Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, 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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 62 of 77
Found at i:12446768 original size:22 final size:22
Alignment explanation
Indices: 12446743--12446912 Score: 108
Period size: 22 Copynumber: 7.2 Consensus size: 22
12446733 ACTTTTATTT
*
12446743 ATAAATAATGTTATATTAATAA
1 ATAAATAATATTATATTAATAA
12446765 ATAAATAATATTATATTAATAA
1 ATAAATAATATTATATTAATAA
*
12446787 ATAATATAATAATAAATATGATTAATTTA
1 ATAA-ATAAT-AT---TAT-ATTAA-TAA
* * *
12446816 ATTAATAAATATTATAATAATAT
1 ATAAAT-AATATTATATTAATAA
* * *
12446839 ATGAATAAATAATATATTACT-A
1 ATAAAT-AATATTATATTAATAA
**
12446861 ATAAATAATATGCTATTAATATA
1 ATAAATAATATTATATTAATA-A
* *
12446884 ATATATTAATAAATATTATTAATAA
1 ATA-AATAAT-ATTA-TATTAATAA
12446909 ATAA
1 ATAA
12446913 TTTAATATAT
Statistics
Matches: 115, Mismatches: 20, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
21 10 0.09
22 30 0.26
23 27 0.23
24 12 0.10
25 8 0.07
26 8 0.07
27 3 0.03
28 9 0.08
29 8 0.07
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (22 bp):
ATAAATAATATTATATTAATAA
Found at i:12446794 original size:15 final size:15
Alignment explanation
Indices: 12446771--12446913 Score: 109
Period size: 15 Copynumber: 9.4 Consensus size: 15
12446761 ATAAATAAAT
*
12446771 AATATTATATTAATA
1 AATAATATATTAATA
*
12446786 AATAATATAATAATA
1 AATAATATATTAATA
*
12446801 AAT-ATGATTAATTTAATT
1 AATAAT-A-T-A-TTAATA
12446819 AATAA-ATATT-AT-
1 AATAATATATTAATA
*
12446831 AATAATATATGAATA
1 AATAATATATTAATA
12446846 AATAATATATTACTAATA
1 AATAATATA-T--TAATA
** *
12446864 AATAATATGCTATTA
1 AATAATATATTAATA
12446879 ATATAATATATTAATA
1 A-ATAATATATTAATA
12446895 AAT-AT-TATTAATA
1 AATAATATATTAATA
12446908 AATAAT
1 AATAAT
12446914 TTAATATATT
Statistics
Matches: 103, Mismatches: 12, Indels: 27
0.73 0.08 0.19
Matches are distributed among these distances:
12 5 0.05
13 17 0.17
14 10 0.10
15 34 0.33
16 15 0.15
17 2 0.02
18 19 0.18
19 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (15 bp):
AATAATATATTAATA
Found at i:12446812 original size:13 final size:13
Alignment explanation
Indices: 12446796--12446911 Score: 55
Period size: 13 Copynumber: 8.7 Consensus size: 13
12446786 AATAATATAA
12446796 TAATAAATATGAT
1 TAATAAATATGAT
*
12446809 TAAT---T-TAAT
1 TAATAAATATGAT
*
12446818 TAATAAATATTA-
1 TAATAAATATGAT
12446830 TAATAATATATGAAT
1 TAATAA-ATATG-AT
* * *
12446845 AAATAATATATTAC
1 TAATAA-ATATGAT
12446859 TAATAAATAATATGCTAT
1 TAAT--A-AATATG--AT
12446877 TAATATAATAT-AT
1 TAATA-AATATGAT
*
12446890 TAATAAATATTAT
1 TAATAAATATGAT
12446903 TAATAAATA
1 TAATAAATA
12446912 ATTTAATATA
Statistics
Matches: 81, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
9 7 0.09
10 1 0.01
12 12 0.15
13 28 0.35
14 5 0.06
15 10 0.12
16 12 0.15
17 1 0.01
18 5 0.06
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (13 bp):
TAATAAATATGAT
Found at i:12446820 original size:37 final size:37
Alignment explanation
Indices: 12446754--12446912 Score: 118
Period size: 37 Copynumber: 4.4 Consensus size: 37
12446744 TAAATAATGT
*
12446754 TATATTAATAAATAAATAATATTATATTAATAAATAA
1 TATAATAATAAATAAATAATATTATATTAATAAATAA
* *
12446791 TATAATAATAAATATGATTAAT-TTA-ATTAATAAATAT
1 TATAATAATAAATA--AATAATATTATATTAATAAATAA
* * * *
12446828 TATAATAATATATGAATAAATAATATATTACT-AATAA
1 TATAATAATAAATAAAT-AATATTATATTAATAAATAA
** * *
12446865 -ATAAT-ATGCTATTAAT-ATAATATATTAATAAAT-A
1 TATAATAAT-AAATAAATAATATTATATTAATAAATAA
*
12446899 T-TATTAATAAATAA
1 TATAATAATAAATAA
12446913 TTTAATATAT
Statistics
Matches: 97, Mismatches: 16, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
34 19 0.20
35 9 0.09
36 14 0.14
37 42 0.43
38 8 0.08
39 5 0.05
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (37 bp):
TATAATAATAAATAAATAATATTATATTAATAAATAA
Found at i:12446901 original size:10 final size:11
Alignment explanation
Indices: 12446754--12446907 Score: 52
Period size: 11 Copynumber: 13.2 Consensus size: 11
12446744 TAAATAATGT
12446754 TATATTAATAA
1 TATATTAATAA
* *
12446765 -ATAAATAATAT
1 TAT-ATTAATAA
12446776 TATATTAATAAA
1 TATATTAAT-AA
12446788 TAATATAATAATAAA
1 T-ATAT--TAAT-AA
*
12446803 TATGATTAAT-T
1 TAT-ATTAATAA
12446814 TA-ATTAATAA
1 TATATTAATAA
12446824 -ATATTATAATAA
1 TATA-T-TAATAA
12446836 TATATGAATAAATAA
1 TATAT---T-AATAA
*
12446851 TATATTACTAA
1 TATATTAATAA
*
12446862 TA-AATAAT-A
1 TATATTAATAA
*
12446871 TGCTATTAATATAA
1 T-ATATT-A-ATAA
12446885 TATATTAATAA
1 TATATTAATAA
*
12446896 -ATATTATTAA
1 TATATTAATAA
12446906 TA
1 TA
12446908 AATAATTTAA
Statistics
Matches: 109, Mismatches: 13, Indels: 42
0.66 0.08 0.26
Matches are distributed among these distances:
9 9 0.08
10 16 0.15
11 27 0.25
12 14 0.13
13 17 0.16
14 6 0.06
15 20 0.18
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (11 bp):
TATATTAATAA
Found at i:12452837 original size:48 final size:48
Alignment explanation
Indices: 12452762--12452858 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
12452752 CCTAGACAAA
* *
12452762 TATATGAATATGACATGTTTCACACATAATCTTTAACCAATAACAATG
1 TATATGAATATAACATGTTTCACACATAATCTTTAAACAATAACAATG
* *
12452810 TATATGAATATAACATGTTTCATACATAATCTTTAAACAATAATAATG
1 TATATGAATATAACATGTTTCACACATAATCTTTAAACAATAACAATG
12452858 T
1 T
12452859 CATTACAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (48 bp):
TATATGAATATAACATGTTTCACACATAATCTTTAAACAATAACAATG
Found at i:12460544 original size:1 final size:1
Alignment explanation
Indices: 12460538--12460567 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
12460528 ATTGGCTGAG
*
12460538 TTTTTTTTTTTTTTTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12460568 CTAAAGGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:12462691 original size:18 final size:19
Alignment explanation
Indices: 12462665--12462700 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12462655 ATTAATTATT
12462665 ATTCCAATT-ATTGTTTCG
1 ATTCCAATTAATTGTTTCG
*
12462683 ATTCTAATTAATTGTTTC
1 ATTCCAATTAATTGTTTC
12462701 TAAACCCCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.53
Consensus pattern (19 bp):
ATTCCAATTAATTGTTTCG
Found at i:12466992 original size:13 final size:13
Alignment explanation
Indices: 12466974--12467013 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
12466964 TGATTGCCTA
12466974 AAATATTTTTATT
1 AAATATTTTTATT
12466987 AAATATTTTTATAT
1 AAATATTTTTAT-T
*
12467001 GAAT-TTTTTATT
1 AAATATTTTTATT
12467013 A
1 A
12467014 TTAGACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 1 0.04
13 19 0.79
14 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (13 bp):
AAATATTTTTATT
Found at i:12469797 original size:22 final size:22
Alignment explanation
Indices: 12469771--12470051 Score: 97
Period size: 22 Copynumber: 12.8 Consensus size: 22
12469761 AATAATCATC
12469771 GATAATTTAATAGTAAATTAAT
1 GATAATTTAATAGTAAATTAAT
* * *
12469793 GATAACTTAATAATAAATGAAT
1 GATAATTTAATAGTAAATTAAT
* * *
12469815 AATAATTCAATAATAAA-TAATT
1 GATAATTTAATAGTAAATTAA-T
*
12469837 GATAACTTT-TTAGTAAA-TAAGT
1 GATAA-TTTAATAGTAAATTAA-T
* * * * *
12469859 AATAATATAATAATATA-TGAT
1 GATAATTTAATAGTAAATTAAT
* ** *
12469880 AATACCTTAATAGTAAATCAAT
1 GATAATTTAATAGTAAATTAAT
* * * *
12469902 TATAATATAGTTGTAAATGT-AT
1 GATAATTTAATAGTAAAT-TAAT
* ** * * *
12469924 AATAACATAATACTAAATCAAG
1 GATAATTTAATAGTAAATTAAT
* * * * *
12469946 GATAACTTAACA-AAAAATATGT
1 GATAATTTAATAGTAAATTA-AT
* * *
12469968 GATAATTTAGTAGTTAATTATT
1 GATAATTTAATAGTAAATTAAT
* * * *
12469990 GATAACTTAGTAATAAATCAAT
1 GATAATTTAATAGTAAATTAAT
* * *
12470012 GATAATTTAATTGTAGATTAGT
1 GATAATTTAATAGTAAATTAAT
*
12470034 AATAATTTAATAGTAAAT
1 GATAATTTAATAGTAAAT
12470052 CAATTTCAGT
Statistics
Matches: 182, Mismatches: 69, Indels: 16
0.68 0.26 0.06
Matches are distributed among these distances:
21 21 0.12
22 155 0.85
23 6 0.03
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (22 bp):
GATAATTTAATAGTAAATTAAT
Found at i:12469854 original size:44 final size:43
Alignment explanation
Indices: 12469772--12469873 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 43
12469762 ATAATCATCG
*
12469772 ATAATTTAATAGTAAATTAATGATAACTTAATAATAAATGAA-TA
1 ATAA-TTAATAATAAATTAATGATAACTTAATAATAAAT-AAGTA
** *
12469816 ATAATTCAATAATAAA-TAATTGATAACTTTTTAGTAAATAAGTA
1 ATAATT-AATAATAAATTAA-TGATAACTTAATAATAAATAAGTA
12469860 ATAATATAATAATA
1 ATAAT-TAATAATA
12469874 TATGATAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
43 7 0.14
44 42 0.84
45 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (43 bp):
ATAATTAATAATAAATTAATGATAACTTAATAATAAATAAGTA
Found at i:12470104 original size:22 final size:22
Alignment explanation
Indices: 12470079--12470173 Score: 70
Period size: 22 Copynumber: 4.4 Consensus size: 22
12470069 AATTAATTGA
*
12470079 TAGTAAATCAATGACAAATTAG
1 TAGTAAATCAATGATAAATTAG
*
12470101 TAGTAAAT-AATTGATAATTTAG
1 TAGTAAATCAA-TGATAAATTAG
* * * * *
12470123 TAATTAATTATTGA-AAACTTAA
1 TAGTAAATCAATGATAAA-TTAG
* *
12470145 AAGTAAATCAAT-ATAATTTAG
1 TAGTAAATCAATGATAAATTAG
12470166 TAGTAAAT
1 TAGTAAAT
12470174 AATTTATAAT
Statistics
Matches: 54, Mismatches: 15, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
21 15 0.28
22 38 0.70
23 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (22 bp):
TAGTAAATCAATGATAAATTAG
Found at i:12470195 original size:65 final size:66
Alignment explanation
Indices: 12470080--12470238 Score: 173
Period size: 65 Copynumber: 2.4 Consensus size: 66
12470070 ATTAATTGAT
* * * * * *
12470080 AGTAAATCAATGACAAATTAGTAGTAAATAATTGATAATTTAGTAATTAATTATTGAA-AACTTA
1 AGTAAATCAAT-ATAATTTAGTAGTAAATAATTGATAATATAATAATTAATCAGT-AATAACTTA
12470144 A-A
64 ATA
* *
12470146 AGTAAATCAATATAATTTAGTAGTAAATAATTTATAATATAATAGTTAATCAGTAATAACTTAAT
1 AGTAAATCAATATAATTTAGTAGTAAATAATTGATAATATAATAATTAATCAGTAATAACTTAAT
12470211 A
66 A
* *
12470212 A-TAAATCATGTATAATTTAAT-GTAAAT
1 AGTAAATCA-ATATAATTTAGTAGTAAAT
12470239 TAGTAATAAC
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
64 2 0.03
