Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 95 of 182
Found at i:28696871 original size:25 final size:25
Alignment explanation
Indices: 28696837--28696888 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
28696827 TGCCCCCTAA
28696837 ATTGAAAGATCCTGGGAGCTTTACC
1 ATTGAAAGATCCTGGGAGCTTTACC
28696862 ATTGAAAGATCCTGGGAGCTTTACC
1 ATTGAAAGATCCTGGGAGCTTTACC
28696887 AT
1 AT
28696889 CCCATGATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (25 bp):
ATTGAAAGATCCTGGGAGCTTTACC
Found at i:28698695 original size:15 final size:15
Alignment explanation
Indices: 28698675--28698704 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28698665 CCCAGCCCAT
*
28698675 AACCAAATTAATAAA
1 AACCAAAATAATAAA
28698690 AACCAAAATAATAAA
1 AACCAAAATAATAAA
28698705 TTAAATGTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (15 bp):
AACCAAAATAATAAA
Found at i:28704835 original size:10 final size:9
Alignment explanation
Indices: 28704820--28704850 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28704810 TATGAGTTTT
28704820 AAAAAAATC
1 AAAAAAATC
28704829 AAAAAAATC
1 AAAAAAATC
*
28704838 AAAAAAATG
1 AAAAAAATC
28704847 AAAA
1 AAAA
28704851 TAATGGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.81, C:0.06, G:0.03, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:28704865 original size:6 final size:6
Alignment explanation
Indices: 28704856--28704895 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
28704846 GAAAATAATG
* *
28704856 GAAAAA G-AAAA GAAAAA GAAAAG GAAAAA GAAAAG GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
28704896 GGAGAGGCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:28704870 original size:11 final size:11
Alignment explanation
Indices: 28704856--28704896 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
28704846 GAAAATAATG
28704856 GAAAAAGAAAA
1 GAAAAAGAAAA
28704867 GAAAAAGAAAA
1 GAAAAAGAAAA
28704878 GGAAAAAGAAAA
1 -GAAAAAGAAAA
*
28704890 GGAAAAG
1 GAAAAAG
28704897 GAGAGGCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:28704882 original size:12 final size:12
Alignment explanation
Indices: 28704855--28704895 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
28704845 TGAAAATAAT
28704855 GGAAAAAGAAAA
1 GGAAAAAGAAAA
28704867 -GAAAAAGAAAA
1 GGAAAAAGAAAA
28704878 GGAAAAAGAAAA
1 GGAAAAAGAAAA
28704890 GGAAAA
1 GGAAAA
28704896 GGAGAGGCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
GGAAAAAGAAAA
Found at i:28704886 original size:18 final size:18
Alignment explanation
Indices: 28704863--28704898 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28704853 ATGGAAAAAG
28704863 AAAAGAAAAAGAAAAGGA
1 AAAAGAAAAAGAAAAGGA
*
28704881 AAAAGAAAAGGAAAAGGA
1 AAAAGAAAAAGAAAAGGA
28704899 GAGGCCAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAGGA
Found at i:28707129 original size:45 final size:45
Alignment explanation
Indices: 28707081--28707707 Score: 831
Period size: 45 Copynumber: 13.9 Consensus size: 45
28707071 AAAAAAATAG
* * *
28707081 CAGATCTTGTCTTTCTGTATTGGCAGTGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* *
28707126 CAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * * *
28707171 TAGATCTTGTCTTCCTATATTGGCAGCAAAGTAGATCGAAGACAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * * * * *
28707216 CAAATCTTGTCTTCCTATATTGGTAGCGAAGTACATCAAAGATAG
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * * *
28707261 CAGATCTTGTTTTCCTGTACTGCCAGCGAAGTAGATTGAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * *
28707306 CAGATCTTGTCTTCCTATATTGGCAGCAAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * *
28707351 CAGATCTTGTCTTTCTGTATTGGCAGCGAAGCAGATTGAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * *
28707396 TAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAGAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * * * * *
28707441 TAGATCTTGTCTTCCTGCATTTGCAACAAAGTAGATTGAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
*
28707486 TAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * * *
28707531 TAGATCTTGTCTTCCTGTATTTGCAGTGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * * *
28707576 TAGATCTTGTCTTCTTGTATTGGCTGCTAAGTAGATCGAAGATAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
* * *
28707621 CAGATCTTGTCTTTCTGTATTGACAGCGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
*
28707666 TAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
28707708 CCCAAGCCTT
Statistics
Matches: 505, Mismatches: 77, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 505 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (45 bp):
CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAA
Found at i:28707870 original size:132 final size:132
Alignment explanation
Indices: 28707719--28708057 Score: 520
Period size: 132 Copynumber: 2.6 Consensus size: 132
28707709 CCAAGCCTTA
**
28707719 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTCCCAAGGTAGTAGGGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAA
* ** *
28707784 ACAGATTTAAGCCACCAGTCCTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATGGATCT
66 ACAGATTTAAGCCACCAGTCCTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATACATCC
28707849 TG
131 TG
28707851 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAAT-TGTATCTTCCCAAGGTAGTA-GGA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCT-TATCTTCCCAAGGTAGTAGGGA
* * * * *
28707914 AAGCAGGTTTAAGCCATCAGTCCTGTCTCCCTAAGCAGCTGTGGAGTAGGTTGAGGATTGTACAT
65 AA-CAGATTTAAGCCACCAGTCCTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATACAT
28707979 CCTG
129 CCTG
* *
28707983 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTTCCAAGGTAGTAGAGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAA
*
28708048 GCAGATTTAA
66 ACAGATTTAA
28708058 AACACCGGTC
Statistics
Matches: 188, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
131 6 0.03
132 178 0.95
133 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (132 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAA
ACAGATTTAAGCCACCAGTCCTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATACATCC
TG
Found at i:28708167 original size:50 final size:50
Alignment explanation
Indices: 28708083--28708223 Score: 156
Period size: 50 Copynumber: 2.8 Consensus size: 50
28708073 TCTTTTGCAT
* * *
28708083 TACAGTGGAACAGATTGAAGCTACAATAGCGAATCTTACTTCCCAGGCAC
1 TACAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCAGACAC
** * *** *
28708133 TGTAGTGGAACAGATTGAAGCTACAACAATGAATCTCGTTTCCCAGACAT
1 TACAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCAGACAC
** * *
28708183 TACAGTTAAATAGATTGAAGTTACAACAACGAATCTTACTT
1 TACAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTT
28708224 TCCTAGCGTT
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (50 bp):
TACAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCAGACAC
Found at i:28708285 original size:44 final size:43
Alignment explanation
Indices: 28708235--28708377 Score: 128
Period size: 44 Copynumber: 3.2 Consensus size: 43
28708225 CCTAGCGTTG
* *
28708235 CAGTGGAACAAGTTGAAGATAAAAGCCTTATCTCCTTGAAGTTA
1 CAGTGGAGCAAG-TGAAGATAAAAGTCTTATCTCCTTGAAGTTA
* * * *
28708279 CAGTGGAGCAGGCTGAAGATAACGAA-TCTTTTGTCCTAGAAGTTA
1 CAGTGGAGCAAG-TGAAGATAA--AAGTCTTATCTCCTTGAAGTTA
** * *
28708324 C-GTGGAGCAGAGTGAAGATTGCAAGTCTTATCCCCTTGAAGTTG
1 CAGTGGAGCA-AGTGAAGA-TAAAAGTCTTATCTCCTTGAAGTTA
28708368 CAGTGGAGCA
1 CAGTGGAGCA
28708378 GAAAGAAGAT
Statistics
Matches: 78, Mismatches: 15, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
43 2 0.03
44 48 0.62
45 26 0.33
46 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.26
Consensus pattern (43 bp):
CAGTGGAGCAAGTGAAGATAAAAGTCTTATCTCCTTGAAGTTA
Found at i:28708401 original size:45 final size:45
Alignment explanation
Indices: 28708261--28708403 Score: 139
Period size: 45 Copynumber: 3.2 Consensus size: 45
28708251 AGATAAAAGC
* ** *
28708261 CTTATCTCCTTGAAGTTACAGTGGAGCAGGCTGAAGATAACGAAT
1 CTTATCCCCTTGAAGTTACAGTGGAGCAGAATGAAGATGACGAAT
* ** * *
28708306 CTTTTGTCCTAGAAGTTAC-GTGGAGCAGAGTGAAGATTG-C-AAGT
1 CTTATCCCCTTGAAGTTACAGTGGAGCAGAATGAAGA-TGACGAA-T
* *
28708350 CTTATCCCCTTGAAGTTGCAGTGGAGCAGAAAGAAGATGACGAAT
1 CTTATCCCCTTGAAGTTACAGTGGAGCAGAATGAAGATGACGAAT
*
28708395 CCTATCCCC
1 CTTATCCCC
28708404 CTGACGTGGC
Statistics
Matches: 79, Mismatches: 14, Indels: 10
0.77 0.14 0.10
Matches are distributed among these distances:
43 2 0.03
44 33 0.42
45 42 0.53
46 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (45 bp):
CTTATCCCCTTGAAGTTACAGTGGAGCAGAATGAAGATGACGAAT
Found at i:28708630 original size:15 final size:15
Alignment explanation
Indices: 28708610--28708639 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28708600 CCCAGCCCAT
*
28708610 AACCAAATTAATAAA
1 AACCAAAATAATAAA
28708625 AACCAAAATAATAAA
1 AACCAAAATAATAAA
28708640 TTAAATGTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (15 bp):
AACCAAAATAATAAA
Found at i:28708769 original size:18 final size:19
Alignment explanation
Indices: 28708740--28708775 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28708730 ACCCGTATGG
*
28708740 CCCAATACCCAATTACATA
1 CCCAATACCCAAATACATA
28708759 CCCAA-ACCCAAATACAT
1 CCCAATACCCAAATACAT
28708776 CAAGCCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.44, C:0.39, G:0.00, T:0.17
Consensus pattern (19 bp):
CCCAATACCCAAATACATA
Found at i:28710927 original size:60 final size:60
Alignment explanation
Indices: 28710834--28711015 Score: 355
Period size: 60 Copynumber: 3.0 Consensus size: 60
28710824 TTGTTTACAC
28710834 AAAAGTTTTCAAAAATAATGCGATACTCGAAATTTGGGGTCCTCAAGAAGATTGTACCCT
1 AAAAGTTTTCAAAAATAATGCGATACTCGAAATTTGGGGTCCTCAAGAAGATTGTACCCT
28710894 AAAAGTTTTCAAAAATAATGCGATACTCGAAATTTGGGGTCCTCAAGAAGATTGTACCCT
1 AAAAGTTTTCAAAAATAATGCGATACTCGAAATTTGGGGTCCTCAAGAAGATTGTACCCT
*
28710954 AAAAGTTTTCAAAAATAATGCGATACTCGAAATTTGGGGTCCTCAAGAAGATTTTACCCT
1 AAAAGTTTTCAAAAATAATGCGATACTCGAAATTTGGGGTCCTCAAGAAGATTGTACCCT
28711014 AA
1 AA
28711016 CTCATTGGGT
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 121 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (60 bp):
AAAAGTTTTCAAAAATAATGCGATACTCGAAATTTGGGGTCCTCAAGAAGATTGTACCCT
Found at i:28716106 original size:17 final size:17
Alignment explanation
