Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 121 of 343
Found at i:40593014 original size:54 final size:55
Alignment explanation
Indices: 40592853--40593015 Score: 186
Period size: 55 Copynumber: 2.9 Consensus size: 55
40592843 GAGATTGGCG
* * * * * * *
40592853 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGA-CTTGAATATATAGCA
* * *
40592910 CTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGACTTGAATATATAGCA
*
40592965 CTAAGTGTGCGAG-TTGATTATATAGCACTGAGTGTGCGGACTT-AATATATA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGC-GACTTGAATATATA
40593016 CTTTTGAATC
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
54 29 0.31
55 30 0.32
56 20 0.21
57 15 0.16
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.34
Consensus pattern (55 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGACTTGAATATATAGCA
Found at i:40598838 original size:40 final size:40
Alignment explanation
Indices: 40598718--40598898 Score: 158
Period size: 40 Copynumber: 4.5 Consensus size: 40
40598708 TGAATGCTGT
* *
40598718 CGGGCTAAGTCCCGAAGGC-TTTG-GCTA-AGTGACTAAATC
1 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAATC
** * * * *
40598757 CGGACTAAGAT-CCGAAGGTATTTGTGGCGAGTTATTAATTC
1 CGGGTTAAG-TCCCGAAGGCATTTGT-GCGAGATACTAAATC
* *
40598798 CGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATTC
1 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATC
* **
40598838 CGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TTTTAAAATC
1 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACT-AAATC
40598878 CGGGTTAAGT-CCGAAGGCATT
1 CGGGTTAAGTCCCGAAGGCATT
40598899 GAATGAGTTA
Statistics
Matches: 118, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
39 28 0.24
40 61 0.52
41 25 0.21
42 4 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
CGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATC
Found at i:40598880 original size:80 final size:81
Alignment explanation
Indices: 40598718--40598895 Score: 199
Period size: 80 Copynumber: 2.2 Consensus size: 81
40598708 TGAATGCTGT
* * * *
40598718 CGGGCTAAGTCCCGAAGG-CTTTGGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGTATTTGT
1 CGGGTTAAGTCCCGAAGGCCTTTGGCGAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTCGT
*
40598782 GGCGAGTTATTAATTC
66 GGCGAGTTATTAAATC
* **
40598798 CGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTAATTCCGGGTTAAG-TCCCGAAGGCATT
1 CGGGTTAAGTCCCGAAGGCCTTTG-GCGAAG-TGACTAAATCCGGACTAAGAT-CCGAAGGCATT
40598860 CGT-GCGAGTT-TTAAAATC
63 CGTGGCGAGTTATT-AAATC
40598878 CGGGTTAAGT-CCGAAGGC
1 CGGGTTAAGTCCCGAAGGC
40598896 ATTGAATGAG
Statistics
Matches: 85, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
79 10 0.12
80 39 0.46
81 33 0.39
82 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (81 bp):
CGGGTTAAGTCCCGAAGGCCTTTGGCGAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTCGT
GGCGAGTTATTAAATC
Found at i:40606592 original size:39 final size:39
Alignment explanation
Indices: 40606496--40606678 Score: 192
Period size: 40 Copynumber: 4.6 Consensus size: 39
40606486 TTGAATGCTG
* * *
40606496 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTA-TAAT
** *
40606535 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATAAT
* *
40606575 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-TAAT
* * *
40606615 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTAT-AAT
40606655 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40606679 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 1 0.01
39 30 0.24
40 84 0.68
41 8 0.07
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATAAT
Found at i:40606632 original size:79 final size:81
Alignment explanation
Indices: 40606496--40606675 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 81
40606486 TTGAATGCTG
* * *
40606496 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
40606560 TGTGCGAGTTAT-AAT
66 CGTGCGAGTTATAAAA
**
40606575 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
*
40606636 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTATAAAA
40606655 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
40606676 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
78 2 0.02
79 54 0.61
80 32 0.36
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTATAAAA
Found at i:40606691 original size:79 final size:78
Alignment explanation
Indices: 40606549--40606714 Score: 199
Period size: 79 Copynumber: 2.1 Consensus size: 78
40606539 GGACTAAGAT
* * * * **
40606549 CCGAAGGTATTTGTGCGAGTTATAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAA
1 CCGAAGGCATTCGTGCGAGTTATAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACTAA
* *
40606614 TTCCGGGTTAAGTC
66 -ACCGGGCTAAGTC
* * *
40606628 CCGAAGGCATTCGTGCGAGTTTTAAAATCCGGGTTAAGTCCCGAAGG-CATTGAATGAGTTACTA
1 CCGAAGGCATTCGTGCGAGTTAT-AAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACTA
*
40606692 AACCGGGCTATGTC
65 AACCGGGCTAAGTC
40606706 CCGAAGGCA
1 CCGAAGGCA
40606715 CTTGAACGAG
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
78 19 0.26
79 33 0.45
80 22 0.30
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (78 bp):
CCGAAGGCATTCGTGCGAGTTATAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACTAA
ACCGGGCTAAGTC
Found at i:40611928 original size:28 final size:28
Alignment explanation
Indices: 40611863--40612013 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
40611853 GAGATTGGCG
* * * *
40611863 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
40611892 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
40611920 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
40611948 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
40611976 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
40612003 CTGAGTGTGCG
1 CTAAGTGTGCG
40612014 GACTTAATAT
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 24 0.21
28 76 0.66
29 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:40620840 original size:40 final size:40
Alignment explanation
Indices: 40620792--40620997 Score: 308
Period size: 40 Copynumber: 5.2 Consensus size: 40
40620782 GGACTAAGAT
* *
40620792 CCGAAGGCATTTGTGCTAGTGATTATATCCGAGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
40620832 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
40620872 CCTAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
40620912 CCGAAGGCATTTGTGCTAGTGACTATGTCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* * * *
40620952 CCGAAGGCATTCGTGCGAGTTG-CTATATCC-GGCTAAATT
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC
40620991 CCGAAGG
1 CCGAAGG
40620998 TACTTGGGTT
Statistics
Matches: 155, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 14 0.09
40 139 0.90
41 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:40624052 original size:51 final size:51
Alignment explanation
Indices: 40623997--40624093 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
40623987 CGAATCTTAG
* * * *
40623997 GAATAAAATAGCTTTGGA-TGCAAGTGTGGTACTATGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTT-GACTACAAGGGTGGTACAATATGAAGGCCACTTTGT
40624048 GAATAAAATAGCTTTGACTACAAGGGTGGTACAATATGAAGGCCAC
1 GAATAAAATAGCTTTGACTACAAGGGTGGTACAATATGAAGGCCAC
40624094 CATGTATTCG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 2 0.05
51 39 0.95
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (51 bp):
GAATAAAATAGCTTTGACTACAAGGGTGGTACAATATGAAGGCCACTTTGT
Found at i:40629463 original size:16 final size:16
Alignment explanation
Indices: 40629439--40629482 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
40629429 GGCAAAAGCT
* *
40629439 GAAATGTCGAAATGCC
1 GAAAAGTCGAAATACC
40629455 GAAAAGTCGAAATACC
1 GAAAAGTCGAAATACC
* *
40629471 AAAAAGCCGAAA
1 GAAAAGTCGAAA
40629483 GTTTGGCTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.18, G:0.20, T:0.11
Consensus pattern (16 bp):
GAAAAGTCGAAATACC
Found at i:40629805 original size:28 final size:28
Alignment explanation
Indices: 40629693--40629807 Score: 133
Period size: 29 Copynumber: 4.0 Consensus size: 28
40629683 GTGAGCGTGA
* * *
40629693 ATATGAATGTGACTAGGCCTAACGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
*
40629721 ATATAAATGTGACTTGGGCCTAATGGGCC
1 ATATGAATGTGA-TTGGGCCTAATGGGCC
*
40629750 ATATTCAA-GTGATTGGGGCCTAATGGGCC
1 ATA-TGAATGTGATT-GGGCCTAATGGGCC
* *
40629779 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
40629807 A
1 A
40629808 GATACAGGCA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
28 30 0.40
29 42 0.56
30 3 0.04
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.27
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:40641121 original size:17 final size:18
Alignment explanation
Indices: 40641099--40641148 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
40641089 TTTTACTTTA
40641099 GTTTTCAAATAAGA-ATG
1 GTTTTCAAATAAGACATG
*
40641116 GTTTTC-AATGAAAACATG
1 GTTTTCAAAT-AAGACATG
*
40641134 GTTTTCAAAAAAGAC
1 GTTTTCAAATAAGAC
40641149 TTCAATGTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 3 0.11
17 9 0.33
18 13 0.48
19 2 0.07
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (18 bp):
GTTTTCAAATAAGACATG
Found at i:40642603 original size:19 final size:20
Alignment explanation
Indices: 40642581--40642627 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
40642571 GATTTTTGGG
*
40642581 CTATCTTTC-TTTCTCTCTT
1 CTATCTTTCGATTCTCTCTT
* *
40642600 CTAT-TTCCGATTCTCTTTT
1 CTATCTTTCGATTCTCTCTT
40642619 CTATCTTTC
1 CTATCTTTC
40642628 AACACTGGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 3 0.14
19 16 0.73
20 3 0.14
ACGTcount: A:0.09, C:0.30, G:0.02, T:0.60
Consensus pattern (20 bp):
CTATCTTTCGATTCTCTCTT
