Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 108 of 160
Found at i:20441731 original size:22 final size:23
Alignment explanation
Indices: 20441706--20441749 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
20441696 TTCAAAGGAG
20441706 TAAAAAATTTTACTA-TTATTTA
1 TAAAAAATTTTACTATTTATTTA
* *
20441728 TAAAGACTTTTACTATTTATTT
1 TAAAAAATTTTACTATTTATTT
20441750 TCAACGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (23 bp):
TAAAAAATTTTACTATTTATTTA
Found at i:20441939 original size:2 final size:2
Alignment explanation
Indices: 20441932--20441957 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20441922 AAATTGGTGG
20441932 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
20441958 GTAAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20442616 original size:21 final size:22
Alignment explanation
Indices: 20442579--20442620 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
20442569 CAAAACTCTC
*
20442579 CATCATTTTGTAAATTTAAATG
1 CATCATTTTGCAAATTTAAATG
20442601 CATCATTTT-CAAATTTAAAT
1 CATCATTTTGCAAATTTAAAT
20442621 TTAACAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (22 bp):
CATCATTTTGCAAATTTAAATG
Found at i:20443170 original size:13 final size:14
Alignment explanation
Indices: 20443149--20443177 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20443139 AAAATTACAA
20443149 AAAAGATTTTTATT
1 AAAAGATTTTTATT
20443163 AAAA-ATTTTTATT
1 AAAAGATTTTTATT
20443176 AA
1 AA
20443178 TCAGTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
AAAAGATTTTTATT
Found at i:20443816 original size:18 final size:19
Alignment explanation
Indices: 20443789--20443834 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
20443779 TTTTTTGAAA
*
20443789 ATAAATTTTCATAAAG-TT
1 ATAAATTTTCAAAAAGTTT
*
20443807 ATATATTTTCAAAAAGTTT
1 ATAAATTTTCAAAAAGTTT
20443826 ATAAATTTT
1 ATAAATTTT
20443835 TGGAAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (19 bp):
ATAAATTTTCAAAAAGTTT
Found at i:20453777 original size:163 final size:163
Alignment explanation
Indices: 20453588--20453916 Score: 640
Period size: 163 Copynumber: 2.0 Consensus size: 163
20453578 ATCGGCTTTA
20453588 TGAATCATATTGTAATACTATACTCCATTTAAAACCATATTTCAATAAGCACAGTAAAACCCTGG
1 TGAATCATATTGTAATACTATACTCCATTTAAAACCATATTTCAATAAGCACAGTAAAACCCTGG
*
20453653 TCCATGGAATAATTGAGATATGGAAAAAAGCATAATAAAGAACTGCATTGATTGTGAACTTCTTC
66 TCCATGGAATAATTGAGATATGGAAAAAAACATAATAAAGAACTGCATTGATTGTGAACTTCTTC
20453718 AAAAACTGGGAGTAAGTCTAGGCTGAATATGAT
131 AAAAACTGGGAGTAAGTCTAGGCTGAATATGAT
20453751 TGAATCATATTGTAATACTATACTCCATTTAAAACCATATTTCAATAAGCACAGTAAAACCCTGG
1 TGAATCATATTGTAATACTATACTCCATTTAAAACCATATTTCAATAAGCACAGTAAAACCCTGG
*
20453816 TCCATGGGATAATTGAGATATGGAAAAAAACATAATAAAGAACTGCATTGATTGTGAACTTCTTC
66 TCCATGGAATAATTGAGATATGGAAAAAAACATAATAAAGAACTGCATTGATTGTGAACTTCTTC
20453881 AAAAACTGGGAGTAAGTCTAGGCTGAATATGAT
131 AAAAACTGGGAGTAAGTCTAGGCTGAATATGAT
20453914 TGA
1 TGA
20453917 TTTTCCTTAC
Statistics
Matches: 164, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 164 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (163 bp):
TGAATCATATTGTAATACTATACTCCATTTAAAACCATATTTCAATAAGCACAGTAAAACCCTGG
TCCATGGAATAATTGAGATATGGAAAAAAACATAATAAAGAACTGCATTGATTGTGAACTTCTTC
AAAAACTGGGAGTAAGTCTAGGCTGAATATGAT
Found at i:20461532 original size:2 final size:2
Alignment explanation
Indices: 20461525--20461567 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
20461515 AATTTAAAAC
20461525 GA GA GA GA 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 GA GA GA GA
20461567 G
1 G
20461568 TCTGTATACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:20471335 original size:30 final size:30
Alignment explanation
Indices: 20471299--20471358 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
20471289 TAAAATATTA
* **
20471299 TATTAATTAAATGTTTTCATTTGATTTACT
1 TATTAATGAAATGTCATCATTTGATTTACT
**
20471329 TATTAATGAGTTGTCATCATTTGATTTACT
1 TATTAATGAAATGTCATCATTTGATTTACT
20471359 GATAATATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (30 bp):
TATTAATGAAATGTCATCATTTGATTTACT
Found at i:20475020 original size:28 final size:29
Alignment explanation
Indices: 20474954--20475021 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
20474944 ATAAAAACCT
20474954 CCAAAACCA-TTTCTTTAAAAAGAAAATC
1 CCAAAACCATTTTCTTTAAAAAGAAAATC
* * *
20474982 CCGAAATCATTTTC-TTAAAAAGAAGATC
1 CCAAAACCATTTTCTTTAAAAAGAAAATC
*
20475010 CTAAAACCATTT
1 CCAAAACCATTT
20475022 AAGAAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 29 0.88
29 4 0.12
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.28
Consensus pattern (29 bp):
CCAAAACCATTTTCTTTAAAAAGAAAATC
Found at i:20475620 original size:16 final size:19
Alignment explanation
Indices: 20475599--20475635 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
20475589 ATAATTCCGA
20475599 AATTAT-TTA-ACAA-AAC
1 AATTATATTATACAACAAC
20475615 AATTATATTATACAACAAC
1 AATTATATTATACAACAAC
20475634 AA
1 AA
20475636 CAAACTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
17 3 0.17
18 4 0.22
19 5 0.28
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTATATTATACAACAAC
Found at i:20486121 original size:19 final size:20
Alignment explanation
Indices: 20486099--20486136 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
20486089 TGGTTTTTGG
20486099 TTTTAGGTTTTATT-TTTAA
1 TTTTAGGTTTTATTATTTAA
**
20486118 TTTTATTTTTTATTATTTA
1 TTTTAGGTTTTATTATTTA
20486137 TGATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTAGGTTTTATTATTTAA
Found at i:20486150 original size:22 final size:19
Alignment explanation
Indices: 20486106--20486149 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 19
20486096 TGGTTTTAGG
20486106 TTTTATTTTTAATTTTATT
1 TTTTATTTTTAATTTTATT
20486125 TTTTATTATTTATGATTTT-TT
1 TTTTATT-TTTA--ATTTTATT
20486146 TTTT
1 TTTT
20486150 TGCTAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 6 0.27
22 5 0.23
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTATTTTTAATTTTATT
Found at i:20487084 original size:22 final size:22
Alignment explanation
Indices: 20487050--20487091 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20487040 TAAAACCTAT
* *
20487050 AAGATTTGTGTGTTGACCCATC
1 AAGAGTTGCGTGTTGACCCATC
20487072 AAGAGTTGCGTGTTGACCCA
1 AAGAGTTGCGTGTTGACCCA
20487092 CTCCAGACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (22 bp):
AAGAGTTGCGTGTTGACCCATC
Found at i:20487168 original size:23 final size:21
Alignment explanation
Indices: 20487142--20487186 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
20487132 TCAATTTTGA
20487142 TTTGATTTGATTTTCTTATATTT
1 TTTGATTTGATTTT-TT-TATTT
* *
20487165 TTTGTTTTTATTTTTTTATTT
1 TTTGATTTGATTTTTTTATTT
20487186 T
1 T
20487187 ATTTTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 2 0.10
23 12 0.60
ACGTcount: A:0.13, C:0.02, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTGATTTGATTTTTTTATTT
Found at i:20487418 original size:20 final size:19
Alignment explanation
Indices: 20487393--20487430 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
20487383 TATTGGCATG
20487393 TTGCATGATATTTTATATTA
1 TTGCATGATATTTT-TATTA
*
20487413 TTGCATGATGTTTTTATT
1 TTGCATGATATTTTTATT
20487431 GCATGGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.24, C:0.05, G:0.13, T:0.58
Consensus pattern (19 bp):
TTGCATGATATTTTTATTA
Found at i:20487431 original size:16 final size:16
Alignment explanation
Indices: 20487410--20487445 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
20487400 ATATTTTATA
*
20487410 TTATTGCATGATGTTT
1 TTATTGCATGATATTT
*
20487426 TTATTGCATGGTATTT
1 TTATTGCATGATATTT
20487442 TTAT
1 TTAT
20487446 ATATGATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (16 bp):
TTATTGCATGATATTT
Found at i:20488989 original size:17 final size:17
Alignment explanation
Indices: 20488951--20488991 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
20488941 TAAAATATTT
20488951 TAAAAT-TTTATTTTAA
1 TAAAATATTTATTTTAA
20488967 TAAAAATATTT-TTATTAA
1 T-AAAATATTTATT-TTAA
20488985 TAAAATA
1 TAAAATA
20488992 ATAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.05
17 13 0.59
18 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAATATTTATTTTAA
Found at i:20489228 original size:11 final size:11
Alignment explanation
Indices: 20489210--20489252 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
20489200 ATATATATTT
20489210 TTTATTTTTTA
1 TTTATTTTTTA
*
20489221 TCTA-TTTTTA
1 TTTATTTTTTA
*
20489231 TTTCATTATTTA
1 TTT-ATTTTTTA
20489243 TTTATTTTTT
1 TTTATTTTTT
20489253 TGGTTTACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 8 0.31
11 10 0.38
12 8 0.31
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:20493223 original size:52 final size:52
Alignment explanation
Indices: 20493154--20493258 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
20493144 ATTCTTGTAA
20493154 ATCCAGTAGTTGAACTGTCATTATACATATTAATATATAGATAGTAAATAGT
1 ATCCAGTAGTTGAACTGTCATTATACATATTAATATATAGATAGTAAATAGT
20493206 ATCCAGTAGTTGAACTGTCATTATACATATTAATATATAGATAGTAAATAGT
