Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000886.1 Hibiscus syriacus cultivar Beakdansim tig00001731_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 974096
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 4
Found at i:331471 original size:9 final size:8
Alignment explanation
Indices: 331393--331472 Score: 54
Period size: 9 Copynumber: 9.1 Consensus size: 8
331383 AAAATGATAT
*
331393 GAAAAAAT
1 GAAAAAAA
331401 GAAAAAAAA
1 G-AAAAAAA
331410 TGAAAAAAA
1 -GAAAAAAA
331419 -AAATGAAAA
1 GAAA--AAAA
331428 TGAAAAAAGA
1 -GAAAAAA-A
*
331438 GAAAATAA
1 GAAAAAAA
331446 GAAAAATAA
1 GAAAAA-AA
*
331455 GAAGAAAA
1 GAAAAAAA
331463 GAATAAAAA
1 GAA-AAAAA
331472 G
1 G
331473 GGGGTTCAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
7 3 0.05
8 12 0.21
9 38 0.66
10 2 0.03
11 3 0.05
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (8 bp):
GAAAAAAA
Found at i:336924 original size:36 final size:36
Alignment explanation
Indices: 336795--336932 Score: 172
Period size: 35 Copynumber: 3.8 Consensus size: 36
336785 AAACAAGTCA
** *
336795 ATCTTAAGCCTTCAC-GAAGGAGTAGTGAAGTGAGTTA
1 ATCTTAAGCCTTCACGGAA-GAGTAGTGAAG-GAAATC
* * * *
336832 ATCTTAAGCCTTCATGGAATAGTAGAGAAGCAAATC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGGAAATC
*
336868 ATCTT-AGCATTCACGGAAGAGTAGTGAAGGAAATC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGGAAATC
336903 ATCTTAAGCCTTCACGGAAGAGTAGTGAAG
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAG
336933 CGAATCAGTC
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
35 30 0.35
36 30 0.35
37 23 0.27
38 3 0.03
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.25
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGGAAATC
Found at i:336927 original size:71 final size:73
Alignment explanation
Indices: 336795--336939 Score: 188
Period size: 71 Copynumber: 2.0 Consensus size: 73
336785 AAACAAGTCA
* ** * *
336795 ATCTTAAGCCTTCACGAAGGAGTAGTGAAGTGAGTTAATCTTAAGCCTTCATGGAATAGTAGAGA
1 ATCTTAAGCATTCACGAAGGAGTAGTGAAGTGAAATAATCTTAAGCCTTCACGGAAGAGTAGAGA
336860 AGCAAATC
66 AGCAAATC
* *
336868 ATCTT-AGCATTCACGGAA-GAGTAGTGAAG-GAAATCATCTTAAGCCTTCACGGAAGAGTAGTG
1 ATCTTAAGCATTCAC-GAAGGAGTAGTGAAGTGAAATAATCTTAAGCCTTCACGGAAGAGTAGAG
*
336930 AAGCGAATC
65 AAGCAAATC
336939 A
1 A
336940 GTCTCGAGTC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 36 0.57
72 19 0.30
73 8 0.13
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (73 bp):
ATCTTAAGCATTCACGAAGGAGTAGTGAAGTGAAATAATCTTAAGCCTTCACGGAAGAGTAGAGA
AGCAAATC
Found at i:336939 original size:36 final size:36
Alignment explanation
Indices: 336795--336939 Score: 170
Period size: 36 Copynumber: 4.0 Consensus size: 36
336785 AAACAAGTCA
* * *
336795 ATCTTAAGCCTTCAC-GAAGGAGTAGTGAAGTGAGTTA
1 ATCTTAAGCCTTCACGGAA-GAGTAGTGAAGCGA-ATC
* * * *
336832 ATCTTAAGCCTTCATGGAATAGTAGAGAAGCAAATC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCGAATC
*
336868 ATCTT-AGCATTCACGGAAGAGTAGTGAAG-GAAATC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCG-AATC
336903 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCGAATC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCGAATC
336939 A
1 A
336940 GTCTCGAGTC
Statistics
Matches: 91, Mismatches: 13, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
35 29 0.32
36 34 0.37
37 25 0.27
38 3 0.03
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCGAATC
Found at i:337047 original size:55 final size:55
Alignment explanation
Indices: 336982--337186 Score: 236
Period size: 55 Copynumber: 3.7 Consensus size: 55
336972 AGTAGACCCA
* *
336982 TTTTCAGAAGATTATTCGAGTTCTATACACCTTGAAAGAATAGGGAGCGAACTC-G
1 TTTTC-GAAGATTGTTCGAGTTCTATACTCCTTGAAAGAATAGGGAGCGAACTCAG
* * * *
337037 TTTTCAGAAGATTGTTCGAGTTCTATACTCCTTGAAAGAATACGGAGCGGACCCGG
1 TTTTC-GAAGATTGTTCGAGTTCTATACTCCTTGAAAGAATAGGGAGCGAACTCAG
* * * * *
337093 TTGTCGAAGATTGTTCGAG-TCTTATACTCCCTAAAAGAATTGGGAGC-ATACTCAT
1 TTTTCGAAGATTGTTCGAGTTC-TATACTCCTTGAAAGAATAGGGAGCGA-ACTCAG
* *
337148 TTTTCGAAGATTGTTCGAGTACTATACTCTTTGAAAGAA
1 TTTTCGAAGATTGTTCGAGTTCTATACTCCTTGAAAGAA
337187 AAGGACTGGA
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
54 2 0.02
55 119 0.94
56 6 0.05
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (55 bp):
TTTTCGAAGATTGTTCGAGTTCTATACTCCTTGAAAGAATAGGGAGCGAACTCAG
Found at i:337173 original size:110 final size:110
Alignment explanation
Indices: 336988--337186 Score: 278
Period size: 110 Copynumber: 1.8 Consensus size: 110
336978 CCCATTTTCA
* *
336988 GAAGATTATTCGAGTTCTATACACCTTGAAAGAATAGGGAGCGAACTCGTTTTCAGAAGATTGTT
1 GAAGATTATTCGAGTTCTATACACCCTAAAAGAATAGGGAGCGAACTCGTTTTCAGAAGATTGTT
*
337053 CGAGTTCTATACTCCTTGAAAGAATACGGAGCGGACCCGGTTGTC
66 CGAGTACTATACTCCTTGAAAGAATACGGAGCGGACCCGGTTGTC
* * * *
337098 GAAGATTGTTCGAG-TCTTATACTCCCTAAAAGAATTGGGAGC-ATACTCATTTTTC-GAAGATT
1 GAAGATTATTCGAGTTC-TATACACCCTAAAAGAATAGGGAGCGA-ACTC-GTTTTCAGAAGATT
*
337160 GTTCGAGTACTATACTCTTTGAAAGAA
63 GTTCGAGTACTATACTCCTTGAAAGAA
337187 AAGGACTGGA
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
109 3 0.04
110 70 0.90
111 5 0.06
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (110 bp):
GAAGATTATTCGAGTTCTATACACCCTAAAAGAATAGGGAGCGAACTCGTTTTCAGAAGATTGTT
CGAGTACTATACTCCTTGAAAGAATACGGAGCGGACCCGGTTGTC
Found at i:345311 original size:59 final size:59
Alignment explanation
Indices: 345155--345618 Score: 253
Period size: 59 Copynumber: 7.9 Consensus size: 59
345145 TGGCTCTATG
* * * * * * * *
345155 TGTGCTAAAATGATAAGGAAATTATACTGAGTGTATAGATTTCCATATGGAGCATTGAG
1 TGTGCTAAAAAGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGAGCATTTAA
* * * * * *** *
345214 TGTTCT--AATGATATGGAAATCATATTGAAAATATGGATTTCCAGATAGAGCATTTTA
1 TGTGCTAAAAAGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGAGCATTTAA
* * * *
345271 TATGCTAAAAAGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCA-CTAA
1 TGTGCTAAAAAGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGAGCATTTAA
* * * * * * * * * * *
345329 GGGCGCTACAATGATAAGGAAATCATACT-AATAGTATGGATTTTCACATAGGGAATTTTA
1 -TGTGCTAAAAAGGTAAGGAAATCATACTGAGT-GTATGGATTTCCAGATAGAGCATTTAA
* * * * *
345389 TGTTCTAAAAAGGTAAGGGAATCATACTGAGTGTATGGATTTCCCGATAAAGCA-CTAA
1 TGTGCTAAAAAGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGAGCATTTAA
* * * * * ** * * *
345447 GGGTGCTACAAAGTTAAGGAAATCATACTAAGGGTATGGATTTTAACATAGGGCATTTCA
1 -TGTGCTAAAAAGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGAGCATTTAA
* ** * * ** * * *
345507 TGTGCTAAAATGGTAACAAAATCATACT-AATGTATGAATTT-TTGAATAGGGCACTTAG
1 TGTGCTAAAAAGGTAAGGAAATCATACTGAGTGTATGGATTTCCAG-ATAGAGCATTTAA
* * * * *
345565 TGTGCT-AAAATGAAAGGGAAAGCATACTAAGCGTAT-GATTTTCCAGATAGAGCA
1 TGTGCTAAAAAGGTAA-GGAAATCATACTGAGTGTATGGA-TTTCCAGATAGAGCA
345619 CTGAGAATGC
Statistics
Matches: 293, Mismatches: 99, Indels: 26
0.70 0.24 0.06
Matches are distributed among these distances:
57 49 0.17
58 42 0.14
59 195 0.67
60 7 0.02
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (59 bp):
TGTGCTAAAAAGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGAGCATTTAA
Found at i:345397 original size:118 final size:117
Alignment explanation
Indices: 345220--345522 Score: 426
Period size: 118 Copynumber: 2.6 Consensus size: 117
345210 TGAGTGTTCT
* * * * * * *
345220 AATGATATGGAAATCATATTGAAAATATGGATTTCCAGATAGAGCATTTTATATGCTAAAAAGGT
1 AATGATAAGGAAATCATACT-AAAGTATGGATTTTCACATAGGGCATTTTATGTGCTAAAAAGGT
345285 AAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGGCGCTAC
65 AAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGGCGCTAC
* *
345338 AATGATAAGGAAATCATACTAATAGTATGGATTTTCACATAGGGAATTTTATGTTCTAAAAAGGT
1 AATGATAAGGAAATCATACTAA-AGTATGGATTTTCACATAGGGCATTTTATGTGCTAAAAAGGT
* *
345403 AAGGGAATCATACTGAGTGTATGGATTTCCCGATAAAGCACTAAGGGTGCTAC
65 AAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGGCGCTAC
* * * * * *
345456 AAAGTTAAGGAAATCATACTAAGGGTATGGATTTTAACATAGGGCATTTCATGTGCTAAAATGGT
1 AATGATAAGGAAATCATACTAA-AGTATGGATTTTCACATAGGGCATTTTATGTGCTAAAAAGGT
345521 AA
65 AA
345523 CAAAATCATA
Statistics
Matches: 164, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
117 2 0.01
118 162 0.99
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (117 bp):
AATGATAAGGAAATCATACTAAAGTATGGATTTTCACATAGGGCATTTTATGTGCTAAAAAGGTA
AGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGGCGCTAC
Found at i:345606 original size:58 final size:59
Alignment explanation
Indices: 345462--345606 Score: 147
Period size: 58 Copynumber: 2.5 Consensus size: 59
345452 CTACAAAGTT
* * *
345462 AAGGAAATCATACTAAGGGTATGGA-TTTTAACATAGGGCATTTCATGTGCTAAAATGGT
1 AAGGAAATCATACTAAGCGTAT-GATTTTTAACATAGGGCACTTCATGTGCTAAAATGGA
** * *
345521 AACAAAATCATACTAA-TGTATGAATTTTTGA-ATAGGGCACTT-AGTGTGCTAAAAT-GA
1 AAGGAAATCATACTAAGCGTATG-ATTTTTAACATAGGGCACTTCA-TGTGCTAAAATGGA
*
345578 AAGGGAAAGCATACTAAGCGTATGATTTT
1 AA-GGAAATCATACTAAGCGTATGATTTT
345607 CCAGATAGAG
Statistics
Matches: 71, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
57 5 0.07
58 42 0.59
59 24 0.34
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.30
Consensus pattern (59 bp):
AAGGAAATCATACTAAGCGTATGATTTTTAACATAGGGCACTTCATGTGCTAAAATGGA
Found at i:345760 original size:44 final size:44
Alignment explanation
Indices: 345710--345867 Score: 280
Period size: 44 Copynumber: 3.6 Consensus size: 44
345700 TAAATAAGGT
* *
345710 TAATGGTAAGTATATTGGTAGAATAAGCTTACGAGCTTATGGAA
1 TAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTATGGAA
345754 TAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTATGGAA
1 TAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTATGGAA
*
345798 TAATGGTGAGTATATTGGTAAAATAAGCTTATGAGCTTATGGAA
1 TAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTATGGAA
*
345842 TAATGGTAAGTATGTTGGTAAAATAA
1 TAATGGTAAGTATATTGGTAAAATAA
345868 TGGTAAGTAT
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 109 1.00
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (44 bp):
TAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTATGGAA
Found at i:345866 original size:23 final size:23
Alignment explanation
Indices: 345840--345890 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
345830 GAGCTTATGG
*
345840 AATAATGGTAAGTATGTTGGTAA
1 AATAATGGTAAGTATATTGGTAA
345863 AATAATGGTAAGTATATTGGTAA
1 AATAATGGTAAGTATATTGGTAA
345886 AATAA
1 AATAA
345891 GCTTACGAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.22, T:0.33
Consensus pattern (23 bp):
AATAATGGTAAGTATATTGGTAA
Found at i:345877 original size:67 final size:68