Found at i:40643940 original size:26 final size:26
Alignment explanation
Indices: 40643856--40643985 Score: 138
Period size: 27 Copynumber: 4.9 Consensus size: 26
40643846 AACACCCCGA
* * *
40643856 TTTGTAAAATTATCGAAATACCCCAGG
1 TTTGTAAAATTACCAAAATACCCTA-G
*
40643883 TTTGTAAAATTACCGAAATACCCCTAG
1 TTTGTAAAATTACCAAAATA-CCCTAG
* *
40643910 ATTGTAAAATTACTAAAATACCCTAG
1 TTTGTAAAATTACCAAAATACCCTAG
40643936 TTTGTAAAATTACCAAAATACCCTTA-
1 TTTGTAAAATTACCAAAATACCC-TAG
*
40643962 TAGTT-TAAAATTACCGAAATACCC
1 T--TTGTAAAATTACCAAAATACCC
40643986 CTGTAGGGTA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
26 28 0.31
27 57 0.63
28 6 0.07
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (26 bp):
TTTGTAAAATTACCAAAATACCCTAG
Found at i:40643945 original size:53 final size:55
Alignment explanation
Indices: 40643857--40643986 Score: 169
Period size: 53 Copynumber: 2.4 Consensus size: 55
40643847 ACACCCCGAT
*
40643857 TTGTAAAATTA-TCGAAATACCCCAGGTTTGTAAAATTACCGAAATACCCCTAGA-
1 TTGTAAAATTACT-GAAATACCCCAGGTTTGTAAAATTACCAAAATACCCCTAGAG
* * * *
40643911 TTGTAAAATTACTAAAATACCCTA-GTTTGTAAAATTACCAAAATACCCTTATAG
1 TTGTAAAATTACTGAAATACCCCAGGTTTGTAAAATTACCAAAATACCCCTAGAG
*
40643965 TT-TAAAATTACCGAAATACCCC
1 TTGTAAAATTACTGAAATACCCC
40643987 TGTAGGGTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
53 43 0.65
54 22 0.33
55 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (55 bp):
TTGTAAAATTACTGAAATACCCCAGGTTTGTAAAATTACCAAAATACCCCTAGAG
Found at i:40644872 original size:16 final size:16
Alignment explanation
Indices: 40644851--40644889 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
40644841 GTTTCCAATG
*
40644851 AAAACATGGTTTTCGA
1 AAAACACGGTTTTCGA
40644867 AAAACACGGTTTTCGA
1 AAAACACGGTTTTCGA
40644883 AAAACAC
1 AAAACAC
40644890 TTCAATGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (16 bp):
AAAACACGGTTTTCGA
Found at i:40645775 original size:29 final size:29
Alignment explanation
Indices: 40645737--40645834 Score: 119
Period size: 29 Copynumber: 3.4 Consensus size: 29
40645727 GAACATGTGA
*
40645737 CCTAACGGGCCATATAAATGTGATTTGGG
1 CCTAATGGGCCATATAAATGTGATTTGGG
* *
40645766 CCTAATGGGCCATATTCAA-GTGATTGGGG
1 CCTAATGGGCCATA-TAAATGTGATTTGGG
* *
40645795 CCTAATGGGCCATATGAATATGA-TTGGG
1 CCTAATGGGCCATATAAATGTGATTTGGG
*
40645823 CTTAATGGGCCA
1 CCTAATGGGCCA
40645835 GATACAGGCA
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
28 18 0.30
29 39 0.65
30 3 0.05
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.28
Consensus pattern (29 bp):
CCTAATGGGCCATATAAATGTGATTTGGG
Found at i:40653720 original size:26 final size:27
Alignment explanation
Indices: 40653690--40653773 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
40653680 GGTCGTTAAG
* *
40653690 ACCCCGA-TTTGTAAAATTATCGAAAT
1 ACCCCGATTTTCTAAAATTACCGAAAT
*
40653716 ACCCCTATTTTCTAAAATTACCGAAAT
1 ACCCCGATTTTCTAAAATTACCGAAAT
* ** *
40653743 ACCCTTG-TAGTATAAAATTACCGAAAT
1 ACCC-CGATTTTCTAAAATTACCGAAAT
40653770 ACCC
1 ACCC
40653774 TTGTAGGGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
26 6 0.12
27 42 0.88
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (27 bp):
ACCCCGATTTTCTAAAATTACCGAAAT
Found at i:40653774 original size:27 final size:27
Alignment explanation
Indices: 40653701--40653779 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
40653691 CCCCGATTTG
* * * ** *
40653701 TAAAATTATCGAAATACCCCTATTTTC
1 TAAAATTACCGAAATACCCTTGTAGTA
40653728 TAAAATTACCGAAATACCCTTGTAGTA
1 TAAAATTACCGAAATACCCTTGTAGTA
40653755 TAAAATTACCGAAATACCCTTGTAG
1 TAAAATTACCGAAATACCCTTGTAG
40653780 GGTAAAATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTTGTAGTA
Found at i:40653785 original size:27 final size:27
Alignment explanation
Indices: 40653728--40653787 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
40653718 CCCTATTTTC
*
40653728 TAAAATTACCGAAATACCCTTGTAGTA
1 TAAAATTACCGAAATACCCTTGTAGGA
*
40653755 TAAAATTACCGAAATACCCTTGTAGGG
1 TAAAATTACCGAAATACCCTTGTAGGA
40653782 TAAAAT
1 TAAAAT
40653788 GACTGTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTTGTAGGA
Found at i:40654194 original size:22 final size:22
Alignment explanation
Indices: 40654146--40654205 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
40654136 GTAATCTGAT
40654146 TATGGCTCTGTGCCAACCTAAA
1 TATGGCTCTGTGCCAACCTAAA
* * *
40654168 AATGGCTCTGTGCC-ATCTCGAA
1 TATGGCTCTGTGCCAACCT-AAA
*
40654190 TATGGCTTTGTGCCAA
1 TATGGCTCTGTGCCAA
40654206 ATGTATTTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 3 0.10
22 27 0.87
23 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (22 bp):
TATGGCTCTGTGCCAACCTAAA
Found at i:40658054 original size:26 final size:26
Alignment explanation
Indices: 40657970--40658099 Score: 138
Period size: 27 Copynumber: 4.9 Consensus size: 26
40657960 AACACCCCGA
* * *
40657970 TTTGTAAAATTATCGAAATACCCCAGG
1 TTTGTAAAATTACCAAAATACCCTA-G
*
40657997 TTTGTAAAATTACCGAAATACCCCTAG
1 TTTGTAAAATTACCAAAATA-CCCTAG
* *
40658024 ATTGTAAAATTACTAAAATACCCTAG
1 TTTGTAAAATTACCAAAATACCCTAG
40658050 TTTGTAAAATTACCAAAATACCCTTA-
1 TTTGTAAAATTACCAAAATACCC-TAG
*
40658076 TAGTT-TAAAATTACCGAAATACCC
1 T--TTGTAAAATTACCAAAATACCC
40658100 CTGTAGGGTA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
26 28 0.31
27 57 0.63
28 6 0.07
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (26 bp):
TTTGTAAAATTACCAAAATACCCTAG
Found at i:40658059 original size:53 final size:55
Alignment explanation
Indices: 40657971--40658100 Score: 169
Period size: 53 Copynumber: 2.4 Consensus size: 55
40657961 ACACCCCGAT
*
40657971 TTGTAAAATTA-TCGAAATACCCCAGGTTTGTAAAATTACCGAAATACCCCTAGA-
1 TTGTAAAATTACT-GAAATACCCCAGGTTTGTAAAATTACCAAAATACCCCTAGAG
* * * *
40658025 TTGTAAAATTACTAAAATACCCTA-GTTTGTAAAATTACCAAAATACCCTTATAG
1 TTGTAAAATTACTGAAATACCCCAGGTTTGTAAAATTACCAAAATACCCCTAGAG
*
40658079 TT-TAAAATTACCGAAATACCCC
1 TTGTAAAATTACTGAAATACCCC
40658101 TGTAGGGTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
53 43 0.65
54 22 0.33
55 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (55 bp):
TTGTAAAATTACTGAAATACCCCAGGTTTGTAAAATTACCAAAATACCCCTAGAG
Found at i:40661535 original size:43 final size:43
Alignment explanation
Indices: 40661453--40661538 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
40661443 TATCCTAGAA
* * * *
40661453 AAAAAAGAATTTAAAAAGATGAGATGATAATCTTGGGTTGTTG
1 AAAAAAGAATTTAAAAAGATGAGAAGATAAACATAGGTTGTTG
*
40661496 AAAATAGAATTTAAAAAGATGAGAAGATAAACATAGGTTGTTG
1 AAAAAAGAATTTAAAAAGATGAGAAGATAAACATAGGTTGTTG
40661539 GATTTACCCT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.22, T:0.28
Consensus pattern (43 bp):
AAAAAAGAATTTAAAAAGATGAGAAGATAAACATAGGTTGTTG
Found at i:40663583 original size:53 final size:52
Alignment explanation
Indices: 40663469--40663601 Score: 143
Period size: 53 Copynumber: 2.7 Consensus size: 52
40663459 GTAGTATGCA
* * ** *
40663469 TAGTAGCCTGCACTTAGTAG---TACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTAGTACTACACACGTGACCAACCATCCGATACACG
* *
40663518 TAGTAGCATGCACTTAGTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTAGTACTACACACGTGACC-AACCATCCGATACACG
*
40663571 TAGTAGCCTGCAC-T--CAGTACTACACACGTGA
1 TAGTAGCCTGCACTTAGTAGTACTACACACGTGA
40663602 TCGAAGTTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
49 19 0.27
50 16 0.23
52 12 0.17
53 24 0.34
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (52 bp):
TAGTAGCCTGCACTTAGTAGTACTACACACGTGACCAACCATCCGATACACG
Found at i:40666299 original size:33 final size:33
Alignment explanation
Indices: 40666262--40666327 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
40666252 TGTCCTGTTC
*
40666262 TGACAAGGAGTAGTTGGATTGTGTGGTATCCTT
1 TGACAAGGAGTAGCTGGATTGTGTGGTATCCTT
40666295 TGACAAGGAGTAGCTGGATTGTGTGGTATCCTT
1 TGACAAGGAGTAGCTGGATTGTGTGGTATCCTT
40666328 ACTCGACAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.21, C:0.11, G:0.33, T:0.35
Consensus pattern (33 bp):
TGACAAGGAGTAGCTGGATTGTGTGGTATCCTT
Found at i:40673282 original size:33 final size:33
Alignment explanation
Indices: 40673236--40673302 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
40673226 TCATATTAGA
40673236 ACCATTTGCACATATATAAACAACATCAAGTTC
1 ACCATTTGCACATATATAAACAACATCAAGTTC
* *
40673269 ACCATTTGTACATATATAAACATCATCAAGTTC
1 ACCATTTGCACATATATAAACAACATCAAGTTC
40673302 A
1 A
40673303 TCATCTTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.30
Consensus pattern (33 bp):
ACCATTTGCACATATATAAACAACATCAAGTTC
Found at i:40673795 original size:28 final size:28
Alignment explanation
Indices: 40673751--40673824 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
40673741 TCAATGCCTT
*
40673751 GCACACTAAGTGTCATACTCGATATCTA
1 GCACACTAAGTGCCATACTCGATATCTA
* * *
40673779 GCACACTAAGTGCCATACTTGGTATCTC
1 GCACACTAAGTGCCATACTCGATATCTA
40673807 GCACACTAAGTGCCATAC
1 GCACACTAAGTGCCATAC
40673825 ATTGCTGAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (28 bp):
GCACACTAAGTGCCATACTCGATATCTA
Found at i:40673875 original size:40 final size:40
Alignment explanation
Indices: 40673805--40673897 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 40
40673795 ACTTGGTATC
* *
40673805 TCGCACACTAAGTGCCATACATTGCTGAAGCTATCTCGAA
1 TCGCACACTAAGTACCATACATAGCTGAAGCTATCTCGAA
* * * *
40673845 TTGCACACTAAGTACCATATATAG-TCGAAGCTATGTCGTA
1 TCGCACACTAAGTACCATACATAGCT-GAAGCTATCTCGAA
*
40673885 TCACACACTAAGT
1 TCGCACACTAAGT
40673898 GCCACAAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 1 0.02
40 43 0.98
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (40 bp):
TCGCACACTAAGTACCATACATAGCTGAAGCTATCTCGAA
Found at i:40676739 original size:42 final size:41
Alignment explanation
Indices: 40676681--40676795 Score: 131
Period size: 44 Copynumber: 2.7 Consensus size: 41
