Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 93 of 199
Found at i:28528472 original size:15 final size:17
Alignment explanation
Indices: 28528452--28528483 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
28528442 TTTTTAGAAA
28528452 GATCTC-TTAT-TCATT
1 GATCTCATTATGTCATT
28528467 GATCTCATTATGTCATT
1 GATCTCATTATGTCATT
28528484 TTAGAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.22, C:0.19, G:0.09, T:0.50
Consensus pattern (17 bp):
GATCTCATTATGTCATT
Found at i:28531412 original size:17 final size:18
Alignment explanation
Indices: 28531377--28531412 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
28531367 TAAAAATCAC
28531377 TTAACAACACAAATTTAA
1 TTAACAACACAAATTTAA
*
28531395 TTAACAAC-CAAGTTTAA
1 TTAACAACACAAATTTAA
28531412 T
1 T
28531413 AATCTATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.31
Consensus pattern (18 bp):
TTAACAACACAAATTTAA
Found at i:28537939 original size:2 final size:2
Alignment explanation
Indices: 28537932--28537974 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28537922 TATAATAAGG
28537932 TA TA 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 TA TA
28537974 T
1 T
28537975 GCATATGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28538156 original size:11 final size:11
Alignment explanation
Indices: 28538140--28538177 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
28538130 TTTTAGACAT
*
28538140 AAAAAAAATTA
1 AAAAAAAATGA
28538151 AAAAAAAATGA
1 AAAAAAAATGA
*
28538162 AAAAAGAA-GA
1 AAAAAAAATGA
28538172 AAAAAA
1 AAAAAA
28538178 GTACACAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAAAATGA
Found at i:28541320 original size:32 final size:31
Alignment explanation
Indices: 28541229--28541322 Score: 111
Period size: 32 Copynumber: 3.1 Consensus size: 31
28541219 ATACATATTA
* *
28541229 CATTTTCATACCCTGT-ATCATTCACATTTG
1 CATTTTCATACCCTGTAATTATTCACATTTT
* **
28541259 C-TTATCATACCCTGTAATTGGTCACATTTT
1 CATTTTCATACCCTGTAATTATTCACATTTT
*
28541289 CATTTTTCATACCCTGTAATTATTCATATTTT
1 CA-TTTTCATACCCTGTAATTATTCACATTTT
28541321 CA
1 CA
28541323 CATTTCATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
29 13 0.25
30 12 0.23
32 27 0.52
ACGTcount: A:0.24, C:0.23, G:0.06, T:0.46
Consensus pattern (31 bp):
CATTTTCATACCCTGTAATTATTCACATTTT
Found at i:28541329 original size:32 final size:32
Alignment explanation
Indices: 28541263--28541330 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
28541253 CATTTGCTTA
* **
28541263 TCATACCCTGTAATTGGTCACATTTTCATTTT
1 TCATACCCTGTAATTAGTCACATTTTCACATT
* *
28541295 TCATACCCTGTAATTATTCATATTTTCACATT
1 TCATACCCTGTAATTAGTCACATTTTCACATT
28541327 TCAT
1 TCAT
28541331 TTATTCAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (32 bp):
TCATACCCTGTAATTAGTCACATTTTCACATT
Found at i:28544016 original size:17 final size:18
Alignment explanation
Indices: 28543994--28544033 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
28543984 CGATTAATTC
28543994 ATTAATTTAGA-AATTTA
1 ATTAATTTAGATAATTTA
* *
28544011 ATTAATTTATATGATTTA
1 ATTAATTTAGATAATTTA
28544029 ATTAA
1 ATTAA
28544034 ATAAATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTAATTTAGATAATTTA
Found at i:28548823 original size:20 final size:20
Alignment explanation
Indices: 28548798--28548836 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
28548788 TATAATATTT
28548798 GTAATAATTT-GTGTAATTAG
1 GTAAT-ATTTGGTGTAATTAG
28548818 GTAATATTTGGTGTAATTA
1 GTAATATTTGGTGTAATTA
28548837 AAGCCGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
GTAATATTTGGTGTAATTAG
Found at i:28548834 original size:29 final size:25
Alignment explanation
Indices: 28548770--28548835 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 25
28548760 ATCAGACAGT
*
28548770 TTTGTGTAATTTGTGTTATATAATA
1 TTTGTGTAATTTGTGTAATATAATA
*
28548795 TTTGTAATAATTTGTGTAATTAGGTAATA
1 TTTGT-GTAATTTGTGTAA-TA--TAATA
28548824 TTTGGTGTAATT
1 TTT-GTGTAATT
28548836 AAAGCCGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 5 0.15
26 11 0.33
27 2 0.06
29 13 0.39
30 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (25 bp):
TTTGTGTAATTTGTGTAATATAATA
Found at i:28557513 original size:63 final size:63
Alignment explanation
Indices: 28557430--28557676 Score: 284
Period size: 63 Copynumber: 3.9 Consensus size: 63
28557420 TACCTATTGA
** * * *
28557430 GAAGGTGTTGATGC-GTGGAATGATTGTGGGTGTTATGGTGCTTATGTAAAATAAACTGGTGCT
1 GAAGGTGTTGATGCAG-GGAATGATTGTGCATGTTGTGGTGCTTGTGTAAAATAAACTGGAGCT
* * * * * * *
28557493 AAATGTGCTGATGCAGGGAATAATTGTGCATGTTGTGGTGTTTTTGTAAAATAAACTAGAGCT
1 GAAGGTGTTGATGCAGGGAATGATTGTGCATGTTGTGGTGCTTGTGTAAAATAAACTGGAGCT
* * * * *
28557556 GAAGGTGTTGATACGGGGAATGTTATGTG--TGTTGTGGTGTTTGTGTAAAATAAACTGGAGTT
1 GAAGGTGTTGATGCAGGGAATGAT-TGTGCATGTTGTGGTGCTTGTGTAAAATAAACTGGAGCT
* *
28557618 GAAGGTGTTGATGCAAGGAATGATTGTGCATGTTGTGGTACTTGTGTAAAATAAACTGG
1 GAAGGTGTTGATGCAGGGAATGATTGTGCATGTTGTGGTGCTTGTGTAAAATAAACTGG
28557677 GTTAGCACAA
Statistics
Matches: 153, Mismatches: 27, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
61 4 0.03
62 50 0.33
63 94 0.61
64 5 0.03
ACGTcount: A:0.27, C:0.06, G:0.32, T:0.35
Consensus pattern (63 bp):
GAAGGTGTTGATGCAGGGAATGATTGTGCATGTTGTGGTGCTTGTGTAAAATAAACTGGAGCT
Found at i:28557638 original size:125 final size:126
Alignment explanation
Indices: 28557430--28557674 Score: 330
Period size: 125 Copynumber: 2.0 Consensus size: 126
28557420 TACCTATTGA
* * * *
28557430 GAAGGTGTTGATGCGTGGAATGATTGTGGGTGTTATGGTGCTTATGTAAAATAAACTGGTGCTAA
1 GAAGGTGTTGATACGGGGAATGATTATGGGTGTTATGGTGCTTATGTAAAATAAACTGGAGCTAA
* * ** *
28557495 ATGTGCTGATGCAGGGAATAATTGTGCATGTTGTGGTGTTTTTGTAAAATAAACTAGAGCT
66 AGGTGCTGATGCAAGGAATAATTGTGCATGTTGTGGTACTTGTGTAAAATAAACTAGAGCT
* * * * * *
28557556 GAAGGTGTTGATACGGGGAATG-TTATGTGTGTTGTGGTGTTTGTGTAAAATAAACTGGAGTTGA
1 GAAGGTGTTGATACGGGGAATGATTATGGGTGTTATGGTGCTTATGTAAAATAAACTGGAGCTAA
* *
28557620 AGGTGTTGATGCAAGGAATGATTGTGCATGTTGTGGTACTTGTGTAAAATAAACT
66 AGGTGCTGATGCAAGGAATAATTGTGCATGTTGTGGTACTTGTGTAAAATAAACT
28557675 GGGTTAGCAC
Statistics
Matches: 102, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
125 82 0.80
126 20 0.20
ACGTcount: A:0.27, C:0.06, G:0.32, T:0.35
Consensus pattern (126 bp):
GAAGGTGTTGATACGGGGAATGATTATGGGTGTTATGGTGCTTATGTAAAATAAACTGGAGCTAA
AGGTGCTGATGCAAGGAATAATTGTGCATGTTGTGGTACTTGTGTAAAATAAACTAGAGCT
Found at i:28561404 original size:11 final size:11
Alignment explanation
Indices: 28561376--28561416 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
28561366 GCTTAATCAA
28561376 ATTTTTTCTT-C
1 ATTTTTT-TTCC
28561387 ATATTTTTTTCC
1 AT-TTTTTTTCC
28561399 -TTTTTTTTCC
1 ATTTTTTTTCC
28561409 ATTTTTTT
1 ATTTTTTT
28561417 AAGAACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.33
11 12 0.44
12 6 0.22
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTTTTTTTCC
Found at i:28562343 original size:6 final size:6
Alignment explanation
Indices: 28562330--28562400 Score: 106
Period size: 6 Copynumber: 11.8 Consensus size: 6
28562320 AGTACAACTG
* * *
28562330 AAAATC AGAATC AGAATC AAAATC AAAATC AAAATT AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
*
28562378 AAAATT AAAATC AAAATC AAAAT
1 AAAATC AAAATC AAAATC AAAAT
28562401 AAATAAAACA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.65, C:0.13, G:0.03, T:0.20
Consensus pattern (6 bp):
AAAATC
Found at i:28563973 original size:14 final size:14
Alignment explanation
Indices: 28563944--28563972 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28563934 TAATAAAAGT
28563944 AATAATAATATAAA
1 AATAATAATATAAA
28563958 AATAATAA-ATAAA
1 AATAATAATATAAA
28563971 AA
1 AA
28563973 AGTGAAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAATAATATAAA
Found at i:28564489 original size:141 final size:141
Alignment explanation
Indices: 28564235--28564504 Score: 531
Period size: 141 Copynumber: 1.9 Consensus size: 141
28564225 CGAAGAGAAA
28564235 AGGAAGCCATGGGTGTGTATGTGGACTATGTTGGGCCATACGACCGTGTGAGTTGACTATGTTAC
1 AGGAAGCCATGGGTGTGTATGTGGACTATGTTGGGCCATACGACCGTGTGAGTTGACTATGTTAC
28564300 TCATTGTGCTCGTGTGGCCTATTTTAAAGTATTGCTCCACTGTTCACATGGCTTGTCACATGCCA
66 TCATTGTGCTCGTGTGGCCTATTTTAAAGTATTGCTCCACTGTTCACATGGCTTGTCACATGCCA
28564365 GAAAAGAAAGG
131 GAAAAGAAAGG
*
28564376 AGGAAGCCATGGGTGTGTATGTGGACTATGTTGGGCCATATGACCGTGTGAGTTGACTATGTTAC
1 AGGAAGCCATGGGTGTGTATGTGGACTATGTTGGGCCATACGACCGTGTGAGTTGACTATGTTAC
28564441 TCATTGTGCTCGTGTGGCCTATTTTAAAGTATTGCTCCACTGTTCACATGGCTTGTCACATGCC
66 TCATTGTGCTCGTGTGGCCTATTTTAAAGTATTGCTCCACTGTTCACATGGCTTGTCACATGCC
28564505 CATGTGTCTA
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 128 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.32
Consensus pattern (141 bp):
AGGAAGCCATGGGTGTGTATGTGGACTATGTTGGGCCATACGACCGTGTGAGTTGACTATGTTAC
TCATTGTGCTCGTGTGGCCTATTTTAAAGTATTGCTCCACTGTTCACATGGCTTGTCACATGCCA
GAAAAGAAAGG
Found at i:28568457 original size:52 final size:50
Alignment explanation
Indices: 28568391--28568513 Score: 151
Period size: 50 Copynumber: 2.4 Consensus size: 50
28568381 ATGAGCAAAT
*
28568391 GAGTTACTTAATGCATTACTTAATTTAATGATGCAAACTTTAACTAAAATGA
1 GAGTTACATAATGCATTACTTAATTT-ATGATGCAAAC-TTAACTAAAATGA
* * * *
28568443 GAGTTAGATAATGCATGT-CATAATTTATGATGCCAACTTAACTAACATGA
1 GAGTTACATAATGCAT-TACTTAATTTATGATGCAAACTTAACTAAAATGA
28568493 GAGTTACATAATG-ATTCACTT
1 GAGTTACATAATGCATT-ACTT
28568514 TATTAAATAC
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
48 1 0.02
49 2 0.03
50 26 0.43
51 10 0.16
52 21 0.34
53 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (50 bp):
GAGTTACATAATGCATTACTTAATTTATGATGCAAACTTAACTAAAATGA
Found at i:28574562 original size:23 final size:22
Alignment explanation
Indices: 28574524--28574573 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
28574514 GATTTTAAAA
*
28574524 ATTTAAATTATTTAGTGATAGT
1 ATTTAAATTATTTAGTGATAAT
*
28574546 ATTTAAGATTTTTTAGTGATAAT
1 ATTTAA-ATTATTTAGTGATAAT
28574569 ATTTA
1 ATTTA
28574574 GGAAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (22 bp):
ATTTAAATTATTTAGTGATAAT
Found at i:28575634 original size:28 final size:28
Alignment explanation
Indices: 28575580--28575635 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
28575570 TCGTAAAACC
**
28575580 AGCCTAATATTATAATTTTTTTTAAAAT
1 AGCCTAATATTATAATTTTTTAAAAAAT
