Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_pilon, whole genome shotgun sequence
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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 62
Found at i:3464894 original size:21 final size:20
Alignment explanation
Indices: 3464833--3464894 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
3464823 ATTTACTTAT
3464833 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
* *
3464854 TCGCAACT-CGAAATTAGAAAA
1 TCGC-ATTGCG-AATTGGAAAA
3464875 TCGCATTGCGAATCTGGAAA
1 TCGCATTGCGAAT-TGGAAA
3464895 CTGATTTGCG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 5 0.15
21 22 0.67
22 6 0.18
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:3466929 original size:63 final size:63
Alignment explanation
Indices: 3466830--3466954 Score: 196
Period size: 63 Copynumber: 2.0 Consensus size: 63
3466820 TATTGAAAAT
* *
3466830 CAAGTTGATAAGTCGGAGGAGCCACCGGAAAAGAAACAATGCCTTGAAACAGATACATCAAAC
1 CAAGTAGATAAGTCGGAGGAGCCACCAGAAAAGAAACAATGCCTTGAAACAGATACATCAAAC
* * * *
3466893 CAAGTAGATAAGTTGGAGGAGCCATCAGCAAAGAAACAATGTCTTGAAACAGATACATCAAA
1 CAAGTAGATAAGTCGGAGGAGCCACCAGAAAAGAAACAATGCCTTGAAACAGATACATCAAA
3466955 GAGTGCAACC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (63 bp):
CAAGTAGATAAGTCGGAGGAGCCACCAGAAAAGAAACAATGCCTTGAAACAGATACATCAAAC
Found at i:3469141 original size:20 final size:21
Alignment explanation
Indices: 3469103--3469144 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3469093 AAAAGAGTAG
*
3469103 AAAATGTTAAATAAAATAAAA
1 AAAATATTAAATAAAATAAAA
*
3469124 AAAATATTAAAT-ACATAAAA
1 AAAATATTAAATAAAATAAAA
3469144 A
1 A
3469145 TGGGAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAATATTAAATAAAATAAAA
Found at i:3469227 original size:37 final size:39
Alignment explanation
Indices: 3469146--3469230 Score: 95
Period size: 37 Copynumber: 2.2 Consensus size: 39
3469136 ACATAAAAAT
* *
3469146 GGGAAAAAATAGAAAATAAAAATAAAATAATAAATCGAA
1 GGGAAAAAATAGAAAATAAAAATAAAATAACAAATCAAA
* * *
3469185 TGGAAAAAGTA-AAAAT-AATA-AAAATAAACAAATCAAA
1 GGGAAAAAATAGAAAATAAAAATAAAAT-AACAAATCAAA
3469222 GGGAAAAAA
1 GGGAAAAAA
3469231 ACAAACTGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
36 5 0.13
37 19 0.50
38 5 0.13
39 9 0.24
ACGTcount: A:0.69, C:0.04, G:0.13, T:0.14
Consensus pattern (39 bp):
GGGAAAAAATAGAAAATAAAAATAAAATAACAAATCAAA
Found at i:3471286 original size:106 final size:106
Alignment explanation
Indices: 3471101--3472241 Score: 1848
Period size: 106 Copynumber: 11.0 Consensus size: 106
3471091 TATTGTTCCA
* ** *** *
3471101 AGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGGTTTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
3471166 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** ** *
3471207 AGTCCAATATCCTTCGCAGTGAAGTTGAAATTGGCTCTGAGTTTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
3471272 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
3471313 AGTCC-A-ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
3471376 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
3471417 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
*
3471482 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
3471523 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
3471588 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
3471629 AGTCCAATATCCTTCTTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
3471694 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
3471735 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
*
3471800 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
3471841 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
3471906 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
3471947 AGTCCAATATCCTTCGTTGTGAAGTTGAAA-----T-TG-----G-GAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
3472000 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
3472041 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
3472106 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
3472147 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG----G--A---AG---TTATTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
* *
3472200 CAGCGGTCCCTTCGTCGTGAAGTTAAACTTGTGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
3472241 A
1 A
3472242 AGCTGCAAAA
Statistics
Matches: 995, Mismatches: 26, Indels: 40
0.94 0.02 0.04
Matches are distributed among these distances:
94 142 0.14
95 1 0.00
97 2 0.00
99 1 0.00
100 5 0.01
101 1 0.00
102 1 0.00
104 99 0.10
105 3 0.00
106 740 0.74
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:3471975 original size:43 final size:43
Alignment explanation
Indices: 3471914--3472069 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 43
3471904 ACCAGCGGTC
3471914 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** ***
3471957 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
3472007 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
3472051 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
3472070 ATTGGCTCTG
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
43 40 0.48
44 1 0.01
45 3 0.04
46 7 0.08
48 7 0.08
49 3 0.04
50 1 0.01
51 22 0.26
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:3472039 original size:94 final size:94
Alignment explanation
Indices: 3471878--3472241 Score: 566
Period size: 94 Copynumber: 3.7 Consensus size: 94
3471868 AAATTGGCTC
* *
3471878 TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
3471943 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
3471972 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
3472037 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
3472066 TGAAATTGGCTCTGAAATTGAGAAATGGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1 TGAAATTGG----GAAA-T------T-GTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
3472131 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
54 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* * * *
3472172 TGAAATTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGTGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
3472237 CTGGA
66 CTGGA
3472242 AGCTGCAAAA
Statistics
Matches: 252, Mismatches: 6, Indels: 24
0.89 0.02 0.09
Matches are distributed among these distances:
94 153 0.61
95 1 0.00
98 4 0.02
99 1 0.00
101 1 0.00
102 3 0.01
105 1 0.00
106 88 0.35
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (94 bp):
TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGT
Found at i:3475790 original size:11 final size:11
Alignment explanation
Indices: 3475756--3475798 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
3475746 AAAAGAGTAG
*
3475756 AAAATGTTAAA
1 AAAATATTAAA
3475767 TAAAATA--AAA
1 -AAAATATTAAA
3475777 AAAATATTAAA
1 AAAATATTAAA
3475788 AAAATATTAAA
1 AAAATATTAAA
3475799 TACATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 6 0.21
10 3 0.11
11 14 0.50
12 5 0.18
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (11 bp):
AAAATATTAAA
Found at i:3475891 original size:37 final size:39
Alignment explanation
Indices: 3475810--3475894 Score: 95
Period size: 37 Copynumber: 2.2 Consensus size: 39
3475800 ACATAAAAAT
* *
3475810 GGGAAAAAATAGAAAATAAAAATAAAATAATAAATCGAA
1 GGGAAAAAATAGAAAATAAAAATAAAATAACAAATCAAA
* * *
3475849 TGGAAAAAGTA-AAAAT-AATA-AAAATAAACAAATCAAA
1 GGGAAAAAATAGAAAATAAAAATAAAAT-AACAAATCAAA
3475886 GGGAAAAAA
1 GGGAAAAAA
3475895 ACAAACTGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
36 5 0.13
37 19 0.50
38 5 0.13
39 9 0.24
ACGTcount: A:0.69, C:0.04, G:0.13, T:0.14
Consensus pattern (39 bp):
GGGAAAAAATAGAAAATAAAAATAAAATAACAAATCAAA
Found at i:3478018 original size:61 final size:61
Alignment explanation
Indices: 3477935--3478058 Score: 203
Period size: 61 Copynumber: 2.0 Consensus size: 61
3477925 TTTATTTAAA
* * *
3477935 ATTATGTATCCGTGTTAGTTTGTTTAATGTTCGTAAACAAGCTTATATAGCGTTCACTAAC
1 ATTACGTAGCCGTGTTAGTTTGTTTAATGTTCGTAAACAAGCTCATATAGCGTTCACTAAC
* *
3477996 ATTACGTAGCCGTGTTAGTTTGTTTAATGTTCGTAAACAAGCTCATTTAGTGTTCACTAAC
1 ATTACGTAGCCGTGTTAGTTTGTTTAATGTTCGTAAACAAGCTCATATAGCGTTCACTAAC
3478057 AT
1 AT
3478059 CTTAGCATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (61 bp):
ATTACGTAGCCGTGTTAGTTTGTTTAATGTTCGTAAACAAGCTCATATAGCGTTCACTAAC
Found at i:3491748 original size:42 final size:42
Alignment explanation
Indices: 3491689--3491808 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
3491679 TTTCCCCGGA
*
3491689 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTGGTTTTCCGGAAAATGTT
*
3491731 TTCCCGTGTTTGTTTCACGTAATTGGTTTTCCGAAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTGGTTTTCCGGAAAATGTT
*
3491773 TTCCAGTGTTTGTTTCACGTAATTGGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTGGTTTTCCGGAA
3491809 CGTAATTCAT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.45
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTGGTTTTCCGGAAAATGTT
Found at i:3492027 original size:22 final size:23
Alignment explanation
Indices: 3491997--3492040 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3491987 TTTATTTATT
3491997 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
3492020 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
3492041 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:3492059 original size:36 final size:34
