Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 17 of 129
Found at i:3219475 original size:12 final size:13
Alignment explanation
Indices: 3219446--3219480 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
3219436 TAATATTAGA
3219446 ATATTTTATTATT
1 ATATTTTATTATT
3219459 ATATTTT-TTATT
1 ATATTTTATTATT
*
3219471 TTATTTTATT
1 ATATTTTATT
3219481 TGTTAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATATTTTATTATT
Found at i:3219490 original size:20 final size:21
Alignment explanation
Indices: 3219445--3219491 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
3219435 TTAATATTAG
3219445 AATATTTTATTATTATATTTT
1 AATATTTTATTATTATATTTT
*
3219466 -TTATTTTATT-TTAT-TTGTT
1 AATATTTTATTATTATATT-TT
3219485 AATATTT
1 AATATTT
3219492 GCTAGCTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
AATATTTTATTATTATATTTT
Found at i:3234828 original size:33 final size:32
Alignment explanation
Indices: 3234790--3234893 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 32
3234780 TATATTTGTG
3234790 TTTTATAAAATATTAAAATATAAATATTTTATA
1 TTTTATAAAA-ATTAAAATATAAATATTTTATA
* * * *
3234823 TTTTATATGAAAATT-ATATAT-TATAATTTAAA
1 TTTTATA--AAAATTAAAATATAAATATTTTATA
*
3234855 TTATTATAAAAATATAAAATATACATATTTT-TA
1 TT-TTATAAAAAT-TAAAATATAAATATTTTATA
3234888 TTTTAT
1 TTTTAT
3234894 TAAATCTATA
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
31 5 0.09
32 15 0.26
33 25 0.44
34 9 0.16
35 3 0.05
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (32 bp):
TTTTATAAAAATTAAAATATAAATATTTTATA
Found at i:3235938 original size:18 final size:19
Alignment explanation
Indices: 3235915--3235959 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
3235905 ATGAGTTTTG
*
3235915 TTTATTTAATTATTAT-TA
1 TTTATTTAATTATGATGTA
*
3235933 TTTATTTATTTATGATGTA
1 TTTATTTAATTATGATGTA
3235952 TTTCATTT
1 TTT-ATTT
3235960 GATTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 14 0.61
19 5 0.22
20 4 0.17
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTATTTAATTATGATGTA
Found at i:3237694 original size:13 final size:13
Alignment explanation
Indices: 3237676--3237700 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3237666 AATCTAATCT
3237676 TATTATATTATTA
1 TATTATATTATTA
3237689 TATTATATTATT
1 TATTATATTATT
3237701 TTATCATAAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTATATTATTA
Found at i:3243366 original size:4 final size:4
Alignment explanation
Indices: 3243326--3243356 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3243316 ATATATATAG
3243326 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
3243357 TATATATATA
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:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:3247130 original size:2 final size:2
Alignment explanation
Indices: 3247123--3247149 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3247113 AATTCTTTGA
3247123 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3247150 ATTTTACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3247256 original size:30 final size:25
Alignment explanation
Indices: 3247195--3247244 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3247185 GTTTAATGGA
3247195 ATAAATAGACTTGATTAAGATAAGG
1 ATAAATAGACTTGATTAAGATAAGG
*
3247220 ATAAATAGGCTTGATTAAGATAAGG
1 ATAAATAGACTTGATTAAGATAAGG
3247245 CATTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.22, T:0.28
Consensus pattern (25 bp):
ATAAATAGACTTGATTAAGATAAGG
Found at i:3250075 original size:25 final size:25
Alignment explanation
Indices: 3250041--3250092 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
3250031 CACCATATCA
* *
3250041 CACTGGTATGCATGATACTCCTTAC
1 CACTAGTATGCATCATACTCCTTAC
*
3250066 CACTAGTATGCATCATTCTCCTTAC
1 CACTAGTATGCATCATACTCCTTAC
3250091 CA
1 CA
3250093 AGACTATACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.33
Consensus pattern (25 bp):
CACTAGTATGCATCATACTCCTTAC
Found at i:3255107 original size:21 final size:21
Alignment explanation
Indices: 3255052--3255100 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
3255042 TGAGTCACCA
*
3255052 TACCATAATAATAAGTCATTG
1 TACCATAATAATGAGTCATTG
3255073 TACCATAATAATGAGTCATTG
1 TACCATAATAATGAGTCATTG
3255094 TACCATA
1 TACCATA
3255101 GTTATGACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (21 bp):
TACCATAATAATGAGTCATTG
Found at i:3256278 original size:18 final size:20
Alignment explanation
Indices: 3256245--3256289 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
3256235 ATATTTTATT
3256245 AATTAAAATAATAAAAA-TA
1 AATTAAAATAATAAAAACTA
*
3256264 AATTAAAAT-ATAAAAACTC
1 AATTAAAATAATAAAAACTA
3256283 AATTAAA
1 AATTAAA
3256290 CTCACGAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
AATTAAAATAATAAAAACTA
Found at i:3256962 original size:2 final size:2
Alignment explanation
Indices: 3256955--3256981 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3256945 TCCACCTAAC
3256955 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3256982 ATTGAGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3257352 original size:2 final size:2
Alignment explanation
Indices: 3257345--3257372 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3257335 GGAATTAGGA
3257345 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
3257373 GTGTGTGTGT
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:3257377 original size:2 final size:2
Alignment explanation
Indices: 3257372--3257398 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3257362 TATATATATA
3257372 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
3257399 ATGTATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3257508 original size:2 final size:2
Alignment explanation
Indices: 3257501--3257557 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
3257491 TTAAATTAAG
3257501 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
3257543 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
3257558 GAAAGAAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3258080 original size:24 final size:25
Alignment explanation
Indices: 3258042--3258093 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
3258032 AAATTATTAT
*
3258042 AATTTAATTCACTGATAATATATAA
1 AATTTAATACACTGATAATATATAA
*
3258067 AATTT-ATACACTGATAATATATTA
1 AATTTAATACACTGATAATATATAA
3258091 AAT
1 AAT
3258094 ATAACCTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (25 bp):
AATTTAATACACTGATAATATATAA
Found at i:3260491 original size:89 final size:89
Alignment explanation
Indices: 3260340--3260518 Score: 322
Period size: 89 Copynumber: 2.0 Consensus size: 89
3260330 CCCCCTATCC
*
3260340 CCATCCTCTTTCAGTTTTTAACACCTTAGCTATATCAGAGAAAACCCACCAAATCCCATCCTCTT
1 CCATCCTATTTCAGTTTTTAACACCTTAGCTATATCAGAGAAAACCCACCAAATCCCATCCTCTT
*
3260405 TCTCTTTTCCCTTTGTCCCCAGCT
66 TCTCTCTTCCCTTTGTCCCCAGCT
*
3260429 CCATCCTATTTCAGTTTTTTACACCTTAGCTATATCAGAGAAAACCCACCAAATCCCATCCTCTT
1 CCATCCTATTTCAGTTTTTAACACCTTAGCTATATCAGAGAAAACCCACCAAATCCCATCCTCTT
*
3260494 TCTCTCTTCCCTTTGTCCCCTGCT
66 TCTCTCTTCCCTTTGTCCCCAGCT
3260518 C
1 C
3260519 TTCTGTATAG
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.22, C:0.36, G:0.07, T:0.35
Consensus pattern (89 bp):
CCATCCTATTTCAGTTTTTAACACCTTAGCTATATCAGAGAAAACCCACCAAATCCCATCCTCTT
TCTCTCTTCCCTTTGTCCCCAGCT
Found at i:3263304 original size:18 final size:18
Alignment explanation
Indices: 3263246--3263304 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
3263236 CATATCTGAA
* *
3263246 AAAAAAATATGATTATTT
1 AAAAAAATATAATTATAT
* * * *
3263264 AAATAAAATTTATTTAAAC
1 AAA-AAAATATAATTATAT
3263283 AAAAAAATATAATTATAT
1 AAAAAAATATAATTATAT
3263301 AAAA
1 AAAA
3263305 TATCATAATT
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAAAAATATAATTATAT
Found at i:3265651 original size:27 final size:27
Alignment explanation
Indices: 3265621--3265677 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
3265611 TTAAGTCTCT
*
3265621 GTTTGCATAAGCACATTACTTGTTGAA
1 GTTTGCATAAGCACATTACTTATTGAA
3265648 GTTTGCATAAGCACATTACTTATTGAA
1 GTTTGCATAAGCACATTACTTATTGAA
3265675 GTT
1 GTT
3265678 AAGGAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (27 bp):
