Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 190 of 427
Found at i:52494715 original size:40 final size:40
Alignment explanation
Indices: 52494641--52494782 Score: 167
Period size: 40 Copynumber: 3.5 Consensus size: 40
52494631 CCGCACCAAG
* * * * * *
52494641 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
52494681 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * *
52494721 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
52494761 GCCTTCGGGTCTTAACCCGGAT
1 GCCTTCGGGTCTTAGCCCGGAT
52494783 GTAATTTTCA
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:52494801 original size:40 final size:40
Alignment explanation
Indices: 52494673--52494824 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
52494663 ATCACGATTT
* * * * *
52494673 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
52494713 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
* * * **
52494753 GCACAATTGCCTTCGGGTCTTAACCCGGATGTA-ATTTTCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACT-A
* * *
52494793 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
52494825 CATTCAATTT
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 4 0.04
40 89 0.94
41 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
Found at i:52498633 original size:43 final size:43
Alignment explanation
Indices: 52498511--52498668 Score: 182
Period size: 44 Copynumber: 3.7 Consensus size: 43
52498501 TATGTGTTTT
* * *
52498511 GTGTAAGACCACGTCTAGGATGCTGGCATCG-ACTTATGATTTAC
1 GTGTAAGACCATGTCTAGGACGTTGGCATCGTA-TT-TGATTTAC
52498555 GTGTAAGACCATGTCTAGGACGTTGGCATCGTATTTGATTT-C
1 GTGTAAGACCATGTCTAGGACGTTGGCATCGTATTTGATTTAC
*
52498597 GTGTAAGACC-TGTCTGGGACAG-TGGCAATCGATATTTG-TTTAC
1 GTGTAAGACCATGTCTAGGAC-GTTGGC-ATCG-TATTTGATTTAC
* *
52498640 ATGTAAGATCATGTCTAGGACGTTGGCAT
1 GTGTAAGACCATGTCTAGGACGTTGGCAT
52498669 TGTACGAGCT
Statistics
Matches: 100, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
41 13 0.13
42 19 0.19
43 24 0.24
44 43 0.43
45 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
GTGTAAGACCATGTCTAGGACGTTGGCATCGTATTTGATTTAC
Found at i:52499949 original size:39 final size:40
Alignment explanation
Indices: 52499837--52499954 Score: 166
Period size: 39 Copynumber: 2.9 Consensus size: 40
52499827 TATGGTAACC
* *
52499837 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACTT
*
52499878 CGCAACAATTGCCTTGCTCGGCTTAGCCCGGATATCACAA-TT
1 CGC-ACAATTGCCTT-C-GGGCTTAGCCCGGATATCACAACTT
52499920 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
52499955 TCGAACATTC
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
39 19 0.27
40 1 0.01
41 14 0.20
42 15 0.21
43 19 0.27
44 2 0.03
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (40 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTT
Found at i:52507877 original size:40 final size:39
Alignment explanation
Indices: 52507833--52508014 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
52507823 GTTCAAAACA
* * ** * *
52507833 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
52507873 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
52507913 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
52507952 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
52507991 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
52508015 CTCGAACATT
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 88 0.69
40 40 0.31
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:52507944 original size:39 final size:39
Alignment explanation
Indices: 52507863--52508015 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
52507853 TATGGTAACC
* *
52507863 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
52507903 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
52507942 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
52507981 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
52508016 TCGAACATTC
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:52515944 original size:40 final size:39
Alignment explanation
Indices: 52515900--52516081 Score: 229
Period size: 39 Copynumber: 4.6 Consensus size: 39
52515890 GTTCAAAACA
* * ** * *
52515900 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
52515940 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
52515980 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* * * *
52516019 CCTTCGGGCTTAGCCCGGATACCACAATTCGCACAATTA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
52516058 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
52516082 CTCGAACATT
Statistics
Matches: 125, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 85 0.68
40 40 0.32
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:52516011 original size:39 final size:39
Alignment explanation
Indices: 52515930--52516082 Score: 234
Period size: 39 Copynumber: 3.9 Consensus size: 39
52515920 TATGGTAACC
* *
52515930 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
52515970 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
* *
52516009 CGCACAATTGCCTTCGGGCTTAGCCCGGATACCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
52516048 CGCACAATTACCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
52516083 TCGAACATTC
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 86 0.83
40 17 0.17
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:52531026 original size:29 final size:29
Alignment explanation
Indices: 52530994--52531228 Score: 298
Period size: 29 Copynumber: 8.2 Consensus size: 29
52530984 ATCCCACATA
52530994 AATGTGAATTGGGCCTAATGGGCCATATG
1 AATGTGAATTGGGCCTAATGGGCCATATG
* * * *
52531023 AATGTGAATTAGG-CTGGATGAGCCATATA
1 AATGTGAATTGGGCCT-AATGGGCCATATG
*
52531052 AATGAG-ATTGGGCCTAATGGGCCATATG
1 AATGTGAATTGGGCCTAATGGGCCATATG
**
52531080 AATGTGAATTGGGCCGGATGGGCCATATG
1 AATGTGAATTGGGCCTAATGGGCCATATG
*
52531109 AATGTGAATTGGGCGTAATGGGCCATATG
1 AATGTGAATTGGGCCTAATGGGCCATATG
*
52531138 AATGTGAATTGGGCCTGATGGGCCATATG
1 AATGTGAATTGGGCCTAATGGGCCATATG
* *
52531167 AATGTGAATTGGG-CTGGATGGGCCATATA
1 AATGTGAATTGGGCCT-AATGGGCCATATG
* *
52531196 AATGAG-ATTGGGCCTAGTGGGCCATATG
1 AATGTGAATTGGGCCTAATGGGCCATATG
*
52531224 CATGT
1 AATGT
52531229 ATGAGGGGTT
Statistics
Matches: 177, Mismatches: 24, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
28 43 0.24
29 134 0.76
ACGTcount: A:0.27, C:0.13, G:0.33, T:0.27
Consensus pattern (29 bp):
AATGTGAATTGGGCCTAATGGGCCATATG
Found at i:52534896 original size:29 final size:29
Alignment explanation
Indices: 52534863--52534965 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
52534853 CCTCCGAACT
** * * *
52534863 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
52534892 TGCACACTTAGTGCCAAATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
52534921 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
52534950 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
52534966 ATCTCGTCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:52542403 original size:29 final size:29
Alignment explanation
Indices: 52542303--52542403 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
52542293 CCTCCGAACT
* * * *
52542303 CGCACAC-CAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
52542331 TGCACACTTAGTGCCA-ATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
52542359 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
52542388 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
52542404 ATCTCGTCAC
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
28 31 0.48
29 34 0.52
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:52542422 original size:57 final size:57
Alignment explanation
Indices: 52542311--52542422 Score: 127
Period size: 57 Copynumber: 2.0 Consensus size: 57
52542301 CTCGCACACC
* * ** * * *
52542311 AGTGCCGTATTTTTCCAGCTTGCACACTTAGTGCCAATATTTCCAGCACGCACACTT
1 AGTGCCATATATTTCCAGCACGCACACTTAGTGCCAATATGTCCACCACACACACTT
* *
52542368 AGTGCCATATATTTCCAGCACGCACACTTAGTGCCAATCTCGT-CACCATACACAC
1 AGTGCCATATATTTCCAGCACGCACACTTAGTGCCAATAT-GTCCACCACACACAC
52542423 GTATTGCCCG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
57 44 0.98
58 1 0.02
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (57 bp):
AGTGCCATATATTTCCAGCACGCACACTTAGTGCCAATATGTCCACCACACACACTT
Found at i:52547075 original size:80 final size:80
Alignment explanation
Indices: 52546991--52547139 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
52546981 TATGGTAACC
* * * *
52546991 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
52547055 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
52547071 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
52547136 CCGG
66 CCGG
52547140 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:52547081 original size:40 final size:38
Alignment explanation
Indices: 52547032--52547139 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
52547022 ATCACGATTT
*
52547032 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
52547072 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
52547112 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
52547140 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:52555188 original size:80 final size:80
Alignment explanation
Indices: 52555104--52555252 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
52555094 TATGGTAACC
* * * *
52555104 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
52555168 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
52555184 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
52555249 CCGG
66 CCGG
52555253 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:52555194 original size:40 final size:38
Alignment explanation
Indices: 52555145--52555252 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
52555135 ATCACGATTT
*
52555145 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
52555185 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
