Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 22 of 26
Found at i:9314775 original size:2 final size:2
Alignment explanation
Indices: 9314762--9314803 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
9314752 ACATGGAATT
* *
9314762 TA TA TA TT TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9314804 AACAAGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9324973 original size:6 final size:6
Alignment explanation
Indices: 9324962--9324988 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9324952 TTGTTTGGCC
9324962 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
9324989 TAGGCACAGA
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:9329229 original size:5 final size:5
Alignment explanation
Indices: 9329219--9329243 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9329209 GGCACCCACA
9329219 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
9329244 CAGACCTTCC
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:9329771 original size:14 final size:13
Alignment explanation
Indices: 9329750--9329789 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
9329740 TCTTACAACT
9329750 AGAAAGAAGAGAGAA
1 AGAAAGAA-A-AGAA
9329765 A-AAAGAAAAGAA
1 AGAAAGAAAAGAA
9329777 AGAAAGAAAAGAA
1 AGAAAGAAAAGAA
9329790 CTCTTACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.21
13 12 0.50
14 6 0.25
15 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAAGAA
Found at i:9333903 original size:20 final size:20
Alignment explanation
Indices: 9333866--9333904 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9333856 TATACCAAAT
*
9333866 TTAATATTATTTTAAATTTA
1 TTAATATTAATTTAAATTTA
9333886 TTAAT-TTAATTTATAATTT
1 TTAATATTAATTTA-AATTT
9333905 TCATTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAATATTAATTTAAATTTA
Found at i:9354223 original size:2 final size:2
Alignment explanation
Indices: 9354177--9354204 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9354167 TGTGATAAAC
9354177 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
9354205 CTTTGTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9358914 original size:2 final size:2
Alignment explanation
Indices: 9358907--9358938 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9358897 AGATGACCTT
9358907 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9358939 GTAGGGAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9359767 original size:2 final size:2
Alignment explanation
Indices: 9359760--9359792 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9359750 CGCATCAGGA
9359760 AT 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 AT A
9359793 AAATGTTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9371428 original size:25 final size:25
Alignment explanation
Indices: 9371400--9371448 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
9371390 TCATCTGATG
9371400 CTACTACCATGGCAAAAGAATCTAT
1 CTACTACCATGGCAAAAGAATCTAT
9371425 CTACTACCATGGCAAAAGAATCTA
1 CTACTACCATGGCAAAAGAATCTA
9371449 ACACTAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.22
Consensus pattern (25 bp):
CTACTACCATGGCAAAAGAATCTAT
Found at i:9381060 original size:63 final size:63
Alignment explanation
Indices: 9380981--9381107 Score: 211
Period size: 63 Copynumber: 2.0 Consensus size: 63
9380971 TATAGGAGAA
*
9380981 AGTAAACCTGCGGGGGATTAATCATCTAACATTGACCGGGACAGTCT-TGTGTCCATGAGATAG
1 AGTAAACCTGCGGGGGATTAATCATCTAACATTGACCGAGACAGTCTGT-TGTCCATGAGATAG
* *
9381044 AGTAAACCTGTGGGGGATTAATCATCTTACATTGACCGAGACAGTCTGTTGTCCATGAGATAG
1 AGTAAACCTGCGGGGGATTAATCATCTAACATTGACCGAGACAGTCTGTTGTCCATGAGATAG
9381107 A
1 A
9381108 TTATGTGCTT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 59 0.98
64 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (63 bp):
AGTAAACCTGCGGGGGATTAATCATCTAACATTGACCGAGACAGTCTGTTGTCCATGAGATAG
Found at i:9393513 original size:11 final size:11
Alignment explanation
Indices: 9393486--9393524 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
9393476 TATAAATTTA
9393486 TTATTTATAAGT
1 TTATTTA-AAGT
*
9393498 TTATTTAAATT
1 TTATTTAAAGT
9393509 TTATTTTAAAGT
1 TTA-TTTAAAGT
9393521 TTAT
1 TTAT
9393525 ATTGTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (11 bp):
TTATTTAAAGT
Found at i:9403372 original size:3 final size:3
Alignment explanation
Indices: 9403330--9403355 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9403320 GCTTGACATT
9403330 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
9403356 ATCAGTTTGA
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:9412844 original size:21 final size:22
Alignment explanation
Indices: 9412811--9412851 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
9412801 CCGGCTGAGG
* *
9412811 TGTCTCCTGCGTCTG-CGTATC
1 TGTCGCCTCCGTCTGACGTATC
9412832 TGTCGCCTCCGTCTGACGTA
1 TGTCGCCTCCGTCTGACGTA
9412852 GAAGTGCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.07, C:0.34, G:0.24, T:0.34
Consensus pattern (22 bp):
TGTCGCCTCCGTCTGACGTATC
Found at i:9434913 original size:2 final size:2
Alignment explanation
Indices: 9434906--9434939 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9434896 AAATCTCAAG
9434906 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9434940 GTTTTTATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9444783 original size:66 final size:66
Alignment explanation
Indices: 9444706--9444836 Score: 217
Period size: 66 Copynumber: 2.0 Consensus size: 66
9444696 ACATTACTAG
** **
9444706 TACTAAATTCAAAGCAACCCGAAGGGGTAGCATAACCCCCTAAAATTTTTTAAATTTTTTATTTA
1 TACTAAATTCAAAGCAACCAAAAGGGGTAGCATAACCCCCTAAAATTTTTTAAACGTTTTATTTA
9444771 T
66 T
*
9444772 TACTAAATTCAAAGCAACTAAAAGGGGTAGCATAACCCCCTAAAATTTTTTAAACGTTTTATTTA
1 TACTAAATTCAAAGCAACCAAAAGGGGTAGCATAACCCCCTAAAATTTTTTAAACGTTTTATTTA
9444837 ATACATATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (66 bp):
TACTAAATTCAAAGCAACCAAAAGGGGTAGCATAACCCCCTAAAATTTTTTAAACGTTTTATTTA
T
Found at i:9445576 original size:28 final size:28
Alignment explanation
Indices: 9445545--9445604 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
9445535 AATAAAAATT
9445545 ATGAAAACAAAACTCCAAAACAAAATGA
1 ATGAAAACAAAACTCCAAAACAAAATGA
* * * * *
9445573 ATGATAAGAAAATTTCAGAACAAAATGA
1 ATGAAAACAAAACTCCAAAACAAAATGA
9445601 ATGA
1 ATGA
9445605 TAAATTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.17
Consensus pattern (28 bp):
ATGAAAACAAAACTCCAAAACAAAATGA
Found at i:9446445 original size:21 final size:21
Alignment explanation
Indices: 9446416--9446457 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9446406 TTGTGAAAAC
9446416 TGAGAGAGAAGATGGGTAAAT
1 TGAGAGAGAAGATGGGTAAAT
* * *
9446437 TGAGGGAGAAGGTGGTTAAAT
1 TGAGAGAGAAGATGGGTAAAT
9446458 AATGTTGCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.21
Consensus pattern (21 bp):
TGAGAGAGAAGATGGGTAAAT
Found at i:9448843 original size:3 final size:3
Alignment explanation
Indices: 9448835--9448859 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9448825 TCAAGGCTTT
9448835 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
9448860 GAGAGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:9449902 original size:82 final size:81
Alignment explanation
Indices: 9449696--9449904 Score: 190
Period size: 82 Copynumber: 2.5 Consensus size: 81
9449686 TGATAGGAGG
* * * *
9449696 CTAGCAGAGTCGTTGCAAACGTTAGGAGGGTGGCTAATGGAGATGAAGATAGAGGTATTGGAGGA
1 CTAGCGGAGTCATTGCAAA-GTTA-GAGGGTGGCTAATGGAGATGAAGATAAAGGTATTAGAGGA
*
9449761 AATGGAGGTGAAGGGACA
64 AATGGAGCTGAAGGGACA
* * * * *
9449779 CTGGCGGAGTCATTGCAAAAGCTGAGGGGGTTGGCTCATGGAGATGAAGGTAAAGGTA-TAGA-G
1 CTAGCGGAGTCATTGC-AAAG-TTAGAGGG-TGGCTAATGGAGATGAAGATAAAGGTATTAGAGG
* *
9449842 AATTGTG-GCTGACGGGACA
63 AAATG-GAGCTGAAGGGACA
* *
9449861 CTAGCGGAGTCTTTGCAGAAGTTAAGAAGGGTGGCGAATGGAGA
1 CTAGCGGAGTCATTGCA-AAGTT-AG-AGGGTGGCTAATGGAGA
9449905 CGCAAATGGG
Statistics
Matches: 101, Mismatches: 18, Indels: 15
0.75 0.13 0.11
Matches are distributed among these distances:
81 2 0.02
82 45 0.45
83 25 0.25
84 29 0.29
ACGTcount: A:0.30, C:0.11, G:0.39, T:0.20
Consensus pattern (81 bp):
CTAGCGGAGTCATTGCAAAGTTAGAGGGTGGCTAATGGAGATGAAGATAAAGGTATTAGAGGAAA
TGGAGCTGAAGGGACA
Found at i:9470622 original size:42 final size:42
Alignment explanation
Indices: 9470576--9470787 Score: 253
Period size: 42 Copynumber: 5.0 Consensus size: 42
9470566 CCTCCTACCA
* * *
9470576 TACCGATCCTCTGGTGAGTAGGAACGATCCCGTCTTCGGTAG
1 TACCGATCATCAGGTGAGTAGGAACGATCCCGTCTTCTGTAG
