Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 144 of 335
Found at i:42426649 original size:48 final size:48
Alignment explanation
Indices: 42426596--42426789 Score: 325
Period size: 48 Copynumber: 4.0 Consensus size: 48
42426586 CGAATGGCTA
*
42426596 ATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
42426644 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
42426692 ATATGTATATATGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
42426740 ATATGTATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
42426788 AT
1 AT
42426790 GGGTGTATAT
Statistics
Matches: 138, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 138 1.00
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:42426695 original size:126 final size:126
Alignment explanation
Indices: 42426470--42426721 Score: 459
Period size: 126 Copynumber: 2.0 Consensus size: 126
42426460 TATGTATGAG
* *
42426470 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGGAATATGTATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATATGTATGAGATATGTATATGTGGTAA
* * *
42426535 AGCCGAATGGCTAATGTGGAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
66 AGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATATGGTAAAGCCGAATGGCTA
42426596 ATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATATGTATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATATGTATGAGATATGTATATGTGGTAA
42426661 AGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATATGGTAAAGCCGAATGGCTA
66 AGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATATGGTAAAGCCGAATGGCTA
42426722 GTGTGAAATA
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 121 1.00
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (126 bp):
ATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATATGTATGAGATATGTATATGTGGTAA
AGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATATGGTAAAGCCGAATGGCTA
Found at i:42426712 original size:174 final size:174
Alignment explanation
Indices: 42426422--42426769 Score: 624
Period size: 174 Copynumber: 2.0 Consensus size: 174
42426412 AGATAAATAT
*
42426422 ATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCAAATGGATAATGTGAAATATGTATGAGATATGTATATGTGGTAA
* * *
42426487 AGCCGAATGGCTAATGTGGAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGT
66 AGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATATGGTAAAGCCGAATGGCTAATGT
*
42426552 GGAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
131 GAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
*
42426596 ATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATATGTATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCAAATGGATAATGTGAAATATGTATGAGATATGTATATGTGGTAA
*
42426661 AGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATATGGTAAAGCCGAATGGCTAGTGT
66 AGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATATGGTAAAGCCGAATGGCTAATGT
*
42426726 GAAATATGTATGAGATATGTATATGTGGTAAAGCTGAATGGCTA
131 GAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
42426770 GTGTGAAATA
Statistics
Matches: 166, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 166 1.00
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.31
Consensus pattern (174 bp):
ATATGTATATGTGGTAAAGCCAAATGGATAATGTGAAATATGTATGAGATATGTATATGTGGTAA
AGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATATGGTAAAGCCGAATGGCTAATGT
GAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
Found at i:42426980 original size:37 final size:37
Alignment explanation
Indices: 42426930--42427032 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
42426920 GGAAATATAT
42426930 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
42426967 TCCGGGTAAGACCCGATGACTACATGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
42427004 CCCGGGTAAAACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
42427033 GGACTATTCG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.23
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:42428480 original size:6 final size:6
Alignment explanation
Indices: 42428465--42428598 Score: 87
Period size: 6 Copynumber: 21.8 Consensus size: 6
42428455 ATTCTGTTAC
* * *
42428465 CTGATA CTGATT CTGATT TTGATT CTG-TT ACCTGATA CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT
* * * *
42428514 CTAATT CTG-TCAC CTAATT CTGATT CTGATT CTGATT CTGATT CTG-TCAC
1 CTGATT CTGAT--T CTGATT CTGATT CTGATT CTGATT CTGATT CTGAT--T
* * *
42428564 CTAATT TTGATT TTGATT CTGATT CT-AGTT CTGAT
1 CTGATT CTGATT CTGATT CTGATT CTGA-TT CTGAT
42428599 AATGTTTCTT
Statistics
Matches: 100, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
5 5 0.05
6 84 0.84
7 8 0.08
8 3 0.03
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (6 bp):
CTGATT
Found at i:42428493 original size:31 final size:31
Alignment explanation
Indices: 42428455--42428553 Score: 153
Period size: 31 Copynumber: 3.2 Consensus size: 31
42428445 CTGATTTTTT
*
42428455 ATTCTGTTACCTGATACTGATTCTGATTTTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
*
42428486 ATTCTGTTACCTGATACTGATTCTGATTCTA
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
* * *
42428517 ATTCTGTCACCTAATTCTGATTCTGATTCTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
42428548 ATTCTG
1 ATTCTG
42428554 ATTCTGTCAC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.46
Consensus pattern (31 bp):
ATTCTGTTACCTGATACTGATTCTGATTCTG
Found at i:42428506 original size:37 final size:36
Alignment explanation
Indices: 42428465--42428587 Score: 130
Period size: 37 Copynumber: 3.5 Consensus size: 36
42428455 ATTCTGTTAC
* * *
42428465 CTGATACTGATTCTGATTTTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGA-TTTGATTCTGTCACCTAATA
*
42428502 CTGATTCTGATTCT-A----ATTCTGTCACCTAATT
1 CTGATTCTGATTCTGATTTGATTCTGTCACCTAATA
*
42428533 CTGATTCTGATTCTGATTCTGATTCTGTCACCTAATT
1 CTGATTCTGATTCTGATT-TGATTCTGTCACCTAATA
* *
42428570 TTGATTTTGATTCTGATT
1 CTGATTCTGATTCTGATT
42428588 CTAGTTCTGA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
31 27 0.36
32 1 0.01
36 1 0.01
37 45 0.61
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (36 bp):
CTGATTCTGATTCTGATTTGATTCTGTCACCTAATA
Found at i:42428575 original size:31 final size:31
Alignment explanation
Indices: 42428472--42428589 Score: 119
Period size: 31 Copynumber: 3.6 Consensus size: 31
42428462 TACCTGATAC
* * * **
42428472 TGATTCTGATTTTGATTCTGTTACCTGATAC
1 TGATTCTGATTCTGATTCTGTCACCTAATTT
*
42428503 TGATTCTGATTCTAATTCTGTCACCTAATTCTGATT
1 TGATTCTGATTCTGATTCTGTCACCTAA---T--TT
42428539 CTGATTCTGATTCTGATTCTGTCACCTAATTT
1 -TGATTCTGATTCTGATTCTGTCACCTAATTT
*
42428571 TGATTTTGATTCTGATTCT
1 TGATTCTGATTCTGATTCT
42428590 AGTTCTGATA
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
31 42 0.58
32 2 0.03
34 2 0.03
37 27 0.37
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (31 bp):
TGATTCTGATTCTGATTCTGTCACCTAATTT
Found at i:42428588 original size:37 final size:37
Alignment explanation
Indices: 42428496--42428596 Score: 157
Period size: 37 Copynumber: 2.7 Consensus size: 37
42428486 ATTCTGTTAC
*
42428496 CTGATACTGATTCTGATTCTAATTCTGTCACCTAATT
1 CTGATTCTGATTCTGATTCTAATTCTGTCACCTAATT
*
42428533 CTGATTCTGATTCTGATTCTGATTCTGTCACCTAATT
1 CTGATTCTGATTCTGATTCTAATTCTGTCACCTAATT
* * *
42428570 TTGATTTTGATTCTGATTCTAGTTCTG
1 CTGATTCTGATTCTGATTCTAATTCTG
42428597 ATAATGTTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.48
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTAATTCTGTCACCTAATT
Found at i:42430796 original size:42 final size:41
Alignment explanation
Indices: 42430713--42430855 Score: 130
Period size: 43 Copynumber: 3.3 Consensus size: 41
42430703 TCCCAGGCGT
* *
42430713 GGTCTTACATGTAATCAAATATCGATGCCACTAT-CCCAGACAG
1 GGTCTTACACGAAATCAAATAT-GATGCCA--ATGCCCAGACAG
*
42430756 GGTCTTACACGAAATCAAATATGATGCCAATGCCCAAGACAT
1 GGTCTTACACGAAATCAAATATGATGCCAATGCCC-AGACAG
* * *
42430798 GGTCTTACACATAAATCATAAGT-TGATGCCAACGTCCCAGA-TG
1 GGTCTTACAC-GAAATCA-AA-TATGATGCCAATG-CCCAGACAG
42430841 TGGTCTTACACGAAA
1 -GGTCTTACACGAAA
42430856 ACACATATCG
Statistics
Matches: 85, Mismatches: 8, Indels: 14
0.79 0.07 0.13
Matches are distributed among these distances:
40 2 0.02
41 3 0.04
42 22 0.26
43 29 0.34
44 25 0.29
45 4 0.05
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
GGTCTTACACGAAATCAAATATGATGCCAATGCCCAGACAG
Found at i:42434313 original size:5 final size:5
Alignment explanation
Indices: 42434303--42434327 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42434293 CATGGAGACA
42434303 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
42434328 GGTCAAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:42435389 original size:70 final size:70
Alignment explanation
Indices: 42435306--42435590 Score: 498
Period size: 70 Copynumber: 4.1 Consensus size: 70
42435296 AGTTTATTAT
*
42435306 TAATTAATATGCTGCTGTTATACTGTAAATTATTGGCTATCCAAATTAGGACAAATTCATGGTGC
1 TAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTATCCAAATTAGGACAAATTCATGGTGC
42435371 TTAGC
66 TTAGC
*
42435376 TAATTAATATGCTGCTGTAATATTGTAAATTATTGGCTATCCAAATTAGGACAAATTCATGGTGC
1 TAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTATCCAAATTAGGACAAATTCATGGTGC
42435441 TTAGC
66 TTAGC
* * *
42435446 TAATTAATATGCCGCTGTTATACTGTAAATTATTGGCTGTCCAAATTAGGACAAATTCATGGTGC
1 TAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTATCCAAATTAGGACAAATTCATGGTGC
42435511 TTAGC
66 TTAGC
* * *
42435516 TAATTAATATGCTGCTGTAATATTGTAAATTATTGGCTATCCAAATTAGTACAAATTCATGGTGT
1 TAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTATCCAAATTAGGACAAATTCATGGTGC
42435581 TTAGC
66 TTAGC
42435586 TAATT
1 TAATT
42435591 CAAGGAAGAT
Statistics
Matches: 203, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 203 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (70 bp):
TAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTATCCAAATTAGGACAAATTCATGGTGC
TTAGC
