TTACTATTAAATTATCATTGAT
* * *
5542223 TTACTATTAAGTTATCACTAAT
1 TTACTATTAAATTATCATTGAT
*
5542245 TTACTTTTAAATTATCATTGAT
1 TTACTATTAAATTATCATTGAT
5542267 TT-CTTATTAA
1 TTAC-TATTAA
5542277 GTTTTCAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 1 0.02
22 42 0.98
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (22 bp):
TTACTATTAAATTATCATTGAT
Found at i:5542654 original size:22 final size:22
Alignment explanation
Indices: 5542629--5542676 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5542619 GCTATTAATA
*
5542629 ATTTATTACTAATTTAT-AAATG
1 ATTTACTACTAATTTATGAAA-G
*
5542651 ATTTACTAGTAATTTATGAAAG
1 ATTTACTACTAATTTATGAAAG
5542673 ATTT
1 ATTT
5542677 GTCATTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (22 bp):
ATTTACTACTAATTTATGAAAG
Found at i:5542690 original size:33 final size:33
Alignment explanation
Indices: 5542653--5542721 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
5542643 TATAAATGAT
*
5542653 TTACTAGTAATTTATGAAAGATTTGTCATTAAG
1 TTACTAGTAATTTATGAAAGATTTATCATTAAG
*
5542686 TTACTATTAATTTATGAAAGATTTATCATTAAG
1 TTACTAGTAATTTATGAAAGATTTATCATTAAG
5542719 TTA
1 TTA
5542722 TGAATGATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.45
Consensus pattern (33 bp):
TTACTAGTAATTTATGAAAGATTTATCATTAAG
Found at i:5542716 original size:22 final size:22
Alignment explanation
Indices: 5542691--5542733 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5542681 TTAAGTTACT
*
5542691 ATTAATTTATGAAAGATTTATC
1 ATTAAGTTATGAAAGATTTATC
*
5542713 ATTAAGTTATGAATGATTTAT
1 ATTAAGTTATGAAAGATTTAT
5542734 GAATAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (22 bp):
ATTAAGTTATGAAAGATTTATC
Found at i:5542732 original size:33 final size:33
Alignment explanation
Indices: 5542653--5542736 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
5542643 TATAAATGAT
* *
5542653 TTACTAGTAATTTATGAAAGATTTGTCATTAAG
1 TTACTAATAATTTATGAAAGATTTATCATTAAG
*
5542686 TTACTATTAATTTATGAAAGATTTATCATTAAG
1 TTACTAATAATTTATGAAAGATTTATCATTAAG
*
5542719 TTA-TGAATGATTTATGAA
1 TTACT-AATAATTTATGAA
5542737 TAATTGTTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.02
33 45 0.98
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (33 bp):
TTACTAATAATTTATGAAAGATTTATCATTAAG
Found at i:5543191 original size:22 final size:22
Alignment explanation
Indices: 5543166--5543239 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
5543156 TGTCAATCTT
*
5543166 AGTTATTGATGATTTATTATAA
1 AGTTATTAATGATTTATTATAA
5543188 AGTTA-TAACTGATTTATTACTAA
1 AGTTATTAA-TGATTTATTA-TAA
* *
5543211 TA-TT-TTAATGATTTACTAAAA
1 -AGTTATTAATGATTTATTATAA
5543232 AGTTATTA
1 AGTTATTA
5543240 GTAATTAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
20 1 0.02
21 6 0.14
22 27 0.63
23 8 0.19
24 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.47
Consensus pattern (22 bp):
AGTTATTAATGATTTATTATAA
Found at i:5543276 original size:11 final size:11
Alignment explanation
Indices: 5543247--5543495 Score: 97
Period size: 11 Copynumber: 22.9 Consensus size: 11
5543237 TTAGTAATTA
5543247 ACTAATTTATT
1 ACTAATTTATT
*
5543258 ACTAAATTTATC
1 ACT-AATTTATT
*
5543270 ACTAATTTATA
1 ACTAATTTATT
*
5543281 ACTAAGTTATT
1 ACTAATTTATT
* *
5543292 AGTAATTTACT
1 ACTAATTTATT
*
5543303 A-TTATATTATT
1 ACTAAT-TTATT
* *
5543314 AGTAATTTACT
1 ACTAATTTATT
*
5543325 ACTAAGTTA-T
1 ACTAATTTATT
5543335 --TAATTTATT
1 ACTAATTTATT
* *
5543344 ACTAAATTATC
1 ACTAATTTATT
*
5543355 AATAATTTATT
1 ACTAATTTATT
5543366 A-TAATATTATT
1 ACTAAT-TTATT
*
5543377 ATATATATTTATT
1 A-CTA-ATTTATT
*
5543390 A-T-A-TTATC
1 ACTAATTTATT
* *
5543398 ATTAATTTACT
1 ACTAATTTATT
*
5543409 ATTTAATTT-TT
1 A-CTAATTTATT
* * *
5543420 AATTATTTATC
1 ACTAATTTATT
* *
5543431 A-TAAAATTATC
1 ACT-AATTTATT
*
5543442 ACTGATTTATT
1 ACTAATTTATT
*
5543453 ACTAAATTATCT
1 ACTAATTTAT-T
* *
5543465 A-TGATTTACT
1 ACTAATTTATT
*
5543475 ACTAAGTTATT
1 ACTAATTTATT
*
5543486 ACTATTTTAT
1 ACTAATTTAT
5543496 ATTAAATTAT
Statistics
Matches: 178, Mismatches: 41, Indels: 38
0.69 0.16 0.15
Matches are distributed among these distances:
8 11 0.06
9 3 0.02
10 17 0.10
11 114 0.64
12 23 0.13
13 8 0.04
14 2 0.01
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (11 bp):
ACTAATTTATT
Found at i:5543295 original size:53 final size:51
Alignment explanation
Indices: 5543193--5543311 Score: 134
Period size: 53 Copynumber: 2.3 Consensus size: 51
5543183 TATAAAGTTA
*
5543193 TAACTGATTTATTACTAATATTTTAATGATTTACTAAAAAGTTATTAGTAAT
1 TAACT-ATTTATTACTAATATTTTAATAATTTACTAAAAAGTTATTAGTAAT
* *
5543245 TAACTAATTTATTACTAA-ATTTATCACTAATTTA-TAACTAAGTTATTAGTAAT
1 TAACT-ATTTATTACTAATATTT-T-AATAATTTACTAA-AAAGTTATTAGTAAT
*
5543298 TTACTATTATATTA
1 TAACTATT-TATTA
5543312 TTAGTAATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
51 4 0.07
52 24 0.41
53 30 0.52
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (51 bp):
TAACTATTTATTACTAATATTTTAATAATTTACTAAAAAGTTATTAGTAAT
Found at i:5543300 original size:75 final size:74
Alignment explanation
Indices: 5543177--5543325 Score: 167
Period size: 75 Copynumber: 2.0 Consensus size: 74
5543167 GTTATTGATG
* * * *
5543177 ATTTATTATAAAGTTATAACTGATTTATTACTAATATTTTAATGATTTACTA-AAAAGTTATTAG
1 ATTTATTATAAAGTTATAACTAATTTATAACTAATATATTAATAATTTACTATAAAA-TTATTAG
5543241 TAATTAACTA
65 TAATTAACTA
* * * * *
5543251 ATTTATTACTAAATTTATCACTAATTTATAACTAAGT-TATTAGTAATTTACTATTATATTATTA
1 ATTTATTA-TAAAGTTATAACTAATTTATAACTAA-TATATTAATAATTTACTATAAAATTATTA
*
5543315 GTAATTTACTA
64 GTAATTAACTA
5543326 CTAAGTTATT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
74 8 0.13
75 51 0.82
76 3 0.05
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (74 bp):
ATTTATTATAAAGTTATAACTAATTTATAACTAATATATTAATAATTTACTATAAAATTATTAGT
AATTAACTA
Found at i:5543340 original size:19 final size:19
Alignment explanation
Indices: 5543311--5543353 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
5543301 CTATTATATT
*
5543311 ATTAGTAATTTACTACTAA
1 ATTATTAATTTACTACTAA
* *
5543330 GTTATTAATTTATTACTAA
1 ATTATTAATTTACTACTAA
5543349 ATTAT
1 ATTAT
5543354 CAATAATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49
Consensus pattern (19 bp):
ATTATTAATTTACTACTAA
Found at i:5543381 original size:13 final size:13
Alignment explanation
Indices: 5543359--5543393 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5543349 ATTATCAATA
5543359 ATTTATTATA-AT
1 ATTTATTATATAT
5543371 A-TTATTATATAT
1 ATTTATTATATAT
5543383 ATTTATTATAT
1 ATTTATTATAT
5543394 TATCATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.38
12 4 0.19
13 9 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTATTATATAT
Found at i:5543540 original size:22 final size:22
Alignment explanation
Indices: 5543247--5543578 Score: 132
Period size: 22 Copynumber: 15.3 Consensus size: 22
5543237 TTAGTAATTA
* * *
5543247 ACTAATTTATTACTAAATTTATC
1 ACTAATTTACTATTAAA-TTATT
* *
5543270 ACTAATTTA-TAACTAAGTTATT
1 ACTAATTTACT-ATTAAATTATT
* *
5543292 AGTAATTTACTATTATATTATT
1 ACTAATTTACTATTAAATTATT
* * *
5543314 AGTAATTTACTACTAAGTTA-T
1 ACTAATTTACTATTAAATTATT
* * *
5543335 --TAATTTATTACTAAATTATC
1 ACTAATTTACTATTAAATTATT
* *
5543355 AATAATTTATTA-TAATATTATT
1 ACTAATTTACTATTAA-ATTATT
* *
5543377 A-TATATATT--TATTATATTATC
1 ACTA-AT-TTACTATTAAATTATT
* * *
5543398 ATTAATTTACTATTTAATTTTT
1 ACTAATTTACTATTAAATTATT
* * * *
5543420 AATTATTTA-TCATAAAATTATC
1 ACTAATTTACT-ATTAAATTATT
* * *
5543442 ACTGATTTATTACTAAATTATCT
1 ACTAATTTACTATTAAATTAT-T
* * *
5543465 A-TGATTTACTACTAAGTTATT
1 ACTAATTTACTATTAAATTATT
*
5543486 ACTATTTTA-TATTAAATTA-T
1 ACTAATTTACTATTAAATTATT
* *
5543506 GCATTATTTACTATTAAATTATT
1 AC-TAATTTACTATTAAATTATT
* * * *
5543529 ACTAATTAACTATTATACTATC
1 ACTAATTTACTATTAAATTATT
* * * *
5543551 AATGATTTACCACTAAATTA-T
1 ACTAATTTACTATTAAATTATT
5543572 ACTAATT
1 ACTAATT
5543579 AACTTTTTTT
Statistics
Matches: 235, Mismatches: 55, Indels: 40
0.71 0.17 0.12
Matches are distributed among these distances:
19 16 0.07
20 4 0.02
21 37 0.16