GTTTGCATAAGCACATTACTTATTGAA
Found at i:3275883 original size:16 final size:16
Alignment explanation
Indices: 3275841--3275986 Score: 91
Period size: 16 Copynumber: 9.2 Consensus size: 16
3275831 AGGTTTGAGA
*
3275841 TTTCGGATTTTATGAGG
1 TTTCGGATTTTA-GGGG
*
3275858 TTTTGGATTTTAGGGG
1 TTTCGGATTTTAGGGG
* *
3275874 TTTCGCATTTTA-GGA
1 TTTCGGATTTTAGGGG
* **
3275889 TTTTGGATTTTAGAAG
1 TTTCGGATTTTAGGGG
* *
3275905 TTT-GGATTTAAGGGA
1 TTTCGGATTTTAGGGG
* *
3275920 TTTTGGATCTTAGGGG
1 TTTCGGATTTTAGGGG
** *
3275936 TTTCAAATTTTA-GGA
1 TTTCGGATTTTAGGGG
* *
3275951 TTTTGGATCTTAGGGG
1 TTTCGGATTTTAGGGG
* *
3275967 ATTTTGGATTTTAAGGG
1 -TTTCGGATTTTAGGGG
3275984 TTT
1 TTT
3275987 TAGAAACCCA
Statistics
Matches: 96, Mismatches: 29, Indels: 9
0.72 0.22 0.07
Matches are distributed among these distances:
15 33 0.34
16 38 0.40
17 25 0.26
ACGTcount: A:0.20, C:0.04, G:0.29, T:0.47
Consensus pattern (16 bp):
TTTCGGATTTTAGGGG
Found at i:3275896 original size:31 final size:31
Alignment explanation
Indices: 3275858--3275966 Score: 130
Period size: 31 Copynumber: 3.5 Consensus size: 31
3275848 TTTTATGAGG
* *
3275858 TTTTGGATTTTAGGGGTTTCGCATTTTAGGA
1 TTTTGGATCTTAGGGGTTTCGAATTTTAGGA
* ** * *
3275889 TTTTGGATTTTAGAAGTTT-GGATTTAAGGGA
1 TTTTGGATCTTAGGGGTTTCGAATTTTA-GGA
*
3275920 TTTTGGATCTTAGGGGTTTCAAATTTTAGGA
1 TTTTGGATCTTAGGGGTTTCGAATTTTAGGA
3275951 TTTTGGATCTTAGGGG
1 TTTTGGATCTTAGGGG
3275967 ATTTTGGATT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
30 6 0.09
31 55 0.83
32 5 0.08
ACGTcount: A:0.20, C:0.05, G:0.29, T:0.46
Consensus pattern (31 bp):
TTTTGGATCTTAGGGGTTTCGAATTTTAGGA
Found at i:3275970 original size:17 final size:17
Alignment explanation
Indices: 3275905--3275975 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 17
3275895 ATTTTAGAAG
*
3275905 TTTGGAT-TTAAGGGAT
1 TTTGGATCTTAGGGGAT
3275921 TTTGGATCTTAGGGG-T
1 TTTGGATCTTAGGGGAT
*** *
3275937 TTCAAATTTTA--GGAT
1 TTTGGATCTTAGGGGAT
3275952 TTTGGATCTTAGGGGAT
1 TTTGGATCTTAGGGGAT
3275969 TTTGGAT
1 TTTGGAT
3275976 TTTAAGGGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
14 2 0.05
15 8 0.19
16 15 0.36
17 17 0.40
ACGTcount: A:0.21, C:0.04, G:0.30, T:0.45
Consensus pattern (17 bp):
TTTGGATCTTAGGGGAT
Found at i:3275985 original size:48 final size:47
Alignment explanation
Indices: 3275895--3275986 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 47
3275885 AGGATTTTGG
*
3275895 ATTTTAGAAGTTTGGATTTAAGGGATTTTGGATCTTAGGGGTTTCAA
1 ATTTTAGAAGTTTGGATTTAAGGGATTTTGGATCTTAAGGGTTTCAA
* * * *
3275942 ATTTTAGGATTTTGGATCTTAGGGGATTTTGGATTTTAAGGGTTT
1 ATTTTAGAAGTTTGGAT-TTAAGGGATTTTGGATCTTAAGGGTTT
3275987 TAGAAACCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 15 0.38
48 24 0.62
ACGTcount: A:0.23, C:0.03, G:0.28, T:0.46
Consensus pattern (47 bp):
ATTTTAGAAGTTTGGATTTAAGGGATTTTGGATCTTAAGGGTTTCAA
Found at i:3276453 original size:11 final size:11
Alignment explanation
Indices: 3276439--3276471 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
3276429 ATATATCTAT
3276439 AAATTTAAAAA
1 AAATTTAAAAA
3276450 AAATTT-AAAA
1 AAATTTAAAAA
3276460 AAATTTAAAAA
1 AAATTTAAAAA
3276471 A
1 A
3276472 TTTTTTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATTTAAAAA
Found at i:3276474 original size:9 final size:10
Alignment explanation
Indices: 3276439--3276471 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
3276429 ATATATCTAT
3276439 AAATTTAAAAA
1 AAATTT-AAAA
3276450 AAATTTAAAA
1 AAATTTAAAA
3276460 AAATTTAAAA
1 AAATTTAAAA
3276470 AA
1 AA
3276472 TTTTTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAATTTAAAA
Found at i:3276754 original size:28 final size:28
Alignment explanation
Indices: 3276693--3276746 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
3276683 CACAGATCCT
**
3276693 CTTATGCTTGAAACGACGTCGTTTTGGC
1 CTTATGCTCAAAACGACGTCGTTTTGGC
*
3276721 CCTATGCTCAAAACGACGTCGTTTTG
1 CTTATGCTCAAAACGACGTCGTTTTG
3276747 CTTTTATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.33
Consensus pattern (28 bp):
CTTATGCTCAAAACGACGTCGTTTTGGC
Found at i:3277451 original size:19 final size:20
Alignment explanation
Indices: 3277429--3277466 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3277419 GTTTGTCTCT
*
3277429 CTTTCTTTTCTT-TTTTTTC
1 CTTTCTTTTATTATTTTTTC
*
3277448 CTTTTTTTTATTATTTTTT
1 CTTTCTTTTATTATTTTTT
3277467 TTATTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (20 bp):
CTTTCTTTTATTATTTTTTC
Found at i:3281171 original size:21 final size:22
Alignment explanation
Indices: 3281127--3281171 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3281117 ATAATCACCT
*
3281127 AATCAATATCTAATATTTTTTA
1 AATCAATATCTAATATTATTTA
3281149 AATCAATATC-AA-ATTAATTTA
1 AATCAATATCTAATATT-ATTTA
3281170 AA
1 AA
3281172 ATATTATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 8 0.38
22 10 0.48
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (22 bp):
AATCAATATCTAATATTATTTA
Found at i:3282684 original size:2 final size:2
Alignment explanation
Indices: 3282679--3282707 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3282669 AACTAAGAGT
3282679 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
3282708 TGAAGTTACA
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:3284366 original size:64 final size:64
Alignment explanation
Indices: 3284264--3284388 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 64
3284254 CTCACAAGGA
* * * * *
3284264 TGTGAATCTTGACAGGAAGGTTGATCCGAGACGTCGAAAGGATGAATGTCCGGGTTTCGGACCT
1 TGTGAATCCTGACAGGAAGATTGATCCGAGACGCCGAAAGGATGAATGCCCGGATTTCGGACCT
* *
3284328 TGTGAATCCTGACAGGAAGATTGATCCGGGACGCCGAAAGGGTGAATGCCCGGATTTCGGA
1 TGTGAATCCTGACAGGAAGATTGATCCGAGACGCCGAAAGGATGAATGCCCGGATTTCGGA
3284389 GCCGCGTGAG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (64 bp):
TGTGAATCCTGACAGGAAGATTGATCCGAGACGCCGAAAGGATGAATGCCCGGATTTCGGACCT
Found at i:3290145 original size:95 final size:94
Alignment explanation
Indices: 3290025--3290212 Score: 252
Period size: 95 Copynumber: 2.0 Consensus size: 94
3290015 CAGATATGGT
* * *
3290025 ACATCTTATCTTGATTTAAGGGACTGAATAACTTATTTAC-CTCAAATTTTTCTTACAAAAAAAA
1 ACATCTTATCTTAATTTAAGAGACTGAACAACTTATTTACACT-AAATTTTTCTTA-AAAAAAAA
* * *
3290089 GTAACAATTTTAAGGACATATTAGTTTATCC
64 ATAACAACTTTAAGGACATATTAATTTATCC
* * *
3290120 ACATCTTATCTTAATTTGAGAGACTGAACAATTTATTTACACTGAATTTTTCTTAAAAAAAAAAT
1 ACATCTTATCTTAATTTAAGAGACTGAACAACTTATTTACACTAAATTTTTCTTAAAAAAAAAAT
* *
3290185 ATCAACTTTAAGGACATGTTAATTTATC
66 AACAACTTTAAGGACATATTAATTTATC
3290213 TAATTAAAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 33 0.41
95 46 0.57
96 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (94 bp):
ACATCTTATCTTAATTTAAGAGACTGAACAACTTATTTACACTAAATTTTTCTTAAAAAAAAAAT
AACAACTTTAAGGACATATTAATTTATCC
Found at i:3304262 original size:18 final size:19
Alignment explanation
Indices: 3304231--3304270 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3304221 ACTCAGTCAA
*
3304231 CAAAAAACCAAAAAAAAGG
1 CAAAAAACCAAAAAAAACG
*
3304250 CAAAAAGCC-AAAAAAACG
1 CAAAAAACCAAAAAAAACG
3304268 CAA
1 CAA
3304271 CCATCATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.70, C:0.20, G:0.10, T:0.00
Consensus pattern (19 bp):
CAAAAAACCAAAAAAAACG
Found at i:3316205 original size:20 final size:21
Alignment explanation
Indices: 3316162--3316222 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 21
3316152 CCGATCCGAC
3316162 TTAAAATTAATAAAATATTATATT
1 TTAAAA-T-ATAAAATATTAT-TT
3316186 TTAAAATATAAAATATTATTT
1 TTAAAATATAAAATATTATTT
*
3316207 TTTAAATAT-AAATATT
1 TTAAAATATAAAATATT
3316223 TAAAAATATC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 7 0.19
21 10 0.28
22 12 0.33
23 1 0.03
24 6 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAAATATAAAATATTATTT
Found at i:3317793 original size:25 final size:25
Alignment explanation
Indices: 3317764--3317812 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3317754 GATTTATTTC
* *
3317764 ATTATTCTTTT-TTTTTTTTTGGTTT
1 ATTA-TCTTTTCTTCTTGTTTGGTTT
3317789 ATTATCTTTTCTTCTTGTTTGGTT
1 ATTATCTTTTCTTCTTGTTTGGTT
3317813 GAAGAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.08, C:0.08, G:0.10, T:0.73
