Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 18 of 31
Found at i:4119998 original size:2 final size:2
Alignment explanation
Indices: 4119991--4120026 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4119981 TCAGATACAA
4119991 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4120027 TCGACATGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4122563 original size:36 final size:36
Alignment explanation
Indices: 4122523--4122595 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
4122513 AGAAGTGAAT
4122523 AAAATTGTGAAGATACTAGAGTGAGCAATATCATAC
1 AAAATTGTGAAGATACTAGAGTGAGCAATATCATAC
4122559 AAAATTGTGAAGATACTAGAGTGAGCAATATCATAC
1 AAAATTGTGAAGATACTAGAGTGAGCAATATCATAC
4122595 A
1 A
4122596 CTAAGTGGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (36 bp):
AAAATTGTGAAGATACTAGAGTGAGCAATATCATAC
Found at i:4125473 original size:10 final size:10
Alignment explanation
Indices: 4125458--4125488 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
4125448 ATATATACAT
*
4125458 ATAAGCCGAC
1 ATAAGCTGAC
4125468 ATAAGCTGAC
1 ATAAGCTGAC
4125478 ATAAGCTGAC
1 ATAAGCTGAC
4125488 A
1 A
4125489 AATTCAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (10 bp):
ATAAGCTGAC
Found at i:4126036 original size:2 final size:2
Alignment explanation
Indices: 4125987--4126017 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4125977 ATTTAAAACA
4125987 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4126018 ACTTACAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4127245 original size:54 final size:53
Alignment explanation
Indices: 4127163--4127264 Score: 125
Period size: 54 Copynumber: 1.9 Consensus size: 53
4127153 TTTTTTAAGA
* * *
4127163 TTTACATATGTAAATAAAAAATAGTGTTTATTGAAATTATTATTGGTTTAGGG
1 TTTAAATATGTAAATAAAAAATAGTGTTTACTGAAACTATTATTGGTTTAGGG
* * *
4127216 TTTAAATATTTAAATTAAAAAACTA-TGTTTGCTGATACTATTATTGGTT
1 TTTAAATATGTAAA-TAAAAAA-TAGTGTTTACTGAAACTATTATTGGTT
4127265 GTTTTCGCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
53 12 0.29
54 27 0.66
55 2 0.05
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (53 bp):
TTTAAATATGTAAATAAAAAATAGTGTTTACTGAAACTATTATTGGTTTAGGG
Found at i:4130424 original size:73 final size:73
Alignment explanation
Indices: 4130261--4130407 Score: 276
Period size: 73 Copynumber: 2.0 Consensus size: 73
4130251 ATAAAGAAGG
*
4130261 TCACAAGAAAAGAGGTTGTTCATTTAAGGGTATTGAGGTAATTTTTAATTTTATCTTATTCATTT
1 TCACAAGAAAAGAGGTTGTTCATTCAAGGGTATTGAGGTAATTTTTAATTTTATCTTATTCATTT
4130326 GACTTTAT
66 GACTTTAT
*
4130334 TCACAAGAAAAGAGGTTGTTCATTCAAGGGTATTGAGGTAATTTTTAGTTTTATCTTATTCATTT
1 TCACAAGAAAAGAGGTTGTTCATTCAAGGGTATTGAGGTAATTTTTAATTTTATCTTATTCATTT
4130399 GACTTTAT
66 GACTTTAT
4130407 T
1 T
4130408 ATATACGTAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (73 bp):
TCACAAGAAAAGAGGTTGTTCATTCAAGGGTATTGAGGTAATTTTTAATTTTATCTTATTCATTT
GACTTTAT
Found at i:4132330 original size:18 final size:18
Alignment explanation
Indices: 4132307--4132341 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4132297 GTAAAAAGGG
4132307 ATTTTTTATAATT-TTATA
1 ATTTTTTA-AATTATTATA
4132325 ATTTTTTAAATTATTAT
1 ATTTTTTAAATTATTAT
4132342 TTTTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTTTAAATTATTATA
Found at i:4133143 original size:14 final size:14
Alignment explanation
Indices: 4133121--4133159 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
4133111 TGTTTAAATA
*
4133121 TATTATATTATATT
1 TATTTTATTATATT
*
4133135 TATTTTATTATTTT
1 TATTTTATTATATT
4133149 TATATTTATTA
1 TAT-TTTATTA
4133160 AATATATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTTTATTATATT
Found at i:4133681 original size:24 final size:24
Alignment explanation
Indices: 4133654--4133706 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
4133644 TTATATATTT
4133654 TTTTATATAAATATAAAAATATAA
1 TTTTATATAAATATAAAAATATAA
* * *
4133678 TTTTATATATATATATATATATAA
1 TTTTATATAAATATAAAAATATAA
4133702 TTTTA
1 TTTTA
4133707 AAACAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTTATATAAATATAAAAATATAA
Found at i:4137092 original size:2 final size:2
Alignment explanation
Indices: 4137085--4137116 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4137075 GCTTGCAAAG
*
4137085 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4137117 TAGTTTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4137790 original size:2 final size:2
Alignment explanation
Indices: 4137783--4137816 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4137773 TGGATTCTTG
4137783 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
4137817 AATCTATCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4140580 original size:2 final size:2
Alignment explanation
Indices: 4140575--4140599 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4140565 TTACTAAGAG
4140575 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
4140600 CCCTATGCAA
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:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4141172 original size:14 final size:14
Alignment explanation
Indices: 4141153--4141187 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
4141143 AATTCTTCAG
4141153 TTTTTTATTT-TTT
1 TTTTTTATTTCTTT
4141166 CTTTTTTATTTCTTT
1 -TTTTTTATTTCTTT
4141181 TTTTTTA
1 TTTTTTA
4141188 ATGGTTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTATTTCTTT
Found at i:4141616 original size:20 final size:22
Alignment explanation
Indices: 4141585--4141627 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
4141575 GGGCTCATCG
4141585 TTCCCATTCTCC-CTTTCTTCT
1 TTCCCATTCTCCACTTTCTTCT
*
4141606 TTCCC-TTCTCCATTTTCTTCT
1 TTCCCATTCTCCACTTTCTTCT
4141627 T
1 T
4141628 CTTCTTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.05, C:0.40, G:0.00, T:0.56
Consensus pattern (22 bp):
TTCCCATTCTCCACTTTCTTCT
Found at i:4142938 original size:19 final size:18
Alignment explanation
Indices: 4142902--4142937 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4142892 CAGCGGTAAT
4142902 TAAATTAGCAATAAAAAA
1 TAAATTAGCAATAAAAAA
4142920 TAAATTAGCAATAAAAAA
1 TAAATTAGCAATAAAAAA
4142938 AGAAATTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (18 bp):
TAAATTAGCAATAAAAAA
Found at i:4142943 original size:19 final size:18
Alignment explanation
Indices: 4142903--4142944 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
4142893 AGCGGTAATT
*
4142903 AAATTAGCAATAAAAAAT
1 AAATTAGCAATAAAAAAG
4142921 AAATTAGCAATAAAAAAAG
1 AAATTAGCAAT-AAAAAAG
4142940 AAATT
1 AAATT
4142945 TCCAATGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATTAGCAATAAAAAAG
Found at i:4142950 original size:19 final size:18
Alignment explanation
Indices: 4142903--4142950 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
4142893 AGCGGTAATT
* *
4142903 AAATTAGCAATAAAAAAT
1 AAATTACCAATAAAAAAG
*
4142921 AAATTAGCAATAAAAAAAG
1 AAATTACCAAT-AAAAAAG
*
4142940 AAATTTCCAAT
1 AAATTACCAAT
4142951 GTAAATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.23
Consensus pattern (18 bp):
AAATTACCAATAAAAAAG
Found at i:4144312 original size:32 final size:31
Alignment explanation
Indices: 4144235--4144333 Score: 101
Period size: 32 Copynumber: 3.1 Consensus size: 31
4144225 TTTTAATATA
* *
4144235 ATATAATTATATAATATAAA-AAATTAAAATATG
1 ATATAA-TATA-AATATAAATATATTAAAAT-TT
* *
4144268 ATATGATTTAAATAATAAATATATTAAAATTT
1 ATATAATATAAAT-ATAAATATATTAAAATTT
*
4144300 ATATAATATAAATTATTAATATATTAAAATTT
1 ATATAATATAAA-TATAAATATATTAAAATTT
4144332 AT
1 AT
4144334 TTAAAATATT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
31 3 0.05
32 38 0.68
33 15 0.27
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (31 bp):
ATATAATATAAATATAAATATATTAAAATTT
Found at i:4144333 original size:18 final size:18
