Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 109 of 120
Found at i:31981331 original size:117 final size:117
Alignment explanation
Indices: 31981116--31981332 Score: 296
Period size: 117 Copynumber: 1.9 Consensus size: 117
31981106 AAACTATCCA
*
31981116 AAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATT
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTCAACCCCGATTTCACCAAAAATT
* * ** * *
31981181 ACCATTTTACCCTCGAACTTTCCAAAATCCCATTTTTAACCCCAGTTTCACC
66 ACCATTTTACCCCCAAAAGTTCAAAAATACCATTTTTAACCCCAGTTTCACC
** *
31981233 AAAATTACCATTTTACCCCCGAA-TTTCCTAAAATCCCATTTTCGGCTCCGATTTCACCAAAAAT
1 AAAATTACCATTTTACCCCCGAACTTTCC-AAAATCCCATTTTCAACCCCGATTTCACCAAAAAT
31981297 TA-CATTTTTACCCCCAAAAGTT-AAAAATTACCATTT
65 TACCA-TTTTACCCCCAAAAGTTCAAAAA-TACCATTT
31981333 CACCCCCGGG
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
116 11 0.13
117 76 0.87
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.32
Consensus pattern (117 bp):
AAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTCAACCCCGATTTCACCAAAAATT
ACCATTTTACCCCCAAAAGTTCAAAAATACCATTTTTAACCCCAGTTTCACC
Found at i:31986792 original size:21 final size:22
Alignment explanation
Indices: 31986768--31986817 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
31986758 AAATAATAAT
* *
31986768 TTAAGTACCAATAT-AAAAAAA
1 TTAAATACCAAAATGAAAAAAA
*
31986789 TTAAATACTAAAATGAAAAAAA
1 TTAAATACCAAAATGAAAAAAA
*
31986811 TAAAATA
1 TTAAATA
31986818 ATTCAAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.24
Consensus pattern (22 bp):
TTAAATACCAAAATGAAAAAAA
Found at i:32013360 original size:13 final size:14
Alignment explanation
Indices: 32013344--32013385 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
32013334 TTTTTATTTT
32013344 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
32013357 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
32013372 ATTTTAAGTAATAT
1 ATTTTAA-TAATAT
32013386 TTTTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 10 0.42
16 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:32013376 original size:15 final size:16
Alignment explanation
Indices: 32013349--32013378 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
32013339 ATTTTATTTT
32013349 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
32013365 AATAAT-AATTTTAA
1 AATAATAAATTTTAA
32013379 GTAATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:32039223 original size:50 final size:50
Alignment explanation
Indices: 32039165--32039265 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
32039155 CCCACGCTCA
*
32039165 GCTCATTATTTAAGTAAAATGCTGAAGATAATTGAATTATAAATAATATT
1 GCTCATTATTTAAGTAAAATGCTGAAGATAATTGAATTATAAAAAATATT
32039215 GCTCATTATTTAAGTAAAATGCTGAAGATAATTGAATTATAAAAAATATT
1 GCTCATTATTTAAGTAAAATGCTGAAGATAATTGAATTATAAAAAATATT
32039265 G
1 G
32039266 TTAAGAGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.37
Consensus pattern (50 bp):
GCTCATTATTTAAGTAAAATGCTGAAGATAATTGAATTATAAAAAATATT
Found at i:32065563 original size:36 final size:37
Alignment explanation
Indices: 32065516--32065589 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
32065506 GATATCTTCA
32065516 ACAAAATTTTTTATCCTATTTAACCCCATGTTTTGAT
1 ACAAAATTTTTTATCCTATTTAACCCCATGTTTTGAT
*
32065553 ACAAAATTTTTTATCTTATTTAACCCCATGTTTTGAT
1 ACAAAATTTTTTATCCTATTTAACCCCATGTTTTGAT
32065590 TTGATGGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (37 bp):
ACAAAATTTTTTATCCTATTTAACCCCATGTTTTGAT
Found at i:32076834 original size:35 final size:34
Alignment explanation
Indices: 32076795--32076863 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
32076785 GTTGTCAAAG
*
32076795 AAGACTGTATAGAGACAAGAGATGAGGTGACACAA
1 AAGACTGTATAGAGA-AAGAGATGAAGTGACACAA
* *
32076830 AAGACTGTATAGAGATAGATATGAAGTGACACAA
1 AAGACTGTATAGAGAAAGAGATGAAGTGACACAA
32076864 CGGCAATGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 16 0.52
35 15 0.48
ACGTcount: A:0.46, C:0.10, G:0.26, T:0.17
Consensus pattern (34 bp):
AAGACTGTATAGAGAAAGAGATGAAGTGACACAA
Found at i:32097986 original size:58 final size:56
Alignment explanation
Indices: 32097840--32097986 Score: 170
Period size: 58 Copynumber: 2.5 Consensus size: 56
32097830 ATATATTATA
* *
32097840 ATTTTTACTAATTCATATTTTAATAATAATTATATTAAAAAATATTATTAAATTACAT
1 ATTTTTATTAATT-ATA-TTTAATAATAATTATATTAAAAAATATTAATAAATTACAT
* * *
32097898 ATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTA-AT
1 A-T-TTTTATT-AATTATATTTAATAATAATTATATTAAAAAAT-ATT-AATAAATTACAT
32097958 ATTTTTATTCAATTATATTTAATAATAAT
1 ATTTTTATT-AATTATATTTAATAATAAT
32097987 CATTAAAATT
Statistics
Matches: 77, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
58 26 0.34
59 25 0.32
60 14 0.18
61 12 0.16
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (56 bp):
ATTTTTATTAATTATATTTAATAATAATTATATTAAAAAATATTAATAAATTACAT
Found at i:32098172 original size:46 final size:44
Alignment explanation
Indices: 32098080--32098173 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
32098070 ATTACAACAT
* *
32098080 CATTCCATTCAACCAAACACAAGAATATTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
*
32098124 CATTCCAATCAACCAAACA-ATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACA-AGAA-TA-TGATTACAGCTCTATTC
32098170 CATT
1 CATT
32098174 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 2 0.05
46 20 0.45
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
Found at i:32098176 original size:16 final size:16
Alignment explanation
Indices: 32098155--32098210 Score: 103
Period size: 16 Copynumber: 3.5 Consensus size: 16
32098145 TGAATTACTG
32098155 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
32098171 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
32098187 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
32098203 ATTACAGC
1 ATTACAGC
32098211 GAACCAAACG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.27, C:0.32, G:0.05, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:32101087 original size:29 final size:29
Alignment explanation
Indices: 32101055--32101110 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
32101045 GTTTTGGTGC
32101055 TTTTTTTACTATTTTAGTTGCTGTTTTTG
1 TTTTTTTACTATTTTAGTTGCTGTTTTTG
* *
32101084 TTTTTTTACTGTTTTAGTTGTTGTTTT
1 TTTTTTTACTATTTTAGTTGCTGTTTT
32101111 CGTGTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.09, C:0.05, G:0.14, T:0.71
Consensus pattern (29 bp):
TTTTTTTACTATTTTAGTTGCTGTTTTTG
Found at i:32101125 original size:29 final size:28
Alignment explanation
Indices: 32101066--32101125 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
32101056 TTTTTTACTA
*
32101066 TTTTAGTTGCTGTTTTTGTTTTTTTACTG
1 TTTTAGTTGCTGTTTTTGTTATTTTA-TG
*
32101095 TTTTAGTTGTTGTTTTCGTGTTATTTT-TG
1 TTTTAGTTGCTGTTTT--TGTTATTTTATG
32101124 TT
1 TT
32101126 GCTGTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.07, C:0.05, G:0.18, T:0.70
Consensus pattern (28 bp):
TTTTAGTTGCTGTTTTTGTTATTTTATG
Found at i:32101141 original size:44 final size:44
Alignment explanation
Indices: 32101086--32101177 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
32101076 TGTTTTTGTT
*
32101086 TTTTTACTG-TTTTAGTTGTTGTTTT-CGTGTTATTTTTGTTGCTG
1 TTTTTACTGTTTTTA-ATGTTGTTTTGC-TGTTATTTTTGTTGCTG
*
32101130 TTTTTATTGTTTTTAATGTTGTTTTGCTGTTATTTTTGTTGCTG
1 TTTTTACTGTTTTTAATGTTGTTTTGCTGTTATTTTTGTTGCTG
32101174 TTTT
1 TTTT
32101178 GGTTATTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
44 38 0.86
45 6 0.14
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.68
Consensus pattern (44 bp):
TTTTTACTGTTTTTAATGTTGTTTTGCTGTTATTTTTGTTGCTG
Found at i:32101178 original size:23 final size:22
Alignment explanation
Indices: 32101095--32101177 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 22
32101085 TTTTTTACTG
* *
32101095 TTTTAGTTGTTGTTTTCGTGTTA
1 TTTTTGTTGCTGTTTTC-TGTTA
* *
32101118 TTTTTGTTGCTGTTTT-TATTG
1 TTTTTGTTGCTGTTTTCTGTTA
** *
32101139 TTTTTAATGTTGTTTTGCTGTTA
1 TTTTTGTTGCTGTTTT-CTGTTA
32101162 TTTTTGTTGCTGTTTT
1 TTTTTGTTGCTGTTTT
32101178 GGTTATTAAT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
21 16 0.35
23 30 0.65
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.69
Consensus pattern (22 bp):
TTTTTGTTGCTGTTTTCTGTTA
Found at i:32101407 original size:38 final size:38
Alignment explanation
Indices: 32101324--32101408 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 38
32101314 TAATATAAAT
* * * *
