Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 59 of 85
Found at i:20598416 original size:44 final size:44
Alignment explanation
Indices: 20598368--20598552 Score: 117
Period size: 44 Copynumber: 4.2 Consensus size: 44
20598358 CCAGTAATTC
20598368 TATCTCCCTGGGCAGTAGTAGAATAAATTAAATATTACAGATCT
1 TATCTCCCTGGGCAGTAGTAGAATAAATTAAATATTACAGATCT
** * ** * * *** *
20598412 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGGTAGATTT
1 TATCTCCCTGGGCAGTAGTAGAATAAATTAAATATTACAGATCT
* * * * * * * * * *
20598456 TACCTCCTTGAGGTTA-CAGTGGAGTACATTAAAGCCAGTA-A-TTC-
1 TATCTCCCTG-GG-CAGTAGTAGAATAAATTAAA--TATTACAGATCT
20598500 TATCTCCCTGGGCAGTAGTAGAATAAATTAAATATTACAGATCT
1 TATCTCCCTGGGCAGTAGTAGAATAAATTAAATATTACAGATCT
20598544 TATCTCCCT
1 TATCTCCCT
20598553 AAGTAGTAGT
Statistics
Matches: 97, Mismatches: 36, Indels: 16
0.65 0.24 0.11
Matches are distributed among these distances:
41 3 0.03
42 2 0.02
43 17 0.18
44 57 0.59
45 15 0.15
46 2 0.02
47 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (44 bp):
TATCTCCCTGGGCAGTAGTAGAATAAATTAAATATTACAGATCT
Found at i:20598520 original size:132 final size:132
Alignment explanation
Indices: 20598312--20599293 Score: 1557
Period size: 132 Copynumber: 7.5 Consensus size: 132
20598302 GGAGCAGGTT
* *
20598312 GATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTAAAGCCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* * * * *
20598377 GGGCAGTAGTAGAATAAATTAAATATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
20598442 AA
131 AA
* ** * *
20598444 TATGGTAGATTTTACCTCCTTGAGGTTACAGTGGAGTACATTAAAGCCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* * * * * * *
20598509 GGGCAGTAGTAGAATAAATTAAATATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
*
20598574 AG
131 AA
20598576 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* *
20598641 GGGCAGCAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCTAAACAGTAGTGGAGCAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
*
20598706 AG
131 AA
20598708 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* *
20598773 GGGCAGCAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATGA
66 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
*
20598838 AT
131 AA
*
20598840 GATAGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* * *
20598905 GAGCAGCAGTGGAATATATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGAGGAGCAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
20598970 AA
131 AA
20598972 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
*
20599037 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
66 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
20599102 AA
131 AA
* * * *
20599104 GATGGCGAATTTTACCTCCATGAGGTTACAGTGGAGTACATT-------G-AATTCCATCTCCAT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
*
20599161 GGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
20599226 AA
131 AA
* * *
20599228 GATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTATATTGAAGCCAGTAATTCTAACTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
20599293 G
66 G
20599294 ATCGGTAGTG
Statistics
Matches: 794, Mismatches: 48, Indels: 16
0.93 0.06 0.02
Matches are distributed among these distances:
124 115 0.14
125 1 0.00
131 1 0.00
132 677 0.85
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
AA
Found at i:20598680 original size:44 final size:44
Alignment explanation
Indices: 20598632--20599223 Score: 190
Period size: 44 Copynumber: 13.6 Consensus size: 44
20598622 CCAGTAATTC
*
20598632 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAAATCT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAAATCT
*** * * * ** ** *
20598676 TATCTCCCTAAACAGTAGTGGAGCAGA-TCAAGGATGGCGGATTT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAA-GATTACAAATCT
* * * * *
20598720 TACCTCCCTGAGGTTA-CAGTGGAGTACATTGAAGCCAGT--AATTC-
1 TATCTCCCTG-GG-CAGCAGTGGAGTAGATTGAAG--ATTACAAATCT
*
20598764 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAAATCT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAAATCT
** * * ** *
20598808 TATCTCCCTAAGCAGTAGTGGAGCAGA-TGAATGA-TAGCGGATTT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAA-GATTA-CAAATCT
* * * * *
20598852 TACCTCCCTGAGGTTA-CAGTGGAGTACATTGAAGCCAGT--AATTC-
1 TATCTCCCTG-GG-CAGCAGTGGAGTAGATTGAAG--ATTACAAATCT
* * * *
20598896 TATCTCCCTGAGCAGCAGTGGAATATATTGAAGATTACAGATCT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAAATCT
** * * * ** ** ** *
20598940 TATCTCCCTAAGCAGTAGAGGAGCAGATCAAAGATGGCGGATTT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAAATCT
* * * * *
20598984 TACCTCCCTGAGGTTA-CAGTGGAGTACATTGAAGCCAGT--AATTC-
1 TATCTCCCTG-GG-CAGCAGTGGAGTAGATTGAAG--ATTACAAATCT
* *
20599028 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAAATCT
** * * * ** * *
20599072 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATTT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAAATCT
* * * *
20599116 TACCTCCATGAGGTTA-CAGTGGAGTACATTG-A-ATT-C----C-
1 TATCTCCCTG-GG-CAGCAGTGGAGTAGATTGAAGATTACAAATCT
* * * *
20599153 -ATCTCCATGGGCAACAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAAATCT
** * *
20599196 TATCTCCCTAAGCAGTAGTGGAGCAGAT
1 TATCTCCCTGGGCAGCAGTGGAGTAGAT
20599224 CAAAGATGGT
Statistics
Matches: 378, Mismatches: 128, Indels: 84
0.64 0.22 0.14
Matches are distributed among these distances:
34 1 0.00
35 15 0.04
36 9 0.02
37 3 0.01
38 1 0.00
41 6 0.02
42 5 0.01
43 74 0.20
44 200 0.53
45 49 0.13
46 11 0.03
47 3 0.01
48 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAAATCT
Found at i:20599221 original size:124 final size:124
Alignment explanation
Indices: 20599023--20599272 Score: 428
Period size: 124 Copynumber: 2.0 Consensus size: 124
20599013 TGAAGCCAGT
* * *
20599023 AATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
1 AATTCCATCTCCATGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
*
20599088 AGTGGAGCAGATCGAAGATGGCGAATTTTACCTCCATGAGGTTACAGTGGAGTACATTG
66 AGTGGAGCAGATCAAAGATGGCGAATTTTACCTCCATGAGGTTACAGTGGAGTACATTG
20599147 AATTCCATCTCCATGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
1 AATTCCATCTCCATGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
* * * *
20599212 AGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTATATTG
66 AGTGGAGCAGATCAAAGATGGCGAATTTTACCTCCATGAGGTTACAGTGGAGTACATTG
20599271 AA
1 AA
20599273 GCCAGTAATT
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 118 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (124 bp):
AATTCCATCTCCATGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCAAAGATGGCGAATTTTACCTCCATGAGGTTACAGTGGAGTACATTG
Found at i:20599416 original size:44 final size:44
Alignment explanation
Indices: 20599309--20599422 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 44
20599299 TAGTGGAATC
* * * * *
20599309 GATCGAAGAAAG-AAGATATTGCCTTCATGTATTAGCGTGGAGTA
1 GATCAAAGAAAGCAA-ATCTTGTCTTCATGTATTAGCATGAAGTA
* * *
20599353 GATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTA
1 GATCAAAGAAAGCAAATCTTGTCTTCATGTATTAGCATGAAGTA
*
20599397 GATCAAAGAGAGCAAATCTTGTCTTC
1 GATCAAAGAAAGCAAATCTTGTCTTC
20599423 CCATACTGGT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
44 59 0.98
45 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (44 bp):
GATCAAAGAAAGCAAATCTTGTCTTCATGTATTAGCATGAAGTA
Found at i:20608974 original size:18 final size:18
Alignment explanation
Indices: 20608939--20608976 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
20608929 TTTTGTTTTC
20608939 TAAAAAACCAGAATATTA
1 TAAAAAACCAGAATATTA
*
20608957 TAAAATAACCATAA-ATTA
1 TAAAA-AACCAGAATATTA
20608975 TA
1 TA
20608977 GGGTAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAAAAACCAGAATATTA
Found at i:20622541 original size:44 final size:44
Alignment explanation
Indices: 20622470--20622700 Score: 257
Period size: 44 Copynumber: 5.2 Consensus size: 44
20622460 CATAGCAAAC
* ** * *
20622470 CTTATCTCCCAGAAGTTGTAGTGGAGCAAATTGAAGCTACGAAT
1 CTTATCTCCCTGAAGTTACAGTAGAGCAGATTGAAGCTACGAAT
* * * * *
20622514 CTCATCTCTCTGAAGTTACAATAGAGCAGATTGGAGCTATGAAT
1 CTTATCTCCCTGAAGTTACAGTAGAGCAGATTGAAGCTACGAAT
* * *
20622558 CTTATCTCCCT-AGAGTTGCAGTAGAGCAGATTGGAGTTACGAAT
1 CTTATCTCCCTGA-AGTTACAGTAGAGCAGATTGAAGCTACGAAT
* *
20622602 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGCTACAAAT
1 CTTATCTCCCTGAAGTTACAGTAGAGCAGATTGAAGCTACGAAT
* * * * *
20622646 CTTATCTCCTTGAAGTTATAGTGGAGCAGATTGAAGCAACAAAT
1 CTTATCTCCCTGAAGTTACAGTAGAGCAGATTGAAGCTACGAAT
*
20622690 TTTATCTCCCT
1 CTTATCTCCCT
20622701 AAAACTGCAG
Statistics
Matches: 159, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
43 1 0.01
44 157 0.99
45 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTACAGTAGAGCAGATTGAAGCTACGAAT
Found at i:20622710 original size:132 final size:132
Alignment explanation
Indices: 20622470--20622711 Score: 315
Period size: 132 Copynumber: 1.8 Consensus size: 132
20622460 CATAGCAAAC
* * *
20622470 CTTATCTCCCAGAAGTTGTAGTGGAGCAAATTGAAGCTACGAATCTCATCTCTCTGAAGTTACAA
1 CTTATCTCCCAGAAGTTGCAGTAGAGCAAATTGAAGCTACAAATCTCATCTCTCTGAAGTTACAA
* * ** * **
20622535 TAGAGCAGATTGGAGCTATGAATCTTATCTCCCTAGAGTTGCAGTAGAGCAGATTGGAGTTACGA
66 TAGAGCAGATTGAAGCAACAAATCTTATCTCCCTAAAACTGCAGTAGAGCAGATTGGAGTTACGA
20622600 AT
131 AT
* * * *
20622602 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGCTACAAATCTTATCTC-CTTGAAGTTATA
1 CTTATCTCCCAGAAGTTGCAGTAGAGCAAATTGAAGCTACAAATCTCATCTCTC-TGAAGTTACA
* * *
20622666 GTGGAGCAGATTGAAGCAACAAATTTTATCTCCCTAAAACTGCAGT
65 ATAGAGCAGATTGAAGCAACAAATCTTATCTCCCTAAAACTGCAGT
20622712 GGAACAAGAC
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
131 1 0.01
132 91 0.99
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (132 bp):
CTTATCTCCCAGAAGTTGCAGTAGAGCAAATTGAAGCTACAAATCTCATCTCTCTGAAGTTACAA
TAGAGCAGATTGAAGCAACAAATCTTATCTCCCTAAAACTGCAGTAGAGCAGATTGGAGTTACGA
AT
Found at i:20622711 original size:88 final size:88
Alignment explanation
Indices: 20622465--20622700 Score: 285
Period size: 88 Copynumber: 2.7 Consensus size: 88
20622455 GTCACCATAG
* * * * *
20622465 CAAACCTTATCTCCCAGAAGTTGTAGTGGAGCAAATTGAAGCTACGAATCTCATCTCTCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCTACGAATCTTATCTCCCTGAAGT
* * *
20622530 TACAATAGAGCAGATTGGAGCTA
66 TGCAGTAGAGCAGATTGAAGCTA
** * * * *
20622553 TGAATCTTATCTCCCT-AGAGTTGCAGTAGAGCAGATTGGAGTTACGAATCTTATCTCCCTGAAG
1 CAAATCTTATCTCCCTGA-AGTTGTAGTGGAGCAGATTGAAGCTACGAATCTTATCTCCCTGAAG
20622617 TTGCAGTAGAGCAGATTGAAGCTA
65 TTGCAGTAGAGCAGATTGAAGCTA
* * * * *
20622641 CAAATCTTATCTCCTTGAAGTTATAGTGGAGCAGATTGAAGCAACAAATTTTATCTCCCT
1 CAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCTACGAATCTTATCTCCCT
20622701 AAAACTGCAG
Statistics
