Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 165 of 310
Found at i:54140031 original size:25 final size:25
Alignment explanation
Indices: 54139991--54140118 Score: 111
Period size: 25 Copynumber: 5.1 Consensus size: 25
54139981 CATTATTTAT
* *
54139991 CTCTTATGAGCATCCC-ACTATATGG
1 CTCTCATGAGCTTCCCGA-TATATGG
** *
54140016 CTCTCACAAGCTTCCCGATATTTGG
1 CTCTCATGAGCTTCCCGATATATGG
*
54140041 CACTCATGAGCTTCCCGAT-TAATGG
1 CTCTCATGAGCTTCCCGATAT-ATGG
54140066 CTCTCATGAGCTTCCCGATA-ATTGG
1 CTCTCATGAGCTTCCCGATATA-TGG
* * *
54140091 CT-TGCAAGAGCTTCCCGTTACATGG
1 CTCT-CATGAGCTTCCCGATATATGG
54140116 CTC
1 CTC
54140119 GGAAGAGCTT
Statistics
Matches: 84, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
24 3 0.04
25 79 0.94
26 2 0.02
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (25 bp):
CTCTCATGAGCTTCCCGATATATGG
Found at i:54140066 original size:50 final size:50
Alignment explanation
Indices: 54140012--54140118 Score: 137
Period size: 50 Copynumber: 2.1 Consensus size: 50
54140002 ATCCCACTAT
* *
54140012 ATGGCTCTCACAAGCTTCCCGATATTTGGCACT-CATGAGCTTCCCGATTA-
1 ATGGCTCTCACAAGCTTCCCGATAATTGGC-CTGCAAGAGCTTCCCG-TTAC
** *
54140062 ATGGCTCTCATGAGCTTCCCGATAATTGGCTTGCAAGAGCTTCCCGTTAC
1 ATGGCTCTCACAAGCTTCCCGATAATTGGCCTGCAAGAGCTTCCCGTTAC
54140112 ATGGCTC
1 ATGGCTC
54140119 GGAAGAGCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
49 4 0.08
50 46 0.92
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.30
Consensus pattern (50 bp):
ATGGCTCTCACAAGCTTCCCGATAATTGGCCTGCAAGAGCTTCCCGTTAC
Found at i:54140124 original size:25 final size:24
Alignment explanation
Indices: 54140048--54140131 Score: 96
Period size: 25 Copynumber: 3.4 Consensus size: 24
54140038 TGGCACTCAT
* *
54140048 GAGCTTCCCGATTAATGGCTCTCAT
1 GAGCTTCCCG-TTAATGGCTCGCAA
* *
54140073 GAGCTTCCCGATAATTGGCTTGCAA
1 GAGCTTCCCGTTAA-TGGCTCGCAA
*
54140098 GAGCTTCCCGTTACATGGCTCGGAA
1 GAGCTTCCCGTTA-ATGGCTCGCAA
54140123 GAGCTTCCC
1 GAGCTTCCC
54140132 ATTTACATGC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.06
25 46 0.92
26 1 0.02
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (24 bp):
GAGCTTCCCGTTAATGGCTCGCAA
Found at i:54140127 original size:50 final size:50
Alignment explanation
Indices: 54140024--54140131 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
54140014 GGCTCTCACA
* * * *
54140024 AGCTTCCCGATATTTGGCACTCATGAGCTTCCCGATTAATGGCTCTCATG
1 AGCTTCCCGATAATTGGCACTCAAGAGCTTCCCGATTAATGGCTCGCAAG
* *
54140074 AGCTTCCCGATAATTGGC-TTGCAAGAGCTTCCCG-TTACATGGCTCGGAAG
1 AGCTTCCCGATAATTGGCACT-CAAGAGCTTCCCGATTA-ATGGCTCGCAAG
54140124 AGCTTCCC
1 AGCTTCCC
54140132 ATTTACATGC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
49 4 0.08
50 46 0.92
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (50 bp):
AGCTTCCCGATAATTGGCACTCAAGAGCTTCCCGATTAATGGCTCGCAAG
Found at i:54142725 original size:48 final size:46
Alignment explanation
Indices: 54142622--54142836 Score: 299
Period size: 46 Copynumber: 4.6 Consensus size: 46
54142612 TGTGTGCTAA
* * *
54142622 TGTAAGACATGTCTGGGACATGCATTGGCCA-T-ATTATGAGAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCGG-CATTGA-GATGAAAGCCAG
* * * *
54142668 TGTAAGACATGTTTGGGATATGCATCGGCCTTGAGATATACAAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCGGCATTGAGAT-GA-AAGCCAG
*
54142716 TGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGAAAGCTAG
1 TGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGAAAGCCAG
*
54142762 TGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGAAAGCTAG
1 TGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGAAAGCCAG
54142808 TGTAAGACATGTCTGGGACATGCATCGGC
1 TGTAAGACATGTCTGGGACATGCATCGGC
54142837 CTCTAGATAT
Statistics
Matches: 153, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
45 1 0.01
46 109 0.71
47 3 0.02
48 40 0.26
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (46 bp):
TGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGAAAGCCAG
Found at i:54142853 original size:94 final size:94
Alignment explanation
Indices: 54142617--54142877 Score: 305
Period size: 94 Copynumber: 2.8 Consensus size: 94
54142607 TGATATGTGT
* * * * * *
54142617 GCTAATGTAAGACATGTCTGGGACATGCATTGGCCATA-TTATGAGAGCCAGTGTAAGACATGTT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTAGATAT-AAAGCTAGTGTAAGACATGTT
* * *
54142681 TGGGATATGCATCGGCCTTGAGATATACAA
65 TGGGACATGCATCGGCATTGAGATAGACAA
* * * *
54142711 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGAT-GAAAGCTAGTGTAAGACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTT-AGATATAAAGCTAGTGTAAGACATGTT
54142775 TGGGACATGCATCGGCATTGAGAT-GA-AA
65 TGGGACATGCATCGGCATTGAGATAGACAA
* * * *
54142803 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCTAGATATACAAGCTAATGAAAAACCTGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-TAGATATA-AAGCTAGTGTAAGACATGT
54142868 TTGGGACATG
64 TTGGGACATG
54142878 GCGTCATCTT
Statistics
Matches: 141, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
92 40 0.28
93 3 0.02
94 96 0.68
95 1 0.01
96 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTAGATATAAAGCTAGTGTAAGACATGTTT
GGGACATGCATCGGCATTGAGATAGACAA
Found at i:54142874 original size:140 final size:140
Alignment explanation
Indices: 54142617--54142877 Score: 357
Period size: 140 Copynumber: 1.9 Consensus size: 140
54142607 TGATATGTGT
* * * *
54142617 GCTAATGTAAGACATGTCTGGGACATGCATTGGCCATATTATGAGAGCCAGTGTAAGACATGTTT
1 GCTAATGTAAGACATGTCTGGGACATGCATCGGCCATATGATGAAAGCCAGTGTAAGACATGTCT
* * * *
54142682 GGGATATGCATCGGCCTTGAGATATACAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCAT
66 GGGACATGCATCGGCCTTGAGATATACAAGCCAATGAAAAACATGTCTGGGACATGCATCGGCAT
54142747 TGAGATGAAA
131 TGAGATGAAA
* *
54142757 GCTAGTGTAAGACATGTCTGGGACATGCATCGG-CAT-TGAGATGAAAGCTAGTGTAAGACATGT
1 GCTAATGTAAGACATGTCTGGGACATGCATCGGCCATAT--GATGAAAGCCAGTGTAAGACATGT
* * *
54142820 CTGGGACATGCATCGGCCTCT-AGATATACAAGCTAATGAAAAACCTGTTTGGGACATG
64 CTGGGACATGCATCGGCCT-TGAGATATACAAGCCAATGAAAAACATGTCTGGGACATG
54142878 GCGTCATCTT
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
138 1 0.01
139 3 0.03
140 100 0.95
141 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (140 bp):
GCTAATGTAAGACATGTCTGGGACATGCATCGGCCATATGATGAAAGCCAGTGTAAGACATGTCT
GGGACATGCATCGGCCTTGAGATATACAAGCCAATGAAAAACATGTCTGGGACATGCATCGGCAT
TGAGATGAAA
Found at i:54143033 original size:49 final size:48
Alignment explanation
Indices: 54142656--54143075 Score: 158
Period size: 46 Copynumber: 8.9 Consensus size: 48
54142646 TTGGCCATAT
* * * * * *
54142656 TATGAGAGCCAGTGTAAGACATGTTTGGGATAT--GCATCGGCCTTGAGA
1 TATGAAAGCCAGTGTAAGACCTGTCTAGGACATGAGCATCGACCTT--GA
* * * *
54142704 TAT-ACAAGCCAGTGTAAGACATGTCTGGGACAT--GCATCGGCATTGA
1 TATGA-AAGCCAGTGTAAGACCTGTCTAGGACATGAGCATCGACCTTGA
* * * * * *
54142750 GATGAAAGCTAGTGTAAGACATGTCTGGGACAT--GCATCGGCATTGA
1 TATGAAAGCCAGTGTAAGACCTGTCTAGGACATGAGCATCGACCTTGA
* * * * *
54142796 GATGAAAGCTAGTGTAAGACATGTCTGGGACAT--GCATCGGCCTCTAGA
1 TATGAAAGCCAGTGTAAGACCTGTCTAGGACATGAGCATCGACCT-T-GA
* * * * * * * *
54142844 TAT-ACAAGCTAATGAAAAACCTGTTTGGGACATG-GCGTC-ATCTTG-
1 TATGA-AAGCCAGTGTAAGACCTGTCTAGGACATGAGCATCGACCTTGA
*** * ** * * * *
54142889 T-TGTGTGTCAGTGTAAGATTTGTCTAGGATAT-TGCATTGACAC-CGA
1 TATGAAAGCCAGTGTAAGACCTGTCTAGGACATGAGCATCGAC-CTTGA
* * *
54142935 TAGATGAGAGCCAGTGTAAGACCTGTCTAGGACA-CAGCATCGGCCTTGATA
1 T--ATGAAAGCCAGTGTAAGACCTGTCTAGGACATGAGCATCGACCTTG--A
* *
54142986 TATGAAAGTCAGTGTAAGACCTGTCTAGGACATGA-CATCGACTTTGA
1 TATGAAAGCCAGTGTAAGACCTGTCTAGGACATGAGCATCGACCTTGA
* ** * *
54143033 TGTGCTAGCCAATGTAAGACCATGTCTAGGACATG-GCGTCGAC
1 TATGAAAGCCAGTGTAAGACC-TGTCTAGGACATGAGCATCGAC
54143076 ATCTTATCCC
Statistics
Matches: 297, Mismatches: 54, Indels: 42
0.76 0.14 0.11
Matches are distributed among these distances:
44 20 0.07
45 3 0.01
46 89 0.30
47 22 0.07
48 87 0.29
49 73 0.25
50 1 0.00
51 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (48 bp):
TATGAAAGCCAGTGTAAGACCTGTCTAGGACATGAGCATCGACCTTGA
Found at i:54154102 original size:27 final size:27
Alignment explanation
Indices: 54154072--54154344 Score: 317
Period size: 27 Copynumber: 10.3 Consensus size: 27
54154062 GTAATGACCA
54154072 AAATACCCCCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
*
54154099 AAATA-CCCCA-AGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGATCG
*
54154124 AAATA-CCCTATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
* *
54154150 AAATACCCACATAGGGTAAAAT-AACTG
1 AAATACCCCCATAGGGTAAAATGATC-G
* *
54154177 AAATACCCCTATAGGATAAAATGA-CTG
1 AAATACCCCCATAGGGTAAAATGATC-G
*
54154204 AAATACCCCCATAGGATAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
* * * * * * * *
54154231 AAATGCTCCAATATGATAAAATAACCA
1 AAATACCCCCATAGGGTAAAATGATCG
* *
54154258 AAATACCCCCATAGGG-AAAATGACCA
1 AAATACCCCCATAGGGTAAAATGATCG
54154284 AAATA-CCCCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
*
54154310 AAATACCCCCATAGGGTAAAATGATCA
1 AAATACCCCCATAGGGTAAAATGATCG
54154337 AAATACCC
1 AAATACCC
54154345 TTGTAAGGTA
Statistics
Matches: 213, Mismatches: 26, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
25 33 0.15
26 53 0.25
27 125 0.59
28 2 0.01
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.18
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGATCG
Found at i:54154743 original size:18 final size:18
Alignment explanation
Indices: 54154720--54154762 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
54154710 CGTTTACTGC
54154720 TACTGCACTGTATACCGT
1 TACTGCACTGTATACCGT
54154738 TACTGCACTGTATACCGT
1 TACTGCACTGTATACCGT
54154756 TACTGCA
1 TACTGCA
54154763 AAGGGCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (18 bp):
TACTGCACTGTATACCGT
Found at i:54157878 original size:27 final size:27
Alignment explanation
Indices: 54157539--54157867 Score: 451
Period size: 27 Copynumber: 12.2 Consensus size: 27
54157529 GGGCCGAAGT
*
54157539 AATGACCGAAATACCCCCGTAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* * * *
54157566 AATAATCGAAGTACCCCTATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* *
54157593 AATGACCGAAGTACCCCTATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
54157620 AATGACCGAAATACCCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* * *
54157647 AATGATCAAAATACCCCCATAAGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
** *
54157674 AATGATTGAAATACCCCCATAAGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* * *
54157701 AATGATCGAAATTCTCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
*
54157728 AATGACCAAAATACCCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* * *
54157755 AATGATCGAAATACCCCTATAGGATAA
1 AATGACCGAAATACCCCCATAGGGTAA
* *
54157782 AATGACCAAAATACCCCCATAGGATAA
1 AATGACCGAAATACCCCCATAGGGTAA
*
54157809 AATGACCGAAATACCCCTATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
54157836 AATGACCGAAATACCCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
54157863 AATGA
1 AATGA
54157868 TTGTAATACC
Statistics
Matches: 269, Mismatches: 33, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 269 1.00
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (27 bp):
AATGACCGAAATACCCCCATAGGGTAA
Found at i:54162668 original size:42 final size:41
Alignment explanation
Indices: 54162621--54162775 Score: 195
Period size: 42 Copynumber: 3.7 Consensus size: 41
54162611 AATCATTCCA
*
54162621 ATGCCATATTCCAGATATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACAT-GGATCTCATATCG
* *
54162663 ATGCCAATAGCCCAGCTATGGTCTTACAT-GATTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACATGGA-TCTCATATCG
* * * *
54162705 ATGCCATATCCCAGACATGGTCTTACACGAAATCTCATAACG
1 ATGCCATATCCCAGATATGGTCTTACATG-GATCTCATATCG
*
54162747 AGGCCATATCCCAGATATGGTCTTACATG
1 ATGCCATATCCCAGATATGGTCTTACATG
54162776 TAAACTCATA
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
41 21 0.22
42 55 0.57
43 21 0.22
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (41 bp):
ATGCCATATCCCAGATATGGTCTTACATGGATCTCATATCG
Found at i:54162784 original size:84 final size:84
Alignment explanation
Indices: 54162621--54162785 Score: 215
Period size: 84 Copynumber: 2.0 Consensus size: 84
54162611 AATCATTCCA
* * * ** * * *
54162621 ATGCCATATTCCAGATATGGTCTTACATGGGATCTCATATCGATGCCAATAGCCCAGCTATGGTC
1 ATGCCATATCCCAGACATGGTCTTACACGAAATCTCATAACGAGGCCAATAGCCCAGATATGGTC
**
54162686 TTACATGATTCTCATATCG
66 TTACATGAAACTCATATCG
*
54162705 ATGCCATATCCCAGACATGGTCTTACACGAAATCTCATAACGAGGCC-ATATCCCAGATATGGTC
1 ATGCCATATCCCAGACATGGTCTTACACGAAATCTCATAACGAGGCCAATAGCCCAGATATGGTC
54162769 TTACATGTAAACTCATA
66 TTACATG-AAACTCATA
54162786 ACCCTAATAC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
83 22 0.32
84 47 0.68
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (84 bp):
ATGCCATATCCCAGACATGGTCTTACACGAAATCTCATAACGAGGCCAATAGCCCAGATATGGTC
TTACATGAAACTCATATCG
Found at i:54169739 original size:47 final size:46
Alignment explanation
