Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 142 of 226
Found at i:47283551 original size:99 final size:100
Alignment explanation
Indices: 47283414--47283716 Score: 378
Period size: 100 Copynumber: 3.0 Consensus size: 100
47283404 ATCTCTTTGG
* * *
47283414 CATTACAGTGGAATAGATTGAAGCCACAATGGTGAATCTTACTTCCCTGGCGATGTAGTGGAACA
1 CATTACAGTGGAATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGTGGTGTAGTGGAACA
*
47283479 AATTGAAGTCACGACGGTGAATCT-ATTTCCTCGA
66 GATTGAAGTCACGACGGTGAATCTGATTTCCTCGA
* ** * *
47283513 TATTACAGTGGAATAGATTGAAGCCACAACGGCAAATCTTACTTCCCTAGTGGTGTGGTGGAACA
1 CATTACAGTGGAATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGTGGTGTAGTGGAACA
*
47283578 GATTGAAG-CTACGACGGTGAATCTGGTTTCCTCGA
66 GATTGAAGTC-ACGACGGTGAATCTGATTTCCTCGA
* * ** * * * *
47283613 CATTGCAATTAAAAAGATTGAAGCCACAACTGTGAATCTTACCTCCCTGGTGGTGTAGTGGAATA
1 CATTACAGTGGAATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGTGGTGTAGTGGAACA
* * *
47283678 GATTGAAGTCATGACGGCGAATCTTG-TTTCCCCGA
66 GATTGAAGTCACGACGGTGAATC-TGATTTCCTCGA
47283713 CATT
1 CATT
47283717 GCAATTAAAC
Statistics
Matches: 174, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
98 1 0.01
99 78 0.45
100 92 0.53
101 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (100 bp):
CATTACAGTGGAATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGTGGTGTAGTGGAACA
GATTGAAGTCACGACGGTGAATCTGATTTCCTCGA
Found at i:47283981 original size:41 final size:42
Alignment explanation
Indices: 47283746--47283983 Score: 169
Period size: 41 Copynumber: 5.7 Consensus size: 42
47283736 AAAATAATCC
* * * **
47283746 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAAT-CAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAGCATACAG-TCT
*** * *
47283788 TATCTCTCTGAAGTTGCAGAATAGCAGA-TCGCATCCAGTCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAGCATACAGTCT
* * * * * * *
47283829 TATCTCTCTGAAGTTGTAGTGGGGCAGATTGAAGAAAATAATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATT--AGCATACAGTCT
* * * *
47283873 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAACAT-CAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAGCATACAG-TCT
*** * *
47283915 TATCTCTCTGAAGTTGCAAAAGAACAGA-TCGCATACAGTCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAGCATACAGTCT
*
47283956 TATCTCTCTGAAGTTGCAGTGGAACAGA
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA
47283984 CAGAAGAAAC
Statistics
Matches: 148, Mismatches: 42, Indels: 13
0.73 0.21 0.06
Matches are distributed among these distances:
41 62 0.42
42 56 0.38
44 30 0.20
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (42 bp):
TATCTCTCTGAAGTTGCAGTGGAGCAGATTAGCATACAGTCT
Found at i:47284059 original size:127 final size:127
Alignment explanation
Indices: 47283732--47284073 Score: 472
Period size: 127 Copynumber: 2.7 Consensus size: 127
47283722 TAAACAAATT
*
47283732 GAAGAAAATAATCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATCAGATCTTATCTCTCT
1 GAAGAAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCT
* * * ** **
47283797 GAAGTTGCAGAATAGCAGATCGCATCCAGTCTTATCTCTCTGAAGTTGTAGTGGGGCAGATT
66 GAAGTTGCAGAAGAGCAGATCGCATACAGTCTTATCTCTCTGAAGTTGCAGTGGAACAGACA
* *
47283859 GAAGAAAATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAACATCAGATCTTATCTCTCT
1 GAAGAAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCT
* *
47283924 GAAGTTGCAAAAGAACAGATCGCATACAGTCTTATCTCTCTGAAGTTGCAGTGGAACAGACA
66 GAAGTTGCAGAAGAGCAGATCGCATACAGTCTTATCTCTCTGAAGTTGCAGTGGAACAGACA
** * * * *
47283986 GAAGAAACCAATCCTATCTCCCTGAAGTTTCAGTGGAGTGGATTAAAAAACAAATCTTATCTC-C
1 GAAGAAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAATCAGATCTTATCTCTC
* *
47284050 AT-AAATTGCAGAAGAGCAGGTCGC
65 -TGAAGTTGCAGAAGAGCAGATCGC
47284074 GTCAACTCTC
Statistics
Matches: 189, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
127 173 0.92
128 16 0.08
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (127 bp):
GAAGAAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCT
GAAGTTGCAGAAGAGCAGATCGCATACAGTCTTATCTCTCTGAAGTTGCAGTGGAACAGACA
Found at i:47285611 original size:25 final size:24
Alignment explanation
Indices: 47285565--47285611 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
47285555 TACTTTTATT
*
47285565 ATTATTATTGTATTATATATCACC
1 ATTATTATTGTATTATAGATCACC
* *
47285589 ATTATTTTTAGTATTATCGATCA
1 ATTATTATT-GTATTATAGATCA
47285612 TTGTTATGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (24 bp):
ATTATTATTGTATTATAGATCACC
Found at i:47296705 original size:25 final size:25
Alignment explanation
Indices: 47296652--47296712 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
47296642 TTGAGCCAGT
* *
47296652 ATTCTTTTATTCTTTTTGAGTAATT
1 ATTCTTTTATTCTTTTTGACTAATC
*
47296677 ATTCTTTTATTCTTTTT-TCTACATC
1 ATTCTTTTATTCTTTTTGACTA-ATC
47296702 ATTC-TTTATTC
1 ATTCTTTTATTC
47296713 ATTTCATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.28
25 23 0.72
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.64
Consensus pattern (25 bp):
ATTCTTTTATTCTTTTTGACTAATC
Found at i:47300238 original size:5 final size:5
Alignment explanation
Indices: 47300220--47300313 Score: 92
Period size: 5 Copynumber: 19.4 Consensus size: 5
47300210 TACTTTTCTT
*
47300220 AAAA- AAAAG AAAAAG AAAAG AAAAG AAAAG AAAAG AAAAG TAAAG -AAA-
1 AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
* *
47300268 AAAAG -AAAG AAAGAA AAAAGG AGAAG -AAAG -AAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAA-AG AAAA-G AAAAG AAAAG AAAAG AAAAG AAAAG AA
47300314 GAAAAAAAGG
Statistics
Matches: 77, Mismatches: 5, Indels: 15
0.79 0.05 0.15
Matches are distributed among these distances:
4 21 0.27
5 44 0.57
6 12 0.16
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:47300250 original size:21 final size:22
Alignment explanation
Indices: 47300220--47300322 Score: 114
Period size: 21 Copynumber: 5.0 Consensus size: 22
47300210 TACTTTTCTT
47300220 AAAA-AAAAGAA-AAAGAAAAG
1 AAAAGAAAAGAAGAAAGAAAAG
47300240 AAAAGAAAAG-A-AAAGAAAAG
1 AAAAGAAAAGAAGAAAGAAAAG
* *
47300260 TAAAGAAAAAAAGAAAG-AAAG
1 AAAAGAAAAGAAGAAAGAAAAG
*
47300281 AAAA-AAGGAGAAGAAAG-AAAG
1 AAAAGAA-AAGAAGAAAGAAAAG
47300302 AAAAGAAAAGAAGAAA-AAAAG
1 AAAAGAAAAGAAGAAAGAAAAG
47300323 GGAAAATGAG
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
20 24 0.34
21 41 0.58
22 6 0.08
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (22 bp):
AAAAGAAAAGAAGAAAGAAAAG
Found at i:47301633 original size:40 final size:40
Alignment explanation
Indices: 47301588--47302165 Score: 200
Period size: 44 Copynumber: 13.8 Consensus size: 40
47301578 AACATCCAAA
** * *
47301588 TCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAG
1 TCTTATCTCCCTGAAGTTACAGAGAGCAGATAGCATCCAG
* * * *
47301628 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGGA-AGAATAAATCAA
1 TCTTATCTCCCTGAAGTTACAG-AGAGCA-GATAGCAT---CCAG
* * * ** *
47301672 TCCTATCTCCCTGAAGTTGCAGCGGAGTGGATTAACATCCAG
1 TCTTATCTCCCTGAAGTTACAG-AGAGCAGA-TAGCATCCAG
** * * *
47301714 ATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATCCAG
1 -TCTTATCTCCCTGAAGTTACAGAGAGCAGATAGCATCCAG
* *
47301755 TCTTATCTCCCTGAAGTTACAGTGGAGCAGGCAGAATA-AAT-CAA
1 TCTTATCTCCCTGAAGTTACA---GAG-A-GCAG-ATAGCATCCAG
* * * ** *
47301799 TCCTATCTCCCTGAAGTTGCAGCGGAGTGGATTAACATCCAG
1 TCTTATCTCCCTGAAGTTACAG-AGAGCAGA-TAGCATCCAG
** * *
47301841 ATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAG
1 -TCTTATCTCCCTGAAGTTACAGAGAGCAGATAGCATCCAG
* *
47301882 TCTTATCT-CCTGAAGTTACAGTGGAGCAGGCAGAATA-AAT-CAA
1 TCTTATCTCCCTGAAGTTACA---GAG-A-GCAG-ATAGCATCCAG
* * * * ** *
47301925 TCCTATCTCCTTGAAGTTGCAGCGGAGTGGATTAACATCCAG
1 TCTTATCTCCCTGAAGTTACAG-AGAGCAGA-TAGCATCCAG
* ** * * *
47301967 ATTTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATCCAG
1 -TCTTATCTCCCTGAAGTTACAGAGAGCAGATAGCATCCAG
* * *
47302008 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACAGA-AGAAAT-CAA
1 TCTTATCTCCCTGAAGTTAC-A--GAG-AG-CAGATAG-CATCCAG
* * * * * *
47302052 TCCTATCCCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAG
1 TCTTATCTCCCTGAAGTTACAG-AGAGCAGA-TAGCATCCAG
* ** * ** *
47302094 ATCTTATTTTTCTGAGGTTGTAGAGAGCAGATCGCATCCAG
1 -TCTTATCTCCCTGAAGTTACAGAGAGCAGATAGCATCCAG
* *
47302135 TCTTATCTCCCTAAAGTTACAGTGGAGCAGA
1 TCTTATCTCCCTGAAGTTACAG-AGAGCAGA
47302166 CTAATGATAG
Statistics
Matches: 388, Mismatches: 107, Indels: 85
0.67 0.18 0.15
Matches are distributed among these distances:
39 12 0.03
40 85 0.22
41 62 0.16
42 38 0.10
43 85 0.22
44 87 0.22
45 17 0.04
46 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (40 bp):
TCTTATCTCCCTGAAGTTACAGAGAGCAGATAGCATCCAG
Found at i:47301942 original size:44 final size:44
Alignment explanation
Indices: 47301504--47301951 Score: 162
Period size: 44 Copynumber: 10.5 Consensus size: 44
47301494 ACTTCAGTCT
* * * *
47301504 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAT-CAATCC
1 TATCTCCCTGAAGTTACAGCGGAG-AGGCAGAATAAATCCAATCC
* * * *
47301548 TATCTCCCTGAAGTTGCAGCGGAG-TG--GATTAACATCCAAATCT
1 TATCTCCCTGAAGTTACAGCGGAGAGGCAGAATAA-ATCC-AATCC
** * ** * *
47301591 TATCTTTCTGAGGTTACA---GAGA-GCAG-ATCGCATCCAGTCT
1 TATCTCCCTGAAGTTACAGCGGAGAGGCAGAAT-AAATCCAATCC
* ** *
47301631 TATCTCCCTGAAGTTGCAGTAGAGCAGGAAGAATAAAT-CAATCC
1 TATCTCCCTGAAGTTACAGCGGAG-AGGCAGAATAAATCCAATCC
* * * *
47301675 TATCTCCCTGAAGTTGCAGCGGAG-TG--GATTAACATCCAGATCT
1 TATCTCCCTGAAGTTACAGCGGAGAGGCAGAATAA-ATCCA-ATCC
** * * ** * *
47301718 TATCTTTCTGAGGTT---GCAGAGA-GCAG-ATCGCATCCAGTCT
1 TATCTCCCTGAAGTTACAGCGGAGAGGCAGAAT-AAATCCAATCC
*
47301758 TATCTCCCTGAAGTTACAGTGGAGCAGGCAGAATAAAT-CAATCC
1 TATCTCCCTGAAGTTACAGCGGAG-AGGCAGAATAAATCCAATCC
* * * *
47301802 TATCTCCCTGAAGTTGCAGCGGAG-TG--GATTAACATCCAGATCT
1 TATCTCCCTGAAGTTACAGCGGAGAGGCAGAATAA-ATCCA-ATCC
** * ** * *
47301845 TATCTTTCTGAGGTTACA---GAGA-GCAG-ATCGCATCCAGTCT
1 TATCTCCCTGAAGTTACAGCGGAGAGGCAGAAT-AAATCCAATCC
*
47301885 TATCT-CCTGAAGTTACAGTGGAGCAGGCAGAATAAAT-CAATCC
1 TATCTCCCTGAAGTTACAGCGGAG-AGGCAGAATAAATCCAATCC
* *
47301928 TATCTCCTTGAAGTTGCAGCGGAG
1 TATCTCCCTGAAGTTACAGCGGAG
47301952 TGGATTAACA
Statistics
Matches: 297, Mismatches: 67, Indels: 80
0.67 0.15 0.18
Matches are distributed among these distances:
39 10 0.03
40 69 0.23
41 23 0.08
42 13 0.04
43 67 0.23
44 98 0.33
45 13 0.04
46 4 0.01
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGAAGTTACAGCGGAGAGGCAGAATAAATCCAATCC
Found at i:47302036 original size:253 final size:254
Alignment explanation
Indices: 47301498--47302164 Score: 1174
Period size: 253 Copynumber: 2.6 Consensus size: 254
47301488 GGTGAAACTT
47301498 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
*
47301563 GCAGCGGAGTGGATTAACATCCAAATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAG
66 GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAG
* *
47301628 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGGAAGAATAAATCAATCCTATCTCCCTGAAGTTGCA
131 TCTTATCTCCCTGAAGTTACAGTGGAGCAGGAAGAATAAATCAATCCTATCTCCCTGAAGTTGCA
47301693 GCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
196 GCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
* * *
47301752 CAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGGCAGAATAAATCAATCCTATCTCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
47301817 GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAG
66 GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAG
* *
47301882 TCTTATCT-CCTGAAGTTACAGTGGAGCAGGCAGAATAAATCAATCCTATCTCCTTGAAGTTGCA
131 TCTTATCTCCCTGAAGTTACAGTGGAGCAGGAAGAATAAATCAATCCTATCTCCCTGAAGTTGCA
*
47301946 GCGGAGTGGATTAACATCCAGATTTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
196 GCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
* *
47302005 CAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACAGAAGAAATCAATCCTATCCCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
* * * **
47302070 GCAGTGGAGCGGATTAACATCCAGATCTTATTTTTCTGAGGTTGTAGAGAGCAGATCGCATCCAG
66 GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAG
*
47302135 TCTTATCTCCCTAAAGTTACAGTGGAGCAG
131 TCTTATCTCCCTGAAGTTACAGTGGAGCAG
47302165 ACTAATGATA
Statistics
Matches: 392, Mismatches: 20, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
253 238 0.61
254 154 0.39
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (254 bp):
CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAG
TCTTATCTCCCTGAAGTTACAGTGGAGCAGGAAGAATAAATCAATCCTATCTCCCTGAAGTTGCA
GCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
Found at i:47302165 original size:127 final size:127
Alignment explanation
Indices: 47301498--47302166 Score: 1135
Period size: 127 Copynumber: 5.3 Consensus size: 127
47301488 GGTGAAACTT
* *
47301498 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACAGAATAAATCAATCCTATCTCCCTGAAGTT
* *
47301563 GCAGCGGAGTGGATTAACATCCAAATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATC
66 GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
* *
47301625 CAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGGA-AGAATAAATCAATCCTATCTCCCTGAAGT
1 CAGTCTTATCTCCCTGAAGTTACAGTGGAGCA-GACAGAATAAATCAATCCTATCTCCCTGAAGT
47301689 TGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
65 TGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
*
47301752 CAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGGCAGAATAAATCAATCCTATCTCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACAGAATAAATCAATCCTATCTCCCTGAAGTT
*
47301817 GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATC
66 GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
* *
47301879 CAGTCTTATCT-CCTGAAGTTACAGTGGAGCAGGCAGAATAAATCAATCCTATCTCCTTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACAGAATAAATCAATCCTATCTCCCTGAAGTT
*
47301943 GCAGCGGAGTGGATTAACATCCAGATTTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
66 GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
* * * *
47302005 CAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACAGAAGAAATCAATCCTATCCCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACAGAATAAATCAATCCTATCTCCCTGAAGTT
* * * *
47302070 GCAGTGGAGCGGATTAACATCCAGATCTTATTTTTCTGAGGTTGTAGAGAGCAGATCGCATC
66 GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
*
47302132 CAGTCTTATCTCCCTAAAGTTACAGTGGAGCAGAC
1 CAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGAC
47302167 TAATGATAGC
Statistics
Matches: 514, Mismatches: 25, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
126 124 0.24
127 388 0.75
128 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (127 bp):
CAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACAGAATAAATCAATCCTATCTCCCTGAAGTT
GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
Found at i:47303747 original size:15 final size:17
Alignment explanation
Indices: 47303712--47303748 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
47303702 TTTATTAATA
*
47303712 TATTTTGCTTATATTTT
1 TATTTTGCTTATATTTG
47303729 TATTTTG-TT-TATTTG
1 TATTTTGCTTATATTTG
47303744 TATTT
1 TATTT
47303749 ATTTCTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 2 0.11
17 7 0.37
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.73
Consensus pattern (17 bp):
TATTTTGCTTATATTTG
Found at i:47303794 original size:15 final size:15
Alignment explanation
Indices: 47303782--47303810 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
47303772 ATACATATTA
47303782 TATATATATATATAT
1 TATATATATATATAT
47303797 TATATATATATATA
1 TATATATATATATA
47303811 ACTTTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:47303809 original size:17 final size:17
Alignment explanation
Indices: 47303771--47303810 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
47303761 TTTAGATGCC
*
47303771 TATACATATTATATATA
1 TATATATATTATATATA
47303788 TATATATATTATATATA
1 TATATATATTATATATA
47303805 TATATA
1 TATATA
47303811 ACTTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TATATATATTATATATA
Found at i:47303823 original size:2 final size:2
Alignment explanation
Indices: 47303771--47303810 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
47303761 TTTAGATGCC
*
47303771 TA TA CA TA T- TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47303811 ACTTTATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47305962 original size:40 final size:40
Alignment explanation
Indices: 47305878--47306005 Score: 129
Period size: 40 Copynumber: 3.2 Consensus size: 40
47305868 CGTTTGGATA
* **
47305878 AAAAACGCCGCTAAAAATC-AATCATTAGCGGCGC-AATCT
1 AAAAACGCCGCTAAAAATCGAGT-ATTAGCGGCGCTTTTCT
*
47305917 AAAAAACGCCGCTAAAGATCGAGTATTAGCGGCGCTTTTCT
1 -AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCTTTTCT
* * * *
47305958 AAAAATGCCGTTAAAAAT-GAGCATTAGCGGCG-TTTTCC
1 AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCTTTTCT
47305996 AAAAAGCGCC
1 AAAAA-CGCC
47306006 ACAAAAACCT
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
38 10 0.13
39 16 0.21
40 44 0.59
41 5 0.07
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCTTTTCT
Found at i:47306113 original size:41 final size:41
Alignment explanation
Indices: 47306052--47306246 Score: 309
Period size: 41 Copynumber: 4.8 Consensus size: 41
47306042 TTTTTGGGGA
* *
47306052 TTTAGCGGCGTTTTTTAAGAAGCGTCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTC
47306093 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTC
* *
47306134 TTTAGAGGCGTTTTTGAAGAAGCGCCGCTAATGCTCCGGTC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTC
** *
47306175 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTAAGGAC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTC
* *
47306216 TTTCGCGGCGTTTTTTAAGAAGCGCCGCTAA
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAA
47306247 AAACATTTTA
Statistics
Matches: 144, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 144 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTC
Found at i:47306565 original size:14 final size:14
Alignment explanation
Indices: 47306518--47306565 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
47306508 TATCACTATA
* * *
47306518 GTTTAGGGTTTTTA
1 GTTTAGGGATTATG
*
47306532 GTTTAGGGAGTATGG
1 GTTTAGGGATTAT-G
47306547 GTTTAGGGATTATG
1 GTTTAGGGATTATG
47306561 GTTTA
1 GTTTA
47306566 AGGGTTGGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (14 bp):
GTTTAGGGATTATG
Found at i:47306569 original size:15 final size:15
Alignment explanation
Indices: 47306532--47306565 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
47306522 AGGGTTTTTA
47306532 GTTTAGGGAGTATGG
1 GTTTAGGGAGTATGG
*
47306547 GTTTAGGGATTAT-G
1 GTTTAGGGAGTATGG
47306561 GTTTA
1 GTTTA
47306566 AGGGTTGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (15 bp):
GTTTAGGGAGTATGG
Found at i:47306604 original size:15 final size:15
Alignment explanation
Indices: 47306584--47306632 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
47306574 GATTTAATGT
47306584 TTAGGGG-TTAGAGGG
1 TTAGGGGTTTAG-GGG
47306599 TTAGGGGTTTAGGGG
1 TTAGGGGTTTAGGGG
**
47306614 TTAGATGTGTTAGGGG
1 TTAGGGGT-TTAGGGG
47306630 TTA
1 TTA
47306633 AGAGTTAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 16 0.53
16 14 0.47
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.35
Consensus pattern (15 bp):
TTAGGGGTTTAGGGG
Found at i:47306609 original size:23 final size:24
Alignment explanation
Indices: 47306582--47306631 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
47306572 GGGATTTAAT
47306582 GTTTAGGGGTTAGA-GGGTTAGGG
1 GTTTAGGGGTTAGATGGGTTAGGG
*
47306605 GTTTAGGGGTTAGATGTGTTAGGG
1 GTTTAGGGGTTAGATGGGTTAGGG
47306629 GTT
1 GTT
47306632 AAGAGTTAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (24 bp):
GTTTAGGGGTTAGATGGGTTAGGG
Found at i:47306639 original size:23 final size:23
Alignment explanation
Indices: 47306590--47306640 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
47306580 ATGTTTAGGG
* *
47306590 GTTAGAGGGTTAGGGGTTTAGGG
1 GTTAGAGGGTTAGGGGTTTAAGA
*
47306613 GTTAGATGTGTTAGGGG-TTAAGA
1 GTTAGA-GGGTTAGGGGTTTAAGA
47306636 GTTAG
1 GTTAG
47306641 GGATTTAGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.22, C:0.00, G:0.45, T:0.33
Consensus pattern (23 bp):
GTTAGAGGGTTAGGGGTTTAAGA
Found at i:47306648 original size:38 final size:38
Alignment explanation
Indices: 47306580--47306652 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
47306570 TTGGGATTTA
* *
47306580 ATGTTTAGGGGTTAGAGGGTTAGGGGTTTAGGGGTTAG
1 ATGTTTAGGGGTTAGAGAGTTAGGGATTTAGGGGTTAG
47306618 ATGTGTTAGGGGTTA-AGAGTTAGGGATTTAGGGGT
1 ATGT-TTAGGGGTTAGAGAGTTAGGGATTTAGGGGT
47306653 CGGGTTAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
38 22 0.69
39 10 0.31
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (38 bp):
ATGTTTAGGGGTTAGAGAGTTAGGGATTTAGGGGTTAG
Found at i:47306845 original size:15 final size:15
Alignment explanation
Indices: 47306815--47306861 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
47306805 TATTTTAAGG
* *
47306815 TTTAGGGAGTACGGA
1 TTTAGGGATTATGGA
47306830 TTTAGGGATTATGGA
1 TTTAGGGATTATGGA
*
47306845 -TTAGCGATTAT-GA
1 TTTAGGGATTATGGA
47306858 TTTA
1 TTTA
47306862 AGGGTTGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.07
14 13 0.46
15 13 0.46
ACGTcount: A:0.28, C:0.04, G:0.30, T:0.38
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:47306898 original size:36 final size:37
Alignment explanation
Indices: 47306856--47306945 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 37
47306846 TAGCGATTAT
* *
47306856 GATTTAAGGGTTGGGATGTAAG-GTTTAGGGGTTAGG
1 GATTTAAGGGTTGGGATGTAAGTGTTTAAGAGTTAGG
* * *
47306892 GGTTTAAGGGTT-AGATGTTAGTGTTTAAGAGTTAGG
1 GATTTAAGGGTTGGGATGTAAGTGTTTAAGAGTTAGG
*
47306928 GATTTAAGGTTTAGGGAT
1 GATTTAAGGGTT-GGGAT
47306946 TTAGGGATCG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
35 7 0.16
36 33 0.77
38 3 0.07
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (37 bp):
GATTTAAGGGTTGGGATGTAAGTGTTTAAGAGTTAGG
Found at i:47313097 original size:42 final size:42
Alignment explanation
Indices: 47313068--47313340 Score: 314
Period size: 43 Copynumber: 6.4 Consensus size: 42
47313058 GTGTTTTTGC
* * * *
47313068 GAGAAGCGCCGGTAAAGGTTTATTCTTTAGCGGCATTTGTGA
1 GAGAAGCGCCGCTAAAGGTTTAGTCTTTAGCGGCGTTTGTGG
* * * * *
47313110 TAAAAGTGCCGCTAAAGGTTAGAGTCTTTAGCGGCGTTTTTGG
1 GAGAAGCGCCGCTAAAGGTT-TAGTCTTTAGCGGCGTTTGTGG
* *
47313153 AAGAAGCG-CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGG
1 GAGAAGCGCCGCTAAAGGT-TTAGTCTTTAGCGGCGTTTGTGG
*
47313195 GAGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGG
1 GAGAAGCGCCGCTAAAGGT-TTAGTCTTTAGCGGCGTTTGTGG
* * *
47313238 GAGAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCATTTGTGG
1 GAGAAGCGCCGCTAAAGGT-TTAGTCTTTAGCGGCGTTTGTGG
* * * *
47313281 AAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTTG
1 GAGAAGCGCCGCTAAAGGT-TTAGTCTTTAGCGGCGTTTGTGG
*
47313324 GAAAAGCGCCGCTAAAG
1 GAGAAGCGCCGCTAAAG
47313341 TTAGCGACGC
Statistics
Matches: 204, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
42 52 0.25
43 152 0.75
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (42 bp):
GAGAAGCGCCGCTAAAGGTTTAGTCTTTAGCGGCGTTTGTGG
Found at i:47313288 original size:86 final size:86
Alignment explanation
Indices: 47313068--47313340 Score: 376
Period size: 86 Copynumber: 3.2 Consensus size: 86
47313058 GTGTTTTTGC
* * *
47313068 GAGAAGCGCCGGTAAAGGTTTAT--TCTTTAGCGGCATTTGT-GATAAAAGTGCCGCTAAAGGT-
1 GAGAAGCGCCGCTAAAGG-TCATGGTCTTTAGCGGCATTTGTGGA-AAAAGCGCCGCTAAAGGTC
* *
47313129 TAGAGTCTTTAGCGGCGTTTTTGG
64 TTG-GTCTTTAGCGGCGTTTGTGG
* * * * *
47313153 AAGAAGCG-CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTT
1 GAGAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCTT
47313217 GGTCTTTAGCGGCGTTTGTGG
66 GGTCTTTAGCGGCGTTTGTGG
47313238 GAGAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCTT
1 GAGAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCTT
*
47313303 GGTCTTTAGCGGCGTTTGTTG
66 GGTCTTTAGCGGCGTTTGTGG
*
47313324 GAAAAGCGCCGCTAAAG
1 GAGAAGCGCCGCTAAAG
47313341 TTAGCGACGC
Statistics
Matches: 166, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
83 2 0.01
84 8 0.05
85 65 0.39
86 91 0.55
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (86 bp):
GAGAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCTT
GGTCTTTAGCGGCGTTTGTGG
Found at i:47315916 original size:21 final size:21
Alignment explanation
Indices: 47315892--47315934 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
47315882 ACGGGTTAGT
*
47315892 TTGACTATAATAGTTAATAAA
1 TTGACCATAATAGTTAATAAA
*
47315913 TTGACCATAATAGTTCATAAA
1 TTGACCATAATAGTTAATAAA
47315934 T
1 T
47315935 AATATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (21 bp):
TTGACCATAATAGTTAATAAA
Found at i:47335097 original size:20 final size:21
Alignment explanation
Indices: 47335074--47335115 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
47335064 TATCATTAGA
47335074 AATTT-TAAAAAATCAAAAAT
1 AATTTATAAAAAATCAAAAAT
* *
47335094 AATTTATAAAAATTGAAAAAT
1 AATTTATAAAAAATCAAAAAT
47335115 A
1 A
47335116 CTAAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AATTTATAAAAAATCAAAAAT
Found at i:47337972 original size:18 final size:18
Alignment explanation
Indices: 47337946--47337990 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
47337936 ATGTGAGAAT
*
47337946 TGATGTTCACATTTTAAA
1 TGATGTTCACATTTCAAA
*
47337964 TGATATTCACATTTCAAA
1 TGATGTTCACATTTCAAA
47337982 TGATGTTCA
1 TGATGTTCA
47337991 AATTGATGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (18 bp):
TGATGTTCACATTTCAAA
Found at i:47338519 original size:72 final size:72
Alignment explanation
Indices: 47338414--47338585 Score: 233
Period size: 72 Copynumber: 2.4 Consensus size: 72
47338404 AACAACAATG
* * * * *
47338414 CTAAA-CTAGTTTTATCAATAGTTATTTACGTTTGGTTTTTGGATATTGAATTTATGTTCTACTT
