Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397267.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_204.0, 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: 6982396
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 27749 characters in sequence are not A, C, G, or T
File 9 of 12
Found at i:5320634 original size:15 final size:14
Alignment explanation
Indices: 5320616--5320654 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
5320606 TCTTCTCAGT
5320616 AATCACATTCTCAAC
1 AATCACATTC-CAAC
*
5320631 AATCAGATATCCAAC
1 AATCACAT-TCCAAC
5320646 AATCACATT
1 AATCACATT
5320655 ACTAGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 1 0.05
15 18 0.86
16 2 0.10
ACGTcount: A:0.44, C:0.28, G:0.03, T:0.26
Consensus pattern (14 bp):
AATCACATTCCAAC
Found at i:5329388 original size:7 final size:7
Alignment explanation
Indices: 5329376--5329400 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5329366 GATATATTTA
5329376 TTTTATT
1 TTTTATT
5329383 TTTTATT
1 TTTTATT
5329390 TTTTATT
1 TTTTATT
5329397 TTTT
1 TTTT
5329401 TGTGAAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:5330816 original size:32 final size:32
Alignment explanation
Indices: 5330780--5330850 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
5330770 TGGTATATAA
* * *
5330780 TTTTTTTATTTAAAAAGTAAAATTTGAATTAT
1 TTTTTTTATATAAAAAATAAAATTTAAATTAT
* * * *
5330812 TTTTTTAATATAAAAAATCATATTTAAATTTT
1 TTTTTTTATATAAAAAATAAAATTTAAATTAT
5330844 TTTTTTT
1 TTTTTTT
5330851 TGTCTCTAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (32 bp):
TTTTTTTATATAAAAAATAAAATTTAAATTAT
Found at i:5336270 original size:2 final size:2
Alignment explanation
Indices: 5336263--5336287 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5336253 TCCATTGTCA
5336263 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 A
5336288 GTGTTAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5336434 original size:39 final size:40
Alignment explanation
Indices: 5336365--5336442 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 40
5336355 AATAATTATT
* * * *
5336365 TTATTAAAATATAACTTTTTAATGGTTATATTATGAAAGG
1 TTATTAAAATATAACTTTTGAATAGCTATATTATAAAAGG
5336405 TTATT-AAATATAA-TTATTGAATAGCTATATTATAAAAG
1 TTATTAAAATATAACTT-TTGAATAGCTATATTATAAAAG
5336443 TAAACAAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.06
39 26 0.79
40 5 0.15
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (40 bp):
TTATTAAAATATAACTTTTGAATAGCTATATTATAAAAGG
Found at i:5347509 original size:30 final size:30
Alignment explanation
Indices: 5347473--5347532 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
5347463 AGCCACCGCC
5347473 TGCATTGACTCAGGTCAACTTCAAGTGCAA
1 TGCATTGACTCAGGTCAACTTCAAGTGCAA
5347503 TGCATTGACTCAGGTCAACTTCAAGTGCAA
1 TGCATTGACTCAGGTCAACTTCAAGTGCAA
5347533 CTAAGTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (30 bp):
TGCATTGACTCAGGTCAACTTCAAGTGCAA
Found at i:5349133 original size:2 final size:2
Alignment explanation
Indices: 5349126--5349151 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5349116 CCTCCCTCCC
5349126 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
5349152 ATGTGCGTAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5350642 original size:14 final size:14
Alignment explanation
Indices: 5350622--5350665 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
5350612 ACATAACAAT
5350622 GTAATGTGA-TACA
1 GTAATGTGATTACA
*
5350635 GTTAATGTAATTACAA
1 G-TAATGTGATTAC-A
5350651 GTAATGTGATTACA
1 GTAATGTGATTACA
5350665 G
1 G
5350666 GGAAAATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 1 0.04
14 9 0.35
15 14 0.54
16 2 0.08
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (14 bp):
GTAATGTGATTACA
Found at i:5350864 original size:18 final size:16
Alignment explanation
Indices: 5350814--5350869 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 16
5350804 ATATAAGTTT
5350814 AATATATTATATTTTT-
1 AATATATTA-ATTTTTA
5350830 -AT-TATTAATTTTTA
1 AATATATTAATTTTTA
*
5350844 AATAATATTCATTTCTTA
1 AAT-ATATTAATTT-TTA
5350862 AATATATT
1 AATATATT
5350870 TTAAATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
13 6 0.18
14 5 0.15
15 4 0.12
17 13 0.38
18 6 0.18
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (16 bp):
AATATATTAATTTTTA
Found at i:5350967 original size:28 final size:28
Alignment explanation
Indices: 5350805--5351232 Score: 143
Period size: 29 Copynumber: 15.4 Consensus size: 28
5350795 ATTATTAAAA
* *
5350805 TATAAGTTTAATATATTATATTTT-TAT
1 TATAATTTTAATATAATATATTTTATAT
5350832 TATTAATTTTTAA-ATAATATTCATTTCT-TA-
1 TA-TAA-TTTTAATATAATA-T-ATTT-TATAT
*
5350862 AATATATTTTAA-ATATATATATTTTAT-T
1 TATA-ATTTTAATATA-ATATATTTTATAT
* *
5350890 T-T-A-TTTATTATTATAATATTTTATAT
1 TATAATTTTAATATAAT-ATATTTTATAT
* * *
5350916 TTTATTTTTAATATATTTATATTTTATAT
1 TATAATTTTAATATA-ATATATTTTATAT
*
5350945 TATAATTTT-ATATAATATCATTTCT-TAA
1 TATAATTTTAATATAATAT-ATTT-TATAT
* *
5350973 TAT-ATTTTAATGTCATATA-TTTAT-T
1 TATAATTTTAATATAATATATTTTATAT
* *
5350998 T-T-A-TTTATTATTATAATATTTTATAT
1 TATAATTTTAATATAAT-ATATTTTATAT
* * * *
5351024 TTTATTTTTAATATATTATATTATATAT
1 TATAATTTTAATATAATATATTTTATAT
*
5351052 TATTAATTTT-ATATAATATCATATTT-TAAA
1 TA-TAATTTTAATATAATAT-AT-TTTAT-AT
* * * *
5351082 TATATTTTTAATGTCATATATTTTTTATT
1 TATAATTTTAATATAATATATTTTATA-T
* * *
5351111 TATTTATATTATAATTTTATATATTTTAT-T
1 TA--TA-ATTTTAATATAATATATTTTATAT
* *
5351141 T-TCATTTCTTAA-AT-ATATTTTTTATAT
1 TAT-AATT-TTAATATAATATATTTTATAT
* * * * *
5351168 TATATATTTTATTTTAATTTGTTTTATCT
1 TATA-ATTTTAATATAATATATTTTATAT
* *
5351197 ATATTATTATAATATAA-AT-TTTTATAT
1 -TATAATTTTAATATAATATATTTTATAT
*
5351224 T-TTATTTTA
1 TATAATTTTA
5351233 TTTTAATTTT
Statistics
Matches: 301, Mismatches: 56, Indels: 90
0.67 0.13 0.20
Matches are distributed among these distances:
23 8 0.03
24 11 0.04
25 26 0.09
26 18 0.06
27 32 0.11
28 66 0.22
29 91 0.30
30 27 0.09
31 5 0.02
32 17 0.06
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (28 bp):
TATAATTTTAATATAATATATTTTATAT
Found at i:5351033 original size:108 final size:110
Alignment explanation
Indices: 5350811--5351142 Score: 500
Period size: 108 Copynumber: 3.0 Consensus size: 110
5350801 AAAATATAAG
*
5350811 TTTAATATATTATATTTT-TATTATTAATTTTTAAATAATATTCATTTCTTAAATATATTTTAAA
1 TTTAATATATTATATTTTATATTATTAA-TTTTATATAATA-TCATTTCTTAAATATATTTT-AA
*
5350875 TAT-ATATATTTTATTTTATTTATTATTATAATATTTTATATTTTATT
63 TGTCATATATTTTATTTTATTTATTATTATAATATTTTATATTTTATT
5350922 TTTAATATATTTATATTTTATATTA-TAATTTTATATAATATCATTTCTT-AATATATTTTAATG
1 TTTAATATA-TTATATTTTATATTATTAATTTTATATAATATCATTTCTTAAATATATTTTAATG
5350985 TCATATA-TTTATTTTATTTATTATTATAATATTTTATATTTTATT
65 TCATATATTTTATTTTATTTATTATTATAATATTTTATATTTTATT
*
5351030 TTTAATATATTATATTATATATTATTAATTTTATATAATATCATATT-TTAAATATATTTTTAAT
1 TTTAATATATTATATTTTATATTATTAATTTTATATAATATCAT-TTCTTAAATATA-TTTTAAT
*
5351094 GTCATATATTTTTTATTTATTTA-TATTATAAT-TTTATATATTTTATT
64 GTCATATATTTTAT-TTTATTTATTATTATAATATTT-TATATTTTATT
5351141 TT
1 TT
5351143 CATTTCTTAA
Statistics
Matches: 207, Mismatches: 4, Indels: 20
0.90 0.02 0.09
Matches are distributed among these distances:
107 14 0.07
108 72 0.35
109 23 0.11
110 27 0.13
111 46 0.22
112 20 0.10
113 5 0.02
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (110 bp):
TTTAATATATTATATTTTATATTATTAATTTTATATAATATCATTTCTTAAATATATTTTAATGT
CATATATTTTATTTTATTTATTATTATAATATTTTATATTTTATT
Found at i:5351075 original size:26 final size:26
Alignment explanation
Indices: 5350940--5351075 Score: 82
Period size: 26 Copynumber: 5.1 Consensus size: 26
5350930 ATTTATATTT
5350940 TATATTA-TAATTTTATATAATATCA
1 TATATTATTAATTTTATATAATATCA
* * * * *
5350965 TTTCTTAATATATTTTAATGTCATAT-A
1 TATATTATTA-ATTTT-ATATAATATCA
* * **
5350992 TTTATT-TTATTTATTATTATAATATTT
1 TATATTATTAATT-TTA-TATAATATCA
* *
5351019 TATATT-TTATTTTTAATATATTATATTA
1 TATATTATTAATTTT-ATATA--ATATCA
5351047 TATATTATTAATTTTATATAATATCA
1 TATATTATTAATTTTATATAATATCA
5351073 TAT
1 TAT
5351076 TTTAAATATA
Statistics
Matches: 87, Mismatches: 14, Indels: 19
0.73 0.12 0.16
Matches are distributed among these distances:
25 8 0.09
26 26 0.30
27 23 0.26
28 23 0.26
29 7 0.08
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.60
Consensus pattern (26 bp):
TATATTATTAATTTTATATAATATCA
Found at i:5351128 original size:22 final size:20
Alignment explanation
Indices: 5351104--5351187 Score: 59
Period size: 21 Copynumber: 4.2 Consensus size: 20
5351094 GTCATATATT
