Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 11 of 32
Found at i:5886767 original size:140 final size:140
Alignment explanation
Indices: 5886515--5886801 Score: 529
Period size: 140 Copynumber: 2.0 Consensus size: 140
5886505 AACAAGACTT
5886515 TAATTTTTGTCGCCACGAAATCTTGTCAGACTGATTGATCGATGACCGAAAGCCCGGAACAACTA
1 TAATTTTTGTCGCCACGAAATCTTGTCAGACTGATTGATCGATGACCGAAAGCCCGGAACAACTA
5886580 ATCTCCGTTTCAAATTGAACAGAGAACACAACCAGAGGCGGAGGGGAGGGGGACAAGTGGGGGCC
66 ATCTCCGTTTCAAATTGAACAGAGAACACAACCAGAGGCGGAGGGGAGGGGGACAAGTGGGGGCC
5886645 CGCCTCTCAA
131 CGCCTCTCAA
* *
5886655 TAATTTTTGTCGTCACGAAATCTTGTCAGACTGATTGATCGATGACCGACAGCCCGGAACAACTA
1 TAATTTTTGTCGCCACGAAATCTTGTCAGACTGATTGATCGATGACCGAAAGCCCGGAACAACTA
* * *
5886720 ATCTCCGTTTCAAATTGAACGGAGAACACAACCAGAGGCGGAGGGGAGGGGGGCTAGTGGGGGCC
66 ATCTCCGTTTCAAATTGAACAGAGAACACAACCAGAGGCGGAGGGGAGGGGGACAAGTGGGGGCC
5886785 CGCCTCTCAA
131 CGCCTCTCAA
5886795 TAATTTT
1 TAATTTT
5886802 AAATTTTTAT
Statistics
Matches: 142, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 142 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (140 bp):
TAATTTTTGTCGCCACGAAATCTTGTCAGACTGATTGATCGATGACCGAAAGCCCGGAACAACTA
ATCTCCGTTTCAAATTGAACAGAGAACACAACCAGAGGCGGAGGGGAGGGGGACAAGTGGGGGCC
CGCCTCTCAA
Found at i:5891101 original size:5 final size:5
Alignment explanation
Indices: 5891091--5891117 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5891081 AACGAGAGGA
5891091 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
5891118 GAAAAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5899370 original size:24 final size:25
Alignment explanation
Indices: 5899341--5899397 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
5899331 AATATGATAT
5899341 TTTATTAATAAA-ATAAAATTAAAA
1 TTTATTAATAAATATAAAATTAAAA
* *
5899365 TTTATTAA-AAATTTAAAATTAAAT
1 TTTATTAATAAATATAAAATTAAAA
*
5899389 TTTAATAAT
1 TTTATTAAT
5899398 TATTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTATTAATAAATATAAAATTAAAA
Found at i:5900710 original size:13 final size:14
Alignment explanation
Indices: 5900681--5900710 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5900671 CTCGATTATA
5900681 AATAAAAAATTTGT
1 AATAAAAAATTTGT
5900695 AATAAAAAATTT-T
1 AATAAAAAATTTGT
5900708 AAT
1 AAT
5900711 TATATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
AATAAAAAATTTGT
Found at i:5901388 original size:2 final size:2
Alignment explanation
Indices: 5901381--5901405 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5901371 CTTGAATAGA
5901381 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
5901406 GCCATTACCA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5913035 original size:17 final size:17
Alignment explanation
Indices: 5912996--5913043 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
5912986 TTTTGAAAGC
5912996 TATTAAAAAT-AAA-TA
1 TATTAAAAATAAAATTA
*
5913011 TA--ATAAATAAAATTA
1 TATTAAAAATAAAATTA
*
5913026 TATTAAAAATATAATTA
1 TATTAAAAATAAAATTA
5913043 T
1 T
5913044 TTTATTCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
13 5 0.19
14 3 0.12
15 6 0.23
17 12 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATTAAAAATAAAATTA
Found at i:5913249 original size:18 final size:19
Alignment explanation
Indices: 5913226--5913280 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
5913216 TTTAAATTAT
5913226 AAAAAATAAAATTCACAA-
1 AAAAAATAAAATTCACAAG
* *
5913244 AAAAAA-AAAACATGACAAG
1 AAAAAATAAAA-TTCACAAG
5913263 TAAAAAATAAAATTCACA
1 -AAAAAATAAAATTCACA
5913281 TATGACATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 4 0.14
18 11 0.38
20 10 0.34
21 4 0.14
ACGTcount: A:0.71, C:0.11, G:0.04, T:0.15
Consensus pattern (19 bp):
AAAAAATAAAATTCACAAG
Found at i:5926060 original size:6 final size:6
Alignment explanation
Indices: 5926028--5926057 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5926018 TGAAGAGATC
*
5926028 GGGTGG GGGTGG GGGTGG GGGTGG TGGTGG
1 GGGTGG GGGTGG GGGTGG GGGTGG GGGTGG
5926058 TGGCGGAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.80, T:0.20
Consensus pattern (6 bp):
GGGTGG
Found at i:5926819 original size:17 final size:17
Alignment explanation
Indices: 5926797--5926829 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5926787 TTATGGTCGT
5926797 TATTAGTTTTTAACAAA
1 TATTAGTTTTTAACAAA
5926814 TATTAGTTTTTAACAA
1 TATTAGTTTTTAACAA
5926830 TGGAAAAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (17 bp):
TATTAGTTTTTAACAAA
Found at i:5932705 original size:13 final size:13
Alignment explanation
Indices: 5932687--5932713 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5932677 AAATCAATGA
5932687 AATTCACCTAAAC
1 AATTCACCTAAAC
5932700 AATTCACCTAAAC
1 AATTCACCTAAAC
5932713 A
1 A
5932714 GCTATTTATG
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:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (13 bp):
AATTCACCTAAAC
Found at i:5935634 original size:93 final size:93
Alignment explanation
Indices: 5935474--5935661 Score: 331
Period size: 93 Copynumber: 2.0 Consensus size: 93
5935464 TTTCTTCAGT
*
5935474 GTCTACATTAGAATAAAGGTAACAAACGAGTGGAAATTACAATACCCAGGCTCTTCCACCAATAT
1 GTCTACATTAGAATAAAGGTAACAAACGAGTGGAAATTACAATACCCAGGCTCTTCCACCAACAT
*
5935539 GTCAGTGATCTAACTTTTTCCCTCTGCA
66 GTCAGTGATCTAACTTTTTCCCTCCGCA
* * *
5935567 GTCTACATTAGAATGAAGGTATCAAACGAGTGGAAATTACAATACCCAGGTTCTTCCACCAACAT
1 GTCTACATTAGAATAAAGGTAACAAACGAGTGGAAATTACAATACCCAGGCTCTTCCACCAACAT
5935632 GTCAGTGATCTAACTTTTTCCCTCCGCA
66 GTCAGTGATCTAACTTTTTCCCTCCGCA
5935660 GT
1 GT
5935662 GTTCTTTTAA
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (93 bp):
GTCTACATTAGAATAAAGGTAACAAACGAGTGGAAATTACAATACCCAGGCTCTTCCACCAACAT
GTCAGTGATCTAACTTTTTCCCTCCGCA
Found at i:5938624 original size:14 final size:14
Alignment explanation
Indices: 5938604--5939069 Score: 115
Period size: 15 Copynumber: 33.1 Consensus size: 14
5938594 TTATAATTAA
5938604 AATAAAAAATAT-T
1 AATAAAAAATATAT
5938617 AATAAAAAATATAT
1 AATAAAAAATATAT
* *
5938631 AATATAAGAATA-AA
1 AATA-AAAAATATAT
*
5938645 AATTAAAATAA-AAAT
1 AA-TAAAA-AATATAT
5938660 AAATATAAAAA-AT-T
1 -AATA-AAAAATATAT
* ** *
5938674 AACATTTATATATAT
1 AATA-AAAAATATAT
*
5938689 AGTAAAACAA-AT-T
1 AATAAAA-AATATAT
5938702 AA-AATAAAAT-TAT
1 AATAA-AAAATATAT
*
5938715 AATATAAAATATAT
1 AATAAAAAATATAT
*
5938729 -A-AAAAAATA-AA
1 AATAAAAAATATAT
*
5938740 AAT-AAATATATA-
1 AATAAAAAATATAT
*
5938752 AATTATAAAAATAAAT
1 AA-TA-AAAAATATAT
*
5938768 AAAAATAAAATATAT
1 AATAA-AAAATATAT
*
5938783 GACATTAAAATAATATTT
1 -A-A-TAAAA-AATATAT
* **
5938801 AAGAAATGATAT-T
1 AATAAAAAATATAT
*
5938814 ATATAAAAATTA-AT
1 A-ATAAAAAATATAT
* *
5938828 AATATAAATATAAAT
1 AATA-AAAAATATAT
*
5938843 ATATTAAAAATA-A-
1 A-ATAAAAAATATAT
5938856 AATATAAAAATATTAT
1 AATA-AAAAATA-TAT
* *
5938872 AATAATAAATA-AA
1 AATAAAAAATATAT
*
5938885 AATAAAATATATA-
1 AATAAAAAATATAT
*
5938898 ACATTAAAAATATAT
1 A-ATAAAAAATATAT
* *
5938913 -TTAAGAAATGATAT
1 AATAAAAAAT-ATAT
*
5938927 TATATAAAAAT-TAAT
1 AATA-AAAAATAT-AT
*
5938942 AATAAAAATATAAAT
1 AATAAAAA-ATATAT
*
5938957 ATATTAAAAATA-A-
1 A-ATAAAAAATATAT
*
5938970 AATATAAAATATTAT
1 AATAAAAAATA-TAT
* *
5938985 AATAATAAATA-AA
1 AATAAAAAATATAT
*
5938998 AATAAAATATATGAT
1 AATAAAAAATAT-AT
* *
5939013 ATTAAAAATATATTT
1 AATAAAAA-ATATAT
* *
5939028 AAGAAATAATAT-T
1 AATAAAAAATATAT
*
5939041 ATATAAAAATTA-AT
1 A-ATAAAAAATATAT
5939055 AATAAAAAA-ATAT
1 AATAAAAAATATAT
5939068 AA
1 AA
5939070 ATATATTAAA
Statistics
Matches: 329, Mismatches: 69, Indels: 110
0.65 0.14 0.22
Matches are distributed among these distances:
11 1 0.00
12 32 0.10
13 87 0.26
14 75 0.23
15 92 0.28
16 30 0.09
17 4 0.01
18 8 0.02
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.32
Consensus pattern (14 bp):
AATAAAAAATATAT
Found at i:5938666 original size:35 final size:33
Alignment explanation
Indices: 5938595--5938667 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 33
5938585 TTATTAATAT
* *
5938595 TATAATTAAAATAAAAAATATTAATAAAAAATA
1 TATAATTAAAATAAAAAATATAAATAAAAAAAA
*
5938628 TATAATATAAGAATAAAAATTA-AAATAAAAATAAA
1 TATAAT-TAA-AATAAAAAATATAAATAAAAA-AAA
5938663 TATAA
1 TATAA
5938668 AAAATTAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 6 0.18
34 11 0.32
35 17 0.50
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (33 bp):
TATAATTAAAATAAAAAATATAAATAAAAAAAA
Found at i:5938752 original size:36 final size:38
Alignment explanation
Indices: 5938685--5938777 Score: 106
Period size: 37 Copynumber: 2.5 Consensus size: 38
5938675 ACATTTATAT
