Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 31
Found at i:5467119 original size:2 final size:2
Alignment explanation
Indices: 5467112--5467137 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5467102 TACTTAACAG
5467112 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
5467138 TAACTTTATA
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:5468665 original size:18 final size:17
Alignment explanation
Indices: 5468642--5468684 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
5468632 ATATATACAT
5468642 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
5468660 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
5468677 ATAA-AATA
1 ATAATAATA
5468685 TCCATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:5470021 original size:105 final size:105
Alignment explanation
Indices: 5469833--5470970 Score: 1827
Period size: 105 Copynumber: 11.0 Consensus size: 105
5469823 GCATTGTTCA
* * ** **
5469833 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
5469893 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
5469933 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
*
5469998 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
5470038 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
5470103 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5470143 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
*
5470208 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
5470248 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGAGAA---GTTATTGATAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
*
5470310 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5470350 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
5470415 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5470455 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA---GTTGTTGACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
*
5470517 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5470557 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
5470622 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5470662 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA---GTTGTTGACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
5470724 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
5470764 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCACTGAAATTGAGAAGTTGTTGTTGACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
*
5470829 CAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
5470869 GAGTCTAATATCCTTCGTTGTGAAATTGAAATTAGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAG
* * *
5470934 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
5470971 CCTCGAGTGC
Statistics
Matches: 971, Mismatches: 52, Indels: 24
0.93 0.05 0.02
Matches are distributed among these distances:
100 36 0.04
101 1 0.00
102 294 0.30
103 2 0.00
104 2 0.00
105 594 0.61
106 42 0.04
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:5470362 original size:207 final size:208
Alignment explanation
Indices: 5469833--5470970 Score: 1874
Period size: 207 Copynumber: 5.5 Consensus size: 208
5469823 GCATTGTTCA
* * ** * *
5469833 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AATTTTGTTGACAAACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
* *
5469895 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTT
* * *
5469960 GAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
5470025 CTTGCATTGTCTG
196 CTTGCGTTGTCTG
** *
5470038 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA--TGTTGTTGACAAG
*
5470103 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAG
*
5470168 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
129 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTG
*
5470233 AACTTGCGTTGTCTC
194 AACTTGCGTTGTCTG
* * * *
5470248 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGAGAA-GTTATTGATAGGCA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
*
5470312 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGAAGTCCAATATCCTTCATTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTT
5470377 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAA
5470442 CTTGCGTTGTCTG
196 CTTGCGTTGTCTG
*
5470455 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-GTTGTTGACAGGCA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
*
5470519 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAAAGTCCAATATCCTTCATTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTT
5470584 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAA
5470649 CTTGCGTTGTCTG
196 CTTGCGTTGTCTG
*
5470662 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-GTTGTTGACAGGCA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
5470726 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTT
* *
5470791 GAAATTGGCACTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGATCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAA
5470856 CTTGCGTTGTCTG
196 CTTGCGTTGTCTG
* * * *
5470869 GAGTCTAATATCCTTCGTTGTGAAATTGAAATTAGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA--TG-TTGTTGACAA
* * *
5470934 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
63 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
5470971 CCTCGAGTGC
Statistics
Matches: 884, Mismatches: 40, Indels: 12
0.94 0.04 0.01
Matches are distributed among these distances:
205 36 0.04
206 1 0.00
207 604 0.68
208 2 0.00
210 198 0.22
211 43 0.05
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (208 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTT
GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGCGTTGTCTG
Found at i:5471748 original size:67 final size:66
Alignment explanation
Indices: 5471613--5471770 Score: 201
Period size: 68 Copynumber: 2.4 Consensus size: 66
5471603 AAGATATCTG
* * **
5471613 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
5471678 TT
65 TT
* * * * *
5471680 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATT-TGTTTTAGGGGAAATAAATTCAAAGG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
5471744 TT
65 TT
*
5471746 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
5471771 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 31 0.39
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:5471786 original size:65 final size:67
Alignment explanation
Indices: 5471614--5471796 Score: 183
Period size: 65 Copynumber: 2.7 Consensus size: 67
5471604 AGATATCTGT
* * * * * ** *
5471614 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAGT
5471679 TTG
65 TTG
* * * *
5471682 TGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
5471746 T-
66 TG
* * * *
5471747 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-GAAAATTTGTTTTAAGGGAAA
5471797 CTGTCTCAAG
Statistics
Matches: 97, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
65 37 0.38
66 7 0.07
67 22 0.23
68 31 0.32
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:5471797 original size:36 final size:35
Alignment explanation
Indices: 5471746--5472026 Score: 272
Period size: 36 Copynumber: 8.0 Consensus size: 35
5471736 TTCAAAGGTT
* *
5471746 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
5471782 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
5471817 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
5471855 TTGTTTCAA-AGAAAACATAT-TCAA-ATATTC----
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
5471885 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
5471919 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
5471956 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
5471991 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
5472027 CTCTTCTAGT
Statistics
Matches: 203, Mismatches: 26, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 16 0.08
30 4 0.02
35 11 0.05
36 135 0.67
37 33 0.16
38 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:5471856 original size:138 final size:137
Alignment explanation
Indices: 5471694--5472007 Score: 414
Period size: 138 Copynumber: 2.3 Consensus size: 137
5471684 TTTCAAGAGT
* * * * * *
5471694 AACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTCTGTTTCAAGGGA
* *
5471759 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
5471823 TCCAAAAGA
129 TCCAAAAGA
** * * * *
5471832 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTCTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTCTGTTTCAAGGGA
* * * * *
5471897 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
5471962 CAAGAGA
131 CAAAAGA
*
5471969 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
5472008 TGTCTCAAGA
Statistics
Matches: 150, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
137 49 0.33
138 101 0.67
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTCTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:5471970 original size:102 final size:102
Alignment explanation
Indices: 5471783--5471970 Score: 288
Period size: 102 Copynumber: 1.8 Consensus size: 102
5471773 AGACGAAAAT
*
5471783 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAG
*
5471848 ACGGAATTTGTTTCAAAGAAAACATATTCAAATATTC
66 ACGAAATTTGTTTCAAAGAAAACATATTCAAATATTC
* * * ** *
5471885 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGGGAAACTGTCTCAAGATAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAG
5471949 ACGAAATTTGTTTCAAGAGAAA
66 ACGAAATTTGTTTCAA-AGAAA
5471971 CTGTCTCAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 36 0.47
102 41 0.53
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAG
ACGAAATTTGTTTCAAAGAAAACATATTCAAATATTC
Found at i:5472048 original size:35 final size:36
Alignment explanation
Indices: 5471883--5472060 Score: 173
Period size: 36 Copynumber: 5.0 Consensus size: 36
5471873 ATTCAAATAT
* *
5471883 TCTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TCTGCTTCAAGGAAAACTGTCTCAAGAGAGACAAAA
* ** * * *
5471919 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TCTGCTTCAAGGAAAACTGTCTCAAGAGAGACAAAA
* *
5471955 TTTGTTTCAA-GAGAAACTGTCTCAAGAGAGACAAAA
1 TCTGCTTCAAGGA-AAACTGTCTCAAGAGAGACAAAA
* * *
5471991 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TCTGCTTCAAGGAAAACTGTCTCAAGAGAGACAAAA
* * *
5472027 -CT-CTTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TCTGCTTCAAG-GAAAACTGTCTCAAGAGAGACAAA
5472061 TCTTGTTTTA
Statistics
Matches: 124, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
34 5 0.04
35 23 0.19
36 95 0.77
37 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (36 bp):
TCTGCTTCAAGGAAAACTGTCTCAAGAGAGACAAAA
Found at i:5472956 original size:22 final size:22
Alignment explanation
Indices: 5472930--5473027 Score: 169
Period size: 22 Copynumber: 4.5 Consensus size: 22
5472920 TATGTTTGGC
5472930 CAAAGGTTTGGCATTTGATGCT
1 CAAAGGTTTGGCATTTGATGCT
*
5472952 CAAAGGTTTAGCATTTGATGCT
1 CAAAGGTTTGGCATTTGATGCT
5472974 CAAAGGTTTGGCATTTGATGCT
1 CAAAGGTTTGGCATTTGATGCT
*
5472996 CATAGGTTTGGCATTTGATGCT
1 CAAAGGTTTGGCATTTGATGCT
*
5473018 CAACGGTTTG
1 CAAAGGTTTG
5473028 ATGGGGTAGC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 71 1.00
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (22 bp):
CAAAGGTTTGGCATTTGATGCT
Found at i:5473639 original size:9 final size:9
Alignment explanation
Indices: 5473627--5473684 Score: 89
Period size: 9 Copynumber: 6.2 Consensus size: 9
5473617 TTTTTGTCCC
5473627 TTTTTCTTT
1 TTTTTCTTT
5473636 TTTTTCTTT
1 TTTTTCTTT
*
5473645 TTGTTCTTT
1 TTTTTCTTT
5473654 TTTTTGCTTTT
1 TTTTT-C-TTT
5473665 TTTTTCTTT
1 TTTTTCTTT
5473674 TTTTTCTTT
1 TTTTTCTTT
5473683 TT
1 TT
5473685 GCCCTTTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
9 35 0.78
10 2 0.04
11 8 0.18
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:5473639 original size:18 final size:18
