Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 89 of 333
Found at i:27890874 original size:81 final size:81
Alignment explanation
Indices: 27890728--27890914 Score: 245
Period size: 81 Copynumber: 2.3 Consensus size: 81
27890718 GCTCCTCGTT
* *
27890728 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
27890793 ATTTAGTAAC-TCGCA
66 ATATAGTAACTTAGCA
* * **
27890808 CAAATGCCTTCGGGACTTAACCCGGATATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* *
27890872 GGATATGGTCACTTAGCA
64 GGATATAGTAACTTAGCA
27890890 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27890915 CATCATTCAA
Statistics
Matches: 93, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
80 28 0.30
81 57 0.61
82 8 0.09
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCA
Found at i:27890914 original size:40 final size:40
Alignment explanation
Indices: 27890728--27890914 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
27890718 GCTCCTCGTT
* *
27890728 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
27890768 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
27890808 CAAATGCCTTCGGGACTTAACCCGGATATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
27890849 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
27890890 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27890915 CATCATTCAA
Statistics
Matches: 130, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
40 86 0.66
41 44 0.34
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:27898762 original size:41 final size:40
Alignment explanation
Indices: 27898638--27898824 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
27898628 GCTCCTCGTT
* *
27898638 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
27898678 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
27898718 CAAATGCCTTCGGGACTTAACCCGGATATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
27898759 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
27898800 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27898825 CATCATTCAA
Statistics
Matches: 128, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
40 85 0.66
41 43 0.34
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:27898784 original size:81 final size:80
Alignment explanation
Indices: 27898615--27898824 Score: 239
Period size: 81 Copynumber: 2.6 Consensus size: 80
27898605 CCTTCGAAAT
* * * *
27898615 TTAA-CCGGATATAGCT-CCTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 TTAACCCGGATATAG-TAACTCGTACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
27898678 CAAATGCCTTCGGGAC
65 CAAATGCCTTCGGGAC
* * *
27898694 TTAACCCGGATTTAGTAACTCGTACAAATGCCTTCGGGACTTAACCCGGATATTAGTATCTCGCA
1 TTAACCCGGATATAGTAACTCGTACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
27898759 CAAATGCCTTC-GGATC
65 CAAATGCCTTCGGGA-C
** * * * *
27898775 TTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TTAACCCGGATATAGTAAC-TCGTACAAATGCCTTCGGGACTTAGCCCGGA
27898825 CATCATTCAA
Statistics
Matches: 111, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
79 5 0.05
80 42 0.38
81 57 0.51
82 7 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (80 bp):
TTAACCCGGATATAGTAACTCGTACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC
AAATGCCTTCGGGAC
Found at i:27912993 original size:40 final size:40
Alignment explanation
Indices: 27912938--27913129 Score: 314
Period size: 40 Copynumber: 4.8 Consensus size: 40
27912928 CGGATGATAA
27912938 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
27912978 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
* *
27913018 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
* *
27913058 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-T
* *
27913098 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
27913130 AGCTATATCC
Statistics
Matches: 142, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
Found at i:27918586 original size:10 final size:10
Alignment explanation
Indices: 27918573--27918644 Score: 62
Period size: 10 Copynumber: 7.4 Consensus size: 10
27918563 GACATGTGAG
27918573 AAAAAATTAT
1 AAAAAATTAT
*
27918583 AAAAAA-TAG
1 AAAAAATTAT
**
27918592 AAATCA--AT
1 AAAAAATTAT
27918600 A-AAAATTAT
1 AAAAAATTAT
27918609 AAAAAATTAT
1 AAAAAATTAT
*
27918619 TAAAAATTAT
1 AAAAAATTAT
27918629 AAAAAAAATTAT
1 --AAAAAATTAT
27918641 AAAA
1 AAAA
27918645 TGCATCATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
7 2 0.04
8 2 0.04
9 9 0.18
10 27 0.55
12 9 0.18
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:27918644 original size:20 final size:20
Alignment explanation
Indices: 27918599--27918645 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
27918589 TAGAAATCAA
*
27918599 TAAAAATTATAAAAAATTAT
1 TAAAAATTATAAAAAATAAT
27918619 TAAAAATTATAAAAAA-AAT
1 TAAAAATTATAAAAAATAAT
27918638 TATAAAAT
1 TA-AAAAT
27918646 GCATCATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAAATTATAAAAAATAAT
Found at i:27918956 original size:58 final size:56
Alignment explanation
Indices: 27918827--27918965 Score: 142
Period size: 57 Copynumber: 2.4 Consensus size: 56
27918817 GTACAATAAT
* * * *
27918827 TTTTATAATTTTTTCTGTATTTCTAT-ATATTTTATATTTTTAACGATTTTTATAAAA
1 TTTTACAATTTTTTTTATATTTTTATGAT-TTTTATATTTTTAAC-ATTTTTATAAAA
*
27918884 TTTTACAATTTTTTTTATTTTTTTATGATTTTTATAGTTTTTCAA-ATTTTTAATAAAA
1 TTTTACAATTTTTTTTATATTTTTATGATTTTTATA-TTTTT-AACATTTTT-ATAAAA
27918942 -TTTA-AATATATTTTTTATATTTTT
1 TTTTACAAT-T-TTTTTTATATTTTT
27918966 CATTTAAATT
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
56 3 0.04
57 39 0.56
58 26 0.37
59 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (56 bp):
TTTTACAATTTTTTTTATATTTTTATGATTTTTATATTTTTAACATTTTTATAAAA
Found at i:27920793 original size:26 final size:26
Alignment explanation
Indices: 27920737--27920801 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
27920727 TATTGCTTTT
* *
27920737 GAAAAGTAATTTTAAAAAGTATAGTG
1 GAAAAGTACTTTTAAAAAATATAGTG
* *
27920763 AAAAAATACTTTTAAAAAATATTA-TG
1 GAAAAGTACTTTTAAAAAATA-TAGTG
27920789 GAAAAGTACTTTT
1 GAAAAGTACTTTT
27920802 GAGAAGTGCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 30 0.94
27 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.34
Consensus pattern (26 bp):
GAAAAGTACTTTTAAAAAATATAGTG
Found at i:27921195 original size:22 final size:21
Alignment explanation
Indices: 27921145--27921201 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
27921135 GTAATTACAT
27921145 ATTAATACATTTATATTATTTTA
1 ATTAATAC-TTT-TATTATTTTA
* *
27921168 A-AAATACTTTTTTTACTTTTA
1 ATTAATACTTTTATTA-TTTTA
*
27921189 ATTAATAATTTTA
1 ATTAATACTTTTA
27921202 AGGCATTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
20 4 0.15
21 9 0.33
22 13 0.48
23 1 0.04
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTAATACTTTTATTATTTTA
Found at i:27924039 original size:11 final size:11
Alignment explanation
Indices: 27924025--27924064 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
27924015 TATTTTCTCT
*
27924025 CTATTTTGCTA
1 CTATTTTACTA
27924036 CTATTTTACTA
1 CTATTTTACTA
* *
27924047 TTATGTTACTA
1 CTATTTTACTA
27924058 CTATTTT
1 CTATTTT
27924065 GTTGTTATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.57
Consensus pattern (11 bp):
CTATTTTACTA
Found at i:27924316 original size:12 final size:12
Alignment explanation
Indices: 27924286--27924318 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
27924276 TATATATTTT
27924286 AAAATT-ATATA
1 AAAATTAATATA
27924297 AAAA-TAATATA
1 AAAATTAATATA
27924308 AAAATTAATAT
1 AAAATTAATAT
27924319 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:27940537 original size:39 final size:40
Alignment explanation
Indices: 27940321--27940527 Score: 244
Period size: 40 Copynumber: 5.2 Consensus size: 40
27940311 CGGATGATAA
* * *
27940321 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA-ATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGTGACTATA-T
*
27940361 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCT-ACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACTATAT
* *
27940401 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
* * *
27940440 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
* * *
27940480 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
27940520 CC-GGCTAA
1 CCGGGCTAA
27940528 ACTCCGAAGG
Statistics
Matches: 149, Mismatches: 13, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
39 44 0.30
40 101 0.68
41 4 0.03
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
Found at i:27940537 original size:79 final size:80
Alignment explanation
Indices: 27940317--27940527 Score: 295
Period size: 79 Copynumber: 2.7 Consensus size: 80
27940307 TGTTCGGATG
27940317 ATAACCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA-ATTCCGGGCTAAGTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAG-GCATTTGAGCTAGTGGCTATA-TCCGGGCTAAGTCCCGAAGG
*
27940380 CATTCGTGCGAGCTACT
64 CATTCGTGCAAGCTACT
* * * ***
27940397 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-CCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGGCTAAGTCCCGAAGGCA
* *
27940461 TTTGTGCAAGTTACT
66 TTCGTGCAAGCTACT
27940476 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCC-GGCTAA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGGCTAA
27940528 ACTCCGAAGG
Statistics
Matches: 113, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
79 76 0.67
80 34 0.30
81 3 0.03
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGGCTAAGTCCCGAAGGCA
TTCGTGCAAGCTACT
Found at i:27943544 original size:12 final size:12
Alignment explanation
Indices: 27943527--27943552 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27943517 AAAATATAAA
27943527 GGTCGTGATCGT
1 GGTCGTGATCGT
27943539 GGTCGTGATCGT
1 GGTCGTGATCGT
27943551 GG
1 GG
27943553 ACGTAGTTGG
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:0.08, C:0.15, G:0.46, T:0.31
Consensus pattern (12 bp):
GGTCGTGATCGT
Found at i:27944114 original size:24 final size:23
Alignment explanation
Indices: 27944087--27944149 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
27944077 TTTTTTGGCA
27944087 TATTTATGTTATTTTAAATATGTT
1 TATTTAT-TTATTTTAAATATGTT
**
27944111 TATTT-TCTTGATTAAAAAATATGTT
1 TATTTAT-TT-ATT-TTAAATATGTT
27944136 TATTTATTTATTTT
1 TATTTATTTATTTT
27944150 GCAAGTTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
23 3 0.10
24 11 0.35
25 16 0.52
26 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (23 bp):
TATTTATTTATTTTAAATATGTT
Found at i:27947771 original size:145 final size:145
Alignment explanation