22 157 0.67
23 21 0.09
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (22 bp):
ACTAATTTACTATTAAATTATT
Found at i:5543551 original size:109 final size:109
Alignment explanation
Indices: 5543337--5543571 Score: 246
Period size: 109 Copynumber: 2.2 Consensus size: 109
5543327 TAAGTTATTA
* *
5543337 ATTTATTACTAAATTATCAATAATTTATTATAATATTATTATATATATTTATTATATTATCATTA
1 ATTTATTACTAAATTATCAATAATTTACTATAATATTATTATATATATTTATTAAATTATCATTA
* * * * * *
5543402 ATTTACTATTTAATTTTTAATTATTTATCATAAAATTATCACTG
66 ATTTACTATTAAATTATTAATAATTAATCATAAAACTATCAATG
* * *
5543446 ATTTATTACTAAATTATCTATGATTTACTACTAA-GTTATTACTAT-T-TTATATTAAATTATGC
1 ATTTATTACTAAATTATCAATAATTTACTA-TAATATTATTA-TATATATT-TATTAAATTAT-C
* * *
5543508 ATT-ATTTACTATTAAATTATTACTAATTAA-CTATTATACTATCAATG
62 ATTAATTTACTATTAAATTATTAATAATTAATC-ATAAAACTATCAATG
**
5543555 ATTTACCACTAAATTAT
1 ATTTATTACTAAATTAT
5543572 ACTAATTAAC
Statistics
Matches: 105, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
108 3 0.03
109 92 0.88
110 10 0.10
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (109 bp):
ATTTATTACTAAATTATCAATAATTTACTATAATATTATTATATATATTTATTAAATTATCATTA
ATTTACTATTAAATTATTAATAATTAATCATAAAACTATCAATG
Found at i:5543651 original size:22 final size:22
Alignment explanation
Indices: 5543623--5543671 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
5543613 AATTAATTAC
5543623 TATTAAACTGA-AACTAATTTAT
1 TATTAAA-TGATAACTAATTTAT
* *
5543645 TATTAAATTATCACTAATTTAT
1 TATTAAATGATAACTAATTTAT
5543667 TATTA
1 TATTA
5543672 GGTTATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTAAATGATAACTAATTTAT
Found at i:5543717 original size:22 final size:22
Alignment explanation
Indices: 5543637--5543719 Score: 85
Period size: 22 Copynumber: 3.8 Consensus size: 22
5543627 AAACTGAAAC
* * *
5543637 TAATTTATTATTAAATTATCAC
1 TAATTTATTATTAAGTTATTAA
* *
5543659 TAATTTATTATTAGGTTATTAT
1 TAATTTATTATTAAGTTATTAA
* * *
5543681 TCATTTATTACTAAGTTTTTAA
1 TAATTTATTATTAAGTTATTAA
*
5543703 TAATTAATTATTAAGTT
1 TAATTTATTATTAAGTT
5543720 GTCATTTATT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (22 bp):
TAATTTATTATTAAGTTATTAA
Found at i:5543820 original size:22 final size:22
Alignment explanation
Indices: 5543753--5543821 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
5543743 TTCTTAACTG
*
5543753 TTATACATTTATAATTATATTA
1 TTATATATTTATAATTATATTA
* ** *
5543775 TAAT-TGATTTACCATTAAATTA
1 TTATAT-ATTTATAATTATATTA
*
5543797 TTATATATTTATTATTATATTA
1 TTATATATTTATAATTATATTA
5543819 TTA
1 TTA
5543822 CTAATTCACT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
22 35 0.97
23 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (22 bp):
TTATATATTTATAATTATATTA
Found at i:5543860 original size:66 final size:66
Alignment explanation
Indices: 5543779--5543916 Score: 179
Period size: 66 Copynumber: 2.1 Consensus size: 66
5543769 ATATTATAAT
* * *
5543779 TGATTTACCATTAAATTATTATAT-ATTTATTATTATATTATTACTAATTCACTAAAAAGTTATC
1 TGATTAACTATTAAATTATTAT-TCATTTATTATTAAATTATTACTAATTCACTAAAAAGTTATC
5543843 AA
65 AA
* * * ** *
5543845 TTATTAACTATTAAATTATTATTCATTTATTATTAAATTATTATTAATTTACTACTAAGTTGTCA
1 TGATTAACTATTAAATTATTATTCATTTATTATTAAATTATTACTAATTCACTAAAAAGTTATCA
5543910 A
66 A
5543911 TGATTA
1 TGATTA
5543917 TTACTAAATT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
65 1 0.02
66 60 0.98
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (66 bp):
TGATTAACTATTAAATTATTATTCATTTATTATTAAATTATTACTAATTCACTAAAAAGTTATCA
A
Found at i:5543874 original size:11 final size:11
Alignment explanation
Indices: 5543853--5543895 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
5543843 AATTATTAAC
*
5543853 TATTAAATTAT
1 TATTAATTTAT
*
5543864 TATTCATTTAT
1 TATTAATTTAT
*
5543875 TATTAAATTAT
1 TATTAATTTAT
5543886 TATTAATTTA
1 TATTAATTTA
5543896 CTACTAAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTAATTTAT
Found at i:5543886 original size:22 final size:21
Alignment explanation
Indices: 5543766--5543898 Score: 97
Period size: 22 Copynumber: 6.0 Consensus size: 21
5543756 TACATTTATA
* * *
5543766 ATTATATTATAATTGATTTACC
1 ATTAAATTATTATT-ATTTACT
*
5543788 ATTAAATTATTATATATTTATT
1 ATTAAATTATTAT-TATTTACT
* * *
5543810 ATTATATTATTACTAATTCACT
1 ATTAAATTATTA-TTATTTACT
* * *
5543832 A-AAAAGTTATCAATTATTAACT
1 ATTAAA-TTAT-TATTATTTACT
*
5543854 ATTAAATTATTATTCATTTATT
1 ATTAAATTATTATT-ATTTACT
5543876 ATTAAATTATTATTAATTTACT
1 ATTAAATTATTATT-ATTTACT
5543898 A
1 A
5543899 CTAAGTTGTC
Statistics
Matches: 86, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
21 5 0.06
22 75 0.87
23 6 0.07
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTAAATTATTATTATTTACT
Found at i:5546158 original size:17 final size:17
Alignment explanation
Indices: 5546138--5546171 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5546128 TATTTAAATT
5546138 TTTTTATTATACATAAA
1 TTTTTATTATACATAAA
*
5546155 TTTTTATTATATATAAA
1 TTTTTATTATACATAAA
5546172 AACATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTATTATACATAAA
Found at i:5547222 original size:17 final size:18
Alignment explanation
Indices: 5547202--5547237 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
5547192 ATTTGTATTT
5547202 TCATTTTA-TATGAAAAA
1 TCATTTTACTATGAAAAA
5547219 TCATTTTACTTATGAAAAA
1 TCATTTTAC-TATGAAAAA
5547238 GAGTGTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
19 9 0.53
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (18 bp):
TCATTTTACTATGAAAAA
Found at i:5558438 original size:22 final size:22
Alignment explanation
Indices: 5558399--5558440 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5558389 GAAATAAAAT
* *
5558399 GAAAGAAAATAGTAATTTTTAA
1 GAAAGAAAAGAATAATTTTTAA
*
5558421 GAAAGAAAAGAATTATTTTT
1 GAAAGAAAAGAATAATTTTT
5558441 TATTTTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.33
Consensus pattern (22 bp):
GAAAGAAAAGAATAATTTTTAA
Found at i:5568366 original size:15 final size:16
Alignment explanation
Indices: 5568346--5568375 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5568336 AAAAAAATAT
5568346 AAATAC-GTTTTTTTA
1 AAATACAGTTTTTTTA
5568361 AAATACAGTTTTTTT
1 AAATACAGTTTTTTT
5568376 TTGTATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (16 bp):
AAATACAGTTTTTTTA
Found at i:5568388 original size:16 final size:16
Alignment explanation
Indices: 5568369--5568402 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5568359 TAAAATACAG
*
5568369 TTTTTTT-TTGTATTA
1 TTTTTTTATCGTATTA
5568384 TTTTTTTATCGTATTA
1 TTTTTTTATCGTATTA
5568400 TTT
1 TTT
5568403 GTGTCGTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTTTTATCGTATTA
Found at i:5570439 original size:39 final size:39
Alignment explanation
Indices: 5570364--5570444 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 39
5570354 GCTGCACCTC
* ** *
5570364 CTTTTCTCTTGCACTTTCTGTTGAATGAGCAGAATCAGG
1 CTTTTCTCTTGCACTTTCTATTGAACCAGCAGAATCAAG
* * *
5570403 CTTTTCTGTTTCACTTTCTATTGAACCAGCATAATCAAG
1 CTTTTCTCTTGCACTTTCTATTGAACCAGCAGAATCAAG
5570442 CTT
1 CTT
5570445 CGCACTTGGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (39 bp):
CTTTTCTCTTGCACTTTCTATTGAACCAGCAGAATCAAG
Found at i:5572300 original size:2 final size:2
Alignment explanation
Indices: 5572293--5572327 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5572283 ATTTGTATTT
*
5572293 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5572328 AAAAATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5572365 original size:31 final size:31
Alignment explanation
Indices: 5572315--5572384 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
5572305 CATATATATA
*
5572315 TATATATAATATAAAAAATTTTATATTTTAATT
1 TATAT-TAATATAAAAAATTTCAT-TTTTAATT
* *
5572348 TATATTAATAT-ATAAATTTCATTTTTTATT
1 TATATTAATATAAAAAATTTCATTTTTAATT
*
5572378 TTTATTA
1 TATATTA
5572385 TACTTATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 13 0.39
31 9 0.27
32 6 0.18
33 5 0.15
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (31 bp):