32101324 TTTTTTAATGTATTTTAAATTTATTTATTTTTTAATGT
1 TTTTTTAATGTATTTTAAATGTATTTATATATTAATGA
32101362 TTGTTTTAATGT-TTTTAAATGTATTTGATATATTATAT-A
1 TT-TTTTAATGTATTTTAAATGTATTT-ATATATTA-ATGA
32101401 TTTTTTAA
1 TTTTTTAA
32101409 ATTTGTTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
38 21 0.52
39 17 0.43
40 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (38 bp):
TTTTTTAATGTATTTTAAATGTATTTATATATTAATGA
Found at i:32101623 original size:5 final size:5
Alignment explanation
Indices: 32101599--32101625 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
32101589 CCGATCCTAT
32101599 CCGAC CCGAC CCGAC CCGAC CCGAC CC
1 CCGAC CCGAC CCGAC CCGAC CCGAC CC
32101626 ATAATAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.63, G:0.19, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:32107557 original size:21 final size:21
Alignment explanation
Indices: 32107533--32107579 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
32107523 GTGAAGGAAT
*
32107533 TGATGGAGCTGAGGTTTTCGA
1 TGATGGAGCTGAGGTCTTCGA
* * *
32107554 TGATGGTGTTGAGGTCTTGGA
1 TGATGGAGCTGAGGTCTTCGA
32107575 TGATG
1 TGATG
32107580 AGGTAGTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.06, G:0.40, T:0.36
Consensus pattern (21 bp):
TGATGGAGCTGAGGTCTTCGA
Found at i:32108729 original size:22 final size:24
Alignment explanation
Indices: 32108704--32108751 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
32108694 CATTCCTTAT
*
32108704 AAAAA-CTCAAGTTTTTCATT-TA
1 AAAAATCTCAAGTATTTCATTGTA
*
32108726 AAAAATCTCAGGTATTTCATTGTA
1 AAAAATCTCAAGTATTTCATTGTA
32108750 AA
1 AA
32108752 CCCCAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (24 bp):
AAAAATCTCAAGTATTTCATTGTA
Found at i:32109058 original size:18 final size:17
Alignment explanation
Indices: 32109030--32109064 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
32109020 AAACGAATTC
*
32109030 TAAAAGATAAAGTAAAT
1 TAAAAGATAAAATAAAT
32109047 TAAAATGATAAAATAAAT
1 TAAAA-GATAAAATAAAT
32109065 GATGAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
TAAAAGATAAAATAAAT
Found at i:32115470 original size:20 final size:20
Alignment explanation
Indices: 32115445--32115501 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
32115435 TAGACCATGT
32115445 CTGGTATTGCTCGATGCTCC
1 CTGGTATTGCTCGATGCTCC
* *
32115465 CTGGTACTGCTCGATGCTTC
1 CTGGTATTGCTCGATGCTCC
* *
32115485 CTGATGTTGCTCGATGC
1 CTGGTATTGCTCGATGC
32115502 ATGCTGGTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.28, G:0.26, T:0.35
Consensus pattern (20 bp):
CTGGTATTGCTCGATGCTCC
Found at i:32124908 original size:16 final size:16
Alignment explanation
Indices: 32124871--32124902 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
32124861 AGTTGGTTGG
32124871 ACAATGATGCATTGAT
1 ACAATGATGCATTGAT
32124887 ACAATGATGCATTGAT
1 ACAATGATGCATTGAT
32124903 GTAATGTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
ACAATGATGCATTGAT
Found at i:32127398 original size:18 final size:18
Alignment explanation
Indices: 32127371--32127412 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
32127361 ACATGAGCTG
*
32127371 TTATTGTTTCA-TATTATT
1 TTATTATTTCAGTATTA-T
*
32127389 TTATTATTTCAGTTTTAT
1 TTATTATTTCAGTATTAT
32127407 TTATTA
1 TTATTA
32127413 ATTAGGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (18 bp):
TTATTATTTCAGTATTAT
Found at i:32128692 original size:37 final size:38
Alignment explanation
Indices: 32128641--32128714 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 38
32128631 GACAGGATAC
* *
32128641 AAGTTAACTTTAGGGTTTAAATATAGGGCTAGTATTAT
1 AAGTTAACTTTAGGGTTTAAAGATAGGACTAGTATTAT
* * *
32128679 AAGTTATC-TTAGGGTTTCAAGCTAGGACTAGTATTA
1 AAGTTAACTTTAGGGTTTAAAGATAGGACTAGTATTA
32128715 AATCTTTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
37 24 0.77
38 7 0.23
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (38 bp):
AAGTTAACTTTAGGGTTTAAAGATAGGACTAGTATTAT
Found at i:32131244 original size:3 final size:3
Alignment explanation
Indices: 32131238--32131270 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
32131228 TCTTCTTCTT
32131238 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
32131271 TTATACACCT
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:32140996 original size:43 final size:42
Alignment explanation
Indices: 32140933--32141020 Score: 104
Period size: 43 Copynumber: 2.1 Consensus size: 42
32140923 ATTGCAAGGC
* ** *
32140933 AATAAAACATAAAATGCATTTTCTTAATCAAGTAAATCTTGGT
1 AATAAAACATAAAATACATTTAATTAATCAAGGAAATCTT-GT
* * *
32140976 AATAAAAGATATAATACATTTAATTAATCTAGGAAATCTTGT
1 AATAAAACATAAAATACATTTAATTAATCAAGGAAATCTTGT
32141018 AAT
1 AAT
32141021 GAACTCAAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 5 0.13
43 33 0.87
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (42 bp):
AATAAAACATAAAATACATTTAATTAATCAAGGAAATCTTGT
Found at i:32143286 original size:22 final size:21
Alignment explanation
Indices: 32143255--32143295 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
32143245 TAAATTATGA
32143255 GAAAAATAAAAGTTTTCAAACC
1 GAAAAAT-AAAGTTTTCAAACC
*
32143277 GAAAATTAAAGTTTTCAAA
1 GAAAAATAAAGTTTTCAAA
32143296 TCAATGATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (21 bp):
GAAAAATAAAGTTTTCAAACC
Found at i:32155078 original size:20 final size:21
Alignment explanation
Indices: 32155044--32155083 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
32155034 ATAAAAAATT
32155044 ATAAAATTTACAAAAATATAA
1 ATAAAATTTACAAAAATATAA
*
32155065 ATAAAA-TTATAAAAATATA
1 ATAAAATTTACAAAAATATA
32155084 TAGTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAAAATTTACAAAAATATAA
Found at i:32155167 original size:26 final size:26
Alignment explanation
Indices: 32155133--32155192 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
32155123 AATTGTAAAA
32155133 AAAATTATAAAAATTATTA-AATATTGT
1 AAAA-TATAAAAATTATTAGAA-ATTGT
* **
32155160 AATATATAAATTTTATTAGAAATTGT
1 AAAATATAAAAATTATTAGAAATTGT
32155186 AAAATAT
1 AAAATAT
32155193 TGTAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (26 bp):
AAAATATAAAAATTATTAGAAATTGT
Found at i:32160398 original size:18 final size:17
Alignment explanation
Indices: 32160355--32160410 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
32160345 CGTTTAACTG
* *
32160355 ATTTTTGTAATTTTATAA
1 ATTTTT-TATTTTTTTAA
32160373 ATTTTTTATTTTTTTAA
1 ATTTTTTATTTTTTTAA
* *
32160390 ATTTATTTATATTATTAA
1 ATTT-TTTATTTTTTTAA
32160408 ATT
1 ATT
32160411 ATTCAAATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 13 0.39
18 20 0.61
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
ATTTTTTATTTTTTTAA
Found at i:32160831 original size:5 final size:5
Alignment explanation
Indices: 32160823--32160870 Score: 96
Period size: 5 Copynumber: 9.6 Consensus size: 5
32160813 AACAACACAA
32160823 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
32160871 TACAAGATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:32175200 original size:27 final size:28
Alignment explanation
Indices: 32175167--32175258 Score: 86
Period size: 32 Copynumber: 3.2 Consensus size: 28
32175157 TAAGATTACT
32175167 ATATAAAAAATTTAAATAAATAAAAAT-
1 ATATAAAAAATTTAAATAAATAAAAATA
*
32175194 ATAT-AAAAATATTAAAT--ATTAAAATA
1 ATATAAAAAAT-TTAAATAAATAAAAATA
32175220 ATATAATATACATATTTAAA-AAATAAAAAATA
1 ATATAA-A-A-A-ATTTAAATAAAT-AAAAATA
32175252 ATATAAA
1 ATATAAA
32175259 TAGACCTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
25 7 0.13
26 10 0.19
27 11 0.21
28 1 0.02
29 1 0.02
30 6 0.11
31 5 0.09
32 12 0.23
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (28 bp):
ATATAAAAAATTTAAATAAATAAAAATA
Found at i:32175205 original size:10 final size:10
Alignment explanation
Indices: 32175180--32175258 Score: 51
Period size: 10 Copynumber: 8.1 Consensus size: 10
32175170 TAAAAAATTT
*
32175180 AAATAAATAA
1 AAATATATAA
32175190 AAATATATAA
1 AAATATATAA
32175200 AAATAT-TAA
1 AAATATATAA
*
32175209 ATAT-TA-AA
1 AAATATATAA
*
32175217 ATAATATAATAT
1 A-AATAT-ATAA
* *
32175229 ACATATTTAA
1 AAATATATAA
32175239 AAA-ATA-AA
1 AAATATATAA
32175247 AAATAATATAA
1 AAAT-ATATAA
32175258 A
1 A
32175259 TAGACCTAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
8 9 0.17
9 10 0.19
10 23 0.44
11 8 0.15
12 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.30
Consensus pattern (10 bp):
AAATATATAA
Found at i:32175227 original size:23 final size:22
Alignment explanation
Indices: 32175201--32175244 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
