Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 85 of 318
Found at i:28928519 original size:43 final size:43
Alignment explanation
Indices: 28928452--28928637 Score: 266
Period size: 43 Copynumber: 4.3 Consensus size: 43
28928442 TCTGCCAAAA
* *
28928452 TTAGCGGCGCTTTT-CCAATAAACGCCACTAAAAGTCAAGGCTT
1 TTAGCGGCGCTTTTACC-ACAAACGCCGCTAAAAGTCAAGGCTT
* *
28928495 TTAACGGCGTTTTTACCACAAACGCCGCTAAAAGTCAAGGCTT
1 TTAGCGGCGCTTTTACCACAAACGCCGCTAAAAGTCAAGGCTT
28928538 TTAGCGGCGCTTTTACCACAAACGCCGCTAAAAGTCAAGGCTT
1 TTAGCGGCGCTTTTACCACAAACGCCGCTAAAAGTCAAGGCTT
* * ** *
28928581 TTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACTT
1 TTAGCGGCGCTTTTACCACAAACGCCGCTAAAAGTCAAGGCTT
*
28928624 TTAGCGGCGTTTTT
1 TTAGCGGCGCTTTT
28928638 TTCAATAAAC
Statistics
Matches: 130, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
43 128 0.98
44 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (43 bp):
TTAGCGGCGCTTTTACCACAAACGCCGCTAAAAGTCAAGGCTT
Found at i:28933130 original size:46 final size:46
Alignment explanation
Indices: 28933031--28933156 Score: 173
Period size: 46 Copynumber: 2.7 Consensus size: 46
28933021 GAGTCATCCA
* * * *
28933031 AACTCGTTGAGTTGCGTTCTGAGTTCACCTATGGATGCAAGCATCCG
1 AACTCGTTGAGTTGTGTTCCGAGTTCA-TTATGGATGCAAGCACCCG
28933078 AACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGCGAA-CACCCG
1 AACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGC-AAGCACCCG
* *
28933124 AGCTCGTTGAGTTGTGTTTCGAGTTCATTATGG
1 AACTCGTTGAGTTGTGTTCCGAGTTCATTATGG
28933157 GTGAGATTAT
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
46 45 0.62
47 27 0.38
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (46 bp):
AACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGCAAGCACCCG
Found at i:28944356 original size:9 final size:9
Alignment explanation
Indices: 28944338--28944372 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
28944328 TCCACTCTTC
28944338 TAAA-TTTT
1 TAAATTTTT
28944346 TAAATTTTT
1 TAAATTTTT
28944355 TAAATTTTT
1 TAAATTTTT
28944364 TAAATTTTT
1 TAAATTTTT
28944373 GTTGTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.15
9 22 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TAAATTTTT
Found at i:28947865 original size:120 final size:120
Alignment explanation
Indices: 28947668--28948530 Score: 1654
Period size: 120 Copynumber: 7.2 Consensus size: 120
28947658 TTTTCAAGTT
28947668 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
28947733 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
28947788 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
28947853 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
28947908 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
28947973 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
*
28948028 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
28948093 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
*
28948148 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
28948213 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
*
28948268 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
28948333 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
28948388 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
28948453 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
28948508 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
28948531 TAAATATGAT
Statistics
Matches: 732, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 732 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
Found at i:28948507 original size:18 final size:17
Alignment explanation
Indices: 28948479--28948513 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28948469 ATTATTAAGA
*
28948479 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
28948496 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
28948514 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:28948704 original size:39 final size:40
Alignment explanation
Indices: 28948655--28948763 Score: 112
Period size: 44 Copynumber: 2.6 Consensus size: 40
28948645 AATTTTTTCC
28948655 ATTATGCTATTACACCTCTATTCCATTCAACCAAACACAAG
1 ATTA-GCTATTACACCTCTATTCCATTCAACCAAACACAAG
* ***
28948696 ATTA-CTATTACGCCTCTATTTCATTACATTCAACCAAACAGTGG
1 ATTAGCTATTACACCTCTA-TTC----CATTCAACCAAACACAAG
*
28948740 ATTAGCTATTACACCTCTAATCCA
1 ATTAGCTATTACACCTCTATTCCA
28948764 ATATACCTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
39 13 0.23
40 5 0.09
41 4 0.07
44 21 0.38
45 13 0.23
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (40 bp):
ATTAGCTATTACACCTCTATTCCATTCAACCAAACACAAG
Found at i:28948773 original size:16 final size:16
Alignment explanation
Indices: 28948749--28948800 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
28948739 GATTAGCTAT
28948749 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
28948765 TATACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
28948781 TACACCTCTAATTCAA
1 TACACCTCTAATCCAA
28948797 TACA
1 TACA
28948801 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:28950776 original size:33 final size:33
Alignment explanation
Indices: 28950738--28950809 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
28950728 TTGAATTAGA
28950738 TAATTTAAAGAAAAGAGAGCAAAAATTGAACCC
1 TAATTTAAAGAAAAGAGAGCAAAAATTGAACCC
*
28950771 TAATTTATAGAAAAGAGAGCAAAAATTGAACCC
1 TAATTTAAAGAAAAGAGAGCAAAAATTGAACCC
28950804 TAATTT
1 TAATTT
28950810 GAGAAAGTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (33 bp):
TAATTTAAAGAAAAGAGAGCAAAAATTGAACCC
Found at i:28952587 original size:23 final size:24
Alignment explanation
Indices: 28952531--28952587 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
28952521 GATTTTTAAT
*
28952531 TAAATAAAATATTTAAAATTAAGAT
1 TAAATAAAA-ATTTAAAATTAAGAA
* *
28952556 TCAAT-AAAATTTAAATTTAA-AA
1 TAAATAAAAATTTAAAATTAAGAA
28952578 TAAATAAAAA
1 TAAATAAAAA
28952588 ATCATCTCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 5 0.19
23 15 0.56
24 3 0.11
25 4 0.15
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAATAAAAATTTAAAATTAAGAA
Found at i:28958768 original size:6 final size:6
Alignment explanation
Indices: 28958757--28958786 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28958747 TTTGACTTCA
*
28958757 CCAGCC CCAGCC CCAGCC ACAGCC CCAGCC
1 CCAGCC CCAGCC CCAGCC CCAGCC CCAGCC
28958787 TCTGCACACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.63, G:0.17, T:0.00
Consensus pattern (6 bp):
CCAGCC
Found at i:28963316 original size:20 final size:22
Alignment explanation
Indices: 28963276--28963317 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
28963266 ATTGTTAATA
*
28963276 TAATAAATATAATTTATTATTT
1 TAATAAATATAATTTAATATTT
28963298 TAATAAAT-T-ATTTAATATTT
1 TAATAAATATAATTTAATATTT
28963318 CAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAAATATAATTTAATATTT
Found at i:28963418 original size:15 final size:15
Alignment explanation
Indices: 28963398--28963454 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
28963388 ATTCAATATT
28963398 AATATTTTAATAATA
1 AATATTTTAATAATA
*
28963413 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
28963432 AATATATTAATAATA
1 AATATTTTAATAATA
*
28963447 AATGTTTT
1 AATATTTT
28963455 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:28964685 original size:19 final size:20
Alignment explanation
Indices: 28964661--28964708 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
28964651 ACTTCATGCT
28964661 ATTTTTATTTA-AATTTTTA
1 ATTTTTATTTATAATTTTTA
* *
28964680 ATTTTT-TATATATTTTTTA
1 ATTTTTATTTATAATTTTTA
28964699 ATTATTTATT
1 ATT-TTTATT
28964709 GATGTGACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.13
19 16 0.70
20 3 0.13
21 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTTATTTATAATTTTTA
Found at i:28967577 original size:13 final size:14
Alignment explanation
Indices: 28967541--28967578 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
28967531 ATATTTTATG
*
28967541 ATATATTTTATATT
1 ATATAGTTTATATT
28967555 ATAATAGTTTATATT
1 AT-ATAGTTTATATT
28967570 AT-TAGTTTA
1 ATATAGTTTA
28967579 CTAAATTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 7 0.32
14 2 0.09
15 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
ATATAGTTTATATT
Found at i:28981722 original size:83 final size:81
Alignment explanation
Indices: 28981630--28981848 Score: 281
Period size: 75 Copynumber: 2.7 Consensus size: 81
28981620 GCAGCTACAT
*
28981630 CATCACTACCTAAAAGCTTCACTGATAACCTTTCATGGCGGATTGTCCGAATATATACATACATA
1 CATCACTACCTAAAAGCTTCACTGATAACCTTTCATGGCGGATTTTCC-AATATATACATA-ATA
*
28981695 CATACATATATTATGCTA
64 CATACATATATAATGCTA
* * *
28981713 CATCACTACCTAAAAGCTTCACTAATAACCCTTCATGGCGGATTTTCC--TA-AT--AT-GTACA
1 CATCACTACCTAAAAGCTTCACTGATAACCTTTCATGGCGGATTTTCCAATATATACATAATACA
28981772 TACATATATAATGCTA
66 TACATATATAATGCTA
* * *
28981788 CATCACTACCTAAAAGCTTCTCTGATAA-CTCTTCATGGAGGATTTTCCTAAAATATACATA
1 CATCACTACCTAAAAGCTTCACTGATAACCT-TTCATGGCGGATTTTCC-AATATATACATA
28981849 TCTATTTGGT
Statistics
Matches: 118, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
74 1 0.01
75 61 0.52
77 2 0.02
78 1 0.01
79 4 0.03
80 2 0.02
81 2 0.02
83 45 0.38
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (81 bp):
CATCACTACCTAAAAGCTTCACTGATAACCTTTCATGGCGGATTTTCCAATATATACATAATACA
TACATATATAATGCTA
Found at i:28982971 original size:17 final size:19
Alignment explanation
Indices: 28982927--28982973 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
28982917 TAGTTGAACC
28982927 AATTTTCTTTATTTTTTAAA
1 AATTTT-TTTATTTTTTAAA
* *
28982947 AATATTTTTA-TTTTT-AT
1 AATTTTTTTATTTTTTAAA
28982964 AATTTTTTTA
1 AATTTTTTTA
28982974 AACTTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.42
18 5 0.21
19 4 0.17
20 5 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
AATTTTTTTATTTTTTAAA
Found at i:28992348 original size:38 final size:38
Alignment explanation
Indices: 28992297--28992411 Score: 158
Period size: 38 Copynumber: 3.0 Consensus size: 38
28992287 TTTCAAATTA
* * *
28992297 ACATGTATAACCATGGCATATCCATTTAACACCACGTT
1 ACATGTTTAACCATGGTATATCCATTTAACACCACATT
* *
28992335 ACATGTTTAACCATGATATATCCACTTAACACCACATT
1 ACATGTTTAACCATGGTATATCCATTTAACACCACATT
* * *
28992373 ACATGTTTAATCGTGGTATATCCATTTAGCACCACATT
1 ACATGTTTAACCATGGTATATCCATTTAACACCACATT
28992411 A
1 A
28992412 ATGAATTAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 67 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (38 bp):
ACATGTTTAACCATGGTATATCCATTTAACACCACATT
Found at i:28992483 original size:48 final size:48
Alignment explanation
Indices: 28992375--28992513 Score: 172
Period size: 48 Copynumber: 2.9 Consensus size: 48
28992365 ACCACATTAC
* * * * *
28992375 ATGTTTAATCGTGGTATATCCATTTAGCACCACATTA-ATGAATTAAT
1 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACATGTATCAAT
* * * * *
28992422 ATATGTAACCGTGGCATATCTACTTAGCACTACGTTACATGTATCAAT
1 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACATGTATCAAT
*
28992470 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACACGTAT
1 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACATGTAT
28992514 AACCATGGTA
Statistics
Matches: 75, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
47 29 0.39
48 46 0.61