Alignment explanation
Indices: 345796--345935 Score: 255
Period size: 67 Copynumber: 2.1 Consensus size: 68
345786 GAGCTTATGG
* *
345796 AATAATGGTGAGTATATTGGTAAAATAAGCTTATGAGCTTATGGAAT-AATGGTAAGTATGTTGG
1 AATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGG
345860 TAA
66 TAA
345863 AATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGG
1 AATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGG
345928 TAA
66 TAA
345931 AATAA
1 AATAA
345936 GCTTACGAGC
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 45 0.64
68 25 0.36
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.33
Consensus pattern (68 bp):
AATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGG
TAA
Found at i:345915 original size:45 final size:45
Alignment explanation
Indices: 345866--345963 Score: 160
Period size: 45 Copynumber: 2.2 Consensus size: 45
345856 TTGGTAAAAT
345866 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATA
* * *
345911 AATGGTAAGTATGTTGGTAAAATAAGCTTACGAGCTTGTGGGATA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATA
*
345956 AGTGGTAA
1 AATGGTAA
345964 ATTTATTGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.31
Consensus pattern (45 bp):
AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATA
Found at i:350005 original size:19 final size:18
Alignment explanation
Indices: 349978--350014 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
349968 TTCTTTTGAA
349978 CCTCATCTTCCCTATATTC
1 CCTCATCTTCCCTA-ATTC
*
349997 CCTCTTCTTCCCTAATTC
1 CCTCATCTTCCCTAATTC
350015 TTACTCGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (18 bp):
CCTCATCTTCCCTAATTC
Found at i:353810 original size:25 final size:25
Alignment explanation
Indices: 353782--353835 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
353772 TGGCACCTAT
*
353782 AGTGCAATTCTACAAGGCATTTTTG
1 AGTGCAATTCTACAAGGCATTTTCG
*
353807 AGTGCAATTCTACGAGGCATTTTCG
1 AGTGCAATTCTACAAGGCATTTTCG
353832 AGTG
1 AGTG
353836 TAAATATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (25 bp):
AGTGCAATTCTACAAGGCATTTTCG
Found at i:355042 original size:24 final size:24
Alignment explanation
Indices: 355015--355107 Score: 107
Period size: 24 Copynumber: 3.9 Consensus size: 24
355005 TTGATCCTAT
**
355015 TTAGTACATTTGTGTACTCCAATA
1 TTAGTACATTTGTGTACTCCTGTA
* * *
355039 TTAGTGCCTTTGTGCAC-CCTGTA
1 TTAGTACATTTGTGTACTCCTGTA
* * *
355062 TTAGTACCTTTGGGTACTCTTGTA
1 TTAGTACATTTGTGTACTCCTGTA
355086 TTAGTACATTTGTGTACTCCTG
1 TTAGTACATTTGTGTACTCCTG
355108 GCACTATATG
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 18 0.32
24 38 0.68
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.43
Consensus pattern (24 bp):
TTAGTACATTTGTGTACTCCTGTA
Found at i:356647 original size:14 final size:14
Alignment explanation
Indices: 356628--356655 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
356618 TCCCAAAATT
356628 CAGATTAACTAAGA
1 CAGATTAACTAAGA
356642 CAGATTAACTAAGA
1 CAGATTAACTAAGA
356656 GACGAGGCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
CAGATTAACTAAGA
Found at i:368244 original size:13 final size:13
Alignment explanation
Indices: 368229--368269 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
368219 ATTTTTTTGT
368229 TTTTTCTTCTTT-
1 TTTTTCTTCTTTC
368241 TTTTT-TT-TTTGC
1 TTTTTCTTCTTT-C
368253 TTTTTCTTCTTTC
1 TTTTTCTTCTTTC
368266 TTTT
1 TTTT
368270 GTTTTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 3 0.12
11 2 0.08
12 10 0.40
13 7 0.28
14 3 0.12
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (13 bp):
TTTTTCTTCTTTC
Found at i:368262 original size:27 final size:25
Alignment explanation
Indices: 368215--368277 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 25
368205 TTTTTCAGAC
*
368215 TTTTATTTTTTTGTTTTTTC-TTCT
1 TTTTTTTTTTTTGTTTTTTCTTTCT
*
368239 TTTTTTTTTTTTGCTTTTTC-TTCT
1 TTTTTTTTTTTTGTTTTTTCTTTCT
368263 TTCTTTTGTTTTTTG
1 TT-TTTT-TTTTTTG
368278 AAAATATAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 24 0.69
25 4 0.11
26 7 0.20
ACGTcount: A:0.02, C:0.10, G:0.06, T:0.83
Consensus pattern (25 bp):
TTTTTTTTTTTTGTTTTTTCTTTCT
Found at i:368269 original size:24 final size:24
Alignment explanation
Indices: 368220--368275 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
368210 CAGACTTTTA
* *
368220 TTTTTTTGTTTTTTCTTCTTTTTT
1 TTTTTTTGCTTTTTCTTCTTTCTT
368244 TTTTTTTGCTTTTTCTTCTTTCTT
1 TTTTTTTGCTTTTTCTTCTTTCTT
368268 TTGTTTTT
1 TT-TTTTT
368276 TGAAAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (24 bp):
TTTTTTTGCTTTTTCTTCTTTCTT
Found at i:368886 original size:50 final size:50
Alignment explanation
Indices: 368763--368889 Score: 218
Period size: 50 Copynumber: 2.5 Consensus size: 50
368753 TCCTATCGAG
* * *
368763 CCCTCCTCGTCGCAATGAAAAGGAAAACACGATAATATGACTCTAACCAA
1 CCCTCCTAGTCGCAATGAAAAGGCAAACACGATAATATGACTCCAACCAA
*
368813 CCCTCCTAGTCGCAATGAAAAGGCAAACACGGTAATATGACTCCAACCAA
1 CCCTCCTAGTCGCAATGAAAAGGCAAACACGATAATATGACTCCAACCAA
368863 CCCTCCTAGTCGCAATGAAAAGGCAAA
1 CCCTCCTAGTCGCAATGAAAAGGCAAA
368890 TTGGAGTGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 73 1.00
ACGTcount: A:0.39, C:0.29, G:0.16, T:0.17
Consensus pattern (50 bp):
CCCTCCTAGTCGCAATGAAAAGGCAAACACGATAATATGACTCCAACCAA
Found at i:373022 original size:19 final size:21
Alignment explanation
Indices: 372999--373048 Score: 77
Period size: 19 Copynumber: 2.4 Consensus size: 21
372989 ATTTTTCAGA
372999 CTTTTTTTTGG-CTTTTTCTT
1 CTTTTTTTTGGCCTTTTTCTT
373019 -TTTTTTTTGGCCTTTTTCTT
1 CTTTTTTTTGGCCTTTTTCTT
373039 CTTCTTTTTT
1 CTT-TTTTTT
373049 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.37
20 9 0.33
21 2 0.07
22 6 0.22
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (21 bp):
CTTTTTTTTGGCCTTTTTCTT
Found at i:375270 original size:54 final size:54
Alignment explanation
Indices: 375212--375495 Score: 403
Period size: 54 Copynumber: 5.3 Consensus size: 54
375202 ACGTACTACA
* *
375212 AATACGGTGATTCACAAACTCATTATGAATTACTTAGGTTGCATACATAGTGCC
1 AATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCC
* * * *
375266 AATACGGTAATTCATAAACTCATTATGAAGTACTTAGGTTGAACACATAGTGCT
1 AATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCC
* * * *
375320 AATACGGTAATTCACAAACTCATTATGAAGTACATAGGTTG-A-ACACAGTGCT
1 AATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCC
**
375372 AATACGGTAATTCACAAACTTGTTATGAATTACTTAGGTTGCACACATAGTG-C
1 AATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCC
* * *
375425 AAAACGGTAATTCAGAAACTCATTATGAATTGCTTAGGTTGCACACATAGTGCC
1 AATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCC
*
375479 AATATGGTAATTCACAA
1 AATACGGTAATTCACAA
375496 CATATATATT
Statistics
Matches: 204, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
52 46 0.23
53 49 0.24
54 109 0.53
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (54 bp):
AATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCC
Found at i:375851 original size:22 final size:22
Alignment explanation
Indices: 375800--375844 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
375790 AGACTGAATA
375800 GTATCGATAC--CTCTCCTATG
1 GTATCGATACTTCTCTCCTATG
*
375820 GTATCGATACTTCTCTTCTATG
1 GTATCGATACTTCTCTCCTATG
375842 GTA
1 GTA
375845 CTGATACCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (22 bp):
GTATCGATACTTCTCTCCTATG
Found at i:383581 original size:29 final size:29
Alignment explanation
Indices: 383533--383624 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
383523 GGCATTTCTA
* *
383533 ATTCTGTATGGGA-TTCGATCCCTGCCCTG
1 ATTCTGCATGGGACTT-GATCCATGCCCTG
** *
383562 ATTCTGCATGGGACTTGATCCATATCATG
1 ATTCTGCATGGGACTTGATCCATGCCCTG
* *
383591 TTTAC-GCATGGGACTTGATCCTTGCCCTG
1 ATT-CTGCATGGGACTTGATCCATGCCCTG
*
383620 TTTCT
1 ATTCT
383625 TTATGAGATT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
28 1 0.02
29 46 0.92
30 3 0.06
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (29 bp):
ATTCTGCATGGGACTTGATCCATGCCCTG
Found at i:390079 original size:15 final size:15
Alignment explanation
Indices: 390059--390092 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
390049 TGTTTCTATG
390059 GCTCCATATCAAATA
1 GCTCCATATCAAATA
*
390074 GCTCCATATCAAATG
1 GCTCCATATCAAATA
390089 GCTC
1 GCTC
390093 TAACGATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.26
Consensus pattern (15 bp):
GCTCCATATCAAATA
Found at i:400119 original size:31 final size:29
Alignment explanation
Indices: 400057--400161 Score: 108
Period size: 28 Copynumber: 3.6 Consensus size: 29
400047 AATAGTGTGT
*
400057 AAAACTTTTAATAAATTA-ACATGAAGTAAAA
1 AAAACTTTTTATAAATTACA-AT-AAG-AAAA
*
400088 AAAACTTTTTATAAATTACAATAA-AGAA
1 AAAACTTTTTATAAATTACAATAAGAAAA
* * *
400116 AAAACATTTTATAATTTACAATAA-AATA
1 AAAACTTTTTATAAATTACAATAAGAAAA
*
400144 AAAACTTATTATAAATTA
1 AAAACTTTTTATAAATTA
400162 AGATAAAATA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 42 0.66
30 2 0.03
31 19 0.30
32 1 0.02
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAACTTTTTATAAATTACAATAAGAAAA
Found at i:400170 original size:28 final size:27
Alignment explanation
Indices: 400087--400258 Score: 123
Period size: 28 Copynumber: 6.0 Consensus size: 27
400077 ATGAAGTAAA
400087 AAAAACTTTTTATAAATTACAATAAAGA-
1 AAAAAC-TTTTATAAATTACAATAAA-AT
*
400115 AAAAACATTTTATAATTTACAATAAAAT
1 AAAAAC-TTTTATAAATTACAATAAAAT
400143 AAAAACTTATTATAAATTA-AGATAAAAT
1 AAAAACTT-TTATAAATTACA-ATAAAAT
*** * *
400171 ACAATTTTTTTTATCAATTACATTAAAAT
1 A-AA-AACTTTTATAAATTACAATAAAAT
* **
400200 GGAAAACTTTTTATAAATTATGATAAAGGAT
1 -AAAAAC-TTTTATAAATTACAATAAA--AT
* *
400231 ACAAAATTTTTATAAAATACAATAAAAT
1 A-AAAACTTTTATAAATTACAATAAAAT
400259 GGATAAAATA
Statistics
Matches: 112, Mismatches: 21, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
27 4 0.04
28 49 0.44
29 34 0.30
30 19 0.17
31 6 0.05
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.36
Consensus pattern (27 bp):
AAAAACTTTTATAAATTACAATAAAAT
Found at i:400219 original size:58 final size:57
Alignment explanation
Indices: 400088--400261 Score: 169
Period size: 58 Copynumber: 3.0 Consensus size: 57
400078 TGAAGTAAAA
* * *
400088 AAAACTTTTTATAAATTACA-ATAAAGA-A-AAAACATTTTATAATTTACAATAAAAT-A
1 AAAACTTATTATAAATTA-AGATAAAGATACAAAA-TTTTTATAA-TTACAATAAAATGG
** *
400144 AAAACTTATTATAAATTAAGATAAA-ATACAATTTTTTTTATCAATTACATTAAAATGG
1 AAAACTTATTATAAATTAAGATAAAGATACAA-AATTTTTAT-AATTACAATAAAATGG
* * *
400202 AAAACTTTTTATAAATTATGATAAAGGATACAAAATTTTTATAAAATACAATAAAATGG
1 AAAACTTATTATAAATTAAGATAAA-GATACAAAATTTTTAT-AATTACAATAAAATGG
400261 A
1 A
400262 TAAAATACGA
