Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold144
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: 3311329
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
File 16 of 21
Found at i:2318803 original size:28 final size:29
Alignment explanation
Indices: 2318732--2318804 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 29
2318722 TACTATAAAT
* *
2318732 ATAAAATATCTTAAATATAATTATGATATC
1 ATAAAAT-TATTAAATATAATAATGATATC
2318762 ATAAAA-TATATAAATATAA-AATG-TATAC
1 ATAAAATTAT-TAAATATAATAATGATAT-C
2318790 ATAAAATTATTAAAT
1 ATAAAATTATTAAAT
2318805 TTATTATAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 3 0.08
28 17 0.45
29 12 0.32
30 6 0.16
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (29 bp):
ATAAAATTATTAAATATAATAATGATATC
Found at i:2319692 original size:22 final size:22
Alignment explanation
Indices: 2319649--2319700 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2319639 TCAAAAATTA
* * *
2319649 TAATTTAA-AAAATTATTTTTT
1 TAATTTAATAAAAATAATATTT
2319670 TAATTTAATAAAAATAATATTT
1 TAATTTAATAAAAATAATATTT
*
2319692 TAAATTAAT
1 TAATTTAAT
2319701 TTTTTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATTTAATAAAAATAATATTT
Found at i:2319692 original size:23 final size:21
Alignment explanation
Indices: 2319649--2319697 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
2319639 TCAAAAATTA
* *
2319649 TAATTTAAAAAATTATTTTTT
1 TAATTTAAAAAATAATATTTT
2319670 TAATTTAATAAAAATAATATTTT
1 TAATTT-A-AAAAATAATATTTT
*
2319693 AAATT
1 TAATT
2319698 AATTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 6 0.26
22 1 0.04
23 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATTTAAAAAATAATATTTT
Found at i:2319697 original size:35 final size:36
Alignment explanation
Indices: 2319658--2319735 Score: 99
Period size: 35 Copynumber: 2.2 Consensus size: 36
2319648 ATAATTTAAA
* **
2319658 AAATTATTTTTTTAATTTAAT-AA-AAATAATATTTT
1 AAATTAATTTTTTAAAATAATAAATAAATAAT-TTTT
2319693 AAATTAATTTTTTAAAATAATAAATAAATAATTTTT
1 AAATTAATTTTTTAAAATAATAAATAAATAATTTTT
2319729 -AATTAAT
1 AAATTAAT
2319736 GCTTATAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 25 0.66
36 6 0.16
37 7 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (36 bp):
AAATTAATTTTTTAAAATAATAAATAAATAATTTTT
Found at i:2319705 original size:13 final size:13
Alignment explanation
Indices: 2319680--2319714 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2319670 TAATTTAATA
2319680 AAAATAATATTTT
1 AAAATAATATTTT
* *
2319693 AAATTAATTTTTT
1 AAAATAATATTTT
2319706 AAAATAATA
1 AAAATAATA
2319715 AATAAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATAATATTTT
Found at i:2321428 original size:21 final size:22
Alignment explanation
Indices: 2321404--2321453 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
2321394 TATTTAATCT
*
2321404 TATTTATTATGTAT-TTAAAAA
1 TATTTATTATATATATTAAAAA
2321425 TATTT-TTATATATAAATTAAAAA
1 TATTTATTATATAT--ATTAAAAA
2321448 TATTTA
1 TATTTA
2321454 AAATTTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.29
21 5 0.21
23 12 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTTATTATATATATTAAAAA
Found at i:2324548 original size:2 final size:2
Alignment explanation
Indices: 2324543--2324576 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2324533 CCCCCCCCCC
*
2324543 CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2324577 GAAAGCCTTC
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:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:2327975 original size:19 final size:19
Alignment explanation
Indices: 2327948--2327985 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2327938 GTCCTTTGGG
2327948 CCCAACCCTCCAGGCTAAA
1 CCCAACCCTCCAGGCTAAA
* *
2327967 CCCACCCCTCCATGCTAAA
1 CCCAACCCTCCAGGCTAAA
2327986 TCTCGGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.50, G:0.08, T:0.13
Consensus pattern (19 bp):
CCCAACCCTCCAGGCTAAA
Found at i:2328878 original size:3 final size:3
Alignment explanation
Indices: 2328872--2328910 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2328862 GGAGGAATAT
*
2328872 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2328911 ATGGGGAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:2331959 original size:22 final size:22
Alignment explanation
Indices: 2331926--2331967 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2331916 ACTATTTTTT
2331926 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
*
2331948 TAAATATT-ATTATGAAAATA
1 TAAAT-TTAATTATAAAAATA
2331968 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:2332692 original size:17 final size:17
Alignment explanation
Indices: 2332672--2332717 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
2332662 TTTACTAATT
2332672 AAATAATTTTATTTAAA
1 AAATAATTTTATTTAAA
*
2332689 AAATATACTTTTATTTTAA
1 AAATA-A-TTTTATTTAAA
*
2332708 AAATAGTTTT
1 AAATAATTTT
2332718 TGTTGCCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 9 0.36
18 1 0.04
19 15 0.60
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
AAATAATTTTATTTAAA
Found at i:2335427 original size:12 final size:13
Alignment explanation
Indices: 2335376--2335432 Score: 59
Period size: 12 Copynumber: 4.6 Consensus size: 13
2335366 AAATTTTTTA
2335376 TTTAAAT-TTAAT
1 TTTAAATATTAAT
*
2335388 TATAAATATTAA-
1 TTTAAATATTAAT
*
2335400 TATAAA-ATTAATT
1 TTTAAATATTAA-T
2335413 TTTAAATATT-AT
1 TTTAAATATTAAT
2335425 TTTAAATA
1 TTTAAATA
2335433 GTAAAATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 5 0.13
12 21 0.54
13 10 0.26
14 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTAAATATTAAT
Found at i:2335430 original size:25 final size:24
Alignment explanation
Indices: 2335375--2335430 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
2335365 AAAATTTTTT
*
2335375 ATTTAAATTTAATTATAAATATTA
1 ATTTAAAATTAATTATAAATATTA
* *
2335399 ATATAAAATTAATTTTTAAATATTA
1 ATTTAAAATTAA-TTATAAATATTA
*
2335424 TTTTAAA
1 ATTTAAA
2335431 TAGTAAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTTAAAATTAATTATAAATATTA
Found at i:2335768 original size:22 final size:21
Alignment explanation
Indices: 2335713--2335777 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 21
2335703 TTGAATTATT
* *
2335713 ATTTAATAAAAAAATTTATTTAA
1 ATTTAATATAAAAA--TATATAA
2335736 ATTTAATTATAAAAATATATAA
1 ATTTAA-TATAAAAATATATAA
2335758 ATATTAATATAAAAATATAT
1 AT-TTAATATAAAAATATAT
2335778 TTTTTAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 21 0.55
23 10 0.26
24 7 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTAATATAAAAATATATAA
Found at i:2337017 original size:2 final size:2
Alignment explanation
Indices: 2337010--2337051 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2337000 AACCACTTTA
2337010 AT AT AT AT AT 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 AT AT AT AT AT
2337052 TTGTTTTGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2337398 original size:2 final size:2
Alignment explanation
Indices: 2337391--2337420 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2337381 TTTGTTTCAT
2337391 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2337421 AATTAGTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2340190 original size:30 final size:29
Alignment explanation
Indices: 2340154--2340248 Score: 100
Period size: 30 Copynumber: 3.2 Consensus size: 29
2340144 TTATTACTAA
* * *
2340154 TAAATAAGTCTTTAATTTTTAATTTGTACC
1 TAAATAA-ACTTTAATTTTTAATTTATATC
* *
2340184 TAAATAAACTTTTAATCTTAAATTTATATC
1 TAAATAAAC-TTTAATTTTTAATTTATATC
* *
2340214 TAAATAAACTCTTAAGTTTTAATTTTTATC
1 TAAATAAACT-TTAATTTTTAATTTATATC
2340244 TAAAT
1 TAAAT
2340249 TATTTTTTAT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 2 0.04
30 52 0.96
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.48
Consensus pattern (29 bp):
TAAATAAACTTTAATTTTTAATTTATATC
Found at i:2349170 original size:55 final size:53
Alignment explanation
Indices: 2349065--2349494 Score: 398
Period size: 55 Copynumber: 7.8 Consensus size: 53
2349055 TAGTACTGTG
* * * *
2349065 ACCTTTTCAAAGTCCACAATTCAGTGGCATTTCTTTTCGAAGTCCTCAACTCCGTGGC
1 ACCTTTT--AAGTCCACAACTCCGTGGCA-TCCTTTT--AAGTCCACAACTCCGTGGC
* *
2349123 ATCCTTTTAAGTCCACAACTCCATGGTATCCTTTTAAAGTCCACAACTCCGTGGC
1 A-CCTTTTAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGC
* * * * * * *
2349178 ACCCTTTTAAAATCCATAACTTCGTGGCATCATTTTAAGTCTATAACTCCATGGC
1 A-CCTTTT-AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGC
* * *
2349233 ACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACCACTCCGTGGC
1 A-CCTTTTAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGC
* * * *
2349288 ACCTTTTTAAGTTCACAACT-C-T-GTATCTTTTTAAGTCCACAACTTCGTGGC
1 ACC-TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGC
* * *
2349339 AGCCTTTTAAGTCCACAACTCTGTGGCATCCGTTTCAAGTCCACAACTCTGTGGC
1 A-CCTTTTAAGTCCACAACTCCGTGGCATCC-TTTTAAGTCCACAACTCCGTGGC
* * * * *
2349394 GCATTTTTAAAGTCCACAACTCCCTGGCACCCTTTTAAGTCCACAACTTCGTGGC
1 AC-CTTTT-AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGC
** *
2349449 ACTCTTTTAAGTCCACAACTTTGTGGCATCCTTTTTAAGCCCACAA
1 AC-CTTTTAAGTCCACAACTCCGTGGCATCC-TTTTAAGTCCACAA
2349495 GTCAGTGGTA
Statistics
Matches: 303, Mismatches: 57, Indels: 27
0.78 0.15 0.07
Matches are distributed among these distances:
51 33 0.11
52 9 0.03
53 2 0.01
54 49 0.16
55 140 0.46
56 47 0.16
57 16 0.05
58 1 0.00
59 6 0.02
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (53 bp):
ACCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGC
Found at i:2349171 original size:28 final size:27
Alignment explanation
Indices: 2349074--2349494 Score: 388
Period size: 27 Copynumber: 15.4 Consensus size: 27
2349064 GACCTTTTCA
* * *
2349074 AAGTCCACAATTCAGTGGCATTTCTTTT
1 AAGTCCACAACTCCGTGGCA-TCCTTTT
*
2349102 CGAAGTCCTCAACTCCGTGGCATCCTTTT
1 --AAGTCCACAACTCCGTGGCATCCTTTT
* *
2349131 AAGTCCACAACTCCATGGTATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
2349158 AAAGTCCACAACTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* * * *
2349186 AAAATCCATAACTTCGTGGCATCATTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* * * * *
2349214 AAGTCTATAACTCCATGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
2349241 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
2349268 AAAGTCCACCACTCCGTGGCA-CCTTTTT
1 -AAGTCCACAACTCCGTGGCATCC-TTTT
* * *
2349296 AAGTTCACAACT-C-T-GTATCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
2349320 AAGTCCACAACTTCGTGGCAGCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
2349347 AAGTCCACAACTCTGTGGCATCCGTTTC
1 AAGTCCACAACTCCGTGGCATCC-TTTT
*
2349375 AAGTCCACAACTCTGTGGCGCAT--TTTT
1 AAGTCCACAACTCCGT-G-GCATCCTTTT
* *
2349402 AAAGTCCACAACTCCCTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
*
2349430 AAGTCCACAACTTCGTGGCA-CTCTTTT
1 AAGTCCACAACTCCGTGGCATC-CTTTT
**
2349457 AAGTCCACAACTTTGTGGCATCCTTTTT
1 AAGTCCACAACTCCGTGGCATCC-TTTT
*
2349485 AAGCCCACAA
1 AAGTCCACAA
2349495 GTCAGTGGTA
Statistics
Matches: 328, Mismatches: 47, Indels: 34
0.80 0.11 0.08
Matches are distributed among these distances:
24 17 0.05
25 3 0.01
26 6 0.02
27 153 0.47
28 121 0.37
29 7 0.02
30 21 0.06
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.31
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCATCCTTTT
Found at i:2349502 original size:28 final size:28
