Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 175 of 292
Found at i:52092862 original size:67 final size:64
Alignment explanation
Indices: 52092740--52092863 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 64
52092730 AGACATTATG
* * * *
52092740 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACTGGATGT
1 ATGTAGCTAGGTCGCATGCGTGATACTATGAGGACACAATGTAGACAAGAGAGCTACTGGATGT
* *
52092804 ATGTAGCTAGGTCGCATGCGTGGTTCTAGGTGAAGGACACAATGTAGACAAGAGAGCTAC
1 ATGTAGCTAGGTCGCATGCGTGATACTA--TG-AGGACACAATGTAGACAAGAGAGCTAC
52092864 GAGATAAACT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 25 0.49
66 2 0.04
67 24 0.47
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGCGTGATACTATGAGGACACAATGTAGACAAGAGAGCTACTGGATGT
Found at i:52093907 original size:4 final size:4
Alignment explanation
Indices: 52093898--52093922 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
52093888 TTATTAATAT
52093898 TTAC TTAC TTAC TTAC TTAC TTAC T
1 TTAC TTAC TTAC TTAC TTAC TTAC T
52093923 AAGCTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAC
Found at i:52095392 original size:42 final size:42
Alignment explanation
Indices: 52095359--52095641 Score: 374
Period size: 42 Copynumber: 6.8 Consensus size: 42
52095349 TCCTAGATAG
* *
52095359 GGTCTTACACAAAATTAGATATGATGCCGATGTCCCAGACAT
1 GGTCTTACACAAAATCAGATACGATGCCGATGTCCCAGACAT
*
52095401 GGTCTTACAC--AATCAGATACGATGCC-ATTTTCCCAGACAT
1 GGTCTTACACAAAATCAGATACGATGCCGA-TGTCCCAGACAT
* *
52095441 GGTCTTACACGAAATCAAATACGATGCCGATGTCCCAGACAT
1 GGTCTTACACAAAATCAGATACGATGCCGATGTCCCAGACAT
* * * *
52095483 GGCCTTACACGAAATCAAATACGATGCCGATGTCCTAGACAT
1 GGTCTTACACAAAATCAGATACGATGCCGATGTCCCAGACAT
* * * *
52095525 AGTCTTACTCAAAACCAGATATGATGCCGATGTCCCAGACAT
1 GGTCTTACACAAAATCAGATACGATGCCGATGTCCCAGACAT
* * * *
52095567 GGTCTTACGCAAAATCAAATACGATGCCAATGTCCCAAACAT
1 GGTCTTACACAAAATCAGATACGATGCCGATGTCCCAGACAT
*
52095609 GGTCTTACACAAAATCAGATACGATGCCAATGT
1 GGTCTTACACAAAATCAGATACGATGCCGATGT
52095642 TGCTTTAGAA
Statistics
Matches: 213, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.00
40 35 0.16
42 176 0.83
43 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (42 bp):
GGTCTTACACAAAATCAGATACGATGCCGATGTCCCAGACAT
Found at i:52102068 original size:40 final size:39
Alignment explanation
Indices: 52102038--52102221 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 39
52102028 GCTACTCGTT
*
52102038 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCG
*
52102076 CACAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCG
1 --CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCG
*
52102116 CACAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCG
1 CA-AATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCG
* * *
52102154 CACAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTCACTTAG
1 --CAAATGCCTTCGGGA-CTTAGCCCGGATTATAGTAAC-TCG
*
52102195 CACAAAGCCTTCGGGACTTAGCCCGGA
1 CA-AATGCCTTCGGGACTTAGCCCGGA
52102222 CATCATTCGA
Statistics
Matches: 125, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
38 25 0.20
39 23 0.18
40 70 0.56
41 7 0.06
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCG
Found at i:52102148 original size:78 final size:81
Alignment explanation
Indices: 52102040--52102221 Score: 257
Period size: 78 Copynumber: 2.3 Consensus size: 81
52102030 TACTCGTTCA
* *
52102040 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
*
52102103 ATTTAGTAAC-TCGCAC
65 ATTTAGTAACTTAGCAC
**
52102119 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
52102182 TTTAGTCACTTAGCAC
66 TTTAGTAACTTAGCAC
*
52102198 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
52102222 CATCATTCGA
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
77 3 0.03
78 49 0.53
79 29 0.32
80 11 0.12
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TTTAGTAACTTAGCAC
Found at i:52106840 original size:45 final size:45
Alignment explanation
Indices: 52106776--52106992 Score: 343
Period size: 45 Copynumber: 4.9 Consensus size: 45
52106766 TGTACAGTAC
* *
52106776 TATTCGTGCCTTTGAGCCTAGCAGGCTATAATGCCGTTGAGATAT
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
52106821 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
*
52106866 TATTCGGGCCTTTGAGCCTCA-CAGGCTATGATGCCGGTGAGATAT
1 TATTCGGGCCTTTGAGCCT-AGCAGGCTATAATGCCGGTGAGATAT
52106911 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
* * *
52106956 TATTTGGGCC-TCGAGCCTAGCAGGCGA-AATG-CGGTGA
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
52106993 ATGAATTCGG
Statistics
Matches: 163, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
42 6 0.04
43 4 0.02
44 16 0.10
45 136 0.83
46 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
Found at i:52114884 original size:45 final size:45
Alignment explanation
Indices: 52114820--52115037 Score: 359
Period size: 45 Copynumber: 4.9 Consensus size: 45
52114810 TGTACAGTAC
*
52114820 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
52114865 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
* * *
52114910 TATTCGGGCCTTTGCGCCTCGCAGGCTATGATGCCGGTGAGATAT
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
52114955 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
* * *
52115000 TATTCGGGCC-TCGAGCCTAGCAGGCGA-AATACCGGTGA
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
52115038 ATGAATTTGG
Statistics
Matches: 163, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
43 10 0.06
44 15 0.09
45 138 0.85
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
Found at i:52116376 original size:2 final size:2
Alignment explanation
Indices: 52116369--52116402 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
52116359 ACCAGAACAG
52116369 AT AT AT AT 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 AT AT AT AT
52116403 GTGGCGAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52117191 original size:27 final size:27
Alignment explanation
Indices: 52117131--52117203 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
52117121 TTCTACCTTA
* *
52117131 CAAGGGTATTTTTGTAATTTCACAAAT
1 CAAGGGTATTTTAGTAATTTCACAAAC
* * * * *
52117158 GAGGGGTATTTTGGTAATTTTATAAAC
1 CAAGGGTATTTTAGTAATTTCACAAAC
52117185 CAAGGGTATTTTAGTAATT
1 CAAGGGTATTTTAGTAATT
52117204 CTACAACTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.41
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTTCACAAAC
Found at i:52123064 original size:40 final size:40
Alignment explanation
Indices: 52122992--52123193 Score: 268
Period size: 40 Copynumber: 5.0 Consensus size: 40
52122982 CAGGATTTAA
* *
52122992 CCGGATATAGCT-ACTCGCTC-AATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
52123031 CTGGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
52123071 CCGGATATAGTAGCTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
52123111 CCGGATGTAATAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
52123151 CCGGA-ACTAGTCACTAGCGCA-AAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACT--CGCACAAATGCCTTCGGGACTTAGC
52123192 CC
1 CC
52123194 AGTTATCATC
Statistics
Matches: 146, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.01
39 16 0.11
40 103 0.71
41 22 0.15
42 4 0.03
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:52124354 original size:5 final size:5
Alignment explanation
Indices: 52124340--52124371 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
52124330 TTAAGCTAAC
52124340 AAAT- AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAA
52124372 ACATGCATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:52136726 original size:43 final size:42
Alignment explanation
Indices: 52136622--52136726 Score: 122
Period size: 43 Copynumber: 2.5 Consensus size: 42
52136612 GAGATTTATG
* * ** *
52136622 TGTAATACCAGGTCTGGGACATCGACATCGTATTTGATTTCA
1 TGTAAGACCACGTCTGGGACAGAGACATCGTATTTGATTACA
* *
52136664 TGTAAGACC-CTGTCAGGGACAGAGGCATCGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGACAGAGACATCG-TATTTGATTACA
52136707 TGTAAGACCACGTCTGGGAC
1 TGTAAGACCACGTCTGGGAC
52136727 GTTGGCATTG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 23 0.44
43 28 0.54
44 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACAGAGACATCGTATTTGATTACA
Found at i:52146350 original size:27 final size:27
Alignment explanation
Indices: 52146114--52146349 Score: 312
Period size: 27 Copynumber: 8.7 Consensus size: 27
52146104 GGGTATTTCG
** *
52146114 GTCATTTTATCACATGAA-GAAAAAATT
1 GTCATTTTATCACAT-AAGGGCAAAATC
* * *
52146141 GACATTTTATCACGTGAGGGCAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
*
52146168 GTCATTTTATCACATGAGGGCAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
* *
52146195 ATCATTTTATCACATAAGGGTAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
* *
52146222 GTCATTTTATCACATAAAGGCAATATC
1 GTCATTTTATCACATAAGGGCAAAATC
* *
52146249 GTCATTTTATCACATAAGGGTAAAATT
1 GTCATTTTATCACATAAGGGCAAAATC
* *
52146276 GTCATTTTATCACATAAGCGCAATATC
1 GTCATTTTATCACATAAGGGCAAAATC
*
52146303 GTCATTTTATCACATAAGGGTAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
52146330 GTCATTTTATCACATAAGGG
1 GTCATTTTATCACATAAGGG
52146350 TTCAACTATG
Statistics
Matches: 182, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 1 0.01
27 181 0.99
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (27 bp):
GTCATTTTATCACATAAGGGCAAAATC
Found at i:52158041 original size:42 final size:40
Alignment explanation
Indices: 52157995--52158085 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 40
52157985 ATAAAAACTA
*
52157995 AAATAAAAATAATATTAAAG-AAAA-TGAAAATAAAAAGTACTT
1 AAATAAAAATAA-A-TAAAGAAAAAGTGAAAATAAAAA-TA-AT
*
52158037 AAAT-AAGATAAATAAAGATAAAAGTGAAAATAAAAATAAT
1 AAATAAAAATAAATAAAGA-AAAAGTGAAAATAAAAATAAT
52158077 AAATAAAAA
1 AAATAAAAA
52158086 GTTTTTAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
39 5 0.12
40 6 0.14
41 15 0.36
42 16 0.38
ACGTcount: A:0.70, C:0.01, G:0.08, T:0.21
Consensus pattern (40 bp):
AAATAAAAATAAATAAAGAAAAAGTGAAAATAAAAATAAT
Found at i:52161000 original size:2 final size:2
Alignment explanation
Indices: 52160993--52161026 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
52160983 CGGCTCTAGC