*
5351104 TTTTATTTATTTATATTATAA
1 TTTTATATATTT-TATTATAA
* *
5351125 TTTTATATATTTTATTTTCAT
1 TTTTATATATTTTATTAT-AA
5351146 TTCTTAAATATATTTT-TTAT-A
1 TT-TT--ATATATTTTATTATAA
*
5351167 --TTATATATTTTATTTTAA
1 TTTTATATATTTTATTATAA
5351185 TTT
1 TTT
5351188 GTTTTATCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
16 9 0.18
17 3 0.06
18 3 0.06
20 6 0.12
21 14 0.29
22 2 0.04
23 3 0.06
24 9 0.18
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATATATTTTATTATAA
Found at i:5351133 original size:10 final size:9
Alignment explanation
Indices: 5350863--5351139 Score: 60
Period size: 9 Copynumber: 31.2 Consensus size: 9
5350853 CATTTCTTAA
5350863 ATATATTTT
1 ATATATTTT
* *
5350872 AAATATATAT
1 ATATAT-TTT
*
5350882 ATTTTATTTT
1 A-TATATTTT
*
5350892 ATTTATTATT
1 ATATATT-TT
5350902 ATA-ATATTT
1 ATATAT-TTT
5350911 -TATATTTT
1 ATATATTTT
*
5350919 AT-T-TTTA
1 ATATATTTT
5350926 ATATA-TTT
1 ATATATTTT
5350934 ATAT-TTTAT
1 ATATATTT-T
5350943 ATTATAATTTT
1 A-TAT-ATTTT
*
5350954 ATATA--AT
1 ATATATTTT
5350961 ATCAT-TTCTT
1 AT-ATATT-TT
5350971 AATATATTTT
1 -ATATATTTT
* *
5350981 A-ATGTCATAT
1 ATATAT--TTT
*
5350991 ATTTATTTT
1 ATATATTTT
*
5351000 ATTTATTATT
1 ATATATT-TT
5351010 ATA-ATATTT
1 ATATAT-TTT
5351019 -TATATTTT
1 ATATATTTT
*
5351027 AT-T-TTTA
1 ATATATTTT
*
5351034 ATATATTAT
1 ATATATTTT
*
5351043 ATTATATATT
1 A-TATATTTT
5351053 AT-TAATTTT
1 ATAT-ATTTT
*
5351062 ATATA--AT
1 ATATATTTT
5351069 ATCATATTTT
1 AT-ATATTTT
5351079 AAATATATTTT
1 --ATATATTTT
* *
5351090 -TA-ATGTC
1 ATATATTTT
5351097 ATATATTTT
1 ATATATTTT
5351106 -T-TA-TTT
1 ATATATTTT
* *
5351112 ATTTATATT
1 ATATATTTT
5351121 ATA-ATTTT
1 ATATATTTT
5351129 ATATATTTT
1 ATATATTTT
5351138 AT
1 AT
5351140 TTTCATTTCT
Statistics
Matches: 195, Mismatches: 31, Indels: 84
0.63 0.10 0.27
Matches are distributed among these distances:
6 3 0.02
7 22 0.11
8 45 0.23
9 63 0.32
10 39 0.20
11 18 0.09
12 5 0.03
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (9 bp):
ATATATTTT
Found at i:5351173 original size:72 final size:70
Alignment explanation
Indices: 5350973--5351177 Score: 172
Period size: 72 Copynumber: 2.9 Consensus size: 70
5350963 CATTTCTTAA
* * * * *
5350973 TATATTTTAATGTCATATA-TTTATTTT-ATTTATT-ATTATAATATTTTATATT-T-TATTTTT
1 TATATTATAATTTTATATATTTTATTTTCATTT-TTAAATAT-ATTTTTTATATTATATATTTTT
5351033 AATATAT
64 AATATAT
* * * *
5351040 TATATTATATATTATTA-AT-TTTATATAATATCATATTTTAAATATATTTTTAATGTCATATAT
1 TATATTATA-ATT-TTATATATTT-TAT--TTTCAT-TTTTAAATATATTTTTTATATTATATAT
* *
5351103 TTTTTATTTATT
60 TTTTAATATA-T
5351115 TATATTATAATTTTATATATTTTATTTTCATTTCTTAAATATATTTTTTATATTATATATTTT
1 TATATTATAATTTTATATATTTTATTTTCATTT-TTAAATATATTTTTTATATTATATATTTT
5351178 ATTTTAATTT
Statistics
Matches: 108, Mismatches: 15, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
67 8 0.07
68 6 0.06
69 5 0.05
71 4 0.04
72 43 0.40
73 10 0.09
74 19 0.18
75 13 0.12
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (70 bp):
TATATTATAATTTTATATATTTTATTTTCATTTTTAAATATATTTTTTATATTATATATTTTTAA
TATAT
Found at i:5351176 original size:35 final size:34
Alignment explanation
Indices: 5351046--5351182 Score: 100
Period size: 35 Copynumber: 3.9 Consensus size: 34
5351036 ATATTATATT
* * * *
5351046 ATATATTATTAATTTTATATAATATCATATTTTAA
1 ATATATTTTTAATATTATATATTTTCAT-TTTTAA
* * *
5351081 ATATATTTTTAATGTCATATATTTTTTATTTATTTATA
1 ATATATTTTTAATATTATATA-TTTTCA-TT-TTTA-A
* *
5351119 TTATAATTTTATATATT-T-TATTTTCATTTCTTAA
1 ATATATTTTTA-ATATTATATATTTTCATTT-TTAA
*
5351153 ATATATTTTTTATATTATATATTTT-ATTTT
1 ATATATTTTTAATATTATATATTTTCATTTT
5351183 AATTTGTTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 18
0.71 0.12 0.16
Matches are distributed among these distances:
33 6 0.08
34 15 0.19
35 29 0.36
36 9 0.11
37 7 0.09
38 11 0.14
39 3 0.04
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (34 bp):
ATATATTTTTAATATTATATATTTTCATTTTTAA
Found at i:5351218 original size:81 final size:85
Alignment explanation
Indices: 5351109--5351271 Score: 185
Period size: 81 Copynumber: 2.0 Consensus size: 85
5351099 ATATTTTTTA
* ** *
5351109 TTTATTTATATTATAATTTTATATA-TTTTAT-TTTCA-TTT-CTTAAATATATT-TT-TTATAT
1 TTTATCTATATTATAATAATATAAATTTTTATATTTCATTTTACTTAAAT-TATTATTCTTATAT
5351168 TATATATTTTATTTTAATTTGT
65 TATATA-TTTATTTTAATTTGT
* * * * *
5351190 TTTATCTATATTATTATAATATAAATTTTTATATTTTATTTTATTTTAATTTTTATTCTTATATT
1 TTTATCTATATTATAATAATATAAATTTTTATATTTCATTTTACTTAAATTATTATTCTTATATT
5351255 ATATATTTATTTTAATT
66 ATATATTTATTTTAATT
5351272 ATAATATTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
81 20 0.30
82 6 0.09
83 4 0.06
84 6 0.09
85 19 0.28
86 12 0.18
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (85 bp):
TTTATCTATATTATAATAATATAAATTTTTATATTTCATTTTACTTAAATTATTATTCTTATATT
ATATATTTATTTTAATTTGT
Found at i:5351234 original size:30 final size:31
Alignment explanation
Indices: 5351196--5351275 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 31
5351186 TTGTTTTATC
* * *
5351196 TATA-TTATTATAATATAAATTTTTATATTT
1 TATATTTATTTTAATATAAATTCTTATATTA
* **
5351226 TAT-TTTATTTTAATTTTTATTCTTATATTA
1 TATATTTATTTTAATATAAATTCTTATATTA
5351256 TATATTTATTTTAATTATAA
1 TATATTTATTTTAA-TATAA
5351276 TATTATAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
30 26 0.68
31 10 0.26
32 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (31 bp):
TATATTTATTTTAATATAAATTCTTATATTA
Found at i:5352240 original size:34 final size:34
Alignment explanation
Indices: 5352202--5352271 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
5352192 TTCCTCGGCT
*
5352202 TCACCTGCCAACCATTTCAAGTCTCCCTCGACCC
1 TCACCTCCCAACCATTTCAAGTCTCCCTCGACCC
* *
5352236 TCACCTCCCAACCATTTCAGGTCTCCCTCGGCCC
1 TCACCTCCCAACCATTTCAAGTCTCCCTCGACCC
5352270 TC
1 TC
5352272 CTTCCTCCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.17, C:0.49, G:0.10, T:0.24
Consensus pattern (34 bp):
TCACCTCCCAACCATTTCAAGTCTCCCTCGACCC
Found at i:5358787 original size:33 final size:33
Alignment explanation
Indices: 5358750--5358812 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
5358740 ATGTTACATT
* *
5358750 ATCATCAGTTATGATATATTAACATATCATATC
1 ATCATCAATTATAATATATTAACATATCATATC
* * *
5358783 ATCATTAATTATAATATTTTAGCATATCAT
1 ATCATCAATTATAATATATTAACATATCAT
5358813 GTGAATTCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.43
Consensus pattern (33 bp):
ATCATCAATTATAATATATTAACATATCATATC
Found at i:5358912 original size:30 final size:30
Alignment explanation
Indices: 5358878--5358935 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
5358868 ATCATAAAAC
* *
5358878 CTTATTTGATTTGAAATAAAAATATAAAGA
1 CTTATTTGACTTAAAATAAAAATATAAAGA
5358908 CTTATTTGACTTAAAATAAAAATATAAA
1 CTTATTTGACTTAAAATAAAAATATAAA
5358936 AATTTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (30 bp):
CTTATTTGACTTAAAATAAAAATATAAAGA
Found at i:5359168 original size:14 final size:14
Alignment explanation
Indices: 5359149--5359175 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5359139 TTGTTAAATT
5359149 TTTTTTATAAGTTC
1 TTTTTTATAAGTTC
5359163 TTTTTTATAAGTT
1 TTTTTTATAAGTT
5359176 ATAATTTTGG
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:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTTTATAAGTTC
Found at i:5367891 original size:2 final size:2
Alignment explanation
Indices: 5367886--5367926 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5367876 ATATAGATAT
5367886 AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG A
5367927 TGGATCTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5372890 original size:13 final size:13
Alignment explanation
Indices: 5372874--5372899 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5372864 GATAGATCCC
5372874 AAAAAACCCAAGT
1 AAAAAACCCAAGT
5372887 AAAAAACCCAAGT
1 AAAAAACCCAAGT
5372900 GTAGGTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.23, G:0.08, T:0.08
Consensus pattern (13 bp):
AAAAAACCCAAGT
Found at i:5379445 original size:28 final size:30
Alignment explanation
Indices: 5379408--5379469 Score: 92
Period size: 28 Copynumber: 2.1 Consensus size: 30
5379398 ATCATTAATC
* *
5379408 ATAAATATTTATTTAA-TTATAA-AAAAAT
1 ATAAAAATTTATTTAATTTAAAATAAAAAT
5379436 ATAAAAATTTATTTAATTTAAAATAAAAAT
1 ATAAAAATTTATTTAATTTAAAATAAAAAT
5379466 ATAA
1 ATAA
5379470 GAGCTTGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 15 0.50
29 5 0.17
30 10 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
ATAAAAATTTATTTAATTTAAAATAAAAAT