28575608 AGCCTAAT-TTGATAATTTTTTAAAAAAT
1 AGCCTAATATT-ATAATTTTTTAAAAAAT
28575636 GACAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (28 bp):
AGCCTAATATTATAATTTTTTAAAAAAT
Found at i:28585450 original size:46 final size:46
Alignment explanation
Indices: 28585397--28585486 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
28585387 ACTCTATTTT
28585397 GATTCTTTTGAAAGTAATAGGAGTAATTTGAATACTTTAAAATAAA
1 GATTCTTTTGAAAGTAATAGGAGTAATTTGAATACTTTAAAATAAA
*
28585443 GATTCTTTTGAAAGTTATAGGAGTAATTTGAATACTTTAAAATA
1 GATTCTTTTGAAAGTAATAGGAGTAATTTGAATACTTTAAAATA
28585487 TTTTAGTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (46 bp):
GATTCTTTTGAAAGTAATAGGAGTAATTTGAATACTTTAAAATAAA
Found at i:28586037 original size:44 final size:44
Alignment explanation
Indices: 28585974--28586062 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
28585964 TTGAGGGGAG
28585974 TGTGTTGATGCTACAACTAAGGGGGAGTGTGCTAATGGTATTAT
1 TGTGTTGATGCTACAACTAAGGGGGAGTGTGCTAATGGTATTAT
28586018 TGTGTTGATGCTACAACTAAGGGGGAGTGTGCTAATGGTATTAT
1 TGTGTTGATGCTACAACTAAGGGGGAGTGTGCTAATGGTATTAT
28586062 T
1 T
28586063 AAGGGGGAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.25, C:0.09, G:0.31, T:0.35
Consensus pattern (44 bp):
TGTGTTGATGCTACAACTAAGGGGGAGTGTGCTAATGGTATTAT
Found at i:28588409 original size:39 final size:39
Alignment explanation
Indices: 28588257--28588401 Score: 139
Period size: 40 Copynumber: 3.6 Consensus size: 39
28588247 AGCGGCACTT
*
28588257 TTAGCGGCGTTTGGACAAAAAACGCCACTAAAAATCAAGCA
1 TTAGCGGCGTTT-TAC-AAAAACGCCACTAAAAATCAAGCA
* * * *
28588298 TTAGTGGCGCTTTTACAAAAACACCACTAAAGATCGAGCA
1 TTAGCGGCG-TTTTACAAAAACGCCACTAAAAATCAAGCA
* *** *
28588338 TTAGCGGCATATTTTGGAAAACGCCGCTAAAAAT-AAGCA
1 TTAGCGGCGT-TTTACAAAAACGCCACTAAAAATCAAGCA
*
28588377 TTAGCGGCGTTTTCCAAAAAGCGCC
1 TTAGCGGCGTTTTACAAAAA-CGCC
28588402 GCAAAAAACC
Statistics
Matches: 83, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
38 7 0.08
39 18 0.22
40 45 0.54
41 10 0.12
42 3 0.04
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (39 bp):
TTAGCGGCGTTTTACAAAAACGCCACTAAAAATCAAGCA
Found at i:28588512 original size:41 final size:41
Alignment explanation
Indices: 28588455--28588890 Score: 665
Period size: 41 Copynumber: 10.6 Consensus size: 41
28588445 GGTCTATAGT
28588455 GGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTACCTTTAGC
1 GGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTACCTTTAGC
* *
28588496 GGCGTTTTTGAAAAAGCACCGCTAATGTTCGTACCTTTAGC
1 GGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTACCTTTAGC
* * *
28588537 GGCATTTTTGAAAAAGCACCGTTAATGCTCGTACCTTTAGC
1 GGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTACCTTTAGC
* * *
28588578 GACGTTTTTGAAAAAGCACCGTTAATGCTCGTACCTTTAGC
1 GGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTACCTTTAGC
* *
28588619 GACGTTTTTGAAAAAGCGCCGCTAATGCTCATACCTTTAGC
1 GGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTACCTTTAGC
* **
28588660 GGTGTTTTTGAAAAAGCGCCGCTAATGCTATTACCTTTAGC
1 GGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTACCTTTAGC
* * *
28588701 GACGTTTTTGAAAAAGTGCCGCTAATGCTCATACCTTTAGC
1 GGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTACCTTTAGC
* *
28588742 TGCGTTTTTGAACAAGCGCCGCTAATGCTCGTACCTTTAGC
1 GGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTACCTTTAGC
* *
28588783 GGCGTTTTTGAAAAAGCGCCGCTAATGCTCATACCTTTAGT
1 GGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTACCTTTAGC
* * *
28588824 GGTGTTTTTGAAGAAGCGCCGCTACTGCTCGTACCTTTAGC
1 GGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTACCTTTAGC
28588865 GGCGTTTTTGAAAAAGCGCCGCTAAT
1 GGCGTTTTTGAAAAAGCGCCGCTAAT
28588891 AATAAAATCT
Statistics
Matches: 359, Mismatches: 36, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 359 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (41 bp):
GGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTACCTTTAGC
Found at i:28591844 original size:15 final size:15
Alignment explanation
Indices: 28591826--28591854 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28591816 AGCTTGTATT
28591826 ATTCAGGTAATCACG
1 ATTCAGGTAATCACG
28591841 ATTCAGGTAATCAC
1 ATTCAGGTAATCAC
28591855 TATAATGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (15 bp):
ATTCAGGTAATCACG
Found at i:28593768 original size:16 final size:16
Alignment explanation
Indices: 28593747--28593781 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28593737 TCAAAAGGTA
*
28593747 TTGCCTTTGTTATATT
1 TTGCCTTTGTTATAAT
28593763 TTGCCTTTGTTATAAT
1 TTGCCTTTGTTATAAT
28593779 TTG
1 TTG
28593782 TCAGTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.60
Consensus pattern (16 bp):
TTGCCTTTGTTATAAT
Found at i:28594796 original size:14 final size:14
Alignment explanation
Indices: 28594777--28594806 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
28594767 TGGATATTTC
28594777 TTGTCAGTTGCATT
1 TTGTCAGTTGCATT
28594791 TTGTCAGTTGCATT
1 TTGTCAGTTGCATT
28594805 TT
1 TT
28594807 CTGTTGTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.20, T:0.53
Consensus pattern (14 bp):
TTGTCAGTTGCATT
Found at i:28594947 original size:27 final size:26
Alignment explanation
Indices: 28594917--28594974 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
28594907 AATTTTGAGG
*
28594917 TTTATAATTTATAATTTTTATTAATT
1 TTTATAATTTATAACTTTTATTAATT
* * * *
28594943 ATTTACATTTTCTCACTTTTATTAATT
1 -TTTATAATTTATAACTTTTATTAATT
28594970 TTTAT
1 TTTAT
28594975 TATTATTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTATAATTTATAACTTTTATTAATT
Found at i:28595251 original size:43 final size:43
Alignment explanation
Indices: 28595181--28595288 Score: 137
Period size: 43 Copynumber: 2.5 Consensus size: 43
28595171 TTTTGGCGAG
* * * *
28595181 AAGCGCCGTTAAAGGTCACGTTCTTTAGCGGCATTTGT-GACAA
1 AAGCGCCGCTAAAGGTCATGGTATTTAGCGGCATTTGTGGA-AA
* *
28595224 AAGCACCGCTAAAGGTCATGGTATTTAGCGGCGTTTGTGGAAA
1 AAGCGCCGCTAAAGGTCATGGTATTTAGCGGCATTTGTGGAAA
*
28595267 AAGCGTCGCTAAAGGTCATGGT
1 AAGCGCCGCTAAAGGTCATGGT
28595289 CTATTTTGTG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 54 0.96
44 2 0.04
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.26
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCATGGTATTTAGCGGCATTTGTGGAAA
Found at i:28606037 original size:25 final size:26
Alignment explanation
Indices: 28605984--28606071 Score: 94
Period size: 25 Copynumber: 3.5 Consensus size: 26
28605974 GTACATGTAG
* *
28605984 GCTCATACGAGC-GATAAA-CGATAA
1 GCTCATACGAGCTGACAAATCGGTAA
* * *
28606008 GCTCATCCGAGCTGA-ATATTGGTAA
1 GCTCATACGAGCTGACAAATCGGTAA
*
28606033 GCTCATACAAGCT-ACAAATCGGTAA
1 GCTCATACGAGCTGACAAATCGGTAA
28606058 GCTCATACGAGCTG
1 GCTCATACGAGCTG
28606072 TGGTGAGTCC
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 14 0.27
25 37 0.73
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (26 bp):
GCTCATACGAGCTGACAAATCGGTAA
Found at i:28613602 original size:25 final size:25
Alignment explanation
Indices: 28613574--28613628 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
28613564 AAGCTTCTTG
*
28613574 GAGCTA-AATATCGGTAAGCTCATAT
1 GAGCTACAA-ATCGGTAAGCTCATAC
**
28613599 GAGCTACAAATTTGTAAGCTCATAC
1 GAGCTACAAATCGGTAAGCTCATAC
28613624 GAGCT
1 GAGCT
28613629 GTGGTGAGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (25 bp):
GAGCTACAAATCGGTAAGCTCATAC
Found at i:28615481 original size:27 final size:27
Alignment explanation
Indices: 28615451--28615568 Score: 114
Period size: 27 Copynumber: 4.4 Consensus size: 27
28615441 TCTTTCAAAC
28615451 AGGTGACTGGCAGACTGTCTCGCTAAT
1 AGGTGACTGGCAGACTGTCTCGCTAAT
* *
28615478 AGGTGACTGGC-GAATTGTCTCGCTAAC
1 AGGTGACTGGCAG-ACTGTCTCGCTAAT
** *
28615505 AGGTGACTGGCAGTTTGTCTCGCTAAA
1 AGGTGACTGGCAGACTGTCTCGCTAAT
* * * * *
28615532 AGATAACTGGCGGACTATCTCGCGAAT
1 AGGTGACTGGCAGACTGTCTCGCTAAT
28615559 AAGG-GACTGG
1 -AGGTGACTGG
28615569 TGGGTTGTCT
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
26 1 0.01
27 70 0.95
28 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (27 bp):
AGGTGACTGGCAGACTGTCTCGCTAAT
Found at i:28615553 original size:54 final size:54
Alignment explanation
Indices: 28615448--28615554 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
28615438 CTATCTTTCA
* * * * *
28615448 AACAGGTGACTGGCAGACTGTCTCGCTAATAGGTGACTGGCGAATTGTCTCGCT
1 AACAGGTGACTGGCAGACTGTCTCGCTAAAAGATAACTGGCGAACTATCTCGCT
** *
28615502 AACAGGTGACTGGCAGTTTGTCTCGCTAAAAGATAACTGGCGGACTATCTCGC
1 AACAGGTGACTGGCAGACTGTCTCGCTAAAAGATAACTGGCGAACTATCTCGC
28615555 GAATAAGGGA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (54 bp):
AACAGGTGACTGGCAGACTGTCTCGCTAAAAGATAACTGGCGAACTATCTCGCT
Found at i:28615567 original size:54 final size:54
Alignment explanation
Indices: 28615451--28615568 Score: 130
Period size: 54 Copynumber: 2.2 Consensus size: 54
28615441 TCTTTCAAAC
* * * * * * *
28615451 AGGTGACTGGCAGACTGTCTCGCTAATAGGTGACTGGCGAATTGTCTCGCTAAC
1 AGGTGACTGGCAGACTGTCTCGCTAAAAGATAACTGGCGAACTATCTCGCGAAA
** *
28615505 AGGTGACTGGCAGTTTGTCTCGCTAAAAGATAACTGGCGGACTATCTCGCGAATA
1 AGGTGACTGGCAGACTGTCTCGCTAAAAGATAACTGGCGAACTATCTCGCGAA-A
28615560 AGG-GACTGG
1 AGGTGACTGG
28615569 TGGGTTGTCT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 50 0.94
55 3 0.06
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (54 bp):
AGGTGACTGGCAGACTGTCTCGCTAAAAGATAACTGGCGAACTATCTCGCGAAA
Found at i:28626436 original size:51 final size:51
Alignment explanation
Indices: 28626380--28626507 Score: 150
Period size: 51 Copynumber: 2.5 Consensus size: 51
28626370 TTTTATGATT
* *
28626380 ATTATGAAATATGATTATTTAATTAAATAAT-AGAAAATTAAATATTTAAAA
1 ATTATGAAATATGATTATTTATTTAAATAATCA-AAAATTAAATAATTAAAA
* * ** * **
28626431 ATTATGAATTATGAATATTTATTTATTTAATCAAAAATTAATTAATTAATT
1 ATTATGAAATATGATTATTTATTTAAATAATCAAAAATTAAATAATTAAAA
*
28626482 ATTATGAAACATGATTATTTATTTAA
1 ATTATGAAATATGATTATTTATTTAA
28626508 TTTTATCCAC
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
51 62 0.98
52 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (51 bp):
ATTATGAAATATGATTATTTATTTAAATAATCAAAAATTAAATAATTAAAA
Found at i:28632931 original size:16 final size:16
Alignment explanation
Indices: 28632910--28632950 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
28632900 GAAGAACTTA
28632910 TTTTATAGAAAAGGTG
