Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 23
Found at i:2990767 original size:19 final size:19
Alignment explanation
Indices: 2990739--2990775 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2990729 AAATATCAAG
*
2990739 TTAAAATATGATTCATTTA
1 TTAAAATATGATTAATTTA
*
2990758 TTAAAGTATGATTAATTT
1 TTAAAATATGATTAATTT
2990776 GTTTCGAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (19 bp):
TTAAAATATGATTAATTTA
Found at i:2991672 original size:3 final size:3
Alignment explanation
Indices: 2991664--2991712 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
2991654 ATTAATATTA
2991664 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
2991712 A
1 A
2991713 TATTTTTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2995193 original size:21 final size:21
Alignment explanation
Indices: 2995136--2995195 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
2995126 GAAGCTGAAG
* *
2995136 CGAGAGAAGTAGAGAAAGCAG
1 CGAGAGAAGTAGAGAGAGCAA
*
2995157 TGAGAGAAGTAGAGAGAGCAA
1 CGAGAGAAGTAGAGAGAGCAA
2995178 CGAGAGAAGTAGAGAGAG
1 CGAGAGAAGTAGAGAGAG
2995196 AATCATCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.47, C:0.07, G:0.40, T:0.07
Consensus pattern (21 bp):
CGAGAGAAGTAGAGAGAGCAA
Found at i:2997545 original size:226 final size:226
Alignment explanation
Indices: 2997133--2997593 Score: 667
Period size: 226 Copynumber: 2.0 Consensus size: 226
2997123 TAACGTAACC
* *
2997133 GGTTAATTAATGAAAACATTAGCAACTATAATAACATAACAGATAGCGTTTATATAACGTAATAT
1 GGTTAATTAATGAAAACATTAGCAACCATAATAACATAACAGATAGCGTTTATATAACGTAATAG
* * * **
2997198 GTAACGTCTTTTTAAAGTTGATGAGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTGTTT
66 GTAACGTCTTTTTAAAGATGATGAGGCCTTAAAAATCCAACGATAACAAAATAGGTTAATTAATT
* * * *
2997263 GATTTGTTATCAATATTATCAACATATTAAGTAGCGCATAAAATGTTATGAAAGTTTAAGCTAAT
131 GATTTGTTATCAATATTATCAACATATTAAATAACGCATAAAATATTATCAAAGTTTAAGCTAAT
*
2997328 -GGAGCCTTAGAAATCTGACGATAACAAAATA
196 AGG-GCCTTAGAAATCAGACGATAACAAAATA
* * * * *
2997359 GGTTAATTATTGGAAACATTATCAACCATAATAACATAACA-AGTAGCGTTTATTTAATGTAATA
1 GGTTAATTAATGAAAACATTAGCAACCATAATAACATAACAGA-TAGCGTTTATATAACGTAATA
*
2997423 GGTAGCGTCTTTTTAAAGATGAT-AGAGCCTTAAAAATCCAACGATAACAAAATAGGTTAATTAA
65 GGTAACGTCTTTTTAAAGATGATGAG-GCCTTAAAAATCCAACGATAACAAAATAGGTTAATTAA
* * * *
2997487 TTGATTTGTTATCAATATTATCAATATATTAAATAACTCCTAAAATATTATCAAAGTTTAAGCTG
129 TTGATTTGTTATCAATATTATCAACATATTAAATAACGCATAAAATATTATCAAAGTTTAAGCTA
*
2997552 GTAGGGCCTTAGAAATCAGACGATAACAAAATA
194 ATAGGGCCTTAGAAATCAGACGATAACAAAATA
2997585 GGTTAATTA
1 GGTTAATTA
2997594 CTTATTTTGT
Statistics
Matches: 209, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
225 3 0.01
226 204 0.98
227 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (226 bp):
GGTTAATTAATGAAAACATTAGCAACCATAATAACATAACAGATAGCGTTTATATAACGTAATAG
GTAACGTCTTTTTAAAGATGATGAGGCCTTAAAAATCCAACGATAACAAAATAGGTTAATTAATT
GATTTGTTATCAATATTATCAACATATTAAATAACGCATAAAATATTATCAAAGTTTAAGCTAAT
AGGGCCTTAGAAATCAGACGATAACAAAATA
Found at i:2997638 original size:108 final size:108
Alignment explanation
Indices: 2997449--2997661 Score: 286
Period size: 108 Copynumber: 2.0 Consensus size: 108
2997439 AGATGATAGA
*
2997449 GCCTTAAAAATCCAACGATAACAAAATAGGTTAATTAATTGATTTGTTATCAATATTATCAATAT
1 GCCTTAAAAATCCAACGATAACAAAATAGGTTAATTAATTGATTTGTTATCAATATTATCAACAT
** * *
2997514 ATTAAATAACTCCTAAAATATTATCAAAGTTTAAGCTGGTAGG
66 ATTAAATAACGACTAAAATATTACCAAAATTTAAGCTGGTAGG
* * *
2997557 GCCTTAGAAAT-CAGACGATAACAAAATAGGTTAATTACTT-ATTTTGTTATTAATATTATCAAC
1 GCCTTAAAAATCCA-ACGATAACAAAATAGGTTAATTAATTGA-TTTGTTATCAATATTATCAAC
** * *
2997620 ATATTAGGTAGCGACTAAAATATTACCAAAATTTAAGGTGGT
64 ATATTAAATAACGACTAAAATATTACCAAAATTTAAGCTGGT
2997662 GAGATTTTTG
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 3 0.03
108 88 0.97
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (108 bp):
GCCTTAAAAATCCAACGATAACAAAATAGGTTAATTAATTGATTTGTTATCAATATTATCAACAT
ATTAAATAACGACTAAAATATTACCAAAATTTAAGCTGGTAGG
Found at i:2997675 original size:108 final size:108
Alignment explanation
Indices: 2997450--2997713 Score: 282
Period size: 108 Copynumber: 2.4 Consensus size: 108
2997440 GATGATAGAG
* * *
2997450 CCTTAAAAATCCA-ACGATAACAAAATAGGTTAATTAATTGA-TTTGTTATCAATATTATCAATA
1 CCTTAGAAAT-CAGACGATAACAAAATAGGTTAATTACTT-ATTTTGTTATCAATATTATCAACA
** * * *
2997513 TATTAAATAACTCCTAAAATATTATCAAAGTTTAAGCTGGTAGGG
64 TATTAAATAACGACTAAAATATTACCAAAATTTAAGCTGGTAGGA
*
2997558 CCTTAGAAATCAGACGATAACAAAATAGGTTAATTACTTATTTTGTTATTAATATTATCAACATA
1 CCTTAGAAATCAGACGATAACAAAATAGGTTAATTACTTATTTTGTTATCAATATTATCAACATA
** * *
2997623 TTAGGTAGCGACTAAAATATTACCAAAATTTAAGGTGGT-GAGA
66 TTAAATAACGACTAAAATATTACCAAAATTTAAGCTGGTAG-GA
** * ** * * * *
2997666 TTTTTGAAATCCTACAACAACAAAATAGATTAATTTCTTATTTTGTTA
1 CCTTAGAAATCAGACGATAACAAAATAGGTTAATTACTTATTTTGTTA
2997714 AAATAAATAT
Statistics
Matches: 131, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
107 4 0.03
108 127 0.97
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (108 bp):
CCTTAGAAATCAGACGATAACAAAATAGGTTAATTACTTATTTTGTTATCAATATTATCAACATA
TTAAATAACGACTAAAATATTACCAAAATTTAAGCTGGTAGGA
Found at i:2998139 original size:75 final size:74
Alignment explanation
Indices: 2998058--2998267 Score: 251
Period size: 75 Copynumber: 2.8 Consensus size: 74
2998048 TACCATTTCC
*
2998058 ATTATTATTAACCTTTAAATAATCCGGTAGTTAGTTTAACGTAATAGGTAGCGCCTATTTTATTT
1 ATTATTATTAACCTTTAAA-AATCCGGTAGTTAGTTTAACGTAATAAGTAGCGCCTATTTTATTT
**
2998123 TATTGTGTAA
65 TACCGTGTAA
* * * * * *
2998133 ATTATTAGTAACCTTTAAACAAGCCGGTAGGTATTTTAACGTAATAAGTAGCACCGATTTTATTT
1 ATTATTATTAACCTTTAAA-AATCCGGTAGTTAGTTTAACGTAATAAGTAGCGCCTATTTTATTT
* *
2998198 TACCGTTTAC
65 TACCGTGTAA
* * *
2998208 ATTATTATTAACTTTTAAGCAAAT-CGGTAGTTAGTTTAACTTAATAAGTAGCGCTTATTT
1 ATTATTATTAACCTTTAA--AAATCCGGTAGTTAGTTTAACGTAATAAGTAGCGCCTATTT
2998268 AACGTAATAG
Statistics
Matches: 112, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
75 109 0.97
76 2 0.02
77 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (74 bp):
ATTATTATTAACCTTTAAAAATCCGGTAGTTAGTTTAACGTAATAAGTAGCGCCTATTTTATTTT
ACCGTGTAA
Found at i:2998300 original size:23 final size:23
Alignment explanation
Indices: 2998242--2998307 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
2998232 CGGTAGTTAG
* * *
2998242 TTTAACTTAATAAGTAGCGCTTA
1 TTTAACATAATAGGTAGCGCCTA
* *
2998265 TTTAACGTAATAGGTAGTGCCTA
1 TTTAACATAATAGGTAGCGCCTA
*
2998288 TTTAACATAATAGGCAGCGC
1 TTTAACATAATAGGTAGCGC
2998308 ATGTTTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (23 bp):
TTTAACATAATAGGTAGCGCCTA
Found at i:2998407 original size:76 final size:74
Alignment explanation
Indices: 2998288--2998471 Score: 228
Period size: 76 Copynumber: 2.4 Consensus size: 74
2998278 GTAGTGCCTA
* *
2998288 TTTAACATAATAGGCAGCGC-ATGTTTTATTTTTACCGTTTACATTATTAGTAACCTTTAAACAA
1 TTTAACATAATAGGCAACGCTAT-TTTTA-TTTTACCGTTTACATTATTAGTAACCTTCAAAC-A
* *
2998352 ATCAGTAGGTAT
63 ACCAGTAGGTAG
* *
2998364 TTTAACGTAATAGGCAACGTCTATTTTTATTTTACCGTTTACATTATTAGTGACCTTCAAACAAC
1 TTTAACATAATAGGCAACG-CTATTTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACAAC
*
2998429 CGGTAGGTAG
65 CAGTAGGTAG
* *
2998439 TTTAACATAATATGTAACGCCTA-TTTTATTTTA
1 TTTAACATAATAGGCAACG-CTATTTTTATTTTA
2998472 ACCGGTTAAG
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
74 10 0.11
75 29 0.31
76 48 0.51
77 6 0.06
78 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (74 bp):
TTTAACATAATAGGCAACGCTATTTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACAACC
AGTAGGTAG
Found at i:2999482 original size:4 final size:4
Alignment explanation
Indices: 2999473--2999512 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
2999463 AGACTGTAAC
*
2999473 AATA AATA AATA AATA ATTA GTAATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA --AATA AATA AATA AATA AA
2999513 ACAAAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 29 0.91
6 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:2999573 original size:19 final size:18
Alignment explanation
Indices: 2999536--2999579 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
2999526 AATGCATAAT
*
2999536 ATATATATAATTCTTTTA
1 ATATATATAATTATTTTA
*
2999554 ATATATACTACTTATTTTA
1 ATATATA-TAATTATTTTA
*
2999573 ACATATA
1 ATATATA
2999580 GACTATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATAATTATTTTA
Found at i:2999667 original size:2 final size:2
Alignment explanation
Indices: 2999660--2999863 Score: 98
Period size: 2 Copynumber: 104.0 Consensus size: 2
2999650 TCTATAAAAT
2999660 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * *
2999700 TT TT TA -A AA CTA CA -A TA TG TA CTA AA TA TA CTA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA
*
2999741 T- TA TA TA -A TA TA TA -A CTA TA TA -A TA TA CTA TA GTA TA AA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA -TA TA TA
* *
2999780 T- TT TA CA TA CTA TA TA -A TA TA -A CTA TA TA CTA TGA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA -TA T-A TA TA TA
*
2999821 -A TA TA T- TA TA CTA TA TA TA TA TA TA TA TA -A TA T- TG TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2999860 TA TA
1 TA TA
2999864 AAATATAAGG
Statistics
Matches: 160, Mismatches: 14, Indels: 56
0.70 0.06 0.24
Matches are distributed among these distances:
1 16 0.10
2 124 0.77
3 20 0.12
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2999840 original size:46 final size:46
Alignment explanation
Indices: 2999725--2999847 Score: 121
Period size: 46 Copynumber: 2.7 Consensus size: 46
2999715 TATGTACTAA
* *
2999725 ATATACTATATATATATTATATA-AT-ATATAACTATATAATATACT
1 ATATAATATAT-TATACTATATATATAATATAACTATATAATATACT
* * *
2999770 ATAGT-ATAAATTTTAC-ATACTATATAATATAACTATATACTATGA-T
1 ATA-TAATATATTATACTATA-TATATAATATAACTATATAATAT-ACT
2999816 ATATAATATATTATACTATATATATATATATA
1 ATATAATATATTATACTATATATATA-ATATA
2999848 TAATATTGTA
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
43 3 0.05
44 5 0.08
45 10 0.16
46 36 0.57
47 9 0.14
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.44
Consensus pattern (46 bp):
ATATAATATATTATACTATATATATAATATAACTATATAATATACT
Found at i:2999841 original size:41 final size:41
Alignment explanation
Indices: 2999738--2999869 Score: 128
Period size: 46 Copynumber: 3.1 Consensus size: 41
2999728 TACTATATAT
2999738 ATATTATA-TA-ATATATAACTATATAATAT-ACTATAGTATAA
1 ATATTATACTATATATATAACTATATAATATGA-TATA-TA-AA
* * *
2999779 ATTTTACATACTATATAATATAACTATATACTATGATATATAAT
1 ATATT--ATACTATAT-ATATAACTATATAATATGATATATAAA
2999823 ATATTATACTATATATATATA-TATATAATATTGTATATATAAA
1 ATATTATACTATATATATA-ACTATATAATA-TG-ATATATAAA