Alignment explanation
Indices: 3491989--3492112 Score: 109
Period size: 36 Copynumber: 3.7 Consensus size: 34
3491979 ATTATTTATT
* *
3491989 TATT-TATTTATTAATATT--TATAATAAT-ATAA
1 TATTATATTT-TTAATATTAATAAAATAATAATTA
3492020 TATTATATTTTTAATATTATATAAAATAATCAATTA
1 TATTATATTTTTAATATTA-ATAAAATAAT-AATTA
*
3492056 TATTATATTTTT-ATTTTAATAATATATAATAATT-
1 TATTATATTTTTAATATTAATAA-A-ATAATAATTA
*
3492090 T-TTATATATTTAATAATTAATAA
1 TATTATATTTTTAAT-ATTAATAA
3492113 TATTTTTATA
Statistics
Matches: 78, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
31 12 0.15
32 5 0.06
33 9 0.12
34 15 0.19
35 17 0.22
36 20 0.26
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (34 bp):
TATTATATTTTTAATATTAATAAAATAATAATTA
Found at i:3492103 original size:25 final size:26
Alignment explanation
Indices: 3492063--3492133 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 26
3492053 TTATATTATA
3492063 TTTT-TATTTTAATA-ATATATAATAAT
1 TTTTATATTTTAATATATA-ATAAT-AT
3492089 TTTTATATATTTAATA-ATTAATAATAT
1 TTTTATAT-TTTAATATA-TAATAATAT
3492116 TTTTATATTTTAATATAT
1 TTTTATATTTTAATATAT
3492134 TTTAATAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
26 12 0.29
27 14 0.34
28 13 0.32
29 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTATATTTTAATATATAATAATAT
Found at i:3492110 original size:35 final size:36
Alignment explanation
Indices: 3492071--3492141 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 36
3492061 TATTTTTATT
*
3492071 TTAATAATATATAATA-ATTTTTATATA-TTTAATAA
1 TTAATAATAT-TAATATATTTTAATATATTTTAATAA
**
3492106 TTAATAATATTTTTATATTTTAATATATTTTAATAA
1 TTAATAATATTAATATATTTTAATATATTTTAATAA
3492142 AGATATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 3 0.10
35 20 0.65
36 8 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (36 bp):
TTAATAATATTAATATATTTTAATATATTTTAATAA
Found at i:3492120 original size:19 final size:18
Alignment explanation
Indices: 3492082--3492141 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
3492072 TAATAATATA
* * *
3492082 TAATAATTTTTATATATT
1 TAATAATTATAATATTTT
3492100 TAATAATTAATAATATTTT
1 TAATAATT-ATAATATTTT
*
3492119 T-AT-ATTTTAATATATTT
1 TAATAATTATAATAT-TTT
3492136 TAATAA
1 TAATAA
3492142 AGATATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
16 6 0.18
17 7 0.21
18 12 0.35
19 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATAATTATAATATTTT
Found at i:3492137 original size:10 final size:10
Alignment explanation
Indices: 3492067--3492140 Score: 56
Period size: 10 Copynumber: 8.0 Consensus size: 10
3492057 ATTATATTTT
3492067 TATTTTAATA
1 TATTTTAATA
*
3492077 -ATATATAATA
1 TAT-TTTAATA
*
3492087 -ATTTTTATA
1 TATTTTAATA
3492096 TA-TTTAATA
1 TATTTTAATA
3492105 -A--TTAATAA
1 TATTTTAAT-A
3492113 TATTTT--TA
1 TATTTTAATA
3492121 TATTTTAATA
1 TATTTTAATA
3492131 TATTTTAATA
1 TATTTTAATA
3492141 AAGATATTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
7 5 0.10
8 9 0.17
9 15 0.29
10 21 0.40
11 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATTTTAATA
Found at i:3492162 original size:23 final size:23
Alignment explanation
Indices: 3492136--3492180 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3492126 TAATATATTT
3492136 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
3492159 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
3492181 ATATATACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:3492285 original size:28 final size:28
Alignment explanation
Indices: 3492235--3492294 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 28
3492225 TTTATTTCAC
*
3492235 TAAAATATACAAAATTAATATTTTATTAA
1 TAAAATATACAAAATTAATA-TTTAATAA
*
3492264 TAAAATTATA-AAAA-TACTATTTAATAA
1 TAAAA-TATACAAAATTAATATTTAATAA
3492291 TAAA
1 TAAA
3492295 TAAGTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 11 0.39
28 4 0.14
29 9 0.32
30 4 0.14
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAAATATACAAAATTAATATTTAATAA
Found at i:3492478 original size:14 final size:14
Alignment explanation
Indices: 3492445--3492472 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3492435 AAATGTAATT
3492445 CATTTTACGGAAAA
1 CATTTTACGGAAAA
3492459 CATTTTACGGAAAA
1 CATTTTACGGAAAA
3492473 GGTTTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
CATTTTACGGAAAA
Found at i:3492521 original size:15 final size:15
Alignment explanation
Indices: 3492503--3492566 Score: 78
Period size: 15 Copynumber: 4.3 Consensus size: 15
3492493 CATTTTCCAG
3492503 AATTCAAATTTCAGT
1 AATTCAAATTTCAGT
*
3492518 AATTCAAATTCCAGT
1 AATTCAAATTTCAGT
*
3492533 AATTC-ATTTTCCAGT
1 AATTCAAATTT-CAGT
3492548 AATTCAAA-TTCTAGT
1 AATTCAAATTTC-AGT
3492563 AATT
1 AATT
3492567 TATTTTCTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
14 4 0.10
15 37 0.88
16 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (15 bp):
AATTCAAATTTCAGT
Found at i:3492548 original size:30 final size:30
Alignment explanation
Indices: 3492488--3492573 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
3492478 TCCATAAATT
** *
3492488 TAATTCATTTTCCAG-AATTCAAATTT-CAG
1 TAATTCAAATTCCAGTAATTC-ATTTTCCAG
3492517 TAATTCAAATTCCAGTAATTCATTTTCCAG
1 TAATTCAAATTCCAGTAATTCATTTTCCAG
* *
3492547 TAATTCAAATTCTAGTAATTTATTTTC
1 TAATTCAAATTCCAGTAATTCATTTTC
3492574 TGGAAAACCA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
29 17 0.34
30 33 0.66
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (30 bp):
TAATTCAAATTCCAGTAATTCATTTTCCAG
Found at i:3492574 original size:15 final size:15
Alignment explanation
Indices: 3492488--3492574 Score: 70
Period size: 15 Copynumber: 5.9 Consensus size: 15
3492478 TCCATAAATT
*
3492488 TAATTCATTTTCCAG
1 TAATTCATTTTCTAG
*
3492503 -AATTCAAATTTC-AG
1 TAATTC-ATTTTCTAG
** *
3492517 TAATTCAAATTCCAG
1 TAATTCATTTTCTAG
*
3492532 TAATTCATTTTCCAG
1 TAATTCATTTTCTAG
**
3492547 TAATTCAAATTCTAG
1 TAATTCATTTTCTAG
*
3492562 TAATTTATTTTCT
1 TAATTCATTTTCT
3492575 GGAAAACCAA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
14 12 0.20
15 47 0.80
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (15 bp):
TAATTCATTTTCTAG
Found at i:3492790 original size:2 final size:2
Alignment explanation
Indices: 3492785--3492809 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3492775 TTTTTTTTAC
3492785 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 T
3492810 TCTTAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3496374 original size:21 final size:21
Alignment explanation
Indices: 3496349--3496392 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3496339 CCGGAGGAGG
*
3496349 AGGAGGAGCACGAGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
* *
3496370 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
3496391 AG
1 AG
3496393 CTCCCGAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.41, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:3497419 original size:13 final size:13
Alignment explanation
Indices: 3497391--3497429 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
3497381 TGGGCAATGT
*
3497391 TTTGAAAA-ACTA
1 TTTGAAAATAATA
3497403 TTTGAAAATAATA
1 TTTGAAAATAATA
*
3497416 TTTGTAAATAATA
1 TTTGAAAATAATA
3497429 T
1 T
3497430 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:3497984 original size:24 final size:24
Alignment explanation
Indices: 3497964--3498026 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
3497954 GCATCAACAT
3497964 GATGAAGCGATGCACATTCAAAGG
1 GATGAAGCGATGCACATTCAAAGG
* *
3497988 GATGCATCGATGCACATTCAAAGG
1 GATGAAGCGATGCACATTCAAAGG
* *
3498012 GATGCATCGATGCAC
1 GATGAAGCGATGCAC
3498027 TGTTAAGTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (24 bp):
GATGAAGCGATGCACATTCAAAGG
Found at i:3502052 original size:15 final size:15
Alignment explanation
Indices: 3502032--3502070 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
3502022 TTCTTGTTCC
*
3502032 TCTTCATCGGAACCT
1 TCTTCATCGAAACCT
3502047 TCTTCATCGAAACCT
1 TCTTCATCGAAACCT
3502062 TCTTCATCG
1 TCTTCATCG
3502071 CTCCATGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.33, G:0.10, T:0.36
Consensus pattern (15 bp):
TCTTCATCGAAACCT
Found at i:3503993 original size:91 final size:91
Alignment explanation
Indices: 3503831--3503996 Score: 237
Period size: 91 Copynumber: 1.8 Consensus size: 91
3503821 GGTGCACTAA
** **
3503831 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGGTC
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAAACTGAGTGCATCGATGCATGGAA
*
3503896 TTGTGCATCGATGCATCAAATGCACT
66 TGGTGCATCGATGCATCAAATGCACT
* *
3503922 GAGTGCATCGATGTATAAAATGCATTCGATG-TTTGAAAAATTAATTG-GTGCATCGATGCATGG
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAA--AACTGAGTGCATCGATGCATGG
3503985 AATGGTGCATCG
64 AATGGTGCATCG
3503997 CTTTGAAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
90 9 0.14
91 55 0.83
92 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (91 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAAACTGAGTGCATCGATGCATGGAA
TGGTGCATCGATGCATCAAATGCACT
Found at i:3515362 original size:25 final size:26
Alignment explanation
Indices: 3515330--3515383 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
3515320 GGGTGATGTG
*
3515330 AAATTATAAAATT-TTAAAAAATATA
1 AAATTATAAAATTAATAAAAAATATA
**
3515355 AAATTATATTATTAATAAAAAATATA
1 AAATTATAAAATTAATAAAAAATATA
3515381 AAA
1 AAA