1 TTTTATAGAAAAGGTG
28632926 TTTTATAGAAAAGGTG
1 TTTTATAGAAAAGGTG
28632942 TTTTATAGA
1 TTTTATAGA
28632951 TTGTTAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (16 bp):
TTTTATAGAAAAGGTG
Found at i:28634229 original size:21 final size:21
Alignment explanation
Indices: 28634205--28634246 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28634195 ATTAACAAAC
28634205 AAACAAAAT-GATTTGGGGAAA
1 AAAC-AAATGGATTTGGGGAAA
*
28634226 AAACTAATGGATTTGGGGAAA
1 AAACAAATGGATTTGGGGAAA
28634247 TTGCAGCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.48, C:0.05, G:0.26, T:0.21
Consensus pattern (21 bp):
AAACAAATGGATTTGGGGAAA
Found at i:28634486 original size:82 final size:82
Alignment explanation
Indices: 28634412--28634572 Score: 200
Period size: 82 Copynumber: 2.0 Consensus size: 82
28634402 TACTTATATC
* * * ** *
28634412 AGCGTTTATGGGAAAAATGTCGTTATCGTTTTAACCCTTTGCGACGTTTATGCAAAAATGCCGTT
1 AGCGTTTATGAGAAAAACGCCACTATCATTTTAACCCTTTGCGACGTTTATGCAAAAATGCCGTT
28634477 ATTGCTTTACCTTTAAT
66 ATTGCTTTACCTTTAAT
* * * *
28634494 GGCGTTTATGAGAAAAACGCCACTATCATTTTAACCTTTTGCGGCGTTTATGCAAAAACT-CCAC
1 AGCGTTTATGAGAAAAACGCCACTATCATTTTAACCCTTTGCGACGTTTATGCAAAAA-TGCC-G
28634558 TT-TTGCTTTACCTTT
64 TTATTGCTTTACCTTT
28634573 TGCGGCGTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
82 64 0.96
83 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (82 bp):
AGCGTTTATGAGAAAAACGCCACTATCATTTTAACCCTTTGCGACGTTTATGCAAAAATGCCGTT
ATTGCTTTACCTTTAAT
Found at i:28634510 original size:41 final size:40
Alignment explanation
Indices: 28634413--28634591 Score: 107
Period size: 41 Copynumber: 4.4 Consensus size: 40
28634403 ACTTATATCA
* *
28634413 GCGTTTATGGGAAAAATGTCGTTATCGTTTTAACCCTTTGC
1 GCGTTTAT-GGAAAAATGCCGTTATCGCTTTAACCCTTTGC
* * *
28634454 GACGTTTATGCAAAAATGCCGTTATTGCTTT-ACCTTTAATG-
1 G-CGTTTATGGAAAAATGCCGTTATCGCTTTAACCCTT--TGC
* ** ** *
28634495 GCGTTTATGAGAAAAACGCCACTATCATTTTAACCTTTTGC
1 GCGTTTATG-GAAAAATGCCGTTATCGCTTTAACCCTTTGC
* * * *
28634536 GGCGTTTATGCAAAAACT-CCACTT-TTGCTTT-ACCTTTTGC
1 -GCGTTTATGGAAAAA-TGCC-GTTATCGCTTTAACCCTTTGC
28634576 GGCGTTTATGGAAAAA
1 -GCGTTTATGGAAAAA
28634592 ACGCCGCTTA
Statistics
Matches: 109, Mismatches: 20, Indels: 19
0.74 0.14 0.13
Matches are distributed among these distances:
40 39 0.36
41 45 0.41
42 25 0.23
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (40 bp):
GCGTTTATGGAAAAATGCCGTTATCGCTTTAACCCTTTGC
Found at i:28634577 original size:40 final size:40
Alignment explanation
Indices: 28634449--28634591 Score: 128
Period size: 40 Copynumber: 3.5 Consensus size: 40
28634439 GTTTTAACCC
* *
28634449 TTTGCGACGTTTATGCAAAAA-TGCC-GTTATTGCTTTACCT
1 TTTGCGGCGTTTATGCAAAAACT-CCACTT-TTGCTTTACCT
*** * * * ***
28634489 TTAATGGCGTTTATGAGAAAAACGCCACTATCATTTTAACCT
1 TTTGCGGCGTTTATG-CAAAAACTCCACTTTTGCTTT-ACCT
28634531 TTTGCGGCGTTTATGCAAAAACTCCACTTTTGCTTTACCT
1 TTTGCGGCGTTTATGCAAAAACTCCACTTTTGCTTTACCT
*
28634571 TTTGCGGCGTTTATGGAAAAA
1 TTTGCGGCGTTTATGCAAAAA
28634592 ACGCCGCTTA
Statistics
Matches: 78, Mismatches: 21, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
40 35 0.45
41 26 0.33
42 17 0.22
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (40 bp):
TTTGCGGCGTTTATGCAAAAACTCCACTTTTGCTTTACCT
Found at i:28634580 original size:82 final size:82
Alignment explanation
Indices: 28634435--28634596 Score: 213
Period size: 82 Copynumber: 2.0 Consensus size: 82
28634425 AAAATGTCGT
* * *
28634435 TATCGTTTTAACCCTTTGCGACGTTTATGCAAAAATGCCGTTATTGCTTTACCTTTAATGGCGTT
1 TATCATTTTAACCCTTTGCGACGTTTATGCAAAAATGCCCTTATTGCTTTACCTTTAACGGCGTT
28634500 TAT-GAGAAAAACGCCAC
66 TATGGA-AAAAACGCCAC
* * **
28634517 TATCATTTTAACCTTTTGCGGCGTTTATGCAAAAACT-CCACTT-TTGCTTTACCTTTTGCGGCG
1 TATCATTTTAACCCTTTGCGACGTTTATGCAAAAA-TGCC-CTTATTGCTTTACCTTTAACGGCG
28634580 TTTATGGAAAAAACGCC
64 TTTATGGAAAAAACGCC
28634597 GCTTACGCTG
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
82 65 0.93
83 5 0.07
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (82 bp):
TATCATTTTAACCCTTTGCGACGTTTATGCAAAAATGCCCTTATTGCTTTACCTTTAACGGCGTT
TATGGAAAAAACGCCAC
Found at i:28634592 original size:41 final size:40
Alignment explanation
Indices: 28634449--28634596 Score: 143
Period size: 41 Copynumber: 3.6 Consensus size: 40
28634439 GTTTTAACCC
* * * **
28634449 TTTGCGACGTTTATGCAAAAATGCCGTTATTGCTTTACCT
1 TTTGCGGCGTTTATGAAAAAACGCCACTATTGCTTTACCT
*** ***
28634489 TTAATGGCGTTTATGAGAAAAACGCCACTATCATTTTAACCT
1 TTTGCGGCGTTTATGA-AAAAACGCCACTATTGCTTT-ACCT
* * *
28634531 TTTGCGGCGTTTATGCAAAAACTCCACTTTTGCTTTACCT
1 TTTGCGGCGTTTATGAAAAAACGCCACTATTGCTTTACCT
28634571 TTTGCGGCGTTTATGGAAAAAACGCC
1 TTTGCGGCGTTTAT-GAAAAAACGCC
28634597 GCTTACGCTG
Statistics
Matches: 83, Mismatches: 22, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
40 29 0.35
41 38 0.46
42 16 0.19
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (40 bp):
TTTGCGGCGTTTATGAAAAAACGCCACTATTGCTTTACCT
Found at i:28636153 original size:61 final size:61
Alignment explanation
Indices: 28636073--28636221 Score: 208
Period size: 63 Copynumber: 2.4 Consensus size: 61
28636063 CTTGGTTAAT
* *
28636073 TGACGAAATTGTAAATTTTTTTTAGGTAACCGACTTAACTGAGAATTTTCAAATAATTCAA
1 TGACCAAATTGGAAATTTTTTTTAGGTAACCGACTTAACTGAGAATTTTCAAATAATTCAA
* * * *
28636134 TGACCAAATTGGAACTTTTTTTTTTAGTTAACTGACTTAACTGAGAATTTTCGAATAATTCAA
1 TGACCAAATTGGAA--ATTTTTTTTAGGTAACCGACTTAACTGAGAATTTTCAAATAATTCAA
* *
28636197 TGACCAAATTAGAAATTTGTTTTAG
1 TGACCAAATTGGAAATTTTTTTTAG
28636222 TTAAGTAACC
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
61 21 0.27
63 56 0.73
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (61 bp):
TGACCAAATTGGAAATTTTTTTTAGGTAACCGACTTAACTGAGAATTTTCAAATAATTCAA
Found at i:28636171 original size:63 final size:63
Alignment explanation
Indices: 28636088--28636206 Score: 211
Period size: 63 Copynumber: 1.9 Consensus size: 63
28636078 AAATTGTAAA
28636088 TTTTTTTTAGGTAACCGACTTAACTGAGAATTTTCAAATAATTCAATGACCAAATTGGAACTT
1 TTTTTTTTAGGTAACCGACTTAACTGAGAATTTTCAAATAATTCAATGACCAAATTGGAACTT
* * *
28636151 TTTTTTTTAGTTAACTGACTTAACTGAGAATTTTCGAATAATTCAATGACCAAATT
1 TTTTTTTTAGGTAACCGACTTAACTGAGAATTTTCAAATAATTCAATGACCAAATT
28636207 AGAAATTTGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (63 bp):
TTTTTTTTAGGTAACCGACTTAACTGAGAATTTTCAAATAATTCAATGACCAAATTGGAACTT
Found at i:28640518 original size:597 final size:597
Alignment explanation
Indices: 28639385--28640581 Score: 2394
Period size: 597 Copynumber: 2.0 Consensus size: 597
28639375 GATGGAGCAG
28639385 AGGACGCAATCGTATGACGAAGGACTATGATACGAGCACATGACCATGAACCTAGTGGAATGCAT
1 AGGACGCAATCGTATGACGAAGGACTATGATACGAGCACATGACCATGAACCTAGTGGAATGCAT
28639450 TAATTTCATATTGAAGGGGACGTGTCATTTGCCAGTAACCTCGATGATTAAGGAAACATATACTT
66 TAATTTCATATTGAAGGGGACGTGTCATTTGCCAGTAACCTCGATGATTAAGGAAACATATACTT
28639515 GACTAGTAGCCTTGTTTCTAAAAGTAAGCTAACACATACACGGGATAGATAAAGGGCAGTTACGT
131 GACTAGTAGCCTTGTTTCTAAAAGTAAGCTAACACATACACGGGATAGATAAAGGGCAGTTACGT
28639580 TTGGTAAGAGTCAATGCTGAAAGATATTAGGTAAAATGTAGAAACCGTGAACTCAATGACGTCAG
196 TTGGTAAGAGTCAATGCTGAAAGATATTAGGTAAAATGTAGAAACCGTGAACTCAATGACGTCAG
28639645 TGTGTCACTTGCAACCAAATTTAGTATTCCGGGTTAAGCAACCCTATAAACCCGACGAATGAGCT
261 TGTGTCACTTGCAACCAAATTTAGTATTCCGGGTTAAGCAACCCTATAAACCCGACGAATGAGCT
28639710 AACTGTGGAGTGTACTACATAGACTTGAGATGAATGACCTGCAACTATGGGAGATTTCAAGCACT
326 AACTGTGGAGTGTACTACATAGACTTGAGATGAATGACCTGCAACTATGGGAGATTTCAAGCACT
28639775 TCATTATCTATGAGCACATGCAATTATGGCATGTGCCTCAACACTTGTAAATTGCATGACCTATG
391 TCATTATCTATGAGCACATGCAATTATGGCATGTGCCTCAACACTTGTAAATTGCATGACCTATG
28639840 TTGACAAAGTTTACAAACTCAAATGCTTGTATAATGTTTGGAAATTTGAATTCCTACCTGTCTCA
456 TTGACAAAGTTTACAAACTCAAATGCTTGTATAATGTTTGGAAATTTGAATTCCTACCTGTCTCA
28639905 GATGAATAGATGTGGCCACCTACCACGCACATTTCTTTTAAGTTGGTATCAAATAAGAACTCGCG
521 GATGAATAGATGTGGCCACCTACCACGCACATTTCTTTTAAGTTGGTATCAAATAAGAACTCGCG
28639970 GTGTAAGACAAA
586 GTGTAAGACAAA
28639982 AGGACGCAATCGTATGACGAAGGACTATGATACGAGCACATGACCATGAACCTAGTGGAATGCAT
1 AGGACGCAATCGTATGACGAAGGACTATGATACGAGCACATGACCATGAACCTAGTGGAATGCAT
28640047 TAATTTCATATTGAAGGGGACGTGTCATTTGCCAGTAACCTCGATGATTAAGGAAACATATACTT
66 TAATTTCATATTGAAGGGGACGTGTCATTTGCCAGTAACCTCGATGATTAAGGAAACATATACTT
28640112 GACTAGTAGCCTTGTTTCTAAAAGTAAGCTAACACATACACGGGATAGATAAAGGGCAGTTACGT
131 GACTAGTAGCCTTGTTTCTAAAAGTAAGCTAACACATACACGGGATAGATAAAGGGCAGTTACGT
28640177 TTGGTAAGAGTCAATGCTGAAAGATATTAGGTAAAATGTAGAAACCGTGAACTCAATGACGTCAG
196 TTGGTAAGAGTCAATGCTGAAAGATATTAGGTAAAATGTAGAAACCGTGAACTCAATGACGTCAG
28640242 TGTGTCACTTGCAACCAAATTTAGTATTCCGGGTTAAGCAACCCTATAAACCCGACGAATGAGCT
261 TGTGTCACTTGCAACCAAATTTAGTATTCCGGGTTAAGCAACCCTATAAACCCGACGAATGAGCT
28640307 AACTGTGGAGTGTACTACATAGACTTGAGATGAATGACCTGCAACTATGGGAGATTTCAAGCACT
326 AACTGTGGAGTGTACTACATAGACTTGAGATGAATGACCTGCAACTATGGGAGATTTCAAGCACT
28640372 TCATTATCTATGAGCACATGCAATTATGGCATGTGCCTCAACACTTGTAAATTGCATGACCTATG
391 TCATTATCTATGAGCACATGCAATTATGGCATGTGCCTCAACACTTGTAAATTGCATGACCTATG
28640437 TTGACAAAGTTTACAAACTCAAATGCTTGTATAATGTTTGGAAATTTGAATTCCTACCTGTCTCA
456 TTGACAAAGTTTACAAACTCAAATGCTTGTATAATGTTTGGAAATTTGAATTCCTACCTGTCTCA
28640502 GATGAATAGATGTGGCCACCTACCACGCACATTTCTTTTAAGTTGGTATCAAATAAGAACTCGCG
521 GATGAATAGATGTGGCCACCTACCACGCACATTTCTTTTAAGTTGGTATCAAATAAGAACTCGCG
28640567 GTGTAAGACAAA
586 GTGTAAGACAAA
28640579 AGG
1 AGG
28640582 TCTATCAAAC
Statistics
Matches: 600, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
597 600 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (597 bp):
AGGACGCAATCGTATGACGAAGGACTATGATACGAGCACATGACCATGAACCTAGTGGAATGCAT
TAATTTCATATTGAAGGGGACGTGTCATTTGCCAGTAACCTCGATGATTAAGGAAACATATACTT
GACTAGTAGCCTTGTTTCTAAAAGTAAGCTAACACATACACGGGATAGATAAAGGGCAGTTACGT
TTGGTAAGAGTCAATGCTGAAAGATATTAGGTAAAATGTAGAAACCGTGAACTCAATGACGTCAG
TGTGTCACTTGCAACCAAATTTAGTATTCCGGGTTAAGCAACCCTATAAACCCGACGAATGAGCT
AACTGTGGAGTGTACTACATAGACTTGAGATGAATGACCTGCAACTATGGGAGATTTCAAGCACT
TCATTATCTATGAGCACATGCAATTATGGCATGTGCCTCAACACTTGTAAATTGCATGACCTATG
TTGACAAAGTTTACAAACTCAAATGCTTGTATAATGTTTGGAAATTTGAATTCCTACCTGTCTCA
GATGAATAGATGTGGCCACCTACCACGCACATTTCTTTTAAGTTGGTATCAAATAAGAACTCGCG
GTGTAAGACAAA
Found at i:28646613 original size:14 final size:14
Alignment explanation
Indices: 28646594--28646622 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28646584 AACGATTTAG
