Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A02
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: 90410113
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3900000 characters in sequence are not A, C, G, or T
File 266 of 268
Found at i:89210603 original size:11 final size:11
Alignment explanation
Indices: 89210584--89210662 Score: 54
Period size: 12 Copynumber: 6.9 Consensus size: 11
89210574 GAGGTTTTTC
* *
89210584 TTTTATTTGGT
1 TTTTTTTTGCT
89210595 TTTTTTTTGCT
1 TTTTTTTTGCT
89210606 TTTTATTTT-CT
1 TTTT-TTTTGCT
*
89210617 CGTTTTTTTTAC-
1 --TTTTTTTTGCT
*
89210629 CTTTTTTTGTCT
1 TTTTTTTTG-CT
*
89210641 TTTTTTTGTCCT
1 TTTTTTT-TGCT
89210653 TTTTTTTTGC
1 TTTTTTTTGC
89210663 CTCCACTGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
10 7 0.13
11 18 0.33
12 23 0.43
13 6 0.11
ACGTcount: A:0.04, C:0.11, G:0.09, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGCT
Found at i:89210609 original size:12 final size:11
Alignment explanation
Indices: 89210594--89210660 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 11
89210584 TTTTATTTGG
*
89210594 TTTTTTTTTGC
1 TTTTTTTTTTC
89210605 TTTTTATTTTCTC
1 TTTTT-TTTT-TC
* *
89210618 GTTTTTTTTAC
1 TTTTTTTTTTC
* *
89210629 CTTTTTTTGTC
1 TTTTTTTTTTC
*
89210640 TTTTTTTTGTCC
1 TTTTTTTT-TTC
89210652 TTTTTTTTT
1 TTTTTTTTT
89210661 GCCTCCACTG
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 22 0.50
12 17 0.39
13 5 0.11
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.79
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:89210636 original size:22 final size:22
Alignment explanation
Indices: 89210611--89210658 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
89210601 TTGCTTTTTA
89210611 TTTTCTCGTTTTTTTT-ACCTTT
1 TTTTCTC-TTTTTTTTGACCTTT
* *
89210633 TTTTGTCTTTTTTTTGTCCTTT
1 TTTTCTCTTTTTTTTGACCTTT
89210655 TTTT
1 TTTT
89210659 TTGCCTCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (22 bp):
TTTTCTCTTTTTTTTGACCTTT
Found at i:89222576 original size:15 final size:15
Alignment explanation
Indices: 89222556--89222600 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
89222546 CAAGAACAAG
*
89222556 AGCAACAACAGCAGC
1 AGCAACAACAACAGC
89222571 AGCAACAACAACAGC
1 AGCAACAACAACAGC
*
89222586 AGCAGCAACAACAGC
1 AGCAACAACAACAGC
89222601 TTCTTGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.49, C:0.33, G:0.18, T:0.00
Consensus pattern (15 bp):
AGCAACAACAACAGC
Found at i:89222579 original size:18 final size:18
Alignment explanation
Indices: 89222558--89222598 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
89222548 AGAACAAGAG
89222558 CAACAACAGCAGCAGCAA
1 CAACAACAGCAGCAGCAA
89222576 CAACAACAGCAGCAGCAA
1 CAACAACAGCAGCAGCAA
89222594 CAACA
1 CAACA
89222599 GCTTCTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.34, G:0.15, T:0.00
Consensus pattern (18 bp):
CAACAACAGCAGCAGCAA
Found at i:89228056 original size:16 final size:17
Alignment explanation
Indices: 89228035--89228074 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
89228025 CTAATTTTTT
89228035 TAAAATTATAAAAAT-A
1 TAAAATTATAAAAATAA
*
89228051 TAAAA-TATTAAAATAA
1 TAAAATTATAAAAATAA
89228067 TAAAATTA
1 TAAAATTA
89228075 CATATTTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 8 0.38
16 11 0.52
17 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATTATAAAAATAA
Found at i:89244637 original size:21 final size:20
Alignment explanation
Indices: 89244603--89244642 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
89244593 GGACGAAAAA
* *
89244603 TAATTTAATATTTATTATTC
1 TAATATAATATTTAATATTC
89244623 TAATATAATTATTTAATATT
1 TAATATAA-TATTTAATATT
89244643 AAAGTTTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TAATATAATATTTAATATTC
Found at i:89260003 original size:13 final size:16
Alignment explanation
Indices: 89259965--89260001 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
89259955 TACCTTACAT
89259965 CACACGACAATTCCAC
1 CACACGACAATTCCAC
89259981 CACACGACAATTCCAC
1 CACACGACAATTCCAC
89259997 CACAC
1 CACAC
89260002 AAACTTGGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.46, G:0.05, T:0.11
Consensus pattern (16 bp):
CACACGACAATTCCAC
Found at i:89263266 original size:35 final size:37
Alignment explanation
Indices: 89263219--89263348 Score: 104
Period size: 40 Copynumber: 3.4 Consensus size: 37
89263209 AAATAGTTTT
* *
89263219 ATAAGTTATGTATTAGTGAAGCTCCCTC-G-TTAGTG
1 ATAAGTTGTGTATTAGAGAAGCTCCCTCAGCTTAGTG
* *
89263254 ATAAGTTGTGTATCA-ACGAAGCTCCCTCATGAGCTTATTG
1 ATAAGTTGTGTATTAGA-GAAGCTCCCTC---AGCTTAGTG
*
89263294 ATAAGTTGTGTATTAGAGAAACTCCCTATGCAAGCTTAAGTG
1 ATAAGTTGTGTATTAGAGAAGCTCCC--T-C-AGCTT-AGTG
*
89263336 ACAAGTTGTGTAT
1 ATAAGTTGTGTAT
89263349 CAGTGAAGTT
Statistics
Matches: 75, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
35 24 0.32
39 1 0.01
40 27 0.36
41 6 0.08
42 16 0.21
43 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (37 bp):
ATAAGTTGTGTATTAGAGAAGCTCCCTCAGCTTAGTG
Found at i:89263346 original size:42 final size:40
Alignment explanation
Indices: 89263248--89263350 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 40
89263238 AGCTCCCTCG
*
89263248 TTAGTGATAAGTTGTGTATCAACGAAGCTCCCTCATGAGC
1 TTAGTGATAAGTTGTGTATCAACGAAACTCCCTCATGAGC
* *
89263288 TTATTGATAAGTTGTGTATTAGA-GAAACTCCCT-ATGCAAGC
1 TTAGTGATAAGTTGTGTATCA-ACGAAACTCCCTCATG--AGC
*
89263329 TTAAGTGACAAGTTGTGTATCA
1 TT-AGTGATAAGTTGTGTATCA
89263351 GTGAAGTTCG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
39 3 0.06
40 28 0.53
41 6 0.11
42 16 0.30
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (40 bp):
TTAGTGATAAGTTGTGTATCAACGAAACTCCCTCATGAGC
Found at i:89295041 original size:23 final size:23
Alignment explanation
Indices: 89295009--89295058 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
89294999 TCCCCATATA
89295009 TTTTCATTTTGAGCATTTAACTT
1 TTTTCATTTTGAGCATTTAACTT
* ** *
89295032 TTTTCTTTTTGTTCTTTTAACTT
1 TTTTCATTTTGAGCATTTAACTT
89295055 TTTT
1 TTTT
89295059 TTTAATTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.14, C:0.12, G:0.06, T:0.68
Consensus pattern (23 bp):
TTTTCATTTTGAGCATTTAACTT
Found at i:89295067 original size:21 final size:23
Alignment explanation
Indices: 89295024--89295069 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
89295014 ATTTTGAGCA
**
89295024 TTTAACTTTTTTCTTTTTGTTCT
1 TTTAACTTTTTTCTTTTAATTCT
89295047 TTTAAC-TTTTT-TTTTAATTCT
1 TTTAACTTTTTTCTTTTAATTCT
89295068 TT
1 TT
89295070 ATTTTCCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 5 0.24
23 6 0.29
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTAACTTTTTTCTTTTAATTCT
Found at i:89297145 original size:2 final size:2
Alignment explanation
Indices: 89297138--89297170 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
89297128 ATCCCCGCCT
*
89297138 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
89297171 GCCTCGCNNN
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:89323101 original size:2 final size:2
Alignment explanation
Indices: 89323094--89323126 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
89323084 ATCCCCGCCT
*
89323094 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
89323127 GCCTCGCGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:89327593 original size:31 final size:31
Alignment explanation
Indices: 89327558--89327619 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
89327548 AACAGCCAAG
* *
89327558 TGATTTAAATAAAATATTTCGAATAGTTCAA
1 TGATTTAAATAAAAGATTTCAAATAGTTCAA
*
89327589 TGATTTAAATAAAAGCTTTCAAATAGTTCAA
1 TGATTTAAATAAAAGATTTCAAATAGTTCAA
89327620 GGACTACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (31 bp):
TGATTTAAATAAAAGATTTCAAATAGTTCAA
Found at i:89331817 original size:23 final size:22
Alignment explanation
Indices: 89331787--89331844 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
89331777 TTATGGAATT
89331787 TATAATTTTTATTATAATAAAAA
1 TATAATTTTTATTATAAT-AAAA
* *
89331810 TATAATTTTACTATTTTAATAAGA
1 TATAATTTT--TATTATAATAAAA
89331834 TAT-ATTTTTAT
1 TATAATTTTTAT
89331845 AATTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
21 3 0.10
23 14 0.45
24 6 0.19
25 8 0.26
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TATAATTTTTATTATAATAAAA
Found at i:89333250 original size:24 final size:24
Alignment explanation
Indices: 89333221--89333266 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
89333211 GAAGTAAAAT
89333221 TCAGGTACCAAAATGGAAAAAAGC
1 TCAGGTACCAAAATGGAAAAAAGC
* *
89333245 TCAGGTACTAAATTGGAAAAAA
1 TCAGGTACCAAAATGGAAAAAA
89333267 AATTGTCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.13, G:0.20, T:0.17
Consensus pattern (24 bp):
TCAGGTACCAAAATGGAAAAAAGC
Found at i:89368086 original size:4 final size:4
Alignment explanation
Indices: 89368077--89368103 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
89368067 AAACTAAGTA
89368077 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
89368104 AATAAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:89373171 original size:103 final size:104
Alignment explanation
Indices: 89372939--89373204 Score: 428
Period size: 103 Copynumber: 2.6 Consensus size: 104
89372929 GTTGTACATA
** *
89372939 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* *
89373004 TTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
89373043 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
89373107 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
89373146 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
89373205 AATAACGGTT
Statistics
Matches: 150, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