Alignment explanation
Indices: 4144285--4144334 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
4144275 TTAAATAATA
4144285 AATATATTAAAATTTA-T
1 AATATATTAAAATTTATT
4144302 -ATA-A-TATAAA-TTATT
1 AATATATTA-AAATTTATT
4144317 AATATATTAAAATTTATT
1 AATATATTAAAATTTATT
4144335 TAAAATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 11
0.71 0.00 0.29
Matches are distributed among these distances:
14 5 0.19
15 5 0.19
16 6 0.22
17 4 0.15
18 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATATATTAAAATTTATT
Found at i:4144351 original size:34 final size:32
Alignment explanation
Indices: 4144276--4144342 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 32
4144266 TGATATGATT
* * *
4144276 TAAATAATAAATATATTAAAATTTATATAATA
1 TAAATTATTAATATATTAAAATTTATAAAATA
4144308 TAAATTATTAATATATTAAAATTTATTTAAAATA
1 TAAATTATTAATATATTAAAATTTA--TAAAATA
4144342 T
1 T
4144343 TTAATATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 23 0.77
34 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
TAAATTATTAATATATTAAAATTTATAAAATA
Found at i:4146547 original size:26 final size:26
Alignment explanation
Indices: 4146511--4146569 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
4146501 CTTTAGTAAA
* *
4146511 AAAAAAAATTACTTTTTATGTTTATC
1 AAAAATAATTACTTTTTATATTTATC
* * *
4146537 AAAAATAATTATTTTTTTTATTTGTC
1 AAAAATAATTACTTTTTATATTTATC
4146563 AAAAATA
1 AAAAATA
4146570 GTGACTTGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (26 bp):
AAAAATAATTACTTTTTATATTTATC
Found at i:4151056 original size:25 final size:25
Alignment explanation
Indices: 4151018--4151089 Score: 110
Period size: 24 Copynumber: 2.9 Consensus size: 25
4151008 AAAAGCCACA
*
4151018 CTTTGTGTTTGTCAAAAATGGTGGTT
1 CTTT-TGTTTGTCAAAAATGGTGGCT
4151044 CTTTTGTTTGTCAAAAATGGTGGCT
1 CTTTTGTTTGTCAAAAATGGTGGCT
*
4151069 -TTTTGTTTGTCAAAATTGGTG
1 CTTTTGTTTGTCAAAAATGGTG
4151090 ACTAATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 20 0.45
25 20 0.45
26 4 0.09
ACGTcount: A:0.19, C:0.08, G:0.25, T:0.47
Consensus pattern (25 bp):
CTTTTGTTTGTCAAAAATGGTGGCT
Found at i:4151072 original size:24 final size:24
Alignment explanation
Indices: 4151018--4151089 Score: 108
Period size: 25 Copynumber: 3.0 Consensus size: 24
4151008 AAAAGCCACA
*
4151018 CTTTGTGTTTGTCAAAAATGGTGG
1 CTTTTTGTTTGTCAAAAATGGTGG
*
4151042 TTCTTTTGTTTGTCAAAAATGGTGG
1 CT-TTTTGTTTGTCAAAAATGGTGG
*
4151067 CTTTTTGTTTGTCAAAATTGGTG
1 CTTTTTGTTTGTCAAAAATGGTG
4151090 ACTAATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 21 0.49
25 22 0.51
ACGTcount: A:0.19, C:0.08, G:0.25, T:0.47
Consensus pattern (24 bp):
CTTTTTGTTTGTCAAAAATGGTGG
Found at i:4155750 original size:32 final size:31
Alignment explanation
Indices: 4155708--4155776 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 31
4155698 TGTATTTAAA
* *
4155708 AATATATTTAAATAAATATTTATATTATATTT
1 AATATATTTAAATAAATATTAACATTATA-TT
*
4155740 AATATCTTTAAATAAATATTAACATTATATT
1 AATATATTTAAATAAATATTAACATTATATT
4155771 AATATA
1 AATATA
4155777 ATATTTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 7 0.21
32 26 0.79
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (31 bp):
AATATATTTAAATAAATATTAACATTATATT
Found at i:4155836 original size:18 final size:18
Alignment explanation
Indices: 4155773--4155858 Score: 50
Period size: 20 Copynumber: 4.4 Consensus size: 18
4155763 ATTATATTAA
* *
4155773 TATAATATTTAATTTAAT
1 TATAATATATAATTTTAT
*
4155791 TATGATATATGATATTTTTAT
1 TAT-A-ATAT-ATAATTTTAT
*
4155812 AAAATAATATATAATATTT-T
1 --TATAATATATAAT-TTTAT
4155832 TATAAGTATTATAATTTTAT
1 TATAA-TA-TATAATTTTAT
4155852 TA-AATAT
1 TATAATAT
4155859 TAAATATAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 19
0.68 0.08 0.24
Matches are distributed among these distances:
17 1 0.02
18 9 0.17
19 8 0.15
20 18 0.34
21 14 0.26
22 1 0.02
23 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (18 bp):
TATAATATATAATTTTAT
Found at i:4155873 original size:23 final size:23
Alignment explanation
Indices: 4155766--4155874 Score: 61
Period size: 23 Copynumber: 4.9 Consensus size: 23
4155756 TATTAACATT
4155766 ATATT-AATATAATATTTAATTTAA
1 ATATTAAATATAATATTT-A-TTAA
* * * *
4155790 TTATGATATATGATATTT-TTATA
1 ATATTAAATATAATATTTATTA-A
* *
4155813 A-AATAATATATAATATTT-TTAT
1 ATATTAA-ATATAATATTTATTAA
* *
4155835 A-AGT-ATTATAAT-TTTATTAA
1 ATATTAAATATAATATTTATTAA
4155855 ATATTAAATATAATATTTAT
1 ATATTAAATATAATATTTAT
4155875 ATTTATTTAA
Statistics
Matches: 63, Mismatches: 15, Indels: 15
0.68 0.16 0.16
Matches are distributed among these distances:
19 3 0.05
20 10 0.16
21 3 0.05
22 15 0.24
23 19 0.30
24 3 0.05
25 10 0.16
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
ATATTAAATATAATATTTATTAA
Found at i:4156596 original size:3 final size:3
Alignment explanation
Indices: 4156588--4156612 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4156578 GCCATGCAAG
4156588 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
4156613 TTACACTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:4159263 original size:11 final size:11
Alignment explanation
Indices: 4159200--4159274 Score: 50
Period size: 10 Copynumber: 7.0 Consensus size: 11
4159190 TATCTATCGG
4159200 TAAATTTAATT
1 TAAATTTAATT
** *
4159211 CGAATTGAA-T
1 TAAATTTAATT
*
4159221 TAAATTT-ATA
1 TAAATTTAATT
*
4159231 TAAATTT-TTT
1 TAAATTTAATT
4159241 TATAATTTAATT
1 TA-AATTTAATT
4159253 T-AATTTAAATT
1 TAAATTT-AATT
*
4159264 AAAATTTAATT
1 TAAATTTAATT
4159275 AATAAAAATA
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
9 1 0.02
10 20 0.42
11 19 0.40
12 8 0.17
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (11 bp):
TAAATTTAATT
Found at i:4159296 original size:17 final size:15
Alignment explanation
Indices: 4159249--4159296 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
4159239 TTTATAATTT
*
4159249 AATTTAATTTAAATTAA
1 AATTTAA-TT-AATAAA
4159266 AATTTAATTAATAAA
1 AATTTAATTAATAAA
4159281 AATATTAATATAATAA
1 AAT-TTAAT-TAATAA
4159297 TATTATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 13 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTTAATTAATAAA
Found at i:4159301 original size:26 final size:27
Alignment explanation
Indices: 4159272--4159327 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
4159262 TTAAAATTTA
4159272 ATTAATAA-AAATATTAATATAAT-AAT
1 ATTAATAATAAATATTAA-ATAATAAAT
* *
4159298 ATT-ATAATATATTTTAAATAATAAAT
1 ATTAATAATAAATATTAAATAATAAAT
4159324 ATTA
1 ATTA
4159328 TACTAACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
ATTAATAATAAATATTAAATAATAAAT
Found at i:4160160 original size:23 final size:23
Alignment explanation
Indices: 4160123--4160191 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
4160113 TTATTTTTAT
*
4160123 ATTTTA-TCATATTTTAAATTAA
1 ATTTTATTTATATTTTAAATTAA
* *
4160145 ATTTTATTTATATTTTATATTAT
1 ATTTTATTTATATTTTAAATTAA
* *
4160168 ATAATTATATTATATTTAAAATTA
1 AT-TTTAT-TTATATTTTAAATTA
4160192 TCAAATTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 6 0.16
23 15 0.39
24 4 0.11
25 13 0.34
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTTATTTATATTTTAAATTAA
Found at i:4160161 original size:11 final size:11
Alignment explanation
Indices: 4160105--4160184 Score: 65
Period size: 11 Copynumber: 7.0 Consensus size: 11
4160095 AATTTTGATA
4160105 TATTTATATTAT
1 TATTTATATT-T
4160117 T-TTTATATTT
1 TATTTATATTT
*
4160127 TA-TCATATTT
1 TATTTATATTT
* *
4160137 TAAATTAAATTT
1 T-ATTTATATTT
4160149 TATTTATATTT
1 TATTTATATTT
*
4160160 TATATTATATAAT
1 TAT-TTATAT-TT
4160173 TATATTATATTT
1 TAT-TTATATTT
4160185 AAAATTATCA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
10 10 0.18
11 20 0.36
12 15 0.27
13 11 0.20
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTATATTT
Found at i:4160191 original size:25 final size:23
Alignment explanation
Indices: 4160131--4160192 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
4160121 ATATTTTATC
* *
4160131 ATATTTTAAATTAAATTTTATTT
1 ATATTTTAAATTATATATTATTT
*
4160154 ATATTTTATATTATATAATTATATT
1 ATATTTTAAATTATAT-ATTAT-TT
*
4160179 ATATTTAAAATTAT
1 ATATTTTAAATTAT
4160193 CAAATTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 14 0.44
24 4 0.12
25 14 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATTTTAAATTATATATTATTT
Found at i:4160530 original size:13 final size:14
Alignment explanation
Indices: 4160509--4160570 Score: 60
Period size: 13 Copynumber: 4.7 Consensus size: 14
4160499 GACTCTTTTT
*
4160509 TTATTATTTTTTAA
1 TTATAATTTTTTAA
4160523 TT-TAA-TTTTT-A
1 TTATAATTTTTTAA
4160534 TTATAATTTTTTAA
1 TTATAATTTTTTAA
* * *
4160548 TCATTA-TTTATAA
1 TTATAATTTTTTAA
4160561 TTATAATTTT
1 TTATAATTTT
4160571 CAATTTATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
11 3 0.08
12 8 0.21
13 17 0.45
14 10 0.26
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATAATTTTTTAA
Found at i:4160542 original size:25 final size:25
Alignment explanation
Indices: 4160504--4160570 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 25
4160494 AATTCGACTC
*
4160504 TTTTT-TTATTATTTTTTAAT-TTAA
1 TTTTTATTATAATTTTTTAATATT-A
4160528 TTTTTATTATAATTTTTTAATCATTA
1 TTTTTATTATAATTTTTTAAT-ATTA
*
4160554 TTTATAATTATAATTTT
1 TTT-TTATTATAATTTT
4160571 CAATTTATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
24 5 0.14
25 14 0.38
26 4 0.11
27 14 0.38
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTTATTATAATTTTTTAATATTA
Found at i:4160578 original size:24 final size:24
Alignment explanation
Indices: 4160509--4160578 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
4160499 GACTCTTTTT
* *
4160509 TTATTATTTTTTAATTTAATTTTTA
1 TTATAATTTTTTAATTT-ATTTTAA
4160534 TTATAATTTTTTAATCATTATTTATAA
1 TTATAATTTTTTAAT--TTATTT-TAA
*
4160561 TTATAA-TTTTCAATTTAT
1 TTATAATTTTTTAATTTAT
4160579 GAATAAATCC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 4 0.10
25 14 0.36
26 11 0.28
27 10 0.26
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATAATTTTTTAATTTATTTTAA
Found at i:4161329 original size:29 final size:30
Alignment explanation
Indices: 4161297--4161367 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
4161287 TTGAATTCTT
4161297 AAATATTTATTTTTA-TCAAATTAAAAC-TC
1 AAATATTTATTTTTATTC-AATTAAAACTTC
* * *
4161326 AAATCTTTACTTTTATTCAATTAAACCTTC
1 AAATATTTATTTTTATTCAATTAAAACTTC
*
4161356 AAACA-TTATTTT
1 AAATATTTATTTT
4161368 CACGAATTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 27 0.79
30 7 0.21
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.46
Consensus pattern (30 bp):
AAATATTTATTTTTATTCAATTAAAACTTC
Found at i:4161661 original size:3 final size:3
Alignment explanation
Indices: 4161653--4161682 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4161643 ATATTGGACA
4161653 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4161683 TACAAAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4162518 original size:19 final size:19
Alignment explanation
Indices: 4162468--4162539 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
4162458 AGTAATAAGA
** *
4162468 AAATTATTTATTAATTTTT
1 AAATTATTTAAAAATTATT
4162487 AAATTATTTTAAAAATTATT
1 AAATTA-TTTAAAAATTATT
*
4162507 ATATTATTT-AAAATATATT
1 AAATTATTTAAAAAT-TATT
*
4162526 AAAAT-TTTAAAAAT
1 AAATTATTTAAAAAT
4162540 ATTTATATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
18 8 0.18
19 21 0.48
20 15 0.34
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTATTTAAAAATTATT
Found at i:4162527 original size:29 final size:27
Alignment explanation
Indices: 4162475--4162529 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
4162465 AGAAAATTAT
* *
4162475 TTATTAATTTTTAAATTATTTTAAAAA
1 TTATTAATTTTTAAAATATATTAAAAA
4162502 TTATTATATTATTTAAAATATATTAAAA
1 TTATTA-ATT-TTTAAAATATATTAAAA
4162530 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 3 0.12
29 15 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATTAATTTTTAAAATATATTAAAAA
Found at i:4162551 original size:19 final size:20
Alignment explanation
Indices: 4162491--4162552 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 20
4162481 ATTTTTAAAT
4162491 TATTTTAAAAAT-TATTATA
1 TATTTTAAAAATATATTATA
4162510 T-TATTT-AAAATATATTA-A
1 TAT-TTTAAAAATATATTATA
*
4162528 AATTTTAAAAATAT-TTATA
1 TATTTTAAAAATATATTATA
4162547 TATTTT
1 TATTTT
4162553 TATAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 13 0.36
19 23 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTTTAAAAATATATTATA
Found at i:4162655 original size:16 final size:16
Alignment explanation
Indices: 4162631--4162667 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4162621 ATAAATTAAA
* *
4162631 AAAAATATATATATTT
1 AAAATTATATAAATTT
4162647 AAAATTATATAAATTT
1 AAAATTATATAAATTT
4162663 AAAAT
1 AAAAT
4162668 CAAATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATTATATAAATTT
Found at i:4163847 original size:3 final size:3
Alignment explanation
Indices: 4163841--4163865 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4163831 ATAATTCCTA
4163841 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
4163866 TTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4164727 original size:29 final size:33
Alignment explanation
Indices: 4164681--4164740 Score: 83
Period size: 30 Copynumber: 1.9 Consensus size: 33
4164671 AAATTAATTT
4164681 TTATTATTATAAATATT-AATTTAAAATAAAAA
1 TTATTATTATAAATATTAAATTTAAAATAAAAA
*
4164713 TTATTATT-T-AA-ATTAAATTTAATATAAA
1 TTATTATTATAAATATTAAATTTAAAATAAA
4164741 TTAAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 14 0.54
31 1 0.04
32 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
TTATTATTATAAATATTAAATTTAAAATAAAAA
Found at i:4164742 original size:16 final size:15
Alignment explanation
Indices: 4164715--4164757 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
4164705 AATAAAAATT
*
4164715 ATTATTTAAATTAAA
1 ATTATATAAATTAAA
*
4164730 TTTAATATAAATTAAA
1 ATT-ATATAAATTAAA
4164746 ATTATA-AAATTA
1 ATTATATAAATTA
4164758 TCAAATCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 6 0.25
15 5 0.21
16 13 0.54
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTATATAAATTAAA
Found at i:4164753 original size:29 final size:31
Alignment explanation
Indices: 4164686--4164753 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 31
4164676 AATTTTTATT
* **
4164686 ATTATAAATATTAATTTAAAATAAAAATTATT
1 ATTATAAATATAAATTT-AAATAAAAATTAAA
*
4164718 ATT-TAAAT-TAAATTT-AATATAAATTAAA
1 ATTATAAATATAAATTTAAATAAAAATTAAA
4164746 ATTATAAA
1 ATTATAAA
4164754 ATTATCAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
28 13 0.42
29 4 0.13
30 6 0.19
31 5 0.16
32 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
ATTATAAATATAAATTTAAATAAAAATTAAA
Found at i:4165162 original size:525 final size:523
Alignment explanation
Indices: 4164311--4165347 Score: 1452
Period size: 525 Copynumber: 2.0 Consensus size: 523
4164301 ATTTTACTAT
* *
4164311 AAATATTTATAAATCGAGTTACAATAAAAAATTTATAATAAAAAGCTTTTAAAAATTAAATTATC
1 AAATATTTATAAATCAAATTACAATAAAAAATTTATAATAAAAAGCTTTTAAAAATTAAATTATC
* * * * * *
4164376 AAATAATTTTTACTTTATTTTTTAAATTTTTATTTTTTTTACAAAGACTTCATTTTAATTTATAA
66 AAATAATTTTTACTTTATTTTTAAAATTTTTAATTTTTATACAAAGACTTAATTTCAAGTTATAA
*
4164441 ATTAAAAAAAGTGACATCAAATATGCTCAAATTATACTCTTTTATCTTTAACTTGAGTAACTTTT
131 ATTAAAAAAAGTGACATCAAATATGCTCAAATTATACTCTTTTATCTTTAACTTAAGTAACTTTT
* * ** * *
4164506 TTCATAAATCGAGTTCGATTGAATTCTGATTTAAAACTTATTTTTTTATTTTAATATGATCTTAA
196 TTCATAAATCAAGTTCAATAAAATTCTAATTTAAAACTTATTTTTTTATCTTAATATGATCTTAA
* * *
4164571 TTCATGAAATTAAATTAATTATAAATCTATTCAATTGTTTAAATAATATTAAATTATTATATTAA
