Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009625.1 Hibiscus syriacus cultivar Beakdansim tig00117017_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: 6938204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 25
Found at i:6243315 original size:35 final size:36
Alignment explanation
Indices: 6243269--6243340 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
6243259 GATAAATTAT
6243269 AATCTACATATCCATGGCTGATT-TTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
* * *
6243304 AATCTACATATCGATGTCTGATTCTTTTATCTCTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
6243340 A
1 A
6243341 TTCCAGAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 21 0.64
36 12 0.36
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.44
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:6245839 original size:37 final size:37
Alignment explanation
Indices: 6245786--6245859 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
6245776 AAAATCCATA
*
6245786 TTATAAACATAGTTTGTACCATCATATACCTTGCATC
1 TTATAAACATACTTTGTACCATCATATACCTTGCATC
*
6245823 TTATAAACATACTTTGTATCATCATATACCTTGCATC
1 TTATAAACATACTTTGTACCATCATATACCTTGCATC
6245860 AAATAAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (37 bp):
TTATAAACATACTTTGTACCATCATATACCTTGCATC
Found at i:6247210 original size:21 final size:21
Alignment explanation
Indices: 6247186--6247233 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
6247176 GCATCGGTAT
6247186 TGTTCATGATATCGATACTAC
1 TGTTCATGATATCGATACTAC
* *
6247207 TGTTCATGGTATCGATACTAG
1 TGTTCATGATATCGATACTAC
6247228 TGTTCA
1 TGTTCA
6247234 CACAATATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (21 bp):
TGTTCATGATATCGATACTAC
Found at i:6249840 original size:21 final size:21
Alignment explanation
Indices: 6249811--6249861 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
6249801 TTAGCATCAG
*
6249811 TACTATTCATGATATCGATAC
1 TACTGTTCATGATATCGATAC
*
6249832 TACTGTTCATGGTATCGATAC
1 TACTGTTCATGATATCGATAC
*
6249853 TATTGTTCA
1 TACTGTTCA
6249862 CACAGTATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (21 bp):
TACTGTTCATGATATCGATAC
Found at i:6251453 original size:14 final size:14
Alignment explanation
Indices: 6251434--6251460 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6251424 AATGAAAATT
6251434 AGAAGGAATTTAGG
1 AGAAGGAATTTAGG
6251448 AGAAGGAATTTAG
1 AGAAGGAATTTAG
6251461 CTAGGAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (14 bp):
AGAAGGAATTTAGG
Found at i:6251698 original size:21 final size:19
Alignment explanation
Indices: 6251653--6251699 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
6251643 ATTAAATATC
6251653 ATATTT-AATATTCCAAAA
1 ATATTTAAATATTCCAAAA
*
6251671 ATAATTTAAATACTTCCTAATA
1 AT-ATTTAAATA-TTCC-AAAA
6251693 ATATTTA
1 ATATTTA
6251700 TAATTTTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.08
19 4 0.17
20 4 0.17
21 9 0.38
22 5 0.21
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATTTAAATATTCCAAAA
Found at i:6252630 original size:16 final size:16
Alignment explanation
Indices: 6252609--6252641 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6252599 AATTTATAAT
6252609 ATGAAACAATCA-AAAA
1 ATGAAAC-ATCATAAAA
6252625 ATGAAACATCATAAAA
1 ATGAAACATCATAAAA
6252641 A
1 A
6252642 CAAAAAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.15
Consensus pattern (16 bp):
ATGAAACATCATAAAA
Found at i:6253853 original size:14 final size:14
Alignment explanation
Indices: 6253834--6253867 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
6253824 TGAAAATAAG
6253834 ATGCAAAACATGTA
1 ATGCAAAACATGTA
6253848 ATGCAAAACATGTA
1 ATGCAAAACATGTA
6253862 ATGCAA
1 ATGCAA
6253868 TGATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (14 bp):
ATGCAAAACATGTA
Found at i:6257367 original size:18 final size:19
Alignment explanation
Indices: 6257332--6257376 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
6257322 TATGATTTCA
*
6257332 AAAATAAAAATTAGACTTT
1 AAAATAAAAATTAAACTTT
6257351 AAAATAAAAA-TAAACTTT
1 AAAATAAAAATTAAACTTT
*
6257369 ATAATAAA
1 AAAATAAA
6257377 TATCAAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATAAAAATTAAACTTT
Found at i:6261741 original size:24 final size:24
Alignment explanation
Indices: 6261709--6261779 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 24
6261699 ACATGACCTT
* *
6261709 AATTATGTTCTGATTTCTGATATG
1 AATTCTGTTATGATTTCTGATATG
* * * * *
6261733 GATTCTGTTATGATATATGTTCTG
1 AATTCTGTTATGATTTCTGATATG
* *
6261757 AATTCTGTTTTCATTTCTGATAT
1 AATTCTGTTATGATTTCTGATAT
6261780 CTCTTCTTAC
Statistics
Matches: 33, Mismatches: 14, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (24 bp):
AATTCTGTTATGATTTCTGATATG
Found at i:6263850 original size:50 final size:50
Alignment explanation
Indices: 6263775--6263879 Score: 210
Period size: 50 Copynumber: 2.1 Consensus size: 50
6263765 ATTAAAGACT
6263775 CTATTGAATCATTCTTATCTTTATAGAAGGTTAAGGGTATTCAAAAATCC
1 CTATTGAATCATTCTTATCTTTATAGAAGGTTAAGGGTATTCAAAAATCC
6263825 CTATTGAATCATTCTTATCTTTATAGAAGGTTAAGGGTATTCAAAAATCC
1 CTATTGAATCATTCTTATCTTTATAGAAGGTTAAGGGTATTCAAAAATCC
6263875 CTATT
1 CTATT
6263880 TTGGTGGGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (50 bp):
CTATTGAATCATTCTTATCTTTATAGAAGGTTAAGGGTATTCAAAAATCC
Found at i:6266719 original size:429 final size:425
Alignment explanation
Indices: 6265923--6266779 Score: 1554
Period size: 429 Copynumber: 2.0 Consensus size: 425
6265913 AGAGATTGTT
6265923 GATTAAAATTCATAATTATGAGTATATATTTTTAATTTATATTGTTCTCATAAAATATGACAAAA
1 GATTAAAATTCATAATTATGAGTATATATTTTTAATTTATATTGTTCTCATAAAATATGACAAAA
*
6265988 TTAAGTGATCAACCATGCTAATAAGTCATAAGGAATTAGAAATATACAACAACAACAACAAAACC
66 TTAAGTGATCAACCATGATAATAAGTCATAAGGAATTAGAAATATACAACAACAACAACAAAACC
*
6266053 CTATTCCCAATATGCAATGGGGTAAAGGGGAGGTAGGGTAGTAGGCTGCCCCCAACGCCAGGTTG
131 CTATTCCCAATATACAATGGGGTAAAGGGGAGGTAGGGTAGTAGGCTGCCCCCAACGCCAGGTTG
*
6266118 AGAGCAACTTCCGTGTAAGACCTTCGGCAATCAGAAAATTAAAAATAAAGATAAAATACAATGCA
196 AGAGCAACTTCCGTGTAAGACCTCCGGCAATCAGAAAATTAAAAATAAAGATAAAATACAATGCA
*
6266183 TGTATAAATATCATGAGAATAAAAGAGTATATATTATTGAAGTTGTATTTATAATTTAACGACAG
261 TGTATAAATATCATAAGAATAAAAGAGTATATATTATTGAAGTTGTATTTATAATTTAACGACAG
*
6266248 ATAAAGTTATAAATACATACAATAACTTATTCTTAAATCAATTATATAATGGGGTTATGGTCCCA
326 AT-AAGTTATAAATACAAACAATAACTTATTCTTAAATCAATTATATAATGGGGTTATGGTCCCA
6266313 AAAATATATCATCTCGTATTTTCTCTTATCCCATTA
390 AAAATATATCATCTCGTATTTTCTCTTATCCCATTA
6266349 GATTAAAATTCATAATTATGAGTATATATTTTTAATTTATATTGTTCTCATAAAATATGACAAAA
1 GATTAAAATTCATAATTATGAGTATATATTTTTAATTTATATTGTTCTCATAAAATATGACAAAA
* *
6266414 TTAAGTGATCAATCATGATAATAAGTCATAAGGTATTAGAAATATACAACAACAACAACAACAAA
66 TTAAGTGATCAACCATGATAATAAGTCATAAGGAATTAGAAATAT---ACAACAACAACAACAAA
* *
6266479 ACCCTATTCCCAATATACAATGGGGTAAGGGGGAGGTAGGGTAGTAGGCTGCCCCCAACGTCAGG
128 ACCCTATTCCCAATATACAATGGGGTAAAGGGGAGGTAGGGTAGTAGGCTGCCCCCAACGCCAGG
* *
6266544 TTGAGAGCAGCTTCCGTGTAAGACCTCCGGCAGTCAGAAAATTAAAAATAAAGATAAAATACAAT
193 TTGAGAGCAACTTCCGTGTAAGACCTCCGGCAATCAGAAAATTAAAAATAAAGATAAAATACAAT
6266609 GCATGTATAAATATCATAAGAATAAAAGAGTATATATTATTGAAGTTGTATTTATAATTTAACGA
258 GCATGTATAAATATCATAAGAATAAAAGAGTATATATTATTGAAGTTGTATTTATAATTTAACGA
6266674 CGAGCAT-AGTTATAAATACAAACAATAACTTATTCTTAAATCAATTATATAATGGGGTTATGGT
323 C-AG-ATAAGTTATAAATACAAACAATAACTTATTCTTAAATCAATTATATAATGGGGTTATGGT
6266738 CCCAAAAATATATCATCTCGTATTTTCTCTTATCCCATTA
386 CCCAAAAATATATCATCTCGTATTTTCTCTTATCCCATTA
6266778 GA
1 GA
6266780 GAGTTTATAC
Statistics
Matches: 415, Mismatches: 11, Indels: 7
0.96 0.03 0.02
Matches are distributed among these distances:
426 107 0.26
429 304 0.73
430 2 0.00
431 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (425 bp):
GATTAAAATTCATAATTATGAGTATATATTTTTAATTTATATTGTTCTCATAAAATATGACAAAA
TTAAGTGATCAACCATGATAATAAGTCATAAGGAATTAGAAATATACAACAACAACAACAAAACC
CTATTCCCAATATACAATGGGGTAAAGGGGAGGTAGGGTAGTAGGCTGCCCCCAACGCCAGGTTG
AGAGCAACTTCCGTGTAAGACCTCCGGCAATCAGAAAATTAAAAATAAAGATAAAATACAATGCA
TGTATAAATATCATAAGAATAAAAGAGTATATATTATTGAAGTTGTATTTATAATTTAACGACAG
ATAAGTTATAAATACAAACAATAACTTATTCTTAAATCAATTATATAATGGGGTTATGGTCCCAA
AAATATATCATCTCGTATTTTCTCTTATCCCATTA
Found at i:6268913 original size:19 final size:19
Alignment explanation
Indices: 6268889--6268926 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
6268879 GAGTGGGACG
6268889 GTCATCCTCATAAGTTTTT
1 GTCATCCTCATAAGTTTTT
6268908 GTCATCCTCATAAGTTTTT
1 GTCATCCTCATAAGTTTTT
6268927 AAATCCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (19 bp):
GTCATCCTCATAAGTTTTT
Found at i:6268932 original size:18 final size:19
Alignment explanation
Indices: 6268892--6268934 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
6268882 TGGGACGGTC
**
6268892 ATCCTCATAAGTTTTTGTC
1 ATCCTCATAAGTTTTTGAA
6268911 ATCCTCATAAGTTTTT-AA
1 ATCCTCATAAGTTTTTGAA
6268929 ATCCTC
1 ATCCTC
6268935 TTATATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (19 bp):
ATCCTCATAAGTTTTTGAA
Found at i:6273333 original size:28 final size:27
Alignment explanation
Indices: 6273259--6273364 Score: 140
Period size: 27 Copynumber: 3.9 Consensus size: 27
6273249 CTTTTTACAA
6273259 CATAAGGGTATTTTCATAATTTTACCC
1 CATAAGGGTATTTTCATAATTTTACCC
* * *
6273286 CATACGGGTATTTTCGTAATTTTAACC
1 CATAAGGGTATTTTCATAATTTTACCC
*
6273313 CATAAGGGTATTTTTTATAATTTTACCC
1 CATAAGGGTA-TTTTCATAATTTTACCC
* * *
6273341 CATAAAGTTATTTTCGTAATTTTA
1 CATAAGGGTATTTTCATAATTTTA
6273365 TCCAACCAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
27 45 0.67
28 22 0.33
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.44
Consensus pattern (27 bp):
CATAAGGGTATTTTCATAATTTTACCC
Found at i:6273353 original size:55 final size:54
Alignment explanation
Indices: 6273259--6273364 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 54
6273249 CTTTTTACAA
**
6273259 CATAAGGGTATTTTCATAATTTTACCCCATACGGGTATTTTCGTAATTTTAACC
1 CATAAGGGTATTTTCATAATTTTACCCCATAAAGGTATTTTCGTAATTTTAACC
* *