2999866 ATAT
1 ATAT
2999870 AAGGAAAACC
Statistics
Matches: 76, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
41 17 0.22
42 12 0.16
43 15 0.20
44 7 0.09
45 4 0.05
46 20 0.26
47 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (41 bp):
ATATTATACTATATATATAACTATATAATATGATATATAAA
Found at i:2999864 original size:14 final size:14
Alignment explanation
Indices: 2999732--2999869 Score: 79
Period size: 15 Copynumber: 9.4 Consensus size: 14
2999722 TAAATATACT
2999732 ATATATATATTATATA
1 ATATAT-TA-TATATA
*
2999748 ATATATAACTATATA
1 ATATATTA-TATATA
*
2999763 ATATACTATAGTATA
1 ATATATTATA-TATA
*
2999778 A-AT-TT-TACATA
1 ATATATTATATATA
* *
2999789 CTATATAATATAACTA
1 ATATATTATAT-A-TA
*
2999805 TATACTATGATATATA
1 -ATA-TATTATATATA
2999821 ATATATTATACTAT-
1 ATATATTATA-TATA
2999835 ATATATATATATATA
1 ATATAT-TATATATA
2999850 ATAT-TGTATATATA
1 ATATAT-TATATATA
*
2999864 AAATAT
1 ATATAT
2999870 AAGGAAAACC
Statistics
Matches: 96, Mismatches: 14, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
11 3 0.03
12 4 0.04
13 2 0.02
14 33 0.34
15 34 0.35
16 10 0.10
17 3 0.03
18 7 0.07
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (14 bp):
ATATATTATATATA
Found at i:2999869 original size:27 final size:29
Alignment explanation
Indices: 2999722--2999870 Score: 93
Period size: 29 Copynumber: 5.3 Consensus size: 29
2999712 CAATATGTAC
2999722 TAAATATACTATAT-ATATATTATA-TA-A
1 TAAATATA-TATATAATATATTATACTATA
* * *
2999749 TATATA-ACTATATAATATACTATAGTATA
1 TAAATATA-TATATAATATATTATACTATA
* * * *
2999778 -AATTTTACATACT-ATATAATATAACTATA
1 TAAATATATATA-TAATATATTAT-ACTATA
*
2999807 T-ACTATGATATATAATATATTATACTATA
1 TAAATAT-ATATATAATATATTATACTATA
*
2999836 TATATATATATATAATAT-TGTATA-TATA
1 TAAATATATATATAATATAT-TATACTATA
2999864 -AAATATA
1 TAAATATA
2999871 AGGAAAACCA
Statistics
Matches: 96, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
26 7 0.07
27 20 0.21
28 20 0.21
29 34 0.35
30 15 0.16
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (29 bp):
TAAATATATATATAATATATTATACTATA
Found at i:3005278 original size:60 final size:60
Alignment explanation
Indices: 3005120--3005280 Score: 259
Period size: 60 Copynumber: 2.7 Consensus size: 60
3005110 ATTCATAATA
* * * *
3005120 ACTTACCCTAGACCCCTAGGAACTAGGAGTCCAATATGAAAGATACATGCATCCATAAGG
1 ACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATGGAAGATACATACATCCATAAGG
*
3005180 ACTTACCCTAGACCACTAGGATCTAAGAGTCCAATATGGAAGATACATACATCCATAAGG
1 ACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATGGAAGATACATACATCCATAAGG
* *
3005240 ACTTACCCTAGGCCACTAGGATCTAGGATTCCAATATGGAA
1 ACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATGGAA
3005281 TATCATAATA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (60 bp):
ACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATGGAAGATACATACATCCATAAGG
Found at i:3013122 original size:43 final size:43
Alignment explanation
Indices: 3013039--3013123 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
3013029 CAGTTGAGAG
* *
3013039 GGTCCTCAGTAGGAGGTCCAAACAAACCAGTGACATTGTAGGA
1 GGTCCTCAGTAGGAGGTCCAAACAAACCAGTAACACTGTAGGA
* * * * *
3013082 GGTCCTTAGTAGGATGTCCAAATAAACTAGTAAGACTGTAGG
1 GGTCCTCAGTAGGAGGTCCAAACAAACCAGTAACACTGTAGG
3013124 GCATATCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (43 bp):
GGTCCTCAGTAGGAGGTCCAAACAAACCAGTAACACTGTAGGA
Found at i:3025184 original size:23 final size:22
Alignment explanation
Indices: 3025151--3025210 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
3025141 CAGCAGTTCG
3025151 AAAAAAA-AAGAAAAAAAAGGA
1 AAAAAAACAAGAAAAAAAAGGA
*
3025172 AAAAAACACAAGAAAAAAATGGA
1 AAAAAA-ACAAGAAAAAAAAGGA
*
3025195 AAACAAAACAACAAAA
1 AAA-AAAACAAGAAAA
3025211 GTGTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 6 0.18
22 1 0.03
23 24 0.71
24 3 0.09
ACGTcount: A:0.80, C:0.08, G:0.10, T:0.02
Consensus pattern (22 bp):
AAAAAAACAAGAAAAAAAAGGA
Found at i:3028673 original size:22 final size:21
Alignment explanation
Indices: 3028648--3028700 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
3028638 TATTCAGGCC
3028648 AGTATCGATACCCCAGCATCA-G
1 AGTATCGATACCCCA--ATCAGG
* *
3028670 AGTATTGATA-CTCAATCAGG
1 AGTATCGATACCCCAATCAGG
3028690 AGTATCGATAC
1 AGTATCGATAC
3028701 TATCTTCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 4 0.15
20 10 0.38
21 3 0.12
22 9 0.35
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (21 bp):
AGTATCGATACCCCAATCAGG
Found at i:3033069 original size:13 final size:13
Alignment explanation
Indices: 3033051--3033110 Score: 77
Period size: 13 Copynumber: 4.6 Consensus size: 13
3033041 GCACAATATT
3033051 AGAAACAACTTTG
1 AGAAACAACTTTG
3033064 AGAAACAACTTTG
1 AGAAACAACTTTG
*
3033077 ATACAA-AACTTTG
1 AGA-AACAACTTTG
*
3033090 AGAGACAACTTTG
1 AGAAACAACTTTG
*
3033103 AGACACAA
1 AGAAACAA
3033111 TTCACAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
12 1 0.02
13 38 0.93
14 2 0.05
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.22
Consensus pattern (13 bp):
AGAAACAACTTTG
Found at i:3033450 original size:3 final size:3
Alignment explanation
Indices: 3033442--3033492 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
3033432 GTTCGATTAT
3033442 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3033490 ATA
1 ATA
3033493 TATTATTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3035318 original size:13 final size:13
Alignment explanation
Indices: 3035299--3035329 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3035289 TCTTTATCTC
3035299 AATTTATTTATTT
1 AATTTATTTATTT
*
3035312 GATTTATTTATTT
1 AATTTATTTATTT
3035325 AATTT
1 AATTT
3035330 TTATCTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (13 bp):
AATTTATTTATTT
Found at i:3035433 original size:5 final size:5
Alignment explanation
Indices: 3035423--3035454 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
3035413 TTTTCCTATT
3035423 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
3035455 CTGTATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:3035433 original size:27 final size:29
Alignment explanation
Indices: 3035368--3035441 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 29
3035358 TAAAACCCCC
3035368 TTTTATCTTTATTATTATTTTTAAATCATT
1 TTTTAT-TTTATTATTATTTTTAAATCATT
* **
3035398 ATTTA--TTATTATTATTTTT-CCT-ATT
1 TTTTATTTTATTATTATTTTTAAATCATT
3035423 TTTTATTTTATT-TTATTTT
1 TTTTATTTTATTATTATTTT
3035442 ATTTTATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
25 7 0.18
26 8 0.21
27 19 0.50
30 4 0.11
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (29 bp):
TTTTATTTTATTATTATTTTTAAATCATT
Found at i:3036936 original size:21 final size:21
Alignment explanation
Indices: 3036898--3036937 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3036888 CAATTTCACT
**
3036898 AGAAAAGTTGGTTACATCCTA
1 AGAAAAGTTCATTACATCCTA
*
3036919 AGAAAAGTTCATTGCATCC
1 AGAAAAGTTCATTACATCC
3036938 CAGGAAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
AGAAAAGTTCATTACATCCTA
Found at i:3041619 original size:20 final size:20
Alignment explanation
Indices: 3041596--3041633 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3041586 AAATCATTAT
3041596 TTATTATTT-TATTATTTTCC
1 TTATT-TTTATATTATTTTCC
3041616 TTATTTTTATATTATTTT
1 TTATTTTTATATTATTTT
3041634 ATTATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATTTTTATATTATTTTCC
Found at i:3041643 original size:20 final size:20
Alignment explanation
Indices: 3041592--3041643 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
3041582 TTTTAAATCA
*
3041592 TTATT-TATTATTTTATTATT
1 TTATTATATT-TTATATTATT
*
3041612 TTCCTTAT-TTTTATATTATT
1 TT-ATTATATTTTATATTATT
3041632 TTATTATATTTT
1 TTATTATATTTT
3041644 TTCAATTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 4 0.15
20 17 0.65
21 4 0.15
22 1 0.04
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (20 bp):
TTATTATATTTTATATTATT
Found at i:3045789 original size:53 final size:52
Alignment explanation
Indices: 3045724--3046196 Score: 624
Period size: 53 Copynumber: 8.9 Consensus size: 52
3045714 TAAAAAAAAG
* * * * * *
3045724 CGGGTTCACTCCCTATTACTTTAGGGAGTAGAACTCGAACAATCTTCTATTTT
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT-TCTA
* * *
3045777 CGGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAAAAAATCTTCTGCTTA
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCG-AACAATCTTCTTC-TA
* * * *
3045831 TGGGTTCGTTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCATCTGCCTA
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT-TCTA
*
3045884 CGGGTTCGTTCCCTCTTGCTTCAGGGAGTAGAACTCGAA-ATATCTTCTTCTTA
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACA-ATCTTCTTC-TA
* * *
3045937 CGGGTTCACTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATATTCTATCTA
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT-TCTA
* *
3045990 CGGGTTCGCTCCCTTTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTTCCTA
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTT-CTA
** *
3046043 CGGGTTCGCTCCCTCTTGCTTCAGGGCTTAGAACTCGAACAATCTTCTGCCTA
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT-TCTA
* *
3046096 CGAGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTTCCTA
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTT-CTA
*
3046149 TGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
3046197 GGTGTGATTC
Statistics
Matches: 372, Mismatches: 38, Indels: 20
0.87 0.09 0.05
Matches are distributed among these distances:
52 3 0.01
53 320 0.86
54 49 0.13
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (52 bp):
CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTTCTA
Found at i:3046061 original size:159 final size:158
Alignment explanation
Indices: 3045724--3046197 Score: 691
Period size: 159 Copynumber: 3.0 Consensus size: 158
3045714 TAAAAAAAAG
* * * * *
3045724 CGGGTTCACTCCCTATTACTTTAGGGAGTAGAACTCGAACAATCTTCTAT-TTTCGGGTTCGCTC
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT-TCTTACGGGTTCGCTC
* * *
3045788 CCTCTTGCTTCAAGGAGTAGAACTCGAAAAAATCTTCTGCTTATGGGTTCGTTCCCTCTTGCTTC
65 CCTCTTGCTTCAAGGAGTAGAACTCG-AACAATCTTCTTC-TATGGGTTCGCTCCCTCTTGCTTC
*
3045853 AGGGAGTAGAACTCGAACAATCATCTGCCTA
128 AGGGAGTAGAACTCGAACAATCTTCTGCCTA
* *
3045884 CGGGTTCGTTCCCTCTTGCTTCAGGGAGTAGAACTCGAA-ATATCTTCTTCTTACGGGTTCACTC
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACA-ATCTTCTTCTTACGGGTTCGCTC
* * *
3045948 CCTCTTGCTTCAAGGAGTAGAACTCGAACAATATTCTATCTACGGGTTCGCTCCCTTTTGCTTCA
65 CCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCT-TCTATGGGTTCGCTCCCTCTTGCTTCA
* *
3046013 AGGAGTAGAACTCGAACAATCTTCTTCCTA
129 GGGAGTAGAACTCGAACAATCTTCTGCCTA
