Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 89 of 250
Found at i:28603944 original size:3 final size:3
Alignment explanation
Indices: 28603936--28603961 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28603926 CATTTCAGTA
28603936 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
28603962 AAGAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28609106 original size:10 final size:10
Alignment explanation
Indices: 28609091--28609121 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
28609081 TTCTTACTAT
28609091 TCATACTGAA
1 TCATACTGAA
28609101 TCATACTGAA
1 TCATACTGAA
28609111 TCATACTGAA
1 TCATACTGAA
28609121 T
1 T
28609122 ATTTTCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (10 bp):
TCATACTGAA
Found at i:28609857 original size:15 final size:15
Alignment explanation
Indices: 28609837--28609865 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28609827 TTACAAGTGA
28609837 TTGTTGTTAAGATAC
1 TTGTTGTTAAGATAC
28609852 TTGTTGTTAAGATA
1 TTGTTGTTAAGATA
28609866 TTGAACCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (15 bp):
TTGTTGTTAAGATAC
Found at i:28610632 original size:15 final size:16
Alignment explanation
Indices: 28610601--28610647 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
28610591 CATAGAAAAT
*
28610601 AAATAT-TATTTAATTA
1 AAATATATATTT-TTTA
28610617 AAATATAT-TTTTTTA
1 AAATATATATTTTTTA
*
28610632 AAATTTATATTTTTTA
1 AAATATATATTTTTTA
28610648 GCGGCGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 10 0.37
16 16 0.59
17 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATATATATTTTTTA
Found at i:28616467 original size:49 final size:50
Alignment explanation
Indices: 28616410--28616657 Score: 205
Period size: 50 Copynumber: 5.0 Consensus size: 50
28616400 AACCGAAGCT
* * * *
28616410 ATCTGGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGGCC-AACA
1 ATCTGGTACACGTAGTAGCTTGCACTTAGTACTACACACGCGACCTAACA
* * * *
28616459 ATCTGGTACACGTAGTAGCTTGCACTTATTACTATACACGTGACCTAACC
1 ATCTGGTACACGTAGTAGCTTGCACTTAGTACTACACACGCGACCTAACA
* * * * * **
28616509 ATATGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGTT
1 ATCTGGTACACGTAGTAGCTTGCACTTAGTACTACACACGCGACCT-AA-CA
* * * * * * * * *
28616560 GTCAGGTACGCATAATAG-TCTGCACTTAGTACTACATATGCAACCTAACT
1 ATCTGGTACACGTAGTAGCT-TGCACTTAGTACTACACACGCGACCTAACA
* * *
28616610 ATCTAGTACACGTAGTAGCTTGCACTTATTACTACACACGTGACCTAA
1 ATCTGGTACACGTAGTAGCTTGCACTTAGTACTACACACGCGACCTAA
28616658 AACCATCTTA
Statistics
Matches: 152, Mismatches: 41, Indels: 11
0.75 0.20 0.05
Matches are distributed among these distances:
49 39 0.26
50 79 0.52
51 33 0.22
52 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (50 bp):
ATCTGGTACACGTAGTAGCTTGCACTTAGTACTACACACGCGACCTAACA
Found at i:28622066 original size:20 final size:20
Alignment explanation
Indices: 28622029--28622067 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28622019 CCTGCAGTCC
* *
28622029 AAAATTTTCAACTTTTTCTT
1 AAAATTTTCAAATGTTTCTT
28622049 AAAATTTTCAAATGTTTCT
1 AAAATTTTCAAATGTTTCT
28622068 GATTTAGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.13, G:0.03, T:0.51
Consensus pattern (20 bp):
AAAATTTTCAAATGTTTCTT
Found at i:28622984 original size:58 final size:60
Alignment explanation
Indices: 28622882--28623004 Score: 205
Period size: 58 Copynumber: 2.1 Consensus size: 60
28622872 CATGTGAATT
*
28622882 TAGTTGATAGGACTTATGTGAGAAAATTTAGAAATGTGCTAGGCAAATGCAAGTGGCCT-A
1 TAGTTGAGAGGACTTATGTGAG-AAATTTAGAAATGTGCTAGGCAAATGCAAGTGGCCTAA
*
28622942 TAGTTGAGATGACTTATGTGAG-AATTTAGAAATGTGCTAGGCAAATGCAAGTGGCCTAA
1 TAGTTGAGAGGACTTATGTGAGAAATTTAGAAATGTGCTAGGCAAATGCAAGTGGCCTAA
28623001 TAGT
1 TAGT
28623005 GCATGTAATC
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
58 35 0.58
59 5 0.08
60 20 0.33
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (60 bp):
TAGTTGAGAGGACTTATGTGAGAAATTTAGAAATGTGCTAGGCAAATGCAAGTGGCCTAA
Found at i:28624569 original size:40 final size:40
Alignment explanation
Indices: 28624514--28624724 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
28624504 ATTTGAATGA
*
28624514 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
28624554 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
28624594 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * *
28624634 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * * * *
28624674 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
28624714 TATCC-GGCTAA
1 TATCCGGGCTAA
28624725 ATTCCGAAGA
Statistics
Matches: 156, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 7 0.04
40 146 0.94
41 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:28632687 original size:40 final size:40
Alignment explanation
Indices: 28632632--28632842 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
28632622 ATTTGAATGA
*
28632632 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
28632672 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
28632712 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * *
28632752 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * * * *
28632792 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
28632832 TATCC-GGCTAA
1 TATCCGGGCTAA
28632843 ATTCGAAGAA
Statistics
Matches: 156, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 7 0.04
40 146 0.94
41 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:28634263 original size:15 final size:15
Alignment explanation
Indices: 28634231--28634272 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
28634221 GTTACATCAC
*
28634231 CAAAATATAGAATTT
1 CAAAATATAAAATTT
28634246 CAAAA-ATAAAATTAT
1 CAAAATATAAAATT-T
*
28634261 CAATATATAAAA
1 CAAAATATAAAA
28634273 CAAGACCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 10 0.43
16 6 0.26
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (15 bp):
CAAAATATAAAATTT
Found at i:28638230 original size:31 final size:31
Alignment explanation
Indices: 28638195--28638253 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
28638185 TATTCTAGTC
28638195 AAATTAAATTTTGTAAACAATTTATATATTG
1 AAATTAAATTTTGTAAACAATTTATATATTG
28638226 AAATTAAATTTTGTAAACAATTTATATA
1 AAATTAAATTTTGTAAACAATTTATATA
28638254 AAATTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (31 bp):
AAATTAAATTTTGTAAACAATTTATATATTG
Found at i:28640315 original size:40 final size:40
Alignment explanation
Indices: 28640252--28640331 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
28640242 AACTCCCCTA
* *
28640252 AGGTTCCTCTTTCCACACTTGAAAGTCTGTATGTTCTATC
1 AGGTTCCTCTTTCCACACCTGAAAGTCTGCATGTTCTATC
*
28640292 AGGTTCCTCTTTCTACACCTGAAAGTCTGCATGTTCTATC
1 AGGTTCCTCTTTCCACACCTGAAAGTCTGCATGTTCTATC
28640332 TCTGCTAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.39
Consensus pattern (40 bp):
AGGTTCCTCTTTCCACACCTGAAAGTCTGCATGTTCTATC
Found at i:28643896 original size:16 final size:16
Alignment explanation
Indices: 28643865--28643898 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28643855 ATACAATACT
* *
28643865 AAAAAAGAAGAGGAAA
1 AAAAAAGAAAAAGAAA
28643881 AAAAAAGAAAAAGAAA
1 AAAAAAGAAAAAGAAA
28643897 AA
1 AA
28643899 TATTGCAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAGAAA
Found at i:28647429 original size:18 final size:18
Alignment explanation
Indices: 28647406--28647440 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28647396 AAACATTATT
28647406 TAATTTT-TTTTCAAAATA
1 TAATTTTATTTT-AAAATA
28647424 TAATTTTATTTTAAAAT
1 TAATTTTATTTTAAAAT
28647441 TTTGTTAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTTTATTTTAAAATA
Found at i:28652071 original size:39 final size:39
Alignment explanation
Indices: 28652027--28652225 Score: 299
Period size: 39 Copynumber: 5.1 Consensus size: 39
28652017 ATTCAAGACA
* *
28652027 CTGGAAATGTATCCGGGCTAAAGTCCCGTAGGCTTCGTA
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
28652066 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
** * *
28652105 CTGGAAATGTATCTAGGCTAAAGTCTCGTAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
28652144 CTGGAAATGTATCCGGGCTAAAGTTCCGCATGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* * *
28652183 TTGGAAATGTATCCAGGCTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
28652222 CTGG
1 CTGG
28652226 TAATATAATT
Statistics
Matches: 142, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 142 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:28657974 original size:40 final size:40
Alignment explanation
Indices: 28657850--28658154 Score: 375
Period size: 40 Copynumber: 7.7 Consensus size: 40
28657840 TTGAATGCTG
* * * * *
28657850 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAA
** * * *
28657890 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGGTA-CAAGT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAA-A
* *
28657930 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
*
28657970 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
*
28658010 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
*
28658050 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* *
28658090 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* * *
28658129 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
28658155 AACGAGGAGC
Statistics
Matches: 236, Mismatches: 23, Indels: 12
0.87 0.08 0.04
Matches are distributed among these distances:
39 34 0.14
40 192 0.81
41 10 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
Found at i:28667017 original size:46 final size:44
Alignment explanation
Indices: 28666964--28667232 Score: 188
Period size: 46 Copynumber: 5.8 Consensus size: 44
28666954 GGGTTATTGT
*
28666964 GAGCTAGTGTAAGACATGTATGGGACATGCATCAGCCACATT-ATGA-
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATC-G--ACATTGA-GAC
28667010 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGAC
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACATTGAGAC
* * * ***
28667056 GAGTGCTAGTGTAAGGCATGTCTAGGACATGCATCGGCCCCGAGAC
1 GA--GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGAC
* *
28667102 GCAAG-TCAGTGTAAGACATGTCTGGGACATGCATCGGC-TATGAGAT
1 G--AGCT-AGTGTAAGACATGTCTGGGACATGCATCGACAT-TGAGAC
* * * *
28667148 GTG-TCAATGTAAGACCATGTCTGGGACATAGCATCGACATAGATATGC
1 GAGCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGACATTGAGA--C
*
28667196 TAGAGCTTGTGTAAGACCATGTCTGGGACATGGCATC
1 --GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATC
28667233 AGCACCTTTC
Statistics
Matches: 183, Mismatches: 22, Indels: 32
0.77 0.09 0.14