TATATTAATATAAAAAATTTCATTTTTAATT
Found at i:5572442 original size:13 final size:12
Alignment explanation
Indices: 5572424--5572482 Score: 54
Period size: 13 Copynumber: 5.0 Consensus size: 12
5572414 ATAATATCAC
5572424 TTTTATATATAT
1 TTTTATATATAT
5572436 TTATTAT-TATTAT
1 TT-TTATATA-TAT
*
5572449 TTTCATAT-T-T
1 TTTTATATATAT
5572459 TTTTATAT-TAT
1 TTTTATATATAT
5572470 TTTTATATTATAT
1 TTTTATA-TATAT
5572483 CATTTAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
10 9 0.23
11 9 0.23
12 8 0.21
13 13 0.33
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTATATATAT
Found at i:5572456 original size:21 final size:21
Alignment explanation
Indices: 5572432--5572478 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5572422 ACTTTTATAT
5572432 ATATTTATTAT-TATTATTTTC
1 ATATTT-TTATATATTATTTTC
* *
5572453 ATATTTTTTTATATTATTTTT
1 ATATTTTTATATATTATTTTC
5572474 ATATT
1 ATATT
5572479 ATATCATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
ATATTTTTATATATTATTTTC
Found at i:5572479 original size:11 final size:11
Alignment explanation
Indices: 5572424--5572480 Score: 71
Period size: 11 Copynumber: 5.0 Consensus size: 11
5572414 ATAATATCAC
5572424 TTTTATATATAT
1 TTTTATAT-TAT
5572436 TTATTATTATTAT
1 TT-TTA-TATTAT
*
5572449 TTTCATATT-T
1 TTTTATATTAT
5572459 TTTTATATTAT
1 TTTTATATTAT
5572470 TTTTATATTAT
1 TTTTATATTAT
5572481 ATCATTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 9 0.22
11 16 0.40
12 4 0.10
13 8 0.20
14 3 0.08
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:5576986 original size:70 final size:70
Alignment explanation
Indices: 5576897--5577040 Score: 236
Period size: 70 Copynumber: 2.1 Consensus size: 70
5576887 TAATATAATA
*
5576897 AAAATACTATTTAACATATTATTT-TTACTTTTTACTTTTTTATTTTATTAACAAAATTATTATT
1 AAAAGACTATTTAACATATT-TTTGTTACTTTTTACTTTTTTATTTTATTAACAAAATTATTATT
5576961 TATCAT
65 TATCAT
* * *
5576967 AAAAGACTATTTAATATATTTTTGTTATTTTTTATTTTTTTATTTTATTAACAAAATTATTATTT
1 AAAAGACTATTTAACATATTTTTGTTACTTTTTACTTTTTTATTTTATTAACAAAATTATTATTT
5577032 ATCAT
66 ATCAT
5577037 AAAA
1 AAAA
5577041 ATATTTTTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 3 0.04
70 66 0.96
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (70 bp):
AAAAGACTATTTAACATATTTTTGTTACTTTTTACTTTTTTATTTTATTAACAAAATTATTATTT
ATCAT
Found at i:5577050 original size:70 final size:68
Alignment explanation
Indices: 5576894--5577075 Score: 224
Period size: 70 Copynumber: 2.6 Consensus size: 68
5576884 CTTTAATATA
* * *
5576894 ATAAAAATACTATTTAACATATTATTTTTACTTTTTACTTTTTTATTTTATTAACAAAATTATTA
1 ATAAAAATA-T-TTTAAAATATT-TTTTTATTTTTTAATTTTTTATTTTATTAACAAAATTATTA
5576959 TTTATC
63 TTTATC
* *
5576965 ATAAAAGACTA-TTTAATATATTTTTGTTATTTTTTATTTTTTTATTTTATTAACAAAATTATTA
1 ATAAAA-A-TATTTTAAAATATTTTT-TTATTTTTTAATTTTTTATTTTATTAACAAAATTATTA
5577029 TTTATC
63 TTTATC
*
5577035 ATAAAAATATTTTTAAAAT-TTTTTATTATTTATTAATTTTT
1 ATAAAAATA-TTTTAAAATATTTTT-TTATTTTTTAATTTTT
5577076 ATAAGTTAAA
Statistics
Matches: 99, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
68 2 0.02
69 23 0.23
70 65 0.66
71 6 0.06
72 1 0.01
73 2 0.02
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.58
Consensus pattern (68 bp):
ATAAAAATATTTTAAAATATTTTTTTATTTTTTAATTTTTTATTTTATTAACAAAATTATTATTT
ATC
Found at i:5577296 original size:38 final size:39
Alignment explanation
Indices: 5577229--5577316 Score: 160
Period size: 38 Copynumber: 2.3 Consensus size: 39
5577219 TCACTATAGT
*
5577229 AACTAATCACATCTCTACTATTGTTTTTAATCTTACTGA
1 AACTAATCTCATCTCTACTATTGTTTTTAATCTTACTGA
5577268 AACTAATCTCATCTC-ACTATTGTTTTTAATCTTACTGA
1 AACTAATCTCATCTCTACTATTGTTTTTAATCTTACTGA
5577306 AACTAATCTCA
1 AACTAATCTCA
5577317 CAATCTATCC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 34 0.71
39 14 0.29
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.42
Consensus pattern (39 bp):
AACTAATCTCATCTCTACTATTGTTTTTAATCTTACTGA
Found at i:5580025 original size:2 final size:2
Alignment explanation
Indices: 5580020--5580044 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5580010 TGTGTGTGTT
5580020 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 T
5580045 TTCAAAGGCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5582861 original size:44 final size:44
Alignment explanation
Indices: 5582807--5582890 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
5582797 CCAGTTGGAT
* *
5582807 GAAAATTAAGTGTTACACCA-TAGGAGCCACTTCTAAAATCCTAC
1 GAAAACTAAGTGTTACA-CAGTAGGAACCACTTCTAAAATCCTAC
* *
5582851 GAAAACTAAGTGTTATACAGTAGGAACCACTTCTAGAATC
1 GAAAACTAAGTGTTACACAGTAGGAACCACTTCTAAAATC
5582891 TCAACATTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 2 0.06
44 33 0.94
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.25
Consensus pattern (44 bp):
GAAAACTAAGTGTTACACAGTAGGAACCACTTCTAAAATCCTAC
Found at i:5584677 original size:13 final size:13
Alignment explanation
Indices: 5584659--5584683 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5584649 TAGGATAGAT
5584659 ATCATAAATGTTA
1 ATCATAAATGTTA
5584672 ATCATAAATGTT
1 ATCATAAATGTT
5584684 TCTAAGCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
ATCATAAATGTTA
Found at i:5585851 original size:51 final size:51
Alignment explanation
Indices: 5585788--5585893 Score: 160
Period size: 51 Copynumber: 2.1 Consensus size: 51
5585778 TGAATAAAAT
* * *
5585788 AATAACAGAATATACCTCGCACCGTCCATCAAATAGAA-TATTAATTAATTG
1 AATAACAGAATATACCTAGCACCGTCCATCAAATA-AAGAATCAATTAATTG
*
5585839 AATAACAGAATATACCTAGCATCGTCCATCAAATAAAGAATCAATTAATTG
1 AATAACAGAATATACCTAGCACCGTCCATCAAATAAAGAATCAATTAATTG
5585890 AATA
1 AATA
5585894 GTGATTAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
50 2 0.04
51 48 0.96
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.26
Consensus pattern (51 bp):
AATAACAGAATATACCTAGCACCGTCCATCAAATAAAGAATCAATTAATTG
Found at i:5593087 original size:17 final size:18
Alignment explanation
Indices: 5593057--5593098 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
5593047 TCTATACAAA
5593057 AAATATATATATACCAATC
1 AAAT-TATATATACCAATC
* *
5593076 AAATTATA-ATACCCATG
1 AAATTATATATACCAATC
5593093 AAATTA
1 AAATTA
5593099 AAAAACCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 13 0.62
18 4 0.19
19 4 0.19
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATTATATATACCAATC
Found at i:5594342 original size:22 final size:22
Alignment explanation
Indices: 5594300--5594344 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5594290 TATAAAATAA
** *
5594300 AATGTTTAATCTTAAATTAAGT
1 AATGTTTAATCCCAAACTAAGT
5594322 AATGTTTAATCCCAAACTAAGT
1 AATGTTTAATCCCAAACTAAGT
5594344 A
1 A
5594345 TTTAGCCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (22 bp):
AATGTTTAATCCCAAACTAAGT
Found at i:5601504 original size:2 final size:2
Alignment explanation
Indices: 5601497--5601538 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5601487 CAATCGGTCT
5601497 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5601538 T
1 T
5601539 TGGGTTTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5601589 original size:22 final size:21
Alignment explanation
Indices: 5601563--5601604 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5601553 TTAACCCTTA
*
5601563 TTATTTTTATTCTTATTATTTC
1 TTATTTTGATT-TTATTATTTC
*
5601585 TTATTTTGATTTTTTTATTT
1 TTATTTTGATTTTATTATTT
5601605 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (21 bp):
TTATTTTGATTTTATTATTTC
Found at i:5601670 original size:31 final size:31
Alignment explanation
Indices: 5601625--5601690 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
5601615 TTAACCTTTA
*
5601625 TTTACTCTTATTTTGATTTTGATT-TTATTTT
1 TTTACTCTTATTTTG-TTTTGATTATGATTTT
*
5601656 TTTACTTCTT-TTTTGTTTTTATTATGATTTT
1 TTTAC-TCTTATTTTGTTTTGATTATGATTTT
5601687 TTTA
1 TTTA
5601691 AAAAAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 7 0.23
31 20 0.65
32 4 0.13
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (31 bp):
TTTACTCTTATTTTGTTTTGATTATGATTTT