52555225 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
52555253 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:52560731 original size:28 final size:28
Alignment explanation
Indices: 52560698--52560756 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
52560688 GTATTATTTT
*
52560698 ATGTGTTGTAGTATGATTTTATGAGCGC
1 ATGTGTTATAGTATGATTTTATGAGCGC
* *
52560726 ATGTGTTATAGTTTGATTTTATGAGTGC
1 ATGTGTTATAGTATGATTTTATGAGCGC
52560754 ATG
1 ATG
52560757 AAAATTATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.22, C:0.05, G:0.27, T:0.46
Consensus pattern (28 bp):
ATGTGTTATAGTATGATTTTATGAGCGC
Found at i:52562277 original size:24 final size:24
Alignment explanation
Indices: 52562213--52562307 Score: 140
Period size: 24 Copynumber: 4.0 Consensus size: 24
52562203 GCTTTATCAT
*
52562213 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
52562238 ATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
52562261 ATAACTAGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
52562285 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
52562308 GTACTTCCTT
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.26
24 40 0.62
25 8 0.12
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:52562382 original size:20 final size:19
Alignment explanation
Indices: 52562353--52562423 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 19
52562343 GCATTTATGA
52562353 ATAC-ATCATGTGCATATC
1 ATACAATCATGTGCATATC
52562371 ATACAGATCATGTGCATATC
1 ATACA-ATCATGTGCATATC
52562391 ATACATATCATGTGCATATC
1 ATACA-ATCATGTGCATATC
52562411 ATATCAATCATGT
1 ATA-CAATCATGT
52562424 ATATCAAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 4 0.08
20 43 0.88
21 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (19 bp):
ATACAATCATGTGCATATC
Found at i:52562391 original size:11 final size:11
Alignment explanation
Indices: 52562357--52562412 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
52562347 TTATGAATAC
52562357 ATCATGTGCAT
1 ATCATGTGCAT
* *
52562368 ATCA--TACAG
1 ATCATGTGCAT
52562377 ATCATGTGCAT
1 ATCATGTGCAT
*
52562388 ATCA--TACAT
1 ATCATGTGCAT
52562397 ATCATGTGCAT
1 ATCATGTGCAT
52562408 ATCAT
1 ATCAT
52562413 ATCAATCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:52562502 original size:25 final size:24
Alignment explanation
Indices: 52562460--52562507 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
52562450 ATAATTAAAC
* * *
52562460 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTC-TTTTTA
52562485 CCTAGGGGCAAAACGGTCTTTTT
1 CCTAGGGGCAAAACGGTCTTTTT
52562508 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (24 bp):
CCTAGGGGCAAAACGGTCTTTTTA
Found at i:52570319 original size:24 final size:24
Alignment explanation
Indices: 52570255--52570349 Score: 140
Period size: 24 Copynumber: 4.0 Consensus size: 24
52570245 GCTTTATCAT
*
52570255 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
52570280 ATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
52570303 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
52570327 ATAATTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
52570350 GTACTTCCTC
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
23 18 0.27
24 40 0.61
25 8 0.12
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:52570504 original size:25 final size:24
Alignment explanation
Indices: 52570462--52570509 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
52570452 ATAATTAAAC
* * *
52570462 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTC-TTTTTA
52570487 CCTAGGGGCAAAACGGTCTTTTT
1 CCTAGGGGCAAAACGGTCTTTTT
52570510 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (24 bp):
CCTAGGGGCAAAACGGTCTTTTTA
Found at i:52574163 original size:20 final size:21
Alignment explanation
Indices: 52574124--52574163 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52574114 GTCCTAATGG
*
52574124 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCGCGTTGCCCTT
52574145 CCACACGGGCGCG-TGCCCT
1 CCACACGGGCGCGTTGCCCT
52574164 GTTTCTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.42, G:0.30, T:0.17
Consensus pattern (21 bp):
CCACACGGGCGCGTTGCCCTT
Found at i:52576538 original size:42 final size:41
Alignment explanation
Indices: 52576427--52576548 Score: 136
Period size: 43 Copynumber: 2.9 Consensus size: 41
52576417 TAATATACCA
* * * *
52576427 ATGCCATATCCTAGATATGGTCTTACATAGGATCTCATATCG
1 ATGCAATATCCTAGATATGGTCTTACAGA-AATCTCACATCG
* *
52576469 ATGTCAATAGCCTAGCTATGGTCTTACACGAAATCTCACATCG
1 ATG-CAATATCCTAGATATGGTCTTACA-GAAATCTCACATCG
* *
52576512 ATGCTATATCCTAGATATGGTCTTACATGTAATCTCA
1 ATGCAATATCCTAGATATGGTCTTACA-GAAATCTCA
52576549 ATAACCCTAA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 32 0.48
43 34 0.51
44 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.33
Consensus pattern (41 bp):
ATGCAATATCCTAGATATGGTCTTACAGAAATCTCACATCG
Found at i:52581081 original size:87 final size:87
Alignment explanation
Indices: 52580944--52581117 Score: 330
Period size: 87 Copynumber: 2.0 Consensus size: 87
52580934 CAACTCTTGC
* *
52580944 AACTTTGCTTTCAACTCTTTCAACTCTATGGGAGCCATTCTTTACGGTGCTATCGATATCAGTGA
1 AACTTTGCTTTCAACTCTTTCAACTCTATGGGAGCAATTCTTTACAGTGCTATCGATATCAGTGA
52581009 TGTTCCTGATACTAACTCAATG
66 TGTTCCTGATACTAACTCAATG
52581031 AACTTTGCTTTCAACTCTTTCAACTCTATGGGAGCAATTCTTTACAGTGCTATCGATATCAGTGA
1 AACTTTGCTTTCAACTCTTTCAACTCTATGGGAGCAATTCTTTACAGTGCTATCGATATCAGTGA
52581096 TGTTCCTGATACTAACTCAATG
66 TGTTCCTGATACTAACTCAATG
52581118 GAAACTTCGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (87 bp):
AACTTTGCTTTCAACTCTTTCAACTCTATGGGAGCAATTCTTTACAGTGCTATCGATATCAGTGA
TGTTCCTGATACTAACTCAATG
Found at i:52583171 original size:24 final size:25
Alignment explanation
Indices: 52583144--52583195 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
52583134 TTTGAACATG
52583144 ATTCACATA-TACATATCATA-ACTC
1 ATTCACATACT-CATATCATATACTC
* *
52583168 ATTCTCATACTTATATCATATACTC
1 ATTCACATACTCATATCATATACTC
52583193 ATT
1 ATT
52583196 AAGGTACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTCACATACTCATATCATATACTC
Found at i:52583453 original size:42 final size:43
Alignment explanation
Indices: 52583351--52583508 Score: 173
Period size: 43 Copynumber: 3.7 Consensus size: 43
52583341 AGCTCGTACA
* * *
52583351 ATGCCAACGTCCTAGACATGATCTTACATGTAAA-CAAATATCG
1 ATGCCAACGTCCTAGACAGGGTCTTACACGTAAATCAAATA-CG
*
52583394 ATGCC-ACTGTCCCAGACAGGGTCTTACACG-AAATCAAATACG
1 ATGCCAAC-GTCCTAGACAGGGTCTTACACGTAAATCAAATACG
*
52583436 ATGCCAACGTCCTAGACATGGTCTTACACGTAAATCATAAGT-CG
1 ATGCCAACGTCCTAGACAGGGTCTTACACGTAAATCA-AA-TACG
* *
52583480 ATGCCAGCATCCTAGAC-GTGGTCTTACAC
1 ATGCCAACGTCCTAGACAG-GGTCTTACAC
52583509 AAAAACACAT
Statistics
Matches: 99, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
42 32 0.32
43 37 0.37
44 29 0.29
45 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCTAGACAGGGTCTTACACGTAAATCAAATACG
Found at i:52587291 original size:40 final size:39
Alignment explanation
Indices: 52587205--52587388 Score: 147
Period size: 40 Copynumber: 4.6 Consensus size: 39
52587195 AAATTGAATG
* * * * *
52587205 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGAA-AATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC--AAGTAGT
* * *
52587245 ACATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAG-T
* *
52587285 ATATCCGGGCCAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTAG-T
* * * *
52587325 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAGT
* * *
52587364 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
52587389 CTTGGTGCGG
Statistics
Matches: 116, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
38 1 0.01
39 5 0.04
40 108 0.93
41 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAGT
Found at i:52595368 original size:38 final size:40
Alignment explanation
Indices: 52595311--52595410 Score: 123
Period size: 38 Copynumber: 2.5 Consensus size: 40
52595301 AAATTGAATG
*
52595311 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAAT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAAAT
* * * * **
52595350 -TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAAAT
52595389 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
52595411 GCATTCGTGC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
38 28 0.55
39 3 0.06
40 20 0.39
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAAAT
Found at i:52595403 original size:40 final size:40
Alignment explanation
Indices: 52595311--52595460 Score: 162
Period size: 40 Copynumber: 3.8 Consensus size: 40
52595301 AAATTGAATG
* * * * *
52595311 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAAT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGAT
* *
52595350 -TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGAT
* * *
52595389 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGAT
* *
52595429 AAATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
52595461 AAATCGTGAT
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
38 28 0.30
39 6 0.06
40 58 0.62
41 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGAT
Found at i:52595475 original size:40 final size:39
Alignment explanation
Indices: 52595350--52595492 Score: 160
Period size: 40 Copynumber: 3.6 Consensus size: 39
52595340 TGCTGAAAAT
* * *
52595350 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAG-TA
* *
52595390 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAG-TA
* * *
52595430 AATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTGA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAGT-A
* * *
52595470 TATCCGGGTTAAGTCCCGTAGGC
1 TATCCGGGCTAAGACCCGAAGGC
52595493 CTTGGTGCGG
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 1 0.01
40 87 0.99
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAGTA
Found at i:52597406 original size:29 final size:29
Alignment explanation
Indices: 52597373--52597437 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
