Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 17 of 202
Found at i:5153592 original size:47 final size:47
Alignment explanation
Indices: 5153523--5153617 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
5153513 GTTCGAGGTA
*
5153523 AGTCCATTGCAGATTTTGGCCGAGAAGGTGTTATAAAAATAAGAGCC
1 AGTCCATGGCAGATTTTGGCCGAGAAGGTGTTATAAAAATAAGAGCC
5153570 AGTCCATGGCAGATTTTGGCCGAGAAGGTGTTATAAAAATAAGAGCC
1 AGTCCATGGCAGATTTTGGCCGAGAAGGTGTTATAAAAATAAGAGCC
5153617 A
1 A
5153618 ATGTGAAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (47 bp):
AGTCCATGGCAGATTTTGGCCGAGAAGGTGTTATAAAAATAAGAGCC
Found at i:5158512 original size:21 final size:23
Alignment explanation
Indices: 5158462--5158516 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
5158452 TTTTGCTTAT
*
5158462 TCAAATAAAATCATAATTTATACA
1 TCAAATAAAAT-ATAATCTATACA
5158486 TCAAATAAAAT-TAATCTA-ACA
1 TCAAATAAAATATAATCTATACA
*
5158507 TGAAATAAAA
1 TCAAATAAAA
5158517 CACGGTGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.41
22 6 0.21
24 11 0.38
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (23 bp):
TCAAATAAAATATAATCTATACA
Found at i:5158869 original size:8 final size:8
Alignment explanation
Indices: 5158820--5158871 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 8
5158810 ATATGTATGT
5158820 ATATATAA
1 ATATATAA
5158828 AT-TATAA
1 ATATATAA
5158835 AGTATA-AA
1 A-TATATAA
5158843 ATATATAA
1 ATATATAA
* *
5158851 GTATGTAA
1 ATATATAA
5158859 ATATATAA
1 ATATATAA
5158867 ATATA
1 ATATA
5158872 CACTTATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 10 0.27
8 25 0.68
9 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.37
Consensus pattern (8 bp):
ATATATAA
Found at i:5158910 original size:16 final size:16
Alignment explanation
Indices: 5158891--5158924 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5158881 AAATTAAAAT
5158891 ATATATGTAGACATAA
1 ATATATGTAGACATAA
*
5158907 ATATATGTATACATAA
1 ATATATGTAGACATAA
5158923 AT
1 AT
5158925 TATAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (16 bp):
ATATATGTAGACATAA
Found at i:5159992 original size:4 final size:4
Alignment explanation
Indices: 5159983--5160009 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5159973 ATATGAGAGA
5159983 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
5160010 AGCTGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5160910 original size:50 final size:50
Alignment explanation
Indices: 5160852--5161173 Score: 221
Period size: 50 Copynumber: 6.4 Consensus size: 50
5160842 AATCTGTCAT
* *
5160852 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAAATTCACTGTTGTAG
1 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
**** ** *** ** ** *
5160902 CTTCAATCTGTTCCGTTGCACCGCCAGAAAAGTAAGATTCGCCATTGTGG
1 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
*
5160952 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
1 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
**** ** *** ** * **
5161002 CTTCAATCTGTTCCGTTGCACCGCCAGAAAAGTAAGATTCACCATTGTAG
1 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
* * * *
5161052 CTTCAATCTTTTTAACTGCAATGTTGGGGGAGCAAGATCCGCTGTTGTAG
1 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
** * ** * * * * * *
5161102 CTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAG
1 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
*
5161152 CTTCAATCTTTTTAACTGCAAT
1 CTTCAATCTGTTTAACTGCAAT
5161174 ATCGGAGAAA
Statistics
Matches: 189, Mismatches: 83, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
50 189 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (50 bp):
CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
Found at i:5161025 original size:100 final size:100
Alignment explanation
Indices: 5160852--5161173 Score: 500
Period size: 100 Copynumber: 3.2 Consensus size: 100
5160842 AATCTGTCAT
* * *
5160852 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAAATTCACTGTTGTAGCTTCAATCTGTTCCG
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
*
5160917 TTGCACCGCCAGAAAAGTAAGATTCGCCATTGTGG
66 TTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
5160952 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
*
5161017 TTGCACCGCCAGAAAAGTAAGATTCACCATTGTAG
66 TTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
* * * *
5161052 CTTCAATCTTTTTAACTGCAATGTTGGGGGAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
* * * * * * *
5161117 CTACACCGCTAGGAAAGTAAGATCCGCTATTATAG
66 TTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
5161152 CTTCAATCTTTTTAACTGCAAT
1 CTTCAATCTTTTTAACTGCAAT
5161174 ATCGGAGAAA
Statistics
Matches: 205, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 205 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (100 bp):
CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
TTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
Found at i:5161189 original size:50 final size:50
Alignment explanation
Indices: 5161049--5161189 Score: 122
Period size: 50 Copynumber: 2.8 Consensus size: 50
5161039 TTCACCATTG
* * * * * *
5161049 TAGCTTCAATCTTTTTAACTGCAATGTTGGGGGAGCAAGATCCGCTGTTG
1 TAGCTTCAATCTTTTTAACTGCAATATAGGAGAAGCAAGATCCGCTATTA
* ** * *** *
5161099 TAGCTTCAATCTGTTCCACTACACCGCTAGGA-AAGTAAGATCCGCTATTA
1 TAGCTTCAATCTTTTTAACTGCA-ATATAGGAGAAGCAAGATCCGCTATTA
* *
5161149 TAGCTTCAATCTTTTTAACTGCAATATCGGAGAAACAAGAT
1 TAGCTTCAATCTTTTTAACTGCAATATAGGAGAAGCAAGAT
5161190 TCGTCAATTT
Statistics
Matches: 66, Mismatches: 23, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
49 4 0.06
50 59 0.89
51 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (50 bp):
TAGCTTCAATCTTTTTAACTGCAATATAGGAGAAGCAAGATCCGCTATTA
Found at i:5161210 original size:100 final size:100
Alignment explanation
Indices: 5160852--5161221 Score: 481
Period size: 100 Copynumber: 3.7 Consensus size: 100
5160842 AATCTGTCAT
* * * * *
5160852 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAAATTCACTGTTGTAGCTTCAATCTGTTCCG
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCA
* *
5160917 TTGCACCGCCAGAAAAGTAAGATTCGCCATTGTGG
66 CTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
* *
5160952 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCA
* *
5161017 TTGCACCGCCAGAAAAGTAAGATTCACCATTGTAG
66 CTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
* *
5161052 CTTCAATCTTTTTAACTGCAATGTTGGGGGAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCA
* * * * * *
5161117 CTACACCGCTAGGAAAGTAAGATCCGCTATTATAG
66 CTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
* * * * ** * *
5161152 CTTCAATCTTTTTAACTGCAATATCGGAGAAACAAGATTCGTCAATT-TGGCTTTAATCTGTTCC
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCG-CTGTTGTAGCTTCAATCTGTTCC
5161216 ACTGCA
65 ACTGCA
5161222 TCGCTTGGGG
Statistics
Matches: 241, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
100 238 0.99
101 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (100 bp):
CTTCAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCA
CTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
Found at i:5161237 original size:100 final size:100
Alignment explanation
Indices: 5160896--5161259 Score: 307
Period size: 100 Copynumber: 3.6 Consensus size: 100
5160886 AAATTCACTG
** * * * * * * *
5160896 TTGTAGCTTCAATCTGTTCCGTTGCACCGCCAGAAAAGTAAGATTCGCCATTGTGGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAGCTTCAATCT
* * * ** * **
5160961 TTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTG
66 TTTTAACTGCAATATCGGAGAAACAAGATCCGCAA
** * * * * * * *
5160996 TTGTAGCTTCAATCTGTTCCGTTGCACCGCCAGAAAAGTAAGATTCACCATTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAGCTTCAATCT
* * * * * **
5161061 TTTTAACTGCAATGTTGGGGGAGCAAGATCCGCTG
66 TTTTAACTGCAATATCGGAGAAACAAGATCCGCAA
5161096 TTGTAGCTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAGCTTCAATCT
*
5161161 TTTTAACTGCAATATCGGAGAAACAAGATTCGTCAA
66 TTTTAACTGCAATATCGGAGAAACAAGATCCG-CAA
* * * * * *** * * *
5161197 TT-TGGCTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTATTGTAGCTTTAATC
1 TTGTAGCTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAGCTTCAATC
5161260 AAGATTCACC
Statistics
Matches: 230, Mismatches: 33, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
100 227 0.99
101 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (100 bp):
TTGTAGCTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAGCTTCAATCT
TTTTAACTGCAATATCGGAGAAACAAGATCCGCAA
Found at i:5161357 original size:125 final size:125
Alignment explanation
Indices: 5161200--5161509 Score: 448
Period size: 125 Copynumber: 2.5 Consensus size: 125
5161190 TCGTCAATTT
5161200 GGCTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTATTGTAGCTTTAATCAAGAT
1 GGCTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTATTGTAGCTTTAATCAAGAT
* * *
5161265 TCACCGATGTGGCTTTAATCTTTTTAACTGTAATGT-AGGGGAA-GCAAGATTCACCGATGC
66 TCACCGATGTGGCTTTAATCTTTTTAACCGCAATGTCA--GAAAGGCAAGATTCACCGATGC
* *
5161325 GGTTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGAT
1 GGCTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTATTGTAGCTTTAATCAAGAT
* *
5161390 TCACCGATGTGGCTTTAATCTTTTTAACCGCAATGTCAGAAAGGCAAGATTCACCGTTGT
66 TCACCGATGTGGCTTTAATCTTTTTAACCGCAATGTCAGAAAGGCAAGATTCACCGATGC
* * * * *
5161450 GGCTTTAATCTATTCCACTGCACCGCCTGAGAG-GTAAGATTTGCTGA-TGTAGCTTTAATC
1 GGCTTTAATCTGTTCCACTGCATCGCTTG-GGGCGTAAGATTCGCT-ATTGTAGCTTTAATC
5161510 TTCTTAATTG
Statistics
Matches: 167, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
124 3 0.02
125 161 0.96
126 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (125 bp):
GGCTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTATTGTAGCTTTAATCAAGAT
TCACCGATGTGGCTTTAATCTTTTTAACCGCAATGTCAGAAAGGCAAGATTCACCGATGC
Found at i:5161489 original size:50 final size:50
Alignment explanation
Indices: 5161384--5161510 Score: 119
Period size: 50 Copynumber: 2.5 Consensus size: 50
5161374 TAGCTTTAAT
* * * *
5161384 CAAGATTCACCGATGTGGCTTTAATCTTTTTAACCGCAATGTCAGAAAGG
1 CAAGATTCACCGATGTGGCTTTAATCTATTCAACCGCAACGCCAGAAAGG
* * * * * *
5161434 CAAGATTCACCGTTGTGGCTTTAATCTATTCCACTGCACCGCCTGAGAGG
1 CAAGATTCACCGATGTGGCTTTAATCTATTCAACCGCAACGCCAGAAAGG
* ** * *
5161484 TAAGATTTGCTGATGTAGCTTTAATCT
1 CAAGATTCACCGATGTGGCTTTAATCT
5161511 TCTTAATTGC
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (50 bp):
CAAGATTCACCGATGTGGCTTTAATCTATTCAACCGCAACGCCAGAAAGG
Found at i:5161560 original size:100 final size:98
Alignment explanation
Indices: 5161385--5161679 Score: 322
Period size: 100 Copynumber: 3.0 Consensus size: 98
5161375 AGCTTTAATC
* ** * * * *
5161385 AAGATTCACCGATGTGGCTTTAATCTTTTTAACCGCAATGTCA-GAAAGGCAAGATTCACCGTTG
1 AAGATTCGCCGATGTGGCTTTAATC-TTTTAATTGCAATGTCAGGGAA-GTAAGATCCGCCGTTG
* * * **
5161449 TGGCTTTAATCTATTCCACTGCACCGCCTGAGAGGT