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (48 bp):
ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACATGTATCAAT
Found at i:28995037 original size:21 final size:21
Alignment explanation
Indices: 28995011--28995227 Score: 184
Period size: 21 Copynumber: 10.3 Consensus size: 21
28995001 GTACATCATT
28995011 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
** *
28995032 AACAGAAGCTTGTAAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
** * *
28995053 AACAGAAGCTTGTAAAAGCTT
1 AACAGAAGCTCATAAGAGCTG
* * *
28995074 AACAGAAACTCATAAGAGTTA
1 AACAGAAGCTCATAAGAGCTG
* *
28995095 AATAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* *
28995116 AACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
* * *
28995137 AACAGAAGCTCGTCATAGCTG
1 AACAGAAGCTCATAAGAGCTG
* * * * *
28995158 AATAGAAACTTATAAGAGTTT
1 AACAGAAGCTCATAAGAGCTG
* *
28995179 AACAGAAACTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* *
28995200 AACAAAAGCTCGA-AAGAGCTA
1 AACAGAAGCTC-ATAAGAGCTG
28995221 AACAGAA
1 AACAGAA
28995228 AGTAAAATAT
Statistics
Matches: 151, Mismatches: 44, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
21 151 1.00
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:28995228 original size:42 final size:42
Alignment explanation
Indices: 28995011--28995227 Score: 249
Period size: 42 Copynumber: 5.2 Consensus size: 42
28995001 GTACATCATT
* * ** *
28995011 AACAGAAGCTCATAAGAGCTGAACAGAAGCTTGTAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTA
* * *
28995053 AACAGAAGCTTGTAAAAGCTTAACAGAAACTCATAAGAGTTA
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTA
* *
28995095 AATAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTA
* * * * *
28995137 AACAGAAGCTCGTCATAGCTGAATAGAAACTTATAAGAGTTT
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTA
* *
28995179 AACAGAAACTCGTAAGAGCTGAACA-AAAGCTCGA-AAGAGCTA
1 AACAGAAGCTCGTAAGAGCTGAACAGAAA-CTC-ATAAGAGTTA
28995221 AACAGAA
1 AACAGAA
28995228 AGTAAAATAT
Statistics
Matches: 147, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
41 3 0.02
42 143 0.97
43 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (42 bp):
AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTA
Found at i:28997499 original size:44 final size:45
Alignment explanation
Indices: 28997432--28997535 Score: 131
Period size: 44 Copynumber: 2.4 Consensus size: 45
28997422 CTCCAGTCCG
* ** *
28997432 CTCCACTGTAACTTCAGGGAGATGAGGCTTGTAATTTTAACCT-A
1 CTCCACTGCAACTTCAGAAAGATGAGGCTTGTAATTTCAACCTGA
* * *
28997476 CTCCACTACAACTTCAGAAAGATGAGGTTTGTAATTTCGACCTGA
1 CTCCACTGCAACTTCAGAAAGATGAGGCTTGTAATTTCAACCTGA
28997521 -TCCACTGCAACTTCA
1 CTCCACTGCAACTTCA
28997536 AAGAGATAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 50 0.98
45 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGAAAGATGAGGCTTGTAATTTCAACCTGA
Found at i:28997641 original size:45 final size:44
Alignment explanation
Indices: 28997572--28998055 Score: 162
Period size: 45 Copynumber: 10.6 Consensus size: 44
28997562 TTCAATTTGT
* *
28997572 TCCACTGCAACTTCAGGAAAATAAGATTTGCTATATTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATATTCAGTCTGC
* ** * * *
28997617 TCCACTACAACTTCAGGGAGATAAGGCTTGT-T-TTGA-CCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATATTCAGTCTGC
* * * * *
28997658 TCTACTGCAACTTCAGAGAGATAGGATCTGTA-ATTGACAGCTTCGATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATATT--CA-----G-TCTGC
* * *
28997709 TCTACTACAACTTCAGGGAAATAAGATTTGCTATATTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATATTCAGTCTGC
* * * ** * *
28997754 TCCACTACGACTTCAGAGAGATAAGGCTTGT-T-TTGA-CCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATATTCAGTCTGC
* * * * * * *
28997795 TCTACTGCAACTTTAGAGAGATAGGATCTGTAATTTATAGCTTCAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGA--T-T--TGTATA--TTCAGTCTGC
* *
28997846 TCCACTGTAACTTCAGGGAAATAAGATTTGCTATATTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATATTCAGTCTGC
* ** ** * * *
28997891 TCTACTGCGGCTTCAGGGAGATAAGGCTTG-CT-TTGA-CCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATATTCAGTCTGC
* * * * * * *
28997932 ACTACTGCAACTTTAGAGAGATAGGATCTGTAATTTATAGCTTC-GATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGA--T-T--TGTATA--TTCAG-TCTGC
** * * * *
28997983 TCTGCTGCAACTTCAGGAAAATAAAATTTGCTATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATATTCAGTCTGC
*
28998028 TCCACTGCGACTTCAGGGAGATAAGATT
1 TCCACTGCAACTTCAGGGAGATAAGATT
28998056 GATGACTTTA
Statistics
Matches: 309, Mismatches: 93, Indels: 74
0.65 0.20 0.16
Matches are distributed among these distances:
41 74 0.24
42 11 0.04
43 3 0.01
44 5 0.02
45 113 0.37
46 7 0.02
47 9 0.03
48 2 0.01
49 2 0.01
50 5 0.02
51 73 0.24
52 2 0.01
53 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTGTATATTCAGTCTGC
Found at i:28997686 original size:137 final size:137
Alignment explanation
Indices: 28997524--28998052 Score: 779
Period size: 137 Copynumber: 3.9 Consensus size: 137
28997514 GACCTGATCC
* * ** * *
28997524 ACTGCAACTTCAAAGAGATAAGATCTGCGATTCATAGCTTCAATTTGTTCCACTGCAACTTCAGG
1 ACTGCAACTTCAGAGAGATAGGATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGG
*
28997589 AAAATAAGATTTGCTATATTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGGCTTGTTTTGAC
66 AAAATAAGATTTGCTATATTCAGTCTGCTCCACTACGACTTCAGGGAGATAAGGCTTGTTTTGAC
28997654 CTACTCT
131 CTACTCT
* * * * *
28997661 ACTGCAACTTCAGAGAGATAGGATCTGTAATTGACAGCTTCGATCTGTTCTACTACAACTTCAGG
1 ACTGCAACTTCAGAGAGATAGGATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGG
* *
28997726 GAAATAAGATTTGCTATATTCAGTCTGCTCCACTACGACTTCAGAGAGATAAGGCTTGTTTTGAC
66 AAAATAAGATTTGCTATATTCAGTCTGCTCCACTACGACTTCAGGGAGATAAGGCTTGTTTTGAC
*
28997791 CTGCTCT
131 CTACTCT
* *
28997798 ACTGCAACTTTAGAGAGATAGGATCTGTAATTTATAGCTTCAATCTGTTCCACTGTAACTTCAGG
1 ACTGCAACTTCAGAGAGATAGGATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGG
* * * * *
28997863 GAAATAAGATTTGCTATATTCAGTCTGCTCTACTGCGGCTTCAGGGAGATAAGGCTTGCTTTGAC
66 AAAATAAGATTTGCTATATTCAGTCTGCTCCACTACGACTTCAGGGAGATAAGGCTTGTTTTGAC
* *
28997928 CTGCACT
131 CTACTCT
* * **
28997935 ACTGCAACTTTAGAGAGATAGGATCTGTAATTTATAGCTTCGATCTGTTCTGCTGCAACTTCAGG
1 ACTGCAACTTCAGAGAGATAGGATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGG
* * *
28998000 AAAATAAAATTTGCTATCTTCAGTCTGCTCCACTGCGACTTCAGGGAGATAAG
66 AAAATAAGATTTGCTATATTCAGTCTGCTCCACTACGACTTCAGGGAGATAAG
28998053 ATTGATGACT
Statistics
Matches: 356, Mismatches: 36, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
137 356 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (137 bp):
ACTGCAACTTCAGAGAGATAGGATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGG
AAAATAAGATTTGCTATATTCAGTCTGCTCCACTACGACTTCAGGGAGATAAGGCTTGTTTTGAC
CTACTCT
Found at i:29009679 original size:127 final size:127
Alignment explanation
Indices: 29009542--29009858 Score: 411
Period size: 128 Copynumber: 2.5 Consensus size: 127
29009532 TCCAACAAAA
* * * * **
29009542 AAATCAAAACCCAACACGGTAGGGCACGATTCCTCGAACTTCTAAACATTGAACATTGTCTTGTT
1 AAATCGAAACCCAGCACGGTAGGGCACGATTCC-CGAATTTCCAAACATCAAACATTGTCTTGTT
* * ** * *
29009607 TTAGGATTTA-AAGAATGCGAATGAAATTCTAAAGGAATATTTGATTATTTTGAACAAACGAG
65 TTAGAATTTAGAAAAACACGAATGAAATTCTAAAGGAAAATTCGATTATTTTGAACAAACGAG
** * * *
29009669 AAATCGAAACCCAGCACAATAGGGCACGATTCCCCGAATTTCCAAGCATCAAACGTTGCCTTGTT
1 AAATCGAAACCCAGCACGGTAGGGCACGATT-CCCGAATTTCCAAACATCAAACATTGTCTTGTT
*
29009734 TTAGAATTTAGAAAAACACGAGTGAAATTCTAAAGGAAAATTCGATTATTTTGAACAAACGAG
65 TTAGAATTTAGAAAAACACGAATGAAATTCTAAAGGAAAATTCGATTATTTTGAACAAACGAG
* * *
29009797 AAAACGAAACCTAGCACGGTAGGGCACGATTTCCCAAATTTCCAAACATCAAACATTGTCTT
1 AAATCGAAACCCAGCACGGTAGGGCACGA-TTCCCGAATTTCCAAACATCAAACATTGTCTT
29009859 CGTCTTAAGG
Statistics
Matches: 161, Mismatches: 26, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
127 60 0.37
128 99 0.61
129 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (127 bp):
AAATCGAAACCCAGCACGGTAGGGCACGATTCCCGAATTTCCAAACATCAAACATTGTCTTGTTT
TAGAATTTAGAAAAACACGAATGAAATTCTAAAGGAAAATTCGATTATTTTGAACAAACGAG
Found at i:29013685 original size:43 final size:43
Alignment explanation
Indices: 29013637--29013723 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
29013627 GGCCCTTAAT
*
29013637 CATTTCTTAA-CTACTTAACTATTATAATTAATAACCCAATAAC
1 CATTTCTTAATC-ACTTAACTATTATAATTAACAACCCAATAAC
* * *
29013680 CATTTCTTAATCATTTAATTATTATAATTAACAACTCAATAAC
1 CATTTCTTAATCACTTAACTATTATAATTAACAACCCAATAAC
29013723 C
1 C
29013724 CACTAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 38 0.97
44 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (43 bp):
CATTTCTTAATCACTTAACTATTATAATTAACAACCCAATAAC
Found at i:29016583 original size:42 final size:37
Alignment explanation
Indices: 29016536--29016636 Score: 116
Period size: 36 Copynumber: 2.6 Consensus size: 37
29016526 TTCTTTTAGA
*
29016536 TAAATATAAAATATTTAAAATTATAATACATACTTTTAATTT
1 TAAATA-AAAATATAT-AAATTAT-AT--ATACTTTTAATTT
*
29016578 TAAATAAAAA-ATATAGATTATATATACTTTTAATTT
1 TAAATAAAAATATATAAATTATATATACTTTTAATTT
*
29016614 TAAATAAAAA-ATATAGATTATAT
1 TAAATAAAAATATATAAATTATAT
29016637 GAACTTATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
36 36 0.63
38 2 0.04
39 6 0.11
40 3 0.05
41 4 0.07
42 6 0.11
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (37 bp):
TAAATAAAAATATATAAATTATATATACTTTTAATTT
Found at i:29016612 original size:36 final size:36
Alignment explanation
Indices: 29016565--29016636 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
29016555 ATTATAATAC
29016565 ATACTTTTAATTTTAAATAAAAAATATAGATTATAT
1 ATACTTTTAATTTTAAATAAAAAATATAGATTATAT
29016601 ATACTTTTAATTTTAAATAAAAAATATAGATTATAT
1 ATACTTTTAATTTTAAATAAAAAATATAGATTATAT
29016637 GAACTTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (36 bp):
ATACTTTTAATTTTAAATAAAAAATATAGATTATAT
Found at i:29036039 original size:9 final size:10
Alignment explanation
Indices: 29036010--29036041 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
29036000 AAATATTTAG
29036010 ATTTCTCTTC
1 ATTTCTCTTC
29036020 ATTTCTCTTC
1 ATTTCTCTTC
29036030 ATTT-TCTTC
1 ATTTCTCTTC
29036039 ATT
1 ATT
29036042 CTCATTAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTCTCTTC
Found at i:29041344 original size:19 final size:21
Alignment explanation
Indices: 29041322--29041371 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
29041312 TTTTAGGAGG
29041322 TAATTTTTATTT-T-TTATTT
1 TAATTTTTATTTCTATTATTT
* *
29041341 TAATATTTTGTTTCTATTTTTT
1 TAAT-TTTTATTTCTATTATTT
29041363 TAATTTTTA
1 TAATTTTTA
29041372 ATCAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 4 0.16
20 7 0.28
21 5 0.20
22 9 0.36
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (21 bp):
TAATTTTTATTTCTATTATTT
Found at i:29044978 original size:11 final size:11
Alignment explanation
Indices: 29044962--29044986 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29044952 GAACTTAAGG
29044962 AAAAAAAAACA
1 AAAAAAAAACA
29044973 AAAAAAAAACA
1 AAAAAAAAACA
29044984 AAA
1 AAA
29044987 TCGCTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:29050593 original size:16 final size:17
Alignment explanation
Indices: 29050572--29050606 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
29050562 AAAAATTGTT