Matches are distributed among these distances:
44 11 0.06
45 22 0.12
46 75 0.41
47 28 0.15
48 17 0.09
50 29 0.16
51 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.23
Consensus pattern (44 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGAC
Found at i:28671399 original size:40 final size:40
Alignment explanation
Indices: 28671187--28671392 Score: 342
Period size: 40 Copynumber: 5.2 Consensus size: 40
28671177 AACCCAAGTA
* * *
28671187 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
*
28671226 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAGATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
* *
28671266 CCTTCGGGACTTAGCCCAGATATAGTAACTAGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
28671306 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
*
28671346 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
28671386 CCTTCGG
1 CCTTCGG
28671393 ATCTTAGTCC
Statistics
Matches: 156, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 13 0.08
40 143 0.92
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
Found at i:28672784 original size:13 final size:13
Alignment explanation
Indices: 28672766--28672791 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28672756 ATTTTTATTT
28672766 TTAACATAAAATA
1 TTAACATAAAATA
28672779 TTAACATAAAATA
1 TTAACATAAAATA
28672792 ATTATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:28677264 original size:40 final size:40
Alignment explanation
Indices: 28677194--28677411 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
28677184 AAGCCAAGTA
* * * * *
28677194 CCTTCGGGATTTA-ACCGGGTATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
28677233 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
28677273 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
28677313 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
28677353 CCTTCGAGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
28677393 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
28677412 TTATCATCCA
Statistics
Matches: 163, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 13 0.08
40 150 0.92
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:28679385 original size:8 final size:9
Alignment explanation
Indices: 28679363--28679395 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
28679353 TTTTGACTCG
28679363 GTTTTTGAT
1 GTTTTTGAT
28679372 GTTTTTGAT
1 GTTTTTGAT
28679381 GTTTTTGAT
1 GTTTTTGAT
28679390 GTTTTT
1 GTTTTT
28679396 TGTGATCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.09, C:0.00, G:0.21, T:0.70
Consensus pattern (9 bp):
GTTTTTGAT
Found at i:28681962 original size:26 final size:26
Alignment explanation
Indices: 28681925--28681979 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
28681915 TGACACTCTG
*
28681925 TTTTAAAATATGTTTTCAAGT-TATGT
1 TTTTAAAATATGTTTT-AAATATATGT
*
28681951 TTTTAAACTATGTTTTAAATATATGT
1 TTTTAAAATATGTTTTAAATATATGT
28681977 TTT
1 TTT
28681980 ATGTGTGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 3 0.12
26 23 0.88
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.56
Consensus pattern (26 bp):
TTTTAAAATATGTTTTAAATATATGT
Found at i:28681980 original size:13 final size:12
Alignment explanation
Indices: 28681923--28681980 Score: 62
Period size: 13 Copynumber: 4.6 Consensus size: 12
28681913 TTTGACACTC
28681923 TGTTTTAAAATA
1 TGTTTTAAAATA
**
28681935 TGTTTTCAAGTTA
1 TGTTTT-AAAATA
*
28681948 TGTTTTTAAACTA
1 TG-TTTTAAAATA
28681961 TGTTTTAAATATA
1 TGTTTTAAA-ATA
28681974 TGTTTTA
1 TGTTTTA
28681981 TGTGTGTTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
12 13 0.34
13 21 0.55
14 4 0.11
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.55
Consensus pattern (12 bp):
TGTTTTAAAATA
Found at i:28682459 original size:59 final size:59
Alignment explanation
Indices: 28682395--28682512 Score: 186
Period size: 59 Copynumber: 2.0 Consensus size: 59
28682385 CTCAGCCATT
*
28682395 CTAATAA-GACAAATATGTGAGCATGTTTTCCTGTTA-TTCGTTTTCAAACAATAACAAAC
1 CTAATAAGGA-AAATATGTGAGCATG-TTTCCTGTTATTTCATTTTCAAACAATAACAAAC
*
28682454 CTAATAAGGAAAATATGTGAGCATGTTTCCTGTTATTTTATTTTCAAACAATAACAAAC
1 CTAATAAGGAAAATATGTGAGCATGTTTCCTGTTATTTCATTTTCAAACAATAACAAAC
28682513 TAAGTTTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
58 10 0.18
59 43 0.78
60 2 0.04
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (59 bp):
CTAATAAGGAAAATATGTGAGCATGTTTCCTGTTATTTCATTTTCAAACAATAACAAAC
Found at i:28691846 original size:21 final size:22
Alignment explanation
Indices: 28691791--28691847 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
28691781 GAAACAAGGC
28691791 ACACGCCCGTGTGGAAGGACGA
1 ACACGCCCGTGTGGAAGGACGA
* **
28691813 ACACACCTATGTGGAAGGAC-A
1 ACACGCCCGTGTGGAAGGACGA
28691834 ACACGCCCGTGTGG
1 ACACGCCCGTGTGG
28691848 CCATTTCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.28, C:0.28, G:0.32, T:0.12
Consensus pattern (22 bp):
ACACGCCCGTGTGGAAGGACGA
Found at i:28693139 original size:46 final size:46
Alignment explanation
Indices: 28692992--28693208 Score: 156
Period size: 46 Copynumber: 4.6 Consensus size: 46
28692982 GTGCTGATGC
* * **
28692992 CATGTCCCAGACATGGTCTTACACAAGCTCTAG-CATATTGGTGCCAATG
1 CATGTCCCAGACATGGTCTTACACTAGC-CTCGTC-TA--AATGCCAATG
* * * ** * *
28693041 CCATGTCCCAGACATGGTCTTACATTGGCTTACGTCTCGAGGCCGATG
1 -CATGTCCCAGACATGGTCTTACACTAGCCT-CGTCTAAATGCCAATG
*
28693089 CATGTTCCAGACAT-GTCTTACACTAGCCTCGTCTAAATGCCAATG
1 CATGTCCCAGACATGGTCTTACACTAGCCTCGTCTAAATGCCAATG
** * * *
28693134 CCATGTCATAGACATGGTCTTACACT-GGCTC-TCGTAATGTGGCCGATG
1 -CATGTCCCAGACATGGTCTTACACTAGCCTCGTC-TAA-AT-GCCAATG
28693182 CATGTCCCAGACAT-GTCTTACACTAGC
1 CATGTCCCAGACATGGTCTTACACTAGC
28693209 TCACACAAGT
Statistics
Matches: 133, Mismatches: 26, Indels: 19
0.75 0.15 0.11
Matches are distributed among these distances:
45 14 0.11
46 40 0.30
47 37 0.28
48 13 0.10
49 1 0.01
50 27 0.20
51 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGGTCTTACACTAGCCTCGTCTAAATGCCAATG
Found at i:28693155 original size:93 final size:93
Alignment explanation
Indices: 28693033--28693208 Score: 266
Period size: 93 Copynumber: 1.9 Consensus size: 93
28693023 AGCATATTGG
* * * *
28693033 TGCCAATGCCATGTCCCAGACATGGTCTTACATTGGCT-TACGT-CTCGAGGCCGATGCATGTTC
1 TGCCAATGCCATGTCACAGACATGGTCTTACACTGGCTCT-CGTAAT-GAGGCCGATGCATGTCC
28693096 CAGACATGTCTTACACTAGCCTCGTCTAAA
64 CAGACATGTCTTACACTAGCCTCGTCTAAA
* *
28693126 TGCCAATGCCATGTCATAGACATGGTCTTACACTGGCTCTCGTAATGTGGCCGATGCATGTCCCA
1 TGCCAATGCCATGTCACAGACATGGTCTTACACTGGCTCTCGTAATGAGGCCGATGCATGTCCCA
28693191 GACATGTCTTACACTAGC
66 GACATGTCTTACACTAGC
28693209 TCACACAAGT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
93 73 0.97
94 2 0.03
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (93 bp):
TGCCAATGCCATGTCACAGACATGGTCTTACACTGGCTCTCGTAATGAGGCCGATGCATGTCCCA
GACATGTCTTACACTAGCCTCGTCTAAA
Found at i:28710292 original size:21 final size:21
Alignment explanation
Indices: 28710268--28710322 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
28710258 AAAACAGGGT
*
28710268 ACACGCCCGTGTGGAAGGGCA
1 ACACGCCCGTGTGGAAGGGAA
*
28710289 ACACGCCCATGTGGAAGGGAA
1 ACACGCCCGTGTGGAAGGGAA
*
28710310 AAACGCCCGTGTG
1 ACACGCCCGTGTG
28710323 ACCAACTCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.35, T:0.11
Consensus pattern (21 bp):
ACACGCCCGTGTGGAAGGGAA
Found at i:28711524 original size:49 final size:49
Alignment explanation
Indices: 28711451--28711707 Score: 248
Period size: 49 Copynumber: 5.4 Consensus size: 49
28711441 CTCAAACACG
*
28711451 AGACATGGTCTTACATTGGCTATCATCATCGAGGCTGATGCCATGTCCC
1 AGACATGGTCTTACATTGGCTATCATCATCGAGGCCGATGCCATGTCCC
*
28711500 GGACATGGTCTTACATTGGCTATCATCATCGAGGCCGATGCCATGTCCC
1 AGACATGGTCTTACATTGGCTATCATCATCGAGGCCGATGCCATGTCCC
* * * *
28711549 AGACATGGTCTTATACTGAC-A-CATC-TCGTA-GCCGATG-GATGTCCC
1 AGACATGGTCTTACATTGGCTATCATCATCG-AGGCCGATGCCATGTCCC
* * * *
28711594 AAACAT-GTCTGACACTGGCTTAT-GTC-TCGAGGCCGAT-CCATGTCCC
1 AGACATGGTCTTACATTGGC-TATCATCATCGAGGCCGATGCCATGTCCC
* * * * * ** *
28711640 AAACAT-ATCTTACACTAGCTCTCATC-TTAATGCCGATGCCATGTCCC
1 AGACATGGTCTTACATTGGCTATCATCATCGAGGCCGATGCCATGTCCC
*
28711687 AGACATGGTCTTACACTGGCT
1 AGACATGGTCTTACATTGGCT
28711708 TACACCAATG
Statistics
Matches: 175, Mismatches: 24, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
44 10 0.06
45 15 0.09
46 55 0.31
47 19 0.11
48 13 0.07
49 63 0.36
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (49 bp):
AGACATGGTCTTACATTGGCTATCATCATCGAGGCCGATGCCATGTCCC
Found at i:28711666 original size:92 final size:94
Alignment explanation
Indices: 28711487--28711709 Score: 226
Period size: 94 Copynumber: 2.4 Consensus size: 94
28711477 CATCGAGGCT
** * * * *
28711487 GATGCCATGTCCCGGACATGGTCTTACATTGGC-TATCATCATCGAGGCCGATGCCATGTCCCAG
1 GATGCCATGTCCCAAACATGGTCTGACACTGGCTTAT-GTC-TCGAGGCCGATGCCATGTCCCAA
* *
28711551 ACATGGTCTTATACTGACACATCTCGT-A-GCC
64 ACATGATCTTACACTGACACATCT--TAATGCC
*
28711582 GATG-GATGTCCCAAACAT-GTCTGACACTGGCTTATGTCTCGAGGCCGAT-CCATGTCCCAAAC
1 GATGCCATGTCCCAAACATGGTCTGACACTGGCTTATGTCTCGAGGCCGATGCCATGTCCCAAAC
* *
28711644 AT-ATCTTACACTAGCTCTCATCTTAATGCC
66 ATGATCTTACACT-G-ACACATCTTAATGCC
* *
28711674 GATGCCATGTCCCAGACATGGTCTTACACTGGCTTA
1 GATGCCATGTCCCAAACATGGTCTGACACTGGCTTA
28711710 CACCAATGAC
Statistics
Matches: 107, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
90 9 0.08
91 16 0.15
92 24 0.22
93 25 0.23
94 29 0.27
95 4 0.04
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (94 bp):
GATGCCATGTCCCAAACATGGTCTGACACTGGCTTATGTCTCGAGGCCGATGCCATGTCCCAAAC
ATGATCTTACACTGACACATCTTAATGCC
Found at i:28719248 original size:46 final size:47
Alignment explanation
Indices: 28719055--28719310 Score: 222
Period size: 46 Copynumber: 5.4 Consensus size: 47
28719045 CATGTCTTAG
*
28719055 ACATGGTCTTACACTGGCTATCATCATCGAGGCCTATGCCATGTCCCAA
1 ACATGGTCTTACACTGGCTATCATC-TCGAGGCCGAT-CCATGTCCCAA
* * * *
28719104 ACATGGTCTTACACTAGCTTTCGCATATTCG-TGCCGATTCCATGTCCCAA
1 ACATGGTCTTACACTGGCTAT--CAT-CTCGAGGCCGA-TCCATGTCCCAA
* * * *
28719154 ACATGGTCTTATACTGGC-A-CATCTC-ATAGTCGATGCATGTCCCAA
1 ACATGGTCTTACACTGGCTATCATCTCGA-GGCCGATCCATGTCCCAA
* *
28719199 ACAT-GTCTTACACTGGCTTAT-GTCTCGAGGCCGATACATGTCCCAA
1 ACATGGTCTTACACTGGC-TATCATCTCGAGGCCGATCCATGTCCCAA
* * * * *
28719245 ACAT-GTCTTACACTAGC-ACTCATCTCAATGCTGATGCCATGTCCCAG
1 ACATGGTCTTACACTGGCTA-TCATCTCGAGGCCGAT-CCATGTCCCAA
28719292 ACATGGTCTTACACTGGCT
1 ACATGGTCTTACACTGGCT
28719311 CACACCAATG
Statistics