Alignment explanation
Indices: 2349066--2350367 Score: 618
Period size: 28 Copynumber: 45.6 Consensus size: 28
2349056 AGTACTGTGA
* *
2349066 CCTTTTCAAAGTCCACAATTCAGTGGCATT
1 CCTTTT-AAAGCCCACAAGTCAGTGGCA-T
* * * * * *
2349096 TCTTTTCGAAGTCCTCAACTCCGTGGCAT
1 CCTTTT-AAAGCCCACAAGTCAGTGGCAT
* * *
2349125 CCTTTT-AAGTCCACAACTCCA-TGGTAT
1 CCTTTTAAAGCCCACAAGT-CAGTGGCAT
* * * *
2349152 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
** * *
2349180 CCTTTTAAAATCCATAACTTC-GTGGCAT
1 CCTTTTAAAGCCCACAA-GTCAGTGGCAT
* * * * *
2349208 CATTTT-AAGTCTATAACTCCA-TGGCA-
1 CCTTTTAAAGCCCACAAGT-CAGTGGCAT
* * * * *
2349234 CCCTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
* * * *
2349262 CCTTTTAAAGTCCACCACTCCGTGGCA-
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
* ** * *
2349289 CCTTTTTAAGTTCACAACTC--T-GTAT
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
* * * *
2349314 -CTTTTTAAGTCCACAACTTC-GTGGCAG
1 CCTTTTAAAGCCCACAA-GTCAGTGGCAT
* * *
2349341 CCTTTT-AAGTCCACAACTCTGTGGCAT
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
* * * * *
2349368 CCGTTTCAAGTCCACAACTCTGTGGCGCAT
1 CCTTTTAAAGCCCACAAGTCAGT-G-GCAT
* * ** *
2349398 --TTTTAAAGTCCACAACTCCCTGGCAC
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
* *
2349424 CCTTTT-AAGTCCACAACTTC-GTGGCA-
1 CCTTTTAAAGCCCACAA-GTCAGTGGCAT
* * **
2349450 CTCTTTT-AAGTCCACAACTTTGTGGCAT
1 C-CTTTTAAAGCCCACAAGTCAGTGGCAT
* * *
2349478 CCTTTTTAAGCCCACAAGTCAGTGGTAC
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
** * * * * *
2349506 CCTTCCAAAGTCTACAACTCAGTGACACC
1 CCTTTTAAAGCCCACAAGTCAGTGGCA-T
* *
2349535 CCTTTTTAAGCTCACAAGTCAGTGGCAT
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
** * **
2349563 TATTTCAAAGCCCACACAAGTTGGTGGCAACT
1 CCTTTTAAAG-CC-CACAAGTCAGTGGC-A-T
* * *
2349595 CATTTGAAAGCCCACACAAGTCAGTGGCAAC
1 CCTTTTAAAG-CC-CACAAGTCAGTGGC-AT
* * * *
2349626 CCATTTCACAGCCCACACAAGTCAGTGGTAAC
1 CC-TTTTAAAG-CC-CACAAGTCAGTGG-CAT
*
2349658 CCATTTCAAAGCCCACAAGTCAGTGGCAT
1 CC-TTTTAAAGCCCACAAGTCAGTGGCAT
* * * *
2349687 CATTTCAAAGCCCACACAAGTCGGTGGCAA
1 CCTTTTAAAG-CC-CACAAGTCAGTGGCAT
* * ** *
2349717 CTTATTTGAAAGGCCATACAAGTTGGTGGCAA
1 CCT-TTT-AAA-GCC-CACAAGTCAGTGGCAT
* ** *
2349749 CCTATTTCAAAGCCTATACAAGTTGGTGGCAAC
1 CCT-TTT-AAAGCC--CACAAGTCAGTGGC-AT
* *
2349782 CCATTTTAAAGCCCACACAAGTCGGTGGCAAC
1 CC-TTTTAAAG-CC-CACAAGTCAGTGGC-AT
* * * *
2349814 CCATTTCAAAGCTCACAAATCAGTGGCAC
1 CC-TTTTAAAGCCCACAAGTCAGTGGCAT
* *
2349843 CCTTTCAAAGCCCATAAGTCAGTGGCAT
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
2349871 CCTTTTCAAAGCCCACAAGTCAGTGGCAT
1 CCTTTT-AAAGCCCACAAGTCAGTGGCAT
* * *
2349900 CCTTTCAAAGTCCACAAGTCGGTGGCAT
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
* * *
2349928 CATTTTCAAAGCCCACAAGTCGGTGGTAT
1 CCTTTT-AAAGCCCACAAGTCAGTGGCAT
* *
2349957 -CTTTTCAAAGCCCACAAATCAGTGGCAC
1 CCTTTT-AAAGCCCACAAGTCAGTGGCAT
*
2349985 CCTTTCAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
* * *
2350013 TCTTTCAAAGTCCACAAGTCAGTGGCAT
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
*
2350041 CCTTTTCAAAGCCCACAAGTCGGTGGCAT
1 CCTTTT-AAAGCCCACAAGTCAGTGGCAT
* * *
2350070 -CTTTTCAAAACCCATAAGTTAGTGGCAT
1 CCTTTT-AAAGCCCACAAGTCAGTGGCAT
* ** * * *
2350098 -CTTTTCCAAGCTAAAAAATCAGTGGCAC
1 CCTTTT-AAAGCCCACAAGTCAGTGGCAT
* *
2350126 CCTTTCAAAGCCCACAAGTTAGTGGCAT
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
* *
2350154 CCTTTTAAAGTCCACAAGTCAATGGCAT
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
* *
2350182 CATTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTT-AAAGCCCACAAGTCAGTGGCAT
* * *
2350211 CCTTTCAAAGCCCATAAGTCAGTGGTAT
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
* * *
2350239 CCTTTCAAAGTCCAAAAGTCAGTGGCAT
1 CCTTTTAAAGCCCACAAGTCAGTGGCAT
* * * *
2350267 CCTTTTCCAAGCCCACAAGTCGGTAGTAT
1 CCTTTT-AAAGCCCACAAGTCAGTGGCAT
** *
2350296 -CTTTTCAAAGCTTACAAGTCAGAGGCAT
1 CCTTTT-AAAGCCCACAAGTCAGTGGCAT
* ** *
2350324 -CTTCTCAAAATCCACAAGTTAGTGGCAT
1 CCTT-TTAAAGCCCACAAGTCAGTGGCAT
2350352 CCTTTTAAAGCCCACA
1 CCTTTTAAAGCCCACA
2350368 CAAGTCGGTG
Statistics
Matches: 1030, Mismatches: 192, Indels: 102
0.78 0.15 0.08
Matches are distributed among these distances:
24 17 0.02
25 3 0.00
26 14 0.01
27 134 0.13
28 471 0.46
29 155 0.15
30 80 0.08
31 10 0.01
32 136 0.13
33 9 0.01
34 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (28 bp):
CCTTTTAAAGCCCACAAGTCAGTGGCAT
Found at i:2349535 original size:110 final size:111
Alignment explanation
Indices: 2349104--2349540 Score: 298
Period size: 110 Copynumber: 4.0 Consensus size: 111
2349094 TTTCTTTTCG
* * * ** * * * *
2349104 AAGTCCTCAACTCCGTGGCATCCTTTTAAGTCCACAACTCCATGGTATCCTTTTAAAGTCCACAA
1 AAGTCCACAACTTCGTGGCAGCCTTTTAAGTCCACAACTCTGTGGCATCCGTTTCAAGCCCACAA
* * ** * * * * * *
2349169 CTCCGTGGCACCCTTTTAAAATCCATAACTTC-GTGGCA-TCATTTT
66 CTCAGTGGCACACTTCCAAAGTCCACAAC-TCACTGACACCCCTTTT
* * * * * * * * * * * *
2349214 AAGTCTATAACTCCATGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACCA
1 AAGTCCACAACTTCGTGGCAGCCTTTTAAGTCCACAACTCTGTGGCATCCGTTTCAAGCCCACAA
* *** * * * *
2349279 CTCCGTGGCAC-CTTTTTAAGTTCACAACT--CTG-TA-TCTTTTT
66 CTCAGTGGCACACTTCCAAAGTCCACAACTCACTGACACCCCTTTT
*
2349320 AAGTCCACAACTTCGTGGCAGCCTTTTAAGTCCACAACTCTGTGGCATCCGTTTCAAGTCCACAA
1 AAGTCCACAACTTCGTGGCAGCCTTTTAAGTCCACAACTCTGTGGCATCCGTTTCAAGCCCACAA
* * * ** * *
2349385 CTCTGTGGCGCATTTTTAAAGTCCACAACTCCCTGGCA-CCCTTTT
66 CTCAGTGGCACACTTCCAAAGTCCACAACTCACTGACACCCCTTTT
* * *
2349430 AAGTCCACAACTTCGTGGCA-CTCTTTTAAGTCCACAACTTTGTGGCATCCTTTTTAAGCCCACA
1 AAGTCCACAACTTCGTGGCAGC-CTTTTAAGTCCACAACTCTGTGGCATCCGTTTCAAGCCCACA
* * * * *
2349494 AGTCAGTGGTACCCTTCCAAAGTCTACAACTCAGTGACACCCCTTTT
65 ACTCAGTGGCACACTTCCAAAGTCCACAACTCACTGACACCCCTTTT
2349541 TAAGCTCACA
Statistics
Matches: 269, Mismatches: 52, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
106 70 0.26
107 17 0.06
108 1 0.00
109 17 0.06
110 157 0.58
111 7 0.03
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (111 bp):
AAGTCCACAACTTCGTGGCAGCCTTTTAAGTCCACAACTCTGTGGCATCCGTTTCAAGCCCACAA
CTCAGTGGCACACTTCCAAAGTCCACAACTCACTGACACCCCTTTT
Found at i:2349610 original size:32 final size:32
Alignment explanation
Indices: 2349564--2350068 Score: 380
Period size: 32 Copynumber: 16.9 Consensus size: 32
2349554 CAGTGGCATT
* *
2349564 ATTTCAAAGCCCACACAAGTTGGTGGCAACTC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
* *
2349596 ATTTGAAAGCCCACACAAGTCAGTGGCAACCC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
* * *
2349628 ATTTCACAGCCCACACAAGTCAGTGGTAACCC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
* *
2349660 ATTTCAAAG-CC-CACAAGTCAGTGGC-A-TC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
**
2349688 ATTTCAAAGCCCACACAAGTCGGTGGCAACTT
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
* * * * *
2349720 ATTTGAAAGGCCATACAAGTTGGTGGCAACCT
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
* * *
2349752 ATTTCAAAGCCTATACAAGTTGGTGGCAACCC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
*
2349784 ATTTTAAAGCCCACACAAGTCGGTGGCAACCC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
* *
2349816 ATTTCAAAGCTCACA-AA-TCAGTGGC-ACCC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
* * *
2349845 -TTTCAAAG-CC-CATAAGTCAGTGGC-ATCC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
* * *
2349873 TTTTCAAAG-CC-CACAAGTCAGTGGC-ATCC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
* *
2349902 -TTTCAAAG-TC-CACAAGTCGGTGGC-A-TC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
* *
2349929 ATTTTCAAAG-CC-CACAAGTCGGTGG-TA-TC
1 A-TTTCAAAGCCCACACAAGTCGGTGGCAACCC
* *
2349958 TTTTCAAAGCCCACA-AA-TCAGTGGC-ACCC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
* **
2349987 -TTTCAAAG-CC-CACAAGTCAGTGGC-ATTC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
* * *
2350015 -TTTCAAAG-TC-CACAAGTCAGTGGC-ATCC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
*
2350043 TTTTCAAAG-CC-CACAAGTCGGTGGCA
1 ATTTCAAAGCCCACACAAGTCGGTGGCA
2350069 TCTTTTCAAA
Statistics
Matches: 411, Mismatches: 44, Indels: 38
0.83 0.09 0.08
Matches are distributed among these distances:
26 4 0.01
27 8 0.02
28 111 0.27
29 86 0.21
30 35 0.09
31 5 0.01
32 162 0.39
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.23
Consensus pattern (32 bp):
ATTTCAAAGCCCACACAAGTCGGTGGCAACCC
Found at i:2349743 original size:156 final size:154
Alignment explanation
Indices: 2349547--2350283 Score: 534
Period size: 141 Copynumber: 5.0 Consensus size: 154
2349537 TTTTTAAGCT
*
2349547 CACAAGTCAGTGGCATTATTTCAAAGCCCACACAAGTTGGTGGCAA-CTCATTTGAAAGCCCACA
1 CACAAGTCAGTGGCATTATTTCAAAGCCCACACAAGTTGGTGGCAACCT-ATTTCAAAGCCCACA
* *
2349611 CAAGTCAGTGGCAACCCATTTCACAGCCCACACAAGTCAGTGGTAACCCATTTCAAAGCCCACAA
65 CAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACAA
* *
2349676 GTCAGTGGCATCATTTCAAAGCCCA
130 ATCAGTGGCACCATTTCAAAGCCCA
* * * * * *
2349701 CACAAGTCGGTGGCAACTTATTTGAAAGGCCATACAAGTTGGTGGCAACCTATTTCAAAGCCTAT
1 CACAAGTCAGTGGC-A-TTATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCAC
** * * *
2349766 ACAAGTTGGTGGCAACCCATTTTAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCTCACA
64 ACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACA
*
2349831 AATCAGTGGCACCCTTTCAAAG-CC-
129 AATCAGTGGCACCATTTCAAAGCCCA
* ** * *
2349855 CATAAGTCAGTGGCATCCT-TTTCAAAG-CC-CACAAGTCAGTGGCATCC--TTTCAAAG-TC-C
1 CACAAGTCAGTGGCAT--TATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCAC
* * * * * *
2349913 ACAAGTCGGTGGC-A-TCATTTTCAAAG-CC-CACAAGTCGGTGG-TA-TCTTTTCAAAGCCCAC
64 ACAAGTCAGTGGCAACCCA-TTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCAC
*
2349972 AAATCAGTGGCACCCTTTCAAAG-CC-
128 AAATCAGTGGCACCATTTCAAAGCCCA
* * ** *
2349997 CACAAGTCAGTGGCATTCTTTCAAAG-TC-CACAAGTCAGTGGCATCCT-TTTCAAAG-CC-CAC
1 CACAAGTCAGTGGCATTATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACAC
* * * * * * * * * ** *
2350057 AAGTCGGTGGC-A-TCTTTTCAAA-ACC-CATAAGTTAGTGGC-A-TCTTTTCCAAGCTAAAAAA
66 AAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACAAA
*
2350116 TCAGTGGCACCCTTTCAAAG-CC-
131 TCAGTGGCACCATTTCAAAGCCCA
* ** * * *** * *
2350138 CACAAGTTAGTGGCATCCTTTTAAAG-TC-CACAAGTCAATGGCATCAT-TTTCAAAG-CC-CAC
1 CACAAGTCAGTGGCATTATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACAC
* * * *
2350198 AAGTCAGTGGC-ACCC-TTTCAAAG-CC-CATAAGTCAGTGG-TATCC-TTTCAAAGTCCA-AAA
66 AAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACAAA
* *
2350256 GTCAGTGGCATCCTTTTCCAAGCCCA
131 -TCAGTGGCA-CCATTTCAAAGCCCA
2350282 CA
1 CA
2350284 AGTCGGTAGT
Statistics
Matches: 505, Mismatches: 60, Indels: 46
0.83 0.10 0.08
Matches are distributed among these distances:
140 4 0.01
141 189 0.37
142 90 0.18
143 3 0.01
144 15 0.03
145 4 0.01
146 8 0.02
147 12 0.02
149 8 0.02
151 14 0.03
152 3 0.01
153 8 0.02
154 26 0.05
155 3 0.01
156 116 0.23
157 2 0.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (154 bp):
CACAAGTCAGTGGCATTATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACAC
AAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACAAA
TCAGTGGCACCATTTCAAAGCCCA
Found at i:2349888 original size:57 final size:57
Alignment explanation
Indices: 2349471--2350367 Score: 669
Period size: 57 Copynumber: 15.4 Consensus size: 57
2349461 CCACAACTTT
* ** * * * * * *