** *
9470618 TACCGATTGTCAGGTGAGTAGGAAAGATCCCGTCTTCTGTAG
1 TACCGATCATCAGGTGAGTAGGAACGATCCCGTCTTCTGTAG
*
9470660 TACCGATCATCAGGTGCGTAGGAACGATCCCGTCTTCTGTAG
1 TACCGATCATCAGGTGAGTAGGAACGATCCCGTCTTCTGTAG
* * * ** * *
9470702 TGCTGATCGTTTGGTGAGTAGGAACGATCCCGCCTTCTGTAA
1 TACCGATCATCAGGTGAGTAGGAACGATCCCGTCTTCTGTAG
* * * * *
9470744 TACCGATCATCAGGAGAGTAGGAATGGTCACGTCTTCTATAG
1 TACCGATCATCAGGTGAGTAGGAACGATCCCGTCTTCTGTAG
9470786 TA
1 TA
9470788 GCAGTCATCT
Statistics
Matches: 141, Mismatches: 29, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 141 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (42 bp):
TACCGATCATCAGGTGAGTAGGAACGATCCCGTCTTCTGTAG
Found at i:9474159 original size:19 final size:19
Alignment explanation
Indices: 9474132--9474168 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9474122 GATTTATGAT
* *
9474132 GTTTGTAGATTTTATTATG
1 GTTTATAGATATTATTATG
9474151 GTTTATAGATATTATTAT
1 GTTTATAGATATTATTAT
9474169 TTTATTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.57
Consensus pattern (19 bp):
GTTTATAGATATTATTATG
Found at i:9474500 original size:25 final size:26
Alignment explanation
Indices: 9474445--9474500 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
9474435 TATTGTATTC
*
9474445 ATATT-TATTTATATAACTATTAATA
1 ATATTATATTTATATAACTAATAATA
*
9474470 GT-TTATATTTATATAA-TAATAATA
1 ATATTATATTTATATAACTAATAATA
9474494 ATATTAT
1 ATATTAT
9474501 TATTATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
ATATTATATTTATATAACTAATAATA
Found at i:9488665 original size:80 final size:80
Alignment explanation
Indices: 9488536--9488683 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
9488526 GGTCGGACAA
* * * *
9488536 TTTCTCTCTTCACTCTTTTCTTTTTTTCTCAAACTACCCAATACTAGATCCGGTCGAATCTCCTC
1 TTTCTCTCTTCACTATTTTCCTTTTTTCTCAAACTACCCAATACCAGATCCAGTCGAATCTCCTC
9488601 AGATTGCACAATGCC
66 AGATTGCACAATGCC
* * * * *
9488616 TTTCTCTTTTCACTATTTTCCTTTTTTCTCATA-T-CGCACAATGCCAGATCCAGTTGGATCTCC
1 TTTCTCTCTTCACTATTTTCCTTTTTTCTCAAACTAC-C-CAATACCAGATCCAGTCGAATCTCC
9488679 TCAGA
64 TCAGA
9488684 CCGTGCAATG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
78 1 0.02
79 2 0.04
80 54 0.95
ACGTcount: A:0.20, C:0.30, G:0.09, T:0.41
Consensus pattern (80 bp):
TTTCTCTCTTCACTATTTTCCTTTTTTCTCAAACTACCCAATACCAGATCCAGTCGAATCTCCTC
AGATTGCACAATGCC
Found at i:9509026 original size:14 final size:15
Alignment explanation
Indices: 9509009--9509042 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
9508999 AGATTACAAT
9509009 AAATTAAAT-TAGTA
1 AAATTAAATCTAGTA
9509023 AAATTAAATCTAGTA
1 AAATTAAATCTAGTA
9509038 AAATT
1 AAATT
9509043 GCTGTCGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (15 bp):
AAATTAAATCTAGTA
Found at i:9530284 original size:2 final size:2
Alignment explanation
Indices: 9530279--9530305 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9530269 ACACACACAC
9530279 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9530306 GCTATTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9531709 original size:13 final size:14
Alignment explanation
Indices: 9531683--9531711 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9531673 GCATAACAAC
9531683 TGCTGAAAACATCA
1 TGCTGAAAACATCA
9531697 TGCTGAAAA-ATCA
1 TGCTGAAAACATCA
9531710 TG
1 TG
9531712 GGGTGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (14 bp):
TGCTGAAAACATCA
Found at i:9535593 original size:14 final size:14
Alignment explanation
Indices: 9535574--9535604 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9535564 ATACCATTGT
*
9535574 TTTTATGTAAAATA
1 TTTTATGAAAAATA
9535588 TTTTATGAAAAATA
1 TTTTATGAAAAATA
9535602 TTT
1 TTT
9535605 CAACGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
TTTTATGAAAAATA
Found at i:9537352 original size:12 final size:13
Alignment explanation
Indices: 9537335--9537387 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
9537325 AAATTTGTAA
9537335 AAAATTA-AAAAT
1 AAAATTATAAAAT
9537347 AAAATTATAAAATTT
1 AAAATTATAAAA--T
** *
9537362 AAAAAAATAAAAA
1 AAAATTATAAAAT
9537375 AAAATTATAAAAT
1 AAAATTATAAAAT
9537388 TTTAAATCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
12 7 0.22
13 14 0.44
15 11 0.34
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAATTATAAAAT
Found at i:9541204 original size:15 final size:16
Alignment explanation
Indices: 9541165--9541213 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
9541155 AACAACAAAT
*
9541165 AAGAGAAGAGTAGAAA
1 AAGAAAAGAGTAGAAA
9541181 AAGAAAAGAGTAGAAA
1 AAGAAAAGAGTAGAAA
*
9541197 AAG-CAAGAGTAAGAAA
1 AAGAAAAGAGT-AGAAA
9541213 A
1 A
9541214 GTGTTATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 6 0.20
16 24 0.80
ACGTcount: A:0.65, C:0.02, G:0.27, T:0.06
Consensus pattern (16 bp):
AAGAAAAGAGTAGAAA
Found at i:9545053 original size:3 final size:3
Alignment explanation
Indices: 9545045--9545086 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
9545035 AATAAACATG
9545045 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9545087 CAAAAAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:9546908 original size:27 final size:27
Alignment explanation
Indices: 9546876--9546928 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
9546866 ATTTTTTACA
* **
9546876 TTAAAATGTTAATAATTTATAATTTAT
1 TTAAAATATTAATAATCAATAATTTAT
9546903 TTAAAATATTAATAATCAATAATTTA
1 TTAAAATATTAATAATCAATAATTTA
9546929 ATATTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
TTAAAATATTAATAATCAATAATTTAT
Found at i:9547355 original size:16 final size:17
Alignment explanation
Indices: 9547334--9547366 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
9547324 TAAGTTAAAC
9547334 ATTAATA-TTTTAAAAT
1 ATTAATACTTTTAAAAT
9547350 ATTAATACTTTTAAAAT
1 ATTAATACTTTTAAAAT
9547367 TTTTAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTAATACTTTTAAAAT
Found at i:9547724 original size:31 final size:32
Alignment explanation
Indices: 9547689--9547775 Score: 86
Period size: 32 Copynumber: 2.8 Consensus size: 32
9547679 TTTGATGAAG
9547689 TGGCACTGACATGATGACGTGGT-GTGCCACA
1 TGGCACTGACATGATGACGTGGTAGTGCCACA
* * * * *
9547720 TGGCACCGACACGATAATGTGGTAGTGCCACG
1 TGGCACTGACATGATGACGTGGTAGTGCCACA
* * * *
9547752 TGGCATTGATATAATGACATGGTA
1 TGGCACTGACATGATGACGTGGTA
9547776 CTAAAATGTT
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
31 19 0.45
32 23 0.55
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (32 bp):
TGGCACTGACATGATGACGTGGTAGTGCCACA
Found at i:9547756 original size:32 final size:31
Alignment explanation
Indices: 9547688--9547756 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
9547678 TTTTGATGAA
* * *
9547688 GTGGCACTGACATGATGACGTGGTGTGCCAC
1 GTGGCACCGACACGATAACGTGGTGTGCCAC
* *
9547719 ATGGCACCGACACGATAATGTGGTAGTGCCAC
1 GTGGCACCGACACGATAACGTGGT-GTGCCAC
9547751 GTGGCA
1 GTGGCA
9547757 TTGATATAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
31 19 0.61
32 12 0.39
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.20
Consensus pattern (31 bp):
GTGGCACCGACACGATAACGTGGTGTGCCAC
Found at i:9549433 original size:18 final size:18
Alignment explanation
Indices: 9549410--9549445 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9549400 TTATTCAATC
* *
9549410 TATTTTTTATTCGGTCAA
1 TATTTTTGAGTCGGTCAA
9549428 TATTTTTGAGTCGGTCAA
1 TATTTTTGAGTCGGTCAA
9549446 AAGTATAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (18 bp):
TATTTTTGAGTCGGTCAA
Found at i:9551824 original size:29 final size:31
Alignment explanation
Indices: 9551769--9551827 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
9551759 TTAATCATTA
* *
9551769 ATTATAAAACTTATTTTAATAAAAATAAAAT
1 ATTATAAAACTTAATTAAATAAAAATAAAAT
*
9551800 ATTA-AAAACTTAATTAAAT-ATAATAAAA
1 ATTATAAAACTTAATTAAATAAAAATAAAA
9551828 AATTTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.32
30 13 0.52
31 4 0.16
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (31 bp):
ATTATAAAACTTAATTAAATAAAAATAAAAT
Found at i:9551828 original size:21 final size:21
Alignment explanation
Indices: 9551794--9551839 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
9551784 TTAATAAAAA
* *
9551794 TAAA-ATATTAAAAACTTAAT
1 TAAATATAATAAAAAATTAAT
*
9551814 TAAATATAATAAAAAATTTAT
1 TAAATATAATAAAAAATTAAT
9551835 TAAAT
1 TAAAT
9551840 TATTTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATATAATAAAAAATTAAT
Found at i:9552332 original size:4 final size:4
Alignment explanation
Indices: 9552323--9552361 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
