Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397266.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_20.0, 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: 7441454
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 92215 characters in sequence are not A, C, G, or T
File 9 of 18
Found at i:3594623 original size:30 final size:28
Alignment explanation
Indices: 3594587--3594662 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 28
3594577 AATCATCAAT
3594587 TATAAAAATATATTTAACT-TAAAATAAAAA
1 TATAAAAATATATTTAA-TGT--AATAAAAA
* *
3594617 TATAAAAATTTAAATTAATGTAATAAAAA
1 TATAAAAATAT-ATTTAATGTAATAAAAA
3594646 TATAAAAA-ATTATTTAA
1 TATAAAAATA-TATTTAA
3594663 ATTTTTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 5 0.13
29 17 0.44
30 11 0.28
31 6 0.15
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (28 bp):
TATAAAAATATATTTAATGTAATAAAAA
Found at i:3603659 original size:6 final size:7
Alignment explanation
Indices: 3603626--3603827 Score: 81
Period size: 6 Copynumber: 29.0 Consensus size: 7
3603616 TAAAATATAA
*
3603626 ATTTAAT
1 ATTTTAT
3603633 ATATTTAT
1 AT-TTTAT
3603641 ATTTTAT
1 ATTTTAT
3603648 ATTTT-T
1 ATTTTAT
3603654 AATTTTTAT
1 -A-TTTTAT
* *
3603663 AATATCAT
1 -ATTTTAT
*
3603671 CTTTTAT
1 ATTTTAT
*
3603678 A-TATAT
1 ATTTTAT
3603684 -TTTTA-
1 ATTTTAT
3603689 ATGTTATAT
1 AT-TT-TAT
3603698 ATTTTAT
1 ATTTTAT
3603705 -TTTTAT
1 ATTTTAT
3603711 -TTTT-T
1 ATTTTAT
*
3603716 ATTATA-
1 ATTTTAT
3603722 ATTTTAT
1 ATTTTAT
3603729 ATATTT-T
1 AT-TTTAT
3603736 ATTTTA-
1 ATTTTAT
*
3603742 ATTTTTTT
1 A-TTTTAT
* *
3603750 AATATAATT
1 -ATTTTA-T
3603759 ATTTT-T
1 ATTTTAT
3603765 ATTTTAT
1 ATTTTAT
3603772 ATTTTA-
1 ATTTTAT
3603778 ATTTTA-
1 ATTTTAT
*
3603784 ATTTTTT
1 ATTTTAT
3603791 A-TTTAT
1 ATTTTAT
*
3603797 ATTATATAA
1 ATT-T-TAT
3603806 ATTTTAAT
1 ATTTT-AT
*
3603814 TTTTTAT
1 ATTTTAT
3603821 ATTTTAT
1 ATTTTAT
3603828 TTTAATTTTT
Statistics
Matches: 148, Mismatches: 23, Indels: 48
0.68 0.11 0.22
Matches are distributed among these distances:
5 1 0.01
6 53 0.36
7 49 0.33
8 33 0.22
9 12 0.08
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (7 bp):
ATTTTAT
Found at i:3603707 original size:20 final size:19
Alignment explanation
Indices: 3603697--3603787 Score: 60
Period size: 20 Copynumber: 4.6 Consensus size: 19
3603687 TAATGTTATA
* *
3603697 TATTTT-ATTTTTATTTTT
1 TATTTTAATTTATATATTT
*
3603715 TATTATAATTTTATATATTT
1 TATTTTAA-TTTATATATTT
* *
3603735 TATTTTAATTTTTTTAATATAAT
1 TATTTTAA--TTTAT-ATAT-TT
*
3603758 TATTTTTATTT-TATATTT
1 TATTTTAATTTATATATTT
3603776 TAATTTTAATTT
1 T-ATTTTAATTT
3603788 TTTATTTATA
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
18 7 0.12
19 14 0.24
20 17 0.29
21 8 0.14
22 4 0.07
23 8 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTTAATTTATATATTT
Found at i:3603731 original size:10 final size:9
Alignment explanation
Indices: 3603638--3603737 Score: 53
Period size: 7 Copynumber: 12.1 Consensus size: 9
3603628 TTAATATATT
3603638 TATATTTTA
1 TATATTTTA
3603647 TAT-TTTTA
1 TATATTTTA
3603655 -AT-TTTTA
1 TATATTTTA
* *
3603662 TA-ATATCA
1 TATATTTTA
*
3603670 TCT-TTTATA
1 TATATTT-TA
3603679 TATATTTT-
1 TATATTTTA
*
3603687 TA-ATGTTA
1 TATATTTTA
3603695 TATA-TTT-
1 TATATTTTA
3603702 TAT-TTTTA
1 TATATTTTA
3603710 T-T-TTTTA
1 TATATTTTA
3603717 TTATAATTTTA
1 -TAT-ATTTTA
3603728 TATATTTTA
1 TATATTTTA
3603737 T
1 T
3603738 TTTAATTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 26
0.67 0.08 0.25
Matches are distributed among these distances:
7 23 0.33
8 20 0.29
9 16 0.23
10 6 0.09
11 5 0.07
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (9 bp):
TATATTTTA
Found at i:3603748 original size:61 final size:62
Alignment explanation
Indices: 3603674--3603837 Score: 153
Period size: 62 Copynumber: 2.7 Consensus size: 62
3603664 ATATCATCTT
* *
3603674 TTATAT-ATATTTTTAATGTTATATATTTTATTTTTATTTTTTATTATAATTTTATATATTT-TA
1 TTATATAAT-TTTTTAATATTATATATTTTATTTTTATTTTTAATTATAATTTT-T-TATTTATA
* *
3603737 TT-T-TAATTTTTTTAATATAAT-TATTTT-TATTTTATATTTTAATTTTAATTTTTTATTTATA
1 TTATATAA-TTTTTTAATATTATATATTTTAT-TTTTAT-TTTTAATTATAATTTTTTATTTATA
* * * *
3603798 TTATATAA-ATTTTAATTTTTTATATTTTATTTTAATTTTT
1 TTATATAATTTTTTAATATTATATATTTTATTTTTATTTTT
3603838 GATGCTTATA
Statistics
Matches: 83, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
60 6 0.07
61 31 0.37
62 39 0.47
63 7 0.08
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.70
Consensus pattern (62 bp):
TTATATAATTTTTTAATATTATATATTTTATTTTTATTTTTAATTATAATTTTTTATTTATA
Found at i:3603756 original size:34 final size:34
Alignment explanation
Indices: 3603687--3603782 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 34
3603677 TATATATTTT
* * *
3603687 TAATGTTATATATTTTATTTTTA-TTTTTTATTA
1 TAATTTTATATATTTTATTTTAATTTTTTTAATA
3603720 TAATTTTATATATTTTATTTTAATTTTTTTAATA
1 TAATTTTATATATTTTATTTTAATTTTTTTAATA
*
3603754 TAATTATT-TTTATTTTATATTTTAATTTT
1 TAATT-TTATATA-TTT-TATTTTAATTTT
3603783 AATTTTTTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
33 21 0.38
34 17 0.31
35 5 0.09
36 12 0.22
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (34 bp):
TAATTTTATATATTTTATTTTAATTTTTTTAATA
Found at i:3603764 original size:49 final size:47
Alignment explanation
Indices: 3603699--3603837 Score: 123
Period size: 42 Copynumber: 3.0 Consensus size: 47
3603689 ATGTTATATA
* *
3603699 TTTTATTTTTATT-TTTTATTATAATTTTATATATTTTATTTTAATTT
1 TTTTATATATATTATTTTATT-TAATTTTATATATTTTATTTTAATTT
*
3603746 TTTTA-ATATA--ATTATT-TTT-ATTTTATAT-TTTAATTTTAA-TT
1 TTTTATATATATTATT-TTATTTAATTTTATATATTTTATTTTAATTT
* ** *
3603787 TTTTATTTATATTATATAAATTTTAATTTTTTATATTTTATTTTAATTT
1 TTTTATATATATTAT-TTTA-TTTAATTTTATATATTTTATTTTAATTT
3603836 TT
1 TT
3603838 GATGCTTATA
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
41 7 0.10
42 14 0.19
43 9 0.12
44 3 0.04
45 5 0.07
46 8 0.11
47 13 0.18
48 10 0.14
49 4 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (47 bp):
TTTTATATATATTATTTTATTTAATTTTATATATTTTATTTTAATTT
Found at i:3603773 original size:41 final size:46
Alignment explanation
Indices: 3603728--3603837 Score: 131
Period size: 49 Copynumber: 2.4 Consensus size: 46
3603718 TATAATTTTA
*
3603728 TATATTTTATTTTAATTTTT-TTAATA-TA-AT-TATTTT-TATTT
1 TATATTTTATTTTAATTTTTATTAATATTATATAAATTTTATATTT
* *
3603769 TATATTTTAATTTTAATTTTTTATTTATATTATATAAATTTTAATTTTT
1 TATATTTT-ATTTTAA-TTTTTATTAATATTATATAAATTTT-ATATTT
3603818 TATATTTTATTTTAATTTTT
1 TATATTTTATTTTAATTTTT
3603838 GATGCTTATA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
41 8 0.14
42 7 0.12
43 5 0.09
44 5 0.09
45 2 0.03
46 2 0.03
47 10 0.17
48 7 0.12
49 12 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (46 bp):
TATATTTTATTTTAATTTTTATTAATATTATATAAATTTTATATTT
Found at i:3603814 original size:56 final size:55
Alignment explanation
Indices: 3603701--3603836 Score: 145
Period size: 56 Copynumber: 2.5 Consensus size: 55
3603691 GTTATATATT
* * * *
3603701 TTATTTTTATTTTTTATTATAATTTTATATATTTTATTTTAATTTTTTTAATATAA
1 TTATTTTTA-TTTTTATTTTAATTTTATATATTTTATTTTAATTATATAAATATAA
* *
3603757 TTATTTTTATTTTATATTTTAATTTTA-ATTTTTTA-TTTATATTATATAAATTTTAA
1 TTATTTTTATTTT-TATTTTAATTTTATATATTTTATTTTA-ATTATATAAA-TATAA
3603813 -T-TTTTTATATTTTATTTTAATTTT
1 TTATTTTTAT-TTTTATTTTAATTTT
3603837 TGATGCTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
54 23 0.33
55 22 0.31
56 25 0.36
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (55 bp):
TTATTTTTATTTTTATTTTAATTTTATATATTTTATTTTAATTATATAAATATAA
Found at i:3603822 original size:90 final size:89
Alignment explanation
Indices: 3603604--3603837 Score: 235
Period size: 90 Copynumber: 2.6 Consensus size: 89
3603594 TTTTTTAAAT
** *
3603604 TTTTTTATTTATTAAAATATAAA-TTTAATATATTTATATTTTATATTTTTAATTTTTATAATAT
1 TTTTTTATTTA-TATTATATAAATTTTAAT-TTTTTATA-TTT-TA-TTTTAATTTTTATAATAT
*
3603668 CATCTTTTATATATATTTTTAATGTTATA
61 AATCTTTTATATATATTTTTAATGTTATA
* * ** * * *
3603697 TATTTTATTTTTATT-T-TTTATTATAATTTTATATATTTTATTTTAATTTTTTTAATATAAT-T
1 TTTTTTATTTATATTATATAAATTTTAATTTTTTATATTTTATTTTAATTTTTATAATATAATCT
* * *
3603759 ATTTTTATTTTATATTTTAATTTTA-A
66 -TTTATA-TATAT-TTTTAATGTTATA
3603785 TTTTTTATTTATATTATATAAATTTTAATTTTTTATATTTTATTTTAATTTTT
1 TTTTTTATTTATATTATATAAATTTTAATTTTTTATATTTTATTTTAATTTTT
3603838 GATGCTTATA
Statistics
Matches: 115, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
86 1 0.01
87 24 0.21
88 20 0.17
89 14 0.12
90 39 0.34
91 6 0.05
92 2 0.02
93 9 0.08
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (89 bp):
TTTTTTATTTATATTATATAAATTTTAATTTTTTATATTTTATTTTAATTTTTATAATATAATCT
TTTATATATATTTTTAATGTTATA
Found at i:3603858 original size:48 final size:48
Alignment explanation
Indices: 3603766--3603858 Score: 136
Period size: 48 Copynumber: 1.9 Consensus size: 48
3603756 ATTATTTTTA
*
3603766 TTTTATATTTTAATTTTAATTTTTTATTTATATTATATAAATTTTAATT
1 TTTTATATTTTAATTTTAATTTTTGATTTATATTATAT-AATTTTAATT
3603815 TTTTATATTTT-ATTTTAATTTTTGATGCTTATATTATAT-ATTTT