Matches: 121, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
87 1 0.01
88 119 0.98
89 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (88 bp):
CAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCTACGAATCTTATCTCCCTGAAGT
TGCAGTAGAGCAGATTGAAGCTA
Found at i:20622925 original size:44 final size:43
Alignment explanation
Indices: 20622842--20622939 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 43
20622832 ATCTTATTTT
* *
20622842 CCTGAAGTTGTAGTGGACGAAGATGAAGCTACAACTCCTATATC
1 CCTGAAGTTGTAGTGGAC-AAGATGAAACTACAACTCCTATACC
* * *
20622886 CCTGAATTTGTAGTGGATC-AGATTGAAACTATAATTCCTATACC
1 CCTGAAGTTGTAGTGGA-CAAGA-TGAAACTACAACTCCTATACC
*
20622930 CCTGAGGTTG
1 CCTGAAGTTG
20622940 CAGTAGGTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
43 3 0.07
44 41 0.91
45 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (43 bp):
CCTGAAGTTGTAGTGGACAAGATGAAACTACAACTCCTATACC
Found at i:20623700 original size:7 final size:7
Alignment explanation
Indices: 20623684--20623730 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
20623674 GCAAAATATG
*
20623684 AAAAAGA
1 AAAAACA
20623691 AAAAACA
1 AAAAACA
20623698 AAAAACA
1 AAAAACA
20623705 AAAAACA
1 AAAAACA
*
20623712 AAAAAGA
1 AAAAACA
*
20623719 AAAAAGA
1 AAAAACA
20623726 AAAAA
1 AAAAA
20623731 AGAAGGTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:20623701 original size:14 final size:14
Alignment explanation
Indices: 20623684--20623730 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
20623674 GCAAAATATG
20623684 AAAAAGAAAAAACA
1 AAAAAGAAAAAACA
*
20623698 AAAAACAAAAAACA
1 AAAAAGAAAAAACA
*
20623712 AAAAAGAAAAAAGA
1 AAAAAGAAAAAACA
20623726 AAAAA
1 AAAAA
20623731 AGAAGGTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAACA
Found at i:20633047 original size:239 final size:239
Alignment explanation
Indices: 20632628--20633105 Score: 940
Period size: 239 Copynumber: 2.0 Consensus size: 239
20632618 GTAAAATTAC
20632628 ACTTTAACCCCCTAAATATAATAAAATTTTAATTTAATCTTTTAAAAATTATATTTTTACTATAT
1 ACTTTAACCCCCTAAATATAATAAAATTTTAATTTAATCTTTTAAAAATTATATTTTTACTATAT
20632693 TAAAATTTACAATTTAACTTCAGCCCCTAAAATATTTTATGACTTCGCCTTGCATAGGAGAGTTG
66 TAAAATTTACAATTTAACTTCAGCCCCTAAAATATTTTATGACTTCGCCTTGCATAGGAGAGTTG
20632758 AGTGATATGTATAAGTATGTGTTTGATAGATAACCCATTAGGGATTGTTTTTAAATATAGGTATA
131 AGTGATATGTATAAGTATGTGTTTGATAGATAACCCATTAGGGATTGTTTTTAAATATAGGTATA
20632823 TATTTTATTGCAGTTAATGAAGCCAGATCCAATGTTTGTGGCTA
196 TATTTTATTGCAGTTAATGAAGCCAGATCCAATGTTTGTGGCTA
20632867 ACTTTAACCCCCTAAAATATAAT-AAATTTTAATTTAATCTTTTAAAAATTATATTTTTACTATA
1 ACTTTAACCCCCT-AAATATAATAAAATTTTAATTTAATCTTTTAAAAATTATATTTTTACTATA
20632931 TTAAAATTTACAATTTAACTTCAGCCCCTAAAATATTTTATGACTTCGCCTTGCATAGGAGAGTT
65 TTAAAATTTACAATTTAACTTCAGCCCCTAAAATATTTTATGACTTCGCCTTGCATAGGAGAGTT
20632996 GAGTGATATGTATAAGTATGTGTTTGATAGATAACCCATTAGGGATTGTTTTTAAATATAGGTAT
130 GAGTGATATGTATAAGTATGTGTTTGATAGATAACCCATTAGGGATTGTTTTTAAATATAGGTAT
20633061 ATATTTTATTGCAGTTAATGAAGCCAGATCCAATGTTTGTGGCTA
195 ATATTTTATTGCAGTTAATGAAGCCAGATCCAATGTTTGTGGCTA
20633106 CGAAACTGTT
Statistics
Matches: 238, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
239 229 0.96
240 9 0.04
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (239 bp):
ACTTTAACCCCCTAAATATAATAAAATTTTAATTTAATCTTTTAAAAATTATATTTTTACTATAT
TAAAATTTACAATTTAACTTCAGCCCCTAAAATATTTTATGACTTCGCCTTGCATAGGAGAGTTG
AGTGATATGTATAAGTATGTGTTTGATAGATAACCCATTAGGGATTGTTTTTAAATATAGGTATA
TATTTTATTGCAGTTAATGAAGCCAGATCCAATGTTTGTGGCTA
Found at i:20635455 original size:31 final size:30
Alignment explanation
Indices: 20635401--20635481 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
20635391 ACTTTTTCTT
* * *
20635401 AATTTGGTACTTAAACTTTTTTTAAGGCCC
1 AATTTGGTACCTAAATTTTTTTTTAGGCCC
* ***
20635431 AATTTGGTACCTAAGTTTTTTTTTAGGTTT
1 AATTTGGTACCTAAATTTTTTTTTAGGCCC
20635461 AATTTGGTACCTAAATTTTTT
1 AATTTGGTACCTAAATTTTTT
20635482 AAATGTTATA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.51
Consensus pattern (30 bp):
AATTTGGTACCTAAATTTTTTTTTAGGCCC
Found at i:20635705 original size:24 final size:23
Alignment explanation
Indices: 20635667--20635712 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
20635657 TTTCAACTAA
20635667 TAAAATAATTAAATAAATAAAAC
1 TAAAATAATTAAATAAATAAAAC
* *
20635690 TAAAAGTAATTGAATATATAAAA
1 TAAAA-TAATTAAATAAATAAAA
20635713 TACAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (23 bp):
TAAAATAATTAAATAAATAAAAC
Found at i:20635760 original size:104 final size:104
Alignment explanation
Indices: 20635646--20635843 Score: 380
Period size: 104 Copynumber: 1.9 Consensus size: 104
20635636 AACTTAAAAT
20635646 AAATTCATTATTTTCAACTAATAAAAT-AATTAAATAAATAAAACTAAAAGTAATTGAATATATA
1 AAATTCATTATTTTCAACTAATAAAATAAATTAAAT-AATAAAACTAAAAGTAATTGAATATATA
20635710 AAATACAAAAAAAATCATGTCATCTGTCACCACAACTTAA
65 AAATACAAAAAAAATCATGTCATCTGTCACCACAACTTAA
20635750 AAATTCATTATTTTCAACTAATAAAATAAATTAAATAATAAAACTAAAAGTAATTGAATATATAA
1 AAATTCATTATTTTCAACTAATAAAATAAATTAAATAATAAAACTAAAAGTAATTGAATATATAA
20635815 AATACAAAAAAAATCATGTCATCTGTCAC
66 AATACAAAAAAAATCATGTCATCTGTCAC
20635844 ATGTCGATTA
Statistics
Matches: 93, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
104 85 0.91
105 8 0.09
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (104 bp):
AAATTCATTATTTTCAACTAATAAAATAAATTAAATAATAAAACTAAAAGTAATTGAATATATAA
AATACAAAAAAAATCATGTCATCTGTCACCACAACTTAA
Found at i:20635985 original size:31 final size:31
Alignment explanation
Indices: 20635950--20636101 Score: 132
Period size: 31 Copynumber: 5.0 Consensus size: 31
20635940 CAAAAAAAAG
20635950 TAGGTACCAAATTAGGAAAAAGAGTCAAGTT
1 TAGGTACCAAATTAGGAAAAAGAGTCAAGTT
* **** ** *
20635981 TAGGTACCAAA--ATGAACCCCCA-AAAAGAT
1 TAGGTACCAAATTAGGAA-AAAGAGTCAAGTT
* * * *
20636010 TAAGTACCAACTTAAGAAAAAGTGTCAAGTT
1 TAGGTACCAAATTAGGAAAAAGAGTCAAGTT
20636041 TAGGTACCAAATTAGGAAAAA-ATGTCAAGTT
1 TAGGTACCAAATTAGGAAAAAGA-GTCAAGTT
* *
20636072 TAGGTACCAAATTAGAAAAAAGTGTCAAGT
1 TAGGTACCAAATTAGGAAAAAGAGTCAAGT
20636102 CATATTAAGC
Statistics
Matches: 90, Mismatches: 25, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
29 17 0.19
30 1 0.01
31 72 0.80
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.22
Consensus pattern (31 bp):
TAGGTACCAAATTAGGAAAAAGAGTCAAGTT
Found at i:20641031 original size:226 final size:227
Alignment explanation
Indices: 20640626--20641079 Score: 901
Period size: 226 Copynumber: 2.0 Consensus size: 227
20640616 ACAAGTTTTA
20640626 AAAATATAATGTATAATAAAATTATATAAATAATTTAATATTTGTAGAAAATAAATTTCTCCTTT
1 AAAATATAATGTATAATAAAATTATATAAATAATTTAATATTTGTAGAAAATAAATTTCTCCTTT
20640691 GAGTAGCATAATTTTTTTGAACCACTAACTAGCATAATTTTAATTTTTAATTAATTTGATAAATG
66 GAGTAGCATAATTTTTTTGAACCACTAACTAGCATAATTTTAATTTTTAATTAATTTGATAAATG
20640756 ATTTGACACTAATTCAGATTATTAGTGATACATATTGCTTATTGTGGATTTAAAAATTAAAAATA
131 ATTTGACACTAATTCAGATTATTAGTGATACATATTGCTTATTGTGGATTTAAAAATTAAAAATA
20640821 AATAGAACACATAATAATCTCTTAATCAATTT
196 AATAGAACACATAATAATCTCTTAATCAATTT
20640853 AAAATATAAT-TATAATAAAATTATATAAATAATTTAATATTTGTAGAAAATAAATTTCTCCTTT
1 AAAATATAATGTATAATAAAATTATATAAATAATTTAATATTTGTAGAAAATAAATTTCTCCTTT
20640917 GAGTAGCATAATTTTTTTGAACCACTAACTAGCATAATTTTAATTTTTAATTAATTTGATAAATG
66 GAGTAGCATAATTTTTTTGAACCACTAACTAGCATAATTTTAATTTTTAATTAATTTGATAAATG
20640982 ATTTGACACTAATTCAGATTATTAGTGATACATATTGCTTATTGTGGATTTAAAAATTAAAAATA
131 ATTTGACACTAATTCAGATTATTAGTGATACATATTGCTTATTGTGGATTTAAAAATTAAAAATA
20641047 AATAGAACACATAATAATCTCTTAATCAATTT
196 AATAGAACACATAATAATCTCTTAATCAATTT
20641079 A
1 A
20641080 TAAGATTAAA
Statistics
Matches: 227, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
226 217 0.96
227 10 0.04
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (227 bp):
AAAATATAATGTATAATAAAATTATATAAATAATTTAATATTTGTAGAAAATAAATTTCTCCTTT
GAGTAGCATAATTTTTTTGAACCACTAACTAGCATAATTTTAATTTTTAATTAATTTGATAAATG
ATTTGACACTAATTCAGATTATTAGTGATACATATTGCTTATTGTGGATTTAAAAATTAAAAATA
AATAGAACACATAATAATCTCTTAATCAATTT
Found at i:20656366 original size:13 final size:13
Alignment explanation
Indices: 20656348--20656398 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
20656338 AAAAAACTCC
20656348 TAAAATTAATAAA
1 TAAAATTAATAAA
**
20656361 TAAAATGGA-AAA
1 TAAAATTAATAAA
*
20656373 -AAAATTGATAAA
1 TAAAATTAATAAA
20656385 TAAAATTAATAAA
1 TAAAATTAATAAA
20656398 T
1 T
20656399 GCATAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 7 0.22
12 6 0.19
13 19 0.59
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (13 bp):
TAAAATTAATAAA
Found at i:20656583 original size:60 final size:60
Alignment explanation
Indices: 20656516--20656643 Score: 229
Period size: 60 Copynumber: 2.1 Consensus size: 60
20656506 ATACTATACT
*
20656516 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
*
20656576 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAT
1 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
*
20656636 AAAAACAA
1 AAACACAA
20656644 AAAAAATTGC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.31
Consensus pattern (60 bp):
AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:20663307 original size:6 final size:6
Alignment explanation
Indices: 20663298--20663326 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
20663288 TAAAAATAAT
20663298 ATGAAG ATGAAG ATGAAG ATGAAG ATGAA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAA
20663327 TACTTCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
ATGAAG
Found at i:20665023 original size:3 final size:3
Alignment explanation
Indices: 20665015--20665045 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
20665005 CCGAATGCAC
20665015 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
20665046 AAGGTGTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:20675075 original size:6 final size:6
Alignment explanation
Indices: 20675064--20675091 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20675054 TTATGTTATA
20675064 TCTGAT TCTGAT TCTGAT TCTGAT TCTG
1 TCTGAT TCTGAT TCTGAT TCTGAT TCTG
20675092 GGCATTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (6 bp):
TCTGAT
Found at i:20688027 original size:46 final size:45
Alignment explanation
Indices: 20687960--20688114 Score: 193
Period size: 46 Copynumber: 3.6 Consensus size: 45
20687950 TTTGAGTACT
*
20687960 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCGACACTTA
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGC-ACACTTA
*
20688006 TCTGATCAAGTGAAAAAGTGATAA---GT-GC--T---ACACTTA
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCACACTTA
*
20688042 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCAACACTTA
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGC-ACACTTA
*