Indices: 28716084--28716138 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
28716074 TATTCTATTA
28716084 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
* *
28716101 ATTTATCAAGA-TAAAT
1 ATTTATTAAGATTTAAT
* *
28716117 ATTAGATTGA-ATTTAAT
1 ATT-TATTAAGATTTAAT
28716134 ATTTA
1 ATTTA
28716139 AGTGATTAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Found at i:28718090 original size:53 final size:53
Alignment explanation
Indices: 28718010--28718115 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
28718000 AATTCAATCC
*
28718010 AACTTTCTAAATCCAAGGGATTAGATATGCTCAAATCAATCTGATTTGATTCT
1 AACTTTCTAAATCCAAGGGATTAGATATGCTCAAATCAATCTAATTTGATTCT
*
28718063 AACTTTCTAAATCCAATGGATTAGATATGCTCAAATCAATCTAATTTGATTCT
1 AACTTTCTAAATCCAAGGGATTAGATATGCTCAAATCAATCTAATTTGATTCT
28718116 CCAAATATGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (53 bp):
AACTTTCTAAATCCAAGGGATTAGATATGCTCAAATCAATCTAATTTGATTCT
Found at i:28718562 original size:21 final size:21
Alignment explanation
Indices: 28718523--28718562 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28718513 AACCTTATTT
*
28718523 TGTTTTTTTTTCTTATTTCAA
1 TGTTTTTTTTTATTATTTCAA
28718544 TGTTTTTTATTTATT-TTTC
1 TGTTTTTT-TTTATTATTTC
28718563 TAACAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (21 bp):
TGTTTTTTTTTATTATTTCAA
Found at i:28720996 original size:17 final size:17
Alignment explanation
Indices: 28720974--28721028 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
28720964 TATTCTATTA
28720974 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
* *
28720991 ATTTATCAAGA-TAAAT
1 ATTTATTAAGATTTAAT
* *
28721007 ATTAGATTGA-ATTTAAT
1 ATT-TATTAAGATTTAAT
28721024 ATTTA
1 ATTTA
28721029 AGTGATTAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Found at i:28723399 original size:21 final size:21
Alignment explanation
Indices: 28723360--28723399 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28723350 AACCTTATTT
*
28723360 TGTTTTTTTTTCTTATTTCAA
1 TGTTTTTTTTTATTATTTCAA
28723381 TGTTTTTTATTTATT-TTTC
1 TGTTTTTT-TTTATTATTTC
28723400 TAACAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (21 bp):
TGTTTTTTTTTATTATTTCAA
Found at i:28725833 original size:17 final size:17
Alignment explanation
Indices: 28725811--28725865 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
28725801 TATTCTATTA
28725811 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
* *
28725828 ATTTATCAAGA-TAAAT
1 ATTTATTAAGATTTAAT
* *
28725844 ATTAGATTGA-ATTTAAT
1 ATT-TATTAAGATTTAAT
28725861 ATTTA
1 ATTTA
28725866 AGTGATTAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Found at i:28728236 original size:21 final size:21
Alignment explanation
Indices: 28728197--28728236 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28728187 AACCTTATTT
*
28728197 TGTTTTTTTTTCTTATTTCAA
1 TGTTTTTTTTTATTATTTCAA
28728218 TGTTTTTTATTTATT-TTTC
1 TGTTTTTT-TTTATTATTTC
28728237 TAACAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (21 bp):
TGTTTTTTTTTATTATTTCAA
Found at i:28732559 original size:87 final size:87
Alignment explanation
Indices: 28732424--28732591 Score: 266
Period size: 87 Copynumber: 1.9 Consensus size: 87
28732414 AGGCAGCATT
*
28732424 GAGAGAAGCTGAGGTCCAAAGAAAATATGAAGAACTCCAACTACAACTTAAAG-TAGATGTAGCA
1 GAGAGAAGCTGAGGTCCAAAGAAAATATGAAGAACTCCAACTACAACTTAAAGCT-GATGCAGCA
* *
28732488 GCAAGGGAAGTAGAGGCAGTAGC
65 ACAAGGGAAGCAGAGGCAGTAGC
* * *
28732511 GAGAGAAGCTGATGTTCAAAGAAAATATGAAGAACTTCAACTACAACTTAAAGCTGATGCAGCAA
1 GAGAGAAGCTGAGGTCCAAAGAAAATATGAAGAACTCCAACTACAACTTAAAGCTGATGCAGCAA
28732576 CAAGGGAAGCAGAGGC
66 CAAGGGAAGCAGAGGC
28732592 TGCAGCGCGG
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
87 73 0.99
88 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.15
Consensus pattern (87 bp):
GAGAGAAGCTGAGGTCCAAAGAAAATATGAAGAACTCCAACTACAACTTAAAGCTGATGCAGCAA
CAAGGGAAGCAGAGGCAGTAGC
Found at i:28732956 original size:43 final size:43
Alignment explanation
Indices: 28732916--28733018 Score: 179
Period size: 43 Copynumber: 2.4 Consensus size: 43
28732906 TAAAAAAAAA
*
28732916 GCCGCTAAAAGTCATGATCTATAGCGGCGTTTGGGGAAAAAGT
1 GCCGCTAAAAGTCATGATCTATAGCGGCGTTTGCGGAAAAAGT
28732959 GCCGCTAAAAGTCATGATCTATAGCGGCGTTTGCGGAAAAAGT
1 GCCGCTAAAAGTCATGATCTATAGCGGCGTTTGCGGAAAAAGT
**
28733002 GCCGCTAATGGTCATGA
1 GCCGCTAAAAGTCATGA
28733019 CTTTTAGTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.23
Consensus pattern (43 bp):
GCCGCTAAAAGTCATGATCTATAGCGGCGTTTGCGGAAAAAGT
Found at i:28734793 original size:17 final size:17
Alignment explanation
Indices: 28734771--28734825 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
28734761 TATTCTATTA
28734771 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
* *
28734788 ATTTATCAAGA-TAAAT
1 ATTTATTAAGATTTAAT
* *
28734804 ATTAGATTGA-ATTTAAT
1 ATT-TATTAAGATTTAAT
28734821 ATTTA
1 ATTTA
28734826 AGTGATTAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Found at i:28735050 original size:260 final size:260
Alignment explanation
Indices: 28734589--28735111 Score: 1028
Period size: 260 Copynumber: 2.0 Consensus size: 260
28734579 CGAGCCGACA
28734589 GAAACCAAATCACCTTGGGGTGTCGGCGGTAGCGACGGCGGCAATCCGACGACCGAAAAATGAGA
1 GAAACCAAATCACCTTGGGGTGTCGGCGGTAGCGACGGCGGCAATCCGACGACCGAAAAATGAGA
*
28734654 TTCTATCAGAGAATTTGATTTCAGATTAATTATTCAAAAATATAGACTTAATATTAAAGTGATTA
66 CTCTATCAGAGAATTTGATTTCAGATTAATTATTCAAAAATATAGACTTAATATTAAAGTGATTA
*
28734719 TTTTAATGTTTAGTTTAATTTAATGTTTATCTTGTACATAAATATTCTATTAATTTATTAAGATT
131 TCTTAATGTTTAGTTTAATTTAATGTTTATCTTGTACATAAATATTCTATTAATTTATTAAGATT
28734784 TAATATTTATCAAGATAAATATTAGATTGAATTTAATATTTAAGTGATTAAGTTTAATCATAGTT
196 TAATATTTATCAAGATAAATATTAGATTGAATTTAATATTTAAGTGATTAAGTTTAATCATAGTT
28734849 GAAACCAAATCACCTTGGGGTGTCGGCGGTAGCGACGGCGGCAATCCGACGACCGAAAAATGAGA
1 GAAACCAAATCACCTTGGGGTGTCGGCGGTAGCGACGGCGGCAATCCGACGACCGAAAAATGAGA
28734914 CTCTATCAGAGAATTTGATTTCAGATTAATTATTCAAAAATATAGACTTAATATTAAAGTGATTA
66 CTCTATCAGAGAATTTGATTTCAGATTAATTATTCAAAAATATAGACTTAATATTAAAGTGATTA
28734979 TCTTAATGTTTAGTTTAATTTAATGTTTATCTTGTACATAAATATTCTATTAATTTATTAAGATT
131 TCTTAATGTTTAGTTTAATTTAATGTTTATCTTGTACATAAATATTCTATTAATTTATTAAGATT
28735044 TAATATTTATCAAGATAAATATTAGATTGAATTTAATATTTAAGTGATTAAGTTTAATCATAGTT
196 TAATATTTATCAAGATAAATATTAGATTGAATTTAATATTTAAGTGATTAAGTTTAATCATAGTT
28735109 GAA
1 GAA
28735112 CTCTCTAAAC
Statistics
Matches: 261, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
260 261 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (260 bp):
GAAACCAAATCACCTTGGGGTGTCGGCGGTAGCGACGGCGGCAATCCGACGACCGAAAAATGAGA
CTCTATCAGAGAATTTGATTTCAGATTAATTATTCAAAAATATAGACTTAATATTAAAGTGATTA
TCTTAATGTTTAGTTTAATTTAATGTTTATCTTGTACATAAATATTCTATTAATTTATTAAGATT
TAATATTTATCAAGATAAATATTAGATTGAATTTAATATTTAAGTGATTAAGTTTAATCATAGTT
Found at i:28735053 original size:17 final size:17
Alignment explanation
Indices: 28735031--28735085 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
28735021 TATTCTATTA
28735031 ATTTATTAAGATTTAAT
1 ATTTATTAAGATTTAAT
* *
28735048 ATTTATCAAGA-TAAAT
1 ATTTATTAAGATTTAAT
* *
28735064 ATTAGATTGA-ATTTAAT
1 ATT-TATTAAGATTTAAT
28735081 ATTTA
1 ATTTA
28735086 AGTGATTAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTTATTAAGATTTAAT
Found at i:28735197 original size:77 final size:76
Alignment explanation
Indices: 28735105--28735249 Score: 281
Period size: 77 Copynumber: 1.9 Consensus size: 76
28735095 GTTTAATCAT
28735105 AGTTGAACTCTCTAAACTCTCCCTATATAAAGAGAGTCTTGGGTCATTATTTTTCACACACTTGA
1 AGTTGAACTCTCTAAACTCTCCCTATATAAAGAGAGTCTTGGGTCATTATTTTTCACACACTTGA
28735170 ATTCGAGAGGA
66 ATTCGAGAGGA
28735181 AGTTGGAACTCTCTAAACTCTCCCTATATAAAGAGAGTCTTGGGTCATTATTTTTCACACACTTG
1 AGTT-GAACTCTCTAAACTCTCCCTATATAAAGAGAGTCTTGGGTCATTATTTTTCACACACTTG
28735246 AATT
65 AATT
28735250 GTAGCAGTTC
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 4 0.06
77 64 0.94
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (76 bp):
AGTTGAACTCTCTAAACTCTCCCTATATAAAGAGAGTCTTGGGTCATTATTTTTCACACACTTGA
ATTCGAGAGGA
Found at i:28737373 original size:43 final size:44
Alignment explanation
Indices: 28737311--28737409 Score: 164
Period size: 43 Copynumber: 2.3 Consensus size: 44
28737301 CAGTGTTTAT
**
28737311 ATGTAAGACCATAGTTGGGCTATTGGCATCGATTTGAGATTT-C
1 ATGTAAGACCATAGTTGGGCTATTGGCATCGATACGAGATTTCC
*
28737354 GTGTAAGACCATAGTTGGGCTATTGGCATCGATACGAGATTTCC
1 ATGTAAGACCATAGTTGGGCTATTGGCATCGATACGAGATTTCC
28737398 ATGTAAGACCAT
1 ATGTAAGACCAT
28737410 GTCTCTGACT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 39 0.76
44 12 0.24
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (44 bp):
ATGTAAGACCATAGTTGGGCTATTGGCATCGATACGAGATTTCC
Found at i:28746028 original size:39 final size:39
Alignment explanation
Indices: 28745930--28746090 Score: 159
Period size: 40 Copynumber: 4.1 Consensus size: 39
28745920 AATGATGTCT
*
28745930 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-AAGT-ACTATATCC
*
28745970 GGACTAAGAT-CCGAAGGCATTTGTGCAAGATACTA-ATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCAAG-TACTATA-TCC
* *
28746010 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCAAG-TACTATATCC
* ** *
28746049 GGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCAAGTA-CTATATCC
28746089 GG
1 GG
28746091 TTAAATTCCG
Statistics
Matches: 103, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
39 35 0.34
40 59 0.57
41 9 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (39 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCAAGTACTATATCC
Found at i:28746365 original size:47 final size:47
Alignment explanation
Indices: 28746296--28747262 Score: 1862
Period size: 47 Copynumber: 20.6 Consensus size: 47
28746286 AAGGGTTGGT