Statistics
Matches: 97, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
55 2 0.02
56 23 0.24
57 19 0.20
58 25 0.26
59 22 0.23
60 6 0.06
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.36
Consensus pattern (57 bp):
AAAACTTATTATAAATTAAGATAAAGATACAAAATTTTTATAATTACAATAAAATGG
Found at i:409110 original size:17 final size:18
Alignment explanation
Indices: 409078--409111 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
409068 AATGTTACTT
409078 ATAAAGATAAAATATTTG
1 ATAAAGATAAAATATTTG
*
409096 ATAAA-ATAAATTATTT
1 ATAAAGATAAAATATTT
409112 ATTTCATCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
ATAAAGATAAAATATTTG
Found at i:409984 original size:39 final size:39
Alignment explanation
Indices: 409930--410005 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
409920 TGATGTGTAC
* *
409930 ACAAAGACAAGCAGTAGCACATATTGAATAGATAATCAG
1 ACAAAGACAAGCAGTAACACAGATTGAATAGATAATCAG
*
409969 ACAAAGACAAGCAGTAACATAGATTGAATAGATAATC
1 ACAAAGACAAGCAGTAACACAGATTGAATAGATAATC
410006 TTATTAGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.18
Consensus pattern (39 bp):
ACAAAGACAAGCAGTAACACAGATTGAATAGATAATCAG
Found at i:411052 original size:3 final size:3
Alignment explanation
Indices: 411046--411097 Score: 88
Period size: 3 Copynumber: 17.3 Consensus size: 3
411036 ATGTTTTTTT
411046 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
411092 -AA TAA T
1 TAA TAA T
411098 GACTATTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:413251 original size:40 final size:40
Alignment explanation
Indices: 413205--413310 Score: 176
Period size: 40 Copynumber: 2.6 Consensus size: 40
413195 ACTAAGTGTA
413205 ATATGGTGGGCACGACCTTATGTGTAATGTACGTCGGTGC
1 ATATGGTGGGCACGACCTTATGTGTAATGTACGTCGGTGC
* * *
413245 ATATGGTGGGCATGAGCTTATGTGTAATGTACTTCGGTGC
1 ATATGGTGGGCACGACCTTATGTGTAATGTACGTCGGTGC
*
413285 ATATGGTGGGTACGACCTTATGTGTA
1 ATATGGTGGGCACGACCTTATGTGTA
413311 GCACTACGGT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.21, C:0.14, G:0.32, T:0.33
Consensus pattern (40 bp):
ATATGGTGGGCACGACCTTATGTGTAATGTACGTCGGTGC
Found at i:420305 original size:40 final size:40
Alignment explanation
Indices: 420258--420376 Score: 161
Period size: 40 Copynumber: 3.0 Consensus size: 40
420248 ACTAAGTGTA
*
420258 ATATGGTGGGCTCGACCTTATGTGTAATGTACTTCGGTGC
1 ATATGGTGGGCACGACCTTATGTGTAATGTACTTCGGTGC
* *
420298 ATATGGTGGGCACGACCTTATGTGGAATGTACTTCGGTGA
1 ATATGGTGGGCACGACCTTATGTGTAATGTACTTCGGTGC
* * * *
420338 ATATGCTGGGAACAACCTTATGTGT-A-GTACTACGGTGC
1 ATATGGTGGGCACGACCTTATGTGTAATGTACTTCGGTGC
420376 A
1 A
420377 GGTATTACTT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
38 11 0.16
39 1 0.01
40 58 0.83
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (40 bp):
ATATGGTGGGCACGACCTTATGTGTAATGTACTTCGGTGC
Found at i:426259 original size:30 final size:31
Alignment explanation
Indices: 426203--426260 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
426193 GAATTATGGG
*
426203 AGATGATAAGGTTTAGGTGTCATGGTTTGGA
1 AGATGATAAGGTTTAGGCGTCATGGTTTGGA
*
426234 AGATGATAAGG-TTAGGCGTCTTGGTTT
1 AGATGATAAGGTTTAGGCGTCATGGTTT
426261 AATGGTAATT
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:0.24, C:0.05, G:0.34, T:0.36
Consensus pattern (31 bp):
AGATGATAAGGTTTAGGCGTCATGGTTTGGA
Found at i:426984 original size:28 final size:29
Alignment explanation
Indices: 426952--427009 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
426942 GAAAAATTTA
*
426952 GGGACC-ATTTTGTAATTTTTGAAAAGTT
1 GGGACCAATTTGGTAATTTTTGAAAAGTT
426980 GGGACCAATTTGGTAATTTTTGAAAAGTT
1 GGGACCAATTTGGTAATTTTTGAAAAGTT
427009 G
1 G
427010 TGAATGGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (29 bp):
GGGACCAATTTGGTAATTTTTGAAAAGTT
Found at i:427932 original size:40 final size:40
Alignment explanation
Indices: 427886--428031 Score: 204
Period size: 40 Copynumber: 3.6 Consensus size: 40
427876 ACTAATTGTA
* *
427886 ATATGGTGGACACGACCTTATGTGTAATGTACTTCAGTTC
1 ATATGGTGGACACGACCTTATGTGTAATGTACTTCGGTGC
* * *
427926 ATATGGTGGCCATGACCTTATGTGTAATGCACTTCGGTGC
1 ATATGGTGGACACGACCTTATGTGTAATGTACTTCGGTGC
*
427966 ATATGGTGGGA-ACGACCTTATGTGTAATATACTTCGGTGC
1 ATATGGT-GGACACGACCTTATGTGTAATGTACTTCGGTGC
* *
428006 ATATGGTGGGCACAACCTTATGTGTA
1 ATATGGTGGACACGACCTTATGTGTA
428032 GCACTGTGGT
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
39 2 0.02
40 89 0.96
41 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
ATATGGTGGACACGACCTTATGTGTAATGTACTTCGGTGC
Found at i:433440 original size:177 final size:178
Alignment explanation
Indices: 433127--433450 Score: 426
Period size: 177 Copynumber: 1.8 Consensus size: 178
433117 AATTTTTTCT
* * *
433127 TGTGATAATTTTTCTATAACAATAATTATAATATATAGTTACAAAAATTGTCACTATATAACATT
1 TGTGATAATTTTTCTATAACAATAACTATAATATATAATTACAAAAATTGTCAC-ATAAAACATT
* * * * * * * *
433192 TTTGACACCAAAAAATAGGGAAAAATGTTTATGATATTATATTTTTTCGTAATTATTAAAATTTA
65 TTTGACAACAAAAAATAGAGAAAAATGTTTATGACAATATATGTTATCCTAATAATTAAAATTTA
433257 TAACTACAAAAATAATTGATTACAAAAAAACTTGAATTTTATTATTTGA
130 TAACTACAAAAATAATTGATTACAAAAAAACTTGAATTTTATTATTTGA
*
433306 TGTGATAACTTTTTCTATAACAATAACTATAA-ATTATAATTACAAAACTTGTCA-ATAAAAC-T
1 TGTGATAA-TTTTTCTATAACAATAACTATAATA-TATAATTACAAAAATTGTCACATAAAACAT
*
433368 TTTTGA-AACAAAAAAGTAGAGAAAACTAG-TTATGACAATATATGTTATCACT-ATAATTAAAA
64 TTTTGACAACAAAAAA-TAGAGAAAAAT-GTTTATGACAATATATGTTATC-CTAATAATTAAAA
*
433430 TTTATAACTACAAATATAATT
126 TTTATAACTACAAAAATAATT
433451 TGTCACAAAA
Statistics
Matches: 126, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
176 8 0.06
177 61 0.48
178 8 0.06
179 9 0.07
180 40 0.32
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (178 bp):
TGTGATAATTTTTCTATAACAATAACTATAATATATAATTACAAAAATTGTCACATAAAACATTT
TTGACAACAAAAAATAGAGAAAAATGTTTATGACAATATATGTTATCCTAATAATTAAAATTTAT
AACTACAAAAATAATTGATTACAAAAAAACTTGAATTTTATTATTTGA
Found at i:433626 original size:18 final size:18
Alignment explanation
Indices: 433603--433647 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
433593 AAAATATATA
433603 ACTACAAACATTTTTTTC
1 ACTACAAACATTTTTTTC
433621 ACTACAAACATTTTTTTC
1 ACTACAAACATTTTTTTC
*
433639 ACTAAAAAC
1 ACTACAAAC
433648 TTGAATCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.38
Consensus pattern (18 bp):
ACTACAAACATTTTTTTC
Found at i:433891 original size:15 final size:16
Alignment explanation
Indices: 433863--433892 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
433853 TTTTGTGCCA
433863 TAGTTACTAAAACTTT
1 TAGTTACTAAAACTTT
433879 TAGTTAC-AAAACTT
1 TAGTTACTAAAACTT
433893 GTCACTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (16 bp):
TAGTTACTAAAACTTT
Found at i:434308 original size:37 final size:37
Alignment explanation
Indices: 434250--434346 Score: 142
Period size: 37 Copynumber: 2.6 Consensus size: 37
434240 CCTTTTCGTC
434250 CTACTA-GAATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTATG-ATTCAAACTCCTAAAAATAGGATAGAATT
* * *
434287 TTGCTATGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
*
434324 CTACTATGATTTAAACTCCTAAA
1 CTACTATGATTCAAACTCCTAAA
434347 GATATGATCC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
37 52 0.98
38 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:434913 original size:19 final size:19
Alignment explanation
Indices: 434825--434914 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 19
434815 TTTTTTACAC
*
434825 TATATAT-TA-TTATTATA
1 TATATATATATTTATTATT
*
434842 TATACATATAGTTT-TTATT
1 TATATATATA-TTTATTATT
* *
434861 TATTTATATTCATTTGGTTATT
1 TATATATA-T-ATTT-ATTATT
*
434883 TTTAATACTATATTTATTATT
1 TAT-ATA-TATATTTATTATT
434904 TATATATATAT
1 TATATATATAT
434915 ATACTTTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
17 6 0.11
18 2 0.04
19 15 0.27
20 9 0.16
21 8 0.14
22 11 0.20
23 3 0.05
24 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
TATATATATATTTATTATT
Found at i:435223 original size:4 final size:4
Alignment explanation
Indices: 435210--435239 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
435200 TATATTTTAA
435210 TATT TCATT TATT TATT TATT TATT TATT T
1 TATT T-ATT TATT TATT TATT TATT TATT T
435240 TTCCTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:435261 original size:12 final size:12
Alignment explanation
Indices: 435246--435279 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
435236 ATTTTTCCTT
435246 TTATTTTTTTTC
1 TTATTTTTTTTC
435258 TTA-TTTTTTTC
1 TTATTTTTTTTC
435269 TTCATTTTTTT
1 TT-ATTTTTTT
435280 CATTTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 10 0.50
12 4 0.20
13 6 0.30
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (12 bp):
TTATTTTTTTTC
Found at i:435264 original size:11 final size:12
Alignment explanation
Indices: 435250--435280 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
435240 TTCCTTTTAT
435250 TTTTTTTCTT-A
1 TTTTTTTCTTCA
435261 TTTTTTTCTTCA
1 TTTTTTTCTTCA
435273 TTTTTTTC
1 TTTTTTTC
435281 ATTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTCTTCA
Found at i:439767 original size:17 final size:17
Alignment explanation
Indices: 439718--439783 Score: 70
Period size: 18 Copynumber: 4.1 Consensus size: 17
439708 TCCAATCAAG
*
439718 AACAAAA-AAGAAAAGA
1 AACAAAAGAAAAAAAGA
*
439734 AGCAAAAG--AAAAA-A
1 AACAAAAGAAAAAAAGA
439748 AAC-AAAGAAAAAAGAGA
1 AACAAAAGAAAAAA-AGA
439765 AACAAAAGAAAAAAAGA
1 AACAAAAGAAAAAAAGA
439782 AA
1 AA
439784 GAACAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
13 4 0.10
14 3 0.07
15 8 0.20
16 7 0.17
17 9 0.22
18 10 0.24
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (17 bp):
AACAAAAGAAAAAAAGA
Found at i:439774 original size:31 final size:30
Alignment explanation
Indices: 439718--439779 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 30
439708 TCCAATCAAG
*
439718 AACAAAAAAGAAAAGAAGCAAAAGAAAAAA
1 AACAAAAAAGAAAAGAAACAAAAGAAAAAA
439748 AACAAAGAAA-AAAGAGAAACAAAAGAAAAAA
1 AACAAA-AAAGAAA-AGAAACAAAAGAAAAAA
439779 A
1 A
439780 GAAAGAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 9 0.31
31 20 0.69
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (30 bp):
AACAAAAAAGAAAAGAAACAAAAGAAAAAA
Found at i:441500 original size:106 final size:106
Alignment explanation
Indices: 441369--442424 Score: 1520
Period size: 106 Copynumber: 10.0 Consensus size: 106
441359 ATATCGTGCC
* * * * *
441369 ACTCAAGACAACACAAGTTCAACTTCACGAAGAAGGGACGGTTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * *
441434 AATTTCAGAGCCAATTTCAACTTCACAGTGAATGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