1 TTTTATATTTTAATTTTAATTTTTGAT--TTATATTATATAATTTT
3603859 CTTTCAATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
48 19 0.46
49 11 0.27
50 11 0.27
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.68
Consensus pattern (48 bp):
TTTTATATTTTAATTTTAATTTTTGATTTATATTATATAATTTTAATT
Found at i:3608130 original size:30 final size:29
Alignment explanation
Indices: 3608096--3608172 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
3608086 AATCATTAAT
*
3608096 TATAAAAACTTATTTAGATCAAAATAAAAA
1 TATAAAAACTTATTTA-AACAAAATAAAAA
* *
3608126 TATAAATACTT-TATTAAACATAATAAAAA
1 TATAAAAACTTAT-TTAAACAAAATAAAAA
* *
3608155 AATAAAAATTTATTTAAA
1 TATAAAAACTTATTTAAA
3608173 TTTTATTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 25 0.64
30 14 0.36
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (29 bp):
TATAAAAACTTATTTAAACAAAATAAAAA
Found at i:3615011 original size:34 final size:33
Alignment explanation
Indices: 3614947--3615012 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
3614937 AAGAGAGAGA
* *
3614947 AAATATTAAAGTGAACAAGTTAATTGAAGATAG
1 AAATATTAAAGTGAAAAAGGTAATTGAAGATAG
3614980 AAATATTAAAGTGACAAAAGGTAATCT-AAGATA
1 AAATATTAAAGTGA-AAAAGGTAAT-TGAAGATA
3615013 TTGTAACAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 14 0.48
34 14 0.48
35 1 0.03
ACGTcount: A:0.53, C:0.05, G:0.17, T:0.26
Consensus pattern (33 bp):
AAATATTAAAGTGAAAAAGGTAATTGAAGATAG
Found at i:3630178 original size:121 final size:123
Alignment explanation
Indices: 3630007--3630247 Score: 362
Period size: 121 Copynumber: 2.0 Consensus size: 123
3629997 GCCCATTCTT
*
3630007 GTCTTATCTCTGTGGCATGCTGGCCTTGTGCATGTTATGATCTAGGATTTCTCTCCAGAAATGAG
1 GTCTTATCTCTGTGGCATACTGGCCTTGTGCATGTTATGATCTAGGATTTCTCTCCAGAAATGAG
* * *
3630072 GAGCCTTATTTCAA-TTGCTGACTTCATTAGTGACCTCAGATTTCTGGTTCTGATGTC
66 GAGCCTTATTTCAATTTGCTGACTTCACTAGGGACATCAGATTTCTGGTTCTGATGTC
* * *
3630129 GTCTTATCTCTGT-GCATACTGGTCC-TGTGCATGTTATGATCTATGATTTCTCTCCGGGAATGA
1 GTCTTATCTCTGTGGCATACTGG-CCTTGTGCATGTTATGATCTAGGATTTCTCTCCAGAAATGA
* * *
3630192 GGAGCTTTGTTTCAATTTGCTTACTTCACTAGGGACATCAGATTTCTGGTTCTGAT
65 GGAGCCTTATTTCAATTTGCTGACTTCACTAGGGACATCAGATTTCTGGTTCTGAT
3630248 TCCAAGTTCA
Statistics
Matches: 107, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
121 56 0.52
122 51 0.48
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (123 bp):
GTCTTATCTCTGTGGCATACTGGCCTTGTGCATGTTATGATCTAGGATTTCTCTCCAGAAATGAG
GAGCCTTATTTCAATTTGCTGACTTCACTAGGGACATCAGATTTCTGGTTCTGATGTC
Found at i:3634345 original size:18 final size:18
Alignment explanation
Indices: 3634318--3634353 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3634308 TTTAGATAGG
*
3634318 TAATTAAAAATGATTAAT
1 TAATTAAAAATGAATAAT
*
3634336 TAATTCAAAATGAATAAT
1 TAATTAAAAATGAATAAT
3634354 GGGTGTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.36
Consensus pattern (18 bp):
TAATTAAAAATGAATAAT
Found at i:3642350 original size:28 final size:28
Alignment explanation
Indices: 3642319--3642375 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
3642309 AAAAGTTATG
*
3642319 CACAGGATGTTAATTGAGAAAAAAGATA
1 CACAGGATGCTAATTGAGAAAAAAGATA
* * *
3642347 CACAGGGTGCTAATTGGGAAAAATGATA
1 CACAGGATGCTAATTGAGAAAAAAGATA
3642375 C
1 C
3642376 CTAGAAGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.21
Consensus pattern (28 bp):
CACAGGATGCTAATTGAGAAAAAAGATA
Found at i:3647279 original size:31 final size:29
Alignment explanation
Indices: 3647241--3647302 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 29
3647231 AATATCCAAA
* *
3647241 TAGTCCATGTATTCATACATTTTCATCAATT
1 TAGTCCATATATTCA-A-AATTTCATCAATT
*
3647272 TAGTCCATATATTCAAAATTTGATCAATT
1 TAGTCCATATATTCAAAATTTCATCAATT
3647301 TA
1 TA
3647303 AGTTTTCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 13 0.46
30 1 0.04
31 14 0.50
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (29 bp):
TAGTCCATATATTCAAAATTTCATCAATT
Found at i:3657478 original size:25 final size:26
Alignment explanation
Indices: 3657430--3657480 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3657420 ATACAAAAAA
*
3657430 ATTTAAATAAATTTTTATTTTTTTAT
1 ATTTAAATAAATTTTTATTATTTTAT
* *
3657456 ATTTAATTAAGTTTTTA-TATTTTAT
1 ATTTAAATAAATTTTTATTATTTTAT
3657481 TTTGAGTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
ATTTAAATAAATTTTTATTATTTTAT
Found at i:3657640 original size:33 final size:33
Alignment explanation
Indices: 3657579--3657658 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
3657569 ATGCGAAATT
* * *
3657579 AACATTTTATGTTATCATTAATTTTAATATATC
1 AACATATTATATTATCATTAATTATAATATATC
* * * *
3657612 AACATATTATATTATTATTGATTATAATATGTT
1 AACATATTATATTATCATTAATTATAATATATC
*
3657645 AACATATCATATTA
1 AACATATTATATTA
3657659 ATAGTAGACG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (33 bp):
AACATATTATATTATCATTAATTATAATATATC
Found at i:3657810 original size:30 final size:30
Alignment explanation
Indices: 3657776--3657872 Score: 99
Period size: 30 Copynumber: 3.3 Consensus size: 30
3657766 GTTATAAGGG
*
3657776 TTTATTTGGCTCTAAATAAAAATATAAGAT
1 TTTATTTGGCTCAAAATAAAAATATAAGAT
* *
3657806 TTTATTTGACTCAAAATAAAAGTATAAAGAT
1 TTTATTTGGCTCAAAATAAAAATAT-AAGAT
* ** **
3657837 TTAATTAAG-T-AAAATAAAAATATAAGGG
1 TTTATTTGGCTCAAAATAAAAATATAAGAT
3657865 TTTATTTG
1 TTTATTTG
3657873 ATTTTTTCTA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
28 8 0.15
29 12 0.23
30 23 0.43
31 10 0.19
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.38
Consensus pattern (30 bp):
TTTATTTGGCTCAAAATAAAAATATAAGAT
Found at i:3662283 original size:14 final size:14
Alignment explanation
Indices: 3662248--3662293 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
3662238 TATATTTGTT
3662248 TATTTTATTTTTAA
1 TATTTTATTTTTAA
* *
3662262 AATATTATTTTTAA
1 TATTTTATTTTTAA
* *
3662276 TTTTTTATTATTAA
1 TATTTTATTTTTAA
3662290 TATT
1 TATT
3662294 AATAAGATTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTATTTTTAA
Found at i:3665497 original size:16 final size:16
Alignment explanation
Indices: 3665476--3665510 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3665466 CCCCATACAT
3665476 ATAATTTACATACTCA
1 ATAATTTACATACTCA
*
3665492 ATAATTTACATACTGA
1 ATAATTTACATACTCA
3665508 ATA
1 ATA
3665511 TTCATTAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (16 bp):
ATAATTTACATACTCA
Found at i:3681269 original size:30 final size:30
Alignment explanation
Indices: 3681229--3681287 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
3681219 CTCTTACCAC
3681229 CTCCCCGCTTGATTCAATGATGGAATTTAA
1 CTCCCCGCTTGATTCAATGATGGAATTTAA
*
3681259 CTCCCGGCTTGATTCAATGATGGAATTTA
1 CTCCCCGCTTGATTCAATGATGGAATTTA
3681288 TCTAATTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (30 bp):
CTCCCCGCTTGATTCAATGATGGAATTTAA
Found at i:3698064 original size:48 final size:50
Alignment explanation
Indices: 3697980--3698119 Score: 160
Period size: 54 Copynumber: 2.8 Consensus size: 50
3697970 AGGTAGAGGC
* *
3697980 AATGTTGGTGTTGATGTTAGTAGTTC-ATATATTGGTAG-AGA-CAAAGGG
1 AATGTTGGTGTTGATGCTAGTAGTTCAAT-TAGTGGTAGTAGAGCAAAGGG
* *
3698028 ATTGTTGGTGTTGATGCTAGTAGTTCAATTAGTGGTAAAGGTAGAGGCAGAGGG
1 AATGTTGGTGTTGATGCTAGTAGTTCAATTAGTGGT--A-GTAGA-GCAAAGGG
* *
3698082 AATATTGGTGTTGGTGCTAGTAGTTCAATTAGTGGTAG
1 AATGTTGGTGTTGATGCTAGTAGTTCAATTAGTGGTAG
3698120 GGGTAGAAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
48 30 0.38
49 2 0.03
50 1 0.01
51 2 0.03
52 4 0.05
54 39 0.50
ACGTcount: A:0.26, C:0.05, G:0.34, T:0.35
Consensus pattern (50 bp):
AATGTTGGTGTTGATGCTAGTAGTTCAATTAGTGGTAGTAGAGCAAAGGG
Found at i:3698126 original size:54 final size:54
Alignment explanation
Indices: 3698013--3698118 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 54
3698003 TTCATATATT
* *
3698013 GGTAGAGACAAAGGGATTGTTGGTGTTGATGCTAGTAGTTCAATTAGTGGTAAA
1 GGTAGAGACAAAGGGAATATTGGTGTTGATGCTAGTAGTTCAATTAGTGGTAAA
* * *
3698067 GGTAGAGGCAGAGGGAATATTGGTGTTGGTGCTAGTAGTTCAATTAGTGGTA
1 GGTAGAGACAAAGGGAATATTGGTGTTGATGCTAGTAGTTCAATTAGTGGTA
3698119 GGGGTAGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.31
Consensus pattern (54 bp):
GGTAGAGACAAAGGGAATATTGGTGTTGATGCTAGTAGTTCAATTAGTGGTAAA
Found at i:3718371 original size:21 final size:21
Alignment explanation
Indices: 3718346--3718407 Score: 124
Period size: 21 Copynumber: 3.0 Consensus size: 21
3718336 TTGAATGTTG
3718346 GTGGTATCATGGCAGTGAATT
1 GTGGTATCATGGCAGTGAATT
3718367 GTGGTATCATGGCAGTGAATT
1 GTGGTATCATGGCAGTGAATT
3718388 GTGGTATCATGGCAGTGAAT
1 GTGGTATCATGGCAGTGAAT
3718408 ATGGTCTTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.24, C:0.10, G:0.34, T:0.32
Consensus pattern (21 bp):
GTGGTATCATGGCAGTGAATT
Found at i:3733559 original size:16 final size:16
Alignment explanation
Indices: 3733540--3733587 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 16
3733530 TATTTTTTAT
3733540 TATTAATTTTATATAA
1 TATTAATTTTATATAA
3733556 TATT-ATTTT-TA-AA
1 TATTAATTTTATATAA
*
3733569 TA-TATTTTTAATATAA
1 TATTAATTTT-ATATAA