*
5938685 ATATAGTAAAACAAATTAAAATAAAATTAT-AA-TATAAA
1 ATATA-TAAAA-AAATAAAAATAAAATTATAAATTATAAA
5938723 ATATATAAAAAAATAAAAAT-AAATATATAAATTATAAA
1 ATATATAAAAAAATAAAAATAAAAT-TATAAATTATAAA
5938761 A-ATA-AATAAAAATAAAA
1 ATATATAA-AAAAATAAAA
5938778 TATATGACAT
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
35 4 0.08
36 14 0.28
37 20 0.40
38 12 0.24
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (38 bp):
ATATATAAAAAAATAAAAATAAAATTATAAATTATAAA
Found at i:5938840 original size:21 final size:21
Alignment explanation
Indices: 5938814--5938886 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
5938804 AAATGATATT
5938814 ATATAAAAATTAATAATATAA
1 ATATAAAAATTAATAATATAA
*
5938835 ATATAAATATATTAAAAATA-AA
1 ATATAAA-A-ATTAATAATATAA
*
5938857 ATATAAAAATATTATAATAATAA
1 ATATAAAAAT-TAATAAT-ATAA
5938880 ATA-AAAA
1 ATATAAAA
5938887 TAAAATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
20 2 0.05
21 13 0.30
22 15 0.34
23 14 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
ATATAAAAATTAATAATATAA
Found at i:5938908 original size:50 final size:51
Alignment explanation
Indices: 5938824--5939025 Score: 171
Period size: 50 Copynumber: 3.8 Consensus size: 51
5938814 ATATAAAAAT
* * *
5938824 TAAT-AATATAAATATAAATATATTAAAAAT-AAAATATA-AAAATATTATAA
1 TAATAAATAAAAATA-AAATATA-TAATATTAAAAATATATAAAATATTATAA
*
5938874 TAATAAATAAAAATAAAATATATAACATTAAAAATATATTTAAGAA-ATGATATTATA
1 TAATAAATAAAAATAAAATATATAATATTAAAAATATA--TAA-AATAT--TA-TA-A
* *
5938931 TAA-AAATTAATAATAAAAATATAAATATATTAAAAATAAAATATAAAATATTATAA
1 TAATAAA-TAAAAAT-AAAATATATA-ATATTAAAAAT---ATATAAAATATTATAA
*
5938987 TAATAAATAAAAATAAAATATATGATATTAAAAATATAT
1 TAATAAATAAAAATAAAATATATAATATTAAAAATATAT
5939026 TTAAGAAATA
Statistics
Matches: 125, Mismatches: 9, Indels: 35
0.74 0.05 0.21
Matches are distributed among these distances:
49 5 0.04
50 19 0.15
51 13 0.10
53 4 0.03
54 13 0.10
55 10 0.08
56 15 0.12
57 15 0.12
58 11 0.09
59 12 0.10
60 5 0.04
62 3 0.02
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (51 bp):
TAATAAATAAAAATAAAATATATAATATTAAAAATATATAAAATATTATAA
Found at i:5939008 original size:23 final size:23
Alignment explanation
Indices: 5938938--5939008 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 23
5938928 ATATAAAAAT
*
5938938 TAAT-AATAAAAATATAAATATAT
1 TAATAAATAAAAATA-AAATATAA
5938961 TAA-AAATAAAATATAAAATATTATAA
1 TAATAAATAAAA-AT-AAA-A-TATAA
5938987 TAATAAATAAAAATAAAATATA
1 TAATAAATAAAAATAAAATATA
5939009 TGATATTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
23 14 0.34
24 5 0.12
25 5 0.12
26 9 0.22
27 8 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
TAATAAATAAAAATAAAATATAA
Found at i:5939047 original size:113 final size:113
Alignment explanation
Indices: 5938707--5939079 Score: 583
Period size: 114 Copynumber: 3.3 Consensus size: 113
5938697 AAATTAAAAT
* * * * *
5938707 AAAATT-ATAATATAAAATATATAAAAAAATAAAAAT-AAATATATAA-ATTATAAAAATAAATA
1 AAAATTAATAATA-AAAATATA-AATATATTAAAAATAAAATATAAAATATTATAATAATAAATA
5938769 AAAATAAAATATATGACATT-AAAATAATATTTAAGAAATGATATTATATA
64 AAAATAAAATATATGACATTAAAAAT-ATATTTAAGAAATGATATTATATA
*
5938819 AAAATTAATAATATAAATATAAATATATTAAAAATAAAATATAAAAATATTATAATAATAAATAA
1 AAAATTAATAATAAAAATATAAATATATTAAAAATAAAATAT-AAAATATTATAATAATAAATAA
*
5938884 AAATAAAATATATAACATTAAAAATATATTTAAGAAATGATATTATATA
65 AAATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATA
5938933 AAAATTAATAATAAAAATATAAATATATTAAAAATAAAATATAAAATATTATAATAATAAATAAA
1 AAAATTAATAATAAAAATATAAATATATTAAAAATAAAATATAAAATATTATAATAATAAATAAA
* *
5938998 AATAAAATATATGATATTAAAAATATATTTAAGAAATAATATTATATA
66 AATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATA
5939046 AAAATTAATAATAAAAAAATATAAATATATTAAA
1 AAAATTAATAAT--AAAAATATAAATATATTAAA
5939080 CTTATATTTT
Statistics
Matches: 243, Mismatches: 11, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
111 11 0.05
112 19 0.08
113 89 0.37
114 99 0.41
115 25 0.10
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (113 bp):
AAAATTAATAATAAAAATATAAATATATTAAAAATAAAATATAAAATATTATAATAATAAATAAA
AATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATA
Found at i:5942782 original size:212 final size:214
Alignment explanation
Indices: 5942389--5942791 Score: 632
Period size: 212 Copynumber: 1.9 Consensus size: 214
5942379 GATATTATGT
* * *
5942389 ATACATATATTTAATTTATAAATAAGTATTATTATAACTTATAATATATTTTATTTATATAATTA
1 ATACATATATTTAATTTATAAATAAGTATTACTATAACTTATAATAAACTTTATTTATATAATTA
* *
5942454 TATTTAATAACTTTATTAATTATCACCTTACATGTTATAATATATTGTTTATAATTAGTTATTAT
66 CATTTAATAACTTTATTAATTATCACCTTACATGTTATAACATATTGTTTATAATTAGTTATTAT
* *
5942519 TTATACAAATTTTGATATAAAACATTTTAACATATAATGTGTATCATTAATTATATATATAATAA
131 TTATACAAATTTTGATATAAAACATTATAACATATAATGTATATCATTAATTATATATATAATAA
5942584 AATAATATATTATATATAC
196 AATAATATATTATATATAC
* *
5942603 ATACATATATTTAA-TTATATATAAGTATTACTATAACTTATAATAAACTTTATTTGTATAATTA
1 ATACATATATTTAATTTATAAATAAGTATTACTATAACTTATAATAAACTTTATTTATATAATTA
* * * * * *
5942667 CATTTAATAAGTTTATTAGTTATTATCTTAGAT-TTTTAACATATTGTTTATAATTAGTTATTAT
66 CATTTAATAACTTTATTAATTATCACCTTACATGTTATAACATATTGTTTATAATTAGTTATTAT
*
5942731 TTATACAAATTTTGATATAAAACATTATAACATATAAAT-TATATTATTAATTATATATATA
131 TTATACAAATTTTGATATAAAACATTATAACATAT-AATGTATATCATTAATTATATATATA
5942792 TAATTATGGA
Statistics
Matches: 172, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
212 83 0.48
213 75 0.44
214 14 0.08
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (214 bp):
ATACATATATTTAATTTATAAATAAGTATTACTATAACTTATAATAAACTTTATTTATATAATTA
CATTTAATAACTTTATTAATTATCACCTTACATGTTATAACATATTGTTTATAATTAGTTATTAT
TTATACAAATTTTGATATAAAACATTATAACATATAATGTATATCATTAATTATATATATAATAA
AATAATATATTATATATAC
Found at i:5942787 original size:14 final size:14
Alignment explanation
Indices: 5942762--5942798 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
5942752 ACATTATAAC
5942762 ATATA-AATTATAT
1 ATATATAATTATAT
5942775 -TAT-TAATTATAT
1 ATATATAATTATAT
5942787 ATATATAATTAT
1 ATATATAATTAT
5942799 GGATGCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.52
13 3 0.14
14 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATAATTATAT
Found at i:5944036 original size:1 final size:1
Alignment explanation
Indices: 5944030--5944055 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
5944020 TTTCCCAATG
5944030 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
5944056 GTCTTTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5944838 original size:17 final size:19
Alignment explanation
Indices: 5944816--5944854 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5944806 TAATAATGAT
*
5944816 TATGTATA-A-ATTAAATA
1 TATGTATATATATAAAATA
5944833 TATGTATATATATAAAATA
1 TATGTATATATATAAAATA
5944852 TAT
1 TAT
5944855 TACTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
TATGTATATATATAAAATA
Found at i:5944998 original size:22 final size:22
Alignment explanation
Indices: 5944969--5945018 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
5944959 TGTAATCATA
*
5944969 TAAATAAAGTTTAT-TATAAAT
1 TAAATAAAGCTTATCTATAAAT
5944990 TATAATAAAGCTTATCTATAAAT
1 TA-AATAAAGCTTATCTATAAAT
5945013 TAAATA
1 TAAATA
5945019 TATGTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 2 0.08
22 15 0.58
23 9 0.35
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
TAAATAAAGCTTATCTATAAAT
Found at i:5945375 original size:27 final size:27
Alignment explanation
Indices: 5945319--5945375 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
5945309 TTAATTCTTC
* * *
5945319 TTAATATATATAAAAATATTTTATATA
1 TTAATATATATAAAAATATTATAAAAA
*
5945346 TTAATATATATATAAATA-TATACAAAA
1 TTAATATATATAAAAATATTATA-AAAA
5945373 TTA
1 TTA
5945376 GTTTGGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
TTAATATATATAAAAATATTATAAAAA
Found at i:5946236 original size:22 final size:22
Alignment explanation
Indices: 5946205--5946246 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5946195 GACATTCATT
* *
5946205 CTAGCCTATATTCATCAATAAA
1 CTAGCATATACTCATCAATAAA
*
5946227 CTAGCATATACTCATTAATA
1 CTAGCATATACTCATCAATA
5946247 TTATATAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.33
Consensus pattern (22 bp):
CTAGCATATACTCATCAATAAA
Found at i:5946259 original size:2 final size:2
Alignment explanation
Indices: 5946244--5946277 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5946234 ATACTCATTA
5946244 AT AT -T AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5946278 CGTCTAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5947666 original size:22 final size:22