52160993 AT AT AT AT 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 AT AT AT AT
52161027 GTTTGCACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52161825 original size:39 final size:39
Alignment explanation
Indices: 52161772--52161895 Score: 146
Period size: 38 Copynumber: 3.2 Consensus size: 39
52161762 CCGCGTCAAT
* *
52161772 TCCCGAA-GCATTTGTGCGAGTTACCAAACCGGGTTAAG
1 TCCCGAAGGCATTTGTGCGAGTTACTAAACCGGGCTAAG
*
52161810 TCCCGAAGGCATTTGTGCGAG-TACTAAATCC-GGCTAAT
1 TCCCGAAGGCATTTGTGCGAGTTACTAAA-CCGGGCTAAG
* * * *
52161848 TCCCGAAGGCAATTGTGCGAATCACTATAACCGGGCTATG
1 TCCCGAAGGCATTTGTGCGAGTTACTA-AACCGGGCTAAG
52161888 TCCCGAAG
1 TCCCGAAG
52161896 ACAATCGAGC
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
38 37 0.51
39 21 0.29
40 15 0.21
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (39 bp):
TCCCGAAGGCATTTGTGCGAGTTACTAAACCGGGCTAAG
Found at i:52166102 original size:39 final size:38
Alignment explanation
Indices: 52166053--52166166 Score: 156
Period size: 39 Copynumber: 2.9 Consensus size: 38
52166043 TATCACGATT
*
52166053 TGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAAC
1 TGCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAAC
* *
52166092 TGCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCTAC
1 TGCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAAC
*
52166131 TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAA
1 T-GCACAA-TGCCTTCGGGTCTTAGCCCGGATATAA
52166167 TTTCCAGCAT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
39 38 0.57
40 29 0.43
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (38 bp):
TGCACAATGCCTTCGGGTCTTAGCCCGGATATAACAAC
Found at i:52166160 original size:40 final size:40
Alignment explanation
Indices: 52166022--52166204 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
52166012 CCGCACCAAG
* * * * * * * *
52166022 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* *
52166062 GCCTTCGGGTCTTAGCCCGGATTTAACAACT-GCACGAA-T
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCAC-AATT
*
52166101 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* * * * *
52166141 GCCTTCGGGTCTTAACCCGGATATAATTTCCAGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* *
52166181 GTCTTCGGGGCTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
52166205 CATTCAATTT
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
39 35 0.29
40 86 0.71
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
Found at i:52174173 original size:39 final size:38
Alignment explanation
Indices: 52174115--52174300 Score: 155
Period size: 39 Copynumber: 4.8 Consensus size: 38
52174105 CCGCACCAAG
* * *
52174115 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAA-T
1 GCCTTCGGGTCTTAGCCCGGATAT-AC-ATTTGCACAATT
* * *
52174154 GCCTTCGGGTCTTAGCCCGGATTTAACAAGTGGCACGAA-T
1 GCCTTCGGGTCTTAGCCCGGATAT-AC-ATTTGCAC-AATT
* *
52174194 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATA-C-ATTTGCACAATT
* *
52174234 GCCTTCGGGTCTTAACCCGGATATA-ATTTCAGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATACATTT--GCACAATT
* *
52174273 GTCTTCGGGGCTTAGCCCGGATAT-CATT
1 GCCTTCGGGTCTTAGCCCGGATATACATT
52174301 CAATTTCTCA
Statistics
Matches: 122, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
37 2 0.02
39 62 0.51
40 58 0.48
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (38 bp):
GCCTTCGGGTCTTAGCCCGGATATACATTTGCACAATT
Found at i:52174197 original size:40 final size:39
Alignment explanation
Indices: 52174115--52174296 Score: 159
Period size: 40 Copynumber: 4.6 Consensus size: 39
52174105 CCGCACCAAG
* * * * * * *
52174115 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTAGCACAAT
* * *
52174154 GCCTTCGGGTCTTAGCCCGGATTTAACAAGTGGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTAGCAC-AAT
* *
52174194 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTAGCACAA-T
* *** *
52174234 GCCTTCGGGTCTTAACCCGGATATAATTTC-AGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTAGCACAA-T
* *
52174273 GTCTTCGGGGCTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
52174297 CATTCAATTT
Statistics
Matches: 120, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
39 59 0.49
40 61 0.51
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (39 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTAGCACAAT
Found at i:52179118 original size:38 final size:39
Alignment explanation
Indices: 52179026--52179187 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
52179016 TGTGTATGAA
*
52179026 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
52179065 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAA-
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
52179103 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
52179142 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
52179182 TGTGCG
1 TGTGCG
52179188 GGTTACCATA
Statistics
Matches: 114, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
38 36 0.32
39 61 0.54
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:52179203 original size:40 final size:39
Alignment explanation
Indices: 52179026--52179217 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
52179016 TGTGTATGAA
* *
52179026 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
52179065 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAA-
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
52179103 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
52179142 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
* ** * *
52179182 TGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGG
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGG
52179218 TGTTTTGAAC
Statistics
Matches: 137, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
38 36 0.26
39 61 0.45
40 40 0.29
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.23
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:52188838 original size:47 final size:48
Alignment explanation
Indices: 52188784--52188905 Score: 160
Period size: 48 Copynumber: 2.6 Consensus size: 48
52188774 ATTACATGTT
*
52188784 TAACCGTGGTATATCCACTTAGCACGACGTTA-ATGA-ATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACAT-ATATCAATATATG
* * *
52188831 TAACCGTGGCATATCAACTTAGCACCACGTTACATATATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATATATCAATATATG
*
52188879 TAA-TGATGGTATATCCACTTAGCACCA
1 TAACCG-TGGTATATCCACTTAGCACCA
52188906 TGTTTTTCCA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
47 31 0.48
48 34 0.52
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATATATCAATATATG
Found at i:52190973 original size:20 final size:19
Alignment explanation
Indices: 52190948--52190989 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
52190938 TCTTTCTTTA
*
52190948 TTTTTTTTATAATTTTGAAC
1 TTTTTTTCAT-ATTTTGAAC
52190968 TTTTTTTCATATTTTGAAC
1 TTTTTTTCATATTTTGAAC
52190987 TTT
1 TTT
52190990 GTACAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTTTCATATTTTGAAC
Found at i:52193015 original size:27 final size:26
Alignment explanation
Indices: 52192977--52193207 Score: 201
Period size: 27 Copynumber: 8.6 Consensus size: 26
52192967 ATACTTTAGT
*
52192977 TTACCAAAATACCACTAGTTTGTAAAA
1 TTACCAAAATACC-CTGGTTTGTAAAA
* * *
52193004 TTACTAGAATACCCTTGGTTTATAAAA
1 TTACCAAAATACCC-TGGTTTGTAAAA
*
52193031 TCACCAAAATACTCCTGGTTTGTAAAA
1 TTACCAAAATAC-CCTGGTTTGTAAAA
52193058 TTACCAAAATACCCCTGGTTTGTAAAA
1 TTACCAAAATA-CCCTGGTTTGTAAAA
* *
52193085 TTATCAAAATACCCCTAGTTTGTAAAA
1 TTACCAAAATA-CCCTGGTTTGTAAAA
* * *
52193112 TTATCAAAATATCCCTGATTTGTGAAA
1 TTACCAAAATA-CCCTGGTTTGTAAAA
** ***
52193139 TTACTGAAATACCCTCGACCTGTAAAA
1 TTACCAAAATACCCT-GGTTTGTAAAA
*** **
52193166 TTATTGAAATACCCTCGACTTGTAAAA
1 TTACCAAAATACCCT-GGTTTGTAAAA
*
52193193 TTACCAAAGTACCCT
1 TTACCAAAATACCCT
52193208 TAATTTACAG
Statistics
Matches: 173, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
26 5 0.03
27 165 0.95
28 3 0.02
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (26 bp):
TTACCAAAATACCCTGGTTTGTAAAA
Found at i:52193259 original size:27 final size:27
Alignment explanation
Indices: 52193136--52193260 Score: 90
Period size: 27 Copynumber: 4.6 Consensus size: 27
52193126 CTGATTTGTG
* * **
52193136 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCGAAATACCCTCGACTTACA
** **
52193163 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCGAAATACCCTCGACTTACA
** *
52193190 AAATTACC-AAAGTACCCTTAATTTACA
1 AAATTACCGAAA-TACCCTCGACTTACA
* *** *
52193217 GAATTACCGTTTTACCCTCGATTTACA
1 AAATTACCGAAATACCCTCGACTTACA
52193244 AAATTACCGAAATACCC
1 AAATTACCGAAATACCC
52193261 CTGTAGGGTA
Statistics
Matches: 77, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
26 3 0.04
27 74 0.96
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGACTTACA
Found at i:52193275 original size:27 final size:27
Alignment explanation
Indices: 52193245--52193439 Score: 277
Period size: 27 Copynumber: 7.3 Consensus size: 27
52193235 CGATTTACAA
52193245 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
52193272 AATTACC-AGAATACCCCTGTAGGGTAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
*
52193299 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
52193326 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
52193353 AATTACCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
52193380 AATTACTAAAATACCCCTATAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
52193407 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
52193433 AATTACC
1 AATTACC
52193440 ATTTTGTCCC
Statistics
Matches: 150, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
26 16 0.11
27 134 0.89
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:52194328 original size:19 final size:19
Alignment explanation
Indices: 52194304--52194367 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
52194294 ATTCTAATTT
52194304 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
* * **
52194323 TGATTCTAATT--CTAATTT
1 TGATTCT-GTTACCTGATAC
*
52194341 TGATTCTGTTACCTGATGC
1 TGATTCTGTTACCTGATAC
52194360 TGATTCTG
1 TGATTCTG
52194368 ATTTTAATTT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
17 2 0.06
18 11 0.32
19 19 0.56
20 2 0.06