Found at i:5380076 original size:29 final size:29
Alignment explanation
Indices: 5380044--5380104 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
5380034 TCAACTAGAA
5380044 ATTAAATAGTCATATTCTCACTATATTTT
1 ATTAAATAGTCATATTCTCACTATATTTT
5380073 ATTAAATAGTCATATTCTCACTATATTTT
1 ATTAAATAGTCATATTCTCACTATATTTT
5380102 ATT
1 ATT
5380105 GAATGTACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.49
Consensus pattern (29 bp):
ATTAAATAGTCATATTCTCACTATATTTT
Found at i:5380702 original size:29 final size:30
Alignment explanation
Indices: 5380641--5380710 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
5380631 TTTATATTTT
* *
5380641 TAATTATATTATATAAATATAAAATATTAA
1 TAATTATATTAAATAAATATAAAATATAAA
*
5380671 TAATTATA-TAAATAAATAT-GAATATAACA
1 TAATTATATTAAATAAATATAAAATATAA-A
5380700 TAATTA-ATTAA
1 TAATTATATTAA
5380711 TTATATTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 7 0.20
29 20 0.57
30 8 0.23
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (30 bp):
TAATTATATTAAATAAATATAAAATATAAA
Found at i:5389921 original size:9 final size:9
Alignment explanation
Indices: 5389907--5389936 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
5389897 AATTATATAT
5389907 ATTTTTAAA
1 ATTTTTAAA
5389916 ATTTTTAAA
1 ATTTTTAAA
5389925 ATTTTTAAA
1 ATTTTTAAA
5389934 ATT
1 ATT
5389937 AAATTTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:5392048 original size:11 final size:10
Alignment explanation
Indices: 5392029--5392062 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
5392019 AAATAAATTC
5392029 TTATAATTAA
1 TTATAATTAA
5392039 TTATTAATTAA
1 TTA-TAATTAA
*
5392050 TTATCATTAA
1 TTATAATTAA
5392060 TTA
1 TTA
5392063 AAATATCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (10 bp):
TTATAATTAA
Found at i:5398686 original size:22 final size:22
Alignment explanation
Indices: 5398658--5398708 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
5398648 AGTTCTTATA
* *
5398658 TTTTTATTTTAAGTTAAATAAG
1 TTTTTATTTTAAATCAAATAAG
5398680 TTTTTATTTTAAATCAAATAAG
1 TTTTTATTTTAAATCAAATAAG
5398702 TTTTTAT
1 TTTTTAT
5398709 AATTAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (22 bp):
TTTTTATTTTAAATCAAATAAG
Found at i:5398687 original size:28 final size:26
Alignment explanation
Indices: 5398615--5398708 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 26
5398605 AATAAAATTC
* *
5398615 AAATAAGTCTTTATATTTTATTATGTT
1 AAATAAGTTTTTAT-TTTTATTAAGTT
*
5398642 CAATCAAGTTCTTATATTTTTATTTTAAGTT
1 AAAT-AAGTT-TT-TATTTTTA--TTAAGTT
*
5398673 AAATAAGTTTTTA-TTTTA--AA-TC
1 AAATAAGTTTTTATTTTTATTAAGTT
5398695 AAATAAGTTTTTAT
1 AAATAAGTTTTTAT
5398709 AATTAATAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
22 14 0.25
23 2 0.04
27 8 0.14
28 6 0.11
29 9 0.16
30 8 0.14
31 9 0.16
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.53
Consensus pattern (26 bp):
AAATAAGTTTTTATTTTTATTAAGTT
Found at i:5400202 original size:55 final size:55
Alignment explanation
Indices: 5400091--5400248 Score: 208
Period size: 55 Copynumber: 2.9 Consensus size: 55
5400081 CCAAGTGGAG
* *
5400091 TTATGTTGAAAAGTTAATTATTACACGCTATATTAAAATAATATAATTATTATATA
1 TTATGTTGAAAATTTAATTATTACACGCTATGTTAAAA-AATATAATTATTATATA
* * * * *
5400147 TTATGTTAAAAATTTAGTTATTACACGTTATGTTGAAAAATATATTTATTATATA
1 TTATGTTGAAAATTTAATTATTACACGCTATGTTAAAAAATATAATTATTATATA
* * * *
5400202 TTATATTGAAGATTTAATTGTTACACGCTATGTTAAAAAATTTAATT
1 TTATGTTGAAAATTTAATTATTACACGCTATGTTAAAAAATATAATT
5400249 GTTACAAGTT
Statistics
Matches: 86, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
55 54 0.63
56 32 0.37
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (55 bp):
TTATGTTGAAAATTTAATTATTACACGCTATGTTAAAAAATATAATTATTATATA
Found at i:5400205 original size:28 final size:28
Alignment explanation
Indices: 5400130--5400211 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 28
5400120 ATATTAAAAT
5400130 AATATAATTATTATATATTATGTT-AAA
1 AATATAATTATTATATATTATGTTGAAA
* * * **
5400157 AATTTAGTTATTACACGTTATGTTGAAA
1 AATATAATTATTATATATTATGTTGAAA
* *
5400185 AATATATTTATTATATATTATATTGAA
1 AATATAATTATTATATATTATGTTGAA
5400212 GATTTAATTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 19 0.44
28 24 0.56
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (28 bp):
AATATAATTATTATATATTATGTTGAAA
Found at i:5400268 original size:28 final size:28
Alignment explanation
Indices: 5400213--5400269 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
5400203 TATATTGAAG
* **
5400213 ATTTAATTGTTACACGCTATGTTAAAAA
1 ATTTAATTGTTACAAGCTATCATAAAAA
* *
5400241 ATTTAATTGTTACAAGTTATCATGAAAA
1 ATTTAATTGTTACAAGCTATCATAAAAA
5400269 A
1 A
5400270 GTTGTTGCGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.39
Consensus pattern (28 bp):
ATTTAATTGTTACAAGCTATCATAAAAA
Found at i:5402390 original size:2 final size:2
Alignment explanation
Indices: 5402383--5402412 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5402373 TGCTTCAAAC
5402383 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
5402413 TTGAAAAGCT
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:5411500 original size:22 final size:20
Alignment explanation
Indices: 5411456--5411502 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
5411446 TGGTTTATTA
* *
5411456 TTTATTTTTAAATAATTATT
1 TTTATTATTAAATAATTAAT
5411476 TTTATTATTAATATAAATTAAT
1 TTTATTATTAA-AT-AATTAAT
5411498 TTTAT
1 TTTAT
5411503 ATTTTATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 2 0.09
22 11 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTATTAAATAATTAAT
Found at i:5416234 original size:2 final size:2
Alignment explanation
Indices: 5416229--5416263 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5416219 TTAGAAACAG
*
5416229 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5416264 GCTTTTGGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5421234 original size:12 final size:11
Alignment explanation
Indices: 5421212--5421255 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
5421202 AATATTCATT
5421212 TTTTAATTTATA
1 TTTT-ATTTATA
5421224 TTATTATTTAT-
1 TT-TTATTTATA
*
5421235 TTTTATTTTTA
1 TTTTATTTATA
5421246 TTTTATTTAT
1 TTTTATTTAT
5421256 TCATATATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 7 0.25
11 11 0.39
12 8 0.29
13 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTATTTATA
Found at i:5421236 original size:24 final size:22
Alignment explanation
Indices: 5421204--5421256 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
5421194 TCACACTTAA
*
5421204 TATTCATTTTTTAATTTATATTAT
1 TATTTATTTTTT-ATTTATATT-T
*
5421228 TATTTA-TTTTTATTTTTATTT
1 TATTTATTTTTTATTTATATTT
5421249 TATTTATT
1 TATTTATT
5421257 CATATATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 7 0.27
22 9 0.35
23 5 0.19
24 5 0.19
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TATTTATTTTTTATTTATATTT
Found at i:5421241 original size:16 final size:17
Alignment explanation
Indices: 5421203--5421255 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
5421193 ATCACACTTA
5421203 ATATTCATT-TTTTAATTT
1 ATATT-ATTATTTT-ATTT
5421221 ATATTATTA-TTTATTT
1 ATATTATTATTTTATTT
* *
5421237 TTATTTTTATTTTATTT
1 ATATTATTATTTTATTT
5421254 AT
1 AT
5421256 TCATATATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 11 0.37
17 14 0.47
18 5 0.17
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (17 bp):
ATATTATTATTTTATTT
Found at i:5422738 original size:22 final size:21
Alignment explanation
Indices: 5422687--5422738 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
5422677 CATGTTTATT
*
5422687 TATTAATATTTTAAATTATCA
1 TATTAATATTTTAAATTATAA
* **
5422708 TTTTAAATATTTTTTATTATTAA
1 TATT-AATATTTTAAATTA-TAA
5422731 TATTAATA
1 TATTAATA
5422739 AGATTTATCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 3 0.12
22 16 0.67
23 5 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTAATATTTTAAATTATAA
Found at i:5424196 original size:2 final size:2
Alignment explanation
Indices: 5424189--5424216 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5424179 ACTCAGAAGG
5424189 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5424217 AGTAGGAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5426328 original size:2 final size:2
Alignment explanation
Indices: 5426321--5426348 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5426311 CAGAACTTTG
5426321 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
5426349 TGTAATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5442515 original size:2 final size:2