65 55 0.69
66 23 0.29
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (66 bp):
AGTAAATCAATATAATTTAGTAGTAAATAATTGATAATATAATAATTAATCAGTAATAACTTAAT
A
Found at i:12470204 original size:22 final size:21
Alignment explanation
Indices: 12470141--12470493 Score: 73
Period size: 22 Copynumber: 16.3 Consensus size: 21
12470131 TATTGAAAAC
* *
12470141 TTAAAAGTAAATCAAT-ATAA
1 TTAATAGTAAATCAGTAATAA
* * * *
12470161 TTTAGTAGTAAATAATTTATAA
1 -TTAATAGTAAATCAGTAATAA
*
12470183 TATAATAGTTAATCAGTAATAA
1 T-TAATAGTAAATCAGTAATAA
*
12470205 CTTAATAATAAATCATGT-ATAA
1 -TTAATAGTAAATCA-GTAATAA
*
12470227 TTTAAT-GTAAATTAGTAATAA
1 -TTAATAGTAAATCAGTAATAA
* * *
12470248 CTTGATCA-TGAATCA-CAGATAA
1 -TTAAT-AGTAAATCAGTA-ATAA
* *
12470270 TTTAAT-GATAAATCAGTGACAA
1 -TTAATAG-TAAATCAGTAATAA
** * *
12470292 TTTTGTAGTAAAT-AATCAAAAA
1 -TTAATAGTAAATCAGT-AATAA
* * * *
12470314 TTAAGTAGTAATTCAATGATAC
1 TTAA-TAGTAAATCAGTAATAA
* *
12470336 TCTAATAGTAAAT-ATATAAAAA
1 T-TAATAGTAAATCA-GTAATAA
* * *
12470358 TGTAATAATAAATCATTTATAA
1 T-TAATAGTAAATCAGTAATAA
12470380 TTTAATAGTAAAT---TAATAA
1 -TTAATAGTAAATCAGTAATAA
** *
12470399 TTTAGCAGTAAATCACTAATAA
1 -TTAATAGTAAATCAGTAATAA
* *
12470421 TATAATAGTAAATTATTAATAA
1 T-TAATAGTAAATCAGTAATAA
* * *
12470443 TTTAATTA-TAAATTAATGATAA
1 -TTAA-TAGTAAATCAGTAATAA
* * *
12470465 TTCAATAGTATATTAGCTAATCA
1 TT-AATAGTAAATCAG-TAATAA
12470488 TTAATA
1 TTAATA
12470494 ACTTTTTAAT
Statistics
Matches: 245, Mismatches: 59, Indels: 55
0.68 0.16 0.15
Matches are distributed among these distances:
19 16 0.07
20 2 0.01
21 38 0.16
22 168 0.69
23 21 0.09
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (21 bp):
TTAATAGTAAATCAGTAATAA
Found at i:12470250 original size:43 final size:43
Alignment explanation
Indices: 12470147--12470286 Score: 122
Period size: 43 Copynumber: 3.2 Consensus size: 43
12470137 AAACTTAAAA
* * * * * * *
12470147 GTAAATCAAT-ATAATTTAGTAGTAAATAATTTATAATATAAT
1 GTAAATCAGTAATAACTTAATAATAAATCATGTATAATTTAAT
*
12470189 AGTTAATCAGTAATAACTTAATAATAAATCATGTATAATTTAAT
1 -GTAAATCAGTAATAACTTAATAATAAATCATGTATAATTTAAT
* * * * *
12470233 GTAAATTAGTAATAACTTGATCATGAATCACAG-ATAATTTAAT
1 GTAAATCAGTAATAACTTAATAATAAATCA-TGTATAATTTAAT
12470276 GATAAATCAGT
1 G-TAAATCAGT
12470287 GACAATTTTG
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
43 44 0.56
44 35 0.44
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.37
Consensus pattern (43 bp):
GTAAATCAGTAATAACTTAATAATAAATCATGTATAATTTAAT
Found at i:12470455 original size:44 final size:43
Alignment explanation
Indices: 12470338--12470455 Score: 123
Period size: 41 Copynumber: 2.7 Consensus size: 43
12470328 AATGATACTC
* * * * *
12470338 TAATAGTAAATATATAAAAATGTAATAATAAATCATTTATAATT
1 TAATAGTAAATAT-TAATAATTTAATAATAAATCACTAATAATA
** *
12470382 TAATAGT-AA-ATTAATAATTTAGCAGTAAATCACTAATAATA
1 TAATAGTAAATATTAATAATTTAATAATAAATCACTAATAATA
*
12470423 TAATAGTAAATTATTAATAATTTAATTATAAAT
1 TAATAGTAAA-TATTAATAATTTAATAATAAAT
12470456 TAATGATAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
41 29 0.49
42 4 0.07
43 2 0.03
44 24 0.41
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (43 bp):
TAATAGTAAATATTAATAATTTAATAATAAATCACTAATAATA
Found at i:12470465 original size:44 final size:42
Alignment explanation
Indices: 12470266--12470474 Score: 127
Period size: 44 Copynumber: 4.8 Consensus size: 42
12470256 TGAATCACAG
* * * ** *
12470266 ATAATTTAATGATAAATCAGTGACAATTTTGTAGTAAATAATCA
1 ATAATTTAATAATAAATCAATGATAA-TTAATAGTAAAT-ATTA
* * * *
12470310 A-AAATTAAGTAGTAATTCAATGATACTCTAATAGTAAATATATA
1 ATAATTTAA-TAATAAATCAATGATAAT-TAATAGTAAATAT-TA
* * * *
12470354 AAAATGTAATAATAAATCATTTATAATTTAATAGT-AA-ATTA
1 ATAATTTAATAATAAATCAATGATAA-TTAATAGTAAATATTA
** * * *
12470395 ATAATTTAGCAGTAAATCACTAATAATATAATAGTAAATTATTA
1 ATAATTTAATAATAAATCAATGATAAT-TAATAGTAAA-TATTA
* *
12470439 ATAATTTAATTATAAATTAATGATAATTCAATAGTA
1 ATAATTTAATAATAAATCAATGATAATT-AATAGTA
12470475 TATTAGCTAA
Statistics
Matches: 124, Mismatches: 31, Indels: 20
0.71 0.18 0.11
Matches are distributed among these distances:
40 1 0.01
41 28 0.23
42 4 0.03
43 12 0.10
44 73 0.59
45 6 0.05
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (42 bp):
ATAATTTAATAATAAATCAATGATAATTAATAGTAAATATTA
Found at i:12470595 original size:21 final size:22
Alignment explanation
Indices: 12470539--12470589 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
12470529 AACTTTATAA
*
12470539 TAAATCATCAATAATTTAGTAG
1 TAAATCATCAATAATTTAATAG
*
12470561 TAAATCACCAATAATTTAATAG
1 TAAATCATCAATAATTTAATAG
12470583 -AAATCAT
1 TAAATCAT
12470590 TCATAACTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (22 bp):
TAAATCATCAATAATTTAATAG
Found at i:12471117 original size:43 final size:43
Alignment explanation
Indices: 12471070--12471160 Score: 100
Period size: 43 Copynumber: 2.1 Consensus size: 43
12471060 AGTAATTAAT
12471070 TGATAAATTTAATAGTAAATTA-TATAATTTAATAA-TAAATCAA
1 TGATAAATTTAATAGTAAATTATTA-AATTTAA-AACTAAATCAA
* **
12471113 TGAT-AATTTAGTAGTTTATTATTGAAATTTAAAACTAAATCAA
1 TGATAAATTTAATAGTAAATTATT-AAATTTAAAACTAAATCAA
12471156 T-ATAA
1 TGATAA
12471161 CTTAGTAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
42 18 0.44
43 22 0.54
44 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (43 bp):
TGATAAATTTAATAGTAAATTATTAAATTTAAAACTAAATCAA
Found at i:12471134 original size:42 final size:42
Alignment explanation
Indices: 12471070--12471170 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 42
12471060 AGTAATTAAT
*
12471070 TGATAAATTTAATAGTAAATTA-TATAATTTAATAA-TAAATCAA
1 TGAT-AATTTAGTAGTAAATTATTA-AATTTAA-AACTAAATCAA
**
12471113 TGATAATTTAGTAGTTTATTATTGAAATTTAAAACTAAATCAA
1 TGATAATTTAGTAGTAAATTATT-AAATTTAAAACTAAATCAA
*
12471156 T-ATAACTTAGTAGTA
1 TGATAATTTAGTAGTA
12471171 GTTAATCATC
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
42 28 0.56
43 21 0.42
44 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.41
Consensus pattern (42 bp):
TGATAATTTAGTAGTAAATTATTAAATTTAAAACTAAATCAA
Found at i:12471279 original size:21 final size:22
Alignment explanation
Indices: 12471250--12471300 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
12471240 GATAACTTGA
* *
12471250 TAATGAATC-ATGCTTAATTTG
1 TAATAAATCTATGATTAATTTG
*
12471271 TAATAAATCTATGATTATTTTG
1 TAATAAATCTATGATTAATTTG
*
12471293 TAGTAAAT
1 TAATAAAT
12471301 ATTCAAAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (22 bp):
TAATAAATCTATGATTAATTTG
Found at i:12471353 original size:24 final size:22
Alignment explanation
Indices: 12471312--12471355 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
12471302 TTCAAAAACT
12471312 AAATAGTAAATTAATGATAACA
1 AAATAGTAAATTAATGATAACA
*
12471334 AAATAGTGATAATTAGTGATAA
1 AAATAGT-A-AATTAATGATAA
12471356 TTTAGTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 11 0.58
ACGTcount: A:0.55, C:0.02, G:0.14, T:0.30
Consensus pattern (22 bp):
AAATAGTAAATTAATGATAACA
Found at i:12471416 original size:22 final size:22
Alignment explanation
Indices: 12471391--12471568 Score: 94
Period size: 22 Copynumber: 8.1 Consensus size: 22
12471381 GATATTTTTG
*
12471391 TAGTAAATTATCAATAAATTAA
1 TAGTAAATTATCAATAATTTAA
* * *
12471413 TAGTAAATCAGT-TATAATTTTAT
1 TAGTAAATTA-TCAATAA-TTTAA
* * *
12471436 TA-CAAATCATCAATAATTTAG
1 TAGTAAATTATCAATAATTTAA
* *
12471457 TAGTAAATTATTAACAATTTAA
1 TAGTAAATTATCAATAATTTAA
* ** * *
12471479 TAGTAAATAATTTATAACTTAG
1 TAGTAAATTATCAATAATTTAA
* *
12471501 TAATAAATTATTC-ATAAGTTAA
1 TAGTAAATTA-TCAATAATTTAA
* ** *
12471523 TAATAAATTAAT-GTTAATTTAG
1 TAGTAAATT-ATCAATAATTTAA
**
12471545 TAGTAAATTATTGATAATTTAA
1 TAGTAAATTATCAATAATTTAA
12471567 TA
1 TA
12471569 ATATATCACT
Statistics
Matches: 120, Mismatches: 28, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
21 9 0.08
22 103 0.86
23 8 0.07
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (22 bp):
TAGTAAATTATCAATAATTTAA
Found at i:12471501 original size:44 final size:45
Alignment explanation
Indices: 12471448--12471622 Score: 176
Period size: 44 Copynumber: 4.0 Consensus size: 45
12471438 CAAATCATCA
* * *
12471448 ATAATTTAGTAGTAAATTATTAACAATTTAATAGTAAA-TAATTT
1 ATAATTTAGTAGTAAATTATTAATAATTTAATAATAAATTAATGT
* * * *
12471492 ATAACTTAGTAATAAATTATTCATAAGTTAATAATAAATTAATGT
1 ATAATTTAGTAGTAAATTATTAATAATTTAATAATAAATTAATGT
* * * *
12471537 -TAATTTAGTAGTAAATTATTGATAATTTAATAATATATCACTG-
1 ATAATTTAGTAGTAAATTATTAATAATTTAATAATAAATTAATGT
* * * * * *
12471580 ATAGTTTAGTAATAAATCATTGATAATATAATAATATATTAAT
1 ATAATTTAGTAGTAAATTATTAATAATTTAATAATAAATTAAT
12471623 AATAACTTAA
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
44 104 0.95
45 5 0.05
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (45 bp):
ATAATTTAGTAGTAAATTATTAATAATTTAATAATAAATTAATGT
Found at i:12471541 original size:88 final size:88
Alignment explanation
Indices: 12471449--12471622 Score: 224
Period size: 88 Copynumber: 2.0 Consensus size: 88
12471439 AAATCATCAA
* * * *
12471449 TAATTTAGTAGTAAATTATTAACAATTTAATAGTAAATAATTTATAACTTAGTAATAAATTATTC
1 TAATTTAGTAGTAAATTATTAACAATTTAATAATAAATAACTGATAACTTAGTAATAAATCATTC
12471514 ATAAGT-TAATAATAAATTAATGT
66 ATAA-TATAATAATAAATTAATGT
* * * * ** *
12471537 TAATTTAGTAGTAAATTATTGATAATTTAATAATATATCACTGATAGTTTAGTAATAAATCATTG
1 TAATTTAGTAGTAAATTATTAACAATTTAATAATAAATAACTGATAACTTAGTAATAAATCATTC
*
12471602 ATAATATAATAATATATTAAT
66 ATAATATAATAATAAATTAAT
12471623 AATAACTTAA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
87 1 0.01
88 72 0.99
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (88 bp):
TAATTTAGTAGTAAATTATTAACAATTTAATAATAAATAACTGATAACTTAGTAATAAATCATTC
ATAATATAATAATAAATTAATGT
Found at i:12471581 original size:22 final size:22
Alignment explanation
Indices: 12471556--12471618 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
12471546 AGTAAATTAT
12471556 TGATAATTTAATAATATATCAC
1 TGATAATTTAATAATATATCAC
* * * *
12471578 TGATAGTTTAGTAATAAATCAT
1 TGATAATTTAATAATATATCAC
*
12471600 TGATAATATAATAATATAT
1 TGATAATTTAATAATATAT