20688088 TCTGATCAAGTGAAAAAGTGATAAGTG
1 TCTGATCAAGAGAAAAAGTGATAAGTG
20688115 CTANNNNNNN
Statistics
Matches: 93, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
36 29 0.31
39 2 0.02
40 3 0.03
42 3 0.03
43 2 0.02
46 54 0.58
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (45 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCACACTTA
Found at i:20688040 original size:36 final size:36
Alignment explanation
Indices: 20687999--20688117 Score: 130
Period size: 36 Copynumber: 3.0 Consensus size: 36
20687989 AGCTTTAGCG
20687999 ACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCT
1 ACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCT
* *
20688035 ACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 ACACTTATCTGATCAAGTGAAAAAGTGATAA---GT-GC--T
20688077 AGCAACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCT
1 ----ACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCT
20688117 A
1 A
20688118 NNNNNNNNNN
Statistics
Matches: 69, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
36 30 0.43
39 2 0.03
40 3 0.04
42 3 0.04
43 2 0.03
46 29 0.42
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
ACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCT
Found at i:20688097 original size:82 final size:82
Alignment explanation
Indices: 20687960--20688117 Score: 298
Period size: 82 Copynumber: 1.9 Consensus size: 82
20687950 TTTGAGTACT
* *
20687960 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCGACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCAACACTTATCTGATCAAGTGAAAAAGT
20688025 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
20688042 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCAACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCAACACTTATCTGATCAAGTGAAAAAGT
20688107 GATAAGTGCTA
66 GATAAGTGCTA
20688118 NNNNNNNNNN
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCAACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:20694406 original size:3 final size:3
Alignment explanation
Indices: 20694398--20694446 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
20694388 AAGTTAAACA
20694398 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20694446 T
1 T
20694447 TATTTGAGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20709544 original size:22 final size:22
Alignment explanation
Indices: 20709519--20709561 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20709509 ATATATATAT
*
20709519 ATAT-ATATAATATTTTAGATTG
1 ATATGATATAAT-TATTAGATTG
20709541 ATATGATATAATTATTAGATT
1 ATATGATATAATTATTAGATT
20709562 AGTTCAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
ATATGATATAATTATTAGATTG
Found at i:20713828 original size:3 final size:3
Alignment explanation
Indices: 20713820--20713845 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20713810 TATTCTTTCT
20713820 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
20713846 TTTGGGTTGA
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:20714935 original size:35 final size:34
Alignment explanation
Indices: 20714896--20714975 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 34
20714886 AACATGTAAC
*
20714896 CTTAAACTCTTAAACCTTG-AACCCGAACCC-TAAA
1 CTTAAACTCAT-AA-CTTGTAACCCGAACCCTTAAA
20714930 TCTTAAACTCATAACTTGTAACCCGAACCCTTAAA
1 -CTTAAACTCATAACTTGTAACCCGAACCCTTAAA
20714965 CATTAAACTCA
1 C-TTAAACTCA
20714976 AACCATAAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
33 4 0.10
34 14 0.34
35 23 0.56
ACGTcount: A:0.39, C:0.30, G:0.05, T:0.26
Consensus pattern (34 bp):
CTTAAACTCATAACTTGTAACCCGAACCCTTAAA
Found at i:20715014 original size:13 final size:14
Alignment explanation
Indices: 20714955--20715088 Score: 70
Period size: 13 Copynumber: 9.9 Consensus size: 14
20714945 TTGTAACCCG
*
20714955 AACCCTTAAACATTA
1 AACCC-TAAACCTTA
* *
20714970 AACTC-AAACCATA
1 AACCCTAAACCTTA
20714983 AA-CCTCAAATCCTTA
1 AACCCT-AAA-CCTTA
*
20714998 AACCCTAAATC-TA
1 AACCCTAAACCTTA
20715011 AA-CCTAAACCTTA
1 AACCCTAAACCTTA
* **
20715024 AACCTTAAACCCAA
1 AACCCTAAACCTTA
*
20715038 AACCC-AAACTCGT-
1 AACCCTAAAC-CTTA
*
20715051 -ACCCAAAACCTTA
1 AACCCTAAACCTTA
*
20715064 AATCCTAAATCC--A
1 AACCCTAAA-CCTTA
20715077 AACCCTAAACCT
1 AACCCTAAACCT
20715089 CAGGATTTGG
Statistics
Matches: 90, Mismatches: 17, Indels: 26
0.68 0.13 0.20
Matches are distributed among these distances:
12 16 0.18
13 33 0.37
14 23 0.26
15 15 0.17
16 3 0.03
ACGTcount: A:0.46, C:0.34, G:0.01, T:0.20
Consensus pattern (14 bp):
AACCCTAAACCTTA
Found at i:20715017 original size:6 final size:7
Alignment explanation
Indices: 20714958--20715034 Score: 70
Period size: 7 Copynumber: 11.3 Consensus size: 7
20714948 TAACCCGAAC
20714958 CCTTAAA
1 CCTTAAA
*
20714965 CATTAAA
1 CCTTAAA
*
20714972 -CTCAAA
1 CCTTAAA
*
20714978 CCATAAA
1 CCTTAAA
*
20714985 CCTCAAA
1 CCTTAAA
20714992 TCCTTAAA
1 -CCTTAAA
*
20715000 CCCTAAA
1 CCTTAAA
*
20715007 TC-TAAA
1 CCTTAAA
20715013 CC-TAAA
1 CCTTAAA
20715019 CCTTAAA
1 CCTTAAA
20715026 CCTTAAA
1 CCTTAAA
20715033 CC
1 CC
20715035 CAAAACCCAA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
6 15 0.27
7 35 0.62
8 6 0.11
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.23
Consensus pattern (7 bp):
CCTTAAA
Found at i:20715032 original size:26 final size:28
Alignment explanation
Indices: 20714981--20715032 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
20714971 ACTCAAACCA
20714981 TAAACCTCAAATCCTTAAACCCTAAATC
1 TAAACCTCAAATCCTTAAACCCTAAATC
*
20715009 TAAACCT-AAA-CCTTAAACCTTAAA
1 TAAACCTCAAATCCTTAAACCCTAAA
20715033 CCCAAAACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 13 0.57
27 3 0.13
28 7 0.30
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (28 bp):
TAAACCTCAAATCCTTAAACCCTAAATC
Found at i:20715035 original size:33 final size:33
Alignment explanation
Indices: 20714974--20715088 Score: 108
Period size: 33 Copynumber: 3.4 Consensus size: 33
20714964 ACATTAAACT
*
20714974 CAAACCATAAACCTCAAATCCTTAAACCCTAAATC
1 CAAACC-TAAACCT-AAAACCTTAAACCCTAAATC
* * * *
20715009 TAAACCTAAACCTTAAACCTTAAACCCAAAACC
1 CAAACCTAAACCTAAAACCTTAAACCCTAAATC
* *
20715042 CAAACTCGT--ACCCAAAACCTTAAATCCTAAATC
1 CAAAC-C-TAAACCTAAAACCTTAAACCCTAAATC
20715075 CAAACCCTAAACCT
1 CAAA-CCTAAACCT
20715089 CAGGATTTGG
Statistics
Matches: 63, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
32 1 0.02
33 44 0.70
34 12 0.19
35 6 0.10
ACGTcount: A:0.45, C:0.35, G:0.01, T:0.19
Consensus pattern (33 bp):
CAAACCTAAACCTAAAACCTTAAACCCTAAATC
Found at i:20715086 original size:7 final size:7
Alignment explanation
Indices: 20714996--20715087 Score: 52
Period size: 7 Copynumber: 13.9 Consensus size: 7
20714986 CTCAAATCCT
20714996 TAAACCC
1 TAAACCC
*
20715003 TAAA-TC
1 TAAACCC
20715009 TAAA-CC
1 TAAACCC
*
20715015 TAAACCT
1 TAAACCC
*
20715022 TAAACCT
1 TAAACCC
20715029 TAAACCC
1 TAAACCC
*
20715036 AAAACCC
1 TAAACCC
*
20715043 -AAACTCG
1 TAAAC-CC
20715050 T--ACCC
1 TAAACCC
* *
20715055 AAAACCT
1 TAAACCC
*
20715062 TAAATCC
1 TAAACCC
*
20715069 TAAATCC
1 TAAACCC
20715076 -AAACCC
1 TAAACCC
20715082 TAAACC
1 TAAACC
20715088 TCAGGATTTG
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
5 1 0.02
6 21 0.32
7 44 0.67
ACGTcount: A:0.46, C:0.35, G:0.01, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:20717346 original size:18 final size:18
Alignment explanation
Indices: 20717306--20717346 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
20717296 ATTTTAATCC
20717306 TAATTATAAAAATATTAAA
1 TAATTATAAAAATA-TAAA
20717325 -AATTATAAAAATA-AATA
1 TAATTATAAAAATATAA-A
20717342 TAATT
1 TAATT
20717347 TTTTNNNNNN
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.10
17 1 0.05
18 17 0.85
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATTATAAAAATATAAA
Found at i:20723027 original size:22 final size:22
Alignment explanation
Indices: 20723000--20723041 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20722990 TTCCAAACAA
* *
20723000 AATATTTTGATATTAAAAAAAC
1 AATATTTTAATAATAAAAAAAC
20723022 AATATTTTAATAATAAAAAA
1 AATATTTTAATAATAAAAAA
20723042 TCCATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AATATTTTAATAATAAAAAAAC
Found at i:20729798 original size:30 final size:30
Alignment explanation
Indices: 20729764--20729830 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
20729754 TTCAAATTCA
*
20729764 CCTTATCTTTCATTTGAAAATATTTAGTTT
1 CCTTATCTTTCATTTGAAAATATTCAGTTT
* *
20729794 CCTTATTTTTCATTTGATAATATTCAGTTT
1 CCTTATCTTTCATTTGAAAATATTCAGTTT
20729824 CCTTATC
1 CCTTATC
20729831 AAAAAGAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.24, C:0.16, G:0.06, T:0.54
Consensus pattern (30 bp):
CCTTATCTTTCATTTGAAAATATTCAGTTT
Found at i:20730597 original size:17 final size:17
Alignment explanation
Indices: 20730575--20730607 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20730565 AAGAGACGCG
*
20730575 CTACAATTGTCTTAGCA
1 CTACAACTGTCTTAGCA
20730592 CTACAACTGTCTTAGC
1 CTACAACTGTCTTAGC
20730608 CATGCTCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (17 bp):
CTACAACTGTCTTAGCA
Found at i:20730910 original size:22 final size:24
Alignment explanation
Indices: 20730872--20730918 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
20730862 TATGAAAGAA
20730872 AAAAATATAGAAATATGTATATAT
1 AAAAATATAGAAATATGTATATAT
*
20730896 AAAAAT-TA-AAATATGTATGTAT
1 AAAAATATAGAAATATGTATATAT
20730918 A
1 A
20730919 TAGGTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
23 2 0.09
24 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (24 bp):
AAAAATATAGAAATATGTATATAT
Found at i:20731174 original size:3 final size:3
Alignment explanation
Indices: 20731166--20731332 Score: 77
Period size: 3 Copynumber: 54.0 Consensus size: 3
20731156 TTACGTAGTG
* *
20731166 ATA ATA ATA ATA ACTA AGA ATA ATA ATAA ATA ATC ATA CATTA ATA A-A
1 ATA ATA ATA ATA A-TA ATA ATA ATA AT-A ATA ATA ATA -A-TA ATA ATA
** * * * * *
20731214 CGA ATA ATA GTA GTA CATAA ATAA ATA AGA GTA ACA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA -AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * * * **
20731262 GTA GTA AAA AGA GTA ATA GTA ATA ACA GTA ATA ATA GTA ACG A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20731309 ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
20731333 TCAAATTTAT
Statistics
Matches: 123, Mismatches: 33, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
2 2 0.02
3 103 0.84
4 15 0.12
5 3 0.02
ACGTcount: A:0.60, C:0.05, G:0.08, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:20733979 original size:6 final size:6
Alignment explanation
Indices: 20733968--20733993 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20733958 CTCTGTAAGA
20733968 AAGATG AAGATG AAGATG AAGATG AA