2349471 GTGGCATCCTTTTTAAGCCCACAAGTCAGTGGTA-CCCTTCCAAAGTCTACAACTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCA
* ** * **
2349527 GTGACACCCCTTTTTAAGCTCACAAGTCAGTGGCAT--TATTTCAAAGCCCACACAAGTTG
1 GTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCATCCT-TTTCAAAG-CC-CACAAGTCA
* * * * *
2349586 GTGGCAACTCATTTGAAAGCCCACACAAGTCAGTGGCAACCCATTTCACAGCCCACACAAGTCA
1 GTGGC-AC-CCTTTCAAAG-CC-CACAAGTCAGTGGC-ATCCTTTTCAAAG-CC-CACAAGTCA
* * *
2349650 GTGGTAACCCATTTCAAAGCCCACAAGTCAGTGGCAT-CATTTCAAAGCCCACACAAGTCG
1 GTGG-CACCC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAG-CC-CACAAGTCA
** * * ** * * **
2349710 GTGGCAACTTATTTGAAAGGCCATACAAGTTGGTGGCAACCTATTTCAAAGCCTATACAAGTTG
1 GTGGC-AC-CCTTTCAAA-GCC-CACAAGTCAGTGGCATCCT-TTTCAAAGCC--CACAAGTCA
* * * * * *
2349774 GTGGCAACCCATTTTAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCTCACAAATCA
1 GTGGC-ACCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ATCCTTTTCAAAGCCCACAAGTCA
*
2349836 GTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCA
* * * * *
2349893 GTGGCATCCTTTCAAAGTCCACAAGTCGGTGGCATCATTTTCAAAGCCCACAAGTCG
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCA
* * * * *
2349950 GTGGTATCTTTTCAAAGCCCACAAATCAGTGGCA-CCCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCA
** * *
2350006 GTGGCATTCTTTCAAAGTCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCG
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCA
* * * * * * ** * *
2350063 GTGGCATCTTTTCAAAACCCATAAGTTAGTGGCAT-CTTTTCCAAGCTAAAAAATCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCA
* *
2350119 GTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTT-AAAGTCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCA
* ** * *
2350175 ATGGCATCATTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCATAAGTCA
1 GTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCA
* * * * * *
2350232 GTGGTATCCTTTCAAAGTCCAAAAGTCAGTGGCATCCTTTTCCAAGCCCACAAGTCG
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCA
* * * * ** * * ** *
2350289 GTAGTATCTTTTCAAAGCTTACAAGTCAGAGGCAT-CTTCTCAAAATCCACAAGTTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCA
* *
2350345 GTGGCATCCTTTTAAAGCCCACA
1 GTGGCACCCTTTCAAAGCCCACA
2350368 CAAGTCGGTG
Statistics
Matches: 675, Mismatches: 137, Indels: 58
0.78 0.16 0.07
Matches are distributed among these distances:
56 173 0.26
57 274 0.41
58 13 0.02
59 12 0.02
60 48 0.07
61 9 0.01
62 50 0.07
63 8 0.01
64 85 0.13
65 3 0.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (57 bp):
GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCA
Found at i:2349925 original size:85 final size:85
Alignment explanation
Indices: 2349334--2350367 Score: 628
Period size: 85 Copynumber: 11.9 Consensus size: 85
2349324 CCACAACTTC
* * * * * * *
2349334 GTGGCAGCCTTTT--AAGTCCACAACTCTGTGGCATCCGTTTC-AAGTCCACAACTCTGTGGCGC
1 GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGTCCACAAGTCAGTGGCAC
** * * * *
2349396 ATTTTTAAAGTCCACAACTCC
65 CCTTTCAAAGCCCACAAGTCA
* * * * * * **
2349417 CTGGCACCCTTTT--AAGTCCACAACTTC-GTGGCA-CTCTTT-TAAGTCCACAACTTTGTGGCA
1 GTGGCATCCTTTTCAAAGCCCACAA-GTCAGTGGCATC-CTTTCAAAGTCCACAAGTCAGTGGCA
* **
2349477 TCCTTTTTAAGCCCACAAGTCA
64 CCCTTTCAAAGCCCACAAGTCA
* * * * * * * * **
2349499 GTGGTA-CCCTTCCAAAGTCTACAACTCAGTGACACCCCTTTTTAAG-CTCACAAGTCAGTGGCA
1 GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGTC-CACAAGTCAGTGGCA
*** **
2349562 TTATTTCAAAGCCCACACAAGTTG
64 CCCTTTCAAAG-CC-CACAAGTCA
* * * * * *
2349586 GTGGCAACTCATTTGAAAGCCCACACAAGTCAGTGGCAACCCATTTCACAGCCCACACAAGTCAG
1 GTGGCATC-CTTTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-TTTCAAAG-TC-CACAAGTCAG
*
2349651 TGGTAACCCATTTCAAAGCCCACAAGTCA
59 TGG-CACCC-TTTCAAAGCCCACAAGTCA
* * ** * * **
2349680 GTGGCAT-CATTTCAAAGCCCACACAAGTCGGTGGCAACTTATTTGAAAGGCCATACAAGTTGGT
1 GTGGCATCCTTTTCAAAG-CC-CACAAGTCAGTGGC-A-TCCTTTCAAAGTCC--ACAAGTCAGT
* * **
2349744 GGCAACCTATTTCAAAGCCTATACAAGTTG
60 GGC-ACC-CTTTCAAAGCC--CACAAGTCA
* * * *
2349774 GTGGCAACCCATTTT-AAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAG-CTCACAAATCAG
1 GTGGC-ATCC-TTTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-TTTCAAAGTC-CACAAGTCAG
*
2349837 TGGCACCCTTTCAAAGCCCATAAGTCA
59 TGGCACCCTTTCAAAGCCCACAAGTCA
*
2349864 GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGTCCACAAGTCGGTGGCATC
1 GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGGCA-C
** *
2349929 ATTTTCAAAGCCCACAAGTCG
65 CCTTTCAAAGCCCACAAGTCA
* * * * **
2349950 GTGGTAT-CTTTTCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATT
1 GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGGCACC
*
2350014 CTTTCAAAGTCCACAAGTCA
66 CTTTCAAAGCCCACAAGTCA
* * ** * * *
2350034 GTGGCATCCTTTTCAAAGCCCACAAGTCGGTGGCATCTTTTCAAAACCCATAAGTTAGTGGCATC
1 GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGGCACC
* * ** * *
2350099 TTTTCCAAGCTAAAAAATCA
66 CTTTCAAAGCCCACAAGTCA
* * * *
2350119 GTGGCA-CCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGTCCACAAGTCAATGGCATC
1 GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGGCA-C
**
2350183 ATTTTCAAAGCCCACAAGTCA
65 CCTTTCAAAGCCCACAAGTCA
* * * *
2350204 GTGGCA-CCCTTTCAAAGCCCATAAGTCAGTGGTATCCTTTCAAAGTCCAAAAGTCAGTGGCATC
1 GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGGCA-C
* * *
2350268 CTTTTCCAAGCCCACAAGTCG
65 CCTTTCAAAGCCCACAAGTCA
* * ** * * * *
2350289 GTAGTAT-CTTTTCAAAGCTTACAAGTCAGAGGCAT-CTTCTCAAAATCCACAAGTTAGTGGCAT
1 GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAGTCCACAAGTCAGTGGCAC
*
2350352 CCTTTTAAAGCCCACA
65 CCTTTCAAAGCCCACA
2350368 CAAGTCGGTG
Statistics
Matches: 758, Mismatches: 152, Indels: 81
0.76 0.15 0.08
Matches are distributed among these distances:
81 4 0.01
82 43 0.06
83 42 0.06
84 92 0.12
85 301 0.40
86 30 0.04
87 25 0.03
88 7 0.01
89 14 0.02
90 12 0.02
91 15 0.02
92 73 0.10
93 3 0.00
94 48 0.06
95 5 0.01
96 41 0.05
97 3 0.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.25
Consensus pattern (85 bp):
GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGGCACC
CTTTCAAAGCCCACAAGTCA
Found at i:2350022 original size:113 final size:113
Alignment explanation
Indices: 2349471--2350367 Score: 762
Period size: 113 Copynumber: 7.7 Consensus size: 113
2349461 CCACAACTTT
* * * * * * *
2349471 GTGGCATCCTTTT-TAAGCCCACAAGTCAGTGGTACCCTTCCAAAGTCTACAACTCAGTGACACC
1 GTGGCAT-CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-C
** * * *
2349535 CCTTTTTAAGCTCACAAGTCAGTGGCATTA-TTTCAAAGCCCACACAAGTTG
64 CCTTTCAAAGCCCACAAGTCAGTGGCATCATTTTCAAAG-CC-CACAAGTCG
* * *
2349586 GTGGCAACTCATTTGAAAGCCCACACAAGTCAGTGGCAACCCATTTCACAGCCCACACAAGTCAG
1 GTGGC-A-TCTTTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-CACAAGTCAG
*
2349651 TGGTAACCCATTTCAAAGCCCACAAGTCAGTGGCATCA-TTTCAAAGCCCACACAAGTCG
58 TGG-CACCC-TTTCAAAGCCCACAAGTCAGTGGCATCATTTTCAAAG-CC-CACAAGTCG
* * * ** * * **
2349710 GTGGCAACTTATTTGAAAGGCCATACAAGTTGGTGGCAACCTATTTCAAAGCCTATACAAGTTGG
1 GTGGCATC-T-TTTCAAA-GCC-CACAAGTCAGTGGC-ACC-CTTTCAAAGCC--CACAAGTCAG
* * * * * *
2349775 TGGCAACCCATTTTAAAGCCCACACAAGTCGGTGGCAACCCA-TTTCAAAGCTCACAAATCA
58 TGGC-ACCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCATTTTCAAAGCCCACAAGTCG
* * * * *
2349836 GTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATC
1 GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCACC
* *
2349901 CTTTCAAAGTCCACAAGTCGGTGGCATCATTTTCAAAGCCCACAAGTCG
65 CTTTCAAAGCCCACAAGTCAGTGGCATCATTTTCAAAGCCCACAAGTCG
* * **
2349950 GTGGTATCTTTTCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATTC
1 GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* *
2350015 TTTCAAAGTCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCG
66 TTTCAAAGCCCACAAGTCAGTGGCATCATTTTCAAAGCCCACAAGTCG
* * * * * * ** * *
2350063 GTGGCATCTTTTCAAAACCCATAAGTTAGTGGCATCTTTTCCAAGCTAAAAAATCAGTGGCACCC
1 GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * * *
2350128 TTTCAAAGCCCACAAGTTAGTGGCATCCTTTT-AAAGTCCACAAGTCA
66 TTTCAAAGCCCACAAGTCAGTGGCATCATTTTCAAAGCCCACAAGTCG
* * * *
2350175 ATGGCATCATTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTCAGTGGTATC
1 GTGGCATC-TTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
2350240 CTTTCAAAGTCCAAAAGTCAGTGGCATCCTTTTCCAAGCCCACAAGTCG
65 CTTTCAAAGCCCACAAGTCAGTGGCATCATTTTCAAAGCCCACAAGTCG
* * ** * * ** * *
2350289 GTAGTATCTTTTCAAAGCTTACAAGTCAGAGGCA-TCTTCTCAAAATCCACAAGTTAGTGGCATC
1 GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTT-TCAAAGCCCACAAGTCAGTGGCACC
*
2350353 CTTTTAAAGCCCACA
65 CTTTCAAAGCCCACA
2350368 CAAGTCGGTG
Statistics
Matches: 645, Mismatches: 111, Indels: 54
0.80 0.14 0.07
Matches are distributed among these distances:
112 23 0.04
113 287 0.44
114 63 0.10
115 19 0.03
116 6 0.01
117 11 0.02
118 5 0.01
119 24 0.04
120 4 0.01
121 17 0.03
122 14 0.02
123 19 0.03
124 111 0.17
125 3 0.00
126 27 0.04
127 2 0.00
128 10 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (113 bp):
GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
TTTCAAAGCCCACAAGTCAGTGGCATCATTTTCAAAGCCCACAAGTCG
Found at i:2355070 original size:64 final size:64
Alignment explanation
Indices: 2354986--2355411 Score: 304
Period size: 64 Copynumber: 6.7 Consensus size: 64
2354976 GGTCCAAATT
* * *
2354986 TTTAGAAAAAGACAATTTTGACTTTTAACTTATTTAGAAAGACATAGGTTCAAATTTTGACTTA
1 TTTAGAAAGAGATAAGTTTGACTTTTAACTTATTTAGAAAGACATAGGTTCAAATTTTGACTTA
* * ** * * * * * ****
2355050 -CTCGAAAAGAGAT-AGATTTGACTCCTAACCTATTCAAAAATATATAGGTTTGGCTTTTGACTT
1 TTTAG-AAAGAGATAAG-TTTGACTTTTAACTTATTTAGAAAGACATAGGTTCAAATTTTGACTT
*
2355113 G
64 A
* * * * *
2355114 TTTAGAATGAGAAAAGTTTGACTTCTGACTTATTTAGAAAGGCATAGGTTCAAATTTTGACTTA
1 TTTAGAAAGAGATAAGTTTGACTTTTAACTTATTTAGAAAGACATAGGTTCAAATTTTGACTTA
* * * * * * ** *
2355178 TTTAGAAAGTGATAAGTTTAACTTTTAACCTATTCAGAAAGATAGAGGTT-AGGCTTTTGACTTG
1 TTTAGAAAGAGATAAGTTTGACTTTTAACTTATTTAGAAAGACATAGGTTCA-AATTTTGACTTA
* * * * *
2355242 TTTAGAAAGAGATAAGTTTGATTTTTGACTTATTT-GAAAAGACATAAGTTCAAGTTTTGAGTTG
1 TTTAGAAAGAGATAAGTTTGACTTTTAACTTATTTAG-AAAGACATAGGTTCAAATTTTGACTT-
2355306 A
64 A
* * * * * * * **** *
2355307 -TCAAAAAGAGACAAGTTTAACTTTTAACTTATTTAGAAAGATACAAGTTTGGCTTTTGACTTG
1 TTTAGAAAGAGATAAGTTTGACTTTTAACTTATTTAGAAAGACATAGGTTCAAATTTTGACTTA
* * * *
2355370 TTTAGAATGAGACAAGTTTGACTTTTAACCTATTCAGAAAGA
1 TTTAGAAAGAGATAAGTTTGACTTTTAACTTATTTAGAAAGA
2355412 TGCAAGTTTG
Statistics
Matches: 271, Mismatches: 81, Indels: 20
0.73 0.22 0.05
Matches are distributed among these distances:
63 5 0.02
64 260 0.96
65 6 0.02
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.37
Consensus pattern (64 bp):
TTTAGAAAGAGATAAGTTTGACTTTTAACTTATTTAGAAAGACATAGGTTCAAATTTTGACTTA
Found at i:2355153 original size:128 final size:127
Alignment explanation
Indices: 2355002--2355411 Score: 500
Period size: 128 Copynumber: 3.2 Consensus size: 127
2354992 AAAAGACAAT
*
2355002 TTTGACTTTTAACTTATTTAGAAAGACATAGGTTCAAATTTTGACTTACTCGAAAAGAGAT-AGA
1 TTTGACTTTTAACTTATTTAGAAAGACATAGGTTCAAATTTTGACTTA-TCAAAAAGAGATAAG-
* ** * * *
2355066 TTTGACTCCTAACCTATTCAAAAATATATAGGTTTGGCTTTTGACTTGTTTAGAATGAGAAAAG
64 TTTAACTTTTAACCTATTCAGAAAGATACAGGTTTGGCTTTTGACTTGTTTAGAATGAGAAAAG
* * * * * *
2355130 TTTGACTTCTGACTTATTTAGAAAGGCATAGGTTCAAATTTTGACTTATTTAGAAAGTGATAAGT
1 TTTGACTTTTAACTTATTTAGAAAGACATAGGTTCAAATTTTGACTTA-TCAAAAAGAGATAAGT
* * * *
2355195 TTAACTTTTAACCTATTCAGAAAGATAGAGGTTAGGCTTTTGACTTGTTTAGAAAGAGATAAG