** * * *
3046043 CGGGTTCGCTCCCTCTTGCTTCAGGGCTTAGAACTCGAACAATCTTCTGCCTACGAGTTCGCTCC
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTTCTTACGGGTTCGCTCC
3046108 CTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTTCCTATGGGTTCGCTCCCTCTTGCTTCAG
66 CTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTT-CTATGGGTTCGCTCCCTCTTGCTTCAG
3046173 GGAGTAGAACTCGAACAATCTTCTG
130 GGAGTAGAACTCGAACAATCTTCTG
3046198 GTGTGATTCT
Statistics
Matches: 281, Mismatches: 28, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
158 1 0.00
159 199 0.71
160 81 0.29
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (158 bp):
CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTTCTTACGGGTTCGCTCC
CTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTTCTATGGGTTCGCTCCCTCTTGCTTCAGG
GAGTAGAACTCGAACAATCTTCTGCCTA
Found at i:3046702 original size:42 final size:42
Alignment explanation
Indices: 3046600--3046702 Score: 170
Period size: 42 Copynumber: 2.5 Consensus size: 42
3046590 TATCATCTCA
**
3046600 CTCGAAAGACTTACAAATGACCCGAAGGATTTAATCATCATG
1 CTCGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATG
*
3046642 CTCGAAAGACTTACTGATGACCCGAAGGATTTCATCATCATG
1 CTCGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATG
*
3046684 CTCGAAAGACTTATTGATG
1 CTCGAAAGACTTACTGATG
3046703 GCACTTACTG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (42 bp):
CTCGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATG
Found at i:3046838 original size:80 final size:80
Alignment explanation
Indices: 3046705--3046956 Score: 414
Period size: 80 Copynumber: 3.1 Consensus size: 80
3046695 TATTGATGGC
* * *
3046705 ACTTACTGACGTATTTGCTTCACTACTCTTCCATGAAGGCTTAAAAATTACCCGAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
3046770 TATCATGCTCGAAAG
66 TATCATGCTCGAAAG
* *
3046785 ACTTACTGATGGGTTTGCTTCACTACTCTTCGGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
3046850 TATCATGCTCGAAAG
66 TATCATGCTCGAAAG
* ** *
3046865 ACTTACTGATGAATTTGCTTCACTACTCTTCCGTGAAGGCTTACCAGTTACCCGAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
*
3046930 CATCATGCTCGAAAG
66 TATCATGCTCGAAAG
3046945 ACTTACTGATGG
1 ACTTACTGATGG
3046957 CCCGAAGGAC
Statistics
Matches: 159, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 159 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (80 bp):
ACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
TATCATGCTCGAAAG
Found at i:3047136 original size:41 final size:41
Alignment explanation
Indices: 3047079--3047184 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 41
3047069 CCCGAAGGTT
* ** * *
3047079 TTACAGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTACAGATGACCCGAAGGACTTATCATCAAGCTCGAAAGAC
* *
3047120 TTACAGATGACCCGAAGGATTTAAACATCAAGCTCGAAAGAC
1 TTACAGATGACCCGAAGGACTT-ATCATCAAGCTCGAAAGAC
* *
3047162 TTACTGATGACCCG-ACGACTTAT
1 TTACAGATGACCCGAAGGACTTAT
3047185 AAATTATGAA
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
40 1 0.02
41 25 0.47
42 27 0.51
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (41 bp):
TTACAGATGACCCGAAGGACTTATCATCAAGCTCGAAAGAC
Found at i:3047316 original size:212 final size:214
Alignment explanation
Indices: 3046900--3047339 Score: 697
Period size: 212 Copynumber: 2.1 Consensus size: 214
3046890 CTCTTCCGTG
* * * * *
3046900 AAGGCTTACCAG-TTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
1 AAGGCTTA-CAGATGACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGACCCGAAC
* * *
3046964 GACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAGTTTCATCTTCTCAAAA
65 GACTTATAAATTATGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTCAAAA
** * *
3047029 CATCGCTTTTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTACAGATGGCCCGA
130 CATC-AATTTTCATTTTCAAATTCATGTAAAAACATCATACCCGAAGGTTTTACAGATGGCCCGA
3047094 AGGACTTATCATCTTGCTCTA
194 AGGACTTATCATCTTGCTCTA
3047115 AAGGCTTACAGATGACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGACCCG-ACG
1 AAGGCTTACAGATGACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGACCCGAACG
*
3047179 ACTTATAAATTATGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAAC
66 ACTTATAAATTATGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTCAAAAC
* **
3047244 AT-AATTTTCATTTTTAAATTCATGTAAAAACATCATACCCGAAGGTTTTATGGATGGCCCGAAG
131 ATCAATTTTCATTTTCAAATTCATGTAAAAACATCATACCCGAAGGTTTTACAGATGGCCCGAAG
3047308 GACTTATCATCTTGCTCTA
196 GACTTATCATCTTGCTCTA
3047327 AAGGCTTACAGAT
1 AAGGCTTACAGAT
3047340 AGATTTGCTT
Statistics
Matches: 208, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
212 87 0.42
214 68 0.33
215 53 0.25
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (214 bp):
AAGGCTTACAGATGACCCGAAGGATTTAAACATCAAGCTCGAAAGACTTACTGATGACCCGAACG
ACTTATAAATTATGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTCAAAAC
ATCAATTTTCATTTTCAAATTCATGTAAAAACATCATACCCGAAGGTTTTACAGATGGCCCGAAG
GACTTATCATCTTGCTCTA
Found at i:3047438 original size:39 final size:39
Alignment explanation
Indices: 3047327--3047440 Score: 132
Period size: 34 Copynumber: 3.1 Consensus size: 39
3047317 TCTTGCTCTA
* *
3047327 AAGGCTTAC-AGATAGATTTGCTTCACTACTCTTCCGTG
1 AAGGCTTACAAGATGGATTTGCTTCACTACTCTTCGGTG
* *
3047365 AAGGCTT--AAGATGG---TGTTTCACTACCCTTCGGTG
1 AAGGCTTACAAGATGGATTTGCTTCACTACTCTTCGGTG
* *
3047399 AAGGCTTACAAAATGGATTTGCTTCACTACTCTTTGGTG
1 AAGGCTTACAAGATGGATTTGCTTCACTACTCTTCGGTG
3047438 AAG
1 AAG
3047441 ACTTGACTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
34 24 0.39
36 6 0.10
37 5 0.08
38 7 0.11
39 20 0.32
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (39 bp):
AAGGCTTACAAGATGGATTTGCTTCACTACTCTTCGGTG
Found at i:3053177 original size:45 final size:45
Alignment explanation
Indices: 3053128--3053231 Score: 172
Period size: 45 Copynumber: 2.3 Consensus size: 45
3053118 CATCATCTTG
* *
3053128 GACATTTGTTCTTTTATCTCTCTTATGTCCTTGTGCTCTCCGTCA
1 GACATTTGTTCTTTTATCTCTCTTATCTCATTGTGCTCTCCGTCA
3053173 GACATTTGTTCTTTTATCTCTCTTATCTCATTGTGCTCTCCGTCA
1 GACATTTGTTCTTTTATCTCTCTTATCTCATTGTGCTCTCCGTCA
* *
3053218 GACATATGATCTTT
1 GACATTTGTTCTTT
3053232 ATGTGCGCAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.14, C:0.25, G:0.12, T:0.48
Consensus pattern (45 bp):
GACATTTGTTCTTTTATCTCTCTTATCTCATTGTGCTCTCCGTCA
Found at i:3053530 original size:6 final size:6
Alignment explanation
Indices: 3053499--3053528 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3053489 TGCTAATAAG
*
3053499 AATGCA AATGCA AATGCA AATGCA CATGCA
1 AATGCA AATGCA AATGCA AATGCA AATGCA
3053529 CAAGGTGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.17
Consensus pattern (6 bp):
AATGCA
Found at i:3059337 original size:13 final size:13
Alignment explanation
Indices: 3059319--3059374 Score: 85
Period size: 13 Copynumber: 4.3 Consensus size: 13
3059309 AATCTTAGAA
3059319 ACAACTTTGAGAG
1 ACAACTTTGAGAG
*
3059332 ACAACTTTGAGAT
1 ACAACTTTGAGAG
*
3059345 AAAACTTTGAGAG
1 ACAACTTTGAGAG
*
3059358 ACAACTTTGAGAC
1 ACAACTTTGAGAG
3059371 ACAA
1 ACAA
3059375 TTCACAAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (13 bp):
ACAACTTTGAGAG
Found at i:3060673 original size:26 final size:26
Alignment explanation
Indices: 3060637--3060686 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
3060627 TGATCCATTA
3060637 ATATGCAACAAATGGATAAAGATTTG
1 ATATGCAACAAATGGATAAAGATTTG
3060663 ATATGCAACAAATGGATAAAGATT
1 ATATGCAACAAATGGATAAAGATT
3060687 GACAATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (26 bp):
ATATGCAACAAATGGATAAAGATTTG
Found at i:3061208 original size:3 final size:3
Alignment explanation
Indices: 3061200--3061236 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
3061190 ATTTATTTAT
*
3061200 TTA TTA TTA TTA TAA TTA TTA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
3061237 AAATATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3061242 original size:19 final size:19
Alignment explanation
Indices: 3061204--3061244 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3061194 ATTTATTTAT
**
3061204 TATTATTATAATTATTATA
1 TATTATTATAATTAAAATA
*
3061223 TATTATTATTATTAAAATA
1 TATTATTATAATTAAAATA
3061242 TAT
1 TAT
3061245 ATATATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTATTATAATTAAAATA
Found at i:3061266 original size:25 final size:21
Alignment explanation
Indices: 3061201--3061266 Score: 53
Period size: 22 Copynumber: 2.9 Consensus size: 21
3061191 TTTATTTATT
*
3061201 TATTATTATT-ATAATTATTATA
1 TATTATTATTAATAA--AATATA
*
3061223 TATTATTATTATTAAAATATA
1 TATTATTATTAATAAAATATA
3061244 TATATATATATATAATAATAATA
1 TAT-TAT-TAT-TAATAA-AATA
3061267 ATAAAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 8 0.22
22 13 0.36
23 6 0.17
24 5 0.14
25 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTATTATTAATAAAATATA
Found at i:3062602 original size:23 final size:22
Alignment explanation
Indices: 3062548--3062602 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
3062538 TAATTGTATT
* * *
3062548 TTTATTGTTTTAATTTTACTTG
1 TTTATTATTTAAATATTACTTG
*
3062570 TTTATATATTTAAATATTATTTG
1 TTTAT-TATTTAAATATTACTTG
3062593 TATTATTATT
1 T-TTATTATT
3062603 ATATAGTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.19
23 18 0.67
24 4 0.15
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (22 bp):
TTTATTATTTAAATATTACTTG
Found at i:3062672 original size:27 final size:28
Alignment explanation
Indices: 3062620--3062674 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
3062610 CATATAAATA
3062620 TATATATAATAAATAATAATTTATATTTT
1 TATATATAATAAAT-ATAATTTATATTTT
*
3062649 TATATAT-ATAAAT-TATTTTAATATTT
1 TATATATAATAAATATAATTT-ATATTT
3062675 ATTTATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.21
27 6 0.25
28 6 0.25
29 7 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TATATATAATAAATATAATTTATATTTT
Found at i:3062675 original size:25 final size:25
Alignment explanation
Indices: 3062616--3062676 Score: 61
Period size: 27 Copynumber: 2.4 Consensus size: 25
3062606 TAGTCATATA
*
3062616 AATATATATATAATAAATAATAATTT
1 AATATTTATATAATAAAT-ATAATTT
* *
3062642 ATATTTTTATATATATAAAT-TATTTT
1 A-ATATTTATATA-ATAAATATAATTT
3062668 AATATTTAT
1 AATATTTAT
3062677 TTATTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 7 0.24
26 7 0.24
27 9 0.31
28 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
AATATTTATATAATAAATATAATTT
Found at i:3062809 original size:23 final size:22
Alignment explanation
Indices: 3062763--3062807 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3062753 ATATTATAAA
3062763 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
3062785 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