Alignment explanation
Indices: 5473616--5473658 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5473606 TTTGCATGTG
*
5473616 TTTTTTGTCCCTTT-TTC
1 TTTTTTTTCCCTTTGTTC
**
5473633 TTTTTTTTCTTTTTGTTC
1 TTTTTTTTCCCTTTGTTC
5473651 TTTTTTTT
1 TTTTTTTT
5473659 GCTTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (18 bp):
TTTTTTTTCCCTTTGTTC
Found at i:5473693 original size:29 final size:29
Alignment explanation
Indices: 5473633--5473693 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
5473623 TCCCTTTTTC
***
5473633 TTTTTTTTCTTTTTGTTCTTTTTTTTGCT
1 TTTTTTTTCTTTTTGTTCTTTTTTGCCCT
*
5473662 TTTTTTTTCTTTTTTTTC-TTTTTGCCCT
1 TTTTTTTTCTTTTTGTTCTTTTTTGCCCT
5473690 TTTT
1 TTTT
5473694 ATTCTGATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (29 bp):
TTTTTTTTCTTTTTGTTCTTTTTTGCCCT
Found at i:5474886 original size:8 final size:8
Alignment explanation
Indices: 5474870--5474908 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
5474860 ATTGTAGATG
5474870 AAAATGCA
1 AAAATGCA
*
5474878 AAAAGGCA
1 AAAATGCA
5474886 AAAATGC-
1 AAAATGCA
5474893 AAAATGCA
1 AAAATGCA
*
5474901 AGAATGCA
1 AAAATGCA
5474909 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:5474896 original size:15 final size:15
Alignment explanation
Indices: 5474870--5474908 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5474860 ATTGTAGATG
5474870 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
5474886 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
5474901 AGAATGCA
1 AAAATGCA
5474909 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:5478049 original size:18 final size:17
Alignment explanation
Indices: 5478026--5478068 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
5478016 ATATATACAT
5478026 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
5478044 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
5478061 ATAA-AATA
1 ATAATAATA
5478069 TCCATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:5484292 original size:25 final size:25
Alignment explanation
Indices: 5484262--5484312 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
5484252 ATAAGATAAT
5484262 ATTTCATAAAACTAGCCTTTATGTG
1 ATTTCATAAAACTAGCCTTTATGTG
*
5484287 ATTTCATAAAATTAGCCTTTATGTG
1 ATTTCATAAAACTAGCCTTTATGTG
5484312 A
1 A
5484313 CACTTGGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (25 bp):
ATTTCATAAAACTAGCCTTTATGTG
Found at i:5486411 original size:14 final size:14
Alignment explanation
Indices: 5486392--5486419 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5486382 TAAACTCTAA
5486392 TATTATATTATTTT
1 TATTATATTATTTT
5486406 TATTATATTATTTT
1 TATTATATTATTTT
5486420 GATGGATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATATTATTTT
Found at i:5487319 original size:143 final size:137
Alignment explanation
Indices: 5487043--5487326 Score: 397
Period size: 143 Copynumber: 2.0 Consensus size: 137
5487033 CCACACCATG
* * *
5487043 ATGCCTTCCTCAGCTTTGCATGTCAGCACCCTTATGTGTTCATACCTATTCCACTAGCATGCTCA
1 ATGCCTACCTCAGCTTCGCATGTCAGCACCCTTATGTGTTCATACCTATTCCACTAGCATACTCA
* *
5487108 GAATACATGTAATACAATACAATTATTAATGTGGCATTGAGCTCGTAAGCTCAACCTCTGAAATG
66 GAATACATGTAATACAATACAATTATTAATGTGGCACTGAGCTCATAAGCTCAACCTCTGAAATG
5487173 TTTTTCC
131 TTTTTCC
* *
5487180 ATGCCTACCTCAGCTTCGCATGTCATCATCCTTATGTGTTCATACCTATTCCACTAGCATACTCA
1 ATGCCTACCTCAGCTTCGCATGTCAGCACCCTTATGTGTTCATACCTATTCCACTAGCATACTC-
* * * * * *
5487245 TATAGTGAATGCATGTAGTATAATACAATTATTAGTGTGGTACTGAGCTCATAAGCTCAACCTTT
65 ---A--GAATACATGTAATACAATACAATTATTAATGTGGCACTGAGCTCATAAGCTCAACCTCT
5487310 GAAATGTTTTTCC
125 GAAATGTTTTTCC
5487323 ATGC
1 ATGC
5487327 GCAGGTTCAT
Statistics
Matches: 128, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
137 59 0.46
141 1 0.01
143 68 0.53
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (137 bp):
ATGCCTACCTCAGCTTCGCATGTCAGCACCCTTATGTGTTCATACCTATTCCACTAGCATACTCA
GAATACATGTAATACAATACAATTATTAATGTGGCACTGAGCTCATAAGCTCAACCTCTGAAATG
TTTTTCC
Found at i:5496064 original size:32 final size:32
Alignment explanation
Indices: 5496023--5496087 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
5496013 AAGAAAGAAC
5496023 TTATCTTGGCACCTATAGTACAATCACCCAAT
1 TTATCTTGGCACCTATAGTACAATCACCCAAT
5496055 TTATCTTGGCACCTATAGTACAATCACCCAAT
1 TTATCTTGGCACCTATAGTACAATCACCCAAT
5496087 T
1 T
5496088 GGGATTGTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (32 bp):
TTATCTTGGCACCTATAGTACAATCACCCAAT
Found at i:5502368 original size:21 final size:21
Alignment explanation
Indices: 5502342--5502383 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5502332 TAAATTATAG
5502342 TTTTTAAATGAGTATTTAAAA
1 TTTTTAAATGAGTATTTAAAA
5502363 TTTTTAAATGAGTATTTAAAA
1 TTTTTAAATGAGTATTTAAAA
5502384 AGAAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (21 bp):
TTTTTAAATGAGTATTTAAAA
Found at i:5509381 original size:20 final size:20
Alignment explanation
Indices: 5509356--5509409 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
5509346 GATACTCATG
*
5509356 GGAGTATCGATA-TGTAGTGT
1 GGAGTATCGATATTG-ACTGT
5509376 GGAGTATCGATATTGACTGT
1 GGAGTATCGATATTGACTGT
5509396 GGAGTATCGATATT
1 GGAGTATCGATATT
5509410 CTAAGTAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.26, C:0.07, G:0.31, T:0.35
Consensus pattern (20 bp):
GGAGTATCGATATTGACTGT
Found at i:5517010 original size:45 final size:45
Alignment explanation
Indices: 5516751--5517000 Score: 322
Period size: 45 Copynumber: 5.6 Consensus size: 45
5516741 CTTTTCATTC
* * * * *
5516751 ATGCAACGTTATGAATTTCATTGATGGCATCCTTTAATGCCGGTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCGTTA
* * *
5516796 ATGCACCATTATGCATTTCATTTATGGAATCCTTTCACGCCGTTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCGTTA
*
5516841 ATGCACCGTTATGCATTTCATTTATGGCATCCTTCCATGCCGTTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCGTTA
* * * * **
5516886 ATGCACAGTTTTGCATTTCATTTATGTCATACTTTCATGTTGTTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCGTTA
* *
5516931 ATGCACCGTTATGCATTTCATTGATGGCATCCTTTCATG-CATGTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCGT-TA
*
5516976 ATGCACTGTTATGCATTTCATTTAT
1 ATGCACCGTTATGCATTTCATTTAT
5517001 TTATTCCTTT
Statistics
Matches: 176, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
44 1 0.01
45 175 0.99
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (45 bp):
ATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCGTTA
Found at i:5519074 original size:45 final size:45
Alignment explanation
Indices: 5519010--5519252 Score: 360
Period size: 45 Copynumber: 5.4 Consensus size: 45
5519000 CCTTTCATTG
* * * * *
5519010 ATGCACTGTTATGCATTTCATTGATGGCATCCTTTCATGCCGGTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGTCGTTA
*
5519055 ATGCACTGTTATGCATTTCATTTATGGCATCATTTCATGTCGTTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGTCGTTA
* *
5519100 AAGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGTCGTTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGTCGTTA
* *
5519145 ATGCACCGTTATTCATTTCATTGATGGCATCATTTCATGTCGTTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGTCGTTA
* * * *
5519190 ATGCACCATTATACATTTCATTTATGACATCATTTCATGCCGTTA
1 ATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGTCGTTA
5519235 ATGCACCGTTATGCATTT
1 ATGCACCGTTATGCATTT
5519253 GGTAATGTAC
Statistics
Matches: 180, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 180 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (45 bp):
ATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGTCGTTA
Found at i:5519258 original size:22 final size:22
Alignment explanation
Indices: 5519233--5519274 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5519223 TTCATGCCGT
*
5519233 TAATGCACCGTTATGCATTTGG
1 TAATGCACCATTATGCATTTGG
* *
5519255 TAATGTACTATTATGCATTT
1 TAATGCACCATTATGCATTT
5519275 CATTATTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (22 bp):
TAATGCACCATTATGCATTTGG
Found at i:5521377 original size:45 final size:45
Alignment explanation
Indices: 5521298--5521456 Score: 212
Period size: 45 Copynumber: 3.5 Consensus size: 45
5521288 ATCCTTTAAT
*
5521298 TAATGCACCGTTATGCATTTCATTGATGGTATCCTTTCATGTC-GG
1 TAATGCACCGTTATGCATTTCATTGATGGCATCCTTTCAT-TCTGG
* * * * *
5521343 TAATACAACGTTATGCATTTCATTTATGGCATCCTTTCAATCTGT
1 TAATGCACCGTTATGCATTTCATTGATGGCATCCTTTCATTCTGG
* * *
5521388 TAATGCACCGTTATGCATTTTATTGATCGCATCCTTTCATACTGG
1 TAATGCACCGTTATGCATTTCATTGATGGCATCCTTTCATTCTGG
*
5521433 TAATGCACCATTATGCATTTCATT
1 TAATGCACCGTTATGCATTTCATT
5521457 TATTCATTCA
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
44 2 0.02
45 95 0.98
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (45 bp):
TAATGCACCGTTATGCATTTCATTGATGGCATCCTTTCATTCTGG
Found at i:5521423 original size:90 final size:85
Alignment explanation
Indices: 5521275--5521459 Score: 237
Period size: 90 Copynumber: 2.1 Consensus size: 85
5521265 TATCCTTTAT
* * *
5521275 TTTCATTTATAGCATCCTTTAATTAATGCACCGTTATGCATTTCATTGATGGTATCCTTTCAT-G
1 TTTCATTTATAGCATCCTTTAATTAATGCACCGTTATGCATTTCATTGATCGCATCCTTTCATAC
*
5521339 TCGGTAATACAACGTTATGCA
66 T-GGTAATACAACATTATGCA
* *
5521360 TTTCATTTATGGCATCCTTTCAATCTGTTAATGCACCGTTATGCATTTTATTGATCGCATCCTTT
1 TTTCATTTATAGCATCCTTT-AA----TTAATGCACCGTTATGCATTTCATTGATCGCATCCTTT
* *
5521425 CATACTGGTAATGCACCATTATGCA
61 CATACTGGTAATACAACATTATGCA
5521450 TTTCATTTAT
1 TTTCATTTAT
5521460 TCATTCATTT
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
85 19 0.22
86 2 0.02
90 64 0.74
91 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (85 bp):
TTTCATTTATAGCATCCTTTAATTAATGCACCGTTATGCATTTCATTGATCGCATCCTTTCATAC
TGGTAATACAACATTATGCA
Found at i:5521556 original size:21 final size:21
Alignment explanation
Indices: 5521519--5521580 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
5521509 TTTCATACAC
5521519 ATAATG-AAAAC--ATATTAA
1 ATAATGTAAAACATATATTAA
5521537 ATAATGTAAAACATATATTAA
1 ATAATGTAAAACATATATTAA
* *
5521558 ATATTGTAAAACATACATTAA
1 ATAATGTAAAACATATATTAA
5521579 AT
1 AT
5521581 TAAAACATTC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
18 6 0.15
19 5 0.13
21 28 0.72
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.32
Consensus pattern (21 bp):
ATAATGTAAAACATATATTAA
Found at i:5521877 original size:120 final size:120
Alignment explanation
Indices: 5521664--5521905 Score: 484
Period size: 120 Copynumber: 2.0 Consensus size: 120
5521654 ATCCTGGCTA
5521664 ATAAAGTGTAATGATATCTGGCTATTCAGCAACTTTATATTTGCCCTTTTTGTTGCTAGACTCAA
1 ATAAAGTGTAATGATATCTGGCTATTCAGCAACTTTATATTTGCCCTTTTTGTTGCTAGACTCAA
5521729 GATGTTGGTTATGATCTACACAAACATATATTTAAACACACATATCATACCAAAT
66 GATGTTGGTTATGATCTACACAAACATATATTTAAACACACATATCATACCAAAT
5521784 ATAAAGTGTAATGATATCTGGCTATTCAGCAACTTTATATTTGCCCTTTTTGTTGCTAGACTCAA
1 ATAAAGTGTAATGATATCTGGCTATTCAGCAACTTTATATTTGCCCTTTTTGTTGCTAGACTCAA
5521849 GATGTTGGTTATGATCTACACAAACATATATTTAAACACACATATCATACCAAAT
66 GATGTTGGTTATGATCTACACAAACATATATTTAAACACACATATCATACCAAAT
5521904 AT
1 AT
5521906 TAGTATATTC
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 122 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (120 bp):
ATAAAGTGTAATGATATCTGGCTATTCAGCAACTTTATATTTGCCCTTTTTGTTGCTAGACTCAA
GATGTTGGTTATGATCTACACAAACATATATTTAAACACACATATCATACCAAAT
Found at i:5523648 original size:15 final size:14
Alignment explanation
Indices: 5523610--5523650 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
5523600 GAAACAAATG
5523610 ATGATATAAGA-AT
1 ATGATATAAGATAT
5523623 AT--TATAAGATAT
1 ATGATATAAGATAT
5523635 ATGATATGAAGATAT
1 ATGATAT-AAGATAT
5523650 A
1 A
5523651 ATAGTGAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 7 0.29
12 4 0.17
13 2 0.08
14 3 0.12
15 8 0.33
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (14 bp):
ATGATATAAGATAT
Found at i:5523964 original size:31 final size:31