103 84 0.56
104 66 0.44
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:89375801 original size:40 final size:40
Alignment explanation
Indices: 89375755--89375938 Score: 235
Period size: 40 Copynumber: 4.6 Consensus size: 40
89375745 CTCGCACAAG
* *
89375755 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * **
89375795 GCCTTCGGGACTTAGCCCGGATATAATCGTTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
89375835 ACCTTCGGGTCTTAGCCCGGATATAG-CAACTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
89375875 GCCTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
*
89375915 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
89375939 CATTCGAATA
Statistics
Matches: 121, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
39 1 0.01
40 119 0.98
41 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:89375850 original size:80 final size:80
Alignment explanation
Indices: 89375719--89375938 Score: 245
Period size: 80 Copynumber: 2.8 Consensus size: 80
89375709 ACCCAAGTAT
* * * * *
89375719 CTTCGGGAT-TTAG-CCGGATACAACCACTCGCAC-AAGGCCTTCGGGTCTTAGCCCGGATATGG
1 CTTC-GGATCTTAGCCCGGATATAATCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAG
*
89375781 TC-ACTAGCATAAATGC
65 -CAACTAGCACAAATGC
**
89375797 CTTCGGGA-CTTAGCCCGGATATAATCGTTAGCACAAATA-CCTTCGGGTCTTAGCCCGGATATA
1 CTTC-GGATCTTAGCCCGGATATAATCACTAGCACAAA-AGCCTTCGGGTCTTAGCCCGGATATA
*
89375860 GCAACTTGCACAAATGC
64 GCAACTAGCACAAATGC
* * * *
89375877 CTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAAGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGATCTTAGCCCGGATATAATCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATAT
89375939 CATTCGAATA
Statistics
Matches: 120, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
78 12 0.10
79 20 0.17
80 88 0.73
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (80 bp):
CTTCGGATCTTAGCCCGGATATAATCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGC
AACTAGCACAAATGC
Found at i:89380878 original size:17 final size:18
Alignment explanation
Indices: 89380851--89380884 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
89380841 TCTTCCATCT
89380851 AGAAGTATTTTTTGAAAA
1 AGAAGTATTTTTTGAAAA
89380869 AGAA-TATTTTTTGAAA
1 AGAAGTATTTTTTGAAA
89380885 TGCTTCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (18 bp):
AGAAGTATTTTTTGAAAA
Found at i:89381448 original size:17 final size:18
Alignment explanation
Indices: 89381422--89381457 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
89381412 CATATCATTT
89381422 ATATAAAATAAA-ATTAA
1 ATATAAAATAAACATTAA
*
89381439 ATATATAATAAACATTAA
1 ATATAAAATAAACATTAA
89381457 A
1 A
89381458 GAATATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
ATATAAAATAAACATTAA
Found at i:89386653 original size:34 final size:34
Alignment explanation
Indices: 89386610--89386677 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
89386600 AACTCAAGCA
89386610 AATCAACTATTGAAAAGCACTAAAACATTATTAT
1 AATCAACTATTGAAAAGCACTAAAACATTATTAT
89386644 AATCAACTATTGAAAAGCACTAAAACATTATTAT
1 AATCAACTATTGAAAAGCACTAAAACATTATTAT
89386678 TTGGTGCGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (34 bp):
AATCAACTATTGAAAAGCACTAAAACATTATTAT
Found at i:89389222 original size:35 final size:35
Alignment explanation
Indices: 89389176--89389247 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
89389166 TCGAATAACT
89389176 TTTCATAATTAAATAATAAAAAATAAATTTATTAA
1 TTTCATAATTAAATAATAAAAAATAAATTTATTAA
89389211 TTTCATAATTAAATAATAAAAAATAAATTTATTAA
1 TTTCATAATTAAATAATAAAAAATAAATTTATTAA
89389246 TT
1 TT
89389248 GTTGAATGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (35 bp):
TTTCATAATTAAATAATAAAAAATAAATTTATTAA
Found at i:89391827 original size:20 final size:21
Alignment explanation
Indices: 89391802--89391843 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
89391792 TGGACAATTC
89391802 AATT-AAATAAATATTAAAAA
1 AATTAAAATAAATATTAAAAA
*
89391822 AATTAAAAATATATATTAAAAA
1 AATT-AAAATAAATATTAAAAA
89391844 TCGATTCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
22 15 0.79
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AATTAAAATAAATATTAAAAA
Found at i:89393612 original size:21 final size:22
Alignment explanation
Indices: 89393586--89393632 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
89393576 CTCTGCTCAA
*
89393586 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
89393607 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
89393629 ACTC
1 ACTC
89393633 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:89402151 original size:20 final size:20
Alignment explanation
Indices: 89402114--89402154 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
89402104 AGATATTAAT
* **
89402114 ATTAAATTTTAAGGAAATTA
1 ATTAAAATTTAAAAAAATTA
89402134 ATTAAAATTTAAAAAAATTA
1 ATTAAAATTTAAAAAAATTA
89402154 A
1 A
89402155 AATTTTTGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
ATTAAAATTTAAAAAAATTA
Found at i:89404222 original size:32 final size:30
Alignment explanation
Indices: 89404150--89404222 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 30
89404140 TGAAATTTTA
*
89404150 AAATTCAAAAAGTACAATAACCAAAATCAAT
1 AAATT-AAAAAGTACAATAACCAAAATCAAC
* * *
89404181 GAATCTAAAAAGTACAAATAACTAAAATTAACC
1 AAAT-TAAAAAGTAC-AATAACCAAAATCAA-C
89404214 AAATTAAAA
1 AAATTAAAA
89404223 CATAGGGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
31 12 0.35
32 19 0.56
33 3 0.09
ACGTcount: A:0.62, C:0.14, G:0.04, T:0.21
Consensus pattern (30 bp):
AAATTAAAAAGTACAATAACCAAAATCAAC
Found at i:89419334 original size:7 final size:7
Alignment explanation
Indices: 89419322--89419347 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
89419312 AATTTAGTAG
89419322 ATTTTCA
1 ATTTTCA
89419329 ATTTTCA
1 ATTTTCA
89419336 ATTTTCA
1 ATTTTCA
89419343 ATTTT
1 ATTTT
89419348 AACACAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTCA
Found at i:89420474 original size:16 final size:16
Alignment explanation
Indices: 89420449--89420482 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
89420439 TGTTTAACGT
89420449 AATTGCATGC-ATGGC
1 AATTGCATGCAATGGC
89420464 AATTGGCATGCAATGGC
1 AATT-GCATGCAATGGC
89420481 AA
1 AA
89420483 AATGATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 6 0.35
17 7 0.41
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (16 bp):
AATTGCATGCAATGGC
Found at i:89420845 original size:6 final size:6
Alignment explanation
Indices: 89420835--89420874 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
89420825 TTTTTTAACT
* *
89420835 TTACAA GTACAA GTACAA TTACAA TTACAA TTACAA TTAC
1 TTACAA TTACAA TTACAA TTACAA TTACAA TTACAA TTAC
89420875 GAGATGTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.30
Consensus pattern (6 bp):
TTACAA
Found at i:89421573 original size:38 final size:38
Alignment explanation
Indices: 89421522--89421595 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
89421512 TAATAAAATA
89421522 TTTAATTAATTTTCATATTAATAAAATTTTTAAACATC
1 TTTAATTAATTTTCATATTAATAAAATTTTTAAACATC
* *
89421560 TTTAATTAATTTTCATATTAATATATTTTTTAAACA
1 TTTAATTAATTTTCATATTAATAAAATTTTTAAACA
89421596 ATCTGGTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.53
Consensus pattern (38 bp):
TTTAATTAATTTTCATATTAATAAAATTTTTAAACATC
Found at i:89424491 original size:17 final size:17
Alignment explanation
Indices: 89424460--89424505 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
89424450 AATTATAAAA
*
89424460 TAAAA-TCAAACAAATG
1 TAAAATTCAAATAAATG
89424476 TAAAATTCAAATAAATG
1 TAAAATTCAAATAAATG
*
89424493 -AATAATTGAAATA
1 TAA-AATTCAAATA
89424506 TAACTGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.26
Consensus pattern (17 bp):
TAAAATTCAAATAAATG
Found at i:89430807 original size:15 final size:15
Alignment explanation
Indices: 89430787--89430818 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
89430777 AGTGAAAATT
89430787 AAATTAATTATTTCA
1 AAATTAATTATTTCA
89430802 AAATTAATTATTTCA
1 AAATTAATTATTTCA
89430817 AA
1 AA
89430819 GTTAGTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTAATTATTTCA
Found at i:89450296 original size:107 final size:107
Alignment explanation
Indices: 89450100--89450416 Score: 553
Period size: 107 Copynumber: 3.0 Consensus size: 107
89450090 TTAAACTTAA
* *
89450100 AATTATATAATCTGTAGAAGAATTAAATTATAATTTTACAATTTTTACAGGGACTAGAATTGAAT
1 AATTTTATAATCTGTAGAAGAATTAAACTATAATTTTACAATTTTTACAGGGACTAGAATTGAAT
*
89450165 TATAAATTTTTTGATAAATAAAAATATTATATATTATTTTAC
66 TATAAATTTTTTGATAAATTAAAATATTATATATTATTTTAC
* *
89450207 AATTTTATAGTCTGTAGAATAATTAAACTATAATTTTACAATTTTTACAGGGACTAGAATTGAAT
1 AATTTTATAATCTGTAGAAGAATTAAACTATAATTTTACAATTTTTACAGGGACTAGAATTGAAT
*
89450272 TATAAATTTTTTGATAAATTAAAATATTATTTATTATTTTAC
66 TATAAATTTTTTGATAAATTAAAATATTATATATTATTTTAC
* *
89450314 AATTTTACAATCTGTAGAAGAATTAAACTATAATTTTACAATTTTTAAAGGGACTAGAATTGAAT
1 AATTTTATAATCTGTAGAAGAATTAAACTATAATTTTACAATTTTTACAGGGACTAGAATTGAAT
*
89450379 TATAATTTTTTTGATAAATTAAAATATTATATATTATT
66 TATAAATTTTTTGATAAATTAAAATATTATATATTATT
89450417 ATATTAATAA
Statistics
Matches: 198, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 198 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (107 bp):
AATTTTATAATCTGTAGAAGAATTAAACTATAATTTTACAATTTTTACAGGGACTAGAATTGAAT
TATAAATTTTTTGATAAATTAAAATATTATATATTATTTTAC
Found at i:89450848 original size:13 final size:13
Alignment explanation
Indices: 89450830--89450854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89450820 TTTTATAAAT
89450830 TATAAAAAAATTA
1 TATAAAAAAATTA
89450843 TATAAAAAAATT
1 TATAAAAAAATT