3515384 CAATATCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AAATTATAAAATTAATAAAAAATATA
Found at i:3527264 original size:15 final size:16
Alignment explanation
Indices: 3527246--3527275 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3527236 ACCATAACCG
3527246 AAAA-TAACCCGAATC
1 AAAAGTAACCCGAATC
3527261 AAAAGTAACCCGAAT
1 AAAAGTAACCCGAAT
3527276 ATGATTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.23, G:0.10, T:0.13
Consensus pattern (16 bp):
AAAAGTAACCCGAATC
Found at i:3527373 original size:3 final size:3
Alignment explanation
Indices: 3527365--3527457 Score: 186
Period size: 3 Copynumber: 31.0 Consensus size: 3
3527355 TATTTATATT
3527365 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
3527413 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
3527458 TACTTTTGGC
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:3528484 original size:65 final size:63
Alignment explanation
Indices: 3528365--3528574 Score: 214
Period size: 65 Copynumber: 3.3 Consensus size: 63
3528355 TTTTTCAGAG
* *
3528365 TGATGCA-CAGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATG
1 TGATGCATC-GATGCA-CAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATG
3528426 CATT
60 CATT
* *
3528430 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
3528494 T
63 T
* * * * *
3528495 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
3528559 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
3528575 TCTTAGTGCA
Statistics
Matches: 125, Mismatches: 11, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 47 0.38
65 68 0.54
66 6 0.05
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:3534391 original size:24 final size:24
Alignment explanation
Indices: 3534364--3534444 Score: 84
Period size: 24 Copynumber: 3.5 Consensus size: 24
3534354 TCACTTAACA
3534364 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
3534388 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
3534410 -TGCATCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
3534432 GTGCATCGATGCA
1 GTGCATCGATGCA
3534445 CATGGTCATG
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
20 3 0.06
21 12 0.26
22 1 0.02
23 15 0.32
24 16 0.34
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:3534430 original size:44 final size:44
Alignment explanation
Indices: 3534365--3534467 Score: 147
Period size: 44 Copynumber: 2.3 Consensus size: 44
3534355 CACTTAACAG
* * *
3534365 TGCATCGATGCATCCCTTTGAATGTGCATCGATTCATCATGTTGA
1 TGCATCGATGCATCCCTTTGAATGTGCATCGATGCA-CATGGTCA
3534410 TGCATCGATGCA-CGCC-TTGAATGTGCATCGATGCACATGGTCA
1 TGCATCGATGCATC-CCTTTGAATGTGCATCGATGCACATGGTCA
3534453 TGCATCGATGCATCC
1 TGCATCGATGCATCC
3534468 ATCGGGTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
43 19 0.36
44 20 0.38
45 14 0.26
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.30
Consensus pattern (44 bp):
TGCATCGATGCATCCCTTTGAATGTGCATCGATGCACATGGTCA
Found at i:3536009 original size:21 final size:21
Alignment explanation
Indices: 3535967--3536010 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3535957 ACTCCGGGAG
* *
3535967 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
3535988 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
3536009 CT
1 CT
3536011 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:3537249 original size:64 final size:64
Alignment explanation
Indices: 3537043--3537252 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
3537033 TTTTTCAGAG
* * ** *
3537043 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATCAAATGCA
1 TGATGCATCGATGCACCAA-CCATGCATCGATGCACTC-TGGA-TATTTTGAAACATCGAATGCA
3537106 TT
63 TT
* * * **
3537108 TCATGCATTGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATGCATCGATGCACTCTGGATATTT-TG-AAACATCGAATGCA
3537171 TT
63 TT
* * *
3537173 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
3537237 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
3537253 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 50 0.42
65 61 0.51
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
Found at i:3537252 original size:17 final size:19
Alignment explanation
Indices: 3537224--3537272 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3537214 TATTTTGAAA
3537224 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
3537242 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
3537261 CACCGATGCACT
1 CATCGATGCACT
3537273 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:3537268 original size:64 final size:63
Alignment explanation
Indices: 3537093--3537272 Score: 168
Period size: 65 Copynumber: 2.8 Consensus size: 63
3537083 AATTAAATTG
* * * * * * *
3537093 AACATCAAATGCATTTCATGCATTGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCACTTGATGCATCGATGCAC-CAGC-TGCACCGATGCACTCAGGATTTTATGAA
* * * *
3537158 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTT-TG-
1 AACATCGAATGCACTTGATGCATCGATGCACCAG-C-TGCACCGATGCACTCAGGAT-TTTATGA
3537221 A
63 A
3537222 AACATCGAATGCACTTGATGCATCGATGCACTCTTAG-TGCACCGATGCACT
1 AACATCGAATGCACTTGATGCATCGATGCAC-C--AGCTGCACCGATGCACT
3537273 AAGGGTCCAA
Statistics
Matches: 99, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
64 45 0.45
65 49 0.49
66 3 0.03
67 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCACTTGATGCATCGATGCACCAGCTGCACCGATGCACTCAGGATTTTATGAA
Found at i:3541643 original size:15 final size:15
Alignment explanation
Indices: 3541623--3541652 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3541613 AGCCCGATCT
3541623 GAAATGACCCAATCC
1 GAAATGACCCAATCC
3541638 GAAATGACCCAATCC
1 GAAATGACCCAATCC
3541653 AAACCCGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.33, G:0.13, T:0.13
Consensus pattern (15 bp):
GAAATGACCCAATCC
Found at i:3543406 original size:19 final size:19
Alignment explanation
Indices: 3543368--3543407 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3543358 TTGTTAGTGC
*
3543368 AAATGTTTGTCTAATTTTA
1 AAATGTTTGTCTAATGTTA
3543387 AAATGTTT-TCTAAGTGTTA
1 AAATGTTTGTCTAA-TGTTA
3543406 AA
1 AA
3543408 GGACAAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (19 bp):
AAATGTTTGTCTAATGTTA
Found at i:3548046 original size:167 final size:167
Alignment explanation
Indices: 3547776--3548093 Score: 457
Period size: 167 Copynumber: 1.9 Consensus size: 167
3547766 TGTTGCATTG
* * *
3547776 AATTCGAATCAAACTCTAACAACAAAGATAAGAGGTTATGAATGATTACCTCATGTTAAGGAGAA
1 AATTCAAATCAAACTCTAACAACAAAGATAAGAGATTATGAATGATTACCTAATGTTAAGGAGAA
* *
3547841 GAATAAGCAAAAGCACGGCTGAAAGGAAGGGCTTTTCATGGTTATGTTTTTTAG-TTTGCAGTTA
66 GAATAAGCAAAAGCAAGGCTGAAAGGAAGGGCTTTTCATGGTTATGTTGTTTAGTTTTGCA-TTA
* *
3547905 TTGGTCTGTACTCTGGTTTCAGAACTTGTGTCACATCA
130 TTGGTCTATACTCTAGTTTCAGAACTTGTGTCACATCA
3547943 AATTCAAATCAAACTCTAA-AACAATAGATAAGAGATTATGAA-GATTACCTAATGTTAAGGATG
1 AATTCAAATCAAACTCTAACAACAA-AGATAAGAGATTATGAATGATTACCTAATGTTAAGGA-G
* * *
3548006 -AGAATAAGCAAAAGCAAGGCTGAAAAGG-AGGGATTTTTCATGGTTTTGTTGTTTAGTTTTTCA
64 AAGAATAAGCAAAAGCAAGGCTG-AAAGGAAGGG-CTTTTCATGGTTATGTTGTTTAGTTTTGCA
*
3548069 TTGTTGGTCTATACTCTAGTTTCAG
127 TTATTGGTCTATACTCTAGTTTCAG
3548094 GTAGTGTAGA
Statistics
Matches: 135, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
166 48 0.36
167 82 0.61
168 5 0.04
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (167 bp):
AATTCAAATCAAACTCTAACAACAAAGATAAGAGATTATGAATGATTACCTAATGTTAAGGAGAA
GAATAAGCAAAAGCAAGGCTGAAAGGAAGGGCTTTTCATGGTTATGTTGTTTAGTTTTGCATTAT
TGGTCTATACTCTAGTTTCAGAACTTGTGTCACATCA
Found at i:3561193 original size:2 final size:2
Alignment explanation
Indices: 3561188--3561244 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
3561178 CCAAAAAAAG
3561188 TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
3561230 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
3561245 GGTGTTTTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3561994 original size:20 final size:20
Alignment explanation
Indices: 3561956--3562008 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
3561946 ACCTAAATAA
* *
3561956 TAAAAAAAT-ATTATTTTTAT
1 TAAAAAAATAATGA-TTTAAT
3561976 TCAAAAAAATAATGATTTAAT
1 T-AAAAAAATAATGATTTAAT
*
3561997 TGAAAAAATAAT
1 TAAAAAAATAAT
3562009 ATATAGAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 11 0.39
21 14 0.50
22 3 0.11
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (20 bp):
TAAAAAAATAATGATTTAAT
Found at i:3567990 original size:12 final size:12
Alignment explanation
Indices: 3567973--3567997 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3567963 TGTTTATTTA
3567973 AATAAATAAATT
1 AATAAATAAATT
3567985 AATAAATAAATT
1 AATAAATAAATT
3567997 A
1 A
3567998 CATATTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAAATAAATT
Found at i:3568703 original size:51 final size:51
Alignment explanation
Indices: 3568627--3568731 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
3568617 ACTTGCATGC
* *
3568627 ATAACCACTGAGTCAACCTCCGCACTTGGGCTGTATTTTACAGCATAATGT
1 ATAACCACTGAGTCAACATCCGCACTTGGGCTGTATTTTACAGCATAATAT
3568678 ATAACCACTGAGTCAACATCCGCACTTGGGCTGTATTTTACAGCATAATAT
1 ATAACCACTGAGTCAACATCCGCACTTGGGCTGTATTTTACAGCATAATAT
3568729 ATA
1 ATA
3568732 TTTGTATAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (51 bp):
ATAACCACTGAGTCAACATCCGCACTTGGGCTGTATTTTACAGCATAATAT
Found at i:3581528 original size:2 final size:2
Alignment explanation