12471619 TAATAATAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (22 bp):
TGATAATTTAATAATATATCAC
Found at i:12471613 original size:19 final size:19
Alignment explanation
Indices: 12471589--12471626 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12471579 GATAGTTTAG
*
12471589 TAATAA-ATCATTGATAATA
1 TAATAATAT-ATTAATAATA
12471608 TAATAATATATTAATAATA
1 TAATAATATATTAATAATA
12471627 ACTTAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (19 bp):
TAATAATATATTAATAATA
Found at i:12471964 original size:22 final size:21
Alignment explanation
Indices: 12471939--12472022 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 21
12471929 TATTAATTAT
*
12471939 TAAAATTACATCAAGAGGTTAC
1 TAAAATTATATCAAGA-GTTAC
*
12471961 TAAAATTTTATCAATGA-TTA-
1 TAAAATTATATCAA-GAGTTAC
*
12471981 TCAAAATTATATCAAAAGTTAC
1 T-AAAATTATATCAAGAGTTAC
*
12472003 TAAAATTTTATCTAA-AGTTA
1 TAAAATTATATC-AAGAGTTA
12472023 TCAAAATCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
20 2 0.04
21 33 0.63
22 15 0.29
23 2 0.04
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (21 bp):
TAAAATTATATCAAGAGTTAC
Found at i:12471988 original size:21 final size:20
Alignment explanation
Indices: 12471962--12472029 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
12471952 AGAGGTTACT
12471962 AAAATTTTATCAATGATTATC
1 AAAATTTTATCAA-GATTATC
* *
12471983 AAAATTATATCAAAAGTTA-C
1 AAAATTTTATCAAGA-TTATC
12472003 TAAAATTTTATCTAA-AGTTATC
1 -AAAATTTTATC-AAGA-TTATC
12472025 AAAAT
1 AAAAT
12472030 CAAAATTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 2 0.05
21 35 0.88
22 3 0.08
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (20 bp):
AAAATTTTATCAAGATTATC
Found at i:12472014 original size:42 final size:44
Alignment explanation
Indices: 12471934--12472029 Score: 135
Period size: 42 Copynumber: 2.2 Consensus size: 44
12471924 TAGAATATTA
* * *
12471934 ATTATTAAAATTACATCAAGAGGTTACTAAAATTTTATC-AATG
1 ATTATCAAAATTACATCAAGAAGTTACTAAAATTTTATCTAAAG
*
12471977 ATTATCAAAATTATATCAA-AAGTTACTAAAATTTTATCTAAAG
1 ATTATCAAAATTACATCAAGAAGTTACTAAAATTTTATCTAAAG
12472020 -TTATCAAAAT
1 ATTATCAAAAT
12472030 CAAAATTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
42 28 0.58
43 20 0.42
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (44 bp):
ATTATCAAAATTACATCAAGAAGTTACTAAAATTTTATCTAAAG
Found at i:12476747 original size:2 final size:2
Alignment explanation
Indices: 12476737--12476770 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
12476727 TCCAGAGAGG
12476737 AT AT A- 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 AT A
12476771 GAACTATAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12480143 original size:19 final size:20
Alignment explanation
Indices: 12480119--12480157 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12480109 TTATTGTTTT
12480119 ATTTA-TATGAATTATTTAA
1 ATTTATTATGAATTATTTAA
* *
12480138 ATTTATTATTAATTTTTTAA
1 ATTTATTATGAATTATTTAA
12480158 TTGTTGCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
ATTTATTATGAATTATTTAA
Found at i:12480209 original size:31 final size:31
Alignment explanation
Indices: 12480168--12480226 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
12480158 TTGTTGCATT
* *
12480168 TTATATTTTTAATTTTGAAGTAAATTTATTA
1 TTATACTTTTAATTTTGAAATAAATTTATTA
12480199 TTATACTTTTAATTTTGAAATAAATTTA
1 TTATACTTTTAATTTTGAAATAAATTTA
12480227 ATCAATGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (31 bp):
TTATACTTTTAATTTTGAAATAAATTTATTA
Found at i:12480276 original size:14 final size:13
Alignment explanation
Indices: 12480241--12480278 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
12480231 ATGTGTAACA
*
12480241 AAAATATTTT-GT
1 AAAATATTTTATT
12480253 AAAATATTTTATT
1 AAAATATTTTATT
12480266 AAAATTATTTTAT
1 AAAA-TATTTTAT
12480279 AATTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.43
13 5 0.22
14 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
AAAATATTTTATT
Found at i:12485827 original size:42 final size:41
Alignment explanation
Indices: 12485759--12485856 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 41
12485749 CCTTAAATGG
*
12485759 AAGATGTAGCTGAGGTAATAGGAATGAAAGGGTAAAAAATCA
1 AAGATGTAGCTGAGGTAATAGGAATGAAAGGATAAAAAAT-A
* * *
12485801 AAGATGTAGCT-ATGTTAAT-GGAAATGAAAGGATAAGAAATG
1 AAGATGTAGCTGA-GGTAATAGG-AATGAAAGGATAAAAAATA
*
12485842 AAGATGTAGTTGAGG
1 AAGATGTAGCTGAGG
12485857 CAGCAAGAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
41 14 0.30
42 33 0.70
ACGTcount: A:0.45, C:0.03, G:0.30, T:0.22
Consensus pattern (41 bp):
AAGATGTAGCTGAGGTAATAGGAATGAAAGGATAAAAAATA
Found at i:12485915 original size:33 final size:33
Alignment explanation
Indices: 12485870--12485948 Score: 79
Period size: 33 Copynumber: 2.4 Consensus size: 33
12485860 CAAGAATGGA
*
12485870 AAATGAAA-ATGTAACTAAGGCAGTAAGGACAGG
1 AAAT-AAAGATGTAACTAAGGCAATAAGGACAGG
* * **
12485903 AAATAAAGATGTATCTGAGGCAATAAGGGTAGG
1 AAATAAAGATGTAACTAAGGCAATAAGGACAGG
**
12485936 AAATGGAGATGTA
1 AAATAAAGATGTA
12485949 TCTAGGATAG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 3 0.08
33 35 0.92
ACGTcount: A:0.46, C:0.06, G:0.29, T:0.19
Consensus pattern (33 bp):
AAATAAAGATGTAACTAAGGCAATAAGGACAGG
Found at i:12489546 original size:28 final size:27
Alignment explanation
Indices: 12489514--12489582 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
12489504 CATCATCAGG
* *
12489514 TTGCTTTTATAAATGTAGCTTTTTTCTA
1 TTGCTTTTATAAATCTAGC-ATTTTCTA
12489542 TTGCTTTTATAAATCTAGCATTTTCTA
1 TTGCTTTTATAAATCTAGCATTTTCTA
* *
12489569 TTACTTCTATAAAT
1 TTGCTTTTATAAAT
12489583 TCAACTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 19 0.51
28 18 0.49
ACGTcount: A:0.26, C:0.13, G:0.07, T:0.54
Consensus pattern (27 bp):
TTGCTTTTATAAATCTAGCATTTTCTA
Found at i:12489579 original size:27 final size:28
Alignment explanation
Indices: 12489521--12489602 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 28
12489511 AGGTTGCTTT
* * * *
12489521 TATAAATGTAGCTTTTTTCTATTGCTTT
1 TATAAATCTAGCTATTTTCTATTACTTC
12489549 TATAAATCTAGC-ATTTTCTATTACTTC
1 TATAAATCTAGCTATTTTCTATTACTTC
* *
12489576 TATAAAT-TCAACTATTTTTTATTACTT
1 TATAAATCT-AGCTATTTTCTATTACTT
12489603 TTCTATCATT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.02
27 21 0.46
28 24 0.52
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (28 bp):
TATAAATCTAGCTATTTTCTATTACTTC
Found at i:12489921 original size:21 final size:21
Alignment explanation
Indices: 12489897--12489964 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
12489887 AATTTTGACC
12489897 TCAAAATACTAAATTCTCTCT
1 TCAAAATACTAAATTCTCTCT
* * * ** *
12489918 TCAAGAT-CTTTCAATTTTGACC
1 TCAAAATAC--TAAATTCTCTCT
12489940 TCAAAATACTAAATTCTCTCT
1 TCAAAATACTAAATTCTCTCT
12489961 TCAA
1 TCAA
12489965 CTGCATATTC
Statistics
Matches: 32, Mismatches: 12, Indels: 6
0.64 0.24 0.12
Matches are distributed among these distances:
20 1 0.03
21 17 0.53
22 13 0.41
23 1 0.03
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (21 bp):
TCAAAATACTAAATTCTCTCT
Found at i:12489929 original size:43 final size:43
Alignment explanation
Indices: 12489881--12489964 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
12489871 TTTACTACTT
12489881 TCTTTCAATTTTGACCTCAAAATACTAAATTCTCTCTTCAAGA
1 TCTTTCAATTTTGACCTCAAAATACTAAATTCTCTCTTCAAGA
12489924 TCTTTCAATTTTGACCTCAAAATACTAAATTCTCTCTTCAA
1 TCTTTCAATTTTGACCTCAAAATACTAAATTCTCTCTTCAA
12489965 CTGCATATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (43 bp):
TCTTTCAATTTTGACCTCAAAATACTAAATTCTCTCTTCAAGA
Found at i:12491370 original size:13 final size:13
Alignment explanation
Indices: 12491352--12491378 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12491342 ATCCAATTAC
12491352 TTAACAATGATTG
1 TTAACAATGATTG
12491365 TTAACAATGATTG
1 TTAACAATGATTG
12491378 T
1 T
12491379 GCCAAACACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TTAACAATGATTG
Found at i:12491870 original size:19 final size:19
Alignment explanation
Indices: 12491806--12491879 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
12491796 TTATAATTCG
*
12491806 AATATT-TATATTATATAA
1 AATATTATATTTTATATAA
*
12491824 AATATTGATAATTTTA-ATATT
1 AATATT-AT-ATTTTATATA-A
12491845 AATATTATATTTTATATAA
1 AATATTATATTTTATATAA
* *
12491864 AAAATTATATATTATA
1 AATATTATATTTTATA
12491880 AATTATGTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 20 0.43
20 9 0.20
21 11 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (19 bp):
AATATTATATTTTATATAA
Found at i:12491961 original size:22 final size:22
Alignment explanation
Indices: 12491918--12491962 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
12491908 ATTATTTAAT
*
12491918 TTTTTATTAAATTTATATATAA
1 TTTTTATTAAATTTATAAATAA
12491940 TTTTTATTAAAATTT-TAAATAA
1 TTTTTATT-AAATTTATAAATAA
12491962 T
1 T
12491963 ATCGCTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTTATTAAATTTATAAATAA
Found at i:12498475 original size:30 final size:29
Alignment explanation
Indices: 12498414--12498475 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
12498404 ATCATTGTAA
* * *
12498414 TATTTTTTTTTTATAATTTTATAAACTTT
1 TATTTTTTATTCATAATTTTATAAACATT
* *
12498443 TATTTTTTATTCATACATTTTTTACACATT
1 TATTTTTTATTCATA-ATTTTATAAACATT
12498473 TAT
1 TAT
12498476 ATATATTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (29 bp):
TATTTTTTATTCATAATTTTATAAACATT
Found at i:12499960 original size:68 final size:68
Alignment explanation
Indices: 12499851--12499981 Score: 253
Period size: 68 Copynumber: 1.9 Consensus size: 68
12499841 AAAGGTCTAG
*
12499851 TGTACTCACCCCCATTATCAATCCTTATACATTTCAATTTCAACCCTATTTGTTTTTCAACTAGC
1 TGTACTCACCCCCATTATCAATCCTTATACATTTCAATTTCAACCCCATTTGTTTTTCAACTAGC
12499916 TAA
66 TAA
12499919 TGTACTCACCCCCATTATCAATCCTTATACATTTCAATTTCAACCCCATTTGTTTTTCAACTA
1 TGTACTCACCCCCATTATCAATCCTTATACATTTCAATTTCAACCCCATTTGTTTTTCAACTA
12499982 AGGCATGAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.27, C:0.29, G:0.04, T:0.40
Consensus pattern (68 bp):
TGTACTCACCCCCATTATCAATCCTTATACATTTCAATTTCAACCCCATTTGTTTTTCAACTAGC
