Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 115 of 311
Found at i:38231552 original size:17 final size:17
Alignment explanation
Indices: 38231532--38231570 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
38231522 GAAATATTTG
*
38231532 AATATAATTTAATATAA
1 AATATAATTTAAAATAA
38231549 AATATAATTTAAAATAA
1 AATATAATTTAAAATAA
38231566 AATAT
1 AATAT
38231571 TTTAATGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATATAATTTAAAATAA
Found at i:38235784 original size:6 final size:6
Alignment explanation
Indices: 38235775--38235822 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
38235765 TTAATATGAA
38235775 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
38235823 TTTAATGTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:38239232 original size:20 final size:21
Alignment explanation
Indices: 38239200--38239248 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
38239190 TATTGACTTC
* *
38239200 ATATTATTCTATGTA-AATAT
1 ATATTTTTTTATGTAGAATAT
*
38239220 ATATTTTTTTATGTATGTATAT
1 ATATTTTTTTATGTA-GAATAT
38239242 ATATTTT
1 ATATTTT
38239249 CCTTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.54
22 11 0.46
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (21 bp):
ATATTTTTTTATGTAGAATAT
Found at i:38250850 original size:54 final size:52
Alignment explanation
Indices: 38250726--38250879 Score: 224
Period size: 54 Copynumber: 3.0 Consensus size: 52
38250716 AAGGGAAGAA
*
38250726 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGA-T-TTAAAAA-AAAAAGG
1 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACTAATAAAAATAAAAAGG
* *
38250775 ACCAAAGTGAAAACCCGCAAAGGGCACTTTGAGACCTAATAAAAATGAAAAAGG
1 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGA-CTAATAAAAAT-AAAAAGG
*
38250829 GCCAAAGTGAAAACCCACAAAGGGCGCTTTGAGACTCAATAAAAATAAAAA
1 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACT-AATAAAAATAAAAA
38250880 AAAAACAAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
49 32 0.34
51 1 0.01
52 6 0.06
53 7 0.08
54 47 0.51
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (52 bp):
GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACTAATAAAAATAAAAAGG
Found at i:38252166 original size:43 final size:46
Alignment explanation
Indices: 38252087--38252185 Score: 120
Period size: 43 Copynumber: 2.3 Consensus size: 46
38252077 AGTCCCAAGC
* * *
38252087 CTTATC-TCTCTGAGGTAGCAAGAGAGCAGGTAGAAGATTG-AG-T
1 CTTATCTTCTCTGAGGTAGCAAGAAAACAGCTAGAAGATTGAAGAT
38252130 CTTATCTTC-CTGAGGTAGCAAGAAAACAGACT-GAAGATTGAAGAT
1 CTTATCTTCTCTGAGGTAGCAAGAAAACAG-CTAGAAGATTGAAGAT
38252175 CTTATC-TCTCT
1 CTTATCTTCTCT
38252186 AAACAGTAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
43 32 0.67
44 7 0.15
45 9 0.19
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (46 bp):
CTTATCTTCTCTGAGGTAGCAAGAAAACAGCTAGAAGATTGAAGAT
Found at i:38252301 original size:176 final size:176
Alignment explanation
Indices: 38251995--38253042 Score: 1457
Period size: 176 Copynumber: 6.0 Consensus size: 176
38251985 TGATGAAGTT
* *
38251995 AGATCTTATCTCCCTAAAAAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCG
1 AGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCG
* * *
38252060 GCAATGGAGCAAATTTAAGTCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTAGAAGAT
66 GCAATGGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAT
*
38252125 TGAGTCTTATCTTCCTGAGGTAGCAAGAAAACAGACTGAAGATTGA
131 TGAGTCTTATCTTCCTGAGGTAGCAAGAAAGCAGACTGAAGATTGA
* *
38252171 AGATCTTATCTCTCTAAACAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCTATGTATCG
1 AGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCG
* * *
38252236 GCAATGAAGTAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGTAGGTTGAAGAT
66 GCAATGGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAT
* *
38252301 TGAGTCTTATCTTCCTGAGGTAGCAAGGAACCAGACTGAAGATTGA
131 TGAGTCTTATCTTCCTGAGGTAGCAAGAAAGCAGACTGAAGATTGA
* **
38252347 AGATCTTATCTCCCTAAACAGTAGAGGAGCAGATTAAAGATGGCGAATCTTATCTCCATGTATCG
1 AGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCG
** *
38252412 AAAATGGAGCAAATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAT
66 GCAATGGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAT
*
38252477 TGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGA
131 TGAGTCTTATCTTCCTGAGGTAGCAAGAAAGCAGACTGAAGATTGA
* * *
38252523 AGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGAACCTTATCTCCATGTATCG
1 AGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCG
*
38252588 ACAATGGAGCAGA-TTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAT
66 GCAATGGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAT
* *
38252652 TGAGTCTTATCTTCCAGAGGTAGCAAGGAAGC-GACTGAAGATTGA
131 TGAGTCTTATCTTCCTGAGGTAGCAAGAAAGCAGACTGAAGATTGA
* * * *
38252697 AGATCTTATCT-CCTCAAATAGTA-TAGAAGCAGATCGAAGATAGCGAATCTTATTTCCATGTAT
1 AGATCTTATCTCCCT-AAACAGTAGT-GGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTAT
* ** * * *
38252760 CGGCAATGGTGCAGATTTAAGCCCCAAGTTTTATCTCTCTGAGATAACAAGAGAGCAGGTTAAAG
64 CGGCAATGGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAG
* * *
38252825 ATTGAGTCTTATCTTTCC-GAGGTAGCAAGAAAGTAGATTGAAAATTGA
129 ATTGAGTCTTATC-TTCCTGAGGTAGCAAGAAAGCAGACTGAAGATTGA
* * * *
38252873 AGATTTTATCTCCC-AAAGCAATAGTGGAGCAGATCAAAAGA-GGCGACTCTTATCTCCATGTAT
1 AGATCTTATCTCCCTAAA-CAGTAGTGGAGCAGATC-GAAGATGGCGAATCTTATCTCCATGTAT
* * * * * * * * * * *
38252936 TGGCAATGGAGCAGATTTTAGCCGCTAGTCTTATCTTTTTGAGGAATCAAGAGAGCAGATTGGCA
64 CGGCAATGGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTT-GAA
* *
38253001 -ATTGTAGTCTTATCTTCCTAAGTTAGCAA-AGAAGCAGACTGA
128 GATTG-AGTCTTATCTTCCTGAGGTAGCAAGA-AAGCAGACTGA
38253043 TTGTAGATCT
Statistics
Matches: 782, Mismatches: 77, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
173 4 0.01
174 76 0.10
175 156 0.20
176 512 0.65
177 34 0.04
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (176 bp):
AGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCG
GCAATGGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAT
TGAGTCTTATCTTCCTGAGGTAGCAAGAAAGCAGACTGAAGATTGA
Found at i:38252495 original size:43 final size:46
Alignment explanation
Indices: 38252439--38252533 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 46
38252429 AGCCCCAAGC
**
38252439 CTTATC-TCTCTGAGGTAGCAA-GAGAGCAGGTTGAAGATTG-AG-T
1 CTTATCTTCTCTGAGGTAGCAAGGA-AGCAGACTGAAGATTGAAGAT
38252482 CTTATCTTC-CTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGAT
1 CTTATCTTCTCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGAT
38252527 CTTATCT
1 CTTATCT
38252534 CCCTAAGCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
43 32 0.70
44 6 0.13
45 8 0.17
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (46 bp):
CTTATCTTCTCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGAT
Found at i:38252661 original size:43 final size:45
Alignment explanation
Indices: 38252614--38252708 Score: 110
Period size: 43 Copynumber: 2.2 Consensus size: 45
38252604 AGCCCCAAGC
* **
38252614 CTTATCTCT-CTGAGGTAGCAA-GAGAGCAGGTTGAAGATTG-AG-T
1 CTTATCTCTCCAGAGGTAGCAAGGA-AGC-GACTGAAGATTGAAGAT
38252657 CTTATCT-TCCAGAGGTAGCAAGGAAGCGACTGAAGATTGAAGAT
1 CTTATCTCTCCAGAGGTAGCAAGGAAGCGACTGAAGATTGAAGAT
38252701 CTTATCTC
1 CTTATCTC
38252709 CTCAAATAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
42 11 0.25
43 23 0.52
44 10 0.23
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27
Consensus pattern (45 bp):
CTTATCTCTCCAGAGGTAGCAAGGAAGCGACTGAAGATTGAAGAT
Found at i:38252989 original size:526 final size:529
Alignment explanation
Indices: 38251995--38253042 Score: 1504
Period size: 526 Copynumber: 2.0 Consensus size: 529
38251985 TGATGAAGTT
*
38251995 AGATCTTATCTCCCTAAAAAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCG
1 AGATCTTATCTCCCTAAAAAGTAGCGGAGCAGATCGAAGATGGCGAACCTTATCTCCATGTATCG
* *
38252060 GCAATGGAGCAAATTTAAGTCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTAGAAGAT
66 ACAATGGAGCAAATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTAGAAGAT
*
38252125 TGAGTCTTATCTTCCTGAGGTAGCAAGAAAACAGACTGAAGATTGAAGATCTTATCTCTCTAAAC
131 TGAGTCTTATCTTCCAGAGGTAGCAAGAAAACAGACTGAAGATTGAAGATCTTATCTCTCTAAAC
* * * *
38252190 AGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCTATGTATCGGCAATGAAGTAGATTTAAG
196 AGTAGTGAAGCAGATCGAAGATAGCGAATCTTATCTCCATGTATCGGCAATGAAGCAGATTTAAG
* * * *
38252255 CCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGTAGGTTGAAGATTGAGTCTTATCTTCCTGAG
261 CCCCAAGCCTTATCTCTCTGAGATAACAAGAGAGCAGGTTAAAGATTGAGTCTTATCTTCCTGAG
* * * *
38252320 GTAGCAAGGAACCAGACTGAAGATTGAAGATCTTATCTCCCTAAACAGTAGAGGAGCAGATTAAA
326 GTAGCAAGAAACCAGACTGAAAATTGAAGATCTTATCTCCCTAAACAATAGAGGAGCAGATAAAA
38252385 GATGGCGAATCTTATCTCCATGTATCGAAAATGGAGCAAATTTAAGCCCCAAGCCTTATCTCTCT
391 GATGGCGAATCTTATCTCCATGTATCGAAAATGGAGCAAATTTAAGCCCCAAGCCTTATCTCTCT
* * * *
38252450 GAGGTAGCAAGAGAGCAGGTT-GAAGATTG-AGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGAC
456 GAGGAAGCAAGAGAGCAGATTGGAA-ATTGTAGTCTTATCTTCCTAAGGTAGCAAAGAAGCAGAC
38252513 TGAAGATTGA
520 TGAAGATTGA
* *
38252523 AGATCTTATCTCCCTAAGCAA-TAGTGGAGCAGATCGAAGATGGCGAACCTTATCTCCATGTATC
1 AGATCTTATCTCCCTAA-AAAGTAGCGGAGCAGATCGAAGATGGCGAACCTTATCTCCATGTATC
* *
38252587 GACAATGGAGCAGA-TTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGA
65 GACAATGGAGCAAATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTAGAAGA
* *
38252651 TTGAGTCTTATCTTCCAGAGGTAGCAAGGAAGC-GACTGAAGATTGAAGATCTTATCTC-CTCAA
130 TTGAGTCTTATCTTCCAGAGGTAGCAAGAAAACAGACTGAAGATTGAAGATCTTATCTCTCT-AA
* * **
38252714 ATAGTA-TAGAAGCAGATCGAAGATAGCGAATCTTATTTCCATGTATCGGCAATGGTGCAGATTT