28746296 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746343 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746390 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746437 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746484 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746531 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746578 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746625 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746672 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746719 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746766 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746813 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746860 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746907 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28746954 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28747001 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28747048 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28747095 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28747142 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
28747189 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
28747236 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
28747263 TCCCGAAGGG
Statistics
Matches: 910, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 910 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:28747437 original size:37 final size:37
Alignment explanation
Indices: 28747381--28747459 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
28747371 CCGAGCTCTA
* * *
28747381 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
28747418 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
28747455 AAGAC
1 AAGAC
28747460 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:28749981 original size:40 final size:40
Alignment explanation
Indices: 28749921--28750011 Score: 139
Period size: 40 Copynumber: 2.3 Consensus size: 40
28749911 GTTCTGTTTT
* *
28749921 TAGCAGGCTTATTGTCAGTGAATTTTTTAGACTTAATGTC
1 TAGCAGGCTTATTGTCAGTGAAATTTTCAGACTTAATGTC
*
28749961 TAGCAGGCTTATTG-CTAGTGAAATTTTCAGACTTAATGTG
1 TAGCAGGCTTATTGTC-AGTGAAATTTTCAGACTTAATGTC
28750001 TAGCAGGCTTA
1 TAGCAGGCTTA
28750012 ATGCCGGTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 1 0.02
40 46 0.98
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.38
Consensus pattern (40 bp):
TAGCAGGCTTATTGTCAGTGAAATTTTCAGACTTAATGTC
Found at i:28759983 original size:41 final size:40
Alignment explanation
Indices: 28759938--28760077 Score: 106
Period size: 40 Copynumber: 3.5 Consensus size: 40
28759928 AGCGGCACTT
* *
28759938 TTAGCGGCGTTTGGACAAAAAACGCCACTAACA-ATCGAGCA
1 TTAGCGGCGTTT-GACAAAAAACACC-CTAAAATATCGAGCA
* * * *
28759979 TTAGCGGCATTTTACAAAAAACACCGTAAAATATTGAGCA
1 TTAGCGGCGTTTGACAAAAAACACCCTAAAATATCGAGCA
* ** * * *
28760019 TTAGCGGCGCTACATAAAAAACACCGCT-AAA-ACCAAGCA
1 TTAGCGGCGTTTGACAAAAAACACC-CTAAAATATCGAGCA
* *
28760058 TTAGCAGCGTTTTACAAAAA
1 TTAGCGGCGTTTGACAAAAA
28760078 GCGCCGCAAT
Statistics
Matches: 77, Mismatches: 20, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
39 24 0.31
40 41 0.53
41 12 0.16
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (40 bp):
TTAGCGGCGTTTGACAAAAAACACCCTAAAATATCGAGCA
Found at i:28760258 original size:98 final size:95
Alignment explanation
Indices: 28760084--28760366 Score: 403
Period size: 98 Copynumber: 3.0 Consensus size: 95
28760074 AAAAGCGCCG
*
28760084 CAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTTCCCA
1 CAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTGCCCA
* * *
28760149 AGCACCGCTAATACTCCCTTCTTCAGCGGCG
66 AGCGCCGCTAATACTCCGTTCTTCAGCGG-A
* * *
28760180 CTTTATGGAGTAACACAGAACGACACCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTGCC
1 C--AATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTGCC
*
28760245 CAAGCGCCGCTAATACTTCGTTCTTCA----A
64 CAAGCGCCGCTAATACTCCGTTCTTCAGCGGA
* **
28760273 CAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACACTAGTGATGGTTTTGCCCA
1 CAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTGCCCA
*
28760338 AACGCCGCTAATACTCCGTTCTTCAGCGG
66 AGCGCCGCTAATACTCCGTTCTTCAGCGG
28760367 TGTTTGGCGT
Statistics
Matches: 165, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
91 81 0.49
93 1 0.01
96 1 0.01
98 82 0.50
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (95 bp):
CAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTGCCCA
AGCGCCGCTAATACTCCGTTCTTCAGCGGA
Found at i:28760344 original size:91 final size:91
Alignment explanation
Indices: 28760187--28760362 Score: 298
Period size: 91 Copynumber: 1.9 Consensus size: 91
28760177 GCGCTTTATG
* * *
28760187 GAGTAACACAGAACGACACCGTTTTCATATATTTGGGAACATTAGTGGCGGTTTTGCCCAAGCGC
1 GAGTAACACAGAACGACACCGTTTTCATATATTTGGGAACACTAGTGACGGTTTTGCCCAAACGC
*
28760252 CGCTAATACTTCGTTCTTCAACAATA
66 CGCTAATACTCCGTTCTTCAACAATA
* *
28760278 GAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACACTAGTGATGGTTTTGCCCAAACGC
1 GAGTAACACAGAACGACACCGTTTTCATATATTTGGGAACACTAGTGACGGTTTTGCCCAAACGC
28760343 CGCTAATACTCCGTTCTTCA
66 CGCTAATACTCCGTTCTTCA
28760363 GCGGTGTTTG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 79 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (91 bp):
GAGTAACACAGAACGACACCGTTTTCATATATTTGGGAACACTAGTGACGGTTTTGCCCAAACGC
CGCTAATACTCCGTTCTTCAACAATA
Found at i:28760583 original size:41 final size:41
Alignment explanation
Indices: 28760520--28760597 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
28760510 CTAATGTTCC
* * *
28760520 GGTCTATAGCGGCGTTCTTGTAACAGCGCCGGTAATTCTTG
1 GGTCTATAGCGGCGTTCTTGTAAAAACGCCGCTAATTCTTG
28760561 GGTCTATAGCGGCGTT-TGTGTAAAAACGCCGCTAATT
1 GGTCTATAGCGGCGTTCT-TGTAAAAACGCCGCTAATT
28760598 AGAAAATCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 1 0.03
41 32 0.97
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (41 bp):
GGTCTATAGCGGCGTTCTTGTAAAAACGCCGCTAATTCTTG
Found at i:28760639 original size:8 final size:8
Alignment explanation
Indices: 28760626--28760687 Score: 61
Period size: 8 Copynumber: 7.1 Consensus size: 8
28760616 TTTCATTCTT
28760626 TTATATTA
1 TTATATTA
28760634 TTATATTA
1 TTATATTA
*
28760642 TTATAATAA
1 TTAT-ATTA
28760651 GTTATATTA
1 -TTATATTA
*
28760660 TTATGTTTGAA
1 TTAT-ATT--A
28760671 TTATATTA
1 TTATATTA
28760679 TTATATTA
1 TTATATTA
28760687 T
1 T
28760688 AAGTTATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
8 26 0.58
9 8 0.18
10 6 0.13
11 5 0.11
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (8 bp):
TTATATTA
Found at i:28760699 original size:19 final size:20
Alignment explanation
Indices: 28760634--28760701 Score: 83
Period size: 19 Copynumber: 3.6 Consensus size: 20
28760624 TTTTATATTA
28760634 TTATATTATTATA--ATAAG
1 TTATATTATTATATTATAAG
*
28760652 TTATATTATTATGTT-TGAA-
1 TTATATTATTATATTAT-AAG
28760671 TTATATTATTATATTATAAG
1 TTATATTATTATATTATAAG
28760691 TTATA-TATTAT
1 TTATATTATTAT
28760702 GAAGCATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
18 12 0.28
19 23 0.53
20 8 0.19
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (20 bp):
TTATATTATTATATTATAAG
Found at i:28760718 original size:37 final size:38
Alignment explanation
Indices: 28760630--28760723 Score: 93
Period size: 38 Copynumber: 2.4 Consensus size: 38
28760620 ATTCTTTTAT
* **
28760630 ATTATTATATTATTATAATAAGTTATATTATTATGTTTGA
1 ATTA-TATATTA-TATTATAAGTTATATTATTATGTAAGA
*
28760670 ATTATATTATTATATTATAAGTTATA-TATTATG-AAGC
1 ATTATA-TATTATATTATAAGTTATATTATTATGTAAGA
28760707 ATATATATATTAATATT
1 AT-TATATATT-ATATT
28760724 GTGTTAGTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
37 7 0.15
38 16 0.34
39 15 0.32
40 9 0.19
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.52
Consensus pattern (38 bp):
ATTATATATTATATTATAAGTTATATTATTATGTAAGA
Found at i:28763090 original size:16 final size:16
Alignment explanation
Indices: 28763066--28763096 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28763056 ATTTTTCCTC
28763066 TTCTAAAATCCCTAAG
1 TTCTAAAATCCCTAAG
*
28763082 TTCTGAAATCCCTAA
1 TTCTAAAATCCCTAA
28763097 CTCCATTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TTCTAAAATCCCTAAG
Found at i:28770648 original size:21 final size:21
Alignment explanation
Indices: 28770622--28770672 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
28770612 CTACAACTTA
* *
28770622 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
28770643 AAGCAGAGGCAGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
*
28770664 AAGCTGAGG
1 AAGCAGAGG
28770673 TTCAACGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:28770667 original size:87 final size:87
Alignment explanation
Indices: 28770556--28770753 Score: 256
Period size: 87 Copynumber: 2.3 Consensus size: 87
28770546 ACACAACTTA
* * * *
28770556 AAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAAC
1 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAACAACTCCAGC-AGCAAC
*
28770619 TTAAAGCAGATGCGGCAGCGAGAG
64 TTAAAGCAGATGCGACAGCGAGAG
* * *
28770643 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAACAACTCCAGCAGTAGCTT
1 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAACAACTCCAGCAGCAACTT
28770708 AAAGCAGATGCGACAGCGAGAG
66 AAAGCAGATGCGACAGCGAGAG
* * * *
28770730 AAGCAGCGGCTGCAGTGAGGGAAG
1 AAGCAGAGGCAGCAGCGAGAGAAG
28770754 TAGAGGCTGC
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
86 1 0.01
87 92 0.95
88 4 0.04
ACGTcount: A:0.38, C:0.19, G:0.32, T:0.12
Consensus pattern (87 bp):
AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAACAACTCCAGCAGCAACTT
AAAGCAGATGCGACAGCGAGAG
Found at i:28770753 original size:21 final size:21
Alignment explanation
Indices: 28770729--28770778 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
28770719 GACAGCGAGA
*
28770729 GAAGCAGCGGCTGCAGTGAGG
1 GAAGCAGAGGCTGCAGTGAGG
*
28770750 GAAGTAGAGGCTGCAGTGAGG
1 GAAGCAGAGGCTGCAGTGAGG
28770771 GAAGCAGA
1 GAAGCAGA
28770779 ACAACTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.14, G:0.46, T:0.10
Consensus pattern (21 bp):
GAAGCAGAGGCTGCAGTGAGG
Found at i:28771180 original size:43 final size:42
Alignment explanation
Indices: 28771113--28771534 Score: 423
Period size: 43 Copynumber: 9.8 Consensus size: 42
28771103 GGTGTTTTTT
* * *
28771113 AAGCACCGCTAAAGACCAAGGTCTATAGCGGCGTTTGATGGGA
1 AAGCGCCGCTAAAGACC-TGGTCTATAGCGGCGTTTGATGGAA
* * * **
28771156 AAGCGCCGCGAAAGATCCTAGTCTATAGCGGCGTTTTATGGTT
1 AAGCGCCGCTAAAGA-CCTGGTCTATAGCGGCGTTTGATGGAA
* * *
28771199 AAGCGCCGCGAAAGATCCTGGTCTATAGCGGCGTTTTATGGGA
1 AAGCGCCGCTAAAGA-CCTGGTCTATAGCGGCGTTTGATGGAA
* * *
28771242 AAGCGCCGCGAAAGATCCTGGTCTATAGCGGCATTTTATGGAA
1 AAGCGCCGCTAAAGA-CCTGGTCTATAGCGGCGTTTGATGGAA
* * * **
28771285 AAGCACCGCGAAAGATCCTGGTCTATAGCGGCGTTTGACGGGT