52597363 GTGACGAGAT
*
52597373 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
52597402 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
52597431 CGGCACT
1 TGGCACT
52597438 GGGTGTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:52605335 original size:29 final size:28
Alignment explanation
Indices: 52605265--52605327 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
52605255 TGACGAGATT
* *
52605265 GGCACTAAGTGTGCATGCTGGAATATAT
1 GGCACTAAGTGTGCATGCTGGAAAATAC
52605293 GGCACTAAGTGTGCATGCTGGAAAAATAC
1 GGCACTAAGTGTGCATGCTGG-AAAATAC
52605322 GGCACT
1 GGCACT
52605328 GGGTGTGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 21 0.66
29 11 0.34
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (28 bp):
GGCACTAAGTGTGCATGCTGGAAAATAC
Found at i:52607077 original size:39 final size:39
Alignment explanation
Indices: 52607023--52607176 Score: 238
Period size: 39 Copynumber: 3.9 Consensus size: 39
52607013 TGTGAATGAA
52607023 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
*
52607062 TGTGCGAATTCTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
52607101 TGTGC-AAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAA-TTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
52607140 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGC
52607177 GTTTGTACGG
Statistics
Matches: 105, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
38 2 0.02
39 93 0.89
40 10 0.10
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:52609252 original size:21 final size:20
Alignment explanation
Indices: 52609224--52609263 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
52609214 CAAAACTTGT
52609224 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
52609244 ATAATCTATCATCAATCATT
1 ATAA-CTATCATCAAACATT
52609264 AAATCTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:52612273 original size:19 final size:19
Alignment explanation
Indices: 52612249--52612293 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
52612239 TTTTTAATAT
52612249 TTTATTTTCTTAAATC-TCA
1 TTTATTTTCTTAAATCAT-A
*
52612268 TTTATTTTTTTAAATCATA
1 TTTATTTTCTTAAATCATA
52612287 TTTATTT
1 TTTATTT
52612294 GTATTCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTTTCTTAAATCATA
Found at i:52614310 original size:26 final size:26
Alignment explanation
Indices: 52614242--52614321 Score: 65
Period size: 25 Copynumber: 3.0 Consensus size: 26
52614232 TATTGTTTCA
*
52614242 TTTAATAAAATAAAAGTTGTTTTTAATAT
1 TTTAATAAAAT--AA-TTATTTTTAATAT
**
52614271 TTTAATAGTA-AATTATTTTT-ATATT
1 TTTAATAAAATAATTATTTTTAATA-T
*
52614296 TTTAATAAAATAATTCTTTTTGAATA
1 TTTAATAAAATAATTATTTTT-AATA
52614322 AGGCAATAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
24 3 0.07
25 16 0.39
26 11 0.27
28 3 0.07
29 8 0.20
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (26 bp):
TTTAATAAAATAATTATTTTTAATAT
Found at i:52617544 original size:126 final size:124
Alignment explanation
Indices: 52617312--52617705 Score: 467
Period size: 126 Copynumber: 3.1 Consensus size: 124
52617302 GCCAAACAGA
* *
52617312 AACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCA-TCAATTTTGTTGACAGTGCATC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAAATTTTG-TGACAGTGCATC
52617376 CTGCTTGAAGCAT-TTTTTACACTATTTGTTCAGAACCATCTTCTCAAAATTATTTATTCAGG
65 CTGCTTGAA--ATGTTTTTACACTATTTGTTCAGAACCATCTTCTCAAAATTATTT-TTCAGG
**
52617438 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGT-ACCTTTGCTGACAGTGCATC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAAATTTTG-TGACAGTGCATC
* * *
52617502 CTGCTTGAAATGTTTTTGACACTATTTGTTCAAAATCGTCTTCTCAAAATTATTTTTTCAGG
65 CTGCTTGAAATGTTTTT-ACACTATTTGTTCAGAACCATCTTCTCAAAATTA-TTTTTCAGG
* * * * *
52617564 AACTACTGTAGAAAAAGAG-GACC-TGTGTAGAAGCTTTTTTCAGTAATTTTTGTGATAGTGCAT
1 AACTACTGTAGAAAAAGAGCGTCCACGTG--GGAGCTTTTTTCAGTAAATTTTGTGACAGTGCAT
** * * * *
52617627 CCTGCTTGAAGCGTTTTTCACATTATCTT-TTTAGAACCATCTTCTCAAAATTAATTTTCTGG
64 CCTGCTTGAAATGTTTTT-ACACTAT-TTGTTCAGAACCATCTTCTCAAAATTATTTTTCAGG
*
52617689 AAACAACTGTAGAAAAA
1 -AACTACTGTAGAAAAA
52617706 AAATAAAATC
Statistics
Matches: 235, Mismatches: 24, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
124 5 0.02
125 15 0.06
126 204 0.87
127 11 0.05
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (124 bp):
AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAAATTTTGTGACAGTGCATCC
TGCTTGAAATGTTTTTACACTATTTGTTCAGAACCATCTTCTCAAAATTATTTTTCAGG
Found at i:52617816 original size:34 final size:33
Alignment explanation
Indices: 52617760--52617894 Score: 150
Period size: 34 Copynumber: 4.0 Consensus size: 33
52617750 CCTAAACACA
52617760 AATTTATTTTTTAAAAA-ACTAAACCCTAATTT
1 AATTTATTTTTTAAAAACACTAAACCCTAATTT
* *
52617792 AATTTATTTTCTTAAAAACTCTAAACTCTAATTT
1 AATTTATTTT-TTAAAAACACTAAACCCTAATTT
* *
52617826 AACTTATTTATTTAAAAGC-CTTAAACCCTAATTT
1 AATTTATTT-TTTAAAAACAC-TAAACCCTAATTT
* *
52617860 AA-CTACTTTTTTAAAAAACACTAAACCTTAATTT
1 AATTTA-TTTTTT-AAAAACACTAAACCCTAATTT
52617894 A
1 A
52617895 TTTTTTAAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
32 10 0.11
33 13 0.15
34 63 0.72
35 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.01, T:0.42
Consensus pattern (33 bp):
AATTTATTTTTTAAAAACACTAAACCCTAATTT
Found at i:52633712 original size:3 final size:3
Alignment explanation
Indices: 52633704--52633735 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
52633694 TTAATAACAT
*
52633704 AGA AGA AGA TGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
52633736 CAGCTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:52642408 original size:49 final size:50
Alignment explanation
Indices: 52642354--52642454 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
52642344 TTCGGTTATT
52642354 TTAGTTTAACTAATTAAGTTGTTAT-AATTGTCTTTAGTTGCTTAAATAA
1 TTAGTTTAACTAATTAAGTTGTTATGAATTGTCTTTAGTTGCTTAAATAA
* * * *
52642403 TTAGTTTAATTATTTAAGTTGTTTTGAATTTTCTTTAGTTGCTTAAATAA
1 TTAGTTTAACTAATTAAGTTGTTATGAATTGTCTTTAGTTGCTTAAATAA
52642453 TT
1 TT
52642455 TCAGCATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 22 0.47
50 25 0.53
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (50 bp):
TTAGTTTAACTAATTAAGTTGTTATGAATTGTCTTTAGTTGCTTAAATAA
Found at i:52644692 original size:30 final size:30
Alignment explanation
Indices: 52644659--52644716 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
52644649 ATTAATACAT
52644659 AAAATAATAATATAATATATAACTATTACTA
1 AAAATAATAATA-AATATATAACTATTACTA
* *
52644690 AAAATATTAATACATATATAACTATTA
1 AAAATAATAATAAATATATAACTATTA
52644717 TTATAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (30 bp):
AAAATAATAATAAATATATAACTATTACTA
Found at i:52645123 original size:238 final size:248
Alignment explanation
Indices: 52644703--52645178 Score: 679
Period size: 238 Copynumber: 1.9 Consensus size: 248
52644693 ATATTAATAC
*
52644703 ATATATAACTATTATTATAATATAGATTATAATAAAAGATAAAATATTACATGTGATATTATAAT
1 ATATATAACTATTATTATAATATAGATTACAATAAAAGATAAAATATTACA-GTGATATTATAAT
* * * *
52644768 GTTTAATTATCAGTGCATTTATATATAAACTATTAATATATTATATGATATGGTATGATATAATA
65 GCTTAATCATCAGTGCATATATATATAAACTATTAATATATTATATGATA--GTATGATATAACA
52644833 TTATAGTAGGAGGGCTAACTTTCAAATGTAAGAAAAATATAGGGACTTAGAGCATATTTTAACTA
128 TTATAGTAGGAGGGCTAACTTTCAAATGTAAGAAAAATATAGGGACTTAGAGCATATTTTAACTA
* *
52644898 GTATAATAAT-AAACGGTAATATA-TATAATAAGTAATATATAATGAACTGCTATT
193 GTATAATAATAAAACAGTAATATATTATAATAAGTAACATATAATGAACTGCTATT
* * *
52644952 ATATATAACTATTATTATAATATAGATTACAATAAAAGATATAGTATTACA-TGATATTGTAATG
1 ATATATAACTATTATTATAATATAGATTACAATAAAAGATAAAATATTACAGTGATATTATAATG
* * *
52645016 CTTAATCAT-TGATGCATATATATATATA-TA-TAA-ACTGTTA-AT-ATA-T-T-ATATAACAT
66 CTTAATCATCAG-TGCATATATATATAAACTATTAATA-TATTATATGATAGTATGATATAACAT
*
52645072 TATAGTAGGAGGGCTAACTTTCAAATGTAAGAAAAATATAGGGATTTAGAGCATATTTTAACTAG
129 TATAGTAGGAGGGCTAACTTTCAAATGTAAGAAAAATATAGGGACTTAGAGCATATTTTAACTAG
* *
52645137 TATAATAATAAAATAGTAATATATTATAATAATTAACATATA
194 TATAATAATAAAACAGTAATATATTATAATAAGTAACATATA
52645179 GAGGTGCTCA
Statistics
Matches: 207, Mismatches: 16, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
238 81 0.39
239 12 0.06
240 17 0.08
243 3 0.01
244 3 0.01
245 7 0.03
246 3 0.01
247 33 0.16
249 48 0.23
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (248 bp):
ATATATAACTATTATTATAATATAGATTACAATAAAAGATAAAATATTACAGTGATATTATAATG
CTTAATCATCAGTGCATATATATATAAACTATTAATATATTATATGATAGTATGATATAACATTA
TAGTAGGAGGGCTAACTTTCAAATGTAAGAAAAATATAGGGACTTAGAGCATATTTTAACTAGTA
TAATAATAAAACAGTAATATATTATAATAAGTAACATATAATGAACTGCTATT
Found at i:52649480 original size:25 final size:25
Alignment explanation
Indices: 52649446--52649515 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
52649436 GCGGACACAC
*
52649446 CACAGCTCATATGAGCTTACCGATT
1 CACAGCTCATATGAGCATACCGATT
52649471 CACAGCTCATGA-GAGCATACCGATT
1 CACAGCTCAT-ATGAGCATACCGATT
*
52649496 CATAGCTCATATGAGCATAC
1 CACAGCTCATATGAGCATAC
52649516 ATGTACAGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 1 0.02
25 39 0.95
26 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (25 bp):
CACAGCTCATATGAGCATACCGATT
Found at i:52653207 original size:29 final size:29
Alignment explanation
Indices: 52653175--52653273 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 29
52653165 ATATATAGCG
*
52653175 ATCTCAGTTATAACGAAGCCTTTATGGAA
1 ATCTCAGTTATAACGAAGCCTTTGTGGAA
* * **
52653204 ATCTTAGTTA-AATGAATGCCTTTGTGGTG
1 ATCTCAGTTATAACGAA-GCCTTTGTGGAA
* * **
52653233 ATCTCTGTTATAAGGAAGCCTTTGTGGCT
1 ATCTCAGTTATAACGAAGCCTTTGTGGAA
*
52653262 ATCTTAGTTATA
1 ATCTCAGTTATA
52653274 TGAATGCCTT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
28 5 0.09
29 46 0.82
30 5 0.09
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.38
Consensus pattern (29 bp):
ATCTCAGTTATAACGAAGCCTTTGTGGAA
Found at i:52653282 original size:29 final size:29
Alignment explanation
Indices: 52653204--52653492 Score: 162
Period size: 29 Copynumber: 10.0 Consensus size: 29