64 TAGCTTCAATCTGTTCCACTGCACCGCCTG-GAAAT
* * * *
5161485 AAGATTTGCTGATGTAGCTTTAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGT
1 AAGATTCGCCGATGTGGCTTTAATCTT-TTAATTGCAATGTCAGGGAAGTAAGATCCGCCGTTGT
5161550 AGCTTCAATCTGTTCCACTGCACCGCCTGGAAAT
65 AGCTTCAATCTGTTCCACTGCACCGCCTGGAAAT
* * * ** *
5161584 AAGATTCGCCGTTGTGGCCTCAATCTTTGGATTGCAATGTCAGGGAAGTGAGATCCGCCGTTGTA
1 AAGATTCGCCGATGTGGCTTTAATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCCGTTGTA
* * *
5161649 GCTTCAACCTGTTCCGCTGCACCGCTTGGAA
66 GCTTCAATCTGTTCCACTGCACCGCCTGGAA
5161680 TGTAAGTTCC
Statistics
Matches: 164, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
98 62 0.38
99 26 0.16
100 73 0.45
101 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (98 bp):
AAGATTCGCCGATGTGGCTTTAATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCCGTTGTA
GCTTCAATCTGTTCCACTGCACCGCCTGGAAAT
Found at i:5161641 original size:98 final size:99
Alignment explanation
Indices: 5161443--5161679 Score: 296
Period size: 98 Copynumber: 2.4 Consensus size: 99
5161433 GCAAGATTCA
* * * ** * * * *
5161443 CCGTTGTGGCTTTAATCTATTCCACTGCACCGCCTGAGAGGTAAGATTTGCTGATGTAGCTTTAA
1 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTG-GAAATAAGATTCGCCGATGTAGCCTCAA
*
5161508 TCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCG
65 TCTTCTGAATTGCAATGTCAGGGAAGTAAGATCCG
* * *
5161543 CTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAAT
1 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCGATGTAGCCTCAAT
* *
5161608 CTT-TGGATTGCAATGTCAGGGAAGTGAGATCCG
66 CTTCTGAATTGCAATGTCAGGGAAGTAAGATCCG
* * *
5161641 CCGTTGTAGCTTCAACCTGTTCCGCTGCACCGCTTGGAA
1 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAA
5161680 TGTAAGTTCC
Statistics
Matches: 118, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
98 62 0.53
99 24 0.20
100 32 0.27
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (99 bp):
CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCGATGTAGCCTCAAT
CTTCTGAATTGCAATGTCAGGGAAGTAAGATCCG
Found at i:5161643 original size:49 final size:50
Alignment explanation
Indices: 5161516--5161663 Score: 147
Period size: 49 Copynumber: 3.0 Consensus size: 50
5161506 AATCTTCTTA
* *
5161516 ATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
1 ATTGCAATGTCAGGGAAGTAAGATCCGCCGTTGTAGCCTCAATCTGTTCC
* ** ** * * * **
5161566 ACTGCACCG-CCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCT-TTGG
1 ATTGCAATGTCAGGGAAGTAAGATCCGCCGTTGTAGCCTCAATCTGTTCC
* * *
5161614 ATTGCAATGTCAGGGAAGTGAGATCCGCCGTTGTAGCTTCAACCTGTTCC
1 ATTGCAATGTCAGGGAAGTAAGATCCGCCGTTGTAGCCTCAATCTGTTCC
5161664 GCTGCACCGC
Statistics
Matches: 71, Mismatches: 25, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
48 8 0.11
49 55 0.77
50 8 0.11
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (50 bp):
ATTGCAATGTCAGGGAAGTAAGATCCGCCGTTGTAGCCTCAATCTGTTCC
Found at i:5161959 original size:86 final size:86
Alignment explanation
Indices: 5161777--5162209 Score: 615
Period size: 86 Copynumber: 5.1 Consensus size: 86
5161767 ATCTGCTATC
* * * * ** * * *
5161777 TTCGACCTGCTTCGCTATCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAACTCCA-TCACA
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACT-TCTTTAACCAGCTCCACT-GCA
* *
5161841 ACCGA-G-AGGCAAGG-TTTATT
64 ACCAATGAAGGCAAGGCTTTGTT
* * *
5161861 TTCGATCTGCTTCGTTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
5161926 CAATGAAGGCAAGGCTTTGTT
66 CAATGAAGGCAAGGCTTTGTT
* *
5161947 TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGTAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
*
5162012 CAATGAAGGCAAGTC-TTGTT
66 CAATGAAGGCAAGGCTTTGTT
* * * *
5162032 TTCGATCTACTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCGATTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
5162097 CAATGAAGGCAAGGCTTTGTT
66 CAATGAAGGCAAGGCTTTGTT
5162118 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
*
5162183 CAATGAAGGCAATGCTTTGTT
66 CAATGAAGGCAAGGCTTTGTT
5162204 TTCGAT
1 TTCGAT
5162210 GTTCACTAAT
Statistics
Matches: 313, Mismatches: 31, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
83 20 0.06
84 36 0.12
85 86 0.27
86 171 0.55
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (86 bp):
TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
CAATGAAGGCAAGGCTTTGTT
Found at i:5162067 original size:171 final size:171
Alignment explanation
Indices: 5161777--5162209 Score: 633
Period size: 171 Copynumber: 2.5 Consensus size: 171
5161767 ATCTGCTATC
* * * ** * * *
5161777 TTCGACCTGCTTCGCTATCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAACTCCA-TCACA
1 TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTACT-TCTTTAACCAGCTCCACT-GCA
* * * *
5161841 ACCGA-G-AGGCAAGGT-TTATTTTCGATCTGCTTCGTTGTTAACGCAGGAAGGCAAGATCTGCT
64 ACCAATGAAGGCAA-GTCTTGTTTTCGATCTACTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT
5161903 TCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTT
128 TCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTT
*
5161947 TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGTAAC
1 TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
*
5162012 CAATGAAGGCAAGTCTTGTTTTCGATCTACTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCT
66 CAATGAAGGCAAGTCTTGTTTTCGATCTACTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCT
* *
5162077 TTAACCAGCTCGATTGCAACCAATGAAGGCAAGGCTTTGTT
131 TTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTT
*
5162118 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
5162183 CAATGAAGGCAA-TGCTTTGTTTTCGAT
66 CAATGAAGGCAAGT-C-TTGTTTTCGAT
5162210 GTTCACTAAT
Statistics
Matches: 239, Mismatches: 18, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
169 19 0.08
170 42 0.18
171 167 0.70
172 11 0.05
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (171 bp):
TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
CAATGAAGGCAAGTCTTGTTTTCGATCTACTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCT
TTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTT
Found at i:5163405 original size:14 final size:14
Alignment explanation
Indices: 5163386--5163435 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
5163376 CCTTAGCCTC
5163386 TTCATTTTTACTTT
1 TTCATTTTTACTTT
* *
5163400 TTCATTTTTTCATT
1 TTCATTTTTACTTT
*
5163414 TTCATTTTTATTTT
1 TTCATTTTTACTTT
5163428 TCTCATTT
1 T-TCATTT
5163436 CTTCTTCTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 24 0.80
15 6 0.20
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCATTTTTACTTT
Found at i:5163442 original size:3 final size:3
Alignment explanation
Indices: 5163434--5163461 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5163424 TTTTTCTCAT
5163434 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
5163462 CTTTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5168560 original size:21 final size:23
Alignment explanation
Indices: 5168510--5168564 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
5168500 TTTTGCTTAT
*
5168510 TCAAATAAAATCATAATTTATACA
1 TCAAATAAAAT-ATAATCTATACA
5168534 TCAAATAAAAT-TAATCTA-ACA
1 TCAAATAAAATATAATCTATACA
*
5168555 TGAAATAAAA
1 TCAAATAAAA
5168565 CACGGTGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.41
22 6 0.21
24 11 0.38
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (23 bp):
TCAAATAAAATATAATCTATACA
Found at i:5170115 original size:4 final size:4
Alignment explanation
Indices: 5170106--5170132 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5170096 ATATGAGAGA
5170106 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
5170133 AGCTGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5173498 original size:13 final size:13
Alignment explanation
Indices: 5173480--5173520 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
5173470 TATCATATTT
5173480 TATATTTCAAAAA
1 TATATTTCAAAAA
5173493 TATATTT-ATAAAA
1 TATATTTCA-AAAA
5173506 -ATATTTCAAAAA
1 TATATTTCAAAAA
5173518 TAT
1 TAT
5173521 TTTATTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATTTCAAAAA
Found at i:5185080 original size:23 final size:24
Alignment explanation
Indices: 5185054--5185107 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
5185044 GACGGCTGGT
5185054 GAGAGGAAGACAAGT-G-GAGAAAG
1 GAGAGGAA-ACAAGTGGAGAGAAAG
* *
5185077 GAGATTGAAACACGTGGAGAGAAAG
1 GAGA-GGAAACAAGTGGAGAGAAAG
5185102 GAGAGG
1 GAGAGG
5185108 TGGGGAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 9 0.36
24 5 0.20
25 11 0.44
ACGTcount: A:0.44, C:0.06, G:0.43, T:0.07
Consensus pattern (24 bp):
GAGAGGAAACAAGTGGAGAGAAAG
Found at i:5186639 original size:3 final size:3
Alignment explanation
Indices: 5186631--5186656 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5186621 GTCCACAGTT
5186631 AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AG
5186657 GCATTGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:5189192 original size:23 final size:22
Alignment explanation
Indices: 5189141--5189182 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
5189131 TTTTAATATT
*
5189141 AAATTATTTTTTATCTGAATCA
1 AAATTATTATTTATCTGAATCA
5189163 AATATTATTATTTATC-GAAT
1 AA-ATTATTATTTATCTGAAT
5189183 ATCCAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (22 bp):
AAATTATTATTTATCTGAATCA
Found at i:5190602 original size:20 final size:20
Alignment explanation
Indices: 5190570--5190623 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
5190560 TATATAAATA
*
5190570 ATTTTAAAAAATAAAAACAC
1 ATTTTATAAAATAAAAACAC
* *
5190590 A-TTTATAATAAT-ATAACTC
1 ATTTTATAA-AATAAAAACAC
5190609 ATTTTATAAAATAAA
1 ATTTTATAAAATAAA
5190624 TAGTCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTTTATAAAATAAAAACAC
Found at i:5198169 original size:11 final size:11
Alignment explanation
Indices: 5198155--5198194 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
5198145 TATTTTCTCC
5198155 CTATTTTGCTA
1 CTATTTTGCTA
*
5198166 CTATTTTACTA
1 CTATTTTGCTA
* *
5198177 TTATGTTGCTA
1 CTATTTTGCTA
5198188 CTATTTT
1 CTATTTT
5198195 ATTGTTATTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:5198269 original size:30 final size:30
Alignment explanation
Indices: 5198235--5198294 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
5198225 TATTTTATTA
5198235 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
5198265 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
5198295 CTTGTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:5199540 original size:55 final size:55
Alignment explanation
Indices: 5199435--5199540 Score: 142
Period size: 55 Copynumber: 1.9 Consensus size: 55
5199425 GTGAGCTTGA
* * *
5199435 AAAATAAGATAGCTTTGAAGACATATCTAGCTACCTTGAAGGTATACAGACATAG
1 AAAATAAGATAGCTTTGAAGACATATCTAGCCACCTTGAAAGTAGACAGACATAG
* * *