3733585 TAT
1 TAT
3733588 ATTTTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 9
0.72 0.03 0.25
Matches are distributed among these distances:
12 1 0.04
13 8 0.31
14 2 0.08
15 7 0.27
16 8 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTAATTTTATATAA
Found at i:3733561 original size:29 final size:28
Alignment explanation
Indices: 3733529--3733636 Score: 94
Period size: 29 Copynumber: 3.7 Consensus size: 28
3733519 ATCATTATTT
3733529 TTATTTTTTATTATTAATTTTATATAATA
1 TTATTTTTTATTA-TAATTTTATATAATA
* * *
3733558 TTATTTTTAAATATATTTTTAATATAATA
1 TTATTTTTTATTATAATTTT-ATATAATA
* * *
3733587 -TATTTTATTTTTAT-TTTTTATTATAATT
1 TTATTTT-TTATTATAATTTTA-TATAATA
3733615 TTATATATTTTATTATAATTTT
1 TTAT-T-TTTTATTATAATTTT
3733637 TCCTTTTTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
27 1 0.02
28 23 0.37
29 26 0.41
30 7 0.11
31 6 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TTATTTTTTATTATAATTTTATATAATA
Found at i:3733565 original size:28 final size:28
Alignment explanation
Indices: 3733533--3733636 Score: 72
Period size: 28 Copynumber: 3.6 Consensus size: 28
3733523 TTATTTTTAT
3733533 TTTTTATTATTAATTTTATATAATATTA
1 TTTTTATTATTAATTTTATATAATATTA
* *
3733561 TTTTTA-AATATATTTTTAATATAATA-TA
1 TTTTTATTAT-TAATTTT-ATATAATATTA
* * *
3733589 -TTTTATTTTTATTTTTTATTATAATTTTATA
1 TTTTTATTATTA-ATTTTA-TATAA-TAT-TA
3733620 TATTTTATTA-TAATTTT
1 T-TTTTATTATTAATTTT
3733637 TCCTTTTTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
27 10 0.17
28 25 0.42
29 9 0.15
31 6 0.10
32 2 0.03
33 7 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTTATTATTAATTTTATATAATATTA
Found at i:3733601 original size:27 final size:29
Alignment explanation
Indices: 3733533--3733618 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 29
3733523 TTATTTTTAT
* *
3733533 TTTTTATTATTAATTTT-ATATAATATTA
1 TTTTTATTTTTATTTTTAATATAATATTA
** *
3733561 TTTTTAAATATATTTTTAATATAATA-TA
1 TTTTTATTTTTATTTTTAATATAATATTA
* *
3733589 -TTTTATTTTTATTTTTTATTATAATTTTA
1 TTTTTATTTTTA-TTTTTAATATAATATTA
3733618 T
1 T
3733619 ATATTTTATT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
27 8 0.18
28 26 0.59
29 10 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTTATTTTTATTTTTAATATAATATTA
Found at i:3733621 original size:10 final size:11
Alignment explanation
Indices: 3733602--3733636 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3733592 TATTTTTATT
3733602 TTTTATTATAA
1 TTTTATTATAA
3733613 TTTTA-TAT-A
1 TTTTATTATAA
3733622 TTTTATTATAA
1 TTTTATTATAA
3733633 TTTT
1 TTTT
3733637 TCCTTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 6 0.27
10 6 0.27
11 10 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTATTATAA
Found at i:3733621 original size:33 final size:33
Alignment explanation
Indices: 3733523--3733637 Score: 117
Period size: 33 Copynumber: 3.4 Consensus size: 33
3733513 GTAATCATCA
*
3733523 TTATTTTTATTTTTTATTATTAATTTTATATAATA
1 TTATTTTTATTTTTTATTA-TAATTTTATAT-ATT
* * * *
3733558 TTATTTTTAAATATATT-TT-TAATATAATATATT
1 TTATTTTT--ATTTTTTATTATAATTTTATATATT
3733591 TTATTTTTATTTTTTATTATAATTTTATATATT
1 TTATTTTTATTTTTTATTATAATTTTATATATT
* *
3733624 TTATTATAATTTTT
1 TTATTTTTATTTTT
3733638 CCTTTTTAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
31 5 0.08
32 2 0.03
33 34 0.52
34 9 0.14
35 8 0.12
36 2 0.03
37 5 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (33 bp):
TTATTTTTATTTTTTATTATAATTTTATATATT
Found at i:3733627 original size:20 final size:19
Alignment explanation
Indices: 3733593--3733637 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
3733583 AATATATTTT
*
3733593 ATTTTTATTTTTTATTATA
1 ATTTTTATATTTTATTATA
3733612 ATTTTATATATTTTATTATA
1 ATTTT-TATATTTTATTATA
3733632 ATTTTT
1 ATTTTT
3733638 CCTTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTTATATTTTATTATA
Found at i:3733787 original size:36 final size:37
Alignment explanation
Indices: 3733720--3733794 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 37
3733710 AAATCTATAT
* *
3733720 AAAAAATCAAATTATAATATTATAAATTATTTTTAAC
1 AAAAAATAAAATTATAATAGTATAAATTATTTTTAAC
3733757 AAAATAATAAAATTATAA-AGTA-AAATTATTTTTAAC
1 AAAA-AATAAAATTATAATAGTATAAATTATTTTTAAC
3733793 AA
1 AA
3733795 CATTGTGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
36 16 0.46
37 7 0.20
38 12 0.34
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (37 bp):
AAAAAATAAAATTATAATAGTATAAATTATTTTTAAC
Found at i:3737566 original size:73 final size:74
Alignment explanation
Indices: 3737489--3737629 Score: 203
Period size: 74 Copynumber: 1.9 Consensus size: 74
3737479 ATAAATAGAA
* * * * * *
3737489 TAAATCTTACTAATTATTATAAT-AAAAATATTTTAATAATTATTATTTGATGAATACATGTTTA
1 TAAATCTCACTAATAATTAAAATAAAAAATATTTCAATAATTATTATTTAATAAATACATGTTTA
3737553 TAATTGGTT
66 TAATTGGTT
* *
3737562 TAAATCTCACTAATAATTAAAATAAAAAATATTTCAATAGTTGTTATTTAATAAATACATGTTTA
1 TAAATCTCACTAATAATTAAAATAAAAAATATTTCAATAATTATTATTTAATAAATACATGTTTA
3737627 TAA
66 TAA
3737630 GTATAGGTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
73 20 0.34
74 39 0.66
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.44
Consensus pattern (74 bp):
TAAATCTCACTAATAATTAAAATAAAAAATATTTCAATAATTATTATTTAATAAATACATGTTTA
TAATTGGTT
Found at i:3748824 original size:14 final size:14
Alignment explanation
Indices: 3748797--3748843 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
3748787 TTTCAATTAT
* *
3748797 ACACACACACACAC
1 ACACATACATACAC
3748811 ACACATACATACAC
1 ACACATACATACAC
* *
3748825 ACACATTCATACAT
1 ACACATACATACAC
3748839 ACACA
1 ACACA
3748844 CATATACCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.49, C:0.38, G:0.00, T:0.13
Consensus pattern (14 bp):
ACACATACATACAC
Found at i:3748826 original size:18 final size:18
Alignment explanation
Indices: 3748803--3748845 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3748793 TTATACACAC
3748803 ACACACACACACATACAT
1 ACACACACACACATACAT
**
3748821 ACACACACATTCATACAT
1 ACACACACACACATACAT
3748839 ACACACA
1 ACACACA
3748846 TATACCCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.37, G:0.00, T:0.14
Consensus pattern (18 bp):
ACACACACACACATACAT
Found at i:3751741 original size:21 final size:21
Alignment explanation
Indices: 3751717--3751757 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3751707 TTAAATTAGT
*
3751717 TCAAAAATCATTTAAACAAAA
1 TCAAAAATCATTCAAACAAAA
**
3751738 TCAAATCTCATTCAAACAAA
1 TCAAAAATCATTCAAACAAA
3751758 TTTAGAACTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (21 bp):
TCAAAAATCATTCAAACAAAA
Found at i:3755516 original size:13 final size:13
Alignment explanation
Indices: 3755498--3755531 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3755488 AGTTAGACTC
3755498 GATAATGAGTGAA
1 GATAATGAGTGAA
**
3755511 GATAATTCGTGAA
1 GATAATGAGTGAA
3755524 GATAATGA
1 GATAATGA
3755532 CTGATTTCTA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.26, T:0.26
Consensus pattern (13 bp):
GATAATGAGTGAA
Found at i:3756519 original size:42 final size:42
Alignment explanation
Indices: 3756418--3756539 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 42
3756408 GCCATAATGT
* * * * * *
3756418 TTCTTCTCTTAGAGGTGTTTTGAATACTATTCATAATATTTC
1 TTCTTCTCCTAGAGGTGTTCTAAATACAACTCGTAATATTTC
* ** * * *
3756460 TTCTTCTTCGGGTGGTGTTCCAAATACAACTCGTAATGTTTC
1 TTCTTCTCCTAGAGGTGTTCTAAATACAACTCGTAATATTTC
*
3756502 TTCTTCTCCTAGAGGTGTTCTAAATACAACTCGCAATA
1 TTCTTCTCCTAGAGGTGTTCTAAATACAACTCGTAATA
3756540 CTTTTTTTTT
Statistics
Matches: 61, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.42
Consensus pattern (42 bp):
TTCTTCTCCTAGAGGTGTTCTAAATACAACTCGTAATATTTC
Found at i:3758799 original size:29 final size:29
Alignment explanation
Indices: 3758757--3758813 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
3758747 AGATATCCAA
* *
3758757 TATATCTTGCTTAGGTATTGTGAATATTG
1 TATATCTTGCTTAGCTACTGTGAATATTG
* * *
3758786 TATATTTTGTTTAGCTACTGTGGATATT
1 TATATCTTGCTTAGCTACTGTGAATATT
3758814 ATAAATATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.23, C:0.07, G:0.19, T:0.51
Consensus pattern (29 bp):
TATATCTTGCTTAGCTACTGTGAATATTG
Found at i:3768242 original size:75 final size:75
Alignment explanation
Indices: 3768151--3768297 Score: 242
Period size: 75 Copynumber: 2.0 Consensus size: 75
3768141 AGAGGGGCAA
3768151 AATTGTTGGAACAGGTAATAGATTTATGAACAATATTAGCAATTGGTTGTTCATGAGT-GCTTTT
1 AATTGTTGGAACAGGTAATAGATTTATGAACAATATTAGCAATTGGTTGTTCATGAGTGGC-TTT
3768215 AAGAAGAACAG
65 AAGAAGAACAG
* * * *
3768226 AATTGTTGGAAGAGGTAGTAGATTTATGAATAATGTTAGCAATTGGTTGTTCATGAGTGGCTTTA
1 AATTGTTGGAACAGGTAATAGATTTATGAACAATATTAGCAATTGGTTGTTCATGAGTGGCTTTA
3768291 AGAAGAA
66 AGAAGAA
3768298 TTTCATGAGC
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
75 65 0.97
76 2 0.03
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.34
Consensus pattern (75 bp):
AATTGTTGGAACAGGTAATAGATTTATGAACAATATTAGCAATTGGTTGTTCATGAGTGGCTTTA
AGAAGAACAG
Found at i:3783408 original size:39 final size:36
Alignment explanation
