Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397263.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_86.0, 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: 8461613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 85630 characters in sequence are not A, C, G, or T
File 6 of 18
Found at i:3014535 original size:21 final size:21
Alignment explanation
Indices: 3014505--3014544 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3014495 ATAAAAAAAA
*
3014505 ATGTATAAGTAATT-AGCTGCC
1 ATGTACAAGT-ATTAAGCTGCC
3014526 ATGTACAAGTATTAAGCTG
1 ATGTACAAGTATTAAGCTG
3014545 TCAAGCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (21 bp):
ATGTACAAGTATTAAGCTGCC
Found at i:3031266 original size:62 final size:62
Alignment explanation
Indices: 3031169--3031293 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
3031159 CGCCTTCATT
3031169 TTCGGAATCTAGAGCTTACCGAAGAAAACAATCAATTAGATAAAGAGCAAGCTCGCTTTGGC
1 TTCGGAATCTAGAGCTTACCGAAGAAAACAATCAATTAGATAAAGAGCAAGCTCGCTTTGGC
*
3031231 TTCGGAATCTAGAGCTTACCGAAGAAAACAATCAATTAGATAAAGAGCACGCTCGCTTTGGC
1 TTCGGAATCTAGAGCTTACCGAAGAAAACAATCAATTAGATAAAGAGCAAGCTCGCTTTGGC
3031293 T
1 T
3031294 AACTTTTGAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (62 bp):
TTCGGAATCTAGAGCTTACCGAAGAAAACAATCAATTAGATAAAGAGCAAGCTCGCTTTGGC
Found at i:3043442 original size:15 final size:16
Alignment explanation
Indices: 3043407--3043495 Score: 60
Period size: 16 Copynumber: 5.5 Consensus size: 16
3043397 ATAATAAAAC
*
3043407 ATTAATATTTTATAA-T
1 ATTAATATATTA-AATT
3043423 ATTAATA-ATTAAATT
1 ATTAATATATTAAATT
*
3043438 ATTAATATTTTAAATT
1 ATTAATATATTAAATT
* *
3043454 ATCAAT-TATTACTATT
1 ATTAATATATTA-AATT
*
3043470 -TGTAATAAATTATAAATT
1 AT-TAATATA-T-TAAATT
3043488 ATTAATAT
1 ATTAATAT
3043496 TTATAAGATA
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
14 2 0.04
15 16 0.29
16 25 0.45
17 1 0.02
18 9 0.16
19 3 0.05
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (16 bp):
ATTAATATATTAAATT
Found at i:3043452 original size:16 final size:16
Alignment explanation
Indices: 3043407--3043455 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
3043397 ATAATAAAAC
3043407 ATTAATATTTTATAA-T
1 ATTAATATTTTA-AATT
*
3043423 ATTAATA-ATTAAATT
1 ATTAATATTTTAAATT
3043438 ATTAATATTTTAAATT
1 ATTAATATTTTAAATT
3043454 AT
1 AT
3043456 CAATTATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 2 0.07
15 11 0.38
16 16 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAATATTTTAAATT
Found at i:3043610 original size:149 final size:153
Alignment explanation
Indices: 3043308--3043664 Score: 401
Period size: 149 Copynumber: 2.3 Consensus size: 153
3043298 NNNNNNNNTC
* * *
3043308 AATTATTAATGTTTTAAATAAATTATAAATTATAAATATTTAAAAAATAAAATAAAATAAAATAA
1 AATTACTAATGTTGTAAATAAATTATAAATTATTAATATTTAAAAAATAAAATAAAAT--AATAA
* * *
3043373 AAATAATCATAATAATATTTAATTATAATAAAACATTAATATTTTATAATATTAATAATTAAATT
64 AAATAATCATAATAATATTAAATTATAATAAAACATTAATATTATATAATACTAATAATTAAATT
* * *
3043438 ATTAATATTTTAAATTATCAA-T-T
129 ATTAAAATATTAAATTATAAATTAT
* * *
3043461 -ATTACT-AT-TTGT-AATAAATTATAAATTATTAATATTTATAAGATAAAATGAAAT-A-AAAA
1 AATTACTAATGTTGTAAATAAATTATAAATTATTAATATTTAAAAAATAAAATAAAATAATAAAA
* * *
3043520 ATAATCATAATAATAATTAAATTATAATAAAATC-TTAATATTATATGATGCTAATGATTAAATT
66 ATAATCATAATAAT-ATTAAATTATAATAAAA-CATTAATATTATATAATACTAATAATTAAATT
3043584 ATCAATAAAATATTAACATT-TAAATTAT
129 AT---TAAAATATTAA-ATTATAAATTAT
* * *
3043612 CAATTAGTAATGTTTTAAATAAATTATAAATTATTAATATTTTAAAAATAAAA
1 -AATTACTAATGTTGTAAATAAATTATAAATTATTAATATTTAAAAAATAAAA
3043665 AATAAAAGCA
Statistics
Matches: 171, Mismatches: 20, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
145 18 0.11
146 44 0.26
147 1 0.01
149 50 0.29
150 7 0.04
151 3 0.02
152 5 0.03
153 5 0.03
154 2 0.01
155 3 0.02
156 33 0.19
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (153 bp):
AATTACTAATGTTGTAAATAAATTATAAATTATTAATATTTAAAAAATAAAATAAAATAATAAAA
ATAATCATAATAATATTAAATTATAATAAAACATTAATATTATATAATACTAATAATTAAATTAT
TAAAATATTAAATTATAAATTAT
Found at i:3043643 original size:27 final size:27
Alignment explanation
Indices: 3043604--3043657 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3043594 TATTAACATT
* *
3043604 TAAATTATCAATTAGTAATGTTTTAAA
1 TAAATTATAAATTAGTAATATTTTAAA
*
3043631 TAAATTATAAATTATTAATATTTTAAA
1 TAAATTATAAATTAGTAATATTTTAAA
3043658 AATAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (27 bp):
TAAATTATAAATTAGTAATATTTTAAA
Found at i:3043843 original size:16 final size:16
Alignment explanation
Indices: 3043824--3043854 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3043814 TACGTAATAA
*
3043824 CTATTTTATTCTATTT
1 CTATCTTATTCTATTT
3043840 CTATCTTATTCTATT
1 CTATCTTATTCTATT
3043855 CCCTTAGAAT
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:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (16 bp):
CTATCTTATTCTATTT
Found at i:3046555 original size:20 final size:22
Alignment explanation
Indices: 3046527--3046566 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
3046517 AAAGACTCAC
3046527 AAAACACAAA-AAA-AAAAAAA
1 AAAACACAAAGAAAGAAAAAAA
*
3046547 AAAAGACAAAGAAAGAAAAA
1 AAAACACAAAGAAAGAAAAA
3046567 GAGCTGATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 3 0.18
22 5 0.29
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.00
Consensus pattern (22 bp):
AAAACACAAAGAAAGAAAAAAA
Found at i:3046865 original size:20 final size:20
Alignment explanation
Indices: 3046837--3046874 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3046827 ATGTTTTATG
*
3046837 ATATTTTAAAAAAATATTTA
1 ATATATTAAAAAAATATTTA
*
3046857 ATATATTAAAAAATTATT
1 ATATATTAAAAAAATATT
3046875 ATTTTATATA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATTAAAAAAATATTTA
Found at i:3048668 original size:68 final size:68
Alignment explanation
Indices: 3048555--3048698 Score: 263
Period size: 68 Copynumber: 2.1 Consensus size: 68
3048545 AAAGATCCAC
3048555 TATT-TTCAATGGCACATTGCTACTACCCCAAAGTCTACTTTAATACCAACTGTTACGATTCATC
1 TATTGTTCAATGGCACATTGCTACTACCCCAAAGTCTACTTTAATACCAACTGTTACGATTCATC
3048619 AAG
66 AAG
* *
3048622 TATTGTTCAATGGCACATTGCTATTACCCCAAAGTCTATTTTAATACCAACTGTTACGATTCATC
1 TATTGTTCAATGGCACATTGCTACTACCCCAAAGTCTACTTTAATACCAACTGTTACGATTCATC
3048687 AAG
66 AAG
3048690 TATTGTTCA
1 TATTGTTCA
3048699 CTTTGGCCCA
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 4 0.05
68 70 0.95
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (68 bp):
TATTGTTCAATGGCACATTGCTACTACCCCAAAGTCTACTTTAATACCAACTGTTACGATTCATC
AAG
Found at i:3051508 original size:17 final size:17
Alignment explanation
Indices: 3051476--3051510 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3051466 AACAAGTAAG
3051476 TTTTTTTTTTCTTCTTT
1 TTTTTTTTTTCTTCTTT
3051493 TTTTTCTTTTTC-TCTTT
1 TTTTT-TTTTTCTTCTTT
3051510 T
1 T
3051511 ATTTGGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTTCTTCTTT
Found at i:3051792 original size:3 final size:3
Alignment explanation
Indices: 3051778--3051811 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3051768 CAAGTAAGTT
*
3051778 TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3051812 CTTTTATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:3058091 original size:26 final size:26
Alignment explanation
Indices: 3058061--3058343 Score: 125
Period size: 26 Copynumber: 10.5 Consensus size: 26
3058051 TACAATCCTC
*
3058061 AAATATTAATGA-TTAAATTATAAATA
1 AAATATTAAT-ATTTAAATAATAAATA
3058087 AAATATTAATATTTAAATAATAAAT-
1 AAATATTAATATTTAAATAATAAATA
*
3058112 ---TATTAATATTTTAAATAA-ACTATA
1 AAATATTAATA-TTTAAATAATA-AATA
* * *
3058136 AATTATTAATATATAAA-AATTAATA
1 AAATATTAATATTTAAATAATAAATA
* * * *
3058161 ATCATAATAATATTTAACTTATAAATA
1 A-AATATTAATATTTAAATAATAAATA
*
3058188 AAATATTAATATTTTTAAATATTAATGATTA
1 AAATATTAATA--TTTAAATAATAA--A-TA
* ** *
3058219 AAATATAATAAAATATTAATATTTTAATTATC
1 AAATAT--TAATAT-TTAA-ATAATAA--ATA
* * *
3058251 AATTATTAATATTTGAAATAA-ATGATC
1 AAATATTAATATTT-AAATAATA-AATA
* *
3058278 AATTATTAATATTTAGA-AATAAATA
1 AAATATTAATATTTAAATAATAAATA
** * * *
3058303 ATCCTAATAATATTTAAATTATGAATA
1 A-AATATTAATATTTAAATAATAAATA
3058330 AAATATTAATATTT
1 AAATATTAATATTT
3058344 TTAAAAATTA
Statistics
Matches: 195, Mismatches: 38, Indels: 48
0.69 0.14 0.17
Matches are distributed among these distances:
22 9 0.05
23 11 0.06
25 12 0.06
26 71 0.36
27 39 0.20
28 10 0.05
29 4 0.02
30 8 0.04
31 9 0.05
32 10 0.05
33 12 0.06
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
AAATATTAATATTTAAATAATAAATA
Found at i:3058136 original size:27 final size:23
Alignment explanation
Indices: 3058083--3058556 Score: 109
Period size: 27 Copynumber: 20.1 Consensus size: 23
3058073 TTAAATTATA
*
3058083 AATAAAATATTAATA-TTTAAAT
1 AATAAATTATTAATATTTTAAAT
3058105 AATAAATTATTAATATTTTAAAT
1 AATAAATTATTAATATTTTAAAT
*
3058128 AAACTATAAATTATTAATA-TATAAA-
1 --A--ATAAATTATTAATATTTTAAAT
* *
3058153 AATTAATAATCATAATAATATTTAACTTAT
1 AATAAATTAT--TAAT-AT-TTTAA---AT
*
3058183 AAATAAAATATTAATATTTTTAAAT
1 -AATAAATTATTAATA-TTTTAAAT
* * *
3058208 -ATTAATGATTAA-A----ATAT
1 AATAAATTATTAATATTTTAAAT
*
3058225 AATAAAATATTAATATTTT-AAT
1 AATAAATTATTAATATTTTAAAT
* * *
3058247 TATCAATTATTAATATTTGAAAT
1 AATAAATTATTAATATTTTAAAT
*
3058270 AAATGATCAATTATTAATATTTAGAAAT
1 -AAT-A--AATTATTAATATTT-TAAAT
* *
3058298 AA-ATAATCCTAATAATATTTAAATTAT
1 AATA-AAT--TATTAATATTTTAA--AT
*
3058325 GAATAAAATATTAATATTTTTAAA-
1 -AATAAATTATTAATA-TTTTAAAT
* *
3058349 AATTAATGATTAA-A--TT--AT
1 AATAAATTATTAATATTTTAAAT
* *
3058367 AATAAAATATTAATA-TGTAAAGT
1 AATAAATTATTAATATTTTAAA-T
*
3058390 -ATCAATTATTAATATAATGATTAAAT
1 AATAAATTATTAATAT--T--TTAAAT
* *
3058416 TATAAATTATTAATATTTAAAAAT
1 AATAAATTATTAATATTT-TAAAT