Found at i:42436057 original size:48 final size:47
Alignment explanation
Indices: 42435985--42436206 Score: 214
Period size: 48 Copynumber: 4.7 Consensus size: 47
42435975 TATGTGTGCT
* * * **
42435985 AGTGTAAGAACATGTTTGGAACATGGCATCAACCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACA-TATGAGAGCC
* * *** * *
42436033 AGTGTAAGACCATGTCTGGGACATGACATTGGCGTTGATATGTGCA-CT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CACATATGAG-AGCC
42436081 AGTGTAA-ACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACA-TATGAGAGCC
* * * *
42436128 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGACATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATATGAGAGCC
* * *
42436176 AATGTAAGACCATGTCTAGGACATAGCATCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCG
42436207 ACAATTTACC
Statistics
Matches: 141, Mismatches: 27, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
46 2 0.01
47 36 0.26
48 100 0.71
49 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATATGAGAGCC
Found at i:42436125 original size:95 final size:95
Alignment explanation
Indices: 42435972--42436208 Score: 296
Period size: 95 Copynumber: 2.5 Consensus size: 95
42435962 GACATTTGGG
* * * * *
42435972 TGATATGTGTGCTAGTGTAAGAACATGTTTGGAACATGGCATCAACCACATTATGAGAGCCAGTG
1 TGATATGTG-ACTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACATTATGAGAGCCAGTG
* *
42436037 TAAGACCATGTCTGGGACATGACATTGGCGT
65 TAAGACCATGTCTGGGACATGACATCGGCCT
*
42436068 TGATATGTGCACTAGTGTAA-ACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCCAGTG
1 TGATATGTG-ACTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACATTATGAGAGCCAGTG
* *
42436132 TAAGACCATGTTTGGGACATGGCATCGGCCT
65 TAAGACCATGTCTGGGACATGACATCGGCCT
* * * * * *
42436163 CGACATGTGAGCCAATGTAAGACCATGTCTAGGACATAGCATCGAC
1 TGATATGTGA-CTAGTGTAAGACCATGTCTGGGACATGGCATCGAC
42436209 AATTTACCCT
Statistics
Matches: 121, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
94 1 0.01
95 80 0.66
96 40 0.33
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (95 bp):
TGATATGTGACTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACATTATGAGAGCCAGTGT
AAGACCATGTCTGGGACATGACATCGGCCT
Found at i:42440246 original size:22 final size:21
Alignment explanation
Indices: 42440199--42440246 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
42440189 AAATTAATTT
*
42440199 TTTCTTAAAAACAATCACTTCT
1 TTTCTTAAAAACAA-CACTTCA
42440221 TTTCTTAAAAATCAA-AGCTTCA
1 TTTCTTAAAAA-CAACA-CTTCA
42440243 TTTC
1 TTTC
42440247 AAATTAGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 1 0.04
22 19 0.83
23 3 0.13
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTCTTAAAAACAACACTTCA
Found at i:42440459 original size:150 final size:151
Alignment explanation
Indices: 42440196--42440500 Score: 411
Period size: 150 Copynumber: 2.0 Consensus size: 151
42440186 GCAAAATTAA
*
42440196 TTTTTTCTTAAAAACAATCACTTCTTTTCTTAAAAATCAAAGCTTCATTTCAAATTAGTTGAAAA
1 TTTTTTCTTAAAAAAAATCACTTCTTTTCTTAAAAATCAAAGCTTCATTTCAAATTAGTTGAAAA
* * * *
42440261 AGATCAAAACTTTGTTTTCAAAATTTAAAATTTTCCTTTAAAATGACTA-AAAAAATATTTTTAT
66 AGATCAAAAATTTATTTTAAAAATTTAAAATTTTCCTTTAAAATGACTAGAAAAAAGATTTTTAT
*
42440325 TTTTACAAATATAAAAATTCTC
131 TTTGA-AAATATAAAAATTCTC
* * * *
42440347 TTTTTT-TTAAAAAAAATCACTAT-TTTTCTTAAAAATTAAAGTTTTATTTTGAAA-TAGTTGAA
1 TTTTTTCTTAAAAAAAATCACT-TCTTTTCTTAAAAATCAAAGCTTCA-TTTCAAATTAGTTGAA
* * *
42440409 AAAGTTCAAAAATTTATTTTAAAAATTTAAACTTTTCCTTTAAAATGACTAGAAAATAGATTTTT
64 AAAGATCAAAAATTTATTTTAAAAATTTAAAATTTTCCTTTAAAATGACTAGAAAAAAGATTTTT
* **
42440474 ATTTTGAAAATCTAAACTTTCTC
129 ATTTTGAAAATATAAAAATTCTC
42440497 TTTT
1 TTTT
42440501 AAAACAAAAA
Statistics
Matches: 135, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
150 105 0.78
151 30 0.22
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (151 bp):
TTTTTTCTTAAAAAAAATCACTTCTTTTCTTAAAAATCAAAGCTTCATTTCAAATTAGTTGAAAA
AGATCAAAAATTTATTTTAAAAATTTAAAATTTTCCTTTAAAATGACTAGAAAAAAGATTTTTAT
TTTGAAAATATAAAAATTCTC
Found at i:42445232 original size:20 final size:20
Alignment explanation
Indices: 42445207--42445251 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
42445197 GAACTATTCT
*
42445207 ATTTACTTTCTTACCATTTC
1 ATTTACTTACTTACCATTTC
*
42445227 ATTTACTTACTTTCCATTTC
1 ATTTACTTACTTACCATTTC
42445247 ATTTA
1 ATTTA
42445252 TTTAGCATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTACTTACTTACCATTTC
Found at i:42446532 original size:30 final size:30
Alignment explanation
Indices: 42446496--42446563 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
42446486 TATGTGACCA
* *
42446496 GCCTGTGTGCCCTTCGTAATGGCCTCAGAG
1 GCCTGTGTGCCATTCGTAATGGCCTCAGAC
42446526 GCCTGTGTGCCATTCGTAATGGCCTCAGAC
1 GCCTGTGTGCCATTCGTAATGGCCTCAGAC
42446556 GCCTGTGT
1 GCCTGTGT
42446564 CGCAGACCGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.13, C:0.29, G:0.29, T:0.28
Consensus pattern (30 bp):
GCCTGTGTGCCATTCGTAATGGCCTCAGAC
Found at i:42451863 original size:29 final size:29
Alignment explanation
Indices: 42451821--42451936 Score: 126
Period size: 29 Copynumber: 4.0 Consensus size: 29
42451811 GCGAGCATGA
* * *
42451821 ATATGAATATGATTTGGGTCTGATGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
42451850 ATATAAATGTGATTTGGGCCTGATGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
** * * * *
42451879 ATATAAATGCAAATTAGGCCTAACGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
* *
42451908 ATACAAATGTGA-TTGGGCCTGGTGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
42451936 A
1 A
42451937 GATACAGGTA
Statistics
Matches: 71, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
28 13 0.18
29 58 0.82
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTGATGGGCC
Found at i:42452251 original size:26 final size:27
Alignment explanation
Indices: 42452221--42452275 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
42452211 AACCGTAATA
* * *
42452221 AAAGG-AAAAATTACTGAAATGCCCCT
1 AAAGGCAAAAATGACCGAAATACCCCT
42452247 AAAGGCAAAAATGACCGAAATACCCCT
1 AAAGGCAAAAATGACCGAAATACCCCT
42452274 AA
1 AA
42452276 GTGTTGAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.49, C:0.22, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAGGCAAAAATGACCGAAATACCCCT
Found at i:42455512 original size:14 final size:14
Alignment explanation
Indices: 42455475--42455506 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
42455465 GTACGAACAC
42455475 TATGAGTTTTTGGT
1 TATGAGTTTTTGGT
42455489 TATGAGTTTTTGGT
1 TATGAGTTTTTGGT
42455503 TATG
1 TATG
42455507 CATTTTGGAC
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:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (14 bp):
TATGAGTTTTTGGT
Found at i:42460818 original size:36 final size:36
Alignment explanation
Indices: 42460776--42460847 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
42460766 ATAGTAGTCA
42460776 AATTTAATCATTTTCGGCCATAACATATTAAAAATT
1 AATTTAATCATTTTCGGCCATAACATATTAAAAATT
42460812 AATTTAATCATTTTCGGCCATAACATATTAAAAATT
1 AATTTAATCATTTTCGGCCATAACATATTAAAAATT
42460848 CTACATTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.39
Consensus pattern (36 bp):
AATTTAATCATTTTCGGCCATAACATATTAAAAATT
Found at i:42470779 original size:28 final size:28
Alignment explanation
Indices: 42470713--42470811 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
42470703 TCATGAATTG
* **
42470713 GCACTAAGTGTGCGGGTTCAAATTGA-ATA
1 GCACTAAGTGTGCGAGTT-TGATT-ATATA
42470742 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
42470770 GCACTAAGTGTCCGAGTTTGACTAT-TAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
42470798 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42470812 GGCTTATTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
27 2 0.03
28 43 0.69
29 17 0.27
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:42477547 original size:32 final size:32
Alignment explanation
Indices: 42477511--42477592 Score: 146
Period size: 32 Copynumber: 2.6 Consensus size: 32
42477501 GGTTTGATAT
42477511 TGAAATGGGCTAGGCCTAACTGATATTGATTC
1 TGAAATGGGCTAGGCCTAACTGATATTGATTC
*
42477543 TGAAATGGGCTAGGCCCAACTGATATTGATTC
1 TGAAATGGGCTAGGCCTAACTGATATTGATTC
*
42477575 TGAGATGGGCTAGGCCTA
1 TGAAATGGGCTAGGCCTA
42477593 GTTGAGACTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (32 bp):
TGAAATGGGCTAGGCCTAACTGATATTGATTC
Found at i:42478338 original size:21 final size:22
Alignment explanation
Indices: 42478296--42478338 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
42478286 TTTTCATTTA
*
42478296 TTTCACAATTTAACCACAAAAT
1 TTTCACAATTTAACCAAAAAAT
42478318 TTTCAC-ATTTAA-CAAATAAAT
1 TTTCACAATTTAACCAAA-AAAT
42478339 CCTTATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 10 0.53
22 6 0.32
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTCACAATTTAACCAAAAAAT
Found at i:42488958 original size:38 final size:40
Alignment explanation
Indices: 42488868--42489081 Score: 257
Period size: 39 Copynumber: 5.5 Consensus size: 40
42488858 CAAGTATCTT
* *
42488868 GGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCTTC
1 GGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTC
* **
42488907 GGGTCTTAGCCCGGATATAGTCACTAGCATGAAT-CCTTC
1 GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
42488946 -GGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
1 GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
42488985 GGGACTTAGCCC-G-TATAG-CAACTACTCGCACAAATGCCTTC
1 GGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGCCTTC
* *
42489026 GGGACTTAGCCC-GATATAGTAACTTGCACAAATGCCTTC
1 GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
42489065 GGGACTTAG-CCGGATAT
1 GGGACTTAGCCCGGATAT
42489082 CATCCGAATA
Statistics
Matches: 154, Mismatches: 10, Indels: 22
0.83 0.05 0.12
Matches are distributed among these distances:
37 1 0.01
38 41 0.27
39 46 0.30
40 30 0.19
41 28 0.18
42 8 0.05
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