28646594 CTTGATTTAGAAGT
1 CTTGATTTAGAAGT
28646608 CTTGATTTAGAAGT
1 CTTGATTTAGAAGT
28646622 C
1 C
28646623 ATCGTGACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (14 bp):
CTTGATTTAGAAGT
Found at i:28648321 original size:33 final size:32
Alignment explanation
Indices: 28648262--28648336 Score: 91
Period size: 33 Copynumber: 2.4 Consensus size: 32
28648252 TTTAAATAAA
* * *
28648262 TTTT-AAA-ATTTCTTTTTAGTTTATTTTTAT
1 TTTTAAAATATTTCTCTTTAATTAATTTTTAT
*
28648292 TTATTAAATTATTTCTCTTTAATTAATTTTTAT
1 TT-TTAAAATATTTCTCTTTAATTAATTTTTAT
28648325 TTTTAAAATATT
1 TTTTAAAATATT
28648337 ATTGTTCATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 2 0.05
31 2 0.05
32 11 0.30
33 22 0.59
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (32 bp):
TTTTAAAATATTTCTCTTTAATTAATTTTTAT
Found at i:28649317 original size:15 final size:15
Alignment explanation
Indices: 28649297--28649326 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28649287 AATATTAAAT
28649297 AAAAATATTTTTTTA
1 AAAAATATTTTTTTA
28649312 AAAAATATTTTTTTA
1 AAAAATATTTTTTTA
28649327 TTTTTTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AAAAATATTTTTTTA
Found at i:28657443 original size:156 final size:153
Alignment explanation
Indices: 28657021--28657479 Score: 564
Period size: 157 Copynumber: 3.0 Consensus size: 153
28657011 GATTTTTTTT
* *
28657021 AAGAGAAAGTTTAGATTTTTAAAAAT-AAAA--T-TTTTTTTATTCATTTTAAAGGAAAGTTTAC
1 AAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTTAGTCATTTTAAAGGAAAGTTTAA
28657082 ATTTTTAAAATAAATTTTTGATTTTTTTTTCAACTATTTCGAAATAAAAGCTTTGATCTTTAAGA
66 ATTTTTAAAATAAA-TTTTGA--TTTTTTTCAACTATTTCGAAATAAAAGCTTTGAT-TTTAAGA
***
28657147 AAAATAGT-ATTTTTT--TTTAAAAAA
127 AAAATAGTGATTTTTTAAAGAAAAAAA
* * *
28657171 AAGTGAAAGTTTAGA-TTTTAAAAATTAATAATCTG-TTTCTTAGTCATTTTAAAGGAAAGTTTA
1 AAGAGAAAGTTTAGATTTTTAAAAA-TAAAAATCTGTTTTTTTAGTCATTTTAAAGGAAAGTTTA
* * *
28657234 AAATTTTAAAACAAATTTTTATTTCTTTTCAACTATTTCGAAATAAAAGCTTTGATATTTAAGAA
65 AATTTTTAAAATAAATTTTGATTT-TTTTCAACTATTTCGAAATAAAAGCTTTGAT-TTTAAGAA
*
28657299 AAGTAGTGATTTTTTAAAAGAAAAAAA
128 AAATAGTGATTTTTT-AAAGAAAAAAA
* * *
28657326 AAGAGAAAGTTTGGATTTTTAAAAATAAAAATCTGTTTTTTTAGTCATTTTAAATGAAAATTTTA
1 AAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTTAGTCATTTTAAA-GGAAAGTTTA
28657391 AATTTTTAAAATAAAGTTTTGATCTTTTTT-AACTATTTCGAAATAAAA-CTTTGATTTTAAAGA
65 AATTTTTAAAATAAA-TTTTGAT-TTTTTTCAACTATTTCGAAATAAAAGCTTTGATTTT-AAG-
28657454 AAAAATTA-TGATTTTTTTAAAGAAAA
126 AAAAA-TAGTGA-TTTTTTAAAGAAAA
28657480 CTTTGATTTT
Statistics
Matches: 267, Mismatches: 23, Indels: 31
0.83 0.07 0.10
Matches are distributed among these distances:
149 9 0.03
150 18 0.07
151 48 0.18
152 12 0.04
153 39 0.15
155 31 0.12
156 36 0.13
157 54 0.20
158 18 0.07
159 2 0.01
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (153 bp):
AAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTTAGTCATTTTAAAGGAAAGTTTAA
ATTTTTAAAATAAATTTTGATTTTTTTCAACTATTTCGAAATAAAAGCTTTGATTTTAAGAAAAA
TAGTGATTTTTTAAAGAAAAAAA
Found at i:28657479 original size:21 final size:22
Alignment explanation
Indices: 28657445--28657489 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
28657435 AAAACTTTGA
*
28657445 TTTTAAAGAAAAAATTATGATTT
1 TTTTAAAGAAAAACTT-TGATTT
28657468 TTTTAAAG-AAAACTTTGATTT
1 TTTTAAAGAAAAACTTTGATTT
28657489 T
1 T
28657490 GCAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 6 0.29
23 8 0.38
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (22 bp):
TTTTAAAGAAAAACTTTGATTT
Found at i:28658761 original size:3 final size:3
Alignment explanation
Indices: 28658753--28658782 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
28658743 AAGTCTTTTA
28658753 AAT AAT AAT AAT AATT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AA
28658783 AAGATCGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28658771 original size:13 final size:13
Alignment explanation
Indices: 28658755--28658780 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28658745 GTCTTTTAAA
28658755 TAATAATAATAAT
1 TAATAATAATAAT
28658768 TAATAATAATAAT
1 TAATAATAATAAT
28658781 AAAAGATCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:28660625 original size:23 final size:23
Alignment explanation
Indices: 28660598--28660695 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
28660588 ATTGTTATTG
*
28660598 ATCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28660621 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28660644 -TCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28660666 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28660689 ATCAGTG
1 ATCAGTG
28660696 TGGCACTTAT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
22 22 0.31
23 50 0.69
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:28660664 original size:45 final size:46
Alignment explanation
Indices: 28660598--28660695 Score: 171
Period size: 45 Copynumber: 2.2 Consensus size: 46
28660588 ATTGTTATTG
*
28660598 ATCAGTGGTAGCTTCGACTACATTTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGACTACATATCAGTGGTAGCTTCGGCTACAT
*
28660644 -TCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGACTACATATCAGTGGTAGCTTCGGCTACAT
28660689 ATCAGTG
1 ATCAGTG
28660696 TGGCACTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 43 0.88
46 6 0.12
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGACTACATATCAGTGGTAGCTTCGGCTACAT
Found at i:28668117 original size:23 final size:23
Alignment explanation
Indices: 28668090--28668187 Score: 180
Period size: 23 Copynumber: 4.3 Consensus size: 23
28668080 ATTGTTATTG
28668090 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28668113 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28668136 -TCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28668158 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28668181 ATCAGTG
1 ATCAGTG
28668188 TGGCACTTAT
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
22 22 0.30
23 51 0.70
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:28668155 original size:45 final size:46
Alignment explanation
Indices: 28668090--28668187 Score: 180
Period size: 45 Copynumber: 2.2 Consensus size: 46
28668080 ATTGTTATTG
*
28668090 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
28668136 -TCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
28668181 ATCAGTG
1 ATCAGTG
28668188 TGGCACTTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 44 0.88
46 6 0.12
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
Found at i:28670716 original size:14 final size:14
Alignment explanation
Indices: 28670683--28670743 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 14
28670673 AATACATAAA
28670683 TTTTCTCTCT-TTTT
1 TTTTCT-TCTATTTT
28670697 TGTTTCTTCTATTTT
1 T-TTTCTTCTATTTT
*
28670712 TTTTCATCTACTCTTT
1 TTTTCTTCTA-T-TTT
* *
28670728 TCTTCTTATATTTT
1 TTTTCTTCTATTTT
28670742 TT
1 TT
28670744 ACCAGAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
14 16 0.42
15 12 0.32
16 10 0.26
ACGTcount: A:0.08, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTTCTTCTATTTT
Found at i:28675339 original size:15 final size:16
Alignment explanation
Indices: 28675308--28675340 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
28675298 ACTTGTGTGA
*
28675308 TTAATATATGTTTTAG
1 TTAATATATGTTCTAG
28675324 TTAATA-ATGTTCTAG
1 TTAATATATGTTCTAG
28675339 TT
1 TT
28675341 CATGGTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (16 bp):
TTAATATATGTTCTAG
Found at i:28680429 original size:25 final size:26
Alignment explanation
Indices: 28680376--28680442 Score: 100
Period size: 25 Copynumber: 2.6 Consensus size: 26
28680366 CTCGGGCCGT
*
28680376 TAACACTAGCTTCAGATCAAGGTTGC
1 TAACACTAGCTTCAGATCAAGGTTAC
* *
28680402 TAACACTAGCTT-AGTTCAATGTTAC
1 TAACACTAGCTTCAGATCAAGGTTAC
28680427 TAACACTAGCTTCAGA
1 TAACACTAGCTTCAGA
28680443 GAATCCGCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
25 22 0.61
26 14 0.39
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (26 bp):
TAACACTAGCTTCAGATCAAGGTTAC
Found at i:28681469 original size:103 final size:103
Alignment explanation
Indices: 28681351--28681558 Score: 389
Period size: 103 Copynumber: 2.0 Consensus size: 103
28681341 AAAAATGAAA
*
28681351 ACAAAAGATAATAATGTTTTTTCTTATGTTTTAGTTTTATCCTTTTAACATATATTAATAATTTA
1 ACAAAAGATAATAATGTTTTTTCTTATGTTTTAGTTTTATCCATTTAACATATATTAATAATTTA
28681416 ATTAATATTTTCATATATAATTCACTCAAATCTAAGCC
66 ATTAATATTTTCATATATAATTCACTCAAATCTAAGCC
*
28681454 ACAAAAGATAATAATGTTTTTTCTTATGTTTTAGTTTTATCCATTTAACATGTATTAATAATTTA
1 ACAAAAGATAATAATGTTTTTTCTTATGTTTTAGTTTTATCCATTTAACATATATTAATAATTTA
*
28681519 ATTAATATTTTCATATATAGTTCACTCAAATCTAAGCC
66 ATTAATATTTTCATATATAATTCACTCAAATCTAAGCC
28681557 AC
1 AC
28681559 TCATCGACTA
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (103 bp):
ACAAAAGATAATAATGTTTTTTCTTATGTTTTAGTTTTATCCATTTAACATATATTAATAATTTA
ATTAATATTTTCATATATAATTCACTCAAATCTAAGCC
Found at i:28682458 original size:41 final size:41
Alignment explanation
Indices: 28682401--28682482 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
28682391 ACTTGTTCTT
28682401 GTGATGCCTTCATTGTATTTTCATAATGGAACTAGTCTATC
1 GTGATGCCTTCATTGTATTTTCATAATGGAACTAGTCTATC
*
28682442 GTGATGCCTTCTTTGTATTTTCATAATGGAACTAGTCTATC
1 GTGATGCCTTCATTGTATTTTCATAATGGAACTAGTCTATC
28682483 TTATCTTAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (41 bp):
GTGATGCCTTCATTGTATTTTCATAATGGAACTAGTCTATC
Found at i:28689589 original size:12 final size:12
Alignment explanation
Indices: 28689572--28689596 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28689562 ACTTAATCAC
28689572 TTTAATATTAAA
1 TTTAATATTAAA
28689584 TTTAATATTAAA
1 TTTAATATTAAA
28689596 T
1 T
28689597 CTTATTACAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:28691544 original size:17 final size:17
Alignment explanation
Indices: 28691522--28691560 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28691512 AAGTCTGATA
*
28691522 AAATAATTAAAATAAAT
1 AAATAACTAAAATAAAT
*
28691539 AAATAACTAAGATAAAT
1 AAATAACTAAAATAAAT
28691556 AAATA
1 AAATA
28691561 GAACAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATAACTAAAATAAAT
Found at i:28693681 original size:21 final size:20
Alignment explanation