9552313 CCCTAAATCT
* * *
9552323 TTTA TTTA TTTA TTTA TTTA TTCA TTCA TTTG TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
9552362 TCGAAGTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:9553563 original size:21 final size:18
Alignment explanation
Indices: 9553536--9553581 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
9553526 TGGTCAGGAT
9553536 ACTGCTGCTGCCGGTACC
1 ACTGCTGCTGCCGGTACC
9553554 ACTGCTGCTGCCGGTACC
1 ACTGCTGCTGCCGGTACC
*
9553572 ACAGCTGCTG
1 ACTGCTGCTG
9553582 ATCAGGCCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.13, C:0.37, G:0.28, T:0.22
Consensus pattern (18 bp):
ACTGCTGCTGCCGGTACC
Found at i:9553778 original size:22 final size:22
Alignment explanation
Indices: 9553736--9553787 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
9553726 AATACTATTG
*
9553736 ATAATTAAATTATTAATTTTAT
1 ATAATTAAATTATTAAATTTAT
9553758 ATAATTAAA-TATATAAATTTAT
1 ATAATTAAATTAT-TAAATTTAT
9553780 -TAAATTAA
1 AT-AATTAA
9553788 TTAAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAATTAAATTATTAAATTTAT
Found at i:9558127 original size:10 final size:10
Alignment explanation
Indices: 9558104--9558138 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
9558094 AAATATTTTT
9558104 ATTAAATAATA
1 ATTAAAT-ATA
9558115 ATTAAATATA
1 ATTAAATATA
9558125 ATTAAA-ATA
1 ATTAAATATA
9558134 ATTAA
1 ATTAA
9558139 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.33
10 9 0.38
11 7 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAATATA
Found at i:9558382 original size:34 final size:34
Alignment explanation
Indices: 9558339--9558409 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
9558329 GTCTACGTCG
9558339 AAGTGGAGTTATAGCTGACATGAAATGAACCAAT
1 AAGTGGAGTTATAGCTGACATGAAATGAACCAAT
9558373 AAGTGGAGTTATAGCTGACATGAAATGAACCAAT
1 AAGTGGAGTTATAGCTGACATGAAATGAACCAAT
9558407 AAG
1 AAG
9558410 ATCGTTCCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.23
Consensus pattern (34 bp):
AAGTGGAGTTATAGCTGACATGAAATGAACCAAT
Found at i:9560343 original size:16 final size:17
Alignment explanation
Indices: 9560322--9560359 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
9560312 TGGATTAAAT
9560322 TTTAATCTTA-ATTC-AA
1 TTTAATC-TACATTCAAA
9560338 TTTAATCTACATTCAAA
1 TTTAATCTACATTCAAA
9560355 TTTAA
1 TTTAA
9560360 ATATACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 2 0.10
16 11 0.55
17 7 0.35
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAATCTACATTCAAA
Found at i:9560433 original size:12 final size:12
Alignment explanation
Indices: 9560418--9560461 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
9560408 TTTTATCTTA
9560418 ATTTTAAAATAT
1 ATTTTAAAATAT
9560430 ATTTTAAAATACT
1 ATTTTAAAATA-T
* *
9560443 AATCTAAAATAT
1 ATTTTAAAATAT
9560455 CATTTTA
1 -ATTTTA
9560462 TTATACGGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAT
Found at i:9560771 original size:16 final size:17
Alignment explanation
Indices: 9560750--9560782 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
9560740 TCACCTAATG
9560750 GTTAAAT-ATATAAATA
1 GTTAAATAATATAAATA
9560766 GTTAAATAATATAAATA
1 GTTAAATAATATAAATA
9560783 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
GTTAAATAATATAAATA
Found at i:9562556 original size:17 final size:16
Alignment explanation
Indices: 9562527--9562559 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
9562517 TCACATAATC
9562527 ATTAAATATATAAATA
1 ATTAAATATATAAATA
9562543 ATTAAATAATATAAATA
1 ATTAAAT-ATATAAATA
9562560 GAAAAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAAATATATAAATA
Found at i:9562876 original size:17 final size:17
Alignment explanation
Indices: 9562854--9562895 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
9562844 GGAATCATTT
*
9562854 TAAATATATATAATAAA
1 TAAATATATATAAAAAA
*
9562871 TAAATAGT-TTTAAAAAA
1 TAAATA-TATATAAAAAA
9562888 TAAATATA
1 TAAATATA
9562896 AAAATTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.05
17 19 0.90
18 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TAAATATATATAAAAAA
Found at i:9590579 original size:21 final size:21
Alignment explanation
Indices: 9590549--9590589 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9590539 TGCAATATAA
* *
9590549 TAAAGGTTTTGGTTTTAAATT
1 TAAAGATTTTGGTTCTAAATT
9590570 TAAAGATTTTGGTTCTAAAT
1 TAAAGATTTTGGTTCTAAAT
9590590 CTGAAGTTCC
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:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (21 bp):
TAAAGATTTTGGTTCTAAATT
Found at i:9610461 original size:16 final size:17
Alignment explanation
Indices: 9610431--9610467 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
9610421 TTTATTTTTT
9610431 TATTTATATTATTTAAC
1 TATTTATATTATTTAAC
9610448 TATTTATA-TATTTAAC
1 TATTTATATTATTTAAC
9610464 TATT
1 TATT
9610468 ATGTGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTATATTATTTAAC
Found at i:9610501 original size:21 final size:21
Alignment explanation
Indices: 9610477--9610527 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
9610467 TATGTGAAAT
*
9610477 TTTATATATTGT-ATTTATATA
1 TTTATATATTATAATTT-TATA
*
9610498 TTTATGTATTATAATTTTATA
1 TTTATATATTATAATTTTATA
9610519 TTTA-ATATT
1 TTTATATATT
9610528 TAAATATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 18 0.69
22 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTATATATTATAATTTTATA
Found at i:9611680 original size:20 final size:20
Alignment explanation
Indices: 9611643--9611681 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9611633 AAAAAATTAA
*
9611643 TAAAATAATTTTATTATATC
1 TAAAATAATTATATTATATC
9611663 TAAAATAAATTATA-TATAT
1 TAAAAT-AATTATATTATAT
9611682 AATAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAAATAATTATATTATATC
Found at i:9611694 original size:20 final size:18
Alignment explanation
Indices: 9611642--9611690 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
9611632 AAAAAAATTA
*
9611642 ATAAAATAATTTTATTATAT
1 ATAAAATAA-ATTA-TATAT
*
9611662 CTAAAATAAATTATATAT
1 ATAAAATAAATTATATAT
9611680 ATAATAATAAA
1 ATAA-AATAAA
9611691 ATTAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAAATAAATTATATAT
Found at i:9621529 original size:22 final size:22
Alignment explanation
Indices: 9621503--9621647 Score: 123
Period size: 22 Copynumber: 6.7 Consensus size: 22
9621493 AGTGTTGGTG
*
9621503 GTTTTTAGGTATTGCATGATTA
1 GTTTTTAAGTATTGCATGATTA
* * *
9621525 GTTTTTAAGCATTACATGGTT-
1 GTTTTTAAGTATTGCATGATTA
** ** *
9621546 GACTTTGGGTATTGCATGACTA
1 GTTTTTAAGTATTGCATGATTA
* * * *
9621568 GTTTTTAAGCATTACGTGACTA
1 GTTTTTAAGTATTGCATGATTA
* *
9621590 ATTTTTAAGTATTGCGTGATT-
1 GTTTTTAAGTATTGCATGATTA
* *
9621611 GATTTTAAGCATTGCATGATTA
1 GTTTTTAAGTATTGCATGATTA
9621633 GTTTTTAAGTATTGC
1 GTTTTTAAGTATTGC
9621648 GTGACTGACT
Statistics
Matches: 92, Mismatches: 29, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
21 30 0.33
22 62 0.67
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.46
Consensus pattern (22 bp):
GTTTTTAAGTATTGCATGATTA
Found at i:9621617 original size:43 final size:43
Alignment explanation
Indices: 9621570--9621651 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
9621560 CATGACTAGT
*
9621570 TTTTAAGCATTACGTGACTAATTTTTAAGTATTGCGTGATTGA
1 TTTTAAGCATTACATGACTAATTTTTAAGTATTGCGTGATTGA
* * *
9621613 TTTTAAGCATTGCATGATTAGTTTTTAAGTATTGCGTGA
1 TTTTAAGCATTACATGACTAATTTTTAAGTATTGCGTGA
9621652 CTGACTAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.45
Consensus pattern (43 bp):
TTTTAAGCATTACATGACTAATTTTTAAGTATTGCGTGATTGA
Found at i:9621694 original size:23 final size:23
Alignment explanation
Indices: 9621653--9621730 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
9621643 ATTGCGTGAC
* *
9621653 TGACTAGTTGAT-AGGCATTTCG
1 TGACTAGTTAATAAGGCATTGCG
* *
9621675 TGACTTGTTAATAAGGCATTGCA
1 TGACTAGTTAATAAGGCATTGCG
* *
9621698 TGACTAGTTAGTAAGGTATTGCG
1 TGACTAGTTAATAAGGCATTGCG
9621721 TGACTAGTTA
1 TGACTAGTTA
9621731 GTACGACATT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 10 0.21
23 37 0.79
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.36
Consensus pattern (23 bp):
TGACTAGTTAATAAGGCATTGCG
Found at i:9631529 original size:24 final size:23
Alignment explanation
Indices: 9631493--9631539 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
9631483 TTTTTTGTGT
9631493 TGAGTATAAAATATTGAAACAAAG
1 TGAGTATAAAATATTGAAA-AAAG
* *
9631517 TGAGTGTAGAATATTGAAAAAAG
1 TGAGTATAAAATATTGAAAAAAG