5199490 AAAATTAGATAGCTTTGAATG-CATATCTAGCCACTTTGAAAGTAGGCAGAC
1 AAAATAAGATAGCTTTGAA-GACATATCTAGCCACCTTGAAAGTAGACAGAC
5199541 TTTTTTGAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
55 43 0.98
56 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (55 bp):
AAAATAAGATAGCTTTGAAGACATATCTAGCCACCTTGAAAGTAGACAGACATAG
Found at i:5203464 original size:23 final size:23
Alignment explanation
Indices: 5203437--5203483 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
5203427 CATGTTAGTT
*
5203437 TTTGATTACTTTCATTAGTCACG
1 TTTGATTACTTTCACTAGTCACG
*
5203460 TTTGATTACTTTCGCTAGTCACG
1 TTTGATTACTTTCACTAGTCACG
5203483 T
1 T
5203484 CAATATTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (23 bp):
TTTGATTACTTTCACTAGTCACG
Found at i:5203933 original size:17 final size:17
Alignment explanation
Indices: 5203872--5203934 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 17
5203862 CCGAATTATA
5203872 TATTAAATATATATTTT
1 TATTAAATATATATTTT
5203889 TATT---T-TAT-TTTT
1 TATTAAATATATATTTT
* * *
5203901 AATCAAATATA-CTTTT
1 TATTAAATATATATTTT
5203917 TATTAAATATATATTTT
1 TATTAAATATATATTTT
5203934 T
1 T
5203935 GGACTTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
12 6 0.17
13 3 0.09
14 1 0.03
15 1 0.03
16 15 0.43
17 9 0.26
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTAAATATATATTTT
Found at i:5209398 original size:3 final size:3
Alignment explanation
Indices: 5209390--5209482 Score: 186
Period size: 3 Copynumber: 31.0 Consensus size: 3
5209380 ACTACTTAGA
5209390 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
5209438 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
5209483 CCAGATGTGG
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5213403 original size:135 final size:135
Alignment explanation
Indices: 5213156--5213410 Score: 321
Period size: 135 Copynumber: 1.9 Consensus size: 135
5213146 CAAAAACTAT
* * * *
5213156 AATTTCCTCCAGAAAATATAATACTGTCAGCCTCAACGAAGGAACATTTATTCAGATGAACTGCC
1 AATTCCCTCCAGAAAATATAAAACTGTCAGCCTCAACAAAGGAACATTTATTCAGATGAACTCCC
* * * * *
5213221 ACTATAGAATCCCATCATGAACTAGTAGAACTATCATGTTTCAAATGAACTTTTAAAACAGTTCA
66 ACTAGAGAATCCCACCACGAACAAGTAGAACTATCAAGTTTCAAATGAACTTTTAAAACAGTTCA
5213286 ACCAG
131 ACCAG
* * * * ** * * *
5213291 AATTCCCTCCAGAAAATATAAAATTGTTAGCCTCAATAAAGGGATGTTTATTTAGGTGGACTCCC
1 AATTCCCTCCAGAAAATATAAAACTGTCAGCCTCAACAAAGGAACATTTATTCAGATGAACTCCC
* * *
5213356 ACTCGAGAATCCCACCACGAACAAGTAGAATTATGAAGTTTCAAATGAACTTTTA
66 ACTAGAGAATCCCACCACGAACAAGTAGAACTATCAAGTTTCAAATGAACTTTTA
5213411 GAAATGCTGA
Statistics
Matches: 99, Mismatches: 21, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
135 99 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (135 bp):
AATTCCCTCCAGAAAATATAAAACTGTCAGCCTCAACAAAGGAACATTTATTCAGATGAACTCCC
ACTAGAGAATCCCACCACGAACAAGTAGAACTATCAAGTTTCAAATGAACTTTTAAAACAGTTCA
ACCAG
Found at i:5216627 original size:6 final size:6
Alignment explanation
Indices: 5216616--5216646 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
5216606 AACAAGAAGA
5216616 GATGTG GATGTG GATGTG GATGTG GATGTG G
1 GATGTG GATGTG GATGTG GATGTG GATGTG G
5216647 GTTTTCTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GATGTG
Found at i:5217199 original size:20 final size:19
Alignment explanation
Indices: 5217156--5217207 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
5217146 AATGACATCA
5217156 AAACAACAACAAACAGTAG
1 AAACAACAACAAACAGTAG
* * *
5217175 AAACAACAGCAAAGTAGTGG
1 AAACAACAACAAA-CAGTAG
*
5217195 AAACAATAACAAA
1 AAACAACAACAAA
5217208 ACACAATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.62, C:0.17, G:0.13, T:0.08
Consensus pattern (19 bp):
AAACAACAACAAACAGTAG
Found at i:5224023 original size:28 final size:28
Alignment explanation
Indices: 5223930--5224028 Score: 67
Period size: 28 Copynumber: 3.5 Consensus size: 28
5223920 TTATTTAATA
* * *
5223930 AATTAAAATTTATAAAGATTATAAGACATT
1 AATTAAAA-TTATAAA-AATATTAGAAATT
** * *
5223960 AATTAAAACCAT-AAAATTTTATAAAATT
1 AATTAAAATTATAAAAATATTA-GAAATT
*
5223988 AGA-AAAAATTATAAAAATATTAGAAATT
1 A-ATTAAAATTATAAAAATATTAGAAATT
*
5224016 AATTAAAAATATA
1 AATTAAAATTATA
5224029 TATAAAAATT
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
27 5 0.10
28 27 0.53
29 11 0.22
30 8 0.16
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (28 bp):
AATTAAAATTATAAAAATATTAGAAATT
Found at i:5224043 original size:24 final size:25
Alignment explanation
Indices: 5223993--5224060 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 25
5223983 AAATTAGAAA
*
5223993 AAATTATAAAA-ATAT-TAGAAATT
1 AAATTATAAAATATATATAAAAATT
5224016 -AATTA-AAAATATATATAAAAATT
1 AAATTATAAAATATATATAAAAATT
*
5224039 AAATTATAAAAT-TTTATAAAAA
1 AAATTATAAAATATATATAAAAA
5224061 ATAATTTCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.10
22 9 0.23
23 7 0.18
24 14 0.36
25 5 0.13
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (25 bp):
AAATTATAAAATATATATAAAAATT
Found at i:5225866 original size:6 final size:6
Alignment explanation
Indices: 5225845--5225896 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
5225835 CAAACCACAA
* * *
5225845 CAACAG CATCAG CAACAA CAACAA CAACAG CAACAG CAACAG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
5225893 CAAC
1 CAAC
5225897 GGGAACATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.52, C:0.35, G:0.12, T:0.02
Consensus pattern (6 bp):
CAACAG
Found at i:5225903 original size:18 final size:18
Alignment explanation
Indices: 5225841--5225896 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
5225831 TCGGCAAACC
*
5225841 ACAACAACAGCATCAGCA
1 ACAACAACAGCAACAGCA
*
5225859 ACAACAACAACAACAGCA
1 ACAACAACAGCAACAGCA
*
5225877 ACAGCAACAGCAACAGCA
1 ACAACAACAGCAACAGCA
5225895 AC
1 AC
5225897 GGGAACATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.54, C:0.34, G:0.11, T:0.02
Consensus pattern (18 bp):
ACAACAACAGCAACAGCA
Found at i:5227976 original size:30 final size:30
Alignment explanation
Indices: 5227916--5227995 Score: 72
Period size: 30 Copynumber: 2.5 Consensus size: 30
5227906 ATCTTATATA
* * *
5227916 TTTATAATTTTTAAAAGATTAAATTAAATT
1 TTTATTATTTTTAAAAGAGTAAATGAAATT
*
5227946 TTTATTATTTTTAAAAG-GTAAAGTGCAATT
1 TTTATTATTTTTAAAAGAGTAAA-TGAAATT
5227976 TTACTATTATTAATTTAAAA
1 TT--TATTATT--TTTAAAA
5227996 TTTTATAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 4 0.10
30 23 0.56
32 7 0.17
34 7 0.17
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (30 bp):
TTTATTATTTTTAAAAGAGTAAATGAAATT
Found at i:5231105 original size:5 final size:5
Alignment explanation
Indices: 5231095--5231119 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5231085 CAGATATATG
5231095 TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA
5231120 GGCATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:5231824 original size:12 final size:12
Alignment explanation
Indices: 5231807--5231831 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5231797 ACCAAAACTG
5231807 GCTTTTAGCGGC
1 GCTTTTAGCGGC
5231819 GCTTTTAGCGGC
1 GCTTTTAGCGGC
5231831 G
1 G
5231832 ATTAAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.36, T:0.32
Consensus pattern (12 bp):
GCTTTTAGCGGC
Found at i:5232185 original size:114 final size:113
Alignment explanation
Indices: 5231943--5232543 Score: 853
Period size: 114 Copynumber: 5.3 Consensus size: 113
5231933 AAAATAAGCA
* * * *
5231943 TTAGCGGCGTTTATTTGAAAGCGCCGCAAAAAGCCTAAGCCAAACGGTACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* ** * *
5232008 TGGGGGTCTTTAGTGGCGTTTCTATAAAGCGCCGCTAATTCTCAGGTCT
66 T-GGGGTCTTTAGCGGCGTTTCTGCAATGCGCCGCTAATGCTCAGGTCT
* * * * *
5232057 GTAGCGGCGGTTTTTTAACAGCGCCGCAAAAAGCCTAAACCCAACGGTACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
*
5232122 TGGGGTCTTTAGCGGCGTTTCTGCACTGCGCCGCTAATGCTCAGGTCT
66 TGGGGTCTTTAGCGGCGTTTCTGCAATGCGCCGCTAATGCTCAGGTCT
* *
5232170 TTAGCGGCGTTTTTTTAAAAGCGCCGCAACAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* * * * * *
5232235 TGGGGGTCTTTCGCGGCATTTTTGTAATGCGCCGCTAATTCTTAGGTCTT
66 T-GGGGTCTTTAGCGGCGTTTCTGCAATGCGCCGCTAATGCTCAGGTC-T
* *
5232285 TTAGCGGCGTTTTGTTAAAAGCGCCGCAAAAAGCCTAAGCCAAACGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* * * *
5232350 TGGGGTCTTTAGCGGCGTTTTTTCAAAGCGCCGCTAATGCTCAGGTGT
66 TGGGGTCTTTAGCGGCGTTTCTGCAATGCGCCGCTAATGCTCAGGTCT
* *
5232398 TTAGCAGCGTTTTTTTAAAAGCGCCGCAAAAAGCTTAAGCCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
*
5232463 TAGGGTCTTTAGCGGCGTTTCTG-AATAAGCGCCGCTAATGCTCAGGTCT
66 TGGGGTCTTTAGCGGCGTTTCTGCAAT--GCGCCGCTAATGCTCAGGTCT
*
5232512 TTAGCGGCGTTTTTTAAAAAGCGCCGCAAAAA
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAA
5232544 CATTTTATCT
Statistics
Matches: 435, Mismatches: 48, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
112 2 0.00
113 184 0.42
114 186 0.43
115 63 0.14
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (113 bp):
TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
TGGGGTCTTTAGCGGCGTTTCTGCAATGCGCCGCTAATGCTCAGGTCT
Found at i:5233087 original size:15 final size:14
Alignment explanation
Indices: 5233061--5233095 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
5233051 TTAGACTAAG
5233061 TAATATATATTAAA
1 TAATATATATTAAA
*
5233075 TTATATAATATTAAA
1 TAATAT-ATATTAAA
5233090 TAATAT
1 TAATAT
5233096 TGTTTAGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TAATATATATTAAA
Found at i:5233109 original size:7 final size:7
Alignment explanation
Indices: 5233097--5233137 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
5233087 AAATAATATT
5233097 GTTTAGG
1 GTTTAGG
*
5233104 GGTTAGG
1 GTTTAGG
5233111 GATTTAGG
1 G-TTTAGG
5233119 G-TTAGG
1 GTTTAGG
5233125 GTTTAGG
1 GTTTAGG
5233132 GTTTAG
1 GTTTAG
5233138 ATTAATTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 18 0.60
8 6 0.20
ACGTcount: A:0.17, C:0.00, G:0.44, T:0.39
Consensus pattern (7 bp):
GTTTAGG
Found at i:5233292 original size:93 final size:91
Alignment explanation
Indices: 5233119--5233373 Score: 340
Period size: 93 Copynumber: 2.8 Consensus size: 91
5233109 GGGATTTAGG
* *
5233119 GTTAGGGTTTAGGGTTTAGATTAATTAGTGTTTTTTAA-TT-GATATATTAAATAATGTTTAGGG
1 GTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTACATATATTAAATAATGTTTAGGG
*
5233182 GTTAGGGGTTAGTGATTCGGGGTCGA
66 GTTAGGGGTTAGTGATTCGGGGTCCA
* *
5233208 GTTAGGGTTTAGGATTTATATTAATTAGT-TTTTTTAATTTATATATATTAATAAATAATGTTTA
1 GTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTACATATA-T--TAAATAATGTTTA
*
5233272 GGGGTTTGGGGTTAGTGATTCGGGGTCCA
63 GGGGTTAGGGGTTAGTGATTCGGGGTCCA
* * * *
5233301 ATTAGGGTTTAAGATTTAGATTGATTAGTGTTTTATAATTTAC--ATATTAAATAATGTTTAGGG
1 GTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTACATATATTAAATAATGTTTAGGG
* *
5233364 TTTATGGGTT
66 GTTAGGGGTT
5233374 TGGGGTTTGT
Statistics