1 CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACTG
47338478 ATTTAT-
66 ATTTATA
* * *
47338484 GTGTAATCTAGTTTTATTAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACT
1 CT-AAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACT
47338549 GATTTATA
65 GATTTATA
*
47338557 CTAAAT-TAATTTTATCAATAGTTGTTTAT
1 CTAAATCTAGTTTTATCAATAGTTGTTTAT
47338586 ATATGATTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
70 1 0.01
71 23 0.26
72 62 0.71
73 1 0.01
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.53
Consensus pattern (72 bp):
CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACTG
ATTTATA
Found at i:47338608 original size:71 final size:72
Alignment explanation
Indices: 47338423--47338609 Score: 191
Period size: 72 Copynumber: 2.6 Consensus size: 72
47338413 GCTAAACTAG
* ** * * * * * * *
47338423 TTTTATCAATAGTTATTTACGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
1 TTTTATCAATAGTTGTTTATATATGATATTTGGATATTAAATTTATGTTCTACTGATTTATCTGA
*
47338488 AATCTAG
66 AATCTAA
* * * *
47338495 TTTTATTAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACTGATTTATACT-
1 TTTTATCAATAGTTGTTTATATATGATATTTGGATATTAAATTTATGTTCTACTGATTTAT-CTG
47338559 AAAT-TAA
65 AAATCTAA
*
47338566 TTTTATCAATAGTTGTTTATATATGAT-TTTGGATGTTCAAATTT
1 TTTTATCAATAGTTGTTTATATATGATATTTGGATATT-AAATTT
47338610 TTTCATAGGT
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
70 9 0.09
71 31 0.31
72 58 0.59
73 1 0.01
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (72 bp):
TTTTATCAATAGTTGTTTATATATGATATTTGGATATTAAATTTATGTTCTACTGATTTATCTGA
AATCTAA
Found at i:47339982 original size:3 final size:3
Alignment explanation
Indices: 47339974--47340027 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
47339964 GTCGAGAAAG
* * * * * *
47339974 TGA TGA TGA TGA CGA CGA CGA CGA TGA TGA CGA TGA TGA TGA TGG TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
47340022 TGA TGA
1 TGA TGA
47340028 CGGTGAATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.31, C:0.09, G:0.35, T:0.24
Consensus pattern (3 bp):
TGA
Found at i:47340032 original size:12 final size:12
Alignment explanation
Indices: 47339996--47340033 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
47339986 CGACGACGAC
*
47339996 GATGATGACGAT
1 GATGATGACGGT
*
47340008 GATGATGATGGT
1 GATGATGACGGT
47340020 GATGATGACGGT
1 GATGATGACGGT
47340032 GA
1 GA
47340034 ATCAAACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.29, C:0.05, G:0.39, T:0.26
Consensus pattern (12 bp):
GATGATGACGGT
Found at i:47344423 original size:126 final size:124
Alignment explanation
Indices: 47344170--47344735 Score: 740
Period size: 124 Copynumber: 4.5 Consensus size: 124
47344160 GATAAAATCA
* * * * * * * * * *
47344170 AAGCAGGATGATTTATCAAAAGGATTTTTGAAGTCACTCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * * * *
47344235 AGATCCTGGAAAAATAATTTTGAGTTAACGTTTCTAAGCAAATAGTTTAAAAAAAGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTAT-AAAAACGCTTC
*
47344295 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * * * *
47344360 TGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTTTAAAAAACGTTTC
66 AGGTCCTGGAA-AAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTAT-AAAAACGCTTC
47344421 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCAT-GTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCC-TCGTGGACGCGCTTTTGCTACAG
* * *
47344485 TAGGTCCTGAAAAAATAATTTCGAGTTAACGTTTTTGAGCAAATAGTATAAAAACGCTGC
65 TAGGTCCTGGAAAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTATAAAAACGCTTC
* * *
47344545 AAGTAGGATGCTATT-TTAGAAGAATTTGTGAAATCACGCCCTCGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * * * *
47344609 TAGGTTCTGGAAAAATAATTTCGACTTGACATTTCTGAGCAAATAGTATAAAATCGCTTC
65 TAGGTCCTGGAAAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTATAAAAACGCTTC
* * * * *
47344669 TAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACATGGACACACTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
47344734 AG
66 AG
47344736 CATGTTTGGG
Statistics
Matches: 391, Mismatches: 45, Indels: 11
0.87 0.10 0.02
Matches are distributed among these distances:
123 3 0.01
124 173 0.44
125 100 0.26
126 114 0.29
127 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (124 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTATAAAAACGCTTC
Found at i:47347918 original size:21 final size:21
Alignment explanation
Indices: 47347892--47348052 Score: 198
Period size: 21 Copynumber: 7.6 Consensus size: 21
47347882 CCAAATTATA
47347892 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
47347913 TTTAAGTTAAGTGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * *
47347934 TTTTATTTAAGGGTTACGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
47347955 TTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * * * *
47347977 CTTAATTTAAGTGTTACGATT
1 TTTAAGTTAAGGGTTAGGGTT
*
47347998 TTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
47348020 TTTAAGTTAAGGGTTAGGG-T
1 TTTAAGTTAAGGGTTAGGGTT
47348040 TTTAAGTTAAGGG
1 TTTAAGTTAAGGG
47348053 GTTATGTAAT
Statistics
Matches: 116, Mismatches: 22, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
20 14 0.12
21 68 0.59
22 34 0.29
ACGTcount: A:0.25, C:0.02, G:0.29, T:0.44
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:47347991 original size:64 final size:63
Alignment explanation
Indices: 47347895--47348050 Score: 206
Period size: 64 Copynumber: 2.4 Consensus size: 63
47347885 AATTATATTT
* * ** *
47347895 AAGTTAAGGGTTAGGGTTTTTAAGTTAAGTGTTAGGGTTTTTTATTTAAGGG-TTACGGTTTTA
1 AAGTTAAGGGTTAGGG-TTTTAAGTTAAGTGTTACGATTTTAAAGTTAAGGGTTTACGGTTTTA
* * *
47347958 AAGTTAAGGGTTTAGGGTTCTTAATTTAAGTGTTACGATTTTAAAGTTAAGGGTTTAGGGTTTTT
1 AAGTTAAGGG-TTAGGGTT-TTAAGTTAAGTGTTACGATTTTAAAGTTAAGGGTTTACGGTTTTA
47348023 AAGTTAAGGGTTAGGGTTTTAAGTTAAG
1 AAGTTAAGGGTTAGGGTTTTAAGTTAAG
47348051 GGGTTATGTA
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
63 21 0.26
64 41 0.51
65 19 0.23
ACGTcount: A:0.26, C:0.02, G:0.28, T:0.44
Consensus pattern (63 bp):
AAGTTAAGGGTTAGGGTTTTAAGTTAAGTGTTACGATTTTAAAGTTAAGGGTTTACGGTTTTA
Found at i:47348052 original size:85 final size:85
Alignment explanation
Indices: 47347893--47348052 Score: 223
Period size: 85 Copynumber: 1.9 Consensus size: 85
47347883 CAAATTATAT
* * * * * *
47347893 TTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGTGTTAGGGTTTTTTATTTAAGGGTTACGGTTTTA
1 TTAAGTTAAGGGTTACGATTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTACGGTTTTA
47347958 AAGTTAAGGGTTTAGGGTTC
66 AAGTTAAGGGTTTAGGGTTC
* * *
47347978 TTAATTTAAGTGTTACGATTTTAAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTT
1 TTAAGTTAAGGGTTACGATTTTAAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTACGGTTTT
47348043 -AAGTTAAGGG
65 AAAGTTAAGGG
47348053 GTTATGTAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
85 37 0.57
86 28 0.43
ACGTcount: A:0.26, C:0.02, G:0.29, T:0.44
Consensus pattern (85 bp):
TTAAGTTAAGGGTTACGATTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTACGGTTTTA
AAGTTAAGGGTTTAGGGTTC
Found at i:47348055 original size:43 final size:43
Alignment explanation
Indices: 47347892--47348052 Score: 218
Period size: 43 Copynumber: 3.8 Consensus size: 43
47347882 CCAAATTATA
* * *
47347892 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGTG-TTAGGGTT
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
* *
47347934 TTTTATTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
* * * *
47347977 CTTAATTTAAGTGTTACGATTTTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
*
47348020 TTTAAGTTAAGGGTTAGGGTTTT-AAGTTAAGGG
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGG
47348053 GTTATGTAAT
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
42 39 0.38
43 65 0.62
ACGTcount: A:0.25, C:0.02, G:0.29, T:0.44
Consensus pattern (43 bp):
TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
Found at i:47350588 original size:46 final size:46
Alignment explanation
Indices: 47350513--47350784 Score: 401
Period size: 46 Copynumber: 6.0 Consensus size: 46
47350503 TATGGCAAAG
* *
47350513 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
* *
47350559 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAATCATACT--G-
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
* *
47350602 T-T-AAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
* * * * *
47350646 TGTTAAAAGTAGGTATGATGTATCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
47350692 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
*
47350738 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
47350784 T
1 T
47350785 ATAGCAATGT
Statistics
Matches: 206, Mismatches: 15, Indels: 10
0.89 0.06 0.04
Matches are distributed among these distances:
41 34 0.17
42 1 0.00
43 2 0.01
44 2 0.01
45 1 0.00
46 166 0.81
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
Found at i:47351199 original size:43 final size:44
Alignment explanation
Indices: 47351139--47351532 Score: 443
Period size: 43 Copynumber: 9.2 Consensus size: 44
47351129 GTGTTACAGG
*
47351139 TTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGCG-
1 TTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGT
* *
47351182 TTAGGGTTTTTAAGTTAA-GGGTTAGAGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGT
* *
47351225 TTATGGTTTTTAAGTTAA-GGTTTAGGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGT
* *
47351268 TTAGGGTTTTTAAGTTAAGGGGTTAAGG-TTTTAAGTTAAAGGT
1 TTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGT
* * * * * *
47351311 TTAGTGTTTTAAATTTAAGGGTTTAGGGTTTTAAATTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGT
**
47351355 TTAAAG-TTTTAAGTTAA-GGGTTAGGG-TTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGT
* * * * * *
47351396 TTAGAGTTTTTAATTTAAGGGTTTAAGATTTTTAAGTTAATGAG-
1 TTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAA-GGGT
* * * * *
47351440 TTA-GGTTTTTAGGTTACGGGTTTATGATTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGT
*
47351483 TTAGGGTTTTTAATTTAAGGGG-TAGGAG-TTTTAAGTTAA-GGT
1 TTAGGGTTTTTAAGTTAAGGGGTTAGG-GTTTTTAAGTTAAGGGT
47351525 TTAGGGTT
1 TTAGGGTT
47351533 AGGGTTTTTA
Statistics
Matches: 297, Mismatches: 44, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
41 18 0.06
42 52 0.18
43 174 0.59
44 51 0.17
45 2 0.01
ACGTcount: A:0.26, C:0.01, G:0.29, T:0.45
Consensus pattern (44 bp):
TTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGT
Found at i:47351530 original size:27 final size:28
Alignment explanation
Indices: 47351500--47351555 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
47351490 TTTTAATTTA
47351500 AGGGGTAGGAG-TTTTAAGTT-AAGGTTT
1 AGGGGTAGG-GTTTTTAAGTTAAAGGTTT
* *
47351527 AGGGTTAGGGTTTTTAGGTTAAAGGTTT
1 AGGGGTAGGGTTTTTAAGTTAAAGGTTT
47351555 A
1 A
47351556 AGGTTTGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 1 0.04
27 16 0.64
28 8 0.32
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (28 bp):
AGGGGTAGGGTTTTTAAGTTAAAGGTTT
Found at i:47351553 original size:21 final size:22
Alignment explanation
Indices: 47351139--47351532 Score: 452
Period size: 22 Copynumber: 18.4 Consensus size: 22
47351129 GTGTTACAGG
*
47351139 TTAGGGTTTTTAAGTTAAGGGG
1 TTAGGGTTTTTAAGTTAAGGGT
*
47351161 TTAGGGTTTTTAAGTTAAGCG-
1 TTAGGGTTTTTAAGTTAAGGGT
47351182 TTAGGGTTTTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGT
* *
47351203 TTAGAGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
*
47351225 TTATGGTTTTTAAGTTAA-GGT
1 TTAGGGTTTTTAAGTTAAGGGT
47351246 TTAGGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
*
47351268 TTAGGGTTTTTAAGTTAAGGGG
1 TTAGGGTTTTTAAGTTAAGGGT
* *
47351290 TTAAGG-TTTTAAGTTAAAGGT
1 TTAGGGTTTTTAAGTTAAGGGT
* * *
47351311 TTAGTGTTTTAAATTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
* *
47351333 TTAGGGTTTTAAATTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
**
47351355 TTAAAG-TTTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGT
47351375 TTAGGG-TTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
* *
47351396 TTAGAGTTTTTAATTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
* * *
47351418 TTAAGATTTTTAAGTTAATGAG-
1 TTAGGGTTTTTAAGTTAA-GGGT
* *
47351440 TTA-GGTTTTTAGGTTACGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
* *
47351461 TTATGATTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
*
47351483 TTAGGGTTTTTAATTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGT
*
47351504 GTAGGAG-TTTTAAGTTAA-GGT
1 TTAGG-GTTTTTAAGTTAAGGGT
47351525 TTAGGGTT
1 TTAGGGTT
47351533 AGGGTTTTTA
Statistics
Matches: 317, Mismatches: 44, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
20 23 0.07
21 126 0.40
22 166 0.52
23 2 0.01
ACGTcount: A:0.26, C:0.01, G:0.29, T:0.45
Consensus pattern (22 bp):
TTAGGGTTTTTAAGTTAAGGGT
Found at i:47352979 original size:20 final size:20
Alignment explanation