3062808 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:3073881 original size:9 final size:10
Alignment explanation
Indices: 3073862--3073916 Score: 58
Period size: 10 Copynumber: 5.3 Consensus size: 10
3073852 CTTGAAGAAT
3073862 AAAAACAAAA
1 AAAAACAAAA
3073872 AAAAACAAAA
1 AAAAACAAAA
3073882 AAGGAAA-AAAA
1 AA--AAACAAAA
*
3073893 AGAAAAGAAAA
1 A-AAAACAAAA
*
3073904 AAAAAGAAAA
1 AAAAACAAAA
3073914 AAA
1 AAA
3073917 GGGTGTCAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
10 27 0.66
11 10 0.24
12 4 0.10
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:3073889 original size:15 final size:14
Alignment explanation
Indices: 3073856--3073913 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
3073846 ATTATGCTTG
* *
3073856 AAGAATAAAAACAA
1 AAGAAAAAAAAGAA
3073870 AA-AAAAACAAA-AA
1 AAGAAAAA-AAAGAA
*
3073883 AGGAAAAAAAAGAA
1 AAGAAAAAAAAGAA
3073897 AAGAAAAAAAAAGAA
1 AAG-AAAAAAAAGAA
3073912 AA
1 AA
3073914 AAAGGGTGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 10 0.27
14 14 0.38
15 13 0.35
ACGTcount: A:0.84, C:0.03, G:0.10, T:0.02
Consensus pattern (14 bp):
AAGAAAAAAAAGAA
Found at i:3075164 original size:110 final size:112
Alignment explanation
Indices: 3074937--3075245 Score: 430
Period size: 110 Copynumber: 2.7 Consensus size: 112
3074927 GAATGTGCTC
* *
3074937 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAACCACAGAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--TGAACCACAAAACCAAT
* *
3075002 CATTGAATTTGAAAGATGAAGGTGATCATAGTAGAAATAAGAAGACCTA
64 CATTGAATTTGAAAGATGAAGGTGATCATAGTACAAATAAGAAGACCCA
**
3075051 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT-CCCCA-AAAACCAATCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTGAACCACAAAACCAATCA
* *
3075114 TT-AGATTTGAAAGATGAATGTGCTCATAGTACAAATAA-AGAGACCCA
66 TTGA-ATTTGAAAGATGAAGGTGATCATAGTACAAATAAGA-AGACCCA
*
3075161 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACCACAGAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT--GAACCACAAAACCAAT
*
3075226 CATTGGAA-TTAAAAGATGAA
64 CATT-GAATTTGAAAGATGAA
3075246 CTGCATGATC
Statistics
Matches: 175, Mismatches: 12, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
109 2 0.01
110 96 0.55
111 3 0.02
112 1 0.01
113 3 0.02
114 68 0.39
115 1 0.01
116 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (112 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTGAACCACAAAACCAATCA
TTGAATTTGAAAGATGAAGGTGATCATAGTACAAATAAGAAGACCCA
Found at i:3076172 original size:113 final size:112
Alignment explanation
Indices: 3075970--3076452 Score: 535
Period size: 113 Copynumber: 4.3 Consensus size: 112
3075960 TTCCAGAAAA
* * * * * *
3075970 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTACTTAAATTCATCACTCAGTGGAACAGCAGT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGATCAGCATT
* *
3076035 ACCAGTTAGAGTTCATAATGAGAAGAAATCACCTAAAGAAGGAAGAAG
66 ACCAGTTAGAGTTCATAATGAGAAGAACTCATCTAAAGAA-GAAGAAG
* *
3076083 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGATCAGCATT
* * *
3076148 ACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAG
66 ACCAGTTAGAGTTCATAATGAGAAGAACTCATCTAAAGAA-GAAGAAG
* * * ** * *
3076196 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATTAACATT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGATCAGCATT
* * * * **
3076261 GCCAGGTAGAGTTCATAATGAGAACAACTCGTC-ATCTGAAGAAGAAG
66 ACCAGTTAGAGTTCATAATGAGAAGAACTCATCTA-AAGAAGAAGAAG
* * * * * *
3076308 AAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTT-GATGGATCAGCTT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTCAATGGATCAGCAT
* * ** * *
3076372 TTCTAGAGAAAGTTCATAATGAGAAGAACTCAT-T--TGAAGAAGAAG
65 TACCAGTTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGAAGAAG
* *
3076417 AAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGC
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
3076453 ATAATTCTAT
Statistics
Matches: 319, Mismatches: 48, Indels: 10
0.85 0.13 0.03
Matches are distributed among these distances:
109 43 0.13
112 86 0.27
113 190 0.60
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (112 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGATCAGCATT
ACCAGTTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGAAGAAG
Found at i:3076388 original size:225 final size:222
Alignment explanation
Indices: 3075970--3076452 Score: 542
Period size: 225 Copynumber: 2.2 Consensus size: 222
3075960 TTCCAGAAAA
* * *
3075970 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTACTTAAATTCATCACTCAGTGGAACAGCAGT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCAGTGGAACAACAGT
* * * *
3076035 ACCAGTTAGAGTTCATAATGAGAAGAAATCACCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAG
66 ACCAGGTAGAGTTCATAATGAGAACAAATCACATAAAGAAGGAAGAAGAAATTCATAATGAGAAG
* ** * ****
3076100 AACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCGAGTTCATA
131 AACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAGAGAAAGTTCATA
3076165 ATAAGAAGAACTCATCTGAAGAAGGAAGAAG
196 ATAAGAAGAACTCAT-T--AGAA-GAAGAAG
* * * ** ** *
3076196 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTA-TTTGATGGATTAACAT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCAG-TGGAACAACAG
* * * **
3076260 TGCCAGGTAGAGTTCATAATGAGAACAACTCGTCAT-CTGAA-GAAGAAGAAATTCATAATGAGA
65 TACCAGGTAGAGTTCATAATGAGAACAAATC-ACATAAAGAAGGAAGAAGAAATTCATAATGAGA
* * * * *
3076323 AGAATTTGTTCAACCTTTTGCTCAAATCCATCACTT-GATGGATCAGCTTTTCTAGAGAAAGTTC
129 AGAACTTGTTCAACCTTTTGCTCAAATCCATCA-TTCAATGGATCAGCATTACCAGAGAAAGTTC
* *
3076387 ATAATGAGAAGAACTCATTTGAAGAAGAAG
193 ATAATAAGAAGAACTCATTAGAAGAAGAAG
* *
3076417 AAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGC
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
3076453 ATAATTCTAT
Statistics
Matches: 215, Mismatches: 39, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
221 39 0.18
222 3 0.01
224 1 0.00
225 88 0.41
226 82 0.38
227 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (222 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCAGTGGAACAACAGT
ACCAGGTAGAGTTCATAATGAGAACAAATCACATAAAGAAGGAAGAAGAAATTCATAATGAGAAG
AACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAGAGAAAGTTCATA
ATAAGAAGAACTCATTAGAAGAAGAAG
Found at i:3076550 original size:20 final size:20
Alignment explanation
Indices: 3076527--3076592 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
3076517 ACTCATCTGA
3076527 AGAAGAAGAAGTTCATAATG
1 AGAAGAAGAAGTTCATAATG
** *
3076547 AGAAGAACTCA--TC-TGAAGG
1 AGAAGAA-GAAGTTCAT-AATG
3076566 AGAAAGAAGAAGTTCATAATG
1 AG-AAGAAGAAGTTCATAATG
3076587 AGAAGA
1 AGAAGA
3076593 GCTTATTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 1 0.03
19 8 0.24
20 16 0.47
21 8 0.24
22 1 0.03
ACGTcount: A:0.50, C:0.08, G:0.26, T:0.17
Consensus pattern (20 bp):
AGAAGAAGAAGTTCATAATG
Found at i:3076551 original size:36 final size:39
Alignment explanation
Indices: 3076504--3076592 Score: 148
Period size: 40 Copynumber: 2.3 Consensus size: 39
3076494 CCAGAGAATC
3076504 CATAATGAGAAGAACTCATCTG-A-AG-AAGAAGAAGTT
1 CATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTT
3076540 CATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTT
1 CATAATGAGAAGAACTCATCTGAA-GAGAAAGAAGAAGTT
3076580 CATAATGAGAAGA
1 CATAATGAGAAGA
3076593 GCTTATTCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
36 22 0.45
37 1 0.02
39 2 0.04
40 24 0.49
ACGTcount: A:0.48, C:0.10, G:0.24, T:0.18
Consensus pattern (39 bp):
CATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTT
Found at i:3076666 original size:158 final size:152
Alignment explanation
Indices: 3076381--3076688 Score: 393
Period size: 158 Copynumber: 2.0 Consensus size: 152
3076371 TTTCTAGAGA
* * *
3076381 AAGTTCATAATGAGAAGAACTCATTTGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAAC
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTATTCAAA
* * * * ** *
3076446 CTTTTGCATAATTCTATTACAGAAAGAGATAGATTAGCATCAGCTTTTCCAGAGAATCCATAATG
66 CTTTTGAATAATTCTATCACAGAAAGAAATAGATTAACATCA-C-TCCCCAGAAAATCCATAATG
3076511 AGAAGAACTCATCTGAAGAAGAAG
129 AGAAGAACTCATCTGAAGAAGAAG
*
3076535 AAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATT
1 AAGTTCATAATGAGAAGAACTCATCTG-A--AG-AAGAAGAAGTTCACAATGAGAAGAGCTTATT
* * * *
3076600 CAAACTTTTGAATGATTCTATCACAGAAGGAAATAGGTTAACATCA-TCCCCAGCAAAAATTTCA
62 CAAACTTTTGAATAATTCTATCACAGAAAGAAATAGATTAACATCACTCCCCAG--AAAA-TCCA
3076664 TAATGAGAAGAACTCATCTGAAGAA
124 TAATGAGAAGAACTCATCTGAAGAA
3076689 AGAGAAGAAT
Statistics
Matches: 132, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
154 26 0.20
155 6 0.05
157 5 0.04
158 95 0.72
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (152 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTATTCAAA
CTTTTGAATAATTCTATCACAGAAAGAAATAGATTAACATCACTCCCCAGAAAATCCATAATGAG
AAGAACTCATCTGAAGAAGAAG
Found at i:3076861 original size:3 final size:3
Alignment explanation
Indices: 3076853--3076882 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3076843 ATTTATTTAT
3076853 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3076883 AAAAAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3078101 original size:28 final size:29
Alignment explanation
Indices: 3078054--3078111 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
3078044 TCATAAAATA
3078054 TATATAATAAATAATAATTTATATT-TTTT
1 TATATAATAAATAATAATTTAT-TTATTTT
* *
3078083 TATAT-ATAAATATTTATTTATTTATTTT
1 TATATAATAAATAATAATTTATTTATTTT
3078111 T
1 T
3078112 CAATATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 2 0.08
28 19 0.73
29 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TATATAATAAATAATAATTTATTTATTTT
Found at i:3079786 original size:18 final size:16
Alignment explanation
Indices: 3079763--3079807 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 16
3079753 TGTTTATGAG
3079763 GGAATTGGAATTTGTGAA
1 GGAATTGGAATTTGT--A
3079781 GGAATTGGAATTTGTA
1 GGAATTGGAATTTGTA
*
3079797 GAAATTGGAAT
1 GGAATTGGAAT
3079808 CCAATTTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 11 0.42
18 15 0.58
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (16 bp):
GGAATTGGAATTTGTA
Found at i:3080440 original size:39 final size:37
Alignment explanation
Indices: 3080382--3080476 Score: 154
Period size: 39 Copynumber: 2.5 Consensus size: 37
3080372 TTTTCACCCT
3080382 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTT-AAA
*
3080421 AAACCCGACCTGACTCCGACCCGAATATCACACTTAAA
1 AAACCCGACCCGAC-CCGACCCGAATATCACACTTAAA
3080459 AAACCCGACCCGACCCGA
1 AAACCCGACCCGACCCGA
3080477 ACAAAATAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
37 4 0.08
38 22 0.42
39 27 0.51
ACGTcount: A:0.38, C:0.40, G:0.12, T:0.11