Alignment explanation
Indices: 5947625--5947667 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5947615 AGACAAAAGA
* * *
5947625 AAAAAAAGAAAAATATATTGTT
1 AAAAAAACAAAAAAAAATTGTT
5947647 AAAAAAACAAAAAAAAATTGT
1 AAAAAAACAAAAAAAAATTGT
5947668 CAATGAACAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (22 bp):
AAAAAAACAAAAAAAAATTGTT
Found at i:5951118 original size:23 final size:23
Alignment explanation
Indices: 5951092--5951143 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
5951082 TAAGTTTATA
5951092 CTTTTGTGGAAATGAACTAATAC
1 CTTTTGTGGAAATGAACTAATAC
5951115 CTTTTGTGGAAATGAACTAATAC
1 CTTTTGTGGAAATGAACTAATAC
5951138 CTTTTG
1 CTTTTG
5951144 CAATTCTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38
Consensus pattern (23 bp):
CTTTTGTGGAAATGAACTAATAC
Found at i:5958162 original size:15 final size:14
Alignment explanation
Indices: 5958117--5958163 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
5958107 TTTAAAAGTT
5958117 TTTATTTTTA-TTA
1 TTTATTTTTATTTA
5958130 -TTATTATTTAGTTTA
1 TTTATT-TTTA-TTTA
5958145 TTTATTTTTATTTTA
1 TTTATTTTTA-TTTA
5958160 TTTA
1 TTTA
5958164 CTCATACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 5 0.17
13 4 0.14
15 15 0.52
16 5 0.17
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTATTTTTATTTA
Found at i:5958163 original size:19 final size:20
Alignment explanation
Indices: 5958116--5958163 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
5958106 TTTTAAAAGT
*
5958116 TTTTATTTTTATTATTATTA
1 TTTTATTTATATTATTATTA
*
5958136 -TTTAGTTTAT-TTATTTTTA
1 TTTTA-TTTATATTATTATTA
5958155 TTTTATTTA
1 TTTTATTTA
5958164 CTCATACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTATTTATATTATTATTA
Found at i:5958315 original size:16 final size:16
Alignment explanation
Indices: 5958296--5958334 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
5958286 TTTTCTGTTA
*
5958296 TATAAATTTTATTTTT
1 TATAAATTTTAATTTT
5958312 TAT-AATTTTAATTTT
1 TATAAATTTTAATTTT
5958327 TA-AAATTT
1 TATAAATTT
5958335 AATAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATAAATTTTAATTTT
Found at i:5958619 original size:20 final size:20
Alignment explanation
Indices: 5958590--5958628 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
5958580 ATTTTACACT
5958590 TTATAATTTTTT-ATTTTTA
1 TTATAATTTTTTAATTTTTA
5958609 TTATCAATTTTTTAATTTTT
1 TTAT-AATTTTTTAATTTTT
5958629 GATTGAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 8 0.44
21 6 0.33
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATAATTTTTTAATTTTTA
Found at i:5959868 original size:5 final size:5
Alignment explanation
Indices: 5959858--5959888 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
5959848 GACCATGAAG
*
5959858 AAGAA AAGAA AAGAA AAGAA AAGAG AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
5959889 CCATCAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:5995688 original size:18 final size:18
Alignment explanation
Indices: 5995654--5995711 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
5995644 NNNNNNCTCG
*
5995654 ATCACGATCACGGTCCCT
1 ATCACGATCACGCTCCCT
* *
5995672 ATCGCGTTCACGCTCCCT
1 ATCACGATCACGCTCCCT
*
5995690 ATCACGATCACGCTCTCT
1 ATCACGATCACGCTCCCT
5995708 ATCA
1 ATCA
5995712 TGGTCATGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.21, C:0.40, G:0.14, T:0.26
Consensus pattern (18 bp):
ATCACGATCACGCTCCCT
Found at i:5998025 original size:24 final size:24
Alignment explanation
Indices: 5997998--5998069 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
5997988 TAATCTCTTA
5997998 AACATATATAAATAAAATCAACTT
1 AACATATATAAATAAAATCAACTT
* * *
5998022 AACATGTGT---T--AATC-TCTT
1 AACATATATAAATAAAATCAACTT
5998040 AAACATATATAAATAAAATCAACTT
1 -AACATATATAAATAAAATCAACTT
5998065 AACAT
1 AACAT
5998070 CCTTTCTGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
18 3 0.09
19 11 0.31
21 1 0.03
22 1 0.03
24 16 0.46
25 3 0.09
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (24 bp):
AACATATATAAATAAAATCAACTT
Found at i:5998045 original size:43 final size:43
Alignment explanation
Indices: 5997984--5998069 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
5997974 AATGAATCCC
5997984 GTGTTAATCTCTTAAACATATATAAATAAAATCAACTTAACAT
1 GTGTTAATCTCTTAAACATATATAAATAAAATCAACTTAACAT
5998027 GTGTTAATCTCTTAAACATATATAAATAAAATCAACTTAACAT
1 GTGTTAATCTCTTAAACATATATAAATAAAATCAACTTAACAT
5998070 CCTTTCTGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.35
Consensus pattern (43 bp):
GTGTTAATCTCTTAAACATATATAAATAAAATCAACTTAACAT
Found at i:6013313 original size:2 final size:2
Alignment explanation
Indices: 6013306--6013334 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6013296 AAACAGTTAA
6013306 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6013335 AATAAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6027502 original size:14 final size:16
Alignment explanation
Indices: 6027469--6027512 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
6027459 AATTATAAAA
6027469 ATTAATATTTAAAATT
1 ATTAATATTTAAAATT
6027485 -TTAAT-TTT-AAATT
1 ATTAATATTTAAAATT
6027498 ATTAATATTTTAAAA
1 ATTAATA-TTTAAAA
6027513 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.21
14 8 0.33
15 5 0.21
16 3 0.12
17 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTAATATTTAAAATT
Found at i:6029939 original size:41 final size:40
Alignment explanation
Indices: 6029876--6029956 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
6029866 TCATCTATTA
* *
6029876 AATATATTTTTAATATCGTATATTTTATTTTTATTTCTTT
1 AATATATTTTTAATATCATATATTTTATTTTAATTTCTTT
* *
6029916 AATATAATTTTTGATATTATATATTTTATTTTAATTTCTTT
1 AATAT-ATTTTTAATATCATATATTTTATTTTAATTTCTTT
6029957 TACCTATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 5 0.14
41 31 0.86
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (40 bp):
AATATATTTTTAATATCATATATTTTATTTTAATTTCTTT
Found at i:6030005 original size:50 final size:48
Alignment explanation
Indices: 6029917--6030040 Score: 119
Period size: 50 Copynumber: 2.6 Consensus size: 48
6029907 TATTTCTTTA
* * * * *
6029917 ATATAATTTTTGATATTATATATTTTATTTTAATTTCTTTTACCTATATT
1 ATATAAATTTTAATTTTTTATATTTTATTTTAATTTCTTATA-CTATA-T
* *
6029967 ATATAAATTTTAATTTTTTATATTTTATTTTTGA-TTCTTATATTATAT
1 ATATAAATTTTAATTTTTTATATTTTA-TTTTAATTTCTTATACTATAT
*
6030015 ATAT-TATTTTAATATTTTT-TATTTTA
1 ATATAAATTTTAAT-TTTTTATATTTTA
6030041 ATTATAATAT
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
47 15 0.23
48 10 0.16
49 4 0.06
50 30 0.47
51 5 0.08
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (48 bp):
ATATAAATTTTAATTTTTTATATTTTATTTTAATTTCTTATACTATAT
Found at i:6030061 original size:42 final size:43
Alignment explanation
Indices: 6029962--6030068 Score: 98
Period size: 41 Copynumber: 2.6 Consensus size: 43
6029952 TCTTTTACCT
* * * * *
6029962 ATATTATATAAATTTTAATTTT-TTATATTTTATTTTTGATTCTT
1 ATATTATA-AAATATT-ATTTTAATATATTTTATTTTTAATTATA
* *
6030006 ATATTAT-ATATATTATTTTAATATTTTTTA-TTTTAATTATA
1 ATATTATAAAATATTATTTTAATATATTTTATTTTTAATTATA
6030047 ATATTATAAAATA-T-TTTTAATA
1 ATATTATAAAATATTATTTTAATA
6030069 AGGTAATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
40 8 0.15
41 21 0.40
42 17 0.32
44 7 0.13
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (43 bp):
ATATTATAAAATATTATTTTAATATATTTTATTTTTAATTATA
Found at i:6030197 original size:37 final size:39
Alignment explanation
Indices: 6030155--6030246 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 39
6030145 AATTACAATT
** *
6030155 ATATTATATTTATTGA-CTGTAATGTAAT-TATATTATA
1 ATATTATATTTATTGATCTGTAATAAAATAAATATTATA
* *
6030192 ATATTATATTATAGTGATCTGTTATAAAATAAATATTATA
1 ATATTATATT-TATTGATCTGTAATAAAATAAATATTATA
*
6030232 ATATTAT-TTAATTGA
1 ATATTATATTTATTGA
6030247 ATACAAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
37 10 0.22
38 9 0.20
39 11 0.24
40 15 0.33
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (39 bp):
ATATTATATTTATTGATCTGTAATAAAATAAATATTATA
Found at i:6036529 original size:36 final size:36
Alignment explanation
Indices: 6036482--6036552 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
6036472 CTTGCAGCAA
6036482 TTCATGTTTATACAGCATTTCTTAACCAAAATTTGC
1 TTCATGTTTATACAGCATTTCTTAACCAAAATTTGC
* *
6036518 TTCATGTTTATACAGCATTTCTTGACCCAAATTTG
1 TTCATGTTTATACAGCATTTCTTAACCAAAATTTG
6036553 ATTGGTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (36 bp):
TTCATGTTTATACAGCATTTCTTAACCAAAATTTGC