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.47
Consensus pattern (19 bp):
TGATTCTGTTACCTGATAC
Found at i:52194332 original size:31 final size:31
Alignment explanation
Indices: 52194294--52194459 Score: 113
Period size: 31 Copynumber: 5.2 Consensus size: 31
52194284 TTGCATTCAC
52194294 ATTCTAATTTTGATTCTGTTACCTGATACTG
1 ATTCTAATTTTGATTCTGTTACCTGATACTG
*
52194325 ATTCTAATTCTAATTTTGATTCTGTTACCTGATGCTG
1 ------ATTCTAATTTTGATTCTGTTACCTGATACTG
* * *
52194362 ATTCTGATTTTAATT-TGGTTACCTGATACTA
1 ATTCTAATTTTGATTCT-GTTACCTGATACTG
* * * * * *
52194393 ATTTTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTAATTTTGATTCTGTTACCTGATACTG
* * * *
52194424 ATTCTGATTCTGATTTTGATT--CTGATTCTG
1 ATTCTAATTTTGATTCTG-TTACCTGATACTG
52194454 ATTCTA
1 ATTCTA
52194460 GTTCTGATAA
Statistics
Matches: 109, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
30 14 0.13
31 63 0.58
32 2 0.02
37 30 0.28
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (31 bp):
ATTCTAATTTTGATTCTGTTACCTGATACTG
Found at i:52194344 original size:37 final size:37
Alignment explanation
Indices: 52194294--52194377 Score: 141
Period size: 37 Copynumber: 2.3 Consensus size: 37
52194284 TTGCATTCAC
52194294 ATTCTAATTTTGATTCTGTTACCTGATACTGATTCTA
1 ATTCTAATTTTGATTCTGTTACCTGATACTGATTCTA
* *
52194331 ATTCTAATTTTGATTCTGTTACCTGATGCTGATTCTG
1 ATTCTAATTTTGATTCTGTTACCTGATACTGATTCTA
*
52194368 ATTTTAATTT
1 ATTCTAATTT
52194378 GGTTACCTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.51
Consensus pattern (37 bp):
ATTCTAATTTTGATTCTGTTACCTGATACTGATTCTA
Found at i:52194368 original size:6 final size:6
Alignment explanation
Indices: 52194294--52194467 Score: 88
Period size: 6 Copynumber: 28.3 Consensus size: 6
52194284 TTGCATTCAC
* * * * * *
52194294 ATTCTA ATTTTG ATTCTG -TTACCTG ATACTG ATTCTA ATTCTA ATTTTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * * * *
52194343 ATTCTG -TTACCTG ATGCTG ATTCTG ATTTTA ATT-TG GTTACCTG ATACTA
1 ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG
* * * *
52194393 ATTTTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG ATTTTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
52194442 ATTCTG ATTCTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG A-TTCTG AT
52194468 AATGTTTCTT
Statistics
Matches: 126, Mismatches: 28, Indels: 28
0.69 0.15 0.15
Matches are distributed among these distances:
5 9 0.07
6 102 0.81
7 9 0.07
8 6 0.05
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:52205008 original size:36 final size:36
Alignment explanation
Indices: 52204961--52205032 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
52204951 AACCTAATGG
52204961 TCTAATTACCATTTAAGGACCTCTACTTCAATTATA
1 TCTAATTACCATTTAAGGACCTCTACTTCAATTATA
52204997 TCTAATTACCATTTAAGGACCTCTACTTCAATTATA
1 TCTAATTACCATTTAAGGACCTCTACTTCAATTATA
52205033 CTCTTCAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (36 bp):
TCTAATTACCATTTAAGGACCTCTACTTCAATTATA
Found at i:52205589 original size:53 final size:53
Alignment explanation
Indices: 52205490--52205593 Score: 131
Period size: 53 Copynumber: 2.0 Consensus size: 53
52205480 AGGTGTAATA
* *
52205490 AAATATTAGTTTTGTGGTGTTGGAGGTGTGAATATTCTATAGTGTATATATTT
1 AAATATTAGTTTTATGGTGTTGGAGGTGTGAATATTCTAGAGTGTATATATTT
* * *
52205543 AAATATTAGTTTTATGGTGTCTTG-GTTGTGAATGTTCTACGA-TGTATATAT
1 AAATATTAGTTTTATGGTGT-TGGAGGTGTGAATATTCTA-GAGTGTATATAT
52205594 ATTTGAAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
53 41 0.93
54 3 0.07
ACGTcount: A:0.26, C:0.04, G:0.23, T:0.47
Consensus pattern (53 bp):
AAATATTAGTTTTATGGTGTTGGAGGTGTGAATATTCTAGAGTGTATATATTT
Found at i:52220425 original size:43 final size:41
Alignment explanation
Indices: 52220368--52220521 Score: 157
Period size: 43 Copynumber: 3.6 Consensus size: 41
52220358 ATGCCATATC
* * * *
52220368 CCAGATATGGTCTTACATGTTATCAAATATCGATGCCACTGT
1 CCAGACATGGTCTTACACGTAATCAAATA-CGATGCCAATGT
* *
52220410 CCAAGACA-GAGTCTTACACGTAATCGATTAACGATGCCAATGTT
1 CC-AGACATG-GTCTTACACGTAATCAAAT-ACGATGCCAATG-T
* *
52220454 CCAGACATGGTCTTACACGTAATCACAATACAAAGCCAATGT
1 CCAGACATGGTCTTACACGTAATCA-AATACGATGCCAATGT
*
52220496 CCTAGACATGGTCTTACATGTAATCA
1 CC-AGACATGGTCTTACACGTAATCA
52220522 CATCTCGGTA
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
42 6 0.06
43 81 0.86
44 7 0.07
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (41 bp):
CCAGACATGGTCTTACACGTAATCAAATACGATGCCAATGT
Found at i:52224654 original size:49 final size:49
Alignment explanation
Indices: 52224595--52224694 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
52224585 CCCAAAAGAG
*
52224595 ATCATTGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
1 ATCATCGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
52224644 ATCATCGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
1 ATCATCGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
52224693 AT
1 AT
52224695 TCAAACATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (49 bp):
ATCATCGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
Found at i:52227290 original size:43 final size:41
Alignment explanation
Indices: 52227233--52227386 Score: 157
Period size: 43 Copynumber: 3.6 Consensus size: 41
52227223 ATGCCATATC
* * * *
52227233 CCAGATATGGTCTTACATGTTATCAAATATCGATGCCACTGT
1 CCAGACATGGTCTTACACGTAATCAAATA-CGATGCCAATGT
* *
52227275 CCAAGACA-GAGTCTTACACGTAATCGATTAACGATGCCAATGTT
1 CC-AGACATG-GTCTTACACGTAATCAAAT-ACGATGCCAATG-T
* *
52227319 CCAGACATGGTCTTACACGTAATCACAATACAAAGCCAATGT
1 CCAGACATGGTCTTACACGTAATCA-AATACGATGCCAATGT
*
52227361 CCTAGACATGGTCTTACATGTAATCA
1 CC-AGACATGGTCTTACACGTAATCA
52227387 CATCTCGGTA
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
42 6 0.06
43 81 0.86
44 7 0.07
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (41 bp):
CCAGACATGGTCTTACACGTAATCAAATACGATGCCAATGT
Found at i:52231519 original size:49 final size:49
Alignment explanation
Indices: 52231460--52231559 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
52231450 CCCAAAAGAG
*
52231460 ATCATTGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
1 ATCATCGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
52231509 ATCATCGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
1 ATCATCGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
52231558 AT
1 AT
52231560 TCAAACATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (49 bp):
ATCATCGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
Found at i:52234155 original size:43 final size:41
Alignment explanation
Indices: 52234098--52234251 Score: 157
Period size: 43 Copynumber: 3.6 Consensus size: 41
52234088 ATGCCATATC
* * * *
52234098 CCAGATATGGTCTTACATGTTATCAAATATCGATGCCACTGT
1 CCAGACATGGTCTTACACGTAATCAAATA-CGATGCCAATGT
* *
52234140 CCAAGACA-GAGTCTTACACGTAATCGATTAACGATGCCAATGTT
1 CC-AGACATG-GTCTTACACGTAATCAAAT-ACGATGCCAATG-T
* *
52234184 CCAGACATGGTCTTACACGTAATCACAATACAAAGCCAATGT
1 CCAGACATGGTCTTACACGTAATCA-AATACGATGCCAATGT
*
52234226 CCTAGACATGGTCTTACATGTAATCA
1 CC-AGACATGGTCTTACACGTAATCA
52234252 CATCTCGGTA
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
42 6 0.06
43 81 0.86
44 7 0.07
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (41 bp):
CCAGACATGGTCTTACACGTAATCAAATACGATGCCAATGT
Found at i:52238385 original size:49 final size:49
Alignment explanation
Indices: 52238326--52238425 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
52238316 CCCAAAAGAG
*
52238326 ATCATTGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
1 ATCATCGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
52238375 ATCATCGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
1 ATCATCGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
52238424 AT
1 AT
52238426 TCAAACATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (49 bp):
ATCATCGTAAACCATTTAATTACAAATGCTTTACTCAGCTATCCTTACA
Found at i:52241021 original size:43 final size:41
Alignment explanation
Indices: 52240964--52241117 Score: 150
Period size: 43 Copynumber: 3.6 Consensus size: 41
52240954 ATGCCATATC
* * *
52240964 CCAGATATGGTCTTACATGTTATCAAATATCGATGCCACTGT
1 CCAGACATGGTCTTACATGTAATCAAATA-CGATGCCAATGT
* * *
52241006 CCGAGACA-GAGTCTTACACGTAATCGATTAACGATGCCAATGTT
1 CC-AGACATG-GTCTTACATGTAATCAAAT-ACGATGCCAATG-T
* *
52241050 CCAGACATGGTCTTACACT-TAATCACAATACAAAGCCAATGT
1 CCAGACATGGTCTTACA-TGTAATCA-AATACGATGCCAATGT
52241092 CCTAGACATGGTCTTACATGTAATCA
1 CC-AGACATGGTCTTACATGTAATCA
52241118 CATCTCGGTA
Statistics
Matches: 92, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
42 7 0.08
43 78 0.85
44 7 0.08
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (41 bp):
CCAGACATGGTCTTACATGTAATCAAATACGATGCCAATGT
Found at i:52244689 original size:13 final size:13
Alignment explanation
Indices: 52244671--52244695 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52244661 ACAAAGAATA
52244671 AAATTTTCACACG
1 AAATTTTCACACG
52244684 AAATTTTCACAC
1 AAATTTTCACAC
52244696 ATATCAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:52254958 original size:9 final size:9
Alignment explanation
Indices: 52254944--52254970 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
52254934 GAAATGGGCC
52254944 GAAAATGGA
1 GAAAATGGA
52254953 GAAAATGGA
1 GAAAATGGA
52254962 GAAAATGGA
1 GAAAATGGA
52254971 CCCACGTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.33, T:0.11
Consensus pattern (9 bp):
GAAAATGGA
Found at i:52262954 original size:3 final size:3
Alignment explanation
Indices: 52262946--52263012 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
52262936 GTCTTGTTTA
52262946 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
52262994 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
52263013 TACATATTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:52265862 original size:26 final size:26
Alignment explanation
Indices: 52265833--52265882 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
52265823 TTTATACTGA
52265833 TTACTGGCAGCTTTGCTGCAATACCG
1 TTACTGGCAGCTTTGCTGCAATACCG
* *
52265859 TTACTGTCAGCTTTGCTGCGATAC
1 TTACTGGCAGCTTTGCTGCAATAC
52265883 TGATATTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCAATACCG
Found at i:52270834 original size:40 final size:40
Alignment explanation
Indices: 52270749--52270899 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
52270739 AATTGAATGA
* * *
52270749 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
52270789 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
52270830 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
52270869 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
52270900 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:52270913 original size:40 final size:40
Alignment explanation
Indices: 52270786--52270915 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
52270776 ATGCTGGAAA
* * * *
52270786 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
52270826 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
52270866 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
52270906 TTATATCCGG
1 TTATATCCGG
52270916 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:52286649 original size:40 final size:39
Alignment explanation
Indices: 52286543--52286655 Score: 136
Period size: 39 Copynumber: 2.8 Consensus size: 39
52286533 ATCACGATTT
* *
52286543 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTT
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
* * *
52286583 GCACGATGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
1 GCACAATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
* * *
52286622 GCACAATTGCCTTCGGGTATTAACCCGGTTATAA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATATAA
52286656 TTTCCAGCAT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
39 35 0.56
40 27 0.44
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
Found at i:52286670 original size:40 final size:40
Alignment explanation
Indices: 52286543--52286693 Score: 108
Period size: 40 Copynumber: 3.8 Consensus size: 40
52286533 ATCACGATTT
* * * * * **
52286543 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTT
1 GCACAATTGCCTTCGGGTATTAACCCGGATATAACTACCA
* * * * *
52286583 GCACGA-TGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
1 GCACAATTGCCTTCGGGTATTAACCCGGATATAACTACCA
* * *
52286622 GCACAATTGCCTTCGGGTATTAACCCGGTTATAATTTCCA
1 GCACAATTGCCTTCGGGTATTAACCCGGATATAACTACCA
* * * *
52286662 GCATAATTGTCTTCAGGG-CTTAGCCCGGATAT
1 GCACAATTGCCTTC-GGGTATTAACCCGGATAT
52286694 CATTCAATTT
Statistics
Matches: 91, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
39 34 0.37
40 54 0.59
41 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTATTAACCCGGATATAACTACCA
Found at i:52296592 original size:39 final size:39
Alignment explanation
Indices: 52296529--52296691 Score: 272
Period size: 39 Copynumber: 4.2 Consensus size: 39
52296519 ATTTGATGTG
52296529 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
* *
52296568 TATCTGGACTTAGGGTCCGTAGGCTATGTGCTGGAATTA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
52296607 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
* * *
52296646 TATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
*
52296685 TGTCCGG
1 TATCCGG
52296692 GCTAAAGTCC
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 116 1.00
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (39 bp):
TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
Found at i:52296724 original size:78 final size:78
Alignment explanation
Indices: 52296529--52296729 Score: 219
Period size: 78 Copynumber: 2.6 Consensus size: 78
52296519 ATTTGATGTG
** * * * * *
52296529 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCTGGACTTAGGGTCCGTAGGCTA
1 TATCCGGACTTAAAGTCCGCAGGCTATGAGCTAGAATTATATCCGGACTTAAGGTCCGCAGGCTA
* *
52296594 TGTGCTGGAATTA
66 CGTGCTGGAAATA
** * *
52296607 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGGCTA
1 TATCCGGACTTAAAGTCCGCAGGCTATGAGCTAGAATTATATCCGGACTTAAGGTCCGCAGGCTA
52296672 CGTGCTGGAAATA
66 CGTGCTGGAAATA
* * *
52296685 TGTCCGGGC-TAAAGTCCCGCAGGCT-TCGAGCTAGTATTATA-CCGG
1 TATCCGGACTTAAAGT-CCGCAGGCTAT-GAGCTAGAATTATATCCGG
52296730 GTTTAAATTC
Statistics
Matches: 109, Mismatches: 12, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
77 9 0.08
78 100 0.92
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.27
Consensus pattern (78 bp):
TATCCGGACTTAAAGTCCGCAGGCTATGAGCTAGAATTATATCCGGACTTAAGGTCCGCAGGCTA
CGTGCTGGAAATA
Found at i:52296945 original size:2 final size:2
Alignment explanation
Indices: 52296938--52296970 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
52296928 TCAAAGAAGA
52296938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52296971 GATTGATGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52302935 original size:20 final size:19
Alignment explanation
Indices: 52302907--52302955 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
52302897 TGTCCATGGG
52302907 CAAGCCACACAGGCATGTTC
1 CAAGCCACACAGGCATG-TC
* *
52302927 CAGGCCACACGGGCATGTC
1 CAAGCCACACAGGCATGTC
52302946 CAAGCCACAC
1 CAAGCCACAC
52302956 GGGCGTGTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.29, C:0.39, G:0.22, T:0.10
Consensus pattern (19 bp):
CAAGCCACACAGGCATGTC
Found at i:52302952 original size:19 final size:20
Alignment explanation
Indices: 52302907--52302959 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
52302897 TGTCCATGGG
*
52302907 CAAGCCACACAGGCATGTTC
1 CAAGCCACACGGGCATGTTC
*
52302927 CAGGCCACACGGGCATG-TC
1 CAAGCCACACGGGCATGTTC
52302946 CAAGCCACACGGGC
1 CAAGCCACACGGGC
52302960 GTGTGCCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.26, C:0.38, G:0.26, T:0.09
Consensus pattern (20 bp):
CAAGCCACACGGGCATGTTC
Found at i:52311921 original size:40 final size:40
Alignment explanation
Indices: 52311877--52311969 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
52311867 ACTATGATCG
* * *
52311877 GCACTAAGTGTGCGATTTGAAATAGCTTCGGCTATAAATA
1 GCACTAAGTGTGCGAATTGAAATAACATCGGCTATAAATA
* ** *
52311917 GCACTAAGTGTGCGAATTGGAATAACATCGGCTATATGTC
1 GCACTAAGTGTGCGAATTGAAATAACATCGGCTATAAATA
52311957 GCACTAAGTGTGC
1 GCACTAAGTGTGC
52311970 AATATTGAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (40 bp):
GCACTAAGTGTGCGAATTGAAATAACATCGGCTATAAATA
Found at i:52313051 original size:55 final size:55
Alignment explanation
Indices: 52312985--52313091 Score: 169
Period size: 55 Copynumber: 1.9 Consensus size: 55
52312975 GGGCACCCGG
* * * * *
52312985 GCGTGTGGCTAGTCGTGTGACCTAAGTCAGTGTCGACCACGGCTAAGGCACACCA
1 GCGTGTAGCTAGCCGTGTGACCCAAGTCAGTGTCGACCACGGCCAAGACACACCA
52313040 GCGTGTAGCTAGCCGTGTGACCCAAGTCAGTGTCGACCACGGCCAAGACACA
1 GCGTGTAGCTAGCCGTGTGACCCAAGTCAGTGTCGACCACGGCCAAGACACA
52313092 TGGGCATGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.23, C:0.29, G:0.30, T:0.18
Consensus pattern (55 bp):
GCGTGTAGCTAGCCGTGTGACCCAAGTCAGTGTCGACCACGGCCAAGACACACCA
Found at i:52317268 original size:37 final size:38
Alignment explanation
Indices: 52317174--52317343 Score: 254
Period size: 38 Copynumber: 4.5 Consensus size: 38
52317164 GCAGGGTATA
52317174 TGCTGG-AATTATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGTAA-TATATCCGGGTTAAATCCCGCAGGCTTCG
*
52317212 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCA
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
*
52317250 TGCT-ATAATATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
* * *
52317287 TGCTGGTAGTATATCCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
* *
52317325 TGCTGGTATTATATTCGGG
1 TGCTGGTAATATATCCGGG
52317344 CCTTCGTGCC
Statistics
Matches: 121, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
37 35 0.29
38 84 0.69
39 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (38 bp):
TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
Found at i:52317328 original size:38 final size:38
Alignment explanation
Indices: 52317146--52317343 Score: 242
Period size: 38 Copynumber: 5.2 Consensus size: 38
52317136 ATTTGATGTG
* * *
52317146 TATCCGGGCCTAAAACCCGCAGGGTATA-TGCTGG-AATTA
1 TATCCGGG-TTAAATCCCGCAGGCT-TAGTGCTGGTAA-TA
*
52317185 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAATA
*
52317223 TATCCGGGTTAAATCCCGCAGGCTTCA-TGCT-ATAATA
1 TATCCGGGTTAAATCCCGCAGGCTT-AGTGCTGGTAATA
* *
52317260 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAGTA
1 TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAATA
* *
52317298 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAATA
*
52317336 TATTCGGG
1 TATCCGGG
52317344 CCTTCGTGCC
Statistics
Matches: 141, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
37 35 0.25
38 96 0.68
39 10 0.07
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAATA
Found at i:52317384 original size:43 final size:43
Alignment explanation
Indices: 52317336--52317490 Score: 256
Period size: 43 Copynumber: 3.6 Consensus size: 43
52317326 GCTGGTATTA
52317336 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
52317379 TATTCGGGCATTCGTGCCTAGCAGGCTTCGTGCCGATGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* * * *
52317422 TATTTGGGCCTTCGTGCTTAGCAAGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
52317465 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
52317491 GTAATGCCGG
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 101 1.00
ACGTcount: A:0.12, C:0.25, G:0.32, T:0.31
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:52323670 original size:41 final size:40
Alignment explanation
Indices: 52323583--52323723 Score: 122
Period size: 40 Copynumber: 3.4 Consensus size: 40
52323573 GACTATGATC
* * * * **
52323583 GGCACTAAGTGTGCGATTTGAAAAAGCTTTGGCTATAAAT
1 GGCACTAAGTGTGCGAATTGGAATAGCTTGGGCTATATGT
*
52323623 AGCACTAAGTGTGCGAATTGGAATAGCTTGGGGCTATATGT
1 GGCACTAAGTGTGCGAATTGGAATAGCTT-GGGCTATATGT
* * **
52323664 GGCACTAAGTGTGC-AATATTGAGATAGTTTCGGTTTAATATGAT
1 GGCACTAAGTGTGCGAAT-TGGA-ATAGCTT-GGGCT-ATATG-T
52323708 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
52323724 TATTTTATAG
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
40 28 0.34
41 24 0.29
42 9 0.11
43 5 0.06
44 15 0.18
45 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.30
Consensus pattern (40 bp):
GGCACTAAGTGTGCGAATTGGAATAGCTTGGGCTATATGT
Found at i:52324644 original size:31 final size:31
Alignment explanation
Indices: 52324601--52324714 Score: 196
