Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 62 of 208
Found at i:23284857 original size:18 final size:19
Alignment explanation
Indices: 23284821--23284859 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
23284811 ACTAAATAAT
23284821 AAAATATAATAATTATTTA
1 AAAATATAATAATTATTTA
23284840 AAAATAT-AT-ATTACTTTA
1 AAAATATAATAATTA-TTTA
23284858 AA
1 AA
23284860 TTTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 8 0.42
19 7 0.37
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATATAATAATTATTTA
Found at i:23286009 original size:12 final size:12
Alignment explanation
Indices: 23285992--23286016 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23285982 AATTTATGCT
23285992 TATGATATGTGA
1 TATGATATGTGA
23286004 TATGATATGTGA
1 TATGATATGTGA
23286016 T
1 T
23286017 GCATATTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (12 bp):
TATGATATGTGA
Found at i:23287887 original size:20 final size:20
Alignment explanation
Indices: 23287859--23287897 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23287849 ATGATTGATG
* *
23287859 TATGGTGTGATTGGTGGTTC
1 TATGATGTGATTAGTGGTTC
23287879 TATGATGTGATTAGTGGTT
1 TATGATGTGATTAGTGGTT
23287898 AGTGAGGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.03, G:0.36, T:0.46
Consensus pattern (20 bp):
TATGATGTGATTAGTGGTTC
Found at i:23297298 original size:22 final size:20
Alignment explanation
Indices: 23297270--23297327 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
23297260 TCGCGTTGAC
23297270 ATATAAAGACTAATTTTTAATA
1 ATATAAAGACTAATTTTT--TA
*
23297292 ATATAAATGA-AAATTTTTTA
1 ATATAAA-GACTAATTTTTTA
* *
23297312 ATAAAAATACTAATTT
1 ATATAAAGACTAATTT
23297328 ACTCTTTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.03
20 13 0.43
22 14 0.47
23 2 0.07
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
ATATAAAGACTAATTTTTTA
Found at i:23302857 original size:12 final size:12
Alignment explanation
Indices: 23302842--23302868 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
23302832 ATATACATCC
23302842 AAATATACCTAT
1 AAATATACCTAT
23302854 AAATATACCTAT
1 AAATATACCTAT
23302866 AAA
1 AAA
23302869 GATGTGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATATACCTAT
Found at i:23307485 original size:52 final size:52
Alignment explanation
Indices: 23307407--23307514 Score: 216
Period size: 52 Copynumber: 2.1 Consensus size: 52
23307397 CTTATAAATG
23307407 AAAGATTGTTCATAGTTAAAAGAATAAAACAATGAAGCCTTAAATACAAAAC
1 AAAGATTGTTCATAGTTAAAAGAATAAAACAATGAAGCCTTAAATACAAAAC
23307459 AAAGATTGTTCATAGTTAAAAGAATAAAACAATGAAGCCTTAAATACAAAAC
1 AAAGATTGTTCATAGTTAAAAGAATAAAACAATGAAGCCTTAAATACAAAAC
23307511 AAAG
1 AAAG
23307515 TTAACTAAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.55, C:0.11, G:0.12, T:0.22
Consensus pattern (52 bp):
AAAGATTGTTCATAGTTAAAAGAATAAAACAATGAAGCCTTAAATACAAAAC
Found at i:23314021 original size:6 final size:6
Alignment explanation
Indices: 23313982--23314008 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
23313972 TACTCACAAG
23313982 ATAAAA ATAAAA ATAAAA ATAAAA ATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATA
23314009 TATTAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:23314829 original size:29 final size:29
Alignment explanation
Indices: 23314776--23314832 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
23314766 ATTACTTTAT
*
23314776 AATTTTTATAATTTTTAATGATTAAATTA
1 AATTTTTATAATTTTTAAAGATTAAATTA
23314805 AATTTTTAT-ATTTTTGAAA-AGTTAAATT
1 AATTTTTATAATTTTT-AAAGA-TTAAATT
23314833 GTAATTTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.54
Consensus pattern (29 bp):
AATTTTTATAATTTTTAAAGATTAAATTA
Found at i:23320700 original size:21 final size:22
Alignment explanation
Indices: 23320674--23320722 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
23320664 AGAAAAACTT
23320674 ATATTAAGTAAA-A-ATTTAAA
1 ATATTAAGTAAACATATTTAAA
*
23320694 ATAATT-ATTAAACATATTTAAA
1 AT-ATTAAGTAAACATATTTAAA
23320716 ATATTAA
1 ATATTAA
23320723 ATGTTGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 7 0.29
21 7 0.29
22 10 0.42
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATTAAGTAAACATATTTAAA
Found at i:23323919 original size:48 final size:48
Alignment explanation
Indices: 23323712--23324447 Score: 857
Period size: 48 Copynumber: 14.9 Consensus size: 48
23323702 TACTCCCCAC
* * *
23323712 CACCACCCAAGGAGCCTTACAAGTATAAGTCTCCACCACCTCCTCCACCAGT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCA-C-CC-CCACCA-T
** * * * * *
23323764 GCATTATCCTCCA-CCCCCTTACGAGTACAAGTCTCCTCCGCCACCCCCGCCAT
1 -CACCA-CC-CAAGCACCCTTACAAGTACAAG--T-CTCCACCACCCCCACCAT
* *
23323817 CACCACCCAAGCATCCC-TATAAGTACAAGTCT---CCACCTCCACCAT
1 CACCACCCAAGCA-CCCTTACAAGTACAAGTCTCCACCACCCCCACCAT
23323862 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCCCCACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCCCCACCAT
* *
23323910 CACCACCCAAGCACCCCTACAAGTACAAGTCTCCTCCACCACCTCCACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAG--T-CTCCACCACCCCCACCAT
* *
23323961 CACCACCCAAGCACCCCTACAAGTATAAGTCTCCACCACCCCCACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCCCCACCAT
*
23324009 CACCACCCAAGCATCCTTACAAGTACAAGTCTCCACCACCACCACCACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCA-C-CC-CCACCAT
* * *
23324060 CACCACCCAAGCACCCCTACAAGTACAAGTCTCCTCCACCTCCACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCCCCACCAT
* *
23324108 CACCACCCAAGCATCCTTACAAGTACAAGTCTCCACCACCACCACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCCCCACCAT
* *
23324156 CACCACCCAAGCACCCCTACAAGTACAAGTCTCCTCCACCCCCACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCCCCACCAT
23324204 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCACCTCCACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCA-C-CC-CCACCAT
23324255 CACCACCCAAGCACCCTTACAAGTACAAGTCT---CCACCCCCACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCCCCACCAT
23324300 CACCACCCAAGCATCCC-TACAAGTACAAGTCTCCACCCCCACCCCCACCCCCACCCT
1 CACCACCCAAGCA-CCCTTACAAGTACAAGTCTCCA---CCACCCCCA---CCA---T
* *
23324357 CACCACCCAAGCACCCCTACAAGTACAAGTCT---CCACCCCCACCCT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCCCCACCAT
* *
23324402 CACCACCCAAGCACCCTTACAAGTATAAGTCTCCCCCACCACCCAC
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACC-CCCAC
23324448 TCCAGTCTAC
Statistics
Matches: 601, Mismatches: 44, Indels: 80
0.83 0.06 0.11
Matches are distributed among these distances:
44 3 0.00
45 104 0.17
46 5 0.01
47 1 0.00
48 235 0.39
49 10 0.02
50 8 0.01
51 157 0.26
52 6 0.01
53 4 0.01
54 23 0.04
55 4 0.01
56 5 0.01
57 36 0.06
ACGTcount: A:0.29, C:0.49, G:0.07, T:0.14
Consensus pattern (48 bp):
CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCCCCACCAT
Found at i:23323982 original size:99 final size:98
Alignment explanation
Indices: 23323712--23324444 Score: 911
Period size: 99 Copynumber: 7.4 Consensus size: 98
23323702 TACTCCCCAC
* * * * * ** *
23323712 CACCACCCAAGGAGCCTTACAAGTATAAGTCTCCACCACCTCCTCCACCAGTGCATTATCCTCCA
1 CACCACCCAAGCATCCTTACAAGTACAAGTCTCCTCCACCACCTCCACCA-T-CACCA-CC-CAA
* *
23323777 -C-CCCCTTACGAGTACAAGTCTCCTCCGCCACCCCCGCCAT
62 GCACCCC-TACAAGTACAAG--T-CTCC-CCACCCCCACCAT
* *
23323817 CACCACCCAAGCATCCCTATAAGTACAAG--T-CT---CCACCTCCACCATCACCACCCAAGCAC
1 CACCACCCAAGCATCCTTACAAGTACAAGTCTCCTCCACCACCTCCACCATCACCACCCAAGCAC
*
23323876 CCTTACAAGTACAAGTCTCCACCACCCCCACCAT
66 CCCTACAAGTACAAGTCTCC-CCACCCCCACCAT
* *
23323910 CACCACCCAAGCACCCCTACAAGTACAAGTCTCCTCCACCACCTCCACCATCACCACCCAAGCAC
1 CACCACCCAAGCATCCTTACAAGTACAAGTCTCCTCCACCACCTCCACCATCACCACCCAAGCAC
*
23323975 CCCTACAAGTATAAGTCTCCACCACCCCCACCAT
66 CCCTACAAGTACAAGTCTCC-CCACCCCCACCAT
* *
23324009 CACCACCCAAGCATCCTTACAAGTACAAGTCTCCACCACCACCACCACCATCACCACCCAAGCAC
1 CACCACCCAAGCATCCTTACAAGTACAAGTCTCCTCCACCACCTCCACCATCACCACCCAAGCAC
*
23324074 CCCTACAAGTACAAGTCTCCTCCACCTCCACCAT
66 CCCTACAAGTACAAGTCTCC-CCACCCCCACCAT
*
23324108 CACCACCCAAGCATCCTTACAAGTACAAG--T-CTCCACCACCACCACCATCACCACCCAAGCAC
1 CACCACCCAAGCATCCTTACAAGTACAAGTCTCCTCCACCACCTCCACCATCACCACCCAAGCAC
23324170 CCCTACAAGTACAAGTCTCCTCCACCCCCACCAT
66 CCCTACAAGTACAAGTCTCC-CCACCCCCACCAT
* *
23324204 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCACCTCCACCATCACCACCCAAGCAC
1 CACCACCCAAGCATCCTTACAAGTACAAGTCTCCTCCACCACCTCCACCATCACCACCCAAGCAC
*
23324269 CCTTACAAGTACAAGTCT--CCACCCCCACCAT
66 CCCTACAAGTACAAGTCTCCCCACCCCCACCAT
* * * *
23324300 CACCACCCAAGCATCCCTACAAGTACAAGTCTCCACCCCCACCCCCACCCCCACCCTCACCACCC
1 CACCACCCAAGCATCCTTACAAGTACAAGTCT---CCTCCA---CCACCTCCACCATCACCACCC
*
23324365 AAGCACCCCTACAAGTACAAGTCT--CCACCCCCACCCT
60 AAGCACCCCTACAAGTACAAGTCTCCCCACCCCCACCAT
* * *
23324402 CACCACCCAAGCACCCTTACAAGTATAAGTCTCCCCCACCACC
1 CACCACCCAAGCATCCTTACAAGTACAAGTCTCCTCCACCACC
23324445 CACTCCAGTC
Statistics
Matches: 570, Mismatches: 41, Indels: 43
0.87 0.06 0.07
Matches are distributed among these distances:
93 43 0.08
94 1 0.00
95 3 0.01
96 156 0.27
97 7 0.01
98 2 0.00
99 249 0.44
102 84 0.15
103 1 0.00
105 24 0.04
ACGTcount: A:0.29, C:0.49, G:0.07, T:0.14
Consensus pattern (98 bp):
CACCACCCAAGCATCCTTACAAGTACAAGTCTCCTCCACCACCTCCACCATCACCACCCAAGCAC
CCCTACAAGTACAAGTCTCCCCACCCCCACCAT
Found at i:23324104 original size:147 final size:144
Alignment explanation
Indices: 23323712--23324447 Score: 877
Period size: 147 Copynumber: 5.0 Consensus size: 144
23323702 TACTCCCCAC
* * * ** *
23323712 CACCACCCAAGGAGCCTTACAAGTATAAGTCTCCACCACCTCCTCCACCAGTGCATTATCCTCCA
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACC-CC-CCACCA-T-CACCA-CC-CAA
* * * *
23323777 -C-CCCCTTACGAGTACAAGTCTCCTCCGCCACCCCCGCCATCACCACCCAAGCATCCC-TATAA
60 GCACCCC-TACAAGTACAAGTCTCCT---CCACCTCCACCATCACCACCCAAGCA-CCCTTACAA
*
23323839 GTACAAGTCT--CCACCTCCACCAT
120 GTACAAGTCTCCCCACCCCCACCAT
23323862 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCA-CCCCCACCATCACCACCCAAGCACCC
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCCCCCACCATCACCACCCAAGCACCC
* *
23323926 CTACAAGTACAAGTCTCCTCCACCACCTCCACCATCACCACCCAAGCACCCCTACAAGTATAAGT
