Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 95 of 125
Found at i:18488319 original size:89 final size:87
Alignment explanation
Indices: 18488064--18488362 Score: 284
Period size: 89 Copynumber: 3.4 Consensus size: 87
18488054 GGGTTTGAAA
* * * *
18488064 TTTTAGGGTTTGAAAAGTTTAGGGTTTTGATTTTAGGGTTTAGA-GATT-AGATTTTTTATTTTA
1 TTTTAAGGTTTG-AAAGTTTAGGGTTTTGATTTTAGGGTTTAGAGGTTTAAGGTTTGTT-TTTTA
18488127 GGGTTTAAAGGGTTTA-AGCTTTTAG
64 GGGTTTAAAGGGTTTAGAG--TTTAG
* * * * * *
18488152 TTTTATGGTTTGGAAGATTTAGGATTTTGATTTTAGGGTTTAGGGGGTTTAGGGTTT-TGATTTT
1 TTTTAAGGTTTGAAAG-TTTAGGGTTTTGATTTTAGGGTTTA-GAGGTTTAAGGTTTGT-TTTTT
*
18488216 AGGATTTAAAGGGTTTAGAGTTTAG
63 AGGGTTTAAAGGGTTTAGAGTTTAG
* * *
18488241 TTTTAAGGTTTGAAAGTTTAGAGTTTTGATTTTAGGATTTATAAGGTTTAAGGTTTCGTTTTTTA
1 TTTTAAGGTTTGAAAGTTTAGGGTTTTGATTTTAGGGTTTA-GAGGTTTAAGGTTT-GTTTTTTA
* * * *
18488306 GGGCTTT-GAGGGTTTAGGGATTAA
64 GGG-TTTAAAGGGTTTAGAGTTTAG
* * *
18488330 TTTTAAGGTTTGAAGGTTTGGGGTTTTCATTTT
1 TTTTAAGGTTTGAAAGTTTAGGGTTTTGATTTT
18488363 TTTTAATTTT
Statistics
Matches: 174, Mismatches: 28, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
87 3 0.02
88 68 0.39
89 69 0.40
90 28 0.16
91 6 0.03
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.48
Consensus pattern (87 bp):
TTTTAAGGTTTGAAAGTTTAGGGTTTTGATTTTAGGGTTTAGAGGTTTAAGGTTTGTTTTTTAGG
GTTTAAAGGGTTTAGAGTTTAG
Found at i:18488678 original size:18 final size:17
Alignment explanation
Indices: 18488641--18488685 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
18488631 AAGGAAAAAA
* *
18488641 ATTATTATTTAATTATT
1 ATTATTTTTTAATGATT
18488658 ATTATTTTTTATATGATT
1 ATTATTTTTTA-ATGATT
18488676 ATTATTTTTT
1 ATTATTTTTT
18488686 TAGCATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
ATTATTTTTTAATGATT
Found at i:18488874 original size:11 final size:10
Alignment explanation
Indices: 18488853--18488887 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
18488843 AAAAAAATTT
18488853 AAAATTTAAA
1 AAAATTTAAA
*
18488863 AACATTTAAA
1 AAAATTTAAA
*
18488873 AAAATTTTAA
1 AAAATTTAAA
18488883 AAAAT
1 AAAAT
18488888 AATAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:18488893 original size:21 final size:20
Alignment explanation
Indices: 18488853--18488896 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
18488843 AAAAAAATTT
*
18488853 AAAATTTAAAAACATTTAAA
1 AAAATTTAAAAACATATAAA
18488873 AAAATTTTAAAAA-ATAATAAA
1 AAAA-TTTAAAAACAT-ATAAA
18488894 AAA
1 AAA
18488897 TACTTGAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATTTAAAAACATATAAA
Found at i:18490031 original size:17 final size:16
Alignment explanation
Indices: 18489993--18490039 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
18489983 GTTTTTTGTT
18489993 TTTTAATTAATT-ATTA
1 TTTTAATT-ATTAATTA
18490009 TATTTAATTATTAATTGA
1 T-TTTAATTATTAATT-A
18490027 TTTTAA-TATTAAT
1 TTTTAATTATTAAT
18490040 AAATAGAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 11 0.39
17 15 0.54
18 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTAATTATTAATTA
Found at i:18490708 original size:334 final size:336
Alignment explanation
Indices: 18490082--18490762 Score: 1159
Period size: 334 Copynumber: 2.0 Consensus size: 336
18490072 AGACCCGAAT
18490082 AAAATTCGATGTCTACAGCTACCCCTCTTTATGCATTATTGAGAATCAGGAATAGAAAAAAGACA
1 AAAATTCGATGTCTACAGCTACCCCTCTTTATGCATTATTGAGAATCAGGAATAGAAAAAAGACA
* * * * * *
18490147 TAGACAACAATTTTGTCTAGAAGCAAATCATGAATTTTTCAAAAGTTTTTTTTTCTTTTTTTTTT
66 CAAACAACAATTTTATCCAAAAGCAAATCATGAATTTTTCAAAAG-------TTCATTTTTTTTT
* *
18490212 TGTTTTGAACCACAAGTCAAGTGATAAAGAAAATGACTGGAATGACACCGCGAGCTGAAAAGTAA
124 TATTTTAAACCACAAGTCAAGTGATAAAGAAAATGACTGGAATGACACCGCGAGCTGAAAAGTAA
18490277 AGATTGACTAGGACAACACCGTAAGTCAATAAATAAATAATCGACTAGGACAACACCATGAGTCG
189 AGATTGACTAGGACAACACCGTAAGTCAATAAATAAATAATCGACTAGGACAACACCATGAGTCG
* * *
18490342 AAATTAAAGATCGACTATGATGATATTGCAAGTCGAGAAATAAAGAATCGATCGGGACAACACTG
254 AAATTAAAGATCGACTATGACGATACTGCAAGTCGAGAAATAAAGAATCGATCGGGACAACACTA
18490407 TAAATCGAAATTATGCCC
319 TAAATCGAAATTATGCCC
18490425 AAAATTCGATGTCTACAGCTACCCCTCTTTATGCATTATTGAGAATCAGGAATAGAAAAAAGACA
1 AAAATTCGATGTCTACAGCTACCCCTCTTTATGCATTATTGAGAATCAGGAATAGAAAAAAGACA
18490490 CAAACAACAATTTTATCCAAAAGCAAATCATGAATTTTTCAAAAG-T-ATTTTTTTTTTATTTTA
66 CAAACAACAATTTTATCCAAAAGCAAATCATGAATTTTTCAAAAGTTCATTTTTTTTTTATTTTA
* *
18490553 AATCACAAGTCAAGTGATAAAGAAAATGACTGGGATGACACCGCGAGCTGAAAAGTAAAGATTGA
131 AACCACAAGTCAAGTGATAAAGAAAATGACTGGAATGACACCGCGAGCTGAAAAGTAAAGATTGA
18490618 CTAGGACAACACCGTAAGTCAATAAATAAATAATCGACTAGGACAACACCATGAGTCGAAATTAA
196 CTAGGACAACACCGTAAGTCAATAAATAAATAATCGACTAGGACAACACCATGAGTCGAAATTAA
*
18490683 AGATTGACTATGACGATACTGCAAGTCGAGAAATAAAGAATCGATCGGGACAACACTATAAATCG
261 AGATCGACTATGACGATACTGCAAGTCGAGAAATAAAGAATCGATCGGGACAACACTATAAATCG
18490748 AAATTATGCCC
326 AAATTATGCCC
18490759 AAAA
1 AAAA
18490763 GTCTTAAGGA
Statistics
Matches: 324, Mismatches: 14, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
334 218 0.67
335 1 0.00
343 105 0.32
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (336 bp):
AAAATTCGATGTCTACAGCTACCCCTCTTTATGCATTATTGAGAATCAGGAATAGAAAAAAGACA
CAAACAACAATTTTATCCAAAAGCAAATCATGAATTTTTCAAAAGTTCATTTTTTTTTTATTTTA
AACCACAAGTCAAGTGATAAAGAAAATGACTGGAATGACACCGCGAGCTGAAAAGTAAAGATTGA
CTAGGACAACACCGTAAGTCAATAAATAAATAATCGACTAGGACAACACCATGAGTCGAAATTAA
AGATCGACTATGACGATACTGCAAGTCGAGAAATAAAGAATCGATCGGGACAACACTATAAATCG
AAATTATGCCC
Found at i:18490709 original size:72 final size:72
Alignment explanation
Indices: 18490608--18490753 Score: 168
Period size: 72 Copynumber: 2.0 Consensus size: 72
18490598 AGCTGAAAAG
* * * *
18490608 TAAAGATTGACTAGGACAACACCGTAAGTCAATAAATAAATAATCGA-CTAGGACAACACCATGA
1 TAAAGATTGACTAGGACAACACCGCAAGTCAAGAAATAAAGAATCGATC-AGGACAACACCATAA
*
18490672 GTCGAAAT
65 ATCGAAAT
* * * * * * *
18490680 TAAAGATTGACTATGACGATACTGCAAGTCGAGAAATAAAGAATCGATCGGGACAACACTATAAA
1 TAAAGATTGACTAGGACAACACCGCAAGTCAAGAAATAAAGAATCGATCAGGACAACACCATAAA
18490745 TCGAAAT
66 TCGAAAT
18490752 TA
1 TA
18490754 TGCCCAAAAG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