6273313 CATAAGGGTATTTTTTATAATTTTACCCCATAAAGTTATTTTCGTAATTTTA
1 CATAAGGGTA-TTTTCATAATTTTACCCCATAAAGGTATTTTCGTAATTTTA
6273365 TCCAACCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 10 0.21
55 37 0.79
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.44
Consensus pattern (54 bp):
CATAAGGGTATTTTCATAATTTTACCCCATAAAGGTATTTTCGTAATTTTAACC
Found at i:6273994 original size:22 final size:24
Alignment explanation
Indices: 6273969--6274015 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
6273959 TCGACGGTTG
*
6273969 GACCAGTCAA-AGTCAAC-GGTCA
1 GACCAATCAATAGTCAACGGGTCA
*
6273991 GACCAATCAATGGTCAACGGGTCA
1 GACCAATCAATAGTCAACGGGTCA
6274015 G
1 G
6274016 GTAAAAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 6 0.29
24 6 0.29
ACGTcount: A:0.34, C:0.26, G:0.26, T:0.15
Consensus pattern (24 bp):
GACCAATCAATAGTCAACGGGTCA
Found at i:6274045 original size:19 final size:20
Alignment explanation
Indices: 6274018--6274055 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
6274008 CGGGTCAGGT
6274018 AAAAGTCAATTGG-TCGAGTC
1 AAAAGTCAA-TGGATCGAGTC
6274038 AAAA-TCAATGGATCGAGT
1 AAAAGTCAATGGATCGAGT
6274056 TTGGTTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 10 0.59
20 4 0.24
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (20 bp):
AAAAGTCAATGGATCGAGTC
Found at i:6276374 original size:36 final size:35
Alignment explanation
Indices: 6276269--6276409 Score: 106
Period size: 35 Copynumber: 4.0 Consensus size: 35
6276259 GTCACTTTAG
* *
6276269 ATCCGTAAGGAATTACCAGCTCGATCGGTCTGAAC
1 ATCCGTAAGGAATTACCAGTTTGATCGGTCTGAAC
*** * * *
6276304 ATAAATAAGGAATTACCAATTTGACCGAG-ATGAAC
1 ATCCGTAAGGAATTACCAGTTTGATCG-GTCTGAAC
* *
6276339 CTCCCGTAAGGAATTACCAGTTTAATCGGTCTGAAC
1 AT-CCGTAAGGAATTACCAGTTTGATCGGTCTGAAC
*** **
6276375 ATATATAAGGAATTACTTGTTTGATCGAG-CTGAAC
1 ATCCGTAAGGAATTACCAGTTTGATCG-GTCTGAAC
6276410 CTACAGAGAC
Statistics
Matches: 79, Mismatches: 23, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
35 52 0.66
36 27 0.34
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (35 bp):
ATCCGTAAGGAATTACCAGTTTGATCGGTCTGAAC
Found at i:6277498 original size:27 final size:26
Alignment explanation
Indices: 6277468--6277572 Score: 102
Period size: 27 Copynumber: 3.9 Consensus size: 26
6277458 CTTTTTACAA
* * *
6277468 CATAAGGGTATTTTCATAAATTTGCAC
1 CATAAGGGTATTTTCGTAATTTTAC-C
* * *
6277495 CATAATGATACTTTCGTAATTTTACCC
1 CATAAGGGTATTTTCGTAATTTTA-CC
*
6277522 CATAAGAGTATTTTCGTAATTTTACC
1 CATAAGGGTATTTTCGTAATTTTACC
* *
6277548 TCAAAAGGGTATTTTTGTAATTTTA
1 -CATAAGGGTATTTTCGTAATTTTA
6277573 ACCAACCAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
26 2 0.03
27 60 0.95
28 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.42
Consensus pattern (26 bp):
CATAAGGGTATTTTCGTAATTTTACC
Found at i:6280122 original size:24 final size:22
Alignment explanation
Indices: 6280095--6280152 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
6280085 AAGTTTTTTT
6280095 AATTTATTTTATTAATTTTATTGC
1 AATTTATTTTATT--TTTTATTGC
*
6280119 AATTTTATTTATATTTTTTATTGT
1 AA-TTTATTT-TATTTTTTATTGC
*
6280143 ACTTTATTTT
1 AATTTATTTT
6280153 TCAATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.03
23 7 0.23
24 11 0.37
25 7 0.23
26 4 0.13
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (22 bp):
AATTTATTTTATTTTTTATTGC
Found at i:6281080 original size:28 final size:26
Alignment explanation
Indices: 6281049--6281119 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 26
6281039 TAATTCTTTC
*
6281049 TTTTAAAAATTTTTATATATACTTATT
1 TTTTAAATATTTTTATATATA-TTATT
* *
6281076 ATTTTCATAATATTTATATGTATATTATT
1 -TTTT-A-AATATTTTTATATATATTATT
6281105 TTTT-AATATTTTTAT
1 TTTTAAATATTTTTAT
6281120 TTTATTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
25 10 0.27
28 8 0.22
29 6 0.16
30 13 0.35
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (26 bp):
TTTTAAATATTTTTATATATATTATT
Found at i:6286809 original size:15 final size:15
Alignment explanation
Indices: 6286789--6286845 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
6286779 CTTCATGGGG
*
6286789 TAAGAAGACAACGTC
1 TAAGAAGAAAACGTC
6286804 TAAGAAGAAAACGTC
1 TAAGAAGAAAACGTC
*
6286819 AAAGAAGAAAACGTC
1 TAAGAAGAAAACGTC
6286834 TAAGAAGGAAAA
1 TAAGAA-GAAAA
6286846 AAGAAAGCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 33 0.87
16 5 0.13
ACGTcount: A:0.56, C:0.12, G:0.21, T:0.11
Consensus pattern (15 bp):
TAAGAAGAAAACGTC
Found at i:6290837 original size:39 final size:39
Alignment explanation
Indices: 6290749--6290843 Score: 99
Period size: 39 Copynumber: 2.4 Consensus size: 39
6290739 GGAATAGGGT
*
6290749 AAAGGAGAAGGGACACCGCAAAGGAAAAAGGAAGAGGAG
1 AAAGGAGAAGGGACACCGCAAAGGAAAAAAGAAGAGGAG
*
6290788 AAAGAAGAAGGGACACCG-AAGAGGGAAAGAAAGAA-A-GA-
1 AAAGGAGAAGGGACACCGCAA-A-GGAAA-AAAGAAGAGGAG
*
6290826 AAAGGAGGAAGGAACACC
1 AAAGGA-GAAGGGACACC
6290844 ATAAAGGAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
38 7 0.15
39 30 0.62
40 6 0.12
41 5 0.10
ACGTcount: A:0.54, C:0.11, G:0.36, T:0.00
Consensus pattern (39 bp):
AAAGGAGAAGGGACACCGCAAAGGAAAAAAGAAGAGGAG
Found at i:6291365 original size:12 final size:12
Alignment explanation
Indices: 6291348--6291373 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6291338 CCCGGGTTTT
6291348 TTTTTCATTTGA
1 TTTTTCATTTGA
6291360 TTTTTCATTTGA
1 TTTTTCATTTGA
6291372 TT
1 TT
6291374 ATCAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (12 bp):
TTTTTCATTTGA
Found at i:6291878 original size:17 final size:17
Alignment explanation
Indices: 6291856--6291890 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6291846 AAATTTTCTG
6291856 ATACACATCTA-TCATAC
1 ATACACAT-TAGTCATAC
6291873 ATACACATTAGTCATAC
1 ATACACATTAGTCATAC
6291890 A
1 A
6291891 ACTATCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.43, C:0.26, G:0.03, T:0.29
Consensus pattern (17 bp):
ATACACATTAGTCATAC
Found at i:6292775 original size:2 final size:2
Alignment explanation
Indices: 6292764--6292842 Score: 106
Period size: 2 Copynumber: 40.0 Consensus size: 2
6292754 TTTGTCAATC
* *
6292764 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
6292805 TA TA TT TA TA TT TA TA TA TC TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6292843 ATTTCTGAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:6293180 original size:85 final size:85
Alignment explanation
Indices: 6292914--6293164 Score: 353
Period size: 85 Copynumber: 3.0 Consensus size: 85
6292904 AATGACACAT
* * * * *
6292914 AATGTAAGTCATATATGCATGTCATAAATTTATGACACACAAATGTATGTCAAGC--AGATTTAT
1 AATGTAAGTCATACATGCGTGTCATAAATTTATAACACACAAATGTGTGTC-ATCTTA-ATTTAT
**
6292977 GATTGGGGCTTCAATGACGCGC
64 GACGGGGGCTTCAATGACGCGC
* * *
6292999 AATGTAAGTTATACATGTGTGTCATAAATTTATGACACACAAATGTGTGTCATCTTAATTTATGA
1 AATGTAAGTCATACATGCGTGTCATAAATTTATAACACACAAATGTGTGTCATCTTAATTTATGA
6293064 CGGGGGCTTCAATGACGCGC
66 CGGGGGCTTCAATGACGCGC
* * *
6293084 AATGTAAGTCATACATGCGTGTCAAAAATTTATAACTCACAAATGTGTGTCATCTTAATTTATGG
1 AATGTAAGTCATACATGCGTGTCATAAATTTATAACACACAAATGTGTGTCATCTTAATTTATGA
6293149 CGGGGGCTTCAATGAC
66 CGGGGGCTTCAATGAC
6293165 ACTCAAAGAA
Statistics
Matches: 150, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
84 2 0.01
85 147 0.98
86 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (85 bp):
AATGTAAGTCATACATGCGTGTCATAAATTTATAACACACAAATGTGTGTCATCTTAATTTATGA
CGGGGGCTTCAATGACGCGC
Found at i:6293187 original size:85 final size:85
Alignment explanation
Indices: 6292917--6293197 Score: 327
Period size: 85 Copynumber: 3.3 Consensus size: 85
6292907 GACACATAAT
* * * * * *
6292917 GTAAGTCATATATGCATGTCATAAATTTATGACACACAAATGTATGTCAAGC--AGATTTATGAT
1 GTAAGTCATACATGCGTGTCATAAATTTATAACACACAAATGTGTGTC-ATCTTA-ATTTATGAC
* * *
6292980 TGGGGCTTCAATGACGCGCAAT
64 GGGGGCTTCAATGACACGCAAA
* * *
6293002 GTAAGTTATACATGTGTGTCATAAATTTATGACACACAAATGTGTGTCATCTTAATTTATGACGG
1 GTAAGTCATACATGCGTGTCATAAATTTATAACACACAAATGTGTGTCATCTTAATTTATGACGG
* *
6293067 GGGCTTCAATGACGCGCAAT
66 GGGCTTCAATGACACGCAAA
* * *
6293087 GTAAGTCATACATGCGTGTCAAAAATTTATAACTCACAAATGTGTGTCATCTTAATTTATGGCGG
1 GTAAGTCATACATGCGTGTCATAAATTTATAACACACAAATGTGTGTCATCTTAATTTATGACGG
*
6293152 GGGCTTCAATGACACTCAAA
66 GGGCTTCAATGACACGCAAA
*
6293172 G-AACGTCATTA-ATGCGCGTCATAAAT
1 GTAA-GTCA-TACATGCGTGTCATAAAT
6293198 GGGCGCCATA
Statistics
Matches: 173, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
84 4 0.02
85 166 0.96
86 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (85 bp):
GTAAGTCATACATGCGTGTCATAAATTTATAACACACAAATGTGTGTCATCTTAATTTATGACGG
GGGCTTCAATGACACGCAAA
Found at i:6301215 original size:22 final size:19
Alignment explanation
Indices: 6301164--6301215 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
6301154 ATCCACATTC
6301164 TTCAAAGATGATAGTTTTT
1 TTCAAAGATGATAGTTTTT
*
6301183 CTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAG-TT-T-TT
*
6301205 TTCAAATATGA
1 TTCAAAGATGA
6301216 AAGCTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.48
20 2 0.07
21 1 0.04
22 11 0.41
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (19 bp):
TTCAAAGATGATAGTTTTT
Found at i:6301917 original size:45 final size:45
Alignment explanation
Indices: 6301853--6302199 Score: 550
Period size: 45 Copynumber: 7.7 Consensus size: 45
6301843 GATTTTCATA
*
6301853 GGGTCATCTGTAAGCCCTTCATTGCATGATGTTTTCAAAACCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
* *
6301898 GGGTCATCTATAAGCCCTTCAGTGCATGATGTTATCAAAACCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
*
6301943 GGGTCATCTGTAAGCCCTTCAGTGTATGATGTTTTCAAAACCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
* *
6301988 GGGTCATCTGTAAGCCCTTCAGTGCATGTTGTTATCAAAACCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
*
6302033 GGGTCATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAACCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
* * *
6302078 AGGTCATCTGTAAACCCTTCAATGCATGATGTTTTCAAAACCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
* *
