Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, 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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 28 of 117
Found at i:3929051 original size:20 final size:21
Alignment explanation
Indices: 3929020--3929076 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
3929010 AAGTTAGGAT
*
3929020 TTAAT-TTGATTTGATTCAAAA
1 TTAATATT-ATTTGATTAAAAA
* *
3929041 -TAATATTATTTTAATAAAAA
1 TTAATATTATTTGATTAAAAA
*
3929061 TTAATTTTATTTGATT
1 TTAATATTATTTGATT
3929077 TTAATTAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (21 bp):
TTAATATTATTTGATTAAAAA
Found at i:3929133 original size:13 final size:13
Alignment explanation
Indices: 3929106--3929158 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
3929096 TATTAATTTA
3929106 TTAATTTTAATAT
1 TTAATTTTAATAT
3929119 TTAATATTTAA-A-
1 TTAAT-TTTAATAT
3929131 TT--TTTTAATATT
1 TTAATTTTAATA-T
3929143 TTAATTTTAAATAT
1 TTAATTTT-AATAT
3929157 TT
1 TT
3929159 GCATTTGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
9 5 0.15
10 2 0.06
12 4 0.12
13 6 0.18
14 12 0.36
15 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTAATTTTAATAT
Found at i:3929136 original size:23 final size:23
Alignment explanation
Indices: 3929110--3929154 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3929100 AATTTATTAA
3929110 TTTTAATA-TTTAATATTTAAATT
1 TTTTAATATTTTAAT-TTTAAATT
3929133 TTTTAATATTTTAATTTTAAAT
1 TTTTAATATTTTAATTTTAAAT
3929155 ATTTGCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTAATATTTTAATTTTAAATT
Found at i:3929137 original size:16 final size:16
Alignment explanation
Indices: 3929118--3929150 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3929108 AATTTTAATA
3929118 TTTAATATTTAAATTT
1 TTTAATATTTAAATTT
*
3929134 TTTAATATTTTAATTT
1 TTTAATATTTAAATTT
3929150 T
1 T
3929151 AAATATTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTAATATTTAAATTT
Found at i:3929279 original size:19 final size:19
Alignment explanation
Indices: 3929257--3929316 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 19
3929247 TTATATAGTA
*
3929257 AATAATTTTATATTATTTT
1 AATAATTTAATATTATTTT
*
3929276 AATAA-TTAATATT-GTTT
1 AATAATTTAATATTATTTT
*
3929293 AAT-ATAATAATATTATTTT
1 AATAAT-TTAATATTATTTT
3929312 AATAA
1 AATAA
3929317 CATGATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 1 0.03
17 6 0.18
18 14 0.42
19 11 0.33
20 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
AATAATTTAATATTATTTT
Found at i:3929298 original size:45 final size:47
Alignment explanation
Indices: 3929214--3929312 Score: 105
Period size: 48 Copynumber: 2.1 Consensus size: 47
3929204 TAAATAGTAT
* *
3929214 TTTTTTATTATTTTAATAATAAATAATAAATATTTATATAGTAA-ATAA
1 TTTTATATTATTTTAATAAT--ATAATAAATATTTATATAATAATATAA
* * *
3929262 TTTTATATTATTTTAATAAT-TAAT-ATTGTTTAATATAATAATATTA
1 TTTTATATTATTTTAATAATATAATAAATATTT-ATATAATAATATAA
3929308 TTTTA
1 TTTTA
3929313 ATAACATGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
44 5 0.11
45 12 0.27
46 8 0.18
48 19 0.43
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (47 bp):
TTTTATATTATTTTAATAATATAATAAATATTTATATAATAATATAA
Found at i:3929474 original size:29 final size:29
Alignment explanation
Indices: 3929429--3929500 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 29
3929419 TAAATAAATA
* *
3929429 ATAAAT-TTGTTACAATTT-AATAATAAT
1 ATAAATATTTTTAAAATTTAAATAATAAT
3929456 AGTAAATATTTTTAAAATTTAAATAATAA-
1 A-TAAATATTTTTAAAATTTAAATAATAAT
*
3929485 ATAAA-ATATTTAAAAT
1 ATAAATATTTTTAAAAT
3929501 ATTATTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 11 0.28
28 9 0.23
29 11 0.28
30 8 0.21
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (29 bp):
ATAAATATTTTTAAAATTTAAATAATAAT
Found at i:3929806 original size:13 final size:14
Alignment explanation
Indices: 3929778--3929807 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3929768 TTTTATTGAC
3929778 AATAATTTTTTAAA
1 AATAATTTTTTAAA
3929792 AATAATTTTTTAAA
1 AATAATTTTTTAAA
3929806 AA
1 AA
3929808 ATGAACATAT
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:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAATTTTTTAAA
Found at i:3930267 original size:15 final size:15
Alignment explanation
Indices: 3930238--3930307 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 15
3930228 TAAAAATTTG
3930238 AAATTATTTATTATT
1 AAATTATTTATTATT
*
3930253 AAATTATTATATATTTT
1 AAATTATT-TAT-TATT
*
3930270 AATAATAATATTTAATATT
1 -A-AAT--TATTTATTATT
3930289 AAATTATTGTATT-TT
1 AAATTATT-TATTATT
3930304 AAAT
1 AAAT
3930308 ATAAAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
15 18 0.41
16 6 0.14
17 6 0.14
18 2 0.05
19 6 0.14
20 2 0.05
21 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (15 bp):
AAATTATTTATTATT
Found at i:3930282 original size:36 final size:36
Alignment explanation
Indices: 3930242--3930345 Score: 106
Period size: 36 Copynumber: 2.9 Consensus size: 36
3930232 AATTTGAAAT
* *
3930242 TATTTATTATTAAATTATTATATATTTTAATA-ATAA
1 TATTTATTATTAAATTATTATAT-TTTAAATATAAAA
* *
3930278 TATTTAATATTAAATTATTGTATTTTAAATATAAAA
1 TATTTATTATTAAATTATTATATTTTAAATATAAAA
* * * *
3930314 TATATATT-TTAAATT-TTTTAATTTATATATAA
1 TATTTATTATTAAATTATTATATTTTAAATATAA
3930346 TTTTTGTTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
34 14 0.24
35 14 0.24
36 30 0.52
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (36 bp):
TATTTATTATTAAATTATTATATTTTAAATATAAAA
Found at i:3930982 original size:13 final size:14
Alignment explanation
Indices: 3930955--3930984 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3930945 AAATTTAAAT
3930955 TTTATTAATAATTA
1 TTTATTAATAATTA
3930969 TTTATTAA-AATTA
1 TTTATTAATAATTA
3930982 TTT
1 TTT
3930985 TAAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTATTAATAATTA
Found at i:3930986 original size:14 final size:15
Alignment explanation
Indices: 3930953--3930986 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
3930943 TTAAATTTAA
3930953 ATTTTATTAATAATT
1 ATTTTATTAATAATT
3930968 A-TTTATTAA-AATT
1 ATTTTATTAATAATT
3930981 ATTTTA
1 ATTTTA
3930987 AATATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.28
14 12 0.67
15 1 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTATTAATAATT
Found at i:3933860 original size:27 final size:26
Alignment explanation
Indices: 3933830--3933885 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
3933820 TTTGAAAAGA
*
3933830 TTTTTTA-CTTTATTTTTTATTTTTTCG
1 TTTTTTATCTTTATCTTTT-TTTTTT-G
3933857 -TTTTTATCTTTATCTTTTTTTTTTG
1 TTTTTTATCTTTATCTTTTTTTTTTG
3933882 TTTT
1 TTTT
3933886 CAAAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 1 0.04
26 15 0.58
27 10 0.38
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.80
Consensus pattern (26 bp):
TTTTTTATCTTTATCTTTTTTTTTTG
Found at i:3933977 original size:17 final size:16
Alignment explanation
Indices: 3933951--3934057 Score: 74
Period size: 17 Copynumber: 6.4 Consensus size: 16
3933941 ATAAAGTCAG
3933951 TAAAATAAAATAAATAA
1 TAAAATAAAATAAA-AA
* *
3933968 TAAAAGAAAACTGAAAA
1 TAAAATAAAA-TAAAAA
* **
3933985 TAAAATAAAATGAACT
1 TAAAATAAAATAAAAA
*
3934001 TAAAAT-AATTAAAAA
1 TAAAATAAAATAAAAA
3934016 -ATAAATAAAATCAAATAA
1 TA-AAATAAAAT-AAA-AA
3934034 TACAAATAAAATGAAAAA
1 TA-AAATAAAAT-AAAAA
*
3934052 AAAAAT
1 TAAAAT
3934058 TTTGATTCGG
Statistics
Matches: 71, Mismatches: 13, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
14 1 0.01
15 9 0.13
16 13 0.18
17 27 0.38
18 8 0.11
19 13 0.18
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.21
Consensus pattern (16 bp):
TAAAATAAAATAAAAA
Found at i:3934013 original size:25 final size:24
Alignment explanation
Indices: 3933952--3934055 Score: 74
Period size: 25 Copynumber: 4.4 Consensus size: 24
3933942 TAAAGTCAGT
*
3933952 AAAATAAAATAA-ATAATAAAA-G
1 AAAATAAAATAATAAAATAAAATG
*
3933974 AAAACT-GAA-AATAAAATAAAATG
1 AAAA-TAAAATAATAAAATAAAATG
** *
3933997 AACTTAAAATAATTAAAAAATAAAT-
1 AAAATAAAATAA-TAAAATA-AAATG
*
3934022 AAAATCAAATAATACAAATAAAATG
1 AAAATAAAATAATA-AAATAAAATG
*
3934047 AAAAAAAAA
1 AAAATAAAA
3934056 ATTTTGATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
21 2 0.03
22 15 0.25
23 6 0.10
24 8 0.13
25 26 0.43
26 4 0.07
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (24 bp):
AAAATAAAATAATAAAATAAAATG
Found at i:3934040 original size:14 final size:14
Alignment explanation
Indices: 3933932--3934057 Score: 52
Period size: 14 Copynumber: 9.1 Consensus size: 14
3933922 TAAAACTACT
*
3933932 TAAATAAAAATAAAG
1 TAAAT-AAAATAAAA
* *
3933947 TCAGTAAAATAAAA
