Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009014.1 Hibiscus syriacus cultivar Beakdansim tig00112402_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3470424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:2203070 original size:20 final size:20
Alignment explanation
Indices: 2203057--2203094 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2203047 TATATATGTT
2203057 ATGTATAAACTATATATACC
1 ATGTATAAACTATATATACC
2203077 ATGTATAAACTATA-ATAC
1 ATGTATAAACTATATATAC
2203095 TATATAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (20 bp):
ATGTATAAACTATATATACC
Found at i:2203148 original size:11 final size:11
Alignment explanation
Indices: 2203134--2203171 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
2203124 TCTACATAGT
2203134 TTATATATAAA
1 TTATATATAAA
*
2203145 TTATATATGAA
1 TTATATATAAA
2203156 TTATATATAAA
1 TTATATATAAA
*
2203167 CTATA
1 TTATA
2203172 CAATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:2203197 original size:17 final size:17
Alignment explanation
Indices: 2203177--2203230 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2203167 CTATACAATT
* *
2203177 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
2203194 TATAATTATAAATAATA
1 TATATTTATAAATTATA
2203211 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
2203229 TA
1 TA
2203231 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:2203250 original size:22 final size:19
Alignment explanation
Indices: 2203129--2203279 Score: 85
Period size: 22 Copynumber: 7.6 Consensus size: 19
2203119 TAGAATCTAC
2203129 ATAGTTTATATATAAATTAT
1 ATAGTTTATATATAAA-TAT
*
2203149 ATATGAATTATATATAAACTAT
1 ATA-G-TTTATATATAAA-TAT
* * * *
2203171 ACAATTTATATTTATATAT
1 ATAGTTTATATATAAATAT
*
2203190 -TA-TGTATAATTATAAATAAT
1 ATAGTTTAT-A-TATAAAT-AT
* *
2203210 ATA-TATTGTATA-AATTAT
1 ATAGT-TTATATATAAATAT
2203228 ATAGTTTATTAATATAAACTAT
1 ATAGTTTA-T-ATATAAA-TAT
*
2203250 ATAGTTTATATATATATAT
1 ATAGTTTATATATAAATAT
*
2203269 ATAGTATATAT
1 ATAGTTTATAT
2203280 GGTTTAAGGT
Statistics
Matches: 101, Mismatches: 18, Indels: 25
0.70 0.12 0.17
Matches are distributed among these distances:
17 4 0.04
18 9 0.09
19 26 0.26
20 25 0.25
21 8 0.08
22 29 0.29
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (19 bp):
ATAGTTTATATATAAATAT
Found at i:2203290 original size:7 final size:7
Alignment explanation
Indices: 2203280--2203318 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
2203270 TAGTATATAT
2203280 GGTTTAA
1 GGTTTAA
2203287 GGTTTAA
1 GGTTTAA
2203294 GGTTTAA
1 GGTTTAA
*
2203301 GGTTTAT
1 GGTTTAA
*
2203308 GATTTAA
1 GGTTTAA
2203315 GGTT
1 GGTT
2203319 AATTTATTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (7 bp):
GGTTTAA
Found at i:2203427 original size:11 final size:11
Alignment explanation
Indices: 2203367--2203420 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
2203357 TAGTAGTATT
2203367 TAAACTATATA
1 TAAACTATATA
2203378 TAAAC-A-ATA
1 TAAACTATATA
2203387 TAAACTA-ACT-
1 TAAACTATA-TA
* *
2203397 TATACTATATG
1 TAAACTATATA
2203408 TAAACTATATA
1 TAAACTATATA
2203419 TA
1 TA
2203421 CTATATAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 8 0.22
10 10 0.28
11 18 0.50
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.35
Consensus pattern (11 bp):
TAAACTATATA
Found at i:2203519 original size:24 final size:24
Alignment explanation
Indices: 2203473--2203522 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2203463 CTACGTAAAC
*
2203473 TATATAGTTTACATATGACCTATA
1 TATATAGTTTACATATGAACTATA
*
2203497 TATATAGTTTA-TTAGTGAACTATA
1 TATATAGTTTACATA-TGAACTATA
2203521 TA
1 TA
2203523 AACTATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (24 bp):
TATATAGTTTACATATGAACTATA
Found at i:2203591 original size:20 final size:19
Alignment explanation
Indices: 2203568--2203612 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2203558 AATTATAGTT
2203568 TATATTTATATACTACATAC
1 TATATTTATAT-CTACATAC
* *
2203588 TATAGTTTATATTTATATAC
1 TATA-TTTATATCTACATAC
2203608 TATAT
1 TATAT
2203613 ATATGAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 14 0.64
21 7 0.32
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (19 bp):
TATATTTATATCTACATAC
Found at i:2203622 original size:13 final size:13
Alignment explanation
Indices: 2203606--2203657 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 13
2203596 ATATTTATAT
2203606 ACTATATATATGA
1 ACTATATATATGA
2203619 ACTATAGTTTACATATGA
1 ACTATA---T--ATATGA
*
2203637 ACTATATATATAA
1 ACTATATATATGA
2203650 ACTATATA
1 ACTATATA
2203658 GTTTACATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
13 19 0.58
15 1 0.03
16 1 0.03
18 12 0.36
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (13 bp):
ACTATATATATGA
Found at i:2203623 original size:33 final size:32
Alignment explanation
Indices: 2203543--2203701 Score: 112
Period size: 33 Copynumber: 5.2 Consensus size: 32
2203533 TAGTATATAC
*
2203543 TATATA-TA-ATATATAAATTATAGTTTATATT
1 TATATACTATATATAT-AACTATAGTTTATATT
*
2203574 TATATAC----TACAT-ACTATAGTTTATATT
1 TATATACTATATATATAACTATAGTTTATATT
*
2203601 TATATACTATATATATGAACTATAGTTTACA--
1 TATATACTATATATAT-AACTATAGTTTATATT
*
2203632 TATGA-ACTATATATATAAACTATATAGTTTACA--
1 TAT-ATACTATATATAT-AAC--TATAGTTTATATT
*
2203665 TATGA-ACTATATATATAA-TATAGTTGATATT
1 TAT-ATACTATATATATAACTATAGTTTATATT
2203696 TATATA
1 TATATA
2203702 TGAACTATAG
Statistics
Matches: 108, Mismatches: 7, Indels: 26
0.77 0.05 0.18
Matches are distributed among these distances:
27 21 0.19
29 13 0.12
30 1 0.01
31 31 0.29
32 3 0.03
33 39 0.36
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (32 bp):
TATATACTATATATATAACTATAGTTTATATT
Found at i:2203634 original size:18 final size:18
Alignment explanation
Indices: 2203613--2203974 Score: 197
Period size: 18 Copynumber: 19.7 Consensus size: 18
2203603 TATACTATAT
2203613 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
2203631 ATATGAACTATA---T--
1 ATATGAACTATAGTTTAC
*
2203644 ATATAAACTATATAGTTTAC
1 ATATGAAC--TATAGTTTAC
2203664 ATATGAACTATA-TATATA-
1 ATATGAACTATAGT-T-TAC
** *
2203682 ATAT-AGTTGATA-TTTAT
1 ATATGAACT-ATAGTTTAC
2203699 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
2203717 ATATAAACTATATAGTTTAT
1 ATATGAAC--TATAGTTTAC
2203737 ATACT-AACTATAGTTTAC
1 ATA-TGAACTATAGTTTAC
*
2203755 ATATAAACTATAGTTGATATTTAC
1 ATATGAACTATA---G---TTTAC
*
2203779 ATATGAACTATATTTTAC
1 ATATGAACTATAGTTTAC
2203797 ATATGAACTATA---T--
1 ATATGAACTATAGTTTAC
*
2203810 ATATAAACTATATAGTTTAC
1 ATATGAAC--TATAGTTTAC
2203830 ATATGAACTATA-TATATAC
1 ATATGAACTATAGT-T-TAC
** *
2203849 -TAT-AGTTGATA-TTTAT
1 ATATGAACT-ATAGTTTAC
2203865 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
2203883 ATATAAACTATATAGTTTAT
1 ATATGAAC--TATAGTTTAC
2203903 ATACT-AACTATAGTTTAC
1 ATA-TGAACTATAGTTTAC
*
2203921 ATATAAACTATAGTTGATATTTAC
1 ATATGAACTATA---G---TTTAC
2203945 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
2203963 ATATGAACTATA
1 ATATGAACTATA
2203975 TATATAAACT
Statistics
Matches: 274, Mismatches: 24, Indels: 92
0.70 0.06 0.24
Matches are distributed among these distances:
13 14 0.05
15 10 0.04
16 4 0.01
17 23 0.08
18 137 0.50
19 5 0.02
20 44 0.16
21 5 0.02
24 32 0.12
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (18 bp):
ATATGAACTATAGTTTAC
Found at i:2203714 original size:53 final size:54
Alignment explanation
Indices: 2203641--2203896 Score: 222
Period size: 53 Copynumber: 4.6 Consensus size: 54
2203631 ATATGAACTA
2203641 TATATATAAACTATATAGTTTACATATGAACTATATATATAATATAGTTGATA-TT
1 TATATATAAAC--TATAGTTTACATATGAACTATATATATAATATAGTTGATACTT
* * * ** *
2203696 TATATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTAACT-ATAGTT
1 TATATATAAACTATAGTTTACATATGAACTATATA-TATA-ATA-TAGTTGATACTT
* * * *
2203752 TACATATAAACTATAGTTGATATTTACATATGAACTATAT-T-TTACATA--TGA-ACTA
1 TATATATAAACTATA---G---TTTACATATGAACTATATATATAATATAGTTGATACTT
*
2203807 TATATATAAACTATATAGTTTACATATGAACTATATATATACTATAGTTGATA-TT
1 TATATATAAAC--TATAGTTTACATATGAACTATATATATAATATAGTTGATACTT
* *
2203862 TATATATGAACTATAGTTTACATATAAACTATATA
1 TATATATAAACTATAGTTTACATATGAACTATATA
2203897 GTTTATATAC
Statistics
Matches: 164, Mismatches: 19, Indels: 38
0.74 0.09 0.17
Matches are distributed among these distances:
51 18 0.11
52 1 0.01
53 50 0.30
54 4 0.02
55 43 0.26
56 20 0.12
57 6 0.04
58 2 0.01
59 2 0.01
60 1 0.01
62 17 0.10
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (54 bp):
TATATATAAACTATAGTTTACATATGAACTATATATATAATATAGTTGATACTT
Found at i:2203733 original size:166 final size:164
Alignment explanation
Indices: 2203613--2203987 Score: 696
Period size: 166 Copynumber: 2.3 Consensus size: 164
2203603 TATACTATAT
2203613 ATATGAACTATAGTTTACATATGAACTATATATATAAACTATATAGTTTACATATGAACTATATA
1 ATATGAACTATAGTTTACATATGAACTATATATATAAACTATATAGTTTACATATGAACTATATA
2203678 TATAATATAGTTGATATTTATATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTA
66 TATAATATAGTTGATATTTATATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTA
2203743 ACTATAGTTTACATATAAACTATAGTTGATATTTAC
131 ACTATA--TTACATATAAACTATAGTTGATATTTAC
*
2203779 ATATGAACTATATTTTACATATGAACTATATATATAAACTATATAGTTTACATATGAACTATATA
1 ATATGAACTATAGTTTACATATGAACTATATATATAAACTATATAGTTTACATATGAACTATATA
*
2203844 TATACTATAGTTGATATTTATATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTA
66 TATAATATAGTTGATATTTATATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTA
2203909 ACTATAGTTTACATATAAACTATAGTTGATATTTAC
131 ACTATA--TTACATATAAACTATAGTTGATATTTAC
2203945 ATATGAACTATAGTTTACATATGAACTATATATATAAACTATA
1 ATATGAACTATAGTTTACATATGAACTATATATATAAACTATA
2203988 GTTTATATTT
Statistics
Matches: 206, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 206 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.41
Consensus pattern (164 bp):
ATATGAACTATAGTTTACATATGAACTATATATATAAACTATATAGTTTACATATGAACTATATA
TATAATATAGTTGATATTTATATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTA
ACTATATTACATATAAACTATAGTTGATATTTAC
Found at i:2203796 original size:80 final size:79
Alignment explanation
Indices: 2203626--2203976 Score: 406
Period size: 80 Copynumber: 4.5 Consensus size: 79
2203616 TGAACTATAG
*
2203626 TTTACATATGAACTATA---T--ATATAAACTATATAGTTTACATA-TGAACTATA--T--ATAT
1 TTTACATATGAACTATAGTTTACATATAAACTATATAGTTTATATACT-AACTATATTTACATAT
2203681 -AA-TATAGTTGATA
65 AAACTATAGTTGATA
*
2203694 TTTATATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTAACTATAGTTTACATAT
1 TTTACATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTAACTATA-TTTACATAT
2203759 AAACTATAGTTGATA
65 AAACTATAGTTGATA
* * * * **
2203774 TTTACATATGAACTATATTTTACATATGAACTATATA-TATAAACTATATAGTTTAC-ATATGAA
1 TTTACATATGAACTATAGTTTACATATAAACTATATAGT-T----TATATA-CTAACTATATTTA
2203837 CTATATATATACTATAGTTGATA
60 C-ATATA-A-ACTATAGTTGATA
*
2203860 TTTATATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTAACTATAGTTTACATAT
1 TTTACATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTAACTATA-TTTACATAT
2203925 AAACTATAGTTGATA
65 AAACTATAGTTGATA
*
2203940 TTTACATATGAACTATAGTTTACATATGAACTATATA
