Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397263.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_86.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8461613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 85630 characters in sequence are not A, C, G, or T
File 4 of 18
Found at i:1986667 original size:31 final size:30
Alignment explanation
Indices: 1986577--1986677 Score: 120
Period size: 31 Copynumber: 3.4 Consensus size: 30
1986567 AATAAATTAT
* *
1986577 TTAAATAAATTTTTATATTTTTA--TTATA
1 TTAAATAAAATTTTATATTTTTATTTTAAA
*
1986605 TT-TAT-AAATTATTATATTTTTATTTTAAA
1 TTAAATAAAATT-TTATATTTTTATTTTAAA
*
1986634 TTAAATAAAATTTTATATTTTTATTTTTTAA
1 TTAAATAAAATTTTATATTTTTA-TTTTAAA
1986665 TTAAATAAAATTT
1 TTAAATAAAATTT
1986678 AATAATTAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
26 4 0.06
27 13 0.21
28 2 0.03
29 6 0.10
30 13 0.21
31 24 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTAAATAAAATTTTATATTTTTATTTTAAA
Found at i:1986903 original size:25 final size:25
Alignment explanation
Indices: 1986875--1986922 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1986865 ATATATATAA
*
1986875 AATAATAAATATTATT-TTAATTAAT
1 AATAATAAAT-TAATTATTAATTAAT
*
1986900 AATAATTAATTAATTATTAATTA
1 AATAATAAATTAATTATTAATTA
1986923 TAAAGATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AATAATAAATTAATTATTAATTAAT
Found at i:1988836 original size:21 final size:21
Alignment explanation
Indices: 1988812--1988854 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1988802 TGGAATAAAT
1988812 AAATCAGCAGAAGGGGAGAGG
1 AAATCAGCAGAAGGGGAGAGG
1988833 AAATCAGCAGAAGGGGAGAGG
1 AAATCAGCAGAAGGGGAGAGG
1988854 A
1 A
1988855 TAGATAGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.42, T:0.05
Consensus pattern (21 bp):
AAATCAGCAGAAGGGGAGAGG
Found at i:1992875 original size:30 final size:29
Alignment explanation
Indices: 1992835--1992900 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
1992825 GGGGCGGGTC
**
1992835 GGGGGGAATCAGGTTTGACTCGCGGGAGG
1 GGGGGGAATCAGGTCGGACTCGCGGGAGG
*
1992864 GGGGGGAAATCAGGTCGGACTTGCGGGAGG
1 GGGGGG-AATCAGGTCGGACTCGCGGGAGG
1992894 GTGGGGG
1 G-GGGGG
1992901 CCTGGGGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 6 0.19
30 21 0.66
31 5 0.16
ACGTcount: A:0.17, C:0.12, G:0.56, T:0.15
Consensus pattern (29 bp):
GGGGGGAATCAGGTCGGACTCGCGGGAGG
Found at i:1992941 original size:41 final size:40
Alignment explanation
Indices: 1992864--1992942 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 40
1992854 TCGCGGGAGG
* *
1992864 GGGGGGAAATCAGGTCGGACTTGCGGGAGGGTGGGGGCCT
1 GGGGGGAAATAAGGTCGGACTCGCGGGAGGGTGGGGGCCT
** *
1992904 GGGGGGAGAATAAGGTCTGGACTCGTTGGAGGGGGGGGG
1 GGGGGGA-AATAAGGTC-GGACTCGCGGGAGGGTGGGGG
1992943 GGGGGGGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 7 0.22
41 8 0.25
42 17 0.53
ACGTcount: A:0.16, C:0.11, G:0.57, T:0.15
Consensus pattern (40 bp):
GGGGGGAAATAAGGTCGGACTCGCGGGAGGGTGGGGGCCT
Found at i:1992994 original size:32 final size:32
Alignment explanation
Indices: 1992958--1993024 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
1992948 GGAATCAGGG
1992958 CGGGATTCACCGGAGGGGGGAAGGAGTTAGAT
1 CGGGATTCACCGGAGGGGGGAAGGAGTTAGAT
* * *
1992990 CGGGATTCGCCGGGGGGGGGAAGGAGTTAGGT
1 CGGGATTCACCGGAGGGGGGAAGGAGTTAGAT
1993022 CGG
1 CGG
1993025 CGATGGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.19, C:0.13, G:0.52, T:0.15
Consensus pattern (32 bp):
CGGGATTCACCGGAGGGGGGAAGGAGTTAGAT
Found at i:1999994 original size:39 final size:39
Alignment explanation
Indices: 1999938--2000025 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
1999928 CTGCTGGTTC
*
1999938 AACAGAAAAGCCTGATTCTGCT-AGTTC-ACAAGAAAGTAA
1 AACAGAAAAGCCAGATTCTGCTCA-TTCAAC-AGAAAGTAA
*
1999977 AACAGAAAAGCCAGATTCTGCTCATTCAACAGAAAGTGA
1 AACAGAAAAGCCAGATTCTGCTCATTCAACAGAAAGTAA
*
2000016 AAGAGAAAAG
1 AACAGAAAAG
2000026 GAGGTGCAGC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
39 41 0.93
40 3 0.07
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (39 bp):
AACAGAAAAGCCAGATTCTGCTCATTCAACAGAAAGTAA
Found at i:2011286 original size:21 final size:21
Alignment explanation
Indices: 2011251--2011291 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2011241 TCATAATTTT
* * *
2011251 AATAAAAATATATATTTATTA
1 AATAAAAAAAGATATGTATTA
2011272 AATAAAAAAAGATATGTATT
1 AATAAAAAAAGATATGTATT
2011292 TATAAACTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
AATAAAAAAAGATATGTATTA
Found at i:2011304 original size:25 final size:24
Alignment explanation
Indices: 2011249--2011304 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
2011239 ATTCATAATT
2011249 TTAATAAAAATATATATTTATTAAA
1 TTAA-AAAAATATATATTTATTAAA
* *
2011274 TAAAAAAAGATATGTATTTA-TAAA
1 TTAAAAAA-ATATATATTTATTAAA
2011298 CTTAAAA
1 -TTAAAA
2011305 TCTTATTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (24 bp):
TTAAAAAAATATATATTTATTAAA
Found at i:2019382 original size:12 final size:12
Alignment explanation
Indices: 2019365--2019390 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2019355 ACACGGGGGA
2019365 GAGAGAGAGAGT
1 GAGAGAGAGAGT
2019377 GAGAGAGAGAGT
1 GAGAGAGAGAGT
2019389 GA
1 GA
2019391 TGGTATGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.50, T:0.08
Consensus pattern (12 bp):
GAGAGAGAGAGT
Found at i:2021916 original size:18 final size:18
Alignment explanation
Indices: 2021893--2021930 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2021883 TTTTCACAAC
*
2021893 AAAAAATTGTGGTATTCA
1 AAAAAATTGTGATATTCA
*
2021911 AAAAAATTTTGATATTCA
1 AAAAAATTGTGATATTCA
2021929 AA
1 AA
2021931 TATTTTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (18 bp):
AAAAAATTGTGATATTCA
Found at i:2023602 original size:30 final size:28
Alignment explanation
Indices: 2023518--2023604 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 28
2023508 ATTATTAAAT
** *
2023518 TATTTTTAAAAAATAAAATAAATTTTTA
1 TATTTTTATTAAATTAAATAAATTTTTA
** *
2023546 TATTTTTATTACGTTTAATCAAATTTTTA
1 TATTTTTATTAAATTAAAT-AAATTTTTA
2023575 TATTTTTATTTTAAATTAAATAAATTTTTA
1 TATTTTTA--TTAAATTAAATAAATTTTTA
2023605 CGATTAATAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 13 0.28
29 17 0.36
30 9 0.19
31 8 0.17
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (28 bp):
TATTTTTATTAAATTAAATAAATTTTTA
Found at i:2023743 original size:19 final size:19
Alignment explanation
Indices: 2023713--2023749 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
2023703 ATTTTTTATT
2023713 TTTTATATTAATAAATAATA
1 TTTTATATTAAT-AATAATA
2023733 TTTTA-ATTAATAATAAT
1 TTTTATATTAATAATAAT
2023750 TAATCAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 6 0.35
20 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTATATTAATAATAATA
Found at i:2030336 original size:13 final size:13
Alignment explanation
Indices: 2030318--2030344 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2030308 TGCAGATTAA
2030318 ATTTTTATTTTTT
1 ATTTTTATTTTTT
2030331 ATTTTTATTTTTT
1 ATTTTTATTTTTT
2030344 A
1 A
2030345 AATTGACTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:2030911 original size:19 final size:19
Alignment explanation
Indices: 2030874--2030928 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 19
2030864 AATGATTTTA
* *
2030874 TTAAAAATTATTTTTTAATT
1 TTAAAAA-TATTATATAATT
2030894 TTAAAAATATTATATAA-T
1 TTAAAAATATTATATAATT
2030912 TT--AAATATTA-ATAATT
1 TTAAAAATATTATATAATT
2030928 T
1 T
2030929 AAATTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 4 0.12
16 10 0.31
18 3 0.09
19 8 0.25
20 7 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAAAATATTATATAATT
Found at i:2030927 original size:15 final size:16
Alignment explanation
Indices: 2030898--2030932 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
2030888 TTAATTTTAA
2030898 AAATATTATATAATTT
1 AAATATTATATAATTT
2030914 AAATATTA-ATAATTT