29050572 TTACTTTTC-TATATTA
1 TTACTTTTCATATATTA
29050588 TTACTTTTCATATATTA
1 TTACTTTTCATATATTA
29050605 TT
1 TT
29050607 TCATGTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (17 bp):
TTACTTTTCATATATTA
Found at i:29050653 original size:13 final size:14
Alignment explanation
Indices: 29050635--29050666 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
29050625 ATATATTTTC
29050635 ATTATTTTATAT-T
1 ATTATTTTATATAT
29050648 ATTA-TTTATATAT
1 ATTATTTTATATAT
29050661 ATTATT
1 ATTATT
29050667 ATCCTTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 9 0.53
14 1 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTATTTTATATAT
Found at i:29050716 original size:36 final size:35
Alignment explanation
Indices: 29050676--29050755 Score: 81
Period size: 36 Copynumber: 2.2 Consensus size: 35
29050666 TATCCTTAAC
29050676 TATTATATTTTATTAATCAAT-TACTTATAAACTATA
1 TATTATATTTTA--AATCAATATACTTATAAACTATA
* * * * *
29050712 TATTACGATTTTAAATCCATATACTTTTATATTATA
1 TATTA-TATTTTAAATCAATATACTTATAAACTATA
29050748 TATTATAT
1 TATTATAT
29050756 AATTATTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
35 8 0.22
36 22 0.61
37 6 0.17
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (35 bp):
TATTATATTTTAAATCAATATACTTATAAACTATA
Found at i:29063421 original size:18 final size:18
Alignment explanation
Indices: 29063400--29063459 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
29063390 AATAAATTAT
*
29063400 TAATTATATATATTTTTA
1 TAATTAAATATATTTTTA
*
29063418 TAATTAAATTTATTTTT-
1 TAATTAAATATATTTTTA
*
29063435 TAA-AAAATA-ATTATTTA
1 TAATTAAATATATT-TTTA
29063452 -AATTAAAT
1 TAATTAAAT
29063460 TCGGGTTCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 3 0.09
16 9 0.26
17 7 0.21
18 15 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAAATATATTTTTA
Found at i:29063882 original size:24 final size:25
Alignment explanation
Indices: 29063845--29063900 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 25
29063835 ATGGACCAAC
*
29063845 TTTTAACAATAAAAATAAATGTACT
1 TTTTAATAATAAAAATAAATGTACT
*
29063870 TTTTAATAA-AAAAATAAATTTACT
1 TTTTAATAATAAAAATAAATGTACT
29063894 TTTTAAT
1 TTTTAAT
29063901 CTAACATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 21 0.72
25 8 0.28
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (25 bp):
TTTTAATAATAAAAATAAATGTACT
Found at i:29071922 original size:22 final size:20
Alignment explanation
Indices: 29071884--29071923 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
29071874 TCTTTACATA
29071884 AAAACAATATATTAATGTCG
1 AAAACAATATATTAATGTCG
29071904 AAAACATATATAATTAATGT
1 AAAACA-ATAT-ATTAATGT
29071924 ATTTAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 8 0.44
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (20 bp):
AAAACAATATATTAATGTCG
Found at i:29072037 original size:29 final size:30
Alignment explanation
Indices: 29071995--29072051 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
29071985 TTATTTTCAT
*
29071995 GTGTAATTTAATACAT-AAACTTTGATTTA
1 GTGTAATTTAATACATAAAACTTGGATTTA
29072024 GTGTAA-TTATATACATAAAACTTGGATT
1 GTGTAATTTA-ATACATAAAACTTGGATT
29072052 ACGATTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 12 0.48
30 10 0.40
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (30 bp):
GTGTAATTTAATACATAAAACTTGGATTTA
Found at i:29073143 original size:29 final size:31
Alignment explanation
Indices: 29073094--29073173 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
29073084 AAATTTAATC
* *
29073094 AAATCAAAATTTAATATATAA-AAT-CACACA
1 AAATCAAAA-TTCATGTATAACAATGCACACA
* **
29073124 AAATCAAAATTCATGTATAACATTGCACATT
1 AAATCAAAATTCATGTATAACAATGCACACA
*
29073155 AAATCAAAGTTCATGTATA
1 AAATCAAAATTCATGTATA
29073174 GTTTAATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 9 0.21
30 11 0.26
31 22 0.52
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (31 bp):
AAATCAAAATTCATGTATAACAATGCACACA
Found at i:29076420 original size:11 final size:11
Alignment explanation
Indices: 29076404--29076440 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
29076394 TTTAAGTAAA
29076404 TATTATTTTAT
1 TATTATTTTAT
29076415 TATTATTTTAT
1 TATTATTTTAT
*
29076426 TATTATATTA-
1 TATTATTTTAT
29076436 TATTA
1 TATTA
29076441 GTTAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:29080112 original size:30 final size:29
Alignment explanation
Indices: 29080076--29080136 Score: 113
Period size: 30 Copynumber: 2.1 Consensus size: 29
29080066 AGTTGGAAGT
29080076 TTTGGCACTAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGATTT-AACTAGC
29080106 TTTGGCACTAAGTGTGCGATTTAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAACTAGC
29080135 TT
1 TT
29080137 CGGCTACTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (29 bp):
TTTGGCACTAAGTGTGCGATTTAACTAGC
Found at i:29087439 original size:22 final size:22
Alignment explanation
Indices: 29087410--29087477 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
29087400 TGCACAAACG
29087410 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
29087432 TACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
* *
29087454 AACAGGGAGCACTTAACGTGCTA
1 AACAGAGAGCAC-TAAAGTGCTA
29087477 A
1 A
29087478 TAATAGTACA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 28 0.74
23 8 0.21
24 1 0.03
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:29088662 original size:5 final size:5
Alignment explanation
Indices: 29088652--29088703 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
29088642 TTATGTTTTA
* * * *
29088652 TATAT TATAT TATAT ATAATAT AATAA TATAA TATAA TATAT TATAT TATAT
1 TATAT TATAT TATAT -T-ATAT TATAT TATAT TATAT TATAT TATAT TATAT
29088704 ATTAATACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
5 36 0.88
6 1 0.02
7 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (5 bp):
TATAT
Found at i:29088719 original size:14 final size:13
Alignment explanation
Indices: 29088653--29088722 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 13
29088643 TATGTTTTAT
*
29088653 ATATT-ATATTAT
1 ATATTAATATTAA
*
29088665 ATA-TAATATAATA
1 ATATTAATATTA-A
29088678 ATA-TAATA-TAA
1 ATATTAATATTAA
*
29088689 TATATT-ATATTAT
1 -ATATTAATATTAA
29088702 ATATTAATACTTAA
1 ATATTAATA-TTAA
29088716 ATATTAA
1 ATATTAA
29088723 GTTAATATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
11 2 0.04
12 20 0.43
13 14 0.30
14 10 0.22
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATTAATATTAA
Found at i:29096002 original size:14 final size:14
Alignment explanation
Indices: 29095983--29096096 Score: 72
Period size: 12 Copynumber: 8.9 Consensus size: 14
29095973 TTTACTTTTC
*
29095983 TTATATTTTATATA
1 TTATATTATATATA
29095997 TTATATTATATATA
1 TTATATTATATATA
*
29096011 --ATATAATATA-A
1 TTATATTATATATA
*
29096022 TAATA-TA-ATATA
1 TTATATTATATATA
29096034 TTATATTATATAT-
1 TTATATTATATATA
*
29096047 TAATACTTA-A-ATA
1 TTATA-TTATATATA
29096060 TTA-AGTTA-ATATA
1 TTATA-TTATATATA
* *
29096073 ATATATAATATATA
1 TTATATTATATATA
29096087 TT-T-TTATATA
1 TTATATTATATA
29096097 AAAAATATCT
Statistics
Matches: 79, Mismatches: 11, Indels: 22
0.71 0.10 0.20
Matches are distributed among these distances:
11 4 0.05
12 28 0.35
13 20 0.25
14 27 0.34
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (14 bp):
TTATATTATATATA
Found at i:29096003 original size:5 final size:5
Alignment explanation
Indices: 29095983--29096044 Score: 54
Period size: 5 Copynumber: 12.2 Consensus size: 5
29095973 TTTACTTTTC
* * * * *
29095983 TTATA TTTTA -TATA TTATA TTATA TATAATA TAATA TAATA ATATA ATATA
1 TTATA TTATA TTATA TTATA TTATA T-T-ATA TTATA TTATA TTATA TTATA
29096034 TTATA TTATA T
1 TTATA TTATA T
29096045 ATTAATACTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 3 0.06
5 40 0.83
6 1 0.02
7 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (5 bp):
TTATA
Found at i:29096070 original size:44 final size:37
Alignment explanation
Indices: 29095992--29096087 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 37
29095982 CTTATATTTT
29095992 ATATATTATATTATATATAATATAATATAATAATATA
1 ATATATTATATTATATATAATATAATATAATAATATA
29096029 ATATATTATATTATATATTAATACTTAAATATTAAGTTAATATA
1 ATATATTATATTATATA-TAATA--T-AATA-TAA--TAATATA
*
29096073 ATATATAATA-TATAT
1 ATATATTATATTATAT
29096088 TTTTATATAA
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
37 17 0.33
38 5 0.10
40 1 0.02
41 4 0.08
42 3 0.06
43 5 0.10
44 16 0.31
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (37 bp):
ATATATTATATTATATATAATATAATATAATAATATA
Found at i:29097241 original size:30 final size:29
Alignment explanation
Indices: 29097205--29097265 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
29097195 AGTAGGAAGT
*
29097205 TTTGGCACTAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCAATTT-AACTAGC
29097235 TTTGGCACTAAGTGTGCAATTTAACTAGC
1 TTTGGCACTAAGTGTGCAATTTAACTAGC
29097264 TT
1 TT
29097266 CGACTACTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (29 bp):
TTTGGCACTAAGTGTGCAATTTAACTAGC
Found at i:29101325 original size:29 final size:30
Alignment explanation
Indices: 29101266--29101323 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
29101256 TCCGAGCCTT
*
29101266 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
29101296 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
29101324 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:29101553 original size:13 final size:13
Alignment explanation
Indices: 29101535--29101565 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
29101525 TTCCAGCAAC
29101535 TATGAATTTATTT
1 TATGAATTTATTT
29101548 TATGAATTTATTT
1 TATGAATTTATTT
*
29101561 GATGA
1 TATGA
29101566 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:29101735 original size:50 final size:50
Alignment explanation
Indices: 29101660--29101902 Score: 378
Period size: 50 Copynumber: 4.8 Consensus size: 50
29101650 ATTTGGGTAA
29101660 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
29101710 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
29101760 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
29101810 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
29101860 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
29101903 TGTTATTATC
Statistics
Matches: 175, Mismatches: 17, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
50 141 0.81
51 34 0.19
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:29103961 original size:43 final size:42
Alignment explanation
Indices: 29103898--29104021 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 42
29103888 TCTGAACTCA
* *
29103898 TTCACCGGCATTTCGCCTGCTAGGCTTGAAGCCCGATATCAT
1 TTCACCGGCATTTAGCCTGCTAGGCTCGAAGCCCGATATCAT
* * ** *
29103940 TTCACCGCCATTGTAGCCTGCTAGGCCCGAAGCCTAATATTAT
1 TTCACCGGCATT-TAGCCTGCTAGGCTCGAAGCCCGATATCAT
* *
29103983 CTCATCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATA
1 TTCACCGGCATT-TAGCCTGCTAGGCTCGAAGCCCGATA
29104022 ATATTATTCA
Statistics
Matches: 67, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 11 0.16
43 56 0.84
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.27
Consensus pattern (42 bp):
TTCACCGGCATTTAGCCTGCTAGGCTCGAAGCCCGATATCAT
Found at i:29118060 original size:314 final size:314
Alignment explanation