Consensus pattern (25 bp):
ATTATCTTTTCTTCTTGTTTGGTTT
Found at i:3323795 original size:6 final size:6
Alignment explanation
Indices: 3323784--3323811 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3323774 CCTCTTTCTG
3323784 CTCCTA CTCCTA CTCCTA CTCCTA CTCC
1 CTCCTA CTCCTA CTCCTA CTCCTA CTCC
3323812 CATCTCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.54, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCCTA
Found at i:3332663 original size:14 final size:14
Alignment explanation
Indices: 3332621--3332664 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3332611 TAATTTTTTT
3332621 ATAAATATATATTA
1 ATAAATATATATTA
* * *
3332635 ATATATATTTTTTA
1 ATAAATATATATTA
*
3332649 ATAAAAATATATTA
1 ATAAATATATATTA
3332663 AT
1 AT
3332665 TTTAATTAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAAATATATATTA
Found at i:3332731 original size:51 final size:51
Alignment explanation
Indices: 3332633--3332731 Score: 112
Period size: 51 Copynumber: 1.9 Consensus size: 51
3332623 AAATATATAT
* * * *
3332633 TAATATATATTTTTTAATAAAAATATATTAATTTTAATTAATCTAAAATAA
1 TAATATATATTATTTAATAAAAATATATTAATATTAAATAATATAAAATAA
* *
3332684 TAATTTATATTATTTAATAAAAA-A-GTTATATATTAAATATATATAAAA
1 TAATATATATTATTTAATAAAAATATATTA-ATATTAAATA-ATATAAAA
3332732 ATATATATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
49 3 0.08
50 9 0.22
51 28 0.70
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (51 bp):
TAATATATATTATTTAATAAAAATATATTAATATTAAATAATATAAAATAA
Found at i:3339707 original size:22 final size:22
Alignment explanation
Indices: 3339682--3339725 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3339672 TTAAATCTTT
3339682 CTTAATTCTA-AGGATACAAATA
1 CTTAATTCTAGA-GATACAAATA
3339704 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
3339726 TAAATATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:3343213 original size:23 final size:23
Alignment explanation
Indices: 3343157--3343238 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
3343147 AAAGGGTTCG
* *
3343157 GCAATGAAGGCCTAAACAGGATTC-
1 GCAATGAAGGCCTAAA-A-AAGTCA
3343181 GACAATGAAGGCCTAAAAAAGTCA
1 G-CAATGAAGGCCTAAAAAAGTCA
* *
3343205 GCAATGAAGGCCTAAACAAGTTA
1 GCAATGAAGGCCTAAAAAAGTCA
*
3343228 ACAATGAAGGC
1 GCAATGAAGGC
3343239 TGAAAATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 33 0.65
24 3 0.06
25 15 0.29
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (23 bp):
GCAATGAAGGCCTAAAAAAGTCA
Found at i:3354565 original size:2 final size:2
Alignment explanation
Indices: 3354558--3354584 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3354548 TGCAATCTCT
3354558 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3354585 CATCGAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3366699 original size:14 final size:14
Alignment explanation
Indices: 3366680--3366712 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3366670 TCTTATCTCT
3366680 TTAATATATT-AAAA
1 TTAATA-ATTAAAAA
3366694 TTAATAATTAAAAA
1 TTAATAATTAAAAA
3366708 TTAAT
1 TTAAT
3366713 TTTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAATAATTAAAAA
Found at i:3369324 original size:2 final size:2
Alignment explanation
Indices: 3369319--3369343 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3369309 TATATATATA
3369319 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
3369344 ATGGTCCTAA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3372672 original size:2 final size:2
Alignment explanation
Indices: 3372667--3372691 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3372657 AAAAAAAAAA
3372667 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
3372692 CTCTGTTTAC
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:3374368 original size:25 final size:25
Alignment explanation
Indices: 3374295--3374368 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 25
3374285 CTGTCTTTTT
* * * *
3374295 TTTTTTTATATCTCAAAATTATGTCTT
1 TTTTTTTATCTTTTAAAATTAT-T-TA
* *
3374322 TTTTTTTA-CATTTAAAA-CATTTA
1 TTTTTTTATCTTTTAAAATTATTTA
3374345 TTTTTTTATCTTTTAAAATTATTT
1 TTTTTTTATCTTTTAAAATTATTT
3374369 TTTATAATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
23 9 0.24
24 9 0.24
25 6 0.16
26 5 0.14
27 8 0.22
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.62
Consensus pattern (25 bp):
TTTTTTTATCTTTTAAAATTATTTA
Found at i:3375047 original size:28 final size:25
Alignment explanation
Indices: 3375008--3375066 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 25
3374998 AATTTTAATT
*
3375008 TAAAAATGTTAATTTTATTTATATTTAA
1 TAAAAATGTTAA-TTT-TTTAT-TTAAA
*
3375036 TAAAAATTTTAATTTTTTATTTAAA
1 TAAAAATGTTAATTTTTTATTTAAA
3375061 TAAAAA
1 TAAAAA
3375067 AAATGATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 10 0.34
26 5 0.17
27 3 0.10
28 11 0.38
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TAAAAATGTTAATTTTTTATTTAAA
Found at i:3377213 original size:21 final size:20
Alignment explanation
Indices: 3377187--3377225 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3377177 TCAAATTTAA
*
3377187 TTTAATTAGTTTAATTAATTT
1 TTTAATTA-TTTAAATAATTT
3377208 TTTAATTATTTAAATAAT
1 TTTAATTATTTAAATAAT
3377226 AAATATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTAATTATTTAAATAATTT
Found at i:3377250 original size:16 final size:16
Alignment explanation
Indices: 3377214--3377251 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
3377204 ATTTTTTAAT
3377214 TATTTAAATAATAAATA
1 TATTTAAAT-ATAAATA
3377231 TATTTAAAT-TAAATTA
1 TATTTAAATATAAA-TA
3377247 TATTT
1 TATTT
3377252 TAAACTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTAAATATAAATA
Found at i:3377469 original size:12 final size:12
Alignment explanation
Indices: 3377449--3377477 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3377439 ATTAAAAATT
3377449 AAATT-TTTTTA
1 AAATTATTTTTA
3377460 AAATTATTTTTA
1 AAATTATTTTTA
3377472 AAATTA
1 AAATTA
3377478 ATTAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AAATTATTTTTA
Found at i:3379443 original size:14 final size:15
Alignment explanation
Indices: 3379419--3379447 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3379409 GTTTATGTTC
3379419 GTTTAAAATTTATTT
1 GTTTAAAATTTATTT
3379434 GTTT-AAATTTATTT
1 GTTTAAAATTTATTT
3379448 AATCATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
GTTTAAAATTTATTT
Found at i:3379547 original size:23 final size:23
Alignment explanation
Indices: 3379499--3379541 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3379489 CATGTTCGTT
*
3379499 AATAAATTTATTTAATATTTACA
1 AATAAATTTATTTAATATTAACA
*
3379522 AATAATTTTATTTAAT-TTAA
1 AATAAATTTATTTAATATTAA
3379542 TTAAATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AATAAATTTATTTAATATTAACA
Found at i:3388667 original size:18 final size:19
Alignment explanation
Indices: 3388644--3388688 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
3388634 GTAGTTCACG
3388644 AATTTAATTAAATTTTT-T
1 AATTTAATTAAATTTTTAT
*
3388662 AATTTAA-TATATTTTTAT
1 AATTTAATTAAATTTTTAT
*
3388680 TATTTAATT
1 AATTTAATT
3388689 CAAAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.35
18 14 0.61
19 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTTAATTAAATTTTTAT
Found at i:3389808 original size:16 final size:17
Alignment explanation
Indices: 3389787--3389820 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3389777 GATTAACTGG
*
3389787 TATTTATAAAA-TATAT
1 TATTTAAAAAATTATAT
3389803 TATTTAAAAAATTATAT
1 TATTTAAAAAATTATAT
3389820 T
1 T
3389821 TGATGCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTAAAAAATTATAT
Found at i:3393567 original size:13 final size:14
Alignment explanation
Indices: 3393549--3393577 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3393539 ACCCCATTCT
3393549 TTGTTGCTT-TTGC
1 TTGTTGCTTGTTGC
3393562 TTGTTGCTTGTTGC
1 TTGTTGCTTGTTGC
3393576 TT
1 TT
3393578 CCTCGAGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.14, G:0.24, T:0.62
Consensus pattern (14 bp):
TTGTTGCTTGTTGC
Found at i:3393570 original size:7 final size:7
Alignment explanation
Indices: 3393549--3393577 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3393539 ACCCCATTCT