1 AAATATTATATAATTT
2030929 AAAT
1 AAAT
2030933 TAATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATATTATATAATTT
Found at i:2030971 original size:16 final size:16
Alignment explanation
Indices: 2030948--2030984 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2030938 TTTTTAAAAA
2030948 TAAA-TTTTAATATTT
1 TAAATTTTTAATATTT
*
2030963 TTAATTTTTAATATTT
1 TAAATTTTTAATATTT
2030979 TAAATT
1 TAAATT
2030985 AAATATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TAAATTTTTAATATTT
Found at i:2031026 original size:15 final size:16
Alignment explanation
Indices: 2030982--2031026 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
2030972 AATATTTTAA
2030982 ATTAAATATTAATATTC
1 ATTAAAT-TTAATATTC
2030999 ATTAAATTT-ATATTC
1 ATTAAATTTAATATTC
*
2031014 A-TGAATTTAATAT
1 ATTAAATTTAATAT
2031027 AATAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 6 0.23
15 11 0.42
16 2 0.08
17 7 0.27
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (16 bp):
ATTAAATTTAATATTC
Found at i:2039816 original size:31 final size:31
Alignment explanation
Indices: 2039781--2039841 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
2039771 AATTATTAAT
*
2039781 TATAAAAAGTTATTTACTTCAAAATAAAAAA
1 TATAAAAAGTTATTTAATTCAAAATAAAAAA
* * *
2039812 TATAATAATTTATTTAATTTAAAATAAAAA
1 TATAAAAAGTTATTTAATTCAAAATAAAAA
2039842 TCTAAAAGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (31 bp):
TATAAAAAGTTATTTAATTCAAAATAAAAAA
Found at i:2052408 original size:17 final size:16
Alignment explanation
Indices: 2052386--2052429 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2052376 AATATAGATA
**
2052386 TAATTAACTTATTTTTT
1 TAATTAACTT-TTAATT
2052403 TAATTAACTTTTAATT
1 TAATTAACTTTTAATT
2052419 TAATTAA-TTTT
1 TAATTAACTTTT
2052430 TTATACTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 4 0.16
16 11 0.44
17 10 0.40
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATTAACTTTTAATT
Found at i:2053663 original size:13 final size:14
Alignment explanation
Indices: 2053628--2053693 Score: 64
Period size: 13 Copynumber: 4.7 Consensus size: 14
2053618 TAATTAAATT
**
2053628 ATATTATAATATTT
1 ATATTATAATATAA
*
2053642 ATTTTATAATA-AA
1 ATATTATAATATAA
2053655 ATATTATAATATAA
1 ATATTATAATATAA
*
2053669 A-ATTTTAATATAA
1 ATATTATAATATAA
2053682 TCATATTATAAT
1 --ATATTATAAT
2053694 TAAGAATGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
13 21 0.50
14 13 0.31
15 1 0.02
16 7 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATTATAATATAA
Found at i:2053786 original size:36 final size:37
Alignment explanation
Indices: 2053746--2053821 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
2053736 ATTATACTGT
* *
2053746 ATTTTATAATGTTTTT-AAAGATATTTTTAAT-TTTTA
1 ATTTTATAAT-TTTTTGAAAAATATTTTTAATATTATA
*
2053782 ATTTTATTATTTTTTGAAAAATATTTTTAATATTATA
1 ATTTTATAATTTTTTGAAAAATATTTTTAATATTATA
2053819 ATT
1 ATT
2053822 AAATAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 5 0.14
36 23 0.66
37 7 0.20
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (37 bp):
ATTTTATAATTTTTTGAAAAATATTTTTAATATTATA
Found at i:2053854 original size:28 final size:26
Alignment explanation
Indices: 2053823--2053938 Score: 91
Period size: 24 Copynumber: 4.5 Consensus size: 26
2053813 ATTATAATTA
*
2053823 AATAAAAAATATTAAAAATAATATATAT
1 AATAAAAAA-ATT-AAAATAAAATATAT
*
2053851 AATATAAAAATTAAAATAAAATATA-
1 AATAAAAAAATTAAAATAAAATATAT
* *
2053876 AA-AAATTAAAATT--TATATAATATA-
1 AATAAA--AAAATTAAAATAAAATATAT
*
2053900 AGT-AAAAAATTAAAATAAAATATAT
1 AATAAAAAAATTAAAATAAAATATAT
*
2053925 AACATAAAAAATTA
1 AATA-AAAAAATTA
2053939 TATTAAAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
22 6 0.09
24 23 0.33
25 3 0.04
26 18 0.26
27 12 0.17
28 8 0.11
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (26 bp):
AATAAAAAAATTAAAATAAAATATAT
Found at i:2053874 original size:26 final size:26
Alignment explanation
Indices: 2053823--2053934 Score: 97
Period size: 26 Copynumber: 4.4 Consensus size: 26
2053813 ATTATAATTA
* *
2053823 AATAAAAAATATTAAAAATAATATATAT
1 AATATAAAA-ATT-AAAATAAAATATAT
*
2053851 AATATAAAAATTAAAATAAAATATAA
1 AATATAAAAATTAAAATAAAATATAT
* * * *
2053877 AAAATTAAAATT--TATATAATATA-
1 AATATAAAAATTAAAATAAAATATAT
*
2053900 AGTA-AAAAATTAAAATAAAATATAT
1 AATATAAAAATTAAAATAAAATATAT
*
2053925 AACATAAAAA
1 AATATAAAAA
2053935 ATTATATTAA
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
22 6 0.09
23 2 0.03
24 18 0.27
25 2 0.03
26 27 0.41
27 3 0.05
28 8 0.12
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (26 bp):
AATATAAAAATTAAAATAAAATATAT
Found at i:2053908 original size:48 final size:47
Alignment explanation
Indices: 2053813--2053941 Score: 154
Period size: 48 Copynumber: 2.7 Consensus size: 47
2053803 TATTTTTAAT
* * *
2053813 ATTATAATTAAATA-AAAAATATTAAAAATAATATATATAATATAAAA
1 ATTAAAATAAAATATAAAAA-ATTAAAAATTATATATATAATATAAAA
*
2053860 ATTAAAATAAAATATAAAAAATTAAAATTTATATAATATAAGTA-AAAA
1 ATTAAAATAAAATATAAAAAATTAAAAATTATAT-ATATAA-TATAAAA
* * *
2053908 ATTAAAATAAAATATATAACATAAAAAATTATAT
1 ATTAAAATAAAATATAAAAAATTAAAAATTATAT
2053942 TAAAAAATTA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
47 24 0.34
48 45 0.63
49 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.33
Consensus pattern (47 bp):
ATTAAAATAAAATATAAAAAATTAAAAATTATATATATAATATAAAA
Found at i:2053958 original size:13 final size:13
Alignment explanation
Indices: 2053902--2053959 Score: 71
Period size: 13 Copynumber: 4.4 Consensus size: 13
2053892 ATAATATAAG
2053902 TAAAAAATTAAAA
1 TAAAAAATTAAAA
* *
2053915 TAAAATATATAACA
1 TAAAAAAT-TAAAA
* *
2053929 TAAAAAATTATAT
1 TAAAAAATTAAAA
2053942 TAAAAAATTAAAA
1 TAAAAAATTAAAA
2053955 TAAAA
1 TAAAA
2053960 GATATAAGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
13 25 0.69
14 11 0.31
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAAAAATTAAAA
Found at i:2065553 original size:71 final size:71
Alignment explanation
Indices: 2065471--2065605 Score: 182
Period size: 71 Copynumber: 1.9 Consensus size: 71
2065461 ATATATTACT
* * * * * *
2065471 TTATAATATAATTTGAGTATAGGTAATGT-AATTACTTATAATGATTTAAATGTAAGAAAAATAA
1 TTATAATATAATGTGAGTATAAGTAATATGAA-TACTTATAATAATTAAAATATAAGAAAAATAA
2065535 TATAGTG
65 TATAGTG
* *
2065542 TTATAATATAATGTGATTATAAGTAATATGAATATTTATAATAATTAAAATATAAGAAAAATAA
1 TTATAATATAATGTGAGTATAAGTAATATGAATACTTATAATAATTAAAATATAAGAAAAATAA
2065606 CATTACGGTG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
71 53 0.96
72 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.11, T:0.39
Consensus pattern (71 bp):
TTATAATATAATGTGAGTATAAGTAATATGAATACTTATAATAATTAAAATATAAGAAAAATAAT
ATAGTG
Found at i:2065705 original size:19 final size:19
Alignment explanation
Indices: 2065648--2065708 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
2065638 AATTTTTTAT
*
2065648 TTATTAATATTTTATTATAAA
1 TTATTTATA-TTTATTA-AAA
2065669 TGTAATATTA-ATTT-TTAAAA
1 T-T-AT-TTATATTTATTAAAA
2065689 TTATTTATATTTATTAAAA
1 TTATTTATATTTATTAAAA
2065708 T
1 T
2065709 GTAAGTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
17 3 0.09
18 6 0.18
19 8 0.24
20 4 0.12
21 4 0.12
22 4 0.12
23 3 0.09
24 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTTATATTTATTAAAA
Found at i:2065737 original size:41 final size:41
Alignment explanation
Indices: 2065637--2065748 Score: 108
Period size: 39 Copynumber: 2.8 Consensus size: 41
2065627 GATAGTATTA
* **
2065637 TAATTTTTTATTTATTAATAT-TTTATTATAAATGTAATAT
1 TAATTTTTTATTAATTTTTATATTTATTATAAATGTAATAT
*
2065677 TAA-TTTTTA-AAATTATTTATATTTATTA-AAATGTAAGT-T
1 TAATTTTTTATTAATT-TTTATATTTATTATAAATGTAA-TAT
*
2065716 TAATTTTTTTATTAATTTTTATATAATATTATA
1 TAA-TTTTTTATTAATTTTTATAT-TTATTATA
2065749 TAATATTGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
38 3 0.05
39 21 0.36
40 11 0.19
41 13 0.22
42 9 0.16
43 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (41 bp):