441475 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
441540 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
441581 ACTCCAGACAACGCAAGTTCAAATTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
441646 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * * *
441687 ACTCCAGACAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
441752 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
441793 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
441858 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
441899 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTTTCAAC-AACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * *
441963 AATTTCAGAGCCAGTTTCAACTTCGCAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
442004 ACTCCAGACAACACAAGTTCAAATTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
442069 AATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
442110 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
442175 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * *
442216 AC-CCAAGACAACACAAGCCCAACTTCACGACGAAGGG-GCGCTGATTGTCAAC-AA-AATTT--
1 ACTCC-AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
** *
442275 C-A-TTCAGAGTTAATTTCAACTTCACAGCGAATGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
442315 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
** * *
442380 GGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
442421 ACTC
1 ACTC
442425 GGAACAATGC
Statistics
Matches: 863, Mismatches: 76, Indels: 22
0.90 0.08 0.02
Matches are distributed among these distances:
99 64 0.07
100 14 0.02
101 3 0.00
102 5 0.01
103 4 0.00
104 3 0.00
105 108 0.13
106 662 0.77
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:442161 original size:423 final size:423
Alignment explanation
Indices: 441369--442424 Score: 1642
Period size: 423 Copynumber: 2.5 Consensus size: 423
441359 ATATCGTGCC
* * * * *
441369 ACTCAAGACAACACAAGTTCAACTTCACGAAGAAGGGACGGTTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* * * *
441434 AATTTCAGAGCCAATTTCAACTTCACAGTGAATGATATTAGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACACAAGTTCAACT
* * * *
441499 TCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACAACGAAGGGACAGCTGGTTGTCAA-CAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
* * *
441564 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAATTCACGATGAAGGGACCGCTGGTTG
195 ACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAAATTCACGACGAAGGGACCGCTGGTTG
*
441629 TCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
260 TCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
* *
441694 ACAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
325 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
441759 GAGCCAATTTCAACTTCACAACGAAGGATATTGG
390 GAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
441793 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
441858 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACACAAGTTCAACT
* * * * *
441923 TCACAACGAAGGGACGGCTAGTTTTCAACAACAATTTCCCAATTTCAGAGCCAGTTTCAACTTCG
131 TCACAACGAAGGGACAGCTGGTTGTCAACAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
441988 CAACGAAGGATATTGGACTCCAGACAACACAAGTTCAAATTCACGACGAAGGGACCGCTGGTTGT
196 CAACGAAGGATATTGGACTCCAGACAACACAAGTTCAAATTCACGACGAAGGGACCGCTGGTTGT
*
442053 CAATAAACAATTTCCCAATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGA
261 CAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
442118 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
326 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
* * *
442183 AGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
391 AGCCAATTTCAACTTCACAACGAAGGATATTGG
** * *
442216 AC-CCAAGACAACACAAGCCCAACTTCACGACGAAGGG-GCGCTGATTGTCAAC-AA-AA-TT-T
1 ACTCC-AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCT
** *
442275 C-A-TTCAGAGTTAATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACACAAGTTCAAC
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACACAAGTTCAAC
** *
442338 TTCACAACGAAGGGACAGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTT
130 TTCACAACGAAGGGACAGCTGGTTGTCAAC-AACAATTTCCCAATTTCAGAGCCAATTTCAACTT
* *
442403 CACGACGGAGGATATTGGACTC
194 CACAACGAAGGATATTGGACTC
442425 GGAACAATGC
Statistics
Matches: 580, Mismatches: 50, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
416 84 0.14
417 50 0.09
418 2 0.00
419 2 0.00
420 2 0.00
421 2 0.00
422 14 0.02
423 283 0.49
424 141 0.24
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (423 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACACAAGTTCAACT
TCACAACGAAGGGACAGCTGGTTGTCAACAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
CAACGAAGGATATTGGACTCCAGACAACACAAGTTCAAATTCACGACGAAGGGACCGCTGGTTGT
CAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
AGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:443211 original size:37 final size:37
Alignment explanation
Indices: 443122--443225 Score: 131
Period size: 37 Copynumber: 2.8 Consensus size: 37
443112 CATTTTCGTC
*
443122 CTACTAGAATTCAAACTCCTAAAAA-AGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
443158 TTGCTAGGATTCAAACTCCTAAAAATAGGATA-AAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAA-TT
* * *
443195 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
443226 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
36 24 0.41
37 34 0.59
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:443717 original size:20 final size:20
Alignment explanation
Indices: 443689--443782 Score: 52
Period size: 20 Copynumber: 4.5 Consensus size: 20
443679 TTGATTTTTT
443689 TACACTATATATTATTTTATA
1 TACA-TATATATTATTTTATA
*
443710 TACATATATTTTTATTTATTTATA
1 TACATATA-TATTA--T-TTTATA
* *
443734 TTCAT-T-TGGTTATTTTA-A
1 TACATATAT-ATTATTTTATA
*
443752 TACTATATTTATTATTTT-TA
1 TAC-ATATATATTATTTTATA
*
443772 TATATATATAT
1 TACATATATAT
443783 ACTTTTTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
18 3 0.05
19 13 0.23
20 16 0.28
21 10 0.18
22 3 0.05
23 2 0.04
24 10 0.18
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (20 bp):
TACATATATATTATTTTATA
Found at i:443826 original size:2 final size:2
Alignment explanation
Indices: 443814--443881 Score: 127
Period size: 2 Copynumber: 33.5 Consensus size: 2
443804 ATAAGCGTAT
443814 TA TA CTA 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 TA TA TA
443857 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
443882 TGTAATTATC
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 63 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:444153 original size:16 final size:16
Alignment explanation
Indices: 444132--444172 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
444122 CATTCATTTA
*
444132 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
444148 TTTATTT-TTTTTACT
1 TTTATTTATTTTTACT
444163 TATT-TTTATT
1 T-TTATTTATT
444173 CTTCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:448457 original size:22 final size:22
Alignment explanation
Indices: 448422--448469 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
448412 TCTTTTTTTG
448422 TTTTTGTTAA-TTTTTTCATTT
1 TTTTTGTTAATTTTTTTCATTT
*
448443 TTTTTGTTTACTTTTTTTCATTT
1 TTTTTG-TTAATTTTTTTCATTT
448466 TTTT
1 TTTT
448470 ATGAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 6 0.25
22 3 0.12
23 15 0.62
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTTTGTTAATTTTTTTCATTT
Found at i:460732 original size:18 final size:20
Alignment explanation
Indices: 460690--460734 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
460680 GATTATGCTG
*
460690 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAGTGTT
460710 GAAATTGAT-TTAGAGTG-T
1 GAAATTGATGTTAGAGTGTT
460728 GAAATTG
1 GAAATTG
460735 GGTCATTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.33
19 8 0.33
20 8 0.33
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.38
Consensus pattern (20 bp):
GAAATTGATGTTAGAGTGTT
Found at i:461982 original size:59 final size:60
Alignment explanation
Indices: 461913--462095 Score: 192
Period size: 59 Copynumber: 3.1 Consensus size: 60
461903 CATATTCAGG
* * * * *
461913 TTAGCCCTAAAGGATACCTAGAT-CATATGATGGATATGACCTTATGTGTCATATTTGGT
1 TTAGCACTAAAGGATACCTAGATGCAGATGATGGACACGACCTTATGTGTAATATTTGGT
* *
461972 TTAGCACTAAAGGATACCTA-ATGCAGATGGTGGGCACGACCTTATGTGTAATATTTGGT
1 TTAGCACTAAAGGATACCTAGATGCAGATGATGGACACGACCTTATGTGTAATATTTGGT
* * * * ** * * * *
462031 TCAGCACTAAAGGATACCTAG-TGTAGATGGTGGGCAATACCTTATGTTTTATATTCGAT
1 TTAGCACTAAAGGATACCTAGATGCAGATGATGGACACGACCTTATGTGTAATATTTGGT
462090 TTAGCA
1 TTAGCA
462096 ACCTAGTGCA
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
58 2 0.02
59 104 0.98
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (60 bp):
TTAGCACTAAAGGATACCTAGATGCAGATGATGGACACGACCTTATGTGTAATATTTGGT
Found at i:464491 original size:12 final size:12
Alignment explanation
Indices: 464474--464498 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
464464 TACTCATGTG
464474 ATGAATGCATAT
1 ATGAATGCATAT
464486 ATGAATGCATAT
1 ATGAATGCATAT
464498 A
1 A
464499 GTACATTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGAATGCATAT
Found at i:473837 original size:21 final size:21
Alignment explanation
Indices: 473811--473857 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
473801 GCAAATGAGG
473811 TACAATTGGATATGTTGGATA
1 TACAATTGGATATGTTGGATA
473832 TACAATTGGATATGTTGGATA
1 TACAATTGGATATGTTGGATA
473853 TACAA
1 TACAA
473858 ATGAAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (21 bp):
TACAATTGGATATGTTGGATA
Found at i:485451 original size:13 final size:15
Alignment explanation
Indices: 485433--485469 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
485423 GAGTCAATCC
485433 AGTCAAC-C-CACTG
1 AGTCAACTCTCACTG
*
485446 AGTCAACTCTCATTG
1 AGTCAACTCTCACTG
485461 AGTCAACTC
1 AGTCAACTC
485470 AGACCAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.33
14 1 0.05
15 13 0.62
ACGTcount: A:0.30, C:0.32, G:0.14, T:0.24
Consensus pattern (15 bp):
AGTCAACTCTCACTG
Found at i:487355 original size:13 final size:13
Alignment explanation
Indices: 487337--487361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
487327 AAAAACTCAA
487337 TCTCTAATATATG
1 TCTCTAATATATG
487350 TCTCTAATATAT
1 TCTCTAATATAT
487362 AATATATATG
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:0.32, C:0.16, G:0.04, T:0.48
Consensus pattern (13 bp):
TCTCTAATATATG
Found at i:487883 original size:2 final size:2
Alignment explanation