Indices: 27947554--27947832 Score: 468
Period size: 145 Copynumber: 1.9 Consensus size: 145
27947544 AACAAAAACG
27947554 TATTTCACCAAAATTATTCTTCACCCATGATCTTGAGAAAAGAGGTGATATAAATGTTCAACAAA
1 TATTTCACCAAAATTATTCTTCACCCATGATCTTGAGAAAAGAGGTGATATAAATGTTCAACAAA
* * *
27947619 TTTGTTCTAGTGAGAATTTAATAGATCTTTTTATTAAGGCATTACCAACTCCAACATTTGAAAGA
66 TTCGTTCTAGTGAGAATTTAACAGATCTTTTTACTAAGGCATTACCAACTCCAACATTTGAAAGA
27947684 CTACAGAACGAAATA
131 CTACAGAACGAAATA
* * *
27947699 TATTTCACCAAAATTATTCTTCACCTATGATCTTGAGAAAAGATGTGCTATAAATGTTCAACAAA
1 TATTTCACCAAAATTATTCTTCACCCATGATCTTGAGAAAAGAGGTGATATAAATGTTCAACAAA
* * * *
27947764 TTCGTTCTAGTGAGAATTTAGCAGATCTTTTTACTAAGGTATTGCCAACTTCAACATTTGAAAGA
66 TTCGTTCTAGTGAGAATTTAACAGATCTTTTTACTAAGGCATTACCAACTCCAACATTTGAAAGA
27947829 CTAC
131 CTAC
27947833 TACACAAGAT
Statistics
Matches: 124, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
145 124 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (145 bp):
TATTTCACCAAAATTATTCTTCACCCATGATCTTGAGAAAAGAGGTGATATAAATGTTCAACAAA
TTCGTTCTAGTGAGAATTTAACAGATCTTTTTACTAAGGCATTACCAACTCCAACATTTGAAAGA
CTACAGAACGAAATA
Found at i:27962952 original size:40 final size:40
Alignment explanation
Indices: 27962866--27963123 Score: 346
Period size: 40 Copynumber: 6.5 Consensus size: 40
27962856 AAGCCAAGTA
* * *
27962866 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
27962904 CCTTCGGGACATAGCCTGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
27962944 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
27962984 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
27963024 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
** *
27963064 CCTTCGGGACTTAAACCGGA-ACTAGTCACTAGCGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATG
27963105 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
27963124 TTATCATCCA
Statistics
Matches: 197, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
38 12 0.06
39 16 0.08
40 143 0.73
41 22 0.11
42 4 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:27971598 original size:20 final size:20
Alignment explanation
Indices: 27971573--27971612 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
27971563 ACCGTGTGTC
27971573 ACACACGGCTGAGACACACA
1 ACACACGGCTGAGACACACA
27971593 ACACACGGCTGAGACACACA
1 ACACACGGCTGAGACACACA
27971613 TCCGTGTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.35, G:0.20, T:0.05
Consensus pattern (20 bp):
ACACACGGCTGAGACACACA
Found at i:27972544 original size:22 final size:23
Alignment explanation
Indices: 27972489--27972586 Score: 87
Period size: 22 Copynumber: 4.3 Consensus size: 23
27972479 GTCATGGTCG
* *
27972489 GTAAGCTCTCTTGAGCTGATAAATA
1 GTAAGCTCTATTGAGCTG--AAACA
*
27972514 GCAAGCTCTATTGAGCTG-AACA
1 GTAAGCTCTATTGAGCTGAAACA
*
27972536 GTAAGCTCT-TTCGAGCTGAATCA
1 GTAAGCTCTATT-GAGCTGAAACA
* *
27972559 GTAA-CTCCAATGAGCTGAAACA
1 GTAAGCTCTATTGAGCTGAAACA
27972581 -TAAGCT
1 GTAAGCT
27972587 TTTATGAGCT
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
21 5 0.08
22 32 0.52
23 8 0.13
25 16 0.26
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (23 bp):
GTAAGCTCTATTGAGCTGAAACA
Found at i:27974814 original size:39 final size:39
Alignment explanation
Indices: 27974778--27974903 Score: 135
Period size: 39 Copynumber: 3.2 Consensus size: 39
27974768 AAGCATATAT
** **
27974778 CAATACTCATATAATTACATAATGTTTGAGCACATATCG
1 CAATACTCATATAATTACATAACATTCAAGCACATATCG
* * * *
27974817 CAATGCTTATATAATCACATAACATTCAAGCATATATCG
1 CAATACTCATATAATTACATAACATTCAAGCACATATCG
* * * * *
27974856 CAATACTCATATAATTAAACAACATTTAAGCATATGTCG
1 CAATACTCATATAATTACATAACATTCAAGCACATATCG
27974895 CAATACTCA
1 CAATACTCA
27974904 AAAACATGTT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (39 bp):
CAATACTCATATAATTACATAACATTCAAGCACATATCG
Found at i:27974890 original size:76 final size:75
Alignment explanation
Indices: 27974748--27974890 Score: 173
Period size: 76 Copynumber: 1.9 Consensus size: 75
27974738 TCACATTACA
* * * ** *
27974748 TATACAATCACATTAAATTTAAGCATATATCAATACTCATATAATTACATAATGTTTGAGCACAT
1 TATACAATCACATTAAATTCAAGCATATATCAATACTCATATAATTAAACAACATTTAAG-ACAT
27974813 ATCGCAATGCT
65 ATCGCAATGCT
*
27974824 TATATAATCACA-TAACATTCAAGCATATATCGCAATACTCATATAATTAAACAACATTTAAG-C
1 TATACAATCACATTAA-ATTCAAGCATATAT--CAATACTCATATAATTAAACAACATTTAAGAC
27974887 ATAT
63 ATAT
27974891 GTCGCAATAC
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
75 3 0.05
76 29 0.51
78 25 0.44
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.33
Consensus pattern (75 bp):
TATACAATCACATTAAATTCAAGCATATATCAATACTCATATAATTAAACAACATTTAAGACATA
TCGCAATGCT
Found at i:27974896 original size:78 final size:76
Alignment explanation
Indices: 27974748--27974898 Score: 187
Period size: 78 Copynumber: 2.0 Consensus size: 76
27974738 TCACATTACA
* * * ** *
27974748 TATACAATCACATTAAATTTAAGCATATATCAATACTCATATAATTACATAATGTTTGAGCACAT
1 TATACAATCACATTAAATTCAAGCATATATCAATACTCATATAATTAAACAACATTTAAGCACAT
27974813 ATCGCAATGCT
66 ATCGCAATGCT
*
27974824 TATATAATCACA-TAACATTCAAGCATATATCGCAATACTCATATAATTAAACAACATTTAAGCA
1 TATACAATCACATTAA-ATTCAAGCATATAT--CAATACTCATATAATTAAACAACATTTAAGCA
* *
27974888 TATGTCGCAAT
63 CATATCGCAAT
27974899 ACTCAAAAAC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
75 3 0.05
76 24 0.38
78 36 0.57
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.32
Consensus pattern (76 bp):
TATACAATCACATTAAATTCAAGCATATATCAATACTCATATAATTAAACAACATTTAAGCACAT
ATCGCAATGCT
Found at i:27976559 original size:105 final size:102
Alignment explanation
Indices: 27976395--27976613 Score: 241
Period size: 105 Copynumber: 2.1 Consensus size: 102
27976385 CATGGCCCTG
* * * ** *
27976395 CCATGGTCTTACACTCATAGTGCTATAACCTAGTTATGGTTTTATTATCAGGATGCCATAGCCCA
1 CCATGGTCTTATACTCATAGTGCCATAACCTAATTATGGTTTTATTATCAAAATACCATAGCCCA
*
27976460 -ACTATGGTTTTACACTTATATACA-TACTGCCATAG-TCCAA
66 GA-TATGGTCTTACA-TT-TA-ACACT-CTGCCAT-GTTCCAA
* *
27976500 CCATGGTCTTATATTCATGGTGCCATAACCTAATTATGGTTTT-TTCA-CTAAAATACCATAGCC
1 CCATGGTCTTATACTCATAGTGCCATAACCTAATTATGGTTTTATT-ATC-AAAATACCATAGCC
*
27976563 CAGATATGGTCTTACATTTAACACTTTGCCATGTTCCAA
64 CAGATATGGTCTTACATTTAACACTCTGCCATGTTCCAA
27976602 CCATGGTCTTAT
1 CCATGGTCTTAT
27976614 CCGTCAATTT
Statistics
Matches: 99, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
101 1 0.01
102 26 0.26
103 3 0.03
104 5 0.05
105 63 0.64
106 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36
Consensus pattern (102 bp):
CCATGGTCTTATACTCATAGTGCCATAACCTAATTATGGTTTTATTATCAAAATACCATAGCCCA
GATATGGTCTTACATTTAACACTCTGCCATGTTCCAA
Found at i:27976721 original size:17 final size:17
Alignment explanation
Indices: 27976701--27976735 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27976691 TCATATTATT
27976701 ACAATAACCATATTTCA
1 ACAATAACCATATTTCA
**
27976718 ACAATAATGATATTTCA
1 ACAATAACCATATTTCA
27976735 A
1 A
27976736 TAACAAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (17 bp):
ACAATAACCATATTTCA
Found at i:27977482 original size:21 final size:21
Alignment explanation
Indices: 27977458--27977497 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
27977448 AAATGTCTAG
27977458 ATTT-CTTTAAATTTCATTTTT
1 ATTTACTTT-AATTTCATTTTT
*
27977479 ATTTACTTTAATTTTATTT
1 ATTTACTTTAATTTCATTT
27977498 ATTTCCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTACTTTAATTTCATTTTT
Found at i:27981137 original size:24 final size:25
Alignment explanation
Indices: 27981083--27981139 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
27981073 GAGGTAGTAC
27981083 AATAGAACAAAGCAAAACAAAACAG
1 AATAGAACAAAGCAAAACAAAACAG
* * **
27981108 AGTAGAACAACGCAATTC-AAACAG
1 AATAGAACAAAGCAAAACAAAACAG
27981132 AATAGAAC
1 AATAGAAC
27981140 CGAATAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.60, C:0.18, G:0.14, T:0.09
Consensus pattern (25 bp):
AATAGAACAAAGCAAAACAAAACAG
Found at i:27986761 original size:73 final size:73
Alignment explanation
Indices: 27986675--27986816 Score: 239
Period size: 73 Copynumber: 1.9 Consensus size: 73
27986665 TATGACAACA
* *
27986675 TGCAAACGCTTTAATTGGGTTTTATTAAAGAATGATTGACAATTTAATTGATGTTATAACATGTG
1 TGCAAACGCTTTAATTGGGTTTTATTAAAGAATGATTGACAATTGAATTGATATTATAACATGTG
27986740 TTTAAACC
66 TTTAAACC
* * *
27986748 TGCAAATGCTTTAATTGGGTTTTATTAAAGAATGATTGACCATTGAATTTATATTATAACATGTG
1 TGCAAACGCTTTAATTGGGTTTTATTAAAGAATGATTGACAATTGAATTGATATTATAACATGTG
27986813 TTTA
66 TTTA
27986817 TGATATGTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (73 bp):
TGCAAACGCTTTAATTGGGTTTTATTAAAGAATGATTGACAATTGAATTGATATTATAACATGTG
TTTAAACC
Found at i:27988517 original size:22 final size:21
Alignment explanation
Indices: 27988492--27988532 Score: 73
Period size: 21 Copynumber: 1.9 Consensus size: 21
27988482 TTATCATTTT
27988492 GAATTTAGGTATCGATACTTTG
1 GAATTT-GGTATCGATACTTTG
27988514 GAATTTGGTATCGATACTT
1 GAATTTGGTATCGATACTT
27988533 GACGATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (21 bp):
GAATTTGGTATCGATACTTTG
Found at i:27995678 original size:48 final size:47
Alignment explanation
Indices: 27995574--27995704 Score: 129
Period size: 48 Copynumber: 2.7 Consensus size: 47
27995564 TATGTGTAAC
* * * * * *
27995574 CGTGTAAGACCATTTCTGGGATATGGCATCGACATTGTTATGTGATCT
1 CGTGTAAGA-CAATTCTAGGACATGGCATTGGCATTGTTATGTGAGCT
*
27995622 CGTATAAGACAAATTCTAGGACATGGCATTGGCATTGTTATGTGAGC-
1 CGTGTAAGAC-AATTCTAGGACATGGCATTGGCATTGTTATGTGAGCT
* * *
27995669 CAGTGTAAGACCATGTCTCGGACTTGGCATTGGCAT
1 C-GTGTAAGACAAT-TCTAGGACATGGCATTGGCAT
27995705 GAGGCATCAT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
47 4 0.06
48 65 0.94
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (47 bp):
CGTGTAAGACAATTCTAGGACATGGCATTGGCATTGTTATGTGAGCT
Found at i:27997615 original size:13 final size:13
Alignment explanation
Indices: 27997597--27997625 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
27997587 GGTTGTTTAT
27997597 TAAACTAATTAAC
1 TAAACTAATTAAC
27997610 TAAACTAATTAAC
1 TAAACTAATTAAC
27997623 TAA
1 TAA
27997626 TCAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:28000490 original size:7 final size:6
Alignment explanation
Indices: 28000473--28000506 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
28000463 AATAAAATTG
*
28000473 AAATGA AAATAAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAAT-AA AAATAA AAATAA AAATAA AAA
28000507 GATAGGAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:28000495 original size:19 final size:19
Alignment explanation
Indices: 28000453--28000506 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
28000443 TATGTCTTTC
