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 67 of 310
Found at i:21441252 original size:14 final size:15
Alignment explanation
Indices: 21441228--21441262 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
21441218 TACTTTAATC
21441228 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
21441243 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
21441258 ATGGT
1 ATGGT
21441263 AATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:21448639 original size:34 final size:33
Alignment explanation
Indices: 21448597--21448662 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
21448587 TTGTTTGCAT
21448597 ACTATACTGAAATGGGCTAAGGCCCAAACTGCC
1 ACTATACTGAAATGGGCTAAGGCCCAAACTGCC
* *
21448630 ACTATTACTGAAATGGGCTCAGGCCCAGACTGC
1 ACTA-TACTGAAATGGGCTAAGGCCCAAACTGC
21448663 TACTGCTACC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 4 0.13
34 26 0.87
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (33 bp):
ACTATACTGAAATGGGCTAAGGCCCAAACTGCC
Found at i:21450219 original size:48 final size:48
Alignment explanation
Indices: 21450163--21450307 Score: 175
Period size: 48 Copynumber: 3.0 Consensus size: 48
21450153 CATGAGGTTA
*
21450163 CATTGAGTTGGCTTCAGGCTATAATATTAGAACTTCGGGTGCGAGATT
1 CATTGAGTTGGCTTCAGGCCATAATATTAGAACTTCGGGTGCGAGATT
* * * * * *
21450211 CATTGAGTTGGATTCAGGCCATGATATTGGTACTTCTGGTGTGAGATT
1 CATTGAGTTGGCTTCAGGCCATAATATTAGAACTTCGGGTGCGAGATT
* * * *
21450259 CATTGAGTTGGCTTC-GAGCCATAAGATTAGCACTTAGGGTGCAAGATT
1 CATTGAGTTGGCTTCAG-GCCATAATATTAGAACTTCGGGTGCGAGATT
21450307 C
1 C
21450308 TCGAGTATTC
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
47 1 0.01
48 79 0.99
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (48 bp):
CATTGAGTTGGCTTCAGGCCATAATATTAGAACTTCGGGTGCGAGATT
Found at i:21452626 original size:29 final size:29
Alignment explanation
Indices: 21452563--21452670 Score: 112
Period size: 29 Copynumber: 3.8 Consensus size: 29
21452553 TTCACATACC
* * * *
21452563 TGTATTTGGCCCATTAAG-CCTAATCATA
1 TGTATATGGCCCATTAGGCCCAAATCACA
21452591 T-TCATATGGCCCATTAGGCCCAAATCACA
1 TGT-ATATGGCCCATTAGGCCCAAATCACA
*
21452620 TGTATATGGCCAATTAGGCCCAAATCACA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* * **
21452649 TTTATATAGCCTGTTAGGCCCA
1 TGTATATGGCCCATTAGGCCCA
21452671 GTCACTTTCA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.01
28 14 0.21
29 52 0.76
30 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCACA
Found at i:21452906 original size:8 final size:8
Alignment explanation
Indices: 21452893--21452935 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
21452883 GTAGCCAAAC
21452893 TTTCGGCT
1 TTTCGGCT
*
21452901 TTTCGGCA
1 TTTCGGCT
*
21452909 TTTCAGCT
1 TTTCGGCT
*
21452917 TTTCGGCA
1 TTTCGGCT
*
21452925 TTTCGACT
1 TTTCGGCT
21452933 TTT
1 TTT
21452936 GCCGATTCAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.09, C:0.23, G:0.19, T:0.49
Consensus pattern (8 bp):
TTTCGGCT
Found at i:21452917 original size:16 final size:16
Alignment explanation
Indices: 21452893--21452928 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
21452883 GTAGCCAAAC
*
21452893 TTTCGGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
21452909 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
21452925 TTTC
1 TTTC
21452929 GACTTTTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.25, G:0.19, T:0.47
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCA
Found at i:21452934 original size:16 final size:16
Alignment explanation
Indices: 21452893--21452935 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
21452883 GTAGCCAAAC
*
21452893 TTTCGGCTTTTCGGCA
1 TTTCGACTTTTCGGCA
21452909 TTTC-AGCTTTTCGGCA
1 TTTCGA-CTTTTCGGCA
21452925 TTTCGACTTTT
1 TTTCGACTTTT
21452936 GCCGATTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.09, C:0.23, G:0.19, T:0.49
Consensus pattern (16 bp):
TTTCGACTTTTCGGCA
Found at i:21457029 original size:8 final size:8
Alignment explanation
Indices: 21457018--21457072 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 8
21457008 ACTTTCAGCT
21457018 TTTCGGCA
1 TTTCGGCA
*
21457026 TTTCGGCT
1 TTTCGGCA
21457034 TTTCGGCA
1 TTTCGGCA
* *
21457042 TTTCAGCT
1 TTTCGGCA
* *
21457050 TTTCGACT
1 TTTCGGCA
*
21457058 TTTCGACA
1 TTTCGGCA
21457066 TTTCGGC
1 TTTCGGC
21457073 TTTTACCGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.44
Consensus pattern (8 bp):
TTTCGGCA
Found at i:21457061 original size:16 final size:16
Alignment explanation
Indices: 21457010--21457054 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
21457000 ATAGCCAAAC
21457010 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
*
21457026 TTTCGGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
21457042 TTTCAGCTTTTCG
1 TTTCAGCTTTTCG
21457055 ACTTTTCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.09, C:0.24, G:0.20, T:0.47
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCA
Found at i:21457069 original size:16 final size:16
Alignment explanation
Indices: 21457016--21457072 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
21457006 AAACTTTCAG
*
21457016 CTTTTCGGCATTTCGG
1 CTTTTCGGCATTTCGA
21457032 CTTTTCGGCATTTC-A
1 CTTTTCGGCATTTCGA
* *
21457047 GCTTTTCGACTTTTCGA
1 -CTTTTCGGCATTTCGA
*
21457064 CATTTCGGC
1 CTTTTCGGC
21457073 TTTTACCGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 33 0.97
17 1 0.03
ACGTcount: A:0.11, C:0.26, G:0.19, T:0.44
Consensus pattern (16 bp):
CTTTTCGGCATTTCGA
Found at i:21457074 original size:24 final size:24
Alignment explanation
Indices: 21457018--21457076 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
21457008 ACTTTCAGCT
* * *
21457018 TTTCGGCATTTCGGCTTTTCGGCA
1 TTTCGGCTTTTCGACTTTTCGACA
*
21457042 TTTCAGCTTTTCGACTTTTCGACA
1 TTTCGGCTTTTCGACTTTTCGACA
21457066 TTTCGGCTTTT
1 TTTCGGCTTTT
21457077 ACCGATTCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.10, C:0.24, G:0.19, T:0.47
Consensus pattern (24 bp):
TTTCGGCTTTTCGACTTTTCGACA
Found at i:21461633 original size:25 final size:25
Alignment explanation
Indices: 21461595--21461673 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
21461585 CAGCCCGCAA
* *
21461595 GAGCATCCCGTTATTTAGCTCTTAT
1 GAGCATCCCATTATTTGGCTCTTAT
* * *
21461620 GAGCATCCCATTATATGGCTCTCAC
1 GAGCATCCCATTATTTGGCTCTTAT
* *
21461645 GAGCTTCTCGA-TATTTGGCTCTTAT
1 GAGCATC-CCATTATTTGGCTCTTAT
21461670 GAGC
1 GAGC
21461674 TTGCCGATTA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
25 41 0.95
26 2 0.05
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.35
Consensus pattern (25 bp):
GAGCATCCCATTATTTGGCTCTTAT
Found at i:21461762 original size:25 final size:25
Alignment explanation
Indices: 21461612--21461773 Score: 79
Period size: 25 Copynumber: 6.6 Consensus size: 25
21461602 CCGTTATTTA
* *
21461612 GCTCTTATGAGCATCCCATTATATG
1 GCTCTTATGAGCTTTCCATTATATG
* * * *
21461637 GCTCTCACGAGCTTCTCGA-TATTTG
1 GCTCTTATGAGCTT-TCCATTATATG
*
21461662 GCTCTTATGAGCTTGCCGATTA-ATG
1 GCTCTTATGAGCTTTCC-ATTATATG
* *
21461687 GCTCTCTA-GAG-GTTCC-TGATATTG
1 GCTCT-TATGAGCTTTCCATTATA-TG
* * *
21461711 GCT-TGCATGAGC-TTCCTACT-TACG
1 GCTCT-TATGAGCTTTCC-ATTATATG
*
21461735 GCTCTTATGAGCTTTCCATTACATG
1 GCTCTTATGAGCTTTCCATTATATG
**
21461760 GCTCACATGAGCTT
1 GCTCTTATGAGCTT
21461774 CGTGTTATAT
Statistics
Matches: 99, Mismatches: 25, Indels: 26
0.66 0.17 0.17
Matches are distributed among these distances:
22 2 0.02
23 3 0.03
24 28 0.28
25 60 0.61
26 6 0.06
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (25 bp):
GCTCTTATGAGCTTTCCATTATATG
Found at i:21467060 original size:45 final size:45
Alignment explanation
Indices: 21466957--21467071 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 45
21466947 CATACCGGAG
* * * * *
21466957 ACGAGTAAAACCATAGCTAAAAGACGTTATGGCATCATAATTTTA
1 ACGAGTAAAACCATAGCTGAAAGACATTATGACATCACAATTCTA
* * * * ** *
21467002 ATGAATAAGACCATAGCCGAAAGTTATTATGACATCACGATTCTA
1 ACGAGTAAAACCATAGCTGAAAGACATTATGACATCACAATTCTA
21467047 ACGAGTAAAACCATAGCTGAAAGAC
1 ACGAGTAAAACCATAGCTGAAAGAC
21467072 GCTATAGCAT
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (45 bp):
ACGAGTAAAACCATAGCTGAAAGACATTATGACATCACAATTCTA
Found at i:21467095 original size:45 final size:44
Alignment explanation
Indices: 21466957--21467105 Score: 120
Period size: 45 Copynumber: 3.3 Consensus size: 44
21466947 CATACCGGAG
* * *
21466957 ACGAGTAAAACCATAGCTAAAAGACGTTATGGCATCAT-AATTTTA
1 ACGAATAAAACCATAGCTGAAAGACGTTAT-GCATCATGAA-TCTA
* * * *** * *
21467002 ATGAATAAGACCATAGCCGAAAGTTATTATGACATCACGATTCTA
1 ACGAATAAAACCATAGCTGAAAGACGTTATG-CATCATGAATCTA
* * *
21467047 ACGAGTAAAACCATAGCTGAAAGACGCTATAGCATCATGAATCAA
1 ACGAATAAAACCATAGCTGAAAGACGTTAT-GCATCATGAATCTA
*
21467092 ACGAATAAGACCAT
1 ACGAATAAAACCAT
21467106 GGTTGAAATA
Statistics
Matches: 77, Mismatches: 24, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
44 1 0.01
45 74 0.96
46 2 0.03
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (44 bp):
ACGAATAAAACCATAGCTGAAAGACGTTATGCATCATGAATCTA
Found at i:21467113 original size:45 final size:46
Alignment explanation
Indices: 21467046--21467167 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 46
21467036 TCACGATTCT
* * * * * * * *
21467046 AACGAGTAAAACCATAGCTGAAAGACGCTATAGCATCATGA-ATCA
1 AACGAATAAGACCATGGTTGAAAGACACTATAGCAACACGATATAA
* * * *
21467091 AACGAATAAGACCATGGTTGAAATACATTATGGCAACACGATGTAA
1 AACGAATAAGACCATGGTTGAAAGACACTATAGCAACACGATATAA
*
21467137 AATGAATAAGACCATGGTTGAAAGACACTAT
1 AACGAATAAGACCATGGTTGAAAGACACTAT
21467168 GGAATCAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
45 31 0.51
46 30 0.49