Found at i:5603438 original size:15 final size:16
Alignment explanation
Indices: 5603418--5603451 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5603408 TTAATTTAAA
*
5603418 AATATAAAA-ATTTAT
1 AATATAAAATAATTAT
5603433 AATATAAAATAATTAT
1 AATATAAAATAATTAT
5603449 AAT
1 AAT
5603452 TTTAAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATAAAATAATTAT
Found at i:5608541 original size:47 final size:47
Alignment explanation
Indices: 5608472--5608565 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
5608462 TTAGCAACAA
5608472 TTAAGCAAATGCAATAGGACAATCG-GGGAAATGTGGGAATCAAAGGG
1 TTAAGCAAATGCAATAGGACAAT-GTGGGAAATGTGGGAATCAAAGGG
5608519 TTAAGCAAATGCAATAGGACAATGTGGGAAATGTGGGAATCAAAGGG
1 TTAAGCAAATGCAATAGGACAATGTGGGAAATGTGGGAATCAAAGGG
5608566 GGTACCTTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 1 0.02
47 45 0.98
ACGTcount: A:0.40, C:0.10, G:0.32, T:0.18
Consensus pattern (47 bp):
TTAAGCAAATGCAATAGGACAATGTGGGAAATGTGGGAATCAAAGGG
Found at i:5617887 original size:23 final size:24
Alignment explanation
Indices: 5617854--5617933 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 24
5617844 TATATATATA
5617854 TTTATATATAATTAGTAAATAATT-T
1 TTTATA-ATAATTA-TAAATAATTAT
*
5617879 TTTA-AATAA-TATAAATTATTAT
1 TTTATAATAATTATAAATAATTAT
*
5617901 TTTATATTAATTA-AAATTAATATATT
1 TTTATAATAATTATAAA-TAAT-TA-T
5617927 TTTATAA
1 TTTATAA
5617934 AAAATATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
21 8 0.18
22 7 0.16
23 11 0.24
24 6 0.13
25 6 0.13
26 7 0.16
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
TTTATAATAATTATAAATAATTAT
Found at i:5618085 original size:6 final size:6
Alignment explanation
Indices: 5618074--5618103 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5618064 TATATATGAG
5618074 AATAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA
5618104 TTTAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:5627116 original size:56 final size:57
Alignment explanation
Indices: 5627055--5627176 Score: 147
Period size: 60 Copynumber: 2.1 Consensus size: 57
5627045 TACTTTATAA
* *
5627055 ATAAGC-ATGCATCTTTCACTCTTAAAAACCTAAGTCAGTAACCATTTTTAAATATG
1 ATAAGCAATACATCCTTCACTCTTAAAAACCTAAGTCAGTAACCATTTTTAAATATG
* * * * *
5627111 ATAAGCAAGTATATATCCTTCACTTTTAAAAACTTAAGTCAGTAGCTATTTTTAAATATG
1 ATAAGC-A--ATACATCCTTCACTCTTAAAAACCTAAGTCAGTAACCATTTTTAAATATG
5627171 ATAAGC
1 ATAAGC
5627177 TCTTTAAGAG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
56 6 0.11
60 49 0.89
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (57 bp):
ATAAGCAATACATCCTTCACTCTTAAAAACCTAAGTCAGTAACCATTTTTAAATATG
Found at i:5628135 original size:30 final size:31
Alignment explanation
Indices: 5628068--5628145 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 31
5628058 TATTATTTTT
* * *
5628068 TTAAATAAATTGTTATATTTTTATTGTATCA
1 TTAAATAAATTATTATTTTTTTATTGTATAA
5628099 --AAATAAA-TATTTATTTTTTTATT-TATAA
1 TTAAATAAATTA-TTATTTTTTTATTGTATAA
5628127 TTAAATAAATTATTATTTT
1 TTAAATAAATTATTATTTT
5628146 AAATAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
28 5 0.12
29 19 0.47
30 14 0.35
31 2 0.05
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (31 bp):
TTAAATAAATTATTATTTTTTTATTGTATAA
Found at i:5628188 original size:18 final size:18
Alignment explanation
Indices: 5628133--5628188 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 18
5628123 ATAATTAAAT
5628133 AAATTATTATTTTAAATA-A
1 AAATT-TTA-TTTAAATATA
* *
5628152 AAATTTAATTTATAT-TA
1 AAATTTTATTTAAATATA
*
5628169 AAATTTTATTTAGATATA
1 AAATTTTATTTAAATATA
5628187 AA
1 AA
5628189 TTAAAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 20 0.65
18 6 0.19
19 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AAATTTTATTTAAATATA
Found at i:5628199 original size:30 final size:29
Alignment explanation
Indices: 5628165--5628296 Score: 119
Period size: 30 Copynumber: 4.4 Consensus size: 29
5628155 TTTAATTTAT
5628165 ATTAAAATTTTATTTAGATATAAATTAAAA
1 ATTAAAA-TTTATTTAGATATAAATTAAAA
* *
5628195 ATTAAAGATCTATTTAAATATAAATTAAAA
1 ATTAAA-ATTTATTTAGATATAAATTAAAA
* *
5628225 GTTAAAATTTTATTT-GAGTGTAAATTAAAA
1 ATTAAAA-TTTATTTAGA-TATAAATTAAAA
*
5628255 ATCAATAATTTATTTA-A-ATACAA-TAAAA
1 ATTAA-AATTTATTTAGATATA-AATTAAAA
5628283 ATATAAAAATTTAT
1 AT-T-AAAATTTAT
5628297 CGAAGTAATT
Statistics
Matches: 84, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
28 9 0.11
29 11 0.13
30 61 0.73
31 3 0.04
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (29 bp):
ATTAAAATTTATTTAGATATAAATTAAAA
Found at i:5628292 original size:60 final size:61
Alignment explanation
Indices: 5628167--5628296 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 61
5628157 TAATTTATAT
* *
5628167 TAAAATTTTATTTAGATATAAATTAAAAATTAAAGATCTATTTAAATATAAATTAAAAGT-
1 TAAAATTTTATTTAGATATAAATTAAAAATCAAAGATCTATTTAAATATAAATTAAAAATA
* * *
5628227 TAAAATTTTATTT-GAGTGTAAATTAAAAATCAATA-ATTTATTTAAATA-CAA-TAAAAATA
1 TAAAATTTTATTTAGA-TATAAATTAAAAATCAA-AGATCTATTTAAATATAAATTAAAAATA
*
5628286 TAAAAATTTAT
1 TAAAATTTTAT
5628297 CGAAGTAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
58 6 0.10
59 14 0.23
60 40 0.66
61 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (61 bp):
TAAAATTTTATTTAGATATAAATTAAAAATCAAAGATCTATTTAAATATAAATTAAAAATA
Found at i:5628440 original size:11 final size:11
Alignment explanation
Indices: 5628424--5628448 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5628414 ATAGAGTAAC
5628424 ATAATATAAAA
1 ATAATATAAAA
5628435 ATAATATAAAA
1 ATAATATAAAA
5628446 ATA
1 ATA
5628449 TAATATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:5628453 original size:13 final size:12
Alignment explanation
Indices: 5628424--5628456 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
5628414 ATAGAGTAAC
5628424 ATAATAT-AAAA
1 ATAATATAAAAA
5628435 ATAATATAAAAA
1 ATAATATAAAAA
5628447 TATAATATAA
1 -ATAATATAA
5628457 TTTAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 4 0.20
13 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAATATAAAAA
Found at i:5647052 original size:17 final size:17
Alignment explanation
Indices: 5647032--5647066 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5647022 TAGAATTCTA
*
5647032 AATAAAAATCCCCAGGC
1 AATAAAAATCCACAGGC
*
5647049 AATAATAATCCACAGGC
1 AATAAAAATCCACAGGC
5647066 A
1 A
5647067 GTTCCATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.26, G:0.11, T:0.14
Consensus pattern (17 bp):
AATAAAAATCCACAGGC
Found at i:5651775 original size:35 final size:34
Alignment explanation
Indices: 5651736--5651817 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 34
5651726 TATTTGAACT
5651736 AGAAAATAAAAATAATCTAT-TAAATTTATTATCAA
1 AGAAAATAAAAA-AATCTATATAAATTTA-TATCAA
* * * *
5651771 AGAAAATTAAAAAATTTATATTAATTTATATTAA
1 AGAAAATAAAAAAATCTATATAAATTTATATCAA
5651805 A-AAAATAAAAAAA
1 AGAAAATAAAAAAA
5651818 ATAAAATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 11 0.27
34 12 0.29
35 18 0.44
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (34 bp):
AGAAAATAAAAAAATCTATATAAATTTATATCAA
Found at i:5659180 original size:11 final size:11
Alignment explanation
Indices: 5659161--5659228 Score: 51
Period size: 11 Copynumber: 6.8 Consensus size: 11
5659151 AATTTAAAAT
5659161 TTTAA-ATATA
1 TTTAATATATA
5659171 TTTAATATATA
1 TTTAATATATA
**
5659182 TACAA-A-AT-
1 TTTAATATATA
5659190 TTT-A-A-ATA
1 TTTAATATATA
*
5659198 TTAAATATATA
1 TTTAATATATA
5659209 TTTAATATATA
1 TTTAATATATA
*
5659220 TTTAGTATA
1 TTTAATATA
5659229 GAAAAATAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
7 4 0.09
8 3 0.07
9 3 0.07
10 7 0.15
11 29 0.63
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (11 bp):
TTTAATATATA
Found at i:5659206 original size:27 final size:29
Alignment explanation
Indices: 5659156--5659209 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
5659146 AATTTAATTT
*
5659156 AAAATTTTAAATATATTTAATATATATAC
1 AAAATTTTAAATATATTAAATATATATAC
5659185 AAAATTTT-AA-ATATTAAATATATAT
1 AAAATTTTAAATATATTAAATATATAT
