Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 140 of 199
Found at i:42339882 original size:131 final size:131
Alignment explanation
Indices: 42339543--42339871 Score: 543
Period size: 131 Copynumber: 2.5 Consensus size: 131
42339533 TATCAAGCCT
* *
42339543 TATCTCCCTGAGCAGCAGTAGAGTAGGTCGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGG
* *
42339608 AGCAGATCGAAGACGACGAATCTTATCTTCTCGAGATAGTAGGAAGCAGATTTAAGCCACCAGTC
66 AGCAGATCGAAGACGACAAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCACCAGTC
42339673 C
131 C
* *
42339674 TATCTCCCTGAACAACAGTGGAGTAGGTTGAAGA-TAGTAGATCTTATCTCCCTAAGCAGTAGTG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTA-TAGATCTTATCTCCCTAAGCAGTAGTG
* ** *
42339738 AAGCAGATCGAAGACGGTAAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGGCACCAGT
65 GAGCAGATCGAAGACGACAAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCACCAGT
42339803 CC
130 CC
*
42339805 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGCAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGG
42339870 AG
66 AG
42339872 TAGGTTGAAG
Statistics
Matches: 182, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
130 2 0.01
131 178 0.98
132 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (131 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACGACAAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCACCAGTC
C
Found at i:42339918 original size:131 final size:133
Alignment explanation
Indices: 42339543--42339920 Score: 470
Period size: 131 Copynumber: 2.9 Consensus size: 133
42339533 TATCAAGCCT
* * *
42339543 TATCTCCCTGAGCAGCAGTAGAGTAGGTCGAAGATTA-TAGATCTTATCTCCCTAAGCAGTAGTG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTACTAGATCTTATCTCCCTAAGCAGCAGTG
* * * *
42339607 GAGCAGATCGAAGACGA-CGAATCTTATCT-TCT-CGAGATAGTAGGAAGCAGATTTAAGCCACC
66 GAGCAGATCGAAGACGATAG-ATCTTATCTCCCTAAGAG-TAGTAGGAAGCAGATTTAAGGCACC
42339669 AGTCC
129 AGTCC
* * * *
42339674 TATCTCCCTGAACAACAGTGGAGTAGGTTGAAGA-TAGTAGATCTTATCTCCCTAAGCAGTAGTG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTACTAGATCTTATCTCCCTAAGCAGCAGTG
* * * *
42339738 AAGCAGATCGAAGACGGTAAATCTTATCTTCCC-GAGA-TAGTAGGAAGCAGATTTAAGGCACCA
66 GAGCAGATCGAAGACGATAGATCTTATC-TCCCTAAGAGTAGTAGGAAGCAGATTTAAGGCACCA
42339801 GTCC
130 GTCC
42339805 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTA-TAGATCTTATCTCCCTAAGCAGCAGTG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTACTAGATCTTATCTCCCTAAGCAGCAGTG
* * * **
42339869 GAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGAT
66 GAGCAGATCGAAGACGATAGATCTTATCTCCCTAAG-AGTAGTAGGAAGCAGAT
42339921 CGAAGATGAC
Statistics
Matches: 215, Mismatches: 23, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
130 6 0.03
131 196 0.91
132 6 0.03
133 7 0.03
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (133 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTACTAGATCTTATCTCCCTAAGCAGCAGTG
GAGCAGATCGAAGACGATAGATCTTATCTCCCTAAGAGTAGTAGGAAGCAGATTTAAGGCACCAG
TCC
Found at i:42340071 original size:176 final size:175
Alignment explanation
Indices: 42339712--42340073 Score: 503
Period size: 176 Copynumber: 2.1 Consensus size: 175
42339702 TGAAGATAGT
** *
42339712 AGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGACGGTAAATCTTATCTTCCCGAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGACGACAAATCTTATCTTCCCAAGATA
* *
42339777 GTAGGAAGCAGATTTAAGGCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTA
66 GTAGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTA
* * * ** *
42339842 TAGATCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTAT
131 TAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACGAG
* * * *
42339887 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACGAATCTTATCTTCCCAAGGTA
1 AGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGACGACAAATCTTATCTTCCCAAGATA
* * *
42339952 TTAGGGAAGCAGATTTAAGCCACCAG-CCTTATCTCCTTAAGCTGCAGTGGAGTAGGTTGAAGAT
66 GTA-GGAAGCAGATTTAAGCCACCAGTCC-TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGAT
* *
42340016 TATAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGACG
129 TATAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACGA-G
42340064 A-ATCTTATCT
1 AGATCTTATCT
42340074 TTCCAAGGTA
Statistics
Matches: 164, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
175 62 0.38
176 101 0.62
177 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (175 bp):
AGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGACGACAAATCTTATCTTCCCAAGATA
GTAGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTA
TAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACGAG
Found at i:42340117 original size:176 final size:175
Alignment explanation
Indices: 42339712--42340120 Score: 459
Period size: 176 Copynumber: 2.3 Consensus size: 175
42339702 TGAAGATAGT
* **** * *
42339712 AGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGACGGTAAATCTTATCTTCCCGAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCACCAACCTTATCTTCCCAAGATA
* *
42339777 GTAGGAAGCAGATTTAAGGCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTA
66 GTAGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTA
* * * ** *
42339842 TAGATCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTAT
131 TAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACGAG
** * * *
42339887 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACGAATCTTATCTTCCCAAGGTA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCACCAACCTTATCTTCCCAAGATA
* * *
42339952 TTAGGGAAGCAGATTTAAGCCACCAG-CCTTATCTCCTTAAGCTGCAGTGGAGTAGGTTGAAGAT
66 GTA-GGAAGCAGATTTAAGCCACCAGTCC-TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGAT
* *
42340016 TATAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGACG
129 TATAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACGA-G
* * * **
42340064 A-ATCTTATCTTTCC-AAGGTATTAG-GGAAGCAGATTTAAG-CCACCAACCTTATCTTCC
1 AGATCTTATC-TCCCTAA-GCAGTAGTGG-AGCAGATCGAAGACCACCAACCTTATCTTCC
42340121 TGAGCAGCAG
Statistics
Matches: 199, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
175 62 0.31
176 118 0.59
177 19 0.10
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (175 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCACCAACCTTATCTTCCCAAGATA
GTAGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTA
TAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACGAG
Found at i:42340229 original size:266 final size:264
Alignment explanation
Indices: 42339847--42340389 Score: 890
Period size: 266 Copynumber: 2.0 Consensus size: 264
42339837 GATTATAGAT
*
42339847 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGT
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGT
*
42339912 GGAGCAGATCGAAGATGACGAATCTTATCTTCCCAAGGTATTAGGGAAGCAGATTTAAGCCACCA
66 GGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGGTATTAGGGAAGCAGATTTAAGCCACCA
* *
42339977 GCCTTATC-TCCTTAAGCTGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCTCTAAGCAGT
131 GCCTTATCTTCC-TAAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGT
* *
42340041 AGTGGAGCAGATCGAAGACGACGAATCTTATCTTTCCAAGGTATTAGGGAAGCAGATTTAAGCCA
195 AGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCA
42340106 CCAAC
260 CCAAC
* *
42340111 CTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGGCAGGTA
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAA-GCA-GTA
** *
42340176 GTGGAGCAGATCGAAGACGGGGAATCTTATCTTTCCAAGGTATTAGGGAAGCAGATTTAAGCCAC
64 GTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGGTATTAGGGAAGCAGATTTAAGCCAC
* * *
42340241 CAGCCTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCCG
129 CAGCCTTATCTTCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAG
* **
42340306 TAGTGGAGCAGATCGAAGATGGGGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCC
194 TAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCC
*
42340371 ACCAGC
259 ACCAAC
42340377 CTTATCTCCCTGA
1 CTTATCTCCCTGA
42340390 AGTTGCAGTG
Statistics
Matches: 257, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
264 54 0.21
265 3 0.01
266 197 0.77
267 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (264 bp):
CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGT
GGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGGTATTAGGGAAGCAGATTTAAGCCACCA
GCCTTATCTTCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCAC
CAAC
Found at i:42340389 original size:132 final size:132
Alignment explanation
Indices: 42339847--42340389 Score: 888
Period size: 132 Copynumber: 4.1 Consensus size: 132
42339837 GATTATAGAT
*
42339847 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGT
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGT
*
42339912 GGAGCAGATCGAAGATGACGAATCTTATCTTCCCAAGGTATTAGGGAAGCAGATTTAAGCCACCA
66 GGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGGTATTAGGGAAGCAGATTTAAGCCACCA
42339977 GC
131 GC
* * * *
42339979 CTTATCTCCTTAAGCTGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCTCTAAGCAGTAGT
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGT
*
42340044 GGAGCAGATCGAAGACGACGAATCTTATCTTTCCAAGGTATTAGGGAAGCAGATTTAAGCCACCA
66 GGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGGTATTAGGGAAGCAGATTTAAGCCACCA
*
42340109 AC
131 GC
* *
42340111 CTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGGCAGGTA
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAA-GCA-GTA
** *
42340176 GTGGAGCAGATCGAAGACGGGGAATCTTATCTTTCCAAGGTATTAGGGAAGCAGATTTAAGCCAC
64 GTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGGTATTAGGGAAGCAGATTTAAGCCAC
42340241 CAGC
129 CAGC
* * *
42340245 CTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCCGTAGT
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGT
* ** *
42340310 GGAGCAGATCGAAGATGGGGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCA
66 GGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGGTATTAGGGAAGCAGATTTAAGCCACCA
42340375 GC
131 GC
42340377 CTTATCTCCCTGA
1 CTTATCTCCCTGA
42340390 AGTTGCAGTG
Statistics
Matches: 389, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
132 258 0.66
133 5 0.01
134 126 0.32
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (132 bp):
CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGT
GGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGGTATTAGGGAAGCAGATTTAAGCCACCA
GC
Found at i:42340405 original size:44 final size:44
Alignment explanation
Indices: 42340357--42340581 Score: 203
Period size: 44 Copynumber: 5.2 Consensus size: 44
42340347 GTAGTAGGGA
* * *
42340357 AGCAGATTTAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTGAAGACACCAGTCTTATCTCCCTGAAGTTGCAGTGG
* *
42340401 AGCAGATT-AA-A-ACCATAGATCTTATCTCTCTGAAGTTGCAGTAG
1 AGCAGATTGAAGACACC--AG-TCTTATCTCCCTGAAGTTGCAGTGG
* *
42340445 AGCAGATT---G-CACCTAGTCTTATATCCTTGAAGTTGCAGTGG
1 AGCAGATTGAAGACACC-AGTCTTATCTCCCTGAAGTTGCAGTGG
** * * *
42340486 AGCAGACAGAAGAAACCAATCTTATCTCCCTAAAGTTGCAGTGG
1 AGCAGATTGAAGACACCAGTCTTATCTCCCTGAAGTTGCAGTGG
* * * * *
42340530 AACAGATTGAAAAAACCAATCTTATCTCCCTGAAGTTCCAGTGG
1 AGCAGATTGAAGACACCAGTCTTATCTCCCTGAAGTTGCAGTGG
*
42340574 AGCGGATT
1 AGCAGATT
42340582 AAAATGATGG
Statistics
Matches: 149, Mismatches: 23, Indels: 18
0.78 0.12 0.09
Matches are distributed among these distances:
41 30 0.20
42 3 0.02
43 7 0.05
44 106 0.71
45 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (44 bp):