Found at i:42489061 original size:80 final size:78
Alignment explanation
Indices: 42488868--42489081 Score: 258
Period size: 80 Copynumber: 2.7 Consensus size: 78
42488858 CAAGTATCTT
* * * * *
42488868 GGGATTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTCACTA
1 GGGACTTAGCCCGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
**
42488933 GCATGAATCCTTC
66 GCACAAATCCTTC
*
42488946 -GGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCC-G-TATAG-CAAC
1 GGGACTTAGCCC-GATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTC-AC
42489007 TACTCGCACAAATGCCTTC
64 TA---GCACAAAT-CCTTC
*
42489026 GGGACTTAGCCCGATATAGTAACTTGCACAAATGCCTTCGGGACTTAG-CCGGATAT
1 GGGACTTAGCCCGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
42489082 CATCCGAATA
Statistics
Matches: 117, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
75 1 0.01
76 9 0.08
77 10 0.09
78 35 0.30
79 8 0.07
80 40 0.34
81 14 0.12
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (78 bp):
GGGACTTAGCCCGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
GCACAAATCCTTC
Found at i:42494166 original size:80 final size:80
Alignment explanation
Indices: 42494082--42494230 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
42494072 TATGGTAACC
* * * *
42494082 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
42494146 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
42494162 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
42494227 CCGG
66 CCGG
42494231 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:42494172 original size:40 final size:38
Alignment explanation
Indices: 42494123--42494230 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
42494113 ATCACGATTT
*
42494123 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
42494163 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
42494203 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
42494231 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:42496611 original size:34 final size:34
Alignment explanation
Indices: 42496572--42496640 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
42496562 TAAAACACCA
*
42496572 TAGTTTTTAATTAAGGGCATTTTGGTCATTTAGT
1 TAGTTTCTAATTAAGGGCATTTTGGTCATTTAGT
42496606 TAGTTTCTAATTAAGGGCATTTTGGTCATTTAGT
1 TAGTTTCTAATTAAGGGCATTTTGGTCATTTAGT
42496640 T
1 T
42496641 GTTAAAATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.49
Consensus pattern (34 bp):
TAGTTTCTAATTAAGGGCATTTTGGTCATTTAGT
Found at i:42499489 original size:23 final size:23
Alignment explanation
Indices: 42499457--42499562 Score: 63
Period size: 24 Copynumber: 4.5 Consensus size: 23
42499447 CTGAGTTGAT
* *
42499457 AAACAATAAGCTTTATTGAGCTA
1 AAACAGTAAGCTTCATTGAGCTA
** *
42499480 AAACAGTAAGCTCTTTTTCAAGCT-
1 AAACAGTAAGCT-TCATT-GAGCTA
* * *
42499504 GAACAGTAAGC-TCATACGAGCTG
1 AAACAGTAAGCTTCAT-TGAGCTA
* *
42499527 AAACAGTAAGCTCCAATGAGCTAA
1 AAACAGTAAGCTTCATTGAGCT-A
*
42499551 AAATAGTAAGCT
1 AAACAGTAAGCT
42499563 CTTTCGAGCT
Statistics
Matches: 63, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
22 6 0.10
23 26 0.41
24 27 0.43
25 4 0.06
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.25
Consensus pattern (23 bp):
AAACAGTAAGCTTCATTGAGCTA
Found at i:42502196 original size:47 final size:47
Alignment explanation
Indices: 42502127--42502420 Score: 473
Period size: 47 Copynumber: 6.3 Consensus size: 47
42502117 CCCTTCGGGA
* *
42502127 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
42502174 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
42502221 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
42502268 CTTATCACACATATGCACTTTCACATTCATCACA-TGGCCATTAGGC
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
42502314 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
42502361 CTTATCACACATATACACTTTCACATTCATCACATGGGCCATTAGGC
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
42502408 CTTATCATCACAT
1 CTTATCA-CACAT
42502421 GGCCATTAGG
Statistics
Matches: 228, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
46 42 0.18
47 181 0.79
48 5 0.02
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.31
Consensus pattern (47 bp):
CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:42502300 original size:25 final size:25
Alignment explanation
Indices: 42502224--42502301 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
42502214 ATTCGGCCTT
*
42502224 ATCACACATATACACTTTCACATTC
1 ATCACACATATGCACTTTCACATTC
* * *
42502249 AT--CACAT-TGGC-CATTCGGCCTT-
1 ATCACACATAT-GCACTTTC-ACATTC
42502271 ATCACACATATGCACTTTCACATTC
1 ATCACACATATGCACTTTCACATTC
42502296 ATCACA
1 ATCACA
42502302 TGGCCATTAG
Statistics
Matches: 39, Mismatches: 7, Indels: 14
0.65 0.12 0.23
Matches are distributed among these distances:
22 7 0.18
23 9 0.23
24 10 0.26
25 13 0.33
ACGTcount: A:0.31, C:0.32, G:0.06, T:0.31
Consensus pattern (25 bp):
ATCACACATATGCACTTTCACATTC
Found at i:42502380 original size:140 final size:141
Alignment explanation
Indices: 42502127--42502420 Score: 554
Period size: 140 Copynumber: 2.1 Consensus size: 141
42502117 CCCTTCGGGA
42502127 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
42502192 TTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATATACACTTTCACATTCATCACATT
66 TTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATATACACTTTCACATTCATCACATG
*
42502257 GGCCATTCGGC
131 GGCCATTAGGC
42502268 CTTATCACACATATGCACTTTCACATTCATCACAT-GGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
42502332 TTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATATACACTTTCACATTCATCACATG
66 TTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATATACACTTTCACATTCATCACATG
42502397 GGCCATTAGGC
131 GGCCATTAGGC
42502408 CTTATCATCACAT
1 CTTATCA-CACAT
42502421 GGCCATTAGG
Statistics
Matches: 150, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
140 110 0.73
141 40 0.27
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.31
Consensus pattern (141 bp):
CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATATACACTTTCACATTCATCACATG
GGCCATTAGGC
Found at i:42502429 original size:24 final size:25
Alignment explanation
Indices: 42502387--42502438 Score: 97
Period size: 24 Copynumber: 2.1 Consensus size: 25
42502377 ACTTTCACAT
42502387 TCATCACATGGGCCATTAGGCCTTA
1 TCATCACATGGGCCATTAGGCCTTA
42502412 TCATCACAT-GGCCATTAGGCCTTA
1 TCATCACATGGGCCATTAGGCCTTA
42502436 TCA
1 TCA
42502439 CATATATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (25 bp):
TCATCACATGGGCCATTAGGCCTTA
Found at i:42502435 original size:71 final size:70
Alignment explanation
Indices: 42502341--42502489 Score: 237
Period size: 71 Copynumber: 2.1 Consensus size: 70
42502331 CTTTCACATC
*
42502341 CATCACATTGGCCATTCGGCCTTATCACACATATACACTTTCACATTCATCACATGGGCCATTAG
1 CATCACA-TGGCCATTAGGCCTTATCACACATATACACTTTCACA-TCATCACATGGGCCATTAG
42502406 GCCTTAT
64 GCCTTAT
* * *
42502413 CATCACATGGCCATTAGGCCTTATCACATATATACACTTTCACATCATCACATTGGCCATTCGGC
1 CATCACATGGCCATTAGGCCTTATCACACATATACACTTTCACATCATCACATGGGCCATTAGGC
42502478 CTTAT
66 CTTAT
42502483 CA-CACAT
1 CATCACAT
42502490 ATACACTTTC
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
69 5 0.07
70 26 0.36
71 35 0.48
72 7 0.10
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.30
Consensus pattern (70 bp):
CATCACATGGCCATTAGGCCTTATCACACATATACACTTTCACATCATCACATGGGCCATTAGGC
CTTAT
Found at i:42502436 original size:164 final size:164
Alignment explanation
Indices: 42502247--42502583 Score: 543
Period size: 164 Copynumber: 2.1 Consensus size: 164
42502237 ACTTTCACAT
* *
42502247 TCATCACATTGGCCATTCGGCCTTATCACACATATGCACTTTCACATTCATCACA-TGGCCATTA
1 TCATCACA-TGGCCATTAGGCCTTATCACACATATACACTTTCACA-TCATCACATTGGCCATTA
* * *
42502311 GGCCTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATATA
64 GGCCTTATCACACATATACACTTTCACATCCATCACATGGGCCATTAGGCCTTATCACACATATA
42502376 CACTTTCACATTCATCACATGGGCCATTAGGCCTTA
129 CACTTTCACATTCATCACATGGGCCATTAGGCCTTA
* *
42502412 TCATCACATGGCCATTAGGCCTTATCACATATATACACTTTCACATCATCACATTGGCCATTCGG
1 TCATCACATGGCCATTAGGCCTTATCACACATATACACTTTCACATCATCACATTGGCCATTAGG
* *
42502477 CCTTATCACACATATACACTTTCACATTCATCACATGGGCCATTAGGCCTTATCACATATATACA
66 CCTTATCACACATATACACTTTCACATCCATCACATGGGCCATTAGGCCTTATCACACATATACA
* *
42502542 CTTTCACATTCATCACATTGGCCATTTGGCCTTA
131 CTTTCACATTCATCACATGGGCCATTAGGCCTTA
42502576 TCA-CACAT
1 TCATCACAT
42502584 ATATGTATAT
Statistics
Matches: 160, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
163 13 0.08
164 139 0.87
165 8 0.05
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.31
Consensus pattern (164 bp):
TCATCACATGGCCATTAGGCCTTATCACACATATACACTTTCACATCATCACATTGGCCATTAGG
CCTTATCACACATATACACTTTCACATCCATCACATGGGCCATTAGGCCTTATCACACATATACA
CTTTCACATTCATCACATGGGCCATTAGGCCTTA
Found at i:42502510 original size:71 final size:71
Alignment explanation
Indices: 42502362--42502512 Score: 180
Period size: 70 Copynumber: 2.1 Consensus size: 71
42502352 CCATTCGGCC
* * *
42502362 TTATCACACATATACACTTTCACATTCATCACATGGGCCATTAGGCCTTATCATCACATGGCCAT
1 TTATCACATATATACACTTTCACATTCATCACATGGGCCATTAGGCCTTATCATCACATAGACAT
** *
42502427 TAGGCC
66 TACACA
* * *
42502433 TTATCACATATATACACTTTCACA-TCATCACATTGGCCATTCGGCCTTATCA-CACATATACAC
1 TTATCACATATATACACTTTCACATTCATCACATGGGCCATTAGGCCTTATCATCACATAGACA-
*
42502496 TTTCACA
65 TTACACA
42502503 TTCATCACAT
1 TT-ATCACAT
42502513 GGGCCATTAG
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
69 7 0.10
70 31 0.46
71 30 0.44
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (71 bp):
TTATCACATATATACACTTTCACATTCATCACATGGGCCATTAGGCCTTATCATCACATAGACAT
TACACA
Found at i:42502510 original size:117 final size:118
Alignment explanation
Indices: 42502294--42502531 Score: 469
Period size: 117 Copynumber: 2.0 Consensus size: 118
42502284 ACTTTCACAT
42502294 TCATCACATGGCCATTAGGCCTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCG
1 TCATCACATGGCCATTAGGCCTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCG
42502359 GCCTTATCACACATATACACTTTCACATTCATCACATGGGCCATTAGGCCTTA
66 GCCTTATCACACATATACACTTTCACATTCATCACATGGGCCATTAGGCCTTA
42502412 TCATCACATGGCCATTAGGCCTTATCACATATATACACTTTCACAT-CATCACATTGGCCATTCG
1 TCATCACATGGCCATTAGGCCTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCG
42502476 GCCTTATCACACATATACACTTTCACATTCATCACATGGGCCATTAGGCCTTA
66 GCCTTATCACACATATACACTTTCACATTCATCACATGGGCCATTAGGCCTTA
42502529 TCA
1 TCA
42502532 CATATATACA
Statistics
Matches: 120, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
117 74 0.62
118 46 0.38
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.31
Consensus pattern (118 bp):
TCATCACATGGCCATTAGGCCTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCG
GCCTTATCACACATATACACTTTCACATTCATCACATGGGCCATTAGGCCTTA
Found at i:42502518 original size:93 final size:93
Alignment explanation
Indices: 42502412--42502586 Score: 325
Period size: 93 Copynumber: 1.9 Consensus size: 93
42502402 TTAGGCCTTA
42502412 TCATCACATGGCCATTAGGCCTTATCACATATATACACTTTCACA-TCATCACATTGGCCATTCG
1 TCATCACATGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCG
42502476 GCCTTATCACACATATACACTTTCACAT
66 GCCTTATCACACATATACACTTTCACAT
*
42502504 TCATCACATGGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTT
1 TCATCACAT-GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTC
42502569 GGCCTTATCACACATATA
65 GGCCTTATCACACATATA
42502587 TGTATATCAT
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
92 9 0.11
93 36 0.45
94 35 0.44
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (93 bp):
TCATCACATGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCG
GCCTTATCACACATATACACTTTCACAT
Found at i:42502526 original size:47 final size:47
Alignment explanation
Indices: 42502412--42502586 Score: 291
Period size: 47 Copynumber: 3.8 Consensus size: 47
42502402 TTAGGCCTTA
*
42502412 TCATCACA-TGGCCATTAGGCCTTATCACATATATACACTTTCACA-
1 TCATCACATTGGCCATTAGGCCTTATCACACATATACACTTTCACAT
*
42502457 TCATCACATTGGCCATTCGGCCTTATCACACATATACACTTTCACAT
1 TCATCACATTGGCCATTAGGCCTTATCACACATATACACTTTCACAT
* *
42502504 TCATCACATGGGCCATTAGGCCTTATCACATATATACACTTTCACAT
1 TCATCACATTGGCCATTAGGCCTTATCACACATATACACTTTCACAT
*
42502551 TCATCACATTGGCCATTTGGCCTTATCACACATATA
1 TCATCACATTGGCCATTAGGCCTTATCACACATATA
42502587 TGTATATCAT
Statistics
Matches: 120, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
45 8 0.07
46 35 0.29
47 77 0.64
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (47 bp):
TCATCACATTGGCCATTAGGCCTTATCACACATATACACTTTCACAT
Found at i:42506964 original size:46 final size:45
Alignment explanation
Indices: 42506914--42507089 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
42506904 TGGTTGAGCA
42506914 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
42506960 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
42507007 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
42507053 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42507090 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:42507070 original size:93 final size:93
Alignment explanation
Indices: 42506911--42507081 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
42506901 GGATGGTTGA
* *
42506911 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42506976 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
42507004 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42507069 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
42507082 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:42510654 original size:47 final size:49
Alignment explanation
Indices: 42510585--42510809 Score: 193
Period size: 47 Copynumber: 4.8 Consensus size: 49
42510575 TAAGGTGCCA
**
42510585 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCTC-AAATTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAACCG
* * *
42510632 ATGCCATGTCCCAGACATGGTCTTACACTGTCT-ATCATCTCGTAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAACCG
* * * ** *
42510680 AT-ACATGTCCCAGACAT-GTCTTACACTGGCTTA-CGTCTCGAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAACCG
* * * ** * *
42510726 ATG-TATGTCCTAGACAT-GTCTTACACTAGCTC-TGGTCT-TAATGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAA-ACCG
*
42510772 ATGCCAAGTCCCAGACATGGTCTTACACTGGCTC-TCAT
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAT
42510810 AATGTGGCTG
Statistics
Matches: 145, Mismatches: 25, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
45 1 0.01
46 61 0.42
47 63 0.43
48 20 0.14
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAACCG
Found at i:42510719 original size:46 final size:46
Alignment explanation
Indices: 42510589--42510846 Score: 197
Period size: 46 Copynumber: 5.5 Consensus size: 46
42510579 GTGCCAATGC
* ****
42510589 CATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCT-CAAATTGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTC-TCATCTGTAGGCCGATG
* * *
42510635 CCATGTCCCAGACATGGTCTTACACTGTCTATCATCTCGTA-GCCGATA
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCT-GTAGGCCGATG
* *
42510683 CATGTCCCAGACATGTCTTACACTGGCT-TACGTCTCG-AGGCTGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCT-CATCT-GTAGGCCGATG
* * * ** *
42510729 TATGTCCTAGACATGTCTTACACTAGCTCTGGTCT-TAATGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTCATCTGT-AGGCCGATG
* * *
42510775 CCAAGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT-GGCTGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTGTAGGCCGATG
42510823 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
42510847 AGCCAGCAAT
Statistics
Matches: 172, Mismatches: 27, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
45 2 0.01
46 71 0.41
47 71 0.41
48 25 0.15
49 2 0.01
50 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTCTCATCTGTAGGCCGATG
Found at i:42515639 original size:17 final size:15
Alignment explanation
Indices: 42515603--42515637 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
42515593 AGGCTGTGCA
42515603 GCACAACCGTGTGTC
1 GCACAACCGTGTGTC
42515618 GCACAACCGTGTGTC
1 GCACAACCGTGTGTC
42515633 GCACA
1 GCACA
42515638 CAGCTGAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.17
Consensus pattern (15 bp):
GCACAACCGTGTGTC
Found at i:42516582 original size:23 final size:25
Alignment explanation
Indices: 42516536--42516592 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
42516526 TCATGGTCAG
*
42516536 TAAGCTCCTCTTGAGCTGAGAAACAA
1 TAAGCT-CTATTGAGCTGAGAAACAA
*
42516562 TAAGCTCTATTGAGCT-A-AAACAG
1 TAAGCTCTATTGAGCTGAGAAACAA
42516585 TAAGCTCT
1 TAAGCTCT
42516593 TTTTCGAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 13 0.45
24 1 0.03
25 9 0.31
26 6 0.21
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (25 bp):
TAAGCTCTATTGAGCTGAGAAACAA
Found at i:42516601 original size:25 final size:23
Alignment explanation
Indices: 42516533--42516663 Score: 86
Period size: 24 Copynumber: 5.5 Consensus size: 23
42516523 CTGTCATGGT
*
42516533 CAGTAAGCTCCTCTTGAGCTGAGAAA
1 CAGTAAGCT-CTATTGAGCT-A-AAA
*
42516559 CAATAAGCTCTATTGAGCTAAAA
1 CAGTAAGCTCTATTGAGCTAAAA
* *
42516582 CAGTAAGCTCTTTTTCGAGCT-GAA
1 CAGTAAGCTC-TATT-GAGCTAAAA
* ** *
42516606 TAGTAAGCTC-ATACAAGCTGAAA
1 CAGTAAGCTCTAT-TGAGCTAAAA
* * *
42516629 CGGTAAGCTCTAATGAGTTGAAAA
1 CAGTAAGCTCTATTGAGCT-AAAA
42516653 CAGTAAGCTCT
1 CAGTAAGCTCT
42516664 TTCGACTGAT
Statistics
Matches: 81, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
22 5 0.06
23 25 0.31
24 29 0.36
25 14 0.17
26 8 0.10
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (23 bp):
CAGTAAGCTCTATTGAGCTAAAA
Found at i:42516690 original size:72 final size:69
Alignment explanation
Indices: 42516562--42516697 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 69
42516552 TGAGAAACAA
*
42516562 TAAGCTCTATTGAGCTAAAACAGTAAGCTCTTTTTCGAGCTGAATAGTAAGCTCATACAAGCTGA
1 TAAGCTCTAATGAGCTAAAACAGTAAGCTC-TTTTCGAGCTGAATAGTAAGCTCATACAAGCTGA
42516627 AACGG
65 AACGG
* *
42516632 TAAGCTCTAATGAGTTGAAAACAGTAAGCTC-TTTCGA-CTGATATATCGGTAAGCTCATACGAG
1 TAAGCTCTAATGAGCT-AAAACAGTAAGCTCTTTTCGAGCTGA-ATA---GTAAGCTCATACAAG
42516695 CTG
61 CTG
42516698 TGGTGAGTCC
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
68 4 0.07
69 9 0.16
70 14 0.24
71 14 0.24
72 17 0.29
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (69 bp):
TAAGCTCTAATGAGCTAAAACAGTAAGCTCTTTTCGAGCTGAATAGTAAGCTCATACAAGCTGAA
ACGG
Found at i:42524595 original size:2 final size:2
Alignment explanation
Indices: 42524588--42524621 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
42524578 CATTCAAATC
42524588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42524622 AACTAAGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42527606 original size:10 final size:9
Alignment explanation
Indices: 42527592--42527644 Score: 58
Period size: 9 Copynumber: 6.0 Consensus size: 9
42527582 ATTTAAATAA
*
42527592 ATTTTTATT
1 ATTTTTAAT
42527601 ATTTTTAAT
1 ATTTTTAAT
42527610 ATTTTT-AT
1 ATTTTTAAT
42527618 -TTTTATAA-
1 ATTTT-TAAT
42527626 ATTTTTAAT
1 ATTTTTAAT
42527635 AATTTTTAAT
1 -ATTTTTAAT
42527645 TGAATTAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
7 4 0.11
8 6 0.16
9 19 0.50
10 9 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:42527619 original size:15 final size:16
Alignment explanation
Indices: 42527588--42527632 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
42527578 ATAGATTTAA
42527588 ATAAATTTTTATTATTT
1 ATAAATTTTTATT-TTT
*
42527605 TTAATATTTTTATTTTT
1 ATAA-ATTTTTATTTTT
42527622 ATAAATTTTTA
1 ATAAATTTTTA
42527633 ATAATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.28
17 9 0.36
18 9 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATAAATTTTTATTTTT
Found at i:42527629 original size:25 final size:25
Alignment explanation