Indices: 487876--487901 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
487866 ACGCTTCACC
487876 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
487902 CTTATCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:490032 original size:14 final size:14
Alignment explanation
Indices: 490015--490055 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
490005 ATTTTTGTTT
490015 TATTATTGATATTG
1 TATTATTGATATTG
490029 TATTATTCGATATTG
1 TATTATT-GATATTG
*
490044 -GTTATTGATATT
1 TATTATTGATATT
490056 TTATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 6 0.24
14 12 0.48
15 7 0.28
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (14 bp):
TATTATTGATATTG
Found at i:493013 original size:31 final size:31
Alignment explanation
Indices: 492975--493125 Score: 188
Period size: 31 Copynumber: 5.0 Consensus size: 31
492965 CCCGAATGAC
* *
492975 CAGTCCATAGATTCCGAAGAACCTAGGTAAT
1 CAGTCCATAGATTCCGAAGAACATAGGTAAA
*
493006 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATTCCGAAGAACATAGGTAAA
*
493037 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATTCCGAAGAACATAGGTAAA
493068 CAGTCCAT--ATGTCCGAAGAACATAGGTAAA
1 CAGTCCATAGAT-TCCGAAGAACATAGGTAAA
*
493098 CAGTCCAT--ATTCCCAAGAACATAGGTAA
1 CAGTCCATAGATTCCGAAGAACATAGGTAA
493126 CCCTCGACCC
Statistics
Matches: 112, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
29 18 0.16
30 28 0.25
31 65 0.58
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATAGATTCCGAAGAACATAGGTAAA
Found at i:493055 original size:62 final size:61
Alignment explanation
Indices: 492975--493125 Score: 236
Period size: 62 Copynumber: 2.5 Consensus size: 61
492965 CCCGAATGAC
* * *
492975 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAACAGTCCATATGT-CCGAAGAACATAGGTAAA
493037 CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCGAAGAACATAGGTAAA
493098 CAGTCCATAT-TCCC-AAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
493126 CCCTCGACCC
Statistics
Matches: 85, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
59 14 0.16
60 4 0.05
61 28 0.33
62 38 0.45
63 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (61 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCGAAGAACATAGGTAAA
Found at i:501051 original size:13 final size:13
Alignment explanation
Indices: 501033--501057 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
501023 TTTAAATAAA
501033 AAAATATAAATTT
1 AAAATATAAATTT
501046 AAAATATAAATT
1 AAAATATAAATT
501058 ATTTAAAAAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATATAAATTT
Found at i:501089 original size:20 final size:18
Alignment explanation
Indices: 501064--501100 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
501054 AATTATTTAA
501064 AAATATTAAGAATATTAAAC
1 AAATATTAA-AA-ATTAAAC
501084 AAATATTAAAAATTAAA
1 AAATATTAAAAATTAAA
501101 AACTTTCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (18 bp):
AAATATTAAAAATTAAAC
Found at i:504723 original size:30 final size:31
Alignment explanation
Indices: 504679--504750 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 31
504669 TTTTTTCCCG
* * **
504679 CTCAAGCGCGCGATTTCAGTCCAAAACT-CT
1 CTCAATCGCACGATTTCAACCCAAAACTACT
*
504709 CTCAATCGCACGATTTCAACCCAAAAGTACT
1 CTCAATCGCACGATTTCAACCCAAAACTACT
*
504740 CTCGATCGCAC
1 CTCAATCGCAC
504751 CTGAATCGCG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 23 0.66
31 12 0.34
ACGTcount: A:0.29, C:0.35, G:0.14, T:0.22
Consensus pattern (31 bp):
CTCAATCGCACGATTTCAACCCAAAACTACT
Found at i:506716 original size:24 final size:24
Alignment explanation
Indices: 506680--506746 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
506670 TTTTATCTTT
* * *
506680 GTTTTAGGAATTTTAGTTTAAATA
1 GTTTTAAGTATTTTAATTTAAATA
506704 GTTTTAAGTATTTTAATTTAAATA
1 GTTTTAAGTATTTTAATTTAAATA
506728 GTTTTAAGTATTTTAATTT
1 GTTTTAAGTATTTTAATTT
506747 GAATTTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (24 bp):
GTTTTAAGTATTTTAATTTAAATA
Found at i:507691 original size:14 final size:14
Alignment explanation
Indices: 507654--507702 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
507644 TCATATTTAA
507654 TTATCTATTTTATT
1 TTATCTATTTTATT
507668 TTAT-TATTTTATT
1 TTATCTATTTTATT
507681 CTTATCT-TTTTATCT
1 -TTATCTATTTTAT-T
507696 TTATCTA
1 TTATCTA
507703 AAATTCTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.29
14 20 0.65
15 2 0.06
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATCTATTTTATT
Found at i:512476 original size:12 final size:13
Alignment explanation
Indices: 512453--512487 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
512443 CTTTATTTCA
512453 ATTTATTTTGTTT
1 ATTTATTTTGTTT
512466 ATTTA-TTTGTTT
1 ATTTATTTTGTTT
512478 ATTTAGTTTT
1 ATTTA-TTTT
512488 TATCTCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.60
13 5 0.25
14 3 0.15
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (13 bp):
ATTTATTTTGTTT
Found at i:512572 original size:28 final size:27
Alignment explanation
Indices: 512541--512593 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
512531 TATCTTTATC
*
512541 ATTATCTTATAATTATTTTCTATTTTTT
1 ATTATCTTATAATTATCTTCT-TTTTTT
* *
512569 ATTATTTTATCATTATCTTCTTTTT
1 ATTATCTTATAATTATCTTCTTTTT
512594 AAAATAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (27 bp):
ATTATCTTATAATTATCTTCTTTTTTT
Found at i:512649 original size:14 final size:14
Alignment explanation
Indices: 512612--512660 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
512602 TCATATTTAA
512612 TTATCTATTTTATT
1 TTATCTATTTTATT
512626 TTAT-TATTTTATT
1 TTATCTATTTTATT
512639 CTTATCT-TTTTATCT
1 -TTATCTATTTTAT-T
512654 TTATCTA
1 TTATCTA
512661 AAATTCTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.29
14 20 0.65
15 2 0.06
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATCTATTTTATT
Found at i:513461 original size:12 final size:12
Alignment explanation
Indices: 513444--513474 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
513434 TGCCTCTCAG
513444 TCTGTGGGCGAT
1 TCTGTGGGCGAT
513456 TCTGTGGGCGAT
1 TCTGTGGGCGAT
*
513468 TATGTGG
1 TCTGTGG
513475 AGGAACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.13, G:0.42, T:0.35
Consensus pattern (12 bp):
TCTGTGGGCGAT
Found at i:515480 original size:7 final size:7
Alignment explanation
Indices: 515444--515576 Score: 77
Period size: 7 Copynumber: 19.6 Consensus size: 7
515434 AATTTACAAA
515444 ATATATT
1 ATATATT
515451 ATA-ATT
1 ATATATT
* *
515457 ATTTTTT
1 ATATATT
* *
515464 ATAAAAT
1 ATATATT
515471 ATATATT
1 ATATATT
515478 ATA-ATT
1 ATATATT
515484 ACTATATTT
1 A-TATA-TT
515493 ATATATT
1 ATATATT
515500 ATTATATT
1 A-TATATT
*
515508 TTA-ATT
1 ATATATT
*
515514 ATTTATT
1 ATATATT
515521 ATAT-TT
1 ATATATT
515527 A-ATATT
1 ATATATT
515533 -TAATATT
1 AT-ATATT
515540 AT-TCATT
1 ATAT-ATT
515547 AT-TATT
1 ATATATT
515553 AT-TATT
1 ATATATT
* *
515559 ATGTTTT
1 ATATATT
*
515566 ATTTATT
1 ATATATT
515573 ATAT
1 ATAT
515577 TCATTTAATT
Statistics
Matches: 98, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
5 2 0.02
6 30 0.31
7 51 0.52
8 12 0.12
9 3 0.03
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (7 bp):
ATATATT
Found at i:515500 original size:16 final size:15
Alignment explanation
Indices: 515470--515514 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
515460 TTTTATAAAA
515470 TATATATTATAATTAC
1 TATAT-TTATAATTAC
*
515486 TATATTTATATATTAT
1 TATATTTATA-ATTAC
515502 TATATTT-TAATTA
1 TATATTTATAATTA
515515 TTTATTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 4 0.15
15 7 0.26
16 16 0.59
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATTTATAATTAC
Found at i:515502 original size:43 final size:41
Alignment explanation
Indices: 515443--515542 Score: 100
Period size: 43 Copynumber: 2.4 Consensus size: 41
515433 AAATTTACAA
515443 AATATATTATA-ATTATT-T-TTTATAAAATATATATTATAATT
1 AATAT-TTATATATTATTATATTT-T-AAATATATATTATAATT
* * *
515484 ACTATATTTATATATTATTATATTTTAATTATTTATTATATTT
1 A--ATATTTATATATTATTATATTTTAAATATATATTATAATT
515527 AATATTTA-ATATTATT
1 AATATTTATATATTATT
515543 CATTATTATT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
40 8 0.16
41 8 0.16
42 5 0.10
43 25 0.49
44 2 0.04
45 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (41 bp):
AATATTTATATATTATTATATTTTAAATATATATTATAATT
Found at i:515523 original size:26 final size:26
Alignment explanation
Indices: 515488--515577 Score: 89
Period size: 26 Copynumber: 3.5 Consensus size: 26
515478 ATAATTACTA
515488 TATTTA-TATATTATTATATTTTAAT
1 TATTTATTATATTATTATATTTTAAT
* *
515513 TATTTATTATATT-TAATATTTAATAT
1 TATTTATTATATTATTATATTTTA-AT
* *
515539 TATTCATTATTATTATTATTATGTT--T
1 TATTTATTA-TATTATTA-TATTTTAAT
515565 TATTTATTATATT
1 TATTTATTATATT
515578 CATTTAATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
25 18 0.34
26 25 0.47
27 4 0.08
28 2 0.04
29 4 0.08
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (26 bp):
TATTTATTATATTATTATATTTTAAT
Found at i:515534 original size:16 final size:16
Alignment explanation
Indices: 515486--515534 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 16
515476 TTATAATTAC
515486 TATATTT-ATATATTAT
1 TATATTTAATAT-TTAT
515502 TATATTTTAATTATTTAT
1 TATA-TTTAA-TATTTAT
515520 TATATTTAATATTTA
1 TATATTTAATATTTA
515535 ATATTATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.33
17 8 0.27
18 9 0.30
19 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATTTAATATTTAT
Found at i:515557 original size:16 final size:17
Alignment explanation
Indices: 515498--515559 Score: 58
Period size: 16 Copynumber: 3.7 Consensus size: 17
515488 TATTTATATA
*
515498 TTATTATATTTTAATTAT
1 TTATTAT-TATTAATTAT
515516 TTATTA-TATTTAA-TAT
1 TTATTATTA-TTAATTAT
* *
515532 TTAATATTATTCATTA-
1 TTATTATTATTAATTAT
515548 TTATTATTATTA
1 TTATTATTATTA
515560 TGTTTTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
16 22 0.61
17 8 0.22
18 6 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATTATTATTAATTAT
Found at i:524086 original size:31 final size:31
Alignment explanation
Indices: 524048--524110 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
524038 GCATGAACAT
524048 GCTATTAAATGATCATGCAATTGATCTTATG
1 GCTATTAAATGATCATGCAATTGATCTTATG
524079 GCTATTAAATGATCATGCAATTGATCTTATG
1 GCTATTAAATGATCATGCAATTGATCTTATG
524110 G
1 G
524111 TTTATGAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (31 bp):
GCTATTAAATGATCATGCAATTGATCTTATG
Found at i:527145 original size:15 final size:15
Alignment explanation
Indices: 527125--527163 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
527115 TGCTAAAAGA