TAATTTTTTATTAATTTTTATATTTATTATAAATGTAATAT
Found at i:2066283 original size:64 final size:66
Alignment explanation
Indices: 2066175--2066297 Score: 187
Period size: 64 Copynumber: 1.9 Consensus size: 66
2066165 ATTTGGACTT
*
2066175 ATATATTACAAAGCCCCATAAAAAAAAAGGAAAACAAACGTCTTCCCCAACTTAAATCTCCTCAC
1 ATATATTACAAAGCCCCATAAAAAAAAAGGAAAACAAACGTCTTCACCAACTTAAATCTCCTCAC
2066240 A
66 A
* * * *
2066241 ATATATTACAAAGCCCC-TAAAAAGAAA-GAGAACAAATGTCTTCACCATCTTAAATCT
1 ATATATTACAAAGCCCCATAAAAAAAAAGGAAAACAAACGTCTTCACCAACTTAAATCT
2066298 GTTACAAATC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
64 26 0.50
65 9 0.17
66 17 0.33
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.22
Consensus pattern (66 bp):
ATATATTACAAAGCCCCATAAAAAAAAAGGAAAACAAACGTCTTCACCAACTTAAATCTCCTCAC
A
Found at i:2066561 original size:6 final size:6
Alignment explanation
Indices: 2066539--2066572 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
2066529 AAACTAATCA
*
2066539 TTTATT TGTTTTT TTTATT TTTATT TTTATT TTT
1 TTTATT T-TTATT TTTATT TTTATT TTTATT TTT
2066573 TATAGTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:2066563 original size:19 final size:19
Alignment explanation
Indices: 2066539--2066575 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2066529 AAACTAATCA
2066539 TTTATTTGTT-TTTTTTATT
1 TTTATTT-TTATTTTTTATT
2066558 TTTATTTTTATTTTTTAT
1 TTTATTTTTATTTTTTAT
2066576 AGTATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.84
Consensus pattern (19 bp):
TTTATTTTTATTTTTTATT
Found at i:2066572 original size:13 final size:13
Alignment explanation
Indices: 2066539--2066575 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2066529 AAACTAATCA
2066539 TTTATTTGTTT-TT
1 TTTATTT-TTTATT
2066552 TTTA-TTTTTATT
1 TTTATTTTTTATT
2066564 TTTATTTTTTAT
1 TTTATTTTTTAT
2066576 AGTATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.14
12 8 0.36
13 11 0.50
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.84
Consensus pattern (13 bp):
TTTATTTTTTATT
Found at i:2067831 original size:17 final size:17
Alignment explanation
Indices: 2067809--2067843 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2067799 ACAACTTGTC
*
2067809 TTTTTTT-CTTTTCTTT
1 TTTTTTTCCTTTGCTTT
2067825 TTTTTTTCCTTTGCTTT
1 TTTTTTTCCTTTGCTTT
2067842 TT
1 TT
2067844 GAGAGTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (17 bp):
TTTTTTTCCTTTGCTTT
Found at i:2070498 original size:25 final size:25
Alignment explanation
Indices: 2070464--2070515 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
2070454 AATTTTTTTA
2070464 TTCAAAGATT-TTTAAGTAGTTTCAT
1 TTCAAAGATTATTTAA-TAGTTTCAT
* * *
2070489 TTCAAGGATTATTTTATATTTTCAT
1 TTCAAAGATTATTTAATAGTTTCAT
2070514 TT
1 TT
2070516 GATATTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.54
Consensus pattern (25 bp):
TTCAAAGATTATTTAATAGTTTCAT
Found at i:2070709 original size:18 final size:18
Alignment explanation
Indices: 2070682--2070722 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2070672 TTTATATTTA
2070682 TTATTAACTTTTATTAAT
1 TTATTAACTTTTATTAAT
* * *
2070700 TTATTGACTTTTTTTTAT
1 TTATTAACTTTTATTAAT
2070718 TTATT
1 TTATT
2070723 TACACACATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (18 bp):
TTATTAACTTTTATTAAT
Found at i:2071961 original size:20 final size:21
Alignment explanation
Indices: 2071924--2071962 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2071914 ATCTCTTTTC
*
2071924 AAAATTTTATATTATTAAATA
1 AAAATATTATATTATTAAATA
*
2071945 AAAATATTA-ATTTTTAAA
1 AAAATATTATATTATTAAA
2071963 ATTAATAATT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAATATTATATTATTAAATA
Found at i:2087218 original size:14 final size:14
Alignment explanation
Indices: 2087190--2087243 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
2087180 GGCTTCCACC
*
2087190 TTTCGTTTTTGTTT
1 TTTCCTTTTTGTTT
2087204 TTTCCTCTTTT-TTT
1 TTTCCT-TTTTGTTT
2087218 TTTCCTTTTTGTTT
1 TTTCCTTTTTGTTT
*
2087232 GTTTTCTTTTTG
1 -TTTCCTTTTTG
2087244 AAGAGTGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 4 0.11
14 17 0.49
15 14 0.40
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.78
Consensus pattern (14 bp):
TTTCCTTTTTGTTT
Found at i:2092869 original size:23 final size:23
Alignment explanation
Indices: 2092843--2092887 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2092833 TTAATTAATA
*
2092843 AAAATT-ATATAATAATAAATTTT
1 AAAATTAATA-AAAAATAAATTTT
2092866 AAAATTAATAAAAAATAAATTT
1 AAAATTAATAAAAAATAAATTT
2092888 ATTATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATTAATAAAAAATAAATTTT
Found at i:2105277 original size:29 final size:30
Alignment explanation
Indices: 2105245--2105316 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 30
2105235 TTAACAAGTG
* *
2105245 TTTAAATTATTTTTTTA-TTTTTATTTTTA
1 TTTAAATTATTTATTTATTTTTTATTTTAA
**
2105274 TTT-AATTAAGTATTTATTTTTTATTTTAA
1 TTTAAATTATTTATTTATTTTTTATTTTAA
* *
2105303 ATTAAATAATTTAT
1 TTTAAATTATTTAT
2105317 AATTAATGAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
28 10 0.30
29 16 0.48
30 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (30 bp):
TTTAAATTATTTATTTATTTTTTATTTTAA
Found at i:2107734 original size:2 final size:2
Alignment explanation
Indices: 2107721--2107761 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2107711 TCTCAAGTAA
*
2107721 TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2107762 TTGTGTATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.46, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2115859 original size:17 final size:18
Alignment explanation
Indices: 2115839--2115875 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2115829 TTAAAAGTAA
2115839 TAAAATAATAAAA-AATT
1 TAAAATAATAAAATAATT
*
2115856 TAAAATTATAAAATAATT
1 TAAAATAATAAAATAATT
2115874 TA
1 TA
2115876 TAAACTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATAATAAAATAATT
Found at i:2138066 original size:6 final size:6
Alignment explanation
Indices: 2138055--2138080 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2138045 GAAAAATTCT
2138055 CTGGTG CTGGTG CTGGTG CTGGTG CT
1 CTGGTG CTGGTG CTGGTG CTGGTG CT
2138081 TGCCTTTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.46, T:0.35
Consensus pattern (6 bp):
CTGGTG
Found at i:2141255 original size:14 final size:14
Alignment explanation
Indices: 2141236--2141264 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2141226 TGATGGAAGG
2141236 ATACTTATAGAGTA
1 ATACTTATAGAGTA
2141250 ATACTTATAGAGTA
1 ATACTTATAGAGTA
2141264 A
1 A
2141265 CTTACAATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (14 bp):
ATACTTATAGAGTA
Found at i:2142779 original size:15 final size:15
Alignment explanation
Indices: 2142759--2142790 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2142749 ACGTCTATAT
2142759 ATAAAATTAAAATCC
1 ATAAAATTAAAATCC
2142774 ATAAAATTAAAATCC
1 ATAAAATTAAAATCC
2142789 AT
1 AT
2142791 CTCATATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAAAATTAAAATCC
Found at i:2152345 original size:13 final size:13
Alignment explanation
Indices: 2152293--2152327 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2152283 ATATGTGATA
*
2152293 ATGA-ATAATGAC
1 ATGATATAATCAC
2152305 ATGATATAATCAC
1 ATGATATAATCAC
2152318 ATGATATAAT
1 ATGATATAAT
2152328 TATATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (13 bp):
ATGATATAATCAC
Found at i:2162928 original size:2 final size:2
Alignment explanation
Indices: 2162921--2162950 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2162911 TGTTATTGAA
2162921 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
2162951 TAGTAAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2166976 original size:29 final size:29
Alignment explanation
Indices: 2166922--2166977 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
2166912 TAAGTAGCCA
* * *
2166922 CTCTCTCAGCTTTGGTTTAACTAGGGTTT