Indices: 28693650--28693690 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
28693640 GACTAAAATA
*
28693650 ATAATTTTTAAAAAATAATT
1 ATAATTTTTAAAAAACAATT
*
28693670 ATAATATTTTAAGAAACAATT
1 ATAAT-TTTTAAAAAACAATT
28693691 CTAAGAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
ATAATTTTTAAAAAACAATT
Found at i:28695174 original size:7 final size:7
Alignment explanation
Indices: 28695159--28695190 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
28695149 GTGGGGGGAA
*
28695159 TTTTGTT
1 TTTTATT
28695166 TTTTATT
1 TTTTATT
28695173 TTTTATT
1 TTTTATT
28695180 TTTTATT
1 TTTTATT
28695187 TTTT
1 TTTT
28695191 TCCTATTCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:28709075 original size:23 final size:23
Alignment explanation
Indices: 28709049--28709092 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
28709039 AACTTTTGGT
*
28709049 CCAGTAGTAAAATTTGTAAAAGC
1 CCAGTAATAAAATTTGTAAAAGC
28709072 CCAGTAATAAAATTTGTAAAA
1 CCAGTAATAAAATTTGTAAAA
28709093 CACTTCCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (23 bp):
CCAGTAATAAAATTTGTAAAAGC
Found at i:28712811 original size:8 final size:8
Alignment explanation
Indices: 28712789--28712818 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
28712779 TACTTCAATT
28712789 TTATTTTA
1 TTATTTTA
28712797 TTTATTTTA
1 -TTATTTTA
28712806 TTATTTTA
1 TTATTTTA
28712814 TTATT
1 TTATT
28712819 CTATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTATTTTA
Found at i:28722479 original size:46 final size:45
Alignment explanation
Indices: 28722408--28722573 Score: 167
Period size: 46 Copynumber: 3.9 Consensus size: 45
28722398 AATAAATCAT
*
28722408 ACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAAA
1 ACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAG-AAAA
* *
28722454 ACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAG-ATA
1 ACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAAAA
* * *
28722498 ACGGATCTTG---TC---T-C---CGTGGAGTAGGTCGAAG-AAA
1 ACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAAAA
* *
28722532 ACAGATCGTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA
1 ACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGA
28722574 TAGTAGGTCC
Statistics
Matches: 96, Mismatches: 13, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
34 24 0.25
37 3 0.03
38 1 0.01
40 1 0.01
41 3 0.03
44 25 0.26
46 39 0.41
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (45 bp):
ACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAAAA
Found at i:28722544 original size:34 final size:34
Alignment explanation
Indices: 28722478--28722544 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
28722468 CATGTACTGG
* * *
28722478 CGTGAAGTAGATCAAAGATAACGGATCTTGTCTC
1 CGTGAAGTAGATCAAAGAAAACAGATCGTGTCTC
* * *
28722512 CGTGGAGTAGGTCGAAGAAAACAGATCGTGTCT
1 CGTGAAGTAGATCAAAGAAAACAGATCGTGTCT
28722545 TCATGTACTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.24
Consensus pattern (34 bp):
CGTGAAGTAGATCAAAGAAAACAGATCGTGTCTC
Found at i:28723078 original size:169 final size:170
Alignment explanation
Indices: 28722882--28723264 Score: 570
Period size: 169 Copynumber: 2.3 Consensus size: 170
28722872 TAGATCGAAT
*
28722882 ATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAACCAATCCAATCTCCTTGA
1 ATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGTAACCAATCCAATCTCCTTGA
*
28722947 AGTTACAACGGGGCGGATTAAAACCGCAAATCTCATCTCTCTGAAGTTGCAGTAGAGCAGATCGC
66 AGTTACAACGGAGCGGATTAAAACCGCAAATCTCATCTCTCTGAAGTTGCAGTAGAGCAGATCGC
* * *
28723012 ATC-AGATTTACCTTTAAGTTGTAGCATAACAAATCAAAG
131 ATCAAGATTTACCCTTAAATTGTAGCAGAACAAATCAAAG
* *
28723051 ATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGTAACCAATCCTATCTCCTTGA
1 ATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGTAACCAATCCAATCTCCTTGA
* * * * * *
28723116 AGTTGCGATGGAGTGGATTAAAATCGCAAATCTCATCTCTCTGAAGTTGCAGTAGAGCAGATTGC
66 AGTTACAACGGAGCGGATTAAAACCGCAAATCTCATCTCTCTGAAGTTGCAGTAGAGCAGATCGC
* * * **
28723181 GTCAAGATTTACCCTTAAATTGTAGCAGAACTAGTTGAAG
131 ATCAAGATTTACCCTTAAATTGTAGCAGAACAAATCAAAG
* * *
28723221 CTATAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAG
1 ATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG
28723265 ATAGCAACTT
Statistics
Matches: 191, Mismatches: 22, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
169 122 0.64
170 69 0.36
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (170 bp):
ATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGTAACCAATCCAATCTCCTTGA
AGTTACAACGGAGCGGATTAAAACCGCAAATCTCATCTCTCTGAAGTTGCAGTAGAGCAGATCGC
ATCAAGATTTACCCTTAAATTGTAGCAGAACAAATCAAAG
Found at i:28727636 original size:18 final size:18
Alignment explanation
Indices: 28727613--28727648 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28727603 ACAATAACAC
28727613 ATAGTGCACCATACGTGT
1 ATAGTGCACCATACGTGT
28727631 ATAGTGCACCATACGTGT
1 ATAGTGCACCATACGTGT
28727649 TTCATGTTGA
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:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (18 bp):
ATAGTGCACCATACGTGT
Found at i:28728270 original size:10 final size:9
Alignment explanation
Indices: 28728253--28728288 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
28728243 TACAAGTTAT
28728253 TTTTAATAA
1 TTTTAATAA
28728262 TTCTTAATAA
1 TT-TTAATAA
28728272 TTTTTAATAA
1 -TTTTAATAA
28728282 TTTTAAT
1 TTTTAAT
28728289 TGTTTATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.36
10 14 0.56
11 2 0.08
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTTAATAA
Found at i:28728276 original size:20 final size:19
Alignment explanation
Indices: 28728251--28728288 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
28728241 TCTACAAGTT
28728251 ATTTTTAATAATTCTTAATA
1 ATTTTTAATAATT-TTAATA
28728271 ATTTTTAATAATTTTAAT
1 ATTTTTAATAATTTTAAT
28728289 TGTTTATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTTAATAATTTTAATA
Found at i:28731596 original size:5 final size:5
Alignment explanation
Indices: 28731588--28731619 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
28731578 TTATAATGTT
28731588 AATAA AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AA
28731620 GATGATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:28732502 original size:26 final size:26
Alignment explanation
Indices: 28732464--28732532 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
28732454 CATTCTGACC
* * *
28732464 CACAACTCATGTGAGCAGGCCCATTT
1 CACAGCTCGTGTGAGCAGACCCATTT
*
28732490 CACAGCTCGTGTGAGCAGACTCATTT
1 CACAGCTCGTGTGAGCAGACCCATTT
*
28732516 CACAGCTTGTGTGAGCA
1 CACAGCTCGTGTGAGCA
28732533 ACCATGCATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCAGACCCATTT
Found at i:28737595 original size:13 final size:13
Alignment explanation
Indices: 28737577--28737631 Score: 65
Period size: 13 Copynumber: 3.9 Consensus size: 13
28737567 AAATTATCCA
28737577 ACCCAACCCAATT
1 ACCCAACCCAATT
*
28737590 ACCCAATCCAATT
1 ACCCAACCCAATT
28737603 ACCAACCCAACCCAATT
1 ----ACCCAACCCAATT
28737620 ACCCAACCCAAT
1 ACCCAACCCAAT
28737632 AAAACTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
13 24 0.67
17 12 0.33
ACGTcount: A:0.40, C:0.45, G:0.00, T:0.15
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:28737610 original size:30 final size:31
Alignment explanation
Indices: 28737568--28737631 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
28737558 TAATAAATAA
*
28737568 AATTATCCAACCCAACCCAATTACCCAATCC
1 AATTATCCAACCCAACCCAATTACCCAACCC
28737599 AATTA-CCAACCCAACCCAATTACCCAACCC
1 AATTATCCAACCCAACCCAATTACCCAACCC
28737629 AAT
1 AAT
28737632 AAAACTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.41, C:0.42, G:0.00, T:0.17
Consensus pattern (31 bp):
AATTATCCAACCCAACCCAATTACCCAACCC
Found at i:28737612 original size:17 final size:18
Alignment explanation
Indices: 28737590--28737631 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
28737580 CAACCCAATT
28737590 ACCCAATCCAATTA-CCA
1 ACCCAATCCAATTACCCA
*
28737607 ACCCAACCCAATTACCCA
1 ACCCAATCCAATTACCCA
28737625 ACCCAAT
1 ACCCAAT
28737632 AAAACTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.40, C:0.45, G:0.00, T:0.14
Consensus pattern (18 bp):
ACCCAATCCAATTACCCA
Found at i:28737670 original size:38 final size:39
Alignment explanation
Indices: 28737612--28737689 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
28737602 TACCAACCCA
*
28737612 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
28737651 ACCCAATTA-CCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
28737689 A
1 A
28737690 ACTCTTAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 29 0.76
39 9 0.24
ACGTcount: A:0.51, C:0.28, G:0.03, T:0.18
Consensus pattern (39 bp):
ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
Found at i:28737842 original size:17 final size:17
Alignment explanation
Indices: 28737822--28737884 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
28737812 TAATTTCAAG
28737822 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
28737839 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
28737857 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
28737876 AATTATGTA
1 AATTATGTA
28737885 GTGATTCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 18 0.53
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:28737846 original size:37 final size:37
Alignment explanation
Indices: 28737819--28737893 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
28737809 TGTTAATTTC
* *
28737819 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
* *
28737856 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
28737893 A
1 A
28737894 TTCGGGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
Found at i:28737906 original size:9 final size:9
Alignment explanation
Indices: 28737892--28737922 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28737882 GTAGTGATTC
*
28737892 AATTCGGGT
1 AATTCGGTT
28737901 AATTCGGTT
1 AATTCGGTT
28737910 AATTCGGTT
1 AATTCGGTT
28737919 AATT
1 AATT
28737923 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:28740873 original size:231 final size:231
Alignment explanation
Indices: 28740448--28740943 Score: 726
Period size: 231 Copynumber: 2.1 Consensus size: 231
28740438 ATTTAGGTTG
* * * * *
28740448 AACAAAAGTCCTGTAACAGTCACACTTGTATAACGTAATCATTTGTTTCTTGAATACTAAGTAGA