*
28000453 AAAA-GAAAATAATAAAATT
1 AAAATGAAAATAA-AAAATA
*
28000472 GAAATGAAAATAAAAAATA
1 AAAATGAAAATAAAAAATA
*
28000491 AAAATAAAAATAAAAA
1 AAAATGAAAATAAAAA
28000507 GATAGGAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (19 bp):
AAAATGAAAATAAAAAATA
Found at i:28006002 original size:13 final size:13
Alignment explanation
Indices: 28005984--28006012 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
28005974 GGTTGTTTAT
28005984 TAAACTAATTAAC
1 TAAACTAATTAAC
28005997 TAAACTAATTAAC
1 TAAACTAATTAAC
28006010 TAA
1 TAA
28006013 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:28012634 original size:187 final size:188
Alignment explanation
Indices: 28012297--28012673 Score: 630
Period size: 187 Copynumber: 2.0 Consensus size: 188
28012287 ACCGTGTAAC
*
28012297 AACCTGTGACTGTGTGTGATAAACCTGCACCAAAATTAAATAGTCCATATGGCCATGTGGTGTGA
1 AACCTGTGACCGTGTGTGATAAACCTGCACCAAAATTAAATAGTCCATATGGCCATGTGGTGTGA
* * * * * * **
28012362 TCGTGGGTGGCACACGACTGTGTGCACCTAAATTAGCTTCCAAAATAAGGCAAACCAACACCAAT
66 CCATGGGTGGCACACGACTGTGTGCACCTAAATTAGATTCAAAAACAAGGCAAACAAACAAAAAT
*
28012427 TTCTTAGGCTCTAAGCCAAACCAAAATCAACCATTAACAGGCCTTTAAAACACATCAA
131 TTCTTAGGCTCTAAGCCAAACCAAAATCAAACATTAACAGGCCTTTAAAACACATCAA
*
28012485 AACCTGTGACCGTGTGTGATAAACCTGCACCAAAATTAAATAGTCCATATGGTCATGTGGTGTGA
1 AACCTGTGACCGTGTGTGATAAACCTGCACCAAAATTAAATAGTCCATATGGCCATGTGGTGTGA
*
28012550 CCAT-GGTGGCATACGACTGTGTGCACCTAAATTAGATTCAAAAACAAGGCAAACAAACAAAAAT
66 CCATGGGTGGCACACGACTGTGTGCACCTAAATTAGATTCAAAAACAAGGCAAACAAACAAAAAT
*
28012614 TTCTTAGGCTCTAAGCCAAACCAAAATCAAACATTAACATGCCTTTAAAACACATCAA
131 TTCTTAGGCTCTAAGCCAAACCAAAATCAAACATTAACAGGCCTTTAAAACACATCAA
28012672 AA
1 AA
28012674 TAAGCTTAAA
Statistics
Matches: 176, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
187 111 0.63
188 65 0.37
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (188 bp):
AACCTGTGACCGTGTGTGATAAACCTGCACCAAAATTAAATAGTCCATATGGCCATGTGGTGTGA
CCATGGGTGGCACACGACTGTGTGCACCTAAATTAGATTCAAAAACAAGGCAAACAAACAAAAAT
TTCTTAGGCTCTAAGCCAAACCAAAATCAAACATTAACAGGCCTTTAAAACACATCAA
Found at i:28016255 original size:29 final size:29
Alignment explanation
Indices: 28016222--28016281 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
28016212 TTACCAAAGT
*
28016222 ATGATTTATGGACTGATTTGAACAATGTA
1 ATGATTTATCGACTGATTTGAACAATGTA
28016251 ATGATTTATCGACTGATTTGAACAATGTA
1 ATGATTTATCGACTGATTTGAACAATGTA
28016280 AT
1 AT
28016282 AATTAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (29 bp):
ATGATTTATCGACTGATTTGAACAATGTA
Found at i:28022954 original size:26 final size:26
Alignment explanation
Indices: 28022918--28022970 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28022908 ATTTGCTTTG
28022918 AGGGCTATGAACACTCAGTTGGCCTT
1 AGGGCTATGAACACTCAGTTGGCCTT
28022944 AGGGCTATGAACACTCAGTTGGCCTT
1 AGGGCTATGAACACTCAGTTGGCCTT
28022970 A
1 A
28022971 TTAGATGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (26 bp):
AGGGCTATGAACACTCAGTTGGCCTT
Found at i:28025819 original size:48 final size:48
Alignment explanation
Indices: 28025767--28025910 Score: 202
Period size: 47 Copynumber: 3.0 Consensus size: 48
28025757 CTATTGGAAA
* *
28025767 CGATCTATGATCCTATGTAAGATCATGTCTGGGACATGGCATTGGCAT
1 CGATCTATGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
*
28025815 CGATCTA-GATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCAT
1 CGATCTATGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
* * * *
28025862 CGATATGTGATCCCATGTAAGACCATAT-TCGGGATATGGCATTGGCAT
1 CGATCTATGATCCCATGTAAGACCATGTCT-GGGACATGGCATTGGCAT
28025910 C
1 C
28025911 CTACCATGTG
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
47 43 0.50
48 43 0.50
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (48 bp):
CGATCTATGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
Found at i:28029748 original size:40 final size:40
Alignment explanation
Indices: 28029666--28029922 Score: 324
Period size: 40 Copynumber: 6.5 Consensus size: 40
28029656 AAGCCAAGTA
* * *
28029666 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
28029704 CCTTCGGGACATAGCCCGGATATAGTAACTTGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
28029744 CCTTCGGGACTTAGCTCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
28029784 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
28029824 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * **
28029864 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGTGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
28029904 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
28029923 TTATCATCCG
Statistics
Matches: 195, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
38 12 0.06
39 16 0.08
40 167 0.86
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:28037904 original size:40 final size:40
Alignment explanation
Indices: 28037844--28038034 Score: 260
Period size: 40 Copynumber: 4.8 Consensus size: 40
28037834 GGATATGGCT
* *
28037844 ACTCGCTC-AATGCCTTCGGGACATAGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
*
28037883 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
28037923 GCTCGCACAAATGCCTTCGGGACTTAGCCCGGATGTAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
28037963 ACTTGCACAAATGCCTTCGGGACTTAGCCCAGA-ACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTA
* *
28038003 ACTAGCGCAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
28038035 TTATCATCCG
Statistics
Matches: 135, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 7 0.05
40 128 0.95
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:28046335 original size:40 final size:40
Alignment explanation
Indices: 28046280--28046355 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
28046270 CCGATACCTG
*
28046280 TGTAGTTACATCCTGACTGTCTGCTTGTGTGAGTAGCCCA
1 TGTAGTTACATCCTGACTGTCAGCTTGTGTGAGTAGCCCA
*
28046320 TGTAGTTACGTCCTGACTGTCAGCTTGTGTGAGTAG
1 TGTAGTTACATCCTGACTGTCAGCTTGTGTGAGTAG
28046356 GCCCGTGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.36
Consensus pattern (40 bp):
TGTAGTTACATCCTGACTGTCAGCTTGTGTGAGTAGCCCA
Found at i:28049479 original size:40 final size:40
Alignment explanation
Indices: 28049442--28049626 Score: 189
Period size: 40 Copynumber: 4.7 Consensus size: 40
28049432 GCTACTCGTT
*
28049442 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* * * *
28049482 CAATTGCCTTCGGGACTTAACCTGGATTTAGTAACTCGCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
28049522 CAAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
28049561 CAAATGCCTTC-GGATCTTAGTCCGGGTATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28049602 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28049627 CATCATTCAA
Statistics
Matches: 117, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
38 2 0.02
39 30 0.26
40 72 0.62
41 13 0.11
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28062051 original size:20 final size:20
Alignment explanation
Indices: 28062022--28062072 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
28062012 CGAGCTGAGG
28062022 ACAC-GGCGTGTCCCAAGCC
1 ACACGGGCGTGTCCCAAGCC
28062041 ACACGGGCGTGTCCCAAGCC
1 ACACGGGCGTGTCCCAAGCC
* *
28062061 ATAGGGGCGTGT
1 ACACGGGCGTGT
28062073 GTAACTACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.14
Consensus pattern (20 bp):
ACACGGGCGTGTCCCAAGCC
Found at i:28062908 original size:22 final size:23
Alignment explanation
Indices: 28062862--28062908 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
28062852 GGAAAGACAG
* * *
28062862 TTTTCTATACTTATGTATGTTCT
1 TTTTCTATACTTAGGTAAGTGCT
28062885 TTTTCTATACTTAGGTAAG-GCT
1 TTTTCTATACTTAGGTAAGTGCT
28062907 TT
1 TT
28062909 GATCCTCCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (23 bp):
TTTTCTATACTTAGGTAAGTGCT
Found at i:28063821 original size:18 final size:18
Alignment explanation
Indices: 28063798--28063840 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
28063788 AATATTTAAA
28063798 GAATAAAAGATAACTTTG
1 GAATAAAAGATAACTTTG
28063816 GAATAAAAGATAACTTTG
1 GAATAAAAGATAACTTTG
*
28063834 GTATAAA
1 GAATAAA
28063841 TGACTTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28
Consensus pattern (18 bp):
GAATAAAAGATAACTTTG
Found at i:28064106 original size:43 final size:43
Alignment explanation
Indices: 28063999--28064092 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 43
28063989 TTAATAACTT
* *
28063999 ATATCTATCATATCATAACTTACATAACTTACATAATACATAA
1 ATATATATTATATCATAACTTACATAACTTACATAATACATAA
*
28064042 ATATATATTATATCATAACTTACATAACTTA-ATTATACTTATAA
1 ATATATATTATATCATAACTTACATAACTTACATAATAC--ATAA
28064086 ATATATA
1 ATATATA
28064093 ACTTATTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 6 0.13
43 29 0.63
44 11 0.24
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (43 bp):
ATATATATTATATCATAACTTACATAACTTACATAATACATAA
Found at i:28064135 original size:28 final size:24
Alignment explanation
Indices: 28064065--28064121 Score: 105
Period size: 24 Copynumber: 2.3 Consensus size: 24
28064055 CATAACTTAC
28064065 ATAACTTAATTATACTTATAAATAT
1 ATAACTT-ATTATACTTATAAATAT
28064090 ATAACTTATTATACTTATAAATAT
1 ATAACTTATTATACTTATAAATAT
28064114 ATAACTTA
1 ATAACTTA
28064122 CTTGTGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 25 0.78
25 7 0.22
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAACTTATTATACTTATAAATAT
Found at i:28070055 original size:49 final size:49
Alignment explanation
Indices: 28069999--28070603 Score: 937
Period size: 49 Copynumber: 12.6 Consensus size: 49
28069989 TATTTGAATA
*
28069999 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
28070048 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGACCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
28070097 AAAGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
28070146 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
28070193 AATGTAAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28070242 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
28070291 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
28070338 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28070387 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * * *
28070436 AATGTGAAAGTG--TATATGTGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28070483 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * * *
28070530 AATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
28070577 GATGTGAAAGTGTATA-A-ATGTGATAAG
1 AATGTGAAAGTGTATATATATGTGATAAG
28070604 TCCCGAAGGG
Statistics
Matches: 520, Mismatches: 30, Indels: 14
