Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 22 of 310
Found at i:5810677 original size:47 final size:47
Alignment explanation
Indices: 5810620--5810876 Score: 213
Period size: 47 Copynumber: 5.4 Consensus size: 47
5810610 AGTGCCATTT
*
5810620 TAAGACCATGTCTGGGACATGGCATCGGCGTAGAGATGAGTA-CCAGTG
1 TAAGACCATGTCTGGGACAT-GCATCGGCCTAGAGATGA-TAGCCAGTG
*
5810668 TAAGA-CATGTCTGGGACATGCATCGGCCTCGATGATGATAGCCAGTG
1 TAAGACCATGTCTGGGACATGCATCGGCCTAGA-GATGATAGCCAGTG
* * * * * *
5810715 TAAGA-CGTGTCTGGAACATGTATCGG-TTA-AGAGTCAT-GCTAGTG
1 TAAGACCATGTCTGGGACATGCATCGGCCTAGAGA-TGATAGCCAGTG
* * * * * * * *
5810759 TAAGA-CATGTCCGGGACATGCATCAGCACGTATATACGAAAGCTAGTA
1 TAAGACCATGTCTGGGACATGCATCGGC-C-TAGAGATGATAGCCAGTG
* * *
5810807 TAAGACCATGTCTGGAACATGGCATCGGCCTTGATGATGATAGCCTGTG
1 TAAGACCATGTCTGGGACAT-GCATCGGCCTAGA-GATGATAGCCAGTG
*
5810856 TGAGACCATGTCTGGGACATG
1 TAAGACCATGTCTGGGACATG
5810877 GAATCGGTAA
Statistics
Matches: 165, Mismatches: 33, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
44 29 0.18
45 4 0.02
46 14 0.08
47 51 0.31
48 21 0.13
49 39 0.24
50 7 0.04
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
TAAGACCATGTCTGGGACATGCATCGGCCTAGAGATGATAGCCAGTG
Found at i:5810726 original size:94 final size:92
Alignment explanation
Indices: 5810566--5810876 Score: 265
Period size: 94 Copynumber: 3.3 Consensus size: 92
5810556 ATTTCTTGTG
* * * * *
5810566 TACCAGTGTAAGACATGTCTAGGACATGCATCGATCAC-ATTATAAGT-GCCATTTTAAGACCAT
1 TACCAGTGTAAGACATGTCTGGGACATGCATCG-GCACGA-TATGA-TAGCCAGTATAAGACCAT
* *
5810629 GTCTGGGACATGGCATCGGCGTAGAGATGA
63 GTCTGGAACATGGCATCGGCCTAGAGATGA
* * *
5810659 GTACCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATGATGATAGCCAGTGTAAGA-CGT
1 -TACCAGTGTAAGACATGTCTGGGACATGCATCGG-CACGAT-ATGATAGCCAGTATAAGACCAT
* * *
5810723 GTCTGGAACAT-GTATCGG-TTA-AGAGTCA
63 GTCTGGAACATGGCATCGGCCTAGAGA-TGA
* * * * * *
5810751 TGCTAGTGTAAGACATGTCCGGGACATGCATCAGCACGTATATACGAAAGCTAGTATAAGACCAT
1 TACCAGTGTAAGACATGTCTGGGACATGCATCGGCACG-ATAT--GATAGCCAGTATAAGACCAT
*
5810816 GTCTGGAACATGGCATCGGCCTTGATGATGA
63 GTCTGGAACATGGCATCGGCCTAGA-GATGA
* *
5810847 TAGCCTGTGTGAGACCATGTCTGGGACATG
1 TA-CCAGTGTAAGA-CATGTCTGGGACATG
5810877 GAATCGGTAA
Statistics
Matches: 173, Mismatches: 29, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
90 5 0.03
91 35 0.20
92 17 0.10
93 19 0.11
94 54 0.31
95 15 0.09
96 4 0.02
97 10 0.06
98 14 0.08
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (92 bp):
TACCAGTGTAAGACATGTCTGGGACATGCATCGGCACGATATGATAGCCAGTATAAGACCATGTC
TGGAACATGGCATCGGCCTAGAGATGA
Found at i:5811727 original size:55 final size:55
Alignment explanation
Indices: 5811643--5811777 Score: 202
Period size: 55 Copynumber: 2.5 Consensus size: 55
5811633 GCACTTAAAA
* * *
5811643 TTTT-AAGTCAGT-TTAGTACACGGGTAGGCCACACGGGCGTGTGTCATGATCGTG
1 TTTTAAAGTCAGTGTT-GTACACGGGCAGGCCACACGGGCGTATGTCATGACCGTG
*
5811697 TTTTAAAGTCAGTGTTGTACACGGGCAGGCCACACGGGCGTATGTCATGGCCGTG
1 TTTTAAAGTCAGTGTTGTACACGGGCAGGCCACACGGGCGTATGTCATGACCGTG
*
5811752 TTTTAAAGTCAGTGTTGCACACGGGC
1 TTTTAAAGTCAGTGTTGTACACGGGC
5811778 TAAGGGCACG
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
54 4 0.05
55 68 0.92
56 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (55 bp):
TTTTAAAGTCAGTGTTGTACACGGGCAGGCCACACGGGCGTATGTCATGACCGTG
Found at i:5815351 original size:20 final size:19
Alignment explanation
Indices: 5815328--5815373 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5815318 AAAAAATTCT
5815328 AAATTATAAAAACATCAAAA
1 AAATTATAAAAA-ATCAAAA
* * *
5815348 AAATCATAAAAATTTAAAA
1 AAATTATAAAAAATCAAAA
5815367 AAATTAT
1 AAATTAT
5815374 CATGAAGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATTATAAAAAATCAAAA
Found at i:5815492 original size:31 final size:30
Alignment explanation
Indices: 5815456--5815527 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 30
5815446 AAAAAAACTA
*
5815456 AAATTCATCTATTTTTGAAAGGTTGATGGTC
1 AAATTCATCTATTTTTGAAAGGTT-AAGGTC
* *
5815487 AAATTCGA-CTTTTTTTTTAAAGGTTAAGGTC
1 AAATTC-ATC-TATTTTTGAAAGGTTAAGGTC
*
5815518 AAATTTATCT
1 AAATTCATCT
5815528 CAGAAAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
30 2 0.06
31 18 0.53
32 14 0.41
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (30 bp):
AAATTCATCTATTTTTGAAAGGTTAAGGTC
Found at i:5816781 original size:5 final size:5
Alignment explanation
Indices: 5816762--5816796 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
5816752 TAAAAATCTG
5816762 TTTATT TTTATT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTA-T TTTA-T TTTAT TTTAT TTTAT TTTAT TTT
5816797 CACAAAGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTAT
Found at i:5819158 original size:14 final size:14
Alignment explanation
Indices: 5819139--5819166 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5819129 AAAACAGAAT
5819139 TAGAAGAGAAATTA
1 TAGAAGAGAAATTA
5819153 TAGAAGAGAAATTA
1 TAGAAGAGAAATTA
5819167 AACCTCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.21
Consensus pattern (14 bp):
TAGAAGAGAAATTA
Found at i:5823231 original size:36 final size:36
Alignment explanation
Indices: 5823162--5823235 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 36
5823152 ATTTTGTCTC
*
5823162 TTTCTTAGATTTTTTTCTTTTTTAAGTTTTATATTAT
1 TTTCTTAGATTTTTTTCTTATTTAAG-TTTATATTAT
5823199 TTTCTTA-ATTTATTTTGCTTATTTAA-TTTATATTAT
1 TTTCTTAGATTT-TTTT-CTTATTTAAGTTTATATTAT
5823235 T
1 T
5823236 AATTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 15 0.44
37 11 0.32
38 8 0.24
ACGTcount: A:0.22, C:0.05, G:0.04, T:0.69
Consensus pattern (36 bp):
TTTCTTAGATTTTTTTCTTATTTAAGTTTATATTAT
Found at i:5823240 original size:18 final size:17
Alignment explanation
Indices: 5823189--5823236 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
5823179 TTTTTTAAGT
*
5823189 TTTATATTATTTTCTTAA
1 TTTATATTATTAT-TTAA
* *
5823207 TTTATTTTGCTTATTTAA
1 TTTATATT-ATTATTTAA
5823225 TTTATATTATTA
1 TTTATATTATTA
5823237 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATATTATTATTTAA
Found at i:5823249 original size:22 final size:21
Alignment explanation
Indices: 5823223--5823312 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 21
5823213 TTGCTTATTT
*
5823223 AATTTATATTATTAATTTTAAA
1 AATTTATAATATT-ATTTTAAA
*
5823245 AATTTGTAATA-TATATTTAAA
1 AATTTATAATATTAT-TTTAAA
* *
5823266 ATGTTTTATAATATT-TTTTTAA
1 A--ATTTATAATATTATTTTAAA
5823288 AATTT-TAATTATTATTTTTAAA
1 AATTTATAA-TATTA-TTTTAAA
5823310 AAT
1 AAT
5823313 ATTTTTTAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
19 3 0.06
20 9 0.17
21 8 0.15
22 24 0.44
23 9 0.17
24 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AATTTATAATATTATTTTAAA
Found at i:5823293 original size:21 final size:21
Alignment explanation
Indices: 5823238--5823310 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
5823228 ATATTATTAA
* * *
5823238 TTTTAAAAATTTGTAATATAT
1 TTTTAAAATTTTATAATATTT
*
5823259 ATTTAAAATGTTTTATAATATTT
1 TTTTAAAA--TTTTATAATATTT
*
5823282 TTTTAAAATTTTA-ATTATTAT
1 TTTTAAAATTTTATAATATT-T
5823303 TTTTAAAA
1 TTTTAAAA
5823311 ATATTTTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.12
21 21 0.49
23 17 0.40
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TTTTAAAATTTTATAATATTT
Found at i:5823360 original size:24 final size:23
Alignment explanation
Indices: 5823333--5823423 Score: 71
Period size: 24 Copynumber: 3.8 Consensus size: 23
5823323 TTTATATATA
5823333 TTTATATATATTTGAAATTAATTT
1 TTTATATATATTTGAAATT-ATTT
* *
5823357 TTTATAAAT-TTTAAAAATGTATTT
1 TTTATATATATTT-GAAAT-TATTT
*
5823381 TTTAAAT-TAGTTTTGAAATTATTAGT
1 TTTATATATA--TTTGAAATTATT--T
5823407 TTTATA-ATATTTGAAAT
1 TTTATATATATTTGAAAT
5823424 GTATGTTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
23 4 0.08
24 33 0.62
25 5 0.09
26 11 0.21
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (23 bp):
TTTATATATATTTGAAATTATTT
Found at i:5823824 original size:26 final size:28
Alignment explanation
Indices: 5823793--5823857 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
5823783 TTTAAATACA
*
5823793 ATTTTTAAATACATTTAAAAAATTATAAT
1 ATTTTTAAATA-ATATAAAAAATTATAAT
*
5823822 -TTTTT-AATAATATAAGAAATTATAAT
1 ATTTTTAAATAATATAAAAAATTATAAT
5823848 A-TTTTAAATA
1 ATTTTTAAATA
5823858 TTTTTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 19 0.59
27 8 0.25
28 5 0.16
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
ATTTTTAAATAATATAAAAAATTATAAT
Found at i:5823851 original size:28 final size:27
Alignment explanation
Indices: 5823792--5823857 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
5823782 TTTTAAATAC
*
5823792 AATTTTTAAATACATTTAAAAAATTAT
1 AATTTTTAAATACATATAAAAAATTAT
* *
5823819 AATTTTTTAATA-ATATAAGAAATTAT
1 AATTTTTAAATACATATAAAAAATTAT
5823845 AATATTTTAAATA
1 AAT-TTTTAAATA
5823858 TTTTTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 15 0.44
27 19 0.56
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
AATTTTTAAATACATATAAAAAATTAT
Found at i:5823915 original size:35 final size:36
Alignment explanation
Indices: 5823858--5823926 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
5823848 ATTTTAAATA
*
5823858 TTTTTTTAAAATTTTGTCTTTTTCCTT-TTTTTTAC
1 TTTTTTGAAAATTTTGTCTTTTTCCTTATTTTTTAC
* *
5823893 TTTTTTGAAATTTTATGT-TTTTTTCTTATTTTTT
1 TTTTTTGAAAATTT-TGTCTTTTTCCTTATTTTTT
5823927 TTGTTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 20 0.69
36 9 0.31
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.74
Consensus pattern (36 bp):
TTTTTTGAAAATTTTGTCTTTTTCCTTATTTTTTAC
Found at i:5824025 original size:20 final size:22
Alignment explanation