65 TTAACTTTTAACCTATTCAGAAAGATACAGGTTTGGCTTTTGACTTGTTTAGAATGAGAAAAG
* * * * * *
2355258 TTTGATTTTTGACTTATTT-GAAAAGACATAAGTTCAAGTTTTGAGTTGATCAAAAAGAGACAAG
1 TTTGACTTTTAACTTATTTAG-AAAGACATAGGTTCAAATTTTGACTT-ATCAAAAAGAGATAAG
* * * *
2355322 TTTAACTTTTAACTTATTTAGAAAGATACAAGTTTGGCTTTTGACTTGTTTAGAATGAGACAAG
64 TTTAACTTTTAACCTATTCAGAAAGATACAGGTTTGGCTTTTGACTTGTTTAGAATGAGAAAAG
* *
2355386 TTTGACTTTTAACCTATTCAGAAAGA
1 TTTGACTTTTAACTTATTTAGAAAGA
2355412 TGCAAGTTTG
Statistics
Matches: 240, Mismatches: 38, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
127 1 0.00
128 235 0.98
129 4 0.02
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.38
Consensus pattern (127 bp):
TTTGACTTTTAACTTATTTAGAAAGACATAGGTTCAAATTTTGACTTATCAAAAAGAGATAAGTT
TAACTTTTAACCTATTCAGAAAGATACAGGTTTGGCTTTTGACTTGTTTAGAATGAGAAAAG
Found at i:2355268 original size:32 final size:32
Alignment explanation
Indices: 2354986--2355411 Score: 232
Period size: 32 Copynumber: 13.3 Consensus size: 32
2354976 GGTCCAAATT
* * * *
2354986 TTTAGAAAAAGACAATTTTGACTTTTAACTTA
1 TTTAGAAAGAGATAAGTTTGACTTTTGACTTA
* * ** *
2355018 TTTAGAAAGACATAGGTTCAAATTTTGACTTA
1 TTTAGAAAGAGATAAGTTTGACTTTTGACTTA
* * ** * *
2355050 -CTCGAAAAGAGAT-AGATTTGACTCCTAACCTA
1 TTTAG-AAAGAGATAAG-TTTGACTTTTGACTTA
* * * * * * *
2355082 TTCAAAAATATATAGGTTTGGCTTTTGACTTG
1 TTTAGAAAGAGATAAGTTTGACTTTTGACTTA
* * *
2355114 TTTAGAATGAGAAAAGTTTGACTTCTGACTTA
1 TTTAGAAAGAGATAAGTTTGACTTTTGACTTA
* ** *
2355146 TTTAGAAAG-GCATAGGTTCAAATTTTGACTTA
1 TTTAGAAAGAG-ATAAGTTTGACTTTTGACTTA
* * * *
2355178 TTTAGAAAGTGATAAGTTTAACTTTTAACCTA
1 TTTAGAAAGAGATAAGTTTGACTTTTGACTTA
* * * * * * *
2355210 TTCAGAAAGATAGAGGTTAGGCTTTTGACTTG
1 TTTAGAAAGAGATAAGTTTGACTTTTGACTTA
*
2355242 TTTAGAAAGAGATAAGTTTGATTTTTGACTTA
1 TTTAGAAAGAGATAAGTTTGACTTTTGACTTA
* ** * *
2355274 TTT-GAAAAGACATAAGTTCAAGTTTTGAGTTGA
1 TTTAG-AAAGAGATAAGTTTGACTTTTGACTT-A
* * * * *
2355307 -TCAAAAAGAGACAAGTTTAACTTTTAACTTA
1 TTTAGAAAGAGATAAGTTTGACTTTTGACTTA
* * * *
2355338 TTTAGAAAGATACAAGTTTGGCTTTTGACTTG
1 TTTAGAAAGAGATAAGTTTGACTTTTGACTTA
* * * *
2355370 TTTAGAATGAGACAAGTTTGACTTTTAACCTA
1 TTTAGAAAGAGATAAGTTTGACTTTTGACTTA
*
2355402 TTCAGAAAGA
1 TTTAGAAAGA
2355412 TGCAAGTTTG
Statistics
Matches: 282, Mismatches: 102, Indels: 20
0.70 0.25 0.05
Matches are distributed among these distances:
31 6 0.02
32 273 0.97
33 3 0.01
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.37
Consensus pattern (32 bp):
TTTAGAAAGAGATAAGTTTGACTTTTGACTTA
Found at i:2356943 original size:13 final size:13
Alignment explanation
Indices: 2356925--2356955 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2356915 ACATTTCATC
2356925 ATGTATCGATACA
1 ATGTATCGATACA
2356938 ATGTATCGATACA
1 ATGTATCGATACA
*
2356951 TTGTA
1 ATGTA
2356956 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2356943 original size:33 final size:33
Alignment explanation
Indices: 2356903--2356968 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2356893 CCATTACAAG
* *
2356903 CAATGTATCTATACATT-TCATCATGTATCGATA
1 CAATGTATCGATACATTGT-ACCATGTATCGATA
2356936 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGTACCATGTATCGATA
2356969 TAAATAGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (33 bp):
CAATGTATCGATACATTGTACCATGTATCGATA
Found at i:2357029 original size:20 final size:20
Alignment explanation
Indices: 2357004--2357053 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
2356994 TAGTTTCATA
* **
2357004 TATCGATACAATTGTCCATG
1 TATCGATACAAGTGAACATG
2357024 TATCGATAC-AGTGAACATG
1 TATCGATACAAGTGAACATG
2357043 TATCGATACAA
1 TATCGATACAA
2357054 AGCAAGATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (20 bp):
TATCGATACAAGTGAACATG
Found at i:2365742 original size:33 final size:33
Alignment explanation
Indices: 2365702--2365770 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
2365692 CCGTTACAAG
*
2365702 CAATGTATCGATACATT-TCATCATGTATCGATA
1 CAATGTATCGATACATTAT-ACCATGTATCGATA
2365735 CAATGTATCGATACATTATACCATGTATCGATA
1 CAATGTATCGATACATTATACCATGTATCGATA
2365768 CAA
1 CAA
2365771 ATAGTGATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACATTATACCATGTATCGATA
Found at i:2365755 original size:20 final size:20
Alignment explanation
Indices: 2365732--2365769 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2365722 TCATGTATCG
2365732 ATACAATGTATCGATACATT
1 ATACAATGTATCGATACATT
*
2365752 ATACCATGTATCGATACA
1 ATACAATGTATCGATACA
2365770 AATAGTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (20 bp):
ATACAATGTATCGATACATT
Found at i:2365768 original size:13 final size:13
Alignment explanation
Indices: 2365702--2365749 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
2365692 CCGTTACAAG
2365702 CAATGTATCGATA
1 CAATGTATCGATA
2365715 C-AT-T-TC-AT-
1 CAATGTATCGATA
2365723 C-ATGTATCGATA
1 CAATGTATCGATA
2365735 CAATGTATCGATA
1 CAATGTATCGATA
2365748 CA
1 CA
2365750 TTATACCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
8 3 0.10
9 3 0.10
10 4 0.13
11 3 0.10
12 3 0.10
13 14 0.47
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2365857 original size:13 final size:13
Alignment explanation
Indices: 2365839--2365865 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2365829 TACAGTGAAC
2365839 ATGTATCGATACA
1 ATGTATCGATACA
2365852 ATGTATCGATACA
1 ATGTATCGATACA
2365865 A
1 A
2365866 AGCAAGATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2372916 original size:19 final size:17
Alignment explanation
Indices: 2372894--2372936 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
2372884 TTGATCCCTC
*
2372894 TTTAAAAGGTTTGATTATT
1 TTTAAAAGGATTG-TT-TT
*
2372913 TTTAAAATGATTGTTTT
1 TTTAAAAGGATTGTTTT
2372930 TTTAAAA
1 TTTAAAA
2372937 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.41
18 2 0.09
19 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (17 bp):
TTTAAAAGGATTGTTTT
Found at i:2377573 original size:39 final size:39
Alignment explanation
Indices: 2377481--2377575 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
2377471 GAACAATTGT
* * * *
2377481 CAATGAAACAAGCAGCTCTGAGATTGAGATGGCGGTGGC
1 CAATGAAACAAGCAGCTCTGAGATTCAGACGACGGTGAC
* *
2377520 CAATGAAACTAGCAGCTCTGAGATTCAGACGATGGTGAC
1 CAATGAAACAAGCAGCTCTGAGATTCAGACGACGGTGAC
*
2377559 CAGT-AATACAAGCAGCT
1 CAATGAA-ACAAGCAGCT
2377576 TTAATGAAAC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 2 0.04
39 45 0.96
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (39 bp):
CAATGAAACAAGCAGCTCTGAGATTCAGACGACGGTGAC
Found at i:2388356 original size:192 final size:190
Alignment explanation
Indices: 2388027--2388406 Score: 634
Period size: 192 Copynumber: 2.0 Consensus size: 190
2388017 ATTTATTACT
* * * * *
2388027 ATAATCATAAGTAAGAACTGATAATCATTGTTGCGAACACTTTCCTGATGTGCTAGATTGATAAG
1 ATAATCATAAATAAAAACTGATAATCATTGATGCAAACACTCTCCTGATGTGCTAGATTGATAAG
* *
2388092 GACATTTTTTGTGGGTGTGACTTTCATTCCTGTATAATCTACAATGCTTTGGTTGGCATTTCTCC
66 GACATTTTTTATGGGTGTGACTTTCATTCCTATATAATCTACAATGCTTTGGTTGGCATTTCTCC
*
2388157 CTAAAGTCCATTTCATTATACATATAACTTGATTTTGGTCGACAATCATTCCGCATTTCTCG
131 CTAAAGTCCATTTCATTAT--ATATAACTTGATTTTGGTCGACAATCACTCCGCATTTCTCG
2388219 ATAATCATAAATAAAAACTGATAATCATTGATGCAAACACTCTCCTGATGTGCTAGATTGATAAG
1 ATAATCATAAATAAAAACTGATAATCATTGATGCAAACACTCTCCTGATGTGCTAGATTGATAAG
* *
2388284 GACATTTTTTATGGGTGTGACTTTCATTCTTATATAATCTACAATGCTTTGGTTGGCGTTTCTCC
66 GACATTTTTTATGGGTGTGACTTTCATTCCTATATAATCTACAATGCTTTGGTTGGCATTTCTCC
* *
2388349 TTAAAGTCCATTTCATTATATATGACTTGATTTTGGTCGACAATCACTCCGCATTTCT
131 CTAAAGTCCATTTCATTATATATAACTTGATTTTGGTCGACAATCACTCCGCATTTCT
2388407 TGATTTGGGC
Statistics
Matches: 176, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
190 37 0.21
192 139 0.79
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.39
Consensus pattern (190 bp):
ATAATCATAAATAAAAACTGATAATCATTGATGCAAACACTCTCCTGATGTGCTAGATTGATAAG
GACATTTTTTATGGGTGTGACTTTCATTCCTATATAATCTACAATGCTTTGGTTGGCATTTCTCC
CTAAAGTCCATTTCATTATATATAACTTGATTTTGGTCGACAATCACTCCGCATTTCTCG
Found at i:2399779 original size:34 final size:34
Alignment explanation
Indices: 2399701--2399780 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
2399691 TTGTTAAGTG
* * *
2399701 TGTTAGGTGAAGCATATTAGGTATGCTAGGTGATA
1 TGTTAGGTG-AGAATATTAGGTATGCTAAGTAATA
* * * *
2399736 TATTTGGTGAGAATGTTAGGTATGTTAAGTAATA
1 TGTTAGGTGAGAATATTAGGTATGCTAAGTAATA
2399770 TGTTAGGTGAG
1 TGTTAGGTGAG
2399781 TAAGATATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
34 29 0.81
35 7 0.19
ACGTcount: A:0.29, C:0.03, G:0.31, T:0.38
Consensus pattern (34 bp):
TGTTAGGTGAGAATATTAGGTATGCTAAGTAATA
Found at i:2401327 original size:18 final size:17
Alignment explanation
Indices: 2401293--2401346 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
2401283 TATTCAAAAT
2401293 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
2401310 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
2401327 A-TTTATA-TTATATAA
1 ATTTTATATTTATATAA
2401342 ATTTT
1 ATTTT
2401347 GAAACATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.09
14 2 0.06
15 5 0.16
16 6 0.19
17 7 0.22
18 6 0.19
19 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:2406749 original size:73 final size:73
Alignment explanation
Indices: 2406643--2406840 Score: 227
Period size: 73 Copynumber: 2.7 Consensus size: 73
2406633 AGCATGTGTG
* * * * * * *
2406643 CATTGTGACTTAGTGTCGCTCGCTTATAGGATTATGTTGCAAGTGGACCTTTGATGTCATCTTAG
1 CATTGTGACTTGGTGTCACTCACTTATAGGATTATGTAGCAAGTAGACCTTTGAGGTCATCTTAA
2406708 TATGTTTA
66 TATGTTTA
* * * **
2406716 CATTATGACTTGGTGTCACTCACTTATATGATTATGTAGTAAGTAGACCTTTGAGGTTGTCTTAA
1 CATTGTGACTTGGTGTCACTCACTTATAGGATTATGTAGCAAGTAGACCTTTGAGGTCATCTTAA
2406781 TATGTTTA
66 TATGTTTA
* * * * *
2406789 CATTGTGACTTGGTGTCGCTTATTTATA-CATTTATGTAGCAAGTAGATCTTT
1 CATTGTGACTTGGTGTCACTCACTTATAGGA-TTATGTAGCAAGTAGACCTTT
2406841 AAGAGTGTCT
Statistics
Matches: 105, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
72 1 0.01
73 104 0.99
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (73 bp):
CATTGTGACTTGGTGTCACTCACTTATAGGATTATGTAGCAAGTAGACCTTTGAGGTCATCTTAA
TATGTTTA
Found at i:2414818 original size:2 final size:2
Alignment explanation
Indices: 2414811--2414850 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2414801 ATAAGAAAAG
*
2414811 GA GA GA GA GA GA GA GA GA GA GA GA GA GA TA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2414851 AGGAGCAGAA
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:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
GA
Found at i:2414870 original size:10 final size:10
Alignment explanation
Indices: 2414844--2414894 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
2414834 AGAGATAGAG
2414844 AGAGAGAAGG-
1 AGAGA-AAGGA
*
2414854 AGCAGAAAGGC
1 AG-AGAAAGGA
2414865 AGAG-AAGGA
1 AGAGAAAGGA
*
2414874 AGGGAAAGGA
1 AGAGAAAGGA
2414884 AGAGAAAGGA
1 AGAGAAAGGA
2414894 A
1 A
2414895 AGAGCAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 7 0.20
10 23 0.66
11 5 0.14
ACGTcount: A:0.53, C:0.04, G:0.43, T:0.00
Consensus pattern (10 bp):
AGAGAAAGGA
Found at i:2418184 original size:2 final size:2
Alignment explanation
Indices: 2418177--2418219 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2418167 GTATGCAAAG
2418177 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2418219 T