66 CTACAAGTACAAGTCTCCT---CCACCTCCACCATCACCACCCAAGCACCCTTACAAGTACAAGT
23323991 CTCCACCACCCCCACCAT
128 CTCC-CCACCCCCACCAT
*
23324009 CACCACCCAAGCATCCTTACAAGTACAAGTCTCCACCACCACCACCACCATCACCACCCAAGCAC
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACC-CC-CCACCATCACCACCCAAGCAC
*
23324074 CCCTACAAGTACAAGTCTCCTCCACCTCCACCATCACCACCCAAGCATCCTTACAAGTACAAGTC
64 CCCTACAAGTACAAGTCTCCTCCACCTCCACCATCACCACCCAAGCACCCTTACAAGTACAAGTC
*
23324139 TCCACCACCACCACCAT
129 TCC-CCACCCCCACCAT
* *
23324156 CACCACCCAAGCACCCCTACAAGTACAAGTCTCCTCCA-CCCCCACCATCACCACCCAAGCACCC
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCCCCCACCATCACCACCCAAGCACCC
* *
23324220 TTACAAGTACAAGTCTCCACCACCACCTCCACCATCACCACCCAAGCACCCTTACAAGTACAAGT
66 CTACAAGTACAAGTCT---CCTCCACCTCCACCATCACCACCCAAGCACCCTTACAAGTACAAGT
23324285 CT--CCACCCCCACCAT
128 CTCCCCACCCCCACCAT
*
23324300 CACCACCCAAGCATCCC-TACAAGTACAAGTCTCCACCCCCACCCCCACCCCCACCCTCACCACC
1 CACCACCCAAGCA-CCCTTACAAGTACAAGTCTCCA---CCA----C-CCCCCACCATCACCACC
* *
23324364 CAAGCACCCCTACAAGTACAAG--T-CTCCACCCCCACCCTCACCACCCAAGCACCCTTACAAGT
57 CAAGCACCCCTACAAGTACAAGTCTCCTCCACCTCCACCATCACCACCCAAGCACCCTTACAAGT
*
23324426 ATAAGTCTCCCCCACCACCCAC
122 ACAAGTCT-CCCCACC-CCCAC
23324448 TCCAGTCTAC
Statistics
Matches: 528, Mismatches: 32, Indels: 51
0.86 0.05 0.08
Matches are distributed among these distances:
143 5 0.01
144 139 0.26
145 12 0.02
146 2 0.00
147 239 0.45
148 3 0.01
149 3 0.01
150 82 0.16
151 6 0.01
153 37 0.07
ACGTcount: A:0.29, C:0.49, G:0.07, T:0.14
Consensus pattern (144 bp):
CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCCCCCACCATCACCACCCAAGCACCC
CTACAAGTACAAGTCTCCTCCACCTCCACCATCACCACCCAAGCACCCTTACAAGTACAAGTCTC
CCCACCCCCACCAT
Found at i:23324350 original size:5 final size:6
Alignment explanation
Indices: 23324332--23324365 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
23324322 GTACAAGTCT
*
23324332 CCACCC CCACCC CCACCC CCACCC TCACCAC CCA
1 CCACCC CCACCC CCACCC CCACCC CCACC-C CCA
23324366 AGCACCCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 22 0.88
7 3 0.12
ACGTcount: A:0.21, C:0.76, G:0.00, T:0.03
Consensus pattern (6 bp):
CCACCC
Found at i:23324394 original size:39 final size:40
Alignment explanation
Indices: 23324349--23324436 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 40
23324339 CACCCCCACC
23324349 CCCACCCTCACCACCCAAGCACCCCTACAAGTACAAGTCT
1 CCCACCCTCACCACCCAAGCACCCCTACAAGTACAAGTCT
* *
23324389 CCACCCCCACCCTCACCACCCAAGCACCCTTACAAGTATAAGTCT
1 -----CCCACCCTCACCACCCAAGCACCCCTACAAGTACAAGTCT
23324434 CCC
1 CCC
23324437 CCACCACCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
40 3 0.07
45 38 0.93
ACGTcount: A:0.28, C:0.51, G:0.07, T:0.14
Consensus pattern (40 bp):
CCCACCCTCACCACCCAAGCACCCCTACAAGTACAAGTCT
Found at i:23324394 original size:57 final size:57
Alignment explanation
Indices: 23324287--23324410 Score: 212
Period size: 57 Copynumber: 2.2 Consensus size: 57
23324277 GTACAAGTCT
*
23324287 CCACCCCCACCATCACCACCCAAGCATCCCTACAAGTACAAGTCTCCACCCCCACCC
1 CCACCCCCACCATCACCACCCAAGCACCCCTACAAGTACAAGTCTCCACCCCCACCC
*
23324344 CCACCCCCACCCTCACCACCCAAGCACCCCTACAAGTACAAGTCTCCACCCCCACCC
1 CCACCCCCACCATCACCACCCAAGCACCCCTACAAGTACAAGTCTCCACCCCCACCC
*
23324401 TCACCACCCA
1 CCACC-CCCA
23324411 AGCACCCTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
57 59 0.94
58 4 0.06
ACGTcount: A:0.27, C:0.58, G:0.05, T:0.10
Consensus pattern (57 bp):
CCACCCCCACCATCACCACCCAAGCACCCCTACAAGTACAAGTCTCCACCCCCACCC
Found at i:23324487 original size:36 final size:37
Alignment explanation
Indices: 23324417--23324519 Score: 97
Period size: 36 Copynumber: 2.8 Consensus size: 37
23324407 CCCAAGCACC
*
23324417 CTTACAAGTATAAGTCTCC-CCCACCACCCACTCCAG
1 CTTACAAATATAAGTCTCCTCCCACCACCCACTCCAG
*
23324453 -TCTACAAATATAAGTCTCCTCCC-CCTCCTC-CTCCAG
1 CT-TACAAATATAAGTCTCCTCCCACCACC-CACTCCAG
* * *
23324489 CTTACTATTACAAGTCTCCTCCTCCACCACC
1 CTTACAAATATAAGTCTCCT-C-CCACCACC
23324520 ACCCCATTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
35 1 0.02
36 41 0.76
37 6 0.11
38 2 0.04
39 4 0.07
ACGTcount: A:0.24, C:0.45, G:0.06, T:0.25
Consensus pattern (37 bp):
CTTACAAATATAAGTCTCCTCCCACCACCCACTCCAG
Found at i:23325058 original size:23 final size:22
Alignment explanation
Indices: 23325014--23325060 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
23325004 TTAATTTAAT
*
23325014 TAAAAATAAAAAAAATCACTTA
1 TAAAAATAAAAAAAATAACTTA
**
23325036 TAAAAATAAAATTAATAACCTTA
1 TAAAAATAAAAAAAATAA-CTTA
23325059 TA
1 TA
23325061 TATTCTTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAAAATAAAAAAAATAACTTA
Found at i:23331160 original size:73 final size:73
Alignment explanation
Indices: 23331053--23331191 Score: 185
Period size: 73 Copynumber: 1.9 Consensus size: 73
23331043 TTCTCAGTAA
** * *
23331053 GCGCCGCAAAAAGACTTCAGCCTCACGATGCCGTTTTTTGAGCTTTC-GGGGATTTAGTGGTGTT
1 GCGCCGCAAAAAGACTTCAGCCTCACGACACCG-TTTCTGAGCTTTCGGGGGATTTAGTGGCGTT
23331117 TTTGGGGAT
65 TTTGGGGAT
*
23331126 GCGCCGC-AAACGTACTTCAGCC-CAACGACACCGTTTCTGAGCTTTCGGGGGATTTAGTGGCGT
1 GCGCCGCAAAAAG-ACTTCAGCCTC-ACGACACCGTTTCTGAGCTTTCGGGGGATTTAGTGGCGT
23331189 TTT
64 TTT
23331192 CATGCAATCG
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
72 17 0.29
73 41 0.71
ACGTcount: A:0.18, C:0.23, G:0.29, T:0.30
Consensus pattern (73 bp):
GCGCCGCAAAAAGACTTCAGCCTCACGACACCGTTTCTGAGCTTTCGGGGGATTTAGTGGCGTTT
TTGGGGAT
Found at i:23331305 original size:114 final size:114
Alignment explanation
Indices: 23331104--23331677 Score: 656
Period size: 114 Copynumber: 5.0 Consensus size: 114
23331094 GCTTTCGGGG
* * * * * *
23331104 ATTTAGTGGTGTTTTTGGGGATGCGCCGCAAACGTACTTCAGCCCAACGACACCG-TTTCTGAGC
1 ATTTAGCGGCGTTTTTGGGAAAGCGCCGCAAACATACTTCAGCCCAACGACGCCGTTTTCTGAGC
* * * * *
23331168 TTTCGGGGGATTTAGTGGCGTTTTCATGCAATCGCCGCGAATGCTCAGGT
66 TTTC-GGGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATACTCAGGT
* * * * * * * *
23331218 CTTTAGCAGCGTTTTTGGGAAAGCGCCGTAAACGTACTTCAGTCAAACAACACCGTTTTCTGAGC
1 ATTTAGCGGCGTTTTTGGGAAAGCGCCGCAAACATACTTCAGCCCAACGACGCCGTTTTCTGAGC
*
23331283 TTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGCCGCTAATACTCAGAG-
66 TTTCGGGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATACTCAG-GT
* * *
23331332 ATTTAGCGGCATTTTTGTGAAAGCGCCAC-AACAATACTTCAGCCCAACGACGCCGTTTTCTGAG
1 ATTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAC-ATACTTCAGCCCAACGACGCCGTTTTCTGAG
* * *
23331396 CTTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGCCGTTAATACTCAGGG
65 CTTTCGGGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATACTCAGGT
* * *
23331446 ATTTAGCGTCGTTTTTGTGAAAGCGCCACAATA-ATACTTCAGCCCAACGACGCCGTTTTCTGAG
1 ATTTAGCGGCGTTTTTGGGAAAGCGCCGCAA-ACATACTTCAGCCCAACGACGCCGTTTTCTGAG
** *** * * * *
23331510 C-TGAGAATAATTTAGTGGCGTTTTTTTGTATGCGCCGCTAATGCTCAGGT
65 CTTTCG-GGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATACTCAGGT
* * * * *
23331560 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACTTCAGCCCAACGACGTCGTTTTTTTAGC
1 ATTTAGCGGCGTTTTTGGGAAAGCGCCGCAAACATACTTCAGCCCAACGACGCCGTTTTCTGAGC
* *
23331625 TTTCGGGGATTTAGTGGCGTTTTTATG-AAGCGCCACTAATACTCAGGG
66 TTTCGGGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATACTCAGGT
23331673 ATTTA
1 ATTTA
23331678 AAATAATTTA
Statistics
Matches: 391, Mismatches: 60, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
113 28 0.07
114 345 0.88
115 17 0.04
116 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (114 bp):
ATTTAGCGGCGTTTTTGGGAAAGCGCCGCAAACATACTTCAGCCCAACGACGCCGTTTTCTGAGC
TTTCGGGGATTTAGTGGCGTTTTTATGAAAGCGCCGCTAATACTCAGGT
Found at i:23331319 original size:187 final size:185
Alignment explanation
Indices: 23330921--23331319 Score: 428
Period size: 187 Copynumber: 2.1 Consensus size: 185
23330911 AAAATAAGCA
* **
23330921 TTAGCGGCGTTTTTGGTAAAGCGCCGCAAAAGACTTCAGCCCAACGATGCCGTTTTCTGAGCTGA
1 TTAGTGGCGTTTTTGGTAAAGCGCCGCAAAAGACTTCAGCCCAACGACACCGTTTTCTGAGCTGA
* * *
23330986 GAAGGATTTAGTGGCGATTTTATGAAAGCGCCGCCAATTATCAGTCTTTAGCGGCTTTTCTCAGT
66 GAAGGATTTAGTGGCGATTTTATGAAAGCGCCGCCAATGATCAGTCTTTAGCAGCTTTTCTCAGA
** * ** *
23331051 AAGCGCCGCAAAAAGACTTCAGCCTCACGATGCCGTTTTTTGAGCTTTCGGGGAT
131 AAGCGCCGCAAAAAGACTTCAGCCAAACAACACCGTTTTCTGAGCTTTCGGGGAT
* ** * *
23331106 TTAGTGGTGTTTTTGGGGATGCGCCGCAAACGTACTTCAGCCCAACGACACCG-TTTCTGAGCTT
1 TTAGTGGCGTTTTTGGTAAAGCGCCGCAAAAG-ACTTCAGCCCAACGACACCGTTTTCTGAGC-T
** ** * * * *
23331170 TCGGGGGATTTAGTGGCG-TTTTCATGCAATCGCCGCGAATGCTCAGGTCTTTAGCAGCGTTTT-
64 GAGAAGGATTTAGTGGCGATTTT-ATGAAAGCGCCGCCAATGATCA-GTCTTTAGCAGC-TTTTC
** * * *
23331233 TGGGAAAGCGCCG-TAAACGTACTTCAGTCAAACAACACCGTTTTCTGAGCTTTCGGGGAT
126 TCAGAAAGCGCCGCAAAAAG-ACTTCAGCCAAACAACACCGTTTTCTGAGCTTTCGGGGAT
**
23331293 TTAGTGGCGTTTTTATTAAAGCGCCGC
1 TTAGTGGCGTTTTTGGTAAAGCGCCGC
23331320 TAATACTCAG
Statistics
Matches: 172, Mismatches: 36, Indels: 10
0.79 0.17 0.05
Matches are distributed among these distances:
185 39 0.23
186 54 0.31
187 75 0.44
188 4 0.02
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.30
Consensus pattern (185 bp):
TTAGTGGCGTTTTTGGTAAAGCGCCGCAAAAGACTTCAGCCCAACGACACCGTTTTCTGAGCTGA
GAAGGATTTAGTGGCGATTTTATGAAAGCGCCGCCAATGATCAGTCTTTAGCAGCTTTTCTCAGA
AAGCGCCGCAAAAAGACTTCAGCCAAACAACACCGTTTTCTGAGCTTTCGGGGAT
Found at i:23331938 original size:14 final size:15
Alignment explanation
Indices: 23331905--23331938 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
23331895 TAAGTTTTAT
23331905 AGATTATGGAATTAG
1 AGATTATGGAATTAG
23331920 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
*
23331934 TGATT
1 AGATT
23331939 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.38
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:23331985 original size:7 final size:7
Alignment explanation
Indices: 23331972--23332011 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
23331962 TAAGGTTTAT
23331972 GGGTTAG
1 GGGTTAG
*
23331979 GGATTAG
1 GGGTTAG
23331986 GGGTTAG
1 GGGTTAG
23331993 GGGTTA-
1 GGGTTAG
23331999 -GGTTAG
1 GGGTTAG