52653194 CTTTATGGAA
52653204 ATCTTAGTTAAATGAATGCCTTTGTGG-T
1 ATCTTAGTTAAATGAATGCCTTTGTGGCT
*
52653232 GATCTCT-GTTATAAGGAA-GCCTTTGTGGCT
1 -ATCT-TAGTTA-AATGAATGCCTTTGTGGCT
* * * *
52653262 ATCTTAGTTATATGAATGCCTTTTTAGCG
1 ATCTTAGTTAAATGAATGCCTTTGTGGCT
* **
52653291 ATCTCT-GTTGAAA-GTATGCCTTTGTGATT
1 ATCT-TAGTT-AAATGAATGCCTTTGTGGCT
* * ** * *
52653320 ATCTAAATTAAATGAATGATTTTATGGCG
1 ATCTTAGTTAAATGAATGCCTTTGTGGCT
* * * * *
52653349 ATTTTTGTTAAAAGGATGCCTTTGTGGGT
1 ATCTTAGTTAAATGAATGCCTTTGTGGCT
* * * *
52653378 ATCTCAATTAAATGAATGTCTTTATGGCT
1 ATCTTAGTTAAATGAATGCCTTTGTGGCT
* * * *
52653407 ATCTGT-GTTAAAAGGATGTCTTTGTGGCC
1 ATCT-TAGTTAAATGAATGCCTTTGTGGCT
* * *
52653436 ATCTTTGTTAAAGGAATGCC-TTGTGGCA
1 ATCTTAGTTAAATGAATGCCTTTGTGGCT
* *
52653464 AACTCT-GTTAAAATGAATGCCTTCGTGGC
1 ATCT-TAGTT-AAATGAATGCCTTTGTGGC
52653493 AGAATCTGAA
Statistics
Matches: 191, Mismatches: 55, Indels: 27
0.70 0.20 0.10
Matches are distributed among these distances:
28 22 0.12
29 153 0.80
30 16 0.08
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (29 bp):
ATCTTAGTTAAATGAATGCCTTTGTGGCT
Found at i:52653312 original size:58 final size:58
Alignment explanation
Indices: 52653172--52653492 Score: 268
Period size: 58 Copynumber: 5.5 Consensus size: 58
52653162 AGCATATATA
* * * * * ** *
52653172 GCGATCTCAGTTATAACGAAGCCTTTATGGAAATCTTAGTTAAATGAATGCCTTTGTG
1 GCGATCTCTGTTAAAAGGATGCCTTTGTGGCTATCTTAGTTAAATGAATGCCTTTTTG
* * * * *
52653230 GTGATCTCTGTTATAAGGAAGCCTTTGTGGCTATCTTAGTTATATGAATGCCTTTTTA
1 GCGATCTCTGTTAAAAGGATGCCTTTGTGGCTATCTTAGTTAAATGAATGCCTTTTTG
* * ** * * *
52653288 GCGATCTCTGTTGAAAGTATGCCTTTGTGATTATCTAAATTAAATGAATG-ATTTTATG
1 GCGATCTCTGTTAAAAGGATGCCTTTGTGGCTATCTTAGTTAAATGAATGCCTTTT-TG
* * * * * * *
52653346 GCGATTTTTGTTAAAAGGATGCCTTTGTGGGTATCTCAATTAAATGAATGTCTTTATG
1 GCGATCTCTGTTAAAAGGATGCCTTTGTGGCTATCTTAGTTAAATGAATGCCTTTTTG
* * * * * * *
52653404 GCTATCTGTGTTAAAAGGATGTCTTTGTGGCCATCTTTGTTAAAGGAATGCC-TTGTG
1 GCGATCTCTGTTAAAAGGATGCCTTTGTGGCTATCTTAGTTAAATGAATGCCTTTTTG
* * * *
52653461 GCAAACTCTGTTAAAATGAATGCCTTCGTGGC
1 GCGATCTCTGTTAAAA-GGATGCCTTTGTGGC
52653493 AGAATCTGAA
Statistics
Matches: 212, Mismatches: 48, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
57 21 0.10
58 188 0.89
59 3 0.01
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.39
Consensus pattern (58 bp):
GCGATCTCTGTTAAAAGGATGCCTTTGTGGCTATCTTAGTTAAATGAATGCCTTTTTG
Found at i:52653447 original size:116 final size:116
Alignment explanation
Indices: 52653132--52653492 Score: 269
Period size: 116 Copynumber: 3.1 Consensus size: 116
52653122 TTGCATATGT
* ** * * * * * * *
52653132 AAGCCTTTGTCGCTATCTCTGTTATAA-GAAAGCATATATAGCGATCTCAGTTATAACGAAGCCT
1 AAGCCTTTGTGGCTATCTCAATTA-AATGAATGCCTTTATAGCGATCTCTGTTAAAAGGATGCCT
* * * * * *
52653196 TTATGGA-AATCTTAGTTAAATGAATGCCTTTGTGGTGATCTCTGTTATAAGG
65 TTGT-GACCATCTTAGTTAAATGAATGACTTTATGGCGATCTCTGTTAAAAGG
* * * * * *
52653248 AAGCCTTTGTGGCTATCTTAGTTATATGAATGCCTTTTTAGCGATCTCTGTTGAAAGTATGCCTT
1 AAGCCTTTGTGGCTATCTCAATTAAATGAATGCCTTTATAGCGATCTCTGTTAAAAGGATGCCTT
** * * * * *
52653313 TGTGATTATCTAAATTAAATGAATGATTTTATGGCGATTTTTGTTAAAAGG
66 TGTGACCATCTTAGTTAAATGAATGACTTTATGGCGATCTCTGTTAAAAGG
* * * * * * *
52653364 ATGCCTTTGTGGGTATCTCAATTAAATGAATGTCTTTATGGCTATCTGTGTTAAAAGGATGTCTT
1 AAGCCTTTGTGGCTATCTCAATTAAATGAATGCCTTTATAGCGATCTCTGTTAAAAGGATGCCTT
* * * * * * * *
52653429 TGTGGCCATCTTTGTTAAAGGAATG-CCTTGTGGCAAACTCTGTTAAAATG
66 TGTGACCATCTTAGTTAAATGAATGACTTTATGGCGATCTCTGTTAAAAGG
*
52653479 AATGCCTTCGTGGC
1 AA-GCCTTTGTGGC
52653493 AGAATCTGAA
Statistics
Matches: 186, Mismatches: 56, Indels: 6
0.75 0.23 0.02
Matches are distributed among these distances:
115 21 0.11
116 165 0.89
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (116 bp):
AAGCCTTTGTGGCTATCTCAATTAAATGAATGCCTTTATAGCGATCTCTGTTAAAAGGATGCCTT
TGTGACCATCTTAGTTAAATGAATGACTTTATGGCGATCTCTGTTAAAAGG
Found at i:52656383 original size:24 final size:24
Alignment explanation
Indices: 52656356--52656418 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
52656346 CTTATTATGT
52656356 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
52656380 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
52656404 TCGCACACATAGTGC
1 TCGCACACATAGTGC
52656419 ATTTGAGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:52658588 original size:40 final size:40
Alignment explanation
Indices: 52658422--52658606 Score: 180
Period size: 40 Copynumber: 4.6 Consensus size: 40
52658412 TTCGAATGAT
* * *
52658422 ATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAA
** * *
52658462 ATCCGGAATAAGAT-CCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
52658502 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGCGAGCTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAA
* *
52658542 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTGTA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACT-AA
*
52658583 A-CCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATT
52658607 TGAATGTGTA
Statistics
Matches: 120, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.01
40 111 0.93
41 8 0.07
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:52658600 original size:80 final size:80
Alignment explanation
Indices: 52658422--52658609 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
52658412 TTCGAATGAT
* *
52658422 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGAATAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGAATAAGATCCGAAGGCATA
52658487 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* * **
52658502 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-GAGCT-ACTAAATCCGGGTTAAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGAATAAGAT-CCGAAGG
* *
52658563 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
52658583 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
52658610 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGAATAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:52666563 original size:40 final size:40
Alignment explanation
Indices: 52666397--52666581 Score: 180
Period size: 40 Copynumber: 4.6 Consensus size: 40
52666387 TTCGAATGAT
* * *
52666397 ATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAA
** * *
52666437 ATCCGGAATAAGAT-CCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
52666477 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGCGAGCTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAA
* *
52666517 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTGTA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACT-AA
*
52666558 A-CCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATT
52666582 TGAATGTGTA
Statistics
Matches: 120, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.01
40 111 0.93
41 8 0.07
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:52666575 original size:80 final size:80
Alignment explanation
Indices: 52666397--52666584 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
52666387 TTCGAATGAT
* *
52666397 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGAATAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGAATAAGATCCGAAGGCATA
52666462 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* * **
52666477 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-GAGCT-ACTAAATCCGGGTTAAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGAATAAGAT-CCGAAGG
* *
52666538 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
52666558 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
52666585 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGAATAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:52670188 original size:22 final size:23
Alignment explanation
Indices: 52670122--52670237 Score: 130
Period size: 23 Copynumber: 5.0 Consensus size: 23
52670112 TAGGCTCCTC
52670122 TCGAGCTGATGAACAGTAAGCTCTA
1 TCGAGCTGA--AACAGTAAGCTCTA
* *
52670147 TTGAGCTGAAACGGTAAGCTCTA
1 TCGAGCTGAAACAGTAAGCTCTA
52670170 TCGAGCTG-AACAGTAAGCTC-A
1 TCGAGCTGAAACAGTAAGCTCTA
52670191 TACGAGCTGAAACAGTAAGCTCTAA
1 T-CGAGCTGAAACAGTAAGCTCT-A
* *
52670216 T-GAGCTAAAAATAGTAAGCTCT
1 TCGAGCT-GAAACAGTAAGCTCT
52670238 TACAAGCTGA
Statistics
Matches: 80, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
21 2 0.03
22 18 0.22
23 37 0.46
24 13 0.16
25 10 0.12
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.23
Consensus pattern (23 bp):
TCGAGCTGAAACAGTAAGCTCTA
Found at i:52678697 original size:68 final size:67
Alignment explanation
Indices: 52678621--52678772 Score: 175
Period size: 67 Copynumber: 2.3 Consensus size: 67
52678611 CATCATGTGT
* * * * *
52678621 ACAAGAGAGCTACGAGACATTATGATGTAGCTAAGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTACGAGA-A-TAT-ATGTAGCTAAGCCGCATGCGTGATACCAGTGAAGGACACCA
52678684 TGTAG
63 TGTAG
* * *
52678689 ACAAGAGAGCTACGAG-ATATATGTAGCTAGGCCGCATGCGTGGTTCCAGGTGAAGGACACCATG
1 ACAAGAGAGCTACGAGAATATATGTAGCTAAGCCGCATGCGTGATACCA-GTGAAGGACACCATG
52678753 TAG
65 TAG
52678756 ACAAGAGAGCTACGAGA
1 ACAAGAGAGCTACGAGA
52678773 TGAAGTGGCT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
64 22 0.31
65 3 0.04
66 3 0.04
67 28 0.39
68 16 0.22
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (67 bp):
ACAAGAGAGCTACGAGAATATATGTAGCTAAGCCGCATGCGTGATACCAGTGAAGGACACCATGT
AG
Found at i:52680860 original size:52 final size:49
Alignment explanation
Indices: 52680680--52680869 Score: 194
Period size: 47 Copynumber: 3.9 Consensus size: 49
52680670 ACATAGTCAT
* ** * *
52680680 ATATCACA-TACCGAGGCCATAGCCCAGCCATGGTCTTACACGG-ATCAC
1 ATATCACACT-CCGATGCCATAGCCCAGATATGGTCTTATACGGAAGCAC
* * *
52680728 ATATCACACT--GATGCCATATCCCAGATATGGTCTTATACAGTAGCAC
1 ATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAGCAC
* *
52680775 ATATCACA--CCGATGCCATATCCCGGATATGGTCTTATACGGAAGCAC
1 ATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAGCAC
* *
52680822 ATATCACATTTCTCCGAAGCCATAGCCCAGCTATGGTCTTATACGGAA