1 TTTACATATGAACTATAGTTTACATATAAACTATATA
2203977 TATAAACTAT
Statistics
Matches: 240, Mismatches: 18, Indels: 38
0.81 0.06 0.13
Matches are distributed among these distances:
68 16 0.07
71 1 0.00
73 29 0.12
74 1 0.00
76 1 0.00
78 4 0.02
79 3 0.01
80 94 0.39
81 4 0.02
82 14 0.06
83 6 0.03
84 14 0.06
85 4 0.02
86 48 0.20
87 1 0.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (79 bp):
TTTACATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTAACTATATTTACATATA
AACTATAGTTGATA
Found at i:2203819 original size:31 final size:32
Alignment explanation
Indices: 2203779--2203847 Score: 113
Period size: 33 Copynumber: 2.2 Consensus size: 32
2203769 TGATATTTAC
*
2203779 ATATGAACTATAT-TTTACATATGAACTATAT
1 ATATAAACTATATATTTACATATGAACTATAT
2203810 ATATAAACTATATAGTTTACATATGAACTATAT
1 ATATAAACTATATA-TTTACATATGAACTATAT
2203843 ATATA
1 ATATA
2203848 CTATAGTTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 12 0.34
33 23 0.66
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.41
Consensus pattern (32 bp):
ATATAAACTATATATTTACATATGAACTATAT
Found at i:2203847 original size:33 final size:33
Alignment explanation
Indices: 2203606--2203748 Score: 134
Period size: 33 Copynumber: 4.2 Consensus size: 33
2203596 ATATTTATAT
*
2203606 ACTATATATATGAAC--TATAGTTTACATATGA
1 ACTATATATATAAACTATATAGTTTACATATGA
2203637 ACTATATATATAAACTATATAGTTTACATATGA
1 ACTATATATATAAACTATATAGTTTACATATGA
*
2203670 ACTATATATATAATA-TAGTTGATA-TTTATATATGA
1 ACTATATATATAA-ACTA--T-ATAGTTTACATATGA
*
2203705 ACTATAGTTTACATATAAACTATATAGTTTATATACT-A
1 ACTATA---T--ATATAAACTATATAGTTTACATA-TGA
2203743 ACTATA
1 ACTATA
2203749 GTTTACATAT
Statistics
Matches: 96, Mismatches: 2, Indels: 21
0.81 0.02 0.18
Matches are distributed among these distances:
31 14 0.15
33 31 0.32
34 1 0.01
35 17 0.18
36 3 0.03
37 3 0.03
38 17 0.18
39 2 0.02
40 8 0.08
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.41
Consensus pattern (33 bp):
ACTATATATATAAACTATATAGTTTACATATGA
Found at i:2203944 original size:62 final size:57
Alignment explanation
Indices: 2203878--2204037 Score: 148
Period size: 60 Copynumber: 2.7 Consensus size: 57
2203868 TGAACTATAG
2203878 TTTACATATAAACTATATAGTTTATATACT-AACTATAGTTTACATATAAACTATAGTTGATA
1 TTTACATATAAACTATATAGTTTATATA-TGAACTATA---T--ATATAAACTATAGTTGATA
* * *
2203940 TTTACATATGAAC--TATAGTTTACATATGAACTATATATATAAACTATAGTTTATA
1 TTTACATATAAACTATATAGTTTATATATGAACTATATATATAAACTATAGTTGATA
* * *
2203995 TTTATATACTACATACTATAT-TTTATATATATAAACTATATAT
1 TTTACATA-TA-A-ACTATATAGTT-TATATATGAACTATATAT
2204038 TATATATATA
Statistics
Matches: 83, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
55 25 0.30
56 1 0.01
57 2 0.02
58 2 0.02
59 3 0.04
60 38 0.46
62 12 0.14
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (57 bp):
TTTACATATAAACTATATAGTTTATATATGAACTATATATATAAACTATAGTTGATA
Found at i:2203994 original size:20 final size:19
Alignment explanation
Indices: 2203991--2204065 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 19
2203981 AACTATAGTT
* *
2203991 TATATTTATATACTACATAC
1 TATATTTATATA-TATAAAC
2204011 TATATTTTATATATATAAAC
1 TATA-TTTATATATATAAAC
2204031 TATATATTATATATATAAAC
1 TATAT-TTATATATATAAAC
*
2204051 TATATATACTATATA
1 TATATTTA-TATATA
2204066 GTATAATTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
19 3 0.06
20 38 0.78
21 8 0.16
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATTTATATATATAAAC
Found at i:2204014 original size:27 final size:27
Alignment explanation
Indices: 2203982--2204041 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
2203972 ATATATATAA
* *
2203982 ACTATAGTTTATATTTATATACTACAT
1 ACTATAGTTTATATATATAAACTACAT
* *
2204009 ACTATATTTTATATATATAAACTATAT
1 ACTATAGTTTATATATATAAACTACAT
*
2204036 ATTATA
1 ACTATA
2204042 TATATAAACT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (27 bp):
ACTATAGTTTATATATATAAACTACAT
Found at i:2204034 original size:11 final size:11
Alignment explanation
Indices: 2204020--2204058 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
2204010 CTATATTTTA
2204020 TATATATAAAC
1 TATATATAAAC
*
2204031 TATATAT-TA-
1 TATATATAAAC
2204040 TATATATAAAC
1 TATATATAAAC
2204051 TATATATA
1 TATATATA
2204059 CTATATAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 7 0.29
10 2 0.08
11 15 0.62
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (11 bp):
TATATATAAAC
Found at i:2204043 original size:18 final size:18
Alignment explanation
Indices: 2203641--2204355 Score: 161
Period size: 18 Copynumber: 39.3 Consensus size: 18
2203631 ATATGAACTA
2203641 TATATATAAACTATATAGTT
1 TATATATAAACTATATA--T
* *
2203661 TACATATGAACTATATA-
1 TATATATAAACTATATAT
* *
2203678 TATA-ATATAGT-TGATATT
1 TATATATAAACTAT-ATA-T
*
2203696 TATATATGAACTATAGT-T
1 TATATATAAACTATA-TAT
*
2203714 TACATATAAACTATATAGT
1 TATATATAAACTATATA-T
2203733 T-TATATACTAACTATAGT-T
1 TATATATA--AACTATA-TAT
*
2203752 TACATATAAACTATAGTTGATATT
1 TATATATAAAC--TA--T-ATA-T
* * *
2203776 TACATATGAACTATATTT
1 TATATATAAACTATATAT
* *
2203794 TACATATGAAC----TA-
1 TATATATAAACTATATAT
2203807 TATATATAAACTATATAGTT
1 TATATATAAACTATATA--T
* *
2203827 TACATATGAACTATATA-
1 TATATATAAACTATATAT
**
2203844 TATACTAT-AGTTGATAT-T
1 TATA-TATAAACT-ATATAT
*
2203862 TATATATGAACTATAGT-T
1 TATATATAAACTATA-TAT
*
2203880 TACATATAAACTATATAGT
1 TATATATAAACTATATA-T
2203899 T-TATATACTAACTATAGT-T
1 TATATATA--AACTATA-TAT
*
2203918 TACATATAAACTATAGTTGATATT
1 TATATATAAAC--TA--T-ATA-T
* *
2203942 TACATATGAACTATAGT-T
1 TATATATAAACTATA-TAT
* *
2203960 TACATATGAACTATATA-
1 TATATATAAACTATATAT
* * * *
2203977 TATAAACTATAGTTTATATT
1 TATATA-TAAACTATATA-T
*
2203997 TATATACTACATACTATATTTT
1 TATATA-TA-A-ACTATA-TAT
2204019 ATATATATAAACTATATATT
1 -TATATATAAACTATATA-T
2204039 ATATATATAAACTATATA-
1 -TATATATAAACTATATAT
*
2204057 TACTATAT--AGTATA-AT
1 TA-TATATAAACTATATAT
*
2204073 T-TCCATATGAACTATATA-
1 TAT--ATATAAACTATATAT
* * *
2204091 TA-A-A-AACCATATAAAC
1 TATATATAAAC-TATATAT
* *
2204107 TATATACTATAGT-TGATAT
1 TATATA-TAAACTAT-ATAT
*
2204126 T-TATAT--ACTATATAA
1 TATATATAAACTATATAT
** *
2204141 TATA-ATTTA-TACTATAG
1 TATATATAAACTA-TATAT
2204158 TATATATAAACTATA-AT
1 TATATATAAACTATATAT
2204175 ATATATATAAACTATATAT
1 -TATATATAAACTATATAT
* *
2204194 TATATAGT--TC-AT-TAG
1 TATATA-TAAACTATATAT
**
2204209 TATATATAAACTATATGG
1 TATATATAAACTATATAT
*
2204227 TATATATAAAACTATACAT
1 TATATAT-AAACTATATAT
* *
2204246 TATATAGT---TTAT-TAG
1 TATATA-TAAACTATATAT
*
2204261 TATATATAAACTATATAA
1 TATATATAAACTATATAT
**
2204279 TATATATAAACTATATGG
1 TATATATAAACTATATAT
* *
2204297 TATATATAAATTATACAT
1 TATATATAAACTATATAT
** *
2204315 TATATAT-ATTTCAT-TAG
1 TATATATAAACT-ATATAT
2204332 TATATATAAACTATATAT
1 TATATATAAACTATATAT
2204350 TATATA
1 TATATA
2204356 GTTCATTAGT
Statistics
Matches: 521, Mismatches: 82, Indels: 186
0.66 0.10 0.24
Matches are distributed among these distances:
13 9 0.02
14 6 0.01
15 31 0.06
16 31 0.06
17 56 0.11
18 200 0.38
19 41 0.08
20 98 0.19
21 3 0.01
22 15 0.03
23 9 0.02
24 22 0.04
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.43
Consensus pattern (18 bp):
TATATATAAACTATATAT
Found at i:2204139 original size:7 final size:6
Alignment explanation
Indices: 2204122--2204355 Score: 55
Period size: 7 Copynumber: 38.2 Consensus size: 6
2204112 ACTATAGTTG
* * *
2204122 ATATTT ATATACT ATATA- ATATA- ATTTAT ACTATAGT ATATAT AAACTAT
1 ATATAT ATATA-T ATATAT ATATAT ATATAT A-TATA-T ATATAT ATA-TAT
* *
2204172 A-ATAT ATATAT AAACTAT ATAT-T ATATAGT -TCAT-T AGTATAT ATAAACT
1 ATATAT ATATAT ATA-TAT ATATAT ATATA-T AT-ATAT A-TATAT ATATA-T
* * * * *
2204221 ATATGGT ATATAT A-AAACT ATACAT -TATAT AGTTTAT -TAGTAT ATATAA
1 ATAT-AT ATATAT ATATA-T ATATAT ATATAT A-TATAT ATA-TAT ATATAT
* * * *
2204270 ACTATAT A-ATAT ATATAA ACTATAT GGTATAT ATAAAT -TATAC AT-TAT
1 A-TATAT ATATAT ATATAT A-TATAT -ATATAT ATATAT ATATAT ATATAT
* *
2204318 ATATAT TTCAT-T AGTATAT ATAAACT ATATAT -TATAT A
1 ATATAT AT-ATAT A-TATAT ATATA-T ATATAT ATATAT A
2204356 GTTCATTAGT
Statistics
Matches: 167, Mismatches: 29, Indels: 64
0.64 0.11 0.25
Matches are distributed among these distances:
5 43 0.26
6 53 0.32
7 69 0.41
8 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (6 bp):
ATATAT
Found at i:2204223 original size:26 final size:25
Alignment explanation
Indices: 2204155--2204277 Score: 76
Period size: 26 Copynumber: 4.8 Consensus size: 25
2204145 ATTTATACTA
2204155 TAGTATATATAAACTATA-A-TATAT
1 TAGTATATATAAACTATATAGT-TAT
* * *
2204179 ATA-TAAACTATATATTATATAGTTCAT
1 -TAGTATA-TATAAACTATATAGTT-AT
*
2204206 TAGTATATATAAACTATAT-GGTAT
1 TAGTATATATAAACTATATAGTTAT
* * *
2204230 ATA-TAAAACTATACATTATATAGTTTAT
1 -TAGT-ATA-TATAAACTATATAGT-TAT
2204258 TAGTATATATAAACTATATA
1 TAGTATATATAAACTATATA
2204278 ATATATATAA
Statistics
Matches: 73, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
24 6 0.08
25 17 0.23
26 35 0.48
27 11 0.15
28 4 0.05
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (25 bp):
TAGTATATATAAACTATATAGTTAT
Found at i:2204283 original size:33 final size:33
Alignment explanation
Indices: 2204226--2204533 Score: 256
Period size: 33 Copynumber: 9.6 Consensus size: 33
2204216 AAACTATATG
* *
2204226 GTATATATAAAACTATACATTATATAGTTTATTA
1 GTATATAT-AAACTATATATTATATAGTTCATTA
** *
2204260 GTATATATAAACTATATAATATATATA-AACTATATG
1 GTATATATAAACTATAT-AT-TATATAGTTC-AT-TA
* * *
2204296 GTATATATAAATTATACATTATATATATTTCATTA
1 GTATATATAAACTATATA-T-TATATAGTTCATTA
2204331 GTATATATAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
* *
2204364 GTATATATAACCTATATAGTATAT-G-------
1 GTATATATAAACTATATATTATATAGTTCATTA
* *
2204389 GTATATACAAACTATATATTATATAGTGCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
* * *
2204422 GTATATATAACCTATGTAGTATAT-G-------
1 GTATATATAAACTATATATTATATAGTTCATTA
*
2204447 GTATATACAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
*
2204480 GTATATATAAACTATATATTGA-AAAGTTCATTA
1 GTATATATAAACTATATATT-ATATAGTTCATTA
*
2204513 GTATATATAACCTATATATTA
1 GTATATATAAACTATATATTA
2204534 ATTTATTAAT
Statistics
Matches: 222, Mismatches: 29, Indels: 48
0.74 0.10 0.16
Matches are distributed among these distances:
25 41 0.18
26 2 0.01
32 3 0.01
33 111 0.50
34 12 0.05
35 26 0.12
36 26 0.12
37 1 0.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.42
Consensus pattern (33 bp):
GTATATATAAACTATATATTATATAGTTCATTA
Found at i:2204372 original size:2 final size:2
Alignment explanation
Indices: 2203971--2204355 Score: 61
Period size: 2 Copynumber: 185.0 Consensus size: 2
2203961 ACATATGAAC
* * * *
2203971 TA TA TA TA TA AA CTA TA GTT TA TA TT TA TA TA CTA CA TA CTA TA
1 TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA -TA TA TA -TA TA
* * *
2204015 T- TT TA TA TA TA TA AA CTA TA TA T- TA TA TA TA TA AA CTA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * * *
2204057 TA CTA TA TA GTA TA -A TT TC CA TA TGA -A CTA TA TA TA AA AA CCA
1 TA -TA TA TA -TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA TA -TA
* *
2204100 TA TA AA CTA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA -A TA