1 AAGATG AAGATG AAGATG AAGATG AA
20733994 CTCAACTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.31, T:0.15
Consensus pattern (6 bp):
AAGATG
Found at i:20742715 original size:22 final size:22
Alignment explanation
Indices: 20742675--20742717 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20742665 ACACCAATAC
* **
20742675 AGGCTTTTAGCGGTGCTTTTTT
1 AGGCCTTTAGCGGCACTTTTTT
20742697 AGGCCTTTAGCGGCACTTTTT
1 AGGCCTTTAGCGGCACTTTTT
20742718 AGCGCCGCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCGGCACTTTTTT
Found at i:20742904 original size:42 final size:43
Alignment explanation
Indices: 20742810--20743138 Score: 432
Period size: 42 Copynumber: 7.7 Consensus size: 43
20742800 TTTTTAGAAA
20742810 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
20742853 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
20742895 AAACGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTTTCACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
20742938 AAACGCCACT-AAGACCAGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
20742980 AAACGCCGCTAAAGACCAGGAACTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * ** *
20743023 AAATGCCGCTATAGACCATGACCTTTAGCGGCACTTTTATCAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * ** *
20743066 AAACGCCACTAAAGAACAA-ACCTTTAGCGGCACTTTTATCAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
20743108 AAACGCCACTAAAGAACAA-ACCTTTAGCGGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGC
20743139 ACTTCCGCTA
Statistics
Matches: 261, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
42 133 0.51
43 128 0.49
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:20742911 original size:85 final size:86
Alignment explanation
Indices: 20742810--20743138 Score: 432
Period size: 85 Copynumber: 3.9 Consensus size: 86
20742800 TTTTTAGAAA
*
20742810 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGACCAAGAC
20742875 CTTTAGCGGCGC-TTTCCCAC
66 CTTTAGCGGCGCTTTTCCCAC
* * *
20742895 AAACGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTTTCACACAAACGCCACT-AAGACCAGGAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGACCAAGAC
20742959 CTTTAGCGGCGCTTTTCCCAC
66 CTTTAGCGGCGCTTTTCCCAC
* * * * * * *
20742980 AAACGCCGCTAAAGACCAGGAACTTTAGCGACGCTTTTCCCACAAATGCCGCTATAGACCATGAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGACCAAGAC
* ** *
20743045 CTTTAGCGGCACTTTTATCAA
66 CTTTAGCGGCGCTTTTCCCAC
* * * ** * *
20743066 AAACGCCACTAAAGAACAA-ACCTTTAGCGGCACTTTTATCAAAAACGCCACTAAAGAACAA-AC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGACCAAGAC
20743129 CTTTAGCGGC
66 CTTTAGCGGC
20743139 ACTTCCGCTA
Statistics
Matches: 211, Mismatches: 31, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
84 34 0.16
85 135 0.64
86 42 0.20
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (86 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGACCAAGAC
CTTTAGCGGCGCTTTTCCCAC
Found at i:20744301 original size:16 final size:16
Alignment explanation
Indices: 20744280--20744310 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20744270 AGTCCCAAAC
20744280 TATTGTAAACATCAGT
1 TATTGTAAACATCAGT
20744296 TATTGTAAACATCAG
1 TATTGTAAACATCAG
20744311 ATAGGTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
TATTGTAAACATCAGT
Found at i:20748045 original size:41 final size:39
Alignment explanation
Indices: 20748000--20748205 Score: 198
Period size: 41 Copynumber: 5.0 Consensus size: 39
20747990 TATTGCCCTA
20748000 AGCATTAGCGACGCTTCATTAAAAACGCCGCTAAAGACCCG
1 AGCATTAGCGACGCTT--TTAAAAACGCCGCTAAAGACCCG
* * * *
20748041 AGCATTAGCGGCGCTTTTGAGAAAGCGCCGTTAAAGACCTG
1 AGCATTAGCGACGCTTTT-A-AAAACGCCGCTAAAGACCCG
* * *
20748082 ATCATTAGCGGCGCTTTCCGAAAAACGCCGCTAAAGACCCG
1 AGCATTAGCGACGCTTT--TAAAAACGCCGCTAAAGACCCG
* *
20748123 ATCATTAGCGACGCTTTTTTAAAAACGCCGCTAAA-ACCATG
1 AGCATTAGCGACGC--TTTTAAAAACGCCGCTAAAGACC-CG
* * *
20748164 AGCATTAGCGTCGCTTTTTAAAAAACGCCACTAAAGCCCCG
1 AGCATTAGCGACGC-TTTT-AAAAACGCCGCTAAAGACCCG
20748205 A
1 A
20748206 AAACTAAAAA
Statistics
Matches: 139, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
39 2 0.01
40 9 0.06
41 122 0.88
42 3 0.02
43 3 0.02
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (39 bp):
AGCATTAGCGACGCTTTTAAAAACGCCGCTAAAGACCCG
Found at i:20748097 original size:82 final size:81
Alignment explanation
Indices: 20748000--20748205 Score: 236
Period size: 82 Copynumber: 2.5 Consensus size: 81
20747990 TATTGCCCTA
*
20748000 AGCATTAGCGACGCTTCATTAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGC-TTTTGAGAA
1 AGCATTAGCGACGCTTC-TTAAAAACGCCGCTAAAGACCCGAGCATTAGCGACGCTTTTTGA-AA
* *
20748064 AGCGCCGTTAAAGACC-TG
64 AACGCCGCTAAA-ACCATG
* * ** * *
20748082 ATCATTAGCGGCGCTTTCCGAAAAACGCCGCTAAAGACCCGATCATTAGCGACGCTTTTTTAAAA
1 AGCATTAGCGACGC-TTCTTAAAAACGCCGCTAAAGACCCGAGCATTAGCGACGCTTTTTGAAAA
20748147 ACGCCGCTAAAACCATG
65 ACGCCGCTAAAACCATG
* * * *
20748164 AGCATTAGCGTCGCTTTTTAAAAAACGCCACTAAAGCCCCGA
1 AGCATTAGCGACGCTTCTT-AAAAACGCCGCTAAAGACCCGA
20748206 AAACTAAAAA
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
81 5 0.05
82 91 0.88
83 8 0.08
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (81 bp):
AGCATTAGCGACGCTTCTTAAAAACGCCGCTAAAGACCCGAGCATTAGCGACGCTTTTTGAAAAA
CGCCGCTAAAACCATG
Found at i:20748307 original size:39 final size:39
Alignment explanation
Indices: 20748240--20748349 Score: 98
Period size: 40 Copynumber: 2.8 Consensus size: 39
20748230 GCTTAGATTT
* * *
20748240 TTTGCGACGCTTTTTGAAAAA-CGGCGCTAA-AAATAAGC
1 TTTGCGGCG-TTTTTAAAAAAGCGCCGCTAATAAATAAGC
** *
20748278 ATTTGCGGCGTTTTTAAAAAAGCGCCGCTAATACTTAATC
1 -TTTGCGGCGTTTTTAAAAAAGCGCCGCTAATAAATAAGC
** *
20748318 TTTAGCGGCGTTTTTTTAAAAGTGCCGCTAAT
1 TTT-GCGGCGTTTTTAAAAAAGCGCCGCTAAT
20748350 GCTTGATTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
38 10 0.17
39 19 0.32
40 30 0.51
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (39 bp):
TTTGCGGCGTTTTTAAAAAAGCGCCGCTAATAAATAAGC
Found at i:20748373 original size:40 final size:40
Alignment explanation
Indices: 20748282--20748374 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
20748272 ATAAGCATTT
*
20748282 GCGGCGTTTTTAAAAAAGCGCCGCTAATACTTAATCTTTA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATACTTAATCTTTA
* * * * *
20748322 GCGGCGTTTTTTTAAAAGTGCCGCTAATGCTTGATTTTTA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATACTTAATCTTTA
20748362 GCGGCGTTTTTTA
1 GCGGCGTTTTTTA
20748375 TCCAAACGCC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.39
Consensus pattern (40 bp):
GCGGCGTTTTTTAAAAAGCGCCGCTAATACTTAATCTTTA
Found at i:20751365 original size:16 final size:16
Alignment explanation
Indices: 20751344--20751411 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
20751334 TAGTTCGCTA
20751344 TAATGGAATAGAGGTG
1 TAATGGAATAGAGGTG
20751360 TAATGGAATAGAGGTG
1 TAATGGAATAGAGGTG
*
20751376 TAATGGAATAGAGCTG
1 TAATGGAATAGAGGTG
* *
20751392 TAATAGAATAGAGGCG
1 TAATGGAATAGAGGTG
20751408 TAAT
1 TAAT
20751412 AGTAATTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.40, C:0.03, G:0.32, T:0.25
Consensus pattern (16 bp):
TAATGGAATAGAGGTG
Found at i:20751707 original size:55 final size:54
Alignment explanation
Indices: 20751598--20751721 Score: 130
Period size: 55 Copynumber: 2.3 Consensus size: 54
20751588 GATTATTAAC
* *
20751598 ATAAATAATACATAATTTAATCATATTTTATCATAATTATTATTAAATATAATTTA
1 ATAAA-AATACATAATTTAATAAAATTTTATCATAATTATTATT-AATATAATTTA
* *
20751654 ATAAAAATATATAATTTAATAAAATTCTTAAT-ATAATTATTCTT-ATATGAATTTA
1 ATAAAAATACATAATTTAATAAAATT-TT-ATCATAATTATTATTAATAT-AATTTA
*
20751709 CT-AAAAT-CATAAT
1 ATAAAAATACATAAT
20751722 ATATAATACT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
53 5 0.08
54 9 0.15
55 25 0.42
56 18 0.31
57 2 0.03
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (54 bp):
ATAAAAATACATAATTTAATAAAATTTTATCATAATTATTATTAATATAATTTA
Found at i:20765317 original size:31 final size:31
Alignment explanation
Indices: 20765282--20765344 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
20765272 CGATCCTCCC
20765282 TATTTTCCCATTTT-TAGTTCTTTATTATTAT
1 TATTTTCCCATTTTATA-TTCTTTATTATTAT
*** *
20765313 TATTTTGTTATTTTATATTTTTTATTATTAT
1 TATTTTCCCATTTTATATTCTTTATTATTAT
20765344 T
1 T
20765345 TTCTTTAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (31 bp):
TATTTTCCCATTTTATATTCTTTATTATTAT
Found at i:20765561 original size:21 final size:21
Alignment explanation
Indices: 20765533--20765583 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
20765523 GGTTACTATA
*
20765533 TATT-TTATTA-TTCTTTTTAT
1 TATTCTTATTACTT-TTGTTAT
*
20765553 TCTTCTTATTACTTTTGTTAT
1 TATTCTTATTACTTTTGTTAT
20765574 TATTCTTATT
1 TATTCTTATT
20765584 TTAAGTATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 3 0.12
21 21 0.81
22 2 0.08
ACGTcount: A:0.18, C:0.10, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTCTTATTACTTTTGTTAT
Found at i:20774997 original size:21 final size:21
Alignment explanation
Indices: 20774964--20775033 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
20774954 TTATCGGCTT
*
20774964 TGTCG-ATCAGGCACTATATG
1 TGTCGTATTAGGCACTATATG
**
20774984 TGTCGTATTAGGCAGC-ACGTG
1 TGTCGTATTAGGCA-CTATATG
* *
20775005 TGTCAT-TTCAGGCACTTTATG
1 TGTCGTATT-AGGCACTATATG
20775026 TGTCGTAT
1 TGTCGTAT
20775034 ACTGCTTCTG
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 8 0.22
21 27 0.73
22 2 0.05
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (21 bp):
TGTCGTATTAGGCACTATATG
Found at i:20778990 original size:48 final size:48
Alignment explanation
Indices: 20778917--20779057 Score: 159
Period size: 47 Copynumber: 3.0 Consensus size: 48
20778907 CACACCATTT
*
20778917 GTGGACAAGCCACCACATAGA-TGTCGATAAATGGTCACATAAG-ATATC
1 GTGGACAAGCCACCACATA-ATTGTCGAT-AATGGTCACATAAGCACATC
*
20778965 GTGGA-AGAGCCACCACATAATTGTCGATAATGG-C-CGTATAGCACATC
1 GTGGACA-AGCCACCACATAATTGTCGATAATGGTCACATA-AGCACATC
* *
20779012 GTGGACAAGCCACCACATAATTG-CTGATAACGGTCACATAATCACA
1 GTGGACAAGCCACCACATAATTGTC-GATAATGGTCACATAAGCACA
20779058 GTTAAACTGC
Statistics
Matches: 80, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
45 3 0.04
46 4 0.05
47 39 0.49
48 31 0.39
49 3 0.04
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (48 bp):
GTGGACAAGCCACCACATAATTGTCGATAATGGTCACATAAGCACATC
Found at i:20779522 original size:20 final size:21
Alignment explanation
Indices: 20779497--20779536 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
20779487 CAAATTAATT
20779497 AATTAAATAACATT-TATTTA
1 AATTAAATAACATTATATTTA
20779517 AATTAAATAACATTATATTT
1 AATTAAATAACATTATATTT
20779537 CACTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTAAATAACATTATATTTA
Found at i:20792810 original size:18 final size:18
Alignment explanation