1 ATATCACA---CTCCGATGCCATAGCCCAGATATGGTCTTATACGGAA
52680870 ATCACAGTTC
Statistics
Matches: 119, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
46 25 0.21
47 54 0.45
48 8 0.07
49 1 0.01
52 31 0.26
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (49 bp):
ATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAGCAC
Found at i:52687320 original size:15 final size:17
Alignment explanation
Indices: 52687302--52687333 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
52687292 AGTCCGAGAC
52687302 AAAGAAA-T-CCAAGAT
1 AAAGAAACTCCCAAGAT
52687317 AAAGAAACTCCCAAGAT
1 AAAGAAACTCCCAAGAT
52687334 TCAGAAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.12
Consensus pattern (17 bp):
AAAGAAACTCCCAAGAT
Found at i:52696318 original size:138 final size:138
Alignment explanation
Indices: 52696065--52696485 Score: 641
Period size: 138 Copynumber: 3.1 Consensus size: 138
52696055 TGGAAAAATG
* * * * *
52696065 AATTATATTATTTCTAAAAGAATATTAATTTCTATGTCTTTTATATTTTGACCAAACTTCATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAA
52696130 TATAACTGTTTATATTAATAAATTTAGTAAAATATATACAATTAACATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTTAGTAAAATATATACAATTAACATTTTGTATGAATCAAATT
*
52696195 CATATATT
131 AATATATT
*
52696203 AATTATATTCTTTCCATAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAA
*
52696268 TATAACTGTTTATATTAATAAATTCAGTAAAATATAAATACAATT-A-ATTTTGTATGAATCAAA
66 TATAACTGTTTATATTAATAAATTTAGTAAAATAT--ATACAATTAACATTTTGTATGAATCAAA
52696331 TTAATATATT
129 TTAATATATT
* * * *
52696341 AATTATATTCTTTCCAAAATAATATTAATTTCCATGTCTTTTACATTTTGA-AAAAAATAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAA
* * * * *
52696405 TATAGCTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGCATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTTAGTAAAATATATACAATTAACATTTTGTATGAATCAAATT
*
52696470 TATATATT
131 AATATATT
52696478 AATTATAT
1 AATTATAT
52696486 CTATGTTCTC
Statistics
Matches: 260, Mismatches: 19, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
135 8 0.03
136 1 0.00
137 75 0.29
138 167 0.64
139 1 0.00
140 8 0.03
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAA
TATAACTGTTTATATTAATAAATTTAGTAAAATATATACAATTAACATTTTGTATGAATCAAATT
AATATATT
Found at i:52697894 original size:23 final size:22
Alignment explanation
Indices: 52697845--52697895 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
52697835 AAATTAGCAA
52697845 ATTCATTACATAACATAATAAC
1 ATTCATTACATAACATAATAAC
* *
52697867 TTTCATGTACATAGCAT-ATAAGC
1 ATTCAT-TACATAACATAATAA-C
52697890 ATTCAT
1 ATTCAT
52697896 ACTTTCATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (22 bp):
ATTCATTACATAACATAATAAC
Found at i:52699087 original size:98 final size:98
Alignment explanation
Indices: 52698973--52699170 Score: 396
Period size: 98 Copynumber: 2.0 Consensus size: 98
52698963 TCTTTGAATA
52698973 TTTGGTGGTGAAGATGAAAGAAAGATGATATCTTTCTTTTCTTTACTTAATTTTATGTTAATTTT
1 TTTGGTGGTGAAGATGAAAGAAAGATGATATCTTTCTTTTCTTTACTTAATTTTATGTTAATTTT
52699038 TCAATTTACCTTTTTAACCTTATACATTAACCT
66 TCAATTTACCTTTTTAACCTTATACATTAACCT
52699071 TTTGGTGGTGAAGATGAAAGAAAGATGATATCTTTCTTTTCTTTACTTAATTTTATGTTAATTTT
1 TTTGGTGGTGAAGATGAAAGAAAGATGATATCTTTCTTTTCTTTACTTAATTTTATGTTAATTTT
52699136 TCAATTTACCTTTTTAACCTTATACATTAACCT
66 TCAATTTACCTTTTTAACCTTATACATTAACCT
52699169 TT
1 TT
52699171 AAAAATCACT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 100 1.00
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.48
Consensus pattern (98 bp):
TTTGGTGGTGAAGATGAAAGAAAGATGATATCTTTCTTTTCTTTACTTAATTTTATGTTAATTTT
TCAATTTACCTTTTTAACCTTATACATTAACCT
Found at i:52701579 original size:12 final size:12
Alignment explanation
Indices: 52701552--52701585 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
52701542 TTAGCCTTAG
*
52701552 CCTTAGCCTTTT
1 CCTTTGCCTTTT
52701564 -CTTTGCCTTTT
1 CCTTTGCCTTTT
52701575 CCTTTGCCTTT
1 CCTTTGCCTTT
52701586 GCCCTTGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.03, C:0.32, G:0.09, T:0.56
Consensus pattern (12 bp):
CCTTTGCCTTTT
Found at i:52702631 original size:9 final size:9
Alignment explanation
Indices: 52702617--52702641 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52702607 GGACTAAAAT
52702617 ATGAAATAA
1 ATGAAATAA
52702626 ATGAAATAA
1 ATGAAATAA
52702635 ATGAAAT
1 ATGAAAT
52702642 GTGTGGACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (9 bp):
ATGAAATAA
Found at i:52703236 original size:42 final size:43
Alignment explanation
Indices: 52703132--52703270 Score: 110
Period size: 42 Copynumber: 3.2 Consensus size: 43
52703122 TGTGATTTTG
* *
52703132 TGTAAGACCATGTCTTGGA-AGTTGGCATCGACT-TCT-ATTTTACG
1 TGTAAGACCATGTCTGGGACAG-TGGCATCGA-TATCTGA--TTACA
* *
52703176 CGTAAGACCATGTCTGGGACA-TCGGCATCG-TATCTGATTTCA
1 TGTAAGACCATGTCTGGGACAGT-GGCATCGATATCTGATTACA
* * * *
52703218 TGTAAGATCC-TGTTTGGGATAGTGGCATCGATGTTTGATTACA
1 TGTAAGA-CCATGTCTGGGACAGTGGCATCGATATCTGATTACA
52703261 TGTAAGACCA
1 TGTAAGACCA
52703271 CATCTCAGAC
Statistics
Matches: 77, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
42 28 0.36
43 23 0.30
44 25 0.32
45 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGATATCTGATTACA
Found at i:52709835 original size:9 final size:9
Alignment explanation
Indices: 52709806--52709864 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
52709796 ATTCATTAAC
52709806 AAACACATT
1 AAACACATT
*
52709815 AAAACAAATT
1 -AAACACATT
*
52709825 AAACACTTT
1 AAACACATT
*
52709834 AAGCACATT
1 AAACACATT
*
52709843 AAGCACATT
1 AAACACATT
*
52709852 AAACATATT
1 AAACACATT
52709861 AAAC
1 AAAC
52709865 TTAATTAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
9 34 0.81
10 8 0.19
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.24
Consensus pattern (9 bp):
AAACACATT
Found at i:52710008 original size:34 final size:34
Alignment explanation
Indices: 52709909--52710011 Score: 116
Period size: 37 Copynumber: 2.9 Consensus size: 34
52709899 TAACAATAAA
* * * * * *
52709909 TTATTCCAACATCTAAATTAACTAAGATAAGCAT
1 TTATTCCAGCAACTCAATTAACTAAAATGAGTAT
*
52709943 TTATTCTAGCAACTCAATTAATAACTAAAATGAGTAT
1 TTATTCCAGCAACTCAA-T--TAACTAAAATGAGTAT
52709980 TTATTCCAGCAACTCAATTAACTAAAATGAGT
1 TTATTCCAGCAACTCAATTAACTAAAATGAGT
52710012 TTAATTAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
34 27 0.47
35 1 0.02
36 1 0.02
37 29 0.50
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.33
Consensus pattern (34 bp):
TTATTCCAGCAACTCAATTAACTAAAATGAGTAT
Found at i:52712001 original size:39 final size:39
Alignment explanation
Indices: 52711947--52712109 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
52711937 TGTGAATGAA
52711947 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
52711986 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
** *
52712025 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * **
52712064 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCGTT
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
52712104 TGTGCG
1 TGTGCG
52712110 GGTTACCATA
Statistics
Matches: 115, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 99 0.86
40 16 0.14
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.25
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:52721113 original size:17 final size:18
Alignment explanation
Indices: 52721091--52721124 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52721081 CAATTTGGGC
52721091 CGTGT-GACCCACACGGA
1 CGTGTGGACCCACACGGA
*
52721108 CGTGTGGGCCCACACGG
1 CGTGTGGACCCACACGG
52721125 GAAGGGCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.35, G:0.35, T:0.12
Consensus pattern (18 bp):
CGTGTGGACCCACACGGA
Found at i:52723381 original size:39 final size:39
Alignment explanation
Indices: 52723334--52723516 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
52723324 AATGTTCGAG
52723334 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
52723373 TGATATCCGGGCTAAGCCCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
52723412 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
52723451 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
52723491 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
52723517 GTTTGAACGA
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:52730833 original size:38 final size:39
Alignment explanation
Indices: 52730760--52730941 Score: 231
Period size: 39 Copynumber: 4.6 Consensus size: 39
52730750 AATGTTCGAG
52730760 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
52730799 TGATATCCGGGCTAAG-CCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
52730837 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
52730876 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
52730916 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
52730942 GTTTGAACGA
Statistics
Matches: 124, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
38 37 0.30
39 49 0.40
40 38 0.31
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:52737632 original size:21 final size:21
Alignment explanation
Indices: 52737606--52737699 Score: 161
Period size: 21 Copynumber: 4.5 Consensus size: 21
52737596 TGTGGTCCAA
52737606 GGGACACGCCCGTGTGACCCT
1 GGGACACGCCCGTGTGACCCT
*
52737627 GGGACACTCCCGTGTGACCCT
1 GGGACACGCCCGTGTGACCCT
52737648 GGGACACGCCCGTGTGACCCT
1 GGGACACGCCCGTGTGACCCT
* *
52737669 GGGACACACCCGTTTGACCCT
1 GGGACACGCCCGTGTGACCCT
52737690 GGGACACGCC
1 GGGACACGCC
52737700 TGTGCTAGAG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 68 1.00
ACGTcount: A:0.16, C:0.38, G:0.31, T:0.15
Consensus pattern (21 bp):
GGGACACGCCCGTGTGACCCT
Found at i:52740970 original size:61 final size:61
Alignment explanation
Indices: 52740875--52740995 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 61
52740865 GTGAGCAGGG
52740875 CCATTGATAGCTCTAGTGTGAGCAGTATATGTGATATGAGATTGAGATAGCTTCGGCTATC
1 CCATTGATAGCTCTAGTGTGAGCAGTATATGTGATATGAGATTGAGATAGCTTCGGCTATC
*