527125 TGATGAGCCAGATAT
1 TGATGAGCCAGATAT
527140 TGATGAGCCAGATAT
1 TGATGAGCCAGATAT
527155 TGATGAGCC
1 TGATGAGCC
527164 TATGACAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (15 bp):
TGATGAGCCAGATAT
Found at i:528600 original size:8 final size:8
Alignment explanation
Indices: 528587--528611 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
528577 ATCCTGTATA
528587 TATATATG
1 TATATATG
528595 TATATATG
1 TATATATG
528603 TATATATG
1 TATATATG
528611 T
1 T
528612 CTTCTCATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TATATATG
Found at i:532086 original size:5 final size:5
Alignment explanation
Indices: 532073--532194 Score: 57
Period size: 5 Copynumber: 25.0 Consensus size: 5
532063 ACTTCACCTA
*
532073 AAAAG AAAATA AAAAG AAAAG AAAA- AATAA- AAAAG AAGAAG AAAAG
1 AAAAG AAAA-G AAAAG AAAAG AAAAG AA-AAG AAAAG AA-AAG AAAAG
* * * *
532119 AAAA- AATAG AAAAATG AGAA- AAATG AAAA- AAGAG AAAA- AAGAA-
1 AAAAG AAAAG -AAAA-G AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG
*
532162 AAACA- AAAAG AAAA- AAAAG AAAA- AAAAT AAAAG
1 AAA-AG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
532195 GGGGTTCAAG
Statistics
Matches: 92, Mismatches: 11, Indels: 28
0.70 0.08 0.21
Matches are distributed among these distances:
4 24 0.26
5 52 0.57
6 15 0.16
7 1 0.01
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (5 bp):
AAAAG
Found at i:532114 original size:25 final size:24
Alignment explanation
Indices: 532089--532193 Score: 94
Period size: 23 Copynumber: 4.4 Consensus size: 24
532079 AAATAAAAAG
532089 AAAAGAAAAAATAAAAAAGAAGAA
1 AAAAGAAAAAATAAAAAAGAAGAA
532113 GAAAAGAAAAAATAGAAAAATG-AGAA
1 -AAAAGAAAAAATA-AAAAA-GAAGAA
* * *
532139 AAATGAAAAAAGAGAAAA-AAGAA
1 AAAAGAAAAAATAAAAAAGAAGAA
532162 AAACA-AAAAGAA-AAAAAAGAA-AA
1 AAA-AGAAAA-AATAAAAAAGAAGAA
*
532185 AAAATAAAA
1 AAAAGAAAA
532194 GGGGGTTCAA
Statistics
Matches: 68, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
22 1 0.01
23 25 0.37
24 8 0.12
25 24 0.35
26 9 0.13
27 1 0.01
ACGTcount: A:0.81, C:0.01, G:0.13, T:0.05
Consensus pattern (24 bp):
AAAAGAAAAAATAAAAAAGAAGAA
Found at i:532140 original size:16 final size:15
Alignment explanation
Indices: 532089--532185 Score: 72
Period size: 16 Copynumber: 6.3 Consensus size: 15
532079 AAATAAAAAG
* *
532089 AAAAGAAAAAATAAAA
1 AAAAGAAAAAA-GAGA
*
532105 AAGAAGAAGAAAAGAAA
1 AA-AAGAA-AAAAGAGA
*
532122 AAATAGAAAAATGAGA
1 AAA-AGAAAAAAGAGA
532138 AAAATGAAAAAAGAGA
1 AAAA-GAAAAAAGAGA
* *
532154 AAAA-AGAAAA-ACA
1 AAAAGAAAAAAGAGA
*
532167 AAAAGAAAAAAAAGA
1 AAAAGAAAAAAGAGA
532182 AAAA
1 AAAA
532186 AAATAAAAGG
Statistics
Matches: 67, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
13 6 0.09
14 10 0.15
15 7 0.10
16 26 0.39
17 14 0.21
18 4 0.06
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.04
Consensus pattern (15 bp):
AAAAGAAAAAAGAGA
Found at i:532187 original size:9 final size:9
Alignment explanation
Indices: 532072--532193 Score: 90
Period size: 9 Copynumber: 13.1 Consensus size: 9
532062 TACTTCACCT
532072 AAAAAGAAAA
1 AAAAAG-AAA
532082 TAAAAAGAAA
1 -AAAAAGAAA
532092 AGAAAA-AATA
1 A-AAAAGAA-A
532102 AAAAAGAAGA
1 AAAAAGAA-A
532112 AGAAAAGAAA
1 A-AAAAGAAA
*
532122 AAATAG--A
1 AAAAAGAAA
* *
532129 AAAATGAGA
1 AAAAAGAAA
*
532138 AAAATGAAA
1 AAAAAGAAA
*
532147 AAAGAGAAA
1 AAAAAGAAA
532156 AAAGAA-AAA
1 AAA-AAGAAA
532165 CAAAAAGAAA
1 -AAAAAGAAA
532175 AAAAAGAAA
1 AAAAAGAAA
*
532184 AAAAATAAA
1 AAAAAGAAA
532193 A
1 A
532194 GGGGGTTCAA
Statistics
Matches: 93, Mismatches: 9, Indels: 20
0.76 0.07 0.16
Matches are distributed among these distances:
7 5 0.05
9 53 0.57
10 22 0.24
11 13 0.14
ACGTcount: A:0.81, C:0.01, G:0.13, T:0.05
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:532193 original size:7 final size:7
Alignment explanation
Indices: 532072--532186 Score: 76
Period size: 7 Copynumber: 15.7 Consensus size: 7
532062 TACTTCACCT
532072 AAAAAGA
1 AAAAAGA
*
532079 AAATAAAA
1 AAA-AAGA
532087 AGAAAAGA
1 A-AAAAGA
*
532095 AAAAATA
1 AAAAAGA
532102 AAAAAG-
1 AAAAAGA
*
532108 AAGAAGA
1 AAAAAGA
532115 AAAGAA-A
1 AAA-AAGA
*
532122 AAATAGA
1 AAAAAGA
532129 AAAATGAGA
1 AAAA--AGA
*
532138 AAAATGAA
1 AAAAAG-A
532146 AAAAGAGA
1 AAAA-AGA
532154 AAAAAGA
1 AAAAAGA
532161 AAAACA-A
1 AAAA-AGA
532168 AAAGAA-A
1 AAA-AAGA
532175 AAAAAGA
1 AAAAAGA
532182 AAAAA
1 AAAAA
532187 AATAAAAGGG
Statistics
Matches: 86, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
6 8 0.09
7 46 0.53
8 22 0.26
9 10 0.12
ACGTcount: A:0.81, C:0.01, G:0.14, T:0.04
Consensus pattern (7 bp):
AAAAAGA
Found at i:533754 original size:15 final size:15
Alignment explanation
Indices: 533736--533770 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
533726 CGAGGGTATT
533736 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
*
533751 GTAGTCCTTCGGGAT
1 GTAGTCCTTCGGGAC
533766 GTAGT
1 GTAGT
533771 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.20, G:0.34, T:0.31
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:533781 original size:18 final size:18
Alignment explanation
Indices: 533754--533801 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
533744 TCGGGACGTA
* *
533754 GTCCTTCGGGATGTAGTG
1 GTCCTACGGGACGTAGTG
533772 GTCCTACGGGACGTAGTG
1 GTCCTACGGGACGTAGTG
533790 GTCCTACGGGAC
1 GTCCTACGGGAC
533802 ATATATAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (18 bp):
GTCCTACGGGACGTAGTG
Found at i:536608 original size:192 final size:191
Alignment explanation
Indices: 536282--536666 Score: 752
Period size: 192 Copynumber: 2.0 Consensus size: 191
536272 CAAAGACAAA
536282 GAGATGGAAGAAATTTCTATCGTTAGAGATTCTCTGATATATTCCCTGCAGAATTGCCAGGTTTA
1 GAGATGGAAGAAATTTCTATCGTTAGAGATTCTCTGATATATTCCCTGCAGAATTGCCAGGTTTA
536347 CCTCCGGACAGAGAGGTAGAATTTCAGATTGAGATAATGTCGGGAACAACGCCCATTGCAATGGC
66 CCTCCGGACAGAGAGGTAGAATTTCAGATTGAGATAATGTCGGGAACAACGCCCATTGCAATGGC
536412 GCCATACAGAATGGCTCCAAAAGAGTTGCAAGAGTTAAAGATTCAATTACAAGAATTTCTG
131 GCCATACAGAATGGCTCCAAAAGAGTTGCAAGAGTTAAAGATTCAATTACAAGAATTTCTG
536473 GAGATGGAAGAAATTTCTATCGTTAGAGAGTTCTCTGATATATTCCCTGCAGAATTGCCAGGTTT
1 GAGATGGAAGAAATTTCTATCGTTAGAGA-TTCTCTGATATATTCCCTGCAGAATTGCCAGGTTT
*
536538 ACCTCCGGACAGAGAGGTAGAATTTCAGATTGAGATAATGTCGGGAACAGCGCCCATTGCAATGG
65 ACCTCCGGACAGAGAGGTAGAATTTCAGATTGAGATAATGTCGGGAACAACGCCCATTGCAATGG
536603 CGCCATACAGAATGGCTCCAAAAGAGTTGCAAGAGTTAAAGATTCAATTACAAGAATTTCTG
130 CGCCATACAGAATGGCTCCAAAAGAGTTGCAAGAGTTAAAGATTCAATTACAAGAATTTCTG
536665 GA
1 GA
536667 CAAAGGTTTT
Statistics
Matches: 192, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
191 29 0.15
192 163 0.85
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (191 bp):
GAGATGGAAGAAATTTCTATCGTTAGAGATTCTCTGATATATTCCCTGCAGAATTGCCAGGTTTA
CCTCCGGACAGAGAGGTAGAATTTCAGATTGAGATAATGTCGGGAACAACGCCCATTGCAATGGC
GCCATACAGAATGGCTCCAAAAGAGTTGCAAGAGTTAAAGATTCAATTACAAGAATTTCTG
Found at i:540010 original size:21 final size:20
Alignment explanation
Indices: 539971--540008 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
539961 AGTATGTCCA
539971 GGGGGTATCGATTCCCCCTG
1 GGGGGTATCGATTCCCCCTG
539991 GGGGGTATCGATTCCCCC
1 GGGGGTATCGATTCCCCC
540009 CTAAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTG
Found at i:542784 original size:133 final size:132
Alignment explanation
Indices: 542497--542819 Score: 418
Period size: 133 Copynumber: 2.4 Consensus size: 132
542487 GCAAATTGAA
* * * *
542497 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACGTTTCTAGATATGATTTTCCTAAA
1 CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTGATTTTCCTAAA
*
542562 GAAGCAGCAAAGCAGATCCCTTGTTTTTCCAGATTTGATTTTCCCCAAGGAACAATGGAACAAGT
66 GAAGCAGCAAAGCAAATCCC-T-TTTTTCCAGATTTGATTTTCCCCAAGGAACAATGGAACAAGT
*
542627 CTAT
129 CTAC
* *
542631 CTCGATTCAATATTCCCTGAAGAATAGTGGAATGAATCAACGTCTCCAGATCTGATTTTCCCTAA
1 CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTGATTTT-CCTAA
* * *
542696 AGAAGTAGCGAAA-CAAATCCC-TTTTTCCAGATTTGATCTTT-CCCGAGGAAGCAGTGGAACAA
65 AGAAGCAGC-AAAGCAAATCCCTTTTTTCCAGATTTGAT-TTTCCCCAAGGAA-CAATGGAACAA
*
542758 GTCTGC
127 GTCTAC
* * * * *
542764 CTCGATTCAATATTCACTGAAGAACAGTCGAATTAATAAACGTTTCCATATCTGAT
1 CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTGAT
542820 CTACCCTGAA
Statistics
Matches: 166, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
132 24 0.14
133 66 0.40
134 53 0.32
135 20 0.12
136 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (132 bp):
CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTGATTTTCCTAAA
GAAGCAGCAAAGCAAATCCCTTTTTTCCAGATTTGATTTTCCCCAAGGAACAATGGAACAAGTCT
AC
Found at i:543062 original size:19 final size:17
Alignment explanation
Indices: 543039--543096 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 17
543029 CTTATTAATG
543039 TTATTAATTATTATTATT
1 TTATTAATTATT-TTATT
*
543057 TCTATTATTTATTTTATT
1 T-TATTAATTATTTTATT
543075 TTATTTATATTATCTTTATT
1 TTA-TTA-ATTAT-TTTATT
543095 TT
1 TT
543097 TATTTCTCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 2 0.06
18 10 0.29
19 14 0.41
20 8 0.24
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTAATTATTTTATT
Found at i:543080 original size:14 final size:15
Alignment explanation
Indices: 543061--543100 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
543051 ATTATTTCTA
*
543061 TTATTTATTTTAT-T
1 TTATTTATATTATCT
543075 TTATTTATATTATCT
1 TTATTTATATTATCT
*
543090 TTATTTTTATT
1 TTATTTATATT
543101 TCTCAGGCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (15 bp):
TTATTTATATTATCT
Found at i:544257 original size:106 final size:105
Alignment explanation
Indices: 544056--544280 Score: 267
Period size: 106 Copynumber: 2.1 Consensus size: 105
544046 TCCCCTTAAG
* * * *
544056 TTAGCAGTGTTTTTCCATGTTAGTCACTTGTGAGGACCTAAGTTGTATTTACCCATTTTCATGCA
1 TTAGC-GTGTTTTTACATGTTAGTCACCTGTGAGGACCGAAGTTGTATTTACCCATTTTCATGAA
* *
544121 TGCTATATATTTTTAGGGTATTGTTGTTTAGTCCCCCATAGT
65 TGCTATATATTTTTAGGATATTGTTATTTAGTCCCCCATA-T
*
544163 TTAGCGTGTTTTTACATGTTGGTCACCTGT-AGGACCGAAG-TGT-TATTACCCATTTTCATGAA
1 TTAGCGTGTTTTTACATGTTAGTCACCTGTGAGGACCGAAGTTGTAT-TTACCCATTTTCATGAA
* * * * *
544225 TGTTATGTATTTTTTGGAATATTTTCTATTTAGTCCCCCTTAT
65 TGCTATATATTTTTAGG-ATATTGT-TATTTAGTCCCCCATAT
544268 TTAGGCGTGTTTT
1 TTA-GCGTGTTTT
544281 GCATTTTGGT
Statistics
Matches: 102, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
103 1 0.01
104 33 0.32
105 18 0.18
106 45 0.44
107 5 0.05
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (105 bp):
TTAGCGTGTTTTTACATGTTAGTCACCTGTGAGGACCGAAGTTGTATTTACCCATTTTCATGAAT