Indices: 5823982--5824025 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
5823972 ATTTAAAATG
5823982 TTTTATAATATAGTTTTTACAA
1 TTTTATAATATAGTTTTTACAA
5824004 TTTTA-AATATTA-TTTTTA-AA
1 TTTTATAATA-TAGTTTTTACAA
5824024 TT
1 TT
5824026 CTTTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.19
21 10 0.48
22 7 0.33
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTATAATATAGTTTTTACAA
Found at i:5824156 original size:18 final size:18
Alignment explanation
Indices: 5824133--5824180 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
5824123 GTGACTATTA
5824133 ATAAATTTAAATATAAAT
1 ATAAATTTAAATATAAAT
5824151 ATAAATTTAAA-A-AAAT
1 ATAAATTTAAATATAAAT
*
5824167 ATATA-TTAAATATA
1 ATAAATTTAAATATA
5824181 TTTTTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.19
16 9 0.33
17 2 0.07
18 11 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATTTAAATATAAAT
Found at i:5827218 original size:30 final size:30
Alignment explanation
Indices: 5827174--5827296 Score: 174
Period size: 30 Copynumber: 4.1 Consensus size: 30
5827164 AGTCCCAAGC
*
5827174 AGTTCATATAACCCGGACATAGGTGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* * *
5827204 AGTTCGTATCACCCGGACATGGGTGATTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* *
5827234 AGTTCATATCATCCGGACATGGGTGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* *
5827264 AGTTCATATCACCCGGATATAGGCGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
5827294 AGT
1 AGT
5827297 CCATTTGACT
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 82 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (30 bp):
AGTTCATATCACCCGGACATAGGTGGTTCG
Found at i:5830832 original size:31 final size:34
Alignment explanation
Indices: 5830773--5830844 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 34
5830763 GTTTTATAAT
5830773 ATATT-TTTTTATAAATATTAAAAATATATTTTCA
1 ATATTATTTTTATAAATATT-AAAATATATTTTCA
*
5830807 A-ATTATTTTT-TAAATATT-AAATATATTTTTA
1 ATATTATTTTTATAAATATTAAAATATATTTTCA
5830838 ATATTAT
1 ATATTAT
5830845 AAAACATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
31 13 0.37
32 5 0.14
33 11 0.31
34 6 0.17
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (34 bp):
ATATTATTTTTATAAATATTAAAATATATTTTCA
Found at i:5830882 original size:29 final size:29
Alignment explanation
Indices: 5830850--5830912 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
5830840 ATTATAAAAC
*
5830850 ATTTAAAATGATTTAAAATATTTTTTAAT
1 ATTTAAAATGATTTAAAATATTTTTTAAA
* * *
5830879 ATTTTAAATGCTTTTAAATATTTTTTAAA
1 ATTTAAAATGATTTAAAATATTTTTTAAA
5830908 ATTTA
1 ATTTA
5830913 CATAGAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (29 bp):
ATTTAAAATGATTTAAAATATTTTTTAAA
Found at i:5830887 original size:19 final size:19
Alignment explanation
Indices: 5830798--5830902 Score: 70
Period size: 19 Copynumber: 5.4 Consensus size: 19
5830788 TATTAAAAAT
5830798 ATATTTTCAAATTATTTTTTA
1 ATATTTT-AAA-TATTTTTTA
*
5830819 A-ATATTAAATATATTTTTA
1 ATATTTTAAATAT-TTTTTA
* * **
5830838 ATATTATAAA-ACATTTAAA
1 ATATTTTAAATA-TTTTTTA
*
5830857 ATGATTTAAAATATTTTTTA
1 AT-ATTTTAAATATTTTTTA
** *
5830877 ATATTTTAAATGCTTTTAA
1 ATATTTTAAATATTTTTTA
5830896 ATATTTT
1 ATATTTT
5830903 TTAAAATTTA
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
18 3 0.05
19 37 0.58
20 22 0.34
21 2 0.03
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (19 bp):
ATATTTTAAATATTTTTTA
Found at i:5831005 original size:8 final size:8
Alignment explanation
Indices: 5830992--5831018 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
5830982 ACAAATTTTA
5830992 TTTAAAAG
1 TTTAAAAG
5831000 TTTAAAAG
1 TTTAAAAG
5831008 TTTAAAAG
1 TTTAAAAG
5831016 TTT
1 TTT
5831019 TATATATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (8 bp):
TTTAAAAG
Found at i:5831053 original size:18 final size:20
Alignment explanation
Indices: 5831016--5831055 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
5831006 AGTTTAAAAG
5831016 TTTTATATATCTTTAAATTA
1 TTTTATATATCTTTAAATTA
*
5831036 TTTTA-ATAT-TTTATATTA
1 TTTTATATATCTTTAAATTA
5831054 TT
1 TT
5831056 AAAAATATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATATATCTTTAAATTA
Found at i:5831609 original size:37 final size:36
Alignment explanation
Indices: 5831539--5831609 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
5831529 AATAATTATT
*
5831539 TTTTTAAAATTTTAAAAAATTAATTTGAAAAATACA
1 TTTTTAAAATTTTAAAAAATTAATTTCAAAAATACA
* *
5831575 TTTTTAAAATTTATAAATAATTAATTTCACAAATA
1 TTTTTAAAATTT-TAAAAAATTAATTTCAAAAATA
5831610 TATATAAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 12 0.39
37 19 0.61
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (36 bp):
TTTTTAAAATTTTAAAAAATTAATTTCAAAAATACA
Found at i:5831657 original size:22 final size:24
Alignment explanation
Indices: 5831629--5831715 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 24
5831619 TTAAAAATAT
5831629 TTTTAAAAATAATAAT-TAAAA-A
1 TTTTAAAAATAATAATATAAAACA
*
5831651 TTTT-AAAA-AATATTATAAAACA
1 TTTTAAAAATAATAATATAAAACA
* **
5831673 TTTTAAATAT-AT-AT-TACAAATT
1 TTTTAAAAATAATAATATA-AAACA
*
5831695 TTTTAAAATTAATAATATAAA
1 TTTTAAAAATAATAATATAAA
5831716 TTAAATAAGC
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
20 5 0.10
21 11 0.22
22 21 0.42
23 7 0.14
24 4 0.08
25 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTTAAAAATAATAATATAAAACA
Found at i:5831659 original size:23 final size:22
Alignment explanation
Indices: 5831622--5831679 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
5831612 TATAAAGTTA
* *
5831622 AAAATATTTTTAAAAATAATAATT
1 AAAACATTTTAAAAAAT-ATAA-T
*
5831646 AAAA-ATTTTAAAAAATATTAT
1 AAAACATTTTAAAAAATATAAT
5831667 AAAACATTTTAAA
1 AAAACATTTTAAA
5831680 TATATATTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 5 0.16
22 11 0.35
23 11 0.35
24 4 0.13
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAACATTTTAAAAAATATAAT
Found at i:5831716 original size:23 final size:22
Alignment explanation
Indices: 5831627--5831717 Score: 62
Period size: 23 Copynumber: 4.1 Consensus size: 22
5831617 AGTTAAAAAT
*
5831627 ATTTTTAAAAATAATAAT-TAA
1 ATTTTTTAAAATAATAATATAA
** *
5831648 AAATTTTAAAA-AATATTATAAA
1 ATTTTTTAAAATAATAATAT-AA
** * *
5831670 ACATTTT-AAATATATATTACAA
1 ATTTTTTAAAATA-ATAATATAA
5831692 ATTTTTTAAAATTAATAATATAA
1 ATTTTTTAAAA-TAATAATATAA
5831715 ATT
1 ATT
5831718 AAATAAGCAA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
20 5 0.09
21 12 0.22
22 16 0.30
23 19 0.35
24 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTTTAAAATAATAATATAA
Found at i:5831745 original size:36 final size:37
Alignment explanation
Indices: 5831705--5831778 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
5831695 TTTTAAAATT
*
5831705 AATAATAT-AAA-TTAAATAAGCAAAATAAAT-TAAGAA
1 AATAATATAAAACTTAAAAAAG-AAAA-AAATCTAAGAA
5831741 AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
1 AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
5831778 A
1 A
5831779 GAGACAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 12 0.35
37 14 0.41
38 8 0.24
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.22
Consensus pattern (37 bp):
AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
Found at i:5831750 original size:18 final size:18
Alignment explanation
Indices: 5831700--5831751 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
5831690 AAATTTTTTA
*
5831700 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
** *
5831718 AAATAAGCAAAATAAATT
1 AAATAAATAATATAAATT
5831736 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
5831752 ACTTAAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:5831808 original size:9 final size:9
Alignment explanation
Indices: 5831794--5831836 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
5831784 AAAATATAAG
5831794 AAAAAAAGT
1 AAAAAAAGT
5831803 AAAAAAAGT
1 AAAAAAAGT
*
5831812 TAAAAAAGT
1 AAAAAAAGT
5831821 AAAAAAAGT
1 AAAAAAAGT
5831830 AAAAAAA
1 AAAAAAA
5831837 AATATAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (9 bp):
AAAAAAAGT
Found at i:5833887 original size:22 final size:21
Alignment explanation
Indices: 5833854--5833899 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
5833844 GCTTAATTTC
5833854 TTTTATATAGTTT-ATAAATT
1 TTTTATATAGTTTGATAAATT
*
5833874 TTTTATATTAAGTTTGATACATT
1 TTTTATA-T-AGTTTGATAAATT
5833897 TTT
1 TTT
5833900 AGTTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 1 0.05
22 5 0.23
23 9 0.41
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (21 bp):
TTTTATATAGTTTGATAAATT
Found at i:5838034 original size:46 final size:46
Alignment explanation
Indices: 5837984--5838159 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
5837974 TGGTTGAGCA
5837984 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5838030 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
5838075 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5838123 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5838160 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5838140 original size:93 final size:93
Alignment explanation
Indices: 5837981--5838152 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
5837971 GGATGGTTGA
* *
5837981 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5838046 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
5838074 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5838139 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
5838153 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:5845615 original size:46 final size:46
Alignment explanation
Indices: 5845565--5845877 Score: 583