1 TAAATAAAATAAAA
3933961 TAAATAATAA-AAGAA
1 TAAATAA-AATAA-AA
*
3933976 -AACTGAAAATAAAA
1 TAAAT-AAAATAAAA
**
3933990 TAAAATGAACTTAAAA
1 T-AAAT-AAAATAAAA
*
3934006 T-AAT-TAA-AAAA
1 TAAATAAAATAAAA
*
3934017 TAAATAAAATCAAA
1 TAAATAAAATAAAA
3934031 T-AATACAAATAAAA
1 TAAATA-AAATAAAA
*
3934045 TGAA-AAAA-AAAA
1 TAAATAAAATAAAA
3934057 T
1 T
3934058 TTTGATTCGG
Statistics
Matches: 85, Mismatches: 15, Indels: 25
0.68 0.12 0.20
Matches are distributed among these distances:
11 5 0.06
12 8 0.09
13 9 0.11
14 38 0.45
15 13 0.15
16 12 0.14
ACGTcount: A:0.71, C:0.04, G:0.05, T:0.21
Consensus pattern (14 bp):
TAAATAAAATAAAA
Found at i:3934050 original size:6 final size:5
Alignment explanation
Indices: 3933951--3934054 Score: 56
Period size: 5 Copynumber: 20.0 Consensus size: 5
3933941 ATAAAGTCAG
* **
3933951 TAAAA TAAAA TAAATAA TAAAA GAAAA CTGAAAA TAAAA TAAAA TGAACT
1 TAAAA TAAAA T-AA-AA TAAAA TAAAA -T-AAAA TAAAA TAAAA T-AAAA
*
3934001 TAAAA TAATTAA -AAAA T-AAA TAAAA TCAAA T--AA TACAAA TAAAA
1 TAAAA TAA--AA TAAAA TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA
3934045 TGAAAA -AAAA
1 T-AAAA TAAAA
3934055 AATTTTGATT
Statistics
Matches: 79, Mismatches: 7, Indels: 27
0.70 0.06 0.24
Matches are distributed among these distances:
3 3 0.04
4 10 0.13
5 39 0.49
6 18 0.23
7 9 0.11
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:3934051 original size:36 final size:33
Alignment explanation
Indices: 3933952--3934055 Score: 99
Period size: 31 Copynumber: 3.1 Consensus size: 33
3933942 TAAAGTCAGT
* *
3933952 AAAATAAAATAAATAATAAAAGAAAACTGAAAAT
1 AAAATAAAATAAATAATAAAATAAAA-TGAAAAA
* *
3933986 AAAATAAAATGAACT--TAAAAT--AATTAAAAA
1 AAAATAAAAT-AAATAATAAAATAAAATGAAAAA
3934016 ATAAATAAAATCAAATAATACAAATAAAATGAAAAA
1 A-AAATAAAAT-AAATAATA-AAATAAAATGAAAAA
3934052 AAAA
1 AAAA
3934056 ATTTTGATTC
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
30 6 0.11
31 14 0.25
33 7 0.12
34 14 0.25
35 6 0.11
36 9 0.16
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (33 bp):
AAAATAAAATAAATAATAAAATAAAATGAAAAA
Found at i:3934834 original size:3 final size:3
Alignment explanation
Indices: 3934826--3934852 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3934816 AAGAGGAAGG
3934826 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
3934853 TAACAAGTAG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3935062 original size:3 final size:3
Alignment explanation
Indices: 3935056--3935119 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
3935046 CTACCAAAAA
* * *
3935056 AAT AAT AAT AAT -AT AAT -AT AAT ATT ATAC AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
*
3935100 AAT AAT AAT ACT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
3935120 AAATCAGTCC
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
2 4 0.08
3 45 0.90
4 1 0.02
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:3936810 original size:22 final size:21
Alignment explanation
Indices: 3936765--3936811 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
3936755 GTTTAAGTCT
**
3936765 TTTTTTTGTTGTTTTTTATTC
1 TTTTTTTGTTGTTTTTTACCC
*
3936786 TTTTTTTGCTTTTTTTTTACCC
1 TTTTTTTG-TTGTTTTTTACCC
3936808 TTTT
1 TTTT
3936812 CGTATCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.04, C:0.11, G:0.06, T:0.79
Consensus pattern (21 bp):
TTTTTTTGTTGTTTTTTACCC
Found at i:3941959 original size:32 final size:31
Alignment explanation
Indices: 3941857--3941993 Score: 112
Period size: 32 Copynumber: 4.3 Consensus size: 31
3941847 ATAAATCTGC
* * *
3941857 TTTTGAAAATGATCTGAAAATTTTTACATAAT
1 TTTTTAAAATGATAT-AAAATTTTTACTTAAT
* * * *
3941889 ATTTTAAAATGATATAGAGTTTTTATTTAAT
1 TTTTTAAAATGATATAAAATTTTTACTTAAT
* * *
3941920 TTCTTAAATTGATATAAAAATGTTTACTTAAT
1 TTTTTAAAATGATAT-AAAATTTTTACTTAAT
** * **
3941952 TTTTTAAAATGATATGTAATTTTAACAAAAT
1 TTTTTAAAATGATATAAAATTTTTACTTAAT
3941983 TATTTTAAAAT
1 T-TTTTAAAAT
3941994 TTTCAACTTA
Statistics
Matches: 81, Mismatches: 22, Indels: 4
0.76 0.21 0.04
Matches are distributed among these distances:
31 35 0.43
32 46 0.57
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (31 bp):
TTTTTAAAATGATATAAAATTTTTACTTAAT
Found at i:3943461 original size:6 final size:7
Alignment explanation
Indices: 3943448--3943476 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3943438 GATAAATATT
3943448 AATAAAA
1 AATAAAA
3943455 AATAAAA
1 AATAAAA
3943462 AATAAAA
1 AATAAAA
3943469 AATAAAA
1 AATAAAA
3943476 A
1 A
3943477 GATTCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AATAAAA
Found at i:3943737 original size:22 final size:23
Alignment explanation
Indices: 3943683--3943753 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 23
3943673 ATTTAATTTT
* * *
3943683 TAAAAAT-TTAATTAATAAGTGTT
1 TAAAAATATTAATTAA-AAATATA
*
3943706 TATAAATATTAATTAAAAATA-A
1 TAAAAATATTAATTAAAAATATA
* *
3943728 TAAAAATATTATTTAAATATATA
1 TAAAAATATTAATTAAAAATATA
3943751 TAA
1 TAA
3943754 TGCATTTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 18 0.46
23 13 0.33
24 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (23 bp):
TAAAAATATTAATTAAAAATATA
Found at i:3952979 original size:62 final size:63
Alignment explanation
Indices: 3952867--3952986 Score: 170
Period size: 62 Copynumber: 1.9 Consensus size: 63
3952857 GGAACAATCC
* * * * *
3952867 CCATTTCCGTATTTTTTTTTTCCTTGTAATTGTTCTTATTGTTTCCGATGTGGGTTTTCTTCA
1 CCATTTCCATATTTGTTTTTTCATTGTAATTATTCTTATTATTTCCGATGTGGGTTTTCTTCA
* *
3952930 CCATTTCCATATTTGTTTTTT-ATTTTAATTATTCTTATTATTTCTGATGTGGGTTTT
1 CCATTTCCATATTTGTTTTTTCATTGTAATTATTCTTATTATTTCCGATGTGGGTTTT
3952987 GATTGGCTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
62 31 0.62
63 19 0.38
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.59
Consensus pattern (63 bp):
CCATTTCCATATTTGTTTTTTCATTGTAATTATTCTTATTATTTCCGATGTGGGTTTTCTTCA
Found at i:3960771 original size:261 final size:260
Alignment explanation
Indices: 3960260--3960778 Score: 986
Period size: 260 Copynumber: 2.0 Consensus size: 260
3960250 TGCAAAAGAA
3960260 AATTCTAAGAGAAAAAAAATTCTTAATATGCAAGTTTGACTTGCAGAAAAAGAATTCTAAAAGGA
1 AATTCTAAGAGAAAAAAAATTCTTAATATGCAAGTTTGACTTGCAGAAAAAGAATTCTAAAAGGA
*
3960325 AATGGATCTTAATAGGCAAGTTTGTATGGTTATAAATAGGTGAAGTTTCTGTAAGGTTAGGTATG
66 AATGGATCTTAATAGGCAAGTTTGTATGGTTATAAATAGGTGAAGTCTCTGTAAGGTTAGGTATG
3960390 AGAAAAAGATATAAAAGAGTTGTAGAGTTTTATAGGATAGACACCCATAGGACTACTGAAGATTT
131 AGAAAAAGATATAAAAGAGTTGTAGAGTTTTATAGGATAGACACCCATAGGACTACTGAAGATTT
3960455 ACTTCTTGTGGGTGTATATGTTTAAATGTATGTGAGTGGACTAAAGGAGATTGAAAGGGTTCAAG
196 ACTTCTTGTGGGTGTATATGTTTAAATGTATGTGAGTGGACTAAAGGAGATTGAAAGGGTTCAAG
3960520 AATTCTAAGAGAAAAAAAATTCTTAATATGCAAGTTTGACTTGCAGAAAAAGAATTCTAAAAGGA
1 AATTCTAAGAGAAAAAAAATTCTTAATATGCAAGTTTGACTTGCAGAAAAAGAATTCTAAAAGGA
3960585 AATGGATCTTAATAGGCAAGTTTGTATGGTTATAAATAGGTGAAGTCTCTGTAAGGTTAGGTATG
66 AATGGATCTTAATAGGCAAGTTTGTATGGTTATAAATAGGTGAAGTCTCTGTAAGGTTAGGTATG
* *
3960650 AGAAAAAGATGTAAAAGAGTTGTAGAGTTTTATAGGATAGACACCCCATAGGACTATTGAAGATT
131 AGAAAAAGATATAAAAGAGTTGTAGAGTTTTATAGGATAGACA-CCCATAGGACTACTGAAGATT
3960715 TACTTCTTGTGGGTGTATATGTTTAAATGTATGTGAGTGGACTAGAA-GAGATTGAAAGGGTTCA
195 TACTTCTTGTGGGTGTATATGTTTAAATGTATGTGAGTGGACTA-AAGGAGATTGAAAGGGTTCA
3960779 TAGGTATGGT
Statistics
Matches: 254, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
260 171 0.67
261 81 0.32
262 2 0.01
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.31
Consensus pattern (260 bp):
AATTCTAAGAGAAAAAAAATTCTTAATATGCAAGTTTGACTTGCAGAAAAAGAATTCTAAAAGGA
AATGGATCTTAATAGGCAAGTTTGTATGGTTATAAATAGGTGAAGTCTCTGTAAGGTTAGGTATG
AGAAAAAGATATAAAAGAGTTGTAGAGTTTTATAGGATAGACACCCATAGGACTACTGAAGATTT
ACTTCTTGTGGGTGTATATGTTTAAATGTATGTGAGTGGACTAAAGGAGATTGAAAGGGTTCAAG
Found at i:3961590 original size:23 final size:23
Alignment explanation
Indices: 3961564--3961615 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3961554 AAACTCTTTA
* **
3961564 TTTTAAATAGACTTATTTATCTG
1 TTTTAAACAGACTTAACTATCTG
*
3961587 TTTTGAACAGACTTAACTATCTG
1 TTTTAAACAGACTTAACTATCTG
3961610 TCTTTA
1 T-TTTA
3961616 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (23 bp):
TTTTAAACAGACTTAACTATCTG
Found at i:3968037 original size:19 final size:16
Alignment explanation
Indices: 3967998--3968030 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3967988 AACGATTTGA
3967998 ATGATAATGATGATTT
1 ATGATAATGATGATTT
3968014 ATGATAATGATGATTT
1 ATGATAATGATGATTT
3968030 A
1 A
3968031 CGATGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (16 bp):
ATGATAATGATGATTT
Found at i:3970992 original size:54 final size:54