Found at i:6047013 original size:21 final size:21
Alignment explanation
Indices: 6046984--6047023 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6046974 GATAGCCAGG
* *
6046984 AAGATCTTGTCAAGAGGCATC
1 AAGACCTTGCCAAGAGGCATC
*
6047005 AAGACCTTGCCCAGAGGCA
1 AAGACCTTGCCAAGAGGCA
6047024 GCAAACGGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (21 bp):
AAGACCTTGCCAAGAGGCATC
Found at i:6053997 original size:17 final size:18
Alignment explanation
Indices: 6053959--6053999 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
6053949 TAATTTATAT
*
6053959 ATTA-TATAAAATTATTT
1 ATTATTATAAAATTATTA
*
6053976 TTTATTATAAAATT-TTA
1 ATTATTATAAAATTATTA
6053993 ATTATTA
1 ATTATTA
6054000 ATAATTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTATAAAATTATTA
Found at i:6054007 original size:14 final size:13
Alignment explanation
Indices: 6053990--6054032 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
6053980 TTATAAAATT
6053990 TTAATTATTAATAA
1 TTAATT-TTAATAA
*
6054004 TTAAATTTAATATA
1 TTAATTTTAATA-A
*
6054018 TTAATTTTAAAAA
1 TTAATTTTAATAA
6054031 TT
1 TT
6054033 TCTAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAATTTTAATAA
Found at i:6055903 original size:20 final size:21
Alignment explanation
Indices: 6055878--6055921 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
6055868 CCTAATGATA
6055878 AATGATAGA-TAAAGATTTTG
1 AATGATAGATTAAAGATTTTG
*
6055898 AATGATAGATTTAAGATTTTG
1 AATGATAGATTAAAGATTTTG
6055919 AAT
1 AAT
6055922 AAAAAGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (21 bp):
AATGATAGATTAAAGATTTTG
Found at i:6061882 original size:3 final size:3
Alignment explanation
Indices: 6061874--6061906 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
6061864 TATATGCATT
6061874 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6061907 TGTTTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6077182 original size:2 final size:2
Alignment explanation
Indices: 6077175--6077215 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
6077165 AGCAAGACAA
* * *
6077175 AT AT AT AT AA AT AA AT AT AT AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6077216 CTCAAGTTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:6077198 original size:18 final size:18
Alignment explanation
Indices: 6077175--6077215 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
6077165 AGCAAGACAA
6077175 ATATATATAAATAAATAT
1 ATATATATAAATAAATAT
*
6077193 ATATATATATATAAATAT
1 ATATATATAAATAAATAT
6077211 ATATA
1 ATATA
6077216 CTCAAGTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATATATAAATAAATAT
Found at i:6081317 original size:19 final size:19
Alignment explanation
Indices: 6081293--6081361 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 19
6081283 TTAACACATT
6081293 AATATTAAACTATAAATAA
1 AATATTAAACTATAAATAA
* *
6081312 AATATTAATAGTTTAAAATCATA
1 AATATTAA-ACTAT-AAAT-A-A
* *
6081335 AAAATTAAATTATAAATAA
1 AATATTAAACTATAAATAA
6081354 AATATTAA
1 AATATTAA
6081362 TATTTAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 16 0.40
20 4 0.10
21 8 0.20
22 4 0.10
23 8 0.20
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (19 bp):
AATATTAAACTATAAATAA
Found at i:6081327 original size:41 final size:41
Alignment explanation
Indices: 6081266--6081369 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 41
6081256 TCCAACTTTT
* * * *
6081266 AATAATATATTAATATTTTAACA-CATTAATATTAAACTATA
1 AATAAAATATTAATA-TTTAAAATCATAAAAATTAAACTATA
*
6081307 AATAAAATATTAATAGTTTAAAATCATAAAAATTAAATTATA
1 AATAAAATATTAATA-TTTAAAATCATAAAAATTAAACTATA
6081349 AATAAAATATTAATATTTAAA
1 AATAAAATATTAATATTTAAA
6081370 TTATAAATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 26 0.46
42 30 0.54
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (41 bp):
AATAAAATATTAATATTTAAAATCATAAAAATTAAACTATA
Found at i:6081381 original size:22 final size:22
Alignment explanation
Indices: 6081307--6081504 Score: 83
Period size: 22 Copynumber: 9.0 Consensus size: 22
6081297 TTAAACTATA
*
6081307 AATAAAATATTAATAGTTTAAAAT
1 AATAAATTATTAATA-TTT-AAAT
* *
6081331 CATAAA-AATTAA-ATTATAAAT
1 AATAAATTATTAATATT-TAAAT
6081352 -A-AAA-TATTAATATTTAAAT
1 AATAAATTATTAATATTTAAAT
* ** *
6081371 TATAAATTATTCCTATTTAAAA
1 AATAAATTATTAATATTTAAAT
** **
6081393 AATAAATTAAAAATAAATAAGCAT
1 AATAAATTATTAATATTTAA--AT
* *
6081417 -A-AAATCATTTAA-A-TTATAT
1 AATAAATTA-TTAATATTTAAAT
* *
6081436 -ATAAAATATTAATAATTAAAT
1 AATAAATTATTAATATTTAAAT
*
6081457 AATCAATTATTAATATTTTAAAT
1 AATAAATTATTAATA-TTTAAAT
6081480 AAATGACCAATTATTAATATTTAAA
1 -AAT-A--AATTATTAATATTTAAA
6081505 ATAAAATAAG
Statistics
Matches: 131, Mismatches: 26, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
19 20 0.15
20 10 0.08
21 16 0.12
22 45 0.34
23 14 0.11
24 9 0.07
26 6 0.05
27 11 0.08
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
AATAAATTATTAATATTTAAAT
Found at i:6081482 original size:42 final size:41
Alignment explanation
Indices: 6081295--6081482 Score: 132
Period size: 42 Copynumber: 4.4 Consensus size: 41
6081285 AACACATTAA
* * *
6081295 TATTAAACTATAAATAAAATATTAATAGTTTAAAATCATAAA-
1 TATTAAATTATAAATAAAATATTAATA-ATT-AAATAATAAAT
* * *
6081337 AATTAAATTATAAATAAAATATTAATATTTAAATTATAAAT
1 TATTAAATTATAAATAAAATATTAATAATTAAATAATAAAT
** * *
6081378 TATTCCTATT-TAAA-AAATAAATTAA-AAATAAATAAGCATAAAAT
1 TATT-AAATTATAAATAAA-ATATTAATAATTAAAT-A--AT-AAAT
* * *
6081422 CATTTAAATTATATATAAAATATTAATAATTAAATAATCAAT
1 TA-TTAAATTATAAATAAAATATTAATAATTAAATAATAAAT
*
6081464 TATTAATATTTTAAATAAA
1 TATTAA-ATTATAAATAAA
6081483 TGACCAATTA
Statistics
Matches: 114, Mismatches: 20, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
40 18 0.16
41 20 0.18
42 42 0.37
43 4 0.04
44 8 0.07
45 12 0.11
46 10 0.09
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (41 bp):
TATTAAATTATAAATAAAATATTAATAATTAAATAATAAAT
Found at i:6081581 original size:16 final size:16
Alignment explanation
Indices: 6081560--6081611 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
6081550 AAATTAAATT
6081560 AAATATTAATATTTTA
1 AAATATTAATATTTTA
6081576 AAATATTAATGA--TTA
1 AAATATTAAT-ATTTTA
*
6081591 AATTATTAATATTTTA
1 AAATATTAATATTTTA
6081607 AAATA
1 AAATA
6081612 AAACAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 1 0.03
15 12 0.39
16 17 0.55
17 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
AAATATTAATATTTTA
Found at i:6081666 original size:96 final size:94
Alignment explanation
Indices: 6081426--6081672 Score: 261
Period size: 96 Copynumber: 2.5 Consensus size: 94
6081416 TAAAATCATT
* *
6081426 TAAATTATAT-ATAAAATATTAATAATTAAATAATCAATTATTAATATTTT-AAATAAATGACCA
1 TAAATT-TATCATAAAATATTTA-AATTAAATAA--AA-TATTAATATTTTAAAATAAATGACAA
*
6081489 ATTATTAATATTTAAAATAAAATAAGAATAAATAAAA
61 ATTATTAATATTT---ATAAAATAAGAAAAAATAAAA
* *
6081526 TAAAATTTAATCATAATAATATTTAAATTAAATTAAATATTAATATTTTAAAATATTAATGATTA
1 T-AAATTT-ATCATAA-AATATTTAAATTAAATAAAATATTAATATTTTAAAATA--AATGA-CA
6081591 AATTATTAATATTT-TAAAATAA-AACAAAATAAAA
60 AATTATTAATATTTATAAAATAAGAA-AAAATAAAA
*
6081625 T-AATTTATCATAACAATATTTAAATTAAATAAAATATTAATATATTAA
1 TAAATTTATCATAA-AATATTTAAATTAAATAAAATATTAATATTTTAA
6081673 TGACTAAATT
Statistics
Matches: 130, Mismatches: 8, Indels: 22
0.81 0.05 0.14
Matches are distributed among these distances:
96 39 0.30
97 5 0.04
98 2 0.02
99 29 0.22
100 9 0.07
101 7 0.05
102 18 0.14
103 21 0.16
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (94 bp):
TAAATTTATCATAAAATATTTAAATTAAATAAAATATTAATATTTTAAAATAAATGACAAATTAT
TAATATTTATAAAATAAGAAAAAATAAAA
Found at i:6081814 original size:42 final size:41
Alignment explanation
Indices: 6081661--6081954 Score: 155
Period size: 42 Copynumber: 7.1 Consensus size: 41
6081651 AAATAAAATA
* *
6081661 TTAATATATTAATGACTAAATTATAAAT-AAATATTAAT-AT
1 TTAAAATATTAATGATTAAATT-TAAATAAAATATTAATAAT
* * * * *
6081701 TT-AAATGGTCAATTATTAATATTTTAAAATAAAACA-AAATAA-
1 TTAAAAT-ATTAATGATTAA-A-TTT-AAATAAAATATTAATAAT
* * **
6081743 TTAATCATAATAAT-ATATAAA-TT-AA-AAAATATTAATGTT
1 TTAA-AATATTAATGAT-TAAATTTAAATAAAATATTAATAAT
6081782 TTAAAATATTAATGATTAAATTATAAATAAAATATTAAT-AT
1 TTAAAATATTAATGATTAAATT-TAAATAAAATATTAATAAT
* * * **
6081823 TTAAATTATCAATTATTAATATTTGAAATAAAATAAAACAAAATAAT
1 TTAAAATATTAATGATTAA-ATTT-AAATAAAAT---A-TTAATAAT
* ** * * *
6081870 TGATCATAATAATGTTTAAA-TTAAATAAAATATTAATATT
1 TTAAAATATTAATGATTAAATTTAAATAAAATATTAATAAT
*
6081910 TTAAAATATTAATGATTAAATTATAAATGAAATATT--TAAT
1 TTAAAATATTAATGATTAAATT-TAAATAAAATATTAATAAT
6081950 TTAAA