89450855 TTCATTTTAG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TATAAAAAAATTA
Found at i:89457979 original size:29 final size:28
Alignment explanation
Indices: 89457905--89457979 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
89457895 GTATTTATAT
* *
89457905 TTTTCAAAATTTTGAAATTTAGTCTTTTTA
1 TTTTC-AAATTTT-AAATTTAGTCCTTTAA
* **
89457935 TTTTTATTTTTATAAATTTAGTCCTTTAA
1 TTTTCAAATTT-TAAATTTAGTCCTTTAA
89457964 CTTTTCAAATTTTAAA
1 -TTTTCAAATTTTAAA
89457980 ATTCAGGTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (28 bp):
TTTTCAAATTTTAAATTTAGTCCTTTAA
Found at i:89468475 original size:29 final size:29
Alignment explanation
Indices: 89468381--89468477 Score: 72
Period size: 29 Copynumber: 3.3 Consensus size: 29
89468371 TTTGATTTTA
*
89468381 GTCACTCAACTATGAAAAGTTACAAAATG
1 GTCACTCAACTATGAAATGTTACAAAATG
* * * ****
89468410 ATCA-TCAACTATTAGTAAT-TTTCTTTTTTG
1 GTCACTCAACTA-T-GAAATGTTAC-AAAATG
*
89468440 GTTACTCAACTATGAAATGTTACAAAATG
1 GTCACTCAACTATGAAATGTTACAAAATG
89468469 GTCACTCAA
1 GTCACTCAA
89468478 GTATTAGCCA
Statistics
Matches: 46, Mismatches: 17, Indels: 10
0.63 0.23 0.14
Matches are distributed among these distances:
28 7 0.15
29 21 0.46
30 11 0.24
31 7 0.15
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (29 bp):
GTCACTCAACTATGAAATGTTACAAAATG
Found at i:89468515 original size:63 final size:59
Alignment explanation
Indices: 89468376--89468515 Score: 165
Period size: 59 Copynumber: 2.3 Consensus size: 59
89468366 TTGTTTTTGA
* * *
89468376 TTTTAGTCACTCAACTATGAAAAGTTACAAAATGATCATCAACTATTAGTAATTTTCTT
1 TTTTGGTCACTCAACTATGAAAAGTTACAAAATGATCATCAACTATTAGAAATTATCTT
* * * *
89468435 TTTTGGTTACTCAACTATGAAATGTTACAAAATGGTCACTCAAGTATTAGCCAAAATTATCTT
1 TTTTGGTCACTCAACTATGAAAAGTTACAAAATGATCA-TCAACTATTAG---AAATTATCTT
89468498 TTTTGGTCA-TCCAACTAT
1 TTTTGGTCACT-CAACTAT
89468516 TTTTATTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
59 34 0.50
60 10 0.15
62 1 0.01
63 23 0.34
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (59 bp):
TTTTGGTCACTCAACTATGAAAAGTTACAAAATGATCATCAACTATTAGAAATTATCTT
Found at i:89472790 original size:24 final size:24
Alignment explanation
Indices: 89472735--89472790 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
89472725 TTTGACCCGT
89472735 TAATTATATTTATTTTTCATTTTAG
1 TAATTA-ATTTATTTTTCATTTTAG
*
89472760 -AATTTAATTT-TTTTTCCATTTTGG
1 TAA-TTAATTTATTTTT-CATTTTAG
89472784 TAATTAA
1 TAATTAA
89472791 ACTATTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
23 5 0.19
24 17 0.63
25 5 0.19
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (24 bp):
TAATTAATTTATTTTTCATTTTAG
Found at i:89474668 original size:204 final size:201
Alignment explanation
Indices: 89474313--89474827 Score: 634
Period size: 204 Copynumber: 2.5 Consensus size: 201
89474303 AAAATTGTGA
* * *
89474313 TGTCATAGATTAAGACCAATTGG-TCCATAACT-AGGTTTTATTCACATAGGACAGTCTATAGTT
1 TGTCTTAGATTAAGACCAATTGGAT-CATAACTCAGGTTTTGTTCACATAGGACAGTCTAGAGTT
* * ** *
89474376 GAGATTGCTGTACCTAAGCTGCATTTTGGGAATATAGAATTCTTTGGAGAGATTACTGTTCAAGC
65 GAGATTGTTGTACCTAAGCTGCATTTTTGGAATATAGAATTCTGGGGAGAGATTACCGTTCAAGC
* * * * *
89474441 CGGACTGATACAATATCTGGACATGGCGCTGTCGGAAAATAGATAGGGCAGTCTTTAGCTAAGAA
130 CGGACGGATACAATATCTGGACATGGCACGGTCGG--AATACATAGGGCAATCTTTAGCTAAGAA
89474506 ATTGTGTGTTC
193 A-T-TGTGTTC
*
89474517 TGTCTTAGATTAAGGCCAATTGGATCATAACTCA-GTTTTGTTCACATAGGACAGTCTAGAGTTG
1 TGTCTTAGATTAAGACCAATTGGATCATAACTCAGGTTTTGTTCACATAGGACAGTCTAGAGTTG
* *
89474581 AGATTGTTGTACTTAAGCTGCATTTTTGGAATATAGAATTCTGGGGAGAGATTACCGTTCAGGCC
66 AGATTGTTGTACCTAAGCTGCATTTTTGGAATATAGAATTCTGGGGAGAGATTACCGTTCAAGCC
*
89474646 GGACGGATACAATATCTGGACATGGCACGGTCGGAATACATAGGGCAATCTTTAGCTGAGAAATT
131 GGACGGATACAATATCTGGACATGGCACGGTCGGAATACATAGGGCAATCTTTAGCTAAGAAATT
89474711 GTGTTC
196 GTGTTC
* * * *
89474717 TATCTTTAGTTTAAGACCAACCTATTGTTGGACCGTAAC-CAGGTTTTGTTTCACATAAGG-CAG
1 TGTC-TTAGATTAAGACC-A---A---TTGGATCATAACTCAGGTTTTG-TTCACAT-AGGACAG
89474780 TCTAGAGTTGAGA---TTGTACCTAAGCTGCA-TTTTGGAAATATAGAATTC
56 TCTAGAGTTGAGATTGTTGTACCTAAGCTGCATTTTTGG-AATATAGAATTC
89474828 CTTTTATGAA
Statistics
Matches: 274, Mismatches: 23, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
200 10 0.04
201 12 0.04
202 27 0.10
204 145 0.53
205 9 0.03
206 27 0.10
207 2 0.01
208 16 0.06
209 23 0.08
210 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (201 bp):
TGTCTTAGATTAAGACCAATTGGATCATAACTCAGGTTTTGTTCACATAGGACAGTCTAGAGTTG
AGATTGTTGTACCTAAGCTGCATTTTTGGAATATAGAATTCTGGGGAGAGATTACCGTTCAAGCC
GGACGGATACAATATCTGGACATGGCACGGTCGGAATACATAGGGCAATCTTTAGCTAAGAAATT
GTGTTC
Found at i:89477535 original size:96 final size:96
Alignment explanation
Indices: 89477371--89477562 Score: 384
Period size: 96 Copynumber: 2.0 Consensus size: 96
89477361 CAAAATGCAA
89477371 TCCGACTCTTTTATTATTCTTAAAGTAATCATGTTGGAACCCGTATCCAAAGCATATTCAAACAT
1 TCCGACTCTTTTATTATTCTTAAAGTAATCATGTTGGAACCCGTATCCAAAGCATATTCAAACAT
89477436 GATTATAGGAATATAAAGCCTCCTAATAGGG
66 GATTATAGGAATATAAAGCCTCCTAATAGGG
89477467 TCCGACTCTTTTATTATTCTTAAAGTAATCATGTTGGAACCCGTATCCAAAGCATATTCAAACAT
1 TCCGACTCTTTTATTATTCTTAAAGTAATCATGTTGGAACCCGTATCCAAAGCATATTCAAACAT
89477532 GATTATAGGAATATAAAGCCTCCTAATAGGG
66 GATTATAGGAATATAAAGCCTCCTAATAGGG
89477563 GCGTAGACAG
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (96 bp):
TCCGACTCTTTTATTATTCTTAAAGTAATCATGTTGGAACCCGTATCCAAAGCATATTCAAACAT
GATTATAGGAATATAAAGCCTCCTAATAGGG
Found at i:89485349 original size:169 final size:165
Alignment explanation
Indices: 89485065--89485382 Score: 383
Period size: 169 Copynumber: 1.9 Consensus size: 165
89485055 TCATGGACCA
** * **
89485065 AGTGAACAAATGCTGCAAGCTAAGCTTGAATGGTAGAAAACACTTGCATTAAGCTAAACTTTTAA
1 AGTGAACAAATGCTGCAAGCTAAGCTAAAATAGTAGAAAACACTCACATTAAGCTAAACTTTTAA
* * * * *
89485130 AGAAATTATGGCAGAGATCCCTTAAAAACTTGCATAAATGGGATAAATTGAAATTAAGCTACAAC
66 AGAAATCATGACAGAAAGCCCATAAAAACTTGCATAAATGGGATAAATTGAAATTAAG---CAAC
*
89485195 TTCTTATGAACCACACATCAAAACAACATAAAAAACCC
128 TTCTTAAGAACCACACATCAAAACAACATAAAAAACCC
* * *
89485233 AGTGACCAAATGCTGCAAGCT-AGCTCAAATATAGTGGAAAACACTCACGTTAAGCTAAACTTTT
1 AGTGAACAAATGCTGCAAGCTAAGCT-AAA-ATAGTAGAAAACACTCACATTAAGCTAAACTTTT
*
89485297 ACTA-AAATCATGACAGAAAGCCCAT-AAAACTTACGCAT-AATGGGATAAATTGAAATTAAGCA
64 A-AAGAAATCATGACAGAAAGCCCATAAAAACTT--GCATAAATGGGATAAATTGAAATTAAGCA
* *
89485359 ACTTCTTAAGAACCGCATATCAAA
126 ACTTCTTAAGAACCACACATCAAA
89485383 TCAATTTACA
Statistics
Matches: 128, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
166 23 0.18
167 4 0.03
168 28 0.22
169 68 0.53
170 5 0.04
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (165 bp):
AGTGAACAAATGCTGCAAGCTAAGCTAAAATAGTAGAAAACACTCACATTAAGCTAAACTTTTAA
AGAAATCATGACAGAAAGCCCATAAAAACTTGCATAAATGGGATAAATTGAAATTAAGCAACTTC
TTAAGAACCACACATCAAAACAACATAAAAAACCC
Found at i:89493366 original size:395 final size:387
Alignment explanation
Indices: 89492632--89493679 Score: 1381
Period size: 395 Copynumber: 2.7 Consensus size: 387
89492622 TATAATTAAA
* ** *
89492632 GGTATGTTCATTTAACAGAAGCTATAATTCACTACATGTTGGATGGTGTTTGCTTTTATGGCAAA
1 GGTATGTTCATTTAACACAAGCTATAATTCACTACATGTTGGATCATG-TTGCTTTTATGACAAA
89492697 TAAAAATATGAATCTCATAGGTTAGTAATTATCTAGCTCTCGAAGTAATACAAGACTTCAGAAAT
65 TAAAAATATGAATCTCATA-GTTAGT-ATTATCTAGCTCTCGAAGTAATACAAGACTTCAGAAAT
* **
89492762 TCATGACCGAACGAACCTTGATCCATCCA------TT-TTCCTACTGAAAATGAGATCAATGTAA
128 TCATGACCGAA-G-ACCTTGATCCATCCATTTTTGTTGTTCCTATTGAAAATGAGATTGATGTAA
* * * *
89492820 AAGTTTCCAGTTTTGTATCTTGTCTCACTTTCTGAATAATTGCTTTGTCTCTTCCCTTTGTTCTC
191 AAGTTCCCAGTTTTGTATCTTGT-TAACTTTCTGATTAATTGCTTCGTCTCTTCCCTTTGTTCTC
* * *
89492885 TCATATATGTGTGTTAGCAAGTTAAATTGAATTTTCTGTGTAAGTTCAGAAATAAGAATTTTTGA
255 TCATATGTGTGTGTTAGCAAGTTAAATTGAATTTTCTGTGCAACTTCAGAAATAAGAATTTTTGA
** * * * *
89492950 GTGATGGGGCTGGAGTTCGCTAGAAACTTATTATGAAACTATCTTGTGTATGATTAATGACCAAA
320 GTGACAGGGCTGGAATTCGCTAGAAACTCATAATGAAACTATATTGTGTATGATTAATGACCAAA
89493015 AGC-
385 A-CT
* * * * **
89493018 GGTATGTTCATTTAACATAAGCTATATAATTCACTACGTGTTGGATCATGTTGCTCTCATGATGA
1 GGTATGTTCATTTAACACAAGC--TATAATTCACTACATGTTGGATCATGTTGCTTTTATGACAA
89493083 ATAAAAATATGAATCTCATA-TCTAGTCATTATCTAGCTCTCGAAGTAATA-AGAGACTTCAGAA
64 ATAAAAATATGAATCTCATAGT-TAGT-ATTATCTAGCTCTCGAAGTAATACA-AGACTTCAGAA
*
89493146 ATTCATGACCGAATGAGCCTTGATCCATTCATTTTTGTTGTTCCTATTGAAAATGAGATTGATGT
126 ATTCATGACCGAA-GA-CCTTGATCCATCCATTTTTGTTGTTCCTATTGAAAATGAGATTGATGT
* * *
89493211 AAAAAAGTTCCCATTTTTGTATCTTGTTAAACTTTCTGATTAATTGCTTCGACTCTTCACTTTGT
189 --AAAAGTTCCCAGTTTTGTATCTTGTT-AACTTTCTGATTAATTGCTTCGTCTCTTCCCTTTGT
* *
89493276 TC-CATCATATGTGTGTGTTAGGAAGTTAAATTGAATTTTCTGTGCAACTTCAGAATTAAGAATT
251 TCTC-TCATATGTGTGTGTTAGCAAGTTAAATTGAATTTTCTGTGCAACTTCAGAAATAAGAATT
* *
89493340 TTTTAGTGACAGTGCTGGAATTCGCTAGAAACTCATAATGAAACTATATTGTGTATGATTAATGA
315 TTTGAGTGACAGGGCTGGAATTCGCTAGAAACTCATAATGAAACTATATTGTGTATGATTAATGA
89493405 CCAAAACT
380 CCAAAACT
* *
89493413 GGTATTTTCATTTAATACAAGC--T-ATTCACTACATGTTGGATCATGTTGCTTTTATGACAAAT
1 GGTATGTTCATTTAACACAAGCTATAATTCACTACATGTTGGATCATGTTGCTTTTATGACAAAT
* * *
89493475 GAAAATATGAATCTCATAGGTTAGTACTTATCTAGCTCTCAAAGTGATACAAGACTTCAGAAATT
66 AAAAATATGAATCTCATA-GTTAGTA-TTATCTAGCTCTCGAAGTAATACAAGACTTCAGAAATT
* * *
89493540 CATGACCG-A-ACCTTGTTCCATCCATTTTTGTTGTCCCTATTGAAAATGATATTGATGTAAAAG
129 CATGACCGAAGACCTTGATCCATCCATTTTTGTTGTTCCTATTGAAAATGAGATTGATGTAAAAG
* ***
89493603 TTCCCAGTTTTATATCTTGTTGAACTTTCTGATTAATTGCTTCGTCTCTTCCCTCCATTCTCTCA
194 TTCCCAGTTTTGTATCTTGTT-AACTTTCTGATTAATTGCTTCGTCTCTTCCCTTTGTTCTCTCA
89493668 TATGTGTGTGTT
258 TATGTGTGTGTT
89493680 GTTGCATGCC
Statistics
Matches: 582, Mismatches: 58, Indels: 45