Indices: 47352941--47352979 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
47352931 CTTTTATTTT
*
47352941 TAAAATCTACATAATAATTG
1 TAAAATCTACATAAAAATTG
47352961 TAAAATCTA-ATATAAAATT
1 TAAAATCTACATA-AAAATT
47352980 TACCTCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAAATCTACATAAAAATTG
Found at i:47354013 original size:11 final size:11
Alignment explanation
Indices: 47353993--47354061 Score: 102
Period size: 11 Copynumber: 6.2 Consensus size: 11
47353983 TAAATTTGGA
*
47353993 AGGAATTTGAG
1 AGGAAATTGAG
*
47354004 AGCAAATTGAG
1 AGGAAATTGAG
*
47354015 AGGAAATTTAG
1 AGGAAATTGAG
47354026 AGGAAATTGAG
1 AGGAAATTGAG
47354037 AGGAAATTGAG
1 AGGAAATTGAG
47354048 AGGAAATTTGAG
1 AGGAAA-TTGAG
47354060 AG
1 AG
47354062 AGGATTAGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
11 45 0.87
12 7 0.13
ACGTcount: A:0.43, C:0.01, G:0.33, T:0.22
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:47354036 original size:33 final size:33
Alignment explanation
Indices: 47353984--47354061 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 33
47353974 GATTTCAGAT
* *
47353984 AAATTTGGAAGGAATTTGAGAGCAAATTGAGAGG
1 AAATTTAG-AGGAAATTGAGAGCAAATTGAGAGG
*
47354018 AAATTTAGAGGAAATTGAGAGGAAATTGAGAGG
1 AAATTTAGAGGAAATTGAGAGCAAATTGAGAGG
47354051 AAATTTGAGAG
1 AAATTT-AGAG
47354062 AGGATTAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 29 0.73
34 11 0.28
ACGTcount: A:0.44, C:0.01, G:0.32, T:0.23
Consensus pattern (33 bp):
AAATTTAGAGGAAATTGAGAGCAAATTGAGAGG
Found at i:47354307 original size:40 final size:42
Alignment explanation
Indices: 47354256--47354350 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 42
47354246 CATGCTGATA
* * * *
47354256 TGGACGTGATTTACTGCCACGTTAGCT-A-ACCGCGCTGACG
1 TGGACGCGATTTACTGACACGTCACCTGACACCGCGCTGACG
* * *
47354296 TGGACGCGATTTGCTGACACGTCCCCTGACATCGCGCTGACG
1 TGGACGCGATTTACTGACACGTCACCTGACACCGCGCTGACG
*
47354338 TGGACGCAATTTA
1 TGGACGCGATTTA
47354351 AAGGAAAATG
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
40 21 0.48
41 1 0.02
42 22 0.50
ACGTcount: A:0.20, C:0.28, G:0.27, T:0.24
Consensus pattern (42 bp):
TGGACGCGATTTACTGACACGTCACCTGACACCGCGCTGACG
Found at i:47364084 original size:18 final size:18
Alignment explanation
Indices: 47364053--47364100 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
47364043 ATATAATTTT
*
47364053 AAATAATTTTTAAAATTCA
1 AAAT-ATTTATAAAATTCA
*
47364072 AAATATTTATAAAAATTCT
1 AAATATTTAT-AAAATTCA
47364091 AAA-ATTTATA
1 AAATATTTATA
47364101 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 11 0.42
19 14 0.54
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATTTATAAAATTCA
Found at i:47364136 original size:20 final size:20
Alignment explanation
Indices: 47364106--47364144 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
47364096 TTATATTTTT
47364106 TAAAAATTATAAA-AAATTC
1 TAAAAATTATAAAGAAATTC
47364125 TAAAAATATATAAAGAAATT
1 TAAAAAT-TATAAAGAAATT
47364145 AAAACATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 6 0.33
21 5 0.28
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (20 bp):
TAAAAATTATAAAGAAATTC
Found at i:47364147 original size:19 final size:18
Alignment explanation
Indices: 47364104--47364157 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
47364094 ATTTATATTT
47364104 TTTAAAAATTATAAAAAA
1 TTTAAAAATTATAAAAAA
47364122 TTCTAAAAATATATAAAGAAA
1 TT-TAAAAAT-TATAAA-AAA
47364143 -TTAAAACATTA-AAAA
1 TTTAAAA-ATTATAAAA
47364158 TTTTCTAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.03
18 5 0.16
19 14 0.44
20 9 0.28
21 3 0.09
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
TTTAAAAATTATAAAAAA
Found at i:47372038 original size:29 final size:29
Alignment explanation
Indices: 47372005--47372063 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
47371995 CATCTCTTGG
47372005 TAAGCATTTAATTTCACTACCTCTTTTAC
1 TAAGCATTTAATTTCACTACCTCTTTTAC
47372034 TAAGCATTTAATTTCACTACCTCTTTTAC
1 TAAGCATTTAATTTCACTACCTCTTTTAC
47372063 T
1 T
47372064 TTCTGGTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (29 bp):
TAAGCATTTAATTTCACTACCTCTTTTAC
Found at i:47372213 original size:66 final size:65
Alignment explanation
Indices: 47372131--47372266 Score: 245
Period size: 66 Copynumber: 2.1 Consensus size: 65
47372121 CAAATTAGTT
47372131 TATACGTTGTGGGTGTTACATAAATACTTATTTTACTTTGATTATCGGGAATTATACACCTTTCA
1 TATACGTTGTGGGTGTTACATAAATACTTATTTTACTTTGATTATC-GGAATTATACACCTTTCA
47372196 C
65 C
* *
47372197 TATACGTTGTGGGTGTTATATAAATACTTTTTTTACTTTGATTATCGGAATTATACACCTTTCAC
1 TATACGTTGTGGGTGTTACATAAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCAC
47372262 TATAC
1 TATAC
47372267 TTAAATCTGC
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 24 0.35
66 44 0.65
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (65 bp):
TATACGTTGTGGGTGTTACATAAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCAC
Found at i:47372864 original size:314 final size:323
Alignment explanation
Indices: 47372402--47373118 Score: 829
Period size: 314 Copynumber: 2.2 Consensus size: 323
47372392 TTCACCTTTT
* * * * *
47372402 ACCTTTCACCATACCTATACCTCTATTTTATTATAAATGCGTACTTTATTTTTTTTAATAAGTAG
1 ACCTTTCACTATACCTAAACCTCTATTTTATTAT-AATGCTTATTTTGTTTTTTTTAATAAGTAG
* * *
47372467 AACGATTTTCGAATTATATATCCTTTAACGATACTTAAAATTTATATTTCATTATATATTATAAA
65 AACGATTTTCAAATTAGATATCCTTTAACGATACTTAAAATTTATATTTCAGTATATATTATAAA
* * * * * * *
47372532 TGCTTATTTTGCTTTGGTTTTCGGAATCATACACCTTTCACCATATC-TATATCTCTATTCTGTT
130 TACTTATTTTGCTTTGGTTATAGGAATCATACACCTTCCACCATA-CGTAAACCTCTATTCTATT
* * * *
47372596 ATAAATGCGTAATTTGTTTTTGTTTTAATAAGTAAAACGATTTTCGAATTATATATCTTTTAACG
194 ATAAATGCGTAATTTGTTTCTCTTTTAATAAGTAAAACGATTTTCAAATTATATATCTTTCAACG
* * *
47372661 ATA-T-A-TTT-CA-TGGA-TGT-TA-TATAAATGCTT-ATTTTTCTTTGGTTATCGGAACCATA
259 ATACTAAGTTTACATTGCATTGTGTACTATAAATG-TTAATTTTGCTTTCGTTATCGGAACCATA
47372717 C
323 C
47372718 ACCTTTCACTATACCTAAACCTCTATTTTA-T-T-ATGCTTATTTTGTTTTTGTTTCAATAAGTA
1 ACCTTTCACTATACCTAAACCTCTATTTTATTATAATGCTTATTTTGTTTTT-TTT-AATAAGTA
* * * *
47372780 -AATTG-TTTTCAAATTAGATATCTTTTAACGATACTTAAAGTTTATATTTTACGAGTGT-TA-T
64 GAA-CGATTTTCAAATTAGATATCCTTTAACGATACTTAAAATTTATA-TTT-C-AGTATATATT
* * *
47372841 ATAAATACTTATTTTGCTTTGGTTATAGGAATCATACACCTTCCGCTATACGTAAACCTCTATTT
125 ATAAATACTTATTTTGCTTTGGTTATAGGAATCATACACCTTCCACCATACGTAAACCTCTATTC
* * * *
47372906 TATTATAAATGCTTATTTTGTTTCTCTTTTAATAAGTAAGACGGTTTTCAAATTATATATCTTTC
190 TATTATAAATGCGTAATTTGTTTCTCTTTTAATAAGTAAAACGATTTTCAAATTATATATCTTTC
* *
47372971 AACGATACTTAAAGTTTATATTTCATTGTGTACTATAAATGTTAATTTTGCTTTCGTTATCGGAA
255 AACGATAC-T-AAGTTTACATTGCATTGTGTACTATAAATGTTAATTTTGCTTTCGTTATCGGAA
* *
47373036 TCATCC
318 CCATAC
47373042 ACCTTTCACTATACCTAAACCTCTATTTTATTATAGATGCTTACTTTTGTTTTTATTTTAATAAG
1 ACCTTTCACTATACCTAAACCTCTATTTTATTATA-ATGCTTA-TTTTG-TTTT-TTTTAATAAG
* *
47373107 TATAATGATTTT
62 TAGAACGATTTT
47373119 TGAATTATAA
Statistics
Matches: 337, Mismatches: 37, Indels: 40
0.81 0.09 0.10
Matches are distributed among these distances:
312 14 0.04
313 43 0.13
314 131 0.39
315 4 0.01
316 32 0.09
318 1 0.00
319 3 0.01
320 1 0.00
321 2 0.01
322 3 0.01
323 4 0.01
324 61 0.18
325 1 0.00
326 1 0.00
328 7 0.02
329 15 0.04
330 13 0.04
331 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (323 bp):
ACCTTTCACTATACCTAAACCTCTATTTTATTATAATGCTTATTTTGTTTTTTTTAATAAGTAGA
ACGATTTTCAAATTAGATATCCTTTAACGATACTTAAAATTTATATTTCAGTATATATTATAAAT
ACTTATTTTGCTTTGGTTATAGGAATCATACACCTTCCACCATACGTAAACCTCTATTCTATTAT
AAATGCGTAATTTGTTTCTCTTTTAATAAGTAAAACGATTTTCAAATTATATATCTTTCAACGAT
ACTAAGTTTACATTGCATTGTGTACTATAAATGTTAATTTTGCTTTCGTTATCGGAACCATAC
Found at i:47373127 original size:165 final size:159
Alignment explanation
Indices: 47372662--47373613 Score: 649
Period size: 160 Copynumber: 5.9 Consensus size: 159
47372652 CTTTTAACGA
* * *
47372662 TATATTTCATGGATGTTATATAAATGCTTATTTTTCTTTGGTTATCGGAACCATACACCTTTCAC
1 TATATTTCATTG-TG-TATATAAATG-TTATTTTGCTTTGGTTATCGGAATCATACACCTTTCAC
* *
47372727 TATACCTAAACCTCTATTTTA-T-T-ATGCTTATTTTGTTTTTGTTTCAATAAGTAAATTGTTTT
63 TATACCTAAACCTCTATTTTATTATAATGCTTATTTTGTTTTTATTTTAATAAGTAAA-TGTTTT
* *
47372789 CAAATTAGATATCTTTTAACGATACTTAAAGTT
127 CAAATTATATATCTTTCAACGATACTTAAAGTT
* * * * *
47372822 TATATTTTACGAGTGT-TATATAAATACTTATTTTGCTTTGGTTATAGGAATCATACACCTTCCG
1 TATA-TTT-C-ATTGTGTATATAAAT-GTTATTTTGCTTTGGTTATCGGAATCATACACCTTTCA
* * * *
47372886 CTATACGTAAACCTCTATTTTATTATAAATGCTTATTTTGTTTCTCTTTTAATAAGTAAGACGGT
62 CTATACCTAAACCTCTATTTTATTAT-AATGCTTATTTTGTTTTTATTTTAATAAGTAA-A-TGT
47372951 TTTCAAATTATATATCTTTCAACGATACTTAAAGTT
124 TTTCAAATTATATATCTTTCAACGATACTTAAAGTT
* *
47372987 TATATTTCATTGTGTACTATAAATGTTAATTTTGCTTTCGTTATCGGAATCATCCACCTTTCACT
1 TATATTTCATTGTGTA-TATAAATGTT-ATTTTGCTTTGGTTATCGGAATCATACACCTTTCACT
47373052 ATACCTAAACCTCTATTTTATTATAGATGCTTACTTTTGTTTTTATTTTAATAAGTATAATGATT
64 ATACCTAAACCTCTATTTTATTATA-ATGCTTA-TTTTGTTTTTATTTTAATAAGTA-AATG---
* *
47373117 TTTGAATTATAATGAATTATATATCTTTTAACGATACTTAAAGTT
123 --T---TT-TCA--AATTATATATCTTTCAACGATACTTAAAGTT
* * * * * * *
47373162 TATATTTCATCGTACTTTATAAATGCTTATTTTACTTCT-TTTA-C--AATACCTA-AAC-TT--
1 TATATTTCATTGT-GTATATAAATG-TTATTTTGCTT-TGGTTATCGGAAT-CATACACCTTTCA
* * * * * *
47373219 GTAT---T-----T-TATTATA-AATGAT--TAT-TTT-GTTTTTGTTTTAATAAATAAAATGGT
62 CTATACCTAAACCTCTATTTTATTATAATGCT-TATTTTGTTTTTATTTTAATAAGT-AAAT-GT
* *
47373270 TTTCAATTTATATATCTTTTAACGATACTTAAAGTT
124 TTTCAAATTATATATCTTTCAACGATACTTAAAGTT
* * * * * * * *
47373306 TATATTCCATCGTGTTTCATAAATACTTATTTCGCTTTTGTTATCGGAATCATACATCTTGT-AT
1 TATATTTCATTGTGTAT-ATAAAT-GTTATTTTGCTTTGGTTATCGGAATCATACACCTT-TCAC
* * *
47373370 TATACTTAAACTTGC-ATTTTATTATAAATGCTTATTTTGTTTTTA--TTATTAAGTAAGATGGT
63 TATACCTAAACCT-CTATTTTATTAT-AATGCTTATTTTGTTTTTATTTTAATAAGTAA-AT-GT
* * * * *
47373432 TTTCGAATTAGATATCTTTTAACGACGAC-TAAA-TC
124 TTTCAAATTATATATCTTTCAACGA-TACTTAAAGTT
* * * * * * * *
47373467 TATACTCCATCGTGTCTTATAAATGCTTATTTT-CTTTGGTTATTGAAAACATACACCTTTTACT
1 TATATTTCATTGTGT-ATATAAATG-TTATTTTGCTTTGGTTATCGGAATCATACACCTTTCACT
* * * *
47373531 ATACCTAAACC-CGTATTTTATTATAAATACTTATTTTGTATATTATTTTAATATGCAAATTGGT
64 ATACCTAAACCTC-TATTTTATTAT-AATGCTTATTTTGT-TTTTATTTTAATAAGTAAA-T-GT
*
47373595 TTTCAAATTATGTATCTTT
124 TTTCAAATTATATATCTTT
47373614 TAGAATACTT
Statistics
Matches: 638, Mismatches: 84, Indels: 137
0.74 0.10 0.16
Matches are distributed among these distances:
143 4 0.01
144 60 0.09
145 1 0.00
146 5 0.01
147 7 0.01
148 1 0.00
149 1 0.00
150 4 0.01
153 1 0.00
154 19 0.03
155 5 0.01
156 1 0.00
157 1 0.00
158 4 0.01
159 8 0.01
160 130 0.20
161 40 0.06
162 49 0.08
163 42 0.07
164 107 0.17
165 63 0.10
166 2 0.00
169 4 0.01
171 2 0.00
172 7 0.01
173 4 0.01
174 1 0.00
175 61 0.10
176 4 0.01
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (159 bp):
TATATTTCATTGTGTATATAAATGTTATTTTGCTTTGGTTATCGGAATCATACACCTTTCACTAT
ACCTAAACCTCTATTTTATTATAATGCTTATTTTGTTTTTATTTTAATAAGTAAATGTTTTCAAA
TTATATATCTTTCAACGATACTTAAAGTT
Found at i:47379619 original size:2 final size:2
Alignment explanation
Indices: 47379612--47379637 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47379602 TCCTTTATTA
47379612 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
47379638 TTGTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47380222 original size:2 final size:2
Alignment explanation
Indices: 47380215--47380249 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
47380205 AAATATAAAC
*
47380215 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47380250 AATTATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:47380222 original size:12 final size:12
Alignment explanation
Indices: 47380207--47380247 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
47380197 ATAAAGAAAA
*
47380207 ATATAAACATAT
1 ATATAAATATAT
*
47380219 ATATATATATAT
1 ATATAAATATAT
47380231 ATATAAATATAT
1 ATATAAATATAT
47380243 ATATA
1 ATATA
47380248 TAAATTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATAAATATAT
Found at i:47380262 original size:14 final size:14
Alignment explanation
Indices: 47380205--47380262 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
47380195 AAATAAAGAA
47380205 AAATATAAACATATAT
1 AAATAT-AA-ATATAT
* *
47380221 ATATATATATATAT
1 AAATATAAATATAT
*
47380235 AAATATATATATAT
1 AAATATAAATATAT
47380249 AAATTATGAAATAT
1 AAA-TAT-AAATAT
47380263 GTGTTTAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 22 0.61
15 4 0.11
16 10 0.28
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (14 bp):
AAATATAAATATAT
Found at i:47380487 original size:28 final size:30
Alignment explanation
Indices: 47380456--47380511 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 30
47380446 TTTTTTAAAA
47380456 TGTATGTATACTAT-TATAA-AA-AATAATG
1 TGTATGTATA-TATATATAATAATAATAATG
47380484 TGTATGTATATATATATAATAATAATAA
1 TGTATGTATATATATATAATAATAATAA