AGCAGATTGAAGACACCAGTCTTATCTCCCTGAAGTTGCAGTGG
Found at i:42340596 original size:44 final size:44
Alignment explanation
Indices: 42340377--42340624 Score: 188
Period size: 44 Copynumber: 5.7 Consensus size: 44
42340367 AGCCACCAGC
*
42340377 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT---AAAACCATAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAAAAACC--A-AT
* * * * *
42340421 CTTATCTCTCTGAAGTTGCAGTAGAGCAGATTG----CACCTAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAAAAACC-AAT
* * * ** *
42340462 CTTATATCCTTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAAAAACCAAT
* * *
42340506 CTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAAAAACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAAAAACCAAT
* * ***
42340550 CTTATCTCCCTGAAGTTCCAGTGGAGCGGATT-AAAATGATGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAAA-AACCAAT
* * *
42340594 CTTATCTCTCTGAAGTTGCAATAGAGCGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCGGAT
42340625 CGCATCAGAC
Statistics
Matches: 167, Mismatches: 31, Indels: 12
0.80 0.15 0.06
Matches are distributed among these distances:
41 28 0.17
42 2 0.01
43 7 0.04
44 127 0.76
45 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAAAAACCAAT
Found at i:42342405 original size:20 final size:19
Alignment explanation
Indices: 42342365--42342409 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
42342355 AATTTATTTG
42342365 TATATA-TATGTACATACT
1 TATATATTATGTACATACT
* *
42342383 TATATATTATTTATATACTT
1 TATATATTATGTACATAC-T
42342403 TATATAT
1 TATATAT
42342410 AAACATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 9 0.39
20 8 0.35
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (19 bp):
TATATATTATGTACATACT
Found at i:42348341 original size:40 final size:40
Alignment explanation
Indices: 42348286--42348367 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
42348276 ACCACTGCTG
42348286 CTAAGTCCAAATCATGGGTAGGGTAGATACACTTATGTGA
1 CTAAGTCCAAATCATGGGTAGGGTAGATACACTTATGTGA
42348326 CTAAGTCCAAATCATGGGTAGGGTAGATACACTTATGTGA
1 CTAAGTCCAAATCATGGGTAGGGTAGATACACTTATGTGA
42348366 CT
1 CT
42348368 TAAGCTGCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (40 bp):
CTAAGTCCAAATCATGGGTAGGGTAGATACACTTATGTGA
Found at i:42357121 original size:30 final size:30
Alignment explanation
Indices: 42357087--42357149 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
42357077 AATAATATCA
* * *
42357087 ATATAT-AA-AAAGACAAGTATGTATATAT
1 ATATATAAATAAAAACAAGCATGTATACAT
*
42357115 ATATATAAATAAAAACATGCATGTATACAT
1 ATATATAAATAAAAACAAGCATGTATACAT
42357145 ATATA
1 ATATA
42357150 AATTATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.21
29 2 0.07
30 21 0.72
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (30 bp):
ATATATAAATAAAAACAAGCATGTATACAT
Found at i:42357414 original size:2 final size:2
Alignment explanation
Indices: 42357407--42357436 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
42357397 AAAGATTTAA
*
42357407 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42357437 TTTAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42357885 original size:66 final size:67
Alignment explanation
Indices: 42357786--42357912 Score: 152
Period size: 66 Copynumber: 1.9 Consensus size: 67
42357776 ATAAAAAAGG
* * *
42357786 ATATATATATGTGTATATATATATATAGGAGTTAT-GAAATATAAAACACATATAT-TATAAGAA
1 ATATATATATATATATATATATATATAGAAGTTATAG-AATATAAAACACATATATGTATAAGAA
42357849 TGC
65 TGC
* * * *
42357852 ATATATATATATATATATATATATTTTA-AAGTTATAGAATATACAATACGTATATGTATAA
1 ATATATATATATATATATATATA-TATAGAAGTTATAGAATATAAAACACATATATGTATAA
42357913 ATAAAAAGCA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
66 42 0.82
67 9 0.18
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.39
Consensus pattern (67 bp):
ATATATATATATATATATATATATATAGAAGTTATAGAATATAAAACACATATATGTATAAGAAT
GC
Found at i:42358257 original size:114 final size:113
Alignment explanation
Indices: 42358054--42358620 Score: 512
Period size: 114 Copynumber: 5.0 Consensus size: 113
42358044 TAATCATTCC
* * * *
42358054 CGGCGTTT-TTGAGAAAGCGCCGCAAAAAACCT-AGCGCAACGACG-CTGTTTCCCTAGCATTC-
1 CGGCGTTTCTTG-GAAAGCGCCGCAAAAAAACTAAGCCCAACGACGTC-GTTTCCCGAGCTTTCA
* *
42358115 GATGATTTAGCGGCGTTTTTCAGT-AAGCGCCGCTAATGCTCAAGGCTTTAG
64 G-GGATTTAGCGGCGTTTTT-AATAAAGCGCCGCTAATGCTCAAGGCTTTAG
* *
42358166 CGGCGTTTCTAGGAAAGCGCCGCAAAAATAACTAAGCCCAACGATGTCGTTTCCCGAGCTTTCAG
1 CGGCGTTTCTTGGAAAGCGCCGCAAAAA-AACTAAGCCCAACGACGTCGTTTCCCGAGCTTTCAG
* * * *
42358231 GGATTTAGCGGTGCTTTCT-ATAAAGCGCCGCTAATGGT-TAGGTCTTTAG
65 GGATTTAGCGGCG-TTTTTAATAAAGCGCCGCTAATGCTCAAGG-CTTTAG
* * * ** * *
42358280 CAGCGTTTC-TGGAAAAGTGCTGCTACTTAAAACT-AGCGCAACGACGTCGTCTCCCGAGCTTTC
1 CGGCGTTTCTTGG-AAAGCGCCGC-A-AAAAAACTAAGCCCAACGACGTCGTTTCCCGAGCTTTC
* * * *
42358343 AGGGATTTAGCGGCGCTTTTACAGAAAGCGCCGCTAATGCTGAAGTCTTTAG
63 AGGGATTTAGCGGCGTTTTTA-ATAAAGCGCCGCTAATGCTCAAGGCTTTAG
* * * * * * *
42358395 CGGCGTTT-TTGTTAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTG-GATTTCGG
1 CGGCGTTTCTTG-GAAAGCGCCGCAAAAAAACTAAGCCCAACGACGTCGTTTCCCGAGCTTTCAG
** * *
42358458 GGATTTTAGCGGCGTTTTTGTTAAAGCGCCGCTAATGTTC-AGTCTTTAG
65 GGA-TTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCTCAAGGCTTTAG
* * * * * * *
42358507 CGGCGTTTTTTGGAAAGCGCCGCAAAAAAAACTAAGCGCAACGTCGTCGTTTTCTGTGCTTTTGA
1 CGGCGTTTCTTGGAAAGCGCCGC-AAAAAAACTAAGCCCAACGACGTCGTTTCCCGAGC-TTTCA
* *
42358572 GGGATTTAGCGGCGTTTTTAGA-AAAGCGCCGCTAATGATCAAGGATTTA
64 GGGATTTAGCGGCGTTTTTA-ATAAAGCGCCGCTAATGCTCAAGGCTTTA
42358621 AAATAATTTA
Statistics
Matches: 370, Mismatches: 61, Indels: 45
0.78 0.13 0.09
Matches are distributed among these distances:
112 51 0.14
113 75 0.20
114 176 0.48
115 64 0.17
116 4 0.01
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (113 bp):
CGGCGTTTCTTGGAAAGCGCCGCAAAAAAACTAAGCCCAACGACGTCGTTTCCCGAGCTTTCAGG
GATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCTCAAGGCTTTAG
Found at i:42358485 original size:228 final size:226
Alignment explanation
Indices: 42358056--42358620 Score: 603
Period size: 228 Copynumber: 2.5 Consensus size: 226
42358046 ATCATTCCCG
* * *
42358056 GCGTTTT-TGAGAAAGCGCCGC-AAAAAACCTAGCGCAACGACG-CTGTTTCCCTAGCATTC-GA
1 GCGTTTTCTG-GAAAGCGCCGCAAAAAAAACTAGCGCAACGACGTC-GTTTCCCGAGCTTTCAG-
* * *
42358117 TGATTTAGCGGCGTTTTTCAGTAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTCTAGGAAA
63 GGATTTAGCGGCGTTTTACAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTCTAGGAAA
* * * *
42358182 GCGCCGCAAAAATAACTAAGCCCAACGATGTCGTTTCCCGAGCTTTCAGGGATTTAGCGGTGCTT
128 GCGCCGCAAAAATAACTAAGCCCAACGACGCCGTTTCCCGAGATTTCAGGGATTTAGCGGCGCTT
42358247 TCTATAAAGCGCCGCTAATGGTT-AGGTCTTTAGCA
193 TCTATAAAGCGCCGCTAAT-GTTCA-GTCTTTAGCA
* * *** *
42358282 GCG-TTTCTGGAAAAGTGCTGCTACTTAAAACTAGCGCAACGACGTCGTCTCCCGAGCTTTCAGG
1 GCGTTTTCTGG-AAAGCGCCGC-AAAAAAAACTAGCGCAACGACGTCGTTTCCCGAGCTTTCAGG
* * * *
42358346 GATTTAGCGGCGCTTTTACAGAAAGCGCCGCTAATGCTGAAGTCTTTAGCGGCGTTT-TTGTTAA
64 GATTTAGCGGCG-TTTTACAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTCTAG-GAA
* * * *
42358410 AGCGCCGCAAAAA-ACCTAAGCCCAACGACGCCGTTTTCTG-GATTTCGGGGATTTTAGCGGCG-
127 AGCGCCGCAAAAATAACTAAGCCCAACGACGCCGTTTCCCGAGATTTCAGGGA-TTTAGCGGCGC
* * *
42358472 TTTTTGTTAAAGCGCCGCTAATGTTCAGTCTTTAGCG
191 TTTCT-ATAAAGCGCCGCTAATGTTCAGTCTTTAGCA
* * * * * *
42358509 GCGTTTTTTGGAAAGCGCCGCAAAAAAAACTAAGCGCAACGTCGTCGTTTTCTGTGCTTTTGAGG
1 GCGTTTTCTGGAAAGCGCCGCAAAAAAAACT-AGCGCAACGACGTCGTTTCCCGAGC-TTTCAGG
* * *
42358574 GATTTAGCGGCGTTTT-TAGAAAAGCGCCGCTAATGATCAAGGATTTA
64 GATTTAGCGGCGTTTTACAG-AAAGCGCCGCTAATGCTCAAGGCTTTA
42358621 AAATAATTTA
Statistics
Matches: 280, Mismatches: 44, Indels: 29
0.79 0.12 0.08
Matches are distributed among these distances:
225 4 0.01
226 22 0.08
227 83 0.30
228 114 0.41
229 57 0.20
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (226 bp):
GCGTTTTCTGGAAAGCGCCGCAAAAAAAACTAGCGCAACGACGTCGTTTCCCGAGCTTTCAGGGA
TTTAGCGGCGTTTTACAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTCTAGGAAAGCG
CCGCAAAAATAACTAAGCCCAACGACGCCGTTTCCCGAGATTTCAGGGATTTAGCGGCGCTTTCT
ATAAAGCGCCGCTAATGTTCAGTCTTTAGCA
Found at i:42358903 original size:7 final size:7
Alignment explanation
Indices: 42358893--42358953 Score: 86
Period size: 7 Copynumber: 8.4 Consensus size: 7
42358883 AGAGTTAAAA
42358893 TTTAGGG
1 TTTAGGG
42358900 TTTAGAGG
1 TTTAG-GG
42358908 TTTAGGG
1 TTTAGGG
42358915 TTTAGGG
1 TTTAGGG
42358922 TTTAGGG
1 TTTAGGG
42358929 TTTAGGG
1 TTTAGGG
**
42358936 ATTTCTGG
1 -TTTAGGG
42358944 TTTAGGG
1 TTTAGGG
42358951 TTT
1 TTT
42358954 GAACGGTAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
7 36 0.75
8 12 0.25
ACGTcount: A:0.15, C:0.02, G:0.38, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:42358913 original size:15 final size:14
Alignment explanation
Indices: 42358893--42358953 Score: 86
Period size: 15 Copynumber: 4.2 Consensus size: 14
42358883 AGAGTTAAAA
42358893 TTTAGGGTTTAGAGG
1 TTTAGGGTTTAG-GG
42358908 TTTAGGGTTTAGGG
1 TTTAGGGTTTAGGG
42358922 TTTAGGGTTTAGGG
1 TTTAGGGTTTAGGG
**
42358936 ATTTCTGGTTTAGGG
1 -TTTAGGGTTTAGGG
42358951 TTT
1 TTT
42358954 GAACGGTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
14 19 0.44
15 24 0.56
ACGTcount: A:0.15, C:0.02, G:0.38, T:0.46
Consensus pattern (14 bp):
TTTAGGGTTTAGGG
Found at i:42358920 original size:22 final size:22
Alignment explanation
Indices: 42358892--42358953 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
42358882 AAGAGTTAAA
42358892 ATTTAGGGTTTAGAGGTTTAGGG
1 ATTTAGGGTTTAG-GGTTTAGGG
42358915 -TTTAGGGTTTAGGGTTTAGGG
1 ATTTAGGGTTTAGGGTTTAGGG
**
42358936 ATTTCTGGTTTAGGGTTT
1 ATTTAGGGTTTAGGGTTT
42358954 GAACGGTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 9 0.25
22 27 0.75
ACGTcount: A:0.16, C:0.02, G:0.37, T:0.45
Consensus pattern (22 bp):
ATTTAGGGTTTAGGGTTTAGGG
Found at i:42358926 original size:29 final size:29
Alignment explanation
Indices: 42358893--42358953 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
42358883 AGAGTTAAAA
42358893 TTTAGGGTTTAGAGG-TTTAGGGTTTAGGG
1 TTTAGGGTTTAG-GGATTTAGGGTTTAGGG
**
42358922 TTTAGGGTTTAGGGATTTCTGGTTTAGGG
1 TTTAGGGTTTAGGGATTTAGGGTTTAGGG
42358951 TTT
1 TTT
42358954 GAACGGTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.15, C:0.02, G:0.38, T:0.46
Consensus pattern (29 bp):
TTTAGGGTTTAGGGATTTAGGGTTTAGGG
Found at i:42359268 original size:31 final size:32
Alignment explanation
Indices: 42359225--42359299 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 32
42359215 AATAAAATTT
* *
42359225 TTTAGGGGTTATGGTTTAGGGGTTAAAGGAG-
1 TTTAGGGGTTATGCTTTAAGGGTTAAAGGAGA
* *
42359256 TTTAGGGTTTATGCTTTAAGGGTTAAAGGGGA
1 TTTAGGGGTTATGCTTTAAGGGTTAAAGGAGA
42359288 TTTAGGGGTTAT
1 TTTAGGGGTTAT
42359300 ATATGGGNNN
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
31 27 0.71
32 11 0.29
ACGTcount: A:0.23, C:0.01, G:0.37, T:0.39
Consensus pattern (32 bp):
TTTAGGGGTTATGCTTTAAGGGTTAAAGGAGA
Found at i:42362464 original size:22 final size:23
Alignment explanation
Indices: 42362439--42362501 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 23
42362429 AATAAAATTA
42362439 TATTAAAATTATTATTA-AATAT
1 TATTAAAATTATTATTAGAATAT
*
42362461 TATTAATAATTA-TATTAGTAATGT
1 TATTAA-AATTATTATTAG-AATAT
42362485 TATT-AAATTATATATTA