1 TA TA TA -TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA TA TA
* *
2204143 TA -A TT TA TA CTA TA GTA TA TA TA AA CTA TA -A 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
* * *
2204184 AA CTA TA TA T- TA TA TA GT- TCA T- TA GTA TA TA TA AA CTA TA TGG
1 TA -TA TA TA TA TA TA TA -TA T-A TA TA -TA TA TA TA TA -TA TA T-A
* * *
2204227 TA TA TA TA -A AA CTA TA CA T- TA TA TA GTT TA T- TA GTA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA
* * * *
2204267 TA AA CTA TA TA -A TA TA TA TA AA CTA TA TGG TA TA TA TA AA T-
1 TA TA -TA TA TA TA TA TA TA TA TA -TA TA T-A TA TA TA TA TA TA
* * *
2204308 TA TA CA T- TA TA TA TA TT TCA T- TA GTA TA TA TA AA CTA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA -TA TA TA TA TA -TA TA TA
2204349 T- TA TA TA
1 TA TA TA TA
2204356 GTTCATTAGT
Statistics
Matches: 276, Mismatches: 54, Indels: 106
0.63 0.12 0.24
Matches are distributed among these distances:
1 19 0.07
2 212 0.77
3 45 0.16
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:2204385 original size:18 final size:18
Alignment explanation
Indices: 2204153--2204387 Score: 174
Period size: 18 Copynumber: 13.6 Consensus size: 18
2204143 TAATTTATAC
2204153 TATAGTATATATAAACTA
1 TATAGTATATATAAACTA
2204171 TAATA-TATATATAAACTA
1 T-ATAGTATATATAAACTA
**
2204189 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
2204205 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
*
2204222 TATGGTATATATAAAACTA
1 TATAGTATATAT-AAACTA
* ***
2204241 TACA-T-TATATAGTTTA
1 TATAGTATATATAAACTA
2204257 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
*
2204274 TATAATATATATAAACTA
1 TATAGTATATATAAACTA
* *
2204292 TATGGTATATATAAATTA
1 TATAGTATATATAAACTA
* * **
2204310 TACATTATATAT-ATTTCA
1 TATAGTATATATAAACT-A
2204328 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
**
2204345 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
*
2204361 T-TAGTATATATAACCTA
1 TATAGTATATATAAACTA
2204378 TATAGTATAT
1 TATAGTATAT
2204388 GGTATATACA
Statistics
Matches: 169, Mismatches: 30, Indels: 36
0.72 0.13 0.15
Matches are distributed among these distances:
15 9 0.05
16 21 0.12
17 46 0.27
18 82 0.49
19 11 0.07
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:2204402 original size:58 final size:58
Alignment explanation
Indices: 2204331--2204497 Score: 298
Period size: 58 Copynumber: 2.9 Consensus size: 58
2204321 TATTTCATTA
*
2204331 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
* *
2204389 GTATATACAAACTATATATTATATAGTGCATTAGTATATATAACCTATGTAGTATATG
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
*
2204447 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATA
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATA
2204498 TTGAAAAGTT
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 103 1.00
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (58 bp):
GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
Found at i:2204403 original size:25 final size:25
Alignment explanation
Indices: 2204364--2204470 Score: 88
Period size: 25 Copynumber: 4.0 Consensus size: 25
2204354 TAGTTCATTA
* *
2204364 GTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATAGTATATG
*
2204389 GTATATACAAACTATATATTATATAG
1 GTATATACAAACTATATAGTATAT-G
* *
2204415 TGCATTAGTATATATAACCTATGTAGTATATG
1 -G---TA-TATACA-AA-CTATATAGTATATG
*
2204447 GTATATACAAACTATATATTATAT
1 GTATATACAAACTATATAGTATAT
2204471 AGTTCATTAG
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
25 32 0.49
26 3 0.05
27 6 0.09
28 2 0.03
30 2 0.03
31 6 0.09
32 3 0.05
33 11 0.17
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.40
Consensus pattern (25 bp):
GTATATACAAACTATATAGTATATG
Found at i:2205197 original size:113 final size:113
Alignment explanation
Indices: 2205048--2205271 Score: 326
Period size: 113 Copynumber: 2.0 Consensus size: 113
2205038 TGTTCTTCAT
* * *
2205048 TTGTTCATCCTAGTTCTTCCCCAAAACCCTCATTTGATCTTCGAAAACACCGAAACACAAGCCAT
1 TTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCGAAACACAAACCAT
* * *
2205113 TTCGTGTTGTTTTGGATCAAACACCCA-AATATTCATCCA-TGTTCATCC
66 TTCATATT-TTTTCGATCAAACACCCATAA-ATTCATCCATTGTTCATCC
* * *
2205161 TTGTTCATCCCAGTTCTTCTCCAAAACCCTCCTTTGATCTTCAAAAACACCGAAACCCAAACCAT
1 TTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCGAAACACAAACCAT
*
2205226 TTCATATTTTTTCGATCAAACACCCATAAATTCATCTATTGTTCAT
66 TTCATATTTTTTCGATCAAACACCCATAAATTCATCCATTGTTCAT
2205272 ATGTGTTCTT
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
112 25 0.25
113 74 0.75
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (113 bp):
TTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCGAAACACAAACCAT
TTCATATTTTTTCGATCAAACACCCATAAATTCATCCATTGTTCATCC
Found at i:2205424 original size:6 final size:6
Alignment explanation
Indices: 2205409--2205548 Score: 68
Period size: 6 Copynumber: 23.5 Consensus size: 6
2205399 TCTAACCCTT
* * * * **
2205409 AACCCG AACCCA AACCCG ATCCCA AACCCA AACCCG AACCTG AA-CCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * * * * ** *
2205456 AAACCA GAACCGA AACCCA AACCCG AACCC- ACCCCG AACATA AACCCG
1 AACCCA -AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * * * * * *
2205504 AACCCC ACCCCG AACCCA AACCTA AACCCC ACCCCG AACCCA AAC
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AAC
2205549 TCATACTCGA
Statistics
Matches: 98, Mismatches: 33, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
5 7 0.07
6 87 0.89
7 4 0.04
ACGTcount: A:0.41, C:0.49, G:0.08, T:0.03
Consensus pattern (6 bp):
AACCCA
Found at i:2205426 original size:12 final size:12
Alignment explanation
Indices: 2205409--2205548 Score: 93
Period size: 12 Copynumber: 11.2 Consensus size: 12
2205399 TCTAACCCTT
2205409 AACCCGAACCCA
1 AACCCGAACCCA
*
2205421 AACCCGATCCCA
1 AACCCGAACCCA
* *
2205433 AACCCAAACCCG
1 AACCCGAACCCA
* *
2205445 AACCTGAACCAA
1 AACCCGAACCCA
2205457 AACCAGAACCGAAACCCA
1 AA-C----CCG-AACCCA
2205475 AACCCGAACCC-
1 AACCCGAACCCA
* **
2205486 ACCCCGAACATA
1 AACCCGAACCCA
*
2205498 AACCCGAACCCC
1 AACCCGAACCCA
*
2205510 ACCCCGAACCCA
1 AACCCGAACCCA
** *
2205522 AACCTAAACCCC
1 AACCCGAACCCA
*
2205534 ACCCCGAACCCA
1 AACCCGAACCCA
2205546 AAC
1 AAC
2205549 TCATACTCGA
Statistics
Matches: 93, Mismatches: 28, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
11 8 0.09
12 71 0.76
13 4 0.04
17 3 0.03
18 7 0.08
ACGTcount: A:0.41, C:0.49, G:0.08, T:0.03
Consensus pattern (12 bp):
AACCCGAACCCA
Found at i:2205438 original size:18 final size:18
Alignment explanation
Indices: 2205409--2205548 Score: 102
Period size: 18 Copynumber: 7.8 Consensus size: 18
2205399 TCTAACCCTT
*
2205409 AACCCGAACCCAAACCCG
1 AACCCAAACCCAAACCCG
*
2205427 ATCCCAAACCCAAACCCG
1 AACCCAAACCCAAACCCG
** * *
2205445 AACCTGAACCAAAACCAG
1 AACCCAAACCCAAACCCG
*
2205463 AACCGAAACCCAAACCCG
1 AACCCAAACCCAAACCCG
* * ***
2205481 AACCC-ACCCCGAACATA
1 AACCCAAACCCAAACCCG
* * *
2205498 AACCCGAACCCCACCCCG
1 AACCCAAACCCAAACCCG
* *
2205516 AACCCAAACCTAAACCCC
1 AACCCAAACCCAAACCCG
* *
2205534 ACCCCGAACCCAAAC
1 AACCCAAACCCAAAC
2205549 TCATACTCGA
Statistics
Matches: 90, Mismatches: 31, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
17 12 0.13
18 78 0.87
ACGTcount: A:0.41, C:0.49, G:0.08, T:0.03
Consensus pattern (18 bp):
AACCCAAACCCAAACCCG
Found at i:2205492 original size:24 final size:24
Alignment explanation
Indices: 2205469--2205548 Score: 117
Period size: 24 Copynumber: 3.4 Consensus size: 24
2205459 CCAGAACCGA
2205469 AACCCAAACCCGAA-CCCACCCCG
1 AACCCAAACCCGAACCCCACCCCG
**
2205492 AACATAAACCCGAACCCCACCCCG
1 AACCCAAACCCGAACCCCACCCCG
**
2205516 AACCCAAACCTAAACCCCACCCCG
1 AACCCAAACCCGAACCCCACCCCG
2205540 AACCCAAAC
1 AACCCAAAC
2205549 TCATACTCGA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
23 12 0.24
24 38 0.76
ACGTcount: A:0.39, C:0.53, G:0.06, T:0.03
Consensus pattern (24 bp):
AACCCAAACCCGAACCCCACCCCG
Found at i:2205892 original size:63 final size:63
Alignment explanation
Indices: 2205788--2206009 Score: 302
Period size: 63 Copynumber: 3.5 Consensus size: 63
2205778 TATATACTGG
* * **
2205788 TTTATTGTTGTTGATGTAAATGATATACTGTCAGAAACATTTAATGTAAACTAACTTTGGTTT
1 TTTATTGCTGTTGATGTAAATGATATACTGTCAGAAGCATTTAATGTAAACTAACCATGGTTT
* * * *
2205851 TTTATTGCTGCTGATGTAAATGATATACTGTCAGAAGCATTTCATATAAACTAACCCTGGTTTT
1 TTTATTGCTGTTGATGTAAATGATATACTGTCAGAAGCATTTAATGTAAACTAACCATGG-TTT
* *
2205915 TTTATTGCTGTTGATGTAAATGATATACTGTCAGAAGCATTTAATGAAAACTAACCATGATTT
1 TTTATTGCTGTTGATGTAAATGATATACTGTCAGAAGCATTTAATGTAAACTAACCATGGTTT
* **
2205978 TTT-TTGCAAGGGGATGTAAATGATATACTGTC
1 TTTATTGC-TGTTGATGTAAATGATATACTGTC
2206010 CAAAGCAATT
Statistics
Matches: 141, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
62 4 0.03
63 80 0.57
64 57 0.40
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (63 bp):
TTTATTGCTGTTGATGTAAATGATATACTGTCAGAAGCATTTAATGTAAACTAACCATGGTTT
Found at i:2208277 original size:20 final size:20
Alignment explanation
Indices: 2208249--2208293 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2208239 TTCTGCTTTA
*
2208249 TTCTATTTTATATTATTTGC
1 TTCTATTTTATATTACTTGC
* *
2208269 TTCTGTTTTATATTGCTTGC
1 TTCTATTTTATATTACTTGC
2208289 TTCTA
1 TTCTA
2208294 CTTGATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.13, G:0.09, T:0.62
Consensus pattern (20 bp):
TTCTATTTTATATTACTTGC
Found at i:2208448 original size:23 final size:23
Alignment explanation
Indices: 2208395--2208448 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
2208385 CTTAATGCAG
** *
2208395 GATGCTTGCTGAATTGATGCAAC
1 GATGCTTGCCAAATTGATACAAC
* * *
2208418 GATTCTTGCCAAATTGGTACAAT
1 GATGCTTGCCAAATTGATACAAC
2208441 GATGCTTG
1 GATGCTTG
2208449 TCAGTTGTTG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (23 bp):
GATGCTTGCCAAATTGATACAAC
Found at i:2209404 original size:31 final size:32
Alignment explanation
Indices: 2209328--2209409 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 32
2209318 ATTAACCAGG
2209328 TCAATCTCGGGTTCGGGTTCATATCAGTCGGAT
1 TCAAT-TCGGGTTCGGGTTCATATCAGTCGGAT
* * **
2209361 GCAATTCAGGTTCGGGTATCATAT-TTTCGG-T
1 TCAATTCGGGTTCGGGT-TCATATCAGTCGGAT
*
2209392 TCAATTCGGGTTCAGGTT
1 TCAATTCGGGTTCGGGTT
2209410 GTTCTCAGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
30 1 0.02
31 15 0.37
32 15 0.37
33 10 0.24
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (32 bp):
TCAATTCGGGTTCGGGTTCATATCAGTCGGAT
Found at i:2209430 original size:11 final size:11
Alignment explanation
Indices: 2209415--2209444 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2209405 AGGTTGTTCT
2209415 CAGGTCGGATG
1 CAGGTCGGATG
*
2209426 TAGGTCGGATG
1 CAGGTCGGATG
2209437 CAGGTCGG
1 CAGGTCGG
2209445 GTTCAGATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.47, T:0.20
Consensus pattern (11 bp):
CAGGTCGGATG
Found at i:2212807 original size:2 final size:2
Alignment explanation
Indices: 2212800--2212850 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2212790 AGATTATCTA
2212800 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
2212842 AT AT AT AT A
1 AT AT AT AT A
2212851 AGTTATTATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2216746 original size:21 final size:20