Indices: 42527592--42527642 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
42527582 ATTTAAATAA
*
42527592 ATTTTTATTATTTTTAAT-ATTTTT
1 ATTTTTATAATTTTTAATAATTTTT
42527616 ATTTTTATAAATTTTTAATAATTTTT
1 ATTTTTAT-AATTTTTAATAATTTTT
42527642 A
1 A
42527643 ATTGAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 8 0.33
25 9 0.38
26 7 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
ATTTTTATAATTTTTAATAATTTTT
Found at i:42527654 original size:26 final size:25
Alignment explanation
Indices: 42527601--42527657 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
42527591 AATTTTTATT
* **
42527601 ATTTTTAATATTTTTATTTTTATAA
1 ATTTTTAATATTTTTAATTGAATAA
*
42527626 ATTTTTAATAATTTTTAATTGAATTA
1 ATTTTTAAT-ATTTTTAATTGAATAA
42527652 ATTTTT
1 ATTTTT
42527658 TTTGGAAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
ATTTTTAATATTTTTAATTGAATAA
Found at i:42528117 original size:30 final size:30
Alignment explanation
Indices: 42528083--42528145 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
42528073 AATTAACAAG
42528083 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
42528113 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
42528143 CAA
1 CAA
42528146 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:42528459 original size:5 final size:5
Alignment explanation
Indices: 42528449--42528491 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
42528439 AACAGGTCTA
* *
42528449 ATTAT ATTAT ACTAT ATTAT ATTAT ATTAG ATTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT
42528492 TGAAGATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (5 bp):
ATTAT
Found at i:42536307 original size:40 final size:40
Alignment explanation
Indices: 42536230--42536450 Score: 297
Period size: 40 Copynumber: 5.5 Consensus size: 40
42536220 ACCCAAGTAT
* *
42536230 CTTCGGGAT-TTAG-CCGGATATA-ACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
*
42536269 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
42536309 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
42536349 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
42536389 CTTCGGATCTTAGTCCGGATATAGTCACTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
42536429 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
42536451 CATTCGAATA
Statistics
Matches: 161, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
38 1 0.01
39 12 0.07
40 146 0.91
41 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:42544559 original size:40 final size:40
Alignment explanation
Indices: 42544482--42544702 Score: 297
Period size: 40 Copynumber: 5.5 Consensus size: 40
42544472 ACCCAAGTAT
* *
42544482 CTTCGGGAT-TTAG-CCGGATATA-ACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
*
42544521 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
42544561 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
42544601 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
42544641 CTTCGGATCTTAGTCCGGATATAGTCACTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
42544681 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
42544703 CATTCGAATA
Statistics
Matches: 161, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
38 1 0.01
39 12 0.07
40 146 0.91
41 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:42552814 original size:40 final size:40
Alignment explanation
Indices: 42552737--42552957 Score: 297
Period size: 40 Copynumber: 5.5 Consensus size: 40
42552727 ACCCAAGTAT
* *
42552737 CTTCGGGAT-TTAG-CCGGATATA-ACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
*
42552776 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
42552816 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
42552856 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
42552896 CTTCGGATCTTAGTCCGGATATAGTCACTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
42552936 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
42552958 CATTCGAATA
Statistics
Matches: 161, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
38 1 0.01
39 12 0.07
40 146 0.91
41 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:42559219 original size:49 final size:48
Alignment explanation
Indices: 42559144--42559326 Score: 213
Period size: 49 Copynumber: 3.8 Consensus size: 48
42559134 TATTCGGATA
42559144 TGATGGGCCACTGGTAGGGCATGTTAGTTGCTAACCAAGTTGGCGTATG
1 TGATGGGCCACTGGTAGGGCATGTTAGTTGCTAACCAAGTTGGCG-ATG
* * * * *
42559193 TGTTGGGCCACTAGTAGGGCATGTTAGTTGCTAACCAGGTTGCCAGAGG
1 TGATGGGCCACTGGTAGGGCATGTTAGTTGCTAACCAAGTTGGC-GATG
* * * * *
42559242 TGACGGGCCATTGGTAGGTCATGTTAGTTGCTAAACAAGTTGGAGCATG
1 TGATGGGCCACTGGTAGGGCATGTTAGTTGCTAACCAAGTTGGCG-ATG
* ** *
42559291 TGCTGGGTTATTGGTAGGGCATGTTAGTTGCTAACC
1 TGATGGGCCACTGGTAGGGCATGTTAGTTGCTAACC
42559327 GGCCCGACGT
Statistics
Matches: 111, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
48 1 0.01
49 109 0.98
50 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.30
Consensus pattern (48 bp):
TGATGGGCCACTGGTAGGGCATGTTAGTTGCTAACCAAGTTGGCGATG
Found at i:42559317 original size:98 final size:98
Alignment explanation
Indices: 42559148--42559326 Score: 268
Period size: 98 Copynumber: 1.8 Consensus size: 98
42559138 CGGATATGAT
* * * *
42559148 GGGCCACTGGTAGGGCATGTTAGTTGCTAACCAAGTTGGCGTATGTGTTGGGCCACTAGTAGGGC
1 GGGCCACTGGTAGGGCATGTTAGTTGCTAAACAAGTTGGAGCATGTGCTGGGCCACTAGTAGGGC
42559213 ATGTTAGTTGCTAACCAGGTTGCCAGAGGTGAC
66 ATGTTAGTTGCTAACCAGGTTGCCAGAGGTGAC
* * ** * *
42559246 GGGCCATTGGTAGGTCATGTTAGTTGCTAAACAAGTTGGAGCATGTGCTGGGTTATTGGTAGGGC
1 GGGCCACTGGTAGGGCATGTTAGTTGCTAAACAAGTTGGAGCATGTGCTGGGCCACTAGTAGGGC
42559311 ATGTTAGTTGCTAACC
66 ATGTTAGTTGCTAACC
42559327 GGCCCGACGT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
98 71 1.00
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (98 bp):
GGGCCACTGGTAGGGCATGTTAGTTGCTAAACAAGTTGGAGCATGTGCTGGGCCACTAGTAGGGC
ATGTTAGTTGCTAACCAGGTTGCCAGAGGTGAC
Found at i:42559392 original size:16 final size:16
Alignment explanation
Indices: 42559373--42559403 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42559363 GTTAGTTGTT
42559373 AACCATGGCAAAGAGA
1 AACCATGGCAAAGAGA
*
42559389 AACCATGGGAAAGAG
1 AACCATGGCAAAGAG
42559404 CTTTGATCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.29, T:0.06
Consensus pattern (16 bp):
AACCATGGCAAAGAGA
Found at i:42559934 original size:2 final size:2
Alignment explanation
Indices: 42559927--42559970 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
42559917 ACATGTTCTC
42559927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42559969 AT
1 AT
42559971 GACTCTTATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42561694 original size:18 final size:18
Alignment explanation
Indices: 42561673--42561707 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42561663 TTATTTAATT
*
42561673 TATATAATATAATAATAA
1 TATAAAATATAATAATAA
42561691 TATAAAATATAATAATA
1 TATAAAATATAATAATA
42561708 TTTTCTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAAAATATAATAATAA
Found at i:42564426 original size:2 final size:2
Alignment explanation
Indices: 42564419--42564449 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42564409 ATAAATACTC
42564419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42564450 ATTGGTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42566423 original size:22 final size:22
Alignment explanation
Indices: 42566378--42566425 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
42566368 ATTTATTAAT
* ** *
42566378 AATTTTTTTAAAAAATCACTAA
1 AATTTTTTAAAAAAAAAACCAA
42566400 AATTTTTTAAAAAAAAAACCAA
1 AATTTTTTAAAAAAAAAACCAA
42566422 AATT
1 AATT
42566426 ATAAATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.35
Consensus pattern (22 bp):
AATTTTTTAAAAAAAAAACCAA
Found at i:42567900 original size:23 final size:21
Alignment explanation
Indices: 42567858--42567906 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
42567848 AATTTTAATT
*
42567858 TTTTATAATAAAAATTAAATA
1 TTTTATAATAAAAATAAAATA
*
42567879 TTTTATATTTAAAAATGAAAATA
1 TTTTATA-ATAAAAAT-AAAATA
*
42567902 ATTTA
1 TTTTA
42567907 AAATTTCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 7 0.30
22 7 0.30
23 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTTATAATAAAAATAAAATA
Found at i:42575039 original size:34 final size:34
Alignment explanation
Indices: 42574996--42575094 Score: 110
Period size: 34 Copynumber: 2.9 Consensus size: 34
42574986 AAGCAAGTTT
*
42574996 ATTGCTACTGTATTGATTTATTATAACCATGTTA
1 ATTGCTACTGTATTGATTTATTATAAACATGTTA
* *
42575030 ATTGCTACTGTATTGACTTGA-TATAAACATGTTT
1 ATTGCTACTGTATTGA-TTTATTATAAACATGTTA
* * * * *
42575064 ATTGCTACCGTAATGATCTGTTATAAGCATG
1 ATTGCTACTGTATTGATTTATTATAAACATG
42575095 AATATTTTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
33 1 0.02
34 50 0.93
35 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (34 bp):
ATTGCTACTGTATTGATTTATTATAAACATGTTA
Found at i:42575366 original size:21 final size:21
Alignment explanation
Indices: 42575340--42575380 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42575330 AATTTTTATT
*
42575340 ATTAGTAGTTCATCTACAACA
1 ATTAGTAGTTCATCCACAACA
*
42575361 ATTAGTGGTTCATCCACAAC
1 ATTAGTAGTTCATCCACAAC
42575381 GTGGTGTAAG
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:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (21 bp):
ATTAGTAGTTCATCCACAACA
Found at i:42577226 original size:3 final size:3
Alignment explanation
Indices: 42577218--42577258 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42577208 ATTAATGTGA
42577218 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
42577259 AGATGCGGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:42580480 original size:9 final size:10
Alignment explanation
Indices: 42580466--42580506 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
42580456 AAAGGAAAAC
42580466 ATACATA-AT
1 ATACATATAT