Indices: 54169663--54169979 Score: 244
Period size: 47 Copynumber: 6.8 Consensus size: 46
54169653 AGGGTGTAAC
54169663 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-CATCAA
* * * *
54169710 GTCGATGCCATGTCCCAGACATGGACTTACACTGACT-ATCGAAATCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC---ATC-AA
* * *
54169759 GCCAACGCCATGTCCCAGACATGGT-TTACACTAGCTC-TCA-CATATA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATC--A-A
* * * *
54169805 CGTGCCAATGCCATATCCCAAACATGGTCTTACACTGGCACATC-TCATA
1 ---GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCA-A
* * *
54169854 GCTGATG-CATGTCCCAGAAAT-GTCTTACACTGGCTTACATC-TCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC-T-CATCATC-AA
* *
54169900 GCCGATG-CATGTCCCATACAT-GTCTTACACTAGCTC-TCATCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCA--TCAA
54169945 TGCCGATGCCATGTCCCAGACAT-GTCTTACACTGG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGG
54169980 TACACAAATA
Statistics
Matches: 218, Mismatches: 31, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
43 2 0.01
44 15 0.07
45 16 0.07
46 52 0.24
47 59 0.27
48 14 0.06
49 47 0.22
50 10 0.05
51 3 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCAA
Found at i:54169943 original size:145 final size:144
Alignment explanation
Indices: 54169667--54169979 Score: 346
Period size: 145 Copynumber: 2.2 Consensus size: 144
54169657 TGTAACGCCG
* * * *
54169667 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAGTCGATGCCATGTCCCAGACAT
1 ATGCCATATCCCAAACATGGTCTTACACTGGCACATCCAT-AAGTCGATGCCATGTCCCAGAAAT
54169732 GGACTTACACTGACTATCGAAATCGAGGCCAACGCCATGTCCCAGACATGGTTTACACTAGCTCT
65 GGACTTACACTGACTATCGAAATCGAGGCCAACGCCATGTCCCAGACATGGTTTACACTAGCTCT
54169797 CACATATACGTGCCA
130 CACATATACGTGCCA
54169812 ATGCCATATCCCAAACATGGTCTTACACTGGCACATCTCAT-AG-CTGATG-CATGTCCCAGAAA
1 ATGCCATATCCCAAACATGGTCTTACACTGGCACATC-CATAAGTC-GATGCCATGTCCCAGAAA
* * ** * * *
54169874 T-GTCTTACACTGGCT-TAC-ATCTCGAGGCCGATG-CATGTCCCATACAT-GTCTTACACTAGC
64 TGGACTTACACTGACTAT-CGAAATCGAGGCCAACGCCATGTCCCAGACATGGT-TTACACTAGC
*
54169934 TCTCATC-TCA-A--TGCCG
127 TCTCA-CAT-ATACGTGCCA
* *
54169950 ATGCCATGTCCCAGACAT-GTCTTACACTGG
1 ATGCCATATCCCAAACATGGTCTTACACTGG
54169980 TACACAAATA
Statistics
Matches: 148, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
137 12 0.08
138 20 0.14
139 2 0.01
140 30 0.20
141 14 0.09
142 13 0.09
143 14 0.09
144 6 0.04
145 34 0.23
146 3 0.02
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (144 bp):
ATGCCATATCCCAAACATGGTCTTACACTGGCACATCCATAAGTCGATGCCATGTCCCAGAAATG
GACTTACACTGACTATCGAAATCGAGGCCAACGCCATGTCCCAGACATGGTTTACACTAGCTCTC
ACATATACGTGCCA
Found at i:54176526 original size:625 final size:625
Alignment explanation
Indices: 54175337--54176586 Score: 2500
Period size: 625 Copynumber: 2.0 Consensus size: 625
54175327 ACCGGTAAGT
54175337 TAGAGAATACAAACCTCGTGTGCCATACCCCAATGCGACAAGGAAACATTGCTCAGATGAACAAT
1 TAGAGAATACAAACCTCGTGTGCCATACCCCAATGCGACAAGGAAACATTGCTCAGATGAACAAT
54175402 TTGGTAAATTCTTTAAATCTTAAAAAAATTACATATTAACTTATTGTTTATTGAAGCTCTATCAC
66 TTGGTAAATTCTTTAAATCTTAAAAAAATTACATATTAACTTATTGTTTATTGAAGCTCTATCAC
54175467 AGATGCCAAACGCAATGAAATTTTTAAAGGAGCTTTTAGCAAATAAGAAAAAGTTGGACGAGGCT
131 AGATGCCAAACGCAATGAAATTTTTAAAGGAGCTTTTAGCAAATAAGAAAAAGTTGGACGAGGCT
54175532 TCACATGTGAAGCTAAACGCAGTTTGCTTAGTTATTCTACATAATAAACTACCCAACAAATTGAA
196 TCACATGTGAAGCTAAACGCAGTTTGCTTAGTTATTCTACATAATAAACTACCCAACAAATTGAA
54175597 AGATCCAGGGAGTTTTACAATTCCTTGCTTAATTGGTAGTTTAGATGTTAATAATGCATTAGCTA
261 AGATCCAGGGAGTTTTACAATTCCTTGCTTAATTGGTAGTTTAGATGTTAATAATGCATTAGCTA
54175662 ATTTAGGGGCTAGTATTAACGTCATGCCTTACCAGATGTTTAAACAATTAGGTCTTGGGAAACCC
326 ATTTAGGGGCTAGTATTAACGTCATGCCTTACCAGATGTTTAAACAATTAGGTCTTGGGAAACCC
54175727 AAACAGACTAGGATGAGCATTCAATTAGCAGATAAAACTATAAGGTTTCCTAGGGGTATTATTGA
391 AAACAGACTAGGATGAGCATTCAATTAGCAGATAAAACTATAAGGTTTCCTAGGGGTATTATTGA
54175792 AGATGTGCTAGATAAAATCGATAAATTTATATTTCCTGTTGACTTCATTGTTCTAGACATAGAGC
456 AGATGTGCTAGATAAAATCGATAAATTTATATTTCCTGTTGACTTCATTGTTCTAGACATAGAGC
54175857 AGGATAGGAACACTCCTTTGATTTTAGGAAGGCCCTTTTTAGCAACTGTTAGAACGATTATTGAT
521 AGGATAGGAACACTCCTTTGATTTTAGGAAGGCCCTTTTTAGCAACTGTTAGAACGATTATTGAT
54175922 GTTGGCACAGGTGAACTCACACTTCATGAGGGAGACGAAA
586 GTTGGCACAGGTGAACTCACACTTCATGAGGGAGACGAAA
54175962 TAGAGAATACAAACCTCGTGTGCCATACCCCAATGCGACAAGGAAACATTGCTCAGATGAACAAT
1 TAGAGAATACAAACCTCGTGTGCCATACCCCAATGCGACAAGGAAACATTGCTCAGATGAACAAT
54176027 TTGGTAAATTCTTTAAATCTTAAAAAAATTACATATTAACTTATTGTTTATTGAAGCTCTATCAC
66 TTGGTAAATTCTTTAAATCTTAAAAAAATTACATATTAACTTATTGTTTATTGAAGCTCTATCAC
54176092 AGATGCCAAACGCAATGAAATTTTTAAAGGAGCTTTTAGCAAATAAGAAAAAGTTGGACGAGGCT
131 AGATGCCAAACGCAATGAAATTTTTAAAGGAGCTTTTAGCAAATAAGAAAAAGTTGGACGAGGCT
54176157 TCACATGTGAAGCTAAACGCAGTTTGCTTAGTTATTCTACATAATAAACTACCCAACAAATTGAA
196 TCACATGTGAAGCTAAACGCAGTTTGCTTAGTTATTCTACATAATAAACTACCCAACAAATTGAA
54176222 AGATCCAGGGAGTTTTACAATTCCTTGCTTAATTGGTAGTTTAGATGTTAATAATGCATTAGCTA
261 AGATCCAGGGAGTTTTACAATTCCTTGCTTAATTGGTAGTTTAGATGTTAATAATGCATTAGCTA
54176287 ATTTAGGGGCTAGTATTAACGTCATGCCTTACCAGATGTTTAAACAATTAGGTCTTGGGAAACCC
326 ATTTAGGGGCTAGTATTAACGTCATGCCTTACCAGATGTTTAAACAATTAGGTCTTGGGAAACCC
54176352 AAACAGACTAGGATGAGCATTCAATTAGCAGATAAAACTATAAGGTTTCCTAGGGGTATTATTGA
391 AAACAGACTAGGATGAGCATTCAATTAGCAGATAAAACTATAAGGTTTCCTAGGGGTATTATTGA
54176417 AGATGTGCTAGATAAAATCGATAAATTTATATTTCCTGTTGACTTCATTGTTCTAGACATAGAGC
456 AGATGTGCTAGATAAAATCGATAAATTTATATTTCCTGTTGACTTCATTGTTCTAGACATAGAGC
54176482 AGGATAGGAACACTCCTTTGATTTTAGGAAGGCCCTTTTTAGCAACTGTTAGAACGATTATTGAT
521 AGGATAGGAACACTCCTTTGATTTTAGGAAGGCCCTTTTTAGCAACTGTTAGAACGATTATTGAT
54176547 GTTGGCACAGGTGAACTCACACTTCATGAGGGAGACGAAA
586 GTTGGCACAGGTGAACTCACACTTCATGAGGGAGACGAAA
54176587 CAGTCACCCT
Statistics
Matches: 625, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
625 625 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (625 bp):
TAGAGAATACAAACCTCGTGTGCCATACCCCAATGCGACAAGGAAACATTGCTCAGATGAACAAT
TTGGTAAATTCTTTAAATCTTAAAAAAATTACATATTAACTTATTGTTTATTGAAGCTCTATCAC
AGATGCCAAACGCAATGAAATTTTTAAAGGAGCTTTTAGCAAATAAGAAAAAGTTGGACGAGGCT
TCACATGTGAAGCTAAACGCAGTTTGCTTAGTTATTCTACATAATAAACTACCCAACAAATTGAA
AGATCCAGGGAGTTTTACAATTCCTTGCTTAATTGGTAGTTTAGATGTTAATAATGCATTAGCTA
ATTTAGGGGCTAGTATTAACGTCATGCCTTACCAGATGTTTAAACAATTAGGTCTTGGGAAACCC
AAACAGACTAGGATGAGCATTCAATTAGCAGATAAAACTATAAGGTTTCCTAGGGGTATTATTGA
AGATGTGCTAGATAAAATCGATAAATTTATATTTCCTGTTGACTTCATTGTTCTAGACATAGAGC
AGGATAGGAACACTCCTTTGATTTTAGGAAGGCCCTTTTTAGCAACTGTTAGAACGATTATTGAT
GTTGGCACAGGTGAACTCACACTTCATGAGGGAGACGAAA
Found at i:54179351 original size:6 final size:6
Alignment explanation
Indices: 54179346--54179426 Score: 87
Period size: 6 Copynumber: 13.8 Consensus size: 6
54179336 ATGATGTTTA
* * * *
54179346 ATTTT- ATTTT- ATCTTT- ATTTTT ATTTTT ATTTTT ATTTTT ATTTTC
1 ATTTTC ATTTTC AT-TTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC
*
54179392 ATTTTC ATTTTC ATTTTC ATTTTA ATTTTC ATTTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
54179427 ATGTTTTTAT
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
5 10 0.14
6 61 0.86
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (6 bp):
ATTTTC
Found at i:54179369 original size:12 final size:12
Alignment explanation
Indices: 54179342--54179437 Score: 95
Period size: 12 Copynumber: 8.0 Consensus size: 12
54179332 GATGATGATG
*
54179342 TTTAATTTTA-T
1 TTTATTTTTATT
*
54179353 TTTATCTTTATT
1 TTTATTTTTATT
54179365 TTTATTTTTATT
1 TTTATTTTTATT
54179377 TTTATTTTTATT
1 TTTATTTTTATT
* *
54179389 TTCATTTTCATT
1 TTTATTTTTATT
* *
54179401 TTCATTTTCATT
1 TTTATTTTTATT
* *
54179413 TTAATTTTCATT
1 TTTATTTTTATT
*
54179425 TTATGTTTTTATT
1 TT-TATTTTTATT
54179438 AATTTCACCT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
11 8 0.11
12 59 0.80
13 7 0.09
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (12 bp):
TTTATTTTTATT
Found at i:54181488 original size:13 final size:13
Alignment explanation
Indices: 54181470--54181509 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
54181460 GAAGTAATCA
54181470 CACACGGGCGTGT
1 CACACGGGCGTGT
*
54181483 CACACGGGCGTGC
1 CACACGGGCGTGT
*
54181496 CACATGGGCGTGT
1 CACACGGGCGTGT
54181509 C
1 C
54181510 CCTACAGAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.15, C:0.33, G:0.38, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:54192089 original size:40 final size:40
Alignment explanation
Indices: 54192052--54192276 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
54192042 GCTACTCGTT
* *
54192052 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
54192092 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
54192132 CAAATGCCTTCGGGCCTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
54192172 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
54192211 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
54192252 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
54192277 CATCATTCAA
Statistics
Matches: 166, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 33 0.20
40 118 0.71
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:54192236 original size:119 final size:120
Alignment explanation
Indices: 54192052--54192276 Score: 296
Period size: 119 Copynumber: 1.9 Consensus size: 120
54192042 GCTACTCGTT
*
54192052 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* * *
54192117 ATTTAGTAAC-TCGCACAAATGCCTTCGGGCCTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
54192172 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
54192234 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
54192277 CATCATTCAA
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
118 4 0.04
119 65 0.71
120 22 0.24
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:54200173 original size:79 final size:82
Alignment explanation
Indices: 54200062--54200246 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
54200052 GCTACTCGTT
* *
54200062 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
54200125 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
54200142 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
54200205 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
54200222 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54200247 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:54200246 original size:40 final size:40
Alignment explanation
Indices: 54200043--54200246 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
54200033 CGGAATTTAA
** *
54200043 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54200083 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
54200123 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54200162 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
54200202 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
54200242 CCGGA
1 CCGGA
54200247 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
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:54208634 original size:47 final size:47
Alignment explanation
Indices: 54208573--54208696 Score: 131
Period size: 47 Copynumber: 2.6 Consensus size: 47
54208563 GTGCGAATAA
* * ** * * * *
54208573 TACCTTGAGTTGGCTACGGGCCATGATTTAGGTATTTTGTGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGATATACATACTTCGGGAGAAGT
* * *
54208620 TACCTTGATTTGGCTATGGGCCATGGTATACATACTTCGGGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGATATACATACTTCGGGAGAAGT
* *
54208667 TACCTTGATTTGGCTACAGGCCATGGTATA
1 TACCTTGATTTGGCTACGGGCCATGATATA
54208697 GGTTCTTATC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 64 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGATATACATACTTCGGGAGAAGT
Found at i:54210375 original size:93 final size:93
Alignment explanation
Indices: 54210263--54210433 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
54210253 GCCCATAAGT
* *
54210263 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54210328 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
54210356 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
54210421 CGAGTTCGGATGC
66 CGAGCTCGGATGC
54210434 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:54210430 original size:46 final size:46
Alignment explanation
Indices: 54210255--54210430 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
54210245 TGTAACCCGC
* *
54210255 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
54210301 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
54210347 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
54210394 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
54210431 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:54212865 original size:30 final size:30
Alignment explanation
Indices: 54212821--54212909 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
54212811 CAAAGATAAC
*
54212821 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
*