Matches: 146, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
88 8 0.05
89 52 0.36
90 5 0.03
91 2 0.01
92 3 0.02
93 65 0.45
94 11 0.08
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (91 bp):
GTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTACATATATTAAATAATGTTTAGGG
GTTAGGGGTTAGTGATTCGGGGTCCA
Found at i:5233393 original size:14 final size:15
Alignment explanation
Indices: 5233356--5233394 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
5233346 ATTAAATAAT
5233356 GTTTAGGGTTTATGG
1 GTTTAGGGTTTATGG
* *
5233371 GTTTGGGGTTTGT-G
1 GTTTAGGGTTTATGG
5233385 GTTTAGGGTT
1 GTTTAGGGTT
5233395 AAGAGTTAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.08, C:0.00, G:0.44, T:0.49
Consensus pattern (15 bp):
GTTTAGGGTTTATGG
Found at i:5233435 original size:17 final size:19
Alignment explanation
Indices: 5233408--5233447 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5233398 AGTTAGTGAT
5233408 TTAAGGGTTT-AGATCAGA
1 TTAAGGGTTTAAGATCAGA
*
5233426 TTAA-GGTTTAAGCTCAGA
1 TTAAGGGTTTAAGATCAGA
5233444 TTAA
1 TTAA
5233448 TTAGTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (19 bp):
TTAAGGGTTTAAGATCAGA
Found at i:5236143 original size:34 final size:35
Alignment explanation
Indices: 5236087--5236183 Score: 115
Period size: 38 Copynumber: 2.7 Consensus size: 35
5236077 CATAAGTTAG
* *
5236087 TTAATTAAAATACATAAATTACATAACTAATTACA
1 TTAATTAAAATACATAACTTACATAACTAAGTACA
**
5236122 TTAA-TACTATACATAACTTACATATATAACTAAGTACA
1 TTAATTAAAATACATAACTTAC----ATAACTAAGTACA
5236160 TTAATTAAAATACATAACTTACAT
1 TTAATTAAAATACATAACTTACAT
5236184 TAATATTATA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
34 14 0.27
35 6 0.12
38 16 0.31
39 15 0.29
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.35
Consensus pattern (35 bp):
TTAATTAAAATACATAACTTACATAACTAAGTACA
Found at i:5236209 original size:126 final size:121
Alignment explanation
Indices: 5236065--5236341 Score: 482
Period size: 126 Copynumber: 2.2 Consensus size: 121
5236055 GCTTGAAATA
5236065 ATACTTAAATTACATAAGTTAGTTAATTAAAATACATAAATTACATAACTAATTACATTAATACT
1 ATACTTAAATTACATAAGTTAGTTAATTAAAATACATAAATTACATAACTAATTACATTAATACT
5236130 ATACATAACTTACATATATAACTAAGTACATTAATTAAAATACATAACTTACATTAATATT
66 ATACATAACTTAC----ATAACTAAGTACATTAA-TAAAATACATAACTTACATTAATATT
5236191 ATACTTAAATTACATAAGTTAGTTAATTAAAATACATAAATTACATAACTAATTACATTAATACT
1 ATACTTAAATTACATAAGTTAGTTAATTAAAATACATAAATTACATAACTAATTACATTAATACT
**
5236256 ATACATAACTTACATAACTAAGTACATTAATATTATACATAACTTACATTAATATT
66 ATACATAACTTACATAACTAAGTACATTAATAAAATACATAACTTACATTAATATT
*
5236312 ATACTTAAAGTACATAAGTTAGTTAATTAA
1 ATACTTAAATTACATAAGTTAGTTAATTAA
5236342 TATTATACTT
Statistics
Matches: 148, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
121 53 0.36
122 17 0.11
126 78 0.53
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.37
Consensus pattern (121 bp):
ATACTTAAATTACATAAGTTAGTTAATTAAAATACATAAATTACATAACTAATTACATTAATACT
ATACATAACTTACATAACTAAGTACATTAATAAAATACATAACTTACATTAATATT
Found at i:5236220 original size:34 final size:34
Alignment explanation
Indices: 5236178--5236304 Score: 138
Period size: 34 Copynumber: 3.8 Consensus size: 34
5236168 AATACATAAC
*
5236178 TTACATTAATATTATACTTAAATTACATAAGTTAG
1 TTACATTAATATTATACATAAATTACATAA-TTAG
* *
5236213 TTA-ATTAA-A--ATACATAAATTACATAACTAA
1 TTACATTAATATTATACATAAATTACATAATTAG
* * *
5236243 TTACATTAATACTATACATAACTTACATAACTAAG
1 TTACATTAATATTATACATAAATTACATAA-TTAG
*
5236278 -TACATTAATATTATACATAACTTACAT
1 TTACATTAATATTATACATAAATTACAT
5236305 TAATATTATA
Statistics
Matches: 79, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
30 5 0.06
31 21 0.27
32 1 0.01
33 1 0.01
34 47 0.59
35 4 0.05
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (34 bp):
TTACATTAATATTATACATAAATTACATAATTAG
Found at i:5236303 original size:56 final size:56
Alignment explanation
Indices: 5236243--5236349 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
5236233 ACATAACTAA
**
5236243 TTACATTAATACTATACATAACTTACATAACTAAG-TACATTAATATTATACATAAC
1 TTACATTAATACTATACATAAAGTACATAACTAAGTTA-ATTAATATTATACATAAC
* * * *
5236299 TTACATTAATATTATACTTAAAGTACATAAGTTAGTTAATTAATATTATAC
1 TTACATTAATACTATACATAAAGTACATAACTAAGTTAATTAATATTATAC
5236350 TTAAATTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
56 42 0.95
57 2 0.05
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (56 bp):
TTACATTAATACTATACATAAAGTACATAACTAAGTTAATTAATATTATACATAAC
Found at i:5236325 original size:22 final size:22
Alignment explanation
Indices: 5236275--5236326 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
5236265 TTACATAACT
5236275 AAGTACATTAATATTATACATA
1 AAGTACATTAATATTATACATA
** *
5236297 ACTTACATTAATATTATACTTA
1 AAGTACATTAATATTATACATA
5236319 AAGTACAT
1 AAGTACAT
5236327 AAGTTAGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (22 bp):
AAGTACATTAATATTATACATA
Found at i:5236504 original size:31 final size:32
Alignment explanation
Indices: 5236440--5236523 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 32
5236430 AATTGCTTAA
* * *
5236440 AATAATACTTAAATTACATAAGTTAGTTAATT
1 AATAATACATAAATTACATAAGCTAATTAATT
5236472 AA-AATACATAAATTACATAA-CTAATTACATT
1 AATAATACATAAATTACATAAGCTAATTA-ATT
*
5236503 AATATTATACATAACTTACAT
1 AATA--ATACATAAATTACAT
5236524 TAATATTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
30 5 0.11
31 22 0.50
32 3 0.07
34 14 0.32
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.37
Consensus pattern (32 bp):
AATAATACATAAATTACATAAGCTAATTAATT
Found at i:5236515 original size:56 final size:56
Alignment explanation
Indices: 5236466--5236579 Score: 158
Period size: 56 Copynumber: 2.0 Consensus size: 56
5236456 CATAAGTTAG
5236466 TTAATTAAAATACATAAATTACATAA-CTAATTACATTAATATTATACATAACTTACA
1 TTAA-TAAAATACATAAATTACATAAGCTAATTA-ATTAATATTATACATAACTTACA
** * * *
5236523 TTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACA
1 TTAATAAAATACATAAATTACATAAGCTAATTAATTAATATTATACATAACTTACA
5236579 T
1 T
5236580 AACTTACATA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
56 42 0.82
57 9 0.18
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (56 bp):
TTAATAAAATACATAAATTACATAAGCTAATTAATTAATATTATACATAACTTACA
Found at i:5236524 original size:22 final size:22
Alignment explanation
Indices: 5236494--5236545 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
5236484 TTACATAACT
5236494 AATTACATTAATATTATACATA
1 AATTACATTAATATTATACATA
* *
5236516 ACTTACATTAATATTATACTTA
1 AATTACATTAATATTATACATA
5236538 AATTACAT
1 AATTACAT
5236546 AAGTTAGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTACATTAATATTATACATA
Found at i:5236562 original size:34 final size:34
Alignment explanation
Indices: 5236522--5236634 Score: 136
Period size: 34 Copynumber: 3.1 Consensus size: 34
5236512 CATAACTTAC
5236522 ATTAATATTATACTTAAATTACATAAGTTAGTTA
1 ATTAATATTATACTTAAATTACATAAGTTAGTTA
* * * *
5236556 ATTAATATTATACATAACTTACATAACTTACATAACTTA
1 ATTAATATTATACTTAAATTACATAA-GT---T-AGTTA
5236595 CATTAATATTATACTTAAATTACATAAGTTAGTTA
1 -ATTAATATTATACTTAAATTACATAAGTTAGTTA
5236630 ATTAA
1 ATTAA
5236635 CTTACATTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
34 29 0.45
35 5 0.08
36 1 0.02
38 1 0.02
39 5 0.08
40 24 0.37
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.42
Consensus pattern (34 bp):
ATTAATATTATACTTAAATTACATAAGTTAGTTA
Found at i:5236580 original size:9 final size:9
Alignment explanation
Indices: 5236566--5236789 Score: 72
Period size: 9 Copynumber: 24.7 Consensus size: 9
5236556 ATTAATATTA
5236566 TACATAACT
1 TACATAACT
5236575 TACATAACT
1 TACATAACT
5236584 TACATAACT
1 TACATAACT
*
5236593 TACATTAATATT
1 TACA-T-A-ACT
* *
5236605 ATACTTAAAT
1 -TACATAACT
*
5236615 TACATAAGT
1 TACATAACT
**
5236624 TAGTTAA-T
1 TACATAACT
*
5236632 TA-ACTTACAT
1 TACA-TAAC-T
*
5236642 TA-ATATCT
1 TACATAACT
5236650 TACATAACT
1 TACATAACT
5236659 TAC--AACT
1 TACATAACT
5236666 TACATAACT
1 TACATAACT
*
5236675 TACATTAATATT
1 TACA-T-A-ACT
* *
5236687 ATACTTAAAT
1 -TACATAACT
*
5236697 TACATAAGT
1 TACATAACT
**
5236706 TAGTTAA-T
1 TACATAACT
* *
5236714 TA-ACT-TCGA
1 TACA-TAAC-T
5236723 TACATAACT
1 TACATAACT
5236732 TACATAACT
1 TACATAACT
*
5236741 TACATAAAT
1 TACATAACT
* *
5236750 AAC-T-TCT
1 TACATAACT
5236757 TACATAACT
1 TACATAACT
** *
5236766 TATGTGACT
1 TACATAACT
5236775 TACATAACT
1 TACATAACT
5236784 TACATA
1 TACATA
5236790 GCATAATTTT
Statistics
Matches: 158, Mismatches: 36, Indels: 42
0.67 0.15 0.18
Matches are distributed among these distances:
7 10 0.06
8 14 0.09
9 106 0.67
10 12 0.08
11 4 0.03
12 6 0.04
13 6 0.04
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:5236657 original size:22 final size:21
Alignment explanation
Indices: 5236556--5236701 Score: 96
Period size: 22 Copynumber: 7.1 Consensus size: 21
5236546 AAGTTAGTTA
5236556 ATTAATATTATACATAACTTAC
1 ATTAATATT-TACATAACTTAC
*
5236578 A-T-A-ACTTACATAACTTAC
1 ATTAATATTTACATAACTTAC
* *
5236596 ATTAATATTATACTTAAATTAC
1 ATTAATATT-TACATAACTTAC
*
5236618 A-TAAGTTAGTTA-ATTAACTTAC
1 ATTAA--TATTTACA-TAACTTAC
5236640 ATTAATATCTTACATAACTTAC
1 ATTAATAT-TTACATAACTTAC
*
5236662 ----A-ACTTACATAACTTAC
1 ATTAATATTTACATAACTTAC
* *
5236678 ATTAATATTATACTTAAATTAC
1 ATTAATATT-TACATAACTTAC
5236700 AT
1 AT
5236702 AAGTTAGTTA
Statistics
Matches: 96, Mismatches: 12, Indels: 32
0.69 0.09 0.23
Matches are distributed among these distances:
16 13 0.14
17 1 0.01
18 14 0.15
19 3 0.03
20 3 0.03
21 10 0.10
22 45 0.47
23 7 0.07
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.40
Consensus pattern (21 bp):
ATTAATATTTACATAACTTAC
Found at i:5236669 original size:16 final size:16
Alignment explanation
Indices: 5236648--5236678 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5236638 ACATTAATAT
5236648 CTTACATAACTTACAA
1 CTTACATAACTTACAA
5236664 CTTACATAACTTACA
1 CTTACATAACTTACA
5236679 TTAATATTAT
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:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (16 bp):
CTTACATAACTTACAA
Found at i:5236735 original size:35 final size:34
Alignment explanation
Indices: 5236662--5236781 Score: 111
Period size: 35 Copynumber: 3.6 Consensus size: 34
5236652 CATAACTTAC
* *
5236662 AACTTACATAACTTACATTAAT-A-TT-ATACTT
1 AACTTACATAACTTACATAAATAACTTCATACAT
* * ** *
5236693 AAATTACATAAGTTAGTTAATTAACTTCGATACAT
1 AACTTACATAACTTACATAAATAACTTC-ATACAT
*
5236728 AACTTACATAACTTACATAAATAACTTCTTACAT
1 AACTTACATAACTTACATAAATAACTTCATACAT
** *
5236762 AACTTATGTGACTTACATAA
1 AACTTACATAACTTACATAA
5236782 CTTACATAGC
Statistics
Matches: 69, Mismatches: 16, Indels: 5
0.77 0.18 0.06
Matches are distributed among these distances:
31 16 0.23
32 1 0.01
33 2 0.03
34 22 0.32
35 28 0.41
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (34 bp):