72 60 0.98
73 1 0.02
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (72 bp):
TAAAGATTGACTAGGACAACACCGCAAGTCAAGAAATAAAGAATCGATCAGGACAACACCATAAA
TCGAAAT
Found at i:18490994 original size:22 final size:22
Alignment explanation
Indices: 18490967--18491038 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
18490957 ACCACAAATC
**
18490967 AAAATTATGCTTGGAGGACTTA
1 AAAATTATGCCAGGAGGACTTA
*
18490989 AAAATTATGCCAGGAGGTCTTA
1 AAAATTATGCCAGGAGGACTTA
* *
18491011 AAAATCATGCCCA-GAGGTCTTA
1 AAAATTATG-CCAGGAGGACTTA
18491033 CAAAAT
1 -AAAAT
18491039 AGATCGGGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
22 36 0.82
23 8 0.18
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (22 bp):
AAAATTATGCCAGGAGGACTTA
Found at i:18491024 original size:23 final size:22
Alignment explanation
Indices: 18490979--18491038 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
18490969 AATTATGCTT
* *
18490979 GGAGGACTTAAAAATTATGCCA
1 GGAGGTCTTAAAAATCATGCCA
18491001 GGAGGTCTTAAAAATCATGCCCA
1 GGAGGTCTTAAAAATCATG-CCA
18491024 -GAGGTCTTACAAAAT
1 GGAGGTCTTA-AAAAT
18491039 AGATCGGGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (22 bp):
GGAGGTCTTAAAAATCATGCCA
Found at i:18491474 original size:37 final size:37
Alignment explanation
Indices: 18491433--18491504 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
18491423 CAACACCGTA
*
18491433 AGTCAAAAAATAAGAAAA-CAATTGGGACAACACCACG
1 AGTCAAAAAATAA-AAAATCAATCGGGACAACACCACG
* * *
18491470 AGTCAAAAAGTAAAAAATCGATCGGGATAACACCA
1 AGTCAAAAAATAAAAAATCAATCGGGACAACACCA
18491505 TAAATCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 4 0.13
37 26 0.87
ACGTcount: A:0.53, C:0.18, G:0.17, T:0.12
Consensus pattern (37 bp):
AGTCAAAAAATAAAAAATCAATCGGGACAACACCACG
Found at i:18491790 original size:33 final size:33
Alignment explanation
Indices: 18491737--18491973 Score: 196
Period size: 33 Copynumber: 7.2 Consensus size: 33
18491727 AGTTACGTTA
* *
18491737 GGCTTAAAACTTCATTTGGGGGCCAGATAAACTG
1 GGCTTAAAATTTCA-TTGAGGGCCAGATAAACTG
* *
18491771 GGTTTAAAATTTTATTG-GGGTCCAGATAAACTG
1 GGCTTAAAATTTCATTGAGGG-CCAGATAAACTG
* * *
18491804 GGCTTAAAACTTCATTGATGGCTAGATAAACTG
1 GGCTTAAAATTTCATTGAGGGCCAGATAAACTG
* * * *
18491837 GGCTTAAAATTTCCTTAAGGGCCAGCTAAACTA
1 GGCTTAAAATTTCATTGAGGGCCAGATAAACTG
* * * *
18491870 GGTTTAAAACTTCATTGATGG-C--ATAAACTA
1 GGCTTAAAATTTCATTGAGGGCCAGATAAACTG
* * * *
18491900 GGCTT-AAATATTCTTTGAAGGCCAGATAAATTA
1 GGCTTAAAAT-TTCATTGAGGGCCAGATAAACTG
* * * *
18491933 GGCTTAAGATTTCATTAAGGGCCAAATAAATTG
1 GGCTTAAAATTTCATTGAGGGCCAGATAAACTG
*
18491966 AGCTTAAA
1 GGCTTAAA
18491974 TCTTATGTAG
Statistics
Matches: 162, Mismatches: 34, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
29 3 0.02
30 20 0.12
31 1 0.01
32 4 0.02
33 118 0.73
34 16 0.10
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (33 bp):
GGCTTAAAATTTCATTGAGGGCCAGATAAACTG
Found at i:18493975 original size:25 final size:25
Alignment explanation