194 ACAGTAGT-GAAGCAGATCGAAGATAGCGAATCTTATCTCCATGTATCGGCAATGAAGCAGATTT
**
38252778 AAGCCCCAAGTTTTATCTCTCTGAGATAACAAGAGAGCAGGTTAAAGATTGAGTCTTATCTTTCC
258 AAGCCCCAAGCCTTATCTCTCTGAGATAACAAGAGAGCAGGTTAAAGATTGAGTCTTATC-TTCC
** * * *
38252843 -GAGGTAGCAAGAAAGTAGATTGAAAATTGAAGATTTTATCTCCC-AAAGCAATAGTGGAGCAGA
322 TGAGGTAGCAAGAAACCAGACTGAAAATTGAAGATCTTATCTCCCTAAA-CAATAGAGGAGCAGA
* * ** * * * * *
38252906 TCAAAAGA-GGCGACTCTTATCTCCATGTATTGGCAATGGAGCAGATTTTAGCCGCTAGTCTTAT
386 T-AAAAGATGGCGAATCTTATCTCCATGTATCGAAAATGGAGCAAATTTAAGCCCCAAGCCTTAT
* * * * *
38252970 CTTTTTGAGGAATCAAGAGAGCAGATTGGCAATTGTAGTCTTATCTTCCTAAGTTAGCAAAGAAG
450 CTCTCTGAGGAAGCAAGAGAGCAGATTGGAAATTGTAGTCTTATCTTCCTAAGGTAGCAAAGAAG
38253035 CAGACTGA
515 CAGACTGA
38253043 TTGTAGATCT
Statistics
Matches: 461, Mismatches: 51, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
525 6 0.01
526 260 0.56
527 123 0.27
528 70 0.15
529 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (529 bp):
AGATCTTATCTCCCTAAAAAGTAGCGGAGCAGATCGAAGATGGCGAACCTTATCTCCATGTATCG
ACAATGGAGCAAATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTAGAAGAT
TGAGTCTTATCTTCCAGAGGTAGCAAGAAAACAGACTGAAGATTGAAGATCTTATCTCTCTAAAC
AGTAGTGAAGCAGATCGAAGATAGCGAATCTTATCTCCATGTATCGGCAATGAAGCAGATTTAAG
CCCCAAGCCTTATCTCTCTGAGATAACAAGAGAGCAGGTTAAAGATTGAGTCTTATCTTCCTGAG
GTAGCAAGAAACCAGACTGAAAATTGAAGATCTTATCTCCCTAAACAATAGAGGAGCAGATAAAA
GATGGCGAATCTTATCTCCATGTATCGAAAATGGAGCAAATTTAAGCCCCAAGCCTTATCTCTCT
GAGGAAGCAAGAGAGCAGATTGGAAATTGTAGTCTTATCTTCCTAAGGTAGCAAAGAAGCAGACT
GAAGATTGA
Found at i:38253300 original size:6 final size:7
Alignment explanation
Indices: 38253282--38253308 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
38253272 TATAATAAAT
38253282 CAAAAAC
1 CAAAAAC
38253289 CAAAAAC
1 CAAAAAC
38253296 CAAAAAC
1 CAAAAAC
38253303 CAAAAA
1 CAAAAA
38253309 ATATGTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.26, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAAAC
Found at i:38255545 original size:47 final size:49
Alignment explanation
Indices: 38255427--38255603 Score: 189
Period size: 44 Copynumber: 3.8 Consensus size: 49
38255417 TGTAACCCGC
* * *
38255427 CCATAAGCGAACTCGGACTCAACTCAACGAG--C---TGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
38255471 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
38255521 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
38255564 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
38255604 TCAACCATCC
Statistics
Matches: 110, Mismatches: 9, Indels: 23
0.77 0.06 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 32 0.29
45 2 0.02
46 30 0.27
47 29 0.26
48 2 0.02
49 4 0.04
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:38255591 original size:93 final size:91
Alignment explanation
Indices: 38255434--38255603 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 91
38255424 CGCCCATAAG
*
38255434 CGAACTCGGACTCAACTCAACGAGCTGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 CGAACTCGGACTCAACTCAACGAGCTGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
38255499 GAGTTCGGATGCCTAGTTACATCTCA
66 GAGTTCGGATGCCTAGTTACATCTCA
*
38255525 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCT-GG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
38255590 ACGAGTTCGGATGC
64 ACGAGTTCGGATGC
38255604 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 25 0.33
92 2 0.03
93 48 0.64
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (91 bp):
CGAACTCGGACTCAACTCAACGAGCTGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCA
Found at i:38262252 original size:93 final size:93
Alignment explanation
Indices: 38262140--38262311 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
38262130 CGCCCATAAG
* *
38262140 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
38262205 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
38262233 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
38262298 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
38262312 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:38262308 original size:46 final size:46
Alignment explanation
Indices: 38262133--38262308 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
38262123 TGTAACCCGC
* * *
38262133 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
38262179 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
38262229 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
38262272 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
38262309 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:38292158 original size:1 final size:1
Alignment explanation
Indices: 38292152--38292231 Score: 160
Period size: 1 Copynumber: 80.0 Consensus size: 1
38292142 TGACTGGTCA
38292152 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
38292217 GGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGG
38292232 CTGACCTCGT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 79 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:38292349 original size:1 final size:1
Alignment explanation
Indices: 38292343--38292377 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
38292333 ATACACGACC
* *
38292343 AAAAAAAGAAAAAAAAAAAAAAGAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38292378 CTAATTATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:38292363 original size:15 final size:15
Alignment explanation
Indices: 38292343--38292377 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
38292333 ATACACGACC
38292343 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
38292358 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
38292373 AAAAA
1 AAAAA
38292378 CTAATTATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAA
Found at i:38298200 original size:40 final size:40
Alignment explanation
Indices: 38298116--38298299 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
38298106 TTGAATGCTG
* * * *
38298116 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
38298155 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
38298196 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
38298236 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
38298276 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
38298300 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:38298253 original size:80 final size:81
Alignment explanation
Indices: 38298116--38298296 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
38298106 TTGAATGCTG
* * *
38298116 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
38298180 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
38298196 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
38298257 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
38298276 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
38298297 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:38298320 original size:39 final size:39
Alignment explanation
Indices: 38298184--38298346 Score: 141
Period size: 40 Copynumber: 4.1 Consensus size: 39
38298174 GGTATTTGTG
* * * **
38298184 CGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTG
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGG-CATTGAA
* * **
38298224 CGAGATACT-AATTCCGGGTTAAGTCCCGAAGGCATTCGTG
1 CGAGTTA-TAAAATCCGGGTTAAGTCCCGAAGGCATT-GAA
*
38298264 CGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
* * * *
38298303 TGAGTTAATATAA-CCGGGCTATGTCCCGAAGGCACTTGAA
1 CGAGTT-ATAAAATCCGGGTTAAGTCCCGAAGGCA-TTGAA
38298343 CGAG
1 CGAG
38298347 GAGCTAAATC
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
39 29 0.28
40 75 0.71
41 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (39 bp):
CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
Found at i:38305051 original size:166 final size:164
Alignment explanation
Indices: 38304774--38305082 Score: 501
Period size: 166 Copynumber: 1.9 Consensus size: 164
38304764 ATATCAAACC
*
38304774 AAGAATTAAGCACATATAATTGAGAACAAAATCTAAGTATTTATTAAGTAAAATAAAAATCAAAC
1 AAGAATTAAGCACACATAATTGAGAACAAAATCTAAGTATTTATTAAGTAAAATAAAAATCAAAC
* ** *
38304839 AACAAAATTCATTATAGGGTTCATCTCCCTAGGTATTTGGAAAATTAGTTTATGCTTAAAAAAAT
66 AACAAAATTCATCATAGGGTTCATCTCCCTAGGTATTTAAAAAATTAGTTCATGCTT--AAAAAT
38304904 AAAAACATACAATATATAGTATAATCGGATGAAAAA
129 AAAAACATACAATATATAGTATAATCGGATGAAAAA
* **
38304940 AAGAATTAAGCACACATAATTGAGAACAAGATCTAAGTATTTATTGGGTAAAATAAAAATCAAAC
1 AAGAATTAAGCACACATAATTGAGAACAAAATCTAAGTATTTATTAAGTAAAATAAAAATCAAAC
* *
38305005 GACAGAATTCATCATAGGGTTCATCTCCCTAGGTATTTAAAAAATTAGTTCATGCTTAAAAATAA
66 AACAAAATTCATCATAGGGTTCATCTCCCTAGGTATTTAAAAAATTAGTTCATGCTTAAAAATAA
*
38305070 AAACATCCAATAT
131 AAACATACAATAT
38305083 GCAATATAAT
Statistics
Matches: 132, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
164 20 0.15
166 112 0.85
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (164 bp):
AAGAATTAAGCACACATAATTGAGAACAAAATCTAAGTATTTATTAAGTAAAATAAAAATCAAAC
AACAAAATTCATCATAGGGTTCATCTCCCTAGGTATTTAAAAAATTAGTTCATGCTTAAAAATAA
AAACATACAATATATAGTATAATCGGATGAAAAA
Found at i:38306968 original size:10 final size:11
Alignment explanation
Indices: 38306945--38306973 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
38306935 ATCAAAAAAA
38306945 TTAAACATCAT
1 TTAAACATCAT
38306956 TTAAACA-CAT
1 TTAAACATCAT
38306966 TTAAACAT
1 TTAAACAT
38306974 ACCATTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (11 bp):
TTAAACATCAT
Found at i:38325974 original size:29 final size:29
Alignment explanation
Indices: 38325916--38326012 Score: 103
Period size: 28 Copynumber: 3.4 Consensus size: 29
38325906 GATAAGGTGA
*
38325916 CAGAGTCACCAGATAC--ATATA-ATCGTGG
1 CAGAGCCACCAGA-ACAGATATATAT-GTGG