1 ATCCAGTAGTTGAACTGTCATTATACATATTAATATATAGATAGTAAATAGT
20493258 A
1 A
20493259 ATGCGATACC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (52 bp):
ATCCAGTAGTTGAACTGTCATTATACATATTAATATATAGATAGTAAATAGT
Found at i:20494824 original size:22 final size:23
Alignment explanation
Indices: 20494776--20494825 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
20494766 CTCAACAATG
* *
20494776 ATAAAATAAATTTAAATTTTATT
1 ATAAATTAAATTTAAATTATATT
20494799 -TAAATTAAATTTAAA-TATATT
1 ATAAATTAAATTTAAATTATATT
20494820 ATAAAT
1 ATAAAT
20494826 ATTAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATAAATTAAATTTAAATTATATT
Found at i:20495438 original size:21 final size:18
Alignment explanation
Indices: 20495399--20495447 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 18
20495389 TTAAATACAT
*
20495399 ATTTTATTATAAATTTTA
1 ATTTTATTATAAATATTA
20495417 ATTTTATTATCATAATAATTA
1 ATTTTATTAT-A-AAT-ATTA
*
20495438 AATTTATTAT
1 ATTTTATTAT
20495448 TATCGTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 10 0.38
19 1 0.04
20 3 0.12
21 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTATTATAAATATTA
Found at i:20496010 original size:19 final size:19
Alignment explanation
Indices: 20495988--20496078 Score: 66
Period size: 19 Copynumber: 4.9 Consensus size: 19
20495978 TTTTATATAA
20495988 ATATTAAAT-TTATATATTT
1 ATATTAAATATTATA-ATTT
*
20496007 ATATTATATATTATAATTT
1 ATATTAAATATTATAATTT
* * **
20496026 ATATT-AATATAAAAATAA
1 ATATTAAATATTATAATTT
* *
20496044 ATA-TATAT-TTTTAATTT
1 ATATTAAATATTATAATTT
20496061 -TATTAAATATATATAATT
1 ATATTAAATAT-TATAATT
20496079 ATTAAAATTT
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
16 2 0.04
17 9 0.17
18 14 0.26
19 23 0.43
20 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTAAATATTATAATTT
Found at i:20496086 original size:45 final size:49
Alignment explanation
Indices: 20495982--20496121 Score: 119
Period size: 49 Copynumber: 2.8 Consensus size: 49
20495972 ATATTTTTTT
* * *
20495982 ATATAAATATTAAATTTATATATTTATATTATATATTATAATTTATATTA
1 ATATAAA-AATAAATATATATATTTATATTATATATTATAATATATATTA
*
20496032 ATATAAAAATAAATATATATTTTTA-ATT-T-TATTA-AATATATA-TA
1 ATATAAAAATAAATATATATATTTATATTATATATTATAATATATATTA
* *
20496076 ATTATTAAAATTTTAAATCTTATATATTTATATATATATATATATA
1 A-TA-TAAAA--ATAAAT-ATATATATTTATAT-TATATAT-TATA
20496122 TGTCCCCTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
44 3 0.04
45 9 0.12
46 10 0.14
47 1 0.01
48 8 0.11
49 24 0.33
50 9 0.12
51 1 0.01
52 1 0.01
53 3 0.04
54 2 0.03
55 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (49 bp):
ATATAAAAATAAATATATATATTTATATTATATATTATAATATATATTA
Found at i:20496155 original size:14 final size:14
Alignment explanation
Indices: 20496136--20496169 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
20496126 CCCTTTGTAT
20496136 TTAAATTTTTACTC
1 TTAAATTTTTACTC
20496150 TTAAA-TTTTACTC
1 TTAAATTTTTACTC
*
20496163 CTAAATT
1 TTAAATT
20496170 ATTGCTGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (14 bp):
TTAAATTTTTACTC
Found at i:20498372 original size:2 final size:2
Alignment explanation
Indices: 20498365--20498389 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20498355 AGTGTGATGA
20498365 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
20498390 ATTCTTTCTT
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:20500100 original size:35 final size:35
Alignment explanation
Indices: 20500061--20500179 Score: 102
Period size: 42 Copynumber: 3.3 Consensus size: 35
20500051 TATTTTGTTT
20500061 TTTTATTATTAAATAATATTAATAAATAAAATTTA
1 TTTTATTATTAAATAATATTAATAAATAAAATTTA
* *
20500096 TTTTA-TA-T-AATAA-AATAATAAATAAACTTTA
1 TTTTATTATTAAATAATATTAATAAATAAAATTTA
* *
20500127 TTTTTATTTTTTATTAAACAATAAATTAATAAATAACATTTA
1 -TTTTA----TTATTAAATAAT--ATTAATAAATAAAATTTA
20500169 TTATTATTATT
1 TT-TTATTATT
20500180 TTAAATTATT
Statistics
Matches: 66, Mismatches: 6, Indels: 21
0.71 0.06 0.23
Matches are distributed among these distances:
31 16 0.24
32 10 0.15
33 1 0.02
34 2 0.03
35 5 0.08
37 2 0.03
38 6 0.09
39 4 0.06
41 2 0.03
42 18 0.27
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.50
Consensus pattern (35 bp):
TTTTATTATTAAATAATATTAATAAATAAAATTTA
Found at i:20500115 original size:27 final size:30
Alignment explanation
Indices: 20500062--20500128 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
20500052 ATTTTGTTTT
*
20500062 TTTATTATTAAATAATATTAATAAATAAAA
1 TTTATTATTAAATAATATAAATAAATAAAA
* * *
20500092 TTTATT-TTATATAATAAAATAATAAATAAAC
1 TTTATTATTAAATAAT-ATA-AATAAATAAAA
20500123 TTTATT
1 TTTATT
20500129 TTTATTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 8 0.26
30 7 0.23
31 16 0.52
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (30 bp):
TTTATTATTAAATAATATAAATAAATAAAA
Found at i:20502856 original size:6 final size:7
Alignment explanation
Indices: 20502816--20502879 Score: 53
Period size: 7 Copynumber: 9.3 Consensus size: 7
20502806 TTATCCTTTC
*
20502816 TATATAT
1 TATATAA
20502823 TATA-AA
1 TATATAA
*
20502829 TTATGTAA
1 -TATATAA
*
20502837 CATATAA
1 TATATAA
20502844 TATATAA
1 TATATAA
20502851 -ATATAA
1 TATATAA
20502857 -ATAATAA
1 TAT-ATAA
*
20502864 TATATAT
1 TATATAA
20502871 TATATAA
1 TATATAA
20502878 TA
1 TA
20502880 AAAAAAAGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
6 9 0.20
7 33 0.72
8 4 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (7 bp):
TATATAA
Found at i:20507533 original size:20 final size:20
Alignment explanation
Indices: 20507508--20507545 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20507498 TAGGACTAGT
* *
20507508 AGTGAATATGATCATTATCA
1 AGTGAACATAATCATTATCA
20507528 AGTGAACATAATCATTAT
1 AGTGAACATAATCATTAT
20507546 TGCTTTATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (20 bp):
AGTGAACATAATCATTATCA
Found at i:20516292 original size:20 final size:19
Alignment explanation
Indices: 20516268--20516315 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
20516258 AGTTTTTGCA
*
20516268 CAATTTTGACTTTGTTTGAC
1 CAATTTTGACTTT-ATTGAC
* *
20516288 TAATTTTAACTTTATTGAC
1 CAATTTTGACTTTATTGAC
20516307 CAATTTTGA
1 CAATTTTGA
20516316 TCGAATTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.50
Consensus pattern (19 bp):
CAATTTTGACTTTATTGAC
Found at i:20516632 original size:19 final size:18
Alignment explanation
Indices: 20516584--20516633 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
20516574 CTTTCTTTCT
*
20516584 TTTTTTTTGTGTTTTGTTA
1 TTTTTTTTGT-TATTGTTA
*
20516603 TCTTTTATTGTTATTGTTA
1 T-TTTTTTTGTTATTGTTA
20516622 TTTTTGTTTGTT
1 TTTTT-TTTGTT
20516634 TGTTTTGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 4 0.15
19 14 0.54
20 8 0.31
ACGTcount: A:0.08, C:0.02, G:0.14, T:0.76
Consensus pattern (18 bp):
TTTTTTTTGTTATTGTTA
Found at i:20517066 original size:32 final size:34
Alignment explanation
Indices: 20517030--20517096 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
20517020 GGCTTAGAAA
*
20517030 TTCATT-GGG-CTAGATAAACTAAGCTTACAATT
1 TTCATTAGGGACTAGATAAACTAAGCTTAAAATT
*
20517062 TTCATTAGGGACTAGATAAACTAGGCTTAAAATT
1 TTCATTAGGGACTAGATAAACTAAGCTTAAAATT
20517096 T
1 T
20517097 CATCGAAGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 6 0.19
33 3 0.10
34 22 0.71
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (34 bp):
TTCATTAGGGACTAGATAAACTAAGCTTAAAATT
Found at i:20517078 original size:34 final size:32
Alignment explanation
Indices: 20517030--20517128 Score: 101
Period size: 33 Copynumber: 3.0 Consensus size: 32
20517020 GGCTTAGAAA
*
20517030 TTCATTGGGCTAGATAAACTAAGCTTACAATT
1 TTCATTGGGCTAGATAAACTAAGCTTAAAATT
*
20517062 TTCATTAGGGACTAGATAAACTAGGCTTAAAA-T
1 TTCATT-GGG-CTAGATAAACTAAGCTTAAAATT
* * **
20517095 TTCATCGAAGGCCAGATAAACTGGGCTTAAAATT
1 TTCATTG--GGCTAGATAAACTAAGCTTAAAATT
20517129 AAGTGACAGC
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
32 7 0.12
33 28 0.49
34 22 0.39
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (32 bp):
TTCATTGGGCTAGATAAACTAAGCTTAAAATT
Found at i:20517324 original size:34 final size:34
Alignment explanation
Indices: 20517219--20517403 Score: 121
Period size: 34 Copynumber: 5.5 Consensus size: 34
20517209 AAGCAAGGTT
* *
20517219 TTAAAATCTTCATTGGGTG-TCAAGTAAACTGGGC
1 TTAAAATCTTTATTGGGTGCT-AGGTAAACTGGGC
* ** * **
20517253 TTAAAATCATTT-TTTGGTGCTAAATAAATTGTAC
1 TTAAAATC-TTTATTGGGTGCTAGGTAAACTGGGC
20517287 TTAAAATCTTTATTGGGTGCTAGGTAAACTGGGC
1 TTAAAATCTTTATTGGGTGCTAGGTAAACTGGGC
* * *
20517321 TT-AAA-CTTTCACT-GATGCTAGGTAAACTAGGC
1 TTAAAATCTTT-ATTGGGTGCTAGGTAAACTGGGC
* * * * * * * *
20517353 TTGAAACCTTTCTTTGGTGCAAGATAAATTGAGC
1 TTAAAATCTTTATTGGGTGCTAGGTAAACTGGGC
*
20517387 TTAAAAT-TTCATTGGGT
1 TTAAAATCTTTATTGGGT
20517404 AATAACTAAG
Statistics
Matches: 116, Mismatches: 28, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
32 23 0.20
33 19 0.16
34 71 0.61
35 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (34 bp):
TTAAAATCTTTATTGGGTGCTAGGTAAACTGGGC
Found at i:20517520 original size:32 final size:33