9631540 ATTAAGTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.51, C:0.02, G:0.21, T:0.26
Consensus pattern (23 bp):
TGAGTATAAAATATTGAAAAAAG
Found at i:9632209 original size:14 final size:15
Alignment explanation
Indices: 9632192--9632220 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9632182 ATTATATAAT
9632192 TTTAT-TATTTTTTA
1 TTTATATATTTTTTA
9632206 TTTATATATTTTTTA
1 TTTATATATTTTTTA
9632221 AAAAGCTCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATATATTTTTTA
Found at i:9649428 original size:30 final size:32
Alignment explanation
Indices: 9649388--9649446 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
9649378 TTTAATGAAG
9649388 TTTTAGTA-TTTTTATTTTGAA-TCAAATAGGT
1 TTTTAGTATTTTTTATTTT-AAGTCAAATAGGT
9649419 TTTTA-TATTTTTTATTTTAAGTCAAATA
1 TTTTAGTATTTTTTATTTTAAGTCAAATA
9649447 AATATTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (32 bp):
TTTTAGTATTTTTTATTTTAAGTCAAATAGGT
Found at i:9649455 original size:31 final size:31
Alignment explanation
Indices: 9649396--9649456 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
9649386 AGTTTTAGTA
** *
9649396 TTTTTATTTTGAATCAAATAGGTTTTTATAT
1 TTTTTATTTTGAATCAAATAAATATTTATAT
9649427 TTTTTATTTT-AAGTCAAATAAATATTTATA
1 TTTTTATTTTGAA-TCAAATAAATATTTATA
9649457 ATTAATGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (31 bp):
TTTTTATTTTGAATCAAATAAATATTTATAT
Found at i:9649743 original size:29 final size:32
Alignment explanation
Indices: 9649677--9649743 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 32
9649667 GTTTATTTGA
9649677 TTTAAAAAATATATAAATATTTAATTAAATGT
1 TTTAAAAAATATATAAATATTTAATTAAATGT
** * *
9649709 AATAAAAAA-ATA-AAA-ATTTATTTAAATTT
1 TTTAAAAAATATATAAATATTTAATTAAATGT
9649738 TTTAAA
1 TTTAAA
9649744 TAATCTATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
29 16 0.55
30 3 0.10
31 3 0.10
32 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (32 bp):
TTTAAAAAATATATAAATATTTAATTAAATGT
Found at i:9659385 original size:4 final size:4
Alignment explanation
Indices: 9659376--9659409 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
9659366 CAAAGACTTG
*
9659376 AGCC AGCC AGCC AGCC AGCC AGCC AGCT AGCC AG
1 AGCC AGCC AGCC AGCC AGCC AGCC AGCC AGCC AG
9659410 AGGAAACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.26, C:0.44, G:0.26, T:0.03
Consensus pattern (4 bp):
AGCC
Found at i:9661669 original size:16 final size:17
Alignment explanation
Indices: 9661648--9661679 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9661638 ATGTACTCAG
9661648 AGAAAA-AAAAAAGGGT
1 AGAAAAGAAAAAAGGGT
9661664 AGAAAAGAAAAAAGGG
1 AGAAAAGAAAAAAGGG
9661680 GGGAAAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (17 bp):
AGAAAAGAAAAAAGGGT
Found at i:9661685 original size:17 final size:16
Alignment explanation
Indices: 9661647--9661685 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
9661637 CATGTACTCA
9661647 GAGAAAAAAAAAAGGG
1 GAGAAAAAAAAAAGGG
*
9661663 TAGAAAAGAAAAAAGGG
1 GAGAAAA-AAAAAAGGG
*
9661680 GGGAAA
1 GAGAAA
9661686 GATAGGCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (16 bp):
GAGAAAAAAAAAAGGG
Found at i:9663422 original size:344 final size:344
Alignment explanation
Indices: 9662363--9664086 Score: 2508
Period size: 345 Copynumber: 5.0 Consensus size: 344
9662353 CCTGCTGATT
* * * * *
9662363 AATGGATTAGATGAGAATGAATAGACTGCATTGTTTTTAGATTTTGATCGGACAGGTTTGGCACT
1 AATGGATTAGGTGAGAATGAATGGACTGCATCGATTTTAGATTTTGGTCGGACAGGTTTGGCACT
*
9662428 AAATTTTGGAGTTAGCTGAAATGGTAATTGAAAAATGATTGGAAAGAAAAAGAAACTATAAGTTA
66 AAATTTTGGAGTTAGCTGGAATGGTAATTGAAAAATGATTGGAAAGAAAAAGAAACTATAAGTTA
* * *
9662493 TTTTGGAAAATCTACTTTAGCTTCCAGATCTTGTTGATATGCTGTCCAAACCTCCCTGCACATTT
131 TTTTGAAAAATCCACTTTAGCTTCCAGATCTTGCTGATATGCTGTCCAAACCT-CCTGCACATTT
*
9662558 CTTTTCGATAAAATCTTCTCTGGAAACACA-AGAAAGATCTCAAAGCAGATGCTCAAGTTAAGTG
195 CTTTTCGATAAAATCTTCTCTGGAAACACAGA-AAAGATCTCAAAGCAGGTGCTCAAGTTAAGTG
* * *
9662622 ATTTGGCCTCAACTATGCCAACTTCATCTTATAT-AGCCTGATAGTCTTCAACTGGGTTTTTTTT
259 ATTCGGCCTCAACTATGCCAACTTCATCTTAT-TCAGCCTTATAGTCTTCAACTGGGTTCTTTTT
*
9662686 TCAAGAGTTGAGGGGCTTGCCC
323 TCAAGAGTTGGGGGGCTTGCCC
* ** * *
9662708 AATGGATTAGGTGAGAATGAATGGATTGCATCGGCTTTAGATTTTGGTTGGACAAGTTTGGCACT
1 AATGGATTAGGTGAGAATGAATGGACTGCATCGATTTTAGATTTTGGTCGGACAGGTTTGGCACT
* *
9662773 AAACTTTGAAGTTAGCTGGAATGGTAATTGAAAAATGATTGGAAAGAAAAAGAAACTATAAGTTA
66 AAATTTTGGAGTTAGCTGGAATGGTAATTGAAAAATGATTGGAAAGAAAAAGAAACTATAAGTTA
* * * * * * *
9662838 TTTTGGAAAATCCACTTTAGCTTCTAAATCTTACTAATATGCTGTCCAAACCTCTTTCCACATTT
131 TTTTGAAAAATCCACTTTAGCTTCCAGATCTTGCTGATATGCTGTCCAAACCTC-CTGCACATTT
* * * *
9662903 CTTTTCGATAAAATCTTCTTTGAAAACACAGAAAAGATCTCAAAACAGGTGCTCAAGTTAAATGA
195 CTTTTCGATAAAATCTTCTCTGGAAACACAGAAAAGATCTCAAAGCAGGTGCTCAAGTTAAGTGA
* * *
9662968 TTCGGCCTCAACTATGCCAACTTCATCTTATTCAGCCCTATAGTATTCAGA-TGAGCTT-TTTTT
260 TTCGGCCTCAACTATGCCAACTTCATCTTATTCAGCCTTATAGTCTTCA-ACTG-GGTTCTTTTT
* *
9663031 TCAAGAGTTGGGGGGTTTGCCT
323 TCAAGAGTTGGGGGGCTTGCCC
*
9663053 AATGGATTCAGG-GAGAATGAATGGACTGCATCGATTTTAGATTTTGGTCGAACAGGTTTGGCAC
1 AATGGATT-AGGTGAGAATGAATGGACTGCATCGATTTTAGATTTTGGTCGGACAGGTTTGGCAC
* *
9663117 TAAATTTTGGAGTTAGTTGGAATGGTAATTGAAAAATGATTGAAAAGAAAAAGAAACTATAAGTT
65 TAAATTTTGGAGTTAGCTGGAATGGTAATTGAAAAATGATTGGAAAGAAAAAGAAACTATAAGTT
* * * *
9663182 ATTTTGAAAAATTCACTTTAGCTTCCAGATCTTGCTGATATGCTGTCAAAACCTCCGGCGCATTT
130 ATTTTGAAAAATCCACTTTAGCTTCCAGATCTTGCTGATATGCTGTCCAAACCTCCTGCACATTT
* * * * *
9663247 CTTTTTGATAAAATTTTCCCTGGAAACACAGAAAAGATCTCAAAGTAGGTGCTCAAGTGAAGTGA
195 CTTTTCGATAAAATCTTCTCTGGAAACACAGAAAAGATCTCAAAGCAGGTGCTCAAGTTAAGTGA
* * *
9663312 TTCGGCTTCAACTATGCCAACTTCATCTTATTCAACCTTATAGTTTTCAACTGGGTTCTTTTTTC
260 TTCGGCCTCAACTATGCCAACTTCATCTTATTCAGCCTTATAGTCTTCAACTGGGTTCTTTTTTC
*
9663377 AAGAGTTGGGGGGCTTGTCC
325 AAGAGTTGGGGGGCTTGCCC
* **
9663397 AATGGATTAGGTAAGAATGAATGGACTGCATCGATTTTAGATTTTGGTTAGACAGGTTTGGCACT
1 AATGGATTAGGTGAGAATGAATGGACTGCATCGATTTTAGATTTTGGTCGGACAGGTTTGGCACT
* *
9663462 AAATTTTAGAGTTAGCTGGAATGGTAATTGAAAAATGATTGGAAAGAAAAA-AAACTATAAATTA
66 AAATTTTGGAGTTAGCTGGAATGGTAATTGAAAAATGATTGGAAAGAAAAAGAAACTATAAGTTA
* * *
9663526 TTCTGAAAAATCCACTTTAGCTTCCAGATCTTGCTGATATGCTATCCAAACCTCCCTGAACATTT
131 TTTTGAAAAATCCACTTTAGCTTCCAGATCTTGCTGATATGCTGTCCAAACCT-CCTGCACATTT
* * *
9663591 CTTTTCGATAAAATCTTTTCTGGAAACACAAAAAATATCTCAAAGCAGGTGCTCAAGTTAAGTGA
195 CTTTTCGATAAAATCTTCTCTGGAAACACAGAAAAGATCTCAAAGCAGGTGCTCAAGTTAAGTGA
* * ** *
9663656 TTCGGCCTAAACTATGCCAACTTCATCTTATTCAGCCCTATAGTCTTCAGTTGGGCTCTTTTTTC
260 TTCGGCCTCAACTATGCCAACTTCATCTTATTCAGCCTTATAGTCTTCAACTGGGTTCTTTTTTC
9663721 AAGAGTTGGGGGGCTTGCCC
325 AAGAGTTGGGGGGCTTGCCC
* * *
9663741 AATGGATTAGGTGAGAATGAATGGACTGCTTCGGTTTTAGATTTTGGTTGGACAGGTTTGGCACT
1 AATGGATTAGGTGAGAATGAATGGACTGCATCGATTTTAGATTTTGGTCGGACAGGTTTGGCACT
* *
9663806 AAATTTTAGAGTTAACTGGAATGGTAATTGAAAAATGATTGGAAAGAAAAAGAAACTATAAGTTA
66 AAATTTTGGAGTTAGCTGGAATGGTAATTGAAAAATGATTGGAAAGAAAAAGAAACTATAAGTTA
* * * *
9663871 TTCT-AGAAAACCCATTTTAGCTTCCAGATCTTGCTGATATGCTATCCAAACCTCCTTGCACATT
131 TTTTGA-AAAATCCACTTTAGCTTCCAGATCTTGCTGATATGCTGTCCAAACCTCC-TGCACATT
* * * *
9663935 TCTTTTCGATAAAATCTTCTCTAGAAACATAGAAAAGATCTCAAAGCAAGTGCTCAAGTTAAATG
194 TCTTTTCGATAAAATCTTCTCTGGAAACACAGAAAAGATCTCAAAGCAGGTGCTCAAGTTAAGTG
* * * * * *
9664000 ATTTGGCCTAAACTATGCCAACTTCATCTTATTCAACCTTATAATCTTCAGCTGGGCTCTTTTTT
259 ATTCGGCCTCAACTATGCCAACTTCATCTTATTCAGCCTTATAGTCTTCAACTGGGTTCTTTTTT
*
9664065 CAAGAGTTGGTGGGCTTGCCC
324 CAAGAGTTGGGGGGCTTGCCC
9664086 A
1 A
9664087 GATTATAGAC
Statistics
Matches: 1241, Mismatches: 125, Indels: 26
0.89 0.09 0.02
Matches are distributed among these distances:
343 68 0.05
344 495 0.40
345 670 0.54
346 8 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (344 bp):
AATGGATTAGGTGAGAATGAATGGACTGCATCGATTTTAGATTTTGGTCGGACAGGTTTGGCACT
AAATTTTGGAGTTAGCTGGAATGGTAATTGAAAAATGATTGGAAAGAAAAAGAAACTATAAGTTA
TTTTGAAAAATCCACTTTAGCTTCCAGATCTTGCTGATATGCTGTCCAAACCTCCTGCACATTTC
TTTTCGATAAAATCTTCTCTGGAAACACAGAAAAGATCTCAAAGCAGGTGCTCAAGTTAAGTGAT
TCGGCCTCAACTATGCCAACTTCATCTTATTCAGCCTTATAGTCTTCAACTGGGTTCTTTTTTCA
AGAGTTGGGGGGCTTGCCC
Found at i:9673932 original size:2 final size:2
Alignment explanation
Indices: 9673925--9673949 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9673915 GCAGTTATGC
9673925 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
9673950 TTTTCAAGGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9698912 original size:10 final size:9
Alignment explanation
Indices: 9698897--9698935 Score: 51