* *
3058440 AAATAACCATCA-TAATATTTAAATTAT
1 -AATAA--ATTATTAATATTTTAA--AT
* * *
3058467 AGAGAAAATATTAATACTTTATAAT
1 A-ATAAATTATTAATATTTTA-AAT
* * * *
3058492 -GTTAATGATTAA-ATTATAAAT
1 AATAAATTATTAATATTTTAAAT
3058513 -A-AAA-TATTAATA-TTTAAAT
1 AATAAATTATTAATATTTTAAAT
* * *
3058532 TATCAATTATTAATGTTTTAAAT
1 AATAAATTATTAATATTTTAAAT
3058555 AA
1 AA
3058557 ATTATAAATT
Statistics
Matches: 330, Mismatches: 61, Indels: 121
0.64 0.12 0.24
Matches are distributed among these distances:
17 4 0.01
18 19 0.06
19 15 0.05
20 5 0.02
21 12 0.04
22 57 0.17
23 51 0.15
24 10 0.03
25 20 0.06
26 44 0.13
27 64 0.19
28 15 0.05
29 7 0.02
31 7 0.02
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (23 bp):
AATAAATTATTAATATTTTAAAT
Found at i:3058231 original size:41 final size:43
Alignment explanation
Indices: 3058184--3058382 Score: 140
Period size: 41 Copynumber: 4.4 Consensus size: 43
3058174 TTAACTTATA
3058184 AATAAAATATTAATATTT-TTAAATATTAATGA-TTAAAATAT
1 AATAAAATATTAATATTTATTAAATATTAATGATTTAAAATAT
*
3058225 AATAAAATATTAATATTTTAATTATCAATTATTAAT-ATTTGAAATA-
1 AATAAAATATTAATA-TTT-ATTA--AA-TATTAATGATTTAAAATAT
* * * *
3058271 AATGATCAATTATTAATATTTAGAAATAAATAATCCTAATAATATTTAAATTAT
1 AAT-A--AAATATTAATATTT---ATTAAAT-AT--TAAT--GATTTAAAATAT
* *
3058325 GAATAAAATATTAATATTT-TTAAAAATTAATGA-TTAAATTAT
1 -AATAAAATATTAATATTTATTAAATATTAATGATTTAAAATAT
3058367 AATAAAATATTAATAT
1 AATAAAATATTAATAT
3058383 GTAAAGTATC
Statistics
Matches: 129, Mismatches: 9, Indels: 40
0.72 0.05 0.22
Matches are distributed among these distances:
41 31 0.24
42 12 0.09
43 1 0.01
44 3 0.02
45 4 0.03
46 6 0.05
47 18 0.14
48 11 0.09
49 10 0.08
50 8 0.06
52 13 0.10
53 8 0.06
54 1 0.01
55 3 0.02
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (43 bp):
AATAAAATATTAATATTTATTAAATATTAATGATTTAAAATAT
Found at i:3058238 original size:142 final size:143
Alignment explanation
Indices: 3058062--3058878 Score: 847
Period size: 142 Copynumber: 5.7 Consensus size: 143
3058052 ACAATCCTCA
* *
3058062 AATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATAATAAATTATTAATATTTTAAA
1 AATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAA
* * *
3058127 TAAACTATAAATTATTAATATATAAAAATTAATAATCATAATAATATTTAACTTATAAATAAAAT
66 TAAATTATAAATTATTAATATTTAAAAATTAATAATCATAATAATATTTAAATTAT-AATAAAAT
3058192 ATTAATATTTTTA-
130 ATTAATATTTTTAT
* * *
3058205 AATATTAATGATTAAAATAT-AATAAAATATTAATATTTTAATTATCAATTATTAATATTTGAAA
1 AATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAA
* * * * *
3058269 TAAATGATCAATTATTAATATTTAGAAATAAATAATCCTAATAATATTTAAATTATGAATAAAAT
66 TAAATTATAAATTATTAATATTTAAAAATTAATAATCATAATAATATTTAAATTAT-AATAAAAT
3058334 ATTAATATTTTTA-
130 ATTAATATTTTTAT
* * * ** * *
3058347 AAAATTAATGATTAAATTAT-AATAAAATATTAATATGTAAAGTATCAATTATTAATATAATGAT
1 AATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAA
* * * *
3058411 TAAATTATAAATTATTAATATTTAAAAATAAATAACCATCATAATATTTAAATTATAGAGAAAAT
66 TAAATTATAAATTATTAATATTTAAAAATTAATAATCATAATAATATTTAAATTATA-ATAAAAT
*
3058476 ATTAATA-CTTTAT
130 ATTAATATTTTTAT
* *
3058489 AATGTTAATGATTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATGTTTTAAA
1 AATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAA
* * * * *
3058554 TAAATTATAAATTATAAATATTTAAAAA-TAA-AAT-A-AATAA-AATAAAAATATCATAATAAT
66 TAAATTATAAATTATTAATATTTAAAAATTAATAATCATAATAATATTTAAATTATAATAA-AAT
* *
3058614 ATT-A-ATTATAAT
130 ATTAATATTTTTAT
* * *
3058626 AACATTAAT-ATTTTATAATATTATAATTAAATTA-TAATATTTTAAATTATCAATTATTAATAT
1 AATATTAATGA---T-TAA-ATTATAAATAAAATATTAATA-TTTAAATTATCAATTATTAATAT
* * * *
3058689 TTGT-AATAAATTATAAATTATTAATATTTATAAGATAAAATGAAATAAAAATAATCATAATAAT
60 TT-TAAATAAATTATAAATTATTAATATTTA-AAAAT-TAAT--AATCATAATAAT-AT--T--T
* * *
3058753 AATTAAATATAATAAAATCTTAATA-TTATAT
115 -A--AATTATAATAAAATATTAATATTTTTAT
* ** * * * *
3058784 GATGCTAATGATTAAATTATCAATAAAATATTAACATTTAAATTATCAATTAGTAATGTTTTAAA
1 AATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAA
3058849 TAAATTATAAATTATTAATATTTTAAAAAT
66 TAAATTATAAATTATTAATA-TTTAAAAAT
3058879 AAAAATAAAA
Statistics
Matches: 560, Mismatches: 79, Indels: 59
0.80 0.11 0.08
Matches are distributed among these distances:
136 2 0.00
137 14 0.03
138 14 0.03
139 5 0.01
140 9 0.02
141 69 0.12
142 250 0.45
143 83 0.15
144 2 0.00
147 3 0.01
148 1 0.00
149 5 0.01
151 1 0.00
153 2 0.00
154 61 0.11
155 11 0.02
156 2 0.00
157 5 0.01
158 19 0.03
159 2 0.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (143 bp):
AATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAA
TAAATTATAAATTATTAATATTTAAAAATTAATAATCATAATAATATTTAAATTATAATAAAATA
TTAATATTTTTAT
Found at i:3058379 original size:25 final size:26
Alignment explanation
Indices: 3058344--3058420 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 26
3058334 ATTAATATTT
3058344 TTAAAA-ATTAATGATTAAATTATAA
1 TTAAAATATTAATGATTAAATTATAA
*
3058369 -TAAAATATTAAT-ATGTAAAGTATCAA
1 TTAAAATATTAATGAT-TAAATTAT-AA
*
3058395 TTATTAATA-TAATGATTAAATTATAA
1 TTA-AAATATTAATGATTAAATTATAA
3058421 ATTATTAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
24 7 0.16
25 13 0.30
26 4 0.09
27 13 0.30
28 6 0.14
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.40
Consensus pattern (26 bp):
TTAAAATATTAATGATTAAATTATAA
Found at i:3058748 original size:22 final size:22
Alignment explanation
Indices: 3058723--3058765 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3058713 TATTTATAAG
3058723 ATAA-AATGAAATAAAAATAATC
1 ATAATAAT-AAATAAAAATAATC
* *
3058745 ATAATAATAATTAAATATAAT
1 ATAATAATAAATAAAAATAAT
3058766 AAAATCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
ATAATAATAAATAAAAATAATC
Found at i:3058861 original size:27 final size:27
Alignment explanation
Indices: 3058822--3058875 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3058812 TATTAACATT
* *
3058822 TAAATTATCAATTAGTAATGTTTTAAA
1 TAAATTATAAATTAGTAATATTTTAAA
*
3058849 TAAATTATAAATTATTAATATTTTAAA
1 TAAATTATAAATTAGTAATATTTTAAA
3058876 AATAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (27 bp):
TAAATTATAAATTAGTAATATTTTAAA
Found at i:3059062 original size:16 final size:16
Alignment explanation
Indices: 3059038--3059068 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3059028 TACGTAATAA
*
3059038 CTATTTTATTCTATTT
1 CTATCTTATTCTATTT
3059054 CTATCTTATTCTATT
1 CTATCTTATTCTATT
3059069 CCCTTAGAAT
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:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (16 bp):
CTATCTTATTCTATTT
Found at i:3063890 original size:29 final size:29
Alignment explanation
Indices: 3063833--3063891 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
3063823 TAAAAATTAA
* *
3063833 AGACTTAATTAATATTTAATAACTAAATT
1 AGACTTAAATAATATTTAATAAATAAATT
3063862 AGACTTAAATAAT-TTT-ATAAAATAGAATT
1 AGACTTAAATAATATTTAAT-AAATA-AATT
3063891 A
1 A
3063892 TCATTTCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 2 0.08
28 7 0.27
29 17 0.65
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (29 bp):
AGACTTAAATAATATTTAATAAATAAATT
Found at i:3064201 original size:35 final size:35
Alignment explanation
Indices: 3064137--3064226 Score: 114
Period size: 35 Copynumber: 2.6 Consensus size: 35
3064127 ACATTATTTT
* *
3064137 ATGCAGAATAACTAAAA-AA-CGAAGTGTTACTTC
1 ATGCAAAATAACTAAAATAAGTGAAGTGTTACTTC
*
3064170 ATG-AATAATAATTAAAATAAGTGAAGTGTTACTTC
1 ATGCAA-AATAACTAAAATAAGTGAAGTGTTACTTC
*
3064205 ATGCAAAATAACTAGAATAAGT
1 ATGCAAAATAACTAAAATAAGT
3064227 AAAGCACTCC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
32 1 0.02
33 13 0.27
34 2 0.04
35 30 0.62
36 2 0.04
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (35 bp):
ATGCAAAATAACTAAAATAAGTGAAGTGTTACTTC
Found at i:3067462 original size:22 final size:23
Alignment explanation
Indices: 3067414--3067459 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3067404 CTTATTAATT
*
3067414 CAAAACTACTCAAAATTAGAAAC
1 CAAAACTACTCAAAATCAGAAAC
*
3067437 CAAAACTACTTAAATATCA-AAAC
1 CAAAACTACTCAAA-ATCAGAAAC
3067460 AAACCATGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.57, C:0.22, G:0.02, T:0.20
Consensus pattern (23 bp):
CAAAACTACTCAAAATCAGAAAC
Found at i:3070758 original size:2 final size:2
Alignment explanation
Indices: 3070751--3070776 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3070741 TTTGGTAAAC
3070751 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
3070777 GCTAATACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3085990 original size:2 final size:2
Alignment explanation
Indices: 3085985--3086012 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3085975 TGCGTGTGTG
3085985 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
3086013 AAATTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3090111 original size:2 final size:2
Alignment explanation
Indices: 3090104--3090136 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3090094 CTTAATTACG
3090104 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
3090137 ACGATTGTTT
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:3090788 original size:2 final size:2
Alignment explanation
Indices: 3090781--3090805 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3090771 CGATTGAGTT
3090781 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
3090806 CTAATTAGCC
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:3091539 original size:18 final size:18
Alignment explanation
Indices: 3091513--3091547 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3091503 TATCTCTACT
*
3091513 TCAAGTTTATAATTTATA
1 TCAAGTTTATAACTTATA
*
3091531 TCAATTTTATAACTTAT
1 TCAAGTTTATAACTTAT
3091548 GATTTGATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (18 bp):
TCAAGTTTATAACTTATA