52740936 CCATTGATAGCTCTAGTGTGAGTAGTATATGTGATATGAGATTGAGATAGCTTCGGCTAT
1 CCATTGATAGCTCTAGTGTGAGCAGTATATGTGATATGAGATTGAGATAGCTTCGGCTAT
52740996 ATATATGGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (61 bp):
CCATTGATAGCTCTAGTGTGAGCAGTATATGTGATATGAGATTGAGATAGCTTCGGCTATC
Found at i:52752535 original size:47 final size:47
Alignment explanation
Indices: 52752459--52752584 Score: 225
Period size: 47 Copynumber: 2.7 Consensus size: 47
52752449 GGATGGTTGA
*
52752459 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAG
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAG
*
52752506 GCATTCAAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAG
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAG
*
52752553 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTC
52752585 ACTTATGGAT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 75 1.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (47 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:52755617 original size:14 final size:15
Alignment explanation
Indices: 52755568--52755617 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
52755558 GTATCTTGGG
* *
52755568 TTTCTTTGTCCTGGA
1 TTTCTTTATTCTGGA
*
52755583 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
52755598 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
52755612 TTTCTT
1 TTTCTT
52755618 GTTATCTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.08, C:0.18, G:0.14, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:52758119 original size:47 final size:47
Alignment explanation
Indices: 52758050--52758172 Score: 237
Period size: 47 Copynumber: 2.6 Consensus size: 47
52758040 GATGCGAATG
52758050 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
52758097 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
*
52758144 TCCGAACTCGTTGAGTGGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
52758173 ACCTATGGAT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 75 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
Found at i:52763410 original size:24 final size:24
Alignment explanation
Indices: 52763383--52763430 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
52763373 ACACAAAGTA
52763383 AGCTTTCAAAAGCTTAGCAAGCTC
1 AGCTTTCAAAAGCTTAGCAAGCTC
52763407 AGCTTTCAAAAGCTTAGCAAGCTC
1 AGCTTTCAAAAGCTTAGCAAGCTC
52763431 GTACTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (24 bp):
AGCTTTCAAAAGCTTAGCAAGCTC
Found at i:52765090 original size:8 final size:7
Alignment explanation
Indices: 52765073--52765104 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
52765063 AATTTGAACG
52765073 AGGGTTT
1 AGGGTTT
52765080 AGGGTTTT
1 AGGG-TTT
52765088 AGGGTTT
1 AGGGTTT
52765095 AGGGTTT
1 AGGGTTT
52765102 AGG
1 AGG
52765105 TATAGGGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.16, C:0.00, G:0.44, T:0.41
Consensus pattern (7 bp):
AGGGTTT
Found at i:52765093 original size:15 final size:15
Alignment explanation
Indices: 52765073--52765101 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52765063 AATTTGAACG
52765073 AGGGTTTAGGGTTTT
1 AGGGTTTAGGGTTTT
52765088 AGGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
52765102 AGGTATAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.45
Consensus pattern (15 bp):
AGGGTTTAGGGTTTT
Found at i:52778943 original size:24 final size:24
Alignment explanation
Indices: 52778916--52778978 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
52778906 CTTATTATGT
52778916 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
52778940 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
52778964 TCGCACACATAGTGC
1 TCGCACACATAGTGC
52778979 ATTTGAGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:52786731 original size:24 final size:24
Alignment explanation
Indices: 52786704--52786790 Score: 174
Period size: 24 Copynumber: 3.6 Consensus size: 24
52786694 CTTATTATGT
52786704 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
52786728 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
52786752 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
52786776 TCGCACACATAGTGC
1 TCGCACACATAGTGC
52786791 ATTTGAGATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:52792682 original size:40 final size:40
Alignment explanation
Indices: 52792361--52792669 Score: 460
Period size: 40 Copynumber: 7.7 Consensus size: 40
52792351 AATGATAACG
*
52792361 GGGCTAAGGCCCGAAGGCATTTGTGCGAGCTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTCC
* *
52792401 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTCC
52792441 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTCC
* * *
52792481 TGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTCC
* * *
52792521 GGGCTAAGTCTCGAAGGCATTTGTGCGAGCTACTATTTCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTCC
* *
52792561 AGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAAT-TCC
* *
52792601 GGGCTAAGTCCCGAAGGCATTTGTGTGAACTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAAT-TCC
*
52792641 GGGCTAAGTCCCGAAGGCATTTGAGCGAG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG
52792670 TAGCTATATC
Statistics
Matches: 242, Mismatches: 26, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
39 1 0.00
40 241 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTCC
Found at i:52795580 original size:42 final size:42
Alignment explanation
Indices: 52795468--52795631 Score: 206
Period size: 42 Copynumber: 3.9 Consensus size: 42
52795458 TACTGTACCA
* * *
52795468 ATGCCATATCCCAGATATGGCCTTACATGTAATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATCG
* * * *
52795510 ATGCCAATAGCCTAGCTATGGTCTTACACG-AAGTCTCACATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGTAA-TCTCATATCG
* *
52795553 ATGCCATATCCCAGATATGGTCTTACACG-AAGTGTTATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGTAA-TCTCATATCG
52795595 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
52795632 GTAACCCTAA
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
42 70 0.67
43 34 0.33
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATCG
Found at i:52795594 original size:85 final size:84
Alignment explanation
Indices: 52795468--52795631 Score: 215
Period size: 85 Copynumber: 1.9 Consensus size: 84
52795458 TACTGTACCA
* * * *
52795468 ATGCCATATCCCAGATATGGCCTTACATGTAATCTCGTATCGATGCCAATAGCCTAGCTATGGTC
1 ATGCCATATCCCAGATATGGCCTTACACGTAATCTCATATCGATGCC-ATAGCCCAGATATGGTC
52795533 TTACACG-AAGTCTCACATCG
65 TTACACGTAA-TCTCACATCG
* * * *
52795553 ATGCCATATCCCAGATATGGTCTTACACG-AAGTGTTATATCGATGCCATATCCCAGATATGGTC
1 ATGCCATATCCCAGATATGGCCTTACACGTAA-TCTCATATCGATGCCATAGCCCAGATATGGTC
52795617 TTACACGTAATCTCA
65 TTACACGTAATCTCA
52795632 GTAACCCTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
84 28 0.41
85 41 0.59
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (84 bp):
ATGCCATATCCCAGATATGGCCTTACACGTAATCTCATATCGATGCCATAGCCCAGATATGGTCT
TACACGTAATCTCACATCG
Found at i:52813832 original size:28 final size:29
Alignment explanation
Indices: 52813790--52813904 Score: 101
Period size: 29 Copynumber: 4.0 Consensus size: 29
52813780 TACCTGTATC
* *
52813790 TGACCCATTAAGCCC-AATCATATTCATA
1 TGACCCATTAGGCCCAAATCACATTCATA
*
52813818 TGACCCATTAGGCCCAAATCAC-TTGTATA
1 TGACCCATTAGGCCCAAATCACATT-CATA
* * *
52813847 TGGCCTATTAGGCCCAAATCACATTTATA
1 TGACCCATTAGGCCCAAATCACATTCATA
* * * * *
52813876 TGGCTCGTCAGGCCC-AGTCACATTCATA
1 TGACCCATTAGGCCCAAATCACATTCATA
52813904 T
1 T
52813905 TCATGCTTAC
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
28 28 0.38
29 43 0.59
30 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
TGACCCATTAGGCCCAAATCACATTCATA
Found at i:52813878 original size:29 final size:29
Alignment explanation
Indices: 52813793--52813879 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
52813783 CTGTATCTGA
* * * *
52813793 CCCATTAAGCCC-AATCATATTCATATGA
1 CCCATTAGGCCCAAATCACATTTATATGG
52813821 CCCATTAGGCCCAAATCAC-TTGTATATGG
1 CCCATTAGGCCCAAATCACATT-TATATGG
*
52813850 CCTATTAGGCCCAAATCACATTTATATGG
1 CCCATTAGGCCCAAATCACATTTATATGG
52813879 C
1 C
52813880 TCGTCAGGCC
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
28 13 0.25
29 36 0.71
30 2 0.04
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.29
Consensus pattern (29 bp):
CCCATTAGGCCCAAATCACATTTATATGG
Found at i:52814136 original size:16 final size:16
Alignment explanation
Indices: 52814115--52814149 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
52814105 GTAGCCAAAC
52814115 TTTCGACATTTCGGCA
1 TTTCGACATTTCGGCA
*
52814131 TTTCGACATTTTGGCA
1 TTTCGACATTTCGGCA
52814147 TTT
1 TTT
52814150 TGGCTTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (16 bp):
TTTCGACATTTCGGCA
Found at i:52818432 original size:29 final size:29
Alignment explanation
Indices: 52818330--52818419 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 29
52818320 TACCTATATC
* *
52818330 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCATATTTATA
* ** *
52818358 TGGCCCATTAGGCCTAAATCACCTGTATA
1 TGGCCCATTAGGCCCAAATCATATTTATA
52818387 TGGCCCATTAGGCCCAAATCATATTTATA
1 TGGCCCATTAGGCCCAAATCATATTTATA
52818416 TGGC
1 TGGC
52818420 TTGTTAGGCC
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 13 0.25
29 38 0.75
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCATATTTATA
Found at i:52818680 original size:16 final size:16
Alignment explanation
Indices: 52818655--52818691 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
52818645 GTAGCCAAAC
* *
52818655 TTTTGGCTTTTCGGCA
1 TTTTGACTTTTCGACA
52818671 TTTTGACTTTTCGACA
1 TTTTGACTTTTCGACA
52818687 TTTTG
1 TTTTG
52818692 GTATTTCGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.16, G:0.19, T:0.54
Consensus pattern (16 bp):
TTTTGACTTTTCGACA
Found at i:52828227 original size:28 final size:28
Alignment explanation
Indices: 52828187--52828257 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 28
52828177 TATAGTAAGT
*
52828187 TCGCACACTTAGTGCT-TAATAATCAAAC