1 AAGCGCCGCTAAAGA-CCTGGTCTATAGCGGCGTTTGATGGAA
* *
28771328 AAGCGCCGCTAAAGACCATGGTCTATCGCGGCGTTTGATGCAA
1 AAGCGCCGCTAAAGACC-TGGTCTATAGCGGCGTTTGATGGAA
* * * **
28771371 AAGTGCCGCTAAAGACCATGGTCTATGGCGGCGATTGATGCCA
1 AAGCGCCGCTAAAGACC-TGGTCTATAGCGGCGTTTGATGGAA
* * * *
28771414 AAGCGCTGCTAAAGACCACGGTCTATAGTGGCGTTTGATGCAA
1 AAGCGCCGCTAAAGACC-TGGTCTATAGCGGCGTTTGATGGAA
* * ** *
28771457 AAGCGCCCCTAAAGACCACGGTCTATAGCGGCGTTT-ATTTAT
1 AAGCGCCGCTAAAGACC-TGGTCTATAGCGGCGTTTGATGGAA
*
28771499 AAGCGCCGCTAAAGACCATTGTCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGACC-TGGTCTATAGCGGCGTTT
28771535 ATTGTAAAAA
Statistics
Matches: 332, Mismatches: 45, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
42 38 0.11
43 292 0.88
44 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (42 bp):
AAGCGCCGCTAAAGACCTGGTCTATAGCGGCGTTTGATGGAA
Found at i:28771353 original size:129 final size:129
Alignment explanation
Indices: 28771113--28771556 Score: 468
Period size: 129 Copynumber: 3.4 Consensus size: 129
28771103 GGTGTTTTTT
* * * * *
28771113 AAGCACCGCTAAAGACCAAGGTCTATAGCGGCGTTTGATGGGAAAGCGCCGCGAAAGATCCTAGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCATTTGATGGAAAAGCGCCGCGAAAGATCCTGGT
* * * **
28771178 CTATAGCGGCGTTTTATGGTTAAGCGCCGCGAAAGATCC-TGGTCTATAGCGGCGTTTTATGGGA
66 CTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGA-CCATGGTCTATAGCGGCGTTTTATGCAA
* * *
28771242 AAGCGCCGCGAAAGATCC-TGGTCTATAGCGGCATTTTATGGAAAAGCACCGCGAAAGATCCTGG
1 AAGCGCCGCTAAAGA-CCATGGTCTATAGCGGCATTTGATGGAAAAGCGCCGCGAAAGATCCTGG
* * * *
28771306 TCTATAGCGGCGTTTGACGGGTAAGCGCCGCTAAAGACCATGGTCTATCGCGGCGTTTGATGCAA
65 TCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTTATGCAA
* * ** * * *
28771371 AAGTGCCGCTAAAGACCATGGTCTATGGCGGCGA-TTGATGCCAAAGCGCTGCTAAAGA-CCACG
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGC-ATTTGATGGAAAAGCGCCGCGAAAGATCC-TG
* * * * * **
28771434 GTCTATAGTGGCGTTTGATGCAAAAGCGCCCCTAAAGACCACGGTCTATAGCGGCG-TTTATTTA
64 GTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTTATGCA
*
28771498 T
129 A
* * * *
28771499 AAGCGCCGCTAAAGACCATTGTCTATAGCGGCGTTT-ATTGTAAAAAGCGGCGCGAAAG
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCATTTGA-TG-GAAAAGCGCCGCGAAAG
28771557 TTACCGACGC
Statistics
Matches: 260, Mismatches: 47, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
127 1 0.00
128 44 0.17
129 212 0.82
130 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (129 bp):
AAGCGCCGCTAAAGACCATGGTCTATAGCGGCATTTGATGGAAAAGCGCCGCGAAAGATCCTGGT
CTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTTATGCAA
Found at i:28783672 original size:73 final size:73
Alignment explanation
Indices: 28783553--28783695 Score: 214
Period size: 73 Copynumber: 2.0 Consensus size: 73
28783543 CGATGATCGG
* * *
28783553 AAAATGAGTCTCTATCACAGAGTTTGATTTTAGATCAATGATTCAAAAATAATATTATTGTAATA
1 AAAATGAGACTCTATCACAGAATTTGATTTCAGATCAATGATTCAAAAATAATATTATTGTAATA
28783618 GATTTCAA
66 GATTTCAA
* * * *
28783626 AAAATGAGACTCTATCAGAGAATTTGATTTCAGATTAATTATTCAAAAATAATATTATTTTAATA
1 AAAATGAGACTCTATCACAGAATTTGATTTCAGATCAATGATTCAAAAATAATATTATTGTAATA
*
28783691 TATTT
66 GATTT
28783696 AATATTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39
Consensus pattern (73 bp):
AAAATGAGACTCTATCACAGAATTTGATTTCAGATCAATGATTCAAAAATAATATTATTGTAATA
GATTTCAA
Found at i:28799515 original size:15 final size:14
Alignment explanation
Indices: 28799494--28799529 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
28799484 ATAATCCTTA
*
28799494 ATAATTATCTTAAT
1 ATAATTATCCTAAT
28799508 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
28799523 ATAATTA
1 ATAATTA
28799530 AAATAGAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:28805965 original size:5 final size:5
Alignment explanation
Indices: 28805955--28806005 Score: 59
Period size: 5 Copynumber: 10.0 Consensus size: 5
28805945 TATTTATTTA
* *
28805955 TTATT TTATT TT-CT TTACTT TAATT CTTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTA-TT TTATT -TTATT TTATT TTATT TTATT TTATT
28806006 ATATATTACT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 3 0.08
5 29 0.74
6 7 0.18
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:28806226 original size:22 final size:21
Alignment explanation
Indices: 28806167--28806226 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
28806157 GCCCAGAATG
*
28806167 CCTGCAGCCAAACTACCCTATT
1 CCTGCAGCCAAAC-ACCCTATC
* *
28806189 CCTACAGCCAACCACCCTTATC
1 CCTGCAGCCAAACACCC-TATC
*
28806211 CCTGCACCCAAACACC
1 CCTGCAGCCAAACACC
28806227 ACCCCTCAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.28, C:0.48, G:0.07, T:0.17
Consensus pattern (21 bp):
CCTGCAGCCAAACACCCTATC
Found at i:28811613 original size:29 final size:29
Alignment explanation
Indices: 28811559--28811614 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
28811549 GCTTTTAAAG
* *
28811559 ATATTTACAAAAAGAGACAGCTAATTTCA
1 ATATTTACAAAAAGAGACACCAAATTTCA
*
28811588 ATATTTACAAAAATA-ACAACCAAATTT
1 ATATTTACAAAAAGAGAC-ACCAAATTT
28811615 TGTGAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (29 bp):
ATATTTACAAAAAGAGACACCAAATTTCA
Found at i:28816826 original size:27 final size:27
Alignment explanation
Indices: 28816807--28816977 Score: 224
Period size: 27 Copynumber: 6.4 Consensus size: 27
28816797 GGGTATAACA
*
28816807 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* * *
28816834 ATCATTTTACCCTATAGGAGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCG
28816861 GTCATTTTACCCTAT-GGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
*
28816887 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCG
28816914 GTCATTTTACCCTATCA-GGGTATTTCG
1 GTCATTTTACCCTAT-AGGGGTATTTCG
* * *
28816941 ATCATTTTACCCTGT-GGGGACATTT-G
1 GTCATTTTACCCTATAGGGG-TATTTCG
28816967 GTCATTTTACC
1 GTCATTTTACC
28816978 TATTTTAGGG
Statistics
Matches: 127, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
26 38 0.30
27 88 0.69
28 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTCG
Found at i:28816895 original size:53 final size:54
Alignment explanation
Indices: 28816807--28816953 Score: 251
Period size: 53 Copynumber: 2.7 Consensus size: 54
28816797 GGGTATAACA
*
28816807 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGAGTATTTTG
1 GTCATTTTACCCTATCGGGGTATTTCGATCATTTTACCCTATAGGAGTATTTTG
* *
28816861 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATCGGGGTATTTCGATCATTTTACCCTATAGGAGTATTTTG
*
28816914 GTCATTTTACCCTATCAGGGTATTTCGATCATTTTACCCT
1 GTCATTTTACCCTATCGGGGTATTTCGATCATTTTACCCT
28816954 GTGGGGACAT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
53 51 0.58
54 37 0.42
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (54 bp):
GTCATTTTACCCTATCGGGGTATTTCGATCATTTTACCCTATAGGAGTATTTTG
Found at i:28816937 original size:80 final size:80
Alignment explanation
Indices: 28816807--28816977 Score: 247
Period size: 80 Copynumber: 2.1 Consensus size: 80
28816797 GGGTATAACA
* * *
28816807 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGAGTATTTTGGTCATTTTACC
1 GTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATAGGAGTATTTCGATCATTTTACC
*
28816872 CTATGGGG-TATTTCG
66 CTATGGGGACATTT-G
* *
28816887 GTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATCAGG-GTATTTCGATCATTTTAC
1 GTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTAT-AGGAGTATTTCGATCATTTTAC
*
28816951 CCTGTGGGGACATTTG
65 CCTATGGGGACATTTG
28816967 GTCATTTTACC
1 GTCATTTTACC
28816978 TATTTTAGGG
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
80 75 0.91
81 7 0.09
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (80 bp):
GTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATAGGAGTATTTCGATCATTTTACC
CTATGGGGACATTTG
Found at i:28816967 original size:53 final size:52
Alignment explanation
Indices: 28816807--28816977 Score: 245
Period size: 53 Copynumber: 3.2 Consensus size: 52
28816797 GGGTATAACA
*
28816807 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGAGTATTTTG
1 GTCATTTTACCCTAT-GGGGTATTTCGATCATTTTACCCTATAGG-GGATTTTG
*
28816861 GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGTATTTCGATCATTTTACCCTATAGGGG-ATTTTG
* * *
28816914 GTCATTTTACCCTATCAGGGTATTTCGATCATTTTACCCTGT-GGGGACATTTG
1 GTCATTTTACCCTAT-GGGGTATTTCGATCATTTTACCCTATAGGGGA-TTTTG
28816967 GTCATTTTACC
1 GTCATTTTACC
28816978 TATTTTAGGG
Statistics
Matches: 108, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
52 2 0.02
53 68 0.63
54 38 0.35
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (52 bp):
GTCATTTTACCCTATGGGGTATTTCGATCATTTTACCCTATAGGGGATTTTG
Found at i:28827869 original size:28 final size:28
Alignment explanation
Indices: 28827836--28827906 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
28827826 TTGACTTTCG
* *
28827836 ACACTAAGTGTGCGAGTTTAATTGTAAA
1 ACACTAAGTGTGCGAGTTTAATGGAAAA
*
28827864 GCACTAAGTGTGCGAGTTTAATGGAAAA
1 ACACTAAGTGTGCGAGTTTAATGGAAAA
28827892 ACACTAAGTGTGCGA
1 ACACTAAGTGTGCGA
28827907 ACTTCTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (28 bp):
ACACTAAGTGTGCGAGTTTAATGGAAAA
Found at i:28829992 original size:37 final size:37
Alignment explanation
Indices: 28829942--28830020 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
28829932 TTATTACGAA
* *
28829942 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCAG
1 GTCTTACCCGGACAAAATTCT-CACACGAAGTCATCAG
* *
28829979 GTCTTACCCGGACAAAATTCTCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCTCACACGAAGTCATCAG
28830016 GTCTT
1 GTCTT
28830021 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 34 0.92
38 3 0.08
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCTCACACGAAGTCATCAG
Found at i:28830259 original size:49 final size:49
Alignment explanation
Indices: 28830139--28830621 Score: 848
Period size: 49 Copynumber: 9.9 Consensus size: 49
28830129 CCCTTCGAGA
* * * * * *
28830139 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
28830186 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
28830233 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
28830282 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
28830331 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
28830380 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
28830429 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