54212850 GAGAAACCCGGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGGAATAAAGAAATCCAAG-ATA
* * *
54212880 AAGAGATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
54212910 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 9 0.18
30 34 0.68
31 7 0.14
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:54212869 original size:15 final size:14
Alignment explanation
Indices: 54212821--54212903 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
54212811 CAAAGATAAC
*
54212821 AAGAAAACCGAATA
1 AAGAAACCCGAATA
* *
54212835 AAGAAATCCAAGATA
1 AAGAAACCCGA-ATA
*
54212850 GAGAAACCCGGAATA
1 AAGAAACCC-GAATA
*
54212865 AAGAAATCCAGAATA
1 AAGAAA-CCCGAATA
* * *
54212880 AAGAGATCCAGGATA
1 AAGA-AACCCGAATA
54212895 AAGAAACCC
1 AAGAAACCC
54212904 AAGATACGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.22
15 38 0.70
16 4 0.07
ACGTcount: A:0.55, C:0.17, G:0.18, T:0.10
Consensus pattern (14 bp):
AAGAAACCCGAATA
Found at i:54212909 original size:15 final size:15
Alignment explanation
Indices: 54212832--54212909 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
54212822 AGAAAACCGA
54212832 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
54212847 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
54212861 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
54212876 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
54212892 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
54212907 ATA
1 ATA
54212910 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:54215945 original size:93 final size:93
Alignment explanation
Indices: 54215833--54216004 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
54215823 GCCCATAAGT
* *
54215833 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54215898 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
54215926 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
54215991 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
54216005 CAAATATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:54216000 original size:46 final size:46
Alignment explanation
Indices: 54215825--54216000 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
54215815 TGTAACCCGC
* *
54215825 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
54215871 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
54215917 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
54215964 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
54216001 TGCCCAAATA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:54225751 original size:17 final size:16
Alignment explanation
Indices: 54225729--54225774 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
54225719 TAATTATATA
54225729 TATTAAATATATAAAAT
1 TATTAAATAT-TAAAAT
*
54225746 TATTAATTATTAAAAT
1 TATTAAATATTAAAAT
54225762 CTA-TAAA-ATTAAA
1 -TATTAAATATTAAA
54225775 CTTTAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 6 0.23
16 9 0.35
17 11 0.42
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TATTAAATATTAAAAT
Found at i:54225883 original size:30 final size:30
Alignment explanation
Indices: 54225849--54225916 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
54225839 ATTAAATTTG
*
54225849 TATATTACTAATAC-ATAAAATAATAATATA
1 TATATTACTAATACTA-AAAATAATAATACA
* * *
54225879 TATATAACTATTACTAAAAATATTAATACA
1 TATATTACTAATACTAAAAATAATAATACA
54225909 TATGATTA
1 TAT-ATTA
54225917 GTATTAATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.38
Consensus pattern (30 bp):
TATATTACTAATACTAAAAATAATAATACA
Found at i:54226435 original size:22 final size:22
Alignment explanation
Indices: 54226414--54226460 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
54226404 TAATGAAATA
*
54226414 ATATAT-TTTATAAGTATTAAT
1 ATATATATTTATAACTATTAAT
*
54226435 ATATATATTTATAACTATTATT
1 ATATATATTTATAACTATTAAT
54226457 ATAT
1 ATAT
54226461 TATAGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATATATTTATAACTATTAAT
Found at i:54228678 original size:3 final size:3
Alignment explanation
Indices: 54228670--54228705 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
54228660 CACATATTTG
54228670 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
54228706 ATTTTTTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:54233174 original size:47 final size:46
Alignment explanation
Indices: 54233121--54233383 Score: 240
Period size: 47 Copynumber: 5.6 Consensus size: 46
54233111 TGGGGTAAAG
54233121 TGCCGATGCTATGTCCCAGACATGGTCTTACACTAGCTCAT-ATCTC-A
1 TGCCGATGC-ATGTCCCAGACATGGTCTTACACT-GCTC-TCATCTCAA
* *
54233168 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTC-G
1 TGCCGATG-CATGTCCCAGACATGGTCTTACACTG-CTCTCATCTCAA
* *
54233215 TAGCCGATGCATGTCCCAGACAT-GTCTTACACTGACT-TCTGTCTCGA
1 T-GCCGATGCATGTCCCAGACATGGTCTTACACTG-CTCTC-ATCTCAA
* * * *
54233262 GGCCGATGCATGTCTCAGACAT-GTCTTACACTAGCACTCGTCTCAA
1 TGCCGATGCATGTCCCAGACATGGTCTTACACT-GCTCTCATCTCAA
*
54233308 TACCGATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCA--T-AA
1 TGCCGATG-CATGTCCCAGACATGGTCTTACACT-GCTCTCATCTCAA
*
54233353 TGTGGCCGATGCATGTCTCAGACAT-GTCTTA
1 --T-GCCGATGCATGTCCCAGACATGGTCTTA
54233384 AAATAGCTCA
Statistics
Matches: 187, Mismatches: 16, Indels: 27
0.81 0.07 0.12
Matches are distributed among these distances:
45 4 0.02
46 70 0.37
47 84 0.45
48 29 0.16
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.29
Consensus pattern (46 bp):
TGCCGATGCATGTCCCAGACATGGTCTTACACTGCTCTCATCTCAA
Found at i:54233368 original size:94 final size:91
Alignment explanation
Indices: 54233122--54233383 Score: 275
Period size: 94 Copynumber: 2.8 Consensus size: 91
54233112 GGGGTAAAGT
* * * *
54233122 GCCGATGCTATGTCCCAGACATGGTCTTACACTAG--CTCATATCTCATGCCGATGCCATGTCCC
1 GCCGATGC-ATGTCCCAGACATGGTCTTACACTGGCTCTCATATGT--GGCCGATG-CATGTCTC
*
54233185 AGACATGGTCTTACACTGACTATCATCTCGTA
62 AGACAT-GTCTTACACTGAC-ATCATCTCATA
* * * *
54233217 GCCGATGCATGTCCCAGACAT-GTCTTACACTGACT-TCTGTCTCGAGGCCGATGCATGTCTCAG
1 GCCGATGCATGTCCCAGACATGGTCTTACACTGGCTCTC-ATAT-GTGGCCGATGCATGTCTCAG
*
54233280 ACATGTCTTACACT-AGCACTCGTCTCAATA
64 ACATGTCTTACACTGA-CA-TCATCTC-ATA
54233310 -CCGATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCTCAG
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATGTGGCCGATGCATGTCTCAG
54233374 ACATGTCTTA
64 ACATGTCTTA
54233384 AAATAGCTCA
Statistics
Matches: 142, Mismatches: 14, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
91 2 0.01
92 23 0.16
93 39 0.27
94 65 0.46
95 13 0.09
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (91 bp):
GCCGATGCATGTCCCAGACATGGTCTTACACTGGCTCTCATATGTGGCCGATGCATGTCTCAGAC
ATGTCTTACACTGACATCATCTCATA
Found at i:54233383 original size:140 final size:141
Alignment explanation
Indices: 54233122--54233383 Score: 379
Period size: 140 Copynumber: 1.9 Consensus size: 141
54233112 GGGGTAAAGT
* *
54233122 GCCGATGCTATGTCCCAGACATGGTCTTACACTAGCTCATATCTCATGCCGATGCCATGTCCCAG
1 GCCGATGCTATGTCCCAGACATGGTCTTACACTAGCACATATCTCATACCGATGCCATGTCCCAG
*
54233187 ACATGGTCTTACACTGACTATCATCTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGACT
66 ACATGGTCTTACACTGACTATCATATCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGACT
54233252 TCTGTCTCGAG
131 TCTGTCTCGAG
* * *
54233263 GCCGATGC-ATGTCTCAGACAT-GTCTTACACTAGCAC-TCGTCTCAATACCGATGTCATGTCCC
1 GCCGATGCTATGTCCCAGACATGGTCTTACACTAGCACAT-ATCTC-ATACCGATGCCATGTCCC
* * * *
54233325 AGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATGCATGTCTCAGACATGTCTTA
64 AGACATGGTCTTACACTGACTATCAT-ATCGTAGCCGATGCATGTCCCAGACATGTCTTA
54233384 AAATAGCTCA
Statistics
Matches: 108, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
138 1 0.01
139 18 0.17
140 80 0.74
141 9 0.08
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (141 bp):
GCCGATGCTATGTCCCAGACATGGTCTTACACTAGCACATATCTCATACCGATGCCATGTCCCAG
ACATGGTCTTACACTGACTATCATATCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGACT
TCTGTCTCGAG
Found at i:54235230 original size:21 final size:21
Alignment explanation
Indices: 54235205--54235271 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
54235195 ATTTTATGTA
54235205 ATTATATTATTATCATACATT
1 ATTATATTATTATCATACATT
* *
54235226 TTTATATTATT-TCAT-TATT
1 ATTATATTATTATCATACATT
* *
54235245 ATTATCATTATTATCATATAGT
1 ATTAT-ATTATTATCATACATT
54235267 ATTAT
1 ATTAT
54235272 TAATTGAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 7 0.18
20 10 0.26
21 14 0.36
22 8 0.21
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.57
Consensus pattern (21 bp):
ATTATATTATTATCATACATT
Found at i:54249767 original size:94 final size:93
Alignment explanation
Indices: 54249632--54250240 Score: 593
Period size: 94 Copynumber: 6.5 Consensus size: 93
54249622 ATCAAAGTTT
54249632 CAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATACCCT
1 CAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATACCC-
* *
54249697 TGAAGTTGCAATAGTTTGAAATAAAATTA
65 TGAAGTTGCAATAGGTTGAAATGAAATTA
* * * * *
54249726 CAATAGCAAATCTTATCTCCCTAAAGTTGCAATGAAACAAGATGAAGCTACAAATCCTATATCCC
1 CAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATA-CCC
* * * * * **
54249791 AGAAGTTGCAGT-GGGTCAGATTGAAGCTA
65 TGAAGTTGCAATAGGTTGA-AATGAAATTA
*
54249820 CAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATAAAGCTACAAAT-CTCATACCC
1 CAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCT-ATACCC
* * *
54249884 T-ATAGTTGCAGTGGGTTGGAATG-AATCTA
65 TGA-AGTTGCAATAGGTTGAAATGAAAT-TA
* ** * *
54249913 CAATAGTGAATCTTATCTCCCTGAAGTTATAGTGGAACAAGATTAAGCTACAAATCCTATACCAC
1 CAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATACC-C
** *
54249978 TGAAGTTGCTGTAGG-TCAGAATG-AATCTA
65 TGAAGTTGCAATAGGTTGA-AATGAAAT-TA
** * * * * *
54250007 CCGTAGCGAATCTTATCTCTCTGAAGTTGTAGTGGAACAAGATAAAGCTACAAATTCTATACCCC
1 CAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATA-CCC
* *
54250072 TGAAGTTTCAATAGGTTGGAATGAAATTA
65 TGAAGTTGCAATAGGTTGAAATGAAATTA
* * * * * * *
54250101 CAATGGCAAACCTTATCTCACTGAAGTTGCAATGGAGCAAGAAGAAGTTACAAATCCTATATCCC
1 CAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATA-CCC
* * * *
54250166 TGAAGTTGCAAT-GGAATGGATTGAAACTA
65 TGAAGTTGCAATAGG-TTGAAATGAAATTA
** * * * *
54250195 CAATAGTAAATCTTATCTCCTTGAAGCTGCAATTGAGCAAGATGAA
1 CAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAA
54250241 ACTGTAACAC
Statistics
Matches: 427, Mismatches: 74, Indels: 28
0.81 0.14 0.05
Matches are distributed among these distances:
92 2 0.00
93 80 0.19
94 335 0.78
95 10 0.02
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (93 bp):
CAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATACCCT
GAAGTTGCAATAGGTTGAAATGAAATTA
Found at i:54249778 original size:50 final size:50
Alignment explanation
Indices: 54249724--54249872 Score: 134
Period size: 50 Copynumber: 3.1 Consensus size: 50
54249714 GAAATAAAAT
* *
54249724 TACAATAGCAAATCTTATCTCCCTAAAGTTGCAATGAAACAAGATGAAG-
1 TACAATAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAACAAGATGAAGC
* * **
54249773 --C--TA-CAAATCCTATATCCC-AGAAGTTGCAGTGGGTC-AGATTGAAGC
1 TACAATAGCAAATCTTATCTCCCTA-AAGTTGCAGTGGAACAAGA-TGAAGC
* * * *
54249818 TACAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATAAAGC
1 TACAATAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAACAAGATGAAGC
54249868 TACAA
1 TACAA
54249873 ATCTCATACC
Statistics
Matches: 77, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
43 4 0.05
44 29 0.38
45 2 0.03
47 2 0.03
49 2 0.03
50 35 0.45
51 3 0.04
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (50 bp):
TACAATAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAACAAGATGAAGC
Found at i:54250118 original size:281 final size:282
Alignment explanation
Indices: 54249632--54250220 Score: 688
Period size: 281 Copynumber: 2.1 Consensus size: 282
54249622 ATCAAAGTTT
* * *
54249632 CAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATACCCT
1 CAATAGTGAATCTTATCTCCCTGAAGTTACAGTGGAACAAGATGAAGCTACAAATCCTATACCCT
**
54249697 TGAAGTTGCAATAGTTTGAAATAAAATTACAATAGCAAATCTTATCTCCCTAAAGTTGCAATGAA
66 TGAAGTTGCAATAGTCAGAAATAAAATTACAATAGCAAATCTTATCTCCCTAAAGTTGCAATGAA
* * * * * *
54249762 ACAAGATGAAGCTACAAATCCTATATCCCAGAAGTTGCAGTGGGTCAGATTGAAGCTACAATAGC
131 ACAAGATAAAGCTACAAATCCTATACCCCAGAAGTTGCAATAGGTCAGAATGAAACTACAATAGC
* * * *
54249827 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATA-AAGCTACAAAT-CTCATA-CCCT-ATA
196 AAACCTTATCTCACTGAAGTTGCAATGGAGCAAGA-AGAAGCTACAAATCCT-ATATCCCTGA-A
* ** *
54249888 GTTGCAGTGGGTTGGAATGAATCTA
258 GTTGCAATGGAATGGAATGAAACTA
* *
54249913 CAATAGTGAATCTTATCTCCCTGAAGTTATAGTGGAACAAGATTAAGCTACAAATCCTATACCAC
1 CAATAGTGAATCTTATCTCCCTGAAGTTACAGTGGAACAAGATGAAGCTACAAATCCTATACC-C
** * ** * * * * *
54249978 -TGAAGTTGCTGTAGGTCAG-AAT-GAATCTACCGTAGCGAATCTTATCTCTCTGAAGTTGTAGT
65 TTGAAGTTGCAATA-GTCAGAAATAAAAT-TACAATAGCAAATCTTATCTCCCTAAAGTTGCAAT
* * * * ** *
54250040 GGAACAAGATAAAGCTACAAATTCTATACCCCTGAAGTTTCAATAGGTTGGAATGAAATTACAAT