1 CTCTCTCAGCGTTGGATTAACAAGGGTTT
2166951 CTCTCTCAGTCGTTGGATTAA-AAGGGT
1 CTCTCTCAG-CGTTGGATTAACAAGGGT
2166978 CACGTGCGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 14 0.61
30 9 0.39
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (29 bp):
CTCTCTCAGCGTTGGATTAACAAGGGTTT
Found at i:2167493 original size:31 final size:32
Alignment explanation
Indices: 2167436--2167502 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
2167426 ATATCATATG
2167436 AATTAAATGAAACAAAAAATATAAAATACAAA
1 AATTAAATGAAACAAAAAATATAAAATACAAA
* *
2167468 AATTAAAT-AAA-ATAAAATTATAAAATACAAT
1 AATTAAATGAAACA-AAAAATATAAAATACAAA
2167499 AATT
1 AATT
2167503 GAATTGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 1 0.03
31 23 0.72
32 8 0.25
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.25
Consensus pattern (32 bp):
AATTAAATGAAACAAAAAATATAAAATACAAA
Found at i:2180306 original size:18 final size:18
Alignment explanation
Indices: 2180267--2180306 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2180257 ATAATGCCAG
* * *
2180267 GGCTGCTAGAAAAGGTAT
1 GGCTGCCAGAAAAGCTAC
2180285 GGCTGCCAGAAAAGCTAC
1 GGCTGCCAGAAAAGCTAC
2180303 GGCT
1 GGCT
2180307 TCCAAGAGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.33, T:0.17
Consensus pattern (18 bp):
GGCTGCCAGAAAAGCTAC
Found at i:2189261 original size:43 final size:43
Alignment explanation
Indices: 2189208--2189289 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
2189198 CTGATTACAT
* *
2189208 AGCTGTTTCTTTATATTTCTTCATCATCTTAAGTTTCCAACAG
1 AGCTGGTTCTTTATATTTCTTCATCATCTCAAGTTTCCAACAG
*
2189251 AGCTGGTTCTTTATATTTGTTCATCATCTCAAGTTTCCA
1 AGCTGGTTCTTTATATTTCTTCATCATCTCAAGTTTCCA
2189290 GCTGTGGAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.46
Consensus pattern (43 bp):
AGCTGGTTCTTTATATTTCTTCATCATCTCAAGTTTCCAACAG
Found at i:2196659 original size:21 final size:22
Alignment explanation
Indices: 2196635--2196680 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2196625 AGGAGACAAG
*
2196635 AGAAGAAG-AAACAGAGGAAAC
1 AGAAGAAGAAAACAGAGAAAAC
2196656 AGAAGAAGAAAACAGAGAAAAC
1 AGAAGAAGAAAACAGAGAAAAC
2196678 AGA
1 AGA
2196681 GGACTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.65, C:0.09, G:0.26, T:0.00
Consensus pattern (22 bp):
AGAAGAAGAAAACAGAGAAAAC
Found at i:2200888 original size:32 final size:33
Alignment explanation
Indices: 2200852--2200915 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
2200842 TAGGGTAGCA
* * *
2200852 ACATGTTGATGTGGCATTGCCACGTCA-CCTTC
1 ACATGTTGACGTGGCAGTGCCACATCATCCTTC
*
2200884 ACATGTTGACGTGGTAGTGCCACATCATCCTT
1 ACATGTTGACGTGGCAGTGCCACATCATCCTT
2200916 TTACGGTCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 23 0.85
33 4 0.15
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (33 bp):
ACATGTTGACGTGGCAGTGCCACATCATCCTTC
Found at i:2201242 original size:20 final size:22
Alignment explanation
Indices: 2201204--2201250 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
2201194 TAAAATAATC
* *
2201204 TTTTTCTCATTTTTTCC-TTCT
1 TTTTTCTCATTTCTACCTTTCT
2201225 TTTTTCTC-TTTCTACCTTTCT
1 TTTTTCTCATTTCTACCTTTCT
2201246 TTTTT
1 TTTTT
2201251 TTTTCTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTCTCATTTCTACCTTTCT
Found at i:2205128 original size:34 final size:30
Alignment explanation
Indices: 2205053--2205148 Score: 126
Period size: 29 Copynumber: 3.3 Consensus size: 30
2205043 AATCATTAGT
* *
2205053 TATAAAGACTTATTTAACTTAAAATAAAAA
1 TATAAAAATTTATTTAACTTAAAATAAAAA
*
2205083 TATAAAAATTTATTT-ATTTAAAATAAAAA
1 TATAAAAATTTATTTAACTTAAAATAAAAA
*
2205112 TATAAAAATTTGATTTAAC--ATAATAAAAA
1 TATAAAAATTT-ATTTAACTTAAAATAAAAA
2205141 TATAAAAA
1 TATAAAAA
2205149 AATTTAAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
29 41 0.69
30 17 0.29
31 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.35
Consensus pattern (30 bp):
TATAAAAATTTATTTAACTTAAAATAAAAA
Found at i:2208277 original size:21 final size:21
Alignment explanation
Indices: 2208230--2208278 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2208220 ATAAAAATAT
2208230 AATATTTAAAAAAACTATTAA
1 AATATTTAAAAAAACTATTAA
* *
2208251 ACTATTTAAAAAAA-TTTTAAA
1 AATATTTAAAAAAACTATT-AA
2208272 AATATTT
1 AATATTT
2208279 TTTTTATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
AATATTTAAAAAAACTATTAA
Found at i:2222549 original size:2 final size:2
Alignment explanation
Indices: 2222542--2222567 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2222532 TAGACGTGTT
2222542 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2222568 ATTTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2234519 original size:23 final size:23
Alignment explanation
Indices: 2234493--2234537 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2234483 CGTAGAAAAA
*
2234493 GACAGAGTGTTAACCTTTTTTAT
1 GACAGAGAGTTAACCTTTTTTAT
2234516 GACAGAGAGTTAACCTTTTTTA
1 GACAGAGAGTTAACCTTTTTTA
2234538 GATTTAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (23 bp):
GACAGAGAGTTAACCTTTTTTAT
Found at i:2239002 original size:228 final size:227
Alignment explanation
Indices: 2238582--2239432 Score: 837
Period size: 228 Copynumber: 3.7 Consensus size: 227
2238572 ACGGAGACGA
* * * * * * *
2238582 AGAACAAGGTGAAGGGTAGACT-CTTTCTGAATGTTATAATCAGCTAAAGTCCTCCCATCCTCCA
1 AGAACAAGGTGAAGAGTTGACTCCTTT-TGGATGTTATAATCAGCCAAAGTACGCCCGTCCT-CA
* * * * * *
2238646 A-TTGTTTCCCGGCAAAGAT-AAGCCTTTGCTGATCTGGG-GGGATTCCTTCCTTATCCTGAATC
64 AGCTGTTTCCCGGCGAAGATGAA-CCGTTGCTGGTC-GGGTGGGATCCCTTCCTTATCCTGGATC
* * * * * * *
2238708 TTTGCCTTGACGTTATCGATTGTATCCGAACTTTCCACCTCCAAGGTGATTGTTTTTCCAGTCAA
127 TTGGCCTTAACGTTATCAATCGTGTCCGAACTCTCGACCTCCAAGGTGATTG-TTTTCCAGTCAA
* * * * * *
2238773 GGTCTTGACAAAAATCTGCATTCCTCCACGAAGCCTC
191 GGTTTTGACAAAGATTTGCATACCCCCACGAAGCCTG
* * * * * * * * *
2238810 AAAACAAGATGAAGGGTTGATTCCTTTTGTATGTTGTAATCAGCCAAGGTCCTCCCGTCCTCAAG
1 AGAACAAGGTGAAGAGTTGACTCCTTTTGGATGTTATAATCAGCCAAAGTACGCCCGTCCTCAAG
* * * * * *
2238875 CTGCTTCCCGGCGAAGATCAAACGTTGTTGGTCTGGTGGGATCCCTTCCTTATCTTGGATCTTGG
66 CTGTTTCCCGGCGAAGATGAACCGTTGCTGGTCGGGTGGGATCCCTTCCTTATCCTGGATCTTGG
* * *
2238940 CCTTAACGTTATCAATCGTGTCCGAGCTCTCGACCTCCAAGGTTATTGTCTTTCCTGTCAAGGTT
131 CCTTAACGTTATCAATCGTGTCCGAACTCTCGACCTCCAAGGTGATTGT-TTTCCAGTCAAGGTT
*
2239005 TTGACAAAGATTTGCATGCCCCCACGAAGCCTG
195 TTGACAAAGATTTGCATACCCCCACGAAGCCTG
* * * *
2239038 AGGACAAGGTGGAGAGTTGACTCCTTTTGGATGTTATAATCAGCCAAAGTACGGCCGTCCTCCAG
1 AGAACAAGGTGAAGAGTTGACTCCTTTTGGATGTTATAATCAGCCAAAGTACGCCCGTCCTCAAG
* * * * * * *
2239103 CTGTTTCCCGGCGAAGATGAGCCGCTGTTGGTCGGGAGGGATGCCTTCCTTGTCCTGGATTTTGG
66 CTGTTTCCCGGCGAAGATGAACCGTTGCTGGTCGGGTGGGATCCCTTCCTTATCCTGGATCTTGG
* * * * * * * * *
2239168 CCTTGACGTTGTCAATCGTGTCGGAACTCTCGACTTCGAGGGTGATGGTTTTGCCGGTCAAAGTT
131 CCTTAACGTTATCAATCGTGTCCGAACTCTCGACCTCCAAGGTGATTGTTTT-CCAGTCAAGGTT
* * * *
2239233 TTGACGAAGATTTGCATACCGCCACGAAGACGG
195 TTGACAAAGATTTGCATACCCCCACGAAGCCTG
* * * * * * * * *
2239266 AGGACCAGGTGGAGAGTTGACTCCTTCTGGATGTTATAATCCGCCAAGGTACGACCGTCTTCGAG
1 AGAACAAGGTGAAGAGTTGACTCCTTTTGGATGTTATAATCAGCCAAAGTACGCCCGTCCTCAAG
* * * *
2239331 CTGTTTCCCGGCGAAGATGAGCCTTTGCTGGTCGGGTGGGATCCCTTCCTTGTCTTGGATCTTGG
66 CTGTTTCCCGGCGAAGATGAACCGTTGCTGGTCGGGTGGGATCCCTTCCTTATCCTGGATCTTGG
* * * *
2239396 CCTTAACGTTGTCGATGGTGTCGGAACTCTCGACCTC
131 CCTTAACGTTATCAATCGTGTCCGAACTCTCGACCTC
2239433 GAGAGTTATG
Statistics
Matches: 523, Mismatches: 94, Indels: 12
0.83 0.15 0.02
Matches are distributed among these distances:
227 9 0.02
228 508 0.97
229 6 0.01
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (227 bp):
AGAACAAGGTGAAGAGTTGACTCCTTTTGGATGTTATAATCAGCCAAAGTACGCCCGTCCTCAAG
CTGTTTCCCGGCGAAGATGAACCGTTGCTGGTCGGGTGGGATCCCTTCCTTATCCTGGATCTTGG
CCTTAACGTTATCAATCGTGTCCGAACTCTCGACCTCCAAGGTGATTGTTTTCCAGTCAAGGTTT
TGACAAAGATTTGCATACCCCCACGAAGCCTG
Found at i:2239452 original size:228 final size:228