Alignment explanation
Indices: 5523928--5524077 Score: 221
Period size: 31 Copynumber: 4.8 Consensus size: 31
5523918 TGTGACAGAA
5523928 CTATGTTCTTCGGGACATATGGACTGTTTAC
1 CTATGTTCTTCGGGACATATGGACTGTTTAC
* *
5523959 CTATGTTCTTCAGCACATATGGACTGTTTAC
1 CTATGTTCTTCGGGACATATGGACTGTTTAC
* *
5523990 CTATGTTCTTCGGGACATATGAATTGTTTAC
1 CTATGTTCTTCGGGACATATGGACTGTTTAC
*
5524021 CTATGTTCTTCGGGACATATGGACTGATTAC
1 CTATGTTCTTCGGGACATATGGACTGTTTAC
* *
5524052 CTAGGTTCTTCGGAATC-TATGGACTG
1 CTATGTTCTTCGGGA-CATATGGACTG
5524078 GTCCTTCGGG
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
31 106 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
CTATGTTCTTCGGGACATATGGACTGTTTAC
Found at i:5528733 original size:29 final size:31
Alignment explanation
Indices: 5528681--5528745 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
5528671 TAGCTATTCT
* *
5528681 TTATACTATTAGACTTTTAATTTT-TTT-AA
1 TTATAATATTAGAATTTTAATTTTATTTCAA
5528710 TTATAATATTA-AATTTTAATTTTTATTTCAA
1 TTATAATATTAGAATTTTAA-TTTTATTTCAA
5528741 TTATA
1 TTATA
5528746 TCCTTGAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 7 0.23
29 14 0.45
30 3 0.10
31 7 0.23
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (31 bp):
TTATAATATTAGAATTTTAATTTTATTTCAA
Found at i:5529183 original size:22 final size:22
Alignment explanation
Indices: 5529158--5529204 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5529148 ATAATATATT
*
5529158 TTTATATATAAAATTTTATAAA
1 TTTATATATAAAATTTCATAAA
* * *
5529180 TTTATTTTTATAATTTCATAAA
1 TTTATATATAAAATTTCATAAA
5529202 TTT
1 TTT
5529205 GTTCTTAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATATATAAAATTTCATAAA
Found at i:5534153 original size:18 final size:17
Alignment explanation
Indices: 5534103--5534156 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
5534093 AATTTAGTAA
5534103 AAATAAATAAATTTAAAGT
1 AAATAAA-AAATTTAAA-T
* *
5534122 GAAGAAAAAA-TTAAAT
1 AAATAAAAAATTTAAAT
5534138 AAATAAAAAACTTTAAAT
1 AAATAAAAAA-TTTAAAT
5534156 A
1 A
5534157 CTAAATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 9 0.31
17 5 0.17
18 10 0.34
19 5 0.17
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.26
Consensus pattern (17 bp):
AAATAAAAAATTTAAAT
Found at i:5538857 original size:2 final size:2
Alignment explanation
Indices: 5538844--5538894 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
5538834 ATTATGGACC
*
5538844 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5538885 AT AT AT AT AT
1 AT AT AT AT AT
5538895 GTGTGTGTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5541260 original size:6 final size:6
Alignment explanation
Indices: 5541249--5541317 Score: 63
Period size: 6 Copynumber: 12.0 Consensus size: 6
5541239 AGTTGAAGAG
* ** * * *
5541249 GGAGAA GGAGAA GAAGAA TAAGAA -G-G-A GGAGAA GAATAA GAAGAA
1 GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA
5541294 GGAGAA GGAGAA GGAGAA GGAGAA
1 GGAGAA GGAGAA GGAGAA GGAGAA
5541318 TAATAATAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 1 0.02
6 49 0.92
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (6 bp):
GGAGAA
Found at i:5541264 original size:18 final size:18
Alignment explanation
Indices: 5541260--5541317 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
5541250 GAGAAGGAGA
* *
5541260 AGAAGAATAAGAAGGAGG
1 AGAAGAAGAAGAAGAAGG
*
5541278 AGAAGAATAAGAAGAAGG
1 AGAAGAAGAAGAAGAAGG
* *
5541296 AGAAGGAGAAGGAGAAGG
1 AGAAGAAGAAGAAGAAGG
5541314 AGAA
1 AGAA
5541318 TAATAATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (18 bp):
AGAAGAAGAAGAAGAAGG
Found at i:5542218 original size:33 final size:33
Alignment explanation
Indices: 5542169--5542235 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
5542159 GTCCAAACTT
*
5542169 TACCCAACCTGGAGTATATCTCCCGAACAATAC
1 TACCCAACCTGAAGTATATCTCCCGAACAATAC
*
5542202 TACCCAGCCTGAAGTATATCTCCCGAACAATAC
1 TACCCAACCTGAAGTATATCTCCCGAACAATAC
5542235 T
1 T
5542236 TGCCATCAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.33, G:0.12, T:0.22
Consensus pattern (33 bp):
TACCCAACCTGAAGTATATCTCCCGAACAATAC
Found at i:5547001 original size:5 final size:5
Alignment explanation
Indices: 5546991--5547017 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5546981 AACCACTAAC
5546991 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
5547018 TATATATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:5547125 original size:111 final size:111
Alignment explanation
Indices: 5546921--5547342 Score: 452
Period size: 111 Copynumber: 3.6 Consensus size: 111
5546911 CTCTTATTAC
*
5546921 TCGACCTTGTGGTGACCCGATCTGGGGTAAGATCCACATTATTATGGTTCGAACTTTGCTAACCA
1 TCGACCTTGTGGTGACCCGATCCGGGGTAAGATCCACATTATTATGGTTCGAAC--T-CT----A
* *
5546986 CTAACTTATTTTATTTTATTTTATTTTATTTTTATATATTTGTTTACATTATTCGAT
59 CTAAC-CA--TTAATTT-TTTTATTTTATTTTTATATATTTGTTTACATTATTCGAT
* * *
5547043 TCGACCTTATGGTGACCCGATCCGAGGTAAGACCCACATTATTATGGTTCGAACTCTACTAACCA
1 TCGACCTTGTGGTGACCCGATCCGGGGTAAGATCCACATTATTATGGTTCGAACTCTACTAACCA
*
5547108 TTAACTTTTTTATTTTATTTTTATATATTTGTTTACATTATTCGAT
66 TTAATTTTTTTATTTTATTTTTATATATTTGTTTACATTATTCGAT
* *
5547154 TCGACCTTGTGGTGACCCGAAT-CGGGGTAAGATCCACATTATTATGGTTCGAAATCTGCTAACC
1 TCGACCTTGTGGTGACCCG-ATCCGGGGTAAGATCCACATTATTATGGTTCGAACTCTACTAACC
* *
5547218 ACTAATTTTTTTATTTTATTTGTTTTATTTTAGTTTTATGTATTTGTTTGCATTATTCGAT
65 ATTAATTTTTTTATTTTA-------T-TTTTA----TA--TATTTGTTTACATTATTCGAT
* * * *
5547279 TCGACCTAT-TGGTGACTCGATCCGGGGTAAGATCCACACTATTATGGTTCGGACCCTACTAACC
1 TCGACCT-TGTGGTGACCCGATCCGGGGTAAGATCCACATTATTATGGTTCGAACTCTACTAACC
5547343 CCCTAACTTT
Statistics
Matches: 262, Mismatches: 21, Indels: 31
0.83 0.07 0.10
Matches are distributed among these distances:
111 111 0.42
112 7 0.03
114 1 0.00
115 6 0.02
118 1 0.00
119 7 0.03
120 1 0.00
122 50 0.19
123 2 0.01
124 2 0.01
125 73 0.28
126 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (111 bp):
TCGACCTTGTGGTGACCCGATCCGGGGTAAGATCCACATTATTATGGTTCGAACTCTACTAACCA
TTAATTTTTTTATTTTATTTTTATATATTTGTTTACATTATTCGAT
Found at i:5547341 original size:125 final size:125
Alignment explanation
Indices: 5547115--5547342 Score: 343
Period size: 125 Copynumber: 1.8 Consensus size: 125
5547105 CCATTAACTT
*
5547115 TTTTATTTTATTTTTATATATTTGTTTACATTATTCGATTCGACCTTGTGGTGACCCGAATCGGG
1 TTTTATTTTAGTTTTATATATTTGTTTACATTATTCGATTCGACCTTGTGGTGACCCGAATCGGG
* * *
5547180 GTAAGATCCACATTATTATGGTTCGAAATCTGCTAACCACTAATTTTTTTATTTTATTTG
66 GTAAGATCCACACTATTATGGTTCGAAACCTACTAACCACTAATTTTTTTATTTTATTTG
* * *
5547240 TTTTATTTTAGTTTTATGTATTTGTTTGCATTATTCGATTCGACCTAT-TGGTGACTCG-ATCCG
1 TTTTATTTTAGTTTTATATATTTGTTTACATTATTCGATTCGACCT-TGTGGTGACCCGAAT-CG
* *
5547303 GGGTAAGATCCACACTATTATGGTTCGGACCCTACTAACC
64 GGGTAAGATCCACACTATTATGGTTCGAAACCTACTAACC
5547343 CCCTAACTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
124 2 0.02
125 89 0.97
126 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (125 bp):
TTTTATTTTAGTTTTATATATTTGTTTACATTATTCGATTCGACCTTGTGGTGACCCGAATCGGG
GTAAGATCCACACTATTATGGTTCGAAACCTACTAACCACTAATTTTTTTATTTTATTTG
Found at i:5547380 original size:125 final size:125
Alignment explanation
Indices: 5547115--5547387 Score: 302
Period size: 125 Copynumber: 2.2 Consensus size: 125
5547105 CCATTAACTT
* *
5547115 TTTTATTTTATTTTTATATATTTGTTTACATTATTCGATTCGACCTTGTGGTGACCCGAATCGGG
1 TTTTAGTTTAGTTTTATATATTTGTTTACATTATTCGATTCGACCTTGTGGTGACCCGAATCGGG
* * * * ** *** *
5547180 GTAAGATCCACATTATTATGGTTCGAAATCTGCTAACCACTAATTTTTTTATTTTATTTG
66 GTAAGATCCACACTATTATGGTTCGAAACCTACTAACCACTAACTTTTAAATGCAATTTA
* * * *
5547240 TTTTATTTTAGTTTTATGTATTTGTTTGCATTATTCGATTCGACCTAT-TGGTGACTCG-ATCCG
1 TTTTAGTTTAGTTTTATATATTTGTTTACATTATTCGATTCGACCT-TGTGGTGACCCGAAT-CG
* * *
5547303 GGGTAAGATCCACACTATTATGGTTCGGACCCTACTAACCCCCTAACTTTTAAATGCAATTTA
64 GGGTAAGATCCACACTATTATGGTTCGAAACCTACTAA-CCACTAACTTTTAAATGCAATTTA
*
5547366 TTTCT-GTTTA-TTTTATTTATTT
1 TTT-TAGTTTAGTTTTATATATTT
5547388 TCTAGCACTT
Statistics
Matches: 125, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
124 2 0.02
125 98 0.78
126 24 0.19
127 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (125 bp):
TTTTAGTTTAGTTTTATATATTTGTTTACATTATTCGATTCGACCTTGTGGTGACCCGAATCGGG
GTAAGATCCACACTATTATGGTTCGAAACCTACTAACCACTAACTTTTAAATGCAATTTA
Found at i:5547756 original size:16 final size:17
Alignment explanation
Indices: 5547731--5547770 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5547721 TTTATTTCAA
*
5547731 GTTTTT-TTA-TGTATT
1 GTTTTTATTATTGTACT
5547746 GTTTTTATTATTGTACT
1 GTTTTTATTATTGTACT
5547763 -TTTTTATT
1 GTTTTTATT
5547771 TTATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 6 0.27
16 11 0.50
17 5 0.23
ACGTcount: A:0.15, C:0.03, G:0.10, T:0.72
Consensus pattern (17 bp):
GTTTTTATTATTGTACT
Found at i:5553026 original size:16 final size:16
Alignment explanation
Indices: 5553005--5553037 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5552995 TTGTAGCTTT
5553005 TTCAGAGTTCATTCAA
1 TTCAGAGTTCATTCAA
5553021 TTCAGAGTTCATTCAA
1 TTCAGAGTTCATTCAA
5553037 T
1 T
5553038 GTAGAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (16 bp):
TTCAGAGTTCATTCAA
Found at i:5553047 original size:16 final size:16
Alignment explanation
Indices: 5553005--5553052 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
5552995 TTGTAGCTTT
*
5553005 TTCAGAGTTCATTCAA
1 TTCAGAATTCATTCAA
*
5553021 TTCAGAGTTCATTCAA
1 TTCAGAATTCATTCAA
*
5553037 TGT-AGAATTCAATCAA
1 T-TCAGAATTCATTCAA
5553053 GTTTTCAGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 28 0.97
17 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (16 bp):
TTCAGAATTCATTCAA
Found at i:5553296 original size:46 final size:47
Alignment explanation
Indices: 5553223--5553328 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 47
5553213 TTTTCGGTGT
*** * *
5553223 TCAATCAATGCACCATTTCAGTTACTTTTCAAAGGTCATTTATTGCA-
1 TCAAT-AATGCACCATTTCAACAACTTTTCAAAGGTAATTTACTGCAG
* *
5553270 TCAATAATGCACCATTTCAACAACTTTTCAGATGTAATTTACTGCAG
1 TCAATAATGCACCATTTCAACAACTTTTCAAAGGTAATTTACTGCAG
5553317 T-AATAATGCACC
1 TCAATAATGCACC
5553329 GATTGGCTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
46 45 0.88
47 6 0.12
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (47 bp):
TCAATAATGCACCATTTCAACAACTTTTCAAAGGTAATTTACTGCAG
Found at i:5557174 original size:60 final size:60
Alignment explanation
Indices: 5557077--5557208 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
5557067 ATCATATGTA
* * ** * *
5557077 CCCAAACTAT-AACTCTTATTTTAAATTAGTCCTTAAACTTTTGAATATTTCAA-TCTCAT
1 CCCAAACTATGAACTCTCATTCTAAATTAAACCCTAAACTTTTGAACATTTCAATTC-CAT
*
5557136 CACCAAACTATGAA-TCTCATTCTAAATTAAACCCTAAACTTTTGAACATTTTAATTCCAT
1 C-CCAAACTATGAACTCTCATTCTAAATTAAACCCTAAACTTTTGAACATTTCAATTCCAT
5557196 CCCTAAACTATGA
1 CCC-AAACTATGA
5557209 CTTTCTAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 3 0.05
60 55 0.89
61 4 0.06
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (60 bp):
CCCAAACTATGAACTCTCATTCTAAATTAAACCCTAAACTTTTGAACATTTCAATTCCAT
Found at i:5557493 original size:60 final size:60
Alignment explanation
Indices: 5557381--5557518 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
5557371 GTATATACGT
* * *
5557381 ATAGTTTGAGATGAAATTAGAATGTTCAAAAAAGTTTAGGGATCAATTTAGAATGA-AGGTC
1 ATAGTTTGGGATGAAATTAGAATGTT-AAAAAAGTTTAAGAATCAATTTAGAATGATA-GTC
* * * *
5557442 ATAGTTTGGGGATGAAATTTGAATGTT-TAGAAGTTTAAGAATTAATTTAGAATGATAGTC
1 ATAGTTT-GGGATGAAATTAGAATGTTAAAAAAGTTTAAGAATCAATTTAGAATGATAGTC
*
5557502 ATAGTTAGGGATGAAAT
1 ATAGTTTGGGATGAAAT
5557519 CGAAATATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
59 10 0.15
60 32 0.48
61 8 0.12
62 17 0.25
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTAGAATGTTAAAAAAGTTTAAGAATCAATTTAGAATGATAGTC