TAA
Found at i:12501958 original size:16 final size:17
Alignment explanation
Indices: 12501924--12501959 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12501914 TCTTAAGATT
*
12501924 AAATAATCTTAGGAAAA
1 AAATAATCTTAGCAAAA
12501941 AAATAATCTT-GCAAAA
1 AAATAATCTTAGCAAAA
12501957 AAA
1 AAA
12501960 ATTAGAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.22
Consensus pattern (17 bp):
AAATAATCTTAGCAAAA
Found at i:12502171 original size:16 final size:18
Alignment explanation
Indices: 12502150--12502187 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
12502140 ACAAGCCATA
*
12502150 TTTTCTC-CTTTTCTTT-
1 TTTTCTCTCTATTCTTTC
12502166 TTTTCTCTCTATTCTTTC
1 TTTTCTCTCTATTCTTTC
12502184 TTTT
1 TTTT
12502188 TGTTGCCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTCTCTCTATTCTTTC
Found at i:12503309 original size:13 final size:13
Alignment explanation
Indices: 12503291--12503315 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12503281 TGATCTATCA
12503291 ATTTTAATTTTTG
1 ATTTTAATTTTTG
12503304 ATTTTAATTTTT
1 ATTTTAATTTTT
12503316 ATTAAATCAT
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:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
ATTTTAATTTTTG
Found at i:12511902 original size:3 final size:3
Alignment explanation
Indices: 12511894--12511945 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
12511884 ATGCTTAAAG
* * * *
12511894 AAT AAT AAT AAT AAT AAT -CT AAA AAT AAT AAT AAT AAG AAT -AG AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12511940 AAT AAT
1 AAT AAT
12511946 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:12511940 original size:20 final size:22
Alignment explanation
Indices: 12511891--12511945 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
12511881 AAAATGCTTA
*
12511891 AAGAATAATAATAATAATAATCT
1 AAGAATAATAATAATAAGAA-CT
*
12511914 AAAAATAATAATAATAAGAA-T
1 AAGAATAATAATAATAAGAACT
12511935 -AGAATAATAAT
1 AAGAATAATAAT
12511946 TTTTTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.34
21 1 0.03
23 18 0.62
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.27
Consensus pattern (22 bp):
AAGAATAATAATAATAAGAACT
Found at i:12512045 original size:3 final size:3
Alignment explanation
Indices: 12512039--12512067 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12512029 AAAAAGACTA
12512039 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12512068 ATTTTCATAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12512248 original size:13 final size:13
Alignment explanation
Indices: 12512204--12512254 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
12512194 ATAAAGTTCG
12512204 AAACCCTAAAATCA
1 AAACCCT-AAATCA
* *
12512218 AAAACCT-AATCCCC
1 AAACCCTAAAT--CA
12512232 AAACCCTAAATCA
1 AAACCCTAAATCA
12512245 AAACCCTAAA
1 AAACCCTAAA
12512255 CTTTCCAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
12 3 0.10
13 11 0.37
14 13 0.43
15 3 0.10
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.14
Consensus pattern (13 bp):
AAACCCTAAATCA
Found at i:12514231 original size:12 final size:13
Alignment explanation
Indices: 12514211--12514245 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
12514201 TAAAGTTAGG
12514211 AAAAAAAAAG-AA
1 AAAAAAAAAGTAA
12514223 AACAAAAAAAGTAA
1 AA-AAAAAAAGTAA
12514237 AAAAAAAAA
1 AAAAAAAAA
12514246 AGGGATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.10
13 15 0.71
14 4 0.19
ACGTcount: A:0.89, C:0.03, G:0.06, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAGTAA
Found at i:12514231 original size:14 final size:14
Alignment explanation
Indices: 12514211--12514247 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
12514201 TAAAGTTAGG
12514211 AAAAAAAAAG-AAA
1 AAAAAAAAAGTAAA
*
12514224 ACAAAAAAAGTAAA
1 AAAAAAAAAGTAAA
12514238 AAAAAAAAAG
1 AAAAAAAAAG
12514248 GGATTTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGTAAA
Found at i:12515534 original size:4 final size:4
Alignment explanation
Indices: 12515513--12515584 Score: 65
Period size: 4 Copynumber: 18.0 Consensus size: 4
12515503 GTTTTGTCAA
* * **
12515513 TCAT GCAT TCAC TCAT TCAT TCAT TCAT TCAT TTGT GT-AT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT -TCAT TCAT TCAT
** *
12515561 TTGT GCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT
12515585 CTATTTATGT
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
3 1 0.02
4 51 0.96
5 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.49
Consensus pattern (4 bp):
TCAT
Found at i:12515554 original size:16 final size:16
Alignment explanation
Indices: 12515534--12515577 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
12515524 CTCATTCATT
12515534 CATTCATTCATTTGTG
1 CATTCATTCATTTGTG
*
12515550 TATTCATTCATTTGTG
1 CATTCATTCATTTGTG
12515566 CATTCATTCATT
1 CATTCATTCATT
12515578 CATTCATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.09, T:0.52
Consensus pattern (16 bp):
CATTCATTCATTTGTG
Found at i:12517280 original size:15 final size:15
Alignment explanation
Indices: 12517259--12517296 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
12517249 AGTAATGCCT
12517259 TAAAAAAATAAAACAA
1 TAAAAAAATAAAA-AA
*
12517275 -AAAAAAGTAAAAAA
1 TAAAAAAATAAAAAA
12517289 TAAAAAAA
1 TAAAAAAA
12517297 AATTTGAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.84, C:0.03, G:0.03, T:0.11
Consensus pattern (15 bp):
TAAAAAAATAAAAAA
Found at i:12519764 original size:28 final size:28
Alignment explanation
Indices: 12519732--12519806 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
12519722 ATAAATATGG
*
12519732 TTTTAAGCCCAGTGTAGCTGACCCTCAA
1 TTTTAAGCCCAGTTTAGCTGACCCTCAA
* * *
12519760 TTTTAAGCCTAGTTTAGTTGACCCTTAA
1 TTTTAAGCCCAGTTTAGCTGACCCTCAA
*
12519788 TTTAAAGCCCAGTTTAGCT
1 TTTTAAGCCCAGTTTAGCT
12519807 AGCCATCAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (28 bp):
TTTTAAGCCCAGTTTAGCTGACCCTCAA
Found at i:12519833 original size:33 final size:33
Alignment explanation
Indices: 12519787--12520102 Score: 177
Period size: 33 Copynumber: 9.6 Consensus size: 33
12519777 TTGACCCTTA
*
12519787 ATTTAAAGCCCAGTTTAGCTAGCCATCAATAAAG
1 ATTT-AAGCCCAGTTTATCTAGCCATCAATAAAG
* * * * ** *
12519821 ATTTAATCCCAGTTTAGCTGGCCTTTGATGAAG
1 ATTTAAGCCCAGTTTATCTAGCCATCAATAAAG
* * *
12519854 -TTTAAGCCCAATTTA-CTTAGCCTTTAA-AGAAG
1 ATTTAAGCCCAGTTTATC-TAGCCATCAATA-AAG
*
12519886 ATTTAAGCCC-GATTTATCTAGCCATCAATGAAG
1 ATTTAAGCCCAG-TTTATCTAGCCATCAATAAAG
* * * * * *
12519919 TTTTAAGCCCAATCTAGCTAGCCCTTAA-AGAA-
1 ATTTAAGCCCAGTTTATCTAGCCATCAATA-AAG
* *
12519951 ATTTTAAGCCTAGTTTATCT-GACCATTAATGAAA-
1 A-TTTAAGCCCAGTTTATCTAG-CCATCAAT-AAAG
* * * *
12519985 TTTTAAGCTCAGTTTATCTGGCCATCAATGAAG
1 ATTTAAGCCCAGTTTATCTAGCCATCAATAAAG
** * * * *
12520018 ATTTAAATCTAGTTTACCTGGCCTTCAA-AGAAG
1 ATTTAAGCCCAGTTTATCTAGCCATCAATA-AAG
*
12520051 ATTTAAACCC-GATTTATCTAGCCATCAATAAAG
1 ATTTAAGCCCAG-TTTATCTAGCCATCAATAAAG
12520084 -TCTTAAGCCCAGTTTATCT
1 AT-TTAAGCCCAGTTTATCT
12520103 GGCTCCCAAA
Statistics
Matches: 216, Mismatches: 47, Indels: 39
0.72 0.16 0.13
Matches are distributed among these distances:
31 1 0.00
32 29 0.13
33 175 0.81
34 10 0.05
35 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (33 bp):
ATTTAAGCCCAGTTTATCTAGCCATCAATAAAG
Found at i:12520105 original size:66 final size:65
Alignment explanation
Indices: 12519787--12520105 Score: 224
Period size: 66 Copynumber: 4.8 Consensus size: 65
12519777 TTGACCCTTA
* * **
12519787 ATTTAAAGCCCAGTTTAGCTAGCCATCAATAAAGATTTAATCCCAGTTTAGCTGGCCTTTGATGA
1 ATTT-AAGCCCA-TTTAGCTAGCCATCAATAAAGATTTAAGCCCAGTTTATCTGGCCTTCAATGA
12519852 AG
64 AG
* * * *
12519854 -TTTAAGCCCAATTTA-CTTAGCCTTTAA-AGAAGATTTAAGCCC-GATTTATCTAGCCATCAAT
1 ATTTAAGCCC-ATTTAGC-TAGCCATCAATA-AAGATTTAAGCCCAG-TTTATCTGGCCTTCAAT
12519915 GAAG
62 GAAG
* * * * * *
12519919 TTTTAAGCCCAATCTAGCTAGCCCTTAA-AGAA-ATTTTAAGCCTAGTTTATCTGACCATT-AAT
1 ATTTAAGCCC-ATTTAGCTAGCCATCAATA-AAGA-TTTAAGCCCAGTTTATCTGGCC-TTCAAT
12519981 GAA-
62 GAAG
* * * * ** * * *
12519984 ATTTTAAGCTCAGTTTATCTGGCCATCAATGAAGATTTAAATCTAGTTTACCTGGCCTTCAAAGA
1 A-TTTAAGCCCA-TTTAGCTAGCCATCAATAAAGATTTAAGCCCAGTTTATCTGGCCTTCAATGA
12520049 AG
64 AG
* *
12520051 ATTTAAACCCGATTTATCTAGCCATCAATAAAG-TCTTAAGCCCAGTTTATCTGGC
1 ATTTAAGCCC-ATTTAGCTAGCCATCAATAAAGAT-TTAAGCCCAGTTTATCTGGC
12520106 TCCCAAAGAA
Statistics
Matches: 200, Mismatches: 35, Indels: 35
0.74 0.13 0.13
Matches are distributed among these distances:
64 3 0.01
65 51 0.25
66 140 0.70
67 6 0.03
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (65 bp):
ATTTAAGCCCATTTAGCTAGCCATCAATAAAGATTTAAGCCCAGTTTATCTGGCCTTCAATGAAG
Found at i:12520121 original size:33 final size:34
Alignment explanation
Indices: 12520084--12520171 Score: 126
Period size: 33 Copynumber: 2.6 Consensus size: 34
12520074 ATCAATAAAG
12520084 TCTTAAGCCCAGTTTATCTGGCTCCC-AAAGAAA
1 TCTTAAGCCCAGTTTATCTGGCTCCCTAAAGAAA
* * * *
12520117 TCTTAAGCTCAGTCTAGCTGG-TCCCTAAGGAAA
1 TCTTAAGCCCAGTTTATCTGGCTCCCTAAAGAAA
12520150 TCTTAAGCCCAGTTTATCTGGC
1 TCTTAAGCCCAGTTTATCTGGC
12520172 CTCCAATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
32 4 0.09
33 42 0.91
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (34 bp):
TCTTAAGCCCAGTTTATCTGGCTCCCTAAAGAAA
Found at i:12520350 original size:28 final size:28
Alignment explanation
Indices: 12520308--12520365 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
12520298 CCCAAAAGAT
* *
12520308 GTTTTAAGCCTAATTTAGCTGGCCTTCA
1 GTTTTAAGCCCAATTCAGCTGGCCTTCA
*
12520336 GTTTTAAGCCCAATTCATCTGGCCTTCA
1 GTTTTAAGCCCAATTCAGCTGGCCTTCA
12520364 GT
1 GT
12520366 AAATTTTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (28 bp):
GTTTTAAGCCCAATTCAGCTGGCCTTCA
Found at i:12520864 original size:74 final size:75
Alignment explanation
Indices: 12520783--12521106 Score: 202
Period size: 75 Copynumber: 4.3 Consensus size: 75
12520773 GATTCTTTAT
* *
12520783 TTCTCGACTTGCAATGTTGTCCTAGTCG-ATTCTTTACTTTTCGACTCGCGATGTTATCCCTATC
1 TTCTCGACTTGCAATGTTGTCCTAGTCGTATTCATTACTTTTCGACTCGCGATGTTATCCCGATC