3393549 TTGTTGC
1 TTGTTGC
3393556 TT-TTGC
1 TTGTTGC
3393562 TTGTTGC
1 TTGTTGC
3393569 TTGTTGC
1 TTGTTGC
3393576 TT
1 TT
3393578 CCTCGAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.14, G:0.24, T:0.62
Consensus pattern (7 bp):
TTGTTGC
Found at i:3393824 original size:51 final size:52
Alignment explanation
Indices: 3393714--3393827 Score: 153
Period size: 51 Copynumber: 2.2 Consensus size: 52
3393704 CACCTTATAA
*
3393714 ACTGGACACCCCTAAAAATTGAAAAATAAGAAAATTTGAAGGGAAATTTTCT
1 ACTGGACACCCCTAAAAATTGAAAAATAAGAAAATTTGAAGGGAAATTTTCC
* * *
3393766 A-TCGGACACCCC-CAAAATTGAAAAATAAGAAATTTTG-GGGGAAAATTTTCC
1 ACT-GGACACCCCTAAAAATTGAAAAATAAGAAAATTTGAAGGG-AAATTTTCC
3393817 ACTGGACACCC
1 ACTGGACACCC
3393828 AAAATTTTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
50 3 0.05
51 41 0.75
52 11 0.20
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (52 bp):
ACTGGACACCCCTAAAAATTGAAAAATAAGAAAATTTGAAGGGAAATTTTCC
Found at i:3398992 original size:22 final size:22
Alignment explanation
Indices: 3398950--3398992 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3398940 TTCTTTTTAC
*
3398950 AAAAAAATTATAGTCTAAAAAA
1 AAAAAAATCATAGTCTAAAAAA
*
3398972 AAAAAAATACATA-TCTTAAAA
1 AAAAAAAT-CATAGTCTAAAAA
3398993 TTTGAACACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.23
Consensus pattern (22 bp):
AAAAAAATCATAGTCTAAAAAA
Found at i:3399982 original size:22 final size:22
Alignment explanation
Indices: 3399948--3399992 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3399938 TTTTAATATC
* *
3399948 TAAAATTTTTATTTTTTGTATTT
1 TAAAATTTATATTTTATG-ATTT
3399971 TAAAA-TTATATTTTATGATTT
1 TAAAATTTATATTTTATGATTT
3399992 T
1 T
3399993 TTTATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 10 0.50
23 5 0.25
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TAAAATTTATATTTTATGATTT
Found at i:3401655 original size:19 final size:19
Alignment explanation
Indices: 3401628--3401666 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3401618 TTGAGGGTAG
* *
3401628 ATTTTGTAATTAATCTAAA
1 ATTTGGTAATAAATCTAAA
*
3401647 ATTTGGTAATAAATGTAAA
1 ATTTGGTAATAAATCTAAA
3401666 A
1 A
3401667 GAAGAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (19 bp):
ATTTGGTAATAAATCTAAA
Found at i:3401855 original size:4 final size:4
Alignment explanation
Indices: 3401846--3401876 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3401836 AAAACCCAAT
3401846 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
3401877 TATATATATA
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:3405453 original size:2 final size:2
Alignment explanation
Indices: 3405446--3405478 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3405436 CACCTGAATC
3405446 TA TA 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 TA TA T
3405479 GCATGATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3415458 original size:26 final size:29
Alignment explanation
Indices: 3415429--3415496 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
3415419 AAAATATATT
3415429 TTTTTATTTAATTT-TT-TA-TATATAAA
1 TTTTTATTTAATTTATTATATTATATAAA
*
3415455 TTTTTATTTATTTTATTGATATTATATAAA
1 TTTTTATTTAATTTATT-ATATTATATAAA
*
3415485 ATTTTATCTTAA
1 TTTTTAT-TTAA
3415497 CTGATAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 13 0.38
27 2 0.06
29 2 0.06
30 14 0.41
31 3 0.09
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (29 bp):
TTTTTATTTAATTTATTATATTATATAAA
Found at i:3416839 original size:69 final size:70
Alignment explanation
Indices: 3416744--3416876 Score: 223
Period size: 69 Copynumber: 1.9 Consensus size: 70
3416734 TTATGTTAAT
* *
3416744 GTTATTAGATCTGATTATTTGTTTGTTTGATCTGTTTTGCAACAT-GGTTTTTAATGTTGGAAAC
1 GTTATTACATCTGATTATTTGTTTGTTTGATCTGTTTTGCAACATAGATTTTTAATGTTGGAAAC
3416808 AACAC
66 AACAC
* *
3416813 GTTATTACATCTGATTGTTTGTTTGTTTGATCTGTTTTGCAGCATAGATTTTTAATGTTGGAAA
1 GTTATTACATCTGATTATTTGTTTGTTTGATCTGTTTTGCAACATAGATTTTTAATGTTGGAAA
3416877 TTATGTGTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
69 42 0.71
70 17 0.29
ACGTcount: A:0.23, C:0.09, G:0.20, T:0.48
Consensus pattern (70 bp):
GTTATTACATCTGATTATTTGTTTGTTTGATCTGTTTTGCAACATAGATTTTTAATGTTGGAAAC
AACAC
Found at i:3417063 original size:23 final size:23
Alignment explanation
Indices: 3417003--3417065 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 23
3416993 TTTTTATTGG
* *
3417003 TTTATATGCAAGAAAGGTCTAATC
1 TTTAT-TGCAAGAAAGTTCTTATC
3417027 TTTATT----GAAAGTTCTTATC
1 TTTATTGCAAGAAAGTTCTTATC
3417046 TTTATTGCAAGAAAGTTCTT
1 TTTATTGCAAGAAAGTTCTT
3417066 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
19 17 0.52
23 11 0.33
24 5 0.15
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (23 bp):
TTTATTGCAAGAAAGTTCTTATC
Found at i:3425284 original size:21 final size:22
Alignment explanation
Indices: 3425258--3425304 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
3425248 CCGAGAGAGT
3425258 TAGAGAATGAAGTGAAGTG-AA
1 TAGAGAATGAAGTGAAGTGAAA
3425279 TAGAGAATGAAGTGAAGTGAAA
1 TAGAGAATGAAGTGAAGTGAAA
3425301 TAGA
1 TAGA
3425305 ACTCCATCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.32, T:0.19
Consensus pattern (22 bp):
TAGAGAATGAAGTGAAGTGAAA
Found at i:3427734 original size:24 final size:24
Alignment explanation
Indices: 3427685--3427732 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
3427675 ATATTAACAG
* *
3427685 TAAATATATTATTTTATTAATAAA
1 TAAATATATTAATTCATTAATAAA
3427709 TAAATATATTTAATTCATTAATAA
1 TAAATATA-TTAATTCATTAATAA
3427733 TATATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAATATATTAATTCATTAATAAA
Found at i:3433082 original size:23 final size:23
Alignment explanation
Indices: 3433039--3433093 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
3433029 ACAATGATTT
*
3433039 TATATCAAATTTTATTTAAATAA
1 TATATAAAATTTTATTTAAATAA
3433062 -AT-TAAAATTTTATATTAAAATAA
1 TATATAAAATTTTAT-TT-AAATAA
3433085 TATATAAAA
1 TATATAAAA
3433094 ATTAAAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 10 0.37
22 4 0.15
23 6 0.22
24 2 0.07
25 5 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TATATAAAATTTTATTTAAATAA
Found at i:3433184 original size:22 final size:22
Alignment explanation
Indices: 3433128--3433184 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
3433118 AATCAATAAA
* *
3433128 ATTCGATTCG-ATTCAGTTTAG
1 ATTCGAATCGAATTCAGTTCAG
3433149 A-TCGAAT-GAAAATTCAGTTCAG
1 ATTCGAATCG--AATTCAGTTCAG
3433171 ATTCGAATCGAATT
1 ATTCGAATCGAATT
3433185 TTAAATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
19 1 0.03
20 5 0.17
21 1 0.03
22 15 0.52
23 6 0.21
24 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (22 bp):
ATTCGAATCGAATTCAGTTCAG
Found at i:3434377 original size:26 final size:25
Alignment explanation
Indices: 3434327--3434381 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 25
3434317 TTAATATAAC
3434327 TATTAAAATATTAAAAATTATTTAT
1 TATTAAAATATTAAAAATTATTTAT
**
3434352 TATTAAAATATATTGAAATTATTTAT
1 TATTAAAATAT-TAAAAATTATTTAT
3434378 TATT
1 TATT
3434382 TAATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TATTAAAATATTAAAAATTATTTAT
Found at i:3434502 original size:23 final size:23
Alignment explanation
Indices: 3434476--3434734 Score: 148
Period size: 23 Copynumber: 11.0 Consensus size: 23
3434466 ATTATTCTTT
3434476 ATATTATTTATTAATATATTATA
1 ATATTATTTATTAATATATTATA
*
3434499 ATATTAATTATTAATAATATTAATA
1 ATATTATTTATTAAT-ATATT-ATA
3434524 ATA-TATTATATTAATA-A-TATA
1 ATATTATT-TATTAATATATTATA
* *
3434545 CTATTTATTCA-T-ATATTATTATA
1 ATA-TTATTTATTAATA-TATTATA
3434568 ATA-T-TTTATTAAT-TAATTTGATA
1 ATATTATTTATTAATAT-A-TT-ATA
*
3434591 ATATTTATTATATTATTAT-TTATTA
1 ATA-TTATT-TATTAATATATTA-TA
*
3434616 ATATAATATTATTTTAAATATATTATA
1 ATAT--TATT-TATT-AATATATTATA
* *
3434643 ATATTATTTCTTAATGTTATTTATTA
1 ATATTATTTATTAAT-ATA-TTA-TA
* *
3434669 A-ACTATTATATTAATAGTA-TATT
1 ATATTATT-TATTAATA-TATTATA
*
3434692 AT-TTA-TTAATAATATATTATA
1 ATATTATTTATTAATATATTATA
*
3434713 ATATTATTTATTAATATGTTAT
1 ATATTATTTATTAATATATTAT
3434735 TTATTAATCT
Statistics
Matches: 184, Mismatches: 20, Indels: 64
0.69 0.07 0.24