1 TATTAAAATTAT-TATTA
42362502 TTTTATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 16 0.46
23 6 0.17
24 13 0.37
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
TATTAAAATTATTATTAGAATAT
Found at i:42362500 original size:12 final size:11
Alignment explanation
Indices: 42362433--42362513 Score: 50
Period size: 12 Copynumber: 7.5 Consensus size: 11
42362423 CTTAATAATA
42362433 AAATTA-TATT
1 AAATTATTATT
42362443 AAAATTATTATT
1 -AAATTATTATT
42362455 AAA-TATTATT
1 AAATTATTATT
42362465 AATAATTA-TATT
1 -A-AATTATTATT
*
42362477 AGTAA-TGTTATT
1 A--AATTATTATT
42362489 AAATTATATATT
1 AAATTAT-TATT
42362501 --ATT-TTATT
1 AAATTATTATT
42362509 AAATT
1 AAATT
42362514 GTACTTAACA
Statistics
Matches: 58, Mismatches: 2, Indels: 21
0.72 0.02 0.26
Matches are distributed among these distances:
8 4 0.07
9 1 0.02
10 15 0.26
11 14 0.24
12 22 0.38
13 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (11 bp):
AAATTATTATT
Found at i:42362670 original size:9 final size:9
Alignment explanation
Indices: 42362636--42363088 Score: 207
Period size: 9 Copynumber: 52.8 Consensus size: 9
42362626 AACAACTCAA
42362636 AACTTACAT
1 AACTTACAT
* *
42362645 AACCTAAAT
1 AACTTACAT
*
42362654 AACCTACAT
1 AACTTACAT
42362663 AACTTACAT
1 AACTTACAT
*
42362672 AA--TACAA
1 AACTTACAT
*
42362679 AACTCACAT
1 AACTTACAT
*
42362688 AACTTAAAT
1 AACTTACAT
** *
42362697 CTCTTACAC
1 AACTTACAT
42362706 AACTTACAT
1 AACTTACAT
42362715 AACCTT-CAT
1 AA-CTTACAT
42362724 AA--TACATTT
1 AACTTACA--T
42362733 AACTTACAT
1 AACTTACAT
42362742 AACTTACAT
1 AACTTACAT
*
42362751 AATACATA-AT
1 -A-ACTTACAT
42362761 AACTTAC--
1 AACTTACAT
42362768 AACTTACAT
1 AACTTACAT
42362777 AA--TACATCT
1 AACTTACA--T
42362786 AACTTAC--
1 AACTTACAT
42362793 AACTTACAT
1 AACTTACAT
42362802 AA--TACATCT
1 AACTTACA--T
42362811 AACTTAC--
1 AACTTACAT
42362818 AACTTACAT
1 AACTTACAT
42362827 AA--TACATTT
1 AACTTACA--T
42362836 AACTTAC--
1 AACTTACAT
42362843 AACTTACAT
1 AACTTACAT
42362852 AA--TACATTT
1 AACTTACA--T
42362861 AACTTACAT
1 AACTTACAT
*
42362870 AACTTACGT
1 AACTTACAT
* *
42362879 AA-TCCATCTT
1 AACT-TA-CAT
42362889 AACTTACAT
1 AACTTACAT
*
42362898 AATACATA-AT
1 -A-ACTTACAT
42362908 AACTTAC--
1 AACTTACAT
42362915 AACTTACAT
1 AACTTACAT
*
42362924 AACATACAT
1 AACTTACAT
* **
42362933 TACTTTGAT
1 AACTTACAT
42362942 AACTTACAT
1 AACTTACAT
42362951 AAC-T---T
1 AACTTACAT
42362956 -ACTTACAT
1 AACTTACAT
42362964 AACTTACAT
1 AACTTACAT
42362973 AACTTACAT
1 AACTTACAT
*
42362982 AACTAACAT
1 AACTTACAT
* *
42362991 TA--TACAC
1 AACTTACAT
42362998 AACTTACAT
1 AACTTACAT
42363007 AA--TACAT
1 AACTTACAT
*
42363014 TACTTACAT
1 AACTTACAT
42363023 AACTTAAAGCAT
1 AACTT--A-CAT
42363035 AA--TA-AT
1 AACTTACAT
42363041 AACTTACAT
1 AACTTACAT
*
42363050 AA--TACAC
1 AACTTACAT
42363057 AACTTACAT
1 AACTTACAT
* *
42363066 AGCTTACAC
1 AACTTACAT
42363075 AA--TACAT
1 AACTTACAT
42363082 AACTTAC
1 AACTTAC
42363089 CCGTGCAATT
Statistics
Matches: 335, Mismatches: 47, Indels: 124
0.66 0.09 0.25
Matches are distributed among these distances:
4 2 0.01
5 2 0.01
6 5 0.01
7 81 0.24
8 14 0.04
9 184 0.55
10 15 0.04
11 27 0.08
12 5 0.01
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:42362688 original size:43 final size:43
Alignment explanation
Indices: 42362633--42362716 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
42362623 CTGAACAACT
* *
42362633 CAAAACTTACATAACCTAAATAACCTACATAACTTACATAATA
1 CAAAACTCACATAACCTAAATAACCTACACAACTTACATAATA
* ** *
42362676 CAAAACTCACATAACTTAAATCTCTTACACAACTTACATAA
1 CAAAACTCACATAACCTAAATAACCTACACAACTTACATAA
42362717 CCTTCATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (43 bp):
CAAAACTCACATAACCTAAATAACCTACACAACTTACATAATA
Found at i:42362893 original size:19 final size:19
Alignment explanation
Indices: 42362868--42362915 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
42362858 TTTAACTTAC
* * *
42362868 ATAACTTACGTAATCCATC
1 ATAACTTACATAATACATA
*
42362887 TTAACTTACATAATACATA
1 ATAACTTACATAATACATA
42362906 ATAACTTACA
1 ATAACTTACA
42362916 ACTTACATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAACTTACATAATACATA
Found at i:42362959 original size:13 final size:13
Alignment explanation
Indices: 42362943--42362970 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42362933 TACTTTGATA
42362943 ACTTACATAACTT
1 ACTTACATAACTT
42362956 ACTTACATAACTT
1 ACTTACATAACTT
42362969 AC
1 AC
42362971 ATAACTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (13 bp):
ACTTACATAACTT
Found at i:42363026 original size:25 final size:26
Alignment explanation
Indices: 42362706--42363051 Score: 290
Period size: 25 Copynumber: 13.4 Consensus size: 26
42362696 TCTCTTACAC
42362706 AACTTACATAACCTT-CATAATACATTT
1 AACTTACATAA-CTTACATAATACA-TT
42362733 AACTTACATAACTTACATAATACATAAT
1 AACTTACATAACTTACATAATACAT--T
42362761 AACTTAC--AACTTACATAATACATCT
1 AACTTACATAACTTACATAATACAT-T
42362786 AACTTAC--AACTTACATAATACATCT
1 AACTTACATAACTTACATAATACAT-T
42362811 AACTTAC--AACTTACATAATACATTT
1 AACTTACATAACTTACATAATACA-TT
42362836 AACTTAC--AACTTACATAATACATTT
1 AACTTACATAACTTACATAATACA-TT
* *
42362861 AACTTACATAACTTACGTAATCCATCTT
1 AACTTACATAACTTACATAATACA--TT
42362889 AACTTACATAA--TACATAATA-ACTT
1 AACTTACATAACTTACATAATACA-TT
* *
42362913 ACAACTTACATAACATACAT--TACTTTGAT
1 --AACTTACATAACTTACATAATAC-AT--T
42362942 AACTTACATAACTTAC-T--TACA-T
1 AACTTACATAACTTACATAATACATT
42362964 AACTTACATAACTTACATAACTAACATT
1 AACTTACATAACTTACATAA-T-ACATT
*
42362992 -A--TACACAACTTACATAATACATT
1 AACTTACATAACTTACATAATACATT
42363015 -ACTTACATAACTTAAAGCATAATA-A-T
1 AACTTACATAACTT--A-CATAATACATT
42363041 AACTTACATAA
1 AACTTACATAA
42363052 TACACAACTT
Statistics
Matches: 281, Mismatches: 11, Indels: 54
0.81 0.03 0.16
Matches are distributed among these distances:
22 17 0.06
23 7 0.02
24 4 0.01
25 106 0.38
26 47 0.17
27 65 0.23
28 34 0.12
29 1 0.00
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.34
Consensus pattern (26 bp):
AACTTACATAACTTACATAATACATT
Found at i:42363043 original size:59 final size:56
Alignment explanation
Indices: 42362942--42363066 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 56
42362932 TTACTTTGAT
*
42362942 AACTTACAT-AACTTACTTACATAACTTACATAACTTACATAACTAACATTATACAC
1 AACTTACATAAACTTACTTACATAACTTACATAAC-TACATAACTAACATAATACAC
*
42362998 AACTTACATAATACATTACTTACATAACTTAAAGCATAA-TA-ATAACTTACATAATACAC
1 AACTTACATAA-AC-TTACTTACATAACTT--A-CATAACTACATAACTAACATAATACAC
42363057 AACTTACATA
1 AACTTACATA
42363067 GCTTACACAA
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
56 9 0.15
57 1 0.02
58 2 0.03
59 41 0.67
60 2 0.03
61 1 0.02
62 5 0.08
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (56 bp):
AACTTACATAAACTTACTTACATAACTTACATAACTACATAACTAACATAATACAC
Found at i:42363045 original size:43 final size:43
Alignment explanation
Indices: 42362956--42363088 Score: 141
Period size: 43 Copynumber: 3.1 Consensus size: 43
42362946 TACATAACTT
*
42362956 ACTTACATAACTTACATAACTTACATAAC-T-AACATTATACACA
1 ACTTACATAA--TACATAACTTACATAACTTAAACATAATACACA
* *
42362999 ACTTACATAATACATTACTTACATAACTTAAAGCATAATA-ATA
1 ACTTACATAATACATAACTTACATAACTTAAA-CATAATACACA
* * * *
42363042 ACTTACATAATACACAACTTACATAGCTT--ACACAATACATA
1 ACTTACATAATACATAACTTACATAACTTAAACATAATACACA
42363083 ACTTAC
1 ACTTAC
42363089 CCGTGCAATT
Statistics
Matches: 79, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
40 6 0.08
41 26 0.33
42 1 0.01
43 40 0.51
44 6 0.08
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.30
Consensus pattern (43 bp):
ACTTACATAATACATAACTTACATAACTTAAACATAATACACA
Found at i:42368684 original size:66 final size:65
Alignment explanation
Indices: 42368576--42368741 Score: 199
Period size: 66 Copynumber: 2.5 Consensus size: 65
42368566 GAGCAAATTA
* * * * *
42368576 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGATGTTCAAAG-AAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAG-TATGAAGAACTCCA
42368640 G
65 G
*
42368641 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCA
42368706 G
65 G
* * ** *
42368707 CAGCAGCTTAGAGCAGATGTGGCAGCAAGAGAAGC
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGC
42368742 AGTGGCGGCA
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 82 0.94
67 3 0.03
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.14
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCAG
Found at i:42368790 original size:21 final size:20
Alignment explanation
Indices: 42368766--42368829 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
42368756 GAGAAGTACG
42368766 GGCTACTAAGAGGGAAGCAGA
1 GGCTAC-AAGAGGGAAGCAGA
*
42368787 GGCTA-AAGCGAGGGAAGTAGA
1 GGCTACAA--GAGGGAAGCAGA
* *
42368808 GGCTGCAGCGAGGGAAGCAGA
1 GGCTACA-AGAGGGAAGCAGA
42368829 G
1 G
42368830 CAGCGTCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 2 0.06
21 32 0.91
22 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.44, T:0.08
Consensus pattern (20 bp):
GGCTACAAGAGGGAAGCAGA
Found at i:42371445 original size:22 final size:24
Alignment explanation
Indices: 42371417--42371460 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
42371407 TATGGCAAGA
42371417 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
42371439 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
42371461 AACTTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:42372056 original size:37 final size:39
Alignment explanation
Indices: 42371997--42372092 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
42371987 CGGATAGATT
* * * *
42371997 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
42372034 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
42372073 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
42372093 TACTGGAGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:42376673 original size:2 final size:2
Alignment explanation
Indices: 42376666--42376702 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
42376656 GGTGCTTTTA
42376666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42376703 AAATAGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42377815 original size:18 final size:19
Alignment explanation
Indices: 42377789--42377836 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
42377779 ATTATTTTTA
* *
42377789 CATTCTTATTGTATTA-AT
1 CATTATTATTATATTATAT
42377807 CATTATTATTATATTATAT
1 CATTATTATTATATTATAT
42377826 -ATTATTATTAT
1 CATTATTATTAT
42377837 TATTGTACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.58
Consensus pattern (19 bp):
CATTATTATTATATTATAT
Found at i:42377816 original size:3 final size:3
Alignment explanation
Indices: 42377808--42377840 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
42377798 TGTATTAATC
42377808 ATT ATT ATT A-T ATT ATAT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
42377841 GTACCTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:42378182 original size:30 final size:30
Alignment explanation
Indices: 42378074--42378189 Score: 106
Period size: 34 Copynumber: 3.6 Consensus size: 30
42378064 ATTAATTTCA
*
42378074 ATATATGTAATTATTATTATTTGTTTTTATATAT
1 ATATATGT-A-TATAATTA-TT-TTTTTATATAT
* *
42378108 ATATATATATGTAATTATCTTTTTTATAATCTAT
1 ATATATGTATATAATTAT-TTTTTTAT-A--TAT
42378142 ATATATGTATATAATTATTTTTTTATATAT
1 ATATATGTATATAATTATTTTTTTATATAT