Period size: 46 Copynumber: 6.8 Consensus size: 46
5845555 TGGTTGAGCA
5845565 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
5845611 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
5845657 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
5845703 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
5845749 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
5845795 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
5845841 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5845878 GCGGGTTACA
Statistics
Matches: 263, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
45 2 0.01
46 261 0.99
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5856781 original size:20 final size:20
Alignment explanation
Indices: 5856756--5856807 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
5856746 GAGGAAAAGC
5856756 ACACGCCCGTGTGCTTAGGG
1 ACACGCCCGTGTGCTTAGGG
5856776 ACACGCCCGTGTGCTTAGGG
1 ACACGCCCGTGTGCTTAGGG
5856796 ACACGCCCGTGT
1 ACACGCCCGTGT
5856808 CCCTTACCCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.33, G:0.33, T:0.19
Consensus pattern (20 bp):
ACACGCCCGTGTGCTTAGGG
Found at i:5861943 original size:26 final size:26
Alignment explanation
Indices: 5861890--5861944 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
5861880 CTCAGTACAG
* *
5861890 TTTCAAAAAGTACTAACTATAGCGTT
1 TTTCAAAAAGTACTAACTAAAGCATT
* * *
5861916 TTTCAGAAAGTTCTAACTAAAGTATT
1 TTTCAAAAAGTACTAACTAAAGCATT
5861942 TTT
1 TTT
5861945 TAAATTCAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (26 bp):
TTTCAAAAAGTACTAACTAAAGCATT
Found at i:5862255 original size:14 final size:14
Alignment explanation
Indices: 5862236--5862263 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5862226 CATAACACAA
5862236 AATTTCATATACAG
1 AATTTCATATACAG
5862250 AATTTCATATACAG
1 AATTTCATATACAG
5862264 TCAGATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
AATTTCATATACAG
Found at i:5864508 original size:39 final size:39
Alignment explanation
Indices: 5864438--5864692 Score: 384
Period size: 39 Copynumber: 6.5 Consensus size: 39
5864428 NNNNNNNNNN
* * * **
5864438 CTTTAACCCGGATACATTTTCATCATTAAGCCTGCGGGA
1 CTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGA
* * *
5864477 CTTTGGCCCTGATACATTTCCAGCACGAAGCCTGCAGGA
1 CTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGA
*
5864516 CTTTGGCCCGGATACATTTCCAGCACGAAGCCTGCGGGA
1 CTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGA
*
5864555 CTTTAGTCCGGATACATTTCCAGCACGAAGCCTGCGGGA
1 CTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGA
* * *
5864594 CTTTAGCCCAGATATATTTCTAGCACGAAGCCTGCGGGA
1 CTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGA
*
5864633 CTTTAGCCCGGATTCATTTCCAGCACGAAGCCTGCGGGA
1 CTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGA
5864672 CTTTAGCCCGGATACATTTCC
1 CTTTAGCCCGGATACATTTCC
5864693 GAATTTACCT
Statistics
Matches: 195, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 195 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (39 bp):
CTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGA
Found at i:5865648 original size:6 final size:6
Alignment explanation
Indices: 5865632--5865666 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
5865622 GGGTTGTTAC
5865632 AAAAAT AAAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT AAAA
5865667 CAAGACCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:5872167 original size:40 final size:39
Alignment explanation
Indices: 5872136--5872345 Score: 233
Period size: 40 Copynumber: 5.3 Consensus size: 39
5872126 GGACTAAGAT
* *
5872136 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
5872176 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
5872216 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* ** *
5872256 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGAT-ACAAATCCGGGTTAAGTC
* * * * *
5872296 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
5872335 CCGAAGGCATT
1 CCGAAGGCATT
5872346 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
39 33 0.22
40 117 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:5872299 original size:120 final size:120
Alignment explanation
Indices: 5872083--5872345 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
5872073 TTGAATGCTG
* *
5872083 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
5872147 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
5872203 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * * * *
5872266 TCGTGCGAGTTGTTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
5872322 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
5872346 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 38 0.32
120 73 0.61
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:5872365 original size:79 final size:80
Alignment explanation
Indices: 5872136--5872380 Score: 228
Period size: 80 Copynumber: 3.1 Consensus size: 80
5872126 GGACTAAGAT
* * * * * * * ** *
5872136 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGA-GATAC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-GC
5872199 TAAATCCGGGTTAAGTC
64 TAAATCCGGGTTAAGTC
* * * ** ** *
5872216 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
5872281 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
5872296 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
5872360 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
5872374 CCGAAGG
1 CCGAAGG
5872381 TACGTGATTT
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
78 14 0.10
79 46 0.33
80 75 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:5880115 original size:40 final size:40
Alignment explanation
Indices: 5880032--5880374 Score: 467
Period size: 40 Copynumber: 8.6 Consensus size: 40
5880022 TTGAATGCTG
* * * * * *
5880032 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
5880072 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
5880112 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
5880152 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
5880192 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
5880232 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
5880272 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
5880312 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
5880351 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
5880375 TGAACGAGGA
Statistics
Matches: 281, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.12
40 238 0.85
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:5887338 original size:15 final size:16
Alignment explanation
Indices: 5887313--5887354 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
5887303 ATTTATTATT
5887313 AAATAATTTTTAAAATA
1 AAAT-ATTTTTAAAATA
**
5887330 AAATATTTTTAACGTA
1 AAATATTTTTAAAATA
5887346 AAATATTTT
1 AAATATTTT
5887355 ATTTTACCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
AAATATTTTTAAAATA
Found at i:5888825 original size:18 final size:19
Alignment explanation
Indices: 5888791--5888830 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5888781 TATAACTTTT
5888791 ATTTTAAATTAATTTTTAA
1 ATTTTAAATTAATTTTTAA
5888810 ATTTT-AATTACA-TTTTAA
1 ATTTTAAATTA-ATTTTTAA
5888828 ATT
1 ATT
5888831 ATCGATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTAAATTAATTTTTAA
Found at i:5888905 original size:14 final size:15
Alignment explanation
Indices: 5888873--5888919 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
5888863 ATTAAAACAT
*
5888873 TAATCTAAATTTTATA
1 TAAT-TAAATTTTAAA
5888889 TAATTAAA-TTTAAA
1 TAATTAAATTTTAAA
*
5888903 TAA-AAAATTTTAAA
1 TAATTAAATTTTAAA
5888917 TAA
1 TAA
5888920 AAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.11
14 17 0.61
15 4 0.14
16 4 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATTAAATTTTAAA
Found at i:5888920 original size:14 final size:14
Alignment explanation
Indices: 5888879--5888922 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
5888869 ACATTAATCT
* *
5888879 AAATTTTATATAATT
1 AAATTTTAAATAA-A
5888894 AAA-TTTAAATAAA
1 AAATTTTAAATAAA
5888907 AAATTTTAAATAAA
1 AAATTTTAAATAAA
5888921 AA
1 AA
5888923 TAAAATATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 3 0.12
14 20 0.77
15 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATTTTAAATAAA
Found at i:5890547 original size:3 final size:3
Alignment explanation
Indices: 5890541--5890570 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5890531 TCAACCATGG
*
5890541 TGA TGA TGA TGA TGA TGA TGA TTA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
5890571 GTACAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (3 bp):
TGA
Found at i:5894415 original size:16 final size:16
Alignment explanation
Indices: 5894367--5894418 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
5894357 TTTGGTTCGC
*
5894367 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
* *
5894383 CGTATTGAATTAGAGG
1 TGTATTGGATTAGAGG
5894399 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5894415 TGTA
1 TGTA
5894419 ATAGCTAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:5894675 original size:18 final size:17
Alignment explanation
Indices: 5894654--5894688 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5894644 TTATTATTAA
*
5894654 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5894672 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5894689 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5894908 original size:121 final size:120
Alignment explanation
Indices: 5894637--5895030 Score: 761
Period size: 120 Copynumber: 3.3 Consensus size: 120