Alignment explanation
Indices: 20517311--20517601 Score: 104
Period size: 33 Copynumber: 8.8 Consensus size: 33
20517301 GGGTGCTAGG
* * * *
20517311 TAAACTGGGCTTAAACTTTCACTGATG-CTAGG
1 TAAACTAGGCTTAAACTTTCATTGATGCCAAGA
* *
20517343 TAAACTAGGCTTGAAACCTTTCTTTGGTG-CAAGA
1 TAAACTAGGCTT-AAA-CTTTCATTGATGCCAAGA
* * ** *
20517377 TAAA-TTGAGCTTAAAATTTCATTG--GGTAATAA
1 TAAACTAG-GCTTAAACTTTCATTGATGCCAA-GA
** * * * * *
20517409 CTAAGTTAAGCTTAAACTTTCATTGGT-ACTAGG
1 -TAAACTAGGCTTAAACTTTCATTGATGCCAAGA
* ** * *
20517442 TAAACTAGGCTTTAAATTTTCATCAAGTGGC-AGC
1 TAAACTAGGC-TTAAACTTTCATTGA-TGCCAAGA
* *
20517476 TAAACCATGCTTAAACTTTCATTGATGCCAAG-
1 TAAACTAGGCTTAAACTTTCATTGATGCCAAGA
* *
20517508 TAAACT-GAGCTTAAAATCTTTCTTTGGTGCC-AGA
1 TAAACTAG-GCTT-AAA-CTTTCATTGATGCCAAGA
* * *
20517542 TAAACTAGGTTTAAA-TTTCATTAGGA-G-CTAGC
1 TAAACTAGGCTTAAACTTTCATT--GATGCCAAGA
*
20517574 TAAGCTAGGCTTAAACTTTCATTGATGC
1 TAAACTAGGCTTAAACTTTCATTGATGC
20517602 TAGGTAAACT
Statistics
Matches: 190, Mismatches: 45, Indels: 47
0.67 0.16 0.17
Matches are distributed among these distances:
30 1 0.01
31 11 0.06
32 55 0.29
33 67 0.35
34 54 0.28
35 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (33 bp):
TAAACTAGGCTTAAACTTTCATTGATGCCAAGA
Found at i:20517604 original size:32 final size:32
Alignment explanation
Indices: 20517304--20517611 Score: 160
Period size: 32 Copynumber: 9.4 Consensus size: 32
20517294 CTTTATTGGG
* * *
20517304 TGCTAGGTAAACTGGGCTTAAACTTTCACTGA
1 TGCTAGCTAAACTAGGCTTAAACTTTCATTGA
* * *
20517336 TGCTAGGTAAACTAGGCTTGAAACCTTTCTTTGG
1 TGCTAGCTAAACTAGGCTT-AAA-CTTTCATTGA
* * * * *
20517370 TGCAAGATAAA-TTGAGCTTAAAATTTCATTGGG
1 TGCTAGCTAAACTAG-GCTTAAACTTTCATT-GA
** * ** * *
20517403 TAATAACTAAGTTAAGCTTAAACTTTCATTGG
1 TGCTAGCTAAACTAGGCTTAAACTTTCATTGA
* * * **
20517435 TACTAGGTAAACTAGGCTTTAAATTTTCATCAA
1 TGCTAGCTAAACTAGGC-TTAAACTTTCATTGA
* *
20517468 GTGGC-AGCTAAACCATGCTTAAACTTTCATTGA
1 -T-GCTAGCTAAACTAGGCTTAAACTTTCATTGA
* * *
20517501 TGCCAAG-TAAACT-GAGCTTAAAATCTTTCTTTGG
1 TG-CTAGCTAAACTAG-GCTT-AAA-CTTTCATTGA
* * *
20517535 TGCCAGATAAACTAGGTTTAAA-TTTCATTAGGA
1 TGCTAGCTAAACTAGGCTTAAACTTTCATT--GA
*
20517568 -GCTAGCTAAGCTAGGCTTAAACTTTCATTGA
1 TGCTAGCTAAACTAGGCTTAAACTTTCATTGA
*
20517599 TGCTAGGTAAACT
1 TGCTAGCTAAACT
20517612 GAGCTTCACT
Statistics
Matches: 208, Mismatches: 49, Indels: 38
0.71 0.17 0.13
Matches are distributed among these distances:
31 9 0.04
32 75 0.36
33 71 0.34
34 51 0.25
35 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (32 bp):
TGCTAGCTAAACTAGGCTTAAACTTTCATTGA
Found at i:20517846 original size:22 final size:21
Alignment explanation
Indices: 20517798--20517848 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
20517788 AGCTAATCCA
* *
20517798 AGCTTATGTGCCAACTAATTT
1 AGCTTATGTGCCAACTAACTG
20517819 AGGCTTATGTGCCAACTAAACTG
1 A-GCTTATGTGCCAACT-AACTG
20517842 AGCTTAT
1 AGCTTAT
20517849 ATGCTAGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.81
23 4 0.15
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (21 bp):
AGCTTATGTGCCAACTAACTG
Found at i:20519380 original size:5 final size:5
Alignment explanation
Indices: 20519342--20519378 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
20519332 TCATAACCAT
20519342 TTTTC TTTTC TTTTC TTTTC TTTT- TTTTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
20519379 TTACATCCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (5 bp):
TTTTC
Found at i:20520616 original size:5 final size:5
Alignment explanation
Indices: 20520568--20520626 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
20520558 TTTTTTGTCT
* * * *
20520568 TTTTC -TTTC TTTTA TTCTTC CTTTC CTTTC CTTTC ATTTT- TTTTC TTTTC
1 TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC
20520618 TTTTC TTTT
1 TTTTC TTTT
20520627 GTATTCTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 8 0.17
5 32 0.70
6 6 0.13
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:20523512 original size:4 final size:4
Alignment explanation
Indices: 20523488--20523535 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
20523478 TAGATACATA
* * * *
20523488 AATG GATG AATG GATG GATG AATG AATG AATG AATG AATG AACG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
20523536 CACAAATGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.44, C:0.02, G:0.31, T:0.23
Consensus pattern (4 bp):
AATG
Found at i:20528823 original size:145 final size:142
Alignment explanation
Indices: 20528609--20529003 Score: 454
Period size: 145 Copynumber: 2.7 Consensus size: 142
20528599 TTAAAACACA
* * * *
20528609 AAAATTCATGAAATATTATAAAATTGAGATATGAAAAGTTTCATGAAAATTAGAGCTCGAAAAGT
1 AAAATTAATGAAATATTATAAAATTAAGATCTGAAAAGTTTCATGAAAATTA-AGCTCGAAAAGG
20528674 TCAAATTACAAAAATACTCCTAAAGGGTATTTTGATAATTTCACACCTCCT-GTGGTACTACTAT
65 TCAAATTACAAAAATAC-CCTAAAGGGTATTTTGATAATTTCACACCTCCTAG-GGTACTACTAT
20528738 G-GTTTCAAATGCACC
128 GAGTTTC-AATGCACC
* * * * *
20528753 AAAATTTATGAAATATTATAAAATTAAGATCTAAAAAAGTTTCATAAAAATCCAAGCTCAAAAAG
1 AAAATTAATGAAATATTATAAAATTAAGATCT-GAAAAGTTTCATGAAAAT-TAAGCTCGAAAAG
** * ** * * * * *
20528818 GTCAAATTATGAAAATACCTTTATAAAAGTATTTTGGTAATTTCACACTTTCTAGGGTATTATTA
64 GTCAAATTACAAAAATACC-CTA-AAGGGTATTTTGATAATTTCACACCTCCTAGGGTACTACTA
* *
20528883 TGATTTTCAATGCAGC
127 TGAGTTTCAATGCACC
* * * *
20528899 AAAAATAACGAAATATTATAAAATTAAGATCTGAAAAGTTTCATGAAAATTTGAGCTTGAAAAGA
1 AAAATTAATGAAATATTATAAAATTAAGATCTGAAAAGTTTCATGAAAA-TTAAGCTCGAAAAG-
20528964 GT-AAATTACAAAAATACCCTAAAGGGTATTTTGATAATTT
64 GTCAAATTACAAAAATACCCTAAAGGGTATTTTGATAATTT
20529004 TATACTTTTC
Statistics
Matches: 208, Mismatches: 35, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
143 16 0.08
144 32 0.15
145 81 0.39
146 74 0.36
147 5 0.02
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (142 bp):
AAAATTAATGAAATATTATAAAATTAAGATCTGAAAAGTTTCATGAAAATTAAGCTCGAAAAGGT
CAAATTACAAAAATACCCTAAAGGGTATTTTGATAATTTCACACCTCCTAGGGTACTACTATGAG
TTTCAATGCACC
Found at i:20531095 original size:22 final size:22
Alignment explanation
Indices: 20531070--20531116 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
20531060 TGGATGTAAA
*
20531070 AGTTACATAATCATCCTAATGG
1 AGTTACATAATCATCCAAATGG
*
20531092 AGTTACATAATCTTCCAAATGG
1 AGTTACATAATCATCCAAATGG
20531114 AGT
1 AGT
20531117 CACCACTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (22 bp):
AGTTACATAATCATCCAAATGG
Found at i:20531680 original size:236 final size:234
Alignment explanation
Indices: 20531194--20531637 Score: 528
Period size: 236 Copynumber: 1.9 Consensus size: 234
20531184 AGGAATTGTT
* *
20531194 AATCGATTTATTTATGTCTAAGGAATCAATGCCAGTTTCAATGTCACAATTTTATCTTTACAAAA
1 AATCAATTTATTTATGTCTAAGGAATCAATGCCAGTTTCAAGGTCACAATTTTATCTTTACAAAA
* * * *
20531259 AAACTTGGTTTAGATATAGTAAATAGGATATTAGAGGAATCAAAGCTCTAAAACCTATCTAAGAT
66 AAACTTGATTCAAATATAGTAAATAGGATATTAGAGGAATCAAAGCTCTAAAACCTACCTAAGAT
* * * *
20531324 AAACCTAACCTTTACTTAGCCATTTTACACTAACACTTGACTGGCTTACAAACTAAAAAACATGT
131 AAACCTAACCTCTACTTAGCCATTTTACACTAACACTCGACTAGCTTACAAACTAAAAAACATGA
* * ***** *
20531389 CTTTTCATTTTGAAATCCAAGCTTTTGATTAGGAATCATC
196 CTCTCCATTTTGAAATCCAAGCAACCAATGAGG-ATCATC
* ** ** * *
20531429 AATCAATTTATTTATGTCTAAGGAATTAATGTTAGTTTTGAGGTCATAGTTTTTATCTTTACAAA
1 AATCAATTTATTTATGTCTAAGGAATCAATGCCAGTTTCAAGGTCACA-ATTTTATCTTTACAAA
* * * * *
20531494 AAAACTTGATTCAAATTTAGTAAATAGGATATTAGAGGAATTAAAGCTCTAAAACTTGCCTGAGA
65 AAAACTTGATTCAAATATAGTAAATAGGATATTAGAGGAATCAAAGCTCTAAAACCTACCTAAGA
* * * * * *
20531559 TAAACCTTACCTCTACTTATCCATTTTACACTAACACCTCGACTAGCTTACGAATTAAAGAGCAT
130 TAAACCTAACCTCTACTTAGCCATTTTACACTAACA-CTCGACTAGCTTACAAACTAAAAAACAT
*
20531624 GACTCTCCCTTTTG
194 GACTCTCCATTTTG
20531638 TACCTTGTAG
Statistics
Matches: 176, Mismatches: 31, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
235 40 0.23
236 104 0.59
237 32 0.18
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (234 bp):
AATCAATTTATTTATGTCTAAGGAATCAATGCCAGTTTCAAGGTCACAATTTTATCTTTACAAAA
AAACTTGATTCAAATATAGTAAATAGGATATTAGAGGAATCAAAGCTCTAAAACCTACCTAAGAT
AAACCTAACCTCTACTTAGCCATTTTACACTAACACTCGACTAGCTTACAAACTAAAAAACATGA
CTCTCCATTTTGAAATCCAAGCAACCAATGAGGATCATC
Found at i:20532819 original size:31 final size:32
Alignment explanation
Indices: 20532784--20532865 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 32
20532774 AGTTTGTACA
*
20532784 ATTCATTTGAATTTATTTAATAAAAATAT-AT
1 ATTCATTTGAATTTATTTAATAAAAAGATAAT
20532815 ATTCATTTGAATTTATTTAATAAAAAGATAAT
1 ATTCATTTGAATTTATTTAATAAAAAGATAAT
* *
20532847 ATT-TTTTG-AGTTATTTAAT
1 ATTCATTTGAATTTATTTAAT
20532866 GGAAATTATT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
30 10 0.21
31 32 0.68
32 5 0.11
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.50
Consensus pattern (32 bp):
ATTCATTTGAATTTATTTAATAAAAAGATAAT
Found at i:20534557 original size:26 final size:26
Alignment explanation
Indices: 20534528--20534580 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
20534518 ATAACCAAAT
*
20534528 AAAT-AATTAAAAAAATCCTATATAAA
1 AAATAAATT-AAAAAATCCTACATAAA
*