Matches: 167, Mismatches: 25, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
44 13 0.08
45 18 0.11
46 53 0.32
47 14 0.08
48 12 0.07
49 19 0.11
50 31 0.19
51 7 0.04
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (47 bp):
ACATGGTCTTACACTGGCTATCATCTCGAGGCCGATCCATGTCCCAA
Found at i:28719296 original size:138 final size:143
Alignment explanation
Indices: 28719055--28719309 Score: 335
Period size: 138 Copynumber: 1.8 Consensus size: 143
28719045 CATGTCTTAG
* *
28719055 ACATGGTCTTACACTGGCTATCATCATCGAGGCCTATGCCATGTCCCAAACATGGTCTTACACTA
1 ACATGGTCTTACACTGGCTATCATCATCGAGGCCGATGACATGTCCCAAACATGGTCTTACACTA
* * * * *
28719120 GCTTTCGCATATTCGTGCCGATTCCATGTCCCAAACATGGTCTTATACTGGCACATCTCATAGTC
66 GC-TACGCATACTCATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCACATCTCATAGTC
28719185 GATGCATGTCCCAA
130 GATGCATGTCCCAA
*
28719199 ACAT-GTCTTACACTGGCTTAT-GTC-TCGAGGCCGAT-ACATGTCCCAAACAT-GTCTTACACT
1 ACATGGTCTTACACTGGC-TATCATCATCGAGGCCGATGACATGTCCCAAACATGGTCTTACACT
* * *
28719259 AGC-ACTCAT-CTCAATGCTGATGCCATGTCCCAGACATGGTCTTACACTGGC
65 AGCTACGCATACTC-ATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGC
28719310 TCACACCAAT
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
137 2 0.02
138 37 0.38
140 13 0.13
141 14 0.14
142 10 0.10
143 15 0.15
144 7 0.07
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (143 bp):
ACATGGTCTTACACTGGCTATCATCATCGAGGCCGATGACATGTCCCAAACATGGTCTTACACTA
GCTACGCATACTCATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCACATCTCATAGTCG
ATGCATGTCCCAA
Found at i:28725937 original size:15 final size:15
Alignment explanation
Indices: 28725919--28725962 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
28725909 GAAGCCCAGA
28725919 ATAAGGAAATCCAAG
1 ATAAGGAAATCCAAG
* *
28725934 ATAAAGAAATCCATG
1 ATAAGGAAATCCAAG
28725949 ATAAGGAAATCCAA
1 ATAAGGAAATCCAA
28725963 TTTACAGCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.16
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Found at i:28739908 original size:22 final size:22
Alignment explanation
Indices: 28739825--28739895 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
28739815 GTAGTGGAGT
* *
28739825 GGTGGTTGTATGGTGGTGGTTC
1 GGTGGATGTATGATGGTGGTTC
*
28739847 GATGGATGTATGATGGTGGTTC
1 GGTGGATGTATGATGGTGGTTC
28739869 GGTGGATGTATGATGGTGGTTC
1 GGTGGATGTATGATGGTGGTTC
28739891 GGTGG
1 GGTGG
28739896 TTGTTAGGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.11, C:0.04, G:0.48, T:0.37
Consensus pattern (22 bp):
GGTGGATGTATGATGGTGGTTC
Found at i:28740166 original size:13 final size:13
Alignment explanation
Indices: 28740150--28740209 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 13
28740140 AGTGGTGTAT
28740150 CACACGGCCTGGA
1 CACACGGCCTGGA
* *
28740163 CACACGGGCTTG-
1 CACACGGCCTGGA
28740175 CGACACGGCCGTGTGTA
1 C-ACACGGCC-TG-G-A
28740192 TCACACGGCCTGGA
1 -CACACGGCCTGGA
28740206 CACA
1 CACA
28740210 TGGGCGTGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
12 1 0.03
13 21 0.57
14 2 0.05
15 2 0.05
16 2 0.05
17 8 0.22
18 1 0.03
ACGTcount: A:0.22, C:0.35, G:0.30, T:0.13
Consensus pattern (13 bp):
CACACGGCCTGGA
Found at i:28740179 original size:41 final size:43
Alignment explanation
Indices: 28740122--28740217 Score: 133
Period size: 43 Copynumber: 2.3 Consensus size: 43
28740112 AAAAAGAATC
* *
28740122 CACACGGGGGTGCGACACAG-TG-GTGTATCACACGGCCTGGA
1 CACACGGGCGTGCGACACAGCCGTGTGTATCACACGGCCTGGA
* *
28740163 CACACGGGCTTGCGACACGGCCGTGTGTATCACACGGCCTGGA
1 CACACGGGCGTGCGACACAGCCGTGTGTATCACACGGCCTGGA
*
28740206 CACATGGGCGTG
1 CACACGGGCGTG
28740218 TCCCAGGTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 17 0.36
42 1 0.02
43 29 0.62
ACGTcount: A:0.20, C:0.29, G:0.35, T:0.16
Consensus pattern (43 bp):
CACACGGGCGTGCGACACAGCCGTGTGTATCACACGGCCTGGA
Found at i:28750825 original size:40 final size:40
Alignment explanation
Indices: 28750745--28750864 Score: 188
Period size: 40 Copynumber: 3.0 Consensus size: 40
28750735 TGTTTGACAA
*
28750745 CGATTCGAGATAGCTTTGGCTATAT-TGGCACTTAGTGTG
1 CGATTCGAGATAGCTTCGGCTATATATGGCACTTAGTGTG
28750784 CGATTCGAGATAGCTTCGGCTATATATGGCACTTAGTGTG
1 CGATTCGAGATAGCTTCGGCTATATATGGCACTTAGTGTG
* * * *
28750824 CGACTCGAAATATCCTCGGCTATATATGGCACTTAGTGTG
1 CGATTCGAGATAGCTTCGGCTATATATGGCACTTAGTGTG
28750864 C
1 C
28750865 AAGACTGAGG
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 24 0.32
40 51 0.68
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (40 bp):
CGATTCGAGATAGCTTCGGCTATATATGGCACTTAGTGTG
Found at i:28759199 original size:37 final size:37
Alignment explanation
Indices: 28759140--28759211 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
28759130 AGCTCAGACG
*
28759140 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
*
28759177 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGA
28759212 ATATATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (37 bp):
AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
Found at i:28759481 original size:48 final size:48
Alignment explanation
Indices: 28759357--28759541 Score: 300
Period size: 48 Copynumber: 3.8 Consensus size: 48
28759347 GCACATCGCC
*
28759357 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* * *
28759405 TATTTATATTTCACATT-GACAATTCGGCTTTACCACATATGCATATCTCA
1 TA--CATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
28759455 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
28759503 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
28759542 TGCATGTTCA
Statistics
Matches: 126, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
48 82 0.65
49 2 0.02
50 42 0.33
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:28759546 original size:98 final size:97
Alignment explanation
Indices: 28759357--28759540 Score: 309
Period size: 98 Copynumber: 1.9 Consensus size: 97
28759347 GCACATCGCC
*
28759357 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATTTATATTTCACATT
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA-TCATATTTCACATT
28759422 GACAATTCGGCTTTACCACATATGCATATCTCA
65 GACAATTCGGCTTTACCACATATGCATATCTCA
*
28759455 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATA-CATATTTCACATT-
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATCATATTTCACATTG
*
28759518 AGCCATTCGGCTTTACCACATAT
66 A-CAATTCGGCTTTACCACATAT
28759541 ATGCATGTTC
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
95 1 0.01
96 32 0.39
98 49 0.60
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.36
Consensus pattern (97 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATCATATTTCACATTG
ACAATTCGGCTTTACCACATATGCATATCTCA
Found at i:28759590 original size:47 final size:47
Alignment explanation
Indices: 28759511--28759704 Score: 289
Period size: 47 Copynumber: 4.1 Consensus size: 47
28759501 CATACATATT
* * * *
28759511 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
28759558 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
28759605 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
28759652 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
28759699 TCACAT
1 TCACAT
28759705 AAAATCCTAA
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 133 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:28759631 original size:22 final size:22
Alignment explanation
Indices: 28759604--28759675 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
28759594 GCTCACATTC
28759604 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
28759626 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
28759650 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
28759673 ATC
1 ATC
28759676 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:28759632 original size:94 final size:94
Alignment explanation
Indices: 28759464--28759704 Score: 290
Period size: 94 Copynumber: 2.6 Consensus size: 94
28759454 ATACATATTT
* * * *
28759464 CACATTAGCCATTCGGCTTTA-C-CACATATACATATCTCATACATAT-TTCACATTAGCCATTC
1 CACATTGGCCATTCGGCCTTATCACACATATACACA-CTC--ACAT-TCATCACATTAGCCATTC
* *
28759526 GGCTTTACCACATATATGCATGTTCATATTCAC
62 GGCCTTACCACATATATGCATGTTCACATTCAC
* ** *
28759559 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCC
1 CACATTGGCCATTCGGCCTTATCACACATATACACACTCACATTCATCACATTAGCCATTCGGCC
* *
28759624 TTATCACATATATGCATGTTCACATTCAT
66 TTACCACATATATGCATGTTCACATTCAC
* * *
28759653 CACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT
1 CACATTGGCCATTCGGCCTTATCACACATATACACACTCACATTCATCACAT
28759705 AAAATCCTAA
Statistics
Matches: 127, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
93 1 0.01
94 93 0.73
95 19 0.15
96 4 0.03
97 10 0.08
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (94 bp):
CACATTGGCCATTCGGCCTTATCACACATATACACACTCACATTCATCACATTAGCCATTCGGCC
TTACCACATATATGCATGTTCACATTCAC
Found at i:28765175 original size:40 final size:40
Alignment explanation
Indices: 28765098--28765320 Score: 360
Period size: 40 Copynumber: 5.6 Consensus size: 40
28765088 AACCCAAGTA
* *
28765098 CCTTCGGGATTTA-CCCGGATATAG-CAACTCGGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-T-AGCACAAATG
* * *
28765138 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGTACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
28765178 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
28765218 CCTTCGGGACTTAGCGCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
28765258 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
28765298 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
28765321 CATTCGATTA
Statistics
Matches: 171, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
40 156 0.91
41 12 0.07
42 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:28773369 original size:40 final size:40
Alignment explanation
Indices: 28773295--28773516 Score: 358
Period size: 40 Copynumber: 5.6 Consensus size: 40
28773285 AACCCAAGTA
* *
28773295 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* *
28773334 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
28773374 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
28773414 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
28773454 CCTCCGGGACTTAGCCCGGATATAGCCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
28773494 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
28773517 CATTCGAATA
Statistics
Matches: 170, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 12 0.07
40 155 0.91
41 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:28781583 original size:40 final size:40
Alignment explanation