Alignment explanation
Indices: 3970895--3971001 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
3970885 AAAATCACTT
* * * *
3970895 ATGTCAAGATGAATGATTTTATCAATTCAGTCAATCTATTATTGATTATAAACC
1 ATGTCAAGACGAATGATTTTAACAATTCAGTCAACCTACTATTGATTATAAACC
* * * *
3970949 ATGTCAAGACGAATGATTTTAACAATTGAGTTAACCTGCTATTGGTTATAAAC
1 ATGTCAAGACGAATGATTTTAACAATTCAGTCAACCTACTATTGATTATAAAC
3971002 AATATAAACC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (54 bp):
ATGTCAAGACGAATGATTTTAACAATTCAGTCAACCTACTATTGATTATAAACC
Found at i:3972301 original size:2 final size:2
Alignment explanation
Indices: 3972294--3972329 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3972284 TTAAGGCTTT
3972294 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3972330 GTGGTGCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3979490 original size:27 final size:27
Alignment explanation
Indices: 3979459--3979528 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
3979449 AATTTTTAAT
*
3979459 TAAATTATTAATTAAAATTTATATTTA
1 TAAATTATTAATTAAAATTGATATTTA
*
3979486 TAAATATATT-ATTAAAGTTGATATTTA
1 TAAAT-TATTAATTAAAATTGATATTTA
* *
3979513 -AATTTATAAATTAAAA
1 TAAATTATTAATTAAAA
3979529 AAATTTTATG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
25 3 0.08
26 9 0.25
27 20 0.56
28 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (27 bp):
TAAATTATTAATTAAAATTGATATTTA
Found at i:3980244 original size:57 final size:58
Alignment explanation
Indices: 3980156--3980271 Score: 180
Period size: 57 Copynumber: 2.0 Consensus size: 58
3980146 CCAAAAATAT
* *
3980156 AGAAAGAAAAGAAAAGAAAAAATAATTGATCACTAAAAGAGCTATCACTATGACACTA
1 AGAAAGAAAAGAAAAGAAAAAATAATTGATCACTAAAAGAGATATCAATATGACACTA
* * *
3980214 AGAAAG-AAAGAAAAGAATACATAATTGATCACTAAAAGAGATATCAATATGACGCTA
1 AGAAAGAAAAGAAAAGAAAAAATAATTGATCACTAAAAGAGATATCAATATGACACTA
3980271 A
1 A
3980272 CTTTAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 47 0.89
58 6 0.11
ACGTcount: A:0.56, C:0.11, G:0.15, T:0.18
Consensus pattern (58 bp):
AGAAAGAAAAGAAAAGAAAAAATAATTGATCACTAAAAGAGATATCAATATGACACTA
Found at i:3980560 original size:2 final size:2
Alignment explanation
Indices: 3980553--3980584 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3980543 GTTCGAATTG
3980553 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3980585 AGATAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3980595 original size:21 final size:21
Alignment explanation
Indices: 3980553--3980597 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3980543 GTTCGAATTG
* *
3980553 ATATATATATATATATATATA
1 ATATATATATAGATATAAATA
3980574 ATATATATATAAGATA-AAATA
1 ATATATATAT-AGATATAAATA
3980595 ATA
1 ATA
3980598 ATTTTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATATATATATAGATATAAATA
Found at i:3995310 original size:22 final size:23
Alignment explanation
Indices: 3995279--3995330 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
3995269 GAGTATTTAT
*
3995279 AAAAAA-TTTTCAATA-TAATAA
1 AAAAAATTTTTCAAAAGTAATAA
*
3995300 AAAAAATTTTTTAAAAGTAATAA
1 AAAAAATTTTTCAAAAGTAATAA
3995323 AAAAAATT
1 AAAAAATT
3995331 GATGAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 6 0.22
22 7 0.26
23 14 0.52
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAAATTTTTCAAAAGTAATAA
Found at i:3995555 original size:11 final size:11
Alignment explanation
Indices: 3995533--3995563 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
3995523 CAATTTTTTA
3995533 AATAAGAATATT
1 AATAA-AATATT
3995545 AATAAAATATT
1 AATAAAATATT
3995556 AATAAAAT
1 AATAAAAT
3995564 TTCTAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
AATAAAATATT
Found at i:3996025 original size:19 final size:20
Alignment explanation
Indices: 3995993--3996030 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3995983 AAAATTATCT
3995993 TTTTAATAAATTTTTATTAA
1 TTTTAATAAATTTTTATTAA
*
3996013 TTTTAA-AATTTTTTATTA
1 TTTTAATAAATTTTTATTA
3996031 CAAGGATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAATAAATTTTTATTAA
Found at i:4005835 original size:47 final size:47
Alignment explanation
Indices: 4005781--4006238 Score: 561
Period size: 49 Copynumber: 9.7 Consensus size: 47
4005771 AGAAGATATT
* * *
4005781 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGTTTTTTCAAGTGAGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAATGAGA
*
4005828 TTTTAAAGTTGTTGAGCCTCTGATGAGAGGAGCTTTTTCAAATGAGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAATGAGA
* **
4005875 TTTTTAAAGTTGTTGAGGCTCTGCTGAGAGGAGCCATTTCTAAGATGAGA
1 -TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC-AA-ATGAGA
4005925 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAATGAGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAATGAGA
* * ** *
4005972 TTTTAAAAGTTGTTGAGCATCTGCTGAGATGAGCCATTTCTAAGATAAGA
1 TTTT-AAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC-AA-ATGAGA
* *
4006022 TTTTAAAGTTGTTGAGCCTCTGCTGAGAAGAGCATTTTTTTAAA--A-A
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC--TTTTTCAAATGAGA
* *
4006068 TTTTAAAGTCGTTGAGCCTCTGTTGAGAGGAGCCTTTTTC--A--AGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAATGAGA
*
4006112 TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAATGAGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAATGAGA
* * * * *
4006159 TTTTAAAATTATTGAGCCTCTGTTGAGAGGAACCCTTTTTCAAATGAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGG-A-GCTTTTTCAAATGAGA
*
4006208 TTTTAAAGTTGTTGAGCATCTGCTGAGAGGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGA
4006239 TTTCAATAAA
Statistics
Matches: 361, Mismatches: 34, Indels: 31
0.85 0.08 0.07
Matches are distributed among these distances:
43 9 0.02
44 32 0.09
45 6 0.02
46 30 0.08
47 86 0.24
48 70 0.19
49 108 0.30
50 17 0.05
51 3 0.01
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (47 bp):
TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAATGAGA
Found at i:4005952 original size:97 final size:97
Alignment explanation
Indices: 4005780--4006238 Score: 575
Period size: 97 Copynumber: 4.8 Consensus size: 97
4005770 AAGAAGATAT
* ***
4005780 TTTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGTTTTTTC-AAG-TGAGATTTTAAAGTTGTTGA
1 TTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCATTTCTAAGATGAGATTTTAAAGTTGTTGA
*
4005843 GCCTCTGATGAGAGGAGCTTTTTCAAATGAGA
66 GCCTCTGCTGAGAGGAGCTTTTTCAAATGAGA
*
4005875 TTTTTAAAGTTGTTGAGGCTCTGCTGAGAGGAGCCATTTCTAAGATGAGATTTTAAAGTTGTTGA
1 TTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCATTTCTAAGATGAGATTTTAAAGTTGTTGA
4005940 GCCTCTGCTGAGAGGAGCTTTTTCAAATGAGA
66 GCCTCTGCTGAGAGGAGCTTTTTCAAATGAGA
* * * *
4005972 TTTTAAAAGTTGTTGAGCATCTGCTGAGATGAGCCATTTCTAAGATAAGATTTTAAAGTTGTTGA
1 TTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCATTTCTAAGATGAGATTTTAAAGTTGTTGA
* *
4006037 GCCTCTGCTGAGAAGAGCATTTTTTTAAA--A-A
66 GCCTCTGCTGAGAGGAGC--TTTTTCAAATGAGA
* * **
4006068 -TTTTAAAGTCGTTGAGCCTCTGTTGAGAGGAGCC-TTT-T-TCA--AGATTTTAAAGTTGTTGA
1 TTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCATTTCTAAGATGAGATTTTAAAGTTGTTGA
*
4006127 GCCTCTGTTGAGAGGAGCTTTTTCAAATGAGA
66 GCCTCTGCTGAGAGGAGCTTTTTCAAATGAGA
* * * * * * *
4006159 -TTTTAAAATTATTGAGCCTCTGTTGAGAGGAACCCTTTTTCAA-ATGAAATTTTAAAGTTGTTG
1 TTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCATTTCT-AAGATGAGATTTTAAAGTTGTTG
*
4006222 AGCATCTGCTGAGAGGA
65 AGCCTCTGCTGAGAGGA
4006239 TTTCAATAAA
Statistics
Matches: 320, Mismatches: 31, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
88 8 0.03
90 35 0.11
91 31 0.10
92 4 0.01
93 2 0.01
94 4 0.01
95 64 0.20
96 35 0.11
97 129 0.40
99 8 0.03
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (97 bp):
TTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCATTTCTAAGATGAGATTTTAAAGTTGTTGA
GCCTCTGCTGAGAGGAGCTTTTTCAAATGAGA
Found at i:4006443 original size:18 final size:18
Alignment explanation
Indices: 4006420--4006466 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
4006410 CGTAATATAG
*
4006420 TATATAAAATATTGAAAT-
1 TATATAAAA-AATGAAATA
4006438 TATATAAAAAATGAAATAA
1 TATATAAAAAATGAAAT-A
4006457 TATATAAAAA
1 TATATAAAAA
4006467 TACCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.27
18 9 0.35
19 10 0.38
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (18 bp):
TATATAAAAAATGAAATA
Found at i:4006454 original size:17 final size:17
Alignment explanation
Indices: 4006420--4006467 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
4006410 CGTAATATAG
*
4006420 TATATAAAATATTGAAAT
1 TATATAAAA-AATGAAAT
4006438 TATATAAAAAATGAAAT
1 TATATAAAAAATGAAAT