20534554 AAATAAATTAATAAATCCTACATAAA
1 AAATAAATTAAAAAATCCTACATAAA
20534580 A
1 A
20534581 CTCGAAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.26
Consensus pattern (26 bp):
AAATAAATTAAAAAATCCTACATAAA
Found at i:20537287 original size:26 final size:29
Alignment explanation
Indices: 20537257--20537328 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 29
20537247 AAGCATTTTT
*
20537257 TTTATGTATTTGATTTATTATTTG-TT-G
1 TTTATGTATTTGATTTATTATATGATTGG
*
20537284 -TTATGCTA-TGGATTTATTATATGATTGG
1 TTTATG-TATTTGATTTATTATATGATTGG
20537312 TTTGATGTATTTGATTT
1 TTT-ATGTATTTGATTT
20537329 GTTAGGTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
26 18 0.50
27 4 0.11
28 1 0.03
29 4 0.11
30 9 0.25
ACGTcount: A:0.21, C:0.01, G:0.18, T:0.60
Consensus pattern (29 bp):
TTTATGTATTTGATTTATTATATGATTGG
Found at i:20540984 original size:13 final size:13
Alignment explanation
Indices: 20540966--20540999 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
20540956 TAAATAAAAA
20540966 ATATTAAATTTAC
1 ATATTAAATTTAC
*
20540979 ATATTAAATTTAT
1 ATATTAAATTTAC
20540992 ATA-TAAAT
1 ATATTAAAT
20541000 AATTAACGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATTAAATTTAC
Found at i:20542443 original size:18 final size:18
Alignment explanation
Indices: 20542416--20542471 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
20542406 AGCCCAATTT
20542416 AAGTCCAATTCTAAATCA
1 AAGTCCAATTCTAAATCA
* * *
20542434 AAGTCTAATTGTGAATCA
1 AAGTCCAATTCTAAATCA
* *
20542452 AA-CCCAATTATAAAATCA
1 AAGTCCAATTCT-AAATCA
20542470 AA
1 AA
20542472 CCTCAACTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 6 0.20
18 24 0.80
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27
Consensus pattern (18 bp):
AAGTCCAATTCTAAATCA
Found at i:20553386 original size:42 final size:42
Alignment explanation
Indices: 20553340--20553453 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 42
20553330 TTTTATTTTG
20553340 TATATTTATGTAATTATATATTAATATATT-TTTAA-ATAAAAA
1 TATATTTAT-TAATTATATATTAATATATTATTTAATA-AAAAA
* *
20553382 TATA-TTATTAATCTAAAATAATAATTTATATTATTTAATAAAAAA
1 TATATTTATTAAT-T-ATATATTAA--TATATTATTTAATAAAAAA
* * *
20553427 TTTATTTATTAAATATATATAAATATA
1 TATATTTATTAATTATATATTAATATA
20553454 GATAAGATAC
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
40 4 0.07
41 5 0.09
42 15 0.26
44 12 0.21
45 14 0.24
46 8 0.14
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (42 bp):
TATATTTATTAATTATATATTAATATATTATTTAATAAAAAA
Found at i:20555243 original size:56 final size:57
Alignment explanation
Indices: 20555142--20555250 Score: 184
Period size: 56 Copynumber: 1.9 Consensus size: 57
20555132 ATTTTCTTTG
20555142 CTTTAAAGTTTGAAATAATTTTAAAGATACTTTTTACTTGATTATTGTGATTTATTT
1 CTTTAAAGTTTGAAATAATTTTAAAGATACTTTTTACTTGATTATTGTGATTTATTT
** *
20555199 CTTTAAAGTTTGAAATAA-TTTAAAGATGTTTTTTACTTGGTTATTGTGATTT
1 CTTTAAAGTTTGAAATAATTTTAAAGATACTTTTTACTTGATTATTGTGATTT
20555251 GTTTGTTATC
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
56 31 0.63
57 18 0.37
ACGTcount: A:0.30, C:0.05, G:0.13, T:0.52
Consensus pattern (57 bp):
CTTTAAAGTTTGAAATAATTTTAAAGATACTTTTTACTTGATTATTGTGATTTATTT
Found at i:20560010 original size:26 final size:26
Alignment explanation
Indices: 20559963--20560012 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
20559953 TCAGATATGA
* *
20559963 ATATCCAATAAATTTTATAACTTATC
1 ATATCCAATAAATTATAAAACTTATC
* *
20559989 ATATCTAATAAGTTATAAAACTTA
1 ATATCCAATAAATTATAAAACTTA
20560013 CAAAATATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.40
Consensus pattern (26 bp):
ATATCCAATAAATTATAAAACTTATC
Found at i:20560238 original size:17 final size:16
Alignment explanation
Indices: 20560200--20560240 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
20560190 TTTTTTTTTT
20560200 AATTTATAAGATATAA
1 AATTTATAAGATATAA
*
20560216 ATATTTAGTAAGTTATAA
1 A-ATTTA-TAAGATATAA
20560234 AATTTAT
1 AATTTAT
20560241 CGAATATGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.09
17 10 0.45
18 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (16 bp):
AATTTATAAGATATAA
Found at i:20566330 original size:2 final size:2
Alignment explanation
Indices: 20566317--20566350 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
20566307 CTGAGATTAA
*
20566317 AT AT AC 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
20566351 GAATAGGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20575714 original size:99 final size:99
Alignment explanation
Indices: 20575543--20575744 Score: 404
Period size: 99 Copynumber: 2.0 Consensus size: 99
20575533 TTGGGTTAAG
20575543 CAGTAGAGGGTTTTTAAGAATAAGAACAAGACATTGGGTAAAAGGGATGAGTAAGTGGAATAGTT
1 CAGTAGAGGGTTTTTAAGAATAAGAACAAGACATTGGGTAAAAGGGATGAGTAAGTGGAATAGTT
20575608 GTTCATTTATTTTATTTTACTGTTTTATGTTCAA
66 GTTCATTTATTTTATTTTACTGTTTTATGTTCAA
20575642 CAGTAGAGGGTTTTTAAGAATAAGAACAAGACATTGGGTAAAAGGGATGAGTAAGTGGAATAGTT
1 CAGTAGAGGGTTTTTAAGAATAAGAACAAGACATTGGGTAAAAGGGATGAGTAAGTGGAATAGTT
20575707 GTTCATTTATTTTATTTTACTGTTTTATGTTCAA
66 GTTCATTTATTTTATTTTACTGTTTTATGTTCAA
20575741 CAGT
1 CAGT
20575745 TTGAGCTTGT
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 103 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.37
Consensus pattern (99 bp):
CAGTAGAGGGTTTTTAAGAATAAGAACAAGACATTGGGTAAAAGGGATGAGTAAGTGGAATAGTT
GTTCATTTATTTTATTTTACTGTTTTATGTTCAA
Found at i:20589625 original size:11 final size:11
Alignment explanation
Indices: 20589609--20589635 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20589599 TAGAAATTAC
20589609 TTTTATTATTT
1 TTTTATTATTT
20589620 TTTTATTATTT
1 TTTTATTATTT
20589631 TTTTA
1 TTTTA
20589636 GAAAGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTATTATTT
Found at i:20590537 original size:14 final size:14
Alignment explanation
Indices: 20590518--20590558 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
20590508 GATTTCCCCT
20590518 TTCCCTTCTTTCTC
1 TTCCCTTCTTTCTC
20590532 TTCCCTT-TTT-T-
1 TTCCCTTCTTTCTC
20590543 TTCCCTTCTTTTCTC
1 TTCCCTTC-TTTCTC
20590558 T
1 T
20590559 CTATCCGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 7 0.30
12 1 0.04
13 6 0.26
14 8 0.35
15 1 0.04
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (14 bp):
TTCCCTTCTTTCTC
Found at i:20590546 original size:11 final size:12
Alignment explanation
Indices: 20590517--20590554 Score: 51
Period size: 11 Copynumber: 3.1 Consensus size: 12
20590507 AGATTTCCCC
20590517 TTTCCCTTCTTT
1 TTTCCCTTCTTT
20590529 CTCTTCCCTT-TTT
1 -T-TTCCCTTCTTT
20590542 TTTCCCTTCTTT
1 TTTCCCTTCTTT
20590554 T
1 T
20590555 CTCTCTATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 7 0.30
12 5 0.22
13 4 0.17
14 7 0.30
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTCCCTTCTTT
Found at i:20592344 original size:94 final size:94
Alignment explanation
Indices: 20592168--20592345 Score: 250
Period size: 94 Copynumber: 1.9 Consensus size: 94
20592158 TGCTTCTCTA
* * *
20592168 GTTACACTTTCCTGCTTTATATATGGCATGAATTGTTATGTTTGTATAAATTTGATTAATAACAT
1 GTTACACTTTCCTGCTCTATATATGACATGAATTGTTATGTTTATATAAATTTGATTAATAACAT
* **
20592233 AATAATTTGCATTATTAATTATACCATTT
66 AATAATATGCACCATTAATTATACCATTT
* * * *
20592262 GTTACACTTTCTTGCTCTATATGTGACATGAATTGTTATGTTTATATAAATTTGATTGATAGCA-
1 GTTACACTTTCCTGCTCTATATATGACATGAATTGTTATGTTTATATAAATTTGATTAATAACAT
20592326 AGATAATATGCACCATTAAT
66 A-ATAATATGCACCATTAAT
20592346 GGTACTATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
93 1 0.01
94 72 0.99
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.44
Consensus pattern (94 bp):
GTTACACTTTCCTGCTCTATATATGACATGAATTGTTATGTTTATATAAATTTGATTAATAACAT
AATAATATGCACCATTAATTATACCATTT
Found at i:20593934 original size:13 final size:13
Alignment explanation
Indices: 20593918--20593947 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20593908 AAATTATAAC
*
20593918 TTCAAATCCTAGA
1 TTCAAATCCTACA
20593931 TTCAAATCCTACA
1 TTCAAATCCTACA
20593944 TTCA
1 TTCA
20593948 TAGTGTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (13 bp):
TTCAAATCCTACA
Found at i:20601582 original size:15 final size:15
Alignment explanation
Indices: 20601558--20601594 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
20601548 TGTCATTTGT
20601558 AGTTAATTATGTTAG
1 AGTTAATTATGTTAG
*
20601573 AGTTAGTTATGTTAG
1 AGTTAATTATGTTAG
20601588 AGGTTAA
1 A-GTTAA
20601595 AATTTAGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.43
Consensus pattern (15 bp):
AGTTAATTATGTTAG
Found at i:20605226 original size:306 final size:306
Alignment explanation
Indices: 20604666--20605271 Score: 903
Period size: 306 Copynumber: 2.0 Consensus size: 306
20604656 GCTCTGATAC
* ** * *
20604666 CACTTGTCACGGGTCGAGACTTAAGCTCCGAATCCGCGTAGCTCTAGGACCCAGGTATTCACCCT
1 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCACAGCTCCAGGACCCAGGCATTCACCCT
* * * *
20604731 TCCGACGTCCCGGATCAGCCTGACCGCCACGGTTCACACCCTTGTGAGGTATTGTTCGCTCTGGC
66 TCCGACGTCCCAGATCAGCCTGACCGCCACGATTCACACCCTTGTGAGGTATTGTCCGCTCTGAC
* * *
20604796 CTCCCTGACCTCACGGTTTTGTCCTACAAAAGGCGCCTCACAAGACGGAAATGGTGTGAACCCTT