5659210 TTAATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.58
28 2 0.08
29 8 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAATTTTAAATATATTAAATATATATAC
Found at i:5660111 original size:11 final size:11
Alignment explanation
Indices: 5660073--5660111 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5660063 GATATGATTT
5660073 AAAATTTTAATA
1 AAAATTTT-ATA
*
5660085 AAAATTATATA
1 AAAATTTTATA
*
5660096 TAAATTTTATA
1 AAAATTTTATA
5660107 AAAAT
1 AAAAT
5660112 AAAAAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATTTTATA
Found at i:5662372 original size:21 final size:20
Alignment explanation
Indices: 5662330--5662392 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 20
5662320 TTATCTAATC
5662330 AAAAAAATAAATAAAG-GAAA
1 AAAAAAATAAA-AAAGAGAAA
5662350 AATAAAAATAAAAAAGATGAAA
1 AA-AAAAATAAAAAAGA-GAAA
5662372 AAACAAAA-AAAAGAA-AGAAA
1 AAA-AAAATAAAA-AAGAGAAA
5662392 A
1 A
5662393 TCAAGTTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
20 11 0.29
21 15 0.39
22 12 0.32
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.08
Consensus pattern (20 bp):
AAAAAAATAAAAAAGAGAAA
Found at i:5662373 original size:23 final size:22
Alignment explanation
Indices: 5662332--5662389 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
5662322 ATCTAATCAA
* *
5662332 AAAAATAAATAAAG-GAAAAAT
1 AAAAATAAAGAAAGAGAAAAAC
5662353 AAAAATAAA-AAAGATGAAAAAAC
1 AAAAATAAAGAAAGA-G-AAAAAC
5662376 AAAAA-AAAGAAAGA
1 AAAAATAAAGAAAGA
5662390 AAATCAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.12
21 9 0.28
22 4 0.12
23 15 0.47
ACGTcount: A:0.79, C:0.02, G:0.10, T:0.09
Consensus pattern (22 bp):
AAAAATAAAGAAAGAGAAAAAC
Found at i:5662667 original size:16 final size:16
Alignment explanation
Indices: 5662647--5662676 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5662637 AGCATGACCA
5662647 AAAAAATTTA-AAATT
1 AAAAAATTTATAAATT
5662662 AAAAAATTTATAAAT
1 AAAAAATTTATAAAT
5662677 ATATAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAAATTTATAAATT
Found at i:5662754 original size:7 final size:7
Alignment explanation
Indices: 5662742--5662771 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5662732 AAATCTTTTT
5662742 AAAAAGA
1 AAAAAGA
5662749 AAAAAGA
1 AAAAAGA
5662756 AAAAA-A
1 AAAAAGA
5662762 AAAAAGA
1 AAAAAGA
5662769 AAA
1 AAA
5662772 CTTGATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:5662764 original size:13 final size:13
Alignment explanation
Indices: 5662742--5662771 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5662732 AAATCTTTTT
*
5662742 AAAAAGAAAAAAG
1 AAAAAAAAAAAAG
5662755 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
5662768 AAAA
1 AAAA
5662772 CTTGATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:5663697 original size:35 final size:35
Alignment explanation
Indices: 5663657--5663727 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
5663647 TAAAGAGGGG
5663657 TCCTAAGATTAACTTAGATATCTTTAAATAATAGA
1 TCCTAAGATTAACTTAGATATCTTTAAATAATAGA
5663692 TCCTAAGATTAACTTAGATATCTTTAAATAATAGA
1 TCCTAAGATTAACTTAGATATCTTTAAATAATAGA
5663727 T
1 T
5663728 TTTGATCCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.38
Consensus pattern (35 bp):
TCCTAAGATTAACTTAGATATCTTTAAATAATAGA
Found at i:5666917 original size:30 final size:30
Alignment explanation
Indices: 5666783--5666918 Score: 122
Period size: 29 Copynumber: 4.6 Consensus size: 30
5666773 GCTTTTAGGT
* * * *
5666783 TTTGATTTTAGGTTTTGGA-TGTTTAGGGT
1 TTTGATTTTAGGGTTTGAAGGGTTTAGGGA
* **
5666812 TTTAATTTTAAGACTTTG-AGGGTTTA-GGA
1 TTTGATTTT-AGGGTTTGAAGGGTTTAGGGA
5666841 TTT-AGTTTTAGGGTTT-ATAGGGTTTAGGGA
1 TTTGA-TTTTAGGGTTTGA-AGGGTTTAGGGA
*
5666871 TTTG-TTTTATGGTTTGAAGGGTTTAGGGA
1 TTTGATTTTAGGGTTTGAAGGGTTTAGGGA
*
5666900 TTTGATTTCAGGGTTTGAA
1 TTTGATTTTAGGGTTTGAA
5666919 ATGTTTTAGG
Statistics
Matches: 88, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
28 6 0.07
29 52 0.59
30 30 0.34
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (30 bp):
TTTGATTTTAGGGTTTGAAGGGTTTAGGGA
Found at i:5667146 original size:3 final size:3
Alignment explanation
Indices: 5667138--5667189 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
5667128 TTATGAAAAT
5667138 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5667186 TTA T
1 TTA T
5667190 ACTTTTTATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5667204 original size:15 final size:15
Alignment explanation
Indices: 5667150--5667216 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
5667140 ATTATTATTA
*
5667150 TTATTATTATTA-TTA
1 TTATTATTA-TACTTT
*
5667165 TTATTATTATTA-TTA
1 TTATTATTA-TACTTT
5667180 TTATTATTATACTTT
1 TTATTATTATACTTT
* *
5667195 TTATTGTTATGCTTT
1 TTATTATTATACTTT
*
5667210 TTTTTAT
1 TTATTAT
5667217 ATAATTCTCC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 2 0.04
15 44 0.96
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (15 bp):
TTATTATTATACTTT
Found at i:5674329 original size:12 final size:12
Alignment explanation
Indices: 5674304--5674369 Score: 62
Period size: 12 Copynumber: 5.2 Consensus size: 12
5674294 GTTTTTTTTT
5674304 TAAAATAATTTAA
1 TAAAA-AATTTAA
*
5674317 TAAAAATTTTAA
1 TAAAAAATTTAA
*
5674329 TAAAAAATTAAA
1 TAAAAAATTTAA
5674341 TAAATAAAATTTAA
1 T-AA-AAAATTTAA
*
5674355 TGTAAAAA-TTAA
1 T-AAAAAATTTAA
5674367 TAA
1 TAA
5674370 TATATAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
11 1 0.02
12 22 0.50
13 11 0.25
14 10 0.23
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
TAAAAAATTTAA
Found at i:5674391 original size:12 final size:12
Alignment explanation
Indices: 5674362--5674398 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5674352 TAATGTAAAA
*
5674362 ATTAATAATA-T
1 ATTAAAAATATT
5674373 A-TAAAAATATT
1 ATTAAAAATATT
5674384 ATTAAAAATATT
1 ATTAAAAATATT
5674396 ATT
1 ATT
5674399 TATAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
10 7 0.30
11 3 0.13
12 13 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATTAAAAATATT
Found at i:5674563 original size:20 final size:20
Alignment explanation
Indices: 5674538--5674577 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5674528 CAATAAAACC
5674538 TTTTAATTTATTAATTTTTA
1 TTTTAATTTATTAATTTTTA
*
5674558 TTTTAATTTATTCATTTTTA
1 TTTTAATTTATTAATTTTTA
5674578 ATTAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTAATTTATTAATTTTTA
Found at i:5675299 original size:21 final size:22
Alignment explanation
Indices: 5675269--5675314 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
5675259 ATTAATTATA
* *
5675269 TGAATTAATTAAA-TTAAGTTT
1 TGAATGAATTAAATTTAAGGTT
5675290 TGAATGAATTAAATTTAAGGTT
1 TGAATGAATTAAATTTAAGGTT
5675312 TGA
1 TGA
5675315 GACTTAGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.43
Consensus pattern (22 bp):
TGAATGAATTAAATTTAAGGTT
Found at i:5676669 original size:24 final size:26
Alignment explanation
Indices: 5676632--5676685 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 26
5676622 ATGATTTGTT
*
5676632 TATTGTTTATGAACATGTTCA-TTTA
1 TATTGTTTATGAACATGTTCACTTAA
*
5676657 TATT-TTTGTGAACATGTTCACTTAA
1 TATTGTTTATGAACATGTTCACTTAA
5676682 TATT
1 TATT
5676686 CACTATGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.52
Consensus pattern (26 bp):
TATTGTTTATGAACATGTTCACTTAA
Found at i:5678804 original size:101 final size:105
Alignment explanation
Indices: 5678561--5678805 Score: 284
Period size: 107 Copynumber: 2.4 Consensus size: 105
5678551 TGCGTTTAGC
* * *
5678561 TTAAAAAAAACACAATAATTGACAAACCCATGATAAACACTCATTAAATCAAAAGCCATCAAGTC
1 TTAAAAAAAACACAATAATTGACATACCCATAATAAACACTCATTAAATAAAAAGCCATCAAGTC
*
5678626 AAACAGATAAAAAAAATTAAATGACAAATACTATGTTTTTG
66 AAACAGATAAAAAAAA-TAAATGACAAATACTATATTTTTG
* * * * * *
5678667 TTAAAAAAAAACACAGTAATTGTCATACCCATAATAAATACTTATTAGATAAAAAGTCAT-ACAG
1 TT-AAAAAAAACACAATAATTGACATACCCATAATAAACACTCATTAAATAAAAAGCCATCA-AG
* * * *
5678731 TTAAACA-A-ATAAAAAA-AAA-GTCAAATACTGTATTTTTG
64 TCAAACAGATAAAAAAAATAAATGACAAATACTATATTTTTG
* *