* * *
42378172 GTACATGTATATATTTAT
1 ATATATGTATATAATTAT
42378190 ATATTTTTTC
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
30 18 0.26
31 8 0.11
32 9 0.13
33 9 0.13
34 26 0.37
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (30 bp):
ATATATGTATATAATTATTTTTTTATATAT
Found at i:42378192 original size:24 final size:24
Alignment explanation
Indices: 42378139--42378193 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
42378129 TTTTATAATC
* *
42378139 TATATATATGTATATAATTATTTT
1 TATATATATGTACATAATTATATT
* *
42378163 TTTATATATGTACAT-GTATATATT
1 TATATATATGTACATAAT-TATATT
42378187 TATATAT
1 TATATAT
42378194 TTTTTCTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.56
Consensus pattern (24 bp):
TATATATATGTACATAATTATATT
Found at i:42378569 original size:13 final size:12
Alignment explanation
Indices: 42378536--42378582 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
42378526 TCATAGGTTA
42378536 TTATTT-TTTGT
1 TTATTTATTTGT
* *
42378547 ATATTAATTTCGT
1 TTATTTATTT-GT
42378560 TTATTTATTTGT
1 TTATTTATTTGT
42378572 TTATATTATTT
1 TTAT-TTATTT
42378583 CTATGCCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 4 0.14
12 9 0.31
13 16 0.55
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.70
Consensus pattern (12 bp):
TTATTTATTTGT
Found at i:42378888 original size:2 final size:2
Alignment explanation
Indices: 42378881--42378913 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
42378871 AAAGATTTAA
42378881 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42378914 ATAAGAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42381146 original size:13 final size:12
Alignment explanation
Indices: 42381100--42381146 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
42381090 CGTTATAGAT
42381100 TAAATTAATTTA
1 TAAATTAATTTA
* *
42381112 TAAAATATTTTA
1 TAAATTAATTTA
42381124 -AAATTTAATTGTA
1 TAAA-TTAATT-TA
42381137 TAAATTAATT
1 TAAATTAATT
42381147 CAATCTATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
11 3 0.11
12 14 0.50
13 8 0.29
14 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
TAAATTAATTTA
Found at i:42383020 original size:29 final size:29
Alignment explanation
Indices: 42382926--42383025 Score: 105
Period size: 29 Copynumber: 3.4 Consensus size: 29
42382916 CAAAAAATAA
*
42382926 AAATTACATTTTAACCCCTAATATTTT-GT
1 AAATTACATTTTAACCCCT-ATATTTTCAT
** * * *
42382955 AAATTACATTCGAGCCCCTAAACTTTCTAT
1 AAATTACATTTTAACCCCTATATTTTC-AT
42382985 AAATTACATTTTAACCCC-ATATTTTCAT
1 AAATTACATTTTAACCCCTATATTTTCAT
42383013 GAAATTACATTTT
1 -AAATTACATTTT
42383026 TGCCCCAGAA
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
28 7 0.12
29 34 0.60
30 16 0.28
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (29 bp):
AAATTACATTTTAACCCCTATATTTTCAT
Found at i:42383031 original size:59 final size:59
Alignment explanation
Indices: 42382926--42383040 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 59
42382916 CAAAAAATAA
* *
42382926 AAATTACATTTTAACCCCTAATATTTTGTAAATTACATTCGAGCCCC-TAAACTTTCTAT
1 AAATTACATTTTAACCCC-AATATTTTATAAATTACATTCGAGCCCCAGAAACTTTCTAT
***
42382985 AAATTACATTTTAACCCC-ATATTTTCATGAAATTACATTTTTGCCCCAGAAACTTT
1 AAATTACATTTTAACCCCAATATTTT-AT-AAATTACATTCGAGCCCCAGAAACTTT
42383041 GCACCCGTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
57 7 0.15
58 1 0.02
59 33 0.69
60 7 0.15
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (59 bp):
AAATTACATTTTAACCCCAATATTTTATAAATTACATTCGAGCCCCAGAAACTTTCTAT
Found at i:42383333 original size:17 final size:17
Alignment explanation
Indices: 42383289--42383334 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
42383279 CCCTCGCCAC
*
42383289 CGTCGCGCCACCACCGT
1 CGTCGCGCCACCACCAT
*
42383306 CGTTGCGCCACCACCAT
1 CGTCGCGCCACCACCAT
*
42383323 CGTCGCTCCACC
1 CGTCGCGCCACC
42383335 GCCGAAACCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.13, C:0.52, G:0.20, T:0.15
Consensus pattern (17 bp):
CGTCGCGCCACCACCAT
Found at i:42383404 original size:24 final size:23
Alignment explanation
Indices: 42383366--42383415 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
42383356 AAGCAAGCAT
42383366 AAACAAAAAAAACAGCAAACAAG
1 AAACAAAAAAAACAGCAAACAAG
*
42383389 AAACAACAAAAAACAGCAAAGAAG
1 AAACAA-AAAAAACAGCAAACAAG
42383413 AAA
1 AAA
42383416 AAGGAGAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.74, C:0.16, G:0.10, T:0.00
Consensus pattern (23 bp):
AAACAAAAAAAACAGCAAACAAG
Found at i:42384087 original size:10 final size:10
Alignment explanation
Indices: 42384074--42384126 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
42384064 TTTTTAAGTA
42384074 TTTTTTTA-T
1 TTTTTTTATT
*
42384083 TTTTTGTATT
1 TTTTTTTATT
42384093 TATGTTTTTATT
1 T-T-TTTTTATT
*
42384105 TTATTTTATT
1 TTTTTTTATT
*
42384115 TTATTTTATT
1 TTTTTTTATT
42384125 TT
1 TT
42384127 ATTCGTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
9 7 0.18
10 21 0.55
11 2 0.05
12 8 0.21
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:42384108 original size:5 final size:5
Alignment explanation
Indices: 42384098--42384129 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
42384088 GTATTTATGT
42384098 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
42384130 CGTTAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:42384459 original size:18 final size:18
Alignment explanation
Indices: 42384436--42384481 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
42384426 AAACTAATTG
42384436 TGTTTCAAAAATTT-TCA
1 TGTTTCAAAAATTTCTCA
*
42384453 TGTTTTC-AAAATTTCTCG
1 TG-TTTCAAAAATTTCTCA
42384471 TGTTTCAAAAA
1 TGTTTCAAAAA
42384482 ATAATACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (18 bp):
TGTTTCAAAAATTTCTCA
Found at i:42384550 original size:17 final size:17
Alignment explanation
Indices: 42384530--42384761 Score: 117
Period size: 18 Copynumber: 12.8 Consensus size: 17
42384520 AAAAAAACTT
42384530 CGTGTTTCAAAAATTTC
1 CGTGTTTCAAAAATTTC
* *
42384547 CGTGTTTTTAAAAATTTT
1 CGTG-TTTCAAAAATTTC
* * *
42384565 CGCGTTTTAAAAATTTT
1 CGTGTTTCAAAAATTTC
42384582 CGTGTTTTCAAAAAAATTTCC
1 CGTG-TTTC--AAAAATTT-C
42384603 CGTGTTTTCAAAAA-TTC
1 CGTG-TTTCAAAAATTTC
* **
42384620 TCGTATTTC-GTAATTTC
1 -CGTGTTTCAAAAATTTC
* *
42384637 CTTGTTTTTAGAAAAAATTTC
1 C--GTGTTT--CAAAAATTTC
* * *
42384658 CATGTTTTATAAATTTC
1 CGTGTTTCAAAAATTTC
*
42384675 CGTGTTTTCAAAAAATTC
1 CGTG-TTTCAAAAATTTC
* * *
42384693 CTGTCTTTTAAAAATTTT
1 C-GTGTTTCAAAAATTTC
* *
42384711 TGTGGTTTCAAAAAAATTGAC
1 CGT-GTTTC--AAAAATT-TC
*
42384732 CGTGTTTCATAAATTTC
1 CGTGTTTCAAAAATTTC
42384749 CGTGTTTCAAAAA
1 CGTGTTTCAAAAA
42384762 AAATCCTCGT
Statistics
Matches: 163, Mismatches: 34, Indels: 36
0.70 0.15 0.15
Matches are distributed among these distances:
16 3 0.02
17 54 0.33
18 57 0.35
19 11 0.07
20 20 0.12
21 18 0.11
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (17 bp):
CGTGTTTCAAAAATTTC
Found at i:42384577 original size:35 final size:35
Alignment explanation
Indices: 42384528--42384595 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
42384518 AAAAAAAAAC
* *
42384528 TTCGTGTTTCAAAAATTTCCGTGTTTTTAAAAATT
1 TTCGCGTTTCAAAAATTTCCGTGTTTTCAAAAATT
* *
42384563 TTCGCGTTTTAAAAATTTTCGTGTTTTCAAAAA
1 TTCGCGTTTCAAAAATTTCCGTGTTTTCAAAAA
42384596 AATTTCCCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (35 bp):
TTCGCGTTTCAAAAATTTCCGTGTTTTCAAAAATT
Found at i:42384606 original size:21 final size:20
Alignment explanation
Indices: 42384538--42384763 Score: 86
Period size: 17 Copynumber: 12.2 Consensus size: 20
42384528 TTCGTGTTTC
*
42384538 AAAAATTTCCGTGTTTT--T
1 AAAAATTTCCGTGTTTTCAA
* *
42384556 AAAAATTTTCGCGTTTT---
1 AAAAATTTCCGTGTTTTCAA
*
42384573 AAAAATTTTCGTGTTTTCAA
1 AAAAATTTCCGTGTTTTCAA
42384593 AAAAATTTCCCGTGTTTTC--
1 AAAAATTT-CCGTGTTTTCAA
*
42384612 AAAAA-TTCTCGT-ATTTC--
1 AAAAATTTC-CGTGTTTTCAA
** * *
42384629 -GTAATTTCCTTGTTTTTAGA
1 AAAAATTTCCGTGTTTTCA-A
*
42384649 AAAAATTTCCATGTTTT---
1 AAAAATTTCCGTGTTTTCAA
*
42384666 ATAAATTTCCGTGTTTTC-A
1 AAAAATTTCCGTGTTTTCAA
*
42384685 AAAAA-TTCC-TGTCTTT--T
1 AAAAATTTCCGTGT-TTTCAA
** *
42384702 AAAAATTTTTGTGGTTTCAA
1 AAAAATTTCCGTGTTTTCAA
*
42384722 AAAAATTGACCGTG-TTTC--
1 AAAAATT-TCCGTGTTTTCAA
*
42384740 ATAAATTTCCGTG-TTTCAA
1 AAAAATTTCCGTGTTTTCAA
42384759 AAAAA
1 AAAAA
42384764 ATCCTCGTGT
Statistics
Matches: 160, Mismatches: 27, Indels: 41
0.70 0.12 0.18
Matches are distributed among these distances:
16 4 0.03
17 59 0.37
18 38 0.24
19 15 0.09
20 19 0.12
21 25 0.16
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (20 bp):
AAAAATTTCCGTGTTTTCAA
Found at i:42384689 original size:37 final size:36
Alignment explanation
Indices: 42384631--42384763 Score: 119
Period size: 38 Copynumber: 3.6 Consensus size: 36
42384621 CGTATTTCGT
* *
42384631 AATTTCCTTGTTTTTAGAAAAAATTTCCATGTTTTATA
1 AATTTCCGTGTTTTCA-AAAAAATTTCC-TGTTTTATA
*
42384669 AATTTCCGTGTTTTC-AAAAAA-TTCCTGTCTTTTAAA
1 AATTTCCGTGTTTTCAAAAAAATTTCCTG--TTTTATA
** * * *
42384705 AATTTTTGTGGTTTCAAAAAAATTGACCGTGTTTCATA
1 AATTTCCGTGTTTTCAAAAAAATT-TCC-TGTTTTATA
42384743 AATTTCCGTG-TTTCAAAAAAA
1 AATTTCCGTGTTTTCAAAAAAA
42384764 ATCCTCGTGT
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
34 2 0.03
35 4 0.05
36 24 0.31
37 17 0.22
38 27 0.35
39 2 0.03
40 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.44
Consensus pattern (36 bp):
AATTTCCGTGTTTTCAAAAAAATTTCCTGTTTTATA
Found at i:42384702 original size:36 final size:35
Alignment explanation
Indices: 42384530--42384780 Score: 122
Period size: 37 Copynumber: 6.9 Consensus size: 35
42384520 AAAAAAACTT
* * * *
42384530 CGTG-TTTCAAAAATTTCCGTGTTTTTAAAAATTTT
1 CGTGTTTTCAAAAAATTCC-TGTTTTCATAAATTTC
* * * *
42384565 CGCGTTTT-AAAAATTTTCGTGTTTTCAAAAAAATTTCC
1 CGTGTTTTCAAAAA-ATTCCTGTTTTC--ATAAATTT-C
*
42384603 CGTGTTTTC-AAAAATT-CTCGTATTTCGT-AATTTC
1 CGTGTTTTCAAAAAATTCCT-GT-TTTCATAAATTTC
* *
42384637 CTTGTTTTTAGAAAAAATTTCCATGTTTT-ATAAATTTC
1 CGTG-TTTT-CAAAAAA-TTCC-TGTTTTCATAAATTTC
* * *
42384675 CGTGTTTTCAAAAAATTCCTGTCTTTTAAAAATTTT
1 CGTGTTTTCAAAAAATTCCTGT-TTTCATAAATTTC
* *
42384711 TGTGGTTTCAAAAAAATTGACC-GTGTTTCATAAATTTC
1 CGTGTTTTC-AAAAAATT--CCTGT-TTTCATAAATTTC
*
42384749 CGTG-TTTCAAAAAAAATCCTCGTGTTTCATAA
1 CGTGTTTTC-AAAAAATTCCT-GT-TTTCATAA
42384781 TTTATCAAAA
Statistics
Matches: 170, Mismatches: 24, Indels: 42
0.72 0.10 0.18
Matches are distributed among these distances:
34 7 0.04
35 32 0.19
36 28 0.16
37 53 0.31
38 44 0.26
39 5 0.03
40 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.44
Consensus pattern (35 bp):
CGTGTTTTCAAAAAATTCCTGTTTTCATAAATTTC
Found at i:42384773 original size:37 final size:37
Alignment explanation
Indices: 42384595--42384780 Score: 127
Period size: 37 Copynumber: 5.1 Consensus size: 37
42384585 GTTTTCAAAA
* *
42384595 AAATTTCCCGTGTTTTC--AAAAATT-CTCGTATTTCGT
1 AAATTT-CCGTG-TTTCAAAAAAATTCCTCGTGTTTCAT
* * * * *
42384631 -AATTTCCTTGTTTTTAGAAAAAATTTC-CATGTTTTAT
1 AAATTTCCGTG-TTTCA-AAAAAATTCCTCGTGTTTCAT
* * *
42384668 AAATTTCCGTGTTTTC-AAAAAATTCCT-GTCTTTTAA
1 AAATTTCCGTG-TTTCAAAAAAATTCCTCGTGTTTCAT
** *
42384704 AAATTTTTGTGGTTTCAAAAAAATTGAC-CGTGTTTCAT
1 AAATTTCCGT-GTTTCAAAAAAATT-CCTCGTGTTTCAT
*
42384742 AAATTTCCGTGTTTCAAAAAAAATCCTCGTGTTTCAT
1 AAATTTCCGTGTTTCAAAAAAATTCCTCGTGTTTCAT
42384779 AA
1 AA
42384781 TTTATCAAAA
Statistics