Alignment explanation
Indices: 2238825--2239477 Score: 840
Period size: 228 Copynumber: 2.9 Consensus size: 228
2238815 AAGATGAAGG
* * * * ** *
2238825 GTTGATTCCTTTTGTATGTTGTAATCAGCCAAGGTCCTCCCGTCCTCAAGCTGCTTCCCGGCGAA
1 GTTGACTCCTTTTGGATGTTATAATCAGCCAAGGTACGACCGTCCTCAAGCTGTTTCCCGGCGAA
* ** * * *
2238890 GATCAAACGTTGTTGGTCTGGTGGGATCCCTTCCTTATCTTGGATCTTGGCCTTAACGTTATCAA
66 GATGAGCCGTTGTTGGTCGGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTAACGTTGTCAA
* * * * * * *
2238955 TCGTGTCCGAGCTCTCGACCTCCA-AGGTTATTGTCTTTCCTGTCAAGGTTTTGACAAAGATTTG
131 TCGTGTCGGAACTCTCGACCTCGAGA-GTTATGGTCTTGCCGGTCAAGGTTTTGACGAAGATTTG
* * *
2239019 CATGCCCCCACGAAGCCTGAGGACAAGGTGGAGA
195 CATACCCCCACGAAGACGGAGGACAAGGTGGAGA
* * *
2239053 GTTGACTCCTTTTGGATGTTATAATCAGCCAAAGTACGGCCGTCCTCCAGCTGTTTCCCGGCGAA
1 GTTGACTCCTTTTGGATGTTATAATCAGCCAAGGTACGACCGTCCTCAAGCTGTTTCCCGGCGAA
* * * * * *
2239118 GATGAGCCGCTGTTGGTCGGGAGGGATGCCTTCCTTGTCCTGGATTTTGGCCTTGACGTTGTCAA
66 GATGAGCCGTTGTTGGTCGGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTAACGTTGTCAA
* * * * *
2239183 TCGTGTCGGAACTCTCGACTTCGAGGGTGATGGTTTTGCCGGTCAAAGTTTTGACGAAGATTTGC
131 TCGTGTCGGAACTCTCGACCTCGAGAGTTATGGTCTTGCCGGTCAAGGTTTTGACGAAGATTTGC
* *
2239248 ATACCGCCACGAAGACGGAGGACCAGGTGGAGA
196 ATACCCCCACGAAGACGGAGGACAAGGTGGAGA
* * * *
2239281 GTTGACTCCTTCTGGATGTTATAATCCGCCAAGGTACGACCGTCTTCGAGCTGTTTCCCGGCGAA
1 GTTGACTCCTTTTGGATGTTATAATCAGCCAAGGTACGACCGTCCTCAAGCTGTTTCCCGGCGAA
* * *
2239346 GATGAGCCTTTGCTGGTCGGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTAACGTTGTCGA
66 GATGAGCCGTTGTTGGTCGGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTAACGTTGTCAA
* * * *
2239411 TGGTGTCGGAACTCTCGACCTCGAGAGTTATGGTCTTGCCGGTCAGGGTTTTCACGAAGATCTGC
131 TCGTGTCGGAACTCTCGACCTCGAGAGTTATGGTCTTGCCGGTCAAGGTTTTGACGAAGATTTGC
2239476 AT
196 AT
2239478 CTTCTAAAAA
Statistics
Matches: 362, Mismatches: 62, Indels: 2
0.85 0.15 0.00
Matches are distributed among these distances:
228 362 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.30
Consensus pattern (228 bp):
GTTGACTCCTTTTGGATGTTATAATCAGCCAAGGTACGACCGTCCTCAAGCTGTTTCCCGGCGAA
GATGAGCCGTTGTTGGTCGGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTAACGTTGTCAA
TCGTGTCGGAACTCTCGACCTCGAGAGTTATGGTCTTGCCGGTCAAGGTTTTGACGAAGATTTGC
ATACCCCCACGAAGACGGAGGACAAGGTGGAGA
Found at i:2245448 original size:2 final size:2
Alignment explanation
Indices: 2245441--2245474 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2245431 GTACTAACAA
*
2245441 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2245475 TATGTACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2254754 original size:19 final size:20
Alignment explanation
Indices: 2254730--2254769 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2254720 AAAGATTTAT
*
2254730 TTAATTTAAAATAA-AAAAA
1 TTAATTGAAAATAATAAAAA
*
2254749 TTAATTGAAAGTAATAAAAA
1 TTAATTGAAAATAATAAAAA
2254769 T
1 T
2254770 ATAAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
TTAATTGAAAATAATAAAAA
Found at i:2261904 original size:2 final size:2
Alignment explanation
Indices: 2261883--2261926 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
2261873 TGAGCAGGAG
* * * *
2261883 AT AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2261925 AT
1 AT
2261927 TACATATGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2266673 original size:12 final size:12
Alignment explanation
Indices: 2266656--2266683 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2266646 AATCTAAGCA
2266656 AAAAAACAAAAC
1 AAAAAACAAAAC
2266668 AAAAAACAAAAC
1 AAAAAACAAAAC
2266680 AAAA
1 AAAA
2266684 CAAGGCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAC
Found at i:2267389 original size:2 final size:2
Alignment explanation
Indices: 2267382--2267407 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2267372 AGTTGGATCC
2267382 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
2267408 TTTTCAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2274086 original size:2 final size:2
Alignment explanation
Indices: 2274079--2274105 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2274069 CTGCACAAAA
2274079 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2274106 TATGCAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2285466 original size:19 final size:20
Alignment explanation
Indices: 2285429--2285468 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2285419 TGTTTTACAC
*
2285429 TAATTTTTGTTATAGTATTA
1 TAATTTTTGTTAAAGTATTA
*
2285449 TAATTTTT-TTAAATTATTA
1 TAATTTTTGTTAAAGTATTA
2285468 T
1 T
2285469 TTTAACAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TAATTTTTGTTAAAGTATTA
Found at i:2292625 original size:22 final size:21
Alignment explanation
Indices: 2292602--2292675 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
2292592 TAAATAAAAT
*
2292602 TTTATAATTAATAATTAATTA
1 TTTATCATTAATAATTAATTA
*
2292623 TTTATCATTAATTAAATAATTA
1 TTTATCATTAA-TAATTAATTA
*
2292645 TTTATCA-TATATCATATAATTA
1 TTTATCATTA-ATAAT-TAATTA
2292667 TTTTATCAT
1 -TTTATCAT
2292676 ATTATATTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
21 14 0.32
22 23 0.52
23 7 0.16
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTATCATTAATAATTAATTA
Found at i:2292686 original size:22 final size:21
Alignment explanation
Indices: 2292615--2292686 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 21
2292605 ATAATTAATA
2292615 ATTAATTATTTATCATTAATTA-
1 ATTAATTATTTATCA-T-ATTAT
*
2292637 AATAATTATTTATCATA-TAT
1 ATTAATTATTTATCATATTAT
2292657 CATATAATTATTTTATCATATTAT
1 -AT-TAATTA-TTTATCATATTAT
2292681 ATTAAT
1 ATTAAT
2292687 ATGTCATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
19 2 0.05
20 1 0.02
21 2 0.05
22 24 0.56
23 11 0.26
24 3 0.07
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTAATTATTTATCATATTAT
Found at i:2293154 original size:2 final size:2
Alignment explanation
Indices: 2293147--2293177 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2293137 GGCAAAAGAA
2293147 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2293178 CAAGGTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2295630 original size:51 final size:51
Alignment explanation
Indices: 2295570--2295668 Score: 198
Period size: 51 Copynumber: 1.9 Consensus size: 51
2295560 GTAACATAAA
2295570 CATCTTACTTCTGGAATTGAGCTTTTCTGGGGGAGGCAAAGTTCAAGGGTT
1 CATCTTACTTCTGGAATTGAGCTTTTCTGGGGGAGGCAAAGTTCAAGGGTT
2295621 CATCTTACTTCTGGAATTGAGCTTTTCTGGGGGAGGCAAAGTTCAAGG
1 CATCTTACTTCTGGAATTGAGCTTTTCTGGGGGAGGCAAAGTTCAAGG
2295669 TTTTCCAGGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.32
Consensus pattern (51 bp):
CATCTTACTTCTGGAATTGAGCTTTTCTGGGGGAGGCAAAGTTCAAGGGTT
Found at i:2303973 original size:16 final size:19
Alignment explanation
Indices: 2303935--2303975 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 19
2303925 TGCTATATTA
2303935 AAAATATAATATAAAAGTT
1 AAAATATAATATAAAAGTT
2303954 -AAAT-TAA-ATAAAA-TT
1 AAAATATAATATAAAAGTT
2303969 AAAATAT
1 AAAATAT
2303976 TAAGAAATNN
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
15 2 0.10
16 10 0.50
17 4 0.20
18 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAATATAATATAAAAGTT
Found at i:2308747 original size:25 final size:25
Alignment explanation
Indices: 2308719--2308768 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2308709 TTTAATGATC
* *
2308719 TTCAATTAATAATAGTTTT-TTTAAT
1 TTCAATAAAAAATA-TTTTATTTAAT
2308744 TTCAATAAAAAATATTTTATTTAAT
1 TTCAATAAAAAATATTTTATTTAAT
2308769 AAAAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (25 bp):
TTCAATAAAAAATATTTTATTTAAT
Found at i:2308786 original size:17 final size:17
Alignment explanation
Indices: 2308752--2308783 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2308742 ATTTCAATAA
2308752 AAAATATTTTATTTAAT
1 AAAATATTTTATTTAAT
2308769 AAAA-ATTTTATTTAA
1 AAAATATTTTATTTAA