Found at i:3093207 original size:599 final size:600
Alignment explanation
Indices: 3091886--3093688 Score: 3497
Period size: 599 Copynumber: 3.0 Consensus size: 600
3091876 AAGCTTATAG
3091886 TGGACAATTCTATGAACAATACTCCATTGGTTGTTCACAACAACCTTTCCTTTATGGACGCATTC
1 TGGACAATTCTATGAACAATACTCCATTGGTTGTTCACAACAACCTTTCCTTTATGGACGCATTC
*
3091951 CTTACTTCAGATGGTGAAGAGGCCTATTTCCAAAGTGATAGTGAATTTTCTGAGGATTTTAAGGA
66 CTTACTTCAGATGGTGAAGAGGCCTATTTCCAAAGTGACAGTGAATTTTCTGAGGATTTTAAGGA
3092016 TGATAAGGAGTCTGAGATGGATTGTAACTCAGATGCATCTGATGAAGAGGATTTTGAATATGGAT
131 TGATAAGGAGTCTGAGATGGATTGTAACTCAGATGCATCTGATGAAGAGGATTTTGAATATGGAT
*
3092081 TC-ATATTGAAGGGTTCCCTTTAATCACGGTTTTTAATCGGAGGCAAGATACATTACAAAGACAT
196 TCAATATTGAAGGGTTCCCTTTAATCACGGTTTCTAATCGGAGGCAAGATACATTACAAAGACAT
3092145 AGCATAACTCAATTATTGTATAGCTGCTAGGTTGCCCAATTTCATAAAAAGTACTTTGTGAGAAA
261 AGCATAACTCAATTATTGTATAGCTGCTAGGTTGCCCAATTTCATAAAAAGTACTTTGTGAGAAA
* *
3092210 GTTGTTAATCTTTGGAAACCAATAAAATGATATATTATTGTGGATTTGGATGATAACTGTTTTAT
326 GTTGCTAATCTTTGGAAACCAATAAAATGATATATTATTGTGGATTTGGATGATAATTGTTTTAT
3092275 TGTCCACTTTGTGAGAAAGGAGGATTACTTGAGAGCCTTATTGGCTGGACCATGGGTAATTATAG
391 TGTCCACTTTGTGAGAAAGGAGGATTACTTGAGAGCCTTATTGGCTGGACCATGGGTAATTATAG
3092340 GGCATTACCTGATTGTCAATCTCTAAATGCCTAA-TTTTCCAC-AATATGCAAGAACTCACAGTA
456 GGCATTACCTGATTGTCAATCTCTAAATGCCTAATTTTTCCACAAATATGCAAGAACTCACAGTA
3092403 GTGGTGACGTGGGTTCAGTTTCCTCACATTCTACTTCACTTGTATTACAAATCGATTCTTAGGCG
521 GTGGTGACGTGGGTTCAGTTTCCTCACATTCTACTTCACTTGTATTACAAATCGATTCTTAGGCG
3092468 AATTACCTCTTTGAT
586 AATTACCTCTTTGAT
3092483 TGGACAATTCTATGAACAATACTCCATTGGTTGTTCACAACAACCTTTCCTTTATGGACGCATTC
1 TGGACAATTCTATGAACAATACTCCATTGGTTGTTCACAACAACCTTTCCTTTATGGACGCATTC
3092548 CTTACTTCAGATGGTGAAGAGGCCTATTTCCAAAGTGACAGTGAATTTTCTGAGGATTTTAAGGA
66 CTTACTTCAGATGGTGAAGAGGCCTATTTCCAAAGTGACAGTGAATTTTCTGAGGATTTTAAGGA
3092613 TGATAAGGAGTCTGAGATGGATTGTAACTCAGATGCATCTGATGAAGAGGATTTTGAATATGGAT
131 TGATAAGGAGTCTGAGATGGATTGTAACTCAGATGCATCTGATGAAGAGGATTTTGAATATGGAT
3092678 TCAATATTGAAGGGTTCCCTTTAATCACGGTTTCTAATCGGAGGCAAGATACATTACAAAGACAT
196 TCAATATTGAAGGGTTCCCTTTAATCACGGTTTCTAATCGGAGGCAAGATACATTACAAAGACAT
3092743 AGCATAACTCAATTATTGTATAGCTGCTAGGTTGCCCAATTTCATAAAAAGTACTTTGTGAGAAA
261 AGCATAACTCAATTATTGTATAGCTGCTAGGTTGCCCAATTTCATAAAAAGTACTTTGTGAGAAA
3092808 GTTGCTAATCTTTGGAAACCAATAAAATGATATA-TATTGTGGATTTGGATGATAATTGTTTTAT
326 GTTGCTAATCTTTGGAAACCAATAAAATGATATATTATTGTGGATTTGGATGATAATTGTTTTAT
3092872 TGTCCACTTTGTGAGAAAGGAGGATTACTTGAGAGCCTTATTGGCTGGACCATGGGTAATTATAG
391 TGTCCACTTTGTGAGAAAGGAGGATTACTTGAGAGCCTTATTGGCTGGACCATGGGTAATTATAG
3092937 GGCATTACCTGATTGTCAATCTCTAAATGCCTAATTTTTCCACAAATATGCAAGAACTCACAGTA
456 GGCATTACCTGATTGTCAATCTCTAAATGCCTAATTTTTCCACAAATATGCAAGAACTCACAGTA
3093002 GTGGTGACGTGGGTTCAGTTTCCTCACATTCTACTTCACTTGTATTACAAATCGATTCTTAGGCG
521 GTGGTGACGTGGGTTCAGTTTCCTCACATTCTACTTCACTTGTATTACAAATCGATTCTTAGGCG
3093067 AATTACCTCTTTGAT
586 AATTACCTCTTTGAT
3093082 TGGACAATTCTATGAACAATACTCCATTGGTTGTTCACAACAACCTTTCCTTTATGGACGCATTC
1 TGGACAATTCTATGAACAATACTCCATTGGTTGTTCACAACAACCTTTCCTTTATGGACGCATTC
*
3093147 CTTACTTCAGATGGTGAAGAGGCCTACTTCCAAAGTGACAGTGAATTTTCTGAGGATTTTAAGGA
66 CTTACTTCAGATGGTGAAGAGGCCTATTTCCAAAGTGACAGTGAATTTTCTGAGGATTTTAAGGA
3093212 TGATAAGGAGTCTGAGATGGATTGTAACTCAGATGCATCTGATGAAGAGGATTTTGAATATGGAT
131 TGATAAGGAGTCTGAGATGGATTGTAACTCAGATGCATCTGATGAAGAGGATTTTGAATATGGAT
*
3093277 TCAATATTGAAGGGTTCCCTTTAATCACGGTTTCTAATCTGAGGCAAGATACATTACAAAGACAT
196 TCAATATTGAAGGGTTCCCTTTAATCACGGTTTCTAATCGGAGGCAAGATACATTACAAAGACAT
3093342 AGCATAACTCAATTATTGTATAGCTGCTAGGTTGCCCAATTTCATAAAAAGTACTTTGTGAGAAA
261 AGCATAACTCAATTATTGTATAGCTGCTAGGTTGCCCAATTTCATAAAAAGTACTTTGTGAGAAA
3093407 GTTGCTAATCTTTGGAAACCAATAAAATGATATATTATTGTGGATTTGGATGATAATTGTTTTAT
326 GTTGCTAATCTTTGGAAACCAATAAAATGATATATTATTGTGGATTTGGATGATAATTGTTTTAT
*
3093472 TGTCCACTTTATGAGAAAGGAGGATTACTTGAGAGCCTTATTGGCTGGACCATGGGTAATTATAG
391 TGTCCACTTTGTGAGAAAGGAGGATTACTTGAGAGCCTTATTGGCTGGACCATGGGTAATTATAG
*
3093537 GGCATTACCTGATTGTCAATCTCTAAATGCCTAATTTTTCCAAACAATATGCAAGAACTCACAGT
456 GGCATTACCTGATTGTCAATCTCTAAATGCCTAATTTTTCCACA-AATATGCAAGAACTCACAGT
3093602 AGTGGTGACGTGGGTTCAGTTTCCTCACATTCTACTTCACTTGTATTACAAATCGATTCTTAGGC
520 AGTGGTGACGTGGGTTCAGTTTCCTCACATTCTACTTCACTTGTATTACAAATCGATTCTTAGGC
3093667 GAATTACCTCTTTGAT
585 GAATTACCTCTTTGAT
3093683 TGGACA
1 TGGACA
3093689 TCTTTTGAAA
Statistics
Matches: 1193, Mismatches: 8, Indels: 6
0.99 0.01 0.00
Matches are distributed among these distances:
597 324 0.27
598 167 0.14
599 458 0.38
600 137 0.11
601 107 0.09
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (600 bp):
TGGACAATTCTATGAACAATACTCCATTGGTTGTTCACAACAACCTTTCCTTTATGGACGCATTC
CTTACTTCAGATGGTGAAGAGGCCTATTTCCAAAGTGACAGTGAATTTTCTGAGGATTTTAAGGA
TGATAAGGAGTCTGAGATGGATTGTAACTCAGATGCATCTGATGAAGAGGATTTTGAATATGGAT
TCAATATTGAAGGGTTCCCTTTAATCACGGTTTCTAATCGGAGGCAAGATACATTACAAAGACAT
AGCATAACTCAATTATTGTATAGCTGCTAGGTTGCCCAATTTCATAAAAAGTACTTTGTGAGAAA
GTTGCTAATCTTTGGAAACCAATAAAATGATATATTATTGTGGATTTGGATGATAATTGTTTTAT
TGTCCACTTTGTGAGAAAGGAGGATTACTTGAGAGCCTTATTGGCTGGACCATGGGTAATTATAG
GGCATTACCTGATTGTCAATCTCTAAATGCCTAATTTTTCCACAAATATGCAAGAACTCACAGTA
GTGGTGACGTGGGTTCAGTTTCCTCACATTCTACTTCACTTGTATTACAAATCGATTCTTAGGCG
AATTACCTCTTTGAT
Found at i:3105019 original size:29 final size:30
Alignment explanation
Indices: 3104945--3105020 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
3104935 ACCGTTAGTC
* *
3104945 ATAAAGACTTATTTAACTAAAACTAAAAAT
1 ATAAAAACTTATTTAAATAAAACTAAAAAT
* *
3104975 ATAAAAGCTTGA-TTAAATACAA-TAAAAGA-
1 ATAAAAACTT-ATTTAAATAAAACTAAAA-AT
3105004 ATAAAAACTTATTTAAA
1 ATAAAAACTTATTTAAA
3105021 ATTTTCTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 1 0.03
29 19 0.50
30 17 0.45
31 1 0.03
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (30 bp):
ATAAAAACTTATTTAAATAAAACTAAAAAT
Found at i:3116709 original size:31 final size:31
Alignment explanation
Indices: 3116671--3116742 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
3116661 GTGAGGTGTC
3116671 TATGTCCTCAGCCAAACTCGACTTTTATTTG
1 TATGTCCTCAGCCAAACTCGACTTTTATTTG
3116702 TATGTCCTCAGCCAAACTCGACTTTTATTTG
1 TATGTCCTCAGCCAAACTCGACTTTTATTTG
*
3116733 TGTGTCCTCA
1 TATGTCCTCA
3116743 CATTTAGTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (31 bp):
TATGTCCTCAGCCAAACTCGACTTTTATTTG
Found at i:3132390 original size:18 final size:16
Alignment explanation
Indices: 3132359--3132392 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
3132349 GATTAATAGC
3132359 AGTGTAAAAATTGAAA
1 AGTGTAAAAATTGAAA
3132375 AGTGATAAAGAATTGAAA
1 AGTG-TAAA-AATTGAAA
3132393 TTTGTTAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (16 bp):
AGTGTAAAAATTGAAA
Found at i:3134826 original size:17 final size:16
Alignment explanation
Indices: 3134800--3134831 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3134790 TTTATTTTTT
3134800 TTTCTCTTTCTTGGTG
1 TTTCTCTTTCTTGGTG
3134816 TTTCTTCTTTCTTGGT
1 TTTC-TCTTTCTTGGT
3134832 CGTAAGGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.19, G:0.16, T:0.66
Consensus pattern (16 bp):
TTTCTCTTTCTTGGTG
Found at i:3136298 original size:26 final size:28
Alignment explanation
Indices: 3136244--3136300 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 28
3136234 GGGAAAAAAT
3136244 GGAAAAAGAAAATTGCTTCAAATTAGAAGG
1 GGAAAAAG-AAATTGCTT-AAATTAGAAGG
*
3136274 GGAAAAAG-AATTGCTT-AATTGGAAGG
1 GGAAAAAGAAATTGCTTAAATTAGAAGG
3136300 G
1 G
3136301 TCTGAGAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 10 0.38
28 8 0.31
30 8 0.31
ACGTcount: A:0.46, C:0.05, G:0.28, T:0.21
Consensus pattern (28 bp):
GGAAAAAGAAATTGCTTAAATTAGAAGG
Found at i:3138098 original size:21 final size:22
Alignment explanation
Indices: 3138058--3138098 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3138048 TTCCAAAACT
3138058 TCAATTTTTTTGCTGCAATCAG
1 TCAATTTTTTTGCTGCAATCAG
3138080 TCAAGTTTTTTT-CTG-AATC
1 TCAA-TTTTTTTGCTGCAATC
3138099 CTTTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 7 0.39
23 7 0.39
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.49
Consensus pattern (22 bp):
TCAATTTTTTTGCTGCAATCAG
Found at i:3152386 original size:2 final size:2
Alignment explanation
Indices: 3152379--3152418 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
3152369 ATTAAACATG
* *
3152379 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TT TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3152419 GAACATTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3155528 original size:28 final size:27
Alignment explanation
Indices: 3155472--3155528 Score: 62
Period size: 28 Copynumber: 2.0 Consensus size: 27
3155462 TTATTATATT
**
3155472 TTTAATAATTTTAATAAAATAAATTTAA
1 TTTAATAA-TTTAATAAAATAAAAATAA
3155500 TTTAATAA-TTAATATAAATAAAAAATAA
1 TTTAATAATTTAATA-AAAT-AAAAATAA
3155528 T
1 T
3155529 AAAATAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 6 0.24
27 4 0.16
28 15 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TTTAATAATTTAATAAAATAAAAATAA
Found at i:3155970 original size:18 final size:18
Alignment explanation
Indices: 3155945--3155986 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3155935 TAATTTACTC
3155945 ATTA-TATAAA-ATTATTA
1 ATTATTATAAATATT-TTA
*
3155962 TTTATTATAAATATTTTA
1 ATTATTATAAATATTTTA
3155980 ATTATTA
1 ATTATTA
3155987 ATTAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 15 0.71
19 3 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTATTATAAATATTTTA
Found at i:3160684 original size:29 final size:29
Alignment explanation
Indices: 3160652--3160727 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
3160642 TTTTGCATAC
3160652 AAGTCTGAAGAACAAGTACTTTTCAAAAA