38325944 CAGAGCCACCAGAACAGATATATATGTGG
1 CAGAGCCACCAGAACAGATATATATGTGG
** *
38325973 CAGAGCCACCAGATTAGATA-ATTTGTGG
1 CAGAGCCACCAGAACAGATATATATGTGG
*
38326001 CATAGCCACCAG
1 CAGAGCCACCAG
38326013 GACGCTTCCG
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
27 2 0.03
28 30 0.49
29 27 0.44
30 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (29 bp):
CAGAGCCACCAGAACAGATATATATGTGG
Found at i:38326442 original size:8 final size:8
Alignment explanation
Indices: 38326426--38326457 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
38326416 CATAAAATAC
38326426 CGGCTTTT
1 CGGCTTTT
*
38326434 CGGCATTT
1 CGGCTTTT
38326442 CGGCTTTT
1 CGGCTTTT
38326450 CGGCTTTT
1 CGGCTTTT
38326458 GCCGATCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.25, G:0.25, T:0.47
Consensus pattern (8 bp):
CGGCTTTT
Found at i:38327457 original size:24 final size:24
Alignment explanation
Indices: 38327430--38327500 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
38327420 CTAGATTTCC
**
38327430 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
38327454 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
38327478 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
38327501 CTCCTGACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.38, G:0.01, T:0.35
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:38327467 original size:48 final size:48
Alignment explanation
Indices: 38327407--38327500 Score: 120
Period size: 48 Copynumber: 1.9 Consensus size: 48
38327397 ACCTCTTGTT
* **
38327407 CCTTGATCAACTCCTAGATTTCC-TCCCTTATCTGCTCCTAAATCCTATC
1 CCTTGATCAACTCCTA-A-ATCCATCCCTTATCAACTCCTAAATCCTATC
38327456 CCTT-ATCAACTCCTAAATCCTATCCCTTATCAACTCCTAAATCCT
1 CCTTGATCAACTCCTAAATCC-ATCCCTTATCAACTCCTAAATCCT
38327501 CTCCTGACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
46 3 0.08
47 1 0.03
48 32 0.80
49 4 0.10
ACGTcount: A:0.24, C:0.37, G:0.03, T:0.35
Consensus pattern (48 bp):
CCTTGATCAACTCCTAAATCCATCCCTTATCAACTCCTAAATCCTATC
Found at i:38333852 original size:28 final size:29
Alignment explanation
Indices: 38333785--38333856 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
38333775 CATATAATCA
*
38333785 TGGCAGAGCAACCAGAACAGATATATATG
1 TGGCAGAGCCACCAGAACAGATATATATG
* *
38333814 TGGCAGAGCCACCAGATCAGATA-ATTTG
1 TGGCAGAGCCACCAGAACAGATATATATG
*
38333842 TGGCATAGCCACCAG
1 TGGCAGAGCCACCAG
38333857 GACGCTTCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 18 0.46
29 21 0.54
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (29 bp):
TGGCAGAGCCACCAGAACAGATATATATG
Found at i:38334306 original size:8 final size:8
Alignment explanation
Indices: 38334273--38334309 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
38334263 AAAATACCGA
38334273 CTTTTCGG
1 CTTTTCGG
*
38334281 CATTTCGG
1 CTTTTCGG
*
38334289 CATTTCGG
1 CTTTTCGG
38334297 CTTTTCGG
1 CTTTTCGG
38334305 CTTTT
1 CTTTT
38334310 GCCGATCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.05, C:0.24, G:0.22, T:0.49
Consensus pattern (8 bp):
CTTTTCGG
Found at i:38335306 original size:24 final size:24
Alignment explanation
Indices: 38335276--38335346 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
38335266 CTAGATTTCC
*
38335276 TCCCTTATCTACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
*
38335300 TCTCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
38335324 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
38335347 CTCCTGACAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:38350331 original size:42 final size:42
Alignment explanation
Indices: 38350283--38350375 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
38350273 CTAAGGCTAT
* *
38350283 GTGTAAGGCCATA-TCTGGGATATGACATCTATATAAGACTTC
1 GTGTAAGACCATATTCT-GGATATGACATCGATATAAGACTTC
* * *
38350325 GTGTAAGACCATATTCTGGATATGGCATCGATATGAGACTTT
1 GTGTAAGACCATATTCTGGATATGACATCGATATAAGACTTC
38350367 GTGTAAGAC
1 GTGTAAGAC
38350376 TATAGTTGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
42 42 0.93
43 3 0.07
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (42 bp):
GTGTAAGACCATATTCTGGATATGACATCGATATAAGACTTC
Found at i:38350598 original size:16 final size:15
Alignment explanation
Indices: 38350573--38350602 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
38350563 GTACTAAAAA
38350573 CTCATATGTGATGAG
1 CTCATATGTGATGAG
38350588 CTCATTATGTGATGA
1 CTCA-TATGTGATGA
38350603 ACCCTCGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (15 bp):
CTCATATGTGATGAG
Found at i:38353117 original size:31 final size:30
Alignment explanation
Indices: 38353060--38353118 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
38353050 GTAAATACTC
* * * *
38353060 AAAATTTGAGGGATTAAAGTGTAAATATGA
1 AAAAGTTGAAGGACTAAAGTGCAAATATGA
38353090 AAAAGTTGAAGGACTAATAGTGCAAATAT
1 AAAAGTTGAAGGACTAA-AGTGCAAATAT
38353119 TTTAAGGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.47, C:0.03, G:0.22, T:0.27
Consensus pattern (30 bp):
AAAAGTTGAAGGACTAAAGTGCAAATATGA
Found at i:38353379 original size:29 final size:31
Alignment explanation
Indices: 38353331--38353394 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
38353321 TTTATAGTTA
*
38353331 TTTAATTAGATAATTATTATT-TATTTAATAT
1 TTTAATAAGATAATTATTATTAT-TTTAATAT
*
38353362 TTTAATAAGAT-ATT-TTATTATTTTATTAT
1 TTTAATAAGATAATTATTATTATTTTAATAT
38353391 TTTA
1 TTTA
38353395 TTTAGTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTAATAAGATAATTATTATTATTTTAATAT
Found at i:38353383 original size:8 final size:8
Alignment explanation
Indices: 38353372--38353396 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
38353362 TTTAATAAGA
38353372 TATTTTAT
1 TATTTTAT
38353380 TATTTTAT
1 TATTTTAT
38353388 TATTTTAT
1 TATTTTAT
38353396 T
1 T
38353397 TAGTCTATAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:38356851 original size:12 final size:12
Alignment explanation
Indices: 38356834--38356862 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
38356824 CTGCAAAATT
38356834 GTAAAAATAATA
1 GTAAAAATAATA
38356846 GTAAAAATAATA
1 GTAAAAATAATA
38356858 GTAAA
1 GTAAA
38356863 GGGGAAGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (12 bp):
GTAAAAATAATA
Found at i:38357792 original size:10 final size:10
Alignment explanation
Indices: 38357773--38357822 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
38357763 TGAAATTCTA
38357773 AAAGATAAAT
1 AAAGATAAAT
38357783 ATAA-ATAAAT
1 A-AAGATAAAT
*
38357793 AAAGATAATT
1 AAAGATAAAT
38357803 AAAGATAAAT
1 AAAGATAAAT
*
38357813 AAAAATAAAT
1 AAAGATAAAT
38357823 CCTAAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:38358651 original size:96 final size:97
Alignment explanation
Indices: 38358487--38358668 Score: 312
Period size: 96 Copynumber: 1.9 Consensus size: 97
38358477 ATTTTATTTA
* * * *
38358487 TTTATTTTTACTTAGGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAACCAAGCACCCTA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAACCAAGCACCCCA
*
38358552 CCCCGGTTACTTAGCCCAACATACTCCTAATT
66 CCCCGGTTACTCAGCCCAACATACTCCTAATT
38358584 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAACCAAGCACCCCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAACCAAGCACCCCA
38358648 CCCCGGTTACTCAGCCCAACA
66 CCCCGGTTACTCAGCCCAACA
38358669 CATTCTTAGA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
96 71 0.89
97 9 0.11
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAACCAAGCACCCCA
CCCCGGTTACTCAGCCCAACATACTCCTAATT
Found at i:38361326 original size:19 final size:19
Alignment explanation
Indices: 38361260--38361326 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
38361250 TTTTATTAAT
*
38361260 ATAATAAAA-TAATAAAAA
1 ATAATAAAAGAAATAAAAA
*
38361278 ATAAACAAAATGAAAT--AAA
1 AT-AATAAAA-GAAATAAAAA
*
38361297 ATAA-AGTAAGAAATAAAAA
1 ATAATA-AAAGAAATAAAAA
38361316 ATAATAAAAGA
1 ATAATAAAAGA
38361327 TAGAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
17 6 0.16
18 6 0.16
19 22 0.58
20 1 0.03
21 3 0.08
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (19 bp):
ATAATAAAAGAAATAAAAA
Found at i:38364890 original size:40 final size:40
Alignment explanation
Indices: 38364835--38365016 Score: 287
Period size: 40 Copynumber: 4.6 Consensus size: 40
38364825 TATTCGAATG
38364835 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
38364875 ATATCTGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
38364915 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
38364955 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
38364995 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
38365017 TACTTGGGTT
Statistics
Matches: 131, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 14 0.11
40 115 0.88
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:38375825 original size:17 final size:17
Alignment explanation
Indices: 38375803--38375835 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38375793 AAAATGGAAA
38375803 AAAATAAACAAAGTTTG
1 AAAATAAACAAAGTTTG
*
38375820 AAAATAAAGAAAGTTT
1 AAAATAAACAAAGTTT
38375836 CTTATGTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.03, G:0.12, T:0.24
Consensus pattern (17 bp):
AAAATAAACAAAGTTTG
Found at i:38376529 original size:10 final size:10
Alignment explanation
Indices: 38376508--38376559 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
38376498 AATGAAATTC
38376508 TAAAAGATAAA
1 TAAAA-ATAAA
38376519 TAAAAATAAA
1 TAAAAATAAA
* *
38376529 TAAAGATAAT
1 TAAAAATAAA
*
38376539 TAAAGATAAA
1 TAAAAATAAA
*
38376549 TGAAAATAAA
1 TAAAAATAAA
38376559 T
1 T
38376560 CCTAAAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
10 31 0.86
11 5 0.14