Indices: 3783357--3783472 Score: 121
Period size: 39 Copynumber: 3.1 Consensus size: 36
3783347 AATCTTTTCA
3783357 AAAAATTAAAATAAAATATATAATATATAAAATTATATT
1 AAAAA-TAAAATAAAATATATAATAT-TAAAA-TATATT
* *
3783396 AAGAAATAAAATAAAATATATAAGATTATAATA-A--
1 AA-AAATAAAATAAAATATATAATATTAAAATATATT
*
3783430 AAAAATAAAAATAAAATATATGATATTAAAAATATATT
1 AAAAAT-AAAATAAAATATATAATATT-AAAATATATT
*
3783468 TAAAA
1 AAAAA
3783473 GATGATATTA
Statistics
Matches: 65, Mismatches: 6, Indels: 13
0.77 0.07 0.15
Matches are distributed among these distances:
33 4 0.06
34 20 0.31
35 5 0.08
36 2 0.03
37 2 0.03
38 8 0.12
39 21 0.32
40 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (36 bp):
AAAAATAAAATAAAATATATAATATTAAAATATATT
Found at i:3783414 original size:32 final size:33
Alignment explanation
Indices: 3783364--3783450 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 33
3783354 TCAAAAAATT
*
3783364 AAAATAAAATATATAATATATAAAATTAT-ATTAA
1 AAAATAAAATA-A-AATATATAAAATTATAATAAA
* *
3783398 GAAATAAAATAAAATATATAAGATTATAATAAA
1 AAAATAAAATAAAATATATAAAATTATAATAAA
3783431 AAAATAAAAATAAAATATAT
1 AAAAT-AAAATAAAATATAT
3783451 GATATTAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
32 14 0.30
33 9 0.19
34 24 0.51
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (33 bp):
AAAATAAAATAAAATATATAAAATTATAATAAA
Found at i:3784230 original size:19 final size:19
Alignment explanation
Indices: 3784206--3784244 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3784196 AATTTATAAT
3784206 TTTTAATATAAAAGTCAAA
1 TTTTAATATAAAAGTCAAA
*
3784225 TTTTAATATAAAGGTCAAA
1 TTTTAATATAAAAGTCAAA
3784244 T
1 T
3784245 GCTTTATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (19 bp):
TTTTAATATAAAAGTCAAA
Found at i:3785765 original size:21 final size:22
Alignment explanation
Indices: 3785725--3785765 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3785715 TTGATTTCTT
* *
3785725 AAATTTTATTTTTCATATTTCA
1 AAATTTTATATTTAATATTTCA
3785747 AAATTTTA-ATTTAATATTT
1 AAATTTTATATTTAATATTT
3785766 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (22 bp):
AAATTTTATATTTAATATTTCA
Found at i:3820084 original size:2 final size:2
Alignment explanation
Indices: 3820077--3820102 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3820067 TTCATTCTTA
3820077 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
3820103 CGTATAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3828435 original size:43 final size:43
Alignment explanation
Indices: 3828374--3828467 Score: 179
Period size: 43 Copynumber: 2.2 Consensus size: 43
3828364 GCCTCCTAAG
*
3828374 TTAGCTATCCCATATTCAAGTGTCATTCTCCCATCTCCCATAA
1 TTAGCAATCCCATATTCAAGTGTCATTCTCCCATCTCCCATAA
3828417 TTAGCAATCCCATATTCAAGTGTCATTCTCCCATCTCCCATAA
1 TTAGCAATCCCATATTCAAGTGTCATTCTCCCATCTCCCATAA
3828460 TTAGCAAT
1 TTAGCAAT
3828468 TCTCCTATGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.34
Consensus pattern (43 bp):
TTAGCAATCCCATATTCAAGTGTCATTCTCCCATCTCCCATAA
Found at i:3839760 original size:18 final size:18
Alignment explanation
Indices: 3839727--3839765 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3839717 AGATAAAAGG
** *
3839727 CATAACTGTTTGTAGTTT
1 CATAACTGTTAATAGTGT
3839745 CATAACTGTTAATAGTGT
1 CATAACTGTTAATAGTGT
3839763 CAT
1 CAT
3839766 GTTTAAAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (18 bp):
CATAACTGTTAATAGTGT
Found at i:3843573 original size:3 final size:3
Alignment explanation
Indices: 3843565--3843589 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3843555 GACAAACCCT
3843565 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
3843590 TACACGCTAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3844211 original size:24 final size:21
Alignment explanation
Indices: 3844161--3844212 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
3844151 AGTCTTTTCA
3844161 TTTTGTTGTTGTATTATTGGT
1 TTTTGTTGTTGTATTATTGGT
3844182 TTTTGTTGTTGTATTATTGGT
1 TTTTGTTGTTGTATTATTGGT
**
3844203 AATTGTTGTT
1 TTTTGTTGTT
3844213 TTTGTTCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.12, C:0.00, G:0.23, T:0.65
Consensus pattern (21 bp):
TTTTGTTGTTGTATTATTGGT
Found at i:3851143 original size:3 final size:3
Alignment explanation
Indices: 3851135--3851169 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3851125 CTGAACATAT
*
3851135 TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3851170 ATTTTCTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3851153 original size:14 final size:14
Alignment explanation
Indices: 3851134--3851162 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3851124 ACTGAACATA
3851134 TTTATTATTATTAT
1 TTTATTATTATTAT
3851148 TTTATTATTATTAT
1 TTTATTATTATTAT
3851162 T
1 T
3851163 ATAATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTATTATTAT
Found at i:3851590 original size:21 final size:23
Alignment explanation
Indices: 3851566--3851626 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 23
3851556 AAATAAAAAT
*
3851566 AAAATATATA-AAATT-ATATTA
1 AAAATATATATAAATTAATAATA
3851587 AAAATA-ATATAAATTAATAATA
1 AAAATATATATAAATTAATAATA
* *
3851609 AAAATATAAATATATTAA
1 AAAATATATATAAATTAA
3851627 ACTTATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.09
21 11 0.32
22 11 0.32
23 9 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAATATATATAAATTAATAATA
Found at i:3851611 original size:33 final size:34
Alignment explanation
Indices: 3851522--3851616 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 34
3851512 AAAAAAATTA
*
3851522 AAATAAAATATATAATATAAT-AAATTATATTAAC
1 AAATAAAA-ATAAAATATAATAAAATTATATTAAC
3851556 AAATAAAAATAAAATAT-ATAAAATTATATTAA-
1 AAATAAAAATAAAATATAATAAAATTATATTAAC
* * *
3851588 AAAT-AATATAAATTAATAATAAAAATATA
1 AAATAAAAATAAAAT-ATAATAAAATTATA
3851617 AATATATTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
31 8 0.15
32 8 0.15
33 30 0.56
34 8 0.15
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (34 bp):
AAATAAAAATAAAATATAATAAAATTATATTAAC
Found at i:3851616 original size:19 final size:21
Alignment explanation
Indices: 3851563--3851626 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 21
3851553 AACAAATAAA
3851563 AATAAAATATATAAAATTATATT
1 AATAAAA-ATAT-AAATTATATT
3851586 AA-AAATAATATAAATTA-A-T
1 AATAAA-AATATAAATTATATT
3851605 AATAAAAATATAAA-TATATT
1 AATAAAAATATAAATTATATT
3851625 AA
1 AA
3851627 ACTTATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
18 2 0.05
19 12 0.32
20 7 0.19
21 6 0.16
22 7 0.19
23 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AATAAAAATATAAATTATATT
Found at i:3851660 original size:49 final size:48
Alignment explanation
Indices: 3851557--3851665 Score: 123
Period size: 49 Copynumber: 2.2 Consensus size: 48
3851547 TATATTAACA
*
3851557 AATAAAAATAAAATATATAAAATTATATTAAAAATAATATAAATTAAT
1 AATAAAAATAAAATATATAAAATTATATTAAAAATAATATAAAATAAT
* **
3851605 AATAAAAATATAAATATATTAAACTTATATT-TTAATAA-ATAAAAATAAT
1 AATAAAAATA-AAATATA-TAAAATTATATTAAAAATAATAT-AAAATAAT
**
3851654 TTTAAAAATAAA
1 AATAAAAATAAA
3851666 CATTATATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
48 14 0.27
49 27 0.52
50 11 0.21
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (48 bp):
AATAAAAATAAAATATATAAAATTATATTAAAAATAATATAAAATAAT
Found at i:3851679 original size:21 final size:21
Alignment explanation
Indices: 3851624--3851683 Score: 74
Period size: 19 Copynumber: 3.0 Consensus size: 21
3851614 ATAAATATAT
3851624 TAAAC-TTATATTTTAATAAA
1 TAAACATTATATTTTAATAAA
*
3851644 TAAA-AATA-ATTTTAA-AAA
1 TAAACATTATATTTTAATAAA
3851662 TAAACATTATATTTTTAATAAA
1 TAAACATTATA-TTTTAATAAA
3851684 ATACTTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 7 0.21
19 10 0.30
20 7 0.21
21 6 0.18
22 3 0.09
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAACATTATATTTTAATAAA
Found at i:3855795 original size:385 final size:387
Alignment explanation
Indices: 3855078--3855839 Score: 1343
Period size: 385 Copynumber: 2.0 Consensus size: 387
3855068 AGAAAAATAT
*
3855078 AGAAGTAGAGTTGCAGAAAGCAAATGAAGAAACTCATTCACAAACTAACAAGTTTGCTGAGACTA
1 AGAAATAGAGTTGCAGAAAGCAAATGAAGAAACTCATTCACAAACTAACAAGTTTGCTGAGACTA
*
3855143 GTGAGGCTAGAAAGTCACTTGAGGAGGCATTGTCACTGGCAGAAAATAACATTTCCTTGCTTATC
66 GTGAGGCTAGAAAGTCACTTGAAGAGGCATTGTCACTGGCAGAAAATAACATTTCCTTGCTTATC
3855208 AGTGAGAAAGAGGAGGCTCAAGGTAGCAGAGCTGCCTCAGAGATGGAGGTGGAGAAAATGAGGGA
131 AGTGAGAAAGAGGAGGCTCAAGGTAGCAGAGCTGCCTCAGAGATGGAGGTGGAGAAAATGAGGGA
* * *
3855273 GGAAGTTGCTATTCAGACCAGCAGGCTCACAGAAGCATATAATACTATAAAGTCACTTGAATATG
196 GGAAGTTGCTATTCAGACCAGCAGACTCACAGAAGCATATAACACTATAAAGTCACTTGAAAATG
*
3855338 CACTTTCTCAGGCAGAGATGAATGTTGCTTCACTAACTGAACAAAGTAACAATTCACAAGTGGAA
261 CACTTTCCCAGGCAGAGATGAATGTTGCTTCACTAACTGAACAAAGTAACAATTCACAAGTGGAA
3855403 ATAACCAACTTAGAGAATGAGCTAAAGA-AGCTAAAAGATGAAACTGAGACCCAGAAAGCAAC
326 ATAACCAACTTAGAGAATGAGCTAAA-ACAGCTAAAAGATGAAACTGAGACCCAGAAAGCAAC
* *
3855465 AGAAATAGAGTTGCAGAAAGC-AATCGAGGAAGCTCATTCACAAACTAACAAGTTTGCTGAGACT