23332005 GGGTTAG
1 GGGTTAG
23332012 ATGTTAAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
7 24 0.83
ACGTcount: A:0.17, C:0.00, G:0.53, T:0.30
Consensus pattern (7 bp):
GGGTTAG
Found at i:23332017 original size:14 final size:12
Alignment explanation
Indices: 23331973--23332011 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
23331963 AAGGTTTATG
*
23331973 GGTTAGGGATTA
1 GGTTAGGGGTTA
23331985 GGGGTTAGGGGTTA
1 --GGTTAGGGGTTA
23331999 GGTTAGGGGTTA
1 GGTTAGGGGTTA
23332011 G
1 G
23332012 ATGTTAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.54
14 11 0.46
ACGTcount: A:0.18, C:0.00, G:0.51, T:0.31
Consensus pattern (12 bp):
GGTTAGGGGTTA
Found at i:23332017 original size:19 final size:21
Alignment explanation
Indices: 23331982--23332027 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
23331972 GGGTTAGGGA
*
23331982 TTAGGGGTTAGGGGTT-AG-G
1 TTAGGGGTTAGAGGTTAAGAG
*
23332001 TTAGGGGTTAGATGTTAAGAG
1 TTAGGGGTTAGAGGTTAAGAG
23332022 TTAGGG
1 TTAGGG
23332028 ATTTAGGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 14 0.61
20 2 0.09
21 7 0.30
ACGTcount: A:0.22, C:0.00, G:0.46, T:0.33
Consensus pattern (21 bp):
TTAGGGGTTAGAGGTTAAGAG
Found at i:23332017 original size:26 final size:26
Alignment explanation
Indices: 23331973--23332026 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
23331963 AAGGTTTATG
* * *
23331973 GGTTAGGGATTAGGGGTTAGGGGTTA
1 GGTTAGGGATTAGAGGTTAAGAGTTA
* *
23331999 GGTTAGGGGTTAGATGTTAAGAGTTA
1 GGTTAGGGATTAGAGGTTAAGAGTTA
23332025 GG
1 GG
23332027 GATTTAGGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.46, T:0.31
Consensus pattern (26 bp):
GGTTAGGGATTAGAGGTTAAGAGTTA
Found at i:23332123 original size:7 final size:7
Alignment explanation
Indices: 23332111--23332199 Score: 72
Period size: 7 Copynumber: 12.6 Consensus size: 7
23332101 TAAATAAGGT
23332111 TTAGGGG
1 TTAGGGG
23332118 TTAGGGG
1 TTAGGGG
23332125 TTAGGGG
1 TTAGGGG
*
23332132 TTAGAGG
1 TTAGGGG
* *
23332139 TCATGGG
1 TTAGGGG
*
23332146 TTAAGGGT
1 TT-AGGGG
23332154 TTA-GGG
1 TTAGGGG
*
23332160 TTAAGGG
1 TTAGGGG
* *
23332167 TTAAGAG
1 TTAGGGG
*
23332174 TTAAGGG
1 TTAGGGG
*
23332181 TTAAGGG
1 TTAGGGG
23332188 TTAAGGGG
1 TT-AGGGG
23332196 TTAG
1 TTAG
23332200 AGATTGGGTT
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
6 5 0.07
7 52 0.76
8 11 0.16
ACGTcount: A:0.24, C:0.01, G:0.45, T:0.30
Consensus pattern (7 bp):
TTAGGGG
Found at i:23332525 original size:19 final size:19
Alignment explanation
Indices: 23332483--23332524 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
23332473 TCAAAATTAC
*
23332483 AAAAAAT-AAAATGAAAAT
1 AAAAAATAAAAAAGAAAAT
23332501 AAAAAATAAAAAAG-AAAT
1 AAAAAATAAAAAAGAAAAT
23332519 AAAAAA
1 AAAAAA
23332525 ACTAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (19 bp):
AAAAAATAAAAAAGAAAAT
Found at i:23332531 original size:18 final size:19
Alignment explanation
Indices: 23332483--23332532 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
23332473 TCAAAATTAC
23332483 AAAAAATAAAATGAAAAT-
1 AAAAAATAAAATGAAAATA
*
23332501 AAAAAATAAAA-AAGAAATA
1 AAAAAATAAAATGA-AAATA
23332520 AAAAAACTAAAAT
1 AAAAAA-TAAAAT
23332533 TTTTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 1 0.04
18 15 0.56
19 6 0.22
20 5 0.19
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (19 bp):
AAAAAATAAAATGAAAATA
Found at i:23333358 original size:198 final size:197
Alignment explanation
Indices: 23332999--23333409 Score: 700
Period size: 198 Copynumber: 2.1 Consensus size: 197
23332989 GGCGCTTATG
* *
23332999 TATAAACGCCACAATTTACAGAATTGTTTAGGAAAACGGCTCCGTTTTCTTATTTAACTTTAGTG
1 TATAAACGCCGCAAATTACAGAATTGTTTAGGAAAACGGCTCCGTTTTCTTATTTAACTTTAGTG
* *
23333064 GCGCTTTTAGTAAACGCCGCAAAAATGTTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAAAA
66 GCACTTTTAGTAAACGCCGCAAAAATGTTTTAATTTTTATGGAGACAATGCCGTTTTCTCTAAAA
* *
23333129 CGCCATGAGTTTGAGTTAACTGATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTGG
131 CGCCATGAGTTTCAATTAACTGATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTGG
23333194 TA
196 TA
* *
23333196 TATAAACACCGCAAATTACAGAAATTG-TTAGGGAAAACGGCTTCGTTTTCTTATTT-ACTTTTA
1 TATAAACGCCGCAAATTACAG-AATTGTTTA-GGAAAACGGCTCCGTTTTCTTATTTAAC-TTTA
23333259 GTGGCACTTTTAGTAAACGCCGCAAAAATGTTTTAATTTTTATGGAGACAATGCCGTTTTCTCTA
63 GTGGCACTTTTAGTAAACGCCGCAAAAATGTTTTAATTTTTATGGAGACAATGCCGTTTTCTCTA
23333324 AAACGCCATGAGTTTCAATTAACTGATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGC
128 AAACGCCATGAGTTTCAATTAACTGATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGC
23333389 TGGTA
193 TGGTA
*
23333394 TACAAACGCCGCAAAT
1 TATAAACGCCGCAAAT
23333410 GGGTTAGTTA
Statistics
Matches: 201, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
197 23 0.11
198 178 0.89
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (197 bp):
TATAAACGCCGCAAATTACAGAATTGTTTAGGAAAACGGCTCCGTTTTCTTATTTAACTTTAGTG
GCACTTTTAGTAAACGCCGCAAAAATGTTTTAATTTTTATGGAGACAATGCCGTTTTCTCTAAAA
CGCCATGAGTTTCAATTAACTGATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTGG
TA
Found at i:23334350 original size:296 final size:296
Alignment explanation
Indices: 23333809--23334402 Score: 1116
Period size: 296 Copynumber: 2.0 Consensus size: 296
23333799 ATTAGTTTCC
* *
23333809 ATTGCTACCATGTTGAATCATTTACTGCTGTTTTGTCGAAAATTGCAAAATTGTTCAAAACCTAT
1 ATTGCTACCATGTTGAATCATTTACTGCTGTTCTGTCGAAAATTGCAAAACTGTTCAAAACCTAT
23333874 TGAATGATATCTATTAATATTTGCTATGGCAGGGCTACTATACTACTATTAGAAAAAATCCAATA
66 TGAATGATATCTATTAATATTTGCTATGGCAGGGCTACTATACTACTATTAGAAAAAATCCAATA
*
23333939 GTGGCAAGGAACTGAACACTACAGCACTGTTCAAAACTTGTAAGTTCAAATTTCTAAAGAGCAAA
131 GTGGCAAGGAACTGAACACTACAGCACTGTTCAAAACTTGTAAGTTCAAACTTCTAAAGAGCAAA
* * *
23334004 GTAATATTTTTGGTTGAAATCTGAGATTCAATCTTTTTTTTTTGTTTTATAATATATTTAAAATT
196 GTAATATTTTTGGTTGAAATATGAGATTCAATCTTTTTTTTTTCTTTTATAATATACTTAAAATT
23334069 TATATACATTTTTAATATATAATATATATAGTTTTA
261 TATATACATTTTTAATATATAATATATATAGTTTTA
* *
23334105 ATTGCTACCATGTTGAATCATTTACTGTTGTTCTGTCGAAATTTGCAAAACTGTTCAAAACCTAT
1 ATTGCTACCATGTTGAATCATTTACTGCTGTTCTGTCGAAAATTGCAAAACTGTTCAAAACCTAT
23334170 TGAATGATATCTATTAATATTTGCTATGGCAGGGCTACTATACTACTATTAGAAAAAATCCAATA
66 TGAATGATATCTATTAATATTTGCTATGGCAGGGCTACTATACTACTATTAGAAAAAATCCAATA
23334235 GTGGCAAGGAACTGAACACTACAGCACTGTTCAAAACTTGTAAGTTCAAACTTCTAAAGAGCAAA
131 GTGGCAAGGAACTGAACACTACAGCACTGTTCAAAACTTGTAAGTTCAAACTTCTAAAGAGCAAA
23334300 GTAATATTTTTGGTTGAAATATGAGATTCAATCTTTTTTTTTTCTTTTATAATATACTTAAAATT
196 GTAATATTTTTGGTTGAAATATGAGATTCAATCTTTTTTTTTTCTTTTATAATATACTTAAAATT
23334365 TATATACATTTTTAATATATAATATATATAGTTTTA
261 TATATACATTTTTAATATATAATATATATAGTTTTA
23334401 AT
1 AT
23334403 ATCTAGTTTA
Statistics
Matches: 290, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
296 290 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.39
Consensus pattern (296 bp):
ATTGCTACCATGTTGAATCATTTACTGCTGTTCTGTCGAAAATTGCAAAACTGTTCAAAACCTAT
TGAATGATATCTATTAATATTTGCTATGGCAGGGCTACTATACTACTATTAGAAAAAATCCAATA
GTGGCAAGGAACTGAACACTACAGCACTGTTCAAAACTTGTAAGTTCAAACTTCTAAAGAGCAAA
GTAATATTTTTGGTTGAAATATGAGATTCAATCTTTTTTTTTTCTTTTATAATATACTTAAAATT
TATATACATTTTTAATATATAATATATATAGTTTTA
Found at i:23334662 original size:18 final size:19
Alignment explanation
Indices: 23334639--23334682 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
23334629 CAGAAATTTC
*
23334639 TGTTTCTCTAGCA-TGTTA
1 TGTTTCTCTACCATTGTTA
* *
23334657 TGTTTCTGTACCATTTTTA
1 TGTTTCTCTACCATTGTTA
23334676 TGTTTCT
1 TGTTTCT
23334683 TTATTTTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.57
Consensus pattern (19 bp):
TGTTTCTCTACCATTGTTA
Found at i:23334701 original size:22 final size:22
Alignment explanation
Indices: 23334671--23334716 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
23334661 TCTGTACCAT
*
23334671 TTTTATGTTTCT-TTATTTTCTG
1 TTTTATGTTT-TGCTATTTTCTG
*
23334693 TTTTCTGTTTTGCTATTTTCTG
1 TTTTATGTTTTGCTATTTTCTG
23334715 TT
1 TT
23334717 GAATGAAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.07, C:0.11, G:0.11, T:0.72
Consensus pattern (22 bp):
TTTTATGTTTTGCTATTTTCTG
Found at i:23335307 original size:13 final size:13
Alignment explanation
Indices: 23335285--23335439 Score: 82
Period size: 13 Copynumber: 11.8 Consensus size: 13
23335275 TTTTACTCTT
*
23335285 AATATATTACTTG
1 AATATATTACTTA
*
23335298 AATATGTTACTTA
1 AATATATTACTTA
*
23335311 AATAAATTACTTA
1 AATATATTACTTA
*
23335324 AATACATTACTTA
1 AATATATTACTTA
*
23335337 CTAA-A-ATTTCGTTA
1 --AATATATTAC-TTA
* *
23335351 AATTTTTTACTTA
1 AATATATTACTTA
* *
23335364 AATATGTTACTCA
1 AATATATTACTTA
* *
23335377 GATACATTACTTA
1 AATATATTACTTA
* **
23335390 CTAAAAT-TTGGTTA
1 --AATATATTACTTA
* *
23335404 AATTTTTTACTTA
1 AATATATTACTTA
*
23335417 AATATGTTACTTA
1 AATATATTACTTA
*
23335430 AATACATTAC
1 AATATATTAC
23335440 CCGCTATAAA
Statistics
Matches: 105, Mismatches: 29, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
12 5 0.05
13 84 0.80
14 12 0.11
15 4 0.04
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (13 bp):
AATATATTACTTA
Found at i:23335361 original size:53 final size:53
Alignment explanation
Indices: 23335304--23335439 Score: 227
Period size: 53 Copynumber: 2.6 Consensus size: 53
23335294 CTTGAATATG
**
23335304 TTACTTAAATAAATTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
1 TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
* * *
23335357 TTACTTAAATATGTTACTCAGATACATTACTTACTAAAATTTGGTTAAATTTT
1 TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
23335410 TTACTTAAATATGTTACTTAAATACATTAC
1 TTACTTAAATATGTTACTTAAATACATTAC
23335440 CCGCTATAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 76 1.00
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (53 bp):
TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
Found at i:23335608 original size:9 final size:9
Alignment explanation
Indices: 23335588--23335825 Score: 140
Period size: 9 Copynumber: 27.3 Consensus size: 9
23335578 TACAAGAACC
*
23335588 TACATAATT
1 TACATAACT
*
23335597 TACACAACT
1 TACATAACT