47380512 ATGATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 3 0.12
28 15 0.60
29 2 0.08
30 5 0.20
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (30 bp):
TGTATGTATATATATATAATAATAATAATG
Found at i:47380520 original size:16 final size:16
Alignment explanation
Indices: 47380499--47380530 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
47380489 GTATATATAT
*
47380499 ATAATAATAATAAATG
1 ATAATAATAACAAATG
47380515 ATAATAATAACAAATG
1 ATAATAATAACAAATG
47380531 GGGATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (16 bp):
ATAATAATAACAAATG
Found at i:47382124 original size:41 final size:40
Alignment explanation
Indices: 47382061--47382203 Score: 142
Period size: 41 Copynumber: 3.5 Consensus size: 40
47382051 ATTAGTAACG
* * * **
47382061 TTTTTGCATAAAAGCCACAAAAGGTAAAGTAATAGTGGCA
1 TTTTTTCATAAACGCCGCAAAAGGTAAAGTAATAGCCGCA
* * *
47382101 TTTTTCTCATAAACGCCGCAAAAGGTAAAGCAACAACCGCA
1 TTTTT-TCATAAACGCCGCAAAAGGTAAAGTAATAGCCGCA
** * **
47382142 TTTTTTCATAAACGCCGTTAAAGGTAAAGTAATAGCAGTG
1 TTTTTTCATAAACGCCGCAAAAGGTAAAGTAATAGCCGCA
*
47382182 TTTTTTCCATAAATGCCGCAAA
1 TTTTTT-CATAAACGCCGCAAA
47382204 TATTTTTTAT
Statistics
Matches: 82, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
40 38 0.46
41 44 0.54
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (40 bp):
TTTTTTCATAAACGCCGCAAAAGGTAAAGTAATAGCCGCA
Found at i:47382556 original size:20 final size:20
Alignment explanation
Indices: 47382519--47382557 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
47382509 AAACTCTATC
*
47382519 TATTTTGGTTTTACATGAAG
1 TATTTTGGTTCTACATGAAG
*
47382539 TATTTTGGTTCTATATGAA
1 TATTTTGGTTCTACATGAA
47382558 ATGAATTATT
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:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (20 bp):
TATTTTGGTTCTACATGAAG
Found at i:47388835 original size:29 final size:29
Alignment explanation
Indices: 47388802--47388860 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
47388792 CATCTCTTGG
47388802 TAAGCATTTAATTTCACTACCTCTTTTAC
1 TAAGCATTTAATTTCACTACCTCTTTTAC
47388831 TAAGCATTTAATTTCACTACCTCTTTTAC
1 TAAGCATTTAATTTCACTACCTCTTTTAC
47388860 T
1 T
47388861 TTCTGGTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (29 bp):
TAAGCATTTAATTTCACTACCTCTTTTAC
Found at i:47389033 original size:66 final size:65
Alignment explanation
Indices: 47388941--47389076 Score: 254
Period size: 66 Copynumber: 2.1 Consensus size: 65
47388931 GCTTAAGGTT
*
47388941 TATACGTTGTGGGTGTTACATGAATACTTATTTTACTTTGATTATCGGGAATTATACACCTTTCA
1 TATACGTTGTGGGTGTTACATAAATACTTATTTTACTTTGATTATC-GGAATTATACACCTTTCA
47389006 C
65 C
47389007 TATACGTTGTGGGTGTTACATAAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCAC
1 TATACGTTGTGGGTGTTACATAAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCAC
47389072 TATAC
1 TATAC
47389077 TTAAATCTGC
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 24 0.35
66 45 0.65
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (65 bp):
TATACGTTGTGGGTGTTACATAAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCAC
Found at i:47389340 original size:162 final size:160
Alignment explanation
Indices: 47389119--47390595 Score: 1099
Period size: 162 Copynumber: 9.2 Consensus size: 160
47389109 CCTAAACTAC
* * * * * *
47389119 ATCTTTCAACTATGCTTAAAGTTTATATTTTATGAGTGTTATATAAATGCTTGTTTTGCTTTGGT
1 ATCTTTTAACGATACTTAAAATTTATATTTCAT---TGTTATATAAATGCTTATTTTGCTTTGGT
* * * *
47389184 TATCGGAATCATACACCTTTCACCATACCTATACCTCTATTTTATTATAAATGCGTACTTTATTT
63 TATCGGAATCATACACCTTTCACTATACCTAAACCTCTATTTTATTATAAATGCTTACTTTGTTT
*
47389249 T-TTTTAATAAGTAGAACGATTTTCGAATTATAT
128 TATTTTAATAAGTA-AACGGTTTTCGAATTATAT
*
47389282 ATCTTTTAACGATACTTAAAATTTATATTTCATTATATATTATAAATGCTTATTTTGCTTTGGTT
1 ATCTTTTAACGATACTTAAAATTTATATTTCATTGT-TA-TATAAATGCTTATTTTGCTTTGGTT
* * * * * *
47389347 ATCGGAATCATACACCTTTCACCATATCTATACCTCTATTTTGTTATAAATGCATAATTTGTTTT
64 ATCGGAATCATACACCTTTCACTATACCTAAACCTCTATTTTATTATAAATGCTTACTTTG-TTT
*
47389412 TGTTTTAATAAGTAAATCGGTTTTCGAATTATAT
128 TATTTTAATAAGTAAA-CGGTTTTCGAATTATAT
* ** *
47389446 ATCTTTTAACGATA--T---ATTT-CA-TGGA-TGTTATATAAATGCTTATTTTTCTTTGGTTAT
1 ATCTTTTAACGATACTTAAAATTTATATTTCATTGTTATATAAATGCTTATTTTGCTTTGGTTAT
* *
47389503 CGGAACCATACACCTTTCACTATACCTAAACCTCTATTTTA-T-T--ATGCTTATTTTGTTTT-T
66 CGGAATCATACACCTTTCACTATACCTAAACCTCTATTTTATTATAAATGCTTACTTTGTTTTAT
* * *
47389563 GTTTCAATAAGTAAATAGGTTTTCAAATTAGAT
131 -TTT-AATAAGTAAA-CGGTTTTCGAATTATAT
* * *
47389596 ATCTTTTAACGATACTTAAAGTTTATATTTTACGAGTGTTATATAAATACTTATTTTGCTTTGGT
1 ATCTTTTAACGATACTTAAAATTTATA-TTT-C-ATTGTTATATAAATGCTTATTTTGCTTTGGT
* * * * *
47389661 TATAGGAATCATACACCTTCCGCTATACCTAAACCTTTATTTTATTATAAATGCTTATTTTGTTT
63 TATCGGAATCATACACCTTTCACTATACCTAAACCTCTATTTTATTATAAATGCTTACTTTGTTT
47389726 CTATTTTAATAAGTAAGACGGTTTTCGAATTATAT
128 -TATTTTAATAAGTAA-ACGGTTTTCGAATTATAT
*
47389761 ATCTTTTAACGATACTAATTAAAGTTTATATTTCATTGTGTACTATAAATG-TTAATTTTGCTTT
1 ATCTTTTAACGATAC---TTAAAATTTATATTTCATTGT-TA-TATAAATGCTT-ATTTTGCTTT
* * * *
47389825 CGTTATCGGAATCATCCACCTTTCACTATACCTAAACCTCTATTTTATCATAGATGCTTACTTTT
60 GGTTATCGGAATCATACACCTTTCACTATACCTAAACCTCTATTTTATTATAAATGCTTAC-TTT
*
47389890 GTTTTTATTTTAATAAGTATAATGATTTTTGAATTATAAT-GAATTATAT
124 G-TTTTATTTTAATAAGTA-AACG------G--TT-T--TCGAATTATAT
* * * * *
47389939 ATCTTTTAACGATATTTAAAGTTTATATTTCATCG-TACGTTATAAATGCTTATTTTACTTCT-T
1 ATCTTTTAACGATACTTAAAATTTATATTTCATTGTTA---TATAAATGCTTATTTTGCTT-TGG
* * * * ** * *
47390002 TTA-C--AATACCTA-AACTTGT-ATTTTATGATAAA--T-GA--TTATT-T---TG-TT-C-CT
62 TTATCGGAAT-CATACACCTT-TCACTATA-CCTAAACCTCTATTTTATTATAAATGCTTACTTT
* * *
47390050 G-----TTTTAATAAGCAAAATGG-TTTCAAATTATAT
124 GTTTTATTTTAATAAG-TAAACGGTTTTCGAATTATAT
* * * * * *
47390082 ATCTTTTAACGATACCTAAAGTTTATATTCCATTGTGTTCTATAAATACTTATTTTGCTTTCGTT
1 ATCTTTTAACGATACTTAAAATTTATATTTCA-T-TGTTATATAAATGCTTATTTTGCTTTGGTT
* * ** * * *
47390147 ATCGGAATCGTACACTTTTTTCTATACCTAAACTTATATTTTTATTATAAATGCTTATTTTGTTT
64 ATCGGAATCATACACCTTTCACTATACCTAAACCTCTA-TTTTATTATAAATGCTTACTTTG-TT
* *
47390212 TTGTTTTAATAAGTAAAATGGTTTTC-AATTTATAT
127 TTATTTTAATAAGT-AAACGGTTTTCGAA-TTATAT
* * * * * *
47390247 ATCTTTTAACGATACTTAAAGTTTATATTCCATCGTGTTTTATAAATTCTTATTTCGCTTTCGTT
1 ATCTTTTAACGATACTTAAAATTTATATTTCAT--TGTTATATAAATGCTTATTTTGCTTTGGTT
* * * * * * * *
47390312 ATTGGAATCATACATCTTTTATTATACTTAAACTTGTATTTTATTATAAATGCTTATTTTGTTTT
64 ATCGGAATCATACACCTTTCACTATACCTAAACCTCTATTTTATTATAAATGCTTACTTTGTTTT
* * * *
47390377 -TATTATTAAGTAAGATGGTTTTCAAATTATAT
129 ATTTTAATAAGTAA-ACGGTTTTCGAATTATAT
* * *
47390409 ATCTTTTAACGATGAC-T-AAATCTATACTCCATCATGTCT-TATAAATGCTTATTTT-CTTTGG
1 ATCTTTTAACGAT-ACTTAAAATTTATATTTCAT--TGT-TATATAAATGCTTATTTTGCTTTGG
* * * * *
47390470 TTATTGAAATCATACACCTTTTACTATACCTAAACC-CGTATTTTATTATAAATACTTATTTTGT
62 TTATCGGAATCATACACCTTTCACTATACCTAAACCTC-TATTTTATTATAAATGCTTACTTTGT
* * * * **
47390534 ATTTATTTTAATATGCAAATTGGTTTTCAAATTAGGT
126 -TTTATTTTAATAAGTAAA-CGGTTTTCGAATTATAT
* **
47390571 ATCTTTT-ACAATACTTGTAATTTAT
1 ATCTTTTAACGATACTTAAAATTTAT
47390596 GTTAATAAGT
Statistics
Matches: 1090, Mismatches: 128, Indels: 193
0.77 0.09 0.14
Matches are distributed among these distances:
142 2 0.00
143 58 0.05
144 3 0.00
145 10 0.01
146 10 0.01
147 1 0.00
148 3 0.00
149 7 0.01
150 49 0.04
151 5 0.00
152 3 0.00
153 1 0.00
154 76 0.07
155 8 0.01
156 5 0.00
157 2 0.00
158 4 0.00
159 4 0.00
160 68 0.06
161 109 0.10
162 159 0.15
163 45 0.04
164 86 0.08
165 156 0.14
166 10 0.01
167 74 0.07
168 36 0.03
169 4 0.00
170 1 0.00
171 1 0.00
172 11 0.01
173 9 0.01
174 2 0.00
175 38 0.03
176 5 0.00
177 1 0.00
178 23 0.02
179 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (160 bp):
ATCTTTTAACGATACTTAAAATTTATATTTCATTGTTATATAAATGCTTATTTTGCTTTGGTTAT
CGGAATCATACACCTTTCACTATACCTAAACCTCTATTTTATTATAAATGCTTACTTTGTTTTAT
TTTAATAAGTAAACGGTTTTCGAATTATAT
Found at i:47389661 original size:161 final size:164
Alignment explanation
Indices: 47389471--47390586 Score: 902
Period size: 165 Copynumber: 6.9 Consensus size: 164
47389461 ATTTCATGGA
* * *
47389471 TGTTATATAAATGCTTATTTTTCTTTGGTTATCGGAACCATACACCTTTCACTATACCTAAACCT
1 TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
* * *
47389536 CTATTTTA-T-T-ATGCTTATTTTGTTTTTGTTTCAATAAGTAAATAGGTTTTCAAATTAGATAT
66 CTATTTTATTATAATGCTTATTTTGTTTTTATTTTAATAAGTAAATAGGTTTTCAAATTATATAT
**
47389598 CTTTTAACGATACTTAAAGTTTATATTTTA-CGAG
131 CTTTTAACGATACTTAAAGTTTATATTCCATC-AG
* * * * *
47389632 TGTTATATAAATACTTATTTTGCTTTGGTTATAGGAATCATACACCTTCCGCTATACCTAAACCT
1 TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
* * * *
47389697 TTATTTTATTATAAATGCTTATTTTGTTTCTATTTTAATAAGTAAGA-CGGTTTTCGAATTATAT
66 CTATTTTATTAT-AATGCTTATTTTGTTTTTATTTTAATAAGTAA-ATAGGTTTTCAAATTATAT
* *
47389761 ATCTTTTAACGATACTAATTAAAGTTTATATTTCAT-TG
129 ATCTTTTAACGATAC---TTAAAGTTTATATTCCATCAG
*
47389799 TG-TACTATAAATG-TTAATTTTGCTTTCGTTATCGGAATCATCCACCTTTCACTATACCTAAAC
1 TGTTA-TATAAATGCTT-ATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAAC
* * *
47389862 CTCTATTTTATCATAGATGCTTACTTTTGTTTTTATTTTAATAAGTATAATGATTTTTGAATTAT
64 CTCTATTTTATTATA-ATGCTTA-TTTTGTTTTTATTTTAATAAGTA-AAT-A-----G-GTTTT
* * *
47389927 AATGAATTATATATCTTTTAACGATATTTAAAGTTTATATTTCATC-G
119 CA--AATTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCAG
* * * * **
47389974 TACG-T-TATAAATGCTTATTTTAC-TTC-TT-T---TA-CA-ATACC--T-A--A-ACTTGTA-
1 T--GTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAAC
* * ** * * ** * *
47390022 TTTTATGATA-AATGAT--TAT-TTT-GTTCCTGTTTTAATAAGCAAA-ATGG-TTTCAAATTAT
64 CTCTATTTTATTATAATGCT-TATTTTGTTTTTATTTTAATAAGTAAATA-GGTTTTCAAATTAT
* *
47390080 ATATCTTTTAACGATACCTAAAGTTTATATTCCAT-TG
127 ATATCTTTTAACGATACTTAAAGTTTATATTCCATCAG
* * * * ** *
47390117 TGTTCTATAAATACTTATTTTGCTTTCGTTATCGGAATCGTACACTTTTTTCTATACCTAAACTT
1 TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
* * *
47390182 ATATTTTTATTATAAATGCTTATTTTGTTTTTGTTTTAATAAGTAAA-ATGGTTTTCAATTTATA
66 CTA-TTTTATTAT-AATGCTTATTTTGTTTTTATTTTAATAAGTAAATA-GGTTTTCAAATTATA
47390246 TATCTTTTAACGATACTTAAAGTTTATATTCCATC-G
128 TATCTTTTAACGATACTTAAAGTTTATATTCCATCAG
* * * * * * * * *
47390282 TGTTTTATAAATTCTTATTTCGCTTTCGTTATTGGAATCATACATCTTTTATTATACTTAAACTT
1 TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
* *
47390347 GTATTTTATTATAAATGCTTATTTTGTTTTTA--TTATTAAGTAAGAT-GGTTTTCAAATTATAT
66 CTATTTTATTAT-AATGCTTATTTTGTTTTTATTTTAATAAGTAA-ATAGGTTTTCAAATTATAT
* *
47390409 ATCTTTTAACGATGAC-TAAA-TCTATACTCCATCA-
129 ATCTTTTAACGAT-ACTTAAAGTTTATATTCCATCAG
* * * *
47390443 TGTCT-TATAAATGCTTATTTT-CTTTGGTTATTGAAATCATACACCTTTTACTATACCTAAACC
1 TGT-TATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACC
* * * * * **
47390506 -CGTATTTTATTATAAATACTTATTTTGTATTTATTTTAATATGCAAATTGGTTTTCAAATTAGG
65 TC-TATTTTATTAT-AATGCTTATTTTGTTTTTATTTTAATAAGTAAATAGGTTTTCAAATTATA
*
47390570 TATCTTTT-ACAATACTT
128 TATCTTTTAACGATACTT
47390587 GTAATTTATG
Statistics
Matches: 783, Mismatches: 106, Indels: 132
0.77 0.10 0.13
Matches are distributed among these distances:
141 1 0.00
142 1 0.00
143 56 0.07
144 3 0.00
145 5 0.01
146 1 0.00
147 2 0.00
149 1 0.00
150 1 0.00
151 4 0.01
153 3 0.00
154 15 0.02
155 3 0.00
156 2 0.00
157 5 0.01
158 6 0.01
159 5 0.01
160 75 0.10
161 107 0.14
162 75 0.10
163 8 0.01
164 51 0.07
165 160 0.20
166 6 0.01
167 74 0.09
168 41 0.05
169 2 0.00
172 1 0.00
173 2 0.00
174 3 0.00
175 35 0.04
176 5 0.01
177 2 0.00
178 22 0.03
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (164 bp):
TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
CTATTTTATTATAATGCTTATTTTGTTTTTATTTTAATAAGTAAATAGGTTTTCAAATTATATAT
CTTTTAACGATACTTAAAGTTTATATTCCATCAG
Found at i:47390148 original size:318 final size:313
Alignment explanation
Indices: 47389135--47390586 Score: 1002
Period size: 315 Copynumber: 4.5 Consensus size: 313
47389125 CAACTATGCT
** * * * *
47389135 TAAAGTTTATATTTTATGAGTGTTATATAAATGCTTGTTTTGCTTTGGTTATCGGAATCATACAC
1 TAAAGTTTATATTCCAT-TGTGTTCTATAAAT-CTTATTTTGCTTTCGTTATCGGAATCATACAC
* * * * * * *
47389200 CTTTCACCATACCTATACCTCTATTTTATTATAAATGCGTACTTT-ATTTT-TTTTAATAAGTAG
64 CTTTTACTATACCTAAACCTCTATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTAA
* * * * ** **
47389263 AACGATTTTCGAA-TTATATATCTTTTAACGATACTTAAAATTTATATTTCATTATATATTATAA
129 AATGGTTTTC-AATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTACGTTATAA
* * * * * * * * * * *
47389327 ATGCTTATTTTGCTTTGGTTATCGGAATCATACACCTTTCACCATATCTATACCTCTATTTTGTT
193 A----TA--TT-C-GTCGTTAT---TAT-ATACATCTTTTACAATACCTAAACTTGTATTTTATT
* * * *
47389392 ATAAATGCATAATTTGTTTTTGTTTTAATAAGTAA-ATCGGTTTTCGAATTATATATCTTTTAAC
246 ATAAATGCTTATTTTG-TTCT-TTTTAATAAGTAAGAT-GGTTTTCAAATTATATATCTTTTAAC
47389456 G--A--
308 GATACC
* * * * *
47389458 T--A---TAT-TT-CATGGATGTTATATAAATGCTTATTTTTCTTTGGTTATCGGAACCATACAC
1 TAAAGTTTATATTCCATTG-TGTTCTATAAAT-CTTATTTTGCTTTCGTTATCGGAATCATACAC
* * *