0.92 0.05 0.02
Matches are distributed among these distances:
47 227 0.44
48 1 0.00
49 292 0.56
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (49 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:28070187 original size:145 final size:145
Alignment explanation
Indices: 28069999--28070603 Score: 1002
Period size: 145 Copynumber: 4.2 Consensus size: 145
28069989 TATTTGAATA
*
28069999 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
* *
28070064 TATATGTGATAAGGCCGAATGACCAATGTGATGAAAGTGAAAGTGTATATATATGTGATAAGGCC
64 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
28070129 TAATGGCCGATGTGATG
129 TAATGGCCGATGTGATG
*
28070146 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTAAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
28070211 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
66 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
28070276 ATGGCCGATGTGATG
131 ATGGCCGATGTGATG
28070291 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
28070356 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
66 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
28070421 ATGGCCGATGTGATG
131 ATGGCCGATGTGATG
* * * *
28070436 AATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
* * * * *
28070499 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCCGA
66 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
* * *
28070562 GTGGCCAACGTGATG
131 ATGGCCGATGTGATG
* *
28070577 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
28070604 TCCCGAAGGG
Statistics
Matches: 438, Mismatches: 20, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
141 53 0.12
143 45 0.10
145 328 0.75
147 12 0.03
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (145 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
ATGGCCGATGTGATG
Found at i:28070188 original size:96 final size:97
Alignment explanation
Indices: 28069999--28070603 Score: 949
Period size: 96 Copynumber: 6.3 Consensus size: 97
28069989 TATTTGAATA
28069999 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG-ATA
*
28070064 TATATGTGATAAGGCCGAATGACCAATGTGATG
65 TATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28070097 AAAGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TAT
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGATAT
28070161 ATATGTGATAAGGCCGAATGGCCAATGTGATG
66 ATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28070193 AATGTAAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG-ATA
* *
28070258 TATATGTGATAAGGCCTAATGGCCGATGTGATG
65 TATATGTGATAAGGCCGAATGGCCAATGTGATG
*
28070291 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG-ATA
28070354 TATATGTGATAAGGCCGAATGGCCAATGTGATG
65 TATATGTGATAAGGCCGAATGGCCAATGTGATG
*
28070387 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TAT
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGATAT
* * * *
28070451 ATGTGTGATAAGGCCTAATAGCCGATGTGATG
66 ATATGTGATAAGGCCGAATGGCCAATGTGATG
*
28070483 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TAT
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGATAT
* * * *
28070545 ATATGTGACAGGGCCGAGTGGCCAACGTGATG
66 ATATGTGATAAGGCCGAATGGCCAATGTGATG
*
28070577 GATGTGAAAGTGTATA-A-ATGTGATAAG
1 AATGTGAAAGTGTATATATATGTGATAAG
28070604 TCCCGAAGGG
Statistics
Matches: 474, Mismatches: 27, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
94 95 0.20
95 1 0.00
96 230 0.49
98 148 0.31
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (97 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGATAT
ATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:28073760 original size:13 final size:14
Alignment explanation
Indices: 28073744--28073772 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28073734 TTTTAAATAT
28073744 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
28073757 TTATAATGGTTTAA
1 TTATAATGGTTTAA
28073771 TT
1 TT
28073773 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:28074608 original size:43 final size:43
Alignment explanation
Indices: 28074556--28074899 Score: 206
Period size: 43 Copynumber: 8.1 Consensus size: 43
28074546 GAATGGTACT
*
28074556 TTTAATGGCGTTTGTGATAAAAGCACCGCTAAAGGT-ACTATTC
1 TTTAGTGGCGTTTGTGATAAAAGCACCGCTAAAGGTCA-TATTC
* * * *
28074599 TTTAGTGGCGTTTGTGAAAAAAACACCGCTAAAAGTCATGCTT-
1 TTTAGTGGCGTTTGTGATAAAAGCACCGCTAAAGGTCAT-ATTC
* *** * *
28074642 TATAGCAACGTTTGTTTG-TAAAA-CCCCGCTAAAGGTCATGTTC
1 TTTAGTGGCGTTTG--TGATAAAAGCACCGCTAAAGGTCATATTC
* * * * * *
28074685 TTCAGCGGCGTTTGTGATAAAAGCGCCGATAAAGGACATGTTC
1 TTTAGTGGCGTTTGTGATAAAAGCACCGCTAAAGGTCATATTC
* ** * * * * * * *
28074728 TATAGCAGCATTTGTAAAAAAAACGCCGCTAAAGGGCATGTTC
1 TTTAGTGGCGTTTGTGATAAAAGCACCGCTAAAGGTCATATTC
* * * *
28074771 TTTAGCGGCGTTTGTGATAAAAGCATCGCTAAAGTTCATGTTC
1 TTTAGTGGCGTTTGTGATAAAAGCACCGCTAAAGGTCATATTC
* * *
28074814 -----TGGCATTTGTGATAAAAGCGCCGCTAAAGGTCATGTT-
1 TTTAGTGGCGTTTGTGATAAAAGCACCGCTAAAGGTCATATTC
** * * *
28074851 TTATAGCAGCTTTTGTGGGT-AAAGCACCGCTAAAGGTCATGTTC
1 TT-TAGTGGCGTTTGT-GATAAAAGCACCGCTAAAGGTCATATTC
28074895 TTTAG
1 TTTAG
28074900 CGGTGTTTTT
Statistics
Matches: 237, Mismatches: 49, Indels: 30
0.75 0.16 0.09
Matches are distributed among these distances:
38 32 0.14
41 2 0.01
42 7 0.03
43 183 0.77
44 11 0.05
45 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (43 bp):
TTTAGTGGCGTTTGTGATAAAAGCACCGCTAAAGGTCATATTC
Found at i:28074671 original size:86 final size:86
Alignment explanation
Indices: 28074581--28074900 Score: 255
Period size: 86 Copynumber: 3.8 Consensus size: 86
28074571 GATAAAAGCA
* * * * *
28074581 CCGCTAAAGGT-ACTATTCTTTAGTGGCGTTTGTGAAAAAAACACCGCTAAAAGTCATGCTT-TA
1 CCGCTAAAGGTCA-TGTTCTTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAAGACATG-TTCTA
* ****
28074644 TAGCAACGTTTGTTTGTAAAACC
64 TAGCAACATTTGTAAAAAAAACC
* * * *
28074667 CCGCTAAAGGTCATGTTCTTCAGCGGCGTTTGTGATAAAAGCGCCGATAAAGGACATGTTCTATA
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAAGACATGTTCTATA
* *
28074732 GCAGCATTTGTAAAAAAAACG
66 GCAACATTTGTAAAAAAAACC
* * *
28074753 CCGCTAAAGGGCATGTTCTTTAGCGGCGTTTGTGATAAAAGCATCGCT-AAAGTTCATGTTC--T
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAAG-ACATGTTCTAT
* * * * *
28074815 -G--GCATTTGTGATAAAAGCG
65 AGCAACATTTGTAAAAAAAACC
* * * * * *
28074834 CCGCTAAAGGTCATGTT-TTATAGCAGCTTTTGTGGGT-AAAGCACCGCTAAAGGTCATGTTCTT
1 CCGCTAAAGGTCATGTTCTT-TAGCGGCGTTTGT-GATAAAAGCACCGCTAAAAGACATGTTCTA
28074897 TAGC
64 TAGC
28074901 GGTGTTTTTT
Statistics
Matches: 192, Mismatches: 32, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
80 2 0.01
81 60 0.31
82 5 0.03
83 2 0.01
84 2 0.01
85 5 0.03
86 115 0.60
87 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (86 bp):
CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAAGACATGTTCTATA
GCAACATTTGTAAAAAAAACC
Found at i:28074783 original size:129 final size:124
Alignment explanation
Indices: 28074561--28074907 Score: 351
Period size: 129 Copynumber: 2.8 Consensus size: 124
28074551 GTACTTTTAA
* * * ** *
28074561 TGGCGTTTGTGATAAAAGCACCGCTAAAGGTAC-TATTCTTTAGTGGCGTTTGTGAAAAAAACAC
1 TGGCGTTTGTGATAAAAGCGCCGCTAAAGG-ACATGTTCTATAGCAGCATTTGTGAAAAAAACAC
* * ** *
28074625 CGCTAAAAGTCATGCTT-TATAGCAACGTTTGTTTG-TAAAA-CCCCGCTAAAGGTCATGTTC
65 CGCTAAAGGTCATG-TTCTTTAGCGGCGTTTG--TGATAAAAGCACCGCTAAAGGTCATGTTC
* *
28074685 TTCAGCGGCGTTTGTGATAAAAGCGCCGATAAAGGACATGTTCTATAGCAGCATTTGTAAAAAAA
1 -T----GGCGTTTGTGATAAAAGCGCCGCTAAAGGACATGTTCTATAGCAGCATTTGTGAAAAAA
* * * *
28074750 ACGCCGCTAAAGGGCATGTTCTTTAGCGGCGTTTGTGATAAAAGCATCGCTAAAGTTCATGTTC
61 ACACCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCATGTTC
* * * * *** *
28074814 TGGCATTTGTGATAAAAGCGCCGCTAAAGGTCATGTTTTATAGCAGCTTTTGTGGGTAAAGCACC
1 TGGCGTTTGTGATAAAAGCGCCGCTAAAGGACATGTTCTATAGCAGCATTTGTGAAAAAAACACC
*
28074879 GCTAAAGGTCATGTTCTTTAGCGGTGTTT
66 GCTAAAGGTCATGTTCTTTAGCGGCGTTT
28074908 TTTCACATAA
Statistics
Matches: 184, Mismatches: 30, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
124 80 0.43
125 1 0.01
127 2 0.01
128 10 0.05
129 91 0.49
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (124 bp):
TGGCGTTTGTGATAAAAGCGCCGCTAAAGGACATGTTCTATAGCAGCATTTGTGAAAAAAACACC
GCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCATGTTC
Found at i:28074875 original size:81 final size:81
Alignment explanation
Indices: 28074661--28074895 Score: 249
Period size: 81 Copynumber: 2.8 Consensus size: 81
28074651 GTTTGTTTGT
* * * * * * *
28074661 AAAACCCCGCTAAAGGTCATGTTCTTCAGCGGCGTTTGTGATAAAAGCGCCGATAAAGGACATGT
1 AAAACGCCGCTAAAGGGCATGTTCTTTAGCAGCGTTTGTGATAAAAGCACCGCTAAAGGTCATGT
28074726 TCTATAGCAGCATTTGTAAAA
66 TC--T-G--GCATTTGTAAAA
* * *
28074747 AAAACGCCGCTAAAGGGCATGTTCTTTAGCGGCGTTTGTGATAAAAGCATCGCTAAAGTTCATGT
1 AAAACGCCGCTAAAGGGCATGTTCTTTAGCAGCGTTTGTGATAAAAGCACCGCTAAAGGTCATGT
* *
28074812 TCTGGCATTTGTGATA
66 TCTGGCATTTGTAAAA
* * * *
28074828 AAAGCGCCGCTAAAGGTCATGTT-TTATAGCAGCTTTTGTGGGT-AAAGCACCGCTAAAGGTCAT
1 AAAACGCCGCTAAAGGGCATGTTCTT-TAGCAGCGTTTGT-GATAAAAGCACCGCTAAAGGTCAT
28074891 GTTCT
64 GTTCT
28074896 TTAGCGGTGT
Statistics
Matches: 130, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
80 2 0.02
81 65 0.50
82 2 0.02
83 1 0.01
84 1 0.01
86 59 0.45
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (81 bp):
AAAACGCCGCTAAAGGGCATGTTCTTTAGCAGCGTTTGTGATAAAAGCACCGCTAAAGGTCATGT
TCTGGCATTTGTAAAA
Found at i:28076171 original size:25 final size:26
Alignment explanation
Indices: 28076143--28076196 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
28076133 TAATTAGTAT
*
28076143 AAAATATT-AATAATTGAAT-AAATTG
1 AAAA-ATTAAATAATTAAATAAAATTG
28076168 AAAAATTAAATAATTAAATAAAATTG
1 AAAAATTAAATAATTAAATAAAATTG
28076194 AAA
1 AAA
28076197 TTTAGGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 3 0.12
25 14 0.54
26 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (26 bp):
AAAAATTAAATAATTAAATAAAATTG
Found at i:28076963 original size:31 final size:31
Alignment explanation
Indices: 28076904--28076963 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
28076894 CCTTTCAAAA
* * *
28076904 ATATTTACAAAAAGAGGCATCTATTTTTGTT
1 ATATTTACAAAAAGAGGCACCAAATTTTGTT
28076935 ATATTTACAAAAAGA-GCAACCAAATTTTG
1 ATATTTACAAAAAGAGGC-ACCAAATTTTG
28076964 AAAATAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (31 bp):
ATATTTACAAAAAGAGGCACCAAATTTTGTT
Found at i:28079434 original size:42 final size:42
Alignment explanation
Indices: 28079321--28079436 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 42
28079311 GACATCTGTC
* * *
28079321 TGAGATGTCGTGTAAGACCGTGTCTGGGACACAAGCCTCGAT