6302123 GGGTCACCTGTAAGCCCTTCAGTGCATGATGTTATCAAAATCCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA-CCTTC
* * *
6302169 GGGTCATCTGTAAGACCTACAGTGCAAGATG
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATG
6302200 ATAAGACCTC
Statistics
Matches: 278, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
45 246 0.88
46 32 0.12
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (45 bp):
GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
Found at i:6302361 original size:3 final size:3
Alignment explanation
Indices: 6302353--6302393 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
6302343 CATTTTCATT
6302353 TTA TTA TTA TTA TTA TTA TTA -TA TTA -TA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
6302394 AATAAACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:6334004 original size:39 final size:39
Alignment explanation
Indices: 6333960--6334074 Score: 126
Period size: 39 Copynumber: 2.9 Consensus size: 39
6333950 AATTTTCAAG
* *
6333960 AAAATAAATTCAACTATTTATTTCCTTTCACAAACCAGA
1 AAAATAAATTCAACTATTTATTTCCTTTTACAAAACAGA
* * * *
6333999 AAAATAAATAT-AACTATTAATTTTCTTTTACAAAATAGG
1 AAAATAAAT-TCAACTATTTATTTCCTTTTACAAAACAGA
* *
6334038 AAAATAAA-TCCATTGATTTATTTCCTTTTACAAAACA
1 AAAATAAATTCAACT-ATTTATTTCCTTTTACAAAACA
6334075 AAATCATATA
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
37 1 0.02
38 2 0.03
39 58 0.94
40 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.37
Consensus pattern (39 bp):
AAAATAAATTCAACTATTTATTTCCTTTTACAAAACAGA
Found at i:6334644 original size:58 final size:58
Alignment explanation
Indices: 6334411--6334647 Score: 323
Period size: 58 Copynumber: 4.1 Consensus size: 58
6334401 TTCCTTGGTA
* * * *
6334411 AGAATCATTTGAGATTCTTAAGAAAATAAATTCAACTATTTATTTTCTTTACAAAGTT
1 AGAATCATTTAAGATTCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAAAGTT
* * *
6334469 ATAATCAATTAAGATTCTCAAGGGAATAAATTCAACTATTTATTTTCCTTACAAAGTT
1 AGAATCATTTAAGATTCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAAAGTT
* * ** *
6334527 ACAATCATTTAAGATTCTTAAGGAAATAAATTCAAGGAATTATTTTCCTTACAAAGTT
1 AGAATCATTTAAGATTCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAAAGTT
* * *
6334585 AGAATCATTTAAAATTCTCAAGGAAATAAATTCAA-TAATTTATTTTCTTTACGAAGTT
1 AGAATCATTTAAGATTCTCAAGGAAATAAATTCAACT-ATTTATTTTCCTTACAAAGTT
6334643 AGAAT
1 AGAAT
6334648 GTAACCCCCC
Statistics
Matches: 157, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
58 157 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.38
Consensus pattern (58 bp):
AGAATCATTTAAGATTCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAAAGTT
Found at i:6344124 original size:45 final size:44
Alignment explanation
Indices: 6344049--6344331 Score: 291
Period size: 45 Copynumber: 6.3 Consensus size: 44
6344039 GTTTATCAAC
* * *
6344049 CCAACAATTAAAAGGAACTAATCC-TTGATTTTAATTTCCACAA
1 CCAATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTCACAA
* *
6344092 TCCAATAATCAAAAAGAACTAATCTTTTGATTTTAATTTTCACAA
1 -CCAATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTCACAA
*
6344137 CCTAATAATCGAAAGGAACTAATCCTTTGATTTTAA-TTTCAGCAA
1 CC-AATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTCA-CAA
* * * * **
6344182 CCTAATAATCAAAATGAACTAATTCTCTGATTTTACTTTTGGCAA
1 CC-AATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTCACAA
* * * * * **
6344227 CTCAATGAGCAAAAGGAACTAATCGTTTGGTTTTACTTTTGGCAA
1 C-CAATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTCACAA
* * *
6344272 CTCAATAATTAAAAGGAACTAATCCTTTGATTTTACTTTTGACAA
1 C-CAATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTCACAA
6344317 CTCAATAATCAAAAG
1 C-CAATAATCAAAAG
6344332 CTTTAGATTG
Statistics
Matches: 205, Mismatches: 29, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
44 27 0.13
45 174 0.85
46 4 0.02
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (44 bp):
CCAATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTCACAA
Found at i:6345838 original size:31 final size:31
Alignment explanation
Indices: 6345803--6345874 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
6345793 CTCTTAACAG
* **
6345803 AATATTGTTTTTAAAGTTAAGATATTAATAA
1 AATATTGTTTTTAAAGTTAAAATAAGAATAA
* *
6345834 AATATAT-TTTTTCAATTTAAAATAAGAATAA
1 AATAT-TGTTTTTAAAGTTAAAATAAGAATAA
*
6345865 AATATAGTTT
1 AATATTGTTT
6345875 AAGTGAAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (31 bp):
AATATTGTTTTTAAAGTTAAAATAAGAATAA
Found at i:6345954 original size:24 final size:24
Alignment explanation
Indices: 6345909--6345972 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
6345899 TATTTTTATA
* *
6345909 TTAAATTAAAAAAAATTAAATATATT
1 TTAAATT--AAAATATTTAATATATT
* *
6345935 TTAAATTAAGATATTTAATATCTT
1 TTAAATTAAAATATTTAATATATT
*
6345959 TTACATTAAAATAT
1 TTAAATTAAAATAT
6345973 AAATAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 25 0.78
26 7 0.22
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (24 bp):
TTAAATTAAAATATTTAATATATT
Found at i:6346014 original size:30 final size:30
Alignment explanation
Indices: 6345978--6346042 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
6345968 AATATAAATA
* *
6345978 AAAAATAAAAAATATTTAATAAGTTAAGAC
1 AAAAATAAAAAATATTTAATAAATTAAAAC
* *
6346008 AAAAATAAAATATGTTTAATAAATTAAAAC
1 AAAAATAAAAAATATTTAATAAATTAAAAC
6346038 AAAAA
1 AAAAA
6346043 CAGTGGATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (30 bp):
AAAAATAAAAAATATTTAATAAATTAAAAC
Found at i:6348239 original size:16 final size:15
Alignment explanation
Indices: 6348202--6348240 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
6348192 AAGGTAAATA
6348202 TTTTTTTGTTTTTAT
1 TTTTTTTGTTTTTAT
*
6348217 TTCTTTTTGTTTTTCCT
1 TT-TTTTTGTTTTT-AT
6348234 TTTTTTT
1 TTTTTTT
6348241 CTACACCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 16 0.76
17 3 0.14
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.85
Consensus pattern (15 bp):
TTTTTTTGTTTTTAT
Found at i:6348884 original size:3 final size:3
Alignment explanation
Indices: 6348878--6348929 Score: 79
Period size: 3 Copynumber: 17.0 Consensus size: 3
6348868 GTAAAAAAAG
6348878 ATA ATA ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATAA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
6348924 ATA ATA
1 ATA ATA
6348930 TTATTATTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.04
3 39 0.85
4 5 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:6349324 original size:42 final size:41
Alignment explanation
Indices: 6349247--6349348 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
6349237 AAGGTCTTAT
*
6349247 AGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTGAC
1 AGATGACCCGAAGGACTTATCATCTTGCTCAAAAGACTGAC
* * * * *
6349288 AGATTACCCGAAGGATTTAATCATCTTTCTCGAAAGACTTAC
1 AGATGACCCGAAGGACTT-ATCATCTTGCTCAAAAGACTGAC
* *
6349330 TGATGGCCCGAAGGACTTA
1 AGATGACCCGAAGGACTTA
6349349 CCAATTTTGG
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (41 bp):
AGATGACCCGAAGGACTTATCATCTTGCTCAAAAGACTGAC
Found at i:6349642 original size:258 final size:258
Alignment explanation
Indices: 6349179--6350499 Score: 1812
Period size: 258 Copynumber: 5.1 Consensus size: 258
6349169 TTACTGGGTA
* * *
6349179 AGAAACTTTGGAAATCACTTTCTCATTTTTCAAAAATCATGTGGAAACATCCTGCCCGAAGGTCT
1 AGAAACTTTGGAAATCGCTTTCTTATTTTTCAAAAATCATGTGGAAACATCCTGCCCGAAAGTCT
*
6349244 TATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTGACAGATTACCCGAAGGATTTAAT
66 TATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAAT
* *
6349309 CATCTTTCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTATTGGG
131 CATCATTCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTACTGGG
*
6349374 TAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAATATTTCATTTTCTGAAAACATTAAATG
196 TAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACATTAAATG
* * * * * *
6349437 AGACACTTTGGAAATCGCTTTCTTATTTTTCAAAAAGCATGTGGAAACTTCTTACCCGAATGTCT
1 AGAAACTTTGGAAATCGCTTTCTTATTTTTCAAAAATCATGTGGAAACATCCTGCCCGAAAGTCT
* * * * **
6349502 TATAGATGGCCCGAAGAACTTATCATCTTGCTCAAAAGACTGAAAGAGGACCCAAAATATTTAAT
66 TATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAAT
*
6349567 CATCATTCTCGAAAGACTTATTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTACTGGG
131 CATCATTCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTACTGGG
* * * *
6349632 TAATAAACTTTGGAAAT--C--GCTTACTATTCAAAAATTTCATTTTCTGAAAATATTAAATG
196 TAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACATTAAATG
* ** * * *
6349691 AGAAACTTTGAAAATCATTTTCCCT-TTTTTCGAAAATCATGTGGAAACATCCTACCCGAAAGTC
1 AGAAACTTTGGAAATCGCTTT-CTTATTTTTCAAAAATCATGTGGAAACATCCTGCCCGAAAGTC
* * * *
6349755 TTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGATCCGAAGGATTTAA
65 TTATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAA
* * * *
6349820 TCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAG
130 TCATCATTCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTACTGG
* ** * * * *
6349885 GTAAGAAACTTTGAAAATTGCTTTTTTACTTTTCAAAAATATCATTTTCTGAAAAGATTTAAATA
195 GTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACA-TTAAATG
* * * * * *
6349950 AGATACTTTGGAAATCTCTTTCTTATTTTTCAAAAATCTTGTTGAAACATCCTGCCTGAAGGTCT
1 AGAAACTTTGGAAATCGCTTTCTTATTTTTCAAAAATCATGTGGAAACATCCTGCCCGAAAGTCT
* *
6350015 TATAGATGGCCCGAAGGACTTATCATCTTGCTCAAGAGACTGACAGATTACCCGAAGGATTTAAT
66 TATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAAT
* *
6350080 CATAATTCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTATTGGG
131 CATCATTCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTACTGGG
*
6350145 TAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAATATTTCATTTTCTGAAAACATTAAATG
196 TAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACATTAAATG
* * * * *
6350208 AGAAACTTTGCAAATCGCTTT-TTCATTTTTCGAAAATCATGTGGGAACATCCTGGCCAAAAGTC
1 AGAAACTTTGGAAATCGCTTTCTT-ATTTTTCAAAAATCATGTGGAAACATCCTGCCCGAAAGTC
* * * * * *
6350272 TTATCGATGGCACAAATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAA
65 TTATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAA
* * * * * * * *
6350337 GCATCATGCTCGAAAGACTTACTGATGGCCCAAAAGACTTACAAATTTTGGAAATAATTTACAGG
130 TCATCATTCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTACTGG
** * * *
6350402 GTACA-AAACTTTGGAAATTGCTTTCTTACTTTTTAAAAATTTCA-TTTCAGAAAAGATTTAAAT
195 GTA-AGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACA-TTAAAT
6350465 G
258 G
*
6350466 AGAAACTTTGGAAATCGCTTTCTCATTTTTCAAA
1 AGAAACTTTGGAAATCGCTTTCTTATTTTTCAAA
6350500 TTTAATGGTT
Statistics
Matches: 927, Mismatches: 125, Indels: 22
0.86 0.12 0.02
Matches are distributed among these distances:
254 219 0.24
255 2 0.00
256 2 0.00
257 12 0.01
258 466 0.50
259 226 0.24
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (258 bp):
AGAAACTTTGGAAATCGCTTTCTTATTTTTCAAAAATCATGTGGAAACATCCTGCCCGAAAGTCT
TATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAAT
CATCATTCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTACTGGG
TAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACATTAAATG
Found at i:6349834 original size:42 final size:41
Alignment explanation
Indices: 6349747--6349860 Score: 138
Period size: 42 Copynumber: 2.8 Consensus size: 41
6349737 ACATCCTACC
* * * * *
6349747 CGAAAGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCT
1 CGAAAGACTTACAGATGACCCGAAGGACTTATCATCATGCT
* *
6349788 CGAAAGACTTACAGATGATCCGAAGGATTTAATCATCATGCT
1 CGAAAGACTTACAGATGACCCGAAGGACTT-ATCATCATGCT
* *
6349830 CGAAAGACTTACTGATGGCCCGAAGGACTTA
1 CGAAAGACTTACAGATGACCCGAAGGACTTA
6349861 CAAATTTTGG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 25 0.41
42 36 0.59
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (41 bp):
CGAAAGACTTACAGATGACCCGAAGGACTTATCATCATGCT
Found at i:6350413 original size:517 final size:512
Alignment explanation
Indices: 6349179--6350499 Score: 1921
Period size: 517 Copynumber: 2.6 Consensus size: 512
6349169 TTACTGGGTA
* * * *
6349179 AGAAACTTTGGAAATCACTTTCTCATTTTTCAAAAATCATGTGGAAACATCCTGCCCGAAGGTCT
1 AGAAACTTTGAAAATC-CTTTTTCATTTTTCGAAAATCATGTGGAAACATCCTGCCCGAAAGTCT
* * * *
6349244 TATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTGACAGATTACCCGAAGGATTTAAT
65 TATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAT
* * * * **
6349309 CATCTTTCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTATTGGG
130 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACAGGG
** * *
6349374 TAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAATATTTCATTTTCTGAAAACA-TTAAATGA
195 TAAGAAACTTTGGAAATTGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAGATTTAAATGA
* * * *
6349438 GACACTTTGGAAATCGCTTTCTTATTTTTCAAAAAGCATGTGGAAACTTCTTACCCGAATGTCTT
260 GAAACTTTGGAAATCGCTTTCTTATTTTTCAAAAAGCATGTGGAAACATCCTACCCGAAGGTCTT
*
6349503 ATAGATGGCCCGAAGAACTTATCATCTTGCTCAAAAGACTGAAAGAGGACCCAAAATATTTAATC
325 ATAGATGGCCCGAAGAACTTATCATCTTGCTCAAAAGACTGAAAGAGGACCCAAAAGATTTAATC
* *
6349568 ATCATTCTCGAAAGACTTATTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTACTGGGT
390 ATAATTCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTACTGGGT
* *
6349633 AATAAACTTTGGAAATCGCTTACTATTCAAAAATTTCATTTTCTGAAAATATTAAATG
455 AAGAAACTTTGGAAATCGCTTACTATTCAAAAATTTCATTTTCTGAAAACATTAAATG
* * * *
6349691 AGAAACTTTGAAAATCATTTTCCCTTTTTTCGAAAATCATGTGGAAACATCCTACCCGAAAGTCT
1 AGAAACTTTGAAAATCCTTTT-TCATTTTTCGAAAATCATGTGGAAACATCCTGCCCGAAAGTCT
*
6349756 TATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGATCCGAAGGATTTAAT
65 TATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAT
6349821 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACTA-G
130 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTAC-AGG
* * * *
6349885 GTAAGAAACTTTGAAAATTGCTTTTTTACTTTTCAAAAATATCATTTTCTGAAAAGATTTAAATA
194 GTAAGAAACTTTGGAAATTGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAGATTTAAATG
* * * * * * *
6349950 AGATACTTTGGAAATCTCTTTCTTATTTTTCAAAAATCTTGTTGAAACATCCTGCCTGAAGGTCT
259 AGAAACTTTGGAAATCGCTTTCTTATTTTTCAAAAAGCATGTGGAAACATCCTACCCGAAGGTCT
* * * ** * *
6350015 TATAGATGGCCCGAAGGACTTATCATCTTGCTCAAGAGACTGACAGATTACCCGAAGGATTTAAT
324 TATAGATGGCCCGAAGAACTTATCATCTTGCTCAAAAGACTGAAAGAGGACCCAAAAGATTTAAT
*
6350080 CATAATTCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTATTGGG
389 CATAATTCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTACTGGG
* * *
6350145 TAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAATATTTCATTTTCTGAAAACATTAAATG
454 TAAGAAACTTTGGAAAT--C--GCTTACTATTCAAAAATTTCATTTTCTGAAAACATTAAATG
* * * *
6350208 AGAAACTTTGCAAATCGCTTTTTCATTTTTCGAAAATCATGTGGGAACATCCTGGCCAAAAGTCT
1 AGAAACTTTGAAAATC-CTTTTTCATTTTTCGAAAATCATGTGGAAACATCCTGCCCGAAAGTCT
* * * *
6350273 TATCGATGGCACAAATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
65 TATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAT
* * *
6350338 CATCATGCTCGAAAGACTTACTGATGGCCCAAAAGACTTACAAATTTTGGAAATAATTTACAGGG
130 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACAGGG
* *
6350403 TACA-AAACTTTGGAAATTGCTTTCTTACTTTTTAAAAATTTCA-TTTCAGAAAAGATTTAAATG
195 TA-AGAAACTTTGGAAATTGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAGATTTAAATG
*
6350466 AGAAACTTTGGAAATCGCTTTCTCATTTTTCAAA
259 AGAAACTTTGGAAATCGCTTTCTTATTTTTCAAA
6350500 TTTAATGGTT
Statistics
Matches: 721, Mismatches: 78, Indels: 16
0.88 0.10 0.02
Matches are distributed among these distances:
511 3 0.00
512 220 0.31
513 196 0.27
515 1 0.00
516 50 0.07
517 246 0.34
518 5 0.01
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (512 bp):
AGAAACTTTGAAAATCCTTTTTCATTTTTCGAAAATCATGTGGAAACATCCTGCCCGAAAGTCTT
ATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAATC
ATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATAGTTTACAGGGT
AAGAAACTTTGGAAATTGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAGATTTAAATGAG
AAACTTTGGAAATCGCTTTCTTATTTTTCAAAAAGCATGTGGAAACATCCTACCCGAAGGTCTTA
TAGATGGCCCGAAGAACTTATCATCTTGCTCAAAAGACTGAAAGAGGACCCAAAAGATTTAATCA
TAATTCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTCTACTGGGTA
AGAAACTTTGGAAATCGCTTACTATTCAAAAATTTCATTTTCTGAAAACATTAAATG
Found at i:6359486 original size:3 final size:3
Alignment explanation
Indices: 6359480--6359537 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
6359470 GTAAAAAAAG
* * *
6359480 ATA ATA AAA ATA A-A ATA AAA ATA AAA ATTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
6359525 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
6359538 ATATTAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:6359500 original size:12 final size:13
Alignment explanation
Indices: 6359471--6359538 Score: 54
Period size: 13 Copynumber: 5.3 Consensus size: 13
6359461 GTTGGGTCTG
6359471 TAAAAAA-AGATAA
1 TAAAAAATA-ATAA
6359484 T-AAAAATAA-AA
1 TAAAAAATAATAA
*
6359495 T-AAAAATAAAAA
1 TAAAAAATAATAA
* *
6359507 TTAATAATAATAA
1 TAAAAAATAATAA
6359520 TAATAATAATAATAA
1 TAA-AA-AATAATAA
6359535 TAAA
1 TAAA
6359539 TATTAATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
11 11 0.24
12 9 0.20
13 13 0.28
14 2 0.04
15 11 0.24
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (13 bp):
TAAAAAATAATAA
Found at i:6361044 original size:22 final size:22
Alignment explanation
Indices: 6360960--6361072 Score: 105
Period size: 22 Copynumber: 5.5 Consensus size: 22
6360950 ATAATCAACG
*
6360960 AATTCGCAACGCG-ATTT--CA
1 AATTCGCAACACGAATTTCCCA
* *
6360979 AATTTGCAACACGAA-CT-CCA
1 AATTCGCAACACGAATTTCCCA
* * * *
6360999 ATTTCGAAATAC-AGTTT-CCA
1 AATTCGCAACACGAATTTCCCA
*
6361019 AATTCGCAATACGAATTTCCCA
1 AATTCGCAACACGAATTTCCCA
6361041 AATTCGCAACACGAATTTCCCA
1 AATTCGCAACACGAATTTCCCA
6361063 AATTCGCAAC
1 AATTCGCAAC
6361073 TCGGTTTTCA
Statistics
Matches: 76, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
19 13 0.17
20 25 0.33
21 4 0.05
22 34 0.45
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.26
Consensus pattern (22 bp):
AATTCGCAACACGAATTTCCCA
Found at i:6361081 original size:22 final size:22
Alignment explanation
Indices: 6361016--6361099 Score: 102
Period size: 22 Copynumber: 3.9 Consensus size: 22
6361006 AATACAGTTT
6361016 CCAAATTCGCAA-TACGAATTTC
1 CCAAATTCGCAACT-CGAATTTC
*
6361038 CCAAATTCGCAACACGAATTTC
1 CCAAATTCGCAACTCGAATTTC
*
6361060 CCAAATTCGCAACTCG-GTTT-
1 CCAAATTCGCAACTCGAATTTC
* *
6361080 TCAAATTCGCAATTCGAATT
1 CCAAATTCGCAACTCGAATT
6361100 CGGATTTCGC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
20 14 0.26
21 5 0.09
22 35 0.65
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (22 bp):
CCAAATTCGCAACTCGAATTTC
Found at i:6361178 original size:22 final size:22
Alignment explanation
Indices: 6361150--6361198 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
6361140 ATAAAAAATC
*
6361150 CGCAACTCGAGTTCGCCAATTT
1 CGCAACTCGAATTCGCCAATTT
6361172 CGCAACTCGAATTCGCCAATTT
1 CGCAACTCGAATTCGCCAATTT
6361194 CGCAA
1 CGCAA
6361199 TTCAATTACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.24
Consensus pattern (22 bp):
CGCAACTCGAATTCGCCAATTT
Found at i:6361206 original size:87 final size:85
Alignment explanation
Indices: 6361085--6361270 Score: 275
Period size: 87 Copynumber: 2.2 Consensus size: 85
6361075 GGTTTTCAAA
* * *
6361085 TTCGCAATTCGAATTCGGATTTCGCAACTCAATTACCGATATAGGTAAACACAGTATAAAAAATC
1 TTCGCAACTCGAATTCGAATTTCGCAACTCAATTACCGATATAGGTAAACACAGTAGAAAAAATC
* *
6361150 CGCAACTCGAGTTCGCCAAT
66 CGCAACTCGAATTCACCAAT
* *
6361170 TTCGCAACTCGAATTCGCCAATTTCGCAATTCAATTACCGATATAGGTAAACACGGTAGAAAAAA
1 TTCGCAACTCGAATTCG--AATTTCGCAACTCAATTACCGATATAGGTAAACACAGTAGAAAAAA
6361235 TCCGCAACTCGAATTCACCAAT
64 TCCGCAACTCGAATTCACCAAT
*
6361257 TTTGCAACT-GAATT
1 TTCGCAACTCGAATT
6361271 TTTTACCTAT
Statistics
Matches: 91, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
85 16 0.18
86 5 0.05
87 70 0.77
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (85 bp):
TTCGCAACTCGAATTCGAATTTCGCAACTCAATTACCGATATAGGTAAACACAGTAGAAAAAATC
CGCAACTCGAATTCACCAAT
Found at i:6361576 original size:20 final size:20
Alignment explanation