*
4006455 AATATATAAAAAT
1 TATATA-AAAAAT
4006468 ACCAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (17 bp):
TATATAAAAAATGAAAT
Found at i:4006467 original size:18 final size:18
Alignment explanation
Indices: 4006420--4006467 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 18
4006410 CGTAATATAG
*
4006420 TATATAAAATATTGAAATTA
1 TATATAAAA-A-TGAAATAA
4006440 TATA-AAAAATGAAATAA
1 TATATAAAAATGAAATAA
4006457 TATATAAAAAT
1 TATATAAAAAT
4006468 ACCAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 11 0.42
18 7 0.27
19 4 0.15
20 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
TATATAAAAATGAAATAA
Found at i:4007839 original size:20 final size:19
Alignment explanation
Indices: 4007794--4007842 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
4007784 TTTTTTAAAA
4007794 AGTAATAAAATAAAAATTG
1 AGTAATAAAATAAAAATTG
* *
4007813 A-TGAATATATTAAAAATATG
1 AGT-AATAAAATAAAAAT-TG
4007833 AGTAATAAAA
1 AGTAATAAAA
4007843 ATGAGAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
18 1 0.04
19 13 0.57
20 8 0.35
21 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (19 bp):
AGTAATAAAATAAAAATTG
Found at i:4008036 original size:11 final size:11
Alignment explanation
Indices: 4008014--4008044 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
4008004 CAATTTTTTA
4008014 AATAAGAATATT
1 AATAA-AATATT
4008026 AATAAAATATT
1 AATAAAATATT
4008037 AATAAAAT
1 AATAAAAT
4008045 TTCTAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
AATAAAATATT
Found at i:4008797 original size:14 final size:14
Alignment explanation
Indices: 4008780--4008818 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4008770 TTGGAATTGA
4008780 ATTAATTGAATTAT
1 ATTAATTGAATTAT
* * *
4008794 ATTAATTTATTTTT
1 ATTAATTGAATTAT
4008808 ATTAATTGAAT
1 ATTAATTGAAT
4008819 CAAAATTTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (14 bp):
ATTAATTGAATTAT
Found at i:4009164 original size:24 final size:22
Alignment explanation
Indices: 4009137--4009181 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4009127 TAAAATTTTT
4009137 TAAAAATAATTTTTGATAATTAAC
1 TAAAAATAA--TTTGATAATTAAC
*
4009161 TAAAATTAATTTGATAATTAA
1 TAAAAATAATTTGATAATTAA
4009182 TTAATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
24 8 0.40
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (22 bp):
TAAAAATAATTTGATAATTAAC
Found at i:4009533 original size:21 final size:20
Alignment explanation
Indices: 4009494--4009533 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4009484 TAAAATAACC
*
4009494 AATAAATTAAAATATAATTA
1 AATAAATTAAAATAAAATTA
*
4009514 AATAAATTTAACATAAAATT
1 AATAAA-TTAAAATAAAATT
4009534 GAATTATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
AATAAATTAAAATAAAATTA
Found at i:4010413 original size:24 final size:23
Alignment explanation
Indices: 4010386--4010442 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 23
4010376 AATTTGAGTT
4010386 TAAAAATTTTATTAATTAAAATAA
1 TAAAAATTTTATTAATTAAAAT-A
*
4010410 TAAAAA---TA-T-ATTTAAATA
1 TAAAAATTTTATTAATTAAAATA
4010428 TAAAAATTTTATTAA
1 TAAAAATTTTATTAA
4010443 AATCGTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 11
0.69 0.03 0.28
Matches are distributed among these distances:
18 7 0.26
19 7 0.26
20 1 0.04
21 4 0.15
22 1 0.04
23 1 0.04
24 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAAAATTTTATTAATTAAAATA
Found at i:4010440 original size:19 final size:19
Alignment explanation
Indices: 4010400--4010445 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
4010390 AATTTTATTA
4010400 ATTAAAATAATAAAAATAT
1 ATTAAAATAATAAAAATAT
* *
4010419 ATTTAAAT-ATAAAAATTTT
1 ATTAAAATAATAAAAA-TAT
4010438 ATTAAAAT
1 ATTAAAAT
4010446 CGTAAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTAAAATAATAAAAATAT
Found at i:4014343 original size:54 final size:55
Alignment explanation
Indices: 4014244--4014349 Score: 124
Period size: 54 Copynumber: 1.9 Consensus size: 55
4014234 TCTCATTTTG
*
4014244 AATTTCTAAATTTTTCACCATTTGGATCAATTTAAAAATAGTTTTT-TTTTTCAA
1 AATTTCTAAATTTTTCACCATTTGGATCAATTTAAAAATACTTTTTATTTTTCAA
* *** * * * *
4014298 AATTTTTAAATTTTTCATTGTTTGGGTCTATTTAGAAATTCTTTTTATTTTT
1 AATTTCTAAATTTTTCACCATTTGGATCAATTTAAAAATACTTTTTATTTTT
4014350 TTTTGGAAAG
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
54 37 0.88
55 5 0.12
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (55 bp):
AATTTCTAAATTTTTCACCATTTGGATCAATTTAAAAATACTTTTTATTTTTCAA
Found at i:4014685 original size:25 final size:25
Alignment explanation
Indices: 4014639--4014687 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
4014629 TCTTCACCTA
*
4014639 GAAATTTTATAAAAATTTATCATTT
1 GAAATTTTATAAAAATTCATCATTT
*
4014664 GAAATTTT-TATAAATTCCATCATT
1 GAAATTTTATAAAAATT-CATCATT
4014688 GGATAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (25 bp):
GAAATTTTATAAAAATTCATCATTT
Found at i:4014783 original size:22 final size:22
Alignment explanation
Indices: 4014755--4014797 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4014745 TAACTATGCA
4014755 AAAATACTAAA-AATATAAAAAT
1 AAAATACTAAATAA-ATAAAAAT
4014777 AAAATACTAAATAAATAAAAA
1 AAAATACTAAATAAATAAAAA
4014798 ATACCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAATACTAAATAAATAAAAAT
Found at i:4015398 original size:16 final size:16
Alignment explanation
Indices: 4015377--4015407 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4015367 ACTCCAAAAT
4015377 TTTTTTTGCTTTTTAC
1 TTTTTTTGCTTTTTAC
*
4015393 TTTTTTTTCTTTTTA
1 TTTTTTTGCTTTTTA
4015408 TGTGTGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.10, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTTTGCTTTTTAC
Found at i:4015398 original size:17 final size:16
Alignment explanation
Indices: 4015376--4015407 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
4015366 AACTCCAAAA
4015376 TTTTTTTTGCTTTTTAC
1 TTTTTTTT-CTTTTTAC
4015393 TTTTTTTTCTTTTTA
1 TTTTTTTTCTTTTTA
4015408 TGTGTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTTTTCTTTTTAC
Found at i:4015525 original size:24 final size:24
Alignment explanation
Indices: 4015498--4015550 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
4015488 TTTAACTTTT
*
4015498 AACTCCAAATTTTAATATCACTTA
1 AACTCCAAATTTTAATACCACTTA
*** *
4015522 AACTTTTAATTTTAATCCCACTTA
1 AACTCCAAATTTTAATACCACTTA
4015546 AACTC
1 AACTC
4015551 TTTATATTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (24 bp):
AACTCCAAATTTTAATACCACTTA
Found at i:4015968 original size:43 final size:43
Alignment explanation
Indices: 4015872--4015977 Score: 137
Period size: 42 Copynumber: 2.5 Consensus size: 43
4015862 AGGCTCAACG
* *
4015872 ACTTTGAAAAAATTAAAATG-TTCATCTAAACAGAGGCACCATA
1 ACTTTGAAAAAA-TAAAATGCTTCATCTAAACAGAAGCACCACA
* *
4015915 ACTTTAAAAAAATAAATTGCTTC-TCTAAACAGAAGCACCACA
1 ACTTTGAAAAAATAAAATGCTTCATCTAAACAGAAGCACCACA
4015957 ACTTTTG-AAAAATAAAATGCT
1 AC-TTTGAAAAAATAAAATGCT
4015978 CCTTAACGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
42 38 0.69
43 17 0.31
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.26
Consensus pattern (43 bp):
ACTTTGAAAAAATAAAATGCTTCATCTAAACAGAAGCACCACA
Found at i:4017011 original size:79 final size:79
Alignment explanation
Indices: 4016919--4017067 Score: 212
Period size: 79 Copynumber: 1.9 Consensus size: 79
4016909 TATCATTTAA
*
4016919 TCACAGGCTTCTCAGCATTAA-CAGTCTCAGAATAAATTTTATCAAT-TGATCCATATTATGTTC
1 TCACAGGCTTCTCAGCATTAACCA-TCTCAGAATAAATTTTATC-ATCTGATCCACATTATGTTC
4016982 ATCACTTGATCACCAT
64 ATCACTTGATCACCAT
* * * * *
4016998 TCACAGTCTTCTCAGCATTAACCATTTCAGAATGAATTTTGTCCTCTGATCCACATTATGTTCAT
1 TCACAGGCTTCTCAGCATTAACCATCTCAGAATAAATTTTATCATCTGATCCACATTATGTTCAT
4017063 CACTT
66 CACTT
4017068 CATTATCAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
78 1 0.02
79 59 0.95
80 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (79 bp):
TCACAGGCTTCTCAGCATTAACCATCTCAGAATAAATTTTATCATCTGATCCACATTATGTTCAT
CACTTGATCACCAT
Found at i:4017089 original size:79 final size:80
Alignment explanation
Indices: 4016917--4017098 Score: 210
Period size: 79 Copynumber: 2.3 Consensus size: 80
4016907 CATATCATTT
* *
4016917 AATCACAGGCTTCTCAGCATTAA-CAGTCTCAGAATAAATTTTATCAATTGATCCATATTATGTT
1 AATCACAGGTTTCTCAGCATTAACCAGTCTCAGAATAAATTTTATCAATTGATCCACATTATGTT
*
4016981 CATCACTTGATCACC
66 CATCACTTCATCACC
* * * * *
4016996 ATTCACA-GTCTTCTCAGCATTAACCA-TTTCAGAATGAATTTTGTC-CTCTGATCCACATTATG
1 AATCACAGGT-TTCTCAGCATTAACCAGTCTCAGAATAAATTTTATCAAT-TGATCCACATTATG
* *
4017058 TTCATCACTTCATTATC
64 TTCATCACTTCATCACC
* *
4017075 AATCATAGGTTTCTCAGCACTAAC