Indices: 28781509--28781770 Score: 447
Period size: 40 Copynumber: 6.6 Consensus size: 40
28781499 AACCCAAGTA
* *
28781509 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* *
28781548 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
28781588 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
28781628 CCTTCGGGACTTAGCTCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
28781668 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
28781708 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
28781748 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
28781771 CATTCAATTA
Statistics
Matches: 211, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
39 12 0.06
40 196 0.93
41 3 0.01
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:28791814 original size:40 final size:40
Alignment explanation
Indices: 28791734--28791846 Score: 165
Period size: 40 Copynumber: 2.9 Consensus size: 40
28791724 TGTTTGACAA
*
28791734 CGATTCGAGATAGCTTTGGCTATAT-TGGCACTTAATGTG
1 CGATTCGAGATAGCTTCGGCTATATATGGCACTTAATGTG
*
28791773 CGATTCGAGATAGCTTCGGCTATATATGGCACTTAGTGTG
1 CGATTCGAGATAGCTTCGGCTATATATGGCACTTAATGTG
* * * *
28791813 CGACTCAAAATATCTTCGGCTATATATGGCACTT
1 CGATTCGAGATAGCTTCGGCTATATATGGCACTT
28791847 TGTTTGCAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 24 0.36
40 43 0.64
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (40 bp):
CGATTCGAGATAGCTTCGGCTATATATGGCACTTAATGTG
Found at i:28795771 original size:27 final size:27
Alignment explanation
Indices: 28795728--28795801 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
28795718 AAATGACTAA
*
28795728 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
28795755 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
28795782 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
28795802 TGATGAATAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:28796630 original size:26 final size:26
Alignment explanation
Indices: 28796601--28796775 Score: 273
Period size: 26 Copynumber: 6.8 Consensus size: 26
28796591 GATGAAGTGC
* *
28796601 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
28796627 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
28796653 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
28796679 AAAAGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
* *
28796705 AAAAGGGCTTATGCCCAAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
28796731 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
28796756 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28796776 ATTAAAGAGG
Statistics
Matches: 138, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 32 0.23
26 106 0.77
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATCG
Found at i:28796679 original size:52 final size:52
Alignment explanation
Indices: 28796601--28796775 Score: 309
Period size: 52 Copynumber: 3.4 Consensus size: 52
28796591 GATGAAGTGC
*
28796601 AAAAGGGCTTATGCCCTAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
28796653 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
28796705 AAAAGGGCTTATGCCCAAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
28796756 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28796776 ATTAAAGAGG
Statistics
Matches: 118, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
50 9 0.08
51 24 0.20
52 85 0.72
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
Found at i:28798741 original size:40 final size:40
Alignment explanation
Indices: 28798642--28798832 Score: 269
Period size: 40 Copynumber: 4.8 Consensus size: 40
28798632 TGGATGATAA
* * * * **
28798642 CCGGGCTAAGTCCCGAAGGCATCTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
28798682 CCGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
28798721 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
28798761 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTCTAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
* *
28798801 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
28798833 AGCTATATCC
Statistics
Matches: 138, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
39 33 0.24
40 103 0.75
41 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:28806824 original size:40 final size:40
Alignment explanation
Indices: 28806724--28806954 Score: 331
Period size: 40 Copynumber: 5.8 Consensus size: 40
28806714 TGGATGATAA
* * * * **
28806724 CCGGGCTAAGTCCCGAAGGCATCTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
28806764 CTGGG-TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
28806803 CAGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
28806843 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
28806883 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTCTAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
* *
28806923 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
28806955 AGCTATATCC
Statistics
Matches: 175, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 32 0.18
40 141 0.81
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:28808397 original size:42 final size:42
Alignment explanation
Indices: 28808338--28808429 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
28808328 TACACTCCCC
* ** *
28808338 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
28808380 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
28808422 AAATGGGC
1 AAATGGGC
28808430 CTAAGGGTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:28811251 original size:29 final size:30
Alignment explanation
Indices: 28811210--28811274 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
28811200 TATGGCCAAG
*
28811210 ACACAC-AGCCGTGTTCTAGGCCGTGTGGC
1 ACACACGAGCCGTGTTCTAGGCCATGTGGC
*
28811239 ACACACGA-CCGTGTTCTAGGCTATGTGGC
1 ACACACGAGCCGTGTTCTAGGCCATGTGGC
28811268 ACACACG
1 ACACACG
28811275 GCTGAGACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 32 0.97
30 1 0.03
ACGTcount: A:0.22, C:0.31, G:0.28, T:0.20
Consensus pattern (30 bp):
ACACACGAGCCGTGTTCTAGGCCATGTGGC
Found at i:28826971 original size:48 final size:48
Alignment explanation
Indices: 28826900--28827081 Score: 265
Period size: 48 Copynumber: 3.8 Consensus size: 48
28826890 TCATATCGAA
* * * ** *
28826900 GCCATGTCCTAGACATGGTCTTACACGAAATCACATATCGATGCCAAT
1 GCCATGTCCCAAACATGGTCTTACATGGGATCTCATATCGATGCCAAT
* * *
28826948 GCCATATCCCAGACATGGCCTTACATGGGATCTCATATCGATGCCAAT
1 GCCATGTCCCAAACATGGTCTTACATGGGATCTCATATCGATGCCAAT
*
28826996 GCCATGTCCTAAACATGGTCTTACATGGGATCTCATATCGATGCCAAT
1 GCCATGTCCCAAACATGGTCTTACATGGGATCTCATATCGATGCCAAT
*
28827044 GTCATGTCCCAAACATGGTCTTACATGGGATCTCATAT
1 GCCATGTCCCAAACATGGTCTTACATGGGATCTCATAT
28827082 AACCCTAATG
Statistics
Matches: 121, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 121 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27
Consensus pattern (48 bp):
GCCATGTCCCAAACATGGTCTTACATGGGATCTCATATCGATGCCAAT
Found at i:28827676 original size:21 final size:22
Alignment explanation
Indices: 28827646--28827686 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
28827636 TAGTAAAAGT
28827646 CATTTCTCTAACCA-TAAACATG
1 CATTTCTCT-ACCATTAAACATG
28827668 CATTT-TCTACCATTAAACA
1 CATTTCTCTACCATTAAACA
28827687 CAAAAATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (22 bp):
CATTTCTCTACCATTAAACATG
Found at i:28837595 original size:29 final size:29
Alignment explanation
Indices: 28837532--28837646 Score: 137
Period size: 29 Copynumber: 4.0 Consensus size: 29
28837522 TTCACATACT
* * *
28837532 TGTATCTGGCCCATTAAGCCC-AATCATA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* *
28837560 T-TAATATGGCCCATTAGACCCAAATCACC
1 TGT-ATATGGCCCATTAGGCCCAAATCACA
28837589 TGTATATGGCCCATTAGGCCCAAATCACA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* *
28837618 TTTATATGGCCCGTTAGGCCC-AATCACA
1 TGTATATGGCCCATTAGGCCCAAATCACA
28837646 T
1 T
28837647 TCATAATCAT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.01
28 24 0.32
29 49 0.65
30 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCACA
Found at i:28837599 original size:57 final size:57
Alignment explanation
Indices: 28837532--28837644 Score: 156
Period size: 57 Copynumber: 2.0 Consensus size: 57
28837522 TTCACATACT
* *
28837532 TGTATCTGGCCCATTAAGCCC-AATCATATTAATATGGCCCATTAGACCCAAATCACC
1 TGTATATGGCCCATTAAGCCCAAATCACATTAATATGGCCCATTAGACCC-AATCACC
* * * *
28837589 TGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCCCAATCAC
1 TGTATATGGCCCATTAAGCCCAAATCACATTAATATGGCCCATTAGACCCAATCAC
28837645 ATTCATAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
57 25 0.51
58 24 0.49
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (57 bp):
TGTATATGGCCCATTAAGCCCAAATCACATTAATATGGCCCATTAGACCCAATCACC
Found at i:28837995 original size:34 final size:34
Alignment explanation
Indices: 28837952--28838022 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
28837942 TGCGATCTCC
28837952 TTAGCCCAAACCTACAATCGATATCACTCAAAGA
1 TTAGCCCAAACCTACAATCGATATCACTCAAAGA
28837986 TTAGCCCAAACCTACAATCGATATCACTCAAAGA
1 TTAGCCCAAACCTACAATCGATATCACTCAAAGA
28838020 TTA
1 TTA
28838023 ATCTTACATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.41, C:0.28, G:0.08, T:0.23
Consensus pattern (34 bp):
TTAGCCCAAACCTACAATCGATATCACTCAAAGA
Found at i:28840851 original size:34 final size:31
Alignment explanation
Indices: 28840813--28840894 Score: 83
Period size: 34 Copynumber: 2.5 Consensus size: 31
28840803 ATATCTGTAT
*
28840813 TGATACTGTCACTGAATTGGGCTAAGGCCTACAC
1 TGATACTGT-ACTGAA-AGGGCTAAGGCCTA-AC
*
28840847 TGATACTGATACTGTAAAGGGCTAAGGCCTAGC
1 TGATACTG-TACTG-AAAGGGCTAAGGCCTAAC
*
28840880 TGAAACTGTTACTGA
1 TGATACTG-TACTGA
28840895 TACAGGCTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
32 1 0.02
33 13 0.31
34 25 0.60
35 3 0.07
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (31 bp):
TGATACTGTACTGAAAGGGCTAAGGCCTAAC
Found at i:28850655 original size:39 final size:40
Alignment explanation
Indices: 28850610--28850818 Score: 107
Period size: 41 Copynumber: 5.2 Consensus size: 40
28850600 CGGGGTTTAG
* * *
28850610 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
28850649 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * * **
28850689 CCGGATATAGTCGCTAGCACAAATGCCTTC-AGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
28850729 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
* ** * * * *
28850770 TCGGATATAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
28850811 CCGGATAT
1 CCGGATAT
28850819 CATTCGAGTA
Statistics