*
23335606 TACATAACC
1 TACATAACT
23335615 TACATAACT
1 TACATAACT
23335624 TACATAA--
1 TACATAACT
*
23335631 TACA-AAGGT
1 TACATAA-CT
23335640 TACATAACT
1 TACATAACT
* * *
23335649 GAAATAGCT
1 TACATAACT
*
23335658 TACACAACT
1 TACATAACT
23335667 TACATAACT
1 TACATAACT
* *
23335676 TACAGAAGT
1 TACATAACT
* *
23335685 TATATAATACA
1 TACAT-A-ACT
23335696 TA-ATAACT
1 TACATAACT
23335704 TAC--AACT
1 TACATAACT
*
23335711 TACATAACA
1 TACATAACT
*
23335720 TACATTACT
1 TACATAACT
**
23335729 TTGATAACT
1 TACATAACT
*
23335738 TACATAAGT
1 TACATAACT
23335747 TACATAA--
1 TACATAACT
*
23335754 TACACAACT
1 TACATAACT
**
23335763 TACATAGTT
1 TACATAACT
*
23335772 TACTTAA--
1 TACATAACT
23335779 TACATAACT
1 TACATAACT
*
23335788 TATATAACT
1 TACATAACT
*
23335797 T--ATACACG
1 TACATA-ACT
23335805 TACATAACT
1 TACATAACT
*
23335814 TACATAATT
1 TACATAACT
23335823 TAC
1 TAC
23335826 TTAATACATA
Statistics
Matches: 172, Mismatches: 41, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
6 2 0.01
7 26 0.15
8 7 0.04
9 126 0.73
10 8 0.05
11 3 0.02
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:23335768 original size:25 final size:25
Alignment explanation
Indices: 23335732--23335836 Score: 104
Period size: 25 Copynumber: 4.2 Consensus size: 25
23335722 CATTACTTTG
23335732 ATAACTTACATAAGTTACATAATAC
1 ATAACTTACATAAGTTACATAATAC
* *
23335757 ACAACTTACAT-AGTTTACTTAATAC
1 ATAACTTACATAAG-TTACATAATAC
* * * * *
23335782 ATAACTTATATAACTTATACACGTAC
1 ATAACTTACATAAGTTACATA-ATAC
* *
23335808 ATAACTTACATAATTTACTTAATAC
1 ATAACTTACATAAGTTACATAATAC
23335833 ATAA
1 ATAA
23335837 ATATATATCA
Statistics
Matches: 62, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
24 2 0.03
25 40 0.65
26 20 0.32
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (25 bp):
ATAACTTACATAAGTTACATAATAC
Found at i:23341308 original size:21 final size:21
Alignment explanation
Indices: 23341282--23341352 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
23341272 CTACAACTTA
* *
23341282 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
23341303 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
23341324 AAGCGGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
23341345 AAGCAGAG
1 AAGCAGAG
23341353 CAGAGCAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.31, C:0.18, G:0.48, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:23355155 original size:3 final size:3
Alignment explanation
Indices: 23355147--23355193 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
23355137 AAACCTATTG
* * * *
23355147 CTT CTT CTT CTT CTT CTT CTT CTT CCT CCT CCT C-T CTT TTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
23355194 TCCTTCTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:23356506 original size:18 final size:18
Alignment explanation
Indices: 23356472--23356507 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
23356462 GGGATAGGAT
*
23356472 TTTTAGTTAATATAAATA
1 TTTTAGTTAATAAAAATA
*
23356490 TTTTAGTTAGTAAAAATA
1 TTTTAGTTAATAAAAATA
23356508 AGAAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (18 bp):
TTTTAGTTAATAAAAATA
Found at i:23360608 original size:24 final size:23
Alignment explanation
Indices: 23360548--23360610 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
23360538 TTTTTAGCAG
* *
23360548 TTTTATATTTTTATTTATTTTAAA
1 TTTTATA-TATTATTTATATTAAA
*
23360572 TTTTATATATTATTTATATTAGA
1 TTTTATATATTATTTATATTAAA
*
23360595 TTGTTTTATATTATTT
1 TT-TTATATATTATTT
23360611 TAGATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 15 0.44
24 19 0.56
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (23 bp):
TTTTATATATTATTTATATTAAA
Found at i:23360858 original size:14 final size:14
Alignment explanation
Indices: 23360841--23360874 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
23360831 GAGACCTCTT
23360841 TTTTATATTTTTTA
1 TTTTATATTTTTTA
*
23360855 TTTTAAATTTTTTA
1 TTTTATATTTTTTA
23360869 TTTTAT
1 TTTTAT
23360875 GTACTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATATTTTTTA
Found at i:23360865 original size:23 final size:23
Alignment explanation
Indices: 23360839--23360886 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
23360829 TTGAGACCTC
* *
23360839 TTTTTTATATTT-TTTATTTTAAA
1 TTTTTTAT-TTTATGTACTTTAAA
23360862 TTTTTTATTTTATGTACTTTAAA
1 TTTTTTATTTTATGTACTTTAAA
23360885 TT
1 TT
23360887 GTTCTTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTTTTATTTTATGTACTTTAAA
Found at i:23363223 original size:6 final size:6
Alignment explanation
Indices: 23363212--23363238 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
23363202 ATTTGTATAA
23363212 AATTAT AATTAT AATTAT AATTAT AAT
1 AATTAT AATTAT AATTAT AATTAT AAT
23363239 ACTAACTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:23366176 original size:39 final size:40
Alignment explanation
Indices: 23366025--23366194 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 40
23366015 GGACTAAGAT
* * * *
23366025 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGTGAGTTACTAAATCCGGGTTAAGTC
* * * *
23366065 CCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGTGAGTTACTAAATCCGGGTTAAGTC
** *
23366105 CCGAAGGCATTCGTGTGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGTGAGTTACTAAATCCGGGTTAAGTC
* * * *
23366145 CCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGTGAGTTACTAAATCCGGGTTAAGTC
23366184 CCGAAGGCATT
1 CCGAAGGCATT
23366195 TGAACGAGGA
Statistics
Matches: 112, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 33 0.29
40 79 0.71
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGTGAGTTACTAAATCCGGGTTAAGTC
Found at i:23366194 original size:79 final size:80
Alignment explanation
Indices: 23366048--23366194 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 80
23366038 TGCGAGATAC
* * * *
23366048 TAAATCCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
23366113 ATTCGTGTGAGTTGT
66 ATTCGTGTGAGTTGT
* * * *
23366128 TAAATCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
23366192 ATT
66 ATT
23366195 TGAACGAGGA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 35 0.59
80 24 0.41
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (80 bp):
TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGTGTGAGTTGT
Found at i:23366214 original size:79 final size:80
Alignment explanation
Indices: 23366047--23366229 Score: 199
Period size: 79 Copynumber: 2.3 Consensus size: 80
23366037 GTGCGAGATA
* * * *
23366047 CTAAATCCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*** **
23366112 CATTCGTGTGAGTTG
66 CATTCGAACGAGGAG
* * * * *
23366127 TTAAATCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
23366191 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
23366206 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
23366230 TACGTGATTT
Statistics
Matches: 84, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
78 14 0.17
79 46 0.55
80 24 0.29
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:23369682 original size:43 final size:43
Alignment explanation
Indices: 23369634--23369904 Score: 357
Period size: 43 Copynumber: 6.3 Consensus size: 43
23369624 GCGTCGCTAA
* ** * *
23369634 CTTTAGCGGCGTTTTTAGAAAAAACGCTGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
23369677 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
* * * *
23369720 CTTCAGCGGTGTTTTTACCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
* *
23369763 CTTTAGCGGCGCTTTT-CTCACTAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTAC-CACAAACGCCGCTAAAGACCAAGAC
* * * *
23369806 CTTTAGCGGCGCTTTTCCCACTAACGCCGCTATAGACCATGAC
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
* * *
23369849 CTTTAGTGGCGCTTTTATCACAAACGCCGCTAAAGAACAA-AC
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
23369891 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
23369905 CTAGCAAAAA
Statistics
Matches: 204, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
42 16 0.08
43 187 0.92
44 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
Found at i:23371972 original size:27 final size:28
Alignment explanation
Indices: 23371942--23372036 Score: 76
Period size: 27 Copynumber: 3.5 Consensus size: 28
23371932 ACTTTCAAGT
23371942 TTTTTA-TTATTTTATAATTTTTATATA
1 TTTTTATTTATTTTATAATTTTTATATA
* ** *
23371969 -TTTTATTTCTTTTATAAAATTTATGTA
1 TTTTTATTTATTTTATAATTTTTATATA
*
23371996 TTTTTAATTTGTTTTA-AACTTTTT-TA-A
1 TTTTT-ATTTATTTTATAA-TTTTTATATA
*
23372023 GTTTTA-TTATTTTA
1 TTTTTATTTATTTTA
23372037 AATACAAGTA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
25 7 0.13
26 6 0.11
27 22 0.41
28 7 0.13
29 12 0.22
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.67
Consensus pattern (28 bp):
TTTTTATTTATTTTATAATTTTTATATA
Found at i:23374396 original size:37 final size:36
Alignment explanation
Indices: 23374317--23374397 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 36
23374307 AAAAATTATT
*
23374317 TTATTTAAACTAATATTTAAATATATATCTATTAAT
1 TTATTTAAACTAATATTTAAATATATATCTATTAAC
*
23374353 TCTATTTAAACTAATATTTAAATATAT-TTTATTTAAAC
1 T-TATTTAAACTAATATTTAAATATATATCTA-TT-AAC
23374391 TTATTTA
1 TTATTTA
23374398 TTAATTCTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
36 4 0.10
37 33 0.82
38 3 0.08
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (36 bp):
TTATTTAAACTAATATTTAAATATATATCTATTAAC
Found at i:23374420 original size:25 final size:25
Alignment explanation
Indices: 23374330--23374422 Score: 111
Period size: 25 Copynumber: 3.7 Consensus size: 25
23374320 TTTAAACTAA
*
23374330 TATTTAAA-TATATATCTATTAATTC
1 TATTTAAACTA-ATATTTATTAATTC
* *
23374355 TATTTAAACTAATATTTAAATATATTT
1 TATTTAAACTAATATTT-ATTA-ATTC
23374382 TATTTAAACT--TATTTATTAATTC
1 TATTTAAACTAATATTTATTAATTC
23374405 TATTTAAACTAATATTTA
1 TATTTAAACTAATATTTA
23374423 AATATATCAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
23 13 0.22
24 3 0.05
25 24 0.41
26 5 0.09
27 13 0.22
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTTAAACTAATATTTATTAATTC
Found at i:23374756 original size:14 final size:14