1 AATCACAGGTTTCTCAGCATTAAC
4017099 TATTACTTGG
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
78 2 0.02
79 80 0.93
80 4 0.05
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (80 bp):
AATCACAGGTTTCTCAGCATTAACCAGTCTCAGAATAAATTTTATCAATTGATCCACATTATGTT
CATCACTTCATCACC
Found at i:4017796 original size:8 final size:8
Alignment explanation
Indices: 4017783--4017812 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
4017773 GTCTTCATTT
4017783 TTTTTTCA
1 TTTTTTCA
4017791 TTTTTTCA
1 TTTTTTCA
*
4017799 TTCTTTCA
1 TTTTTTCA
4017807 TTTTTT
1 TTTTTT
4017813 TTCTCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:4017819 original size:16 final size:15
Alignment explanation
Indices: 4017780--4017840 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 15
4017770 TGAGTCTTCA
4017780 TTTTTT-TTTCATTT
1 TTTTTTCTTTCATTT
*
4017794 TTTCATTCTTTCATTT
1 TTT-TTTCTTTCATTT
*
4017810 TTTTTCTCTTT-TTTT
1 TTTTT-TCTTTCATTT
* *
4017825 TTTTTTTTTTTATTT
1 TTTTTTCTTTCATTT
4017840 T
1 T
4017841 CATCCATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 7 0.18
15 15 0.39
16 16 0.42
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTCTTTCATTT
Found at i:4021946 original size:54 final size:53
Alignment explanation
Indices: 4021883--4021985 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 53
4021873 TCTTTTTTTT
*
4021883 ATTTCTAAATTTTTCACCA-TTGGAGTCAATTTAGAAATATTATTTTTTTTCAAA
1 ATTTCTAAA-TTTTCACCATTTCG-GTCAATTTAGAAATATTATTTTTTTTCAAA
* * * * *
4021937 ATTTTTAAATTTTCATCATTTCGGTCTATTTAGAAATTTTTTTTTTTTT
1 ATTTCTAAATTTTCACCATTTCGGTCAATTTAGAAATATTATTTTTTTT
4021986 GGAAAATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
53 31 0.74
54 11 0.26
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (53 bp):
ATTTCTAAATTTTCACCATTTCGGTCAATTTAGAAATATTATTTTTTTTCAAA
Found at i:4022272 original size:25 final size:25
Alignment explanation
Indices: 4022243--4022303 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
4022233 ATAAATTCAG
4022243 ATAAAATTTCTCACTTAAAAATTTT
1 ATAAAATTTCTCACTTAAAAATTTT
* *
4022268 ATAAAAATTTAC-CATTTAAAATTTTT
1 AT-AAAATTT-CTCACTTAAAAATTTT
4022294 AT-AAATTTCT
1 ATAAAATTTCT
4022304 TCATTGGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 1 0.03
24 6 0.19
25 2 0.06
26 21 0.68
27 1 0.03
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (25 bp):
ATAAAATTTCTCACTTAAAAATTTT
Found at i:4022274 original size:26 final size:26
Alignment explanation
Indices: 4022245--4022298 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
4022235 AAATTCAGAT
4022245 AAAATTT-CTCACTTAAAAATTTTATA
1 AAAATTTAC-CACTTAAAAATTTTATA
* *
4022271 AAAATTTACCATTTAAAATTTTTATA
1 AAAATTTACCACTTAAAAATTTTATA
4022297 AA
1 AA
4022299 TTTCTTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (26 bp):
AAAATTTACCACTTAAAAATTTTATA
Found at i:4022308 original size:25 final size:25
Alignment explanation
Indices: 4022245--4022308 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
4022235 AAATTCAGAT
4022245 AAAATTTCTCACTTAAAAATTTTATA
1 AAAATTTCTCA-TTAAAAATTTTATA
*
4022271 AAAATTTAC-CATTTAAAATTTT-TA
1 AAAATTT-CTCATTAAAAATTTTATA
*
4022295 TAAATTTCTTCATT
1 AAAATTTC-TCATT
4022309 GGATAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
23 1 0.03
24 8 0.24
25 14 0.42
26 9 0.27
27 1 0.03
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (25 bp):
AAAATTTCTCATTAAAAATTTTATA
Found at i:4023218 original size:15 final size:15
Alignment explanation
Indices: 4023174--4023224 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
4023164 AAACTTCTCC
4023174 TATTTTTCATTTTTT
1 TATTTTTCATTTTTT
*
4023189 CTAGCCTTTTCATTTTTT
1 -TA--TTTTTCATTTTTT
*
4023207 TATTTTTTATTTTTT
1 TATTTTTCATTTTTT
4023222 TAT
1 TAT
4023225 ATATTAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 14 0.47
16 2 0.07
17 2 0.07
18 12 0.40
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.75
Consensus pattern (15 bp):
TATTTTTCATTTTTT
Found at i:4023984 original size:30 final size:30
Alignment explanation
Indices: 4023898--4024100 Score: 106
Period size: 29 Copynumber: 7.1 Consensus size: 30
4023888 CTCAAATTCA
* * * **
4023898 AAAATTGAAACCTTAAACCCTCCAAATCTT
1 AAAATTGAAACCCTAAACCATCCAAACCCC
*
4023928 AAAATTG-AACCCTAAACCATCTAAACCCC
1 AAAATTGAAACCCTAAACCATCCAAACCCC
* * *
4023957 GAAATTGAAACCCTAAA-TATCCCAAACCCT
1 AAAATTGAAACCCTAAACCAT-CCAAACCCC
** * *
4023987 AAAATCAAAACCCTAAACC-T-CAAATCCT
1 AAAATTGAAACCCTAAACCATCCAAACCCC
* * *
4024015 AAAA-TCAAACCC-AAACC-T-CAAGCCCT
1 AAAATTGAAACCCTAAACCATCCAAACCCC
** * *
4024041 AAAATCAAAATCCTAAA-CATCCAAACTCC
1 AAAATTGAAACCCTAAACCATCCAAACCCC
* *
4024070 AAAA-TCAATACCCTAAA--ATCAAAACCCC
1 AAAATTGAA-ACCCTAAACCATCCAAACCCC
4024098 AAA
1 AAA
4024101 CTTTCAAGTC
Statistics
Matches: 135, Mismatches: 30, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
26 16 0.12
27 12 0.09
28 29 0.21
29 40 0.30
30 38 0.28
ACGTcount: A:0.48, C:0.32, G:0.02, T:0.18
Consensus pattern (30 bp):
AAAATTGAAACCCTAAACCATCCAAACCCC
Found at i:4023999 original size:14 final size:14
Alignment explanation
Indices: 4023964--4024096 Score: 105
Period size: 14 Copynumber: 9.4 Consensus size: 14
4023954 CCCGAAATTG
*
4023964 AAACCCTAAATATCCC
1 AAACCCTAAA-AT-CA
4023980 AAACCCTAAAATCA
1 AAACCCTAAAATCA
*
4023994 AAACCCTAAACCTC-
1 AAACCCTAAA-ATCA
*
4024008 AAATCCTAAAATC-
1 AAACCCTAAAATCA
*
4024021 AAACCC-AAACCTC-
1 AAACCCTAAA-ATCA
*
4024034 AAGCCCTAAAATCA
1 AAACCCTAAAATCA
* *
4024048 AAATCCTAAACATCC
1 AAACCCTAAA-ATCA
4024063 AAACTCC-AAAATCA
1 AAAC-CCTAAAATCA
*
4024077 ATACCCTAAAATCA
1 AAACCCTAAAATCA
4024091 AAACCC
1 AAACCC
4024097 CAAACTTTCA
Statistics
Matches: 95, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
12 3 0.03
13 18 0.19
14 49 0.52
15 13 0.14
16 12 0.13
ACGTcount: A:0.50, C:0.34, G:0.01, T:0.16
Consensus pattern (14 bp):
AAACCCTAAAATCA
Found at i:4024041 original size:26 final size:27
Alignment explanation
Indices: 4023935--4024086 Score: 121
Period size: 29 Copynumber: 5.3 Consensus size: 27
4023925 CTTAAAATTG
* * *
4023935 AACCCTAAACCATCTAAACCCCGAAATTGA
1 AACCCTAAACC-TC-AAA-CCCTAAAATCA
4023965 AACCCTAAATATCC-CAAACCCTAAAATCAA
1 AACCCT-AA-A-CCTCAAACCCTAAAATC-A
*
4023995 AACCCTAAACCTCAAATCCTAAAATCA
1 AACCCTAAACCTCAAACCCTAAAATCA
*
4024022 AACCC-AAACCTCAAGCCCTAAAATCAA
1 AACCCTAAACCTCAAACCCTAAAATC-A
* *
4024049 AATCCTAAACATCCAAACTCC-AAAATCA
1 AACCCTAAACCT-CAAAC-CCTAAAATCA
4024077 ATACCCTAAA
1 A-ACCCTAAA
4024087 ATCAAAACCC
Statistics
Matches: 102, Mismatches: 10, Indels: 21
0.77 0.08 0.16
Matches are distributed among these distances:
26 18 0.18
27 13 0.13
28 21 0.21
29 26 0.25
30 18 0.18
31 3 0.03
32 1 0.01
33 2 0.02
ACGTcount: A:0.48, C:0.34, G:0.02, T:0.16
Consensus pattern (27 bp):
AACCCTAAACCTCAAACCCTAAAATCA
Found at i:4027278 original size:18 final size:19
Alignment explanation
Indices: 4027242--4027281 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
4027232 TTAATTTTTT
*
4027242 ATATTGATTTAATTTAATA
1 ATATTGATTCAATTTAATA
4027261 ATATTGATTCAA-TTAATA
1 ATATTGATTCAATTTAATA
4027279 ATA
1 ATA
4027282 ATGTTACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (19 bp):
ATATTGATTCAATTTAATA
Found at i:4027455 original size:31 final size:32
Alignment explanation
Indices: 4027420--4027510 Score: 114
Period size: 31 Copynumber: 2.9 Consensus size: 32
4027410 TGTAAATATT
*
4027420 TTATATTCGTACAAAATTTAAAATTTAATT-A
1 TTATATTCGTACGAAATTTAAAATTTAATTCA
* *
4027451 TTATATTCGTATGAAATTTGAAATTTAATTCA
1 TTATATTCGTACGAAATTTAAAATTTAATTCA
** *
4027483 -TATGCTCGCACGAAATTTAAAATTTAAT
1 TTATATTCGTACGAAATTTAAAATTTAAT
4027511 CTCTTTAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 50 0.98
32 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.43
Consensus pattern (32 bp):
TTATATTCGTACGAAATTTAAAATTTAATTCA
Found at i:4027625 original size:14 final size:13
Alignment explanation
Indices: 4027608--4027691 Score: 57
Period size: 14 Copynumber: 6.2 Consensus size: 13
4027598 TTTATTATAT
4027608 ATAATTAATTATTA
1 ATAATTAA-TATTA
*
4027622 ATAATATCATATTA
1 ATAAT-TAATATTA
*
4027636 ATAA-TATTATT-
1 ATAATTAATATTA
* *
4027647 ATCATTTATATTA
1 ATAATTAATATTA
4027660 ATCAATTATAATATTA
1 AT-AA-T-TAATATTA
4027676 ATAATTTAA-ATTA
1 ATAA-TTAATATTA
4027689 ATA
1 ATA
4027692 TATCAAGTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
11 3 0.05
12 10 0.18
13 9 0.16
14 18 0.32
15 7 0.12
16 9 0.16
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
ATAATTAATATTA
Found at i:4027645 original size:40 final size:40
Alignment explanation