0.85 0.08 0.07
Matches are distributed among these distances:
385 75 0.13
386 87 0.15
387 74 0.13
388 24 0.04
390 53 0.09
391 47 0.08
392 4 0.01
393 22 0.04
394 3 0.01
395 193 0.33
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (387 bp):
GGTATGTTCATTTAACACAAGCTATAATTCACTACATGTTGGATCATGTTGCTTTTATGACAAAT
AAAAATATGAATCTCATAGTTAGTATTATCTAGCTCTCGAAGTAATACAAGACTTCAGAAATTCA
TGACCGAAGACCTTGATCCATCCATTTTTGTTGTTCCTATTGAAAATGAGATTGATGTAAAAGTT
CCCAGTTTTGTATCTTGTTAACTTTCTGATTAATTGCTTCGTCTCTTCCCTTTGTTCTCTCATAT
GTGTGTGTTAGCAAGTTAAATTGAATTTTCTGTGCAACTTCAGAAATAAGAATTTTTGAGTGACA
GGGCTGGAATTCGCTAGAAACTCATAATGAAACTATATTGTGTATGATTAATGACCAAAACT
Found at i:89496452 original size:14 final size:15
Alignment explanation
Indices: 89496433--89496461 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
89496423 TTTAAAACCT
89496433 ATTAAA-ATTTTAAA
1 ATTAAATATTTTAAA
89496447 ATTAAATATTTTAAA
1 ATTAAATATTTTAAA
89496462 TTACAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAAATATTTTAAA
Found at i:89499585 original size:27 final size:27
Alignment explanation
Indices: 89499547--89499600 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
89499537 TCACTGTCAA
*
89499547 AAACCTTGCCAAAGAAAGGCAGGTGAG
1 AAACCTTACCAAAGAAAGGCAGGTGAG
89499574 AAACCTTACCAAAGAAAGGCAGGTGAG
1 AAACCTTACCAAAGAAAGGCAGGTGAG
89499601 TTTGCATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.19, G:0.28, T:0.11
Consensus pattern (27 bp):
AAACCTTACCAAAGAAAGGCAGGTGAG
Found at i:89500999 original size:23 final size:24
Alignment explanation
Indices: 89500972--89501016 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
89500962 AATTGATTTA
* *
89500972 TGTTAATT-TTTTTCTAATTTTTT
1 TGTTAATTGATTTTCAAATTTTTT
89500995 TGTTAATTGATTTTCAAATTTT
1 TGTTAATTGATTTTCAAATTTT
89501017 AGTCAATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (24 bp):
TGTTAATTGATTTTCAAATTTTTT
Found at i:89504402 original size:6 final size:6
Alignment explanation
Indices: 89504393--89504422 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
89504383 TAATATTTTA
89504393 AAAAAT AAAAAT AAAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT -AAAAAT AAAAAT AAAAA
89504423 CTCTCTCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:89504409 original size:13 final size:13
Alignment explanation
Indices: 89504391--89504422 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
89504381 ACTAATATTT
89504391 TAAAAAATAAAAA
1 TAAAAAATAAAAA
89504404 TAAAAAATAAAAA
1 TAAAAAATAAAAA
89504417 TAAAAA
1 TAAAAA
89504423 CTCTCTCAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:89507368 original size:39 final size:39
Alignment explanation
Indices: 89507325--89507947 Score: 750
Period size: 39 Copynumber: 16.2 Consensus size: 39
89507315 TGTTCAGCAG
*
89507325 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCATGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
** * * *
89507364 GAAGAGAGAAG-G-AGGCA-CG--TGAA-CT--AGAA-GA
1 GAAGAGA-AAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
*
89507395 GAAAGAGAAGGAGAAGAAATTGAAGGAAGCTCGTGAACGA
1 G-AAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * * * *
89507435 GAAGAGAATGAGAAGAGATTGAGGGAGGATCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
*
89507474 GAAGAGATAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * * * *
89507513 GAAGAGAATGAGAAGAGATTGAGGGAGGCTCGTGAGCGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * *
89507552 GAAGAGAAAGAGAAGAAA--G-AGGAGGCACATGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
89507588 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
89507627 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * *
89507666 GAAGAGAATGAGAGGAGATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * **
89507705 GAAGAGAATGAGAAGAGATTGAAGGAAATTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
** *
89507744 GAAGAGAAAGAGAAGAAAGAGAAGG-AGGTACGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCT-CGTGAACGA
* *
89507783 GAAGAGAAAGAGAAGAAATTGAAAGAAGCTCGTGAACAA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * *
89507822 GAAGAGAATGAGCAGAGATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* * * *
89507861 GAAGAGAATGAGAAGAGATTGAAGGAAGCTTGTGAACAA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
* *
89507900 GAAGAGAATGAGAAGAGATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
89507939 GAAGAGAAA
1 GAAGAGAAA
89507948 TTGAAGGAAG
Statistics
Matches: 503, Mismatches: 65, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
31 5 0.01
32 10 0.02
33 3 0.01
34 3 0.01
35 3 0.01
36 34 0.07
37 4 0.01
38 6 0.01
39 426 0.85
40 9 0.02
ACGTcount: A:0.47, C:0.07, G:0.35, T:0.11
Consensus pattern (39 bp):
GAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGA
Found at i:89507953 original size:30 final size:30
Alignment explanation
Indices: 89507909--89508037 Score: 199
Period size: 30 Copynumber: 4.4 Consensus size: 30
89507899 AGAAGAGAAT
89507909 GAGAAGAG--ATTGAAGGAAGCTCGTGAAC
1 GAGAAGAGAAATTGAAGGAAGCTCGTGAAC
*
89507937 GAGAAGAGAAATTGAAGGAAGCTTGTGAAC
1 GAGAAGAGAAATTGAAGGAAGCTCGTGAAC
89507967 GAGAAGAGAAATTGAAGGAAGCTCGTGAAC
1 GAGAAGAGAAATTGAAGGAAGCTCGTGAAC
** * *
89507997 GAGAAGAGAAAGAGAAGGAGGCACGTGAAC
1 GAGAAGAGAAATTGAAGGAAGCTCGTGAAC
89508027 GAGAAGAGAAA
1 GAGAAGAGAAA
89508038 GAGAGGAAAG
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
28 8 0.09
30 85 0.91
ACGTcount: A:0.45, C:0.09, G:0.36, T:0.11
Consensus pattern (30 bp):
GAGAAGAGAAATTGAAGGAAGCTCGTGAAC
Found at i:89511014 original size:29 final size:29
Alignment explanation
Indices: 89510981--89511038 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
89510971 AGATTTTTTT
* *
89510981 TAATATGGTATTTGTGTTA-GTTTTTGGTC
1 TAATATGCTACTTGTGTTATG-TTTTGGTC
89511010 TAATATGCTACTTGTGTTATGTTTTGGTC
1 TAATATGCTACTTGTGTTATGTTTTGGTC
89511039 CAGTTTGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.17, C:0.07, G:0.22, T:0.53
Consensus pattern (29 bp):
TAATATGCTACTTGTGTTATGTTTTGGTC
Found at i:89512912 original size:12 final size:12
Alignment explanation
Indices: 89512895--89512919 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
89512885 ATTTTATAGC
89512895 ATAAATATTGTT
1 ATAAATATTGTT
89512907 ATAAATATTGTT
1 ATAAATATTGTT
89512919 A
1 A
89512920 ATAGTCTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAATATTGTT
Found at i:89517333 original size:53 final size:53
Alignment explanation
Indices: 89517253--89517404 Score: 243
Period size: 53 Copynumber: 2.9 Consensus size: 53
89517243 TTTTTAACCG
*
89517253 ATTGGCTTGACGCTCACATTCGAGACACGAAATTCGTCCTCCAAAAGCCGGTC
1 ATTGGCTCGACGCTCACATTCGAGACACGAAATTCGTCCTCCAAAAGCCGGTC
* *
89517306 ATTGGCTCAACGCTCACATTCGAGACACGAAATTCATCCTCCAAAAGCCGGTC
1 ATTGGCTCGACGCTCACATTCGAGACACGAAATTCGTCCTCCAAAAGCCGGTC
* *
89517359 ATTGGCTCGACGCTCACATTCGAGACTA-GGAATCCGTCCTCCAAAA
1 ATTGGCTCGACGCTCACATTCGAGAC-ACGAAATTCGTCCTCCAAAA
89517405 TCCGATCCTT
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 90 0.99
54 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (53 bp):
ATTGGCTCGACGCTCACATTCGAGACACGAAATTCGTCCTCCAAAAGCCGGTC
Found at i:89518490 original size:31 final size:32
Alignment explanation
Indices: 89518442--89518515 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 32
89518432 GATATTTTGA
*
89518442 TATTTTA-TAATTATTTAATTAGATA-AATAT
1 TATTTTATTAATTATTTAATAAGATATAATAT
*
89518472 TATTTTATTAA-TACTTTAATAAGATATTTATTAT
1 TATTTTATTAATTA-TTTAATAAGATA--TAATAT
89518506 TATTTTATTA
1 TATTTTATTA
89518516 GTATATAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
30 9 0.24
31 14 0.38
34 14 0.38
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (32 bp):
TATTTTATTAATTATTTAATAAGATATAATAT
Found at i:89520706 original size:38 final size:40
Alignment explanation
Indices: 89520652--89520905 Score: 257
Period size: 46 Copynumber: 6.0 Consensus size: 40
89520642 CTGATATGAA
89520652 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-TG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATG
*
89520691 -TGTGTAAGACTATGGTTGAAAGATACCATGGCAACC-TG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATG
89520729 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC----ATG
* *
89520772 AAATGTGTAAGACTATGTTTGAAAGATACCATGGCAACCTGATATGAG
1 --ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC----AT--G
89520820 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC----CATG
* **
89520864 AAAAGAATAAGACCATGGTTGAAAGATACCATGGCAA-CATG
1 --ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATG
89520905 A
1 A
89520906 CAGAAAATGA
Statistics
Matches: 190, Mismatches: 9, Indels: 32
0.82 0.04 0.14
Matches are distributed among these distances:
38 72 0.38
39 1 0.01
41 4 0.02
43 2 0.01
44 1 0.01
46 108 0.57
48 1 0.01
50 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (40 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATG
Found at i:89520796 original size:46 final size:46
Alignment explanation
Indices: 89520729--89520945 Score: 283
Period size: 46 Copynumber: 4.7 Consensus size: 46
89520719 TGGCAACCTG
*
89520729 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* * * *
89520775 TGTGTAAGACTATGTTTGAAAGATACCATGGCAACCTGATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
*
89520821 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* ** *
89520867 AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATG-AAA
* * * * *
89520913 TGAGTAAGACTATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
89520946 TCACGTCAAA
Statistics
Matches: 152, Mismatches: 18, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
45 1 0.01
46 151 0.99