1 TTAAA
6081955 TGATAATTAT
Statistics
Matches: 188, Mismatches: 41, Indels: 50
0.67 0.15 0.18
Matches are distributed among these distances:
37 5 0.03
38 16 0.09
39 10 0.05
40 41 0.22
41 24 0.13
42 49 0.26
43 12 0.06
44 11 0.06
45 3 0.02
46 4 0.02
47 13 0.07
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.40
Consensus pattern (41 bp):
TTAAAATATTAATGATTAAATTTAAATAAAATATTAATAAT
Found at i:6081889 original size:121 final size:120
Alignment explanation
Indices: 6081591--6081970 Score: 427
Period size: 128 Copynumber: 3.1 Consensus size: 120
6081581 TTAATGATTA
* * * *
6081591 AATTATTAATATTTTAAAATAAAACAAAATAAAATAATTTATCATAACAATAT-TTAAATTAAAT
1 AATTATTAATA-TTT-AAATAAAATAAAACAAAATAATTAATCATAATAATATATTAAA--AAAT
* * * *
6081655 A--AA-ATATTAATATATTAATGACTAAATTATAAATAAATATTAATATTTAAATGGTC
62 ATTAATATTTTAAAATATTAATGATTAAATTATAAATAAATATTAATATTTAAATGATC
6081711 AATTATTAATATTT---TAAAATAAAACAAAATAATTAATCATAATAATATATAAATTAAAAAAT
1 AATTATTAATATTTAAATAAAATAAAACAAAATAATTAATCATAAT-A-ATAT--ATTAAAAAAT
* *
6081773 ATTAATGTTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATTATC
62 ATTAATATTTTAAAATATTAATGATTAAATTATAAAT-AAATATTAATATTTAAATGATC
* *
6081833 AATTATTAATATTTGAAATAAAATAAAACAAAATAATTGATCATAATAATGTTTAAATTAAATAA
1 AATTATTAATATTT-AAATAAAATAAAACAAAATAATTAATCATAATAA----TATATT-AA-AA
*
6081898 AATATTAATATTTTAAAATATTAATGATTAAATTATAAATGAAATATTTA-ATTTAAATGAT-
59 AATATTAATATTTTAAAATATTAATGATTAAATTATAAAT-AAATATTAATATTTAAATGATC
6081959 AATTATTAATAT
1 AATTATTAATAT
6081971 ATTTTAATTA
Statistics
Matches: 225, Mismatches: 16, Indels: 32
0.82 0.06 0.12
Matches are distributed among these distances:
115 25 0.11
116 1 0.00
117 4 0.02
118 5 0.02
119 3 0.01
120 18 0.08
121 27 0.12
122 34 0.15
124 1 0.00
125 1 0.00
126 43 0.19
127 12 0.05
128 51 0.23
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (120 bp):
AATTATTAATATTTAAATAAAATAAAACAAAATAATTAATCATAATAATATATTAAAAAATATTA
ATATTTTAAAATATTAATGATTAAATTATAAATAAATATTAATATTTAAATGATC
Found at i:6081904 original size:64 final size:62
Alignment explanation
Indices: 6081589--6081917 Score: 195
Period size: 64 Copynumber: 5.4 Consensus size: 62
6081579 TATTAATGAT
* * * *
6081589 TAAATTATTAATATTTTAAAATAAAACAAAATAAAATAATTTATCATAACAATATTTAAATTAAA
1 TAAAATATTAATA-TTTAAAATAAAATAAAACAAAATAA-TTATCATAATAATATTTAAATT-AA
* * ** **
6081654 TAAAATATTAATATATT--AAT-GACTAAATTATAAATAA--AT-AT--TAATATTTAAA-TGG
1 TAAAATATTAATAT-TTAAAATAAAATAAAACA-AAATAATTATCATAATAATATTTAAATTAA
* * *
6081709 TCAATTATTAATATTT----TAAAATAAAACAAAATAATTAATCATAATAATATATAAATTAA
1 TAAAATATTAATATTTAAAATAAAATAAAACAAAATAATT-ATCATAATAATATTTAAATTAA
* * * ** * ** *
6081768 -AAAATATTAATGTTTTAAAATATTAATGATTAA-ATTATAAATAAAATATTAATATTTAAATT-
1 TAAAATATTAAT-ATTTAAAATA-AAAT-A-AAACAAAATAATTATCATAATAATATTTAAATTA
6081830 A
62 A
* * * *
6081831 TCAATTATTAATATTTGAAATAAAATAAAACAAAATAATTGATCATAATAATGTTTAAATTAAA
1 TAAAATATTAATATTTAAAATAAAATAAAACAAAATAATT-ATCATAATAATATTTAAATT-AA
6081895 TAAAATATTAATATTTTAAAATA
1 TAAAATATTAATA-TTTAAAATA
6081918 TTAATGATTA
Statistics
Matches: 195, Mismatches: 45, Indels: 48
0.68 0.16 0.17
Matches are distributed among these distances:
52 7 0.04
53 6 0.03
54 2 0.01
55 14 0.07
56 3 0.02
57 10 0.05
58 19 0.10
59 6 0.03
60 4 0.02
61 7 0.04
62 25 0.13
63 20 0.10
64 41 0.21
65 29 0.15
66 2 0.01
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (62 bp):
TAAAATATTAATATTTAAAATAAAATAAAACAAAATAATTATCATAATAATATTTAAATTAA
Found at i:6081974 original size:128 final size:126
Alignment explanation
Indices: 6081591--6081970 Score: 502
Period size: 126 Copynumber: 3.1 Consensus size: 126
6081581 TTAATGATTA
* * * *
6081591 AATTATTAATATTTTAAAATAAAACAAAATAAAATAATTTATCATAACAATATTTAAATTAAATA
1 AATTATTAATA-TTT-AAATAAAATAAAACAAAATAATTAATCATAATAATATTTAAATTAAATA
* *
6081656 AAATATT-A-A---T---ATATTAATGACTAAATTATAAATAAATATTAATATTTAAATGGTC
64 AAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAATATTAATATTTAAATGATC
*
6081711 AATTATTAATATTT---TAAAATAAAACAAAATAATTAATCATAATAATATATAAATT-AA-AAA
1 AATTATTAATATTTAAATAAAATAAAACAAAATAATTAATCATAATAATATTTAAATTAAATAAA
* *
6081771 ATATTAATGTTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATTATC
66 ATATTAATATTTTAAAATATTAATGATTAAATTATAAAT-AAATATTAATATTTAAATGATC
* *
6081833 AATTATTAATATTTGAAATAAAATAAAACAAAATAATTGATCATAATAATGTTTAAATTAAATAA
1 AATTATTAATATTT-AAATAAAATAAAACAAAATAATTAATCATAATAATATTTAAATTAAATAA
*
6081898 AATATTAATATTTTAAAATATTAATGATTAAATTATAAATGAAATATTTA-ATTTAAATGAT-
65 AATATTAATATTTTAAAATATTAATGATTAAATTATAAAT-AAATATTAATATTTAAATGATC
6081959 AATTATTAATAT
1 AATTATTAATAT
6081971 ATTTTAATTA
Statistics
Matches: 229, Mismatches: 16, Indels: 24
0.85 0.06 0.09
Matches are distributed among these distances:
113 8 0.03
114 3 0.01
115 36 0.16
118 1 0.00
119 3 0.01
120 11 0.05
121 22 0.10
122 34 0.15
126 50 0.22
127 12 0.05
128 49 0.21
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (126 bp):
AATTATTAATATTTAAATAAAATAAAACAAAATAATTAATCATAATAATATTTAAATTAAATAAA
ATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAATATTAATATTTAAATGATC
Found at i:6081981 original size:28 final size:29
Alignment explanation
Indices: 6081944--6081998 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
6081934 AAATGAAATA
6081944 TTTAATTTAAATGATA-ATTATTAATATAT
1 TTTAATTTAAATGATAGA-TATTAATATAT
*
6081973 TTTAA-TTAAATTATAGATATTAATAT
1 TTTAATTTAAATGATAGATATTAATAT
6081999 TTAAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (29 bp):
TTTAATTTAAATGATAGATATTAATATAT
Found at i:6082825 original size:14 final size:14
Alignment explanation
Indices: 6082806--6082843 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
6082796 TTTATTTACT
*
6082806 TATTTTATTTTTGA
1 TATTTTATTTTTAA
6082820 TATTTTAATTTTTAA
1 TATTTT-ATTTTTAA
6082835 T-TTTTATTT
1 TATTTTATTT
6082844 ATTATTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 10 0.45
15 8 0.36
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (14 bp):
TATTTTATTTTTAA
Found at i:6083024 original size:17 final size:18
Alignment explanation
Indices: 6082986--6083026 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
6082976 AAAACTCTTA
*
6082986 AAAAAATAACTGTATTTT
1 AAAAAATAAATGTATTTT
6083004 AAAAAATAAAT-T-TTTT
1 AAAAAATAAATGTATTTT
6083020 GAAAAAA
1 -AAAAAA
6083027 AGCTTTAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 7 0.33
18 10 0.48
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (18 bp):
AAAAAATAAATGTATTTT
Found at i:6085109 original size:30 final size:30
Alignment explanation
Indices: 6085069--6085127 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
6085059 AATTTTTAAT
*
6085069 TATAATAATTTATTTGATTAAAAATAAAAA
1 TATAAAAATTTATTTGATTAAAAATAAAAA
*
6085099 TATAAAAATTTATTTGATTTAAAATAAAA
1 TATAAAAATTTATTTGATTAAAAATAAAA
6085128 TAATTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (30 bp):
TATAAAAATTTATTTGATTAAAAATAAAAA
Found at i:6085132 original size:24 final size:23
Alignment explanation
Indices: 6085095--6085156 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 23
6085085 ATTAAAAATA
6085095 AAAATATAAAAATT-TATTTGATTT
1 AAAATA-AAAAATTATATTTGA-TT
6085119 AAAATAAAATAATTAATATTTGATT
1 AAAATAAAA-AATT-ATATTTGATT
6085144 AAATATAATAAAA
1 AAA-ATAA-AAAA
6085157 GTGTAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
23 3 0.09
24 10 0.30
25 5 0.15
26 13 0.39
27 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (23 bp):
AAAATAAAAAATTATATTTGATT
Found at i:6087599 original size:26 final size:24
Alignment explanation
Indices: 6087554--6087609 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
6087544 AATCATACTA
6087554 TTTTTTTTTTCTGTTTCTCTGCTT
1 TTTTTTTTTTCTGTTTCTCTGCTT
* *
6087578 TTTTTTTTATTTTTTTTGCTCTGCTT
1 TTTTTTTT-TTCTGTTT-CTCTGCTT
*
6087604 TCTTTT
1 TTTTTT
6087610 GCTCTTTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 8 0.30
25 6 0.22
26 13 0.48
ACGTcount: A:0.02, C:0.14, G:0.07, T:0.77
Consensus pattern (24 bp):
TTTTTTTTTTCTGTTTCTCTGCTT
Found at i:6099461 original size:20 final size:20
Alignment explanation
Indices: 6099436--6099474 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6099426 TTTAATCAAT
6099436 ATTAATATTTAACTTAAAAC
1 ATTAATATTTAACTTAAAAC
*
6099456 ATTAATATTTAATTTAAAA
1 ATTAATATTTAACTTAAAA
6099475 AATAACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTAATATTTAACTTAAAAC
Found at i:6099664 original size:13 final size:14
Alignment explanation
Indices: 6099633--6099665 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6099623 ATCATTTAAA