Alignment explanation
Indices: 23374686--23374772 Score: 63
Period size: 14 Copynumber: 6.1 Consensus size: 14
23374676 ACCCCTGAAT
*
23374686 CCCTATACCTTAAA
1 CCCTAAACCTTAAA
*
23374700 TCCCT-AACTCTTAAC
1 -CCCTAAAC-CTTAAA
* *
23374715 CCCT-AACGTTTAAC
1 CCCTAAAC-CTTAAA
23374729 CCCTAAACCCTTAAA
1 CCCTAAA-CCTTAAA
23374744 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
*
23374758 GCCC-AACCCTTAAA
1 -CCCTAAACCTTAAA
23374772 C
1 C
23374773 TATAATCCGT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
13 1 0.02
14 34 0.56
15 25 0.41
16 1 0.02
ACGTcount: A:0.34, C:0.39, G:0.02, T:0.24
Consensus pattern (14 bp):
CCCTAAACCTTAAA
Found at i:23375551 original size:40 final size:41
Alignment explanation
Indices: 23375443--23375595 Score: 213
Period size: 41 Copynumber: 3.8 Consensus size: 41
23375433 TAAAATGCTT
*
23375443 TTAGCGA-GCTTTTTCAAAAATGCCGCTAAAG-CCCTGAGCA
1 TTAGCGACGCTTTTTCAAAAACGCCGCTAAAGACCC-GAGCA
* *
23375483 TTAGCGTCGCTTTTTCAAAAATGCCGCTAAAGACCCGAGCA
1 TTAGCGACGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCA
*
23375524 TTAGCGACGC-TGTTCAAAAACGCCGCTAAAGACCCGAGCA
1 TTAGCGACGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCA
* * *
23375564 TTAGCGGCGCTTTTTTAATAACGCCGCTAAAG
1 TTAGCGACGCTTTTTCAAAAACGCCGCTAAAG
23375596 CTCGAAAATG
Statistics
Matches: 102, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
40 43 0.42
41 56 0.55
42 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (41 bp):
TTAGCGACGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCA
Found at i:23375681 original size:40 final size:41
Alignment explanation
Indices: 23375637--23375766 Score: 149
Period size: 40 Copynumber: 3.2 Consensus size: 41
23375627 GGTTTTTTGT
23375637 GGCGTTTTTTCAAAAAACGCCGCTAATGCTC-ATTTTTAGC
1 GGCGTTTTTTCAAAAAACGCCGCTAATGCTCAATTTTTAGC
* * * *
23375677 GGCGTTTTTT-GAGAAACGCCGCTAATGCTCAATCTTTAGT
1 GGCGTTTTTTCAAAAAACGCCGCTAATGCTCAATTTTTAGC
* ** * * *
23375717 GGCG-ATTTTCATTAAGCGCCGCTAATGCTCTATTTTTACC
1 GGCGTTTTTTCAAAAAACGCCGCTAATGCTCAATTTTTAGC
23375757 GGCGTTTTTT
1 GGCGTTTTTT
23375767 GTTCAAACGC
Statistics
Matches: 73, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
39 22 0.30
40 47 0.64
41 4 0.05
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.38
Consensus pattern (41 bp):
GGCGTTTTTTCAAAAAACGCCGCTAATGCTCAATTTTTAGC
Found at i:23382426 original size:18 final size:19
Alignment explanation
Indices: 23382393--23382432 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
23382383 TTATTATTTT
23382393 TATATCTTATAAATAAAAA
1 TATATCTTATAAATAAAAA
*
23382412 TATATCTTA-AAATAATAA
1 TATATCTTATAAATAAAAA
23382430 TAT
1 TAT
23382433 TTAAATACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATCTTATAAATAAAAA
Found at i:23383731 original size:16 final size:18
Alignment explanation
Indices: 23383710--23383742 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
23383700 TATTATTAGA
23383710 TTAAATA-AAA-AATTAT
1 TTAAATATAAATAATTAT
23383726 TTAAATATAAATAATTA
1 TTAAATATAAATAATTA
23383743 ATAATTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAATATAAATAATTAT
Found at i:23385211 original size:50 final size:50
Alignment explanation
Indices: 23385152--23385260 Score: 218
Period size: 50 Copynumber: 2.2 Consensus size: 50
23385142 GATTGTTGAT
23385152 ATATTTTTACCTATTACTTATGAGAATGTGATAATTTTAACTAGCAAATA
1 ATATTTTTACCTATTACTTATGAGAATGTGATAATTTTAACTAGCAAATA
23385202 ATATTTTTACCTATTACTTATGAGAATGTGATAATTTTAACTAGCAAATA
1 ATATTTTTACCTATTACTTATGAGAATGTGATAATTTTAACTAGCAAATA
23385252 ATATTTTTA
1 ATATTTTTA
23385261 TTGCAAATAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (50 bp):
ATATTTTTACCTATTACTTATGAGAATGTGATAATTTTAACTAGCAAATA
Found at i:23390426 original size:23 final size:23
Alignment explanation
Indices: 23390391--23390435 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
23390381 CCTTATTTAA
**
23390391 TTCAAATTGATTAT-AATATTATT
1 TTCAAATAAATTATCAA-ATTATT
23390414 TTCAAATAAATTATCAAATTAT
1 TTCAAATAAATTATCAAATTAT
23390436 AAAATGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TTCAAATAAATTATCAAATTATT
Found at i:23393741 original size:92 final size:91
Alignment explanation
Indices: 23393584--23393792 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
23393574 TTGATTTTAG
* * *
23393584 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATGACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
23393649 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
23393676 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
23393740 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
23393768 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
23393793 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:23393755 original size:24 final size:25
Alignment explanation
Indices: 23393720--23393767 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
23393710 TTATGAAATT
23393720 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
23393744 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
23393768 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:23393952 original size:120 final size:120
Alignment explanation
Indices: 23393815--23394220 Score: 710
Period size: 120 Copynumber: 3.4 Consensus size: 120
23393805 TTAAATTATT
* * * *
23393815 TTAAATAATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-TTTATAG
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-ATTTTACAG
23393877 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
63 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
*
23393935 TTAAATTATATAGTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
*
23394000 CATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
23394055 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
23394120 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
23394175 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
23394221 TAAATATGAT
Statistics
Matches: 275, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
119 6 0.02
120 267 0.97
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
Found at i:23393968 original size:15 final size:15
Alignment explanation
Indices: 23393942--23393984 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
23393932 TTATTAAATT
23393942 ATATAGTTTAATTATA
1 ATATA-TTTAATTATA
*
23393958 ATATATTTAATAATA
1 ATATATTTAATTATA
23393973 AT-TATGTTAATT
1 ATATAT-TTAATT
23393985 TATATTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 16 0.67
16 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
ATATATTTAATTATA
Found at i:23394042 original size:66 final size:66
Alignment explanation
Indices: 23393966--23394163 Score: 190
Period size: 66 Copynumber: 3.2 Consensus size: 66
23393956 TAATATATTT
23393966 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATAAAA
1 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATAAAA
23394031 G
66 G
* * * * *
23394032 AATATTAATTAT-TAAGAATTT-TA--TTA-A--ATTATATATT-TTAATT-A-T-AA-T-AT-A
1 AATAATAATTATGT--TAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATAA
***
23394083 TTT
64 AAG
*
23394086 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATAAAA
23394151 G
66 G
*
23394152 AATATTAATTAT
1 AATAATAATTAT
23394164 TAAGAATTTT
Statistics
Matches: 98, Mismatches: 18, Indels: 32
0.66 0.12 0.22
Matches are distributed among these distances:
53 5 0.05
54 14 0.14
55 3 0.03
56 4 0.04
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 4 0.04
65 3 0.03
66 24 0.24
67 5 0.05
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (66 bp):
AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATAAAA
G
Found at i:23394066 original size:61 final size:61
Alignment explanation
Indices: 23394001--23394188 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 61
23393991 TTACAGTATC
23394001 ATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * ** * * * * *
23394062 ATATATTTTAATTAT-AATATATTTAATAATAATTATGTTAA-T-TT-A-TATTTTA-CAGTATC
1 ATATATTATGATT-TGAGTA-AATTCATAA-AAGAATATTAATTATTAAGAATTTTATTA-AATT
*
23394121 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAAATT
23394182 ATATATT
1 ATATATT
23394189 TTAATTATAA
Statistics
Matches: 92, Mismatches: 25, Indels: 20
0.67 0.18 0.15
Matches are distributed among these distances:
57 8 0.09
58 9 0.10
59 24 0.26
60 2 0.02
61 31 0.34
62 10 0.11
63 8 0.09
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:23394088 original size:15 final size:15
Alignment explanation
Indices: 23394053--23394104 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
23394043 TTAAGAATTT
*
23394053 TATTAAATTAT-ATA
1 TATTTAATTATAATA
23394067 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
23394081 TATTTAATAATAAT-
1 TATTTAATTATAATA
23394095 TATGTTAATT
1 TAT-TTAATT
23394105 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:23394126 original size:59 final size:59
Alignment explanation
Indices: 23393942--23394127 Score: 173
Period size: 59 Copynumber: 3.1 Consensus size: 59
23393932 TTATTAAATT
*
23393942 ATATAGTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATC
1 ATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATC
* * * * * ** * * * * *
23394001 ATATATTATGATT-TGAGTA-AATTCATAA-AAGAATATTAATTATTAAGAATTTTATTA-AATT
1 ATATATTTTAATTAT-AATATATTTAATAATAATTATGTTAA-T-TT-A-TATTTTA-CAGTATC
23394062 ATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATC
1 ATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATC
23394121 ATATATT
1 ATATATT
23394128 ATGATTTGAG
Statistics
Matches: 92, Mismatches: 25, Indels: 20
0.67 0.18 0.15
Matches are distributed among these distances:
57 8 0.09
58 10 0.11
59 30 0.33
60 2 0.02
61 24 0.26
62 10 0.11
63 8 0.09
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (59 bp):
ATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATC
Found at i:23394203 original size:16 final size:16
Alignment explanation
Indices: 23394182--23394223 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
23394172 TTATTAAATT
*