Indices: 29117485--29118113 Score: 1096
Period size: 314 Copynumber: 2.0 Consensus size: 314
29117475 GGCTGCCTCG
*
29117485 CCTTAGTCTGTCCAGCTCCTCTACCCGGTGCTCTCTGCCTACAGCCCATACTGTTACCACCCCTA
1 CCTTAGTCTGTCCAGCACCTCTACCCGGTGCTCTCTGCCTACAGCCCATACTGTTACCACCCCTA
* *
29117550 GCATGACCACTGCTCCTAGATGGCTGCAAAACTACCCTCGGTGGCTATGCAGTACTAGAACTCGG
66 GCATGACCACGGCTCCTAGATGGCTGCAAAACTACCCTCGGTGGCTATGCAGTACTAAAACTCGG
* * *
29117615 AGCTTGTATTTGATCGGCCCTTAGCGAATACTCATGAATGCTGTTCTCAGTAGACCCACATCTTA
131 AGCTTGTATTTGATCGGCCCTCAACGAATACTCATGAATGCTGTGCTCAGTAGACCCACATCTTA
* *
29117680 AGTATATCACAGTCATCCTCTAACATTCACCTGGATGACATCTACCACAATGCTCACAACGCAAG
196 AGCATATCACAGTCATCCTCTAACATTCACCTGGATGACATCTACCACAATGCCCACAACGCAAG
*
29117745 TTCCCAGTAAGTACAACAGGAGGCCCAACTTTAACTGGGTTCATCAGATTTGAC
261 TTCCCAGTAAGTACAACAGGAGGCCCAACTTTAACTGGGCTCATCAGATTTGAC
*
29117799 CCTTAGTCTGTCCAGCACCTCTACCCGGTGCTCTCTGCCTACAGCCCATATTGTTACCACCCCTA
1 CCTTAGTCTGTCCAGCACCTCTACCCGGTGCTCTCTGCCTACAGCCCATACTGTTACCACCCCTA
* *
29117864 GCATGTCCACGGCTCCTAGATGGCTGCAAAACTACCCTCGGTGGCTGTGCAGTACTAAAACTCGG
66 GCATGACCACGGCTCCTAGATGGCTGCAAAACTACCCTCGGTGGCTATGCAGTACTAAAACTCGG
*
29117929 AGCTTGTATTTGATCGGCCCTCAACGGATACTCATGAATGCTGTGCTCAGTAGACCCACATCTTA
131 AGCTTGTATTTGATCGGCCCTCAACGAATACTCATGAATGCTGTGCTCAGTAGACCCACATCTTA
* * * *
29117994 AGCATATCCCAGTCATCCTCTAACATTCGCCTGGATGACGTCTACCACAATGCCCACAAGGCAAG
196 AGCATATCACAGTCATCCTCTAACATTCACCTGGATGACATCTACCACAATGCCCACAACGCAAG
*
29118059 TTCCTAGTAAGTACAACAGGAGGCCCAACTTTAACTGGGCTCATCAGATTTGAC
261 TTCCCAGTAAGTACAACAGGAGGCCCAACTTTAACTGGGCTCATCAGATTTGAC
29118113 C
1 C
29118114 TTTTTCTTAG
Statistics
Matches: 297, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
314 297 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (314 bp):
CCTTAGTCTGTCCAGCACCTCTACCCGGTGCTCTCTGCCTACAGCCCATACTGTTACCACCCCTA
GCATGACCACGGCTCCTAGATGGCTGCAAAACTACCCTCGGTGGCTATGCAGTACTAAAACTCGG
AGCTTGTATTTGATCGGCCCTCAACGAATACTCATGAATGCTGTGCTCAGTAGACCCACATCTTA
AGCATATCACAGTCATCCTCTAACATTCACCTGGATGACATCTACCACAATGCCCACAACGCAAG
TTCCCAGTAAGTACAACAGGAGGCCCAACTTTAACTGGGCTCATCAGATTTGAC
Found at i:29121682 original size:22 final size:22
Alignment explanation
Indices: 29121642--29121683 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
29121632 ATATTTGAGC
**
29121642 ATTGGTATTGAATTTAAATTGA
1 ATTGGTATTGAATCCAAATTGA
*
29121664 ATTGGTATTTAATCCAAATT
1 ATTGGTATTGAATCCAAATT
29121684 TTAATTAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (22 bp):
ATTGGTATTGAATCCAAATTGA
Found at i:29127851 original size:18 final size:18
Alignment explanation
Indices: 29127809--29127874 Score: 107
Period size: 18 Copynumber: 3.7 Consensus size: 18
29127799 TTCAATAATA
29127809 TGCAATCTTAGATATGA-
1 TGCAATCTTAGATATGAT
*
29127826 TACAATCTTAGATATGAT
1 TGCAATCTTAGATATGAT
29127844 TGCAATCTTAGATATGAT
1 TGCAATCTTAGATATGAT
29127862 ATGCAATCTTAGA
1 -TGCAATCTTAGA
29127875 AGATATGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.36
18 17 0.38
19 12 0.27
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (18 bp):
TGCAATCTTAGATATGAT
Found at i:29127881 original size:17 final size:19
Alignment explanation
Indices: 29127806--29127874 Score: 117
Period size: 17 Copynumber: 3.8 Consensus size: 19
29127796 ATTTTCAATA
29127806 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
29127825 ATA--CAATCTTAGATATG
1 ATATGCAATCTTAGATATG
29127842 AT-TGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
29127860 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
29127875 AGATATGATT
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.34
18 16 0.34
19 15 0.32
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:29127900 original size:22 final size:22
Alignment explanation
Indices: 29127806--29127897 Score: 73
Period size: 17 Copynumber: 4.7 Consensus size: 22
29127796 ATTTTCAATA
29127806 ATATGCAATCTT---AGATATG
1 ATATGCAATCTTAGAAGATATG
29127825 ATA--CAATCTT---AGATATG
1 ATATGCAATCTTAGAAGATATG
29127842 AT-TGCAATCTT---AGATATG
1 ATATGCAATCTTAGAAGATATG
29127860 ATATGCAATCTTAGAAGATATG
1 ATATGCAATCTTAGAAGATATG
* *
29127882 ATTTTGTAATCTTAGA
1 A-TATGCAATCTTAGA
29127898 GATTTAATTT
Statistics
Matches: 64, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
17 16 0.25
18 16 0.25
19 12 0.19
22 8 0.12
23 12 0.19
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (22 bp):
ATATGCAATCTTAGAAGATATG
Found at i:29134657 original size:52 final size:52
Alignment explanation
Indices: 29134510--29134660 Score: 160
Period size: 52 Copynumber: 2.9 Consensus size: 52
29134500 TAACATGCCA
* * *
29134510 ATGCCATATCCCAGATATGGTCTTATACGGAATCACATTATCACATCACACCG
1 ATGCCATAACCCAGCTATGGTCTTATACGGAAACACA-TATCACATCACACCG
* * * ***
29134563 ATGCCATAACCCAGCTACGGTCTTATACAGAAACTCGA-ATCACATTGTACCG
1 ATGCCATAACCCAGCTATGGTCTTATACGGAAACAC-ATATCACATCACACCG
* * * *
29134615 ATGCCATAGCCCATCTATGGTCTTATATGGAAGCACATATCACATC
1 ATGCCATAACCCAGCTATGGTCTTATACGGAAACACATATCACATC
29134661 TTTTCCGTCA
Statistics
Matches: 79, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
51 1 0.01
52 47 0.59
53 30 0.38
54 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (52 bp):
ATGCCATAACCCAGCTATGGTCTTATACGGAAACACATATCACATCACACCG
Found at i:29139916 original size:28 final size:28
Alignment explanation
Indices: 29139883--29139942 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
29139873 ATGCCCAAAA
29139883 CATTGACTTATAAATCTTGATAAAATAG
1 CATTGACTTATAAATCTTGATAAAATAG
29139911 CATTGACTTATAAATCTTGATAAAATAG
1 CATTGACTTATAAATCTTGATAAAATAG
29139939 CATT
1 CATT
29139943 CTTTTATCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (28 bp):
CATTGACTTATAAATCTTGATAAAATAG
Found at i:29140722 original size:52 final size:51
Alignment explanation
Indices: 29140525--29140724 Score: 198
Period size: 52 Copynumber: 4.0 Consensus size: 51
29140515 CACATTACAC
* * * *
29140525 ACCGAAGCCATAGCCCTGCCATGGTCTTACACGG-ATCACATA--ACA-TG
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCACATTG
* ** **
29140572 -CCGATGCCATATCCCAAATATGGTCTTATACGGAATCACATTATCACATCAC
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACA-TATCACAT-TG
* *
29140624 ACCGATGCCATAGCCCAGCTATGGTCTTATATGGGAACTC-GA-ATCACATTG
1 ACCGATGCCATAGCCCAGCTATGGTCTTATA-CGGAA-TCACATATCACATTG
*
29140675 TACCGATGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACAT
1 -ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCACAT
29140725 CTTTTCTGTC
Statistics
Matches: 122, Mismatches: 19, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
46 26 0.21
47 6 0.05
48 2 0.02
50 4 0.03
51 5 0.04
52 45 0.37
53 27 0.22
54 5 0.04
55 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCACATTG
Found at i:29143492 original size:11 final size:11
Alignment explanation
Indices: 29143476--29143501 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29143466 AAATCAATAA
29143476 AACAAGGTAAG
1 AACAAGGTAAG
29143487 AACAAGGTAAG
1 AACAAGGTAAG
29143498 AACA
1 AACA
29143502 TCATGATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.12, G:0.23, T:0.08
Consensus pattern (11 bp):
AACAAGGTAAG
Found at i:29145087 original size:46 final size:46
Alignment explanation
Indices: 29145035--29145445 Score: 515
Period size: 46 Copynumber: 9.0 Consensus size: 46
29145025 GCTTTCTGAA
** *
29145035 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
29145081 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
29145127 ATGAAATGTGTAAGACCATGGTTGAAAGATATCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * * *
29145173 GGGAAATGAATAAAACCATGGTTG-AAGATACCATGGTAGCGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
29145218 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
29145264 ATGAGAA-GAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGA-AATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
29145310 ATGAGAA-GAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGA-AATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
29145356 ATGAAAAGAATAAGACAATGGCTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * * * *
29145402 A-GAAAATGAGTAAAACTATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
29145446 TCAAAGATAA
Statistics
Matches: 333, Mismatches: 28, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
45 41 0.12
46 290 0.87
47 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:29145348 original size:183 final size:184
Alignment explanation
Indices: 29145035--29145445 Score: 515
Period size: 183 Copynumber: 2.2 Consensus size: 184
29145025 GCTTTCTGAA
** * **
29145035 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCAT
* ** *
29145100 GGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATATCATGGC
66 GGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGC
* * * *
29145165 AACATGACGGGAAATGAATAAAACCATGGTTG-AAGATACCATGGTAGCGTGAC
131 AACATGACAGGAAAAGAATAAAACAATGGCTGAAAGATACCATGGTAGCGTGAC
*
29145218 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAGAA-GAATAAGACCA
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGA-AATGAATAAGACCA
*
29145282 TGGTTGAAAGATACCATGGCAACGTGACATGAGAA-GAATAAGACCATGGTTGAAAGATACCATG
65 TGGTTGAAAGATACCATGGCAACATGACATGA-AATGAATAAGACCATGGTTGAAAGATACCATG
* * * * * *
29145346 GCAACGTGACATGAAAAGAATAAGACAATGGCTGAAAGATACCATGGCAACATGAC
129 GCAACATGACAGGAAAAGAATAAAACAATGGCTGAAAGATACCATGGTAGCGTGAC
* * * * * * *
29145402 A-GAAAATGAGTAAAACTATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
29145446 TCAAAGATAA
Statistics
Matches: 195, Mismatches: 29, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
183 139 0.71
184 56 0.29
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.20
Consensus pattern (184 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCAT
GGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGC
AACATGACAGGAAAAGAATAAAACAATGGCTGAAAGATACCATGGTAGCGTGAC
Found at i:29145461 original size:229 final size:228
Alignment explanation
Indices: 29145045--29145461 Score: 568
Period size: 229 Copynumber: 1.8 Consensus size: 228
29145035 ATGAAATGTG
* **
29145045 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
* * ** * * * *
29145110 TACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATATCATGGCAACATGACGG
66 TACCATGGCAACATGACATGAAAAGAATAAGACAATGGCTGAAAGATACCATGGCAACATGACAG
* * * * * *
29145175 GAAATGAATAAAACCATGGTTGAAGATACCATGGTAGCGTGACATGAAATGAATAAGACCATGGT
131 AAAATGAATAAAACCATAGTTGAAGACACCATGGCAGCATGACA-GAAATAAATAAGACCATGGT
29145240 TGAAAGATACCATGGCAACGTGACATGAGAAGAA
195 TGAAAGATACCATGGCAACGTGACATGAGAAGAA
*
29145274 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAGAA-GAATAAGACCATGGTTGAAAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGA-AATGAATAAGACCATGGTTGAAAG
*
29145338 ATACCATGGCAACGTGACATGAAAAGAATAAGACAATGGCTGAAAGATACCATGGCAACATGACA
65 ATACCATGGCAACATGACATGAAAAGAATAAGACAATGGCTGAAAGATACCATGGCAACATGACA
* * * * *
29145403 GAAAATGAGTAAAACTATAGTTGAAAGACACTATGGCATCATGTCA-AAGATAAATAAGA
130 GAAAATGAATAAAACCATAGTTG-AAGACACCATGGCAGCATGACAGAA-ATAAATAAGA
29145462 TACCATGGCA
Statistics
Matches: 161, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
228 2 0.01
229 141 0.88
230 18 0.11
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (228 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