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:38376533 original size:20 final size:21
Alignment explanation
Indices: 38376510--38376559 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
38376500 TGAAATTCTA
38376510 AAAGATAAATAAAAATAAAT-
1 AAAGATAAATAAAAATAAATG
* *
38376530 AAAGATAATTAAAGATAAATG
1 AAAGATAAATAAAAATAAATG
38376551 AAA-ATAAAT
1 AAAGATAAAT
38376560 CCTAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (21 bp):
AAAGATAAATAAAAATAAATG
Found at i:38378271 original size:14 final size:14
Alignment explanation
Indices: 38378252--38378278 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38378242 ATTTCACTTG
38378252 GCCATATATATATA
1 GCCATATATATATA
38378266 GCCATATATATAT
1 GCCATATATATAT
38378279 CAAATCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (14 bp):
GCCATATATATATA
Found at i:38379043 original size:23 final size:24
Alignment explanation
Indices: 38379017--38379065 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
38379007 TTTATAACAC
38379017 ATCATTCATT-T-ATATATATTCAT
1 ATCATTCATTGTCATATAT-TTCAT
*
38379040 ATCATTCGTTGTCATATATTTCAT
1 ATCATTCATTGTCATATATTTCAT
38379064 AT
1 AT
38379066 ATGGTCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 8 0.35
25 6 0.26
ACGTcount: A:0.31, C:0.14, G:0.04, T:0.51
Consensus pattern (24 bp):
ATCATTCATTGTCATATATTTCAT
Found at i:38379259 original size:42 final size:45
Alignment explanation
Indices: 38379187--38379307 Score: 160
Period size: 42 Copynumber: 2.8 Consensus size: 45
38379177 AACCATTTAG
* * *
38379187 AATATCGATGCCACTGTCCCAGACAGGGTCTTACACG-AAATCA-
1 AATATCGATGCCAATGTCCCAAACATGGTCTTACACGTAAATCAC
38379230 AATA-CGATGCCAATGTCCCAAACATGGTCTTACACGTAAATCAC
1 AATATCGATGCCAATGTCCCAAACATGGTCTTACACGTAAATCAC
* * *
38379274 AA-ATCAATGCCAACGTTCCAAACATGGTCTTACA
1 AATATCGATGCCAATGTCCCAAACATGGTCTTACA
38379308 TGATAACACA
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
42 29 0.42
43 11 0.16
44 29 0.42
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (45 bp):
AATATCGATGCCAATGTCCCAAACATGGTCTTACACGTAAATCAC
Found at i:38379295 original size:44 final size:42
Alignment explanation
Indices: 38379194--38379307 Score: 133
Period size: 44 Copynumber: 2.7 Consensus size: 42
38379184 TAGAATATCG
* * *
38379194 ATGCC-ACTGTCCCAGACAGGGTCTTACACGAAATCAAATACG
1 ATGCCAAC-GTCCCAAACATGGTCTTACACGAAATCAAATACA
*
38379236 ATGCCAATGTCCCAAACATGGTCTTACACGTAAATCACAA-ATCA
1 ATGCCAACGTCCCAAACATGGTCTTACACG-AAATCA-AATA-CA
*
38379280 ATGCCAACGTTCCAAACATGGTCTTACA
1 ATGCCAACGTCCCAAACATGGTCTTACA
38379308 TGATAACACA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
42 25 0.40
43 8 0.13
44 29 0.47
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (42 bp):
ATGCCAACGTCCCAAACATGGTCTTACACGAAATCAAATACA
Found at i:38385434 original size:42 final size:42
Alignment explanation
Indices: 38385375--38385528 Score: 170
Period size: 42 Copynumber: 3.6 Consensus size: 42
38385365 CTAAGATAAT
*
38385375 GTGTAAGACTATATCTGGGATATGGCATCTATATAGAACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCTATATAGAACTTC
38385417 GTGTAAGACCATATCTGGGATATGGCAT-TGATAT-GATACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCT-ATATAGA-ACTTC
* * * * * *
38385459 GTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATCCT-
1 GTGTAAGACCATATCTGGGATA-TGGCATCTATA-TAGAACTTC
* *
38385502 ATGTATGACCATATCTGGGATATGGCA
1 GTGTAAGACCATATCTGGGATATGGCA
38385529 ATTGTATAGT
Statistics
Matches: 95, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
41 3 0.03
42 61 0.64
43 27 0.28
44 2 0.02
45 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCTATATAGAACTTC
Found at i:38390399 original size:29 final size:29
Alignment explanation
Indices: 38390318--38390432 Score: 110
Period size: 29 Copynumber: 4.0 Consensus size: 29
38390308 TAAATACATG
* *
38390318 CATATAGCCCACTAGGCCCAA-TCTTATT
1 CATATGGCCCACTAGGCCCAATTCATATT
* * *
38390346 CAAATGGCCCATCT-GGCCTAGTTCATATT
1 CATATGGCCCA-CTAGGCCCAATTCATATT
**
38390375 -ATTATGGCCCACTAGGCCCAATTCACCTT
1 CA-TATGGCCCACTAGGCCCAATTCATATT
* *
38390404 CATATGGCCCATTAGGCCCAAATCATATT
1 CATATGGCCCACTAGGCCCAATTCATATT
38390433 ATACTCATGC
Statistics
Matches: 68, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
28 17 0.25
29 50 0.74
30 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (29 bp):
CATATGGCCCACTAGGCCCAATTCATATT
Found at i:38390432 original size:58 final size:57
Alignment explanation
Indices: 38390324--38390434 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 57
38390314 CATGCATATA
* * **
38390324 GCCCACTAGGCCCAATCTTATTCAAATGGCCCATCTGGCCTAGTTCATATTATTATG
1 GCCCACTAGGCCCAATCTCATTCAAATGGCCCATCTGGCCCAAATCATATTATTATG
*
38390381 GCCCACTAGGCCCAAT-TCACCTTCATATGGCCCAT-TAGGCCCAAATCATATTAT
1 GCCCACTAGGCCCAATCTCA--TTCAAATGGCCCATCT-GGCCCAAATCATATTAT
38390435 ACTCATGCTC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
56 2 0.04
57 17 0.37
58 27 0.59
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (57 bp):
GCCCACTAGGCCCAATCTCATTCAAATGGCCCATCTGGCCCAAATCATATTATTATG
Found at i:38390676 original size:16 final size:17
Alignment explanation
Indices: 38390655--38390698 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
38390645 AACTTTCGAT
38390655 TTTTCGG-TATTTTAGC
1 TTTTCGGCTATTTTAGC
38390671 TTTTCGGCT-TTTTAGC
1 TTTTCGGCTATTTTAGC
*
38390687 ATTTCGGCTATT
1 TTTTCGGCTATT
38390699 GCCGATTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.11, C:0.16, G:0.18, T:0.55
Consensus pattern (17 bp):
TTTTCGGCTATTTTAGC
Found at i:38396460 original size:42 final size:42
Alignment explanation
Indices: 38396401--38396554 Score: 186
Period size: 42 Copynumber: 3.6 Consensus size: 42
38396391 CTAAGATAAT
*
38396401 GTGTAAGACTATATCTGGGATATGGCATCTATATGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCTATATGAGACTTC
*
38396443 GTGTAAGACCATATCTGGGATATGGCAT-TGATATGATACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCT-ATATGAGACTTC
* * * * *
38396485 GTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGA-TCC
1 GTGTAAGACCATATCTGGGATA-TGGCATCTATATGAGACTTC
* *
38396527 TATGTATGACCATATCTGGGATATGGCA
1 -GTGTAAGACCATATCTGGGATATGGCA
38396555 ATTGTATGGT
Statistics
Matches: 96, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
41 1 0.01
42 65 0.68
43 30 0.31
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCTATATGAGACTTC
Found at i:38396543 original size:85 final size:84
Alignment explanation
Indices: 38396401--38396562 Score: 211
Period size: 85 Copynumber: 1.9 Consensus size: 84
38396391 CTAAGATAAT
* * * * * *
38396401 GTGTAAGACTATATCTGGGATATGGCATCTATATGAGACTTCGTGTAAGACCATATCTGGGATAT
1 GTGTAAGACCATAGCTGGGATATGGCATCGATACGAGACCTCATGTAAGACCATATCTGGGATAT
38396466 GGC-ATTGATATGATACTTC
66 GGCAATTG-TATGATACTTC
* *
38396485 GTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATCCT-ATGTATGACCATATCTGGGAT
1 GTGTAAGACCATAGCTGGGATA-TGGCATCGATACGAGA-CCTCATGTAAGACCATATCTGGGAT
38396549 ATGGCAATTGTATG
64 ATGGCAATTGTATG
38396563 GTACCATGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
84 19 0.28
85 42 0.63
86 6 0.09
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.31
Consensus pattern (84 bp):
GTGTAAGACCATAGCTGGGATATGGCATCGATACGAGACCTCATGTAAGACCATATCTGGGATAT
GGCAATTGTATGATACTTC
Found at i:38400307 original size:17 final size:18
Alignment explanation
Indices: 38400285--38400319 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38400275 TTACATTGAA
38400285 GTGTTTT-AGTGAAAACC
1 GTGTTTTCAGTGAAAACC
*
38400302 GTGTTTTCATTGAAAACC
1 GTGTTTTCAGTGAAAACC
38400320 CTTCTTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (18 bp):
GTGTTTTCAGTGAAAACC
Found at i:38401427 original size:29 final size:29
Alignment explanation
Indices: 38401348--38401459 Score: 86
Period size: 29 Copynumber: 3.9 Consensus size: 29
38401338 ACCCCTAAAT
* * *
38401348 ACATGCATATAGCCTACTAGGCCCAA-TC
1 ACATTCATATGGCCCACTAGGCCCAATTC
* * * *
38401376 -CTATCCAAATGGCCCATCT-GGCCTAGTTC
1 AC-ATTCATATGGCCCA-CTAGGCCCAATTC
* *
38401405 ATATTCTTATGGCCCACTAGGCCCAATTC
1 ACATTCATATGGCCCACTAGGCCCAATTC
* *
38401434 ACCTTCATATGGCCCATTAGGCCCAA
1 ACATTCATATGGCCCACTAGGCCCAA
38401460 ATCATATTAT
Statistics
Matches: 63, Mismatches: 16, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
27 1 0.02
28 17 0.27
29 45 0.71
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAATTC
Found at i:38401710 original size:8 final size:8
Alignment explanation
Indices: 38401699--38401749 Score: 66
Period size: 8 Copynumber: 6.4 Consensus size: 8
38401689 TTTTTTGGTA
38401699 TTTCAGCT
1 TTTCAGCT
*
38401707 TTTCGGCT
1 TTTCAGCT
38401715 TTTCAGCT
1 TTTCAGCT
*
38401723 TTTCGGCT
1 TTTCAGCT
*
38401731 TTTCAGCA
1 TTTCAGCT
*
38401739 TTTCGGCT
1 TTTCAGCT
38401747 TTT
1 TTT
38401750 GCCGATTCAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.08, C:0.24, G:0.18, T:0.51
Consensus pattern (8 bp):
TTTCAGCT
Found at i:38401718 original size:16 final size:16
Alignment explanation
Indices: 38401699--38401749 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
38401689 TTTTTTGGTA
38401699 TTTCAGCTTTTCGGCT
1 TTTCAGCTTTTCGGCT
38401715 TTTCAGCTTTTCGGCT
1 TTTCAGCTTTTCGGCT
*
38401731 TTTCAGCATTTCGGCT
1 TTTCAGCTTTTCGGCT
38401747 TTT
1 TTT
38401750 GCCGATTCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.08, C:0.24, G:0.18, T:0.51
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCT
Found at i:38410500 original size:40 final size:40
Alignment explanation
Indices: 38410402--38410664 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
38410392 TCCTCGTTCA
* * * * *
38410402 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
38410441 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