Period size: 31 Copynumber: 3.7 Consensus size: 31
52324591 TTAGTCTTGA
*
52324601 CATAT-ACT-GGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
52324630 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
52324661 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
52324692 CATATCACTGGACCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
52324715 ACTGTAAACG
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 5 0.06
30 3 0.04
31 73 0.90
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:52324783 original size:41 final size:42
Alignment explanation
Indices: 52324738--52324828 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
52324728 TGGCCCTTAG
*
52324738 GCCCATTTCAA-ATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
52324779 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
52324821 GCCCATTT
1 GCCCATTT
52324829 GGGGAGACTA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 11 0.23
42 37 0.77
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:52325009 original size:25 final size:25
Alignment explanation
Indices: 52324976--52325045 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
52324966 CTCTTTTAAT
*
52324976 AACTAGGGCAAAGCCCTTTCTGA-TA
1 AACTGGGGCAAAGCCCTTT-TGAGTA
*
52325001 AACTGGGGCAAAGCCCTTTTTAGTA
1 AACTGGGGCAAAGCCCTTTTGAGTA
* *
52325026 AACTGGGGTAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
52325046 AGCACTTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 2 0.05
25 38 0.95
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTGAGTA
Found at i:52325916 original size:27 final size:27
Alignment explanation
Indices: 52325855--52325918 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
52325845 GGCATATTCA
52325855 TCATTTTACCATACAAGGGTATTACGG
1 TCATTTTACCATACAAGGGTATTACGG
* * *
52325882 TCACTTTACCCTACAGGGGCT-TTACGG
1 TCATTTTACCATACAAGGG-TATTACGG
*
52325909 TCTTTTTACC
1 TCATTTTACC
52325919 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (27 bp):
TCATTTTACCATACAAGGGTATTACGG
Found at i:52326001 original size:27 final size:27
Alignment explanation
Indices: 52325949--52326184 Score: 184
Period size: 27 Copynumber: 8.7 Consensus size: 27
52325939 TTTCATCCTA
* * * *
52325949 AAGGGTGTTTTGGTAAATCTACAAACC
1 AAGGGTATTTCGGTAATTTTACAAACC
* **
52325976 AAGGGTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTCGGTAATTTTACAAACC
* ** * *
52326003 AATGGTATTTCTATAATTTTTAGAAAGTC
1 AAGGGTATTTCGGTAA-TTTTACAAA-CC
* ** *
52326032 AAGGGTATTTCTGTAATTTTGTAAATC
1 AAGGGTATTTCGGTAATTTTACAAACC
* * **
52326059 AGGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTCGGTAATTTTACAAACC
* *
52326086 GAGGGTATTTCGGTAATTTCACAAACC
1 AAGGGTATTTCGGTAATTTTACAAACC
* * *
52326113 AATGGTATTTCGATAATTTTACAAACT
1 AAGGGTATTTCGGTAATTTTACAAACC
* * *
52326140 AGGGGTATTTTGGTAATTTTACAAACT
1 AAGGGTATTTCGGTAATTTTACAAACC
* *
52326167 AGGGGTATTTTGGTAATT
1 AAGGGTATTTCGGTAATT
52326185 CTACCCTACA
Statistics
Matches: 169, Mismatches: 38, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
27 140 0.83
28 14 0.08
29 15 0.09
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
AAGGGTATTTCGGTAATTTTACAAACC
Found at i:52326201 original size:81 final size:81
Alignment explanation
Indices: 52326059--52326217 Score: 193
Period size: 81 Copynumber: 2.0 Consensus size: 81
52326049 TTTGTAAATC
*
52326059 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAATGGTATTTC
1 AGGGGTATTTTGGTAATTTTACAAATAGAGGGTATTTCGGTAATTTCACAAACCAATGGTATTTC
*
52326124 -GATAATTTTACAAACT
66 AG-TAATTTCACAAACT
* **
52326140 AGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTGGTAA-TTCTACCCTA-CAGA-GGTA
1 AGGGGTATTTTGGTAATTTTACAAA-TAGAGGGTATTTCGGTAATTTC-A-CAAACCA-ATGGTA
52326201 TTTCAGTAATTTCACAA
62 TTTCAGTAATTTCACAA
52326218 TCGAGGGTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
80 3 0.04
81 59 0.87
82 6 0.09
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAATAGAGGGTATTTCGGTAATTTCACAAACCAATGGTATTTC
AGTAATTTCACAAACT
Found at i:52326281 original size:54 final size:54
Alignment explanation
Indices: 52326216--52326399 Score: 280
Period size: 54 Copynumber: 3.4 Consensus size: 54
52326206 GTAATTTCAC
* * * *
52326216 AATCGAGGGTAAAACGATAATTTTGTAAA-CTGAGGTTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATC-GAGGGTAAAATGGTAATTCTATA
52326270 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
* * *
52326324 AATCGAGGGTAAAACGGTAATTTTGTAAATCAAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
*
52326378 AATCGAGGGTAAAATGGTAATT
1 AATCGAGGGTAAAACGGTAATT
52326400 CTACGAATCG
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
54 120 0.99
55 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (54 bp):
AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
Found at i:52326402 original size:27 final size:27
Alignment explanation
Indices: 52326216--52326399 Score: 253
Period size: 27 Copynumber: 6.8 Consensus size: 27
52326206 GTAATTTCAC
*
52326216 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* *
52326243 AA-CTGAGGTTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTTTGTA
52326270 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * *
52326297 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
52326324 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * * *
52326351 AATCAAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
52326378 AATCGAGGGTAAAATGGTAATT
1 AATCGAGGGTAAAACGGTAATT
52326400 CTACGAATCG
Statistics
Matches: 137, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
26 1 0.01
27 135 0.99
28 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:52326425 original size:81 final size:81
Alignment explanation
Indices: 52326259--52326433 Score: 242
Period size: 81 Copynumber: 2.2 Consensus size: 81
52326249 GGTTAAAATG
* * * *
52326259 GTAATTTTGTAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
1 GTAATTTTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTACA
* *
52326324 AATCGAGGGTAAAACG
66 AATCGAGGGCAAAACA
* *
52326340 GTAATTTTGTAAATCAAGGGTGAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTACG
1 GTAATTTTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTACA
***
52326405 AATCGAGGGCATTTCA
66 AATCGAGGGCAAAACA
*
52326421 GTAATTTGGTAAA
1 GTAATTTTGTAAA
52326434 CTAAAGTATT
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (81 bp):
GTAATTTTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTACA
AATCGAGGGCAAAACA
Found at i:52328336 original size:55 final size:55
Alignment explanation
Indices: 52328265--52328395 Score: 199
Period size: 55 Copynumber: 2.4 Consensus size: 55
52328255 CTTGGCCATG
* * * *
52328265 GCCAAGGCACATGGGCGTGTGGCTAGCCGTGTGACCCAAGTCAGTGTCGACCACA
1 GCCAAGGCACACGGGCGTGTAGCTAGCCATGTGACCCAAGTCAGCGTCGACCACA
*
52328320 GCCAAGGCACACGGGCGTGTAGCTAGCCATGTGACCCAAGTCAGCGTCGACCACG
1 GCCAAGGCACACGGGCGTGTAGCTAGCCATGTGACCCAAGTCAGCGTCGACCACA
* *
52328375 GCCAAGACACACGGGCATGTA
1 GCCAAGGCACACGGGCGTGTA
52328396 ATGTGGCCGT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 69 1.00
ACGTcount: A:0.24, C:0.31, G:0.31, T:0.14
Consensus pattern (55 bp):
GCCAAGGCACACGGGCGTGTAGCTAGCCATGTGACCCAAGTCAGCGTCGACCACA
Found at i:52342720 original size:24 final size:24
Alignment explanation
Indices: 52342688--52342739 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
52342678 ATGCTCTGCC
52342688 TCATCTTTAGAATAAATTAGAATA
1 TCATCTTTAGAATAAATTAGAATA
52342712 TCATCTTTAGAATAAATTAGAATA
1 TCATCTTTAGAATAAATTAGAATA
52342736 TCAT
1 TCAT
52342740 TGATGAACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (24 bp):
TCATCTTTAGAATAAATTAGAATA
Found at i:52349644 original size:2 final size:2
Alignment explanation
Indices: 52349637--52349668 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52349627 TCATGACATG
52349637 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
52349669 CTAGTCTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52361760 original size:27 final size:28
Alignment explanation
Indices: 52361730--52361792 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
52361720 CCCTATAGTA
*
52361730 TAGAATTACT-AAAATACCTTTGTAGGG
1 TAGAATTACTCAAAATACCCTTGTAGGG
* * *
52361757 TAGATTTA-TCGAGATACCCTTGTAGGG
1 TAGAATTACTCAAAATACCCTTGTAGGG
*
52361784 TAAAATTAC
1 TAGAATTAC
52361793 CATTTTGCCC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (28 bp):
TAGAATTACTCAAAATACCCTTGTAGGG
Found at i:52362245 original size:27 final size:26
Alignment explanation
Indices: 52362201--52362254 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
52362191 GGAGGAAGCA
* *
52362201 TTCTGGTGGCTATGCCACAAATATCTG
1 TTCTGATGGCTATACCAC-AATATCTG
*
52362228 TTCTGATGGCTTTACCACAATATCTG
1 TTCTGATGGCTATACCACAATATCTG
52362254 T
1 T
52362255 ACCTGGTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (26 bp):
TTCTGATGGCTATACCACAATATCTG
Found at i:52364607 original size:27 final size:27
Alignment explanation
Indices: 52364575--52364663 Score: 106
Period size: 27 Copynumber: 3.3 Consensus size: 27
52364565 CTTGATTTAC
*
52364575 AAAATTATTGAAATACCCCTGTAGGGT
1 AAAATTACTGAAATACCCCTGTAGGGT
*
52364602 AGAATTACTGAAATACCCCTGTAGGGT
1 AAAATTACTGAAATACCCCTGTAGGGT
* * * * * *
52364629 AAAATTACCGAGATACACTTGTGGGGA
1 AAAATTACTGAAATACCCCTGTAGGGT
52364656 AAAATTAC
1 AAAATTAC
52364664 CATTTTGCCC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (27 bp):
AAAATTACTGAAATACCCCTGTAGGGT
Found at i:52365115 original size:28 final size:27
Alignment explanation
Indices: 52365075--52365161 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 27
52365065 GGAAGCGTTT
*
52365075 TGGTTGCTATGCCACAAATATCTATTTC
1 TGGTGGCTATGCCACAAATATCT-TTTC
*
52365103 TGGTGGCTATGCCACAAATATCTGTTC
1 TGGTGGCTATGCCACAAATATCTTTTC
* * * *
52365130 TGGTAGCTCTACCAC-AATATCTGTATC
1 TGGTGGCTATGCCACAAATATCT-TTTC
52365157 TGGTG
1 TGGTG
52365162 ACTCTATCAC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
26 7 0.14
27 21 0.42
28 22 0.44
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.36
Consensus pattern (27 bp):
TGGTGGCTATGCCACAAATATCTTTTC
Found at i:52365144 original size:27 final size:25
Alignment explanation
Indices: 52365086--52365184 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 25