1 AGAAATAGAGTTGCAGAAAGCAAAT-GAAGAAACTCATTCACAAACTAACAAGTTTGCTGAGACT
3855529 AGTGAGGCTAGAAAGTCACTTGAAGAGGCATTGTCACTGGCAGAAAATAA-ATTTCCTTGCTTAT
65 AGTGAGGCTAGAAAGTCACTTGAAGAGGCATTGTCACTGGCAGAAAATAACATTTCCTTGCTTAT
* *
3855593 CAGTGA-AAAGAGGAGGCTCAAGGTAGCAGAGCTGCTTCAGAGATGGAGGTGGAGAAAGTGAGGG
130 CAGTGAGAAAGAGGAGGCTCAAGGTAGCAGAGCTGCCTCAGAGATGGAGGTGGAGAAAATGAGGG
* * * *
3855657 AGGAAGTTGCTATTCAGACCTGCAGACTTAGAGAGGCATATAACACTATAAAGTCACTTGAAAAT
195 AGGAAGTTGCTATTCAGACCAGCAGACTCACAGAAGCATATAACACTATAAAGTCACTTGAAAAT
3855722 GCACTTTCCCAGGCAGAGATGAATGTTGCTTCACTAACTGAACAAAGTAACAATTCACAAGTGGA
260 GCACTTTCCCAGGCAGAGATGAATGTTGCTTCACTAACTGAACAAAGTAACAATTCACAAGTGGA
*
3855787 AATAACCAACTTGGAGAATGAGCTAAAACAGCTAAAAGATGAAACTGAGACCC
325 AATAACCAACTTAGAGAATGAGCTAAAACAGCTAAAAGATGAAACTGAGACCC
3855840 TGGCTAGCAA
Statistics
Matches: 358, Mismatches: 15, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
384 1 0.00
385 228 0.64
386 23 0.06
387 106 0.30
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (387 bp):
AGAAATAGAGTTGCAGAAAGCAAATGAAGAAACTCATTCACAAACTAACAAGTTTGCTGAGACTA
GTGAGGCTAGAAAGTCACTTGAAGAGGCATTGTCACTGGCAGAAAATAACATTTCCTTGCTTATC
AGTGAGAAAGAGGAGGCTCAAGGTAGCAGAGCTGCCTCAGAGATGGAGGTGGAGAAAATGAGGGA
GGAAGTTGCTATTCAGACCAGCAGACTCACAGAAGCATATAACACTATAAAGTCACTTGAAAATG
CACTTTCCCAGGCAGAGATGAATGTTGCTTCACTAACTGAACAAAGTAACAATTCACAAGTGGAA
ATAACCAACTTAGAGAATGAGCTAAAACAGCTAAAAGATGAAACTGAGACCCAGAAAGCAAC
Found at i:3865934 original size:40 final size:40
Alignment explanation
Indices: 3865879--3865959 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
3865869 TCTTTGATGA
3865879 TAATCTATTTGATGTTATGCCTCAGTGGGATTGTTTTTCT
1 TAATCTATTTGATGTTATGCCTCAGTGGGATTGTTTTTCT
3865919 TAATCTATTTGATGTTATGCCTCAGTGGGATTGTTTTTCT
1 TAATCTATTTGATGTTATGCCTCAGTGGGATTGTTTTTCT
3865959 T
1 T
3865960 TGCAATCTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.17, C:0.12, G:0.20, T:0.51
Consensus pattern (40 bp):
TAATCTATTTGATGTTATGCCTCAGTGGGATTGTTTTTCT
Found at i:3872181 original size:15 final size:16
Alignment explanation
Indices: 3872161--3872196 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3872151 AACTCCCCTC
3872161 TATTACTTTT-TAATA
1 TATTACTTTTGTAATA
3872176 TATTACTTTTGTAATA
1 TATTACTTTTGTAATA
*
3872192 AATTA
1 TATTA
3872197 TTATTTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (16 bp):
TATTACTTTTGTAATA
Found at i:3881653 original size:14 final size:16
Alignment explanation
Indices: 3881636--3881672 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
3881626 CACCTTAGAG
3881636 TTTATAA-TA-TATTA
1 TTTATAATTAGTATTA
3881650 TTTATAATTAGTTATTA
1 TTTATAATTAG-TATTA
3881667 TTTATA
1 TTTATA
3881673 TAAACTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.35
15 2 0.10
17 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTATAATTAGTATTA
Found at i:3881800 original size:204 final size:205
Alignment explanation
Indices: 3881532--3882143 Score: 709
Period size: 204 Copynumber: 3.0 Consensus size: 205
3881522 TATTTATATA
* * **
3881532 AATATAT--TATATATATTTAGTTTATACATAAACATTGCTATAATTTATAATAAATTTAATTTA
1 AATATATCATATATATATATAATTTATACATAAGTATTGCTATAATTTATAATAAATTT-ATTTA
* * *
3881595 TATGATTGCACTTAATAACTTTATTAGTTATCACCTTAGAGTTTATAATATATTATTTATAATTA
65 TATGATTACAATTAATAACTTTATTAGTTATCACCTTAGA-TTTATAACATATTATTTATAATTA
* *
3881660 GTTATTATTTATATAAACTTAGATATAAAACATTATAACATATAAGTTATATAATTAATTTCATA
129 GTTATTATTTATATAAACTTTGATATAAAACATTATAACATATAAGTTATATCATTAATTT-ATA
*
3881725 TAT-GCATAAAAT
193 TATAGAATAAAAT
* * * *
3881737 AA-A-GTCATAT-TATATATAATTTATACATAAGTATTACTATAACTTATAATAGACTTTATTTA
1 AATATATCATATATATATATAATTTATACATAAGTATTGCTATAATTTATAATA-AATTTATTTA
* * * * *
3881799 TACGATTACAATTAATAACTTTATTAATTATCACTTTAAATTTTATAACATAATATTTATAATTA
65 TATGATTACAATTAATAACTTTATTAGTTATCACCTTAGA-TTTATAACATATTATTTATAATTA
* * * * *
3881864 GTTATTATTTATACAAACTTTGATACAAAACGTTTTAACATATAATTTATATCATTAATTTTATA
129 GTTATTATTTATATAAACTTTGATATAAAACATTATAACATATAAGTTATATCATTAA-TTTATA
* *
3881929 TATATAATAAAGT
193 TATAGAATAAAAT
* *
3881942 AATATATCATATATAAATATATTTAATTTATATATAAGTATTGCTTTAATTTATAATAAAATTTA
1 AATATATCATATAT--ATATA--TAATTTATACATAAGTATTGCTATAATTTATAAT-AAATTTA
* * * * * *
3882007 TTTATATGATTACATTTAAT-AGTTTGTTAGCTATC-CCTTTAGATTTATAGCATATTGTTTATA
61 TTTATATGATTACAATTAATAACTTTATTAGTTATCACC-TTAGATTTATAACATATTATTTATA
* * *
3882070 ATTAGTTATTATTTTTTATAAATTTTGATGTAAAACATTATAACATATAAGTTATATCATTAATT
125 ATTAGTTATTA-TTTATATAAACTTTGATATAAAACATTATAACATATAAGTTATATCATTAATT
3882135 ATATATATA
189 -TATATATA
3882144 TTTATAATTA
Statistics
Matches: 339, Mismatches: 52, Indels: 26
0.81 0.12 0.06
Matches are distributed among these distances:
203 1 0.00
204 154 0.45
205 20 0.06
206 1 0.00
207 6 0.02
208 1 0.00
210 36 0.11
211 66 0.19
212 53 0.16
213 1 0.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (205 bp):
AATATATCATATATATATATAATTTATACATAAGTATTGCTATAATTTATAATAAATTTATTTAT
ATGATTACAATTAATAACTTTATTAGTTATCACCTTAGATTTATAACATATTATTTATAATTAGT
TATTATTTATATAAACTTTGATATAAAACATTATAACATATAAGTTATATCATTAATTTATATAT
AGAATAAAAT
Found at i:3881976 original size:21 final size:21
Alignment explanation
Indices: 3881950--3882010 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
3881940 GTAATATATC
3881950 ATATATAAATATATTTAATTT
1 ATATATAAATATATTTAATTT
* *
3881971 ATATATAAGTATTGCTTTAATTT
1 ATATATAAATA-T-ATTTAATTT
*
3881994 ATA-ATAAAATTTATTTA
1 ATATAT-AAATATATTTA
3882011 TATGATTACA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 14 0.44
22 4 0.12
23 14 0.44
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (21 bp):
ATATATAAATATATTTAATTT
Found at i:3888415 original size:26 final size:26
Alignment explanation
Indices: 3888376--3888436 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
3888366 ACTGAGGGTG
* *
3888376 TGCGTGAATGCAGTAGGGGTTAACAT
1 TGCGTGACTACAGTAGGGGTTAACAT
*
3888402 TGCGTGACTACAGTAGGGTTTAACAT
1 TGCGTGACTACAGTAGGGGTTAACAT
3888428 TGCGTGACT
1 TGCGTGACT
3888437 GATTGATATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.30
Consensus pattern (26 bp):
TGCGTGACTACAGTAGGGGTTAACAT
Found at i:3888455 original size:23 final size:23
Alignment explanation
Indices: 3888425--3888482 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
3888415 TAGGGTTTAA
* *
3888425 CATTGCGTGAC-TGATTGATATGT
1 CATTGCGTGACAT-ATTGAAAGGT
3888448 CATTGCGTGACATATTGAAAGGT
1 CATTGCGTGACATATTGAAAGGT
3888471 CATTGCGTGACA
1 CATTGCGTGACA
3888483 AGGTGACTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (23 bp):
CATTGCGTGACATATTGAAAGGT
Found at i:3888566 original size:23 final size:23
Alignment explanation
Indices: 3888538--3888612 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
3888528 TAAGGATTAA
3888538 CATTGCATGACTGGTTGATAGGT
1 CATTGCATGACTGGTTGATAGGT
* ** **
3888561 CATTGCATTACCT-AATGATAAAT
1 CATTGCATGA-CTGGTTGATAGGT
** *
3888584 CATTGTGTGATTGGTTGATAGGT
1 CATTGCATGACTGGTTGATAGGT
3888607 CATTGC
1 CATTGC
3888613 GTTAGCTAAT
Statistics
Matches: 36, Mismatches: 14, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
22 1 0.03
23 33 0.92
24 2 0.06
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (23 bp):
CATTGCATGACTGGTTGATAGGT
Found at i:3891211 original size:22 final size:22
Alignment explanation
Indices: 3891181--3891238 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
3891171 CGTACTGCCC
*
3891181 CAACGTCACGCAATACATAACAA
1 CAAC-TCACGCAATACATAAAAA
3891204 CAACTCAC-CATATACATAAAAA
1 CAACTCACGCA-ATACATAAAAA
*
3891226 CCACTCACGCAAT
1 CAACTCACGCAAT
3891239 GTCTCAATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 2 0.06
22 23 0.74
23 6 0.19
ACGTcount: A:0.47, C:0.33, G:0.05, T:0.16
Consensus pattern (22 bp):
CAACTCACGCAATACATAAAAA
Found at i:3902464 original size:2 final size:2
Alignment explanation
Indices: 3902457--3902482 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3902447 TTTATGGTGC
3902457 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
3902483 TGTGTGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3903151 original size:27 final size:28
Alignment explanation
Indices: 3903097--3903153 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
3903087 AACAAATTGA
*
3903097 AAAAAATAAAAAGCCAAATAAACAAAAT
1 AAAAAATAAAAAGCCAAAGAAACAAAAT
*
3903125 AAAAAATAAAAAG-GAAAGAAA-AGAAAT
1 AAAAAATAAAAAGCCAAAGAAACA-AAAT
3903152 AA
1 AA
3903154 TTGAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.04
27 12 0.46
28 13 0.50
ACGTcount: A:0.77, C:0.05, G:0.09, T:0.09
Consensus pattern (28 bp):
AAAAAATAAAAAGCCAAAGAAACAAAAT
Found at i:3904078 original size:26 final size:25
Alignment explanation
Indices: 3904040--3904089 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3904030 CTCTTCCTTG
*
3904040 TTCTCTCTGTCTTTTTGTTTTTCTCC
1 TTCTCTCTGTC-TTTGGTTTTTCTCC
* *
3904066 TTCTTTCTTTCTTTGGTTTTTCTC
1 TTCTCTCTGTCTTTGGTTTTTCTC
3904090 TTTTGTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.00, C:0.24, G:0.08, T:0.68
Consensus pattern (25 bp):
TTCTCTCTGTCTTTGGTTTTTCTCC