1 AAGTCTGAAGAACAAGTACTTTTCAAAAA
*
3160681 AAGTCTGAAGAACAATTACTTTTCAAAAA
1 AAGTCTGAAGAACAAGTACTTTTCAAAAA
* *
3160710 ACGTCCGAAGAACAAGTA
1 AAGTCTGAAGAACAAGTA
3160728 AAACACAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTCTGAAGAACAAGTACTTTTCAAAAA
Found at i:3163787 original size:5 final size:5
Alignment explanation
Indices: 3163777--3163808 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
3163767 GTGTTAAATG
*
3163777 ATTTT ATTTT ATTTT ATTTT ATTTT GTTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
3163809 AAGGTGTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:3177162 original size:24 final size:22
Alignment explanation
Indices: 3177128--3177187 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
3177118 AAATATTATG
*
3177128 TAAGTACTATTTAAATATAAATGA
1 TAAGTAATATTTAAAT-T-AATGA
*
3177152 TAAGTAATATTTTAATTAATGA
1 TAAGTAATATTTAAATTAATGA
*
3177174 TAATTAATAATTTA
1 TAAGTAAT-ATTTA
3177188 TTAATCATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 12 0.39
23 5 0.16
24 14 0.45
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (22 bp):
TAAGTAATATTTAAATTAATGA
Found at i:3177175 original size:22 final size:22
Alignment explanation
Indices: 3177128--3177197 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
3177118 AAATATTATG
* *
3177128 TAAGTACTATTTAAATATAAATGA
1 TAAGTAATATTTTAAT-T-AATGA
3177152 TAAGTAATATTTTAATTAATGA
1 TAAGTAATATTTTAATTAATGA
* * *
3177174 TAATTAATAATTT-ATTAATCA
1 TAAGTAATATTTTAATTAATGA
3177195 TAA
1 TAA
3177198 AAATTTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 10 0.24
22 16 0.39
23 1 0.02
24 14 0.34
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (22 bp):
TAAGTAATATTTTAATTAATGA
Found at i:3182227 original size:2 final size:2
Alignment explanation
Indices: 3182220--3182254 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3182210 AATTGAATAG
*
3182220 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3182255 GTGCATCAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3193296 original size:2 final size:2
Alignment explanation
Indices: 3193289--3193325 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3193279 GATAAAGAAG
3193289 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3193326 GCATCAAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3193821 original size:4 final size:4
Alignment explanation
Indices: 3193812--3193846 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
3193802 TATTGACTTT
3193812 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
3193847 TATATACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:3195172 original size:21 final size:21
Alignment explanation
Indices: 3195148--3195188 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3195138 TTAATGATAT
3195148 TATAAGTTCAAATAATTTATA
1 TATAAGTTCAAATAATTTATA
* * *
3195169 TATATGTTTAATTAATTTAT
1 TATAAGTTCAAATAATTTAT
3195189 TTAAATGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
TATAAGTTCAAATAATTTATA
Found at i:3202844 original size:12 final size:12
Alignment explanation
Indices: 3202827--3202851 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3202817 ATAAAAAATG
3202827 CTGATAATTGCC
1 CTGATAATTGCC
3202839 CTGATAATTGCC
1 CTGATAATTGCC
3202851 C
1 C
3202852 AGAATCATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (12 bp):
CTGATAATTGCC
Found at i:3210120 original size:59 final size:59
Alignment explanation
Indices: 3210009--3210122 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 59
3209999 AACTAAATCT
* * * * *
3210009 TCAACATGACATGTAACAATTATATTTTTTAACATAGCGTGCAACAACTAAATTTTTTA
1 TCAACATGACATATAACAATTACATTTTTCAACATAACGTACAACAACTAAATTTTTTA
* * * * *
3210068 TCAACATGGCATATAACAATTACATTTTTCAACATAATGTATAATAATTAAATTT
1 TCAACATGACATATAACAATTACATTTTTCAACATAACGTACAACAACTAAATTT
3210123 CAATATGACA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
59 45 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (59 bp):
TCAACATGACATATAACAATTACATTTTTCAACATAACGTACAACAACTAAATTTTTTA
Found at i:3210158 original size:28 final size:28
Alignment explanation
Indices: 3209993--3210281 Score: 124
Period size: 27 Copynumber: 10.6 Consensus size: 28
3209983 CATCATAATG
* * *
3209993 TGTAACAACTA-AATCTTCAACATGACA
1 TGTAACAACTACATTTTTTAACATGACA
* * *
3210020 TGTAACAATTATATTTTTTAACAT-AGCG
1 TGTAACAACTACATTTTTTAACATGA-CA
* * *
3210048 TGCAACAACTAAATTTTTTATCAACATGGCA
1 TGTAACAACTACA-TTTTT-T-AACATGACA
* * *
3210079 TATAACAATTACATTTTTCAACAT-A-A
1 TGTAACAACTACATTTTTTAACATGACA
* * *
3210105 TGT-ATAA-TA-ATTAAATTTCAATATGACA
1 TGTAACAACTACATT---TTTTAACATGACA
*
3210133 TGTAATAACTACATTTTTTAACATGACA
1 TGTAACAACTACATTTTTTAACATGACA
* * *
3210161 TGTAACAACTA-AATTTTTAATATGACG
1 TGTAACAACTACATTTTTTAACATGACA
* * * * *
3210188 TATAATAAATACA-TTTTCAACATGATA
1 TGTAACAACTACATTTTTTAACATGACA
* ** **
3210215 TGTAACAA-T-TA-TTTCCAACATGATG
1 TGTAACAACTACATTTTTTAACATGACA
* *
3210240 TGTAAC-ACTAAATTTTTTAACATGACG
1 TGTAACAACTACATTTTTTAACATGACA
3210267 T-TAACAA-TAC-TTTTT
1 TGTAACAACTACATTTTT
3210282 CCAATACTCT
Statistics
Matches: 201, Mismatches: 42, Indels: 40
0.71 0.15 0.14
Matches are distributed among these distances:
23 3 0.01
24 3 0.01
25 28 0.14
26 19 0.09
27 62 0.31
28 51 0.25
29 9 0.04
30 8 0.04
31 18 0.09
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (28 bp):
TGTAACAACTACATTTTTTAACATGACA
Found at i:3210174 original size:54 final size:54
Alignment explanation
Indices: 3209993--3210273 Score: 182
Period size: 54 Copynumber: 5.1 Consensus size: 54
3209983 CATCATAATG
* * *
3209993 TGTAACAACTAAATCTTCAACATGACATGTAACAATTATATTTTTTAACAT-AGCG
1 TGTAACAACTAAAT-TTCAACATGACATGTAACAACTACATTTTTTAACATGA-CA
* * * * *
3210048 TGCAACAACTAAATTTTTTATCAACATGGCATATAACAATTACATTTTTCAACAT-A-A
1 TGTAACAACTAAA----TT-TCAACATGACATGTAACAACTACATTTTTTAACATGACA
* * * *
3210105 TGTATAATAATTAAATTTCAATATGACATGTAATAACTACATTTTTTAACATGACA
1 TG--TAACAACTAAATTTCAACATGACATGTAACAACTACATTTTTTAACATGACA
* * * * * * * *
3210161 TGTAACAACTAAATTTTTAATATGACGTATAATAAATACA-TTTTCAACATGATA
1 TGTAACAACTAAA-TTTCAACATGACATGTAACAACTACATTTTTTAACATGACA
* ** * *
3210215 TGTAACAA-T-TATTTCCAACATGATGTGTAAC-ACTAAATTTTTTAACATGACG
1 TGTAACAACTAAATTT-CAACATGACATGTAACAACTACATTTTTTAACATGACA
3210267 T-TAACAA
1 TGTAACAA
3210274 TACTTTTTCC
Statistics
Matches: 180, Mismatches: 34, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
51 13 0.07
52 24 0.13
53 1 0.01
54 58 0.32
55 37 0.21
56 3 0.02
57 2 0.01
58 1 0.01
59 41 0.23
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (54 bp):
TGTAACAACTAAATTTCAACATGACATGTAACAACTACATTTTTTAACATGACA
Found at i:3234833 original size:251 final size:252
Alignment explanation
Indices: 3234319--3234893 Score: 619
Period size: 251 Copynumber: 2.3 Consensus size: 252
3234309 TTACGTCAAA
** * *
3234319 ATTTAAAAATTAAAATTTGCATATTGTTAAACACTTTTAGTTTGAGAATATAAATTTAAATATTT
1 ATTTAAAAATTAAAATTTATATATTGTTAAACACTTTTAGTTCGAAAATATAAATTTAAATA-TT
* ** * * *
3234384 TATTTTTCACTAAAGTTAGATTTTTTTTACTTAATTGACTTGTTAAGTTAACTTCTACACTTTTA
65 TATTTTTCACTAAAATTAGAAATATTTTACTTAATTGACTTATTAAGTTAACTTCTACACATTTA
*
3234449 CGTTAAGATTTAAAATTTAGTTATTCTACATTTATAAGTTTTTATATCAATTCTCGTTGTTTAAC
130 CGTTAAGATTTAAAATTTAGTTATTCTACATTTATAAGTTTTTACATCAATTCTCGTTGTTTAAC
** * * * *********
3234514 GTCAAGATTTTTCTGTATTAATTTTGAAGTATAATTATTTTGATCTTTANNNNNNNNN
195 AACAAGATTTTTCTATATTAATTTTAAACTATAATTATTTTGATCTTTAATTATTTTT
* * * * * *
3234572 NTTTAAAAATTAAAATTTATATATTGTTAAATACTTTTAATCCGAAAATATAAATATAAATGTTT
1 ATTTAAAAATTAAAATTTATATATTGTTAAACACTTTTAGTTCGAAAATATAAATTTAAATATTT
*
3234637 ATTTTTCACTAAAATTA-AAATATTTTACTTAATTGACTTATTATGTTAACTT-TCACACATTTA
66 ATTTTTCACTAAAATTAGAAATATTTTACTTAATTGACTTATTAAGTTAACTTCT-ACACATTTA
* * * ** *
3234700 CTTTAAGATTT-AAATTTAGTTATT-TCACTTTTATAAGTTTTTACGTCAATT-TTTTTAGTTTT
130 CGTTAAGATTTAAAATTTAGTTATTCT-ACATTTATAAGTTTTTACATCAATTCTCGTT-GTTTA
* *
3234762 ACAACAAGGTTTATT-TATGTTAATTTTAAACTATAATTATTTT-AT-TATTATTATTATTTTT
193 ACAACAAGATTT-TTCTATATTAATTTTAAACTATAATTATTTTGATCT-TTA--ATTATTTTT
* * *
3234823 ATTTAAAAATTAAAATCTATATATCGTTAAACAATTTTAGTTC-AAGAATATAAATTTAAATATT
1 ATTTAAAAATTAAAATTTATATATTGTTAAACACTTTTAGTTCGAA-AATATAAATTTAAATATT
3234887 TATTTTT
65 TATTTTT
3234894 TATTAAAANN
Statistics
Matches: 265, Mismatches: 49, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
248 1 0.00
249 9 0.03
250 75 0.28
251 109 0.41
252 19 0.07
253 52 0.20
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.49
Consensus pattern (252 bp):
ATTTAAAAATTAAAATTTATATATTGTTAAACACTTTTAGTTCGAAAATATAAATTTAAATATTT
ATTTTTCACTAAAATTAGAAATATTTTACTTAATTGACTTATTAAGTTAACTTCTACACATTTAC
GTTAAGATTTAAAATTTAGTTATTCTACATTTATAAGTTTTTACATCAATTCTCGTTGTTTAACA
ACAAGATTTTTCTATATTAATTTTAAACTATAATTATTTTGATCTTTAATTATTTTT
Found at i:3235108 original size:24 final size:24
Alignment explanation
Indices: 3235076--3235122 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3235066 ACAATTTTAA
*
3235076 ATTACATATGTTTTTATTT-TTATT
1 ATTACATAT-TTTTAATTTATTATT
*
3235100 ATTATATATTTTTAATTTATTAT
1 ATTACATATTTTTAATTTATTAT
3235123 AATGATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (24 bp):
ATTACATATTTTTAATTTATTATT
Found at i:3235111 original size:16 final size:18
Alignment explanation
Indices: 3235090--3235123 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3235080 CATATGTTTT
3235090 TATTTTT-A-TTATTATA
1 TATTTTTAATTTATTATA
3235106 TATTTTTAATTTATTATA
1 TATTTTTAATTTATTATA
3235124 ATGATAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTTTAATTTATTATA
Found at i:3235299 original size:14 final size:15
Alignment explanation
Indices: 3235273--3235317 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
3235263 ATTTTTTACA
*
3235273 AATTTTAAA-TTAAT