TACCATGGCAACATGACATGAAAAGAATAAGACAATGGCTGAAAGATACCATGGCAACATGACAG
AAAATGAATAAAACCATAGTTGAAGACACCATGGCAGCATGACAGAAATAAATAAGACCATGGTT
GAAAGATACCATGGCAACGTGACATGAGAAGAA
Found at i:29145508 original size:77 final size:77
Alignment explanation
Indices: 29145381--29145538 Score: 307
Period size: 77 Copynumber: 2.1 Consensus size: 77
29145371 CAATGGCTGA
*
29145381 AAGATACCATGGCAACATGACAGAAAATGAGTAAAACTATAGTTGAAAGACACTATGGCATCATG
1 AAGATACCATGGCAACATGACAGAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCATCATG
29145446 TCAAAGATAAAT
66 TCAAAGATAAAT
29145458 AAGATACCATGGCAACATGACAGAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCATCATG
1 AAGATACCATGGCAACATGACAGAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCATCATG
29145523 TCAAAGATAAAT
66 TCAAAGATAAAT
29145535 AAGA
1 AAGA
29145539 CCGTGGATAG
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (77 bp):
AAGATACCATGGCAACATGACAGAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCATCATG
TCAAAGATAAAT
Found at i:29151479 original size:20 final size:19
Alignment explanation
Indices: 29151434--29151487 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
29151424 ACGCTTAATG
* *
29151434 TTAATTAAGTAAAGGTTAA
1 TTAATTAATTAAAGATTAA
29151453 TTAAATTAATTAAAGATTAA
1 TT-AATTAATTAAAGATTAA
29151473 TCTAATTATATTAAA
1 T-TAATTA-ATTAAA
29151488 AGACAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.07
20 21 0.70
21 7 0.23
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (19 bp):
TTAATTAATTAAAGATTAA
Found at i:29155413 original size:203 final size:203
Alignment explanation
Indices: 29155054--29155667 Score: 1169
Period size: 203 Copynumber: 3.0 Consensus size: 203
29155044 TTAAAGAAAT
29155054 AAATA-ATAAA-ATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
1 AAATACATAAACATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
*
29155117 ATTACATTTAAGGGATCTATTAATACCAAGAAACTGGATGATAGTTAGAATAAGTAGTGCTAGTA
66 ATTACATTTAAGGGATCTATTAATACCAAGAAACTGGATGATAGTTAGAATAAGTGGTGCTAGTA
*
29155182 CTTCAAAATCTGTAAGTACTATAGAATATATGTCGTCAGGAGATAGATTATTTTTTAAAAATAAT
131 CTTCAAAACCTGTAAGTACTATAGAATATATGTCGTCAGGAGATAGATTATTTTTTAAAAATAAT
29155247 GCTATAAC
196 GCTATAAC
29155255 AAATACATAAACATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
1 AAATACATAAACATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
*
29155320 ATTACATTTAAGGGATCTATTGATACCAAGAAACTGGATGATAGTTAGAATAAGTGGTGCTAGTA
66 ATTACATTTAAGGGATCTATTAATACCAAGAAACTGGATGATAGTTAGAATAAGTGGTGCTAGTA
29155385 CTTCAAAACCTGTAAGTACTATAGAATATATGTCGTCAGGAGATAGATTATTTTTTAAAAATAAT
131 CTTCAAAACCTGTAAGTACTATAGAATATATGTCGTCAGGAGATAGATTATTTTTTAAAAATAAT
29155450 GCTATAAC
196 GCTATAAC
29155458 AAATACATAAACATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
1 AAATACATAAACATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
*
29155523 ATTGCATTTAAGGGATCTATTAATACCAAGAAACTGGATGATAGTTAGAATAAGTGGTGCTAGTA
66 ATTACATTTAAGGGATCTATTAATACCAAGAAACTGGATGATAGTTAGAATAAGTGGTGCTAGTA
29155588 CTTCAAAACCTGTAAGTACTATAGAATATATGTCGTCAGGAGATAGATTATTTTTTAAAAATAAT
131 CTTCAAAACCTGTAAGTACTATAGAATATATGTCGTCAGGAGATAGATTATTTTTTAAAAATAAT
*
29155653 GTTATAAC
196 GCTATAAC
29155661 AAATACA
1 AAATACA
29155668 AATGATAATT
Statistics
Matches: 405, Mismatches: 6, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
201 5 0.01
202 5 0.01
203 395 0.98
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (203 bp):
AAATACATAAACATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
ATTACATTTAAGGGATCTATTAATACCAAGAAACTGGATGATAGTTAGAATAAGTGGTGCTAGTA
CTTCAAAACCTGTAAGTACTATAGAATATATGTCGTCAGGAGATAGATTATTTTTTAAAAATAAT
GCTATAAC
Found at i:29159455 original size:17 final size:17
Alignment explanation
Indices: 29159413--29159456 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
29159403 TTTATTTTGG
*
29159413 TTTTTATTGTTTTCTAA
1 TTTTTTTTGTTTTCTAA
29159430 TTTTCTTTTGTTTT-TAA
1 TTTT-TTTTGTTTTCTAA
29159447 TTGTTTTTTG
1 TT-TTTTTTG
29159457 GATTTCTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.11, C:0.05, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTTTTTGTTTTCTAA
Found at i:29159462 original size:28 final size:28
Alignment explanation
Indices: 29159400--29159463 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
29159390 TAAGCTTTAA
*
29159400 GGATTTATTTTGGTTTTTATTGTTTTCT
1 GGATTTCTTTTGGTTTTTATTGTTTTCT
* *
29159428 -AATTTTCTTTT-GTTTTTAATTGTTTTTT
1 GGA-TTTCTTTTGGTTTTT-ATTGTTTTCT
29159456 GGATTTCT
1 GGATTTCT
29159464 GGTGTTGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
27 7 0.24
28 21 0.72
29 1 0.03
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.69
Consensus pattern (28 bp):
GGATTTCTTTTGGTTTTTATTGTTTTCT
Found at i:29167418 original size:9 final size:11
Alignment explanation
Indices: 29167393--29167421 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
29167383 AACAGATTGA
29167393 GAGAGAAAGGG
1 GAGAGAAAGGG
29167404 GAGAGAAAGGG
1 GAGAGAAAGGG
29167415 GAGAGAA
1 GAGAGAA
29167422 TTACTCAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (11 bp):
GAGAGAAAGGG
Found at i:29176718 original size:26 final size:27
Alignment explanation
Indices: 29176689--29176741 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
29176679 TTTTATTTAT
* *
29176689 TTTTTTTATTTTTTTAATCAT-TAAAA
1 TTTTATTATTTTTTAAATCATCTAAAA
*
29176715 TTTTATTCTTTTTTAAATCATCTAAAA
1 TTTTATTATTTTTTAAATCATCTAAAA
29176742 ATTGATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTTATTATTTTTTAAATCATCTAAAA
Found at i:29180811 original size:23 final size:23
Alignment explanation
Indices: 29180785--29180839 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
29180775 TTAAGAATAA
29180785 ATTTATATTATTTTAAATTTAAT
1 ATTTATATTATTTTAAATTTAAT
* * **
29180808 ATTTA-ATAAATTTAAATTTTTT
1 ATTTATATTATTTTAAATTTAAT
29180830 ATTT-TATTAT
1 ATTTATATTAT
29180840 AAGTTTAAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTATATTATTTTAAATTTAAT
Found at i:29185892 original size:17 final size:18
Alignment explanation
Indices: 29185858--29185910 Score: 81
Period size: 17 Copynumber: 2.9 Consensus size: 18
29185848 AATCATATAT
29185858 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
29185876 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
29185893 TCTAAGATTGCATATCAT
1 TCTAAGATTGCA-ATCAT
29185911 TGAAGATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 16 0.52
18 10 0.32
19 5 0.16
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:29186375 original size:44 final size:45
Alignment explanation
Indices: 29186259--29186532 Score: 200
Period size: 45 Copynumber: 6.1 Consensus size: 45
29186249 GGAAGGCGAT
* * *** *
29186259 ATCTGCTATCTTTGATCTGCTTCTTATCTAATACAGAGGCGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
*
29186304 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * *
29186349 ATTTGCT-TCTTC-AGTTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGCTATCTTCGA-TCTGCTCCCCGTCTAATACAGAGACGCCAA
** * * * * * *
29186393 ATCTATTATCTCCGATTTGTTCCCTGTATAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * * * * *
29186438 ATCTG-TCATCTTGGATCTG--CCTCGATGTAA-ACACATGAAGGTCAG
1 ATCTGCT-ATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ACGCCAA
* *
29186483 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACATAGATGCCAA
1 ATCTGCTA--TCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
29186530 ATC
1 ATC
29186533 ATCTTAGATC
Statistics
Matches: 180, Mismatches: 36, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
43 8 0.04
44 43 0.24
45 97 0.54
46 2 0.01
47 17 0.09
48 5 0.03
49 8 0.04
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.32
Consensus pattern (45 bp):
ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
Found at i:29186603 original size:78 final size:78
Alignment explanation
Indices: 29186472--29186766 Score: 448
Period size: 78 Copynumber: 3.8 Consensus size: 78
29186462 ATGTAAACAC
*
29186472 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACATAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
*
29186537 TAGATCTGCTTCA
66 TGGATCTGCTTCA
* * * *
29186550 ATGAAGGTCCA-ATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATAATA
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
*
29186614 TTGGATCTACTTCA
65 TTGGATCTGCTTCA
* *
29186628 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCTCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
29186693 TGGATCTGCTTCA
66 TGGATCTGCTTCA
** * **
29186706 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTTCGTCGAATATGGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
29186767 TGTTTCTTCG
Statistics
Matches: 196, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
77 2 0.01
78 192 0.98
79 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:29187029 original size:44 final size:44
Alignment explanation
Indices: 29186974--29187245 Score: 204
Period size: 44 Copynumber: 6.3 Consensus size: 44
29186964 GTCGAATATG
* * * *
29186974 GAGATGCCAAATCTACTATC-TCTGATTTGCTCTCTGACCATACA
1 GAGATGTCAAATCTACTATCTTC-GATCTGCTCCCTGACAATACA
*
29187018 GAGATGTCAAATCTGCTATCTTCGATCTGCTCCCTGACAATACA
1 GAGATGTCAAATCTACTATCTTCGATCTGCTCCCTGACAATACA
* * * * *
29187062 GGGATGTCAAATCTGCT-TCTTGGATTTGC-CCCTCGTCAAATAC-
1 GAGATGTCAAATCTACTATCTTCGATCTGCTCCCT-GAC-AATACA
* * * * *
29187105 GAAGATGCCAAA--T-C-ATCTTGGATCTGCTCCCCGTCGAATACG
1 G-AGATGTCAAATCTACTATCTTCGATCTGCTCCCTGAC-AATACA
* * *
29187147 GAGATGCCAAATAT-C-ATCTTCGATCTGCTCTCTGACAATACA
1 GAGATGTCAAATCTACTATCTTCGATCTGCTCCCTGACAATACA
*** * * *
29187189 GAGACACCAAATCTGCTATCTTTGATCTGCTCTCTGACAATACA
1 GAGATGTCAAATCTACTATCTTCGATCTGCTCCCTGACAATACA
*
29187233 GAGATGCCAAATC
1 GAGATGTCAAATC
29187246 ATCTTGGATC
Statistics
Matches: 192, Mismatches: 25, Indels: 22
0.80 0.10 0.09
Matches are distributed among these distances:
41 30 0.16
42 25 0.13
43 33 0.17
44 102 0.53
45 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (44 bp):
GAGATGTCAAATCTACTATCTTCGATCTGCTCCCTGACAATACA
Found at i:29197955 original size:19 final size:20
Alignment explanation
Indices: 29197931--29197969 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29197921 GATATGATAC
*
29197931 TAAAAT-TATTAAAAAAAAT
1 TAAAATATATAAAAAAAAAT
29197950 TAAAATATATAAAAAAAAAT
1 TAAAATATATAAAAAAAAAT
29197970 CAGGGTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAATATATAAAAAAAAAT
Found at i:29198269 original size:23 final size:22
Alignment explanation
Indices: 29198226--29198283 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
29198216 AGGTATCTTC
* *
29198226 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
29198247 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
29198270 TGCATATCATATCT
1 TACAAATCATATCT
29198284 AATATTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:29198298 original size:18 final size:19
Alignment explanation
Indices: 29198262--29198324 Score: 96
Period size: 18 Copynumber: 3.5 Consensus size: 19
29198252 AATCATATCT
29198262 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
29198281 TCTAATATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
29198299 TCTAAGATTGCATATCAT-
1 TCTAAGATTGCATATCATA
29198317 TC-AAGATT
1 TCTAAGATT
29198325 ATATTTCCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.15