GCTATATATTTTTAGGATATTGTTATTTAGTCCCCCATAT
Found at i:546133 original size:38 final size:38
Alignment explanation
Indices: 546038--546342 Score: 193
Period size: 38 Copynumber: 7.8 Consensus size: 38
546028 GATTCCAAAA
* * *
546038 AAAAAAAATCCAATGATTTATTTCTTTTACAAAATAGG
1 AAAATAAATCTAATGATTTATTTCCTTTACAAAATAGG
* *
546076 -AAATAAATTTAACTG-TTTATTTCCTTTGCAAAATAGG
1 AAAATAAATCTAA-TGATTTATTTCCTTTACAAAATAGG
*
546113 AAAATAAATCTAATGATTTATTTCTTTTTACAAAATAGG
1 AAAATAAATCTAATGATTTATTTC-CTTTACAAAATAGG
* * *
546152 AAAA-AAATCCT-ACGATTTA-TTCAATTTTACAAAACAGG
1 AAAATAAAT-CTAATGATTTATTTC--CTTTACAAAATAGG
546190 AAAATAAATCGTACGATTTGTTTCAATTTATTTCCTGTTAC-AAATAGG
1 AAAATAAATC-TA--A--TG-----ATTTATTTCCT-TTACAAAATAGG
* * ** *
546238 AAATTAAATATAACAATTTATTTCCTTTTACAAACTA-G
1 AAAATAAATCTAATGATTTATTTCC-TTTACAAAATAGG
* * *
546276 AAACTAAATTCT-ATGATTTATTTCCTTTTTCAATATAGG
1 AAAATAAA-TCTAATGATTTATTTCC-TTTACAAAATAGG
546315 --AATAAATCT-ATCGA-TTATTTCCTTTACA
1 AAAATAAATCTAAT-GATTTATTTCCTTTACA
546343 TATCAAAATC
Statistics
Matches: 214, Mismatches: 28, Indels: 53
0.73 0.09 0.18
Matches are distributed among these distances:
35 5 0.02
36 13 0.06
37 41 0.19
38 92 0.43
39 31 0.14
42 1 0.00
44 1 0.00
45 1 0.00
47 2 0.01
48 15 0.07
49 9 0.04
50 3 0.01
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (38 bp):
AAAATAAATCTAATGATTTATTTCCTTTACAAAATAGG
Found at i:546449 original size:96 final size:92
Alignment explanation
Indices: 546315--546519 Score: 245
Period size: 96 Copynumber: 2.2 Consensus size: 92
546305 TCAATATAGG
546315 AATAAA-TCTATCGA-TTATTTCCTTTACATATCAAAATCATACAAGATTCATAGGAAAATAAAT
1 AATAAATTCTAT-GATTTA-TTCCTTTACATATCAAAATCATACAAGATTCATAGG-AAAT-AAT
*
546378 TTACCAATTTATTTCATTTTTCAAAACACAAA
62 TTACCAATTTATTTC-CTTTTCAAAACACAAA
* * *
546410 AAGT-AATTCTATGATTTATTCCTTTTACATATCAGAATCATACAAGGTTCTTAGGAAATAATTT
1 AA-TAAATTCTATGATTTATTCC-TTTACATATCAAAATCATACAAGATTCATAGGAAATAATTT
*** *
546474 ATTGATTTATTTCCTTTTCAAAACACGAA
64 ACCAATTTATTTCCTTTTCAAAACACAAA
*
546503 AATAAATTTTATGATTT
1 AATAAATTCTATGATTT
546520 CCTTTTACAA
Statistics
Matches: 96, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
92 1 0.01
93 28 0.29
94 15 0.16
95 14 0.15
96 38 0.40
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (92 bp):
AATAAATTCTATGATTTATTCCTTTACATATCAAAATCATACAAGATTCATAGGAAATAATTTAC
CAATTTATTTCCTTTTCAAAACACAAA
Found at i:546554 original size:35 final size:34
Alignment explanation
Indices: 546482--546554 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 34
546472 TTATTGATTT
*** *
546482 ATTTCCTTTTCAAAACACGAAAATAAATTTTATG
1 ATTTCCTTTTCAAAACACGAAAATAAATCGAACG
* *
546516 ATTTCCTTTTACAAAATAGGAAAATAAATCGAACG
1 ATTTCCTTTT-CAAAACACGAAAATAAATCGAACG
546551 ATTT
1 ATTT
546555 ATTTCCTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 10 0.31
35 22 0.69
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (34 bp):
ATTTCCTTTTCAAAACACGAAAATAAATCGAACG
Found at i:546676 original size:39 final size:39
Alignment explanation
Indices: 546594--546678 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
546584 AATTCATAGG
* *
546594 AAAATAAATTTAACGATTTATTTTATTCTACAAAACATG
1 AAAATAAATTTAACGATTTATTTCATTCTACAAAACATA
* * *
546633 AAAATAAATTCT-ACGATTTATTTCCTTTTACACAATCA-A
1 AAAATAAATT-TAACGATTTATTTCATTCTACA-AAACATA
546672 AAAATAA
1 AAAATAA
546679 CAAAACAGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
39 34 0.87
40 5 0.13
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (39 bp):
AAAATAAATTTAACGATTTATTTCATTCTACAAAACATA
Found at i:546682 original size:55 final size:54
Alignment explanation
Indices: 546623--546747 Score: 180
Period size: 55 Copynumber: 2.3 Consensus size: 54
546613 ATTTTATTCT
* *
546623 ACAAAACATGAAAATAAATTCTACGATTTATTTCCTTTTACACAATCAAAAAATA
1 ACAAAACAAGAAAATAAATTCAACGATTTATTTCCTTTTACACAAT-AAAAAATA
* * **
546678 ACAAAACAGGAAACTAAATTCAACGATTTATTTCCTTTTACACAATAGGAAATA
1 ACAAAACAAGAAAATAAATTCAACGATTTATTTCCTTTTACACAATAAAAAATA
546732 AC-AAACAAGAAAATAA
1 ACAAAACAAGAAAATAA
546748 TTTAACAAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
53 12 0.19
54 8 0.13
55 43 0.68
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.26
Consensus pattern (54 bp):
ACAAAACAAGAAAATAAATTCAACGATTTATTTCCTTTTACACAATAAAAAATA
Found at i:546708 original size:225 final size:223
Alignment explanation
Indices: 546234--546732 Score: 525
Period size: 225 Copynumber: 2.2 Consensus size: 223
546224 CTGTTACAAA
* * *
546234 TAGGAAATTAAATATAACAATTTATTTCCTTTTACAAACTAGAAACTAAATTCTATGATTTATTT
1 TAGGAAA-TAAAT-TAACGATTTATTTCCTTTTACAAACTAGAAAATAAATTCTATGATTGATTT
* * * * *
546299 CCTTTTTCAATATAGGAATAAATCTATCGATTATTTCCTTTACATATCAAAATCATACAAGATTC
64 CCTTTTACAAAATAGGAATAAATCGAACGATTATTTCCTTTACATATCAAAATCATACAAAATTC
* * * *
546364 ATAGGAAAATAAATTTACCAATTTATTTCATTTTTCAAAACACAAAAAGTAATTCTATGATTTAT
129 ATAGGAAAATAAATTTAACAATTTATTTCATTCTACAAAACACAAAAAGTAATTCTACGATTTAT
* ** **
546429 TCCTTTTACATATCAGAATCATACAAGGTTC
194 TCCTTTTACAAATCAGAAAAATACAA-GAAC
* **
546460 TTAGGAAATAATTTATTGATTTATTTCCTTTT-CAAAAC-ACGAAAATAAATT-T-T-A-TGATT
1 -TAGGAAATAAATTAACGATTTATTTCCTTTTAC-AAACTA-GAAAATAAATTCTATGATTGATT
* *
546519 TCCTTTTACAAAATAGGAAAATAAATCGAACGATTTATTTCCTTTTACATATCATAATCATATAA
63 TCCTTTTACAAAATAGG--AATAAATCGAACGA-TTATTTCC-TTTACATATCAAAATCATACAA
* * **
546584 AATTCATAGGAAAATAAATTTAACGATTTATTTTATTCTACAAAACATGAAAA-TAAATTCTACG
124 AATTCATAGGAAAATAAATTTAACAATTTATTTCATTCTACAAAACACAAAAAGT-AATTCTACG
546648 ATTTATTTCCTTTTACACAATCA-AAAAATAACAA-AAC
188 ATTTA-TTCCTTTTACA-AATCAGAAAAAT-ACAAGAAC
*
546685 -AGGAAACTAAATTCAACGATTTATTTCCTTTTACACAA-TAGGAAATAA
1 TAGGAAA-TAAATT-AACGATTTATTTCCTTTTACA-AACTAGAAAATAA
546733 CAAACAAGAA
Statistics
Matches: 227, Mismatches: 30, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
221 19 0.08
222 1 0.00
223 19 0.08
224 17 0.07
225 133 0.59
226 23 0.10
227 15 0.07
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (223 bp):
TAGGAAATAAATTAACGATTTATTTCCTTTTACAAACTAGAAAATAAATTCTATGATTGATTTCC
TTTTACAAAATAGGAATAAATCGAACGATTATTTCCTTTACATATCAAAATCATACAAAATTCAT
AGGAAAATAAATTTAACAATTTATTTCATTCTACAAAACACAAAAAGTAATTCTACGATTTATTC
CTTTTACAAATCAGAAAAATACAAGAAC
Found at i:546871 original size:58 final size:58
Alignment explanation
Indices: 546774--547061 Score: 294
Period size: 58 Copynumber: 5.1 Consensus size: 58
546764 TTTTAAATGA
* * * ** * * *
546774 TAGAATCATCTACGATTCTCAAGAAAATAAATTTGACAATTTATTTTTCTTATAAAGT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATCTATTTTCCTTACAAAGT
* * *
546832 TAAAATCATTCAATATT-TCCAAGGAAATAAATTCAAC-A---A------TTACAAAGT
1 TAGAATCATTTAAGATTCT-CAAGGAAATAAATTCAACAATCTATTTTCCTTACAAAGT
*
546880 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATCTATTTTCCTTACAAATT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATCTATTTTCCTTACAAAGT
* * * * *
546938 TAGAATCATTAAAGATTCTCAAGGAAATATATTTAA-AGATATATTTTCCTTACAAAGC
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACA-ATCTATTTTCCTTACAAAGT
* * *
546996 TAGAATCATTTAAGATTCCCAAGTAAATAAATTCAAAAATCTATTTTCCTTACAAAGT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATCTATTTTCCTTACAAAGT
547054 TAGAATCA
1 TAGAATCA
547062 ATGCAAGATT
Statistics
Matches: 190, Mismatches: 26, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
48 40 0.21
49 2 0.01
52 1 0.01
54 1 0.01
57 3 0.02
58 142 0.75
59 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (58 bp):
TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATCTATTTTCCTTACAAAGT
Found at i:546903 original size:48 final size:48
Alignment explanation
Indices: 546827--546919 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 48
546817 TTTTTCTTAT
*
546827 AAAGTTAAAATCATTCAATATTTCCAAGGAAATAAATTCAACAATTAC
1 AAAGTTAAAATCATTCAAGATTTCCAAGGAAATAAATTCAACAATTAC
* *
546875 AAAGTTAGAATCATTTAAGA-TTCTCAAGGAAATAAATTCAACAAT
1 AAAGTTAAAATCATTCAAGATTTC-CAAGGAAATAAATTCAACAAT
546920 CTATTTTCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 3 0.07
48 38 0.93
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (48 bp):
AAAGTTAAAATCATTCAAGATTTCCAAGGAAATAAATTCAACAATTAC
Found at i:546912 original size:106 final size:106
Alignment explanation
Indices: 546774--547061 Score: 281
Period size: 106 Copynumber: 2.6 Consensus size: 106
546764 TTTTAAATGA
* ** * * *
546774 TAGAATCATCTACGATTCTCAAGAAAATAAATTTGACAATTTATTTTTCTTATAAAGTTAAAATC
1 TAGAATCATCTAAGATTCTCAAGAAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAAAATC
* *
546839 ATTCAATATT-TCCAAGGAAATAAATTCAACAATTACAAAGT
66 ATTAAAGATTCT-CAAGGAAATAAATTCAACAATTACAAAGT
* * * *
546880 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATCTATTTTCCTTACAAATTTAGAATC
1 TAGAATCATCTAAGATTCTCAAGAAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAAAATC
* * * *
546945 ATTAAAGATTCTCAAGGAAATATATTTAAAGATATATTTTCCTTACAAAGC
66 ATTAAAGATTCTCAAGGAAATA-AATT-CA-ACA-A------TTACAAAGT
* * * * *
546996 TAGAATCATTTAAGATTCCCAAGTAAATAAATTCAAAAATCTATTTTCCTTACAAAGTTAGAATC
1 TAGAATCATCTAAGATTCTCAAGAAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAAAATC
547061 A
66 A
547062 ATGCAAGATT
Statistics
Matches: 151, Mismatches: 20, Indels: 12
0.83 0.11 0.07
Matches are distributed among these distances:
106 73 0.48
107 4 0.03
108 1 0.01
109 2 0.01
110 1 0.01
116 70 0.46
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (106 bp):
TAGAATCATCTAAGATTCTCAAGAAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAAAATC
ATTAAAGATTCTCAAGGAAATAAATTCAACAATTACAAAGT
Found at i:547287 original size:44 final size:43
Alignment explanation
Indices: 547235--547413 Score: 211
Period size: 44 Copynumber: 4.1 Consensus size: 43
547225 CCAAAAATCA
* *
547235 AAAGGAACTAATCCTTTGATTTTAATTTTGCAATCCAATAATTG
1 AAAGGAACTAATCCTTTGATTTTACTTTTGCAA-CCAATAATTC
* *
547279 AAAGGAACTAATCCTTTGATTTTACTTTTGGAAACAATAA-TC
1 AAAGGAACTAATCCTTTGATTTTACTTTTGCAACCAATAATTC
* *
547321 AAAGGAACTAATCCATTGATTTTACTTTGGCAACACAATAATAATC
1 AAAGGAACTAATCCTTTGATTTTACTTTTGCAAC-CAATAAT--TC
*
547367 AAATGAAC-AATCCTTTGATTTTACTTTTGACAAACCCAATAA-TC
1 AAAGGAACTAATCCTTTGATTTTACTTTTG-C-AA-CCAATAATTC
547411 AAA
1 AAA
547414 AGCCTTGGAT
Statistics
Matches: 117, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
42 31 0.26
43 12 0.10
44 36 0.31
45 19 0.16
46 10 0.09
47 8 0.07
48 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (43 bp):
AAAGGAACTAATCCTTTGATTTTACTTTTGCAACCAATAATTC
Found at i:547342 original size:86 final size:88
Alignment explanation
Indices: 547225--547413 Score: 242
Period size: 86 Copynumber: 2.1 Consensus size: 88