Found at i:3904098 original size:25 final size:24
Alignment explanation
Indices: 3904049--3904103 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
3904039 GTTCTCTCTG
3904049 TCTT-TTT-GTTTTTCTCCTTCTT
1 TCTTCTTTGGTTTTTCTCCTTCTT
*
3904071 TCTTTCTTTGGTTTTTCT-CTTTTGT
1 TC-TTCTTTGGTTTTTCTCCTTCT-T
3904096 TCTTCTTT
1 TCTTCTTT
3904104 CTTTTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 2 0.07
23 2 0.07
24 13 0.46
25 11 0.39
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.73
Consensus pattern (24 bp):
TCTTCTTTGGTTTTTCTCCTTCTT
Found at i:3904119 original size:21 final size:20
Alignment explanation
Indices: 3904088--3904133 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3904078 TTGGTTTTTC
*
3904088 TCTTTTGTTCT-TCTTTCTTT
1 TCTTTTGTTCTCTCTTT-TGT
3904108 TCTTTTGTTTCTCTCTTTTGT
1 TCTTTTG-TTCTCTCTTTTGT
3904129 TCTTT
1 TCTTT
3904134 GGGCCTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 11 0.48
22 5 0.22
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.74
Consensus pattern (20 bp):
TCTTTTGTTCTCTCTTTTGT
Found at i:3904123 original size:33 final size:32
Alignment explanation
Indices: 3904065--3904132 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
3904055 TGTTTTTCTC
*
3904065 CTTCTTTCTTTCTTTGGTTTTTCTCTTTTGTT
1 CTTCTTTCTTTCTTTGGTTTCTCTCTTTTGTT
*
3904097 CTTCTTTCTTTTCTTTTGTTTCTCTCTTTTGTT
1 CTTCTTTC-TTTCTTTGGTTTCTCTCTTTTGTT
3904130 CTT
1 CTT
3904133 TGGGCCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 8 0.24
33 25 0.76
ACGTcount: A:0.00, C:0.21, G:0.07, T:0.72
Consensus pattern (32 bp):
CTTCTTTCTTTCTTTGGTTTCTCTCTTTTGTT
Found at i:3918724 original size:15 final size:15
Alignment explanation
Indices: 3918700--3918733 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3918690 AAATTTTACG
* *
3918700 TAATTTATTATAATT
1 TAATTAATTATAATA
3918715 TAATTAATTATAATA
1 TAATTAATTATAATA
3918730 TAAT
1 TAAT
3918734 ATTTTATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTAATTATAATA
Found at i:3928436 original size:62 final size:62
Alignment explanation
Indices: 3928351--3928476 Score: 227
Period size: 62 Copynumber: 2.0 Consensus size: 62
3928341 TATACATTGA
3928351 ATAAATTCAGTAGTGCTCCAAACTTAAATTTATTATTTTCATTCATTATTTTTATGAGTCCT
1 ATAAATTCAGTAGTGCTCCAAACTTAAATTTATTATTTTCATTCATTATTTTTATGAGTCCT
*
3928413 ATAAATT-AGGTAGTGCTCCAAACTTCAATTTATTATTTTCATTCATTATTTTTATGAGTCCT
1 ATAAATTCA-GTAGTGCTCCAAACTTAAATTTATTATTTTCATTCATTATTTTTATGAGTCCT
3928475 AT
1 AT
3928477 TTATTGACTA
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
61 1 0.02
62 61 0.98
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (62 bp):
ATAAATTCAGTAGTGCTCCAAACTTAAATTTATTATTTTCATTCATTATTTTTATGAGTCCT
Found at i:3928847 original size:29 final size:29
Alignment explanation
Indices: 3928814--3928871 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
3928804 AAATAAGAAT
3928814 TGAGAAAAAAACTAT-TGGTTTATTTCTCA
1 TGAGAAAAAAACT-TCTGGTTTATTTCTCA
* *
3928843 TGAGAGAAGAACTTCTGGTTTATTTCTCA
1 TGAGAAAAAAACTTCTGGTTTATTTCTCA
3928872 ATATTTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (29 bp):
TGAGAAAAAAACTTCTGGTTTATTTCTCA
Found at i:3931139 original size:18 final size:18
Alignment explanation
Indices: 3931116--3931166 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
3931106 GAATTTATGC
3931116 CTCTTTTGGGGCAATAAG
1 CTCTTTTGGGGCAATAAG
3931134 CTCTTTTGGGGCAATAAG
1 CTCTTTTGGGGCAATAAG
* * *
3931152 TTTTTTTGGAGCAAT
1 CTCTTTTGGGGCAAT
3931167 TCGTGCCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.39
Consensus pattern (18 bp):
CTCTTTTGGGGCAATAAG
Found at i:3931184 original size:39 final size:40
Alignment explanation
Indices: 3931134--3931211 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 40
3931124 GGGCAATAAG
* * *
3931134 CTCTTTTGGGGCAATAAGTTTTTTTGGAGCA-ATTCGTGC
1 CTCTTTAGGGGCAATAAGCTCTTTTGGAGCAGATTCGTGC
**
3931173 CTCTTTAGGGGCAATGGGCTCTTTTGGAGCAGATTCGTG
1 CTCTTTAGGGGCAATAAGCTCTTTTGGAGCAGATTCGTG
3931212 ATTTTTCCCC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 26 0.79
40 7 0.21
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.37
Consensus pattern (40 bp):
CTCTTTAGGGGCAATAAGCTCTTTTGGAGCAGATTCGTGC
Found at i:3934347 original size:29 final size:29
Alignment explanation
Indices: 3934315--3934372 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
3934305 AGAAAATAAT
*
3934315 TGAGAAAAAAACTTCT-GATTTATTTCTCA
1 TGAGAAAAAAACTTCTAG-TTCATTTCTCA
*
3934344 TGAGAGAAAAACTTCTAGTTCATTTCTCA
1 TGAGAAAAAAACTTCTAGTTCATTTCTCA
3934373 CTATTTCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (29 bp):
TGAGAAAAAAACTTCTAGTTCATTTCTCA
Found at i:3935106 original size:69 final size:69
Alignment explanation
Indices: 3934995--3935130 Score: 195
Period size: 69 Copynumber: 2.0 Consensus size: 69
3934985 TGAATGCAAC
**
3934995 AAACAAGCTACTAATAAAAAATCACGAGTCTACCTATTTCTTGAAATGAATGCT-AAATCATTTA
1 AAACAAGCTACTAATAAAAAATCACGAACCTACCTATTTCTTGAAATGAATG-TGAAATCATTTA
3935059 ATATT
65 ATATT
* * *
3935064 AAACAAGCTACTAATAAAAAATCATGAACCTGTCC-ATTTCTTGAAGTGAATGTGAAATCATTTA
1 AAACAAGCTACTAATAAAAAATCACGAACCT-ACCTATTTCTTGAAATGAATGTGAAATCATTTA
3935128 ATA
65 ATA
3935131 ATTATGGTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 1 0.02
69 57 0.95
70 2 0.03
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.31
Consensus pattern (69 bp):
AAACAAGCTACTAATAAAAAATCACGAACCTACCTATTTCTTGAAATGAATGTGAAATCATTTAA
TATT
Found at i:3938831 original size:23 final size:24
Alignment explanation
Indices: 3938804--3938852 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
3938794 TTTGTATATC
*
3938804 AAATTCA-TCATCTCTATTTATGT
1 AAATTCATTCATCTCCATTTATGT
* *
3938827 AAATTTATTCTTCTCCATTTATGT
1 AAATTCATTCATCTCCATTTATGT
3938851 AA
1 AA
3938853 GCCTATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (24 bp):
AAATTCATTCATCTCCATTTATGT
Found at i:3939785 original size:21 final size:19
Alignment explanation
Indices: 3939759--3939804 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
3939749 ATCAGACAAA
* *
3939759 TATTATACTTAATTATTTAT
1 TATTATAATAAATTA-TTAT
3939779 GTATTATAATAAATTATTAT
1 -TATTATAATAAATTATTAT
3939799 TATTAT
1 TATTAT
3939805 TCGAATTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 4 0.17
21 13 0.57
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TATTATAATAAATTATTAT
Found at i:3940035 original size:2 final size:2
Alignment explanation
Indices: 3940023--3940053 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3940013 ATTGTACTAT
*
3940023 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3940054 CTAAAACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3949021 original size:2 final size:2
Alignment explanation
Indices: 3949014--3949044 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3949004 ATTATCTAGA
*
3949014 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3949045 ATGTAACTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3954292 original size:2 final size:2
Alignment explanation
Indices: 3954285--3954311 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3954275 AAATGTGATT
3954285 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3954312 TCAATTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3962776 original size:19 final size:21
Alignment explanation
Indices: 3962738--3962778 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
3962728 GCATTGTGTA
3962738 TTAATATGTTACTATATATAG
1 TTAATATGTTACTATATATAG
3962759 TTAATAT-TTACT-TATATAG
1 TTAATATGTTACTATATATAG
3962778 T
1 T
3962779 ATATAAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 5 0.25
21 7 0.35
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (21 bp):
TTAATATGTTACTATATATAG
Found at i:3962840 original size:20 final size:20
Alignment explanation
Indices: 3962815--3962874 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
3962805 ACATATATAC
*
3962815 TATATAATAGTATATTGTTA
1 TATATAATAGTAAATTGTTA
3962835 TATATAATAGTAAATTGTTA
1 TATATAATAGTAAATTGTTA
3962855 TATATAATAGTAAATTGTTA
1 TATATAATAGTAAATTGTTA
3962875 GAGTAATTAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (20 bp):
TATATAATAGTAAATTGTTA
Found at i:3962948 original size:22 final size:20
Alignment explanation
Indices: 3962880--3962970 Score: 53
Period size: 20 Copynumber: 4.3 Consensus size: 20
3962870 TGTTAGAGTA
*
3962880 ATTAGTATATTAATAAGTATACT
1 ATTA-TATATT-ATAA-TATATT
3962903 A-TATA-ATATATAATATATT
1 ATTATATAT-TATAATATATT
*
3962922 GTTATATATTATAATATAGTT
1 ATTATATATTATAATATA-TT
*
3962943 AATTAT-TAATATAAGTTATATT
1 -ATTATATATTATAA--TATATT
*
3962965 ACTATA
1 ATTATA
3962971 GAATACTAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
19 5 0.09
20 19 0.35
21 18 0.33
22 8 0.15
23 5 0.09
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (20 bp):
ATTATATATTATAATATATT
Found at i:3962965 original size:18 final size:18
Alignment explanation
Indices: 3962926--3963014 Score: 66
Period size: 18 Copynumber: 5.2 Consensus size: 18
3962916 TATATTGTTA
3962926 TATATTA-TAATAT-AGT