Alignment explanation
Indices: 2216708--2216746 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2216698 CAAAATGCAA
* *
2216708 GATAACAAAATAAGACATTC
1 GATAAAAAAATAAAACATTC
2216728 GATAAAAAATATAAAACAT
1 GATAAAAAA-ATAAAACAT
2216747 GCATGAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.21
Consensus pattern (20 bp):
GATAAAAAAATAAAACATTC
Found at i:2218403 original size:91 final size:92
Alignment explanation
Indices: 2218293--2218478 Score: 270
Period size: 91 Copynumber: 2.0 Consensus size: 92
2218283 AATGGACGAG
* * * *
2218293 CCAAGGTTGAATAAGTTCTTCTTATTATGAACTTCTTCTCCCTCATTTG-ATGAGTTCTTCTCAT
1 CCAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCA-TCGAATGAGTTCTTCTCAT
*
2218357 TATG-AA-CTCTTCATTGGAAATGTTGAT
65 TATGAAACCT-TTCATTAGAAATGTTGAT
* *
2218384 CCAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTTTCCCTTATCGAATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATCGAATGAGTTCTTCTCATT
2218449 ATGAAACCTTTCATTAGAAATGTTGAT
66 ATGAAACCTTTCATTAGAAATGTTGAT
2218476 CCA
1 CCA
2218479 CCTCCTTCTG
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
90 2 0.02
91 59 0.69
92 22 0.26
93 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (92 bp):
CCAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATCGAATGAGTTCTTCTCATT
ATGAAACCTTTCATTAGAAATGTTGAT
Found at i:2218778 original size:116 final size:117
Alignment explanation
Indices: 2218588--2218813 Score: 350
Period size: 116 Copynumber: 1.9 Consensus size: 117
2218578 TGAAAACGAG
* * *
2218588 CTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGGTGAGTTATTCTCATT
1 CTAAGGTTAAACAAGTTCTTCTCAATATGAACTTCTTCTCCCTCATCAGGTGAGTTATTCTCATT
*
2218653 ATGAACTCTCCACTGGAAATGTTAATCCTA-CTCATTT-TGTGATGGTATTGAA
66 ATGAACTCTCCACTGGAAATATTAATCC-ACCTC-TTTCTGTGATGGTATTGAA
* *
2218705 CTAAGGTTAAACAAG-TCTTCTCAATATGAACTTCTTCTCCCTCGTCAGGTGAGTTCTTCTCATT
1 CTAAGGTTAAACAAGTTCTTCTCAATATGAACTTCTTCTCCCTCATCAGGTGAGTTATTCTCATT
*
2218769 ATGAACTCTCCACTGGAAATATTGATCCACCTCTTTCTGTGATGG
66 ATGAACTCTCCACTGGAAATATTAATCCACCTCTTTCTGTGATGG
2218814 AATCGAACAA
Statistics
Matches: 100, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
115 4 0.04
116 82 0.82
117 14 0.14
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (117 bp):
CTAAGGTTAAACAAGTTCTTCTCAATATGAACTTCTTCTCCCTCATCAGGTGAGTTATTCTCATT
ATGAACTCTCCACTGGAAATATTAATCCACCTCTTTCTGTGATGGTATTGAA
Found at i:2218980 original size:319 final size:320
Alignment explanation
Indices: 2218386--2219313 Score: 1391
Period size: 319 Copynumber: 2.9 Consensus size: 320
2218376 ATGTTGATCC
* * * ** *
2218386 AAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTTTCCCTTATC-GAATGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCAG-GTGAGTTCTTCTCATTA
* * * * *
2218450 TGAAAC-CTTTCATTAGAAATGTTGATCCACCTCCTTCTGTGATGGAATCAAACAAAGTGATGAT
65 TG-AACTC-TCCACTGGAAATGTTGATCCACCTCTTTCTGTGATGGAATCGAACAAAGTGATGAT
*
2218514 GTTGATCCAACTCCATATGCGATGGTTGAGCCAAGTATTGGTGTTGTTCCAAC-TCTTTATGTGA
128 GTTGATCCAACTCCATATGCGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTTC-TTATGTGA
* *
2218578 TGAAAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGGTGAGT
192 TGGAAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGT
* * * * *
2218643 TATTCTCATTATGAACTCTCCACTGGAAATGTTAATCCTACTCATTTTGTGATGGTATTGAACT
257 TCTTCTCATTATGAACTCTCCACTAGAAATGTTAATCATACTCATTTTGTGATGGAATCGAACT
*
2218707 AAGGTTAAACAAG-TCTTCTCAATATGAACTTCTTCTCCCTCGTCAGGTGAGTTCTTCTCATTAT
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCAGGTGAGTTCTTCTCATTAT
* *
2218771 GAACTCTCCACTGGAAATATTGATCCACCTCTTTCTGTGATGGAATCGAACAAAGTGATGATGCT
66 GAACTCTCCACTGGAAATGTTGATCCACCTCTTTCTGTGATGGAATCGAACAAAGTGATGATGTT
* * *
2218836 GATCCAACTCTATATACGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTTCATATGTGATGGA
131 GATCCAACTCCATATGCGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTTCTTATGTGATGGA
* * * *
2218901 AATGAGCTAAGGTTGAACAAATCCTTCTCATTATGAACTTCTTCTCCCTCATCGGATTAGTTCTT
196 AACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTT
* *
2218966 CTCATTATGAACTCTCCACTAGAAATTTTGATCATACTCATTTTGTGATGGAATCGAACT
261 CTCATTATGAACTCTCCACTAGAAATGTTAATCATACTCATTTTGTGATGGAATCGAACT
* * *
2219026 AAGATTAAACAAGTTCTTATCATTATGAACTTCTTCTCCCTCGTCATGTGAGTTCTTCTCATTAT
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCAGGTGAGTTCTTCTCATTAT
*
2219091 GAACTCTCCACTGG-AATGTTGATCCACCT-TCTTCTGTTATGGAATCGAACAAAGTGATGATGT
66 GAACTCTCCACTGGAAATGTTGATCCACCTCT-TTCTGTGATGGAATCGAACAAAGTGATGATGT
* *
2219154 TGATCCAACTCCATATGCGATGGATGAGCCAAGTATTGGTGTTGTTCTAACTCCTTATGTGATGG
130 TGATCCAACTCCATATGCGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTTCTTATGTGATGG
* * *
2219219 AAACGAGCTTAGGTTCAACAAGTTCTTCTCATTATGAGCTTCTTCTCCCTCATCGGATGAGTTCT
195 AAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCT
* *
2219284 TCTTATTATGAACTCTCCACTCGAAATGTT
260 TCTCATTATGAACTCTCCACTAGAAATGTT
2219314 GATTAGTTTA
Statistics
Matches: 549, Mismatches: 53, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
318 1 0.00
319 426 0.78
320 109 0.20
321 13 0.02
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (320 bp):
AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCAGGTGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATGTTGATCCACCTCTTTCTGTGATGGAATCGAACAAAGTGATGATGTT
GATCCAACTCCATATGCGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTTCTTATGTGATGGA
AACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTT
CTCATTATGAACTCTCCACTAGAAATGTTAATCATACTCATTTTGTGATGGAATCGAACT
Found at i:2219098 original size:117 final size:116
Alignment explanation
Indices: 2218892--2219102 Score: 309
Period size: 117 Copynumber: 1.8 Consensus size: 116
2218882 CAACTTCATA
* * * *
2218892 TGTGATGGAAATGAGCTAAGGTTGAACAAATCCTTCTCATTATGAACTTCTTCTCCCTCATCGGA
1 TGTGATGGAAATGAACTAAGATTAAACAAATCCTTATCATTATGAACTTCTTCTCCCTCATC-GA
2218957 TTAGTTCTTCTCATTATGAACTCTCCACTAGAAATTTTGATCATACTCATTT
65 TTAGTTCTTCTCATTATGAACTCTCCACTAGAAATTTTGATCATACTCATTT
* * *
2219009 TGTGATGG-AATCGAACTAAGATTAAACAAGTTCTTATCATTATGAACTTCTTCTCCCTCGTC-A
1 TGTGATGGAAAT-GAACTAAGATTAAACAAATCCTTATCATTATGAACTTCTTCTCCCTCATCGA
2219072 TGTGAGTTCTTCTCATTATGAACTCTCCACT
65 T-T-AGTTCTTCTCATTATGAACTCTCCACT
2219103 GGAATGTTGA
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
115 2 0.02
116 4 0.05
117 78 0.93
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (116 bp):
TGTGATGGAAATGAACTAAGATTAAACAAATCCTTATCATTATGAACTTCTTCTCCCTCATCGAT
TAGTTCTTCTCATTATGAACTCTCCACTAGAAATTTTGATCATACTCATTT
Found at i:2225390 original size:23 final size:23
Alignment explanation
Indices: 2225344--2225418 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
2225334 AGAACCCGAT
2225344 GGGGATATCGATTCCC--T-AAAG
1 GGGGA-ATCGATTCCCATTCAAAG
*
2225365 GGGGAATTGATTCCCATTCAAAG
1 GGGGAATCGATTCCCATTCAAAG
* *
2225388 GGGGAATCGGTTCCCCTTC-AAG
1 GGGGAATCGATTCCCATTCAAAG
2225410 GGGGAATCG
1 GGGGAATCG
2225419 GTTCTTCCTG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
20 9 0.19
21 5 0.11
22 13 0.28
23 20 0.43
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (23 bp):
GGGGAATCGATTCCCATTCAAAG
Found at i:2225410 original size:22 final size:23
Alignment explanation
Indices: 2225361--2225422 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2225351 TCGATTCCCT
* *
2225361 AAAGGGGGAATTGATTCCCATTC
1 AAAGGGGGAATCGGTTCCCATTC
*
2225384 AAAGGGGGAATCGGTTCCCCTTC
1 AAAGGGGGAATCGGTTCCCATTC
2225407 -AAGGGGGAATCGGTTC
1 AAAGGGGGAATCGGTTC
2225423 TTCCTGCACT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 16 0.44
23 20 0.56
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (23 bp):
AAAGGGGGAATCGGTTCCCATTC
Found at i:2228507 original size:12 final size:12
Alignment explanation
Indices: 2228475--2228514 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2228465 TGCGGGAAAA
2228475 TTAAAATC-A-T
1 TTAAAATCTATT
2228485 TT-AAATCTATT
1 TTAAAATCTATT
*
2228496 TTAAAATTTATT
1 TTAAAATCTATT
2228508 TTAAAAT
1 TTAAAAT
2228515 ATAGATTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 3 0.12
12 15 0.58
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAAAATCTATT
Found at i:2228526 original size:22 final size:22
Alignment explanation
Indices: 2228501--2229209 Score: 979
Period size: 22 Copynumber: 32.2 Consensus size: 22
2228491 CTATTTTAAA
*
2228501 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
2228523 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
***
2228545 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
2228567 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
2228589 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
2228611 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
2228633 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
2228655 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2228677 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2228699 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
** ***
2228721 ATTTATTTTAAAATATAAAAAA
1 ATTTATTTTAAAATATGGATTG
*
2228743 ATTTATTTTAAAATATTGATTG
1 ATTTATTTTAAAATATGGATTG
***
2228765 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
*
2228787 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
2228809 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
2228831 ATTTATTTTCAAATATGGATAG
1 ATTTATTTTAAAATATGGATTG
*
2228853 ATTTATTTTAGAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2228875 ATTTATTTTAAAAATATGGATTG
1 ATTTATTTT-AAAATATGGATTG
2228898 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
2228920 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
* ***
2228942 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
2228964 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
***
2228986 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
* *
2229008 AATTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
* *
2229030 ATTCATTTTAAAATATGTATTG
1 ATTTATTTTAAAATATGGATTG
2229052 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2229074 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
2229096 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
**
2229118 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
2229139 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
*
2229162 ATTTATTTTAATATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2229184 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2229206 ATTT
1 ATTT
2229210 CATTATTGCA
Statistics
Matches: 605, Mismatches: 79, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
21 1 0.00
22 582 0.96
23 22 0.04
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:2235442 original size:14 final size:14
Alignment explanation
Indices: 2235425--2235454 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2235415 AAAGTGCAAT
2235425 AATTAAAGGATTGA
1 AATTAAAGGATTGA
*
2235439 AATTAAAGTATTGA
1 AATTAAAGGATTGA
2235453 AA
1 AA
2235455 AATGAGGGGC
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:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (14 bp):
AATTAAAGGATTGA