Consensus pattern (37 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
Found at i:3080732 original size:37 final size:38
Alignment explanation
Indices: 3080647--3080734 Score: 169
Period size: 38 Copynumber: 2.3 Consensus size: 38
3080637 CCCTAAACTC
3080647 AAACCCGACCCGACTCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGACTCGACCCGAATATCACACTTAAAA
3080685 AAACCCGACCCGACTCGACCCGAATATCACACTT-AAA
1 AAACCCGACCCGACTCGACCCGAATATCACACTTAAAA
3080722 AAACCCGACCCGA
1 AAACCCGACCCGA
3080735 ACAAAATAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 16 0.32
38 34 0.68
ACGTcount: A:0.39, C:0.39, G:0.11, T:0.11
Consensus pattern (38 bp):
AAACCCGACCCGACTCGACCCGAATATCACACTTAAAA
Found at i:3080872 original size:249 final size:252
Alignment explanation
Indices: 3080342--3080944 Score: 835
Period size: 249 Copynumber: 2.4 Consensus size: 252
3080332 TATAAGGTAA
* * * * *
3080342 AATTATATAT-TTTTTGGATCGGTCTGGTTTTTTTCACCCTAAACCCGAACCCGAC-C-CGACCC
1 AATTATATATATTTTTGGGTCGGTCCGGCTTTTTTCACCCTAAACTCAAACCCGACACTCGACCC
*
3080404 GAATATCACACTTAAAAAAACCCGACCTGACTCCGACCCGAATATCACACTTAAAAAACCCGACC
66 GAATATCACACTTAAAAAAACCCGACCCGACT-CGACCCGAATATCACACTTAAAAAA--C-ACC
*
3080469 CGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCGACCCGA
127 CGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCAAATATATGAATTAGAAATCCGACCCGA
3080534 GCCGACCCGAAATAATAAAAAATCATTTTTATTTAATAAAAAGAGTGACTTAATCCGACCCGACC
192 --C-A--C-AAATAATAAAAAATCATTTTTATTTAATAAAAAGAGTGACTTAATCCGACCCGACC
3080599 CG
251 CG
*
3080601 AATTATATATATTTTCGGGTCGGTCCGG-TTTTTTCACCCTAAACTCAAACCCGACCCGACTCGA
1 AATTATATATATTTTTGGGTCGGTCCGGCTTTTTTCACCCTAAACTCAAACCCGA--C-ACTCGA
3080665 CCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTT-AAAAA-ACCC
63 CCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACACCC
3080728 GACCCGAACAAAATAAAGTTTCATCCGACCCGACCCAAATATATGAATTAGAAATCCGACCCG--
128 GACCCGAACAAAATAAAGTTTCATCCGACCCGACCCAAATATATGAATTAGAAATCCGACCCGAC
* * *
3080791 --AAATAATAAAAAAATTATTTTTATTTAATAAAAATAGTGACTTAATCCGACCCGACCTG
193 ACAAATAAT-AAAAAATCATTTTTATTTAATAAAAAGAGTGACTTAATCCGACCCGACCCG
*
3080850 AATTATATATATTTTTGGGTCGGTCCGGCTTTTTTC-GCC---A-T-AAACCCGA-ACTCGACCC
1 AATTATATATATTTTTGGGTCGGTCCGGCTTTTTTCACCCTAAACTCAAACCCGACACTCGACCC
* *
3080908 GAATATCACACTTAAAAAAACCCGATCCGACCCGACC
66 GAATATCACACTTAAAAAAACCCGACCCGACTCGACC
3080945 AAAATAAAGT
Statistics
Matches: 322, Mismatches: 14, Indels: 35
0.87 0.04 0.09
Matches are distributed among these distances:
240 44 0.14
244 8 0.02
245 1 0.00
246 1 0.00
248 7 0.02
249 77 0.24
250 7 0.02
258 66 0.20
259 34 0.11
260 14 0.04
261 1 0.00
262 5 0.02
263 20 0.06
264 37 0.11
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.24
Consensus pattern (252 bp):
AATTATATATATTTTTGGGTCGGTCCGGCTTTTTTCACCCTAAACTCAAACCCGACACTCGACCC
GAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACACCCGAC
CCGAACAAAATAAAGTTTCATCCGACCCGACCCAAATATATGAATTAGAAATCCGACCCGACACA
AATAATAAAAAATCATTTTTATTTAATAAAAAGAGTGACTTAATCCGACCCGACCCG
Found at i:3083171 original size:39 final size:39
Alignment explanation
Indices: 3083115--3083228 Score: 165
Period size: 39 Copynumber: 2.9 Consensus size: 39
3083105 CTTAATTTCT
*
3083115 AAGAAAATAAATTCAACAATTTATTTTCTTTTATAAAAC
1 AAGAAAATAAATTCAACAATTTATTTTCTTTTACAAAAC
* * *
3083154 AGGAAAATAAATCCAACAATTTATTTTCCTTTACAAAAC
1 AAGAAAATAAATTCAACAATTTATTTTCTTTTACAAAAC
* * *
3083193 AATAAAATAAATTCAACGATTTATTTCCTTTTACAA
1 AAGAAAATAAATTCAACAATTTATTTTCTTTTACAA
3083229 CCCAAAATCA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (39 bp):
AAGAAAATAAATTCAACAATTTATTTTCTTTTACAAAAC
Found at i:3083312 original size:136 final size:133
Alignment explanation
Indices: 3083115--3083437 Score: 355
Period size: 136 Copynumber: 2.4 Consensus size: 133
3083105 CTTAATTTCT
* * * *
3083115 AAGAAAATAAATTCAACAATTTATTTTCTTTTATAAAACAGGAAAATAAATCCAACAATTTATT-
1 AAGAAAATAAATTCAATAATTTA-TTACTTTTACAAAACA-GAAAATAAATACAACAATTTATTA
* *
3083179 TTCCTTTACAAAACA-ATAAAATAAATTCAACGATTTATTTCCTTTTACAACCCAA-AATCATAT
64 TT--TTTACAAAACAGA-AAAATAAATCCAACGATTTATTTCCTTTTACAA-ACAAGAATCATAT
* *
3083242 AAGATTATC
125 AAGATCATA
**
3083251 AAGAAAATAAATTCAATAATTTATTACCTTTTACAAAACATGAAAATAAATACAATTATTTATTA
1 AAGAAAATAAATTCAATAATTTATTA-CTTTTACAAAACA-GAAAATAAATACAACAATTTATTA
* * ** * *
3083316 GTTTTTAGAAAATAGAAAAATAAATCCAACGATTTATTTTGTTTTACAAACAAGAATCATGTGAG
64 -TTTTTACAAAACAGAAAAATAAATCCAACGATTTATTTCCTTTTACAAACAAGAATCATATAAG
* *
3083381 GTCCTA
128 ATCATA
*
3083387 AAGAAAATAAATTCAATAATTTATTTACTTTTACAAAATAGAAAAATAAAT
1 AAGAAAATAAATTCAATAATTTA-TTACTTTTACAAAACAG-AAAATAAAT
3083438 CCAAAGATTT
Statistics
Matches: 160, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
135 6 0.04
136 148 0.93
137 4 0.03
138 2 0.01
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (133 bp):
AAGAAAATAAATTCAATAATTTATTACTTTTACAAAACAGAAAATAAATACAACAATTTATTATT
TTTACAAAACAGAAAAATAAATCCAACGATTTATTTCCTTTTACAAACAAGAATCATATAAGATC
ATA
Found at i:3083322 original size:39 final size:38
Alignment explanation
Indices: 3083252--3083340 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 38
3083242 AAGATTATCA
*
3083252 AGAAAATAAATTCAATAATTTATTACCTTTTACAAAAC
1 AGAAAATAAATACAATAATTTATTACCTTTTACAAAAC
* ** * *
3083290 ATGAAAATAAATACAATTATTTATTAGTTTTTAGAAAAT
1 A-GAAAATAAATACAATAATTTATTACCTTTTACAAAAC
3083329 AGAAAAATAAAT
1 AG-AAAATAAAT
3083341 CCAACGATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
38 2 0.05
39 41 0.95
ACGTcount: A:0.53, C:0.07, G:0.06, T:0.35
Consensus pattern (38 bp):
AGAAAATAAATACAATAATTTATTACCTTTTACAAAAC
Found at i:3083393 original size:97 final size:95
Alignment explanation
Indices: 3083292--3083556 Score: 284
Period size: 94 Copynumber: 2.8 Consensus size: 95
3083282 TACAAAACAT
* * * *
3083292 GAAAATAAATACAATTATTTATTAGTTTTTAGAAAATAGAAAAATAAATCCAACGATTTATTTTG
1 GAAAATAAATTCAATAATTTATTA-CTTTTACAAAATAGAAAAATAAATCCAACGATTTATTTT-
* *
3083357 TTTTACAAA-CAAGAATCATGTGAGGTCCTAAA
64 TTTTACAAATC-AGAATCATCTGAGATCCTAAA
* *
3083389 GAAAATAAATTCAATAATTTATTTACTTTTACAAAATAGAAAAATAAATCCAAAGA-TT-TTGTT
1 GAAAATAAATTCAATAATTTA-TTACTTTTACAAAATAGAAAAATAAATCCAACGATTTATTTTT
* * * *
3083452 TTTGCAAATCAGAATCATCTGAGATTCTCAG
65 TTTACAAATCAGAATCATCTGAGATCCTAAA
* * * * * * *
3083483 GAAAATAAATTTAATGATTTATTTCCTTTTACACAATAGGAAAATAAATCAAACGATTTATTTCC
1 GAAAATAAATTCAATAATTTA-TTACTTTTACAAAATAGAAAAATAAATCCAACGATTTATTT-T
3083548 TTTTACAAA
64 TTTTACAAA
3083557 ATAGAAAACT
Statistics
Matches: 141, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
94 73 0.52
95 6 0.04
96 4 0.03
97 55 0.39
98 3 0.02
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.35
Consensus pattern (95 bp):
GAAAATAAATTCAATAATTTATTACTTTTACAAAATAGAAAAATAAATCCAACGATTTATTTTTT
TTACAAATCAGAATCATCTGAGATCCTAAA
Found at i:3083541 original size:39 final size:38
Alignment explanation
Indices: 3083481--3083714 Score: 202
Period size: 39 Copynumber: 6.0 Consensus size: 38
3083471 TGAGATTCTC
* * *
3083481 AGGAAAATAAATTTAATGATTTATTTCCTTTTACACAAT
1 AGGAAAATAAA-TCAACGATTTATTTCCTTTTACAAAAT
3083520 AGGAAAATAAATCAAACGATTTATTTCCTTTTACAAAAT
1 AGGAAAATAAATC-AACGATTTATTTCCTTTTACAAAAT
* * *
3083559 A-GAAAACTAAATTCAACAATTTATTTCATTTTTCAAAAT
1 AGGAAAA-TAAA-TCAACGATTTATTTCCTTTTACAAAAT
* * * * *
3083598 AGGAAATTAAGTTCAACAATTTATTTTCTTTTACAAAAC
1 AGGAAAATAA-ATCAACGATTTATTTCCTTTTACAAAAT
* * * * *
3083637 ATGAAAATAAATTTAATG-TTTTTTTCATTTTACAAAAT
1 AGGAAAATAAA-TCAACGATTTATTTCCTTTTACAAAAT
* ** * *
3083675 AGAAAAATAAATTCAAATATTTATTTTCTTTTTCAAAAT
1 AGGAAAATAAA-TCAACGATTTATTTCCTTTTACAAAAT
3083714 A
1 A
3083715 AAATCATTCA
Statistics
Matches: 157, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
38 35 0.22
39 116 0.74
40 6 0.04
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (38 bp):
AGGAAAATAAATCAACGATTTATTTCCTTTTACAAAAT
Found at i:3083697 original size:77 final size:75
Alignment explanation
Indices: 3083483--3083712 Score: 264
Period size: 78 Copynumber: 3.0 Consensus size: 75
3083473 AGATTCTCAG
* * *
3083483 GAAAATAAATTTAATGATTTATTTCCTTTTACACAATAGGAAAATAAA-TCAAACGATTTATTTC
1 GAAAATAAATTTAATG-TTTATTTCATTTTACAAAATAGGAAAATAAATTCAAA--ATTTATTTT
*
3083547 CTTTTACAAAATA
63 CTTTTACAAAACA
* ** * * *
3083560 GAAAACTAAATTCAACAATTTATTTCATTTTTCAAAATAGGAAATTAAGTTCAACAATTTATTTT
1 GAAAA-TAAATTTAA-TGTTTATTTCATTTTACAAAATAGGAAAATAAATTCAA-AATTTATTTT
3083625 CTTTTACAAAACA
63 CTTTTACAAAACA
* *
3083638 TGAAAATAAATTTAATGTTTTTTTCATTTTACAAAATAGAAAAATAAATTCAAATATTTATTTTC
1 -GAAAATAAATTTAATGTTTATTTCATTTTACAAAATAGGAAAATAAATTCAAA-ATTTATTTTC
*
3083703 TTTTTCAAAA
64 TTTTACAAAA
3083713 TAAAATCATT
Statistics
Matches: 128, Mismatches: 19, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
76 1 0.01
77 55 0.43
78 62 0.48
79 9 0.07
80 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.40
Consensus pattern (75 bp):
GAAAATAAATTTAATGTTTATTTCATTTTACAAAATAGGAAAATAAATTCAAAATTTATTTTCTT
TTACAAAACA
Found at i:3083698 original size:116 final size:117
Alignment explanation
Indices: 3083499--3083714 Score: 303
Period size: 116 Copynumber: 1.9 Consensus size: 117
3083489 AAATTTAATG
* * *
3083499 ATTTATTTCCTTTTACACAATAGGAAAATAAATCAAACGATTTATTTCCTTTTACAAAATAGAAA
1 ATTTATTTCCTTTTACAAAACAGGAAAATAAATCAAACGATTTATTTCATTTTACAAAATAGAAA
*
3083564 ACTAAATTCAACAATTTA-TTTCATTTTTCAAAATAGGAAATTAAGTTCAACA
66 AATAAATTCAACAATTTATTTTC-TTTTTCAAAATAGGAAATTAAGTTCAACA
* * ** * *
3083616 ATTTATTTTCTTTTACAAAACATGAAAATAAATTTAATG-TTTTTTTCATTTTACAAAATAGAAA
1 ATTTATTTCCTTTTACAAAACAGGAAAATAAATCAAACGATTTATTTCATTTTACAAAATAGAAA
3083680 AATAAATTCAA-ATATTTATTTTCTTTTTCAAAATA
66 AATAAATTCAACA-ATTTATTTTCTTTTTCAAAATA
3083715 AAATCATTCA
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
115 1 0.01
116 50 0.57
117 36 0.41
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (117 bp):
ATTTATTTCCTTTTACAAAACAGGAAAATAAATCAAACGATTTATTTCATTTTACAAAATAGAAA
AATAAATTCAACAATTTATTTTCTTTTTCAAAATAGGAAATTAAGTTCAACA
Found at i:3084052 original size:58 final size:58
Alignment explanation
Indices: 3083975--3084121 Score: 208
Period size: 58 Copynumber: 2.5 Consensus size: 58
3083965 TCAAGATTCA
* **
3083975 CAAGAAAATAAATTTAACAATTTATTTCTTTTTATAAA-ATAAAATCATTTGAGAGTCT
1 CAAGAAAATAAATTCAACAATTTATTTCTTTTTA-AAAGATAAAATCATTAAAGAGTCT
* *
3084033 CGAGAAAATAAATTCAACAATTTATTT-TCTTTTAAAAGATAAAATCATTAAAGATTCT
1 CAAGAAAATAAATTCAACAATTTATTTCT-TTTTAAAAGATAAAATCATTAAAGAGTCT
*
3084091 CAAGAAAATAAATTCAATAATTTATTTCTTT
1 CAAGAAAATAAATTCAACAATTTATTTCTTT
3084122 ATTCAATATT
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
57 4 0.05
58 74 0.94
59 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.39