AACTTACATAACTTACATAAATAACTTCATACAT
Found at i:5236751 original size:22 final size:22
Alignment explanation
Indices: 5236662--5236754 Score: 66
Period size: 22 Copynumber: 4.2 Consensus size: 22
5236652 CATAACTTAC
*
5236662 AACTTACATAACTTACATTAAT
1 AACTTACATAACTTACATAAAT
* * * *
5236684 -ATTATACTTAAATTACATAAGT
1 AACT-TACATAACTTACATAAAT
* * *
5236706 TAGTTA-ATTAACTT-CGATACAT
1 AACTTACA-TAACTTAC-ATAAAT
5236728 AACTTACATAACTTACATAAAT
1 AACTTACATAACTTACATAAAT
5236750 AACTT
1 AACTT
5236755 CTTACATAAC
Statistics
Matches: 52, Mismatches: 13, Indels: 12
0.68 0.17 0.16
Matches are distributed among these distances:
21 3 0.06
22 45 0.87
23 4 0.08
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (22 bp):
AACTTACATAACTTACATAAAT
Found at i:5236761 original size:82 final size:77
Alignment explanation
Indices: 5236513--5236754 Score: 318
Period size: 82 Copynumber: 3.1 Consensus size: 77
5236503 AATATTATAC
5236513 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTAC
1 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATT-A-ATTATACATAACTTAC
5236578 ATAACTTAC-----
64 ATAACTTACATTAA
*
5236587 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAACTTACATTA-ATATCTT
1 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAA-TT--A-TACATAACTT
*
5236651 ACATAACTTACAACTTAC
62 ACATAACTTAC-A-TTAA
5236669 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAACTTCGATACATAACTTA
1 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAA-TT--ATACATAACTTA
5236734 CATAACTTACA-TAA
63 CATAACTTACATTAA
5236748 ATAACTT
1 ATAACTT
5236755 CTTACATAAC
Statistics
Matches: 151, Mismatches: 5, Indels: 19
0.86 0.03 0.11
Matches are distributed among these distances:
72 1 0.01
73 3 0.02
74 46 0.30
75 18 0.12
76 2 0.01
79 9 0.06
81 3 0.02
82 69 0.46
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.40
Consensus pattern (77 bp):
ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATTATACATAACTTACAT
AACTTACATTAA
Found at i:5242369 original size:66 final size:66
Alignment explanation
Indices: 5242293--5242419 Score: 202
Period size: 66 Copynumber: 1.9 Consensus size: 66
5242283 AGCAAATTAC
*
5242293 ACAACTTAAAGCAGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCTAG
1 ACAACTTAAAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCTAG
5242357 TT
65 TT
* * *
5242359 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTC
1 ACAACTTAAAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTC
5242420 CAACAACAGC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
66 52 0.93
67 4 0.07
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.17
Consensus pattern (66 bp):
ACAACTTAAAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCTAGT
T
Found at i:5242438 original size:66 final size:66
Alignment explanation
Indices: 5242293--5242440 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 66
5242283 AGCAAATTAC
* * * **
5242293 ACAACTTAAAGCAGAGGCAACATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCTAGT
1 ACAACTTAAAGCAGATGCAACAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAAC
*
5242358 T
66 A
* *
5242359 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAA
1 ACAACTTAAAGCAGATGCAACAGCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAA
5242423 CA
65 CA
* *
5242425 ACAGCTTAGAGCAGAT
1 ACAACTTAAAGCAGAT
5242441 ACGGCGGCAA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
66 67 0.94
67 4 0.06
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.16
Consensus pattern (66 bp):
ACAACTTAAAGCAGATGCAACAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAAC
A
Found at i:5242454 original size:66 final size:66
Alignment explanation
Indices: 5242293--5242462 Score: 171
Period size: 66 Copynumber: 2.6 Consensus size: 66
5242283 AGCAAATTAC
** * * * * **
5242293 ACAACTTAAAGCAGAGGCAACATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCTAGT
1 ACAACTTAAAGCAGATACAGCAGCAAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAAC
*
5242358 T
66 A
* * *
5242359 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAA
1 ACAACTTAAAGCAGATACAGCAGCAAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAA
5242423 CA
65 CA
* * * * *
5242425 ACAGCTTAGAGCAGATACGGCGGCAAGAGAAGCAGAGG
1 ACAACTTAAAGCAGATACAGCAGCAAGAGAAGCTGAGG
5242463 CGGCAGCGAG
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
66 84 0.95
67 4 0.05
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.14
Consensus pattern (66 bp):
ACAACTTAAAGCAGATACAGCAGCAAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAAC
A
Found at i:5242506 original size:21 final size:21
Alignment explanation
Indices: 5242453--5242545 Score: 105
Period size: 21 Copynumber: 4.4 Consensus size: 21
5242443 GGCGGCAAGA
* *
5242453 GAAGCAGAGGCGGCAGCGAGA
1 GAAGCAGAGGCTGCAGCGAGG
* *
5242474 GAAGTACAGGCTGCAGCGAGG
1 GAAGCAGAGGCTGCAGCGAGG
** *
5242495 GAAGCAGAGGCTAAAGTGAGG
1 GAAGCAGAGGCTGCAGCGAGG
**
5242516 GAAATAGAGGCTGCAGCGAGG
1 GAAGCAGAGGCTGCAGCGAGG
5242537 GAAGCAGAG
1 GAAGCAGAG
5242546 CAGCGTCAAA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.34, C:0.15, G:0.44, T:0.06
Consensus pattern (21 bp):
GAAGCAGAGGCTGCAGCGAGG
Found at i:5242973 original size:43 final size:43
Alignment explanation
Indices: 5242917--5243258 Score: 176
Period size: 43 Copynumber: 8.0 Consensus size: 43
5242907 GTTTTTGGTC
* *
5242917 AAAGCGCCGCTAAAGATTAGGGTCTTTTGCGGCGTTTGT-G-G
1 AAAGCGCCACTAAAGATTAGGGTCTTTAGCGGCGTTTGTAGTG
* * *
5242958 AAAAGGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTTGTAGTG
1 -AAA-GCGCCACTAAAGATTAGGGTCTTTAGCGGCGTTTGTAGTG
* * * * *
5243003 AAAGCGCCACTAAAGATTCGGTTCTTTAGTGGCGTTTGTTGTC
1 AAAGCGCCACTAAAGATTAGGGTCTTTAGCGGCGTTTGTAGTG
* * * * * * * * ***
5243046 TATGCGCCGCTATAGATCAGGGTCTATAGCGGCGCTTATACCA
1 AAAGCGCCACTAAAGATTAGGGTCTTTAGCGGCGTTTGTAGTG
* * * * ****
5243089 AAAACGCCACTAAAGATCAGGGTCTTTAGCGGCGCTTATCCCA
1 AAAGCGCCACTAAAGATTAGGGTCTTTAGCGGCGTTTGTAGTG
* * * * * * *
5243132 AAAACGCCGCTAAAGATCAGGGTCTTTGGCGGCGCTTCTACT-
1 AAAGCGCCACTAAAGATTAGGGTCTTTAGCGGCGTTTGTAGTG
* * * * *
5243174 AAAGCACCGCTAAAAGTCTTA--TTCTTCAGCGGCGTTTGT-GAT-
1 AAAGCGCCACT-AAAG-ATTAGGGTCTTTAGCGGCGTTTGTAG-TG
* * * *
5243216 AGAAGCGCCGCTAAAGATCAGTGTCTTTAGCGGCGTTTTTAGT
1 A-AAGCGCCACTAAAGATTAGGGTCTTTAGCGGCGTTTGTAGT
5243259 AAAAAACGCC
Statistics
Matches: 234, Mismatches: 56, Indels: 19
0.76 0.18 0.06
Matches are distributed among these distances:
41 2 0.01
42 31 0.13
43 193 0.82
44 7 0.03
45 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (43 bp):
AAAGCGCCACTAAAGATTAGGGTCTTTAGCGGCGTTTGTAGTG
Found at i:5243053 original size:86 final size:86
Alignment explanation
Indices: 5242917--5243258 Score: 219
Period size: 86 Copynumber: 4.0 Consensus size: 86
5242907 GTTTTTGGTC
* * * *
5242917 AAAGCGCCGCTAAAGATTAGGGTCTTTTGCGGCGTTTGTGGAAAAGGCGCCACTAAAGCTCATGG
1 AAAGCGCCACTAAAGATTAGGGTCTTTAGCGGCGTTTGTGGAAAAGGCGCCACTAAAGATCAGGG
*
5242982 TCTTTAGCGGCGTTTGTAGTG
66 TCTATAGCGGCGTTTGTAGTG
* * * * *** * * *
5243003 AAAGCGCCACTAAAGATTCGGTTCTTTAGTGGCGTTTGTTGTCTATGCGCCGCTATAGATCAGGG
1 AAAGCGCCACTAAAGATTAGGGTCTTTAGCGGCGTTTGTGGAAAAGGCGCCACTAAAGATCAGGG
* * ***
5243068 TCTATAGCGGCGCTTATACCA
66 TCTATAGCGGCGTTTGTAGTG
* * * * ** * *
5243089 AAAACGCCACTAAAGATCAGGGTCTTTAGCGGCGCTTATCCCAAAA-ACGCCGCTAAAGATCAGG
1 AAAGCGCCACTAAAGATTAGGGTCTTTAGCGGCGTTTGT-GGAAAAGGCGCCACTAAAGATCAGG
* * * * *
5243153 GTCTTTGGCGGCGCTTCTACT-
65 GTCTATAGCGGCGTTTGTAGTG
* * * * * *
5243174 AAAGCACCGCTAAAAGTCTTA--TTCTTCAGCGGCGTTTGT-GATAGAA-GCGCCGCTAAAGATC
1 AAAGCGCCACT-AAAG-ATTAGGGTCTTTAGCGGCGTTTGTGGA-A-AAGGCGCCACTAAAGATC
* * *
5243235 AGTGTCTTTAGCGGCGTTTTTAGT
62 AGGGTCTATAGCGGCGTTTGTAGT
5243259 AAAAAACGCC
Statistics
Matches: 197, Mismatches: 54, Indels: 11
0.75 0.21 0.04
Matches are distributed among these distances:
83 1 0.01
84 1 0.01
85 57 0.29
86 135 0.69
87 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (86 bp):
AAAGCGCCACTAAAGATTAGGGTCTTTAGCGGCGTTTGTGGAAAAGGCGCCACTAAAGATCAGGG
TCTATAGCGGCGTTTGTAGTG
Found at i:5243748 original size:39 final size:40
Alignment explanation
Indices: 5243681--5243759 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 40
5243671 TAAAAAGTAT
* * *
5243681 TTATATTAACAAATACTACCATAAATATAATAAATATTTTC
1 TTATATTAAAAAACACTA-CATAAATATAATAAACATTTTC
5243722 TTATATTAAAAAACACTA-ATAAATATAATAAACATTTT
1 TTATATTAAAAAACACTACATAAATATAATAAACATTTT
5243760 ACTGTATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 19 0.54
41 16 0.46
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (40 bp):
TTATATTAAAAAACACTACATAAATATAATAAACATTTTC
Found at i:5246651 original size:34 final size:34
Alignment explanation
Indices: 5246607--5246690 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 34
5246597 TTTAGCTTTT
* * *
5246607 ATATATTTTATATTTTATAGATATATACATATTC
1 ATATTTTTTATATTTTAAAGATATATACATATAC
** * *
5246641 AT-TTCTTTTATGCTGTAAATATATATACATATAC
1 ATATT-TTTTATATTTTAAAGATATATACATATAC
5246675 ATATTTTTTATATTTT
1 ATATTTTTTATATTTT
5246691 CATTTTACTT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
33 1 0.03
34 35 0.92
35 2 0.05
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.55
Consensus pattern (34 bp):
ATATTTTTTATATTTTAAAGATATATACATATAC
Found at i:5248672 original size:19 final size:20
Alignment explanation
Indices: 5248635--5248674 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5248625 TCTTTTCGCA
* *
5248635 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
5248655 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
5248674 T
1 T
5248675 AAACACAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:5250542 original size:19 final size:19
Alignment explanation
Indices: 5250518--5250557 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5250508 GCAAATATTC
*
5250518 TTTCATT-CTTTACGATTTT
1 TTTCATTCCTTCA-GATTTT
5250537 TTTCATTCCTTCAGATTTT
1 TTTCATTCCTTCAGATTTT
5250556 TT
1 TT
5250558 CTGCCAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.15, C:0.17, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTCATTCCTTCAGATTTT
Found at i:5251508 original size:6 final size:7
Alignment explanation
Indices: 5251496--5251541 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
5251486 AAAAGTGATG
5251496 TGAAAAA
1 TGAAAAA
5251503 TGAAAAGA
1 TGAAAA-A
5251511 TG-AAAA
1 TGAAAAA
5251517 TGAAAAA
1 TGAAAAA
5251524 TGAAAAA
1 TGAAAAA
5251531 -GTAAAAA
1 TG-AAAAA
5251538 TGAA
1 TGAA
5251542 GAGGCTAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 4 0.11
7 27 0.77
8 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (7 bp):
TGAAAAA
Found at i:5252868 original size:45 final size:45
Alignment explanation
Indices: 5252768--5252960 Score: 189
Period size: 45 Copynumber: 4.3 Consensus size: 45
5252758 GGCAGGTTGA
* * * *