47389516 CTTTCACTATACCTAAACCTCTATTTTA-T-T--ATGCTTATTTTGTTTTTGTTTCAATAAGT-A
64 CTTTTACTATACCTAAACCTCTATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTAA
* * ** *
47389576 AATAGGTTTTCAAATTAGATATCTTTTAACGATACTTAAAGTTTATATTTTA-CG-AGTGTTATA
129 AAT-GGTTTTCAATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTA-CG-T-TA
* * * * *** *
47389639 TAAATACTTATTTTGCTTTGGTTATAGGAATCATACACCTTCCGCTATACCTAAACCTT-TATTT
190 T-AA-A--TA--TT-C-GTCGTTAT---TAT-ATACATCTTTTACAATACCTAAA-CTTGTATTT
* *
47389703 TATTATAAATGCTTATTTTGTTTCTATTTTAATAAGTAAGACGGTTTTCGAATTATATATCTTTT
242 TATTATAAATGCTTATTTTG-TTCT-TTTTAATAAGTAAGATGGTTTTCAAATTATATATCTTTT
*
47389768 AACGATACTAAT
305 AACGATAC---C
* * * *
47389780 TAAAGTTTATATTTCATTGTGTACTATAAATGTTAATTTTGCTTTCGTTATCGGAATCATCCACC
1 TAAAGTTTATATTCCATTGTGTTCTATAAATCTT-ATTTTGCTTTCGTTATCGGAATCATACACC
* * *
47389845 TTTCACTATACCTAAACCTCTATTTTATCATAGATGCTTACTTTTGTTTTTATTTTAATAAGTAT
65 TTTTACTATACCTAAACCTCTATTTTATTATAAATGCTTA-TTTTGTTTTTATTTTAATAAGTA-
** * * *
47389910 AATGATTTTTGAATTATAATGAATTATATATCTTTTAACGATATTTAAAGTTTATATTTCATCGT
128 AA--ATGGTT---TT-CAAT---TTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGT
* *
47389975 ACGTTAT-AA-A-T-G-C-TTATT-T-TACTTCTTTTACAATACCTAAACTTGTATTTTATGATA
184 ACGTTATAAATATTCGTCGTTATTATATACATCTTTTACAATACCTAAACTTGTATTTTATTATA
* * *
47390032 AATGATTATTTTGTTCCTGTTTTAATAAGCAAAATGG-TTTCAAATTATATATCTTTTAACGATA
249 AATGCTTATTTTGTT-CT-TTTTAATAAGTAAGATGGTTTTCAAATTATATATCTTTTAACGATA
47390096 CC
312 CC
* *
47390098 TAAAGTTTATATTCCATTGTGTTCTATAAATACTTATTTTGCTTTCGTTATCGGAATCGTACACT
1 TAAAGTTTATATTCCATTGTGTTCTATAAAT-CTTATTTTGCTTTCGTTATCGGAATCATACACC
* * * *
47390163 TTTTTCTATACCTAAACTTATATTTTTATTATAAATGCTTATTTTGTTTTTGTTTTAATAAGTAA
65 TTTTACTATACCTAAACCTCTA-TTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTAA
***
47390228 AATGGTTTTCAATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTGTTTTATAAA
129 AATGGTTTTCAATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTACGTTATAAA
** *
47390293 TTCTTATTTCGCTTTCGTTATTGGAATCATACATCTTTTATTATACTTAAACTTGTATTTTATTA
194 ----TA-TTCG---TCGTTATT---AT-ATACATCTTTTACAATACCTAAACTTGTATTTTATTA
*
47390358 TAAATGCTTATTTTGTT-TTTATTATTAAGTAAGATGGTTTTCAAATTATATATCTTTTAACGAT
247 TAAATGCTTATTTTGTTCTTT-TTAATAAGTAAGATGGTTTTCAAATTATATATCTTTTAACGAT
47390422 GA-C
311 -ACC
* * ** * * *
47390425 TAAA-TCTATACTCCATCATG-TCTTATAAATGCTTATTTT-CTTTGGTTATTGAAATCATACAC
1 TAAAGTTTATATTCCATTGTGTTC-TATAAAT-CTTATTTTGCTTTCGTTATCGGAATCATACAC
* * * *
47390487 CTTTTACTATACCTAAACC-CGTATTTTATTATAAATACTTATTTTGTATTTATTTTAATATGCA
64 CTTTTACTATACCTAAACCTC-TATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTA
* * ** *
47390551 AATTGGTTTTCAAATTAGGTATCTTTT-ACAATACTT
128 AAATGGTTTTCAATTTATATATCTTTTAACGATACTT
47390587 GTAATTTATG
Statistics
Matches: 933, Mismatches: 122, Indels: 148
0.78 0.10 0.12
Matches are distributed among these distances:
308 44 0.05
309 2 0.00
311 3 0.00
312 12 0.01
313 9 0.01
314 54 0.06
315 118 0.13
316 76 0.08
317 7 0.01
318 99 0.11
319 18 0.02
321 34 0.04
322 62 0.07
323 9 0.01
324 61 0.07
325 41 0.04
326 42 0.05
327 36 0.04
328 117 0.13
329 4 0.00
330 1 0.00
332 7 0.01
333 21 0.02
335 2 0.00
336 3 0.00
337 2 0.00
339 3 0.00
340 3 0.00
342 3 0.00
343 36 0.04
344 3 0.00
345 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (313 bp):
TAAAGTTTATATTCCATTGTGTTCTATAAATCTTATTTTGCTTTCGTTATCGGAATCATACACCT
TTTACTATACCTAAACCTCTATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTAAAA
TGGTTTTCAATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTACGTTATAAATA
TTCGTCGTTATTATATACATCTTTTACAATACCTAAACTTGTATTTTATTATAAATGCTTATTTT
GTTCTTTTTAATAAGTAAGATGGTTTTCAAATTATATATCTTTTAACGATACC
Found at i:47395314 original size:15 final size:15
Alignment explanation
Indices: 47395294--47395367 Score: 66
Period size: 15 Copynumber: 5.2 Consensus size: 15
47395284 CTCCTATGTC
*
47395294 TGGTGAACTCACATA
1 TGGTGAACTCACCTA
*
47395309 TGGTGAAC-C-CTTA
1 TGGTGAACTCACCTA
**
47395322 TGGCAAACTCACCTA
1 TGGTGAACTCACCTA
*
47395337 TGGTGAAC-C-CTTA
1 TGGTGAACTCACCTA
*
47395350 TCGTGAACTCACCTA
1 TGGTGAACTCACCTA
47395365 TGG
1 TGG
47395368 CAAACCCCTA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
13 19 0.42
14 4 0.09
15 22 0.49
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (15 bp):
TGGTGAACTCACCTA
Found at i:47395358 original size:28 final size:28
Alignment explanation
Indices: 47395296--47395386 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 28
47395286 CCTATGTCTG
* *
47395296 GTGAACTCACATATGGTGAACCCTTATG
1 GTGAACTCACCTATGGTGAACCCTTATC
**
47395324 GCAAACTCACCTATGGTGAACCCTTATC
1 GTGAACTCACCTATGGTGAACCCTTATC
** *
47395352 GTGAACTCACCTATGGCAAACCCCTATC
1 GTGAACTCACCTATGGTGAACCCTTATC
47395380 GTGAACT
1 GTGAACT
47395387 GCCTTAATTC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (28 bp):
GTGAACTCACCTATGGTGAACCCTTATC
Found at i:47399171 original size:32 final size:32
Alignment explanation
Indices: 47399133--47399194 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
47399123 CCCGTTTTTT
* **
47399133 AAATAAATATCAAAAATTTATTTTAAAAATTA
1 AAATAAAAATCAAAAAAGTATTTTAAAAATTA
*
47399165 AAATAAAAATTAAAAAAGTATTTTAAAAAT
1 AAATAAAAATCAAAAAAGTATTTTAAAAAT
47399195 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (32 bp):
AAATAAAAATCAAAAAAGTATTTTAAAAATTA
Found at i:47399234 original size:41 final size:40
Alignment explanation
Indices: 47399151--47399292 Score: 205
Period size: 40 Copynumber: 3.5 Consensus size: 40
47399141 ATCAAAAATT
47399151 TATTTTAAAAATTAAAATAAAAATT-AAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAAGTATTTTAAAAA
47399194 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
* *
47399234 AATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAA-TTAAAAAAAGTATTTTAAAAA
*
47399275 TATTTTAAAGTTAAAAAA
1 TATTTTAAAATTAAAAAA
47399293 TAAAAATAAA
Statistics
Matches: 93, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
39 7 0.08
40 38 0.41
41 36 0.39
42 6 0.06
43 6 0.06
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:47399273 original size:11 final size:11
Alignment explanation
Indices: 47399259--47399283 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
47399249 AAAATTTAAA
47399259 AAAAGTATTTT
1 AAAAGTATTTT
47399270 AAAAGTATTTT
1 AAAAGTATTTT
47399281 AAA
1 AAA
47399284 GTTAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:47399309 original size:41 final size:40
Alignment explanation
Indices: 47399151--47399309 Score: 160
Period size: 41 Copynumber: 3.9 Consensus size: 40
47399141 ATCAAAAATT
*
47399151 TATTTTAAAAATTAAAATAA-AAATTAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAA-AATAAA--AAAAAAATATTTTAAAAA
* *
47399194 TATTTTAAAATTAAAAAA-ATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAATA-AAAAAAAAATATTTTAAAAA
* ** * *
47399234 AATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATT-AAAAAATAAAAAAAAAATATTTTAAAAA
*
47399275 TATTTTAAAGTTAAAAAATAAAAATAAAAATATTT
1 TATTTTAAAATTAAAAAATAAAAA-AAAAATATTT
47399310 ATTATTCGGG
Statistics
Matches: 103, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
40 39 0.38
41 47 0.46
42 11 0.11
43 6 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAATAAAAAAAAAATATTTTAAAAA
Found at i:47401331 original size:29 final size:28
Alignment explanation
Indices: 47401291--47401345 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
47401281 TTTAAATTTA
* *
47401291 AAAAATTCAAATATATAAAAAGTATTTCT
1 AAAAATTAAAAT-TATAAAAACTATTTCT
*
47401320 AAAAATTAAAATTATTAAAACTATTT
1 AAAAATTAAAATTATAAAAACTATTT
47401346 AAAATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.36
Consensus pattern (28 bp):
AAAAATTAAAATTATAAAAACTATTTCT
Found at i:47405461 original size:11 final size:11
Alignment explanation
Indices: 47405439--47405478 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
47405429 AACTAATCCT
47405439 CTCTCAAATTTC
1 CTCTC-AATTTC
47405451 CTCTCAATTTC
1 CTCTCAATTTC
47405462 CTCTCAATTTC
1 CTCTCAATTTC
47405473 CT-TCAA
1 CTCTCAA
47405479 AAATTCTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.14
11 19 0.68
12 5 0.18
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:47406704 original size:7 final size:7
Alignment explanation
Indices: 47406692--47406716 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
47406682 AGTCGATTGA
47406692 TATTTAG
1 TATTTAG
47406699 TATTTAG
1 TATTTAG
47406706 TATTTAG
1 TATTTAG
47406713 TATT
1 TATT
47406717 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:47407855 original size:25 final size:25
Alignment explanation
Indices: 47407827--47407940 Score: 109
Period size: 25 Copynumber: 4.8 Consensus size: 25
47407817 TATTTTGATA
47407827 TTATTTGATGTAATAAAATAGGAGT
1 TTATTTGATGTAATAAAATAGGAGT
*
47407852 TTATTTGATGTAATAAAATA-GAAT
1 TTATTTGATGTAATAAAATAGGAGT
* * **
47407876 TT-TTTTA-GT--T--ATTTTGA-T
1 TTATTTGATGTAATAAAATAGGAGT
*
47407894 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGGAGT
47407920 TTATTTGATGTAATAAAATAG
1 TTATTTGATGTAATAAAATAG
47407941 AAATTTTTGA
Statistics
Matches: 71, Mismatches: 9, Indels: 18
0.72 0.09 0.18
Matches are distributed among these distances:
18 3 0.04
19 4 0.06
20 5 0.07
21 2 0.03
22 2 0.03
23 5 0.07
24 5 0.07
25 44 0.62
26 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGGAGT
Found at i:47407959 original size:9 final size:9
Alignment explanation
Indices: 47407945--47407990 Score: 85
Period size: 9 Copynumber: 5.2 Consensus size: 9
47407935 AAATAGAAAT
47407945 TTTTGAATA
1 TTTTGAATA
47407954 TTTTGAATA
1 TTTTGAATA
47407963 TTTTGAATA
1 TTTTGAATA
47407972 TTTTGAATA
1 TTTTGAATA
47407981 TTTTG-ATA
1 TTTTGAATA
47407989 TT
1 TT
47407991 ATTTGAGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 5 0.14
9 32 0.86
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (9 bp):
TTTTGAATA
Found at i:47407964 original size:68 final size:67
Alignment explanation
Indices: 47407805--47407964 Score: 257
Period size: 68 Copynumber: 2.3 Consensus size: 67
47407795 TTATTTGTAC
*
47407805 AAATATTTTGAATATTTTGATATTATTTGATGTAATAAAATAGGAGTTTATTTGATGTAATAAAA
1 AAAT-TTTTGAATATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAA
47407870 TAG
65 TAG
* * *
47407873 AATTTTTTTAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAA
1 AAATTTTTGA-ATATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAA
47407938 TAG
65 TAG
47407941 AAATTTTTGAATATTTTGAATATT
1 AAATTTTTGAATATTTTG-ATATT
47407965 TTGAATATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
67 12 0.14
68 71 0.86
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.47
Consensus pattern (67 bp):
AAATTTTTGAATATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAAT
AG
Found at i:47408047 original size:23 final size:23
Alignment explanation
Indices: 47408021--47408415 Score: 419
Period size: 23 Copynumber: 17.8 Consensus size: 23
47408011 ATTAATACCC
*
47408021 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
**
47408044 TTAAATTAAAAACCCTAACC-CC
1 TTAAATTAAAAACCCTAACCTAA
* *
47408066 TTAATTTAAAAATCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
47408089 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
47408112 TTAAATTAAAAACTCTAACC--C
1 TTAAATTAAAAACCCTAACCTAA
* *
47408133 TTAACTTAAAAA-TC-AACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
47408154 TTAAATTAAAAACCCTAACCT-C
1 TTAAATTAAAAACCCTAACCTAA
* *
47408176 TTAACTTAAAAACTCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
47408199 TTAAATTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCTAA
*
47408220 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
47408243 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
47408266 TTAAATTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCTAA
* *
47408287 TTAACTTAAAAACCCTAACTTAA
1 TTAAATTAAAAACCCTAACCTAA
*
47408310 TTTAATTAAAAACCCTAA---AA
1 TTAAATTAAAAACCCTAACCTAA
* * *
47408330 CCTTAACTTAAAAACACTAAACC--C
1 --TTAAATTAAAAACCCT-AACCTAA
* * *
47408354 TTAACTTAAAAATCCTAACC--C
1 TTAAATTAAAAACCCTAACCTAA
*
47408375 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
47408398 TTAAATTAAAAACCCTAA
1 TTAAATTAAAAACCCTAA
47408416 ACGAAATTAA
Statistics
Matches: 315, Mismatches: 40, Indels: 34
0.81 0.10 0.09
Matches are distributed among these distances:
19 4 0.01
20 4 0.01
21 83 0.26
22 65 0.21
23 159 0.50
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (23 bp):
TTAAATTAAAAACCCTAACCTAA
Found at i:47408218 original size:155 final size:156
Alignment explanation
Indices: 47408019--47408415 Score: 624
Period size: 155 Copynumber: 2.6 Consensus size: 156
47408009 CCATTAATAC
* * *
47408019 CCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCCTTAATTTAAAAATCCTAA
1 CCTTAACTTAAAAACACTAACCTAATTAAATTAAAAACCCTAA-CCCTTAACTTAAAAACCCTAA
* *
47408084 CCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACTCTAACCCTTAACTTAAAAA-TC-