Found at i:2236921 original size:14 final size:14
Alignment explanation
Indices: 2236904--2236933 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2236894 AAAGTGCAAT
2236904 AATTAAAGGATTGA
1 AATTAAAGGATTGA
*
2236918 AATTAAAGTATTGA
1 AATTAAAGGATTGA
2236932 AA
1 AA
2236934 AATGAGGGGC
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:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (14 bp):
AATTAAAGGATTGA
Found at i:2239881 original size:42 final size:42
Alignment explanation
Indices: 2239758--2239944 Score: 248
Period size: 42 Copynumber: 4.4 Consensus size: 42
2239748 TATCATGAGC
* *
2239758 CCTTTTGTGGCGTTTGTATCCAAAAACACCGCTATAGATCTGA
1 CCTTTTGCGGCGTTTGT-TCAAAAAACACCGCTATAGATCTGA
* *
2239801 CCTTTTGCGGTGTTTGTTTCAAAAAAGCGCCGCTATAGATCTGA
1 CCTTTTGCGGCGTTTG-TTCAAAAAA-CACCGCTATAGATCTGA
* * *
2239845 CATTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATTTGA
1 CCTTTTGCGGCGTTTGTTCAAAAAACACCGCTATAGATCTGA
* * *
2239887 CCTTTTGCGGTGTTTGTTCCAAAAACACTGCTATAGATCTTGA
1 CCTTTTGCGGCGTTTGTTCAAAAAACACCGCTATAGATC-TGA
2239930 CCTTTTGCGGCGTTT
1 CCTTTTGCGGCGTTT
2239945 TTGGATATCG
Statistics
Matches: 127, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
42 49 0.39
43 47 0.37
44 31 0.24
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (42 bp):
CCTTTTGCGGCGTTTGTTCAAAAAACACCGCTATAGATCTGA
Found at i:2239910 original size:86 final size:86
Alignment explanation
Indices: 2239760--2239944 Score: 266
Period size: 86 Copynumber: 2.2 Consensus size: 86
2239750 TCATGAGCCC
* * *
2239760 TTTTGTGGCGTTTGTATCCAAAAACACCGCTATAGATCTGACCTTTTGCGGTGTTTGTTTCAAAA
1 TTTTGCGGCGTTTGTATCAAAAAACACCGCTATAGATCTGACCTTTTGCGGTGTTTG-TTCCAAA
*
2239825 AAGCGCCGCTATAGATC-TGACA
65 AA-CACCGCTATAGATCTTGACA
* *
2239847 TTTTGCGGCGTTTGT-TCAAAAAACGCCGCTATAGATTTGACCTTTTGCGGTGTTTGTTCCAAAA
1 TTTTGCGGCGTTTGTATCAAAAAACACCGCTATAGATCTGACCTTTTGCGGTGTTTGTTCCAAAA
* *
2239911 ACACTGCTATAGATCTTGACC
66 ACACCGCTATAGATCTTGACA
2239932 TTTTGCGGCGTTT
1 TTTTGCGGCGTTT
2239945 TTGGATATCG
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
84 12 0.13
85 25 0.28
86 38 0.43
87 14 0.16
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (86 bp):
TTTTGCGGCGTTTGTATCAAAAAACACCGCTATAGATCTGACCTTTTGCGGTGTTTGTTCCAAAA
ACACCGCTATAGATCTTGACA
Found at i:2239996 original size:69 final size:69
Alignment explanation
Indices: 2239885--2240015 Score: 172
Period size: 69 Copynumber: 1.9 Consensus size: 69
2239875 CTATAGATTT
** * * * * *
2239885 GACCTTTTGCGGTGTTTGTTCCAAAAACACTGCTATAGATCTTGACCTTTTGCGGCGTTTTTGGA
1 GACCTTTTGCGACGATTGTTCCAAAAACACCGCGATAGATCTTGACCTATTGCAGCGTTTTTGGA
2239950 TATC
66 TATC
* * *
2239954 GACCTTTTGCGACGATTGTTCCAAAAACGCCGGGATATATCTTGACCTATTGCAGCGTTTTT
1 GACCTTTTGCGACGATTGTTCCAAAAACACCGCGATAGATCTTGACCTATTGCAGCGTTTTT
2240016 TGTTCTCAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 52 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (69 bp):
GACCTTTTGCGACGATTGTTCCAAAAACACCGCGATAGATCTTGACCTATTGCAGCGTTTTTGGA
TATC
Found at i:2243305 original size:20 final size:19
Alignment explanation
Indices: 2243264--2243306 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
2243254 AAACTTATTT
*
2243264 TTCATTTTTTAAAAAAGCA
1 TTCATTTTTTAAAAAAGAA
2243283 TTCATTTTAATTAAAAAA-AA
1 TTCATTTT--TTAAAAAAGAA
2243303 TTCA
1 TTCA
2243307 CAGTATGCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 5 0.24
21 8 0.38
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (19 bp):
TTCATTTTTTAAAAAAGAA
Found at i:2243886 original size:131 final size:131
Alignment explanation
Indices: 2243644--2243959 Score: 416
Period size: 131 Copynumber: 2.4 Consensus size: 131
2243634 ATAATTTTAA
* * * * * *
2243644 GAGAGAAAACGATAATATCTAATAATTTCTAATTGAGAATAAATAACCTTTCATGCCTTAAAACA
1 GAGAGAAAACGATAATATCAAATAATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAACA
* * * * *
2243709 GTCATTTATTACTCCAATCGAAACAAAGATATATTACTATTTCGTCTTAAAATTCAATATCAATT
66 GTCATTTATTACTCCAATCAAAACAAAGAGATATCACTATTCCGTCTTAAAAATCAATATCAATT
2243774 C
131 C
* * * **
2243775 GAGTGAAAACGATAATATCCAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGTA
1 GAGAGAAAACGATAATATCAAATAATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAACA
* * **
2243840 GTCATTTATTACTCCAATCAAAATAAAGAGATATCGCTATTCCGTCTTAAAAATCAATATTGATT
66 GTCATTTATTACTCCAATCAAAACAAAGAGATATCACTATTCCGTCTTAAAAATCAATATCAATT
2243905 C
131 C
* * * *
2243906 GAGAGAAAACGGTAATATCAAATTATTTCCAATCGATAATAAATGATCTCTCAT
1 GAGAGAAAACGATAATATCAAATAATTTCCAATCGAGAATAAATGACCTCTCAT
2243960 GCCAAATAAA
Statistics
Matches: 160, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
131 160 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCAAATAATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAACA
GTCATTTATTACTCCAATCAAAACAAAGAGATATCACTATTCCGTCTTAAAAATCAATATCAATT
C
Found at i:2245704 original size:3 final size:3
Alignment explanation
Indices: 2245698--2245732 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2245688 GTTATTATAT
*
2245698 TAC TAC TAC TAC TAT TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
2245733 ATAACAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (3 bp):
TAC
Found at i:2245744 original size:6 final size:6
Alignment explanation
Indices: 2245735--2246575 Score: 1553
Period size: 6 Copynumber: 142.2 Consensus size: 6
2245725 TACTACTAAT
* * *
2245735 AACAAC AACAAC AACAAG AACAAG AACAAG AACAAG AACATG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2245783 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2245831 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2245879 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2245927 AACAAG AACAAG AACAAG AAC--- AACAAG AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2245972 AACAAG AAC-A- AACAAG AACAAG AACAAG AACAAG AAC-A- AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2246016 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
*
2246064 AACAAG AACAAT AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2246112 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2246160 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG -ACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2246207 AACAAG AACAAG AACAAG AACAAG AAC-A- AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2246253 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2246301 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
*
2246349 AAC-AG AACAAG AACAAG AACAAG AAC-AT AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2246395 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2246443 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2246491 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG
2246539 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG A
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG A
2246576 GAATAGGAAT
Statistics
Matches: 816, Mismatches: 7, Indels: 24
0.96 0.01 0.03
Matches are distributed among these distances:
3 3 0.00
4 9 0.01
5 20 0.02
6 784 0.96
ACGTcount: A:0.67, C:0.17, G:0.16, T:0.00
Consensus pattern (6 bp):
AACAAG
Found at i:2246585 original size:6 final size:6
Alignment explanation
Indices: 2246576--2246664 Score: 178
Period size: 6 Copynumber: 14.8 Consensus size: 6
2246566 AAGAACAAGA
2246576 GAATAG GAATAG GAATAG GAATAG GAATAG GAATAG GAATAG GAATAG
1 GAATAG GAATAG GAATAG GAATAG GAATAG GAATAG GAATAG GAATAG
2246624 GAATAG GAATAG GAATAG GAATAG GAATAG GAATAG GAATA
1 GAATAG GAATAG GAATAG GAATAG GAATAG GAATAG GAATA
2246665 TAATATAATA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 83 1.00
ACGTcount: A:0.51, C:0.00, G:0.33, T:0.17
Consensus pattern (6 bp):
GAATAG
Found at i:2246677 original size:3 final size:3
Alignment explanation
Indices: 2246664--2246731 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
2246654 GAATAGGAAT
2246664 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2246711 ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
2246732 CAGGACGAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2261529 original size:79 final size:79
Alignment explanation
Indices: 2261441--2261588 Score: 190
Period size: 80 Copynumber: 1.9 Consensus size: 79
2261431 CATTTATTAC
** * *
2261441 TCCAATCGAAATGAAGAGATTAT-TATTTTGTCTTAAAATTCAAAATCGATTCGAGTGAAAACGA
1 TCCAATCGAAATGAAGAGA-TATCTATTCCGTCTTAAAAATCAAAATCGATTCGAGAGAAAACGA
2261505 TAATATCTAATGATT
65 TAATATCTAATGATT
* * * * *
2261520 TCCAATCGAAATTAAGAGATATCCTATTCCGTCTTAAAAATCAATATTGATTGGAGAGAAAACGG
1 TCCAATCGAAATGAAGAGATAT-CTATTCCGTCTTAAAAATCAAAATCGATTCGAGAGAAAACGA
2261585 TAAT
65 TAAT
2261589 GTAACACCCG
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
78 3 0.05
79 18 0.31
80 37 0.64
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (79 bp):
TCCAATCGAAATGAAGAGATATCTATTCCGTCTTAAAAATCAAAATCGATTCGAGAGAAAACGAT
AATATCTAATGATT
Found at i:2262227 original size:30 final size:31
Alignment explanation
Indices: 2262193--2262277 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 31
2262183 CCCGAAGGAC
*
2262193 CTATCCAGAGGTCACAAGGAACCTC-GGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGGTAA
* *
2262223 CTATCCAGAGGTCATAAAGATCCTCGGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGGTAA
* * * *
2262254 CTGTCCATAGGTCCCGAAGAACCT
1 CTATCCAGAGGTCACAAAGAACCT
2262278 AGGTATACTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 22 0.49
31 23 0.51
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (31 bp):
CTATCCAGAGGTCACAAAGAACCTCGGGTAA
Found at i:2262266 original size:31 final size:30
Alignment explanation
Indices: 2262193--2262291 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 30
2262183 CCCGAAGGAC
*
2262193 CTATCCAGAGGTCACAAGGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
* *
2262223 CTATCCAGAGGTCATAAAGATCCTCGGGTAA
1 CTATCCAGAGGTCACAAAGAACCTC-GGTAA
* * * * *
2262254 CTGTCCATAGGTCCCGAAGAACCTAGGTATA
1 CTATCCAGAGGTCACAAAGAACCTCGGTA-A
*
2262285 CTGTCCA
1 CTATCCA
2262292 TATGTTCCTT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
30 26 0.46
31 31 0.54
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGTAA
Found at i:2262292 original size:31 final size:31
Alignment explanation
Indices: 2262249--2262376 Score: 118
Period size: 31 Copynumber: 4.1 Consensus size: 31
2262239 AAGATCCTCG
* *
2262249 GGTA-ACTGTCCATAGGTCCCGAAGAACCTA
1 GGTATACTGTCCATATGTCCCGAAGAACATA
* **
2262279 GGTATACTGTCCATATGTTCCTTAGAACATA
1 GGTATACTGTCCATATGTCCCGAAGAACATA
* *
2262310 GGTATACTATCCATATGTCCCGAA-AGGCATA
1 GGTATACTGTCCATATGTCCCGAAGA-ACATA
* * *
2262341 GGTAATTA-TGTCTATATGTTCCGTAGAACATA
1 GGT-A-TACTGTCCATATGTCCCGAAGAACATA
2262373 GGTA
1 GGTA
2262377 AACCCTCGAC
Statistics
Matches: 78, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
30 5 0.06
31 49 0.63
32 21 0.27
33 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (31 bp):
GGTATACTGTCCATATGTCCCGAAGAACATA
Found at i:2266692 original size:31 final size:31
Alignment explanation
Indices: 2266654--2266773 Score: 100
Period size: 31 Copynumber: 3.8 Consensus size: 31
2266644 ATCCTCGGCA
* *
2266654 ATTGTCCATAGGTCCCGAAGAACCTAGGTAT