Indices: 20792787--20792830 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
20792777 AATTTATAAG
20792787 TTTTTTTA-AAATTTGAA
1 TTTTTTTATAAATTTGAA
20792804 TTTTTTTATAAATTTGAA
1 TTTTTTTATAAATTTGAA
*
20792822 TTTATTTAT
1 TTTTTTTAT
20792831 TGATATGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (18 bp):
TTTTTTTATAAATTTGAA
Found at i:20794345 original size:34 final size:35
Alignment explanation
Indices: 20794291--20794359 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
20794281 TGGTTTCAAC
20794291 AATGTTAGAATTGAGATCTAACAGGTCCATTTACT
1 AATGTTAGAATTGAGATCTAACAGGTCCATTTACT
20794326 AATGTTAGAA-TGAGATCTAACAGGTCCATTTACT
1 AATGTTAGAATTGAGATCTAACAGGTCCATTTACT
20794360 CGAAATCGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 24 0.71
35 10 0.29
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (35 bp):
AATGTTAGAATTGAGATCTAACAGGTCCATTTACT
Found at i:20798793 original size:84 final size:84
Alignment explanation
Indices: 20798650--20798835 Score: 336
Period size: 84 Copynumber: 2.2 Consensus size: 84
20798640 AAACACCAAT
*
20798650 ATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCTTTAGTGGCGT
1 ATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGT
*
20798715 TTTTTGTCTAGCGCCGCTA
66 TTTTTGTCAAGCGCCGCTA
* *
20798734 ATGGTTTGTGTTTTTAGCAAAATATAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGT
1 ATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGT
20798799 TTTTTGTCAAGCGCCGCTA
66 TTTTTGTCAAGCGCCGCTA
20798818 ATGGTCTGTGTTTTTAGC
1 ATGGTCTGTGTTTTTAGC
20798836 GGCGTTTTAA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 97 1.00
ACGTcount: A:0.16, C:0.18, G:0.28, T:0.38
Consensus pattern (84 bp):
ATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGT
TTTTTGTCAAGCGCCGCTA
Found at i:20799110 original size:188 final size:188
Alignment explanation
Indices: 20798668--20799137 Score: 753
Period size: 188 Copynumber: 2.5 Consensus size: 188
20798658 TGTTTTTAGC
* *
20798668 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCTTTAGTGGCGTTTTTTGTCTAGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
* *
20798733 AATGGTTTGTGTTTTTAGCAAAATATAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCG
66 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTA---------GGTGGCCTTAGTGGCG
* *
20798798 TTTTTTGTCAAGCGCCGCTAATGGTCTGTGTTTTTAGCGGCGTTTTAAAAAAAATGCCGCAAAAA
122 TTTTTTGTCAAGCGCCGCTAATGGTCTGTGTTTTGAGCGGCGTTTTAAAAAAAACGCCGCAAAAA
20798863 AT
187 AT
20798865 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
*
20798930 AATGGTCTGTGTTTTTAGCAAAATACAATGGCGTCGTTTA-GTGGCCTTAGTGGCGTTTTTTGTC
66 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGGTGGCCTTAGTGGCGTTTTTTGTC
** *
20798994 TTGCGCCGCTAATGGTCTGTGTTTTGAGCGGCGTTTTCAGAAAAAACGCCGCAAAAAAT
131 AAGCGCCGCTAATGGTCTGTGTTTTGAGCGGCGTTTT-AAAAAAAACGCCGCAAAAAAT
20799053 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
20799118 AATGGTCTGTGTTTTTAGCA
66 AATGGTCTGTGTTTTTAGCA
20799138 GTATTTTTAG
Statistics
Matches: 262, Mismatches: 10, Indels: 11
0.93 0.04 0.04
Matches are distributed among these distances:
187 58 0.22
188 104 0.40
197 100 0.38
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.34
Consensus pattern (188 bp):
AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGGTGGCCTTAGTGGCGTTTTTTGTC
AAGCGCCGCTAATGGTCTGTGTTTTGAGCGGCGTTTTAAAAAAAACGCCGCAAAAAAT
Found at i:20799245 original size:113 final size:114
Alignment explanation
Indices: 20798970--20799424 Score: 631
Period size: 114 Copynumber: 4.1 Consensus size: 114
20798960 GCGTCGTTTA
* * * *
20798970 GTGGCCTTAGTGGCGTTTTTTGTCTTGCGCCGCTAATGGTCTGTGTTTTGAGCGGCGTTTTCAGA
1 GTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCTAATGGTCTGTGTTTTTAGCGGCGTTTTCAGG
20799035 AAAAACGCCGCAAAAAATAAAATACAACGGCGTCGTTTAGTGGCCTTCG
66 AAAAACGCCGCAAAAAATAAAATACAACGGCGTCGTTTAGTGGCCTTCG
* ** *
20799084 GTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCTAATGGTCTGTGTTTTTAGCAGTATTTTTAGG
1 GTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCTAATGGTCTGTGTTTTTAGCGGCGTTTTCAGG
* *
20799149 AAGAACGCCGCAAAAAATAAAATACAACGGCGTCGTTTAGTGG-CTACG
66 AAAAACGCCGCAAAAAATAAAATACAACGGCGTCGTTTAGTGGCCTTCG
* * *
20799197 GTGGCGTTAGTGGCGTTTTTGGTCTTGCGCCGCTAATGGTCTATGTTTTTAGCGGCGTTTTCAGG
1 GTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCTAATGGTCTGTGTTTTTAGCGGCGTTTTCAGG
* * * *
20799262 ATAAACACCGCAAAAAATAAAATACAATGGCGTTGTTTAGTGGCCTTCG
66 AAAAACGCCGCAAAAAATAAAATACAACGGCGTCGTTTAGTGGCCTTCG
* * * * *
20799311 GTGGCCCTAGTGGCATTTTTGGTATAGTGCCGCTAATGGTCT-T-TTTTTAGCGGCGTTTTCTGG
1 GTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCTAATGGTCTGTGTTTTTAGCGGCGTTTTCAGG
*
20799374 AAAAACGCCACAAAAAATAAAAT---A---CGTCGTTTAGTGGCCTTCG
66 AAAAACGCCGCAAAAAATAAAATACAACGGCGTCGTTTAGTGGCCTTCG
*
20799417 ATGGCCTT
1 GTGGCCTT
20799425 TTACCTTAAT
Statistics
Matches: 304, Mismatches: 36, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
106 24 0.08
109 1 0.00
112 39 0.13
113 101 0.33
114 139 0.46
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.32
Consensus pattern (114 bp):
GTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCTAATGGTCTGTGTTTTTAGCGGCGTTTTCAGG
AAAAACGCCGCAAAAAATAAAATACAACGGCGTCGTTTAGTGGCCTTCG
Found at i:20799345 original size:227 final size:225
Alignment explanation
Indices: 20798970--20799398 Score: 662
Period size: 227 Copynumber: 1.9 Consensus size: 225
20798960 GCGTCGTTTA
* *
20798970 GTGGCCTTAGTGGCGTTTTTTGTCTTGCGCCGCTAATGGTCTGTGTTTTGAGCGGCGTTTTCAGA
1 GTGGCCTTAGTGGCGTTTTTGGTCTTGCGCCGCTAATGGTCTATGTTTTGAGCGGCGTTTTCAGA
* * *
20799035 AAAAACGCCGCAAAAAATAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGT
66 AAAAACACCGCAAAAAATAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCCTAGTGGCAT
* * * *
20799100 TTTTGGTCTAGCGCCGCTAATGGTCTGTGTTTTTAGCAGTATTTT-TAGGAAGAACGCCGCAAAA
131 TTTTGGTATAGCGCCGCTAATGGTCT-T-TTTTTAGCAGCATTTTCT-GGAAAAACGCCACAAAA
20799164 AATAAAATACAACGGCGTCGTTTAGTGGCTACG
193 AATAAAATACAACGGCGTCGTTTAGTGGCTACG
* * *
20799197 GTGGCGTTAGTGGCGTTTTTGGTCTTGCGCCGCTAATGGTCTATGTTTTTAGCGGCGTTTTCAGG
1 GTGGCCTTAGTGGCGTTTTTGGTCTTGCGCCGCTAATGGTCTATGTTTTGAGCGGCGTTTTCAGA
* * *
20799262 ATAAACACCGCAAAAAATAAAATACAATGGCGTTGTTTAGTGGCCTTCGGTGGCCCTAGTGGCAT
66 AAAAACACCGCAAAAAATAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCCTAGTGGCAT
* * *
20799327 TTTTGGTATAGTGCCGCTAATGGTCTTTTTTTAGCGGCGTTTTCTGGAAAAACGCCACAAAAAAT
131 TTTTGGTATAGCGCCGCTAATGGTCTTTTTTTAGCAGCATTTTCTGGAAAAACGCCACAAAAAAT
20799392 AAAATAC
196 AAAATAC
20799399 GTCGTTTAGT
Statistics
Matches: 183, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
225 38 0.21
226 2 0.01
227 143 0.78
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (225 bp):
GTGGCCTTAGTGGCGTTTTTGGTCTTGCGCCGCTAATGGTCTATGTTTTGAGCGGCGTTTTCAGA
AAAAACACCGCAAAAAATAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCCTAGTGGCAT
TTTTGGTATAGCGCCGCTAATGGTCTTTTTTTAGCAGCATTTTCTGGAAAAACGCCACAAAAAAT
AAAATACAACGGCGTCGTTTAGTGGCTACG
Found at i:20800807 original size:15 final size:15
Alignment explanation
Indices: 20800787--20800819 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
20800777 TGGCCGAGAT
20800787 TTAAGGGTTTAGGGG
1 TTAAGGGTTTAGGGG
20800802 TTAAGGGTTTAGGGG
1 TTAAGGGTTTAGGGG
20800817 TTA
1 TTA
20800820 GATGTTAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.36
Consensus pattern (15 bp):
TTAAGGGTTTAGGGG
Found at i:20801614 original size:28 final size:28
Alignment explanation
Indices: 20801595--20802433 Score: 1660
Period size: 28 Copynumber: 30.0 Consensus size: 28
20801585 AAAAGAAATA
20801595 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801623 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801651 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801679 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801707 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801735 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801763 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801791 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801819 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801847 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801875 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801903 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801931 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801959 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20801987 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802015 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802043 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802071 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802099 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802127 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802155 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802183 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802211 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802239 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802267 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802295 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802323 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802351 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
20802379 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
* *
20802407 AAAACACTAAAATTTATAATTATTAGT
1 AAAACACTAAAATTTAAAAATATTAGT
20802434 ACTATATATT
Statistics
Matches: 809, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 809 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (28 bp):
AAAACACTAAAATTTAAAAATATTAGTG
Found at i:20804005 original size:14 final size:14
Alignment explanation
Indices: 20803986--20804015 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20803976 ATAAAAGGTT
20803986 TTTAGTTAATCATC
1 TTTAGTTAATCATC
20804000 TTTAGTTAATCATC
1 TTTAGTTAATCATC
20804014 TT
1 TT
20804016 GCTGTTCGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (14 bp):
TTTAGTTAATCATC
Found at i:20804595 original size:22 final size:22
Alignment explanation
Indices: 20804484--20804595 Score: 69
Period size: 22 Copynumber: 5.2 Consensus size: 22
20804474 GTTAAAACCT
20804484 ATATTTTTAATATATGCAAAATGG
1 ATATTTTTAATATATGC--AATGG
* *
20804508 ATATTTTTTAGAAATAT-CAAT-T
1 ATA-TTTTTA-ATATATGCAATGG
*
20804530 ATATTTTT-TTA-AT---ATAGG
1 ATATTTTTAATATATGCAAT-GG
**
20804548 ATATTTTTAATATATGCAATCT
1 ATATTTTTAATATATGCAATGG
20804570 ATATTTTTAATATATGGC-ATGG
1 ATATTTTTAATATAT-GCAATGG
20804592 ATAT
1 ATAT
20804596 GTAACATATA
Statistics
Matches: 68, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
16 2 0.03
18 10 0.15
19 3 0.04
20 2 0.03