1 AACACAAGTCCTGTAGCAGTCACACTTGTATAGCATAATCATTTGATTCTTGAATACTAAGTAGA
28740513 CTAAGACAAACTAATGAGTCTTATATACCATATCAACTCATTTGAGCATGGTCATCCATTTATAG
66 CTAAGACAAACTAATGAGTCTTATATACCATATCAACTCATTTGAGCATGGTCATCCATTTATAG
*** * * *
28740578 TCTCACTTGATCAAAAAACCTGGGATATCACTCCTATTAAGTAGGAGAGACAAATCGAATCTTGA
131 TCTCACTTGATCAAAAAACCTAACATATCACTCCTATTAAATAGGAGAGAAAAATCCAATCTTGA
** * * *
28740643 TCGTTTATATAC-CACTACATAGATTGTGGCATACCT
196 TCAATCACAT-CTCACTACATAGATTGTGGCATACCC
*
28740679 AACACAAGTCCTGTAGTAGTCACACTTGTATAGCATAATCATTTGATTCTTGAATACTAAGTAGA
1 AACACAAGTCCTGTAGCAGTCACACTTGTATAGCATAATCATTTGATTCTTGAATACTAAGTAGA
* *
28740744 CTAAGACAAACTAATGAGTCTTATAT-CTCATATCAACTCATTTGAGCATGGTCATGCATTTCTA
66 CTAAGACAAACTAATGAGTCTTATATAC-CATATCAACTCATTTGAGCATGGTCATCCATTTATA
* * *
28740808 GTCTCACTTGATCAAAATACCTAACATATCACTCCTATTAAATAGGAGGGAAAAATCCTATCTTG
130 GTCTCACTTGATCAAAAAACCTAACATATCACTCCTATTAAATAGGAGAGAAAAATCCAATCTTG
*
28740873 ATCAATCACATCTCACTACATGGATTGTGGCATACCC
195 ATCAATCACATCTCACTACATAGATTGTGGCATACCC
** *
28740910 AACACAAGTCCCATAGCAGTCACACTTGGATAGC
1 AACACAAGTCCTGTAGCAGTCACACTTGTATAGC
28740944 CCTATAGAAC
Statistics
Matches: 236, Mismatches: 27, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
230 2 0.01
231 234 0.99
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (231 bp):
AACACAAGTCCTGTAGCAGTCACACTTGTATAGCATAATCATTTGATTCTTGAATACTAAGTAGA
CTAAGACAAACTAATGAGTCTTATATACCATATCAACTCATTTGAGCATGGTCATCCATTTATAG
TCTCACTTGATCAAAAAACCTAACATATCACTCCTATTAAATAGGAGAGAAAAATCCAATCTTGA
TCAATCACATCTCACTACATAGATTGTGGCATACCC
Found at i:28743498 original size:12 final size:12
Alignment explanation
Indices: 28743481--28743508 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28743471 CTAAAGAAAA
28743481 AAAATCCAAGTG
1 AAAATCCAAGTG
28743493 AAAATCCAAGTG
1 AAAATCCAAGTG
28743505 AAAA
1 AAAA
28743509 ACTCTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (12 bp):
AAAATCCAAGTG
Found at i:28763361 original size:21 final size:19
Alignment explanation
Indices: 28763320--28763366 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
28763310 TAAATAATGT
*
28763320 AAAAATTTTAAAGGTTAAA
1 AAAAATTTTAAAAGTTAAA
*
28763339 AAAAAGTTTATAAAAGTTCAA
1 AAAAA-TTT-TAAAAGTTAAA
28763360 AAAAATT
1 AAAAATT
28763367 AGCATGCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 5 0.21
21 14 0.58
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (19 bp):
AAAAATTTTAAAAGTTAAA
Found at i:28769293 original size:3 final size:3
Alignment explanation
Indices: 28769287--28769321 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28769277 AGTAGCAATT
28769287 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
28769322 TTGAAAGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:28769514 original size:12 final size:12
Alignment explanation
Indices: 28769497--28769522 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28769487 TAACAAGCAA
28769497 TAATAATAATAG
1 TAATAATAATAG
28769509 TAATAATAATAG
1 TAATAATAATAG
28769521 TA
1 TA
28769523 CCAACTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (12 bp):
TAATAATAATAG
Found at i:28771689 original size:43 final size:42
Alignment explanation
Indices: 28771625--28771751 Score: 161
Period size: 43 Copynumber: 3.0 Consensus size: 42
28771615 AGGATTTTTT
28771625 ATATGTGTTATCGTGTAAGACCACGTCTGGGACGTTGGCATCG
1 ATATGTGTTA-CGTGTAAGACCACGTCTGGGACGTTGGCATCG
*
28771668 ACT-TGTGTTTACGTGTAAGACC-CTGTCTAGGACAG-TGGCATCG
1 A-TATGTG-TTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCG
*
28771711 ATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 ATATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCAT
28771752 TGTACGAGTT
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
42 3 0.04
43 64 0.88
44 6 0.08
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (42 bp):
ATATGTGTTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
Found at i:28772420 original size:14 final size:15
Alignment explanation
Indices: 28772396--28772430 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
28772386 TACTTTAATC
28772396 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
28772411 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
28772426 ATGGT
1 ATGGT
28772431 AATGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:28772796 original size:21 final size:21
Alignment explanation
Indices: 28772772--28772812 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28772762 AAAAAATTGA
* *
28772772 ATATGTGCTATTCAATTTTGT
1 ATATATGCTATTAAATTTTGT
*
28772793 ATATATGCTGTTAAATTTTG
1 ATATATGCTATTAAATTTTG
28772813 ACGTATAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (21 bp):
ATATATGCTATTAAATTTTGT
Found at i:28772856 original size:47 final size:47
Alignment explanation
Indices: 28772794--28773183 Score: 628
Period size: 47 Copynumber: 8.4 Consensus size: 47
28772784 CAATTTTGTA
* *
28772794 TATATGCTGTTAAATTTTGACGTATAAATGCAGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
*
28772841 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATGTG
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
28772888 TATATGCTGTCAAATTTTGATGTAT-AATGCAGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
* *
28772934 TAAATGCTGTCAAATTTTGATGTATAAATGTAGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
28772981 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
28773028 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
* * *
28773075 TATATGCTGTCAAATTTTGATGTATAAGTGCAGTCCAATT-T-TGTA
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
* * * *
28773120 TATATGCTGTTAAATTTTGATGTATAAATGCAATCCAATT-T-TGTA
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
*
28773165 TATATGCTGTCCAATTTTG
1 TATATGCTGTCAAATTTTG
28773184 GTGAAAAAAA
Statistics
Matches: 326, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
45 61 0.19
46 45 0.14
47 220 0.67
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (47 bp):
TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
Found at i:28773121 original size:21 final size:21
Alignment explanation
Indices: 28772784--28773183 Score: 116
Period size: 24 Copynumber: 17.4 Consensus size: 21
28772774 ATGTGCTATT
* *
28772784 CAATTTTGTATATATGCTGTT
1 CAATTTTGTATATATGCAGTC
* *
28772805 AAATTTTGACGTATAAATGCAGTC
1 CAATTTT---GTATATATGCAGTC
* * *
28772829 CAATTATATATGTATATGCTGTC
1 CAATT-T-TGTATATATGCAGTC
* *
28772852 AAATTTTGATGTATAAATGCAGTC
1 CAA-TTT--TGTATATATGCAGTC
* *
28772876 CAATTATATGTGTATATGCTGTC
1 CAATT-T-TGTATATATGCAGTC
* *
28772899 AAATTTTGATGTATAATGCAGTC
1 CAATTTTG-TATAT-ATGCAGTC
* * * *
28772922 CAATTATATATGTAAATGCTGTC
1 CAATT-T-TGTATATATGCAGTC
* * *
28772945 AAATTTTGATGTATAAATGTAGTC
1 CAA-TTT--TGTATATATGCAGTC
* * *
28772969 CAATTATATATGTATATGCTGTC
1 CAATT-T-TGTATATATGCAGTC
* *
28772992 AAATTTTGATGTATAAATGCAGTC
1 CAA-TTT--TGTATATATGCAGTC
* * *
28773016 CAATTATATATGTATATGCTGTC
1 CAATT-T-TGTATATATGCAGTC
* *
28773039 AAATTTTGATGTATAAATGCAGTC
1 CAA-TTT--TGTATATATGCAGTC
* * *
28773063 CAATTATATATGTATATGCTGTC
1 CAATT-T-TGTATATATGCAGTC
* *
28773086 AAATTTTGATGTATAAGTGCAGTC
1 CAATTTTG-TATAT-A-TGCAGTC
* *
28773110 CAATTTTGTATATATGCTGTT
1 CAATTTTGTATATATGCAGTC
* * *
28773131 AAATTTTGATGTATAAATGCAATC
1 CAA-TTT--TGTATATATGCAGTC
*
28773155 CAATTTTGTATATATGCTGTC
1 CAATTTTGTATATATGCAGTC
28773176 CAATTTTG
1 CAATTTTG
28773184 GTGAAAAAAA
Statistics
Matches: 281, Mismatches: 71, Indels: 54
0.69 0.17 0.13
Matches are distributed among these distances:
21 36 0.13
22 16 0.06
23 112 0.40
24 114 0.41
25 2 0.01
26 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (21 bp):
CAATTTTGTATATATGCAGTC
Found at i:28773228 original size:23 final size:23
Alignment explanation
Indices: 28773202--28773253 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
28773192 AAATGTTGCT
*
28773202 CAAATTGTTGTATATATGCTGCC
1 CAAATTGCTGTATATATGCTGCC
*
28773225 CAAATTGCTGTATATATGCTGTC
1 CAAATTGCTGTATATATGCTGCC
28773248 CAAATT
1 CAAATT
28773254 TTGGTGTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (23 bp):
CAAATTGCTGTATATATGCTGCC
Found at i:28778898 original size:43 final size:43
Alignment explanation
Indices: 28778840--28778953 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
28778830 TGTGTTATTG
* * * *
28778840 TGTAAAACGACGTCTGGGACGTTGGCATCGACT-TGTGTTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGA-TATGTGATTACA
*
28778883 TGTAAGACC-CTGTCTGGGACAG-TGACATCGATATGTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGATTACA
28778926 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
28778954 TGTACGAGTT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
42 3 0.05
43 55 0.92
44 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACA
Found at i:28779999 original size:21 final size:21
Alignment explanation
Indices: 28779970--28780010 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28779960 AAAAAAGCGA
* *
28779970 ATATGTGCTGTTCAATTTTGT
1 ATATATGCTGTTAAATTTTGT
28779991 ATATATGCTGTTAAATTTTG
1 ATATATGCTGTTAAATTTTG
28780011 ATGTATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.51
Consensus pattern (21 bp):
ATATATGCTGTTAAATTTTGT
Found at i:28780306 original size:185 final size:185
Alignment explanation
Indices: 28779992--28780334 Score: 546
Period size: 185 Copynumber: 1.9 Consensus size: 185
28779982 CAATTTTGTA
* * * *
28779992 TATATGCTGTTAAATTTTGATGTATAAATTCAGTCCAATTATATATGTATATGCTGTCAAATTTT
1 TATATGCCGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATATATATGCTGTCAAATTTT
*
28780057 GATGTATAAATGCAGTCCAATTATATGTGTATATGCTGTCAAATTTTGATGTATAAATGCAGTCC
66 GATGTATAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGTATAAATGCAGTCC
*
28780122 AATTATATATGTATATGCTGTCAAATTTTGATGTATAATGCGGTCCAATTATATATG
131 AATT-T-TATATATATGCTGTCAAATTTTGATGTATAATGCGGTCCAATTATATATG
* *
28780179 TATATGCCGTCAAATTTTGATGTATAAATGCAGTCCAATT-T-TGTATATATGCTGTTAAATTTT
1 TATATGCCGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATATATATGCTGTCAAATTTT
* *
28780242 GATGTATAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGTTGTTTAAATGCAGTCC
66 GATGTATAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGTATAAATGCAGTCC
* *
28780307 AATTTTGTATATATGCTGTCCAATTTTG
131 AATTTTATATATATGCTGTCAAATTTTG
28780335 GTGAAAAAAA
Statistics