Consensus pattern (58 bp):
CAAGAAAATAAATTCAACAATTTATTTCTTTTTAAAAGATAAAATCATTAAAGAGTCT
Found at i:3084173 original size:159 final size:159
Alignment explanation
Indices: 3083879--3084218 Score: 484
Period size: 159 Copynumber: 2.1 Consensus size: 159
3083869 ATTTTCAAGG
* * * *
3083879 AAATAAATTCAACAATATATTTCCTTTGAAAAGATAGAATAATTAAATATTCTCAATAAAATAAA
1 AAATAAATTCAACAATTTATTTCCTTTGAAAAGATAAAATAATTAAAGATTCTCAAGAAAATAAA
*
3083944 TTCAACAATTTATTTCGATATTCAAGATTCACAAGAAAATAAATTTAACAATTTATTTCTTTTTA
66 TTCAACAATTTATTTCGATATTCAAGATTCACAAGAAAATAAATTTAACAATTTATTTCATTTTA
* *
3084009 TAAAATAAAATCATTTGAGAGTCTC-GAGA
131 GAAAATAAAATCATTTAAGAGTCTCAG-GA
* * *
3084038 AAATAAATTCAACAATTTATTTTCTTTTAAAAGATAAAATCATTAAAGATTCTCAAGAAAATAAA
1 AAATAAATTCAACAATTTATTTCCTTTGAAAAGATAAAATAATTAAAGATTCTCAAGAAAATAAA
* ** * * *
3084103 TTCAATAATTTATTTCTTTATTCAATATTCCCAAGAAAATAAGTTTAACAATTTATTTCATTTTA
66 TTCAACAATTTATTTCGATATTCAAGATTCACAAGAAAATAAATTTAACAATTTATTTCATTTTA
* *
3084168 GAAAATAATATCATTTAAGATTCTCAGGA
131 GAAAATAAAATCATTTAAGAGTCTCAGGA
* *
3084197 AAATAAATTTAACAAATTATTT
1 AAATAAATTCAACAATTTATTT
3084219 ATAAAAAAAT
Statistics
Matches: 160, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
159 159 0.99
160 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (159 bp):
AAATAAATTCAACAATTTATTTCCTTTGAAAAGATAAAATAATTAAAGATTCTCAAGAAAATAAA
TTCAACAATTTATTTCGATATTCAAGATTCACAAGAAAATAAATTTAACAATTTATTTCATTTTA
GAAAATAAAATCATTTAAGAGTCTCAGGA
Found at i:3084217 original size:101 final size:101
Alignment explanation
Indices: 3084035--3084218 Score: 264
Period size: 101 Copynumber: 1.8 Consensus size: 101
3084025 GAGAGTCTCG
3084035 AGAAAATAAATTCAACAATTTATTTTCTTTTAAAAGATAAAATCATTAAAGATTCTCAAGAAAAT
1 AGAAAATAAATTCAACAATTTATTTTCTTTTAAAAGATAAAATCATTAAAGATTCTCAAGAAAAT
* *
3084100 AAATTCAATAATTTATTTCTTTATTCAATATTCCCA
66 AAATTCAACAAATTATTTCTTTATTCAATATTCCCA
* * * * *
3084136 AGAAAATAAGTTTAACAATTTA-TTTCATTTTAGAAA-ATAATATCATTTAAGATTCTCAGGAAA
1 AGAAAATAAATTCAACAATTTATTTTC-TTTTA-AAAGATAAAATCATTAAAGATTCTCAAGAAA
*
3084199 ATAAATTTAACAAATTATTT
64 ATAAATTCAACAAATTATTT
3084219 ATAAAAAAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
100 4 0.05
101 66 0.90
102 3 0.04
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (101 bp):
AGAAAATAAATTCAACAATTTATTTTCTTTTAAAAGATAAAATCATTAAAGATTCTCAAGAAAAT
AAATTCAACAAATTATTTCTTTATTCAATATTCCCA
Found at i:3084948 original size:45 final size:45
Alignment explanation
Indices: 3084865--3085085 Score: 230
Period size: 45 Copynumber: 4.8 Consensus size: 45
3084855 AAAGTAAAAG
* * * * *
3084865 GATTAGTTCTTTTTAATTATTGTGTTGCCAAAAGTAAAATCAAAT
1 GATTAGTTCCTTTTGATTATTGGGTTGCTAAAATTAAAATCAAAT
* * *
3084910 AATTAATTCCTTTTGATTTTTGGGTTGCTAAAATTAAAATCAAA-
1 GATTAGTTCCTTTTGATTATTGGGTTGCTAAAATTAAAATCAAAT
** ** *
3084954 GTATTAGTTCCTTTTGATT-TCTCAGTTTTTATTAAAATTAAAATCAAAG
1 G-ATTAGTTCCTTTTGATTAT-T--G-GGTTGCTAAAATTAAAATCAAAT
* *
3085003 GATTAGTTCCTTTTGATTATTGGGTTGCGAAAATTAAAATCCAAT
1 GATTAGTTCCTTTTGATTATTGGGTTGCTAAAATTAAAATCAAAT
* *
3085048 GCTTAGTTCCTTTTAATTATTGGGTTGCTAAAATTAAA
1 GATTAGTTCCTTTTGATTATTGGGTTGCTAAAATTAAA
3085086 GGATTAATTC
Statistics
Matches: 145, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
44 1 0.01
45 104 0.72
46 1 0.01
47 1 0.01
48 36 0.25
49 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (45 bp):
GATTAGTTCCTTTTGATTATTGGGTTGCTAAAATTAAAATCAAAT
Found at i:3085036 original size:39 final size:40
Alignment explanation
Indices: 3084993--3085104 Score: 109
Period size: 45 Copynumber: 2.7 Consensus size: 40
3084983 TATTAAAATT
3084993 AAAATCAAAGGATTAGTTCCTTTTGATTATTGGGTTGCGAAAA
1 AAAATCAAAGGATTAGTTCCTTTTGATTATTGGGTTGCG---A
* * * * *
3085036 TTAAAATCCAATGCTTAGTTCCTTTTAATTATTGGGTTGC-T
1 --AAAATCAAAGGATTAGTTCCTTTTGATTATTGGGTTGCGA
* *
3085077 AAAATTAAAGGATTAATTCCTTTTGATT
1 AAAATCAAAGGATTAGTTCCTTTTGATT
3085105 TTTTAATTGG
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
39 22 0.39
45 34 0.61
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (40 bp):
AAAATCAAAGGATTAGTTCCTTTTGATTATTGGGTTGCGA
Found at i:3085309 original size:58 final size:58
Alignment explanation
Indices: 3085233--3085356 Score: 151
Period size: 58 Copynumber: 2.1 Consensus size: 58
3085223 AATCTTGCGT
* * **
3085233 TGATTCTAACTTCGTAAGGAAAATAAATCATTAAATTCATT-TCCTTAAGAATCTTGAA
1 TGATTCTAAATTCGTAAGGAAAATAAATCATTAAATTCATTAT-CTTAAGAATATCAAA
* * * * *
3085291 TGATTCTAAATTTGTAAGGAAAATAGATCGTTGAATTTATTATCTTAAGAATATCAAA
1 TGATTCTAAATTCGTAAGGAAAATAAATCATTAAATTCATTATCTTAAGAATATCAAA
3085349 TGATTCTA
1 TGATTCTA
3085357 TCTTTTAATT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 55 0.98
59 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (58 bp):
TGATTCTAAATTCGTAAGGAAAATAAATCATTAAATTCATTATCTTAAGAATATCAAA
Found at i:3091849 original size:21 final size:20
Alignment explanation
Indices: 3091823--3091920 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
3091813 ATCAGTTTCC
3091823 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* *
3091844 AAAATCGCAATGCGATAGTAT-
1 AAAATCGCAACGCGAT--TTTG
* ** *
3091865 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-G
* * *
3091886 AGAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
3091906 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
3091921 ACACATAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
19 2 0.03
20 14 0.23
21 42 0.70
22 1 0.02
23 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:3091949 original size:20 final size:20
Alignment explanation
Indices: 3091888--3092075 Score: 193
Period size: 20 Copynumber: 9.4 Consensus size: 20
3091878 GATTTTCCAG
* ** *
3091888 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3091908 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3091928 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
3091948 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3091968 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3091988 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3092008 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3092028 AATCGCAACG-ATAATCCGT-
1 AATCGCAACGCGT-ATCCGTA
* * *
3092047 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3092067 AATCACAAC
1 AATCGCAAC
3092076 ACTGAAATTT
Statistics
Matches: 141, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 17 0.12
20 122 0.87
21 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:3092799 original size:24 final size:24
Alignment explanation
Indices: 3092760--3092806 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3092750 GAAATTGGTC
**
3092760 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATAAACGGACTTTGATA
*
3092784 TTGGTCAATAAACGGATTTTGAT
1 TTGGTCAATAAACGGACTTTGAT
3092807 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATAAACGGACTTTGATA
Found at i:3095395 original size:53 final size:53
Alignment explanation
Indices: 3095324--3095579 Score: 489
Period size: 53 Copynumber: 4.9 Consensus size: 53
3095314 CGGAAATGAA
3095324 AATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
3095376 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
3095429 AATCGCAATGCGTAAATG-AAATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
3095481 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
3095534 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
3095580 TTGCGATTCT
Statistics
Matches: 200, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
52 62 0.31
53 138 0.69
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:3095643 original size:54 final size:52
Alignment explanation
Indices: 3095575--3095692 Score: 218
Period size: 54 Copynumber: 2.2 Consensus size: 52
3095565 GAAATGAAAA
3095575 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
3095628 TCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
3095681 TCGCATTGCGAT
1 TCGCATTGCGAT
3095693 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
52 11 0.17
53 20 0.31
54 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:3095700 original size:19 final size:19
Alignment explanation
Indices: 3095594--3095692 Score: 136
Period size: 19 Copynumber: 5.4 Consensus size: 19
3095584 GATTCTCTCG
3095594 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3095614 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
3095634 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3095648 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3095667 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3095686 TTGCGAT
1 TTGCGAT
3095693 AGTCATTTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 5 0.07
17 6 0.08
18 3 0.04
19 26 0.36
20 26 0.36
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3095817 original size:14 final size:14
Alignment explanation
Indices: 3095798--3095834 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3095788 CATCAATTAC
3095798 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3095812 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3095826 ACAAATCAA
1 ACAAATCAA
3095835 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3097770 original size:19 final size:19
Alignment explanation
Indices: 3097728--3097898 Score: 141
Period size: 19 Copynumber: 9.6 Consensus size: 19
3097718 TAGTTTACTT
* *
3097728 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
3097748 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
3097767 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
3097786 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3097805 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3097824 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3097838 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
3097856 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
3097870 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
3097888 TCGCAATGCGA
1 TCGCAACGCGA
3097899 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 15, Indels: 22
0.77 0.09 0.13
Matches are distributed among these distances:
13 1 0.01
14 17 0.13
16 9 0.07
17 5 0.04
18 21 0.17
19 61 0.48
20 12 0.10
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3097841 original size:14 final size:14
Alignment explanation
Indices: 3097822--3097877 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
3097812 GCGAAATGAA
*
3097822 AATCGCAACGACAG
1 AATCGCAACGAAAG
3097836 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
3097853 AAATCGCAACGAGAG
1 -AATCGCAACGAAAG
3097868 AATCGCAACG
1 AATCGCAACG
3097878 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 18 0.50
15 1 0.03