1 TGAGATTTCGTGTAAGACCATGTCTGGGACACAAGCATCGAT
* *
28079363 TGAGATTTACATATAAGACCATGTCTGGGACATCAA-CATCGTAT
1 TGAGATTT-CGTGTAAGACCATGTCTGGGACA-CAAGCATCG-AT
* *
28079407 T-TGATTTCGTGTAAGACCCTGTCTGGGACA
1 TGAGATTTCGTGTAAGACCATGTCTGGGACA
28079437 GAGGCATTGA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
42 27 0.44
43 29 0.47
44 6 0.10
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (42 bp):
TGAGATTTCGTGTAAGACCATGTCTGGGACACAAGCATCGAT
Found at i:28086628 original size:42 final size:42
Alignment explanation
Indices: 28086525--28086641 Score: 123
Period size: 43 Copynumber: 2.8 Consensus size: 42
28086515 TGAGACATCA
* *
28086525 TGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAGATTTACG
1 TGTAAGACCATGTCTGGGACACAGGCATCGATT-AGATTTACG
*
28086568 TATAAGACCATGTCTGGGACATCA-GCATCGTATCT-GATTT-CG
1 TGTAAGACCATGTCTGGGACA-CAGGCATCG-AT-TAGATTTACG
* * *
28086610 TGTAAGACCCTGTCTGGGATAGAGGCATCGAT
1 TGTAAGACCATGTCTGGGACACAGGCATCGAT
28086642 ATTGAATTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
41 3 0.05
42 26 0.41
43 29 0.46
44 4 0.06
45 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACACAGGCATCGATTAGATTTACG
Found at i:28095394 original size:46 final size:46
Alignment explanation
Indices: 28095344--28095519 Score: 223
Period size: 46 Copynumber: 3.8 Consensus size: 46
28095334 TGGTTGAGCA
*
28095344 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*** *
28095390 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GAA--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
*
28095437 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
28095483 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28095520 GCGGGTTGCA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 1 0.01
46 68 0.61
47 32 0.29
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28095502 original size:93 final size:93
Alignment explanation
Indices: 28095343--28095511 Score: 302
Period size: 93 Copynumber: 1.8 Consensus size: 93
28095333 ATGGTTGAGC
* *
28095343 ATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGTTG
28095408 AGTCCGAGTTCGAGAGATGTAACTAGGA
66 AGTCCGAGTTCGAGAGATGTAACTAGGA
* *
28095436 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGTTG
28095501 AGTCCGAGTTC
66 AGTCCGAGTTC
28095512 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGTTG
AGTCCGAGTTCGAGAGATGTAACTAGGA
Found at i:28098502 original size:15 final size:15
Alignment explanation
Indices: 28098464--28098507 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
28098454 TATAGTATCG
* *
28098464 TATCTTGGGTTTCTT
1 TATCTTGGATTTCTC
28098479 TAT-TCTGGATTTCTC
1 TATCT-TGGATTTCTC
28098494 TATCTTGGATTTCT
1 TATCTTGGATTTCT
28098508 TTATTCGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Found at i:28100961 original size:46 final size:45
Alignment explanation
Indices: 28100911--28101086 Score: 221
Period size: 46 Copynumber: 3.8 Consensus size: 45
28100901 TGGTTGAGCA
28100911 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** *
28100957 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GAA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
28101004 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
28101050 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28101087 GCGGGTTACA
Statistics
Matches: 113, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 1 0.01
46 69 0.61
47 32 0.28
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:28101069 original size:93 final size:93
Alignment explanation
Indices: 28100910--28101078 Score: 302
Period size: 93 Copynumber: 1.8 Consensus size: 93
28100900 ATGGTTGAGC
* *
28100910 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTG
28100975 AGTCCGAGTTCGAGAGATGTAACTAGGA
66 AGTCCGAGTTCGAGAGATGTAACTAGGA
* *
28101003 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTG
28101068 AGTCCGAGTTC
66 AGTCCGAGTTC
28101079 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTG
AGTCCGAGTTCGAGAGATGTAACTAGGA
Found at i:28106267 original size:13 final size:13
Alignment explanation
Indices: 28106248--28106278 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28106238 GGGTTTGTTT
28106248 ACTAAACTAATTA
1 ACTAAACTAATTA
*
28106261 TCTAAACTAATTA
1 ACTAAACTAATTA
28106274 ACTAA
1 ACTAA
28106279 TTTAATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
ACTAAACTAATTA
Found at i:28130224 original size:20 final size:21
Alignment explanation
Indices: 28130199--28130237 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28130189 CAAAGCAAAT
28130199 AAGGGC-ACACGCCCGTGTAA
1 AAGGGCGACACGCCCGTGTAA
28130219 AAGGGCGACACGCCCGTGT
1 AAGGGCGACACGCCCGTGT
28130238 GTCTTCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.26, C:0.31, G:0.33, T:0.10
Consensus pattern (21 bp):
AAGGGCGACACGCCCGTGTAA
Found at i:28131528 original size:48 final size:48
Alignment explanation
Indices: 28131476--28131794 Score: 379
Period size: 48 Copynumber: 6.6 Consensus size: 48
28131466 ATGTCGAGGT
* * * * * *
28131476 CGATGCCATGTCCCAGACATGGTCTTAAACTGGCTTTCATAATATCAC
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTAC
* *
28131524 CGATGCCATGTTCCAAACATGGTCTTACACTGCCTCTCATAACATTGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTAC
* * * * *
28131572 CAATGCCATGATCCAAACATGGTCTTACATTAGCTCTCATAACATTTC
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTAC
* * * *
28131620 CGATGCAATGTTCCAATCATGGTCTTACACTGGCTCTTATAACATTAT
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTAC
28131668 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTAC
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTAC
* * *** **
28131716 TGATGCCATGTTTCAAAACATGGTCTTACACT-GCTCTCATAGTGTGGC
1 CGATGCCATG-TTCCAAACATGGTCTTACACTGGCTCTCATAACATTAC
* * *
28131764 CAATGTCATGTCCCAAACATGGTCTTACACT
1 CGATGCCATGTTCCAAACATGGTCTTACACT
28131795 AACACACATA
Statistics
Matches: 231, Mismatches: 39, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
47 19 0.08
48 192 0.83
49 20 0.09
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (48 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTAC
Found at i:28138690 original size:54 final size:54
Alignment explanation
Indices: 28138512--28138713 Score: 228
Period size: 54 Copynumber: 3.7 Consensus size: 54
28138502 ACTTACCATA
* * * *
28138512 GCCATGTCTTGACATGGTCTTACGTGGTATCCTTACCTTAT-AAACTCACCAAT
1 GCCATGCCTTGACATGGTCTTACATGATATCCTTACCTTATAAAACTCATCAAT
* ** ** * *
28138565 GCCATGCCTTGGCATGGTCTTTTATGGGA-CCTTTTCCTTATAGTAACTCATCAAT
1 GCCATGCCTTGACATGGTCTTACATGATATCC-TTACCTTATA-AAACTCATCAAT
* * * *
28138620 GCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTATAAAATTTATCAAT
1 GCCATGCCTTGACATGGTCTTACATGATATCCTTACCTTATAAAACTCATCAAT
*
28138674 GCCATGCCTTGGCATGGTCTTACATGATATCCTTACCTTA
1 GCCATGCCTTGACATGGTCTTACATGATATCCTTACCTTA
28138714 CCAAATGCCA
Statistics
Matches: 122, Mismatches: 23, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
52 2 0.02
53 31 0.25
54 46 0.38
55 41 0.34
56 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.37
Consensus pattern (54 bp):
GCCATGCCTTGACATGGTCTTACATGATATCCTTACCTTATAAAACTCATCAAT
Found at i:28138807 original size:47 final size:47
Alignment explanation
Indices: 28138686--28138807 Score: 199
Period size: 47 Copynumber: 2.6 Consensus size: 47
28138676 CATGCCTTGG
* *
28138686 CATGGTCTTACATGATATCCTTACCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
*
28138733 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
* *
28138780 CATGGTTTTACATGGTATCCCTATCTTA
1 CATGGTCTTACATGGTATCCTTATCTTA
28138808 GTGCCAATGC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.35
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
Found at i:28146633 original size:48 final size:48
Alignment explanation
Indices: 28146472--28146789 Score: 354
Period size: 48 Copynumber: 6.7 Consensus size: 48
28146462 GGGTAATTTA
* * ** **
28146472 CCGATGCCATG-TCTCAGACATGGTCTTACACTGG-TCACATGTCAAGG
1 CCGATGCCATGTTC-CAAACATGGTCTTACACTGGCTCTCATAACATTG
* * *
28146519 CCGATGCCATGTCCCAAATATGGTCTTACACTGGCTC-GATAACATTG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTG
**
28146566 CCGATGCCATGTTATAAACATGGTCTTACACTGGCTCTCATAACATTG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTG
* * * *
28146614 TCGATGTCATGCTCCAAACATGATCTTACACTGGCTCTCATAACATTG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTG
* *
28146662 CCGATGCCATGTTCCAAACAAGGTCTTATACTGGCTCTCATAACATTG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTG
* ** * * ** *
28146710 CTGATGATATGTTCAAAACATGGTCTTACACTGGCTCACATAATGTGG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTG
* * *
28146758 CCAATGCCATGTCCCAGACATGGTCTTACACT
1 CCGATGCCATGTTCCAAACATGGTCTTACACT
28146790 AGCACACATA
Statistics
Matches: 226, Mismatches: 42, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
47 67 0.30
48 159 0.70
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (48 bp):
CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACATTG
Found at i:28146658 original size:25 final size:24
Alignment explanation
Indices: 28146582--28146659 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
28146572 CCATGTTATA
28146582 AACATGGTCTTACACTGGCTCTCAT
1 AACAT-GTCTTACACTGGCTCTCAT
28146607 AACATTGTCGATGT-CA-T-GCTC-CA-
1 AACA-TGTC--T-TACACTGGCTCTCAT
28146630 AACATGATCTTACACTGGCTCTCAT
1 AACATG-TCTTACACTGGCTCTCAT
28146655 AACAT
1 AACAT
28146660 TGCCGATGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 20
0.68 0.00 0.32
Matches are distributed among these distances:
20 1 0.02
21 3 0.07
22 3 0.07
23 10 0.23
24 4 0.09
25 16 0.37
26 2 0.05
27 3 0.07
28 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (24 bp):
AACATGTCTTACACTGGCTCTCAT
Found at i:28155818 original size:65 final size:65
Alignment explanation
Indices: 28155714--28155846 Score: 266
Period size: 65 Copynumber: 2.0 Consensus size: 65
28155704 CCTAAACTTT
28155714 CTTGATATAAAATTCTAAATAACTTAAAATATCCAAAATTTGAAATAAATAAATAAATAATAAAA
1 CTTGATATAAAATTCTAAATAACTTAAAATATCCAAAATTTGAAATAAATAAATAAATAATAAAA
28155779 CTTGATATAAAATTCTAAATAACTTAAAATATCCAAAATTTGAAATAAATAAATAAATAATAAAA
1 CTTGATATAAAATTCTAAATAACTTAAAATATCCAAAATTTGAAATAAATAAATAAATAATAAAA
28155844 CTT
1 CTT
28155847 AATCAATGCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (65 bp):
CTTGATATAAAATTCTAAATAACTTAAAATATCCAAAATTTGAAATAAATAAATAAATAATAAAA
Found at i:28160427 original size:88 final size:89
Alignment explanation
Indices: 28160313--28160509 Score: 258
Period size: 88 Copynumber: 2.2 Consensus size: 89
28160303 AAGTAATTAG
* * *