Matches: 146, Mismatches: 20, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
39 17 0.12
40 61 0.42
41 66 0.45
42 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:28850768 original size:41 final size:41
Alignment explanation
Indices: 28850633--28850818 Score: 243
Period size: 41 Copynumber: 4.6 Consensus size: 41
28850623 CTCGCACAAG
* * * * * *
28850633 GCCTTCGGGTCTTAACCCGGATATGGTCAC-TAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
*
28850673 GCCTTCGGGACTTAGCCCGGATATAGTCGC-TAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
* * *
28850713 GCCTTC-AGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGCTTAGCACAAAA
*
28850754 GCCTTCGGGACTTAGCTCGGATATAGTCGCTTAGCACAAAA
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
28850795 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
28850819 CATTCGAGTA
Statistics
Matches: 129, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
39 2 0.02
40 59 0.46
41 66 0.51
42 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (41 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
Found at i:28854311 original size:46 final size:48
Alignment explanation
Indices: 28854238--28854340 Score: 138
Period size: 46 Copynumber: 2.2 Consensus size: 48
28854228 GACAGGACAG
* * * *
28854238 GACAGAAATGAGCCATGTAAGTCCATATCA-GT-TATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
* *
28854284 GATAGGAATGAGCCATGTAAGCCCATATTATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
28854332 GACAGGAAT
1 GACAGGAAT
28854341 AATCATGTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 26 0.54
47 1 0.02
48 21 0.44
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (48 bp):
GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
Found at i:28869082 original size:40 final size:40
Alignment explanation
Indices: 28869038--28869229 Score: 287
Period size: 40 Copynumber: 4.8 Consensus size: 40
28869028 GGGTATAGCT
* * * *
28869038 ACTCGCTCGAATGCCTTCGGGACATAGCCCAGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
*
28869078 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
28869118 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
* *
28869158 ACTCGCACAAATGCCTTTGGGACTTAGCCCGGA-ACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTA
* *
28869198 ACTAGCGCAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
28869230 TTATCATCCA
Statistics
Matches: 141, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 1 0.01
40 140 0.99
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:28881994 original size:57 final size:57
Alignment explanation
Indices: 28881917--28882030 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
28881907 GGTACAACCG
28881917 ATACAAGTGTCTTCCATCAGTGGTAAGCTGAATCTCTAAGCAGTGATACAACATATT
1 ATACAAGTGTCTTCCATCAGTGGTAAGCTGAATCTCTAAGCAGTGATACAACATATT
28881974 ATACAAGTGTCTTCCATCAGTGGTAAGCTGAATCTCTAAGCAGTGATACAACATATT
1 ATACAAGTGTCTTCCATCAGTGGTAAGCTGAATCTCTAAGCAGTGATACAACATATT
28882031 TCATGCATTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (57 bp):
ATACAAGTGTCTTCCATCAGTGGTAAGCTGAATCTCTAAGCAGTGATACAACATATT
Found at i:28884144 original size:42 final size:42
Alignment explanation
Indices: 28884080--28884195 Score: 115
Period size: 42 Copynumber: 2.8 Consensus size: 42
28884070 AATAAGATGC
* * * ** *
28884080 CAATGCCATGTCTCAGACATGGTCTTACATGGGATCTTACAT
1 CAATGCCATATCCCAGATATGGTCTTACATGAAATCTCACAT
* * * *
28884122 CGATGCCATATCCCAGATATGGTCTTATACGAAATCTCATAT
1 CAATGCCATATCCCAGATATGGTCTTACATGAAATCTCACAT
* * *
28884164 CAACGCCATATCCTAGATATAGTCTTACATGA
1 CAATGCCATATCCCAGATATGGTCTTACATGA
28884196 TAACTCATAC
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (42 bp):
CAATGCCATATCCCAGATATGGTCTTACATGAAATCTCACAT
Found at i:28895013 original size:47 final size:47
Alignment explanation
Indices: 28894960--28895380 Score: 637
Period size: 47 Copynumber: 9.0 Consensus size: 47
28894950 TTAGGATTTT
* *
28894960 ATGTGATGAATGTGAACACGCATATATGTGATGAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
28895007 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
28895054 ATGTGGTGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCT
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
28895101 ATGTGATGAATGTGAACATGCATATATGTGATGAA-GCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGAT-AAGGCCGAATGGCCA
* *
28895148 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
28895195 ATGTGGTGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
28895242 ATGTGATAAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
28895289 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
28895336 ATGTGGTGAATATGAAAATGCATATATGCGGTAAAGCCGAATGGC
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC
28895381 TAGTGTGAAA
Statistics
Matches: 340, Mismatches: 32, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
46 2 0.01
47 336 0.99
48 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:28895134 original size:25 final size:25
Alignment explanation
Indices: 28895100--28895228 Score: 80
Period size: 25 Copynumber: 5.4 Consensus size: 25
28895090 CCGAATGGCC
28895100 TATGTGATGAATGTGAACATGCATA
1 TATGTGATGAATGTGAACATGCATA
* *
28895125 TATGTGATGAA-GCCG-A-ATGGC-CA
1 TATGTGATGAATG-TGAACAT-GCATA
*
28895148 -ATGTGATGAATGTGAGCATGCATA
1 TATGTGATGAATGTGAACATGCATA
* * * *
28895172 TGTGTGAT-AAGGCCG-A-ATGGC-CA
1 TATGTGATGAATG-TGAACAT-GCATA
*
28895195 -ATGTGGTGAATGTGAACATGCATA
1 TATGTGATGAATGTGAACATGCATA
28895219 TATGTGATGA
1 TATGTGATGA
28895229 GGCCGAATGG
Statistics
Matches: 74, Mismatches: 16, Indels: 28
0.63 0.14 0.24
Matches are distributed among these distances:
22 17 0.23
23 15 0.20
24 15 0.20
25 27 0.36
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.28
Consensus pattern (25 bp):
TATGTGATGAATGTGAACATGCATA
Found at i:28895213 original size:141 final size:141
Alignment explanation
Indices: 28894959--28895388 Score: 729
Period size: 141 Copynumber: 3.0 Consensus size: 141
28894949 TTTAGGATTT
* *
28894959 TATGTGATGAATGTGAACACGCATATATGTGATGAGGCCGAATGGCCAATGTGATGAATGTGAGC
1 TATGTGATGAATGTGAACATGCATATATGTGATGAAGCCGAATGGCCAATGTGATGAATGTGAGC
28895024 ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGATAAG
66 ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGATAAG
28895089 GCCGAATGGCC
131 GCCGAATGGCC
28895100 TATGTGATGAATGTGAACATGCATATATGTGATGAAGCCGAATGGCCAATGTGATGAATGTGAGC
1 TATGTGATGAATGTGAACATGCATATATGTGATGAAGCCGAATGGCCAATGTGATGAATGTGAGC
* *
28895165 ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATGTGAACATGCATATATGTGATGAG
66 ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGATAAG
28895230 GCCGAATGGCC
131 GCCGAATGGCC
* * *
28895241 AATGTGATAAATGTGAGCATGCATATATGTGAT-AAGGCCGAATGGCCAATGTGATGAATGTGAG
1 TATGTGATGAATGTGAACATGCATATATGTGATGAA-GCCGAATGGCCAATGTGATGAATGTGAG
* * *
28895305 CATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAAAATGCATATATGCGGTAA
65 CATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGATAA
*
28895370 AGCCGAATGG-C
130 GGCCGAATGGCC
28895381 TAGTGTGA
1 TA-TGTGA
28895389 AATATGTAGG
Statistics
Matches: 273, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
140 4 0.01
141 269 0.99
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.26
Consensus pattern (141 bp):
TATGTGATGAATGTGAACATGCATATATGTGATGAAGCCGAATGGCCAATGTGATGAATGTGAGC
ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGCATATATGTGATAAG
GCCGAATGGCC
Found at i:28895344 original size:25 final size:25
Alignment explanation
Indices: 28895269--28895344 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
28895259 ATGCATATAT
28895269 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
28895294 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
28895316 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
28895341 GTGA
1 GTGA
28895345 ATATGAAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:28895593 original size:37 final size:37
Alignment explanation
Indices: 28895543--28895657 Score: 185
Period size: 37 Copynumber: 3.1 Consensus size: 37
28895533 GGAAATATAT
*
28895543 TCCGGGTGAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
28895580 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
28895617 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTACG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
28895654 TCCG
1 TCCG
28895658 AGCTAAAGGT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:28907230 original size:6 final size:6
Alignment explanation
Indices: 28907216--28907246 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
28907206 AAAACACAAT
*
28907216 TTGGTA TTGGCA TTGGCA TTGGCA TTGGCA T
1 TTGGCA TTGGCA TTGGCA TTGGCA TTGGCA T
28907247 CCCCCTTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.32, T:0.39
Consensus pattern (6 bp):
TTGGCA
Found at i:28915511 original size:28 final size:29
Alignment explanation
Indices: 28915467--28915522 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
28915457 AAATTTTAAA
*
28915467 AAAAAAGTATTTTAAAA-TAAAAAAAATC
1 AAAAAAGTATTTAAAAATTAAAAAAAATC
*
28915495 AAAAAAGT-TCTTAAAAATTCAAAAAAAT
1 AAAAAAGTAT-TTAAAAATTAAAAAAAAT
28915523 AACATGAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 1 0.04
28 14 0.58
29 9 0.38
ACGTcount: A:0.66, C:0.05, G:0.04, T:0.25
Consensus pattern (29 bp):
AAAAAAGTATTTAAAAATTAAAAAAAATC
Found at i:28917644 original size:48 final size:48
Alignment explanation
Indices: 28917565--28917658 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
28917555 AGGGAATTCT
* *
28917565 GTTGAATCCTTTATTGTTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
28917613 GTTGAATCCATTATTGGTG-GAAGTT-AGGCTGACTTAGGCGTTTTTA
1 GTTGAATCCATTATTGGTGCG-AGTTGA-GCTGACTTAGGCGTTTTTA
28917659 AGCCAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 2 0.05
48 40 0.95
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
Found at i:28918426 original size:31 final size:31
Alignment explanation
Indices: 28918382--28918450 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
28918372 TACAAAATGG
* *
28918382 TCACTAAATTATTCAAAAGTTTTCATTTAAA
1 TCACTAAACTATTCAAAAATTTTCATTTAAA
* *
28918413 TCGCTAAACTATTCAAAAATTTTTATTTAAA
1 TCACTAAACTATTCAAAAATTTTCATTTAAA
28918444 TCACTAA
1 TCACTAA
28918451 GTTGTTAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.41
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAATTTTCATTTAAA
Found at i:28927983 original size:37 final size:37
Alignment explanation
Indices: 28927933--28928011 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