23394182 ATATATTTTAATTATA
1 ATATATTTTAATAATA
23394198 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
23394213 AT-TATGTTTAA
1 ATATAT-TTTAA
23394224 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:23394208 original size:15 final size:15
Alignment explanation
Indices: 23394173--23394214 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
23394163 TTAAGAATTT
*
23394173 TATTAAATTAT-ATA
1 TATTTAATTATAATA
23394187 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
23394201 TATTTAATAATAAT
1 TATTTAATTATAAT
23394215 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:23397288 original size:20 final size:20
Alignment explanation
Indices: 23397263--23397306 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
23397253 AAAATTAAAA
23397263 TAATT-ATTTAATTTATGACT
1 TAATTAATTTAATTTATGA-T
23397283 TAATTAATTTAATTTATGAT
1 TAATTAATTTAATTTATGAT
23397303 TAAT
1 TAAT
23397307 ATAAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (20 bp):
TAATTAATTTAATTTATGAT
Found at i:23404043 original size:11 final size:11
Alignment explanation
Indices: 23404027--23404052 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
23404017 AATTGATTGC
23404027 ATTTTCATGTT
1 ATTTTCATGTT
23404038 ATTTTCATGTT
1 ATTTTCATGTT
23404049 ATTT
1 ATTT
23404053 GCCCATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (11 bp):
ATTTTCATGTT
Found at i:23408777 original size:44 final size:44
Alignment explanation
Indices: 23408714--23408804 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
23408704 AACTCTGTTT
*
23408714 TTAGTTTTCTACTTAAACTCTGATGAGTGTAAT-TTATTTTAATA
1 TTAGTTTTCTACTTAAACTCTAATGAGTGT-ATGTTATTTTAATA
*
23408758 TTAG-TTTCTCACTTAAACTCTAATTAGTGTATGTTATTTTAATA
1 TTAGTTTTCT-ACTTAAACTCTAATGAGTGTATGTTATTTTAATA
23408802 TTA
1 TTA
23408805 TTTGACCTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 7 0.16
44 36 0.84
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.51
Consensus pattern (44 bp):
TTAGTTTTCTACTTAAACTCTAATGAGTGTATGTTATTTTAATA
Found at i:23410737 original size:44 final size:44
Alignment explanation
Indices: 23410687--23410771 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
23410677 CTCTATTTTA
23410687 AGTTTCCCACTTAAACTCTGATTAGTATAGGTTATTTTAATGTT
1 AGTTTCCCACTTAAACTCTGATTAGTATAGGTTATTTTAATGTT
* *
23410731 AGTTTCCCACTTAAACTTTGATTAGTGTAGGTTATTTTAAT
1 AGTTTCCCACTTAAACTCTGATTAGTATAGGTTATTTTAAT
23410772 ATTATTTGGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (44 bp):
AGTTTCCCACTTAAACTCTGATTAGTATAGGTTATTTTAATGTT
Found at i:23411474 original size:21 final size:20
Alignment explanation
Indices: 23411452--23411489 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23411442 GCATAGTATA
23411452 AAAAAATAATTTTAAAATAT
1 AAAAAATAATTTTAAAATAT
* *
23411472 AAAATATTATTTTAAAAT
1 AAAAAATAATTTTAAAAT
23411490 TTATTTCAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAAATAATTTTAAAATAT
Found at i:23421983 original size:14 final size:14
Alignment explanation
Indices: 23421964--23421996 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
23421954 ATCCTAAACT
*
23421964 AAAAAAA-AGGAAG
1 AAAAAAAGAAGAAG
23421977 AAAAAAAGAAGAAG
1 AAAAAAAGAAGAAG
23421991 AAAAAA
1 AAAAAA
23421997 CCCAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAGAAG
Found at i:23432022 original size:22 final size:21
Alignment explanation
Indices: 23431974--23432022 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
23431964 AACTAAATCC
* * *
23431974 TTTCTCTCAATTTCTCTCTAA
1 TTTCTCTCAACTCCTCTCAAA
23431995 TATTCTCTCAAACTCCTCTCAAA
1 T-TTCTCTC-AACTCCTCTCAAA
23432018 TTTCT
1 TTTCT
23432023 ATTTAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 11 0.48
23 11 0.48
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTCTCTCAACTCCTCTCAAA
Found at i:23433406 original size:18 final size:18
Alignment explanation
Indices: 23433370--23433412 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
23433360 TGCCAGGTGC
* *
23433370 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
*
23433388 GTATCCTAACTCTTATAT
1 GTATCCTAACCCTTATAT
*
23433406 GTTTCCT
1 GTATCCT
23433413 TTTTCTAGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:23434786 original size:94 final size:94
Alignment explanation
Indices: 23434571--23434845 Score: 270
Period size: 94 Copynumber: 2.9 Consensus size: 94
23434561 CGTAACCCTA
* * * *
23434571 AACCCCAAATCCTGATTTATTTGAGTTTTTACTTAAAAATCCTAAACACTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGA-TTTTTACTTAAAAACCCTAAACACTAAACCCTAATCTAAT
*
23434636 TTTATAAAAATTTATAATTAATTTACTCAAGT
65 TTTATAAAAA--TATAATTAAATTACTCAAGT
* * * * *
23434668 AACCCTGAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACTA-TAAACCCTAATTTGAT
1 AACCCTAAACCCTAATTTATTTGATTTTTACTTAAAAACCCTAAAC-ACTAAACCCTAATCTAAT
* *
23434732 TTTTTAAAAA-ATGAATTAAATTACTTAAGT
65 TTTATAAAAATAT-AATTAAATTACTCAAGT
* * * ** * *
23434762 AACCTTAAACCCTAATTTAATTGATTTTTTCTTAAAAAACAATAAACACGAAA-CCTAATCCAAT
1 AACCCTAAACCCTAATTTATTTGATTTTTACTT-AAAAACCCTAAACACTAAACCCTAATCTAAT
*
23434826 TTTGA-AAAATTTATAATTAA
65 TTT-ATAAAA-ATATAATTAA
23434846 TTTAATTGAC
Statistics
Matches: 146, Mismatches: 25, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
93 2 0.01
94 60 0.41
95 19 0.13
96 44 0.30
97 21 0.14
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.37
Consensus pattern (94 bp):
AACCCTAAACCCTAATTTATTTGATTTTTACTTAAAAACCCTAAACACTAAACCCTAATCTAATT
TTATAAAAATATAATTAAATTACTCAAGT
Found at i:23436344 original size:14 final size:15
Alignment explanation
Indices: 23436321--23436349 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
23436311 TTCTTAAAAT
23436321 AATTTAAATAAATAA
1 AATTTAAATAAATAA
23436336 AATTT-AATAAATAA
1 AATTTAAATAAATAA
23436350 TTAGATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTTAAATAAATAA
Found at i:23437467 original size:21 final size:22
Alignment explanation
Indices: 23437443--23437492 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
23437433 TTCAGTTATT
23437443 TAATTATAATT-AATTAAAT-AA
1 TAATTA-AATTAAATTAAATGAA
23437464 TAATTAAATTAAATTAAATGAA
1 TAATTAAATTAAATTAAATGAA
*
23437486 TTATTAA
1 TAATTAA
23437493 GTCATCTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.15
21 14 0.54
22 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TAATTAAATTAAATTAAATGAA
Found at i:23437468 original size:15 final size:16
Alignment explanation
Indices: 23437448--23437477 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23437438 TTATTTAATT
23437448 ATAATT-AATTAAATA
1 ATAATTAAATTAAATA
23437463 ATAATTAAATTAAAT
1 ATAATTAAATTAAAT
23437478 TAAATGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAATTAAATTAAATA
Found at i:23441011 original size:20 final size:19
Alignment explanation
Indices: 23440969--23441013 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
23440959 CTGGTATTTT
* *
23440969 AAAT-ATTATAAAAATAAG
1 AAATAATTAAAAAAAAAAG
23440987 AAATAATTAAAAAAAAAAG
1 AAATAATTAAAAAAAAAAG
23441006 AGAATAAT
1 A-AATAAT
23441014 AGATAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 13 0.57
20 6 0.26
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (19 bp):
AAATAATTAAAAAAAAAAG
Found at i:23444619 original size:24 final size:24
Alignment explanation
Indices: 23444570--23444620 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
23444560 ATTTCTAATA
*
23444570 TTTGTCTTCAATTTCTATCATCTTT
1 TTTGTCTTCAATTTC-ATCATATTT
*
23444595 TTTGTCTTCACCTTTC-TCATATTT
1 TTTGTCTTCA-ATTTCATCATATTT
23444619 TT
1 TT
23444621 ACTTGTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 9 0.39
25 10 0.43
26 4 0.17
ACGTcount: A:0.14, C:0.22, G:0.04, T:0.61
Consensus pattern (24 bp):
TTTGTCTTCAATTTCATCATATTT
Found at i:23448907 original size:25 final size:26
Alignment explanation
Indices: 23448873--23448926 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
23448863 AACAATAATC
* *
23448873 AAATTGTTATGTTTAATTTT-ATCCA
1 AAATTATTATATTTAATTTTGATCCA
* *
23448898 AAATTATTATATTTAGTTTTGGTCCA
1 AAATTATTATATTTAATTTTGATCCA
23448924 AAA
1 AAA
23448927 CAACAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.48
Consensus pattern (26 bp):
AAATTATTATATTTAATTTTGATCCA
Found at i:23453282 original size:3 final size:3
Alignment explanation
Indices: 23453274--23453307 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
23453264 AGTATCCCCA
23453274 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
23453308 GGGTGTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:23455581 original size:3 final size:3
Alignment explanation
Indices: 23455573--23455597 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23455563 ACCAAAATAT
23455573 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
23455598 GAAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:23460637 original size:13 final size:14
Alignment explanation
Indices: 23460615--23460647 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
23460605 AACCATGACC
*
23460615 CTGAATCCTGAACT
1 CTGAACCCTGAACT
23460629 C-GAACCCTGAACT
1 CTGAACCCTGAACT
23460642 CTGAAC
1 CTGAAC
23460648 TTCAAACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.21
Consensus pattern (14 bp):
CTGAACCCTGAACT
Found at i:23460660 original size:21 final size:20
Alignment explanation
Indices: 23460622--23460661 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
23460612 ACCCTGAATC
* *
23460622 CTGAACTCGAACCCTGAACT
1 CTGAACTCAAACCATGAACT
23460642 CTGAACTTCAAACCATGAAC
1 CTGAAC-TCAAACCATGAAC
23460662 CCTAACCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.33, G:0.12, T:0.20
Consensus pattern (20 bp):
CTGAACTCAAACCATGAACT
Found at i:23460678 original size:27 final size:26
Alignment explanation
Indices: 23460627--23460695 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
23460617 GAATCCTGAA
* *
23460627 CTCGAACCCTGAACTCTGAACTTCAAAC
1 CTCGAACCCT-AACCCTAAACTTC-AAC
23460655 CAT-GAACCCTAACCCTAAACTTCAAC
1 C-TCGAACCCTAACCCTAAACTTCAAC
*
23460681 CTCGAACCCGAACCC
1 CTCGAACCCTAACCC
23460696 AAATCCGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 1 0.03