32175191 AATATATAAA
32175201 AATATTAAATA-TTAAAATAATAT
1 AATA-TAAATATTTAAAA-AATAT
*
32175224 AATATACATATTTAAAAAATA
1 AATATAAATATTTAAAAAATA
32175245 AAAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AATATAAATATTTAAAAAATAT
Found at i:32188420 original size:102 final size:102
Alignment explanation
Indices: 32188244--32188437 Score: 352
Period size: 102 Copynumber: 1.9 Consensus size: 102
32188234 GAAGATGAGA
32188244 AGAATGAAATAGTTACTGAAAATAATGCATTTGTGCATGGGAAACCACCTCAAGATGCTGCTGGA
1 AGAATGAAATAGTTACTGAAAATAATGCATTTGTGCATGGGAAACCACCTCAAGATGCTGCTGGA
32188309 CCTCCGAAAGTTGAATCTGATATGGAAATTGTTGATG
66 CCTCCGAAAGTTGAATCTGATATGGAAATTGTTGATG
* * * *
32188346 AGAATGAAATAGTTACTGAAAGTACTGCATTTGTGCATGGGGAACCACTTCAAGATGCTGCTGGA
1 AGAATGAAATAGTTACTGAAAATAATGCATTTGTGCATGGGAAACCACCTCAAGATGCTGCTGGA
32188411 CCTCCGAAAGTTGAATCTGATATGGAA
66 CCTCCGAAAGTTGAATCTGATATGGAA
32188438 GTTCTTCATG
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 88 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (102 bp):
AGAATGAAATAGTTACTGAAAATAATGCATTTGTGCATGGGAAACCACCTCAAGATGCTGCTGGA
CCTCCGAAAGTTGAATCTGATATGGAAATTGTTGATG
Found at i:32188756 original size:43 final size:44
Alignment explanation
Indices: 32188661--32188767 Score: 128
Period size: 43 Copynumber: 2.4 Consensus size: 44
32188651 TAACTTTCAG
* *
32188661 TACTC-ACATCTGCAATAGAAGCTTGAATCTTGTATCTGGTTATTT
1 TACTCAACATCT-TAAT-GAAGCTTGAATCTTGTATCTGATTATTT
* * *
32188706 TAATCAACATCTTAATGAAGCTTGAATCTT-TATCTTATTCTTT
1 TACTCAACATCTTAATGAAGCTTGAATCTTGTATCTGATTATTT
*
32188749 TACTCAACATCTTGATGAA
1 TACTCAACATCTTAATGAA
32188768 ACTATACTGA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 27 0.50
44 14 0.26
45 7 0.13
46 6 0.11
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (44 bp):
TACTCAACATCTTAATGAAGCTTGAATCTTGTATCTGATTATTT
Found at i:32199502 original size:51 final size:52
Alignment explanation
Indices: 32199431--32199536 Score: 151
Period size: 51 Copynumber: 2.1 Consensus size: 52
32199421 AAGAAGAACT
32199431 TAAACTTTGTCACTTCATTTAAATAAGCTCTTATAATTTTACTACATCCAAA
1 TAAACTTTGTCACTTCATTTAAATAAGCTCTTATAATTTTACTACATCCAAA
* * * ** *
32199483 TAAACTTT-TCATTTTATTTAAATAAGTTCTTATTCTTTTATTACATCCAAA
1 TAAACTTTGTCACTTCATTTAAATAAGCTCTTATAATTTTACTACATCCAAA
32199534 TAA
1 TAA
32199537 GCCGTTAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 40 0.83
52 8 0.17
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.45
Consensus pattern (52 bp):
TAAACTTTGTCACTTCATTTAAATAAGCTCTTATAATTTTACTACATCCAAA
Found at i:32216039 original size:21 final size:21
Alignment explanation
Indices: 32216013--32216052 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
32216003 TTATATATTA
32216013 TTTGAAG-ATAAAGTTTTTTTT
1 TTTGAAGTATAAA-TTTTTTTT
32216034 TTTGAAGTATAAATTTTTT
1 TTTGAAGTATAAATTTTTT
32216053 CAAATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TTTGAAGTATAAATTTTTTTT
Found at i:32216741 original size:2 final size:2
Alignment explanation
Indices: 32216734--32216761 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32216724 TATCAACCAA
32216734 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
32216762 GATGAGATAG
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:32219395 original size:55 final size:55
Alignment explanation
Indices: 32219336--32219471 Score: 164
Period size: 55 Copynumber: 2.5 Consensus size: 55
32219326 TGTTTGGAGG
* * * * *
32219336 CACACGGGCGTGTGTTAGGGTGTGTGCCTGTTCTATTTGGTGGCACACGGGTTGA
1 CACACGGGCGTGTGTTAGGGTGTGTGCCTATACTATTTGGAGGCACACAGGCTGA
* * * * *
32219391 CACACGGGCATGTGTTAGGGTGCGTGCGTATACTGTTTGGAGGCACACAGGCTGG
1 CACACGGGCGTGTGTTAGGGTGTGTGCCTATACTATTTGGAGGCACACAGGCTGA
* *
32219446 CACACGGGCGTGTGTCAGGATGTGTG
1 CACACGGGCGTGTGTTAGGGTGTGTG
32219472 TGGCACACGA
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.15, C:0.19, G:0.39, T:0.26
Consensus pattern (55 bp):
CACACGGGCGTGTGTTAGGGTGTGTGCCTATACTATTTGGAGGCACACAGGCTGA
Found at i:32219477 original size:41 final size:41
Alignment explanation
Indices: 32219432--32219513 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
32219422 ACTGTTTGGA
* *
32219432 GGCACAC-AGGCTGGCACACGGGCGTGTGTC-AGGATGTGTGT
1 GGCACACGA-GCTGGCACACAGGCGTATGTCAAGG-TGTGTGT
*
32219473 GGCACACGAGCTGGCACATAGGCGTATGTCAAGGTGTGTGT
1 GGCACACGAGCTGGCACACAGGCGTATGTCAAGGTGTGTGT
32219514 ATACTGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 32 0.89
42 4 0.11
ACGTcount: A:0.20, C:0.21, G:0.39, T:0.21
Consensus pattern (41 bp):
GGCACACGAGCTGGCACACAGGCGTATGTCAAGGTGTGTGT
Found at i:32222757 original size:3 final size:3
Alignment explanation
Indices: 32222749--32222775 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
32222739 TTGCAAATAA
32222749 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
32222776 TCGAGAGGAT
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:32223143 original size:17 final size:19
Alignment explanation
Indices: 32223103--32223147 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
32223093 TCACTAAGGT
*
32223103 TTTTTTTTATGTTGACTAA
1 TTTTTTTTATGTTGACCAA
*
32223122 ATTTTTTTAT-TT-ACCAA
1 TTTTTTTTATGTTGACCAA
32223139 TTTTTTTTA
1 TTTTTTTTA
32223148 AAAAAGGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 12 0.52
18 2 0.09
19 9 0.39
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTTTTTATGTTGACCAA
Found at i:32223662 original size:18 final size:17
Alignment explanation
Indices: 32223629--32223662 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
32223619 AATTTAAAAG
*
32223629 TTTTTAAAATTATTATT
1 TTTTTAAAAATATTATT
32223646 TTTTTAAAAATAGTTAT
1 TTTTTAAAAATA-TTAT
32223663 GAAAAGACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTTAAAAATATTATT
Found at i:32228325 original size:12 final size:12
Alignment explanation
Indices: 32228308--32228332 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32228298 ACTATTAAAA
32228308 ACTGGATGAAAT
1 ACTGGATGAAAT
32228320 ACTGGATGAAAT
1 ACTGGATGAAAT
32228332 A
1 A
32228333 ACCAAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (12 bp):
ACTGGATGAAAT
Found at i:32233404 original size:18 final size:20
Alignment explanation
Indices: 32233372--32233409 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
32233362 TTAATTATTT
32233372 TATATTATATGAAATAAATA
1 TATATTATATGAAATAAATA
32233392 TATATTAT-T-AAATAAATA
1 TATATTATATGAAATAAATA
32233410 AAAATAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
TATATTATATGAAATAAATA
Found at i:32237672 original size:16 final size:16
Alignment explanation
Indices: 32237650--32237691 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
32237640 ATTTTATATT
32237650 ATTTTAATATTAAATA
1 ATTTTAATATTAAATA
* *
32237666 TTTTTAAAATTAAATA
1 ATTTTAATATTAAATA
*
32237682 AATTTAATAT
1 ATTTTAATAT
32237692 AATTGATTCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAATATTAAATA
Found at i:32238344 original size:6 final size:6
Alignment explanation
Indices: 32238333--32238358 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
32238323 ATTATACAGA
32238333 CCTACT CCTACT CCTACT CCTACT CC
1 CCTACT CCTACT CCTACT CCTACT CC
32238359 ATCATTGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (6 bp):
CCTACT
Found at i:32246452 original size:29 final size:27
Alignment explanation
Indices: 32246420--32246481 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
32246410 TATAATTCTC
*
32246420 TTTTAATTTTTATAAACTTTTTTTATAAT
1 TTTTAATTTTT-TAAA-TATTTTTATAAT
* * *
32246449 TTTTAGTTTTTTGAATATTTTTATATT
1 TTTTAATTTTTTAAATATTTTTATAAT
32246476 TTTTAA
1 TTTTAA
32246482 AATCATTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 15 0.54
28 3 0.11
29 10 0.36
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (27 bp):
TTTTAATTTTTTAAATATTTTTATAAT
Found at i:32246621 original size:24 final size:23
Alignment explanation
Indices: 32246594--32246644 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
32246584 ATTAATATTT
32246594 TAATTAGTA-TTTTTGTTAAAAAAA
1 TAATTAG-ACTTTTT-TTAAAAAAA
* *
32246618 TAATTTGACTTTTTTTAAAAAAT
1 TAATTAGACTTTTTTTAAAAAAA
32246641 TAAT
1 TAAT
32246645 GATCAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (23 bp):
TAATTAGACTTTTTTTAAAAAAA
Found at i:32254470 original size:6 final size:6
Alignment explanation
Indices: 32254459--32254525 Score: 84
Period size: 6 Copynumber: 11.2 Consensus size: 6
32254449 TCTAAATTTG
* *