Matches: 117, Mismatches: 22, Indels: 21
0.73 0.14 0.13
Matches are distributed among these distances:
34 8 0.07
35 5 0.04
36 28 0.24
37 47 0.40
38 29 0.25
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (37 bp):
AAATTTCCGTGTTTCAAAAAAATTCCTCGTGTTTCAT
Found at i:42384831 original size:19 final size:19
Alignment explanation
Indices: 42384804--42384845 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42384794 TTGTGTTCTC
* *
42384804 AAAATAAAATTTTGTATTT
1 AAAAAAAAATTGTGTATTT
*
42384823 AAAAAAAAATTGTGTTTTT
1 AAAAAAAAATTGTGTATTT
42384842 AAAA
1 AAAA
42384846 TTATTGTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (19 bp):
AAAAAAAAATTGTGTATTT
Found at i:42384845 original size:17 final size:16
Alignment explanation
Indices: 42384825--42384866 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
42384815 TTGTATTTAA
42384825 AAAAAAATTGTGTTTTT
1 AAAAAAATTGTG-TTTT
**
42384842 AAAATTATTGTGTTTT
1 AAAAAAATTGTGTTTT
42384858 AAAAAAATT
1 AAAAAAATT
42384867 TCATGCTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (16 bp):
AAAAAAATTGTGTTTT
Found at i:42391391 original size:1 final size:1
Alignment explanation
Indices: 42391387--42391454 Score: 55
Period size: 1 Copynumber: 68.0 Consensus size: 1
42391377 TAAAAAAGAC
* * * * * * * * *
42391387 AAAAAAAAATAAAAATAAAAAAATAAAAACAAAAAAATAAAAAAAAACAAAGAAAAGAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
42391452 AAA
1 AAA
42391455 TCAAGATGAA
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.87, C:0.03, G:0.04, T:0.06
Consensus pattern (1 bp):
A
Found at i:42391406 original size:14 final size:13
Alignment explanation
Indices: 42391387--42391448 Score: 79
Period size: 14 Copynumber: 4.5 Consensus size: 13
42391377 TAAAAAAGAC
42391387 AAAAAAAAATAAA
1 AAAAAAAAATAAA
42391400 AATAAAAAAATAAA
1 AA-AAAAAAATAAA
42391414 AACAAAAAAATAAA
1 AA-AAAAAAATAAA
*
42391428 AAAAAACAAAGAAA
1 AAAAAA-AAATAAA
*
42391442 AGAAAAA
1 AAAAAAA
42391449 GAAAAATCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
13 7 0.16
14 37 0.84
ACGTcount: A:0.87, C:0.03, G:0.03, T:0.06
Consensus pattern (13 bp):
AAAAAAAAATAAA
Found at i:42391442 original size:22 final size:22
Alignment explanation
Indices: 42391388--42391431 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
42391378 AAAAAAGACA
*
42391388 AAAAAAAATAAAAATAAAAAAAT
1 AAAAACAA-AAAAATAAAAAAAT
42391411 AAAAACAAAAAAATAAAAAAA
1 AAAAACAAAAAAATAAAAAAA
42391432 AACAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.89, C:0.02, G:0.00, T:0.09
Consensus pattern (22 bp):
AAAAACAAAAAAATAAAAAAAT
Found at i:42392566 original size:158 final size:156
Alignment explanation
Indices: 42392239--42393002 Score: 810
Period size: 158 Copynumber: 4.8 Consensus size: 156
42392229 TATTTTTTAA
* * * *
42392239 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTTGGGT-CATGATGAGGTATTTCTTTAA
1 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTA
* * **
42392303 AATATCTGTTTTT---TAAATCAACTCATAATATGAGAGGTGAGTTGAGCCTCGGGTCACGCTGA
66 AATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGA
*
42392365 GGTATTTTTTTAAATTTAATTTCTGTTTTC
131 GGTATTTTTTTAAA-TT--TCT-TGTTTTC
* * *
42392395 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTGTTTCTTTT
1 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTT
* * *
42392459 AAATTTCTGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCGCACGC
65 AAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT--CACGC
42392524 TGAGGTATTTCTTTTAAATTTC-TGTTTTC
128 TGAGGTATTT-TTTTAAATTTCTTGTTTTC
* *
42392553 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTT-TTTT
1 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTT
*
42392616 AAATTTCTGTTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGC
65 AAATTTCTG--TTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGC
*
42392680 TGAGGTATTTTTTTTAAATTTAAATTCTATTTTTTTTC
128 TGAGGTA-TTTTTTTAAA--T---TTC---TTGTTTTC
*
42392718 AAAAAAATCAACTCATAATAC-AGAGGTGAGTCGAGCCTCGGGT-CACGCTGAGGTATTTCTTTT
1 -AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTT
* * *
42392781 AATTTAATTTCTATTTTTTCAAAAAAATCAACTCATAATAC-AGATGTGAGTTGAGCCTCGGGTC
65 -A---AATTTCT-GTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC
*
42392845 ACGCTGAGGTA--TTTTTAAATTTCTATTTTTTTC
124 ACGCTGAGGTATTTTTTTAAATTTC--TTGTTTTC
* *
42392878 AAAAAATCAACTCATAATAC-AGAGGTGAGTTGTGCCTCGGGTCACAC-ATCGAGGTA--T-TTT
1 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC-CACGCT-GAGGTATTTCTTT
** * * *
42392938 CCAATTTCTATTTTTTCAAAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTTGGGTCAC
64 TAAATTTCT-GTTTTTC--AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
42393003 ATGCCGATGT
Statistics
Matches: 537, Mismatches: 36, Indels: 70
0.84 0.06 0.11
Matches are distributed among these distances:
154 15 0.03
155 59 0.11
156 42 0.08
157 44 0.08
158 110 0.20
159 46 0.09
160 46 0.09
161 15 0.03
162 17 0.03
163 7 0.01
164 16 0.03
165 10 0.02
166 30 0.06
167 17 0.03
168 6 0.01
169 40 0.07
170 17 0.03
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (156 bp):
AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTA
AATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGA
GGTATTTTTTTAAATTTCTTGTTTTC
Found at i:42392597 original size:78 final size:76
Alignment explanation
Indices: 42392239--42393002 Score: 751
Period size: 80 Copynumber: 9.6 Consensus size: 76
42392229 TATTTTTTAA
* * * *
42392239 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTTGGGTCATGATGAGGTATTTCTTTAAA
1 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT-TTTTAA
*
42392304 ATATCTGTTTT-
65 ATTTCTGTTTTC
** *
42392315 -TTAAATCAACTCATAATATGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTAAA
1 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTT--A
42392379 TTTAATTTCTGTTTTC
64 ---AATTTCTGTTTTC
* * *
42392395 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTGTTTCTTTT
1 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTATTT-TTTT
42392459 AAATTTCTGCTTTTC
63 AAATTTCTG-TTTTC
* * *
42392474 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCGCACGCTGAGGTATTTCTTTT
1 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTATTT-TTTT
42392539 AAATTTCTGTTTTC
63 AAATTTCTGTTTTC
* *
42392553 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTA
1 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTATTTTTTTA
42392617 AATTTCTGTTTTTTTC
64 AATTTCTG---TTTTC
* *
42392633 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAA
1 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TTTTTTTAA
*
42392697 ATTTAAATTCTATTTTTTTTC
65 A--T---TTC----TGTTTTC
*
42392718 AAAAAAATCAACTCATAATAC-AGAGGTGAGTCGAGCCTCGGGTCACGCTGAGGTATTTCTTTTA
1 -AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT-TTTT-
*
42392782 ATTTAATTTCTATTTTTTC
63 A---AATTTC--TGTTTTC
*
42392801 AAAAAAATCAACTCATAATAC-AGATGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--TTTTTAA
1 -AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTAA
*
42392863 ATTTCTATTTTTTTC
65 ATTTC---TGTTTTC
* * **
42392878 AAAAAATCAACTCATAATAC-AGAGGTGAGTTGTGCCTCGGGTCACACATCGAGGTA--TTTTCC
1 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGC-T-GAGGTATTTTTTTA
*
42392940 AATTTCTATTTTTTC
64 AATTTC--TGTTTTC
* * *
42392955 AAAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTTGGGTCAC
1 --AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCAC
42393003 ATGCCGATGT
Statistics
Matches: 614, Mismatches: 37, Indels: 70
0.85 0.05 0.10
Matches are distributed among these distances:
74 3 0.00
75 51 0.08
76 51 0.08
77 28 0.05
78 94 0.15
79 51 0.08
80 181 0.29
81 3 0.00
82 14 0.02
83 65 0.11
84 3 0.00
85 11 0.02
86 37 0.06
87 18 0.03
88 2 0.00
90 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (76 bp):
AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTAAA
TTTCTGTTTTC
Found at i:42393004 original size:78 final size:76
Alignment explanation
Indices: 42392786--42393051 Score: 313
Period size: 76 Copynumber: 3.4 Consensus size: 76
42392776 CTTTTAATTT
* *
42392786 AATTTCTATTTTTTCAAAAAAATCAACTCATAATACAGATGTGAGTTGAGCCTCGGGTCAC-GCT
1 AATTTCTATTTTTTCAAAAAAATCAACTCATAATACAGAAGTGAGTTGAGCCTCGGGTCACATC-
*
42392850 GAGGTATTTTTA
65 GAGGTATTTTTC
* *
42392862 AATTTCTATTTTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGTGCCTCGGGTCACACA
1 AATTTCTA-TTTTTTCAAAAAAATCAACTCATAATACAGAAGTGAGTTGAGCCTCGGGT--CACA
*
42392926 TCGAGGTATTTTCC
63 TCGAGGTATTTTTC
* *
42392940 AATTTCTATTTTTTCAAAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTTGGGTCACAT
1 AATTTCTATTTTTTC-AAAAAAATCAACTCATAATAC-AGAAGTGAGTTGAGCCTCGGGTCACAT
*
42393005 GCCGATGTATTTTTC
64 --CGAGGTATTTTTC
** *
42393020 AATTTTCGT-TTTTTAAAAAAAAATTAACTCAT
1 AA-TTTC-TATTTTTTCAAAAAAATCAACTCAT
42393052 GGCTCGAGAG
Statistics
Matches: 165, Mismatches: 14, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
76 48 0.29
77 14 0.08
78 26 0.16
79 20 0.12
80 47 0.28
81 9 0.05
82 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (76 bp):
AATTTCTATTTTTTCAAAAAAATCAACTCATAATACAGAAGTGAGTTGAGCCTCGGGTCACATCG
AGGTATTTTTC
Found at i:42393472 original size:29 final size:28
Alignment explanation
Indices: 42393396--42393479 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 28
42393386 CAAAAAATAA
*
42393396 AAATTACATTTTAACCCCTAATATTTTGT
1 AAATTACATTTTAA-CCCTAATATTTTAT
** *
42393425 AAATTACATTCGAGCCCCTAA-ACTTTCTAT
1 AAATTACATTTTA-ACCCTAATA-TTT-TAT
42393455 AAATTACATTTTAACCCT-ATATTTT
1 AAATTACATTTTAACCCTAATATTTT
42393480 CGTGACATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
27 1 0.02
28 5 0.11
29 25 0.57
30 13 0.30
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.42
Consensus pattern (28 bp):
AAATTACATTTTAACCCTAATATTTTAT
Found at i:42393501 original size:59 final size:60
Alignment explanation
Indices: 42393396--42393510 Score: 146
Period size: 59 Copynumber: 1.9 Consensus size: 60
42393386 CAAAAAATAA
*
42393396 AAATTACATTTTAACCCCTAATATTTTGTAAATTACATTCGAGCCCC-TAAACTTTCTAT
1 AAATTACATTTTAACCCCTAATATTTTGTAAATTACATTCGAGCCCCAGAAACTTTCTAT
* ***
42393455 AAATTACATTTTAA-CCCT-ATATTTTCGTGACATTACATTTTTGCCCCAGAAACTTT
1 AAATTACATTTTAACCCCTAATATTTT-GT-AAATTACATTCGAGCCCCAGAAACTTT
42393511 GCACCAGTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
57 7 0.15
58 6 0.12
59 28 0.58
60 7 0.15
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
AAATTACATTTTAACCCCTAATATTTTGTAAATTACATTCGAGCCCCAGAAACTTTCTAT
Found at i:42393856 original size:24 final size:23
Alignment explanation
Indices: 42393818--42393867 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
42393808 AAGCAAGCAT
42393818 AAACAAAAAAAACAGCAAACAAG
1 AAACAAAAAAAACAGCAAACAAG
*
42393841 AAACAACAAAAAACAGCAAAGAAG
1 AAACAA-AAAAAACAGCAAACAAG
42393865 AAA
1 AAA
42393868 AAAGAGAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.74, C:0.16, G:0.10, T:0.00
Consensus pattern (23 bp):
AAACAAAAAAAACAGCAAACAAG
Found at i:42394536 original size:11 final size:10
Alignment explanation
Indices: 42394509--42394535 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
42394499 TATTATCGCA
42394509 TATTTTTAAG
1 TATTTTTAAG
42394519 TATTTTTAAG
1 TATTTTTAAG
42394529 TATTTTT
1 TATTTTT
42394536 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (10 bp):
TATTTTTAAG
Found at i:42394552 original size:13 final size:13