26 15 0.42
27 11 0.31
28 8 0.22
29 1 0.03
ACGTcount: A:0.33, C:0.41, G:0.09, T:0.17
Consensus pattern (26 bp):
CTCGAACCCTAACCCTAAACTTCAAC
Found at i:23461208 original size:21 final size:20
Alignment explanation
Indices: 23461184--23461223 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
23461174 TATTCGTATA
* *
23461184 TATTTTAATTTTAATCTATTG
1 TATTATAATTATAAT-TATTG
23461205 TATTATAATTATAATTATT
1 TATTATAATTATAATTATT
23461224 CGAATGTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (20 bp):
TATTATAATTATAATTATTG
Found at i:23462762 original size:3 final size:3
Alignment explanation
Indices: 23462754--23462784 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
23462744 CTGGAAAGGA
*
23462754 AAG AAG AAG AAG AAG AAG AAC AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
23462785 GGTTAAGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:23469431 original size:31 final size:30
Alignment explanation
Indices: 23469396--23469503 Score: 85
Period size: 31 Copynumber: 3.5 Consensus size: 30
23469386 ACATTAATGC
*
23469396 TAAATTGATAAAATACTATCAAGATAATTAT
1 TAAATTAATAAAATACTATCAAGATAA-TAT
* ** * *
23469427 TAAATCAAATTTAATA-TTTCACA-TTAATAT
1 TAAAT-TAATAAAATACTATCA-AGATAATAT
*
23469457 TAAATTAATAAAATACTATCAAGATAAATAA
1 TAAATTAATAAAATACTATCAAGAT-AATAT
*
23469488 TAAATTTATTAAAATA
1 TAAA-TTAATAAAATA
23469504 ATATTATTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
29 8 0.14
30 13 0.22
31 20 0.34
32 17 0.29
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (30 bp):
TAAATTAATAAAATACTATCAAGATAATAT
Found at i:23474493 original size:44 final size:44
Alignment explanation
Indices: 23474430--23474892 Score: 193
Period size: 44 Copynumber: 10.6 Consensus size: 44
23474420 GATCTACTCT
* * * * *
23474430 ACTGTAA-CTTCAGTGAGATAAGATCATTTGTTTTAATCCGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCACTAGCTTCAATCCGCTCC
* * * *
23474474 ACTGTAATCTCAGGTAGATAGGATTACTAGCTTCAATCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCACTAGCTTCAATCCGCTCC
* * ** * * *
23474518 GCTGTAATCTCAGGGAGATAAGA-C-CTGAAATTCTTCGGTCTGTTTC
1 ACTGTAATCTCAGGGAGATAAGATCACT---A-GCTTCAATCCGCTCC
* * * * ** *
23474564 ACTGTAATCTCAGGGAAATAAGA-C-CT-GGTGCGATCTACTCT
1 ACTGTAATCTCAGGGAGATAAGATCACTAGCTTCAATCCGCTCC
* * * *
23474605 ACTGTAA-CTTCAGAGAGATAAGATC-CTTGGTTTTAATCCGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCAC-TAGCTTCAATCCGCTCC
* * * **
23474649 ACTGTAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCC
1 ACTGTAATCTCAGGGAGATAAGATCACTAGCTTCAATCCGCTCC
* * ** * * *
23474693 GCTGTAATCTCAGGGAGATAAGATCTGA-AATTTTTCAGTCTGTTCC
1 ACTGTAATCTCAGGGAGATAAGATC--ACTA-GCTTCAATCCGCTCC
* * * * ** *
23474739 ACTGTAATCTCAGGGAAATAAGA-C-CT-GGTGCGATCTACTCT
1 ACTGTAATCTCAGGGAGATAAGATCACTAGCTTCAATCCGCTCC
* *
23474780 ACTGTAA-CTTCAGAGG-GATAAGATC-CTTTA-TTTTAATCCGCTCC
1 ACTGTAATC-TCAG-GGAGATAAGATCAC--TAGCTTCAATCCGCTCC
* * ** *
23474824 ACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCACTAGCTTCAATCCGCTCC
* *
23474868 GCTGTAATCTCAGAGAGATAAGATC
1 ACTGTAATCTCAGGGAGATAAGATC
23474893 TGCAATTCTT
Statistics
Matches: 312, Mismatches: 82, Indels: 50
0.70 0.18 0.11
Matches are distributed among these distances:
40 2 0.01
41 50 0.16
42 8 0.03
43 5 0.02
44 173 0.55
45 8 0.03
46 66 0.21
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
ACTGTAATCTCAGGGAGATAAGATCACTAGCTTCAATCCGCTCC
Found at i:23474679 original size:175 final size:174
Alignment explanation
Indices: 23474411--23474979 Score: 958
Period size: 175 Copynumber: 3.3 Consensus size: 174
23474401 GGGAGGTAAA
* * *
23474411 ACCTGATGCGATCTACTCTACTGTAACTTCAGTGAGATAAGATCATTTGTTTTAATCCGCTCCAC
1 ACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCAC
23474476 TGTAATCTCAGGTAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
66 TGTAATCTCAGG-AGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
* *
23474541 CCTGAAATTCTTCGGTCTGTTTCACTGTAATCTCAGGGAAATAAG
130 TCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAG
*
23474586 ACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTGGTTTTAATCCGCTCCAC
1 ACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCAC
*
23474651 TGTAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGA
66 TGTAATCTCAG-GAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
* *
23474716 TCTGAAATTTTTCAGTCTGTTCCACTGTAATCTCAGGGAAATAAG
130 TCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAG
* *
23474761 ACCTGGTGCGATCTACTCTACTGTAACTTCAGAGGGATAAGATCCTTTATTTTAATCCGCTCCAC
1 ACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCAC
** *
23474826 TGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGA
66 TGTAATCTCA-GGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
* *
23474891 TCTGCAATTCTTCGGTCTGTTCCACCGTAATCTCAGGGAAATAAG
130 TCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAG
*
23474936 ACCTGGTGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATC
1 ACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
23474980 ATTTCTTCAA
Statistics
Matches: 370, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
175 368 0.99
176 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (174 bp):
ACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCAC
TGTAATCTCAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
CTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAG
Found at i:23475093 original size:87 final size:87
Alignment explanation
Indices: 23474983--23475237 Score: 261
Period size: 87 Copynumber: 2.9 Consensus size: 87
23474973 TAAGATCATT
* * * * * **
23474983 TCTTCAATCAGCTTCACTGCAACCGATGGGGGCAATGCTTTGTTTTCGATCTGCTTCGTTGTTAA
1 TCTTCAATCAGCTTCACTACAACCGATGGAGACAATACTTTGTTTTCAATCTGCTTCACTGTTAA
23475048 CGCAGGAAGGCAAGA-TCTGCTA
66 CGCAGGAAGGCAAGACT-TGCTA
23475070 TCTTCAATCAGC-TCTACTACAACCGATGGAGACAATACTTTGTTTTCAATCTGCTTCACTGTTA
1 TCTTCAATCAGCTTC-ACTACAACCGATGGAGACAATACTTTGTTTTCAATCTGCTTCACTGTTA
*
23475134 ACGCAGGAAGGCCAGACTTGCTA
65 ACGCAGGAAGGCAAGACTTGCTA
* ** * *
23475157 TCATCAA-CTAG-TTCCACCGCAACTGATGGAGACAA-AGC-TTGTATCTTCGATCTGCTTCACT
1 TCTTCAATC-AGCTT-CACTACAACCGATGGAGACAATA-CTTTGT-T-TTCAATCTGCTTCACT
* * *
23475218 GTCAAGGCAGGAAAGCAAGA
61 GTTAACGCAGGAAGGCAAGA
23475238 TCTGTTGTCT
Statistics
Matches: 143, Mismatches: 17, Indels: 15
0.82 0.10 0.09
Matches are distributed among these distances:
86 8 0.06
87 102 0.71
88 33 0.23
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (87 bp):
TCTTCAATCAGCTTCACTACAACCGATGGAGACAATACTTTGTTTTCAATCTGCTTCACTGTTAA
CGCAGGAAGGCAAGACTTGCTA
Found at i:23476463 original size:7 final size:7
Alignment explanation
Indices: 23476449--23476541 Score: 83
Period size: 7 Copynumber: 14.0 Consensus size: 7
23476439 TTAGCCTCTC
23476449 CATTTTT
1 CATTTTT
*
23476456 CCTTTTT
1 CATTTTT
*
23476463 CCTTTTT
1 CATTTTT
23476470 CATTTTT
1 CATTTTT
23476477 CATTTTTT
1 CA-TTTTT
23476485 CATTCTTT
1 CATT-TTT
23476493 CA-TTTT
1 CATTTTT
23476499 CA-TTTT
1 CATTTTT
23476505 CA-TTTT
1 CATTTTT
23476511 CA-TTTT
1 CATTTTT
23476517 C--TTTT
1 CATTTTT
*
23476522 CTTTTTT
1 CATTTTT
*
23476529 CTTTTTT
1 CATTTTT
23476536 C-TTTTT
1 CATTTTT
23476542 TACTCAAAGT
Statistics
Matches: 80, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
5 5 0.06
6 27 0.34
7 36 0.45
8 12 0.15
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (7 bp):
CATTTTT
Found at i:23476484 original size:8 final size:8
Alignment explanation
Indices: 23476465--23476498 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
23476455 TCCTTTTTCC
23476465 TTTTTCA-
1 TTTTTCAT
23476472 TTTTTCAT
1 TTTTTCAT
23476480 TTTTTCAT
1 TTTTTCAT
*
23476488 TCTTTCAT
1 TTTTTCAT
23476496 TTT
1 TTT
23476499 CATTTTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTCAT
Found at i:23476499 original size:6 final size:6
Alignment explanation
Indices: 23476466--23476526 Score: 63
Period size: 6 Copynumber: 9.7 Consensus size: 6
23476456 CCTTTTTCCT
23476466 TTTTCA TTTTTCA TTTTTTCA TTCTTTCA TTTTCA TTTTCA TTTTCA TTTTC-
1 TTTTCA -TTTTCA --TTTTCA -T-TTTCA TTTTCA TTTTCA TTTTCA TTTTCA
23476518 TTTTC- TTTT
1 TTTTCA TTTT
23476527 TTCTTTTTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
5 9 0.17
6 22 0.42
7 9 0.17
8 12 0.23
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTCA
Found at i:23477394 original size:10 final size:10
Alignment explanation
Indices: 23477379--23477446 Score: 66
Period size: 10 Copynumber: 6.5 Consensus size: 10
23477369 TGACCTCTCC
23477379 TTTTTCTTTT
1 TTTTTCTTTT
23477389 TTTTTCTTTT
1 TTTTTCTTTT
**
23477399 TTTCCCTATTT
1 TTTTTCT-TTT
23477410 TTTCCTTCTTTT
1 TTT--TTCTTTT
*
23477422 TTCTTT-TTCT
1 TT-TTTCTTTT
23477432 TTTTTCTTTT
1 TTTTTCTTTT
23477442 TTTTT
1 TTTTT
23477447 TTGATTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
9 3 0.06
10 28 0.60
11 8 0.17
12 5 0.11
13 3 0.06
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:23477427 original size:7 final size:7
Alignment explanation
Indices: 23477415--23477448 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
23477405 TATTTTTTCC
23477415 TTCTTTT
1 TTCTTTT
23477422 TTC-TTT
1 TTCTTTT
23477428 TTCTTTT
1 TTCTTTT
23477435 TTCTTTT
1 TTCTTTT
23477442 TT-TTTT
1 TTCTTTT
23477448 T
1 T
23477449 GATTTTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 11 0.42
7 15 0.58
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTCTTTT
Found at i:23477437 original size:13 final size:13
Alignment explanation
Indices: 23477415--23477448 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
23477405 TATTTTTTCC
23477415 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
23477428 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
23477441 TT-TTTTTT
1 TTCTTTTTT
23477449 GATTTTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTCTTTTTTCTTT
Found at i:23477454 original size:13 final size:13
Alignment explanation
Indices: 23477451--23477491 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
23477441 TTTTTTTTGA
23477451 TTTTTTGATTTTT
1 TTTTTTGATTTTT
*