131 CCCCCTGACCTCACGGTTCTATCCTACAAAAGGCGCCTCACAAGACGGAAATGGTGTGAACCCTT
* * * *
20604861 TTATACCCCAGTGACCCTCCTATTATGTTCGATGTGAGATTCAGGACTCTCCTTTAGGTCCGTGA
196 ATATACCCCAGTGACCCTCCTATTATGTTCGATGTGAGATTCAAGACTCCCCCTTAGGTCCGTGA
20604926 CATTCTC-CTGCACCCAACCTCGTGACGCCCTCGTCACGGAAGTTGG
261 CATTCTCTC-GCACCCAACCTCGTGACGCCCTCGTCACGGAAGTTGG
*
20604972 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCACAGCTCCGGGACCCAGGCATTCACCCT
1 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCACAGCTCCAGGACCCAGGCATTCACCCT
* * ** *
20605037 TCCGGCGTCTCAGATCAG-CTTTCCTGTCACGATTCACACCCTTGTGAGGTATTGTCCGCTCTGA
66 TCCGACGTCCCAGATCAGCCTGACC-GCCACGATTCACACCCTTGTGAGGTATTGTCCGCTCTGA
* * **
20605101 CCCCCCT-AGCCTCACGGTTCTATCCTACAAAAGGTGCCTCACAAGGCGGAGGTGGTGTGAACCC
130 CCCCCCTGA-CCTCACGGTTCTATCCTACAAAAGGCGCCTCACAAGACGGAAATGGTGTGAACCC
*
20605165 TTATATACCCCAGTGACCCTCCTATTATGTTCGATGTGGGATTCAAGACTCCCCCTTAGGTCCGT
194 TTATATACCCCAGTGACCCTCCTATTATGTTCGATGTGAGATTCAAGACTCCCCCTTAGGTCCGT
* *
20605230 GACATTCTTTCGCACCCAACCTCGTGATGCCCTCGTCACGGA
259 GACATTCTCTCGCACCCAACCTCGTGACGCCCTCGTCACGGA
20605272 GGCTGGCCAC
Statistics
Matches: 268, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
305 5 0.02
306 262 0.98
307 1 0.00
ACGTcount: A:0.20, C:0.33, G:0.22, T:0.25
Consensus pattern (306 bp):
CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCACAGCTCCAGGACCCAGGCATTCACCCT
TCCGACGTCCCAGATCAGCCTGACCGCCACGATTCACACCCTTGTGAGGTATTGTCCGCTCTGAC
CCCCCTGACCTCACGGTTCTATCCTACAAAAGGCGCCTCACAAGACGGAAATGGTGTGAACCCTT
ATATACCCCAGTGACCCTCCTATTATGTTCGATGTGAGATTCAAGACTCCCCCTTAGGTCCGTGA
CATTCTCTCGCACCCAACCTCGTGACGCCCTCGTCACGGAAGTTGG
Found at i:20605659 original size:370 final size:370
Alignment explanation
Indices: 20604972--20605817 Score: 1363
Period size: 370 Copynumber: 2.3 Consensus size: 370
20604962 CGGAAGTTGG
* *
20604972 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCACAGCTCCGGGACCC-AGGCATTCACCC
1 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGGGACCCGA-GCATTCACCC
* *
20605036 TTCCGGCGTCTCAGATCAGCTTTCCTGTCACGATTCACACCCTTGTGAGGTATTGTCCGCTCTGA
65 TTCC-GCGTCTCAGATCAGCCTTCCTGTCACGGTTCACACCCTTGTGAGGTATTGTCCGCTCTGA
**
20605101 CCCCCCTAGCCTCACGGTTCTATCCTACAAAAGGTGCCTCACAAGGCGGAGGTGGTGTGAACCCT
129 CCCCCCTAGCCTCACGGTTCTATCCTACAAAAGGTGCCTCACAAAACGGAGGTGGTGTGAACCCT
20605166 TATATACCCCAGTGACCCTCCTATTATGTTCGATGTGGGATTCAAGACTCCCCCTTAGGTCCGTG
194 TATATACCCCAGTGACCCTCCTATTATGTTCGATGTGGGATTCAAGACTCCCCCTTAGGTCCGTG
** * *
20605231 ACATTCTTTCGCACCCAACCTCGTGATGCCCTCGTCACGGAGGCTGGCCACTCTGCCTACCTCCC
259 ACATTCTCCCGCACCCAACCTCGTGACGCCCTCGTCACGGAGGCTGGCCACCCTGCCTACCTCCC
*
20605296 TCGAGGTGCTTGGAGTGGATCGAACGGTTTAGGGCTGGCTCTGATAC
324 TCGAGGTGCTTGGAGTGCATCGAACGGTTTAGGGCTGGCTCTGATAC
20605343 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGGGACCCGAGCATTCACCCT
1 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGGGACCCGAGCATTCACCCT
* *
20605408 TCCAGCGTCTCAGATCAGCCTTCC-GCCACGGTTCACACCCTTGTGAGGTATTGTTCGCTCTGAC
66 TCC-GCGTCTCAGATCAGCCTTCCTGTCACGGTTCACACCCTTGTGAGGTATTGTCCGCTCTGAC
** * * *
20605472 CCCTTTGGCCTCACGGTTTTGTCCTACAAAAGGTGCCTCACAAAACGGAGGTGGTGTGAACCCTT
130 CCCCCTAGCCTCACGGTTCTATCCTACAAAAGGTGCCTCACAAAACGGAGGTGGTGTGAACCCTT
* * **
20605537 ATATACCCCAGTGACCCTCTTATTATGTTCGATGTGGGATTCAGGACTTTCCCTTAGGTCCGTGA
195 ATATACCCCAGTGACCCTCCTATTATGTTCGATGTGGGATTCAAGACTCCCCCTTAGGTCCGTGA
*
20605602 CATTCTCCCGCACCCAACCTCGTGACGCTCTCGTCACGGAGGCTGGCCACCCTGCCTACCTCCCT
260 CATTCTCCCGCACCCAACCTCGTGACGCCCTCGTCACGGAGGCTGGCCACCCTGCCTACCTCCCT
*
20605667 CGAGGTGCTTGGCGTGCATCGAACGGTTTAGGGCTGGCTCTGATAC
325 CGAGGTGCTTGGAGTGCATCGAACGGTTTAGGGCTGGCTCTGATAC
* * * *
20605713 CACTTGTCACGGGTTGAGACTCAAGCTCCAAACCCGCGCGGCTCCGGGACCCGGGCATTCACCCT
1 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGGGACCCGAGCATTCACCCT
* * *
20605778 TCCGACGTCCCATATTAGCCTTCCTGTCACGGTTCACACC
66 TCCG-CGTCTCAGATCAGCCTTCCTGTCACGGTTCACACC
20605818 ATCTCTTCCT
Statistics
Matches: 439, Mismatches: 33, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
369 1 0.00
370 340 0.77
371 97 0.22
372 1 0.00
ACGTcount: A:0.18, C:0.34, G:0.24, T:0.24
Consensus pattern (370 bp):
CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGGGACCCGAGCATTCACCCT
TCCGCGTCTCAGATCAGCCTTCCTGTCACGGTTCACACCCTTGTGAGGTATTGTCCGCTCTGACC
CCCCTAGCCTCACGGTTCTATCCTACAAAAGGTGCCTCACAAAACGGAGGTGGTGTGAACCCTTA
TATACCCCAGTGACCCTCCTATTATGTTCGATGTGGGATTCAAGACTCCCCCTTAGGTCCGTGAC
ATTCTCCCGCACCCAACCTCGTGACGCCCTCGTCACGGAGGCTGGCCACCCTGCCTACCTCCCTC
GAGGTGCTTGGAGTGCATCGAACGGTTTAGGGCTGGCTCTGATAC
Found at i:20606916 original size:16 final size:16
Alignment explanation
Indices: 20606892--20606922 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20606882 GAAATAACAT
*
20606892 TCTAGATGGATTGAAG
1 TCTAAATGGATTGAAG
20606908 TCTAAATGGATTGAA
1 TCTAAATGGATTGAA
20606923 TATAGTTCTC
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:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (16 bp):
TCTAAATGGATTGAAG
Found at i:20609508 original size:13 final size:13
Alignment explanation
Indices: 20609490--20609525 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
20609480 ATTAATACTT
20609490 AAAAATAAATAAG
1 AAAAATAAATAAG
20609503 AAAAATAAAT-AG
1 AAAAATAAATAAG
*
20609515 TAAAATAAATA
1 AAAAATAAATA
20609526 CCAAAGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (13 bp):
AAAAATAAATAAG
Found at i:20611286 original size:23 final size:22
Alignment explanation
Indices: 20611260--20611311 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
20611250 GTACCTAGAG
20611260 GTTTTAAGAAGT-ATTACCCAAAA
1 GTTTTAA-AAGTGA-TACCCAAAA
* *
20611283 GTTTTAAAATTGATACTCAAAA
1 GTTTTAAAAGTGATACCCAAAA
20611305 GTTTTAA
1 GTTTTAA
20611312 CAAATGTACG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (22 bp):
GTTTTAAAAGTGATACCCAAAA
Found at i:20611472 original size:13 final size:13
Alignment explanation
Indices: 20611435--20611472 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
20611425 TGATGCATAA
20611435 AATGCATGAAATGC
1 AATGCATG-AATGC
20611449 -ATGCATTGAATGC
1 AATGCA-TGAATGC
20611462 AATGCATGAAT
1 AATGCATGAAT
20611473 TTATATGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (13 bp):
AATGCATGAATGC
Found at i:20616907 original size:4 final size:4
Alignment explanation
Indices: 20616900--20616930 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
20616890 ATAGATAATT
20616900 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
20616931 TAAATAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:20620206 original size:12 final size:12
Alignment explanation
Indices: 20620189--20620220 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
20620179 TAAATTTTAT
20620189 ATTATTAGTGTA
1 ATTATTAGTGTA
20620201 ATTATTAGTGTA
1 ATTATTAGTGTA
20620213 ATTTATTA
1 A-TTATTA
20620221 ATATTTTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (12 bp):
ATTATTAGTGTA
Found at i:20625126 original size:13 final size:13
Alignment explanation
Indices: 20625108--20625144 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
20625098 TAAATTAGCA
20625108 GAAACCCTAAAGT
1 GAAACCCTAAAGT
*
20625121 GAAACCCTAATGT
1 GAAACCCTAAAGT
20625134 GAAACCCTAAA
1 GAAACCCTAAA
20625145 ATTCTAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.16
Consensus pattern (13 bp):
GAAACCCTAAAGT
Found at i:20625178 original size:27 final size:28
Alignment explanation
Indices: 20625122--20625179 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
20625112 CCCTAAAGTG
* * **
20625122 AAACCCTAATGTGAAACCCTAAAATTCT
1 AAACCCTAAGGTGAAACCCGAAAACCCT
20625150 AAACCCT-AGGTGAAACCCGAAAACCCT
1 AAACCCTAAGGTGAAACCCGAAAACCCT
20625177 AAA
1 AAA
20625180 GTAAAATCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.45, C:0.28, G:0.10, T:0.17
Consensus pattern (28 bp):
AAACCCTAAGGTGAAACCCGAAAACCCT
Found at i:20629218 original size:3 final size:3
Alignment explanation
Indices: 20629210--20629261 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
20629200 AAAAGCAAAT
20629210 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20629258 TAA T
1 TAA T
20629262 GATATTATAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:20630027 original size:13 final size:12
Alignment explanation
Indices: 20630009--20630038 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
20629999 AAATGTCTTT
20630009 AAAAAAGAGAAAA
1 AAAAAAG-GAAAA
20630022 AAAAAAGGAAAA
1 AAAAAAGGAAAA
20630034 AAAAA
1 AAAAA
20630039 GAAAAGGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAGGAAAA
Found at i:20631229 original size:19 final size:18
Alignment explanation
Indices: 20631200--20631235 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20631190 GTGAAAGAAT
*
20631200 GAAAAAGAAAAAGTGAAG
1 GAAAAAGAAAAAATGAAG
20631218 GAAAAGAGAAAAAATGAA
1 GAAAA-AGAAAAAATGAA
20631236 ATAAAGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (18 bp):
GAAAAAGAAAAAATGAAG
Found at i:20631878 original size:22 final size:22
Alignment explanation
Indices: 20631825--20631891 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