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.20
Consensus pattern (46 bp):
AACGAATAAGACCATGGTTGAAAGACACTATAGCAACACGATATAA
Found at i:21467121 original size:90 final size:90
Alignment explanation
Indices: 21466957--21467132 Score: 212
Period size: 90 Copynumber: 2.0 Consensus size: 90
21466947 CATACCGGAG
* * ** *
21466957 ACGAGTAAAACCATAGCTAAAAGACGTTATGGCATCATAATTTTAATGAATAAGACCATAGCCGA
1 ACGAGTAAAACCATAGCTAAAAGACGCTATAGCATCATAATTCAAACGAATAAGACCATAGCCGA
* *
21467022 AAGTTATTATGACATCACGATTCTA
66 AAGTCATTATGACAACACGATTCTA
* * **
21467047 ACGAGTAAAACCATAGCTGAAAGACGCTATAGCATCATGAA-TCAAACGAATAAGACCATGGTTG
1 ACGAGTAAAACCATAGCTAAAAGACGCTATAGCATCAT-AATTCAAACGAATAAGACCATAGCCG
*
21467111 AAA-TACATTATGGCAACACGAT
65 AAAGT-CATTATGACAACACGAT
21467133 GTAAAATGAA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
89 1 0.01
90 69 0.96
91 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (90 bp):
ACGAGTAAAACCATAGCTAAAAGACGCTATAGCATCATAATTCAAACGAATAAGACCATAGCCGA
AAGTCATTATGACAACACGATTCTA
Found at i:21467233 original size:45 final size:45
Alignment explanation
Indices: 21467137--21467235 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 45
21467127 CACGATGTAA
* * *
21467137 AATGAATAAGACCATGGTTGAAAGACACTATGGAATCAAATTAGC
1 AATGAATAAGACCATAGTTGAAAGACACAATGGAATCAAATAAGC
* * * *
21467182 AGTGAATAAGACTATAGTTGAAAGACACAATGGCATCAAGTCAAG-
1 AATGAATAAGACCATAGTTGAAAGACACAATGGAATCAAAT-AAGC
21467227 AATGAATAA
1 AATGAATAA
21467236 TACCTTGGTG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
45 43 0.96
46 2 0.04
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.21
Consensus pattern (45 bp):
AATGAATAAGACCATAGTTGAAAGACACAATGGAATCAAATAAGC
Found at i:21480919 original size:196 final size:197
Alignment explanation
Indices: 21480577--21480968 Score: 671
Period size: 196 Copynumber: 2.0 Consensus size: 197
21480567 CCGAAATTTC
*
21480577 AATGTAGAATTTACAGCACATATTTTCTATAAAATTTAGAATTTTTTCTTTAATTTTCACAACTT
1 AATGTAGAATTTACAGCACATATTTTCTATAAAATTTAGAATTTTTTCTTCAATTTTCACAACTT
21480642 TACATTTTAGTACCTAAACCATATTTTCATCAAAAATCACTTTGTAAAAATTATTTATCTATCAA
66 TACATTTTAGTACCTAAACCATATTTTCATCAAAAATCACTTTGTAAAAATTATTTATCTATCAA
* *
21480707 CAACCTTTCATTTTCTACCATAAATTTTAAATTTTTAGCATATTCAT-TCATAACCTGATTTCCA
131 CAACCTTTCATTTTCTACCATAAATTTTAAATTTTCAGCATATTCATCT-ATAACCTAATTTCCA
21480771 TAA
195 TAA
*
21480774 AATGTAGAATTTACAGCACATATTTTCTATCAAATTTAGAA-TTTTTCTTCAATTTTCACAACTT
1 AATGTAGAATTTACAGCACATATTTTCTATAAAATTTAGAATTTTTTCTTCAATTTTCACAACTT
* * * *
21480838 TACATTTTAGTACCTAAATCATGTTTTCATCAAAAATCACTTTGTAAAAGTTGTTTATCTATCAA
66 TACATTTTAGTACCTAAACCATATTTTCATCAAAAATCACTTTGTAAAAATTATTTATCTATCAA
* *
21480903 CAACTTTTCGTTTTCTACCATAAATTTTAAATTTTCAGCATATTCATCTATAACCTAATTTCCAT
131 CAACCTTTCATTTTCTACCATAAATTTTAAATTTTCAGCATATTCATCTATAACCTAATTTCCAT
21480968 A
196 A
21480969 CTTTGATAAC
Statistics
Matches: 184, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
196 143 0.78
197 41 0.22
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (197 bp):
AATGTAGAATTTACAGCACATATTTTCTATAAAATTTAGAATTTTTTCTTCAATTTTCACAACTT
TACATTTTAGTACCTAAACCATATTTTCATCAAAAATCACTTTGTAAAAATTATTTATCTATCAA
CAACCTTTCATTTTCTACCATAAATTTTAAATTTTCAGCATATTCATCTATAACCTAATTTCCAT
AA
Found at i:21486039 original size:25 final size:24
Alignment explanation
Indices: 21485985--21486039 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
21485975 ATATAAATTA
21485985 AAAAAAGTGGTTAGAAAGAAAAAG
1 AAAAAAGTGGTTAGAAAGAAAAAG
* *
21486009 ACAAAAAG-GAGTTAGATAAGGAAAGG
1 A-AAAAAGTG-GTTAGA-AAGAAAAAG
21486035 AAAAA
1 AAAAA
21486040 GACAAGAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 2 0.08
25 16 0.62
26 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.25, T:0.11
Consensus pattern (24 bp):
AAAAAAGTGGTTAGAAAGAAAAAG
Found at i:21490956 original size:46 final size:48
Alignment explanation
Indices: 21490829--21490960 Score: 168
Period size: 46 Copynumber: 2.8 Consensus size: 48
21490819 GGGTTAGTTG
21490829 TGTGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGAGGA
1 TGTGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCA-TGAGAGGA
* *
21490878 -GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-T-ACGA-GA
1 TGTGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATGA-GAGGA
* *
21490921 TGTGTCAGTGTAAGACCATGTCTAGGACCTGGCATCGGCA
1 TGTGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCA
21490961 CAGATATGTG
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
43 3 0.04
44 15 0.21
45 12 0.17
46 16 0.22
47 13 0.18
48 13 0.18
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (48 bp):
TGTGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATGAGAGGA
Found at i:21492986 original size:22 final size:22
Alignment explanation
Indices: 21492958--21493008 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
21492948 TGAGGAAACA
*
21492958 GGCGTGTCCCTATTTCCACACG
1 GGCGTGTCCCTATGTCCACACG
21492980 GGCGTGTCCCTATGTCCACACG
1 GGCGTGTCCCTATGTCCACACG
21493002 GGCGTGT
1 GGCGTGT
21493009 GACCCTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.12, C:0.33, G:0.29, T:0.25
Consensus pattern (22 bp):
GGCGTGTCCCTATGTCCACACG
Found at i:21495444 original size:20 final size:22
Alignment explanation
Indices: 21495409--21495448 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
21495399 GTCGTTGCGA
21495409 TGAAAACATCATCGATACTTTT
1 TGAAAACATCATCGATACTTTT
21495431 TGAAAA-AT-ATCGATACTT
1 TGAAAACATCATCGATACTT
21495449 CTTGTAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (22 bp):
TGAAAACATCATCGATACTTTT
Found at i:21496767 original size:7 final size:7
Alignment explanation
Indices: 21496741--21496780 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
21496731 AAAACTACAA
21496741 TAACTAC
1 TAACTAC
*
21496748 TAAGC-AT
1 TAA-CTAC
21496755 TAACTAC
1 TAACTAC
21496762 TAACTAC
1 TAACTAC
21496769 TAACTAC
1 TAACTAC
21496776 TAACT
1 TAACT
21496781 GCCCCATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 1 0.03
7 27 0.93
8 1 0.03
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.30
Consensus pattern (7 bp):
TAACTAC
Found at i:21509041 original size:16 final size:16
Alignment explanation
Indices: 21509020--21509051 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21509010 AAGTTTAAAT
*
21509020 TGACAATTTACACAAC
1 TGACAATTCACACAAC
21509036 TGACAATTCACACAAC
1 TGACAATTCACACAAC
21509052 ACTAAAGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.28, G:0.06, T:0.22
Consensus pattern (16 bp):
TGACAATTCACACAAC
Found at i:21516697 original size:46 final size:46
Alignment explanation
Indices: 21516630--21516811 Score: 231
Period size: 46 Copynumber: 4.0 Consensus size: 46
21516620 AGTGTGCTCT
* *
21516630 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
21516676 CTGATATGAGATGTGTAAGACCATGGTCGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
21516722 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
21516768 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGACATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
21516812 TCACGTCAAA
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.01
46 119 0.99
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:21517117 original size:23 final size:25
Alignment explanation
Indices: 21517072--21517118 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
21517062 AATAAATATA
*
21517072 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
21517097 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
21517119 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:21525994 original size:42 final size:42
Alignment explanation
Indices: 21525932--21526046 Score: 137
Period size: 42 Copynumber: 2.8 Consensus size: 42
21525922 AAAAGAATGT
* *
21525932 CGCTAAA-ACCATGACTTTTAGCGGCGCATTTT-TATAAACGC
1 CGCTAAAGACCATGACTTTTAGCGGCGC-TTTTACACAAACGC
* *
21525973 CGCTAAAGACCATGACCTTTAGCGGTGCTTTTCACACAAACGC
1 CGCTAAAGACCATGACTTTTAGCGGCGCTTTT-ACACAAACGC
* *
21526016 CACTAAAGA-CATGAGTTTTAGCGGCGCTTTT
1 CGCTAAAGACCATGACTTTTAGCGGCGCTTTT
21526047 CTCACGCCGC
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
41 11 0.17
42 37 0.59
43 15 0.24
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (42 bp):
CGCTAAAGACCATGACTTTTAGCGGCGCTTTTACACAAACGC
Found at i:21526118 original size:22 final size:22
Alignment explanation
Indices: 21526080--21526133 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
21526070 CTTTAAAAAA
*
21526080 ATTATTTTATTTTAAATAATAT
1 ATTATTTTATGTTAAATAATAT
*
21526102 -TTATTTCTATGTTAAATATTAT
1 ATTATTT-TATGTTAAATAATAT
21526124 ATTATGTTTA
1 ATTAT-TTTA
21526134 ATTTTTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 6 0.22
22 13 0.48
23 6 0.22
24 2 0.07
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (22 bp):
ATTATTTTATGTTAAATAATAT
Found at i:21530179 original size:37 final size:37
Alignment explanation
Indices: 21530137--21530218 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 37
21530127 TTAGCACCAG
*
21530137 CTTTTATTTCACATCTTCTTCGTTACTCTCAGTAACC
1 CTTTTATTTCACATCTTCCTCGTTACTCTCAGTAACC
21530174 C---T-TTT-ACATCTTCCTCGTTACTCTCAGTAACC
1 CTTTTATTTCACATCTTCCTCGTTACTCTCAGTAACC
*
21530206 ATTTTATTTCACA
1 CTTTTATTTCACA
21530219 GTTTATAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
32 26 0.68
33 3 0.08
34 1 0.03
35 1 0.03
36 3 0.08
37 4 0.11
ACGTcount: A:0.21, C:0.29, G:0.05, T:0.45
Consensus pattern (37 bp):
CTTTTATTTCACATCTTCCTCGTTACTCTCAGTAACC
Found at i:21530192 original size:32 final size:32
Alignment explanation
Indices: 21530142--21530211 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