23477464 TTTATTGA-TTTT
1 TTTTTTGATTTTT
23477476 TTTTTTGAATTTTT
1 TTTTTTG-ATTTTT
23477490 TT
1 TT
23477492 AAGTCTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.42
13 8 0.33
14 6 0.25
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTTTGATTTTT
Found at i:23477454 original size:20 final size:20
Alignment explanation
Indices: 23477415--23477481 Score: 75
Period size: 21 Copynumber: 3.4 Consensus size: 20
23477405 TATTTTTTCC
*
23477415 TTCTTTTTTCTTTTT-CTTTT
1 TTCTTTTTT-TTTTTGATTTT
23477435 TTCTTTTTTTTTTTGATTTT
1 TTCTTTTTTTTTTTGATTTT
* *
23477455 TTGATTTTTTTTATTGATTTT
1 TT-CTTTTTTTTTTTGATTTT
23477476 TT-TTTT
1 TTCTTTT
23477482 GAATTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
19 9 0.21
20 15 0.36
21 18 0.43
ACGTcount: A:0.06, C:0.06, G:0.04, T:0.84
Consensus pattern (20 bp):
TTCTTTTTTTTTTTGATTTT
Found at i:23482244 original size:14 final size:15
Alignment explanation
Indices: 23482221--23482249 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
23482211 ATATAAGTTG
23482221 TAAAATATATATATA
1 TAAAATATATATATA
23482236 TAAAA-ATATATATA
1 TAAAATATATATATA
23482250 CATATATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATATATATATA
Found at i:23482246 original size:18 final size:18
Alignment explanation
Indices: 23482225--23482300 Score: 57
Period size: 18 Copynumber: 4.2 Consensus size: 18
23482215 AAGTTGTAAA
23482225 ATATATATATATAAAAAT
1 ATATATATATATAAAAAT
* * *
23482243 ATATATACATATATACAT
1 ATATATATATATAAAAAT
* * *
23482261 ATATGT-TACAAAAATAAT
1 ATATATATATATAAA-AAT
*
23482279 GTAT-TATATCATAAAAAT
1 ATATATATAT-ATAAAAAT
23482297 ATAT
1 ATAT
23482301 GCACGTATTT
Statistics
Matches: 42, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
17 5 0.12
18 33 0.79
19 4 0.10
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
ATATATATATATAAAAAT
Found at i:23482256 original size:12 final size:12
Alignment explanation
Indices: 23482191--23482257 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
23482181 ATGAAAATGA
23482191 AAATATATATAT
1 AAATATATATAT
* *
23482203 AGATATGTATAT
1 AAATATATATAT
* *
23482215 AAGT-TGTA-A-
1 AAATATATATAT
23482224 AATATATATATAT
1 AA-ATATATATAT
*
23482237 AAAAATATATAT
1 AAATATATATAT
*
23482249 ACATATATA
1 AAATATATA
23482258 CATATATGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
9 2 0.05
10 2 0.05
11 7 0.17
12 29 0.69
13 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (12 bp):
AAATATATATAT
Found at i:23485006 original size:16 final size:16
Alignment explanation
Indices: 23484961--23485006 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
23484951 GTGATATTTA
*
23484961 AATATTTTATTGAAGT
1 AATATTTTATTTAAGT
*
23484977 AATATTTTAATTAAGAT
1 AATATTTTATTTAAG-T
23484994 AAT-TTTTATTTAA
1 AATATTTTATTTAA
23485007 TAAATTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (16 bp):
AATATTTTATTTAAGT
Found at i:23498038 original size:26 final size:24
Alignment explanation
Indices: 23497979--23498038 Score: 59
Period size: 26 Copynumber: 2.3 Consensus size: 24
23497969 TGAATAAATC
*
23497979 AAAATTTTAATACCAATACCTCAT
1 AAAATTTTAATACCAATACCACAT
23498003 AAAAGGTTTTAATA-CAGATACCACAT
1 AAAA--TTTTAATACCA-ATACCACAT
23498029 ATTAAATTTT
1 A--AAATTTT
23498039 TGGATTTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
24 4 0.13
25 2 0.07
26 21 0.70
28 3 0.10
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (24 bp):
AAAATTTTAATACCAATACCACAT
Found at i:23502492 original size:22 final size:23
Alignment explanation
Indices: 23502451--23502497 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
23502441 GTAACTAAGC
*
23502451 TTCAAAGAAATAATTAAATTTAT
1 TTCAAAGAAATAAATAAATTTAT
*
23502474 TTCAAA-AATTAAATAAATTTAT
1 TTCAAAGAAATAAATAAATTTAT
23502496 TT
1 TT
23502498 TTAAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
TTCAAAGAAATAAATAAATTTAT
Found at i:23505202 original size:31 final size:31
Alignment explanation
Indices: 23505167--23505240 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
23505157 TTTTATGTCC
**
23505167 AATTTAGTACTTGAACTCGACATTTTTTCTT
1 AATTTAGTACTTGAACTCGACACATTTTCTT
* *
23505198 AATTTAGTACATGAACTTGACACATTTTCTT
1 AATTTAGTACTTGAACTCGACACATTTTCTT
*
23505229 AATTTGGTACTT
1 AATTTAGTACTT
23505241 CATCTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (31 bp):
AATTTAGTACTTGAACTCGACACATTTTCTT
Found at i:23506502 original size:18 final size:18
Alignment explanation
Indices: 23506458--23506502 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
23506448 AAATTGGTAT
*
23506458 AATAAATTACACTAAATA
1 AATAAAATACACTAAATA
* **
23506476 TATTTAATACACTAAATA
1 AATAAAATACACTAAATA
23506494 AATAAAATA
1 AATAAAATA
23506503 AAATTTATAT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAAAATACACTAAATA
Found at i:23520991 original size:17 final size:19
Alignment explanation
Indices: 23520956--23520992 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
23520946 ACCTACAATC
*
23520956 ATATAAACCACAACGAATT
1 ATATAAACCACAACAAATT
23520975 ATATAAA-CA-AACAAATT
1 ATATAAACCACAACAAATT
23520992 A
1 A
23520993 AACATTCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 2 0.12
19 7 0.41
ACGTcount: A:0.59, C:0.16, G:0.03, T:0.22
Consensus pattern (19 bp):
ATATAAACCACAACAAATT
Found at i:23521170 original size:16 final size:17
Alignment explanation
Indices: 23521149--23521183 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
23521139 TAAAAAAGAA
23521149 AAAAATATG-CATATAT
1 AAAAATATGACATATAT
23521165 AAAAATATGTACATATAT
1 AAAAATATG-ACATATAT
23521183 A
1 A
23521184 TATAGGTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (17 bp):
AAAAATATGACATATAT
Found at i:23521629 original size:3 final size:3
Alignment explanation
Indices: 23521618--23521693 Score: 109
Period size: 3 Copynumber: 25.3 Consensus size: 3
23521608 CAATAATACC
* * *
23521618 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
23521663 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
23521694 GCAAAGTACT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
2 1 0.02
3 64 0.98
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:23522731 original size:15 final size:16
Alignment explanation
Indices: 23522711--23522743 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
23522701 TTGATGATTT
23522711 TGGGTTA-TTGGGCTG
1 TGGGTTAGTTGGGCTG
23522726 TGGGTTAGTTTGGGCTG
1 TGGGTTAG-TTGGGCTG
23522743 T
1 T
23522744 TAATTAGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.06, C:0.06, G:0.45, T:0.42
Consensus pattern (16 bp):
TGGGTTAGTTGGGCTG
Found at i:23524070 original size:30 final size:30
Alignment explanation
Indices: 23524036--23524110 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
23524026 CTCTTATGTG
*
23524036 ATTAAATTTTACTACAAAGCTTTGAATTTT-
1 ATTAAATTTTACCACAAA-CTTTGAATTTTA
* * * * *
23524066 ATTAAACTCTGCCACCAACTTTGATTTTTA
1 ATTAAATTTTACCACAAACTTTGAATTTTA
23524096 ATTAAATTTTACCAC
1 ATTAAATTTTACCAC
23524111 TCAATATTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 10 0.29
30 25 0.71
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (30 bp):
ATTAAATTTTACCACAAACTTTGAATTTTA
Found at i:23536563 original size:16 final size:16
Alignment explanation
Indices: 23536542--23536593 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
23536532 TTTGGTTCGC
*
23536542 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
23536558 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
23536574 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
23536590 TGTA
1 TGTA
23536594 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:23536640 original size:45 final size:44
Alignment explanation
Indices: 23536574--23536668 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
23536564 GGATTAGAGG
* *
23536574 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTCTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTCTGGTTGAA
* ** *
23536619 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTCTGGTTGAA
23536663 TGTAAT
1 TGTAAT
23536669 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 17 0.39
45 27 0.61
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTCTGGTTGAA
Found at i:23536851 original size:18 final size:17
Alignment explanation
Indices: 23536830--23536864 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
23536820 TTATTATTTA
*
23536830 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
23536848 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
23536865 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:23536858 original size:28 final size:27
Alignment explanation
Indices: 23536788--23536860 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
23536778 TTTATTATCA
*
23536788 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
23536816 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
23536843 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
23536861 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:23536998 original size:18 final size:17
Alignment explanation
Indices: 23536977--23537011 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
23536967 TTATTATTAA
*
23536977 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
23536995 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
23537012 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:23537023 original size:147 final size:149
Alignment explanation
Indices: 23536749--23537023 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 149
23536739 ATGATTATTG
*
23536749 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
23536814 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
23536879 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
* *
23536898 TTATT-TTATTTAAATTTTAATAATATTA-TTAATATCAATAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
23536961 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
23537024 ATATTCTTAT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
147 95 0.78
148 22 0.18
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Done.