1 TCGCACACTTAGTGCTAT-ACAATCAAAC
52828215 TCGCACACTTAGTGCTATACAATCAAAC
1 TCGCACACTTAGTGCTATACAATCAAAC
52828243 TCGCACACTTAGTGC
1 TCGCACACTTAGTGC
52828258 CAATCTCATT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 40 0.98
29 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
TCGCACACTTAGTGCTATACAATCAAAC
Found at i:52828819 original size:2 final size:2
Alignment explanation
Indices: 52828812--52828847 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
52828802 GCCATACATT
52828812 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52828848 GCCGAATGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52836057 original size:40 final size:40
Alignment explanation
Indices: 52836012--52836218 Score: 222
Period size: 40 Copynumber: 5.2 Consensus size: 40
52836002 CGGAATATAA
* *
52836012 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATAAC-TCGCACAAATGCCTTCGGGCCTTAGC
* *
52836052 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATAACTCGCACAAATGCCTTCGGGCCTTAGC
* *
52836092 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATAACTCGCACAAATGCCTTCGGGCCTTAGC
** * * * *
52836132 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATAACTCGCACAAATGCCTTCGGGCCTTAGC
** * * *
52836172 CCGGATATAATTTC-CAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATAACTC-GCACAAATGCCTTCGGGCCTTAGC
52836211 CCGGATAT
1 CCGGATAT
52836219 CATTCAATTT
Statistics
Matches: 146, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
39 14 0.10
40 132 0.90
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAATAACTCGCACAAATGCCTTCGGGCCTTAGC
Found at i:52837067 original size:17 final size:19
Alignment explanation
Indices: 52837044--52837089 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
52837034 AAGAAGCATG
52837044 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
52837062 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
52837080 AATCATGCTC
1 AATCATGCTC
52837090 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:52843342 original size:46 final size:46
Alignment explanation
Indices: 52843289--52843461 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 46
52843279 TTGTGAGCAT
52843289 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* * *
52843335 CGAACTCGTTGAG-TGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TC
* *
52843381 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
*
52843427 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52843462 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 9, Indels: 20
0.79 0.07 0.15
Matches are distributed among these distances:
41 2 0.02
42 5 0.05
44 3 0.03
45 13 0.12
46 63 0.58
47 13 0.12
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
Found at i:52846428 original size:15 final size:15
Alignment explanation
Indices: 52846389--52846467 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
52846379 GTATCTTGGG
*
52846389 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
52846404 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
52846419 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
52846433 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
52846448 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
52846462 TTTCTT
1 TTTCTT
52846468 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:52846452 original size:29 final size:29
Alignment explanation
Indices: 52846380--52846466 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
52846370 CATAGTATCG
* * * *
52846380 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GGATTTCTC
*
52846410 TAT-TCTGGATTTCTTTATTCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGATTTCTC
*
52846439 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGATTTCT
52846467 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 32 0.65
30 17 0.35
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGATTTCTC
Found at i:52848884 original size:46 final size:46
Alignment explanation
Indices: 52848834--52849009 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
52848824 TGGTTGAGCA
52848834 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
52848880 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
52848925 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
52848973 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52849010 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:52848990 original size:93 final size:93
Alignment explanation
Indices: 52848831--52849001 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
52848821 GGATGGTTGA
* *
52848831 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
52848896 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
52848924 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
52848989 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
52849002 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:52852706 original size:43 final size:42
Alignment explanation
Indices: 52852655--52852779 Score: 137
Period size: 44 Copynumber: 2.9 Consensus size: 42
52852645 GTATAACACG
52852655 AACGTCCCAGATGTGGTCTTACATGTAATCACATATCGATGCC
1 AACGTCCCAGATGTGGTCTTACA-GTAATCACATATCGATGCC
* * *
52852698 -ACTGTCCCAGATAG-GGTCTTACACGTAAATTAAAAATCGATGCC
1 AAC-GTCCCAGAT-GTGGTCTTACA-GT-AATCACATATCGATGCC
* **
52852742 AACGTCCCAGACGTGGTCTTACACCAATCACATATCGA
1 AACGTCCCAGATGTGGTCTTACAGTAATCACATATCGA
52852780 AATCCTATGT
Statistics
Matches: 67, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
42 12 0.18
43 21 0.31
44 32 0.48
45 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (42 bp):
AACGTCCCAGATGTGGTCTTACAGTAATCACATATCGATGCC
Found at i:52853900 original size:13 final size:13
Alignment explanation
Indices: 52853882--52853906 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52853872 ACAAACGATA
52853882 AAATTTTCACACG
1 AAATTTTCACACG
52853895 AAATTTTCACAC
1 AAATTTTCACAC
52853907 ATATAATATA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:52859093 original size:58 final size:57
Alignment explanation
Indices: 52859021--52859131 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 57
52859011 TGAATGTGAC
* * **
52859021 TGGGCCTAACGGGCCATATAAATGTGATTTGGGCCTAATGGGCCCTATACAGGTGATT
1 TGGGCCTAACGGGCCATATAAATATGA-TTGGGCCTAAGGGGCCAAATACAGGTGATT
* * *
52859079 TGGGCCTAATGGGCCATATGAATATGATTGGGCTTAAGGGGCCAAATACAGGT
1 TGGGCCTAACGGGCCATATAAATATGATTGGGCCTAAGGGGCCAAATACAGGT
52859132 ATGTGAGTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 22 0.48
58 24 0.52
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (57 bp):
TGGGCCTAACGGGCCATATAAATATGATTGGGCCTAAGGGGCCAAATACAGGTGATT
Found at i:52859120 original size:28 final size:29
Alignment explanation
Indices: 52859008--52859122 Score: 128
Period size: 29 Copynumber: 4.0 Consensus size: 29
52858998 GTGAGCATGA
* *
52859008 ATATGAATGTGA-CTGGGCCTAACGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
52859036 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
52859065 CTAT-ACAGGTGATTTGGGCCTAATGGGCC
1 ATATGA-ATGTGATTTGGGCCTAATGGGCC
* * *
52859094 ATATGAATATGA-TTGGGCTTAAGGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
52859122 A
1 A
52859123 AATACAGGTA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
28 27 0.36
29 46 0.62
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:52869496 original size:15 final size:15
Alignment explanation
Indices: 52869478--52869510 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52869468 TATGTGCTTG
*
52869478 AATTATTACAGTATA
1 AATTATTACAGCATA
52869493 AATTATTACAGCATA
1 AATTATTACAGCATA
52869508 AAT
1 AAT
52869511 GAGATTGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (15 bp):
AATTATTACAGCATA
Found at i:52869646 original size:46 final size:45
Alignment explanation
Indices: 52869588--52869808 Score: 166
Period size: 46 Copynumber: 4.7 Consensus size: 45
52869578 ATTCGTGTGT
* *
52869588 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGA-
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATC-GCCACATGA-GAC
* *
52869634 GAGCCAGTGTAAGACCATGTCTGGAACATGGTATCG--ACATTGAGAC
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGCCACA-TGAGAC
* *
52869680 GAGGGCTAGTGTAAGACATGTCTGGGACATGCATCGGC-CATGAGAC
1 GA--GCCAGTGTAAGACATGTCTGGGACATGCATCGCCACATGAGAC
* * *
52869726 GTAAGCCAATGTAAGACATGTCTAGGACATGCATCAGCTAC-TAGAGGA-
1 G--AGCCAGTGTAAGACATGTCTGGGACATGCATC-GCCACAT-GA-GAC
* * *
52869774 TAGTCAGTGTAAGACCATGTTTGGGACATGGCATC
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
52869809 TACTTGAGAT
Statistics
Matches: 142, Mismatches: 17, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
45 5 0.04
46 68 0.48
47 43 0.30
48 24 0.17
49 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.23
Consensus pattern (45 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGCCACATGAGAC
Found at i:52869842 original size:140 final size:141
Alignment explanation
Indices: 52869595--52869856 Score: 325
Period size: 140 Copynumber: 1.9 Consensus size: 141
52869585 TGTGAGCTAG
* * *
52869595 TGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGGAA
1 TGTAAGACATGTCTAGGACATGCATCAGCCACATGAGGAGAGCCAGTGTAAGACCATGTCTGGAA
* * * * *
52869660 CATGGTATCGACATTGAGACGAGGGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCATGAG
66 CATGGCATCGACATTGAGACGAGAGCCAATGTAAGACATGTCTAGGACATGGCATCGGCCATGAG
52869724 ACGTAAGCCAA
131 ACGTAAGCCAA
* * * * *
52869735 TGTAAGACATGTCTAGGACATGCATCAGCTAC-TAGAGGATAGTCAGTGTAAGACCATGTTTGGG
1 TGTAAGACATGTCTAGGACATGCATCAGCCACAT-GAGGAGAGCCAGTGTAAGACCATGTCTGGA
* * *
52869799 ACATGGCATCTAC-TTGAGA-TATGAGCCAATGTAAGACCGTGTCTAGGACATGGCATCG
65 ACATGGCATCGACATTGAGACGA-GAGCCAATGTAAGA-CATGTCTAGGACATGGCATCG
52869857 ACACCTTACC
Statistics
Matches: 102, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
138 1 0.01
139 18 0.18
140 77 0.75
141 6 0.06
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (141 bp):
TGTAAGACATGTCTAGGACATGCATCAGCCACATGAGGAGAGCCAGTGTAAGACCATGTCTGGAA