21530132 ACCAGCTTTT
* *
21530142 ATTTCACATCTTCTTCGTTACTCTCAGTAACC
1 ATTTTACATCTTCCTCGTTACTCTCAGTAACC
*
21530174 CTTTTACATCTTCCTCGTTACTCTCAGTAACC
1 ATTTTACATCTTCCTCGTTACTCTCAGTAACC
21530206 ATTTTA
1 ATTTTA
21530212 TTTCACAGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.21, C:0.30, G:0.06, T:0.43
Consensus pattern (32 bp):
ATTTTACATCTTCCTCGTTACTCTCAGTAACC
Found at i:21531582 original size:16 final size:17
Alignment explanation
Indices: 21531561--21531593 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21531551 TTTTTTAATT
21531561 TTTTAA-ATATTTTTTA
1 TTTTAATATATTTTTTA
*
21531577 TTTTAATTTATTTTTTA
1 TTTTAATATATTTTTTA
21531594 CATTCTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTAATATATTTTTTA
Found at i:21536412 original size:8 final size:8
Alignment explanation
Indices: 21536363--21536393 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
21536353 TATTTCTTTA
21536363 AAAAAATT
1 AAAAAATT
21536371 AAAAAATT
1 AAAAAATT
21536379 AAAAAATT
1 AAAAAATT
21536387 GAAAAAA
1 -AAAAAA
21536394 AAACTACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (8 bp):
AAAAAATT
Found at i:21540498 original size:26 final size:26
Alignment explanation
Indices: 21540469--21540576 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
21540459 TGATACAAAT
*
21540469 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
21540495 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
21540521 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
21540547 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
21540573 TGAT
1 TGAT
21540577 GGGAATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:21543314 original size:16 final size:16
Alignment explanation
Indices: 21543284--21543313 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21543274 GGTTTACAAA
21543284 AAAAACAAAGATTTTC
1 AAAAACAAAGATTTTC
21543300 AAAAACAAA-ATTTT
1 AAAAACAAAGATTTT
21543314 TTTATAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAAACAAAGATTTTC
Found at i:21549862 original size:70 final size:71
Alignment explanation
Indices: 21549743--21549885 Score: 252
Period size: 70 Copynumber: 2.0 Consensus size: 71
21549733 TACCGGAAAT
* *
21549743 TCCATAAGCCTCAAACATGGGGTAGGGTGTCGATGCCGTGTCCCAGACATGGTCTTACACTGGCT
1 TCCATAAGCCTCAAACATGGGGTAAGGTGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCT
21549808 CATATC
66 CATATC
*
21549814 TCCAT-AGCCTCAAACGTGGGGTAAGGTGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCT
1 TCCATAAGCCTCAAACATGGGGTAAGGTGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCT
21549878 CATATC
66 CATATC
21549884 TC
1 TC
21549886 AAGTCGATGC
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
70 64 0.93
71 5 0.07
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.26
Consensus pattern (71 bp):
TCCATAAGCCTCAAACATGGGGTAAGGTGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCT
CATATC
Found at i:21549932 original size:47 final size:48
Alignment explanation
Indices: 21549841--21549966 Score: 161
Period size: 47 Copynumber: 2.7 Consensus size: 48
21549831 GGGGTAAGGT
*
21549841 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTC-AA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACTCATATCTCGAA
** *
21549888 GTCGATGCCATGTCCTGGACATGGTCTTACACTGACT-ATCATCTCGTA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACTCAT-ATCTCGAA
* *
21549936 GCCGATG-CATGTCCCAAACAT-GTCTTACACT
1 GTCGATGCCATGTCCCAGACATGGTCTTACACT
21549967 AGCACTCGTC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
46 12 0.17
47 50 0.72
48 7 0.10
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (48 bp):
GTCGATGCCATGTCCCAGACATGGTCTTACACTGACTCATATCTCGAA
Found at i:21551941 original size:94 final size:94
Alignment explanation
Indices: 21551819--21551990 Score: 256
Period size: 94 Copynumber: 1.8 Consensus size: 94
21551809 TATCTCAAGT
* * *
21551819 CGATGCCATGTTCTGGACATGGTCTTACACTGACTATCAT-CTCGTAGCCGATGCATGTCCCAAA
1 CGATGCCATGTCCTAGACATGGTCTTACACTGACTATCATAAT-GTAGCCGATGCATGTCCCAAA
21551883 CATGTCTTACACTAGCACTCGTCTTGATGC
65 CATGTCTTACACTAGCACTCGTCTTGATGC
* * * * *
21551913 CGATTCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGAC
1 CGATGCCATGTCCTAGACATGGTCTTACACTGACTATCATAATGTAGCCGATGCATGTCCCAAAC
21551978 ATGTCTTACACTA
66 ATGTCTTACACTA
21551991 ACCCATGATA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
94 68 0.99
95 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (94 bp):
CGATGCCATGTCCTAGACATGGTCTTACACTGACTATCATAATGTAGCCGATGCATGTCCCAAAC
ATGTCTTACACTAGCACTCGTCTTGATGC
Found at i:21551970 original size:47 final size:46
Alignment explanation
Indices: 21551780--21551989 Score: 169
Period size: 47 Copynumber: 4.5 Consensus size: 46
21551770 GTCGATGCCG
* *
21551780 TGTCCCAGACATGGTCTTACACTGG--CTCATATCTCAAGTCGATGCCA
1 TGTCCCAGACATGGTCTTACACTGGCTCTCATATGT--AGCCGATG-CA
* ** * * *
21551827 TGTTCTGGACATGGTCTTACACTGACTATCATCTCGTAGCCGATGCA
1 TGTCCCAGACATGGTCTTACACTGGCTCTCATAT-GTAGCCGATGCA
* * * * * *
21551874 TGTCCCAAACAT-GTCTTACACTAGCACTCGTCT-TGATGCCGATTCCA
1 TGTCCCAGACATGGTCTTACACTGGCTCTCATATGT-A-GCCGA-TGCA
* *
21551921 TGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCA
1 TGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATGTAGCCGATGCA
21551968 TGTCCCAGACAT-GTCTTACACT
1 TGTCCCAGACATGGTCTTACACT
21551990 AACCCATGAT
Statistics
Matches: 127, Mismatches: 27, Indels: 19
0.73 0.16 0.11
Matches are distributed among these distances:
44 1 0.01
45 1 0.01
46 31 0.24
47 58 0.46
48 28 0.22
49 6 0.05
50 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (46 bp):
TGTCCCAGACATGGTCTTACACTGGCTCTCATATGTAGCCGATGCA
Found at i:21562603 original size:40 final size:39
Alignment explanation
Indices: 21562566--21562657 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
21562556 GCTACTCGTT
*
21562566 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
21562606 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
21562645 CAAATGCCTTCGG
1 CAAATGCCTTCGG
21562658 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:21562637 original size:39 final size:40
Alignment explanation
Indices: 21562547--21562710 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
21562537 CGGAATTTAA
** *
21562547 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
21562587 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
21562626 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
21562666 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
21562706 CCGGA
1 CCGGA
21562711 CATCATTCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.30
40 58 0.55
41 12 0.11
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:21569016 original size:17 final size:16
Alignment explanation
Indices: 21568985--21569018 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
21568975 CCACACGACC
21568985 TGGCTACACGACCATG
1 TGGCTACACGACCATG
*
21569001 TGGCTCACATGACCATG
1 TGGCT-ACACGACCATG
21569018 T
1 T
21569019 ATTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (16 bp):
TGGCTACACGACCATG
Found at i:21569151 original size:6 final size:6
Alignment explanation
Indices: 21569131--21569309 Score: 218
Period size: 6 Copynumber: 29.8 Consensus size: 6
21569121 TTTATTTATT
* * * * * **
21569131 TTTTCTG TTTTTG TTTCTG TTTCTG TTTCTG TTTCTA TTTTTG TTTCCG
1 TTTT-TG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
*
21569180 TTTCTG TTTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
* * *
21569229 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTA TTTTTA TTTTT- ATTTT-
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
*
21569275 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTA TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
21569310 TAGTATGCAC
Statistics
Matches: 158, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
5 8 0.05
6 141 0.89
7 9 0.06
ACGTcount: A:0.03, C:0.04, G:0.13, T:0.80
Consensus pattern (6 bp):
TTTTTG
Found at i:21569190 original size:1 final size:1
Alignment explanation
Indices: 21569186--21569310 Score: 79
Period size: 1 Copynumber: 125.0 Consensus size: 1
21569176 TCCGTTTCTG
* * * * * * * * * *
21569186 TTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * *
21569251 TGTTTTTATTTTTATTTTTATTTTTTTTTGTTTTTGTTTTTGTTTTTGTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
21569311 AGTATGCACT
Statistics
Matches: 86, Mismatches: 38, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 86 1.00
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (1 bp):
T
Found at i:21571756 original size:16 final size:18
Alignment explanation
Indices: 21571724--21571756 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
21571714 TTTTTCACTA
21571724 ATAGCACTTATAAATAAG
1 ATAGCACTTATAAATAAG
21571742 ATAGCA-TTA-AAATAA
1 ATAGCACTTATAAATAA
21571757 CCTAGGTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (18 bp):
ATAGCACTTATAAATAAG
Found at i:21573191 original size:22 final size:22
Alignment explanation
Indices: 21573161--21573208 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
21573151 TTCTTTCCTG
21573161 TTTCGTTTTCAATTCTCTATTTC
1 TTTCGTTTTCAATT-TCTATTTC
* * *
21573184 TTTCTTTTTCTATTTTTATTTC
1 TTTCGTTTTCAATTTCTATTTC
21573206 TTT
1 TTT
21573209 ATTCTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTCGTTTTCAATTTCTATTTC
Found at i:21573219 original size:22 final size:22
Alignment explanation
Indices: 21573178--21573219 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
21573168 TTCAATTCTC
*
21573178 TATTTCTTTCTTTTTCTATTTT
1 TATTTCTTTATTTTTCTATTTT
21573200 TATTTCTTTATTCTTT-TATT
1 TATTTCTTTATT-TTTCTATT