40676671 TCGGTTCAAC
* * *
40676681 TGTCCTAGACAAGGTCTTACACAAAATCATATGCGATGCCAA
1 TGTCCCAGACATGGTCTTACACAAAATCAAAT-CGATGCCAA
*
40676723 TGTCCCAGACATGGTCTTACACGTAAATCTCAAATCGATGCCAA
1 TGTCCCAGACATGGTCTTACAC--AAA-ATCAAATCGATGCCAA
* * *
40676767 CGTCCCAGACGTGGTCTTACACGAAATCA
1 TGTCCCAGACATGGTCTTACACAAAATCA
40676796 CATATCATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
41 3 0.05
42 22 0.35
44 32 0.52
45 5 0.08
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (41 bp):
TGTCCCAGACATGGTCTTACACAAAATCAAATCGATGCCAA
Found at i:40682312 original size:79 final size:82
Alignment explanation
Indices: 40682201--40682385 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
40682191 GCTACTCGTT
* * *
40682201 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
40682264 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
40682281 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
40682344 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
40682361 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40682386 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:40682385 original size:40 final size:40
Alignment explanation
Indices: 40682182--40682385 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
40682172 CGGAATTTAA
** *
40682182 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
40682222 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
40682262 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40682301 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
40682341 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40682381 CCGGA
1 CCGGA
40682386 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40690106 original size:39 final size:40
Alignment explanation
Indices: 40690056--40690182 Score: 147
Period size: 38 Copynumber: 3.3 Consensus size: 40
40690046 CTACTCGTTC
*
40690056 AATGCCTTCGGGACAT-GCCCGG-TTATAGTAACTCGCACA
1 AATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCACA
* *
40690095 ATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCACA
* * * *
40690135 AATGCCTTC-GG-CTTAGCCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCACA
40690173 AATG-CTTCGG
1 AATGCCTTCGG
40690183 ATCTTAGTCC
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
37 4 0.05
38 29 0.37
39 16 0.21
40 27 0.35
41 2 0.03
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCACA
Found at i:40690127 original size:40 final size:40
Alignment explanation
Indices: 40690056--40690226 Score: 169
Period size: 39 Copynumber: 4.4 Consensus size: 40
40690046 CTACTCGTTC
*
40690056 AATGCCTTCGGGACAT-GCCCGG-TTATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACA
* *
40690095 ATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
* *
40690135 AATGCCTTC-GG-CTTAGCCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
* * * * *
40690173 AATG-CTTC-GGATCTTAGTCC-GATATGGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACA
40690212 AA-GCCTTCGGGACTT
1 AATGCCTTCGGGACTT
40690227 TGCCNNNNNN
Statistics
Matches: 111, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
37 6 0.05
38 35 0.32
39 38 0.34
40 30 0.27
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
Found at i:40690169 original size:38 final size:39
Alignment explanation
Indices: 40690081--40690188 Score: 148
Period size: 38 Copynumber: 2.8 Consensus size: 39
40690071 TGCCCGGTTA
* *
40690081 TAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTC-GGACTTAACCCGGAAT
*
40690121 TAGTAACTCGCACAAATGCCTTCGG-CTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGAAT
*
40690159 TAGTATCTCGCACAAATG-CTTCGGATCTTA
1 TAGTAACTCGCACAAATGCCTTCGGA-CTTA
40690189 GTCCGATATG
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
37 6 0.10
38 28 0.45
39 6 0.10
40 22 0.35
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (39 bp):
TAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGAAT
Found at i:40692102 original size:40 final size:40
Alignment explanation
Indices: 40691997--40692213 Score: 316
Period size: 40 Copynumber: 5.5 Consensus size: 40
40691987 CGGATGATAA
* *
40691997 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
40692037 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
40692076 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
40692116 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
40692156 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
40692196 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
40692214 TACTTGGTTT
Statistics
Matches: 166, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
39 51 0.31
40 115 0.69
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:40692211 original size:119 final size:119
Alignment explanation
Indices: 40691993--40692213 Score: 331
Period size: 119 Copynumber: 1.9 Consensus size: 119
40691983 TATTCGGATG
* *
40691993 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
* * *
40692058 TTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
66 TTGAGCAAGTTACTATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
*
40692112 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGC
*
40692176 ATTTGAGCAAG-TAGCTATATCC-GGCTAAATTCCGAAGG
64 ATTTGAGCAAGTTA-CTATATCCGGGCTAAATCCCGAAGG
40692214 TACTTGGTTT
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
118 2 0.02
119 64 0.70
120 26 0.28
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (119 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
TTGAGCAAGTTACTATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
Found at i:40700314 original size:40 final size:40
Alignment explanation
Indices: 40700073--40700300 Score: 372
Period size: 40 Copynumber: 5.7 Consensus size: 40
40700063 TATTCGGATG
* *
40700073 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40700113 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
40700152 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
40700192 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
40700232 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
40700272 ATAACCGGGCTAAGAT-CCGAAGGCATTTG
1 ATAACCGGGCTAAG-TCCCGAAGGCATTTG
40700301 AGCAAGTAGC
Statistics
Matches: 178, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
39 36 0.20
40 141 0.79
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:40704557 original size:30 final size:30
Alignment explanation
Indices: 40704521--40704586 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
40704511 GGACTGACCG
40704521 TGTGTCACACACGACCTAGAAACATGCCCA
1 TGTGTCACACACGACCTAGAAACATGCCCA
* * *
40704551 TGTGTCACACACGGCCTAGACACATGCCCG
1 TGTGTCACACACGACCTAGAAACATGCCCA
40704581 TGTGTC
1 TGTGTC
40704587 TACCCGTGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.20
Consensus pattern (30 bp):
TGTGTCACACACGACCTAGAAACATGCCCA
Found at i:40706362 original size:22 final size:22
Alignment explanation
Indices: 40706334--40706376 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
40706324 ATATATTTGG
40706334 GAAACCTCACATTCAAATTAAT
1 GAAACCTCACATTCAAATTAAT
40706356 GAAACCTCACATTCAAATTAA
1 GAAACCTCACATTCAAATTAA
40706377 GGAATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.26
Consensus pattern (22 bp):
GAAACCTCACATTCAAATTAAT
Found at i:40717217 original size:40 final size:40
Alignment explanation
Indices: 40717143--40717306 Score: 258
Period size: 40 Copynumber: 4.1 Consensus size: 40
40717133 AACCCAAGTA
* ** *
40717143 CCTTCGGGATTTAG-CCGGATATAACAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40717182 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40717222 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
40717262 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40717302 CCTTC
1 CCTTC
40717307 AGATCTTAGT
Statistics
Matches: 116, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 12 0.10
40 104 0.90
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40721155 original size:43 final size:42
Alignment explanation
Indices: 40720998--40721156 Score: 144
Period size: 43 Copynumber: 3.7 Consensus size: 42
40720988 TATGTGATAT
* * *
40720998 CATGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGGTATTTA
1 CATGTAAGACCATGTCTAGGACGTTGGCATC-ATATTTG-A-TTA
* * * *
40721042 -AGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTC
1 CA-TGTAAGACCATGTCTAGGACGTTGGCATCATATTTGATTA
* *
40721084 CATGTAAGACCCTGTCTAGGATAG-TGGCATCAATATTTGATTA
1 CATGTAAGACCATGTCTAGGA-CGTTGGCATC-ATATTTGATTA
* *
40721127 CATGTAATACCATATCTAGGACGTTGGCAT
1 CATGTAAGACCATGTCTAGGACGTTGGCAT
40721157 TGTACGATCT
Statistics
Matches: 94, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
42 27 0.29
43 37 0.39
44 30 0.32
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (42 bp):
CATGTAAGACCATGTCTAGGACGTTGGCATCATATTTGATTA
Found at i:40742781 original size:18 final size:19
Alignment explanation
Indices: 40742758--40742796 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40742748 TTTATCTCAA
*
40742758 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
40742776 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
40742795 TT
1 TT
40742797 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:40742824 original size:30 final size:30
Alignment explanation
Indices: 40742790--40742856 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
40742780 TTGTTCACAT
**
40742790 TCTTTTTCTCTCTCAAACTCTTTTTCATTC
1 TCTTTTTCAATCTCAAACTCTTTTTCATTC
*** *
40742820 TCTTTTTCAATCTCATTTTCTTTTTCATTT
1 TCTTTTTCAATCTCAAACTCTTTTTCATTC
40742850 TCTTTTT
1 TCTTTTT
40742857 GTTTTTCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (30 bp):
TCTTTTTCAATCTCAAACTCTTTTTCATTC
Found at i:40742856 original size:18 final size:18