Found at i:5557549 original size:59 final size:60
Alignment explanation
Indices: 5557410--5557555 Score: 172
Period size: 59 Copynumber: 2.5 Consensus size: 60
5557400 GAATGTTCAA
* * * *
5557410 AAAAGTTTAGGGATCAATTTAGAATGAAGGTCATAGTTTGGGGATGAAATTTGAATGTTT
1 AAAAGTTTAAGGATCAATTTAGAATGAAGGTCATAGTTTAGGGATGAAATTCGAATATTT
* * *
5557470 AGAAGTTTAAGAATTAATTTAGAATGATA-GTCATAG-TTAGGGATGAAA-TCGAAATATTT
1 AAAAGTTTAAGGATCAATTTAGAATGA-AGGTCATAGTTTAGGGATGAAATTCG-AATATTT
* *
5557529 AAAAGTTTAAGGATCGATTTAAAATGA
1 AAAAGTTTAAGGATCAATTTAGAATGA
5557556 GAGTAATGGT
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
58 2 0.03
59 39 0.54
60 30 0.42
61 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (60 bp):
AAAAGTTTAAGGATCAATTTAGAATGAAGGTCATAGTTTAGGGATGAAATTCGAATATTT
Found at i:5559975 original size:54 final size:54
Alignment explanation
Indices: 5559917--5560031 Score: 133
Period size: 54 Copynumber: 2.1 Consensus size: 54
5559907 AAGTGCTATT
* *
5559917 CTTTTTTAGAGATGTATATACTTACATCAGT-ATAAGTACATGTTAAGTGTAACA
1 CTTTTTTAGAGATGTACATACTTACA-CAGTCATAAGTACATGTTAAATGTAACA
* * * * ** *
5559971 CTTTTTGAGATATGTACATACTTACACCGTCGTAAGTATGTGTTAAATGTTACA
1 CTTTTTTAGAGATGTACATACTTACACAGTCATAAGTACATGTTAAATGTAACA
5560025 CTTTTTT
1 CTTTTTT
5560032 TATTTTATTC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
53 3 0.06
54 47 0.94
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (54 bp):
CTTTTTTAGAGATGTACATACTTACACAGTCATAAGTACATGTTAAATGTAACA
Found at i:5561097 original size:2 final size:2
Alignment explanation
Indices: 5561090--5561118 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5561080 TTTTAATTAT
5561090 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5561119 TGTATCGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5561331 original size:2 final size:2
Alignment explanation
Indices: 5561324--5561359 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5561314 AAATTACCAT
5561324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5561360 AAGTTAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5562253 original size:21 final size:21
Alignment explanation
Indices: 5562219--5562263 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5562209 CTAAACCCGT
*
5562219 AATAGCGCCTGCTACGGTCGC
1 AATAGCGCCTGCTACGGCCGC
*
5562240 AATAGCG-CTCGCTATGGCCGC
1 AATAGCGCCT-GCTACGGCCGC
5562261 AAT
1 AAT
5562264 CACGGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.20
Consensus pattern (21 bp):
AATAGCGCCTGCTACGGCCGC
Found at i:5568907 original size:31 final size:31
Alignment explanation
Indices: 5568871--5568929 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
5568861 AACTTAAAAG
* *
5568871 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
5568902 AGTTTTACAATATTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
5568930 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:5568977 original size:22 final size:22
Alignment explanation
Indices: 5568952--5568994 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
5568942 AATAAATTAA
5568952 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
5568974 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
5568995 CTAATTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:5569180 original size:22 final size:22
Alignment explanation
Indices: 5569154--5569384 Score: 177
Period size: 22 Copynumber: 10.0 Consensus size: 22
5569144 TAATAAATTA
5569154 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
5569176 TTT-AAAT-AATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
5569196 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
* * *
5569219 ATAAATTATTTAAAAAATCAATTCATAT
1 -T---TTA--AAATAAATCAATCCATAT
*
5569247 TTTAAAATAAATC-ATCTATACT
1 TTTAAAATAAATCAATCCATA-T
**
5569269 AATAAATTATTTAAACTCAATCCATAT
1 TTTAAA--A--TAAA-TCAATCCATAT
5569296 TTT-AAAT-AATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
* *
5569316 TTTAAAATAAATCAACATACTAATTT
1 TTTAAAATAAATC-A-AT-C-CATAT
5569342 ATTTAAAATAAATCAATCCATAT
1 -TTTAAAATAAATCAATCCATAT
5569365 TTTAAAATAAATC-ATCCATA
1 TTTAAAATAAATCAATCCATA
5569385 CTAATAATTA
Statistics
Matches: 168, Mismatches: 18, Indels: 47
0.72 0.08 0.20
Matches are distributed among these distances:
20 29 0.17
21 26 0.15
22 44 0.26
23 5 0.03
24 9 0.05
25 3 0.02
26 10 0.06
27 21 0.12
28 7 0.04
29 14 0.08
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:5569187 original size:124 final size:122
Alignment explanation
Indices: 5569036--5569762 Score: 367
Period size: 124 Copynumber: 6.1 Consensus size: 122
5569026 CAACTACAAT
5569036 AATAAATC-ATCCATA-TTTAAATAAATCAATCATACTAATAAATTATTTAAAAT-AATCCATAC
1 AATAAATCAATCCATATTTTAAAT-AATCAATCATACT-ATAAA-TATTTAAAATAAATCCATAC
*
5569098 AACTACAATAATAATCAATCCATATTTT-AAATAAATCAATCTATACTAATAAATTATTTAA
63 AA-TAAAATAATAATCAATCCATATTTTAAAATAAATC-ATCTATACTAATAAATTATTTAA
* * * *
5569159 AATAAATCAATCCATATTTTAAATAATCAATTCATATTTTAAA-A--T-AAATCAATCCATACTA
1 AATAAATCAATCCATATTTTAAATAATCAA-TCATACTATAAATATTTAAAATAAATCCATACAA
* *
5569220 TAAATTATTTAAAAAATCAATTCATATTTTAAAATAAATCATCTATACTAATAAATTATTT--
65 TAAA--A--T-AATAATCAATCCATATTTTAAAATAAATCATCTATACTAATAAATTATTTAA
*
5569281 -A-AACTCAATCCATATTTTAAATAATCAATC---C-AT--AT-TTTAAAATAAATCAACATACT
1 AATAAATCAATCCATATTTTAAATAATCAATCATACTATAAATATTTAAAATAAATC--CATAC-
* *
5569337 AATTTATTTAA-AATAAATCAATCCATATTTTAAAATAAATCATCCATACTAAT-AATTATTTAA
63 AA--TA--AAATAAT-AATCAATCCATATTTTAAAATAAATCATCTATACTAATAAATTATTTAA
* *** *
5569400 AATAAATCAATTCATACAACTACAATAATAAATCA-ATCTAT--AT-TTTAAAATAAATCAATCC
1 AATAAATCAATCCATA-TTTTA-AATAATCAATCATA-CTATAAATATTTAAAAT--A--AATCC
*
5569461 ATACTAATAATTATTTAAAATAAATC-ATCCATATTTTAAAATAAAT--TC-ATACT-ATAAATT
59 ATAC-AATAA--A---ATAAT-AATCAATCCATATTTTAAAATAAATCATCTATACTAATAAATT
5569521 ATTTAA
117 ATTTAA
* * *
5569527 AAT--A--AAT---TATTTAAAATAAATCAATC---C-AT--AT-TTT-AAATAAATCAAT-CCA
1 AATAAATCAATCCATATTTTAAAT-AATCAATCATACTATAAATATTTAAAATAAATCCATACAA
* * *
5569576 T--ACTAAT--T-AAT---TATTTTAAAATAAATCAATCCATAC-AACTACA--A--T--
65 TAAAATAATAATCAATCCATATTTTAAAATAAATC-ATCTATACTAA-TAAATTATTTAA
5569621 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATATTTAAAATAAATCATCC
1 AATAAATCAATCCATATTTT-AAAT-AATCAAT-CATACT-ATAAATATTTAAAAT-AA--ATCC
* *
5569686 ATACAACTACAATAATAA--AAT-CATCATATTTAAAATAAATCAATCTATACAAATAAATTATT
59 ATACAA-TAAAATAATAATCAATCCAT-AT-TTTAAAATAAATC-ATCTATACTAATAAATTATT
5569748 TAA
120 TAA
5569751 AATAAATCAATC
1 AATAAATCAATC
5569763 TATACTATAA
Statistics
Matches: 477, Mismatches: 38, Indels: 171
0.70 0.06 0.25
Matches are distributed among these distances:
94 3 0.01
95 15 0.03
96 2 0.00
98 9 0.02
99 5 0.01
100 3 0.01
101 8 0.02
102 12 0.03
103 1 0.00
104 1 0.00
106 1 0.00
108 4 0.01
109 1 0.00
110 8 0.02
111 3 0.01
112 5 0.01
113 3 0.01
114 4 0.01
115 14 0.03
116 11 0.02
117 11 0.02
118 44 0.09
119 23 0.05
120 43 0.09
121 16 0.03
122 4 0.01
123 25 0.05
124 79 0.17
125 25 0.05
126 4 0.01
127 33 0.07
128 3 0.01
129 9 0.02
130 33 0.07
131 12 0.03
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (122 bp):
AATAAATCAATCCATATTTTAAATAATCAATCATACTATAAATATTTAAAATAAATCCATACAAT
AAAATAATAATCAATCCATATTTTAAAATAAATCATCTATACTAATAAATTATTTAA
Found at i:5569188 original size:20 final size:21
Alignment explanation
Indices: 5569152--5569216 Score: 96
Period size: 20 Copynumber: 3.1 Consensus size: 21
5569142 ACTAATAAAT
*
5569152 TATTTAAAATAAATCAATCCA
1 TATTTTAAATAAATCAATCCA
*
5569173 TATTTTAAAT-AATCAATTCA
1 TATTTTAAATAAATCAATCCA
5569193 TATTTTAAAATAAATCAATCCA
1 TATTTT-AAATAAATCAATCCA
5569215 TA
1 TA
5569217 CTATAAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
20 15 0.38
21 13 0.33
22 11 0.28
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.38
Consensus pattern (21 bp):
TATTTTAAATAAATCAATCCA
Found at i:5569252 original size:20 final size:20
Alignment explanation
Indices: 5569152--5569253 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
5569142 ACTAATAAAT
* *
5569152 TATTTAAAATAAATCAATCCA
1 TATTTTAAA-AAATCAATTCA
*
5569173 TATTTTAAATAATCAATTCA
1 TATTTTAAAAAATCAATTCA
5569193 TATTTTAAAATAAATCAATCCATACTA
1 TATTTT-AAA-AAATCAAT---T-C-A
5569220 TAAATTATTTAAAAAATCAATTCA
1 T--A-T-TTTAAAAAATCAATTCA
5569244 TATTTTAAAA
1 TATTTTAAAA
5569254 TAAATCATCT
Statistics
Matches: 66, Mismatches: 4, Indels: 23
0.71 0.04 0.25
Matches are distributed among these distances:
20 22 0.33
21 12 0.18
22 8 0.12
24 2 0.03
25 2 0.03
26 2 0.03
27 2 0.03
29 9 0.14
30 4 0.06
31 3 0.05
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
TATTTTAAAAAATCAATTCA
Found at i:5569301 original size:18 final size:18
Alignment explanation
Indices: 5569278--5569328 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
5569268 TAATAAATTA
*
5569278 TTTAAACTCAATCCATAT
1 TTTAAAATCAATCCATAT
5569296 TTTAAATAATCAATCCATAT
1 TTT-AA-AATCAATCCATAT
*
5569316 TTTAAAATAAATC
1 TTTAAAATCAATC
5569329 AACATACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 10 0.34
19 4 0.14
20 15 0.52
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAAAATCAATCCATAT
Found at i:5569315 original size:69 final size:69
Alignment explanation
Indices: 5569227--5569384 Score: 196
Period size: 69 Copynumber: 2.3 Consensus size: 69
5569217 CTATAAATTA
* * * **
5569227 TTTAAAAAATCAATTCATATTTTAAAATAAATCATCTATACTAA-TAAATT-ATTTAAACTCAAT
1 TTTAAATAATCAATCCATATTTTAAAATAAATCAAC-ATACTAATTAAATTAAAATAAA-TCAAT
5569290 CCATAT
64 CCATAT
* *
5569296 TTTAAATAATCAATCCATATTTTAAAATAAATCAACATACTAATTTATTTAAAATAAATCAATCC
1 TTTAAATAATCAATCCATATTTTAAAATAAATCAACATACTAATTAAATTAAAATAAATCAATCC
5569361 ATAT
66 ATAT
5569365 TTTAAAATAAATC-ATCCATA
1 TTT-AAAT-AATCAATCCATA
5569385 CTAATAATTA
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
68 7 0.09
69 51 0.65
70 16 0.21
71 4 0.05
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (69 bp):
TTTAAATAATCAATCCATATTTTAAAATAAATCAACATACTAATTAAATTAAAATAAATCAATCC
ATAT
Found at i:5569363 original size:49 final size:51
Alignment explanation
Indices: 5569293--5569415 Score: 189
Period size: 49 Copynumber: 2.5 Consensus size: 51
5569283 ACTCAATCCA
*
5569293 TATTTTAAAT-AATCAATCCATATTTTAAAATAAATCA-ACATACTAAT-T
1 TATTTAAAATAAATCAATCCATATTTTAAAATAAATCATACATACTAATAT
*
5569341 TATTTAAAATAAATCAATCCATATTTTAAAATAAATCATCCATACTAATAAT
1 TATTTAAAATAAATCAATCCATATTTTAAAATAAATCATACATACTAAT-AT
*
5569393 TATTTAAAATAAATCAATTCATA
1 TATTTAAAATAAATCAATCCATA
5569416 CAACTACAAT
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
48 9 0.13
49 27 0.40
50 9 0.13
52 23 0.34
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (51 bp):
TATTTAAAATAAATCAATCCATATTTTAAAATAAATCATACATACTAATAT
Found at i:5569464 original size:48 final size:46
Alignment explanation
Indices: 5569005--5569668 Score: 239
Period size: 48 Copynumber: 13.7 Consensus size: 46
5568995 CTAATTAATA
*
5569005 TTTAAAATAAATCAATCCATACAACTACAATAATAAATC-ATCCATA-
1 TTTAAAATAAATCAATCCATACAA-TA-AATAATAAATCAATCTATAT
* * *
5569051 TTT-AAATAAATCAAT-CATACTAATAAATTATTTAAAAT-AATCCATACA
1 TTTAAAATAAATCAATCCATAC-AATAAA-TA-AT-AAATCAATCTATA-T
** * *** * *
5569099 ACTACAATAATAATCAATCCATATTTTAAATAAATCAATCTATACTAATAAATT
1 TTTAAAAT-A-AATCAATCCATACAATAAAT-AATAAATCAAT-CT-AT--A-T
*** *
5569153 ATTTAAAATAAATCAATCCATATTTTAAATAATCAAT---TC-ATAT
1 -TTTAAAATAAATCAATCCATACAATAAATAATAAATCAATCTATAT
* *
5569196 TTTAAAATAAATCAATCCATACTATAAATTATTTAAAAAATCAAT-TCATAT
1 TTTAAAATAAATCAATCCATACAAT-AA--A--TAATAAATCAATCT-ATAT
* * *
5569247 TTTAAAATAAATC-ATCTATACTAATAAATTATTTAAACTCAATCCATAT
1 TTTAAAATAAATCAATCCATAC-AATAAA-TA-ATAAA-TCAATCTATAT
** * *
5569296 TTT-AAAT-AATCAATCCATA-TTTTAA-AATAAATCAACATACTAATTT
1 TTTAAAATAAATCAATCCATACAATAAATAATAAATC-A-AT-CT-ATAT
** *
5569342 ATTTAAAATAAATCAATCCATA-TTTTAA-AATAAATCATCCATACTAATAATT