Indices: 18493927--18493977 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
18493917 AAAAAAATGG
* *
18493927 TCATGTAGAATGAACAAGAGAAGGA
1 TCATATAGAATGAACAAGAAAAGGA
**
18493952 TCATATAGAATGAATTAGAAAAGGA
1 TCATATAGAATGAACAAGAAAAGGA
18493977 T
1 T
18493978 TATGTGGGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.49, C:0.06, G:0.24, T:0.22
Consensus pattern (25 bp):
TCATATAGAATGAACAAGAAAAGGA
Found at i:18496215 original size:4 final size:4
Alignment explanation
Indices: 18496189--18496285 Score: 88
Period size: 4 Copynumber: 24.2 Consensus size: 4
18496179 TGCATTATAT
* * * **
18496189 TGAA TGAA T-ACA TAAA TGGA TGAA TGAA TGAA TGAA TGAA TGCA CAAA
1 TGAA TGAA TGA-A TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA
* * ** *
18496237 TGGA TGAA TGAA TGAA TGCA CAAA TGAA TGAA TGAA TGAA TGAG TGAA
1 TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA
18496285 T
1 T
18496286 ACGTAACTGA
Statistics
Matches: 72, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
3 1 0.01
4 70 0.97
5 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (4 bp):
TGAA
Found at i:18496216 original size:24 final size:24
Alignment explanation
Indices: 18496211--18496278 Score: 127
Period size: 24 Copynumber: 2.8 Consensus size: 24
18496201 TAAATGGATG
18496211 AATGAATGAATGAATGAATGCACA
1 AATGAATGAATGAATGAATGCACA
*
18496235 AATGGATGAATGAATGAATGCACA
1 AATGAATGAATGAATGAATGCACA
18496259 AATGAATGAATGAATGAATG
1 AATGAATGAATGAATGAATG
18496279 AGTGAATACG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.49, C:0.06, G:0.24, T:0.22
Consensus pattern (24 bp):
AATGAATGAATGAATGAATGCACA
Found at i:18496238 original size:32 final size:32
Alignment explanation
Indices: 18496189--18496254 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
18496179 TGCATTATAT
*
18496189 TGAATGAATACATAAATGGATGAATGAATGAA
1 TGAATGAATACACAAATGGATGAATGAATGAA
*
18496221 TGAATGAATGCACAAATGGATGAATGAATGAA
1 TGAATGAATACACAAATGGATGAATGAATGAA
18496253 TG
1 TG
18496255 CACAAATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (32 bp):
TGAATGAATACACAAATGGATGAATGAATGAA
Found at i:18499657 original size:28 final size:28
Alignment explanation
Indices: 18499601--18499674 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
18499591 TAGGGCTTGA
*
18499601 ATTTTAGGGTTTGAAAAGTTTAGGATTTTC
1 ATTTTAGGGTTT--AAAGATTAGGATTTTC
* *
18499631 ATTTTAGGGTTTAAAGATTAGGTTTTTT
1 ATTTTAGGGTTTAAAGATTAGGATTTTC
*
18499659 ATTTTGGGGTTTAAAG
1 ATTTTAGGGTTTAAAG
18499675 GGTTTAAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 28 0.70
30 12 0.30
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (28 bp):
ATTTTAGGGTTTAAAGATTAGGATTTTC
Found at i:18499701 original size:88 final size:83
Alignment explanation
Indices: 18499600--18499891 Score: 222
Period size: 89 Copynumber: 3.4 Consensus size: 83
18499590 TTAGGGCTTG
*
18499600 AATTTTAGGGTTTGAAAAGTTTAGGATTTTCATTTTAGGGTTTAAAGATTAGGTTTTTTATTTTG
1 AATTTTA-AGTTTG-AAAGTTTAGGATTTTCATTTTAGGGTTTAAAGATTAGGTTTTTTATTTT-
18499665 GGGTTTAAAGGGTTTAAGGTTTT
63 GGGTTTAAAGGGTTT-AGG-TTT