261 TTCACGAAATTAAATTAATTATAAATCTATTCAATTATTTAAATAATATTAAATTATTAGATTAA
* *
4164636 -TTTTTTATAAATATTCATTATTAAATATAAATAAAAAATTAATTTTTATTATTAT-AA-A-T-A
326 TTTTTTTATAAATATTAATTATTAAATATAAATAAAAAATTAATTATTATTATTATAAATATTAA
4164696 -TTAATTTAAAAT-AAAAATTATTATTTAAATTAAATTTAATATAAATTAAAATTATAAAATTAT
391 TTTAATTTAAAATAAAAAATTATTATTTAAATTAAATTTAATATAAATTAAAATTATAAAATTAT
*
4164759 CAAATCAATAGTCCTAGGGCCCTGGCCCTAGCCCTAGCTATAGTCCTAGGTGAAAGATAATTAAA
456 CAAATCAATAGTACTA--G----GG-CCTAGCCCTAGCTATAGTCCTAGGTGAAAGATAATTAAA
4164824 AAAATATTTA
514 AAAATATTTA
* * * *
4164834 AAATATTTATAAATTAAATTATAATTAAAAATTTATAATAAATAG-TCTTTAAAAATTAAATTAT
1 AAATATTTATAAATCAAATTACAATAAAAAATTTATAATAAAAAGCT-TTTAAAAATTAAATTAT
* * * *
4164898 TAAATAATTTTTATTTTATTTTTAAAATTTTTAAATTTTTAT-GAAAG-TTTAATTTCAAGTTAT
65 CAAATAATTTTTACTTTATTTTTAAAATTTTT-AATTTTTATACAAAGACTTAATTTCAAGTTAT
* * * * * *
4164961 AAATTAAAAAAAGTGAGATCAAATATGCTTAAATTATGCTCTTTTAT-TTTTATTCTAATTAGA-
129 AAATTAAAAAAAGTGACATCAAATATGCTCAAATTATACTCTTTTATCTTTAACT-TAAGTA-AC
* *
4165024 TTTTTTCATAAATTAAGTTCAATAAAATTTTAATTTAAAA-TATATTTTATTTTTATCTTAATAT
192 TTTTTTCATAAATCAAGTTCAATAAAATTCTAATTTAAAACT-TA--TT-TTTTTATCTTAATAT
* * *
4165088 GATCTTAATTTACGAGATTAAATTAATTATAAGTCTATTCAATTATTTAAATAATATTAAATTAT
253 GATCTTAATTCACGAAATTAAATTAATTATAAATCTATTCAATTATTTAAATAATATTAAATTAT
4165153 TAGATTAATTTTTTTATAAATATTAATTATTAAATATAAATAAAAAATTAATTATTATTATTATA
318 TAGATTAATTTTTTTATAAATATTAATTATTAAATATAAATAAAAAATTAATTATTATTATTATA
* * *
4165218 AATATTAATTTAATTTAAAATAAAAAATTATTATTTAAATTTAATTTAATATGAATTAAATTTAT
383 AATATTAATTTAATTTAAAATAAAAAATTATTATTTAAATTAAATTTAATATAAATTAAAATTAT
*
4165283 AAAATTATCAAATCAATAGTACTAGGGCCTAGCCCTAGCTCTAGTCCTAGGTGAAAGATAATTAA
448 AAAATTATCAAATCAATAGTACTAGGGCCTAGCCCTAGCTATAGTCCTAGGTGAAAGATAATTAA
4165348 TGGGTGGGTG
Statistics
Matches: 455, Mismatches: 44, Indels: 28
0.86 0.08 0.05
Matches are distributed among these distances:
521 6 0.01
522 96 0.21
523 90 0.20
524 9 0.02
525 118 0.26
526 55 0.12
527 2 0.00
528 1 0.00
529 1 0.00
530 2 0.00
531 12 0.03
532 63 0.14
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (523 bp):
AAATATTTATAAATCAAATTACAATAAAAAATTTATAATAAAAAGCTTTTAAAAATTAAATTATC
AAATAATTTTTACTTTATTTTTAAAATTTTTAATTTTTATACAAAGACTTAATTTCAAGTTATAA
ATTAAAAAAAGTGACATCAAATATGCTCAAATTATACTCTTTTATCTTTAACTTAAGTAACTTTT
TTCATAAATCAAGTTCAATAAAATTCTAATTTAAAACTTATTTTTTTATCTTAATATGATCTTAA
TTCACGAAATTAAATTAATTATAAATCTATTCAATTATTTAAATAATATTAAATTATTAGATTAA
TTTTTTTATAAATATTAATTATTAAATATAAATAAAAAATTAATTATTATTATTATAAATATTAA
TTTAATTTAAAATAAAAAATTATTATTTAAATTAAATTTAATATAAATTAAAATTATAAAATTAT
CAAATCAATAGTACTAGGGCCTAGCCCTAGCTATAGTCCTAGGTGAAAGATAATTAAAAAAATAT
TTA
Found at i:4166289 original size:16 final size:16
Alignment explanation
Indices: 4166270--4166311 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4166260 TTAATTTTTA
4166270 AAATTATCATATATAT
1 AAATTATCATATATAT
4166286 AAATATAT-ATATATAT
1 AAAT-TATCATATATAT
* *
4166302 GAATTTTCAT
1 AAATTATCAT
4166312 CTTATGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.09
16 17 0.77
17 3 0.14
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (16 bp):
AAATTATCATATATAT
Found at i:4169678 original size:2 final size:2
Alignment explanation
Indices: 4169665--4169697 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4169655 CACCTCAAAA
*
4169665 AT AT AT AA AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4169698 GCCAAATATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4181515 original size:2 final size:2
Alignment explanation
Indices: 4181508--4181536 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4181498 CAGTATTGAA
4181508 AT 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 AT A
4181537 AAAAGTTAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4186736 original size:18 final size:17
Alignment explanation
Indices: 4186715--4186759 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
4186705 TAATCTTTAT
4186715 ATAAATTTTAATATATCA
1 ATAAATTTTAATAT-TCA
*
4186733 AT-AATTTT--TATTCT
1 ATAAATTTTAATATTCA
4186747 ATAAATTTTAATA
1 ATAAATTTTAATA
4186760 AATTCATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
14 4 0.17
15 9 0.39
17 8 0.35
18 2 0.09
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
ATAAATTTTAATATTCA
Found at i:4189139 original size:13 final size:14
Alignment explanation
Indices: 4189121--4189149 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4189111 TTGACTAAAC
4189121 TACTG-TTGATTTT
1 TACTGTTTGATTTT
4189134 TACTGTTTGATTTT
1 TACTGTTTGATTTT
4189148 TA
1 TA
4189150 AACAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.17, C:0.07, G:0.14, T:0.62
Consensus pattern (14 bp):
TACTGTTTGATTTT
Found at i:4189380 original size:19 final size:19
Alignment explanation
Indices: 4189356--4189395 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4189346 ATTTTTTAAA
* *
4189356 ATTAATATAAGTTTATATT
1 ATTAATAAAAGTTTAAATT
*
4189375 ATTAATAAAATTTTAAATT
1 ATTAATAAAAGTTTAAATT
4189394 AT
1 AT
4189396 AATCTTGTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
ATTAATAAAAGTTTAAATT
Found at i:4190910 original size:21 final size:21
Alignment explanation
Indices: 4190886--4190948 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 21
4190876 AAAATTATTG
4190886 TTTAATAAAAAATAAT-TTAAA
1 TTTAATAAAAAATAATATT-AA
*
4190907 TTTAATTATAAAAT-ATATTAA
1 TTTAA-TAAAAAATAATATTAA
4190928 TATTAATATAAAAATAATATT
1 T-TTAATA-AAAAATAATATT
4190949 TTAAATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
21 12 0.34
22 18 0.51
23 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTAATAAAAAATAATATTAA
Found at i:4191069 original size:25 final size:25
Alignment explanation
Indices: 4191038--4191096 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
4191028 AATTTATTAA
4191038 ATTATAATTCAATCCATAAATATAT
1 ATTATAATTCAATCCATAAATATAT
4191063 ATTATAATTCAATCCATAAATATAT
1 ATTATAATTCAATCCATAAATATAT
4191088 ATTATAATT
1 ATTATAATT
4191097 AGTGAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTATAATTCAATCCATAAATATAT
Found at i:4193559 original size:16 final size:17
Alignment explanation
Indices: 4193538--4193570 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4193528 TTTATTTATG
4193538 AAATAAA-TAAATTTAA
1 AAATAAATTAAATTTAA
4193554 AAATAAATTAAATTTAA
1 AAATAAATTAAATTTAA
4193571 TTTCAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAATTAAATTTAA
Found at i:4194648 original size:36 final size:35
Alignment explanation
Indices: 4194603--4194687 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 35
4194593 TATATATTCA
4194603 TATTAAATTTATATTA-ATTTGTATTAT-TTTAAAATT
1 TATT-AATTTATATTATATTT-TATTATATTTAAAA-T
*
4194639 TAATTAATTTTTATTATATTTTATTATATTTAAAAT
1 T-ATTAATTTATATTATATTTTATTATATTTAAAAT
4194675 TATTAAGTTTATA
1 TATTAA-TTTATA
4194688 AATCATAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
35 5 0.12
36 24 0.56
37 14 0.33
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (35 bp):
TATTAATTTATATTATATTTTATTATATTTAAAAT
Found at i:4195049 original size:28 final size:31
Alignment explanation
Indices: 4195018--4195117 Score: 79
Period size: 30 Copynumber: 3.3 Consensus size: 31
4195008 ATTATATAAG
4195018 TATAATATAATTAA-A-ATA-ATTAAAA-TA
1 TATAATATAATTAATAGATATATTAAAATTA
* *
4195045 TTATATTAT-ATTAATAGATATTTTAAAATTA
1 -TATAATATAATTAATAGATATATTAAAATTA
* *
4195076 TATAATATAAAATATTA-ATAT-TTAAAACTTA
1 TATAATAT-AATTAATAGATATATTAAAA-TTA
4195107 TATAAATATAA
1 TAT-AATATAA
4195118 AATATTTTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
27 5 0.08
28 8 0.14
29 3 0.05
30 19 0.32
31 14 0.24
32 10 0.17
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (31 bp):
TATAATATAATTAATAGATATATTAAAATTA