42580475 ATACATATAT
1 ATACATATAT
*
42580485 ATATATATAT
1 ATACATATAT
*
42580495 A-AAATATAT
1 ATACATATAT
42580504 ATA
1 ATA
42580507 TGAGATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 15 0.54
10 13 0.46
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (10 bp):
ATACATATAT
Found at i:42580503 original size:19 final size:19
Alignment explanation
Indices: 42580479--42580527 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
42580469 CATAATATAC
*
42580479 ATATATATATATATATAAA
1 ATATATATATAGATATAAA
42580498 ATATATATATGAGATATAAA
1 ATATATATAT-AGATATAAA
*
42580518 A-ATGTATATA
1 ATATATATATA
42580528 CATGGTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 1 0.04
19 17 0.63
20 9 0.33
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (19 bp):
ATATATATATAGATATAAA
Found at i:42580505 original size:21 final size:21
Alignment explanation
Indices: 42580479--42580527 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
42580469 CATAATATAC
*
42580479 ATATATATAT-ATATAT-AAA
1 ATATATATATGAGATATAAAA
42580498 ATATATATATGAGATATAAAA
1 ATATATATATGAGATATAAAA
*
42580519 ATGTATATA
1 ATATATATA
42580528 CATGGTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 10 0.38
20 5 0.19
21 11 0.42
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (21 bp):
ATATATATATGAGATATAAAA
Found at i:42582728 original size:43 final size:43
Alignment explanation
Indices: 42582481--42582782 Score: 175
Period size: 43 Copynumber: 7.0 Consensus size: 43
42582471 TCGATTTGTG
* * *
42582481 AATTCAACATGTTACCCTACTGCTTA-GGGTTTAAGGTCTGTA
1 AATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCTGTA
* ** * * * * *
42582523 AGTTTGGCTTGCTACCCTACTGCTTAGGGGGTTGAGCTC-AT-
1 AATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCTGTA
* ** * * * *
42582564 CATCTTTGATCTGTTTCCCTACTGCTTAGGGGATTAAGATCTGTA
1 AAT-TCAG-CCTGTTACCCTACTGCTTAGGGGGTTAAGGTCTGTA
** * * **
42582609 AATTCAGCCTGCTTCACTGTAACT--TCAGGGGG-AAAAATCTGTA
1 AATTCAGCCTG-TT-ACCCT-ACTGCTTAGGGGGTTAAGGTCTGTA
* * * *
42582652 ATTTTCAGCCTATTACCCTACTGCTTAGAGGGTTAAGGTCTGCA
1 A-ATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCTGTA
* * ** * *
42582696 AATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCTTTG
1 AATTCAGCCTGTTACCCTACTGCTTAGGGGGTT-AAGGTCTGTA
* *
42582740 AATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCTGTA
1 AATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCTGTA
42582783 CATTTAGTCT
Statistics
Matches: 187, Mismatches: 60, Indels: 25
0.69 0.22 0.09
Matches are distributed among these distances:
41 4 0.02
42 27 0.14
43 88 0.47
44 61 0.33
45 4 0.02
46 3 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (43 bp):
AATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCTGTA
Found at i:42598203 original size:13 final size:13
Alignment explanation
Indices: 42598185--42598210 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42598175 AAGCCACCTA
42598185 GACTTAACCTATT
1 GACTTAACCTATT
42598198 GACTTAACCTATT
1 GACTTAACCTATT
42598211 ATTATTAATC
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:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
GACTTAACCTATT
Found at i:42601707 original size:28 final size:28
Alignment explanation
Indices: 42601684--42601738 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
42601674 CAAAGCAATC
*
42601684 ATTCTAGCTTAAATAACATTAAGCTAAA
1 ATTCTAGCTTAAATAAAATTAAGCTAAA
42601712 ATTCTAGCTTAAATAAAATTAAGCTAA
1 ATTCTAGCTTAAATAAAATTAAGCTAA
42601739 CATTTTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (28 bp):
ATTCTAGCTTAAATAAAATTAAGCTAAA
Found at i:42603473 original size:34 final size:35
Alignment explanation
Indices: 42603435--42603558 Score: 135
Period size: 35 Copynumber: 3.6 Consensus size: 35
42603425 TCCATGAAAA
* *
42603435 AGTTGTGAAACTTTGGTATGGTATCATCCA-ACTG
1 AGTTGTGAAACGTAGGTATGGTATCATCCATACTG
* *
42603469 AGTTGTGAAGCGTAGGTATGGTATTATCCATACTG
1 AGTTGTGAAACGTAGGTATGGTATCATCCATACTG
** * *
42603504 AGTTAAGAAACGTAGGTATGGTAT-TTCCCATACCG
1 AGTTGTGAAACGTAGGTATGGTATCAT-CCATACTG
* *
42603539 AGTTGTAAAATGTAGGTATG
1 AGTTGTGAAACGTAGGTATG
42603559 ATATTTCAAT
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
34 27 0.36
35 48 0.64
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (35 bp):
AGTTGTGAAACGTAGGTATGGTATCATCCATACTG
Found at i:42607785 original size:40 final size:40
Alignment explanation
Indices: 42607740--42607869 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
42607730 CGGAATACAA
42607740 CCGGATATAACCAC-ATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTA-GCACGAATGCCTTCGGGTCTTAGC
* * *
42607780 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * * *
42607820 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
42607860 CCGGATATAA
1 CCGGATATAA
42607870 TTTCCAGCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 2 0.03
40 74 0.97
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:42614240 original size:34 final size:34
Alignment explanation
Indices: 42614202--42614292 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 34
42614192 ATCCATGACA
* *
42614202 AAGTTGTGAAACTTCGGTATGGTATCATCCAACT
1 AAGTTGTGAAACGTAGGTATGGTATCATCCAACT
* *
42614236 AAGTTGTGAAACGTAGGTATGGTATTATCCATCTT
1 AAGTTGTGAAACGTAGGTATGGTATCATCCAAC-T
* **
42614271 GAGTTAAGAAACGTAGGTATGG
1 AAGTTGTGAAACGTAGGTATGG
42614293 CATTTCCCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 29 0.59
35 20 0.41
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (34 bp):
AAGTTGTGAAACGTAGGTATGGTATCATCCAACT
Found at i:42614289 original size:35 final size:35
Alignment explanation
Indices: 42614217--42614331 Score: 101
Period size: 35 Copynumber: 3.3 Consensus size: 35
42614207 GTGAAACTTC
* * * **
42614217 GGTATGGTATCATCCAAC-TAAGTTGTGAAACGTA
1 GGTATGGTATTATCCATCTTGAGTTAAGAAACGTA
42614251 GGTATGGTATTATCCATCTTGAGTTAAGAAACGTA
1 GGTATGGTATTATCCATCTTGAGTTAAGAAACGTA
* * * * *
42614286 GGTATGGCATT-TCCCATATCGAGTTGTA-AAATGTA
1 GGTATGGTATTAT-CCATCTTGAGTT-AAGAAACGTA
42614321 GGTATGGTATT
1 GGTATGGTATT
42614332 TCAATGAGGA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
34 17 0.25
35 49 0.73
36 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (35 bp):
GGTATGGTATTATCCATCTTGAGTTAAGAAACGTA
Found at i:42614333 original size:35 final size:35
Alignment explanation
Indices: 42614237--42614333 Score: 108
Period size: 35 Copynumber: 2.8 Consensus size: 35
42614227 CATCCAACTA
* * *
42614237 AGTTGTGAAACGTAGGTATGGTATTAT-CCATCTTG
1 AGTTGTAAAACGTAGGTATGGTATT-TCCCATATCG
* *
42614272 AGTT-AAGAAACGTAGGTATGGCATTTCCCATATCG
1 AGTTGTA-AAACGTAGGTATGGTATTTCCCATATCG
*
42614307 AGTTGTAAAATGTAGGTATGGTATTTC
1 AGTTGTAAAACGTAGGTATGGTATTTC
42614334 AATGAGGAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
34 1 0.02
35 49 0.96
36 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (35 bp):
AGTTGTAAAACGTAGGTATGGTATTTCCCATATCG
Found at i:42615792 original size:403 final size:403
Alignment explanation
Indices: 42615045--42615840 Score: 1412
Period size: 403 Copynumber: 2.0 Consensus size: 403
42615035 TTTGTAAAAG
42615045 AATAATTATGGGTTATAATTTATACTATTAAAATCCTTAATGAGTCTATTTTTAAAAGAAACAAA
1 AATAATTATGGGTTATAATTTATACTATTAAAATCCTTAATGAGTCTATTTTTAAAAGAAACAAA
* *
42615110 AAATACCATCATATGAATCTCATATGAGGATATAATTAATTTTTAGTGAAGAGTGGTCAGAACCG
66 AAATACCATCATATGAATCTCATATGAGGAGATAATTAATTTTTAGTGAAGAGGGGTCAGAACCG
42615175 TCGGACAGCAAAACAGGGGAGAATTTAAAGAATAAACTGTACTTATTGGCTTGACCAAAAATTCT
131 TCGGACAGCAAAACAGGGGAGAATTTAAAGAATAAACTGTACTTATTGGCTTGACCAAAAATTCT
* *
42615240 GAAAATTTTTGGTAAGAAGATATGTGAGTCTAGTTTCAGGGAAAATTAGAGGATCTTAATTTGGA
196 GAAAATTTTTGGCAAGAAGATATGTGAGTCTAGTTTCAGGGAAAATTAGAGAATCTTAATTTGGA
* *
42615305 GTTTCGTAGCCCAAGATATTAATAATTATTGTGACTATGACTCGAGTGGACAGCTTTAATGTGAA
261 GTTTCGTAGCCCAAGATATTAATAATTATTGTGACTATGACTCAAGTGGACAACTTTAATGTGAA
*
42615370 TATAAGTAAACAATGGAATTTTTGTGTAATTATTCCGTAAACTTTGGTAACATCTTGTAACCCTG
326 TATAAGTAAACAATGGAATTTTTGTGTAATTATTCCGTAAACTTCGGTAACATCTTGTAACCCTG
42615435 TTCCGGTGACAAA
391 TTCCGGTGACAAA
* *
42615448 AATAATTATGGGTTATAATTTATACTATTCAAATCCTTAATGAGTCTATTTTTAAAAGAAATAAA
1 AATAATTATGGGTTATAATTTATACTATTAAAATCCTTAATGAGTCTATTTTTAAAAGAAACAAA
* *
42615513 AAATACCATCATCTGAATCTCATATGAGGAGATAATTAATTTTTAGTGAAGAGGGGTCAGAACTG
66 AAATACCATCATATGAATCTCATATGAGGAGATAATTAATTTTTAGTGAAGAGGGGTCAGAACCG
* *
42615578 TCGGACAGCAAAATAGGGGAGAATTTAAAGAATAAACTGTACTTATTGGCTTGACCAAAAATTTT
131 TCGGACAGCAAAACAGGGGAGAATTTAAAGAATAAACTGTACTTATTGGCTTGACCAAAAATTCT
* * *
42615643 GAAAATTTTTTGCAAGAAGATATGTGAGTTTAGTTTCAGGGAAAATTAGCGAATCTTAATTTGGA
196 GAAAATTTTTGGCAAGAAGATATGTGAGTCTAGTTTCAGGGAAAATTAGAGAATCTTAATTTGGA
* * *
42615708 GTTTCGTAGCTCAAGATATTAATAATTATTGTTACTATGACTCAAGTGGACAACTTTGATGTGAA
261 GTTTCGTAGCCCAAGATATTAATAATTATTGTGACTATGACTCAAGTGGACAACTTTAATGTGAA
*
42615773 TATAAGTAAATAATGGAATTTTTGTGTAATTATTCCGTAAACTTCGGTAACATCTTGTAACCCTG
326 TATAAGTAAACAATGGAATTTTTGTGTAATTATTCCGTAAACTTCGGTAACATCTTGTAACCCTG
42615838 TTC
391 TTC
42615841 TAGTGACGGA
Statistics
Matches: 373, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
403 373 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (403 bp):
AATAATTATGGGTTATAATTTATACTATTAAAATCCTTAATGAGTCTATTTTTAAAAGAAACAAA
AAATACCATCATATGAATCTCATATGAGGAGATAATTAATTTTTAGTGAAGAGGGGTCAGAACCG
TCGGACAGCAAAACAGGGGAGAATTTAAAGAATAAACTGTACTTATTGGCTTGACCAAAAATTCT
GAAAATTTTTGGCAAGAAGATATGTGAGTCTAGTTTCAGGGAAAATTAGAGAATCTTAATTTGGA
GTTTCGTAGCCCAAGATATTAATAATTATTGTGACTATGACTCAAGTGGACAACTTTAATGTGAA
TATAAGTAAACAATGGAATTTTTGTGTAATTATTCCGTAAACTTCGGTAACATCTTGTAACCCTG
TTCCGGTGACAAA
Found at i:42619458 original size:5 final size:5
Alignment explanation
Indices: 42619450--42619476 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
42619440 AAAATTTAAA
42619450 ATTTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT AT