38410481 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
38410521 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
38410561 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
38410601 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
38410641 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
38410665 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:38417689 original size:40 final size:40
Alignment explanation
Indices: 38417591--38417853 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
38417581 TCCTCGTTCA
* * * * *
38417591 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
38417630 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
38417670 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
38417710 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
38417750 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
38417790 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
38417830 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
38417854 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:38419395 original size:28 final size:28
Alignment explanation
Indices: 38419355--38419462 Score: 90
Period size: 28 Copynumber: 3.8 Consensus size: 28
38419345 CACACATATA
*
38419355 GCCCACTAGGCCCAATCTTATTCAAATG
1 GCCCACTAGGCCCAATCATATTCAAATG
* * * **
38419383 GCCCATTTGGCCCATTCATATTCTTATG
1 GCCCACTAGGCCCAATCATATTCAAATG
** * *
38419411 GCCCACTAGGCCCAATTCACCTTTATATG
1 GCCCACTAGGCCCAA-TCATATTCAAATG
* *
38419440 GCCCATTAGGCCTAAATCATATT
1 GCCCACTAGGCC-CAATCATATT
38419463 ATACTCATGC
Statistics
Matches: 61, Mismatches: 17, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
28 34 0.56
29 25 0.41
30 2 0.03
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.31
Consensus pattern (28 bp):
GCCCACTAGGCCCAATCATATTCAAATG
Found at i:38419552 original size:10 final size:10
Alignment explanation
Indices: 38419537--38419583 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
38419527 GGGCCCAACA
*
38419537 GCCCATTCCG
1 GCCCATTCTG
*
38419547 GCCCATT-TA
1 GCCCATTCTG
38419556 GCCCATTCTG
1 GCCCATTCTG
38419566 GCCCATT-TG
1 GCCCATTCTG
*
38419575 GCCAATTCT
1 GCCCATTCT
38419584 CAACCCAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 15 0.48
10 16 0.52
ACGTcount: A:0.15, C:0.38, G:0.17, T:0.30
Consensus pattern (10 bp):
GCCCATTCTG
Found at i:38419560 original size:19 final size:19
Alignment explanation
Indices: 38419536--38419573 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
38419526 TGGGCCCAAC
38419536 AGCCCATTCCGGCCCATTT
1 AGCCCATTCCGGCCCATTT
*
38419555 AGCCCATTCTGGCCCATTT
1 AGCCCATTCCGGCCCATTT
38419574 GGCCAATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.39, G:0.16, T:0.29
Consensus pattern (19 bp):
AGCCCATTCCGGCCCATTT
Found at i:38419582 original size:19 final size:19
Alignment explanation
Indices: 38419536--38419583 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
38419526 TGGGCCCAAC
* *
38419536 AGCCCATTCCGGCCCATTT
1 AGCCAATTCTGGCCCATTT
*
38419555 AGCCCATTCTGGCCCATTT
1 AGCCAATTCTGGCCCATTT
*
38419574 GGCCAATTCT
1 AGCCAATTCT
38419584 CAACCCAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.17, C:0.38, G:0.17, T:0.29
Consensus pattern (19 bp):
AGCCAATTCTGGCCCATTT
Found at i:38422755 original size:17 final size:16
Alignment explanation
Indices: 38422733--38422764 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
38422723 TAAAGTTTCA
38422733 TAGCTATTAGACACCCT
1 TAGCTATTAGA-ACCCT
38422750 TAGCTATTAGAACCC
1 TAGCTATTAGAACCC
38422765 AACTTTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (16 bp):
TAGCTATTAGAACCCT
Found at i:38430707 original size:42 final size:42
Alignment explanation
Indices: 38430648--38430755 Score: 189
Period size: 42 Copynumber: 2.6 Consensus size: 42
38430638 TACAAAGGTC
*
38430648 ACACGCCCGTGTGACTAGGCCGTGTGCCTCACATGGCATTAG
1 ACACGCCCGTGTGACTAGGCCGTGTGCCTCACACGGCATTAG
38430690 ACACGCCCGTGTGACTAGGCCGTGTGCCTCACACGGCATTAG
1 ACACGCCCGTGTGACTAGGCCGTGTGCCTCACACGGCATTAG
* *
38430732 ACAAGCCCGTGTGTCTAGGCCGTG
1 ACACGCCCGTGTGACTAGGCCGTG
38430756 GCAAAATAGG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.19, C:0.31, G:0.30, T:0.20
Consensus pattern (42 bp):
ACACGCCCGTGTGACTAGGCCGTGTGCCTCACACGGCATTAG
Found at i:38430926 original size:109 final size:109
Alignment explanation
Indices: 38430688--38430927 Score: 462
Period size: 109 Copynumber: 2.2 Consensus size: 109
38430678 ACATGGCATT
38430688 AGACACGCCCGTGTGACTAGGCCGTGTGCCTCACACGGCATTAGACAAGCCCGTGTGTCTAGGCC
1 AGACACGCCCGTGTGACTAGGCCGTGTGCCTCACACGGCATTAGACAAGCCCGTGTGTCTAGGCC
38430753 GTGGCAAAATAGGGCATACATACAGACTTAACCACATGGCCACA
66 GTGGCAAAATAGGGCATACATACAGACTTAACCACATGGCCACA
*
38430797 AGACACGCCCGTGTCACTAGGCCGTGTGCCTCACACGGCATTAGACAAGCCCGTGTGTCTAGGCC
1 AGACACGCCCGTGTGACTAGGCCGTGTGCCTCACACGGCATTAGACAAGCCCGTGTGTCTAGGCC
38430862 GTGGCAAAATAGGGCATACATACAGACTTAACCACATGGCCACA
66 GTGGCAAAATAGGGCATACATACAGACTTAACCACATGGCCACA
*
38430906 AGACACGCCCGTGTGTCTAGGC
1 AGACACGCCCGTGTGACTAGGC
38430928 TGTGCTCAAG
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 128 1.00
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.17
Consensus pattern (109 bp):
AGACACGCCCGTGTGACTAGGCCGTGTGCCTCACACGGCATTAGACAAGCCCGTGTGTCTAGGCC
GTGGCAAAATAGGGCATACATACAGACTTAACCACATGGCCACA
Found at i:38441000 original size:81 final size:81
Alignment explanation
Indices: 38440862--38441023 Score: 297
Period size: 81 Copynumber: 2.0 Consensus size: 81
38440852 AATATAAGAA
*
38440862 TGAGTCGATCCAGGATCAATCAATGCAATTACATTAGTATCATAGAGAGAAAATGTACCAGTGAT
1 TGAGTCGATCCAGGATCAATCAAAGCAATTACATTAGTATCATAGAGAGAAAATGTACCAGTGAT
38440927 AACATCAAGGGATGAC
66 AACATCAAGGGATGAC
*
38440943 TGAGTCGATCCAGGATCAATCAAAGCAATTACATTAGTATCATAGAGAGAAATTGTACCAGTGAT
1 TGAGTCGATCCAGGATCAATCAAAGCAATTACATTAGTATCATAGAGAGAAAATGTACCAGTGAT
*
38441008 AACATCAGGGGATGAC
66 AACATCAAGGGATGAC
38441024 GCATCTTTGT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (81 bp):
TGAGTCGATCCAGGATCAATCAAAGCAATTACATTAGTATCATAGAGAGAAAATGTACCAGTGAT
AACATCAAGGGATGAC
Found at i:38442830 original size:36 final size:36
Alignment explanation
Indices: 38442783--38442853 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
38442773 ATTTAGTCCT
*
38442783 TCTAGTCAAATTAAGCACTCAAACGATAAAGTATCG
1 TCTAGTCAAATTAAGCACTCAAACGATAAAATATCG
38442819 TCTAGTCAAATTAAGCACTCAAACGATAAAATATC
1 TCTAGTCAAATTAAGCACTCAAACGATAAAATATC
38442854 TTAACGAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (36 bp):
TCTAGTCAAATTAAGCACTCAAACGATAAAATATCG
Found at i:38449722 original size:27 final size:27
Alignment explanation
Indices: 38449657--38449723 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
38449647 ATGAACCTTA
*
38449657 AAAG-AATGCCTTTGTGGCACAATATG
1 AAAGAAATGCCTTTGTGACACAATATG
38449683 AAATGAACA--CCTTTGTGACA-AACTATG
1 AAA-GAA-ATGCCTTTGTGACACAA-TATG
38449710 AAAGAAATGCCTTT
1 AAAGAAATGCCTTT
38449724 ATGGCGAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
25 1 0.03
26 8 0.24
27 23 0.68
28 1 0.03
29 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (27 bp):
AAAGAAATGCCTTTGTGACACAATATG
Found at i:38456223 original size:63 final size:64
Alignment explanation
Indices: 38456143--38456325 Score: 194
Period size: 66 Copynumber: 2.8 Consensus size: 64
38456133 AGACATTATG
*
38456143 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACG-GATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
38456206 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
38456271 AA
63 AA
* * * *
38456273 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
38456326 CGAACTATAT
Statistics
Matches: 98, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
63 39 0.40
64 5 0.05
65 6 0.06
66 40 0.41
67 5 0.05
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:38460626 original size:68 final size:68
Alignment explanation
Indices: 38460554--38460704 Score: 166
Period size: 68 Copynumber: 2.2 Consensus size: 68
38460544 CATCATGTGT
* * * *
38460554 ACAAGAGAGCTACAAGACATTATGATGTAGCTA-GGTCGCATGGGT-GATACTA-TG-TGTACAC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGGTCGCATGCGTGGATACAAGTGAAGGACAC
38460615 CATGTAG
62 CATGTAG
** * *
38460622 ACAAGAGAGCTACGGGATATATGTAGCTAGGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGGTCGCATGCGTGGATACAAGTGAAGGACACCATG
38460687 TAG
66 TAG
38460690 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
38460705 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
64 9 0.13
65 14 0.20
66 6 0.09
67 2 0.03
68 39 0.56
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.21
Consensus pattern (68 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGGTCGCATGCGTGGATACAAGTGAAGGACACCATG
TAG
Found at i:38468071 original size:18 final size:17
Alignment explanation
Indices: 38468036--38468082 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
38468026 GGCTTTAAAA
38468036 ATATTATAA-TTTATTT
1 ATATTATAATTTTATTT
38468052 ATATTATAATTTTAATTT
1 ATATTATAATTTT-ATTT
* *
38468070 ATTTTATTATTTT
1 ATATTATAATTTT
38468083 TAATATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 9 0.33
17 3 0.11
18 15 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTATAATTTTATTT
Found at i:38469627 original size:25 final size:24
Alignment explanation
Indices: 38469598--38469648 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
38469588 ATATCAAAAA
38469598 TACTAA-AAATATCAAAATAAATATT
1 TACTAACAAAT-TCAAAATAAAT-TT
*
38469623 TACTAACAAATTGAAAATAAATTT
1 TACTAACAAATTCAAAATAAATTT
38469647 TA
1 TA
38469649 AAAAGTATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 16 0.67
26 4 0.17