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
Found at i:89521250 original size:23 final size:25
Alignment explanation
Indices: 89521205--89521251 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
89521195 AATAAATATA
*
89521205 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
89521230 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
89521252 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:89525297 original size:72 final size:71
Alignment explanation
Indices: 89525197--89525439 Score: 317
Period size: 72 Copynumber: 3.4 Consensus size: 71
89525187 AGAGGATGAA
*
89525197 CTCGAGAAGGATGAGGCCTCAAAGAAAGCCGAGGTTAAAGAATCTCGAGAACTGAAAATCGAACA
1 CTCGAGAAGGATGA-GCCTCGAAGAAAGCCGAGGTTAAAGAATCTCGAGAACTGAAAATCGAACA
89525262 CAAGTAT
65 CAAGTAT
* * *
89525269 CTCAAGAAGGATGAGCCCTTGAAGAAAGCCGAGGTTAAAGAATCTCGAGAACTGAAAATTGAACA
1 CTCGAGAAGGATGAG-CCTCGAAGAAAGCCGAGGTTAAAGAATCTCGAGAACTGAAAATCGAACA
*
89525334 CAAGTGT
65 CAAGTAT
* ** * *
89525341 CCCGAGAAGGACAAAGTCTCGAAGAAAGCCGAGGTTAAAGAATC-CGAAGAATTGAAAATCGAAC
1 CTCGAGAAGGA-TGAGCCTCGAAGAAAGCCGAGGTTAAAGAATCTCG-AGAACTGAAAATCGAAC
*
89525405 ACAAATAT
64 ACAAGTAT
* *
89525413 CTCGAGAAAGAGGAAGCCTCGAAGAAA
1 CTCGAGAAGGATG-AGCCTCGAAGAAA
89525440 ACCAAATTTT
Statistics
Matches: 147, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
71 3 0.02
72 142 0.97
73 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.15
Consensus pattern (71 bp):
CTCGAGAAGGATGAGCCTCGAAGAAAGCCGAGGTTAAAGAATCTCGAGAACTGAAAATCGAACAC
AAGTAT
Found at i:89529809 original size:16 final size:17
Alignment explanation
Indices: 89529788--89529825 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
89529778 TTATTCAATG
89529788 TTTTTTAATT-AATAAT
1 TTTTTTAATTAAATAAT
* *
89529804 TTTTTTATTTAAATACT
1 TTTTTTAATTAAATAAT
89529821 TTTTT
1 TTTTT
89529826 ACTCTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTTAATTAAATAAT
Found at i:89532650 original size:22 final size:22
Alignment explanation
Indices: 89532624--89532668 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
89532614 GAAAGGTGAC
89532624 TCACGTGTCAACAAAGGATTTA
1 TCACGTGTCAACAAAGGATTTA
89532646 TCACGTGTCAACAAAGGATTTA
1 TCACGTGTCAACAAAGGATTTA
89532668 T
1 T
89532669 GTTTAGGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (22 bp):
TCACGTGTCAACAAAGGATTTA
Found at i:89534614 original size:15 final size:16
Alignment explanation
Indices: 89534584--89534617 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
89534574 AAAATAGTTA
*
89534584 TTATTTTATAAGTTTT
1 TTATTTTATAACTTTT
89534600 TTATTTTA-AACTTTT
1 TTATTTTATAACTTTT
89534615 TTA
1 TTA
89534618 GCATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (16 bp):
TTATTTTATAACTTTT
Found at i:89548292 original size:126 final size:129
Alignment explanation
Indices: 89548035--89548283 Score: 346
Period size: 129 Copynumber: 2.0 Consensus size: 129
89548025 GGTGTAGGCA
* * * *
89548035 TTAGGGTCTAAGTTCTAAGTCTTACTATGTGTAAATGTGTGTTCAGTGTAATTTTACTATTGTCC
1 TTAGGGTCTAAGTTATAAGTCTTACAATGCGTAAATATGTGTTCAGTGTAATTTTACTATTGTCC
* * *
89548100 TTGTTTAGAATCGTACAATTTTTAAAGGGACTAATAAGGAAATTTTCCATTTTGAGGGGCTGGT
66 TTGTTTAGAATAGTACAATTTATAAAGGGACTAACAAGGAAATTTTCCATTTTGAGGGGCTGGT
*
89548164 TTAGGGTCTAAGTTATAAGTCTTACAATGCGTAAATATG-GCTT-GGTGTAATTTTACTATTGTC
1 TTAGGGTCTAAGTTATAAGTCTTACAATGCGTAAATATGTG-TTCAGTGTAATTTTACTATTGTC
* * *
89548227 CTTGTTTA-AAGTATTACCA-TTATAAGGGGACT-ACAAGGAAATTTTCCATTTTGAGGG
65 CTTGTTTAGAA-TAGTACAATTTATAAAGGGACTAACAAGGAAATTTTCCATTTTGAGGG
89548284 ATCGGTTTAA
Statistics
Matches: 107, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
126 24 0.22
127 13 0.12
128 33 0.31
129 37 0.35
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (129 bp):
TTAGGGTCTAAGTTATAAGTCTTACAATGCGTAAATATGTGTTCAGTGTAATTTTACTATTGTCC
TTGTTTAGAATAGTACAATTTATAAAGGGACTAACAAGGAAATTTTCCATTTTGAGGGGCTGGT
Found at i:89560481 original size:37 final size:37
Alignment explanation
Indices: 89560434--89560521 Score: 89
Period size: 35 Copynumber: 2.5 Consensus size: 37
89560424 AAGTTTGCAA
*
89560434 ATATTAATTTTTTAAAATTT-A-AAATTATATTTATATT
1 ATATTTATTTTTTAAAATTTAATAAATT-T-TTTATATT
*
89560471 ATATTTA--TTTTAATATTTAATAAATTTTTTATATT
1 ATATTTATTTTTTAAAATTTAATAAATTTTTTATATT
*
89560506 -T-TTTATTTGTTAAAAT
1 ATATTTATTTTTTAAAAT
89560522 ATTATATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
33 4 0.09
34 1 0.02
35 25 0.58
36 2 0.05
37 11 0.26
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (37 bp):
ATATTTATTTTTTAAAATTTAATAAATTTTTTATATT
Found at i:89562033 original size:2 final size:2
Alignment explanation
Indices: 89562026--89562059 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
89562016 AATCGTTGAA
89562026 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
89562060 GCAGGACATG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:89567211 original size:39 final size:36
Alignment explanation
Indices: 89567155--89567230 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
89567145 CTTGATTATG
*
89567155 ATAAAATAATAATAATAATAAACTTGAATGGGGTAT
1 ATAAAAAAATAATAATAATAAACTTGAATGGGGTAT
89567191 ATAAAAAAATAATAATAATAAACTTGAATGGGGTAT
1 ATAAAAAAATAATAATAATAAACTTGAATGGGGTAT
89567227 ATAA
1 ATAA
89567231 CACTTAGCAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (36 bp):
ATAAAAAAATAATAATAATAAACTTGAATGGGGTAT
Found at i:89567638 original size:15 final size:16
Alignment explanation
Indices: 89567592--89567640 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 16
89567582 CAATTGAATT
89567592 AAATTTATGATTTTTATTA
1 AAATTTAT-A-TTTTA-TA
*
89567611 AAATTTTTATTTTATA
1 AAATTTATATTTTATA
89567627 AAA-TTATATTTTAT
1 AAATTTATATTTTAT
89567641 CTTAATTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 10 0.36
16 5 0.18
17 5 0.18
18 1 0.04
19 7 0.25
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
AAATTTATATTTTATA
Found at i:89578073 original size:59 final size:59
Alignment explanation
Indices: 89578001--89578114 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
89577991 AGTAAACTAC
* * *
89578001 TATTAGTAAATTTTTATTTAGTTA-TCTAATTATTAAAAGTTATAAAATGATCACTCAAT
1 TATTAGTAAATTTTTATTTAGTCATTC-AACTATGAAAAGTTATAAAATGATCACTCAAT
* *
89578060 TATTAGTAAATTTTTTTTTAGTCATTCAACTATGAAAAGTTATAAAATGGTCACT
1 TATTAGTAAATTTTTATTTAGTCATTCAACTATGAAAAGTTATAAAATGATCACT
89578115 TAACTATTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
59 47 0.96
60 2 0.04
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.45
Consensus pattern (59 bp):
TATTAGTAAATTTTTATTTAGTCATTCAACTATGAAAAGTTATAAAATGATCACTCAAT
Found at i:89582458 original size:82 final size:84
Alignment explanation
Indices: 89582295--89582465 Score: 224
Period size: 82 Copynumber: 2.0 Consensus size: 84
89582285 AAGAATCTTC
* *
89582295 AATTCAGTCCTCTTATAAATAAAAAAAAATTATAAATTAATTTATAGTGAAATTACACTTTAACT
1 AATTCAGTCCTCTTATAAAT-AAAAAAAATTATAAATTAATTAATAGTAAAATTACACTTTAACT
*
89582360 CCCCAAAATATAAAAAAATT
65 CCCCAAAATATAAAAAAAAT
* * *
89582380 AATTCAGTCCTCTTATTAAT-AAAGAAATTATAAATTAA-TAATAGTAAAATTGCA-TTTAAC-C
1 AATTCAGTCCTCTTATAAATAAAAAAAATTATAAATTAATTAATAGTAAAATTACACTTTAACTC
*
89582441 CCCTAAAAATTTAAAAAAAAT
66 CCC--AAAATATAAAAAAAAT
89582462 AATT
1 AATT
89582466 ATTTTTAGTC
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
80 4 0.05
81 6 0.08
82 31 0.40
83 17 0.22
85 19 0.25
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.33
Consensus pattern (84 bp):
AATTCAGTCCTCTTATAAATAAAAAAAATTATAAATTAATTAATAGTAAAATTACACTTTAACTC
CCCAAAATATAAAAAAAAT
Found at i:89582460 original size:85 final size:85
Alignment explanation
Indices: 89582295--89582466 Score: 201
Period size: 85 Copynumber: 2.0 Consensus size: 85
89582285 AAGAATCTTC
* *
89582295 AATTCAGTCCTCTTATAAATAAAAAAAAATTATAAATTAATTTATAGTGAAATTACACTTTAACT
1 AATTCAGTCCTCTTATAAAT-AAAAAAAATTATAAATTAATTAATAGTAAAATTACACTTTAACT
*
89582360 CCCCAAAATATAAAAA-AATT
65 CCCCAAAATAAAAAAATAATT
* * *
89582380 AATTCAGTCCTCTTATTAAT-AAAGAAATTATAAATTAA-TAATAGTAAAATTGCA-TTTAAC-C
1 AATTCAGTCCTCTTATAAATAAAAAAAATTATAAATTAATTAATAGTAAAATTACACTTTAACTC
89582441 CCCTAAAAATTTAAAAAAAATAATT
66 CCC--AAAA--T-AAAAAAATAATT
89582466 A
1 A
89582467 TTTTTAGTCT
Statistics
Matches: 75, Mismatches: 6, Indels: 11
0.82 0.07 0.12
Matches are distributed among these distances:
80 4 0.05
81 6 0.08
82 17 0.23
83 17 0.23
84 1 0.01
85 25 0.33
86 5 0.07
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (85 bp):
AATTCAGTCCTCTTATAAATAAAAAAAATTATAAATTAATTAATAGTAAAATTACACTTTAACTC
CCCAAAATAAAAAAATAATT
Found at i:89584599 original size:2 final size:2
Alignment explanation
Indices: 89584592--89584616 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
89584582 CCAAAGTATA
89584592 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
89584617 AAACACCTCC
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:89586580 original size:20 final size:21
Alignment explanation
Indices: 89586555--89586593 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
89586545 TTATTGAACT
*
89586555 TGACAAAT-GTAAAAATTTGA
1 TGACAAATAATAAAAATTTGA
89586575 TGACAAATAATAAAAATTT
1 TGACAAATAATAAAAATTT
89586594 TGACAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (21 bp):
TGACAAATAATAAAAATTTGA
Found at i:89590585 original size:14 final size:14
Alignment explanation
Indices: 89590566--89590597 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
89590556 ATTTGAACTC
89590566 ATAACCTATAACGT
1 ATAACCTATAACGT
89590580 ATAACCTATAACGT
1 ATAACCTATAACGT
89590594 ATAA
1 ATAA
89590598 GGTATTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (14 bp):
ATAACCTATAACGT