Alignment explanation
Indices: 40742814--40742865 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
40742804 AAACTCTTTT
*
40742814 TCATTCTCTTTTTCAATC
1 TCATTTTCTTTTTCAATC
* *
40742832 TCATTTTCTTTTTCATTT
1 TCATTTTCTTTTTCAATC
* *
40742850 TCTTTTTGTTTTTCAA
1 TCATTTTCTTTTTCAA
40742866 AGGCTTTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.13, C:0.19, G:0.02, T:0.65
Consensus pattern (18 bp):
TCATTTTCTTTTTCAATC
Found at i:40742863 original size:12 final size:12
Alignment explanation
Indices: 40742832--40742856 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40742822 TTTTTCAATC
40742832 TCATTTTCTTTT
1 TCATTTTCTTTT
40742844 TCATTTTCTTTT
1 TCATTTTCTTTT
40742856 T
1 T
40742857 GTTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:40742874 original size:13 final size:13
Alignment explanation
Indices: 40742858--40742890 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
40742848 TTTCTTTTTG
40742858 TTTTTC-AAAGGC
1 TTTTTCAAAAGGC
40742870 TTTTTCAAAAGGC
1 TTTTTCAAAAGGC
40742883 TTTTTCAA
1 TTTTTCAA
40742891 GTTCTCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (13 bp):
TTTTTCAAAAGGC
Found at i:40742946 original size:5 final size:5
Alignment explanation
Indices: 40742936--40742994 Score: 50
Period size: 5 Copynumber: 11.4 Consensus size: 5
40742926 GCCTTTTGTG
*
40742936 TTTCT TTTCT TTT-T ATTTCAT TTTCT TTT-T CTTCT TTTGCTT TTTCT
1 TTTCT TTTCT TTTCT -TTTC-T TTTCT TTTCT TTTCT TTT-C-T TTTCT
*
40742983 TTTCT TCTCT TT
1 TTTCT TTTCT TT
40742995 GTTTTCTCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTCT
Found at i:40742959 original size:16 final size:15
Alignment explanation
Indices: 40742936--40742994 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
40742926 GCCTTTTGTG
40742936 TTTCTTTTCTTTTTA
1 TTTCTTTTCTTTTTA
40742951 TTTCATTTTCTTTTT-
1 TTTC-TTTTCTTTTTA
* *
40742966 CTTCTTTTGCTTTTTCT
1 TTTCTTTT-CTTTTT-A
*
40742983 TTTCTTCTCTTT
1 TTTCTTTTCTTT
40742995 GTTTTCTCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.11
15 13 0.35
16 14 0.38
17 6 0.16
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTCTTTTCTTTTTA
Found at i:40742978 original size:15 final size:14
Alignment explanation
Indices: 40742937--40742983 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 14
40742927 CCTTTTGTGT
*
40742937 TTCTTTTCTTTTTAT
1 TTCTTTTCTTTTT-C
40742952 TTCATTTTCTTTTTC
1 TTC-TTTTCTTTTTC
40742967 TTCTTTTGCTTTTTC
1 TTCTTTT-CTTTTTC
40742982 TT
1 TT
40742984 TTCTTCTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
15 15 0.52
16 10 0.34
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (14 bp):
TTCTTTTCTTTTTC
Found at i:40742995 original size:21 final size:20
Alignment explanation
Indices: 40742956--40742999 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
40742946 TTTTATTTCA
40742956 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTCTTCTTTTG-T
40742977 TTTTC-TTTTCTTCTCTTTGT
1 TTTTCTTTTTCTTCT-TTTGT
40742997 TTT
1 TTT
40743000 CTCGTTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTTCTTCTTTTGT
Found at i:40773474 original size:22 final size:22
Alignment explanation
Indices: 40773449--40773492 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40773439 TTCCATTTAA
40773449 AGACCCCCAATTTATGATACAT
1 AGACCCCCAATTTATGATACAT
*
40773471 AGACCCCGAATTTATGATACAT
1 AGACCCCCAATTTATGATACAT
40773493 GGCAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.27
Consensus pattern (22 bp):
AGACCCCCAATTTATGATACAT
Found at i:40776781 original size:43 final size:42
Alignment explanation
Indices: 40776718--40776873 Score: 181
Period size: 43 Copynumber: 3.7 Consensus size: 42
40776708 AATAGGATTT
* * * *
40776718 TTGATATGTGTTCTCGTGTAAGACCACATCTAGGACATTGGCA
1 TTGATATGTGAT-TCATGTAAGACCACGTCTGGGACATTGGCA
*
40776761 TTGATATGTGATTACATGTAAGACCATGTCTGGGACATTGGCA
1 TTGATATGTGATT-CATGTAAGACCACGTCTGGGACATTGGCA
* * *
40776804 TTG-TATTTGATTCATGTAAGACC-CTGTCTGGGATAGTGGCA
1 TTGATATGTGATTCATGTAAGACCAC-GTCTGGGACATTGGCA
*
40776845 TCGATATGTGATTGCATGTAAGACCACGT
1 TTGATATGTGATT-CATGTAAGACCACGT
40776874 ATGAGATGTT
Statistics
Matches: 97, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
41 27 0.28
42 17 0.18
43 52 0.54
44 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (42 bp):
TTGATATGTGATTCATGTAAGACCACGTCTGGGACATTGGCA
Found at i:40777092 original size:18 final size:19
Alignment explanation
Indices: 40777058--40777095 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
40777048 GATACAAATT
40777058 ATATATGATGTAAATGAAA
1 ATATATGATGTAAATGAAA
*
40777077 ATATATG-TGTATATGAAA
1 ATATATGATGTAAATGAAA
40777095 A
1 A
40777096 GTACATTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (19 bp):
ATATATGATGTAAATGAAA
Found at i:40782790 original size:18 final size:18
Alignment explanation
Indices: 40782747--40782793 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
40782737 TATTGTTTAA
*
40782747 ACTGTTATTGCCCTGATT
1 ACTGTTACTGCCCTGATT
* * *
40782765 ACTATTACTGCTCTGTTT
1 ACTGTTACTGCCCTGATT
40782783 ACTGTTACTGC
1 ACTGTTACTGC
40782794 AATAGGCCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.45
Consensus pattern (18 bp):
ACTGTTACTGCCCTGATT
Found at i:40782872 original size:40 final size:40
Alignment explanation
Indices: 40782783--40782873 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
40782773 TGCTCTGTTT
*
40782783 ACTGTTACTGCAATAGGCCAAAGCCCAAACACATGATTGTT
1 ACTGTTACTG-AATAGGCCAAAGCCCAAACACATGATTGTC
* * * *
40782824 TCTG-TACTGAGATGGGCTAAAGCCCAAACATAT-ATTGTC
1 ACTGTTACTGA-ATAGGCCAAAGCCCAAACACATGATTGTC
40782863 ACTGTTACTGA
1 ACTGTTACTGA
40782874 TATCGGCTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
39 9 0.21
40 30 0.71
41 3 0.07
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (40 bp):
ACTGTTACTGAATAGGCCAAAGCCCAAACACATGATTGTC
Found at i:40784234 original size:16 final size:17
Alignment explanation
Indices: 40784213--40784245 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40784203 CACATTGAAG
40784213 TGTTTT-TTGAAAACCA
1 TGTTTTATTGAAAACCA
40784229 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
40784246 CTTCTTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (17 bp):
TGTTTTATTGAAAACCA
Found at i:40785021 original size:33 final size:33
Alignment explanation
Indices: 40784927--40785022 Score: 99
Period size: 34 Copynumber: 2.9 Consensus size: 33
40784917 TCAAGCCCAT
*
40784927 TGGGCCTAAGCCCTATTCAGATAACAG-AAGGTAC
1 TGGGCCTAAGCCCTTTTCAGATAACAGTAA-G-AC
* *
40784961 TGGGCCGAAGCCCTTTTCA-AAATACAGTAA-AC
1 TGGGCCTAAGCCCTTTTCAGATA-ACAGTAAGAC
*
40784993 TGGGCCTTAGCCCCTTTTCAGATAACAGTA
1 TGGGCCTAAG-CCCTTTTCAGATAACAGTA
40785023 TGGCCCATAG
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
32 10 0.19
33 17 0.33
34 23 0.44
35 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (33 bp):
TGGGCCTAAGCCCTTTTCAGATAACAGTAAGAC
Found at i:40792685 original size:66 final size:68
Alignment explanation
Indices: 40792556--40792685 Score: 176
Period size: 66 Copynumber: 1.9 Consensus size: 68
40792546 GGGATGTATC
*
40792556 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTAC--GAGAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
40792621 AGGACA
63 AGGACA
* *
40792627 CCATGTAGACAAGAGAGCTAC-A-AGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACGAGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
40792686 TTCACCATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
66 24 0.44
67 8 0.15
68 2 0.04
71 21 0.38
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (68 bp):
CCATGTAGACAAGAGAGCTACGAGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGG
ACA
Found at i:40794340 original size:28 final size:28
Alignment explanation
Indices: 40794294--40794358 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
40794284 TCAGTGTACG
* *
40794294 AAATATTGAGAATGGCACTTAATGTGCG
1 AAATATTGAGAATGACACTTAATGTGCA
* *
40794322 AGATATTGAGAATGACACTTAGTGTGCA
1 AAATATTGAGAATGACACTTAATGTGCA
40794350 AAATATTGA
1 AAATATTGA
40794359 ATGATTAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.29
Consensus pattern (28 bp):
AAATATTGAGAATGACACTTAATGTGCA
Found at i:40794477 original size:39 final size:39
Alignment explanation
Indices: 40794431--40794682 Score: 389
Period size: 39 Copynumber: 6.5 Consensus size: 39
40794421 GACTTTATAA
* *
40794431 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCATGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* *
40794470 TGGTGTTATATCCGGGCTAAGTCCCAAAGGCATTCGTAC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
40794509 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
40794548 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* * *
40794587 TGCTATTATATCCGGGCTAAGCCCCGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* * *
40794626 TGGTGTTATATCTGGGCTAAAGTCCCGCAGGC-TTTGTGC
1 TGGTGTTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGC
*
40794665 TGGTATTATATCCGGGCT
1 TGGTGTTATATCCGGGCT
40794683 TAAAGTCTCG
Statistics
Matches: 195, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
39 184 0.94
40 11 0.06
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.30
Consensus pattern (39 bp):
TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
Found at i:40796877 original size:28 final size:28
Alignment explanation
Indices: 40796814--40796911 Score: 171
Period size: 28 Copynumber: 3.5 Consensus size: 28
40796804 ATATTAAGTC
*
40796814 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
40796841 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
40796869 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
40796897 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40796912 GTACAATTTA