52365076 GGTTGCTATG
* * *
52365086 CCACAAATATCTATTTCTGGTGGCTATG
1 CCAC-AATATCT-GTTCTGGT-GCTCTA
52365114 CCACAAATATCTGTTCTGGTAGCTCTA
1 CCAC-AATATCTGTTCTGGT-GCTCTA
52365141 CCACAATATCTGTATCTGGTGACTCTA
1 CCACAATATCTGT-TCTGGTG-CTCTA
* *
52365168 TCACAATATTTGTTCTG
1 CCACAATATCTGTTCTG
52365185 ACAGCCATGC
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
26 14 0.22
27 37 0.59
28 12 0.19
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.36
Consensus pattern (25 bp):
CCACAATATCTGTTCTGGTGCTCTA
Found at i:52366594 original size:26 final size:24
Alignment explanation
Indices: 52366560--52366620 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 24
52366550 GATGTATTTG
* *
52366560 CTCATAAGAGCTTACTGTTTATCA
1 CTCAAAAGAGCTTACTGATTATCA
*
52366584 GCTCAAGAAGAGCTTACTGATTATGA
1 -CTCAA-AAGAGCTTACTGATTATCA
52366610 CTCAAAAGAGC
1 CTCAAAAGAGC
52366621 ACAAATGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 9 0.28
26 17 0.53
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (24 bp):
CTCAAAAGAGCTTACTGATTATCA
Found at i:52367888 original size:48 final size:48
Alignment explanation
Indices: 52367835--52367963 Score: 195
Period size: 48 Copynumber: 2.7 Consensus size: 48
52367825 GTGCTAAATA
*
52367835 TGCCTGTGCAAGACCATGTCTGGGACATGGCATCGGCGATGATATATG
1 TGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATG
* * * *
52367883 TGCCTGTGTAAGACTATGTCCGGGAAATGGCATCGGTGATGATATATG
1 TGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATG
**
52367931 TGCCTAAGTAAGACCATGTCTGGGACATGGCAT
1 TGCCTGTGTAAGACCATGTCTGGGACATGGCAT
52367964 TGTTACTTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (48 bp):
TGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATG
Found at i:52369593 original size:27 final size:27
Alignment explanation
Indices: 52369563--52369637 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
52369553 AATCTCATAT
* * *
52369563 CTGTAGGCTAGTATTACTGAACTGCCC
1 CTGTAGGGTAGAATTACTGAAATGCCC
*
52369590 CTGTAGGGTAGAATTACTGAAATGCCT
1 CTGTAGGGTAGAATTACTGAAATGCCC
*
52369617 TTGTAGGGTAGAATTACTGAA
1 CTGTAGGGTAGAATTACTGAA
52369638 TACCCTTGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (27 bp):
CTGTAGGGTAGAATTACTGAAATGCCC
Found at i:52369666 original size:27 final size:27
Alignment explanation
Indices: 52369636--52369890 Score: 158
Period size: 27 Copynumber: 9.4 Consensus size: 27
52369626 AGAATTACTG
52369636 AATACCCTTGGTTTACAAAATTACCAA
1 AATACCCTTGGTTTACAAAATTACCAA
*
52369663 AATACCAC-TGGTTTATAAAATTACCAA
1 AATACC-CTTGGTTTACAAAATTACCAA
* * ***
52369690 AATACCCCTAGTTTGTGAAATTACCAA
1 AATACCCTTGGTTTACAAAATTACCAA
** **
52369717 AATACCCTTAATTTGA-AAAATTACTGA
1 AATACCCTTGGTTT-ACAAAATTACCAA
** *
52369744 AATACCCTTAATTTAGAAAATTA-CAGA
1 AATACCCTTGGTTTACAAAATTACCA-A
* ** *
52369771 AATACCCCTAATTTACAAAATTACAAA
1 AATACCCTTGGTTTACAAAATTACCAA
* * *
52369798 AATACCCTTGACTTTAAAAAAATTA-TAGA
1 AATACCCTTG-GTTT-ACAAAATTACCA-A
* * **
52369827 AATACCATTGGTTTGCAAAATTACTGA
1 AATACCCTTGGTTTACAAAATTACCAA
* ** * *
52369854 AATACCTTTGGTTTGTAGATTTACCAA
1 AATACCCTTGGTTTACAAAATTACCAA
*
52369881 AACACCCTTG
1 AATACCCTTG
52369891 TAGGGTGAAA
Statistics
Matches: 185, Mismatches: 33, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.01
27 155 0.84
28 10 0.05
29 18 0.10
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (27 bp):
AATACCCTTGGTTTACAAAATTACCAA
Found at i:52369739 original size:81 final size:83
Alignment explanation
Indices: 52369636--52369859 Score: 201
Period size: 81 Copynumber: 2.7 Consensus size: 83
52369626 AGAATTACTG
* * * *
52369636 AATACCCTTG-GTTT-ACAAAATTACCAAAATACCACTGGTTTATAAAATTACCAAAATACCCCT
1 AATACCCTTGAATTTAAAAAAATTACTAAAATACCACTGGTTTACAAAATTACCAAAATACCCCT
* *** *
52369699 AGTTTGTGAAATTACCAA
66 AATTTACAAAATTACAAA
* * ** *
52369717 AATACCCTT-AATTT-GAAAAATTACTGAAATACC-CTTAATTTAGAAAATTA-CAGAAATACCC
1 AATACCCTTGAATTTAAAAAAATTACTAAAATACCAC-TGGTTTACAAAATTACCA-AAATACCC
52369778 CTAATTTACAAAATTACAAA
64 CTAATTTACAAAATTACAAA
* * * **
52369798 AATACCCTTGACTTTAAAAAAATTA-TAGAAATACCATTGGTTTGCAAAATTACTGAAATACC
1 AATACCCTTGAATTTAAAAAAATTACTA-AAATACCACTGGTTTACAAAATTACCAAAATACC
52369860 TTTGGTTTGT
Statistics
Matches: 112, Mismatches: 23, Indels: 14
0.75 0.15 0.09
Matches are distributed among these distances:
80 3 0.03
81 71 0.63
82 5 0.04
83 33 0.29
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (83 bp):
AATACCCTTGAATTTAAAAAAATTACTAAAATACCACTGGTTTACAAAATTACCAAAATACCCCT
AATTTACAAAATTACAAA
Found at i:52369805 original size:54 final size:53
Alignment explanation
Indices: 52369636--52369806 Score: 175
Period size: 54 Copynumber: 3.2 Consensus size: 53
52369626 AGAATTACTG
* * * ** *
52369636 AATACCCTTGGTTTACAAAATTACCAAAATACCACTGGTTTATAAAATTACCAA
1 AATACCCTTAGTTTAGAAAATTACCAAAATACCCCTAATTTA-AAAATTACAAA
* * * **
52369690 AATACCCCTAGTTT-GTGAAATTACCAAAATACCCTTAATTTGAAAAATTACTGA
1 AATACCCTTAGTTTAG-AAAATTACCAAAATACCCCTAATTT-AAAAATTACAAA
*
52369744 AATACCCTTAATTTAGAAAATTA-CAGAAATACCCCTAATTTACAAAATTACAAA
1 AATACCCTTAGTTTAGAAAATTACCA-AAATACCCCTAATTTA-AAAATTACAAA
52369798 AATACCCTT
1 AATACCCTT
52369807 GACTTTAAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
53 3 0.03
54 91 0.95
55 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (53 bp):
AATACCCTTAGTTTAGAAAATTACCAAAATACCCCTAATTTAAAAATTACAAA
Found at i:52369951 original size:27 final size:27
Alignment explanation
Indices: 52369908--52369981 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
52369898 AAATGACTAA
*
52369908 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
* ** *
52369935 AATGCCCCTGTAGGGTAAAGTGATCGT
1 AATACCCCTGTAGGGTAAAAAGACCGT
* *
52369962 AATACCGCTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
52369982 TGACAATTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 2 0.05
27 35 0.95
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:52370211 original size:27 final size:27
Alignment explanation
Indices: 52370125--52370220 Score: 113
Period size: 27 Copynumber: 3.6 Consensus size: 27
52370115 GGAAGTTCTG
* *
52370125 TACTGGTGACTATGTCAC-ATTCACTGT
1 TACTGGTGGCTATGCCACAATT-ACTGT
*
52370152 TACTGGTGGCTATGCCACAATTACTGA
1 TACTGGTGGCTATGCCACAATTACTGT
*
52370179 TACTGGTGGCTTTGCCACAATTACTGT
1 TACTGGTGGCTATGCCACAATTACTGT
* **
52370206 TTCTGGCAGCTATGC
1 TACTGGTGGCTATGC
52370221 TGCATCATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
27 56 0.95
28 3 0.05
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (27 bp):
TACTGGTGGCTATGCCACAATTACTGT
Found at i:52370412 original size:28 final size:28
Alignment explanation
Indices: 52370372--52370463 Score: 96
Period size: 28 Copynumber: 3.1 Consensus size: 28
52370362 ACTATATTGT
* * *
52370372 TACTGCATTGGGCTTAGGCCCACACTGC
1 TACTGTATAGGGCTTAGGCCCAAACTGC
52370400 TACTGTATAGGGCTTAGGCCCAAACTGTAC
1 TACTGTATAGGGCTTAGGCCCAAACTG--C
*
52370430 TGATGCTGTATAGGGCTTAGGCCCAGACTG-
1 T-A--CTGTATAGGGCTTAGGCCCAAACTGC
52370460 TACT
1 TACT
52370464 AATACTGAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
27 2 0.04
28 24 0.44
29 1 0.02
30 3 0.05
31 1 0.02
33 24 0.44
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.27
Consensus pattern (28 bp):
TACTGTATAGGGCTTAGGCCCAAACTGC
Found at i:52370444 original size:33 final size:33
Alignment explanation
Indices: 52370395--52370506 Score: 152
Period size: 33 Copynumber: 3.4 Consensus size: 33
52370385 TTAGGCCCAC
* *
52370395 ACTGCTACTGTATAGGGCTTAGGCCCAAACTGT
1 ACTGATACTGTATAGGGCTTAGGCCCAGACTGT
*
52370428 ACTGATGCTGTATAGGGCTTAGGCCCAGACTGT
1 ACTGATACTGTATAGGGCTTAGGCCCAGACTGT
* * * *
52370461 ACTAATACTGAATAGGGCTTTGGCCCAGATTGT
1 ACTGATACTGTATAGGGCTTAGGCCCAGACTGT
*
52370494 ATTGATACTGTAT
1 ACTGATACTGTAT
52370507 TATTCACTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (33 bp):
ACTGATACTGTATAGGGCTTAGGCCCAGACTGT
Found at i:52377857 original size:48 final size:48
Alignment explanation
Indices: 52377802--52377984 Score: 312
Period size: 48 Copynumber: 3.8 Consensus size: 48
52377792 ATCGTGCTAA
* *
52377802 ATGTGCCTGTGTAAGACCATGACTGGGACATGACATCGGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* *
52377850 ATGTGCCTGTGTAAGACCATGTCTGGGTCATGGCATTGGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
*
52377898 ATGTGCTTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
*
52377946 ATGTGCCTATGTAAGACCATGTCTGGGACATGGCATCGG
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGG
52377985 TATTTTAATT
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 126 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (48 bp):
ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
Found at i:52379729 original size:23 final size:23
Alignment explanation
Indices: 52379702--52379745 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
52379692 GTGTCCCCTC
52379702 GGGTACCCTTTTGAATTAAGTCG
1 GGGTACCCTTTTGAATTAAGTCG
52379725 GGGTACCCTTTTGAATTAAGT
1 GGGTACCCTTTTGAATTAAGT
52379746 AGGTATACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (23 bp):
GGGTACCCTTTTGAATTAAGTCG
Found at i:52379754 original size:23 final size:23
Alignment explanation
Indices: 52379705--52379756 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
52379695 TCCCCTCGGG
* *
52379705 TACCCTTTTGAATTAAGTCGGGG
1 TACCCTTTTGAATTAAGTAGGGA
*
52379728 TACCCTTTTGAATTAAGTAGGTA
1 TACCCTTTTGAATTAAGTAGGGA
52379751 TACCCT
1 TACCCT
52379757 ATAGTTTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (23 bp):
TACCCTTTTGAATTAAGTAGGGA
Found at i:52381091 original size:13 final size:13
Alignment explanation
Indices: 52381073--52381097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52381063 AATCCTAAAC
52381073 GAAATAGAGAGAA
1 GAAATAGAGAGAA
52381086 GAAATAGAGAGA
1 GAAATAGAGAGA
52381098 CGAGGGAAAA
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:0.60, C:0.00, G:0.32, T:0.08
Consensus pattern (13 bp):
GAAATAGAGAGAA
Found at i:52389282 original size:27 final size:27
Alignment explanation
Indices: 52389252--52389341 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
52389242 GTGTACCTGA
* *
52389252 ACCCTAATGAGATAAAATGACTATTTT
1 ACCCTTATGAGATAAAATGACGATTTT
* *