*
12520847 GTTTTCTTAC
66 ATTTTCTTAC
* * * * * * * * *
12520857 TTTTCGACTTGCAGTGTTGTCCTAGTCGTTTTCATTACTTTTTGATTCGTGGTGTTGTCTCGATC
1 TTCTCGACTTGCAATGTTGTCCTAGTCGTATTCATTACTTTTCGACTCGCGATGTTATCCCGATC
12520922 ATTTTCTTAC
66 ATTTTCTTAC
* *** * * * * * * * *
12520932 TTCTCGACTCGTGGTGTTATCCCAATTGTTTTCATTACTTTCCAACTCGCAATGTTATCCC-AGT
1 TTCTCGACTTGCAATGTTGTCCTAGTCGTATTCATTACTTTTCGACTCGCGATGTTATCCCGA-T
*
12520996 CATTTTTTTAAC
65 CATTTTCTT-AC
* ** *** ** * * * * ** * * *
12521008 TTTTATACCCACGGTGTTGTCCCAATCATTTTTTTTACTTTTCGACTCGCGGTATTGTCCCGATC
1 TTCTCGACTTGCAATGTTGTCCTAGTCGTATTCATTACTTTTCGACTCGCGATGTTATCCCGATC
*
12521073 ATTTTTTTAC
66 ATTTTCTTAC
* * *
12521083 TTTTCGACTCGCGATGTTGTCCTA
1 TTCTCGACTTGCAATGTTGTCCTA
12521107 ACCGTTTTCT
Statistics
Matches: 193, Mismatches: 53, Indels: 7
0.76 0.21 0.03
Matches are distributed among these distances:
74 27 0.14
75 109 0.56
76 56 0.29
77 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (75 bp):
TTCTCGACTTGCAATGTTGTCCTAGTCGTATTCATTACTTTTCGACTCGCGATGTTATCCCGATC
ATTTTCTTAC
Found at i:12520944 original size:37 final size:36
Alignment explanation
Indices: 12520443--12521104 Score: 272
Period size: 37 Copynumber: 17.9 Consensus size: 36
12520433 GTTAACTCGG
*
12520443 TCATTTTCTTAC-TTTCAACTCGCGGTGTTGTCTC-A
1 TCATTTTCTTACTTTTCGACTCGCGGTGTTGTC-CGA
* * * **
12520478 GTCGATTCT-TTACTTCTCAACTTACGGTGTTGTCCTGA
1 -TC-ATTTTCTTACTTTTCGACTCGCGGTGTTGTCC-GA
* * *
12520516 TCGATTCT-TTACTTCTCGACTCGCGGTGTTGTCCCA
1 TC-ATTTTCTTACTTTTCGACTCGCGGTGTTGTCCGA
* * *
12520552 TTCATTTTC-T--TTTT-GACTTGCGATGTTGTCCTGG
1 -TCATTTTCTTACTTTTCGACTCGCGGTGTTGTCC-GA
* ** ** *
12520586 TCATTTTTTTACTTTTTAACTTACGGTGTTATCCCGA
1 TCATTTTCTTACTTTTCGACTCGCGGTGTTGT-CCGA
* * * *
12520623 TCATTTTTTTACTTTTTGACTCGCAGTGTTATCCCGA
1 TCATTTTCTTACTTTTCGACTCGCGGTGTTGT-CCGA
* ** * *
12520660 TCATTTTCTTACTTTTCAACTCATGGTATTGTCCCAGT
1 TCATTTTCTTACTTTTCGACTCGCGGTGTTGT-CC-GA
* * * ** *
12520698 TGATTTT-TTACTTCTGGACTCATGGTGTTGTCTCGG
1 TCATTTTCTTACTTTTCGACTCGCGGTGTTGTC-CGA
* * **
12520734 TCGTTTTCTTACTGTTT-AACTCATGGTGTTGTTCCCG-
1 TCATTTTCTTACT-TTTCGACTCGCGGTGTTG-T-CCGA
* * ** *
12520771 TCGATTCT-TTA-TTTCTCGACTTGCAATGTTGTCCTA
1 TC-ATTTTCTTACTTT-TCGACTCGCGGTGTTGTCCGA
* * * *
12520807 GTCGATTCT-TTACTTTTCGACTCGCGATGTTATCCCTA
1 -TC-ATTTTCTTACTTTTCGACTCGCGGTGTTGT-CCGA
* * * *
12520845 TCGTTTTCTTACTTTTCGACTTGCAGTGTTGTCCTA
1 TCATTTTCTTACTTTTCGACTCGCGGTGTTGTCCGA
* * * *
12520881 GTCGTTTTCATTACTTTTTGATTCGTGGTGTTGTCTCGA
1 -TCATTTTC-TTACTTTTCGACTCGCGGTGTTGTC-CGA
* * * *
12520920 TCATTTTCTTACTTCTCGACTCGTGGTGTTATCCCAA
1 TCATTTTCTTACTTTTCGACTCGCGGTGTTGT-CCGA
** * * ** * *
12520957 TTGTTTTCATTACTTTCCAACTCGCAATGTTATCCCA
1 TCATTTTC-TTACTTTTCGACTCGCGGTGTTGTCCGA
* ** * * *
12520994 GTCATTTTTTTAACTTTTATACCCACGGTGTTGTCCCAA
1 -TCATTTTCTT-ACTTTTCGACTCGCGGTGTTGT-CCGA
* *
12521033 TCATTTTTTTTACTTTTCGACTCGCGGTATTGTCCCGA
1 TCA-TTTTCTTACTTTTCGACTCGCGGTGTTGT-CCGA
* *
12521071 TCATTTTTTTACTTTTCGACTCGCGATGTTGTCC
1 TCATTTTCTTACTTTTCGACTCGCGGTGTTGTCC
12521105 TAACCGTTTT
Statistics
Matches: 489, Mismatches: 102, Indels: 70
0.74 0.15 0.11
Matches are distributed among these distances:
33 22 0.04
34 4 0.01
35 4 0.01
36 36 0.07
37 293 0.60
38 117 0.24
39 13 0.03
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.47
Consensus pattern (36 bp):
TCATTTTCTTACTTTTCGACTCGCGGTGTTGTCCGA
Found at i:12521031 original size:38 final size:37
Alignment explanation
Indices: 12520984--12521104 Score: 109
Period size: 38 Copynumber: 3.2 Consensus size: 37
12520974 CAACTCGCAA
* *
12520984 TGTTATCCCAGTCATTTTTTTAACTTTTATACCCACGG
1 TGTTGTCCCAGTCATTTTTTT-ACTTTTAGACCCACGG
* * * *
12521022 TGTTGTCCCAATCATTTTTTTTACTTTTCGACTCGCGG
1 TGTTGTCCCAGTCA-TTTTTTTACTTTTAGACCCACGG
* * * * *
12521060 TATTGTCCC-GATCATTTTTTTACTTTTCGACTCGCGA
1 TGTTGTCCCAG-TCATTTTTTTACTTTTAGACCCACGG
12521097 TGTTGTCC
1 TGTTGTCC
12521105 TAACCGTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
37 29 0.41
38 35 0.49
39 7 0.10
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.46
Consensus pattern (37 bp):
TGTTGTCCCAGTCATTTTTTTACTTTTAGACCCACGG
Found at i:12521184 original size:37 final size:37
Alignment explanation
Indices: 12521038--12521184 Score: 109
Period size: 37 Copynumber: 4.0 Consensus size: 37
12521028 CCCAATCATT
* *
12521038 TTTTTTACTTTTCGACTCGCGGTATTGTCCCGATC-A
1 TTTTTTACTTTTCGACTCACGATATTGTCCCGATCGA
* * ** *
12521074 TTTTTTTACTTTTCGACTCGCGATGTTGTCCTAACCG-
1 -TTTTTTACTTTTCGACTCACGATATTGTCCCGATCGA
* * * * * * *
12521111 TTTTCTTATTTTTTGATTTACGATGTTATCCTGATCGA
1 TTTT-TTACTTTTCGACTCACGATATTGTCCCGATCGA
* * *
12521149 TTCTTTATTTTTCGACTCACGATATTCTCCCGATCG
1 TTTTTTACTTTTCGACTCACGATATTGTCCCGATCG
12521185 TTGTCTTACA
Statistics
Matches: 87, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
36 4 0.05
37 80 0.92
38 3 0.03
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.48
Consensus pattern (37 bp):
TTTTTTACTTTTCGACTCACGATATTGTCCCGATCGA
Found at i:12521402 original size:20 final size:20
Alignment explanation
Indices: 12521377--12521441 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 20
12521367 TAAATATATT
12521377 AATAATAAAAAATACAAACA
1 AATAATAAAAAATACAAACA
12521397 AATAATAAACAAAAAATACAAACA
1 AATAAT----AAAAAATACAAACA
*
12521421 AA-ATTAAAAAATA-AAA-A
1 AATAATAAAAAATACAAACA
12521438 AATA
1 AATA
12521442 GCAGAAAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
17 3 0.08
18 4 0.10
19 8 0.21
20 6 0.15
23 2 0.05
24 16 0.41
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (20 bp):
AATAATAAAAAATACAAACA
Found at i:12521419 original size:13 final size:13
Alignment explanation
Indices: 12521383--12521423 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
12521373 TATTAATAAT
12521383 AAAAAATACAAAC
1 AAAAAATACAAAC
*
12521396 AAATAAT--AAAC
1 AAAAAATACAAAC
12521407 AAAAAATACAAAC
1 AAAAAATACAAAC
12521420 AAAA
1 AAAA
12521424 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
13 14 0.58
ACGTcount: A:0.78, C:0.12, G:0.00, T:0.10
Consensus pattern (13 bp):
AAAAAATACAAAC
Found at i:12521436 original size:24 final size:24
Alignment explanation
Indices: 12521383--12521436 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
12521373 TATTAATAAT
*
12521383 AAAAAATACAAACAAATAATAAAC
1 AAAAAATACAAACAAATAATAAAA
*
12521407 AAAAAATACAAACAAA-ATTAAAA
1 AAAAAATACAAACAAATAATAAAA
12521430 AATAAAA
1 AA-AAAA
12521437 AAATAGCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (24 bp):
AAAAAATACAAACAAATAATAAAA
Found at i:12523076 original size:3 final size:3
Alignment explanation
Indices: 12523070--12523106 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
12523060 AAAAAAATTA
*
12523070 AAT AAT AAT AAT AAT AAT AA- AAC AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12523107 ATTTTCATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:12523398 original size:11 final size:11
Alignment explanation
Indices: 12523382--12523411 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
12523372 ATACCTATAC
12523382 TCAAAACTATT
1 TCAAAACTATT
12523393 TCAAAACTATT
1 TCAAAACTATT
12523404 TCAAAACT
1 TCAAAACT
12523412 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (11 bp):
TCAAAACTATT
Found at i:12532879 original size:20 final size:20
Alignment explanation
Indices: 12532832--12532882 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
12532822 TATTTACCTA
*
12532832 AATT-TTTTAAATGATTAAAT
1 AATTATTTT-AATAATTAAAT
**
12532852 AAAAATTTTAATAATTAAAT
1 AATTATTTTAATAATTAAAT
12532872 AATTATTTTAA
1 AATTATTTTAA
12532883 AAATATGATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AATTATTTTAATAATTAAAT
Found at i:12536677 original size:42 final size:42
Alignment explanation
Indices: 12536629--12536715 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
12536619 CATGTGAAAG
12536629 TATGCATTCTTTTATTAAAGAATATCTTATTTAATTGTTCAA
1 TATGCATTCTTTTATTAAAGAATATCTTATTTAATTGTTCAA
12536671 TATGCATTCTTTTATTAAAGAATATCTTATTTAATTGTTCAA
1 TATGCATTCTTTTATTAAAGAATATCTTATTTAATTGTTCAA
12536713 TAT
1 TAT
12536716 ATCATATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (42 bp):
TATGCATTCTTTTATTAAAGAATATCTTATTTAATTGTTCAA
Found at i:12536694 original size:22 final size:22
Alignment explanation
Indices: 12536629--12536695 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
12536619 CATGTGAAAG
12536629 TATGCATTCTTTTATTAAAGAA
1 TATGCATTCTTTTATTAAAGAA
* * ****
12536651 TAT-C-TTATTTAATTGTTCAA
1 TATGCATTCTTTTATTAAAGAA
12536671 TATGCATTCTTTTATTAAAGAA
1 TATGCATTCTTTTATTAAAGAA
12536693 TAT
1 TAT
12536696 CTTATTTAAT
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
20 13 0.42
21 2 0.06
22 16 0.52
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.49
Consensus pattern (22 bp):
TATGCATTCTTTTATTAAAGAA
Found at i:12540370 original size:20 final size:21
Alignment explanation
Indices: 12540329--12540372 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
12540319 TAAAGGGGAA
12540329 AAATCTAGAACAGATAAAAAG
1 AAATCTAGAACAGATAAAAAG
12540350 AAATCTAGAACAGAT-AAAAG
1 AAATCTAGAACAGATAAAAAG
12540370 AAA
1 AAA
12540373 GACATATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.64, C:0.09, G:0.14, T:0.14
Consensus pattern (21 bp):
AAATCTAGAACAGATAAAAAG
Found at i:12546352 original size:333 final size:332
Alignment explanation
Indices: 12545682--12546625 Score: 1342
Period size: 333 Copynumber: 2.8 Consensus size: 332
12545672 ATTATTGAAT
* * * * *
12545682 GCGGCTTATAATAAAA-ATGCCTTTAATAATC-CGAAAAAATTTTTTTGAGAAAA-TATTGAAGG
1 GCGGCTTATAATAAAAGATGCCTTTAATAATCATG-AAAACTTTTATTAAGAAAATTATTAAAGG
** * *
12545744 TATTGTTATCTGAAATCGTCTTCAGTAATTATATACAAACTGTGATAGAAATTATTAAAGGCGTC
65 CGTTGTTATCTGAAATCGCCTTCAGTAATTATATACAAACTGTGATAGAAATTATTAAAGGCATC
* * * * *
12545809 TATCTTAAATATACGTCTTCAATAACAATGTTACAATATGTGTAGCAGTATATAGAATGCATTTT
130 TATCTTAAATATACGCCTTCAATAACAGTGTTACAATATGTGTAGCGGTATATAGAAGGTATTTT
* * * * * * *
12545874 ACAATAGAAGACGCTTTTAATAATTTTTAAAATATTTAGTGAGAAAATTTTGAAGCCGTCTATTA