Indices: 4027600--4027680 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
4027590 TATTATGTTT
*
4027600 TATTATATATAATTAATTATTAAT-AA-TATCATATTAATAA
1 TATTAT-TATAATTAA-TATTAATCAATTATAATATTAATAA
* *
4027640 TATTATTATCATTTATATTAATCAATTATAATATTAATAA
1 TATTATTATAATTAATATTAATCAATTATAATATTAATAA
4027680 T
1 T
4027681 TTAAATTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 7 0.19
39 9 0.25
40 20 0.56
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (40 bp):
TATTATTATAATTAATATTAATCAATTATAATATTAATAA
Found at i:4027683 original size:29 final size:25
Alignment explanation
Indices: 4027602--4027691 Score: 76
Period size: 26 Copynumber: 3.4 Consensus size: 25
4027592 TTATGTTTTA
*
4027602 TTATATATAATTA-ATTATTAATAAT
1 TTATAT-TAATAATATTATTAATAAT
* *
4027627 ATCATATTAATAATATTATT-ATCAT
1 -TTATATTAATAATATTATTAATAAT
4027652 TTATATTAATCAATTATAATATTAATAAT
1 TTATATTAAT-AA-TAT--TATTAATAAT
*
4027681 TTAAATTAATA
1 TTATATTAATA
4027692 TATCAAGTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
24 9 0.17
25 11 0.21
26 14 0.27
28 5 0.10
29 13 0.25
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (25 bp):
TTATATTAATAATATTATTAATAAT
Found at i:4028223 original size:14 final size:14
Alignment explanation
Indices: 4028204--4028230 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4028194 CCATTAAGTC
4028204 AAAAAATCAATGTA
1 AAAAAATCAATGTA
4028218 AAAAAATCAATGT
1 AAAAAATCAATGT
4028231 TTTGAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (14 bp):
AAAAAATCAATGTA
Found at i:4030351 original size:21 final size:21
Alignment explanation
Indices: 4030325--4030367 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4030315 TAAAATTATA
* *
4030325 ATTTTTGATTTAGTTTGGATT
1 ATTTTTGATTTAATTTGAATT
*
4030346 ATTTTTTATTTAATTTGAATT
1 ATTTTTGATTTAATTTGAATT
4030367 A
1 A
4030368 AGTTTAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (21 bp):
ATTTTTGATTTAATTTGAATT
Found at i:4030834 original size:2 final size:2
Alignment explanation
Indices: 4030822--4030863 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
4030812 ATTTAGCTTC
*
4030822 AT AT GT 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
4030864 GGCTTCCCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4035843 original size:29 final size:29
Alignment explanation
Indices: 4035809--4035868 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
4035799 AAATTTAATT
4035809 TAAAAATAGATTTAAAATATTATAATATTA
1 TAAAAAT-GATTTAAAATATTATAATATTA
** *
4035839 TAAAAATGATTTTTAATATTTTAATATTA
1 TAAAAATGATTTAAAATATTATAATATTA
4035868 T
1 T
4035869 CTTAAATAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (29 bp):
TAAAAATGATTTAAAATATTATAATATTA
Found at i:4042218 original size:9 final size:10
Alignment explanation
Indices: 4042193--4042223 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
4042183 AATCAAATAT
4042193 ATAAAATTTA
1 ATAAAATTTA
4042203 ATAAAATTTA
1 ATAAAATTTA
4042213 ATAAATATTTA
1 ATAAA-ATTTA
4042224 TATTATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATAAAATTTA
Found at i:4042337 original size:21 final size:21
Alignment explanation
Indices: 4042276--4042338 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 21
4042266 GTTTTTATCA
*
4042276 TTTAATAAGTATTTATCAAGTT
1 TTTAAT-AGTATTTATCAAATT
* *
4042298 TTGACTA-TA--TAT-AATATT
1 TTTAATAGTATTTATCAA-ATT
4042316 TTTAATAGTATTTATCAAATT
1 TTTAATAGTATTTATCAAATT
4042337 TT
1 TT
4042339 CATATCAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 11
0.66 0.11 0.23
Matches are distributed among these distances:
17 2 0.06
18 10 0.32
19 2 0.06
20 2 0.06
21 9 0.29
22 6 0.19
ACGTcount: A:0.37, C:0.05, G:0.06, T:0.52
Consensus pattern (21 bp):
TTTAATAGTATTTATCAAATT
Found at i:4045092 original size:13 final size:14
Alignment explanation
Indices: 4045076--4045114 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
4045066 ATGATTGAAT
4045076 AAAAATTAAAAT-A
1 AAAAATTAAAATCA
*
4045089 AAAAATTAAAATCG
1 AAAAATTAAAATCA
*
4045103 ATAAATTAAAAT
1 AAAAATTAAAAT
4045115 GTCTTGTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAAATTAAAATCA
Found at i:4049049 original size:18 final size:18
Alignment explanation
Indices: 4049026--4049060 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4049016 ATTTTTTTTT
*
4049026 CTATTTCAATCATTGATC
1 CTATTTCAATAATTGATC
4049044 CTATTTCAATAATTGAT
1 CTATTTCAATAATTGAT
4049061 TTTGGAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (18 bp):
CTATTTCAATAATTGATC
Found at i:4049846 original size:42 final size:42
Alignment explanation
Indices: 4049757--4049846 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 42
4049747 ACCTGAAGAG
*
4049757 GAAGATGTAGCTAAGATAGCAGGGAATGAAAGGGTAGAATAT
1 GAAGATGTAGCTAAGATAGCAGGGAATGAAAGGATAGAATAT
* * * *
4049799 CAAGATGTAGCTGAA-ATGGTAGGGAATGAAATGATAAGAA-AT
1 GAAGATGTAGCT-AAGATAGCAGGGAATGAAAGGAT-AGAATAT
4049841 GAAGAT
1 GAAGAT
4049847 TTAATTGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
42 34 0.85
43 6 0.15
ACGTcount: A:0.44, C:0.04, G:0.31, T:0.20
Consensus pattern (42 bp):
GAAGATGTAGCTAAGATAGCAGGGAATGAAAGGATAGAATAT
Found at i:4057463 original size:7 final size:8
Alignment explanation
Indices: 4057434--4057460 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
4057424 TAAATTACAT
4057434 TTTTAAAA
1 TTTTAAAA
4057442 TTTTAAAA
1 TTTTAAAA
4057450 TTTTAAAA
1 TTTTAAAA
4057458 TTT
1 TTT
4057461 AAATAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTTAAAA
Found at i:4060076 original size:37 final size:38
Alignment explanation
Indices: 4059940--4060078 Score: 106
Period size: 38 Copynumber: 3.7 Consensus size: 38
4059930 TGACAAAATC
* * * *
4059940 TAATTTAAATATATTATTTTTAAAAATACATTTCTAAA
1 TAATATAAATATATTATTTTTTAAAATAAATTTCTTAA
* ** * *
4059978 TAATCTAAATATA-TATTTTTTTCAATTTAAAATT-TT-C
1 TAATATAAATATATTA-TTTTTT-AAAATAAATTTCTTAA
* **
4060015 TAATATAATGATATATTATCTTTTAAAATAGGTTTCTTAA
1 TAATATAA--ATATATTATTTTTTAAAATAAATTTCTTAA
4060055 TAATATAAATATA-TATTTTTTAAA
1 TAATATAAATATATTATTTTTTAAA
4060079 TCTAAAAACC
Statistics
Matches: 77, Mismatches: 17, Indels: 15
0.71 0.16 0.14
Matches are distributed among these distances:
37 19 0.25
38 29 0.38
39 19 0.25
40 10 0.13
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (38 bp):
TAATATAAATATATTATTTTTTAAAATAAATTTCTTAA
Found at i:4063641 original size:29 final size:30
Alignment explanation
Indices: 4063608--4063665 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
4063598 TTAGGAAAAA
*
4063608 AATAGGAAACATATGTTATTTTTT-ATAAG
1 AATAGGAAACATATATTATTTTTTCATAAG
* *
4063637 AATAGGAAGCTTATATTATTTTTTCATAA
1 AATAGGAAACATATATTATTTTTTCATAA
4063666 TTATTGCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (30 bp):
AATAGGAAACATATATTATTTTTTCATAAG
Found at i:4070234 original size:3 final size:3
Alignment explanation
Indices: 4070226--4070250 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4070216 CTTTAGTTTT
4070226 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
4070251 ACTTGAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4070412 original size:19 final size:20
Alignment explanation
Indices: 4070375--4070423 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
4070365 AATTAATTTA
4070375 AAATAATAATTTATATTATT
1 AAATAATAATTTATATTATT
4070395 AAATAA-AATTT-TATTTATT
1 AAATAATAATTTATA-TTATT
4070414 AAATATATAA
1 AAATA-ATAA
4070424 AGTATGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.08
19 15 0.58
20 7 0.27
21 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATAATAATTTATATTATT
Found at i:4070704 original size:14 final size:14
Alignment explanation
Indices: 4070685--4070712 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4070675 AAAGCACCGG
4070685 CTGCACCATAATAT
1 CTGCACCATAATAT
4070699 CTGCACCATAATAT
1 CTGCACCATAATAT
4070713 AAACAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
CTGCACCATAATAT
Found at i:4071365 original size:46 final size:45
Alignment explanation
Indices: 4071315--4071402 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 45
4071305 TACTTCCGAG
* *
4071315 CCAATTTTAATTCACACTAGCTTTCTTTTCTTTTTAGATATTTGTA
1 CCAATTTTAATTCACACTAGCCTTCGTTTC-TTTTAGATATTTGTA
*
4071361 CCAATTTTAATTCCCACTAGCCTTCGTTTCTTTTAGATATTT
1 CCAATTTTAATTCACACTAGCCTTCGTTTCTTTTAGATATTT
4071403 ATTATGACAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 12 0.31
46 27 0.69
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (45 bp):
CCAATTTTAATTCACACTAGCCTTCGTTTCTTTTAGATATTTGTA
Found at i:4080629 original size:14 final size:14
Alignment explanation