Found at i:89592450 original size:15 final size:16
Alignment explanation
Indices: 89592432--89592461 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
89592422 ATTAATATTA
89592432 TTTTTAT-ATTTATAT
1 TTTTTATCATTTATAT
89592447 TTTTTATCATTTATA
1 TTTTTATCATTTATA
89592462 AATATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTATCATTTATAT
Found at i:89595724 original size:20 final size:20
Alignment explanation
Indices: 89595699--89595739 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
89595689 CAAGATGATT
* *
89595699 TTTTTTAATTATACTATTAA
1 TTTTTTAAGTATAATATTAA
89595719 TTTTTTAAGTATAATATTAA
1 TTTTTTAAGTATAATATTAA
89595739 T
1 T
89595740 ATAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTTTAAGTATAATATTAA
Found at i:89597988 original size:73 final size:72
Alignment explanation
Indices: 89597909--89598071 Score: 178
Period size: 67 Copynumber: 2.3 Consensus size: 72
89597899 ATCGAATATT
* * *
89597909 TATTTTTAAGTTCGAGTTCGAGTTCACTTTAAAATTTAAAGTTTGATGTTCAGTTCAAACTCAAT
1 TATTTTTAAGTTCGAGTTCGAGTTCAC-TTAAAATTCAAAGTTTGATGCTCAGCTCAAACTCAAT
* *
89597974 TGAGTATC
65 TAAGCATC
* * * *
89597982 TATTTTTAAGTTCAAGCTC-A----ACTTGAAATTCAAAGTTTGATGCTCAGCTCAAGCTCAATT
1 TATTTTTAAGTTCGAGTTCGAGTTCACTTAAAATTCAAAGTTTGATGCTCAGCTCAAACTCAATT
89598042 AAGCATC
66 AAGCATC
*
89598049 TA-TTTTAAGTTTGAGTTCG-GTTC
1 TATTTTTAAGTTCGAGTTCGAGTTC
89598072 GATATATAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
66 13 0.18
67 40 0.55
68 2 0.03
72 1 0.01
73 17 0.23
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (72 bp):
TATTTTTAAGTTCGAGTTCGAGTTCACTTAAAATTCAAAGTTTGATGCTCAGCTCAAACTCAATT
AAGCATC
Found at i:89606915 original size:21 final size:22
Alignment explanation
Indices: 89606889--89606935 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
89606879 CTCTGCTCAA
*
89606889 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
89606910 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
89606932 ACTC
1 ACTC
89606936 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:89612850 original size:22 final size:20
Alignment explanation
Indices: 89612803--89612850 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 20
89612793 AATAAATAAA
89612803 AAATTAAAAAATATTAAATAT
1 AAATTAAAAAATA-TAAATAT
89612824 AAAATTAAAAATAATATAAATAT
1 -AAATT-AAAA-AATATAAATAT
89612847 AAAT
1 AAAT
89612851 CTACCAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.38
23 11 0.46
24 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATTAAAAAATATAAATAT
Found at i:89620951 original size:17 final size:18
Alignment explanation
Indices: 89620921--89620966 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
89620911 ATTTAAATTA
89620921 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
89620939 CGGTCGC-GTCGCG-TTT
1 CGGTCGCGGTCGCGTTTT
89620955 --GTCGCGGTCGCG
1 CGGTCGCGGTCGCG
89620967 GACATAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 3 0.11
17 6 0.22
18 7 0.26
ACGTcount: A:0.00, C:0.30, G:0.41, T:0.28
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:89621290 original size:27 final size:25
Alignment explanation
Indices: 89621236--89621290 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
89621226 CAGATGGCCC
* **
89621236 AAAGTAAAAAAATCTAAATATTTTT
1 AAAGTAAAAAAATCTAAATAATCCT
89621261 AAAGTAAAAAAATCTAGATATAATCCT
1 AAAGTAAAAAAATCTA-A-ATAATCCT
89621288 AAA
1 AAA
89621291 AAAAGGCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 16 0.64
26 1 0.04
27 8 0.32
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.29
Consensus pattern (25 bp):
AAAGTAAAAAAATCTAAATAATCCT
Found at i:89622730 original size:18 final size:19
Alignment explanation
Indices: 89622692--89622731 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
89622682 AAATGAATCC
*
89622692 ATATATAAAATATATTATA
1 ATATATAAAATAAATTATA
*
89622711 ATATAT-AAATAAATTCTA
1 ATATATAAAATAAATTATA
89622729 ATA
1 ATA
89622732 CCTTTTTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATATAAAATAAATTATA
Found at i:89625462 original size:20 final size:18
Alignment explanation
Indices: 89625439--89625482 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
89625429 AAAAAATATT
89625439 ATAATAATTAATTGAAGAAA
1 ATAATAA-TAATT-AAGAAA
89625459 ATAATAATAATTAAGAAA
1 ATAATAATAATTAAGAAA
89625477 A-AATAA
1 ATAATAA
89625483 AAAAGGGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.21
18 7 0.29
19 5 0.21
20 7 0.29
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (18 bp):
ATAATAATAATTAAGAAA
Found at i:89625463 original size:17 final size:17
Alignment explanation
Indices: 89625441--89625481 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
89625431 AAAATATTAT
89625441 AATAAT-TAATTGAAGAA
1 AATAATATAATT-AAGAA
89625458 AATAATAATAATTAAGAA
1 AATAAT-ATAATTAAGAA
89625476 AA-AATA
1 AATAATA
89625482 AAAAAGGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.05
17 9 0.41
18 7 0.32
19 5 0.23
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (17 bp):
AATAATATAATTAAGAA
Found at i:89626827 original size:196 final size:195
Alignment explanation
Indices: 89626466--89626828 Score: 469
Period size: 196 Copynumber: 1.9 Consensus size: 195
89626456 GTAAGTCCGT
* * * *
89626466 TAATTAATTCTCCATGTTTTGTAGGCTTATTAAAAGGTAGATGCTTGCCACGAGTTTTAAAGCTG
1 TAATTAATTCTCCATATTCTGTAGGCTTATTAAAAGGTAGATGATTGCCACGAGTTTTAAAACTG
* * * * * * *
89626531 CTGCATACTTAAGGTAAGGATTAAGCTCTCAACTAATGATTAAGGTAGAAGACATATTTACTATC
66 CTCCATACCTAAAGTAAGGATTAAACTCTCAACCAATGATAAAGGTAGAAGACATAATTACTATC
**
89626596 TCACCTAACTCTCGTAGTTAGGAATGTTGAATTTTTTTTCAAGGTATTTATCGGAGCAAACCTAG
131 TCACCTAACTCTCGTAGTTAGGAATGTCAAATTTTTTTTCAAGGTATTTATCGGAGCAAACCTAG
* ** * * *
89626661 TAATTAATTCTCCATATTCTGTAGGTTTATTAAGGGAGTAGATGATTGTCATGAGTTTTAAAATT
1 TAATTAATTCTCCATATTCTGTAGGCTTATTAAAAG-GTAGATGATTGCCACGAGTTTTAAAACT
* * * *
89626726 GCTCCATACCTAGAAG-AATGATTAAACTCTCAACCACTGATAAAGGTAGAAGAGATAATTGCTA
65 GCTCCATACCTA-AAGTAAGGATTAAACTCTCAACCAATGATAAAGGTAGAAGACATAATTACTA
*
89626790 TCTCACCTAACTCTCGTGGTTAGAGAA-GTCAAATTTTTT
129 TCTCACCTAACTCTCGTAGTTAG-GAATGTCAAATTTTTT
89626829 ATTACAAAAC
Statistics
Matches: 141, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
195 31 0.22
196 105 0.74
197 5 0.04
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (195 bp):
TAATTAATTCTCCATATTCTGTAGGCTTATTAAAAGGTAGATGATTGCCACGAGTTTTAAAACTG
CTCCATACCTAAAGTAAGGATTAAACTCTCAACCAATGATAAAGGTAGAAGACATAATTACTATC
TCACCTAACTCTCGTAGTTAGGAATGTCAAATTTTTTTTCAAGGTATTTATCGGAGCAAACCTAG
Found at i:89628323 original size:3 final size:3
Alignment explanation
Indices: 89628315--89628340 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
89628305 TGAACTATGG
89628315 CAA CAA CAA CAA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CA
89628341 TATTTACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:89636289 original size:43 final size:41
Alignment explanation
Indices: 89636242--89636326 Score: 102
Period size: 41 Copynumber: 2.0 Consensus size: 41
89636232 CTCACATTGT
89636242 TTTAAAAATTTTAAAATAATATATT-TTTATTTATAATTTA-ATA
1 TTTAAAAATTTT-AAAT-ATATATTATTTA-TTA-AATTTATATA
* *
89636285 TTTAATAATTTTATATATATATTATTTATTAAATTTATATA
1 TTTAAAAATTTTAAATATATATTATTTATTAAATTTATATA
89636326 T
1 T
89636327 ATATCGTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
40 6 0.16
41 14 0.37
42 7 0.18
43 11 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (41 bp):
TTTAAAAATTTTAAATATATATTATTTATTAAATTTATATA
Found at i:89636321 original size:24 final size:24
Alignment explanation
Indices: 89636270--89636330 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
89636260 ATATATTTTT
* *
89636270 ATTTATA-ATTTAATATTTAATAA
1 ATTTATATATATATTATTTAATAA
* *
89636293 TTTTATATATATATTATTTATTAA
1 ATTTATATATATATTATTTAATAA
89636317 ATTTATATATATAT
1 ATTTATATATATAT
89636331 CGTTTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 6 0.19
24 26 0.81
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTATATATATATTATTTAATAA
Found at i:89636340 original size:24 final size:24
Alignment explanation
Indices: 89636284--89636340 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
89636274 ATAATTTAAT
* * *
89636284 ATTTAATAATTTTATATATATATT
1 ATTTATTAAATTTATATATATATC
89636308 ATTTATTAAATTTATATATATATC
1 ATTTATTAAATTTATATATATATC
* *
89636332 GTTTTTTAA
1 ATTTATTAA
89636341 GGTTTTTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
ATTTATTAAATTTATATATATATC
Found at i:89636986 original size:22 final size:23
Alignment explanation
Indices: 89636937--89636988 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
89636927 TAAAATTTTG
* *
89636937 ATTTAATCTCTTAAAAATTACAT
1 ATTTAATATCGTAAAAATTACAT
*
89636960 TTTTAATATCGTAAAAATTACA-
1 ATTTAATATCGTAAAAATTACAT
89636982 ATTTAAT
1 ATTTAAT
89636989 TTTGGCCTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTTAATATCGTAAAAATTACAT
Found at i:89640780 original size:14 final size:15
Alignment explanation
Indices: 89640750--89640783 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
89640740 TTAATATTCG
*
89640750 AAAATTATAAAACTA
1 AAAATGATAAAACTA
89640765 AAAATGATAAAA-TA
1 AAAATGATAAAACTA
89640779 AAAAT
1 AAAAT
89640784 ACAATTTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAATGATAAAACTA
Found at i:89646531 original size:2 final size:2
Alignment explanation
Indices: 89646524--89646548 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
89646514 CTTAGTTTTG
89646524 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
89646549 AACTTTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:89650388 original size:19 final size:19
Alignment explanation