16 8 0.22
17 1 0.03
18 8 0.22
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3097862 original size:32 final size:32
Alignment explanation
Indices: 3097803--3097893 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 32
3097793 GCGAAACCAA
3097803 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATG-AAATCGCAACGACAG
* *
3097836 AATCGCAATGCGAAATGAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAATCGCAACGACAG
3097868 AATCGCAACGCGAAATGAAATCGCAA
1 AATCGCAACGCGAAATGAAATCGCAA
3097894 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 39 0.71
33 16 0.29
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (32 bp):
AATCGCAACGCGAAATGAAATCGCAACGACAG
Found at i:3097916 original size:19 final size:18
Alignment explanation
Indices: 3097894--3097985 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
3097884 GAAATCGCAA
3097894 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
3097913 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
3097927 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
3097946 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
3097960 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
3097979 TGCGATT
1 TGCGATT
3097986 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:3097929 original size:14 final size:14
Alignment explanation
Indices: 3097910--3097968 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
3097900 TTTGGTTTCG
3097910 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
3097924 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
3097941 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
3097957 CGTTGCGATTTT
1 CGTTGCGATTTT
3097969 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3097936 original size:33 final size:33
Alignment explanation
Indices: 3097894--3098001 Score: 180
Period size: 33 Copynumber: 3.3 Consensus size: 33
3097884 GAAATCGCAA
*
3097894 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
3097927 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
3097960 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
3097993 TGCGATTTT
1 TGCGATTTT
3098002 AAGTTCGTGT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.07, C:0.19, G:0.27, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3097995 original size:14 final size:14
Alignment explanation
Indices: 3097943--3097999 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3097933 TTTGGTTTCG
*
3097943 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
3097957 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3097976 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3097990 CGTTGCGATT
1 CGTTGCGATT
3098000 TTAAGTTCGT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3098014 original size:33 final size:32
Alignment explanation
Indices: 3097894--3098016 Score: 156
Period size: 33 Copynumber: 3.7 Consensus size: 32
3097884 GAAATCGCAA
* *
3097894 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTAG-TTCGCGTTGCGATTCTGTCGT
*
3097927 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTAG-TTCGCGTTGCGATTCTGTCGT
* *
3097960 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTT-AGTTCGCGTTGCGATTCTGTCGT
*
3097993 TGCGATTTTAAGTTCGTGTTGCGA
1 TGCGATTTT-AGTTCGCGTTGCGA
3098017 AAGTAAACTA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.09, C:0.18, G:0.28, T:0.46
Consensus pattern (32 bp):
TGCGATTTTAGTTCGCGTTGCGATTCTGTCGT
Found at i:3099952 original size:20 final size:20
Alignment explanation
Indices: 3099921--3099984 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
3099911 TTTTGGTTGA
3099921 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
3099941 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
3099961 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
3099982 AAT
1 AAT
3099985 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:3099973 original size:21 final size:21
Alignment explanation
Indices: 3099919--3099983 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
3099909 TCTTTTGGTT
3099919 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
3099940 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
3099960 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
3099981 GAA
1 GAA
3099984 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:3099987 original size:14 final size:14
Alignment explanation
Indices: 3099968--3100024 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3099958 GAGAAATGAA
3099968 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3099982 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
3100001 AATCGCAATGAGAG
1 AATCGCAACGAGAG
3100015 AATCGCAACG
1 AATCGCAACG
3100025 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3100000 original size:33 final size:33
Alignment explanation
Indices: 3099919--3100041 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
3099909 TCTTTTGGTT
*
3099919 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
3099960 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
3099993 GAAATGAAAATCGCAATGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3100026 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3100042 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
33 49 0.61
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.28
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3100042 original size:33 final size:33
Alignment explanation
Indices: 3099960--3100043 Score: 159
Period size: 33 Copynumber: 2.5 Consensus size: 33
3099950 CGCAACGAGA
*
3099960 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAATGAGAGAATCGCAACGC
3099993 GAAATGAAAATCGCAATGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAATGAGAGAATCGCAACGC
3100026 GAAATGAAAATCGCAATG
1 GAAATGAAAATCGCAATG
3100044 CGATTTTGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAATGAGAGAATCGCAACGC
Found at i:3100094 original size:21 final size:21
Alignment explanation
Indices: 3100069--3100142 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
3100059 GTTGCGATTC
3100069 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
3100090 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* * *
3100111 TCACGTTGCTATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
3100132 TCTCGTTGCGA
1 TCTCGTTGCGA
3100143 CTCTTCTGCA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
20 5 0.12
21 31 0.74
22 6 0.14
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.49
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:3100264 original size:33 final size:33
Alignment explanation
Indices: 3100222--3100292 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3100212 AATACTAACT
3100222 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
3100255 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
3100288 TGAAA
1 TGAAA
3100293 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:3100696 original size:20 final size:20
Alignment explanation
Indices: 3100671--3100904 Score: 267
Period size: 20 Copynumber: 11.6 Consensus size: 20
3100661 CTTTAAAAAT
3100671 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3100691 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
3100711 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
3100732 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
3100752 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
3100773 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
3100793 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3100813 CGCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3100833 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
3100853 CGTGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3100873 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3100893 CGCGTTGCGATT
1 CGCGTTGCGATT
3100905 CTGGAAAATC
Statistics
Matches: 182, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
20 147 0.81
21 35 0.19
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3101673 original size:19 final size:19
Alignment explanation
Indices: 3101646--3101690 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3101636 TGTTCAATAT
* *
3101646 ATTATTTAAATGAGG-TAGA
1 ATTAATTAAATG-GGCTAAA
3101665 ATTAATTAAATGGGCTAAA
1 ATTAATTAAATGGGCTAAA
3101684 ATTAATT
1 ATTAATT
3101691 GACAATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.38
Consensus pattern (19 bp):
ATTAATTAAATGGGCTAAA
Found at i:3102641 original size:30 final size:29
Alignment explanation
Indices: 3102595--3102713 Score: 148
Period size: 30 Copynumber: 4.0 Consensus size: 29
3102585 AAACCCAAGG
*
3102595 AGCCGGAGAAGCCGAAAGAGGCGGAGAAGA
1 AGCC-GAGAAGCCGAAAGAGGCCGAGAAGA
*
3102625 AGTCCGAGAAGTCGAAAGAGGCCGAGAAGA
1 AG-CCGAGAAGCCGAAAGAGGCCGAGAAGA
*
3102655 AACCTGAGAAGCCGAAAGAGGCCGAGAAGAA
1 AGCC-GAGAAGCCGAAAGAGGCCGAGAAG-A
* * *
3102686 AGCCGAAAAGCCGAAAGAAGCTGAGAAG
1 AGCCGAGAAGCCGAAAGAGGCCGAGAAG
3102714 CCTAAAGAGT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
29 2 0.03
30 70 0.90
31 6 0.08
ACGTcount: A:0.43, C:0.18, G:0.36, T:0.03
Consensus pattern (29 bp):
AGCCGAGAAGCCGAAAGAGGCCGAGAAGA
Found at i:3102672 original size:60 final size:60
Alignment explanation
Indices: 3102600--3102713 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
3102590 CAAGGAGCCG
* * * *
3102600 GAGAAGCCGAAAGAGGCGGAGAAG-AAGTCCGAGAAGTCGAAAGAGGCCGAGAAGAAACCT
1 GAGAAGCCGAAAGAGGCCGAGAAGAAAG-CCGAAAAGCCGAAAGAAGCCGAGAAGAAACCT
*
3102660 GAGAAGCCGAAAGAGGCCGAGAAGAAAGCCGAAAAGCCGAAAGAAGCTGAGAAG
1 GAGAAGCCGAAAGAGGCCGAGAAGAAAGCCGAAAAGCCGAAAGAAGCCGAGAAG
3102714 CCTAAAGAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 45 0.94
61 3 0.06
ACGTcount: A:0.44, C:0.17, G:0.36, T:0.04
Consensus pattern (60 bp):
GAGAAGCCGAAAGAGGCCGAGAAGAAAGCCGAAAAGCCGAAAGAAGCCGAGAAGAAACCT
Found at i:3102705 original size:22 final size:22
Alignment explanation
Indices: 3102663--3102704 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3102653 GAAACCTGAG
3102663 AAGCCGAAAGAGGCCGAGAAGA
1 AAGCCGAAAGAGGCCGAGAAGA
3102685 AAGCCGAAA-A-GCCGA-AAGA
1 AAGCCGAAAGAGGCCGAGAAGA
3102704 A
1 A
3102705 GCTGAGAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 1 0.05
22 9 0.45
ACGTcount: A:0.50, C:0.19, G:0.31, T:0.00
Consensus pattern (22 bp):
AAGCCGAAAGAGGCCGAGAAGA
Found at i:3102754 original size:51 final size:51
Alignment explanation
Indices: 3102658--3102805 Score: 169
Period size: 51 Copynumber: 3.0 Consensus size: 51
3102648 GAGAAGAAAC
* * * *
3102658 CTGAGAAGCCGAAAGAGGC---CGAGAAGAAAGCCGA-AAAGCCGAAAGAAG
1 CTGAGAAGCCTAAAGAGGCTGGGGAGAAGAAGGCCGAGAAA-CCAAAAGAAG
*