* * * * * *
18499688 AGTTTTACAGTTTGGAGGATTTAGGGTTTTGATTTTAGGGTTT----A-T-GG-TTTTGATTTTA
1 AATTTTA-AGTTTGAAAG-TTTAGGATTTTCATTTTAGGGTTTAAAGATTAGGTTTTTTATTTT-
*
18499746 TGGTTTAAAGGGTTTAGAGTTT
63 GGGTTTAAAGGGTTTAG-GTTT
* * * *
18499768 AATTTTAAGGTTTGAAAGTTTAGAATTTTGATTTTATGGTTTAGAAGTTTTAGGGTTTCGTTT-T
1 AATTTTAA-GTTTGAAAGTTTAGGATTTTCATTTTAGGGTTTA-AAG-ATTA-GGTTT--TTTAT
* *
18499832 TTTGGGTTTTAAGGGTTTAGGGATT
60 TTTGGGTTTAAAGGGTTTA-GGTTT
* * *
18499857 AATTTTAGGGTTTGAAGGTTTAGGGTTTTCATTTT
1 AATTTTA-AGTTTGAAAGTTTAGGATTTTCATTTT
18499892 TTTTAATTTT
Statistics
Matches: 161, Mismatches: 26, Indels: 33
0.73 0.12 0.15
Matches are distributed among these distances:
79 22 0.14
80 18 0.11
81 24 0.15
82 2 0.01
83 1 0.01
84 1 0.01
86 1 0.01
87 2 0.01
88 35 0.22
89 48 0.30
90 5 0.03
91 2 0.01
ACGTcount: A:0.22, C:0.01, G:0.26, T:0.50
Consensus pattern (83 bp):
AATTTTAAGTTTGAAAGTTTAGGATTTTCATTTTAGGGTTTAAAGATTAGGTTTTTTATTTTGGG
TTTAAAGGGTTTAGGTTT
Found at i:18499736 original size:21 final size:21
Alignment explanation
Indices: 18499707--18499752 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
18499697 GTTTGGAGGA
18499707 TTTAGGGTTTTGATTTTAGGG
1 TTTAGGGTTTTGATTTTAGGG
* *
18499728 TTTATGGTTTTGATTTTATGG
1 TTTAGGGTTTTGATTTTAGGG
18499749 TTTA
1 TTTA
18499753 AAGGGTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (21 bp):
TTTAGGGTTTTGATTTTAGGG
Found at i:18499891 original size:29 final size:28
Alignment explanation
Indices: 18499726--18499884 Score: 102
Period size: 29 Copynumber: 5.4 Consensus size: 28
18499716 TTGATTTTAG
* * * *
18499726 GGTTTATGGTTTTGATTTTATGGTTTAAA
1 GGTTTA-GGGTTTAATTTTAGGGTTTGAA
* *
18499755 GGGTTTAGAGTTTAATTTTAAGGTTTGAA
1 -GGTTTAGGGTTTAATTTTAGGGTTTGAA
* ** * *
18499784 AGTTTAGAATTTTGATTTTATGGTTTAGAA
1 GGTTTAG-GGTTTAATTTTAGGGTTT-GAA
* ** * *
18499814 GTTTTAGGGTTTCGTTTTTTTGGGTTTTAA
1 GGTTTAGGGTTT--AATTTTAGGGTTTGAA
*
18499844 GGGTTTAGGGATTAATTTTAGGGTTTGAA
1 -GGTTTAGGGTTTAATTTTAGGGTTTGAA
18499873 GGTTTAGGGTTT
1 GGTTTAGGGTTT
18499885 TCATTTTTTT
Statistics
Matches: 99, Mismatches: 25, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
28 17 0.17
29 47 0.47
30 16 0.16
31 19 0.19
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.50
Consensus pattern (28 bp):
GGTTTAGGGTTTAATTTTAGGGTTTGAA
Found at i:18500204 original size:15 final size:16
Alignment explanation
Indices: 18500184--18500213 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18500174 ATTATTCAAT
18500184 TATTATTATT-TTTTA
1 TATTATTATTATTTTA
18500199 TATTATTATTATTTT
1 TATTATTATTATTTT
18500214 TTAGCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTATTATTATTTTA
Found at i:18500205 original size:18 final size:18
Alignment explanation
Indices: 18500182--18500216 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
18500172 TTATTATTCA
18500182 ATTATTATTATTTTTTAT
1 ATTATTATTATTTTTTAT
18500200 ATTATTATTATTTTTTA
1 ATTATTATTATTTTTTA
18500217 GCATTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTATTATTATTTTTTAT
Found at i:18501482 original size:17 final size:16
Alignment explanation
Indices: 18501444--18501490 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
18501434 CTTTTCTTTT
18501444 TTTTAATTAATT-ATTA
1 TTTTAATT-ATTAATTA
18501460 TATTTAATTATTAATTGA
1 T-TTTAATTATTAATT-A
18501478 TTTTAA-TATTAAT
1 TTTTAATTATTAAT
18501491 AAATAGAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 11 0.39
17 15 0.54
18 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTAATTATTAATTA
Found at i:18503978 original size:18 final size:19
Alignment explanation
Indices: 18503957--18503994 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
18503947 ATTAAATTTA
18503957 AATATACAAAATAAT-TAT
1 AATATACAAAATAATATAT
* *
18503975 AATATATAATATAATATAT
1 AATATACAAAATAATATAT
18503994 A
1 A
18503995 TTAAAGGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AATATACAAAATAATATAT
Found at i:18505585 original size:65 final size:66
Alignment explanation
Indices: 18505497--18505693 Score: 217
Period size: 64 Copynumber: 3.0 Consensus size: 66
18505487 GTTGGTGGGA
* * *
18505497 TTAATTTTCAAAAAATTATTTTTAAACCCATGAAAATCCTCTAATA-TGTTGGTATGATTTTAAG
1 TTAATTTTCAAAAAATTATTTTTAAACCCAT-AAAATCCTCCAATAGT-TTGGTAAGAATTTAAG
18505561 AAT
64 AAT
* *
18505564 TTAATTTT-AAAAAA-TATTTTTAAACCTATAAAATCCTCCAATAGTTTGGTAAGAATTTACGAA
1 TTAATTTTCAAAAAATTATTTTTAAACCCATAAAATCCTCCAATAGTTTGGTAAGAATTTAAGAA
18505627 T
66 T
** * * * * * *
18505628 TT-ATCCTCAAAAAATTA-TTTTAAACCTATAAAATCTTCCAACAGTTTGAT-GGAATTTATGAA
1 TTAATTTTCAAAAAATTATTTTTAAACCCATAAAATCCTCCAATAGTTTGGTAAGAATTTAAGAA
18505690 T
66 T
18505691 TTA
1 TTA
18505694 CTTTCTAAAA
Statistics
Matches: 114, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
63 16 0.14
64 67 0.59
65 17 0.15
66 6 0.05
67 8 0.07
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (66 bp):
TTAATTTTCAAAAAATTATTTTTAAACCCATAAAATCCTCCAATAGTTTGGTAAGAATTTAAGAA
T
Found at i:18506817 original size:5 final size:5
Alignment explanation
Indices: 18506807--18506930 Score: 55
Period size: 5 Copynumber: 24.8 Consensus size: 5
18506797 AATTAAAAGG
* *
18506807 ATAAA ATAAA A-ATAG ATAAA CATAAA AGACAA ATAAA GA-AAA GAT-AA
1 ATAAA ATAAA ATA-AA ATAAA -ATAAA ATA-AA ATAAA -ATAAA -ATAAA
* * * * * *
18506854 ATAATTA ATAAA ATACA A-AAT ACAAA AAAAA ATAAA AAAAA ATAAA GTAAA
1 ATAA--A ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
*
18506905 A-CAA AT-AA AT-AA ATAAA ATAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
18506931 GATGGAGAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 24
0.70 0.11 0.18
Matches are distributed among these distances:
4 16 0.17
5 60 0.65
6 11 0.12
7 5 0.05
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:18506893 original size:27 final size:29
Alignment explanation
Indices: 18506852--18506924 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 29
18506842 AAGAAAAGAT
*
18506852 AAAT-AATTAATAAAATACAAAATACAAA-
1 AAATAAATAAATAAAATACAAAATA-AAAC
* * *
18506880 AAA-AAATAAA-AAAAAATAAAGTAAAAC
1 AAATAAATAAATAAAATACAAAATAAAAC