20631815 TCCATTCAGA
*
20631825 AAAAAGAAAAAGTGAAAGAATG
1 AAAAAGAAAAAGTGAAAGAAAG
*
20631847 AAAAAGAAAAAGTGAAGGAAA-
1 AAAAAGAAAAAGTGAAAGAAAG
*
20631868 AGAGAA-AAAAA-TGAAAGAAAG
1 A-AAAAGAAAAAGTGAAAGAAAG
20631889 AAA
1 AAA
20631892 TAAACAGAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 9 0.24
21 7 0.18
22 22 0.58
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (22 bp):
AAAAAGAAAAAGTGAAAGAAAG
Found at i:20633603 original size:32 final size:31
Alignment explanation
Indices: 20633443--20633772 Score: 205
Period size: 32 Copynumber: 10.2 Consensus size: 31
20633433 ATAAAAAGAC
* *
20633443 TTAAGCTTAGTTTAGCTAGCAACC-ATAAAAAT
1 TTAAGC-TAGTTTAGCTGGC-ACCAATGAAAAT
* *
20633475 TTAATCCTAGTTTAGCTGGCACCCCATGAAAAT
1 TTAA-GCTAGTTTAGCTGGCA-CCAATGAAAAT
* * *
20633508 TTAAGTCCAGTTTAGTTGGCACCAATGCAAAT
1 TTAAG-CTAGTTTAGCTGGCACCAATGAAAAT
* * * * *
20633540 TTAAGCCTGGTTTAACTAGCACCCATAAAAAT
1 TTAAG-CTAGTTTAGCTGGCACCAATGAAAAT
*
20633572 TTAAGCTAAGTTTAGCTGGCACTAATGAAAAT
1 TTAAGCT-AGTTTAGCTGGCACCAATGAAAAT
* ** * *
20633604 TTAAGCCCAACTTAGTTGGCACCAATGTAAAT
1 TTAAG-CTAGTTTAGCTGGCACCAATGAAAAT
* *
20633636 TTAAGCCTAGTTTAGTTGGCATCTAATGAAAAT
1 TTAAG-CTAGTTTAGCTGGCA-CCAATGAAAAT
* * * *
20633669 TTAAGTCTAGTATAG-TTGAATCCAATGAATAT
1 TTAAG-CTAGTTTAGCTGGCA-CCAATGAAAAT
* * * *
20633701 TTAAGCCTAGAATTAGTTAGCACCAAAGAAAAT
1 TTAAG-CTAG-TTTAGCTGGCACCAATGAAAAT
* * * * * *
20633734 TGAAGTCCAGATTAGTTGGCACTAATAAAAAT
1 TTAAG-CTAGTTTAGCTGGCACCAATGAAAAT
20633766 TTAAGCT
1 TTAAGCT
20633773 CTATTTAGCA
Statistics
Matches: 233, Mismatches: 56, Indels: 19
0.76 0.18 0.06
Matches are distributed among these distances:
31 4 0.02
32 159 0.68
33 67 0.29
34 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (31 bp):
TTAAGCTAGTTTAGCTGGCACCAATGAAAAT
Found at i:20633642 original size:96 final size:97
Alignment explanation
Indices: 20633443--20633649 Score: 292
Period size: 96 Copynumber: 2.1 Consensus size: 97
20633433 ATAAAAAGAC
* * *
20633443 TTAAGCTTAGTTTAGCTAGCAACCATAAAAATTTAATCCTAGTTTAGCTGGCACCCCATGAAAAT
1 TTAAGCCTAGTTTAACTAGCAACCATAAAAATTTAATCCTAGTTTAGCTGGCACCCAATGAAAAT
* **
20633508 TTAAGTCCAGTTTAGTTGGCACCAATGCAAAT
66 TTAAGCCCAACTTAGTTGGCACCAATGCAAAT
* * * *
20633540 TTAAGCCTGGTTTAACTAGCACCCATAAAAATTTAA-GCTAAGTTTAGCTGGCA-CTAATGAAAA
1 TTAAGCCTAGTTTAACTAGCAACCATAAAAATTTAATCCT-AGTTTAGCTGGCACCCAATGAAAA
*
20633603 TTTAAGCCCAACTTAGTTGGCACCAATGTAAAT
65 TTTAAGCCCAACTTAGTTGGCACCAATGCAAAT
20633636 TTAAGCCTAGTTTA
1 TTAAGCCTAGTTTA
20633650 GTTGGCATCT
Statistics
Matches: 97, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
96 52 0.54
97 45 0.46
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (97 bp):
TTAAGCCTAGTTTAACTAGCAACCATAAAAATTTAATCCTAGTTTAGCTGGCACCCAATGAAAAT
TTAAGCCCAACTTAGTTGGCACCAATGCAAAT
Found at i:20633694 original size:65 final size:63
Alignment explanation
Indices: 20633568--20633787 Score: 171
Period size: 65 Copynumber: 3.4 Consensus size: 63
20633558 GCACCCATAA
*
20633568 AAATTTAAG-CTAAGTTTAGCTGGCACTAATGAAAATTTAAGCCCAACTTAGTTGGCACCAATG
1 AAATTTAAGCCT-AGTTTAGCTGGCACTAATGAAAATTTAAGCCCAACTTAGTTGGAACCAATG
* * * *
20633631 TAAATTTAAGCCTAGTTTAGTTGGCATCTAATGAAAATTTAAG-TCTAGTATAGTT-GAATCCAA
1 -AAATTTAAGCCTAGTTTAGCTGGCA-CTAATGAAAATTTAAGCCCAACT-TAGTTGGAA-CCAA
20633694 TG
62 TG
* * * * * * * * *
20633696 AATATTTAAGCCTAGAATTAGTTAGCACCAAAGAAAATTGAAGTCCAGA-TTAGTTGGCACTAAT
1 AA-ATTTAAGCCTAG-TTTAGCTGGCACTAATGAAAATTTAAGCCCA-ACTTAGTTGGAACCAAT
*
20633760 AA
63 -G
*
20633762 AAATTTAAGCTCTA-TTTAGCAGGCAC
1 AAATTTAAGC-CTAGTTTAGCTGGCAC
20633788 CCAGATTTTA
Statistics
Matches: 126, Mismatches: 19, Indels: 22
0.75 0.11 0.13
Matches are distributed among these distances:
64 36 0.29
65 71 0.56
66 18 0.14
67 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (63 bp):
AAATTTAAGCCTAGTTTAGCTGGCACTAATGAAAATTTAAGCCCAACTTAGTTGGAACCAATG
Found at i:20636517 original size:19 final size:18
Alignment explanation
Indices: 20636459--20636519 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 18
20636449 ATGTTAGAGA
* *
20636459 ATTATTAAATATTAAAA-
1 ATTAATAAATAATAAAAG
20636476 A-TAA-AAATAATAAAAG
1 ATTAATAAATAATAAAAG
20636492 ATTAATAAATAATAATAATG
1 ATTAATAAATAATAA-AA-G
20636512 -TTAATAAA
1 ATTAATAAA
20636520 ATTTTAATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 10 0.27
16 3 0.08
17 4 0.11
18 9 0.24
19 10 0.27
20 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
ATTAATAAATAATAAAAG
Found at i:20636714 original size:20 final size:19
Alignment explanation
Indices: 20636671--20636717 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
20636661 TTAAAATCTG
*
20636671 AAACTCTAGGTAAAACCTA
1 AAACCCTAGGTAAAACCTA
*
20636690 AAACCCTAGGTGAAACCTAA
1 AAACCCTAGGTAAAACCT-A
20636710 AAACCCTA
1 AAACCCTA
20636718 AAATAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.17
Consensus pattern (19 bp):
AAACCCTAGGTAAAACCTA
Found at i:20636745 original size:13 final size:13
Alignment explanation
Indices: 20636709--20636745 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
20636699 GTGAAACCTA
20636709 AAAACCCTAAAAT
1 AAAACCCTAAAAT
* *
20636722 AAAATCTTAAAAT
1 AAAACCCTAAAAT
20636735 AAAACCCTAAA
1 AAAACCCTAAA
20636746 TCATAGGTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAACCCTAAAAT
Found at i:20639663 original size:2 final size:2
Alignment explanation
Indices: 20639656--20639683 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20639646 TATGAATGAG
20639656 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
20639684 GAACTTACCA
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:20642558 original size:17 final size:17
Alignment explanation
Indices: 20642536--20642586 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
20642526 AACTCAAGCT
20642536 TTTTTTTTTAATTTTGA
1 TTTTTTTTTAATTTTGA
*
20642553 TTTTTTTTTATTTTTTGA
1 TTTTTTTTTA-ATTTTGA
*
20642571 TTTTTTTTTTATTTTG
1 TTTTTTTTTAATTTTG
20642587 CTTGAAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 15 0.50
18 15 0.50
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTAATTTTGA
Found at i:20642581 original size:19 final size:19
Alignment explanation
Indices: 20642535--20642585 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
20642525 GAACTCAAGC
*
20642535 TTTTTTTTTTA-ATTTTGA
1 TTTTTTTTTTATTTTTTGA
20642553 -TTTTTTTTTATTTTTTGA
1 TTTTTTTTTTATTTTTTGA
20642571 TTTTTTTTTTATTTT
1 TTTTTTTTTTATTTT
20642586 GCTTGAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 10 0.33
18 6 0.20
19 14 0.47
ACGTcount: A:0.12, C:0.00, G:0.04, T:0.84
Consensus pattern (19 bp):
TTTTTTTTTTATTTTTTGA
Found at i:20642903 original size:83 final size:84
Alignment explanation
Indices: 20642793--20643004 Score: 214
Period size: 83 Copynumber: 2.5 Consensus size: 84
20642783 TGCTCGGAGG
* ** * * * * **
20642793 ACTTAGAGACTATGCCTGAAGGCCTTGCAAATCTCGACGTAAAAACAAATTCAGTTTGGAAGACT
1 ACTTAAAGACTATGCCCAAAGGTCTTGCAAATCTCAACATAAAAACAAATTCAGCTAAGAAGACT
*
20642858 TATC-AATCTTGC-CTAAAAA
66 TA-CAAATCTAGCTC-AAAAA
* * * * *
20642877 ACTTAAA-AGTATGCCCAAAGGTCTTGCAAATCTCAACATGAAAATAGATTTAGCTAAGAAGACT
1 ACTTAAAGACTATGCCCAAAGGTCTTGCAAATCTCAACATAAAAACAAATTCAGCTAAGAAGACT
20642941 TACAAATCTAGCTCAAAAA
66 TACAAATCTAGCTCAAAAA
* * * *
20642960 ACTTAAAGACTATGCCCAGAGGTCTTACCAATCTCAACATGAAAA
1 ACTTAAAGACTATGCCCAAAGGTCTTGCAAATCTCAACATAAAAA
20643005 TAGATACAAC
Statistics
Matches: 106, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
82 1 0.01
83 65 0.61
84 40 0.38
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.25
Consensus pattern (84 bp):
ACTTAAAGACTATGCCCAAAGGTCTTGCAAATCTCAACATAAAAACAAATTCAGCTAAGAAGACT
TACAAATCTAGCTCAAAAA
Found at i:20642994 original size:84 final size:83
Alignment explanation
Indices: 20642851--20643009 Score: 232
Period size: 84 Copynumber: 1.9 Consensus size: 83
20642841 ATTCAGTTTG
* * *
20642851 GAAGACTTATCAATCTTGCCTAAAAAACTTAAAAGTATGCCCAAAGGTCTTGCAAATCTCAACAT
1 GAAGACTTATCAATCTAGCCTAAAAAACTTAAAACTATGCCCAAAGGTCTTACAAATCTCAACAT
20642916 GAAAATAGATTTAGCTAA
66 GAAAATAGATTTAGCTAA
* *
20642934 GAAGACTTA-CAAATCTAG-CTCAAAAAACTTAAAGACTATGCCCAGAGGTCTTACCAATCTCAA
1 GAAGACTTATC-AATCTAGCCT-AAAAAACTTAAA-ACTATGCCCAAAGGTCTTACAAATCTCAA
20642997 CATGAAAATAGAT
63 CATGAAAATAGAT
20643010 ACAACTCTAG
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
82 3 0.04
83 27 0.40
84 38 0.56
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (83 bp):
GAAGACTTATCAATCTAGCCTAAAAAACTTAAAACTATGCCCAAAGGTCTTACAAATCTCAACAT
GAAAATAGATTTAGCTAA
Found at i:20645057 original size:12 final size:12
Alignment explanation
Indices: 20645026--20645092 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
20645016 CTTTTCCTTA
*
20645026 TTTTCTTCT-AT
1 TTTTCTTTTCAT
20645037 TTTTCCTTTTCAT
1 TTTT-CTTTTCAT
20645050 TTTTCTTTTC-T
1 TTTTCTTTTCAT
20645061 TCTTTCATTTTCA-
1 T-TTTC-TTTTCAT
20645074 TTTTCTTTT--T
1 TTTTCTTTTCAT
20645084 TTTTCTTTT
1 TTTTCTTTT
20645093 TAGTTTAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 13
0.78 0.02 0.21