5678769 TTAAAAAAAACACAATAATTGCCATACCTATAATAAA
1 TTAAAAAAAACACAATAATTGACATACCCATAATAAA
5678806 AGAAACACAA
Statistics
Matches: 120, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
101 32 0.27
102 18 0.15
103 3 0.03
105 7 0.06
106 4 0.03
107 56 0.47
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.26
Consensus pattern (105 bp):
TTAAAAAAAACACAATAATTGACATACCCATAATAAACACTCATTAAATAAAAAGCCATCAAGTC
AAACAGATAAAAAAAATAAATGACAAATACTATATTTTTG
Found at i:5678806 original size:32 final size:32
Alignment explanation
Indices: 5678770--5678837 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
5678760 GTATTTTTGT
5678770 TAAAAAAAACACAATAATTGCCATACCTATAA
1 TAAAAAAAACACAATAATTGCCATACCTATAA
* * * *
5678802 TAAAAGAAACACAATTATTGTCATACTTATAA
1 TAAAAAAAACACAATAATTGCCATACCTATAA
5678834 TAAA
1 TAAA
5678838 TACTAATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.26
Consensus pattern (32 bp):
TAAAAAAAACACAATAATTGCCATACCTATAA
Found at i:5679051 original size:100 final size:102
Alignment explanation
Indices: 5678907--5679178 Score: 275
Period size: 100 Copynumber: 2.7 Consensus size: 102
5678897 TGTGTTTTTA
** * * *
5678907 TTTAAAGAAGCACAATAATTG-CTATACACATAATAAACACTCATTAAATCAAAAGTCATAAAGT
1 TTTAAAGAAATACAGTAATTGTC-ATACACATAATAAATACTCATTAAATCAAAAG-CATCAAGT
* *
5678971 CAAAC-A-CAAAAAA-AAATGTCAAACACTACGTTTACC
64 CAAACAATAAAAAAATAAATGCCAAACACTACGTTTACC
* **
5679007 TTTAAAGAAATACAGTAATTGTCATACTCATAATAAATGTTCATTAAATCAAAAGCTATCAAGTC
1 TTTAAAGAAATACAGTAATTGTCATACACATAATAAATACTCATTAAATCAAAAGC-ATCAAGTC
* * * ***
5679072 AAACAGATAAAAAAATTAAATGCCAAATATTATGTTTTTG
65 AAACA-ATAAAAAAA-TAAATGCCAAACACTACGTTTACC
* * * *
5679112 TTCAAA-ACATGCAGTAATTGTCATACCCATAATAAATACTCATTAAATCAAAAGCCATCAAGTC
1 TTTAAAGAAATACAGTAATTGTCATACACATAATAAATACTCATTAAATCAAAAG-CATCAAGTC
5679176 AAA
65 AAA
5679179 TACTGTGTTT
Statistics
Matches: 142, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
99 1 0.01
100 57 0.40
101 1 0.01
102 1 0.01
103 6 0.04
104 54 0.38
105 22 0.15
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.27
Consensus pattern (102 bp):
TTTAAAGAAATACAGTAATTGTCATACACATAATAAATACTCATTAAATCAAAAGCATCAAGTCA
AACAATAAAAAAATAAATGCCAAACACTACGTTTACC
Found at i:5681336 original size:19 final size:21
Alignment explanation
Indices: 5681309--5681348 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5681299 TTTCAAATAG
5681309 AAATATAATGAT-CAAACTTT
1 AAATATAATGATACAAACTTT
*
5681329 AAAT-TAATTATACAAACTTT
1 AAATATAATGATACAAACTTT
5681349 CAACTAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (21 bp):
AAATATAATGATACAAACTTT
Found at i:5682859 original size:18 final size:18
Alignment explanation
Indices: 5682832--5682901 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
5682822 TTAATGAGAT
* *
5682832 TAAAAATAATGATAAAAA
1 TAAAATTAATTATAAAAA
5682850 TAAAATTAATTATTATAATAA
1 TAAAATTAATTA-TA-AA-AA
*
5682871 TAAAATTAATTATAAAAT
1 TAAAATTAATTATAAAAA
*
5682889 TAAAATCAATTAT
1 TAAAATTAATTAT
5682902 GAAATATATG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 23 0.51
19 4 0.09
20 4 0.09
21 14 0.31
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (18 bp):
TAAAATTAATTATAAAAA
Found at i:5682872 original size:21 final size:21
Alignment explanation
Indices: 5682843--5682883 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5682833 AAAAATAATG
5682843 ATAAAAATAAAATTAATTATT
1 ATAAAAATAAAATTAATTATT
*
5682864 ATAATAATAAAATTAATTAT
1 ATAAAAATAAAATTAATTAT
5682884 AAAATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAAAATAAAATTAATTATT
Found at i:5694325 original size:15 final size:15
Alignment explanation
Indices: 5694302--5694337 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5694292 TTCAAAAAAA
*
5694302 AAAAAAAAAACCCCT
1 AAAAGAAAAACCCCT
5694317 AAAAGAAAAACCCCT
1 AAAAGAAAAACCCCT
5694332 AAAAGA
1 AAAAGA
5694338 GAGCAGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.67, C:0.22, G:0.06, T:0.06
Consensus pattern (15 bp):
AAAAGAAAAACCCCT
Found at i:5701548 original size:30 final size:31
Alignment explanation
Indices: 5701494--5701565 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
5701484 TTCCATCCAA
5701494 TTGAGGGCTT-AATTGAGATGAAAATAGATGT
1 TTGAGGG-TTCAATTGAGATGAAAATAGATGT
* *
5701525 TTGAGGGTTCAATTG-GGTGAAAATATATGT
1 TTGAGGGTTCAATTGAGATGAAAATAGATGT
*
5701555 TTAAGGGTTCA
1 TTGAGGGTTCA
5701566 TCTGATCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 25 0.68
31 12 0.32
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (31 bp):
TTGAGGGTTCAATTGAGATGAAAATAGATGT
Found at i:5702162 original size:23 final size:23
Alignment explanation
Indices: 5702122--5702165 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5702112 GTGAACTTTG
5702122 AGTTGGAAAATGATGATGGAGAA
1 AGTTGGAAAATGATGATGGAGAA
*
5702145 AGTTCGGAATATGA-GATGGAG
1 AGTT-GGAAAATGATGATGGAG
5702166 GAGATTGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.39, C:0.02, G:0.36, T:0.23
Consensus pattern (23 bp):
AGTTGGAAAATGATGATGGAGAA
Found at i:5703029 original size:13 final size:13
Alignment explanation
Indices: 5703011--5703041 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
5703001 AAGCCTCGGA
5703011 AGGCAAATGATGC
1 AGGCAAATGATGC
5703024 AGGCAAATGATGC
1 AGGCAAATGATGC
5703037 AGGCA
1 AGGCA
5703042 TTAGAGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.32, T:0.13
Consensus pattern (13 bp):
AGGCAAATGATGC
Found at i:5707074 original size:26 final size:26
Alignment explanation
Indices: 5707044--5707096 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
5707034 TTATTATTTC
5707044 ACAAAAATATTCCTAAAACATATTGG
1 ACAAAAATATTCCTAAAACATATTGG
5707070 ACAAAAATATTCCTAAAACATATTGG
1 ACAAAAATATTCCTAAAACATATTGG
5707096 A
1 A
5707097 GAGAAGCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (26 bp):
ACAAAAATATTCCTAAAACATATTGG
Found at i:5709525 original size:275 final size:275
Alignment explanation
Indices: 5709034--5709585 Score: 1034
Period size: 275 Copynumber: 2.0 Consensus size: 275
5709024 AAGATATTAG
*
5709034 AGGCCTATACCGATGTTGATTATGTAGGATCTCTAGTGAATAGGATGTCAACCTTAGGTTATTAC
1 AGGCCTATACCGATGTTGATTATGTAGGATCTCTAGTGAACAGGATGTCAACCTTAGGTTATTAC
5709099 ACCCTCTTGGGAGAGAATCTTGTAACGTGGAGGAGTAAGAAGCAAAACGTGGTGACAAGATCAAG
66 ACCCTCTTGGGAGAGAATCTTGTAACGTGGAGGAGTAAGAAGCAAAACGTGGTGACAAGATCAAG
* *
5709164 TGCAAAGTTTGAGTTTAGGTCAATAGCAATGGGAATGTGAACTATTGTGGTTAAAGATAATTCTT
131 TGCAAAGTTTGAGTTTAGGTCAATAGCAATAGGAATGTGAACTATTGTGGTTAAAAATAATTCTT
5709229 GATGATTTGAAGATTAAATGGGAAAGACTAATGAGATTATACTGTGAAAACAAATTTGCCATTAG
196 GATGATTTGAAGATTAAATGGGAAAGACTAATGAGATTATACTGTGAAAACAAATTTGCCATTAG
5709294 GATTGCTCATAATCC
261 GATTGCTCATAATCC
*
5709309 AGGCCTATATCGATGTTGATTATGTAGGATCTCTAGTGAACAGGATGTCAACCTTAGGTTATTAC
1 AGGCCTATACCGATGTTGATTATGTAGGATCTCTAGTGAACAGGATGTCAACCTTAGGTTATTAC
* *
5709374 ACCCTCTTGGGAGGGAATCTTGTAACGTGGAGGAGTAAGAAGTAAAACGTGGT-AGCAAGATCAA
66 ACCCTCTTGGGAGAGAATCTTGTAACGTGGAGGAGTAAGAAGCAAAACGTGGTGA-CAAGATCAA
5709438 GTGCAAAGTTTGAGTTTAGGTCAATAGCAATAGGAATGTGAACTATTGTGGTTAAAAATAATTCT
130 GTGCAAAGTTTGAGTTTAGGTCAATAGCAATAGGAATGTGAACTATTGTGGTTAAAAATAATTCT
5709503 TGATGATTTGAAGATTAAATGGGAAAGACTAATGAGATTATACTGTGAAAACAAATTTGCCATTA
195 TGATGATTTGAAGATTAAATGGGAAAGACTAATGAGATTATACTGTGAAAACAAATTTGCCATTA
5709568 GGATTGCTCATAATCC
260 GGATTGCTCATAATCC
5709584 AG
1 AG
5709586 TACAACAAGA
Statistics
Matches: 270, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
274 1 0.00
275 269 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (275 bp):
AGGCCTATACCGATGTTGATTATGTAGGATCTCTAGTGAACAGGATGTCAACCTTAGGTTATTAC
ACCCTCTTGGGAGAGAATCTTGTAACGTGGAGGAGTAAGAAGCAAAACGTGGTGACAAGATCAAG
TGCAAAGTTTGAGTTTAGGTCAATAGCAATAGGAATGTGAACTATTGTGGTTAAAAATAATTCTT
GATGATTTGAAGATTAAATGGGAAAGACTAATGAGATTATACTGTGAAAACAAATTTGCCATTAG
GATTGCTCATAATCC
Found at i:5718834 original size:28 final size:27
Alignment explanation
Indices: 5718762--5718835 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
5718752 TTTATTTTTT
* **