1 -TTTAAAATAAATCAATCCATACAATAAATAATAAATCA---AT-CT-AT-A-T
*
5569394 ATTTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCTATAT
1 -TTTAAAATAAATCAATCCATACAA-TA-AATAATAAATCAATCTATAT
*
5569443 TTTAAAATAAATCAATCCATACTAATAATTATTTAAAATAAATC-ATCCATAT
1 TTTAAAATAAATCAATCCATAC-AATAA--A--T--AATAAATCAATCTATAT
* * *
5569495 TTTAAAATAAAT---T-CATACTATAAATTATTTAAAAT-AA-AT-TA-
1 TTTAAAATAAATCAATCCATACAATAAA-TA-AT-AAATCAATCTATAT
* **
5569536 TTTAAAATAAATCAATCCATATTTTAAATAAATCAATCCATACTAAT-TAATTAT
1 TTTAAAATAAATCAATCCATA----CAATAAAT-AATAAAT-C-AATCT-A-TAT
*
5569590 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACAA-TA-AATAATAAATCAATCTATAT
5569638 TTTAAAATAAATCAATCCATACTAATAAATA
1 TTTAAAATAAATCAATCCATAC-AATAAATA
5569669 TTTAAAATAA
Statistics
Matches: 487, Mismatches: 52, Indels: 157
0.70 0.07 0.23
Matches are distributed among these distances:
41 12 0.02
42 28 0.06
43 11 0.02
44 21 0.04
45 22 0.05
46 22 0.05
47 27 0.06
48 78 0.16
49 62 0.13
50 31 0.06
51 42 0.09
52 59 0.12
53 32 0.07
54 24 0.05
55 7 0.01
56 9 0.02
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.36
Consensus pattern (46 bp):
TTTAAAATAAATCAATCCATACAATAAATAATAAATCAATCTATAT
Found at i:5569476 original size:247 final size:240
Alignment explanation
Indices: 5569110--5569610 Score: 671
Period size: 247 Copynumber: 2.0 Consensus size: 240
5569100 CTACAATAAT
*
5569110 AATCAATCCATATTTTAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA
1 AATCAATCCATATTTTAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
*** *
5569175 TTTTAAATAATCAATTCATATTTTAAAATAAATCAATCCATACTATAAATTATTT-AAA-AAATC
66 AACTAAATAATAAATTCATATTTTAAAATAAATCAATCCATACTATAAATTATTTAAAATAAATC
* * * *
5569238 AATTCATATTTTAAAATAAATCATCTATACTAATAAATTATTTAAACTCAATCCATATTTTAAAT
131 -ATCCATATTTTAAAATAAAT--TC-ATACT-ATAAATTATTTAAAATAAAT---TATTTAAAAT
5569303 -AATCAATCCATATTTTAAAATAAATCAA-CATACTAA-T-TTA-TTTAAAATA
188 AAATCAATCCATATTTT-AAATAAATCAACCATACTAATTATTATTTTAAAATA
*
5569352 AATCAATCCATATTTTAAAATAAATC-ATCCATACTAAT-AATTATTTAAAATAAATCAATTCAT
1 AATCAATCCATATTTT-AAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT
5569415 ACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTA-ATAATTATTTAA
65 A-AACTA-AATAATAAAT---TC-ATATTTTAAAATAAATCAATCCATACTATA-AATTATTTAA
5569479 AATAAATCATCCATATTTTAAAATAAATTCATACTATAAATTATTTAAAATAAATTATTTAAAAT
123 AATAAATCATCCATATTTTAAAATAAATTCATACTATAAATTATTTAAAATAAATTATTTAAAAT
5569544 AAATCAATCCATATTTTAAATAAATCAATCCATACTAATTAATTATTTTAAAATA
188 AAATCAATCCATATTTTAAATAAATCAA-CCATACTAATT-ATTATTTTAAAATA
5569599 AATCAATCCATA
1 AATCAATCCATA
5569611 CAACTACAAT
Statistics
Matches: 232, Mismatches: 10, Indels: 29
0.86 0.04 0.11
Matches are distributed among these distances:
241 45 0.19
242 45 0.19
243 26 0.11
244 19 0.08
245 5 0.02
246 8 0.03
247 57 0.25
248 22 0.09
249 5 0.02
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.38
Consensus pattern (240 bp):
AATCAATCCATATTTTAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
AACTAAATAATAAATTCATATTTTAAAATAAATCAATCCATACTATAAATTATTTAAAATAAATC
ATCCATATTTTAAAATAAATTCATACTATAAATTATTTAAAATAAATTATTTAAAATAAATCAAT
CCATATTTTAAATAAATCAACCATACTAATTATTATTTTAAAATA
Found at i:5569499 original size:21 final size:21
Alignment explanation
Indices: 5569474--5569577 Score: 71
Period size: 21 Copynumber: 5.0 Consensus size: 21
5569464 CTAATAATTA
5569474 TTTAAAATAAATCATCCATAT
1 TTTAAAATAAATCATCCATAT
*
5569495 TTTAAAATAAATTCATACTATAAATT
1 TTTAAAATAAA-TCAT-CCAT--A-T
5569521 ATTTAAAAT-AA--AT---TA-
1 -TTTAAAATAAATCATCCATAT
5569536 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATC-ATCCATAT
5569558 TTT-AAATAAATCAATCCATA
1 TTTAAAATAAATC-ATCCATA
5569578 CTAATTAATT
Statistics
Matches: 68, Mismatches: 1, Indels: 28
0.70 0.01 0.29
Matches are distributed among these distances:
14 8 0.12
15 2 0.03
17 1 0.01
18 2 0.03
19 1 0.01
21 30 0.44
22 7 0.10
23 5 0.07
25 1 0.01
26 3 0.04
27 8 0.12
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAAAATAAATCATCCATAT
Found at i:5569506 original size:52 final size:53
Alignment explanation
Indices: 5569426--5570161 Score: 255
Period size: 52 Copynumber: 15.1 Consensus size: 53
5569416 CAACTACAAT
*
5569426 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAA
5569479 AATAAATC-ATCCATATTTTAAAATAAAT---T-CATACT-ATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT-AATTATTTAA
** * ** *
5569527 AAT--A--AAT---TA-TTTAAAATAAATCAATCCATA-TTTTAAATAAAT-C
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAA
** **
5569570 AATCCATACTAATTAATTATTTTAAAATAAATCAATCCATAC-AACTACA--A--T--
1 AATAAAT-C-AATCCA-TATTTTAAAATAAATCAATCCATACTAA-TA-ATTATTTAA
*
5569621 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAA
* * * * * *
5569674 AATAAATC-ATCCATA----CAACTACAAT-AAT--AAAATCATCA-TATTTAA
1 AATAAATCAATCCATATTTTAAAATA-AATCAATCCATACTAATAATTATTTAA
* * * * * *
5569719 AATAAATCAAT-C-TA---TACAAATAAAT-TAT--TTA-AAATAAATCAATCTAT
1 AATAAATCAATCCATATTTTA-AAATAAATCAATCCATACTAAT-AAT-TATTTAA
* *
5569766 ACT--ATAAAT---TA-TTT-AAATAAATCAATCCATA-T--------TTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAA
*
5569803 AATAAATCAATTCATATTTTAAAATAAATC-ATCCATACTAATAATTA-TTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAA
* *
5569854 AATAATTCAATCCATATTTT-AAAT-AATC-ATCCCTACTAATAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAA
* * *
5569904 AAT--ATCAATCCATATTTT-AAA-AAATCAATCCATATTTAA-AA-TAATCAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATA-CTAATAATTATTTAA
* ** * * *
5569952 TACATACTAATAAAT---TA-TTTAAAATAAATCAATCCATA-TTTTAAATAATCAA
1 -A-ATA--AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAA
* * *
5570004 TCCATACTAATAAAT---TA-TTTAAAAT-AATCAATTCATAC-AACTACA--A--T--
1 --AATA--AATCAATCCATATTTTAAAATAAATCAATCCATACTAA-TA-ATTATTTAA
5570051 AATCAAATCAATCC-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AAT-AAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT-AATTATTTAA
* *
5570105 AATAAATCAAT-CATA-TTTAAAATAAATCAATTCATACTAATAATTA-TTCA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAA
5570155 AATAAAT
1 AATAAAT
5570162 TATTTTAAAA
Statistics
Matches: 535, Mismatches: 60, Indels: 179
0.69 0.08 0.23
Matches are distributed among these distances:
37 5 0.01
39 5 0.01
41 12 0.02
42 4 0.01
43 13 0.02
44 37 0.07
45 40 0.07
46 17 0.03
47 19 0.04
48 93 0.17
49 46 0.09
50 32 0.06
51 52 0.10
52 98 0.18
53 29 0.05
54 30 0.06
55 2 0.00
56 1 0.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (53 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAA
Found at i:5569526 original size:27 final size:27
Alignment explanation
Indices: 5569451--5569534 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
5569441 ATTTTAAAAT
* *
5569451 AAATCAATCCATACTA-ATAATTATTTA
1 AAATAAATTCATACTATA-AATTATTTA
*
5569478 AAATAAA-TCAT-CCAT--A-T-TTTA
1 AAATAAATTCATACTATAAATTATTTA
5569499 AAATAAATTCATACTATAAATTATTTA
1 AAATAAATTCATACTATAAATTATTTA
5569526 AAATAAATT
1 AAATAAATT
5569535 ATTTAAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 11 0.24
22 5 0.11
23 4 0.09
25 3 0.07
26 4 0.09
27 19 0.41
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATAAATTCATACTATAAATTATTTA
Found at i:5569530 original size:79 final size:76
Alignment explanation
Indices: 5569348--5569493 Score: 240
Period size: 78 Copynumber: 1.9 Consensus size: 76
5569338 ATTTATTTAA
* *
5569348 AATAAATCAATCCATATTTTAAAATAAATCATCCATACTAATAATTATTTAAAATAAATCAATTC
1 AATAAATCAATCTATATTTTAAAATAAATCATCCATACTAATAATTATTTAAAATAAATCAATCC
5569413 ATACAACTACAAT
66 AT--AACTACAAT
5569426 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAATTATTTAAAATAAATC-ATC
1 AATAAATCAATCTATATTTTAAAATAAATC-ATCCATACTAATAATTATTTAAAATAAATCAATC
5569490 CATA
65 CATA
5569494 TTTTAAAATA
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
76 1 0.02
78 34 0.52
79 30 0.46
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (76 bp):
AATAAATCAATCTATATTTTAAAATAAATCATCCATACTAATAATTATTTAAAATAAATCAATCC
ATAACTACAAT
Found at i:5569531 original size:79 final size:76
Alignment explanation
Indices: 5568957--5569989 Score: 409
Period size: 73 Copynumber: 13.9 Consensus size: 76
5568947 ATTAATTTAA
*
5568957 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATTAA-TATTTAAAATAAATCAAT
1 AATAAATCAATCTATATTTTAAAATAAATC-ATCCATACTAA-TAATTATTTAAAATAAATCAAT
5569021 CCATACAACTACAAT
64 CCAT--AACTACAAT
* *
5569036 AATAAATC-ATCCATA-TTT-AAATAAATCAAT-CATACTAATAAATTATTTAAAAT-AATCCAT
1 AATAAATCAATCTATATTTTAAAATAAATC-ATCCATACTAAT-AATTATTTAAAATAAATCAAT
*
5569096 --ACAACTACAAT
64 CCATAACTACAAT
* *
5569107 AAT-AATCAATCCATATTTT-AAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCTATATTTTAAAATAAATC-ATCCATACTAAT-AATTATTTAAAATAAATCAAT
***
5569170 CCAT-A-TTTTA-
64 CCATAACTACAAT
5569180 AAT-AATCAAT-TCATATTTTAAAATAAATCAATCCATACT-ATAAATTATTT-AAA-AAATCAA
1 AATAAATCAATCT-ATATTTTAAAATAAATC-ATCCATACTAAT-AATTATTTAAAATAAATCAA
* * **
5569240 TTCAT-ATTTTAA-
63 TCCATAACTACAAT
* * ** * * *
5569252 AATAAATC-ATCTATA--CT--AATAAATTATTTAAACTCAATCCA-TATTTTAAAT-AATCAAT
1 AATAAATCAATCTATATTTTAAAATAAATCATCCATACT-AAT-AATTATTTAAAATAAATCAAT
* **
5569310 CCAT-ATTTTAA-
64 CCATAACTACAAT
* *
5569321 AATAAATCAACATACTAATTTATTTAAAATAAATCA---AT-C-CAT-A-T-TTTAAAATAAATC
1 AATAAATC-A-AT-CT-ATAT-TTTAAAATAAATCATCCATACTAATAATTATTTAAAATAAATC
*
5569378 -ATCCAT-ACTAATAATT
61 AATCCATAACT-ACAA-T
* * * * * ** *
5569394 ATTTAAAATAAATC-A-ATTCATACAACTACAATAATAAAT-C-AAT-CTATATTTTAAAATAAA
1 A-AT-AAATCAATCTATATT-TTA-AAATA-AATCATCCATACTAATAAT-TA-TTTAAAATAAA
*
5569454 TCAATCCAT-ACTAATAATT
59 TCAATCCATAACT-ACAA-T
* *
5569473 ATTTAAAATAAATCATCCATATTTTAAAATAAAT--T-CATACT-ATAAATTATTTAAAATAAAT
1 A-AT-AAATCAATC-T--ATATTTTAAAATAAATCATCCATACTAAT-AATTATTTAAAATAAAT
*
5569534 ---T--AT---T-TAA-
60 CAATCCATAACTACAAT
*
5569541 AATAAATCAATCCATATTTT-AAATAAATCAATCCATACTAATTAATTATTTTAAAATAAATCAA
1 AATAAATCAATCTATATTTTAAAATAAATC-ATCCATACTAA-TAATTA-TTTAAAATAAATCAA
5569605 TCCATACAACTACAAT
63 TCCAT--AACTACAAT
* *
5569621 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATATTTAAAATAAATC-ATC
1 AATAAATCAATCTATATTTTAAAATAAATC-ATCCATACTAATAATTATTTAAAATAAATCAATC
5569685 CATACAACTACAAT
65 CAT--AACTACAAT
* *
5569699 AATAAAATC-ATC-ATA-TTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAAATCAA
1 AAT-AAATCAATCTATATTTTAAAATAAATC-ATCCATACTAAT-AATTATTTAAAATAAATCAA
* *
5569761 TCTAT-ACTATAAATTATTT
63 TCCATAAC--TACA--A--T
* *
5569780 AAATAAATCAATCCATATTTTAAAATAAATCA---AT--TCAT-A-T-TTTAAAATAAATC-ATC
1 -AATAAATCAATCTATATTTTAAAATAAATCATCCATACTAATAATTATTTAAAATAAATCAATC
*
5569836 CAT-ACTAATAATTATT
65 CATAACT-A-CA--A-T
* * *
5569852 AAAATAATTCAATCCATATTTT-AAAT-AATCATCCCTACTAATAATTATTTAAAAT--ATCAAT
1 --AATAAATCAATCTATATTTTAAAATAAATCATCCATACTAATAATTATTTAAAATAAATCAAT
**
5569913 CCAT-A-T--TTT
64 CCATAACTACAAT
* * *
5569922 AAAAAATCAATCCATA-TTTAAAAT-AATCAATACATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCTATATTTTAAAATAAATC-ATCCATACTAAT-AATTATTTAAAATAAATCAAT
5569985 CCATA
64 CCATA
5569990 TTTTAAATAA
Statistics
Matches: 788, Mismatches: 62, Indels: 214
0.74 0.06 0.20
Matches are distributed among these distances:
62 8 0.01
63 7 0.01
65 1 0.00
66 14 0.02
67 16 0.02
68 49 0.06
69 44 0.06
70 42 0.05
71 51 0.06
72 51 0.06
73 97 0.12
74 52 0.07
75 25 0.03
76 54 0.07
77 32 0.04
78 61 0.08
79 91 0.12
80 29 0.04
81 31 0.04
82 10 0.01
83 7 0.01
84 16 0.02
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.36
Consensus pattern (76 bp):
AATAAATCAATCTATATTTTAAAATAAATCATCCATACTAATAATTATTTAAAATAAATCAATCC
ATAACTACAAT
Found at i:5569533 original size:14 final size:14
Alignment explanation
Indices: 5569514--5569547 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
5569504 AATTCATACT
5569514 ATAAATTATTTAAA
1 ATAAATTATTTAAA