21573220 ATCATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (22 bp):
TATTTCTTTATTTTTCTATTTT
Found at i:21573227 original size:8 final size:8
Alignment explanation
Indices: 21573216--21573282 Score: 59
Period size: 8 Copynumber: 8.4 Consensus size: 8
21573206 TTTATTCTTT
*
21573216 TATTATCA
1 TATTATTA
21573224 TATTATTA
1 TATTATTA
*
21573232 -ACTATTA
1 TATTATTA
21573239 TATTATTA
1 TATTATTA
*
21573247 TATTATAA
1 TATTATTA
21573255 T-TTACTTTA
1 TATTA--TTA
21573264 TATTATTA
1 TATTATTA
21573272 T-TTACTTA
1 TATTA-TTA
21573280 TAT
1 TAT
21573283 AATAAGTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 12 0.25
8 29 0.60
9 4 0.08
10 3 0.06
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (8 bp):
TATTATTA
Found at i:21573266 original size:17 final size:16
Alignment explanation
Indices: 21573244--21573287 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
21573234 TATTATATTA
21573244 TTATATTATAATTTAC
1 TTATATTATAATTTAC
*
21573260 TTTATATTATTATTTAC
1 -TTATATTATAATTTAC
*
21573277 TTATATAATAA
1 TTATATTATAA
21573288 GTAAATACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATTATAATTTAC
Found at i:21573485 original size:19 final size:20
Alignment explanation
Indices: 21573451--21573488 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
21573441 GTCGTTTTCA
21573451 CTAAATTAACCTTAATTAAG
1 CTAAATTAACCTTAATTAAG
*
21573471 CTAAATTTA-CTTAATTAA
1 CTAAATTAACCTTAATTAA
21573489 AAATCTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
CTAAATTAACCTTAATTAAG
Found at i:21579286 original size:22 final size:22
Alignment explanation
Indices: 21579235--21579300 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
21579225 GGTATTTGGG
* * *
21579235 AATTGGTTCGAAGTAGTATGG-
1 AATTGGTACGAAATGGTATGGT
21579256 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
21579278 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
21579301 TCAAAGAGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 18 0.47
22 15 0.39
23 5 0.13
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:21583507 original size:14 final size:14
Alignment explanation
Indices: 21583473--21583514 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
21583463 TCCAGAAAAC
*
21583473 AAATAAAAATAATC
1 AAATAAAAATAATA
*
21583487 CAA-AAAAATAATA
1 AAATAAAAATAATA
*
21583500 AAATAAAAGTAATA
1 AAATAAAAATAATA
21583514 A
1 A
21583515 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (14 bp):
AAATAAAAATAATA
Found at i:21585345 original size:18 final size:18
Alignment explanation
Indices: 21585322--21585365 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
21585312 AATAAATTTT
21585322 TAATTAAATAATTTT-AAC
1 TAATTAAA-AATTTTAAAC
*
21585340 TAATTAAAAATTTTAAAT
1 TAATTAAAAATTTTAAAC
21585358 TAATTAAA
1 TAATTAAA
21585366 CTGAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATTAAAAATTTTAAAC
Found at i:21588711 original size:21 final size:21
Alignment explanation
Indices: 21588685--21588726 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21588675 AAGGGTGTAA
21588685 GAATGTATCCCTTAAAGGAGT
1 GAATGTATCCCTTAAAGGAGT
* *
21588706 GAATGTATCCTTTAAGGGAGT
1 GAATGTATCCCTTAAAGGAGT
21588727 TAATATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (21 bp):
GAATGTATCCCTTAAAGGAGT
Found at i:21589098 original size:23 final size:23
Alignment explanation
Indices: 21589071--21589150 Score: 61
Period size: 23 Copynumber: 3.2 Consensus size: 23
21589061 TTGAACTTGG
21589071 ATTTTTAAAAATAAATATAAAAA
1 ATTTTTAAAAATAAATATAAAAA
* * **
21589094 ATTTTAAATTCTGAAAAATAAAGAGATTAA
1 A--TT---TT-T-AAAAATAAATATAAAAA
21589124 ATTTTTAAAAATAAATATAAAAA
1 ATTTTTAAAAATAAATATAAAAA
21589147 ATTT
1 ATTT
21589151 AAATTCCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
23 18 0.43
24 1 0.02
25 4 0.10
28 4 0.10
29 1 0.02
30 14 0.33
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (23 bp):
ATTTTTAAAAATAAATATAAAAA
Found at i:21589734 original size:31 final size:30
Alignment explanation
Indices: 21589699--21589782 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
21589689 ATTTAACATA
*
21589699 ATTAATCATAAATATTGTAAT-TTTTAGTATT
1 ATTAATCATAAATAATGTAATATTTT--TATT
* *
21589730 ATTAAACATATATAATGTAATATTTTTATT
1 ATTAATCATAAATAATGTAATATTTTTATT
* * *
21589760 -TTAATAATAAATAAGGAAATATT
1 ATTAATCATAAATAATGTAATATT
21589783 AATATAACCA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 18 0.41
30 4 0.09
31 18 0.41
32 4 0.09
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.46
Consensus pattern (30 bp):
ATTAATCATAAATAATGTAATATTTTTATT
Found at i:21595176 original size:187 final size:186
Alignment explanation
Indices: 21594812--21595352 Score: 716
Period size: 187 Copynumber: 2.9 Consensus size: 186
21594802 CCAGATGTTT
* * *
21594812 TGTTTTGAAGAATAAAAATGTTGTTTGGCAAGAGAGAAAATGAGAGA-AAAAAATGGCA-AT--C
1 TGTTTTGAAGAAGAAAAATGGTGTTTGGCAAGAGAGAAAATGAGAGAGAAAAAATGGCAGCTGAC
* * * * * * *
21594873 GATAGTAAGGTAAAAACAATGATTTTAAGTTGAAAGTGTGGTGTAAGTTTACAAAAAATTGCACG
66 AATAG-AGGGAAAAAACAATGATTTTAAGTTGAAAGTATGGTGTGAGTTTAC-AAAAATTACACA
* * * * * *
21594938 AAAGCATGATTGTAATCATCGTGATGGAAATTCTTGCAGACGAAATGAGCCAACCATG
129 AAAGCATGATTATAATCATAGTAATGGAAATTCTTGTAGATGAAATGAGCCAACCATA
* *
21594996 TGTTTTGAAGAAGAAAAATGGTGTTTGGGAAGAGAGAAAATGAGAGAGAAAAAATGGTAGCTGAC
1 TGTTTTGAAGAAGAAAAATGGTGTTTGGCAAGAGAGAAAATGAGAGAGAAAAAATGGCAGCTGAC
* *
21595061 AATTGAGGGAAAAAACCAATGATTTTAAGTTGAAAGTATGGTGTGCGTTTACAAAAATTACACAA
66 AATAGAGGGAAAAAA-CAATGATTTTAAGTTGAAAGTATGGTGTGAGTTTACAAAAATTACACAA
* *
21595126 AAGCATTATTATAATCATAGTAATGGAAATTCTTATAGATGAAATGAGCCAACCATA
130 AAGCATGATTATAATCATAGTAATGGAAATTCTTGTAGATGAAATGAGCCAACCATA
* *
21595183 TATTTTGAAGAAGAAAAATGGTGTTTGGCAAGAGAGAAAATCAGAG-GAAAAAAATGGCAGCTGA
1 TGTTTTGAAGAAGAAAAATGGTGTTTGGCAAGAGAGAAAATGAGAGAG-AAAAAATGGCAGCTGA
* * * * * *
21595247 TAGTGGAGGGAAAAAACAATGATTTTAAGCTGAACGTGA-GGTGTGGGTTTACAAAAATTACACA
65 CAATAGAGGGAAAAAACAATGATTTTAAGTTGAAAGT-ATGGTGTGAGTTTACAAAAATTACACA
*
21595311 AAAGCATGATTATAATCATGGTAATGGAAATTCTTGTAGATG
129 AAAGCATGATTATAATCATAGTAATGGAAATTCTTGTAGATG
21595353 TGATCATGGT
Statistics
Matches: 315, Mismatches: 35, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
184 44 0.14
185 10 0.03
186 84 0.27
187 140 0.44
188 37 0.12
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (186 bp):
TGTTTTGAAGAAGAAAAATGGTGTTTGGCAAGAGAGAAAATGAGAGAGAAAAAATGGCAGCTGAC
AATAGAGGGAAAAAACAATGATTTTAAGTTGAAAGTATGGTGTGAGTTTACAAAAATTACACAAA
AGCATGATTATAATCATAGTAATGGAAATTCTTGTAGATGAAATGAGCCAACCATA
Found at i:21595361 original size:30 final size:30
Alignment explanation
Indices: 21595325--21595382 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
21595315 CATGATTATA
*
21595325 ATCATGGTAATGGAAATTCTTGTAGATGTG
1 ATCATGGTAATGGAAATTCTTATAGATGTG
21595355 ATCATGGTAATGGAAATTCTTATAGATG
1 ATCATGGTAATGGAAATTCTTATAGATG
21595383 AAATGAGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (30 bp):
ATCATGGTAATGGAAATTCTTATAGATGTG
Found at i:21602378 original size:19 final size:19
Alignment explanation
Indices: 21602332--21602379 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
21602322 GTATATAATT
21602332 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
21602350 TAAATGTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
21602369 TAAGTTTTATT
1 TAAATTTTATT
21602380 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:21605844 original size:27 final size:27
Alignment explanation
Indices: 21605814--21605903 Score: 128
Period size: 28 Copynumber: 3.3 Consensus size: 27
21605804 TGACAGAGTT
* **
21605814 ACCAGATACAAATA-TTGTGGCGGAGCC
1 ACCAGA-ACAGATATTTGTGGCATAGCC
21605841 ACCAGAACAGATATTTGTGGCATAGCC
1 ACCAGAACAGATATTTGTGGCATAGCC
21605868 ACCAGAAACAGATATTTGTGGCATAGCC
1 ACCAG-AACAGATATTTGTGGCATAGCC
21605896 ACCAGAAC
1 ACCAGAAC
21605904 GCTTCCTCCA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
26 6 0.10
27 25 0.43
28 27 0.47
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (27 bp):
ACCAGAACAGATATTTGTGGCATAGCC
Found at i:21605886 original size:28 final size:27
Alignment explanation
Indices: 21605789--21605902 Score: 124
Period size: 27 Copynumber: 4.2 Consensus size: 27
21605779 AGCATGGCTG
* **
21605789 CCAG-AACAGATATTGTGACAGAGTTA
1 CCAGAAACAGATATTGTGGCAGAGCCA
* * *
21605815 CCAGATACAAATATTGTGGCGGAGCCA
1 CCAGAAACAGATATTGTGGCAGAGCCA
*
21605842 CCAG-AACAGATATTTGTGGCATAGCCA
1 CCAGAAACAGATA-TTGTGGCAGAGCCA
*
21605869 CCAGAAACAGATATTTGTGGCATAGCCA
1 CCAGAAACAGATA-TTGTGGCAGAGCCA
21605897 CCAGAA
1 CCAGAA
21605903 CGCTTCCTCC
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
26 10 0.13
27 36 0.48
28 29 0.39
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (27 bp):
CCAGAAACAGATATTGTGGCAGAGCCA
Found at i:21605900 original size:55 final size:53
Alignment explanation
Indices: 21605789--21605903 Score: 140
Period size: 54 Copynumber: 2.1 Consensus size: 53
21605779 AGCATGGCTG
** * *
21605789 CCAGAACAGATATTGTGACAGAGTTACCAGATACAAATATTGTGGCGGAGCCA
1 CCAGAACAGATATTGTGACAGAGCCACCAGAAACAAATATTGTGGCAGAGCCA
* * * *
21605842 CCAGAACAGATATTTGTGGCATAGCCACCAGAAACAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-TTGTGACAGAGCCACCAGAAACAAATA-TTGTGGCAGAGCCA
21605897 CCAGAAC
1 CCAGAAC
21605904 GCTTCCTCCA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 12 0.23
54 21 0.40
55 19 0.37
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (53 bp):
CCAGAACAGATATTGTGACAGAGCCACCAGAAACAAATATTGTGGCAGAGCCA
Found at i:21607005 original size:79 final size:79
Alignment explanation
Indices: 21606897--21607056 Score: 311
Period size: 79 Copynumber: 2.0 Consensus size: 79
21606887 AGATTCGGAT