21 5 0.07
22 24 0.35
23 7 0.10
24 3 0.04
25 7 0.10
26 5 0.07
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (22 bp):
ATATTTTTAATATATGCAATGG
Found at i:20804596 original size:33 final size:33
Alignment explanation
Indices: 20804559--20804641 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
20804549 TATTTTTAAT
20804559 ATATGCAATC-TATATTTTTAATATATGGCATGG
1 ATATGCAA-CATATATTTTTAATATATGGCATGG
* *
20804592 ATATGTAACATATATTTTTAATATATGGTATGG
1 ATATGCAACATATATTTTTAATATATGGCATGG
*
20804625 ATATGTAACATATATTT
1 ATATGCAACATATATTT
20804642 CAAATTTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 1 0.02
33 46 0.98
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (33 bp):
ATATGCAACATATATTTTTAATATATGGCATGG
Found at i:20804836 original size:9 final size:9
Alignment explanation
Indices: 20804811--20804980 Score: 70
Period size: 9 Copynumber: 19.0 Consensus size: 9
20804801 CTTATATATA
20804811 AACTTACAT
1 AACTTACAT
20804820 AA--TACAT
1 AACTTACAT
20804827 AACTTACAT
1 AACTTACAT
*
20804836 AACTTATAT
1 AACTTACAT
*
20804845 AGAACTTATAT
1 --AACTTACAT
*
20804856 AACAACTTGCAT
1 ---AACTTACAT
20804868 AACTTACAT
1 AACTTACAT
*
20804877 AA-TAACATAAT
1 AACTTAC---AT
*
20804888 AACGTACAT
1 AACTTACAT
*
20804897 -AC-TATAT
1 AACTTACAT
* * *
20804904 AGCCTACGT
1 AACTTACAT
* *
20804913 AAATTGCAT
1 AACTTACAT
*
20804922 AACTCACAT
1 AACTTACAT
*
20804931 AA--TACAC
1 AACTTACAT
20804938 AACTTACAT
1 AACTTACAT
* *
20804947 AACTAAAAT
1 AACTTACAT
20804956 AACTTACAT
1 AACTTACAT
20804965 AA--TACAT
1 AACTTACAT
20804972 AACTTACAT
1 AACTTACAT
20804981 TATTGGTGAA
Statistics
Matches: 119, Mismatches: 27, Indels: 30
0.68 0.15 0.17
Matches are distributed among these distances:
7 23 0.19
8 6 0.05
9 67 0.56
11 13 0.11
12 10 0.08
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.30
Consensus pattern (9 bp):
AACTTACAT
Found at i:20804890 original size:32 final size:31
Alignment explanation
Indices: 20804816--20804890 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
20804806 ATATAAACTT
* *
20804816 ACATAATACATAACTTACATAACTTATATAGA
1 ACATAATA-ACAACTTACATAACTTACATAGA
* * *
20804848 ACTTATATAACAACTTGCATAACTTACATAATA
1 ACATA-ATAACAACTTACATAACTTACAT-AGA
20804881 ACATAATAAC
1 ACATAATAAC
20804891 GTACATACTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
32 26 0.74
33 9 0.26
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (31 bp):
ACATAATAACAACTTACATAACTTACATAGA
Found at i:20804961 original size:18 final size:16
Alignment explanation
Indices: 20804920--20804980 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
20804910 CGTAAATTGC
* *
20804920 ATAACTCACATAATAC
1 ATAACTTACATAATAA
*
20804936 ACAACTTACATAACTAAA
1 ATAACTTACATAA-T-AA
*
20804954 ATAACTTACATAATAC
1 ATAACTTACATAATAA
20804970 ATAACTTACAT
1 ATAACTTACAT
20804981 TATTGGTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
16 23 0.61
17 2 0.05
18 13 0.34
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAACTTACATAATAA
Found at i:20811369 original size:42 final size:41
Alignment explanation
Indices: 20811305--20811474 Score: 250
Period size: 42 Copynumber: 4.1 Consensus size: 41
20811295 NNNNNNNNNN
* * **
20811305 GCGCTTAGAAAAAAACGTCGCTAAAGACCATGTTCTTCAAAG
1 GCGCTTAG-AAAAAACGCCGCTAAAGACCATGTTCTTTAGCG
20811347 GCGCTTAGAGAAAAACGCCGCTAAAGACCATGTTCTTTAGCG
1 GCGCTTAGA-AAAAACGCCGCTAAAGACCATGTTCTTTAGCG
20811389 GCGCTTAGAAAGAAACGCCGCTAAAGACCATGTTCTTTAGCG
1 GCGCTTAGAAA-AAACGCCGCTAAAGACCATGTTCTTTAGCG
* * *
20811431 ACGCTTAGAAAAAAAGTCGCTAAAGACCATGTTCTTTAGCG
1 GCGCTTAGAAAAAACGCCGCTAAAGACCATGTTCTTTAGCG
20811472 GCG
1 GCG
20811475 TTTTTGTTTG
Statistics
Matches: 118, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
41 33 0.28
42 85 0.72
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (41 bp):
GCGCTTAGAAAAAACGCCGCTAAAGACCATGTTCTTTAGCG
Found at i:20819531 original size:13 final size:13
Alignment explanation
Indices: 20819513--20819538 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20819503 TATGAATGTT
20819513 AAATGTTTACTGG
1 AAATGTTTACTGG
20819526 AAATGTTTACTGG
1 AAATGTTTACTGG
20819539 GTATGAATGA
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:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
AAATGTTTACTGG
Found at i:20819828 original size:30 final size:29
Alignment explanation
Indices: 20819760--20819838 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
20819750 CTTGATACGA
*
20819760 TGTCAGCTTGTGTGAGCAAATCCTTTATAT
1 TGTCAGCTTGTGTGAGC-AACCCTTTATAT
*
20819790 TGTCAGCTTGTGTGAGCAACCCTGATT-TTT
1 TGTCAGCTTGTGTGAGCAACCCT--TTATAT
* *
20819820 TGTTAGCTTGTATGAGCAA
1 TGTCAGCTTGTGTGAGCAA
20819839 TATAGTCCTG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.12
30 36 0.84
31 2 0.05
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (29 bp):
TGTCAGCTTGTGTGAGCAACCCTTTATAT
Found at i:20830680 original size:17 final size:17
Alignment explanation
Indices: 20830658--20830691 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20830648 CATGCCTCAG
*
20830658 AGCATTTTATATATTAT
1 AGCATTATATATATTAT
20830675 AGCATTATATATATTAT
1 AGCATTATATATATTAT
20830692 GAAAACGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (17 bp):
AGCATTATATATATTAT
Found at i:20830780 original size:18 final size:18
Alignment explanation
Indices: 20830757--20830791 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20830747 TGTAAATGAA
20830757 TTATTGAACCTTCACTTG
1 TTATTGAACCTTCACTTG
*
20830775 TTATTGAACCTTTACTT
1 TTATTGAACCTTCACTT
20830792 AGTGAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.49
Consensus pattern (18 bp):
TTATTGAACCTTCACTTG
Found at i:20835028 original size:14 final size:15
Alignment explanation
Indices: 20834989--20835030 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
20834979 NNNNAACATA
*
20834989 ATTATTATTAAATAT
1 ATTATAATTAAATAT
20835004 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
20835018 A-TATAATTTAATA
1 ATTATAATTAAATA
20835031 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:20836894 original size:8 final size:8
Alignment explanation
Indices: 20836881--20836920 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
20836871 GTAATGAGCA
20836881 ATACAAAC
1 ATACAAAC
20836889 ATACAAAC
1 ATACAAAC
*
20836897 A-A-AACC
1 ATACAAAC
20836903 ATACAAAC
1 ATACAAAC
20836911 ATACAAAC
1 ATACAAAC
20836919 AT
1 AT
20836921 GCAATCGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 4 0.14
7 2 0.07
8 22 0.79
ACGTcount: A:0.62, C:0.25, G:0.00, T:0.12
Consensus pattern (8 bp):
ATACAAAC
Found at i:20839076 original size:9 final size:9
Alignment explanation
Indices: 20839058--20839096 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
20839048 CCAAATAACT
20839058 AAAATAAAAG
1 AAAAT-AAAG
20839068 AAAATAAAG
1 AAAATAAAG
*
20839077 -TAATAAAG
1 AAAATAAAG
20839085 AAAATAAAG
1 AAAATAAAG
20839094 AAA
1 AAA
20839097 TAATAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 7 0.27
9 14 0.54
10 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (9 bp):
AAAATAAAG
Found at i:20839086 original size:17 final size:17
Alignment explanation
Indices: 20839059--20839099 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
20839049 CAAATAACTA
20839059 AAATAAAAGAAAATAAAG
1 AAAT-AAAGAAAATAAAG
*
20839077 TAATAAAGAAAATAAAG
1 AAATAAAGAAAATAAAG
20839094 AAATAA
1 AAATAA
20839100 TAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (17 bp):
AAATAAAGAAAATAAAG
Found at i:20839106 original size:26 final size:27
Alignment explanation
Indices: 20839058--20839108 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
20839048 CCAAATAACT
*
20839058 AAAATAAAAGAAAATAAAGTAATAAAG
1 AAAATAAAAGAAAATAAAATAATAAAG
20839085 AAAAT-AAAG-AAATAATAATAATAA
1 AAAATAAAAGAAAATAA-AATAATAA
20839109 TAAATAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 11 0.50
27 5 0.23
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.18
Consensus pattern (27 bp):
AAAATAAAAGAAAATAAAATAATAAAG
Found at i:20852494 original size:23 final size:23
Alignment explanation
Indices: 20852467--20852589 Score: 74
Period size: 23 Copynumber: 5.3 Consensus size: 23
20852457 CCCTGTTTTA
* *
20852467 GACAGCGATTATTCAGCAAATTG
1 GACAGCGATTATACATCAAATTG
* *
20852490 GACAGCGATAATATGC-TCAAAATG
1 GACAGCGAT--TATACATCAAATTG
*
20852514 GACAGC-ATTATACATCAAATTA
1 GACAGCGATTATACATCAAATTG
* * *
20852536 GACAGC-ATCAATATACTTAAAATCG
1 GACAGCGAT---TATACATCAAATTG
* *
20852561 GACAGC-ATTATACATTAAAAATG
1 GACAGCGATTATACA-TCAAATTG
20852584 GACAGC
1 GACAGC
20852590 ATCAATACAC
Statistics
Matches: 80, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
21 4 0.05
22 19 0.24
23 23 0.29
24 12 0.15
25 22 0.28
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (23 bp):
GACAGCGATTATACATCAAATTG
Found at i:20852540 original size:46 final size:47
Alignment explanation
Indices: 20852467--20852606 Score: 158
Period size: 46 Copynumber: 3.0 Consensus size: 47
20852457 CCCTGTTTTA
* * * *
20852467 GACAGCGATTATTCAGCAAATTGGACAGCGAT-AATATGCTCAAAAT-G
1 GACAGC-ATTATACATCAAATTAGACAGC-ATCAATATACTCAAAATCG
*
20852514 GACAGCATTATACATCAAATTAGACAGCATCAATATACTTAAAATCG
1 GACAGCATTATACATCAAATTAGACAGCATCAATATACTCAAAATCG
* * * *
20852561 GACAGCATTATACATTAAAAATGGACAGCATCAATACACTCAAAAT
1 GACAGCATTATACA-TCAAATTAGACAGCATCAATATACTCAAAAT
20852607 TNNNNNNNNN
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
45 2 0.03
46 31 0.39
47 21 0.26
48 26 0.32
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.24
Consensus pattern (47 bp):
GACAGCATTATACATCAAATTAGACAGCATCAATATACTCAAAATCG
Found at i:20852590 original size:23 final size:22
Alignment explanation
Indices: 20852508--20852591 Score: 89
Period size: 22 Copynumber: 3.6 Consensus size: 22
20852498 TAATATGCTC
*
20852508 AAAATGGACAGCATTATACATC
1 AAAATGGACAGCATTATACATT
* *
20852530 AAATTAGACAGCATCAATATAC-TT
1 AAAATGGACAGCAT---TATACATT
20852554 AAAATCGGACAGCATTATACATT
1 AAAAT-GGACAGCATTATACATT
20852577 AAAAATGGACAGCAT
1 -AAAATGGACAGCAT
20852592 CAATACACTC
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
22 17 0.33
23 11 0.22
24 10 0.20
25 13 0.25
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (22 bp):
AAAATGGACAGCATTATACATT
Found at i:20852605 original size:24 final size:23
Alignment explanation
Indices: 20852483--20852606 Score: 106
Period size: 24 Copynumber: 5.3 Consensus size: 23
20852473 GATTATTCAG
* **
20852483 CAAATTGGACAGCGATAATATGCT
1 CAAAATGGACAGC-ATAATACACT
*
20852507 CAAAATGGACAGCATTATACA-T
1 CAAAATGGACAGCATAATACACT
* * *
20852529 CAAATTAGACAGCATCAATATACT
1 CAAAATGGACAGCAT-AATACACT
* * *
20852553 TAAAATCGGACAGCATTATACATT
1 CAAAAT-GGACAGCATAATACACT
*
20852577 AAAAATGGACAGCATCAATACACT
1 CAAAATGGACAGCAT-AATACACT