5569528 ATAAATTATTTAAA
1 ATAAATTATTTAAA
5569542 ATAAAT
1 ATAAAT
5569548 CAATCCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAATTATTTAAA
Found at i:5569626 original size:26 final size:26
Alignment explanation
Indices: 5569595--5569704 Score: 88
Period size: 26 Copynumber: 4.2 Consensus size: 26
5569585 ATTATTTTAA
5569595 AATAAATCAATCCATACAACTACAAT
1 AATAAATCAATCCATACAACTACAAT
* **
5569621 AATAAATCAATCCAT---ATTTTAA-
1 AATAAATCAATCCATACAACTACAAT
*
5569643 AATAAATCAATCCATACTAA-TAAATATTT
1 AATAAATCAATCCATAC-AACTACA-A--T
5569672 AAAATAAATC-ATCCATACAACTACAAT
1 --AATAAATCAATCCATACAACTACAAT
5569699 AATAAA
1 AATAAA
5569705 ATCATCATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 23
0.70 0.06 0.24
Matches are distributed among these distances:
22 15 0.22
23 4 0.06
25 8 0.12
26 17 0.25
27 1 0.01
29 3 0.04
30 11 0.16
31 8 0.12
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (26 bp):
AATAAATCAATCCATACAACTACAAT
Found at i:5569639 original size:115 final size:116
Alignment explanation
Indices: 5569426--5569649 Score: 287
Period size: 116 Copynumber: 1.9 Consensus size: 116
5569416 CAACTACAAT
*
5569426 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAATTATTTAAAATAAATCATCC
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAAAATAAATCATCC
*** ** *
5569491 ATATTTTAAAATAAATTCATACTATAAATTA-TTTAAAATAAATTATTTAA
66 ATAAACTAAAATAAATAAATACAATAAATTATTTTAAAATAAATTATTTAA
5569541 AATAAATCAATCCATATTTT-AAATAAATCAATCCATACTAATTAATTATTTTAAAATAAATCAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA-TAATTA-TTTAAAATAAATC-A
* **
5569605 TCCATACAACTACAAT-AATAAAT-CAATCCA-TATTTTAAAATAAAT
63 TCCATA-AACTAAAATAAATAAATACAATAAATTATTTTAAAATAAAT
5569650 CAATCCATAC
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
114 21 0.22
115 27 0.29
116 29 0.31
117 12 0.13
118 5 0.05
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (116 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAAAATAAATCATCC
ATAAACTAAAATAAATAAATACAATAAATTATTTTAAAATAAATTATTTAA
Found at i:5569668 original size:22 final size:23
Alignment explanation
Indices: 5569592--5569666 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
5569582 TTAATTATTT
5569592 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
5569614 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
5569640 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
5569663 TAAA
1 TAAA
5569667 TATTTAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:5569705 original size:30 final size:31
Alignment explanation
Indices: 5569640--5569706 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
5569630 ATCCATATTT
*
5569640 TAAAATAAATCAATCCATACTAATAAATATT
1 TAAAATAAATCAATCCATACTAATAAATATA
5569671 TAAAATAAATC-ATCCATAC-AACTACAATA-A
1 TAAAATAAATCAATCCATACTAA-TA-AATATA
5569701 TAAAAT
1 TAAAAT
5569707 CATCATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
29 2 0.06
30 16 0.48
31 15 0.45
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (31 bp):
TAAAATAAATCAATCCATACTAATAAATATA
Found at i:5569741 original size:18 final size:18
Alignment explanation
Indices: 5569718--5569767 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 18
5569708 ATCATATTTA
5569718 AAATAAATCAATCTATAC
1 AAATAAATCAATCTATAC
*
5569736 AAATAAAT-TAT-T-TA-
1 AAATAAATCAATCTATAC
5569750 AAATAAATCAATCTATAC
1 AAATAAATCAATCTATAC
5569768 TATAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
14 8 0.31
15 4 0.15
16 2 0.08
17 4 0.15
18 8 0.31
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATAAATCAATCTATAC
Found at i:5569753 original size:14 final size:15
Alignment explanation
Indices: 5569712--5569788 Score: 52
Period size: 17 Copynumber: 5.0 Consensus size: 15
5569702 AAAATCATCA
5569712 TATTTAAAATAAATC
1 TATTTAAAATAAATC
*
5569727 AATCTATACAAATAAAT-
1 TAT-T-TA-AAATAAATC
5569744 TATTTAAAATAAATC
1 TATTTAAAATAAATC
* **
5569759 AATCTATACTATAAAT-
1 TAT-T-TAAAATAAATC
5569775 TATTT-AAATAAATC
1 TATTTAAAATAAATC
5569789 AATCCATATT
Statistics
Matches: 47, Mismatches: 8, Indels: 15
0.67 0.11 0.21
Matches are distributed among these distances:
13 6 0.13
14 9 0.19
15 7 0.15
16 5 0.11
17 12 0.26
18 8 0.17
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (15 bp):
TATTTAAAATAAATC
Found at i:5569753 original size:32 final size:31
Alignment explanation
Indices: 5569712--5569792 Score: 137
Period size: 32 Copynumber: 2.6 Consensus size: 31
5569702 AAAATCATCA
5569712 TATTTAAAATAAATCAATCTATACAAATAAAT
1 TATTTAAAATAAATCAATCTATAC-AATAAAT
*
5569744 TATTTAAAATAAATCAATCTATACTATAAAT
1 TATTTAAAATAAATCAATCTATACAATAAAT
5569775 TATTT-AAATAAATCAATC
1 TATTTAAAATAAATCAATC
5569793 CATATTTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 13 0.27
31 11 0.23
32 24 0.50
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (31 bp):
TATTTAAAATAAATCAATCTATACAATAAAT
Found at i:5569761 original size:108 final size:104
Alignment explanation
Indices: 5569638--5569869 Score: 283
Period size: 108 Copynumber: 2.2 Consensus size: 104
5569628 CAATCCATAT
*
5569638 TTTAAAATAAATCAATCCATACTAATAAA-TATTTAAAATAAATC-ATCCATACAACTACAAT-A
1 TTTAAAATAAATCAATCCATACT-ATAAATTATTT-AAATAAATCAATCCATA-AACTAAAATAA
*
5569700 ATAAAATCATCATATTTAAAATAAATCAATCTATACAAATAAATTA
63 ATAAAATCAT-AT-TTTAAAATAAATC-ATCCATACAAAT-AATTA
* *** *
5569746 TTTAAAATAAATCAATCTATACTATAAATTATTTAAATAAATCAATCCATATTTTAAAATAAATC
1 TTTAAAATAAATCAATCCATACTATAAATTATTTAAATAAATCAATCCATAAACTAAAATAAATA
* *
5569811 AATTCATATTTTAAAATAAATCATCCATACTAATAATTA
66 AAATCATATTTTAAAATAAATCATCCATACAAATAATTA
*
5569850 -TTAAAATAATTCAATCCATA
1 TTTAAAATAAATCAATCCATA
5569870 TTTTAAATAA
Statistics
Matches: 110, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
103 18 0.16
104 5 0.05
105 10 0.09
106 13 0.12
107 21 0.19
108 43 0.39
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (104 bp):
TTTAAAATAAATCAATCCATACTATAAATTATTTAAATAAATCAATCCATAAACTAAAATAAATA
AAATCATATTTTAAAATAAATCATCCATACAAATAATTA
Found at i:5569807 original size:22 final size:22
Alignment explanation
Indices: 5569780--5569839 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
5569770 TAAATTATTT
5569780 AAATAAATCAATCCATATTTTA
1 AAATAAATCAATCCATATTTTA
*
5569802 AAATAAATCAATTCATATTTTA
1 AAATAAATCAATCCATATTTTA
5569824 AAATAAATC-ATCCATA
1 AAATAAATCAATCCATA
5569840 CTAATAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 6 0.17
22 30 0.83
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATAAATCAATCCATATTTTA
Found at i:5569924 original size:20 final size:19
Alignment explanation
Indices: 5569897--5570009 Score: 89
Period size: 20 Copynumber: 6.1 Consensus size: 19
5569887 TACTAATAAT
5569897 TATTTAAAATATCAATCCA
1 TATTTAAAATATCAATCCA
*
5569916 TATTTTAAAAAATCAATCCA
1 TA-TTTAAAATATCAATCCA
*
5569936 TATTTAAAATAATCAATACA
1 TATTTAAAAT-ATCAATCCA
*
5569956 TA-CT--AATA--AAT---
1 TATTTAAAATATCAATCCA
5569967 TATTTAAAATAAATCAATCCA
1 TATTTAAAAT--ATCAATCCA
*
5569988 TATTTTAAATAATCAATCCA
1 TATTTAAAAT-ATCAATCCA
5570008 TA
1 TA
5570010 CTAATAAATT
Statistics
Matches: 76, Mismatches: 6, Indels: 23
0.72 0.06 0.22
Matches are distributed among these distances:
11 2 0.03
12 1 0.01
14 6 0.08
16 2 0.03
17 3 0.04
18 3 0.04
19 10 0.13
20 40 0.53
21 9 0.12
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.36
Consensus pattern (19 bp):
TATTTAAAATATCAATCCA
Found at i:5569928 original size:72 final size:71
Alignment explanation
Indices: 5569534--5570009 Score: 292
Period size: 72 Copynumber: 6.3 Consensus size: 71
5569524 TAAAATAAAT
* * * *
5569534 TATTTAAAATAAATCAATCCATATTTTAAATAAATCAATCCATACTAATTAATTATTTTAAAATA
1 TATTTTAAA-AAATCAATCCATATTTAAAAT-AATCAATACATACTAATAAATTA-TTTAAAAT-
5569599 AATCAATCCA
62 AATCAATCCA
** * *
5569609 TACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAA-TATTTA
1 T---A-T--TTTAAAAAATCAATCCATA-TTTAAAAT-AATCAATACATACTAATAAATTATTTA
5569673 AAATAAATC-ATCCA
58 AAAT-AATCAATCCA
*** * * *
5569687 TACAACTACAATAATAAAATCATCATATTTAAAATAAATCAAT-CTATACAAATAAATTATTTAA
1 TA-TTTTA-AAAAAT-CAATC--CATATTTAAAAT-AATCAATAC-ATACTAATAAATTATTTAA
5569751 AATAAATCAATCTATACTA
59 AAT-AATCAATC----C-A
* **
5569770 TAAATTATTTAAATAAATCAATCCATATTTTAAAATAAATCAATTCATA-TTTTAAA--A--T-A
1 T--A-T-TTTAAA-AAATCAATCCATA-TTTAAAAT-AATCAATACATACTAATAAATTATTTAA
* * *
5569829 AATCATCCATACTAA
59 AATAATCAAT-C-CA
* * *
5569844 TAATTATTAAAATAATTCAATCCATATTTTAAATAATC-ATCCCTACTAAT-AATTATTTAAAAT
1 T-ATT-TTAAAA-AA-TCAATCCATATTTAAAATAATCAATACATACTAATAAATTATTTAAAAT
5569907 -ATCAATCCA
62 AATCAATCCA
5569916 TATTTTAAAAAATCAATCCATATTTAAAATAATCAATACATACTAATAAATTATTTAAAATAAAT
1 TATTTTAAAAAATCAATCCATATTTAAAATAATCAATACATACTAATAAATTATTTAAAAT-AAT
5569981 CAATCCA
65 CAATCCA
*
5569988 TATTTTAAATAATCAATCCATA
1 TATTTTAAAAAATCAATCCATA
5570010 CTAATAAATT
Statistics
Matches: 326, Mismatches: 36, Indels: 81
0.74 0.08 0.18
Matches are distributed among these distances:
68 21 0.06
69 12 0.04
70 26 0.08
71 11 0.03
72 48 0.15
73 16 0.05
74 12 0.04
75 12 0.04
76 26 0.08
77 24 0.07
78 15 0.05
79 15 0.05
80 15 0.05
81 30 0.09
82 1 0.00
83 10 0.03
84 19 0.06
85 8 0.02
86 5 0.02
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.36
Consensus pattern (71 bp):
TATTTTAAAAAATCAATCCATATTTAAAATAATCAATACATACTAATAAATTATTTAAAATAATC
AATCCA
Found at i:5569974 original size:31 final size:30
Alignment explanation
Indices: 5569936--5570041 Score: 97
Period size: 31 Copynumber: 3.7 Consensus size: 30
5569926 AATCAATCCA
5569936 TATTTAAAATAATCAATACATACTAATAAAT
1 TATTTAAAATAATCAAT-CATACTAATAAAT
5569967 TATTTAAAATAAATCAATC---C--AT--A-
1 TATTTAAAAT-AATCAATCATACTAATAAAT
*
5569990 T-TTTAAAT-AATCAATCCATACTAATAAAT
1 TATTTAAAATAATCAAT-CATACTAATAAAT
5570019 TATTTAAAATAATCAATTCATAC
1 TATTTAAAATAATCAA-TCATAC
5570042 AACTACAATA
Statistics
Matches: 60, Mismatches: 2, Indels: 26
0.68 0.02 0.30
Matches are distributed among these distances:
20 7 0.12
21 1 0.02
22 6 0.10
23 1 0.02
24 2 0.03
26 4 0.07
28 2 0.03
29 1 0.02
30 6 0.10
31 22 0.37
32 8 0.13
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (30 bp):
TATTTAAAATAATCAATCATACTAATAAAT
Found at i:5570017 original size:21 final size:21
Alignment explanation
Indices: 5569973--5570018 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
5569963 AAATTATTTA
**
5569973 AAATAAATCAATCCATATTTT
1 AAATAAATCAATCCATATAAT
5569994 AAAT-AATCAATCCATACTAAT
1 AAATAAATCAATCCATA-TAAT
5570015 AAAT
1 AAAT
5570019 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAAATCAATCCATATAAT
Found at i:5570084 original size:99 final size:95
Alignment explanation
Indices: 5569960--5570190 Score: 256
Period size: 99 Copynumber: 2.4 Consensus size: 95
5569950 AATACATACT
*
5569960 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAA-TAATCAATCCATACTAATAAAT-TAT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAATTAATCAA--AATA--AATAAATATAT
5570022 TTAAAAT-AATCAATTCATAC-AACTACAATAATCA
62 TTAAAATAAATCAATTCATACTAA-TA-AATAATCA
* ** * * *
5570056 AATCAATCCTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCATAT
1 AATAAAT--TATTTTAAAATAAATCAATCCATA-TTTTAAATTAATCAAAATAAATAAAT-ATAT
* *
5570121 TTAAAATAAATCAATTCATACTAATAATTATTCA
62 TTAAAATAAATCAATTCATACTAATAAATAATCA
5570155 AATAAATTATTTTAAAATAAATCAATCCATATTTTA
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTA
5570191 TAAATTTATT
Statistics
Matches: 114, Mismatches: 12, Indels: 18
0.79 0.08 0.12
Matches are distributed among these distances:
96 9 0.08
97 30 0.26
98 2 0.02
99 46 0.40
100 20 0.18
101 7 0.06
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (95 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTAAATTAATCAAAATAAATAAATATATTTAA
AATAAATCAATTCATACTAATAAATAATCA
Found at i:5570123 original size:20 final size:21
Alignment explanation
Indices: 5570098--5570188 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 21