Indices: 3581476--3581508 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
3581466 ATGAAAAAAA
3581476 AT AT CAT 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
3581509 CAATTCACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3582247 original size:28 final size:29
Alignment explanation
Indices: 3582207--3582267 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
3582197 ATATATCCAC
3582207 TTATTTATTTAAATATCTAAAATATT-TT
1 TTATTTATTTAAATATCTAAAATATTCTT
* *
3582235 TTATTTATTTAAATGTTTAAAATATTCTT
1 TTATTTATTTAAATATCTAAAATATTCTT
3582264 TTAT
1 TTAT
3582268 CAATATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (29 bp):
TTATTTATTTAAATATCTAAAATATTCTT
Found at i:3582286 original size:29 final size:29
Alignment explanation
Indices: 3582244--3582321 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 29
3582234 TTTATTTATT
* * *
3582244 TAAATGTTTAAAATATTCTTTT-ATCAATA
1 TAAATATTGAAAATATT-TTTTAATCAAAA
* * *
3582273 TAAGTATTTCAAATTATTTTTTAATCAAAA
1 TAAATA-TTGAAAATATTTTTTAATCAAAA
3582303 TAAATATTGAAAATATTTT
1 TAAATATTGAAAATATTTT
3582322 ATATGAAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
29 19 0.49
30 20 0.51
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (29 bp):
TAAATATTGAAAATATTTTTTAATCAAAA
Found at i:3582458 original size:38 final size:38
Alignment explanation
Indices: 3582416--3582489 Score: 123
Period size: 38 Copynumber: 1.9 Consensus size: 38
3582406 GCATCTAAAT
*
3582416 TCTAATTTATCTAAATCCTAATAAA-TTCTGAAAAAAAA
1 TCTAATTCATCTAAATCCTAATAAATTTC-GAAAAAAAA
3582454 TCTAATTCATCTAAATCCTAATAAATTTCGAAAAAA
1 TCTAATTCATCTAAATCCTAATAAATTTCGAAAAAA
3582490 TTAACATATG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 31 0.91
39 3 0.09
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.34
Consensus pattern (38 bp):
TCTAATTCATCTAAATCCTAATAAATTTCGAAAAAAAA
Found at i:3590631 original size:15 final size:15
Alignment explanation
Indices: 3590611--3590642 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3590601 GATCTTGAGT
3590611 ATGGTGGTGGTGGTG
1 ATGGTGGTGGTGGTG
3590626 ATGGTGGTGGTGGTG
1 ATGGTGGTGGTGGTG
3590641 AT
1 AT
3590643 TAAACGACGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.00, G:0.56, T:0.34
Consensus pattern (15 bp):
ATGGTGGTGGTGGTG
Found at i:3591515 original size:28 final size:28
Alignment explanation
Indices: 3591483--3591539 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3591473 TTTCCTTTCC
3591483 ATCTATATTTTCATTAATGTATTATGAT
1 ATCTATATTTTCATTAATGTATTATGAT
3591511 ATCTATATTTTCATTAATGTATTATGAT
1 ATCTATATTTTCATTAATGTATTATGAT
3591539 A
1 A
3591540 AGACATTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (28 bp):
ATCTATATTTTCATTAATGTATTATGAT
Found at i:3600450 original size:20 final size:20
Alignment explanation
Indices: 3600427--3600474 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3600417 TGTCCCAAAT
3600427 GACCTATGTATATCCCGAAG
1 GACCTATGTATATCCCGAAG
* *
3600447 GACCTCTGTATGTCCCGAAG
1 GACCTATGTATATCCCGAAG
3600467 GACCTATG
1 GACCTATG
3600475 AACCCTCGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (20 bp):
GACCTATGTATATCCCGAAG
Found at i:3602567 original size:58 final size:58
Alignment explanation
Indices: 3602445--3602573 Score: 140
Period size: 58 Copynumber: 2.2 Consensus size: 58
3602435 TAAAATTTTG
* * **
3602445 AATTTATTTTACCTTAGAATCTTGTGTTGATTCTAACTTTGAAAAGGAAATAAATCGTTG
1 AATTTATTTT-CCTTAGAATCTTGTGATGATTCT-ACTTTGAAAAGAAAATAAATCGTCA
3602505 AATTTATTTTCC-TATGAATCTTGT-ATGATTCT-CTTTGGTAAAAGAAAATAAAAT-GTCA
1 AATTTATTTTCCTTA-GAATCTTGTGATGATTCTACTTT-G-AAAAGAAAAT-AAATCGTCA
3602563 AATTTATTTTC
1 AATTTATTTTC
3602574 TTGGAAATCT
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
56 4 0.07
57 1 0.02
58 31 0.51
59 15 0.25
60 10 0.16
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (58 bp):
AATTTATTTTCCTTAGAATCTTGTGATGATTCTACTTTGAAAAGAAAATAAATCGTCA
Found at i:3606200 original size:83 final size:83
Alignment explanation
Indices: 3606103--3606260 Score: 246
Period size: 83 Copynumber: 1.9 Consensus size: 83
3606093 TGATATATTT
* *
3606103 GTTTAATATTTTAAATTTAAAAGATATTACTATCTGTTTACATTTAAATATTAAAAGA-TATTTA
1 GTTTAATATTTTAAATTTAAAAGATATTACTATCTATTTAAATTTAAATATTAAAAGAGT-TTTA
3606167 GTTGGAGTAAAGCTATCAA
65 GTTGGAGTAAAGCTATCAA
* * * *
3606186 GTTTAATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGATGTTAGAAGAGTTTTAG
1 GTTTAATATTTTAAATTTAAAAGATATTACTATCTATTTAAATTTAAATATTAAAAGAGTTTTAG
3606251 TTGGAGTAAA
66 TTGGAGTAAA
3606261 ACTCTCTCTA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
83 67 0.99
84 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.44
Consensus pattern (83 bp):
GTTTAATATTTTAAATTTAAAAGATATTACTATCTATTTAAATTTAAATATTAAAAGAGTTTTAG
TTGGAGTAAAGCTATCAA
Found at i:3609555 original size:105 final size:103
Alignment explanation
Indices: 3609408--3609597 Score: 229
Period size: 105 Copynumber: 1.8 Consensus size: 103
3609398 GTCAAGTGGT
* * * *
3609408 AAATGAAACTCAAAATCAACTCATCATCGACAGGTTTTTTATTGATTTG-GAGTGATCAACAACA
1 AAATGAAACTCAAAATCAACTCATCATCGACAGATGTTTTATTG-GTTGAGAGTAATCAACAACA
**
3609472 AAATGCTTCTCTTGAAAATGTGTCAGGTGACTCATTGGA
65 AAATAATTCTCTTGAAAATGTGTCAGGTGACTCATTGGA
* ** * *
3609511 AAATGACACTCAACTTCAACTTGCATCATCGACATATGTTTTATTGGTTGAGATTAATCAACAAC
1 AAATGAAACTCAAAATCAAC-T-CATCATCGACAGATGTTTTATTGGTTGAGAGTAATCAACAAC
* *
3609576 ATAATAATTCTCTTGAACATGT
64 AAAATAATTCTCTTGAAAATGT
3609598 AATTGAGCTC
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
103 17 0.24
104 4 0.06
105 50 0.70
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (103 bp):
AAATGAAACTCAAAATCAACTCATCATCGACAGATGTTTTATTGGTTGAGAGTAATCAACAACAA
AATAATTCTCTTGAAAATGTGTCAGGTGACTCATTGGA
Found at i:3620213 original size:15 final size:15
Alignment explanation
Indices: 3620179--3620213 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3620169 TTCTCTACAG
*
3620179 TAAAAAATTAATTAA
1 TAAAAAATTAAATAA
*
3620194 CAAAAAATTAAATAA
1 TAAAAAATTAAATAA
3620209 TAAAA
1 TAAAA
3620214 TATATCATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAAATTAAATAA
Found at i:3620410 original size:20 final size:20
Alignment explanation
Indices: 3620357--3620410 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
3620347 TTTATTCCTG
* *
3620357 ATAATCTTATATTTCTATTA
1 ATAATATTATATTTCCATTA
* * *
3620377 ATAATTTTACATTTCCATTT
1 ATAATATTATATTTCCATTA
3620397 ATAATATTATATTT
1 ATAATATTATATTT
3620411 TATAAATCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (20 bp):
ATAATATTATATTTCCATTA
Found at i:3630283 original size:17 final size:17
Alignment explanation
Indices: 3630261--3630295 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3630251 TCACCCTTGA
3630261 TATGTGTGACTATTCGG
1 TATGTGTGACTATTCGG
3630278 TATGTGTGACTATTCGG
1 TATGTGTGACTATTCGG
3630295 T
1 T
3630296 GTAACATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.29, T:0.43
Consensus pattern (17 bp):
TATGTGTGACTATTCGG
Found at i:3634575 original size:15 final size:16
Alignment explanation
Indices: 3634555--3634588 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3634545 ATTTTTATCA
*
3634555 TTACTAA-TATTTAAT
1 TTACTAATTAATTAAT
3634570 TTACTAATTAATTAAT
1 TTACTAATTAATTAAT
3634586 TTA
1 TTA
3634589 GATCGAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TTACTAATTAATTAAT
Found at i:3634673 original size:12 final size:12
Alignment explanation
Indices: 3634652--3634711 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 12
3634642 TTTAAAACAT
3634652 AAATAAAATTAA
1 AAATAAAATTAA
*
3634664 AAATATAATTAA
1 AAATAAAATTAA
* *
3634676 CAATAGAAAATAAA
1 -AA-ATAAAATTAA
3634690 GAAATAAAATTAA
1 -AAATAAAATTAA
3634703 AAATTAAAA
1 AAA-TAAAA
3634712 AGCATGAAGC
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
12 14 0.37
13 15 0.39
14 9 0.24
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (12 bp):
AAATAAAATTAA
Found at i:3634712 original size:27 final size:26
Alignment explanation
Indices: 3634656--3634706 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
3634646 AAACATAAAT
* * *
3634656 AAAATTAAAAATATAATTAACAATAG
1 AAAATAAAAAATAAAATTAAAAATAG
3634682 AAAATAAAGAAATAAAATTAAAAAT
1 AAAATAAA-AAATAAAATTAAAAAT
3634707 TAAAAAGCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (26 bp):
AAAATAAAAAATAAAATTAAAAATAG
Found at i:3635769 original size:23 final size:23
Alignment explanation
Indices: 3635735--3635803 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
3635725 CACCACAGCT
*
3635735 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
3635758 CGTAGAATTGCACTGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
3635781 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
3635804 TATAAGGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:3636200 original size:2 final size:2
Alignment explanation
Indices: 3636193--3636223 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3636183 TATGTCTTAT
3636193 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 T
3636224 TCACATGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3637474 original size:64 final size:63
Alignment explanation
Indices: 3637405--3637565 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
3637395 TTCCTTTAAA
* * * *
3637405 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCAATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACCAATCACATTCAATGTTTCCATTTTTAA-GAG
* * ** * *