Alignment explanation
Indices: 5442510--5442543 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5442500 AAGAAAAAAG
5442510 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5442544 AGATTAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5454859 original size:23 final size:22
Alignment explanation
Indices: 5454833--5454884 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
5454823 TGAAAAAATT
* *
5454833 AAAATATTTTTTTATTAATTTAA
1 AAAATATTATTATATT-ATTTAA
*
5454856 AAAATTATTATTATATTTTTTAA
1 AAAA-TATTATTATATTATTTAA
5454879 AAAATA
1 AAAATA
5454885 AAAAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 2 0.08
23 13 0.52
24 10 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AAAATATTATTATATTATTTAA
Found at i:5455910 original size:2 final size:2
Alignment explanation
Indices: 5455899--5455929 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5455889 CTTAAAAATG
5455899 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5455930 AAACAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5458334 original size:92 final size:92
Alignment explanation
Indices: 5458175--5458352 Score: 284
Period size: 92 Copynumber: 1.9 Consensus size: 92
5458165 GAATCATTAG
* * * * *
5458175 CATGGTAGAATATTTGGTTAGATAAACGTTGGAGAGTCATCAGCATGTAGAGTTTGAGTTTAGGG
1 CATGGTAGAATATTTGGTTAGATAAACATTGAAGAGTCATCAGCATATAGAGTTTGAGTTAAAGG
*
5458240 TTAATCAAAGGATGAGGCTAACATCAA
66 TTAATCAAAGGATAAGGCTAACATCAA
*
5458267 CATGGTAGAATATTTGGTTAGATAGACATTGAAGAGTCATCAGCATATAGAGTTTGAGTTAAAGG
1 CATGGTAGAATATTTGGTTAGATAAACATTGAAGAGTCATCAGCATATAGAGTTTGAGTTAAAGG
*
5458332 TTAATCAAAGGCTAAGGCTAA
66 TTAATCAAAGGATAAGGCTAA
5458353 GAAATGTTGG
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 78 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (92 bp):
CATGGTAGAATATTTGGTTAGATAAACATTGAAGAGTCATCAGCATATAGAGTTTGAGTTAAAGG
TTAATCAAAGGATAAGGCTAACATCAA
Found at i:5470695 original size:9 final size:9
Alignment explanation
Indices: 5470675--5470717 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
5470665 TGTTGCTGCA
*
5470675 GCTGCTGCT
1 GCTGCTGTT
5470684 GCTGCTGTT
1 GCTGCTGTT
*
5470693 GCTGTTGTT
1 GCTGCTGTT
* *
5470702 GTTGTTGTT
1 GCTGCTGTT
5470711 GCTGCTG
1 GCTGCTG
5470718 CTGATGTTGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.00, C:0.19, G:0.35, T:0.47
Consensus pattern (9 bp):
GCTGCTGTT
Found at i:5471609 original size:86 final size:85
Alignment explanation
Indices: 5471438--5471671 Score: 310
Period size: 86 Copynumber: 2.8 Consensus size: 85
5471428 AAAGCTGTCT
** *
5471438 AAACATCTTAGATAAGA-TCTAATTCTGCCAAGGTGCACTATGAAAAAAGTTTATCAAATGATAT
1 AAACATCTTAGATAAGATTCTAATTCTGCCAAGGTGCACTATGAAAAAAGTTTATCAAACAATAC
*
5471502 AAATGGCTGTTTATTCACAA
66 AAATGGCCGTTTATTCACAA
* *
5471522 AAACATCTTTGATAAGATTCTATTTCTGCCAAGGTGCACTATGGAAAAAAGTTTATCAAACAATA
1 AAACATCTTAGATAAGATTCTAATTCTGCCAAGGTGCACTAT-GAAAAAAGTTTATCAAACAATA
* * *
5471587 CGAATGGCCGTTTTTTCTCAA
65 CAAATGGCCGTTTATTCACAA
* * * * *
5471608 AAATATCTTAAACAAGATTCTAATTCTGCCAAGGTGCATTA-CAAAAAACGTTTATCAAACAATA
1 AAACATCTTAGATAAGATTCTAATTCTGCCAAGGTGCACTATGAAAAAA-GTTTATCAAACAATA
5471672 TGAAAGGCTA
Statistics
Matches: 131, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
84 22 0.17
85 38 0.29
86 71 0.54
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (85 bp):
AAACATCTTAGATAAGATTCTAATTCTGCCAAGGTGCACTATGAAAAAAGTTTATCAAACAATAC
AAATGGCCGTTTATTCACAA
Found at i:5474935 original size:10 final size:10
Alignment explanation
Indices: 5474922--5474946 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5474912 CCAAAAAACT
5474922 AAAAAATTAA
1 AAAAAATTAA
5474932 AAAAAATTAA
1 AAAAAATTAA
5474942 AAAAA
1 AAAAA
5474947 GAAGAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:5476355 original size:33 final size:33
Alignment explanation
Indices: 5476313--5476378 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
5476303 TATCTCTATT
5476313 CAGTATATAACTTGTAGATTCAAGATGAGTTAC
1 CAGTATATAACTTGTAGATTCAAGATGAGTTAC
5476346 CAGTATATAACTTGTAGATTCAAGATGAGTTAC
1 CAGTATATAACTTGTAGATTCAAGATGAGTTAC
5476379 TCCTATTCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (33 bp):
CAGTATATAACTTGTAGATTCAAGATGAGTTAC
Found at i:5495708 original size:23 final size:22
Alignment explanation
Indices: 5495663--5495724 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
5495653 ATACCTTTTC
*
5495663 TTTTT-ATTTTGTTCTGTTGCCCT
1 TTTTTCATTTTGTTC--TTCCCCT
*
5495686 TTTTTCAATTTTTTTCTTCCCCT
1 TTTTTC-ATTTTGTTCTTCCCCT
5495709 TTTTTCATTTTGTTCT
1 TTTTTCATTTTGTTCT
5495725 CTTCTTTCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 9 0.26
23 17 0.50
25 8 0.24
ACGTcount: A:0.06, C:0.19, G:0.06, T:0.68
Consensus pattern (22 bp):
TTTTTCATTTTGTTCTTCCCCT
Found at i:5521511 original size:28 final size:27
Alignment explanation
Indices: 5521480--5521535 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
5521470 TATCATGGCC
*
5521480 TATAAGAATTAAATTTTTTAATATGATA
1 TATAAGAATTAAATTTTTCAATAT-ATA
* *
5521508 TATAATAATTATATTTTTCAATATATA
1 TATAAGAATTAAATTTTTCAATATATA
5521535 T
1 T
5521536 CGAGTGTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (27 bp):
TATAAGAATTAAATTTTTCAATATATA
Found at i:5524663 original size:3 final size:3
Alignment explanation
Indices: 5524657--5524683 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5524647 CATCATCATC
5524657 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
5524684 TTGTAATCCT
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:5524819 original size:62 final size:62
Alignment explanation
Indices: 5524719--5524842 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
5524709 AGTGTGCAAA
5524719 TTTCTCTAACCTCATGAAACTAGAAGCTAGAACCGTAACATTGGAATGGGTGGATTATCATG
1 TTTCTCTAACCTCATGAAACTAGAAGCTAGAACCGTAACATTGGAATGGGTGGATTATCATG
*
5524781 TTTCTCTAACCTCATGAAACTAGAAGCTAGAACTGTAACATTGGAATGGGTGGATTATCATG
1 TTTCTCTAACCTCATGAAACTAGAAGCTAGAACCGTAACATTGGAATGGGTGGATTATCATG
5524843 GCAATTTTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (62 bp):
TTTCTCTAACCTCATGAAACTAGAAGCTAGAACCGTAACATTGGAATGGGTGGATTATCATG
Found at i:5528679 original size:2 final size:2
Alignment explanation
Indices: 5528672--5528707 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5528662 TTGGACTATG
*
5528672 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5528708 ACATTCATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5539682 original size:5 final size:6
Alignment explanation
Indices: 5539640--5539681 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
5539630 GCCTAAAAAG
*
5539640 CTTTTT CTTTTT CTTTTT CTTTTT -TCATTT CATTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CT-TTTT C-TTTTT CTTTT
5539682 CATGAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
5 1 0.03
6 25 0.81
7 4 0.13
8 1 0.03
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:5547084 original size:2 final size:2
Alignment explanation
Indices: 5547079--5547106 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5547069 TTTCTGTGTG
5547079 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5547107 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5547111 original size:2 final size:2
Alignment explanation
Indices: 5547106--5547139 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5547096 ATATATATAT
5547106 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5547140 CCCAAAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5553287 original size:2 final size:2
Alignment explanation
Indices: 5553276--5553315 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
5553266 CATGCATGCG
5553276 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5553316 ATCACAGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5564541 original size:13 final size:13
Alignment explanation
Indices: 5564523--5564560 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5564513 CCACATATGG
5564523 GGAAAAA-AAGGAA
1 GGAAAAAGAA-GAA
5564536 GGAAAAAGAAGAA
1 GGAAAAAGAAGAA
*
5564549 AGAAAAAGAAGA
1 GGAAAAAGAAGA
5564561 TCAATAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 21 0.91
14 2 0.09
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
GGAAAAAGAAGAA
Found at i:5571374 original size:39 final size:39
Alignment explanation
Indices: 5571316--5571391 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
5571306 TGGTTAGCTG
5571316 CTTTAGTTTCTTGGATCTGCTTTGCATTTCAATTCCATA
1 CTTTAGTTTCTTGGATCTGCTTTGCATTTCAATTCCATA
*