5894627 ATCATATTTA
5894637 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
5894702 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
5894757 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
5894822 TATTCTTATATTTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATA-TTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
5894878 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
5894943 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
5894998 AACATAATTATTATTAAATATAATTTAATTAAA
1 AACATAATTATTATTAAATATATTTTAATTAAA
5895031 NNNNNNNNNN
Statistics
Matches: 270, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
120 151 0.56
121 119 0.44
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:5894916 original size:18 final size:17
Alignment explanation
Indices: 5894895--5894929 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5894885 TTATTATTAA
*
5894895 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5894913 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5894930 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5899136 original size:45 final size:46
Alignment explanation
Indices: 5899048--5899138 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
5899038 AAAATATGTC
*
5899048 TATAGTGATTGTATTTTTTGAAAATTTCAAAGTAGGAAATTTAATT
1 TATAGTGATTGTATTTTTTAAAAATTTCAAAGTAGGAAATTTAATT
* * *
5899094 TATAGTGGTTGTATTTTTTAAAAATTTTATAGTAGG-AATTTAATT
1 TATAGTGATTGTATTTTTTAAAAATTTCAAAGTAGGAAATTTAATT
5899139 CTGTGAAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 9 0.22
46 32 0.78
ACGTcount: A:0.35, C:0.01, G:0.15, T:0.48
Consensus pattern (46 bp):
TATAGTGATTGTATTTTTTAAAAATTTCAAAGTAGGAAATTTAATT
Found at i:5899191 original size:25 final size:26
Alignment explanation
Indices: 5899153--5899201 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
5899143 GAAGAATAAG
*
5899153 TTTTATTATAAAAATCATGTTTAATT
1 TTTTATTATAAAAATCAAGTTTAATT
*
5899179 TTTTATT-TCAAAATCAAGTTTAA
1 TTTTATTATAAAAATCAAGTTTAA
5899202 GAATTGGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (26 bp):
TTTTATTATAAAAATCAAGTTTAATT
Found at i:5899475 original size:23 final size:23
Alignment explanation
Indices: 5899445--5899490 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5899435 AGAAGCTAGT
5899445 ATGTAACTTAATCAGGCAGCAGA
1 ATGTAACTTAATCAGGCAGCAGA
5899468 ATGTAACTTAATCAGGCAGCAGA
1 ATGTAACTTAATCAGGCAGCAGA
5899491 CATGAAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (23 bp):
ATGTAACTTAATCAGGCAGCAGA
Found at i:5901832 original size:24 final size:24
Alignment explanation
Indices: 5901783--5901833 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5901773 TTGTTATTAT
*
5901783 TATATTTCTTAATATATATATATA
1 TATATTTCTTAATATATATAGATA
* *
5901807 TATATTCTTTTAATATAT-TAGGTA
1 TATATT-TCTTAATATATATAGATA
5901831 TAT
1 TAT
5901834 TCTAAATTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (24 bp):
TATATTTCTTAATATATATAGATA
Found at i:5901879 original size:25 final size:25
Alignment explanation
Indices: 5901844--5901911 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
5901834 TCTAAATTCT
*
5901844 ATATTACGTATATATATATTA-TACA
1 ATATTATGTATATATAT-TTACTACA
* * *
5901869 ATTTTATGTATATATCTTTACTACT
1 ATATTATGTATATATATTTACTACA
*
5901894 ATATTATTTATATATATT
1 ATATTATGTATATATATT
5901912 ACATGTTATC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
24 3 0.09
25 32 0.91
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (25 bp):
ATATTATGTATATATATTTACTACA
Found at i:5901947 original size:22 final size:23
Alignment explanation
Indices: 5901872--5901983 Score: 73
Period size: 25 Copynumber: 4.7 Consensus size: 23
5901862 TTATACAATT
* *
5901872 TTATGTATATATCTTTACTACTATA
1 TTATGTGTATAT-TTTAC-ATTATA
* * * *
5901897 TTATTTATATATATTACATGTTATC
1 TTATGTGTATATTTTACA--TTATA
5901922 TTATGTGTATATTTTA-ATTATA
1 TTATGTGTATATTTTACATTATA
* *
5901944 TTATGTATGTATTTTTTACACTATA
1 TTATG--TGTATATTTTACATTATA
**
5901969 TTATGTACATATTTT
1 TTATGTGTATATTTT
5901984 TAATATTATC
Statistics
Matches: 69, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
22 9 0.13
23 8 0.12
24 15 0.22
25 37 0.54
ACGTcount: A:0.30, C:0.07, G:0.06, T:0.56
Consensus pattern (23 bp):
TTATGTGTATATTTTACATTATA
Found at i:5901974 original size:25 final size:24
Alignment explanation
Indices: 5901927--5902009 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
5901917 TTATCTTATG
* *
5901927 TGTATATTTTAATTATATTATGTA
1 TGTATTTTTTAACTATATTATGTA
5901951 TGTATTTTTTACACTATATTATGTA
1 TGTATTTTTTA-ACTATATTATGTA
** * *
5901976 CATA-TTTTTAA-TATTATCACGTA
1 TGTATTTTTTAACTA-TATTATGTA
*
5901999 TTTATTTTTTA
1 TGTATTTTTTA
5902010 TATATGTACA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 2 0.04
23 10 0.21
24 22 0.46
25 14 0.29
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (24 bp):
TGTATTTTTTAACTATATTATGTA
Found at i:5901991 original size:20 final size:20
Alignment explanation
Indices: 5901966--5902024 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
5901956 TTTTTACACT
5901966 ATATTATGTACATATTTTTA
1 ATATTATGTACATATTTTTA
** *
5901986 ATATTATCACGTATTTATTTTTT
1 ATATTAT---GTACATATTTTTA
5902009 ATA-TATGTACATATTT
1 ATATTATGTACATATTT
5902025 ATGTAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 3 0.10
23 13 0.42
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATTATGTACATATTTTTA
Found at i:5902163 original size:16 final size:15
Alignment explanation
Indices: 5902139--5902173 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
5902129 TAATTATTAT
5902139 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
5902155 TATTTTAATATTTTA
1 TATTCTAATATTTTA
5902170 TATT
1 TATT
5902174 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:5903236 original size:18 final size:17
Alignment explanation
Indices: 5903198--5903236 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
5903188 GGTTTGAAAA
5903198 TTTTAATTAATTAAATTT
1 TTTTAATTAA-TAAATTT
5903216 TTTTAATTAA-AAATTT
1 TTTTAATTAATAAATTT
5903232 ATTTT
1 -TTTT
5903237 CATCCCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 4 0.20
18 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATTAATAAATTT
Found at i:5905632 original size:16 final size:17
Alignment explanation
Indices: 5905598--5905636 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
5905588 AATAATTTAT
**
5905598 AAAAAAATTTAAGTCTA
1 AAAAAAATTTAAGAATA
5905615 AAAAAAATTTAA-AATA
1 AAAAAAATTTAAGAATA
5905631 AAAAAA
1 AAAAAA
5905637 TTAAATTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAAAAATTTAAGAATA
Found at i:5905820 original size:6 final size:6
Alignment explanation
Indices: 5905809--5905838 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5905799 TGATACTACT
*
5905809 ATCACC ATCACC ATCACC ATCACC ACCACC
1 ATCACC ATCACC ATCACC ATCACC ATCACC
5905839 CCTTATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.53, G:0.00, T:0.13
Consensus pattern (6 bp):
ATCACC
Found at i:5905847 original size:3 final size:3
Alignment explanation
Indices: 5905841--5905884 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
5905831 CCACCACCCC
*
5905841 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5905885 TCCTTTTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5908554 original size:13 final size:13
Alignment explanation
Indices: 5908536--5908569 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
5908526 ACAAATTAAG
5908536 GTCACACGGCCAA
1 GTCACACGGCCAA
5908549 GTCACACGGCCAA
1 GTCACACGGCCAA
5908562 GTCACACG
1 GTCACACG
5908570 CCCGTGTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.38, G:0.24, T:0.09
Consensus pattern (13 bp):
GTCACACGGCCAA
Found at i:5913034 original size:79 final size:81
Alignment explanation
Indices: 5912898--5913080 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
5912888 TTGAATGATG
* *
5912898 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
5912962 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
5912977 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
5913039 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
5913057 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
5913081 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.65
80 30 0.34
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:5913096 original size:40 final size:40
Alignment explanation
Indices: 5912899--5913082 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
5912889 TGAATGATGT
* * * *
5912899 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
5912939 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
5912979 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
5913017 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
5913058 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
5913083 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:5913104 original size:79 final size:79
Alignment explanation
Indices: 5912951--5913115 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
5912941 GGACTAAGAT
* **
5912951 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
5913016 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
5913030 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
5913093 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
5913109 CCGAAGG
1 CCGAAGG
5913116 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:5931509 original size:13 final size:13
Alignment explanation
Indices: 5931493--5931522 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5931483 TACACGGGCA
5931493 TGTCACACGAGCG
1 TGTCACACGAGCG
*