1 T
2418220 CCATGAGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2419191 original size:15 final size:15
Alignment explanation
Indices: 2419171--2419210 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
2419161 AGCTTGTTTA
2419171 TTATTTGTTTAAAGC
1 TTATTTGTTTAAAGC
* *
2419186 TTATTTATTTAAAGT
1 TTATTTGTTTAAAGC
2419201 TTATTTGTTT
1 TTATTTGTTT
2419211 GATTATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.25, C:0.03, G:0.10, T:0.62
Consensus pattern (15 bp):
TTATTTGTTTAAAGC
Found at i:2419422 original size:50 final size:51
Alignment explanation
Indices: 2419363--2419464 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
2419353 ATTTTTCCTC
2419363 AGTTCCACCA-TACCAATGACACCTTTAGAAAGTTTCAAATCTATCTTCAA
1 AGTTCCACCACTACCAATGACACCTTTAGAAAGTTTCAAATCTATCTTCAA
2419413 AGTTCCACCACTACCAATGACACCTTTAGAAAGTTTCAAATCTATCTTCAA
1 AGTTCCACCACTACCAATGACACCTTTAGAAAGTTTCAAATCTATCTTCAA
2419464 A
1 A
2419465 ACTTTTAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 10 0.20
51 41 0.80
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.29
Consensus pattern (51 bp):
AGTTCCACCACTACCAATGACACCTTTAGAAAGTTTCAAATCTATCTTCAA
Found at i:2419480 original size:21 final size:21
Alignment explanation
Indices: 2419450--2419494 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2419440 AGAAAGTTTC
*
2419450 AAATCTATCTTCAAAACTTTT
1 AAATCCATCTTCAAAACTTTT
*
2419471 AAATCCATCTTCAAAGCTTTT
1 AAATCCATCTTCAAAACTTTT
2419492 AAA
1 AAA
2419495 ATTAGTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATCCATCTTCAAAACTTTT
Found at i:2424224 original size:19 final size:20
Alignment explanation
Indices: 2424181--2424235 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
2424171 TGCCAGTTTT
* * *
2424181 ATGTATCGATATAATTATGC
1 ATGTATCGATACAATGATAC
2424201 ATGTATCGATACAATGA-AC
1 ATGTATCGATACAATGATAC
2424220 ATGTATCGATACAATG
1 ATGTATCGATACAATG
2424236 TATCGATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGATAC
Found at i:2424238 original size:13 final size:13
Alignment explanation
Indices: 2424220--2424246 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2424210 TACAATGAAC
2424220 ATGTATCGATACA
1 ATGTATCGATACA
2424233 ATGTATCGATACA
1 ATGTATCGATACA
2424246 A
1 A
2424247 AGCATTATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2426802 original size:13 final size:13
Alignment explanation
Indices: 2426783--2426818 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2426773 ATAGTAACCC
*
2426783 ATGTATCGATACC
1 ATGTATCGATACA
*
2426796 TTGTATCGATACA
1 ATGTATCGATACA
2426809 ATGTATCGAT
1 ATGTATCGAT
2426819 GCAAAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2426882 original size:20 final size:21
Alignment explanation
Indices: 2426851--2426890 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2426841 ATCTGGGTTT
*
2426851 TTTCAGATGTATCGATACATC
1 TTTCAGATGTATCAATACATC
2426872 TTTCA-ATGTATCAATACAT
1 TTTCAGATGTATCAATACAT
2426891 TTTGAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (21 bp):
TTTCAGATGTATCAATACATC
Found at i:2431423 original size:9 final size:9
Alignment explanation
Indices: 2431385--2431421 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2431375 GAGTCAACTA
2431385 CATCATTAT
1 CATCATTAT
*
2431394 CATCATCAT
1 CATCATTAT
2431403 CATCATTAT
1 CATCATTAT
*
2431412 CTTCATTAT
1 CATCATTAT
2431421 C
1 C
2431422 TTTGATGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (9 bp):
CATCATTAT
Found at i:2432968 original size:20 final size:20
Alignment explanation
Indices: 2432943--2432995 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
2432933 TCCCGTTGCT
2432943 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
2432963 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
*
2432983 ATGTATTGATACA
1 ATGTATCGATACA
2432996 TGGATTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:2433149 original size:20 final size:19
Alignment explanation
Indices: 2433124--2433173 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
2433114 CAGTTTCATA
* *
2433124 TATCGATACAATTATGCATG
1 TATCGATACAATGA-ACATG
2433144 TATCGATACAATGAACATG
1 TATCGATACAATGAACATG
2433163 TATCGATACAA
1 TATCGATACAA
2433174 AGCATTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (19 bp):
TATCGATACAATGAACATG
Found at i:2433164 original size:19 final size:20
Alignment explanation
Indices: 2433124--2433191 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
2433114 CAGTTTCATA
* *
2433124 TATCGATACAATTATGCATG
1 TATCGATACAATGATACATG
2433144 TATCGATACAATGA-ACATG
1 TATCGATACAATGATACATG
* *
2433163 TATCGATACAAAGCAT-TATG
1 TATCGATACAATG-ATACATG
2433183 TATCGATAC
1 TATCGATAC
2433192 TTTCAAGGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.38
20 26 0.62
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (20 bp):
TATCGATACAATGATACATG
Found at i:2433185 original size:20 final size:19
Alignment explanation
Indices: 2433140--2433191 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
2433130 TACAATTATG
*
2433140 CATGTATCGATACAATGAA
1 CATGTATCGATACAAAGAA
*
2433159 CATGTATCGATACAAAGCAT
1 CATGTATCGATACAAAG-AA
*
2433179 TATGTATCGATAC
1 CATGTATCGATAC
2433192 TTTCAAGGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAAAGAA
Found at i:2433543 original size:20 final size:20
Alignment explanation
Indices: 2433500--2433543 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2433490 TTTGTATCAT
* *
2433500 AATA-ATAAGTTAATGTATC
1 AATACATAAGTGAATGCATC
2433519 AATACATAAGTGAATGCATC
1 AATACATAAGTGAATGCATC
*
2433539 GATAC
1 AATAC
2433544 TAGACCTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (20 bp):
AATACATAAGTGAATGCATC
Found at i:2439508 original size:32 final size:32
Alignment explanation
Indices: 2439463--2439526 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
2439453 ATAGTCAAAA
2439463 TATATCGACACAATTT-TAATGTATCGATAGAT
1 TATATCGACACAATTTCT-ATGTATCGATAGAT
* *
2439495 TATATCGATACAATTTCTTTGTATCGATAGAT
1 TATATCGACACAATTTCTATGTATCGATAGAT
2439527 CTGGAAGACC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (32 bp):
TATATCGACACAATTTCTATGTATCGATAGAT
Found at i:2449485 original size:34 final size:35
Alignment explanation
Indices: 2449447--2449512 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
2449437 CCTTACAACT
*
2449447 CTATTTTTTCA-AAA-GCTAAGATAGAACCTCTTCC
1 CTATTTTTT-ATAAAGGCTAAGATAAAACCTCTTCC
2449481 CTATTTTTTATAAAGGCTAAGATAAAACCTCT
1 CTATTTTTTATAAAGGCTAAGATAAAACCTCT
2449513 CAATCACTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 1 0.03
34 12 0.41
35 16 0.55
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (35 bp):
CTATTTTTTATAAAGGCTAAGATAAAACCTCTTCC
Found at i:2451350 original size:19 final size:18
Alignment explanation
Indices: 2451304--2451354 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
2451294 ACTACCAGTT
*
2451304 TCATGTATCGATACAATT
1 TCATGTATCGATACAATA
2451322 TCCTATGTATCGATACAATGA
1 T-C-ATGTATCGATACAAT-A
2451343 TCATGTATCGAT
1 TCATGTATCGAT
2451355 GTAATGTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
20 16 0.55
21 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (18 bp):
TCATGTATCGATACAATA
Found at i:2451367 original size:32 final size:33
Alignment explanation
Indices: 2451326--2451387 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
2451316 ACAATTTCCT
* *
2451326 ATGTATCGATACAATG-ATCATGTATCGATGTA
1 ATGTATCGATACAAAGCATAATGTATCGATGTA
2451358 ATGTATCGATACAAAGCATAATGTATCGAT
1 ATGTATCGATACAAAGCATAATGTATCGAT
2451388 ACATCTAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATGTA
Found at i:2456771 original size:13 final size:13
Alignment explanation
Indices: 2456753--2456780 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2456743 AATAGTACCT
2456753 AATGTATCGATAC
1 AATGTATCGATAC
2456766 AATGTATCGATAC
1 AATGTATCGATAC
2456779 AA
1 AA
2456781 GGAATGTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2468733 original size:9 final size:9
Alignment explanation
Indices: 2468719--2468752 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
2468709 TCCGAGTCAC
2468719 CATCATTAT
1 CATCATTAT
2468728 CATCATTAT
1 CATCATTAT
2468737 CATC-TTCAT
1 CATCATT-AT
2468746 CATCATT
1 CATCATT
2468753 CATGGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.44
Consensus pattern (9 bp):
CATCATTAT
Found at i:2470690 original size:13 final size:13
Alignment explanation
Indices: 2470672--2470697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2470662 CAATTTTTTG
2470672 TGTATCGATACAT
1 TGTATCGATACAT
2470685 TGTATCGATACAT
1 TGTATCGATACAT
2470698 ACTTCCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2475341 original size:15 final size:15
Alignment explanation
Indices: 2475321--2475351 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2475311 ATTTCGTTTG
*
2475321 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2475336 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2475351 G
1 G
2475352 GACATTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2477183 original size:21 final size:21
Alignment explanation
Indices: 2477154--2477198 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2477144 AAGTTTTCAT
*
2477154 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2477174 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2477196 TTT
1 TTT
2477199 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2479435 original size:13 final size:13
Alignment explanation
Indices: 2479417--2479442 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2479407 CAATTTTTTG
2479417 TGTATCGATACAT
1 TGTATCGATACAT
2479430 TGTATCGATACAT
1 TGTATCGATACAT
2479443 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2480269 original size:20 final size:20
Alignment explanation
Indices: 2480244--2480297 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2480234 ATTACAAGCA
*
2480244 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
2480264 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
*
2480284 ATGTATCAATACAA
1 ATGTATCGATACAA
2480298 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:2480777 original size:20 final size:20
Alignment explanation
Indices: 2480754--2480826 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
2480744 ACAATTCAAA
2480754 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*
2480774 GTATCGATACATGAAAATG--AT
1 GTATCGATACATG---TTGCAAT
2480795 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2480815 GTATCGATACAT
1 GTATCGATACAT
2480827 AAAAAAGATG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
20 27 0.59
21 15 0.33
23 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2480798 original size:21 final size:21
Alignment explanation
Indices: 2480772--2480847 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
2480762 ACATGTTGCA
2480772 ATGTATCGATACATGAAAATG
1 ATGTATCGATACATGAAAATG
*
2480793 ATGTATCGATACATG---TTG
1 ATGTATCGATACATGAAAATG
* *
2480811 CAATGTATCGATACATAAAAAAG
1 --ATGTATCGATACATGAAAATG
2480834 ATGTATCGATACAT
1 ATGTATCGATACAT
2480848 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
18 2 0.04
20 14 0.30
21 29 0.63
23 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAATG
Found at i:2480805 original size:41 final size:41
Alignment explanation
Indices: 2480754--2480847 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2480744 ACAATTCAAA