5571355 CTTTAGTTTCTTGGGTCTGCTTTGCATTTCAATTCCA
1 CTTTAGTTTCTTGGATCTGCTTTGCATTTCAATTCCA
5571392 ATCAATTTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.16, C:0.21, G:0.14, T:0.49
Consensus pattern (39 bp):
CTTTAGTTTCTTGGATCTGCTTTGCATTTCAATTCCATA
Found at i:5576959 original size:251 final size:246
Alignment explanation
Indices: 5576603--5577072 Score: 576
Period size: 251 Copynumber: 1.9 Consensus size: 246
5576593 ATTAAGTAAA
* * * * *
5576603 AATTTTAATATAAATAAATATTTAAATTTATTTAATCAAGTTAAAAGTATTTAACAATATATAAA
1 AATTTTAATAAAAATAAATATTTAAATTTATTTAACCAAGCTAAAAATATGTAACAATATATAAA
* * *
5576668 TTTTGATTTTAAATAAAAAATAAGAATAAAAATGATTATAGTTCAAAATTGA-TA-TAAAAAAGT
66 TTTTGATTTTAAATAAAAAATAAAAATAAAAATAATTATAGTTAAAAATT-ACTATTAAAAAAG-
* * ** ** * *
5576731 TTTAACGCAAAATTATAAGAATTGAA-GTAAAA-ACTTATAAAGTTGGAATAATTAAATTTTAAA
129 TTTAACACAAAATTATAAAAATT-AACGTAAAATA-TTATAAAAATAAAATAAATAAATTTAAAA
*
5576794 TTTTAACGTAAATGTGTGTGAGTTAATATAATAAGTTAATTAAGTAAAAAAATTT
192 TTTTAACGTAAATGTGTGGGAGTTAATATAATAAGTTAATTAAGTAAAAAAATTT
*
5576849 AATTTTAATAAAAAATAAATATTTATAA-TTATATT-ACC-AGACTAAAAATATGTAACGATATA
1 AATTTTAAT-AAAAATAAATATTTA-AATTTAT-TTAACCAAG-CTAAAAATATGTAACAATATA
* *
5576911 TAACTTTTTATTTTTAAATAAAAAATAATAAAAATAAAAATAATTATAGTTAAAAATTACTATTA
62 TAAATTTTGA-TTTTAAAT--AAAA-AATAAAAATAAAAATAATTATAGTTAAAAATTACTATTA
* * *
5576976 AAAAAGTTTGACATAAAATTGTAAAAATTAACGTAAAATATTATAAAAATAAAATAAATAAATTT
123 AAAAAGTTTAACACAAAATTATAAAAATTAACGTAAAATATTATAAAAATAAAATAAATAAATTT
5577041 AAAATTTTAACGTAAATGTGTGGGAGTTAATA
188 AAAATTTTAACGTAAATGTGTGGGAGTTAATA
5577073 AGTGATAATA
Statistics
Matches: 189, Mismatches: 23, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
246 11 0.06
247 45 0.24
248 12 0.06
250 7 0.04
251 105 0.56
252 9 0.05
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.36
Consensus pattern (246 bp):
AATTTTAATAAAAATAAATATTTAAATTTATTTAACCAAGCTAAAAATATGTAACAATATATAAA
TTTTGATTTTAAATAAAAAATAAAAATAAAAATAATTATAGTTAAAAATTACTATTAAAAAAGTT
TAACACAAAATTATAAAAATTAACGTAAAATATTATAAAAATAAAATAAATAAATTTAAAATTTT
AACGTAAATGTGTGGGAGTTAATATAATAAGTTAATTAAGTAAAAAAATTT
Found at i:5597224 original size:17 final size:16
Alignment explanation
Indices: 5597196--5597250 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
5597186 ATTAAAAATA
5597196 AAAATT-ATAATTTAT
1 AAAATTAATAATTTAT
* *
5597211 ATAATATAATAATTTTT
1 AAAAT-TAATAATTTAT
* *
5597228 AAAATTAATAAATAAT
1 AAAATTAATAATTTAT
5597244 AAAATTA
1 AAAATTA
5597251 TTTAAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 4 0.12
16 16 0.50
17 12 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATTAATAATTTAT
Found at i:5597254 original size:45 final size:48
Alignment explanation
Indices: 5597183--5597289 Score: 111
Period size: 45 Copynumber: 2.4 Consensus size: 48
5597173 AGGAGAGAAA
* * *
5597183 AAAATTAA-AAATAA-AAATTATAATTTATATAATATAAT-A-ATTTTT
1 AAAATTAATAAATAATAAA-TATAATTTAAAAAATATAATCACATTATT
* *
5597228 AAAATTAATAAATAATAAA-ATTATTTAAAAAATATTATCACATTATT
1 AAAATTAATAAATAATAAATATAATTTAAAAAATATAATCACATTATT
5597275 -AAATTAATAAA-AATA
1 AAAATTAATAAATAATA
5597290 TTAATAATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
45 27 0.51
46 18 0.34
47 8 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (48 bp):
AAAATTAATAAATAATAAATATAATTTAAAAAATATAATCACATTATT
Found at i:5598070 original size:16 final size:16
Alignment explanation
Indices: 5598049--5598079 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5598039 CACTTATTAA
*
5598049 AAATTTATTTTAATTC
1 AAATTTATTTAAATTC
5598065 AAATTTATTTAAATT
1 AAATTTATTTAAATT
5598080 TTGATGTATT
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:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATTTATTTAAATTC
Found at i:5598464 original size:10 final size:10
Alignment explanation
Indices: 5598451--5598475 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5598441 AAAAAAGGAC
5598451 AAAAAAAAAG
1 AAAAAAAAAG
5598461 AAAAAAAAAG
1 AAAAAAAAAG
5598471 AAAAA
1 AAAAA
5598476 GAAACTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:5609872 original size:23 final size:23
Alignment explanation
Indices: 5609846--5609893 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
5609836 ATCCATGCTT
*
5609846 TTGTTTTACGACTAGTCACTGTA
1 TTGTTTTACGACTAGTCAATGTA
5609869 TTGTTTTACGACTAGTCAATGTA
1 TTGTTTTACGACTAGTCAATGTA
5609892 TT
1 TT
5609894 ATCATTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.46
Consensus pattern (23 bp):
TTGTTTTACGACTAGTCAATGTA
Found at i:5610463 original size:2 final size:2
Alignment explanation
Indices: 5610458--5610487 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5610448 TGTGTGTGTG
*
5610458 TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5610488 CCCATTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:5611930 original size:3 final size:3
Alignment explanation
Indices: 5611922--5611954 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5611912 TTAACCACTA
5611922 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5611955 ACTACATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:5647598 original size:58 final size:58
Alignment explanation
Indices: 5647533--5647645 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
5647523 CCTTCAATGA
* *
5647533 AAGGAAGTAGCAAAAGGACAAGCAACG-CTCTCATACTTTTGTAAGCTCATCCAATATT
1 AAGGAAGTAGCAAAAGGACAAGCAACGCCT-TCATACTCTGGTAAGCTCATCCAATATT
* * * *
5647591 AAGGAAGTAGCAAAAGGATAGGCAATGCCTTCATGCTCTGGTAAGCTCATCCAAT
1 AAGGAAGTAGCAAAAGGACAAGCAACGCCTTCATACTCTGGTAAGCTCATCCAAT
5647646 TATAAGAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 46 0.96
59 2 0.04
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (58 bp):
AAGGAAGTAGCAAAAGGACAAGCAACGCCTTCATACTCTGGTAAGCTCATCCAATATT
Found at i:5648920 original size:2 final size:2
Alignment explanation
Indices: 5648913--5648950 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5648903 CAAAAATACA
*
5648913 AT AT AT AT AA 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
5648951 CCACAACCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5668289 original size:18 final size:18
Alignment explanation
Indices: 5668261--5668302 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5668251 TGCTTTGAAC
5668261 TAATTATTATCAT-TTCT
1 TAATTATTATCATCTTCT
*
5668278 TAATTGATTATCATCTTTT
1 TAATT-ATTATCATCTTCT
5668297 TAATTA
1 TAATTA
5668303 AAACCATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 9 0.41
19 8 0.36
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (18 bp):
TAATTATTATCATCTTCT
Found at i:5669589 original size:23 final size:24
Alignment explanation
Indices: 5669549--5669609 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
5669539 TAAAAAATAT
* *
5669549 TTTTTATTTAATAAAATATAAAA-A
1 TTTTAATTAAATAAAATA-AAAAGA
*
5669573 -TTTAATTAAATATAATAAAAAGA
1 TTTTAATTAAATAAAATAAAAAGA
*
5669596 TTTTATTTAAATAA
1 TTTTAATTAAATAA
5669610 TTTCAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 4 0.13
23 15 0.50
24 11 0.37
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TTTTAATTAAATAAAATAAAAAGA
Found at i:5674611 original size:64 final size:64
Alignment explanation
Indices: 5674495--5674621 Score: 159
Period size: 64 Copynumber: 2.0 Consensus size: 64
5674485 TTTCTTATCA
* * * *
5674495 ATCAAAGGGATGAAATTCGTCGTGCTTATTTCAAATGTGAGTAATGTCAACTCATTCTTAAGAC
1 ATCAAAGGGAGGAAATTCATCGTGCTTATCTCAAACGTGAGTAATGTCAACTCATTCTTAAGAC
* * *
5674559 ATCAAAGGGGGGAAATTCATCGTGTTTATCTCAAACGT-AG-ACCATGTTAACTCATTCTTAAGA
1 ATCAAAGGGAGGAAATTCATCGTGCTTATCTCAAACGTGAGTA--ATGTCAACTCATTCTTAAGA
5674622 AGTATCCTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 2 0.04
64 51 0.94
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (64 bp):
ATCAAAGGGAGGAAATTCATCGTGCTTATCTCAAACGTGAGTAATGTCAACTCATTCTTAAGAC
Found at i:5677508 original size:47 final size:47
Alignment explanation
Indices: 5677451--5677562 Score: 134
Period size: 47 Copynumber: 2.4 Consensus size: 47
5677441 TGCTTTTAAG
* **
5677451 TAATTTTCTTGCGGTCACAGCCAAACTATACACAAGATACTTTGATT
1 TAATTTTCTTGCAGTCACAGCCAAACTATACACAAGATACACTGATT
* * * * * *
5677498 TACTTTTCTTGCAGTCACTGCCGAAGTATACCCATGATACACTGATT
1 TAATTTTCTTGCAGTCACAGCCAAACTATACACAAGATACACTGATT
*
5677545 TAATTTTGTTGCAGTCAC
1 TAATTTTCTTGCAGTCAC
5677563 CTACAAATGT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (47 bp):
TAATTTTCTTGCAGTCACAGCCAAACTATACACAAGATACACTGATT
Found at i:5683819 original size:22 final size:23
Alignment explanation