1 TATATTATTAATATAAGT
3962942 TA-ATTATTAATATAAGT
1 TATATTATTAATATAAGT
* *
3962959 TATATTACT-ATAGAA--
1 TATATTATTAATATAAGT
* *
3962974 TACTAATATTAATATAACT
1 TA-TATTATTAATATAAGT
*
3962993 TACT-TTAGTAATATAAGT
1 TA-TATTATTAATATAAGT
3963011 TATA
1 TATA
3963015 CGATAGTAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
15 6 0.11
16 13 0.23
17 16 0.28
18 18 0.32
19 4 0.07
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (18 bp):
TATATTATTAATATAAGT
Found at i:3974043 original size:15 final size:16
Alignment explanation
Indices: 3974004--3974045 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
3973994 AATGTGATGA
3974004 TATTAATATATTTATAT
1 TATTAAT-TATTTATAT
**
3974021 TAAAAATTATTTA-AT
1 TATTAATTATTTATAT
3974036 TATTAATTAT
1 TATTAATTAT
3974046 ATTTAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 10 0.48
16 6 0.29
17 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAATTATTTATAT
Found at i:3974101 original size:21 final size:22
Alignment explanation
Indices: 3974072--3974120 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
3974062 TTTTATATCA
* *
3974072 TATT-ATAAATATGTATATACT
1 TATTAATAAAAATATATATACT
*
3974093 T-TTAATAAAAATATATTTACT
1 TATTAATAAAAATATATATACT
3974114 TATTAAT
1 TATTAAT
3974121 TTGTGTTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 16 0.70
22 5 0.22
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTAATAAAAATATATATACT
Found at i:3974157 original size:15 final size:17
Alignment explanation
Indices: 3974127--3974159 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3974117 TAATTTGTGT
3974127 TAACATTATAAAAATTA
1 TAACATTATAAAAATTA
3974144 TAAC-TTAT-AAAATTA
1 TAACATTATAAAAATTA
3974159 T
1 T
3974160 TAATTGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACATTATAAAAATTA
Found at i:3974446 original size:17 final size:17
Alignment explanation
Indices: 3974402--3974460 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
3974392 TAATTACTAT
*
3974402 TATATATA-TTCTAAAA
1 TATATATACTTTTAAAA
* *
3974418 TACTAAATACTTTTAAGA
1 TA-TATATACTTTTAAAA
3974436 TATATATAC-TTTAAATA
1 TATATATACTTTTAAA-A
*
3974453 TAAATATA
1 TATATATA
3974461 TTTACTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
16 7 0.21
17 19 0.56
18 8 0.24
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (17 bp):
TATATATACTTTTAAAA
Found at i:3974472 original size:32 final size:34
Alignment explanation
Indices: 3974387--3974472 Score: 81
Period size: 32 Copynumber: 2.6 Consensus size: 34
3974377 AATTTATAAG
*
3974387 AAATATAATTACTATTATATATATTCTAAAATACT
1 AAATATATTTACT-TTATATATATTCTAAAATACT
***
3974422 AAATACT-TTTAAGATATATATACTT-T-AAATA-T
1 AAATA-TATTTACTTTATATATA-TTCTAAAATACT
3974454 AAATATATTTACTTTATAT
1 AAATATATTTACTTTATAT
3974473 TTTGTATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
31 1 0.02
32 15 0.37
33 5 0.12
34 9 0.22
35 10 0.24
36 1 0.02
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (34 bp):
AAATATATTTACTTTATATATATTCTAAAATACT
Found at i:3981192 original size:41 final size:41
Alignment explanation
Indices: 3981095--3981227 Score: 123
Period size: 41 Copynumber: 3.4 Consensus size: 41
3981085 AACAGTGGTA
* ** * *
3981095 CTATTATAAAAAGCA-TCTTTAAGGATCAATAT-TTGTATG
1 CTATTATAAAAAGCACCCTCCAAGGATCAACATATTGTGTG
*
3981134 CTATTAAAAAAAGCACCCTCCAAGGATCAACATATTGTGTG
1 CTATTATAAAAAGCACCCTCCAAGGATCAACATATTGTGTG
* * * * *
3981175 CTATTATAAAGATCACCCTCTAAAGATTAACA-A-T-TGTG
1 CTATTATAAAAAGCACCCTCCAAGGATCAACATATTGTGTG
*
3981213 CTATTATAAATAGCA
1 CTATTATAAAAAGCA
3981228 GTTCAACAAT
Statistics
Matches: 78, Mismatches: 14, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
38 17 0.22
39 15 0.19
40 14 0.18
41 32 0.41
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.32
Consensus pattern (41 bp):
CTATTATAAAAAGCACCCTCCAAGGATCAACATATTGTGTG
Found at i:3985050 original size:63 final size:62
Alignment explanation
Indices: 3984957--3985086 Score: 158
Period size: 63 Copynumber: 2.1 Consensus size: 62
3984947 AGCTAAAGGG
*
3984957 AAAAAAAAAACCTACTAAATCAAAAATCCTTAACAAGA-A-GACTTAGGCAAACGTTAAGGCAA
1 AAAAAAAAAACCTACTAAATCAAAAATCCTT-ACAA-ATATGACTTAGGCAAAAGTTAAGGCAA
** * *
3985019 AAAAAAAAAAGCCTAC-AAAGTTGAAAATCCTTACAAATATGAGTTAGGCAAAAGTTAGGGCAA
1 AAAAAAAAAA-CCTACTAAA-TCAAAAATCCTTACAAATATGACTTAGGCAAAAGTTAAGGCAA
3985082 AAAAA
1 AAAAA
3985087 TGTATATGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
61 1 0.02
62 18 0.31
63 40 0.68
ACGTcount: A:0.55, C:0.15, G:0.14, T:0.17
Consensus pattern (62 bp):
AAAAAAAAAACCTACTAAATCAAAAATCCTTACAAATATGACTTAGGCAAAAGTTAAGGCAA
Found at i:3988876 original size:28 final size:28
Alignment explanation
Indices: 3988834--3988889 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3988824 TCCCAACAAT
* * * *
3988834 TTCTTCAAATGGTTTTATTGCAATATAC
1 TTCTACAAATAGTTTTATTACAACATAC
3988862 TTCTACAAATAGTTTTATTACAACATAC
1 TTCTACAAATAGTTTTATTACAACATAC
3988890 ATCTTCCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (28 bp):
TTCTACAAATAGTTTTATTACAACATAC
Found at i:3989795 original size:23 final size:23
Alignment explanation
Indices: 3989765--3989829 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
3989755 ATGAAGATCT
3989765 AGCGAAGTTCGTGATCAAGCAGA
1 AGCGAAGTTCGTGATCAAGCAGA
* * *
3989788 AGCGAAGTTTGTGATTAAGCAGT
1 AGCGAAGTTCGTGATCAAGCAGA
**
3989811 ATTGAAGTTCGTGATCAAG
1 AGCGAAGTTCGTGATCAAG
3989830 ATACCAAGCA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.26
Consensus pattern (23 bp):
AGCGAAGTTCGTGATCAAGCAGA
Found at i:3989839 original size:31 final size:30
Alignment explanation
Indices: 3989804--3989867 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
3989794 GTTTGTGATT
* *
3989804 AAGCAGTATTGAAGTTCGTGATCAAGATACC
1 AAGCAGCAGTGAAGTT-GTGATCAAGATACC
* *
3989835 AAGCAGCAGTGAGGTTGTGATCAAGATATC
1 AAGCAGCAGTGAAGTTGTGATCAAGATACC
3989865 AAG
1 AAG
3989868 TGTTCGTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (30 bp):
AAGCAGCAGTGAAGTTGTGATCAAGATACC
Found at i:4002682 original size:3 final size:3
Alignment explanation
Indices: 4002668--4002711 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
4002658 AAACAAGAGT
*
4002668 TTA TTA TGA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4002712 TTGACAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4013878 original size:27 final size:27
Alignment explanation
Indices: 4013839--4013890 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
4013829 CATCAGAACT
* * *
4013839 AAAACACACTTCAATAGATGGAAAGCC
1 AAAAAACACTTCAAGAGAAGGAAAGCC
*
4013866 AAAAAACATTTCAAGAGAAGGAAAG
1 AAAAAACACTTCAAGAGAAGGAAAG
4013891 ACAATGCCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.54, C:0.15, G:0.17, T:0.13
Consensus pattern (27 bp):
AAAAAACACTTCAAGAGAAGGAAAGCC
Found at i:4026421 original size:27 final size:27
Alignment explanation
Indices: 4026391--4026614 Score: 103
Period size: 27 Copynumber: 8.3 Consensus size: 27
4026381 TTCATATTCT
*
4026391 AAAATTTAATATTCACATGTCATGTTG
1 AAAATTTAATATTTACATGTCATGTTG
*
4026418 AAAA--TAAT-TGTTACATGTCATGTTA
1 AAAATTTAATAT-TTACATGTCATGTTG
4026443 AAAATTTAATTATTATACA--TCATGTTG
1 AAAATTTAA-TATT-TACATGTCATGTTG
* ** *
4026470 AAAATTTAGT-TATTACA-CACTAAGTT-
1 AAAATTTAATAT-TTACATGTC-ATGTTG
* * * *
4026496 AAAATATGTACT-TGTTATAAGCCATGTTG
1 AAAAT-T-TAATAT-TTACATGTCATGTTG
* *
4026525 AAAATTTAGT-TGTTACATGTCATGTTT
1 AAAATTTAATAT-TTACATGTCATGTTG
* * *
4026552 AAAATTTAAT-TATTATATGTTATGTTA
1 AAAATTTAATAT-TTACATGTCATGTTG
* *
4026579 AAAATTTAAT-TGTTACATGTTATTTTG
1 AAAATTTAATAT-TTACATGTCATGTTG
4026606 AAAAATTTA
1 -AAAATTTA
4026615 GTTGTTATAC
Statistics
Matches: 157, Mismatches: 26, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
24 1 0.01
25 26 0.17
26 8 0.05
27 88 0.56
28 23 0.15
29 11 0.07
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (27 bp):
AAAATTTAATATTTACATGTCATGTTG
Found at i:4026629 original size:28 final size:28
Alignment explanation
Indices: 4026422--4026692 Score: 157
Period size: 27 Copynumber: 9.9 Consensus size: 28
4026412 ATGTTGAAAA
* *
4026422 TAATTGTTACA-TGTCATGTTAAAAATT
1 TAATTGTTATACTGTTATGTTAAAAATT
* * * *
4026449 TAATTATTATAC-ATCATGTTGAAAATT
1 TAATTGTTATACTGTTATGTTAAAAATT
* * * ** * *
4026476 TAGTTATTACAC-ACTAAGTTAAAATATG
1 TAATTGTTATACTGTTATGTTAAAA-ATT
* * ** *
4026504 TACTTGTTATA-AGCCATGTTGAAAATT
1 TAATTGTTATACTGTTATGTTAAAAATT
* * * *
4026531 TAGTTGTTACA-TGTCATGTTTAAAATT
1 TAATTGTTATACTGTTATGTTAAAAATT
*
4026558 TAATTATTATA-TGTTATGTTAAAAATT
1 TAATTGTTATACTGTTATGTTAAAAATT
* *
4026585 TAATTGTTACA-TGTTATTTTGAAAAATT
1 TAATTGTTATACTGTTATGTT-AAAAATT
* * **
4026613 TAGTTGTTATACT-TTATATTAATGATT
1 TAATTGTTATACTGTTATGTTAAAAATT
* *
4026640 TAGTTGTTATAC-GTTATGTTAAAAAATG
1 TAATTGTTATACTGTTATGTT-AAAAATT
*
4026668 TAATTGTTATAC-GTAATGTTAAAAA
1 TAATTGTTATACTGTTATGTTAAAAA
4026693 ATATAATTAT
Statistics
Matches: 194, Mismatches: 43, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
27 131 0.68
28 62 0.32
29 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (28 bp):