28160313 GTTTTTTTTT--ACTTAATTAGATACTTGAACTTTCAAATTACACCAAAAAGCTC-TCAAACTTT
1 GTTTTTTTTTACACTCAATTAGATACTTGAACTGTCAAAATACACCAAAAAGCTCTTCAAACTTT
*
28160375 TTCAAAGAAAACAATTAAGC-CTTT
66 TTCAAA-AAAACAATAAAGCTCTTT
** * *
28160399 GTTTTTTTTTACACTCAATTAGATACTTGAACTGTCAAAATACATTAAAAAGGTCTTCAAATTTT
1 GTTTTTTTTTACACTCAATTAGATACTTGAACTGTCAAAATACACCAAAAAGCTCTTCAAACTTT
*
28160464 TTCAAAAAAGCAATAAAGCTCTTT
66 TTCAAAAAAACAATAAAGCTCTTT
*
28160488 CTTTGTTTTTTACACTCAATTA
1 GTTT-TTTTTTACACTCAATTA
28160510 TTAATATGCA
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
86 10 0.10
88 48 0.50
89 21 0.22
90 17 0.18
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (89 bp):
GTTTTTTTTTACACTCAATTAGATACTTGAACTGTCAAAATACACCAAAAAGCTCTTCAAACTTT
TTCAAAAAAACAATAAAGCTCTTT
Found at i:28160657 original size:19 final size:18
Alignment explanation
Indices: 28160624--28160688 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 18
28160614 ACGATAAAAA
*
28160624 ATAAAAATCAATAAAAGTT
1 ATAAAAAT-GATAAAAGTT
*
28160643 ATAAAAATGATTAAA-TT
1 ATAAAAATGATAAAAGTT
* *
28160660 TTAATAAAATAGAAAAAAGTT
1 AT-A-AAAAT-GATAAAAGTT
28160681 ATAAAAAT
1 ATAAAAAT
28160689 AGTAAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
17 3 0.08
18 6 0.17
19 18 0.50
20 6 0.17
21 3 0.08
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (18 bp):
ATAAAAATGATAAAAGTT
Found at i:28160686 original size:18 final size:18
Alignment explanation
Indices: 28160663--28160821 Score: 72
Period size: 19 Copynumber: 8.3 Consensus size: 18
28160653 TTAAATTTTA
*
28160663 ATAAAATAG-AAAAAAGTT
1 ATAAAATAGTAAAAAA-AT
28160681 ATAAAAATAGTAAAAAAAT
1 AT-AAAATAGTAAAAAAAT
** *
28160700 ATAAAATTTTATAAAAAT
1 ATAAAATAGTAAAAAAAT
*
28160718 CATAAAATA-TATAGAAATAT
1 -ATAAAATAGTA-A-AAAAAT
* *
28160738 AGAAAAATA-TATAAAAATTT
1 A-TAAAATAGTA-AAAAA-AT
** *
28160758 ATAATGTAGTAAGAAAAT
1 ATAAAATAGTAAAAAAAT
* *
28160776 GATAAAAAATGTAAAGAAAT
1 -ATAAAATA-GTAAAAAAAT
*
28160796 ATAAAATTCGTAAAAAAATT
1 ATAAAA-TAGTAAAAAAA-T
28160816 ATAAAA
1 ATAAAA
28160822 ATTATCATAC
Statistics
Matches: 106, Mismatches: 23, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
18 18 0.17
19 48 0.45
20 40 0.38
ACGTcount: A:0.64, C:0.01, G:0.08, T:0.27
Consensus pattern (18 bp):
ATAAAATAGTAAAAAAAT
Found at i:28160702 original size:19 final size:19
Alignment explanation
Indices: 28160665--28160823 Score: 85
Period size: 20 Copynumber: 8.3 Consensus size: 19
28160655 AAATTTTAAT
*
28160665 AAAATAG-AAAAAAGTTATA
1 AAAATAGTAAAAAA-ATATA
28160684 AAAATAGTAAAAAAATAT-
1 AAAATAGTAAAAAAATATA
** *
28160702 AAAATTTTATAAAAATCATA
1 AAAATAGTAAAAAAAT-ATA
* * *
28160722 AAATATA-TAGAAATATAGA
1 AAA-ATAGTAAAAAAATATA
* *
28160741 AAAATA-TATAAAAATTTA
1 AAAATAGTAAAAAAATATA
** *
28160759 TAATGTAGTAAGAAAATGATA
1 -AAAATAGTAAAAAAAT-ATA
*
28160780 AAAA-ATGTAAAGAAATATA
1 AAAATA-GTAAAAAAATATA
* *
28160799 AAATTCGTAAAAAAATTATA
1 AAAATAGTAAAAAAA-TATA
28160819 AAAAT
1 AAAAT
28160824 TATCATACCA
Statistics
Matches: 105, Mismatches: 25, Indels: 19
0.70 0.17 0.13
Matches are distributed among these distances:
18 24 0.23
19 36 0.34
20 41 0.39
21 4 0.04
ACGTcount: A:0.64, C:0.01, G:0.08, T:0.27
Consensus pattern (19 bp):
AAAATAGTAAAAAAATATA
Found at i:28160717 original size:48 final size:47
Alignment explanation
Indices: 28160645--28160803 Score: 121
Period size: 48 Copynumber: 3.3 Consensus size: 47
28160635 TAAAAGTTAT
*
28160645 AAAAATGATTAAATTTTA-ATAAAATAGAAAAAAGTTATAAAAATAGTAA
1 AAAAAT-ATAAAATTTTATA-AAAATAGAAAAAA-TTATAAAAATAGTAA
* *
28160694 AAAAATATAAAATTTTATAAAAAT-CATAAAATATATAGAAATATAG-AA
1 AAAAATATAAAATTTTATAAAAATAGAAAAAAT-TATA-AAA-ATAGTAA
* * ** *
28160742 AAATATATAAAAATTTAT-AATGTAGTAAGAAAATGATAAAAA-ATGTAA
1 AAAAATATAAAATTTTATAAAAATAG-AA-AAAATTATAAAAATA-GTAA
*
28160790 AGAAATATAAAATT
1 AAAAATATAAAATT
28160804 CGTAAAAAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
46 2 0.02
47 14 0.16
48 52 0.59
49 15 0.17
50 5 0.06
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.29
Consensus pattern (47 bp):
AAAAATATAAAATTTTATAAAAATAGAAAAAATTATAAAAATAGTAA
Found at i:28160723 original size:38 final size:38
Alignment explanation
Indices: 28160681--28160755 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
28160671 GAAAAAAGTT
* * *
28160681 ATAAAA-ATAGTAAAAAAATATAAAATTTTATAAAAATC
1 ATAAAATATA-TAAAAAAATAGAAAAATATATAAAAATC
* *
28160719 ATAAAATATATAGAAATATAGAAAAATATATAAAAAT
1 ATAAAATATATAAAAAAATAGAAAAATATATAAAAAT
28160756 TTATAATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 28 0.90
39 3 0.10
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (38 bp):
ATAAAATATATAAAAAAATAGAAAAATATATAAAAATC
Found at i:28160737 original size:10 final size:10
Alignment explanation
Indices: 28160680--28160761 Score: 73
Period size: 10 Copynumber: 8.5 Consensus size: 10
28160670 AGAAAAAAGT
28160680 TATAAAAATA
1 TATAAAAATA
28160690 GTA-AAAAA-A
1 -TATAAAAATA
* *
28160699 TATAAAATTT
1 TATAAAAATA
28160709 TATAAAAAT-
1 TATAAAAATA
*
28160718 CAT-AAAATA
1 TATAAAAATA
*
28160727 TATAGAAATA
1 TATAAAAATA
*
28160737 TAGAAAAATA
1 TATAAAAATA
*
28160747 TATAAAAATT
1 TATAAAAATA
28160757 TATAA
1 TATAA
28160762 TGTAGTAAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
8 7 0.12
9 9 0.16
10 39 0.68
11 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (10 bp):
TATAAAAATA
Found at i:28161028 original size:19 final size:19
Alignment explanation
Indices: 28160992--28161115 Score: 69
Period size: 19 Copynumber: 6.6 Consensus size: 19
28160982 TAATGCATTC
**
28160992 TATAAATTTTTATGATTTT
1 TATAAATTTTTACAATTTT
*
28161011 TATAAATTTATACAATTTTT
1 TATAAATTTTTACAA-TTTT
* * *
28161031 TATATATTTTTACTATTTA
1 TATAAATTTTTACAATTTT
* *
28161050 TATATA-TATT-CTAATTTT
1 TATAAATTTTTAC-AATTTT
**
28161068 TA-ATTTTTTTA-AATTTT
1 TATAAATTTTTACAATTTT
* * *
28161085 TATTAAAGTTTAATAATTTT
1 TA-TAAATTTTTACAATTTT
28161105 TAT-AATTTTTA
1 TATAAATTTTTA
28161116 TTGATTATTA
Statistics
Matches: 80, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
17 11 0.14
18 18 0.22
19 27 0.34
20 24 0.30
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TATAAATTTTTACAATTTT
Found at i:28161048 original size:20 final size:20
Alignment explanation
Indices: 28161007--28161059 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
28160997 ATTTTTATGA
*
28161007 TTTTTATAAATTTATACAAT
1 TTTTTATATATTTATACAAT
* *
28161027 TTTTTATATATTTTTACTAT
1 TTTTTATATATTTATACAAT
*
28161047 TTATATATATATT
1 TT-TTTATATATT
28161060 CTAATTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTATATATTTATACAAT
Found at i:28161140 original size:8 final size:9
Alignment explanation
Indices: 28160996--28161143 Score: 72
Period size: 9 Copynumber: 16.0 Consensus size: 9
28160986 GCATTCTATA
28160996 AATTTTTAT
1 AATTTTTAT
*
28161005 GATTTTTAT
1 AATTTTTAT
* *
28161014 AAATTTATAC
1 -AATTTTTAT
28161024 AATTTTTTAT
1 AA-TTTTTAT
28161034 ATATTTTTACT
1 A-ATTTTTA-T
*
28161045 -ATTTATAT
1 AATTTTTAT
* *
28161053 -ATATATTCT
1 AAT-TTTTAT
28161062 AA-TTTT-T
1 AATTTTTAT
*
28161069 AATTTTTTT
1 AATTTTTAT
28161078 AAATTTTTATT
1 -AATTTTTA-T
* *
28161089 AAAGTTTAAT
1 -AATTTTTAT
28161099 AATTTTTAT
1 AATTTTTAT
28161108 AATTTTTATT
1 AATTTTTA-T
* *
28161118 GATTATTAT
1 AATTTTTAT
*
28161127 -TTTTTTAT
1 AATTTTTAT
28161135 AATTTTTAT
1 AATTTTTAT
28161144 CACATGTGAC
Statistics
Matches: 106, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
7 3 0.03
8 16 0.15
9 43 0.41
10 34 0.32
11 10 0.09
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
AATTTTTAT
Found at i:28162675 original size:96 final size:96
Alignment explanation
Indices: 28162485--28162723 Score: 388
Period size: 96 Copynumber: 2.5 Consensus size: 96
28162475 GCCTTGTCCT
* * * *
28162485 ACAACGGAACCCCAATACTGTTCTCTTAATGAAGTGTCCTATGAATACACCGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACCGAAGATTCTGAGAC
* *
28162550 CAGGCTTGACGTGGGGCTTCCTGGTTGTGAA
66 CAGGCTTGACGTGAGGCTTCCTGGCTGTGAA
* **
28162581 ACAAAGGAGCCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACATGGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACCGAAGATTCTGAGAC
*
28162646 CAGGCTTGACGTGAGGCTTTCTGGCTGTGAA
66 CAGGCTTGACGTGAGGCTTCCTGGCTGTGAA
28162677 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATA
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATA
28162724 TAGGGAAAAT
Statistics
Matches: 132, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 132 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (96 bp):
ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACCGAAGATTCTGAGAC
CAGGCTTGACGTGAGGCTTCCTGGCTGTGAA
Found at i:28165919 original size:10 final size:10
Alignment explanation
Indices: 28165886--28165929 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
28165876 AAAAGATTAA
28165886 TTTTTATAAT
1 TTTTTATAAT
* *
28165896 ATTTATATATT
1 -TTTTTATAAT
28165907 TTTTTATAAT
1 TTTTTATAAT
28165917 TTTTTATAAT
1 TTTTTATAAT
28165927 TTT
1 TTT
28165930 AAAAAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:28169157 original size:29 final size:30
Alignment explanation
Indices: 28169101--28169161 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
28169091 ATTTCAACAC
*
28169101 TAATCAATGCACAGTTTTTAGGAATTCTAT
1 TAATCAATGCACAGATTTTAGGAATTCTAT
28169131 TAATCAATGCACA-ATTTTAGGAATTCTAT
1 TAATCAATGCACAGATTTTAGGAATTCTAT
28169160 TA
1 TA
28169162 TGACTATGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (30 bp):
TAATCAATGCACAGATTTTAGGAATTCTAT
Found at i:28169706 original size:3 final size:3
Alignment explanation
Indices: 28169698--28169746 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
28169688 AATGATCACT
28169698 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28169746 T
1 T
28169747 GTCCTTTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28170796 original size:37 final size:38
Alignment explanation
Indices: 28170754--28170829 Score: 145
Period size: 37 Copynumber: 2.0 Consensus size: 38
28170744 AAATCACCGA
28170754 ATATGTTTGTACGATGATTTC-AAATCCAAATAAAGGC
1 ATATGTTTGTACGATGATTTCAAAATCCAAATAAAGGC
28170791 ATATGTTTGTACGATGATTTCAAAATCCAAATAAAGGC
1 ATATGTTTGTACGATGATTTCAAAATCCAAATAAAGGC
28170829 A
1 A
28170830 CTAACTGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 21 0.55
38 17 0.45
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (38 bp):
ATATGTTTGTACGATGATTTCAAAATCCAAATAAAGGC
Found at i:28174163 original size:25 final size:25
Alignment explanation
Indices: 28174129--28174178 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
28174119 CGCATGTGAT
*
28174129 TAATGTGTGGATTAGGTGGTTAGGC
1 TAATGTGTGGATTAAGTGGTTAGGC