1 AATTATAAATTTAAT
3235287 AATTAT-AATTTAAT
1 AATTATAAATTTAAT
*
3235301 -TTTATAAATTTAAT
1 AATTATAAATTTAAT
3235315 AAT
1 AAT
3235318 ATTTATTAAN
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 6 0.24
14 18 0.72
15 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTATAAATTTAAT
Found at i:3255020 original size:35 final size:35
Alignment explanation
Indices: 3254973--3255130 Score: 181
Period size: 35 Copynumber: 4.5 Consensus size: 35
3254963 TTAAATTGTA
* *
3254973 CCTAATTAATTAAATTATTTAATTAAATCATTGGG
1 CCTAATTAATTAAATTATTTAATTAAGTTATTGGG
* * *
3255008 CTTAATTAATTAAATTATTTACTTAAGTTATTGGA
1 CCTAATTAATTAAATTATTTAATTAAGTTATTGGG
*** *
3255043 CCTAATTAATTAAATTAAACAATTAAGTTATTGAG
1 CCTAATTAATTAAATTATTTAATTAAGTTATTGGG
* * * *
3255078 CTTAATTGATTAAAATTGTTTAATTAAGTTATTTGG
1 CCTAATTAATT-AAATTATTTAATTAAGTTATTGGG
*
3255114 CCTAATTGATTAAATTA
1 CCTAATTAATTAAATTA
3255131 AACAATTAAG
Statistics
Matches: 100, Mismatches: 22, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
35 72 0.72
36 28 0.28
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.44
Consensus pattern (35 bp):
CCTAATTAATTAAATTATTTAATTAAGTTATTGGG
Found at i:3255053 original size:70 final size:71
Alignment explanation
Indices: 3254948--3255139 Score: 232
Period size: 70 Copynumber: 2.8 Consensus size: 71
3254938 CAAGCACTTG
* * *** *
3254948 ATTAAAATTGTTTAATTAA---ATTGTACCTAATTAATTAAATTATTTAATTAAATCATTGGGCT
1 ATTAAAATTATTTAATTAAGTTATTGGACCTAATTAATTAAATTAAACAATTAAATCATTGAGCT
3255010 TAATTA
66 TAATTA
* * *
3255016 ATT-AAATTATTTACTTAAGTTATTGGACCTAATTAATTAAATTAAACAATTAAGTTATTGAGCT
1 ATTAAAATTATTTAATTAAGTTATTGGACCTAATTAATTAAATTAAACAATTAAATCATTGAGCT
*
3255080 TAATTG
66 TAATTA
* *
3255086 ATTAAAATTGTTTAATTAAGTTATTTGG-CCTAATTGATTAAATTAAACAATTAA
1 ATTAAAATTATTTAATTAAGTTA-TTGGACCTAATTAATTAAATTAAACAATTAA
3255140 GTTAACTAGG
Statistics
Matches: 106, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
67 13 0.12
68 3 0.03
70 44 0.42
71 42 0.40
72 4 0.04
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (71 bp):
ATTAAAATTATTTAATTAAGTTATTGGACCTAATTAATTAAATTAAACAATTAAATCATTGAGCT
TAATTA
Found at i:3255129 original size:71 final size:70
Alignment explanation
Indices: 3254945--3255143 Score: 244
Period size: 71 Copynumber: 2.9 Consensus size: 70
3254935 TCTCAAGCAC
* *** * * *
3254945 TTGATTAAAATTGTTTAATTAA---ATTGTACCTAATTAATTAAATTATTTAATTAAATCATTGG
1 TTGATTAAAATTGTTTAATTAAGTTATTG-GCCTAATTAATTAAATTAAACAATTAAGTTATTGA
3255007 GCTTAA
65 GCTTAA
* * *
3255013 TTAATT-AAATTATTTACTTAAGTTATTGGACCTAATTAATTAAATTAAACAATTAAGTTATTGA
1 TTGATTAAAATTGTTTAATTAAGTTATTGG-CCTAATTAATTAAATTAAACAATTAAGTTATTGA
3255077 GCTTAA
65 GCTTAA
*
3255083 TTGATTAAAATTGTTTAATTAAGTTATTTGGCCTAATTGATTAAATTAAACAATTAAGTTA
1 TTGATTAAAATTGTTTAATTAAGTTA-TTGGCCTAATTAATTAAATTAAACAATTAAGTTA
3255144 ACTAGGCTTC
Statistics
Matches: 111, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
67 13 0.12
68 5 0.05
70 43 0.39
71 46 0.41
72 4 0.04
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (70 bp):
TTGATTAAAATTGTTTAATTAAGTTATTGGCCTAATTAATTAAATTAAACAATTAAGTTATTGAG
CTTAA
Found at i:3255138 original size:35 final size:34
Alignment explanation
Indices: 3255030--3255143 Score: 138
Period size: 35 Copynumber: 3.2 Consensus size: 34
3255020 AATTATTTAC
*
3255030 TTAAGTTATTGGACCTAATTAATTAAATTAAACAA
1 TTAAGTTATTGG-CCTAATTGATTAAATTAAACAA
* ****
3255065 TTAAGTTATTGAGCTTAATTGATTAAAATTGTTTAA
1 TTAAGTTATTG-GCCTAATTGATT-AAATTAAACAA
3255101 TTAAGTTATTTGGCCTAATTGATTAAATTAAACAA
1 TTAAGTTA-TTGGCCTAATTGATTAAATTAAACAA
3255136 TTAAGTTA
1 TTAAGTTA
3255144 ACTAGGCTTC
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
35 35 0.54
36 27 0.42
37 3 0.05
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.42
Consensus pattern (34 bp):
TTAAGTTATTGGCCTAATTGATTAAATTAAACAA
Found at i:3261008 original size:13 final size:14
Alignment explanation
Indices: 3260990--3261022 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3260980 ATATGCTCAG
*
3260990 GAAAAAGAAG-AAA
1 GAAAAAAAAGAAAA
3261003 GAAAAAAAAGAAAA
1 GAAAAAAAAGAAAA
3261017 GAAAAA
1 GAAAAA
3261023 TAAAAATAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAGAAAA
Found at i:3271308 original size:2 final size:2
Alignment explanation
Indices: 3271303--3271335 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3271293 TTTGTGTGAG
3271303 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
3271336 ACACTAGATG
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:3274112 original size:31 final size:31
Alignment explanation
Indices: 3274061--3274128 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
3274051 GGTTCCCCCC
3274061 ACATTTCCCTCCAAAAAGTTTTCCCTCCAAA
1 ACATTTCCCTCCAAAAAGTTTTCCCTCCAAA
3274092 AGCATTTCCCTCC-AAAAGTTTTCCCTCCAAA
1 A-CATTTCCCTCCAAAAAGTTTTCCCTCCAAA
3274123 ACATTT
1 ACATTT
3274129 AGGAGGGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 5 0.14
31 20 0.56
32 11 0.31
ACGTcount: A:0.31, C:0.34, G:0.04, T:0.31
Consensus pattern (31 bp):
ACATTTCCCTCCAAAAAGTTTTCCCTCCAAA
Found at i:3274116 original size:15 final size:15
Alignment explanation
Indices: 3274064--3274123 Score: 93
Period size: 16 Copynumber: 3.9 Consensus size: 15
3274054 TCCCCCCACA
3274064 TTTCCCTCCAAAAAGT
1 TTTCCCTCC-AAAAGT
*
3274080 TTTCCCTCCAAAAGCA
1 TTTCCCTCCAAAAG-T
3274096 TTTCCCTCCAAAAGT
1 TTTCCCTCCAAAAGT
3274111 TTTCCCTCCAAAA
1 TTTCCCTCCAAAA
3274124 CATTTAGGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
15 18 0.44
16 23 0.56
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (15 bp):
TTTCCCTCCAAAAGT
Found at i:3274373 original size:15 final size:15
Alignment explanation
Indices: 3274355--3274425 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
3274345 TGCCACACAT
3274355 CTGCGTGCCGCGTAC
1 CTGCGTGCCGCGTAC
* *
3274370 CTGCGTGCCACGCATC
1 CTGCGTGCCGCGTA-C
3274386 C-GCGTGCCGCGTAC
1 CTGCGTGCCGCGTAC
* * *
3274400 CTACGCGCCACGTAC
1 CTGCGTGCCGCGTAC
3274415 CTGCGTGCCGC
1 CTGCGTGCCGC
3274426 ACATCGATTG
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
14 2 0.05
15 40 0.91
16 2 0.05
ACGTcount: A:0.10, C:0.44, G:0.30, T:0.17
Consensus pattern (15 bp):
CTGCGTGCCGCGTAC
Found at i:3274379 original size:30 final size:30
Alignment explanation
Indices: 3274345--3274425 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
3274335 CCATTTTGCA
* *
3274345 TGCCACACATCTGCGTGCCGCGTACCTGCG
1 TGCCACGCATCTGCGTGCCGCGTACCTACG
*
3274375 TGCCACGCATCCGCGTGCCGCGTACCTACG
1 TGCCACGCATCTGCGTGCCGCGTACCTACG
* * *
3274405 CGCCACGTACCTGCGTGCCGC
1 TGCCACGCATCTGCGTGCCGC
3274426 ACATCGATTG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.12, C:0.43, G:0.27, T:0.17
Consensus pattern (30 bp):
TGCCACGCATCTGCGTGCCGCGTACCTACG
Found at i:3279627 original size:14 final size:15
Alignment explanation
Indices: 3279589--3279648 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 15
3279579 GGTTCCCCCA
3279589 CATTTCCCTCCAAA-
1 CATTTCCCTCCAAAG
*
3279603 -AGTTCCCTCCAAAG
1 CATTTCCCTCCAAAG
3279617 CATTT-CCTCCAAAG
1 CATTTCCCTCCAAAG
*
3279631 -TTTTCCCTCCAAA-
1 CATTTCCCTCCAAAG
3279644 CATTT
1 CATTT
3279649 AAGAGGAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 15 0.39
14 20 0.53
15 3 0.08
ACGTcount: A:0.27, C:0.37, G:0.05, T:0.32
Consensus pattern (15 bp):
CATTTCCCTCCAAAG
Found at i:3279636 original size:28 final size:27
Alignment explanation
Indices: 3279588--3279648 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 27
3279578 AGGTTCCCCC
3279588 ACATTTCCCTCCAAAAGTTCCCTCCAA
1 ACATTTCCCTCCAAAAGTTCCCTCCAA
3279615 AGCATTT-CCTCC-AAAGTTTTCCCTCCAA
1 A-CATTTCCCTCCAAAAG--TTCCCTCCAA
3279643 ACATTT
1 ACATTT
3279649 AAGAGGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 4 0.13
27 11 0.35
28 16 0.52
ACGTcount: A:0.28, C:0.36, G:0.05, T:0.31
Consensus pattern (27 bp):
ACATTTCCCTCCAAAAGTTCCCTCCAA
Found at i:3284229 original size:2 final size:2
Alignment explanation
Indices: 3284222--3284247 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3284212 ACATGTAACA
3284222 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
3284248 TGAAAAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3284913 original size:18 final size:19
Alignment explanation
Indices: 3284872--3284913 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
3284862 TGAAAGAGAG
* *
3284872 AATAAACAATTACATACAA
1 AATAAACAATGACAAACAA
*
3284891 CATAAACAA-GACAAACAA
1 AATAAACAATGACAAACAA
3284909 AATAA
1 AATAA
3284914 GTAGGAATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.67, C:0.17, G:0.02, T:0.14
Consensus pattern (19 bp):
AATAAACAATGACAAACAA
Found at i:3289863 original size:13 final size:13
Alignment explanation
Indices: 3289845--3289869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3289835 CCTTCCCCCT
3289845 TTTTTATTTTTTA
1 TTTTTATTTTTTA
3289858 TTTTTATTTTTT
1 TTTTTATTTTTT
3289870 CTAAAAACTA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:3296394 original size:10 final size:10
Alignment explanation
Indices: 3296377--3296425 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
3296367 CGTAAAATTT
3296377 TAAA-AAAAA
1 TAAATAAAAA
*
3296386 TAAATAAAAT
1 TAAATAAAAA
3296396 TAAA-AATAAA
1 TAAATAA-AAA
3296406 T-AATAATAAA
1 TAAATAA-AAA
3296416 TAAATAAAAA
1 TAAATAAAAA
3296426 CTTTAAAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
9 8 0.24
10 21 0.62
11 5 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:3305408 original size:3 final size:3
Alignment explanation
Indices: 3305400--3305435 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3305390 TATCTTACTT
*
3305400 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3305436 CTCTGCAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3307876 original size:17 final size:16