21606897 ATTGAAAAATAATGAAGAAAGGAAAATAAGGAAAGAGACAGAGAGAGAAGAGTATGGGTTCGACT
1 ATTGAAAAATAATGAAGAAAGGAAAATAAGGAAAGAGACAGAGAGAGAAGAGTATGGGTTCGACT
21606962 ATGGAGAAAAGAAA
66 ATGGAGAAAAGAAA
*
21606976 ATTGAAAAATAATGAAGAAAGGAAAATAAGGAAAGAGACAGAGAGAGAAGAGTATGGGTTCGGCT
1 ATTGAAAAATAATGAAGAAAGGAAAATAAGGAAAGAGACAGAGAGAGAAGAGTATGGGTTCGACT
21607041 ATGGAGAAAAGAAA
66 ATGGAGAAAAGAAA
21607055 AT
1 AT
21607057 ATGGAAGAAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.53, C:0.04, G:0.29, T:0.14
Consensus pattern (79 bp):
ATTGAAAAATAATGAAGAAAGGAAAATAAGGAAAGAGACAGAGAGAGAAGAGTATGGGTTCGACT
ATGGAGAAAAGAAA
Found at i:21607061 original size:16 final size:17
Alignment explanation
Indices: 21607040--21607072 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21607030 TGGGTTCGGC
21607040 TATGG-AGAAAAGAAAA
1 TATGGAAGAAAAGAAAA
21607056 TATGGAAGAAAAGAAAA
1 TATGGAAGAAAAGAAAA
21607073 GGTGAGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (17 bp):
TATGGAAGAAAAGAAAA
Found at i:21626090 original size:13 final size:13
Alignment explanation
Indices: 21626072--21626107 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
21626062 GATACCACAC
21626072 GCTCATGTGGCGT
1 GCTCATGTGGCGT
21626085 GCTCATGTGGCGT
1 GCTCATGTGGCGT
*
21626098 GCTCGTGTGG
1 GCTCATGTGG
21626108 GCCCACACGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.06, C:0.22, G:0.42, T:0.31
Consensus pattern (13 bp):
GCTCATGTGGCGT
Found at i:21629747 original size:6 final size:5
Alignment explanation
Indices: 21629718--21629776 Score: 64
Period size: 6 Copynumber: 10.6 Consensus size: 5
21629708 ATTGAGTCCA
21629718 TTTAT TTTAT TTTAT TTTATT TTTAGT TTTAT TTCTATT TTTAT GTTTAT
1 TTTAT TTTAT TTTAT TTTA-T TTTA-T TTTAT TT-TA-T TTTAT -TTTAT
21629768 TGTTAT TTT
1 T-TTAT TTT
21629777 CTTAGACTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
5 21 0.44
6 24 0.50
7 3 0.06
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:21634803 original size:13 final size:13
Alignment explanation
Indices: 21634785--21634811 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21634775 ATAATTTTTC
21634785 TAATATCTTATCT
1 TAATATCTTATCT
21634798 TAATATCTTATCT
1 TAATATCTTATCT
21634811 T
1 T
21634812 TAGATGAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATATCTTATCT
Found at i:21644404 original size:42 final size:44
Alignment explanation
Indices: 21644344--21644469 Score: 152
Period size: 42 Copynumber: 2.9 Consensus size: 44
21644334 GTTATCAAAT
* * *
21644344 ATCGATGCCACTGACCCAAACAGGGTCTTACACGAAATCAT-AT
1 ATCGATGCCAATGTCCCAAACAGGGTCTTACACGAAATCATCAA
* *
21644387 A-CGATGCTAATGTCCCAAACATGGTCTTACACGTAAATC-TCAA
1 ATCGATGCCAATGTCCCAAACAGGGTCTTACACG-AAATCATCAA
*
21644430 ATCGATGCCAATGTCCCAGAC-GTGGTCTTACACGAAATCA
1 ATCGATGCCAATGTCCCAAACAG-GGTCTTACACGAAATCA
21644470 CATATCAGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
42 29 0.41
43 13 0.19
44 28 0.40
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (44 bp):
ATCGATGCCAATGTCCCAAACAGGGTCTTACACGAAATCATCAA
Found at i:21644488 original size:44 final size:42
Alignment explanation
Indices: 21644323--21644488 Score: 138
Period size: 43 Copynumber: 3.8 Consensus size: 42
21644313 GTTCCAGATG
* ** * *
21644323 TGGTCTTACATGTTATCAAATATCGATGCC-ACTGACCCAAACA
1 TGGTCTTACACGAAATCACATATCGAT-CCTA-TGTCCCAAACA
* * *
21644366 GGGTCTTACACGAAATCATATA-CGATGCTAATGTCCCAAACA
1 TGGTCTTACACGAAATCACATATCGATCCT-ATGTCCCAAACA
* * * * *
21644408 TGGTCTTACACGTAAATCTCAAATCGATGCCAATGTCCCAGACG
1 TGGTCTTACACG-AAATCACATATCGAT-CCTATGTCCCAAACA
21644452 TGGTCTTACACGAAATCACATATCAGAATCCTATGTC
1 TGGTCTTACACGAAATCACATATC-G-ATCCTATGTC
21644489 ATGACATATG
Statistics
Matches: 98, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
41 1 0.01
42 25 0.26
43 35 0.36
44 34 0.35
45 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (42 bp):
TGGTCTTACACGAAATCACATATCGATCCTATGTCCCAAACA
Found at i:21645574 original size:13 final size:13
Alignment explanation
Indices: 21645556--21645580 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21645546 ACAAAAGATA
21645556 AAATTTTCACACG
1 AAATTTTCACACG
21645569 AAATTTTCACAC
1 AAATTTTCACAC
21645581 ATATCACATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:21646595 original size:41 final size:41
Alignment explanation
Indices: 21646544--21646682 Score: 262
Period size: 41 Copynumber: 3.4 Consensus size: 41
21646534 TGCGATTACT
21646544 TGACAGCTTGTGTGAGCAGCACCAAGTAGCTACGTCTTGAC
1 TGACAGCTTGTGTGAGCAGCACCAAGTAGCTACGTCTTGAC
21646585 TGACAGCTTGTGTGAGCAGCACCAAGTAGCTACGTCTTGAC
1 TGACAGCTTGTGTGAGCAGCACCAAGTAGCTACGTCTTGAC
21646626 TGACAGCTTGTGTGAGCAGCACCAAGTAGCTACGTCTTGAC
1 TGACAGCTTGTGTGAGCAGCACCAAGTAGCTACGTCTTGAC
21646667 TGGA-AGCTTGTGTGAG
1 T-GACAGCTTGTGTGAG
21646683 AAGGCCCATT
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
41 95 0.98
42 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (41 bp):
TGACAGCTTGTGTGAGCAGCACCAAGTAGCTACGTCTTGAC
Found at i:21650456 original size:15 final size:17
Alignment explanation
Indices: 21650426--21650457 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
21650416 TTGATACTTG
21650426 TGAATGTGAGTTTGGTA
1 TGAATGTGAGTTTGGTA
21650443 TGAAT-TGA-TTTGGTA
1 TGAATGTGAGTTTGGTA
21650458 AATTATGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (17 bp):
TGAATGTGAGTTTGGTA
Found at i:21657724 original size:37 final size:37
Alignment explanation
Indices: 21657634--21657728 Score: 113
Period size: 37 Copynumber: 2.6 Consensus size: 37
21657624 TCTATCGAGC
*
21657634 CAAATCTTACTGTTATACTGAATGAAGCTCAACCGAG
1 CAAATCTTACTGTTATACTGAATGAAGCTCAACAGAG
* *
21657671 CAAGTCATA-TCGTTATACTGAATGGAA-CTCAACAGAG
1 CAAATCTTACT-GTTATACTGAAT-GAAGCTCAACAGAG
* *
21657708 CAAATTTTACTATTATACTGA
1 CAAATCTTACTGTTATACTGA
21657729 CTAGTGTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
36 1 0.02
37 43 0.90
38 4 0.08
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (37 bp):
CAAATCTTACTGTTATACTGAATGAAGCTCAACAGAG
Found at i:21670810 original size:10 final size:10
Alignment explanation
Indices: 21670795--21670822 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
21670785 CGCCAAATAC
21670795 AGAGATGAGT
1 AGAGATGAGT
21670805 AGAGATGAGT
1 AGAGATGAGT
21670815 AGAGATGA
1 AGAGATGA
21670823 TGGAAAAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.39, T:0.18
Consensus pattern (10 bp):
AGAGATGAGT
Found at i:21676290 original size:308 final size:308
Alignment explanation
Indices: 21675732--21676353 Score: 1235
Period size: 308 Copynumber: 2.0 Consensus size: 308
21675722 TCAGTCTAAA
21675732 AAATTTGGCCTCTTACTTAACCATTGATCGATCTCCCTGAGTGAGGTTCAAAAACCCACTTCTAC
1 AAATTTGGCCTCTTACTTAACCATTGATCGATCTCCCTGAGTGAGGTTCAAAAACCCACTTCTAC
21675797 GAGCATCGATGTAACTTGCTCCCACATACTTCCTTTGGAAGGTAGACTTAAAGAACTACCAAGAC
66 GAGCATCGATGTAACTTGCTCCCACATACTTCCTTTGGAAGGTAGACTTAAAGAACTACCAAGAC
21675862 AGACGGTCGGGCTGAGTGCCCTCCTTAGCGGTCAGCCACCACTAATAGGCCTCATTGCGAAGCAA
131 AGACGGTCGGGCTGAGTGCCCTCCTTAGCGGTCAGCCACCACTAATAGGCCTCATTGCGAAGCAA
21675927 CGAGACAGCACCCCTCAATTTCTACTTAGGGGTACAGTCTAAATCATCCATTATCCTCTTAGTAG
196 CGAGACAGCACCCCTCAATTTCTACTTAGGGGTACAGTCTAAATCATCCATTATCCTCTTAGTAG
*
21675992 CCTCCATTCAGTACTCAGCCACATTAGGGCGACTCCAGTGACACCCTT
261 CCTCCATCCAGTACTCAGCCACATTAGGGCGACTCCAGTGACACCCTT
21676040 AAATTTGGCCTCTTACTTAACCATTGATCGATCTCCCTGAGTGAGGTTCAAAAACCCACTTCTAC
1 AAATTTGGCCTCTTACTTAACCATTGATCGATCTCCCTGAGTGAGGTTCAAAAACCCACTTCTAC
21676105 GAGCATCGATGTAACTTGCTCCCACATACTTCCTTTGGAAGGTAGACTTAAAGAACTACCAAGAC
66 GAGCATCGATGTAACTTGCTCCCACATACTTCCTTTGGAAGGTAGACTTAAAGAACTACCAAGAC
21676170 AGACGGTCGGGCTGAGTGCCCTCCTTAGCGGTCAGCCACCACTAATAGGCCTCATTGCGAAGCAA
131 AGACGGTCGGGCTGAGTGCCCTCCTTAGCGGTCAGCCACCACTAATAGGCCTCATTGCGAAGCAA
21676235 CGAGACAGCACCCCTCAATTTCTACTTAGGGGTACAGTCTAAATCATCCATTATCCTCTTAGTAG
196 CGAGACAGCACCCCTCAATTTCTACTTAGGGGTACAGTCTAAATCATCCATTATCCTCTTAGTAG
21676300 CCTCCATCCAGTACTCAGCCACATTAGGGCGACTCCAGTGACACCCTT
261 CCTCCATCCAGTACTCAGCCACATTAGGGCGACTCCAGTGACACCCTT
21676348 AAATTT
1 AAATTT
21676354 TCAGCTCCAT
Statistics
Matches: 313, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
308 313 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (308 bp):
AAATTTGGCCTCTTACTTAACCATTGATCGATCTCCCTGAGTGAGGTTCAAAAACCCACTTCTAC
GAGCATCGATGTAACTTGCTCCCACATACTTCCTTTGGAAGGTAGACTTAAAGAACTACCAAGAC
AGACGGTCGGGCTGAGTGCCCTCCTTAGCGGTCAGCCACCACTAATAGGCCTCATTGCGAAGCAA
CGAGACAGCACCCCTCAATTTCTACTTAGGGGTACAGTCTAAATCATCCATTATCCTCTTAGTAG
CCTCCATCCAGTACTCAGCCACATTAGGGCGACTCCAGTGACACCCTT
Found at i:21679337 original size:26 final size:28
Alignment explanation
Indices: 21679278--21679338 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
21679268 AGGTGTTTTT
21679278 CTATTTT-TAAATAATAAAAAATAAAAA
1 CTATTTTCTAAATAATAAAAAATAAAAA
*
21679305 CTCTTTTCTAAA-AAT-AAAAATAGAAAA
1 CTATTTTCTAAATAATAAAAAATA-AAAA
21679332 -TATTTTC
1 CTATTTTC
21679339 AGAAACCACT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 13 0.43
27 13 0.43
28 4 0.13
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36
Consensus pattern (28 bp):
CTATTTTCTAAATAATAAAAAATAAAAA
Found at i:21679447 original size:14 final size:14
Alignment explanation
Indices: 21679430--21679456 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21679420 ATGATTGAAA
21679430 ATTTTAAAAATGAT
1 ATTTTAAAAATGAT
21679444 ATTTTAAAAATGA
1 ATTTTAAAAATGA
21679457 AGATAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
ATTTTAAAAATGAT
Found at i:21679955 original size:30 final size:30
Alignment explanation
Indices: 21679919--21679981 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
21679909 ACTTATTTTA