3637469 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATAG
1 GTGCATCGATGCACTCC-TATGCATCGATACACCAATCACATTCAATGTTTCCATTTTTAAGAG
*
3637533 GTGCATCGATGCACTTCCTGTGCATCGATACAC
1 GTGCATCGATGCAC-TCCTATGCATCGATACAC
3637566 ACTGAACAAG
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 2 0.02
64 71 0.87
65 9 0.11
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACCAATCACATTCAATGTTTCCATTTTTAAGAG
Found at i:3642001 original size:29 final size:29
Alignment explanation
Indices: 3641959--3642041 Score: 121
Period size: 29 Copynumber: 2.9 Consensus size: 29
3641949 CCCCCAACAC
3641959 AGGTCGCCATGCACTCCCAGCGACCTACA
1 AGGTCGCCATGCACTCCCAGCGACCTACA
***
3641988 AGGTCGCCATGCACTCCCAGCGACCTTGT
1 AGGTCGCCATGCACTCCCAGCGACCTACA
* *
3642017 AGGTCGCCATGCACGCCCAACGACC
1 AGGTCGCCATGCACTCCCAGCGACC
3642042 AACGTTGTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.22, C:0.41, G:0.23, T:0.14
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCAGCGACCTACA
Found at i:3642370 original size:23 final size:23
Alignment explanation
Indices: 3642332--3642393 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
3642322 AAAGAAAGGG
*
3642332 AGAAGAGAGCAAGGGAAAAGAGGA
1 AGAAGA-AGAAAGGGAAAAGAGGA
3642356 AGAAGAAGAAAGGGAAAAGAGGA
1 AGAAGAAGAAAGGGAAAAGAGGA
3642379 AGAAGAAGAAAGGGA
1 AGAAGAAGAAAGGGA
3642394 TAGCACAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 31 0.84
24 6 0.16
ACGTcount: A:0.58, C:0.02, G:0.40, T:0.00
Consensus pattern (23 bp):
AGAAGAAGAAAGGGAAAAGAGGA
Found at i:3642491 original size:46 final size:42
Alignment explanation
Indices: 3642449--3642556 Score: 118
Period size: 39 Copynumber: 2.5 Consensus size: 42
3642439 TTATTTTAAA
3642449 TTATTAGTTTGTTAGTTTATGGTTTAAGGTAAAACCAAATTTTAG
1 TTATTAGTTTGTTAGTTTA--GTTTAAGGTAAAA-CAAATTTTAG
3642494 TTA--A-TTAT-TTAG-TTAGTTTAAGGTAAAACAAATTTTAG
1 TTATTAGTT-TGTTAGTTTAGTTTAAGGTAAAACAAATTTTAG
*
3642532 TTAATTAGTTTGTCAGTTTAAGTTT
1 TT-ATTAGTTTGTTAGTTT-AGTTT
3642557 TATTATTGTT
Statistics
Matches: 54, Mismatches: 1, Indels: 17
0.75 0.01 0.24
Matches are distributed among these distances:
38 12 0.22
39 14 0.26
41 5 0.09
42 11 0.20
43 4 0.07
44 5 0.09
45 3 0.06
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (42 bp):
TTATTAGTTTGTTAGTTTAGTTTAAGGTAAAACAAATTTTAG
Found at i:3642494 original size:38 final size:38
Alignment explanation
Indices: 3642446--3642553 Score: 132
Period size: 38 Copynumber: 2.8 Consensus size: 38
3642436 TTATTATTTT
** *
3642446 AAATTATTAGTTTGTTAGTTTA-TGGTTTAAGGTAAAACC
1 AAATT-TTAGTTAATTAGTTTAGTAGTTTAAGGTAAAA-C
3642485 AAATTTTAGTTAATTA-TTTAGTTAGTTTAAGGTAAAAC
1 AAATTTTAGTTAATTAGTTTAG-TAGTTTAAGGTAAAAC
3642523 AAATTTTAGTTAATTAGTTT-GTCAGTTTAAG
1 AAATTTTAGTTAATTAGTTTAGT-AGTTTAAG
3642554 TTTTATTATT
Statistics
Matches: 62, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
37 5 0.08
38 35 0.56
39 22 0.35
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (38 bp):
AAATTTTAGTTAATTAGTTTAGTAGTTTAAGGTAAAAC
Found at i:3642937 original size:21 final size:21
Alignment explanation
Indices: 3642911--3642950 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3642901 GATAATGAGT
3642911 TTGTTAGTTTAAATTATATTA
1 TTGTTAGTTTAAATTATATTA
*
3642932 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAATTATAT
3642951 CATATAGAAA
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:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAATTATATTA
Found at i:3643170 original size:371 final size:363
Alignment explanation
Indices: 3642515--3643189 Score: 889
Period size: 371 Copynumber: 1.8 Consensus size: 363
3642505 GTTAGTTTAA
** * * * *
3642515 GGTAAAACAAATTTTAGTTAATTAGTTTGTCAGTTTAAGTTTTATTATTGTTAGTTTAAGTTATA
1 GGTAAAACAAAAATTAGATAATGAGTTTGTCAGTTTAAATTATATTATTGTTAGTTTAAGTTATA
* * * * *
3642580 TCATACATAAATATAAAATTATTTAATTAGTTTGTTTGATGGTTATATATTAAAAAAATAATTAA
66 TCATACAGAAATAAAAAATTATTTAATTAGTATGTTTGATAGTTACATATTAAAAAAATAATTAA
*
3642645 TTAGTGTGTTAATTAGTCTAATATTTAATTAGTTTGTAGTTAGTTAAATAGTTAAGTTATATATA
131 TTAGTGTGTTAATTAGTATAATATTTAATTAGTTTGTAGTTAGTTAAATAGTTAAG-T-TATATA
*
3642710 TTTTGGTTGTTGAATTTATATTATATAAAAAAATTAGTTAATTAGTTTATTAGTAGTTTAAGTTT
194 TTTTGGTTGTTGAATTTATATTATATAAAAAAATTAGTTAATTAGTTTATTAATAG-TTAA----
3642775 TATTATAATAAAAAAATAGTTTATTAGTTTAAGTTATA-TAAAAGAATAATTATTTAAATTATTT
254 TATTATAATAAAAAAATAGTTTATTAGTTTAAGTTATATTAAAAGAATAATTATTTAAATTATTT
3642839 TATTGTTATAAATTATTAGTTAATTAGTTTATTATTATAAATTAG
319 TATTGTTATAAATTATTAGTTAATTAGTTTATTATTATAAATTAG
*
3642884 GGTAAAACAAAAAATTAGATAATGAGTTTGTTAGTTTAAATTATATTATTGTTAGTTTAAGTTAT
1 GGTAAAAC-AAAAATTAGATAATGAGTTTGTCAGTTTAAATTATATTATTGTTAGTTTAAGTTAT
*
3642949 ATCATATAGAAATAAAAAAATTATTTAATTAGTATGTTTGATAGTTACATATTAATAAAAATAAT
65 ATCATACAGAAAT-AAAAAATTATTTAATTAGTATGTTTGATAGTTACATATTAA-AAAAATAAT
* * *
3643014 TAGTTAGTTTGTTAGTCGTTAGTTATATATAAAAAAATATGTAATTAGTTTGT-GTTAGTTAAAT
128 TAATTAGTGTGTTA---ATTAG-TATA-AT------AT-T-TAATTAGTTTGTAGTTAGTTAAAT
* *
3643078 AGTTAAG-T-TATA-TTTGTTTGTTGAATTTATATTATATAAAAAAATTAGTTAATTAGTTTTTT
180 AGTTAAGTTATATATTTTGGTTGTTGAATTTATATTATATAAAAAAATTAGTTAATTAGTTTATT
* *
3643140 AATAG-TAA-ATTATAAT-TAAAAATTGTTTATTAGTTTAAGTTATATTAAAA
245 AATAGTTAATATTATAATAAAAAAATAGTTTATTAGTTTAAGTTATATTAAAA
3643190 ATTAGTTTAT
Statistics
Matches: 267, Mismatches: 22, Indels: 31
0.83 0.07 0.10
Matches are distributed among these distances:
369 8 0.03
370 60 0.22
371 63 0.24
372 34 0.13
375 4 0.01
376 3 0.01
377 5 0.02
379 52 0.19
380 4 0.01
381 1 0.00
383 2 0.01
384 19 0.07
385 12 0.04
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (363 bp):
GGTAAAACAAAAATTAGATAATGAGTTTGTCAGTTTAAATTATATTATTGTTAGTTTAAGTTATA
TCATACAGAAATAAAAAATTATTTAATTAGTATGTTTGATAGTTACATATTAAAAAAATAATTAA
TTAGTGTGTTAATTAGTATAATATTTAATTAGTTTGTAGTTAGTTAAATAGTTAAGTTATATATT
TTGGTTGTTGAATTTATATTATATAAAAAAATTAGTTAATTAGTTTATTAATAGTTAATATTATA
ATAAAAAAATAGTTTATTAGTTTAAGTTATATTAAAAGAATAATTATTTAAATTATTTTATTGTT
ATAAATTATTAGTTAATTAGTTTATTATTATAAATTAG
Found at i:3643198 original size:30 final size:30
Alignment explanation
Indices: 3643137--3643226 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
3643127 TAATTAGTTT
*
3643137 TTTAATAG-TAAA-TTATAATTAAAAATT-G
1 TTTATTAGTTAAAGTTAT-ATTAAAAATTAG
*
3643165 TTTATTAGTTTAAGTTATATTAAAAATTAG
1 TTTATTAGTTAAAGTTATATTAAAAATTAG
3643195 TTTATTAGTTAAAGTTATATTAAAGAA-TAG
1 TTTATTAGTTAAAGTTATATTAAA-AATTAG
3643225 TT
1 TT
3643227 AAAGTTATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
28 7 0.13
29 13 0.24
30 33 0.60
31 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (30 bp):
TTTATTAGTTAAAGTTATATTAAAAATTAG
Found at i:3643219 original size:11 final size:11
Alignment explanation
Indices: 3643203--3643241 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
3643193 AGTTTATTAG
3643203 TTAAAGTTATA
1 TTAAAGTTATA
*
3643214 TTAAAG-AATA
1 TTAAAGTTATA
3643224 GTTAAAGTTATA
1 -TTAAAGTTATA
3643236 TTAAAG
1 TTAAAG
3643242 AATAGTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (11 bp):
TTAAAGTTATA
Found at i:3643226 original size:22 final size:22
Alignment explanation
Indices: 3643200--3643248 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
3643190 ATTAGTTTAT
3643200 TAGTTAAAGTTATATTAAAGAA
1 TAGTTAAAGTTATATTAAAGAA
3643222 TAGTTAAAGTTATATTAAAGAA
1 TAGTTAAAGTTATATTAAAGAA
3643244 TAGTT
1 TAGTT
3643249 TATTAGTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (22 bp):
TAGTTAAAGTTATATTAAAGAA
Found at i:3645612 original size:59 final size:56
Alignment explanation
Indices: 3645549--3645669 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 56
3645539 TATTATAATT
* *
3645549 TCATTACTAGTAATTATTAGTAAATCATTAGTATCAAATAATTAAATATTAATAATAAA
1 TCATTACTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATT--TAA-AAA
*
3645608 TCATTATTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTTAAAAA
1 TCATTACTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTTAAAAA
3645664 TCATTA
1 TCATTA
3645670 ATAAATTCGA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
56 9 0.15
57 3 0.05
59 47 0.80
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.40
Consensus pattern (56 bp):
TCATTACTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTTAAAAA
Found at i:3645770 original size:11 final size:11
Alignment explanation
Indices: 3645754--3646083 Score: 225
Period size: 11 Copynumber: 27.2 Consensus size: 11
3645744 ATTAGCAATA
3645754 ATTATTAAATC
1 ATTATTAAATC
*
3645765 ATTATTATAAAATT
1 ATTA-T-T-AAATC
*
3645779 ATTACTAAATC
1 ATTATTAAATC
3645790 ATTATTAAATC
1 ATTATTAAATC
*
3645801 ATTATTATAATGATT
1 ATTA-T-TAA--ATC
3645816 ATTATTAAATC
1 ATTATTAAATC
* *
3645827 ATTATTATCATT
1 ATTATTA-AATC
3645839 ATTATTAAATC
1 ATTATTAAATC
*
3645850 ATTATTATAATG
1 ATTATTA-AATC
3645862 ATTATTACTAAATC
1 ATTA-T--TAAATC
*
3645876 ATTATTATAATA
1 ATTATTA-AATC
3645888 ATTATTATAAAATC
1 ATTA-T-T-AAATC
*
3645902 ATTACTAAATC
1 ATTATTAAATC
3645913 ATCAAATCATTAAAT-
1 AT----T-ATTAAATC
3645928 ATTA--AAATC
1 ATTATTAAATC
3645937 ATTATTAAATC
1 ATTATTAAATC
*
3645948 ATTATTATAATG
1 ATTATTA-AATC
3645960 ATTATTACTAAATC
1 ATTA-T--TAAATC
3645974 ATTATTAAATC
1 ATTATTAAATC
3645985 ATAATATTAAAATC
1 AT--TATT-AAATC
*
3645999 ATTACTAAATC
1 ATTATTAAATC
3646010 ATAATATTAAAATC
1 AT--TATT-AAATC
*
3646024 ATTACTAAATC
1 ATTATTAAATC
3646035 ATTATTAAATC
1 ATTATTAAATC
3646046 ATTATTAAATC
1 ATTATTAAATC