Indices: 89650331--89650388 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
89650321 TATCTCTTCT
89650331 TTACTATACTGCTAACTCA
1 TTACTATACTGCTAACTCA
* *
89650350 -TAC-ATTCT-CTATCTCTTCA
1 TTACTATACTGCTA--AC-TCA
89650369 TTACTATACTGCTAACTCA
1 TTACTATACTGCTAACTCA
89650388 T
1 T
89650389 GTCAATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
16 3 0.10
17 4 0.14
18 4 0.14
19 7 0.24
20 4 0.14
21 4 0.14
22 3 0.10
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (19 bp):
TTACTATACTGCTAACTCA
Found at i:89651295 original size:34 final size:34
Alignment explanation
Indices: 89651232--89651317 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 34
89651222 TGCAATTTAT
*
89651232 AACAAATAAAAATTAAATTATATACTATAATGTA
1 AACAAATAAAAATTAAATTATATAATATAATGTA
* * *
89651266 AACAAA-AAAAATGTTAAGTTATA-AATATAATTTT
1 AACAAATAAAAA--TTAAATTATATAATATAATGTA
*
89651300 AATAAATAAAAATATAAA
1 AACAAATAAAAAT-TAAA
89651318 AGCATTAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
33 6 0.14
34 22 0.52
35 14 0.33
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (34 bp):
AACAAATAAAAATTAAATTATATAATATAATGTA
Found at i:89652355 original size:27 final size:27
Alignment explanation
Indices: 89652325--89652435 Score: 132
Period size: 27 Copynumber: 4.1 Consensus size: 27
89652315 TGAAAATCAC
* * *
89652325 GGTCCCTTGTATCAACATACCTTTGTT
1 GGTCCCTTGGATCGACATACCTCTGTT
* *
89652352 GGTCCCTCGGATCGACGTACCTCTGTT
1 GGTCCCTTGGATCGACATACCTCTGTT
* *
89652379 GGTCTCTTGGATCGACATACCTTTGTT
1 GGTCCCTTGGATCGACATACCTCTGTT
* * *
89652406 GATCCCTTGTATCGACGTACCTCTGTT
1 GGTCCCTTGGATCGACATACCTCTGTT
89652433 GGT
1 GGT
89652436 TTCCGAAATA
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.37
Consensus pattern (27 bp):
GGTCCCTTGGATCGACATACCTCTGTT
Found at i:89652421 original size:54 final size:54
Alignment explanation
Indices: 89652325--89652435 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 54
89652315 TGAAAATCAC
* *
89652325 GGTCCCTTGTATCAACATACCTTTGTTGGTCCCTCGGATCGACGTACCTCTGTT
1 GGTCCCTTGGATCAACATACCTTTGTTGATCCCTCGGATCGACGTACCTCTGTT
* * * *
89652379 GGTCTCTTGGATCGACATACCTTTGTTGATCCCTTGTATCGACGTACCTCTGTT
1 GGTCCCTTGGATCAACATACCTTTGTTGATCCCTCGGATCGACGTACCTCTGTT
89652433 GGT
1 GGT
89652436 TTCCGAAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.37
Consensus pattern (54 bp):
GGTCCCTTGGATCAACATACCTTTGTTGATCCCTCGGATCGACGTACCTCTGTT
Found at i:89654494 original size:13 final size:13
Alignment explanation
Indices: 89654476--89654501 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89654466 CAATACAAAA
89654476 AATGTTTTATGTT
1 AATGTTTTATGTT
89654489 AATGTTTTATGTT
1 AATGTTTTATGTT
89654502 TAAAAGTGCA
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:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (13 bp):
AATGTTTTATGTT
Found at i:89663710 original size:47 final size:47
Alignment explanation
Indices: 89663601--89663711 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 47
89663591 CCGGGATAAG
* * *
89663601 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
89663648 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
89663695 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
89663712 ACTCAATGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 1 0.02
47 51 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:89673245 original size:22 final size:22
Alignment explanation
Indices: 89673213--89673278 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
89673203 AAATATTATA
89673213 ATTTAA-ATTTAACATTTAATT
1 ATTTAATATTTAACATTTAATT
* * * **
89673234 GTTTAATATTTAAAATTTTAGC
1 ATTTAATATTTAACATTTAATT
*
89673256 ATTTAATATGTCAACATTTAATT
1 ATTTAATAT-TTAACATTTAATT
89673279 TTTCAGTTTA
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
21 5 0.16
22 19 0.59
23 8 0.25
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (22 bp):
ATTTAATATTTAACATTTAATT
Found at i:89676653 original size:24 final size:24
Alignment explanation
Indices: 89676621--89676669 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
89676611 TTTGCATGCT
89676621 AAATGACATTTACCTAACAAGATC
1 AAATGACATTTACCTAACAAGATC
89676645 AAATGACATTTACCTAACAAGATC
1 AAATGACATTTACCTAACAAGATC
89676669 A
1 A
89676670 TGTGTTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.24
Consensus pattern (24 bp):
AAATGACATTTACCTAACAAGATC
Found at i:89681710 original size:22 final size:21
Alignment explanation
Indices: 89681682--89681722 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
89681672 CCTCATCTAT
89681682 ATATATATATATGTATACATAC
1 ATATATATATATGT-TACATAC
89681704 ATATATATATATGTTACAT
1 ATATATATATATGTTACAT
89681723 TGGGTTCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (21 bp):
ATATATATATATGTTACATAC
Found at i:89684148 original size:11 final size:11
Alignment explanation
Indices: 89684132--89684156 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
89684122 GTCTTTAAAG
89684132 ATAGTGATTAT
1 ATAGTGATTAT
89684143 ATAGTGATTAT
1 ATAGTGATTAT
89684154 ATA
1 ATA
89684157 AACATTGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (11 bp):
ATAGTGATTAT
Found at i:89685060 original size:27 final size:27
Alignment explanation
Indices: 89685022--89685074 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
89685012 GAAAATATAC
* * *
89685022 AAAAAATAGAAACACCCAAAATTACAA
1 AAAAAAAAGAAAAACACAAAATTACAA
*
89685049 AAAAAAAAGAAAAACACTAAATTACA
1 AAAAAAAAGAAAAACACAAAATTACA
89685075 CAATGTGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.70, C:0.15, G:0.04, T:0.11
Consensus pattern (27 bp):
AAAAAAAAGAAAAACACAAAATTACAA
Found at i:89692904 original size:3 final size:3
Alignment explanation
Indices: 89692896--89692925 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
89692886 AAATTTAAAA
89692896 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
89692926 GGTGTATTGG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:89693381 original size:20 final size:20
Alignment explanation
Indices: 89693358--89693395 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
89693348 TATATTTTAA
* *
89693358 TAATTGGATTTATTTAATAG
1 TAATTGGACTAATTTAATAG
89693378 TAATTGGACTAATTTAAT
1 TAATTGGACTAATTTAAT
89693396 TTGATCTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (20 bp):
TAATTGGACTAATTTAATAG
Found at i:89693599 original size:21 final size:19
Alignment explanation
Indices: 89693571--89693611 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
89693561 TGAACAGCTT
*
89693571 ATTTATTTTTTATTGTTAAA
1 ATTTATTTTATA-TGTTAAA
89693591 ATTTAATTTTATATGTTAAA
1 ATTT-ATTTTATATGTTAAA
89693611 A
1 A
89693612 AGAAATATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
ATTTATTTTATATGTTAAA
Found at i:89694083 original size:16 final size:18
Alignment explanation
Indices: 89694052--89694084 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
89694042 ATGTAATTTT
89694052 ATTTTTATTAATTTTAAA
1 ATTTTTATTAATTTTAAA
89694070 ATTTTT-TT-ATTTTAA
1 ATTTTTATTAATTTTAA
89694085 GAGGATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTATTAATTTTAAA
Found at i:89698012 original size:31 final size:31
Alignment explanation
Indices: 89697968--89698046 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
89697958 GGGGGGAAAA
89697968 AAACTC-AGCTACCAAATTAAACATGGAAGCC
1 AAACTCAAG-TACCAAATTAAACATGGAAGCC
* * *
89697999 AAACTCAAGTACCAAATTGAACATTGAAGCT
1 AAACTCAAGTACCAAATTAAACATGGAAGCC
* *
89698030 AAACTCAGGTATCAAAT
1 AAACTCAAGTACCAAAT
89698047 GGTATATGAC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 40 0.95
32 2 0.05
ACGTcount: A:0.46, C:0.22, G:0.13, T:0.20
Consensus pattern (31 bp):
AAACTCAAGTACCAAATTAAACATGGAAGCC
Found at i:89703117 original size:23 final size:24
Alignment explanation
Indices: 89703081--89703126 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
89703071 TATATACTAA
89703081 ATATATATATTTTTATTTTTAATC
1 ATATATATATTTTTATTTTTAATC
*
89703105 ATATTTATA-TTTTATTTTTAAT
1 ATATATATATTTTTATTTTTAAT
89703127 TTTAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
ATATATATATTTTTATTTTTAATC
Found at i:89710878 original size:15 final size:16
Alignment explanation
Indices: 89710832--89710881 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
89710822 AATAATCCTA
*
89710832 AAACTTAAAATAATTT
1 AAACTTAAAATAACTT
* *
89710848 AAACTCAAAATTACTT
1 AAACTTAAAATAACTT
89710864 AAA-TTAAAATAACTT
1 AAACTTAAAATAACTT
89710879 AAA
1 AAA
89710882 ATTTTAAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (16 bp):
AAACTTAAAATAACTT
Found at i:89710883 original size:16 final size:16
Alignment explanation
Indices: 89710820--89710884 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
89710810 TGATCTGATC
*
89710820 AAAATAATCCTAAAACTT
1 AAAATAA-CTTAAAA-TT
* * *
89710838 AAAATAATTTAAACTC
1 AAAATAACTTAAAATT
*
89710854 AAAATTACTT-AAATT
1 AAAATAACTTAAAATT
89710869 AAAATAACTTAAAATT
1 AAAATAACTTAAAATT
89710885 TTAAAGAGTA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
15 12 0.32
16 14 0.38
17 4 0.11
18 7 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAATAACTTAAAATT
Found at i:89711421 original size:31 final size:30
Alignment explanation
Indices: 89711354--89711422 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
89711344 ACGATAATGT
* * *
89711354 AAGTGACTAAAATGTAATATTTTAAACATA
1 AAGTGACTAAAATGTAACATGTAAAACATA
89711384 AA-TGACTAAAATGTAACATGAGTAAAACA-A
1 AAGTGACTAAAATGTAACAT--GTAAAACATA
89711414 AAGTGACTA
1 AAGTGACTA
89711423 TTTTTAAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 16 0.48
30 5 0.15
31 12 0.36
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (30 bp):
AAGTGACTAAAATGTAACATGTAAAACATA