28927923 TTATTACGAA
* *
28927933 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
28927970 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
28928007 GTCTT
1 GTCTT
28928012 TAGAGCTTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:28928208 original size:47 final size:47
Alignment explanation
Indices: 28928130--28928652 Score: 875
Period size: 47 Copynumber: 11.1 Consensus size: 47
28928120 CCCTTCGGGA
* * * * * * *
28928130 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28928177 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28928224 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28928271 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28928318 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28928365 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28928412 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28928459 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28928506 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28928553 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28928602 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28928649 CTTA
1 CTTA
28928653 CTATCATTTC
Statistics
Matches: 457, Mismatches: 17, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
47 411 0.90
49 46 0.10
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28942395 original size:13 final size:13
Alignment explanation
Indices: 28942377--28942403 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28942367 TTGTTTAGTC
28942377 AGTTAATTAGTTT
1 AGTTAATTAGTTT
28942390 AGTTAATTAGTTT
1 AGTTAATTAGTTT
28942403 A
1 A
28942404 ATAAACAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (13 bp):
AGTTAATTAGTTT
Found at i:28950728 original size:13 final size:13
Alignment explanation
Indices: 28950710--28950736 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28950700 TAGTTTAATC
28950710 AGTTAATTAGTTT
1 AGTTAATTAGTTT
28950723 AGTTAATTAGTTT
1 AGTTAATTAGTTT
28950736 A
1 A
28950737 ATAAACAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (13 bp):
AGTTAATTAGTTT
Found at i:28951854 original size:42 final size:44
Alignment explanation
Indices: 28951752--28951923 Score: 142
Period size: 43 Copynumber: 4.0 Consensus size: 44
28951742 AGCTCATACA
* * *
28951752 ATGCCAACGTCCCAG--ATGTGTTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACATG-GTTCTTACACGAAATCAAATATCG
* *
28951795 ATGCCATTGTCCCAGACA-GGTTCTTACACGAAATCATATA-CG
1 ATGCCAATGTCCCAGACATGGTTCTTACACGAAATCAAATATCG
* * * *
28951837 ATGCCAATGTCCTAGACATGG-TCTTAGACGAAAATCTCAA-ACCG
1 ATGCCAATGTCCCAGACATGGTTCTTACACG-AAATC-AAATATCG
* * ** *
28951881 ATGCCTACGTCCCAGATGTGG-TCTTACACGAAATCACATATCG
1 ATGCCAATGTCCCAGACATGGTTCTTACACGAAATCAAATATCG
28951924 GAATCCTATG
Statistics
Matches: 103, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
42 27 0.26
43 47 0.46
44 28 0.27
45 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACATGGTTCTTACACGAAATCAAATATCG
Found at i:28956260 original size:16 final size:17
Alignment explanation
Indices: 28956235--28956267 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28956225 AGTAAGTCAT
28956235 AATAAAATA-TCAACTC
1 AATAAAATATTCAACTC
*
28956251 AATAATATATTCAACTC
1 AATAAAATATTCAACTC
28956268 CTTAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAAAATATTCAACTC
Found at i:28956568 original size:50 final size:50
Alignment explanation
Indices: 28956509--28956628 Score: 222
Period size: 50 Copynumber: 2.4 Consensus size: 50
28956499 ATCACTCATC
*
28956509 TGGCCGAATATACAAGATCCAATATAACATCACATATGTACATACCTATA
1 TGGCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATA
28956559 TGGCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATA
1 TGGCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATA
*
28956609 TGGCCGAATATACAAAATCA
1 TGGCCGAATATACAAGATCA
28956629 TTTAGCTCAG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (50 bp):
TGGCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATA
Found at i:28957406 original size:30 final size:30
Alignment explanation
Indices: 28957364--28957428 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
28957354 TACCCAAACA
*
28957364 AGTCC-TCAAATTTCATT-TATTTTGCATTTT
1 AGTCCTTCAAATTT-ATTAT-TTTTGCAATTT
*
28957394 AGTCCTTC-AATTTATTATTTTTTCAATTT
1 AGTCCTTCAAATTTATTATTTTTGCAATTT
28957423 AGTCCT
1 AGTCCT
28957429 AATTACTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 18 0.58
30 11 0.35
31 2 0.06
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (30 bp):
AGTCCTTCAAATTTATTATTTTTGCAATTT
Found at i:28972095 original size:50 final size:49
Alignment explanation
Indices: 28972036--28972193 Score: 212
Period size: 50 Copynumber: 3.4 Consensus size: 49
28972026 ATCACTCATC
28972036 TGGCCGAATATACAAGATCCAATATAACATCACATATGTACATACCTATA
1 TGGCCGAATATACAAGAT-CAATATAACATCACATATGTACATACCTATA
28972086 TGGCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATA
1 TGGCCGAATATACAAGATC-AATATAACATCACATATGTACATACCTATA
*
28972136 TGGCCG-A-AT---AG------ATAACATCACGTATGTACATACCTATA
1 TGGCCGAATATACAAGATCAATATAACATCACATATGTACATACCTATA
28972174 TGGCCGAATATACAAGATCA
1 TGGCCGAATATACAAGATCA
28972194 TTTAGCTCAG
Statistics
Matches: 97, Mismatches: 1, Indels: 23
0.80 0.01 0.19
Matches are distributed among these distances:
38 32 0.33
39 1 0.01
40 2 0.02
43 2 0.02
45 2 0.02
48 2 0.02
49 2 0.02
50 54 0.56
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (49 bp):
TGGCCGAATATACAAGATCAATATAACATCACATATGTACATACCTATA
Found at i:28972151 original size:38 final size:38
Alignment explanation
Indices: 28972109--28972183 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
28972099 AAGATCAAAT
28972109 ATAACATCACATATGTACATACCTATATGGCCGAATAG
1 ATAACATCACATATGTACATACCTATATGGCCGAATAG
*
28972147 ATAACATCACGTATGTACATACCTATATGGCCGAATA
1 ATAACATCACATATGTACATACCTATATGGCCGAATA
28972184 TACAAGATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (38 bp):
ATAACATCACATATGTACATACCTATATGGCCGAATAG
Found at i:28974862 original size:43 final size:43
Alignment explanation
Indices: 28974814--28974952 Score: 131
Period size: 43 Copynumber: 3.3 Consensus size: 43
28974804 TCCCGGATGT
* * * *
28974814 GGTCTTACATGTAATTCAATATTGATGCCTCTGTCCCAGACAG
1 GGTCTTACACGTAATTCAATATCGATGCCTATGTCCCAGACAC
* * *
28974857 GGTCTTACACG-AAATCAGATA-CGATGCCGATGTCCCAGACAT
1 GGTCTTACACGTAATTCA-ATATCGATGCCTATGTCCCAGACAC
* * * * *
28974899 GGTCTTATACGTAAATCCCA-ATCGAGGCCTGTGTCCCAGACAC
1 GGTCTTACACGT-AATTCAATATCGATGCCTATGTCCCAGACAC
28974942 GGTCTTACACG
1 GGTCTTACACG
28974953 ATGTCTCAGA
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
42 33 0.43
43 41 0.53
44 3 0.04
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGTAATTCAATATCGATGCCTATGTCCCAGACAC
Found at i:28998128 original size:20 final size:20
Alignment explanation
Indices: 28998103--28998144 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
28998093 GTTCTTAATC
28998103 GTTACCTTATTAAGTTACCG
1 GTTACCTTATTAAGTTACCG
*
28998123 GTTACCTTATTAAGTTGCCG
1 GTTACCTTATTAAGTTACCG
28998143 GT
1 GT
28998145 AATCAATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
GTTACCTTATTAAGTTACCG
Found at i:29004663 original size:27 final size:27
Alignment explanation
Indices: 29004633--29004810 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
29004623 ATATTGAGCC
* *
29004633 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
29004660 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
29004687 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*** ** *
29004715 CGCACACTTAGTGCCGTATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
29004742 CGCACTCTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
29004769 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
29004796 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29004811 GTACAATTTA
Statistics
Matches: 117, Mismatches: 29, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
26 2 0.02
27 93 0.79
28 22 0.19
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:29004745 original size:55 final size:54
Alignment explanation
Indices: 29004633--29004810 Score: 150
Period size: 54 Copynumber: 3.3 Consensus size: 54
29004623 ATATTGAGCC
* * *
29004633 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
* * * *
29004687 CGCACACTTAGTGCTACATAGTTAGACTCGCACACTTAGTG-C-CGTATGGTCAATT
1 CGCACACTTAGTGCTACATAATCA-ACTCGCACACTTAGTGCCACGTA--ATCAAAT
* * ** * *
29004742 CGCACTCTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAAC-AAAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACGTAA-TCA-AAT
29004796 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29004811 GTACAATTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
53 5 0.05
54 52 0.53
55 40 0.41
56 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
Found at i:29012669 original size:27 final size:27
Alignment explanation
Indices: 29012639--29012816 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
29012629 ATATTGAGCC
* *
29012639 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
29012666 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
29012693 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*** ** *
29012721 CGCACACTTAGTGCCGTATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
29012748 CGCACTCTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
29012775 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
29012802 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29012817 GTACAATTTA
Statistics
Matches: 117, Mismatches: 29, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
26 2 0.02
27 93 0.79
28 22 0.19
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:29012751 original size:55 final size:54
Alignment explanation
Indices: 29012639--29012816 Score: 150
Period size: 54 Copynumber: 3.3 Consensus size: 54
29012629 ATATTGAGCC
* * *
29012639 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
* * * *
29012693 CGCACACTTAGTGCTACATAGTTAGACTCGCACACTTAGTG-C-CGTATGGTCAATT
1 CGCACACTTAGTGCTACATAATCA-ACTCGCACACTTAGTGCCACGTA--ATCAAAT
* * ** * *
29012748 CGCACTCTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAAC-AAAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACGTAA-TCA-AAT
29012802 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29012817 GTACAATTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
53 5 0.05
54 52 0.53
55 40 0.41
56 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