52389279 ACCCTTATGTGATAAAATAACGATTTT
1 ACCCTTATGAGATAAAATGACGATTTT
* * *
52389306 TCCCTTATGAGGTAAAATGACGGTTTT
1 ACCCTTATGAGATAAAATGACGATTTT
*
52389333 GCCCTTATG
1 ACCCTTATG
52389342 TGGCAAAATA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (27 bp):
ACCCTTATGAGATAAAATGACGATTTT
Found at i:52389323 original size:54 final size:54
Alignment explanation
Indices: 52389253--52389368 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
52389243 TGTACCTGAA
* * * *
52389253 CCCTAATGAGATAAAATGACTATTTTACCCTTATGTGATAAAATAACGATTTTT
1 CCCTTATGAGATAAAATGACGATTTTACCCTTATGTGACAAAATAACGATTTTG
* * * * *
52389307 CCCTTATGAGGTAAAATGACGGTTTTGCCCTTATGTGGCAAAATAACTATTTTG
1 CCCTTATGAGATAAAATGACGATTTTACCCTTATGTGACAAAATAACGATTTTG
*
52389361 CCCCTATG
1 CCCTTATG
52389369 TGATGTACGT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (54 bp):
CCCTTATGAGATAAAATGACGATTTTACCCTTATGTGACAAAATAACGATTTTG
Found at i:52389349 original size:27 final size:27
Alignment explanation
Indices: 52389264--52389370 Score: 115
Period size: 27 Copynumber: 4.0 Consensus size: 27
52389254 CCTAATGAGA
* * * *
52389264 TAAAATGACTATTTTACCCTTATGTGA
1 TAAAATAACGATTTTGCCCTTATGTGG
* *
52389291 TAAAATAACGATTTTTCCCTTATGAGG
1 TAAAATAACGATTTTGCCCTTATGTGG
* *
52389318 TAAAATGACGGTTTTGCCCTTATGTGG
1 TAAAATAACGATTTTGCCCTTATGTGG
* * *
52389345 CAAAATAACTATTTTGCCCCTATGTG
1 TAAAATAACGATTTTGCCCTTATGTG
52389371 ATGTACGTGC
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (27 bp):
TAAAATAACGATTTTGCCCTTATGTGG
Found at i:52389737 original size:18 final size:19
Alignment explanation
Indices: 52389693--52389744 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
52389683 GGATTTGCAT
*
52389693 ACTG-TTTACTGTTACTGT
1 ACTGATTTACTGTTACTGC
52389711 ACTGA-TTACTGTTACTGC
1 ACTGATTTACTGTTACTGC
*
52389729 ACT-ATTTACTATTACT
1 ACTGATTTACTGTTACT
52389745 AAATGGGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 1 0.03
18 29 0.97
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (19 bp):
ACTGATTTACTGTTACTGC
Found at i:52393064 original size:41 final size:41
Alignment explanation
Indices: 52393007--52393156 Score: 221
Period size: 41 Copynumber: 3.7 Consensus size: 41
52392997 TCGGGGTTTA
52393007 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAATGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAATGTCAT
*
52393048 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAATGTCAT
* * * * * * *
52393089 AA-CCGAACCTAGTTTCGAAGGGCCTTCGGGCCAATGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAATGTCAT
52393129 AATCCGAGCTTGGTCTCGAAGGGCTTTT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTT
52393157 TGAGTCAGCG
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
40 32 0.34
41 61 0.66
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.28
Consensus pattern (41 bp):
AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAATGTCAT
Found at i:52397065 original size:39 final size:40
Alignment explanation
Indices: 52397007--52397107 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
52396997 AAATTGAATG
* *
52397007 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
52397046 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
52397086 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
52397108 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:52397100 original size:40 final size:40
Alignment explanation
Indices: 52397007--52397189 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
52396997 AAATTGAATG
* * * * *
52397007 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
52397046 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
52397086 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCCAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
52397126 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
52397166 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
52397190 CTTGGTGCGG
Statistics
Matches: 120, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
39 32 0.27
40 86 0.72
41 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:52401738 original size:25 final size:25
Alignment explanation
Indices: 52401710--52401757 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
52401700 TTATACCATG
* * *
52401710 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
52401735 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
52401758 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:52401838 original size:11 final size:11
Alignment explanation
Indices: 52401805--52401858 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
52401795 TATGGTATGT
52401805 ATGATATGCAC
1 ATGATATGCAC
*
52401816 ATGA-ATG--T
1 ATGATATGCAC
52401824 ATGATATGCAC
1 ATGATATGCAC
*
52401835 ATGATATG--T
1 ATGATATGCAC
52401844 ATGATATGCAC
1 ATGATATGCAC
52401855 ATGA
1 ATGA
52401859 GGTAATCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
8 4 0.12
9 11 0.32
10 3 0.09
11 16 0.47
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:52401845 original size:20 final size:20
Alignment explanation
Indices: 52401800--52401858 Score: 111
Period size: 19 Copynumber: 3.0 Consensus size: 20
52401790 ATAAATATGG
52401800 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
52401820 -ATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
52401839 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
52401859 GGTAATCATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.50
20 19 0.50
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:52401967 original size:23 final size:23
Alignment explanation
Indices: 52401909--52402028 Score: 143
Period size: 24 Copynumber: 5.0 Consensus size: 23
52401899 GAGGAAGTGA
52401909 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
52401932 CAAAAGGGATTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
52401956 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
* * *
52401980 GAAAGGGCTTTTGCCCCAATTACT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
52402004 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
52402028 A
1 A
52402029 TGATAAAGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
23 21 0.25
24 53 0.64
25 9 0.11
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:52401978 original size:47 final size:48
Alignment explanation
Indices: 52401909--52402027 Score: 152
Period size: 47 Copynumber: 2.5 Consensus size: 48
52401899 GAGGAAGTGA
*
52401909 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGATTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGATTATGCCCCAATTACT
** * *
52401956 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAATTACT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGATTATGCCCCAATTACT
*
52402004 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
52402028 ATGATAAAGC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
47 41 0.65
48 11 0.17
49 11 0.17
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGATTATGCCCCAATTACT
Found at i:52402254 original size:31 final size:31
Alignment explanation
Indices: 52402219--52402313 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
52402209 CATTTACAGT
52402219 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
52402250 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
52402281 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
52402312 AA
1 AA
52402314 TATGAAAAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:52410752 original size:43 final size:41
Alignment explanation
Indices: 52410705--52410818 Score: 99
Period size: 43 Copynumber: 2.7 Consensus size: 41
52410695 TGTGATTACA
52410705 TGTAAGACCATGCTTGGGACATTGGCATTGTATTAA-GATTAT-G
1 TGTAAGACCATG-TTGGGACATTGGCATT-T-TTAACGATT-TCG
* * *
52410748 TGTAAAACTATGTCTGGGGCATTGGCATTTTTAATCGATTTCG
1 TGTAAGACCATGT-TGGGACATTGGCATTTTTAA-CGATTTCG
*
52410791 TGTAAGA-CACTGTTTGGGACAGTGGCAT
1 TGTAAGACCA-TG-TTGGGACATTGGCAT
52410819 CGATATGTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
41 4 0.07
42 4 0.07
43 49 0.84
44 1 0.02
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.35
Consensus pattern (41 bp):
TGTAAGACCATGTTGGGACATTGGCATTTTTAACGATTTCG
Found at i:52423574 original size:31 final size:31
Alignment explanation
Indices: 52423536--52423599 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
52423526 CCTTTTCATA
52423536 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
52423567 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
52423598 TT
1 TT
52423600 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:52423926 original size:23 final size:23
Alignment explanation
Indices: 52423814--52423956 Score: 189
Period size: 23 Copynumber: 6.1 Consensus size: 23
52423804 CCTAGCCTCT
* *
52423814 TTTAGTAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
** *
52423837 TTTTTTGTAACTGGGGCATAAACCC
1 --TTTAATAACTGGGGCATAAGCCC
* *
52423862 TTTTGATCACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
52423886 TTTAATAACT-GGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
52423908 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
52423931 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
52423954 TTT
1 TTT
52423957 TGCACTTCCT
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
22 22 0.20
23 46 0.43
24 20 0.19
25 20 0.19
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:52423928 original size:45 final size:46
Alignment explanation
Indices: 52423814--52423956 Score: 189
Period size: 45 Copynumber: 3.1 Consensus size: 46
52423804 CCTAGCCTCT
* * ** *
52423814 TTTAGTAACTGGGGCAAAAGCCCTTTTTTGTAACTGGGGCATAAACCC
1 TTTAATAACTGGGGCATAAGCCC--TTTAATAACTGGGGCATAAGCCC
* *
52423862 TTTTGATCACTGGGGCATAAGCCCTTTAATAACT-GGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCC
52423908 TTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCC
52423954 TTT
1 TTT
52423957 TGCACTTCCT
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
45 31 0.37
46 26 0.31
47 8 0.10
49 19 0.23
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (46 bp):
TTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCC
Found at i:52424035 original size:20 final size:20
Alignment explanation