28174154 TAATGTGTGGATTAAGTGGTTAGGC
1 TAATGTGTGGATTAAGTGGTTAGGC
28174179 AGTTAGTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.04, G:0.38, T:0.36
Consensus pattern (25 bp):
TAATGTGTGGATTAAGTGGTTAGGC
Found at i:28174706 original size:27 final size:28
Alignment explanation
Indices: 28174676--28174734 Score: 111
Period size: 27 Copynumber: 2.1 Consensus size: 28
28174666 AATGACCAAG
28174676 TAACATAACATTTGATATTCAAGACA-C
1 TAACATAACATTTGATATTCAAGACACC
28174703 TAACATAACATTTGATATTCAAGACACC
1 TAACATAACATTTGATATTCAAGACACC
28174731 TAAC
1 TAAC
28174735 TTATCACTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (28 bp):
TAACATAACATTTGATATTCAAGACACC
Found at i:28180205 original size:9 final size:9
Alignment explanation
Indices: 28180191--28180220 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
28180181 ACAGAAAAAA
28180191 AAAAGAAAG
1 AAAAGAAAG
*
28180200 AAAAGAAAA
1 AAAAGAAAG
28180209 AAAAGAAAG
1 AAAAGAAAG
28180218 AAA
1 AAA
28180221 GAAGGAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:28182992 original size:20 final size:20
Alignment explanation
Indices: 28182955--28182996 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
28182945 ATTCATTTTT
**
28182955 ATTCATATAAACTGTAATTC
1 ATTCATATAAACAATAATTC
*
28182975 ATTCATATAACCAATAATTC
1 ATTCATATAAACAATAATTC
28182995 AT
1 AT
28182997 CAGTAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (20 bp):
ATTCATATAAACAATAATTC
Found at i:28183012 original size:20 final size:20
Alignment explanation
Indices: 28182968--28183057 Score: 71
Period size: 20 Copynumber: 4.5 Consensus size: 20
28182958 CATATAAACT
28182968 GTAATTCATTCA-TAT-AACCA
1 GTAATTCA-TCAGTATCAA-CA
* *
28182988 ATAATTCATCAGTAAT-AATA
1 GTAATTCATCAGT-ATCAACA
* *
28183008 GTAATTTATCCGTATCAACA
1 GTAATTCATCAGTATCAACA
*
28183028 GTAATTCATTCA-TTTCAACA
1 GTAATTCA-TCAGTATCAACA
28183048 GTAATTCATC
1 GTAATTCATC
28183058 CATTTCAACA
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
19 7 0.12
20 44 0.77
21 6 0.11
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.37
Consensus pattern (20 bp):
GTAATTCATCAGTATCAACA
Found at i:28183061 original size:20 final size:20
Alignment explanation
Indices: 28183007--28183067 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
28182997 CAGTAATAAT
* * *
28183007 AGTAATTTATCCGTATCAAC
1 AGTAATTCATCCATTTCAAC
*
28183027 AGTAATTCATTCATTTCAAC
1 AGTAATTCATCCATTTCAAC
28183047 AGTAATTCATCCATTTCAAC
1 AGTAATTCATCCATTTCAAC
28183067 A
1 A
28183068 TAACTTATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (20 bp):
AGTAATTCATCCATTTCAAC
Found at i:28183267 original size:23 final size:22
Alignment explanation
Indices: 28183235--28183347 Score: 106
Period size: 23 Copynumber: 5.0 Consensus size: 22
28183225 AGGTAATAAT
*
28183235 TAGTAAGCTCTATTGAGCTGAAA
1 TAGTAAGCTCTATCGAGCTG-AA
*
28183258 TGGTAAGCTCTATCGAGCTGAA
1 TAGTAAGCTCTATCGAGCTGAA
*
28183280 TAGTAAGCTC-ATACAAGCTGAA
1 TAGTAAGCTCTAT-CGAGCTGAA
28183302 TCAGTAAGCTCTAAT-GAGCTGAAAA
1 T-AGTAAGCTCT-ATCGAGCTG--AA
*
28183327 CAGTAAGCTCT-TACGAGCTGA
1 TAGTAAGCTCTAT-CGAGCTGA
28183348 TATATATGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
21 2 0.03
22 22 0.29
23 32 0.42
24 16 0.21
25 4 0.05
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (22 bp):
TAGTAAGCTCTATCGAGCTGAA
Found at i:28183299 original size:45 final size:47
Alignment explanation
Indices: 28183250--28183347 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 47
28183240 AGCTCTATTG
* *
28183250 AGCTGAAAT-GGTAAGCTCT-ATCGAGCTG-AATAGTAAGCTCATACA
1 AGCTGAAATCAGTAAGCTCTAAT-GAGCTGAAACAGTAAGCTCATACA
* *
28183295 AGCTG-AATCAGTAAGCTCTAATGAGCTGAAAACAGTAAGCTCTTACG
1 AGCTGAAATCAGTAAGCTCTAATGAGCTG-AAACAGTAAGCTCATACA
28183342 AGCTGA
1 AGCTGA
28183348 TATATATGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
44 3 0.07
45 20 0.45
46 2 0.05
47 19 0.43
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (47 bp):
AGCTGAAATCAGTAAGCTCTAATGAGCTGAAACAGTAAGCTCATACA
Found at i:28183313 original size:68 final size:72
Alignment explanation
Indices: 28183236--28183372 Score: 185
Period size: 68 Copynumber: 1.9 Consensus size: 72
28183226 GGTAATAATT
* **
28183236 AGTAAGCTCTATTGAGCTG-AAATGGTAAGCTC-TATCGAGCTG-A-ATA-GTAAGCTCATACAA
1 AGTAAGCTCTAATGAGCTGAAAACAGTAAGCTCTTA-CGAGCTGAATATATGTAAGCTCATACAA
28183296 GCTGAATC
65 GCTGAATC
*
28183304 AGTAAGCTCTAATGAGCTGAAAACAGTAAGCTCTTACGAGCTGATATATATGTAAGCTCATACGA
1 AGTAAGCTCTAATGAGCTGAAAACAGTAAGCTCTTACGAGCTGA-ATATATGTAAGCTCATACAA
28183369 GCTG
65 GCTG
28183373 TGGTGAGTCT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
68 18 0.31
69 18 0.31
70 2 0.03
71 1 0.02
72 3 0.05
73 17 0.29
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (72 bp):
AGTAAGCTCTAATGAGCTGAAAACAGTAAGCTCTTACGAGCTGAATATATGTAAGCTCATACAAG
CTGAATC
Found at i:28186107 original size:46 final size:47
Alignment explanation
Indices: 28185963--28186234 Score: 213
Period size: 46 Copynumber: 5.8 Consensus size: 47
28185953 TTTGTGTGCT
* * * *
28185963 AGTGTAAGACATGTCTGAGACATGCATTGGCCAC-ATTATG-AGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGTAGAGCC
* * * * *
28186009 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGAGAT-AAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTAGAGCC
28186057 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGCC
* * *
28186103 AGTGTAAGACACT-TCTGGGATATGCATCGG-CTATGAGATGT---GTC
1 AGTGTAAGACA-TGTCTGGGACATGCATCGGCCT-CGAGATGTAGAGCC
* * * * *
28186147 AGTATAAGACTATGTCTGGGACATGACATCGG-CACGAATATGTGAGAACT
1 AGTGTAAGAC-ATGTCTGGGACATG-CATCGGCCTCG-AGATGT-AGAGCC
*
28186197 AGTGTAAGACTATGTCTGGGACATGACGTCGGCCTCGA
1 AGTGTAAGAC-ATGTCTGGGACATG-CATCGGCCTCGA
28186235 TTTTGATAGT
Statistics
Matches: 183, Mismatches: 27, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
44 12 0.07
45 14 0.08
46 71 0.39
47 29 0.16
48 22 0.12
49 1 0.01
50 31 0.17
51 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGCC
Found at i:28193687 original size:47 final size:47
Alignment explanation
Indices: 28193630--28193933 Score: 428
Period size: 47 Copynumber: 6.4 Consensus size: 47
28193620 ATTGATGTAC
* * *
28193630 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * * *
28193677 AAGTATATATATATGTGATAGGGCCGAGTGGCCAACGTGATGAATGTGA
1 AAG--TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* ** * * *
28193726 AAGTGTATATATGTGATAGGGTTGAGTGACCAACGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
28193773 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
28193820 AAGTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
28193867 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
28193914 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
28193934 TCCCGAAGGG
Statistics
Matches: 236, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
47 190 0.81
49 46 0.19
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:28198657 original size:49 final size:50
Alignment explanation
Indices: 28198539--28198666 Score: 145
Period size: 50 Copynumber: 2.6 Consensus size: 50
28198529 TATGAGATGT
* *
28198539 GTCAGTGTAAGACCATGTCTGAGACATGGCATCGACACGGATATGTGAGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGACACCGATATGTGAGA
** * * * *
28198589 G-CTAGTGTAAGATTATGTCTGGGACATGGCGTCGGC-CTCGAT-TTTGATA
1 GTC-AGTGTAAGACCATGTCTGGGACATGGCATCGACAC-CGATATGTGAGA
28198638 GTCAGTGTAAGACCATGTCTGGGACATGG
1 GTCAGTGTAAGACCATGTCTGGGACATGG
28198667 AAACAACATT
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
49 32 0.49
50 33 0.51
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (50 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGCATCGACACCGATATGTGAGA
Found at i:28207612 original size:2 final size:2
Alignment explanation
Indices: 28207605--28207661 Score: 78
Period size: 2 Copynumber: 28.5 Consensus size: 2
28207595 AACGGGATTT
* * * *
28207605 TC TC TC TC TC TC TC TC TC TC TC TC AC TC AC TC AC TC AC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28207647 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
28207662 TGTCGAAACT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.07, C:0.49, G:0.00, T:0.44
Consensus pattern (2 bp):
TC
Found at i:28213057 original size:43 final size:43
Alignment explanation
Indices: 28212900--28213063 Score: 170
Period size: 43 Copynumber: 3.8 Consensus size: 43
28212890 AGCTCGTACA
* * * ** * * *
28212900 ATGCC-ATATCCCAGATATGGTTTTACATGTTATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAATCAAATAACG
* * ** *
28212942 ATGCCGATATCCCAGGTATGGTCTTACACGA-AATCAAATAACA
1 ATGCCAATGTCCCAGACATGGTCTTACAC-ATAATCAAATAACG
* *
28212985 ATGCCAATGTCCCAGACATGGTCTTACACATAATCATATAATG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAATCAAATAACG
28213028 ATGCCAATGTCCCAGACATGGTCTTACACATAATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACATAATCA
28213064 CATCTCGTTA
Statistics
Matches: 104, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
42 6 0.06
43 98 0.94
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACATAATCAAATAACG
Found at i:28213063 original size:86 final size:85
Alignment explanation
Indices: 28212897--28213056 Score: 196
Period size: 86 Copynumber: 1.9 Consensus size: 85
28212887 TATAGCTCGT
* * ** * * **
28212897 ACAATGCCATATCCCAGATATGGTTTTACATGTTATCACATATCGATGCCGATATCCCAGGTATG
1 ACAATGCCATATCCCAGACATGGTCTTACACATAATCACATATCGATGCCAATATCCCAGACATG
28212962 GTCTTACACGAAATCAAATA
66 GTCTTACACGAAATCAAATA
* * *
28212982 ACAATGCCAATGTCCCAGACATGGTCTTACACATAATCATATAAT-GATGCCAATGTCCCAGACA
1 ACAATGCC-ATATCCCAGACATGGTCTTACACATAATCACAT-ATCGATGCCAATATCCCAGACA
28213046 TGGTCTTACAC
64 TGGTCTTACAC
28213057 ATAATCACAT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
85 8 0.13
86 52 0.84
87 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (85 bp):
ACAATGCCATATCCCAGACATGGTCTTACACATAATCACATATCGATGCCAATATCCCAGACATG
GTCTTACACGAAATCAAATA
Found at i:28213583 original size:29 final size:28
Alignment explanation
Indices: 28213540--28213599 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
28213530 CTTTCATTTA
* * *
28213540 TTTCACATTTCAACCCCTCAATTTACACT
1 TTTCACAATTAAACCCCT-AATATACACT
*
28213569 TTTCACAATTAAACCCCTAATATACATT
1 TTTCACAATTAAACCCCTAATATACACT
28213597 TTT
1 TTT
28213600 ACTCAAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (28 bp):
TTTCACAATTAAACCCCTAATATACACT
Found at i:28221857 original size:22 final size:22
Alignment explanation
Indices: 28221829--28221950 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
28221819 TTCCACATCC
28221829 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