32254459 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA ATTAGATA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-A-A TTTAAA TTTAAA
32254507 TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA T
32254526 AAAGATTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
5 9 0.17
6 38 0.72
7 2 0.04
8 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:32256329 original size:163 final size:162
Alignment explanation
Indices: 32256138--32256463 Score: 451
Period size: 163 Copynumber: 2.0 Consensus size: 162
32256128 AATTTTAATT
** ** *
32256138 GGTTTATAATTTAGTCCTTTGACTGTTTGACTGTGCCGGAGGTTGCCACGTGTCATGT-ATTGGA
1 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCAT-TCATTGGA
* *
32256202 TTATTTATGCATTTAGTCCTTTTTTATTTTTTATTTGTTTTAATTTAATCCCCAAATCAAC-TTT
65 TTATTCATGCATTTAGTCC-TTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTT
*
32256266 ATTTTAATTACGAAATTGGCCCAATAA-TTTTTCAA
129 A-TTTAATTACAAAATTGGCCCAA-AATTTTTTCAA
*
32256301 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATTCTTTGGAT
1 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATTCATTGGAT
* * ** *
32256366 TATTCCTTCATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTAT
66 TATTCATGCATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTAT
* *
32256431 TTAATTACAAAATTGGTCTAAAATTTTTTCAA
131 TTAATTACAAAATTGGCCCAAAATTTTTTCAA
32256463 G
1 G
32256464 ATTTCCAAAT
Statistics
Matches: 144, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
161 2 0.01
162 66 0.46
163 76 0.53
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.47
Consensus pattern (162 bp):
GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATTCATTGGAT
TATTCATGCATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTAT
TTAATTACAAAATTGGCCCAAAATTTTTTCAA
Found at i:32256595 original size:30 final size:30
Alignment explanation
Indices: 32256556--32256642 Score: 81
Period size: 30 Copynumber: 2.8 Consensus size: 30
32256546 CCCTAAATTG
32256556 TCCAGAAATTACATTTTACCCCCGAAACTTT-
1 TCCA-AAATTACATTTTACCCCCGAAA-TTTA
* *
32256587 TCCAAAATTATATTTTTAACCCCG--ATTTCA
1 TCCAAAATTACA-TTTTACCCCCGAAATTT-A
*
32256617 TCGAAAATTACCATTTTACCCCCGAA
1 TCCAAAATTA-CATTTTACCCCCGAA
32256643 GCTTCTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
28 3 0.07
29 1 0.02
30 26 0.58
31 15 0.33
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (30 bp):
TCCAAAATTACATTTTACCCCCGAAATTTA
Found at i:32256664 original size:59 final size:59
Alignment explanation
Indices: 32256561--32256934 Score: 572
Period size: 59 Copynumber: 6.3 Consensus size: 59
32256551 AATTGTCCAG
* * **
32256561 AAATTA-CATTTTACCCCCGAAACTTTTCCAAAATTATATTTTTAACCCCGATTTCATCGA
1 AAATTACCATTTTACCCCCGAAGC--TTCTAAAATTCCATTTTTAACCCCGATTTCATCGA
* *
32256621 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCTATTTTTAACCCCGATTTCATCAA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCGA
* * * *
32256680 AAATTACCA-TTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCACCGA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCGA
*
32256738 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCAA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCGA
* * * *
32256797 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAAACCCGATTTCACCGA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCGA
*
32256856 AAATTTCCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCGA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCGA
32256915 AAATTACCATTTTACCCCCG
1 AAATTACCATTTTACCCCCG
32256935 GGTATCCATA
Statistics
Matches: 286, Mismatches: 26, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
58 52 0.18
59 212 0.74
60 6 0.02
61 16 0.06
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (59 bp):
AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCGA
Found at i:32256969 original size:118 final size:118
Alignment explanation
Indices: 32256561--32256934 Score: 635
Period size: 118 Copynumber: 3.2 Consensus size: 118
32256551 AATTGTCCAG
* ** *
32256561 AAATTA-CATTTTACCCCCGAAACTTTTCCAAAATTATATTTTTAACCCCGATTTCATCGAAAAT
1 AAATTACCATTTTACCCCCGAATCTTTT--AAAATTCCATTTTTAACCCCGATTTCACCGAAAAT
*
32256625 TACCATTTTACCCCCGAAGCTTCTAAAATTCTATTTTTAACCCCGATTTCATCAA
64 TACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCAA
*
32256680 AAATTACCA-TTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCACCGAAAATTA
1 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTA
32256744 CCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCAA
66 CCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCAA
* *
32256797 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAAACCCGATTTCACCGAAAATTT
1 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTA
*
32256862 CCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCGA
66 CCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCAA
32256915 AAATTACCATTTTACCCCCG
1 AAATTACCATTTTACCCCCG
32256935 GGTATCCATA
Statistics
Matches: 243, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
117 94 0.39
118 124 0.51
119 23 0.09
120 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (118 bp):
AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTA
CCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCATCAA
Found at i:32271998 original size:136 final size:136
Alignment explanation
Indices: 32271754--32272021 Score: 473
Period size: 136 Copynumber: 2.0 Consensus size: 136
32271744 CAACTGGTTG
* * *
32271754 ATGTTCACTTATCAAATTATATTCCACACAATGGGGAACAGGTCTGCATCAAGATATTAAAGATA
1 ATGTTCACTCATCAAATTATATTCCACACAATAGGGAACAAGTCTGCATCAAGATATTAAAGATA
* *
32271819 GACCACACCAATGCAAAAGGCCTTATATCCTAATAAGGGGGGAAATGGCCAAGAAGATGCTTTTT
66 GACCACAACAATGCAAAAGGCCTTATATCCTAATAAGGGGGGAAATGGCCAAGAAGATGCATTTT
32271884 ATCTTA
131 ATCTTA
*
32271890 ATGTTCACTCATCAAATTATATTCCACAGAATAGGGAACAAGTCTGCATCAAGATATTAAAGATA
1 ATGTTCACTCATCAAATTATATTCCACACAATAGGGAACAAGTCTGCATCAAGATATTAAAGATA
*
32271955 GACCACAACAATGCAAAAGGCCTTGTATCCTAATAAGGGGGGAAATGGCCAAGAAGATGCATTTT
66 GACCACAACAATGCAAAAGGCCTTATATCCTAATAAGGGGGGAAATGGCCAAGAAGATGCATTTT
32272020 AT
131 AT
32272022 TTTTTTCATC
Statistics
Matches: 125, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
136 125 1.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (136 bp):
ATGTTCACTCATCAAATTATATTCCACACAATAGGGAACAAGTCTGCATCAAGATATTAAAGATA
GACCACAACAATGCAAAAGGCCTTATATCCTAATAAGGGGGGAAATGGCCAAGAAGATGCATTTT
ATCTTA
Found at i:32276257 original size:27 final size:26
Alignment explanation
Indices: 32276208--32276256 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
32276198 TAAAAACAAA
32276208 AATTTAAGAATAATTATATTTTTCTGC
1 AATTTAAGAATAATTATATTTTT-TGC
*
32276235 AATTTAAGAA-AA-TATTTTTTTT
1 AATTTAAGAATAATTATATTTTTT
32276257 TTGGAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 8 0.38
26 2 0.10
27 10 0.48
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (26 bp):
AATTTAAGAATAATTATATTTTTTGC
Found at i:32288569 original size:30 final size:32
Alignment explanation
Indices: 32288515--32288576 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 32
32288505 TATAAATTTT
*
32288515 AAAGATTTAAATCAAATTTATATCATTTTTAA
1 AAAGATTTAAATCAAATTTATATCATTATTAA
**
32288547 AAAGA-TTAAATGTAATTT-TATCATTATTAA
1 AAAGATTTAAATCAAATTTATATCATTATTAA
32288577 TTTAAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 11 0.41
31 11 0.41
32 5 0.19
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (32 bp):
AAAGATTTAAATCAAATTTATATCATTATTAA
Found at i:32294563 original size:3 final size:3
Alignment explanation
Indices: 32294548--32294582 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
32294538 ACAATTGGAT
* *
32294548 CAA CAA CAG CAA CAA CAA CCA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
32294583 GTTCGTGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.37, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:32298525 original size:30 final size:30
Alignment explanation
Indices: 32298489--32298550 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
32298479 GTTCATATGA
32298489 TTAATACTGTTTGTTTGATTAATTTAAGAC
1 TTAATACTGTTTGTTTGATTAATTTAAGAC
32298519 TTAATACTGTTTGTTTGATTAATTTAAGAC
1 TTAATACTGTTTGTTTGATTAATTTAAGAC
32298549 TT
1 TT
32298551 CTGCTGCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (30 bp):
TTAATACTGTTTGTTTGATTAATTTAAGAC
Found at i:32298568 original size:30 final size:30
Alignment explanation
Indices: 32298489--32298568 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