Period size: 10 Copynumber: 4.0 Consensus size: 9
9698887 CCAGTCATAA
9698897 GAAACCGATC
1 GAAACCGA-C
9698907 GAAACCGACC
1 GAAACCGA-C
9698917 GAAACCGAC
1 GAAACCGAC
9698926 TGAAACCGAC
1 -GAAACCGAC
9698936 ATTCAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 1 0.04
10 26 0.96
ACGTcount: A:0.41, C:0.33, G:0.21, T:0.05
Consensus pattern (9 bp):
GAAACCGAC
Found at i:9698922 original size:20 final size:20
Alignment explanation
Indices: 9698897--9698935 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
9698887 CCAGTCATAA
9698897 GAAACCGA-TCGAAACCGACC
1 GAAACCGACT-GAAACCGACC
9698917 GAAACCGACTGAAACCGAC
1 GAAACCGACTGAAACCGAC
9698936 ATTCAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.41, C:0.33, G:0.21, T:0.05
Consensus pattern (20 bp):
GAAACCGACTGAAACCGACC
Found at i:9706476 original size:24 final size:24
Alignment explanation
Indices: 9706449--9706517 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
9706439 AATAAATATT
*
9706449 AATATTTAATTTAAAATATTTAAA
1 AATATTTAATTTAAAATATTAAAA
* * *
9706473 AATATTAATATTTAACAT-TAAAAA
1 AATATTTA-ATTTAAAATATTAAAA
*
9706497 AAT-TTTAAGTTAAAATATTAA
1 AATATTTAATTTAAAATATTAA
9706518 CATTAATATT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
22 7 0.20
23 6 0.17
24 14 0.40
25 8 0.23
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (24 bp):
AATATTTAATTTAAAATATTAAAA
Found at i:9709306 original size:27 final size:27
Alignment explanation
Indices: 9709268--9709328 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
9709258 ATTGTTGGAA
*
9709268 CATTTTTACTGTAAACATGATAATTTT
1 CATTTTCACTGTAAACATGATAATTTT
9709295 CATTTTCACTGTAAACATGATAATTTT
1 CATTTTCACTGTAAACATGATAATTTT
9709322 CATTTTC
1 CATTTTC
9709329 TATCAATTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.48
Consensus pattern (27 bp):
CATTTTCACTGTAAACATGATAATTTT
Found at i:9711757 original size:50 final size:50
Alignment explanation
Indices: 9711699--9711802 Score: 199
Period size: 50 Copynumber: 2.1 Consensus size: 50
9711689 CTTAACTTAA
*
9711699 TTTTTCAATGATGATTTTACAATCTCTAGCATGAAACTACCACCTCTGCC
1 TTTTTCAATGATGATTTTACAATCTCTAGCATCAAACTACCACCTCTGCC
9711749 TTTTTCAATGATGATTTTACAATCTCTAGCATCAAACTACCACCTCTGCC
1 TTTTTCAATGATGATTTTACAATCTCTAGCATCAAACTACCACCTCTGCC
9711799 TTTT
1 TTTT
9711803 GGGATCAGTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.38
Consensus pattern (50 bp):
TTTTTCAATGATGATTTTACAATCTCTAGCATCAAACTACCACCTCTGCC
Found at i:9714165 original size:21 final size:21
Alignment explanation
Indices: 9714137--9714188 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
9714127 CCTAGCCAAT
*
9714137 ACCCACCACCCACTCAAAGGT-
1 ACCCACCACCAACTC-AAGGTC
* *
9714158 ATCCACCAGCAACTCAAGGTC
1 ACCCACCACCAACTCAAGGTC
9714179 ACCCACCACC
1 ACCCACCACC
9714189 TAGCCGATGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.33, C:0.48, G:0.10, T:0.10
Consensus pattern (21 bp):
ACCCACCACCAACTCAAGGTC
Found at i:9714300 original size:39 final size:39
Alignment explanation
Indices: 9714257--9714379 Score: 137
Period size: 39 Copynumber: 3.2 Consensus size: 39
9714247 CCTCCAACGT
9714257 ATCCACCACCATCTAGATACCCTCCACCCACTCAAGGTC
1 ATCCACCACCATCTAGATACCCTCCACCCACTCAAGGTC
* * *
9714296 ATCCACCACCTAGGC-A-ATA-CCTGCCACCCACTTAAGGCC
1 ATCCACCACC-A-TCTAGATACCCT-CCACCCACTCAAGGTC
* *
9714335 A-CTCACCACCATCTAGATACCCTCCACCTATTCAAGGTC
1 ATC-CACCACCATCTAGATACCCTCCACCCACTCAAGGTC
9714374 ATCCAC
1 ATCCAC
9714380 GACAAAGGCA
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
37 1 0.01
38 6 0.09
39 54 0.79
40 6 0.09
41 1 0.01
ACGTcount: A:0.28, C:0.44, G:0.09, T:0.19
Consensus pattern (39 bp):
ATCCACCACCATCTAGATACCCTCCACCCACTCAAGGTC
Found at i:9714342 original size:78 final size:78
Alignment explanation
Indices: 9714260--9714419 Score: 232
Period size: 78 Copynumber: 2.1 Consensus size: 78
9714250 CCAACGTATC
**
9714260 CACCACCATCTAGATACCCTCCACCCACTCAAGGTCATCCACCACCTAGGCAATA-CCTGCCACC
1 CACCACCATCTAGATACCCTCCACCCACTCAAGGTCATCCACCACAAAGGCAATATCC-GCCACC
*
9714324 CACTTAAGGCCACT
65 CACTCAAGGCCACT
* * * * *
9714338 CACCACCATCTAGATACCCTCCACCTATTCAAGGTCATCCACGACAAAGGCAATATCCGCCGCCG
1 CACCACCATCTAGATACCCTCCACCCACTCAAGGTCATCCACCACAAAGGCAATATCCGCCACCC
9714403 ACTCAAGGCCACT
66 ACTCAAGGCCACT
9714416 CACC
1 CACC
9714420 GCCTCAAAGC
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 71 0.97
79 2 0.03
ACGTcount: A:0.29, C:0.43, G:0.12, T:0.16
Consensus pattern (78 bp):
CACCACCATCTAGATACCCTCCACCCACTCAAGGTCATCCACCACAAAGGCAATATCCGCCACCC
ACTCAAGGCCACT
Found at i:9714455 original size:96 final size:96
Alignment explanation
Indices: 9714340--9714515 Score: 262
Period size: 96 Copynumber: 1.8 Consensus size: 96
9714330 AGGCCACTCA
* * * * * * *
9714340 CCACCATCTAGATACCCTCCACCTATTCAAGGTCATCCACGACAAAGGCAATATCCGCCGCCGAC
1 CCACCATCAAGATACCCTCCACCAACTCAAGGTCATCCACCACAAAGCCAATATCCGCCACCCAC
9714405 TCAAGGCCACTCACCGCCTCAAAGCTATGCT
66 TCAAGGCCACTCACCGCCTCAAAGCTATGCT
* * *
9714436 CCACCGTCAAGATACCCTCCACCAACTCAAGGTCATCCACCACCAAGCCAATATTCGCCACCCAC
1 CCACCATCAAGATACCCTCCACCAACTCAAGGTCATCCACCACAAAGCCAATATCCGCCACCCAC
9714501 TCAAGGCCACTCACC
66 TCAAGGCCACTCACC
9714516 ACCATCTAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 70 1.00
ACGTcount: A:0.29, C:0.43, G:0.12, T:0.16
Consensus pattern (96 bp):
CCACCATCAAGATACCCTCCACCAACTCAAGGTCATCCACCACAAAGCCAATATCCGCCACCCAC
TCAAGGCCACTCACCGCCTCAAAGCTATGCT
Found at i:9714534 original size:96 final size:96
Alignment explanation
Indices: 9714340--9714536 Score: 243
Period size: 96 Copynumber: 2.1 Consensus size: 96
9714330 AGGCCACTCA
* * * * * * *
9714340 CCACCATCTAGATACCCTCCACCTATTCAAGGTCATCCACGACAAAGGCAATATCCGCCGCCGAC
1 CCACCATCAAGATACCCTCCACCAACTCAAGGTCATCCACCACAAAGCCAATATCCGCCACCCAC
* * **
9714405 TCAAGGCCACTCACCGCCTCAAAGCTATGCT
66 TCAAGGCCACTCACCACCTCAAAGATACCCT
* * *
9714436 CCACCGTCAAGATACCCTCCACCAACTCAAGGTCATCCACCACCAAGCCAATATTCGCCACCCAC
1 CCACCATCAAGATACCCTCCACCAACTCAAGGTCATCCACCACAAAGCCAATATCCGCCACCCAC
*
9714501 TCAAGGCCACTCACCACCATC-TAGATACCCT
66 TCAAGGCCACTCACCACC-TCAAAGATACCCT
9714532 CCACC
1 CCACC
9714537 TACTCAACAC
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
96 83 0.98
97 2 0.02
ACGTcount: A:0.29, C:0.43, G:0.12, T:0.16
Consensus pattern (96 bp):
CCACCATCAAGATACCCTCCACCAACTCAAGGTCATCCACCACAAAGCCAATATCCGCCACCCAC
TCAAGGCCACTCACCACCTCAAAGATACCCT
Found at i:9714536 original size:39 final size:39
Alignment explanation
Indices: 9714436--9714554 Score: 98
Period size: 39 Copynumber: 3.1 Consensus size: 39
9714426 AAGCTATGCT
* *
9714436 CCACCGTCAAGATACCCTCCACCAACTCAAGGTCATCCA
1 CCACCATCAAGATACCCTCCACCAACTCAAGGCCATCCA
* * ** * *
9714475 CCACCAAGCCA-ATATTCGCCACCCACTCAAGGCCA-CTCA
1 CCACC-ATCAAGATACCCTCCACCAACTCAAGGCCATC-CA
* * **
9714514 CCACCATCTAGATACCCTCCACCTACTCAACACCATCCA
1 CCACCATCAAGATACCCTCCACCAACTCAAGGCCATCCA
9714553 CC
1 CC
9714555 TCCCACTCAA
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
38 4 0.07
39 53 0.88
40 3 0.05
ACGTcount: A:0.30, C:0.47, G:0.08, T:0.15
Consensus pattern (39 bp):
CCACCATCAAGATACCCTCCACCAACTCAAGGCCATCCA
Found at i:9715333 original size:19 final size:19
Alignment explanation
Indices: 9715289--9715337 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
9715279 AGGCTTTTAA
**
9715289 AATTTAATTTATTTTTTATG
1 AATTTAATTT-TAATTTATG
*
9715309 AA-TTAATTTTAATTTATT
1 AATTTAATTTTAATTTATG
9715327 AATTTAATTTT
1 AATTTAATTTT
9715338 CATTGGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 8 0.32
19 15 0.60
20 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
AATTTAATTTTAATTTATG
Found at i:9718968 original size:2 final size:2
Alignment explanation
Indices: 9718958--9718988 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9718948 GTGATAAAAA
*
9718958 AT AT CT 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
9718989 AAAGTTATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9727095 original size:31 final size:30
Alignment explanation
Indices: 9727041--9727114 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 30
9727031 TAATTTTATT
9727041 TAATTTAA-TTTTTATATTTAAAATTAAAA
1 TAATTTAATTTTTTATATTTAAAATTAAAA
***
9727070 TAATTTAATTTATTTAT-TTTAAAAATTATTT
1 TAATTTAATTT-TTTATATTT-AAAATTAAAA
9727101 TAATTTAATTTTTT
1 TAATTTAATTTTTT
9727115 TCTAACTACA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.21
30 8 0.21
31 23 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TAATTTAATTTTTTATATTTAAAATTAAAA
Found at i:9727274 original size:17 final size:17