128 GAAACAAGATAAAGCTACAAATCCTATACCCCAGAAGTTGCAATAGGTCAGAATGAAACTACAAT
* *
54250105 GGCAAACCTTATCTCACTGAAGTTGCAATGGAGCAAGAAGAAGTTACAAATCCTATATCCCTGAA
193 AGCAAACCTTATCTCACTGAAGTTGCAATGGAGCAAGAAGAAGCTACAAATCCTATATCCCTGAA
*
54250170 GTTGCAATGGAATGGATTGAAACTA
258 GTTGCAATGGAATGGAATGAAACTA
* *
54250195 CAATAGTAAATCTTATCTCCTTGAAG
1 CAATAGTGAATCTTATCTCCCTGAAG
54250221 CTGCAATTGA
Statistics
Matches: 258, Mismatches: 43, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
280 4 0.02
281 198 0.77
282 55 0.21
283 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (282 bp):
CAATAGTGAATCTTATCTCCCTGAAGTTACAGTGGAACAAGATGAAGCTACAAATCCTATACCCT
TGAAGTTGCAATAGTCAGAAATAAAATTACAATAGCAAATCTTATCTCCCTAAAGTTGCAATGAA
ACAAGATAAAGCTACAAATCCTATACCCCAGAAGTTGCAATAGGTCAGAATGAAACTACAATAGC
AAACCTTATCTCACTGAAGTTGCAATGGAGCAAGAAGAAGCTACAAATCCTATATCCCTGAAGTT
GCAATGGAATGGAATGAAACTA
Found at i:54250173 original size:188 final size:188
Alignment explanation
Indices: 54249596--54250237 Score: 726
Period size: 188 Copynumber: 3.4 Consensus size: 188
54249586 AGTGACTCTC
* * * *
54249596 ATATCCCTGAAGATGCAGT-GGATCAG-ATCAAAGTTTCAATAGCGAATCTTATCTCCCTGAAGT
1 ATATCCCTGAAGTTGCAGTAGG-TCAGAAT-GAAGCTACAATAGCGAATCTTATCTCCCTGAAGT
* * * * * *
54249659 TGCAGTGGAGCAAGATGAAGCTACAAATCCTATACCCTTGAAGTTGCAATAGTTTGAAATAAAAT
64 TGCAGTGGAGCAAGATAAAGCTACAAATTCTATACCCCTGAAGTTGCAATAGGTTGGAATGAAAT
* *
54249724 TACAATAGCAAATCTTATCTCCCTAAAGTTGCAATGAAACAAGATGAAGCTACAAATCCT
129 TACAATAGCAAATCTTATCTCCCTGAAGTTGCAATGGAACAAGATGAAGCTACAAATCCT
* * *
54249784 ATATCCCAGAAGTTGCAGTGGGTCAGATTGAAGCTACAATAGCGAATCTTATCTCCCTGAAGTTG
1 ATATCCCTGAAGTTGCAGTAGGTCAGAATGAAGCTACAATAGCGAATCTTATCTCCCTGAAGTTG
* *
54249849 CAGTGGAGCAAGATAAAGCTACAAA-TCTCATA-CCCT-ATAGTTGCAGTGGGTTGGAATG-AAT
66 CAGTGGAGCAAGATAAAGCTACAAATTCT-ATACCCCTGA-AGTTGCAATAGGTTGGAATGAAAT
** ** * *
54249910 CTACAATAGTGAATCTTATCTCCCTGAAGTTATAGTGGAACAAGATTAAGCTACAAATCCT
129 -TACAATAGCAAATCTTATCTCCCTGAAGTTGCAATGGAACAAGATGAAGCTACAAATCCT
* * ** *
54249971 ATA-CCACTGAAGTTGCTGTAGGTCAGAATGAATCTACCGTAGCGAATCTTATCTCTCTGAAGTT
1 ATATCC-CTGAAGTTGCAGTAGGTCAGAATGAAGCTACAATAGCGAATCTTATCTCCCTGAAGTT
* * *
54250035 GTAGTGGAACAAGATAAAGCTACAAATTCTATACCCCTGAAGTTTCAATAGGTTGGAATGAAATT
65 GCAGTGGAGCAAGATAAAGCTACAAATTCTATACCCCTGAAGTTGCAATAGGTTGGAATGAAATT
* * * * * *
54250100 ACAATGGCAAACCTTATCTCACTGAAGTTGCAATGGAGCAAGAAGAAGTTACAAATCCT
130 ACAATAGCAAATCTTATCTCCCTGAAGTTGCAATGGAACAAGATGAAGCTACAAATCCT
* * * * ** * *
54250159 ATATCCCTGAAGTTGCAAT-GGAAT-GGATTGAAACTACAATAGTAAATCTTATCTCCTTGAAGC
1 ATATCCCTGAAGTTGCAGTAGG--TCAGAATGAAGCTACAATAGCGAATCTTATCTCCCTGAAGT
* *
54250222 TGCAATTGAGCAAGAT
64 TGCAGTGGAGCAAGAT
54250238 GAAACTGTAA
Statistics
Matches: 378, Mismatches: 63, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
186 6 0.02
187 154 0.41
188 208 0.55
189 10 0.03
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (188 bp):
ATATCCCTGAAGTTGCAGTAGGTCAGAATGAAGCTACAATAGCGAATCTTATCTCCCTGAAGTTG
CAGTGGAGCAAGATAAAGCTACAAATTCTATACCCCTGAAGTTGCAATAGGTTGGAATGAAATTA
CAATAGCAAATCTTATCTCCCTGAAGTTGCAATGGAACAAGATGAAGCTACAAATCCT
Found at i:54250936 original size:6 final size:6
Alignment explanation
Indices: 54250925--54250957 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
54250915 TTAAATTTCA
54250925 AAAAAT AAAAAT --AAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
54250958 ACAAAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.16
6 21 0.84
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:54250944 original size:16 final size:16
Alignment explanation
Indices: 54250925--54250955 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
54250915 TTAAATTTCA
54250925 AAAAATAAAAATAAAT
1 AAAAATAAAAATAAAT
54250941 AAAAATAAAAATAAA
1 AAAAATAAAAATAAA
54250956 AAACAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATAAAAATAAAT
Found at i:54250965 original size:12 final size:12
Alignment explanation
Indices: 54250925--54250957 Score: 52
Period size: 10 Copynumber: 2.9 Consensus size: 12
54250915 TTAAATTTCA
54250925 AAAAATAAAAAT
1 AAAAATAAAAAT
54250937 --AAATAAAAAT
1 AAAAATAAAAAT
54250947 AAAAATAAAAA
1 AAAAATAAAAA
54250958 ACAAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.53
12 9 0.47
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:54253944 original size:33 final size:35
Alignment explanation
Indices: 54253884--54253954 Score: 85
Period size: 33 Copynumber: 2.1 Consensus size: 35
54253874 CTCGTAGTGC
* *
54253884 CATAACCCAGTTATGGTCTTTTCATTAAA-A-TGT
1 CATAACCCAGCTATGGTCTTTACATTAAATATTGT
*
54253917 CATATCCCAGCTATGGTC-TTACAATTAAATATTGT
1 CATAACCCAGCTATGGTCTTTAC-ATTAAATATTGT
54253952 CAT
1 CAT
54253955 GGTCCAACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 3 0.09
33 22 0.69
34 1 0.03
35 6 0.19
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (35 bp):
CATAACCCAGCTATGGTCTTTACATTAAATATTGT
Found at i:54268828 original size:16 final size:16
Alignment explanation
Indices: 54268809--54268855 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
54268799 GATTTTATTC
54268809 CAATCAGATTGATTTT
1 CAATCAGATTGATTTT
**
54268825 CAATTTGATTTGATTTT
1 CAATCAGA-TTGATTTT
*
54268842 -ATTCAGATTGATTT
1 CAATCAGATTGATTT
54268856 AAAGGCTTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 7 0.28
16 10 0.40
17 8 0.32
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.51
Consensus pattern (16 bp):
CAATCAGATTGATTTT
Found at i:54271055 original size:63 final size:63
Alignment explanation
Indices: 54270956--54271082 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
54270946 GGTCAAACTA
**
54270956 GAGTGCTCATGGGCCGGGTCGGGCTCAACTAAAAATTTAGGCCTATTTTTTGGGCTCGGGCTG
1 GAGTGCTCATGGGCCGGGTCGGGCTCAACTAAAAATTTAGGCCTATTCATTGGGCTCGGGCTG
*
54271019 GAGTGCTCATGGGCCGGGTCGGGCTCAACTAAAAATTTAGGCTTATTCATTGGGCTCGGGCTG
1 GAGTGCTCATGGGCCGGGTCGGGCTCAACTAAAAATTTAGGCCTATTCATTGGGCTCGGGCTG
54271082 G
1 G
54271083 GCCGAGCCCA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.28
Consensus pattern (63 bp):
GAGTGCTCATGGGCCGGGTCGGGCTCAACTAAAAATTTAGGCCTATTCATTGGGCTCGGGCTG
Found at i:54271358 original size:30 final size:30
Alignment explanation
Indices: 54271324--54271383 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54271314 ACTAAAATAG
*
54271324 CAAATACCTCTAAAT-TAATAACAAAATTAA
1 CAAATACAT-TAAATATAATAACAAAATTAA
* *
54271354 CAAATGCATTTAATATAATAACAAAATTAA
1 CAAATACATTAAATATAATAACAAAATTAA
54271384 TAATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (30 bp):
CAAATACATTAAATATAATAACAAAATTAA
Found at i:54272620 original size:33 final size:33
Alignment explanation
Indices: 54272578--54272644 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
54272568 ACAACAACTT
54272578 TTCATCTCTATTAAAATAGTCATTAAATAAAAA
1 TTCATCTCTATTAAAATAGTCATTAAATAAAAA
54272611 TTCATCTCTATTAAAATAGTCATTAAATAAAAA
1 TTCATCTCTATTAAAATAGTCATTAAATAAAAA
54272644 T
1 T
54272645 AATAAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.37
Consensus pattern (33 bp):
TTCATCTCTATTAAAATAGTCATTAAATAAAAA
Found at i:54272625 original size:17 final size:18
Alignment explanation
Indices: 54272578--54272633 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
54272568 ACAACAACTT
54272578 TTCATCTCTATTAAAATA
1 TTCATCTCTATTAAAATA
* * *
54272596 GTCAT-T-AAATAAAA-A
1 TTCATCTCTATTAAAATA
54272611 TTCATCTCTATTAAAATA
1 TTCATCTCTATTAAAATA
*
54272629 GTCAT
1 TTCAT
54272634 TAAATAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
15 5 0.18
16 7 0.25
17 7 0.25
18 9 0.32
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.39
Consensus pattern (18 bp):
TTCATCTCTATTAAAATA
Found at i:54272641 original size:16 final size:16
Alignment explanation
Indices: 54272589--54272642 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
54272579 TCATCTCTAT
54272589 TAAAATAGTCATTAAA
1 TAAAATAGTCATTAAA
* * *
54272605 TAAAA-ATTCATCTCTAT
1 TAAAATAGTCAT-T-AAA
54272622 TAAAATAGTCATTAAA
1 TAAAATAGTCATTAAA
54272638 TAAAA
1 TAAAA
54272643 ATAATAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
15 5 0.17
16 12 0.41
17 7 0.24
18 5 0.17
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (16 bp):
TAAAATAGTCATTAAA
Found at i:54272643 original size:17 final size:17
Alignment explanation
Indices: 54272590--54272645 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
54272580 CATCTCTATT
54272590 AAAATAGTCATTAAATA
1 AAAATAGTCATTAAATA
** *
54272607 AAAAT--TCATCTCTATT
1 AAAATAGTCAT-TAAATA
54272623 AAAATAGTCATTAAATA
1 AAAATAGTCATTAAATA
54272640 AAAATA
1 AAAATA
54272646 ATAAATTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 4 0.13
16 8 0.27
17 14 0.47
18 4 0.13
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (17 bp):
AAAATAGTCATTAAATA
Found at i:54274281 original size:67 final size:67
Alignment explanation
Indices: 54274173--54274307 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
54274163 TGTGGCCAAA
*
54274173 AATAGGCCATTTGAAAAGCCAATTTGCCACCCTACTCTCAACCATACATTTCAACCAAATTGGTA
1 AATAGGCCATTTGAAAAGCCAATTTGCCACCCTACTCTCAACCATACATTGCAACCAAATTGGTA
54274238 CC
66 CC
54274240 AATAGGCCATTTGAAAAGCCAATTTGCCACCCTACTCTCAACCATACATTGCAACCAAATTGGTA
1 AATAGGCCATTTGAAAAGCCAATTTGCCACCCTACTCTCAACCATACATTGCAACCAAATTGGTA
54274305 CC
66 CC
54274307 A
1 A
54274308 TTTCAATACA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.35, C:0.30, G:0.11, T:0.24
Consensus pattern (67 bp):
AATAGGCCATTTGAAAAGCCAATTTGCCACCCTACTCTCAACCATACATTGCAACCAAATTGGTA
CC
Found at i:54275353 original size:43 final size:43
Alignment explanation
Indices: 54275203--54275370 Score: 162
Period size: 43 Copynumber: 3.9 Consensus size: 43
54275193 ATATAGCTTG
* * * *
54275203 TACAATGCC-ATATCCCAGATATGGTCTTACATGTTATCA-CA
1 TACAATGCCAATATCCCAGACATGGTCTTACACGTAATCATAA
* * * * * *
54275244 TATCGATGCCACTATCCCAGACAGGGCCTTACACGTAACCGATTA
1 TA-CAATGCCAATATCCCAGACATGGTCTTACACGTAATC-ATAA
* *
54275289 -ACAATGCCAATGTACCAGACATGGTCTTACACGTAATCATAA
1 TACAATGCCAATATCCCAGACATGGTCTTACACGTAATCATAA
* * *
54275331 TACAATGCCAATTTCCCAGACATGGTATTACATGTAATCA
1 TACAATGCCAATATCCCAGACATGGTCTTACACGTAATCA
54275371 CATCTCAGTA
Statistics
Matches: 101, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 2 0.02
42 9 0.09
43 87 0.86
44 2 0.02
45 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (43 bp):
TACAATGCCAATATCCCAGACATGGTCTTACACGTAATCATAA
Found at i:54275362 original size:86 final size:85
Alignment explanation
Indices: 54275204--54275367 Score: 186
Period size: 86 Copynumber: 1.9 Consensus size: 85
54275194 TATAGCTTGT
* * * * * * *
54275204 ACAATGCCATATCCCAGATATGGTCTTACATGTTATCACATATCGATGCCACTATCCCAGACAGG
1 ACAATGCCATATACCAGACATGGTCTTACACGTAATCAAATATCAATGCCAATATCCCAGACAGG
*
54275269 GCCTTACACGTAACCGATTA
66 GCATTACACGTAACCGATTA
* *
54275289 ACAATGCCAATGTACCAGACATGGTCTTACACGTAATCATAATA-CAATGCCAATTTCCCAGACA
1 ACAATGCC-ATATACCAGACATGGTCTTACACGTAATCA-AATATCAATGCCAATATCCCAGACA
* * *
54275353 TGGTATTACATGTAA
64 GGGCATTACACGTAA
54275368 TCACATCTCA
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
85 8 0.12
86 53 0.83
87 3 0.05
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (85 bp):
ACAATGCCATATACCAGACATGGTCTTACACGTAATCAAATATCAATGCCAATATCCCAGACAGG
GCATTACACGTAACCGATTA
Found at i:54278268 original size:17 final size:16
Alignment explanation
Indices: 54278246--54278279 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54278236 GGGGATGGTG
54278246 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
54278263 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
54278279 T
1 T
54278280 AATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:54283075 original size:20 final size:20
Alignment explanation
Indices: 54283050--54283091 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
54283040 GTATCAAATC
54283050 GACAAATTAAAAACATTCTT
1 GACAAATTAAAAACATTCTT
54283070 GACAAATTAAAAACATTCTT
1 GACAAATTAAAAACATTCTT
54283090 GA
1 GA
54283092 GAAGGTTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (20 bp):
GACAAATTAAAAACATTCTT
Found at i:54290671 original size:19 final size:18
Alignment explanation
Indices: 54290643--54290704 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
54290633 CATTTTTCAT
* *
54290643 TTTTTCATTTTCTAATTA
1 TTTTTAATTTTTTAATTA
*
54290661 GTTTTTAATTTTTTAATATTT
1 -TTTTTAATTTTTT-A-ATTA
54290682 TTTTTGAATTTTTTAATTA
1 TTTTT-AATTTTTTAATTA
54290701 TTTT
1 TTTT
54290705 CTGACATGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 18 0.50
20 7 0.19
21 11 0.31
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTTAATTTTTTAATTA
Found at i:54290686 original size:21 final size:22
Alignment explanation
Indices: 54290662--54290704 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
54290652 TTCTAATTAG
54290662 TTTTT-AATTTTTTAA-TATTT
1 TTTTTGAATTTTTTAATTATTT
54290682 TTTTTGAATTTTTTAATTATTT
1 TTTTTGAATTTTTTAATTATTT
54290704 T
1 T