Found at i:4195094 original size:13 final size:15
Alignment explanation
Indices: 4195068--4195120 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
4195058 ATAGATATTT
4195068 TAAAATTATATAATA
1 TAAAATTATATAATA
4195083 TAAAA-TAT-TAATA
1 TAAAATTATATAATA
4195096 TTTAAAACTTATATAAATA
1 --TAAAA-TTATAT-AATA
4195115 TAAAAT
1 TAAAAT
4195121 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 5 0.16
14 3 0.09
15 10 0.31
16 1 0.03
17 8 0.25
18 1 0.03
19 4 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAAATTATATAATA
Found at i:4196284 original size:2 final size:2
Alignment explanation
Indices: 4196277--4196314 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4196267 GCCGCAAGGT
4196277 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4196315 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4196319 original size:2 final size:2
Alignment explanation
Indices: 4196314--4196351 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4196304 ATATATATAT
*
4196314 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4196352 TATTTGATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4198466 original size:2 final size:2
Alignment explanation
Indices: 4198459--4198487 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4198449 ATTCATTTTG
4198459 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4198488 AACTCACGTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4201009 original size:2 final size:2
Alignment explanation
Indices: 4201002--4201048 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
4200992 AGTTTGATTT
*
4201002 TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4201044 TA TA T
1 TA TA T
4201049 GCCTTTTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4205494 original size:20 final size:20
Alignment explanation
Indices: 4205469--4205508 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4205459 AATTTTTTAA
4205469 TTTATATATTTTAAAATATT
1 TTTATATATTTTAAAATATT
*
4205489 TTTATATATTTTATAATATT
1 TTTATATATTTTAAAATATT
4205509 ATAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATATATTTTAAAATATT
Found at i:4205601 original size:33 final size:34
Alignment explanation
Indices: 4205561--4205633 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
4205551 TTAATAATTA
*
4205561 TATTATATTAATTTTAAATTTT-TATGT-TATTTT
1 TATTATATTAATATTAAATTTTGTAT-TATATTTT
* *
4205594 TATTATATTTATATTAATTTTTGTATTATATTTT
1 TATTATATTAATATTAAATTTTGTATTATATTTT
*
4205628 AATTAT
1 TATTAT
4205634 TTCTTAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 20 0.59
34 14 0.41
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (34 bp):
TATTATATTAATATTAAATTTTGTATTATATTTT
Found at i:4205602 original size:11 final size:11
Alignment explanation
Indices: 4205578--4205633 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
4205568 TTAATTTTAA
4205578 ATTTTTATGT-T
1 ATTTTTAT-TAT
4205589 ATTTTTATTAT
1 ATTTTTATTAT
*
4205600 ATTTATATTA-
1 ATTTTTATTAT
4205610 ATTTTTGTATTAT
1 A-TTTT-TATTAT
*
4205623 ATTTTAATTAT
1 ATTTTTATTAT
4205634 TTCTTAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 2 0.05
11 26 0.68
12 9 0.24
13 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (11 bp):
ATTTTTATTAT
Found at i:4209844 original size:28 final size:28
Alignment explanation
Indices: 4209804--4209860 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
4209794 CAATTAACCA
*
4209804 GACAAACGCGTTAGTGGGATTCAAATCT
1 GACAAACGCGTTAGTGGAATTCAAATCT
* *
4209832 GACAAACTCGTTAGTGTAATTCAAATCT
1 GACAAACGCGTTAGTGGAATTCAAATCT
4209860 G
1 G
4209861 TTCTTTATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (28 bp):
GACAAACGCGTTAGTGGAATTCAAATCT
Found at i:4214602 original size:19 final size:20
Alignment explanation
Indices: 4214578--4214637 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
4214568 TTATTAATTT
*
4214578 ATATATTTAAAT-TATGATA
1 ATATATTTAAATATATCATA
**
4214597 ATATATTTTTATATATCATA
1 ATATATTTAAATATATCATA
*
4214617 ATCATATTTAAA-ATATTATA
1 AT-ATATTTAAATATATCATA
4214637 A
1 A
4214638 ATTTTGATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 10 0.30
20 16 0.48
21 7 0.21
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (20 bp):
ATATATTTAAATATATCATA
Found at i:4216626 original size:18 final size:19
Alignment explanation
Indices: 4216584--4216628 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
4216574 TTTATTTAAA
4216584 TTTAATTATAAAATATATAT
1 TTTAA-TATAAAATATATAT
*
4216604 ATTAATATAAAATA-ATAT
1 TTTAATATAAAATATATAT
4216622 TTTAATA
1 TTTAATA
4216629 CTATAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 10 0.43
19 9 0.39
20 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAATATAAAATATATAT
Found at i:4217024 original size:32 final size:32
Alignment explanation
Indices: 4216983--4217057 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 32
4216973 CTGTAAAAAT
4216983 GCATTACTATTATTATTATTATTTTGTTCATA
1 GCATTACTATTATTATTATTATTTTGTTCATA
4217015 GCATTAC---TATTATTATTATTTTGTTCATA
1 GCATTACTATTATTATTATTATTTTGTTCATA
*
4217044 GCATTATTATTATT
1 GCATTACTATTATT
4217058 TGATTTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 28 0.72
32 11 0.28
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.56
Consensus pattern (32 bp):
GCATTACTATTATTATTATTATTTTGTTCATA
Found at i:4217035 original size:29 final size:29
Alignment explanation
Indices: 4216993--4217057 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
4216983 GCATTACTAT
4216993 TATTATTATTATTTTGTTCATAGCATTAC
1 TATTATTATTATTTTGTTCATAGCATTAC
*
4217022 TATTATTATTATTTTGTTCATAGCATTAT
1 TATTATTATTATTTTGTTCATAGCATTAC
4217051 TATTATT
1 TATTATT
4217058 TGATTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (29 bp):
TATTATTATTATTTTGTTCATAGCATTAC
Found at i:4217072 original size:7 final size:7
Alignment explanation
Indices: 4217060--4217086 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4217050 TTATTATTTG
4217060 ATTTAAA
1 ATTTAAA
4217067 ATTTAAA
1 ATTTAAA
4217074 ATTTAAA
1 ATTTAAA
4217081 ATTTAA
1 ATTTAA
4217087 GGTTTAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTTAAA
Found at i:4225207 original size:17 final size:16
Alignment explanation
Indices: 4225187--4225228 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4225177 ATTTATTAGA
4225187 TTATAAAAAC-ATTAATT
1 TTATAAAAACAATT--TT
*
4225204 TTATAAATACAATTTT
1 TTATAAAAACAATTTT
4225220 TTATAAAAA
1 TTATAAAAA
4225229 AGTTACTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 10 0.45
17 9 0.41
18 3 0.14
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (16 bp):
TTATAAAAACAATTTT
Found at i:4225578 original size:17 final size:17
Alignment explanation
Indices: 4225556--4225590 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4225546 AATATATATC
*
4225556 TTTTATTTTATATTTAA
1 TTTTATATTATATTTAA
*
4225573 TTTTATATTATTTTTAA
1 TTTTATATTATATTTAA
4225590 T
1 T
4225591 AATTTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATATTATATTTAA
Found at i:4225960 original size:17 final size:16
Alignment explanation
Indices: 4225909--4225963 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
4225899 ATACATGATT
4225909 TAAAATT-TATATAATA
1 TAAAATTATATA-AATA
4225925 -AAAATTAT-TAATATAA
1 TAAAATTATATAA-AT-A
4225941 TAAAATTAATATAAATA
1 TAAAATT-ATATAAATA
4225958 TAAAAT
1 TAAAAT
4225964 ACTTTAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
14 1 0.03
15 10 0.30
16 2 0.06
17 13 0.39
18 4 0.12
19 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAATTATATAAATA
Found at i:4226204 original size:14 final size:15
Alignment explanation
Indices: 4226178--4226221 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
4226168 TTAAGATAAA
4226178 AAAATTATAAATATT
1 AAAATTATAAATATT
4226193 AAAATT-TAAATATT
1 AAAATTATAAATATT
* *