42619477 GGTTGGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:42623720 original size:33 final size:33
Alignment explanation
Indices: 42623683--42623749 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
42623673 TTTAACATAG
42623683 ACTTAACTTATTTATATTGAATTATTGAATATT
1 ACTTAACTTATTTATATTGAATTATTGAATATT
42623716 ACTTAACTTATTTATATTGAATTATTGAATATT
1 ACTTAACTTATTTATATTGAATTATTGAATATT
42623749 A
1 A
42623750 TTGAGTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (33 bp):
ACTTAACTTATTTATATTGAATTATTGAATATT
Found at i:42623770 original size:33 final size:34
Alignment explanation
Indices: 42623683--42623770 Score: 110
Period size: 33 Copynumber: 2.7 Consensus size: 34
42623673 TTTAACATAG
*
42623683 ACTTAACTTATTTATAT-TGAATTATTGAATATT
1 ACTTAACTAATTTATATATGAATTATTGAATATT
*
42623716 ACTTAACTTATTTATAT-TGAATTATTGAATATT
1 ACTTAACTAATTTATATATGAATTATTGAATATT
* * *
42623749 A-TTGAGTAATTTGTATATGAAT
1 ACTTAACTAATTTATATATGAAT
42623771 GTTTCTGTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 11 0.22
33 39 0.78
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (34 bp):
ACTTAACTAATTTATATATGAATTATTGAATATT
Found at i:42626632 original size:45 final size:45
Alignment explanation
Indices: 42626582--42626673 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
42626572 TTTTTGAAAT
42626582 CATCCAAATTAAGCTGAAGTAACATTTTAATGCTTCCCCATTGTA
1 CATCCAAATTAAGCTGAAGTAACATTTTAATGCTTCCCCATTGTA
42626627 CATCCAAATTAAGCTGAAGTAACATTTTAATGCTTCCCCATTGTA
1 CATCCAAATTAAGCTGAAGTAACATTTTAATGCTTCCCCATTGTA
42626672 CA
1 CA
42626674 CATACTCTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.33
Consensus pattern (45 bp):
CATCCAAATTAAGCTGAAGTAACATTTTAATGCTTCCCCATTGTA
Found at i:42629127 original size:2 final size:2
Alignment explanation
Indices: 42629120--42629148 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42629110 TCTTAATTAT
42629120 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42629149 TTGAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42640988 original size:43 final size:43
Alignment explanation
Indices: 42640908--42641041 Score: 124
Period size: 51 Copynumber: 2.9 Consensus size: 43
42640898 GAGATATGTT
** * *
42640908 GCATCCGAGCTCGTTGAGAGGTCTGAGTTTATTATGGATGCAA
1 GCATCCGAGCTCGTTGAGAGGTCCAAGTTCATGATGGATGCAA
*
42640951 GCATCTGAGCTCGTTGAGAGGTCCAAGTTCATGATGGATACGATTCATACA
1 GCATCCGAGCTCGTTGAGAGGTCCAAGTTCATGATGGAT--G---C--A-A
* * *
42641002 ACATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATG
1 GCATCCGAGCTCGTTGAGAGGTCCAAGTTCATGATGGATG
42641042 TGTTACATGT
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
43 34 0.46
45 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 36 0.49
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (43 bp):
GCATCCGAGCTCGTTGAGAGGTCCAAGTTCATGATGGATGCAA
Found at i:42643900 original size:24 final size:24
Alignment explanation
Indices: 42643868--42643916 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
42643858 TAGCACTCTG
*
42643868 CATATTGAACCTGCAAAAAACTTT
1 CATATTGAACCCGCAAAAAACTTT
42643892 CATATTGAACCCGCAAAAAACTTT
1 CATATTGAACCCGCAAAAAACTTT
42643916 C
1 C
42643917 TCAATGTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (24 bp):
CATATTGAACCCGCAAAAAACTTT
Found at i:42647772 original size:25 final size:26
Alignment explanation
Indices: 42647725--42647776 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
42647715 ATAATTGAAT
*
42647725 TAAAAATTATTAAAAATTCATAAAAA
1 TAAAAATTATTAAAAATTAATAAAAA
42647751 TAAAAA-TATTAAAAGA-TAATAAAAA
1 TAAAAATTATTAAAA-ATTAATAAAAA
42647776 T
1 T
42647777 TTATTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (26 bp):
TAAAAATTATTAAAAATTAATAAAAA
Found at i:42649378 original size:23 final size:23
Alignment explanation
Indices: 42649352--42649428 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 23
42649342 TTAAATATAT
*
42649352 ATTTTGAA-ATTATTTTTTTAAAA
1 ATTTTAAACATTA-TTTTTTAAAA
42649375 A-TTTAAACATTATTTTTTAAAA
1 ATTTTAAACATTATTTTTTAAAA
* *
42649397 A--TTAAATA-TATTTTTTAATA
1 ATTTTAAACATTATTTTTTAAAA
* *
42649417 ATATAAAACATT
1 ATTTTAAACATT
42649429 TAAATATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
20 12 0.27
21 6 0.13
22 21 0.47
23 6 0.13
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (23 bp):
ATTTTAAACATTATTTTTTAAAA
Found at i:42649393 original size:22 final size:22
Alignment explanation
Indices: 42649360--42649428 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
42649350 ATATTTTGAA
42649360 ATTATTTTTTTAAAAATTTAAAC
1 ATTA-TTTTTTAAAAATTTAAAC
*
42649383 ATTATTTTTTAAAAA-TTAAAT
1 ATTATTTTTTAAAAATTTAAAC
* *
42649404 A-TATTTTTTAATAATATAAAAC
1 ATTATTTTTTAAAAAT-TTAAAC
42649426 ATT
1 ATT
42649429 TAAATATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 12 0.31
21 6 0.15
22 16 0.41
23 5 0.13
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTATTTTTTAAAAATTTAAAC
Found at i:42649396 original size:21 final size:21
Alignment explanation
Indices: 42649360--42649428 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
42649350 ATATTTTGAA
42649360 ATTATTTTTTTAAAAATTTAAAC
1 ATTA-TTTTTT-AAAATTTAAAC
* *
42649383 ATTATTTTTTAAAAATTAAAT
1 ATTATTTTTTAAAATTTAAAC
*
42649404 A-TATTTTTTAATAATATAAAAC
1 ATTATTTTTTAA-AAT-TTAAAC
42649426 ATT
1 ATT
42649429 TAAATATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 10 0.26
21 12 0.32
22 11 0.29
23 5 0.13
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTATTTTTTAAAATTTAAAC
Found at i:42649429 original size:20 final size:20
Alignment explanation
Indices: 42649365--42649429 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
42649355 TTGAAATTAT
* *
42649365 TTTTTTAAAAATTTAAACATTA
1 TTTTTTAAAAA-TTAAATA-CA
*
42649387 TTTTTTAAAAATTAAATATA
1 TTTTTTAAAAATTAAATACA
*
42649407 TTTTTTAATAATATAAA-ACA
1 TTTTTTAAAAAT-TAAATACA
42649427 TTT
1 TTT
42649430 AAATATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
20 18 0.46
21 10 0.26
22 11 0.28
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTTTAAAAATTAAATACA
Found at i:42649486 original size:9 final size:9
Alignment explanation
Indices: 42649469--42649514 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
42649459 TTATTATTAG
*
42649469 TTTTTAATA
1 TTTTAAATA
42649478 TTTTAAATA
1 TTTTAAATA
*
42649487 TTTTTAAATT
1 -TTTTAAATA
42649497 TTTTATAATA
1 TTTTA-AATA
42649507 TTTTAAAT
1 TTTTAAAT
42649515 TATAATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 16 0.50
10 16 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTAAATA
Found at i:42649500 original size:19 final size:20
Alignment explanation
Indices: 42649469--42649515 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
42649459 TTATTATTAG
*
42649469 TTTTT-AATATTTTA-AATA
1 TTTTTAAATTTTTTATAATA
42649487 TTTTTAAATTTTTTATAATA
1 TTTTTAAATTTTTTATAATA
42649507 -TTTTAAATT
1 TTTTTAAATT
42649516 ATAATATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTAAATTTTTTATAATA
Found at i:42649527 original size:14 final size:15
Alignment explanation
Indices: 42649499--42649531 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
42649489 TTTAAATTTT
42649499 TTATAATATTTTAAA
1 TTATAATATTTTAAA
42649514 TTATAATA-TTTAAA
1 TTATAATATTTTAAA
42649528 TTAT
1 TTAT
42649532 TTTTAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATAATATTTTAAA
Found at i:42649688 original size:21 final size:22
Alignment explanation
Indices: 42649627--42649679 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
42649617 TTAGAAAAAT
42649627 AAAAATAATATTTTAAATTTTA
1 AAAAATAATATTTTAAATTTTA
42649649 AAAAATAATATTTTAAATTTTA
1 AAAAATAATATTTTAAATTTTA
42649671 AAAAATAAT
1 AAAAATAAT
42649680 TTCAAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAAATAATATTTTAAATTTTA
Found at i:42657639 original size:46 final size:47
Alignment explanation
Indices: 42657515--42657640 Score: 143
Period size: 46 Copynumber: 2.7 Consensus size: 47
42657505 TTGAGTTCCG
* * *
42657515 AACTCGTTGAGTTGAGTCCGAGTTCGTTA--GATGTAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCGTTATGGATGCAAC-ACGCA-CCA
* *
42657562 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA-ACGC-CCA
1 AACTCGTTGAGTTGAGTCCGAGTTC-GTTATGGATGCAACACGCACCA
42657608 AACTCGTTGAGTTGAGTCCGAGTTCGTTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCG-TTATGG
42657641 GAAGGTTACA
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
46 32 0.47
47 24 0.35
48 6 0.09
50 6 0.09
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (47 bp):
AACTCGTTGAGTTGAGTCCGAGTTCGTTATGGATGCAACACGCACCA
Found at i:42659372 original size:24 final size:24
Alignment explanation
Indices: 42659345--42659391 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
42659335 TATAAGTATA
42659345 CATGAATGATGGGTTGATGTCTTT
1 CATGAATGATGGGTTGATGTCTTT
42659369 CATGAATGATGGGTTGATGTCTT
1 CATGAATGATGGGTTGATGTCTT
42659392 GGTTGTGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.09, G:0.30, T:0.40
Consensus pattern (24 bp):
CATGAATGATGGGTTGATGTCTTT
Found at i:42662393 original size:19 final size:20
Alignment explanation
Indices: 42662362--42662405 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
42662352 TTAGTGCACC
42662362 TTTTTTAACTGG-TAGATAA
1 TTTTTTAACTGGTTAGATAA
42662381 TATTTTTAA-TGGTTAGATAA
1 T-TTTTTAACTGGTTAGATAA
42662401 TTTTT
1 TTTTT
42662406 CTTTACAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.55
Consensus pattern (20 bp):
TTTTTTAACTGGTTAGATAA
Found at i:42665694 original size:23 final size:21
Alignment explanation
Indices: 42665651--42665694 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
42665641 TAAAACTAAT
* *
42665651 AATAATAAAAGGTTTACAATA
1 AATAATAAAAGATTTAAAATA
42665672 AATAATAAAAAGAATTTAAAATA
1 AATAAT-AAAAG-ATTTAAAATA
42665695 TTTAACATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 8 0.42
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (21 bp):
AATAATAAAAGATTTAAAATA
Found at i:42665771 original size:28 final size:27