5570088 ACTAATAAAT
5570098 TATTTAAAATAAATCAA-TCA
1 TATTTAAAATAAATCAATTCA
5570118 TATTTAAAATAAATCAATTCA
1 TATTTAAAATAAATCAATTCA
* * *
5570139 TACTAATAATTATTCAAATAAATT-A
1 TA-T-TTAA--AAT-AAATCAATTCA
*
5570164 T-TTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATTCA
5570184 TATTT
1 TATTT
5570189 TATAAATTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
19 7 0.12
20 21 0.38
21 8 0.14
22 4 0.07
23 4 0.07
25 4 0.07
26 8 0.14
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTTAAAATAAATCAATTCA
Found at i:5570201 original size:99 final size:99
Alignment explanation
Indices: 5570019--5570211 Score: 259
Period size: 100 Copynumber: 1.9 Consensus size: 99
5570009 ACTAATAAAT
*
5570019 TATTTAAAATAATCAATTCATACAACTACAATAATCAAATCAATCCTATTTTAAAATAAATCAAT
1 TATTTAAAATAATCAATTCATACAACTACAATAATCAAATAAAT-CTATTTTAAAATAAATCAAT
5570084 CCATACTAATAAATTA-TTTAAAATAAATCAATCA
65 CCATACTAATAAATTATTTTAAAATAAATCAATCA
* *
5570118 TATTTAAAATAAATCAATTCATACTAA-TA-ATTATTCAAATAAAT-TATTTTAAAATAAATCAA
1 TATTTAAAAT-AATCAATTCATAC-AACTACAATAATCAAATAAATCTATTTTAAAATAAATCAA
* * *
5570180 TCCATATTTTATAAATTTATTTTAAAGTAAAT
64 TCCATA-CTAATAAA-TTATTTTAAAATAAAT
5570212 TATTTATAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
97 24 0.29
98 6 0.07
99 25 0.30
100 26 0.31
101 2 0.02
ACGTcount: A:0.50, C:0.11, G:0.01, T:0.38
Consensus pattern (99 bp):
TATTTAAAATAATCAATTCATACAACTACAATAATCAAATAAATCTATTTTAAAATAAATCAATC
CATACTAATAAATTATTTTAAAATAAATCAATCA
Found at i:5570216 original size:28 final size:26
Alignment explanation
Indices: 5570184--5570301 Score: 111
Period size: 28 Copynumber: 4.5 Consensus size: 26
5570174 AATCAATCCA
5570184 TATTTT-ATAAATTTATTTTAAAGTAAAT
1 TATTTTAATAAA-TTATTTTAAA-T-AAT
5570212 TATTTATAATAAATTATTTTATAATAAT
1 TATTT-TAATAAATTATTTTA-AATAAT
5570240 TATTTTAAATAAATTATTTTAAATAAT
1 TATTTT-AATAAATTATTTTAAATAAT
* ** *
5570267 AACCTTATTAAATTA-TTT-AA-AAT
1 TATTTTAATAAATTATTTTAAATAAT
5570290 TA-TTTAATAAAT
1 TATTTTAATAAAT
5570302 AAATATATTT
Statistics
Matches: 79, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
22 8 0.10
23 4 0.05
24 2 0.03
25 3 0.04
26 8 0.10
27 10 0.13
28 27 0.34
29 10 0.13
30 7 0.09
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (26 bp):
TATTTTAATAAATTATTTTAAATAAT
Found at i:5570223 original size:64 final size:64
Alignment explanation
Indices: 5570090--5570238 Score: 164
Period size: 64 Copynumber: 2.3 Consensus size: 64
5570080 CAATCCATAC
5570090 TAATAAATTA-TTTAAAATAAATCAATCATATTTAAAATAAATCAATTCATACTAATAATTATTC
1 TAATAAATTATTTTAAAATAAATCAATCATATTT-AAATAAATCAATTCATAC-AATAATTATTC
5570154 A
64 A
* ** *
5570155 -AATAAATTATTTTAAAATAAATCAATCCATATTT-TATAAATTTATT-TTA-AAGTAAATTATT
1 TAATAAATTATTTTAAAATAAATCAAT-CATATTTAAATAAATCAATTCATACAA-T-AATTATT
*
5570216 TA
63 CA
*
5570218 TAATAAATTATTTTATAATAA
1 TAATAAATTATTTTAAAATAA
5570239 TTATTTTAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
61 2 0.03
62 1 0.01
63 10 0.14
64 37 0.51
65 16 0.22
66 7 0.10
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (64 bp):
TAATAAATTATTTTAAAATAAATCAATCATATTTAAATAAATCAATTCATACAATAATTATTCA
Found at i:5570259 original size:14 final size:14
Alignment explanation
Indices: 5570190--5570265 Score: 102
Period size: 14 Copynumber: 5.3 Consensus size: 14
5570180 TCCATATTTT
5570190 ATAAATTTATTTTAA
1 ATAAA-TTATTTTAA
5570205 AGTAAATTA-TTTATA
1 A-TAAATTATTTTA-A
5570220 ATAAATTATTTTATA
1 ATAAATTATTTTA-A
5570235 AT-AATTATTTTAA
1 ATAAATTATTTTAA
5570248 ATAAATTATTTTAA
1 ATAAATTATTTTAA
5570262 ATAA
1 ATAA
5570266 TAACCTTATT
Statistics
Matches: 57, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.05
14 36 0.63
15 14 0.25
16 4 0.07
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (14 bp):
ATAAATTATTTTAA
Found at i:5570318 original size:28 final size:27
Alignment explanation
Indices: 5570209--5570318 Score: 79
Period size: 28 Copynumber: 4.1 Consensus size: 27
5570199 TTTTAAAGTA
5570209 AATTATTT-AT-AATAAATTATTTTAT
1 AATTATTTAATAAATAAATTATTTTAT
* **
5570234 AATAATTATTTTAAATAAATTATTTTA-
1 AATTATT-TAATAAATAAATTATTTTAT
* * * *
5570261 AA-TA-ATAACCTTATTAAATTA-TTTAA
1 AATTATTTAA--TAAATAAATTATTTTAT
5570287 AATTATTTAATAAATAAATATATTTTAT
1 AATTATTTAATAAATAAAT-TATTTTAT
5570315 AATT
1 AATT
5570319 GTTCTTGAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 17
0.68 0.13 0.18
Matches are distributed among these distances:
24 1 0.02
25 10 0.16
26 20 0.32
27 7 0.11
28 25 0.40
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
AATTATTTAATAAATAAATTATTTTAT
Found at i:5570720 original size:2 final size:2
Alignment explanation
Indices: 5570713--5570741 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5570703 ATTATCAGTA
5570713 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5570742 GATTTCAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5570916 original size:2 final size:2
Alignment explanation
Indices: 5570909--5570936 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5570899 ATTATCAGTA
5570909 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5570937 GATAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5570933 original size:195 final size:195
Alignment explanation
Indices: 5570547--5570939 Score: 770
Period size: 195 Copynumber: 2.0 Consensus size: 195
5570537 ACCATTTTTG
5570547 GATTTCAGAATCTACTGCAAGTAACCAGCAAAAAAATGGTTATTTGACTACATTATCAATTATTT
1 GATTTCAGAATCTACTGCAAGTAACCAGCAAAAAAATGGTTATTTGACTACATTATCAATTATTT
5570612 GTTTCTAAGCAGGAAGGGACATGATTTTATGAATAACAAACTTTTACATTTTACGAGAAATGAAG
66 GTTTCTAAGCAGGAAGGGACATGATTTTATGAATAACAAACTTTTACATTTTACGAGAAATGAAG
5570677 TTATAAATTTTAAAGAACAAAAATCGATTATCAGTAATATATATATATATATATAATATATATAT
131 TTATAAATTTTAAAGAACAAAAATCGATTATCAGTAATATATATATATATATATAATATATATAT
5570742 GATTTCAGAATCTACTGCAAGTAACCAGCAAAAAAATGGTTATTTGACTACATTATCAATTATTT
1 GATTTCAGAATCTACTGCAAGTAACCAGCAAAAAAATGGTTATTTGACTACATTATCAATTATTT
5570807 GTTTCTAAGCAGGAAGGGACATGATTTTATGAATAACAAACTTTTACAATTTTACGAGAAATGAA
66 GTTTCTAAGCAGGAAGGGACATGATTTTATGAATAACAAACTTTTAC-ATTTTACGAGAAATGAA
5570872 GTTATAAATTTTAAAGAACAAAAATCGATTATCAGTAATATATATATATATATAT-ATATATATA
130 GTTATAAATTTTAAAGAACAAAAATCGATTATCAGTAATATATATATATATATATAATATATATA
5570936 T
195 T
5570937 GAT
1 GAT
5570940 AAATTAACAT
Statistics
Matches: 197, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
195 125 0.63
196 72 0.37
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (195 bp):
GATTTCAGAATCTACTGCAAGTAACCAGCAAAAAAATGGTTATTTGACTACATTATCAATTATTT
GTTTCTAAGCAGGAAGGGACATGATTTTATGAATAACAAACTTTTACATTTTACGAGAAATGAAG
TTATAAATTTTAAAGAACAAAAATCGATTATCAGTAATATATATATATATATATAATATATATAT
Found at i:5577485 original size:55 final size:55
Alignment explanation
Indices: 5577102--5577471 Score: 562
Period size: 55 Copynumber: 6.7 Consensus size: 55
5577092 CTTATACGTG
*
5577102 AAAATTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
* * *
5577157 AAAATTAAGAAATTCATAATAAATTTATGAATTTCCGTATGGGCACTATGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
* * * *
5577212 AAAACTAA-AAATTTCATAATAATTTTATGAATTTTCATATGGGCATTGTGTGTGC
1 AAAACTAAGAAA-TTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
5577267 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
* * * * *
5577322 AAAACAAAGAAATTCATAATAAGCTTATGAATTTCTGTATGAGCATTGTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
* * *
5577377 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGAGCACTGTGTGTGA
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
* *
5577432 AAAACTAAGAAATTCATTATAAATTTATGAATTTCCGTAT
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
5577472 TGGTAGTGGG
Statistics
Matches: 287, Mismatches: 26, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
54 3 0.01
55 281 0.98
56 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.35
Consensus pattern (55 bp):
AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
Found at i:5582574 original size:18 final size:18
Alignment explanation
Indices: 5582551--5582594 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
5582541 TAAAACCGGA
5582551 AATGTTACACCATGCCCT
1 AATGTTACACCATGCCCT
5582569 AATGTTACACCATGCCCT
1 AATGTTACACCATGCCCT
5582587 AATGTTAC
1 AATGTTAC
5582595 TGGTATGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (18 bp):
AATGTTACACCATGCCCT
Found at i:5589385 original size:21 final size:21
Alignment explanation
Indices: 5589361--5589405 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
5589351 GAAACATGCA
5589361 CTCTACATGCTTCAACATTCT
1 CTCTACATGCTTCAACATTCT
5589382 CTCTACATGCTTCAACATTCT
1 CTCTACATGCTTCAACATTCT
5589403 CTC
1 CTC
5589406 CACCCTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.36, G:0.04, T:0.38
Consensus pattern (21 bp):
CTCTACATGCTTCAACATTCT
Found at i:5589413 original size:19 final size:20
Alignment explanation
Indices: 5589370--5589413 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
5589360 ACTCTACATG
**
5589370 CTTCAACATTCTCTCTACATG
1 CTTCAACATTCTCTC-ACACC
5589391 CTTCAACATTCTCTC-CACC
1 CTTCAACATTCTCTCACACC
5589410 CTTC
1 CTTC
5589414 TCAGTTAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
21 15 0.71
ACGTcount: A:0.20, C:0.41, G:0.02, T:0.36
Consensus pattern (20 bp):
CTTCAACATTCTCTCACACC
Found at i:5590677 original size:3 final size:3
Alignment explanation
Indices: 5590657--5590705 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
5590647 ATTTTTTTAT
*
5590657 TTA TT- TTA TT- TGA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5590703 TTA
1 TTA
5590706 CTACTAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 3 0.07
3 39 0.93
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5591984 original size:29 final size:30
Alignment explanation
Indices: 5591951--5592007 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
5591941 GGCTGTAAAT
5591951 TTTAATATTT-TATATTTTAATC-CTATTAC
1 TTTAAT-TTTATATATTTTAATCACTATTAC
* *
5591980 TTTAATTTTATATGTTTTAGTCACTATT
1 TTTAATTTTATATATTTTAATCACTATT
5592008 TAATTGCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 16 0.67
30 5 0.21
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (30 bp):
TTTAATTTTATATATTTTAATCACTATTAC
Found at i:5592990 original size:26 final size:27
Alignment explanation
Indices: 5592935--5592995 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
5592925 TTATAATTAT
* *
5592935 TTATTTTCAAAATTTTTATATATACTTA
1 TTATTTTCAAAATATATATATATAC-TA
*
5592963 TTATTTTCATAATATATATATATA-TA
1 TTATTTTCAAAATATATATATATACTA
5592989 TTATTTT
1 TTATTTT
5592996 ATTAATGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 9 0.30
28 21 0.70
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (27 bp):
TTATTTTCAAAATATATATATATACTA
Found at i:5593001 original size:26 final size:26
Alignment explanation
Indices: 5592919--5592995 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 26
5592909 TTAAAAATCC
* * *
5592919 ATATATTTATAATTATTTATTTTCAAA
1 ATATATATATACTTA-TTATTTTCATA
*
5592946 ATTTTTATATATACTTATTATTTTCATA
1 A--TATATATATACTTATTATTTTCATA
5592974 ATATATATATA-TATATTATTTT
1 ATATATATATACT-TATTATTTT
5592996 ATTAATGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
25 1 0.02
26 18 0.43
27 1 0.02
28 11 0.26
29 11 0.26
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (26 bp):
ATATATATATACTTATTATTTTCATA
Found at i:5596273 original size:15 final size:15
Alignment explanation
Indices: 5596253--5596284 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5596243 ATCAATACCT
*
5596253 TTTTGCATACATTCA
1 TTTTGCACACATTCA
5596268 TTTTGCACACATTCA
1 TTTTGCACACATTCA
5596283 TT
1 TT
5596285 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCACACATTCA
Found at i:5600089 original size:8 final size:9
Alignment explanation