4226207 ATACTTATTAAATAT
1 AAAATTA-TAAATAT
4226222 AATTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
16 7 0.28
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:4226718 original size:20 final size:21
Alignment explanation
Indices: 4226690--4226730 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
4226680 AAAAATTAAT
4226690 TTTTAAAATTTAAG-AAAAAA
1 TTTTAAAATTTAAGCAAAAAA
* *
4226710 TTTTCAAATTTTAGCAAAAAA
1 TTTTAAAATTTAAGCAAAAAA
4226731 AAACATAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (21 bp):
TTTTAAAATTTAAGCAAAAAA
Found at i:4227288 original size:50 final size:48
Alignment explanation
Indices: 4227162--4227342 Score: 126
Period size: 51 Copynumber: 3.7 Consensus size: 48
4227152 ATTATGCATA
*
4227162 AATTA-TTTTTATATTATATTTTAAATATTT-TATAAATA-T-CATATT
1 AATTATTTTTTAT-TTATATTTTAAATATTTATATAAATATTGTATATT
* ** *
4227207 TA-TATTTTTATATTTA-AAATAAAATAAATTTATATAAATTATTGTATATT
1 AATTATTTTT-TATTTATATTTTAAAT--ATTTATATAAA-TATTGTATATT
*
4227257 AATTATTTTTTATTTATATTTTAACATATTTATATATACGA-ATCGTAT-TT
1 AATTATTTTTTATTTATATTTTAA-ATATTTATATA-A--ATATTGTATATT
* * *
4227307 ATATTATTTTTTATTTTGTATTTTAATTTTTTATAT
1 A-ATTATTTTTTA-TTTATATTTTAAATATTTATAT
4227343 CTATCCATAT
Statistics
Matches: 107, Mismatches: 13, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
44 8 0.07
45 8 0.07
46 7 0.07
47 6 0.06
48 2 0.02
49 1 0.01
50 24 0.22
51 37 0.35
52 13 0.12
53 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (48 bp):
AATTATTTTTTATTTATATTTTAAATATTTATATAAATATTGTATATT
Found at i:4227466 original size:21 final size:21
Alignment explanation
Indices: 4227423--4227476 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
4227413 TTCAGATGGG
*
4227423 AAAAGAG-AGAAAGAAAGAAA
1 AAAAGAGAAAAAAGAAAGAAA
*
4227443 AAAGGAGGAAAAAAGAAA-AAA
1 AAAAGA-GAAAAAAGAAAGAAA
4227464 AAAAGAGAAAAAA
1 AAAAGAGAAAAAA
4227477 TTTTATGTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.41
21 9 0.31
22 8 0.28
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AAAAGAGAAAAAAGAAAGAAA
Found at i:4227474 original size:18 final size:19
Alignment explanation
Indices: 4227423--4227474 Score: 52
Period size: 22 Copynumber: 2.6 Consensus size: 19
4227413 TTCAGATGGG
4227423 AAAAGAGAGAAAGAAAGAAA
1 AAAAGAGA-AAAGAAAGAAA
*
4227443 AAAGGAGGAAAAAAGAAA-AAA
1 AAA--A-GAGAAAAGAAAGAAA
4227464 AAAAGAGAAAA
1 AAAAGAGAAAA
4227475 AATTTTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
18 6 0.22
19 1 0.04
20 3 0.11
21 6 0.22
22 8 0.30
23 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAAGAAAGAAA
Found at i:4227798 original size:12 final size:12
Alignment explanation
Indices: 4227783--4227818 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
4227773 AGAAATATGG
4227783 AAAGAAAAAAAA
1 AAAGAAAAAAAA
*
4227795 AAAGAAAAAAGA
1 AAAGAAAAAAAA
4227807 AAAGAAAGAAAA
1 AAAGAAA-AAAA
4227819 GGAGAGAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 18 0.86
13 3 0.14
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:4228403 original size:15 final size:14
Alignment explanation
Indices: 4228381--4228416 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
4228371 TTATTTGATT
4228381 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
4228395 AAAAGAAAGAAAAAG
1 AAAA-AAAGAAAAAG
4228410 AAAAAAA
1 AAAAAAA
4228417 TTTGTGCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:4228962 original size:15 final size:15
Alignment explanation
Indices: 4228916--4228962 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
4228906 ATACATATTA
*
4228916 TTTTTAAAT-AAATT
1 TTTTTAATTAAAATT
* *
4228930 TTATTAATTATAATT
1 TTTTTAATTAAAATT
4228945 TTTTTAATTAAAATT
1 TTTTTAATTAAAATT
4228960 TTT
1 TTT
4228963 ATAAATACCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 7 0.26
15 20 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTAATTAAAATT
Found at i:4229090 original size:15 final size:16
Alignment explanation
Indices: 4229070--4229106 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
4229060 ATTTAGTTAT
4229070 AAAAGAAAGAAA-AAA
1 AAAAGAAAGAAAGAAA
4229085 AAAAGAAAGAAAGAAA
1 AAAAGAAAGAAAGAAA
4229101 AAAAGA
1 AAAAGA
4229107 GAAAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAAGAAAGAAA
Found at i:4229195 original size:33 final size:33
Alignment explanation
Indices: 4229126--4229219 Score: 113
Period size: 35 Copynumber: 2.8 Consensus size: 33
4229116 TATAGATTCG
4229126 TATTTTTAT-TATTTTTTATATTTAAAATATTA
1 TATTTTTATATATTTTTTATATTTAAAATATTA
4229158 TATTTTTATATATTTTTTAATATATTAATAAT-TTA
1 TATTTTTATATATTTTTT-ATAT-TTAA-AATATTA
4229193 T-TTTATTATATATATATTTTATATTTA
1 TATTT-TTATATAT-T-TTTTATATTTA
4229220 TATAAATTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
32 9 0.16
33 8 0.15
34 7 0.13
35 19 0.35
36 8 0.15
37 4 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (33 bp):
TATTTTTATATATTTTTTATATTTAAAATATTA
Found at i:4229218 original size:27 final size:26
Alignment explanation
Indices: 4229152--4229220 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 26
4229142 TATATTTAAA
*
4229152 ATAT-TATATTTT-TATATATTTTTT
1 ATATATATATTTTATATTTATTTTTT
**
4229176 A-ATATAT-TAATA-ATTTATTTTATT
1 ATATATATATTTTATATTTATTTT-TT
4229200 ATATATATATTTTATATTTAT
1 ATATATATATTTTATATTTAT
4229221 ATAAATTCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
23 12 0.35
24 7 0.21
25 6 0.18
26 3 0.09
27 6 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
ATATATATATTTTATATTTATTTTTT
Found at i:4229223 original size:15 final size:16
Alignment explanation
Indices: 4229191--4229223 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4229181 ATTAATAATT
4229191 TATTTTATTATATATA
1 TATTTTATTATATATA
*
4229207 TATTTTA-TATTTATA
1 TATTTTATTATATATA
4229222 TA
1 TA
4229224 AATTCATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTTATTATATATA
Found at i:4229223 original size:21 final size:21
Alignment explanation
Indices: 4229164--4229223 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
4229154 ATTATATTTT
* *
4229164 TATATATTTTTTA-ATATAT-
1 TATATATTTTATATTTATATA
*
4229183 TA-ATAATTTAT-TTTATTATA
1 TATATATTTTATATTTA-TATA
4229203 TATATATTTTATATTTATATA
1 TATATATTTTATATTTATATA
4229224 AATTCATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 9 0.28
19 5 0.16
20 2 0.06
21 12 0.38
22 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATATTTTATATTTATATA
Found at i:4229586 original size:20 final size:21
Alignment explanation
Indices: 4229557--4229595 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4229547 GACTGAAAAA
4229557 AAAGAGAAAAAAAGAAAAATG
1 AAAGAGAAAAAAAGAAAAATG
*
4229578 AAAGA-AAAAAGAGAAAAA
1 AAAGAGAAAAAAAGAAAAA
4229596 AATTATGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (21 bp):
AAAGAGAAAAAAAGAAAAATG
Found at i:4229654 original size:25 final size:25
Alignment explanation
Indices: 4229617--4229690 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
4229607 TGTATTTGTG
*
4229617 TTTTTTTAAATATTATATTTTTATA
1 TTTTTTTACATATTATATTTTTATA
**
4229642 TTTTTTTACATATTA-ATAATT-TA
1 TTTTTTTACATATTATATTTTTATA
* *
4229665 TTTTTTT-CATGTATATTTTTTTATA
1 TTTTTTTACATAT-TATATTTTTATA
4229690 T
1 T
4229691 ATGCGTATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
22 4 0.10
23 11 0.28
24 7 0.18
25 17 0.44
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (25 bp):
TTTTTTTACATATTATATTTTTATA
Found at i:4230791 original size:16 final size:14
Alignment explanation
Indices: 4230759--4230808 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
4230749 ATTATTATTC
4230759 AAAAAATTTAAATA
1 AAAAAATTTAAATA
*
4230773 AAAAAAGTTTAGATGA
1 AAAAAA-TTTAAAT-A
*
4230789 AAAAAATATATAATA
1 AAAAAATTTA-AATA
4230804 AAAAA
1 AAAAA
4230809 TATAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 6 0.20