3102706 CTGAGAAGCCTAAAGAGTCTGGGGAGAAGAAGGCCGAGAAACCAAAAGAAG
1 CTGAGAAGCCTAAAGAGGCTGGGGAGAAGAAGGCCGAGAAACCAAAAGAAG
* * * * *
3102757 CTGAGAAGCCTAAAGAGGGTTGGGAGAAAAAGGCTGAGAAACCCAAAGA
1 CTGAGAAGCCTAAAGAGGCTGGGGAGAAGAAGGCCGAGAAACCAAAAGA
3102806 GGCGGCGCCC
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
48 17 0.20
51 65 0.76
52 3 0.04
ACGTcount: A:0.44, C:0.16, G:0.33, T:0.07
Consensus pattern (51 bp):
CTGAGAAGCCTAAAGAGGCTGGGGAGAAGAAGGCCGAGAAACCAAAAGAAG
Found at i:3102771 original size:18 final size:18
Alignment explanation
Indices: 3102693--3102772 Score: 53
Period size: 18 Copynumber: 4.6 Consensus size: 18
3102683 GAAAGCCGAA
*
3102693 AAGCCGAAAGAAGCTGAG
1 AAGCCTAAAGAAGCTGAG
*
3102711 AAGCCTAAAG-AGTCTGGG
1 AAGCCTAAAGAAG-CTGAG
* *
3102729 GAG----AAGAAGGCCGAG
1 AAGCCTAAAGAA-GCTGAG
* *
3102744 AAACCAAAAGAAGCTGAG
1 AAGCCTAAAGAAGCTGAG
3102762 AAGCCTAAAGA
1 AAGCCTAAAGA
3102773 GGGTTGGGAG
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
14 3 0.07
15 5 0.11
16 1 0.02
17 2 0.04
18 29 0.64
19 5 0.11
ACGTcount: A:0.45, C:0.16, G:0.31, T:0.07
Consensus pattern (18 bp):
AAGCCTAAAGAAGCTGAG
Found at i:3102932 original size:18 final size:18
Alignment explanation
Indices: 3102909--3102946 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3102899 TGGTGTGGGG
**
3102909 CCTAGCTATTGTGGTGGA
1 CCTAGCTATTACGGTGGA
3102927 CCTAGCTATTACGGTGGA
1 CCTAGCTATTACGGTGGA
3102945 CC
1 CC
3102947 ATCTCAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (18 bp):
CCTAGCTATTACGGTGGA
Found at i:3103559 original size:2 final size:2
Alignment explanation
Indices: 3103552--3103577 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3103542 AAAATCAAAT
3103552 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
3103578 CGTTTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3104548 original size:30 final size:30
Alignment explanation
Indices: 3104484--3104550 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
3104474 GGACTGACAA
* *
3104484 TGAACCGGCTGAAAACCGGTAAAACCGGGG
1 TGAACCGGCTGAAAACCGGCAAAACCAGGG
* **
3104514 TGAACTGGCTGAAAACCGGCAAAACCAGTT
1 TGAACCGGCTGAAAACCGGCAAAACCAGGG
3104544 TGAACCG
1 TGAACCG
3104551 TCGGTTCACT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.24, G:0.28, T:0.13
Consensus pattern (30 bp):
TGAACCGGCTGAAAACCGGCAAAACCAGGG
Found at i:3109742 original size:30 final size:32
Alignment explanation
Indices: 3109692--3109761 Score: 126
Period size: 30 Copynumber: 2.2 Consensus size: 32
3109682 AATTTGTATT
3109692 GATACTTTTCTAAGTATGTGCACCAAATTATC
1 GATACTTTTCTAAGTATGTGCACCAAATTATC
3109724 GATACTTTTCT-A-TATGTGCACCAAATTATC
1 GATACTTTTCTAAGTATGTGCACCAAATTATC
3109754 GATACTTT
1 GATACTTT
3109762 AGGAATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 26 0.68
31 1 0.03
32 11 0.29
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (32 bp):
GATACTTTTCTAAGTATGTGCACCAAATTATC
Found at i:3110077 original size:194 final size:194
Alignment explanation
Indices: 3109748--3110149 Score: 608
Period size: 194 Copynumber: 2.1 Consensus size: 194
3109738 TGTGCACCAA
* ** * *
3109748 ATTATCGATACTTTAGGAATTTAAAAGAATTGCAATGATAGTGCTTATAAAGTATCGATACTTTA
1 ATTATCGATACTTTAGGAATTTAAAAGAATTGCAATAATAGCACCTATAAAGTATAGATACTTTA
* *
3109813 GAAACATATATCGATACATGACAATATAACATGTTAAAATATGACAAAACCAGCTTCAATATGAC
66 GAAACATATATCGATACATGACAATATAACAGGTTAAAATATGAAAAAACCAGCTTCAATATGAC
* * *
3109878 AAAACCGATAAAGAC-CTACCGGATATGTTGAAGGTATTAATACTTTTATAAGTATATGTATCAT
131 AAAACCGATAAAG-CGCTACCAGATATGTTGAAGGTATCAATACTTTTATAAGTATATGTATAAT
* *
3109942 ATTATCGATACTTTATGAATTTAAAAGAATTGCAATAATAGCACCTATAAAGTATATATACTTTA
1 ATTATCGATACTTTAGGAATTTAAAAGAATTGCAATAATAGCACCTATAAAGTATAGATACTTTA
* * * * *
3110007 GAAACATGTATCGATACATGACAATATAACAGGTTAAAATATGAAAAAATCGGTTTTAATATGAC
66 GAAACATATATCGATACATGACAATATAACAGGTTAAAATATGAAAAAACCAGCTTCAATATGAC
* *
3110072 AAAACCGGTAAAGCGCTACCAGATATGTTGAAGGTATCGATACTTTTATAAGTATATGTATAAT
131 AAAACCGATAAAGCGCTACCAGATATGTTGAAGGTATCAATACTTTTATAAGTATATGTATAAT
*
3110136 ATTATTGATACTTT
1 ATTATCGATACTTT
3110150 TAAAAGAAAA
Statistics
Matches: 187, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
193 1 0.01
194 186 0.99
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.33
Consensus pattern (194 bp):
ATTATCGATACTTTAGGAATTTAAAAGAATTGCAATAATAGCACCTATAAAGTATAGATACTTTA
GAAACATATATCGATACATGACAATATAACAGGTTAAAATATGAAAAAACCAGCTTCAATATGAC
AAAACCGATAAAGCGCTACCAGATATGTTGAAGGTATCAATACTTTTATAAGTATATGTATAAT
Found at i:3110344 original size:14 final size:13
Alignment explanation
Indices: 3110327--3110369 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 13
3110317 TATTTATAAG
3110327 TATATTATTATTAT
1 TATATT-TTATTAT
3110341 TATAATTTTATTAT
1 TAT-ATTTTATTAT
3110355 TATAATTTTAATTAT
1 TAT-ATTTT-ATTAT
3110370 AATTTTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 19 0.70
15 8 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATATTTTATTAT
Found at i:3113522 original size:55 final size:55
Alignment explanation
Indices: 3113456--3113583 Score: 202
Period size: 55 Copynumber: 2.3 Consensus size: 55
3113446 TACCTGTTAA
*
3113456 GAGTGTATCGATACCCTTAGAACATAGAGTATCATATGTGTATCGGTACACTGAG
1 GAGTGTATCGATACCCTTAAAACATAGAGTATCATATGTGTATCGGTACACTGAG
* * * *
3113511 GAGTGTATCGATACCCCTAAAACATCGAGTTTCATTTGTGTATCGGTACACTGAG
1 GAGTGTATCGATACCCTTAAAACATAGAGTATCATATGTGTATCGGTACACTGAG
*
3113566 GAGTGTATAGATACCCTT
1 GAGTGTATCGATACCCTT
3113584 GCAATTTCGA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (55 bp):
GAGTGTATCGATACCCTTAAAACATAGAGTATCATATGTGTATCGGTACACTGAG
Found at i:3114188 original size:21 final size:21
Alignment explanation
Indices: 3114164--3114211 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3114154 GTCGAGGATC
* *
3114164 TATGTGGTCCTTCGGGATAAT
1 TATGTGGTCCTTCGGGAAAAA
*
3114185 TATGTGGTCTTTCGGGAAAAA
1 TATGTGGTCCTTCGGGAAAAA
3114206 TATGTG
1 TATGTG
3114212 ACATTTCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.38
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGAAAAA
Found at i:3114237 original size:23 final size:23
Alignment explanation
Indices: 3114210--3114254 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3114200 GAAAAATATG
*
3114210 TGACATTTCAGTGCAACCCTATA
1 TGACACTTCAGTGCAACCCTATA
3114233 TGACACTTCAGTGCAACCCTAT
1 TGACACTTCAGTGCAACCCTAT
3114255 GTGGTACTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (23 bp):
TGACACTTCAGTGCAACCCTATA
Found at i:3114263 original size:23 final size:23
Alignment explanation
Indices: 3114216--3114281 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
3114206 TATGTGACAT
* **
3114216 TTCAGTGCAACCCTATATGACAC
1 TTCAGTGCAACCCTATGTGGTAC
3114239 TTCAGTGCAACCCTATGTGGTAC
1 TTCAGTGCAACCCTATGTGGTAC
3114262 TTC-GATGCAA-CCTATGTGGT
1 TTCAG-TGCAACCCTATGTGGT
3114282 CATTCGGGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 11 0.28
23 28 0.72
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (23 bp):
TTCAGTGCAACCCTATGTGGTAC
Found at i:3114300 original size:21 final size:22
Alignment explanation
Indices: 3114274--3114318 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3114264 CGATGCAACC
*
3114274 TATGTGGTCA-TTCGG-GACAAT
1 TATGTGG-CACTTCGGTGAAAAT
3114295 TATGTGGCACTTCGGTGAAAAT
1 TATGTGGCACTTCGGTGAAAAT
3114317 TA
1 TA
3114319 CGAGCTGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 12 0.57
22 7 0.33
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGAAAAT
Found at i:3120310 original size:21 final size:21
Alignment explanation
Indices: 3120284--3120339 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
3120274 TTTTGGGTCC
3120284 AGTGTATCGATACCTGTTGAG
1 AGTGTATCGATACCTGTTGAG
3120305 AGTGTATCGATACCTGTTGAG
1 AGTGTATCGATACCTGTTGAG
*
3120326 AGTGTATCAATACC
1 AGTGTATCGATACC
3120340 CTTAGAACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (21 bp):
AGTGTATCGATACCTGTTGAG
Found at i:3121775 original size:16 final size:16
Alignment explanation
Indices: 3121749--3121789 Score: 73
Period size: 16 Copynumber: 2.5 Consensus size: 16
3121739 TTTTCTCAAT
3121749 AAATGCATGCGGACTAG
1 AAAT-CATGCGGACTAG
3121766 AAATCATGCGGACTAG
1 AAATCATGCGGACTAG
3121782 AAATCATG
1 AAATCATG
3121790 AGGTTAGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (16 bp):
AAATCATGCGGACTAG
Found at i:3130836 original size:12 final size:12
Alignment explanation
Indices: 3130809--3130878 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
3130799 ATGGAGATAT
* *
3130809 CAGAAATCAAAA
1 CAGAATTCAGAA
*
3130821 CAGAATTCAGAT
1 CAGAATTCAGAA
*
3130833 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
3130845 CAGAATCCAGAT
1 CAGAATTCAGAA
*
3130857 CAGAAATCAGAA
1 CAGAATTCAGAA
*
3130869 CATAATTCAG
1 CAGAATTCAG
3130879 GTAATATATC
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:3130841 original size:24 final size:24
Alignment explanation
Indices: 3130807--3130915 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
3130797 AAATGGAGAT
*
3130807 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
3130831 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
3130855 ATCAGAAATCAGAACATAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * * *
3130879 GTAATATATCAGAACATAATTCA-
1 ATCAGAAATCAGAACAGAATTCAG
*
3130902 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
3130916 TAAAATATTT
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:3136713 original size:17 final size:17
Alignment explanation
Indices: 3136688--3136727 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3136678 TTTTATTTTG
3136688 TTATAAGTATATTATTA
1 TTATAAGTATATTATTA
* *
3136705 TTATCAGTATTTTATTA
1 TTATAAGTATATTATTA
3136722 TTATAA
1 TTATAA
3136728 TTTCTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (17 bp):
TTATAAGTATATTATTA
Found at i:3136799 original size:17 final size:17
Alignment explanation
Indices: 3136777--3136811 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3136767 CAGATTTAAC
*
3136777 CCAAGGCCTAATTACAA
1 CCAAGGCCCAATTACAA
*
3136794 CCAAGGCCCGATTACAA
1 CCAAGGCCCAATTACAA
3136811 C
1 C
3136812 AAAACCCGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.34, G:0.14, T:0.14
Consensus pattern (17 bp):
CCAAGGCCCAATTACAA
Found at i:3137425 original size:20 final size:20
Alignment explanation
Indices: 3137388--3137438 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3137378 AGCCTTACCA
3137388 TCGTCGGA-AAGCCCAAGCG
1 TCGTCGGAGAAGCCCAAGCG
*
3137407 TCGTCGGAGAAGTCCAAGCG
1 TCGTCGGAGAAGCCCAAGCG
**
3137427 TCACCGGAGAAG
1 TCGTCGGAGAAG
3137439 ACGAACTTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.12
Consensus pattern (20 bp):
TCGTCGGAGAAGCCCAAGCG
Done.