32298479 GTTCATATGA
* *
32298489 TTAATACTGTTTGTTTGATTAATTTAAGAC
1 TTAATACTGTTAGTATGATTAATTTAAGAC
* *
32298519 TTAATACTGTTTGTTTGATTAATTTAAGAC
1 TTAATACTGTTAGTATGATTAATTTAAGAC
* *
32298549 TT-CTGCTGCTTAGTATGATT
1 TTAATACTG-TTAGTATGATT
32298569 TAAATATGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 4 0.09
30 41 0.91
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (30 bp):
TTAATACTGTTAGTATGATTAATTTAAGAC
Found at i:32298616 original size:30 final size:30
Alignment explanation
Indices: 32298580--32298640 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
32298570 AAATATGCAA
32298580 ATGCGATACACTAGGTGAAGCAATTATGTT
1 ATGCGATACACTAGGTGAAGCAATTATGTT
32298610 ATGCGATACACTAGGTGAAGCAATTATGTT
1 ATGCGATACACTAGGTGAAGCAATTATGTT
32298640 A
1 A
32298641 ACTCTTTGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (30 bp):
ATGCGATACACTAGGTGAAGCAATTATGTT
Found at i:32307518 original size:9 final size:9
Alignment explanation
Indices: 32307504--32307533 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
32307494 AGTTTACTAC
32307504 TTTTCTTCT
1 TTTTCTTCT
32307513 TTTTCTTCT
1 TTTTCTTCT
*
32307522 TCTTCTTCT
1 TTTTCTTCT
32307531 TTT
1 TTT
32307534 CTTGCTCCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:32307553 original size:3 final size:3
Alignment explanation
Indices: 32307545--32307570 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
32307535 TTGCTCCTGT
32307545 TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TG
32307571 TGTTTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.35, T:0.35
Consensus pattern (3 bp):
TGC
Found at i:32308389 original size:30 final size:29
Alignment explanation
Indices: 32308346--32308407 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
32308336 TTATATTATC
*
32308346 AAAAATTAATATAA-ATTATACA-ATAATAA
1 AAAAATAAATATAACA-TATA-ATATAATAA
32308375 AAAAATAACATATAACATATAATATAATAA
1 AAAAATAA-ATATAACATATAATATAATAA
32308405 AAA
1 AAA
32308408 TGAATGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 8 0.28
30 20 0.69
31 1 0.03
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (29 bp):
AAAAATAAATATAACATATAATATAATAA
Found at i:32314939 original size:7 final size:7
Alignment explanation
Indices: 32314929--32314973 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
32314919 GAGTGAACAT
32314929 TGAAGCA
1 TGAAGCA
32314936 TGAAGCA
1 TGAAGCA
32314943 TGAAGCA
1 TGAAGCA
32314950 TGAAGCA
1 TGAAGCA
32314957 TGAAGCA
1 TGAAGCA
32314964 TGAAGCA
1 TGAAGCA
32314971 TGA
1 TGA
32314974 CCACTGAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.42, C:0.13, G:0.29, T:0.16
Consensus pattern (7 bp):
TGAAGCA
Found at i:32316513 original size:95 final size:95
Alignment explanation
Indices: 32316398--32316587 Score: 380
Period size: 95 Copynumber: 2.0 Consensus size: 95
32316388 AAATATGCTG
32316398 GTTTTTCGTAAAAGTATCATGGAGGCTCTTGAGTCAGATTCAACTTGGGGTGCATGAAAAAAGAG
1 GTTTTTCGTAAAAGTATCATGGAGGCTCTTGAGTCAGATTCAACTTGGGGTGCATGAAAAAAGAG
32316463 GAGAGGAAAATAAGTTTACATTTAATTCAA
66 GAGAGGAAAATAAGTTTACATTTAATTCAA
32316493 GTTTTTCGTAAAAGTATCATGGAGGCTCTTGAGTCAGATTCAACTTGGGGTGCATGAAAAAAGAG
1 GTTTTTCGTAAAAGTATCATGGAGGCTCTTGAGTCAGATTCAACTTGGGGTGCATGAAAAAAGAG
32316558 GAGAGGAAAATAAGTTTACATTTAATTCAA
66 GAGAGGAAAATAAGTTTACATTTAATTCAA
32316588 TTTGGTCCTT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (95 bp):
GTTTTTCGTAAAAGTATCATGGAGGCTCTTGAGTCAGATTCAACTTGGGGTGCATGAAAAAAGAG
GAGAGGAAAATAAGTTTACATTTAATTCAA
Found at i:32318578 original size:17 final size:17
Alignment explanation
Indices: 32318545--32318583 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
32318535 CATAATTATC
32318545 TAAAAAAAATTAACTCAG
1 TAAAAAAAATT-ACTCAG
32318563 TAAAAAAAACTT-CTCAG
1 TAAAAAAAA-TTACTCAG
32318580 TAAA
1 TAAA
32318584 TAAACCTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 9 0.45
19 2 0.10
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.23
Consensus pattern (17 bp):
TAAAAAAAATTACTCAG
Found at i:32319859 original size:13 final size:15
Alignment explanation
Indices: 32319836--32319868 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
32319826 TGCCCACTTG
32319836 TTTTTCTTCTTT-TT
1 TTTTTCTTCTTTATT
32319850 TTTTTC-TCTTTATT
1 TTTTTCTTCTTTATT
32319864 TTTTT
1 TTTTT
32319869 GGTTTAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTCTTCTTTATT
Found at i:32322963 original size:37 final size:38
Alignment explanation
Indices: 32322863--32322965 Score: 91
Period size: 37 Copynumber: 2.7 Consensus size: 38
32322853 GACCTTGAGT
* **
32322863 CGATGAGACACTGGGTGTCATTATTTTACTTCGAATAGATT
1 CGATGAGACACTGGGTGTC---ACTTTACTTCGAATAGAGC
* *** **
32322904 CGATGAGATACTGGGAACCACTTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCACTTTACTTCGAATAGAGC
32322941 CGATGAGACACTGGGTGTCACTTTA
1 CGATGAGACACTGGGTGTCACTTTA
32322966 TTGCTTCGAA
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
37 21 0.43
38 13 0.27
41 15 0.31
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGAATAGAGC
Found at i:32325163 original size:18 final size:18
Alignment explanation
Indices: 32325122--32325164 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
32325112 GCAATTTACT
* *
32325122 ATAAAAAAAAAATAAAAG
1 ATAAAAAAAAAAAAAAAC
*
32325140 AGAAAAAAAAAAAAAAAC
1 ATAAAAAAAAAAAAAAAC
32325158 ATAAAAA
1 ATAAAAA
32325165 TGTATAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.86, C:0.02, G:0.05, T:0.07
Consensus pattern (18 bp):
ATAAAAAAAAAAAAAAAC
Found at i:32325612 original size:21 final size:21
Alignment explanation
Indices: 32325553--32325612 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 21
32325543 ATAATAATTC
32325553 AAAAATTATAATTATAATTATAA
1 AAAAATTA-AATTA-AATTATAA
* *
32325576 AAAAATT-AATAAAAATT-TTA
1 AAAAATTAAAT-TAAATTATAA
32325596 AAAAATTAACATTAAAT
1 AAAAATTAA-ATTAAAT
32325613 ACACGTTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 9 0.29
21 12 0.39
22 3 0.10
23 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAATTAAATTAAATTATAA
Found at i:32325765 original size:24 final size:24
Alignment explanation
Indices: 32325736--32325800 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
32325726 TTTTTTTAAT
*
32325736 TAAAAACTAAATTCAACT-AAAAAA
1 TAAAAACTAAATT-AAATAAAAAAA
*
32325760 TAAAAACCAAA-TAAATAAAAAAA
1 TAAAAACTAAATTAAATAAAAAAA
* *
32325783 TAAAAAATAAATTTAATA
1 TAAAAACTAAATTAAATA
32325801 TTATGCTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 3 0.09
23 16 0.47
24 15 0.44
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.22
Consensus pattern (24 bp):
TAAAAACTAAATTAAATAAAAAAA
Found at i:32325790 original size:15 final size:16
Alignment explanation
Indices: 32325753--32325793 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
32325743 TAAATTCAAC
*
32325753 TAAAAAATAAAAACCA
1 TAAAAAATAAAAACAA
*
32325769 -AATAAATAAAAA-AA
1 TAAAAAATAAAAACAA
32325783 TAAAAAATAAA
1 TAAAAAATAAA
32325794 TTTAATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (16 bp):
TAAAAAATAAAAACAA
Found at i:32327474 original size:29 final size:29
Alignment explanation
Indices: 32327444--32327518 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
32327434 TGATTTGAAA
32327444 TTTAATATATAAAAATTAAAAAGATTAAATT
1 TTTAATATATAAAAA-TAAAAAGATTAAA-T
* *
32327475 TTTAA-AAATAAAAATATAAAGATTAAAT
1 TTTAATATATAAAAATAAAAAGATTAAAT
*
32327503 TTTAAATTTATAAAAA
1 TTT-AATATATAAAAA
32327519 AATATAGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
28 4 0.11
29 14 0.37
30 15 0.39
31 5 0.13
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (29 bp):
TTTAATATATAAAAATAAAAAGATTAAAT
Found at i:32328286 original size:35 final size:35
Alignment explanation
Indices: 32328242--32328316 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
32328232 GCTTAACCAG
* *
32328242 CTTATAAAACAATTCTAAATTATGCTGCCTTAAGC
1 CTTAAAAAACAACTCTAAATTATGCTGCCTTAAGC
*
32328277 CTTAAAAAACAACTCTAAATTATGCTGTCTTAAGC
1 CTTAAAAAACAACTCTAAATTATGCTGCCTTAAGC
32328312 CTTAA
1 CTTAA
32328317 GCATAGAGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (35 bp):
CTTAAAAAACAACTCTAAATTATGCTGCCTTAAGC
Found at i:32330918 original size:23 final size:26
Alignment explanation
Indices: 32330867--32330924 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 26
32330857 GACTTTTTTT
*
32330867 AAATTAAAAACTAAATTCAACTAAAA
1 AAATAAAAAACTAAATTCAACTAAAA
32330893 AAATAAAAAAC-AAATT-AA-TAAAA
1 AAATAAAAAACTAAATTCAACTAAAA
32330916 AAATAAAAA
1 AAATAAAAA