Indices: 6361530--6361617 Score: 81
Period size: 20 Copynumber: 4.5 Consensus size: 20
6361520 CGAATTCGAA
* * *
6361530 TTGCGAATTTGAAAACTGAG
1 TTGCGAATTTGGAAATTGTG
6361550 TTGCGAATTTGGAAATTGTG
1 TTGCGAATTTGGAAATTGTG
* * *
6361570 TTCCGAAATTGG-AGTTCGTG
1 TTGCGAATTTGGAAATT-GTG
* *
6361590 TTGCGAATTT-GAAATCGCG
1 TTGCGAATTTGGAAATTGTG
6361609 TTGCGAATT
1 TTGCGAATT
6361618 CGTCGGTTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
19 15 0.27
20 40 0.73
ACGTcount: A:0.26, C:0.11, G:0.27, T:0.35
Consensus pattern (20 bp):
TTGCGAATTTGGAAATTGTG
Found at i:6363326 original size:2 final size:2
Alignment explanation
Indices: 6363319--6363348 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6363309 TACAAAAATA
6363319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6363349 CAAAATCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6378249 original size:10 final size:10
Alignment explanation
Indices: 6378236--6378288 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
6378226 TTTGACCAGT
6378236 TTTGAACCGG
1 TTTGAACCGG
6378246 TTTG-ACCGG
1 TTTGAACCGG
*
6378255 TTCGAACCGG
1 TTTGAACCGG
*
6378265 GTTG-ACCGG
1 TTTGAACCGG
*
6378274 TCTGAACCGG
1 TTTGAACCGG
*
6378284 GTTGA
1 TTTGA
6378289 CCCGACCCGA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
9 15 0.44
10 19 0.56
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (10 bp):
TTTGAACCGG
Found at i:6378253 original size:9 final size:9
Alignment explanation
Indices: 6378225--6378290 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 9
6378215 TGGAAAACCA
6378225 GTTTGACCAG
1 GTTTGACC-G
*
6378235 TTTTGAACCG
1 GTTTG-ACCG
6378245 GTTTGACCG
1 GTTTGACCG
*
6378254 GTTCGAACCG
1 GTTTG-ACCG
*
6378264 GGTTGACCG
1 GTTTGACCG
*
6378273 GTCTGAACCG
1 GTTTG-ACCG
*
6378283 GGTTGACC
1 GTTTGACC
6378291 CGACCCGACT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
9 18 0.41
10 23 0.52
11 3 0.07
ACGTcount: A:0.17, C:0.24, G:0.32, T:0.27
Consensus pattern (9 bp):
GTTTGACCG
Found at i:6378263 original size:19 final size:19
Alignment explanation
Indices: 6378239--6378290 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
6378229 GACCAGTTTT
*
6378239 GAACCGGTTTGACCGGTTC
1 GAACCGGGTTGACCGGTTC
6378258 GAACCGGGTTGACCGG-TC
1 GAACCGGGTTGACCGGTTC
6378276 TGAACCGGGTTGACC
1 -GAACCGGGTTGACC
6378291 CGACCCGACT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 2 0.06
19 29 0.94
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.21
Consensus pattern (19 bp):
GAACCGGGTTGACCGGTTC
Found at i:6378306 original size:17 final size:17
Alignment explanation
Indices: 6378284--6378341 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
6378274 TCTGAACCGG
6378284 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
6378301 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
6378318 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
6378335 GTTGACC
1 GTTGACC
6378342 GTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:6378343 original size:7 final size:7
Alignment explanation
Indices: 6378331--6378373 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
6378321 GACCCGACCC
6378331 GACCGTT
1 GACCGTT
6378338 GACCG-T
1 GACCGTT
6378344 GACCGTT
1 GACCGTT
6378351 GACCG-T
1 GACCGTT
6378357 GACCGTT
1 GACCGTT
6378364 GACCGTT
1 GACCGTT
6378371 GAC
1 GAC
6378374 TTTCTTTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:6378349 original size:13 final size:13
Alignment explanation
Indices: 6378331--6378369 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
6378321 GACCCGACCC
6378331 GACCGTTGACCGT
1 GACCGTTGACCGT
6378344 GACCGTTGACCGT
1 GACCGTTGACCGT
6378357 GACCGTTGACCGT
1 GACCGTTGACCGT
6378370 TGACTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:6378356 original size:20 final size:20
Alignment explanation
Indices: 6378331--6378373 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
6378321 GACCCGACCC
6378331 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
6378351 GACCG-TGACCGTTGACCGTT
1 GACCGTTGACCG-TGACCGTT
6378371 GAC
1 GAC
6378374 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Found at i:6385153 original size:10 final size:10
Alignment explanation
Indices: 6385124--6385230 Score: 98
Period size: 10 Copynumber: 11.1 Consensus size: 10
6385114 GCTGCTGGAA
6385124 AACCGGTTTG
1 AACCGGTTTG
*
6385134 -ACCAGTTTTG
1 AACC-GGTTTG
6385144 AACCGGTTTG
1 AACCGGTTTG
*
6385154 -ACCGGTTCG
1 AACCGGTTTG
6385163 AACCGGTTT-
1 AACCGGTTTG
*
6385172 AACCGGTCTG
1 AACCGGTTTG
*
6385182 AACCGGGTTG
1 AACCGGTTTG
*
6385192 -ACCGGTCTG
1 AACCGGTTTG
*
6385201 AACCGGGTTG
1 AACCGGTTTG
*
6385211 -ACCGGTCTG
1 AACCGGTTTG
*
6385220 AACCGGGTTG
1 AACCGGTTTG
6385230 A
1 A
6385231 CCCGACCCGA
Statistics
Matches: 76, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
9 33 0.43
10 40 0.53
11 3 0.04
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.25
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:6385167 original size:19 final size:19
Alignment explanation
Indices: 6385142--6385232 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
6385132 TGACCAGTTT
*
6385142 TGAACCGGTTTGACCGGT-
1 TGAACCGGGTTGACCGGTC
* *
6385160 TCGAACCGGTTTAACCGGTC
1 T-GAACCGGGTTGACCGGTC
6385180 TGAACCGGGTTGACCGGTC
1 TGAACCGGGTTGACCGGTC
6385199 TGAACCGGGTTGACCGGTC
1 TGAACCGGGTTGACCGGTC
6385218 TGAACCGGGTTGACC
1 TGAACCGGGTTGACC
6385233 CGACCCGACT
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
18 1 0.01
19 66 0.97
20 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (19 bp):
TGAACCGGGTTGACCGGTC
Found at i:6385193 original size:38 final size:38
Alignment explanation
Indices: 6385124--6385232 Score: 148
Period size: 38 Copynumber: 2.8 Consensus size: 38
6385114 GCTGCTGGAA
* * *
6385124 AACCGGTTTGACCAGTTTTGAACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACC-GGTCTGAACCGGGTTGACCGGTCT-G
*
6385163 AACCGGTTTAACCGGTCTGAACCGGGTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTGAACCGGGTTGACCGGTCTG
*
6385201 AACCGGGTTGACCGGTCTGAACCGGGTTGACC
1 AACCGGTTTGACCGGTCTGAACCGGGTTGACC
6385233 CGACCCGACT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
38 50 0.79
39 13 0.21
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.25
Consensus pattern (38 bp):
AACCGGTTTGACCGGTCTGAACCGGGTTGACCGGTCTG
Found at i:6385248 original size:17 final size:17
Alignment explanation
Indices: 6385226--6385283 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
6385216 TCTGAACCGG
6385226 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
6385243 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
6385260 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
6385277 GTTGACC
1 GTTGACC
6385284 GTTGACCGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:6385285 original size:7 final size:7
Alignment explanation
Indices: 6385273--6385322 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
6385263 GACCCGACCC
6385273 GACCGTT
1 GACCGTT
6385280 GACCGTT
1 GACCGTT
6385287 GACCG-T
1 GACCGTT
6385293 GACCGTT
1 GACCGTT
6385300 GACCG-T
1 GACCGTT
*
6385306 GACCGTA
1 GACCGTT
6385313 GACCGTT
1 GACCGTT
6385320 GAC
1 GAC
6385323 TTTCTTTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 12 0.31
7 27 0.69
ACGTcount: A:0.18, C:0.30, G:0.30, T:0.22
Consensus pattern (7 bp):
GACCGTT
Found at i:6385297 original size:13 final size:13
Alignment explanation
Indices: 6385273--6385318 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
6385263 GACCCGACCC
6385273 GACCGTTGACCGTT
1 GACCG-TGACCGTT
6385287 GACCGTGACCGTT
1 GACCGTGACCGTT
*
6385300 GACCGTGACCGTA
1 GACCGTGACCGTT
6385313 GACCGT
1 GACCGT
6385319 TGACTTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 26 0.84
14 5 0.16
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.22
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:6385298 original size:20 final size:20
Alignment explanation
Indices: 6385273--6385322 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
6385263 GACCCGACCC
6385273 GACCGTTGACCGTTGACCGT-
1 GACCGTTGACCG-TGACCGTA
6385293 GACCGTTGACCGTGACCGTA
1 GACCGTTGACCGTGACCGTA
6385313 GACCGTTGAC
1 GACCGTTGAC
6385323 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.18, C:0.30, G:0.30, T:0.22
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTA
Found at i:6391435 original size:22 final size:22
Alignment explanation
Indices: 6391407--6391450 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6391397 AGAAATAATC
*
6391407 TGCAACTCGAGTTCGCCAATTT
1 TGCAACTCGAATTCGCCAATTT
*
6391429 TGCAACTTGAATTCGCCAATTT
1 TGCAACTCGAATTCGCCAATTT
6391451 CGTAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (22 bp):
TGCAACTCGAATTCGCCAATTT
Found at i:6391471 original size:87 final size:87
Alignment explanation
Indices: 6391360--6391522 Score: 238
Period size: 87 Copynumber: 1.9 Consensus size: 87
6391350 TCGAATTTGG
* * * *
6391360 ATTTCGCAACTCAATTACCGATATAGGTAAACACGGTAGAAATAA-TCTGCAACTCGAGTTCGCC
1 ATTTCGCAACTCAATTACCAATATAGGTAAACACAGTAGAAA-AATTCCGCAACTCGAATTCGCC
*
6391424 AATTTTGCAACTTGAATTCGCCA
65 AATTTCGCAACTTGAATTCGCCA
* * *
6391447 ATTTCGTAACTCAATTACCAATATAGGTAAACACAGTAGAAAAATTCCGCATCTCGAATTTGCCA
1 ATTTCGCAACTCAATTACCAATATAGGTAAACACAGTAGAAAAATTCCGCAACTCGAATTCGCCA
6391512 ATTTCGCAACT
66 ATTTCGCAACT
6391523 CAATTTTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
86 2 0.03
87 65 0.97
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (87 bp):
ATTTCGCAACTCAATTACCAATATAGGTAAACACAGTAGAAAAATTCCGCAACTCGAATTCGCCA
ATTTCGCAACTTGAATTCGCCA
Found at i:6391870 original size:19 final size:20
Alignment explanation
Indices: 6391793--6391876 Score: 75
Period size: 20 Copynumber: 4.2 Consensus size: 20
6391783 TTCGAATTAT
* *
6391793 GAATTTGAAAACTGAGTTGC
1 GAATTTGAAATCTGTGTTGC
6391813 GAATTTGGAAA-CTGTGTTGC
1 GAATTT-GAAATCTGTGTTGC
* * *
6391833 GAAATTGGAGT-TCGTGTTGC
1 GAATTTGAAATCT-GTGTTGC
*
6391853 GAATTTGAAATC-GCGTTGC
1 GAATTTGAAATCTGTGTTGC
6391872 GAATT
1 GAATT