Matches are distributed among these distances:
20 9 0.05
21 21 0.11
22 11 0.06
23 51 0.28
24 18 0.10
25 33 0.18
26 21 0.11
27 16 0.09
28 4 0.02
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
ATATTATTTATTAATATATTATA
Found at i:3434559 original size:66 final size:68
Alignment explanation
Indices: 3434475--3434605 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 68
3434465 TATTATTCTT
* *
3434475 TATATTATTTATTAATATATTATAATATTA-ATTATTAA-TAATATTAATAATA-TATTATATTA
1 TATACTATTTATTAATATATTATAATAATATATTATTAATTAAT-TTAATAATATTATTATATTA
3434537 ATAA
65 ATAA
* * * *
3434541 TATACTATTTATTCATATATTATTATAATATTTTATTAATTAATTTGATAATATTTATTATATTA
1 TATACTATTTATTAATATATTATAATAATATATTATTAATTAATTTAATAATA-TTATTATATTA
3434606 TTATTTATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
66 26 0.47
67 15 0.27
68 4 0.07
69 10 0.18
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.54
Consensus pattern (68 bp):
TATACTATTTATTAATATATTATAATAATATATTATTAATTAATTTAATAATATTATTATATTAA
TAA
Found at i:3434625 original size:18 final size:18
Alignment explanation
Indices: 3434476--3434844 Score: 162
Period size: 18 Copynumber: 20.0 Consensus size: 18
3434466 ATTATTCTTT
3434476 ATATTATTTATTAATATA
1 ATATTATTTATTAATATA
* *
3434494 TTA-TA-ATATTAAT-TA
1 ATATTATTTATTAATATA
* * *
3434509 TTAATA-ATATTAATA-A
1 ATATTATTTATTAATATA
*
3434525 TATATTATATTAATAATATA
1 -ATATTAT-TTATTAATATA
* *
3434545 CTATTTATTCATATATTATTATA
1 --A--TATT-ATTTATTAATATA
* * *
3434568 ATATTTTATTAATTAATTTG
1 ATA--TTATTTATTAATATA
*
3434588 ATAATATTTATT-ATAT-
1 ATATTATTTATTAATATA
3434604 -TATTATTTATTAATATA
1 ATATTATTTATTAATATA
*
3434621 ATATTATTT-TAAATATA
1 ATATTATTTATTAATATA
* * **
3434638 TTATAATATTATTTCT-TA
1 ATATTAT-TTATTAATATA
*
3434656 ATGTTATTTATT-A-A-A
1 ATATTATTTATTAATATA
*
3434671 CTATTA--TATTAATAGT-
1 ATATTATTTATTAATA-TA
3434687 ATATTATTTATTAATA-A
1 ATATTATTTATTAATATA
* *
3434704 TATATTATAATATTATTTATTA
1 -ATATTAT-TTATTA-ATA-TA
*
3434726 ATATGTTATTTATTAATCTA
1 ATA--TTATTTATTAATATA
3434746 ATATTATTTCTTTATTAATATA
1 ATATTA----TTTATTAATATA
3434768 ATATTATTTATCAATATACTATA
1 ATATTATTTAT---TA-A-TATA
3434791 ATATTATTTATTAATAGT-
1 ATATTATTTATTAATA-TA
*
3434809 ATATTATTTATTCATATA
1 ATATTATTTATTAATATA
3434827 ATATTATTTATTAATATA
1 ATATTATTTATTAATATA
3434845 TTGTAATCAA
Statistics
Matches: 269, Mismatches: 39, Indels: 86
0.68 0.10 0.22
Matches are distributed among these distances:
13 4 0.01
14 1 0.00
15 21 0.08
16 27 0.10
17 27 0.10
18 82 0.30
19 18 0.07
20 21 0.08
21 11 0.04
22 24 0.09
23 31 0.12
24 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (18 bp):
ATATTATTTATTAATATA
Found at i:3434662 original size:13 final size:13
Alignment explanation
Indices: 3434476--3434874 Score: 196
Period size: 13 Copynumber: 30.6 Consensus size: 13
3434466 ATTATTCTTT
3434476 ATATTATTTATTA
1 ATATTATTTATTA
3434489 ATA-TA-TTA-TA
1 ATATTATTTATTA
*
3434499 ATATTAATTATTA
1 ATATTATTTATTA
* * *
3434512 ATAATATTAATAA
1 ATATTATTTATTA
*
3434525 TATATTATATTAATA
1 -ATATTAT-TTATTA
3434540 ATATACTATTTATTCA
1 ATAT--TATTTATT-A
3434556 TATATTA-TTA-TA
1 -ATATTATTTATTA
3434568 ATA-T-TTTATTA
1 ATATTATTTATTA
*
3434579 AT-TAATTTGA-TA
1 ATATTATTT-ATTA
3434591 ATATTTATTATATTA
1 ATA-TTATT-TATTA
* *
3434606 TTATTTATTAATATA
1 ATA-TTATTTAT-TA
*
3434621 ATATTATTT-TAA
1 ATATTATTTATTA
3434633 ATA-TA-TTA-TA
1 ATATTATTTATTA
*
3434643 ATATTATTTCTTA
1 ATATTATTTATTA
*
3434656 ATGTTATTTATTAA
1 ATATTATTTATT-A
*
3434670 ACTATTATATTAATA
1 A-TATTAT-TTATTA
3434685 GTATATTATTTATTA
1 --ATATTATTTATTA
*
3434700 ATAATATATTA-TA
1 ATATTAT-TTATTA
3434713 ATATTATTTATTA
1 ATATTATTTATTA
3434726 ATATGTTATTTATTA
1 ATA--TTATTTATTA
* * *
3434741 ATCTAATATTATTT
1 ATATTAT-TTATTA
* *
3434755 CT-TTATTAATATA
1 ATATTATTTAT-TA
*
3434768 ATATTATTTATCA
1 ATATTATTTATTA
*
3434781 ATA-TA-CTA-TA
1 ATATTATTTATTA
3434791 ATATTATTTATTA
1 ATATTATTTATTA
*
3434804 ATAGTA--TATT-
1 ATATTATTTATTA
*
3434814 AT-TTATTCATATA
1 ATATTATTTAT-TA
3434827 ATATTATTTATTA
1 ATATTATTTATTA
*
3434840 ATA-TATTGTAATCA
1 ATATTATT-T-ATTA
*
3434854 ATATTATTTATAA
1 ATATTATTTATTA
*
3434867 ATAATATT
1 ATATTATT
3434875 ATGCTTAAAA
Statistics
Matches: 295, Mismatches: 45, Indels: 92
0.68 0.10 0.21
Matches are distributed among these distances:
9 2 0.01
10 21 0.07
11 26 0.09
12 34 0.12
13 85 0.29
14 57 0.19
15 51 0.17
16 14 0.05
17 5 0.02
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (13 bp):
ATATTATTTATTA
Found at i:3434697 original size:31 final size:27
Alignment explanation
Indices: 3434487--3434726 Score: 123
Period size: 25 Copynumber: 9.0 Consensus size: 27
3434477 TATTATTTAT
*
3434487 TAATATATTATAATATTAATTATT-AA
1 TAATATATTATAATATTATTTATTAAA
*
3434513 TAATAT-TAATAATA-TATTATATT-AA
1 TAATATATTATAATATTATT-TATTAAA
* * * *
3434538 TAATATACTAT-TTATTCATATATTATTA
1 TAATATATTATAATATT-ATTTATTA-AA
* *
3434566 TAATATTTTATTAAT-TAATTTGA-T-AA
1 TAATATATTA-TAATATTATTT-ATTAAA
* *
3434592 T-ATTTATTATATTATTATTTATTAATA
1 TAATATATTATAATATTATTTATTAA-A
*
3434619 TAATATTATTTTAA-A-TA--TATTATAA
1 TAATA-TATTATAATATTATTTATTA-AA
* * *
3434644 TATTAT-TTCTTAATGTTATTTATTAAA
1 TAATATATT-ATAATATTATTTATTAAA
*
3434671 CTATTATATTAATAGTATATTATTTATT-AA
1 -TAATATATT-ATA--ATATTATTTATTAAA
3434701 TAATATATTATAATATTATTTATTAA
1 TAATATATTATAATATTATTTATTAA
3434727 TATGTTATTT
Statistics
Matches: 162, Mismatches: 26, Indels: 51
0.68 0.11 0.21
Matches are distributed among these distances:
23 2 0.01
24 12 0.07
25 43 0.27
26 31 0.19
27 9 0.06
28 30 0.19
29 21 0.13
30 3 0.02
31 11 0.07
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (27 bp):
TAATATATTATAATATTATTTATTAAA
Found at i:3434759 original size:22 final size:22
Alignment explanation
Indices: 3434734--3434799 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
3434724 TAATATGTTA
*
3434734 TTTATTAATCTAATATTATTTC
1 TTTATTAATATAATATTATTTC
*
3434756 TTTATTAATATAATATTATTTA
1 TTTATTAATATAATATTATTTC
** *
3434778 TCAATATACTATAATATTATTT
1 TTTAT-TAATATAATATTATTT
3434800 ATTAATAGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
22 23 0.61
23 15 0.39
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTATTAATATAATATTATTTC
Found at i:3434761 original size:41 final size:40
Alignment explanation
Indices: 3434592--3434838 Score: 141
Period size: 41 Copynumber: 6.0 Consensus size: 40
3434582 AATTTGATAA
**
3434592 TATTTATT-ATATTATTATTTATTAATATAATATTATTTTAAA
1 TATTTATTAATA-T-TTATTTATTAATATAATATTA-TTTATT
* * * *
3434634 TATATTA-TAATA-TTATTTCTTAATGTTAT-TTATTAAACTAT
1 TAT-TTATTAATATTTATTTATTAATATAATATTATT-TA-T-T
* * *
3434675 TATATTAATAGTATATTATTTATTAATA-ATATATTA-TAATAT
1 TAT-TTATTAATAT-TTATTTATTAATATA-ATATTATTTAT-T
* *
3434717 TATTTATTAATATGTTATTTATTAATCTAATATTATTTCTT
1 TATTTATTAATAT-TTATTTATTAATATAATATTATTTATT
* * * *
3434758 TATTAATATAATA-TTATTTATCAATATACTATAATATTATT
1 TATTTAT-TAATATTTATTTATTAATATAATATTAT-TTATT
* * *
3434799 TA-TTAATAGTATATTATTTATTCATATAATATTATTTATT
1 TATTTATTAATAT-TTATTTATTAATATAATATTATTTATT
3434839 AATATATTGT
Statistics
Matches: 160, Mismatches: 29, Indels: 34
0.72 0.13 0.15
Matches are distributed among these distances:
38 2 0.01
39 8 0.05
40 39 0.24
41 64 0.40
42 22 0.14
43 8 0.05
44 14 0.09
45 3 0.02
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (40 bp):
TATTTATTAATATTTATTTATTAATATAATATTATTTATT
Found at i:3434762 original size:70 final size:69
Alignment explanation
Indices: 3434632--3434805 Score: 179
Period size: 70 Copynumber: 2.4 Consensus size: 69
3434622 TATTATTTTA
* *
3434632 AATATATTATAATATTATTTCTTAATGTTATTTATTAAACTATTATATTAATAGTATATTATTTA
1 AATATATTATAATATTATTTATTAATGTTATTTATTAAACTA-TATATTAATACTATATTATTTA
3434697 TTAAT
65 TTAAT
* * *
3434702 AATATATTATAATATTATTTATTAATATGTTATTTATTAATCTA-ATATTATTTCTTTATTAATA
1 AATATATTATAATATTATTTATT-A-ATGTTATTTATTAAACTATATATTAATAC--TA-T-AT-
*
3434766 TAATATTATTTAT
59 T-AT-TTATTAAT
*
3434779 CAATATACTATAATATTATTTATTAAT
1 -AATATATTATAATATTATTTATTAAT
3434806 AGTATATTAT
Statistics
Matches: 87, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
70 29 0.33
71 1 0.01
72 19 0.22
73 1 0.01
74 2 0.02
75 1 0.01
76 4 0.05
77 8 0.09
78 22 0.25