Alignment explanation
Indices: 9727248--9727285 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
9727238 TGACGTGATA
9727248 ATATTAATGTGATATTG
1 ATATTAATGTGATATTG
*
9727265 ATATTGATGTGATATTG
1 ATATTAATGTGATATTG
9727282 ATAT
1 ATAT
9727286 ATTGACATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (17 bp):
ATATTAATGTGATATTG
Found at i:9728807 original size:13 final size:13
Alignment explanation
Indices: 9728789--9728829 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
9728779 TGATGTTGAA
9728789 AATGATAATAAAT
1 AATGATAATAAAT
9728802 AATGATAATAAAT
1 AATGATAATAAAT
*
9728815 AATAATAAT-AAT
1 AATGATAATAAAT
9728827 AAT
1 AAT
9728830 AAAAACAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 6 0.22
13 21 0.78
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (13 bp):
AATGATAATAAAT
Found at i:9728812 original size:3 final size:3
Alignment explanation
Indices: 9728793--9728831 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
9728783 GTTGAAAATG
*
9728793 ATA ATAA ATA ATG ATA ATAA ATA ATA ATA ATA ATA ATA A
1 ATA AT-A ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA A
9728832 AAACAGAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:9732633 original size:5 final size:5
Alignment explanation
Indices: 9732623--9732647 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9732613 ATTACAAAAA
9732623 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
9732648 GGAGGACGGC
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:9738142 original size:19 final size:20
Alignment explanation
Indices: 9738120--9738162 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9738110 TTTATTTTGT
9738120 AAAAGC-TTAATATT-TTTAA
1 AAAAGCTTTAA-ATTATTTAA
*
9738139 AAAATCTTTAAATTATTTAA
1 AAAAGCTTTAAATTATTTAA
9738159 AAAA
1 AAAA
9738163 TTTAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (20 bp):
AAAAGCTTTAAATTATTTAA
Found at i:9745838 original size:14 final size:13
Alignment explanation
Indices: 9745819--9745866 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
9745809 ATAATAATAT
9745819 ATTAAAATTTATAA
1 ATTAAAATTT-TAA
9745833 ATTAAAAGTTTTAA
1 ATTAAAA-TTTTAA
* *
9745847 TTTAATATTTTAA
1 ATTAAAATTTTAA
*
9745860 AATAAAA
1 ATTAAAA
9745867 ACATATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 10 0.36
14 15 0.54
15 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
ATTAAAATTTTAA
Found at i:9746655 original size:15 final size:16
Alignment explanation
Indices: 9746637--9746666 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9746627 ATATTAAAAT
9746637 ATAAA-TTATTTTTTG
1 ATAAATTTATTTTTTG
9746652 ATAAATTTATTTTTT
1 ATAAATTTATTTTTT
9746667 AAATAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
ATAAATTTATTTTTTG
Found at i:9746720 original size:54 final size:53
Alignment explanation
Indices: 9746617--9746720 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 53
9746607 TCTTTTCATG
* * * *
9746617 TAATATTTAAATATTAAAATATAAATTATTTTTTGATAAATTTATTTTTTAAA
1 TAATATTTAAATATTAAAATATAAATGATTTTTTAATAAATTCACTTTTTAAA
* *
9746670 TAATATTTAAATATTATTAATATATA-GATTTTTTAATAAAATTCACTTTTT
1 TAATATTTAAATATTA-AAATATAAATGATTTTTTAAT-AAATTCACTTTTT
9746721 GACACTACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
53 25 0.58
54 18 0.42
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (53 bp):
TAATATTTAAATATTAAAATATAAATGATTTTTTAATAAATTCACTTTTTAAA
Found at i:9758519 original size:26 final size:25
Alignment explanation
Indices: 9758471--9758519 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
9758461 CAATGACAGA
*
9758471 AAAATTCTAAATTTTTTGTATAACT
1 AAAATTCTAAATTTTTTGAATAACT
9758496 AAAATT-TAAATTTGTTGTGAATAA
1 AAAATTCTAAATTT-TT-TGAATAA
9758520 TTTATTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 8 0.38
26 6 0.29
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (25 bp):
AAAATTCTAAATTTTTTGAATAACT
Found at i:9758900 original size:2 final size:2
Alignment explanation
Indices: 9758887--9758922 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
9758877 ACAACTTTCC
9758887 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9758923 TGTTGAACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9762047 original size:2 final size:2
Alignment explanation
Indices: 9762040--9762064 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9762030 AATCTTTAAC
9762040 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
9762065 ATCTTTAGCT
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:9764683 original size:12 final size:12
Alignment explanation
Indices: 9764655--9764702 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
9764645 TTCAAAGTTC
* *
9764655 AAAAAAAGATAA
1 AAAAAAAAATAG
9764667 AAAAATAAAATAG
1 AAAAA-AAAATAG
*
9764680 AAAACAAAATAG
1 AAAAAAAAATAG
9764692 AAAAAAAAATA
1 AAAAAAAAATA
9764703 ATACATGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 22 0.71
13 9 0.29
ACGTcount: A:0.81, C:0.02, G:0.06, T:0.10
Consensus pattern (12 bp):
AAAAAAAAATAG
Found at i:9773498 original size:33 final size:35
Alignment explanation
Indices: 9773442--9773513 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
9773432 TATCATATAT
* *
9773442 TTTTTTAATTATAATCTTATATATTTTAT-TTTTA
1 TTTTTTAATTAGAATCTTATATATTATATATTTTA
* *
9773476 TTTTTTAA-TAGAATTTTTTATATTATATATTTTA
1 TTTTTTAATTAGAATCTTATATATTATATATTTTA
9773510 TTTT
1 TTTT
9773514 AATTTTTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 16 0.48
34 17 0.52
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (35 bp):
TTTTTTAATTAGAATCTTATATATTATATATTTTA
Found at i:9776798 original size:2 final size:2
Alignment explanation
Indices: 9776791--9776828 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
9776781 GTTGACCACG
*
9776791 TC TC TC TC TC TC TC TC TC TC TC TA 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 TC TC
9776829 AGTGCTTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9777669 original size:13 final size:13
Alignment explanation
Indices: 9777651--9777690 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
9777641 AACATATCAA
9777651 GTTTTATTGATAT
1 GTTTTATTGATAT
*
9777664 GTTTTA-TCA-A-
1 GTTTTATTGATAT
9777674 GTTTTATTGATAT
1 GTTTTATTGATAT
9777687 GTTT
1 GTTT
9777691 ATGATTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
10 6 0.27
11 3 0.14
12 3 0.14
13 10 0.45
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.60
Consensus pattern (13 bp):
GTTTTATTGATAT
Found at i:9777675 original size:23 final size:23
Alignment explanation
Indices: 9777645--9777690 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
9777635 AGACTTAACA
9777645 TATCAAGTTTTATTGATATGTTT
1 TATCAAGTTTTATTGATATGTTT
9777668 TATCAAGTTTTATTGATATGTTT
1 TATCAAGTTTTATTGATATGTTT
9777691 ATGATTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (23 bp):
TATCAAGTTTTATTGATATGTTT
Found at i:9786829 original size:24 final size:24
Alignment explanation
Indices: 9786797--9786843 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
9786787 CGCCGTTGTC
*
9786797 GCATAGGAGAG-GGTGATTTACGTA
1 GCATAGGAG-GCGGTGATCTACGTA
9786821 GCATAGGAGGCGGTGATCTACGT
1 GCATAGGAGGCGGTGATCTACGT
9786844 CGCAAGGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.13, G:0.38, T:0.23
Consensus pattern (24 bp):
GCATAGGAGGCGGTGATCTACGTA
Found at i:9786862 original size:24 final size:24
Alignment explanation
Indices: 9786835--9786989 Score: 141
Period size: 24 Copynumber: 6.5 Consensus size: 24
9786825 AGGAGGCGGT
*
9786835 GATCTACGTCGCA-AGGGTGATGGA
1 GATCTACGACGCACA-GGTGATGGA
** ** *
9786859 GATCTACGGTGCACAGGAAACGGA
1 GATCTACGACGCACAGGTGATGGA
* *
9786883 GATCTACGACGTATAGGTGATGGA
1 GATCTACGACGCACAGGTGATGGA
** * * * *
9786907 GATCTGTGGCGCCCAGGCGAAGGA
1 GATCTACGACGCACAGGTGATGGA
*
9786931 GATCTACGACGCACAGGGGATGGA
1 GATCTACGACGCACAGGTGATGGA
* *
9786955 GATCTTCGACGCACAAGTGATGGA
1 GATCTACGACGCACAGGTGATGGA
9786979 GATCTACGACG
1 GATCTACGACG
9786990 TCGAACAGGG
Statistics
Matches: 100, Mismatches: 30, Indels: 2
0.76 0.23 0.02
Matches are distributed among these distances:
24 99 0.99
25 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.35, T:0.17
Consensus pattern (24 bp):
GATCTACGACGCACAGGTGATGGA
Found at i:9787009 original size:27 final size:24
Alignment explanation
Indices: 9786835--9787010 Score: 138
Period size: 24 Copynumber: 7.2 Consensus size: 24
9786825 AGGAGGCGGT
*
9786835 GATCTACGTCGCA-AGGGTGATGGA
1 GATCTACGACGCACAGGG-GATGGA
** ** *
9786859 GATCTACGGTGCACAGGAAACGGA