195 ACAGTAGAAGATGCCTTTAATAA-TTTCAAAATATTTAGTGAAAAAATTTTGAAGGCGACTATTA
** * * *
12545939 TTAACAAACACCTTCAGTAATTGAAGGTGCCTTTTCTAATAAATGCATTCGATTACTATCGTGGT
259 TTAACAAATGCCTTCAGTAATTGAAGGTACATTTTCTAATAAATGCATTCGATTACTATCATGGT
*
12546004 ATATCGAAT
324 ATATCGAAG
* *
12546013 GCGGCTTATAATAAAAGATGCCTTTAATAATCATGGAAACTTTTATTAAGAAAATTATTAAATGC
1 GCGGCTTATAATAAAAGATGCCTTTAATAATCATGAAAACTTTTATTAAGAAAATTATTAAAGGC
* *
12546078 GTTGTTATCTAAAATTGCCTTCAGTTAA-TATATACAAACTGTGATAGAAATTATTAAAGGCATC
66 GTTGTTATCTGAAATCGCCTTCAG-TAATTATATACAAACTGTGATAGAAATTATTAAAGGCATC
* * *
12546142 TATCTTAAATATATGCCTTCACTAACAGTGTTACAATATGTGTAGTGGTATATAGAAGGTATTTT
130 TATCTTAAATATACGCCTTCAATAACAGTGTTACAATATGTGTAGCGGTATATAGAAGGTATTTT
* * *
12546207 ACAGTAGAAGATGCCTTTAATAATTCTCAAAATATTTAATGAAAAAATTTTGAAGGCAACTGTTA
195 ACAGTAGAAGATGCCTTTAATAATT-TCAAAATATTTAGTGAAAAAATTTTGAAGGCGACTATTA
*
12546272 TTAACAAATGCCTTCAGTAATTGAAGGTACATTTTCTAATAAATGCCTTCGATTACTATCATGGT
259 TTAACAAATGCCTTCAGTAATTGAAGGTACATTTTCTAATAAATGCATTCGATTACTATCATGGT
*
12546337 ATATCGAGG
324 ATATCGAAG
* *
12546346 GCGGCTTAAAATAAAAGATGTCTTTAATAATCATGAAAACTTTTATTAAGAAAATTATTAAAGGC
1 GCGGCTTATAATAAAAGATGCCTTTAATAATCATGAAAACTTTTATTAAGAAAATTATTAAAGGC
* * * *
12546411 GTTGTTATCTGAAATCGCCTTCAGTAATTATATATAAACTATGATAGGAATAATTAAAGGCATCT
66 GTTGTTATCTGAAATCGCCTTCAGTAATTATATACAAACTGTGATAGAAATTATTAAAGGCATCT
* * *
12546476 ATCTTAGATATACACCTTCAATAACAGTGTTACAATATGTGTAACGGTATATAGAAGGTATTTTA
131 ATCTTAAATATACGCCTTCAATAACAGTGTTACAATATGTGTAGCGGTATATAGAAGGTATTTTA
12546541 CAGTAGAAGATGCCTTTAATAATTTCTAAAATATTTAGTGAAAAAATTTTGAA-GCTGACTATT-
196 CAGTAGAAGATGCCTTTAATAATTTC-AAAATATTTAGTGAAAAAATTTTGAAGGC-GACTATTA
*
12546604 TCTAACAAATGCCTTCTGTAAT
259 T-TAACAAATGCCTTCAGTAAT
12546626 GGATTACTAA
Statistics
Matches: 545, Mismatches: 59, Indels: 16
0.88 0.10 0.03
Matches are distributed among these distances:
331 16 0.03
332 40 0.07
333 486 0.89
334 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (332 bp):
GCGGCTTATAATAAAAGATGCCTTTAATAATCATGAAAACTTTTATTAAGAAAATTATTAAAGGC
GTTGTTATCTGAAATCGCCTTCAGTAATTATATACAAACTGTGATAGAAATTATTAAAGGCATCT
ATCTTAAATATACGCCTTCAATAACAGTGTTACAATATGTGTAGCGGTATATAGAAGGTATTTTA
CAGTAGAAGATGCCTTTAATAATTTCAAAATATTTAGTGAAAAAATTTTGAAGGCGACTATTATT
AACAAATGCCTTCAGTAATTGAAGGTACATTTTCTAATAAATGCATTCGATTACTATCATGGTAT
ATCGAAG
Found at i:12554980 original size:17 final size:17
Alignment explanation
Indices: 12554948--12555008 Score: 97
Period size: 17 Copynumber: 3.6 Consensus size: 17
12554938 TTAAATTATT
*
12554948 TAATATTTATAAAATTAA
1 TAATAATTA-AAAATTAA
12554966 TAATAATTAAAAATTAA
1 TAATAATTAAAAATTAA
12554983 TAATAATTAAAAATTAA
1 TAATAATTAAAAATTAA
12555000 TAA-AATTAA
1 TAATAATTAA
12555009 TAATATATCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
16 6 0.14
17 28 0.67
18 8 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATTAAAAATTAA
Found at i:12558885 original size:36 final size:37
Alignment explanation
Indices: 12558845--12558923 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 37
12558835 ATCCCATTTT
12558845 CCTTATATATTGTGGATTCTCTATGTCTTTGG-TTTA
1 CCTTATATATTGTGGATTCTCTATGTCTTTGGCTTTA
12558881 CCTTATATATTGTGGATTCTCTATGTCTTTGGCTTTA
1 CCTTATATATTGTGGATTCTCTATGTCTTTGGCTTTA
*
12558918 ACTTAT
1 CCTTAT
12558924 TTTGTTTCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 32 0.78
37 9 0.22
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (37 bp):
CCTTATATATTGTGGATTCTCTATGTCTTTGGCTTTA
Found at i:12559719 original size:21 final size:21
Alignment explanation
Indices: 12559694--12559736 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12559684 CTTTTGTCTG
*
12559694 GATTATGTTTCTGATAGGATT
1 GATTATGTTTCTGATAAGATT
*
12559715 GATTATGTTTTTGATAAGATT
1 GATTATGTTTCTGATAAGATT
12559736 G
1 G
12559737 TATGTTAATT
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:0.02, G:0.23, T:0.49
Consensus pattern (21 bp):
GATTATGTTTCTGATAAGATT
Found at i:12560004 original size:17 final size:17
Alignment explanation
Indices: 12559964--12560004 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
12559954 CATAGAACAA
*
12559964 TTTGTAATTAAAATACT
1 TTTGTAGTTAAAATACT
*
12559981 TTTGTAGTTAAAGTACT
1 TTTGTAGTTAAAATACT
12559998 TTTGTAG
1 TTTGTAG
12560005 CTCGAAACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.49
Consensus pattern (17 bp):
TTTGTAGTTAAAATACT
Found at i:12562395 original size:6 final size:6
Alignment explanation
Indices: 12562386--12562411 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12562376 AAACAATATC
12562386 AATTTA AATTTA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AA
12562412 AATTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:12566140 original size:13 final size:13
Alignment explanation
Indices: 12566122--12566146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12566112 TATAAGCAGA
12566122 TCCCTCCTCCTCC
1 TCCCTCCTCCTCC
12566135 TCCCTCCTCCTC
1 TCCCTCCTCCTC
12566147 TCTCTCTCTC
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:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (13 bp):
TCCCTCCTCCTCC
Found at i:12566151 original size:2 final size:2
Alignment explanation
Indices: 12566144--12566183 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
12566134 CTCCCTCCTC
12566144 CT CT CT CT CT CT CT CT CT CT C- CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
12566184 CCCACACATG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:12566165 original size:21 final size:21
Alignment explanation
Indices: 12566141--12566183 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12566131 CTCCTCCCTC
12566141 CTCCTCTCTCTCTCTCTCTCT
1 CTCCTCTCTCTCTCTCTCTCT
12566162 CTCCTCTCTCTCTCTCTCTCT
1 CTCCTCTCTCTCTCTCTCTCT
12566183 C
1 C
12566184 CCCACACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (21 bp):
CTCCTCTCTCTCTCTCTCTCT
Found at i:12566170 original size:19 final size:19
Alignment explanation
Indices: 12566146--12566184 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
12566136 CCCTCCTCCT
12566146 CTCTCTCTCTCTCTCTCTC
1 CTCTCTCTCTCTCTCTCTC
12566165 CTCTCTCTCTCTCTCTCTC
1 CTCTCTCTCTCTCTCTCTC
12566184 C
1 C
12566185 CCACACATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (19 bp):
CTCTCTCTCTCTCTCTCTC
Found at i:12569845 original size:4 final size:4
Alignment explanation
Indices: 12569836--12569870 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
12569826 TATAAAATTA
12569836 TTAT TTAT TTAT TTAT TTAT TTAT TT-T TATAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTA
12569871 CATATTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 2 0.07
4 25 0.86
5 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:12569915 original size:19 final size:20
Alignment explanation
Indices: 12569891--12569934 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
12569881 AAATTTTATA
*
12569891 TTTATATT-AAAAGTAATAT
1 TTTATATTAAAAAATAATAT
12569910 TTTATATTAAAAAATAATAT
1 TTTATATTAAAAAATAATAT
12569930 TTTAT
1 TTTAT
12569935 TAATTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTATATTAAAAAATAATAT
Found at i:12569937 original size:18 final size:19
Alignment explanation
Indices: 12569888--12569937 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
12569878 ATTAAATTTT
*
12569888 ATATTTATATT-AAAAGTA
1 ATATTTATATTAAAAAATA
12569906 ATATTTTATATTAAAAAATA
1 ATA-TTTATATTAAAAAATA
12569926 ATATTT-TATTAA
1 ATATTTATATTAA
12569938 TTTTAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 9 0.31
19 11 0.38
20 9 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATATTTATATTAAAAAATA
Found at i:12569980 original size:32 final size:33
Alignment explanation
Indices: 12569919--12569980 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
12569909 TTTTATATTA
*
12569919 AAAAATAATATTTTATTAATTTTAAATTAAATT
1 AAAAATAATATTTTATTAATATTAAATTAAATT
12569952 AAAAAT-A-ATTTTATATAATATTAAATTAA
1 AAAAATAATATTTTAT-TAATATTAAATTAA
12569981 TTCGAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 7 0.26
32 14 0.52
33 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AAAAATAATATTTTATTAATATTAAATTAAATT
Found at i:12578567 original size:14 final size:14
Alignment explanation
Indices: 12578548--12578598 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
12578538 GTAACTATTT
12578548 ATTATATATAATTA
1 ATTATATATAATTA
12578562 ATTATATATAA--A
1 ATTATATATAATTA
*
12578574 ATTATTATGTAATTA
1 ATTA-TATATAATTA
*
12578589 ATAATATATA
1 ATTATATATA
12578599 TAGATATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 5 0.16
13 6 0.19
14 16 0.52
15 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
ATTATATATAATTA
Found at i:12578600 original size:29 final size:26
Alignment explanation
Indices: 12578548--12578598 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
12578538 GTAACTATTT
12578548 ATTATATATAATTAATTATATATAAA
1 ATTATATATAATTAATTATATATAAA
* *
12578574 ATTATTATGTAATTAATAATATATA
1 ATTA-TATATAATTAATTATATATA
12578599 TAGATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTATATATAATTAATTATATATAAA
Found at i:12579145 original size:65 final size:65
Alignment explanation
Indices: 12579076--12579197 Score: 142
Period size: 65 Copynumber: 1.9 Consensus size: 65
12579066 ATTGCCTAAC
* * *
12579076 GAAA-CCTCAAAATCGCCCAAACCCCAATAA-TCATTAAAAACTCCT-AAAACCCAAAAAAAACC
1 GAAACCCT-AAAATCGACCAAACCCCAAAAACT-AATAAAAA-TCCTAAAAACCCAAAAAAAACC
12579138 CCT
63 CCT
* **
12579141 GAAACCCTAACATCGATGAAACCCCAAAAACTAATAAAAATCCTAAAAACCCAAAAA
1 GAAACCCTAAAATCGACCAAACCCCAAAAACTAATAAAAATCCTAAAAACCCAAAAA
12579198 CTATCCTTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
64 4 0.08
65 40 0.83
66 4 0.08
ACGTcount: A:0.52, C:0.30, G:0.04, T:0.13
Consensus pattern (65 bp):
GAAACCCTAAAATCGACCAAACCCCAAAAACTAATAAAAATCCTAAAAACCCAAAAAAAACCCCT
Found at i:12579499 original size:65 final size:65
Alignment explanation
Indices: 12579384--12579517 Score: 155
Period size: 65 Copynumber: 2.1 Consensus size: 65
12579374 AAAACACCAT
** * ** *
12579384 AAACTACTAAAATGTCCAAAAACCCAAAAATCGCCCTTGAAGCCTAAAAACCCTTCAAACCACAA