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 22 0.32
28 46 0.68
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:40801703 original size:29 final size:29
Alignment explanation
Indices: 40801670--40801752 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
40801660 TATATTCACA
*
40801670 TGGCCCTTTAGGCCCAAATCACATTTATG
1 TGGCCCATTAGGCCCAAATCACATTTATG
*
40801699 TGGCCCATTAGGCCTAAATCACATTTATG
1 TGGCCCATTAGGCCCAAATCACATTTATG
*
40801728 TGGCCCATTAGGCCCAAGTCACATT
1 TGGCCCATTAGGCCCAAATCACATT
40801753 ATATTCATGC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTATG
Found at i:40808119 original size:41 final size:40
Alignment explanation
Indices: 40808063--40808251 Score: 181
Period size: 41 Copynumber: 4.7 Consensus size: 40
40808053 GTTAACTATT
* * * *
40808063 CCCTTAATTTCACATGTGTGCCCCTATTTGTACCTT-GGTA
1 CCCTAAATTGCACATATGTGCCCCTATTTGTA-CTTCGATA
* * *
40808103 CCCTTGAATTGCACATGTGTGCCCCTGTTTGTACTTCGATA
1 CCC-TAAATTGCACATATGTGCCCCTATTTGTACTTCGATA
* * *
40808144 CCCCTAAATTGCACGTACGTGCCCCTGTTTG---TTC-ATA
1 -CCCTAAATTGCACATATGTGCCCCTATTTGTACTTCGATA
* *
40808181 CCGCTAAATTGCACATATGTGCCCTTATTTGTACTTCGGTA
1 CC-CTAAATTGCACATATGTGCCCCTATTTGTACTTCGATA
*
40808222 CTCCTGAATTGCACATATGTGCCCCTATTT
1 C-CCTAAATTGCACATATGTGCCCCTATTT
40808252 ACACCCTAGT
Statistics
Matches: 125, Mismatches: 15, Indels: 17
0.80 0.10 0.11
Matches are distributed among these distances:
36 2 0.02
37 27 0.22
38 3 0.02
40 9 0.07
41 80 0.64
42 4 0.03
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.37
Consensus pattern (40 bp):
CCCTAAATTGCACATATGTGCCCCTATTTGTACTTCGATA
Found at i:40822556 original size:47 final size:48
Alignment explanation
Indices: 40822481--40822612 Score: 196
Period size: 47 Copynumber: 2.8 Consensus size: 48
40822471 CTTAATCGAT
**
40822481 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACT-TATC-CCA
1 AAGTACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTCT-TCTCCA
* *
40822528 GAGTACCTATACCATGGCCTGTAACCAAATCAAGGTAACTCTTCTCCA
1 AAGTACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTCTTCTCCA
*
40822576 AAATACCTATACCATGGCCTGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCTGTAGCCAAATCAAGGTA
40822613 TAACTCACAC
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
47 38 0.50
48 38 0.50
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTCTTCTCCA
Found at i:40822594 original size:48 final size:47
Alignment explanation
Indices: 40822484--40822612 Score: 188
Period size: 48 Copynumber: 2.7 Consensus size: 47
40822474 AATCGATAAG
** * *
40822484 TACCTATACCATGGCCCATAGCCAAATCAAGGTAACTTATCCCAGAG
1 TACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTTATCCCAAAA
*
40822531 TACCTATACCATGGCCTGTAACCAAATCAAGGTAACTCT-TCTCCAAAA
1 TACCTATACCATGGCCTGTAGCCAAATCAAGGTAACT-TATC-CCAAAA
40822579 TACCTATACCATGGCCTGTAGCCAAATCAAGGTA
1 TACCTATACCATGGCCTGTAGCCAAATCAAGGTA
40822613 TAACTCACAC
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
47 36 0.49
48 38 0.51
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (47 bp):
TACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTTATCCCAAAA
Found at i:40823096 original size:25 final size:25
Alignment explanation
Indices: 40823068--40823117 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
40823058 TTAACTATTT
*
40823068 TAACCTTAATGAAAAACCATTTCAA
1 TAACCTTAATGAAAAACAATTTCAA
40823093 TAACCTTAATGAAAAACAATTTCAA
1 TAACCTTAATGAAAAACAATTTCAA
40823118 ACATTCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.18, G:0.04, T:0.28
Consensus pattern (25 bp):
TAACCTTAATGAAAAACAATTTCAA
Found at i:40825458 original size:49 final size:49
Alignment explanation
Indices: 40825373--40825731 Score: 658
Period size: 49 Copynumber: 7.4 Consensus size: 49
40825363 CCCCCCTAAT
40825373 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
40825420 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
40825469 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
*
40825518 ATGAATGTGAAAGTGTATATATATATGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
40825567 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
*
40825616 ATGAATGTGAAAGTG--TATATATGTAATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
40825663 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
40825710 ATGAATGTGAAAGTGTATATAT
1 ATGAATGTGAAAGTGTATATAT
40825732 GTGACAGGGC
Statistics
Matches: 304, Mismatches: 4, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
47 107 0.35
49 197 0.65
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (49 bp):
ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
Found at i:40825898 original size:37 final size:37
Alignment explanation
Indices: 40825857--40825935 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40825847 CCGAGCTCTA
* * *
40825857 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
40825894 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40825931 AAGAC
1 AAGAC
40825936 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40827420 original size:40 final size:40
Alignment explanation
Indices: 40827149--40827407 Score: 430
Period size: 40 Copynumber: 6.5 Consensus size: 40
40827139 GAGAATTGAG
* *
40827149 AGTGATGTATCTGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
*
40827189 AGTGATGTATCCGGGCTAAGTCTCGAAAAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
*
40827229 AGTGATGTATCCGAGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
*
40827269 AGTAATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
40827309 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
*
40827349 AGTGATGTATCCGGACTAAGT-TCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCT-CGAAGAGCATTCGTGCT
* *
40827389 AGTGATATATCCGTGCTAA
1 AGTGATGTATCCGGGCTAA
40827408 ACCCCGAAGA
Statistics
Matches: 206, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 1 0.00
40 205 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
Found at i:40829632 original size:13 final size:13
Alignment explanation
Indices: 40829614--40829638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40829604 TAATGGTATA
40829614 TTGAATCCATGAT
1 TTGAATCCATGAT
40829627 TTGAATCCATGA
1 TTGAATCCATGA
40829639 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:40831420 original size:49 final size:49
Alignment explanation
Indices: 40831334--40831946 Score: 1084
Period size: 49 Copynumber: 12.7 Consensus size: 49
40831324 AGGATTCTAC
*
40831334 GTGACGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
40831381 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
40831430 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
40831479 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
40831528 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
40831575 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
40831624 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
40831673 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
40831722 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
40831771 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
40831820 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
* * * * * *
40831867 GTGATGAATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAAC
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
*
40831914 GTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAG
40831947 TCCCGAAGGG
Statistics
Matches: 550, Mismatches: 10, Indels: 12
0.96 0.02 0.02
Matches are distributed among these distances:
47 159 0.29
48 1 0.00
49 390 0.71
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (49 bp):
GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
Found at i:40831572 original size:194 final size:194
Alignment explanation
Indices: 40831334--40831946 Score: 1099
Period size: 194 Copynumber: 3.2 Consensus size: 194
40831324 AGGATTCTAC
*
40831334 GTGACGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
40831399 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
66 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
40831464 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
131 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
40831528 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
40831593 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
66 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
40831658 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
131 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
40831722 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
40831787 TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGAT
64 TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
* * * * *
40831850 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAA
129 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGA
*
40831913 C
194 T
* *
40831914 GTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 GTGATGAATGTGAAAGTGTATATATGTGATAAG
40831947 TCCCGAAGGG
Statistics
Matches: 408, Mismatches: 9, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
190 14 0.03
192 40 0.10
194 258 0.63
196 96 0.24
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (194 bp):
GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
Found at i:40832119 original size:37 final size:37
Alignment explanation
Indices: 40832063--40832141 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
40832053 CCGAGCTCTA
* * * *
40832063 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
*
40832100 AAGACCCGATAACTTCGTGTGGAGATTATGTCCAGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
40832137 AAGAC
1 AAGAC
40832142 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