Found at i:29014673 original size:41 final size:41
Alignment explanation
Indices: 29014599--29014760 Score: 227
Period size: 41 Copynumber: 4.0 Consensus size: 41
29014589 CTTAAAAGCC
* * * **
29014599 ATCGGTGGATCCATGATCGGCAAGCAATAATGCGATCCTTA
1 ATCGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTTA
* *
29014640 ATCGGTGGATCCACGGTTGTCAAACAACCATGCGATCCTTA
1 ATCGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTTA
*
29014681 ATCGGTGGATCCACGATCGTCAAGCAACCATGCGAT-CTTCA
1 ATCGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTT-A
*
29014722 ATCGGTGGATCCACGGTCGTCAAGCAACCATGCAATCCT
1 ATCGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCT
29014761 CAATTTCTTC
Statistics
Matches: 107, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
40 3 0.03
41 102 0.95
42 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (41 bp):
ATCGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTTA
Found at i:29015157 original size:54 final size:54
Alignment explanation
Indices: 29015010--29015363 Score: 273
Period size: 54 Copynumber: 6.5 Consensus size: 54
29015000 TACAAGGGTG
* * * * * * * ** *
29015010 TTTGGTAAATCTACAAACCAAGGGCATTTCGGTAATTATACAAACCAATGATAT
1 TTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAATCAGGGGTAT
* ** * * *
29015064 TTTTGTAATTTTTGAAAGTTAAGGGTATTTCT-ATAATTTTATAAATCAGGGGTAT
1 TTTGGTAATTTTACAAA-TCAAGGGTATTT-TGGTAATTTTACAAATCAGGGGTAT
* * * *
29015119 TTCT-GTAATTTTCCAAATCAATGGTATTTTGGTAATTTTCCAAATTAGGGGTAT
1 TT-TGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAATCAGGGGTAT
** * * * * *
29015173 TTTGGTAATTTTACAAATTGAGGGTATTTCGATACTTTTACAAGTC-GATGGTAT
1 TTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAATCAG-GGGTAT
** * * *
29015227 TTTGGTAATTTTACAGGTCAAAGGTATTTTGGTAATTTCACAAATCAAGGGTAT
1 TTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAATCAGGGGTAT
** ** * * *
29015281 TTTAATAATTCCACAAACCAGGGGTATTTTGGTAATTTTACAAACCAGGGGTAT
1 TTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAATCAGGGGTAT
** *
29015335 TTTGGTAATTTTGTAAACCAAGGGTATTT
1 TTTGGTAATTTTACAAATCAAGGGTATTT
29015364 AGTAATTCTG
Statistics
Matches: 227, Mismatches: 66, Indels: 14
0.74 0.21 0.05
Matches are distributed among these distances:
53 3 0.01
54 185 0.81
55 38 0.17
56 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.40
Consensus pattern (54 bp):
TTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAATCAGGGGTAT
Found at i:29015201 original size:81 final size:81
Alignment explanation
Indices: 29015002--29015346 Score: 275
Period size: 81 Copynumber: 4.3 Consensus size: 81
29014992 TTTCACCCTA
* * * ** * * * *
29015002 CAAGGGT-GTTTGGTAAATCTACAAACCAAGGGCATTTCGGTAATTATACAAACCAATGATATTT
1 CAAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCTGTAATTTTACAAACCAATGGTATTT
* **
29015066 TTGTAATTTTTGAAAGT
66 TGGTAATTTTACAAA-T
* * * * * * *
29015083 TAAGGGTATTTCT-ATAATTTTATAAATCAGGGGTATTTCTGTAATTTTCCAAATCAATGGTATT
1 CAAGGGTATTT-TGGTAATTTTACAAATTAAGGGTATTTCTGTAATTTTACAAACCAATGGTATT
*
29015147 TTGGTAATTTTCCAAAT
65 TTGGTAATTTTACAAAT
* * * * ** *
29015164 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTC-GATACTTTTACAAGTCGATGGTATT
1 CAAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCTG-TAATTTTACAAACCAATGGTATT
**
29015228 TTGGTAATTTTACAGGT
65 TTGGTAATTTTACAAAT
* * * * ** **
29015245 CAAAGGTATTTTGGTAATTTCACAAATCAAGGGTATTT-TAATAATTCCACAAACCAGGGGTATT
1 CAAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCT-GTAATTTTACAAACCAATGGTATT
*
29015309 TTGGTAATTTTACAAAC
65 TTGGTAATTTTACAAAT
*
29015326 CAGGGGTATTTTGGTAATTTT
1 CAAGGGTATTTTGGTAATTTT
29015347 GTAAACCAAG
Statistics
Matches: 207, Mismatches: 51, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
80 2 0.01
81 150 0.72
82 54 0.26
83 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (81 bp):
CAAGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCTGTAATTTTACAAACCAATGGTATTT
TGGTAATTTTACAAAT
Found at i:29015352 original size:27 final size:27
Alignment explanation
Indices: 29015010--29015363 Score: 203
Period size: 27 Copynumber: 13.1 Consensus size: 27
29015000 TACAAGGGTG
* * * *
29015010 TTTGGTAAATCTACAAACCAAGGGCAT
1 TTTGGTAATTTTACAAACCAGGGGTAT
* * ** *
29015037 TTCGGTAATTATACAAACCAATGATAT
1 TTTGGTAATTTTACAAACCAGGGGTAT
* ** ** *
29015064 TTTTGTAATTTTTGAAAGTTAAGGGTAT
1 TTTGGTAATTTTACAAA-CCAGGGGTAT
* * *
29015092 TTCT-ATAATTTTATAAATCAGGGGTAT
1 TT-TGGTAATTTTACAAACCAGGGGTAT
* * **
29015119 TTCT-GTAATTTTCCAAATCAATGGTAT
1 TT-TGGTAATTTTACAAACCAGGGGTAT
* **
29015146 TTTGGTAATTTTCCAAATTAGGGGTAT
1 TTTGGTAATTTTACAAACCAGGGGTAT
**
29015173 TTTGGTAATTTTACAAA-TTGAGGGTAT
1 TTTGGTAATTTTACAAACCAG-GGGTAT
* * * ** *
29015200 TTCGATACTTTTACAAGTC-GATGGTAT
1 TTTGGTAATTTTACAAACCAG-GGGTAT
*** **
29015227 TTTGGTAATTTTACAGGTCAAAGGTAT
1 TTTGGTAATTTTACAAACCAGGGGTAT
* * *
29015254 TTTGGTAATTTCACAAATCAAGGGTAT
1 TTTGGTAATTTTACAAACCAGGGGTAT
** **
29015281 TTTAATAATTCCACAAACCAGGGGTAT
1 TTTGGTAATTTTACAAACCAGGGGTAT
29015308 TTTGGTAATTTTACAAACCAGGGGTAT
1 TTTGGTAATTTTACAAACCAGGGGTAT
** *
29015335 TTTGGTAATTTTGTAAACCAAGGGTAT
1 TTTGGTAATTTTACAAACCAGGGGTAT
29015362 TT
1 TT
29015364 AGTAATTCTG
Statistics
Matches: 263, Mismatches: 58, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
26 3 0.01
27 241 0.92
28 18 0.07
29 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.40
Consensus pattern (27 bp):
TTTGGTAATTTTACAAACCAGGGGTAT
Found at i:29015357 original size:81 final size:81
Alignment explanation
Indices: 29015141--29015371 Score: 241
Period size: 81 Copynumber: 2.9 Consensus size: 81
29015131 CCAAATCAAT
* * ** **
29015141 GGTATTTTGGTAATTTTCCAAATTAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGAT
1 GGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTAAT
* ** ** *
29015206 ACTTTTACAAGTCGAT
66 AATTCCACAAACCGAG
** ** *
29015222 GGTATTTTGGTAATTTTACAGGTCAAAGGTATTTTGGTAATTTCACAAATCAAGGGTATTTTAAT
1 GGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTAAT
29015287 AATTCCACAAACC-AGG
66 AATTCCACAAACCGA-G
* ** * *
29015303 GGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTA-TTTAGT
1 GGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTAAT
29015367 AATTC
66 AATTC
29015372 TGCCCTACAG
Statistics
Matches: 122, Mismatches: 27, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
80 11 0.09
81 111 0.91
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (81 bp):
GGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTAAT
AATTCCACAAACCGAG
Found at i:29015396 original size:27 final size:27
Alignment explanation
Indices: 29015361--29015423 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
29015351 ACCAAGGGTA
*
29015361 TTTAGTAATTCTGCCCTACAGGGGCAT
1 TTTAGTAATTCTACCCTACAGGGGCAT
*
29015388 TTTAGTAATTCTACCCTACAGGGGTAT
1 TTTAGTAATTCTACCCTACAGGGGCAT
29015415 TTTAGTAAT
1 TTTAGTAAT
29015424 ACTAGCTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (27 bp):
TTTAGTAATTCTACCCTACAGGGGCAT
Found at i:29015434 original size:27 final size:27
Alignment explanation
Indices: 29015356--29015435 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
29015346 TGTAAACCAA
29015356 GGGTA-TTTAGTAATTCT-GCCCTACAG
1 GGGTATTTTAGTAATTCTAG-CCTACAG
* *
29015382 GGGCATTTTAGTAATTCTACCCTACAG
1 GGGTATTTTAGTAATTCTAGCCTACAG
* *
29015409 GGGTATTTTAGTAATACTAGCTTACAG
1 GGGTATTTTAGTAATTCTAGCCTACAG
29015436 ATATGAGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.09
27 42 0.91
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (27 bp):
GGGTATTTTAGTAATTCTAGCCTACAG
Found at i:29031128 original size:39 final size:39
Alignment explanation
Indices: 29030898--29031127 Score: 370
Period size: 39 Copynumber: 5.9 Consensus size: 39
29030888 TACCAGTACA
* *
29030898 AAGCCTGCGGGACTTTAACCCGGATACATTTCCCGCACG
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
*
29030937 AAGCCTGCGGGACTTTGGCCCGGATACATTTCCAGCACG
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
*
29030976 AAGCCTGCGGGACTTTAGCCCAGATACATTTCCAGCACG
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
*
29031015 AAGCCTGCGGGACTTTGGCCCGGATACATTTCCAGCACG
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
* * * * *
29031054 AAGCCTGCGGGACTTTGGCCCAGATATATTTCCAGTACA
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
29031093 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAG
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAG
29031128 TGTCTTGCAT
Statistics
Matches: 177, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 177 1.00
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (39 bp):
AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
Found at i:29035425 original size:39 final size:40
Alignment explanation
Indices: 29035208--29035415 Score: 278
Period size: 40 Copynumber: 5.2 Consensus size: 40
29035198 CGGATGATAA
* * * * *
29035208 CCGGGATAAGTCCAGAAAGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
29035248 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
29035288 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
29035328 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
29035368 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
29035408 CC-GGCTAA
1 CCGGGCTAA
29035416 ATCTTGAAGG
Statistics
Matches: 152, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 8 0.05
40 143 0.94
41 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:29040024 original size:40 final size:40
Alignment explanation
Indices: 29039955--29040088 Score: 234
Period size: 40 Copynumber: 3.4 Consensus size: 40
29039945 AACCCAAGTA
* *
29039955 CCTTCGGGAATTAG-CCGGATATAGCAACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAATTG
*
29039994 CCTTCAGGACTTAGCCCGGATATAGTAACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAATTG
29040034 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAATTG
29040074 CCTTCGGGACTTAGC
1 CCTTCGGGACTTAGC
29040089 TCGGTTATCA
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 12 0.13
40 78 0.87
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAATTG
Found at i:29041626 original size:13 final size:13
Alignment explanation
Indices: 29041608--29041633 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29041598 ATTTTTATTT
29041608 TTAACATAAAATA
1 TTAACATAAAATA
29041621 TTAACATAAAATA
1 TTAACATAAAATA
29041634 ATTATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:29043794 original size:46 final size:46
Alignment explanation
Indices: 29043708--29043880 Score: 133
Period size: 47 Copynumber: 3.7 Consensus size: 46