Alignment explanation
Indices: 3307841--3307875 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3307831 GCTTTTTTTG
3307841 AAATTTTATTTTTTAA
1 AAATTTTATTTTTTAA
3307857 AAATTTTATTTTTTAA
1 AAATTTTATTTTTTAA
3307873 AAA
1 AAA
3307876 ACCTCTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATTTTATTTTTTAA
Found at i:3308357 original size:31 final size:31
Alignment explanation
Indices: 3308304--3308376 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
3308294 TGAAATGATA
*
3308304 ATTT-TATTTTTTATTAATTTTAAAATTATT
1 ATTTATATTTTTTATTAATTTTAAAATTACT
*
3308334 ATTATATATTTTTTATTCA-TTTAAAATTACT
1 ATT-TATATTTTTTATTAATTTTAAAATTACT
*
3308365 ATTTTTATTTTT
1 ATTTATATTTTT
3308377 AAAAAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 11 0.29
31 15 0.39
32 12 0.32
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (31 bp):
ATTTATATTTTTTATTAATTTTAAAATTACT
Found at i:3325052 original size:18 final size:19
Alignment explanation
Indices: 3325015--3325055 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
3325005 GTAAATTTTT
3325015 TTATAAGTTTTTTTATAAA
1 TTATAAGTTTTTTTATAAA
3325034 TTATAA-TTTTTGTTA-AAA
1 TTATAAGTTTTT-TTATAAA
3325052 TTAT
1 TTAT
3325056 CATAAAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTATAAGTTTTTTTATAAA
Found at i:3325125 original size:17 final size:19
Alignment explanation
Indices: 3325093--3325130 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
3325083 TTATTGTAAT
3325093 TATTTTTAACAAATAAAAA
1 TATTTTTAACAAATAAAAA
3325112 TATTTTT-A-AAATAAAAA
1 TATTTTTAACAAATAAAAA
3325129 TA
1 TA
3325131 AAAATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
18 1 0.05
19 7 0.37
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTTTTAACAAATAAAAA
Found at i:3325155 original size:22 final size:24
Alignment explanation
Indices: 3325092--3325156 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
3325082 ATTATTGTAA
*
3325092 TTATTTTTAACAAATAAAAATATTT
1 TTATATTTAA-AAATAAAAATATTT
**
3325117 TTA-AAATAAAAATAAAAAT-TTT
1 TTATATTTAAAAATAAAAATATTT
3325139 TTATATTTAAAAA-AAAAA
1 TTATATTTAAAAATAAAAA
3325157 GAAAAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
22 11 0.32
23 17 0.50
24 3 0.09
25 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TTATATTTAAAAATAAAAATATTT
Found at i:3325223 original size:17 final size:17
Alignment explanation
Indices: 3325197--3325239 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
3325187 CATAAGCTCT
*
3325197 TTTTTA-AAAAAATTTA
1 TTTTTATAAAAAAGTTA
3325213 TTTTTATAAAAAAGTTA
1 TTTTTATAAAAAAGTTA
*
3325230 TTTTTTTAAA
1 TTTTTATAAA
3325240 GAGTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTTTATAAAAAAGTTA
Found at i:3336643 original size:31 final size:31
Alignment explanation
Indices: 3336607--3336678 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
3336597 TCTAGAAGAA
3336607 ACTATGACATTCAAAACCTTGGTCTAGCCTT
1 ACTATGACATTCAAAACCTTGGTCTAGCCTT
3336638 ACTATGACATTCAAAACCTTGGTCTAGCCTT
1 ACTATGACATTCAAAACCTTGGTCTAGCCTT
3336669 ACATATGACA
1 AC-TATGACA
3336679 GTCTTCAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 33 0.82
32 7 0.17
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (31 bp):
ACTATGACATTCAAAACCTTGGTCTAGCCTT
Found at i:3340476 original size:3 final size:3
Alignment explanation
Indices: 3340468--3340496 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3340458 ACGGGCTGTT
3340468 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3340497 TGATTGGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3342876 original size:6 final size:6
Alignment explanation
Indices: 3342865--3342901 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
3342855 AGACAACAGG
*
3342865 GTTTAT GTTTAT GTTTAT GTTTAT GTTTGT GTTTAT G
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT G
3342902 ATCTTCTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.22, T:0.65
Consensus pattern (6 bp):
GTTTAT
Found at i:3343939 original size:11 final size:12
Alignment explanation
Indices: 3343915--3343942 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3343905 TCTCTAACTC
3343915 TTTAAACTTTTT
1 TTTAAACTTTTT
3343927 TTTAAACTTTTT
1 TTTAAACTTTTT
3343939 TTTA
1 TTTA
3343943 CTCATTGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAAACTTTTT
Found at i:3344474 original size:15 final size:15
Alignment explanation
Indices: 3344454--3344483 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3344444 TTCTTTATTT
*
3344454 ATATTTTATAATAAA
1 ATATTTCATAATAAA
3344469 ATATTTCATAATAAA
1 ATATTTCATAATAAA
3344484 TTTTATATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTTCATAATAAA
Found at i:3348579 original size:15 final size:15
Alignment explanation
Indices: 3348555--3348610 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
3348545 AGGCAGTGAA
*
3348555 GAAGAGGATGATGAT
1 GAAGATGATGATGAT
*
3348570 GAAGATGATGACT-CT
1 GAAGATGATGA-TGAT
* *
3348585 GATGATGATGAGGAT
1 GAAGATGATGATGAT
*
3348600 GAGGATGATGA
1 GAAGATGATGA
3348611 AGAGGCCATG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 32 0.97
16 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.38, T:0.23
Consensus pattern (15 bp):
GAAGATGATGATGAT
Found at i:3351839 original size:26 final size:25
Alignment explanation
Indices: 3351805--3351872 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 25
3351795 CCCCAACATA
* *
3351805 AAAAATGAAAAAAAAGTCCATCAAAC
1 AAAAGTGAAAAAAAAAT-CATCAAAC
3351831 AAAAGTGAAAAAAGAGAAAATCATCAAAC
1 AAAAGTG--AAAA-A-AAAATCATCAAAC
3351860 AAAAGTGAAAAAA
1 AAAAGTGAAAAAA
3351873 GGGAAAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
25 1 0.03
26 7 0.19
27 4 0.11
28 4 0.11
29 16 0.44
30 4 0.11
ACGTcount: A:0.68, C:0.10, G:0.12, T:0.10
Consensus pattern (25 bp):
AAAAGTGAAAAAAAAATCATCAAAC
Found at i:3351856 original size:29 final size:29
Alignment explanation
Indices: 3351823--3351881 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3351813 AAAAAAAGTC
3351823 CATCAAACAAAAGTGAAAAAAGAGAAAAT
1 CATCAAACAAAAGTGAAAAAAGAGAAAAT
*
3351852 CATCAAACAAAAGTGAAAAAAGGGAAAAT
1 CATCAAACAAAAGTGAAAAAAGAGAAAAT
3351881 C
1 C
3351882 TTGGGGGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.63, C:0.12, G:0.15, T:0.10
Consensus pattern (29 bp):
CATCAAACAAAAGTGAAAAAAGAGAAAAT
Found at i:3358779 original size:32 final size:33
Alignment explanation
Indices: 3358717--3358789 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
3358707 GGTGATGATG
* *
3358717 AAAATATTTTTTATAAAATGATTCAAATAATAT
1 AAAATATTTTTGATAAAATGATTCAAATAATAA
* * *
3358750 AAAATATTTTTGATAATAT-ATTTATATAATAA
1 AAAATATTTTTGATAAAATGATTCAAATAATAA
3358782 AAAATATT
1 AAAATATT
3358790 AAAATTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 18 0.51
33 17 0.49
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (33 bp):
AAAATATTTTTGATAAAATGATTCAAATAATAA
Found at i:3366926 original size:4 final size:4
Alignment explanation
Indices: 3366917--3366946 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
3366907 TTATTATTGT
3366917 TTTC TTTC TTTC TTTC TTTC TTTC -TTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
3366947 TTTATTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:3371008 original size:34 final size:34
Alignment explanation
Indices: 3370970--3371039 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
3370960 ATATACCAAT
*
3370970 TGATCTAAAAATGAAAATAGAGAGACCGAAATAA
1 TGATCTAAAAATGAAAATAGAGAGACAGAAATAA
* *
3371004 TGATCTAAATATGAAAATAGAGAGGCAGAAATAA
1 TGATCTAAAAATGAAAATAGAGAGACAGAAATAA
3371038 TG
1 TG
3371040 GTGTCGTGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (34 bp):
TGATCTAAAAATGAAAATAGAGAGACAGAAATAA
Found at i:3380035 original size:25 final size:25
Alignment explanation
Indices: 3379973--3380023 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
3379963 ATTTAAAAAA
*
3379973 ATTTAAATAAAATCTTTTTTTATTAT
1 ATTT-AATCAAATCTTTTTTTATTAT
*
3379999 ATTTAATCAAAT-TTTTATTTTTTAT
1 ATTTAATCAAATCTTTT-TTTATTAT
3380024 TTTGAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 4 0.18
25 14 0.64
26 4 0.18
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTTAATCAAATCTTTTTTTATTAT
Found at i:3381376 original size:12 final size:12
Alignment explanation
Indices: 3381359--3381387 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3381349 ACATTTTCTT
3381359 TTTTATGTATAA
1 TTTTATGTATAA
3381371 TTTTATGTATAA
1 TTTTATGTATAA
3381383 TTTTA
1 TTTTA
3381388 AGATAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (12 bp):
TTTTATGTATAA
Found at i:3381811 original size:10 final size:9
Alignment explanation
Indices: 3381782--3381970 Score: 50
Period size: 9 Copynumber: 21.9 Consensus size: 9
3381772 TCATATATTT
*
3381782 TATTTTCATT
1 TATTTT-ATA
3381792 TATTATTATA
1 TATT-TTATA
3381802 -ATTTTATA
1 TATTTTATA
3381810 TATTTTAT-
1 TATTTTATA
*
3381818 T-TTTAATA
1 TATTTTATA
3381826 TA-TTTATA
1 TATTTTATA
3381834 T-TTTTAT-
1 TATTTTATA
3381841 TA--TTA-A
1 TATTTTATA
3381847 T-TTTTATA
1 TATTTTATA
* *
3381855 TAATATTATC
1 T-ATTTTATA
* **
3381865 TCTTAAATA
1 TATTTTATA
3381874 TATTTTTAGTA
1 TA-TTTTA-TA
* * *
3381885 TAATATATTT
1 TATTTTA-TA
*
3381895 TATTTTCATT
1 TATTTT-ATA
3381905 TATTATTATA
1 TATT-TTATA
*
3381915 -ATCTTATA
1 TATTTTATA
3381923 TA-TTT-TA
1 TATTTTATA
*
3381930 T-TTTTATT
1 TATTTTATA
* *
3381938 TCTTTAATA
1 TATTTTATA
3381947 TATTTT-T-
1 TATTTTATA
*
3381954 TATATTATA
1 TATTTTATA
3381963 TATTTTAT
1 TATTTTAT
3381971 TTTAATTTAT
Statistics
Matches: 128, Mismatches: 29, Indels: 45
0.63 0.14 0.22
Matches are distributed among these distances:
6 4 0.03
7 20 0.16
8 31 0.24
9 33 0.26
10 31 0.24
11 9 0.07
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (9 bp):