Indices: 4080610--4080639 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4080600 CTTCATAGAT
4080610 GAGTTAAGAGTTGA
1 GAGTTAAGAGTTGA
4080624 GAGTTAAGAGTTGA
1 GAGTTAAGAGTTGA
4080638 GA
1 GA
4080640 CCCTGCTTCA
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:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (14 bp):
GAGTTAAGAGTTGA
Found at i:4081651 original size:35 final size:35
Alignment explanation
Indices: 4081588--4081675 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 35
4081578 TTTTATGTAT
4081588 TGTAT-TATTTATTA-TTATTATGTATTAATA-TA
1 TGTATATATTTATTATTTATTATGTATTAATATTA
* * *
4081620 TGTATATATTTATTTATTTATTTTTTGTTAATATTTA
1 TGTATATATTTA-TTATTTATTATGTATTAATA-TTA
*
4081657 TGTCTAT-TTTATTATTTAT
1 TGTATATATTTATTATTTAT
4081676 GTATATATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
32 5 0.11
33 6 0.13
34 3 0.06
35 21 0.45
36 4 0.09
37 8 0.17
ACGTcount: A:0.28, C:0.01, G:0.06, T:0.65
Consensus pattern (35 bp):
TGTATATATTTATTATTTATTATGTATTAATATTA
Found at i:4081734 original size:67 final size:66
Alignment explanation
Indices: 4081587--4081776 Score: 167
Period size: 67 Copynumber: 2.8 Consensus size: 66
4081577 ATTTTATGTA
* *
4081587 TTGTATTATTTATTATTATTATGTAT-TAATATATGTATATATTTATTTATTTATTTTTTGTTAA
1 TTGTATT-TTTATTA-T-TTATGTATAT-ATATATGTATATTTTTTTTTATTTATTTTTTGTTAA
4081651 TATTT
62 TATTT
* * *
4081656 ATGTCTATTTTATTATTTATGTATATATATATGTATATTTTTTTTTATCTT-TTTTATT-TTATT
1 TTGTAT-TTTTATTATTTATGTATATATATATGTATATTTTTTTTTAT-TTATTTT-TTGTTAAT
4081719 CATTT
63 -ATTT
* * *
4081724 TTGTATTTTTACTTATCTA-AT-TATATATCTGATATATTTTTTTATTA-TTATTT
1 TTGTATTTTTA-TTATTTATGTATATATATATG-TATATTTTTTT-TTATTTATTT
4081777 ATCCTATAAT
Statistics
Matches: 102, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
66 11 0.11
67 56 0.55
68 23 0.23
69 11 0.11
70 1 0.01
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (66 bp):
TTGTATTTTTATTATTTATGTATATATATATGTATATTTTTTTTTATTTATTTTTTGTTAATATT
T
Found at i:4082279 original size:20 final size:20
Alignment explanation
Indices: 4082256--4082294 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4082246 CCAGTTTCCG
*
4082256 GCGAGGAATCCCAGAAACCA
1 GCGAAGAATCCCAGAAACCA
* *
4082276 GCGAATATTCCCAGAAACC
1 GCGAAGAATCCCAGAAACC
4082295 GGTAGACTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.21, T:0.10
Consensus pattern (20 bp):
GCGAAGAATCCCAGAAACCA
Found at i:4082918 original size:60 final size:57
Alignment explanation
Indices: 4082851--4083127 Score: 378
Period size: 59 Copynumber: 4.7 Consensus size: 57
4082841 AAAGTTCCAA
* *
4082851 AAAAAAATATTTTTTGGGAAAAGTTGAAAGTATCAATTTTTCTCAGAAATAAATTTC
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
*
4082908 AAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCATAAATAAATTTC
1 ---AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
*
4082968 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA-TTTC
** *
4083026 AAAAAAAGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCT-TGAAAATCGAAATTTC
1 AAAAAAA-TATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTCAG-AAAT--AAATTTC
* *
4083086 CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
4083128 CTACAAAAAA
Statistics
Matches: 199, Mismatches: 11, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
57 51 0.26
58 13 0.07
59 67 0.34
60 65 0.33
61 3 0.02
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (57 bp):
AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
Found at i:4087625 original size:56 final size:57
Alignment explanation
Indices: 4087539--4087650 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 57
4087529 GGCCTTTTCA
*
4087539 TTCCTTTATTTTGAATCTCCTATCCAGAAAAG-GTCAGGGGACCGTTATAAATCATG
1 TTCCTTTATTTTGAATCGCCTATCCAGAAAAGTGTCAGGGGACCGTTATAAATCATG
*
4087595 TTCCTTTATTTTGAATCGCCTATGCAGAAAAGTGTCAGGGGACCGTTATAAATCAT
1 TTCCTTTATTTTGAATCGCCTATCCAGAAAAGTGTCAGGGGACCGTTATAAATCAT
4087651 ATGCCTCATC
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
56 30 0.57
57 23 0.43
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (57 bp):
TTCCTTTATTTTGAATCGCCTATCCAGAAAAGTGTCAGGGGACCGTTATAAATCATG
Found at i:4094501 original size:6 final size:6
Alignment explanation
Indices: 4094490--4094519 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
4094480 AGACTCCCTA
4094490 AATGGC AATGGC AATGGC AATGGC AATGGC
1 AATGGC AATGGC AATGGC AATGGC AATGGC
4094520 CATGACAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (6 bp):
AATGGC
Found at i:4094528 original size:18 final size:18
Alignment explanation
Indices: 4094490--4094528 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4094480 AGACTCCCTA
*
4094490 AATGGCAATGGCAATGGC
1 AATGGCAATGGCAATGAC
*
4094508 AATGGCAATGGCCATGAC
1 AATGGCAATGGCAATGAC
4094526 AAT
1 AAT
4094529 TTTAGGAATT
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:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (18 bp):
AATGGCAATGGCAATGAC
Found at i:4095172 original size:16 final size:16
Alignment explanation
Indices: 4095151--4095185 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4095141 ATTCAAACAT
4095151 ATTCAAGTCATGTTAG
1 ATTCAAGTCATGTTAG
* *
4095167 ATTCAAGTTATTTTAG
1 ATTCAAGTCATGTTAG
4095183 ATT
1 ATT
4095186 TAACAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (16 bp):
ATTCAAGTCATGTTAG
Found at i:4098569 original size:11 final size:11
Alignment explanation
Indices: 4098553--4098595 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
4098543 AATCCCATAA
4098553 GAGATTTGTTT
1 GAGATTTGTTT
*
4098564 GAGATTTGTTA
1 GAGATTTGTTT
* * *
4098575 AAAATTTATTT
1 GAGATTTGTTT
4098586 GAGATTTGTT
1 GAGATTTGTT
4098596 AGATATTGCT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:4098763 original size:52 final size:52
Alignment explanation
Indices: 4098651--4098749 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 52
4098641 AGAAAAAAAA
* *
4098651 ATTCTTAATAAGTAAGTTTAACTTGCAAGAGAAAAATTCTAAAAGTAAAGAG
1 ATTCTTAATAAGTAAGTTTAACTTACAAGAGAAAAATTCTAAAAGGAAAGAG
* * * *
4098703 ATTCTTAATAGGTAAGTTTAACTTACAGGAGAAGAATTCTAAGAGGA
1 ATTCTTAATAAGTAAGTTTAACTTACAAGAGAAAAATTCTAAAAGGA
4098750 GATGGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.29
Consensus pattern (52 bp):
ATTCTTAATAAGTAAGTTTAACTTACAAGAGAAAAATTCTAAAAGGAAAGAG
Found at i:4103127 original size:23 final size:23
Alignment explanation
Indices: 4103100--4103146 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4103090 TCGTTTATAT
* * *
4103100 ATGTTCATAAACATATTTATTTA
1 ATGTTCACAAACAAACTTATTTA
*
4103123 ATGTTTACAAACAAACTTATTTA
1 ATGTTCACAAACAAACTTATTTA
4103146 A
1 A
4103147 CTTAATTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (23 bp):
ATGTTCACAAACAAACTTATTTA
Found at i:4107026 original size:51 final size:51
Alignment explanation
Indices: 4106911--4107064 Score: 186
Period size: 52 Copynumber: 3.0 Consensus size: 51
4106901 TATAACCATA
* * * *
4106911 CAAACTTACCTATTAAGAATCACTTTTCTTTTAGAATTCTT-TTTCTGTAAGT
1 CAAACTTACCTATTAAGAATC-CCTTTCTCTTAGAATTCTTCTTT-TGCAAAT
* * * *
4106963 CAAACTTGCCTATGAAGAA-CCCTTTCCTCTTATAATTCTTCTCTTGCAAAT
1 CAAACTTACCTATTAAGAATCCCTTT-CTCTTAGAATTCTTCTTTTGCAAAT
4107014 CAAACTTACCTATTAAGAATCCTCTTTCTCTTAGAATTCTTCTTTTGCAAA
1 CAAACTTACCTATTAAGAATCC-CTTTCTCTTAGAATTCTTCTTTTGCAAA
4107065 GTCTTCTTAT
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
50 4 0.05
51 35 0.41
52 43 0.50
53 4 0.05
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.42
Consensus pattern (51 bp):
CAAACTTACCTATTAAGAATCCCTTTCTCTTAGAATTCTTCTTTTGCAAAT
Found at i:4107684 original size:35 final size:35
Alignment explanation
Indices: 4107618--4107685 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
4107608 TAAAGTATTC
* * * * *
4107618 TCAACCCAAACAAATACATATCTATATGCACCCTT
1 TCAACACAAACAAACACATACCCATACGCACCCTT
*
4107653 TCAACACAACCAAACACATACCCATACGCACCC
1 TCAACACAAACAAACACATACCCATACGCACCC
4107686 ATATATCACA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.41, C:0.38, G:0.03, T:0.18
Consensus pattern (35 bp):
TCAACACAAACAAACACATACCCATACGCACCCTT
Found at i:4107947 original size:52 final size:52
Alignment explanation
Indices: 4107864--4108008 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 52
4107854 TATAACCATA
* *
4107864 CAAACTTGCCTATTAAGAATCTTTTTCCTCTTAGAATTCTTT-TCTTGCAAGT
1 CAAACTTGCCTATTAAGAAT-TTTTTTCTCTTAGAATTCTTTCTCTTACAAGT
*
4107916 CAAACTTGCCTATTAAGAATTATTTTTCTCTTATAATT-TTTCTCTTACAAGT
1 CAAACTTGCCTATTAAGAATT-TTTTTCTCTTAGAATTCTTTCTCTTACAAGT
* * * * *
4107968 CAAACCTACATATTAAGAATCCTCTTTCTCTTAGAATTCTT
1 CAAACTTGCCTATTAAGAAT-TTTTTTCTCTTAGAATTCTT
4108009 CTTTTACTAG