Found at i:40832546 original size:9 final size:9
Alignment explanation
Indices: 40832529--40832559 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40832519 TGCTTACTCC
*
40832529 GTTTGCTCT
1 GTTTCCTCT
40832538 GTTTCCTCT
1 GTTTCCTCT
40832547 GTTTCCTCT
1 GTTTCCTCT
40832556 GTTT
1 GTTT
40832560 TATAGATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.26, G:0.16, T:0.58
Consensus pattern (9 bp):
GTTTCCTCT
Found at i:40835574 original size:43 final size:43
Alignment explanation
Indices: 40835519--40835741 Score: 333
Period size: 43 Copynumber: 5.2 Consensus size: 43
40835509 ATATTGTATA
* *
40835519 ATGCCAACGTCCCAGACGTTGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
40835562 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAATCATATATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
* *
40835605 ATGCTAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
**
40835648 ATGCCAACAACCCAGACGTGGTCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* *
40835691 ATGCCAACGTCCCAGATGTGGTCTTACACGTAATCACATATCA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
40835734 ATGCCAAC
1 ATGCCAAC
40835742 TCAAAAATGT
Statistics
Matches: 162, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
42 3 0.02
43 156 0.96
44 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:40839375 original size:40 final size:40
Alignment explanation
Indices: 40839322--40839477 Score: 224
Period size: 40 Copynumber: 3.9 Consensus size: 40
40839312 CGTGCCTCAC
* * *
40839322 ATAGCCGAAGCTA-TTCTAATTCCCACACTTAGTGCTACTT
1 ATAGCCGAAGCTATTTC-AAATCGCACACTTAGTGCCACTT
*
40839362 ATAGTCGAAGCTATTTCAAATCGCACACTTAGTGCCACTT
1 ATAGCCGAAGCTATTTCAAATCGCACACTTAGTGCCACTT
* *
40839402 ATAGCTGAAGCTATTTCAAATCGCACATTTAGTGCCACTT
1 ATAGCCGAAGCTATTTCAAATCGCACACTTAGTGCCACTT
* *
40839442 ATAGCCGAAGCTATTTCAAATCACACACTTAATGCC
1 ATAGCCGAAGCTATTTCAAATCGCACACTTAGTGCC
40839478 GAACATAGTC
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 101 0.97
41 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (40 bp):
ATAGCCGAAGCTATTTCAAATCGCACACTTAGTGCCACTT
Found at i:40840602 original size:30 final size:30
Alignment explanation
Indices: 40840566--40840625 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
40840556 TTTTCTAACT
40840566 CAGCTTTGTGGTCCCGAAACCACTATTATG
1 CAGCTTTGTGGTCCCGAAACCACTATTATG
*
40840596 CAGCTTTGTGGTCCTGAAACCACTATTATG
1 CAGCTTTGTGGTCCCGAAACCACTATTATG
40840626 ACTAGGGTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (30 bp):
CAGCTTTGTGGTCCCGAAACCACTATTATG
Found at i:40846522 original size:40 final size:40
Alignment explanation
Indices: 40846319--40846522 Score: 202
Period size: 40 Copynumber: 5.1 Consensus size: 40
40846309 CGGAATTTAA
** *
40846319 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
40846359 CCGGTTATAGTAACTCGCACAAATGCCTACGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
40846399 CCGGATTTAGTAACTCGAACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
40846438 CCAGA-ATTAGTAACTCGGACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
40846478 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40846518 CCGGA
1 CCGGA
40846523 CATCATTCGA
Statistics
Matches: 134, Mismatches: 23, Indels: 14
0.78 0.13 0.08
Matches are distributed among these distances:
38 2 0.01
39 31 0.23
40 90 0.67
41 11 0.08
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40854410 original size:40 final size:39
Alignment explanation
Indices: 40854340--40854517 Score: 158
Period size: 40 Copynumber: 4.6 Consensus size: 39
40854330 GCTACTCGTT
*
40854340 CAAATG-CTTC-GACATAGCCC-G-TTATAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATT-TAGTAACTCGCA
*
40854376 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTAACTCGCA
* *
40854416 CCAATGCCTTC-G-CTTAGCCCGGAATTAGTAACT--CA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* * ** *
40854451 CAAATGCCTTCGGATCTTAGTCCGGATATATGGCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTA-GTAAC-TCGCA
40854493 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
40854518 CATCATTCGA
Statistics
Matches: 117, Mismatches: 12, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
35 12 0.10
36 7 0.06
37 23 0.20
38 13 0.11
39 11 0.09
40 24 0.21
41 18 0.15
42 9 0.08
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:40870415 original size:27 final size:27
Alignment explanation
Indices: 40870384--40870561 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40870374 TAAATTGTAC
40870384 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
40870411 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40870437 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
40870465 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
40870493 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40870520 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40870547 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40870562 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40870498 original size:82 final size:81
Alignment explanation
Indices: 40870385--40870540 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40870375 AAATTGTACA
* *
40870385 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
40870449 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
40870466 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
40870531 TGCGAGTTGA
65 TGCGAATTGA
40870541 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40870552 original size:82 final size:81
Alignment explanation
Indices: 40870381--40870561 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
40870371 GATTAAATTG
* *
40870381 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40870446 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
40870462 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
40870526 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40870544 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40870562 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40872643 original size:23 final size:23
Alignment explanation
Indices: 40872613--40872667 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 23
40872603 AAACAAGTTG
40872613 ATTCTTTTGTTTTCTATATTTTA
1 ATTCTTTTGTTTTCTATATTTTA
40872636 ATTCTTTTGTTTTCTATATTTTA
1 ATTCTTTTGTTTTCTATATTTTA
*
40872659 CTATCTTTT
1 AT-TCTTTT
40872668 TATTTATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.16, C:0.11, G:0.04, T:0.69
Consensus pattern (23 bp):
ATTCTTTTGTTTTCTATATTTTA
Found at i:40875986 original size:28 final size:28
Alignment explanation
Indices: 40875928--40876082 Score: 141
Period size: 28 Copynumber: 5.5 Consensus size: 28
40875918 TTATTATTCT
* * *
40875928 AGTGAATTATCTATGTTTTGTATTGTCCC
1 AGTGAACTATCTCTGTGTT-TATTGTCCC
*
40875957 AGTGAACTATCTTTGTGTTTATTGTCCC
1 AGTGAACTATCTCTGTGTTTATTGTCCC
* * * * *
40875985 AGCGGACTATCTCTATATTTACTGTCCC
1 AGTGAACTATCTCTGTGTTTATTGTCCC
* *
40876013 AGT-AGACTATCTCTATGTTTATTATCCC
1 AGTGA-ACTATCTCTGTGTTTATTGTCCC
* * ** *
40876041 CGCGGGCTATCTCTGTGTTTACTGTCCC
1 AGTGAACTATCTCTGTGTTTATTGTCCC
40876069 AGTGAACTATCTCT
1 AGTGAACTATCTCT
40876083 ATAGATGTCA
Statistics
Matches: 99, Mismatches: 25, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
28 83 0.84
29 16 0.16
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (28 bp):
AGTGAACTATCTCTGTGTTTATTGTCCC
Found at i:40876022 original size:56 final size:56
Alignment explanation
Indices: 40875951--40876084 Score: 189
Period size: 56 Copynumber: 2.4 Consensus size: 56
40875941 TGTTTTGTAT
* * *
40875951 TGTCCCAGTGAACTATCTTTGTGTTTATTGTCCCAGCGGACTATCTCTATATTTAC
1 TGTCCCAGTGAACTATCTCTATGTTTATTATCCCAGCGGACTATCTCTATATTTAC
* * * *
40876007 TGTCCCAGT-AGACTATCTCTATGTTTATTATCCCCGCGGGCTATCTCTGTGTTTAC
1 TGTCCCAGTGA-ACTATCTCTATGTTTATTATCCCAGCGGACTATCTCTATATTTAC
40876063 TGTCCCAGTGAACTATCTCTAT
1 TGTCCCAGTGAACTATCTCTAT
40876085 AGATGTCATG
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
55 1 0.01
56 67 0.97
57 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (56 bp):
TGTCCCAGTGAACTATCTCTATGTTTATTATCCCAGCGGACTATCTCTATATTTAC
Found at i:40880930 original size:28 final size:28
Alignment explanation
Indices: 40880879--40880945 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
40880869 GTAAGTCCGT
*
40880879 ACACTTAGTGCTTAATAATCAAACTCGC
1 ACACTTAGTGCTTAACAATCAAACTCGC
*
40880907 ACACTTAGTGC-TATACAATTAAACTCGC
1 ACACTTAGTGCTTA-ACAATCAAACTCGC
40880935 ACACTTAGTGC
1 ACACTTAGTGC
40880946 CAATCTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 2 0.06
28 34 0.94
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.28
Consensus pattern (28 bp):
ACACTTAGTGCTTAACAATCAAACTCGC
Found at i:40882860 original size:43 final size:43
Alignment explanation
Indices: 40882813--40882928 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 43
40882803 TACCACATAT
* * * * *
40882813 CGATGTCACTGTCCCAAACAAGGTCTTACACGA-AATCATAATA
1 CGATGTCAATGTCCCAGACATGGTCTTACAC-ATAATCACAAGA
40882856 CGATGTCAATGTCCCAGACATGGTCTTACACATAATCACAAGA
1 CGATGTCAATGTCCCAGACATGGTCTTACACATAATCACAAGA
* *
40882899 CAATGCCAATGTCCCAGACATGGTCTTACA
1 CGATGTCAATGTCCCAGACATGGTCTTACA
40882929 TGTAGTTACA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.02
43 64 0.98
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (43 bp):
CGATGTCAATGTCCCAGACATGGTCTTACACATAATCACAAGA
Found at i:40884805 original size:42 final size:42
Alignment explanation
Indices: 40884744--40884851 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
40884734 CAGTCCAGCT
* * ** * *
40884744 ATGGTCTTACAC-GATTCTCATATTGATGCCATGTCTCAGAC
1 ATGGTCTTACACAAAATCTCATAACGATGCCATATCCCAGAC
* *
40884785 ATGGTCTTACACAAAATCTCATAACGATGTCATATCCCAGAT