65 CCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCT
*
47408147 AACCTAATTAAATTAAAAACCCT-AAC
130 AACCTAATTAAATTAAAAACCCTAAAA
*
47408173 CTCTTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAA
1 C-CTTAACTTAAAAACACTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAA
47408238 CCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCT
65 CCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCT
* *
47408303 AACTTAATTTAATTAAAAACCCTAAAA
130 AACCTAATTAAATTAAAAACCCTAAAA
* * *
47408330 CCTTAACTTAAAAACACTAAACC--CTTAACTTAAAAATCCTAACCCTTAACTTAAAAACCCTAA
1 CCTTAACTTAAAAACACT-AACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAA
47408393 CCTAATTAAATTAAAAACCCTAA
65 CCTAATTAAATTAAAAACCCTAA
47408416 ACGAAATTAA
Statistics
Matches: 226, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
154 80 0.35
155 102 0.45
156 37 0.16
157 7 0.03
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (156 bp):
CCTTAACTTAAAAACACTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAAC
CTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTA
ACCTAATTAAATTAAAAACCCTAAAA
Found at i:47408271 original size:67 final size:66
Alignment explanation
Indices: 47408017--47408415 Score: 456
Period size: 67 Copynumber: 6.0 Consensus size: 66
47408007 AACCATTAAT
** * *
47408017 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCCTTAATTTAAAAATCCT
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCAATTAAATTAAAAACCCT
47408082 A
66 A
* * * * *
47408083 ACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACTCTAACC-CTTAACTTAAAAATC
1 ACC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCAATTAAATTAAAAA-C
47408147 AACCTA
63 --CCTA
* * * *
47408153 A---TTAAATTAAAAACCCTAACCT-CTTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCC
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC-AATTAAATTAAAAACCC
47408214 TA
65 TA
47408216 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC-AATTAAATTAAAAACCC
47408281 TA
65 TA
* * * *
47408283 ACCCTTAACTTAAAAACCCTAACTTAATTTAATTAAAAACCCTAA--AACCTTAACTTAAAAACA
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCAA--TTAAATTAAAAACC
47408346 CTAA
64 CT-A
* * *
47408350 ACCCTTAACTTAAAAATCCTAACC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCC
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC-AATTAAATTAAAAACCC
47408413 TA
65 TA
47408415 A
1 A
47408416 ACGAAATTAA
Statistics
Matches: 292, Mismatches: 24, Indels: 35
0.83 0.07 0.10
Matches are distributed among these distances:
63 5 0.02
64 21 0.07
65 40 0.14
66 62 0.21
67 116 0.40
68 43 0.15
70 5 0.02
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (66 bp):
ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCAATTAAATTAAAAACCCT
A
Found at i:47408380 original size:199 final size:198
Alignment explanation
Indices: 47408017--47408415 Score: 583
Period size: 199 Copynumber: 2.0 Consensus size: 198
47408007 AACCATTAAT
** * *
47408017 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCCTTAATTTAAAAATCCT
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCAATTAAATTAAAAACCCT
* *
47408082 AACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACTCTAACCCTTAACTTAAAAATC
66 AACC-AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACCTTAACTTAAAAATC
*
47408147 AACCTAATTAAATTAAAAACCCTAACCTCTTAACTTAAAAACTCTAACCTAATTAAATTAAAAAC
130 AACCTAATTAAATTAAAAACCCTAACCTCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAAC
47408212 CCTA
195 CCTA
47408216 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC-AATTAAATTAAAAACCC
* * * *
47408281 TAACC-CTTAACTTAAAAACCCTAACTTAATTTAATTAAAAACCCTAAAACCTTAACTTAAAAA-
65 TAACCAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCT-AAACCTTAACTTAAAAAT
* *
47408344 C-A-CTAAACCCTTAACTTAAAAATCCTAACC-CTTAACTTAAAAACCCTAACCTAATTAAATTA
129 CAACCT-AA---TTAAATTAAAAACCCTAACCTCTTAACTTAAAAACCCTAACCTAATTAAATTA
47408406 AAAACCCTA
190 AAAACCCTA
47408415 A
1 A
47408416 ACGAAATTAA
Statistics
Matches: 181, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
196 2 0.01
197 3 0.02
198 36 0.20
199 104 0.57
200 36 0.20
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (198 bp):
ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCAATTAAATTAAAAACCCT
AACCAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACCTTAACTTAAAAATCA
ACCTAATTAAATTAAAAACCCTAACCTCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACC
CTA
Found at i:47408499 original size:17 final size:17
Alignment explanation
Indices: 47408479--47408548 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
47408469 CCTGGTACTA
47408479 ATAATTAATAATTTTAT
1 ATAATTAATAATTTTAT
*
47408496 ATAATTTGATAATTTTACT
1 ATAA-TTAATAATTTTA-T
* *
47408515 AATCATTAATACAATTTAT
1 -ATAATTAATA-ATTTTAT
*
47408534 -CAATTAATAATTTTA
1 ATAATTAATAATTTTA
47408549 CATTCACATA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 11 0.26
18 11 0.26
19 7 0.17
20 8 0.19
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (17 bp):
ATAATTAATAATTTTAT
Found at i:47408555 original size:115 final size:116
Alignment explanation
Indices: 47408420--47408662 Score: 391
Period size: 115 Copynumber: 2.1 Consensus size: 116
47408410 CCCTAAACGA
* * *
47408420 AATTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAAAAAATTT-CCTGGTACTAATAAT
1 AATTAATAATTTTACATTCACATAATGTTAGATTT-GAAAAAAAAATTTGACTGGTACTAACAAT
*
47408484 TAATAATTTTATATAATTTGATAA-TTTTACTAATCATTAATACAATTTATC
65 TAATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
* ***
47408535 AATTAATAATTTTACATTCACATAATGTTAGATTTGTAAAAACGTTTTGACTGGTACTAACAATT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGAAAAAAAAATTTGACTGGTACTAACAATT
47408600 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
66 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
47408651 AATTAATAATTT
1 AATTAATAATTT
47408663 CACAAACTTA
Statistics
Matches: 118, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
114 9 0.08
115 71 0.60
116 38 0.32
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (116 bp):
AATTAATAATTTTACATTCACATAATGTTAGATTTGAAAAAAAAATTTGACTGGTACTAACAATT
AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
Found at i:47411826 original size:17 final size:18
Alignment explanation
Indices: 47411793--47411826 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47411783 TGTTAACACT
*
47411793 TAAAATAATATTATATAG
1 TAAAATAATAGTATATAG
47411811 TAAAATAAT-GTATATA
1 TAAAATAATAGTATATA
47411827 CAAAAAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TAAAATAATAGTATATAG
Found at i:47414881 original size:123 final size:124
Alignment explanation
Indices: 47414546--47414923 Score: 614
Period size: 126 Copynumber: 3.0 Consensus size: 124
47414536 CCCAAACATG
* *
47414546 CTACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTTCACAAATTCTTCTCAAATAGCATCCTT
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTG
* *
47414611 CTAGAAGCGATTTTATACTATTTACTCAGAAACGTCAAAAAAATTTTATTTCTTCCATGAC
66 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA--TTATTTCTTCTATGAC
* *
47414672 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCTATTTTCACAAATTCTTCTCAAATAGCATCATG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTG
*
47414737 CTAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAATTATTTCTTCTATGAC
66 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCTATGAC
*
47414796 CTACTGTAGCAAAAGCGCGTCCACTAGGGCGCGA-TTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTG
* * *
47414860 CTAGAAGCGATTTTATACTATTTGATCAGAAACGTCAACTCAAAATTATTTCTTCTAGGAC
66 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA--AAAAATTATTTCTTCTATGAC
47414921 CTA
1 CTA
47414924 AAAACCCTAA
Statistics
Matches: 236, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
123 65 0.28
124 47 0.20
125 22 0.09
126 102 0.43
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTG
CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCTATGAC
Found at i:47415442 original size:60 final size:59
Alignment explanation
Indices: 47415330--47415493 Score: 170
Period size: 60 Copynumber: 2.8 Consensus size: 59
47415320 TAACATTTGG
* * * *
47415330 TACCTAAATTTGATATTTTTTCTTAATTTGGTACCTAAAC-TTTTTGTTGCCCAATTCGA
1 TACCTAAAATCGACATTTTTTC-TAATTTGGTACCTAAACTTTTTTGTGGCCCAATTCGA
* *
47415389 TACCTAAAATCGACACTTTTTTTCTAATTTGGTACCTAAACTTTTTTG-GGCCCAATTTGG
1 TACCTAAAATCGACA--TTTTTTCTAATTTGGTACCTAAACTTTTTTGTGGCCCAATTCGA
* * * * * * *
47415449 TACTTGAACTTGGCATTTTTCCTAATTTGGTACCTAAGCTTTTTT
1 TACCTAAAATCGACATTTTTTCTAATTTGGTACCTAAACTTTTTT
47415494 TTAGGTTCAA
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
58 28 0.31
59 12 0.13
60 36 0.40
61 13 0.15
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (59 bp):
TACCTAAAATCGACATTTTTTCTAATTTGGTACCTAAACTTTTTTGTGGCCCAATTCGA
Found at i:47416008 original size:31 final size:30
Alignment explanation
Indices: 47415971--47416070 Score: 118
Period size: 31 Copynumber: 3.4 Consensus size: 30
47415961 TACCAACTTA
*
47415971 AGAAAAAGTGTCAAATTTAAATATCAAATT
1 AGAAAAAATGTCAAATTTAAATATCAAATT
*
47416001 AGAAAAAAATGTCAAATTTAGATATCAAATT
1 AG-AAAAAATGTCAAATTTAAATATCAAATT
* *
47416032 AGACCAAAA--T-AAATTTAAATACCAAATT
1 AGA-AAAAATGTCAAATTTAAATATCAAATT
47416060 A-AAAAAATGTC
1 AGAAAAAATGTC
47416071 GGTTCCAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.07
27 1 0.02
28 18 0.31
29 1 0.02
30 3 0.05
31 32 0.54
ACGTcount: A:0.56, C:0.09, G:0.08, T:0.27
Consensus pattern (30 bp):
AGAAAAAATGTCAAATTTAAATATCAAATT
Found at i:47417663 original size:3 final size:3
Alignment explanation
Indices: 47417655--47417714 Score: 52
Period size: 3 Copynumber: 19.7 Consensus size: 3
47417645 TATATATTAC
* *
47417655 ATT ATT ATT ACTGA ATT ATT ATT AGT -TT ATT ATT ATT A-T ATT ATAT
1 ATT ATT ATT A-T-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
47417701 ATT TTT ATT ATT AT
1 ATT ATT ATT ATT AT
47417715 ACTTACCGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 3 0.07
3 37 0.80
4 5 0.11
5 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:47417698 original size:14 final size:14
Alignment explanation
Indices: 47417669--47417714 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
47417659 TTATTACTGA
47417669 ATTATTATTAGT-TT
1 ATTATTATTA-TATT
47417683 ATTATTATTATATT
1 ATTATTATTATATT
47417697 ATATATT-TT-TATT
1 AT-TATTATTATATT
47417710 ATTAT
1 ATTAT
47417715 ACTTACCGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.10
13 7 0.23
14 16 0.53
15 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:47418046 original size:5 final size:6
Alignment explanation
Indices: 47418032--47418081 Score: 55
Period size: 6 Copynumber: 7.5 Consensus size: 6
47418022 ATGTTTGTAA
47418032 TTTTAT TTTTAT TTTTAT TTTGTAT AAATTTTATT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTT-TAT ---TTTTA-T TTTTAT TTTTAT TTT
47418082 GTTATTTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 25 0.64
7 8 0.21
9 2 0.05
10 4 0.10
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:47425799 original size:21 final size:21
Alignment explanation
Indices: 47425773--47425812 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
47425763 AGAACATGCT
*
47425773 CTTTAGCGGCGTTTTTTTTAA
1 CTTTAGCGGCATTTTTTTTAA
47425794 CTTTAGCGGCATTTTTTTT
1 CTTTAGCGGCATTTTTTTT
47425813 CTAAGCGCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.55
Consensus pattern (21 bp):
CTTTAGCGGCATTTTTTTTAA
Found at i:47426291 original size:21 final size:21
Alignment explanation
Indices: 47426267--47426306 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
47426257 TTCTTTTGAA
*
47426267 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
47426288 CCTCTGCTTCCCTCGCTGC
1 CCTCTGCTTCCCTCGCTGC
47426307 TGCATCTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.03, C:0.47, G:0.17, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:47426370 original size:87 final size:87
Alignment explanation
Indices: 47426202--47426361 Score: 230
Period size: 87 Copynumber: 1.8 Consensus size: 87
47426192 TTCTGCTCTG
* * * * *
47426202 CTCTGCTTCTCTTGCTGCAGCCTCTACTTTAAGTTTTAGCTGCAGTTCTTCATATTTCTTTTGAA
1 CTCTGCTTCCCTCGCTGCAGCATCTACTTTAAGTTGTAGCTGCAGTTCTTCATATTTCCTTTGAA
** *
47426267 CCTCTGCTTCTCTCGCTGCAGC
66 CCTCAACTTCGCTCGCTGCAGC
* *
47426289 CTCTGCTTCCCTCGCTGCTGCATCTACTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
1 CTCTGCTTCCCTCGCTGCAGCATCTACTTTAAGTTGTAGCTGCAGTTCTTCATATTTCCTTTGAA
47426354 CCTCAACT
66 CCTCAACT
47426362 GTGGTCGCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 64 1.00
ACGTcount: A:0.14, C:0.29, G:0.15, T:0.41
Consensus pattern (87 bp):
CTCTGCTTCCCTCGCTGCAGCATCTACTTTAAGTTGTAGCTGCAGTTCTTCATATTTCCTTTGAA
CCTCAACTTCGCTCGCTGCAGC
Found at i:47428203 original size:20 final size:20
Alignment explanation
Indices: 47428149--47428208 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
47428139 CGTTAAAATG
* * *