547215 TTTTACCAAC
* * * *
547225 CCAAAAATCAAAAGGAACTAATCCTTTGATTTTAATTTTGCAATC-CAATAAT-TGAAAGGAACT
1 CCAATAATC-AAAGGAACTAATCCATTGATTTTAATTTGGCAA-CACAATAATATCAAAGGAAC-
*
547288 AATCCTTTGATTTTACTTTTG-GAAA
63 AATCCTTTGATTTTACTTTTGACAAA
* *
547313 -CAATAATCAAAGGAACTAATCCATTGATTTTACTTTGGCAACACAATAATAATCAAATGAACAA
1 CCAATAATCAAAGGAACTAATCCATTGATTTTAATTTGGCAACACAATAAT-ATCAAAGGAACAA
547377 TCCTTTGATTTTACTTTTGACAAA
65 TCCTTTGATTTTACTTTTGACAAA
547401 CCCAATAATCAAA
1 -CCAATAATCAAA
547414 AGCCTTGGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
85 1 0.01
86 37 0.42
87 28 0.32
88 11 0.12
90 11 0.12
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.33
Consensus pattern (88 bp):
CCAATAATCAAAGGAACTAATCCATTGATTTTAATTTGGCAACACAATAATATCAAAGGAACAAT
CCTTTGATTTTACTTTTGACAAA
Found at i:548333 original size:55 final size:57
Alignment explanation
Indices: 548267--548379 Score: 212
Period size: 56 Copynumber: 2.0 Consensus size: 57
548257 ATCAACTATT
548267 GTGCCTAATAACCGATCA-TACCTTAATTTTAGAAATCATGA-GCGGTCTTGAAAAG
1 GTGCCTAATAACCGATCATTACCTTAATTTTAGAAATCATGATGCGGTCTTGAAAAG
548322 GTGCCTAATAACCGATCATTACCTTAATTTTAGAAATCATGATGCGGTCTTGAAAAG
1 GTGCCTAATAACCGATCATTACCTTAATTTTAGAAATCATGATGCGGTCTTGAAAAG
548379 G
1 G
548380 ATGTCGACCT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
55 18 0.32
56 23 0.41
57 15 0.27
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (57 bp):
GTGCCTAATAACCGATCATTACCTTAATTTTAGAAATCATGATGCGGTCTTGAAAAG
Found at i:548760 original size:10 final size:10
Alignment explanation
Indices: 548745--548774 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
548735 GGAGACTCTA
548745 ATATTAATTT
1 ATATTAATTT
548755 ATATTAATTT
1 ATATTAATTT
*
548765 AAATTAATTT
1 ATATTAATTT
548775 TTAGATTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATATTAATTT
Found at i:549260 original size:27 final size:26
Alignment explanation
Indices: 549226--549285 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
549216 AAATAAATGG
*
549226 AAAAATAAAACATTGATTA-AAATAAA
1 AAAAATAAAA-ATTGAGTACAAATAAA
549252 ATAAAATAAAAATTGAGTACCAAATAAA
1 A-AAAATAAAAATTGAGTA-CAAATAAA
549280 AAAAAT
1 AAAAAT
549286 GAAAGAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 8 0.27
27 14 0.47
28 8 0.27
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (26 bp):
AAAAATAAAAATTGAGTACAAATAAA
Found at i:554738 original size:87 final size:87
Alignment explanation
Indices: 554627--554789 Score: 267
Period size: 87 Copynumber: 1.9 Consensus size: 87
554617 AATCCTGAAT
*
554627 ATTTAATTTAATTAAAAATAATTTAATTAATTTGAAATAAT-AAATCCCTAATATGATTAGGGTA
1 ATTTAATTTAATTAAAAATAATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTA-GGTA
554691 ACTTGGATATAAGAGATTATTAA
65 ACTTGGATATAAGAGATTATTAA
*
554714 ATTTAA-TTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGTA
1 ATTTAATTTAATTAAAAATA-ATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGTA
*
554778 ACTTGGCTATAA
65 ACTTGGATATAA
554790 AAGGGTGTTG
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
86 12 0.17
87 42 0.59
88 17 0.24
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.39
Consensus pattern (87 bp):
ATTTAATTTAATTAAAAATAATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGTAA
CTTGGATATAAGAGATTATTAA
Found at i:559620 original size:44 final size:44
Alignment explanation
Indices: 559557--559644 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
559547 AAAGAGAACG
559557 GATGAATAAGATTCCATATGCTTCGGCTATTGGTTCTATAATGT
1 GATGAATAAGATTCCATATGCTTCGGCTATTGGTTCTATAATGT
559601 GATGAATAAGATTCCATATGCTTCGGCTATTGGTTCTATAATGT
1 GATGAATAAGATTCCATATGCTTCGGCTATTGGTTCTATAATGT
559645 ATGCCATGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (44 bp):
GATGAATAAGATTCCATATGCTTCGGCTATTGGTTCTATAATGT
Found at i:566497 original size:54 final size:53
Alignment explanation
Indices: 566409--566513 Score: 129
Period size: 54 Copynumber: 2.0 Consensus size: 53
566399 ATACAAGGTA
**
566409 CATGCATTGCACCAAAGTGCCAAAATGGAAATTCACAAACTTATTATGAATTC
1 CATGCATTGCACCAAAGTGCCAAAATGGAAATTCACAAACACATTATGAATTC
* * * ** *
566462 CATGGATTGCACACATAGTGCCGAAATGGTTATTCATAAACACATTATGAAT
1 CATGCATTGCAC-CAAAGTGCCAAAATGGAAATTCACAAACACATTATGAAT
566514 ACAATGTGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
53 11 0.26
54 32 0.74
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (53 bp):
CATGCATTGCACCAAAGTGCCAAAATGGAAATTCACAAACACATTATGAATTC
Found at i:566535 original size:54 final size:54
Alignment explanation
Indices: 566414--566528 Score: 126
Period size: 54 Copynumber: 2.1 Consensus size: 54
566404 AGGTACATGC
* * ** * *
566414 ATTGCAC-CAAAGTGCCAAAATGGAAATTCACAAACTTATTATGAATTCCATGG
1 ATTGCACACATAGTGCCGAAATGGAAATTCACAAACACATTATGAATACAATGG
** *
566467 ATTGCACACATAGTGCCGAAATGGTTATTCATAAACACATTATGAATACAATGTG
1 ATTGCACACATAGTGCCGAAATGGAAATTCACAAACACATTATGAATACAATG-G
566522 -TTGCACA
1 ATTGCACA
566529 TTTAGTGTCG
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
53 7 0.14
54 43 0.84
55 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (54 bp):
ATTGCACACATAGTGCCGAAATGGAAATTCACAAACACATTATGAATACAATGG
Found at i:568464 original size:136 final size:135
Alignment explanation
Indices: 568220--568737 Score: 700
Period size: 136 Copynumber: 3.8 Consensus size: 135
568210 GGGTATTATA
* * * *
568220 GATTTGAAATGTCGTGAATCAAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTATTCTCC
1 GATTCGAAATCTCGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * * *
568285 CTTCGA-CGGATGAGTACTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCTTTAAGCAAGG
66 C-TCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAG-AAGG
* *
568349 TGTTACT
129 TATTGCT
* * *
568356 GATTTGAAATACT-GTGAATCGAGCAATAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATC
1 GATTCGAAAT-CTCGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTC
* * * *
568420 CCTTTATCGGATGAGTTCTTCTCATTATGAACTCTCAATTGGAAATGTTGATCCCTCAAGTGAGG
65 CCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAG-AAGG
568485 TATTGCT
129 TATTGCT
* * *
568492 GATTCGAAATGC-CGTGAATCGAGCAATAGGTCCAACAAGTTCTTTTCATTATAAACTTCTTCTC
1 GATTCGAAAT-CTCGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTC
* * * *
568556 CCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTCGAAATGTCAATCCCTCAAGAGTGG
65 CCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGA-AGG
568621 TATTGCT
129 TATTGCT
* * *
568628 GATTCGAAATGTCATGAATCGAGCAATAGGTCGAACAAGTTCTTTTCATTATGAACTTCTTCTCC
1 GATTCGAAATCTCGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* *
568693 CTCTATTGGATGAGTTCTTCTCATTATAAACTCTCCATTGGAAAT
66 CTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
568738 TTTCATTGGT
Statistics
Matches: 338, Mismatches: 39, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
135 2 0.01
136 335 0.99
137 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (135 bp):
GATTCGAAATCTCGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
CTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGAAGGTA
TTGCT
Found at i:569121 original size:42 final size:42
Alignment explanation
Indices: 569054--569167 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
569044 CATCCTTCTT
* * * * * *
569054 GAAAGTCTTATGGATGGCCCAAAGGACTTAATCACCATGCTG
1 GAAAGACTTATAGATGGCCCGAAGGACTTAAGCAACATGCTC
* *
569096 GAAAGACTTATAGATGACCCGAAGGATTTAAGCAACATGCTC
1 GAAAGACTTATAGATGGCCCGAAGGACTTAAGCAACATGCTC
* * *
569138 AAAAGCCTTACTA-ATGGCTCGAAGGACTTA
1 GAAAGACTTA-TAGATGGCCCGAAGGACTTA
569168 CAAAGTAAGA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 56 0.97
43 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (42 bp):
GAAAGACTTATAGATGGCCCGAAGGACTTAAGCAACATGCTC
Found at i:569548 original size:54 final size:54
Alignment explanation
Indices: 569464--569629 Score: 201
Period size: 54 Copynumber: 3.1 Consensus size: 54
569454 TTACAGTTAT
* * * * *
569464 CATCAAGAAGCCCTTAAAAATTAGGCTTAACTTCTTTAAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAAATAGGATTAACTTCTTTAAAAATTCATTTGAAGA
* * *
569518 CATTAAGAAACCCCTAAAAAATAGGATTAACTTC-TGAAAAATTCATTTGGAGA
1 CATCAAGAAACCCCTAAAAAATAGGATTAACTTCTTTAAAAATTCATTTGAAGA
* ** *
569571 CATCAAGAAACCCCT-AAAAATCATGATTAGTTTCTTTTAAAATTCATTTGAAGA
1 CATCAAGAAACCCCTAAAAAAT-AGGATTAACTTCTTTAAAAATTCATTTGAAGA
569625 CATCA
1 CATCA
569630 CATTATTTGG
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
52 6 0.06
53 39 0.41
54 50 0.53
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (54 bp):
CATCAAGAAACCCCTAAAAAATAGGATTAACTTCTTTAAAAATTCATTTGAAGA
Found at i:571624 original size:20 final size:19
Alignment explanation
Indices: 571601--571665 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
571591 GTTTTCTTTC
571601 TTCTTTTATCTTTTTTGGCT
1 TTCTTTTATCTTTTTT-GCT
* *
571621 TTCTTTTCTCTTTTTT-TT
1 TTCTTTTATCTTTTTTGCT
*
571639 TTCTTTTTTTTCTTTTTTGCT
1 TTC--TTTTATCTTTTTTGCT
571660 TTCTTT
1 TTCTTT
571666 ACCTCTATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.11
19 3 0.08
20 27 0.71
21 4 0.11
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (19 bp):
TTCTTTTATCTTTTTTGCT
Found at i:571633 original size:11 final size:11
Alignment explanation
Indices: 571619--571656 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
571609 TCTTTTTTGG
*
571619 CTTTCTTTTCT
1 CTTTTTTTTCT
*
571630 CTTTTTTTTTT
1 CTTTTTTTTCT
571641 CTTTTTTTTCT
1 CTTTTTTTTCT
571652 -TTTTT
1 CTTTTT
571657 GCTTTCTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
CTTTTTTTTCT
Found at i:571680 original size:40 final size:40
Alignment explanation
Indices: 571597--571686 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
571587 GTATGTTTTC
* * *
571597 TTTCTTCTTTTATCTTTTTTGGCTTTCTTTTCTCTTTTTTT
1 TTTCTT-TTTTATCTTTTTTGGCTTTCTTTCCTCTATTCTT
*
571638 TTTCTTTTTTTTCTTTTTT-GCTTTCTTTACCTCTATTCTT
1 TTTCTTTTTTATCTTTTTTGGCTTTCTTT-CCTCTATTCTT
*
571678 TTTCCTTTT
1 TTTCTTTTT
571687 CTCTACATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 9 0.21
40 28 0.65
41 6 0.14
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.74
Consensus pattern (40 bp):
TTTCTTTTTTATCTTTTTTGGCTTTCTTTCCTCTATTCTT
Found at i:576844 original size:19 final size:19
Alignment explanation
Indices: 576812--576850 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
576802 GGTTAAATCT
576812 GGGTCAGGTCTAGTTTTAG
1 GGGTCAGGTCTAGTTTTAG
* *
576831 GGGTCGGGTTTAGTTTTAG
1 GGGTCAGGTCTAGTTTTAG
576850 G
1 G
576851 CCTTGGCTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.08, G:0.41, T:0.38
Consensus pattern (19 bp):
GGGTCAGGTCTAGTTTTAG
Done.