Indices: 5600062--5600092 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
5600052 AAATGGTAAT
5600062 CATTCTTTA
1 CATTCTTTA
5600071 CATTCTTTA
1 CATTCTTTA
5600080 CATT-TTTA
1 CATTCTTTA
5600088 CATTC
1 CATTC
5600093 ATTATTTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (9 bp):
CATTCTTTA
Found at i:5603635 original size:6 final size:6
Alignment explanation
Indices: 5603624--5603679 Score: 71
Period size: 6 Copynumber: 9.7 Consensus size: 6
5603614 GCTTGAAGAA
**
5603624 AAAATG AAAATG AAAA-- AAAATG AAAATG AAAAAA AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
*
5603670 AAAAAG AAAA
1 AAAATG AAAA
5603680 AAATGAATGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
4 4 0.09
6 39 0.91
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (6 bp):
AAAATG
Found at i:5603657 original size:18 final size:18
Alignment explanation
Indices: 5603622--5603680 Score: 95
Period size: 18 Copynumber: 3.3 Consensus size: 18
5603612 ATGCTTGAAG
5603622 AAAAAATGAAAATG--AA
1 AAAAAATGAAAATGAAAA
5603638 AAAAAATGAAAATGAAAA
1 AAAAAATGAAAATGAAAA
5603656 AAAAAATGAAAATGAAAA
1 AAAAAATGAAAATGAAAA
5603674 AGAAAAA
1 A-AAAAA
5603681 AATGAATGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
16 14 0.35
18 21 0.52
19 5 0.12
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAAAATGAAAATGAAAA
Found at i:5603692 original size:18 final size:19
Alignment explanation
Indices: 5603625--5603692 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 19
5603615 CTTGAAGAAA
5603625 AAATGAAAATGAAAAAAAATG
1 AAATGAAAA-G-AAAAAAATG
5603646 AAAATG-AAA-AAAAAAATG
1 -AAATGAAAAGAAAAAAATG
5603664 AAAATGAAAAAGAAAAAAATG
1 -AAATG-AAAAGAAAAAAATG
5603685 -AATGAAAA
1 AAATGAAAA
5603693 ATGATAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
18 19 0.44
19 4 0.09
20 3 0.07
21 12 0.28
22 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (19 bp):
AAATGAAAAGAAAAAAATG
Found at i:5603693 original size:33 final size:32
Alignment explanation
Indices: 5603617--5603693 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 32
5603607 ATATTATGCT
5603617 TGAAGAAAAAATGAAAATGAAAAAAAATGAAAA
1 TGAAGAAAAAATGAAAATGAAAAAAAA-GAAAA
*
5603650 TGAAAAAAAAAATGAAAATGAAAAAGAAA-AAAA
1 TG-AAGAAAAAATGAAAATGAAAAA-AAAGAAAA
5603683 TGAATGAAAAA
1 TGAA-GAAAAA
5603694 TGATAATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 2 0.05
33 13 0.33
34 21 0.54
35 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (32 bp):
TGAAGAAAAAATGAAAATGAAAAAAAAGAAAA
Found at i:5603693 original size:34 final size:33
Alignment explanation
Indices: 5603622--5603686 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 33
5603612 ATGCTTGAAG
5603622 AAAAAATGAAAATGAAAAAAAATGAAAATGAAAA
1 AAAAAATGAAAATGAAAAAAAA-GAAAATGAAAA
5603656 AAAAAATGAAAATGAAAAAGAAA-AAAATGAA
1 AAAAAATGAAAATGAAAAA-AAAGAAAATGAA
5603687 TGAAAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 8 0.27
34 19 0.63
35 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (33 bp):
AAAAAATGAAAATGAAAAAAAAGAAAATGAAAA
Found at i:5603706 original size:2 final size:2
Alignment explanation
Indices: 5603699--5603723 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5603689 AAAAATGATA
5603699 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
5603724 AAAAAAATGA
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:5605001 original size:123 final size:120
Alignment explanation
Indices: 5604782--5605105 Score: 487
Period size: 123 Copynumber: 2.7 Consensus size: 120
5604772 CACTCAATGG
5604782 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCAT
*
5604847 AATGAGAAGAGTTTGTTCAACCTTTGCATGACTCTATCACAGAAGGAGATAGATCAA
65 AATGAGAAGAATTTGTTCAACCTTTGCATGACTCTATCACAGAAGGAGATAGATC-A
* *
5604904 CATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGATGAAGAAGAAGTTCAT
1 -ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCAT
* *
5604969 AAGGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCA
65 AATGAGAAGAATTTGTTCAACC-TTTGCATGACTCTATCACAGAAGGAGATAGATCA
** * * *
5605026 A-C-A--TTTCCAGA-AGTGTTCATAATGAGAAGAACTCATTTTAAAAAGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
5605086 ATGAGAAGAATTTGTTCAAC
66 ATGAGAAGAATTTGTTCAAC
5605106 TTTAAGAGAT
Statistics
Matches: 186, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
116 60 0.32
117 8 0.04
119 1 0.01
120 1 0.01
121 1 0.01
122 35 0.19
123 80 0.43
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (120 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
ATGAGAAGAATTTGTTCAACCTTTGCATGACTCTATCACAGAAGGAGATAGATCA
Found at i:5605326 original size:17 final size:16
Alignment explanation
Indices: 5605297--5605345 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
5605287 AAGATACTCA
5605297 TTTATTTATTTATTTAT
1 TTTATTTATTTA-TTAT
5605314 TTTATTTGA-TTATTAT
1 TTTATTT-ATTTATTAT
5605330 TATTA-TTA-TTATTAT
1 T-TTATTTATTTATTAT
5605345 T
1 T
5605346 ACTAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.30
16 7 0.23
17 13 0.43
18 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTATTTATTTATTAT
Found at i:5605330 original size:3 final size:3
Alignment explanation
Indices: 5605310--5605346 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
5605300 ATTTATTTAT
*
5605310 TTA TT- TTA TT- TGA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5605347 CTAAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 3 0.10
3 27 0.90
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5606731 original size:2 final size:2
Alignment explanation
Indices: 5606718--5606751 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5606708 TATATTAGTC
*
5606718 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5606752 TTGTTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5624419 original size:3 final size:3
Alignment explanation
Indices: 5624400--5624438 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
5624390 TATTTATTTG
*
5624400 ATA AAA ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA AT
5624439 TTTAAAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5624728 original size:73 final size:74
Alignment explanation
Indices: 5624635--5624782 Score: 235
Period size: 74 Copynumber: 2.0 Consensus size: 74
5624625 GAGGATTTAA
* * * *
5624635 ATATCAAAAAGCTCTCGAAGGC-TTTTTGAAAACATCCTGCACTATAGGTCTTATGGATGACTCG
1 ATATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTATAGGTCTTATGGATGACCCC
5624699 AAGGTTTTG
66 AAGGTTTTG
* *
5624708 ATATCAAAAAGCTCCCGAAGGCTTTTTTGAAATCATCATGCACTGTAGGTCTTATGGATGACCCC
1 ATATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTATAGGTCTTATGGATGACCCC
5624773 AAGGTTTTG
66 AAGGTTTTG
5624782 A
1 A
5624783 AAACATCATG
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
73 21 0.31
74 47 0.69
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (74 bp):
ATATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTATAGGTCTTATGGATGACCCC
AAGGTTTTG
Found at i:5624796 original size:45 final size:45
Alignment explanation
Indices: 5624732--5624835 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
5624722 CCGAAGGCTT
* *
5624732 TTTTGAAATCATCATGCACTGTAGGTCTTA-TGGATGACCCCAAGG
1 TTTTGAAAACATCATGCACTGTAAGTCTTACT-GATGACCCCAAGG
* *
5624777 TTTTGAAAACATCATGCACTGTAAGTCTTACTGATGTCCCGAAGG
1 TTTTGAAAACATCATGCACTGTAAGTCTTACTGATGACCCCAAGG
*
5624822 TTTTGAAAATATCA
1 TTTTGAAAACATCA
5624836 AAAAGCTCCC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
45 52 0.98
46 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGTAAGTCTTACTGATGACCCCAAGG
Found at i:5624900 original size:121 final size:119
Alignment explanation
Indices: 5624658--5624911 Score: 359
Period size: 121 Copynumber: 2.1 Consensus size: 119
5624648 CTCGAAGGCT
* * *
5624658 TTTTGAAAACATCCTGCACTATAGGTCTTATGGATGACTCGAAGGTTTTGATATCAAAAAGCTCC
1 TTTTGAAAACATCATGCACTATAAGTCTTATGGATGACCCGAAGGTTTTGATATCAAAAAGCTCC
* **
5624723 CGAAGGCTTTTTTGAAATCATCATGCACTGTAGGTCTTATGGATGACCCCAAGG
66 CGAAGGCTTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCCAAGG
* *
5624777 TTTTGAAAACATCATGCACTGTAAGTCTTACT-GATGTCCCGAAGGTTTTGAAAATATCAAAAAG
1 TTTTGAAAACATCATGCACTATAAGTCTTA-TGGATGACCCGAAGGTTTTG---ATATCAAAAAG
* *
5624841 CTCCCGAAGGC-TTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGTCCCGAAGG
62 CTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCCAAGG
*
5624898 TTTTGAAAATATCA
1 TTTTGAAAACATCA
5624912 AAAAGCTCCC
Statistics
Matches: 120, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
119 43 0.36
120 1 0.01
121 54 0.45
122 22 0.18
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (119 bp):
TTTTGAAAACATCATGCACTATAAGTCTTATGGATGACCCGAAGGTTTTGATATCAAAAAGCTCC
CGAAGGCTTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCCAAGG
Found at i:5624903 original size:76 final size:77
Alignment explanation
Indices: 5624777--5624988 Score: 345
Period size: 76 Copynumber: 2.8 Consensus size: 77
5624767 GACCCCAAGG
* *
5624777 TTTTGAAAACATCATGCACTGTAAGTCTTACTGATGTCCCGAAGGTTTTGAAAATATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGTCCCGAAGGTTTTGAAAATATCAAAAAGC
5624842 TCCCGAAGGC-T
66 TCCCGAAGGCTT
5624853 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGTCCCGAAGGTTTTGAAAATATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGTCCCGAAGGTTTTGAAAATATCAAAAAGC
5624918 TCCCGAAGGCTT
66 TCCCGAAGGCTT
* * ** * *
5624930 TTTTGAAAACATCCTGCACTATAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCA
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGTCCCGAAGGTTTTGAAAATATCA
5624989 TGCACTGTAG
Statistics
Matches: 127, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
76 73 0.57
77 54 0.43
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (77 bp):
TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGTCCCGAAGGTTTTGAAAATATCAAAAAGC
TCCCGAAGGCTT
Found at i:5624977 original size:198 final size:198
Alignment explanation
Indices: 5624593--5625104 Score: 730
Period size: 198 Copynumber: 2.6 Consensus size: 198
5624583 GAGGTCTTAT
* * * * * *
5624593 CATCTTGCACTGCAGGTCTTACAGATGACCCAGAGGA-TTT--AAATATCAAAAAGCTCTCGAAG
1 CATCATGCACTGTAAGTCTTACAGATGTCCC-GAAGATTTTGAAAATATCAAAAAGCTCCCGAAG
* * ** * *
5624655 GCTTTTTGAAAACATCCTGCACTATAGGTCTTATGGATGACTCGAAGGTTTTG---ATATCAAAA
65 GCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGTCCCGAAGGTTTTGAAAATATCAAAA
* *
5624717 AGCTCCCGAAGGCTTTTTTGAAATCATCATGCACTGTAGGTCTTATGGATGACCCCAAGGTTTTG
130 AGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTATAGGTCTTATGGATGACCCCAAGGTTTTG
5624782 AAAA
195 AAAA
* *
5624786 CATCATGCACTGTAAGTCTTACTGATGTCCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGG
1 CATCATGCACTGTAAGTCTTACAGATGTCCCGAAGATTTTGAAAATATCAAAAAGCTCCCGAAGG
5624851 CTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGTCCCGAAGGTTTTGAAAATATCAAAAA
66 CTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGTCCCGAAGGTTTTGAAAATATCAAAAA
* *
5624916 GCTCCCGAAGGCTTTTTTGAAAACATCCTGCACTATAGGTCTTATGGATGACCCGAAGGTTTTGA
131 GCTCCCGAAGGCTTTTTTGAAAACATCATGCACTATAGGTCTTATGGATGACCCCAAGGTTTTGA
5624981 AAA
196 AAA
* * * **
5624984 CATCATGCACTGTAGGTCTTACAGATGTCTCGAAGATTTTGAAAATATCAAAAAGCTTCTAAAGG
1 CATCATGCACTGTAAGTCTTACAGATGTCCCGAAGATTTTGAAAATATCAAAAAGCTCCCGAAGG
* * * *
5625049 CTTTTTGAAAACATTATACACTGTAGGTCTTACAAATGTCCTGAAGGTTTTGAAAA
66 CTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGTCCCGAAGGTTTTGAAAA
5625105 CATCCTGCAC
Statistics
Matches: 284, Mismatches: 29, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
192 3 0.01
193 29 0.10
195 68 0.24
198 184 0.65
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (198 bp):
CATCATGCACTGTAAGTCTTACAGATGTCCCGAAGATTTTGAAAATATCAAAAAGCTCCCGAAGG
CTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGTCCCGAAGGTTTTGAAAATATCAAAAA
GCTCCCGAAGGCTTTTTTGAAAACATCATGCACTATAGGTCTTATGGATGACCCCAAGGTTTTGA
AAA
Done.