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (24 bp):
TACTAACAAATTCAAAATAAATTT
Found at i:38469784 original size:22 final size:23
Alignment explanation
Indices: 38469754--38469798 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
38469744 TATAATATTT
38469754 AAACAATAACAATAAAATAGTAG
1 AAACAATAACAATAAAATAGTAG
* * *
38469777 AAAC-ATAATAGTAAAATGGTAG
1 AAACAATAACAATAAAATAGTAG
38469799 CAAAATAGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (23 bp):
AAACAATAACAATAAAATAGTAG
Found at i:38475574 original size:25 final size:24
Alignment explanation
Indices: 38475544--38475598 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 24
38475534 AGTTAAGGGC
38475544 TGATATTAAAATTGAATCAAAGAA
1 TGATATTAAAATTGAATCAAAGAA
*
38475568 TTGATATTAAAATTGAATCAAAGGA
1 -TGATATTAAAATTGAATCAAAGAA
38475593 TGATAT
1 TGATAT
38475599 AGTTGGTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 6 0.21
25 23 0.79
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.33
Consensus pattern (24 bp):
TGATATTAAAATTGAATCAAAGAA
Found at i:38475690 original size:45 final size:45
Alignment explanation
Indices: 38475626--38475718 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
38475616 CAAATTTAGC
38475626 TTACTTATAGGCCAAACTTGAATGAACAAAAGCAAACAACATAAT
1 TTACTTATAGGCCAAACTTGAATGAACAAAAGCAAACAACATAAT
*
38475671 TTACTTATAGGCCAAACTTGAATGAACAAAAGTAAACAACATAAT
1 TTACTTATAGGCCAAACTTGAATGAACAAAAGCAAACAACATAAT
38475716 TTA
1 TTA
38475719 ACGGGGCAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (45 bp):
TTACTTATAGGCCAAACTTGAATGAACAAAAGCAAACAACATAAT
Found at i:38476977 original size:30 final size:30
Alignment explanation
Indices: 38476919--38476977 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
38476909 ACAGGTTGTC
* *
38476919 ACATAGGCGTGTGTCCAGCCTGTGTGGCTT
1 ACATAGGCGTATGTCCAGCCTGTATGGCTT
*
38476949 ACATAGGTGTATGTCCAGTCC-GTATGGCT
1 ACATAGGCGTATGTCCAG-CCTGTATGGCT
38476978 CTTGAAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.17, C:0.22, G:0.31, T:0.31
Consensus pattern (30 bp):
ACATAGGCGTATGTCCAGCCTGTATGGCTT
Found at i:38477016 original size:11 final size:11
Alignment explanation
Indices: 38477002--38477038 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
38476992 TTTTTCTCTA
38477002 TTTTTTGCTCG
1 TTTTTTGCTCG
38477013 TTTTTTGCTCG
1 TTTTTTGCTCG
*
38477024 TTTTTCGCTC-
1 TTTTTTGCTCG
38477034 TTTTT
1 TTTTT
38477039 GTTCCCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.00, C:0.19, G:0.14, T:0.68
Consensus pattern (11 bp):
TTTTTTGCTCG
Found at i:38478445 original size:7 final size:7
Alignment explanation
Indices: 38478433--38478487 Score: 76
Period size: 7 Copynumber: 7.9 Consensus size: 7
38478423 TTCTGAATCC
38478433 TCAATTT
1 TCAATTT
38478440 TCAATTT
1 TCAATTT
38478447 TCAATTT
1 TCAATTT
*
38478454 TTAATTT
1 TCAATTT
38478461 TCAATTCT
1 TCAATT-T
38478469 T-AATTT
1 TCAATTT
*
38478475 TTAATTT
1 TCAATTT
38478482 TCAATT
1 TCAATT
38478488 ACTTTTTGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
6 2 0.05
7 39 0.91
8 2 0.05
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (7 bp):
TCAATTT
Found at i:38493171 original size:17 final size:18
Alignment explanation
Indices: 38493151--38493185 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38493141 TGGAAAAGGT
38493151 TCTC-CACGACTACCATG
1 TCTCGCACGACTACCATG
*
38493168 TCTCGCCCGACTACCATG
1 TCTCGCACGACTACCATG
38493186 ATAACCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.43, G:0.14, T:0.23
Consensus pattern (18 bp):
TCTCGCACGACTACCATG
Found at i:38495633 original size:86 final size:86
Alignment explanation
Indices: 38495488--38495659 Score: 335
Period size: 86 Copynumber: 2.0 Consensus size: 86
38495478 ATTTGTCGTA
38495488 ATTAAGCAGAGTTGATTGCACGCCTAGAGATAGGGTGACAAGATTTTGCCGGATTAGGGTGAAAC
1 ATTAAGCAGAGTTGATTGCACGCCTAGAGATAGGGTGACAAGATTTTGCCGGATTAGGGTGAAAC
38495553 CTAATAAGGGAGTCCATAGAT
66 CTAATAAGGGAGTCCATAGAT
*
38495574 ATTAAGCGGAGTTGATTGCACGCCTAGAGATAGGGTGACAAGATTTTGCCGGATTAGGGTGAAAC
1 ATTAAGCAGAGTTGATTGCACGCCTAGAGATAGGGTGACAAGATTTTGCCGGATTAGGGTGAAAC
38495639 CTAATAAGGGAGTCCATAGAT
66 CTAATAAGGGAGTCCATAGAT
38495660 CGAGTTAATG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (86 bp):
ATTAAGCAGAGTTGATTGCACGCCTAGAGATAGGGTGACAAGATTTTGCCGGATTAGGGTGAAAC
CTAATAAGGGAGTCCATAGAT
Found at i:38495774 original size:25 final size:25
Alignment explanation
Indices: 38495746--38495795 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
38495736 CGAGAGAGAT
38495746 AATAATATAACTTAGGGATTTCTAC
1 AATAATATAACTTAGGGATTTCTAC
38495771 AATAATATAACTTAGGGATTTCTAC
1 AATAATATAACTTAGGGATTTCTAC
38495796 GGATCAAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (25 bp):
AATAATATAACTTAGGGATTTCTAC
Found at i:38496287 original size:46 final size:46
Alignment explanation
Indices: 38496203--38496373 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 46
38496193 TCACATAGCT
* * *
38496203 GATGCATATTCCAGACATGTCTTACACTGGCT-TACATCTCGAGGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCGAGGCC
* * *
38496249 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAGGCC
* * * * *
38496295 GATGCCATGTCCTAGACATGGTCTGACGCTGGCTCTCATAAT-GTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCGAGGCC
* *
38496343 GATGCATGTCCTAGACATGTTTTACACTGGC
1 GATGCATGTCCCAGACATGTCTTACACTGGC
38496374 ACACAAATAA
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
46 52 0.50
47 28 0.27
48 23 0.22
49 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.29
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAGGCC
Found at i:38498169 original size:47 final size:45
Alignment explanation
Indices: 38498103--38498228 Score: 150
Period size: 47 Copynumber: 2.7 Consensus size: 45
38498093 ATTACGAGCT
*
38498103 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAA-T-GC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTC--AT-AAGTGGC
*
38498149 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATAA-GTGGC
38498197 CGATGCA-GATCCCAGACATGTCTTACACTAGC
1 CGATGCATG-TCCCAGACATGTCTTACACTAGC
38498229 ACACATTTAT
Statistics
Matches: 71, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
45 2 0.03
46 19 0.27
47 27 0.38
48 23 0.32
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAAGTGGC
Found at i:38500854 original size:55 final size:55
Alignment explanation
Indices: 38500777--38500890 Score: 174
Period size: 55 Copynumber: 2.1 Consensus size: 55
38500767 ATAAGGGCTA
* * *
38500777 TGTCTTGACCGTGTGAGACACACGGCCTGGCACATGGGCATATGGTTTGGGCTTG
1 TGTCTTGACCGTGTGAGACACACGGCCTGGCACATGGGCATATGATTTGGCCGTG
* * *
38500832 TGTCTTGACCGTGTGTGACACACGGCCTGGCTCATGGGCATGTGATTTGGCCGTG
1 TGTCTTGACCGTGTGAGACACACGGCCTGGCACATGGGCATATGATTTGGCCGTG
38500887 TGTC
1 TGTC
38500891 CCTTGCATCT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (55 bp):
TGTCTTGACCGTGTGAGACACACGGCCTGGCACATGGGCATATGATTTGGCCGTG
Found at i:38501947 original size:21 final size:21
Alignment explanation
Indices: 38501921--38502059 Score: 109
Period size: 21 Copynumber: 6.6 Consensus size: 21
38501911 GCTCAGAGGC
*
38501921 TAAACAGAAGCTCATTAGAGT
1 TAAACAGAAGCTCATAAGAGT
* * *
38501942 TAAACAGAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGT
* * * *
38501963 TGAACGGAAGCTCGTAAGAGC
1 TAAACAGAAGCTCATAAGAGT
* * * * *
38501984 TGAACGGAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGT
*
38502005 TAAACAGAAGCTCAATAA-AGC
1 TAAACAGAAGCTC-ATAAGAGT
* * *
38502026 TGAACAGAAACTCATATGAGT
1 TAAACAGAAGCTCATAAGAGT
38502047 TAAACAGAAGCTC
1 TAAACAGAAGCTC
38502060 GTGAGAGCTA
Statistics
Matches: 88, Mismatches: 28, Indels: 4
0.73 0.23 0.03
Matches are distributed among these distances:
20 3 0.03
21 81 0.92
22 4 0.05
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (21 bp):
TAAACAGAAGCTCATAAGAGT
Found at i:38501974 original size:42 final size:42
Alignment explanation
Indices: 38501921--38502076 Score: 170
Period size: 42 Copynumber: 3.7 Consensus size: 42
38501911 GCTCAGAGGC
*
38501921 TAAACAGAAGCTCATTAGAGTTAAACAGAAACCCATAAGGGT
1 TAAACAGAAGCTCATTAGAGCTAAACAGAAACCCATAAGGGT
* * * * * *
38501963 TGAACGGAAGCTCGTAAGAGCTGAACGGAAACCCATAAGGGT
1 TAAACAGAAGCTCATTAGAGCTAAACAGAAACCCATAAGGGT
* * * * * *
38502005 TAAACAGAAGCTCAATAAAGCTGAACAGAAACTCATATGAGT
1 TAAACAGAAGCTCATTAGAGCTAAACAGAAACCCATAAGGGT
* *
38502047 TAAACAGAAGCTCGTGAGAGCTAAAC-GAAA
1 TAAACAGAAGCTCATTAGAGCTAAACAGAAA
38502077 AGTAAACACA
Statistics
Matches: 92, Mismatches: 22, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
41 4 0.04
42 88 0.96
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (42 bp):
TAAACAGAAGCTCATTAGAGCTAAACAGAAACCCATAAGGGT
Found at i:38513357 original size:50 final size:50
Alignment explanation
Indices: 38513280--38513390 Score: 177
Period size: 50 Copynumber: 2.2 Consensus size: 50
38513270 AATTCAAATA
* * * *
38513280 TCTCATATCTCGAGGCCGATGCCATGTCCTAGACATGGTCTTACACTAGC
1 TCTCATATCTCGAGACCGATACCATGTCCCAGACATGGTATTACACTAGC
*
38513330 TTTCATATCTCGAGACCGATACCATGTCCCAGACATGGTATTACACTAGC
1 TCTCATATCTCGAGACCGATACCATGTCCCAGACATGGTATTACACTAGC
38513380 TCTCATATCTC
1 TCTCATATCTC
38513391 CCTAGCATCA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (50 bp):
TCTCATATCTCGAGACCGATACCATGTCCCAGACATGGTATTACACTAGC
Found at i:38515598 original size:20 final size:21
Alignment explanation
Indices: 38515567--38515623 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
38515557 GAGCTAAACT
38515567 GAAACCCATAAGGGTTGAAC-
1 GAAACCCATAAGGGTTGAACG
* * * *
38515587 GAAACTCGTAAGAGTTGGACG
1 GAAACCCATAAGGGTTGAACG
38515608 GAAACCCATAAGGGTT
1 GAAACCCATAAGGGTT
38515624 AAACAGAAGC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.18