*
6099633 AAATATATATTTAT
1 AAATATAAATTTAT
6099647 AAATATAAATTT-T
1 AAATATAAATTTAT
6099660 AAATAT
1 AAATAT
6099666 TTTACACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATATAAATTTAT
Found at i:6108322 original size:23 final size:23
Alignment explanation
Indices: 6108296--6108346 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
6108286 TTTAAATAAC
*
6108296 AATTATATATAAAATATAAAAT-T
1 AATTATATAT-AAATAAAAAATAT
*
6108319 AATTATTTATAAATAAAAAATAT
1 AATTATATATAAATAAAAAATAT
6108342 AATTA
1 AATTA
6108347 AACTATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AATTATATATAAATAAAAAATAT
Found at i:6108328 original size:27 final size:30
Alignment explanation
Indices: 6108300--6108367 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 30
6108290 AATAACAATT
* *
6108300 ATATATAAAATATAAAATT-AA-T-TATTT
1 ATATATAAAAAATAAAATTAAACTATAATT
* *
6108327 ATAAATAAAAAATATAATTAAACTATAATT
1 ATATATAAAAAATAAAATTAAACTATAATT
6108357 ATATATAAAAA
1 ATATATAAAAA
6108368 CAAATCATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 16 0.48
28 2 0.06
29 1 0.03
30 14 0.42
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (30 bp):
ATATATAAAAAATAAAATTAAACTATAATT
Found at i:6110022 original size:14 final size:15
Alignment explanation
Indices: 6109993--6110025 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
6109983 TTAAGTATAT
6109993 TATTAATTAATTTTAA
1 TATTAATT-ATTTTAA
6110009 TATTAATT-TTTTAA
1 TATTAATTATTTTAA
6110023 TAT
1 TAT
6110026 ATATGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTAATTATTTTAA
Found at i:6111194 original size:15 final size:15
Alignment explanation
Indices: 6111174--6111211 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
6111164 ATTTGATTGA
*
6111174 ATTTTTTATTTTTTT
1 ATTTTTTATTTTCTT
6111189 A-TTTTTATTTTCTT
1 ATTTTTTATTTTCTT
*
6111203 GTTTTTTAT
1 ATTTTTTAT
6111212 AAAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.82
Consensus pattern (15 bp):
ATTTTTTATTTTCTT
Found at i:6111239 original size:17 final size:18
Alignment explanation
Indices: 6111214--6111251 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
6111204 TTTTTTATAA
*
6111214 AAAATAAAATATTAAT-C
1 AAAACAAAATATTAATAC
*
6111231 AAAACAAAATTTTAATAC
1 AAAACAAAATATTAATAC
6111249 AAA
1 AAA
6111252 TTAACTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAACAAAATATTAATAC
Found at i:6139327 original size:25 final size:25
Alignment explanation
Indices: 6139298--6139346 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
6139288 ATAAATATAA
*
6139298 AATGAT-AAATAATGATTGAATTATT
1 AATGATGAAATAATCATT-AATTATT
*
6139323 AATGATGAATTAATCATTAATTAT
1 AATGATGAAATAATCATTAATTAT
6139347 AATAAGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (25 bp):
AATGATGAAATAATCATTAATTATT
Found at i:6140727 original size:16 final size:17
Alignment explanation
Indices: 6140702--6140743 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
6140692 TTTTTTATAA
*
6140702 TTTAAATATTA-ATATT
1 TTTAATTATTATATATT
6140718 TTTAATTATTATTATATT
1 TTTAATTATTA-TATATT
6140736 TTT-ATTAT
1 TTTAATTAT
6140744 AACATCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 10 0.43
17 5 0.22
18 8 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAATTATTATATATT
Found at i:6140736 original size:18 final size:18
Alignment explanation
Indices: 6140708--6140743 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
6140698 ATAATTTAAA
6140708 TATTAATATTTTTAATTAT
1 TATTAATATTTTT-ATTAT
6140727 TATT-ATATTTTTATTAT
1 TATTAATATTTTTATTAT
6140744 AACATCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTAATATTTTTATTAT
Found at i:6144273 original size:10 final size:11
Alignment explanation
Indices: 6144258--6144297 Score: 57
Period size: 10 Copynumber: 3.8 Consensus size: 11
6144248 TGTTGAAGGA
6144258 TGAAAAA-AAG
1 TGAAAAAGAAG
6144268 TGAAAAAGAAG
1 TGAAAAAGAAG
*
6144279 AGAAAAAGAAG
1 TGAAAAAGAAG
6144290 -GAAAAAGA
1 TGAAAAAGA
6144298 GGGGACTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 15 0.54
11 13 0.46
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (11 bp):
TGAAAAAGAAG
Found at i:6147884 original size:29 final size:29
Alignment explanation
Indices: 6147819--6147885 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
6147809 TACTTCCAAT
*
6147819 AAATGAAAAAGATAAAAAAAATCCCAAACT
1 AAAT-AAAAAGATAAAAAAAATCCCAAACC
6147849 AAATAAAAA-ATAAAATAAAATCCTC-AACC
1 AAATAAAAAGATAAAA-AAAATCC-CAAACC
*
6147878 AACTAAAA
1 AAATAAAA
6147886 TACTAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 6 0.18
29 22 0.67
30 5 0.15
ACGTcount: A:0.67, C:0.15, G:0.03, T:0.15
Consensus pattern (29 bp):
AAATAAAAAGATAAAAAAAATCCCAAACC
Found at i:6153539 original size:37 final size:37
Alignment explanation
Indices: 6153489--6153562 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
6153479 ATGTATATAG
6153489 AAATATTTCAAACATAACAAAAGTACTTATCCATCAA
1 AAATATTTCAAACATAACAAAAGTACTTATCCATCAA
6153526 AAATATTTCAAACATAACAAAAGTACTTATCCATCAA
1 AAATATTTCAAACATAACAAAAGTACTTATCCATCAA
6153563 TTGATGGGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.27
Consensus pattern (37 bp):
AAATATTTCAAACATAACAAAAGTACTTATCCATCAA
Found at i:6155399 original size:139 final size:138
Alignment explanation
Indices: 6155201--6155472 Score: 334
Period size: 139 Copynumber: 2.0 Consensus size: 138
6155191 AGAAGAACAA
* * * *
6155201 AAAATTAAAAGAAGAAAAACCTTAACAACTGAAAGAAGAAGATAATGACAGAATATATATCTTAA
1 AAAATTAAAAGAAGAAAAACCTTAACAACTAAAACAAGAAGATAATGACAAAACATATATCTTAA
** * *
6155266 ATGTCAAAAATTAATT-TTTGAAGATAAAAAAGTTAAAAATATATAACCACCAAGCTACAAAAAT
66 ATGTCAAAAACCAATTCTTT-AAGATAAAAAAGCTAAAAATATATAACAACCAAGCTACAAAAAT
6155330 ATCATGTAG
130 ATCATGTAG
* *
6155339 AAAATT-AAAGCAAGAAAGAACC-TAACAACTCAAAACAAGAAGATAATGGCAAAACATATATTT
1 AAAATTAAAAG-AAGAAA-AACCTTAACAACT-AAAACAAGAAGATAATGACAAAACATATATCT
* * * * ** *
6155402 TAAATGTCAAAAACCAATTCTTTAAGATGAAAAAGCTGACAATATGTAACAATTAAGGTACAAAA
63 TAAATGTCAAAAACCAATTCTTTAAGATAAAAAAGCTAAAAATATATAACAACCAAGCTACAAAA
6155467 ATATCA
128 ATATCA
6155473 CTTATGCCTA
Statistics
Matches: 113, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
137 4 0.04
138 20 0.18
139 86 0.76
140 3 0.03
ACGTcount: A:0.54, C:0.12, G:0.11, T:0.23
Consensus pattern (138 bp):
AAAATTAAAAGAAGAAAAACCTTAACAACTAAAACAAGAAGATAATGACAAAACATATATCTTAA
ATGTCAAAAACCAATTCTTTAAGATAAAAAAGCTAAAAATATATAACAACCAAGCTACAAAAATA
TCATGTAG
Found at i:6167573 original size:2 final size:2
Alignment explanation
Indices: 6167566--6167598 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6167556 ATCAATCGAG
6167566 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
6167599 GATTGATGGG
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:6167899 original size:19 final size:19
Alignment explanation
Indices: 6167875--6167921 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
6167865 ATGCAGATTG
6167875 GCGTACTTTAGCTGAGGCC
1 GCGTACTTTAGCTGAGGCC
6167894 GCGTACTTTAGCTGAGGCC
1 GCGTACTTTAGCTGAGGCC
6167913 GCGTACTTT
1 GCGTACTTT
6167922 GGTTGCTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.15, C:0.26, G:0.30, T:0.30
Consensus pattern (19 bp):
GCGTACTTTAGCTGAGGCC
Found at i:6168205 original size:19 final size:19
Alignment explanation
Indices: 6168181--6168218 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
6168171 TCTAAAAGAA
6168181 AGCAAATAAAAAAAA-TAAT
1 AGCAAA-AAAAAAAACTAAT
6168200 AGCAAAAAAAAAAACTAAT
1 AGCAAAAAAAAAAACTAAT
6168219 TTCAAGCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (19 bp):
AGCAAAAAAAAAAACTAAT
Found at i:6170329 original size:2 final size:2
Alignment explanation
Indices: 6170322--6170361 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
6170312 ATTGCTCTGT
*
6170322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6170362 ATTGGACGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6177413 original size:2 final size:2
Alignment explanation
Indices: 6177408--6177439 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6177398 TCTCTGCTAC
6177408 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6177440 TTCTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6177806 original size:2 final size:2
Alignment explanation
Indices: 6177794--6177827 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6177784 TTGTTGGTTA
*
6177794 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6177828 TAATGTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6180272 original size:27 final size:27