18 19 0.46
19 16 0.39
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:29203804 original size:21 final size:21
Alignment explanation
Indices: 29203754--29203806 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
29203744 GAGGCAAGAA
*
29203754 ATTGTGGTAAGTAAAGGTAAG
1 ATTGTGGTGAGTAAAGGTAAG
*
29203775 GTTGTGGTGAGTAAAGGTAAG
1 ATTGTGGTGAGTAAAGGTAAG
29203796 ATTGTGGTGAG
1 ATTGTGGTGAG
29203807 CCACAGTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.40, T:0.30
Consensus pattern (21 bp):
ATTGTGGTGAGTAAAGGTAAG
Found at i:29205208 original size:14 final size:14
Alignment explanation
Indices: 29205191--29205226 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
29205181 ATTTCCACAA
29205191 GCCACACGAGCGTG
1 GCCACACGAGCGTG
*
29205205 GCCACATGAGCGTG
1 GCCACACGAGCGTG
29205219 GCCACACG
1 GCCACACG
29205227 CCTATGTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.36, G:0.33, T:0.08
Consensus pattern (14 bp):
GCCACACGAGCGTG
Found at i:29206926 original size:10 final size:10
Alignment explanation
Indices: 29206911--29206948 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
29206901 CCTCTCAAAG
29206911 TTATATTAAT
1 TTATATTAAT
29206921 TTATATTAAT
1 TTATATTAAT
29206931 TTA-ATTTAAT
1 TTATA-TTAAT
29206941 TTATATTA
1 TTATATTA
29206949 TCAAAATACC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.04
10 24 0.92
11 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTATATTAAT
Found at i:29211360 original size:19 final size:19
Alignment explanation
Indices: 29211328--29211373 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29211318 ACAACATATA
* * *
29211328 ATAATGTCACATTATTTAC
1 ATAATATCAAATTATTCAC
29211347 ATAATATCAAATTATTCAC
1 ATAATATCAAATTATTCAC
29211366 ATATATAT
1 ATA-ATAT
29211374 ATGCTTACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.41
Consensus pattern (19 bp):
ATAATATCAAATTATTCAC
Found at i:29213798 original size:15 final size:15
Alignment explanation
Indices: 29213773--29213836 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
29213763 AACAACAAAA
*
29213773 CCAAGATAAAGAAAC
1 CCAACATAAAGAAAC
29213788 CCAGA-ATAAAGAAAC
1 CCA-ACATAAAGAAAC
*
29213803 CCAACATAAAGAAAT
1 CCAACATAAAGAAAC
* *
29213818 CCAACATAAGGAAAT
1 CCAACATAAAGAAAC
29213833 CCAA
1 CCAA
29213837 ATTACAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.02
15 43 0.96
16 1 0.02
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (15 bp):
CCAACATAAAGAAAC
Found at i:29220352 original size:15 final size:15
Alignment explanation
Indices: 29220327--29220405 Score: 88
Period size: 15 Copynumber: 5.3 Consensus size: 15
29220317 AACAACAAAA
*
29220327 CCAAGATAAAGAAAC
1 CCAACATAAAGAAAC
29220342 CCAGA-ATAAAGAAAC
1 CCA-ACATAAAGAAAC
*
29220357 CCAACATAAAGAAAT
1 CCAACATAAAGAAAC
*
29220372 CCAACATAAAGAAAT
1 CCAACATAAAGAAAC
* * *
29220387 CCAAGATAAGGAAAT
1 CCAACATAAAGAAAC
29220402 CCAA
1 CCAA
29220406 ATTACAATAT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
14 1 0.02
15 57 0.97
16 1 0.02
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.10
Consensus pattern (15 bp):
CCAACATAAAGAAAC
Found at i:29220366 original size:30 final size:30
Alignment explanation
Indices: 29220327--29220405 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
29220317 AACAACAAAA
29220327 CCAAGATAAAGAAACCCAGA-ATAAAGAAAC
1 CCAAGATAAAGAAACCCA-ACATAAAGAAAC
* * *
29220357 CCAACATAAAGAAATCCAACATAAAGAAAT
1 CCAAGATAAAGAAACCCAACATAAAGAAAC
* *
29220387 CCAAGATAAGGAAATCCAA
1 CCAAGATAAAGAAACCCAA
29220406 ATTACAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 1 0.02
30 42 0.98
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.10
Consensus pattern (30 bp):
CCAAGATAAAGAAACCCAACATAAAGAAAC
Found at i:29228412 original size:23 final size:24
Alignment explanation
Indices: 29228386--29228439 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
29228376 GACACACGGG
*
29228386 GTGCCTGAA-ATACAATACATAAA
1 GTGCCTGAATATACAACACATAAA
*
29228409 GTGCCT-AATATACAACACATAGA
1 GTGCCTGAATATACAACACATAAA
29228432 GTGCCTGA
1 GTGCCTGA
29228440 TCGGCAAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 2 0.07
23 24 0.89
24 1 0.04
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
GTGCCTGAATATACAACACATAAA
Found at i:29239689 original size:29 final size:28
Alignment explanation
Indices: 29239649--29239706 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 28
29239639 ATACTCTTTA
29239649 TATTTTTAGAATTTAGTCTTTATATTTT
1 TATTTTTAGAATTTAGTCTTTATATTTT
*
29239677 TATTTTTAAGAATTTAGTCTTTTTATTTT
1 TATTTTT-AGAATTTAGTCTTTATATTTT
29239706 T
1 T
29239707 TAAATTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.24, C:0.03, G:0.07, T:0.66
Consensus pattern (28 bp):
TATTTTTAGAATTTAGTCTTTATATTTT
Found at i:29239714 original size:29 final size:29
Alignment explanation
Indices: 29239656--29239714 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
29239646 TTATATTTTT
**
29239656 AGAATTTAGTCTTTATATTTTTATTTTTA
1 AGAATTTAGTCTTTATATTTTTATAATTA
*
29239685 AGAATTTAGTCTTTTTATTTTT-TAAATTA
1 AGAATTTAGTCTTTATATTTTTAT-AATTA
29239714 A
1 A
29239715 AAAATTCAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (29 bp):
AGAATTTAGTCTTTATATTTTTATAATTA
Found at i:29245569 original size:137 final size:138
Alignment explanation
Indices: 29245332--29245947 Score: 852
Period size: 137 Copynumber: 4.5 Consensus size: 138
29245322 TTTTATCTCT
* * * * *
29245332 TTGTTTGTATTTTTAAAATATTCAGATTTTAATTTTTAAAATATATTATTTTTGTATTTTA-TTT
1 TTGTTTATATTTTTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTT
* * *
29245396 TTATCTTATTTTAGTACATAATGTTTCAAATATATTA-TCTTAGTGTTTTTAAAATAACCCTAAT
66 TTATCTTATTTTAGAACATAATGTTTCAAATGTATTACT-TTAGTGTTTTTTAAATAACCCTAAT
29245460 TTTGTCCCA
130 TTTGTCCCA
* *
29245469 TTGTTTATATTTTTAAAATTTTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTT
1 TTGTTTATATTTTTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTT
* *
29245534 TTATCTTA-TTTAGAACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTATATAACTCTAATT
66 TTATCTTATTTTAGAACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTAAATAACCCTAATT
29245598 TTGTCCC-
131 TTGTCCCA
*
29245605 TT-TATTAT-TTGTATCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTA
1 TTGT-TTATATT-T-T-TAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTA
* *
29245668 TTTTTTATCTTATTTTAGTAA-ATAATATTTCAAATGTATTACTTTAGTGTTTTTTATATAACCC
62 TTTTTTATCTTATTTTAG-AACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTAAATAACCC
*
29245732 TAATTTTGTCCTTTTA
126 TAATTTTGTCC---CA
* * * * * *
29245748 TTATTTGTATTTCTAAAATATTCGGATTTTAATTTTTAAAATATACTGTTTTCATATTTTA-TTT
1 TTGTTTATATTTTTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTT
* *
29245812 TTATCTTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTAATT
66 TTATCTTATTTTAGAACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTAAATAACCCTAATT
29245877 TTGTCCCA
131 TTGTCCCA
* * *
29245885 TCGTTTATATTTTTAAAATTTTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATT
1 TTGTTTATATTTTTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATT
29245948 ATATTTTTTT
Statistics
Matches: 425, Mismatches: 38, Indels: 31
0.86 0.08 0.06
Matches are distributed among these distances:
135 3 0.01
136 7 0.02
137 164 0.39
138 70 0.16
139 58 0.14
140 70 0.16
141 44 0.10
143 6 0.01
144 3 0.01
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.56
Consensus pattern (138 bp):
TTGTTTATATTTTTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTT
TTATCTTATTTTAGAACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTAAATAACCCTAATT
TTGTCCCA
Found at i:29245807 original size:23 final size:24
Alignment explanation
Indices: 29245755--29245808 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
29245745 TTATTATTTG
*
29245755 TATTTCTAAAATATTCGGATTTTAA
1 TATTT-TAAAATATACGGATTTTAA
* *
29245780 T-TTTTAAAATATACTG-TTTTCA
1 TATTTTAAAATATACGGATTTTAA
29245802 TATTTTA
1 TATTTTA
29245809 TTTTTATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 6 0.24
23 15 0.60
24 3 0.12
25 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (24 bp):
TATTTTAAAATATACGGATTTTAA
Found at i:29245847 original size:279 final size:275
Alignment explanation
Indices: 29245334--29245947 Score: 871
Period size: 279 Copynumber: 2.2 Consensus size: 275
29245324 TTATCTCTTT
* * * *
29245334 GTTTGTATTTTTAAAATATTCAGATTTTAATTTTTAAAATATATTATTTTTGTATTTTA-TTTTT
1 GTTTATATTTTTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTTTT
* *
29245398 ATCTTATTTTAGTACATAATGTTTCAAATATATTATCTTAGTGTTTTTAAAATAACCCTAATTTT
66 ATCTTATTTTAGTAAATAATATTTCAAATATATTATCTTAGTGTTTTTAAAATAACCCTAATTTT
* * * * * *
29245463 GTCCCATTGTTTATATTTTTAAAATTTTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTT
131 GTCCCATTATTTATATTTCTAAAATATTCGGATTTTAATTTTTAAAATATACTATTTTCATATTT
* *
29245528 TATTTTTTATCTTATTTAGAACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTATATAACTC
196 TATTTTTTATCTTATTTAGAACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTAAATAACCC
29245593 TAATTTTGTCCC-T-
261 TAATTTTGTCCCATC
*
29245606 TTATTAT-TTGTATCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATT
1 GT-TTATATT-T-T-TAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATT
* * *
29245670 TTTTATCTTATTTTAGTAAATAATATTTCAAATGTATTA-CTTTAGTGTTTTTTATATAACCCTA
62 TTTTATCTTATTTTAGTAAATAATATTTCAAATATATTATC-TTAGTGTTTTTAAAATAACCCTA
* * *
29245734 ATTTTGTCCTTTTATTATTTGTATTTCTAAAATATTCGGATTTTAATTTTTAAAATATACTGTTT
126 ATTTTGTCC---CATTATTTATATTTCTAAAATATTCGGATTTTAATTTTTAAAATATACTATTT
* *
29245799 TCATATTTTA-TTTTTATCTTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTT
188 TCATATTTTATTTTTTATCTTA-TTTAGAACATAATGTTTCAAATGTATTACTTTAGTGTTTTTT
29245863 AAATAACCCTAATTTTGTCCCATC
252 AAATAACCCTAATTTTGTCCCATC
* * *
29245887 GTTTATATTTTTAAAATTTTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATT
1 GTTTATATTTTTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATT
29245948 ATATTTTTTT
Statistics
Matches: 302, Mismatches: 27, Indels: 20
0.87 0.08 0.06
Matches are distributed among these distances:
272 3 0.01
273 4 0.01
274 1 0.00
275 46 0.15
276 67 0.22
278 58 0.19
279 114 0.38
280 6 0.02
281 3 0.01
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.56
Consensus pattern (275 bp):
GTTTATATTTTTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTTTT
ATCTTATTTTAGTAAATAATATTTCAAATATATTATCTTAGTGTTTTTAAAATAACCCTAATTTT
GTCCCATTATTTATATTTCTAAAATATTCGGATTTTAATTTTTAAAATATACTATTTTCATATTT
TATTTTTTATCTTATTTAGAACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTAAATAACCC
TAATTTTGTCCCATC
Found at i:29246009 original size:12 final size:12
Alignment explanation
Indices: 29245992--29246024 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
29245982 TATTTTTCAT
*
29245992 TAAAAAATAGTA
1 TAAAAAATAATA
29246004 T-AAAAATAATA
1 TAAAAAATAATA
29246015 TAAAAAATAA
1 TAAAAAATAA
29246025 AATACGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
TAAAAAATAATA
Found at i:29249445 original size:10 final size:10
Alignment explanation
Indices: 29249430--29249467 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
29249420 ATTTTAGGAT
29249430 TTATCTTTAA
1 TTATCTTTAA
29249440 TTATCTTTAA
1 TTATCTTTAA
*