32330925 TTAAATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 14 0.45
24 2 0.06
25 5 0.16
26 10 0.32
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (26 bp):
AAATAAAAAACTAAATTCAACTAAAA
Found at i:32330934 original size:24 final size:24
Alignment explanation
Indices: 32330871--32330936 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
32330861 TTTTTTAAAT
* *
32330871 TAAAAACTAAATTCAACTAAAAAAA
1 TAAAAAATAAATTTAA-TAAAAAAA
*
32330896 TAAAAAACAAA-TTAATAAAAAAA
1 TAAAAAATAAATTTAATAAAAAAA
*
32330919 TAAAAATTAAATTTAATA
1 TAAAAAATAAATTTAATA
32330937 TTATGCTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 17 0.49
24 9 0.26
25 9 0.26
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (24 bp):
TAAAAAATAAATTTAATAAAAAAA
Found at i:32331467 original size:57 final size:58
Alignment explanation
Indices: 32331219--32331447 Score: 408
Period size: 58 Copynumber: 4.0 Consensus size: 58
32331209 AAAATTGAGA
* *
32331219 ATCACAGAAAAA-CAAACACACCAACCCAATCATCATTTGTCTAAATCATATTATAAT
1 ATCACAGAAAAAGAAAATACACCAACCCAATCATCATTTGTCTAAATCATATTATAAT
*
32331276 ATCACAGAAAAAGAAAATACACCAACCGAATCATCATTTGTCTAAATCATATTATAAT
1 ATCACAGAAAAAGAAAATACACCAACCCAATCATCATTTGTCTAAATCATATTATAAT
32331334 ATCACAGAAAAAGAAAATACACCAACCCAATCATCATTTGTCTAAATCATATTATAAT
1 ATCACAGAAAAAGAAAATACACCAACCCAATCATCATTTGTCTAAATCATATTATAAT
*
32331392 GTCACAGAAAAAG-AAATACACCAACCCAATCATCATTTGTCTAAATCATATTATAA
1 ATCACAGAAAAAGAAAATACACCAACCCAATCATCATTTGTCTAAATCATATTATAA
32331448 ACACCATTAA
Statistics
Matches: 166, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
57 55 0.33
58 111 0.67
ACGTcount: A:0.48, C:0.21, G:0.06, T:0.25
Consensus pattern (58 bp):
ATCACAGAAAAAGAAAATACACCAACCCAATCATCATTTGTCTAAATCATATTATAAT
Found at i:32359472 original size:17 final size:18
Alignment explanation
Indices: 32359452--32359485 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
32359442 TGGATGCACC
*
32359452 TGAAGATTTTGG-ATATG
1 TGAAGATCTTGGCATATG
32359469 TGAAGATCTTGGCATAT
1 TGAAGATCTTGGCATAT
32359486 TCTCTGAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.38
Consensus pattern (18 bp):
TGAAGATCTTGGCATATG
Found at i:32365236 original size:104 final size:104
Alignment explanation
Indices: 32365043--32365238 Score: 238
Period size: 104 Copynumber: 1.9 Consensus size: 104
32365033 ACAAAAGTGA
* *
32365043 TTTGAGTCTTTTTGAAAGGTTAACGGATAATTTAACTCTAAAATAAAATAAGGATCAAATTAACA
1 TTTGAGTCTTTTTAAAAGGTTAACGGATAATTTAACTCTAAAAAAAAATAAGGATCAAATTAACA
* * *
32365108 AAATTGTAAACATTGATAACTAAATTTTAGCATTATGCC
66 AAAATGTAAACATTAAAAACTAAATTTTAGCATTATGCC
* * *
32365147 TTTGAGTCTTTTTAAAAGGTTAA-TGATTAAATTT-A-TCTAAAAAAAAATATGGGTCAAATTGA
1 TTTGAGTCTTTTTAAAAGGTTAACGGA-T-AATTTAACTCTAAAAAAAAATAAGGATCAAATT-A
* *
32365209 CCAAAAAAT-TAAACATTAAAAATTAAATTT
63 AC-AAAAATGTAAACATTAAAAACTAAATTT
32365239 AACATAATGT
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
103 24 0.31
104 44 0.56
105 10 0.13
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (104 bp):
TTTGAGTCTTTTTAAAAGGTTAACGGATAATTTAACTCTAAAAAAAAATAAGGATCAAATTAACA
AAAATGTAAACATTAAAAACTAAATTTTAGCATTATGCC
Found at i:32366355 original size:24 final size:23
Alignment explanation
Indices: 32366310--32366359 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
32366300 TGACTATGAA
32366310 TTTTATAATTTCATAATTTTTATT
1 TTTTATAATTTCATAA-TTTTATT
32366334 TTTTATAATTTTCAATAA-TTTATT
1 TTTTATAA-TTTC-ATAATTTTATT
32366358 TT
1 TT
32366360 GATATTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 16 0.67
25 4 0.17
26 4 0.17
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTATAATTTCATAATTTTATT
Found at i:32369587 original size:9 final size:9
Alignment explanation
Indices: 32369569--32369601 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
32369559 TCTATTTTGA
*
32369569 TTTTTGATT
1 TTTTTAATT
32369578 TTTTTAA-T
1 TTTTTAATT
32369586 TTTTTAATT
1 TTTTTAATT
32369595 TTTTTAA
1 TTTTTAA
32369602 AGTTGATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTTTAATT
Found at i:32369595 original size:17 final size:17
Alignment explanation
Indices: 32369569--32369601 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
32369559 TCTATTTTGA
*
32369569 TTTTTGATTTTTTTAAT
1 TTTTTAATTTTTTTAAT
32369586 TTTTTAATTTTTTTAA
1 TTTTTAATTTTTTTAA
32369602 AGTTGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTAATTTTTTTAAT
Found at i:32370665 original size:2 final size:2
Alignment explanation
Indices: 32370660--32370689 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
32370650 AAAAAAAAAA
32370660 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
32370690 TATTCTTGAA
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:32390530 original size:153 final size:153
Alignment explanation
Indices: 32390252--32390549 Score: 517
Period size: 153 Copynumber: 1.9 Consensus size: 153
32390242 GGAGCTTTAG
* *
32390252 ATTGAGTTTAACAAGGGCCTGGATCTCACTTTTGACATTATCATCTTTTCTATCCTTGCTTTTGG
1 ATTGAGTTTAACAAGGGCCTGAATCTCACTTTTGAAATTATCATCTTTTCTATCCTTGCTTTTGG
32390317 AACAACTCTTCTCCAACCGTGTTCTCCCCTCCGGTATATCTAACTTATTTACACCTGCCTCCAAG
66 AACAACTCTTCTCCAACCGTGTTCTCCCCTCCGGTATATCTAACTTATTTACACCTGCCTCCAAG
32390382 TTGGAATCCAAAGAACGCCCTGA
131 TTGGAATCCAAAGAACGCCCTGA
* *
32390405 ATTGAGTTTAACAAGGGTCTGAATCTCACTTTTGAAATTATCATCTTTTCTATCGTTGCTTTTGG
1 ATTGAGTTTAACAAGGGCCTGAATCTCACTTTTGAAATTATCATCTTTTCTATCCTTGCTTTTGG
* * *
32390470 AACAACTCTTCTCCAACC-TCGTTCTCCCCTCCTGTATATCTAATTTATTTACACCTGCCTCCAG
66 AACAACTCTTCTCCAACCGT-GTTCTCCCCTCCGGTATATCTAACTTATTTACACCTGCCTCCAA
32390534 GTTGGAATCCAAAGAA
130 GTTGGAATCCAAAGAA
32390550 TCCATAGATC
Statistics
Matches: 137, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
152 1 0.01
153 136 0.99
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.36
Consensus pattern (153 bp):
ATTGAGTTTAACAAGGGCCTGAATCTCACTTTTGAAATTATCATCTTTTCTATCCTTGCTTTTGG
AACAACTCTTCTCCAACCGTGTTCTCCCCTCCGGTATATCTAACTTATTTACACCTGCCTCCAAG
TTGGAATCCAAAGAACGCCCTGA
Found at i:32392848 original size:21 final size:21
Alignment explanation
Indices: 32392824--32392866 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
32392814 TTATGTAATT
* *
32392824 TATATTATAAAAATTTAAATA
1 TATAATATAAAAATATAAATA
* *
32392845 TATAATATTATAATATAAATA
1 TATAATATAAAAATATAAATA
32392866 T
1 T
32392867 TAACAATATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATAATATAAAAATATAAATA
Found at i:32392883 original size:29 final size:29
Alignment explanation
Indices: 32392819--32392884 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
32392809 ATATATTATG
* *
32392819 TAAT-TTATATTATAAAAATTTAAATATA
1 TAATATTATAATATAAAAATTAAAATATA
* *
32392847 TAATATTATAATATAAATATTAACAATATT
1 TAATATTATAATATAAAAATTAA-AATATA
32392877 TAA-ATTAT
1 TAATATTAT
32392885 TTGTATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 4 0.12
29 20 0.62
30 8 0.25
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
TAATATTATAATATAAAAATTAAAATATA
Found at i:32395985 original size:39 final size:39
Alignment explanation
Indices: 32395900--32395988 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
32395890 ATTTATTGAG
* *
32395900 ATGTATACAATTGAATTAAAATCAAAGTTTTATGTATAA
1 ATGTATACATTTGAATTAAAATCAAAGTTTCATGTATAA
* * *
32395939 TTGTATACATTTGAATTACAATCGAAA-TTTCATGTGTAAA
1 ATGTATACATTTGAATTAAAATC-AAAGTTTCATGTAT-AA
32395979 AT-TATACATT
1 ATGTATACATT
32395989 AAATCAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
39 36 0.86
40 6 0.14
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (39 bp):
ATGTATACATTTGAATTAAAATCAAAGTTTCATGTATAA
Found at i:32401150 original size:16 final size:17
Alignment explanation
Indices: 32401117--32401165 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
32401107 AGTTTAAAAA
* *
32401117 ATTTCAAAAACA-TCTT
1 ATTTCAAAAATATTTTT
*
32401133 ATTT-AACAATATTTTT
1 ATTTCAAAAATATTTTT
32401149 ATTTCAAAAATATTTTT
1 ATTTCAAAAATATTTTT
32401166 TGTCCCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 5 0.19
16 11 0.41
17 11 0.41
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTCAAAAATATTTTT
Found at i:32403538 original size:16 final size:18
Alignment explanation
Indices: 32403512--32403545 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
32403502 TCAAATTAAC
32403512 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
32403529 TAAA-TAATTTTCTCAAT
1 TAAATTAATTTTCTCAAT
32403546 CCAATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:32404158 original size:24 final size:27