Alignment explanation
Indices: 42665739--42665824 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 27
42665729 TAATAAATTT
42665739 AAAATAGATAATATATAAAAAAGTTTAA
1 AAAATA-ATAATATATAAAAAAGTTTAA
* *
42665767 AAAAT-A-AATGACATAAAAAAATATTAAAA
1 AAAATAATAAT-ATATAAAAAAGT-TT--AA
* *
42665796 AAAATAATAATATGTAAAACAGTTTAA
1 AAAATAATAATATATAAAAAAGTTTAA
42665823 AA
1 AA
42665825 TGACTAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
25 3 0.07
26 11 0.24
27 6 0.13
28 5 0.11
29 9 0.20
30 9 0.20
31 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (27 bp):
AAAATAATAATATATAAAAAAGTTTAA
Found at i:42665794 original size:53 final size:55
Alignment explanation
Indices: 42665718--42665824 Score: 130
Period size: 53 Copynumber: 2.0 Consensus size: 55
42665708 ACCGTATAAC
* * *
42665718 TAAATAACATATAATAAATTTAAAATAGATAAT-ATA-TAAAAAAGTTTAAAAAA
1 TAAATAACATATAAAAAATTTAAAAAAAATAATAATAGTAAAAAAGTTTAAAAAA
* *
42665771 TAAATGACATA-AAAAAATATTAAAAAAAATAATAATATGTAAAACAGTTTAAAA
1 TAAATAACATATAAAAAAT-TTAAAAAAAATAATAATA-GTAAAAAAGTTTAAAA
42665825 TGACTAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
52 6 0.13
53 22 0.49
54 3 0.07
56 14 0.31
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (55 bp):
TAAATAACATATAAAAAATTTAAAAAAAATAATAATAGTAAAAAAGTTTAAAAAA
Found at i:42670488 original size:3 final size:3
Alignment explanation
Indices: 42670482--42670547 Score: 69
Period size: 3 Copynumber: 22.0 Consensus size: 3
42670472 ATGGTGGTGG
* * * * * * *
42670482 TTA TTA TTA TTG TTA TTG TTA TTG TTA TTG TTG TTG TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42670530 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
42670548 CCTGAACATG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:42670498 original size:12 final size:12
Alignment explanation
Indices: 42670481--42670547 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
42670471 CATGGTGGTG
42670481 GTTATTATTATT
1 GTTATTATTATT
*
42670493 GTTATTGTTATT
1 GTTATTATTATT
* *
42670505 GTTATTGTTGTT
1 GTTATTATTATT
*
42670517 GTTGTTATTATT
1 GTTATTATTATT
*
42670529 ATTATTATTATT
1 GTTATTATTATT
*
42670541 ATTATTA
1 GTTATTA
42670548 CCTGAACATG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 48 1.00
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.66
Consensus pattern (12 bp):
GTTATTATTATT
Found at i:42670765 original size:22 final size:22
Alignment explanation
Indices: 42670737--42670782 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
42670727 AACTGGATAC
42670737 TTGCACGAGTAGAAATTATATG
1 TTGCACGAGTAGAAATTATATG
42670759 TTGCACGAGTAGAAATTATATG
1 TTGCACGAGTAGAAATTATATG
42670781 TT
1 TT
42670783 TCGATAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (22 bp):
TTGCACGAGTAGAAATTATATG
Found at i:42676440 original size:19 final size:19
Alignment explanation
Indices: 42676417--42676468 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
42676407 AATTTTTTTA
42676417 CTTTTT-TTTAACTTTTGT
1 CTTTTTCTTTAACTTTTGT
42676435 CTTTTTCTTTAA-TTTT-T
1 CTTTTTCTTTAACTTTTGT
*
42676452 -TTCTTTCTTTAAGTTTT
1 CTT-TTTCTTTAACTTTT
42676469 ATATTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 2 0.06
17 10 0.32
18 14 0.45
19 5 0.16
ACGTcount: A:0.12, C:0.12, G:0.04, T:0.73
Consensus pattern (19 bp):
CTTTTTCTTTAACTTTTGT
Found at i:42676490 original size:5 final size:5
Alignment explanation
Indices: 42676470--42676529 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
42676460 TTAAGTTTTA
* *
42676470 TATTT TTTTCT TATTT TATTT T-GTT TA-TT TA-TT TATTT TATTT TATTATT
1 TATTT TATT-T TATTT TATTT TATTT TATTT TATTT TATTT TATTT TA-T-TT
42676520 TATTT TATTT
1 TATTT TATTT
42676530 AATTACTAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 11 0.23
5 26 0.55
6 6 0.13
7 4 0.09
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:42676506 original size:17 final size:18
Alignment explanation
Indices: 42676484--42676534 Score: 72
Period size: 17 Copynumber: 3.0 Consensus size: 18
42676474 TTTTTCTTAT
*
42676484 TTTATTTTGTTTAT-TTA
1 TTTATTTTATTTATATTA
42676501 TTTATTTTATTT-TATTA
1 TTTATTTTATTTATATTA
42676518 TTTATTTTATTTA-ATTA
1 TTTATTTTATTTATATTA
42676535 CTAATTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 1 0.03
17 30 0.97
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTATTTTATTTATATTA
Found at i:42676508 original size:22 final size:22
Alignment explanation
Indices: 42676480--42676529 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
42676470 TATTTTTTTC
*
42676480 TTATTTTATTTTGTTTATTTA-T
1 TTATTTTATTTT-ATTATTTATT
42676502 TTATTTTATTTTATTATTTATT
1 TTATTTTATTTTATTATTTATT
42676524 TTATTT
1 TTATTT
42676530 AATTACTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (22 bp):
TTATTTTATTTTATTATTTATT
Found at i:42676541 original size:17 final size:17
Alignment explanation
Indices: 42676504--42676543 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
42676494 TTATTTATTT
* * *
42676504 ATTTTATTTTATTATTT
1 ATTTTATTTAATTACTA
42676521 ATTTTATTTAATTACTA
1 ATTTTATTTAATTACTA
42676538 ATTTTA
1 ATTTTA
42676544 AAAAATTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTATTTAATTACTA
Found at i:42676603 original size:23 final size:22
Alignment explanation
Indices: 42676539--42676614 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
42676529 TAATTACTAA
*
42676539 TTTTAAAAAATTTAAA-ATGTAT
1 TTTTAAAAATTTTAAATAT-TAT
* *
42676561 ATTTGAAATATTTTATAATATATAT
1 -TTTTAAAAATTTTA-AATAT-TAT
*
42676586 TTTTTAAAATTTTAAATATTA-
1 TTTTAAAAATTTTAAATATTAT
42676607 TTTTAAAA
1 TTTTAAAA
42676615 TTATTTTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
21 7 0.16
22 2 0.05
23 16 0.37
24 13 0.30
25 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
TTTTAAAAATTTTAAATATTAT
Found at i:42676604 original size:33 final size:33
Alignment explanation
Indices: 42676561--42676712 Score: 119
Period size: 36 Copynumber: 4.5 Consensus size: 33
42676551 TAAAATGTAT
* *
42676561 ATTTGAAATATT-TTATAATATATATTTTTTAAA
1 ATTTTAAATATTATTATAAAAT-TATTTTTTAAA
* *
42676594 ATTTTAAATATTATTTTAAAATTATTTTTTTAA
1 ATTTTAAATATTATTATAAAATTATTTTTTAAA
* * *
42676627 ATTTTAAATATATATTTTTGAAATTATTTCTTATAA
1 ATTTTAAATAT-TA-TTATAAAATTATTTTTTA-AA
* * * * *
42676663 ATTTTAAAAATATATTTTTGAAACTAATTTTTATAA
1 ATTTTAAATAT-TA-TTATAAAATTATTTTTTA-AA
42676699 A-TTTAAATATTATT
1 ATTTTAAATATTATT
42676713 TTTTAAATAT
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
33 34 0.33
34 11 0.11
35 23 0.22
36 35 0.34
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (33 bp):
ATTTTAAATATTATTATAAAATTATTTTTTAAA
Found at i:42676620 original size:23 final size:25
Alignment explanation
Indices: 42676566--42676621 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
42676556 TGTATATTTG
*
42676566 AAATATTTTATAATATATATTTTTT
1 AAATATTTTATAATATATATTTTTA
42676591 AAA-ATTTTA-AATAT-TA-TTTTA
1 AAATATTTTATAATATATATTTTTA
42676612 AAATTATTTT
1 AAA-TATTTT
42676622 TTTAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 7 0.25
22 2 0.07
23 10 0.36
24 6 0.21
25 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
AAATATTTTATAATATATATTTTTA
Found at i:42676650 original size:22 final size:21
Alignment explanation
Indices: 42676606--42676651 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
42676596 TTTAAATATT
*
42676606 ATTTTAAAATTATTTTTTTAA
1 ATTTTAAAATTATTTTTTGAA
42676627 ATTTT-AAATATATATTTTTGAA
1 ATTTTAAAAT-TAT-TTTTTGAA
42676649 ATT
1 ATT
42676652 ATTTCTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 8 0.36
22 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTTAAAATTATTTTTTGAA
Found at i:42676670 original size:36 final size:34
Alignment explanation
Indices: 42676586--42676720 Score: 168
Period size: 36 Copynumber: 3.9 Consensus size: 34
42676576 TAATATATAT
*
42676586 TTTTTA-AAATTTTAAATATTA-TTTTAAAATTA
1 TTTTTATAAATTTTAAATATTATTTTTGAAATTA
*
42676618 TTTTTTTAAATTTTAAATATATATTTTTGAAATTA
1 TTTTTATAAATTTTAAATAT-TATTTTTGAAATTA
* *
42676653 TTTCTTATAAATTTTAAAAATATATTTTTGAAACTAA
1 TTT-TTATAAATTTTAAATAT-TATTTTTGAAA-TTA
*
42676690 TTTTTATAAA-TTTAAATATTATTTTTTAAAT
1 TTTTTATAAATTTTAAATATTATTTTTGAAAT
42676721 ATTAAATATA
Statistics
Matches: 91, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
32 5 0.05
33 14 0.15
34 12 0.13
35 21 0.23
36 34 0.37
37 5 0.05
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (34 bp):
TTTTTATAAATTTTAAATATTATTTTTGAAATTA
Found at i:42676713 original size:21 final size:21
Alignment explanation
Indices: 42676689--42676753 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 21
42676679 TTTGAAACTA
42676689 ATTTTTATAAATTTAAATATT
1 ATTTTTATAAATTTAAATATT
42676710 ATTTTT-TAAATATTAAATA-T
1 ATTTTTATAAAT-TTAAATATT
*
42676730 ATTTTTAATAATATTTAAACATT
1 ATTTTT-ATAA-ATTTAAATATT
42676753 A
1 A
42676754 AAATTTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
20 12 0.32
21 13 0.34
22 9 0.24
23 4 0.11
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTTATAAATTTAAATATT
Found at i:42676747 original size:29 final size:27
Alignment explanation
Indices: 42676714--42676772 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
42676704 AATATTATTT
* * *
42676714 TTTAAATATTAAATATATTTTTAATAATA
1 TTTAAACATTAAA-AT-TTTTAAATAAAA
42676743 TTTAAACATTAAAATTTTTAAATAAAA
1 TTTAAACATTAAAATTTTTAAATAAAA
42676770 TTT
1 TTT
42676773 TTATAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 13 0.48
28 2 0.07
29 12 0.44
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTAAACATTAAAATTTTTAAATAAAA
Found at i:42676770 original size:13 final size:13
Alignment explanation
Indices: 42676752--42676789 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
42676742 ATTTAAACAT
42676752 TAAAATTTTTAAA
1 TAAAATTTTTAAA
*
42676765 TAAAATTTTTATA
1 TAAAATTTTTAAA
42676778 -AAAATTTTTAAA
1 TAAAATTTTTAAA
42676790 AAAGTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAAATTTTTAAA
Done.