*
21679919 TTGTTAATTTTATTATTATTTTAAAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
21679949 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
21679979 TTG
1 TTG
21679982 CTTGTTAAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:21681569 original size:19 final size:19
Alignment explanation
Indices: 21681545--21681581 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
21681535 TATGAGTTAT
21681545 ATATTTTT-ATAACTTTTTA
1 ATATTTTTAATAA-TTTTTA
21681564 ATATTTTTAATAATTTTT
1 ATATTTTTAATAATTTTT
21681582 TTTAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
ATATTTTTAATAATTTTTA
Found at i:21681692 original size:18 final size:20
Alignment explanation
Indices: 21681635--21681704 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
21681625 AAAAATTAAA
*
21681635 TAAT-AATTTTCATAATATTT
1 TAATGAATTTTTATAA-ATTT
* * *
21681655 T-ATAAATTATAATAAATTT
1 TAATGAATTTTTATAAATTT
*
21681674 T-ATG-ATTTTTATAATTTT
1 TAATGAATTTTTATAAATTT
21681692 TAATGAATTTTTA
1 TAATGAATTTTTA
21681705 CTTACATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
18 12 0.29
19 12 0.29
20 17 0.41
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (20 bp):
TAATGAATTTTTATAAATTT
Found at i:21681702 original size:19 final size:18
Alignment explanation
Indices: 21681639--21681702 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
21681629 ATTAAATAAT
*
21681639 AATTTTCATAATATTTTATA
1 AATTTT-ATAAT-TTTTATG
* *
21681659 AATTATAATAAATTTTATG
1 AATT-TTATAATTTTTATG
*
21681678 ATTTTTATAATTTTTAATG
1 AATTTTATAATTTTT-ATG
21681697 AATTTT
1 AATTTT
21681703 TACTTACATA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
18 9 0.26
19 17 0.49
20 8 0.23
21 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (18 bp):
AATTTTATAATTTTTATG
Found at i:21692948 original size:25 final size:25
Alignment explanation
Indices: 21692914--21692962 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
21692904 TTTAGATTTT
* * *
21692914 TATAATTTTTATAATTTTTTTAAAA
1 TATAAATTTTAGAATTTTTATAAAA
*
21692939 TATAAATTTTGGAATTTTTATAAA
1 TATAAATTTTAGAATTTTTATAAA
21692963 TTTTTTGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
TATAAATTTTAGAATTTTTATAAAA
Found at i:21693878 original size:14 final size:14
Alignment explanation
Indices: 21693859--21693896 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
21693849 TATTTAGATT
21693859 TTTTAT-TTATTAAA
1 TTTTATATT-TTAAA
21693873 TTTTATATTTTAAA
1 TTTTATATTTTAAA
*
21693887 TTTTAAATTT
1 TTTTATATTT
21693897 GCTAACTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 20 0.91
15 2 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTATATTTTAAA
Found at i:21699566 original size:19 final size:19
Alignment explanation
Indices: 21699542--21699586 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
21699532 ATTACTAATT
21699542 ATTCTAAGTTTTAGATAAC
1 ATTCTAAGTTTTAGATAAC
21699561 ATTCTAAGTTTTAGATAAC
1 ATTCTAAGTTTTAGATAAC
21699580 ATTCTAA
1 ATTCTAA
21699587 CATTTTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (19 bp):
ATTCTAAGTTTTAGATAAC
Found at i:21699730 original size:16 final size:16
Alignment explanation
Indices: 21699689--21699732 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
21699679 TAAAAATGTG
21699689 ATAAT-TTTAAT-TGA
1 ATAATATTTAATATGA
*
21699703 ATAAAATATTAATATGA
1 ATAATAT-TTAATATGA
21699720 ATAATATTTAATA
1 ATAATATTTAATA
21699733 ACTATAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 4 0.16
15 1 0.04
16 11 0.44
17 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (16 bp):
ATAATATTTAATATGA
Found at i:21700365 original size:15 final size:15
Alignment explanation
Indices: 21700341--21700383 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
21700331 TGTGAGTTTA
*
21700341 TTTAAAAATTCAATT
1 TTTAATAATTCAATT
21700356 TTTAATAATT-ACATT
1 TTTAATAATTCA-ATT
21700371 TTTAATAA-TCAAT
1 TTTAATAATTCAAT
21700384 ATTAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTAATAATTCAATT
Found at i:21704786 original size:57 final size:58
Alignment explanation
Indices: 21704708--21704830 Score: 221
Period size: 57 Copynumber: 2.1 Consensus size: 58
21704698 TAAACGGAAA
21704708 GAATAAATCCCGAAATAGAATTATTTGATTACGTCTCTATTTGGAAATAAAACAATATC
1 GAATAAA-CCCGAAATAGAATTATTTGATTACGTCTCTATTTGGAAATAAAACAATATC
21704767 GAATAAA-CCGAAATAGAATTATTTGATTACGTCTCTATTTGGAAATAAAACAATATC
1 GAATAAACCCGAAATAGAATTATTTGATTACGTCTCTATTTGGAAATAAAACAATATC
*
21704824 AAATAAA
1 GAATAAA
21704831 ATCTTATTAA
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 56 0.89
59 7 0.11
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (58 bp):
GAATAAACCCGAAATAGAATTATTTGATTACGTCTCTATTTGGAAATAAAACAATATC
Found at i:21704926 original size:86 final size:87
Alignment explanation
Indices: 21704813--21704979 Score: 284
Period size: 86 Copynumber: 1.9 Consensus size: 87
21704803 ATTTGGAAAT
* * *
21704813 AAAACAATATCAAATAAAATCTTATTAAACGGTGGGAATAAATCTCGAAACAGATTTTATTTTAT
1 AAAACAATATCAAATAAAATCTTATTAAACGATGGGAATAAATCTCGAAACAGATTTTATATAAT
21704878 TTAATTTCTCATTTTTAGCAAC
66 TTAATTTCTCATTTTTAGCAAC
21704900 AAAATCAA-ATCAAAT-AAATCTTATTAAACGATGGGAATAAATCTCGAAACAGATTTTATATAA
1 AAAA-CAATATCAAATAAAATCTTATTAAACGATGGGAATAAATCTCGAAACAGATTTTATATAA
21704963 TTTAATTTCTCATTTTT
65 TTTAATTTCTCATTTTT
21704980 GGAAATAAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
86 62 0.82
87 11 0.14
88 3 0.04
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (87 bp):
AAAACAATATCAAATAAAATCTTATTAAACGATGGGAATAAATCTCGAAACAGATTTTATATAAT
TTAATTTCTCATTTTTAGCAAC
Found at i:21705021 original size:86 final size:80
Alignment explanation
Indices: 21704804--21705240 Score: 317
Period size: 78 Copynumber: 5.4 Consensus size: 80
21704794 TACGTCTCTA
* ** *
21704804 TTTGGAAATAAAAC-AATATCAAATAAAATCTTATTAAACGGTGGGAATAAATCTCGAAACAGAT
1 TTTGGAAATAAAACAAATTTGGAATAAAATC--ATTGAACGGTGGGAATAAATCTCGAAAC-GA-
*
21704868 TTTATTTTATTTAATTTCTCATT
62 --T-TTTTATTTTA-TTCTCATT
* * * ** * *
21704891 TTTAGCAACAAAATCAAA--TCAAAT-AAATCTTATTAAACGATGGGAATAAATCTCGAAACAGA
1 TTTGGAAATAAAA-CAAATTTGGAATAAAATC--ATTGAACGGTGGGAATAAATCTCGAAAC-GA
21704953 TTTTATATAATTTAATTTCTCATT
62 TTTT-TAT--TTT-A-TTCTCATT
* * *
21704977 TTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAATGGTGGGAATCAATC-CTGAAACGATTT
1 TTTGGAAATAAAACAAATTTGGAATAAAATCATTGAACGGTGGGAATAAATCTC-GAAACGATTT
*
21705041 TTATTTTA--CTCACT
65 TTATTTTATTCTCATT
* ** * *
21705055 TTTGGAAATAAAA-AAATTTGGAATAAAATCATTGAACGGCGGGAATCGATCCCAAAACGATTTT
1 TTTGGAAATAAAACAAATTTGGAATAAAATCATTGAACGGTGGGAATAAATCTCGAAACGATTTT
*
21705119 TATTTTACT-TC-TT
66 TATTTTATTCTCATT
* * ** * * *
21705132 TTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGACT-GGAATCGATCCCAAAACG-GTT
1 TTTGGAAATAAAACAAATTTGGAATAAAATCATTGAACG-GTGGGAATAAATCTCGAAACGATTT
*
21705195 TTATTTTA--CTCGTTT
65 TTATTTTATTCTC-ATT
*
21705210 TTTGGAAATAAAACAAATTTAGAATAAAATC
1 TTTGGAAATAAAACAAATTTGGAATAAAATC
21705241 GTGGAACGAC
Statistics
Matches: 305, Mismatches: 27, Indels: 45
0.81 0.07 0.12
Matches are distributed among these distances:
76 2 0.01
77 75 0.25
78 95 0.31
81 1 0.00
82 6 0.02
83 4 0.01
84 3 0.01
85 13 0.04
86 78 0.26
87 20 0.07
88 6 0.02
89 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (80 bp):
TTTGGAAATAAAACAAATTTGGAATAAAATCATTGAACGGTGGGAATAAATCTCGAAACGATTTT
TATTTTATTCTCATT
Found at i:21705113 original size:77 final size:78
Alignment explanation
Indices: 21704963--21705285 Score: 411
Period size: 78 Copynumber: 4.1 Consensus size: 78
21704953 TTTTATATAA
* * **
21704963 TTTAATTT-CTCATTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAATGGTGGGAATCAA
1 TTTATTTTACTCATTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGACGGGAATCAA
**
21705027 TCCTGAAACGATT
66 TCCCAAAACGATT
* * * *
21705040 TTTATTTTACTCACTTTTGGAAATAAAA-AAATTTGGAATAAAATCATTGAACGGCGGGAATCGA
1 TTTATTTTACTCATTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGACGGGAATCAA
21705104 TCCCAAAACGATT
66 TCCCAAAACGATT
* *
21705117 TTTATTTTACTTC-TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGACTGGAATCG
1 TTTATTTTAC-TCATTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGACGGGAATCA
*
21705181 ATCCCAAAACG-GT
65 ATCCCAAAACGATT
* * * *
21705194 TTTATTTTACTCGTTTTTTGGAAATAAAACAAATTTAGAATAAAATCGTGGAACGACGGAAATCA
1 TTTATTTTACTC-ATTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGACGGGAATCA
* *
21705259 AGCCCAAAACAATTTT
65 ATCCCAAAACGA--TT
21705275 TTTATTTTACT
1 TTTATTTTACT
21705286 TTTTAATTTC
Statistics
Matches: 217, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
76 2 0.01
77 85 0.39
78 118 0.54
81 12 0.06
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (78 bp):
TTTATTTTACTCATTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGACGGGAATCAA
TCCCAAAACGATT
Found at i:21705178 original size:155 final size:157
Alignment explanation
Indices: 21704975--21705286 Score: 425
Period size: 155 Copynumber: 2.0 Consensus size: 157
21704965 TAATTTCTCA
* * ** *
21704975 TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAATGGTGGGAATCAATCCTGAAACGATT
1 TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGCTGGGAATCAATCCCAAAACG-GT
* * * * *
21705040 TTTATTTTACTC-ACTTTTGGAAATAAAA-AAATTTGGAATAAAATCATTGAACGGCGGGAATCG
65 TTTATTTTACTCGACTTTTGGAAATAAAACAAATTTAGAATAAAATCATGGAACGACGGAAATCA
* *
21705103 ATCCCAAAACGA-TTTTTATTTTACTTC
130 AGCCCAAAACAATTTTTTATTTTACTTC
*
21705130 TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGACT-GGAATCGATCCCAAAACGGT
1 TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACG-CTGGGAATCAATCCCAAAACGGT
** *
21705194 TTTATTTTACTCGTTTTTTGGAAATAAAACAAATTTAGAATAAAATCGTGGAACGACGGAAATCA