* *
2480754 GTATCGATACATGTTGCAATGTATCGATACATGAAAATGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2480795 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2480836 GTATCGATACAT
1 GTATCGATACAT
2480848 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2480904 original size:13 final size:13
Alignment explanation
Indices: 2480886--2480911 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2480876 TACAGCAAGT
2480886 ATGTATCGATACA
1 ATGTATCGATACA
2480899 ATGTATCGATACA
1 ATGTATCGATACA
2480912 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2484996 original size:15 final size:15
Alignment explanation
Indices: 2484976--2485006 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2484966 TAAAAATGTC
*
2484976 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2484991 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2485006 C
1 C
2485007 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2487093 original size:13 final size:13
Alignment explanation
Indices: 2487075--2487112 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2487065 CATTTTTATT
2487075 TGTATCGATACAA
1 TGTATCGATACAA
*
2487088 TGTATCGATACAC
1 TGTATCGATACAA
2487101 TGTATCGATACA
1 TGTATCGATACA
2487113 GGGTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2489583 original size:20 final size:20
Alignment explanation
Indices: 2489560--2489632 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
2489550 ACAATTCAAA
2489560 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*
2489580 GTATCGATACATGAAAATG--AT
1 GTATCGATACATG---TTGCAAT
2489601 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2489621 GTATCGATACAT
1 GTATCGATACAT
2489633 AAAAAAGATG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
20 27 0.59
21 15 0.33
23 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2489604 original size:21 final size:21
Alignment explanation
Indices: 2489578--2489653 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
2489568 ACATGTTGCA
2489578 ATGTATCGATACATGAAAATG
1 ATGTATCGATACATGAAAATG
*
2489599 ATGTATCGATACATG---TTG
1 ATGTATCGATACATGAAAATG
* *
2489617 CAATGTATCGATACATAAAAAAG
1 --ATGTATCGATACATGAAAATG
2489640 ATGTATCGATACAT
1 ATGTATCGATACAT
2489654 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
18 2 0.04
20 14 0.30
21 29 0.63
23 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAATG
Found at i:2489611 original size:41 final size:41
Alignment explanation
Indices: 2489560--2489653 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2489550 ACAATTCAAA
* *
2489560 GTATCGATACATGTTGCAATGTATCGATACATGAAAATGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2489601 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2489642 GTATCGATACAT
1 GTATCGATACAT
2489654 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2489710 original size:13 final size:13
Alignment explanation
Indices: 2489692--2489717 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2489682 TACAGCAAGT
2489692 ATGTATCGATACA
1 ATGTATCGATACA
2489705 ATGTATCGATACA
1 ATGTATCGATACA
2489718 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2491229 original size:13 final size:13
Alignment explanation
Indices: 2491211--2491268 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
2491201 TACAATGAAC
2491211 ATGTATCGATACA
1 ATGTATCGATACA
2491224 ATGTATCGATACCAAGCAA
1 ATGTATCGAT----A-C-A
2491243 TATGTATCGATACA
1 -ATGTATCGATACA
2491257 ATGTATCGATAC
1 ATGTATCGATAC
2491269 CAAGCAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.58
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 1 0.03
20 10 0.26
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2491249 original size:20 final size:20
Alignment explanation
Indices: 2491224--2491288 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
2491214 TATCGATACA
2491224 ATGTATCGATACCAAGCAAT
1 ATGTATCGATACCAAGCAAT
2491244 ATGTATCGAT----A-C-A-
1 ATGTATCGATACCAAGCAAT
2491257 ATGTATCGATACCAAGCAAT
1 ATGTATCGATACCAAGCAAT
2491277 ATGTATCGATAC
1 ATGTATCGATAC
2491289 ATCTGGGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 1 0.03
20 22 0.58
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (20 bp):
ATGTATCGATACCAAGCAAT
Found at i:2491253 original size:33 final size:33
Alignment explanation
Indices: 2491193--2491289 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
2491183 CATTTTATGG
*
2491193 TGTATCGATA-CAATG-AACATGTATCGATACAA
1 TGTATCGATACCAA-GCAATATGTATCGATACAA
2491225 TGTATCGATACCAAGCAATATGTATCGATACAA
1 TGTATCGATACCAAGCAATATGTATCGATACAA
2491258 TGTATCGATACCAAGCAATATGTATCGATACA
1 TGTATCGATACCAAGCAATATGTATCGATACA
2491290 TCTGGGTGTG
Statistics
Matches: 62, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
32 11 0.18
33 51 0.82
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (33 bp):
TGTATCGATACCAAGCAATATGTATCGATACAA
Found at i:2491332 original size:30 final size:30
Alignment explanation
Indices: 2491296--2491356 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2491286 TACATCTGGG
2491296 TGTGTATTAATACATTCAAGGGTTTTGACC
1 TGTGTATTAATACATTCAAGGGTTTTGACC
2491326 TGTGTATTAATACATTCAAGGGTTTTGACC
1 TGTGTATTAATACATTCAAGGGTTTTGACC
2491356 T
1 T
2491357 TTTGTAGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (30 bp):
TGTGTATTAATACATTCAAGGGTTTTGACC
Found at i:2491477 original size:22 final size:21
Alignment explanation
Indices: 2491422--2491482 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
2491412 TTGCAATAAT
*
2491422 TTTACTTC-AAAAACA-TTAA
1 TTTATTTCTAAAAACATTTAA
*
2491441 TTTATTGTTTAAAAAACATTTAAA
1 TTTATT-TCT-AAAAACATTT-AA
2491465 TTTATTTCT-AAAACATTT
1 TTTATTTCTAAAAACATTT
2491483 TTGATATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
19 5 0.15
20 1 0.03
21 9 0.26
22 7 0.21
23 4 0.12
24 8 0.24
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTATTTCTAAAAACATTTAA
Found at i:2491924 original size:20 final size:20
Alignment explanation
Indices: 2491899--2491936 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2491889 CTCCAATTAC
2491899 TTCTTT-AAGGCCCTTTTTCT
1 TTCTTTGAA-GCCCTTTTTCT
2491919 TTCTTTGAAGCCCTTTTT
1 TTCTTTGAAGCCCTTTTT
2491937 ACCCCCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.11, C:0.24, G:0.11, T:0.55
Consensus pattern (20 bp):
TTCTTTGAAGCCCTTTTTCT
Found at i:2492698 original size:13 final size:12
Alignment explanation
Indices: 2492675--2492720 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 12
2492665 AAAAAAATTT
2492675 CTATTTTTTTCA
1 CTATTTTTTTCA
2492687 CTATTCTTTTT--
1 CTATT-TTTTTCA
*
2492698 CTTTTTTTTTCA
1 CTATTTTTTTCA
2492710 -TATTTTTTTCA
1 CTATTTTTTTCA
2492721 TTTTTTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
10 5 0.17
11 14 0.48
12 5 0.17
13 5 0.17
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (12 bp):
CTATTTTTTTCA
Found at i:2492715 original size:11 final size:10
Alignment explanation
Indices: 2492672--2492744 Score: 69
Period size: 10 Copynumber: 7.0 Consensus size: 10
2492662 ATAAAAAAAA
2492672 TTTCTATTTT
1 TTTCTATTTT
2492682 TTTCACTATTCTT
1 TTT--CTATT-TT
*
2492695 TTTCTTTTTT
1 TTTCTATTTT
2492705 TTTCATATTTT
1 TTTC-TATTTT
2492716 TTTC-ATTTT
1 TTTCTATTTT
*
2492725 TTTCAATTTT
1 TTTCTATTTT
2492735 CTTTCT-TTTT
1 -TTTCTATTTT
2492745 GTTTTTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
9 9 0.17
10 18 0.33
11 17 0.31
12 5 0.09
13 5 0.09
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTCTATTTT
Found at i:2492716 original size:20 final size:21
Alignment explanation
Indices: 2492672--2492744 Score: 89
Period size: 20 Copynumber: 3.5 Consensus size: 21
2492662 ATAAAAAAAA
2492672 TTTCTATTTTTTTCACTATTCTT
1 TTTCTATTTTTTTCA-TATT-TT
*
2492695 TTTCTTTTTTTTTCATATTTT
1 TTTCTATTTTTTTCATATTTT
2492716 TTTC-ATTTTTTTCA-ATTTT
1 TTTCTATTTTTTTCATATTTT
2492735 CTTTCT-TTTT
1 -TTTCTATTTT
2492745 GTTTTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
19 5 0.11
20 17 0.37
21 6 0.13
22 4 0.09
23 14 0.30
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTCTATTTTTTTCATATTTT
Found at i:2496292 original size:21 final size:21
Alignment explanation
Indices: 2496268--2496308 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2496258 CTAAGTAAAA
2496268 ATACGTATT-GTATCAATACAT
1 ATAC-TATTGGTATCAATACAT
*
2496289 ATACTATTGGTATTAATACA
1 ATACTATTGGTATCAATACA
2496309 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACTATTGGTATCAATACAT
Found at i:2496374 original size:21 final size:20
Alignment explanation
Indices: 2496345--2496401 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
2496335 AAAACCCTGA
**
2496345 AAAGTATCGATACACATTTT
1 AAAGTATCGATACACATTGC
*
2496365 AAATGTATCGATACAGATTGC
1 AAA-GTATCGATACACATTGC
*
2496386 ATAGTATCGATACACA
1 AAAGTATCGATACACA
2496402 CAAATATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAGTATCGATACACATTGC
Found at i:2496470 original size:53 final size:53
Alignment explanation
Indices: 2496389--2496525 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
2496379 AGATTGCATA
*
2496389 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
* *
2496443 GTATCGATACACGCAATATGTATCGATACAGGTCACTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
*
2496496 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
2496526 TTGGTAGTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 65 0.83
54 13 0.17
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
Found at i:2496568 original size:10 final size:10
Alignment explanation
Indices: 2496549--2496579 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2496539 AATCTCATTT
2496549 TCACTGTTCA
1 TCACTGTTCA
*
2496559 TCACTATTCA
1 TCACTGTTCA
2496569 TCACTGTTCA
1 TCACTGTTCA
2496579 T
1 T
2496580 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:2496601 original size:21 final size:22
Alignment explanation
Indices: 2496567--2496622 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
2496557 CATCACTATT
2496567 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
2496589 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
*
2496610 CATCACGGTTCAT
1 CATCACTGTTCAT
2496623 ATGTCACTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:2496653 original size:14 final size:14
Alignment explanation
Indices: 2496636--2496665 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2496626 TCACTGTTCA
2496636 CACTATTCACGTAT
1 CACTATTCACGTAT
*
2496650 CACTATTCATGTAT
1 CACTATTCACGTAT
2496664 CA
1 CA
2496666 TTAAAAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (14 bp):
CACTATTCACGTAT
Found at i:2508478 original size:20 final size:20
Alignment explanation
Indices: 2508455--2508513 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2508445 AATAGTATCG
*
2508455 ATACATCACATATTGTATTA
1 ATACATCGCATATTGTATTA
* *
2508475 ATACAGTTGCATATTCTATTA
1 ATACA-TCGCATATTGTATTA
* *
2508496 ATATATGGCATATTGTAT
1 ATACATCGCATATTGTAT
2508514 CGATACAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (20 bp):
ATACATCGCATATTGTATTA
Found at i:2508489 original size:21 final size:20
Alignment explanation
Indices: 2508463--2508513 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
2508453 CGATACATCA
*
2508463 CATATTGTATTAATACAGTTG
1 CATATTGTATTAATACA-TGG
* *
2508484 CATATTCTATTAATATATGG
1 CATATTGTATTAATACATGG
2508504 CATATTGTAT
1 CATATTGTAT