15 15 0.50
16 9 0.30
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (14 bp):
AAAAAATTTAAATA
Found at i:4231268 original size:22 final size:23
Alignment explanation
Indices: 4231243--4231286 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
4231233 AAAAAATATG
4231243 TATA-AAATAATAAAAAT-TTATC
1 TATATAAA-AATAAAAATGTTATC
*
4231265 TATATAAAAATAACAATGTTAT
1 TATATAAAAATAAAAATGTTAT
4231287 TTTATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (23 bp):
TATATAAAAATAAAAATGTTATC
Found at i:4232435 original size:19 final size:20
Alignment explanation
Indices: 4232408--4232445 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4232398 ATAAATATAA
*
4232408 ATATTTTAT-ATTAAATTTT
1 ATATATTATAATTAAATTTT
4232427 ATATATTATAATTAAATTT
1 ATATATTATAATTAAATTT
4232446 AAAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATATTATAATTAAATTTT
Found at i:4232475 original size:20 final size:19
Alignment explanation
Indices: 4232420--4232491 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 19
4232410 ATTTTATATT
*
4232420 AAATTTTATATATTATAATT
1 AAATTTTATATATTA-AATA
*
4232440 AAA-TTTA-A-AATAAATA
1 AAATTTTATATATTAAATA
4232456 AATATTTTATATATTAAATA
1 AA-ATTTTATATATTAAATA
*
4232476 AAAATTTA-A-ATTAAAT
1 AAATTTTATATATTAAAT
4232492 TATATTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
16 5 0.11
17 11 0.25
18 6 0.14
19 10 0.23
20 12 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTTTATATATTAAATA
Found at i:4232529 original size:11 final size:11
Alignment explanation
Indices: 4232477--4232536 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
4232467 TATTAAATAA
4232477 AAATTTAAATT
1 AAATTTAAATT
*
4232488 AAA-TTATATT
1 AAATTTAAATT
4232498 AAATTTTTAATATT
1 AAA--TTTAA-ATT
** *
4232512 ATTTTTAATTT
1 AAATTTAAATT
4232523 AAATTTAAATT
1 AAATTTAAATT
4232534 AAA
1 AAA
4232537 CTCAAAATCA
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
10 9 0.24
11 16 0.43
12 5 0.14
13 3 0.08
14 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AAATTTAAATT
Found at i:4233046 original size:20 final size:20
Alignment explanation
Indices: 4233001--4233047 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
4232991 ATTAAATTTT
*
4233001 AAATTA-TTTAAATGTATTA
1 AAATTATTTTAAATATATTA
4233020 AATATTATTTTAAATATA-TA
1 AA-ATTATTTTAAATATATTA
4233040 ATAATTAT
1 A-AATTAT
4233048 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.08
20 12 0.50
21 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AAATTATTTTAAATATATTA
Found at i:4233062 original size:52 final size:50
Alignment explanation
Indices: 4232966--4233062 Score: 113
Period size: 52 Copynumber: 1.9 Consensus size: 50
4232956 GTTTTAAAAA
* * **
4232966 ATTAAATATTTTTTATACAAATCATATTAAATTTTAAATTATTTAAATGT
1 ATTAAATATTTTTTAAACAAATAATATTAAATTTTAAAAAATTTAAATGT
* * *
4233016 ATTAAATATTATTTTAAATATATAATAATTATATTTTAAAAAATTTA
1 ATTAAATATT-TTTTAAACAAATAAT-ATTAAATTTTAAAAAATTTA
4233063 TTTTTATGTC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 10 0.26
51 11 0.29
52 17 0.45
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (50 bp):
ATTAAATATTTTTTAAACAAATAATATTAAATTTTAAAAAATTTAAATGT
Found at i:4233191 original size:10 final size:10
Alignment explanation
Indices: 4233176--4233209 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4233166 CCGCGTATAA
*
4233176 TCTCTCTCTC
1 TCTCTCCCTC
4233186 TCTCTCCCTC
1 TCTCTCCCTC
*
4233196 TCCCTCCCTC
1 TCTCTCCCTC
4233206 TCTC
1 TCTC
4233210 CCGACGGCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (10 bp):
TCTCTCCCTC
Found at i:4245049 original size:23 final size:23
Alignment explanation
Indices: 4244995--4245051 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
4244985 ATATAATTTA
* *
4244995 AAAAAATATATAATTTTTTAAATTT
1 AAAAAA-A-ATAATTTATTAAATGT
* *
4245020 AATAAAAATAATTTATTACATGT
1 AAAAAAAATAATTTATTAAATGT
4245043 AAAAAAAAT
1 AAAAAAAAT
4245052 TAAATGATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 21 0.78
24 1 0.04
25 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AAAAAAAATAATTTATTAAATGT
Found at i:4245580 original size:20 final size:23
Alignment explanation
Indices: 4245555--4245604 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 23
4245545 ATATAAATTA
4245555 TTATATA-TTAATA-ATTTAT-T
1 TTATATATTTAATATATTTATAT
4245575 TTATATATTTTAATATATTTATAT
1 TTATATA-TTTAATATATTTATAT
4245599 TTATAT
1 TTATAT
4245605 GTGAAATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.27
22 6 0.23
23 6 0.23
24 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATATATTTAATATATTTATAT
Found at i:4245580 original size:41 final size:41
Alignment explanation
Indices: 4245501--4245591 Score: 116
Period size: 41 Copynumber: 2.2 Consensus size: 41
4245491 CCTATGATGA
*
4245501 TTAATAT-AATTATTTTTATTATAATTTATTTAAATATATATT
1 TTAATATAAATTATTTATATTATAATTTATTT--ATATATATT
4245543 TT-ATATAAATTATTATATATTAATAATTTATTT-TATATATT
1 TTAATATAAATTATT-TATATT-ATAATTTATTTATATATATT
4245584 TTAATATA
1 TTAATATA
4245592 TTTATATTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
41 14 0.32
42 14 0.32
43 5 0.11
44 11 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (41 bp):
TTAATATAAATTATTTATATTATAATTTATTTATATATATT
Found at i:4245595 original size:18 final size:19
Alignment explanation
Indices: 4245535--4245598 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 19
4245525 TTTATTTAAA
*
4245535 TATATATTTTATATAAATTAT
1 TATATATTTTA-ATATATT-T
* *
4245556 TATATATTAATAATTTATTT
1 TATATATT-TTAATATATTT
4245576 TATATATTTTAATATA-TT
1 TATATATTTTAATATATTT
4245594 TATAT
1 TATAT
4245599 TTATATGTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
18 7 0.19
19 6 0.16
20 9 0.24
21 13 0.35
22 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATATTTTAATATATTT
Found at i:4246065 original size:2 final size:2
Alignment explanation
Indices: 4246060--4246086 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4246050 CACTCCACAT
4246060 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
4246087 GAGATTTTTA
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:4246498 original size:27 final size:27
Alignment explanation
Indices: 4246456--4246531 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
4246446 TAGTTGAATA
*
4246456 TAAAATATTTAT-ATTTATATAAATTT
1 TAAAATATTAATAATTTATATAAATTT
** * * *
4246482 TATTATATTAATAATTTAAATTATTTT
1 TAAAATATTAATAATTTATATAAATTT
*
4246509 TAAAATTTTAATAAATTTATATA
1 TAAAATATTAAT-AATTTATATA
4246532 TTTATATTAT
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
26 9 0.24
27 20 0.54
28 8 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TAAAATATTAATAATTTATATAAATTT
Found at i:4246543 original size:27 final size:25
Alignment explanation
Indices: 4246468--4246545 Score: 66
Period size: 27 Copynumber: 2.9 Consensus size: 25
4246458 AAATATTTAT
*
4246468 ATTTATATAAATTTTATTATATTAATA
1 ATTTATAT--ATTTTATTATTTTAATA
* **
4246495 ATTTAAATTATTTTTAAAATTTTAATAA
1 ATTTATA-TA-TTTTATTATTTTAAT-A
4246523 ATTTATATATTTATATTATTTTA
1 ATTTATATATTT-TATTATTTTA
4246546 TATTATATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
26 4 0.10
27 28 0.70
28 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTTATATATTTTATTATTTTAATA
Found at i:4246563 original size:11 final size:12
Alignment explanation
Indices: 4246525--4246564 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
4246515 TTTAATAAAT
4246525 TTATATATTTATA
1 TTATAT-TTTATA
4246538 -T-TATTTTATA
1 TTATATTTTATA
4246548 TTATATTTTA-A
1 TTATATTTTATA
4246559 TTATAT
1 TTATAT
4246565 AATTATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 6 0.24
11 11 0.44
12 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:4247023 original size:18 final size:18
Alignment explanation
Indices: 4247000--4247097 Score: 83