65 TTTATTTTACTCGACTTTTGGAAATAAAACAAATTTAGAATAAAATCATGGAACGACGGAAATCA
21705259 AGCCCAAAACAATTTTTTTATTTTACTT
130 AGCCCAAAACAA-TTTTTTATTTTACTT
21705287 TTTAATTTCT
Statistics
Matches: 136, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
154 13 0.10
155 69 0.51
156 40 0.29
158 14 0.10
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (157 bp):
TTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGCTGGGAATCAATCCCAAAACGGTT
TTATTTTACTCGACTTTTGGAAATAAAACAAATTTAGAATAAAATCATGGAACGACGGAAATCAA
GCCCAAAACAATTTTTTATTTTACTTC
Found at i:21710893 original size:29 final size:29
Alignment explanation
Indices: 21710860--21710953 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
21710850 TTTTATAATT
21710860 AGACTATATTATGGAAAGTGTAAACAATA
1 AGACTATATTATGGAAAGTGTAAACAATA
* ** * ** * *
21710889 AGACTA-ATTTTTTTATAA-TTTTTATAATT
1 AGACTATA-TTATGGA-AAGTGTAAACAATA
21710918 AGACTATATTATGGAAAGTGTAAACAATA
1 AGACTATATTATGGAAAGTGTAAACAATA
21710947 AGACTAT
1 AGACTAT
21710954 TTTTTTATAA
Statistics
Matches: 45, Mismatches: 16, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (29 bp):
AGACTATATTATGGAAAGTGTAAACAATA
Found at i:21710911 original size:58 final size:57
Alignment explanation
Indices: 21710849--21710966 Score: 227
Period size: 58 Copynumber: 2.1 Consensus size: 57
21710839 ATATCTTATT
21710849 TTTTTATAATTAGACTATATTATGGAAAGTGTAAACAATAAGACTAATTTTTTTATAA
1 TTTTTATAATTAGACTATATTATGGAAAGTGTAAACAATAAGACT-ATTTTTTTATAA
21710907 TTTTTATAATTAGACTATATTATGGAAAGTGTAAACAATAAGACTATTTTTTTATAA
1 TTTTTATAATTAGACTATATTATGGAAAGTGTAAACAATAAGACTATTTTTTTATAA
21710964 TTT
1 TTT
21710967 GTTACTATAC
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 15 0.25
58 45 0.75
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (57 bp):
TTTTTATAATTAGACTATATTATGGAAAGTGTAAACAATAAGACTATTTTTTTATAA
Found at i:21715499 original size:26 final size:26
Alignment explanation
Indices: 21715456--21715506 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
21715446 AAAAAATAGA
*
21715456 AAAAATAAGAAAAAAGAATTTGACAG
1 AAAAATAAGAAAAAAGAAATTGACAG
*
21715482 AAAAATGAAG-AAACAGAAATTGACA
1 AAAAAT-AAGAAAAAAGAAATTGACA
21715507 TCAAATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.65, C:0.06, G:0.16, T:0.14
Consensus pattern (26 bp):
AAAAATAAGAAAAAAGAAATTGACAG
Found at i:21720168 original size:9 final size:9
Alignment explanation
Indices: 21720155--21720240 Score: 86
Period size: 9 Copynumber: 9.6 Consensus size: 9
21720145 ATAAGTATAA
*
21720155 AATTAACCA
1 AATTAACCG
*
21720164 AATTAATCG
1 AATTAACCG
21720173 AATTAACCG
1 AATTAACCG
21720182 AATT-ACCTG
1 AATTAACC-G
21720191 AATT-ACTCG
1 AATTAAC-CG
*
21720200 AATTACCCG
1 AATTAACCG
* *
21720209 AATTACCCA
1 AATTAACCG
*
21720218 AATTAACCT
1 AATTAACCG
21720227 AATTAACCG
1 AATTAACCG
21720236 AATTA
1 AATTA
21720241 TTTGTATAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
8 3 0.05
9 61 0.92
10 2 0.03
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:21720185 original size:27 final size:27
Alignment explanation
Indices: 21720155--21720240 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 27
21720145 ATAAGTATAA
21720155 AATTAACCAAATTAATCGAATTAACCG
1 AATTAACCAAATTAATCGAATTAACCG
* * *
21720182 AATT-ACCTGAATTACTCGAATTACCCG
1 AATTAACC-AAATTAATCGAATTAACCG
* * *
21720209 AATTACCCAAATTAACCTAATTAACCG
1 AATTAACCAAATTAATCGAATTAACCG
21720236 AATTA
1 AATTA
21720241 TTTGTATAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
26 3 0.06
27 43 0.90
28 2 0.04
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (27 bp):
AATTAACCAAATTAATCGAATTAACCG
Found at i:21720809 original size:27 final size:27
Alignment explanation
Indices: 21720771--21720825 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
21720761 ATAGGATTTG
21720771 TTCCTCCTACATATAGGAGAAATATCT
1 TTCCTCCTACATATAGGAGAAATATCT
21720798 TTCCTCCTACATATAGGAGAAATATCT
1 TTCCTCCTACATATAGGAGAAATATCT
21720825 T
1 T
21720826 AGGCTTCTTG
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:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (27 bp):
TTCCTCCTACATATAGGAGAAATATCT
Found at i:21721300 original size:6 final size:6
Alignment explanation
Indices: 21721289--21721332 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
21721279 TTCAACATGA
21721289 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TG
21721333 CATGCATGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
TGTATG
Found at i:21728051 original size:34 final size:36
Alignment explanation
Indices: 21727986--21728060 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 36
21727976 TCTTTGCAAA
21727986 CATAGCCATATTCACCTCATCATCATTACTAGAGT-TT
1 CATAGCCATATTCACCTCATCATC--TACTAGAGTCTT
*
21728023 CATATCCATATTCACCTCATCATC-ACTAGAGTCTT
1 CATAGCCATATTCACCTCATCATCTACTAGAGTCTT
21728058 CAT
1 CAT
21728061 TCTTCTCACA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
34 8 0.22
35 5 0.14
37 23 0.64
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.35
Consensus pattern (36 bp):
CATAGCCATATTCACCTCATCATCTACTAGAGTCTT
Found at i:21731124 original size:16 final size:16
Alignment explanation
Indices: 21731105--21731161 Score: 105
Period size: 16 Copynumber: 3.6 Consensus size: 16
21731095 ATTGGAATAT
21731105 AGGCGTAATGGATTAG
1 AGGCGTAATGGATTAG
21731121 AGGCGTAATGGATTAG
1 AGGCGTAATGGATTAG
*
21731137 AGGCGTAATGGAATAG
1 AGGCGTAATGGATTAG
21731153 AGGCGTAAT
1 AGGCGTAAT
21731162 AGCAAATCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.33, C:0.07, G:0.37, T:0.23
Consensus pattern (16 bp):
AGGCGTAATGGATTAG
Found at i:21731199 original size:45 final size:44
Alignment explanation
Indices: 21731141--21731230 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
21731131 GATTAGAGGC
21731141 GTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAAT
* *
21731186 GTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
21731230 G
1 G
21731231 GAATAGAGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.43
45 23 0.55
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
Found at i:21731412 original size:16 final size:16
Alignment explanation
Indices: 21731375--21731416 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
21731365 TTAATCATAT
*
21731375 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
21731391 TT-AAATATATTATAA
1 TTAAAATATATTATAA
21731406 TTAAAATATAT
1 TTAAAATATAT
21731417 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:21731423 original size:14 final size:15
Alignment explanation
Indices: 21731384--21731425 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21731374 TTTAAACATA
*
21731384 ATTATTATTAAATAT
1 ATTATAATTAAATAT
21731399 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
21731413 A-TATAATTTAATA
1 ATTATAATTAAATA
21731426 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:21731517 original size:120 final size:121
Alignment explanation
Indices: 21731373--21731789 Score: 725
Period size: 120 Copynumber: 3.5 Consensus size: 121
21731363 ATTTAATCAT
*
21731373 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
21731438 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
66 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
21731494 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
21731558 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATA
66 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
* *
21731614 AATTAAA-ATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATA
1 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
*
21731677 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
* * *
21731733 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
21731790 TAAAATAATT
Statistics
Matches: 282, Mismatches: 13, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
119 110 0.39
120 166 0.59
121 6 0.02
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (121 bp):
ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
Found at i:21731536 original size:18 final size:17
Alignment explanation
Indices: 21731515--21731549 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21731505 TTATTATTAA
*
21731515 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
21731533 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
21731550 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:21731657 original size:18 final size:17
Alignment explanation
Indices: 21731617--21731669 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
21731607 AAATATAAAT
21731617 TAAAATA-ATAA-TT-A
1 TAAAATATATAATTTAA
*
21731631 TTAAATATAT--TTTAA
1 TAAAATATATAATTTAA
21731646 TTAAAATATATAATTTAA
1 -TAAAATATATAATTTAA
21731664 TAAAAT
1 TAAAAT
21731670 TCTAATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 9 0.29
17 6 0.19
18 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATATAATTTAA
Found at i:21734009 original size:41 final size:41
Alignment explanation
Indices: 21733952--21734033 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
21733942 AGACAGTGTG
*
21733952 AGTAGAAGAAATTACCAAATGAGGATTCTTGAAAAGATCCT
1 AGTAGAAGAAATTACCAAAGGAGGATTCTTGAAAAGATCCT
21733993 AGTAGAAGAAATTACCAAAGGAGGATTCTTGAAAAGATCCT
1 AGTAGAAGAAATTACCAAAGGAGGATTCTTGAAAAGATCCT
21734034 GCGGGCAACG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (41 bp):
AGTAGAAGAAATTACCAAAGGAGGATTCTTGAAAAGATCCT
Found at i:21734264 original size:38 final size:38
Alignment explanation
Indices: 21734222--21734296 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
21734212 AACAATAAAC
*
21734222 CTAGTTGAAGGGACAACTTATAAAACAACAAAATTTCT
1 CTAGTTAAAGGGACAACTTATAAAACAACAAAATTTCT