3646057 ATAATATTAAAATC
1 AT--TATT-AAATC
*
3646071 ATTACTAAATC
1 ATTATTAAATC
3646082 AT
1 AT
3646084 CAAATCATTA
Statistics
Matches: 259, Mismatches: 23, Indels: 74
0.73 0.06 0.21
Matches are distributed among these distances:
8 4 0.02
9 4 0.02
10 1 0.00
11 112 0.43
12 43 0.17
13 23 0.09
14 52 0.20
15 14 0.05
16 6 0.02
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:3645818 original size:72 final size:72
Alignment explanation
Indices: 3645754--3646083 Score: 333
Period size: 72 Copynumber: 4.5 Consensus size: 72
3645744 ATTAGCAATA
3645754 ATTATTAAATCATTATTA-TAAAATTATTACTAAATCATTATTAAATCATTATTATAATGATTAT
1 ATTATTAAATCATTATTATTAAAATTATTACTAAATCATTATTAAATCATTATTATAATGATTAT
3645818 TATTAAATC
66 TA--AAATC
* * *
3645827 ATTATT--ATCATTATTATTAAATCATTATTA-TAATGATTATTACTAAATCATTATTATAATAA
1 ATTATTAAATCATTATTATTAAA--ATTATTACTAA--ATCATTATTAAATCATTATTATAATGA
3645889 TTATTATAAAATC
62 TTA-T-TAAAATC
* * *
3645902 ATTACTAAATCATCAAATCATT-AAA-TATTA--AAATCATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCAT--TATTATTAAAATTATTACTAAATCATTATTAAATCATTATTATAATGATT
3645963 ATTACTAAATC
64 ATTA--AAATC
* * * *
3645974 ATTATTAAATCA-TAATATTAAAATCATTACTAAATCATAATATTAAAATCATTACTA-AATCAT
1 ATTATTAAATCATTATTATTAAAATTATTACTAAATCAT--TATT-AAATCATTATTATAATGAT
3646037 TATT-AAATC
63 TATTAAAATC
* *
3646046 ATTATTAAATCA-TAATATTAAAATCATTACTAAATCAT
1 ATTATTAAATCATTATTATTAAAATTATTACTAAATCAT
3646084 CAAATCATTA
Statistics
Matches: 221, Mismatches: 16, Indels: 41
0.79 0.06 0.15
Matches are distributed among these distances:
69 4 0.02
70 5 0.02
71 15 0.07
72 90 0.41
73 16 0.07
74 9 0.04
75 55 0.25
76 13 0.06
77 7 0.03
78 2 0.01
79 5 0.02
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (72 bp):
ATTATTAAATCATTATTATTAAAATTATTACTAAATCATTATTAAATCATTATTATAATGATTAT
TAAAATC
Found at i:3645894 original size:98 final size:95
Alignment explanation
Indices: 3645754--3646052 Score: 331
Period size: 98 Copynumber: 3.1 Consensus size: 95
3645744 ATTAGCAATA
* * * * * *
3645754 ATTATTA-AATCATTATTA-TAAAATTATTACTAAATCATTATT-AAATCATTATTATAATGATT
1 ATTATTATAATGATTATTACT-AAATCATTATTAAATAATTATTAAAATCATTACTA-AATCATT
* *
3645816 ATTATTAAATCATTATTATCATTATTATTAAATC
64 ATTATTAAATCATTA-TA-AATCATTATTAAATC
3645850 ATTATTATAATGATTATTACTAAATCATTATTATAATAATTATTATAAAATCATTACTAAATCAT
1 ATTATTATAATGATTATTACTAAATCATTATTA-AATAATTA-T-TAAAATCATTACTAAATCAT
* *
3645915 CAAATCATTAAAT-ATTA-AAATCATTATTAAATC
63 --TATTATTAAATCATTATAAATCATTATTAAATC
*
3645948 ATTATTATAATGATTATTACTAAATCATTATTAAATCATAATATTAAAATCATTACTAAATCA-T
1 ATTATTATAATGATTATTACTAAATCATTATTAAAT-A-ATTATTAAAATCATTACTAAATCATT
*
3646012 AATATTAAAATCATTACTAAATCATTATTAAATC
64 ATTATT-AAATCATTA-TAAATCATTATTAAATC
3646046 ATTATTA
1 ATTATTA
3646053 AATCATAATA
Statistics
Matches: 175, Mismatches: 14, Indels: 26
0.81 0.07 0.12
Matches are distributed among these distances:
94 4 0.02
95 4 0.02
96 11 0.06
97 42 0.24
98 79 0.45
99 5 0.03
100 6 0.03
101 15 0.09
102 9 0.05
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (95 bp):
ATTATTATAATGATTATTACTAAATCATTATTAAATAATTATTAAAATCATTACTAAATCATTAT
TATTAAATCATTATAAATCATTATTAAATC
Found at i:3645943 original size:61 final size:58
Alignment explanation
Indices: 3645754--3646036 Score: 225
Period size: 61 Copynumber: 4.7 Consensus size: 58
3645744 ATTAGCAATA
* * *
3645754 ATTATTAAATCATTATTATAAAATTATTACTAAATCATTATTAAATCAT--TATTATAATGATT
1 ATTATTAAATCATTATTATAAAATCATTACTAAATC---ATCAAATCATAATATTA-AA--ATC
* * * * * * *
3645816 ATTATTAAATCATTATTAT--CATTATTATTAAATCATTATTATAATGATTATTACTAAATC
1 ATTATTAAATCATTATTATAAAATCATTACTAAATCATCA-AATCAT-AATATTA--AAATC
*
3645876 ATTATTATAATAATTATTATAAAATCATTACTAAATCATCAAATCATTAAATATTAAAATC
1 ATTATTA-AATCATTATTATAAAATCATTACTAAATCATCAAATCA-T-AATATTAAAATC
* * *
3645937 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTAAATCATAATATTAAAATC
1 ATTATTAAATCATTATTATAA-AATCATTACTAAATC---ATCAAATCATAATATTAAAATC
* *
3645999 ATTACTAAATCA-TAATATTAAAATCATTACTAAATCAT
1 ATTATTAAATCATTATTA-TAAAATCATTACTAAATCAT
3646037 TATTAAATCA
Statistics
Matches: 185, Mismatches: 22, Indels: 32
0.77 0.09 0.13
Matches are distributed among these distances:
57 4 0.02
58 6 0.03
60 35 0.19
61 58 0.31
62 51 0.28
63 23 0.12
64 8 0.04
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (58 bp):
ATTATTAAATCATTATTATAAAATCATTACTAAATCATCAAATCATAATATTAAAATC
Found at i:3646190 original size:49 final size:51
Alignment explanation
Indices: 3646122--3646245 Score: 180
Period size: 52 Copynumber: 2.4 Consensus size: 51
3646112 TCATTATTAC
* *
3646122 TAATAATTACTAAATCATTACTATCAAATCATTAAATA-T-TAACAATAATT
1 TAATTATTACT-AATCATTACTACCAAATCATTAAATATTATAACAATAATT
*
3646172 TAATTATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATAATT
1 TAATTATTACTAATCATTACTACCAAATCATTAAATATT-ATAACAATAATT
*
3646224 TCATTATTACTAATCATTACTA
1 TAATTATTACTAATCATTACTA
3646246 AATAATTATT
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
49 25 0.37
50 11 0.16
52 31 0.46
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (51 bp):
TAATTATTACTAATCATTACTACCAAATCATTAAATATTATAACAATAATT
Found at i:3651200 original size:3 final size:3
Alignment explanation
Indices: 3651192--3651218 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3651182 ATAATATAAT
3651192 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
3651219 AACCCTATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:3652159 original size:23 final size:23
Alignment explanation
Indices: 3652133--3652176 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3652123 GCTTGGCTGC
*
3652133 AATCTCCCAGCTATGGATGCAGG
1 AATCTCCCAACTATGGATGCAGG
3652156 AATCTCCCAACTATGGATGCA
1 AATCTCCCAACTATGGATGCA
3652177 ACGCATGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (23 bp):
AATCTCCCAACTATGGATGCAGG
Found at i:3653085 original size:21 final size:20
Alignment explanation
Indices: 3653017--3653086 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
3653007 TTATAAAAAG
3653017 AATAATAATTATAAGGGTAA
1 AATAATAATTATAAGGGTAA
* * *
3653037 AAT-AT-ATAATGAGAGGAAA
1 AATAATAATTATAAG-GGTAA
3653056 CAATAATAATTATAAGGGTAA
1 -AATAATAATTATAAGGGTAA
3653077 AATATATAAT
1 AATA-ATAAT
3653087 AGGAAGGAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 6 0.15
19 6 0.15
20 10 0.26
21 11 0.28
22 6 0.15
ACGTcount: A:0.56, C:0.01, G:0.14, T:0.29
Consensus pattern (20 bp):
AATAATAATTATAAGGGTAA
Found at i:3653091 original size:37 final size:38
Alignment explanation
Indices: 3653017--3653091 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 38
3653007 TTATAAAAAG
3653017 AATAATAATTATAAGGGTAAAATATATAATGAGAGGAAAC
1 AATAATAATTATAAGGGTAAAATATATAAT--GAGGAAAC
3653057 AATAATAATTATAAGGGTAAAATATATAAT-AGGAA
1 AATAATAATTATAAGGGTAAAATATATAATGAGGAA
3653092 GGAGGAAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
37 5 0.14
40 30 0.86
ACGTcount: A:0.56, C:0.01, G:0.16, T:0.27
Consensus pattern (38 bp):
AATAATAATTATAAGGGTAAAATATATAATGAGGAAAC
Found at i:3653093 original size:21 final size:20
Alignment explanation
Indices: 3653029--3653093 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
3653019 TAATAATTAT
3653029 AAGGGTAAAATATATAAT-G
1 AAGGGTAAAATATATAATAG
* *
3653048 -AGAGGAAACAATA-ATAATTAT
1 AAG-GGTAA-AATATATAA-TAG
3653069 AAGGGTAAAATATATAATAGG
1 AAGGGTAAAATATATAATA-G
3653090 AAGG
1 AAGG
3653094 AGGAAGGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
18 2 0.06
19 8 0.23
20 11 0.31
21 12 0.34
22 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.22, T:0.23
Consensus pattern (20 bp):
AAGGGTAAAATATATAATAG
Found at i:3658520 original size:18 final size:17
Alignment explanation
Indices: 3658499--3658543 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
3658489 ATGTCTTAAT
3658499 AATAAATAATGAGAAT-AA
1 AATAAATAAT-A-AATAAA
3658517 AATAAATAATAAATGAAA
1 AATAAATAATAAAT-AAA
3658535 AATAAATAA
1 AATAAATAA
3658544 GTAACGCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.12
17 1 0.04
18 21 0.84
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (17 bp):
AATAAATAATAAATAAA
Found at i:3660285 original size:13 final size:14
Alignment explanation
Indices: 3660256--3660288 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3660246 TAATTTTTTT
*
3660256 AAATTTATTATAAA
1 AAATTAATTATAAA
3660270 AAATTAATTA-AAA
1 AAATTAATTATAAA
3660283 AAATTA
1 AAATTA
3660289 TACTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATTAATTATAAA
Found at i:3666690 original size:44 final size:44
Alignment explanation
Indices: 3666640--3666766 Score: 245
Period size: 44 Copynumber: 2.9 Consensus size: 44
3666630 ATGTTCTACC
3666640 TATATCTAATAAAATTTGGCTATCTTAAGGACTCTAATCGAACA
1 TATATCTAATAAAATTTGGCTATCTTAAGGACTCTAATCGAACA
3666684 TATATCTAATAAAATTTGGCTATCTTAAGGACTCTAATCGAACA
1 TATATCTAATAAAATTTGGCTATCTTAAGGACTCTAATCGAACA
*
3666728 TATATCTAATAAAATTTGGCTATCTTAAGGATTCTAATC
1 TATATCTAATAAAATTTGGCTATCTTAAGGACTCTAATC
3666767 ATCGCTTTAT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 82 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (44 bp):
TATATCTAATAAAATTTGGCTATCTTAAGGACTCTAATCGAACA
Found at i:3668066 original size:2 final size:2
Alignment explanation
Indices: 3668055--3668105 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
3668045 AACAATTACC
3668055 TA TA TA -A TA TA TA TA TA TA TA TA TA TA 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