5718762 AAATAAAATTTTATATTCTTATTATATTT
1 AAAT-AAATTTT-TATTTTTATTATATCC
* *
5718791 AAATAAATTCTCATTTTTATTTATATCC
1 AAATAAATTTTTATTTTTA-TTATATCC
5718819 AAATAAATTTTTATTTT
1 AAATAAATTTTTATTTT
5718836 AAATGAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 6 0.16
28 27 0.73
29 4 0.11
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (27 bp):
AAATAAATTTTTATTTTTATTATATCC
Found at i:5718963 original size:30 final size:29
Alignment explanation
Indices: 5718889--5718994 Score: 106
Period size: 29 Copynumber: 3.6 Consensus size: 29
5718879 ATTAAATTTT
* *
5718889 TAAAAATTTATTTAAATACAAATAAAAATCT
1 TAAAAATTTATTTAAATA-TAATAAAAAT-A
* * * *
5718920 TAAGAACTTATTTATATGTACATTAAAAAT-
1 TAAAAATTTATTTAAATATA-A-TAAAAATA
*
5718950 TGAAAATTTATTTAAATATAATAAAAATA
1 TAAAAATTTATTTAAATATAATAAAAATA
5718979 TAAAAATTTATTTAAA
1 TAAAAATTTATTTAAA
5718995 CAAATTTATA
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 7 0.11
29 16 0.26
30 16 0.26
31 15 0.25
32 7 0.11
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.39
Consensus pattern (29 bp):
TAAAAATTTATTTAAATATAATAAAAATA
Found at i:5718986 original size:29 final size:28
Alignment explanation
Indices: 5718888--5718994 Score: 106
Period size: 30 Copynumber: 3.6 Consensus size: 28
5718878 GATTAAATTT
*
5718888 TTAAAAATTTATTTAAATACAAATAAAAA
1 TTAAAAATTTATTTAAATA-TAATAAAAA
* * * *
5718917 TCTTAAGAACTTATTTATATGTACATTAAAAA
1 --TTAAAAATTTATTTAAATATA-A-TAAAAA
*
5718949 TTGAAAATTTATTTAAATATAATAAAAA
1 TTAAAAATTTATTTAAATATAATAAAAA
5718977 TATAAAAATTTATTTAAA
1 T-TAAAAATTTATTTAAA
5718995 CAAATTTATA
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
28 7 0.11
29 16 0.26
30 17 0.27
31 16 0.26
32 6 0.10
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (28 bp):
TTAAAAATTTATTTAAATATAATAAAAA
Found at i:5720589 original size:14 final size:13
Alignment explanation
Indices: 5720544--5720594 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
5720534 TAACTATCAA
5720544 AAATTTTA-TTTT
1 AAATTTTATTTTT
5720556 --ATTTTATTTTT
1 AAATTTTATTTTT
5720567 AAATTTTATTTATT
1 AAATTTTATTT-TT
* *
5720581 CATTTTTATTTTT
1 AAATTTTATTTTT
5720594 A
1 A
5720595 GTTTTTTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.19
11 4 0.12
13 11 0.34
14 11 0.34
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
AAATTTTATTTTT
Found at i:5725828 original size:19 final size:21
Alignment explanation
Indices: 5725780--5725836 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
5725770 GCTTGTCATT
5725780 TTAAGATTTCTTTTAGAGTAA
1 TTAAGATTTCTTTTAGAGTAA
*
5725801 TGTTAAGATTTCTTTTA-TGTAA
1 --TTAAGATTTCTTTTAGAGTAA
5725823 -TAAGATTTCATTTT
1 TTAAGATTTC-TTTT
5725837 TTTATCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 9 0.28
20 4 0.12
22 4 0.12
23 15 0.47
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (21 bp):
TTAAGATTTCTTTTAGAGTAA
Found at i:5727371 original size:23 final size:24
Alignment explanation
Indices: 5727318--5727372 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
5727308 AAAATTTTGG
* * *
5727318 ATGTGAATTTCTAAAGTTATGTGA
1 ATGTGAATCTCAAAAGTTATGTAA
*
5727342 ATGTGAATCTCAAAAGTT-TTTAA
1 ATGTGAATCTCAAAAGTTATGTAA
5727365 ATGTGAAT
1 ATGTGAAT
5727373 ATTTGAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.40
Consensus pattern (24 bp):
ATGTGAATCTCAAAAGTTATGTAA
Found at i:5727544 original size:16 final size:16
Alignment explanation
Indices: 5727523--5727559 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5727513 AATTTTAAAA
*
5727523 TCTTGCGAATATAAGT
1 TCTTGCAAATATAAGT
*
5727539 TCTTGCAAATCTAAGT
1 TCTTGCAAATATAAGT
5727555 TCTTG
1 TCTTG
5727560 TGAAACTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (16 bp):
TCTTGCAAATATAAGT
Found at i:5727709 original size:16 final size:16
Alignment explanation
Indices: 5727690--5727730 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
5727680 AATCTTAAAA
5727690 TCTTATGAATTTAAGT
1 TCTTATGAATTTAAGT
***
5727706 TCTTGCAAATTTAAGT
1 TCTTATGAATTTAAGT
5727722 TCTTATGAA
1 TCTTATGAA
5727731 ACTCAAATTT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (16 bp):
TCTTATGAATTTAAGT
Found at i:5728861 original size:2 final size:2
Alignment explanation
Indices: 5728856--5728906 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
5728846 AAAAAAAAAA
*
5728856 AG AG AG A- AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5728897 AG AG AG AG AG
1 AG AG AG AG AG
5728907 CAAAAGTGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5732834 original size:15 final size:16
Alignment explanation
Indices: 5732799--5732842 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
5732789 GGTGTTTCTT
5732799 AATAATATTTATAAATA
1 AATAATA-TTATAAATA
*
5732816 AATAATATTA-AATTA
1 AATAATATTATAAATA
5732831 AATAATA-TATAA
1 AATAATATTATAA
5732843 TGATAATTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 13 0.52
16 3 0.12
17 7 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATATTATAAATA
Found at i:5734323 original size:13 final size:13
Alignment explanation
Indices: 5734291--5734330 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
5734281 TTTTAATTTT
5734291 TAAAATTTT-ATA
1 TAAAATTTTAATA
**
5734303 TATTATTTTAATA
1 TAAAATTTTAATA
5734316 TAAAATTTTAATA
1 TAAAATTTTAATA
5734329 TA
1 TA
5734331 TTGAAATAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TAAAATTTTAATA
Found at i:5734338 original size:23 final size:25
Alignment explanation
Indices: 5734291--5734338 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5734281 TTTTAATTTT
**
5734291 TAAAATTTTATATATTATTTTAATA
1 TAAAATTTTATATATTATTGAAATA
5734316 TAAAATTTTA-ATA-TATTGAAATA
1 TAAAATTTTATATATTATTGAAATA
5734339 GATTTTGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 3 0.14
25 10 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TAAAATTTTATATATTATTGAAATA
Found at i:5740413 original size:2 final size:2
Alignment explanation
Indices: 5740406--5740436 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5740396 AGCATTGGAT
5740406 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
5740437 CTTTCACATT
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:5741992 original size:13 final size:13
Alignment explanation
Indices: 5741969--5742017 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
5741959 TTTGATTATA
*
5741969 GTTTGTATTTAAT
1 GTTTCTATTTAAT
*
5741982 GTTTCTGTTTAAT
1 GTTTCTATTTAAT
* *
5741995 AATTTCTATTTAAC
1 -GTTTCTATTTAAT
5742009 GTTTCTATT
1 GTTTCTATT
5742018 CAACAATTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.22, C:0.08, G:0.10, T:0.59
Consensus pattern (13 bp):
GTTTCTATTTAAT
Found at i:5742025 original size:27 final size:27
Alignment explanation
Indices: 5741974--5742025 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
5741964 TTATAGTTTG
* * * *
5741974 TATTTAATGTTTCTGTTTAATAATTTC
1 TATTTAACGTTTCTATTCAACAATTTC
5742001 TATTTAACGTTTCTATTCAACAATT
1 TATTTAACGTTTCTATTCAACAATT
5742026 AACATTTTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.54
Consensus pattern (27 bp):
TATTTAACGTTTCTATTCAACAATTTC
Found at i:5743250 original size:105 final size:105
Alignment explanation
Indices: 5743068--5743278 Score: 386
Period size: 105 Copynumber: 2.0 Consensus size: 105
5743058 GGTCGACCTG
*
5743068 ACCTAACTTAGCAAATGACAATCCAATCGTATACTGACATGTTCATATATTCATGTATGTTCATG
1 ACCTAACTTAGCAAATGACAATCCAATCATATACTGACATGTTCATATATTCATGTATGTTCATG
5743133 AGAGTAGATGATTTAGCCAAATTAATGTGAATTCTGATAA
66 AGAGTAGATGATTTAGCCAAATTAATGTGAATTCTGATAA
* *
5743173 ACCTAACTTAGCAAATGACAATCTAATCATATACTGACATGTTCATATGTTCATGTATGTTCATG
1 ACCTAACTTAGCAAATGACAATCCAATCATATACTGACATGTTCATATATTCATGTATGTTCATG
*
5743238 AGAGTAGATGATTTGGCCAAATTAATGTGAATTCTGATAA
66 AGAGTAGATGATTTAGCCAAATTAATGTGAATTCTGATAA
5743278 A
1 A
5743279 TCAAGTCACC
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (105 bp):
ACCTAACTTAGCAAATGACAATCCAATCATATACTGACATGTTCATATATTCATGTATGTTCATG
AGAGTAGATGATTTAGCCAAATTAATGTGAATTCTGATAA
Found at i:5746932 original size:2 final size:2