2508514 CGATACAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
CATATTGTATTAATACATGG
Found at i:2510379 original size:58 final size:59
Alignment explanation
Indices: 2510210--2510390 Score: 212
Period size: 57 Copynumber: 3.2 Consensus size: 59
2510200 GGAACCATGT
* * *
2510210 TGCAATTTTAGGTCATTTAAGGCATTTTTCATGCATTTAGGGACTATTATGTAAATTCA
1 TGCAATTTTAGTTCATTTAAGGCATTTTTCATGCATTTAGGGACTATTATGCAATTTCA
* * * *
2510269 T--AAATTTAGGTT-ATTTAAGTCATTTTTCATGTATTTAGGGAGTA-TATGCAATTTCA
1 TGCAATTTTA-GTTCATTTAAGGCATTTTTCATGCATTTAGGGACTATTATGCAATTTCA
* * * *
2510325 TGCATTTTTAGTTCATTTAAGGCATTTTT-ATGCATTTAGGGACCATTATACAATTCCA
1 TGCAATTTTAGTTCATTTAAGGCATTTTTCATGCATTTAGGGACTATTATGCAATTTCA
2510383 TGC-ATTTT
1 TGCAATTTT
2510391 GGGATCATTT
Statistics
Matches: 101, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
56 11 0.11
57 55 0.54
58 34 0.34
59 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (59 bp):
TGCAATTTTAGTTCATTTAAGGCATTTTTCATGCATTTAGGGACTATTATGCAATTTCA
Found at i:2510489 original size:163 final size:162
Alignment explanation
Indices: 2510145--2510495 Score: 381
Period size: 163 Copynumber: 2.2 Consensus size: 162
2510135 GTCATTTAAG
*
2510145 GACTATATTACAATTTCATGCATTTTTAGTTCATTTAAGATATTTTCATGATTTAGGAACCATGT
1 GACTATA-TACAATTTCATGCATTTTTAGTTCATTTAAGACATTTTCATGATTTAGGAACCATGT
* ** * *
2510210 TGCAATTTTAGGTCATTTAAGGCATTTTTCATGCATTTAGGGACTATTATGTAAATTCATAAATT
65 TACAATTCCAGGTCATTTAAGGCATTTTTCATGAATTTAGGGACTATTATGCAAATTCATAAATT
* *
2510275 TAGGTTATTTAAGTCATTTTTCATGTATTTAGG
130 TAGGTTATTTAAGTCACTTTTCATGTATTTAGA
* * * * *
2510308 GAGTATATGCAATTTCATGCATTTTTAGTTCATTTAAGGCATTTTTATGCATTTAGGGACCAT-T
1 GACTATATACAATTTCATGCATTTTTAGTTCATTTAAGACATTTTCATG-ATTTAGGAACCATGT
* ** * *
2510372 ATACAATTCCATG-CATTTTGGGATCATTTTTTAT-AATTTAGGGACTATTATGCAATTTCATAC
65 -TACAATTCCAGGTCATTTAAGG--CATTTTTCATGAATTTAGGGACTATTATGCAAATTCATA-
*
2510435 ATTTTAGGGTTATTTAAGTCACTTTT-ATGT-TTTA-A
126 AATTTA-GGTTATTTAAGTCACTTTTCATGTATTTAGA
* * * *
2510470 TACTATTTATATTTTTCATGCATTTT
1 GACTATATACA-ATTTCATGCATTTT
2510496 AAGGCCATTT
Statistics
Matches: 156, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
162 52 0.33
163 68 0.44
164 18 0.12
165 18 0.12
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (162 bp):
GACTATATACAATTTCATGCATTTTTAGTTCATTTAAGACATTTTCATGATTTAGGAACCATGTT
ACAATTCCAGGTCATTTAAGGCATTTTTCATGAATTTAGGGACTATTATGCAAATTCATAAATTT
AGGTTATTTAAGTCACTTTTCATGTATTTAGA
Found at i:2510719 original size:75 final size:74
Alignment explanation
Indices: 2510549--2510720 Score: 175
Period size: 75 Copynumber: 2.3 Consensus size: 74
2510539 TTTCTATCAC
* * * * *
2510549 CTTAGGATCATG-AAGAAACTTTCATGTCGAAATATATCCATTAAGGTTATTTAGGTAATAGTAC
1 CTTAGGGTCATGTAAG-AAC-TTCAAGTCGAAACATATCCATTAAGGTTATTTAAGTAATAGCAC
2510613 CCTAAAACCAA
64 CCTAAAACCAA
* ** * * *
2510624 TTCTAGGGTCATGTGGGAACTTCAAGTTGAAACATATCCTTTAAGGTTATTTAAGTAATAGCACT
1 CT-TAGGGTCATGTAAGAACTTCAAGTCGAAACATATCCATTAAGGTTATTTAAGTAATAGCACC
** *
2510689 CTAAAATTGAG
65 CTAAAA-CCAA
2510700 CTTAGGGTCATGTAAGAACTT
1 CTTAGGGTCATGTAAGAACTT
2510721 TCATATAGAT
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
75 62 0.81
76 14 0.18
77 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (74 bp):
CTTAGGGTCATGTAAGAACTTCAAGTCGAAACATATCCATTAAGGTTATTTAAGTAATAGCACCC
TAAAACCAA
Found at i:2513709 original size:2 final size:2
Alignment explanation
Indices: 2513702--2513741 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2513692 TAGCAATAGG
2513702 AT AT AT AT 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 AT AT AT AT
2513742 CGATAAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2514032 original size:19 final size:19
Alignment explanation
Indices: 2514010--2514061 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
2514000 TATTTTTAAA
2514010 TTACTATTATAAATATTT-T
1 TTACTATTATAAA-ATTTAT
2514029 TTACTATTAATAAAATTTAT
1 TTACTATT-ATAAAATTTAT
*
2514049 TTAAT-TTATAAAA
1 TTACTATTATAAAA
2514062 GATTAAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.20
19 14 0.47
20 10 0.33
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (19 bp):
TTACTATTATAAAATTTAT
Found at i:2516490 original size:35 final size:29
Alignment explanation
Indices: 2516417--2516694 Score: 173
Period size: 29 Copynumber: 9.7 Consensus size: 29
2516407 AGCCAACGTT
*
2516417 AATTACACAAGCACAAATATTTCAACCTC
1 AATTACACAAGCACAAATATTCCAACCTC
2516446 AATTACACAAGCACAAATATTCCAACCTC
1 AATTACACAAGCACAAATATTCCAACCTC
* * *
2516475 AATTACAAAAGCACAAATATTCTAATCTC
1 AATTACACAAGCACAAATATTCCAACCTC
* * * *
2516504 AGTTAAACAAGAATATATACATATTCCAA-CTAC
1 AATTACACAAG--CACA-A-ATATTCCAACCT-C
* *
2516537 AATTACACAAGCATAAATATTCCAACCTT
1 AATTACACAAGCACAAATATTCCAACCTC
* * * * *
2516566 AATTAAACAGGGACAAACATTCCATCCTC
1 AATTACACAAGCACAAATATTCCAACCTC
* * *
2516595 --TTAGACACAAGCATAAATTTTCAAACCTC
1 AATT--ACACAAGCACAAATATTCCAACCTC
** * *
2516624 ----ACACACCCAGATATATT-C--CCT-
1 AATTACACAAGCACAAATATTCCAACCTC
* * *
2516645 AGTTACACAAGCACAAAGATTCCAACCTA
1 AATTACACAAGCACAAATATTCCAACCTC
* *
2516674 AATTACTCAAGCACGAATATT
1 AATTACACAAGCACAAATATT
2516695 TTACACAAGC
Statistics
Matches: 189, Mismatches: 44, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
22 3 0.02
25 24 0.13
26 1 0.01
27 2 0.01
28 3 0.02
29 127 0.67
30 3 0.02
31 5 0.03
32 3 0.02
33 18 0.10
ACGTcount: A:0.44, C:0.26, G:0.06, T:0.24
Consensus pattern (29 bp):
AATTACACAAGCACAAATATTCCAACCTC
Found at i:2517426 original size:14 final size:14
Alignment explanation
Indices: 2517409--2517473 Score: 71
Period size: 14 Copynumber: 4.6 Consensus size: 14
2517399 TTATATATTT
2517409 TTTAATTAATTTAA
1 TTTAATTAATTTAA
**
2517423 TTTAATTAAAAATAA
1 TTTAATT-AATTTAA
*
2517438 TTT-ATTATATTT-T
1 TTTAATTA-ATTTAA
2517451 TTTAATTAATTTAA
1 TTTAATTAATTTAA
2517465 TTTAATTAA
1 TTTAATTAA
2517474 AAATAAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 8 0.20
14 25 0.61
15 8 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATTAATTTAA
Found at i:2517552 original size:47 final size:45
Alignment explanation
Indices: 2517457--2517561 Score: 117
Period size: 47 Copynumber: 2.2 Consensus size: 45
2517447 TTTTTTTAAT
2517457 TAATTTAATTTAATTAAAAATAAATTTTAATTGATCAGTCATGTGTA
1 TAATTTAA-TTAATTAAAAATAAA-TTTAATTGATCAGTCATGTGTA
*
2517504 TATATTTAATTAATTATAAAAT-AA-TTAATT-ATGATGTCATAGATGTA
1 TA-ATTTAATTAATTA-AAAATAAATTTAATTGATCA-GTCAT-G-TGTA
2517551 TAATTTAATTA
1 TAATTTAATTA
2517562 GAAATCTTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
44 3 0.06
45 11 0.21
46 10 0.19
47 17 0.33
48 11 0.21
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (45 bp):
TAATTTAATTAATTAAAAATAAATTTAATTGATCAGTCATGTGTA
Found at i:2517630 original size:44 final size:44
Alignment explanation
Indices: 2517576--2517672 Score: 194
Period size: 44 Copynumber: 2.2 Consensus size: 44
2517566 TCTTTTATTT
2517576 AAAAAAATTATCAACTGAAACATGATAATTTATAATTGATAAAA
1 AAAAAAATTATCAACTGAAACATGATAATTTATAATTGATAAAA
2517620 AAAAAAATTATCAACTGAAACATGATAATTTATAATTGATAAAA
1 AAAAAAATTATCAACTGAAACATGATAATTTATAATTGATAAAA
2517664 AAAAAAATT
1 AAAAAAATT
2517673 TCTACAAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (44 bp):
AAAAAAATTATCAACTGAAACATGATAATTTATAATTGATAAAA
Found at i:2517649 original size:21 final size:21
Alignment explanation
Indices: 2517581--2517649 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
2517571 TATTTAAAAA
2517581 AATTATCAACTGAAACATGAT
1 AATTATCAACTGAAACATGAT
* * ** *
2517602 AATTTAT-AATTGATAAAAAAAAA
1 AA-TTATCAACTG--AAACATGAT
2517625 AATTATCAACTGAAACATGAT
1 AATTATCAACTGAAACATGAT
2517646 AATT
1 AATT
2517650 TATAATTGAT
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
21 15 0.44
22 8 0.24
23 11 0.32
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (21 bp):
AATTATCAACTGAAACATGAT
Found at i:2517652 original size:22 final size:22
Alignment explanation
Indices: 2517583--2517652 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
2517573 TTTAAAAAAA
2517583 TTATCAACTGAAACATGATAAT
1 TTATCAACTGAAACATGATAAT
* * ** * *
2517605 TTAT-AATTGATAAAAAAAAAAA
1 TTATCAACTGA-AACATGATAAT
2517627 TTATCAACTGAAACATGATAAT
1 TTATCAACTGAAACATGATAAT
2517649 TTAT
1 TTAT
2517653 AATTGATAAA
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
21 5 0.15
22 24 0.71
23 5 0.15
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (22 bp):
TTATCAACTGAAACATGATAAT
Found at i:2519450 original size:51 final size:50
Alignment explanation
Indices: 2519346--2519518 Score: 175
Period size: 51 Copynumber: 3.4 Consensus size: 50
2519336 TTAAGACCAT
* * ** * * * *
2519346 AAATCCGATCAGGTTTGACATACATGATTCTAATGCTTATGTCATGACCAC
1 AAAT-CGATCAAGTTTGACACAGTTGATTCTAATACTCATGTCAAGACTAC
* * *
2519397 AAAGTCAATCAAGTTTGACACAGTTGATTCTAATATTCATGTTAAGACTAC
1 AAA-TCGATCAAGTTTGACACAGTTGATTCTAATACTCATGTCAAGACTAC
* * *
2519448 AAAACCGATCAAGTTTGACACTGTTGATTCTGATACTCATGTCAAGACTAC
1 -AAATCGATCAAGTTTGACACAGTTGATTCTAATACTCATGTCAAGACTAC
*
2519499 AAATCTGATTAAGTTTGACA
1 AAATC-GATCAAGTTTGACA
2519519 TGGCTGATTT
Statistics
Matches: 100, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
50 4 0.04
51 92 0.92
52 4 0.04
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (50 bp):
AAATCGATCAAGTTTGACACAGTTGATTCTAATACTCATGTCAAGACTAC
Found at i:2519721 original size:45 final size:45
Alignment explanation
Indices: 2519657--2519746 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
2519647 TAGTCTGTAT
2519657 GATGCTATTTGTGCATCATTATACATTATGATCAAGACAAGGATA
1 GATGCTATTTGTGCATCATTATACATTATGATCAAGACAAGGATA
*
2519702 GATGCTATTTGTGCATCATTATACATTATGATCAAGATAAGGATA
1 GATGCTATTTGTGCATCATTATACATTATGATCAAGACAAGGATA
2519747 ACAGCTAGTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (45 bp):
GATGCTATTTGTGCATCATTATACATTATGATCAAGACAAGGATA
Found at i:2535267 original size:46 final size:47
Alignment explanation
Indices: 2535162--2535292 Score: 160
Period size: 46 Copynumber: 2.8 Consensus size: 47
2535152 ATCTTTCTTT
* *
2535162 TTTATCTCTTAATTAATTCAATTTAATTAGAGATAAAAACTCTTTTA
1 TTTATCTCTTAATTAATTTAATTTAATTAGAGATAAAAACTCATTTA
*
2535209 TTTATCTCTTAATTATTTTAATTTAATTAGCA-AT-AAAACAT-ATTTA
1 TTTATCTCTTAATTAATTTAATTTAATTAG-AGATAAAAAC-TCATTTA
* ** *
2535255 TTTATCTTTTAATTAATTTAAACTAATTAAAGATAAAA
1 TTTATCTCTTAATTAATTTAATTTAATTAGAGATAAAA
2535293 TTTGATTGGC
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
45 1 0.01
46 36 0.50
47 34 0.47
48 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.47
Consensus pattern (47 bp):
TTTATCTCTTAATTAATTTAATTTAATTAGAGATAAAAACTCATTTA
Found at i:2538164 original size:165 final size:163
Alignment explanation
Indices: 2537746--2538219 Score: 501
Period size: 165 Copynumber: 2.9 Consensus size: 163
2537736 AGTTTTCTTG
* * * *
2537746 TCCGTGAATTTTTTCAAGGTGATTTTTCTTAG-TTTATAATTTTTAAAATTCATCAAATATTATT
1 TCCGTAAATTTTTTCAAGG-GATTTTTCTAAGTTTTA-AATTTTTAAAAGTCATCAAATATTATC
* * * ** * * *
2537810 ATTTATTTCATATTAATTT-ATTTTTCAAAAAT-TCTTTCATTTCCATGAATTTAGAATTTTTTC
64 ATTTATTTCAT-TTTATTTCAGTTTTAAAAAATAAATTT-ATTTTCATG-ATTTTGGATTTTTTC
* ** *
2537873 CTTGAAATCTTTTTTTTTTTTCAAAATACAGTATTTTCTAC
126 CTTGAAA---TTCTCCTTTTCCAAAATACAGTATTTTCTAC
* ** * *
2537914 TCCGTAAATTTTTTCGAGGGGATTTTTCTAAGTTTTTTA-TTTTGAAAGTCATCAAATATTAACA
1 TCCGTAAATTTTTTC-AAGGGATTTTTCTAAGTTTTAAATTTTTAAAAGTCATCAAATATTATCA
* * *