TATTTTATA
Found at i:3381958 original size:33 final size:33
Alignment explanation
Indices: 3381887--3381972 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 33
3381877 TTTTAGTATA
* *
3381887 ATATATTTTATTTTCATTTATTATTATAATCTT
1 ATATATTTTATTTTTATTTATTAATATAATCTT
* *
3381920 ATATATTTTATTTTTATTTCTTTAATAT-ATTTT
1 ATATATTTTATTTTTATTT-ATTAATATAATCTT
* *
3381953 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
3381973 TAATTTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 31 0.69
34 14 0.31
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.67
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTATTAATATAATCTT
Found at i:3381982 original size:31 final size:32
Alignment explanation
Indices: 3381940--3382066 Score: 91
Period size: 31 Copynumber: 3.8 Consensus size: 32
3381930 TTTTTATTTC
*
3381940 TTTAATATATTTT-TTATATTATATATTTTAT
1 TTTAATTTATTTTATTATATTATATATTTTAT
*
3381971 TTTAATTTATTTTACT-TATTATATAATTTTAATTTT
1 TTTAATTTATTTTATTATATTATAT-ATTTT-A---T
*
3382007 TTTATATTT-TTGATTCTTATATTATATATTTGTAT
1 TTTA-ATTTATT--TTATTATATTATATATTT-TAT
*
3382042 TTTAATGTT-TTTTATTTTAATTATA
1 TTTAAT-TTATTTTATTAT-ATTATA
3382067 ACAATATAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 23
0.73 0.06 0.22
Matches are distributed among these distances:
31 20 0.26
32 6 0.08
33 6 0.08
34 8 0.10
35 9 0.12
36 7 0.09
37 4 0.05
38 8 0.10
39 9 0.12
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (32 bp):
TTTAATTTATTTTATTATATTATATATTTTAT
Found at i:3382006 original size:73 final size:72
Alignment explanation
Indices: 3381805--3382057 Score: 209
Period size: 73 Copynumber: 3.4 Consensus size: 72
3381795 TATTATAATT
* * **
3381805 TTATATATTTTATTTTTAATATATTTATATTTTTATTATTAATTTTTATATAATATTATCTCTTA
1 TTATATATTTTA-TTTTAATTTATTT-TATTATTA-TA-TAA-TTTTAT-TTTTATTATCT-TTA
3381870 A-ATATATTTTTAGTA
59 ATATAT-TTTTTA-TA
* * *
3381885 TAATATATTTTATTTTCATTTATTATTATAATCT-TATATATTTTATTTTTATT-TCTTTAATAT
1 TTATATATTTTATTTTAATTTATT-TTATTAT-TATATA-ATTTTATTTTTATTATCTTTAATAT
3381948 ATTTTTTATA
63 ATTTTTTATA
*
3381958 TTATATATTTTATTTTAATTTATTTTACTTATTATATAATTTTAATTTTT-TTATATTT--T-TG
1 TTATATATTTTATTTTAATTTATTTTA-TTATTATATAATTTT-ATTTTTATTATCTTTAATAT-
*
3382019 A-TTCTTATA
63 ATTTTTTATA
3382028 TTATATATTTGTATTTTAATGTT-TTTTATT
1 TTATATATTT-TATTTTAAT-TTATTTTATT
3382058 TTAATTATAA
Statistics
Matches: 150, Mismatches: 12, Indels: 32
0.77 0.06 0.16
Matches are distributed among these distances:
70 20 0.13
71 16 0.11
72 13 0.09
73 41 0.27
74 10 0.07
75 7 0.05
76 5 0.03
77 8 0.05
78 3 0.02
79 14 0.09
80 13 0.09
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (72 bp):
TTATATATTTTATTTTAATTTATTTTATTATTATATAATTTTATTTTTATTATCTTTAATATATT
TTTTATA
Found at i:3383894 original size:30 final size:30
Alignment explanation
Indices: 3383860--3383985 Score: 130
Period size: 30 Copynumber: 4.2 Consensus size: 30
3383850 AGTATATAAG
*
3383860 TTTATTTGATTTAAAATAAAAATAAAAAAA
1 TTTATTTGATTCAAAATAAAAATAAAAAAA
* * **
3383890 TTTATTTAATTCAAAATAAAAATACAATGA
1 TTTATTTGATTCAAAATAAAAATAAAAAAA
* * *
3383920 CTTATTTGACTCAAAATAAAAATATAAAAAC
1 TTTATTTGATTCAAAATAAAAATA-AAAAAA
* * *
3383951 TTGA-TTGA-TCATAATAAATATAAAAAAA
1 TTTATTTGATTCAAAATAAAAATAAAAAAA
3383979 TTTATTT
1 TTTATTT
3383986 AAATTTTTAT
Statistics
Matches: 76, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
28 8 0.11
29 14 0.18
30 50 0.66
31 4 0.05
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (30 bp):
TTTATTTGATTCAAAATAAAAATAAAAAAA
Found at i:3384020 original size:20 final size:19
Alignment explanation
Indices: 3383982--3384020 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3383972 AAAAAAATTT
*
3383982 ATTTAAATTTTTATGAATA
1 ATTTAAATTTTTATAAATA
*
3384001 ATTTAAAATTTTTTTAAATA
1 ATTT-AAATTTTTATAAATA
3384021 TTATGTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTTAAATTTTTATAAATA
Found at i:3390604 original size:23 final size:26
Alignment explanation
Indices: 3390563--3390610 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
3390553 CACTCTCCAG
*
3390563 AATAGCATCAATCACCAT-AACACAA
1 AATAGCATCAATCAACATAAACACAA
3390588 AATA-CATC-ATCAACATAAACACA
1 AATAGCATCAATCAACATAAACACA
3390611 TCTTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 10 0.48
25 4 0.19
ACGTcount: A:0.54, C:0.27, G:0.02, T:0.17
Consensus pattern (26 bp):
AATAGCATCAATCAACATAAACACAA
Found at i:3406213 original size:27 final size:27
Alignment explanation
Indices: 3406181--3406237 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
3406171 ATGATTCCTT
*
3406181 AATGGAGGAAATCCTATGATTTACGAA
1 AATGGAGGAAATCCCATGATTTACGAA
* *
3406208 AATGGATGAAATCCCATGATTTATGAA
1 AATGGAGGAAATCCCATGATTTACGAA
3406235 AAT
1 AAT
3406238 CCCATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (27 bp):
AATGGAGGAAATCCCATGATTTACGAA
Found at i:3419665 original size:2 final size:2
Alignment explanation
Indices: 3419658--3419685 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3419648 TCATATGATG
3419658 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
3419686 GTATGTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3425509 original size:2 final size:2
Alignment explanation
Indices: 3425502--3425532 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3425492 CATTACTCTA
3425502 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 A
3425533 CGAACACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3427701 original size:2 final size:2
Alignment explanation
Indices: 3427690--3427719 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3427680 ATTTTTACAA
3427690 AT AT -T 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 A
3427720 AAGCTTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3429424 original size:14 final size:14
Alignment explanation
Indices: 3429405--3429434 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3429395 GCAAGTGGAT
3429405 ATCCCGGATCCTGG
1 ATCCCGGATCCTGG
*
3429419 ATCCCGGATCGTGG
1 ATCCCGGATCCTGG
3429433 AT
1 AT
3429435 ATGTTGGCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (14 bp):
ATCCCGGATCCTGG
Found at i:3429559 original size:6 final size:6
Alignment explanation
Indices: 3429544--3429578 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
3429534 AGGACATCTG
*
3429544 CCCAAA CCCAAC CCCAAC CCCAAC CCCAAC CCCAA
1 CCCAAC CCCAAC CCCAAC CCCAAC CCCAAC CCCAA
3429579 TCCAAAACCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.37, C:0.63, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCAAC
Found at i:3435913 original size:5 final size:5
Alignment explanation
Indices: 3435905--3436169 Score: 75
Period size: 5 Copynumber: 52.4 Consensus size: 5
3435895 TAATATCATA
*
3435905 TATTT TATTT TATTT TA-TT TATTAT TATAATCT TA-TA TATTT TATTT
1 TATTT TATTT TATTT TATTT TATT-T TAT--T-T TATTT TATTT TATTT
* * * * * * *
3435952 CA-TT TCTTT AATTT AATTTT TATAT TA-TA TATTT TATTT TAATT TATTT
1 TATTT TATTT TATTT TA-TTT TATTT TATTT TATTT TATTT TATTT TATTT
* * * * * * *
3436001 TACTTAT TATTAT AATCT TA-TA TATTT TATTT CA-TT TCTTT AATAT
1 TA-TT-T TATT-T TATTT TATTT TATTT TATTT TATTT TATTT TATTT
* * * * * * * *
3436047 AATTTT TATAT TA-TA TATTT TATTT TAATT TATTT TA-CT TATAT CATATA
1 TA-TTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TAT-TT
* * * *
3436097 AATTT TAATTT T-TTA TATTT TATTT TATTT TAATTTT TATAT TA-TA
1 TATTT T-ATTT TATTT TATTT TATTT TATTT T-A-TTT TATTT TATTT
*
3436143 TATTT TATTT TAATAT T-TTT TATTT TA
1 TATTT TATTT T-ATTT TATTT TATTT TA
3436170 ATTATAACAT
Statistics
Matches: 186, Mismatches: 51, Indels: 46
0.66 0.18 0.16
Matches are distributed among these distances:
4 27 0.15
5 116 0.62
6 32 0.17
7 7 0.04
8 4 0.02
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (5 bp):
TATTT
Found at i:3435945 original size:27 final size:27
Alignment explanation
Indices: 3435915--3436032 Score: 111
Period size: 27 Copynumber: 4.4 Consensus size: 27
3435905 TATTTTATTT
3435915 TATTTTATTTATTATTATAATCTTATA
1 TATTTTATTTATTATTATAATCTTATA
*
3435942 TATTTTATTTCATT-TCTTTAAT-TTA-A
1 TATTTTATTT-ATTAT-TATAATCTTATA
* * *
3435968 T-TTTTATATTATATATT-TTATTTTAATT
1 TATTTTAT-TTAT-TATTATAATCTT-ATA
*
3435996 TATTTTACTTATTATTATAATCTTATA
1 TATTTTATTTATTATTATAATCTTATA
3436023 TATTTTATTT
1 TATTTTATTT
3436033 CATTTCTTTA
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
25 11 0.15
26 8 0.11
27 31 0.42
28 18 0.25
29 5 0.07
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (27 bp):
TATTTTATTTATTATTATAATCTTATA
Found at i:3435946 original size:32 final size:32
Alignment explanation
Indices: 3435910--3435990 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
3435900 TCATATATTT
3435910 TATTTTATTTTATTT-ATT-ATTATAATCTTATA
1 TATTTTATTTTATTTCATTAATT-TAAT-TTATA
* * *
3435942 TATTTTATTTCATTTCTTTAATTTAATTTTTA
1 TATTTTATTTTATTTCATTAATTTAATTTATA
3435974 TATTATATATTTTATTT
1 TATT-T-TATTTTATTT
3435991 TAATTTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
32 22 0.54
33 7 0.17
34 12 0.29
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (32 bp):
TATTTTATTTTATTTCATTAATTTAATTTATA
Found at i:3436002 original size:81 final size:81
Alignment explanation
Indices: 3435905--3436176 Score: 371
Period size: 81 Copynumber: 3.4 Consensus size: 81
3435895 TAATATCATA
* *
3435905 TATTTTATTTTATTTTATTTATTATTATAATCTTATATATTTTATTTCATTTCTTTAATTTAATT
1 TATTTTAATTTATTTTACTTATTATTATAATCTTATATATTTTATTTCATTTCTTTAATTTAATT
3435970 TTTATATTATATATTT
66 TTTATATTATATATTT
*
3435986 TATTTTAATTTATTTTACTTATTATTATAATCTTATATATTTTATTTCATTTCTTTAATATAATT
1 TATTTTAATTTATTTTACTTATTATTATAATCTTATATATTTTATTTCATTTCTTTAATTTAATT
3436051 TTTATATTATATATTT
66 TTTATATTATATATTT
* * *
3436067 TATTTTAATTTATTTTACTTA-TATCATATAAATTTTA-ATTTTTTATATT--TTAT-TTTATTT