1 AAACTACTAAAAACTCCAAAAAACCAAAAATCGCCCTCAAAGCCTAAAAACCATTCAAACCACAA
* * *
12579449 AAACTACTAAAAACT-CAAAAAACCAAAAATCGCCCCTCAAAGACC-CAAAACCATTGAAACCCC
1 AAACTACTAAAAACTCCAAAAAACCAAAAATCG-CCCTCAAAG-CCTAAAAACCATTCAAACCAC
12579512 AA
64 AA
12579514 AAAC
1 AAAC
12579518 CATTTAAAGC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
64 16 0.28
65 40 0.69
66 2 0.03
ACGTcount: A:0.51, C:0.31, G:0.05, T:0.13
Consensus pattern (65 bp):
AAACTACTAAAAACTCCAAAAAACCAAAAATCGCCCTCAAAGCCTAAAAACCATTCAAACCACAA
Found at i:12580055 original size:20 final size:20
Alignment explanation
Indices: 12580004--12580047 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
12579994 TTGAAACCTC
** * *
12580004 AAAACCCATTAATAACCCTT
1 AAAACCCAAAAATCACCCAT
12580024 AAAACCCAAAAATCACCCAT
1 AAAACCCAAAAATCACCCAT
12580044 AAAA
1 AAAA
12580048 TCCTAAAACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.30, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAACCCAAAAATCACCCAT
Found at i:12580626 original size:28 final size:28
Alignment explanation
Indices: 12580594--12580655 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
12580584 GTTGAGACTC
12580594 AAGACCCGAGA-CCTAAGA-CTTGAAACCT
1 AAGACCCGAGACCCT-AGACCTT-AAACCT
*
12580622 AAGACCCTAGACCCTAGACCTTAAACCT
1 AAGACCCGAGACCCTAGACCTTAAACCT
12580650 AAGACC
1 AAGACC
12580656 ATAAACCCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 25 0.81
29 6 0.19
ACGTcount: A:0.39, C:0.32, G:0.15, T:0.15
Consensus pattern (28 bp):
AAGACCCGAGACCCTAGACCTTAAACCT
Found at i:12580654 original size:14 final size:14
Alignment explanation
Indices: 12580604--12580662 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
12580594 AAGACCCGAG
12580604 ACCTAAGA-CTTGAA
1 ACCTAAGACCTT-AA
*
12580618 ACCTAAGACCCTAGA
1 ACCTAAGACCTTA-A
*
12580633 CCCT-AGACCTTAA
1 ACCTAAGACCTTAA
*
12580646 ACCTAAGACCATAA
1 ACCTAAGACCTTAA
12580660 ACC
1 ACC
12580663 CCAAAACCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.11
14 27 0.73
15 6 0.16
ACGTcount: A:0.41, C:0.32, G:0.10, T:0.17
Consensus pattern (14 bp):
ACCTAAGACCTTAA
Found at i:12580670 original size:22 final size:22
Alignment explanation
Indices: 12580644--12580685 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12580634 CCTAGACCTT
12580644 AAACCTAAGACCATAAACCCCA
1 AAACCTAAGACCATAAACCCCA
*
12580666 AAACCTTAGACCATAAACCC
1 AAACCTAAGACCATAAACCC
12580686 AAGTTCCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.36, G:0.05, T:0.12
Consensus pattern (22 bp):
AAACCTAAGACCATAAACCCCA
Found at i:12580844 original size:22 final size:22
Alignment explanation
Indices: 12580819--12580881 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
12580809 AACTTAAATG
12580819 CTAAACCTTAAATCATAAAACC
1 CTAAACCTTAAATCATAAAACC
12580841 CTAAACCTTAAATCATAAAACC
1 CTAAACCTTAAATCATAAAACC
* * *
12580863 CTAAGCCCTAAACCATAAA
1 CTAAACCTTAAATCATAAA
12580882 CATTAAGACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.21
Consensus pattern (22 bp):
CTAAACCTTAAATCATAAAACC
Found at i:12581082 original size:36 final size:36
Alignment explanation
Indices: 12580991--12581179 Score: 118
Period size: 36 Copynumber: 5.3 Consensus size: 36
12580981 TTGAGACTCG
* * *
12580991 AAACCTGAGAACC-TAAACCTAAGACCCTAAATCTTA
1 AAACCTTA-AACCTTAAACCTAAAACCCTAAATCCTA
* * *
12581027 AAACCTTAAATCTTGAACCTAAAACCCTAAA-CCTC
1 AAACCTTAAACCTTAAACCTAAAACCCTAAATCCTA
* *** *
12581062 AAACCTTTAACCTTTAAACCT-AAACTAAAAACCCTA
1 AAACCTTAAACC-TTAAACCTAAAACCCTAAATCCTA
* * * * * *
12581098 AAACC-TAAACCTGAATCCTGAGACCTTAGATCCTA
1 AAACCTTAAACCTTAAACCTAAAACCCTAAATCCTA
* * * *
12581133 AACCCTAAAACTTTAAATCCTAAAA-CCTAAACCCTA
1 AAACCTTAAACCTTAAA-CCTAAAACCCTAAATCCTA
*
12581169 AAACCTGAAAC
1 AAACCTTAAAC
12581180 TAAAAACCCC
Statistics
Matches: 113, Mismatches: 34, Indels: 12
0.71 0.21 0.08
Matches are distributed among these distances:
34 6 0.05
35 40 0.35
36 62 0.55
37 5 0.04
ACGTcount: A:0.44, C:0.29, G:0.05, T:0.22
Consensus pattern (36 bp):
AAACCTTAAACCTTAAACCTAAAACCCTAAATCCTA
Found at i:12581104 original size:7 final size:7
Alignment explanation
Indices: 12581000--12581262 Score: 78
Period size: 7 Copynumber: 37.0 Consensus size: 7
12580990 GAAACCTGAG
12581000 AACCT-A
1 AACCTAA
12581006 AACCTAA
1 AACCTAA
*
12581013 GACCCTAA
1 -AACCTAA
* *
12581021 ATCTTAA
1 AACCTAA
*
12581028 AACCTTA
1 AACCTAA
* **
12581035 AATCTTG
1 AACCTAA
12581042 AACCTAA
1 AACCTAA
12581049 AACCCT-A
1 AA-CCTAA
*
12581056 AACCTCA
1 AACCTAA
**
12581063 AACCTTT
1 AACCTAA
*
12581070 AACCTTTA
1 AACC-TAA
12581078 AACCT-A
1 AACCTAA
12581084 AA-CTAAA
1 AACCT-AA
12581091 AACCCTAA
1 AA-CCTAA
12581099 AACCT-A
1 AACCTAA
*
12581105 AACCTGA
1 AACCTAA
* *
12581112 ATCCTGA
1 AACCTAA
* *
12581119 GACCTTAG
1 AACC-TAA
*
12581127 ATCCTAA
1 AACCTAA
*
12581134 ACCCTAA
1 AACCTAA
*
12581141 AACTTTAA
1 AAC-CTAA
*
12581149 ATCCTAA
1 AACCTAA
12581156 AACCTAA
1 AACCTAA
*
12581163 ACCCTAA
1 AACCTAA
*
12581170 AACCTGA
1 AACCTAA
12581177 AA-CTAAA
1 AACCT-AA
12581184 AACCCCT-A
1 AA--CCTAA
*
12581192 GACCTTAA
1 AACC-TAA
*
12581200 AACCCAA
1 AACCTAA
*
12581207 AACCTAG
1 AACCTAA
*
12581214 ATCCTAA
1 AACCTAA
12581221 AACCATAA
1 AACC-TAA
*
12581229 ACCCT-A
1 AACCTAA
*
12581235 AACTTTAA
1 AAC-CTAA
12581243 AACCT-A
1 AACCTAA
12581249 AACC-ATA
1 AACCTA-A
12581256 AACCTAA
1 AACCTAA
12581263 GACTTGAGAC
Statistics
Matches: 189, Mismatches: 44, Indels: 47
0.68 0.16 0.17
Matches are distributed among these distances:
5 2 0.01
6 29 0.15
7 110 0.58
8 44 0.23
9 2 0.01
10 2 0.01
ACGTcount: A:0.46, C:0.30, G:0.03, T:0.21
Consensus pattern (7 bp):
AACCTAA
Found at i:12581370 original size:14 final size:15
Alignment explanation
Indices: 12581348--12581384 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
12581338 CTGAGACTTG
12581348 AAACTTAAGACCCTA
1 AAACTTAAGACCCTA
12581363 AAAC-TAAGACCCTA
1 AAACTTAAGACCCTA
*
12581377 AACCTTAA
1 AAACTTAA
12581385 AACCATAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.49, C:0.27, G:0.05, T:0.19
Consensus pattern (15 bp):
AAACTTAAGACCCTA
Found at i:12581464 original size:15 final size:15
Alignment explanation
Indices: 12581444--12581473 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12581434 AACAAAAAAG
12581444 TAAAACCCTAAACCT
1 TAAAACCCTAAACCT
*
12581459 TAAAACCTTAAACCT
1 TAAAACCCTAAACCT
12581474 GAGTCCTAGA
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:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAAACCCTAAACCT
Found at i:12581538 original size:17 final size:18
Alignment explanation
Indices: 12581502--12581540 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12581492 CCAAGACCTT
* *
12581502 AAAACCCTAGAATCACTA
1 AAAACCCCAAAATCACTA
12581520 AAAACCCCAAAATCA-TA
1 AAAACCCCAAAATCACTA
12581537 AAAA
1 AAAA
12581541 TCACTCCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.59, C:0.26, G:0.03, T:0.13
Consensus pattern (18 bp):
AAAACCCCAAAATCACTA
Found at i:12582528 original size:62 final size:60
Alignment explanation
Indices: 12582384--12582607 Score: 328
Period size: 62 Copynumber: 3.7 Consensus size: 60
12582374 TCTTGTGTAG
* * *
12582384 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TATTTTTGAAAATTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTTGA-TTTTAA
*
12582442 GGAAAATTGATACTTCCAACTTTTCCTCAAAAATATATTTTTTTTGAAACTTTGATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTTTTGAAACTTTGATTT-TAA
* *
12582504 GGAAAATTGATACTTTCAATTTTTCCTCAAAAATCTTTTTTTTTGAAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTG-AAACTTTGATTTT-AA
12582566 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
12582608 AAAAATCTTT
Statistics
Matches: 150, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
58 33 0.22
61 26 0.17
62 91 0.61
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTTGATTTTAA
Found at i:12585694 original size:41 final size:41
Alignment explanation
Indices: 12585648--12586260 Score: 941
Period size: 41 Copynumber: 15.0 Consensus size: 41
12585638 TTTTTTTAAA
* * *
12585648 GCTCCTCTAAATAGAGGCTCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
12585689 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAA-TAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
12585729 ACTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
12585770 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
12585811 GCTCCTCTAAACAGAGACACCACGACTTTGAAAA-TAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
12585851 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
12585892 GCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
**
12585934 GCTCCTCTAAGTAGAGGCACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
* *
12585976 GCTCCTCTAAACAGAGACACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
12586017 GCTCCTCTAAATAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
12586058 GCTCCTCTAAACAGAGGCACCATGACTTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
*
12586100 GCTCCTCTAAACAGAGGCA--ACGAACTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAATT
* *
12586140 ACTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* * *
12586181 GCTCCTCTAAACAGAGGCATCATGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
12586222 GCTCCTCTAAACAGAGGCA--ACGAACTTGGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAAT
12586261 ACTCCTAGAC
Statistics
Matches: 527, Mismatches: 36, Indels: 19
0.91 0.06 0.03
Matches are distributed among these distances:
39 2 0.00
40 125 0.24
41 291 0.55
42 109 0.21
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:12585754 original size:81 final size:81
Alignment explanation
Indices: 12585648--12586260 Score: 912
Period size: 81 Copynumber: 7.5 Consensus size: 81
12585638 TTTTTTTAAA
* * *
12585648 GCTCCTCTAAATAGAGGCTCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
12585713 ACTTTGAAAATAAATT
66 ACTTTGAAAATAAATT
*
12585729 ACTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
12585794 ACTTTGAAAAGTAAATT
66 ACTTTGAAAA-TAAATT
*