20852601 CAAAAT
1 CAAAAT
20852607 TNNNNNNNNN
Statistics
Matches: 78, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
22 14 0.18
23 18 0.23
24 38 0.49
25 8 0.10
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (23 bp):
CAAAATGGACAGCATAATACACT
Found at i:20852606 original size:48 final size:46
Alignment explanation
Indices: 20852488--20852606 Score: 150
Period size: 48 Copynumber: 2.5 Consensus size: 46
20852478 TTCAGCAAAT
* * *
20852488 TGGACAGCGAT-AATATGCTCAAAATGGACAGCATTATACATCAAAT
1 TGGACAGC-ATCAATATACTCAAAATGGACAGCATTATACATAAAAA
* *
20852534 TAGACAGCATCAATATACTTAAAATCGGACAGCATTATACATTAAAAA
1 TGGACAGCATCAATATACTCAAAAT-GGACAGCATTATACA-TAAAAA
*
20852582 TGGACAGCATCAATACACTCAAAAT
1 TGGACAGCATCAATATACTCAAAAT
20852607 TNNNNNNNNN
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
45 2 0.03
46 19 0.31
47 15 0.24
48 26 0.42
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (46 bp):
TGGACAGCATCAATATACTCAAAATGGACAGCATTATACATAAAAA
Found at i:20877001 original size:16 final size:13
Alignment explanation
Indices: 20876968--20876992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20876958 AAAGTATAGC
20876968 AATTTCTATAAAT
1 AATTTCTATAAAT
20876981 AATTTCTATAAA
1 AATTTCTATAAA
20876993 GGATAATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTTCTATAAAT
Found at i:20891175 original size:31 final size:31
Alignment explanation
Indices: 20891117--20891176 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
20891107 ATAACCAAAT
** *
20891117 CAGAGTATAGGGGTTGAATACATAATTTACA
1 CAGAGTATAGGGACTGAATACAAAATTTACA
20891148 CAGAGTATAGGGACT-AATAGCAAAATTTA
1 CAGAGTATAGGGACTGAATA-CAAAATTTA
20891177 ACAAAGATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (31 bp):
CAGAGTATAGGGACTGAATACAAAATTTACA
Found at i:20895377 original size:16 final size:14
Alignment explanation
Indices: 20895343--20895369 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20895333 TAAAAAATTC
20895343 AAAATAAATATTTA
1 AAAATAAATATTTA
20895357 AAAATAAATATTT
1 AAAATAAATATTT
20895370 TTAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATAAATATTTA
Found at i:20898935 original size:5 final size:5
Alignment explanation
Indices: 20898916--20899136 Score: 127
Period size: 5 Copynumber: 43.8 Consensus size: 5
20898906 TAGGACTTTG
* * * * * * *
20898916 TATGA TATGA TATGA CATGA TGTGA TGTGA TGTGA TGTGA TGTGA TGTGA
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA
* * * * * * * * * *
20898966 TGTGA TGTGA TGTGA TGTGA TGTGA TGTGA TGTGA TGTGA TGTGA TGTGA
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA
* * * * * * * * *
20899016 TGTGA TGTGA TGTGA TGTGA TGTGA TGTGA TGTGA TGTGA TGTGA TATGA
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA
* * * *
20899066 TATGA TATTA TATTA TATGA TATTA TATGA TATGA TATGA TTTATGA TATGC
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA --TATGA TATGA
* * *
20899118 TTTGG TATGA TAAGA TATG
1 TATGA TATGA TATGA TATG
20899137 TTCCAATATA
Statistics
Matches: 199, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
5 194 0.97
7 5 0.03
ACGTcount: A:0.27, C:0.01, G:0.30, T:0.42
Consensus pattern (5 bp):
TATGA
Found at i:20898941 original size:15 final size:15
Alignment explanation
Indices: 20898933--20899071 Score: 260
Period size: 15 Copynumber: 9.3 Consensus size: 15
20898923 TGATATGACA
20898933 TGATGTGATGTGATG
1 TGATGTGATGTGATG
20898948 TGATGTGATGTGATG
1 TGATGTGATGTGATG
20898963 TGATGTGATGTGATG
1 TGATGTGATGTGATG
20898978 TGATGTGATGTGATG
1 TGATGTGATGTGATG
20898993 TGATGTGATGTGATG
1 TGATGTGATGTGATG
20899008 TGATGTGATGTGATG
1 TGATGTGATGTGATG
20899023 TGATGTGATGTGATG
1 TGATGTGATGTGATG
20899038 TGATGTGATGTGATG
1 TGATGTGATGTGATG
* *
20899053 TGATGTGATATGATA
1 TGATGTGATGTGATG
20899068 TGAT
1 TGAT
20899072 ATTATATTAT
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 122 1.00
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (15 bp):
TGATGTGATGTGATG
Found at i:20899073 original size:10 final size:10
Alignment explanation
Indices: 20898933--20899071 Score: 260
Period size: 10 Copynumber: 13.9 Consensus size: 10
20898923 TGATATGACA
20898933 TGATGTGATG
1 TGATGTGATG
20898943 TGATGTGATG
1 TGATGTGATG
20898953 TGATGTGATG
1 TGATGTGATG
20898963 TGATGTGATG
1 TGATGTGATG
20898973 TGATGTGATG
1 TGATGTGATG
20898983 TGATGTGATG
1 TGATGTGATG
20898993 TGATGTGATG
1 TGATGTGATG
20899003 TGATGTGATG
1 TGATGTGATG
20899013 TGATGTGATG
1 TGATGTGATG
20899023 TGATGTGATG
1 TGATGTGATG
20899033 TGATGTGATG
1 TGATGTGATG
20899043 TGATGTGATG
1 TGATGTGATG
*
20899053 TGATGTGATA
1 TGATGTGATG
*
20899063 TGATATGAT
1 TGATGTGAT
20899072 ATTATATTAT
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
10 127 1.00
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (10 bp):
TGATGTGATG
Found at i:20904179 original size:3 final size:3
Alignment explanation
Indices: 20904171--20904201 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
20904161 ATGGCAAATC
*
20904171 ACA ACA ACA GCA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
20904202 GGTGAGCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.32, G:0.03, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:20912626 original size:17 final size:16
Alignment explanation
Indices: 20912601--20912651 Score: 75
Period size: 17 Copynumber: 3.1 Consensus size: 16
20912591 ACTAAATTTG
20912601 TCATTATACCATTTTTT
1 TCATTATACC-TTTTTT
*
20912618 TCATCATACCCTTTTTT
1 TCATTATA-CCTTTTTT
20912635 TCATTATACCTTTTTT
1 TCATTATACCTTTTTT
20912651 T
1 T
20912652 AACTACCACG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 9 0.29
17 20 0.65
18 2 0.06
ACGTcount: A:0.20, C:0.22, G:0.00, T:0.59
Consensus pattern (16 bp):
TCATTATACCTTTTTT
Found at i:20912844 original size:20 final size:20
Alignment explanation
Indices: 20912802--20912846 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20912792 TATTTAAAAA
* * *
20912802 TAAAAATACATAAATATTTT
1 TAAAAATACATAAAAACTAT
20912822 TAAAAATACATAAAAACTAT
1 TAAAAATACATAAAAACTAT
20912842 TAAAA
1 TAAAA
20912847 TTTATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAATACATAAAAACTAT
Found at i:20926651 original size:16 final size:18
Alignment explanation
Indices: 20926612--20926653 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
20926602 TAAGTTTATG
20926612 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
20926629 ATTTTTATATATTATG-T
1 ATATTTATATATTATGTT
20926646 A-ATTTATA
1 ATATTTATA
20926654 CCACAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:20943037 original size:126 final size:126
Alignment explanation
Indices: 20942807--20943077 Score: 402
Period size: 126 Copynumber: 2.2 Consensus size: 126
20942797 GATTTTGGTT
* * **
20942807 TTTTTCTACAATAGTTTCTGAAAAAATAATTTTAGAAAGACTTTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAATAGTTCCTAAAAAAATAATTTTAGAAAGACGGTTCTGAACAAATAGTGTCAAAA
* *
20942872 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACATAGACGCTC
66 ACACTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACATAGACGCTC
* *
20942933 TTTTTCTATAATAGTTCCTAAAAAAATAATTTTA-AGAAGACGGTTCTGAATAAATAGTGTCAAA
1 TTTTTCTACAATAGTTCCTAAAAAAATAATTTTAGA-AAGACGGTTCTGAACAAATAGTGTCAAA
* *
20942997 AACACTTCAAGCAAGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCCACGTGGACGCTC
65 AACACTTCAAGCAAGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACATAGACGCTC
* *
20943059 CTTTTCTACAGTAGTTCCT
1 TTTTTCTACAATAGTTCCT
20943078 GTTTGGCCTT
Statistics
Matches: 130, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
125 1 0.01
126 128 0.98
127 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAATAGTTCCTAAAAAAATAATTTTAGAAAGACGGTTCTGAACAAATAGTGTCAAAA
ACACTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACATAGACGCTC
Found at i:20946360 original size:30 final size:30
Alignment explanation
Indices: 20946326--20946390 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
20946316 ATTAATTAAA
* *
20946326 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
1 GAGAGCTTTAAGAAATCTAAGGAGAAATTT
*
20946356 GAGAGCTTTAAGAAATCTAGGGAGAAATTT
1 GAGAGCTTTAAGAAATCTAAGGAGAAATTT
20946386 GAGAG
1 GAGAG
20946391 TTTTTTTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.05, G:0.29, T:0.26
Consensus pattern (30 bp):
GAGAGCTTTAAGAAATCTAAGGAGAAATTT
Found at i:20952102 original size:126 final size:126
Alignment explanation
Indices: 20951874--20952164 Score: 483
Period size: 126 Copynumber: 2.3 Consensus size: 126
20951864 CAGGCCAAAA
20951874 AGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCA
1 AGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCA
* * * *
20951939 TCTTGCTTAAAGCGTTTTTGACACTATTTTCTTAGAAACATCTACTCGAAATTATTGTTTC
66 TCTCGCTTAAAGCGTTTTTGACACTATTTACTCAGAAACATCTACTCAAAATTATTGTTTC
* * *
20952000 AGGAGCCACTGTAGCAAAAGCGCGTCCACATGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCA
1 AGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCA
* * * *
20952065 TCTCGCTTAAAGCGTTTTTGACACTATTTACTCAGAAACGTCTTCTCAAAATTATTTTTTT
66 TCTCGCTTAAAGCGTTTTTGACACTATTTACTCAGAAACATCTACTCAAAATTATTGTTTC
20952126 AGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
1 AGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
20952165 TTTTAAATTA
Statistics
Matches: 151, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 151 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (126 bp):
AGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCA
TCTCGCTTAAAGCGTTTTTGACACTATTTACTCAGAAACATCTACTCAAAATTATTGTTTC
Found at i:20956427 original size:26 final size:26
Alignment explanation
Indices: 20956398--20956447 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
20956388 AGAAGCTATG
20956398 TTCATTTCATGTAACGTATATTTAGT
1 TTCATTTCATGTAACGTATATTTAGT
20956424 TTCATTTCATGTAACGTATATTTA
1 TTCATTTCATGTAACGTATATTTA
20956448 ACAATTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (26 bp):
TTCATTTCATGTAACGTATATTTAGT
Found at i:20956933 original size:20 final size:20
Alignment explanation
Indices: 20956901--20956938 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20956891 AATTATCGTT
*
20956901 TTAATAATTTTAACATTTTA
1 TTAATAATTTTAAAATTTTA
20956921 TTAA-AATTATTAAAATTT
1 TTAATAATT-TTAAAATTT
20956939 GAGGTGATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATAATTTTAAAATTTTA
Found at i:20958179 original size:36 final size:38
Alignment explanation
Indices: 20958135--20958221 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 38
20958125 GGAGTTGTAA
* * *
20958135 GTGACTATTCATCTATATCAC-TAAATGC-TAGGAGTT
1 GTGACTATTCATCTACATAACTTAAATACGTAGGAGTT
*
20958171 GTGACTATTCATTTACATAACTTAAATACTGTAGGAGTT
1 GTGACTATTCATCTACATAACTTAAATAC-GTAGGAGTT
20958210 GTGACTATTCAT
1 GTGACTATTCAT