1 GATCTACGACGCACAGGGGATGGA
* * *
9786883 GATCTACGACGTATAGGTGATGGA
1 GATCTACGACGCACAGGGGATGGA
** * * * *
9786907 GATCTGTGGCGCCCAGGCGAAGGA
1 GATCTACGACGCACAGGGGATGGA
9786931 GATCTACGACGCACAGGGGATGGA
1 GATCTACGACGCACAGGGGATGGA
* * *
9786955 GATCTTCGACGCACAAGTGATGGA
1 GATCTACGACGCACAGGGGATGGA
*
9786979 GATCTACGACGTCGAACAGGGGATGGT
1 GATCTACGACG-C--ACAGGGGATGGA
9787006 GATCT
1 GATCT
9787011 GTGACGGCGA
Statistics
Matches: 115, Mismatches: 33, Indels: 5
0.75 0.22 0.03
Matches are distributed among these distances:
24 97 0.84
25 4 0.03
27 14 0.12
ACGTcount: A:0.27, C:0.19, G:0.35, T:0.18
Consensus pattern (24 bp):
GATCTACGACGCACAGGGGATGGA
Found at i:9787031 original size:27 final size:27
Alignment explanation
Indices: 9787001--9787103 Score: 100
Period size: 27 Copynumber: 3.8 Consensus size: 27
9786991 CGAACAGGGG
*
9787001 ATGGTGATCTGTGACGGC-GATTTGATA
1 ATGGTGATCTATGACGGCGGA-TTGATA
* *
9787028 ATGGTGATCTATGACGGCGGATTGGTG
1 ATGGTGATCTATGACGGCGGATTGATA
* * * * *
9787055 ATGGTGATCTACGACGTCGGATAGGTG
1 ATGGTGATCTATGACGGCGGATTGATA
* *
9787082 ATGGTGGTCTATGACGCCGGAT
1 ATGGTGATCTATGACGGCGGAT
9787104 GGGCGACCGT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
27 64 0.97
28 2 0.03
ACGTcount: A:0.20, C:0.14, G:0.37, T:0.29
Consensus pattern (27 bp):
ATGGTGATCTATGACGGCGGATTGATA
Found at i:9787119 original size:27 final size:27
Alignment explanation
Indices: 9787028--9787125 Score: 106
Period size: 27 Copynumber: 3.6 Consensus size: 27
9787018 CGATTTGATA
* * *
9787028 ATGGTGATCTATGACGGCGGATTGGTG
1 ATGGTGATCTACGACGCCGGATAGGTG
*
9787055 ATGGTGATCTACGACGTCGGATAGGTG
1 ATGGTGATCTACGACGCCGGATAGGTG
* * * *
9787082 ATGGTGGTCTATGACGCCGGATGGGCG
1 ATGGTGATCTACGACGCCGGATAGGTG
**
9787109 ACCGTGATCTACGACGC
1 ATGGTGATCTACGACGC
9787126 ACGGGTGTAG
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.19, C:0.18, G:0.38, T:0.24
Consensus pattern (27 bp):
ATGGTGATCTACGACGCCGGATAGGTG
Found at i:9795846 original size:117 final size:117
Alignment explanation
Indices: 9795640--9795865 Score: 380
Period size: 117 Copynumber: 1.9 Consensus size: 117
9795630 GTTGAAGCTC
* ** * * *
9795640 TGAGCTATAATGTGATGATTATTTATGAGGAAACTTATTTATTCCAGTTGAAACCAGAGGGGTGC
1 TGAGCTATAATGTGATGAATATTTATGAGGAAACTTAGCTATGCCAGGTGAAACCAGAAGGGTGC
9795705 TTGTAAACCAGAAATATTGTTGGAATATTTGAGTTTGTAGTTGTTTCAACTA
66 TTGTAAACCAGAAATATTGTTGGAATATTTGAGTTTGTAGTTGTTTCAACTA
* *
9795757 TGAGCTATACTGTGATGAATATTTATGAGGAAACTTAGCTATGCTAGGTGAAACCAGAAGGGTGC
1 TGAGCTATAATGTGATGAATATTTATGAGGAAACTTAGCTATGCCAGGTGAAACCAGAAGGGTGC
9795822 TTGTAAACCAGAAATATTGTTGGAATATTTGAGTTTGTAGTTGT
66 TTGTAAACCAGAAATATTGTTGGAATATTTGAGTTTGTAGTTGT
9795866 CATGTGTTTT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 101 1.00
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (117 bp):
TGAGCTATAATGTGATGAATATTTATGAGGAAACTTAGCTATGCCAGGTGAAACCAGAAGGGTGC
TTGTAAACCAGAAATATTGTTGGAATATTTGAGTTTGTAGTTGTTTCAACTA
Found at i:9796568 original size:68 final size:68
Alignment explanation
Indices: 9796455--9796589 Score: 216
Period size: 68 Copynumber: 2.0 Consensus size: 68
9796445 TCCTTAACTG
**
9796455 AGTGATAGAATGGTTCTTGATTTTTCTTTGGTCAATTCCTGATCTTATTTTGTGACATTCTGCAA
1 AGTGATAGAATGGTTCTTGATTTTTCTTTGGTCAATTCCCAATCTTATTTTGTGACATTCTGCAA
9796520 CAT
66 CAT
* ** *
9796523 AGTGATAGAATGGTTCTTGGTTTTTCTTTGGTCGGTTCCCAATCTTATTTTGTGACATTTTGCAA
1 AGTGATAGAATGGTTCTTGATTTTTCTTTGGTCAATTCCCAATCTTATTTTGTGACATTCTGCAA
9796588 CA
66 CA
9796590 GTGTTACTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (68 bp):
AGTGATAGAATGGTTCTTGATTTTTCTTTGGTCAATTCCCAATCTTATTTTGTGACATTCTGCAA
CAT
Found at i:9798162 original size:42 final size:42
Alignment explanation
Indices: 9798115--9798201 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
9798105 AGGCAACGTC
9798115 CAATCACCCAAGAAGCTTGCCATCACGGGGAAATGCATTATA
1 CAATCACCCAAGAAGCTTGCCATCACGGGGAAATGCATTATA
9798157 CAATCACCCAAGAAGCTTGCCATCACGGGGAAATGCATTATA
1 CAATCACCCAAGAAGCTTGCCATCACGGGGAAATGCATTATA
9798199 CAA
1 CAA
9798202 CAAGATCGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (42 bp):
CAATCACCCAAGAAGCTTGCCATCACGGGGAAATGCATTATA
Found at i:9799048 original size:306 final size:306
Alignment explanation
Indices: 9798470--9799070 Score: 798
Period size: 306 Copynumber: 2.0 Consensus size: 306
9798460 TGCAGCTTTC
* * * * * *
9798470 TTGTCACCAGTGCCTTGGTTACCGTTTTTCCATGCTGGCATCTCGAATTCTTCTGTCTCTGGAAA
1 TTGTCACCAGTGCCTTGGTCACCATTTTTCCATGCTGGAACCACGAATTCTTCTGTATCTGGAAA
* * * *
9798535 TGAATTCTGTGATGAAATGAGCGGCGATAGTAAGGGAATTGCAGCTGGAGAAGTCCCACTAGAGG
66 TGAATACGGTGATGAAATGAGCGGCGACAGTAAGGGAATTGCAGCTGGAGAAGTCCCACCAGAGG
* ** * *
9798600 ACCCAAAAGGGCTGGTACCGGCAGCGGGGGCGTTCATCTGATCAAGCTTAAGAGATGCTGGGGCA
131 ACCCAAAAGGGCAGGTACCGGCAGCGGCAGCGTTCATCCGATCAAGCTTAAGAGATGCCGGGGCA
* ** *
9798665 TGCTTTTGTAACCTGGTGGGTGGTTTCCCCACTATGGCTTTGGTCACGCCAATATGTAGTTGCTC
196 TGCTTTTGTAACCTGGTGGGTGGCTTCCCCACTATGGCTTTGGTCACGCCAATAAATAGGTGCTC
*
9798730 AAATAAGTTCCCACCGTCCTCCATTCTTGAAATGAAACGCCCCGTG
261 AAATAAGTTCCCACCGTCCTCCATCCTTGAAATGAAACGCCCCGTG
* *
9798776 TTGTCATCAGTGCCTTGGTCACCATTTTTCCATGTTGGAACCACGAATTCTTCTGTATCTGGAAA
1 TTGTCACCAGTGCCTTGGTCACCATTTTTCCATGCTGGAACCACGAATTCTTCTGTATCTGGAAA
*
9798841 TGGATACGGTGAT-AAAGTGA-CAGGCGACAGTAAGGGAATTGCAGCCT-GAGAAGTCCCACCAG
66 TGAATACGGTGATGAAA-TGAGC-GGCGACAGTAAGGGAATTGCAG-CTGGAGAAGTCCCACCAG
* * * * *
9798903 AGGTCCCAAAAGGGCAGGTGCCGGCAGCGGCAGTGTTTATCCGATCGAGCTTAAGAGATGCCGGG
128 AGGACCCAAAAGGGCAGGTACCGGCAGCGGCAGCGTTCATCCGATCAAGCTTAAGAGATGCCGGG
* * * * * *
9798968 GCATGCTTTTGTAGCCTGGTGGGTTGCTTCCCTACTTTGG-TCTTGGTCATGCCAATAAATTGCG
193 GCATGCTTTTGTAACCTGGTGGGTGGCTTCCCCACTATGGCT-TTGGTCACGCCAATAAATAG-G
* *
9799032 T-CTCGAATATGTTCCCACCGTCCTCCATCCTTGAAATGA
256 TGCTCAAATAAGTTCCCACCGTCCTCCATCCTTGAAATGA
9799071 GACCCCCTGG
Statistics
Matches: 254, Mismatches: 36, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
305 5 0.02
306 246 0.97
307 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (306 bp):
TTGTCACCAGTGCCTTGGTCACCATTTTTCCATGCTGGAACCACGAATTCTTCTGTATCTGGAAA
TGAATACGGTGATGAAATGAGCGGCGACAGTAAGGGAATTGCAGCTGGAGAAGTCCCACCAGAGG
ACCCAAAAGGGCAGGTACCGGCAGCGGCAGCGTTCATCCGATCAAGCTTAAGAGATGCCGGGGCA
TGCTTTTGTAACCTGGTGGGTGGCTTCCCCACTATGGCTTTGGTCACGCCAATAAATAGGTGCTC
AAATAAGTTCCCACCGTCCTCCATCCTTGAAATGAAACGCCCCGTG
Found at i:9799852 original size:25 final size:25
Alignment explanation
Indices: 9799805--9799852 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
9799795 GGTAACAAAG
* * * *
9799805 AAAATAAAAAGAGAGAGAGAGAAAA
1 AAAAAAAAAAAAGACAGAAAGAAAA
9799830 AAAAAAAAAAAAGACAGAAAGAA
1 AAAAAAAAAAAAGACAGAAAGAA
9799853 GATAAAAGCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAAAAGACAGAAAGAAAA
Found at i:9805460 original size:26 final size:26
Alignment explanation
Indices: 9805431--9805485 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
9805421 ATCCGTGTGC
*
9805431 TCAAAGTTTCAAAGAAGAATATTTTG
1 TCAAAGTTTCAAACAAGAATATTTTG
9805457 TCAAAGTTTCAAACAAGAATATTTTG
1 TCAAAGTTTCAAACAAGAATATTTTG
9805483 TCA
1 TCA
9805486 TATACAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (26 bp):
TCAAAGTTTCAAACAAGAATATTTTG
Found at i:9820158 original size:30 final size:30
Alignment explanation
Indices: 9820124--9820203 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
9820114 GTTATACATA
*
9820124 TTGAAAAAAATATTGTTGTTACATGTCATG
1 TTGAAAAAAATATTGTTGTTACATGCCATG
*
9820154 TTGAAAAAAATATTGTTATTACATGCCATG
1 TTGAAAAAAATATTGTTGTTACATGCCATG
* *
9820184 -TCAAAAAAATATTATTGTTA
1 TTGAAAAAAATATTGTTGTTA
9820204 AATACTGTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 17 0.38
30 28 0.62
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (30 bp):
TTGAAAAAAATATTGTTGTTACATGCCATG
Found at i:9822717 original size:24 final size:24
Alignment explanation
Indices: 9822605--9822717 Score: 75
Period size: 24 Copynumber: 4.7 Consensus size: 24
9822595 AGCTTTTAGG
* *
9822605 GCATGCTTGTCAGTTTCTTGAGTA
1 GCATGCTTCTCAGTTTCATGAGTA
* * *
9822629 GCATACTTGTCAGCTTCATGAGTA
1 GCATGCTTCTCAGTTTCATGAGTA
* * * * * *
9822653 CCAT-CCTCGCTGGTTTTATGAGCA
1 GCATGCTTCTC-AGTTTCATGAGTA
* * * *
9822677 GCATGCTTATTATTTTCATAAGTA
1 GCATGCTTCTCAGTTTCATGAGTA
9822701 GCATGCTTCTCAGTTTC
1 GCATGCTTCTCAGTTTC
9822718 GGAAGCTGTT
Statistics
Matches: 63, Mismatches: 24, Indels: 4
0.69 0.26 0.04
Matches are distributed among these distances:
23 3 0.05
24 58 0.92
25 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (24 bp):