Alignment explanation
Indices: 42394531--42394582 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
42394521 TTTTTAAGTA
42394531 TTTT-TTTTATTT
1 TTTTATTTTATTT
*
42394543 TTTGTA-TTTATGT
1 TTT-TATTTTATTT
42394556 TTTTATTTTATTTT
1 TTTTATTTTA-TTT
42394570 ATTTTATTTTATT
1 -TTTTATTTTATT
42394583 CGTTAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 5 0.15
13 14 0.42
14 4 0.12
15 10 0.30
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:42394566 original size:5 final size:5
Alignment explanation
Indices: 42394529--42394582 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
42394519 TATTTTTAAG
* *
42394529 TATTT T-TTT TATTT T-TTG TATTT ATGTTTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT -T-ATTT TATTT TATTT TATTT TATTT
42394579 TATT
1 TATT
42394583 CGTTAAAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
4 7 0.17
5 29 0.71
6 2 0.05
7 3 0.07
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:42394579 original size:21 final size:21
Alignment explanation
Indices: 42394534--42394579 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
42394524 TTAAGTATTT
*
42394534 TTTTTATTTTTTGTATTTATG
1 TTTTTATTTTTTGTATTTATA
*
42394555 TTTTTATTTTATTTTATTT-TA
1 TTTTTATTTT-TTGTATTTATA
42394576 TTTT
1 TTTT
42394580 ATTCGTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.80
Consensus pattern (21 bp):
TTTTTATTTTTTGTATTTATA
Found at i:42394906 original size:18 final size:18
Alignment explanation
Indices: 42394883--42394928 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
42394873 AAACTAATTG
42394883 TGTTTCAAAAATTT-TCA
1 TGTTTCAAAAATTTCTCA
*
42394900 TGTTTTC-AAAATTTCTCG
1 TG-TTTCAAAAATTTCTCA
42394918 TGTTTCAAAAA
1 TGTTTCAAAAA
42394929 ATAATACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (18 bp):
TGTTTCAAAAATTTCTCA
Found at i:42394995 original size:17 final size:17
Alignment explanation
Indices: 42394975--42395205 Score: 101
Period size: 18 Copynumber: 12.8 Consensus size: 17
42394965 AAAAAAACTT
42394975 CGTGTTTCAAAAATTTC
1 CGTGTTTCAAAAATTTC
*
42394992 CGTGTTTTTAAAAATTTC
1 CGTG-TTTCAAAAATTTC
* *
42395010 CGTGTTTTAAAAATTTT
1 CGTGTTTCAAAAATTTC
42395027 CGTGTTTTCAAAAAAATTTCC
1 CGTG-TTTC--AAAAATTT-C
42395048 CGTGTTTTCAAAAA-TTC
1 CGTG-TTTCAAAAATTTC
* **
42395065 TCGTATTTC-GTAATTTC
1 -CGTGTTTCAAAAATTTC
**
42395082 TTTGTTTTCAGAAAAAATTTC
1 CGTG-TTTC---AAAAATTTC
* * * *
42395103 CATGTTTTATAAATTTT
1 CGTGTTTCAAAAATTTC
*
42395120 CGTGTTTTCAAAAAATTC
1 CGTG-TTTCAAAAATTTC
* * *
42395138 ATGTCTTTTAAAAATTT-
1 -CGTGTTTCAAAAATTTC
*
42395155 -GTGTTTTCAAAAAAATTGAC
1 CGTG-TTTC--AAAAATT-TC
* *
42395175 AGTGTTTCATAAATTTC
1 CGTGTTTCAAAAATTTC
42395192 CGTGTTTCTAAAAA
1 CGTGTTTC-AAAAA
42395206 AATCCTCGTG
Statistics
Matches: 160, Mismatches: 33, Indels: 41
0.68 0.14 0.18
Matches are distributed among these distances:
15 2 0.01
16 6 0.04
17 50 0.31
18 60 0.38
19 7 0.04
20 15 0.09
21 20 0.12
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (17 bp):
CGTGTTTCAAAAATTTC
Found at i:42395004 original size:18 final size:18
Alignment explanation
Indices: 42394983--42395063 Score: 101
Period size: 17 Copynumber: 4.4 Consensus size: 18
42394973 TTCGTGTTTC
42394983 AAAAATTTCCGTGTTTTT
1 AAAAATTTCCGTGTTTTT
42395001 AAAAATTTCCGTG-TTTT
1 AAAAATTTCCGTGTTTTT
* *
42395018 AAAAATTTTCGTGTTTTCAA
1 AAAAATTTCCGTGTTTT--T
*
42395038 AAAAATTTCCCGTGTTTTC
1 AAAAATTT-CCGTGTTTTT
42395057 AAAAATT
1 AAAAATT
42395064 CTCGTATTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
17 16 0.29
18 16 0.29
19 7 0.13
20 8 0.15
21 8 0.15
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (18 bp):
AAAAATTTCCGTGTTTTT
Found at i:42395147 original size:36 final size:36
Alignment explanation
Indices: 42395107--42395208 Score: 102
Period size: 35 Copynumber: 2.8 Consensus size: 36
42395097 AATTTCCATG
42395107 TTTTATAAATTTTCGTGTTTTCAAAAAATT-CATGTC
1 TTTTATAAATTTTCGTGTTTTCAAAAAATTACA-GTC
* *
42395143 TTTTA-AAAATTT-GTGTTTTCAAAAAAATTGACAGTG
1 TTTTATAAATTTTCGTGTTTTC-AAAAAATT-ACAGTC
* * *
42395179 TTTCATAAATTTCCGTGTTTCTAAAAAAAT
1 TTTTATAAATTTTCGTGTTT-TCAAAAAAT
42395209 CCTCGTGTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
34 8 0.15
35 14 0.26
36 11 0.20
37 7 0.13
38 13 0.24
39 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (36 bp):
TTTTATAAATTTTCGTGTTTTCAAAAAATTACAGTC
Found at i:42395226 original size:72 final size:71
Alignment explanation
Indices: 42395040--42395226 Score: 164
Period size: 72 Copynumber: 2.6 Consensus size: 71
42395030 GTTTTCAAAA
* * * * **
42395040 AAATTTCCCGTGTTTT-CAAAAATTCTCGTATTTCGTAATTTCTTTGTTTTCAGAAAAAATTTCC
1 AAATTT-CCGTGTTTTAAAAAAATCCTCGTATTTCATAA-TT-TGTGTTTTCAGAAAAAATTGAC
*
42395104 ATGTTTTAT
63 ATGTTTCAT
* * * * * *
42395113 AAATTTTCGTGTTTTCAAAAAATTCAT-GTCTTTTAAAAATTTGTGTTTTCA-AAAAAATTGACA
1 AAATTTCCGTGTTTT-AAAAAAATCCTCGT-ATTTCATAATTTGTGTTTTCAGAAAAAATTGACA
42395176 GTGTTTCAT
64 -TGTTTCAT
*
42395185 AAATTTCCGTGTTTCTAAAAAAATCCTCGTGTTTCATAATTT
1 AAATTTCCGTGTTT-TAAAAAAATCCTCGTATTTCATAATTT
42395227 ATCAAAATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 13
0.74 0.16 0.11
Matches are distributed among these distances:
71 10 0.11
72 55 0.62
73 13 0.15
74 11 0.12
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.45
Consensus pattern (71 bp):
AAATTTCCGTGTTTTAAAAAAATCCTCGTATTTCATAATTTGTGTTTTCAGAAAAAATTGACATG
TTTCAT
Found at i:42395261 original size:21 final size:19
Alignment explanation
Indices: 42395230--42395345 Score: 69
Period size: 19 Copynumber: 6.0 Consensus size: 19
42395220 ATAATTTATC
*
42395230 AAAATTTTTGTGTTCTCAAAA
1 AAAAATTTTGTGTT-T-AAAA
* *
42395251 TAAAATTTTGTATTTAAAA
1 AAAAATTTTGTGTTTAAAA
*
42395270 AAAAATTTTGTGTTT---T
1 AAAAATTTTGTGTTTAAAA
* *
42395286 TAAAATTATTGTGTTT-TAA
1 AAAAATT-TTGTGTTTAAAA
*
42395305 AAAAATTTCGTGCTTTCAAAA
1 AAAAATTTTGTG-TTT-AAAA
**
42395326 AAAAAAGTTGTGTTTCAAAA
1 AAAAATTTTGTGTTT-AAAA
42395346 TTATCGTGTT
Statistics
Matches: 75, Mismatches: 14, Indels: 13
0.74 0.14 0.13
Matches are distributed among these distances:
16 6 0.08
17 8 0.11
18 4 0.05
19 26 0.35
20 9 0.12
21 22 0.29
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.43
Consensus pattern (19 bp):
AAAAATTTTGTGTTTAAAA
Found at i:42395290 original size:16 final size:16
Alignment explanation
Indices: 42395271--42395306 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
42395261 TATTTAAAAA
42395271 AAAATT-TTGTGTTTTT
1 AAAATTATTGTG-TTTT
42395287 AAAATTATTGTGTTTT
1 AAAATTATTGTGTTTT
42395303 AAAA
1 AAAA
42395307 AAATTTCGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (16 bp):
AAAATTATTGTGTTTT
Found at i:42395290 original size:17 final size:17
Alignment explanation
Indices: 42395270--42395307 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
42395260 GTATTTAAAA
42395270 AAAAATT-TTGTGTTTT
1 AAAAATTATTGTGTTTT
*
42395286 TAAAATTATTGTGTTTT
1 AAAAATTATTGTGTTTT
42395303 AAAAA
1 AAAAA
42395308 AATTTCGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (17 bp):
AAAAATTATTGTGTTTT
Found at i:42395341 original size:20 final size:22
Alignment explanation
Indices: 42395303--42395345 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
42395293 ATTGTGTTTT
*
42395303 AAAAAAATTTCGTGCTTTCAAA
1 AAAAAAAGTTCGTGCTTTCAAA
42395325 AAAAAAAGTT-GTG-TTTCAAA
1 AAAAAAAGTTCGTGCTTTCAAA
42395345 A
1 A
42395346 TTATCGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 3 0.15
22 9 0.45
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (22 bp):
AAAAAAAGTTCGTGCTTTCAAA
Found at i:42396744 original size:3 final size:3
Alignment explanation
Indices: 42396738--42396770 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
42396728 AAAATATTAC
*
42396738 TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42396771 ACTGAATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:42397932 original size:24 final size:24
Alignment explanation
Indices: 42397895--42397940 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
42397885 GACTGTGGAC
*
42397895 ATTTTAAAATTTGGTTTTATTTTT
1 ATTTTAAAATTTGGGTTTATTTTT
42397919 ATTTATAAAA-TTGGGTTTATTT
1 ATTT-TAAAATTTGGGTTTATTT
42397941 GCTAAGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (24 bp):
ATTTTAAAATTTGGGTTTATTTTT
Found at i:42399112 original size:21 final size:21
Alignment explanation
Indices: 42399088--42399130 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
42399078 TTCTTGGGTT
42399088 GCCTCAGGTGTCTTATTGTTC
1 GCCTCAGGTGTCTTATTGTTC
42399109 GCCTCAGGTGTCTTATTGTTC
1 GCCTCAGGTGTCTTATTGTTC
42399130 G
1 G
42399131 GTGTTCCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.23, G:0.26, T:0.42
Consensus pattern (21 bp):
GCCTCAGGTGTCTTATTGTTC
Found at i:42399933 original size:13 final size:13
Alignment explanation
Indices: 42399915--42399942 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42399905 ATTTAGCTTA
42399915 TTCTAGCAATAAT
1 TTCTAGCAATAAT
42399928 TTCTAGCAATAAT
1 TTCTAGCAATAAT
42399941 TT
1 TT
42399943 AAGATAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (13 bp):
TTCTAGCAATAAT
Found at i:42400629 original size:45 final size:45
Alignment explanation
Indices: 42400517--42400682 Score: 187
Period size: 45 Copynumber: 3.7 Consensus size: 45
42400507 TATCGTTGGA
* * * * ** *
42400517 AATATAGGTGGATGCTATGTGCTGATTCCACCCGATA-TTAT-GAA
1 AATAAAGGTGGTTGCTATGTGCTGATTTCACCGGATACCAATAG-T
42400561 AATAAAGGTGGTTGCTATGTGCTGATTTCACCGGATACCAATAGT
1 AATAAAGGTGGTTGCTATGTGCTGATTTCACCGGATACCAATAGT
* * *
42400606 AATATAGGTGGTTGCTATCTGCTGATTTCACCCGG-TACCATTGAGT
1 AATAAAGGTGGTTGCTATGTGCTGATTTCA-CCGGATACCAAT-AGT
42400652 -ATAAAGGTGGTTGCTATGTGCTGATTTCACC
1 AATAAAGGTGGTTGCTATGTGCTGATTTCACC
42400683 AGTACTATTG
Statistics
Matches: 106, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
44 35 0.33
45 63 0.59
46 8 0.08
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (45 bp):
AATAAAGGTGGTTGCTATGTGCTGATTTCACCGGATACCAATAGT
Found at i:42404975 original size:20 final size:20
Alignment explanation
Indices: 42404952--42404990 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42404942 AAATGTAACA
*
42404952 ATTAAATTAAAAATAAAAAT
1 ATTAAAATAAAAATAAAAAT
42404972 ATTAAAATAAAAATAAAAA
1 ATTAAAATAAAAATAAAAA
42404991 ATGGCTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
ATTAAAATAAAAATAAAAAT
Found at i:42440842 original size:20 final size:20
Alignment explanation
Indices: 42440817--42440883 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
42440807 TACTGAAGTA
42440817 CAATCAGGGGCACGTATGTG
1 CAATCAGGGGCACGTATGTG
* *
42440837 CAATCAGGGGTACCG-A---A
1 CAATCAGGGGCA-CGTATGTG
42440854 CAAAT-AGGGGCACGTATGTG
1 C-AATCAGGGGCACGTATGTG
42440874 CAATCAGGGG
1 CAATCAGGGG
42440884 TACCGAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
16 2 0.06
17 8 0.22
18 3 0.08
19 3 0.08
20 18 0.50
21 2 0.06
ACGTcount: A:0.30, C:0.19, G:0.34, T:0.16
Consensus pattern (20 bp):
CAATCAGGGGCACGTATGTG
Found at i:42440863 original size:37 final size:39
Alignment explanation
Indices: 42440805--42440919 Score: 146
Period size: 37 Copynumber: 2.9 Consensus size: 39
42440795 GTGCATTCAA
*
42440805 GGTACTGAAGTAC-AATCAGGGGCACGTATGTGCAATCAGG
1 GGTACCGAA-TACAAAT-AGGGGCACGTATGTGCAATCAGG
42440845 GGTACCG-A-ACAAATAGGGGCACGTATGTGCAATCAGG
1 GGTACCGAATACAAATAGGGGCACGTATGTGCAATCAGG
* * *