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (69 bp):
AATATATTATAATATTATTTATTAATGTTATTTATTAAACTATATATTAATACTATATTATTTAT
TAAT
Found at i:3434798 original size:59 final size:56
Alignment explanation
Indices: 3434709--3434844 Score: 168
Period size: 59 Copynumber: 2.4 Consensus size: 56
3434699 AATAATATAT
* * *
3434709 TATAATATTATTTATTAATAT-GTTATTTATTAATCTAATATTAT-TTCTTTATTAA
1 TATAATATTATTTATTAATATACTTATTTATTAAT-TAATAGTATATTATTTATTAA
* * *
3434764 TATAATATTATTTATCAATATACTATAATATTATTTATTAATAGTATATTATTTATTCA
1 TATAATATTATTTATTAATATACT-T-AT-TTATTAATTAATAGTATATTATTTATTAA
3434823 TATAATATTATTTATTAATATA
1 TATAATATTATTTATTAATATA
3434845 TTGTAATCAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
55 20 0.29
56 1 0.01
57 1 0.01
58 10 0.14
59 37 0.54
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (56 bp):
TATAATATTATTTATTAATATACTTATTTATTAATTAATAGTATATTATTTATTAA
Found at i:3438456 original size:16 final size:18
Alignment explanation
Indices: 3438427--3438464 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3438417 TTTCTATAAA
*
3438427 TTTAATTTTTATATT-AT
1 TTTAATTTTAATATTAAT
3438444 TTTAA-TTTAATATTAAT
1 TTTAATTTTAATATTAAT
3438461 TTTA
1 TTTA
3438465 TTGACGTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTAATTTTAATATTAAT
Found at i:3438465 original size:22 final size:22
Alignment explanation
Indices: 3438425--3438466 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3438415 AATTTCTATA
* *
3438425 AATTTAATTTTTATATTATTTT
1 AATTTAATATTAATATTATTTT
*
3438447 AATTTAATATTAATTTTATT
1 AATTTAATATTAATATTATT
3438467 GACGTGATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
AATTTAATATTAATATTATTTT
Found at i:3440583 original size:31 final size:31
Alignment explanation
Indices: 3440548--3440633 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
3440538 TATAATGTCT
**
3440548 ATAAATTAGATGATATTATTTTATTAATGAA
1 ATAAATTAGATGATAAAATTTTATTAATGAA
3440579 ATAAATTAGATGATAAAATTTTATTAATGAA
1 ATAAATTAGATGATAAAATTTTATTAATGAA
* **
3440610 A-AAATTTAAATTTTAAAATTTTAT
1 ATAAA-TTAGATGATAAAATTTTAT
3440634 ATATTTATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
30 3 0.06
31 46 0.94
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (31 bp):
ATAAATTAGATGATAAAATTTTATTAATGAA
Found at i:3440608 original size:17 final size:18
Alignment explanation
Indices: 3440583--3440616 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3440573 AATGAAATAA
*
3440583 ATTAGATGATAAAATTTT
1 ATTAGATGAAAAAATTTT
3440601 ATTA-ATGAAAAAATTT
1 ATTAGATGAAAAAATTT
3440617 AAATTTTAAA
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:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (18 bp):
ATTAGATGAAAAAATTTT
Found at i:3449051 original size:2 final size:2
Alignment explanation
Indices: 3449044--3449069 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3449034 ATATGGTGTG
3449044 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
3449070 CTAAACCCAA
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:3449641 original size:16 final size:16
Alignment explanation
Indices: 3449620--3449651 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3449610 TAACTTTCTC
3449620 AAAACAAAATCCATAG
1 AAAACAAAATCCATAG
3449636 AAAACAAAATCCATAG
1 AAAACAAAATCCATAG
3449652 TCATTCCAAA
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:0.62, C:0.19, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAACAAAATCCATAG
Found at i:3451329 original size:16 final size:16
Alignment explanation
Indices: 3451305--3451335 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3451295 ACTTTCTAAA
3451305 AAAAAAAATTCCATAG
1 AAAAAAAATTCCATAG
*
3451321 AAAACAAATTCCATA
1 AAAAAAAATTCCATA
3451336 ATATTCAAAA
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:0.61, C:0.16, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAAAAATTCCATAG
Found at i:3453574 original size:10 final size:10
Alignment explanation
Indices: 3453559--3453589 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3453549 AGATGTTGAT
3453559 TCATCATCTA
1 TCATCATCTA
*
3453569 TCATCATCTT
1 TCATCATCTA
3453579 TCATCATCTA
1 TCATCATCTA
3453589 T
1 T
3453590 GAGAATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (10 bp):
TCATCATCTA
Found at i:3467835 original size:17 final size:17
Alignment explanation
Indices: 3467813--3467875 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
3467803 TTGCAACTTG
3467813 CAAACCATGTTTTGTTA
1 CAAACCATGTTTTGTTA
*
3467830 CAAACCATGTGTGATT-TTT
1 CAAACCATGT-T--TTGTTA
* * *
3467849 GAAACCATGTTCTGTTG
1 CAAACCATGTTTTGTTA
3467866 CAAACCATGT
1 CAAACCATGT
3467876 GCTTGCAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 2 0.05
19 11 0.30
20 2 0.05
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (17 bp):
CAAACCATGTTTTGTTA
Found at i:3468518 original size:19 final size:18
Alignment explanation
Indices: 3468494--3468542 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
3468484 ATATGATATA
3468494 TATTTTGTAATTTTTAATT
1 TATTTTGTAATTTTTAA-T
3468513 TATTTTGTAATTTTTAAT
1 TATTTTGTAATTTTTAAT
3468531 TATTTT-TAATTT
1 TATTTTGTAATTT
3468543 AATAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.20
18 7 0.23
19 17 0.57
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (18 bp):
TATTTTGTAATTTTTAAT
Found at i:3469585 original size:20 final size:19
Alignment explanation
Indices: 3469550--3469587 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
3469540 TTTTTGTAAA
3469550 ATTAAATAAAATTATTTTT
1 ATTAAATAAAATTATTTTT
3469569 ATTAATATAATAA-TATTTT
1 ATTAA-ATAA-AATTATTTT
3469588 GAATTAGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 10 0.59
21 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTAAATAAAATTATTTTT
Found at i:3474038 original size:14 final size:14
Alignment explanation
Indices: 3474019--3474049 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3474009 TATTTTTAAT
3474019 TTTAATAATCATAA
1 TTTAATAATCATAA
*
3474033 TTTAATAATGATAA
1 TTTAATAATCATAA
3474047 TTT
1 TTT
3474050 CTTACATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (14 bp):
TTTAATAATCATAA
Found at i:3474429 original size:13 final size:14
Alignment explanation
Indices: 3474398--3474432 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
3474388 AAGCAAAAAG
3474398 ATAATATAATTTAAT
1 ATAAT-TAATTTAAT
3474413 ATAATTAATTT-AT
1 ATAATTAATTTAAT
3474426 ATAATTA
1 ATAATTA
3474433 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 6 0.30
15 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATAATTAATTTAAT
Found at i:3474977 original size:31 final size:31
Alignment explanation
Indices: 3474897--3474977 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
3474887 TATTTACATA
* * *
3474897 AAATTTAAAATTTTATTTATGTACTCGTATG
1 AAATTTAAAATTTTATTTTTGTAATCGTACG
3474928 AAATTTAAAATTTTATTTTTGTAATC-TCACG
1 AAATTTAAAATTTTATTTTTGTAATCGT-ACG
*
3474959 AAATTTAAAATTTAATTTT
1 AAATTTAAAATTTTATTTT
3474978 ATTATTATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 1 0.02
31 44 0.98
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49
Consensus pattern (31 bp):
AAATTTAAAATTTTATTTTTGTAATCGTACG
Found at i:3475165 original size:15 final size:15
Alignment explanation
Indices: 3475106--3475169 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 15
3475096 TAATTATTAA
*
3475106 TAATATTATTATTCATT
1 TAATATTA--ATTAATT
*
3475123 T-ATATTAATCAATT
1 TAATATTAATTAATT
3475137 ATAATATTAA-TAATT
1 -TAATATTAATTAATT
*
3475152 TAATTTTAATTAATT
1 TAATATTAATTAATT
3475167 TAA
1 TAA
3475170 ATATATCATA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 13 0.32
15 13 0.32
16 13 0.32
17 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATATTAATTAATT
Found at i:3476053 original size:20 final size:20
Alignment explanation
Indices: 3476007--3476053 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3475997 TTTAAAATAG
*
3476007 AATATTTTTAAAAAAACTAA
1 AATATTTCTAAAAAAACTAA
* **
3476027 AAAATTTCTAAAAAATTTAA
1 AATATTTCTAAAAAAACTAA
3476047 AATATTT
1 AATATTT
3476054 TATATATTAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATTTCTAAAAAAACTAA
Found at i:3476496 original size:21 final size:21