3668096 TA TA TA TA TA
1 TA TA TA TA TA
3668106 AAGAGTAATG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3671189 original size:21 final size:21
Alignment explanation
Indices: 3671162--3671222 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
3671152 TGGCAGATGG
*
3671162 ACTGCCACGTCAGCACCGTGG
1 ACTGCCACGTCAGCACCGTGA
** *
3671183 A-TCGCCACAACATCACCGTGA
1 ACT-GCCACGTCAGCACCGTGA
*
3671204 ACTACCACGTCAGCACCGT
1 ACTGCCACGTCAGCACCGT
3671223 AACGGTCAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.26, C:0.39, G:0.20, T:0.15
Consensus pattern (21 bp):
ACTGCCACGTCAGCACCGTGA
Found at i:3674522 original size:39 final size:39
Alignment explanation
Indices: 3674478--3674556 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
3674468 TCATATACTG
* *
3674478 TGAGTTATATTACAATAAGGATTAATTATTAGTATTTTA
1 TGAGTTATATTACAATAAGGATTAATTATTAATACTTTA
* * *
3674517 TGAGTTATATTACGATTATGATTAATTATTAATACTTTA
1 TGAGTTATATTACAATAAGGATTAATTATTAATACTTTA
3674556 T
1 T
3674557 TTTCTTAGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (39 bp):
TGAGTTATATTACAATAAGGATTAATTATTAATACTTTA
Found at i:3691937 original size:16 final size:16
Alignment explanation
Indices: 3691916--3691957 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
3691906 GGATGATTGG
3691916 CGGGTGATGGATGGAT
1 CGGGTGATGGATGGAT
*
3691932 CGGGTGATTGATGGAT
1 CGGGTGATGGATGGAT
3691948 CGGGTGATGG
1 CGGGTGATGG
3691958 GTCGGGTCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.17, C:0.07, G:0.50, T:0.26
Consensus pattern (16 bp):
CGGGTGATGGATGGAT
Found at i:3692423 original size:17 final size:17
Alignment explanation
Indices: 3692374--3692423 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
3692364 TTGTTCATGT
3692374 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
3692391 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
3692405 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
3692422 TT
1 TT
3692424 AGAAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:3693418 original size:16 final size:16
Alignment explanation
Indices: 3693397--3693428 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3693387 TATGGCTTCT
3693397 TAAAGTACCCAAGAAC
1 TAAAGTACCCAAGAAC
*
3693413 TAAAGTACCTAAGAAC
1 TAAAGTACCCAAGAAC
3693429 GCTAGATTTT
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:0.50, C:0.22, G:0.12, T:0.16
Consensus pattern (16 bp):
TAAAGTACCCAAGAAC
Found at i:3693858 original size:65 final size:65
Alignment explanation
Indices: 3693777--3693930 Score: 211
Period size: 65 Copynumber: 2.4 Consensus size: 65
3693767 ACCCATTTCA
* *
3693777 AATGCATTTTGTGTACCGATGCACA-AGCCATGCATCGATGTACTCTTGAATATTTTGAAACATC
1 AATGCATTTTGTGTACCGATGCACAGA-CCATGCATCGATGCACTCCTGAATATTTTGAAACATC
3693841 G
65 G
** * *
3693842 AATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGCTCTTTTGAAACATTG
1 AATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATATTTTGAAACATCG
* * *
3693907 AATGTAATTAGTGTACCGATGCAC
1 AATGCATTTTGTGTACCGATGCAC
3693931 CCCTAGTATA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 78 0.99
66 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (65 bp):
AATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATATTTTGAAACATCG
Found at i:3696488 original size:65 final size:65
Alignment explanation
Indices: 3696352--3696511 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
3696342 TGCACAAAGA
* *
3696352 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAACCAGAGTGCATCGATGCATGGCTG
* **
3696416 GTACATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AACCTTAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAACCAGAGTGCATCGATGCATGGCT
*
3696479 AT
65 -G
*
3696481 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
3696512 CAATTTAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 28 0.33
65 54 0.64
66 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAACCAGAGTGCATCGATGCATGGCTG
Found at i:3696531 original size:45 final size:45
Alignment explanation
Indices: 3696481--3696585 Score: 201
Period size: 45 Copynumber: 2.3 Consensus size: 45
3696471 TGCATGGTAT
3696481 GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATG
1 GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATG
3696526 GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATG
1 GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATG
*
3696571 GTGCATCGATACATG
1 GTGCATCGATGCATG
3696586 GATTGGTGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (45 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATG
Found at i:3699157 original size:23 final size:22
Alignment explanation
Indices: 3699127--3699206 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
3699117 GGATGACCCT
3699127 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
3699149 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
3699171 GTGTATTGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
3699193 ATGCATCGATGCAC
1 GTGCATCGATGCAC
3699207 TGTTAGGTGT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
21 14 0.31
22 15 0.33
23 16 0.36
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:3703057 original size:22 final size:21
Alignment explanation
Indices: 3703015--3703054 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3703005 GAGTTTATTT
*
3703015 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3703036 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3703055 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3705129 original size:65 final size:64
Alignment explanation
Indices: 3704996--3705205 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 64
3704986 TGCACAAAGA
* * * * *
3704996 GTGCATTGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAACCACAGTGCATCGATACATGGTTG
*
3705060 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AACCTCAGTGCATCGATACATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAACCACAGTGCATCGATACATGGT-
3705124 T-
63 TG
* * ** * ** * *
3705125 GTGCATCGATGCATGAAATGCATTCGAT-ATTCAATTTAATTCATGGTGCATCAATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAA-CCACAGTGCATCGATACATGG-TT
3705189 G
64 G
*
3705190 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
3705206 CTTTGAAAAA
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 43 0.36
65 67 0.55
66 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAACCACAGTGCATCGATACATGGTTG
Found at i:3707054 original size:19 final size:19
Alignment explanation
Indices: 3707030--3707090 Score: 104
Period size: 19 Copynumber: 3.2 Consensus size: 19
3707020 TTGTTGAGAG
*
3707030 GAAAAATCAAACTTTAGAA
1 GAAAAATCGAACTTTAGAA
*
3707049 GAAAAATTGAACTTTAGAA
1 GAAAAATCGAACTTTAGAA
3707068 GAAAAATCGAACTTTAGAA
1 GAAAAATCGAACTTTAGAA
3707087 GAAA
1 GAAA
3707091 TGGTTAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.56, C:0.08, G:0.15, T:0.21
Consensus pattern (19 bp):
GAAAAATCGAACTTTAGAA
Found at i:3708754 original size:17 final size:17
Alignment explanation
Indices: 3708729--3708768 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3708719 CATAGTTTAG
*
3708729 GACTTTCGTATCCTTAA
1 GACTCTCGTATCCTTAA
3708746 GACTCTCGTATCCTTAA
1 GACTCTCGTATCCTTAA
3708763 GACTCT
1 GACTCT
3708769 AGCTTTAGCT
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:0.23, C:0.28, G:0.12, T:0.38
Consensus pattern (17 bp):
GACTCTCGTATCCTTAA
Found at i:3709595 original size:44 final size:43
Alignment explanation
Indices: 3709512--3709611 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 43
3709502 TTGAGCATAA
* *
3709512 TGCATCGATACACCAGAGAGTGTACCGATGCATCTCTTGAATG
1 TGCATCGATACACCAGAAAGTGCACCGATGCATCTCTTGAATG
*
3709555 TGCATCGATACACCATAAAGGTGCACCGATGCAT-TCCTTGAATG
1 TGCATCGATACACCAGAAA-GTGCACCGATGCATCT-CTTGAATG
3709599 TGCATCGATACAC
1 TGCATCGATACAC
3709612 TCATCGGGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
43 18 0.35
44 34 0.65
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (43 bp):
TGCATCGATACACCAGAAAGTGCACCGATGCATCTCTTGAATG
Found at i:3709601 original size:23 final size:22
Alignment explanation
Indices: 3709535--3709607 Score: 67
Period size: 23 Copynumber: 3.3 Consensus size: 22
3709525 CAGAGAGTGT
3709535 ACCGATGCATCTCTTGAATGTGC
1 ACCGATGCATC-CTTGAATGTGC
* * * * *
3709558 ATCGATACA-CCATAAAGGTGC
1 ACCGATGCATCCTTGAATGTGC
3709579 ACCGATGCATTCCTTGAATGTGC
1 ACCGATGCA-TCCTTGAATGTGC
*
3709602 ATCGAT
1 ACCGAT
3709608 ACACTCATCG
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
21 15 0.41
22 1 0.03
23 21 0.57
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (22 bp):
ACCGATGCATCCTTGAATGTGC
Found at i:3710109 original size:12 final size:13
Alignment explanation
Indices: 3710082--3710144 Score: 112
Period size: 12 Copynumber: 5.0 Consensus size: 13
3710072 CTACATATTA
3710082 ATTTTCAAACATT
1 ATTTTCAAACATT
3710095 ATTTTCAAA-ATT
1 ATTTTCAAACATT
3710107 ATTTTCAAACATT
1 ATTTTCAAACATT
3710120 ATTTTCAAA-ATT
1 ATTTTCAAACATT
3710132 ATTTTCAAACATT
1 ATTTTCAAACATT
3710145 TCCCATTAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
12 24 0.50
13 24 0.50
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTCAAACATT
Found at i:3710112 original size:25 final size:25
Alignment explanation
Indices: 3710082--3710144 Score: 126
Period size: 25 Copynumber: 2.5 Consensus size: 25