54290705 CTGACATGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTGAATTTTTTAATTATTT
Found at i:54291585 original size:31 final size:31
Alignment explanation
Indices: 54291550--54291608 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
54291540 GTCATTGAAC
54291550 TATTCAAAAGTTTTCATTTAAGTCACTAAAA
1 TATTCAAAAGTTTTCATTTAAGTCACTAAAA
* *
54291581 TATTCAAAAGTTTTTATTTAAGTTACTA
1 TATTCAAAAGTTTTCATTTAAGTCACTA
54291609 GATTGTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (31 bp):
TATTCAAAAGTTTTCATTTAAGTCACTAAAA
Found at i:54295395 original size:25 final size:25
Alignment explanation
Indices: 54295364--54295431 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 25
54295354 TGTAAACAGT
* *
54295364 AAGCTCATGGGAGCTGAATAACGGG
1 AAGCTCATGAGAGCTGAATAACGAG
54295389 AAGCTCA-GACGAGCTGAATAACGAG
1 AAGCTCATGA-GAGCTGAATAACGAG
*
54295414 AAGCTCATAAGAGCTGAA
1 AAGCTCATGAGAGCTGAA
54295432 ATCGGTGACC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 36 0.95
26 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.15
Consensus pattern (25 bp):
AAGCTCATGAGAGCTGAATAACGAG
Found at i:54296949 original size:20 final size:22
Alignment explanation
Indices: 54296907--54296951 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
54296897 TTTTTTCCAT
54296907 AAAAATATTAACAAATTAGAAAA
1 AAAAATATTAACAAATTA-AAAA
*
54296930 AAAAATATTAA-ATATTAAAAA
1 AAAAATATTAACAAATTAAAAA
54296951 A
1 A
54296952 TGAAAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 5 0.24
23 11 0.52
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAAATATTAACAAATTAAAAA
Found at i:54297005 original size:10 final size:10
Alignment explanation
Indices: 54296990--54297092 Score: 63
Period size: 10 Copynumber: 10.4 Consensus size: 10
54296980 ATCAAAATAT
*
54296990 AAAAATTCTA
1 AAAAATTATA
*
54297000 ATAAATTATA
1 AAAAATTATA
54297010 AAAAATTAT-
1 AAAAATTATA
54297019 -AAAATTAATA
1 AAAAATT-ATA
*
54297029 AAAAATATTTA
1 AAAAAT-TATA
*
54297040 AAATATT-TA
1 AAAAATTATA
**
54297049 AAATTTTAT-
1 AAAAATTATA
54297058 AAAAATGTAT-
1 AAAAAT-TATA
*
54297068 TAAAATTATA
1 AAAAATTATA
*
54297078 TAAAAATCATA
1 -AAAAATTATA
54297089 AAAA
1 AAAA
54297093 CTTTAACTAG
Statistics
Matches: 74, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
8 6 0.08
9 17 0.23
10 30 0.41
11 20 0.27
12 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (10 bp):
AAAAATTATA
Found at i:54297617 original size:10 final size:9
Alignment explanation
Indices: 54297580--54297685 Score: 69
Period size: 9 Copynumber: 11.7 Consensus size: 9
54297570 AATATTTTAA
54297580 ATAA-TTTT
1 ATAATTTTT
*
54297588 ATCATTTATT
1 ATAATTT-TT
*
54297598 ATAATATTT
1 ATAATTTTT
54297607 ATAAATTTTT
1 AT-AATTTTT
54297617 ATAATTTTAT
1 ATAATTTT-T
54297627 ATCAA-TTTT
1 AT-AATTTTT
*
54297636 ATTATTTTT
1 ATAATTTTT
*
54297645 -TAGATATTT
1 ATA-ATTTTT
54297654 AT-ATTTTAT
1 ATAATTTT-T
*
54297663 ATTATTTTT
1 ATAATTTTT
*
54297672 CT-ATTTTT
1 ATAATTTTT
54297680 ATAATT
1 ATAATT
54297686 ATTTTTACAG
Statistics
Matches: 77, Mismatches: 10, Indels: 21
0.71 0.09 0.19
Matches are distributed among these distances:
8 16 0.21
9 32 0.42
10 27 0.35
11 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:54297635 original size:11 final size:10
Alignment explanation
Indices: 54297564--54297637 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 10
54297554 TACGTTTTTT
*
54297564 ATTTTAAAT-
1 ATTTTATATA
*
54297573 ATTTTAAATA
1 ATTTTATATA
*
54297583 A-TTT-TATC
1 ATTTTATATA
54297591 A-TTTATTATA
1 ATTTTA-TATA
54297601 ATATTTATA-A
1 AT-TTTATATA
54297611 ATTTT-TATA
1 ATTTTATATA
54297620 ATTTTATATCA
1 ATTTTATAT-A
54297631 ATTTTAT
1 ATTTTAT
54297638 TATTTTTTAG
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
8 8 0.15
9 21 0.39
10 11 0.20
11 10 0.19
12 4 0.07
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (10 bp):
ATTTTATATA
Found at i:54297635 original size:19 final size:18
Alignment explanation
Indices: 54297580--54297683 Score: 70
Period size: 19 Copynumber: 5.7 Consensus size: 18
54297570 AATATTTTAA
*
54297580 ATAATTTTAT-CATTTATT
1 ATAATTTTATAAATTT-TT
54297598 ATAATATTTATAAATTTTT
1 ATAAT-TTTATAAATTTTT
54297617 ATAATTTTATATCAA-TTTT
1 ATAATTTTATA--AATTTTT
* * * *
54297636 ATTATTTTTTAGATATTT
1 ATAATTTTATAAATTTTT
*
54297654 AT-ATTTTATATTATTTTT
1 ATAATTTTATA-AATTTTT
* *
54297672 CTATTTTTATAA
1 ATAATTTTATAA
54297684 TTATTTTTAC
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
17 8 0.12
18 22 0.32
19 32 0.47
20 6 0.09
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (18 bp):
ATAATTTTATAAATTTTT
Found at i:54297689 original size:36 final size:38
Alignment explanation
Indices: 54297604--54297689 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 38
54297594 TATTATAATA
54297604 TTTATAAATT-TTTATAATTTTATATCAATTTTATTATT
1 TTTAT-AATTATTTATAATTTTATATCAATTTTATTATT
*
54297642 TTT-TAGA-TATTTAT-ATTTTATAT-TATTTT-TCTATT
1 TTTATA-ATTATTTATAATTTTATATCAATTTTAT-TATT
54297677 TTTATAATTATTT
1 TTTATAATTATTT
54297690 TTACAGGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
34 1 0.02
35 13 0.31
36 18 0.43
37 7 0.17
38 3 0.07
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.66
Consensus pattern (38 bp):
TTTATAATTATTTATAATTTTATATCAATTTTATTATT
Found at i:54303861 original size:22 final size:22
Alignment explanation
Indices: 54303828--54303871 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
54303818 AATTGAATTC
*
54303828 AAATTTTAAAATATGAAATATA
1 AAATTTTAAAATATCAAATATA
*
54303850 AAATTATT-AAATTTCAAATATA
1 AAATT-TTAAAATATCAAATATA
54303872 CAAAAAGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AAATTTTAAAATATCAAATATA
Found at i:54305086 original size:21 final size:21
Alignment explanation
Indices: 54305061--54305125 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
54305051 TAGCCTTCAG
54305061 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
** * *
54305082 GCTT-CAATTAGC-CTT-CGG
1 GCTTCCGTTTAGCACTTATGT
*
54305100 GCTTCCGTTCAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
54305121 GCTTC
1 GCTTC
54305126 AGTTAGACTT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
18 5 0.16
19 8 0.25
20 9 0.28
21 10 0.31
ACGTcount: A:0.14, C:0.28, G:0.20, T:0.38
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTATGT
Found at i:54305093 original size:39 final size:39
Alignment explanation
Indices: 54305043--54305143 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
54305033 GCTCTGGTGA
* *
54305043 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTCAGCACTTATGT
*
54305082 GCTTCAATTAGCCTTCGGGCTTCCGTTCAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTCAGCACTTATGT
*
54305121 GCTTCAGTTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
54305144 AGATCACGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.15, C:0.27, G:0.22, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTCAGCACTTATGT
Found at i:54305144 original size:18 final size:18
Alignment explanation
Indices: 54305043--54305145 Score: 62
Period size: 18 Copynumber: 5.4 Consensus size: 18
54305033 GCTCTGGTGA
* *
54305043 GCTTCAGTTAGCCTTCAG
1 GCTTCAGTTAGACTTCGG
* * *
54305061 GCTTCCGTTTAGCACTTATGT
1 GCTTCAG-TTAG-ACTT-CGG
* *
54305082 GCTTCAATTAGCCTTCGG
1 GCTTCAGTTAGACTTCGG
* * *
54305100 GCTTCCGTTCAGCACTTATGT
1 GCTTCAGTT-AG-ACTT-CGG
54305121 GCTTCAGTTAGACTTCGG
1 GCTTCAGTTAGACTTCGG
54305139 GCTTCAG
1 GCTTCAG
54305146 ATCACGATGT
Statistics
Matches: 61, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
18 22 0.36
19 13 0.21
20 12 0.20
21 14 0.23
ACGTcount: A:0.16, C:0.26, G:0.22, T:0.36
Consensus pattern (18 bp):
GCTTCAGTTAGACTTCGG
Found at i:54313762 original size:23 final size:24
Alignment explanation
Indices: 54313671--54313764 Score: 86
Period size: 24 Copynumber: 3.9 Consensus size: 24
54313661 TTTAATAACA
*
54313671 TTGAATTTTAGAAT-TTTTATATTT
1 TTGAATTTTA-AATATTTTTTATTT
54313695 TT-ATATTTTTAAAATATTTTTTATTT
1 TTGA-A-TTTT-AAATATTTTTTATTT
* *
54313721 TTGAATTTTAAAGAGTTTTTATTT
1 TTGAATTTTAAATATTTTTTATTT
* *
54313745 TT-CATTTTATATATTTTTTA
1 TTGAATTTTAAATATTTTTTA
54313765 CAAATTATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
23 15 0.26
24 18 0.31
25 11 0.19
26 13 0.22
27 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (24 bp):
TTGAATTTTAAATATTTTTTATTT
Found at i:54320928 original size:88 final size:87
Alignment explanation
Indices: 54320684--54320938 Score: 237
Period size: 91 Copynumber: 2.8 Consensus size: 87
54320674 ATTTAAAAAA
* * * **
54320684 AAAAAGAAAAAGTAATTAAGCCCCTATTTTTTTTACATTCAATTGGGTACTTGAACTTTTAAAAT
1 AAAAA-AAAAAGTAATTAAACCCCTATTTTTTTCAC-TT-AATTGAGTACTTGAACTACTAAAAT
* *
54320749 GCATAAAAAAATGCCCTTAAACTTTTT
63 GCATAAAAAAAAGCCCTCAAAC--TTT
* * * *
54320776 CAAAAAAAAAGTAATTAAACTTCTTCT-TTTTTTTCACTTAATT-AGGTACTTGAACTGCCAAAA
1 AAAAAAAAAAGTAATTAAAC--C-CCTATTTTTTTCACTTAATTGA-GTACTTGAACTACTAAAA
*
54320839 TGCATAAAAAAAAGAACTCTCAAAC-TT
62 TGCATAAAAAAAAG--CCCTCAAACTTT
* * * *
54320866 AAAAAAAAAAGCAATTAAACCCCTATTTTTTTCACTTAATTGAGTATTTAAACTACTAAAATGTA
1 AAAAAAAAAAGTAATTAAACCCCTATTTTTTTCACTTAATTGAGTACTTGAACTACTAAAATGCA
*
54320931 TTAAAAAA
66 TAAAAAAA
54320939 GGCTAGCGAC
Statistics
Matches: 135, Mismatches: 20, Indels: 20
0.77 0.11 0.11
Matches are distributed among these distances:
87 2 0.01
88 41 0.30
89 1 0.01
90 20 0.15
91 46 0.34
92 6 0.04
93 17 0.13
94 2 0.01
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.34
Consensus pattern (87 bp):
AAAAAAAAAAGTAATTAAACCCCTATTTTTTTCACTTAATTGAGTACTTGAACTACTAAAATGCA
TAAAAAAAAGCCCTCAAACTTT
Found at i:54322942 original size:27 final size:27
Alignment explanation
Indices: 54322904--54322958 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
54322894 ATGGGAACAC
54322904 ACACCTTGAATAATGCATATAGCTCAA
1 ACACCTTGAATAATGCATATAGCTCAA
54322931 ACACCTTGAATAATGCATATAGCTCAA
1 ACACCTTGAATAATGCATATAGCTCAA
54322958 A
1 A
54322959 AGTTGTCTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (27 bp):
ACACCTTGAATAATGCATATAGCTCAA
Found at i:54325120 original size:33 final size:38
Alignment explanation
Indices: 54325083--54325161 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 38
54325073 ATTGTATTAG
54325083 TTATATTA-TATTT-TT-T-AA-AATATTTATTTATTTT
1 TTATATTATTATTTGTTGTCAATAATATTT-TTTATTTT
54325117 TATATATTATTATTTGTTGTCAATAATATTTTTTATTTT
1 T-TATATTATTATTTGTTGTCAATAATATTTTTTATTTT
54325156 TATATA
1 T-TATA
54325162 AAATTTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
34 1 0.03
35 7 0.18
36 5 0.13
37 2 0.05
38 1 0.03
39 16 0.41
40 7 0.18
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.65
Consensus pattern (38 bp):
TTATATTATTATTTGTTGTCAATAATATTTTTTATTTT
Found at i:54325129 original size:20 final size:20
Alignment explanation
Indices: 54325086--54325162 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
54325076 GTATTAGTTA
*
54325086 TATTATATTTTT-TAAAATATT
1 TATT-TATTTTTATATAATA-T
*
54325107 TATTTATTTTTATATATTAT
1 TATTTATTTTTATATAATAT
* * *
54325127 TATTTGTTGTCA-ATAATAT
1 TATTTATTTTTATATAATAT
*
54325146 TTTTTATTTTTATATAA
1 TATTTATTTTTATATAA
54325163 AATTTAAATT
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
19 14 0.32
20 21 0.48
21 9 0.20
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (20 bp):
TATTTATTTTTATATAATAT
Found at i:54325217 original size:23 final size:22
Alignment explanation
Indices: 54325165--54325221 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
54325155 TTATATAAAA
*
54325165 TTTAAATTTATTATTATATTTT
1 TTTAAATTTTTTATTATATTTT
*
54325187 TTAAAAATATTTTTA-TATATTTCT
1 TT-TAAAT-TTTTTATTATATTT-T
54325211 TTTAAATTTTT
1 TTTAAATTTTT
54325222 AGAGTTAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 6 0.21
23 15 0.52
24 8 0.28
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTAAATTTTTTATTATATTTT
Found at i:54332553 original size:38 final size:38
Alignment explanation
Indices: 54332496--54332658 Score: 220
Period size: 38 Copynumber: 4.2 Consensus size: 38
54332486 TCGAAATATG
54332496 ATATCCGGGCTTAAAATCCCGCAGGCTTCGTGCTGGTAAT
1 ATATCCGGG-TT-AAATCCCGCAGGCTTCGTGCTGGTAAT
* **
54332536 ATAACCGGGTTAAATCCCGCAGGC-TCTGTTTTGGTAAT
1 ATATCCGGGTTAAATCCCGCAGGCTTC-GTGCTGGTAAT
*
54332574 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATT
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAT
* * *
54332612 ATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATT
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAT
*
54332650 ATATTCGGG
1 ATATCCGGG
54332659 CCTTTGAGCC
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
37 2 0.02
38 97 0.87
39 4 0.04
40 8 0.07
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (38 bp):
ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAT
Found at i:54332647 original size:76 final size:78
Alignment explanation
Indices: 54332496--54332659 Score: 244
Period size: 76 Copynumber: 2.1 Consensus size: 78
54332486 TCGAAATATG
54332496 ATATCCGGGCTTAAAATCCCGCAGGCTTCGTGCTGGTAATATAACCGGGTTAAATCCCGCAGGCT