28830478 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
28830527 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
28830576 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTA
28830622 CGCCATACTA
Statistics
Matches: 420, Mismatches: 12, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
46 1 0.00
47 42 0.10
49 377 0.90
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:28833537 original size:22 final size:22
Alignment explanation
Indices: 28833504--28833630 Score: 94
Period size: 23 Copynumber: 5.5 Consensus size: 22
28833494 TTATGCTTAA
28833504 ATGCTGCTCAATTTATTGTATAT
1 ATGCTGC-CAATTTATTGTATAT
* *
28833527 TTGCTGCCAATTTGTTGTATAT
1 ATGCTGCCAATTTATTGTATAT
* * *
28833549 AAGCTGTCCAATTT-TTGGTGCAAAA
1 ATGCTG-CCAATTTATT-GT--ATAT
* *
28833574 ATGCTGCTCAATATGTTGTATAT
1 ATGCTGC-CAATTTATTGTATAT
* *
28833597 ATGCTGCCTAAATTGTTGTATAT
1 ATGCTGCC-AATTTATTGTATAT
28833620 ATGCTGTCCAA
1 ATGCTG-CCAA
28833631 ATTTTGGTGT
Statistics
Matches: 84, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
22 21 0.25
23 44 0.52
24 3 0.04
25 14 0.17
26 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (22 bp):
ATGCTGCCAATTTATTGTATAT
Found at i:28833593 original size:70 final size:71
Alignment explanation
Indices: 28833502--28833639 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 71
28833492 TTTTATGCTT
* * * *
28833502 AAATGCTGCTCAATTTATTGTATATTTGCTGCC-AATTTGTTGTATATAAGCTGTCCAATTTTTG
1 AAATGCTGCTCAATATATTGTATATATGCTGCCTAAATTGTTGTATATAAGCTGTCCAAATTTTG
28833566 GTGCAA
66 GTGCAA
* *
28833572 AAATGCTGCTCAATATGTTGTATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAAATTTTG
1 AAATGCTGCTCAATATATTGTATATATGCTGCCTAAATTGTTGTATATAAGCTGTCCAAATTTTG
28833637 GTG
66 GTG
28833640 TGAAATTGCT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
70 30 0.49
71 31 0.51
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (71 bp):
AAATGCTGCTCAATATATTGTATATATGCTGCCTAAATTGTTGTATATAAGCTGTCCAAATTTTG
GTGCAA
Found at i:28833672 original size:71 final size:70
Alignment explanation
Indices: 28833528--28833672 Score: 155
Period size: 71 Copynumber: 2.1 Consensus size: 70
28833518 ATTGTATATT
* * * *
28833528 TGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGCAAAAATGCTGCTCAATATGTTGT
1 TGCTGCCAAATTGTTGTATATAAGCTGTCCAAATTTTGGTGCAAAAATGCTGCTCAATATGGTAT
* *
28833593 ATATA
66 AAAAA
* ** * * * * *
28833598 TGCTGCCTAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTGAAATTGCTGTTTAGTTTGGTA
1 TGCTGCC-AAATTGTTGTATATAAGCTGTCCAAATTTTGGTGCAAAAATGCTGCTCAATATGGTA
28833663 TAAAAA
65 TAAAAA
28833669 TGCT
1 TGCT
28833673 ATCCATATTG
Statistics
Matches: 60, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
70 7 0.12
71 53 0.88
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.41
Consensus pattern (70 bp):
TGCTGCCAAATTGTTGTATATAAGCTGTCCAAATTTTGGTGCAAAAATGCTGCTCAATATGGTAT
AAAAA
Found at i:28834284 original size:41 final size:41
Alignment explanation
Indices: 28834217--28834401 Score: 117
Period size: 41 Copynumber: 4.5 Consensus size: 41
28834207 GTTTACAAAG
** *
28834217 AAGCG-CTGCTAATGCTCAAGGATTTAGCGACATTTTTGAAA
1 AAGCGCCT-CTAATGCTCGGGGCTTTAGCGACATTTTTGAAA
* * *
28834258 AAGCGCCTCTAATGCTCGGGGCTTTAGCGGCGTATTTG-AA
1 AAGCGCCTCTAATGCTCGGGGCTTTAGCGACATTTTTGAAA
* * ** *
28834298 AAG-GCACTGCTAATGATTC-TGGCTTTAGAAACGTTTTTGAAA
1 AAGCGC-CT-CTAATG-CTCGGGGCTTTAGCGACATTTTTGAAA
* * * * * * *
28834340 AGGCGCCGCTAATGCTTGGTGCTTTAGCGGCATTTGTGAAG
1 AAGCGCCTCTAATGCTCGGGGCTTTAGCGACATTTTTGAAA
* * *
28834381 AAGCACCACTAATGCTAGGGG
1 AAGCGCCTCTAATGCTCGGGG
28834402 ACTTAGTGGC
Statistics
Matches: 108, Mismatches: 29, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
39 2 0.02
40 8 0.07
41 87 0.81
42 9 0.08
43 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (41 bp):
AAGCGCCTCTAATGCTCGGGGCTTTAGCGACATTTTTGAAA
Found at i:28838336 original size:87 final size:87
Alignment explanation
Indices: 28838201--28838368 Score: 266
Period size: 87 Copynumber: 1.9 Consensus size: 87
28838191 AGGCAGCATT
*
28838201 GAGAGAAGCTGAGGTCCAAAGAAAATATGAAGAACTCCAACTACAACTTAAAG-TAGATGTAGCA
1 GAGAGAAGCTGAGGTCCAAAGAAAATATGAAGAACTCCAACTACAACTTAAAGCT-GATGCAGCA
* *
28838265 GCAAGGGAAGTAGAGGCAGTAGC
65 ACAAGGGAAGCAGAGGCAGTAGC
* * *
28838288 GAGAGAAGCTGATGTTCAAAGAAAATATGAAGAACTTCAACTACAACTTAAAGCTGATGCAGCAA
1 GAGAGAAGCTGAGGTCCAAAGAAAATATGAAGAACTCCAACTACAACTTAAAGCTGATGCAGCAA
28838353 CAAGGGAAGCAGAGGC
66 CAAGGGAAGCAGAGGC
28838369 TGCAGCGCGG
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
87 73 0.99
88 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.15
Consensus pattern (87 bp):
GAGAGAAGCTGAGGTCCAAAGAAAATATGAAGAACTCCAACTACAACTTAAAGCTGATGCAGCAA
CAAGGGAAGCAGAGGCAGTAGC
Found at i:28838733 original size:43 final size:43
Alignment explanation
Indices: 28838693--28838795 Score: 179
Period size: 43 Copynumber: 2.4 Consensus size: 43
28838683 TAAAAAAAAA
*
28838693 GCCGCTAAAAGTCATGATCTATAGCGGCGTTTGGGGAAAAAGT
1 GCCGCTAAAAGTCATGATCTATAGCGGCGTTTGCGGAAAAAGT
28838736 GCCGCTAAAAGTCATGATCTATAGCGGCGTTTGCGGAAAAAGT
1 GCCGCTAAAAGTCATGATCTATAGCGGCGTTTGCGGAAAAAGT
**
28838779 GCCGCTAATGGTCATGA
1 GCCGCTAAAAGTCATGA
28838796 CTTTTAGTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.23
Consensus pattern (43 bp):
GCCGCTAAAAGTCATGATCTATAGCGGCGTTTGCGGAAAAAGT
Found at i:28841755 original size:39 final size:39
Alignment explanation
Indices: 28841701--28841788 Score: 158
Period size: 39 Copynumber: 2.3 Consensus size: 39
28841691 AACAACTAAG
28841701 TTCCAAATACCATATGCTAAAATCATCCTTTTATGCCAA
1 TTCCAAATACCATATGCTAAAATCATCCTTTTATGCCAA
*
28841740 TTCCAAATACCATATGCTAAAATCATCCTTTTATGCCAC
1 TTCCAAATACCATATGCTAAAATCATCCTTTTATGCCAA
*
28841779 TTTCAAATAC
1 TTCCAAATAC
28841789 AAAACATATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (39 bp):
TTCCAAATACCATATGCTAAAATCATCCTTTTATGCCAA
Found at i:28842498 original size:29 final size:29
Alignment explanation
Indices: 28842464--28842542 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 29
28842454 CGATACATAG
*
28842464 TACCTGAAACTGTAATCACCAGCACTAAC
1 TACCTGAAACTGTAATCACCAGCACAAAC
* ** * *
28842493 TGCCTGAAACTGTAA-CACTGGTACAAAG
1 TACCTGAAACTGTAATCACCAGCACAAAC
*
28842521 TACCTGATACTGTAATCACCAG
1 TACCTGAAACTGTAATCACCAG
28842543 AAACTAGTGC
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
28 21 0.54
29 18 0.46
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (29 bp):
TACCTGAAACTGTAATCACCAGCACAAAC
Found at i:28864138 original size:42 final size:43
Alignment explanation
Indices: 28864035--28864185 Score: 134
Period size: 43 Copynumber: 3.5 Consensus size: 43
28864025 AATGTGATAT
* * *
28864035 CGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTGAGATTTA
1 CGTGTAAGACCCTGTCTGGGACATTGGCATCGATAT-AGATTTA
28864079 CGTGTAAGACCAC-GTCTGGGACATT-GCAATCG-TATATG-TTTA
1 CGTGTAAGACC-CTGTCTGGGACATTGGC-ATCGATATA-GATTTA
* * * *
28864121 CGTGTAAGACCCTGTCTGGGATAATGGCATCGTTAGTTGA-TTA
1 CGTGTAAGACCCTGTCTGGGACATTGGCATCGATA-TAGATTTA
*
28864164 CATGTAAGACCAC-GTCTGGGAC
1 CGTGTAAGACC-CTGTCTGGGAC
28864186 GTTGACATTG
Statistics
Matches: 90, Mismatches: 8, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
41 1 0.01
42 30 0.33
43 31 0.34
44 28 0.31
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCCTGTCTGGGACATTGGCATCGATATAGATTTA
Found at i:28864181 original size:43 final size:42
Alignment explanation
Indices: 28864076--28864184 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
28864066 GATTTGAGAT
* * *
28864076 TTACGTGTAAGACCACGTCTGGGACATTGCAATCGTATATGT
1 TTACGTGTAAGACCACGTCTGGGAAATGGCAATCGTATATGA
28864118 TTACGTGTAAGACC-CTGTCTGGGATAATGGC-ATCGT-TAGTTGA
1 TTACGTGTAAGACCAC-GTCTGGGA-AATGGCAATCGTATA--TGA
*
28864161 TTACATGTAAGACCACGTCTGGGA
1 TTACGTGTAAGACCACGTCTGGGA
28864185 CGTTGACATT
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
41 3 0.05
42 27 0.47
43 27 0.47
44 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (42 bp):
TTACGTGTAAGACCACGTCTGGGAAATGGCAATCGTATATGA
Found at i:28867445 original size:18 final size:18
Alignment explanation
Indices: 28867408--28867459 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
28867398 TAGGGGTGTG
*
28867408 CAAAATTCGGGTAAAACCGA
1 CAAAATTC-GGT-TAACCGA
28867428 CAAAATTCGGTTAACCGA
1 CAAAATTCGGTTAACCGA
**
28867446 CCGAATTCGGTTAA
1 CAAAATTCGGTTAA
28867460 TCGGTCAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 18 0.62
19 3 0.10
20 8 0.28
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (18 bp):
CAAAATTCGGTTAACCGA
Found at i:28867661 original size:18 final size:18
Alignment explanation
Indices: 28867628--28867680 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
28867618 ATTCACCTAA
*
28867628 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
* *
28867647 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
28867665 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
28867681 CCCAATCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.42, C:0.47, G:0.02, T:0.09
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:28868228 original size:20 final size:18
Alignment explanation
Indices: 28868204--28868255 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
28868194 AATAGTATTT
28868204 TATTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
28868222 GTGATT-ATATTAATATTAAA
1 -T-ATTAAT-TTAATATTAAA
28868242 T-TTAATTTAATATT
1 TATTAATTTAATATT
28868256 TATCTTGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 10 0.33
18 2 0.07
19 4 0.13
20 14 0.47
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:28868296 original size:69 final size:68
Alignment explanation
Indices: 28868163--28868297 Score: 173
Period size: 69 Copynumber: 2.0 Consensus size: 68
28868153 TTTAATAGAT
* * *
28868163 TTAATATTAAATTAATTTTAATACTAATCCTAATAGTATTTTATTAATTTAATATTAAAGTGATT
1 TTAATATTAAATTAATTTTAATACTAATCCTAATAATATTGTATTAATTTAATATCAAAGTGATT
28868228 ATA
66 ATA
* * * * *
28868231 TTAATATTAAATTTAA-TTTAATATTTATCTTGATAAATATTGTATTAATTTAATATCAAATTGA
1 TTAATATTAAA-TTAATTTTAATACTAATCCTAAT-AATATTGTATTAATTTAATATCAAAGTGA
28868295 TTA
64 TTA
28868298 AGTCTAATCA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
68 25 0.44
69 32 0.56
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (68 bp):