5931506 TGTCACACTAGCG
1 TGTCACACGAGCG
5931519 TGTC
1 TGTC
5931523 CTTGTCGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.30, G:0.27, T:0.23
Consensus pattern (13 bp):
TGTCACACGAGCG
Found at i:5940336 original size:21 final size:21
Alignment explanation
Indices: 5940280--5940337 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
5940270 ATATTGATAT
* *
5940280 ACATGATATGAC-CTGATATGC
1 ACATGATATG-CTATGACATGC
*
5940301 ACATGATATGTTATGACATGC
1 ACATGATATGCTATGACATGC
5940322 ACATGATATGCTATGA
1 ACATGATATGCTATGA
5940338 TATACTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (21 bp):
ACATGATATGCTATGACATGC
Found at i:5940470 original size:24 final size:24
Alignment explanation
Indices: 5940388--5940470 Score: 105
Period size: 25 Copynumber: 3.4 Consensus size: 24
5940378 AGGAAGTGCA
*
5940388 AAAAGGGCTTTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTATC
*
5940412 GAAAAGGGCTGTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTATC
*
5940437 AGAAAGGGCTTTGCCCCAG-TTATT
1 A-AAAGGGCTTTGCCCCAGTTTATC
5940461 AAAAGAGGCT
1 AAAAG-GGCT
5940471 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 38 0.73
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATC
Found at i:5947547 original size:21 final size:21
Alignment explanation
Indices: 5947514--5947580 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
5947504 CATGAGATAT
*
5947514 TGATATG--CATGATATGACC
1 TGATATGCACATGATATGACA
**
5947533 TGATATGCACATGATATGTTA
1 TGATATGCACATGATATGACA
*
5947554 TGACATGCACATGATATG-CTA
1 TGATATGCACATGATATGAC-A
5947575 TGATAT
1 TGATAT
5947581 ACTCATTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 7 0.18
21 32 0.82
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.34
Consensus pattern (21 bp):
TGATATGCACATGATATGACA
Found at i:5947662 original size:25 final size:24
Alignment explanation
Indices: 5947628--5947692 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
5947618 AGGAAGTGCA
* *
5947628 AAAAGAGCTTTGCCCTAGTATACC
1 AAAAGGGCTTTGCCCTAATATACC
* * *
5947652 GAAAAGGGCTTTGCCATAATTTATC
1 -AAAAGGGCTTTGCCCTAATATACC
5947677 AGAAAGGGCTTTGCCC
1 A-AAAGGGCTTTGCCC
5947693 CAGTTATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 1 0.03
25 32 0.97
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCTAATATACC
Found at i:5962775 original size:46 final size:46
Alignment explanation
Indices: 5962711--5962928 Score: 366
Period size: 46 Copynumber: 4.7 Consensus size: 46
5962701 AACCCGCCCC
* * *
5962711 TAAGTGAACTCGGACTCAACTCAACGAGCTTAGG-CGTTCGCATCCC
1 TAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCA
* * *
5962757 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
5962803 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
5962849 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
5962895 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
5962929 TGCTCAACCA
Statistics
Matches: 165, Mismatches: 6, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
45 3 0.02
46 162 0.98
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:5967458 original size:13 final size:13
Alignment explanation
Indices: 5967440--5967466 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5967430 GGAATGCCTT
5967440 GGTCCTCTTCGAA
1 GGTCCTCTTCGAA
5967453 GGTCCTCTTCGAA
1 GGTCCTCTTCGAA
5967466 G
1 G
5967467 TCAAGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.26, T:0.30
Consensus pattern (13 bp):
GGTCCTCTTCGAA
Found at i:5973046 original size:48 final size:48
Alignment explanation
Indices: 5972994--5973373 Score: 342
Period size: 48 Copynumber: 8.0 Consensus size: 48
5972984 CGAGGCACTT
*
5972994 TTATTATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 TTATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
* * ** ** *
5973042 TTATTATGTGAGCCAGTGTAAGACCATGTTTGAAACATGGCATCATCT
1 TTATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
* * * * * *
5973090 TTGA-TATGTGTGCTAGTGTAAGACCATGTTTGGGACTTGGCATCGACCA
1 TT-ATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG-GCA
* * *
5973139 -CATT-TGAGAGCCAGTGTAAGACTATGTCTGGGATATGGCATCGGCCA
1 TTATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CA
* * *
5973186 -CATT-TGAGAGCCAGTGTAAGGCCATGTTTGGGACATGGCATCGGCA
1 TTATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
* * * * * * * *
5973232 GTGA-GACGAGAGCTAGTGTAAGCCCATGTCTGAGACATGGCACCGGCC
1 -TTATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
** * * *
5973280 TTGA-CCTGTGAGCCAGTGTAAGACCATATCTGGGATATGGCATCGGCA
1 TT-ATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
* * *
5973328 TTATTATGAGAGCTAGTGTAAGACCATATCTGGGAAATGGCATCGG
1 TTATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG
5973374 AATCAAAATG
Statistics
Matches: 270, Mismatches: 53, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
46 2 0.01
47 77 0.29
48 189 0.70
49 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27
Consensus pattern (48 bp):
TTATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
Found at i:5973171 original size:47 final size:47
Alignment explanation
Indices: 5973003--5973228 Score: 206
Period size: 47 Copynumber: 4.8 Consensus size: 47
5972993 TTTATTATGT
* * * * *
5973003 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG-GCATTATTATGT
1 GAGCCAGTGTAAGACCATGTTTGGGACTTGGCATCGACCA-CATT-TGA
** * *** * *
5973051 GAGCCAGTGTAAGACCATGTTTGAAACATGGCATC-ATCTTTGATATGT
1 GAGCCAGTGTAAGACCATGTTTGGGACTTGGCATCGA-C-CACATTTGA
* *
5973099 GTGCTAGTGTAAGACCATGTTTGGGACTTGGCATCGACCACATTTGA
1 GAGCCAGTGTAAGACCATGTTTGGGACTTGGCATCGACCACATTTGA
* * *
5973146 GAGCCAGTGTAAGACTATGTCTGGGA-TATGGCATCGGCCACATTTGA
1 GAGCCAGTGTAAGACCATGTTTGGGACT-TGGCATCGACCACATTTGA
* *
5973193 GAGCCAGTGTAAGGCCATGTTTGGGACATGGCATCG
1 GAGCCAGTGTAAGACCATGTTTGGGACTTGGCATCG
5973229 GCAGTGAGAC
Statistics
Matches: 145, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
46 1 0.01
47 75 0.52
48 66 0.46
49 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTTTGGGACTTGGCATCGACCACATTTGA
Found at i:5976781 original size:16 final size:16
Alignment explanation
Indices: 5976760--5976803 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
5976750 TATAGTATCG
5976760 TATCTTGGTATTTCTC
1 TATCTTGGTATTTCTC
*
5976776 TATCTTGG-ATTTCTT
1 TATCTTGGTATTTCTC
5976791 TA-CTTGGT-TTTCT
1 TATCTTGGTATTTCT
5976804 TGTTATCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 10 0.38
15 8 0.31
16 8 0.31
ACGTcount: A:0.11, C:0.16, G:0.14, T:0.59
Consensus pattern (16 bp):
TATCTTGGTATTTCTC
Found at i:5978349 original size:47 final size:47
Alignment explanation
Indices: 5978295--5978444 Score: 237
Period size: 47 Copynumber: 3.2 Consensus size: 47
5978285 AGGTTGGTGG
* * *
5978295 CATGGCATCGGCCACATTTGAGAGCCTGTGTAAGATCATGTTTAGGA
1 CATGGCATCGGCCACATTTGAGAGCCTGTGTAAGACCATGTCTGGGA
*
5978342 CATGGCATTGGCCACATTTGAGAGCCTGTGTAAGACCATGTCTGGGA
1 CATGGCATCGGCCACATTTGAGAGCCTGTGTAAGACCATGTCTGGGA
* * *
5978389 CATGGTATCGGCCTCATTTGAGAGCCAGTGTAAGACCATGTCTGGGA
1 CATGGCATCGGCCACATTTGAGAGCCTGTGTAAGACCATGTCTGGGA
5978436 CATGGCATC
1 CATGGCATC
5978445 AGCATTGAGA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 94 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (47 bp):
CATGGCATCGGCCACATTTGAGAGCCTGTGTAAGACCATGTCTGGGA
Found at i:5978481 original size:48 final size:49
Alignment explanation
Indices: 5978360--5978593 Score: 185
Period size: 48 Copynumber: 4.9 Consensus size: 49
5978350 TGGCCACATT
* * * * * * **
5978360 TGAGAGCCTGTGTAAGACCATGTCTGGGACATGGTATCGGC-CTCA-TT
1 TGAGAGCCAGTGTAAGACCATATCTGGGACATGGCATCAGCATTGACGA
*
5978407 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGA-GA
1 TGAGAGCCAGTGTAAGACCATATCTGGGACATGGCATCAGCATTGACGA
* * *
5978455 CGAGAGCTAGTGTAAGACCATATCTGGGACATGGCGTCA-C-TCTCGACG-
1 TGAGAGCCAGTGTAAGACCATATCTGGGACATGGCATCAGCAT-T-GACGA
* * * * * * **
5978503 TGTGAGCCAGTGTAAGACCATATTTGGGATATGGCATC-GAAATCATTA
1 TGAGAGCCAGTGTAAGACCATATCTGGGACATGGCATCAGCATTGACGA
* * * *
5978551 TGAGAGCCAGTGTCAGACCATATTTGGGATATGGCATTAGCAT
1 TGAGAGCCAGTGTAAGACCATATCTGGGACATGGCATCAGCAT
5978594 CGAAATGTGT
Statistics
Matches: 152, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
46 1 0.01
47 41 0.27
48 107 0.70
49 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (49 bp):
TGAGAGCCAGTGTAAGACCATATCTGGGACATGGCATCAGCATTGACGA
Found at i:5978556 original size:96 final size:96
Alignment explanation
Indices: 5978361--5978585 Score: 231
Period size: 96 Copynumber: 2.4 Consensus size: 96
5978351 GGCCACATTT
* * ** * ** *
5978361 GAGAGCCTGTGTAAGACCATGTCTGGGACATGGTATCGGC-CTC-ATTTGAGAGCCAGTGTAAGA
1 GAGAGCCAGTGTAAGACCATATCTGGGACATGGCGTC-ACTCTCGACGTGTGAGCCAGTGTAAGA
* * * *
5978424 CCATGTCTGGGACATGGCATCAGCATTGAGAC
65 CCATATCTGGGACATGGCATCAGAAATCAGAC
*
5978456 GAGAGCTAGTGTAAGACCATATCTGGGACATGGCGTCACTCTCGACGTGTGAGCCAGTGTAAGAC
1 GAGAGCCAGTGTAAGACCATATCTGGGACATGGCGTCACTCTCGACGTGTGAGCCAGTGTAAGAC
* * * *
5978521 CATATTTGGGATATGGCATC-GAAATCATTAT
66 CATATCTGGGACATGGCATCAGAAATCA-GAC
* * *
5978552 GAGAGCCAGTGTCAGACCATATTTGGGATATGGC
1 GAGAGCCAGTGTAAGACCATATCTGGGACATGGC
5978586 ATTAGCATCG
Statistics
Matches: 106, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
94 1 0.01
95 39 0.37
96 66 0.62
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (96 bp):
GAGAGCCAGTGTAAGACCATATCTGGGACATGGCGTCACTCTCGACGTGTGAGCCAGTGTAAGAC
CATATCTGGGACATGGCATCAGAAATCAGAC
Found at i:5986727 original size:21 final size:21
Alignment explanation
Indices: 5986701--5986741 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5986691 GTGTTATACT
*
5986701 GATAGAAGTCTGG-GTTGTATC
1 GATAGAA-CCTGGAGTTGTATC