47428149 TAAAATCTAAACCTTAAACC
1 TAAACTCTAAGCCCTAAACC
* *
47428169 TCAATCTCCAAGCCCTAAACC
1 T-AAACTCTAAGCCCTAAACC
*
47428190 TAAACTCTAAGCCCAAAAC
1 TAAACTCTAAGCCCTAAAC
47428209 ACAAAAATGT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (20 bp):
TAAACTCTAAGCCCTAAACC
Found at i:47428883 original size:133 final size:133
Alignment explanation
Indices: 47428572--47428924 Score: 428
Period size: 133 Copynumber: 2.6 Consensus size: 133
47428562 TTTAACATTT
* * * **
47428572 CGCCACTAAAG-CATAAAAAGGAAACAACAAAACGGTACCGTTTTGCTCAAAAATTTTCCTCAAA
1 CGCCACTAAAGAAAT-AAAATGAAACAATAAAACGGTA-CGTTTTGCTCAAATTTTTTCCTCAAA
* * * *
47428636 TTAGATATCTTTACCGGCGTTTCTCCAATAATGCCACTATATCCCAATATTTGCGGCGTTTTTTA
64 TTAGATATCTTTACCGGCGTTTCTCCAATAACGCCACCATATCCCAATATTTCCGGCATTTTTTA
47428701 CAAGG
129 CAAGG
* *
47428706 CACCACTAAAGAAATAAAATGAAGCAATAAAACGGTAGCGTTTTG-TCCAAATTTTTTCCTCAAA
1 CGCCACTAAAGAAATAAAATGAAACAATAAAACGGTA-CGTTTTGCT-CAAATTTTTTCCTCAAA
* * * *
47428770 TTAGATATCTTTACCGGCGTTTCTCTGAA-AACGCCGCCA-AT-TCAATCTTTTCCGGCATTTTT
64 TTAGATATCTTTACCGGCGTTTCTC-CAATAACGCCACCATATCCCAAT-ATTTCCGGCATTTTT
*
47428832 TACAATG
127 TACAAGG
* *
47428839 CGCCACTAAAGAAATAAAATGAAACAATAAAACGGTACTATTTTGCTCAGATTTTTTCCTCAAAT
1 CGCCACTAAAGAAATAAAATGAAACAATAAAACGGTAC-GTTTTGCTCAAATTTTTTCCTCAAAT
* *
47428904 TTGTTATCTTTACCGGCGTTT
65 TAGATATCTTTACCGGCGTTT
47428925 TTGTTGAAGC
Statistics
Matches: 190, Mismatches: 23, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
132 5 0.03
133 97 0.51
134 84 0.44
135 4 0.02
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32
Consensus pattern (133 bp):
CGCCACTAAAGAAATAAAATGAAACAATAAAACGGTACGTTTTGCTCAAATTTTTTCCTCAAATT
AGATATCTTTACCGGCGTTTCTCCAATAACGCCACCATATCCCAATATTTCCGGCATTTTTTACA
AGG
Found at i:47435571 original size:21 final size:21
Alignment explanation
Indices: 47435526--47435571 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
47435516 AATTCTCAAT
* **
47435526 ATTTATATTTTTTTAATTTTT
1 ATTTATATTTTTTTAAGTTAA
*
47435547 ATTTTTATTTTTTTAAGTTAA
1 ATTTATATTTTTTTAAGTTAA
47435568 ATTT
1 ATTT
47435572 GACCATTAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
ATTTATATTTTTTTAAGTTAA
Found at i:47436853 original size:18 final size:19
Alignment explanation
Indices: 47436827--47436864 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
47436817 AAATATTTTT
47436827 ATAACTTTTT-ATTTTTAA
1 ATAACTTTTTAATTTTTAA
*
47436845 ATAATTTTTTAATTTTTAA
1 ATAACTTTTTAATTTTTAA
47436864 A
1 A
47436865 ATTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
ATAACTTTTTAATTTTTAA
Found at i:47441092 original size:15 final size:15
Alignment explanation
Indices: 47441047--47441095 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
47441037 TTAGTTAAAC
47441047 TTAATTAATCTAAAA-
1 TTAATTAA-CTAAAAT
*
47441062 TAAATTAACTAAAAT
1 TTAATTAACTAAAAT
47441077 TTAATTAACTAAAAT
1 TTAATTAACTAAAAT
47441092 TTAA
1 TTAA
47441096 GCTTAATTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 6 0.19
15 25 0.81
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAATTAACTAAAAT
Found at i:47451762 original size:17 final size:16
Alignment explanation
Indices: 47451725--47451763 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
47451715 AATAAACAAT
47451725 TAAA-TAAATTGGAAA
1 TAAATTAAATTGGAAA
47451740 TAAAATTAAATTGAGAAA
1 T-AAATTAAATTG-GAAA
47451758 TAAATT
1 TAAATT
47451764 TGGATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 12 0.57
18 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (16 bp):
TAAATTAAATTGGAAA
Found at i:47452929 original size:61 final size:60
Alignment explanation
Indices: 47452859--47452972 Score: 147
Period size: 61 Copynumber: 1.9 Consensus size: 60
47452849 ATTCTAAATC
* * * *
47452859 TAAAAAATTCAACAAAATTAGCTCTCAATGTTTACAAAAGTTTTCATTTTAGTTCGAATTG
1 TAAAAAATTCAACAAAATTAGCCCTCAATATTTACAAAA-ATTTCAATTTAGTTCGAATTG
* * * *
47452920 TAAATAATTCAATAAATTTATCCCTCAATATTTACAAAAATTTCAATTTAGTT
1 TAAAAAATTCAACAAAATTAGCCCTCAATATTTACAAAAATTTCAATTTAGTT
47452973 GTAATTCTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
60 12 0.27
61 33 0.73
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.39
Consensus pattern (60 bp):
TAAAAAATTCAACAAAATTAGCCCTCAATATTTACAAAAATTTCAATTTAGTTCGAATTG
Found at i:47454027 original size:17 final size:17
Alignment explanation
Indices: 47453998--47454031 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
47453988 TAGTTTACCC
47453998 TTTAATTTATAAATTTT
1 TTTAATTTATAAATTTT
47454015 TTTATATTT-TAAATTTT
1 TTTA-ATTTATAAATTTT
47454032 ATAAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTAATTTATAAATTTT
Found at i:47454848 original size:2 final size:2
Alignment explanation
Indices: 47454841--47454885 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
47454831 ATATTAGTTA
47454841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47454883 AT A
1 AT A
47454886 GTTAGTAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47460101 original size:5 final size:5
Alignment explanation
Indices: 47460091--47460116 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
47460081 GAGATGAAAT
47460091 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
47460117 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:47460882 original size:31 final size:30
Alignment explanation
Indices: 47460847--47460906 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
47460837 GGAGGTGGGA
*
47460847 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
47460878 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
47460907 CAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:47461133 original size:9 final size:9
Alignment explanation
Indices: 47461119--47461155 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
47461109 TATAGTTTGA
47461119 TATTCGAAT
1 TATTCGAAT
47461128 TATTCGAAT
1 TATTCGAAT
*
47461137 TATTCGAGT
1 TATTCGAAT
47461146 TATTCGAAT
1 TATTCGAAT
47461155 T
1 T
47461156 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:47472135 original size:9 final size:9
Alignment explanation
Indices: 47472121--47472160 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
47472111 GATCAACTAA
47472121 AATTAAATT
1 AATTAAATT
47472130 AATTAAATT
1 AATTAAATT
*
47472139 AATCAAATT
1 AATTAAATT
47472148 AATTAAAATT
1 AATT-AAATT
47472158 AAT
1 AAT
47472161 ATGATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (9 bp):
AATTAAATT
Found at i:47472636 original size:11 final size:11
Alignment explanation
Indices: 47472561--47472636 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
47472551 TTCTAAAAAA
*
47472561 TAATATTATTT
1 TAATATTAATT
47472572 TAATAGGTTAATAT
1 TAATA--TTAAT-T
47472586 TAA-ATTTAATT
1 TAATA-TTAATT
*
47472597 TAATATTGATCT
1 TAATATTAAT-T
47472609 TAATATT-ATT
1 TAATATTAATT
47472619 T--TATTAATT
1 TAATATTAATT
47472628 TAATATTAA
1 TAATATTAA
47472637 AGTGATTATT
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
8 4 0.07
9 4 0.07
10 2 0.04
11 21 0.39
12 14 0.26
13 5 0.09
14 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (11 bp):
TAATATTAATT
Found at i:47472669 original size:37 final size:34
Alignment explanation
Indices: 47472561--47472671 Score: 107
Period size: 37 Copynumber: 3.0 Consensus size: 34
47472551 TTCTAAAAAA
47472561 TAATATTATTTTAATAGGTTAATATTAAATTTAAT-T
1 TAATATTATTTTAATA--TTAA-ATTAAATTTAATAT
* **
47472597 TAATATTGATCTTAATATTATTTTATTAATTTAATAT
1 TAATATT-ATTTTAATATTAAATTA--AATTTAATAT
47472634 TAAAGTGATTATTTTAATATTAAATTAAATTTAATAT
1 T-AA-T-ATTATTTTAATATTAAATTAAATTTAATAT
47472671 T
1 T
47472672 TATCTTGTAG
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
34 3 0.05
35 3 0.05
36 15 0.24
37 21 0.34
38 2 0.03
39 15 0.24
40 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (34 bp):
TAATATTATTTTAATATTAAATTAAATTTAATAT
Found at i:47472860 original size:25 final size:26
Alignment explanation
Indices: 47472825--47472879 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
47472815 TGTAGAAAGA
47472825 AAAATTCTCTAAAGATATTATTTTAG-
1 AAAATTCTCTAAAGATATT-TTTTAGT
*
47472851 AAAATT-TCTAGAGATATTTTTTAGT
1 AAAATTCTCTAAAGATATTTTTTAGT
47472876 AAAA
1 AAAA
47472880 GTTTAGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 6 0.22
25 15 0.56
26 6 0.22
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (26 bp):
AAAATTCTCTAAAGATATTTTTTAGT
Found at i:47472886 original size:24 final size:25
Alignment explanation
Indices: 47472832--47472888 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
47472822 AGAAAAATTC
* *
47472832 TCTAAAGATATTATTTTAGAAAATT
1 TCTAGAGATATTATTTTAGAAAAGT
47472857 TCTAGAGATATT-TTTTAGTAAAAGT
1 TCTAGAGATATTATTTTAG-AAAAGT
47472882 T-TAGAGA
1 TCTAGAGA
47472889 AATTGCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (25 bp):
TCTAGAGATATTATTTTAGAAAAGT
Found at i:47476269 original size:2 final size:2
Alignment explanation
Indices: 47476216--47476252 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
47476206 AACTACTTAC
47476216 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47476253 TAAGAGTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47477545 original size:26 final size:26
Alignment explanation
Indices: 47477509--47477567 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
47477499 CTAAGCCTAA
* * *
47477509 GCGCCGCATGCCTAGGCTCCAGCGCT
1 GCGCCGCATGCCCAGGCTCCAACGCC
47477535 GCGCCGCATGCCCAGGCTCCAACGCC
1 GCGCCGCATGCCCAGGCTCCAACGCC
47477561 GCGCCGC
1 GCGCCGC
47477568 CGCTCTCCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.12, C:0.47, G:0.31, T:0.10
Consensus pattern (26 bp):
GCGCCGCATGCCCAGGCTCCAACGCC
Found at i:47486699 original size:18 final size:18
Alignment explanation
Indices: 47486673--47486732 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 18
47486663 ATGTTTTAAT
*
47486673 ATCATCAAAATTAAGAAC
1 ATCAACAAAATTAAGAAC
*
47486691 ATCAAC--AA--AAGAAT
1 ATCAACAAAATTAAGAAC
* *
47486705 ATCATCAACATTAAGAAC
1 ATCAACAAAATTAAGAAC
47486723 ATCAACAAAA
1 ATCAACAAAA
47486733 GTTTTCTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
14 10 0.32
16 3 0.10
18 18 0.58
ACGTcount: A:0.58, C:0.18, G:0.05, T:0.18
Consensus pattern (18 bp):
ATCAACAAAATTAAGAAC
Found at i:47486711 original size:32 final size:32
Alignment explanation
Indices: 47486670--47486733 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
47486660 GAAATGTTTT
47486670 AATATCATCAAAATTAAGAACATCAACAAAAG
1 AATATCATCAAAATTAAGAACATCAACAAAAG
*
47486702 AATATCATCAACATTAAGAACATCAACAAAAG
1 AATATCATCAAAATTAAGAACATCAACAAAAG
47486734 TTTTCTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.58, C:0.17, G:0.06, T:0.19
Consensus pattern (32 bp):
AATATCATCAAAATTAAGAACATCAACAAAAG
Found at i:47486728 original size:15 final size:15
Alignment explanation
Indices: 47486675--47486729 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
47486665 GTTTTAATAT
*
47486675 CATCAAAATTAAGAA
1 CATCAACATTAAGAA
*
47486690 CATCAACA-AAAGAATA
1 CATCAACATTAAG-A-A
47486706 TCATCAACATTAAGAA
1 -CATCAACATTAAGAA
47486722 CATCAACA
1 CATCAACA
47486730 AAAGTTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 3 0.09
15 16 0.48
16 2 0.06
17 9 0.27
18 3 0.09
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.18
Consensus pattern (15 bp):
CATCAACATTAAGAA
Found at i:47490808 original size:22 final size:23
Alignment explanation
Indices: 47490772--47490815 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
47490762 TAAAATTGAA
47490772 TTAAATATTAATA-TTAAAAATT
1 TTAAATATTAATATTTAAAAATT
* *
47490794 TTAAATCTTATTATTTAAAAAT
1 TTAAATATTAATATTTAAAAAT
47490816 AAAATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAATATTAATATTTAAAAATT
Found at i:47494710 original size:38 final size:37
Alignment explanation
Indices: 47494656--47494776 Score: 224
Period size: 37 Copynumber: 3.2 Consensus size: 37
47494646 CTTCTTCGAG
47494656 TGTTTGAAACGATTCAGTCTACTGGTGATTTCTTTTA
1 TGTTTGAAACGATTCAGTCTACTGGTGATTTCTTTTA
47494693 TGTTTGAAACGATTTCAGTCTACTGGTGATTTCTTTTA
1 TGTTTGAAACGA-TTCAGTCTACTGGTGATTTCTTTTA
47494731 TGTTTGAAACGATTCAGTCTACTGGTGATTTCTTTTA
1 TGTTTGAAACGATTCAGTCTACTGGTGATTTCTTTTA
*
47494768 TCTTTGAAA
1 TGTTTGAAA
47494777 TCATCTTAGT
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
37 45 0.55
38 37 0.45
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (37 bp):
TGTTTGAAACGATTCAGTCTACTGGTGATTTCTTTTA
Found at i:47497144 original size:16 final size:16
Alignment explanation
Indices: 47497091--47497148 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
47497081 ACATTAATAT
47497091 AATATAATT-TTAAAAA
1 AATA-AATTATTAAAAA
**
47497107 AATAATTATTATTTAATCA
1 AATAA--ATTA-TTAAAAA
47497126 AATAAATTATTAAAAA
1 AATAAATTATTAAAAA
47497142 AATAAAT
1 AATAAAT
47497149 CCTTACATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 1 0.03
16 16 0.47
17 7 0.21
19 10 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAAATTATTAAAAA
Done.