TTAATATTAAATTAATTTTAATACTAATCCTAATAATATTGTATTAATTTAATATCAAAGTGATT
ATA
Found at i:28868529 original size:36 final size:37
Alignment explanation
Indices: 28868475--28868548 Score: 141
Period size: 36 Copynumber: 2.0 Consensus size: 37
28868465 AAGTATAGAG
28868475 AAATTGCAAAAATTACCCTACTGGTAATTTTTGTGAA
1 AAATTGCAAAAATTACCCTACTGGTAATTTTTGTGAA
28868512 AAATTGC-AAAATTACCCTACTGGTAATTTTTGTGAA
1 AAATTGCAAAAATTACCCTACTGGTAATTTTTGTGAA
28868548 A
1 A
28868549 GTTTTTCTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 30 0.81
37 7 0.19
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (37 bp):
AAATTGCAAAAATTACCCTACTGGTAATTTTTGTGAA
Found at i:28873708 original size:26 final size:26
Alignment explanation
Indices: 28873679--28873897 Score: 201
Period size: 26 Copynumber: 8.4 Consensus size: 26
28873669 CATAGTCAAT
* *
28873679 TTGGTGAATTTGTTAGGTTAGCCTGG
1 TTGGTTAATTTGTTAGGTTAGCCAGG
* * *
28873705 TTGGTTAATCTATTAGGTTCGCCAGG
1 TTGGTTAATTTGTTAGGTTAGCCAGG
* * *
28873731 TTGGTTAATCTGCTAGGTTTGCCAGG
1 TTGGTTAATTTGTTAGGTTAGCCAGG
* *
28873757 TTAGTTAATTTGTTAGGTTTGCCAGG
1 TTGGTTAATTTGTTAGGTTAGCCAGG
28873783 TTGGTTAATTTGTTAGGTTCA-CCAGG
1 TTGGTTAATTTGTTAGGTT-AGCCAGG
* * *
28873809 TTGTTTAATTTGTTAAGTTCA-CTAGG
1 TTGGTTAATTTGTTAGGTT-AGCCAGG
* * *
28873835 TTGGTTAATCTATTAGGTTCA-CCAAG
1 TTGGTTAATTTGTTAGGTT-AGCCAGG
** **
28873861 TTGGTTAACATGTTAGGTTTTCCAGG
1 TTGGTTAATTTGTTAGGTTAGCCAGG
*
28873887 TTTGTTAATTT
1 TTGGTTAATTT
28873898 TTTGAAGTGT
Statistics
Matches: 161, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 161 1.00
ACGTcount: A:0.20, C:0.11, G:0.26, T:0.44
Consensus pattern (26 bp):
TTGGTTAATTTGTTAGGTTAGCCAGG
Found at i:28875262 original size:16 final size:16
Alignment explanation
Indices: 28875241--28875272 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28875231 TTTATGTTTG
28875241 ACCTAAGGTAAGTATA
1 ACCTAAGGTAAGTATA
28875257 ACCTAAGGTAAGTATA
1 ACCTAAGGTAAGTATA
28875273 CATATTCTAT
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:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (16 bp):
ACCTAAGGTAAGTATA
Found at i:28890323 original size:11 final size:11
Alignment explanation
Indices: 28890259--28890370 Score: 56
Period size: 11 Copynumber: 9.8 Consensus size: 11
28890249 TTCAAAAAAA
*
28890259 TAATATTATTT
1 TAATATTAATT
28890270 TAATAAATTTAATT
1 TAAT--A-TTAATT
28890284 TAATACTT-ATCT
1 TAATA-TTAAT-T
*
28890296 TAATAGT-ATT
1 TAATATTAATT
28890306 T--TATTAATT
1 TAATATTAATT
28890315 TAATATTAAAGTT
1 TAATATT-AA-TT
* *
28890328 ATTATCTTAATAT
1 -TAATATTAAT-T
28890341 TAA-ATTTAATT
1 TAATA-TTAATT
28890352 TAAT-TTAATT
1 TAATATTAATT
28890362 TAATATTAA
1 TAATATTAA
28890371 AGTAATTATG
Statistics
Matches: 79, Mismatches: 8, Indels: 28
0.69 0.07 0.24
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 12 0.15
11 21 0.27
12 19 0.24
13 6 0.08
14 14 0.18
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (11 bp):
TAATATTAATT
Found at i:28890331 original size:20 final size:20
Alignment explanation
Indices: 28890306--28890364 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
28890296 TAATAGTATT
28890306 TTATTAATTTAATATTAAAG
1 TTATTAATTTAATATTAAAG
*
28890326 TTATT-ATCTTAATATTAAAT
1 TTATTAAT-TTAATATTAAAG
28890346 TTAATTTAATTTAAT-TTAA
1 TT-A-TTAATTTAATATTAA
28890365 TATTAAAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
19 2 0.06
20 18 0.53
21 5 0.15
22 7 0.21
23 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TTATTAATTTAATATTAAAG
Found at i:28897959 original size:17 final size:17
Alignment explanation
Indices: 28897939--28898035 Score: 60
Period size: 17 Copynumber: 5.7 Consensus size: 17
28897929 ATTTTAATAG
28897939 ATTTAATATTTAATTTA
1 ATTTAATATTTAATTTA
*
28897956 ATTTAATGTTT-ATCTTA
1 ATTTAATATTTAAT-TTA
* *
28897973 A--TAGTATTTCA-TTA
1 ATTTAATATTTAATTTA
*
28897987 ATTTAATATTAAAGTGATT-
1 ATTTAATATTTAA-T--TTA
*
28898006 ATATTAATATTAAATTTA
1 AT-TTAATATTTAATTTA
*
28898024 ATTTAATGTTTA
1 ATTTAATATTTA
28898036 TCTCATAGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 4 0.06
15 6 0.10
16 10 0.16
17 24 0.39
18 2 0.03
19 3 0.05
20 13 0.21
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (17 bp):
ATTTAATATTTAATTTA
Found at i:28898078 original size:62 final size:59
Alignment explanation
Indices: 28898009--28898125 Score: 180
Period size: 62 Copynumber: 1.9 Consensus size: 59
28897999 AGTGATTATA
* * *
28898009 TTAATATTAAATTTAATTTAATGTTTATCTCATAGATAAATATTCTATTAATTTAATAAGAC
1 TTAATATTAAATTTAATCTAATATTTATCT--T-GATAAATATTATATTAATTTAATAAGAC
28898071 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
28898126 TTAAAGTGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
59 23 0.44
60 1 0.02
62 28 0.54
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAAGAC
Found at i:28901580 original size:13 final size:14
Alignment explanation
Indices: 28901556--28901604 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
28901546 AATTCCACTA
28901556 AAAATTTAAAAAATT
1 AAAA-TTAAAAAATT
*
28901571 AAGA-T-AAAAATT
1 AAAATTAAAAAATT
28901583 AAAATTAAAAAA-T
1 AAAATTAAAAAATT
28901596 AAAATTAAA
1 AAAATTAAA
28901605 GAAAAATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 10 0.33
13 12 0.40
14 5 0.17
15 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (14 bp):
AAAATTAAAAAATT
Found at i:28904253 original size:38 final size:39
Alignment explanation
Indices: 28904192--28904271 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 39
28904182 CAACCCAACC
*
28904192 CTACCCAATTATCCAACCCAATAAAACTAAAACTAAAGT
1 CTACCCAATTATCCAACCCAATAAAAATAAAACTAAAGT
*
28904231 CTACCCAATTA-CCAACCTAATAAAAATAAAACTAAAGT
1 CTACCCAATTATCCAACCCAATAAAAATAAAACTAAAGT
28904269 CTA
1 CTA
28904272 ACTCTTAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 28 0.72
39 11 0.28
ACGTcount: A:0.50, C:0.26, G:0.03, T:0.21
Consensus pattern (39 bp):
CTACCCAATTATCCAACCCAATAAAAATAAAACTAAAGT
Found at i:28904487 original size:9 final size:9
Alignment explanation
Indices: 28904473--28904503 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28904463 GTAATGATTC
*
28904473 AATTCGGGT
1 AATTCGGTT
28904482 AATTCGGTT
1 AATTCGGTT
28904491 AATTCGGTT
1 AATTCGGTT
28904500 AATT
1 AATT
28904504 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:28905263 original size:22 final size:21
Alignment explanation
Indices: 28905210--28905266 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
28905200 TCAAAGTTTG
*
28905210 ATGTCTCGAGACAAAGGTATC
1 ATGTCTCGAGACAAAGGTACC
* *
28905231 ATGTCTTGAGACAAA-GTCCCC
1 ATGTCTCGAGACAAAGGT-ACC
28905252 TATGTCTCGAGACAA
1 -ATGTCTCGAGACAA
28905267 TACCTCATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 15 0.50
22 13 0.43
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (21 bp):
ATGTCTCGAGACAAAGGTACC
Found at i:28911706 original size:106 final size:107
Alignment explanation
Indices: 28911485--28911767 Score: 345
Period size: 106 Copynumber: 2.7 Consensus size: 107
28911475 TAAAGTTGAT
* * *
28911485 GAAATTCTAAATAAACCAAACAAAACCCATCACTCATTTACAACTTTTTAGTCTTGCTTTCAGAA
1 GAAATTTTAAATAAACCAAACAAAACCCATCACTTATTTACAAC-TTTTAGTCTTCCTTTCAGAA
* * * * * *
28911550 TGTATCAAACCATGGAGTCTGCAATTGCAATGTCAGAGTTGAT
65 TGTATCAAACCATGGAATCAGCAAATGCAATATCAGAGTTCAC
* * * * * * * *
28911593 GAAATTTTAAAAAAACCAAACAAAACCAACCACTTATTTACTACATTTAATCTTCCATTCAGTAT
1 GAAATTTTAAATAAACCAAACAAAACCCATCACTTATTTACAACTTTTAGTCTTCCTTTCAGAAT
* *
28911658 GTATC-AACCATGGAATCAGCAAATGCAATATTATAGTTCAC
66 GTATCAAACCATGGAATCAGCAAATGCAATATCAGAGTTCAC
* * *
28911699 GAAATTTTAAATAAACCAAGC-AAACCCATCACTTATTCACAACTTTTAGTCTTTCTTTCAGAAT
1 GAAATTTTAAATAAACCAAACAAAACCCATCACTTATTTACAACTTTTAGTCTTCCTTTCAGAAT
28911763 GTATC
66 GTATC
28911768 GGCCATGTAG
Statistics
Matches: 145, Mismatches: 30, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
105 39 0.27
106 47 0.32
107 21 0.14
108 38 0.26
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.31
Consensus pattern (107 bp):
GAAATTTTAAATAAACCAAACAAAACCCATCACTTATTTACAACTTTTAGTCTTCCTTTCAGAAT
GTATCAAACCATGGAATCAGCAAATGCAATATCAGAGTTCAC
Found at i:28924256 original size:21 final size:21
Alignment explanation
Indices: 28924231--28924276 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
28924221 TGGTTTTTGC
*
28924231 CTTTAAACCTTTGTTTTATAA
1 CTTTAAACCCTTGTTTTATAA
*
28924252 CTTTAAACCCTTGTTTTATAC
1 CTTTAAACCCTTGTTTTATAA
28924273 CTTT
1 CTTT
28924277 TGATTGGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.52
Consensus pattern (21 bp):
CTTTAAACCCTTGTTTTATAA
Found at i:28930861 original size:16 final size:18
Alignment explanation
Indices: 28930840--28930877 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
28930830 TAGGGGGAGC
*
28930840 GAATAAAA-AGTTGG-AT
1 GAATAAAATACTTGGAAT
28930856 GAATAAAATACTTGGAAT
1 GAATAAAATACTTGGAAT
28930874 GAAT
1 GAAT
28930878 TATTAGTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 5 0.26
18 6 0.32
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (18 bp):
GAATAAAATACTTGGAAT
Found at i:28932995 original size:5 final size:5
Alignment explanation
Indices: 28932985--28933021 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
28932975 AAGTGTTTAG
* *
28932985 TAAAA TAAAA TAAAA TAAAA TAGAA TTAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
28933022 TTAAAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:28950630 original size:44 final size:44
Alignment explanation
Indices: 28950564--28950758 Score: 191
Period size: 44 Copynumber: 4.5 Consensus size: 44
28950554 CATATCAAAC
* * *
28950564 CTTATCTCCCTGAAGTTACAGTGGAGTAGGTTGAATATACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAACATACCAAT
* *
28950608 CTTATCTCCCTGAAGTTGCAGTGGAGCATGTTGAAGATACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAACATACCAAT
* * * * * * *
28950652 CATATCTCTCTGAAGTTGCAGTAGAGCA-GAT-CACAT-CAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAACATACCAAT
* * *
28950693 CTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTCAAGCA-ACTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAA-CATACCAAT
** *
28950737 AATATCTCCCTAAAGTTGCAGT
1 CTTATCTCCCTGAAGTTGCAGT
28950759 ATTACGTTTT
Statistics
Matches: 125, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
41 27 0.22
42 5 0.04
43 3 0.02