5986722 GATAGAACCTGGAGTTGTAT
1 GATAGAACCTGGAGTTGTAT
5986742 TGGTAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.27, C:0.10, G:0.32, T:0.32
Consensus pattern (21 bp):
GATAGAACCTGGAGTTGTATC
Found at i:5990526 original size:34 final size:34
Alignment explanation
Indices: 5990483--5990549 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
5990473 GTAAGCTAAG
5990483 ATTTCTAATAGATAAATTAAAAAGATTCTAGAAT
1 ATTTCTAATAGATAAATTAAAAAGATTCTAGAAT
5990517 ATTTCTAATAGATAAATTAAAAAGATTCTAGAA
1 ATTTCTAATAGATAAATTAAAAAGATTCTAGAA
5990550 AAACTGGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (34 bp):
ATTTCTAATAGATAAATTAAAAAGATTCTAGAAT
Found at i:5993459 original size:31 final size:30
Alignment explanation
Indices: 5993424--5993481 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
5993414 GGAAAAATTA
5993424 GAAAAGAGTAGGGACAAAATTGG-AATTTATG
1 GAAAAG-GTAGGGACAAAA-TGGTAATTTATG
* *
5993455 GAAAAGTTAGGGGCAAAATGGTAATTT
1 GAAAAGGTAGGGACAAAATGGTAATTT
5993482 TGCCTAGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 3 0.12
30 15 0.62
31 6 0.25
ACGTcount: A:0.43, C:0.03, G:0.29, T:0.24
Consensus pattern (30 bp):
GAAAAGGTAGGGACAAAATGGTAATTTATG
Found at i:5995719 original size:27 final size:27
Alignment explanation
Indices: 5995690--5995832 Score: 121
Period size: 27 Copynumber: 5.3 Consensus size: 27
5995680 CAAAATAGAC
* * *
5995690 ATTTTACCCTACAAGGGTATATCGGTC
1 ATTTTACACTACAAGGGTATTTCGGTA
* *
5995717 ATTTTACACTGCAAGGGTATTTTGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
* *
5995744 ATTTTACACTACAAAGGTATTTCGATA
1 ATTTTACACTACAAGGGTATTTCGGTA
* * *
5995771 ATTTTACA-AATC-GGGGTTGTTTCGGTA
1 ATTTTACACTA-CAAGGG-TATTTCGGTA
* * *
5995798 ATTTTACA-AACCGAGGGTATTTTGGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
5995825 ATTTTACA
1 ATTTTACA
5995833 AATTGAGGGA
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
26 3 0.03
27 89 0.94
28 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGGTA
Found at i:5995833 original size:27 final size:27
Alignment explanation
Indices: 5995730--5996076 Score: 314
Period size: 27 Copynumber: 12.9 Consensus size: 27
5995720 TTACACTGCA
* *
5995730 AGGGTATTTTGGTAATTTTAC-ACTACA
1 AGGGTATTTTGGTAATTTTACAAAT-CG
* * *
5995757 AAGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTTGGTAATTTTACAAATCG
*
5995784 -GGGT-TGTTTCGGTAATTTTACAAACCG
1 AGGGTAT-TTT-GGTAATTTTACAAATCG
*
5995811 AGGGTATTTTGGTAATTTTACAAATTG
1 AGGGTATTTTGGTAATTTTACAAATCG
***
5995838 AGGG-ATTTCAATAATTTTACAAATCG
1 AGGGTATTTTGGTAATTTTACAAATCG
*
5995864 AGGGTGTTTTGGTAATTTTACAAATCG
1 AGGGTATTTTGGTAATTTTACAAATCG
* *** *
5995891 AGGGTGTTTCAATAATTGTACAAATCG
1 AGGGTATTTTGGTAATTTTACAAATCG
* *
5995918 AGGGTATTTTAGTAATTTTACAAATTG
1 AGGGTATTTTGGTAATTTTACAAATCG
** * *
5995945 AGGGTATTTTAATAATTTTGCAAA-CTA
1 AGGGTATTTTGGTAATTTTACAAATC-G
* *
5995972 ATGGTATTTTGGTAATTTTACAAATTG
1 AGGGTATTTTGGTAATTTTACAAATCG
* *
5995999 -GGGATATTTCGGTAATTTTACAAATTTG
1 AGGG-TATTTTGGTAATTTTACAAA-TCG
*
5996027 -GGGTACTTTGGTAATTTTACAAATCG
1 AGGGTATTTTGGTAATTTTACAAATCG
* *
5996053 -GAGGTACTTCGGTAATTTTACAAA
1 AG-GGTATTTTGGTAATTTTACAAA
5996077 CTGGTAATTT
Statistics
Matches: 265, Mismatches: 44, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
25 1 0.00
26 32 0.12
27 216 0.82
28 15 0.06
29 1 0.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTACAAATCG
Found at i:5996084 original size:16 final size:16
Alignment explanation
Indices: 5996063--5996094 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5996053 GAGGTACTTC
5996063 GGTAATTTTACAAACT
1 GGTAATTTTACAAACT
5996079 GGTAATTTTACAAACT
1 GGTAATTTTACAAACT
5996095 AGGGGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
GGTAATTTTACAAACT
Found at i:5996467 original size:28 final size:28
Alignment explanation
Indices: 5996430--5996493 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
5996420 TGGCTCCTCT
* *
5996430 AAGCCCAATCTCGTTCACATGGCCCATC
1 AAGCCCAATCACATTCACATGGCCCATC
* *
5996458 AGGCCCAATCACATTCATATGGCCCATC
1 AAGCCCAATCACATTCACATGGCCCATC
5996486 AAGCCCAA
1 AAGCCCAA
5996494 CTACTTCCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.38, G:0.14, T:0.19
Consensus pattern (28 bp):
AAGCCCAATCACATTCACATGGCCCATC
Found at i:5997959 original size:48 final size:48
Alignment explanation
Indices: 5997907--5998044 Score: 147
Period size: 48 Copynumber: 2.9 Consensus size: 48
5997897 ACGATGTCTC
* *
5997907 ATATCGATGCCAATACCATATCCCAGATATAG-TCTT-CTATGGGATCGA
1 ATATCGATGCCAATACCATGTCCCAGACAT-GTTCTTAC-ATGGGATCGA
* * * *
5997955 ATATCGATACCGATTCCATGTCCTAGACATGTTCTTACATGGGATCGA
1 ATATCGATGCCAATACCATGTCCCAGACATGTTCTTACATGGGATCGA
* * *
5998003 ATAAT-GATGCCAATGCCATGTCCCAGGCATGGTCTTACATGG
1 AT-ATCGATGCCAATACCATGTCCCAGACATGTTCTTACATGG
5998045 CATCACACAT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
47 1 0.01
48 71 0.95
49 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (48 bp):
ATATCGATGCCAATACCATGTCCCAGACATGTTCTTACATGGGATCGA
Found at i:6005705 original size:48 final size:48
Alignment explanation
Indices: 6005648--6005739 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
6005638 ATGTCTCATG
* *
6005648 TCGATGCCAATGCCATATCCCA-GATATGGTCTTACATGGGATCAAATA
1 TCGACGCCAATGCCATATCCCATG-CATGGTCTTACATGGGATCAAATA
*
6005696 TCGACGCCAATGCCATGTCCCATGCATGGTCTTACATGGGATCA
1 TCGACGCCAATGCCATATCCCATGCATGGTCTTACATGGGATCA
6005740 CACATAACCC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (48 bp):
TCGACGCCAATGCCATATCCCATGCATGGTCTTACATGGGATCAAATA
Found at i:6007894 original size:21 final size:22
Alignment explanation
Indices: 6007869--6007912 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
6007859 TTTCCATGAA
*
6007869 ATTTTTTC-TGTACATATCTAT
1 ATTTTTTCTTATACATATCTAT
6007890 ATTTTTTCTTATACATATCTAT
1 ATTTTTTCTTATACATATCTAT
6007912 A
1 A
6007913 CATGCATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.27, C:0.14, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTTTTTCTTATACATATCTAT
Found at i:6011396 original size:43 final size:43
Alignment explanation
Indices: 6011349--6011433 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
6011339 TGCTATGCTT
*
6011349 GAAGCCCGATATCATTTCACCGGCATTATAACCTGCTAGGCCC
1 GAAGCCCGATATCATCTCACCGGCATTATAACCTGCTAGGCCC
* *
6011392 GAAGCCCGATATTATCTCACCGGCATTATAGCCTGCTAGGCC
1 GAAGCCCGATATCATCTCACCGGCATTATAACCTGCTAGGCC
6011434 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.24
Consensus pattern (43 bp):
GAAGCCCGATATCATCTCACCGGCATTATAACCTGCTAGGCCC
Found at i:6014712 original size:41 final size:43
Alignment explanation
Indices: 6014667--6014758 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 43
6014657 CAGCACGAAG
* * * *
6014667 CCTGCTAGACTTTAAGTCTGA-ACTCA-TTCACCGGCATT-TCA
1 CCTGCTAGACTTGAAGCCCGATA-TCATTTCACCGGCATTATAA
*
6014708 CCTGCTAGGCTTGAAGCCCGATATCATTTCACCGGCATTATAA
1 CCTGCTAGACTTGAAGCCCGATATCATTTCACCGGCATTATAA
6014751 CCTGCTAG
1 CCTGCTAG
6014759 GCCCNNNNNN
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
41 20 0.47
42 13 0.30
43 10 0.23
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (43 bp):
CCTGCTAGACTTGAAGCCCGATATCATTTCACCGGCATTATAA
Found at i:6017901 original size:43 final size:43
Alignment explanation
Indices: 6017793--6017923 Score: 165
Period size: 43 Copynumber: 3.0 Consensus size: 43
6017783 NNNNNNNNNN
* *
6017793 TCATTTCGCCGGCATTATAGCCTGCTAGGCTCAAAGGCTCGAATAA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAA-GCCCG-AT-A
* * *
6017839 T-ATTTCACCGGCATCATAGCCTACTAAGCTCAAAGCCCGATA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGATA
* *
6017881 TCATTTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGATA
6017924 ATATTATTCA
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
42 2 0.03
43 38 0.51
44 4 0.05
45 29 0.39
46 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (43 bp):
TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGATA
Found at i:6019377 original size:14 final size:14
Alignment explanation
Indices: 6019358--6019384 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6019348 TGGCTTCTTC
6019358 TATATATATATTTA
1 TATATATATATTTA
6019372 TATATATATATTT
1 TATATATATATTT
6019385 TAGCTACGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATATATATATTTA
Found at i:6029665 original size:441 final size:441
Alignment explanation
Indices: 6028824--6029706 Score: 1141
Period size: 441 Copynumber: 2.0 Consensus size: 441
6028814 GTCCTTAATC
* * * *
6028824 TTGTTAGGGTATACCTAAAGACCAATCATGAGATGATTGTAATCACATGCTTGTTTTACCTTGTT
1 TTGTTAGAGTATACCAAAAGACCAATCATGAGATGATTGTAATCACATGATTGTTTTACCTTATT
* * * ** * *
6028889 TGTTAATATAAGATATTGCCATTGTTATCTTAGTTTCTTTTTTCTGTGTGTGTAAATAAACTGAT
66 TATTAATATAAGACATTACCATTACTATCTTAGTTTCTTTTTTCTGTGTATATAAATAAACTGAT
* * *
6028954 TAATAATAAAGTCCTAAAAATGACATGATTATTCTTAAAAGGTCCTTAGTTAAGTATTATTGTGC
131 TAATAATAAAGTCCTAAAAAT-A-ATAATTATTCTTAAAAGGTCCATAGTCAAGTATTATTGTGC
* * ** * ** * *
6029019 GTTTGGATATTAATAATGCATTGAGACTAATGTGTAGTTGATTGATGTCAAAGTGTTGCCATTGA
194 GCTTGGACAACAATAATGCATTGAGACTAATGTATAGTTGATTGATAACAAAGAGTTGCCATTCA
* * * *
6029084 AATATGGATGTCAAAATCAATACATGAGTATGAGTTGGAGACAACATACTGGACTGACCCACCAT
259 AATAGGGATGTCAAAATCAATACATCAGTATGAGTTAGAGACAACATACTGAACTGACCCACCAT
* *
6029149 GAACATGTTTCTTGGATTATTATGTAATAGTCACAACATTACTCATAGTGATAACTATGTATACA
324 GAACATGTTTCTTGGATTATTATGTAATAGTCACAACATTACTCATAATGATAACTATATATACA
* **
6029214 ATCTTCAGACTTGAGATCATCATTGTCCCAACATCGTGAGTTGTATATTTTGA
389 ATCCTCAGACTTGAGATCATCATTGTCCCAACATCGTGAGCCGTATATTTTGA
*
6029267 TTGTTAGAGTATGCCAAAAGACCAATCATGAGATGATTGTAATCACAT-ATTCGTTTTACCTTAT