6391877 CGTCGGTTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
19 14 0.27
20 34 0.65
21 4 0.08
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.33
Consensus pattern (20 bp):
GAATTTGAAATCTGTGTTGC
Found at i:6393378 original size:2 final size:2
Alignment explanation
Indices: 6393371--6393396 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6393361 TATAAAAATA
6393371 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6393397 CAAAATCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6397720 original size:27 final size:27
Alignment explanation
Indices: 6397685--6397738 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
6397675 TTTCCTATAG
6397685 AGTTAGATTCTTGAAGGCATCTTGAGT
1 AGTTAGATTCTTGAAGGCATCTTGAGT
* *
6397712 AGTTTGATTCTTGAAGGTATCTTGAGT
1 AGTTAGATTCTTGAAGGCATCTTGAGT
6397739 TCCAAATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (27 bp):
AGTTAGATTCTTGAAGGCATCTTGAGT
Found at i:6400058 original size:17 final size:18
Alignment explanation
Indices: 6400024--6400065 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
6400014 TATATATTTA
6400024 CTTCT-TTTTTCATCTTT
1 CTTCTCTTTTTCATCTTT
*
6400041 CTTCTCTTTTTC-TTTTT
1 CTTCTCTTTTTCATCTTT
6400058 CTTC-CTTT
1 CTTCTCTTT
6400066 ACCATCATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 13 0.57
18 6 0.26
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTCTCTTTTTCATCTTT
Found at i:6424172 original size:18 final size:18
Alignment explanation
Indices: 6424122--6424177 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
6424112 CATAATGTTA
6424122 TTTTATCATAAATATAGA-
1 TTTTATCATAAATAT-GAT
* * * *
6424140 ATATATAATACATATGAT
1 TTTTATCATAAATATGAT
*
6424158 TTTTATCATAAATATTAT
1 TTTTATCATAAATATGAT
6424176 TT
1 TT
6424178 CGGGTATGAA
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (18 bp):
TTTTATCATAAATATGAT
Found at i:6424935 original size:29 final size:30
Alignment explanation
Indices: 6424887--6424944 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
6424877 TAAATGGATT
* *
6424887 TTTAGTGACCAAATTGTAAA-TGTTGAAAA
1 TTTAGTGACCAAAGTATAAACTGTTGAAAA
* *
6424916 TTTAGTGGCCAAAGTATAAACTTTTGAAA
1 TTTAGTGACCAAAGTATAAACTGTTGAAA
6424945 GGTTTAAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (30 bp):
TTTAGTGACCAAAGTATAAACTGTTGAAAA
Found at i:6429994 original size:20 final size:19
Alignment explanation
Indices: 6429950--6430022 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 19
6429940 TTGAAACCCA
* * *
6429950 AAGTTTCGAAACTATAAGGG
1 AAGTTTCGAAACTCTTA-TG
6429970 AAGTTTCGAAACTCTTATG
1 AAGTTTCGAAACTCTTATG
** * * *
6429989 ATAGTTTTAAAACTATTGTT
1 A-AGTTTCGAAACTCTTATG
6430009 AAGTTTCGAAACTC
1 AAGTTTCGAAACTC
6430023 CAAAGTCTAC
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
19 12 0.29
20 29 0.71
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (19 bp):
AAGTTTCGAAACTCTTATG
Found at i:6432424 original size:53 final size:53
Alignment explanation
Indices: 6432344--6432446 Score: 188
Period size: 53 Copynumber: 1.9 Consensus size: 53
6432334 GTTAATTCGG
6432344 TTAACAGACCGAAATAAACAAACTTTGTTAAGTTAGGTTAATATTTTTTTCAC
1 TTAACAGACCGAAATAAACAAACTTTGTTAAGTTAGGTTAATATTTTTTTCAC
* *
6432397 TTAACCGACCGAAATAACCAAACTTTGTTAAGTTAGGTTAATATTTTTTT
1 TTAACAGACCGAAATAAACAAACTTTGTTAAGTTAGGTTAATATTTTTTT
6432447 TAAAAATAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39
Consensus pattern (53 bp):
TTAACAGACCGAAATAAACAAACTTTGTTAAGTTAGGTTAATATTTTTTTCAC
Found at i:6436164 original size:20 final size:20
Alignment explanation
Indices: 6436120--6436157 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6436110 AAGTGAGATT
6436120 TCGGTCCGATTAAGGGGTCG
1 TCGGTCCGATTAAGGGGTCG
*
6436140 TCGGTCCGATTAATGGGT
1 TCGGTCCGATTAAGGGGT
6436158 TTACGGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.37, T:0.29
Consensus pattern (20 bp):
TCGGTCCGATTAAGGGGTCG
Found at i:6440329 original size:3 final size:3
Alignment explanation
Indices: 6440316--6440377 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
6440306 GTAATATGTA
** *
6440316 AAT AA- AAT AAT AAT AAT AAT GCT AAT AAT AAT AATT AA- AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
6440360 GAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT A-AT AA
6440378 AAAAGACCCG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 6 0.13
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6440378 original size:24 final size:23
Alignment explanation
Indices: 6440316--6440379 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
6440306 GTAATATGTA
* *
6440316 AATAA-AATAATAATAATAATGCT
1 AATAATAATAATAA-AATAACGAT
6440339 AATAATAATAATTAAAATAACGAT
1 AATAATAATAA-TAAAATAACGAT
6440363 AATAATAATATATAAAA
1 AATAATAATA-ATAAAA
6440380 AAGACCCGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 5 0.14
24 27 0.75
25 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (23 bp):
AATAATAATAATAAAATAACGAT
Found at i:6440979 original size:134 final size:135
Alignment explanation
Indices: 6440560--6441056 Score: 702
Period size: 135 Copynumber: 3.7 Consensus size: 135
6440550 AGTTCGGGTC
*
6440560 ATCTAAGGGTGACACGGTTCCTACATGATGAGGAAATATTGTCGAGGGATGACACTTCTCATACG
1 ATCTAAGGGTGACACGGTTCCTACATGATGAGGAAATATGGTCGAGGGATGACACTTCTCATACG
6440625 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGC
66 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGC
6440690 TGGTT
131 TGGTT
* *
6440695 ATCTAAGGGTGACACGGTTCCTACATAATGAGGAAATATGGTCGAGGGATGACACTGCTCATACG
1 ATCTAAGGGTGACACGGTTCCTACATGATGAGGAAATATGGTCGAGGGATGACACTTCTCATACG
6440760 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGC
66 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGC
6440825 TGGTT
131 TGGTT
* ** * * *
6440830 ATCTAGGGGTGACACGGTTCCTACGCGATGAGGAGATCTGGTCGGGGGATGACACTTCTCATACG
1 ATCTAAGGGTGACACGGTTCCTACATGATGAGGAAATATGGTCGAGGGATGACACTTCTCATACG
* * *
6440895 TGATGAAGAGTTC-TGGCCATCTTTAGGAAGGGTGATAACAT-AGTTCCTACGTGATGAGGACGT
66 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAAC-TCGGTTCCTACGCGATGAGGACGG
*
6440958 CTAGTT
130 CTGGTT
* ** * * * *
6440964 ATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATTTGATC-AGGAGATGACACAATTC-C-T
1 ATCTAAGGGTGACACGGTTCCTACATGATGAGGAAATATGGTCGAGG-GATGACAC--TTCTCAT
* *
6441026 ACGTGATGAGGACG-GC-TGGCCATCTTTAGGA
63 ACGTGATGAAGA-GTTCTTGGCCATCTTTAGGA
6441057 GTTATGATTT
Statistics
Matches: 334, Mismatches: 23, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
133 2 0.01
134 124 0.37
135 205 0.61
136 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.26
Consensus pattern (135 bp):
ATCTAAGGGTGACACGGTTCCTACATGATGAGGAAATATGGTCGAGGGATGACACTTCTCATACG
TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGC
TGGTT
Found at i:6441156 original size:31 final size:28
Alignment explanation
Indices: 6441064--6441159 Score: 106
Period size: 28 Copynumber: 3.3 Consensus size: 28
6441054 GGAGTTATGA
* * *
6441064 TTTCAAGAGAAACCGATTCAAAGATTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTG
6441092 TTTCAAAAGAAACAGACTCAAAGATTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTG
6441120 TTTCAAGAA-AAACA-AGCTCAAAGATAATGTG
1 TTTCAA-AAGAAACAGA-CTCAAAGAT--T-TG
6441151 TTTCAAAAG
1 TTTCAAAAG
6441160 CAACTGTCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
27 1 0.02
28 45 0.76
29 2 0.03
30 3 0.05
31 8 0.14
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.26
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATTTG
Found at i:6441350 original size:66 final size:62
Alignment explanation
Indices: 6441161--6441343 Score: 168
Period size: 66 Copynumber: 2.8 Consensus size: 62
6441151 TTTCAAAAGC
* ** * *
6441161 AACTGTCTCGAAAGAGACAAAATTCGTTTCAAATGAAACAACTCAAAAGATGACGTTTAAAGGG
1 AACTGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACATCTC-AAAGATGATGTTTAAAGGG
* * ** * * * *
6441225 AATTGTCTCAAGCGAGACAAAATTTGTTTTCAAGGGAAACATTCTCAAATATCGGTGTTTCATGG
1 AACTGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACA-TCTCAAAGAT-GATGTTTAAAGG
6441290 G
62 G
6441291 AAACTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 -AACTGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAAC-ATCTCAAAGATG
6441344 TTTGTTTTGT
Statistics
Matches: 95, Mismatches: 17, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
63 2 0.02
64 17 0.18
65 20 0.21
66 36 0.38
67 20 0.21
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (62 bp):
AACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACATCTCAAAGATGATGTTTAAAGGG
Found at i:6441798 original size:40 final size:40
Alignment explanation
Indices: 6441754--6441833 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
6441744 GTTTTAATAG
6441754 AAACGATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACGATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
6441794 AAACGATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACGATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
6441834 CGAGAGACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (40 bp):
AAACGATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
Found at i:6441887 original size:64 final size:65
Alignment explanation
Indices: 6441815--6441940 Score: 191
Period size: 65 Copynumber: 2.0 Consensus size: 65
6441805 AAGGTGGGTA
* * *
6441815 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTT
* * *
6441879 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
6441941 GGATCACATC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
64 17 0.31
65 38 0.69
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (65 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:6442595 original size:67 final size:67
Alignment explanation
Indices: 6442160--6442594 Score: 802
Period size: 67 Copynumber: 6.5 Consensus size: 67
6442150 TCATTTTAAG
* *
6442160 AGAAACAGATTCAAAGA-TTTT-TTCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
6442223 AA
66 AA
6442225 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
6442290 AA
66 AA