Matches are distributed among these distances:
10 9 0.18
11 10 0.20
12 18 0.37
13 12 0.24
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTCAT
Found at i:20645077 original size:24 final size:23
Alignment explanation
Indices: 20645025--20645093 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 23
20645015 TCTTTTCCTT
* *
20645025 ATTTTCTTCTATTTTTCCTTTTC
1 ATTTTCTTTTATTTTTCATTTTC
*
20645048 ATTTTTCTTTTCTTCTTTCATTTTC
1 A-TTTTCTTTTATT-TTTCATTTTC
*
20645073 ATTTTCTTTT-TTTTTCTTTTT
1 ATTTTCTTTTATTTTTCATTTT
20645094 AGTTTAATAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 8 0.20
23 3 0.08
24 19 0.47
25 10 0.25
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (23 bp):
ATTTTCTTTTATTTTTCATTTTC
Found at i:20645083 original size:6 final size:6
Alignment explanation
Indices: 20645036--20645093 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
20645026 TTTTCTTCTA
* * *
20645036 TTTTTC CTTTTC ATTTTTC -TTTTC TTCTTTC ATTTTC ATTTTC -TTTT-
1 TTTTTC TTTTTC -TTTTTC TTTTTC TT-TTTC TTTTTC TTTTTC TTTTTC
20645083 TTTTTC TTTTT
1 TTTTTC TTTTT
20645094 AGTTTAATAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
5 13 0.30
6 21 0.48
7 10 0.23
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:20645475 original size:61 final size:62
Alignment explanation
Indices: 20645370--20645487 Score: 177
Period size: 61 Copynumber: 1.9 Consensus size: 62
20645360 AATTCTTTAA
*
20645370 GAAAAAAGGTTCAAATAAAGGGTTTTTTTTTTTAATTTCTTTTTTT-TTCTTTTTTTTTTGG
1 GAAAAAAGGTTCAAATAAAGGGTTTTTTTTTTAAATTTCTTTTTTTATTCTTTTTTTTTTGG
* *
20645431 GAAAAAAGGTTTAAATAAA-GGTTTTTTTTTTAAAAATTTCTTTTTTCATTCTTTTTT
1 GAAAAAAGGTTCAAATAAAGGGTTTTTTTTTT--AAATTTCTTTTTTTATTCTTTTTT
20645488 ATTGAATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
60 12 0.24
61 18 0.35
62 12 0.24
63 9 0.18
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (62 bp):
GAAAAAAGGTTCAAATAAAGGGTTTTTTTTTTAAATTTCTTTTTTTATTCTTTTTTTTTTGG
Found at i:20651561 original size:18 final size:17
Alignment explanation
Indices: 20651540--20651581 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
20651530 TTTTTGTTTA
20651540 TTTTTAATTATATATTAC
1 TTTTTAATTAT-TATTAC
* *
20651558 TTTTCAATTATTATTAT
1 TTTTTAATTATTATTAC
20651575 TTTTTAA
1 TTTTTAA
20651582 AAATTATTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTAATTATTATTAC
Found at i:20651578 original size:17 final size:17
Alignment explanation
Indices: 20651537--20651578 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
20651527 TTCTTTTTGT
20651537 TTATTTTTAATTATATA
1 TTATTTTTAATTATATA
*
20651554 TTACTTTTCAATTAT-TA
1 TTA-TTTTTAATTATATA
20651571 TTATTTTT
1 TTATTTTT
20651579 TAAAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 4 0.18
17 8 0.36
18 10 0.45
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTTTAATTATATA
Found at i:20652946 original size:3 final size:3
Alignment explanation
Indices: 20652940--20652980 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
20652930 GATTTTTTTA
20652940 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
20652981 CTACTACTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20653982 original size:17 final size:17
Alignment explanation
Indices: 20653960--20653993 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
20653950 CATATTTTTC
20653960 ATTATTTT-TATTTATTT
1 ATTATTTTAT-TTTATTT
20653977 ATTATTTTATTTTATTT
1 ATTATTTTATTTTATTT
20653994 TAAAAAATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTATTTTATTTTATTT
Found at i:20660532 original size:41 final size:42
Alignment explanation
Indices: 20660485--20660569 Score: 118
Period size: 41 Copynumber: 2.0 Consensus size: 42
20660475 GGGCATTTTT
*
20660485 GGCTAAAAACATCTTGAATAATCCCCTTCAA-TTTTTATGAG
1 GGCTAAAAACATCTTGAATAATCCACTTCAAGTTTTTATGAG
** * *
20660526 GGCTAAAAATGTCTTGAATAATCCATTTCAAGTTTTTATTAG
1 GGCTAAAAACATCTTGAATAATCCACTTCAAGTTTTTATGAG
20660568 GG
1 GG
20660570 ATTATTCAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
41 27 0.71
42 11 0.29
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (42 bp):
GGCTAAAAACATCTTGAATAATCCACTTCAAGTTTTTATGAG
Found at i:20661165 original size:182 final size:182
Alignment explanation
Indices: 20660855--20661201 Score: 457
Period size: 182 Copynumber: 1.9 Consensus size: 182
20660845 TAAATAGGGG
* * * *
20660855 ATTATTTAAGGTGTTTTTGGTAAAAAATACCTTGAATAATACCCTCATAAAAATTGAAGGTGATT
1 ATTATTTAAGGTGTTTTTGGCAAAAAACACCTAGAATAATACCCTCATAAAAATTGAAGGTCATT
* * * * *
20660920 ATTCAATGCGTTTTTGACCAAAAACGCCTTGAATAACCCTCATCAATTCTTTGTAAGGGATTATT
66 ATTCAAGGCATTTTTGACCAAAAACGCATTGAATAACCCTCATCAATTCTTTATAAAGGATTATT
20660985 CAAG-GCATTTCTAGCCAAAAATGTCTTGAATAATTCAAAAAAAAGGCAAGAA
131 CAAGAG-ATTTCTAGCCAAAAATGTCTTGAATAATTCAAAAAAAAGGCAAGAA
* * *
20661037 ATTATTTAAGGTTTTTTTGGCCAAAAACACCTAGAATAATCCCCTCATAAAAATTGAAAGG-CAT
1 ATTATTTAAGGTGTTTTTGGCAAAAAACACCTAGAATAATACCCTCATAAAAATTG-AAGGTCAT
* * * * * *
20661101 TATTGAAGGTATTTTTGACCAGAAATGCATTGAATAACCC-CATTTAATTTTTTATAAAGGATTA
65 TATTCAAGGCATTTTTGACCAAAAACGCATTGAATAACCCTCA-TCAATTCTTTATAAAGGATTA
* *
20661165 TTCAAGAAGTTTTCTAGGCAAAAATGTCTTGAATAAT
129 TTCAAG-AGATTTCTAGCCAAAAATGTCTTGAATAAT
20661202 CCCTAATAAA
Statistics
Matches: 141, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
181 2 0.01
182 108 0.77
183 30 0.21
184 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (182 bp):
ATTATTTAAGGTGTTTTTGGCAAAAAACACCTAGAATAATACCCTCATAAAAATTGAAGGTCATT
ATTCAAGGCATTTTTGACCAAAAACGCATTGAATAACCCTCATCAATTCTTTATAAAGGATTATT
CAAGAGATTTCTAGCCAAAAATGTCTTGAATAATTCAAAAAAAAGGCAAGAA
Found at i:20661363 original size:20 final size:20
Alignment explanation
Indices: 20661325--20661364 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20661315 TTTTTGTAAG
**
20661325 GGAATAATCAAGGTGTTTTT
1 GGAATAATCAAGGCATTTTT
20661345 GGAATAATCAAGGCATTTTT
1 GGAATAATCAAGGCATTTTT
20661365 TATCAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.38
Consensus pattern (20 bp):
GGAATAATCAAGGCATTTTT
Found at i:20661600 original size:11 final size:11
Alignment explanation
Indices: 20661584--20661612 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
20661574 TATAAGGGAT
20661584 TTTTCAAAGCA
1 TTTTCAAAGCA
20661595 TTTTCAAAGCA
1 TTTTCAAAGCA
20661606 TTTTCAA
1 TTTTCAA
20661613 GCCAAACGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (11 bp):
TTTTCAAAGCA
Found at i:20666698 original size:2 final size:2
Alignment explanation
Indices: 20666691--20666719 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20666681 TCCTAAAGTG
20666691 TA 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 TA T
20666720 GACTTGAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20671597 original size:17 final size:17
Alignment explanation
Indices: 20671575--20671615 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
20671565 CACAATGAAA
*
20671575 ATTTATTAATGATTT-TT
1 ATTTATTAA-CATTTATT
20671592 ATTTATTAACATTTATT
1 ATTTATTAACATTTATT
20671609 ATTTATT
1 ATTTATT
20671616 TTTAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTTATTAACATTTATT
Found at i:20672055 original size:21 final size:21
Alignment explanation
Indices: 20672031--20672136 Score: 72
Period size: 21 Copynumber: 4.9 Consensus size: 21
20672021 AGGTTTTGAG
*
20672031 TTAATTTGAATTCAAAT-AAAT
1 TTAATTT-AAATCAAATCAAAT
* *
20672052 TTAAATTTAAATCAATTCAATT
1 TT-AATTTAAATCAAATCAAAT
* *
20672074 TTAAATTAAATCAAATTCAAGT
1 TTAATTTAAATCAAA-TCAAAT
* *
20672096 TCAATTTAACTTCAAAT-AAAT
1 TTAATTTAA-ATCAAATCAAAT
* *
20672117 TTAAACTTGAATCAAATCAA
1 TT-AATTTAAATCAAATCAA
20672137 GTTTTAATAT
Statistics
Matches: 65, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
21 30 0.46
22 30 0.46
23 5 0.08
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (21 bp):
TTAATTTAAATCAAATCAAAT
Found at i:20672058 original size:16 final size:16
Alignment explanation
Indices: 20672033--20672121 Score: 63
Period size: 16 Copynumber: 5.5 Consensus size: 16
20672023 GTTTTGAGTT
*
20672033 AATTTGAATTCAAATA
1 AATTTAAATTCAAATA
* *
20672049 AATTTAAATTTAAATC
1 AATTTAAATTCAAATA
* * *
20672065 AATTCAATTTTAAATTA
1 AATTTAAATTCAAA-TA
* * *
20672082 AA-TCAAATTCAAGTTC
1 AATTTAAATTCAA-ATA
*
20672098 AATTTAACTTCAAATA
1 AATTTAAATTCAAATA
20672114 AATTTAAA
1 AATTTAAA
20672122 CTTGAATCAA
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
16 44 0.80
17 11 0.20
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.39
Consensus pattern (16 bp):
AATTTAAATTCAAATA
Found at i:20672058 original size:22 final size:21
Alignment explanation
Indices: 20672033--20672133 Score: 78
Period size: 22 Copynumber: 4.7 Consensus size: 21
20672023 GTTTTGAGTT
*
20672033 AATTTGAATTCAAATAAATTTA
1 AATTT-AAATCAAATAAATTTA
* *
20672055 AATTTAAATCAATTCAATTTTA
1 AATTTAAATCAAAT-AAATTTA
* * *
20672077 AA-TTAAATCAAATTCAAGTTC
1 AATTTAAATCAAA-TAAATTTA
*
20672098 AATTTAACTTCAAATAAATTTA
1 AATTTAA-ATCAAATAAATTTA
* *
20672120 AACTTGAATCAAAT
1 AATTTAAATCAAAT
20672134 CAAGTTTTAA
Statistics
Matches: 60, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
21 27 0.45