Indices: 5683794--5683840 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
5683784 ATTTATATAT
* *
5683794 ATTTTTTTATTTAG-ATGTTTTA
1 ATTTTATTAATTAGAATGTTTTA
5683816 ATTTTATTAATTAGAAATGTTTTA
1 ATTTTATTAATTAG-AATGTTTTA
5683840 A
1 A
5683841 AATTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
24 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (23 bp):
ATTTTATTAATTAGAATGTTTTA
Found at i:5695578 original size:5 final size:5
Alignment explanation
Indices: 5695568--5695597 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
5695558 GATAGACAAG
5695568 GAAAA GAAAA GAAAA GAAAA GAAAAA GAAA
1 GAAAA GAAAA GAAAA GAAAA G-AAAA GAAA
5695598 GAATATGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:5695586 original size:15 final size:16
Alignment explanation
Indices: 5695568--5695597 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5695558 GATAGACAAG
5695568 GAAAAG-AAAAGAAAA
1 GAAAAGAAAAAGAAAA
5695583 GAAAAGAAAAAGAAA
1 GAAAAGAAAAAGAAA
5695598 GAATATGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
GAAAAGAAAAAGAAAA
Found at i:5710628 original size:225 final size:215
Alignment explanation
Indices: 5710249--5710869 Score: 846
Period size: 225 Copynumber: 2.8 Consensus size: 215
5710239 TTTAAACACG
* * * * * * * *
5710249 TTTGAAGTAACTTGGTGATGATTAAGTTGGTGTCTTCTTTATCAGGAGAGGATGGAAAGGAAAGG
1 TTTGAAGTAACATGATGATGTTTAAGTTGGTGTCTTCTTTATGAGGGGCGGA-GGGAAGGAAATG
* * *
5710314 TAAGTTCATGTTCGACATTCAACAATTAGTTGAACTTTGTTTGAGATTCTTATTGCATTTTTTTA
65 TAAGTTAATGTTAGACGTTCAACAATTAGTTGAACTTTGTTTGAGATTCTTATTGCATTTTTTTA
*
5710379 CATTGTAACTTTGTTGCAAAGATGATAGTACTAAGGACAACNNNNNNNNNNGCACATGCAGTTGT
130 CATTGTAACTTCGTTGCAAAGATGATAGTACTAAGGACAAC----------GCACATGCAGTTGT
5710444 CATGCTGTGATGTTAACGATGTTTAGACATT
185 CATGCTGTGATGTTAACGATGTTTAGACATT
* *
5710475 TTTGAAGTAACGTGATGATGTTTAAGTAGGTGTCTTCTTTATGAGGGGCGGAGGGAAGGAAATGT
1 TTTGAAGTAACATGATGATGTTTAAGTTGGTGTCTTCTTTATGAGGGGCGGAGGGAAGGAAATGT
*
5710540 AAGTTAATGTTAGACGTTCAACAATTAGTTGAACTTTGTTTGAGCTTCTTATTGCATTTTTTTAC
66 AAGTTAATGTTAGACGTTCAACAATTAGTTGAACTTTGTTTGAGATTCTTATTGCATTTTTTTAC
5710605 ATTGTAACTTCGTTGCAAAGATGATAGTACTAAGGACAACNNNNNNNNNNGCACATGCAGTTGTC
131 ATTGTAACTTCGTTGCAAAGATGATAGTACTAAGGACAAC----------GCACATGCAGTTGTC
*
5710670 ATGCTGTGATGTTAGCGATGTTTAGACATT
186 ATGCTGTGATGTTAACGATGTTTAGACATT
5710700 TTTGAAGTAACATGATGATGTTTAAGTTGGTGTCTTCTTTATGAGGGGCGGAGGGAAGGAAATGT
1 TTTGAAGTAACATGATGATGTTTAAGTTGGTGTCTTCTTTATGAGGGGCGGAGGGAAGGAAATGT
* *
5710765 AAGTTAATGTTTGACGTTCAACAATTAGTTGAACTTTGTTTGAGATTCTTATTGCATTTTTGTAC
66 AAGTTAATGTTAGACGTTCAACAATTAGTTGAACTTTGTTTGAGATTCTTATTGCATTTTTTTAC
* * * * *
5710830 ATTTTAACTTCATTGGAAAGATGACAGTAGTAAGGACAAC
131 ATTGTAACTTCGTTGCAAAGATGATAGTACTAAGGACAAC
5710870 ATGTAATTAT
Statistics
Matches: 370, Mismatches: 25, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
225 325 0.88
226 45 0.12
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.36
Consensus pattern (215 bp):
TTTGAAGTAACATGATGATGTTTAAGTTGGTGTCTTCTTTATGAGGGGCGGAGGGAAGGAAATGT
AAGTTAATGTTAGACGTTCAACAATTAGTTGAACTTTGTTTGAGATTCTTATTGCATTTTTTTAC
ATTGTAACTTCGTTGCAAAGATGATAGTACTAAGGACAACGCACATGCAGTTGTCATGCTGTGAT
GTTAACGATGTTTAGACATT
Found at i:5714537 original size:21 final size:21
Alignment explanation
Indices: 5714513--5714560 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
5714503 AACAGTTTAA
*
5714513 AATTACCAAGATATATCAAAT
1 AATTACCAAAATATATCAAAT
*
5714534 AATTAGCAAAATATATCAAAT
1 AATTACCAAAATATATCAAAT
5714555 AATTAC
1 AATTAC
5714561 TTACTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.29
Consensus pattern (21 bp):
AATTACCAAAATATATCAAAT
Found at i:5719353 original size:19 final size:20
Alignment explanation
Indices: 5719329--5719372 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
5719319 TTTGGCTTTT
5719329 TTAAATA-A-TTTAAATAAAA
1 TTAAATATATTTTAAA-AAAA
*
5719348 TTAAATATATTTTAGAAAAA
1 TTAAATATATTTTAAAAAAA
5719368 TTAAA
1 TTAAA
5719373 CAATGAGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 10 0.45
21 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TTAAATATATTTTAAAAAAA
Found at i:5721194 original size:67 final size:67
Alignment explanation
Indices: 5721086--5721220 Score: 211
Period size: 67 Copynumber: 2.0 Consensus size: 67
5721076 ATACAATTAA
*
5721086 ATATGGTTTTGTATGACAACATCTCTTTTATATTTGTATTTTTAACATTAAATTGTCACACACAC
1 ATATGGTTATGTATGACAACATCTCTTTTATATTTGTATTTTTAACATTAAATTGTCACACACAC
5721151 AC
66 AC
* *
5721153 ATATGGTTATGTGTGACAACATCAT-TTTTATA-TTGATATTTTTAACATTAAATTGTCACATAC
1 ATATGGTTATGTATGACAACATC-TCTTTTATATTTG-TATTTTTAACATTAAATTGTCACACAC
5721216 ACAC
64 ACAC
5721220 A
1 A
5721221 AGCATATATA
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
66 3 0.05
67 59 0.94
68 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (67 bp):
ATATGGTTATGTATGACAACATCTCTTTTATATTTGTATTTTTAACATTAAATTGTCACACACAC
AC
Found at i:5721229 original size:2 final size:2
Alignment explanation
Indices: 5721224--5721251 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5721214 ACACACAAGC
5721224 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
5721252 TACCACAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5722111 original size:28 final size:28
Alignment explanation
Indices: 5722073--5722132 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
5722063 AAAATATGTC
*
5722073 ATAAACAAATAAAATACACTAAATATAA
1 ATAAACAAATAAAATACACTAAACATAA
* * * *
5722101 ATAAGCAAATAAATTGCATTAAACATAA
1 ATAAACAAATAAAATACACTAAACATAA
5722129 ATAA
1 ATAA
5722133 CATTTCAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.63, C:0.10, G:0.03, T:0.23
Consensus pattern (28 bp):
ATAAACAAATAAAATACACTAAACATAA
Found at i:5726078 original size:15 final size:15
Alignment explanation
Indices: 5726058--5726126 Score: 93
Period size: 15 Copynumber: 4.6 Consensus size: 15
5726048 TTTACAATGC
* **
5726058 AATGTGATTACATGT
1 AATGTGATTGCAAAT
5726073 AATGTGATTGCAAAT
1 AATGTGATTGCAAAT
5726088 AATGTGATTGCAAAT
1 AATGTGATTGCAAAT
**
5726103 AATGTGATTGCAAGC
1 AATGTGATTGCAAAT
5726118 AATGTGATT
1 AATGTGATT
5726127 ACAGGGAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 49 1.00
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (15 bp):
AATGTGATTGCAAAT
Found at i:5726417 original size:23 final size:23
Alignment explanation
Indices: 5726345--5726418 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
5726335 TTTTAATGTC
*
5726345 ATATATTT-TATTTTCATTTATTA
1 ATATATTTATATTTTTA-TTATTA
* * *
5726368 TTATAATCTTAGATATTTTATTTTTA
1 ATAT-AT-TTATAT-TTTTATTATTA
5726394 ATATATTTATATTTTTATTATTA
1 ATATATTTATATTTTTATTATTA
5726417 AT
1 AT
5726419 TGTTATATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
23 15 0.38
24 7 0.17
25 4 0.10
26 10 0.25
27 4 0.10
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (23 bp):
ATATATTTATATTTTTATTATTA
Found at i:5726427 original size:23 final size:22
Alignment explanation
Indices: 5726361--5726427 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 22
5726351 TTTATTTTCA
* * *
5726361 TTTATTATTATAATCTTAGATAT
1 TTTATTATTA-ATTATTATATAT
*
5726384 TTTATTTTTAATATATT-TATATT
1 TTTATTATTAAT-TATTATATA-T
*
5726407 TTTATTATTAATTGTTATATA
1 TTTATTATTAATTATTATATA
5726428 ATATCATCTC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
22 7 0.20
23 28 0.80
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (22 bp):
TTTATTATTAATTATTATATAT
Found at i:5726482 original size:57 final size:56
Alignment explanation
Indices: 5726288--5726486 Score: 187
Period size: 57 Copynumber: 3.5 Consensus size: 56
5726278 TAGTATATTT
* * *
5726288 ATATTTTTTATTATTAATTT-TTATATAATACCATCTTTTAAATATATTTTTAATGTC
1 ATATATTTTATT-TTTATTTATTATATAATA-CATCTCTTAAATATATTTTTAATGTC
* * *
5726345 ATATATTTTATTTTCATTTATTAT-T-ATA-A--TCTTAGATATTTTATTTTTAATAT-
1 ATATATTTTATTTTTATTTATTATATAATACATCTCTTA-A-A-TATATTTTTAATGTC
* * *
5726398 ATTTATATTTTTATTATTAATTGTTATATAATATCATCTCTTAAATATATTTTTAATGTC
1 A--TATA-TTTTATTTTTATTTATTATATAATA-CATCTCTTAAATATATTTTTAATGTC
5726458 ATATATTTTATTTTTATTTATTATATAAT
1 ATATATTTTATTTTTATTTATTATATAAT
5726487 CTTATATATT
Statistics
Matches: 114, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
51 4 0.04
52 1 0.01
53 3 0.03
54 12 0.11
55 7 0.06
56 22 0.19
57 37 0.32
58 7 0.06
59 12 0.11
60 3 0.03
61 1 0.01
62 5 0.04
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (56 bp):
ATATATTTTATTTTTATTTATTATATAATACATCTCTTAAATATATTTTTAATGTC
Found at i:5726494 original size:32 final size:32
Alignment explanation