21734260 CTAGTTAAAGGGACAACTTATAAAACAACAAAATTTC
1 CTAGTTAAAGGGACAACTTATAAAACAACAAAATTTC
21734297 ATTTTTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (38 bp):
CTAGTTAAAGGGACAACTTATAAAACAACAAAATTTCT
Found at i:21737398 original size:31 final size:31
Alignment explanation
Indices: 21737344--21737406 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
21737334 CAACTTAGTA
**
21737344 ACTTAAATAAAAACTTTTGAATAGATT-AATG
1 ACTTAAATAAAAACTTTCAAATAG-TTCAATG
21737375 ACTTAAATAAAAACTTTCAAATAGTTCAATG
1 ACTTAAATAAAAACTTTCAAATAGTTCAATG
21737406 A
1 A
21737407 TCAAATTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAGTTCAATG
Found at i:21739150 original size:40 final size:42
Alignment explanation
Indices: 21739106--21739188 Score: 134
Period size: 40 Copynumber: 2.0 Consensus size: 42
21739096 TTTATGGGTA
* *
21739106 TGTGGGACTTGCCATTGTGAATCAA-T-AAGTACTTTTATTT
1 TGTGGAACTTGCCATTGTGAATCAATTAAAGTACTTGTATTT
21739146 TGTGGAACTTGCCATTGTGAATCAATTAAAGTACTTGTATTT
1 TGTGGAACTTGCCATTGTGAATCAATTAAAGTACTTGTATTT
21739188 T
1 T
21739189 TATTCATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 24 0.62
41 1 0.03
42 14 0.36
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (42 bp):
TGTGGAACTTGCCATTGTGAATCAATTAAAGTACTTGTATTT
Found at i:21741031 original size:13 final size:13
Alignment explanation
Indices: 21741013--21741039 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21741003 CTGCCAAACA
21741013 TAGTGTTAAAAGT
1 TAGTGTTAAAAGT
21741026 TAGTGTTAAAAGT
1 TAGTGTTAAAAGT
21741039 T
1 T
21741040 TTTCTTTCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
TAGTGTTAAAAGT
Found at i:21748566 original size:29 final size:28
Alignment explanation
Indices: 21748533--21748588 Score: 103
Period size: 29 Copynumber: 2.0 Consensus size: 28
21748523 GAGTTATACC
21748533 GATTTGGCTTCGGGCCATGAATATCAGTT
1 GATTTGGCTTCGGGCCATG-ATATCAGTT
21748562 GATTTGGCTTCGGGCCATGATATCAGT
1 GATTTGGCTTCGGGCCATGATATCAGT
21748589 ATTTCAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.34
Consensus pattern (28 bp):
GATTTGGCTTCGGGCCATGATATCAGTT
Found at i:21749773 original size:3 final size:3
Alignment explanation
Indices: 21749765--21749789 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
21749755 TTTCAGTAGC
21749765 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
21749790 TATCTCCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:21750427 original size:20 final size:20
Alignment explanation
Indices: 21750398--21750435 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21750388 CAAACTTTTA
* *
21750398 TTTATTTTTATTTTTAAAAT
1 TTTATATTTACTTTTAAAAT
21750418 TTTATATTTACTTTTAAA
1 TTTATATTTACTTTTAAA
21750436 GAGTAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATATTTACTTTTAAAAT
Found at i:21752254 original size:3 final size:3
Alignment explanation
Indices: 21752227--21752431 Score: 90
Period size: 3 Copynumber: 65.7 Consensus size: 3
21752217 ATGTTATATA
21752227 ATT ATT -TT ATT ATAT ATT ATAT ATT ATT ATT ATTT ATT ATAT ATT ATT
1 ATT ATT ATT ATT AT-T ATT AT-T ATT ATT ATT A-TT ATT AT-T ATT ATT
* * *
21752275 TTT CATAA ATT ATT ATT ATT -TT A-C ATT ATT ATTT ATAT ATT ATT ATT
1 ATT -AT-T ATT ATT ATT ATT ATT ATT ATT ATT A-TT AT-T ATT ATT ATT
*
21752322 A-T ATT A-T ATGT -TT ATT AATT ATT AATT ATAT ATT ATT TTT A-T ATAT
1 ATT ATT ATT AT-T ATT ATT -ATT ATT -ATT AT-T ATT ATT ATT ATT AT-T
* * *
21752368 ATAT ACTT -TT A-T ATT ATAC ATT ATA ATT A-T ATT ATAT GTT ATT ATGT
1 AT-T A-TT ATT ATT ATT AT-T ATT ATT ATT ATT ATT AT-T ATT ATT AT-T
*
21752415 CATT TTT A-T ATT ATT AT
1 -ATT ATT ATT ATT ATT AT
21752432 ACATTTTTAT
Statistics
Matches: 157, Mismatches: 16, Indels: 58
0.68 0.07 0.25
Matches are distributed among these distances:
2 20 0.13
3 90 0.57
4 44 0.28
5 3 0.02
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:21752303 original size:30 final size:30
Alignment explanation
Indices: 21752215--21752323 Score: 93
Period size: 30 Copynumber: 3.7 Consensus size: 30
21752205 AACCTTATTT
*
21752215 TTATGTTATATAATTATT-TTATTATATATTA
1 TTAT-TTATA-AATTATTATTATTATACATTA
* *
21752246 -TATATTAT-TATTA-T-TTATTATATATTA
1 TTAT-TTATAAATTATTATTATTATACATTA
* * *
21752273 TTTTTCATAAATTATTATTATTTTACATTA
1 TTATTTATAAATTATTATTATTATACATTA
*
21752303 TTATTTATATATTATTATTAT
1 TTATTTATAAATTATTATTAT
21752324 ATTATATGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
27 17 0.27
28 10 0.16
29 1 0.02
30 36 0.56
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (30 bp):
TTATTTATAAATTATTATTATTATACATTA
Found at i:21752448 original size:14 final size:14
Alignment explanation
Indices: 21752423--21752456 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
21752413 GTCATTTTTA
21752423 TATTAT-TATACAT
1 TATTATCTATACAT
*
21752436 TTTTATCTATACAT
1 TATTATCTATACAT
21752450 TATTATC
1 TATTATC
21752457 ATTAAAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTATCTATACAT
Found at i:21753359 original size:38 final size:38
Alignment explanation
Indices: 21753308--21753386 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
21753298 CTAAGTTTTT
* *
21753308 AAGATTTTTAAAATACGAGCAACTGTCTTGGGATTTCA
1 AAGATTTTCAAAATACGAGCAACTGTCTTGGAATTTCA
21753346 AAGATTTTCAAAATACGAGCAACTGTCTTGGAATTTCA
1 AAGATTTTCAAAATACGAGCAACTGTCTTGGAATTTCA
21753384 AAG
1 AAG
21753387 CGTTGTGTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (38 bp):
AAGATTTTCAAAATACGAGCAACTGTCTTGGAATTTCA
Found at i:21763626 original size:92 final size:92
Alignment explanation
Indices: 21763469--21763653 Score: 325
Period size: 92 Copynumber: 2.0 Consensus size: 92
21763459 AACCCGCAAA
*
21763469 GGGCACCTTGTGACCAAAGGGGTTTTGAGTTGAAAACCCGAAAGGGCAGCTCAAATTTTGAAGAG
1 GGGCACCTTGTGACCAAAGGGGTTTTGAGTTGAAAACCCGAAAGGGCAACTCAAATTTTGAAGAG
*
21763534 TACACAATGGTCTTGCTACAAAGAGCG
66 TACACAATGATCTTGCTACAAAGAGCG
**
21763561 GGGCACCTTGTGACCAAAGGGGTTTTGAGTTGAAAACCTTAAAGGGCAACTCAAATTTTGAAGAG
1 GGGCACCTTGTGACCAAAGGGGTTTTGAGTTGAAAACCCGAAAGGGCAACTCAAATTTTGAAGAG
*
21763626 TGCACAATGATCTTGCTACAAAGAGCG
66 TACACAATGATCTTGCTACAAAGAGCG
21763653 G
1 G
21763654 AGAATGCTGC
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.23
Consensus pattern (92 bp):
GGGCACCTTGTGACCAAAGGGGTTTTGAGTTGAAAACCCGAAAGGGCAACTCAAATTTTGAAGAG
TACACAATGATCTTGCTACAAAGAGCG
Found at i:21764936 original size:210 final size:205
Alignment explanation
Indices: 21764388--21765395 Score: 973
Period size: 210 Copynumber: 4.8 Consensus size: 205
21764378 ATAAGCCGCA
* * * **
21764388 ACATAGCAGATCTCACCTTCAGATG-TTCACG-CTGAAGC-AGATCCAAGATGAACAGATTTATC
1 ACATAGCAGATCTCACCTTCAGACGATT-A-GACTGAAACAAGATCCAAGATGATCAG--GCATC
** * * * * *
21764450 TCTTTGTATTTAGCGGGGAGCAGATCGAAGATATAGCTAATTTGACTTTTACGTGTTCACGATGA
62 -C-TTGTA-TTA-CAAGGAGCAAATCGAAGACATAGCTGATTTGACTTTCACGTGTTTACGATGA
* * * *
21764515 AGCAAATCTAAGATGATTTGTCGTCTCTGTACTGTTAGAGAACAAATCAAATTCTGGCATCTCTA
123 AGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCA
21764580 CTTCAATAGAGAGCAGAT
188 CTTCAATAGAGAGCAGAT
* * * * **
21764598 GCATAGCAGATCTGACCTTCAGACGATTAGACTGAAACAATATCTAAGATGATTTGGCATCCTTG
1 ACATAGCAGATCTCACCTTCAGACGATTAGACTGAAACAAGATCCAAGATGATCAGGCATCCTTG
* *
21764663 TACTTACAAGGAGCAAATCGAAGACATAGCTGATTTGACTTTCACATGTTTACGATAAAGCAAAT
66 TA-TTACAAGGAGCAAATCGAAGACATAGCTGATTTGACTTTCACGTGTTTACGATGAAGCAAAT
* * * * * **
21764728 CTAAGATGATTTTTCGCCTCTGTATTGTCAGAGAATAAATCGAAGTCTGGCATTTCCACTTTGAT
130 CTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCAAT
* * *
21764793 GGA-ATTCAGAC
195 AGAGA-GCAGAT
* * * * *
21764804 ACATAGTAGATCTCACCTTCAGATGTTTATG-CTGAAGC-AGATCCAAGATGA-CAGATCTTATC
1 ACATAGCAGATCTCACCTTCAGACGATTA-GACTGAAACAAGATCCAAGATGATCAG-GC--ATC
* * * *
21764866 TCTCTGTATTCAGCAGGGAGCAGATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTACGATGA
62 -CT-TGTATT-A-CAAGGAGCAAATCGAAGACATAGCTGATTTGACTTTCACGTGTTTACGATGA
* *
21764931 AGCAAATCTAAGATGATTTGTCGTCTCTGTATTATCAGAGAACAAATCAAAGTCTGGCATCTCTA
123 AGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCA
21764996 CTTCAATAGAGAGCAGAT
188 CTTCAATAGAGAGCAGAT
* **
21765014 ACATAGTAGATCGATCTGACCTTCAGACGATTAGACTGAAACAAGATCCAAGATGATTTGGCATC
1 ACATAGCAGATC--TC--ACCTTCAGACGATTAGACTGAAACAAGATCCAAGATGATCAGGCATC
* *
21765079 CTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTT-AGCTTTCACGTGCTTACGATGAAG
62 CTTGT-ATTACAAGGAGCAAATCGAAGACATAGCTGATTTGA-CTTTCACGTGTTTACGATGAAG
* *
21765143 TAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACA
125 CAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCAC-
* * * *
21765208 TTTAATGGGGAGCGGAT
189 TTCAATAGAGAGCAGAT
* * * * * * ** ** *
21765225 ACATGGCAGATCTGATCTTTAGACGTTTAGACCGAAGTAAGATCCAAGATGATTTGGTATCCTTG
1 ACATAGCAGATCTCACCTTCAGACGATTAGACTGAAACAAGATCCAAGATGATCAGGCATCCTTG
* * * * * *
21765290 TATTTACAAGGAACAAATCAAAGACATAGCAGATTTGACTCTCA-GATGATCT-C-A--AA-TAA
66 TA-TTACAAGGAGCAAATCGAAGACATAGCTGATTTGACTTTCACG-TG-TTTACGATGAAGCAA
* * * *
21765349 ATCTAAGATAATTTGGCATCTCTGTATTGTCAGAGAATAAATCAAAG
128 ATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCAAAG
21765396 AAGCAGATTT
Statistics
Matches: 665, Mismatches: 106, Indels: 61
0.80 0.13 0.07
Matches are distributed among these distances:
203 45 0.07
204 3 0.00
205 13 0.02
206 142 0.21
207 95 0.14
208 7 0.01
209 10 0.02
210 264 0.40
211 42 0.06
212 6 0.01
213 4 0.01
214 19 0.03
215 14 0.02
216 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (205 bp):
ACATAGCAGATCTCACCTTCAGACGATTAGACTGAAACAAGATCCAAGATGATCAGGCATCCTTG
TATTACAAGGAGCAAATCGAAGACATAGCTGATTTGACTTTCACGTGTTTACGATGAAGCAAATC
TAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCAATA
GAGAGCAGAT
Done.