Alignment explanation
Indices: 3476458--3476510 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3476448 GTGAAAATTG
3476458 ATTTTTAAAAAATATATA-TAT
1 ATTTTTAAAAAATATATACT-T
*
3476479 ATTTTTAAAATACT-TATACTT
1 ATTTTTAAAA-AATATATACTT
3476500 -TTTTTAAAAAA
1 ATTTTTAAAAAA
3476511 ATAGAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 1 0.04
20 9 0.32
21 15 0.54
22 3 0.11
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTTTAAAAAATATATACTT
Found at i:3478020 original size:12 final size:12
Alignment explanation
Indices: 3478003--3478027 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3477993 CCTGCAAAAG
3478003 ATAGGGGAACCA
1 ATAGGGGAACCA
3478015 ATAGGGGAACCA
1 ATAGGGGAACCA
3478027 A
1 A
3478028 GTATCAAGAA
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:0.16, G:0.32, T:0.08
Consensus pattern (12 bp):
ATAGGGGAACCA
Found at i:3484573 original size:14 final size:14
Alignment explanation
Indices: 3484556--3484582 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3484546 TGAAAATTAA
3484556 TTTTTAAAAAATAT
1 TTTTTAAAAAATAT
3484570 TTTTTAAAAAATA
1 TTTTTAAAAAATA
3484583 CTTCTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTTTAAAAAATAT
Found at i:3484919 original size:15 final size:15
Alignment explanation
Indices: 3484901--3484937 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3484891 CTATTCTCAA
3484901 AATATTATATTTATT
1 AATATTATATTTATT
*
3484916 AATATAATATTTATT
1 AATATTATATTTATT
*
3484931 ATTATTA
1 AATATTA
3484938 AAATATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATATTATATTTATT
Found at i:3484934 original size:18 final size:20
Alignment explanation
Indices: 3484899--3484945 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
3484889 TACTATTCTC
3484899 AAAATATTATATTTATTAAT
1 AAAATATTATATTTATTAAT
* *
3484919 ATAATATT-TA-TTATTATT
1 AAAATATTATATTTATTAAT
3484937 AAAATATTA
1 AAAATATTA
3484946 AAATATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 14 0.61
19 2 0.09
20 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAATATTATATTTATTAAT
Found at i:3484963 original size:17 final size:17
Alignment explanation
Indices: 3484941--3484973 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3484931 ATTATTAAAA
*
3484941 TATTAAAATATTTATAC
1 TATTAAAATAGTTATAC
3484958 TATTAAAATAGTTATA
1 TATTAAAATAGTTATA
3484974 TTTTATATTG
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:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
TATTAAAATAGTTATAC
Found at i:3485459 original size:25 final size:25
Alignment explanation
Indices: 3485431--3485483 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
3485421 CTTACTTGAG
*
3485431 TAAAATTACAAAAATATTTTTAA-AT
1 TAAAA-TACAAAAATATATTTAATAT
**
3485456 TAAAATATTAAAATATATTTAATAT
1 TAAAATACAAAAATATATTTAATAT
3485481 TAA
1 TAA
3485484 TATTTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
TAAAATACAAAAATATATTTAATAT
Found at i:3489858 original size:21 final size:17
Alignment explanation
Indices: 3489832--3489884 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 17
3489822 TATATATTAG
3489832 TTATATATTATATCTAACT
1 TTATATATTATAT-T-ACT
3489851 AATTATATATTTAATATTACT
1 --TTATATA-TT-ATATTACT
3489872 TTATATATTATAT
1 TTATATATTATAT
3489885 AATATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.13
18 2 0.07
19 7 0.23
21 10 0.33
22 3 0.10
23 4 0.13
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATATATTATATTACT
Found at i:3489970 original size:47 final size:47
Alignment explanation
Indices: 3489899--3490024 Score: 216
Period size: 47 Copynumber: 2.7 Consensus size: 47
3489889 TATATTATTA
* *
3489899 TACCTGAATACCTAATGTCCTATTTTCTCATACTAAATACATAATGT
1 TACCTAAATACCTAATGTCCTATTTTCTCATACTAAATACATAATGC
* *
3489946 TACCTAAATACCTAATGTCATATTTTCTCATACTAAATACCTAATGC
1 TACCTAAATACCTAATGTCCTATTTTCTCATACTAAATACATAATGC
3489993 TACCTAAATACCTAATGTCCTATTTTCTCATA
1 TACCTAAATACCTAATGTCCTATTTTCTCATA
3490025 TTCTTGAGAA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 74 1.00
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (47 bp):
TACCTAAATACCTAATGTCCTATTTTCTCATACTAAATACATAATGC
Found at i:3491891 original size:20 final size:20
Alignment explanation
Indices: 3491868--3491921 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
3491858 TTTTGCTATG
3491868 ATTTCATTTTTTTTATTTTA
1 ATTTCATTTTTTTTATTTTA
* * *
3491888 ATTTAATTCTTTTTTCTTTTG
1 ATTTCATT-TTTTTTATTTTA
*
3491909 CTTTCATGTTTTT
1 ATTTCAT-TTTTT
3491922 CACCAAAGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 7 0.26
21 19 0.70
22 1 0.04
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (20 bp):
ATTTCATTTTTTTTATTTTA
Found at i:3495102 original size:17 final size:17
Alignment explanation
Indices: 3495080--3495113 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3495070 CCTTCTTTCA
3495080 AATCGTTTGTCATTATT
1 AATCGTTTGTCATTATT
3495097 AATCGTTTGTCATTATT
1 AATCGTTTGTCATTATT
3495114 CAAATACGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (17 bp):
AATCGTTTGTCATTATT
Found at i:3495440 original size:8 final size:7
Alignment explanation
Indices: 3495427--3495568 Score: 66
Period size: 8 Copynumber: 19.3 Consensus size: 7
3495417 TGTTTTTTTA
3495427 ATTATTGT
1 ATTATT-T
3495435 ATTATTT
1 ATTATTT
3495442 A-T-TTT
1 ATTATTT
3495447 ATTATTTT
1 ATTA-TTT
3495455 ATTAGTTT
1 ATTA-TTT
3495463 -TTAATTTT
1 ATT-A-TTT
3495471 AATTATTT
1 -ATTATTT
*
3495479 -TAATTGT
1 ATTATT-T
3495486 -TTATTT
1 ATTATTT
3495492 -TTAGTTT
1 ATTA-TTT
3495499 ATTAGTTT
1 ATTA-TTT
3495507 A-T-TTT
1 ATTATTT
3495512 ATTTATTT
1 A-TTATTT
3495520 ATTATTT
1 ATTATTT
*
3495527 ATTTGTTT
1 A-TTATTT
*
3495535 ATTTTATT
1 ATTAT-TT
3495543 AGTTTATTT
1 A--TTATTT
3495552 ATTATTAT
1 ATTATT-T
3495560 ATTATTT
1 ATTATTT
3495567 AT
1 AT
3495569 AGATATTTAT
Statistics
Matches: 110, Mismatches: 7, Indels: 35
0.72 0.05 0.23
Matches are distributed among these distances:
5 8 0.07
6 10 0.09
7 32 0.29
8 51 0.46
9 4 0.04
10 5 0.05
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (7 bp):
ATTATTT
Found at i:3495499 original size:28 final size:27
Alignment explanation
Indices: 3495422--3495568 Score: 73
Period size: 25 Copynumber: 5.5 Consensus size: 27
3495412 TGCTTTGTTT
* *
3495422 TTTTAATTATTGTATTATTTATTTTATTA
1 TTTTAATTGTT-TATT-TTTAGTTTATTA
* *
3495451 TTTT-ATTAGTTT-TTAATT--TTAATTA
1 TTTTAATT-GTTTATT-TTTAGTTTATTA
3495476 TTTTAATTGTTTATTTTTAGTTTATTA
1 TTTTAATTGTTTATTTTTAGTTTATTA
*
3495503 GTTT-A-T-TTTA--TTTA-TTTATTA
1 TTTTAATTGTTTATTTTTAGTTTATTA
*
3495524 -TTTATTTGTTTATTTTATTAGTTTATTTA
1 TTTTAATTGTTTA-TTT-TTAGTTTA-TTA
*
3495553 TTATTATATTATTTAT
1 TT-TTA-ATTGTTTAT
3495569 AGATATTTAT
Statistics
Matches: 92, Mismatches: 9, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
20 3 0.03
21 7 0.08
22 5 0.05
23 4 0.04
24 4 0.04
25 17 0.18
26 7 0.08
27 17 0.18
28 8 0.09
29 9 0.10
30 1 0.01
31 4 0.04
32 6 0.07
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (27 bp):
TTTTAATTGTTTATTTTTAGTTTATTA
Found at i:3495521 original size:32 final size:30
Alignment explanation
Indices: 3495473--3495568 Score: 92
Period size: 32 Copynumber: 3.1 Consensus size: 30
3495463 TTAATTTTAA
*
3495473 TTATTTTAATTGTTTATTTTTAGTTTATTAGT
1 TTATTTT-ATTATTTATTTTTA-TTTATTAGT
*
3495505 TTA--TT-TTATTTATTTATTATTTATTTGT
1 TTATTTTATTATTTATTT-TTATTTATTAGT
3495533 TTATTTTATTAGTTTATTTATTATTATATTA-T
1 TTATTTTATTA-TTTATTT-TTATT-TATTAGT
3495565 TTAT
1 TTAT
3495569 AGATATTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
28 20 0.36
29 3 0.05
30 4 0.07
31 3 0.05
32 21 0.38
33 4 0.07
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (30 bp):
TTATTTTATTATTTATTTTTATTTATTAGT
Found at i:3495581 original size:4 final size:4
Alignment explanation
Indices: 3495491--3495568 Score: 58
Period size: 4 Copynumber: 19.2 Consensus size: 4
3495481 ATTGTTTATT
*
3495491 TTTA GTTTA -TTA GTTTA TTTTA TTTA TTTA -TTA TTTA TTTG TTTA TTT-
1 TTTA -TTTA TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
3495539 TATTA GTTTA TTTA -TTA -TTA TATTA TTTA T
1 T-TTA -TTTA TTTA TTTA TTTA T-TTA TTTA T
3495569 AGATATTTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
3 13 0.21