Matches: 144, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
183 20 0.14
184 1 0.01
185 85 0.59
186 1 0.01
187 37 0.26
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (185 bp):
TATATGCCGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATATATATGCTGTCAAATTTT
GATGTATAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGTATAAATGCAGTCC
AATTTTATATATATGCTGTCAAATTTTGATGTATAATGCGGTCCAATTATATATG
Found at i:28780347 original size:47 final size:47
Alignment explanation
Indices: 28779992--28780334 Score: 534
Period size: 47 Copynumber: 7.4 Consensus size: 47
28779982 CAATTTTGTA
* *
28779992 TATATGCTGTTAAATTTTGATGTATAAATTCAGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
*
28780039 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATGTG
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
28780086 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
*
28780133 TATATGCTGTCAAATTTTGATGTAT-AATGCGGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
* * *
28780179 TATATGCCGTCAAATTTTGATGTATAAATGCAGTCCAATT-T-TGTA
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
*
28780224 TATATGCTGTTAAATTTTGATGTATAAATGCAGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
* * * *
28780271 TATATGCTGTCAAATTTTGTTGTTTAAATGCAGTCCAATT-T-TGTA
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
*
28780316 TATATGCTGTCCAATTTTG
1 TATATGCTGTCAAATTTTG
28780335 GTGAAAAAAA
Statistics
Matches: 274, Mismatches: 19, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
45 60 0.22
46 47 0.17
47 167 0.61
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (47 bp):
TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATG
Found at i:28780366 original size:92 final size:90
Alignment explanation
Indices: 28779992--28780342 Score: 459
Period size: 92 Copynumber: 3.8 Consensus size: 90
28779982 CAATTTTGTA
* * * *
28779992 TATATGCTGTTAAATTTTGATGTATAAATTCAGTCCAATTATATATGTATATGCTGTCAAATTTT
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATT-T-TGTATATATGCTGTCAAATTTT
* *
28780057 GATGTATAAATGCAGTCCAATTATATGTG
64 GATG-AAAAATG-AGTCCAATTATATATG
* *
28780086 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTT
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATT-T-TGTATATATGCTGTCAAATTTT
* * *
28780151 GATGTATAATGCGGTCCAATTATATATG
64 GATGAAAAATG-AGTCCAATTATATATG
* *
28780179 TATATGCCGTCAAATTTTGATGTATAAATGCAGTCCAATTTTGTATATATGCTGTTAAATTTTGA
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTTTGTATATATGCTGTCAAATTTTGA
*
28780244 TGTATAAATGCAGTCCAATTATATATG
66 TG-AAAAATG-AGTCCAATTATATATG
* * * *
28780271 TATATGCTGTCAAATTTTGTTGTTTAAATGCAGTCCAATTTTGTATATATGCTGTCCAATTTTGG
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTTTGTATATATGCTGTCAAATTTTGA
28780336 TGAAAAA
66 TGAAAAA
28780343 AAATGTTGCT
Statistics
Matches: 234, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
91 27 0.12
92 82 0.35
93 58 0.25
94 67 0.29
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (90 bp):
TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTTTGTATATATGCTGTCAAATTTTGA
TGAAAAATGAGTCCAATTATATATG
Found at i:28780379 original size:23 final size:23
Alignment explanation
Indices: 28780353--28780404 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
28780343 AAATGTTGCT
*
28780353 CAAATTGTTGTATACATGCTGCC
1 CAAATTGCTGTATACATGCTGCC
* *
28780376 CAAATTGCTGTATATATGCTGTC
1 CAAATTGCTGTATACATGCTGCC
28780399 CAAATT
1 CAAATT
28780405 TTGGTGTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (23 bp):
CAAATTGCTGTATACATGCTGCC
Found at i:28780925 original size:44 final size:44
Alignment explanation
Indices: 28780857--28781427 Score: 306
Period size: 44 Copynumber: 12.8 Consensus size: 44
28780847 GGTGTTACAG
* *
28780857 CTTCAATCTGTTCCACTAG-TACTTCAGGGAGATAAGATTGGTAT
1 CTTCAATCTGCTCCACT-GCAACTTCAGGGAGATAAGATTGGTAT
* * * *
28780901 CTTCAACCTGCTCCACTGCAACTTCAGGGAGGTAAGGTTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA-GATTGGTAT
* * *
28780946 CTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGTTA-
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTAT
* * * **
28780990 CTTCAATCTGCTCTATTGCAACTTCAAGG-GATAAGATTCATCAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGT-AT
* * ** * *
28781034 -TTTAATCGGCTCCACTGCAACTTCATTGAAATAAAACTT-GTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTAT
* * *
28781077 CTTCAACCTGCTCCACTGCAACTTCAAGGAGATAGGACTT-G--T
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTAT
* * * * * *
28781119 CGT-GATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGGTAT
* * * *
28781163 CTTCAGTCTACTCCACTGCAACTTCAGGAAGATAAGACTTGTTATGGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTA---T
* * * * * * *
28781211 GGATTTAATC--CAACCTACTACAACTTCAGAGGTG-T-AGGTT-TTAT
1 --CTTCAATCTGC-TCC-ACTGCAACTTCAG-GGAGATAAGATTGGTAT
* * * * * *
28781255 CGTTTTAATCAGCTCCACTGCAATTTCAGGGAGATAGGATTAGTAG
1 C--TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTAT
* * *
28781301 CTTCAATCTGCCCCACTGCAGCTTCAGGGAGATAAGATTTGTAGCCTGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG--G--TAT
* * * * *
28781350 CTTCAATCTGCTCTATTGCAACTTCAAGGAGATAAGGTTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA-GATTGGTAT
* * * *
28781395 CTTCACTCTGCTCGACTACAACTTTAGGGAGAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGAT
28781428 GAGACTTGTC
Statistics
Matches: 398, Mismatches: 94, Indels: 69
0.71 0.17 0.12
Matches are distributed among these distances:
40 1 0.00
41 27 0.07
42 6 0.02
43 36 0.09
44 145 0.36
45 111 0.28
46 5 0.01
47 4 0.01
48 4 0.01
49 38 0.10
50 19 0.05
51 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTAT
Found at i:28781582 original size:50 final size:50
Alignment explanation
Indices: 28781473--28782034 Score: 536
Period size: 50 Copynumber: 11.2 Consensus size: 50
28781463 TAAGATTCAA
* * * * *
28781473 TAGCTTCTATCTATTCCACTACACCACCATGGAAGTAAGATTCGCTGTTG
1 TAGCTTCAATCTTTTCCACTACAACGCCAGGGAAGTAAGATTCGCTGTTG
* ** * * * * *
28781523 TAGCCTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTG
1 TAGCTTCAATCTTTTCCACTACAACGCCAGGGAAGTAAGATTCGCTGTTG
* * * *
28781573 TAGCTTCAATCTATTCCACTACACCGCCAAGGAAGTAAGATTCACTGTTG
1 TAGCTTCAATCTTTTCCACTACAACGCCAGGGAAGTAAGATTCGCTGTTG
* * ** * * * * * *
28781623 TTGCTTCAATATTTTTAACTGCAATGTCGGGGAAGAAAGATTTGCTGTTG
1 TAGCTTCAATCTTTTCCACTACAACGCCAGGGAAGTAAGATTCGCTGTTG
* *
28781673 TAGCTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATTCGCTGTTG
1 TAGCTTCAATCTTTTCCACTACAACGCCAGGGAAGTAAGATTCGCTGTTG
* * * * * *
28781723 TAGCTTCAATCTTTTCAACTACAATGTCGGGGAAGCAAGATTCGTTGTTG
1 TAGCTTCAATCTTTTCCACTACAACGCCAGGGAAGTAAGATTCGCTGTTG
* * * *
28781773 TAGCTTCAATCTATTCCACTACACCGCCAAGGAAGGAAGATTCGCTGTTG
1 TAGCTTCAATCTTTTCCACTACAACGCCAGGGAAGTAAGATTCGCTGTTG
* * * * * * *
28781823 TGGTTTCAATCTTTTCCACTGCAATGTC-GAGGAAGCAAGATTCGCTATTG
1 TAGCTTCAATCTTTTCCACTACAACGCCAG-GGAAGTAAGATTCGCTGTTG
* * * *
28781873 TAGCTTCAAT-TTGTTCCACTGCACCACCAGGGAAGTAAGATTCGTTG-TG
1 TAGCTTCAATCTT-TTCCACTACAACGCCAGGGAAGTAAGATTCGCTGTTG
** * * * *
28781922 TTAGCTTCAATCTTTTTAACTACAATGTCGGGGAAGCAAGATTCGCTGTTG
1 -TAGCTTCAATCTTTTCCACTACAACGCCAGGGAAGTAAGATTCGCTGTTG
* * * *
28781973 TAGCTTCAATCTGTTCCACTACACCGCCAAGGAAGTAAGATTCACTGTTG
1 TAGCTTCAATCTTTTCCACTACAACGCCAGGGAAGTAAGATTCGCTGTTG
28782023 TAGCTTCAATCT
1 TAGCTTCAATCT
28782035 ACAACACTTC
Statistics
Matches: 399, Mismatches: 107, Indels: 12
0.77 0.21 0.02
Matches are distributed among these distances:
49 4 0.01
50 390 0.98
51 5 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (50 bp):
TAGCTTCAATCTTTTCCACTACAACGCCAGGGAAGTAAGATTCGCTGTTG
Found at i:28781646 original size:100 final size:100
Alignment explanation
Indices: 28781473--28782034 Score: 847
Period size: 100 Copynumber: 5.6 Consensus size: 100
28781463 TAAGATTCAA
* * * *
28781473 TAGCTTCTATCTATTCCACTACACCACCATGGAAGTAAGATTCGCTGTTGTAGCCTCAATCTTTT
1 TAGCTTCAATCTATTCCACTACACCGCCAAGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTT
28781538 TAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTG
66 TAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTG
* * *
28781573 TAGCTTCAATCTATTCCACTACACCGCCAAGGAAGTAAGATTCACTGTTGTTGCTTCAATATTTT
1 TAGCTTCAATCTATTCCACTACACCGCCAAGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTT
* *
28781638 TAACTGCAATGTCGGGGAAGAAAGATTTGCTGTTG
66 TAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTG
*
28781673 TAGCTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTT
1 TAGCTTCAATCTATTCCACTACACCGCCAAGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTT
* * *
28781738 CAACTACAATGTCGGGGAAGCAAGATTCGTTGTTG
66 TAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTG
* * *
28781773 TAGCTTCAATCTATTCCACTACACCGCCAAGGAAGGAAGATTCGCTGTTGTGGTTTCAATCTTTT
1 TAGCTTCAATCTATTCCACTACACCGCCAAGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTT
** * *
28781838 CCACTGCAATGTCGAGGAAGCAAGATTCGCTATTG
66 TAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTG
* * * * * *
28781873 TAGCTTCAATTTGTTCCACTGCACCACCAGGGAAGTAAGATTCGTTG-TGTTAGCTTCAATCTTT
1 TAGCTTCAATCTATTCCACTACACCGCCAAGGAAGTAAGATTCGCTGTTG-TAGCTTCAATCTTT
*
28781937 TTAACTACAATGTCGGGGAAGCAAGATTCGCTGTTG
65 TTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTG
* *
28781973 TAGCTTCAATCTGTTCCACTACACCGCCAAGGAAGTAAGATTCACTGTTGTAGCTTCAATCT
1 TAGCTTCAATCTATTCCACTACACCGCCAAGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT
28782035 ACAACACTTC
Statistics
Matches: 413, Mismatches: 47, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
99 2 0.00
100 409 0.99
101 2 0.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (100 bp):
TAGCTTCAATCTATTCCACTACACCGCCAAGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTT
TAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTG
Found at i:28784078 original size:44 final size:44
Alignment explanation
Indices: 28784010--28784129 Score: 159
Period size: 51 Copynumber: 2.6 Consensus size: 44
28784000 TTTGAGTACT
* *
28784010 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTA
1 TCTGATCAGTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTA
28784054 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGAC-------AAGTGGTAGCTTTAGCTACACTTA
28784105 TCTGATCAGTGACAAGTGACAAGTG
1 TCTGATCAGTGACAAGTGACAAGTG