CATGGCATCGACATTGAGACGAGAGCCAATGTAAGACATGTCTAGGACATGGCATCGGCCATGAG
ACGTAAGCCAA
Found at i:52877148 original size:11 final size:10
Alignment explanation
Indices: 52877116--52877152 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
52877106 CATGAGATTT
52877116 TGATAT-ACA
1 TGATATGACA
52877125 TGATATGACA
1 TGATATGACA
52877135 TGATATGCACA
1 TGATATG-ACA
52877146 TGATATG
1 TGATATG
52877153 TTATGAGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.23
10 10 0.38
11 10 0.38
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (10 bp):
TGATATGACA
Found at i:52877148 original size:21 final size:21
Alignment explanation
Indices: 52877122--52877172 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
52877112 ATTTTGATAT
*
52877122 ACATGATATGACATGATATGC
1 ACATGATATGACATGAGATGC
**
52877143 ACATGATATGTTATGAGATGC
1 ACATGATATGACATGAGATGC
*
52877164 ACAAGATAT
1 ACATGATAT
52877173 ATTCATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (21 bp):
ACATGATATGACATGAGATGC
Found at i:52877254 original size:25 final size:24
Alignment explanation
Indices: 52877220--52877290 Score: 106
Period size: 25 Copynumber: 2.9 Consensus size: 24
52877210 GGGAAGTGCA
* *
52877220 AAAAGGGCTTTGCCCTAGTTTATC
1 AAAAGGGCTTTGCCCCAGTTAATC
52877244 GAAAAGGGCTTTGCCCCAGTTAATC
1 -AAAAGGGCTTTGCCCCAGTTAATC
52877269 AGAAAGGGCTTTGCCCCAGTTA
1 A-AAAGGGCTTTGCCCCAGTTA
52877291 CTAAAAGAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 1 0.02
25 42 0.98
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTAATC
Found at i:52882264 original size:46 final size:45
Alignment explanation
Indices: 52882208--52882383 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 45
52882198 TGGTTGAGCA
*
52882208 TCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * * * *
52882254 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
* *
52882299 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGTGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
52882347 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52882384 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 60 0.58
47 28 0.27
48 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:52882364 original size:93 final size:93
Alignment explanation
Indices: 52882205--52882376 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
52882195 GGATGGTTGA
* * **
52882205 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
52882270 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* * *
52882298 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGTGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
52882363 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
52882377 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:52887236 original size:49 final size:49
Alignment explanation
Indices: 52887176--52887335 Score: 252
Period size: 49 Copynumber: 3.3 Consensus size: 49
52887166 GTATGAGATA
52887176 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
52887225 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* * * * *
52887274 TATATATGTGATAAGGCCTAGTGGCCAACGTGATGGATGTGGAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
52887321 TATAAATGTGATAAG
1 TATATATGTGATAAG
52887336 TCCCGAAGGG
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
47 17 0.16
49 88 0.84
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.30
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
Found at i:52889268 original size:15 final size:15
Alignment explanation
Indices: 52889229--52889308 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
52889219 GTATCTTGGG
*
52889229 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
52889244 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
52889259 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
52889274 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
52889289 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
52889303 TTTCTT
1 TTTCTT
52889309 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:52889298 original size:30 final size:30
Alignment explanation
Indices: 52889220--52889307 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
52889210 CATAGTATCG
* * *
52889220 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
52889250 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
52889280 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
52889308 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:52891755 original size:46 final size:46
Alignment explanation
Indices: 52891695--52891870 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
52891685 TGGTTGAGCA
* *
52891695 TCCGAACTCATTGAGTTGAGTCCGAATTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
52891741 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
52891786 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACCTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
52891834 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52891871 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 59 0.57
47 28 0.27
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:52891851 original size:93 final size:93
Alignment explanation
Indices: 52891692--52891863 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
52891682 GGATGGTTGA
* *
52891692 GCATCCGAACTCATTGAGTTGAGTCCGAATTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAATTCACCTATGGATGCGAATGCCCGAACTCGTTGAGT
52891757 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* * * *
52891785 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACCTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAATTCACCTATGGATGCGAATGCCCGAACTCGTTGAGT
52891850 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
52891864 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAATTCACCTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:52897348 original size:10 final size:10
Alignment explanation
Indices: 52897333--52897373 Score: 73
Period size: 10 Copynumber: 4.0 Consensus size: 10
52897323 ATTTTGACAT
52897333 ACATGATATG
1 ACATGATATG
52897343 ACATGATATG
1 ACATGATATG
52897353 ACATGATATG
1 ACATGATATG
52897363 CACATGATATG
1 -ACATGATATG
52897374 TTATGAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 20 0.67
11 10 0.33
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (10 bp):
ACATGATATG
Found at i:52897369 original size:21 final size:21
Alignment explanation
Indices: 52897333--52897393 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
52897323 ATTTTGACAT
52897333 ACATGATATG-ACATGATATG
1 ACATGATATGCACATGATATG
52897353 ACATGATATGCACATGATATG
1 ACATGATATGCACATGATATG
** * *
52897374 TTATGAGATGCACAAGATAT
1 ACATGATATGCACATGATAT
52897394 ATTCATTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 10 0.28
21 26 0.72
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (21 bp):
ACATGATATGCACATGATATG
Found at i:52897499 original size:25 final size:25
Alignment explanation
Indices: 52897440--52897510 Score: 108
Period size: 24 Copynumber: 2.9 Consensus size: 25
52897430 GGGGAAGTGT
* *
52897440 AAAAAGGGCTTTTCCCCAGTTTATC
1 AAAAAGGGCTTTGCCCCAGTTAATC
*
52897465 -GAAAGGGCTTTGCCCCAGTTAATC
1 AAAAAGGGCTTTGCCCCAGTTAATC
52897489 AAAAAGGGCTTTGCCCCAGTTA
1 AAAAAGGGCTTTGCCCCAGTTA
52897511 CTAAAAGAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 21 0.51
25 20 0.49
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (25 bp):
AAAAAGGGCTTTGCCCCAGTTAATC
Found at i:52904594 original size:43 final size:43
Alignment explanation
Indices: 52904533--52904707 Score: 194
Period size: 43 Copynumber: 4.1 Consensus size: 43
52904523 AAAGCTCGTA
* *
52904533 CAATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATAT
1 CAATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATAT
* *
52904576 CAATGCCACTGTCCCAGACAG-GGTCATACACGAAATCAAATA-
1 CAATGCCAATGTCCCAGAC-GTGGTCTTACACGAAATCAAATAT
* * * **
52904618 CGATGCCGATGTCCCAGACATGGTCTTACACGTAAATC-TCTAAT
1 CAATGCCAATGTCCCAGACGTGGTCTTACACG-AAATCAAAT-AT
* * *
52904662 CGATGCCAATGTCCCAGACGTGGTCTTACATGAAATCACATAT
1 CAATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATAT
52904705 CAA
1 CAA
52904708 AATCCTATGT
Statistics
Matches: 109, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
42 27 0.25
43 51 0.47
44 31 0.28
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
CAATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATAT
Found at i:52907187 original size:46 final size:46
Alignment explanation
Indices: 52907120--52907341 Score: 299
Period size: 46 Copynumber: 4.8 Consensus size: 46
52907110 TGTAACCCGC
* *
52907120 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
52907166 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT
* * * *
52907216 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCTGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
52907259 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
52907305 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52907342 TGCCCAAATA
Statistics
Matches: 154, Mismatches: 13, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 2 0.01
45 2 0.01
46 107 0.69
47 28 0.18
48 2 0.01
49 2 0.01
50 3 0.02
51 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:52914044 original size:55 final size:55
Alignment explanation
Indices: 52913952--52914060 Score: 130
Period size: 55 Copynumber: 2.0 Consensus size: 55
52913942 AATTTTAGGT
* *
52913952 CAGTATTGTACACAAGCAGGCCACAAGGGCGTGTGCCATGAG-CATGTTTAAAAGC
1 CAGTATTGTACACAAGCAGGCCACAAGGGCATATGCCATG-GCCATGTTTAAAAGC
** * * * *
52914007 CAGTATTGTACACGGGTAGGCCATACGGGCATATGCCATGGCCATGTTTTAAAG
1 CAGTATTGTACACAAGCAGGCCACAAGGGCATATGCCATGGCCATGTTTAAAAG
52914061 TTAGTGTTGC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
54 1 0.02
55 44 0.98
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (55 bp):
CAGTATTGTACACAAGCAGGCCACAAGGGCATATGCCATGGCCATGTTTAAAAGC
Done.