6442292 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
6442357 AA
66 AA
6442359 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
6442424 AA
66 AA
*
6442426 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
6442491 AA
66 AA
* *
6442493 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
6442558 AA
66 AA
*
6442560 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAA
6442595 CAATCTCAAA
Statistics
Matches: 364, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
65 16 0.04
66 4 0.01
67 344 0.95
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.31
Consensus pattern (67 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:6442672 original size:92 final size:93
Alignment explanation
Indices: 6442481--6442702 Score: 270
Period size: 92 Copynumber: 2.4 Consensus size: 93
6442471 AGAGACAAAA
* *
6442481 TTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAA
1 TTTTGTTTCAAAAGAAAC-AACTCAAAGA--TTT-TTTCAAAAGAAACTATCTCAAGAGAGACAA
* *
6442546 AATTTTGTTTCCAAAGAAACAAACTCAAAGAT
62 AACTTTGTTTCAAAAGAAACAAACTCAAAGAT
* * *
6442578 TTTTGTTTCAAAAGAAACAATCTCAAAGATTTTTTC-ACA-AAATTGTCTCAAGAGAGACAAAAC
1 TTTTGTTTCAAAAGAAACAA-CTCAAAGATTTTTTCAAAAGAAACTATCTCAAGAGAGACAAAAC
* *
6442641 TTTGTTTCAAAATAAATAGAA-TCAAAGAT
65 TTTGTTTCAAAAGAAACA-AACTCAAAGAT
* *
6442670 TTTTTTTTCAAACGAAACAACTCAAAGATTTTT
1 TTTTGTTTCAAAAGAAACAACTCAAAGATTTTT
6442703 ATTCAAAATG
Statistics
Matches: 112, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
91 13 0.12
92 61 0.54
93 4 0.04
94 4 0.04
95 3 0.03
96 2 0.02
97 25 0.22
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.32
Consensus pattern (93 bp):
TTTTGTTTCAAAAGAAACAACTCAAAGATTTTTTCAAAAGAAACTATCTCAAGAGAGACAAAACT
TTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:6442707 original size:28 final size:28
Alignment explanation
Indices: 6442662--6442772 Score: 134
Period size: 29 Copynumber: 3.8 Consensus size: 28
6442652 ATAAATAGAA
* *
6442662 TCAAAGATTTTTTTTTCAAACGAA-ACAAC
1 TCAAAGA-TTTTTATTCAAAAGAACA-AAC
6442691 TCAAAGATTTTTATTCAAAATGAACAAAC
1 TCAAAGATTTTTATTCAAAA-GAACAAAC
*
6442720 TCCAAGATTTTTATTCAAAAGGAACAAAC
1 TCAAAGATTTTTATTCAAAA-GAACAAAC
*
6442749 TCAAAGATTTTTTTCTCAAAAGAA
1 TCAAAGATTTTTAT-TCAAAAGAA
6442773 ATTGTCTTTA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.15
29 55 0.75
30 7 0.10
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.32
Consensus pattern (28 bp):
TCAAAGATTTTTATTCAAAAGAACAAAC
Found at i:6443097 original size:36 final size:36
Alignment explanation
Indices: 6443013--6443116 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
6443003 GAGAAAATGA
* * *
6443013 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
6443047 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
6443083 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
6443117 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:6443144 original size:36 final size:36
Alignment explanation
Indices: 6443014--6443132 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
6443004 AGAAAATGAT
* * * *
6443014 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
6443048 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
6443084 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
6443119 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
6443133 TCAACTTTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 19 0.28
35 12 0.17
36 38 0.55
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:6443264 original size:105 final size:101
Alignment explanation
Indices: 6443084--6443316 Score: 269
Period size: 105 Copynumber: 2.3 Consensus size: 101
6443074 TAGAGAAATT
*
6443084 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
*
6443148 GTGAAACAAATTCGAAATTTGGATCTCAAAGGGA-AAAG
64 GTGAAACAAATTCAAAATTTGGATCTCAAA-GGACAAAG
* *
6443186 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTGTTT
* * *
6443250 -TTAGTGAATA-AAATTCAAAATTTGTATCTCAAAGGACAAAT
61 AAT-GTGAA-ACAAATTCAAAATTTGGATCTCAAAGGACAAAG
*
6443291 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
6443317 AAAATTCTCA
Statistics
Matches: 114, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 8 0.07
105 77 0.68
106 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGACAAAG
Found at i:6443796 original size:4 final size:4
Alignment explanation
Indices: 6443787--6443860 Score: 125
Period size: 4 Copynumber: 19.0 Consensus size: 4
6443777 TTTATGTATC
6443787 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
6443833 ATGT ATGT ATGT ATGT ATGT ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
6443861 GTATACTTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
4 64 0.97
ACGTcount: A:0.24, C:0.01, G:0.26, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:6445078 original size:24 final size:26
Alignment explanation
Indices: 6445041--6445089 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
6445031 CTTTGTCCAC
6445041 TTTCTCTTCTTCTTT-TTTTTACTTTG
1 TTTCTCTTCTTCTTTGTTTTT-CTTTG
6445067 TTTCT-TTC-TCTTTGTTTTTCTTT
1 TTTCTCTTCTTCTTTGTTTTTCTTT
6445090 TCTCTTCGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.41
25 8 0.36
26 5 0.23
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (26 bp):
TTTCTCTTCTTCTTTGTTTTTCTTTG
Found at i:6445739 original size:26 final size:24
Alignment explanation
Indices: 6445709--6445779 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 24
6445699 CAAGGTGGAA
6445709 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
* *
6445733 AGGGAATGTTTCAAGG--TCGAA-A-
1 A--GAATATTTCAAGGTCTCAAAGAG
6445755 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
6445779 A
1 A
6445780 TAGAATGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
20 12 0.32
22 5 0.14
23 2 0.05
24 6 0.16
26 12 0.32
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (24 bp):
AGAATATTTCAAGGTCTCAAAGAG
Found at i:6445764 original size:20 final size:20
Alignment explanation
Indices: 6445696--6445770 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
6445686 AAATACAGTG
*
6445696 TTTCAAGGT-GGAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
* *
6445715 TTTCAAGGTCTCAAAGAGAGGGAATG
1 TTTCAAGG--TCGAA-A-A--GAATA
6445741 TTTCAAGGTCGAAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
6445761 TTTCAAGGTC
1 TTTCAAGGTC
6445771 TCAAAGAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.18
20 14 0.32
21 1 0.02
22 2 0.05
23 2 0.05
24 5 0.11
26 12 0.27
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (20 bp):
TTTCAAGGTCGAAAAGAATA
Found at i:6445784 original size:26 final size:26
Alignment explanation
Indices: 6445706--6445785 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
6445696 TTTCAAGGTG
6445706 GAAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
** *
6445732 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
6445753 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
6445778 GATAGAAT
1 GAAAGAAT
6445786 GTCAAAAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 20 0.49
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:6445786 original size:46 final size:45
Alignment explanation
Indices: 6445694--6445787 Score: 152
Period size: 46 Copynumber: 2.1 Consensus size: 45
6445684 ATAAATACAG
* *
6445694 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
6445739 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
6445785 TGT
1 TGT
6445788 CAAAAAATTG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 11 0.24
46 34 0.76
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:6447246 original size:31 final size:32
Alignment explanation
Indices: 6447190--6447251 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
6447180 TGACAAAATG
6447190 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
6447222 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
6447252 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:6450654 original size:3 final size:3
Alignment explanation
Indices: 6450641--6450702 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
6450631 GTAATATGTA
** *
6450641 AAT AA- AAT AAT AAT AAT AAT GCT AAT AAT AAT AATT AA- AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
6450685 GAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT A-AT AA
6450703 AAAAGACCCG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 6 0.13
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6450703 original size:24 final size:23
Alignment explanation
Indices: 6450641--6450704 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
6450631 GTAATATGTA
* *
6450641 AATAA-AATAATAATAATAATGCT
1 AATAATAATAATAA-AATAACGAT
6450664 AATAATAATAATTAAAATAACGAT
1 AATAATAATAA-TAAAATAACGAT
6450688 AATAATAATATATAAAA
1 AATAATAATA-ATAAAA
6450705 AAGACCCGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 5 0.14
24 27 0.75
25 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (23 bp):
AATAATAATAATAAAATAACGAT
Found at i:6452023 original size:2 final size:2
Alignment explanation
Indices: 6451939--6452008 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
6451929 GTGTAAGATG
6451939 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6451981 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6452009 CACGCAAGTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6453753 original size:13 final size:13
Alignment explanation
Indices: 6453735--6453781 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
6453725 TGCGTCATAA
*
6453735 ATTTATGACGCGC
1 ATTTATGACACGC
*
6453748 ATTTATGACATGC
1 ATTTATGACACGC
6453761 ATTTATGACACGC
1 ATTTATGACACGC
6453774 ATTTATGA
1 ATTTATGA
6453782 TGCTCATTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:6455445 original size:2 final size:2
Alignment explanation
Indices: 6455440--6455490 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
6455430 CACACATTTA
6455440 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6455480 AT AT AT AT AT A
1 AT AT AT AT AT A