22 28 0.47
23 5 0.08
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.39
Consensus pattern (21 bp):
AATTTAAATCAAATAAATTTA
Found at i:20672103 original size:27 final size:27
Alignment explanation
Indices: 20672059--20672117 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
20672049 AATTTAAATT
20672059 TAAA-TCAATTCAATTTTAAATT-AAA
1 TAAATTCAATTCAATTTTAAATTCAAA
*
20672084 TCAAATTCAAGTTCAA-TTTAACTTCAAA
1 T-AAATTCAA-TTCAATTTTAAATTCAAA
20672112 TAAATT
1 TAAATT
20672118 TAAACTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 1 0.03
26 3 0.10
27 16 0.55
28 9 0.31
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAATTCAATTCAATTTTAAATTCAAA
Found at i:20673815 original size:36 final size:39
Alignment explanation
Indices: 20673775--20673853 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 39
20673765 AATCATTTAC
20673775 ATTTTTAATATTTTATTTTAATT-AATT-AA-TTTTAA-A
1 ATTTTTAATA-TTTATTTTAATTCAATTAAATTTTTAATA
*
20673811 ATTTTTAATATTTATTTTTATTCAATTAAATTTTTAATA
1 ATTTTTAATATTTATTTTAATTCAATTAAATTTTTAATA
20673850 ATTT
1 ATTT
20673854 ATTTTCATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
35 11 0.29
36 14 0.37
37 2 0.05
38 6 0.16
39 5 0.13
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (39 bp):
ATTTTTAATATTTATTTTAATTCAATTAAATTTTTAATA
Found at i:20673842 original size:29 final size:30
Alignment explanation
Indices: 20673809--20673876 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
20673799 ATTAATTTTA
*
20673809 AAATTTTTAAT-ATTTATTTTTATTCAATT
1 AAATTTTTAATAATTTATTTTCATTCAATT
*
20673838 AAATTTTTAATAATTTATTTTCATTTAATT
1 AAATTTTTAATAATTTATTTTCATTCAATT
*
20673868 GAATTTTTA
1 AAATTTTTA
20673877 TTTAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 11 0.31
30 24 0.69
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.60
Consensus pattern (30 bp):
AAATTTTTAATAATTTATTTTCATTCAATT
Found at i:20673843 original size:16 final size:14
Alignment explanation
Indices: 20673810--20673878 Score: 50
Period size: 15 Copynumber: 4.7 Consensus size: 14
20673800 TTAATTTTAA
*
20673810 AATTTTTAAT-ATT
1 AATTTTTATTAATT
*
20673823 TATTTTTATTCAATT
1 AATTTTTATT-AATT
*
20673838 AAATTTTTAATAATT
1 -AATTTTTATTAATT
* *
20673853 TATTTTCATTTAATT
1 AATTTTTA-TTAATT
20673868 GAATTTTTATT
1 -AATTTTTATT
20673879 TAATAAAATA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
13 8 0.19
14 6 0.14
15 14 0.33
16 14 0.33
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (14 bp):
AATTTTTATTAATT
Found at i:20673879 original size:16 final size:15
Alignment explanation
Indices: 20673779--20673882 Score: 58
Period size: 16 Copynumber: 7.1 Consensus size: 15
20673769 ATTTACATTT
20673779 TTAATATTTTATTTTAA
1 TTAAT-TTTTA-TTTAA
**
20673796 TTAATTAAT-TTTAA
1 TTAATTTTTATTTAA
*
20673810 --AATTTTTA-AT-A
1 TTAATTTTTATTTAA
* *
20673821 TTTATTTTTATTCAA
1 TTAATTTTTATTTAA
*
20673836 TTAAATTTTTA-ATAA
1 TT-AATTTTTATTTAA
* *
20673851 TTTATTTTCATTTAA
1 TTAATTTTTATTTAA
20673866 TTGAATTTTTATTTAA
1 TT-AATTTTTATTTAA
20673882 T
1 T
20673883 AAAATAAGTA
Statistics
Matches: 63, Mismatches: 16, Indels: 17
0.66 0.17 0.18
Matches are distributed among these distances:
11 1 0.02
12 6 0.10
13 7 0.11
14 11 0.17
15 12 0.19
16 21 0.33
17 5 0.08
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.62
Consensus pattern (15 bp):
TTAATTTTTATTTAA
Found at i:20674724 original size:3 final size:3
Alignment explanation
Indices: 20674716--20674747 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20674706 TTTGTAAATC
20674716 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
20674748 AAAGTAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20675005 original size:13 final size:13
Alignment explanation
Indices: 20674974--20675027 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 13
20674964 TAATAAAACT
*
20674974 TTTTAATTTATTGA
1 TTTTAATTT-TTAA
20674988 TTTTAATTTTTAA
1 TTTTAATTTTTAA
*
20675001 TTTT-ATTTTTTA
1 TTTTAATTTTTAA
*
20675013 TTTAATATTTTTAA
1 TTTTA-ATTTTTAA
20675027 T
1 T
20675028 AAAAAATTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 10 0.29
13 7 0.21
14 17 0.50
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:20678032 original size:25 final size:25
Alignment explanation
Indices: 20677971--20678038 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
20677961 AGACTCTGAA
* *
20677971 CCAAATCCTAATCCTAAACCTTAAG
1 CCAAACCCTAAACCTAAACCTTAAG
* * *
20677996 TCAAACCATAAACACTAAATCTT-AG
1 CCAAACCCTAAAC-CTAAACCTTAAG
*
20678021 CCAAACCCTAAACTTAAA
1 CCAAACCCTAAACCTAAA
20678039 GTCAAACCCA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
24 4 0.12
25 22 0.65
26 8 0.24
ACGTcount: A:0.46, C:0.29, G:0.03, T:0.22
Consensus pattern (25 bp):
CCAAACCCTAAACCTAAACCTTAAG
Found at i:20678295 original size:23 final size:23
Alignment explanation
Indices: 20678269--20678313 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
20678259 CATATGAGTT
*
20678269 TTTAATGATGGTTTCAAAAACAA
1 TTTAATGATAGTTTCAAAAACAA
20678292 TTTAATGATAGTTTCAAAAACA
1 TTTAATGATAGTTTCAAAAACA
20678314 TAACAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (23 bp):
TTTAATGATAGTTTCAAAAACAA
Found at i:20679119 original size:20 final size:21
Alignment explanation
Indices: 20679077--20679121 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
20679067 AATTAATCTA
* *
20679077 AAAT-AAAATTTTATATTATT
1 AAATAAAAAATTTATATTACT
20679097 AAATAAAAAATTTAT-TTACT
1 AAATAAAAAATTTATATTACT
20679117 AAATA
1 AAATA
20679122 TATATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATAAAAAATTTATATTACT
Found at i:20679760 original size:2 final size:2
Alignment explanation
Indices: 20679755--20679784 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20679745 CTCTATATGC
20679755 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
20679785 GATGAAACAC
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:20680269 original size:34 final size:35
Alignment explanation
Indices: 20680200--20680269 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 35
20680190 ATAATAATTT
* * *
20680200 AATTATTAATATTTTTATTTAATCTATTAAGTTTA
1 AATTAGTAATATTTTTACTTAATCTATTAACTTTA
20680235 AATTAGTAAT-TTTTTACTTAAT-TATTAATCTTTA
1 AATTAGTAATATTTTTACTTAATCTATTAA-CTTTA
20680269 A
1 A
20680270 TAATATGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 6 0.19
34 16 0.52
35 9 0.29
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (35 bp):
AATTAGTAATATTTTTACTTAATCTATTAACTTTA
Found at i:20681593 original size:16 final size:15
Alignment explanation
Indices: 20681563--20681596 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
20681553 CTAAAATATT
20681563 TATTAAATATTTAAA
1 TATTAAATATTTAAA
*
20681578 TATTAACATTTTTAAA
1 TATTAA-ATATTTAAA
20681594 TAT
1 TAT
20681597 ATGTGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAAATATTTAAA
Found at i:20681613 original size:6 final size:6
Alignment explanation
Indices: 20681602--20681627 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20681592 AATATATGTG
20681602 AAAATT AAAATT AAAATT AAAATT AA
1 AAAATT AAAATT AAAATT AAAATT AA
20681628 TCTTTATTAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:20683347 original size:22 final size:22
Alignment explanation
Indices: 20683321--20683370 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
20683311 TATTTTTGGT
*
20683321 CTAATTAGTTTTAATTTTGTTAA
1 CTAATTAATTTTAATTTT-TTAA
* *
20683344 -TAATCAATTTTTATTTTTTAA
1 CTAATTAATTTTAATTTTTTAA
20683365 CTAATT
1 CTAATT
20683371 TTAATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (22 bp):
CTAATTAATTTTAATTTTTTAA
Found at i:20688609 original size:13 final size:13
Alignment explanation
Indices: 20688591--20688615 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20688581 CGTTCCTTGC
20688591 TTCTATTTTCTTT
1 TTCTATTTTCTTT
20688604 TTCTATTTTCTT
1 TTCTATTTTCTT
20688616 CTTATGCCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (13 bp):
TTCTATTTTCTTT
Found at i:20689199 original size:27 final size:26
Alignment explanation
Indices: 20689169--20689223 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
20689159 TATTTTAAAA
* *
20689169 TTCAAAAAATACAAAATGAAAATTATT
1 TTCAAAAAAT-CAAAATAAAAAATATT
* *
20689196 TTCAGAAAATGAAAATAAAAAATATT
1 TTCAAAAAATCAAAATAAAAAATATT
20689222 TT
1 TT
20689224 TATAACCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.31
Consensus pattern (26 bp):
TTCAAAAAATCAAAATAAAAAATATT
Found at i:20692091 original size:18 final size:17
Alignment explanation
Indices: 20692055--20692128 Score: 64
Period size: 18 Copynumber: 4.3 Consensus size: 17
20692045 ATTTAGTACT
**
20692055 TTTTTATTTTAT-TCCA
1 TTTTTATTTTATCTTTA
20692071 TTTTTATCTTTATCTTTA
1 TTTTTAT-TTTATCTTTA
*
20692089 TTTTTATTTTTATTCTTATT
1 TTTTTA-TTTTA-TCTT-TA
20692109 TTTTTATTTT-T-TTTA
1 TTTTTATTTTATCTTTA
20692124 TTTTT
1 TTTTT
20692129 TTGTCTTCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
15 6 0.12
16 9 0.18
17 6 0.12
18 12 0.24
19 9 0.18
20 7 0.14
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTATCTTTA
Done.