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
51 4 0.05
52 74 0.93
53 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.44
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATTTTTTTCTCTTAGAATTCTTTCTCTTACAAGT
Found at i:4120796 original size:16 final size:16
Alignment explanation
Indices: 4120775--4120823 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
4120765 TATATGTGAA
4120775 TTATATAAAAATTAAT
1 TTATATAAAAATTAAT
** *
4120791 TTATATAATTATTTAT
1 TTATATAAAAATTAAT
4120807 TTATATATATAAATTAA
1 TTATATA-A-AAATTAA
4120824 ATATAAACTC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 20 0.80
17 1 0.04
18 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATATAAAAATTAAT
Found at i:4127744 original size:43 final size:43
Alignment explanation
Indices: 4127683--4127768 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
4127673 CCTCCGGGGA
4127683 ACCTGATTATCTTGGTTTGCAACTGTTACCTTAAAGCCAATTC
1 ACCTGATTATCTTGGTTTGCAACTGTTACCTTAAAGCCAATTC
4127726 ACCTGATTATCTTGGTTTGCAACTGTTACCTTAAAGCCAATTC
1 ACCTGATTATCTTGGTTTGCAACTGTTACCTTAAAGCCAATTC
4127769 GAAATTGCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (43 bp):
ACCTGATTATCTTGGTTTGCAACTGTTACCTTAAAGCCAATTC
Found at i:4128054 original size:2 final size:2
Alignment explanation
Indices: 4128047--4128113 Score: 82
Period size: 2 Copynumber: 33.5 Consensus size: 2
4128037 ATTTATGTTT
* *
4128047 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA T- TCA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* *
4128089 TA TA TA TG TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4128114 GCTGATGACT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4144021 original size:16 final size:16
Alignment explanation
Indices: 4144000--4144048 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
4143990 TATATGTGAA
4144000 TTATATAAAAATTAAT
1 TTATATAAAAATTAAT
** *
4144016 TTATATAATTATTTAT
1 TTATATAAAAATTAAT
4144032 TTATATATATAAATTAA
1 TTATATA-A-AAATTAA
4144049 ATATAAACTC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 20 0.80
17 1 0.04
18 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATATAAAAATTAAT
Found at i:4148622 original size:46 final size:47
Alignment explanation
Indices: 4148562--4148659 Score: 139
Period size: 46 Copynumber: 2.1 Consensus size: 47
4148552 AAATAATATG
*
4148562 AAAATAAT-ACAAAAA-ATATACATATGATACGATTTAAAATTTTAATA
1 AAAATAATAACAAAAATATATAAATATGATA--ATTTAAAATTTTAATA
*
4148609 AAAATCATAA-AAAAATATATAAATATGATAATTTAAAATTTTAATA
1 AAAATAATAACAAAAATATATAAATATGATAATTTAAAATTTTAATA
4148655 AAAAT
1 AAAAT
4148660 TATATATATT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
46 21 0.45
47 12 0.26
48 14 0.30
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (47 bp):
AAAATAATAACAAAAATATATAAATATGATAATTTAAAATTTTAATA
Found at i:4148688 original size:20 final size:20
Alignment explanation
Indices: 4148643--4148688 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
4148633 ATGATAATTT
*
4148643 AAAAT-TTTAATAAAAATTA
1 AAAATATTTAATAAAAATAA
* *
4148662 TATATATTTAATAAAAATAA
1 AAAATATTTAATAAAAATAA
4148682 AAAATAT
1 AAAATAT
4148689 ATATTTTATA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATATTTAATAAAAATAA
Found at i:4151586 original size:43 final size:43
Alignment explanation
Indices: 4151525--4151610 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
4151515 CCTCCGGGGA
4151525 ACCTGATTATCTTGGTTTGCAACTGTTACCTTAAAGCCAATTC
1 ACCTGATTATCTTGGTTTGCAACTGTTACCTTAAAGCCAATTC
4151568 ACCTGATTATCTTGGTTTGCAACTGTTACCTTAAAGCCAATTC
1 ACCTGATTATCTTGGTTTGCAACTGTTACCTTAAAGCCAATTC
4151611 GAAATTGCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (43 bp):
ACCTGATTATCTTGGTTTGCAACTGTTACCTTAAAGCCAATTC
Found at i:4151896 original size:2 final size:2
Alignment explanation
Indices: 4151889--4151954 Score: 73
Period size: 2 Copynumber: 33.5 Consensus size: 2
4151879 ATTTATGTTT
* *
4151889 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA CA T- TCA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* *
4151930 TA TA TA TG TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4151955 GCTGATGACT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:4162548 original size:17 final size:19
Alignment explanation
Indices: 4162507--4162548 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4162497 CGAATCAAAA
*
4162507 TATATATTTTTATTAATTT
1 TATATATTTTTATAAATTT
4162526 TATATATTTTTA-AAATTT
1 TATATATTTTTATAAATTT
4162544 T-TATA
1 TATATA
4162549 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.18
18 6 0.27
19 12 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATATATTTTTATAAATTT
Found at i:4171571 original size:3 final size:3
Alignment explanation
Indices: 4171563--4171601 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
4171553 ATCATACTAG
*
4171563 ATA ATA ATA ATG AT- ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4171602 CCTAACACGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4171999 original size:52 final size:51
Alignment explanation
Indices: 4171863--4172004 Score: 151
Period size: 52 Copynumber: 2.7 Consensus size: 51
4171853 ACAAGAAGAT
* * * *
4171863 TTACAAAAAAAGAATTCCAAGAGAAAAAAAATT-TTAATAGATAAATTTGAC
1 TTACAAGAAAAGAATTCTAAGAG-AAAAAGATTCTTAATAGACAAATTTGAC
* * * *
4171914 TTGCAAGAAAAAAATTTTAAAAGGAAAAAGATTCTTAATAGACAAATTTGAC
1 TTACAAGAAAAGAATTCTAAGA-GAAAAAGATTCTTAATAGACAAATTTGAC
* * *
4171966 TTACAGGAGAAGAATTCTAAGAGAAGAAGGATTCTTAAT
1 TTACAAGAAAAGAATTCTAAGAGAA-AAAGATTCTTAAT
4172005 GGGCAAGTTT
Statistics
Matches: 73, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
51 27 0.37
52 46 0.63
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (51 bp):
TTACAAGAAAAGAATTCTAAGAGAAAAAGATTCTTAATAGACAAATTTGAC
Found at i:4172063 original size:36 final size:36
Alignment explanation
Indices: 4172011--4172085 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
4172001 TAATGGGCAA
* * *
4172011 GTTTGTATGATTATAAATAGGTGAAGTCTATATAAG
1 GTTTATATGATTATAAATAGATGAAATCTATATAAG
4172047 GTTTATATGATTATAAATAGATGAAATCTATATAAG
1 GTTTATATGATTATAAATAGATGAAATCTATATAAG
4172083 GTT
1 GTT
4172086 AGGTATGAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.40
Consensus pattern (36 bp):
GTTTATATGATTATAAATAGATGAAATCTATATAAG
Found at i:4172525 original size:31 final size:31
Alignment explanation
Indices: 4172487--4172598 Score: 134
Period size: 31 Copynumber: 3.6 Consensus size: 31
4172477 AGGGTTTTAG
* * *
4172487 CCCAACAAATGGTATCAGAGCTGTGATCTTC
1 CCCAACAAATGGTATCAGAACTGTGGTGTTC
* * * *
4172518 CCCAACAAATGGTATCACAACTATGGGGATC
1 CCCAACAAATGGTATCAGAACTGTGGTGTTC
* *
4172549 CCTAACAAATGGTATTAGAACTGTGGTGTTC
1 CCCAACAAATGGTATCAGAACTGTGGTGTTC
*
4172580 CCCAACAAGTGGTATCAGA
1 CCCAACAAATGGTATCAGA
4172599 GCTAAAGGTT
Statistics
Matches: 65, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (31 bp):
CCCAACAAATGGTATCAGAACTGTGGTGTTC
Found at i:4172951 original size:11 final size:11
Alignment explanation
Indices: 4172935--4172974 Score: 80
Period size: 11 Copynumber: 3.6 Consensus size: 11
4172925 AATCCAATAA
4172935 GAGATTTGTTT
1 GAGATTTGTTT
4172946 GAGATTTGTTT
1 GAGATTTGTTT
4172957 GAGATTTGTTT
1 GAGATTTGTTT
4172968 GAGATTT
1 GAGATTT
4172975 ATTAGATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.53
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:4173094 original size:52 final size:52
Alignment explanation
Indices: 4173001--4173105 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 52
4172991 TGGACAAGAA
* *
4173001 GACTTGCAAAAGAAGAATTCTAAAAGAAAAGAAATTCTTAATAGGTAAGTTT
1 GACTTACAAAAGAAGAATTCTAAAAGAAAAGAAATTCTTAATAGGCAAGTTT
* * * * *
4173053 GACTTACAAGAGAAGAATTCTAAGAGGAGAAG-GATTTTTAATAGGCAAGTTT
1 GACTTACAAAAGAAGAATTCTAA-AAGAAAAGAAATTCTTAATAGGCAAGTTT
4173105 G
1 G
4173106 TATAATTATA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 39 0.87
53 6 0.13
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.27
Consensus pattern (52 bp):
GACTTACAAAAGAAGAATTCTAAAAGAAAAGAAATTCTTAATAGGCAAGTTT
Found at i:4174583 original size:21 final size:24
Alignment explanation
Indices: 4174557--4174605 Score: 77
Period size: 21 Copynumber: 2.2 Consensus size: 24
4174547 TCAAATTTGA
4174557 AATTGTTTCAT-A-AAA-AATATG
1 AATTGTTTCATAATAAACAATATG
4174578 AATTGTTTCATAATAAACAATATG
1 AATTGTTTCATAATAAACAATATG
4174602 AATT
1 AATT
4174606 ACTTCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 11 0.44
22 1 0.04
23 3 0.12
24 10 0.40
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (24 bp):
AATTGTTTCATAATAAACAATATG
Done.