12585811 GCTCCTCTAAACAGAGACACCACGACTTTGAAAA-TAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
12585875 ACTTTGAAAAATAAATT
66 ACTTTG-AAAATAAATT
* **
12585892 GCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAGTAAATTGCTCCTCTAAGTAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
12585957 GACTTTGAGAAAGTAAATT
65 GACTTTGA-AAA-TAAATT
* * *
12585976 GCTCCTCTAAACAGAGACACCACGACTTTGGAAAGTAAATTGCTCCTCTAAATAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
12586041 ACTTTGAAAAATAAATT
66 ACTTTG-AAAATAAATT
* *
12586058 GCTCCTCTAAACAGAGGCACCATGACTTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCA--AC
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
12586121 GAACTTGGAAAAGTAAATT
65 G-ACTTTGAAAA-TAAATT
* * * *
12586140 ACTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCATCATG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
12586205 ACTTTGGAAAGTAAATT
66 ACTTT-GAAAATAAATT
*
12586222 GCTCCTCTAAACAGAGGCA--ACGAACTTGGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAAT
12586261 ACTCCTAGAC
Statistics
Matches: 494, Mismatches: 24, Indels: 28
0.90 0.04 0.05
Matches are distributed among these distances:
80 3 0.01
81 193 0.39
82 143 0.29
83 123 0.25
84 32 0.06
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (81 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGAAAATAAATT
Found at i:12585787 original size:122 final size:122
Alignment explanation
Indices: 12585648--12586260 Score: 928
Period size: 122 Copynumber: 5.0 Consensus size: 122
12585638 TTTTTTTAAA
* * *
12585648 GCTCCTCTAAATAGAGGCTCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
12585713 ACTTTGAAAATAAATTACTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
66 ACTTTGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
12585770 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGACACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
12585835 ACTTTGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
66 ACTTTGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* **
12585892 GCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAGTAAATTGCTCCTCTAAGTAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
* *
12585957 GACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGACACCACGACTTTGGAAAGTAAATT
65 GACTTTGA-AAA-TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* * *
12586017 GCTCCTCTAAATAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCATG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
* *
12586082 ACTTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGAACTTGGAAAAGTAAATT
66 AC-TTT-GAAAATAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAATT
* * * *
12586140 ACTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCATCATG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
* *
12586205 ACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGAACTTGGAAAAGTAAAT
66 ACTTT-GAAAATAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAAT
12586261 ACTCCTAGAC
Statistics
Matches: 457, Mismatches: 28, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
122 199 0.44
123 119 0.26
124 63 0.14
125 74 0.16
126 2 0.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (122 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:12590819 original size:60 final size:60
Alignment explanation
Indices: 12590726--12590892 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 60
12590716 TCTTGCGTAG
*
12590726 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAACGTTGATT-TCCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAACGTTGATTCT-CAA
** **
12590786 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTCAGAAATTTTGATTCTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAACGTTGATTCTCAA
* *
12590845 GAAAAATTGATACTTTCAACTTTT-CCTCAAAAATCTTTTTTTTTGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAAT-ATTTTTTTTGAAA
12590893 TTTTATTTTT
Statistics
Matches: 94, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
58 3 0.03
59 47 0.50
60 35 0.37
61 9 0.10
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAACGTTGATTCTCAA
Found at i:12590980 original size:25 final size:25
Alignment explanation
Indices: 12590941--12590989 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
12590931 ATACTCCTCA
* *
12590941 AAATAACTAACATA-CAGAAAAAAGT
1 AAATAAATAAAATACCA-AAAAAAGT
12590966 AAATAAATAAAATACCAAAAAAAG
1 AAATAAATAAAATACCAAAAAAAG
12590990 ATTATCTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.69, C:0.10, G:0.06, T:0.14
Consensus pattern (25 bp):
AAATAAATAAAATACCAAAAAAAGT
Found at i:12593036 original size:18 final size:18
Alignment explanation
Indices: 12593013--12593054 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12593003 TTTTTTTTCT
*
12593013 CTCTTATTCGGACTCCTC
1 CTCTTATTCAGACTCCTC
*
12593031 CTCTTATTCAGATTCCTC
1 CTCTTATTCAGACTCCTC
12593049 CT-TTAT
1 CTCTTAT
12593055 CTTTTTTCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.14, C:0.33, G:0.07, T:0.45
Consensus pattern (18 bp):
CTCTTATTCAGACTCCTC
Found at i:12593302 original size:3 final size:3
Alignment explanation
Indices: 12593294--12593327 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
12593284 CAAAATAAAA
12593294 AAT AAT AAT AAT AAT AAT AAT AAT AAT AGAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
12593328 TTAGAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12593352 original size:24 final size:25
Alignment explanation
Indices: 12593325--12593375 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
12593315 AATAATAGAT
12593325 AATTTA-GAAAAGATAAATAAAAAA
1 AATTTATGAAAAGATAAATAAAAAA
* * *
12593349 AA-TTATTATAGGATAAATAAAAAA
1 AATTTATGAAAAGATAAATAAAAAA
12593373 AAT
1 AAT
12593376 AATATCAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (25 bp):
AATTTATGAAAAGATAAATAAAAAA
Found at i:12593386 original size:23 final size:23
Alignment explanation
Indices: 12593335--12593391 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
12593325 AATTTAGAAA
*
12593335 AGATAAATAAAAAAAATTATTAT
1 AGATAAATAAAAAAAATTAATAT
12593358 AGGATAAATAAAAAAAA-TAATAT
1 A-GATAAATAAAAAAAATTAATAT
*
12593381 CAGATATATAA
1 -AGATAAATAA
12593392 TTAGATAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 14 0.47
24 16 0.53
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (23 bp):
AGATAAATAAAAAAAATTAATAT
Found at i:12593417 original size:9 final size:9
Alignment explanation
Indices: 12593403--12593437 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
12593393 TAGATAAACA
12593403 AAAATAAAT
1 AAAATAAAT
12593412 AAAATAAAT
1 AAAATAAAT
*
12593421 AAAATAAAA
1 AAAATAAAT
12593430 AAAATAAA
1 AAAATAAA
12593438 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAATAAAT
Found at i:12593418 original size:5 final size:5
Alignment explanation
Indices: 12593403--12593440 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
12593393 TAGATAAACA
12593403 AAAAT -AAAT AAAAT -AAAT AAAAT AAAA- AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
12593441 TATATATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 12 0.40
5 18 0.60
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:12593425 original size:14 final size:14
Alignment explanation
Indices: 12593396--12593440 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
12593386 ATATAATTAG
12593396 ATAAACAAAAAT-AA
1 ATAAA-AAAAATAAA
*
12593410 ATAAAATAAATAAA
1 ATAAAAAAAATAAA
12593424 ATAAAAAAAATAAA
1 ATAAAAAAAATAAA
12593438 ATA
1 ATA
12593441 TATATATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 5 0.18
14 23 0.82
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (14 bp):
ATAAAAAAAATAAA
Found at i:12593438 original size:9 final size:9
Alignment explanation
Indices: 12593396--12593438 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
12593386 ATATAATTAG
12593396 ATAAACAAAA
1 ATAAA-AAAA
*
12593406 ATAAATAAA
1 ATAAAAAAA
*
12593415 ATAAATAAA
1 ATAAAAAAA
12593424 ATAAAAAAA
1 ATAAAAAAA
12593433 ATAAAA
1 ATAAAA
12593439 TATATATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
9 26 0.84
10 5 0.16
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:12593443 original size:54 final size:54
Alignment explanation
Indices: 12593361--12593467 Score: 130
Period size: 54 Copynumber: 2.0 Consensus size: 54
12593351 TTATTATAGG
* * *
12593361 ATAAATAAAAAAAATAATATCAGATATATA-ATTAGATAA-ACAAAAATAAATAAA
1 ATAAATAAAAAAAATAAAATAAAATATATATATTAG-TAATA-AAAAATAAATAAA
*
12593415 ATAAATAAAATAAAA-AAAATAAAATATATATATTAGTAATAATAAATAAATAA
1 ATAAATAAAA-AAAATAAAATAAAATATATATATTAGTAATAAAAAATAAATAA
12593468 TAAATACATA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
54 36 0.78
55 10 0.22
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (54 bp):
ATAAATAAAAAAAATAAAATAAAATATATATATTAGTAATAAAAAATAAATAAA
Found at i:12593470 original size:14 final size:14
Alignment explanation
Indices: 12593404--12593470 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
12593394 AGATAAACAA
12593404 AAATAAATAA-AAT
1 AAATAAATAATAAT
*
12593417 AAATAAAATAA-AAA
1 AAAT-AAATAATAAT
12593431 AAAT-AA-AATATAT
1 AAATAAATAATA-AT
* * *
12593444 ATATTAGTAATAAT
1 AAATAAATAATAAT
12593458 AAATAAATAATAA
1 AAATAAATAATAA
12593471 ATACATAGGA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
11 2 0.05
12 3 0.07
13 8 0.19
14 25 0.60
15 4 0.10
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.27
Consensus pattern (14 bp):
AAATAAATAATAAT
Found at i:12596300 original size:37 final size:37
Alignment explanation
Indices: 12596259--12596332 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
12596249 AACTAGTTAA
*
12596259 AATAAAAGAA-TAAACAAAAACAATAGCTAAAATAAAT
1 AATAAAAAAATTAAA-AAAAACAATAGCTAAAATAAAT
* * *
12596296 AATAAAAAAATTATAAAATACAATAGCTAAACTAAAT
1 AATAAAAAAATTAAAAAAAACAATAGCTAAAATAAAT
12596333 GAAAACATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 29 0.91
38 3 0.09
ACGTcount: A:0.68, C:0.08, G:0.04, T:0.20
Consensus pattern (37 bp):
AATAAAAAAATTAAAAAAAACAATAGCTAAAATAAAT
Done.