29043698 TATCTGTGCT
* * * * **
29043708 GATGCTATGTCCTAGATATGGTCTTACACT-G-ACACATCTCGTAGTT
1 GATGC-ATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTCGTAGCA
*
29043754 GATGCATGTCCCAGACATGTCTTACACTAGCT-TACGTCTCG-AGGCA
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATCTCGTA-GCA
* * * *
29043800 GATTCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCA
1 GA-TGCATGTCCCAGACAT-GTCTTACACTAGCTCTCAT-CTCGTAG-CA
29043849 -ATGCATGTCCCAGACATGTCTTACACTAGCTC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTC
29043881 ACACAAGTGA
Statistics
Matches: 103, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
44 10 0.10
45 13 0.13
46 28 0.27
47 30 0.29
48 18 0.17
49 4 0.04
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCGTAGCA
Found at i:29043814 original size:47 final size:46
Alignment explanation
Indices: 29043758--29043880 Score: 135
Period size: 47 Copynumber: 2.6 Consensus size: 46
29043748 GTAGTTGATG
* *
29043758 CATGTCCCAGACATGTCTTACACTAGCT-TACGT-CTCGAGG-CAGATTC
1 CATGTCCCAGACATGTCTTACACTAGCTCT-CATAAT-GAGGCCA-A-TC
* * *
29043805 CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCAATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTCTCATAATGAGGCCAATC
29043852 CATGTCCCAGACATGTCTTACACTAGCTC
1 CATGTCCCAGACATGTCTTACACTAGCTC
29043881 ACACAAGTGA
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
46 14 0.21
47 29 0.44
48 19 0.29
49 4 0.06
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATAATGAGGCCAATC
Found at i:29046664 original size:68 final size:68
Alignment explanation
Indices: 29046498--29046673 Score: 150
Period size: 68 Copynumber: 2.6 Consensus size: 68
29046488 TAGTACCACT
* * * * *
29046498 CATGCGACCTAGC--CA-ATTTGTCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCTACATATATATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAAT
29046560 CACA
65 CACA
* * *
29046564 CATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGT
1 CATGCGACCTAGCTACATATATATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGA
29046626 ATCACA
63 ATCACA
**
29046632 CATGTTACCTAGCTACTATATAGTATCTCGTAGC-CTTCTTGT
1 CATGCGACCTAGCTAC-ATATA-TATCTCGTAGCTC-TCTTGT
29046674 ACACATGATG
Statistics
Matches: 90, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
66 13 0.14
67 1 0.01
68 35 0.39
69 9 0.10
70 6 0.07
71 26 0.29
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (68 bp):
CATGCGACCTAGCTACATATATATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATC
ACA
Found at i:29048087 original size:20 final size:19
Alignment explanation
Indices: 29048046--29048090 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
29048036 ATTAGAATGT
29048046 AAAAATTAAACTAAAAACA
1 AAAAATTAAACTAAAAACA
*
29048065 AAAATATTAAATTAAAATA-A
1 AAAA-ATTAAACTAAAA-ACA
29048085 AAAAAT
1 AAAAAT
29048091 GGCTAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.26
20 16 0.70
21 1 0.04
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAATTAAACTAAAAACA
Found at i:29050474 original size:19 final size:19
Alignment explanation
Indices: 29050452--29050490 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
29050442 ATTGCAATTT
* *
29050452 TAATTTTTATTTTATTTTC
1 TAATTCTTAGTTTATTTTC
*
29050471 TAATTCTTCGTTTATTTTC
1 TAATTCTTAGTTTATTTTC
29050490 T
1 T
29050491 TCTCGCAGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.10, G:0.03, T:0.69
Consensus pattern (19 bp):
TAATTCTTAGTTTATTTTC
Found at i:29053863 original size:25 final size:25
Alignment explanation
Indices: 29053834--29053901 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
29053824 ATCTTTTAAT
29053834 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
29053859 AACTGAGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
* *
29053884 AACTAGGGCATAGCCCTT
1 AACTGGGGCAAAGCCCTT
29053902 CTGCACTTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:29053962 original size:10 final size:10
Alignment explanation
Indices: 29053949--29053983 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
29053939 ATATATGTAT
29053949 ATATCATGGC
1 ATATCATGGC
29053959 ATATCATGTGC
1 ATATCATG-GC
29053970 ATATCATGGC
1 ATATCATGGC
29053980 ATAT
1 ATAT
29053984 TATGTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (10 bp):
ATATCATGGC
Found at i:29053996 original size:21 final size:21
Alignment explanation
Indices: 29053937--29053996 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
29053927 CCCAACCCAT
*
29053937 GCATA-TATGTATATATCATG
1 GCATATTATGTACATATCATG
* *
29053957 GCATATCATGTGCATATCATG
1 GCATATTATGTACATATCATG
*
29053978 GCATATTATGTACAAATCA
1 GCATATTATGTACATATCA
29053997 GTATCACATG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (21 bp):
GCATATTATGTACATATCATG
Found at i:29059885 original size:105 final size:105
Alignment explanation
Indices: 29059765--29059955 Score: 364
Period size: 105 Copynumber: 1.8 Consensus size: 105
29059755 ACCTTGAGCC
* *
29059765 TACTACTAACATCAAGCCCTTTCCCTTTTCCTTTACCTTTTCCCTTCACAATCGATGCCCTAGCC
1 TACTACCAACATCAAGCCCTTTCCCTTTTCCTTTACCTTTGCCCTTCACAATCGATGCCCTAGCC
29059830 ATAGATTCCTTATTTTCCCCTCCTGATTGTGGCCTACCTT
66 ATAGATTCCTTATTTTCCCCTCCTGATTGTGGCCTACCTT
29059870 TACTACCAACATCAAGCCCTTTCCCTTTTCCTTTACCTTTGCCCTTCACAATCGATGCCCTAGCC
1 TACTACCAACATCAAGCCCTTTCCCTTTTCCTTTACCTTTGCCCTTCACAATCGATGCCCTAGCC
29059935 ATAGATTCCTTATTTTCCCCT
66 ATAGATTCCTTATTTTCCCCT
29059956 TCTAATTGAG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 84 1.00
ACGTcount: A:0.19, C:0.36, G:0.08, T:0.37
Consensus pattern (105 bp):
TACTACCAACATCAAGCCCTTTCCCTTTTCCTTTACCTTTGCCCTTCACAATCGATGCCCTAGCC
ATAGATTCCTTATTTTCCCCTCCTGATTGTGGCCTACCTT
Found at i:29063294 original size:12 final size:12
Alignment explanation
Indices: 29063277--29063301 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29063267 GTCGTAAATA
29063277 GCCTACCACACG
1 GCCTACCACACG
29063289 GCCTACCACACG
1 GCCTACCACACG
29063301 G
1 G
29063302 TCTGTGTCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.48, G:0.20, T:0.08
Consensus pattern (12 bp):
GCCTACCACACG
Found at i:29077359 original size:25 final size:25
Alignment explanation
Indices: 29077327--29077384 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
29077317 TACTTTTATC
29077327 TTTA-TTTATCTT-CTTTAAGTACTT
1 TTTATTTTATCTTCCTTTAA-TACTT
* *
29077351 TTTATTTTATTTTCCTTTAATATTT
1 TTTATTTTATCTTCCTTTAATACTT
29077376 TTTCATTTT
1 TTT-ATTTT
29077385 TAGGTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.14
25 14 0.48
26 11 0.38
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTATTTTATCTTCCTTTAATACTT
Found at i:29080517 original size:76 final size:76
Alignment explanation
Indices: 29080404--29080557 Score: 290
Period size: 76 Copynumber: 2.0 Consensus size: 76
29080394 TATGCCTTCA
*
29080404 TCGTGATAATATTTAGTTTCAAGAATGATTAATTATAAATTTTTAAAACCTGTTGCGAATATCAC
1 TCGTGATAATATTTAGTTTCAAGAATGATTAATTATAAATTTTTAAAACCTGTCGCGAATATCAC
29080469 ATATCACGCAC
66 ATATCACGCAC
29080480 TCGTGATAATATTTAGTTTCAAGAATGATTAATTATAAATTTTTAAAACCTGTCGCGAATATCAC
1 TCGTGATAATATTTAGTTTCAAGAATGATTAATTATAAATTTTTAAAACCTGTCGCGAATATCAC
*
29080545 GTATCACGCAC
66 ATATCACGCAC
29080556 TC
1 TC
29080558 ACAAGACTAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (76 bp):
TCGTGATAATATTTAGTTTCAAGAATGATTAATTATAAATTTTTAAAACCTGTCGCGAATATCAC
ATATCACGCAC
Found at i:29083690 original size:52 final size:52
Alignment explanation
Indices: 29083607--29083712 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
29083597 TAATGCCTTC
*
29083607 ATATTTTTAGCGTGAAAACCACCGGAACTAGTTCCAAGTCATGGGTTGGGTA
1 ATATTTTTAGCGTGAAAACCACCGCAACTAGTTCCAAGTCATGGGTTGGGTA
* *
29083659 ATATTTTTAGCGTGAAAACCACTGCAGCTAGTTCCAAGTCATGGGTTGGGTA
1 ATATTTTTAGCGTGAAAACCACCGCAACTAGTTCCAAGTCATGGGTTGGGTA
29083711 AT
1 AT
29083713 TTACCTCGTG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (52 bp):
ATATTTTTAGCGTGAAAACCACCGCAACTAGTTCCAAGTCATGGGTTGGGTA
Found at i:29085175 original size:14 final size:15
Alignment explanation
Indices: 29085158--29085186 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29085148 GCCTAATAGA
29085158 CTTA-TCACAATAAT
1 CTTATTCACAATAAT
29085172 CTTATTCACAATAAT
1 CTTATTCACAATAAT
29085187 TTCAAGCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (15 bp):
CTTATTCACAATAAT
Found at i:29086945 original size:17 final size:18
Alignment explanation
Indices: 29086923--29086956 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29086913 CACATTAAAG
29086923 TGTTTT-ATCGAAAACCT
1 TGTTTTCATCGAAAACCT
*
29086940 TGTTTTCATTGAAAACC
1 TGTTTTCATCGAAAACC
29086957 CTTCTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (18 bp):
TGTTTTCATCGAAAACCT
Found at i:29088261 original size:28 final size:28
Alignment explanation
Indices: 29088219--29088342 Score: 154
Period size: 28 Copynumber: 4.7 Consensus size: 28
29088209 TGGCCCCTTT
* *
29088219 AGGCCCAATCTCATTCATATGGCCCATT
1 AGGCCCAATCACATTCATATGGCCCATC
*
29088247 GGGCCCAATCACATTCATATGG-CC--C
1 AGGCCCAATCACATTCATATGGCCCATC
29088272 A----CAATCACATTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
* *
29088296 AGGCCCAATCACTTTCATATGGCCCGTC
1 AGGCCCAATCACATTCATATGGCCCATC
29088324 AGGCCCAATCACATTCATA
1 AGGCCCAATCACATTCATA
29088343 ATCATGCAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 14
0.80 0.07 0.14
Matches are distributed among these distances:
21 17 0.21
22 2 0.02
24 2 0.02
27 2 0.02
28 59 0.72
ACGTcount: A:0.27, C:0.34, G:0.15, T:0.24
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Found at i:29088278 original size:21 final size:21
Alignment explanation
Indices: 29088252--29088293 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
29088242 CCATTGGGCC
29088252 CAATCACATTCATATGGCCCA
1 CAATCACATTCATATGGCCCA
29088273 CAATCACATTCATATGGCCCA
1 CAATCACATTCATATGGCCCA
29088294 TCAGGCCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.24
Consensus pattern (21 bp):
CAATCACATTCATATGGCCCA
Found at i:29088290 original size:49 final size:49
Alignment explanation
Indices: 29088224--29088320 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
29088214 CCTTTAGGCC
* **
29088224 CAATCTCATTCATATGGCCCATTGGGCCCAATCACATTCATATGGCCCA
1 CAATCACATTCATATGGCCCATCAGGCCCAATCACATTCATATGGCCCA
*
29088273 CAATCACATTCATATGGCCCATCAGGCCCAATCACTTTCATATGGCCC
1 CAATCACATTCATATGGCCCATCAGGCCCAATCACATTCATATGGCCC
29088321 GTCAGGCCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.27, C:0.34, G:0.13, T:0.26
Consensus pattern (49 bp):
CAATCACATTCATATGGCCCATCAGGCCCAATCACATTCATATGGCCCA
Done.