1 ATGGTCTTACACAAAATCTCATAACGATGCCATATCCCAGAC
40884827 ATGGTCTTACACATAAA-CTCATAAC
1 ATGGTCTTACACA-AAATCTCATAAC
40884852 TCTAATGTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 12 0.21
42 42 0.74
43 3 0.05
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (42 bp):
ATGGTCTTACACAAAATCTCATAACGATGCCATATCCCAGAC
Found at i:40885756 original size:104 final size:104
Alignment explanation
Indices: 40885576--40885778 Score: 388
Period size: 104 Copynumber: 2.0 Consensus size: 104
40885566 TACACTTACA
* *
40885576 AGCAATCTTGAAAGTGACAATGTAATGGCCCATCTTTCACGGGCACCGGAAAAGTGAGTTTAGGG
1 AGCAATCTTGAAAGTGACAATGTAACGACCCATCTTTCACGGGCACCGGAAAAGTGAGTTTAGGG
40885641 CTTCCGTCTTAGGAAAATGAGTTCGTAAATATTTTTTTC
66 CTTCCGTCTTAGGAAAATGAGTTCGTAAATATTTTTTTC
40885680 AGCAATCTTGAAAGTGACAATGTAACGACCCATCTTTCACGGGCACCGGAAAAGTGAGTTTAGGG
1 AGCAATCTTGAAAGTGACAATGTAACGACCCATCTTTCACGGGCACCGGAAAAGTGAGTTTAGGG
40885745 CTTCCGTCTTAGGAAAATGAGTTCGTAAATATTT
66 CTTCCGTCTTAGGAAAATGAGTTCGTAAATATTT
40885779 AGAAAAAAAT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 97 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (104 bp):
AGCAATCTTGAAAGTGACAATGTAACGACCCATCTTTCACGGGCACCGGAAAAGTGAGTTTAGGG
CTTCCGTCTTAGGAAAATGAGTTCGTAAATATTTTTTTC
Found at i:40886225 original size:18 final size:17
Alignment explanation
Indices: 40886199--40886236 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
40886189 TTAATTTAGT
40886199 AAATGAAAGAAATAAAATA
1 AAATGAAAG-AAT-AAATA
40886218 AAAT-AAAGAATAAATA
1 AAATGAAAGAATAAATA
40886234 AAA
1 AAA
40886237 ACAAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 3 0.16
18 4 0.21
19 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (17 bp):
AAATGAAAGAATAAATA
Found at i:40886294 original size:12 final size:11
Alignment explanation
Indices: 40886263--40886304 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
40886253 AAAGAAACAG
40886263 AGAAGAAACGAA
1 AGAAGAAA-GAA
*
40886275 A-TAGAAAGAA
1 AGAAGAAAGAA
40886285 AGAAAGAAAGAA
1 AG-AAGAAAGAA
40886297 AGAAGAAA
1 AGAAGAAA
40886305 ATAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 4 0.15
11 11 0.42
12 11 0.42
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.02
Consensus pattern (11 bp):
AGAAGAAAGAA
Found at i:40886323 original size:34 final size:35
Alignment explanation
Indices: 40886248--40886323 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 35
40886238 CAAGAAAAAC
* *
40886248 AAGAGAAAGAAACAGAGAAGAAACGAAATAGAAAG
1 AAGAGAAAGAAACAAAGAAGAAAAGAAATAGAAAG
* *
40886283 AA-AGAAAGAAAGAAAGAAGAAAATAAA-AGAAA-
1 AAGAGAAAGAAACAAAGAAGAAAAGAAATAGAAAG
40886315 AAGGAGAAA
1 AA-GAGAAA
40886324 TTAGGGTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 2 0.06
33 5 0.14
34 26 0.74
35 2 0.06
ACGTcount: A:0.71, C:0.03, G:0.24, T:0.03
Consensus pattern (35 bp):
AAGAGAAAGAAACAAAGAAGAAAAGAAATAGAAAG
Found at i:40893527 original size:3 final size:3
Alignment explanation
Indices: 40893519--40893546 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40893509 AGATATTTAC
40893519 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
40893547 ATTTTATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40893768 original size:17 final size:17
Alignment explanation
Indices: 40893739--40893771 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40893729 GAAGGAACGA
40893739 AATAGAAAGAAAGAAAG
1 AATAGAAAGAAAGAAAG
40893756 AATA-AAAGAAAAGAAA
1 AATAGAAAG-AAAGAAA
40893772 AAGGAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (17 bp):
AATAGAAAGAAAGAAAG
Found at i:40896574 original size:40 final size:40
Alignment explanation
Indices: 40896493--40896713 Score: 295
Period size: 40 Copynumber: 5.6 Consensus size: 40
40896483 AAACCAAGTA
** * *
40896493 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
* *
40896532 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGTACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
40896572 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTA
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* * *
40896612 CCTTCGGGACTTGGCTCGATTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
40896652 CCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
40896692 CCTTCGGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
40896714 CAATCCGAAT
Statistics
Matches: 161, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 26 0.16
40 135 0.84
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.28
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:40901260 original size:21 final size:21
Alignment explanation
Indices: 40901234--40901283 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
40901224 TATGGTAATT
40901234 TCACTTTTTAACACATATGAA
1 TCACTTTTTAACACATATGAA
40901255 TCACTTTTTAACACATATGAA
1 TCACTTTTTAACACATATGAA
40901276 TCACTTTT
1 TCACTTTT
40901284 ACACTTAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (21 bp):
TCACTTTTTAACACATATGAA
Found at i:40904013 original size:22 final size:22
Alignment explanation
Indices: 40903981--40904036 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
40903971 AATTATTGCT
*
40903981 GATGTCGCGACACCAAGGTGTA
1 GATGTCACGACACCAAGGTGTA
*
40904003 GATGTCACGACACCAAGGTGTG
1 GATGTCACGACACCAAGGTGTA
*
40904025 GATGTCAAGACA
1 GATGTCACGACA
40904037 TTGACTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.18
Consensus pattern (22 bp):
GATGTCACGACACCAAGGTGTA
Found at i:40907051 original size:18 final size:18
Alignment explanation
Indices: 40907030--40907087 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
40907020 AAGAAGGATC
*
40907030 GAGATCGAGAAAGGGAAA
1 GAGATCGAGAAAGAGAAA
* * **
40907048 GAGAACGAGATAGAGAGC
1 GAGATCGAGAAAGAGAAA
*
40907066 GAGATAGAGAAAGAGAAA
1 GAGATCGAGAAAGAGAAA
40907084 GAGA
1 GAGA
40907088 AAGAGATCGC
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.52, C:0.05, G:0.38, T:0.05
Consensus pattern (18 bp):
GAGATCGAGAAAGAGAAA
Found at i:40907057 original size:6 final size:6
Alignment explanation
Indices: 40907036--40907093 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
40907026 GATCGAGATC
* * * ** *
40907036 GAGAAA GGGAAA GAGAAC GAGATA GAGAGC GAGATA GAGAAA GAGAAA
1 GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA
40907084 GAGAAA GAGA
1 GAGAAA GAGA
40907094 TCGCTTTAGT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.55, C:0.03, G:0.38, T:0.03
Consensus pattern (6 bp):
GAGAAA
Found at i:40907062 original size:12 final size:12
Alignment explanation
Indices: 40907030--40907094 Score: 67
Period size: 12 Copynumber: 5.4 Consensus size: 12
40907020 AAGAAGGATC
*
40907030 GAGATCGAGAAA
1 GAGATAGAGAAA
* * *
40907042 GGGAAAGAGAAC
1 GAGATAGAGAAA
**
40907054 GAGATAGAGAGC
1 GAGATAGAGAAA
40907066 GAGATAGAGAAA
1 GAGATAGAGAAA
*
40907078 GAGAAAGAGAAA
1 GAGATAGAGAAA
40907090 GAGAT
1 GAGAT
40907095 CGCTTTAGTA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.52, C:0.05, G:0.37, T:0.06
Consensus pattern (12 bp):
GAGATAGAGAAA
Found at i:40914806 original size:39 final size:39
Alignment explanation
Indices: 40914763--40914894 Score: 174
Period size: 39 Copynumber: 3.2 Consensus size: 39
40914753 CGAAATCTAG
40914763 CTGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAA
1 CTGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAA
*
40914802 CTGAAGCACATAAGTGCTAGACGAAAGCCCGGAAGCCCGAAGGCTAA
1 CTGAAGCACATAAGTGCT-----AAA---CGGAAGCCCGGAGGCTAA
*
40914849 CTGAAGCACATAAGTGCTAAATGGAAGCCCGGAGGCTAA
1 CTGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAA
40914888 CTGAAGC
1 CTGAAGC
40914895 TCATTAGAGC
Statistics
Matches: 82, Mismatches: 3, Indels: 16
0.81 0.03 0.16
Matches are distributed among these distances:
39 41 0.50
42 3 0.04
44 3 0.04
47 35 0.43
ACGTcount: A:0.36, C:0.23, G:0.28, T:0.13
Consensus pattern (39 bp):
CTGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAA
Found at i:40914853 original size:47 final size:47
Alignment explanation
Indices: 40914784--40914881 Score: 160
Period size: 47 Copynumber: 2.1 Consensus size: 47
40914774 AAGTGCTAAA
* *
40914784 CGGAAGCCCGGAGGCTAACTGAAGCACATAAGTGCTAGACGAAAGCC
1 CGGAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACGAAAGCC
* *
40914831 CGGAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAATGGAAGCC
1 CGGAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACGAAAGCC
40914878 CGGA
1 CGGA
40914882 GGCTAACTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.35, C:0.24, G:0.30, T:0.11
Consensus pattern (47 bp):
CGGAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACGAAAGCC
Found at i:40914931 original size:21 final size:21
Alignment explanation
Indices: 40914907--40914957 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
40914897 ATTAGAGCTG
40914907 AACTGAAACCCCAGAAGGGTT
1 AACTGAAACCCCAGAAGGGTT
40914928 AACTGAAACCCCAGAAGGGTT
1 AACTGAAACCCCAGAAGGGTT
40914949 AACTGAAAC
1 AACTGAAAC
40914958 TTATATGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.14
Consensus pattern (21 bp):
AACTGAAACCCCAGAAGGGTT
Found at i:40918934 original size:17 final size:15
Alignment explanation
Indices: 40918906--40918989 Score: 105
Period size: 16 Copynumber: 5.2 Consensus size: 15
40918896 ATATTTATTA
40918906 TAATTTTTAAAAATTT
1 TAATTTTTAAAAA-TT
40918922 TAATTTTTAAAAATT
1 TAATTTTTAAAAATT
40918937 TAGATTTTTTAAAAATTT
1 TA-A-TTTTTAAAAA-TT
40918955 TAATTTTTAAAAATT
1 TAATTTTTAAAAATT
*
40918970 TAGATTTTTTAAAAACT
1 TA-A-TTTTTAAAAATT
40918987 TAA
1 TAA
40918990 GTGAAATTAT
Statistics
Matches: 62, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
15 8 0.13
16 26 0.42
17 24 0.39
18 4 0.06
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (15 bp):
TAATTTTTAAAAATT