Alignment explanation
Indices: 5746889--5746921 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5746879 TTTACTTATC
5746889 AT AT AT AT 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 AT AT AT AT A
5746922 CACACATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5747938 original size:6 final size:6
Alignment explanation
Indices: 5747907--5747968 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
5747897 AAAAATATTT
*
5747907 TTTATTA TTT-TA TTTA-A TTT-TCA TTTATA TTTTATA TTTAT- TTAAT-
1 TTTA-TA TTTATA TTTATA TTTAT-A TTTATA -TTTATA TTTATA TTTATA
5747953 TTTATA TTTATA TTTA
1 TTTATA TTTATA TTTA
5747969 AAAATAATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
5 17 0.36
6 20 0.43
7 10 0.21
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:5747940 original size:22 final size:22
Alignment explanation
Indices: 5747906--5747969 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
5747896 AAAAAATATT
*
5747906 TTTTATTATTTTATTTAATTTTCA
1 TTTTA-TATTTTATTTAA-TTTAA
*
5747930 -TTTATATTTTATATTTATTTAA
1 TTTTATATTTTAT-TTAATTTAA
5747952 TTTTATATTTATATTTAA
1 TTTTATATTT-TATTTAA
5747970 AAATAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 12 0.35
23 19 0.56
24 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTATATTTTATTTAATTTAA
Found at i:5747956 original size:16 final size:16
Alignment explanation
Indices: 5747911--5747963 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
5747901 ATATTTTTTA
* *
5747911 TTATTTTATTTAAT-T
1 TTATTTAATTTTATAT
5747926 TTCATTTATATTTTATAT
1 TT-ATTTA-ATTTTATAT
5747944 TTATTTAATTTTATAT
1 TTATTTAATTTTATAT
5747960 TTAT
1 TTAT
5747964 ATTTAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 2 0.06
16 17 0.52
17 11 0.33
18 3 0.09
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTAATTTTATAT
Found at i:5747961 original size:29 final size:27
Alignment explanation
Indices: 5747911--5747967 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 27
5747901 ATATTTTTTA
5747911 TTATTTTATTTAATTTTCATTTATATT
1 TTATTTTATTTAATTTTCATTTATATT
*
5747938 TTATATTTATTTAATTTTATATTTATATT
1 TTAT-TTTATTTAATTTT-CATTTATATT
5747967 T
1 T
5747968 AAAAATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 4 0.15
28 13 0.48
29 10 0.37
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (27 bp):
TTATTTTATTTAATTTTCATTTATATT
Found at i:5747991 original size:20 final size:18
Alignment explanation
Indices: 5747956--5748023 Score: 100
Period size: 19 Copynumber: 3.6 Consensus size: 18
5747946 ATTTAATTTT
5747956 ATATTTATATTTAAAAATA
1 ATATTT-TATTTAAAAATA
5747975 ATATTTTATGTTAAAAATA
1 ATATTTTAT-TTAAAAATA
5747994 ATATTTTATATTTAAAAATA
1 ATA-TTT-TATTTAAAAATA
5748014 ATATTTTATT
1 ATATTTTATT
5748024 AATTTTAAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.15
19 21 0.46
20 15 0.33
21 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (18 bp):
ATATTTTATTTAAAAATA
Found at i:5749245 original size:14 final size:15
Alignment explanation
Indices: 5749226--5749263 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
5749216 TCAAGAATCC
5749226 ATTTTCTTTTAG-AA
1 ATTTTCTTTTAGTAA
5749240 ATTTTCTTTT-GTAA
1 ATTTTCTTTTAGTAA
5749254 ATTTT-TTTTA
1 ATTTTCTTTTA
5749264 TTCATTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (15 bp):
ATTTTCTTTTAGTAA
Found at i:5750721 original size:39 final size:39
Alignment explanation
Indices: 5750669--5750760 Score: 125
Period size: 39 Copynumber: 2.4 Consensus size: 39
5750659 GATTGGATAG
* * *
5750669 GGTGGGGA-AGATTGGGTGTGGTGGGGCT-TTAGGGGGAA
1 GGTGGGGAGGGATTGGGTGTGGT-AGGATGTTAGGGGGAA
5750707 GGTGGGGAGGGATTGGGTGTGGTAGGATGTTAGGGGGAA
1 GGTGGGGAGGGATTGGGTGTGGTAGGATGTTAGGGGGAA
*
5750746 GGTGGAGAGGGATTG
1 GGTGGGGAGGGATTG
5750761 ATGGGGGTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
38 11 0.23
39 37 0.77
ACGTcount: A:0.17, C:0.01, G:0.59, T:0.23
Consensus pattern (39 bp):
GGTGGGGAGGGATTGGGTGTGGTAGGATGTTAGGGGGAA
Found at i:5751084 original size:20 final size:19
Alignment explanation
Indices: 5751046--5751085 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5751036 TGTATTTGAA
*
5751046 TTTTAATATTTTTTTATTG
1 TTTTAATATTTTATTATTG
*
5751065 TTTTGATATTTATATTATTG
1 TTTTAATATTT-TATTATTG
5751085 T
1 T
5751086 CGATTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (19 bp):
TTTTAATATTTTATTATTG
Found at i:5751310 original size:26 final size:26
Alignment explanation
Indices: 5751282--5751330 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
5751272 TAAAAAATAA
*
5751282 AAAATATAGGTTTGAAAA-TTTTATT
1 AAAATATAAGTTTGAAAACTTTTATT
5751307 AAAATATAAGTTTGAAAACTTTTA
1 AAAATATAAGTTTGAAAACTTTTA
5751331 ATTTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAACTTTTATT
Found at i:5753396 original size:39 final size:39
Alignment explanation
Indices: 5753342--5753420 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
5753332 GGTTAGTACT
5753342 TAGTAATTAGTACAACTATTTAAATCTAGCATCTTTTTA
1 TAGTAATTAGTACAACTATTTAAATCTAGCATCTTTTTA
5753381 TAGTAATTAGTACAACTATTTAAATCTAGCATCTTTTTA
1 TAGTAATTAGTACAACTATTTAAATCTAGCATCTTTTTA
5753420 T
1 T
5753421 GATATTATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (39 bp):
TAGTAATTAGTACAACTATTTAAATCTAGCATCTTTTTA
Found at i:5754793 original size:6 final size:6
Alignment explanation
Indices: 5754782--5754812 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5754772 GTCTAGATAA
*
5754782 TGATGG TGATGG AGATGG TGATGG TGATGG T
1 TGATGG TGATGG TGATGG TGATGG TGATGG T
5754813 ACGAATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.48, T:0.32
Consensus pattern (6 bp):
TGATGG
Found at i:5755180 original size:18 final size:18
Alignment explanation
Indices: 5755157--5755281 Score: 105
Period size: 18 Copynumber: 6.9 Consensus size: 18
5755147 ATGATTATTA
5755157 TCCACCTCAAATGTATCC
1 TCCACCTCAAATGTATCC
*
5755175 TCCACCTCCTCAAATATATCC
1 TCCA---CCTCAAATGTATCC
* *
5755196 TTCACCTCAAATGTATCAG
1 TCCACCTCAAATGTATC-C
* * *
5755215 T-TACCACAAATGTACCC
1 TCCACCTCAAATGTATCC
* *
5755232 TCCACCACAAATGTATCA
1 TCCACCTCAAATGTATCC
*
5755250 T---CCTCAAATATATCC
1 TCCACCTCAAATGTATCC
5755265 TCCACCTCAAATGTATC
1 TCCACCTCAAATGTATC
5755282 AAGAACAAAG
Statistics
Matches: 84, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
15 12 0.14
17 1 0.01
18 54 0.64
19 1 0.01
21 16 0.19
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.28
Consensus pattern (18 bp):
TCCACCTCAAATGTATCC
Found at i:5755187 original size:21 final size:21
Alignment explanation
Indices: 5755161--5755203 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5755151 TTATTATCCA
*
5755161 CCTCAAATGTATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
*
5755182 CCTCAAATATATCCTTCACCT
1 CCTCAAATATATCCTCCACCT
5755203 C
1 C
5755204 AAATGTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.42, G:0.02, T:0.30
Consensus pattern (21 bp):
CCTCAAATATATCCTCCACCT
Found at i:5755267 original size:33 final size:34
Alignment explanation
Indices: 5755181--5755282 Score: 134
Period size: 33 Copynumber: 3.0 Consensus size: 34
5755171 ATCCTCCACC
*
5755181 TCCTCAAATATATCCTTCACCTCAAATGTATCAG
1 TCCTCAAATATATCCTCCACCTCAAATGTATCAG
* * * *
5755215 TTACCACAAATGTACCCTCCACCACAAATGTATCA-
1 -T-CCTCAAATATATCCTCCACCTCAAATGTATCAG
5755250 TCCTCAAATATATCCTCCACCTCAAATGTATCA
1 TCCTCAAATATATCCTCCACCTCAAATGTATCA
5755283 AGAACAAAGG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
33 28 0.49
34 1 0.02
35 1 0.02
36 27 0.47
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.28
Consensus pattern (34 bp):
TCCTCAAATATATCCTCCACCTCAAATGTATCAG
Found at i:5767950 original size:21 final size:22
Alignment explanation
Indices: 5767902--5767950 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
5767892 TTTGATGTAT
* *
5767902 TATTAATATATAAATTTTATAA
1 TATTATTATATAAATTTAATAA
*
5767924 -ATTATTA-ATAAGTTTAATAA
1 TATTATTATATAAATTTAATAA
5767944 TATTATT
1 TATTATT
5767951 TTTTAATGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTATTATATAAATTTAATAA
Done.