1 ATATCCGGGCTTAAAATCCCGCAGGCTTCGTGCTGGTAATATAACCGGGTTAAATCCCGCAGGCT
**
54332561 CTGTTTTGGTAAT
66 CTGTGCTGGTAAT
* *
54332574 ATATCCGGG-TT-AAATCCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGC-
1 ATATCCGGGCTTAAAATCCCGCAGGCTTCGTGCTGGTAATATAACCGGGTTAAATCCCGCAGGCT
*
54332636 CTAGTGCTGGTATT
66 CT-GTGCTGGTAAT
*
54332650 ATATTCGGGC
1 ATATCCGGGC
54332660 CTTTGAGCCT
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
75 2 0.03
76 65 0.83
77 2 0.03
78 9 0.12
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (78 bp):
ATATCCGGGCTTAAAATCCCGCAGGCTTCGTGCTGGTAATATAACCGGGTTAAATCCCGCAGGCT
CTGTGCTGGTAAT
Found at i:54332731 original size:46 final size:44
Alignment explanation
Indices: 54332651--54332764 Score: 144
Period size: 46 Copynumber: 2.6 Consensus size: 44
54332641 GCTGGTATTA
* *
54332651 TATTCGGGCCTTT-GAGCCTAGCAGACTATTATGCCGGTGAGACAT
1 TATTCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCGGTGA-A-AT
54332696 TATTCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCGGTGAAAT
1 TATTCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCGGTGAAAT
* *
54332740 GATATCAGGCC--TCGAGCCTAGCAGG
1 TAT-TCGGGCCTTTCGAGCCTAGCAGG
54332765 TGAAATACCG
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
43 14 0.22
44 4 0.06
45 20 0.32
46 25 0.40
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (44 bp):
TATTCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCGGTGAAAT
Found at i:54334592 original size:54 final size:54
Alignment explanation
Indices: 54334515--54334623 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
54334505 GGGTATTCAA
54334515 ATCATTTCATTTTGATACAGAAACAGTAACAATTTTCATCATTTCATTTATCAT
1 ATCATTTCATTTTGATACAGAAACAGTAACAATTTTCATCATTTCATTTATCAT
54334569 ATCATTTCATTTTGATACAGAAACAGTAACAATTTTCATCATTTCATTTATCAT
1 ATCATTTCATTTTGATACAGAAACAGTAACAATTTTCATCATTTCATTTATCAT
54334623 A
1 A
54334624 CATGCTAACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (54 bp):
ATCATTTCATTTTGATACAGAAACAGTAACAATTTTCATCATTTCATTTATCAT
Found at i:54338141 original size:138 final size:137
Alignment explanation
Indices: 54337879--54338145 Score: 320
Period size: 138 Copynumber: 1.9 Consensus size: 137
54337869 ATCAAGAGCG
54337879 AAGCTCCAATAGTCATACTAAGGCTCAAAGGAAAAAAGCCGCAACCTCCAACACAATTAGCGAAA
1 AAGCTCCAATAGTCATACTAAGGCTCAAAGGAAAAAAGCCGCAACCTCCAACACAATTAGCGAAA
* * * * * * * *
54337944 ACAAAGCTCCCAGTTGTCAAACTAAGGTTTGCAGGCAAAGAGCCACAGCCTCTACCACAATTAGT
66 ACAAAGCTCCCAGCTGTCAAACTAAAGCTTACAAGCAAAGAGCCACAGCATCCAACACAATTAGT
54338009 GAGAGTA
131 GAGAGTA
* * ** * * *
54338016 AAGCTCCTAATTGTCATACTAAGGCTCACAGGCGAAGAGCCGCAGCCTCCAACACAATTAGCGAG
1 AAGCTCC-AATAGTCATACTAAGGCTCAAAGGAAAAAAGCCGCAACCTCCAACACAATTAGCGAA
** * * * *
54338081 AGTAAAGCTCTCAGCTGTCATACTAAAGCTTACAAG-AGAAGAGCCGCAGTATCCAACACAATTA
65 AACAAAGCTCCCAGCTGTCAAACTAAAGCTTACAAGCA-AAGAGCCACAGCATCCAACACAATTA
54338145 G
129 G
54338146 CAGAAGCAAA
Statistics
Matches: 107, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
137 8 0.07
138 99 0.93
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (137 bp):
AAGCTCCAATAGTCATACTAAGGCTCAAAGGAAAAAAGCCGCAACCTCCAACACAATTAGCGAAA
ACAAAGCTCCCAGCTGTCAAACTAAAGCTTACAAGCAAAGAGCCACAGCATCCAACACAATTAGT
GAGAGTA
Found at i:54338165 original size:69 final size:69
Alignment explanation
Indices: 54337721--54338176 Score: 274
Period size: 69 Copynumber: 6.6 Consensus size: 69
54337711 CCACAGATTT
* * * * * * * * *
54337721 CAACACAGTCAGCGAGAGCAAAGCTTCCAGCTGTCATAATAAGGCTTGCAGGCGAAAAGCCGTAG
1 CAACACAATTAGCGAGAGCAAAGCTCCCAGCTGTCATACTAAAGCTTACAGGAGAAGAGCCGCAG
54337786 CCTC
66 CCTC
** * * * * * * * * * ** * *
54337790 CAACGTAGTTAGCAAAAGTAAAGCTCCTAACTATCACACTAAATCTTGTAGG-GAAAGAACTGCA
1 CAACACAATTAGCGAGAGCAAAGCTCCCAGCTGTCATACTAAAGCTTACAGGAG-AAGAGCCGCA
*
54337854 ACCTC
65 GCCTC
* * * * * * * * * * * *
54337859 CATCATAGTTATCAAGAGCGAAGCT-CCA-ATAGTCATACTAAGGCTCAAAGGAAAAAAGCCGCA
1 CAACACAATTAGCGAGAGCAAAGCTCCCAGCT-GTCATACTAAAGCTTACAGGAGAAGAGCCGCA
*
54337922 ACCTC
65 GCCTC
* * * * * * * *
54337927 CAACACAATTAGCGAAAACAAAGCTCCCAGTTGTCAAACTAAGGTTTGCAGGCA-AAGAGCCACA
1 CAACACAATTAGCGAGAGCAAAGCTCCCAGCTGTCATACTAAAGCTTACAGG-AGAAGAGCCGCA
54337991 GCCTC
65 GCCTC
* * * * * ** * * *
54337996 TACCACAATTAGTGAGAGTAAAGCTCCTAATTGTCATACTAAGGCTCACAGGCGAAGAGCCGCAG
1 CAACACAATTAGCGAGAGCAAAGCTCCCAGCTGTCATACTAAAGCTTACAGGAGAAGAGCCGCAG
54338061 CCTC
66 CCTC
* * *
54338065 CAACACAATTAGCGAGAGTAAAGCTCTCAGCTGTCATACTAAAGCTTACAAGAGAAGAGCCGCAG
1 CAACACAATTAGCGAGAGCAAAGCTCCCAGCTGTCATACTAAAGCTTACAGGAGAAGAGCCGCAG
**
54338130 TATC
66 CCTC
* *
54338134 CAACACAATTAGC-AGAAGCAAAGCTCCCAGCTGCCATATTAAA
1 CAACACAATTAGCGAG-AGCAAAGCTCCCAGCTGTCATACTAAA
54338177 ACTAGTAGGT
Statistics
Matches: 292, Mismatches: 87, Indels: 16
0.74 0.22 0.04
Matches are distributed among these distances:
67 1 0.00
68 47 0.16
69 242 0.83
70 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (69 bp):
CAACACAATTAGCGAGAGCAAAGCTCCCAGCTGTCATACTAAAGCTTACAGGAGAAGAGCCGCAG
CCTC
Found at i:54338377 original size:57 final size:57
Alignment explanation
Indices: 54338249--54338395 Score: 170
Period size: 57 Copynumber: 2.6 Consensus size: 57
54338239 ACAATCCTCT
* * * *
54338249 AAAATTTTCTAAGAATAAAAAAGTCCGCAGAGTTACATTCCCAACTTGTTACTTTAG
1 AAAATTTTCTAAGTATAAAAAAGTTCGCAGAGTCACATTCCCAACTTATTACTTTAG
** * * *
54338306 AAAAACTTCTAAGTATAAAAAAGTTCGCAGAGTCACATTCCCAGCTTATTATTTTTG
1 AAAATTTTCTAAGTATAAAAAAGTTCGCAGAGTCACATTCCCAACTTATTACTTTAG
* * * *
54338363 AAAGTTTTCCAAGTATAAAATAGCTCGCA-AGTC
1 AAAATTTTCTAAGTATAAAAAAGTTCGCAGAGTC
54338396 CAAATTTGTA
Statistics
Matches: 75, Mismatches: 15, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
56 4 0.05
57 71 0.95
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (57 bp):
AAAATTTTCTAAGTATAAAAAAGTTCGCAGAGTCACATTCCCAACTTATTACTTTAG
Found at i:54354334 original size:27 final size:27
Alignment explanation
Indices: 54354296--54354353 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
54354286 CGAGGGAAAT
54354296 AAAAGTTTT-GGGGGAAAACAAAAGTAA
1 AAAAGTTTTGGGGGGAAAACAAAAG-AA
* *
54354323 AAATGTTTTGGGGGGAAAATAAAAGAA
1 AAAAGTTTTGGGGGGAAAACAAAAGAA
54354350 AAAA
1 AAAA
54354354 AAATGTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.53, C:0.02, G:0.26, T:0.19
Consensus pattern (27 bp):
AAAAGTTTTGGGGGGAAAACAAAAGAA
Found at i:54355427 original size:50 final size:50
Alignment explanation
Indices: 54355369--54355465 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
54355359 AACACAACAA
* *
54355369 AGGCTTTAGCCTCAGCATAAATAGAGCATTATGACACGTTAACAATTAGT
1 AGGCTTTAGACTCAGCATAAATAGAACATTATGACACGTTAACAATTAGT
* * *
54355419 AGGCTTTAGACTTATCATAAATAGAACATTATGACATGTTAACAATT
1 AGGCTTTAGACTCAGCATAAATAGAACATTATGACACGTTAACAATT
54355466 GACATTGTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (50 bp):
AGGCTTTAGACTCAGCATAAATAGAACATTATGACACGTTAACAATTAGT
Found at i:54357619 original size:53 final size:53
Alignment explanation
Indices: 54357538--54357638 Score: 125
Period size: 53 Copynumber: 1.9 Consensus size: 53
54357528 AATTTAGAAT
* *
54357538 AAATATTATATATATATAATAGTGTAAAATAACA-AAGTATATATAAAAACTCCA
1 AAATAATATATATATATAATAGTGTAAAATAA-ATAA-TACATATAAAAACTCCA
* * *
54357592 AAATAATA-ATATGTATGATAGTTTAAAATAAATAATACATATAAAAA
1 AAATAATATATATATATAATAGTGTAAAATAAATAATACATATAAAAA
54357639 TTAAAAAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
52 12 0.29
53 22 0.54
54 7 0.17
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.32
Consensus pattern (53 bp):
AAATAATATATATATATAATAGTGTAAAATAAATAATACATATAAAAACTCCA
Found at i:54359478 original size:45 final size:45
Alignment explanation
Indices: 54359316--54359733 Score: 162
Period size: 44 Copynumber: 9.7 Consensus size: 45
54359306 TTTCTTTCAG
* * *
54359316 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAC
1 TCTGCCCCACTGCAACTTCAGAGAGATAAGACTTGTAGCTTCAAC
* * * *
54359361 T-TGCCCCACTGCAATTTTAGAGGGATAAGGACTCGTAGCTTCAAC
1 TCTGCCCCACTGCAACTTCAGAGAGATAA-GACTTGTAGCTTCAAC
* * * * * *
54359406 -CTACCCCACTACAACTTCAG-GGGATAAGATTTATAGCTTTAAC
1 TCTGCCCCACTGCAACTTCAGAGAGATAAGACTTGTAGCTTCAAC
* * * * * *
54359449 TCTGCTCTACTGCAATTTCAGAGAGATAAGATTTGCTATCTTCGA-
1 TCTGCCCCACTGCAACTTCAGAGAGATAAGACTTG-TAGCTTCAAC
* * * *
54359494 TCCGCTCCACTGCAA--T-----AG----GACTCGTAACTTCAAC
1 TCTGCCCCACTGCAACTTCAGAGAGATAAGACTTGTAGCTTCAAC
* * * * *
54359528 -CTGCCCTACTGCAACTTCAGGGAGGTAAGATTTGCTATCTTCAA-
1 TCTGCCCCACTGCAACTTCAGAGAGATAAGACTTG-TAGCTTCAAC
* * * * * * * * *
54359572 TCCGCTCCACTACAAATTCAGGGAGATAGGACTCGTAACTTTAAC
1 TCTGCCCCACTGCAACTTCAGAGAGATAAGACTTGTAGCTTCAAC
* * * * *
54359617 T-TGTCCCACTACAACTTCA-AGGGGATAAGA-TTGTTATCTTC-AG
1 TCTGCCCCACTGCAACTTCAGA-GAGATAAGACTTG-TAGCTTCAAC
* * * * ** *
54359660 TCTACTCTACTGTAACTTCAG-GAAGATAAGACTTGTAATTTCAGC
1 TCTGCCCCACTGCAACTTCAGAG-AGATAAGACTTGTAGCTTCAAC
* *
54359705 -CTGCTCCACTGCAACTTCAGGGAGATAAG
1 TCTGCCCCACTGCAACTTCAGAGAGATAAG
54359734 GTTTGTTTTG
Statistics
Matches: 272, Mismatches: 73, Indels: 57
0.68 0.18 0.14
Matches are distributed among these distances:
33 18 0.07
34 4 0.01
35 1 0.00
38 2 0.01
40 2 0.01
43 18 0.07
44 129 0.47
45 92 0.34
46 6 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (45 bp):
TCTGCCCCACTGCAACTTCAGAGAGATAAGACTTGTAGCTTCAAC
Found at i:54360101 original size:88 final size:87
Alignment explanation
Indices: 54359973--54360277 Score: 389
Period size: 88 Copynumber: 3.5 Consensus size: 87
54359963 GATTAGCTTT
* * * * * *
54359973 CTTCAATCTACTCCGCTGCAACTTTAGGGAGATAAG-ATTGTGGCTTCGAGCCGCTCCAATGCTA
1 CTTCGATCTACTCCGCTGGAACTTCAAGGAGATAAGAATTGTGGCTTCGAACCGCTCCAATGCCA
*
54360037 TTTCATGGAAAAGGGATTTGTAG
66 TTTCA-GGAAAAGAGATTTGTAG
* * * *
54360060 CTTCGATCTATTCCGCTGGAACTTCAATGAAATACGAATTGTGGCTTCGAACCGCTCCAATGCCA
1 CTTCGATCTACTCCGCTGGAACTTCAAGGAGATAAGAATTGTGGCTTCGAACCGCTCCAATGCCA
* *
54360125 TTTTAGGAAGAAGAAATTTGTAG
66 TTTCAGGAA-AAGAGATTTGTAG
* ** *
54360148 CTTCGATCTACTCCACTAAAACTTCAAGGAGATATA-AATTGTGGCTTCGAACCACTCCAATGCC
1 CTTCGATCTACTCCGCTGGAACTTCAAGGAGATA-AGAATTGTGGCTTCGAACCGCTCCAATGCC
54360212 ATTTCAGGGAAAAGAGATTTGTAG
65 ATTTCA-GGAAAAGAGATTTGTAG
* *
54360236 CTTCGATCTACTCTGCTGGAACTTTAAGGAGATAAGAATTGT
1 CTTCGATCTACTCCGCTGGAACTTCAAGGAGATAAGAATTGT
54360278 TTATTTCAAC
Statistics
Matches: 185, Mismatches: 28, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
87 33 0.18
88 148 0.80
89 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (87 bp):
CTTCGATCTACTCCGCTGGAACTTCAAGGAGATAAGAATTGTGGCTTCGAACCGCTCCAATGCCA
TTTCAGGAAAAGAGATTTGTAG
Found at i:54360151 original size:44 final size:44
Alignment explanation
Indices: 54360098--54360241 Score: 114
Period size: 44 Copynumber: 3.3 Consensus size: 44
54360088 GAAATACGAA
* * *
54360098 TTGTGGCTTCGAACCGCTCCAATGCCATTTTAGGAAGAAGAAAT
1 TTGTAGCTTCGAACCACTCCAATGCCATTTAAGGAAGAAGAAAT
* * * *** * *
54360142 TTGTAGCTTCGATCTACTCCACTAAAACTTCAAGG-AGATATAAA-
1 TTGTAGCTTCGAACCACTCCAATGCCA-TTTAAGGAAGA-AGAAAT
* * *
54360186 TTGTGGCTTCGAACCACTCCAATGCCATTTCAGGGAA-AAGAGAT
1 TTGTAGCTTCGAACCACTCCAATGCCATTT-AAGGAAGAAGAAAT
54360230 TTGTAGCTTCGA
1 TTGTAGCTTCGA
54360242 TCTACTCTGC
Statistics
Matches: 72, Mismatches: 23, Indels: 10
0.69 0.22 0.10
Matches are distributed among these distances:
43 5 0.07
44 57 0.79
45 10 0.14
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (44 bp):
TTGTAGCTTCGAACCACTCCAATGCCATTTAAGGAAGAAGAAAT
Found at i:54360455 original size:130 final size:130
Alignment explanation
Indices: 54360295--54361113 Score: 980
Period size: 130 Copynumber: 6.3 Consensus size: 130
54360285 AACCCGCTCT
* *
54360295 ACTACTAC-TAGGGAGATAGGATGGTAGCTTAAATCTGCTCCACTACTGCTTAGGGAGACAAGAT
1 ACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTGCTTAGGGAGACAAGAT
***** * * * * * *
54360359 TTGTTATATTTGATCTGCTCCACTACTGCTTAAGGAGACAGGACCTACAATCTTTAGCCTACTCC
66 TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTTAGCCTACTCC
* *
54360424 ACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTACTCCACTATTGCTTAGGGAGACAAGAT
1 ACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTGCTTAGGGAGACAAGAT
* * ** * *
54360489 TCGCCGTCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGTAATATTTAGTCTACTCC
66 TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTTAGCCTACTCC
* * *
54360554 ACTACTGCTTAGGGAGATAGGATGGTGACTTAAATCCGCTCCACTACTGTTTAGGGAGACAAGAT
1 ACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTGCTTAGGGAGACAAGAT
* * **
54360619 TCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTTAGCCTACTCC
66 TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTTAGCCTACTCC
*
54360684 ACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTACTTAGGGAGACAAGAT
1 ACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTGCTTAGGGAGACAAGAT
* * * * * * *
54360749 TCACCGTCTTCGATCTGCTCTACTATTGCTTAGGGAGATAAAATCTACAATTTTTAGCTTGCTCT
66 TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTTAGCCTACTCC
* * * * * * * * *
54360814 ACTGCTGCTCAGGGAGACAAGGCTAGTGGCTTAAATCTGCTTCC-CTATTACCTCT-GGAAG-TA
1 ACTACTGCTTAGGGAGA-TAGGATGGTGGCTTAAATCTGC-TCCACTACT-GCT-TAGGGAGACA
* * * * ** *
54360876 AGATTCACCATCTTCGATCTGCTCTACTATTACTTAGGGAGATAAGATCTGTAATCTTCAGCCTA
62 AGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTTAGCCTA
54360941 CTCC
127 CTCC
* *
54360945 ACTACTACTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTACTTAGGGAGACAAGAT
1 ACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTGCTTAGGGAGACAAGAT
* * * * * *
54361010 TCACTGTCTTCGATTTGCTCTACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTGCTCT
66 TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTTAGCCTACTCC
* * * * *
54361075 ACTGCTGCTCAGGGAGACAAGGCTAGTGGCTTAAATCTG
1 ACTACTGCTTAGGGAGA-TAGGATGGTGGCTTAAATCTG
54361114 TTTCCGTACT
Statistics
Matches: 596, Mismatches: 85, Indels: 16
0.86 0.12 0.02
Matches are distributed among these distances:
128 1 0.00
129 16 0.03
130 454 0.76
131 115 0.19
132 9 0.02
133 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (130 bp):
ACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTGCTTAGGGAGACAAGAT
TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTTAGCCTACTCC
Found at i:54360721 original size:86 final size:86
Alignment explanation
Indices: 54360371--54360749 Score: 300
Period size: 86 Copynumber: 4.4 Consensus size: 86
54360361 GTTATATTTG
* * * *
54360371 ATCTGCTCCACTACTGCTTAAGGAGACAGGACCTACAATCTTTAGCCTACTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGACAAGA-TTGCAATCTTTAGCCTACTCCACTACTGCTTAG
*
54360436 GGAGATAGGAT-GGTGGCTTAA
65 GGAGATAAGATCGGTGGCTTAA
* * ** * * *
54360457 ATCTACTCCACTATTGCTTAGGGAGACAAGATTCGCCGTC-TTCGATCTGCTCCACTACTGCTTA
1 ATCTGCTCCACTACTGCTTAGGGAGACAAGATT-GCAATCTTTAG-CCTACTCCACTACTGCTTA
* * *** *
54360521 GAGAGATAAGATCTGTAATATTTA
64 GGGAGATAAGATCGGT-GGCTTAA
* * * * * ** * * * *
54360545 GTCTACTCCACTACTGCTTAGGGAGATAGGATGGTGA-CTTAAATCC-GCTCCACTACTGTTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGACAAGATTGCAATCTT-TAGCCTACTCCACTACTGCTTAG
* ** * **
54360608 GGAGACAAGATTCGCCGTCTTCG
65 GGAGATAAGA-TCGGTGGCTTAA
* * *
54360631 ATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTTAGCCTACTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGACAAGAT-TGCAATCTTTAGCCTACTCCACTACTGCTTAG
*
54360696 GGAGATAGGAT-GGTGGCTTAA
65 GGAGATAAGATCGGTGGCTTAA
*
54360717 ATCTGCTCCACTACTACTTAGGGAGACAAGATT
1 ATCTGCTCCACTACTGCTTAGGGAGACAAGATT
54360750 CACCGTCTTC
Statistics
Matches: 223, Mismatches: 60, Indels: 21
0.73 0.20 0.07
Matches are distributed among these distances:
85 5 0.02
86 147 0.66
87 14 0.06
88 57 0.26
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (86 bp):
ATCTGCTCCACTACTGCTTAGGGAGACAAGATTGCAATCTTTAGCCTACTCCACTACTGCTTAGG
GAGATAAGATCGGTGGCTTAA
Found at i:54360779 original size:86 final size:87
Alignment explanation
Indices: 54360420--54360789 Score: 295
Period size: 86 Copynumber: 4.3 Consensus size: 87
54360410 CTTTAGCCTA
* *
54360420 CTCCACTACTGCTTAGGGAGATAGGAT-GGTGGCTTAAATCTACTCCACTATTGCTTAGGGAGAC
1 CTCCACTACTGCTTAGGGAGATAAGATCGGTGGCTTAAATCTACTCCACTACTGCTTAGGGAGAC
*
54360484 AAGATTCGCCGTCTTCGATCTG
66 AAGATTCACCGTCTTCGATCTG
* * *** * *
54360506 CTCCACTACTGCTTAGAGAGATAAGATCTGTAATATTTAGTCTACTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCGGT-GGCTTAAATCTACTCCACTACTGCTTAGGGAGA
* * *** * ** *
54360571 TAGGA-T-GGTGACTTAAATCCG
65 CAAGATTCACCGTCTTCGATCTG
* * ** * ** * *
54360592 CTCCACTACTGTTTAGGGAGACAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGA-TCGGTGGCTTAAATCTACTCCACTACTGCTTAGGGAGA
* * * * * *
54360657 TAAGATCTGTA--ATCTT-TAGCCTA
65 CAAGAT-T-CACCGTCTTCGA-TCTG
* * *
54360680 CTCCACTACTGCTTAGGGAGATAGGAT-GGTGGCTTAAATCTGCTCCACTACTACTTAGGGAGAC
1 CTCCACTACTGCTTAGGGAGATAAGATCGGTGGCTTAAATCTACTCCACTACTGCTTAGGGAGAC
54360744 AAGATTCACCGTCTTCGATCTG
66 AAGATTCACCGTCTTCGATCTG
* *
54360766 CTCTACTATTGCTTAGGGAGATAA
1 CTCCACTACTGCTTAGGGAGATAA
54360790 AATCTACAAT
Statistics
Matches: 216, Mismatches: 57, Indels: 22
0.73 0.19 0.07
Matches are distributed among these distances:
84 1 0.00
85 1 0.00
86 148 0.69
87 8 0.04
88 58 0.27
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (87 bp):
CTCCACTACTGCTTAGGGAGATAAGATCGGTGGCTTAAATCTACTCCACTACTGCTTAGGGAGAC
AAGATTCACCGTCTTCGATCTG
Found at i:54360781 original size:44 final size:44
Alignment explanation
Indices: 54360322--54361053 Score: 284
Period size: 44 Copynumber: 16.8 Consensus size: 44
54360312 AGGATGGTAG
* * * ***
54360322 CTTAAATCTGCTCCACTACTGCTTAGGGAGACAAGATTTGTTAT
1 CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCGT
* * * * * * * **
54360366 ATTTGATCTGCTCCACTACTGCTTAAGGAGACAGGA-CCTACAAT
1 CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTC-GCCGT
* * * ** *
54360410 CTTTAG-CCTACTCCACTACTGCTTAGGGAGATAGGA-T-GGTGG
1 C-TTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCGT
* * * *
54360452 CTTAAATCTACTCCACTATTGCTTAGGGAGACAAGATTCGCCGT
1 CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCGT
* * ***
54360496 CTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGA-TCTGTAAT
1 CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTC-GCCGT
* * * ** *
54360540 ATTTAG-TCTACTCCACTACTGCTTAGGGAGATAGGA-T-GGTGA
1 -CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCGT
* * * *
54360582 CTTAAATCCGCTCCACTACTGTTTAGGGAGACAAGATTCGCCGT
1 CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCGT
* * ***
54360626 CTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGA-TCTGTAAT
1 CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTC-GCCGT
* * * ** *
54360670 CTTTAG-CCTACTCCACTACTGCTTAGGGAGATAGGA-T-GGTGG
1 C-TTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCGT
* * * *
54360712 CTTAAATCTGCTCCACTACTACTTAGGGAGACAAGATTCACCGT
1 CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCGT
* * * * ***
54360756 CTTCGATCTGCTCTACTATTGCTTAGGGAGATAAAATCTAC-AATT
1 CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGAT-T-CGCCGT
* * * * * * ** * * *
54360801 TTTAGCT-TGCTCTACTGCTGCTCAGGGAGACAAGGCTAG-TGG
1 CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCGT
* * * * * *
54360843 CTTAAATCTGCTTCC-CTATTACCTCT-GGAAG-TAAGATTCACCAT
1 CTTAGATCTGC-TCCACTACT-GCT-TAGGGAGATAAGATTCGCCGT
* * * * ***
54360887 CTTCGATCTGCTCTACTATTACTTAGGGAGATAAGA-TCTGTAAT
1 CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTC-GCCGT
* * * * ** *
54360931 CTTCAG-CCTACTCCACTACTACTTAGGGAGATAGGA-T-GGTGG
1 CTT-AGATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCGT
* * * * *
54360973 CTTAAATCTGCTCCACTACTACTTAGGGAGACAAGATTCACTGT
1 CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCGT
* * *
54361017 CTTCGATTTGCTCTACTACTGCTTAGGGAGATAAGAT
1 CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGAT
54361054 CTACAATCTT
Statistics
Matches: 498, Mismatches: 159, Indels: 62
0.69 0.22 0.09
Matches are distributed among these distances:
41 10 0.02
42 115 0.23
43 29 0.06
44 327 0.66
45 16 0.03
46 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (44 bp):
CTTAGATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCGT
Found at i:54360980 original size:261 final size:262
Alignment explanation
Indices: 54360370--54361190 Score: 1098
Period size: 261 Copynumber: 3.1 Consensus size: 262
54360360 TGTTATATTT
* * * * * * **
54360370 GATCTGCTCCACTACTGCTTAAGGAGACAGGACCTACAATCTTTAGCCTACTCCACTACTGCTTA
1 GATCTGCTCCACTATTACTTAGGGAGATAAGATCTGTAATCTTTAGCCTACTCCACTACTGCTTA
* * * *
54360435 GGGAGATAGGATGGTGGCTTAAATCTACTCCACTATTGCTTAGGGAGACAAGATTCGCCGTCTTC
66 GGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTACTTAGGGAGACAAGATTCACCGTCTTC
* * ** * * * *
54360500 GATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGTAATATTTAG-TCTACTCCACTACTGCTT
131 GATCTGCTCTACTACTGCTTAGGGAGATAAGATCTACAATATTTAGCT-TGCTCTACTGCTGCTC
* * * * * * * * * *
54360564 AGGGAGA-TAGGATGGTGACTTAAATCCGC-T-CC-ACTACTGTTTAGGGAGACAAGATTCGCCG
195 AGGGAGACAAGGCTAGTGGCTTAAATCTGCTTCCCTACTAC-CTCT-GGAAGATAAGATTCGCCA
54360625 TCTTC
258 TCTTC
*
54360630 GATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTTAGCCTACTCCACTACTGCTTA
1 GATCTGCTCCACTATTACTTAGGGAGATAAGATCTGTAATCTTTAGCCTACTCCACTACTGCTTA
54360695 GGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTACTTAGGGAGACAAGATTCACCGTCTTC
66 GGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTACTTAGGGAGACAAGATTCACCGTCTTC
* * *
54360760 GATCTGCTCTACTATTGCTTAGGGAGATAAAATCTACAATTTTTAGCTTGCTCTACTGCTGCTCA
131 GATCTGCTCTACTACTGCTTAGGGAGATAAGATCTACAATATTTAGCTTGCTCTACTGCTGCTCA
* *
54360825 GGGAGACAAGGCTAGTGGCTTAAATCTGCTTCCCTATTACCTCTGGAAG-TAAGATTCACCATCT
196 GGGAGACAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCTGGAAGATAAGATTCGCCATCT
54360889 TC
261 TC
* * *
54360891 GATCTGCTCTACTATTACTTAGGGAGATAAGATCTGTAATCTTCAGCCTACTCCACTACTACTTA
1 GATCTGCTCCACTATTACTTAGGGAGATAAGATCTGTAATCTTTAGCCTACTCCACTACTGCTTA
*
54360956 GGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTACTTAGGGAGACAAGATTCACTGTCTTC
66 GGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTACTTAGGGAGACAAGATTCACCGTCTTC
* * * *
54361021 GATTTGCTCTACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTGCTCTACTGCTGCTCA
131 GATCTGCTCTACTACTGCTTAGGGAGATAAGATCTACAATATTTAGCTTGCTCTACTGCTGCTCA
* * *
54361086 GGGAGACAAGGCTAGTGGCTTAAATCTGTTTCCGTACTACCTCTGAAAGATAAGATTCGCCATCT
196 GGGAGACAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCTGGAAGATAAGATTCGCCATCT
54361151 TC
261 TC
* * *
54361153 GATCTGCTCCATTGA-TACCTCATGGAGATAAGATCTGT
1 GATCTGCTCCACT-ATTA-CTTAGGGAGATAAGATCTGT
54361191 GAATTTACCG
Statistics
Matches: 499, Mismatches: 54, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
260 177 0.35
261 261 0.52
262 34 0.07
263 23 0.05
264 4 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (262 bp):
GATCTGCTCCACTATTACTTAGGGAGATAAGATCTGTAATCTTTAGCCTACTCCACTACTGCTTA
GGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACTACTTAGGGAGACAAGATTCACCGTCTTC
GATCTGCTCTACTACTGCTTAGGGAGATAAGATCTACAATATTTAGCTTGCTCTACTGCTGCTCA
GGGAGACAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCTGGAAGATAAGATTCGCCATCT
TC
Found at i:54361064 original size:44 final size:44
Alignment explanation
Indices: 54360980--54361095 Score: 119
Period size: 44 Copynumber: 2.6 Consensus size: 44
54360970 TGGCTTAAAT
* * ** *
54360980 CTGCTCCACTACTACTTAGGGAGACAAGATTCACTGTCTTC-GAT
1 CTGCTCTACTACTGCTTAGGGAGACAAGATTCACAATCTTCAG-C
* *
54361024 TTGCTCTACTACTGCTTAGGGAGATAAGA-TCTACAATCTTCAGC
1 CTGCTCTACTACTGCTTAGGGAGACAAGATTC-ACAATCTTCAGC
* *
54361068 CTGCTCTACTGCTGCTCAGGGAGACAAG
1 CTGCTCTACTACTGCTTAGGGAGACAAG
54361096 GCTAGTGGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
43 2 0.03
44 56 0.95
45 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (44 bp):
CTGCTCTACTACTGCTTAGGGAGACAAGATTCACAATCTTCAGC
Found at i:54362418 original size:19 final size:19
Alignment explanation
Indices: 54362396--54362438 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
54362386 CAACCTTTCC
* *
54362396 TTTTCTTTTCTTTTTTCTTT
1 TTTTATTTT-TTTTCTCTTT
54362416 TTTTATTTTTTTTCTCTTT
1 TTTTATTTTTTTTCTCTTT
54362435 TTTT
1 TTTT
54362439 TGTGAAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTATTTTTTTTCTCTTT
Found at i:54367941 original size:31 final size:28
Alignment explanation
Indices: 54367875--54367955 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
54367865 AATATGAAGA
* *
54367875 AATTTAACATAAATAATATATGAAAAAT
1 AATTTAAAATAAATAATATATGAAAAAC
*
54367903 AAGTTTAAAATAAATAATATATATATATAAAC
1 AA-TTTAAAATAAATAATATAT-GA-A-AAAC
* *
54367935 AATTTAATATAAGTAATATAT
1 AATTTAAAATAAATAATATAT
54367956 CTGAAATCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 2 0.05
29 18 0.41
30 1 0.02
31 18 0.41
32 5 0.11
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (28 bp):
AATTTAAAATAAATAATATATGAAAAAC
Found at i:54368172 original size:25 final size:25
Alignment explanation
Indices: 54368143--54368205 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
54368133 TGTATGATAG
54368143 TTTAAAATAAACAATACATATTAAAA
1 TTTAAAATAAACAATA-ATATTAAAA
* *
54368169 -TTAAAA-AGAATAATAGTATTAAAA
1 TTTAAAATA-AACAATAATATTAAAA
54368193 TTGTAAAATAAAC
1 TT-TAAAATAAAC
54368206 TTAAAACACA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
24 9 0.30
25 13 0.43
26 7 0.23
27 1 0.03
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (25 bp):
TTTAAAATAAACAATAATATTAAAA
Found at i:54369595 original size:17 final size:17
Alignment explanation
Indices: 54369570--54369611 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
54369560 ACATCAAGTT
* *
54369570 TATTTATTTCATGAAAA
1 TATTAATTTAATGAAAA
54369587 TATTAATTTTAATGAAAA
1 TATTAA-TTTAATGAAAA
54369605 TA-TAATT
1 TATTAATT
54369612 AAAATATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 8 0.36
18 12 0.55
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (17 bp):
TATTAATTTAATGAAAA