1 ATTGTCCATATGTCCCGAAGAACATAGGTAT
* **
2266685 ATTGTCCATATGTTCCTTAGAACATAGGTAT
1 ATTGTCCATATGTCCCGAAGAACATAGGTAT
* * *
2266716 ACTATCCATATGTCCCGAA-AGGCATAGGTA-
1 ATTGTCCATATGTCCCGAAGA-ACATAGGTAT
* * *
2266746 ATTATGTCTATATGTTCCGTAGAACATA
1 A-T-TGTCCATATGTCCCGAAGAACATA
2266774 AGTAGACCCT
Statistics
Matches: 68, Mismatches: 17, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
30 2 0.03
31 48 0.71
32 17 0.25
33 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (31 bp):
ATTGTCCATATGTCCCGAAGAACATAGGTAT
Found at i:2270686 original size:3 final size:3
Alignment explanation
Indices: 2270680--2270720 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2270670 TTAAGGCCTG
2270680 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2270721 CGAGAAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2270951 original size:24 final size:23
Alignment explanation
Indices: 2270906--2270951 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2270896 TAACTATACT
*
2270906 ATAGACTTGGTATTTTTTTTATA
1 ATAGACTTGGTATTTTTATTATA
2270929 ATAGACTTGGTATTTTTAATTAT
1 ATAGACTTGGTATTTTT-ATTAT
2270952 GGACTTAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.54
Consensus pattern (23 bp):
ATAGACTTGGTATTTTTATTATA
Found at i:2270956 original size:21 final size:21
Alignment explanation
Indices: 2270906--2270966 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
2270896 TAACTATACT
*
2270906 ATAGACTTGGTATTTTTTTTATA
1 ATAGACTTGGTA--TTTTTAATA
*
2270929 ATAGACTTGGTATTTTTAATT
1 ATAGACTTGGTATTTTTAATA
* *
2270950 ATGGACTTAGTATTTTT
1 ATAGACTTGGTATTTTT
2270967 GGTTACCTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 22 0.65
23 12 0.35
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (21 bp):
ATAGACTTGGTATTTTTAATA
Found at i:2275358 original size:20 final size:20
Alignment explanation
Indices: 2275333--2275371 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2275323 AGATAATTAA
2275333 AAAATTACAAGTCCATAATT
1 AAAATTACAAGTCCATAATT
2275353 AAAATTACAAGTCCATAAT
1 AAAATTACAAGTCCATAAT
2275372 ATAGTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAATTACAAGTCCATAATT
Found at i:2278693 original size:3 final size:3
Alignment explanation
Indices: 2278680--2278709 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2278670 TGGGTGATTT
*
2278680 GAA GGA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2278710 TCATAATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2279520 original size:18 final size:18
Alignment explanation
Indices: 2279497--2279536 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2279487 GAATTTTTAA
* *
2279497 AAAAATCAGACAAATTTC
1 AAAAATCAGAAAAATTAC
2279515 AAAAATCAGAAAAATTAC
1 AAAAATCAGAAAAATTAC
2279533 AAAA
1 AAAA
2279537 CAATAGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.65, C:0.12, G:0.05, T:0.17
Consensus pattern (18 bp):
AAAAATCAGAAAAATTAC
Found at i:2279578 original size:113 final size:108
Alignment explanation
Indices: 2279419--2279842 Score: 576
Period size: 113 Copynumber: 3.9 Consensus size: 108
2279409 TTTTATTTTT
2279419 CAAAAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCTA
1 CAAAAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCTA
2279484 CTTGAATTTTTAAAAAAATCAGACAAATTTCAAAAATCAGAAAAATTA
66 CTTGAA--TTTAAAAAAATCAGA-AAA-TT-AAAAATCAGAAAAATTA
*
2279532 CAAAACAA-TAGTATTTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCT
1 CAAAA-AATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCT
* *
2279596 ACTTGAA-TTAAAAAAAT-AG-AAA--AAAAATCAAAAAAATCA
65 ACTTGAATTTAAAAAAATCAGAAAATTAAAAATCAGAAAAATTA
* * *
2279635 CAAATAATTAGTATGTTTATTTATCTAATTTCAATTTATTTTTATCTATCTTGCAAATTAATCTA
1 CAAAAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCTA
*
2279700 CTTGAATTTAAAAAAATCAGAAAGATTAAAAAAATAAGAAAAATTA
66 CTTGAATTTAAAAAAATCAGAAA-ATT--AAAAATCAGAAAAATTA
* *
2279746 CACGACAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTA--TATATTGCAATTTAATC
1 CA--AAAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATC
* * *
2279809 TACTTAAATTTAAAAAAATAAAAAAATTACAAAA
64 TACTTGAATTTAAAAAAATCAGAAAATTA-AAAA
2279843 AAAAATTGTA
Statistics
Matches: 280, Mismatches: 18, Indels: 30
0.85 0.05 0.09
Matches are distributed among these distances:
102 2 0.01
103 79 0.28
104 10 0.04
105 2 0.01
106 2 0.01
107 4 0.01
108 1 0.00
109 6 0.02
110 13 0.05
111 53 0.19
113 106 0.38
114 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.40
Consensus pattern (108 bp):
CAAAAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCTA
CTTGAATTTAAAAAAATCAGAAAATTAAAAATCAGAAAAATTA
Found at i:2279730 original size:18 final size:18
Alignment explanation
Indices: 2279707--2279745 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2279697 CTACTTGAAT
* *
2279707 TTAAAAAAATCAGAAAGA
1 TTAAAAAAATAAGAAAAA
2279725 TTAAAAAAATAAGAAAAA
1 TTAAAAAAATAAGAAAAA
2279743 TTA
1 TTA
2279746 CACGACAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (18 bp):
TTAAAAAAATAAGAAAAA
Found at i:2279846 original size:113 final size:113
Alignment explanation
Indices: 2279616--2279845 Score: 312
Period size: 111 Copynumber: 2.1 Consensus size: 113
2279606 AAAAAATAGA
* *
2279616 AAAAAAATCAA-AAAAA-T-CACAAATAATTAGTATGTTTATTTATCTAATTTCAATTTATTTTT
1 AAAAAAAT-AAGAAAAATTACACACA-AATTAGTATGTTTATTTATCTAATTTCAATGTATTTTT
* * * *
2279678 ATCTATCTTGCAAATTAATCTACTTGAATTTAAAAAAATCAGAAAGATT--
64 A-CTATCTTGCAATTTAATCTACTTAAATTTAAAAAAATCAAAAAAATTAC
2279727 AAAAAAATAAGAAAAATTACACGACAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTA
1 AAAAAAATAAGAAAAATTACAC-ACAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTA
*
2279792 -TATATTGCAATTTAATCTACTTAAATTTAAAAAAAT-AAAAAAATTAC
65 CTATCTTGCAATTTAATCTACTTAAATTTAAAAAAATCAAAAAAATTAC
2279839 AAAAAAA
1 AAAAAAA
2279846 AATTGTAGCG
Statistics
Matches: 106, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
110 9 0.08
111 46 0.43
112 8 0.08
113 41 0.39
114 2 0.02
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (113 bp):
AAAAAAATAAGAAAAATTACACACAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTAC
TATCTTGCAATTTAATCTACTTAAATTTAAAAAAATCAAAAAAATTAC
Found at i:2279848 original size:216 final size:214
Alignment explanation
Indices: 2279419--2279834 Score: 642
Period size: 216 Copynumber: 1.9 Consensus size: 214
2279409 TTTTATTTTT
*
2279419 CAAAAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCTA
1 CAAAAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAAATTAATCTA
** * *
2279484 CTTGAATTTTTAAAAAAATCAGACAAATTTCAAAAATCAGAAAAATTACAAAACAATAGTATTTT
66 CTTGAA-TTTTAAAAAAATCAGACAAATTAAAAAAATAAGAAAAATTACAAAACAATAGTATGTT
* *
2279549 TATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCTACTTGAATTAAAAAAATA
130 TATTTATCTAATTTCAATGTATTTTTA-CTATATTGCAATTTAATCTACTTAAATTAAAAAAATA
*
2279614 GAAAAAAAATCAAAAAAATCA
194 GAAAAAAAATAAAAAAAATCA
* *
2279635 CAAATAATTAGTATGTTTATTTATCTAATTTCAATTTATTTTTATCTATCTTGCAAATTAATCTA
1 CAAAAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAAATTAATCTA
**
2279700 CTTGAA-TTTAAAAAAATCAGA-AAGATTAAAAAAATAAGAAAAATTACACGACAAATTAGTATG
66 CTTGAATTTTAAAAAAATCAGACAA-ATTAAAAAAATAAGAAAAATTACAAAAC-AA-TAGTATG
2279763 TTTATTTATCTAATTTCAATGTATTTTTA-TATATTGCAATTTAATCTACTTAAATTTAAAAAAA
128 TTTATTTATCTAATTTCAATGTATTTTTACTATATTGCAATTTAATCTACTTAAA-TTAAAAAAA
2279827 TA-AAAAAA
192 TAGAAAAAA
2279835 TTACAAAAAA
Statistics
Matches: 185, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
213 2 0.01
214 67 0.36
215 13 0.07
216 103 0.56
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.40
Consensus pattern (214 bp):
CAAAAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAAATTAATCTA
CTTGAATTTTAAAAAAATCAGACAAATTAAAAAAATAAGAAAAATTACAAAACAATAGTATGTTT
ATTTATCTAATTTCAATGTATTTTTACTATATTGCAATTTAATCTACTTAAATTAAAAAAATAGA
AAAAAAATAAAAAAAATCA
Found at i:2290701 original size:40 final size:40
Alignment explanation
Indices: 2290657--2290738 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
2290647 GAGATGATAG
*
2290657 TGATTTTCAAGCTTACAATAAAGAAATTGGCTTGAAAAGT
1 TGATTTTCAAGCTTACAATAAAGAAACTGGCTTGAAAAGT
* * *
2290697 TGATTTTCAAGTTTACAATGAAGAAACTGGCTTGAATAGT
1 TGATTTTCAAGCTTACAATAAAGAAACTGGCTTGAAAAGT
2290737 TG
1 TG
2290739 GTTTGAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (40 bp):
TGATTTTCAAGCTTACAATAAAGAAACTGGCTTGAAAAGT
Found at i:2291822 original size:26 final size:27
Alignment explanation
Indices: 2291787--2291852 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
2291777 GCCTCTCTCT
*
2291787 CCTCTACCTCCATC-TCTCCCT-CTTCA
1 CCTCCACCTCCA-CATCTCCCTCCTTCA
*
2291813 CCTTCACCTCCACATCTCCCTCCTTCA
1 CCTCCACCTCCACATCTCCCTCCTTCA
2291840 CCTCCACCTCCAC
1 CCTCCACCTCCAC
2291853 CACTGAGAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 1 0.03
26 17 0.49
27 17 0.49
ACGTcount: A:0.14, C:0.58, G:0.00, T:0.29
Consensus pattern (27 bp):
CCTCCACCTCCACATCTCCCTCCTTCA
Found at i:2291847 original size:27 final size:25
Alignment explanation
Indices: 2291778--2291852 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 25
2291768 AGTAGCAACG
* *
2291778 CCTCTCTCTCCTCTACCTCCATCTCTC
1 CCTCT-TCACCTCCACCTCCA-CTCTC
*
2291805 CCTCTTCACCTTCACCTCCACATCTC
1 CCTCTTCACCTCCACCTCCAC-TCTC
2291831 CCTCCTTCACCTCCACCTCCAC
1 CCT-CTTCACCTCCACCTCCAC
2291853 CACTGAGAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.02
26 19 0.45
27 22 0.52
ACGTcount: A:0.12, C:0.57, G:0.00, T:0.31
Consensus pattern (25 bp):
CCTCTTCACCTCCACCTCCACTCTC
Found at i:2305162 original size:18 final size:18
Alignment explanation
Indices: 2305128--2305162 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2305118 ATACCTAATA
*
2305128 GTATCGGTACCCCTTTGG
1 GTATCGGTACCACTTTGG
*
2305146 GTATCGGTACCATTTTG
1 GTATCGGTACCACTTTG
2305163 CATTCTGGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.23, G:0.26, T:0.37
Consensus pattern (18 bp):
GTATCGGTACCACTTTGG
Found at i:2309780 original size:29 final size:28
Alignment explanation
Indices: 2309747--2309833 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 28
2309737 GACTGTACTA
*
2309747 AAACTTTTAAAATTACCATTTTAGTCCCT
1 AAACTTTTAAAATT-CCATTTTAGTCACT
* **
2309776 AAACTTTTCCAAATTTTATTTTAGTCACT
1 AAACTTTT-AAAATTCCATTTTAGTCACT
* * ** *
2309805 TAACTTTCAAAATTTTATTTTGGTCACT
1 AAACTTTTAAAATTCCATTTTAGTCACT
2309833 A
1 A
2309834 TCCAAAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
28 18 0.38
29 25 0.52
30 5 0.10
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (28 bp):
AAACTTTTAAAATTCCATTTTAGTCACT
Found at i:2309821 original size:28 final size:29
Alignment explanation
Indices: 2309747--2309833 Score: 97
Period size: 28 Copynumber: 3.0 Consensus size: 29
2309737 GACTGTACTA
** *
2309747 AAACTTTT-AAAATTACCATTTTAGTCCCT
1 AAACTTTTCAAAATT-TTATTTTAGTCACT
*
2309776 AAACTTTTCCAAATTTTATTTTAGTCACT
1 AAACTTTTCAAAATTTTATTTTAGTCACT
* *
2309805 TAAC-TTTCAAAATTTTATTTTGGTCACT
1 AAACTTTTCAAAATTTTATTTTAGTCACT
2309833 A
1 A
2309834 TCCAAAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 22 0.45
29 22 0.45
30 5 0.10
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (29 bp):