1 TTGTTAGAGTATACCAAAAGACCAATCATGAGATGATTGTAATCACATGATT-GTTTTACCTTAT
* *
6029331 TTATTAATATAAGACATTACCATTACTAT-TTCAGTTTC-TTTTTCTGTGTATATAATTAAATTG
65 TTATTAATATAAGACATTACCATTACTATCTT-AGTTTCTTTTTTCTGTGTATATAAATAAACTG
*
6029394 AATT-GTAATAAAGTCCTGAGAAAAT-ATAATTATTCTTAAAAGGT-CATAGTCAAGTATTATTG
129 -ATTAATAATAAAGTCCT-A-AAAATAATAATTATTCTTAAAAGGTCCATAGTCAAGTATTATTG
* * *
6029456 TGGGCTTGGACAACAATAATGCATTGAGACTAATGTATAGTTGATTGATAACCAAGAGTTGTCAT
191 TGCGCTTGGACAACAATAATGCATTGAGACTAATGTATAGTTGATTGATAACAAAGAGTTGCCAT
* * * *
6029521 TCACATAGGGATGTCAAAATCAATACATCAGTAT-ATGTTAGAGAATAACATATTGAACTGAGCC
256 TCAAATAGGGATGTCAAAATCAATACATCAGTATGA-GTTAGAG-ACAACATACTGAACTGACCC
* * ** * * *
6029585 GCTATGAGTATGTTTCTTGGATTATTATGTGATAGTCATAATATTACTCATAATGATAACTATAT
319 ACCATGAACATGTTTCTTGGATTATTATGTAATAGTCACAACATTACTCATAATGATAACTATAT
** * * *
6029650 ATATGATCCTCAGACTTGATATTATCATTTTCCCAACATCGTGAGCCGTATATTTTG
384 ATACAATCCTCAGACTTGAGATCATCATTGTCCCAACATCGTGAGCCGTATATTTTG
6029707 GTATAGCCAA
Statistics
Matches: 378, Mismatches: 55, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
439 1 0.00
440 106 0.28
441 139 0.37
442 37 0.10
443 90 0.24
444 5 0.01
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (441 bp):
TTGTTAGAGTATACCAAAAGACCAATCATGAGATGATTGTAATCACATGATTGTTTTACCTTATT
TATTAATATAAGACATTACCATTACTATCTTAGTTTCTTTTTTCTGTGTATATAAATAAACTGAT
TAATAATAAAGTCCTAAAAATAATAATTATTCTTAAAAGGTCCATAGTCAAGTATTATTGTGCGC
TTGGACAACAATAATGCATTGAGACTAATGTATAGTTGATTGATAACAAAGAGTTGCCATTCAAA
TAGGGATGTCAAAATCAATACATCAGTATGAGTTAGAGACAACATACTGAACTGACCCACCATGA
ACATGTTTCTTGGATTATTATGTAATAGTCACAACATTACTCATAATGATAACTATATATACAAT
CCTCAGACTTGAGATCATCATTGTCCCAACATCGTGAGCCGTATATTTTGA
Found at i:6030489 original size:137 final size:138
Alignment explanation
Indices: 6030324--6030597 Score: 401
Period size: 137 Copynumber: 2.0 Consensus size: 138
6030314 TATATAAAAC
*
6030324 TAATATATAAATTTGATTCAATCAAAATATTAATTGTATATATTTTACCG-AATTTATTAATATA
1 TAATATATAAATTTGATTCAATCAAAATATTAATAGTATATATTTTA-CGAAATTTATTAATATA
*
6030388 AACAATTATATTAAATAATTTCGGTCAAAAAATAAAAGACATGGAAATTAATATTCATTTGCAAA
65 AACAATTATATTAAATAATTTCGGTCAAAAAATAAAAAACATGGAAATTAATATTCATTTGCAAA
*
6030453 TAATATAAT
130 GAATATAAT
* *
6030462 TAATAT-TGAATTTGATTC-ATACAAAATATTAATAGTATATATTTTACGAAATTTATTAATATG
1 TAATATATAAATTTGATTCAAT-CAAAATATTAATAGTATATATTTTACGAAATTTATTAATATA
** * * * * *
6030525 AACAATTATATTAGTTAATTTTGGTCAAAATATAAAAAACATGGAAATTAGTATTCTTTTGGAAA
65 AACAATTATATTAAATAATTTCGGTCAAAAAATAAAAAACATGGAAATTAATATTCATTTGCAAA
6030590 GAATATAA
130 GAATATAA
6030598 ATCTTTTTTC
Statistics
Matches: 122, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
136 4 0.03
137 112 0.92
138 6 0.05
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.39
Consensus pattern (138 bp):
TAATATATAAATTTGATTCAATCAAAATATTAATAGTATATATTTTACGAAATTTATTAATATAA
ACAATTATATTAAATAATTTCGGTCAAAAAATAAAAAACATGGAAATTAATATTCATTTGCAAAG
AATATAAT
Found at i:6034126 original size:48 final size:47
Alignment explanation
Indices: 6034067--6034240 Score: 179
Period size: 48 Copynumber: 3.7 Consensus size: 47
6034057 ATATTGAGGG
* *
6034067 CCAGTGTAAGACATATCTGGGATATGCATTGGCCTTGAGATATACCAA
1 CCAGTGTAAGACATGTCTGGGATATGCATCGGCCTTGAGATATA-CAA
* * * ***
6034115 CCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGAT-GAGGG
1 CCAGTGTAAGACATGTCTGGGATATGCATCGGCCTTGAGATATACAA
* * * *
6034161 CTAGTATAAGACATGTCTGGGATATGCATCGGCCTCGAGATATTCAA
1 CCAGTGTAAGACATGTCTGGGATATGCATCGGCCTTGAGATATACAA
* * *
6034208 GCTACTGTAAGACATGTCTGGGACATGGCATCG
1 -CCAGTGTAAGACATGTCTGGGATAT-GCATCG
6034241 ACACCGATAG
Statistics
Matches: 102, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
46 36 0.35
47 1 0.01
48 59 0.58
49 6 0.06
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (47 bp):
CCAGTGTAAGACATGTCTGGGATATGCATCGGCCTTGAGATATACAA
Found at i:6034172 original size:94 final size:94
Alignment explanation
Indices: 6034023--6034240 Score: 280
Period size: 94 Copynumber: 2.3 Consensus size: 94
6034013 TATGTGTGCT
* * *
6034023 AGTGTAAGACATGTTTGGGACATGCATCGGCCACATATTGAGGGCCAGTGTAAGACATATCTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATAATGAGGGCCAGTATAAGACATATCTGGG
* *
6034088 ATATGCATTGGCCTTGAGATATACCAA-CC
66 ATATGCATCGGCCTCGAGATAT-CCAAGCC
* * *
6034117 AGTGTAAGACATGTCTGGGACATGCATCGG-CA-TTGAGATGAGGGCTAGTATAAGACATGTCTG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAT-A-ATGAGGGCCAGTATAAGACATATCTG
* *
6034180 GGATATGCATCGGCCTCGAGATATTCAAGCT
64 GGATATGCATCGGCCTCGAGATATCCAAGCC
*
6034211 ACTGTAAGACATGTCTGGGACATGGCATCG
1 AGTGTAAGACATGTCTGGGACAT-GCATCG
6034241 ACACCGATAG
Statistics
Matches: 109, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
92 1 0.01
93 6 0.06
94 96 0.88
95 6 0.06
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATAATGAGGGCCAGTATAAGACATATCTGGG
ATATGCATCGGCCTCGAGATATCCAAGCC
Found at i:6034201 original size:46 final size:46
Alignment explanation
Indices: 6034023--6034296 Score: 194
Period size: 46 Copynumber: 5.8 Consensus size: 46
6034013 TATGTGTGCT
* * *
6034023 AGTGTAAGACATGTTTGGGACATGCATCGGCCAC-ATATTGAGGGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGA-TGAGGGCC
* * * * * ***
6034069 AGTGTAAGACATATCTGGGATATGCATTGGCCTTGAGATATACCAACC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGAT-GA-GGGCC
* * *
6034117 AGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGAGGGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAGGGCC
* * ** *
6034163 AGTATAAGACATGTCTGGGATATGCATCGGCCTCGAGAT-ATTCAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA---GGGCC
* * *
6034211 ACTGTAAGACATGTCTGGGACATGGCATCGACAC-CGATAGATGAGAGCC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGC-CTCG--AGATGAGGGCC
** * *
6034260 AGTGTAAGACCGGTCTAGGACATGGCATCAGCCTCGA
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCGA
6034297 TATATGAAAG
Statistics
Matches: 178, Mismatches: 38, Indels: 23
0.74 0.16 0.10
Matches are distributed among these distances:
45 1 0.01
46 65 0.37
47 5 0.03
48 61 0.34
49 40 0.22
50 1 0.01
51 4 0.02
52 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAGGGCC
Found at i:6034269 original size:49 final size:48
Alignment explanation
Indices: 6034023--6034381 Score: 170
Period size: 49 Copynumber: 7.5 Consensus size: 48
6034013 TATGTGTGCT
* * * *
6034023 AGTGTAAGACATGTTTGGGACAT-GCATCGGCCAC-ATA-TTGAGGGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGACC-CGATAGATGAGAGCC
* * * * * * * * *
6034069 AGTGTAAGACATATCTGGGATAT-GCATTGGCCTTGAGATAT-ACCAACC
1 AGTGTAAGACATGTCTGGGACATGGCATCGACC-CGATAGATGA-GAGCC
* * *
6034117 AGTGTAAGACATGTCTGGGACAT-GCATCG--GC-ATTGAGATGAGGGCT
1 AGTGTAAGACATGTCTGGGACATGGCATCGACCCGA-T-AGATGAGAGCC
* * * * * * *
6034163 AGTATAAGACATGTCTGGGATAT-GCATCGGCCTCGAGATATTCA-AGCT
1 AGTGTAAGACATGTCTGGGACATGGCATCGACC-CGATAGA-TGAGAGCC
*
6034211 ACTGTAAGACATGTCTGGGACATGGCATCGACACCGATAGATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGAC-CCGATAGATGAGAGCC
** * * * **
6034260 AGTGTAAGACCGGTCTAGGACATGGCATC-AGCCTCGATATATGAAAGTT
1 AGTGTAAGACATGTCTGGGACATGGCATCGA-CC-CGATAGATGAGAGCC
* * * ** **
6034309 AGTGTAAGACCTATTTGGGACATGGCATCGACTTTGAT-G-TGCTAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGAC-CCGATAGATGAGAGCC
6034356 AGTGTAAGACCATGTCTGGGACATGG
1 AGTGTAAGA-CATGTCTGGGACATGG
6034382 TGTCGGCATC
Statistics
Matches: 235, Mismatches: 59, Indels: 36
0.71 0.18 0.11
Matches are distributed among these distances:
44 1 0.00
46 59 0.25
47 17 0.07
48 71 0.30
49 84 0.36
50 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGGCATCGACCCGATAGATGAGAGCC
Found at i:6038416 original size:16 final size:16
Alignment explanation
Indices: 6038392--6038434 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
6038382 TAAAAACAAT
*
6038392 TTAAAATATAAATTTA
1 TTAATATATAAATTTA
*
6038408 TTAATATATATAAATTTG
1 TT-A-ATATATAAATTTA
6038426 TTAATATAT
1 TTAATATAT
6038435 GTAAAAACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 8 0.35
17 2 0.09
18 13 0.57
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TTAATATATAAATTTA
Found at i:6038418 original size:18 final size:18
Alignment explanation
Indices: 6038397--6038439 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
6038387 ACAATTTAAA
6038397 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
6038415 ATATAAATTTGTTAATAT
1 ATATAAATTTATTAATAT
*
6038433 ATGTAAA
1 ATATAAA
6038440 AACAGCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:6039320 original size:40 final size:40
Alignment explanation
Indices: 6039258--6039395 Score: 129
Period size: 40 Copynumber: 3.5 Consensus size: 40
6039248 AACAAACCAG
*
6039258 TTTGGCACCCAGTGCCTCATCGGATAATTTGAAGTAGTAA
1 TTTGACACCCAGTGCCTCATCGGATAATTTGAAGTAGTAA
* * * * ***
6039298 TTTGACACCCAATGTCTTATCGGCTAAACCGAAGTA--AA
1 TTTGACACCCAGTGCCTCATCGGATAATTTGAAGTAGTAA
* *
6039336 -TTGGCACCCAGTGCCTCATCGAATTAATTTGAAGTAGTAA
1 TTTGACACCCAGTGCCTCATCGGA-TAATTTGAAGTAGTAA
* * *
6039376 ATTGACACCCCGTGTCTCAT
1 TTTGACACCCAGTGCCTCAT
6039396 TAACTCGAAG
Statistics
Matches: 74, Mismatches: 20, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
37 17 0.23
38 11 0.15
40 30 0.41
41 16 0.22
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGATAATTTGAAGTAGTAA
Found at i:6040319 original size:20 final size:20
Alignment explanation
Indices: 6040301--6040343 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
6040291 TCCTGTTTCG
6040301 TTTCTATTATGTTTCTTTCTA
1 TTTCT-TTATGTTTCTTTCTA
*
6040322 TTTCTTTTTGTTTCTTT-TA
1 TTTCTTTATGTTTCTTTCTA
6040341 TTT
1 TTT
6040344 ATTATAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 11 0.52
21 5 0.24