Alignment explanation
Indices: 32404106--32404160 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 27
32404096 CTAGGACCGG
32404106 TGAAAAGAAGAGAGGAAGCTAAGGAAAAA
1 TGAAAAGAAGAGAGGAAG--AAGGAAAAA
32404135 TGAAAAGAAGAGAGGAAG-A-GAAAAA
1 TGAAAAGAAGAGAGGAAGAAGGAAAAA
32404160 T
1 T
32404161 ACAAGGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 7 0.27
26 1 0.04
29 18 0.69
ACGTcount: A:0.60, C:0.02, G:0.31, T:0.07
Consensus pattern (27 bp):
TGAAAAGAAGAGAGGAAGAAGGAAAAA
Found at i:32411308 original size:46 final size:46
Alignment explanation
Indices: 32411256--32411348 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
32411246 TAGTTAGAAG
* * * *
32411256 TTAATTATTTGTTGAATTATGTAG-TTTTGTGCTTGTAATTTTTGAT
1 TTAATTAGTTGTAGAATTAT-TAGATTTCGTGCTTGTAATTATTGAT
* *
32411302 TTAATTAGTTGTAGAGTTATTCGATTTCGTGCTTGTAATTATTGAT
1 TTAATTAGTTGTAGAATTATTAGATTTCGTGCTTGTAATTATTGAT
32411348 T
1 T
32411349 CTGATTGGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
45 2 0.05
46 38 0.95
ACGTcount: A:0.23, C:0.04, G:0.18, T:0.55
Consensus pattern (46 bp):
TTAATTAGTTGTAGAATTATTAGATTTCGTGCTTGTAATTATTGAT
Found at i:32419912 original size:2 final size:2
Alignment explanation
Indices: 32419905--32419935 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
32419895 ATCAAATTGC
32419905 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32419936 CATCATACTA
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):
AT
Found at i:32427142 original size:130 final size:129
Alignment explanation
Indices: 32426907--32427239 Score: 461
Period size: 130 Copynumber: 2.6 Consensus size: 129
32426897 AGTTTAGCCG
* * * * *
32426907 AATTTTCAATCCTTTTTCATTTTTCATGCTTTTTCTTAAAATTTCATTTTATTTCCCTTTGTTGA
1 AATTTTCAATTCTTTTTCATTTTCCAT-TTTTTTCTTAAAATTTCATTTTATTTTCCTCTGTTGA
* * * **
32426972 CTGAATTATTTTTTACTGCCTCCACCCGAAGAACTTTGTTACTATAAAAACAACAAAATCAAACC
65 CTGAATTATTCTTCACTACCTCCACCCGAAGAACCCTGTTACTATAAAAACAACAAAATCAAACC
* * *
32427037 AATTTTCAATTCTTTTTCATTTTCCATATTTTTTCTTAAATTTTCATTTTCTTTTACTCTGTTGA
1 AATTTTCAATTCTTTTTCATTTTCCAT-TTTTTTCTTAAAATTTCATTTTATTTTCCTCTGTTGA
* *
32427102 CTGAATTATTCTTCACTACCTCCACCTGAA-AACCCCTGTTACTGTAAAAACAACAAAATCAAAC
65 CTGAATTATTCTTCACTACCTCCACCCGAAGAA-CCCTGTTACTATAAAAACAACAAAATCAAAC
32427166 C
129 C
*
32427167 AATTTTCAATTCTTTTTCATTTTTCACATTTTTTTCTTAAAATTTCATTTTATTTTCCCCTGTTG
1 AATTTTCAATTCTTTTTCA-TTTTC-CATTTTTTTCTTAAAATTTCATTTTATTTTCCTCTGTTG
*
32427232 ATTGAATT
64 ACTGAATT
32427240 TCCAGCGACG
Statistics
Matches: 179, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
129 2 0.01
130 130 0.73
131 44 0.25
132 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (129 bp):
AATTTTCAATTCTTTTTCATTTTCCATTTTTTTCTTAAAATTTCATTTTATTTTCCTCTGTTGAC
TGAATTATTCTTCACTACCTCCACCCGAAGAACCCTGTTACTATAAAAACAACAAAATCAAACC
Found at i:32427821 original size:16 final size:17
Alignment explanation
Indices: 32427800--32427831 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
32427790 AAAGTTAAAC
32427800 ATTTTAAT-AAAATAAT
1 ATTTTAATGAAAATAAT
32427816 ATTTTAATGAAAATAA
1 ATTTTAATGAAAATAA
32427832 CTTTTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
ATTTTAATGAAAATAAT
Found at i:32429343 original size:101 final size:100
Alignment explanation
Indices: 32429221--32429406 Score: 255
Period size: 101 Copynumber: 1.9 Consensus size: 100
32429211 ATTAATGCAT
* * * **
32429221 TAATTAAATTCTATTAATTAATGCAATTAAAGCTGTATATGGGCATAGAATTGCCATTCGAAAGG
1 TAATTAAATTCCATTAATTAATGCAATTAAAGCTGCACATAAGCATAGAATTGCCATTCGAAAGG
*
32429286 CGGAATGGGTCATTAATTGCATAATAGGTTTTAATG
66 CGAAATGGGT-ATTAATTGCATAATAGGTTTTAATG
* * * * *
32429322 TAATTCAATTCCATTAGTTAATGCAATTAAAGTTGCACATAAGCATAGAATTGCCCTTGGAAAGG
1 TAATTAAATTCCATTAATTAATGCAATTAAAGCTGCACATAAGCATAGAATTGCCATTCGAAAGG
*
32429387 CGAAATGGGTTTTAATTGCA
66 CGAAATGGGTATTAATTGCA
32429407 GCAATAAATG
Statistics
Matches: 73, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
100 9 0.12
101 64 0.88
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (100 bp):
TAATTAAATTCCATTAATTAATGCAATTAAAGCTGCACATAAGCATAGAATTGCCATTCGAAAGG
CGAAATGGGTATTAATTGCATAATAGGTTTTAATG
Found at i:32435731 original size:2 final size:2
Alignment explanation
Indices: 32435726--32435753 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32435716 TTTAAATTTA
32435726 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
32435754 TGAGCACATT
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:32439981 original size:23 final size:23
Alignment explanation
Indices: 32439955--32440002 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
32439945 TCCTCCTATT
32439955 TATGTGTTGGGATGGACTATGAA
1 TATGTGTTGGGATGGACTATGAA
32439978 TATGTGTTGGGATGGACTATGAA
1 TATGTGTTGGGATGGACTATGAA
32440001 TA
1 TA
32440003 ATTGTAGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.04, G:0.33, T:0.35
Consensus pattern (23 bp):
TATGTGTTGGGATGGACTATGAA
Found at i:32442880 original size:21 final size:22
Alignment explanation
Indices: 32442844--32442891 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
32442834 TTAAAGTAAT
32442844 TTTATATTAAATAATAATT-AAA
1 TTTATATTAAATAAT-ATTAAAA
*
32442866 TTTATATT-TATAATATTAAAA
1 TTTATATTAAATAATATTAAAA
32442887 TTTAT
1 TTTAT
32442892 GTATTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 13 0.54
22 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTATATTAAATAATATTAAAA
Found at i:32445981 original size:22 final size:23
Alignment explanation
Indices: 32445951--32445993 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
32445941 TAACGTTTGA
*
32445951 GTGACTAAAATAAAATTTTAATG
1 GTGACTAAAATAAAATATTAATG
32445974 GTGA-TAAAATAAAATATTAA
1 GTGACTAAAATAAAATATTAA
32445994 AAAATTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (23 bp):
GTGACTAAAATAAAATATTAATG
Found at i:32446013 original size:30 final size:29
Alignment explanation
Indices: 32445975--32446036 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
32445965 ATTTTAATGG
32445975 TGATAAAAT-AAAATAT-TAAAAAATTCAGA
1 TGATAAAATGAAAATATAT-AAAAATT-AGA
32446004 TGATCAAAATGAAAATATATAAAAATTAGA
1 TGAT-AAAATGAAAATATATAAAAATTAGA
32446034 TGA
1 TGA
32446037 CTAATTGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 4 0.13
30 11 0.37
31 14 0.47
32 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.27
Consensus pattern (29 bp):
TGATAAAATGAAAATATATAAAAATTAGA
Found at i:32446028 original size:31 final size:28
Alignment explanation
Indices: 32445975--32446036 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 28
32445965 ATTTTAATGG
32445975 TGATAAAATAAAATATTAAAAAATTCAGA
1 TGATAAAATAAAATATTAAAAAATT-AGA
32446004 TGATCAAAATGAAAATA-TATAAAAATTAGA
1 TGAT-AAAAT-AAAATATTA-AAAAATTAGA
32446034 TGA
1 TGA
32446037 CTAATTGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 4 0.13
30 13 0.43
31 13 0.43
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.27
Consensus pattern (28 bp):
TGATAAAATAAAATATTAAAAAATTAGA
Found at i:32456680 original size:30 final size:31
Alignment explanation
Indices: 32456644--32456704 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
32456634 AAAGTATTTA
*
32456644 AAAAATTTTAATTAGACCTTTCAA-ATTTTT
1 AAAAATTCTAATTAGACCTTTCAATATTTTT
* * *
32456674 AAAAATTCTCATTATACCTTTTAATATTTTT
1 AAAAATTCTAATTAGACCTTTCAATATTTTT
32456705 TTGAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (31 bp):
AAAAATTCTAATTAGACCTTTCAATATTTTT
Found at i:32458674 original size:20 final size:20
Alignment explanation
Indices: 32458651--32458692 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
32458641 AATTAAATAG
32458651 AATA-ATTAAAAATAAATTTA
1 AATATATTAAAAA-AAATTTA
* *
32458671 AATATCTTTAAAAAAATTTA
1 AATATATTAAAAAAAATTTA
32458691 AA
1 AA
32458693 AAATACATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATATTAAAAAAAATTTA
Found at i:32477631 original size:18 final size:19
Alignment explanation
Indices: 32477590--32477643 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
32477580 TACATGTGCT
32477590 ATTTTTTAA-TTTTTATGA
1 ATTTTTTAATTTTTTATGA
32477608 ACTTTTTTAATTTTTTAT-A
1 A-TTTTTTAATTTTTTATGA
* *
32477627 ATTTTTAAATTATTTAT
1 ATTTTTTAATTTTTTAT
32477644 CAATATGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 15 0.47
19 10 0.31
20 7 0.22
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTTTAATTTTTTATGA
Found at i:32477856 original size:2 final size:2
Alignment explanation