Alignment explanation
Indices: 6180250--6180322 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 27
6180240 ATTTTATATG
6180250 ATTT-TTTAA-ATATTAATAATTTATA
1 ATTTATTTAATATATTAATAATTTATA
6180275 ATTTATTTAATATATTAATAA--T-TA
1 ATTTATTTAATATATTAATAATTTATA
*
6180299 A-TTATTTAAT-TATTAATATTTTAT
1 ATTTATTTAATATATTAATAATTTAT
6180323 TTATAATTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
22 8 0.19
23 9 0.21
24 4 0.10
25 6 0.14
26 5 0.12
27 10 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTATTTAATATATTAATAATTTATA
Found at i:6180286 original size:19 final size:19
Alignment explanation
Indices: 6180262--6180363 Score: 71
Period size: 23 Copynumber: 4.9 Consensus size: 19
6180252 TTTTTAAATA
*
6180262 TTAATAATTTATAATTTAT
1 TTAATAATTAATAATTTAT
6180281 TTAATATATTAATAATTAATTAT
1 TTAATA-ATTAATAA-T--TTAT
* *
6180304 TTAATTATTAATATTTTAT
1 TTAATAATTAATAATTTAT
6180323 TT-ATAATTTAAATAATATTAT
1 TTAATAA-TT-AATAAT-TTAT
*
6180344 GATTAAAATATTAATAATTT
1 --TTAATA-ATTAATAATTT
6180364 TAATAAATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
18 3 0.05
19 14 0.21
20 12 0.18
21 6 0.09
22 9 0.14
23 17 0.26
24 4 0.06
25 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (19 bp):
TTAATAATTAATAATTTAT
Found at i:6180437 original size:19 final size:19
Alignment explanation
Indices: 6180413--6180480 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 19
6180403 TAATAATTAA
6180413 TTATTTAAATATTAGCATT
1 TTATTTAAATATTAGCATT
*
6180432 TTATTTATAAT-TTAATCATT
1 TTATTTA-AATATT-AGCATT
*
6180452 AATATTTTTAAATATTAGCATT
1 --T-TATTTAAATATTAGCATT
6180474 TTATTTA
1 TTATTTA
6180481 TAATTTAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
19 14 0.36
20 9 0.23
22 9 0.23
23 7 0.18
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (19 bp):
TTATTTAAATATTAGCATT
Found at i:6180458 original size:21 final size:21
Alignment explanation
Indices: 6180433--6180500 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
6180423 ATTAGCATTT
6180433 TATTTATAATTTAATCATTAA
1 TATTTATAATTTAATCATTAA
* * *
6180454 TATTTTTAAATATT-AGCATT-T
1 TATTTAT-AAT-TTAATCATTAA
6180475 TATTTATAATTTAATCATTAA
1 TATTTATAATTTAATCATTAA
*
6180496 CATTT
1 TATTT
6180501 GAAAGTATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
19 2 0.06
20 8 0.22
21 16 0.44
22 8 0.22
23 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.54
Consensus pattern (21 bp):
TATTTATAATTTAATCATTAA
Found at i:6180469 original size:42 final size:42
Alignment explanation
Indices: 6180402--6180523 Score: 167
Period size: 42 Copynumber: 2.9 Consensus size: 42
6180392 TTATAATATA
* *
6180402 TTAATAATTAAT-TATTTAAATATTAGCATTTTATTTATAAT
1 TTAATCATTAATATTTTTAAATATTAGCATTTTATTTATAAT
6180443 TTAATCATTAATATTTTTAAATATTAGCATTTTATTTATAAT
1 TTAATCATTAATATTTTTAAATATTAGCATTTTATTTATAAT
* * **
6180485 TTAATCATTAACA-TTTGAAAGTATTAATATTTTATTTAT
1 TTAATCATTAATATTTTTAAA-TATTAGCATTTTATTTAT
6180524 TATGATTAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 17 0.23
42 56 0.77
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.53
Consensus pattern (42 bp):
TTAATCATTAATATTTTTAAATATTAGCATTTTATTTATAAT
Found at i:6180545 original size:183 final size:182
Alignment explanation
Indices: 6180338--6180705 Score: 435
Period size: 183 Copynumber: 2.0 Consensus size: 182
6180328 ATTTAAATAA
* * *
6180338 TATTATGATTAAAATATTAATAATTTTAATAAATTTTTAAATTTAAAAT-ATA-TTT-TATAATA
1 TATTATGATTAAAATATAAATAATTCTAATAAATTTTTAAAATTAAAATGATATTTTGTATAATA
* * *
6180400 TATTAA-TAATTAATTATTTAAA-TATTAGCA-TTTTATTTATAAT-TTAATCATTAATATTTTT
66 TA-TAATTAA--AA-T-TTTAAACTATTAGCATTTTTA-TAATAATATTAATAATTAATA-ATTT
* * *
6180461 AAATATTAGCATTTTATTTATAATTTAATCATTAACATTTGAAAGTATTAATATTTTATT
124 AAATATTAACATTTTATATATAATTTAATCATTAACATTTGAAAATATTAATA-TTTATT
* *
6180521 TATTATGATTAAAATATAAATAATTCTAATTAATTTTTAAAATTAAAATGTTATTTTGTATAATA
1 TATTATGATTAAAATATAAATAATTCTAATAAATTTTTAAAATTAAAATGATATTTTGTATAATA
* ** * *
6180586 TATAATTAAAATTTTAAACTTTTTTCCTTTTTATAATAATATTAATAATTTATAATTTAAATATT
66 TATAATTAAAATTTTAAACTATTAGCATTTTTATAATAATATTAATAATTAATAATTTAAATATT
* * * *
6180651 AATATTTTATATATGATTTAATCATTAATATTTTAAAATATTAATATTTATT
131 AACATTTTATATATAATTTAATCATTAACATTTGAAAATATTAATATTTATT
6180703 TAT
1 TAT
6180706 AATTTAAATG
Statistics
Matches: 158, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
182 15 0.09
183 105 0.66
184 20 0.13
185 6 0.04
186 12 0.08
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (182 bp):
TATTATGATTAAAATATAAATAATTCTAATAAATTTTTAAAATTAAAATGATATTTTGTATAATA
TATAATTAAAATTTTAAACTATTAGCATTTTTATAATAATATTAATAATTAATAATTTAAATATT
AACATTTTATATATAATTTAATCATTAACATTTGAAAATATTAATATTTATT
Found at i:6180639 original size:19 final size:21
Alignment explanation
Indices: 6180615--6180661 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
6180605 TTTTTTCCTT
6180615 TTTATAA-T-AATATTAATAA
1 TTTATAATTAAATATTAATAA
*
6180634 TTTATAATTTAAATATTAATAT
1 TTTATAA-TTAAATATTAATAA
6180656 TTTATA
1 TTTATA
6180662 TATGATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 7 0.29
21 1 0.04
22 16 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTATAATTAAATATTAATAA
Found at i:6180659 original size:41 final size:42
Alignment explanation
Indices: 6180614--6180712 Score: 123
Period size: 41 Copynumber: 2.4 Consensus size: 42
6180604 CTTTTTTCCT
*
6180614 TTTTATA-ATAATATTAATAATTTATAATTT-AAATATTAATA
1 TTTTATATATAAT-TTAATAATTAATAATTTAAAATATTAATA
* * *
6180655 TTTTATATATGATTTAATCATTAATATTTTAAAATATTAATA
1 TTTTATATATAATTTAATAATTAATAATTTAAAATATTAATA
*
6180697 -TTTATTTATAATTTAA
1 TTTTATATATAATTTAA
6180713 ATGTTGTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
41 35 0.70
42 15 0.30
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (42 bp):
TTTTATATATAATTTAATAATTAATAATTTAAAATATTAATA
Found at i:6180808 original size:23 final size:22
Alignment explanation
Indices: 6180749--6180809 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 22
6180739 ATTTTAATTC
*
6180749 ATTTTT-AAATTTAAAATATTA
1 ATTTTTAAAATTTATAATATTA
* * * *
6180770 TTTTTTATAATATATATTATATA
1 ATTTTTAAAATTTATAATAT-TA
6180793 ATTTTTAAAATTTATAA
1 ATTTTTAAAATTTATAA
6180810 AAAATATTTT
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 5 0.17
22 9 0.31
23 15 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTTAAAATTTATAATATTA
Found at i:6194285 original size:12 final size:12
Alignment explanation
Indices: 6194248--6194285 Score: 51
Period size: 11 Copynumber: 3.1 Consensus size: 12
6194238 AAATAAATCT
6194248 TAAGAGAATAAGTA
1 TAAGAGAA-AA-TA
6194262 TAAGAG-AAATA
1 TAAGAGAAAATA
6194273 TAAGAGAAAATA
1 TAAGAGAAAATA
6194285 T
1 T
6194286 TTAAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.35
12 8 0.35
13 1 0.04
14 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (12 bp):
TAAGAGAAAATA
Found at i:6204325 original size:2 final size:2
Alignment explanation
Indices: 6204318--6204354 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6204308 TTTGTAGTTG
6204318 AT AT 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 AT AT A
6204355 GAGAGAGAGA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6204397 original size:2 final size:2
Alignment explanation
Indices: 6204354--6204381 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6204344 ATATATATAT
6204354 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6204382 CTAATTGGTC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6204813 original size:2 final size:2
Alignment explanation
Indices: 6204806--6204830 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6204796 AATGATTGAC
6204806 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
6204831 GATCATTTAT
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:6215665 original size:79 final size:79
Alignment explanation
Indices: 6215571--6215718 Score: 253
Period size: 79 Copynumber: 1.9 Consensus size: 79
6215561 GTATTTTTTA
* * *
6215571 TAATAGGTTTATTGTATTGGATTTTTCATTCATAAGAATAAATATTTATCTTAATTCGAACTTAT
1 TAATAGGTTTATTGTATTGAATTTTTCATTCATAAGAATAAAGACTTATCTTAATTCGAACTTAT
6215636 CTCACTCAATTGTG
66 CTCACTCAATTGTG
6215650 TAAT-GGTTTGATTGTATTGAATTTTTCATTCATAAGAATAAAGACTTATCTTAATTCGAACTTA
1 TAATAGGTTT-ATTGTATTGAATTTTTCATTCATAAGAATAAAGACTTATCTTAATTCGAACTTA
6215714 TCTCA
65 TCTCA
6215719 ATTCTGATAT
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
78 5 0.08
79 60 0.92
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (79 bp):
TAATAGGTTTATTGTATTGAATTTTTCATTCATAAGAATAAAGACTTATCTTAATTCGAACTTAT