Indices: 5726458--5726541 Score: 107
Period size: 32 Copynumber: 2.6 Consensus size: 32
5726448 TTTTAATGTC
5726458 ATATATTTTATTTTTATTTATT-ATATAATCTT
1 ATATATTTTATTTTTATTTATTAATAT-ATCTT
* *
5726490 ATATATTTTATTTTTATTTTTTAATATATTTT
1 ATATATTTTATTTTTATTTATTAATATATCTT
* *
5726522 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
5726542 TAATTTGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
32 34 0.74
33 12 0.26
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (32 bp):
ATATATTTTATTTTTATTTATTAATATATCTT
Found at i:5726519 original size:12 final size:14
Alignment explanation
Indices: 5726488--5726592 Score: 58
Period size: 14 Copynumber: 7.6 Consensus size: 14
5726478 TTATATAATC
*
5726488 TTATATATTTTAT-
1 TTATATTTTTTATA
*
5726501 TTTTATTTTTTA-A
1 TTATATTTTTTATA
5726514 -TATATTTTTTATA
1 TTATATTTTTTATA
* *
5726527 TTATATATTTTATT
1 TTATATTTTTTATA
5726541 TTA-ATTTGTTT-TA
1 TTATATTT-TTTATA
* * * *
5726554 CCTATATTATATAAA
1 -TTATATTTTTTATA
*
5726569 TTTTAATTTTTTATA
1 TTAT-ATTTTTTATA
*
5726584 TTTTATTTT
1 TTATATTTT
5726593 ATTTTAATTT
Statistics
Matches: 68, Mismatches: 16, Indels: 15
0.69 0.16 0.15
Matches are distributed among these distances:
12 10 0.15
13 15 0.22
14 28 0.41
15 15 0.22
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.69
Consensus pattern (14 bp):
TTATATTTTTTATA
Found at i:5726521 original size:18 final size:17
Alignment explanation
Indices: 5726466--5726542 Score: 54
Period size: 17 Copynumber: 4.7 Consensus size: 17
5726456 TCATATATTT
*
5726466 TATTTTTATTTATTATA
1 TATTTTTATTTTTTATA
* * * *
5726483 TAATCTTATATATT-T-
1 TATTTTTATTTTTTATA
5726498 TATTTTTATTTTTTAATA
1 TATTTTTATTTTTT-ATA
* *
5726516 TATTTTT-TATATTATA
1 TATTTTTATTTTTTATA
5726532 TA-TTTTATTTT
1 TATTTTTATTTT
5726543 AATTTGTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 9
0.69 0.17 0.14
Matches are distributed among these distances:
15 14 0.31
16 8 0.18
17 16 0.36
18 7 0.16
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTTTATTTTTTATA
Found at i:5726529 original size:113 final size:114
Alignment explanation
Indices: 5726276--5726505 Score: 392
Period size: 113 Copynumber: 2.0 Consensus size: 114
5726266 AAAATACAAG
* * *
5726276 TTTAGTATATTTATATTTTTTATTATTAATTTTTATATAATACCATCTTTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTGTTATATAATACCATCTCTTAAATATATTTTTAA
5726341 TGTCATATATTTTATTTTCATTTATTATTATAATCTTAGATATTTTATT
66 TGTCATATATTTTATTTTCATTTATTATTATAATCTTAGATATTTTATT
*
5726390 TTTAATATATTTATA-TTTTTATTATTAATTGTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTGTTATATAATACCATCTCTTAAATATATTTTTAA
* *
5726454 TGTCATATATTTTATTTTTATTTATTA-TATAATCTTATATATTTTATT
66 TGTCATATATTTTATTTTCATTTATTATTATAATCTTAGATATTTTATT
5726502 TTTA
1 TTTA
5726506 TTTTTTAATA
Statistics
Matches: 110, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
112 24 0.22
113 72 0.65
114 14 0.13
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (114 bp):
TTTAATATATTTATATTTTTTATTATTAATTGTTATATAATACCATCTCTTAAATATATTTTTAA
TGTCATATATTTTATTTTCATTTATTATTATAATCTTAGATATTTTATT
Found at i:5726583 original size:24 final size:25
Alignment explanation
Indices: 5726556--5726630 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
5726546 TTGTTTTACC
5726556 TATATTATA-TAAATTTTAATTTTT
1 TATATTATATTAAATTTTAATTTTT
* **
5726580 TATATTTTATTTTATTTTAATTTTT
1 TATATTATATTAAATTTTAATTTTT
* *
5726605 GATTCTTATATTATATATTTT-ATTTT
1 TA-TATTATATTA-A-ATTTTAATTTT
5726631 AATTATAACA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
24 8 0.21
25 14 0.36
26 7 0.18
27 5 0.13
28 5 0.13
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (25 bp):
TATATTATATTAAATTTTAATTTTT
Found at i:5733336 original size:43 final size:43
Alignment explanation
Indices: 5733275--5733363 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
5733265 TGACTGGCGC
5733275 ACTTACAGCTATAGATACCACCATGGATAATACATTGTTACAT
1 ACTTACAGCTATAGATACCACCATGGATAATACATTGTTACAT
* *
5733318 ACTTACAGCTATATATACCACCATGGATAATACATTTTTACAT
1 ACTTACAGCTATAGATACCACCATGGATAATACATTGTTACAT
5733361 ACT
1 ACT
5733364 GCATGCATGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (43 bp):
ACTTACAGCTATAGATACCACCATGGATAATACATTGTTACAT
Found at i:5739394 original size:12 final size:12
Alignment explanation
Indices: 5739379--5739435 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
5739369 TCCCCTTCTC
*
5739379 CTTCTTCTTCTT
1 CTTCTTCTTCAT
* *
5739391 CTTCTTCCTCAA
1 CTTCTTCTTCAT
* * *
5739403 CTTCCTCCTCCT
1 CTTCTTCTTCAT
*
5739415 CTTCCTCTTCAT
1 CTTCTTCTTCAT
5739427 CTTCTTCTT
1 CTTCTTCTT
5739436 TCTTATATTC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.05, C:0.42, G:0.00, T:0.53
Consensus pattern (12 bp):
CTTCTTCTTCAT
Found at i:5742103 original size:2 final size:2
Alignment explanation
Indices: 5742096--5742120 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5742086 TATTAAACTT
5742096 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5742121 GCATTACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5743243 original size:15 final size:15
Alignment explanation
Indices: 5743216--5743255 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
5743206 TGTAGGGTTT
5743216 AACTCTGGA-GTTTTA
1 AACTC-GGACGTTTTA
5743231 AACTCGGACGTTTTA
1 AACTCGGACGTTTTA
5743246 AACTCGGACG
1 AACTCGGACG
5743256 GTCGGACCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (15 bp):
AACTCGGACGTTTTA
Found at i:5744269 original size:16 final size:16
Alignment explanation
Indices: 5744246--5744291 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
5744236 AAATTGATAA
5744246 AAAAATTAATAAAATT
1 AAAAATTAATAAAATT
* * **
5744262 ATAAATTAGTAATTTT
1 AAAAATTAATAAAATT
5744278 AAAAATTAATAAAA
1 AAAAATTAATAAAA
5744292 AGTTAAATTA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AAAAATTAATAAAATT
Found at i:5756774 original size:55 final size:55
Alignment explanation
Indices: 5756690--5756800 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
5756680 ACAGTTTCAT
* *
5756690 CAGTATGTGTCTTATGTAGTACTATTTAAAGATTTGGTGATAACAATTTGTTAAA
1 CAGTACGTGTCTCATGTAGTACTATTTAAAGATTTGGTGATAACAATTTGTTAAA
* *
5756745 CAGTACGTGTCTCATGTAGTATTTTTTAAAGATTTGGTGATAACAATTTGTTAAA
1 CAGTACGTGTCTCATGTAGTACTATTTAAAGATTTGGTGATAACAATTTGTTAAA
5756800 C
1 C
5756801 TCTCTCCTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (55 bp):
CAGTACGTGTCTCATGTAGTACTATTTAAAGATTTGGTGATAACAATTTGTTAAA
Found at i:5760159 original size:3 final size:3
Alignment explanation
Indices: 5760151--5760180 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5760141 AAAAGATAGC
5760151 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5760181 GTTCCTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5760606 original size:25 final size:25
Alignment explanation
Indices: 5760578--5760628 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5760568 TGAGTTATGA
5760578 TCCTATATATATATTATCACAAAGT
1 TCCTATATATATATTATCACAAAGT
5760603 TCCTATATATATATTATCACAAAGT
1 TCCTATATATATATTATCACAAAGT
5760628 T
1 T
5760629 TTCTCCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TCCTATATATATATTATCACAAAGT
Found at i:5769557 original size:22 final size:22
Alignment explanation
Indices: 5769532--5769599 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
5769522 TAATAATATT
5769532 AAATATTATTAAATTATAATAA
1 AAATATTATTAAATTATAATAA
** * ** *
5769554 AAATATGT-TTGTATTTTGGTGA
1 AAATAT-TATTAAATTATAATAA
*
5769576 AAATATTATTTAATTATAATAA
1 AAATATTATTAAATTATAATAA
5769598 AA
1 AA
5769600 GGTATTTTGA
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
AAATATTATTAAATTATAATAA
Found at i:5769675 original size:22 final size:22
Alignment explanation
Indices: 5769579--5769677 Score: 58
Period size: 22 Copynumber: 4.4 Consensus size: 22
5769569 TTGGTGAAAA
*
5769579 TATTATTTAATTATAATAAAAGG
1 TATT-TTTAATTTTAATAAAAGG
* * **
5769602 TA-TTTTGATTTTATTACTTAGAG
1 TATTTTTAATTTTAATA-AAAG-G
* * **
5769625 TATTTTTATCTTTTAACAAATAAA
1 TATTTTTA-ATTTTAATAAA-AGG
5769649 T-TTTTTAATTTTAATAAAAGG
1 TATTTTTAATTTTAATAAAAGG
5769670 TATTTTTA
1 TATTTTTA
5769678 TCACTAACCA
Statistics
Matches: 53, Mismatches: 17, Indels: 13
0.64 0.20 0.16
Matches are distributed among these distances:
21 12 0.23
22 18 0.34
23 11 0.21
24 5 0.09
25 7 0.13
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (22 bp):
TATTTTTAATTTTAATAAAAGG
Found at i:5783133 original size:25 final size:25
Alignment explanation
Indices: 5783083--5783133 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