2308784 ATATTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAATATTTTATTTAAT
Found at i:2310911 original size:21 final size:20
Alignment explanation
Indices: 2310886--2310927 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2310876 AATTAATTAA
2310886 TTTAAATGAATCATATTCAAT
1 TTTAAATGAATCA-ATTCAAT
* *
2310907 TTTAAATTAATTAATTCAAT
1 TTTAAATGAATCAATTCAAT
2310927 T
1 T
2310928 CCATAGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTAAATGAATCAATTCAAT
Found at i:2312561 original size:20 final size:20
Alignment explanation
Indices: 2312532--2312575 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
2312522 ACTCAACATA
2312532 TTTTTTAAT-ATATA-ATAT
1 TTTTTTAATAATATATATAT
2312550 CTTTTTTAAATAATATATATAT
1 -TTTTTT-AATAATATATATAT
2312572 TTTT
1 TTTT
2312576 ATATTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.27
20 3 0.14
21 9 0.41
22 4 0.18
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTTAATAATATATATAT
Found at i:2312574 original size:19 final size:19
Alignment explanation
Indices: 2312529--2312576 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2312519 AACACTCAAC
*
2312529 ATATTTTTTAATATATAAT
1 ATATTTTTAAATATATAAT
*
2312548 ATCTTTTTTAAATA-ATATAT
1 AT-ATTTTTAAATATATA-AT
2312568 ATATTTTTA
1 ATATTTTTA
2312577 TATTAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATTTTTAAATATATAAT
Found at i:2312583 original size:20 final size:23
Alignment explanation
Indices: 2312536--2312583 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2312526 AACATATTTT
*
2312536 TTAATATATAATATCTTTTTTAA
1 TTAATATATAATATCTTTTATAA
*
2312559 ATAATATAT-ATAT-TTTTAT-A
1 TTAATATATAATATCTTTTATAA
2312579 TTAAT
1 TTAAT
2312584 TTATTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.23
21 5 0.23
22 4 0.18
23 8 0.36
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAATATATAATATCTTTTATAA
Found at i:2313600 original size:10 final size:10
Alignment explanation
Indices: 2313571--2313600 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2313561 TTTTATAAAA
*
2313571 AAAATTTGAC
1 AAAATTTGAT
2313581 AAAATTTGAT
1 AAAATTTGAT
2313591 AAAATTTGAT
1 AAAATTTGAT
2313601 TGTGGTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.37
Consensus pattern (10 bp):
AAAATTTGAT
Found at i:2314011 original size:7 final size:7
Alignment explanation
Indices: 2314001--2314030 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2313991 TTAAATTTTT
2314001 TTATATA
1 TTATATA
2314008 TTATATA
1 TTATATA
2314015 TTATATA
1 TTATATA
2314022 TTATATA
1 TTATATA
2314029 TT
1 TT
2314031 TTTAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATATA
Found at i:2314051 original size:12 final size:13
Alignment explanation
Indices: 2314034--2314066 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
2314024 ATATATTTTT
2314034 AATAATTTTTA-A
1 AATAATTTTTATA
2314046 AATAATTTTTATTA
1 AATAATTTTTA-TA
2314060 AATAATT
1 AATAATT
2314067 AATATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
14 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATAATTTTTATA
Found at i:2314136 original size:9 final size:9
Alignment explanation
Indices: 2314122--2314150 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
2314112 TTTATTTACA
2314122 TTTTTAAAT
1 TTTTTAAAT
2314131 TTTTTAAAT
1 TTTTTAAAT
2314140 TTTTTAAAT
1 TTTTTAAAT
2314149 TT
1 TT
2314151 GACCGTCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:2314244 original size:24 final size:22
Alignment explanation
Indices: 2314216--2314269 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 22
2314206 AAAAAAAGTT
2314216 TTTATTTGATATATTTATATTTA
1 TTTATTTGAT-TATTTATATTTA
*
2314239 TATTATTATTATTATTTATATTTA
1 T-TTATT-TGATTATTTATATTTA
2314263 TTTATTT
1 TTTATTT
2314270 TTTTTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.04
23 6 0.21
24 18 0.64
25 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTATTTGATTATTTATATTTA
Found at i:2314289 original size:10 final size:9
Alignment explanation
Indices: 2314216--2314289 Score: 60
Period size: 10 Copynumber: 7.8 Consensus size: 9
2314206 AAAAAAAGTT
*
2314216 TTTATTTGA
1 TTTATTTTA
*
2314225 TATATTTATA
1 TTTATTT-TA
*
2314235 TTTATATTA
1 TTTATTTTA
2314244 -TTATTATTA
1 TTTATT-TTA
2314253 TTTATATTTA
1 TTTAT-TTTA
*
2314263 TTTATTTTT
1 TTTATTTTA
2314272 TTTAATTTTA
1 TTT-ATTTTA
2314282 TTCTATTT
1 TT-TATTT
2314290 GTTCATATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
8 4 0.08
9 17 0.33
10 29 0.56
11 2 0.04
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (9 bp):
TTTATTTTA
Found at i:2314418 original size:15 final size:15
Alignment explanation
Indices: 2314400--2314433 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2314390 TTGTTATGTG
2314400 AATTTT-ATTTTTAA
1 AATTTTAATTTTTAA
2314414 TAATTTTAATTTTTAA
1 -AATTTTAATTTTTAA
2314430 AATT
1 AATT
2314434 GAAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTTAATTTTTAA
Found at i:2318332 original size:2 final size:2
Alignment explanation
Indices: 2318277--2318322 Score: 51
Period size: 2 Copynumber: 23.0 Consensus size: 2
2318267 TTAGATTGAC
*
2318277 AT AT AT CAT AC AT AT AT AT AT AT AT AT AT AT AT CA- AT AT AT A-
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
2318319 AT AT
1 AT AT
2318323 GTTCATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 2 0.05
2 33 0.87
3 3 0.08
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2319141 original size:18 final size:19
Alignment explanation
Indices: 2319107--2319142 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2319097 TCTCAACATA
*
2319107 TTTTTTAATATATAATATC
1 TTTTTTAATATAAAATATC
2319126 TTTTTTAA-ATAAAATAT
1 TTTTTTAATATAAAATAT
2319143 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTTAATATAAAATATC
Found at i:2319149 original size:19 final size:19
Alignment explanation
Indices: 2319104--2319151 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2319094 AACTCTCAAC
*
2319104 ATATTTTTTAATATATAAT
1 ATATTTTTTAATATAAAAT
*
2319123 ATCTTTTTTAA-ATAAAAT
1 ATATTTTTTAATATAAAAT
2319141 ATATATTTTTA
1 ATAT-TTTTTA
2319152 TATTAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTTTTTAATATAAAAT
Found at i:2319702 original size:21 final size:21
Alignment explanation
Indices: 2319659--2319702 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2319649 AATTATATCA
*
2319659 ATTTAATTATTTTTTAATTAT
1 ATTTAATTATTTTTTAATAAT
*
2319680 ATTTAATTTTTTTATTAA-AAT
1 ATTTAATTATTTT-TTAATAAT
2319701 AT
1 AT
2319703 GATATCAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTAATTATTTTTTAATAAT
Found at i:2320153 original size:10 final size:10
Alignment explanation
Indices: 2320133--2320162 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
2320123 CCTTTTATAA
2320133 AAAATTTTGAC
1 AAAA-TTTGAC
2320144 AAAATTTGAC
1 AAAATTTGAC
2320154 AAAATTTGA
1 AAAATTTGA
2320163 TTGTGGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (10 bp):
AAAATTTGAC
Found at i:2320330 original size:108 final size:107
Alignment explanation
Indices: 2320204--2320412 Score: 251
Period size: 108 Copynumber: 1.9 Consensus size: 107
2320194 TATAAGAAAT
* * *
2320204 TTTGAGTAATTGTAAATAAAAGGCAAACAAGATAAAAGTTAAACAATT-TCAAAAGAACCTGTGT
1 TTTGAGTAATTGTAAATAAAAGACAAACAAGATAAAAGTTAAACAATTCT-AAAAGAACATGTAT
* * * *
2320268 TTGTAAATTGTGAAAGTTGTAATTTAATCAACATATTTCACTAA
65 TTGTAAATTATAAAAATTATAA-TTAATCAACATATTTCACTAA
* ** * * *
2320312 TTTGAGTAAATT-TAAATAAAAGATAAATTAGATAAGAGTTAAATAATTCTAAAAGAATATGTAT
1 TTTGAGT-AATTGTAAATAAAAGACAAACAAGATAAAAGTTAAACAATTCTAAAAGAACATGTAT
*
2320376 TTGTAAATTATAAAAATTATAATTAATCAATATATTT
65 TTGTAAATTATAAAAATTATAATTAATCAACATATTT
2320413 AATTATTTTG
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
107 14 0.16
108 66 0.78
109 5 0.06
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.35
Consensus pattern (107 bp):
TTTGAGTAATTGTAAATAAAAGACAAACAAGATAAAAGTTAAACAATTCTAAAAGAACATGTATT