4 30 0.48
5 18 0.29
6 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:3495608 original size:93 final size:86
Alignment explanation
Indices: 3495428--3495609 Score: 190
Period size: 85 Copynumber: 2.0 Consensus size: 86
3495418 GTTTTTTTAA
*
3495428 TTATTGTATTATTTATTTTATTATTTTATTAGTTTTTAATTTTAATTATTTTAATTGTTTATTTT
1 TTATTGTATTATTTATTTTATTATTTTATTAGTTTTTAATTTTAATTATTTTAATTATTTATTTT
* * * *
3495493 TAGTTTATTAGTTTATTTTAT
66 TAATTTAATAGTTTAATATAT
*
3495514 TTATT-TATTATTTATTTGT-TTATTTTATTAGTTTATTTATTATTATATTATTTATAGA-TATT
1 TTATTGTATTATTTATTT-TATTATTTTATTAGTTT-TTAATT-TTA-ATTATTT-TA-ATTATT
*
3495576 TATTTAAATATAATTTAATATTTTAATATAT
60 TATTT---T-TAATTTAATAGTTTAATATAT
3495607 TTA
1 TTA
3495610 ATATATAAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
85 27 0.34
86 11 0.14
87 3 0.04
88 7 0.09
89 10 0.13
90 1 0.01
92 1 0.01
93 19 0.24
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.66
Consensus pattern (86 bp):
TTATTGTATTATTTATTTTATTATTTTATTAGTTTTTAATTTTAATTATTTTAATTATTTATTTT
TAATTTAATAGTTTAATATAT
Found at i:3495610 original size:17 final size:18
Alignment explanation
Indices: 3495576--3495628 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
3495566 TATAGATATT
3495576 TATTTAAATATAATTTAA
1 TATTTAAATATAATTTAA
*
3495594 TATTTTAATAT-ATTTAA
1 TATTTAAATATAATTTAA
*
3495611 TATATAAATATAATTTAA
1 TATTTAAATATAATTTAA
3495629 ATAAATATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 15 0.48
18 16 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTAAATATAATTTAA
Found at i:3495631 original size:11 final size:9
Alignment explanation
Indices: 3495576--3495628 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 9
3495566 TATAGATATT
3495576 TATTTAAATA
1 TATTT-AATA
3495586 TAATTTAATA
1 T-ATTTAATA
3495596 T-TTTAATA
1 TATTTAATA
3495604 TATTTAATA
1 TATTTAATA
*
3495613 TA-TAAATA
1 TATTTAATA
3495621 TAATTTAA
1 T-ATTTAA
3495629 ATAAATATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 14 0.38
9 10 0.27
10 9 0.24
11 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TATTTAATA
Found at i:3495973 original size:21 final size:21
Alignment explanation
Indices: 3495949--3496134 Score: 106
Period size: 21 Copynumber: 8.9 Consensus size: 21
3495939 TCAATACCAT
*
3495949 CTTTATCTTCATCATACTGAA
1 CTTTATCTTCGTCATACTGAA
*
3495970 CTTTATCTTCATCATACTGAA
1 CTTTATCTTCGTCATACTGAA
* ** **** * *
3495991 ATGGATCAGAATCAATA-TCAT
1 CTTTATCTTCGTC-ATACTGAA
* *
3496012 CTTTATCTTCGTCAAACTAAA
1 CTTTATCTTCGTCATACTGAA
3496033 CTTTATCTTCGTCATACTGAA
1 CTTTATCTTCGTCATACTGAA
* ** **** * *
3496054 ATGGATCAAAATCAATAC-CAT
1 CTTTATCTTCGTC-ATACTGAA
* * *
3496075 CTTTATCTTCGTTAAACTAAA
1 CTTTATCTTCGTCATACTGAA
*
3496096 CTTTATCTTTGTCATACTGAA
1 CTTTATCTTCGTCATACTGAA
3496117 CTTTATCTTCGTCATACT
1 CTTTATCTTCGTCATACT
3496135 AAAATGGATC
Statistics
Matches: 116, Mismatches: 45, Indels: 8
0.69 0.27 0.05
Matches are distributed among these distances:
20 5 0.04
21 104 0.90
22 7 0.06
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.40
Consensus pattern (21 bp):
CTTTATCTTCGTCATACTGAA
Found at i:3496013 original size:63 final size:63
Alignment explanation
Indices: 3495911--3496116 Score: 313
Period size: 63 Copynumber: 3.3 Consensus size: 63
3495901 AATCAATACA
* * * * * *
3495911 ATCTTCGTTATATTGAAATGGATTAGAATCAATACCATCTTTATCTTCATCATACTGAACTTT
1 ATCTTCGTCATACTGAAATGGATCAGAATCAATACCATCTTTATCTTCGTCAAACTAAACTTT
* *
3495974 ATCTTCATCATACTGAAATGGATCAGAATCAATATCATCTTTATCTTCGTCAAACTAAACTTT
1 ATCTTCGTCATACTGAAATGGATCAGAATCAATACCATCTTTATCTTCGTCAAACTAAACTTT
* *
3496037 ATCTTCGTCATACTGAAATGGATCAAAATCAATACCATCTTTATCTTCGTTAAACTAAACTTT
1 ATCTTCGTCATACTGAAATGGATCAGAATCAATACCATCTTTATCTTCGTCAAACTAAACTTT
*
3496100 ATCTTTGTCATACTGAA
1 ATCTTCGTCATACTGAA
3496117 CTTTATCTTC
Statistics
Matches: 130, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 130 1.00
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.38
Consensus pattern (63 bp):
ATCTTCGTCATACTGAAATGGATCAGAATCAATACCATCTTTATCTTCGTCAAACTAAACTTT
Found at i:3496101 original size:84 final size:84
Alignment explanation
Indices: 3496012--3496179 Score: 255
Period size: 84 Copynumber: 2.0 Consensus size: 84
3496002 TCAATATCAT
*
3496012 CTTTATCTTCGTCAAACTAAACTTTATCTTCGTCATACTGAAATGGATCAAAATCAATACCATCT
1 CTTTATCTTCGTCAAACTAAACTTTATCTTCGTCATACTAAAATGGATCAAAATCAATACCATCT
*
3496077 TTATCTTCGTTAAACTAAA
66 TTATCTTCGTCAAACTAAA
* * * * *
3496096 CTTTATCTTTGTCATACTGAACTTTATCTTCGTCATACTAAAATGGATCAGAATCAATACCATTT
1 CTTTATCTTCGTCAAACTAAACTTTATCTTCGTCATACTAAAATGGATCAAAATCAATACCATCT
* *
3496161 TTGTCTTTGTCAAACTAAA
66 TTATCTTCGTCAAACTAAA
3496180 ATGGATCATA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (84 bp):
CTTTATCTTCGTCAAACTAAACTTTATCTTCGTCATACTAAAATGGATCAAAATCAATACCATCT
TTATCTTCGTCAAACTAAA
Found at i:3496178 original size:42 final size:42
Alignment explanation
Indices: 3496033--3496210 Score: 160
Period size: 42 Copynumber: 4.2 Consensus size: 42
3496023 TCAAACTAAA
* * * *
3496033 CTTTATCTTCGTCATACTGAAATGGATCAAAATCAATACCAT
1 CTTTATCTTTGTCAAACTAAAATGGATCAGAATCAATACCAT
* * * ** **** * *
3496075 CTTTATCTTCGTTAAACTAAACTTTATCTTTGTC-ATACTGAA
1 CTTTATCTTTGTCAAACTAAAATGGATCAGAATCAATAC-CAT
* *
3496117 CTTTATCTTCGTCATACTAAAATGGATCAGAATCAATACCAT
1 CTTTATCTTTGTCAAACTAAAATGGATCAGAATCAATACCAT
* * *
3496159 TTTTGTCTTTGTCAAACTAAAATGGATCATAATCAATACCAT
1 CTTTATCTTTGTCAAACTAAAATGGATCAGAATCAATACCAT
3496201 CTTTATCTTT
1 CTTTATCTTT
3496211 ATCTTTGTCA
Statistics
Matches: 104, Mismatches: 30, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
41 4 0.04
42 96 0.92
43 4 0.04
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (42 bp):
CTTTATCTTTGTCAAACTAAAATGGATCAGAATCAATACCAT
Found at i:3496205 original size:84 final size:84
Alignment explanation
Indices: 3496031--3496209 Score: 216
Period size: 84 Copynumber: 2.1 Consensus size: 84
3496021 CGTCAAACTA
* *
3496031 AACTTTATCTTCGTCATACTGAAATGGATCAAAATCAATACCATCTTTATCTTCGTTAAACTAAA
1 AACTTTATCTTCGTCATACTAAAATGGATCAAAATCAATACCATCTTTATCTTCGTCAAACTAAA
* ** * ** *
3496096 CTTTATCTTTGTCATACTG
66 ATGGATCATAATCATACTC
* * * *
3496115 AACTTTATCTTCGTCATACTAAAATGGATCAGAATCAATACCATTTTTGTCTTTGTCAAACTAAA
1 AACTTTATCTTCGTCATACTAAAATGGATCAAAATCAATACCATCTTTATCTTCGTCAAACTAAA
3496180 ATGGATCATAATCAATAC-C
66 ATGGATCATAATC-ATACTC
*
3496199 ATCTTTATCTT
1 AACTTTATCTT
3496210 TATCTTTGTC
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
84 76 0.95
85 4 0.05
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.39
Consensus pattern (84 bp):
AACTTTATCTTCGTCATACTAAAATGGATCAAAATCAATACCATCTTTATCTTCGTCAAACTAAA
ATGGATCATAATCATACTC
Found at i:3497060 original size:2 final size:2
Alignment explanation
Indices: 3497053--3497089 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3497043 TCTGCGAATG
3497053 TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
3497090 ATAAATGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3498215 original size:23 final size:23
Alignment explanation
Indices: 3498189--3498244 Score: 89
Period size: 22 Copynumber: 2.5 Consensus size: 23
3498179 CCCGAAATTA
3498189 ATAAAATATTTATTTTTTAAAAT
1 ATAAAATATTTATTTTTTAAAAT
*
3498212 ATAAAATA-TTATTTTTTTAAAT
1 ATAAAATATTTATTTTTTAAAAT
3498234 AT-AAATATTTA
1 ATAAAATATTTA
3498245 AAAATATCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 5 0.16
22 18 0.58
23 8 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATAAAATATTTATTTTTTAAAAT
Found at i:3502263 original size:3 final size:3
Alignment explanation
Indices: 3502255--3502282 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3502245 TAGAAGGGAA
3502255 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3502283 GTGTTAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3503618 original size:16 final size:18
Alignment explanation
Indices: 3503588--3503625 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
3503578 CTTATTATTT
3503588 TTATATTTTATTTTCATA
1 TTATATTTTATTTTCATA
3503606 TTATA-TTTA-TTTCATA
1 TTATATTTTATTTTCATA
3503622 TTAT
1 TTAT
3503626 TATATGATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATATTTTATTTTCATA
Done.