CTCACTCAATTGTG
Found at i:6231077 original size:2 final size:2
Alignment explanation
Indices: 6231070--6231101 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6231060 TGTCAAAGTG
6231070 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6231102 ACACCCTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:6238108 original size:6 final size:6
Alignment explanation
Indices: 6238097--6238140 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
6238087 TTTTGCATAA
* *
6238097 GCTAAT GCTAAT GCTAAT GCTAAT GCTAAT ACTAAT ACTAAT GC
1 GCTAAT GCTAAT GCTAAT GCTAAT GCTAAT GCTAAT GCTAAT GC
6238141 GTTATATATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (6 bp):
GCTAAT
Found at i:6239031 original size:41 final size:40
Alignment explanation
Indices: 6238986--6239064 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
6238976 TTTAATACTG
* * * *
6238986 TTTTTAAAGAAAATTTTAAGATGAAATATTTTGATTTTTAT
1 TTTTTAAACAAAATTTCAA-ACGAAATATTTTAATTTTTAT
* *
6239027 TTTTTAATCATAATTTCAAACGAAATATTTTAATTTTT
1 TTTTTAAACAAAATTTCAAACGAAATATTTTAATTTTT
6239065 GAAATAGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (40 bp):
TTTTTAAACAAAATTTCAAACGAAATATTTTAATTTTTAT
Found at i:6239686 original size:15 final size:18
Alignment explanation
Indices: 6239666--6239707 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
6239656 AATTTATATA
6239666 TTTAAAAAAA-TA-TT-T
1 TTTAAAAAAAGTATTTAT
6239681 TTTAAAATAAAGTATTTAT
1 TTTAAAA-AAAGTATTTAT
6239700 TTTAAAAA
1 TTTAAAAA
6239708 TTATAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.30
16 3 0.13
17 2 0.09
18 3 0.13
19 8 0.35
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TTTAAAAAAAGTATTTAT
Found at i:6253136 original size:20 final size:20
Alignment explanation
Indices: 6253111--6253171 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
6253101 GTAGGGATAA
6253111 ATAATTATATATTGGAGTAC
1 ATAATTATATATTGGAGTAC
6253131 ATAATTA-ATCA-T----TA-
1 ATAATTATAT-ATTGGAGTAC
6253145 ATAATTATATATTGGAGTAC
1 ATAATTATATATTGGAGTAC
6253165 ATAATTA
1 ATAATTA
6253172 ATCATTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 16
0.67 0.00 0.33
Matches are distributed among these distances:
14 8 0.24
15 5 0.15
19 5 0.15
20 15 0.45
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (20 bp):
ATAATTATATATTGGAGTAC
Found at i:6253153 original size:34 final size:34
Alignment explanation
Indices: 6253110--6253177 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
6253100 AGTAGGGATA
6253110 AATAATTATATATTGGAGTACATAATTAATCATT
1 AATAATTATATATTGGAGTACATAATTAATCATT
6253144 AATAATTATATATTGGAGTACATAATTAATCATT
1 AATAATTATATATTGGAGTACATAATTAATCATT
6253178 CTTTCTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (34 bp):
AATAATTATATATTGGAGTACATAATTAATCATT
Found at i:6263931 original size:2 final size:2
Alignment explanation
Indices: 6263924--6263956 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6263914 TTATCTAAAC
6263924 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
6263957 AAGGTCACGG
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:6267646 original size:21 final size:20
Alignment explanation
Indices: 6267603--6267646 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
6267593 CAAATAATAC
* **
6267603 TATCTATTTTTTTTTAATTT
1 TATCTATTGTTTTTTAACAT
6267623 TATCTACTTGTTTTTTAACAT
1 TATCTA-TTGTTTTTTAACAT
6267644 TAT
1 TAT
6267647 TTTTTACAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (20 bp):
TATCTATTGTTTTTTAACAT
Found at i:6273886 original size:7 final size:7
Alignment explanation
Indices: 6273876--6273900 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6273866 AATATTGTTT
6273876 ATTCATA
1 ATTCATA
6273883 ATTCATA
1 ATTCATA
6273890 ATTCATA
1 ATTCATA
6273897 ATTC
1 ATTC
6273901 GTGAAATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTCATA
Found at i:6287252 original size:6 final size:6
Alignment explanation
Indices: 6287241--6287266 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6287231 ATACATATTC
6287241 TCTGCT TCTGCT TCTGCT TCTGCT TC
1 TCTGCT TCTGCT TCTGCT TCTGCT TC
6287267 ATACTTCAAA
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:0.00, C:0.35, G:0.15, T:0.50
Consensus pattern (6 bp):
TCTGCT
Found at i:6287576 original size:32 final size:32
Alignment explanation
Indices: 6287539--6287601 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
6287529 TAATTTCAAT
6287539 TGTTAATATTTTCATTAATTTTTTTAATTAAG
1 TGTTAATATTTTCATTAATTTTTTTAATTAAG
*
6287571 TGTTAATATTTTCTTTAATTTTTTTAATTAA
1 TGTTAATATTTTCATTAATTTTTTTAATTAA
6287602 AGAAAGTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (32 bp):
TGTTAATATTTTCATTAATTTTTTTAATTAAG
Found at i:6290177 original size:12 final size:13
Alignment explanation
Indices: 6290162--6290191 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
6290152 TTTCTCACTT
6290162 TCTTTCTTTT-TC
1 TCTTTCTTTTCTC
6290174 TCTTTCTTTTCTC
1 TCTTTCTTTTCTC
6290187 TCTTT
1 TCTTT
6290192 TCATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TCTTTCTTTTCTC
Found at i:6295711 original size:3 final size:3
Alignment explanation
Indices: 6295703--6295727 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6295693 TTTTCTTTCT
6295703 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
6295728 GGGGAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:6308589 original size:16 final size:16
Alignment explanation
Indices: 6308570--6308604 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6308560 ATTTTCCCTC
* *
6308570 TTTTATTATCTTGTTT
1 TTTTAATATATTGTTT
6308586 TTTTAATATATTGTTT
1 TTTTAATATATTGTTT
6308602 TTT
1 TTT
6308605 CTTAACTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTAATATATTGTTT
Found at i:6321875 original size:24 final size:24
Alignment explanation
Indices: 6321837--6321883 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
6321827 ATTAACACAA
*
6321837 TAAATTTATTTTTAAAAAATTTAAG
1 TAAATTTATTATT-AAAAATTTAAG
*
6321862 TAAA-TTATTATTAATAATTTAA
1 TAAATTTATTATTAAAAATTTAA
6321884 ATTTAAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 7 0.35
25 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TAAATTTATTATTAAAAATTTAAG
Found at i:6326166 original size:26 final size:28
Alignment explanation
Indices: 6326137--6326199 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
6326127 TAGGATCTAT
*
6326137 TTGATTTAAAATAA-AAAAT-ATAAAAC
1 TTGATTTAAAATAATAAAATAATAAAAA
* *
6326163 TTGATTGAATATAATAAAATAATAAAAA
1 TTGATTTAAAATAATAAAATAATAAAAA
*
6326191 TTTATTTAA
1 TTGATTTAA
6326200 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 12 0.40
27 5 0.17
28 13 0.43
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (28 bp):
TTGATTTAAAATAATAAAATAATAAAAA
Found at i:6326211 original size:19 final size:20
Alignment explanation
Indices: 6326187--6326234 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
6326177 TAAAATAATA
6326187 AAAATTTATTTAA-TTTTTT
1 AAAATTTATTTAATTTTTTT
6326206 AAAA-TTATTTAATTTTTTT
1 AAAATTTATTTAATTTTTTT
6326225 AAAATATTAT
1 AAAAT-TTAT
6326235 ATCAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.31
19 14 0.54
21 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AAAATTTATTTAATTTTTTT
Found at i:6352213 original size:2 final size:2
Alignment explanation
Indices: 6352206--6352230 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6352196 CTTGTAATCA
6352206 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6352231 AGTTTTCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6361165 original size:14 final size:15
Alignment explanation
Indices: 6361130--6361170 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
6361120 CGATAAAATC
*
6361130 AGACAACAAGAAAACA
1 AGACAA-AAAAAAACA
6361146 AGACAAAAAAAAACA
1 AGACAAAAAAAAACA
6361161 A-ACAAAAAAA
1 AGACAAAAAAA
6361171 CAGAAGCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 9 0.38
15 9 0.38
16 6 0.25
ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00
Consensus pattern (15 bp):
AGACAAAAAAAAACA
Found at i:6363852 original size:32 final size:30
Alignment explanation
Indices: 6363794--6363852 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
6363784 TTATTTTTTT
* *
6363794 AAAAAATAAAATTTAATTTTTTTAATTATA
1 AAAAAATAAAATTTAATTATTATAATTATA
6363824 AAAAAATAAAATTTATAATTATTATAATT
1 AAAAAATAAAA-TT-TAATTATTATAATT
6363853 CAAATTCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.44
31 2 0.08
32 12 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAAAATAAAATTTAATTATTATAATTATA
Done.