29249450 TTAT-TTGTAT
1 TTATCTT-TAA
29249460 TTATCTTT
1 TTATCTTT
29249468 TAGAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:29250271 original size:39 final size:39
Alignment explanation
Indices: 29250196--29250270 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
29250186 CGAAATCCCA
*
29250196 ATCAAAACTTTTAACTCTGTTTTTATTTTATTTTTTTAG
1 ATCAAAACTTTTAACTCAGTTTTTATTTTATTTTTTTAG
*
29250235 ATCAAAACTTTTAATTCAG-TTTT-TTTTATTTCTTTT
1 ATCAAAACTTTTAACTCAGTTTTTATTTTATTT-TTTT
29250271 TCAGGTATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 8 0.24
38 8 0.24
39 17 0.52
ACGTcount: A:0.25, C:0.11, G:0.04, T:0.60
Consensus pattern (39 bp):
ATCAAAACTTTTAACTCAGTTTTTATTTTATTTTTTTAG
Found at i:29253214 original size:19 final size:18
Alignment explanation
Indices: 29253190--29253254 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
29253180 GGCAACCCAA
*
29253190 TTTTTATTTTTTATTTTAT
1 TTTTTA-TTATTATTTTAT
*
29253209 TTTTTATTATTACTCTTT-C
1 TTTTTATTATTA-T-TTTAT
29253228 TTTTTATTATTATTTTAT
1 TTTTTATTATTATTTTAT
29253246 TATTTTATT
1 T-TTTTATT
29253255 TTTTGGATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 3 0.08
18 7 0.18
19 26 0.67
20 3 0.08
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTATTATTATTTTAT
Found at i:29254542 original size:96 final size:97
Alignment explanation
Indices: 29254374--29254555 Score: 276
Period size: 96 Copynumber: 1.9 Consensus size: 97
29254364 TTTAAGAATG
* * * * * *
29254374 TGTTGGGCTGAGTGACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGAT
1 TGTTGGGCTGAATAACCAGGGTGAGGTGCTTGACTGTCATCTCTCTTCGCGTCAAAAGATTCAAT
*
29254439 ATGTTCTTAAG-AAAAATAAAAATTAGGAGCA
66 ATATTCTTAAGCAAAAATAAAAATTAGGAGCA
*
29254470 TGTTGGGCTGAATAACCAGGGTGGGGTGCTTGACTGTCATCTCTCTTCGCGTCAAAAGATTCAAT
1 TGTTGGGCTGAATAACCAGGGTGAGGTGCTTGACTGTCATCTCTCTTCGCGTCAAAAGATTCAAT
*
29254535 ATATTCTTAAGCAACAATAAA
66 ATATTCTTAAGCAAAAATAAA
29254556 TAAATAAATA
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
96 68 0.89
97 8 0.11
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (97 bp):
TGTTGGGCTGAATAACCAGGGTGAGGTGCTTGACTGTCATCTCTCTTCGCGTCAAAAGATTCAAT
ATATTCTTAAGCAAAAATAAAAATTAGGAGCA
Found at i:29255256 original size:20 final size:20
Alignment explanation
Indices: 29255233--29255280 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
29255223 TTATTTTCAT
29255233 TTATCTTTAATTATATT-TAA
1 TTATCTTTAATTAT-TTGTAA
* *
29255253 TTATCTTTATTTATTTGTAT
1 TTATCTTTAATTATTTGTAA
29255273 TTATCTTT
1 TTATCTTT
29255281 TAGAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATCTTTAATTATTTGTAA
Found at i:29262641 original size:4 final size:4
Alignment explanation
Indices: 29262632--29262659 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
29262622 AAACTTGTAC
29262632 AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT
29262660 TAGATCTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:29266333 original size:19 final size:20
Alignment explanation
Indices: 29266309--29266350 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
29266299 AAAAATTCAG
29266309 TATT-AAAAATTAGAAAAA-A
1 TATTAAAAAATTA-AAAAATA
29266328 TATTAAAAAATTAAAAAATA
1 TATTAAAAAATTAAAAAATA
29266348 TAT
1 TAT
29266351 AGAATTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
TATTAAAAAATTAAAAAATA
Found at i:29268417 original size:16 final size:16
Alignment explanation
Indices: 29268396--29268426 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29268386 TTGGGGAAAA
*
29268396 ATTTATCATTATACTT
1 ATTTATAATTATACTT
29268412 ATTTATAATTATACT
1 ATTTATAATTATACT
29268427 AGATTTATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTATAATTATACTT
Found at i:29271142 original size:77 final size:75
Alignment explanation
Indices: 29270980--29271186 Score: 222
Period size: 77 Copynumber: 2.7 Consensus size: 75
29270970 CGAAGGTAAT
* *
29270980 CTCGAGGCTCAACCCATTTTGTG--AACATGAATTTGACTTTTGATAAAATGAAAAATTAAAAGG
1 CTCGAGGCTCAACCCATTTT-TGAAAACA-G-ATTTGACTTTTGATAAAATGAAAAATGAAAAAG
*
29271043 ACATCAAAAATGAT
63 ACATCAAAAA-GAC
* * *
29271057 CTCAAGGCTCAACCCATTTTTGAAAACAGATTTGAGTTTTAATAAAATGAAAAACTGAAAAAGAC
1 CTCGAGGCTCAACCCATTTTTGAAAACAGATTTGACTTTTGATAAAATGAAAAA-TGAAAAAGAC
*
29271122 TTCAACAGAA-AC
65 ATCAA-A-AAGAC
* * * * *
29271134 CTCGAGGCTAAACTCATTTTTGAAAATAGATTCGACTTTTGGTAAAATGAAAA
1 CTCGAGGCTCAACCCATTTTTGAAAACAGATTTGACTTTTGATAAAATGAAAA
29271187 GAAAATACCT
Statistics
Matches: 110, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
76 25 0.23
77 78 0.71
78 5 0.05
79 2 0.02
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (75 bp):
CTCGAGGCTCAACCCATTTTTGAAAACAGATTTGACTTTTGATAAAATGAAAAATGAAAAAGACA
TCAAAAAGAC
Found at i:29271488 original size:76 final size:73
Alignment explanation
Indices: 29271347--29271502 Score: 183
Period size: 76 Copynumber: 2.1 Consensus size: 73
29271337 ACTAAATGGA
* *
29271347 AAGGCTCGATCCCTTTTTGAAAACAAATTCGAGTTTGATAAAAGATAATTAAAAGGACCTCGACA
1 AAGGCTCGATCCCTTTTTGAAAACAAATTCGAGTTTAATAAAAGAAAATTAAAAGGACCTCGACA
29271412 AAAATCTC
66 AAAATCTC
* * *
29271420 AAGGCTTGA-CCCATTTTTAGAAAACAAATTCGATTTTTAATAAAAAGAAAATTGAAAA-GATCT
1 AAGGCTCGATCCC-TTTTT-GAAAACAAATTCGA-GTTTAAT-AAAAGAAAATT-AAAAGGACCT
*
29271483 CGACAACAATCT-
61 CGACAAAAATCTC
29271495 AGAGGCTC
1 A-AGGCTC
29271503 AACACTCTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
72 3 0.04
73 13 0.19
74 14 0.20
75 6 0.09
76 30 0.43
77 4 0.06
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (73 bp):
AAGGCTCGATCCCTTTTTGAAAACAAATTCGAGTTTAATAAAAGAAAATTAAAAGGACCTCGACA
AAAATCTC
Found at i:29271706 original size:46 final size:46
Alignment explanation
Indices: 29271623--29272298 Score: 497
Period size: 46 Copynumber: 14.4 Consensus size: 46
29271613 AAATATCCTT
* * *
29271623 GAGAGAGGTTTGAAAATATCTCTAGGGAAAGTC-AAAAGCATCCTCAA
1 GAGAG-GGTTTGAAAATATCTCAAGAGAGA-TCTAAAAGCATCCTCAA
* * * *
29271670 GATAGAGTTTGAAAATATCTCAATAGAGATCTAAAAGCATCCTTAA
1 GAGAGGGTTTGAAAATATCTCAAGAGAGATCTAAAAGCATCCTCAA
* * * *
29271716 TAGAGGGTTTGAAAATATATCTCATA-AGAGATTTGAAAGCAT-CTTAGA
1 GAGAGGGTTTG-AAA-ATATCTCA-AGAGAGATCTAAAAGCATCCTCA-A
* * * *
29271764 GATAAGGTTTGAAAATATCTCAACATAGATCTAAAAGCATCCTCAA
1 GAGAGGGTTTGAAAATATCTCAAGAGAGATCTAAAAGCATCCTCAA
* ** *
29271810 GAGAGGGCTTGAAAATAAATCTCATAG-GAGATCTGGAAGCATCCTCGA
1 GAGAGGGTTTGAAAAT--ATCTCA-AGAGAGATCTAAAAGCATCCTCAA
* * * **
29271858 GATAGGATTTGAAAATATCTCAAGAGAGATCAAAAAGCATCCTTGA
1 GAGAGGGTTTGAAAATATCTCAAGAGAGATCTAAAAGCATCCTCAA
* * * **
29271904 GAGAGGGTTTGAAAATATATATCAAGGGAGATATAAAAGCATCCTTGA
1 GAGAGGGTTTG-AAA-ATATCTCAAGAGAGATCTAAAAGCATCCTCAA
* * * *
29271952 GGGAGGATTTGAAAATATCTCAAGGGAGATCTAAAAGTATCCTCAAA
1 GAGAGGGTTTGAAAATATCTCAAGAGAGATCTAAAAGCATCCTC-AA
* * * *
29271999 GAGAGGGTTTGAAAATATATTTCATAG-GATATCTGAAAGCATCCTCGA
1 GAGAGGGTTTG-AAA-ATATCTCA-AGAGAGATCTAAAAGCATCCTCAA
* * * * *
29272047 GA-AGGGACTCGAAAGTATCTCAAGGGAGATCTACAAA-TATCCTCAA
1 GAGAGGG-TTTGAAAATATCTCAAGAGAGATCTA-AAAGCATCCTCAA
* * * * * *
29272093 GTGAGGGTTTGAAAATATATCTCAAGAGTGATATGAAAGCATTCTCGA
1 GAGAGGGTTTG-AAA-ATATCTCAAGAGAGATCTAAAAGCATCCTCAA
* * ** * * *
29272141 GGGAGGATTT-ATAAGCATCTCAAGGGAGATCTAAAAGTATCCTTAA
1 GAGAGGGTTTGA-AAATATCTCAAGAGAGATCTAAAAGCATCCTCAA
* * * * *
29272187 GAGAGGGTTTGAAAATATATCTCAAGGGTGATATGAAAGCATCCTTAA
1 GAGAGGGTTTG-AAA-ATATCTCAAGAGAGATCTAAAAGCATCCTCAA
* * * * *
29272235 GAGA-GGATTCAAAAGTATCTCAAGATAGATCTAAAAGTATCATCAA
1 GAGAGGGTTTGAAAA-TATCTCAAGAGAGATCTAAAAGCATCCTCAA
29272281 GAGAGGGTTTGAAAATAT
1 GAGAGGGTTTGAAAATAT
29272299 ATCTAAAAGC
Statistics
Matches: 494, Mismatches: 105, Indels: 61
0.75 0.16 0.09
Matches are distributed among these distances:
45 8 0.02
46 219 0.44
47 69 0.14
48 171 0.35
49 25 0.05
50 2 0.00
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (46 bp):
GAGAGGGTTTGAAAATATCTCAAGAGAGATCTAAAAGCATCCTCAA
Found at i:29271774 original size:94 final size:94
Alignment explanation
Indices: 29271677--29272302 Score: 653
Period size: 94 Copynumber: 6.6 Consensus size: 94
29271667 CAAGATAGAG
* * * *
29271677 TTTGAAAATATCTCAATAGAGATCTAAAAGCATCCTTAATAGAGGGTTTGAAAATATATCTCATA
1 TTTGAAAATATCTCAAGAGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCA-A
* * * *
29271742 -AGAGATTTGAAAGCATCTTAGAGATAAGG-
65 GGGAGATATGAAAGCATCTTCGAGA-GAGGA
* * * * *
29271771 TTTGAAAATATCTCAACATAGATCTAAAAGCATCCTCAAGAGAGGGCTTGAAAATAAATCTCATA
1 TTTGAAAATATCTCAAGAGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCA-A
* * * *
29271836 -GGAGATCTGGAAGCATCCTCGAGATAGGA
65 GGGAGATATGAAAGCATCTTCGAGAGAGGA
* * ** *
29271865 TTTGAAAATATCTCAAGAGAGATCAAAAAGCATCCTTGAGAGAGGGTTTGAAAATATATATCAAG
1 TTTGAAAATATCTCAAGAGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCAAG
* *
29271930 GGAGATATAAAAGCATCCTT-GAGGGAGGA
66 GGAGATATGAAAGCAT-CTTCGAGAGAGGA
* *
29271959 TTTGAAAATATCTCAAGGGAGATCTAAAAGTATCCTCAAAGAGAGGGTTTGAAAATATATTTCAT
1 TTTGAAAATATCTCAAGAGAGATCTAAAAGTATCCTC-AAGAGAGGGTTTGAAAATATATCTCA-
* * *
29272024 A-GGATATCTGAAAGCATCCTCGAGA-AGGGA
64 AGGGAGATATGAAAGCATCTTCGAGAGA-GGA
* * * * *
29272054 CTCGAAAGTATCTCAAGGGAGATCTACAAA-TATCCTCAAGTGAGGGTTTGAAAATATATCTCAA
1 TTTGAAAATATCTCAAGAGAGATCTA-AAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCAA
* * *
29272118 GAGTGATATGAAAGCAT-TCTCGAGGGAGGA
65 GGGAGATATGAAAGCATCT-TCGAGAGAGGA
** * *
29272148 TTT-ATAAGCATCTCAAGGGAGATCTAAAAGTATCCTTAAGAGAGGGTTTGAAAATATATCTCAA
1 TTTGA-AAATATCTCAAGAGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCAA
* *
29272212 GGGTGATATGAAAGCATCCTT-AAGAGAGGA
65 GGGAGATATGAAAGCAT-CTTCGAGAGAGGA
* * *
29272242 -TTCAAAAGTATCTCAAGATAGATCTAAAAGTATCATCAAGAGAGGGTTTGAAAATATATCT
1 TTTGAAAA-TATCTCAAGAGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCT
29272303 AAAAGCATCT
Statistics
Matches: 453, Mismatches: 62, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
93 13 0.03
94 358 0.79
95 77 0.17
96 5 0.01
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.26
Consensus pattern (94 bp):
TTTGAAAATATCTCAAGAGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCAAG
GGAGATATGAAAGCATCTTCGAGAGAGGA
Found at i:29271977 original size:23 final size:25
Alignment explanation
Indices: 29271951--29272016 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 25
29271941 AGCATCCTTG
29271951 AGGGAGGATTTGAAAATAT-CTC-A
1 AGGGAGGATTTGAAAATATCCTCAA
*
29271974 AGGGA-GATCT-AAAAGTATCCTCAA
1 AGGGAGGATTTGAAAA-TATCCTCAA
* *
29271998 AGAGAGGGTTTGAAAATAT
1 AGGGAGGATTTGAAAATAT
29272017 ATTTCATAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 4 0.12
22 7 0.21
23 8 0.24
24 5 0.15
25 6 0.18
26 4 0.12
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (25 bp):
AGGGAGGATTTGAAAATATCCTCAA
Found at i:29271984 original size:188 final size:187
Alignment explanation
Indices: 29271657--29272302 Score: 732
Period size: 188 Copynumber: 3.4 Consensus size: 187
29271647 GGGAAAGTCA
* * * *
29271657 AAAGCATCCTCAAGATA-GAGTTTGAAAATATCTCAATAGAGATCTAAAAGCATCCTTAATAGAG
1 AAAGCATCCTCAAGATAGGA-TTTGAAAATATCTCAAGAGAGATCAAAAAGCATCCTCAAGAGAG
* **
29271721 GGTTTGAAAATATATCTCATA-AGAGATTTGAAAGCATCTTAGAGATAAGG-TTTGAAAATATCT
65 GGTTTGAAAATATATCTCA-AGAGAGATATGAAAGCATCTT-GAG-GGAGGATTTGAAAATATCT
*** * * *
29271784 CAACATAGATCTAAAAGCATCCTCAAGAGAGGGCTTGAAAATAAATCTCATAGGAGATCTG