44 90 0.72
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAACATACCAAT
Found at i:28950743 original size:129 final size:129
Alignment explanation
Indices: 28950525--28950758 Score: 335
Period size: 129 Copynumber: 1.8 Consensus size: 129
28950515 TAACATGTCT
* * * *
28950525 TATCTCTCTTAATTTGCAGTAAAGCAGATCATATCAAACCTTATCTCCCTGAAGTTACAGTGGAG
1 TATCTCTCTGAAGTTGCAGTAAAGCAGATCACATCAAACCTTATCTCCCTAAAGTTACAGTGGAG
* * * ** *
28950590 TAGGTTGAATATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCATGTTGAAGATACCAATCA
66 CAGGTTCAACATACCAATAATATCTCCCTAAAGTTGCAGTGGAGCATGTTGAAGATACCAATCA
* *
28950654 TATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAACCTTATCTCCCTAAAGTTGCAGTGGAG
1 TATCTCTCTGAAGTTGCAGTAAAGCAGATCACATCAAACCTTATCTCCCTAAAGTTACAGTGGAG
*
28950719 CAGGTTCAAGCA-ACTAATAATATCTCCCTAAAGTTGCAGT
66 CAGGTTCAA-CATACCAATAATATCTCCCTAAAGTTGCAGT
28950759 ATTACGTTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
129 90 0.99
130 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (129 bp):
TATCTCTCTGAAGTTGCAGTAAAGCAGATCACATCAAACCTTATCTCCCTAAAGTTACAGTGGAG
CAGGTTCAACATACCAATAATATCTCCCTAAAGTTGCAGTGGAGCATGTTGAAGATACCAATCA
Found at i:28951647 original size:15 final size:16
Alignment explanation
Indices: 28951627--28951656 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28951617 ATAATTTACA
28951627 AATTG-TTGCATATTG
1 AATTGTTTGCATATTG
28951642 AATTGTTTGCATATT
1 AATTGTTTGCATATT
28951657 TGAAGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.50
Consensus pattern (16 bp):
AATTGTTTGCATATTG
Found at i:28955787 original size:14 final size:14
Alignment explanation
Indices: 28955768--28955795 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28955758 TGGGTGCAAC
28955768 TTATTACTTTGGAT
1 TTATTACTTTGGAT
28955782 TTATTACTTTGGAT
1 TTATTACTTTGGAT
28955796 ATGTGTATTC
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:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (14 bp):
TTATTACTTTGGAT
Found at i:28962973 original size:6 final size:6
Alignment explanation
Indices: 28962964--28963009 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
28962954 AAGAAAAAGA
*
28962964 AAAATC AAAATC AAAGTC AAAATC AAAATC AAAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
28963010 AAAGAAGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.67, C:0.15, G:0.02, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:28963033 original size:45 final size:46
Alignment explanation
Indices: 28962982--28963075 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 46
28962972 AATCAAAGTC
28962982 AAAATCAAAATCAAAATCAAAATCA-AAAAA-AGAAGAAAGAA-GAAA
1 AAAATCAAAATCAAAATCAAAATCAGAAAAATA-AAG-AAGAATGAAA
* * *
28963027 AAAATCAAGATCAAAATGAAAATGAGAAAAATAAAGAAGAATGAAA
1 AAAATCAAAATCAAAATCAAAATCAGAAAAATAAAGAAGAATGAAA
28963073 AAA
1 AAA
28963076 GAGAAATCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
45 27 0.63
46 15 0.35
47 1 0.02
ACGTcount: A:0.71, C:0.06, G:0.12, T:0.11
Consensus pattern (46 bp):
AAAATCAAAATCAAAATCAAAATCAGAAAAATAAAGAAGAATGAAA
Found at i:28964010 original size:12 final size:13
Alignment explanation
Indices: 28963993--28964032 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
28963983 GAAAATATGA
28963993 AAAATGAAAAT-G
1 AAAATGAAAATGG
*
28964005 AAAATGGAAATGG
1 AAAATGAAAATGG
28964018 AAAATGAAAAATGG
1 AAAATG-AAAATGG
28964032 A
1 A
28964033 GAGGCTAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.42
13 7 0.29
14 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (13 bp):
AAAATGAAAATGG
Found at i:28964030 original size:7 final size:6
Alignment explanation
Indices: 28963993--28964027 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
28963983 GAAAATATGA
*
28963993 AAAATG AAAATG AAAATG GAAATGG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAAT-G AAAATG AAAA
28964028 ATGGAGAGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:28965449 original size:86 final size:86
Alignment explanation
Indices: 28965239--28965454 Score: 294
Period size: 86 Copynumber: 2.5 Consensus size: 86
28965229 TAGATCAGTG
*
28965239 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCTA
1 AAGATAGCAGATCTTGCCTTCCT-CATTGACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
*
28965304 TCGGTTGCAGTGGAGCTGGTTA
65 TCGGTTGCAGTGGAGCTGGTGA
* * * * *
28965326 AAGA-AGTAGATCTTACCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAATCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCT-CATTGACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
28965390 TCGGTTGCAGTGGAGCT-GTGA
65 TCGGTTGCAGTGGAGCTGGTGA
* *
28965411 AAGATAGCAGATATTGCCCTCCT-ATGTCGACAGTGAAGCAGATC
1 AAGATAGCAGATCTTGCCTTCCTCAT-T-GACAGTGAAGCAGATC
28965455 AAAGATTACA
Statistics
Matches: 113, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
84 2 0.02
85 8 0.07
86 99 0.88
87 4 0.04
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (86 bp):
AAGATAGCAGATCTTGCCTTCCTCATTGACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
CGGTTGCAGTGGAGCTGGTGA
Found at i:28965744 original size:45 final size:44
Alignment explanation
Indices: 28965637--28965746 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 44
28965627 TGAAGAAGTA
* * * * *
28965637 AATCTTATTTCCCTGAGGTTGTAGTGGAGCAGATTGAATTCGAT
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTCAAT
* *
28965681 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGT-AAT
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTCAAT
*
28965724 AAGATCTTATCTCTCTGAAGTTG
1 -A-ATCTTATCTCCCTGAAGTTG
28965747 CAGCAGAGCA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
43 2 0.04
44 35 0.64
45 18 0.33
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTCAAT
Found at i:28966062 original size:16 final size:16
Alignment explanation
Indices: 28966041--28966071 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28966031 GGCCCGTCAA
28966041 TAAAATAAAACCAAAT
1 TAAAATAAAACCAAAT
*
28966057 TAAAATTAAACCAAA
1 TAAAATAAAACCAAA
28966072 AAAAAGGGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAATAAAACCAAAT
Found at i:28972028 original size:11 final size:11
Alignment explanation
Indices: 28972012--28972063 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
28972002 TTTTATACTA
28972012 AATAAAATATT
1 AATAAAATATT
*
28972023 AATAAAATAAT
1 AATAAAATATT
* *
28972034 AAT-ATATCTT
1 AATAAAATATT
*
28972044 ATTAAAATATT
1 AATAAAATATT
*
28972055 AATTAAATA
1 AATAAAATA
28972064 ATATTTATCT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
10 6 0.19
11 25 0.81
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
AATAAAATATT
Found at i:28972050 original size:32 final size:31
Alignment explanation
Indices: 28972005--28972093 Score: 103
Period size: 32 Copynumber: 2.9 Consensus size: 31
28971995 CTTTCCTTTT
*
28972005 TATA-CTAAATAAAATATTAATAAAATAATAA
1 TATATCTAATTAAAATATTAATAAAATAAT-A
* *
28972036 TATATCTTATTAAAATATTAATTAAATAATA
1 TATATCTAATTAAAATATTAATAAAATAATA
*
28972067 TTTATCTAATT-AAATAATT-ATAAAATA
1 TATATCTAATTAAAAT-ATTAATAAAATA
28972094 TCATCAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
30 11 0.22
31 17 0.34
32 22 0.44
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (31 bp):
TATATCTAATTAAAATATTAATAAAATAATA
Found at i:28975118 original size:46 final size:46
Alignment explanation
Indices: 28975051--28975138 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
28975041 TATTGCAATT
* *
28975051 AGAGTTTTAGTTTTATTTATTTTCTTTATTACATCAGGTTTTGTTA
1 AGAGTTTTAGTTTTACTTATTTTCTCTATTACATCAGGTTTTGTTA
* *
28975097 AGAGTTTTAGTTTTACTTATTTTCTCTATTATATTAGGTTTT
1 AGAGTTTTAGTTTTACTTATTTTCTCTATTACATCAGGTTTT
28975139 TACTTCCTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.22, C:0.07, G:0.12, T:0.59
Consensus pattern (46 bp):
AGAGTTTTAGTTTTACTTATTTTCTCTATTACATCAGGTTTTGTTA
Found at i:28976354 original size:21 final size:21
Alignment explanation
Indices: 28976329--28976371 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
28976319 ACATGAACCA
28976329 AATTT-AATGTTAAGTGTGAAC
1 AATTTCAATGTT-AGTGTGAAC
*
28976350 AATTTCATTGTTAGTGTGAAC
1 AATTTCAATGTTAGTGTGAAC
28976371 A
1 A
28976372 CATCTAGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.40
Consensus pattern (21 bp):
AATTTCAATGTTAGTGTGAAC
Found at i:28977622 original size:30 final size:32
Alignment explanation
Indices: 28977562--28977625 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
28977552 CACTTATTTT
28977562 CACCTATGCCGAATGCATACACATAAATATATC
1 CACCTATGCCGAATGCA-ACACATAAATATATC
* *
28977595 CACCTATGCCGAATGCAACATATATATATAT
1 CACCTATGCCGAATGCAACACATAAATATAT
28977626 ATACATATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (32 bp):
CACCTATGCCGAATGCAACACATAAATATATC
Found at i:28977887 original size:41 final size:41
Alignment explanation
Indices: 28977842--28978366 Score: 973
Period size: 41 Copynumber: 12.8 Consensus size: 41
28977832 ACCGGCTCTT
*
28977842 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
28977883 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
28977924 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
28977965 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
28978006 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
28978047 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
28978088 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
28978129 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
28978170 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
28978211 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
28978252 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
28978293 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
28978334 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
28978367 TAACGATAAA
Statistics
Matches: 476, Mismatches: 4, Indels: 8
0.98 0.01 0.02
Matches are distributed among these distances:
39 2 0.00
40 2 0.00
41 467 0.98
42 2 0.00
43 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:28980265 original size:18 final size:20
Alignment explanation
Indices: 28980223--28980266 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
28980213 GTTGTTAAGC
*
28980223 ATGATGAATGGAGAGCAACA
1 ATGATTAATGGAGAGCAACA
*
28980243 ATGATTAAT-GAGATCAA-A
1 ATGATTAATGGAGAGCAACA