5252768 AAGAAAGTAGATCTTGTCTT-CATGTACTGG-CGTGAAGTAGATC-
1 AAGAAAGCAGATCTTGTCTTCCCT-TACTGGTGGCGAAGTAGATCG
* * *
5252811 AGAGATACCAGATCTTGCCTTCCCTTACTGGTGGCGAAGTAGATCG
1 A-AGAAAGCAGATCTTGTCTTCCCTTACTGGTGGCGAAGTAGATCG
** * *
5252857 AAGAAAGCAGATCTTGTCTT-TATGTACTGG-CGTGAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCCCT-TACTGGTGGCGAAGTAGATCG
** *
5252901 AAGAAAGTGGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCCCTTACTGGTGGCGAAGTAGATCG
*
5252946 AAGAAAACAGATCTT
1 AAGAAAGCAGATCTT
5252961 ATCTCCTTAG
Statistics
Matches: 119, Mismatches: 24, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
43 1 0.01
44 58 0.49
45 59 0.50
46 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (45 bp):
AAGAAAGCAGATCTTGTCTTCCCTTACTGGTGGCGAAGTAGATCG
Found at i:5252869 original size:89 final size:89
Alignment explanation
Indices: 5252768--5252960 Score: 289
Period size: 89 Copynumber: 2.2 Consensus size: 89
5252758 GGCAGGTTGA
* *
5252768 AAGAAAGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC-AGAGATACCAGATCTTGCCTT
1 AAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGA-AGAAACCAGATCTTGCCTT
*
5252832 CCCTTACTGGTGGCGAAGTAGATCG
65 CCCATACTGGTGGCGAAGTAGATCG
* *** *
5252857 AAGAAAGCAGATCTTGTCTTTATGTACTGGCGTGAAGTAGATCGAAGAAAGTGGATCTTGTCTTC
1 AAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAAACCAGATCTTGCCTTC
5252922 CCATACTGGTGGCGAAGTAGATCG
66 CCATACTGGTGGCGAAGTAGATCG
*
5252946 AAGAAAACAGATCTT
1 AAGAAAGCAGATCTT
5252961 ATCTCCTTAG
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
89 93 0.99
90 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (89 bp):
AAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAAACCAGATCTTGCCTTC
CCATACTGGTGGCGAAGTAGATCG
Found at i:5253671 original size:44 final size:44
Alignment explanation
Indices: 5252953--5253741 Score: 330
Period size: 44 Copynumber: 17.9 Consensus size: 44
5252943 TCGAAGAAAA
* * *
5252953 CAGATCTTATCT-CCTTAGACAGTAGTGGAGTAGA-TCAAGGATGG
1 CAGATTTTATCTCCCTAAG-CAGTAGTGGAGTAGATTGAA-GATGG
** * * * * **
5252997 TGGATTTTACCTCCCTGAAGTTA-CAGTGGAGTACATTGAAGCCGG
1 CAGATTTTATCTCCCT-AAG-CAGTAGTGGAGTAGATTGAAGATGG
* * * * * * **
5253042 TA-ATTCTATCTCCCTAGGCAGCAGTGGAATAGATTGAATATTA
1 CAGATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGG
* * *
5253085 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
1 CAGATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGG
* * ** * ** * *
5253129 CAGATTTTACCTCCCTGAGGTTGCAGCAGAGTATATTGAAGCTGG
1 CAGATTTTATCTCCCT-AAGCAGTAGTGGAGTAGATTGAAGATGG
* * ** ** * **
5253174 TA-ATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTA
1 CAGATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGG
* * * * *
5253217 TAGATCTTATCTCCCAAAGCAGTAGTGGAGCAGATCGAAGATGG
1 CAGATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGG
* * ** * * * ***
5253261 CAGATTTTACCTCCCTGAGGTTGCAGCGGAGTATATTGAAGCCAG
1 CAGATTTTATCTCCCT-AAGCAGTAGTGGAGTAGATTGAAGATGG
* * ** * * **
5253306 TA-ATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTA
1 CAGATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGG
* * *
5253349 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
1 CAGATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGG
* ** * * * * *
5253393 CAGATTTTACCTCCCTAAGGTTGCAGCGGAGTATATTGAAGCTAG
1 CAGATTTTATCTCCCTAA-GCAGTAGTGGAGTAGATTGAAGATGG
* * ** * * * **
5253438 TA-ATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAAATTA
1 CAGATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGG
* * * *
5253481 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGA
1 CAGATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGG
* * * ***
5253525 CAGATTTTACCTCCCTGAG--GTTACAGTGGAGTACATTGAAGCCAG
1 CAGATTTTATCTCCCTAAGCAG-T--AGTGGAGTAGATTGAAGATGG
* * ** * * **
5253570 TA-ATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTA
1 CAGATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGG
* * *
5253613 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
1 CAGATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGG
* * * * *
5253657 CGGATTTTACCTCCCTGAG--GTTACAGTGGAGTACATTG-A-A-GC
1 CAGATTTTATCTCCCTAAGCAG-T--AGTGGAGTAGATTGAAGATGG
* * *
5253699 CAGTATTCTCATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
1 CAG-ATT-TTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGA
5253742 CCCCAGTCTT
Statistics
Matches: 524, Mismatches: 195, Indels: 51
0.68 0.25 0.07
Matches are distributed among these distances:
42 6 0.01
43 107 0.20
44 303 0.58
45 100 0.19
46 8 0.02
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (44 bp):
CAGATTTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGG
Found at i:5253775 original size:44 final size:44
Alignment explanation
Indices: 5253724--5253870 Score: 109
Period size: 44 Copynumber: 3.3 Consensus size: 44
5253714 CCTAAGCAGT
5253724 AGTGGAGCAGATCGAAGACCCCAGTCTTATCTCCCTGAAGTTGC
1 AGTGGAGCAGATCGAAGACCCCAGTCTTATCTCCCTGAAGTTGC
* ** * * *
5253768 AGTGGAGCA-AACAGAAGTATACCAATCCTATCTCCTTGAAGTTGC
1 AGTGGAGCAGATC-GAAG-ACCCCAGTCTTATCTCCCTGAAGTTGC
* ** * * * * *
5253813 AATGGAGTGGAT-TAAAACCGCAGATCTCATCTCTCTGAAGTTGC
1 AGTGGAGCAGATCGAAGACCCCAG-TCTTATCTCCCTGAAGTTGC
* *
5253857 AGTAGAGCAAATCG
1 AGTGGAGCAGATCG
5253871 CATCAGATTT
Statistics
Matches: 72, Mismatches: 26, Indels: 9
0.67 0.24 0.08
Matches are distributed among these distances:
43 5 0.07
44 38 0.53
45 28 0.39
46 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (44 bp):
AGTGGAGCAGATCGAAGACCCCAGTCTTATCTCCCTGAAGTTGC
Found at i:5253776 original size:132 final size:132
Alignment explanation
Indices: 5252952--5253716 Score: 1230
Period size: 132 Copynumber: 5.8 Consensus size: 132
5252942 ATCGAAGAAA
* * **
5252952 ACAGATCTTATCT-CCTTAGACAGTAGTGGAGTAGATC-AAGGATGGTGGATTTTACCTCCCTGA
1 ACAGATCTTATCTCCCTAAG-CAGTAGTGGAGCAGATCGAA-GATGGCAGATTTTACCTCCCTGA
* * * *
5253015 AGTTACAGTGGAGTACATTGAAGCCGGTAATTCTATCTCCCTAGGCAGCAGTGGAATAGATTGAA
64 GGTTACAGCGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAA
*
5253080 TATT
129 GATT
5253084 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGG
* * * ** *
5253149 TTGCAGCAGAGTATATTGAAGCTGGTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGA
66 TTACAGCGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA
5253214 TT
131 TT
* *
5253216 ATAGATCTTATCTCCCAAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGG
* *
5253281 TTGCAGCGGAGTATATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA
66 TTACAGCGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA
5253346 TT
131 TT
*
5253348 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGG
* * * *
5253413 TTGCAGCGGAGTATATTGAAGCTAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAAA
66 TTACAGCGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA
5253478 TT
131 TT
*
5253480 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAGATTTTACCTCCCTGAGG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGG
*
5253545 TTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA
66 TTACAGCGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA
5253610 TT
131 TT
*
5253612 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGG
*
5253677 TTACAGTGGAGTACATTGAAGCCAGT-ATTCTCATCTCCCT
66 TTACAGCGGAGTACATTGAAGCCAGTAATTCT-ATCTCCCT
5253717 AAGCAGTAGT
Statistics
Matches: 597, Mismatches: 33, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
131 5 0.01
132 585 0.98
133 7 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (132 bp):
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGG
TTACAGCGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA
TT
Found at i:5256654 original size:17 final size:17
Alignment explanation
Indices: 5256632--5256668 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
5256622 AGTGCCACAT
5256632 TAAAAGTTTTGATAAAG
1 TAAAAGTTTTGATAAAG
5256649 TAAAAGTTTTGATAAAG
1 TAAAAGTTTTGATAAAG
5256666 TAA
1 TAA
5256669 GAAGGGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (17 bp):
TAAAAGTTTTGATAAAG
Found at i:5259722 original size:11 final size:11
Alignment explanation
Indices: 5259706--5259733 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5259696 AATTATATCT
5259706 TTATTTTTTAA
1 TTATTTTTTAA
5259717 TTATTTTTTAA
1 TTATTTTTTAA
5259728 TTATTT
1 TTATTT
5259734 AAATTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTATTTTTTAA
Found at i:5259956 original size:20 final size:20
Alignment explanation
Indices: 5259910--5259957 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
5259900 CTGTTTTTTA
*
5259910 TTTTATATATTATAATATAAT
1 TTTTA-ATATTATAACATAAT
*
5259931 TATTAATATTATGAACAT-AT
1 TTTTAATATTAT-AACATAAT
5259951 TTTTAAT
1 TTTTAAT
5259958 GGTTTGCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTAATATTATAACATAAT
Found at i:5269623 original size:2 final size:2
Alignment explanation
Indices: 5269618--5269658 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5269608 ACAAAGTTTG
5269618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5269659 AAGCCTTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5278551 original size:23 final size:21
Alignment explanation
Indices: 5278509--5278552 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5278499 GATCTCATTT
*
5278509 TTTTTTAAAAAAATCAAATTA
1 TTTTTTAAAAAAATAAAATTA
*
5278530 TTTTTTAACGAAAATAATAATTA
1 TTTTTTAA-AAAAATAA-AATTA
5278553 AAACATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 6 0.32
23 5 0.26
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTTTTAAAAAAATAAAATTA
Found at i:5281830 original size:101 final size:100
Alignment explanation
Indices: 5281698--5281914 Score: 301
Period size: 101 Copynumber: 2.1 Consensus size: 100
5281688 TTACCATGAC
* * * * *
5281698 CCAACCATGGTCTTACATTCGTAGTTTCATAACTCAATTATGGTCTTATCATCAGAATGCCATAA
1 CCAACCATGGTCTTACATTCATAG-TCCATAACCCAATTATGGTCTTATCATCAAAATACCATAA
5281763 CCCAACTATGGTCTTACTTATAAATACTGCCATGGT
65 CCCAACTATGGTCTTACTTATAAATACTGCCATGGT
* * *
5281799 CCAACCATGGTCTTACATTCAAATAG-CCATAACCCAATTATGGTCTTTTCATTAAAATATCATA
1 CCAACCATGGTCTTACATTC--ATAGTCCATAACCCAATTATGGTCTTATCATCAAAATACCATA
* * *
5281863 TCTCAGCTATGGTCTTACTTATAAATACTGCCATGGT
64 ACCCAACTATGGTCTTACTTATAAATACTGCCATGGT
5281900 CCAACCATGGTCTTA
1 CCAACCATGGTCTTA
5281915 TCCGTCAATT
Statistics
Matches: 103, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
101 100 0.97
103 3 0.03
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (100 bp):
CCAACCATGGTCTTACATTCATAGTCCATAACCCAATTATGGTCTTATCATCAAAATACCATAAC
CCAACTATGGTCTTACTTATAAATACTGCCATGGT
Found at i:5281842 original size:33 final size:33
Alignment explanation
Indices: 5281691--5281880 Score: 104
Period size: 33 Copynumber: 5.7 Consensus size: 33
5281681 ACATGCATTA
* * *
5281691 CCATGACCCAACCATGGTCTTACATTC--GTAG