Found at i:89715749 original size:24 final size:24
Alignment explanation
Indices: 89715722--89715773 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
89715712 TTAGTAAGTC
*
89715722 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
89715746 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
89715770 AAAT
1 AAAT
89715774 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:89717718 original size:24 final size:24
Alignment explanation
Indices: 89717691--89717742 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
89717681 TTAGTAAGTC
*
89717691 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
89717715 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
89717739 AAAT
1 AAAT
89717743 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:89723892 original size:6 final size:6
Alignment explanation
Indices: 89723881--89723907 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
89723871 CAAGTAATAT
89723881 CCTAAG CCTAAG CCTAAG CCTAAG CCT
1 CCTAAG CCTAAG CCTAAG CCTAAG CCT
89723908 TGTCAGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.37, G:0.15, T:0.19
Consensus pattern (6 bp):
CCTAAG
Found at i:89725508 original size:505 final size:503
Alignment explanation
Indices: 89724531--89725587 Score: 2028
Period size: 505 Copynumber: 2.1 Consensus size: 503
89724521 ACGATCAAGC
* * *
89724531 ATGTAT-A-AATAGGGCTAATCAACAATAAAAGAAATATAGAAAATCATCACATATAAAGGCCTG
1 ATGTATAACAATAGCGCTAACCAACAATCAAAGAAATATAGAAAATCATCACATATAAAGGCCTG
89724594 TAATACTCAACACTACATATCGTTCTGAATGCATTTTTCATTTTAAGCAGTCTTTCACACTAATT
66 TAATACTCAACACTACATATCGTTCTGAATGCATTTTTCATTTTAAGCAGTCTTTCACACTAATT
89724659 GCATTAGAGTACTCATGATATCAACAGCAAGCCTTAGATCATAGCAAAATGCATAAATAGGGCCA
131 GCATTAGAGTACTCATGATATCAACAGCAAGCCTTAGATCATAGCAAAATGCATAAATAGGGCCA
89724724 ATTTACAATCAAAGGTTACCACATATAAAGGCCAGTGATACTCAACACTACACAGATCTGAAACC
196 ATTTACAATCAAAGGTTACCACATATAAAGGCCAGTGATACTCAACACTACACAGATCTGAAACC
89724789 CGAATGTAGGATTGTAATAAGAAACTTTGAACTAAAGATATACTTTTTTTAATGCTAAAACCCGA
261 CGAATGTAGGATTGTAATAAGAAACTTTGAACTAAAGATATACTTTTTTTAATGCTAAAACCCGA
89724854 ATTATGGATCAAATTCAGAATCCTTTTGCTTAAGAGATGCTCATGTTATCCCCCAATTTGCATTC
326 ATTATGGATCAAATTCAGAATCCTTTTGCTTAAGAGATGCTCATGTTATCCCCCAATTTGCATTC
89724919 CATGAGTTAAGAACCAAGCAACATTTATCCAACAATTGCATTACAGTTCTTCCTCATAAGCTAGG
391 CATGAGTTAAGAACCAAGCAACATTTATCCAACAATTGCATTACAGTTCTTCCTCATAAGCTAGG
89724984 CATACAATTAAGCACTAATATCCACATCAAACCCAAGACTATAGCAAA
456 CATACAATTAAGCACTAATATCCACATCAAACCCAAGACTATAGCAAA
89725032 ATGTATAACAATAGCGCTAACCAACAATCAAAGAAATATAGAAAATCATCACATATAAAGGCCTG
1 ATGTATAACAATAGCGCTAACCAACAATCAAAGAAATATAGAAAATCATCACATATAAAGGCCTG
89725097 TAATACTCAACACTACATATCGTTCTGAATGCATTTTTCATTTTAAGCAGTCTTTCACACTAATT
66 TAATACTCAACACTACATATCGTTCTGAATGCATTTTTCATTTTAAGCAGTCTTTCACACTAATT
89725162 GCATTAGAGTACTCATGATATCAACAGCAAGCCTTAGATCATAGCAAAATGCATAAATAGGGCCA
131 GCATTAGAGTACTCATGATATCAACAGCAAGCCTTAGATCATAGCAAAATGCATAAATAGGGCCA
89725227 ATTTACAATCAAAGGTTACCACATATAAAGGCCAGTGATACTCAACACTACACATAGATCTGAAA
196 ATTTACAATCAAAGGTTACCACATATAAAGGCCAGTGATACTCAACACTACAC--AGATCTGAAA
89725292 CCCGAATGTAGGATTGTAATAAGAAACTTTGAACTAAAGATATACTTTTTTTAATGCTAAAACCC
259 CCCGAATGTAGGATTGTAATAAGAAACTTTGAACTAAAGATATACTTTTTTTAATGCTAAAACCC
89725357 GAATTATGGATCAAATTCAGAATCCTTTTGCTTAAGAGATGCTCATGTTATCCCCCAATTTGCAT
324 GAATTATGGATCAAATTCAGAATCCTTTTGCTTAAGAGATGCTCATGTTATCCCCCAATTTGCAT
89725422 TCCATGAGTTAAGAACCAAGCAACATTTATCCAACAATTGCATTACAGTTCTTCCTCATAAGCTA
389 TCCATGAGTTAAGAACCAAGCAACATTTATCCAACAATTGCATTACAGTTCTTCCTCATAAGCTA
89725487 GGCATACAATTAAGCACTAATATCCACATCAAACCCAAGACTATAGCAAA
454 GGCATACAATTAAGCACTAATATCCACATCAAACCCAAGACTATAGCAAA
* **
89725537 ATGTATAACAATAGCGCTAACCAACAATCAAAGCAGCATAGAAAATCATCA
1 ATGTATAACAATAGCGCTAACCAACAATCAAAGAAATATAGAAAATCATCA
89725588 GTTCATCACA
Statistics
Matches: 546, Mismatches: 6, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
501 6 0.01
502 1 0.00
503 236 0.43
505 303 0.55
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (503 bp):
ATGTATAACAATAGCGCTAACCAACAATCAAAGAAATATAGAAAATCATCACATATAAAGGCCTG
TAATACTCAACACTACATATCGTTCTGAATGCATTTTTCATTTTAAGCAGTCTTTCACACTAATT
GCATTAGAGTACTCATGATATCAACAGCAAGCCTTAGATCATAGCAAAATGCATAAATAGGGCCA
ATTTACAATCAAAGGTTACCACATATAAAGGCCAGTGATACTCAACACTACACAGATCTGAAACC
CGAATGTAGGATTGTAATAAGAAACTTTGAACTAAAGATATACTTTTTTTAATGCTAAAACCCGA
ATTATGGATCAAATTCAGAATCCTTTTGCTTAAGAGATGCTCATGTTATCCCCCAATTTGCATTC
CATGAGTTAAGAACCAAGCAACATTTATCCAACAATTGCATTACAGTTCTTCCTCATAAGCTAGG
CATACAATTAAGCACTAATATCCACATCAAACCCAAGACTATAGCAAA
Found at i:89726618 original size:138 final size:138
Alignment explanation
Indices: 89726370--89726622 Score: 325
Period size: 138 Copynumber: 1.8 Consensus size: 138
89726360 ATTTTTTTGG
* ** * *
89726370 GTTAATTAAATGAGTTAATTGCACTAAATGTCCCCAAACTATGACTCATTCTAAATTGGTCCTAA
1 GTTAATTAAATGAGTTAATTGCACAAAACATCCCCAAACTACGACTCATTCTAAATTGCTCCTAA
** * * *
89726435 ACTTTTAAAACATTCTAATTATATCTTCAAACTATCAATGTTATATCAATAAGTTTCTTCCATTA
66 ACTTTTAAAACATTCTAAAAACATCCTCAAACTATCAAGGTTATATCAATAAGTTTCTTCCATTA
89726500 CTAAAATC
131 CTAAAATC
*
89726508 GTTAATT-AA-GAGTTAATTGCACAAAACATCCTCAAACTACGACTCTCATTCTAAATTGCTCCA
1 GTTAATTAAATGAGTTAATTGCACAAAACATCCCCAAACTACGA--CTCATTCTAAATTGCTCC-
* *
89726571 TAAAC-TTTAAATCATTCTAAAAACATTCCT-AAACTATCGAGGTTATATCAAT
63 TAAACTTTTAAAACATTCTAAAAACA-TCCTCAAACTATCAAGGTTATATCAAT
89726623 TAGGTCTTTT
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
136 28 0.29
137 2 0.02
138 60 0.61
139 8 0.08
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (138 bp):
GTTAATTAAATGAGTTAATTGCACAAAACATCCCCAAACTACGACTCATTCTAAATTGCTCCTAA
ACTTTTAAAACATTCTAAAAACATCCTCAAACTATCAAGGTTATATCAATAAGTTTCTTCCATTA
CTAAAATC
Found at i:89726661 original size:138 final size:136
Alignment explanation
Indices: 89726371--89726654 Score: 315
Period size: 138 Copynumber: 2.1 Consensus size: 136
89726361 TTTTTTTGGG
* ** * *
89726371 TTAATTAAATGAGTTAATTGCACTAAATGTCCCCAAACTATGACTCATTCTAAATTGGTCCTAAA
1 TTAATT-AA-GAGTTAATTGCACAAAACATCCCCAAACTACGACTCATTCTAAATTGCTCCTAAA
** * * *
89726436 CTTTTAAAACATTCTAATTATATCTTCAAACTATCAATGTTATATCAATAAGTTTCTTCCATTAC
64 CTTTTAAAACATTCTAAAAACATCCTCAAACTATCAAGGTTATATCAATAAGTTTCTTCCATTAC
*
89726501 TAAAATCG
129 TAAAATCA
*
89726509 TTAATTAAGAGTTAATTGCACAAAACATCCTCAAACTACGACTCTCATTCTAAATTGCTCCATAA
1 TTAATTAAGAGTTAATTGCACAAAACATCCCCAAACTACGA--CTCATTCTAAATTGCTCC-TAA
* * * *
89726574 AC-TTTAAATCATTCTAAAAACATTCCT-AAACTATCGAGGTTATATCAATTAGGTCTT-TT-CG
63 ACTTTTAAAACATTCTAAAAACA-TCCTCAAACTATCAAGGTTATATCAA-TAAGT-TTCTTCCA
89726635 TTACTAAAATCA
125 TTACTAAAATCA
*
89726647 TTATTTAA
1 TTAATTAA
89726655 TTGTTAAATG
Statistics
Matches: 123, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
136 28 0.23
137 2 0.02
138 77 0.63
139 14 0.11
140 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (136 bp):
TTAATTAAGAGTTAATTGCACAAAACATCCCCAAACTACGACTCATTCTAAATTGCTCCTAAACT
TTTAAAACATTCTAAAAACATCCTCAAACTATCAAGGTTATATCAATAAGTTTCTTCCATTACTA
AAATCA
Found at i:89732451 original size:21 final size:19
Alignment explanation
Indices: 89732427--89732468 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
89732417 AAAGTTAAAA
*
89732427 TTTTAAAATTTAAAATATAT
1 TTTTTAAATTTAAAATA-AT
*
89732447 TTTTTAAATTTTAAATAAT
1 TTTTTAAATTTAAAATAAT
89732466 TTT
1 TTT
89732469 ATGTATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTAAATTTAAAATAAT
Found at i:89737070 original size:144 final size:142
Alignment explanation
Indices: 89736828--89737406 Score: 592
Period size: 144 Copynumber: 4.2 Consensus size: 142
89736818 TTTCGAAACA
* * * * * *
89736828 TTTCGAATGAGAAACACACATAAAAGAAAAAACCCTTTCAAATGGAAAACAATGTAAGGGTTCTA
1 TTTCGAATGAGAAACACAC--ACAAGAAAAAA-TCTTTCAAATGCAAGACAATATTAGGGTTCTA
* * * * *
89736893 GCTCAGCTTTGCGCCCTTAACAACACTAGTTGTGACATTGCCTAATAAATTTAGCTTTAGTACAA
63 GCTCGGCTTTGCGCCCTTAACAACACTAGTTGTGCCATTGCCTAGTGAATTTAGCTCTAGTACAA
89736958 AAATGTCCAGAACCC
128 AAATGTCCAGAACCC
89736973 TTTCGAATGAGAAACACACACAAGAAAGAAATCCTTTCAAATGCAAGACAATATTAGGGTTCTAG
1 TTTCGAATGAGAAACACACACAAGAAA-AAAT-CTTTCAAATGCAAGACAATATTAGGGTTCTAG
89737038 CTCGGCTTTGCGCCCTTAACAACACTAGTTGTGCCATTGCCTAGTGAATTTAGCTCTAGTACAAA
64 CTCGGCTTTGCGCCCTTAACAACACTAGTTGTGCCATTGCCTAGTGAATTTAGCTCTAGTACAAA
*
89737103 AATAT-CACGAACCC
129 AATGTCCA-GAACCC
* * * * * *
89737117 TTTTGAATGAGAGAGAGAGACAC-AG-AAAAA---TTCGAATGCAAGACAATATTAAGATTCTAG
1 TTTCGAATGAGA-A-ACACACACAAGAAAAAATCTTTCAAATGCAAGACAATATTAGGGTTCTAG
* * * * *
89737177 CTTGGCTTTGCACCTTTAACAACACTAGTTCTGCCATTGCCTAGTGAATTTAGCTCTACTACAAA
64 CTCGGCTTTGCGCCCTTAACAACACTAGTTGTGCCATTGCCTAGTGAATTTAGCTCTAGTACAAA
*
89737242 AATGTCTTA-AACCC
129 AATGTC-CAGAACCC
* ** *
89737256 TTTCGACA-GAGAAACACATACAA-AAAACCTCTTTCGAATGCAAGACAAT-TTAGGGGTTCTAG
1 TTTCGA-ATGAGAAACACACACAAGAAAAAATCTTTCAAATGCAAGACAATATTA-GGGTTCTAG
* * * *
89737318 CTTGGCTTTGCG-------C--C-CT--TTCTGCCATTGCCTAGTGAATTTAGTTTTAGTACAAA
64 CTCGGCTTTGCGCCCTTAACAACACTAGTTGTGCCATTGCCTAGTGAATTTAGCTCTAGTACAAA
89737371 AATGTCTC-GAACCC
129 AATGTC-CAGAACCC
*
89737385 TTTCGAATGAGACACACACACA
1 TTTCGAATGAGAAACACACACA
89737407 CACACAAAAA
Statistics
Matches: 378, Mismatches: 40, Indels: 48
0.81 0.09 0.10
Matches are distributed among these distances:
128 1 0.00
129 64 0.17
131 2 0.01
132 1 0.00
134 1 0.00
137 5 0.01
138 5 0.01
139 105 0.28
140 4 0.01
141 36 0.10
143 12 0.03
144 114 0.30
145 22 0.06
146 6 0.02
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (142 bp):
TTTCGAATGAGAAACACACACAAGAAAAAATCTTTCAAATGCAAGACAATATTAGGGTTCTAGCT
CGGCTTTGCGCCCTTAACAACACTAGTTGTGCCATTGCCTAGTGAATTTAGCTCTAGTACAAAAA
TGTCCAGAACCC
Done.