TAATTGTTATACTGTTATGTTAAAAATT
Found at i:4026641 original size:55 final size:55
Alignment explanation
Indices: 4026525--4026692 Score: 164
Period size: 55 Copynumber: 3.1 Consensus size: 55
4026515 AGCCATGTTG
* * *
4026525 AAAATTTAGTTGTTACATGTCATGTTT-AAAATTTAATTATTATA-TGTTATGTTA
1 AAAATTTAGTTGTTACATGTTAT-TTTAAAAATTTAATTGTTATACTGTTATATTA
* *
4026579 AAAATTTAATTGTTACATGTTATTTTGAAAAATTTAGTTGTTATACT-TTATATTA
1 AAAATTTAGTTGTTACATGTTATTTT-AAAAATTTAATTGTTATACTGTTATATTA
** * * * * * *
4026634 ATGATTTAGTTGTTATACGTTATGTTAAAAAATGTAATTGTTATAC-GTAATGTTA
1 AAAATTTAGTTGTTACATGTTAT-TTTAAAAATTTAATTGTTATACTGTTATATTA
4026689 AAAA
1 AAAA
4026693 ATATAATTAT
Statistics
Matches: 92, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
53 3 0.03
54 21 0.23
55 65 0.71
56 3 0.03
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (55 bp):
AAAATTTAGTTGTTACATGTTATTTTAAAAATTTAATTGTTATACTGTTATATTA
Found at i:4026692 original size:82 final size:81
Alignment explanation
Indices: 4026422--4026692 Score: 240
Period size: 82 Copynumber: 3.3 Consensus size: 81
4026412 ATGTTGAAAA
* * * * *
4026422 TAATTGTTACATGTCATGTTAAAAATTTAATTATTATACATCATGTTGAAAATTTAGTTATTACA
1 TAATTGTTACATGTCATGTTAAAAATTTAGTTGTTATACTTCATATT-AAAATTTAGTTATTATA
** * *
4026487 CACTAAGTTAAAATATG
65 CGTTATGTTAAAAAATG
* * * * * * * *
4026504 TACTTGTTATAAGCCATGTTGAAAATTTAGTTGTTACA-TGTCATGTTTAAAATTTAATTATTAT
1 TAATTGTTACATGTCATGTTAAAAATTTAGTTGTTATACT-TCAT-ATTAAAATTTAGTTATTAT
* *
4026568 ATGTTATGTT-AAAAATT
64 ACGTTATGTTAAAAAATG
* * * * *
4026585 TAATTGTTACATGTTATTTTGAAAAATTTAGTTGTTATACTTTATATTAATGATTTAGTTGTTAT
1 TAATTGTTACATGTCATGTT-AAAAATTTAGTTGTTATACTTCATATTAA-AATTTAGTTATTAT
4026650 ACGTTATGTTAAAAAATG
64 ACGTTATGTTAAAAAATG
* * *
4026668 TAATTGTTATACGTAATGTTAAAAA
1 TAATTGTTACATGTCATGTTAAAAA
4026693 ATATAATTAT
Statistics
Matches: 146, Mismatches: 37, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
81 23 0.16
82 98 0.67
83 25 0.17
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (81 bp):
TAATTGTTACATGTCATGTTAAAAATTTAGTTGTTATACTTCATATTAAAATTTAGTTATTATAC
GTTATGTTAAAAAATG
Found at i:4026693 original size:28 final size:28
Alignment explanation
Indices: 4026643--4026700 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
4026633 AATGATTTAG
* *
4026643 TTGTTATACGTTATGTTAAAAAATGTAA
1 TTGTTATACGTAATGTTAAAAAATATAA
4026671 TTGTTATACGTAATGTTAAAAAATATAA
1 TTGTTATACGTAATGTTAAAAAATATAA
4026699 TT
1 TT
4026701 ATTACAAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.43
Consensus pattern (28 bp):
TTGTTATACGTAATGTTAAAAAATATAA
Found at i:4033078 original size:27 final size:27
Alignment explanation
Indices: 4033040--4033094 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
4033030 TTATAAAGTT
* *
4033040 GTATCTTTCTAATTCTAGGACGCTGAG
1 GTATCATTCTAATTCTAGAACGCTGAG
*
4033067 GTATCATTCTAATTCTAGAATGCTGAG
1 GTATCATTCTAATTCTAGAACGCTGAG
4033094 G
1 G
4033095 ATGCTAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.36
Consensus pattern (27 bp):
GTATCATTCTAATTCTAGAACGCTGAG
Found at i:4034041 original size:2 final size:2
Alignment explanation
Indices: 4034034--4034058 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4034024 TTGTATGTTT
4034034 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
4034059 ATGCATGTAA
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:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4037510 original size:6 final size:6
Alignment explanation
Indices: 4037490--4037528 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
4037480 GTGATGTCCC
* *
4037490 AAACTA AAACTTA AAACTA AAACTA AAACCA AAGCTA AA
1 AAACTA AAAC-TA AAACTA AAACTA AAACTA AAACTA AA
4037529 TATTTAGAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.64, C:0.18, G:0.03, T:0.15
Consensus pattern (6 bp):
AAACTA
Found at i:4049218 original size:17 final size:17
Alignment explanation
Indices: 4049179--4049220 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
4049169 GTGGATAGAT
4049179 TAAATTTTAATCTTACTC
1 TAAA-TTTAATCTTACTC
4049197 T-AATTTAATC-TACATC
1 TAAATTTAATCTTAC-TC
4049213 TAAATTTA
1 TAAATTTA
4049221 GATATACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 10 0.45
17 8 0.36
18 1 0.05
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATTTAATCTTACTC
Found at i:4053475 original size:28 final size:27
Alignment explanation
Indices: 4053442--4053512 Score: 106
Period size: 28 Copynumber: 2.6 Consensus size: 27
4053432 TCTAGTCTAG
4053442 TGGGTTAAAATTATCAATCAATTTTAGA
1 TGGGTTAAAATTATC-ATCAATTTTAGA
**
4053470 TGGGTTAAAATTATTCATCAATTTTTTA
1 TGGGTTAAAATTA-TCATCAATTTTAGA
4053498 TGGGTTAAAATTATC
1 TGGGTTAAAATTATC
4053513 TACCCACTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.05
28 36 0.90
29 2 0.05
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (27 bp):
TGGGTTAAAATTATCATCAATTTTAGA
Found at i:4054259 original size:8 final size:7
Alignment explanation
Indices: 4054233--4054257 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4054223 CTATATTTTT
4054233 AAAATAA
1 AAAATAA
4054240 AAAATAA
1 AAAATAA
4054247 AAAATAA
1 AAAATAA
4054254 AAAA
1 AAAA
4054258 ATCATTTTGT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:4054796 original size:3 final size:3
Alignment explanation
Indices: 4054790--4054815 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4054780 TAATAATATA
4054790 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
4054816 CTTTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4059132 original size:13 final size:13
Alignment explanation
Indices: 4059114--4059139 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4059104 TAAGGAGCAG
4059114 GTTTGAATCCCCT
1 GTTTGAATCCCCT
4059127 GTTTGAATCCCCT
1 GTTTGAATCCCCT
4059140 TTCCCCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.38
Consensus pattern (13 bp):
GTTTGAATCCCCT
Found at i:4071900 original size:58 final size:58
Alignment explanation
Indices: 4071804--4071922 Score: 186
Period size: 58 Copynumber: 2.1 Consensus size: 58
4071794 GCTTACTACT
*
4071804 CTCTAATCAAGCTACAAAGTGGCCAATCCCCTTACAGGTGAACAACTGCAAAAGTGTG
1 CTCTAATCAAGCTAAAAAGTGGCCAATCCCCTTACAGGTGAACAACTGCAAAAGTGTG
* * *
4071862 CTCTAATCAAGCTAAAAAGTGGCCCATCTCC-TAGCAGGTGAACAACTGCAGAAGTGTG
1 CTCTAATCAAGCTAAAAAGTGGCCAATCCCCTTA-CAGGTGAACAACTGCAAAAGTGTG
4071920 CTC
1 CTC
4071923 AAAAAGTATA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
57 2 0.04
58 54 0.96
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (58 bp):
CTCTAATCAAGCTAAAAAGTGGCCAATCCCCTTACAGGTGAACAACTGCAAAAGTGTG
Found at i:4081273 original size:35 final size:36
Alignment explanation
Indices: 4081229--4081303 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 36
4081219 TGGTGTCAGA
*
4081229 TTACGTTATC-ATGTTTAAAAA-AAAATCAGTCAGTT
1 TTACCTTATCGAT-TTTAAAAAGAAAATCAGTCAGTT
*
4081264 TTACCTTATCGTATTTTAAAAAGAAAATCTGTCAGTT
1 TTACCTTATCG-ATTTTAAAAAGAAAATCAGTCAGTT
4081301 TTA
1 TTA
4081304 TATTTAGCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 9 0.26
36 8 0.23
37 18 0.51
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (36 bp):
TTACCTTATCGATTTTAAAAAGAAAATCAGTCAGTT
Found at i:4083226 original size:42 final size:42
Alignment explanation
Indices: 4083180--4083289 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 42
4083170 TTTGATATAC
4083180 TTATGACCCATGCCATTAGAGTTAATTGT-GGTTTCGATATGA
1 TTATGACCCATGCCA-TAGAGTTAATTGTAGGTTTCGATATGA
* * * * * *
4083222 TTATGACCCATGCTACTGGGGTTAATTGTAGTTTTTGTTATGA
1 TTATGACCCATGCCA-TAGAGTTAATTGTAGGTTTCGATATGA
* *
4083265 TTATGACCTATGTCATAGAGGTTAA
1 TTATGACCCATGCCATAGA-GTTAA
4083290 GTATGGTCAT
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
42 27 0.50
43 27 0.50
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (42 bp):
TTATGACCCATGCCATAGAGTTAATTGTAGGTTTCGATATGA
Found at i:4083288 original size:43 final size:41
Alignment explanation
Indices: 4083180--4083289 Score: 107
Period size: 43 Copynumber: 2.6 Consensus size: 41
4083170 TTTGATATAC
4083180 TTATGACCCATGCCATTAGA-GTTAATTGTGGTTTCGATATGA
1 TTATGACCCATG-CA-TAGAGGTTAATTGTGGTTTCGATATGA
* * * *
4083222 TTATGACCCATGC-TACTGGGGTTAATTGTAGTTTTTGTTATGA
1 TTATGACCCATGCATA--GAGGTTAATTGT-GGTTTCGATATGA
*
4083265 TTATGACCTATGTCATAGAGGTTAA
1 TTATGACCCATG-CATAGAGGTTAA
4083290 GTATGGTCAT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
39 2 0.04
41 2 0.04
42 21 0.38
43 28 0.50
44 1 0.02
45 2 0.04
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (41 bp):
TTATGACCCATGCATAGAGGTTAATTGTGGTTTCGATATGA
Found at i:4084473 original size:31 final size:32
Alignment explanation
Indices: 4084419--4084480 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
4084409 TGAAGCTAAG
* * *
4084419 ATTTTAGGTTTTAGAGGACGAAAAT-AAAAAC
1 ATTTTAGATTTGAAAGGACGAAAATGAAAAAC
*
4084450 ATTTTAGATTTGAAAGGATGAAAATGAAAAA
1 ATTTTAGATTTGAAAGGACGAAAATGAAAAA
4084481 ATTAAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.29
Consensus pattern (32 bp):
ATTTTAGATTTGAAAGGACGAAAATGAAAAAC
Done.