3710072 CTACATATTA
3710082 ATTTTCAAACATTATTTTCAAAATT
1 ATTTTCAAACATTATTTTCAAAATT
3710107 ATTTTCAAACATTATTTTCAAAATT
1 ATTTTCAAACATTATTTTCAAAATT
3710132 ATTTTCAAACATT
1 ATTTTCAAACATT
3710145 TCCCATTAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTTTCAAACATTATTTTCAAAATT
Found at i:3712305 original size:65 final size:65
Alignment explanation
Indices: 3712235--3712388 Score: 195
Period size: 65 Copynumber: 2.4 Consensus size: 65
3712225 ACCAATTTCA
*
3712235 AATGCATTTTGTGTACCGATGCACA-AGCCATGCATCGATGCAC-TCTTGAATATTTTGGAACAT
1 AATGCATTTTGTGTACCGATGCACAGA-CCATGCATCGATGCACTTC-TGAATATTTTGAAACAT
3712298 CG
64 CG
* ** *
3712300 AATGCATTTTGTGTACCGATGCACAGATCATGCATCGATGCACTTCTGGCTCTTTTGAAACATCG
1 AATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTTCTGAATATTTTGAAACATCG
** * *
3712365 AATATAATTAGTGTACCGATGCAC
1 AATGCATTTTGTGTACCGATGCAC
3712389 CCCTAGTGTA
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
65 75 0.96
66 3 0.04
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (65 bp):
AATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTTCTGAATATTTTGAAACATCG
Found at i:3719127 original size:10 final size:10
Alignment explanation
Indices: 3719094--3719181 Score: 68
Period size: 10 Copynumber: 8.1 Consensus size: 10
3719084 GTGTTTGTGT
3719094 TGTTCGTTTA
1 TGTTCGTTTA
*
3719104 TGTTCATTTATTA
1 TGTTC--GT-TTA
3719117 TGTTCGTTTA
1 TGTTCGTTTA
*
3719127 TGTCCTTTCGTTTG
1 TG----TTCGTTTA
3719141 TGTTCGTTTA
1 TGTTCGTTTA
* *
3719151 CGTTCGTTTG
1 TGTTCGTTTA
*
3719161 TGTTCGTTTG
1 TGTTCGTTTA
3719171 TGTTCGTTTA
1 TGTTCGTTTA
3719181 T
1 T
3719182 CATTTACATG
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
10 44 0.70
11 1 0.02
12 1 0.02
13 8 0.13
14 9 0.14
ACGTcount: A:0.08, C:0.12, G:0.20, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:3719158 original size:20 final size:20
Alignment explanation
Indices: 3719133--3719179 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
3719123 TTTATGTCCT
3719133 TTCGTTTGTGTTCGTTTACG
1 TTCGTTTGTGTTCGTTTACG
**
3719153 TTCGTTTGTGTTCGTTTGTG
1 TTCGTTTGTGTTCGTTTACG
3719173 TTCGTTT
1 TTCGTTT
3719180 ATCATTTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.02, C:0.13, G:0.26, T:0.60
Consensus pattern (20 bp):
TTCGTTTGTGTTCGTTTACG
Found at i:3719905 original size:43 final size:43
Alignment explanation
Indices: 3719838--3719947 Score: 148
Period size: 43 Copynumber: 2.6 Consensus size: 43
3719828 TGACAACAAA
* * * * *
3719838 AAACGCCGCAATAGGTCAAGATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGACATTTTTGGAAC
* *
3719881 AAACGCTGCAAATGGTCGATATCTATAGCGACATTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGACATTTTTGGAAC
*
3719924 AAATGCCGCAAAAGGTCGATATCT
1 AAACGCCGCAAAAGGTCGATATCT
3719948 GTGTTTGTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGATATCTATAGCGACATTTTTGGAAC
Found at i:3720036 original size:41 final size:41
Alignment explanation
Indices: 3719981--3720089 Score: 121
Period size: 41 Copynumber: 2.6 Consensus size: 41
3719971 TCTATAGCGG
*
3719981 CGTTTTTGGAACAAACGTCGCAAAAGGTCAAATCTACAACGA
1 CGTTTTTGGAACAAACG-CGCAAAAGGTCAAATCTACAACAA
* * * * * *
3720023 CG-TTTTGTAACAAACGCTGCAAAAGTTTAGATCTATAGCAA
1 CGTTTTTGGAACAAACGC-GCAAAAGGTCAAATCTACAACAA
3720064 CGTTTTTGGAACAAACGCCGCAAAAG
1 CGTTTTTGGAACAAACG-CGCAAAAG
3720090 ATCGAGATCT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
40 1 0.02
41 32 0.57
42 22 0.39
43 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (41 bp):
CGTTTTTGGAACAAACGCGCAAAAGGTCAAATCTACAACAA
Found at i:3720113 original size:42 final size:43
Alignment explanation
Indices: 3719958--3720143 Score: 200
Period size: 42 Copynumber: 4.4 Consensus size: 43
3719948 GTGTTTGTTC
* * *
3719958 CAAAAGATAGAGATCTATAGCGGCGTTTTTGGAACAAACGTCG
1 CAAAAGATCGAGATCTATAGCGACGTTTTTGGAACAAACGCCG
* * * * * *
3720001 CAAAAGGTC-AAATCTACAACGACG-TTTTGTAACAAACGCTG
1 CAAAAGATCGAGATCTATAGCGACGTTTTTGGAACAAACGCCG
** *
3720042 CAAAAG-TTTAGATCTATAGCAACGTTTTTGGAACAAACGCCG
1 CAAAAGATCGAGATCTATAGCGACGTTTTTGGAACAAACGCCG
* ** *
3720084 CAAAAGATCGAGATCTATAGTGTTG-TTTTGGAACAAACGCTG
1 CAAAAGATCGAGATCTATAGCGACGTTTTTGGAACAAACGCCG
3720126 CAAAAGATCGAGATCTAT
1 CAAAAGATCGAGATCTAT
3720144 CGTAAAAGGT
Statistics
Matches: 117, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
40 1 0.01
41 31 0.26
42 66 0.56
43 19 0.16
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (43 bp):
CAAAAGATCGAGATCTATAGCGACGTTTTTGGAACAAACGCCG
Found at i:3723812 original size:15 final size:15
Alignment explanation
Indices: 3723787--3723822 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3723777 GGAGAATTGA
*
3723787 AATAAGGTATGTGAT
1 AATAAGATATGTGAT
*
3723802 TATAAGATATGTGAT
1 AATAAGATATGTGAT
3723817 AATAAG
1 AATAAG
3723823 TTATATGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (15 bp):
AATAAGATATGTGAT
Found at i:3724233 original size:30 final size:30
Alignment explanation
Indices: 3724197--3724289 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
3724187 ATGGTCCTTA
*
3724197 TGGACAGTTACTGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
3724227 TGGACAGTTACCGATGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
3724257 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3724286 TGGA
1 TGGA
3724290 TAAGTCCTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 17 0.30
30 40 0.70
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:3728906 original size:15 final size:15
Alignment explanation
Indices: 3728881--3728916 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3728871 GGAGAATTGA
*
3728881 AATAAGGTATGTGAT
1 AATAAGATATGTGAT
*
3728896 TATAAGATATGTGAT
1 AATAAGATATGTGAT
3728911 AATAAG
1 AATAAG
3728917 TTATATGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (15 bp):
AATAAGATATGTGAT
Found at i:3729386 original size:29 final size:30
Alignment explanation
Indices: 3729291--3729383 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
3729281 GTGGTCCTTA
3729291 TGGACAGTTATCGAGGATCTTTATGACCTC
1 TGGACAGTTATCGAGGATCTTTATGACCTC
* *
3729321 TGGACAGTTACCGAGGATCTTTATGGCCTC
1 TGGACAGTTATCGAGGATCTTTATGACCTC
* * *
3729351 TGGATAGTTATC-AGGGTCTTTGTGACCTC
1 TGGACAGTTATCGAGGATCTTTATGACCTC
3729380 TGGA
1 TGGA
3729384 TAGGTCCTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
29 18 0.32
30 38 0.68
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.33
Consensus pattern (30 bp):
TGGACAGTTATCGAGGATCTTTATGACCTC
Found at i:3731625 original size:44 final size:43
Alignment explanation
Indices: 3731576--3731699 Score: 103
Period size: 43 Copynumber: 2.9 Consensus size: 43
3731566 AAGTATGAGC
3731576 ATTTTTTAAATTAAAACGCCACTAAAGTA-TAAGTATTTAGCGGT
1 ATTTTTT-AATTAAAACGCCACTAAAGTATTAAGT-TTTAGCGGT
** * * *
3731620 ATTTTTTGCTTAAAATGCCATTAAAGTATTACGTTTTAGCGG-
1 ATTTTTTAATTAAAACGCCACTAAAGTATTAAGTTTTAGCGGT
* * * * *
3731662 AGTTTGTTGA--AAAATGCCACTAAAGTACTAGGTTTTAG
1 A-TTTTTTAATTAAAACGCCACTAAAGTATTAAGTTTTAG
3731700 TGGCGTTTGT
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
41 25 0.37
42 1 0.01
43 31 0.46
44 11 0.16
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (43 bp):
ATTTTTTAATTAAAACGCCACTAAAGTATTAAGTTTTAGCGGT
Found at i:3731716 original size:41 final size:41
Alignment explanation
Indices: 3731588--3731709 Score: 113
Period size: 41 Copynumber: 2.9 Consensus size: 41
3731578 TTTTTAAATT
* * * *
3731588 AAAACGCCACTAAAGTA-TAAGTATTTAGCGGTA-TTTTTTGCTT
1 AAAATGCCACTAAAGTACTACGT-TTTAGCGG-AGTTTGTTG--A
* *
3731631 AAAATGCCATTAAAGTATTACGTTTTAGCGGAGTTTGTTGA
1 AAAATGCCACTAAAGTACTACGTTTTAGCGGAGTTTGTTGA
* * *
3731672 AAAATGCCACTAAAGTACTAGGTTTTAGTGGCGTTTGT
1 AAAATGCCACTAAAGTACTACGTTTTAGCGGAGTTTGT
3731710 CTAAAAACCC
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 33 0.49
42 1 0.01
43 29 0.43
44 4 0.06
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.36
Consensus pattern (41 bp):
AAAATGCCACTAAAGTACTACGTTTTAGCGGAGTTTGTTGA
Found at i:3734274 original size:20 final size:20
Alignment explanation
Indices: 3734241--3734296 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
3734231 AATCGCAACT
*
3734241 CGATTTTCCAAATTCACAATG
1 CGATTTT-CAAATTCACAATA
*
3734262 CGATTTTCAAATTCGCAATA
1 CGATTTTCAAATTCACAATA
*
3734282 CGGAATTTCAAATTC
1 C-GATTTTCAAATTC
3734297 TCAACTCGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 12 0.39
21 19 0.61
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
CGATTTTCAAATTCACAATA
Found at i:3734331 original size:21 final size:21
Alignment explanation
Indices: 3734169--3734331 Score: 72
Period size: 20 Copynumber: 8.0 Consensus size: 21
3734159 AATGACCAAC
* *
3734169 AAATTCGCAACGCGAACTAC-
1 AAATTCGCAACGCGAATTTCT
* * * *
3734189 AATTTCGCAACAC-AGTTTCC
1 AAATTCGCAACGCGAATTTCT
* * *
3734209 AAATTCGCAACTC-AGTTTTT
1 AAATTCGCAACGCGAATTTCT
* * * *
3734229 GCAA-TCGCAACTCGATTTTCC
1 -AAATTCGCAACGCGAATTTCT
* * *
3734250 AAATTCACAATGCGATTTTC-
1 AAATTCGCAACGCGAATTTCT
3734270 AAATTCGCAATACG-GAATTTC-
1 AAATTCGC-A-ACGCGAATTTCT
* *
3734291 AAATTCTCAACTCG-ATTTCT
1 AAATTCGCAACGCGAATTTCT
*
3734311 GAATTCGCAACGCGAATTTCT
1 AAATTCGCAACGCGAATTTCT
3734332 TTTTCGCAAC
Statistics
Matches: 109, Mismatches: 25, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
19 10 0.09
20 58 0.53
21 39 0.36
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (21 bp):
AAATTCGCAACGCGAATTTCT
Done.