Found at i:40918949 original size:33 final size:33
Alignment explanation
Indices: 40918909--40918984 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
40918899 TTTATTATAA
40918909 TTTTTAAAAATTTTAATTTTTAAAAATTTAGAT
1 TTTTTAAAAATTTTAATTTTTAAAAATTTAGAT
40918942 TTTTTAAAAATTTTAATTTTTAAAAATTTAGAT
1 TTTTTAAAAATTTTAATTTTTAAAAATTTAGAT
40918975 TTTTTAAAAA
1 TTTTTAAAAA
40918985 CTTAAGTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (33 bp):
TTTTTAAAAATTTTAATTTTTAAAAATTTAGAT
Found at i:40919980 original size:16 final size:18
Alignment explanation
Indices: 40919959--40919991 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
40919949 AATGTCATTA
40919959 GATTAAA-C-TAATTAAG
1 GATTAAAGCTTAATTAAG
40919975 GATTAAAGCTTAATTAA
1 GATTAAAGCTTAATTAA
40919992 TTATAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (18 bp):
GATTAAAGCTTAATTAAG
Found at i:40920512 original size:15 final size:15
Alignment explanation
Indices: 40920480--40920508 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40920470 ATTTTCTGTG
40920480 TTTATAGTGTGTGAA
1 TTTATAGTGTGTGAA
40920495 TTTATA-TGTGTGAA
1 TTTATAGTGTGTGAA
40920509 ATTTTTGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (15 bp):
TTTATAGTGTGTGAA
Found at i:40921691 original size:43 final size:42
Alignment explanation
Indices: 40921630--40921760 Score: 140
Period size: 43 Copynumber: 3.1 Consensus size: 42
40921620 ATAGGATTTC
* *
40921630 CGATATGTGTTCTCGTGTAAGACCACGTTTGGGACGTTGGCAT
1 CGATATGTGAT-TCGTGTAAGACCATGTTTGGGACGTTGGCAT
* * * *
40921673 CGATATGTGATTACGTGTAAGACCATGTCTAGGACATCGGCAT
1 CGATATGTGATT-CGTGTAAGACCATGTTTGGGACGTTGGCAT
* * *
40921716 C-ATATTTGATTCGTGTAAGACCTTATTTGGGACAG-TGGCAT
1 CGATATGTGATTCGTGTAAGACCATGTTTGGGAC-GTTGGCAT
40921757 CGAT
1 CGAT
40921761 TAATCGATAT
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
41 24 0.33
42 12 0.17
43 36 0.50
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
CGATATGTGATTCGTGTAAGACCATGTTTGGGACGTTGGCAT
Found at i:40924728 original size:25 final size:25
Alignment explanation
Indices: 40924691--40924778 Score: 83
Period size: 25 Copynumber: 3.5 Consensus size: 25
40924681 TATCAATTTT
*
40924691 AGCTCGTAAGAGCTTACCGATTCTC
1 AGCTCGTATGAGCTTACCGATTCTC
* *
40924716 AGCTCGTATGAGCTAACTGATT-TAC
1 AGCTCGTATGAGCTTACCGATTCT-C
* *
40924741 AGCTCGTGA-GAACATACCGATTCAT-
1 AGCTCGT-ATGAGCTTACCGATTC-TC
40924766 AGCTCGTATGAGC
1 AGCTCGTATGAGC
40924779 ATATATGTAC
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
24 2 0.04
25 46 0.92
26 1 0.02
27 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATTCTC
Found at i:40928689 original size:27 final size:27
Alignment explanation
Indices: 40928610--40928742 Score: 146
Period size: 27 Copynumber: 5.0 Consensus size: 27
40928600 ACCCTCAGAT
* ** *
40928610 TGTAAAATTACCGAAATACCCCCG-ATT
1 TGTAAAATTACCAAAATACCCTTGTA-G
*
40928637 TGT-AAATTACC-AAATACCCTTATAG
1 TGTAAAATTACCAAAATACCCTTGTAG
*
40928662 TATAAAATTACCAAAATACCCTTGTAG
1 TGTAAAATTACCAAAATACCCTTGTAG
*
40928689 TGTAAAATTACCAAAATACCCTTGTGG
1 TGTAAAATTACCAAAATACCCTTGTAG
* * *
40928716 TGTAAAATTATCGAAATACCCCTGTAG
1 TGTAAAATTACCAAAATACCCTTGTAG
40928743 GGCAAGTGAT
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
25 10 0.11
26 17 0.19
27 64 0.70
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.29
Consensus pattern (27 bp):
TGTAAAATTACCAAAATACCCTTGTAG
Found at i:40933419 original size:41 final size:41
Alignment explanation
Indices: 40933336--40933451 Score: 133
Period size: 41 Copynumber: 2.8 Consensus size: 41
40933326 TAAAAGCCAC
* * *
40933336 CGGTGGATCCACGGTCGTCAAGCAACCATGCGGTCCTTAAT
1 CGGTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAAT
* * *
40933377 CGGTGGATCCACTATTGTCAAGCAACCATGTGATCCTCAAT
1 CGGTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAAT
* * * * *
40933418 CGATGAATCCATGGTCGTCAAGCGACCATGCGAT
1 CGGTGGATCCACGATCGTCAAGCAACCATGCGAT
40933452 TCTTAATTTC
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (41 bp):
CGGTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAAT
Found at i:40933815 original size:54 final size:54
Alignment explanation
Indices: 40933726--40933957 Score: 206
Period size: 54 Copynumber: 4.3 Consensus size: 54
40933716 TACAAACTAA
* * * *
40933726 GGGTATTTCGGTAATTTTGA-AAACTAATGGTATTTCTGTAATTTTGTAAATCAG
1 GGGTATTTCTGTAATTTT-ACAAATTAAGGGTATTTCTGTAATTTTATAAATCAG
* * * *
40933780 GGGTATTTTTATAATTTTCCAAATTAAGGGCATTTC-GATAATTTT-TCAAATCAG
1 GGGTATTTCTGTAATTTTACAAATTAAGGGTATTTCTG-TAATTTTAT-AAATCAG
* * *
40933834 TGGTATTTCTGTAATTTTACAAATCAAGGGTATTT-TGGTAATTTTATAATTC-G
1 GGGTATTTCTGTAATTTTACAAATTAAGGGTATTTCT-GTAATTTTATAAATCAG
* * * * * * *
40933887 AGGGTATTTCGGTAAGTTTACAAACTAGGGGTATTTTTGTAATTTTATAAACCAA
1 -GGGTATTTCTGTAATTTTACAAATTAAGGGTATTTCTGTAATTTTATAAATCAG
40933942 GGGTATTT-TAGTAATT
1 GGGTATTTCT-GTAATT
40933958 CTACCCTACA
Statistics
Matches: 143, Mismatches: 25, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
53 3 0.02
54 137 0.96
55 3 0.02
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (54 bp):
GGGTATTTCTGTAATTTTACAAATTAAGGGTATTTCTGTAATTTTATAAATCAG
Found at i:40933950 original size:27 final size:27
Alignment explanation
Indices: 40933696--40933957 Score: 178
Period size: 27 Copynumber: 9.7 Consensus size: 27
40933686 TTTCACCCTA
* * *
40933696 CAAGGGTGTTTTGGTAAATCTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
40933722 CTAAGGGTATTTCGGTAATTTTGA-AAA-
1 C-AAGGGTATTTTGGTAATTTT-ACAAAT
* **
40933749 CTAATGGTATTTCT-GTAATTTTGTAAAT
1 C-AAGGGTATTT-TGGTAATTTTACAAAT
* ** *
40933777 CAGGGGTATTTTTATAATTTTCCAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * * * *
40933804 TAAGGGCATTTCGATAATTTTTCAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
40933831 C-AGTGGTATTTCT-GTAATTTTACAAAT
1 CAAG-GGTATTT-TGGTAATTTTACAAAT
* *
40933858 CAAGGGTATTTTGGTAATTTTATAATT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
40933885 CGAGGGTATTTCGGTAAGTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * * *
40933911 CTAGGGGTATTTTTGTAATTTTATAAAC
1 C-AAGGGTATTTTGGTAATTTTACAAAT
*
40933939 CAAGGGTATTTTAGTAATT
1 CAAGGGTATTTTGGTAATT
40933958 CTACCCTACA
Statistics
Matches: 186, Mismatches: 38, Indels: 23
0.75 0.15 0.09
Matches are distributed among these distances:
26 6 0.03
27 175 0.94
28 5 0.03
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.42
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:40933956 original size:81 final size:80
Alignment explanation
Indices: 40933718--40933957 Score: 272
Period size: 81 Copynumber: 3.0 Consensus size: 80
40933708 GGTAAATCTA
* * * *
40933718 CAAACTAAGGGTATTTCGGTAATTTTGA-AAACTAATGGTATTTCTGTAATTTTGTAAATCAGGG
1 CAAATTAAGGGTATTTCGGTAATTTT-ACAAACTAGTGGTATTTCTGTAATTTTATAAATCAAGG
40933782 GTATTTTTA-TAATTTT
65 GTA-TTTTAGTAATTTT
* * * *
40933798 CCAAATTAAGGGCATTTCGATAATTTTTCAAA-TCAGTGGTATTTCTGTAATTTTACAAATCAAG
1 -CAAATTAAGGGTATTTCGGTAATTTTACAAACT-AGTGGTATTTCTGTAATTTTATAAATCAAG
*
40933862 GGTATTTTGGTAATTTT
64 GGTATTTTAGTAATTTT
* * * * *
40933879 -ATAATTCGAGGGTATTTCGGTAAGTTTACAAACTAGGGGTATTTTTGTAATTTTATAAACCAAG
1 CA-AATT-AAGGGTATTTCGGTAATTTTACAAACTAGTGGTATTTCTGTAATTTTATAAATCAAG
40933943 GGTATTTTAGTAATT
64 GGTATTTTAGTAATT
40933958 CTACCCTACA
Statistics
Matches: 134, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
79 1 0.01
80 9 0.07
81 123 0.92
82 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (80 bp):
CAAATTAAGGGTATTTCGGTAATTTTACAAACTAGTGGTATTTCTGTAATTTTATAAATCAAGGG
TATTTTAGTAATTTT
Found at i:40936105 original size:17 final size:18
Alignment explanation
Indices: 40936083--40936127 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
40936073 GTGAAATGAT
40936083 CCCGATAAATGAA-AATG
1 CCCGATAAATGAATAATG
*
40936100 CCCGATGAAT-AATAATG
1 CCCGATAAATGAATAATG
*
40936117 GCCGATAAATG
1 CCCGATAAATG
40936128 GTAAATGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (18 bp):
CCCGATAAATGAATAATG
Found at i:40937740 original size:42 final size:42
Alignment explanation
Indices: 40937693--40937783 Score: 173
Period size: 42 Copynumber: 2.2 Consensus size: 42
40937683 ACGGATAGAG
40937693 ACACGGGCGTGTGTCTCAGCCATGTGGTTGACACGGGCTTGA
1 ACACGGGCGTGTGTCTCAGCCATGTGGTTGACACGGGCTTGA
*
40937735 ACACGGGCGTGTGTCTCAGCCGTGTGGTTGACACGGGCTTGA
1 ACACGGGCGTGTGTCTCAGCCATGTGGTTGACACGGGCTTGA
40937777 ACACGGG
1 ACACGGG
40937784 TCATTTGTCC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.16, C:0.24, G:0.37, T:0.22
Consensus pattern (42 bp):
ACACGGGCGTGTGTCTCAGCCATGTGGTTGACACGGGCTTGA
Found at i:40945123 original size:23 final size:22
Alignment explanation
Indices: 40945072--40945123 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
40945062 CCTCGTCTTT
*
40945072 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
40945094 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
40945117 TTCTTTT
1 TTCTTTT
40945124 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:40948951 original size:20 final size:21
Alignment explanation
Indices: 40948912--40948951 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
40948902 GATGATATTT
* *
40948912 TCTTTATTTTATTATTTTTCA
1 TCTTTATTTTATCATCTTTCA
40948933 TCTTTA-TTTATCATCTTTC
1 TCTTTATTTTATCATCTTTC
40948952 CAATTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (21 bp):
TCTTTATTTTATCATCTTTCA
Found at i:40951071 original size:27 final size:26
Alignment explanation
Indices: 40951023--40951082 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
40951013 GCGAGGCTGC
*
40951023 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
40951050 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
40951076 CAGATAT
1 CAGATAT
40951083 ATATATATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Done.