127 CAAGGGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCATAGGAGATCTG
* * **
29271845 GAAGCATCCTCGAGATAGGATTTGAAAATATCTCAAGAGAGATCAAAAAGCATCCTTGAGAGAGG
1 AAAGCATCCTCAAGATAGGATTTGAAAATATCTCAAGAGAGATCAAAAAGCATCCTCAAGAGAGG
* * *
29271910 GTTTGAAAATATATATCAAGGGAGATATAAAAGCATCCTTGAGGGAGGATTTGAAAATATCTCAA
66 GTTTGAAAATATATCTCAAGAGAGATATGAAAGCAT-CTTGAGGGAGGATTTGAAAATATCTCAA
* *
29271975 GGGAGATCTAAAAGTATCCTCAAAGAGAGGGTTTGAAAATATATTTCATAGGATATCTG
130 GGGAGATCTAAAAGTATCCTC-AAGAGAGGGTTTGAAAATATATCTCATAGGAGATCTG
* * * * * * * *
29272034 AAAGCATCCTCGAGA-AGGGACTCGAAAGTATCTCAAGGGAGATCTACAAA-TATCCTCAAGTGA
1 AAAGCATCCTCAAGATA-GGATTTGAAAATATCTCAAGAGAGATC-AAAAAGCATCCTCAAGAGA
* * **
29272097 GGGTTTGAAAATATATCTCAAGAGTGATATGAAAGCATTCTCGAGGGAGGATTT-ATAAGCATCT
64 GGGTTTGAAAATATATCTCAAGAGAGATATGAAAGCA-TCTTGAGGGAGGATTTGA-AAATATCT
* * *
29272161 CAAGGGAGATCTAAAAGTATCCTTAAGAGAGGGTTTGAAAATATATCTCA-AGGGTGATATG
127 CAAGGGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCATA-GGAGATCTG
* * * * * * *
29272222 AAAGCATCCTTAAGAGAGGA-TTCAAAAGTATCTCAAGATAGATCTAAAAGTATCATCAAGAGAG
1 AAAGCATCCTCAAGATAGGATTTGAAAA-TATCTCAAGAGAGATCAAAAAGCATCCTCAAGAGAG
29272286 GGTTTGAAAATATATCT
65 GGTTTGAAAATATATCT
29272303 AAAAGCATCT
Statistics
Matches: 392, Mismatches: 53, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
187 12 0.03
188 214 0.55
189 161 0.41
190 5 0.01
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.26
Consensus pattern (187 bp):
AAAGCATCCTCAAGATAGGATTTGAAAATATCTCAAGAGAGATCAAAAAGCATCCTCAAGAGAGG
GTTTGAAAATATATCTCAAGAGAGATATGAAAGCATCTTGAGGGAGGATTTGAAAATATCTCAAG
GGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCATAGGAGATCTG
Found at i:29272163 original size:283 final size:282
Alignment explanation
Indices: 29271656--29272302 Score: 793
Period size: 283 Copynumber: 2.3 Consensus size: 282
29271646 AGGGAAAGTC
* * * * * *
29271656 AAAAGCATCCTCAAGATA-GAGTTTGAAAATATCTCAATAGAGATCTAAAAGCATCCTTAATAGA
1 AAAAGCATCCTTAAGAGAGGA-TTTGAAAATATCTCAAGAGAGATCTAAAAGTATCCTCAAGAGA
* * * *
29271720 GGGTTTGAAAATATATCTCATAAGAGATTTGAAAGCATCTTAGAGATAAGGTTTGAAAATATCTC
65 GGGTTTGAAAATATATCTCATAAGAGATCTGAAAGCATCCTAGAGATAAGGCTCGAAAATATCTC
* * *
29271785 AACATAGATCTAAAAGCATCCTCAAGAGAGGGCTTGAAAATAAATCTCATAGGAGATCTGGAAGC
130 AACAGAGATCTAAAAGCATCCTCAAGAGAGGGCTTGAAAATAAATCTCATAGGAGATATGAAAGC
* * *
29271850 ATCCTCGAGATAGGATTTGAAAATATCTCAAGAGAGATCAAAAAGCATCCTTGAGAGAGGGTTTG
195 ATCCTCGAGAGAGGATTTGAAAACATCTCAAGAGAGATCAAAAAGCATCCTTAAGAGAGGGTTTG
29271915 AAAATATATATCAAGGGAGATAT
260 AAAATATATATCAAGGGAGATAT
* * *
29271938 AAAAGCATCCTTGAGGGAGGATTTGAAAATATCTCAAGGGAGATCTAAAAGTATCCTCAAAGAGA
1 AAAAGCATCCTTAAGAGAGGATTTGAAAATATCTCAAGAGAGATCTAAAAGTATCCTC-AAGAGA
* * * * * *
29272003 GGGTTTGAAAATATATTTCATAGGATATCTGAAAGCATCCTCGAGA-AGGGACTCGAAAGTATCT
65 GGGTTTGAAAATATATCTCATAAGAGATCTGAAAGCATCCTAGAGATAAGG-CTCGAAAATATCT
** * * * * *
29272067 CAAGGGAGATCTACAAA-TATCCTCAAGTGAGGGTTTGAAAATATATCTCA-AGAGTGATATGAA
129 CAACAGAGATCTA-AAAGCATCCTCAAGAGAGGGCTTGAAAATAAATCTCATAG-GAGATATGAA
* * * * * *
29272130 AGCATTCTCGAGGGAGGATTT-ATAAGCATCTCAAGGGAGATCTAAAAGTATCCTTAAGAGAGGG
192 AGCATCCTCGAGAGAGGATTTGA-AAACATCTCAAGAGAGATCAAAAAGCATCCTTAAGAGAGGG
* *
29272194 TTTGAAAATATATCTCAAGGGTGATAT
256 TTTGAAAATATATATCAAGGGAGATAT
* * * *
29272221 GAAAGCATCCTTAAGAGAGGA-TTCAAAAGTATCTCAAGATAGATCTAAAAGTATCATCAAGAGA
1 AAAAGCATCCTTAAGAGAGGATTTGAAAA-TATCTCAAGAGAGATCTAAAAGTATCCTCAAGAGA
29272285 GGGTTTGAAAATATATCT
65 GGGTTTGAAAATATATCT
29272303 AAAAGCATCT
Statistics
Matches: 310, Mismatches: 48, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
282 82 0.26
283 225 0.73
284 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (282 bp):
AAAAGCATCCTTAAGAGAGGATTTGAAAATATCTCAAGAGAGATCTAAAAGTATCCTCAAGAGAG
GGTTTGAAAATATATCTCATAAGAGATCTGAAAGCATCCTAGAGATAAGGCTCGAAAATATCTCA
ACAGAGATCTAAAAGCATCCTCAAGAGAGGGCTTGAAAATAAATCTCATAGGAGATATGAAAGCA
TCCTCGAGAGAGGATTTGAAAACATCTCAAGAGAGATCAAAAAGCATCCTTAAGAGAGGGTTTGA
AAATATATATCAAGGGAGATAT
Found at i:29272259 original size:23 final size:24
Alignment explanation
Indices: 29272233--29272286 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
29272223 AAGCATCCTT
29272233 AAGAGAGGAT-TCAAAAGTATC-TC
1 AAGAGAGGATCT-AAAAGTATCATC
*
29272256 AAGATA-GATCTAAAAGTATCATC
1 AAGAGAGGATCTAAAAGTATCATC
29272279 AAGAGAGG
1 AAGAGAGG
29272287 GTTTGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 12 0.46
23 13 0.50
24 1 0.04
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.20
Consensus pattern (24 bp):
AAGAGAGGATCTAAAAGTATCATC
Found at i:29278309 original size:12 final size:12
Alignment explanation
Indices: 29278292--29278317 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29278282 GTTCAACTCA
29278292 TTTTAAATTATT
1 TTTTAAATTATT
29278304 TTTTAAATTATT
1 TTTTAAATTATT
29278316 TT
1 TT
29278318 AAATTATATG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTAAATTATT
Found at i:29278317 original size:10 final size:10
Alignment explanation
Indices: 29278291--29278324 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
29278281 AGTTCAACTC
29278291 ATTTTAAATT
1 ATTTTAAATT
29278301 ATTTTTTAAATT
1 A--TTTTAAATT
29278313 ATTTTAAATT
1 ATTTTAAATT
29278323 AT
1 AT
29278325 ATGAATGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 12 0.55
12 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTAAATT
Found at i:29278999 original size:19 final size:16
Alignment explanation
Indices: 29278969--29279011 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 16
29278959 TTGTGTAACT
*
29278969 AAAAATATAATTTACTTA
1 AAAAAAATAATTT--TTA
29278987 AATAAAAATAATTTTTA
1 AA-AAAAATAATTTTTA
29279004 AAAAAAAT
1 AAAAAAAT
29279012 CTTAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 6 0.26
17 5 0.22
18 2 0.09
19 10 0.43
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAAAATAATTTTTA
Found at i:29279727 original size:10 final size:10
Alignment explanation
Indices: 29279712--29279761 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
29279702 TTAATTTAGG
29279712 ATTTAT-TTT
1 ATTTATCTTT
29279721 CATTTATCTTT
1 -ATTTATCTTT
*
29279732 AATTATCTTT
1 ATTTATCTTT
29279742 ATTTAT-TTGT
1 ATTTATCTT-T
29279752 ATTTATCTTT
1 ATTTATCTTT
29279762 TAGAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:29280277 original size:30 final size:30
Alignment explanation
Indices: 29280241--29280309 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
29280231 CTAGCCTTTG
*
29280241 CCACCACCAACTTCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
29280271 CCACCACCAACTCCACTAGCCACACTTGTT
1 CCACCACCAACTCCACTAGCCACACTTGCT
29280301 CCACCACCA
1 CCACCACCA
29280310 CTTGTACCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.28, C:0.49, G:0.06, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:29280867 original size:23 final size:25
Alignment explanation
Indices: 29280819--29280905 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 25
29280809 ATTCTTTTAA
* * *
29280819 TATATTAGGTATAT-TC-TAAATTC
1 TATATTATGTATATATCATTAATAC
*
29280842 TATATTACGTATATAT-ATT-ATAC
1 TATATTATGTATATATCATTAATAC
* *
29280865 TATTTTATGTATATATCTTTAATAC
1 TATATTATGTATATATCATTAATAC
*
29280890 TATATTATTTATATAT
1 TATATTATGTATATAT
29280906 TTTTTTCTAC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
23 30 0.58
24 4 0.08
25 18 0.35
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.53
Consensus pattern (25 bp):
TATATTATGTATATATCATTAATAC
Found at i:29280879 original size:25 final size:25
Alignment explanation
Indices: 29280841--29280982 Score: 87
Period size: 25 Copynumber: 5.7 Consensus size: 25
29280831 ATTCTAAATT
*
29280841 CTATATTACGTATATATA-TT-ATA
1 CTATATTATGTATATATATTTAATA
* *
29280864 CTATTTTATGTATATATCTTTAATA
1 CTATATTATGTATATATATTTAATA
* * *
29280889 CTATATTATTTATATATTTTTTTCTACATG
1 CTATATTATGTATATA---TATT-TA-ATA
* *
29280919 TTATCTTATGTATATAT-TTTAAT-
1 CTATATTATGTATATATATTTAATA
* * * *
29280942 -TATATTATGTATGTATTTTTTACA
1 CTATATTATGTATATATATTTAATA
*
29280966 CTATATTATGTACATAT
1 CTATATTATGTATATAT
29280983 TTTTTTTATA
Statistics
Matches: 93, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
22 14 0.15
23 19 0.20
24 4 0.04
25 33 0.35
26 2 0.02
27 1 0.01
28 3 0.03
29 2 0.02
30 15 0.16
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.56
Consensus pattern (25 bp):
CTATATTATGTATATATATTTAATA
Found at i:29281023 original size:77 final size:73
Alignment explanation
Indices: 29280853--29281023 Score: 162
Period size: 77 Copynumber: 2.2 Consensus size: 73
29280843 ATATTACGTA
* * * *
29280853 TATATATTATACTATTTTATGTATATATCTTTAATACTATATTATTTATATATTTTTTTCTACAT
1 TATATATTATA-TA--TTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTATACAT
*
29280918 GTTATCTTATG
63 GTTATCATATG
* * *
29280929 TATATATTTTAATTATATTATGTATGTATTTTTTACACTATATTATGTACATATTTTTTTTATAT
1 TATATA--TT-A-TATATTATGTATATATCTTTAACACTATATTATGTACATA-TTTTTTTATA-
*
29280994 CTATTTTATACATATG
60 C-ATGTTAT-CATATG
29281010 TATATATTATATAT
1 TATATATTATATAT
29281024 ATCTTAACAT
Statistics
Matches: 78, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
76 6 0.08
77 35 0.45
78 12 0.15
79 6 0.08
80 8 0.10
81 11 0.14
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (73 bp):
TATATATTATATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTATACATGTT
ATCATATG
Found at i:29281077 original size:25 final size:24
Alignment explanation
Indices: 29281049--29281104 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
29281039 GTTATATTTT
*
29281049 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
29281074 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
29281097 CACTATTA
1 CACTATTA
29281105 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:29292100 original size:12 final size:12
Alignment explanation
Indices: 29292085--29292111 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29292075 AAGGCATCTT
29292085 AAAAAAAGAAAA
1 AAAAAAAGAAAA
29292097 AAAAAAAGAAAA
1 AAAAAAAGAAAA
29292109 AAA
1 AAA
29292112 GAGAGGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:29305324 original size:23 final size:24
Alignment explanation
Indices: 29305298--29305376 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 24
29305288 ACTTTTCTTA
*
29305298 ATTTTTATTAT-TTATTATTTATT
1 ATTTTTATTATATTAGTATTTATT
*
29305321 A-TTTTATTTTATTAGTATTTATT
1 ATTTTTATTATATTAGTATTTATT
*
29305344 ATTTTATTTCATTTTATTAGTATTTATT
1 A--TT-TTT-ATTATATTAGTATTTATT
29305372 ATTTT
1 ATTTT
29305377 ATTTTGTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
22 8 0.17
23 13 0.27
25 2 0.04
26 3 0.06
27 3 0.06
28 19 0.40
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (24 bp):
ATTTTTATTATATTAGTATTTATT
Found at i:29305350 original size:28 final size:28
Alignment explanation
Indices: 29305306--29305381 Score: 125
Period size: 28 Copynumber: 2.6 Consensus size: 28
29305296 TAATTTTTAT
29305306 TATTTATTATTTATTATTTTATTTTATTAG
1 TATTTATTA-TT-TTATTTTATTTTATTAG
*
29305336 TATTTATTATTTTATTTCATTTTATTAG
1 TATTTATTATTTTATTTTATTTTATTAG
29305364 TATTTATTATTTTATTTT
1 TATTTATTATTTTATTTT
29305382 GTTATTTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 33 0.75
29 2 0.05
30 9 0.20
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (28 bp):
TATTTATTATTTTATTTTATTTTATTAG
Done.