28221851 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
28221875 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
28221898 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
28221922 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
28221945 ATCACA
1 ATCACA
28221951 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:28222173 original size:49 final size:47
Alignment explanation
Indices: 28221801--28222396 Score: 862
Period size: 47 Copynumber: 12.6 Consensus size: 47
28221791 CCCTTCAGGA
* * *
28221801 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
28221848 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
28221895 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
28221942 CTTATCACACATACACA-TGCTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
28221989 CTTATCACACATACACA-TGTTCACA-TCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
28222035 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
28222082 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
28222129 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
28222178 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
28222225 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
28222274 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
28222321 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
28222370 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28222397 TATTCAAATA
Statistics
Matches: 514, Mismatches: 26, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
46 42 0.08
47 334 0.65
49 137 0.27
50 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:28222201 original size:96 final size:94
Alignment explanation
Indices: 28221801--28222396 Score: 862
Period size: 96 Copynumber: 6.3 Consensus size: 94
28221791 CCCTTCAGGA
* * *
28221801 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
28221866 TTTCACATTCATCACATTGGCCATTCGGC
66 TTTCACATTCATCACATTGGCCATTCGGC
* * * *
28221895 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACA
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
*
28221959 -TGCTCACATTCATCACATTGGCCATTCGGC
65 CT-TTCACATTCATCACATTGGCCATTCGGC
* * * * *
28221989 CTTATCACACATACACA-TGTTCACA-TCATCACATTGGCCACTCGGCCTTATCTCATATATGCA
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
28222052 -TGTTCACATTCATCACATTGGCCATTCGGC
65 CT-TTCACATTCATCACATTGGCCATTCGGC
* *
28222082 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATA
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATA
28222146 CACTTTCACATTCATCACATTGGCCATTCGGC
63 CACTTTCACATTCATCACATTGGCCATTCGGC
* *
28222178 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATAC
* *
28222243 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATTGGCCATTCGGC
*
28222274 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATAC
*
28222339 ACTTTCACATTCATCACATTGGCCATTAGGC
64 ACTTTCACATTCATCACATTGGCCATTCGGC
28222370 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28222397 TATTCAAATA
Statistics
Matches: 466, Mismatches: 29, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
93 89 0.19
94 130 0.28
96 245 0.53
97 2 0.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TTTCACATTCATCACATTGGCCATTCGGC
Found at i:28223906 original size:56 final size:56
Alignment explanation
Indices: 28223839--28223958 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
28223829 TATTAGTTTA
28223839 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
28223895 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
28223951 TTGCCCAT
1 TTGCCCAT
28223959 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:28235595 original size:24 final size:26
Alignment explanation
Indices: 28235564--28235628 Score: 84
Period size: 24 Copynumber: 2.7 Consensus size: 26
28235554 CTCAACCGAT
28235564 TTCGCACACATAGTGCTAAT-C-AAA
1 TTCGCACACATAGTGCTAATGCTAAA
*
28235588 TTCGCACACATAGTGC-CATGCTAAA
1 TTCGCACACATAGTGCTAATGCTAAA
*
28235613 -CCGCACACATAGTGCT
1 TTCGCACACATAGTGCT
28235629 TTGGAAATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 2 0.06
24 31 0.86
25 3 0.08
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.23
Consensus pattern (26 bp):
TTCGCACACATAGTGCTAATGCTAAA
Found at i:28235621 original size:48 final size:47
Alignment explanation
Indices: 28235566--28235723 Score: 147
Period size: 48 Copynumber: 3.3 Consensus size: 47
28235556 CAACCGATTT
*
28235566 CGCACACATAGTGCTAATCAAATTCGCACACATAGTGCCATGCTAAAC
1 CGCACACATAGTGCTAATCAAATTCGCACACATAGTGCCATTC-AAAC
* * * * ** * *
28235614 CGCACACATAGTGCT-TTGGAAATTCACTCATTTATTGACATTCAAAC
1 CGCACACATAGTGCTAAT-CAAATTCGCACACATAGTGCCATTCAAAC
* * * *
28235661 CAGCATACATAGTGCCAATCGATTTCGCACACATAGTGCCATTCAAATC
1 C-GCACACATAGTGCTAATCAAATTCGCACACATAGTGCCATTCAAA-C
*
28235710 CGCACACTTAGTGC
1 CGCACACATAGTGC
28235724 CAATGTTGGC
Statistics
Matches: 83, Mismatches: 23, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
47 6 0.07
48 74 0.89
49 3 0.04
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (47 bp):
CGCACACATAGTGCTAATCAAATTCGCACACATAGTGCCATTCAAAC
Found at i:28235699 original size:24 final size:24
Alignment explanation
Indices: 28235667--28235727 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
28235657 AAACCAGCAT
* * *
28235667 ACATAGTGCCAATCGATTTCGCAC
1 ACATAGTGCCAATCAAATCCGCAC
*
28235691 ACATAGTGCCATTCAAATCCGCAC
1 ACATAGTGCCAATCAAATCCGCAC
*
28235715 ACTTAGTGCCAAT
1 ACATAGTGCCAAT
28235728 GTTGGCTCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.25
Consensus pattern (24 bp):
ACATAGTGCCAATCAAATCCGCAC
Found at i:28238913 original size:19 final size:20
Alignment explanation
Indices: 28238885--28238923 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
28238875 TATTAGTGAT
*
28238885 TACATCTGTAAAT-TTAATA
1 TACATATGTAAATATTAATA
*
28238904 TACATATGTATATATTAATA
1 TACATATGTAAATATTAATA
28238924 AAATATGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (20 bp):
TACATATGTAAATATTAATA
Found at i:28246764 original size:56 final size:60
Alignment explanation
Indices: 28246655--28246788 Score: 179
Period size: 56 Copynumber: 2.3 Consensus size: 60
28246645 ATAATATAAA
* *
28246655 AATAATTATATTAACAATATTATTAAATTATATATTTTATTTTTATTAAATTATATTTAAT
1 AATAATTATATTAA-AATATGATTAAATTATATATTATATTTTTATTAAATTATATTTAAT
* *
28246716 AATAATTATATTAAAATATGGTTAAA-T-TAT-TTAT-TTTTTATTAAATTATTTTTAAT
1 AATAATTATATTAAAATATGATTAAATTATATATTATATTTTTATTAAATTATATTTAAT
28246772 AATAATCT-TATTAAAAT
1 AATAAT-TATATTAAAAT
28246789 TCAATAACAA
Statistics
Matches: 68, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
56 36 0.53
57 4 0.06
58 3 0.04
59 1 0.01
60 10 0.15
61 14 0.21
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (60 bp):
AATAATTATATTAAAATATGATTAAATTATATATTATATTTTTATTAAATTATATTTAAT
Found at i:28246979 original size:16 final size:16
Alignment explanation
Indices: 28246954--28246987 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28246944 TTACTAATTG
28246954 CAACTCTATTCCATTA
1 CAACTCTATTCCATTA
* *
28246970 CAACTTTATTCTATTA
1 CAACTCTATTCCATTA
28246986 CA
1 CA
28246988 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.41
Consensus pattern (16 bp):
CAACTCTATTCCATTA
Found at i:28248371 original size:3 final size:3
Alignment explanation
Indices: 28248363--28248392 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
28248353 AAATCTCTAC
28248363 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
28248393 GAAAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28250828 original size:71 final size:71
Alignment explanation
Indices: 28250703--28250860 Score: 219
Period size: 71 Copynumber: 2.2 Consensus size: 71
28250693 GAAAGAAAGA
* * * * **
28250703 GTATTGTGATATCCACACCTTGGAATCATGATACCTTTAAAAGTATTGAAGAATGGAGGCACCCT
1 GTATCGTGATATCCACACCTTAGAATCATGATACCTCTAAAAGTATTGAAGAATGAAAACACCCT
28250768 TCAATG
66 TCAATG
* *
28250774 GTATCGTGATATCCACACCTTAGAATCGTGATACCTCTAACAA-TATTGACGAATGAAAACACCC
1 GTATCGTGATATCCACACCTTAGAATCATGATACCTCTAA-AAGTATTGAAGAATGAAAACACCC
28250838 TTCAATG
65 TTCAATG
*
28250845 GTATCGCGATATCCAC
1 GTATCGTGATATCCAC
28250861 CTTTCCAAGA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
71 75 0.97
72 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (71 bp):
GTATCGTGATATCCACACCTTAGAATCATGATACCTCTAAAAGTATTGAAGAATGAAAACACCCT
TCAATG
Found at i:28250933 original size:22 final size:22
Alignment explanation
Indices: 28250905--28250959 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
28250895 AAGGTATCGT
28250905 GATATCCTCTTATGAGCATTGC
1 GATATCCTCTTATGAGCATTGC
*
28250927 GATATCCTCTTATGAGCATTTC
1 GATATCCTCTTATGAGCATTGC
28250949 GATATCCTCTT
1 GATATCCTCTT
28250960 GTGGGTATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.40
Consensus pattern (22 bp):
GATATCCTCTTATGAGCATTGC
Found at i:28253904 original size:13 final size:13
Alignment explanation
Indices: 28253888--28253931 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
28253878 TTATAATTAA
28253888 TTCATATAACCAT
1 TTCATATAACCAT
28253901 TTCATATAACCAT
1 TTCATATAACCAT
* *
28253914 TTCATCTAAACAT
1 TTCATATAACCAT
28253927 TTCAT
1 TTCAT
28253932 TTGCGCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:28254155 original size:37 final size:37
Alignment explanation
Indices: 28254103--28254185 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
28254093 GGGAACAATA
* ** * *
28254103 CTCACACAAGCTGTGATTGTAACTGTATCTATCAGTT
1 CTCACACAAGATGTGATTGTAACCATATCTATAAGTG
*
28254140 CTCACACAAGATGTGATTGTAACCATATCTGTAAGTG
1 CTCACACAAGATGTGATTGTAACCATATCTATAAGTG
28254177 CTCACACAA
1 CTCACACAA
28254186 TCTGTGGGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (37 bp):
CTCACACAAGATGTGATTGTAACCATATCTATAAGTG
Found at i:28262280 original size:12 final size:12
Alignment explanation
Indices: 28262263--28262287 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28262253 CACTTAAGAT
28262263 TCCTAAAAAATA
1 TCCTAAAAAATA
28262275 TCCTAAAAAATA
1 TCCTAAAAAATA
28262287 T
1 T
28262288 GTTAGATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (12 bp):
TCCTAAAAAATA
Found at i:28264712 original size:34 final size:34
Alignment explanation
Indices: 28264669--28264736 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
28264659 TAACGCGAAC
28264669 AAGTGTCGAGGTAAGTTTGTGTAACTTAATCCGG
1 AAGTGTCGAGGTAAGTTTGTGTAACTTAATCCGG
28264703 AAGTGTCGAGGTAAGTTTGTGTAACTTAATCCGG
1 AAGTGTCGAGGTAAGTTTGTGTAACTTAATCCGG
28264737 CATGTAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.32
Consensus pattern (34 bp):
AAGTGTCGAGGTAAGTTTGTGTAACTTAATCCGG
Done.