1 TATTTTAATTTATTTTACTTATTAT--TAT-AATCTTATATATTTTAT-TTCATT-TCTTTAATT
3436127 TAATTTTTATATTATATATTT
61 TAATTTTTATATTATATATTT
3436148 TATTTTAATATT-TTTTA-TT-TTAATTATAA
1 TATTTTAAT-TTATTTTACTTATT-ATTATAA
3436177 CATTATAAAA
Statistics
Matches: 176, Mismatches: 7, Indels: 19
0.87 0.03 0.09
Matches are distributed among these distances:
78 2 0.01
79 3 0.02
80 6 0.03
81 143 0.81
82 14 0.08
83 8 0.05
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (81 bp):
TATTTTAATTTATTTTACTTATTATTATAATCTTATATATTTTATTTCATTTCTTTAATTTAATT
TTTATATTATATATTT
Found at i:3440585 original size:30 final size:29
Alignment explanation
Indices: 3440544--3440647 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 29
3440534 AATTATTAAT
3440544 TATAAAGATTTATTTGATTAAAAATAAAAA
1 TATAAA-ATTTATTTGATTAAAAATAAAAA
* * *
3440574 TATAAGAATTTATTTAATTTATAATAAAAA
1 TATAA-AATTTATTTGATTAAAAATAAAAA
*
3440604 TATAAAA---ATTTGCTTAAACGAAATAAAAA
1 TATAAAATTTATTTGATT-AA--AAATAAAAA
3440633 TATAATAATTTATTT
1 TATAA-AATTTATTT
3440648 AAAAAAATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
26 6 0.10
27 1 0.02
29 15 0.25
30 32 0.54
31 1 0.02
33 4 0.07
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (29 bp):
TATAAAATTTATTTGATTAAAAATAAAAA
Found at i:3440649 original size:29 final size:29
Alignment explanation
Indices: 3440565--3440650 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
3440555 ATTTGATTAA
* ***
3440565 AAATAAAAATATAAGAATTTATTTAATTT
1 AAATAAAAATATAAAAATTTATTTAAACG
**
3440594 ATAATAAAAATATAAAAATTTGCTTAAACG
1 A-AATAAAAATATAAAAATTTATTTAAACG
*
3440624 AAATAAAAATATAATAATTTATTTAAA
1 AAATAAAAATATAAAAATTTATTTAAA
3440651 AAAATTTAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 24 0.51
30 23 0.49
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.36
Consensus pattern (29 bp):
AAATAAAAATATAAAAATTTATTTAAACG
Found at i:3452430 original size:4 final size:4
Alignment explanation
Indices: 3452416--3452445 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
3452406 TAGCCGCATA
*
3452416 TTAT CTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
3452446 TAATATAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:3473912 original size:29 final size:29
Alignment explanation
Indices: 3473879--3473938 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
3473869 AATGCGTTAT
3473879 AATTATATAATTATATGATAAAGAATAAC
1 AATTATATAATTATATGATAAAGAATAAC
3473908 AATTATATAATTATATGATAAAGAATAAC
1 AATTATATAATTATATGATAAAGAATAAC
3473937 AA
1 AA
3473939 GTAATATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (29 bp):
AATTATATAATTATATGATAAAGAATAAC
Found at i:3479776 original size:28 final size:28
Alignment explanation
Indices: 3479672--3479822 Score: 139
Period size: 28 Copynumber: 5.4 Consensus size: 28
3479662 AAATGTATGT
*
3479672 CGTGTAAGAAAATAGAAA-TAGT-CAAGGA
1 CGTGTAATAAAATAGAAATTA-TAC-AGGA
* *
3479700 -GTGTAACAAAATAGAAATTAGT-CAGGG
1 CGTGTAATAAAATAGAAATTA-TACAGGA
*
3479727 CGTGTCATAAAATAGAAATTATACAGGA
1 CGTGTAATAAAATAGAAATTATACAGGA
* * *
3479755 CGTGTAATGAAATAGAAATTATAAAGTA
1 CGTGTAATAAAATAGAAATTATACAGGA
* * * * *
3479783 CGTCTAACAAAACAGAGATTATACAGGG
1 CGTGTAATAAAATAGAAATTATACAGGA
3479811 CGTGTAATAAAA
1 CGTGTAATAAAA
3479823 GAAAAATATT
Statistics
Matches: 101, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
27 20 0.20
28 81 0.80
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.23
Consensus pattern (28 bp):
CGTGTAATAAAATAGAAATTATACAGGA
Found at i:3481227 original size:26 final size:27
Alignment explanation
Indices: 3481194--3481252 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 27
3481184 TATTTTATTC
* *
3481194 TTTTATATCTGTTTACATATA-ATTTT
1 TTTTATATCTATTTACATAAAGATTTT
3481220 TTTTATATCTATTTACATAAAGATTTT
1 TTTTATATCTATTTACATAAAGATTTT
3481247 TTTTAT
1 TTTTAT
3481253 TAGTTTCTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (27 bp):
TTTTATATCTATTTACATAAAGATTTT
Found at i:3482502 original size:14 final size:14
Alignment explanation
Indices: 3482485--3482632 Score: 89
Period size: 14 Copynumber: 10.3 Consensus size: 14
3482475 CCCCACCCAC
3482485 TTTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
*** *
3482499 TTTTTAATTCAAAG
1 TTTTCCCTCCAAAG
* *
3482513 TATTCCCCCCAAAAG
1 TTTTCCCTCC-AAAG
*
3482528 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
** *
3482542 TTTTCAATTCAAAG
1 TTTTCCCTCCAAAG
* *
3482556 TATTCCCCCCAAAAG
1 TTTTCCCTCC-AAAG
*
3482571 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
** *
3482585 TTTTCAATTCAAAG
1 TTTTCCCTCCAAAG
* *
3482599 TATTCCCCCCCAAAAG
1 T-TTTCCCTCC-AAAG
*
3482615 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
3482629 TTTT
1 TTTT
3482633 GGAAGGTTCT
Statistics
Matches: 92, Mismatches: 38, Indels: 8
0.67 0.28 0.06
Matches are distributed among these distances:
14 55 0.60
15 33 0.36
16 4 0.04
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (14 bp):
TTTTCCCTCCAAAG
Found at i:3482534 original size:43 final size:43
Alignment explanation
Indices: 3482486--3482632 Score: 276
Period size: 43 Copynumber: 3.4 Consensus size: 43
3482476 CCCACCCACT
*
3482486 TTTCCCTCCAAAGTTTTTAATTCAAAGTATTCCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGA
3482529 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGA
3482572 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTCAATTCAAAGTATT-CCCCCCAAAAGA
3482616 TTTCCCTCCAAAGTTTT
1 TTTCCCTCCAAAGTTTT
3482633 GGAAGGTTCT
Statistics
Matches: 102, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
43 73 0.72
44 29 0.28
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.33
Consensus pattern (43 bp):
TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGA
Found at i:3482541 original size:29 final size:28
Alignment explanation
Indices: 3482508--3482629 Score: 77
Period size: 29 Copynumber: 4.2 Consensus size: 28
3482498 GTTTTTAATT
3482508 CAAAGTATTCCCCCCAAAAGATTTCCCTC
1 CAAAGTATTCCCCCC-AAAGATTTCCCTC
* **** *
3482537 CAAAGTTTTCAATTCAAAG-TATTCCCCC
1 CAAAGTATTCCCCCCAAAGAT-TTCCCTC
* * ** *
3482565 CAAAAG-ATTTCCCTCCAAAGTTTTCAATT
1 C-AAAGTA-TTCCCCCCAAAGATTTCCCTC
3482594 CAAAGTATTCCCCCCCAAAAGATTTCCCTC
1 CAAAGTATT-CCCCCC-AAAGATTTCCCTC
3482624 CAAAGT
1 CAAAGT
3482630 TTTGGAAGGT
Statistics
Matches: 67, Mismatches: 19, Indels: 13
0.68 0.19 0.13
Matches are distributed among these distances:
27 1 0.01
28 17 0.25
29 33 0.49
30 16 0.24
ACGTcount: A:0.33, C:0.32, G:0.07, T:0.28
Consensus pattern (28 bp):
CAAAGTATTCCCCCCAAAGATTTCCCTC
Found at i:3482811 original size:39 final size:39
Alignment explanation
Indices: 3482725--3482848 Score: 232
Period size: 39 Copynumber: 3.2 Consensus size: 39
3482715 CCTGGTGTGA
3482725 CTGGACTGGGCTGGCACCCTCTTGGGCCTCCA-GTGGGT
1 CTGGACTGGGCTGGCACCCTCTTGGGCCTCCAGGTGGGT
3482763 CTGGACTGGGCTGGCACCCTCTTGGGCCTCCAGGTGGGT
1 CTGGACTGGGCTGGCACCCTCTTGGGCCTCCAGGTGGGT
*
3482802 CTGGACTGGGCTGGCACCCTCTTGGGCCTCCTGGTGGGT
1 CTGGACTGGGCTGGCACCCTCTTGGGCCTCCAGGTGGGT
3482841 CTGGACTG
1 CTGGACTG
3482849 TGGCCCGTGA
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
38 32 0.38
39 52 0.62
ACGTcount: A:0.07, C:0.31, G:0.38, T:0.24
Consensus pattern (39 bp):
CTGGACTGGGCTGGCACCCTCTTGGGCCTCCAGGTGGGT
Found at i:3483862 original size:60 final size:60
Alignment explanation
Indices: 3483794--3483910 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
3483784 CTTCCACTTT
* *
3483794 GATGTGGAACTATCTCCCCACCTTGAATGTGGCTTGCCCTCGCCACCATCCCTGGACCTC
1 GATGTGGAACTACCTCCCCACCTGGAATGTGGCTTGCCCTCGCCACCATCCCTGGACCTC
* ** * *
3483854 GATGTGGAACTACCTCTCCACCTGGGGTGTGGCTTGCCCTCGCCACTATCCTTGGAC
1 GATGTGGAACTACCTCCCCACCTGGAATGTGGCTTGCCCTCGCCACCATCCCTGGAC
3483911 TGGCTATCTC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.15, C:0.36, G:0.23, T:0.26
Consensus pattern (60 bp):
GATGTGGAACTACCTCCCCACCTGGAATGTGGCTTGCCCTCGCCACCATCCCTGGACCTC
Found at i:3485326 original size:14 final size:14
Alignment explanation
Indices: 3485309--3485454 Score: 78
Period size: 14 Copynumber: 10.3 Consensus size: 14
3485299 CCCCACCCAC
3485309 TTTT-CCTCCAAAG
1 TTTTCCCTCCAAAG
*** *
3485322 TTTTTAATTCAAAG
1 TTTTCCCTCCAAAG
* * *
3485336 TATTCCCCCCAAAA
1 TTTTCCCTCCAAAG
*
3485350 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
** *
3485364 TTTTCAATTCAAAG
1 TTTTCCCTCCAAAG
* *
3485378 TATTCCCCCCAAAAG
1 TTTTCCCTCC-AAAG
*
3485393 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
** *
3485407 TTTTCAATTCAAAG
1 TTTTCCCTCCAAAG
* *
3485421 TATTCCCCCCCAAAAG
1 T-TTTCCCTCC-AAAG
*
3485437 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
3485451 TTTT
1 TTTT
3485455 GGAAGGTTCT
Statistics
Matches: 90, Mismatches: 39, Indels: 7
0.66 0.29 0.05
Matches are distributed among these distances:
13 4 0.04
14 60 0.67
15 22 0.24
16 4 0.04
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (14 bp):
TTTTCCCTCCAAAG
Found at i:3485401 original size:43 final size:43
Alignment explanation
Indices: 3485313--3485454 Score: 259
Period size: 42 Copynumber: 3.3 Consensus size: 43
3485303 ACCCACTTTT
*
3485313 CCTCCAAAGTTTTTAATTCAAAGTATTCCCCCCAAAA-ATTTC
1 CCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGATTTC
3485355 CCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGATTTC
1 CCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGATTTC
3485398 CCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCCAAAAGATTTC
1 CCTCCAAAGTTTTCAATTCAAAGTATT-CCCCCCAAAAGATTTC
3485442 CCTCCAAAGTTTT
1 CCTCCAAAGTTTT
3485455 GGAAGGTTCT
Statistics
Matches: 97, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
42 36 0.37
43 32 0.33
44 29 0.30
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (43 bp):
CCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGATTTC
Done.