Indices: 52424010--52424053 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
52424000 TGAACACCTA
52424010 ATGTGCATATCATACATATC
1 ATGTGCATATCATACATATC
52424030 ATGTGCATATCATACATATC
1 ATGTGCATATCATACATATC
52424050 ATGT
1 ATGT
52424054 TTATCAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (20 bp):
ATGTGCATATCATACATATC
Found at i:52425395 original size:27 final size:27
Alignment explanation
Indices: 52425375--52425634 Score: 335
Period size: 27 Copynumber: 9.6 Consensus size: 27
52425365 AGGGTATTTT
*
52425375 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
52425402 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
52425429 AGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
52425456 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
52425483 GGTAATTCTGTAAATCGAGGGTAAAA-
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * * *
52425509 TGATAATTATGTAAATCGGGGGTAAAAT
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * * *
52425537 GGTAATTATGTAAATTGGGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
52425564 GGTAATTCTGTAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
52425591 AGTAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
52425618 GGTAATTCTGTAAATCG
1 AGTAATTCTGTAAATCG
52425635 GGAGTACTTT
Statistics
Matches: 208, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
26 2 0.01
27 204 0.98
28 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:52425461 original size:81 final size:80
Alignment explanation
Indices: 52425376--52425634 Score: 376
Period size: 81 Copynumber: 3.2 Consensus size: 80
52425366 GGGTATTTTA
* * * *
52425376 GTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA-AGTAATTCTGTA
52425441 AATCGAGGGTAAAATG
65 AATCGAGGGTAAAATG
* *
52425457 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGATAATTATGTA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAAG-TAATTCTGTA
*
52425522 AATCGGGGGTAAAATG
65 AATCGAGGGTAAAATG
* * *
52425538 GTAATTATGTAAATTGGGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA-AGTAATTCTGTA
*
52425603 AA-CTGAGGGTAAAACG
65 AATC-GAGGGTAAAATG
52425619 GTAATTCTGTAAATCG
1 GTAATTCTGTAAATCG
52425635 GGAGTACTTT
Statistics
Matches: 159, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
80 2 0.01
81 156 0.98
82 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (80 bp):
GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAAGTAATTCTGTAA
ATCGAGGGTAAAATG
Found at i:52428509 original size:31 final size:31
Alignment explanation
Indices: 52428471--52428534 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
52428461 CCTTTTCATA
52428471 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
52428502 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
52428533 TT
1 TT
52428535 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:52428806 original size:23 final size:24
Alignment explanation
Indices: 52428727--52428891 Score: 232
Period size: 23 Copynumber: 7.0 Consensus size: 24
52428717 GCTTTATCAT
*
52428727 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
52428752 ATAACTGGGGCAAAAGCCCTTTTTT
1 ATAACTGGGGCATAAGCCC-TTTTA
*
52428777 GTAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
52428801 AT-ACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
52428823 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
52428846 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
52428869 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
52428892 GCACTTCCTC
Statistics
Matches: 129, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
22 6 0.05
23 78 0.60
24 12 0.09
25 33 0.26
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:52428969 original size:20 final size:20
Alignment explanation
Indices: 52428944--52428987 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
52428934 TGAACACCTA
52428944 ATGTGCATATCATACATATC
1 ATGTGCATATCATACATATC
52428964 ATGTGCATATCATACATATC
1 ATGTGCATATCATACATATC
52428984 ATGT
1 ATGT
52428988 TTATCAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (20 bp):
ATGTGCATATCATACATATC
Found at i:52429064 original size:25 final size:25
Alignment explanation
Indices: 52429022--52429069 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
52429012 TCTTATAAAC
* * *
52429022 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
52429047 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
52429070 CACGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:52430320 original size:27 final size:27
Alignment explanation
Indices: 52430300--52430558 Score: 344
Period size: 27 Copynumber: 9.6 Consensus size: 27
52430290 AGGGTATTTT
*
52430300 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
52430327 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
52430354 AGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
52430381 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
52430408 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
52430435 -GATAATTATGTAAATCG-GGGTAAAAT
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * * *
52430461 GGTAATTATGTAAATTGGGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
52430488 GGTAATTCTGTAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
52430515 AGTAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
52430542 GGTAATTCTGTAAATCG
1 AGTAATTCTGTAAATCG
52430559 GGAGTACTTT
Statistics
Matches: 208, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
26 24 0.12
27 183 0.88
28 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:52430504 original size:134 final size:135
Alignment explanation
Indices: 52430302--52430558 Score: 401
Period size: 134 Copynumber: 1.9 Consensus size: 135
52430292 GGTATTTTAG
* *
52430302 TAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATAA
1 TAATTATGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAGTAATTCTATAA
*
52430367 ATCGAGGGTAAAATGGTAATTCTGTAAA-TCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTA
66 ATCGAGGGTAAAATAGTAATTCTGTAAACT-GAGGGTAAAACGGTAATTCTGTAAATCGAGGGTA
52430431 AAACGA
130 AAACGA
** *** * *
52430437 TAATTATGTAAATCG-GGGTAAAATGGTAATTATGTAAATTGGGGGTAAAACGGTAATTCTGTAA
1 TAATTATGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAGTAATTCTATAA
52430501 ATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTGTAAATCG
66 ATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTGTAAATCG
52430559 GGAGTACTTT
Statistics
Matches: 111, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
134 96 0.86
135 15 0.14
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (135 bp):
TAATTATGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAGTAATTCTATAA
ATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAA
AACGA
Found at i:52430574 original size:107 final size:106
Alignment explanation
Indices: 52430299--52430566 Score: 326
Period size: 107 Copynumber: 2.5 Consensus size: 106
52430289 AAGGGTATTT
* * ** *
52430299 TAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAAC-AGTAATTCT
1 TAGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATC--GGG-AGTACTAGTAATTAT
*
52430363 ATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAA
63 ATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA
** * * * * *
52430407 CGGTAATTCTGTAAATCGAGGGTAAAACGATAATTATGTAAATCGGG-GTAAAATGGTAATTATG
1 TAGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGGGAGT--ACTAGTAATTATA
* *
52430471 TAAATTGGGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA
64 TAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA
52430514 TAGTAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGTAAATCGGGAGTACT
1 TAGTAATTCTGTAAATC-GAGGGTAAAACGGTAATTCTGTAAATCGGGAGTACT
52430567 TTGTAATTTT
Statistics
Matches: 135, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
106 7 0.05
107 88 0.65
108 40 0.30
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.29
Consensus pattern (106 bp):
TAGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGGGAGTACTAGTAATTATATA
AATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA
Found at i:52433437 original size:31 final size:31
Alignment explanation
Indices: 52433399--52433462 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
52433389 CCTTTTCATA
52433399 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
52433430 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
52433461 TT
1 TT
52433463 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:52433762 original size:23 final size:23
Alignment explanation
Indices: 52433677--52433818 Score: 207
Period size: 23 Copynumber: 6.1 Consensus size: 23
52433667 CCTAGCCTCT
* *
52433677 TTTAGTAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
**
52433700 TTTTTTGTAACTGGGGCATAAGCCC
1 --TTTAATAACTGGGGCATAAGCCC
52433725 TTT--TAATCTGGGGCATAAGCCC
1 TTTAATAA-CTGGGGCATAAGCCC
52433747 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
52433770 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
52433793 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
52433816 TTT
1 TTT
52433819 TGCACTTCCT
Statistics
Matches: 112, Mismatches: 2, Indels: 8
0.92 0.02 0.07
Matches are distributed among these distances:
21 3 0.03
22 18 0.16
23 67 0.60
24 3 0.03
25 21 0.19
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:52433768 original size:45 final size:46
Alignment explanation
Indices: 52433656--52433819 Score: 208
Period size: 46 Copynumber: 3.5 Consensus size: 46
52433646 GCTTTATCAT
* * * *
52433656 ATAACTGGAGGCCT-AGCCTCTTTTAGTAACTGGGGCAAAAGCCCTTTTTT
1 ATAACTGG-GGCATAAGCC-CTTTTAAT-ACTGGGGCATAAGCCC--TTTA
*
52433706 GTAACTGGGGCATAAGCCCTTTTAAT-CTGGGGCATAAGCCCTTTA
1 ATAACTGGGGCATAAGCCCTTTTAATACTGGGGCATAAGCCCTTTA
52433751 ATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTTA
1 ATAACTGGGGCATAAGCCCTTTTAAT-ACTGGGGCATAAGCCCTTTA
52433797 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
52433820 GCACTTCCTC
Statistics
Matches: 104, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
44 6 0.06
45 21 0.20
46 38 0.37
47 17 0.16
49 11 0.11
50 11 0.11
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (46 bp):
ATAACTGGGGCATAAGCCCTTTTAATACTGGGGCATAAGCCCTTTA
Done.