42440882 GGTACCGAATTACAAGTAGGGGCACATGTGTGCAATCA
1 GGTACCGAA-TACAAATAGGGGCACGTATGTGCAATCA
42440920 TACAATAATT
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
37 32 0.48
38 4 0.06
39 1 0.01
40 30 0.45
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.19
Consensus pattern (39 bp):
GGTACCGAATACAAATAGGGGCACGTATGTGCAATCAGG
Found at i:42441235 original size:16 final size:15
Alignment explanation
Indices: 42441198--42441240 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
42441188 TTTTCATCTT
*
42441198 TTACTTAATTAGCAT
1 TTACTTAATTAGCAA
*
42441213 TTAACTTAATTATCAAA
1 TT-ACTTAATTAGC-AA
42441230 TTACTTAATTA
1 TTACTTAATTA
42441241 ACCTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 19 0.79
17 3 0.12
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (15 bp):
TTACTTAATTAGCAA
Found at i:42441248 original size:32 final size:31
Alignment explanation
Indices: 42441198--42441269 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
42441188 TTTTCATCTT
* *
42441198 TTACTTAATTAGCATTTAACTTAATTATCA-AA
1 TTACTTAATTAACATTTAA--AAATTATCATAA
*
42441230 TTACTTAATTAACCTTTAAAAATTATCATAA
1 TTACTTAATTAACATTTAAAAATTATCATAA
42441261 TTACATTAA
1 TTAC-TTAA
42441270 AAACCTATCC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.23
31 6 0.17
32 21 0.60
ACGTcount: A:0.43, C:0.12, G:0.01, T:0.43
Consensus pattern (31 bp):
TTACTTAATTAACATTTAAAAATTATCATAA
Found at i:42446600 original size:39 final size:40
Alignment explanation
Indices: 42446551--42446647 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 40
42446541 TATAAACAAC
* *
42446551 GGCACATATGTGCAATCAGAG-TATCGAAGTACAAACAGA
1 GGCACGTATGTGCAATCAGAGTTACCGAAGTACAAACAGA
* * *
42446590 GGCACGTATGTGCAATCAGGGTTACCGAAGTACAAATAGG
1 GGCACGTATGTGCAATCAGAGTTACCGAAGTACAAACAGA
*
42446630 GGCACGTATGCGCAATCA
1 GGCACGTATGTGCAATCA
42446648 TACAATAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 19 0.37
40 32 0.63
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.19
Consensus pattern (40 bp):
GGCACGTATGTGCAATCAGAGTTACCGAAGTACAAACAGA
Found at i:42446950 original size:16 final size:14
Alignment explanation
Indices: 42446927--42446970 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 14
42446917 TTTTCATCTT
42446927 TTACTTAATTAAAA
1 TTACTTAATTAAAA
42446941 TTTAACTTAATTATCAAA
1 -TT-ACTTAATTA--AAA
42446959 TTACTTAATTAA
1 TTACTTAATTAA
42446971 CCTTTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 2 0.08
16 18 0.69
17 2 0.08
18 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (14 bp):
TTACTTAATTAAAA
Found at i:42446977 original size:32 final size:31
Alignment explanation
Indices: 42446927--42446998 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
42446917 TTTTCATCTT
*
42446927 TTACTTAATTAAAATTTAACTTAATTATCA-AA
1 TTACTTAATTAAAATTTAA--AAATTATCATAA
**
42446959 TTACTTAATTAACCTTTAAAAATTATCATAA
1 TTACTTAATTAAAATTTAAAAATTATCATAA
42446990 TTACATTAA
1 TTAC-TTAA
42446999 AACCTATCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.23
31 6 0.17
32 21 0.60
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (31 bp):
TTACTTAATTAAAATTTAAAAATTATCATAA
Found at i:42458011 original size:180 final size:180
Alignment explanation
Indices: 42457692--42458036 Score: 521
Period size: 180 Copynumber: 1.9 Consensus size: 180
42457682 AAGCATGTAA
* * * *
42457692 TAGGGGACATTCCAATTTTGTTTCACCCCCAATGAATACCCATTGAATAGCTCTTTTATTTCCAT
1 TAGGGGAAATTCCAATTCTGTTTCACCCCCAATGAATACCCATTGAATAGCTCTATCATTTCCAT
* *
42457757 TTTACCTTTCCGTTTTCTCACCTCAAGAAAGCTCTCACTCAGCCCGATCTCAGTCCCAACCTCCC
66 TTTACCTTTCCATTTTCTCACCTCAAGAAAGCTCTCACTCAGCCCAATCTCAGTCCCAACCTCCC
* *
42457822 TTGCTTCCTTCGTCTCCAGCCAATAGCAATCCTCCTAGTTAAACCTTTAT
131 TTACTTCCTTCGTCTACAGCCAATAGCAATCCTCCTAGTTAAACCTTTAT
* * * *
42457872 TAGGGGAAATTCCTATTCTGTTTCACCCCTACTGAATACCCATTGAATAGCTCTATCGTTTCCAT
1 TAGGGGAAATTCCAATTCTGTTTCACCCCCAATGAATACCCATTGAATAGCTCTATCATTTCCAT
* * *
42457937 TTTACCTTAT-CATTTTCTCACCTCAAGAAAGCTCTCACTCAGCCTAATCTCAGTCCCGACCTCT
66 TTTACCTT-TCCATTTTCTCACCTCAAGAAAGCTCTCACTCAGCCCAATCTCAGTCCCAACCTCC
* *
42458001 CTTACTTCCTTCGTCTATAGCCAATAGCAGTCCTCC
130 CTTACTTCCTTCGTCTACAGCCAATAGCAATCCTCC
42458037 ATTAGGTACA
Statistics
Matches: 147, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
180 146 0.99
181 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (180 bp):
TAGGGGAAATTCCAATTCTGTTTCACCCCCAATGAATACCCATTGAATAGCTCTATCATTTCCAT
TTTACCTTTCCATTTTCTCACCTCAAGAAAGCTCTCACTCAGCCCAATCTCAGTCCCAACCTCCC
TTACTTCCTTCGTCTACAGCCAATAGCAATCCTCCTAGTTAAACCTTTAT
Found at i:42463223 original size:11 final size:11
Alignment explanation
Indices: 42463209--42463238 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
42463199 TTAGCCCATC
42463209 ATTAATTAGAA
1 ATTAATTAGAA
42463220 ATTAATTAGAA
1 ATTAATTAGAA
*
42463231 CTTAATTA
1 ATTAATTA
42463239 CTAGAGTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (11 bp):
ATTAATTAGAA
Found at i:42466019 original size:17 final size:18
Alignment explanation
Indices: 42465987--42466021 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42465977 CCATGATGTT
*
42465987 CGCCCGTGTGGGCCCACA
1 CGCCCATGTGGGCCCACA
42466005 CGCCCATGT-GGCCCACA
1 CGCCCATGTGGGCCCACA
42466022 TGACCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.46, G:0.29, T:0.11
Consensus pattern (18 bp):
CGCCCATGTGGGCCCACA
Found at i:42470017 original size:13 final size:13
Alignment explanation
Indices: 42470001--42470032 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
42469991 TGGATATAAT
42470001 ATATATACACACA
1 ATATATACACACA
42470014 ATATATACACACA
1 ATATATACACACA
42470027 AT-TATA
1 ATATATA
42470033 ATAATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (13 bp):
ATATATACACACA
Found at i:42470766 original size:22 final size:22
Alignment explanation
Indices: 42470741--42470782 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
42470731 CATAAAATTA
42470741 AAAAAGAA-AAACGAATCAATCC
1 AAAAAGAATAAA-GAATCAATCC
*
42470763 AAAAATAATAAAGAATCAAT
1 AAAAAGAATAAAGAATCAAT
42470783 TCATTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.67, C:0.12, G:0.07, T:0.14
Consensus pattern (22 bp):
AAAAAGAATAAAGAATCAATCC
Found at i:42473252 original size:43 final size:43
Alignment explanation
Indices: 42473200--42473298 Score: 153
Period size: 43 Copynumber: 2.3 Consensus size: 43
42473190 AAAAGGAGAT
*
42473200 TTAATTAAAATTTTATGATAATATATCAATAATTTTAAAATAA
1 TTAATTAAAATTTGATGATAATATATCAATAATTTTAAAATAA
**
42473243 TTAATTAAAAAATGATGATAATATATCAATAATTTTAAAATAA
1 TTAATTAAAATTTGATGATAATATATCAATAATTTTAAAATAA
*
42473286 ATAATTATAAATT
1 TTAATTA-AAATT
42473299 AAAAGCATAG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
43 46 0.94
44 3 0.06
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (43 bp):
TTAATTAAAATTTGATGATAATATATCAATAATTTTAAAATAA
Found at i:42473285 original size:22 final size:22
Alignment explanation
Indices: 42473208--42473285 Score: 61
Period size: 22 Copynumber: 3.6 Consensus size: 22
42473198 ATTTAATTAA
**
42473208 AATTTTATGATAATATATCAAT
1 AATTTTAAAATAATATATCAAT
*
42473230 AATTTTAAAATAAT-TAATTAA-
1 AATTTTAAAATAATAT-ATCAAT
** * **
42473251 AAAATGATGATAATATATCAAT
1 AATTTTAAAATAATATATCAAT
42473273 AATTTTAAAATAA
1 AATTTTAAAATAA
42473286 ATAATTATAA
Statistics
Matches: 39, Mismatches: 14, Indels: 6
0.66 0.24 0.10
Matches are distributed among these distances:
21 14 0.36
22 25 0.64
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTTTAAAATAATATATCAAT
Found at i:42485531 original size:13 final size:13
Alignment explanation
Indices: 42485510--42485554 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
42485500 TGACTTGGGT
*
42485510 CACATGGCCAAGC
1 CACACGGCCAAGC
42485523 CACACGGCCAAGC
1 CACACGGCCAAGC
42485536 CACACGGCCAAGC
1 CACACGGCCAAGC
42485549 CACACG
1 CACACG
42485555 CCTATGTGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.31, C:0.44, G:0.22, T:0.02
Consensus pattern (13 bp):
CACACGGCCAAGC
Found at i:42489073 original size:16 final size:16
Alignment explanation
Indices: 42489052--42489090 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
42489042 TGAATTATTG
*
42489052 ATTACAGCTCTATTCC
1 ATTACAGCCCTATTCC
*
42489068 ATTACAACCCTATTCC
1 ATTACAGCCCTATTCC
42489084 ATTACAG
1 ATTACAG
42489091 TGAACCAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (16 bp):
ATTACAGCCCTATTCC
Found at i:42491782 original size:24 final size:25
Alignment explanation
Indices: 42491745--42491792 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
42491735 TCAAGTTTTC
*
42491745 CGTTATATGGTTCTT-GCGAGCTTCT
1 CGTTATATAGTTCTTCG-GAGCTTCT
42491770 CGTTA-ATAGTTCTTCGGAGCTTC
1 CGTTATATAGTTCTTCGGAGCTTC
42491793 CTGATCAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.42
Consensus pattern (25 bp):
CGTTATATAGTTCTTCGGAGCTTCT
Found at i:42491907 original size:26 final size:25
Alignment explanation
Indices: 42491878--42491926 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
42491868 GAGCTTATTG
*
42491878 ATTAAAGGCTCTTTGTGAGCTTCCTA
1 ATTAAAGGCTCTCTG-GAGCTTCCTA
*
42491904 ATTAATGGCTCTCTGGAGCTTCC
1 ATTAAAGGCTCTCTGGAGCTTCC
42491927 CGATATGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (25 bp):
ATTAAAGGCTCTCTGGAGCTTCCTA
Found at i:42491948 original size:23 final size:23
Alignment explanation
Indices: 42491908--42491955 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
42491898 TTCCTAATTA
* * *
42491908 ATGGCTCTCTGGAGCTTCCCGAT
1 ATGGCTCGCTGGAACTTCCCAAT
*
42491931 ATGGCTCGCTTGAACTTCCCAAT
1 ATGGCTCGCTGGAACTTCCCAAT
42491954 AT
1 AT
42491956 ATGGTTATCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (23 bp):
ATGGCTCGCTGGAACTTCCCAAT
Found at i:42492090 original size:25 final size:25
Alignment explanation
Indices: 42492062--42492109 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42492052 TACAGCCTGG
*
42492062 ATAAGCTTCCCCTTACATGGCTCAC
1 ATAAGATTCCCCTTACATGGCTCAC
* *
42492087 ATAAGATTCCCGTTATATGGCTC
1 ATAAGATTCCCCTTACATGGCTC
42492110 GAGAGAGGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (25 bp):
ATAAGATTCCCCTTACATGGCTCAC
Found at i:42494424 original size:74 final size:73
Alignment explanation
Indices: 42494303--42494447 Score: 263
Period size: 74 Copynumber: 2.0 Consensus size: 73
42494293 TCTCGGGTTT
*
42494303 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTT-AAA
42494368 ACTTGAGGA
65 ACTTGAGGA
*
42494377 AAAAAAGGGATCATGCCTAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
42494442 CTTGAG
66 CTTGAG
42494448 TTTGAAAAGA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 10 0.14
74 59 0.86
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (73 bp):
AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
CTTGAGGA
Found at i:42494855 original size:49 final size:48
Alignment explanation
Indices: 42494801--42495004 Score: 150
Period size: 51 Copynumber: 4.2 Consensus size: 48
42494791 TAAAGAAAAT
* *
42494801 AAAATTATAAAAATATAAAAAGATATATTTGTATATATATATGTATATA
1 AAAATTATAAAAATAT-AAAAGATATATATGTATATATATATATATATA
* * * *
42494850 AAAATTAT-AAAATATAAAATATATATAAGTATGTATATATATACATTTATG
1 AAAATTATAAAAATAT-AAA-AGATAT-A-TATGTATATATATATATATATA
* * * * * *
42494901 AAAATGA-AAAAAT-T--ATGCATATAGATATATATATATATGTGTATA
1 AAAATTATAAAAATATAAAAG-ATATATATGTATATATATATATATATA
* * * *
42494946 TAAATTAT-AAAATATAAAACATATATAAGTATGTATATATATATATAA