ACGTcount: A:0.09, C:0.12, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTCTTTATGTTTCTTTCTA
Found at i:6040321 original size:15 final size:16
Alignment explanation
Indices: 6040294--6040323 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6040284 CTTTTTCTCC
6040294 TGTTTCGTTTCTATTA
1 TGTTTCGTTTCTATTA
6040310 TGTTTC-TTTCTATT
1 TGTTTCGTTTCTATT
6040324 TCTTTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.13, G:0.10, T:0.67
Consensus pattern (16 bp):
TGTTTCGTTTCTATTA
Found at i:6040335 original size:31 final size:34
Alignment explanation
Indices: 6040277--6040341 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 34
6040267 CCCTTTTTCT
*
6040277 TTTCTTTCTTTTTCTCCTGTTTCGTTTCTATTATG
1 TTTCTTTCTATTTCT-CTGTTTCGTTTCTATTATG
*
6040312 TTTCTTTCTATTTCT-T-TTT-GTTTCTTTTAT
1 TTTCTTTCTATTTCTCTGTTTCGTTTCTATTAT
6040342 TTATTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 10 0.36
32 3 0.11
33 1 0.04
35 14 0.50
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.71
Consensus pattern (34 bp):
TTTCTTTCTATTTCTCTGTTTCGTTTCTATTATG
Found at i:6040356 original size:7 final size:7
Alignment explanation
Indices: 6040346--6040405 Score: 63
Period size: 7 Copynumber: 8.6 Consensus size: 7
6040336 TTTTATTTAT
6040346 TATAATA
1 TATAATA
6040353 TATAATA
1 TATAATA
*
6040360 TAAAATA
1 TATAATA
6040367 TAT-ATA
1 TATAATA
6040373 CT-TAATGA
1 -TATAAT-A
6040381 T-TAATA
1 TATAATA
6040387 TATAATA
1 TATAATA
6040394 TTATAATA
1 -TATAATA
6040402 TATA
1 TATA
6040406 TTTTAACTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
6 6 0.13
7 32 0.70
8 8 0.17
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (7 bp):
TATAATA
Found at i:6043565 original size:35 final size:35
Alignment explanation
Indices: 6043511--6043588 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
6043501 GCTAATCCAT
6043511 CACACCAACACTCAAAAGAGATAATCC-ATCCGAAA
1 CACACCAACACTCAAAAGAGATAATCCAAT-CGAAA
** * *
6043546 CACACCAATGCTCAGAAGAGCTAATCCAATCGAAA
1 CACACCAACACTCAAAAGAGATAATCCAATCGAAA
6043581 CACACCAA
1 CACACCAA
6043589 AACAGGGAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 36 0.95
36 2 0.05
ACGTcount: A:0.46, C:0.32, G:0.10, T:0.12
Consensus pattern (35 bp):
CACACCAACACTCAAAAGAGATAATCCAATCGAAA
Found at i:6050314 original size:138 final size:138
Alignment explanation
Indices: 6050018--6050323 Score: 353
Period size: 138 Copynumber: 2.2 Consensus size: 138
6050008 GGAGATACAT
* * * * * *
6050018 GCCTAAGGTAACACTTAAATAAGAGTCGACTTTGTCCAACACTATGCTGACACTTTTGGGTCGAC
1 GCCTAAGGAAACACTTAAATAAGATTCGGCTTTATCCAACACTA-GCTGACACTTTTGGGCCGAA
* * * * * * *
6050083 ACTTTCCTAAGTGTTGGGATAGATTTGCAAACATACACTTCGGCAACTTTTTGTATAAGGGTTGG
65 AATTTCCTAAGTGTTGGGACAGACTTGCAAACATACACTTAGCCAACTTATTGTATAAGAGTTGG
* *
6050148 GATATGCAT
130 AATATGCAC
* * *
6050157 GCGTAAGGAAACACTTAAATAAGATTCGGCTTTATCCAATACTA-CTGACAGTTTTGGGCCGAAA
1 GCCTAAGGAAACACTTAAATAAGATTCGGCTTTATCCAACACTAGCTGACACTTTTGGGCCGAAA
* * ** * *
6050221 ATTTCCTTAGTGTTTGGACAGACTTGCCGATATACACTTTAGCCAACTTATTGTATAAGAGTTGT
66 ATTTCCTAAGTGTTGGGACAGACTTGCAAACATACAC-TTAGCCAACTTATTGTATAAGAGTTGG
6050286 AATATGCAC
130 AATATGCAC
* *
6050295 GCCTAAAGCAACACTTAAATAAGATTCGG
1 GCCTAAGGAAACACTTAAATAAGATTCGG
6050324 ATTGTTCCAG
Statistics
Matches: 139, Mismatches: 27, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
137 46 0.33
138 55 0.40
139 38 0.27
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (138 bp):
GCCTAAGGAAACACTTAAATAAGATTCGGCTTTATCCAACACTAGCTGACACTTTTGGGCCGAAA
ATTTCCTAAGTGTTGGGACAGACTTGCAAACATACACTTAGCCAACTTATTGTATAAGAGTTGGA
ATATGCAC
Found at i:6050457 original size:125 final size:126
Alignment explanation
Indices: 6050222--6050457 Score: 298
Period size: 125 Copynumber: 1.9 Consensus size: 126
6050212 GGGCCGAAAA
* *
6050222 TTTCCTTAGTGTTTGGACAGACTTGCCGATATACACTTTAGCCAACTTATTGTATAAGAGTTGTA
1 TTTCCTAAGTGTTTGGACAGACTTGCCGACATACACTTTAGCCAACTTATTGTATAAGAGTTGTA
6050287 ATATGCACGCCTAAAGCAACACTTAAATAAGATTCGGATTGTTCCAGCATTATACTGACAC
66 ATATGCACGCCTAAAGCAACACTTAAATAAGATTCGGATTGTTCCAGCATTATACTGACAC
* * * * * * *
6050348 TTTCCTAAGTG-TTGGATAGACTTGTCGACATACGCTTTGGCCAACTCT-TTTTGTAAGGGTTG-
1 TTTCCTAAGTGTTTGGACAGACTTGCCGACATACACTTTAGCCAACT-TATTGTATAAGAGTTGT
* * * * * *
6050410 AGATATGCATGTCTAACGTAACACTTAAATAAGATTCGGCTTTTTCCA
65 A-ATATGCACGCCTAAAGCAACACTTAAATAAGATTCGGATTGTTCCA
6050458 ACACTATGCT
Statistics
Matches: 93, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
124 1 0.01
125 81 0.87
126 11 0.12
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (126 bp):
TTTCCTAAGTGTTTGGACAGACTTGCCGACATACACTTTAGCCAACTTATTGTATAAGAGTTGTA
ATATGCACGCCTAAAGCAACACTTAAATAAGATTCGGATTGTTCCAGCATTATACTGACAC
Found at i:6050592 original size:17 final size:18
Alignment explanation
Indices: 6050560--6050594 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
6050550 TACCTAAAAA
*
6050560 TTAATAAATATTATAACC
1 TTAAAAAATATTATAACC
6050578 TTAAAAAAT-TTATAACC
1 TTAAAAAATATTATAACC
6050595 AACCCATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAAAAATATTATAACC
Found at i:6052584 original size:35 final size:35
Alignment explanation
Indices: 6052545--6052656 Score: 206
Period size: 35 Copynumber: 3.2 Consensus size: 35
6052535 CGCAGATAAC
6052545 GTCTATCCCAACCTTTTAAAATTTTCCTTAGAGGA
1 GTCTATCCCAACCTTTTAAAATTTTCCTTAGAGGA
6052580 GTCTATCCCAACCTTTTAAAATTTTCCTTAGAGGA
1 GTCTATCCCAACCTTTTAAAATTTTCCTTAGAGGA
* *
6052615 GTCTATCCCAACCTTTTAAAAGTTTCCTTAGAAGA
1 GTCTATCCCAACCTTTTAAAATTTTCCTTAGAGGA
6052650 GTCTATC
1 GTCTATC
6052657 TCAAATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 75 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.37
Consensus pattern (35 bp):
GTCTATCCCAACCTTTTAAAATTTTCCTTAGAGGA
Found at i:6052778 original size:70 final size:71
Alignment explanation
Indices: 6052545--6052779 Score: 212
Period size: 70 Copynumber: 3.3 Consensus size: 71
6052535 CGCAGATAAC
* * * * * ** *
6052545 GTCTATCCCAACCTTTTAAAATTTTCCTTAGAGGAGTCTATCCC-AAC-CTTTTAAAATTTTCCT
1 GTCTATCCCAACCTTTTAAAAGTTGCCTTAGAAGAGTCTATCCCAAACTTTTTTAAAGTTGACAT
* * *
6052608 TAGAGG
66 AAAATG
* * * *
6052614 AGTCTATCCCAACCTTTTAAAAGTTTCCTTAGAAGAGTCTATCTCAAATTTTTTTAATGTTGACA
1 -GTCTATCCCAACCTTTTAAAAGTTGCCTTAGAAGAGTCTATCCCAAACTTTTTTAAAGTTGACA
*
6052679 TACAATG
65 TAAAATG
* * *
6052686 GTCTATCCCAACCTTTTTAAAGTTGCCTTAGATG-G-CTTATCCCAACCTTTTTTAAAGTT-AGC
1 GTCTATCCCAACCTTTTAAAAGTTGCCTTAGAAGAGTC-TATCCCAAACTTTTTTAAAGTTGA-C
6052748 ATAAAATG
64 ATAAAATG
*
6052756 GTCTATCCTAA-CTCTTTAAAAGTT
1 GTCTATCCCAACCT-TTTAAAAGTT
6052780 AGCATATGAA
Statistics
Matches: 136, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
69 4 0.03
70 87 0.64
71 33 0.24
72 12 0.09
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.38
Consensus pattern (71 bp):
GTCTATCCCAACCTTTTAAAAGTTGCCTTAGAAGAGTCTATCCCAAACTTTTTTAAAGTTGACAT
AAAATG
Found at i:6053929 original size:26 final size:25
Alignment explanation
Indices: 6053873--6053936 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
6053863 TCCAGTCCCA
*
6053873 GTAAGATTTTAACAATTTTACCCCT
1 GTAAAATTTTAACAATTTTACCCCT
* * *
6053898 GATAAAATTTTGACGATTTTATCCCT
1 G-TAAAATTTTAACAATTTTACCCCT
*
6053924 CGTAAATTTTTAA
1 -GTAAAATTTTAA
6053937 GAAAATATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
25 1 0.03
26 29 0.94
27 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (25 bp):
GTAAAATTTTAACAATTTTACCCCT
Found at i:6062447 original size:17 final size:17
Alignment explanation
Indices: 6062425--6062458 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6062415 GGGCTTGTAG
6062425 GCCCATGATTCTGAAAT
1 GCCCATGATTCTGAAAT
6062442 GCCCATGATTCTGAAAT
1 GCCCATGATTCTGAAAT
6062459 TTTCTCTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (17 bp):
GCCCATGATTCTGAAAT
Found at i:6064970 original size:27 final size:27
Alignment explanation
Indices: 6064932--6064983 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
6064922 AATATACTTG
6064932 CTATGACAATGGTAGCATAGCCTTTTT
1 CTATGACAATGGTAGCATAGCCTTTTT
*
6064959 CTATGACAATGGTAGCATCGCCTTT
1 CTATGACAATGGTAGCATAGCCTTT
6064984 CTCTCGAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
CTATGACAATGGTAGCATAGCCTTTTT
Found at i:6070142 original size:34 final size:34
Alignment explanation
Indices: 6070066--6070228 Score: 177
Period size: 34 Copynumber: 4.8 Consensus size: 34
6070056 AAGCACAATT
* * * *
6070066 TGGGTCTAAGCCC-TTTCAATAACAGTAGC-GATA
1 TGGGCCTAAGCCCATTACAGTAACAGTAGCAG-TC
* * * * *
6070099 TGGGTCTGAGCCCGTTGCAGTAATAGTAGCAGTC
1 TGGGCCTAAGCCCATTACAGTAACAGTAGCAGTC
* *
6070133 TGGGCCTGAGCCCATTACAATAACAGTAGCAGTC
1 TGGGCCTAAGCCCATTACAGTAACAGTAGCAGTC
* *
6070167 TGGGCCTAAGCCCATTATAGTAACAGTAGTAGTC
1 TGGGCCTAAGCCCATTACAGTAACAGTAGCAGTC
*
6070201 TGGGCCTAAGCCCATGACAGTAACAGTA
1 TGGGCCTAAGCCCATTACAGTAACAGTA
6070229 TGCAAACAGA
Statistics
Matches: 112, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
33 12 0.11
34 99 0.88
35 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (34 bp):
TGGGCCTAAGCCCATTACAGTAACAGTAGCAGTC
Found at i:6078949 original size:26 final size:26
Alignment explanation
Indices: 6078902--6078974 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 26
6078892 TCTCATCCTT
* **
6078902 ATTTTACCCCTAATAAAATTTTGACG
1 ATTTTACCCCTGATAATTTTTTGACG
* **
6078928 ATTTTACCCCTGGTAATTTTTTTTCG
1 ATTTTACCCCTGATAATTTTTTGACG
* *
6078954 ATTTTACTCCTTGTTAATTTT
1 ATTTTAC-CCCTGATAATTTT
6078975 CAAGAAAATA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 27 0.71
27 11 0.29
ACGTcount: A:0.23, C:0.18, G:0.08, T:0.51
Consensus pattern (26 bp):
ATTTTACCCCTGATAATTTTTTGACG
Done.