1 CCATAACCCAACTATGGTCTTACATTCAAATAG
* * *
5281722 TTTCATAACTCAATTATGGTCTTATCA-TCAGAAT-G
1 --CCATAACCCAACTATGGTCTTA-CATTCA-AATAG
*
5281757 CCATAACCCAACTATGGTCTTAC-TTATAAATACTG
1 CCATAACCCAACTATGGTCTTACATT-CAAATA--G
*** *
5281792 CCATGGTCCAACCATGGTCTTACATTCAAATAG
1 CCATAACCCAACTATGGTCTTACATTCAAATAG
* * *
5281825 CCATAACCCAATTATGGTCTTTTCATTAAAATA-
1 CCATAACCCAACTATGGTC-TTACATTCAAATAG
* * * *
5281858 TCATATCTCAGCTATGGTCTTAC
1 CCATAACCCAACTATGGTCTTAC
5281881 TTATAAATAC
Statistics
Matches: 118, Mismatches: 28, Indels: 23
0.70 0.17 0.14
Matches are distributed among these distances:
32 8 0.07
33 68 0.58
34 13 0.11
35 26 0.22
36 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.33
Consensus pattern (33 bp):
CCATAACCCAACTATGGTCTTACATTCAAATAG
Found at i:5284598 original size:35 final size:36
Alignment explanation
Indices: 5284557--5284638 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
5284547 TTTAATTATA
*
5284557 TATATATATATACAATTAATGATATTTAAA-TATAATT
1 TATAT-TATAT-CAATTAATGATAATTAAATTATAATT
* *
5284594 TATATTATATGAATTTATGATAATTAAATTATAA-T
1 TATATTATATCAATTAATGATAATTAAATTATAATT
*
5284629 GATATTATAT
1 TATATTATAT
5284639 TATTAAATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
35 25 0.62
36 10 0.25
37 5 0.12
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (36 bp):
TATATTATATCAATTAATGATAATTAAATTATAATT
Found at i:5284630 original size:25 final size:23
Alignment explanation
Indices: 5284550--5284646 Score: 62
Period size: 24 Copynumber: 4.1 Consensus size: 23
5284540 TTATTTGTTT
5284550 AATTATAT-ATA-TATAT-A-TA
1 AATTATATGATATTATATAATTA
5284569 CAATTA-ATGATATTTAAATATAATTTA
1 -AATTATATGATA-TT--ATATAA-TTA
*
5284596 TATTATATGA-ATTTATGATAATTA
1 AATTATATGATA-TTAT-ATAATTA
*
5284620 AATTATAATGATATTATATTATTA
1 AATTAT-ATGATATTATATAATTA
5284644 AAT
1 AAT
5284647 GAATTAAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
19 2 0.03
20 8 0.13
22 1 0.02
24 23 0.37
25 13 0.21
26 9 0.15
27 6 0.10
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (23 bp):
AATTATATGATATTATATAATTA
Found at i:5284949 original size:3 final size:3
Alignment explanation
Indices: 5284935--5284985 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
5284925 AAATGATTAA
*
5284935 ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5284983 ATT
1 ATT
5284986 GTGAGATGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5286432 original size:45 final size:45
Alignment explanation
Indices: 5286365--5286465 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
5286355 GCCGACTACT
* ** * *
5286365 GTTACTGTTACCGATTTGGCACTTTGTGTGTCAAATACTGTTACC
1 GTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATAATGTCACC
** *
5286410 GTTACTGTTACAGATTCAGCACTTTGTGTGTGGAATAATGTCACT
1 GTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATAATGTCACC
5286455 GTTACTGTTAC
1 GTTACTGTTAC
5286466 TGCTACCGTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (45 bp):
GTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATAATGTCACC
Found at i:5286641 original size:2 final size:2
Alignment explanation
Indices: 5286634--5286658 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5286624 AATAAGAATG
5286634 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5286659 GTTAATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5288536 original size:55 final size:55
Alignment explanation
Indices: 5288471--5288582 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
5288461 ATTGATGTGT
5288471 ATAGATTGAATCGTTATATGATTTGGTTATCTTGAACTCACCTTACTGTTGCAAA
1 ATAGATTGAATCGTTATATGATTTGGTTATCTTGAACTCACCTTACTGTTGCAAA
5288526 ATAGATTGAATCGTTATATGATTTGGTTATCTTGAACTCACCTTACTGTTGCAAA
1 ATAGATTGAATCGTTATATGATTTGGTTATCTTGAACTCACCTTACTGTTGCAAA
5288581 AT
1 AT
5288583 GTAATAACAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (55 bp):
ATAGATTGAATCGTTATATGATTTGGTTATCTTGAACTCACCTTACTGTTGCAAA
Found at i:5289067 original size:17 final size:17
Alignment explanation
Indices: 5289045--5289153 Score: 69
Period size: 17 Copynumber: 6.5 Consensus size: 17
5289035 ACGACTATAC
5289045 TTTATATGCAAGTTGTG
1 TTTATATGCAAGTTGTG
** *
5289062 TTTATATGTGAGTTGTC
1 TTTATATGCAAGTTGTG
* * *
5289079 TTTATACGTAAGCTG-G
1 TTTATATGCAAGTTGTG
* * * * *
5289095 GTTATGTACGAGTTGTA
1 TTTATATGCAAGTTGTG
* * * *
5289112 TGTATATGCGAGCTATG
1 TTTATATGCAAGTTGTG
5289129 TTTATATGCAAGTTGTG
1 TTTATATGCAAGTTGTG
5289146 -TTATATGC
1 TTTATATGC
5289154 GAACTGCGTT
Statistics
Matches: 65, Mismatches: 26, Indels: 3
0.69 0.28 0.03
Matches are distributed among these distances:
16 16 0.25
17 49 0.75
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (17 bp):
TTTATATGCAAGTTGTG
Found at i:5289152 original size:33 final size:32
Alignment explanation
Indices: 5289105--5289200 Score: 84
Period size: 33 Copynumber: 2.8 Consensus size: 32
5289095 GTTATGTACG
*
5289105 AGTTGTATGTATATGCGAGCTATGTTTATATGCA
1 AGTTGT-T-TATATGCGAGCTATGTTTATACGCA
* ** **
5289139 AGTTGTGTTATATGCGAACTGCGTTTATACGTG
1 AGTTGT-TTATATGCGAGCTATGTTTATACGCA
*
5289172 AGTTGCCTTTATATGCGAGCTATGCTTAT
1 AGTTG--TTTATATGCGAGCTATGTTTAT
5289201 CAATGTGTGG
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
33 24 0.49
34 24 0.49
35 1 0.02
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (32 bp):
AGTTGTTTATATGCGAGCTATGTTTATACGCA
Found at i:5295532 original size:50 final size:50
Alignment explanation
Indices: 5295457--5295555 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
5295447 TTCGGAATTC
* *
5295457 TGACTTCTGATATATAAAACATAAGGAAGAATACGTTTTGTTGGTAAAAT
1 TGACTTCTGATATATAAAACATAAGGAAGAATACATTTTGTGGGTAAAAT
* *
5295507 TGACTTCTGGTATATAAAACATAAGGAAGGATACATTTTGTGGGTAAAA
1 TGACTTCTGATATATAAAACATAAGGAAGAATACATTTTGTGGGTAAAA
5295556 AACTGACTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.32
Consensus pattern (50 bp):
TGACTTCTGATATATAAAACATAAGGAAGAATACATTTTGTGGGTAAAAT
Found at i:5313756 original size:3 final size:3
Alignment explanation
Indices: 5313750--5313789 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5313740 CTTCTTTTTC
5313750 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5313790 CCCAAAATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5321903 original size:15 final size:14
Alignment explanation
Indices: 5321872--5321901 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5321862 TCATATAAAA
5321872 TTATTAAAGATGAT
1 TTATTAAAGATGAT
*
5321886 TTATTTAAGATGAT
1 TTATTAAAGATGAT
5321900 TT
1 TT
5321902 TAAATTGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TTATTAAAGATGAT
Found at i:5332871 original size:23 final size:24
Alignment explanation
Indices: 5332827--5332873 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5332817 TTTTTTTGAA
* * *
5332827 TTTCGAATTTAAATCGAGTTAAAT
1 TTTCGAATTCAAATCAACTTAAAT
5332851 TTTCGAATTCAAAT-AACTTAAAT
1 TTTCGAATTCAAATCAACTTAAAT
5332874 AAATCAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (24 bp):
TTTCGAATTCAAATCAACTTAAAT
Found at i:5338671 original size:22 final size:22
Alignment explanation
Indices: 5338640--5338683 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5338630 TACACCAAAA
* *
5338640 TAGGCTTTTAGCGGCGCTTTTT
1 TAGGCCTTTAGCAGCGCTTTTT
5338662 TAGGCCTTTAGCAGCGCTTTTT
1 TAGGCCTTTAGCAGCGCTTTTT
5338684 AGCGCCACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.11, C:0.20, G:0.25, T:0.43
Consensus pattern (22 bp):
TAGGCCTTTAGCAGCGCTTTTT
Found at i:5338833 original size:43 final size:43
Alignment explanation
Indices: 5338777--5339053 Score: 369
Period size: 43 Copynumber: 6.3 Consensus size: 43
5338767 TTACAGAAAT
* ** * * *
5338777 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGC-TTTACCCAT
1 AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTA-TCAC
5338820 AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
5338863 AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
* * *
5338906 AAACG-CTACTAAAGAACATGATCTTTAACAGCGCTTTTATCAC
1 AAACGCCGA-TAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
5338949 AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
*
5338992 AAACGCCGCTAACGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAT
1 AAACGCCG---A---TAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
*
5339041 AAACGCCGCTAAA
1 AAACGCCGATAAA
5339054 AATACGATTT
Statistics
Matches: 211, Mismatches: 14, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
42 2 0.01
43 161 0.76
44 6 0.03
46 1 0.00
49 41 0.19
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGATAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
Found at i:5339025 original size:49 final size:49
Alignment explanation
Indices: 5338958--5339052 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
5338948 CAAACGCCGA
5338958 TAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAACGC
1 TAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAACGC
*
5339007 TAAAGAACATGATCTTTAGCGGCGCTTTTATCATAAACGCCGCTAA
1 TAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
5339053 AAATACGATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (49 bp):
TAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAACGC
Found at i:5343806 original size:148 final size:144
Alignment explanation
Indices: 5343540--5343921 Score: 595
Period size: 148 Copynumber: 2.6 Consensus size: 144
5343530 NNNNNNNNNN
* * *
5343540 AACGATGCCGTTTTGCTATTATAAATTTTTTTTATTTTTTTATAAATTGATTTATTTTTTGCGGC
1 AACGACGCCATTTTGATATTATAAA-TTTTTTT-TTTTTTTATAAATTGATTTATTTTTTGCGGC
*
5343605 GTTTTTATAGAAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATT
64 GTTTTTATAGAAAACGCCGCTATTGCTTACCTTTAACGGCGCTTCTTATAAAGCGCCGCAAAATT
5343670 TTTTCATTTTGAACAA
129 TTTTCATTTTGAACAA
*
5343686 AACGACGCCATTTTGATATTCTAGTAATTTTTATTTTTTTTATATAAATTGATTTATTTTTTGCG
1 AACGACGCCATTTTGATATTATA--AATTTTT-TTTTTTTT-TATAAATTGATTTATTTTTTGCG
5343751 GCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTAACGGCGCTTCTTATAAAGCGCCGCAAAA
62 GCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTAACGGCGCTTCTTATAAAGCGCCGCAAAA
5343816 TTTTTTCATTTTGAACAA
127 TTTTTTCATTTTGAACAA
* * *
5343834 AACGACGCCATTTTGCTATTATAAATTTTTTTATTTTTTTATAAGTTGATTTATTTTTTGCGGTG
1 AACGACGCCATTTTGATATTATAAATTTTTTT-TTTTTTTATAAATTGATTTATTTTTTGCGGCG
* *
5343899 TTTTT-TACAAAAATGCCGCTATT
65 TTTTTATA-GAAAACGCCGCTATT
5343922 TCATTTTGAA
Statistics
Matches: 219, Mismatches: 11, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
144 2 0.01
145 44 0.20
146 32 0.15
147 11 0.05
148 130 0.59
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (144 bp):
AACGACGCCATTTTGATATTATAAATTTTTTTTTTTTTTATAAATTGATTTATTTTTTGCGGCGT
TTTTATAGAAAACGCCGCTATTGCTTACCTTTAACGGCGCTTCTTATAAAGCGCCGCAAAATTTT
TTCATTTTGAACAA
Found at i:5343877 original size:20 final size:20
Alignment explanation