Period size: 18 Copynumber: 5.4 Consensus size: 18
4246990 AACAGTTGAA
*
4247000 TATATATACATCCATATT
1 TATATATACATACATATT
4247018 TATATATACATACATATAT
1 TATATATACATACATAT-T
* *
4247037 ACATATATATATACATA--
1 -TATATATACATACATATT
* * **
4247054 CATACATACATACATACA
1 TATATATACATACATATT
* *
4247072 TATATATACATACACATA
1 TATATATACATACATATT
4247090 TATATATA
1 TATATATA
4247098 TATATATGAT
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
16 14 0.21
18 38 0.57
19 1 0.01
20 14 0.21
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (18 bp):
TATATATACATACATATT
Found at i:4247025 original size:4 final size:4
Alignment explanation
Indices: 4246999--4247109 Score: 69
Period size: 4 Copynumber: 27.5 Consensus size: 4
4246989 AAACAGTTGA
* ** * * * *
4246999 ATAT ATAT ACAT CCAT ATTT ATAT ATAC ATAC ATAT ATAC ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * * * *
4247047 ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAT ACAT ACAC ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
4247095 ATAT ATAT ATGAT AT
1 ATAT ATAT AT-AT AT
4247110 CATTTATAGT
Statistics
Matches: 90, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
4 86 0.96
5 4 0.04
ACGTcount: A:0.48, C:0.14, G:0.01, T:0.38
Consensus pattern (4 bp):
ATAT
Found at i:4247038 original size:8 final size:8
Alignment explanation
Indices: 4247027--4247101 Score: 78
Period size: 8 Copynumber: 9.4 Consensus size: 8
4247017 TTATATATAC
4247027 ATACATAT
1 ATACATAT
4247035 ATACATAT
1 ATACATAT
* *
4247043 ATATATAC
1 ATACATAT
*
4247051 ATACATAC
1 ATACATAT
*
4247059 ATACATAC
1 ATACATAT
4247067 ATACATAT
1 ATACATAT
* *
4247075 ATATACAT
1 ATACATAT
*
4247083 ACACATAT
1 ATACATAT
*
4247091 ATATATAT
1 ATACATAT
4247099 ATA
1 ATA
4247102 TATGATATCA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 56 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.35
Consensus pattern (8 bp):
ATACATAT
Found at i:4247102 original size:12 final size:12
Alignment explanation
Indices: 4247018--4247109 Score: 94
Period size: 12 Copynumber: 7.6 Consensus size: 12
4247008 CATCCATATT
4247018 TATATATACATA
1 TATATATACATA
*
4247030 CATATATACATA
1 TATATATACATA
4247042 TATATATACATA
1 TATATATACATA
* *
4247054 CATACATACATA
1 TATATATACATA
* * *
4247066 CATACATATATA
1 TATATATACATA
* *
4247078 TACATACACATA
1 TATATATACATA
*
4247090 TATATATATATA
1 TATATATACATA
4247102 TATGATAT
1 TAT-ATAT
4247110 CATTTATAGT
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
12 62 0.94
13 4 0.06
ACGTcount: A:0.49, C:0.13, G:0.01, T:0.37
Consensus pattern (12 bp):
TATATATACATA
Found at i:4248740 original size:2 final size:2
Alignment explanation
Indices: 4248733--4248777 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4248723 AACTCCACAA
*
4248733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4248775 AT A
1 AT A
4248778 AAAGCTAGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4249138 original size:2 final size:2
Alignment explanation
Indices: 4249133--4249197 Score: 94
Period size: 2 Copynumber: 32.5 Consensus size: 2
4249123 TTCGTGTGTG
* *
4249133 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
4249175 CA TT TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
4249198 CATAAGACGG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4249739 original size:69 final size:69
Alignment explanation
Indices: 4249627--4249828 Score: 298
Period size: 69 Copynumber: 2.9 Consensus size: 69
4249617 ATTTAAGCCG
* * *
4249627 AATTTCTTCTTAATAATCCTTGAATTCATACTTAAGCATTGAAATATCATCTTATACATAAAAGA
1 AATTTCTTCTTAATAATCCTTGAATTCATACTTAAACATTGAAATATAATCTTATACATTAAAGA
4249692 GCAA
66 GCAA
* *
4249696 AATTTCTTCTTAATAATCCTTGAATTCATACTTAAATACTGAAATATAATCTTATACATTAAAGA
1 AATTTCTTCTTAATAATCCTTGAATTCATACTTAAACATTGAAATATAATCTTATACATTAAAGA
**
4249761 GCCG
66 GCAA
* * *
4249765 AATTTCTTCTCAATAAT-CTTGGAATTCTTACTTAAACATTGAAATAGAATCTTATACATTAAAG
1 AATTTCTTCTTAATAATCCTT-GAATTCATACTTAAACATTGAAATATAATCTTATACATTAAAG
4249829 CTTTTTTTTA
Statistics
Matches: 120, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
68 3 0.03
69 117 0.98
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (69 bp):
AATTTCTTCTTAATAATCCTTGAATTCATACTTAAACATTGAAATATAATCTTATACATTAAAGA
GCAA
Found at i:4254939 original size:2 final size:2
Alignment explanation
Indices: 4254932--4254956 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4254922 TAGTATTCAC
4254932 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4254957 GCAACTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4256422 original size:14 final size:15
Alignment explanation
Indices: 4256405--4256437 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4256395 ATTATACATG
*
4256405 TATTGTAATATT-TA
1 TATTATAATATTATA
4256419 TATTATAATATTATA
1 TATTATAATATTATA
4256434 TATT
1 TATT
4256438 TATTTTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TATTATAATATTATA
Found at i:4256479 original size:13 final size:14
Alignment explanation
Indices: 4256459--4256491 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
4256449 AATGCAAATT
4256459 ATATAATATATATA
1 ATATAATATATATA
4256473 A-ATAATATATATA
1 ATATAATATATATA
4256486 ATATAA
1 ATATAA
4256492 GTTAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATAATATATATA
Found at i:4258475 original size:32 final size:31
Alignment explanation
Indices: 4258424--4258500 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
4258414 ACAACTTTAT
4258424 TTTATATTTATATAAATTTTAAAATATTAATAA
1 TTTATA-TTATATAAATTTTAAAATATT-ATAA
* * * *
4258457 TTTATATTATATATATTTTAATATATTTTTA
1 TTTATATTATATAAATTTTAAAATATTATAA
4258488 TATTATATTATAT
1 T-TTATATTATAT
4258501 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 3 0.08
32 30 0.77
33 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTATATTATATAAATTTTAAAATATTATAA
Found at i:4258482 original size:12 final size:11
Alignment explanation
Indices: 4258463--4258541 Score: 55
Period size: 10 Copynumber: 7.6 Consensus size: 11
4258453 ATAATTTATA
4258463 TTATATATATT
1 TTATATATATT
4258474 TTA-ATATATT
1 TTATATATATT
*
4258484 TT-TATATTATA
1 TTATATA-TATT
4258495 TTATAT-T-TT
1 TTATATATATT
* *
4258504 TATTTTTATATT
1 T-TATATATATT
4258516 TTA-AT-TATT
1 TTATATATATT
*
4258525 TTTTATATA-T
1 TTATATATATT
4258535 TTATATA
1 TTATATA
4258542 ATATAATCTT
Statistics
Matches: 52, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
9 8 0.15
10 26 0.50
11 12 0.23
12 6 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATATATATT
Found at i:4258485 original size:42 final size:42
Alignment explanation
Indices: 4258447--4258545 Score: 99
Period size: 43 Copynumber: 2.2 Consensus size: 42
4258437 AAATTTTAAA
*
4258447 ATATTAATAATTTATATTATATATATTTTAATATATTTTTATATT
1 ATATT-AT-ATTTATATT-TATATATTTTAATATATTTTAATATT
* * *
4258492 ATATTATATTTTTATTTTTATATTTTAATTATTTTTTATATATTT
1 ATATTATATTTATATTTATATATTTTAA-TATATTTTA-ATA-TT
*
4258537 ATATAATAT
1 ATATTATAT
4258546 AATCTTATCG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
42 11 0.24
43 15 0.33
44 5 0.11
45 15 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (42 bp):
ATATTATATTTATATTTATATATTTTAATATATTTTAATATT
Found at i:4258491 original size:18 final size:18
Alignment explanation
Indices: 4258468--4258541 Score: 66
Period size: 18 Copynumber: 4.2 Consensus size: 18
4258458 TTATATTATA
4258468 TATATTTTAATATATTTT
1 TATATTTTAATATATTTT
* *
4258486 TATATTATATTATATTTT
1 TATATTTTAATATATTTT
4258504 TAT-TTTT-ATAT-TTTAAT
1 TATATTTTAATATATTT--T
* *
4258521 TAT-TTTTTATATATTTA
1 TATATTTTAATATATTTT
4258538 TATA
1 TATA
4258542 ATATAATCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
15 3 0.07
16 3 0.07
17 14 0.30
18 23 0.50
19 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATATTTTAATATATTTT
Done.