TGTAAATTATAAAAATTATAATTAATCAACATATTTCACTAA
Found at i:2320698 original size:21 final size:22
Alignment explanation
Indices: 2320653--2320706 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2320643 TTTATTTAAA
* *
2320653 AATTTATATTTTTTAATTTTTTT
1 AATTTA-ATTTCTTAATTATTTT
2320676 AATTTAATTTCTTAA-TATTTT
1 AATTTAATTTCTTAATTATTTT
*
2320697 AATTTTATTT
1 AATTTAATTT
2320707 AATTTAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 14 0.50
22 8 0.29
23 6 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
AATTTAATTTCTTAATTATTTT
Found at i:2325130 original size:28 final size:28
Alignment explanation
Indices: 2325107--2325162 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
2325097 ATTTGATTTA
2325107 AATAAAAATATAAAATTTAATTGAATAT
1 AATAAAAATATAAAATTTAATTGAATAT
*
2325135 AATAAAAA-ATAAAAATTTAATTAAATAT
1 AATAAAAATAT-AAAATTTAATTGAATAT
2325163 TTTTAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (28 bp):
AATAAAAATATAAAATTTAATTGAATAT
Found at i:2325161 original size:23 final size:25
Alignment explanation
Indices: 2325097--2325161 Score: 64
Period size: 28 Copynumber: 2.6 Consensus size: 25
2325087 ATAAAAACTT
*
2325097 ATTTGATTTAAAT-AAAAATATAAA
1 ATTTAATTTAAATAAAAAATATAAA
2325121 ATTTAATTGAATATAATAAAAAATA-AAA
1 ATTTAATT---TA-AATAAAAAATATAAA
2325149 ATTTAA-TTAAATA
1 ATTTAATTTAAATA
2325162 TTTTTAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
23 4 0.11
24 9 0.26
27 3 0.09
28 12 0.34
29 7 0.20
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (25 bp):
ATTTAATTTAAATAAAAAATATAAA
Found at i:2340821 original size:16 final size:15
Alignment explanation
Indices: 2340802--2340831 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2340792 AAAACTAAAC
2340802 TAATTACAAACAAATT
1 TAATTACAAA-AAATT
2340818 TAATTACAAAAAAT
1 TAATTACAAAAAAT
2340832 GCAAATCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (15 bp):
TAATTACAAAAAATT
Found at i:2344380 original size:122 final size:121
Alignment explanation
Indices: 2344123--2344382 Score: 301
Period size: 122 Copynumber: 2.1 Consensus size: 121
2344113 ATATTTTCTG
2344123 AAAAATCGTAACATA-TTTGAATTAATTGCATGATATGCATAAAAACTTACATTATTACTTCATA
1 AAAAATCGTAACATATTTTGAATTAATTGCATGATATGCATAAAAACTTACATTATTACTTCATA
* * * *
2344187 CTGTTAATATTTTAATAAATTTATCTTGATTTTAAGTTTTGATTAGATGTCTTTTA
66 CTGTTAATATTTTAATAAATTTATCTTGAATTTAAGTTTTAATTAAACGTCTTTTA
* * * * * * * * * **
2344243 TAAAGTCCGTGACATATTTTGAATTAATTGTATGATATGTATGAAGATTTGCATTATTACTTTGT
1 AAAAAT-CGTAACATATTTTGAATTAATTGCATGATATGCATAAAAACTTACATTATTACTTCAT
* * *
2344308 ATTGTTAATTCTTTTAATAAATTTAT-TTTAATTTAA-TATTATAATTAAACGTCTTTTA
65 ACTGTTAA-TATTTTAATAAATTTATCTTGAATTTAAGT-TT-TAATTAAACGTCTTTTA
2344366 AAAAATCGTAACATATT
1 AAAAATCGTAACATATT
2344383 CAAACTTATT
Statistics
Matches: 114, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
120 4 0.04
121 9 0.08
122 67 0.59
123 34 0.30
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (121 bp):
AAAAATCGTAACATATTTTGAATTAATTGCATGATATGCATAAAAACTTACATTATTACTTCATA
CTGTTAATATTTTAATAAATTTATCTTGAATTTAAGTTTTAATTAAACGTCTTTTA
Found at i:2345639 original size:18 final size:18
Alignment explanation
Indices: 2345613--2345649 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2345603 ATAAAATAAA
* *
2345613 AAATTATTTAAATTTTTT
1 AAATAATTTAAAATTTTT
2345631 AAATAATTTAAAATTTTT
1 AAATAATTTAAAATTTTT
2345649 A
1 A
2345650 TAAAATATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATAATTTAAAATTTTT
Found at i:2349601 original size:13 final size:13
Alignment explanation
Indices: 2349574--2349727 Score: 55
Period size: 13 Copynumber: 12.1 Consensus size: 13
2349564 TTATCTTTAA
*
2349574 AAAAATATTAAAAT
1 AAAAATA-TATAAT
2349588 AAAAATATATAAT
1 AAAAATATATAAT
*
2349601 ATAAAATATTATATT
1 A-AAAATA-TATAAT
2349616 AAAAA-ATA-AA-
1 AAAAATATATAAT
*
2349626 AATAAA-ATAT-GT
1 AA-AAATATATAAT
* *
2349638 -AAGAT-TATACT
1 AAAAATATATAAT
*
2349649 AAAAA-ATA-AAA
1 AAAAATATATAAT
2349660 ATAAAATATA-ACAT
1 A-AAAATATATA-AT
* *
2349674 TAAAATATAT-TT
1 AAAAATATATAAT
2349686 AAAAAATATATTATAT
1 -AAAAATATA-TA-AT
2349702 AAAAAT-TAATAAT
1 AAAAATAT-ATAAT
2349715 AAAAATATA-AAT
1 AAAAATATATAAT
2349727 A
1 A
2349728 TATTAAACTT
Statistics
Matches: 107, Mismatches: 14, Indels: 40
0.66 0.09 0.25
Matches are distributed among these distances:
10 7 0.07
11 11 0.10
12 16 0.15
13 36 0.34
14 23 0.21
15 13 0.12
16 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (13 bp):
AAAAATATATAAT
Found at i:2349603 original size:7 final size:7
Alignment explanation
Indices: 2349575--2349729 Score: 67
Period size: 7 Copynumber: 22.1 Consensus size: 7
2349565 TATCTTTAAA
2349575 AAAATATT
1 AAAATA-T
2349583 AAAATA-
1 AAAATAT
2349589 AAAATAT
1 AAAATAT
*
2349596 ATAATAT
1 AAAATAT
2349603 AAAATAT
1 AAAATAT
* *
2349610 TATAT-T
1 AAAATAT
*
2349616 AAAAAAT
1 AAAATAT
2349623 AAAA-AT
1 AAAATAT
2349629 AAAATATGT
1 AAAATA--T
2349638 AAGATTATACT
1 AA-A--ATA-T
*
2349649 AAAAAAT
1 AAAATAT
2349656 AAAA-AT
1 AAAATAT
2349662 AAAATAT
1 AAAATAT
*
2349669 AACAT-T
1 AAAATAT
2349675 AAAATAT
1 AAAATAT
** *
2349682 -ATTTAA
1 AAAATAT
2349688 AAAATAT
1 AAAATAT
**
2349695 ATTATAT
1 AAAATAT
2349702 AAAA-ATT
1 AAAATA-T
2349709 AATAATA-
1 AA-AATAT
2349716 AAAATAT
1 AAAATAT
2349723 -AAATAT
1 AAAATAT
2349729 A
1 A
2349730 TTAAACTTAT
Statistics
Matches: 110, Mismatches: 21, Indels: 33
0.67 0.13 0.20
Matches are distributed among these distances:
6 40 0.36
7 48 0.44
8 10 0.09
9 4 0.04
10 2 0.02
11 3 0.03
12 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (7 bp):
AAAATAT
Found at i:2349615 original size:33 final size:31
Alignment explanation
Indices: 2349578--2349670 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 31
2349568 CTTTAAAAAA
*
2349578 ATATTAAAATAAAAATATATAATATAAAATATT
1 ATATTAAAATAAAAATA-A-AATATAAAAGATT
**
2349611 ATATTAAAAAATAAAAATAAAATATGTAAGATT
1 ATATT--AAAATAAAAATAAAATATAAAAGATT
*
2349644 ATACTAAAAAATAAAAATAAAATATAA
1 ATA-T-TAAAATAAAAATAAAATATAA
2349671 CATTAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
33 36 0.72
34 2 0.04
35 12 0.24
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (31 bp):
ATATTAAAATAAAAATAAAATATAAAAGATT
Found at i:2349718 original size:28 final size:28
Alignment explanation
Indices: 2349571--2349723 Score: 91
Period size: 28 Copynumber: 5.4 Consensus size: 28
2349561 ATATTATCTT
* *
2349571 TAAAAAAATATTA-AAATAAAAATATATAA
1 TAAAAATATATTATATA-AAAAATA-ATAA
* *
2349600 TATAAA-ATATTATATTAAAAAATAAAAA
1 TAAAAATATATTATA-TAAAAAATAATAA
* *
2349628 TAAAATATGTAAGATTATACTAAAAAATAAAAA
1 TAAAA-A--T-ATATTATA-TAAAAAATAATAA
** * * *
2349661 T-AAAATATAACAT-TAAAATATATTTA
1 TAAAAATATATTATATAAAAAATAATAA
*
2349687 -AAAAATATATTATATAAAAATTAATAA
1 TAAAAATATATTATATAAAAAATAATAA
2349714 TAAAAATATA
1 TAAAAATATA
2349724 AATATATTAA
Statistics
Matches: 95, Mismatches: 19, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
26 19 0.20
27 9 0.09
28 26 0.27
29 15 0.16
30 1 0.01
31 1 0.01
32 3 0.03
33 21 0.22
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (28 bp):
TAAAAATATATTATATAAAAAATAATAA
Found at i:2349857 original size:23 final size:22
Alignment explanation
Indices: 2349806--2349864 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
2349796 TATAAATGAA
2349806 ATATTAAAATATTA-TTTTTTAT
1 ATATT-AAATATTATTTTTTTAT
* *
2349828 ATTTTAATTATTATTTTATTTAT
1 ATATTAAATATTATTTT-TTTAT
2349851 ATATTAAATATTAT
1 ATATTAAATATTAT
2349865 AATATTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 7 0.23
22 7 0.23
23 17 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTAAATATTATTTTTTTAT
Found at i:2350304 original size:25 final size:25
Alignment explanation
Indices: 2350271--2350319 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2350261 AATTTAAAAA
2350271 TTTTATTTTTGA-TATATAAGATAAC
1 TTTTATTTTT-ATTATATAAGATAAC
* *
2350296 TTTTTTTTTTATTTTATAAGATAA