1 AAAATTATAAAAATATAAAAGATATATATGTATATATATATATATAT-A
42494994 ATAAATTATAA
1 A-AAATTATAA
42495005 CATTATGTAC
Statistics
Matches: 117, Mismatches: 26, Indels: 23
0.70 0.16 0.14
Matches are distributed among these distances:
45 26 0.22
46 2 0.02
47 25 0.21
48 13 0.11
49 20 0.17
50 3 0.03
51 28 0.24
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.38
Consensus pattern (48 bp):
AAAATTATAAAAATATAAAAGATATATATGTATATATATATATATATA
Found at i:42494996 original size:37 final size:34
Alignment explanation
Indices: 42494940--42495069 Score: 102
Period size: 37 Copynumber: 3.5 Consensus size: 34
42494930 TATATATATG
*
42494940 TGTATATAAAT-TATAAAATATAAAACATATATAAGTA
1 TGTATATATATATAT-AAATATAAAACAT-TAT--GTA
*
42494977 TGTATATATATATATAAATAAATTATAACATTATGTA
1 TGTATATATATATATAAAT--A-TAAAACATTATGTA
42495014 CTTGTATATATATATATATATATTATAAAA-ATGTATGTA
1 --TGTATATATATATATA-A-A-TATAAAACAT-TATGTA
*
42495053 TGTATATATATGTATAA
1 TGTATATATATATATAA
42495070 CGAAATTTGA
Statistics
Matches: 79, Mismatches: 4, Indels: 21
0.76 0.04 0.20
Matches are distributed among these distances:
36 1 0.01
37 32 0.41
38 5 0.06
39 30 0.38
40 9 0.11
41 1 0.01
42 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.42
Consensus pattern (34 bp):
TGTATATATATATATAAATATAAAACATTATGTA
Found at i:42495020 original size:39 final size:39
Alignment explanation
Indices: 42494974--42495069 Score: 119
Period size: 37 Copynumber: 2.5 Consensus size: 39
42494964 ACATATATAA
*
42494974 GTATGTATATATATATATAAATAAATTAT-AACAT-TAT
1 GTATGTATATATATATATAAATAAATTATAAAAATGTAT
*
42495011 GTACTTGTATATATATATAT--ATATATTATAAAAATGTAT
1 GTA--TGTATATATATATATAAATAAATTATAAAAATGTAT
*
42495050 GTATGTATATATATGTATAA
1 GTATGTATATATATATATAA
42495070 CGAAATTTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
37 25 0.50
38 4 0.08
39 21 0.42
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (39 bp):
GTATGTATATATATATATAAATAAATTATAAAAATGTAT
Found at i:42495025 original size:96 final size:95
Alignment explanation
Indices: 42494832--42495045 Score: 272
Period size: 96 Copynumber: 2.2 Consensus size: 95
42494822 GATATATTTG
* *
42494832 TATATATATATGTATATAAAAATTATAAAATATAAAATATATATAAGTATGTATATATATACATT
1 TATATATATATGTATATAAAAATTATAAAATATAAAACATATATAAGTATGTATATATATACATA
*
42494897 TATGAAAATGAAAAAATTATGCATATAGATA
66 AAT-AAAATGAAAAAATTATGCATATAGATA
* * *
42494928 TATATATATATGTGTATATAAATTATAAAATATAAAACATATATAAGTATGTATATATATATATA
1 TATATATATATGTATATAAAAATTATAAAATATAAAACATATATAAGTATGTATATATATACATA
* * * *
42494993 AAT-AAATTATAACATTATG--TACTTGTATA
66 AATAAAATGAAAAAATTATGCATA-TAG-ATA
*
42495022 TATATATATATATATTATAAAAAT
1 TATATATATATGTA-TATAAAAAT
42495046 GTATGTATGT
Statistics
Matches: 102, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
92 2 0.02
93 2 0.02
94 28 0.27
95 8 0.08
96 62 0.61
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.40
Consensus pattern (95 bp):
TATATATATATGTATATAAAAATTATAAAATATAAAACATATATAAGTATGTATATATATACATA
AATAAAATGAAAAAATTATGCATATAGATA
Found at i:42496996 original size:94 final size:94
Alignment explanation
Indices: 42496830--42497000 Score: 211
Period size: 94 Copynumber: 1.8 Consensus size: 94
42496820 GATTCATTAT
* *
42496830 TTTAATCCGCACCACTGCAACTTCTGGGAGATAAGATTATTAGCTTCAGTCTGCTCTACTGCAAC
1 TTTAATCCGCACCACTGCAACTTCAGGGAGATAAGATTATTAGCTTCAATCTGCTCTACTGCAAC
42496895 TTCAGGGAGATAAGACTTGTTATGGTAGA
66 TTCAGGGAGATAAGACTTGTTATGGTAGA
* * * * * * *
42496924 TTTAATTCG-ACCTACTGCAATTTCAGGGAGATAGGATTCATT-GTTTTAATCTGCTCTGCTGTA
1 TTTAATCCGCACC-ACTGCAACTTCAGGGAGATAAGATT-ATTAGCTTCAATCTGCTCTACTGCA
* *
42496987 ATTTTAGGGAGATA
64 ACTTCAGGGAGATA
42497001 GTATTAGTAG
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
93 3 0.05
94 58 0.91
95 3 0.05
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (94 bp):
TTTAATCCGCACCACTGCAACTTCAGGGAGATAAGATTATTAGCTTCAATCTGCTCTACTGCAAC
TTCAGGGAGATAAGACTTGTTATGGTAGA
Found at i:42497091 original size:50 final size:50
Alignment explanation
Indices: 42497037--42497200 Score: 157
Period size: 50 Copynumber: 3.3 Consensus size: 50
42497027 TGCAATGTCG
* * *
42497037 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATATATTCCACTGCACCTCCA
1 GGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTATTCCACTGCACCTCCA
* * * ** ** ***
42497087 GGGAAGGAAGATTCATCGTTGTGGCTTCAATCTTTTTAACTGCAATTTTG
1 GGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTATTCCACTGCACCTCCA
** * * *
42497137 GGGAAACAAGATTCGTCGTTATGGCTTCAATCTGTTCCACTGCACCGCCA
1 GGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTATTCCACTGCACCTCCA
*
42497187 GGAAAGTAAGATTC
1 GGGAAGTAAGATTC
42497201 TCTATTGTCG
Statistics
Matches: 85, Mismatches: 29, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (50 bp):
GGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTATTCCACTGCACCTCCA
Found at i:42497188 original size:100 final size:100
Alignment explanation
Indices: 42497010--42497200 Score: 256
Period size: 100 Copynumber: 1.9 Consensus size: 100
42497000 AGTATTAGTA
* ** *
42497010 GCTTCGATCATTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATATATTCC
1 GCTTCAATCATTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTTATAGCTTCAATATATTCC
* *
42497075 ACTGCACCTCCAGGGAAGGAAGATTCATCGTTGTG
66 ACTGCACCGCCAGGAAAGGAAGATTCATCGTTGTG
* * * * * * *
42497110 GCTTCAATCTTTTTAACTGCAATTTTGGGGAAACAAGATTCGTCGTTATGGCTTCAATCTGTTCC
1 GCTTCAATCATTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTTATAGCTTCAATATATTCC
*
42497175 ACTGCACCGCCAGGAAAGTAAGATTC
66 ACTGCACCGCCAGGAAAGGAAGATTC
42497201 TCTATTGTCG
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
100 77 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (100 bp):
GCTTCAATCATTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTTATAGCTTCAATATATTCC
ACTGCACCGCCAGGAAAGGAAGATTCATCGTTGTG
Found at i:42509165 original size:74 final size:73
Alignment explanation
Indices: 42509082--42509226 Score: 227
Period size: 74 Copynumber: 2.0 Consensus size: 73
42509072 ATCTCAGTTT
* * * * *
42509082 AAAAAAGGGATCATGCCAAGTAAGTTAGGACACGATCTTTTCTTAATTCTCGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCAAGTAAGTTAGAACACGATCTCTTCTTAATTCCCGAGATCATAT-AAA
42509147 ACTTGAGGA
65 ACTTGAGGA
*
42509156 AAAAAAGGGATCATGCCCAGTAAGTTAGAACACGATCTCTTCTTAATTCCCGAGATCATATAAAA
1 AAAAAAGGGATCATGCCAAGTAAGTTAGAACACGATCTCTTCTTAATTCCCGAGATCATATAAAA
42509221 CTTGAG
66 CTTGAG
42509227 TGGAAAAGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
73 10 0.15
74 55 0.85
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (73 bp):
AAAAAAGGGATCATGCCAAGTAAGTTAGAACACGATCTCTTCTTAATTCCCGAGATCATATAAAA
CTTGAGGA
Found at i:42509608 original size:2 final size:2
Alignment explanation
Indices: 42509601--42509668 Score: 52
Period size: 2 Copynumber: 35.5 Consensus size: 2
42509591 ATATAAAAAG
* * * * *
42509601 AT AT AT AT GT AT AT AT AT GT AT AT AA AA AT -T AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
42509641 A- AA AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42509669 CATTTATGAA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
1 3 0.06
2 50 0.94
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:42509653 original size:39 final size:38
Alignment explanation
Indices: 42509584--42509664 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 38
42509574 AAAATAAAAT
* *
42509584 TATAAAAATATAAAAAGATATATATGTATATATATGTA
1 TATAAAAATATAAAAAGATAAATATATATATATATGTA
*
42509622 TATAAAAAT-TATAAAATATAAAATATATATATATATGTA
1 TATAAAAATATA-AAAAGAT-AAATATATATATATATGTA
42509661 TATA
1 TATA
42509665 TATACATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 2 0.05
38 15 0.39
39 21 0.55
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (38 bp):
TATAAAAATATAAAAAGATAAATATATATATATATGTA
Found at i:42509690 original size:99 final size:96
Alignment explanation
Indices: 42509587--42509763 Score: 241
Period size: 97 Copynumber: 1.8 Consensus size: 96
42509577 ATAAAATTAT
* *
42509587 AAAAATAT-AAAAAGATATATATGTATATATATGTATATAAAAATTATAAAATATAAAATATATA
1 AAAAATATCAAAAAGATATATA--TATAGATATGTATAT--AAATTATAAAATATAAAACATATA
42509651 TATA-TATGTATATATATACATTTATGAAAATGAAA
62 TA-AGTATGTATATATATACATTTATGAAAATGAAA
* *
42509686 AAAAATATGCATATAGATATATATATAGATATGTATATAAATTATAAAATATAAAACATATATAA
1 AAAAATAT-CAAAAAGATATATATATAGATATGTATATAAATTATAAAATATAAAACATATATAA
*
42509751 GTATGTGTATATA
65 GTATGTATATATA
42509764 AAATAAATTA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
96 1 0.01
97 36 0.51
99 22 0.31
101 11 0.16
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (96 bp):
AAAAATATCAAAAAGATATATATATAGATATGTATATAAATTATAAAATATAAAACATATATAAG
TATGTATATATATACATTTATGAAAATGAAA
Found at i:42509760 original size:39 final size:37
Alignment explanation
Indices: 42509704--42509778 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 37
42509694 GCATATAGAT
42509704 ATATATATAGATATGTATATAAATTATAAAATATAAAAC
1 ATATATATAGATATGTATATAAA--ATAAAATATAAAAC
* *
42509743 ATATATA-AGTATGTGTATATAAAATAAATTATAAAA
1 ATATATATAG-ATATGTATATAAAATAAAATATAAAA
42509779 TTATGTACGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 12 0.36
38 2 0.06
39 19 0.58
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (37 bp):
ATATATATAGATATGTATATAAAATAAAATATAAAAC
Found at i:42509808 original size:31 final size:32
Alignment explanation
Indices: 42509728--42509829 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 32
42509718 GTATATAAAT
* *
42509728 TATAAAATATAAAACATATATAAGTATGTGTATATAA
1 TATAAATTATAAAA-ATGTAT--GTA-GTGTATAT-A
*
42509765 AATAAATTAT-AAAAT-TATGTACGTGTATATA
1 TATAAATTATAAAAATGTATGTA-GTGTATATA
*
42509796 TATATATTATAAAAATGTATGTA-TGTATATA
1 TATAAATTATAAAAATGTATGTAGTGTATATA
42509827 TAT
1 TAT
42509830 GTATAACGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 20 0.34
32 16 0.28
33 6 0.10
34 3 0.05
35 2 0.03
36 3 0.05
37 8 0.14
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (32 bp):
TATAAATTATAAAAATGTATGTAGTGTATATA
Found at i:42509884 original size:3 final size:3
Alignment explanation
Indices: 42509871--42509903 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
42509861 TGAATGAGTA
*
42509871 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42509904 GATGATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:42512004 original size:50 final size:50
Alignment explanation
Indices: 42511901--42512192 Score: 266
Period size: 50 Copynumber: 5.7 Consensus size: 50
42511891 GGGAATGAGA
* *
42511901 TCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
* *
42511957 TCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * ** *
42512007 TCCCATGTAATACCATGTCTAGGACATGGTGTTGGCACCGAGATGAGGGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * * **
42512057 TCCCCCGTAGGACCATGTCTGGGTCATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * *
42512107 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--G-TATAGAAAGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT-GAGAG-G
* * *
42512156 TCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
42512193 TGTATTATCA
Statistics
Matches: 197, Mismatches: 37, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
47 3 0.02
48 4 0.02
49 32 0.16
50 120 0.61
53 3 0.02
55 1 0.01
56 34 0.17
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Done.