GCATGCTTCTCAGTTTCATGAGTA
Found at i:9837191 original size:21 final size:21
Alignment explanation
Indices: 9837167--9837208 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9837157 AACTCCACTC
9837167 AAATATATCCAAATGCTTCAT
1 AAATATATCCAAATGCTTCAT
*
9837188 AAATATCTCCAAATGCTTCAT
1 AAATATATCCAAATGCTTCAT
9837209 CAGGATTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.33
Consensus pattern (21 bp):
AAATATATCCAAATGCTTCAT
Found at i:9850117 original size:12 final size:12
Alignment explanation
Indices: 9850100--9850146 Score: 94
Period size: 12 Copynumber: 3.9 Consensus size: 12
9850090 AAAAAATCTT
9850100 ATTTTTCTTTTC
1 ATTTTTCTTTTC
9850112 ATTTTTCTTTTC
1 ATTTTTCTTTTC
9850124 ATTTTTCTTTTC
1 ATTTTTCTTTTC
9850136 ATTTTTCTTTT
1 ATTTTTCTTTT
9850147 GCTTTGGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (12 bp):
ATTTTTCTTTTC
Found at i:9850158 original size:24 final size:24
Alignment explanation
Indices: 9850106--9850165 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
9850096 TCTTATTTTT
**
9850106 CTTTTCATTTTTCTTTTCATTTTT
1 CTTTTCATTTTTCTTTTCATTTGG
9850130 CTTTTCATTTTTCTTTTGC-TTTGG
1 CTTTTCATTTTTCTTTT-CATTTGG
* *
9850154 GTTTTCCTTTTT
1 CTTTTCATTTTT
9850166 TTTAATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 30 0.97
25 1 0.03
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.72
Consensus pattern (24 bp):
CTTTTCATTTTTCTTTTCATTTGG
Found at i:9852570 original size:21 final size:20
Alignment explanation
Indices: 9852532--9852570 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
9852522 ATGATTTTAG
* *
9852532 ACTAATTTTATTTCTTATGA
1 ACTAATTTAATTTATTATGA
9852552 ACTAATTATAATTTATTAT
1 ACTAATT-TAATTTATTAT
9852571 TTTAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (20 bp):
ACTAATTTAATTTATTATGA
Found at i:9852595 original size:33 final size:33
Alignment explanation
Indices: 9852536--9852598 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
9852526 TTTTAGACTA
9852536 ATTTTATTTCTTATGAACTAATTATAATTTATT
1 ATTTTATTTCTTATGAACTAATTATAATTTATT
*
9852569 ATTTTAATTT-TTATTAA-TAATATATAATTT
1 ATTTT-ATTTCTTATGAACTAAT-TATAATTT
9852599 GATTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 4 0.15
33 19 0.70
34 4 0.15
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.59
Consensus pattern (33 bp):
ATTTTATTTCTTATGAACTAATTATAATTTATT
Found at i:9856277 original size:303 final size:298
Alignment explanation
Indices: 9855729--9856276 Score: 784
Period size: 303 Copynumber: 1.8 Consensus size: 298
9855719 TCTCACTAGT
*
9855729 ATATATACTATAAGTTTATATAAACAAAAAAATATATATTATAATTAATAATTTTATAAGTTATA
1 ATATATACTATAAGTTTATATAAACAAAAAAATATATATTATAATTAATAATTTTATAAGTTACA
** * *
9855794 ATTTTTGTAATGTTAACATAAAATAGAAAATAAATATGTTTATTTTTAAAATAAATATACTAAAA
66 ATTTTTGTAACATTAACACAAAATAGAAAATAAATATGTTTATATTTAAAAT-AATATACTAAAA
*
9855859 GTATATATATAATAATAATAATAATATTCCTTATAAATTAACACAAAATCGAAAATATATATTAA
130 GCATATATATAATAATAAT-ATAATATTCCTTATAAATTAACACAAAATCGAAAATATATATTAA
* *
9855924 AAGAAATTATAAGTTAATTAATAATCATAATTTTATGAATTAATTTAATAACAATATGAGTTTAT
194 AAGAAATTACAAGTTAATTAATAATCATAATTTTATAAATTAATTTAAT---AATATGAGTTTAT
9855989 TCTTCAGTACATGATTTTTTTCTTTTAAAAGCTAGATATATAC
256 TCTTCAGTACATGATTTTTTTCTTTTAAAAGCTAGATATATAC
* * * *
9856032 ATATATATTATAAGTTTATATAAATAAAGATATATATATTATAATTAATAATTTTATAAGTTACA
1 ATATATACTATAAGTTTATATAAACAAAAAAATATATATTATAATTAATAATTTTATAAGTTACA
* *
9856097 ATTTTTGTAACATTAACACAAAATAGAAAGTAAATATGTTTATATTTAAAAT-ATATATTAAAAG
66 ATTTTTGTAACATTAACACAAAATAGAAAATAAATATGTTTATATTTAAAATAATATACTAAAAG
* * * * *
9856161 CATATATATAATAGTAAT-T-ATATTCTTTATAAA-TAATACAACATATAC-CATATATATATTA
131 CATATATATAATAATAATATAATATTCCTTATAAATTAACACAA-A-AT-CGAAAATATATATTA
*
9856222 AAA-AATATTACAAGTTAATTAATAATTATAATTTTATAAATTAATTTAATTAATA
193 AAAGAA-ATTACAAGTTAATTAATAATCATAATTTTATAAATTAATTTAA-TAATA
9856277 ATATGAGTTT
Statistics
Matches: 220, Mismatches: 20, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
297 11 0.05
298 16 0.07
299 57 0.26
300 2 0.01
301 27 0.12
303 107 0.49
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (298 bp):
ATATATACTATAAGTTTATATAAACAAAAAAATATATATTATAATTAATAATTTTATAAGTTACA
ATTTTTGTAACATTAACACAAAATAGAAAATAAATATGTTTATATTTAAAATAATATACTAAAAG
CATATATATAATAATAATATAATATTCCTTATAAATTAACACAAAATCGAAAATATATATTAAAA
GAAATTACAAGTTAATTAATAATCATAATTTTATAAATTAATTTAATAATATGAGTTTATTCTTC
AGTACATGATTTTTTTCTTTTAAAAGCTAGATATATAC
Found at i:9857086 original size:6 final size:6
Alignment explanation
Indices: 9857075--9857104 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
9857065 ATATACTTAG
*
9857075 CTTTTT CTTTTT CTATTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
9857105 ATCTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:9859577 original size:5 final size:5
Alignment explanation
Indices: 9859554--9859707 Score: 56
Period size: 5 Copynumber: 31.4 Consensus size: 5
9859544 CTGTTATAAT
* * * *
9859554 TAAAA TAAAA -AATAT TAAAA TAAAA T-ATA TAATA TAAGAA T-CAA -AAAA
1 TAAAA TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA TAA-AA TAAAA TAAAA
* ** * *
9859602 TAAAA TAAAA TAAAA TATAAA -AAAT TAAAA T-TTA TATAA TATAAG TAAAA
1 TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA
* * * * * *
9859652 CAAAT TAAAA TAAAA T-ATA TAATA TAAAA -AATA TATTAA -AAAA TAAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA T-AAAA
9859701 TAAAA TA
1 TAAAA TA
9859708 TATAAGATTA
Statistics
Matches: 110, Mismatches: 24, Indels: 30
0.67 0.15 0.18
Matches are distributed among these distances:
4 21 0.19
5 73 0.66
6 16 0.15
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (5 bp):
TAAAA
Found at i:9859606 original size:33 final size:34
Alignment explanation
Indices: 9859548--9859623 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 34
9859538 TTTATACTGT
9859548 TATAAT-TAAAATAAAAAATATTAAAATAAAATA
1 TATAATATAAAATAAAAAATATTAAAATAAAATA
*
9859581 TATAATATAAGAATCAAAAA-A-TAAAATAAAATA
1 TATAATATAA-AATAAAAAATATTAAAATAAAATA
9859614 -A-AATATAAAA
1 TATAATATAAAA
9859624 AATTAAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 2 0.05
31 7 0.17
32 1 0.03
33 18 0.45
34 4 0.10
35 8 0.20
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (34 bp):
TATAATATAAAATAAAAAATATTAAAATAAAATA
Found at i:9859614 original size:24 final size:25
Alignment explanation
Indices: 9859595--9859683 Score: 65
Period size: 30 Copynumber: 3.3 Consensus size: 25
9859585 ATATAAGAAT
9859595 CAAAAAA-TAAAATAAAATAAAATA
1 CAAAAAATTAAAATAAAATAAAATA
* *
9859619 TAAAAAATTAAAATTTATATAATATAAGTA
1 CAAAAAATTAAAA--TA-A-AATA-AAATA
9859649 -AAACAAATTAAAATAAAATATATAATA
1 CAAA-AAATTAAAATAAAATA-A-AATA
*
9859676 TAAAAAAT
1 CAAAAAAT
9859684 ATATTAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
24 6 0.11
25 5 0.09
26 6 0.11
27 10 0.19
28 6 0.11
29 7 0.13
30 13 0.25
ACGTcount: A:0.70, C:0.02, G:0.01, T:0.27
Consensus pattern (25 bp):
CAAAAAATTAAAATAAAATAAAATA
Found at i:9859699 original size:18 final size:17
Alignment explanation
Indices: 9859555--9859702 Score: 55
Period size: 16 Copynumber: 8.7 Consensus size: 17
9859545 TGTTATAATT
*
9859555 AAAATAAAAA-ATAT-T
1 AAAATAAAAATATATAA
9859570 AAAATAAAATATATAATATA
1 AAAATAAAA-ATAT-ATA-A
* *
9859590 AGAATCAAAAA-ATAAAA
1 AAAAT-AAAAATATATAA
9859607 TAAAAT-AAAATATA-AA
1 -AAAATAAAAATATATAA
* *
9859623 AAATTAAAATTTATATAA
1 AAAATAAAA-ATATATAA
* *
9859641 TATAAGTAAAACA-A-AT-T
1 -A-AAATAAAA-ATATATAA
9859658 AAAAT-AAAATATATAA
1 AAAATAAAAATATATAA
* *
9859674 TATA-AAAAATATATTAA
1 AAAATAAAAATATA-TAA
9859691 AAAATAAAAATA
1 AAAATAAAAATA
9859703 AAATATATAA
Statistics
Matches: 98, Mismatches: 16, Indels: 35
0.66 0.11 0.23
Matches are distributed among these distances:
13 1 0.01
14 4 0.04
15 18 0.18
16 21 0.21
17 15 0.15
18 19 0.19
19 4 0.04
20 12 0.12
21 4 0.04
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (17 bp):
AAAATAAAAATATATAA
Found at i:9859717 original size:28 final size:28
Alignment explanation
Indices: 9859686--9859754 Score: 66
Period size: 33 Copynumber: 2.3 Consensus size: 28
9859676 TAAAAAATAT
*
9859686 ATTAAAAAATAAAAATAAAATATATAAG
1 ATTAAAAAATAAAAATAAAATATATAAC
* *
9859714 ATTATAATAATAAATGAAAATAAAATATATGAC
1 A-T-T-A-AA-AAATAAAAATAAAATATATAAC
9859747 ATTAAAAA
1 ATTAAAAA
9859755 TATATTTAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
28 3 0.09
29 3 0.09
30 2 0.06
31 2 0.06
32 3 0.09
33 20 0.61
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (28 bp):
ATTAAAAAATAAAAATAAAATATATAAC
Done.