Indices: 5343852--5343892 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5343842 CATTTTGCTA
**
5343852 TTATAAATTTTTTTATTTTT
1 TTATAAATTGATTTATTTTT
*
5343872 TTATAAGTTGATTTATTTTT
1 TTATAAATTGATTTATTTTT
5343892 T
1 T
5343893 GCGGTGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (20 bp):
TTATAAATTGATTTATTTTT
Found at i:5344591 original size:14 final size:14
Alignment explanation
Indices: 5344572--5344620 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
5344562 AACCTTAAAT
5344572 CCCTAAC-TCTTAAC
1 CCCTAACATC-TAAC
5344586 CCCTAACATCTAAC
1 CCCTAACATCTAAC
5344600 CCCTAAACCA-CTAAC
1 CCCT-AA-CATCTAAC
5344615 CCCTAA
1 CCCTAA
5344621 ACCTTAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 17 0.53
15 13 0.41
16 2 0.06
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.20
Consensus pattern (14 bp):
CCCTAACATCTAAC
Found at i:5344615 original size:15 final size:16
Alignment explanation
Indices: 5344582--5344623 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
5344572 CCCTAACTCT
5344582 TAACCCCT-AA-CATC
1 TAACCCCTAAACCATC
5344596 TAACCCCTAAACCA-C
1 TAACCCCTAAACCATC
5344611 TAACCCCTAAACC
1 TAACCCCTAAACC
5344624 TTAAATCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.31
15 16 0.62
16 2 0.08
ACGTcount: A:0.38, C:0.45, G:0.00, T:0.17
Consensus pattern (16 bp):
TAACCCCTAAACCATC
Found at i:5345267 original size:73 final size:72
Alignment explanation
Indices: 5345184--5345363 Score: 288
Period size: 73 Copynumber: 2.5 Consensus size: 72
5345174 AGATAAAATA
*
5345184 TTTTTAGCGGCGCTTTTCAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGG
1 TTTTTTGCGGCGCTTTTC-AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGG
5345249 GCTTAAGT
65 GCTTAAGT
* * *
5345257 TTTTTTGCGGCGCTTTACCAAAAACGCCGCTAAATCCCTGAAAGTTCAGAAAACGGCGTCGTTGG
1 TTTTTTGCGGCGCTTT-TCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGG
*
5345322 GCTTAGGT
65 GCTTAAGT
5345330 TTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAA
1 TTTTTTGCGGCGCTTT-TCAAAAACGCCGCTAAA
5345364 GCCCTAGGCA
Statistics
Matches: 100, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
73 99 0.99
74 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (72 bp):
TTTTTTGCGGCGCTTTTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGG
CTTAAGT
Found at i:5345465 original size:113 final size:112
Alignment explanation
Indices: 5345276--5345588 Score: 443
Period size: 113 Copynumber: 2.8 Consensus size: 112
5345266 GCGCTTTACC
5345276 AAAAACGCCGCTAAATCCCTGAAAGTTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGC
1 AAAAACGCCGCTAAATCCC-GAAAGTT-AGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGC
* *
5345341 GCTTTATCAAAAACGCCGCTAAAGCCCTAG-GCATTAGCGGCGCTTCCTT
64 GCTTTCTCAAAAACGCCGCTAAAACCC-AGAGCATTAGCGGCGCTTCCTT
* *
5345390 AAAAAGGCCGCTAAATCCTCAAAAGATTA-AAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGC
1 AAAAACGCCGCTAAATCC-CGAAAG-TTAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGC
* * * *
5345454 GCTTTCCCAAAAATGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTCTT
64 GCTTTCTCAAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCCTT
* *
5345503 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGCTTAGG-TTTTTTGCGGC
1 AAAAACGCCGCTAAAT-CCCGAAAG-TTAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGC
*
5345567 GCTTTCTCAAAAACGCCACTAA
64 GCTTTCTCAAAAACGCCGCTAA
5345589 TGCTTATTTT
Statistics
Matches: 178, Mismatches: 16, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
112 1 0.01
113 128 0.72
114 46 0.26
115 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (112 bp):
AAAAACGCCGCTAAATCCCGAAAGTTAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGC
TTTCTCAAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCCTT
Found at i:5345890 original size:2 final size:2
Alignment explanation
Indices: 5345883--5345908 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5345873 TTGAAAATGA
5345883 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5345909 TATCAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5353275 original size:19 final size:19
Alignment explanation
Indices: 5353226--5353277 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
5353216 TTCTCATAAA
5353226 AAATATTAAAAA-ATTATG
1 AAATATTAAAAATATTATG
* * * *
5353244 AAAAATCATAAATATTATT
1 AAATATTAAAAATATTATG
5353263 AAATATTAAAAATAT
1 AAATATTAAAAATAT
5353278 ACAATCACAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATATTAAAAATATTATG
Found at i:5363692 original size:27 final size:27
Alignment explanation
Indices: 5363662--5363764 Score: 136
Period size: 27 Copynumber: 3.8 Consensus size: 27
5363652 TCATCTCCTA
5363662 GGGGTATTTC-GATCATTTTACCATATG
1 GGGGTATTTCAG-TCATTTTACCATATG
* *
5363689 GGGGTATTTCAGCCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCATATG
* *
5363716 GGGGTATTTCAGTCATTTAACCTTATG
1 GGGGTATTTCAGTCATTTTACCATATG
**
5363743 GGGGTATTTTGGTCATTTTACC
1 GGGGTATTTCAGTCATTTTACC
5363765 CTATAAGGCT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 66 0.99
28 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCATATG
Found at i:5363732 original size:54 final size:54
Alignment explanation
Indices: 5363662--5363768 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
5363652 TCATCTCCTA
*
5363662 GGGGTATTTCGATCATTTTACCATATGGGGGTATTTCAGCCATTTTACCCTATG
1 GGGGTATTTCGATCATTTAACCATATGGGGGTATTTCAGCCATTTTACCCTATG
* ** *
5363716 GGGGTATTTC-AGTCATTTAACCTTATGGGGGTATTTTGGTCATTTTACCCTAT
1 GGGGTATTTCGA-TCATTTAACCATATGGGGGTATTTCAGCCATTTTACCCTAT
5363769 AAGGCTATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 1 0.02
54 46 0.98
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (54 bp):
GGGGTATTTCGATCATTTAACCATATGGGGGTATTTCAGCCATTTTACCCTATG
Found at i:5363777 original size:27 final size:27
Alignment explanation
Indices: 5363662--5363791 Score: 134
Period size: 27 Copynumber: 4.8 Consensus size: 27
5363652 TCATCTCCTA
* * *
5363662 GGGGTATTTCGATCATTTTACCATATG
1 GGGGTATTTTGGTCATTTTACCCTATG
** *
5363689 GGGGTATTTCAGCCATTTTACCCTATG
1 GGGGTATTTTGGTCATTTTACCCTATG
** * *
5363716 GGGGTATTTCAGTCATTTAACCTTATG
1 GGGGTATTTTGGTCATTTTACCCTATG
*
5363743 GGGGTATTTTGGTCATTTTACCCTATA
1 GGGGTATTTTGGTCATTTTACCCTATG
* * *
5363770 AGGCTATTTTGGTTATTTTACC
1 GGGGTATTTTGGTCATTTTACC
5363792 TATTTTTGGG
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 88 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (27 bp):
GGGGTATTTTGGTCATTTTACCCTATG
Found at i:5374557 original size:37 final size:39
Alignment explanation
Indices: 5374513--5374593 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 39
5374503 TTCGAAATAA
* * *
5374513 TAAATTGACAACC-GGTGTCTTATC-AGTTAAA-TCGAAG
1 TAAATTGAC-ACCTAGTGTCTCATCGACTTAAAGTCGAAG
5374550 TAAATTGACACCTAGTGTCTCATCGACTTAAAGTCGAAG
1 TAAATTGACACCTAGTGTCTCATCGACTTAAAGTCGAAG
5374589 -AAATT
1 TAAATT
5374594 CCTGAACTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
36 3 0.08
37 18 0.47
38 11 0.29
39 6 0.16
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (39 bp):
TAAATTGACACCTAGTGTCTCATCGACTTAAAGTCGAAG
Found at i:5375477 original size:16 final size:17
Alignment explanation
Indices: 5375453--5375496 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
5375443 TTTCTCTTTA
*
5375453 TTTCTTTCTCTTTTTC-
1 TTTCTTTCTCTGTTTCG
*
5375469 TTTCCTTCTCTGTTTCG
1 TTTCTTTCTCTGTTTCG
5375486 TTTCTTTCTCT
1 TTTCTTTCTCT
5375497 CCTTCTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.00, C:0.27, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTCTTTCTCTGTTTCG
Found at i:5375546 original size:5 final size:5
Alignment explanation
Indices: 5375536--5375687 Score: 295
Period size: 5 Copynumber: 30.4 Consensus size: 5
5375526 TTAATTATTT
*
5375536 TAATA TAATA TAATA TAATA TAATA TAATA TAATA CAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
5375586 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
5375636 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
5375686 TA
1 TA
5375688 CTTAACATTT
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 145 1.00
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (5 bp):
TAATA
Found at i:5375725 original size:38 final size:38
Alignment explanation
Indices: 5375669--5375742 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
5375659 TATAATATAA
5375669 TATAATATAATATAATATA-CTTAACATTTAAGTTTTAT
1 TATAATATAATATAATATATCTTAAC-TTTAAGTTTTAT
* * *
5375707 TATAATATTATATTATATATGTTAACTTTAAGTTTT
1 TATAATATAATATAATATATCTTAACTTTAAGTTTT
5375743 CTAATAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 27 0.84
39 5 0.16
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (38 bp):
TATAATATAATATAATATATCTTAACTTTAAGTTTTAT
Found at i:5378443 original size:35 final size:35
Alignment explanation
Indices: 5378403--5378521 Score: 84
Period size: 33 Copynumber: 3.4 Consensus size: 35
5378393 AATAATGATG
5378403 ACAATATAAATAAAATAATACAAGCAAAATAATAA
1 ACAATATAAATAAAATAATACAAGCAAAATAATAA
* * ** * *
5378438 ACAATA-AAA-ACAATCATACGGGCAAAACAACAA
1 ACAATATAAATAAAATAATACAAGCAAAATAATAA
* * *
5378471 ATAATATGAAACTAAAGTAATA-AAACGAACAATAATAA
1 ACAATAT-AAA-TAAAATAATACAAGC-AA-AATAATAA
*
5378509 AC-ATGTAAATAAA
1 ACAATATAAATAAA
5378522 TGTGTGAACA
Statistics
Matches: 61, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
33 23 0.38
34 3 0.05
35 13 0.21
36 4 0.07
37 11 0.18
38 7 0.11
ACGTcount: A:0.64, C:0.12, G:0.07, T:0.18
Consensus pattern (35 bp):
ACAATATAAATAAAATAATACAAGCAAAATAATAA
Found at i:5382058 original size:15 final size:15
Alignment explanation
Indices: 5382034--5382093 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
5382024 ATCAATACCG
5382034 CCCAACTAGCCTAAA
1 CCCAACTAGCCTAAA
* *
5382049 CCCAATTAGCCTAAG
1 CCCAACTAGCCTAAA
* *
5382064 CCCAA-TACCCT-AG
1 CCCAACTAGCCTAAA
5382077 CCCAACTAGCCTAAA
1 CCCAACTAGCCTAAA
5382092 CC
1 CC
5382094 AGAAGTCAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 7 0.18
14 10 0.26
15 21 0.55
ACGTcount: A:0.35, C:0.42, G:0.08, T:0.15
Consensus pattern (15 bp):
CCCAACTAGCCTAAA
Found at i:5382303 original size:16 final size:16
Alignment explanation
Indices: 5382281--5382323 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
5382271 AAACCAATGG
*
5382281 GATTTTTATTTTATTT
1 GATTTTTATTTCATTT
*
5382297 TATTTTTATTTCATTT
1 GATTTTTATTTCATTT
5382313 GATTTTT-TTTC
1 GATTTTTATTTC
5382324 GGGTTCTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (16 bp):
GATTTTTATTTCATTT
Found at i:5385002 original size:16 final size:15
Alignment explanation
Indices: 5384981--5385011 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
5384971 CTAATAAAAG
5384981 TATTTTTAATTAATAT
1 TATTTTT-ATTAATAT
5384997 TATTTTTATTAATAT
1 TATTTTTATTAATAT
5385012 ACTAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTTTATTAATAT
Done.