1 TTTTATTTTTATTATATAAGATAA
2350320 GATTGTGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (25 bp):
TTTTATTTTTATTATATAAGATAAC
Found at i:2350697 original size:14 final size:15
Alignment explanation
Indices: 2350678--2350706 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2350668 AAATATTTTG
2350678 ATTAATTA-TAAATA
1 ATTAATTATTAAATA
2350692 ATTAATTATTAAATA
1 ATTAATTATTAAATA
2350707 TAAAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAATTATTAAATA
Found at i:2361923 original size:17 final size:15
Alignment explanation
Indices: 2361901--2361936 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
2361891 AAAGGGCCCC
2361901 TTTTCTTTTTCGTTTT
1 TTTTCTTTTTC-TTTT
2361917 ATTTTCTTTTTCTTTT
1 -TTTTCTTTTTCTTTT
2361933 TTTT
1 TTTT
2361937 TAATTTCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 4 0.21
17 11 0.58
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTCTTTTTCTTTT
Found at i:2361959 original size:22 final size:21
Alignment explanation
Indices: 2361912--2361963 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
2361902 TTTCTTTTTC
* *
2361912 GTTTTATTTTCTTTTTCTTTT
1 GTTTTAATTTCTTTTTCATTT
* *
2361933 TTTTTAATTTCTTATTTGATTT
1 GTTTTAATTTCTT-TTTCATTT
2361955 GTTTTAATT
1 GTTTTAATT
2361964 GTAAGTCCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.75
Consensus pattern (21 bp):
GTTTTAATTTCTTTTTCATTT
Found at i:2365761 original size:26 final size:28
Alignment explanation
Indices: 2365708--2365763 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 28
2365698 TTGCACACAA
*
2365708 AGAAGAAGAAGGAGAAGAAGACAGAGAG
1 AGAAGAAGAAGGAGAAGAAGACAAAGAG
* *
2365736 AGAA-AAGAA-GAGAAGAATATAAAGAG
1 AGAAGAAGAAGGAGAAGAAGACAAAGAG
2365762 AG
1 AG
2365764 CACCTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 16 0.64
27 5 0.20
28 4 0.16
ACGTcount: A:0.61, C:0.02, G:0.34, T:0.04
Consensus pattern (28 bp):
AGAAGAAGAAGGAGAAGAAGACAAAGAG
Found at i:2383316 original size:20 final size:20
Alignment explanation
Indices: 2383291--2383335 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
2383281 CAGTCCAAGC
2383291 CTATGTATGAAAGGTCAAAA
1 CTATGTATGAAAGGTCAAAA
2383311 CTATGTATGAAAGGTCAAAA
1 CTATGTATGAAAGGTCAAAA
2383331 CTATG
1 CTATG
2383336 CATGCAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
CTATGTATGAAAGGTCAAAA
Found at i:2395760 original size:2 final size:2
Alignment explanation
Indices: 2395753--2395778 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2395743 AAATTTTGAA
2395753 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
2395779 GAGTTTCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2399494 original size:53 final size:53
Alignment explanation
Indices: 2399423--2399528 Score: 149
Period size: 53 Copynumber: 2.0 Consensus size: 53
2399413 ATAAAGTAAA
* * * *
2399423 AAAATAATGATGACCATCAAGAGTTGAAATTCTATATGGCCCCCAAATATTAG
1 AAAATAATAATAACCATCAAGAGTTGAAATTCTATATAGCCCCCAAACATTAG
* * *
2399476 AAAATAATAATAACCATCAAGAGTTGGAATTTTGTATAGCCCCCAAACATTAG
1 AAAATAATAATAACCATCAAGAGTTGAAATTCTATATAGCCCCCAAACATTAG
2399529 CATGTAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.26
Consensus pattern (53 bp):
AAAATAATAATAACCATCAAGAGTTGAAATTCTATATAGCCCCCAAACATTAG
Found at i:2412131 original size:6 final size:6
Alignment explanation
Indices: 2412120--2412154 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2412110 AAAAAAGACA
* *
2412120 AGCAGT AGCAGT AGCAGT CGCAGT AGCAGC AGCAG
1 AGCAGT AGCAGT AGCAGT AGCAGT AGCAGT AGCAG
2412155 CTATAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.34, T:0.11
Consensus pattern (6 bp):
AGCAGT
Found at i:2428614 original size:3 final size:3
Alignment explanation
Indices: 2428606--2428632 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2428596 CAGACTTTTA
2428606 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
2428633 TTCACATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2431189 original size:15 final size:14
Alignment explanation
Indices: 2431160--2431197 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
2431150 GGGTAGCTTC
2431160 TTTTTTGTT-TTTTG
1 TTTTTT-TTGTTTTG
2431174 TTTTATTTTGTTTTG
1 TTTT-TTTTGTTTTG
2431189 TTTTTTTTG
1 TTTTTTTTG
2431198 GCTTTCTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.03, C:0.00, G:0.13, T:0.84
Consensus pattern (14 bp):
TTTTTTTTGTTTTG
Found at i:2433165 original size:58 final size:58
Alignment explanation
Indices: 2433101--2433210 Score: 220
Period size: 58 Copynumber: 1.9 Consensus size: 58
2433091 ATGGAACATG
2433101 ATAAAACACAATATCTTAGACAGCCTATTTACTCACCTACTTATAAAAGTGTTCCATA
1 ATAAAACACAATATCTTAGACAGCCTATTTACTCACCTACTTATAAAAGTGTTCCATA
2433159 ATAAAACACAATATCTTAGACAGCCTATTTACTCACCTACTTATAAAAGTGT
1 ATAAAACACAATATCTTAGACAGCCTATTTACTCACCTACTTATAAAAGTGT
2433211 ACAAAAGTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (58 bp):
ATAAAACACAATATCTTAGACAGCCTATTTACTCACCTACTTATAAAAGTGTTCCATA
Found at i:2442218 original size:19 final size:18
Alignment explanation
Indices: 2442184--2442219 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2442174 CTATATAAAT
*
2442184 ATTAATATTTTTATTATG
1 ATTAAAATTTTTATTATG
2442202 ATTAAAATTTATTATTAT
1 ATTAAAATTT-TTATTAT
2442220 TAAATTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTAAAATTTTTATTATG
Found at i:2442232 original size:16 final size:16
Alignment explanation
Indices: 2442192--2442232 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2442182 ATATTAATAT
2442192 TTTTATTATGATTAAA
1 TTTTATTATGATTAAA
* *
2442208 ATTTATTATTATTAAA
1 TTTTATTATGATTAAA
*
2442224 TTTTGTTAT
1 TTTTATTAT
2442233 ATTTGATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTTATTATGATTAAA
Found at i:2445103 original size:21 final size:22
Alignment explanation
Indices: 2445079--2445127 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 22
2445069 GAATAAAATC
*
2445079 TTCTTATTCCCTGTAAATA-TT
1 TTCTTATTCCCTCTAAATACTT
2445100 TTC-T-TTCCCTCTAAATACTT
1 TTCTTATTCCCTCTAAATACTT
2445120 TCTCTTAT
1 T-TCTTAT
2445128 AGTTGTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 12 0.52
20 4 0.17
21 5 0.22
22 1 0.04
23 1 0.04
ACGTcount: A:0.20, C:0.24, G:0.02, T:0.53
Consensus pattern (22 bp):
TTCTTATTCCCTCTAAATACTT
Found at i:2445247 original size:39 final size:39
Alignment explanation
Indices: 2445193--2445270 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
2445183 TCTCAAGTTT
2445193 TGGAATTATTATATTTTCATCATCTTCAAGCTTCAAAAG
1 TGGAATTATTATATTTTCATCATCTTCAAGCTTCAAAAG
2445232 TGGAATTATTATATTTTCATCATCTTCAAGCTTCAAAAG
1 TGGAATTATTATATTTTCATCATCTTCAAGCTTCAAAAG
2445271 GGTTCCAGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (39 bp):
TGGAATTATTATATTTTCATCATCTTCAAGCTTCAAAAG
Found at i:2445535 original size:52 final size:54
Alignment explanation
Indices: 2445440--2445561 Score: 167
Period size: 52 Copynumber: 2.3 Consensus size: 54
2445430 GCTATTATAT
*
2445440 AGCTATTAATAAAAAACTATGAATGTCCATTTCCTGAAGTGAATGTGACAAATG
1 AGCTACTAATAAAAAACTATGAATGTCCATTTCCTGAAGTGAATGTGACAAATG
* * **
2445494 AGCTACTAAT-AAAAATTATGAATGTTCA-TTCCTGAAGTGAATGTGACAAACA
1 AGCTACTAATAAAAAACTATGAATGTCCATTTCCTGAAGTGAATGTGACAAATG
* *
2445546 AGATACTGATAAAAAA
1 AGCTACTAATAAAAAA
2445562 ATTATAAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
52 30 0.50
53 21 0.35
54 9 0.15
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (54 bp):
AGCTACTAATAAAAAACTATGAATGTCCATTTCCTGAAGTGAATGTGACAAATG
Found at i:2445683 original size:33 final size:33
Alignment explanation
Indices: 2445646--2445712 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
2445636 AAGTGAATGC
2445646 AATATCATTTAATTATGATGGTCATAACAATTT
1 AATATCATTTAATTATGATGGTCATAACAATTT
2445679 AATATCATTTAATTATGATGGTCATAACAATTT
1 AATATCATTTAATTATGATGGTCATAACAATTT
2445712 A
1 A
2445713 CACAAGCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (33 bp):
AATATCATTTAATTATGATGGTCATAACAATTT
Done.