AAACTTTTCAAAATTTTATTTTAGTCACT
Found at i:2310836 original size:15 final size:17
Alignment explanation
Indices: 2310818--2310849 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2310808 TTTAGGGACC
2310818 AAAAG-TATA-ATTTTA
1 AAAAGTTATATATTTTA
2310833 AAAAGTTATATATTTTA
1 AAAAGTTATATATTTTA
2310850 GCTCATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
AAAAGTTATATATTTTA
Found at i:2313509 original size:15 final size:17
Alignment explanation
Indices: 2313472--2313514 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
2313462 ATTATGAACT
*
2313472 TATTATTATTATCATCA
1 TATTATTATTATCATAA
2313489 TCATTATTATTA-C-TAA
1 T-ATTATTATTATCATAA
2313505 TATTATTATT
1 TATTATTATT
2313515 TATTTTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 3 0.12
17 2 0.08
18 10 0.42
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTATTATTATCATAA
Found at i:2315014 original size:81 final size:81
Alignment explanation
Indices: 2314843--2315458 Score: 804
Period size: 81 Copynumber: 7.6 Consensus size: 81
2314833 AATCAAATCA
* * * * * * * *
2314843 ATAAATGACACCGTTTATGTCAAAATGCACTGCTAAGCATTTAGTCTTTTACCCAAAGGAATTTA
1 ATAATTGACACC-TTTCTGTC-AAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTA
* * *
2314908 GCATTTCATCTAACTTGC
64 ACCTTTCATCTAACTGGC
* * * * * * * *
2314926 ATGATTGACACCTTTATGCCAAATACACAGCTAAGCATTTAATCTTTAACTCAAAGGTATTTAGC
1 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAAC
2314991 CTTTCATCTAACTGGC
66 CTTTCATCTAACTGGC
* *
2315007 ATAATTGACACCTTTTTTTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAAC
*
2315072 CTTTTATCTAACTGGC
66 CTTTCATCTAACTGGC
* * * * *
2315088 ATAACTGACACCTTTCTATCAAATGCACAGCTGGGAAATTAATCTTTTACTCAAAGGAATTTAAC
1 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAAC
2315153 CTTTCATCTAACTGGC
66 CTTTCATCTAACTGGC
* *
2315169 ATAATTGACACCTTTCTGTCAAATGTACATCTAGGCAATTAATCTTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAAC
*
2315234 CTTTAATCTAACTGGC
66 CTTTCATCTAACTGGC
** * * *
2315250 ATAATTGACATATTTCTATCAAATGCACCGCTAGGCAATTAATATTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAAC
*
2315315 CTTTCATCTAACTAGC
66 CTTTCATCTAACTGGC
* * *
2315331 GTAATTGACTCCTTTCTGTCAAAAGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAAC
* *
2315396 ATTTCATCTAACTGAC
66 CTTTCATCTAACTGGC
* * *
2315412 AT-ATTGACACCTTTTTATCAAATGCACA-ATAGGCAATTAATCTTTTA
1 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTA
2315459 TTTAAAACAG
Statistics
Matches: 471, Mismatches: 62, Indels: 4
0.88 0.12 0.01
Matches are distributed among these distances:
79 18 0.04
80 22 0.05
81 414 0.88
82 7 0.01
83 10 0.02
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (81 bp):
ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAAC
CTTTCATCTAACTGGC
Found at i:2322050 original size:53 final size:52
Alignment explanation
Indices: 2321966--2322065 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 52
2321956 ATCTGGGCAT
*
2321966 TTAATATTTAACTCAAAGGCATTTATCCTTTCATTTAACTGTCATAATAACAA
1 TTAATATTTAACTCAAAGGCATTTATCCTTTCATCTAACTGT-ATAATAACAA
* * *
2322019 TTAATCTTTTACTCAAAGGTATTTAAT-CTTTCATCTAACTGTATAAT
1 TTAATATTTAACTCAAAGGCATTT-ATCCTTTCATCTAACTGTATAAT
2322066 TGATACCTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
52 5 0.12
53 35 0.83
54 2 0.05
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (52 bp):
TTAATATTTAACTCAAAGGCATTTATCCTTTCATCTAACTGTATAATAACAA
Found at i:2322131 original size:133 final size:134
Alignment explanation
Indices: 2321889--2322146 Score: 347
Period size: 133 Copynumber: 1.9 Consensus size: 134
2321879 AAGCTTTTAG
* * *
2321889 TCTTTTTCCCAAAGGCATTTAGCCTTTCATCTAACTTGCATGATTGACACATTTCTGCCAAATGC
1 TCTTTTACCCAAAGGCATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGC
* * * * * * *
2321954 ACATCTGGGCATTTAATATTTAACTCAAAGGCATTTATCCTTTCATTTAACTGTCATAATAACAA
66 ACATCTAGGCAATTAATATTTAACTCAAAGGAATTTAACATTTCATCTAACTGGCATAATAACAA
2322019 TTAA
131 TTAA
* * * * * * *
2322023 TCTTTTACTCAAAGGTATTTAATCTTTCATCTAAC-TGTATAATTGATACCTTTCTGTCAAATGC
1 TCTTTTACCCAAAGGCATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGC
*
2322087 ACATCTAGGCAATTAATATTTTACTCAAAGGAATTTAACATTTCATCTAACTGGCATAAT
66 ACATCTAGGCAATTAATATTTAACTCAAAGGAATTTAACATTTCATCTAACTGGCATAAT
2322147 TGACACCTTT
Statistics
Matches: 106, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
133 76 0.72
134 30 0.28
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (134 bp):
TCTTTTACCCAAAGGCATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGC
ACATCTAGGCAATTAATATTTAACTCAAAGGAATTTAACATTTCATCTAACTGGCATAATAACAA
TTAA
Found at i:2322183 original size:81 final size:81
Alignment explanation
Indices: 2322016--2322433 Score: 626
Period size: 81 Copynumber: 5.2 Consensus size: 81
2322006 GTCATAATAA
* *
2322016 CAATTAATCTTTTACTCAAAGGTATTTAATC-TTTCATCTAACT-GTATAATTGATACCTTTCTG
1 CAATTAATCTTTTACTCAAAGGTATTTAA-CATTTCATCTAACTGGCATAATTGACACCTTTCTG
2322079 TCAAATGCACATCTAGG
65 TCAAATGCACATCTAGG
* *
2322096 CAATTAATATTTTACTCAAAGGAATTTAACATTTCATCTAACTGGCATAATTGACACCTTTCTGT
1 CAATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTCTGT
*
2322161 CAAATGCACAGCTAGG
66 CAAATGCACATCTAGG
* * *
2322177 CAATTAATCTTTTACTCAAAGGAATTTAA-ACTTTCATCTAATTGGCATAAGTGACACCTTTCTG
1 CAATTAATCTTTTACTCAAAGGTATTTAACA-TTTCATCTAACTGGCATAATTGACACCTTTCTG
*
2322241 TCAAATGCACATCTAAG
65 TCAAATGCACATCTAGG
* * * * *
2322258 CAATTAATCTTTTACTCAAAGCTATTTAACCTTTAATCTAACTTGCATAATTGACACATTTCTGT
1 CAATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTCTGT
*
2322323 CAAATGCACAACTAGG
66 CAAATGCACATCTAGG
* * * *
2322339 CAATTAATCTTTTAGTCAAAGGTATTTAACCTTTCATCTAAGTGTCATAATTGACACCTTTCTGT
1 CAATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTCTGT
2322404 CAAATGCACATCTAGG
66 CAAATGCACATCTAGG
2322420 CAATTAATCTTTTA
1 CAATTAATCTTTTA
2322434 TTTAAGACAG
Statistics
Matches: 306, Mismatches: 28, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
79 1 0.00
80 40 0.13
81 265 0.87
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (81 bp):
CAATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTCTGT
CAAATGCACATCTAGG
Found at i:2323067 original size:21 final size:21
Alignment explanation
Indices: 2323041--2323086 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
2323031 ATACCATATC
2323041 AGTATCGATACTAATTACATT
1 AGTATCGATACTAATTACATT
*
2323062 AGTATCGATACTTATTACATT
1 AGTATCGATACTAATTACATT
2323083 AGTA
1 AGTA
2323087 CCGGTATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (21 bp):
AGTATCGATACTAATTACATT
Found at i:2324255 original size:11 final size:11
Alignment explanation
Indices: 2324239--2324279 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
2324229 AATGTCTTTA
2324239 ATTTTTATTTG
1 ATTTTTATTTG
*
2324250 ATTTTTACCTTTT
1 ATTTTTA--TTTG
2324263 ATTTTTATTTG
1 ATTTTTATTTG
2324274 ATTTTT
1 ATTTTT
2324280 TCCTTTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (11 bp):
ATTTTTATTTG
Found at i:2324286 original size:24 final size:24
Alignment explanation
Indices: 2324234--2324301 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
2324224 ACTCTAATGT
*
2324234 CTTTAATTTTTATTTGATTTTTAC
1 CTTTTATTTTTATTTGATTTTTAC
*
2324258 CTTTTATTTTTATTTGATTTTTTC
1 CTTTTATTTTTATTTGATTTTTAC
** *
2324282 CTTTTGGTTTTATTTTATTT
1 CTTTTATTTTTATTTGATTT
2324302 CAATTTGGTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.15, C:0.07, G:0.06, T:0.72
Consensus pattern (24 bp):
CTTTTATTTTTATTTGATTTTTAC
Found at i:2324385 original size:3 final size:3
Alignment explanation
Indices: 2324377--2324459 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
2324367 TATCTATGCC
2324377 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2324425 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2324460 CTGTTAAGTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2324644 original size:2 final size:2
Alignment explanation
Indices: 2324637--2324661 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2324627 TTAATGCAAT
2324637 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2324662 TAGATTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2326717 original size:21 final size:21
Alignment explanation
Indices: 2326682--2326725 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2326672 ACCTCCTCGT
*
2326682 TCTCTCGTGTTTCTCTCGTCTG
1 TCTCTCGTGTATCTCTCGT-TG
2326704 TCTCT-GTGTATCTCTCGTTG
1 TCTCTCGTGTATCTCTCGTTG
2326724 TC
1 TC
2326726 CCCTCTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 12 0.57
22 5 0.24
ACGTcount: A:0.02, C:0.30, G:0.18, T:0.50
Consensus pattern (21 bp):
TCTCTCGTGTATCTCTCGTTG
Found at i:2327585 original size:24 final size:24
Alignment explanation
Indices: 2327513--2327586 Score: 103
Period size: 24 Copynumber: 3.1 Consensus size: 24
2327503 AAACGGAGAT
* *
2327513 ATCAGAAATCAAAACAGAATTCAT
1 ATCAGAAATCAGAACAGAATTCAG
* * *
2327537 ATTAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
2327561 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
2327585 AT
1 AT
2327587 AATGTATCAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:2327595 original size:24 final size:24
Alignment explanation
Indices: 2327520--2327604 Score: 93
Period size: 24 Copynumber: 3.6 Consensus size: 24
2327510 GATATCAGAA
* * *
2327520 ATCAAAACAGAATTCATATTAGAT
1 ATCAGAACAGAATTCAGATAAGAT
* * *
2327544 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATTCAGATAAGAT
2327568 ATCAGAACAGAATTCAGATAATG-T
1 ATCAGAACAGAATTCAGATAA-GAT
2327592 ATCAGAA-AGAATT
1 ATCAGAACAGAATT
2327605 TAAGTCGAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
23 6 0.12
24 45 0.87
25 1 0.02
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATAAGAT
Found at i:2327595 original size:48 final size:47
Alignment explanation
Indices: 2327513--2327603 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 47
2327503 AAACGGAGAT
* *
2327513 ATCAGAAATCAAAACAGAATTCATATTAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAA-AGAATCCAG
*
2327561 ATCAGAAATCAGAACAGAATTCAGATAATG-TATCAGAAAGAAT
1 ATCAGAAATCAAAACAGAATTCAGATAA-GATATCAGAAAGAAT
2327604 TTAAGTCGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
47 5 0.13
48 33 0.85
49 1 0.03
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.21
Consensus pattern (47 bp):
ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAAAGAATCCAG
Found at i:2331332 original size:29 final size:27
Alignment explanation
Indices: 2331299--2331353 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2331289 AGATGGGTCG
*
2331299 GATTTACTGCTTCTCAGGTTTGGACCTCT
1 GATTT-CT-CTTCTCAGGTCTGGACCTCT
* *
2331328 GATTTGTCTTCTCGGGTCTGGACCTC
1 GATTTCTCTTCTCAGGTCTGGACCTC
2331354 CGGGTTTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 17 0.74
28 1 0.04
29 5 0.22
ACGTcount: A:0.11, C:0.25, G:0.24, T:0.40
Consensus pattern (27 bp):
GATTTCTCTTCTCAGGTCTGGACCTCT
Found at i:2331375 original size:16 final size:15
Alignment explanation
Indices: 2331337--2331375 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
2331327 TGATTTGTCT
*
2331337 TCTCGGGTCTGGACC
1 TCTCGGGTTTGGACC
2331352 TC-CGGGTTTGGACC