2537978 TTTATTTTATGTTAATTCAGTTTTAAAAAATAAATTTATTTTCATGAGTTTTGGATTTTTTCCTT
65 TTTATTTCATTTTATTTCAGTTTTAAAAAATAAATTTATTTTCATGA-TTTTGGATTTTTTCCTT
* **
2538043 GAAATTCTCCTTTTCCTAAATATGGTATTTTCTAC
129 GAAATTCTCCTTTTCCAAAATACAGTATTTTCTAC
* * * *
2538078 TCTGTATATTTTTTCAAGAGGATTTTTCTCAGTTTTAAATTTTTAAAAGTCATAAAATATTATCA
1 TCCGTAAATTTTTTCAAG-GGATTTTTCTAAGTTTTAAATTTTTAAAAGTCATCAAATATTATCA
* *
2538143 TTTATTTCATTTTATTTCAGTTTTAAAAAATAAATTCATTTTCATGCATTTTGGATTTTTT-ATT
65 TTTATTTCATTTTATTTCAGTTTTAAAAAATAAATTTATTTTCATG-ATTTTGGATTTTTTCCTT
2538207 GAAATTC-CCTTTT
129 GAAATTCTCCTTTT
2538220 TTCTGAGAAA
Statistics
Matches: 257, Mismatches: 41, Indels: 21
0.81 0.13 0.07
Matches are distributed among these distances:
163 8 0.03
164 63 0.25
165 77 0.30
166 6 0.02
167 68 0.26
168 29 0.11
169 6 0.02
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (163 bp):
TCCGTAAATTTTTTCAAGGGATTTTTCTAAGTTTTAAATTTTTAAAAGTCATCAAATATTATCAT
TTATTTCATTTTATTTCAGTTTTAAAAAATAAATTTATTTTCATGATTTTGGATTTTTTCCTTGA
AATTCTCCTTTTCCAAAATACAGTATTTTCTAC
Found at i:2538285 original size:165 final size:165
Alignment explanation
Indices: 2537746--2538290 Score: 417
Period size: 165 Copynumber: 3.3 Consensus size: 165
2537736 AGTTTTCTTG
* * * * * * * **
2537746 TCCGTGAATTTTTTCAAG-GTGATTTTTCTTAGTTTATAATTTTTAAAATTCATCAAATATTATT
1 TCCGTAAATTTTTGCAAGAG-GATTTTTCTCAGTCTAAAATTTTTAAAAGTCATAAAATATTAAC
* * * * *** * * * * *
2537810 ATTTATTTCATATTAATTTATTTTTCAAAAATTCTTTCATTTCCATGAATTTAGAATTTTTTCCT
65 ATTTATTTCATGTTAATTCAGTTTTAAAAAATAAATTCATTTTCATGAGTTTTGGATTTTTTCAT
* ** ** *
2537875 TGAAATCTTTTTTTTTTTTCAAA-ATACAGTATTTTCTAC
130 TGAAAT-TCTCCTTTTCCT-AAATAT-C-CTATTTTCTAC
* * * * * *** * *
2537914 TCCGTAAATTTTTTCGAGGGGATTTTTCTAAGTTTTTTA-TTTTGAAAGTCATCAAATATTAACA
1 TCCGTAAATTTTTGCAAGAGGATTTTTCTCAGTCTAAAATTTTTAAAAGTCATAAAATATTAACA
* * *
2537978 TTTATTTTATGTTAATTCAGTTTTAAAAAATAAATTTATTTTCATGAGTTTTGGATTTTTTCCTT
66 TTTATTTCATGTTAATTCAGTTTTAAAAAATAAATTCATTTTCATGAGTTTTGGATTTTTTCATT
**
2538043 GAAATTCTCCTTTTCCTAAATATGGTATTTTCTAC
131 GAAATTCTCCTTTTCCTAAATATCCTATTTTCTAC
* * * * * *
2538078 TCTGTATATTTTTTCAAGAGGATTTTTCTCAGTTTTAAATTTTTAAAAGTCATAAAATATTATCA
1 TCCGTAAATTTTTGCAAGAGGATTTTTCTCAGTCTAAAATTTTTAAAAGTCATAAAATATTAACA
* *
2538143 TTTATTTCATTTTATTTCAGTTTTAAAAAATAAATTCATTTTCATGCA-TTTTGGATTTTTT-AT
66 TTTATTTCATGTTAATTCAGTTTTAAAAAATAAATTCATTTTCATG-AGTTTTGGATTTTTTCAT
* *
2538206 TGAAATTC-CCTTTTTTCTGAGAA-A-CCTAGTTTTCTTC
130 TGAAATTCTCC-TTTTCCT-A-AATATCCTA-TTTTCTAC
** *
2538243 TCCGTAAATATTTTGGGAGA-GA-TTTTCTTCGGTCTAAAATTTTTAAAA
1 TCCGTAAAT-TTTTGCAAGAGGATTTTTC-TCAGTCTAAAATTTTTAAAA
2538291 TGCATCTAAT
Statistics
Matches: 312, Mismatches: 55, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
163 2 0.01
164 65 0.21
165 115 0.37
166 19 0.06
167 78 0.25
168 32 0.10
169 1 0.00
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (165 bp):
TCCGTAAATTTTTGCAAGAGGATTTTTCTCAGTCTAAAATTTTTAAAAGTCATAAAATATTAACA
TTTATTTCATGTTAATTCAGTTTTAAAAAATAAATTCATTTTCATGAGTTTTGGATTTTTTCATT
GAAATTCTCCTTTTCCTAAATATCCTATTTTCTAC
Found at i:2538858 original size:12 final size:11
Alignment explanation
Indices: 2538831--2538874 Score: 58
Period size: 10 Copynumber: 4.2 Consensus size: 11
2538821 TTTTTCCAGC
2538831 AAGGAGA-AAA
1 AAGGAGAGAAA
2538841 AA-GAGAGAAA
1 AAGGAGAGAAA
2538851 AAGTGAGA-AAA
1 AAG-GAGAGAAA
2538862 AAGGAGAGAAA
1 AAGGAGAGAAA
2538873 AA
1 AA
2538875 AATAAAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 4 0.13
10 11 0.37
11 11 0.37
12 4 0.13
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (11 bp):
AAGGAGAGAAA
Found at i:2538875 original size:12 final size:11
Alignment explanation
Indices: 2538834--2538875 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 11
2538824 TTCCAGCAAG
2538834 GAGAAAAAAGA
1 GAGAAAAAAGA
*
2538845 GAG-AAAAAGT
1 GAGAAAAAAGA
2538855 GAGAAAAAAGGA
1 GAGAAAAAA-GA
2538867 GAGAAAAAA
1 GAGAAAAAA
2538876 ATAAAATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 9 0.33
11 8 0.30
12 10 0.37
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (11 bp):
GAGAAAAAAGA
Found at i:2539995 original size:164 final size:162
Alignment explanation
Indices: 2539792--2540225 Score: 541
Period size: 164 Copynumber: 2.7 Consensus size: 162
2539782 TACATTTCTA
* * * * *
2539792 ATATT-CTCATGGGTATCCGTGGGGTATAGAAGGTTTCAAAACCTTTTTGTATCTTTTCGAGTAT
1 ATATTCCT-ATGGGTATCCGTAGGGTATAAAAGATTTCAAAAACTTTTTGTATCTTTTCGGGTAT
* *
2539856 CCATTAAGGTATGAAATGATTTTTTTTCAAAAATAAATAAATAATATTAAATTTACTCATCGTTA
65 CCATTAAGGTACGAAATGA-TTTTTTTCAAAAATAAATAAATAATATTAAATTCACTCATCGTTA
* * *
2539921 ATTACAACAAATATTAATCAT-TTTTAAATCTTTT
129 ATGACAACAAACATTAATCATGTTTT-AATCGTTT
* *
2539955 ATATTCCTATGGGTATCCGTAAGGGTATAAAAGATTTCAAAAACTTGTTGTATCTTTTTGGGTAT
1 ATATTCCTATGGGTATCCGT-AGGGTATAAAAGATTTCAAAAACTTTTTGTATCTTTTCGGGTAT
* * * *
2540020 CAATTAAGGTACGAAATGATTTTCTTCCAAAATAAATAAATAATATTAAATTCACTCTTCGTTAA
65 CCATTAAGGTACGAAATGATTTTTTTCAAAAATAAATAAATAATATTAAATTCACTCATCGTTAA
* *
2540085 TGACAATAAACATTAATCGTGTTTTAATCGTTT
130 TGACAACAAACATTAATCATGTTTTAATCGTTT
* * * * * *
2540118 ATATTCTTACT-GGTATTCTTAGAGGTACAAAAGATTTTGAAAAACTTTTTGTATTTTTTCGGGT
1 ATATTCCTA-TGGGTATCCGTAG-GGTATAAAAGA-TTTCAAAAACTTTTTGTATCTTTTCGGGT
* * *
2540182 ATCCATTAAGGTACGAAATAATTTTTTCCAAATATAAATAAATA
63 ATCCATTAAGGTACGAAATGATTTTTTTCAAAAATAAATAAATA
2540226 TAAATTTTTT
Statistics
Matches: 233, Mismatches: 32, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
162 2 0.01
163 107 0.46
164 124 0.53
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (162 bp):
ATATTCCTATGGGTATCCGTAGGGTATAAAAGATTTCAAAAACTTTTTGTATCTTTTCGGGTATC
CATTAAGGTACGAAATGATTTTTTTCAAAAATAAATAAATAATATTAAATTCACTCATCGTTAAT
GACAACAAACATTAATCATGTTTTAATCGTTT
Found at i:2541390 original size:158 final size:154
Alignment explanation
Indices: 2540954--2541503 Score: 481
Period size: 156 Copynumber: 3.5 Consensus size: 154
2540944 CTTCTAGGTC
* * * *
2540954 ATCACCGAG-TCCGCTTTTATGCCGAAGGT-GAGCATTTAGGATAGGTTCATC-CCATCTCTAGT
1 ATCACCG-GCTCCACTTTTACGCCGAAGATAG-GCATTTAGGATAGGTTCATCACCATTTCTAGT
* *
2541016 C-TTTTAAGTCCTTTAAGGTTGCCGGAATACTTTTACGTCGAAGGTATACC-CATAGGGGCATTT
64 CTTTTTAAGTCCTTTAGGGTTG-CAGAATACTTTTACGTCGAAGGTATACCTCA-A-GGGCATTT
* *
2541079 TCGTAATTTTTAGAATCGAGTCCTAGGTT
126 TCATAATTTTTAGAATCGAGTCCTAAGTT
** * *
2541108 ATCACCGGCTCTGCTTTTACGCCGAAGATGGGCATTTAGGATAGGTTCATCACCATTTGTAGTCC
1 ATCACCGGCTCCACTTTTACGCCGAAGATAGGCATTTAGGATAGGTTCATCACCATTTCTAGT-C
** * * *
2541173 TTTTTAAGTCCTTTAGAGGTACCAGGATACTTTCACGTCGAAGGTAT-CCTCTAGGGGCATTTTC
65 TTTTTAAGTCCTTTAG-GGTTGCAGAATACTTTTACGTCGAAGGTATACCTC-AAGGGCATTTTC
2541237 ATAATTTTTTCTAGAATCGAGTCCTAAGTT
128 ATAA--TTTT-TAGAATCGAGTCCTAAGTT
* * * * *
2541267 GTCACCGGGTCCAC-TTTATGCTGAAGATAGGCATTTAGGATAGGTTTATCACCATTTCTAGTCT
1 ATCACCGGCTCCACTTTTACGCCGAAGATAGGCATTTAGGATAGGTTCATCACCATTTCTAGTCT
* * * * *
2541331 TTTTAAGT-CTATTAGGGTTGCTGAAACACTTTTACGTCGAAGATATACCTCGAAAGGCATTTTG
66 TTTTAAGTCCT-TTAGGGTTGCAG-AATACTTTTACGTCGAAGGTATACCTC-AAGGGCATTTTC
* * * * * * * *
2541395 GTTATTTTTAGAACCAACTCTTAGGTC
128 ATAATTTTTAGAATCGAGTCCTAAGTT
* * * * * * * * *
2541422 ATCACCGGATCCGCTTTTATGTCGGAGGT-GAGCATTTAGGATAGGTTCATC-CCTTTTATATTC
1 ATCACCGGCTCCACTTTTACGCCGAAGATAG-GCATTTAGGATAGGTTCATCACCATTTCTAGT-
*
2541485 CTTTTTAAGTTCTTTAGGG
64 CTTTTTAAGTCCTTTAGGG
2541504 GTATCGGGTA
Statistics
Matches: 325, Mismatches: 53, Indels: 34
0.79 0.13 0.08
Matches are distributed among these distances:
153 1 0.00
154 44 0.14
155 43 0.13
156 72 0.22
157 71 0.22
158 66 0.20
159 28 0.09
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (154 bp):
ATCACCGGCTCCACTTTTACGCCGAAGATAGGCATTTAGGATAGGTTCATCACCATTTCTAGTCT
TTTTAAGTCCTTTAGGGTTGCAGAATACTTTTACGTCGAAGGTATACCTCAAGGGCATTTTCATA
ATTTTTAGAATCGAGTCCTAAGTT
Found at i:2541492 original size:156 final size:154
Alignment explanation
Indices: 2540947--2541503 Score: 547
Period size: 157 Copynumber: 3.6 Consensus size: 154
2540937 AAATTAACTT
* *
2540947 CTAGGTCATCACC-GAGTCCGCTTTTATGCCGAAGGTGAGCATTTAGGATAGGTTCATC-CCATC
1 CTAGGTCATCACCGGA-TCCGCTTTTATGCCGAAGATGAGCATTTAGGATAGGTTCATCACCATT
* *
2541010 TCTAGTC-TTTTAAGTCCTTTAAGGTTGCCGGAATACTTTTACGTCGAAGGTATACC-CATAGGG
65 TCTAGTCTTTTTAAGTCCTTTAGGGTTG-CAGAATACTTTTACGTCGAAGGTATACCTCA-A-GG
*
2541073 GCATTTTCGTAATTTTTAGAATCGAGTC
127 GCATTTTCGTTATTTTTAGAATCGAGTC
* * * * *
2541101 CTAGGTTATCACCGGCTCTGCTTTTACGCCGAAGATGGGCATTTAGGATAGGTTCATCACCATTT
1 CTAGGTCATCACCGGATCCGCTTTTATGCCGAAGATGAGCATTTAGGATAGGTTCATCACCATTT
* ** * * *
2541166 GTAGTCCTTTTTAAGTCCTTTAGAGGTACCAGGATACTTTCACGTCGAAGGTAT-CCTCTAGGGG
66 CTAGT-CTTTTTAAGTCCTTTAG-GGTTGCAGAATACTTTTACGTCGAAGGTATACCTC-AAGGG
* *
2541230 CATTTTCATAATTTTTTCTAGAATCGAGTC
128 CATTTTCGT--TATTTT-TAGAATCGAGTC
* ** * * * *
2541260 CTAAGTTGTCACCGGGTCCAC-TTTATGCTGAAGAT-AGGCATTTAGGATAGGTTTATCACCATT
1 CTAGGTCATCACCGGATCCGCTTTTATGCCGAAGATGA-GCATTTAGGATAGGTTCATCACCATT
* * * *
2541323 TCTAGTCTTTTTAAGT-CTATTAGGGTTGCTGAAACACTTTTACGTCGAAGATATACCTCGAAAG
65 TCTAGTCTTTTTAAGTCCT-TTAGGGTTGCAG-AATACTTTTACGTCGAAGGTATACCTC-AAGG
* * * *
2541387 GCATTTTGGTTATTTTTAGAACCAACTC
127 GCATTTTCGTTATTTTTAGAATCGAGTC
* * * * *
2541415 TTAGGTCATCACCGGATCCGCTTTTATGTCGGAGGTGAGCATTTAGGATAGGTTCATC-CCTTTT
1 CTAGGTCATCACCGGATCCGCTTTTATGCCGAAGATGAGCATTTAGGATAGGTTCATCACCATTT
* * *
2541479 ATATTCCTTTTTAAGTTCTTTAGGG
66 CTAGT-CTTTTTAAGTCCTTTAGGG
2541504 GTATCGGGTA
Statistics
Matches: 327, Mismatches: 58, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
154 50 0.15
155 42 0.13
156 71 0.22
157 72 0.22
158 64 0.20
159 28 0.09
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (154 bp):
CTAGGTCATCACCGGATCCGCTTTTATGCCGAAGATGAGCATTTAGGATAGGTTCATCACCATTT
CTAGTCTTTTTAAGTCCTTTAGGGTTGCAGAATACTTTTACGTCGAAGGTATACCTCAAGGGCAT
TTTCGTTATTTTTAGAATCGAGTC
Found at i:2542674 original size:21 final size:20
Alignment explanation
Indices: 2542628--2542680 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
2542618 GTAGCCAAAC
**
2542628 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
2542648 -TGTATCGATACACAAAAAAA
1 TTGTATCGATACAC-AAAAAA
2542668 TTGTATCGATACA
1 TTGTATCGATACA
2542681 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:2544912 original size:21 final size:21
Alignment explanation
Indices: 2544879--2544923 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2544869 TTGCAAGTTG
*
2544879 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2544901 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
2544921 AAA
1 AAA
2544924 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2555865 original size:20 final size:19
Alignment explanation
Indices: 2555840--2555945 Score: 91
Period size: 20 Copynumber: 5.7 Consensus size: 19
2555830 TTTTACCTAG
*
2555840 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTT-A
2555860 ATGTATCGATACA-T-TT-
1 ATGTATCGATACATTCTTA
2555876 ATG----GATACATTCTTCA
1 ATGTATCGATACATTCTT-A
*
2555892 ATGTATCGATACATTCATA
1 ATGTATCGATACATTCTTA
**
2555911 CATGTATCGATACATTGAATA
1 -ATGTATCGATACATT-CTTA
2555932 ATGTATCGATACAT
1 ATGTATCGATACAT
2555946 CTAGTTAAAA
Statistics
Matches: 74, Mismatches: 2, Indels: 20
0.77 0.02 0.21
Matches are distributed among these distances:
12 6 0.08
13 1 0.01
14 2 0.03
16 6 0.08
18 2 0.03
19 2 0.03
20 52 0.70
21 3 0.04
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATTCTTA
Done.