20958222 GCATGTGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 18 0.41
37 6 0.14
39 20 0.45
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (38 bp):
GTGACTATTCATCTACATAACTTAAATACGTAGGAGTT
Found at i:20962742 original size:32 final size:32
Alignment explanation
Indices: 20962700--20962775 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
20962690 TGCATGTGTG
* * *
20962700 TAACTTTTCATCTTCAAGTCTCTTCGCATTAT
1 TAACTCTTCATATTCAAGTCTCTTCACATTAT
* **
20962732 TAACTCTTCATATTCAAGTCTTTTCACATTCG
1 TAACTCTTCATATTCAAGTCTCTTCACATTAT
*
20962764 TAACTTTTCATA
1 TAACTCTTCATA
20962776 ATTTATTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.25, C:0.24, G:0.05, T:0.46
Consensus pattern (32 bp):
TAACTCTTCATATTCAAGTCTCTTCACATTAT
Found at i:20967663 original size:21 final size:22
Alignment explanation
Indices: 20967627--20967669 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
20967617 CACTATCTAC
*
20967627 ATATGTTCTGTAGCTCGTTTTAA
1 ATATGTTC-GTAGCTCATTTTAA
20967650 ATATGTTC-TAGCTCATTTTA
1 ATATGTTCGTAGCTCATTTTA
20967670 TAGAAAGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (22 bp):
ATATGTTCGTAGCTCATTTTAA
Found at i:20970179 original size:11 final size:11
Alignment explanation
Indices: 20970163--20970208 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
20970153 GCAAAAAGAA
20970163 TAAAATTTATT
1 TAAAATTTATT
*
20970174 TAAAATTTATA
1 TAAAATTTATT
*
20970185 GAAAA-TTA--
1 TAAAATTTATT
20970193 TAAAATTTATT
1 TAAAATTTATT
20970204 TAAAA
1 TAAAA
20970209 AATTAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
8 4 0.14
9 3 0.10
10 3 0.10
11 19 0.66
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
TAAAATTTATT
Found at i:20970227 original size:30 final size:30
Alignment explanation
Indices: 20970162--20970221 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
20970152 TGCAAAAAGA
**
20970162 ATAAAATTTATTTAAAATTTATAGAAAATT
1 ATAAAATTTATTTAAAAAATATAGAAAATT
20970192 ATAAAATTTATTTAAAAAAT-TA-AAAATT
1 ATAAAATTTATTTAAAAAATATAGAAAATT
20970220 AT
1 AT
20970222 TTAAAAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 8 0.29
29 2 0.07
30 18 0.64
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (30 bp):
ATAAAATTTATTTAAAAAATATAGAAAATT
Found at i:20970228 original size:19 final size:21
Alignment explanation
Indices: 20970174--20970229 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 21
20970164 AAAATTTATT
*
20970174 TAAAATTTA--TAGAAAATTA
1 TAAAATTTATTTAAAAAATTA
20970193 TAAAATTTATTTAAAAAATTA
1 TAAAATTTATTTAAAAAATTA
20970214 -AAAA-TTATTTAAAAAA
1 TAAAATTTATTTAAAAAA
20970230 CAAGGCGGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 21 0.62
20 4 0.12
21 9 0.26
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAATTTATTTAAAAAATTA
Found at i:20971740 original size:8 final size:8
Alignment explanation
Indices: 20971730--20971762 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
20971720 TATTATATTT
*
20971730 ATTTTTTT
1 ATTTTTTA
20971738 ATTTTTTA
1 ATTTTTTA
20971746 ATTTTTTA
1 ATTTTTTA
20971754 ATTTTTTA
1 ATTTTTTA
20971762 A
1 A
20971763 AGGCGAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTTA
Found at i:20972054 original size:3 final size:3
Alignment explanation
Indices: 20972042--20972093 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
20972032 TATCCACTAT
20972042 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20972089 ATA AT
1 ATA AT
20972094 CCACCTCACC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20978695 original size:39 final size:39
Alignment explanation
Indices: 20978592--20978703 Score: 125
Period size: 40 Copynumber: 2.8 Consensus size: 39
20978582 CGTTTGGATA
* * * *
20978592 AAAAACGCCGCTAAAGATCGAGCATTAGCGTCGCTTTTTG
1 AAAAACGCCGCTAAAGAT-AAGCATTAGCGGCGCATTATG
* * *
20978632 GAAAACGTCGTTAAAGATATAGCATTAGCGGCGCATTATG
1 AAAAACGCCGCTAAAGATA-AGCATTAGCGGCGCATTATG
* *
20978672 AAAAACACCGCTAAAAATAAGCATTAGCGGCG
1 AAAAACGCCGCTAAAGATAAGCATTAGCGGCG
20978704 TTTTCCAGAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
39 13 0.22
40 46 0.78
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (39 bp):
AAAAACGCCGCTAAAGATAAGCATTAGCGGCGCATTATG
Found at i:20978819 original size:41 final size:41
Alignment explanation
Indices: 20978766--20979056 Score: 273
Period size: 41 Copynumber: 7.1 Consensus size: 41
20978756 GTTTTGGGGA
* * *
20978766 TTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCTCAGGGA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * *
20978807 TTTAGCGGCGTTTTTGAAAAATCGCCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * * * * *
20978848 TATAGCTGCATTTTTGAGGAGGCGCCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * * * **
20978889 TTTAGCGGCGTTTTTGAGGAGGCGTCGTTAATGCTTGGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * * * *
20978930 TTTAGCGGCATTTTTGAGGAGGTGCCGCTAATGCTCAAGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* **
20978971 TTTAGCGGCATTTTTTGAGAAAGCGCCGCTAATGCTCTA--TT
1 TTTAGCGGC-GTTTTTGAGAAAGCGCCGCTAATGCTC-AGGGC
* * *
20979012 TTTAGCGGCGTTTTCT-AAAAAGCGCCACTAATGCTCAGGGA
1 TTTAGCGGCGTTTT-TGAGAAAGCGCCGCTAATGCTCAGGGC
20979053 TTTA
1 TTTA
20979057 AAATAATTTA
Statistics
Matches: 209, Mismatches: 36, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.00
40 22 0.11
41 162 0.78
42 23 0.11
43 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:20979043 original size:40 final size:41
Alignment explanation
Indices: 20978971--20979047 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 41
20978961 TGCTCAAGGC
* * *
20978971 TTTAGCGGCATTTTTTGAGAAAGCGCCGCTAATGCTCTATT
1 TTTAGCGGCATTTTCTGAAAAAGCGCCACTAATGCTCTATT
*
20979012 TTTAGCGGCGTTTTCT-AAAAAGCGCCACTAATGCTC
1 TTTAGCGGCATTTTCTGAAAAAGCGCCACTAATGCTC
20979048 AGGGATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 18 0.56
41 14 0.44
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCATTTTCTGAAAAAGCGCCACTAATGCTCTATT
Found at i:20979044 original size:123 final size:122
Alignment explanation
Indices: 20978766--20979056 Score: 316
Period size: 123 Copynumber: 2.4 Consensus size: 122
20978756 GTTTTGGGGA
*
20978766 TTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAAAAATCG
1 TTTAGCGGCGTTTTTAA-AAAGCGCCGCTAATGCTCAGGGATTTAGCGGCATTTTTGAAAAATCG
** * * * *
20978831 CCGCTAATGCTCGGGGCTATAGCTGCATTTTTGAGGAGGCGCCGCTAATGCTCGGGGC
65 CCGCTAATGCTCAAGGCTATAGCGGCATTTTTGAGAAAGCGCCGCTAATGCTCGGAGC
** * * * ** * * **
20978889 TTTAGCGGCGTTTTTGAGGAGGCGTCGTTAATGCTTGGGGCTTTAGCGGCATTTTTGAGGAGGT-
1 TTTAGCGGCGTTTTT-AAAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCATTTTTGA-AAAATC
* * **
20978953 GCCGCTAATGCTCAAGGCTTTAGCGGCATTTTTTGAGAAAGCGCCGCTAATGCTC-TATT
64 GCCGCTAATGCTCAAGGCTATAGCGGCA-TTTTTGAGAAAGCGCCGCTAATGCTCGGAGC
*
20979012 TTTAGCGGCGTTTTCTAAAAAGCGCCACTAATGCTCAGGGATTTA
1 TTTAGCGGCGTTTT-TAAAAAGCGCCGCTAATGCTCAGGGATTTA
20979057 AAATAATTTA
Statistics
Matches: 133, Mismatches: 31, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
123 105 0.79
124 28 0.21
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (122 bp):
TTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCATTTTTGAAAAATCGC
CGCTAATGCTCAAGGCTATAGCGGCATTTTTGAGAAAGCGCCGCTAATGCTCGGAGC
Found at i:20979276 original size:14 final size:14
Alignment explanation
Indices: 20979230--20979278 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
20979220 TATCACTGTA
*
20979230 GTTTAGGGTTTTAG
1 GTTTAGGGTTTAAG
* *
20979244 GTTTAGGGTATATG
1 GTTTAGGGTTTAAG
* *
20979258 ATTTAGAGTTTAAG
1 GTTTAGGGTTTAAG
20979272 GTTTAGG
1 GTTTAGG
20979279 TGATACCATT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (14 bp):
GTTTAGGGTTTAAG
Found at i:20979289 original size:28 final size:28
Alignment explanation
Indices: 20979231--20979289 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
20979221 ATCACTGTAG
* * **
20979231 TTTAGGGTTTTAGGTTTAGGGTATATGA
1 TTTAGAGTTTAAGGTTTAGGGTATACCA
20979259 TTTAGAGTTTAAGGTTTA-GGTGATACCA
1 TTTAGAGTTTAAGGTTTAGGGT-ATACCA
20979287 TTT
1 TTT
20979290 TAAGGTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.46
Consensus pattern (28 bp):
TTTAGAGTTTAAGGTTTAGGGTATACCA
Found at i:20980027 original size:21 final size:22
Alignment explanation
Indices: 20980003--20980049 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
20979993 TATGGTTTAT
*
20980003 GGTTTATGGTTTAAAGGTT-GG
1 GGTTTAAGGTTTAAAGGTTAGG
*
20980024 GGTTTAAGGTTTAAGGGTTAGG
1 GGTTTAAGGTTTAAAGGTTAGG
20980046 GGTT
1 GGTT
20980050 AGGGATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.40
Consensus pattern (22 bp):
GGTTTAAGGTTTAAAGGTTAGG
Found at i:20980034 original size:7 final size:7
Alignment explanation
Indices: 20979973--20980015 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
20979963 GGTTACTCCG
20979973 ATGGTTT
1 ATGGTTT
* *
20979980 AGGGATT
1 ATGGTTT
20979987 ATGGTTT
1 ATGGTTT
20979994 ATGGTTT
1 ATGGTTT
20980001 ATGGTTT
1 ATGGTTT
20980008 ATGGTTT
1 ATGGTTT
20980015 A
1 A
20980016 AAGGTTGGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (7 bp):
ATGGTTT
Found at i:20980079 original size:7 final size:7
Alignment explanation
Indices: 20980069--20980116 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
20980059 TGTTTTATAA
20980069 TTTAGGG
1 TTTAGGG
20980076 TTTAGGG
1 TTTAGGG
**
20980083 GATAGGGG
1 TTTA-GGG
20980091 TTTAGGG
1 TTTAGGG
20980098 TTTAGGG
1 TTTAGGG
*
20980105 TTTAGGT
1 TTTAGGG
20980112 TTTAG
1 TTTAG
20980117 ATTAATTAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
7 30 0.86
8 5 0.14
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.42
Consensus pattern (7 bp):
TTTAGGG
Found at i:20980091 original size:15 final size:14
Alignment explanation
Indices: 20980071--20980110 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
20980061 TTTTATAATT
20980071 TAGGGTTTAGGGGA
1 TAGGGTTTAGGGGA
**
20980085 TAGGGGTTTAGGGTT
1 TA-GGGTTTAGGGGA
20980100 TAGGGTTTAGG
1 TAGGGTTTAGG
20980111 TTTTAGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.17, C:0.00, G:0.47, T:0.35
Consensus pattern (14 bp):
TAGGGTTTAGGGGA
Found at i:20980109 original size:36 final size:36
Alignment explanation
Indices: 20980023--20980116 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 36
20980013 TTAAAGGTTG
*
20980023 GGGTTTAAGGTTTAAGGG-TTAGGGGTTAGGGATTTA
1 GGGTTTAAGGTTT-AGGGTTTAGGGGATAGGGATTTA
* * * *
20980059 TGTTTTATA-ATTTAGGGTTTAGGGGATAGGGGTTTA
1 GGGTTTA-AGGTTTAGGGTTTAGGGGATAGGGATTTA
* *
20980095 GGGTTTAGGGTTTAGGTTTTAG
1 GGGTTTAAGGTTTAGGGTTTAG
20980117 ATTAATTAGT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
35 4 0.09
36 40 0.89
37 1 0.02
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.41
Consensus pattern (36 bp):
GGGTTTAAGGTTTAGGGTTTAGGGGATAGGGATTTA
Done.