Consensus pattern (21 bp):
GAAACCCATAAGGGTTGAACG
Found at i:38518057 original size:26 final size:27
Alignment explanation
Indices: 38518004--38518062 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
38517994 TTATTACAGA
38518004 TAAAATCGTTAAAAATTTTACCAAGGG
1 TAAAATCGTTAAAAATTTTACCAAGGG
* * * *
38518031 TAAAATTGTT-AAAATTTTTCTAGGGG
1 TAAAATCGTTAAAAATTTTACCAAGGG
38518057 TAAAAT
1 TAAAAT
38518063 AGGGATGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 19 0.68
27 9 0.32
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (27 bp):
TAAAATCGTTAAAAATTTTACCAAGGG
Found at i:38519697 original size:47 final size:48
Alignment explanation
Indices: 38519628--38519752 Score: 125
Period size: 47 Copynumber: 2.7 Consensus size: 48
38519618 TAAGGTGCCG
* * * *
38519628 ATGCCATATACTAAACATGGTCTTATACTGGCTCA-CATCTCA-AGTCA
1 ATGCCATGTCCTAGACATGGTCTTATACTGGCT-ATCATCTCATAGCCA
* * *
38519675 ATGCCATGTCCTAGACATGGTCTTACACTGACTATCATCTCATAGCCG
1 ATGCCATGTCCTAGACATGGTCTTATACTGGCTATCATCTCATAGCCA
*
38519723 ATG-CATGTCCCAGACAT-GTCTT-TCACTGGC
1 ATGCCATGTCCTAGACATGGTCTTAT-ACTGGC
38519753 ATACGTCTCG
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
46 11 0.17
47 48 0.74
48 6 0.09
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (48 bp):
ATGCCATGTCCTAGACATGGTCTTATACTGGCTATCATCTCATAGCCA
Found at i:38527388 original size:47 final size:46
Alignment explanation
Indices: 38527337--38527586 Score: 188
Period size: 47 Copynumber: 5.3 Consensus size: 46
38527327 GCCATATCCT
* *
38527337 AGACATGGTCTTACACTGACTATCATCTCGTAGCCGATGCATGTCCC
1 AGACAT-GTCTTACACTGGCTCTCATCTCGTAGCCGATGCATGTCCC
* *
38527384 AGACATGTCCTT-CACTGGCAT-ACGTCTCG-AGGCCGATGCATGTCCC
1 AGACATGT-CTTACACTGGC-TCTCATCTCGTA-GCCGATGCATGTCCC
* * * * * *
38527430 CGACATGTCTTAAACTAGCTCTCGTCTC-AATGCCGATACCATGTCCC
1 AGACATGTCTTACACTGGCTCTCATCTCGTA-GCCGAT-GCATGTCCC
* * * * * *
38527477 AAACATGGTCCTACACTGGCTCCCATAAT-ATGGCCGATGCATGTCCC
1 AGACAT-GTCTTACACTGGCTCTCAT-CTCGTAGCCGATGCATGTCCC
* * * *
38527524 AGACATGGTCTTACGCTGGCTCTCATAAT-GTGGCTGATGCATGTCCC
1 AGACAT-GTCTTACACTGGCTCTCAT-CTCGTAGCCGATGCATGTCCC
38527571 AGACATGTCTTACACT
1 AGACATGTCTTACACT
38527587 AGCCAACAAC
Statistics
Matches: 166, Mismatches: 27, Indels: 21
0.78 0.13 0.10
Matches are distributed among these distances:
45 5 0.03
46 63 0.38
47 77 0.46
48 20 0.12
49 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (46 bp):
AGACATGTCTTACACTGGCTCTCATCTCGTAGCCGATGCATGTCCC
Found at i:38527456 original size:46 final size:46
Alignment explanation
Indices: 38527369--38527488 Score: 118
Period size: 46 Copynumber: 2.6 Consensus size: 46
38527359 TCATCTCGTA
* * *
38527369 GCCGATGCATGTCCCAGACATGTCCTTCACTGGCATACGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCCTTAACTAGCATACGTCTCAAG
* * *
38527415 GCCGATGCATGTCCCCGACATGT-CTTAAACTAGC-TCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCCTT-AACTAGCAT-ACGTCTCAAG
* *
38527461 GCCGATACCATGTCCCAAACATGGTCCT
1 GCCGAT-GCATGTCCCAGACAT-GTCCT
38527489 ACACTGGCTC
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
45 4 0.07
46 40 0.67
47 12 0.20
48 2 0.03
49 2 0.03
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.25
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCCTTAACTAGCATACGTCTCAAG
Found at i:38535542 original size:12 final size:12
Alignment explanation
Indices: 38535497--38535609 Score: 53
Period size: 12 Copynumber: 9.8 Consensus size: 12
38535487 ATTCCAAAAA
*
38535497 TAATA-TTATTT
1 TAATATTTAATT
38535508 TAATAGTTTAATAT
1 TAATA-TTTAAT-T
38535522 TAA-ATTTAATT
1 TAATATTTAATT
* *
38535533 TAATACTTAACT
1 TAATATTTAATT
*
38535545 TAATA-GT-ATT
1 TAATATTTAATT
38535555 T--TA-TTAATT
1 TAATATTTAATT
* *
38535564 TAATATTAAAGT
1 TAATATTTAATT
* *
38535576 GATTATCTTAATAT
1 TAATAT-TTAAT-T
*
38535590 T-ACATTTAATT
1 TAATATTTAATT
38535601 TAATATTTA
1 TAATATTTA
38535610 TCTTGTAGAT
Statistics
Matches: 75, Mismatches: 16, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 3 0.04
11 14 0.19
12 36 0.48
13 10 0.13
14 5 0.07
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (12 bp):
TAATATTTAATT
Found at i:38541237 original size:15 final size:17
Alignment explanation
Indices: 38541211--38541244 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
38541201 TATTTAATTA
38541211 TTTATCATCTTT-TAAT
1 TTTATCATCTTTCTAAT
38541227 TTTATCA-CTTTCTAAT
1 TTTATCATCTTTCTAAT
38541243 TT
1 TT
38541245 AGTCCTTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATCATCTTTCTAAT
Found at i:38549753 original size:46 final size:46
Alignment explanation
Indices: 38549686--38549855 Score: 186
Period size: 46 Copynumber: 3.7 Consensus size: 46
38549676 AACCCGCCCC
*
38549686 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
38549732 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * * ** *
38549780 TCA-CGAACTCGGACTCAACTCAATGAGTTCGAACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
38549825 TAGGTGAACTCGGACTCAACTCAACGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
38549856 AGATGCTCAA
Statistics
Matches: 102, Mismatches: 13, Indels: 18
0.77 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 1 0.01
46 57 0.56
47 26 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:38549798 original size:93 final size:93
Alignment explanation
Indices: 38549691--38549861 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
38549681 GCCCCTAAGT
** *
38549691 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
38549756 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCAGATGCCTAGTTACATCTCAC
* * *
38549784 GAACTCGGACTCAACTCAATGAGTTCGAACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
38549849 CGAGTTCAGATGC
66 CGAGTTCAGATGC
38549862 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATCTCAC
Found at i:38550318 original size:30 final size:30
Alignment explanation
Indices: 38550284--38550343 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
38550274 ATTTAATACG
38550284 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
38550314 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
38550344 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:38554162 original size:27 final size:28
Alignment explanation
Indices: 38554078--38554175 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
38554068 CATGAGATTG
* * * *
38554078 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
38554107 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
38554135 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
38554162 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
38554176 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:38554186 original size:27 final size:27
Alignment explanation
Indices: 38554106--38554188 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
38554096 TAAATTGTAC
* *
38554106 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
38554134 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
38554161 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
38554188 A
1 A
38554189 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:38554189 original size:29 final size:27
Alignment explanation
Indices: 38554078--38554189 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
38554068 CATGAGATTG
** * *
38554078 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
38554107 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
38554135 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
38554162 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
38554190 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:38562158 original size:30 final size:29
Alignment explanation
Indices: 38562122--38562218 Score: 101
Period size: 28 Copynumber: 3.4 Consensus size: 29
38562112 CATGAGATTG
* *
38562122 GCACTAAGTGTGGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGGCGAGTTT-AATTATACA
* *
38562152 GCACTAAGTGT-GCGAGTTTGATTATATA
1 GCACTAAGTGTGGCGAGTTTAATTATACA
* *
38562180 GCACTAAGTGT-GCGAG-TTGATTATATA
1 GCACTAAGTGTGGCGAGTTTAATTATACA
*
38562207 GCACTGAGTGTG
1 GCACTAAGTGTG
38562219 CGGACTTAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
27 21 0.34
28 22 0.36
29 7 0.11
30 11 0.18
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32
Consensus pattern (29 bp):
GCACTAAGTGTGGCGAGTTTAATTATACA
Found at i:38562207 original size:27 final size:28
Alignment explanation
Indices: 38562122--38562220 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
38562112 CATGAGATTG
* * * *
38562122 GCACTAAGTGTGGCGGGTTTAAATTGTACA
1 GCACTAAGTGT-GCGAGTTT-GATTATATA
38562152 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
38562180 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
38562207 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
38562221 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 7 0.11
30 11 0.17
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:38562234 original size:29 final size:27
Alignment explanation
Indices: 38562151--38562234 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
38562141 TAAATTGTAC
* *
38562151 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
38562179 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
38562206 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
38562235 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.46
28 22 0.44
29 5 0.10
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:38564354 original size:22 final size:22
Alignment explanation
Indices: 38564329--38564373 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
38564319 CAAAATGGTA
38564329 ATTTTGCCTAGGATAGAAATTG