Indices: 32477849--32477886 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
32477839 TAAATTTGAC
32477849 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32477887 ATTTTATCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32493957 original size:4 final size:4
Alignment explanation
Indices: 32493948--32493974 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
32493938 GTGGAGGGAC
32493948 CATG CATG CATG CATG CATG CATG CAT
1 CATG CATG CATG CATG CATG CATG CAT
32493975 TGCCTAGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (4 bp):
CATG
Found at i:32494692 original size:19 final size:21
Alignment explanation
Indices: 32494668--32494719 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
32494658 TTTTAAAATT
*
32494668 AAAATTTAT-ATT-TCAATAA
1 AAAATTTATAATTATAAATAA
32494687 AAAA-TTATAATTATAAATAA
1 AAAATTTATAATTATAAATAA
* *
32494707 AAATTTTAAAATT
1 AAAATTTATAATT
32494720 CAGTGTTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 4 0.15
19 7 0.26
20 9 0.33
21 7 0.26
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATTTATAATTATAAATAA
Found at i:32497301 original size:161 final size:161
Alignment explanation
Indices: 32497023--32497350 Score: 570
Period size: 161 Copynumber: 2.0 Consensus size: 161
32497013 TAATCCTCAG
*
32497023 TTTC-AGAAATATCGTGTTAACATCTTTCCTTTGACCTTGCACTTTGACATCCACACTCGTCTCA
1 TTTCAAGAAATATCGTGTTAACATCTTTCCTTTGACCTTGCACTTTGACATCCACACTCATCTCA
32497087 GATTGAAGATCCTTGGTATTTCCCCTGAAATTAGTCGGATCAGAAGTACTATCTGCATTTAT-AA
66 GATTGAAGATCCTTGGTATTTCCCCTGAAATTAGTCGGATCAGAAGTACTATCTGCATTTATCAA
*
32497151 TATGAAAATGTGAGGCCCAAAATACTGAAACC
131 -ATGAAAATGTGAGGCCCAAAATACTGAAACA
* * *
32497183 TTTCAAGAAGTATGGTGTTAACGTCTTTCCTTTGACCTTGCACTTTGACATCCACACTCATCTCA
1 TTTCAAGAAATATCGTGTTAACATCTTTCCTTTGACCTTGCACTTTGACATCCACACTCATCTCA
*
32497248 GATTGAATATCCTTGGTATTTCCCCTGAAATTAGTCGGATCAGAAGTACTATCTGCATTTATCAA
66 GATTGAAGATCCTTGGTATTTCCCCTGAAATTAGTCGGATCAGAAGTACTATCTGCATTTATCAA
*
32497313 ATGAAAATGTGAGGCCCAAAATATTGAAACA
131 ATGAAAATGTGAGGCCCAAAATACTGAAACA
32497344 TTTCAAG
1 TTTCAAG
32497351 CTCCAAAAAA
Statistics
Matches: 159, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
160 4 0.03
161 153 0.96
162 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (161 bp):
TTTCAAGAAATATCGTGTTAACATCTTTCCTTTGACCTTGCACTTTGACATCCACACTCATCTCA
GATTGAAGATCCTTGGTATTTCCCCTGAAATTAGTCGGATCAGAAGTACTATCTGCATTTATCAA
ATGAAAATGTGAGGCCCAAAATACTGAAACA
Found at i:32503560 original size:2 final size:2
Alignment explanation
Indices: 32503553--32503577 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32503543 TTAATCCGTA
32503553 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
32503578 CATTTGTGTA
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:32507232 original size:49 final size:49
Alignment explanation
Indices: 32507155--32507250 Score: 165
Period size: 49 Copynumber: 2.0 Consensus size: 49
32507145 TAACAACATC
* *
32507155 GTACATCGTTGCCTATTGTGGTAGGCTTTGGTACCAAATCGTTATGATA
1 GTACATCGTTGCCTATTGTGATAAGCTTTGGTACCAAATCGTTATGATA
*
32507204 GTACATCGTTGCCTATTGTGATAAGCTTTGGTACCAAATTGTTATGA
1 GTACATCGTTGCCTATTGTGATAAGCTTTGGTACCAAATCGTTATGA
32507251 ATACACAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.38
Consensus pattern (49 bp):
GTACATCGTTGCCTATTGTGATAAGCTTTGGTACCAAATCGTTATGATA
Found at i:32513326 original size:22 final size:22
Alignment explanation
Indices: 32513290--32513335 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
32513280 TCCGTACTCA
32513290 TTTACTATTAATAAATTTCAAC
1 TTTACTATTAATAAATTTCAAC
* *
32513312 TTTACTTTTATTAAATTTCAAC
1 TTTACTATTAATAAATTTCAAC
32513334 TT
1 TT
32513336 GGTAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTACTATTAATAAATTTCAAC
Found at i:32519291 original size:31 final size:30
Alignment explanation
Indices: 32519134--32519291 Score: 94
Period size: 31 Copynumber: 5.2 Consensus size: 30
32519124 AATTAGGGCT
* * *
32519134 TGAACTTGGCAATTGTTCCAACATTGGGGCC
1 TGAACTTGGTAATTGTTCCCACATT-GAGCC
* ** *
32519165 TGAACTAGGTAACAGTTCCCACATTGAGACT
1 TGAACTTGGTAATTGTTCCCACATTGAG-CC
**
32519196 TGAACTT--TTGTTG-T-CCA-AGTT-AGTCC
1 TGAACTTGGTAATTGTTCCCACA-TTGAG-CC
* * *
32519222 TTGAATTTGGTAATTGTTCTCATATTGAGGCC
1 -TGAACTTGGTAATTGTTCCCACATTGA-GCC
*
32519254 TAAACTTGGTAATTGTTCCCACATTGGAGCC
1 TGAACTTGGTAATTGTTCCCACATT-GAGCC
32519285 TGAACTT
1 TGAACTT
32519292 TAGGGTTTTC
Statistics
Matches: 93, Mismatches: 23, Indels: 22
0.67 0.17 0.16
Matches are distributed among these distances:
26 4 0.04
27 11 0.12
28 1 0.01
29 6 0.06
30 3 0.03
31 61 0.66
32 6 0.06
33 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (30 bp):
TGAACTTGGTAATTGTTCCCACATTGAGCC
Found at i:32519426 original size:59 final size:57
Alignment explanation
Indices: 32519307--32519419 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 57
32519297 TTTTCAAGGG
* * *
32519307 CTAACTTGGGAAAAAAAGTTCAAGCCCCAATGTGAGAACAATGGCCAAGTTCAAAGC
1 CTAACTTGGCAAAAAAAGTTCAAGCCCCAAAGTGAGAACAATGGCCAAATTCAAAGC
* *
32519364 CTAACTTGGACAAAATAAAGTTCAGGCCCCAAAGTGAGAA-AAGTTGCCAAATTCAA
1 CTAACTTGG-CAAAA-AAAGTTCAAGCCCCAAAGTGAGAACAA-TGGCCAAATTCAA
32519420 GACCTAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 9 0.19
58 6 0.12
59 33 0.69
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (57 bp):
CTAACTTGGCAAAAAAAGTTCAAGCCCCAAAGTGAGAACAATGGCCAAATTCAAAGC
Found at i:32523527 original size:24 final size:23
Alignment explanation
Indices: 32523482--32523527 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
32523472 ATTAATATAA
* * *
32523482 TTTATTTTTAAGAATTTTATTTC
1 TTTATTTTTAACAAATTAATTTC
32523505 TTTAGTTTTTAACAAATTAATTT
1 TTTA-TTTTTAACAAATTAATTT
32523528 TTAACAATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (23 bp):
TTTATTTTTAACAAATTAATTTC
Found at i:32525903 original size:14 final size:14
Alignment explanation
Indices: 32525886--32525956 Score: 53
Period size: 15 Copynumber: 5.1 Consensus size: 14
32525876 TATTTTTAAT
32525886 ATAATATTATTTTA
1 ATAATATTATTTTA
*
32525900 AT-A-A-CA-TTTA
1 ATAATATTATTTTA
32525910 ATGAATATTATTTTA
1 AT-AATATTATTTTA
*
32525925 A-AACAATTATTTTTA
1 ATAA-TATTA-TTTTA
32525940 ATAAATATTATTTTA
1 AT-AATATTATTTTA
32525955 AT
1 AT
32525957 GATTATTGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 17
0.68 0.06 0.26
Matches are distributed among these distances:
10 6 0.14
11 1 0.02
12 2 0.05
13 4 0.09
14 7 0.16
15 18 0.41
16 4 0.09
17 2 0.05
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (14 bp):
ATAATATTATTTTA
Found at i:32525951 original size:16 final size:16
Alignment explanation
Indices: 32525906--32525953 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
32525896 TTTAATAACA
*
32525906 TTTAATGAATATTA-T
1 TTTAATAAATATTATT
32525921 TTTAA-AACA-ATTATT
1 TTTAATAA-ATATTATT
32525936 TTTAATAAATATTATT
1 TTTAATAAATATTATT
32525952 TT
1 TT
32525954 AATGATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 5 0.18
15 13 0.46
16 10 0.36
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TTTAATAAATATTATT
Found at i:32541567 original size:18 final size:18
Alignment explanation
Indices: 32541546--32541585 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
32541536 TCAGTTGTAG
32541546 TTAATTTAAAATT-TTTAA
1 TTAA-TTAAAATTATTTAA
*
32541564 TTAATTAAATTTATTTAA
1 TTAATTAAAATTATTTAA
32541582 TTAA
1 TTAA
32541586 AAATTTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTAAAATTATTTAA
Found at i:32552127 original size:12 final size:12
Alignment explanation
Indices: 32552110--32552155 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
32552100 ATAACATTCA
32552110 AACAACAAAAAT
1 AACAACAAAAAT
*
32552122 AACAACCAAAAT
1 AACAACAAAAAT
*
32552134 AACAGC-AAAAT
1 AACAACAAAAAT
*
32552145 AGCAACAAAAA
1 AACAACAAAAA
32552156 AATAGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.70, C:0.20, G:0.04, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:32552186 original size:21 final size:19
Alignment explanation
Indices: 32552154--32552217 Score: 92
Period size: 21 Copynumber: 3.2 Consensus size: 19
32552144 TAGCAACAAA
32552154 AAAATAGTAAAAACAAAATC
1 AAAATAGTAAAAA-AAAATC
*
32552174 AAAATAGTAAAAAAAAGCACC
1 AAAATAGTAAAAAAAA--ATC
32552195 AAAATAGTAAAAAAAAATC
1 AAAATAGTAAAAAAAAATC
32552214 AAAA
1 AAAA
32552218 CAGCAATCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.22
20 13 0.32
21 18 0.45
ACGTcount: A:0.72, C:0.09, G:0.06, T:0.12
Consensus pattern (19 bp):
AAAATAGTAAAAAAAAATC
Done.