Found at i:54371152 original size:12 final size:12
Alignment explanation
Indices: 54371119--54371156 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
54371109 TTCAAAATTT
*
54371119 ATATTTTTTAAA
1 ATATTTTTAAAA
*
54371131 A-ATTTATAAAA
1 ATATTTTTAAAA
54371142 ATATTTTTAAAA
1 ATATTTTTAAAA
54371154 ATA
1 ATA
54371157 AAGAAAGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATTTTTAAAA
Found at i:54375013 original size:48 final size:48
Alignment explanation
Indices: 54374904--54375165 Score: 322
Period size: 48 Copynumber: 5.5 Consensus size: 48
54374894 GGCCAACGCG
* * *
54374904 ATGTCCCAGACATGGTCTTACACT-AGCTCTCACATATCCGTGCCGATGCC
1 ATGTCCCAGACATGGTCTTACACTGA-CAC-CTC-TATACGTGCCGATGCC
* *
54374954 ATGTCCTAGACATGGTCTTACACTGACACCTCTATACGTTCCGATGCC
1 ATGTCCCAGACATGGTCTTACACTGACACCTCTATACGTGCCGATGCC
* * *
54375002 ATGTCCCAGACATGGTCTTACACTGACACATCTCNTCCGTGCCGATGCC
1 ATGTCCCAGACATGGTCTTACACTGACACCTCT-ATACGTGCCGATGCC
* *
54375051 ATGTCCTAGACATGGTCTTACACTGACACCTCTATACGTTCCGATGCC
1 ATGTCCCAGACATGGTCTTACACTGACACCTCTATACGTGCCGATGCC
* *
54375099 ATGT-CCAGACATGGTCTTACACTGACACAT-T-T-CATAGCCGATG-C
1 ATGTCCCAGACATGGTCTTACACTGACACCTCTATACGT-GCCGATGCC
54375143 ATGTCCCAGACAT-GTCTTACACT
1 ATGTCCCAGACATGGTCTTACACT
54375166 AGCACACAAA
Statistics
Matches: 189, Mismatches: 19, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
44 17 0.09
45 15 0.08
46 1 0.01
47 24 0.13
48 61 0.32
49 45 0.24
50 25 0.13
51 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.27
Consensus pattern (48 bp):
ATGTCCCAGACATGGTCTTACACTGACACCTCTATACGTGCCGATGCC
Found at i:54375060 original size:97 final size:96
Alignment explanation
Indices: 54374904--54375165 Score: 385
Period size: 97 Copynumber: 2.8 Consensus size: 96
54374894 GGCCAACGCG
* * *
54374904 ATGTCCCAGACATGGTCTTACACTAGCTCTCA-CATATCCGTGCCGATGCCATGTCCTAGACATG
1 ATGTCCCAGACATGGTCTTACACT-G-ACACATC-TCTCCGTGCCGATGCCATGTCCTAGACATG
54374968 GTCTTACACTGACACCTCTATACGTTCCGATGCC
63 GTCTTACACTGACACCTCTATACGTTCCGATGCC
54375002 ATGTCCCAGACATGGTCTTACACTGACACATCTCNTCCGTGCCGATGCCATGTCCTAGACATGGT
1 ATGTCCCAGACATGGTCTTACACTGACACATCTC-TCCGTGCCGATGCCATGTCCTAGACATGGT
54375067 CTTACACTGACACCTCTATACGTTCCGATGCC
65 CTTACACTGACACCTCTATACGTTCCGATGCC
* *
54375099 ATGT-CCAGACATGGTCTTACACTGACACAT-T-T-CATAGCCGATG-CATGTCCCAGACAT-GT
1 ATGTCCCAGACATGGTCTTACACTGACACATCTCTCCGT-GCCGATGCCATGTCCTAGACATGGT
54375158 CTTACACT
65 CTTACACT
54375166 AGCACACAAA
Statistics
Matches: 156, Mismatches: 5, Indels: 13
0.90 0.03 0.07
Matches are distributed among these distances:
91 10 0.06
92 15 0.10
93 8 0.05
95 1 0.01
96 30 0.19
97 68 0.44
98 24 0.15
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.27
Consensus pattern (96 bp):
ATGTCCCAGACATGGTCTTACACTGACACATCTCTCCGTGCCGATGCCATGTCCTAGACATGGTC
TTACACTGACACCTCTATACGTTCCGATGCC
Found at i:54375065 original size:49 final size:48
Alignment explanation
Indices: 54374801--54375165 Score: 329
Period size: 49 Copynumber: 7.6 Consensus size: 48
54374791 GGTACAATGT
* * * *
54374801 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAGT--
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTAT-ACGTGC
* * * * * * * *
54374848 TGATGCCATATCCC-GAACATGGTCTTACATTGAC-TATCGAAATTGAGGC
1 CGATGCCATGTCCCAG-ACATGGTCTTACACTGACACATCTATA-CG-TGC
* * * * * *
54374897 CAACGCGATGTCCCAGACATGGTCTTACACTAGCTCTCA-CATATCCGTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATC-TATACGTGC
* * *
54374947 CGATGCCATGTCCTAGACATGGTCTTACACTGACACCTCTATACGTTC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTATACGTGC
* *
54374995 CGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCNTCCGTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACACATCT-ATACGTGC
* * *
54375044 CGATGCCATGTCCTAGACATGGTCTTACACTGACACCTCTATACGTTC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTATACGTGC
*
54375092 CGATGCCATGT-CCAGACATGGTCTTACACTGACACAT-T-T-CATAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTATACGT-GC
54375137 CGATG-CATGTCCCAGACAT-GTCTTACACT
1 CGATGCCATGTCCCAGACATGGTCTTACACT
54375166 AGCACACAAA
Statistics
Matches: 259, Mismatches: 45, Indels: 31
0.77 0.13 0.09
Matches are distributed among these distances:
44 17 0.07
45 16 0.06
46 7 0.03
47 52 0.20
48 63 0.24
49 68 0.26
50 31 0.12
51 3 0.01
52 2 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTATACGTGC
Found at i:54378202 original size:11 final size:11
Alignment explanation
Indices: 54378186--54378215 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
54378176 TGATTAGTAT
54378186 AGATTATTTTA
1 AGATTATTTTA
54378197 AGATTA-TTTA
1 AGATTATTTTA
54378207 AGATTATTT
1 AGATTATTT
54378216 GACCTACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (11 bp):
AGATTATTTTA
Found at i:54382139 original size:2 final size:2
Alignment explanation
Indices: 54382132--54382156 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54382122 CAACAACATT
54382132 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
54382157 TAATTTATCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54384504 original size:53 final size:53
Alignment explanation
Indices: 54384421--54384525 Score: 131
Period size: 53 Copynumber: 2.0 Consensus size: 53
54384411 TGCCCGTGTG
* * *
54384421 ACCCATACACCCAAATTGGCCTCACTCGTGTGGCCCACAAGGCTTAACTCAAA
1 ACCCACACACCCAAATTGGCCTCACCCGTGTGGCCCACAAGGCTAAACTCAAA
* * * *
54384474 ACCCACACGCCCAACTTGGCCT-AGCCCGTGTGGCCTACACGGCTAAACTCAA
1 ACCCACACACCCAAATTGGCCTCA-CCCGTGTGGCCCACAAGGCTAAACTCAA
54384526 GCCACCACAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 1 0.02
53 43 0.98
ACGTcount: A:0.28, C:0.38, G:0.17, T:0.17
Consensus pattern (53 bp):
ACCCACACACCCAAATTGGCCTCACCCGTGTGGCCCACAAGGCTAAACTCAAA
Found at i:54388763 original size:29 final size:29
Alignment explanation
Indices: 54388730--54388787 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
54388720 CCTATAAAGC
54388730 TTATTAACCCGAACAAACTACCCTAACAG
1 TTATTAACCCGAACAAACTACCCTAACAG
54388759 TTATTAACCCGAACAAACTACCCTAACAG
1 TTATTAACCCGAACAAACTACCCTAACAG
54388788 ACTCAATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.31, G:0.07, T:0.21
Consensus pattern (29 bp):
TTATTAACCCGAACAAACTACCCTAACAG
Found at i:54390733 original size:16 final size:16
Alignment explanation
Indices: 54390712--54390754 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
54390702 AAACAGTTTG
*
54390712 TATTTTTAGAAAACCT
1 TATTTTTAGAAAACCA
54390728 TA-TTTTAGTAAAACCA
1 TATTTTTAG-AAAACCA
54390744 TAGTTTTTAGA
1 TA-TTTTTAGA
54390755 GATCAGATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 6 0.26
16 10 0.43
17 1 0.04
18 6 0.26
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (16 bp):
TATTTTTAGAAAACCA
Found at i:54403938 original size:41 final size:40
Alignment explanation
Indices: 54403866--54404022 Score: 113
Period size: 41 Copynumber: 3.8 Consensus size: 40
54403856 GTGATATTCG
* * * *
54403866 GGCTTTAAGCCTAGCAAGCATTGTGCTGGTGAATGTAATTG
1 GGCTTTAAGCCTAGCAGGC-TTTTGCCGGTGAATGTAATTA
* * *
54403907 GGCTTTATGCCTAGCAGGCTTATTGCCGGTGAATATAAAATCA
1 GGCTTTAAGCCTAGCAGGCTT-TTGCCGGTGAATGT--AATTA
* * **
54403950 GACTTTAAGTCTAGCAGGCCTTAAGCCGGTG--TGTAATTCA
1 GGCTTTAAGCCTAGCAGG-CTTTTGCCGGTGAATGTAATT-A
**
54403990 GGC-TTATTCCTAGCAGGCTTTATGCCGGTGAAT
1 GGCTTTAAGCCTAGCAGGCTTT-TGCCGGTGAAT
54404023 TATTAAAAGT
Statistics
Matches: 88, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
38 3 0.03
39 21 0.24
40 5 0.06
41 31 0.35
43 25 0.28
44 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (40 bp):
GGCTTTAAGCCTAGCAGGCTTTTGCCGGTGAATGTAATTA
Found at i:54406473 original size:19 final size:18
Alignment explanation
Indices: 54406446--54406503 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 18
54406436 TTTTTTAAAT
54406446 AATTTTAACTTGATTGAA
1 AATTTTAACTTGATTGAA
*
54406464 AATGTTTAACTCGATTGAA
1 AAT-TTTAACTTGATTGAA
54406483 ATCATTTTAACTTGATT-AA
1 A--ATTTTAACTTGATTGAA
54406502 AA
1 AA
54406504 GTTGATTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
17 1 0.03
18 3 0.09
19 18 0.51
20 11 0.31
21 2 0.06
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (18 bp):
AATTTTAACTTGATTGAA
Found at i:54406936 original size:31 final size:32
Alignment explanation
Indices: 54406898--54407031 Score: 129
Period size: 31 Copynumber: 4.4 Consensus size: 32
54406888 AATATATAGC
*
54406898 TTGGGTGACCAAAATGAAAGTGA-CTTAAAAT
1 TTGGGTGACCAAAATGAAAGTGACCCTAAAAT
54406929 TTGGGTGACCAAAATGAAAGT-ACCCTAAAAT
1 TTGGGTGACCAAAATGAAAGTGACCCTAAAAT
* * * *
54406960 TTAGGTGACCAAAATG--AG-AACACCT-TATT
1 TTGGGTGACCAAAATGAAAGTGAC-CCTAAAAT
* * * *
54406989 TTGGGTGACCAGAATGAAAGCG-TCCTAAAAG
1 TTGGGTGACCAAAATGAAAGTGACCCTAAAAT
54407020 TTGGGTGACCAA
1 TTGGGTGACCAA
54407032 CTAAGTAGTT
Statistics
Matches: 84, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
29 20 0.24
30 7 0.08
31 57 0.68
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (32 bp):
TTGGGTGACCAAAATGAAAGTGACCCTAAAAT
Found at i:54407780 original size:66 final size:66
Alignment explanation
Indices: 54407667--54407796 Score: 165
Period size: 66 Copynumber: 2.0 Consensus size: 66
54407657 TGAAGAAGTT
* *
54407667 GCTGGAGTGCATCATATTTTCTTGTTGCCTCTACTTCCCTCACTGCTGCCTCCGTTTTAAGTTGT
1 GCTGAAGTGCATCATATTTTCTTGTAGCCTCTACTTCCCTCACTGCTGCCTCCGTTTTAAGTTGT
54407732 A
66 A
* * * * *
54407733 GCTGAAGTTCATCATATTTTCTT-TGAGCCTTTGCTTCTCTC-CATGCTGCCTTCGTTTTAAGTT
1 GCTGAAGTGCATCATATTTTCTTGT-AGCCTCTACTTCCCTCAC-TGCTGCCTCCGTTTTAAGTT
54407796 G
64 G
54407797 AGCAATTTGC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
65 2 0.04
66 53 0.96
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (66 bp):
GCTGAAGTGCATCATATTTTCTTGTAGCCTCTACTTCCCTCACTGCTGCCTCCGTTTTAAGTTGT
A
Found at i:54408573 original size:194 final size:194
Alignment explanation
Indices: 54408244--54408633 Score: 744
Period size: 194 Copynumber: 2.0 Consensus size: 194
54408234 GCAGCTTCAG
*
54408244 TACTCATATGAGATACATCTTCCTTTCTATGTTTAATGTCAAAAAGCTAAAGGCGTCCAACTTTT
1 TACTCATATGAGATACATCTTCCTTTCTATATTTAATGTCAAAAAGCTAAAGGCGTCCAACTTTT
54408309 TGACCAGATGACAGTTCCTATAATATAGTATAAAAAATATTATTTAGTAGAAAATAATTAATATT
66 TGACCAGATGACAGTTCCTATAATATAGTATAAAAAATATTATTTAGTAGAAAATAATTAATATT
*
54408374 TGACACAATTAATAAATTCAAAATACTTCGTCATCAGCTACACAAGCAAACTTTTCGACCTAGC
131 TGACACAATTAATAAATTCAAAATACCTCGTCATCAGCTACACAAGCAAACTTTTCGACCTAGC
* *
54408438 TACTCATATGAGATATATCTTTCTTTCTATATTTAATGTCAAAAAGCTAAAGGCGTCCAACTTTT
1 TACTCATATGAGATACATCTTCCTTTCTATATTTAATGTCAAAAAGCTAAAGGCGTCCAACTTTT
54408503 TGACCAGATGACAGTTCCTATAATATAGTATAAAAAATATTATTTAGTAGAAAATAATTAATATT
66 TGACCAGATGACAGTTCCTATAATATAGTATAAAAAATATTATTTAGTAGAAAATAATTAATATT
54408568 TGACACAATTAATAAATTCAAAATACCTCGTCATCAGCTACACAAGCAAACTTTTCGACCTAGC
131 TGACACAATTAATAAATTCAAAATACCTCGTCATCAGCTACACAAGCAAACTTTTCGACCTAGC
54408632 TA
1 TA
54408634 TCTGTGTGAA
Statistics
Matches: 192, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
194 192 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (194 bp):
TACTCATATGAGATACATCTTCCTTTCTATATTTAATGTCAAAAAGCTAAAGGCGTCCAACTTTT
TGACCAGATGACAGTTCCTATAATATAGTATAAAAAATATTATTTAGTAGAAAATAATTAATATT
TGACACAATTAATAAATTCAAAATACCTCGTCATCAGCTACACAAGCAAACTTTTCGACCTAGC
Found at i:54414601 original size:23 final size:22
Alignment explanation
Indices: 54414549--54414601 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
54414539 TCCACGTCTT
*
54414549 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
54414571 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
54414594 TTTCTTTT
1 TTTCTTTT
54414602 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:54420210 original size:21 final size:21
Alignment explanation
Indices: 54420186--54420225 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54420176 ATAAACTTTT
*
54420186 CAATTGATTGTATAAAACAAA
1 CAATAGATTGTATAAAACAAA
*
54420207 CAATAGGTTGTATAAAACA
1 CAATAGATTGTATAAAACA
54420226 GTATACTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (21 bp):
CAATAGATTGTATAAAACAAA
Found at i:54420939 original size:25 final size:25
Alignment explanation
Indices: 54420902--54420949 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
54420892 AAAAACTTAC
54420902 ATGGCAATACAGCAGAGGACTATCA
1 ATGGCAATACAGCAGAGGACTATCA
* *
54420927 ATGGCGATGCAGCAGAGGACTAT
1 ATGGCAATACAGCAGAGGACTAT
54420950 TGACAACGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.17
Consensus pattern (25 bp):
ATGGCAATACAGCAGAGGACTATCA
Found at i:54421002 original size:20 final size:21
Alignment explanation
Indices: 54420970--54421020 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
54420960 GCAGTAGATG
54420970 TTGGGGAAAAAAATAAGGGAT
1 TTGGGGAAAAAAATAAGGGAT
54420991 TTGGGGAAAAAAATAAGGGAT
1 TTGGGGAAAAAAATAAGGGAT
*
54421012 TTCGGGAAA
1 TTGGGGAAA
54421021 CTGATTTGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.45, C:0.02, G:0.33, T:0.20
Consensus pattern (21 bp):
TTGGGGAAAAAAATAAGGGAT
Done.