1 ATTTTGCCTAGGATAGAAATTG
38564351 ATTTTGCCTAGGATAGAAATTG
1 ATTTTGCCTAGGATAGAAATTG
38564373 A
1 A
38564374 GTCCACTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (22 bp):
ATTTTGCCTAGGATAGAAATTG
Found at i:38568256 original size:44 final size:45
Alignment explanation
Indices: 38568182--38568301 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 45
38568172 ATATCTATGT
* *
38568182 CGATGCTATGTTCCAGACAT-TCTCTTCACTGAC-ACATCTCGTA-GC
1 CGATGC-ATGTCCCAGACATGTCT-TACACTGACTACATCTCG-AGGC
*
38568227 CGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGAC-TACATCTCGAGGC
*
38568273 TGATGCATGTCCCAGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
38568302 AGCACTTGTC
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
44 19 0.28
45 10 0.15
46 38 0.57
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTGACTACATCTCGAGGC
Found at i:38568324 original size:46 final size:44
Alignment explanation
Indices: 38568227--38568344 Score: 130
Period size: 46 Copynumber: 2.5 Consensus size: 44
38568217 ATCTCGTAGC
* *
38568227 CGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGG
1 CGATGCATGTCCCAGACATGTCTTACACTGACTTA-ATCTCAAGG
* *
38568272 CTGATGCATGTCCCAGACATGTCTTACACTAGCACTT-GTCTCAATGT
1 C-GATGCATGTCCCAGACATGTCTTACACT-G-ACTTAATCTCAA-GG
38568319 CGATGCTATGTCCCAGACATGGTCTT
1 CGATGC-ATGTCCCAGACAT-GTCTT
38568345 TCGCTAGCTC
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
45 1 0.02
46 38 0.60
47 16 0.25
48 8 0.13
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (44 bp):
CGATGCATGTCCCAGACATGTCTTACACTGACTTAATCTCAAGG
Found at i:38590424 original size:30 final size:30
Alignment explanation
Indices: 38590389--38590446 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
38590379 AAGACTACTT
38590389 CCACACGGGCAGAG-CACACGCCCATGTGAG
1 CCACACGGGCAG-GCCACACGCCCATGTGAG
*
38590419 CCACACGGGCTGGCCACACGCCCATGTG
1 CCACACGGGCAGGCCACACGCCCATGTG
38590447 TCAGCCCGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.22, C:0.40, G:0.29, T:0.09
Consensus pattern (30 bp):
CCACACGGGCAGGCCACACGCCCATGTGAG
Found at i:38594970 original size:52 final size:52
Alignment explanation
Indices: 38594887--38594990 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
38594877 ATTGTGCTAG
* *
38594887 GCCATAAAATTTCTAGTAAAAGGATCGAGGTTGATAAAGCAAAAATTGAAAC
1 GCCACAAAATTTCTAGTAAAAGGATCGAGGTTGATAAAGAAAAAATTGAAAC
38594939 GCCACAAAATTTCTAGTAAAAGGATCGAGGTTGATAAAGAAAAAATTGAAAC
1 GCCACAAAATTTCTAGTAAAAGGATCGAGGTTGATAAAGAAAAAATTGAAAC
38594991 TATTGAGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (52 bp):
GCCACAAAATTTCTAGTAAAAGGATCGAGGTTGATAAAGAAAAAATTGAAAC
Found at i:38597957 original size:17 final size:15
Alignment explanation
Indices: 38597935--38597973 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
38597925 TCCTCTCCCT
38597935 TTTTCTCTTTGCTCTTC
1 TTTTCTC-TT-CTCTTC
38597952 TTTTCTCTTCTCTTC
1 TTTTCTCTTCTCTTC
*
38597967 TCTTCTC
1 TTTTCTC
38597974 CCCCATCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTTCTCTTCTCTTC
Found at i:38599881 original size:6 final size:6
Alignment explanation
Indices: 38599866--38599915 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
38599856 ATTGAGTCCA
* * *
38599866 TTTATC TTTATT TTTATT TTTATT TTTATT TTTATT TTTACT TTTCTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
38599914 TT
1 TT
38599916 CATGCTTAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:38604096 original size:24 final size:24
Alignment explanation
Indices: 38603997--38604097 Score: 157
Period size: 24 Copynumber: 4.2 Consensus size: 24
38603987 AAGTCTGTTA
*
38603997 GGAGAGGATTTAGGAGTTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
38604021 GGATAGGATTTAGGAGTTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
38604045 GGATAGGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
38604069 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
38604093 GGAGA
1 GGAGA
38604098 ACAGTGTTGG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.33, C:0.02, G:0.41, T:0.25
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:38605539 original size:27 final size:26
Alignment explanation
Indices: 38605499--38605609 Score: 141
Period size: 27 Copynumber: 4.2 Consensus size: 26
38605489 AGGAAGCGTC
* *
38605499 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
38605526 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
38605553 CTGGTGGCTCTGCCACGATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
** * *
38605580 CTGGTAACTCTGTCACATTATCTATT
1 CTGGTGGCTCTGCCACATTATCTGTT
38605606 CTGG
1 CTGG
38605610 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
26 15 0.20
27 59 0.78
28 2 0.03
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:38610556 original size:24 final size:24
Alignment explanation
Indices: 38610520--38610596 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
38610510 AAGTCTGTTA
*
38610520 GGAGAGGATTTAGGAGTTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
38610544 GGATAGGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
38610568 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
38610592 GGAGA
1 GGAGA
38610597 ACAGTGTTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.32, C:0.03, G:0.42, T:0.23
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:38612012 original size:27 final size:26
Alignment explanation
Indices: 38611972--38612082 Score: 150
Period size: 27 Copynumber: 4.2 Consensus size: 26
38611962 AGGAAGCGTC
* *
38611972 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
38611999 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
38612026 CTGGTGGCTCTGCCACGATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
* * *
38612053 CTGGTGACTCTGTCACATTATCTATT
1 CTGGTGGCTCTGCCACATTATCTGTT
38612079 CTGG
1 CTGG
38612083 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
26 15 0.19
27 60 0.78
28 2 0.03
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:38620734 original size:5 final size:5
Alignment explanation
Indices: 38620724--38620749 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38620714 TCTTTCATTC
38620724 CCCTT CCCTT CCCTT CCCTT CCCTT C
1 CCCTT CCCTT CCCTT CCCTT CCCTT C
38620750 TCTTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (5 bp):
CCCTT
Found at i:38621562 original size:26 final size:24
Alignment explanation
Indices: 38621522--38621572 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 24
38621512 AAAATCAATA
38621522 AAATAGAGAAATATA-AAAAATATT
1 AAATAGAGAAATATATAAAAA-ATT
38621546 AAATAGAGAAATGTATATAAAAAATT
1 AAATAGAGAAA--TATATAAAAAATT
38621572 A
1 A
38621573 TTATAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 11 0.46
26 8 0.33
27 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (24 bp):
AAATAGAGAAATATATAAAAAATT
Found at i:38627835 original size:24 final size:24
Alignment explanation
Indices: 38627808--38627853 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
38627798 TAAAATTATT
* *
38627808 AAAATTAAAATATTTTTTAAACAG
1 AAAATTAAAATATCTTTAAAACAG
38627832 AAAATTAAAATATCTTTAAAAC
1 AAAATTAAAATATCTTTAAAAC
38627854 TTAGGTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAATTAAAATATCTTTAAAACAG
Found at i:38633331 original size:18 final size:18
Alignment explanation
Indices: 38633308--38633520 Score: 90
Period size: 18 Copynumber: 11.4 Consensus size: 18
38633298 GAACAATTAT
38633308 TTATTCAGTAATAGTCAG
1 TTATTCAGTAATAGTCAG
* * * *
38633326 TTATTCGGTAACAATCAA
1 TTATTCAGTAATAGTCAG
* **
38633344 TTATTCAATAATAACCAG
1 TTATTCAGTAATAGTCAG
*
38633362 TTATTCAGTATCGATCAATTGATCGG
1 TTATTCAGTA---AT--A--G-TCAG
* * *
38633388 TTATCCAGTAACAGTCAA
1 TTATTCAGTAATAGTCAG
*
38633406 TTATTCAGTAA-AATCAG
1 TTATTCAGTAATAGTCAG
* * * * *
38633423 GTATTCAATAACAATTAAG
1 TTATTCAGTAA-TAGTCAG
* *
38633442 TTATTTAGTAACAGTCA-
1 TTATTCAGTAATAGTCAG
* * *
38633459 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAATAGTCAG
*
38633478 TTATTCAGTAAT-GATCAA
1 TTATTCAGTAATAG-TCAG
*
38633496 TTATTCAGTAATATTCAG
1 TTATTCAGTAATAGTCAG
38633514 TTATTCA
1 TTATTCA
38633521 ATAACAGTCT
Statistics
Matches: 142, Mismatches: 39, Indels: 28
0.68 0.19 0.13
Matches are distributed among these distances:
17 15 0.11
18 96 0.68
19 15 0.11
21 3 0.02
23 2 0.01
26 11 0.08
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (18 bp):
TTATTCAGTAATAGTCAG
Found at i:38633339 original size:36 final size:36
Alignment explanation
Indices: 38633299--38633381 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
38633289 TAACAATCAG
* * * **
38633299 AACAATTATTTATTCAGTAATAGTCAGTTATTCGGT
1 AACAATCAATTATTCAATAATAACCAGTTATTCGGT
*
38633335 AACAATCAATTATTCAATAATAACCAGTTATTCAGT
1 AACAATCAATTATTCAATAATAACCAGTTATTCGGT
* *
38633371 ATCGATCAATT
1 AACAATCAATT
38633382 GATCGGTTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (36 bp):
AACAATCAATTATTCAATAATAACCAGTTATTCGGT
Found at i:38633500 original size:54 final size:54
Alignment explanation
Indices: 38633387--38633520 Score: 137
Period size: 54 Copynumber: 2.5 Consensus size: 54
38633377 CAATTGATCG
* *
38633387 GTTATCCAGTAACAGTCAATTATTCAGTAAAATCAGGTATTCAATAACAATTAA
1 GTTATTCAGTAACAGTCAATTATTCAGTAAAATCAGGTATTCAATAACAATCAA
* * * * **
38633441 GTTATTTAGTAACAGTC-ATTCATTCAGTGACAATCAGTTATTCAGTAATGATCAA
1 GTTATTCAGTAACAGTCAATT-ATTCAGT-AAAATCAGGTATTCAATAACAATCAA
* * *
38633496 -TTATTCAGTAATATTCAGTTATTCA
1 GTTATTCAGTAACAGTCAATTATTCA
38633521 ATAACAGTCT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
53 3 0.05
54 40 0.62
55 22 0.34
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (54 bp):
GTTATTCAGTAACAGTCAATTATTCAGTAAAATCAGGTATTCAATAACAATCAA
Done.