6455491 AATTAATAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6460172 original size:85 final size:85
Alignment explanation
Indices: 6460062--6460254 Score: 239
Period size: 85 Copynumber: 2.3 Consensus size: 85
6460052 ACATGAATTT
** ** ** *
6460062 AAGATGACACACAACTGTGCATCATAAATTTATGATGCGCATTTATGACACT-CATTGCGTGTCA
1 AAGATGACACACATTTGTGTGTCATAAATTTATGACACGCATGTATGAC-CTACATTGCGTGTCA
* * *
6460126 TTGAAGCCCCCGTCA-TAAATG
65 TTGAAGCACACGTCATTAAA-A
*
6460147 AAGATGACACACATTTGTGTGTCATAAATTTATGACACGCATGTATGACTTACATTGCGTGTCAT
1 AAGATGACACACATTTGTGTGTCATAAATTTATGACACGCATGTATGACCTACATTGCGTGTCAT
6460212 TGAAGCACACGTCATTAAAA
66 TGAAGCACACGTCATTAAAA
6460232 AAGATGACACACATTCT-TGTGTC
1 AAGATGACACACATT-TGTGTGTC
6460255 GTGAATGTAT
Statistics
Matches: 94, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
84 1 0.01
85 88 0.94
86 5 0.05
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (85 bp):
AAGATGACACACATTTGTGTGTCATAAATTTATGACACGCATGTATGACCTACATTGCGTGTCAT
TGAAGCACACGTCATTAAAA
Found at i:6460281 original size:2 final size:2
Alignment explanation
Indices: 6460274--6460302 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6460264 TTTCGTAAAT
6460274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6460303 TTTTTTTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6460526 original size:10 final size:10
Alignment explanation
Indices: 6460511--6460539 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
6460501 TGTACACAAG
6460511 AAATAATTGA
1 AAATAATTGA
6460521 AAATAATTGA
1 AAATAATTGA
6460531 AAATAATTG
1 AAATAATTG
6460540 TAACAGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (10 bp):
AAATAATTGA
Found at i:6462039 original size:27 final size:27
Alignment explanation
Indices: 6462001--6462056 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
6461991 TTCAATATAC
*
6462001 TCGGTTTAGATGGCTTAACCAGTTAAT
1 TCGGTTTAGATGGATTAACCAGTTAAT
6462028 TCGGTTTAGATGGATTAACCAGTTAAT
1 TCGGTTTAGATGGATTAACCAGTTAAT
6462055 TC
1 TC
6462057 AGTTATAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (27 bp):
TCGGTTTAGATGGATTAACCAGTTAAT
Found at i:6462144 original size:146 final size:146
Alignment explanation
Indices: 6461967--6462258 Score: 584
Period size: 146 Copynumber: 2.0 Consensus size: 146
6461957 GGTTTGGTTA
6461967 TTTCGGTCTTAACAATAAAATCAGTTCAATATACTCGGTTTAGATGGCTTAACCAGTTAATTCGG
1 TTTCGGTCTTAACAATAAAATCAGTTCAATATACTCGGTTTAGATGGCTTAACCAGTTAATTCGG
6462032 TTTAGATGGATTAACCAGTTAATTCAGTTATAGGAATATAAAAACCAAACTGACCAAACCAACTG
66 TTTAGATGGATTAACCAGTTAATTCAGTTATAGGAATATAAAAACCAAACTGACCAAACCAACTG
6462097 GATGCACACCTGTAAT
131 GATGCACACCTGTAAT
6462113 TTTCGGTCTTAACAATAAAATCAGTTCAATATACTCGGTTTAGATGGCTTAACCAGTTAATTCGG
1 TTTCGGTCTTAACAATAAAATCAGTTCAATATACTCGGTTTAGATGGCTTAACCAGTTAATTCGG
6462178 TTTAGATGGATTAACCAGTTAATTCAGTTATAGGAATATAAAAACCAAACTGACCAAACCAACTG
66 TTTAGATGGATTAACCAGTTAATTCAGTTATAGGAATATAAAAACCAAACTGACCAAACCAACTG
6462243 GATGCACACCTGTAAT
131 GATGCACACCTGTAAT
6462259 CTCTCCTGAA
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 146 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (146 bp):
TTTCGGTCTTAACAATAAAATCAGTTCAATATACTCGGTTTAGATGGCTTAACCAGTTAATTCGG
TTTAGATGGATTAACCAGTTAATTCAGTTATAGGAATATAAAAACCAAACTGACCAAACCAACTG
GATGCACACCTGTAAT
Found at i:6462185 original size:27 final size:27
Alignment explanation
Indices: 6462147--6462202 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
6462137 TTCAATATAC
*
6462147 TCGGTTTAGATGGCTTAACCAGTTAAT
1 TCGGTTTAGATGGATTAACCAGTTAAT
6462174 TCGGTTTAGATGGATTAACCAGTTAAT
1 TCGGTTTAGATGGATTAACCAGTTAAT
6462201 TC
1 TC
6462203 AGTTATAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (27 bp):
TCGGTTTAGATGGATTAACCAGTTAAT
Found at i:6462565 original size:38 final size:38
Alignment explanation
Indices: 6462523--6462603 Score: 162
Period size: 38 Copynumber: 2.1 Consensus size: 38
6462513 GCCTTCATCT
6462523 GCATGTAAACATCATAAGTTAAAGCTTATCAACAAGAA
1 GCATGTAAACATCATAAGTTAAAGCTTATCAACAAGAA
6462561 GCATGTAAACATCATAAGTTAAAGCTTATCAACAAGAA
1 GCATGTAAACATCATAAGTTAAAGCTTATCAACAAGAA
6462599 GCATG
1 GCATG
6462604 CAACTAGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.23
Consensus pattern (38 bp):
GCATGTAAACATCATAAGTTAAAGCTTATCAACAAGAA
Found at i:6467960 original size:3 final size:3
Alignment explanation
Indices: 6467952--6467977 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6467942 ATACACATGT
6467952 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
6467978 GCTAACGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:6468153 original size:20 final size:21
Alignment explanation
Indices: 6468130--6468170 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6468120 ATATGTACCT
6468130 ACATATAATAAT-ATATTTAA
1 ACATATAATAATCATATTTAA
* *
6468150 ACATCTAATATTCATATTTAA
1 ACATATAATAATCATATTTAA
6468171 TAACATCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (21 bp):
ACATATAATAATCATATTTAA
Found at i:6470053 original size:15 final size:15
Alignment explanation
Indices: 6470012--6470048 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
6470002 AACCCATTTT
6470012 TATTCTTTTTTTCTTA
1 TATT-TTTTTTTCTTA
6470028 TATTTTTTTTTC-TA
1 TATTTTTTTTTCTTA
6470042 T-TTTTTT
1 TATTTTTT
6470049 CTTTTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.29
14 3 0.14
15 8 0.38
16 4 0.19
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (15 bp):
TATTTTTTTTTCTTA
Found at i:6470061 original size:14 final size:15
Alignment explanation
Indices: 6470033--6470075 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
6470023 TCTTATATTT
*
6470033 TTTTTTCTATTTTTTTC
1 TTTTTTC-A-TTTTTCC
6470050 TTTTTTCATTTTTCC
1 TTTTTTCATTTTTCC
*
6470065 TTTTTTTATTT
1 TTTTTTCATTT
6470076 GTCTACTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 16 0.67
16 1 0.04
17 7 0.29
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTCATTTTTCC
Found at i:6481055 original size:2 final size:2
Alignment explanation
Indices: 6481048--6481077 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6481038 TCATGCATAA
6481048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6481078 CATGGCTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6481381 original size:45 final size:45
Alignment explanation
Indices: 6481327--6481520 Score: 239
Period size: 45 Copynumber: 4.3 Consensus size: 45
6481317 CATGAGTAGA
*
6481327 ACCTTTTATGCCGATAATGCACCATTATGCATTTTCATTA-TAGGC
1 ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTAGT-GGC
** * * * **
6481372 ATTTTTTATGCTGATAATGCAACGCTAT-TTTTTTCATTAGTGGC
1 ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTAGTGGC
*
6481416 ACCTTTTATGCCAATAATGCACCGTTATGCATTTTCATTAGTGGC
1 ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTAGTGGC
* * ** *
6481461 ACCTTTTATACCGATAATGTATTGTTATCCATTTTCATTAGTGGC
1 ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTAGTGGC
6481506 ACCTTTTATGCCGAT
1 ACCTTTTATGCCGAT
6481521 TCGTAGATTT
Statistics
Matches: 124, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
44 34 0.27
45 90 0.73
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (45 bp):
ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTAGTGGC
Found at i:6481478 original size:89 final size:90
Alignment explanation
Indices: 6481327--6481517 Score: 251
Period size: 89 Copynumber: 2.1 Consensus size: 90
6481317 CATGAGTAGA
* ** * *
6481327 ACCTTTTATGCCGATAATGCACCATTATGCATTTTCATTATAGGCATTTTTTATGCTGATAATGC
1 ACCTTTTATGCCAATAATGCACCATTATGCATTTTCATTATAGGCACCTTTTATACCGATAATGC
**
6481392 AACGCTAT-TTTTTTCATTAGTGGC
66 AACGCTATCCATTTTCATTAGTGGC
*
6481416 ACCTTTTATGCCAATAATGCACCGTTATGCATTTTCATTAGT-GGCACCTTTTATACCGATAATG
1 ACCTTTTATGCCAATAATGCACCATTATGCATTTTCATTA-TAGGCACCTTTTATACCGATAATG
* ** *
6481480 TATTGTTATCCATTTTCATTAGTGGC
65 CAACGCTATCCATTTTCATTAGTGGC
6481506 ACCTTTTATGCC
1 ACCTTTTATGCC
6481518 GATTCGTAGA
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
89 61 0.69
90 27 0.31
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (90 bp):
ACCTTTTATGCCAATAATGCACCATTATGCATTTTCATTATAGGCACCTTTTATACCGATAATGC
AACGCTATCCATTTTCATTAGTGGC
Found at i:6482119 original size:18 final size:18
Alignment explanation
Indices: 6482096--6482142 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
6482086 CCTTCTTCTT
*
6482096 AGTATCGATACCCACAGC
1 AGTATCGATACCCAAAGC
6482114 AGTATCGATACCCAAAGC
1 AGTATCGATACCCAAAGC
6482132 AGTATCGATAC
1 AGTATCGATAC
6482143 TAATTGCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (18 bp):
AGTATCGATACCCAAAGC
Found at i:6484144 original size:18 final size:17
Alignment explanation
Indices: 6484118--6484156 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
6484108 AAATATTCTT
6484118 TTTTATTTA-TTCCTTTA
1 TTTTATTTATTTCC-TTA
6484135 TTTTATTTTATTTCCTTA
1 TTTTA-TTTATTTCCTTA
6484153 TTTT
1 TTTT
6484157 TACTTTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTTATTTCCTTA
Found at i:6484157 original size:19 final size:17
Alignment explanation
Indices: 6484116--6484163 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
6484106 TAAAATATTC
6484116 TTTTTTA-TTTATTCCT
1 TTTTTTATTTTATTCCT
6484132 TTATTTTATTTTATTTCCT
1 TT-TTTTATTTTA-TTCCT
6484151 TATTTTTACTTTT
1 T-TTTTTA-TTTT
6484164 CTCTTTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.07
17 5 0.19
18 4 0.15
19 11 0.41
20 5 0.19
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTATTTTATTCCT
Found at i:6499583 original size:20 final size:21
Alignment explanation
Indices: 6499547--6499607 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
6499537 TTTTGGTGCA
*
6499547 GAGGGAA-TCGATACCCCC-AT
1 GAGGGAACT-GATTCCCCCTAT
*
6499567 GAGGGAACTGATTCCCCCTTT
1 GAGGGAACTGATTCCCCCTAT
*
6499588 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACTGATTCCCCC
6499608 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 15 0.44
21 3 0.09
22 1 0.03
23 15 0.44
ACGTcount: A:0.25, C:0.31, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACTGATTCCCCCTAT
Done.