1 TCTCGGGTTTGGACC
2331366 TACTCGGGTT
1 T-CTCGGGTT
2331376 GAACTTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 12 0.57
15 3 0.14
16 6 0.29
ACGTcount: A:0.08, C:0.28, G:0.33, T:0.31
Consensus pattern (15 bp):
TCTCGGGTTTGGACC
Found at i:2331467 original size:3 final size:3
Alignment explanation
Indices: 2331461--2331503 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
2331451 GTATTATTTT
*
2331461 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TTA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2331504 TAAAAAAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2332968 original size:21 final size:21
Alignment explanation
Indices: 2332942--2333002 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
2332932 AAAGAGAATT
2332942 GACGGTTCACACCGGTTTTCA
1 GACGGTTCACACCGGTTTTCA
2332963 GACGGTTCACACCGGTTTTCA
1 GACGGTTCACACCGGTTTTCA
* * *
2332984 GCCGGTTCACCCCGATTTT
1 GACGGTTCACACCGGTTTT
2333003 GCCGGTTCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.16, C:0.31, G:0.23, T:0.30
Consensus pattern (21 bp):
GACGGTTCACACCGGTTTTCA
Found at i:2333006 original size:19 final size:20
Alignment explanation
Indices: 2332944--2333010 Score: 73
Period size: 21 Copynumber: 3.3 Consensus size: 20
2332934 AGAGAATTGA
* *
2332944 CGGTTCACACCGGTTTTCAGA
1 CGGTTCACACCGATTTT-AGC
*
2332965 CGGTTCACACCGGTTTTCAGC
1 CGGTTCACACCGATTTT-AGC
*
2332986 CGGTTCACCCCGATTTT-GC
1 CGGTTCACACCGATTTTAGC
2333005 CGGTTC
1 CGGTTC
2333011 TCATCCGGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 8 0.19
21 35 0.81
ACGTcount: A:0.13, C:0.33, G:0.24, T:0.30
Consensus pattern (20 bp):
CGGTTCACACCGATTTTAGC
Found at i:2340221 original size:15 final size:16
Alignment explanation
Indices: 2340191--2340223 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2340181 CTGCGGCGTA
*
2340191 TCCTTCCTTCTTCTCT
1 TCCTTCCTTCTGCTCT
2340207 TCCTT-CTTCTGCTCT
1 TCCTTCCTTCTGCTCT
2340222 TC
1 TC
2340224 TTCAGCCCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.00, C:0.42, G:0.03, T:0.55
Consensus pattern (16 bp):
TCCTTCCTTCTGCTCT
Found at i:2340729 original size:18 final size:17
Alignment explanation
Indices: 2340683--2340733 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
2340673 TAGGGGTGGA
2340683 TTTGGTTTCTCTTCTT-C
1 TTTGG-TTCTCTTCTTCC
* *
2340700 TTTGGGT-GCTTCTTCC
1 TTTGGTTCTCTTCTTCC
2340716 TTTGGCTTCTCTTCTTCC
1 TTTGG-TTCTCTTCTTCC
2340734 GCTTTCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 6 0.22
16 7 0.26
17 6 0.22
18 8 0.30
ACGTcount: A:0.00, C:0.27, G:0.16, T:0.57
Consensus pattern (17 bp):
TTTGGTTCTCTTCTTCC
Found at i:2342159 original size:18 final size:19
Alignment explanation
Indices: 2342123--2342159 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2342113 TGTTGAGGTG
*
2342123 AAAATGTTATTATTGTAAA
1 AAAATGTAATTATTGTAAA
2342142 AAAATGTAATTATT-TAAA
1 AAAATGTAATTATTGTAAA
2342160 TAATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (19 bp):
AAAATGTAATTATTGTAAA
Found at i:2342261 original size:5 final size:5
Alignment explanation
Indices: 2342253--2342345 Score: 168
Period size: 5 Copynumber: 18.4 Consensus size: 5
2342243 TTTTATATTA
*
2342253 TTACG TTACG TTACG TTACG TTACG TTACG TTACG TTACG TTAAG TTACG
1 TTACG TTACG TTACG TTACG TTACG TTACG TTACG TTACG TTACG TTACG
2342303 TTACG TTACG TTACG TTACG TTAACG TTACG TTACG TTACG TT
1 TTACG TTACG TTACG TTACG TT-ACG TTACG TTACG TTACG TT
2342346 CTGTTCTGTT
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
5 80 0.94
6 5 0.06
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (5 bp):
TTACG
Found at i:2342500 original size:14 final size:14
Alignment explanation
Indices: 2342481--2342523 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2342471 AATATTTTAT
2342481 ATATTTTCATTAAA
1 ATATTTTCATTAAA
2342495 ATATTTT-A-T---
1 ATATTTTCATTAAA
2342504 ATATTTTCATTAAA
1 ATATTTTCATTAAA
2342518 ATATTT
1 ATATTT
2342524 ATAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
9 7 0.29
10 1 0.04
11 1 0.04
12 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATTTTCATTAAA
Found at i:2342539 original size:22 final size:23
Alignment explanation
Indices: 2342467--2342530 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
2342457 AGTGTAACGC
2342467 TTAAAATATTTTATATATTTTCA
1 TTAAAATATTTTATATATTTTCA
2342490 TTAAAATATTTTATATATTTTCA
1 TTAAAATATTTTATATATTTTCA
2342513 TTAAAATA-TTTATA-ATTT
1 TTAAAATATTTTATATATTT
2342531 AATATTAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.10
22 6 0.15
23 31 0.76
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAAAATATTTTATATATTTTCA
Found at i:2348393 original size:27 final size:28
Alignment explanation
Indices: 2348363--2348420 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
2348353 GACTTTTGAT
* *
2348363 TAAGGA-ACCGAGACCCTATTTCTATTC
1 TAAGGACACCAAGACCCTATTTCCATTC
2348390 TAA-GACACCAAGACCCTATTTCCATTC
1 TAAGGACACCAAGACCCTATTTCCATTC
2348417 TAAG
1 TAAG
2348421 TTTAACAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (28 bp):
TAAGGACACCAAGACCCTATTTCCATTC
Found at i:2354637 original size:21 final size:22
Alignment explanation
Indices: 2354612--2354652 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2354602 ATCAAAGTTT
*
2354612 TTTCTTTTCTTT-CATTTTTGC
1 TTTCTTTACTTTACATTTTTGC
2354633 TTTCTTTACTTTACATTTTT
1 TTTCTTTACTTTACATTTTT
2354653 TTATTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTCTTTACTTTACATTTTTGC
Found at i:2360133 original size:17 final size:17
Alignment explanation
Indices: 2360108--2360167 Score: 102
Period size: 17 Copynumber: 3.5 Consensus size: 17
2360098 TGATCGTTGC
*
2360108 TTTGTATTCCTTGGGAA
1 TTTGGATTCCTTGGGAA
2360125 TTTGGATTCCTTGGGAA
1 TTTGGATTCCTTGGGAA
*
2360142 TTTGGATTCCATGGGAA
1 TTTGGATTCCTTGGGAA
2360159 TTTGGATTC
1 TTTGGATTC
2360168 TGCCTCTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.43
Consensus pattern (17 bp):
TTTGGATTCCTTGGGAA
Found at i:2370954 original size:21 final size:20
Alignment explanation
Indices: 2370902--2370947 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2370892 TTTTTTTTCA
*
2370902 AAAAAAACAAAAAAAAAGGC
1 AAAAAAACAAAAAAAAAGCC
2370922 AAAAAAACAAAAAAAAAGCC
1 AAAAAAACAAAAAAAAAGCC
2370942 AAAAAA
1 AAAAAA
2370948 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.83, C:0.11, G:0.07, T:0.00
Consensus pattern (20 bp):
AAAAAAACAAAAAAAAAGCC
Found at i:2375532 original size:21 final size:20
Alignment explanation
Indices: 2375481--2375533 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2375471 TTTTTTTTCA
* *
2375481 AAAAAACAAAAAAAAAAGGC
1 AAAAAACCAAAAAAAAAGCC
*
2375501 AAAAAAACAAAAAAAAAGCC
1 AAAAAACCAAAAAAAAAGCC
2375521 AAAAAAGCCAAAA
1 AAAAAA-CCAAAA
2375534 TTTCAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.79, C:0.13, G:0.08, T:0.00
Consensus pattern (20 bp):
AAAAAACCAAAAAAAAAGCC
Found at i:2375533 original size:20 final size:20
Alignment explanation
Indices: 2375479--2375526 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2375469 ATTTTTTTTT
*
2375479 CAAAAAAACAAAAAAAAAAGG
1 CAAAAAAAC-AAAAAAAAAGC
2375500 CAAAAAAACAAAAAAAAAGC
1 CAAAAAAACAAAAAAAAAGC
2375520 CAAAAAA
1 CAAAAAA
2375527 GCCAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.81, C:0.12, G:0.06, T:0.00
Consensus pattern (20 bp):
CAAAAAAACAAAAAAAAAGC
Found at i:2380110 original size:21 final size:21
Alignment explanation
Indices: 2380055--2380103 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
2380045 ATTTTTTTTT
*
2380055 CAAAAAAACAAAAAAAAAAGG
1 CAAAAAAACAAAAAAAAAAGC
2380076 CAAAAAAACAAAAAAAAAAGC
1 CAAAAAAACAAAAAAAAAAGC
2380097 CAAAAAA
1 CAAAAAA
2380104 GCCAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (21 bp):
CAAAAAAACAAAAAAAAAAGC
Found at i:2386667 original size:14 final size:14
Alignment explanation
Indices: 2386648--2386677 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2386638 ATTTATCATT
2386648 TTAAAAACACACAC
1 TTAAAAACACACAC
2386662 TTAAAAACACACAC
1 TTAAAAACACACAC
2386676 TT
1 TT
2386678 CTCCCCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (14 bp):
TTAAAAACACACAC
Found at i:2388545 original size:26 final size:25
Alignment explanation
Indices: 2388498--2388547 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2388488 CAAAACACAA
*
2388498 TAATTTGAAAATTAACATTTTTTTT
1 TAATTTCAAAATTAACATTTTTTTT
*
2388523 TAATTTCAAAATTTA-ATTTTTTTT
1 TAATTTCAAAATTAACATTTTTTTT
2388547 T
1 T
2388548 GGAAAATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (25 bp):
TAATTTCAAAATTAACATTTTTTTT
Found at i:2388938 original size:22 final size:21
Alignment explanation
Indices: 2388899--2388979 Score: 58
Period size: 22 Copynumber: 3.8 Consensus size: 21
2388889 CAGAACCCCA
*
2388899 GGGGGGTATCGATT-CCCTTG
1 GGGGGGAATCGATTCCCCTTG
* *
2388919 TGGGGGGAATCGGTTCCCCTTCA
1 -GGGGGGAATCGATTCCCCTT-G
** * *
2388942 AAGGGGAATCGGTTCCCTCATG
1 GGGGGGAATCGATTCCC-CTTG
2388964 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGATTCCC
2388980 TCTGCACCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
21 21 0.45
22 24 0.51
23 2 0.04
ACGTcount: A:0.15, C:0.23, G:0.37, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTTG
Found at i:2388968 original size:21 final size:21
Alignment explanation
Indices: 2388899--2388981 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
2388889 CAGAACCCCA
* **
2388899 GGGGGGTATCGATTCCCTTGT
1 GGGGGGAATCGATTCCCTCAT
*
2388920 GGGGGGAATCGGTTCCCCTTCA-
1 GGGGGGAATCGATT-CCC-TCAT
** *
2388942 AAGGGGAATCGGTTCCCTCAT
1 GGGGGGAATCGATTCCCTCAT
*
2388963 GGGGGGGATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
2388982 TGCACCAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
20 3 0.06
21 30 0.61
22 15 0.31
23 1 0.02
ACGTcount: A:0.14, C:0.24, G:0.36, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCTCAT
Found at i:2397787 original size:23 final size:23
Alignment explanation
Indices: 2397746--2397789 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2397736 CCGTCCGTCC
**
2397746 ACCTTCTAGAATCTATTGACTTG
1 ACCTTCTAGAAGATATTGACTTG
*
2397769 ACCTTCTAGAAGATGTTGACT
1 ACCTTCTAGAAGATATTGACT
2397790 CACTGCTACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (23 bp):
ACCTTCTAGAAGATATTGACTTG
Found at i:2398379 original size:25 final size:25
Alignment explanation
Indices: 2398351--2398398 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2398341 GTATATATTC
2398351 AATTATACCTATTAGTTTGTCAAAA
1 AATTATACCTATTAGTTTGTCAAAA
** *
2398376 AATTATAGTTATTAGTTTTTCAA
1 AATTATACCTATTAGTTTGTCAA
2398399 CAATTCTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (25 bp):
AATTATACCTATTAGTTTGTCAAAA
Found at i:2401160 original size:21 final size:20
Alignment explanation
Indices: 2401133--2401186 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
2401123 AGCTATAACA
2401133 CTGAACTAGTTGAAAGGGTAG
1 CTGAACTAGTTGAAAGGG-AG
* * *
2401154 TTGAACTAGATGAATGGGAG
1 CTGAACTAGTTGAAAGGGAG
2401174 CTGAACCTAGTTG
1 CTGAA-CTAGTTG
2401187 GGAAGAAGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.26
Consensus pattern (20 bp):
CTGAACTAGTTGAAAGGGAG
Done.