5783073 TTTTATTTTA
*
5783083 AATTATATAAATTTTTATAATTAAT
1 AATTATATAAATTATTATAATTAAT
* *
5783108 AATTA-ATTAATTATTATTATTCAAT
1 AATTATATAAATTATTATAATT-AAT
5783133 A
1 A
5783134 CATCACTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
AATTATATAAATTATTATAATTAAT
Found at i:5784595 original size:22 final size:22
Alignment explanation
Indices: 5784542--5784596 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
5784532 ATTACTTTTC
* *
5784542 TGATTTTTAAATATTACGTGAT
1 TGATTTTTAGACATTACGTGAT
5784564 T-AGTTTTTAGACATTACGTGAT
1 TGA-TTTTTAGACATTACGTGAT
5784586 TGATTTTTAGA
1 TGATTTTTAGA
5784597 GAATATCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 1 0.03
22 27 0.93
23 1 0.03
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.49
Consensus pattern (22 bp):
TGATTTTTAGACATTACGTGAT
Found at i:5784693 original size:22 final size:21
Alignment explanation
Indices: 5784665--5784736 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 21
5784655 ACACAATGCT
5784665 TAAAAATTAATAATATAATATC
1 TAAAAATTAATAATATAATA-C
* *
5784687 TAAAAATTAATCACATAATAC
1 TAAAAATTAATAATATAATAC
**
5784708 TTAAAAATTAATAATGCAATACC
1 -TAAAAATTAATAATATAATA-C
5784731 TAAAAA
1 TAAAAA
5784737 CTAGTCTCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
21 1 0.02
22 40 0.95
23 1 0.02
ACGTcount: A:0.58, C:0.10, G:0.01, T:0.31
Consensus pattern (21 bp):
TAAAAATTAATAATATAATAC
Found at i:5784757 original size:44 final size:44
Alignment explanation
Indices: 5784610--5784759 Score: 149
Period size: 44 Copynumber: 3.4 Consensus size: 44
5784600 TATCTAAGTT
* * * **
5784610 ACATAACGCTTAAAAATTAATCATGCAATATCTTACTAACTAGTC
1 ACATAATGCTTAAAAATTAATAATGCAATA-CCTAAAAACTAGTC
* ** * * *
5784655 ACACAATGCTTAAAAATTAATAATATAATATCTAAAAATTAATC
1 ACATAATGCTTAAAAATTAATAATGCAATACCTAAAAACTAGTC
*
5784699 ACATAATACTTAAAAATTAATAATGCAATACCTAAAAACTAGTC
1 ACATAATGCTTAAAAATTAATAATGCAATACCTAAAAACTAGTC
* *
5784743 TCGTAATG-TCTAAAAAT
1 ACATAATGCT-TAAAAAT
5784760 CGGTTATGTA
Statistics
Matches: 83, Mismatches: 21, Indels: 3
0.78 0.20 0.03
Matches are distributed among these distances:
43 1 0.01
44 57 0.69
45 25 0.30
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (44 bp):
ACATAATGCTTAAAAATTAATAATGCAATACCTAAAAACTAGTC
Found at i:5785097 original size:18 final size:19
Alignment explanation
Indices: 5785069--5785104 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5785059 TTAAGGATAA
*
5785069 TTTTATCTAAAATTAATTT
1 TTTTATCTAAAAATAATTT
5785088 TTTTAT-TAAAAATAATT
1 TTTTATCTAAAAATAATT
5785105 AAAATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTATCTAAAAATAATTT
Found at i:5788488 original size:15 final size:15
Alignment explanation
Indices: 5788428--5788488 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
5788418 TAAAAATTAA
*
5788428 TTAAAATTATTATTAT
1 TTAAAA-TATTAATAT
*
5788444 TATAATCATATTAATAT
1 T-TAA-AATATTAATAT
5788461 TTAAAATGA-TAATAT
1 TTAAAAT-ATTAATAT
*
5788476 TTAAACTATTAAT
1 TTAAAATATTAAT
5788489 TATTAATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 1 0.03
15 18 0.49
16 5 0.14
17 12 0.32
18 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (15 bp):
TTAAAATATTAATAT
Found at i:5790491 original size:76 final size:76
Alignment explanation
Indices: 5790361--5790510 Score: 255
Period size: 76 Copynumber: 2.0 Consensus size: 76
5790351 GAACCAAAAT
*
5790361 TTGAGAGTTGGCTTTAAAATAGATTTTCAAAAAAACTACCTCTTTGAGACTGGACTAGATGATCA
1 TTGAGAGTTGGCTTTAAAATAGATTTTCAAAAAAACTACCTCCTTGAGACTGGACTAGATGATCA
5790426 CATGACAACTA
66 CATGACAACTA
* * * *
5790437 TTGAGAGTTGGCTTTAAAATAGATTTTCCAAAAAACTGCCTCCTTGGGATTGGACTAGATGATCA
1 TTGAGAGTTGGCTTTAAAATAGATTTTCAAAAAAACTACCTCCTTGAGACTGGACTAGATGATCA
5790502 CATGACAAC
66 CATGACAAC
5790511 CATATTGGTA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 69 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (76 bp):
TTGAGAGTTGGCTTTAAAATAGATTTTCAAAAAAACTACCTCCTTGAGACTGGACTAGATGATCA
CATGACAACTA
Found at i:5792060 original size:45 final size:45
Alignment explanation
Indices: 5791976--5792066 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
5791966 GGGTAGAACC
* ** *
5791976 ACAAAGTCCCGCATTGAAGAGAAACTTTTAACGGAGAGTAAAGGA
1 ACAAAGTCCCACATTGAAGAGAAACTCCTAACAGAGAGTAAAGGA
* *
5792021 ACAAAGTCCCACATTGAAGAGAATCTCCTAACA-AGGAGTAAGGGA
1 ACAAAGTCCCACATTGAAGAGAAACTCCTAACAGA-GAGTAAAGGA
5792066 A
1 A
5792067 GATGTTTTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (45 bp):
ACAAAGTCCCACATTGAAGAGAAACTCCTAACAGAGAGTAAAGGA
Found at i:5792424 original size:12 final size:12
Alignment explanation
Indices: 5792407--5792436 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5792397 AAAATAATAA
5792407 ATATATATAATT
1 ATATATATAATT
5792419 ATATATATAATT
1 ATATATATAATT
*
5792431 TTATAT
1 ATATAT
5792437 CTATAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATATATAATT
Found at i:5798832 original size:5 final size:5
Alignment explanation
Indices: 5798822--5798846 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5798812 AAAGGGATGG
5798822 CATGC CATGC CATGC CATGC CATGC
1 CATGC CATGC CATGC CATGC CATGC
5798847 GCAGCTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (5 bp):
CATGC
Found at i:5801972 original size:2 final size:2
Alignment explanation
Indices: 5801965--5801991 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5801955 TCTTTCTTTC
5801965 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5801992 TAAACATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5803540 original size:4 final size:4
Alignment explanation
Indices: 5803524--5803586 Score: 58
Period size: 4 Copynumber: 16.0 Consensus size: 4
5803514 GTTATATCAC
* * *
5803524 TTAT TTAT GTAT TTAT TTAT ATAA TTAT TTA- TTAT TTAT TATAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTAT
* *
5803572 AT-T TTGT TTAT TTAT
1 TTAT TTAT TTAT TTAT
5803587 AAGATTAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
3 5 0.11
4 38 0.81
5 4 0.09
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:5812163 original size:2 final size:2
Alignment explanation
Indices: 5812152--5812181 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5812142 ATTATCTTTT
5812152 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5812182 TAAATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5835857 original size:21 final size:20
Alignment explanation
Indices: 5835831--5835871 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5835821 TTAAGTAATT
5835831 AAAAATAATAATAATATTTTA
1 AAAAATAA-AATAATATTTTA
*
5835852 AAAAATAACATAATATTTTA
1 AAAAATAAAATAATATTTTA
5835872 TATTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATAAAATAATATTTTA
Found at i:5837143 original size:144 final size:143
Alignment explanation
Indices: 5836883--5837159 Score: 405
Period size: 144 Copynumber: 1.9 Consensus size: 143
5836873 CAATTTGACA
* *
5836883 ATTTCAACTATCTAATGTTAACTTTTGTATGTAACAACGGCCTCTATTATCACAAAATCTGCAAA
1 ATTTCAACTATCTAATGTTAACTTTTGTACGCAACAACGGCCTCTATTATCACAAAATCTGCAAA
** * *
5836948 TGCATACTAGTAGATAGTAATCTTAATTTTGTTCAAGGACTGCATAGGATTATCAACATGTATGA
66 TGCATACTAACAGATAGTAATCTTAATTTTGTTAAAGGACTGCATAGGATTATCAACATGCATGA
5837013 AATCAGCTTGATG
131 AATCAGCTTGATG
* * * *
5837026 ATTTCAACTATCTAATGTTAATTTTTGTACGCAACAACTGCCT-TGATTATCGCAAATATTTGCA
1 ATTTCAACTATCTAATGTTAACTTTTGTACGCAACAACGGCCTCT-ATTATCACAAA-ATCTGCA
* *
5837090 AATGCATACTAACAGATAGTAATCTTAATTTTGTTAAAGGATTGTAT-GAGATTATCAACATGCA
64 AATGCATACTAACAGATAGTAATCTTAATTTTGTTAAAGGACTGCATAG-GATTATCAACATGCA
5837154 TGAAAT
128 TGAAAT
5837160 GCTCTTTATC
Statistics
Matches: 119, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
142 1 0.01
143 50 0.42
144 68 0.57
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (143 bp):
ATTTCAACTATCTAATGTTAACTTTTGTACGCAACAACGGCCTCTATTATCACAAAATCTGCAAA
TGCATACTAACAGATAGTAATCTTAATTTTGTTAAAGGACTGCATAGGATTATCAACATGCATGA
AATCAGCTTGATG
Found at i:5841156 original size:10 final size:10
Alignment explanation
Indices: 5841141--5841202 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
5841131 GTCGATCAAA
5841141 TCTCTCTTTC
1 TCTCTCTTTC
5841151 TCTCTCTATT-
1 TCTCTCT-TTC
*
5841161 TCTTTTCCTTTC
1 TC-TCT-CTTTC
*
5841173 TCTCTCTCTC
1 TCTCTCTTTC
*
5841183 TCTCTCTTTT
1 TCTCTCTTTC
*
5841193 TCTGTCTTTC
1 TCTCTCTTTC
5841203 ATTGAAATCG
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
10 29 0.71
11 8 0.20
12 4 0.10
ACGTcount: A:0.02, C:0.35, G:0.02, T:0.61
Consensus pattern (10 bp):
TCTCTCTTTC
Done.