28980261 ATGATT
1 ATGATT
28980267 GAGAAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (20 bp):
ATGATTAATGGAGAGCAACA
Found at i:28984138 original size:19 final size:19
Alignment explanation
Indices: 28984116--28984154 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28984106 CGTTTTGCTA
28984116 TTCTGT-TTCTATTCTCTTT
1 TTCTGTCTTCTATT-TCTTT
*
28984135 TTCTGTCTTTTATTTCTTT
1 TTCTGTCTTCTATTTCTTT
28984154 T
1 T
28984155 ATTTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.72
Consensus pattern (19 bp):
TTCTGTCTTCTATTTCTTT
Found at i:28986212 original size:30 final size:30
Alignment explanation
Indices: 28986175--28986282 Score: 112
Period size: 30 Copynumber: 3.6 Consensus size: 30
28986165 ATTGAGAAGC
28986175 ATTTTTATATTAATTATATTATGA-AAAAG
1 ATTTTTATATTAATTATATTATGAGAAAAG
* * * * *
28986204 AATGTTTATATTTATTGTATTATGATAAAAT
1 -ATTTTTATATTAATTATATTATGAGAAAAG
* **
28986235 ATTTTTACATTAATTACGTTATGAGAAAATG
1 ATTTTTATATTAATTATATTATGAGAAAA-G
28986266 -TTTTTATATTAATTATA
1 ATTTTTATATTAATTATA
28986283 GGAATAATAT
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
30 57 0.93
31 4 0.07
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (30 bp):
ATTTTTATATTAATTATATTATGAGAAAAG
Found at i:28994470 original size:9 final size:9
Alignment explanation
Indices: 28994456--28994492 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28994446 TATAGTTTGA
28994456 TATTCGAAT
1 TATTCGAAT
28994465 TATTCGAAT
1 TATTCGAAT
*
28994474 TATTCGAGT
1 TATTCGAAT
28994483 TATTCGAAT
1 TATTCGAAT
28994492 T
1 T
28994493 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28996190 original size:9 final size:9
Alignment explanation
Indices: 28996161--28996197 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
28996151 TGAGTTTTCG
28996161 AATTCGAAT
1 AATTCGAAT
*
28996170 AACTCGAAT
1 AATTCGAAT
28996179 AATTCGAAT
1 AATTCGAAT
*
28996188 AATTCAAAT
1 AATTCGAAT
28996197 A
1 A
28996198 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28996926 original size:30 final size:31
Alignment explanation
Indices: 28996892--28996951 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
28996882 AAACCTTTTA
*
28996892 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
28996922 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
28996952 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:29000986 original size:3 final size:3
Alignment explanation
Indices: 29000978--29001023 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
29000968 GTGATTGGCT
29000978 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
29001024 AGCTTCTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29007844 original size:23 final size:22
Alignment explanation
Indices: 29007792--29007844 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
29007782 TCCACGTCTT
*
29007792 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
29007814 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
29007837 TTTCTTTT
1 TTTCTTTT
29007845 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:29016446 original size:19 final size:19
Alignment explanation
Indices: 29016419--29016461 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
29016409 TGTATTCTAA
* *
29016419 ATATTGTATAAAATCATGT
1 ATATAGTATAAAATCATAT
* *
29016438 ATATAGTATGAAATTATAT
1 ATATAGTATAAAATCATAT
29016457 ATATA
1 ATATA
29016462 TTTAATATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (19 bp):
ATATAGTATAAAATCATAT
Found at i:29028396 original size:27 final size:27
Alignment explanation
Indices: 29028340--29028636 Score: 308
Period size: 27 Copynumber: 11.2 Consensus size: 27
29028330 GATTCTTGGG
29028340 AAAATGACCGAAATACCC-CGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
*
29028366 AAAATGATCGAAATACCCTCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
*
29028393 AAAATGATCGAAATACCCTCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* *
29028420 AAAATGATCGAAATACCCTCGAGGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* * *
29028447 AAAATGACCAAAATACCCTCGAATGAT
1 AAAATGACCGAAATACCCTCGAAGGGT
** *
29028474 AAAATGATTGAACTACCC-CAGAAGGGT
1 AAAATGACCGAAATACCCTC-GAAGGGT
29028501 -AAATGACCGAAATACCC-C-AGAGGAGT
1 AAAATGACCGAAATACCCTCGA-AGG-GT
* *
29028527 AAAATAACCGAAATAACCC-CAAAGGGT
1 AAAATGACCGAAAT-ACCCTCGAAGGGT
* *
29028554 -AAATGACCGAAATACCTTTGAA-GGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* **
29028579 AAAATAACTTAAATACCC-CGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* *
29028605 AACATGACCGAAATA-CCTCTGAAGGGC
1 AAAATGACCGAAATACCCTC-GAAGGGT
29028632 AAAAT
1 AAAAT
29028637 AACTGTTATA
Statistics
Matches: 227, Mismatches: 32, Indels: 23
0.80 0.11 0.08
Matches are distributed among these distances:
24 1 0.00
25 14 0.06
26 77 0.34
27 126 0.56
28 8 0.04
29 1 0.00
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (27 bp):
AAAATGACCGAAATACCCTCGAAGGGT
Found at i:29030773 original size:47 final size:48
Alignment explanation
Indices: 29030701--29030798 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 48
29030691 ACTTTAATTT
* *
29030701 TTTTTATATATTACAATCATATATTAGCGT-TAAATTTCATTATGTATTA
1 TTTTTATATATTACAATCATATATTAACATATAAATTT--TTATGTATTA
29030750 TTTTTA-A-ATTACAAT-ATATTATTAACATCATAAATTTTTATGTATTA
1 TTTTTATATATTACAATCATA-TATTAACAT-ATAAATTTTTATGTATTA
29030797 TT
1 TT
29030799 AGATTATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
46 3 0.07
47 27 0.61
48 1 0.02
49 13 0.30
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (48 bp):
TTTTTATATATTACAATCATATATTAACATATAAATTTTTATGTATTA
Found at i:29037660 original size:88 final size:88
Alignment explanation
Indices: 29036890--29037658 Score: 1117
Period size: 88 Copynumber: 8.8 Consensus size: 88
29036880 AACAGATCAG
* * * * *
29036890 TGAATACAGCAGATCTTGCCTTCCTGCATCGACAGGGAAGCAGATCGAAGACACAAGCGTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
*
29036955 CTCTTGGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * *
29036978 TGAAGACAACGGATCTTGCCTTCCTGCATTGACAACGAAGCAAATCGAAGACACAAGCCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
* * *
29037043 CTCTCAGTTTTAGTGAAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* *
29037066 TGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCAAAGACACAAGCCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
* **
29037131 CACTCGGTTGTAGTAAAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * * *
29037154 TGAAGACAGCAGA-CTTGCCTTCCTGCATTGACAGCGAAACAGATCGAAGACACAAGCGTTACCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
29037218 CTCTCGGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * *
29037241 TGAAGACAACAGATCTTGCTTTCCTGCATCGACAGGGAAGCAGATCGAAGACACAAGCCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
29037306 CTCTCGGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
*
29037329 TAAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
29037394 CTCTCGGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* *
29037417 TAAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCATTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
* * *
29037482 CTCTCGGTTGTAGCGAAACTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * * * * * *
29037505 TGAAGACAACAGATCTTTCCTGCTTGTATTGACAGTGAAGCAGATCGAAAACACAGGCCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
* *
29037570 CCCTCGGTTGTAGTGGAGCAGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * * * * * *
29037593 TGAGGATAGCAGATGTTGCCTTCCTGCATTGATAGCGAAGCAGATCGAAGATACAAGCCTTACCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
29037658 C
66 C
29037659 CCAGGCGGTG
Statistics
Matches: 607, Mismatches: 73, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
87 78 0.13
88 529 0.87
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (88 bp):
TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
CTCTCGGTTGTAGTGGAGCTGGT
Found at i:29039105 original size:5 final size:5
Alignment explanation
Indices: 29039095--29039119 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29039085 ATCCTCTTTG
29039095 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
29039120 AATTAGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:29039321 original size:47 final size:48
Alignment explanation
Indices: 29039249--29039346 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 48
29039239 TACTTTAATT
* *
29039249 TTTTTATATATTACAATCATATATTAGCGT-TAAATTTCATTATGTATTA
1 TTTTTATATATTACAATCATATATTAACATATAAATTT--TTATGTATTA
29039298 TTTTTA-A-ATTACAAT-ATATTATTAACATCATAAATTTTTATGTATTA
1 TTTTTATATATTACAATCATA-TATTAACAT-ATAAATTTTTATGTATTA
29039345 TT
1 TT
29039347 AGATTAGATT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
46 3 0.07
47 27 0.61
48 1 0.02
49 13 0.30
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (48 bp):
TTTTTATATATTACAATCATATATTAACATATAAATTTTTATGTATTA
Found at i:29052874 original size:90 final size:90
Alignment explanation
Indices: 29052675--29052878 Score: 252
Period size: 90 Copynumber: 2.3 Consensus size: 90
29052665 GTTTATCTGC
* *
29052675 AAACATTTGTGGTTTATCCACAAATTTACTGCAGCTTTTATCTGCAAAGCTATTGTGCATTCACA
1 AAACACTTGTGGTTTATCCACAAATTTACTGCAGATTTTATCTGCAAAGCTATTGTGCATTCACA
29052740 ACCTACTGGAAGCGTATTAACCTGT
66 ACCTACTGGAAGCGTATTAACCTGT
* * * * * * *
29052765 AAATACTGGTGGTTTATCCACAACTTTTACTAGCATATTTTATTTGCAAA-CTCGTTGTGTATTC
1 AAACACTTGTGGTTTATCCACAA-ATTTACT-GCAGATTTTATCTGCAAAGCT-ATTGTGCATTC
* *
29052829 ACAA-CTACTGGCAGCGTATTAACTTG-
63 ACAACCTACTGGAAGCGTATTAACCTGT
*
29052855 AAACACTTGTGGTTCATCCACAAA
1 AAACACTTGTGGTTTATCCACAAA
29052879 CTGGACTGTC
Statistics
Matches: 96, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
90 40 0.42
91 28 0.29
92 28 0.29
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (90 bp):
AAACACTTGTGGTTTATCCACAAATTTACTGCAGATTTTATCTGCAAAGCTATTGTGCATTCACA
ACCTACTGGAAGCGTATTAACCTGT
Found at i:29054949 original size:14 final size:14
Alignment explanation
Indices: 29054930--29054956 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29054920 CATTTCTTGG
29054930 TCGGTTTAGTTCAC
1 TCGGTTTAGTTCAC
29054944 TCGGTTTAGTTCA
1 TCGGTTTAGTTCA
29054957 ACTGGACCAC
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:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (14 bp):
TCGGTTTAGTTCAC
Done.