28784130 ATAAGTGATA
Statistics
Matches: 67, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
44 24 0.36
51 43 0.64
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTA
Found at i:28784093 original size:51 final size:50
Alignment explanation
Indices: 28784017--28784243 Score: 319
Period size: 50 Copynumber: 4.4 Consensus size: 50
28784007 ACTTCTGATC
*
28784017 AGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
28784068 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
28784119 AGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
1 AGTGAC-------AAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
* *
28784176 AGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
* * *
28784226 AGAGATAAATGATAAGTG
1 AGTGACAAGTGATAAGTG
28784244 ATTTCGTGTA
Statistics
Matches: 164, Mismatches: 5, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
50 59 0.36
51 56 0.34
57 32 0.20
58 17 0.10
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Found at i:28791846 original size:13 final size:13
Alignment explanation
Indices: 28791828--28791852 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28791818 GAATTCAAAA
28791828 TCAGCTAGCTAAC
1 TCAGCTAGCTAAC
28791841 TCAGCTAGCTAA
1 TCAGCTAGCTAA
28791853 ATTTAGACGT
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:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (13 bp):
TCAGCTAGCTAAC
Found at i:28793378 original size:17 final size:17
Alignment explanation
Indices: 28793349--28793390 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
28793339 TGAAGAGAAG
28793349 TAAAAAAAATTCG-AT-
1 TAAAAAAAATTCGAATA
28793364 TAAAAAAATATTTCGAATA
1 TAAAAAAA-A-TTCGAATA
28793383 TAAAAAAA
1 TAAAAAAA
28793391 GGGAAGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.35
16 1 0.04
17 4 0.17
18 2 0.09
19 8 0.35
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (17 bp):
TAAAAAAAATTCGAATA
Found at i:28793783 original size:26 final size:22
Alignment explanation
Indices: 28793735--28793778 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28793725 TGAAACACGA
28793735 GAGGAGTGTCATTTTTTTCTTT
1 GAGGAGTGTCATTTTTTTCTTT
28793757 GAGGAGTGTCATTTTTTTCTTT
1 GAGGAGTGTCATTTTTTTCTTT
28793779 CTTTGTGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.09, G:0.23, T:0.55
Consensus pattern (22 bp):
GAGGAGTGTCATTTTTTTCTTT
Found at i:28796767 original size:13 final size:13
Alignment explanation
Indices: 28796749--28796773 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28796739 GAATTCAAAA
28796749 TCAGCTAGCTAAC
1 TCAGCTAGCTAAC
28796762 TCAGCTAGCTAA
1 TCAGCTAGCTAA
28796774 ATTTAGACGT
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:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (13 bp):
TCAGCTAGCTAAC
Found at i:28798032 original size:17 final size:17
Alignment explanation
Indices: 28798003--28798035 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28797993 TAGGCAGTAG
28798003 AAGAAAAGTAAGAGAAA
1 AAGAAAAGTAAGAGAAA
28798020 AAGAAGAAG-AAGAGAA
1 AAGAA-AAGTAAGAGAA
28798036 GGAATGGAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (17 bp):
AAGAAAAGTAAGAGAAA
Found at i:28798698 original size:33 final size:33
Alignment explanation
Indices: 28798651--28798728 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
28798641 AACCGATTTT
* * *
28798651 CTTTTCTTCTCCTTAATCTCAATCGATCCTTTC
1 CTTTTTTTCCCCTTAATCTCAATCCATCCTTTC
*
28798684 CTTTTTTTCCCCTTAATCTCAATCCATCTTTTC
1 CTTTTTTTCCCCTTAATCTCAATCCATCCTTTC
*
28798717 TTTTCTTTTCCC
1 CTTT-TTTTCCC
28798729 TAAACCCGTC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 32 0.82
34 7 0.18
ACGTcount: A:0.13, C:0.33, G:0.01, T:0.53
Consensus pattern (33 bp):
CTTTTTTTCCCCTTAATCTCAATCCATCCTTTC
Found at i:28798810 original size:21 final size:21
Alignment explanation
Indices: 28798777--28798816 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28798767 CAACGTGGCA
*
28798777 AGTTAACTAGCCACGTCACTT
1 AGTTAACCAGCCACGTCACTT
* *
28798798 AGTTAACCGGCCATGTCAC
1 AGTTAACCAGCCACGTCAC
28798817 CTGTCCCGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (21 bp):
AGTTAACCAGCCACGTCACTT
Found at i:28798912 original size:20 final size:20
Alignment explanation
Indices: 28798883--28798929 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
28798873 CGATAACGTT
*
28798883 AGTGACTGGGTTGAAAGTTG
1 AGTGATTGGGTTGAAAGTTG
28798903 AGTGATTGGGTTGAAAGTTG
1 AGTGATTGGGTTGAAAGTTG
28798923 AGTGATT
1 AGTGATT
28798930 ATTTTGTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.02, G:0.38, T:0.34
Consensus pattern (20 bp):
AGTGATTGGGTTGAAAGTTG
Found at i:28804639 original size:21 final size:21
Alignment explanation
Indices: 28804615--28804654 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28804605 AATAAACATT
28804615 CTCA-ATTTCAATTCTAAATAA
1 CTCATATTTC-ATTCTAAATAA
*
28804636 CTCATTTTTCATTCTAAAT
1 CTCATATTTCATTCTAAAT
28804655 GTCTTCTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (21 bp):
CTCATATTTCATTCTAAATAA
Found at i:28816379 original size:39 final size:39
Alignment explanation
Indices: 28816325--28816406 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
28816315 TGGAATGTGT
28816325 GTGTCTCGGGTCTCCATCTTTCCACCAACGCGCTGATAA
1 GTGTCTCGGGTCTCCATCTTTCCACCAACGCGCTGATAA
28816364 GTGTCTCGGGTCTCCATCTTTCCACCAACGCGCTGATAA
1 GTGTCTCGGGTCTCCATCTTTCCACCAACGCGCTGATAA
28816403 GTGT
1 GTGT
28816407 AGGAACCAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.17, C:0.32, G:0.22, T:0.29
Consensus pattern (39 bp):
GTGTCTCGGGTCTCCATCTTTCCACCAACGCGCTGATAA
Found at i:28820125 original size:24 final size:24
Alignment explanation
Indices: 28820089--28820151 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
28820079 ATGGCGTAGG
* *
28820089 ATCTGATTTTGTATTTGATCATAC
1 ATCTGATTCTGTATCTGATCATAC
* * *
28820113 ATCTGGTTCTGTATCTGATTATGC
1 ATCTGATTCTGTATCTGATCATAC
*
28820137 ATCT-ATCCTGTATCT
1 ATCTGATTCTGTATCT
28820152 AGTTATGGAC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 9 0.28
24 23 0.72
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (24 bp):
ATCTGATTCTGTATCTGATCATAC
Found at i:28821852 original size:74 final size:74
Alignment explanation
Indices: 28821731--28821910 Score: 315
Period size: 74 Copynumber: 2.4 Consensus size: 74
28821721 AAAAATTCAT
* *
28821731 CGTTCTCAATGGCTGGCGGTGATTCTACTTCTAAACCATCACCACCTAAAATTGAATGTTGAAAC
1 CGTTCTTAATGGCTGGTGGTGATTCTACTTCTAAACCATCACCACCTAAAATTGAATGTTGAAAC
28821796 TATCACCAC
66 TATCACCAC
*
28821805 CGTTCTTAATGGCTGGTGGCGATTCTACTTCTAAACCATCACCACCTAAAATTGAATGTTGAAAC
1 CGTTCTTAATGGCTGGTGGTGATTCTACTTCTAAACCATCACCACCTAAAATTGAATGTTGAAAC
*
28821870 TATCACCAT
66 TATCACCAC
*
28821879 CGTTCTTAATGGCTGGTAGTGATTCTACTTCT
1 CGTTCTTAATGGCTGGTGGTGATTCTACTTCT
28821911 CCACCACCTA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 100 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (74 bp):
CGTTCTTAATGGCTGGTGGTGATTCTACTTCTAAACCATCACCACCTAAAATTGAATGTTGAAAC
TATCACCAC
Found at i:28825700 original size:9 final size:9
Alignment explanation
Indices: 28825666--28825715 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
28825656 TTTGTTTAAG
28825666 TTATATATAA
1 TTAT-TATAA
*
28825676 ATATTAT-A
1 TTATTATAA
28825684 TGTA-TATAA
1 T-TATTATAA
28825693 TTATTATAA
1 TTATTATAA
28825702 TTATTATAA
1 TTATTATAA
28825711 TTATT
1 TTATT
28825716 TATTCAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 6 0.17
9 26 0.74
10 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
TTATTATAA
Found at i:28827168 original size:39 final size:39
Alignment explanation
Indices: 28827114--28827196 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 39
28827104 AATTGCCGGC
*
28827114 TTACTGATCAGGCACTTATGTG-CT-GAACTACTGTTACTG
1 TTACTGATCAGGCACTT-TGTGTCTCGAA-TACTGTTACCG
*
28827153 TTACTGATTC-GGCACTTTGTGTGTCGAATACTGTTACCG
1 TTACTGA-TCAGGCACTTTGTGTCTCGAATACTGTTACCG
28827192 TTACT
1 TTACT
28827197 ATTACAGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
38 4 0.10
39 30 0.77
40 5 0.13
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (39 bp):
TTACTGATCAGGCACTTTGTGTCTCGAATACTGTTACCG
Found at i:28827213 original size:45 final size:45
Alignment explanation
Indices: 28827146--28827246 Score: 148
Period size: 45 Copynumber: 2.2 Consensus size: 45
28827136 CTGAACTACT
* * *
28827146 GTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACC
1 GTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGTCACC
* * *
28827191 GTTACTATTACAGATTCAGCACTTTGTGTGTTGAATACTGTCACT
1 GTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGTCACC
28827236 GTTACTGTTAC
1 GTTACTGTTAC
28827247 CGTTACTGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (45 bp):
GTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGTCACC
Found at i:28827261 original size:7 final size:6
Alignment explanation
Indices: 28827226--28827268 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
28827216 GTGTGTTGAA
* *
28827226 TACTGT CACTGT TACTGT TACCGT TACTGAT TACTGTT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG-T TACTG
28827269 GTGTGTTTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
6 19 0.61
7 12 0.39
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (6 bp):
TACTGT
Found at i:28828873 original size:32 final size:32
Alignment explanation
Indices: 28828809--28828873 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
28828799 CCAGACCTTA
* * *
28828809 TGGGTCACACAGGCTGAGTTATTTGGGTCGTG
1 TGGGTCACACAGGCTGAGTTAATTAGGCCGTG
28828841 TGGGTCACACAGGCTG-GTTCAATTAGGCCGTG
1 TGGGTCACACAGGCTGAGTT-AATTAGGCCGTG
28828873 T
1 T
28828874 AGCCCTCACG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 3 0.10
32 26 0.90
ACGTcount: A:0.17, C:0.18, G:0.35, T:0.29
Consensus pattern (32 bp):
TGGGTCACACAGGCTGAGTTAATTAGGCCGTG
Found at i:28830732 original size:18 final size:18
Alignment explanation
Indices: 28830682--28830732 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
28830672 AATTAGAAAA
*
28830682 AAATTTATAAAAAAGAAT
1 AAATTTATAAAAAATAAT
*
28830700 AAATTT-TAGAAAAATATT
1 AAATTTATA-AAAAATAAT
*
28830718 AAATTTATTAAAAAT
1 AAATTTATAAAAAAT
28830733 TAGGATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.07
18 25 0.89
19 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
AAATTTATAAAAAATAAT
Done.