18506907 AAATAAATAAATAAAATA
1 AAATAAATAAATAAAATA
18506925 AAATAAGATG
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
26 3 0.08
27 13 0.36
28 15 0.42
29 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.18
Consensus pattern (29 bp):
AAATAAATAAATAAAATACAAAATAAAAC
Found at i:18507847 original size:46 final size:46
Alignment explanation
Indices: 18507797--18507888 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
18507787 CTTCACAAGT
18507797 AAAAATATAAACAAGTAACATTCTTAACAATTTCTATCATTATTCA
1 AAAAATATAAACAAGTAACATTCTTAACAATTTCTATCATTATTCA
18507843 AAAAATATAAACAAGTAACATTCTTAACAATTTCTATCATTATTCA
1 AAAAATATAAACAAGTAACATTCTTAACAATTTCTATCATTATTCA
18507889 TTTCTTGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (46 bp):
AAAAATATAAACAAGTAACATTCTTAACAATTTCTATCATTATTCA
Found at i:18508150 original size:3 final size:3
Alignment explanation
Indices: 18508142--18508284 Score: 170
Period size: 3 Copynumber: 48.7 Consensus size: 3
18508132 GTATAGTATG
* * *
18508142 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA -TA GTA -TA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
18508188 -TG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
18508235 TTA TTA TTA TTA TATA GTA -TA GTA -TA TTG TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
18508280 TTA TT
1 TTA TT
18508285 TTCATTTTTT
Statistics
Matches: 127, Mismatches: 6, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
2 9 0.07
3 114 0.90
4 4 0.03
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:18508190 original size:48 final size:48
Alignment explanation
Indices: 18508103--18508222 Score: 215
Period size: 48 Copynumber: 2.5 Consensus size: 48
18508093 TATTATTAGC
* *
18508103 ATTATTATT-TTTTTACTATTATTACTATAGTATAGTATGTTATTATT
1 ATTATTATTATTATTATTATTATTACTATAGTATAGTATGTTATTATT
18508150 ATTATTATTATTATTATTATTATTACTATAGTATAGTATGTTATTATT
1 ATTATTATTATTATTATTATTATTACTATAGTATAGTATGTTATTATT
18508198 ATTATTATTATTATTATTATTATTA
1 ATTATTATTATTATTATTATTATTA
18508223 TTATTATTAT
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
47 9 0.13
48 61 0.87
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (48 bp):
ATTATTATTATTATTATTATTATTACTATAGTATAGTATGTTATTATT
Found at i:18509018 original size:20 final size:20
Alignment explanation
Indices: 18508993--18509030 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18508983 CGATCATAGG
*
18508993 TTTTCCTTTTTTCATTTTAT
1 TTTTCCTTTTTTAATTTTAT
18509013 TTTTCCTTTTTTAATTTT
1 TTTTCCTTTTTTAATTTT
18509031 TTTATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTCCTTTTTTAATTTTAT
Found at i:18509058 original size:21 final size:21
Alignment explanation
Indices: 18509035--18509086 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
18509025 AATTTTTTTA
18509035 TTTATTTTATATTTTAAATTAT
1 TTTATTTTAT-TTTTAAATTAT
18509057 TTTATTTTATTTTT--ATT-T
1 TTTATTTTATTTTTAAATTAT
18509075 TTTA-TTTATTTT
1 TTTATTTTATTTT
18509087 ACTGACTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.27
18 5 0.17
19 3 0.10
21 4 0.13
22 10 0.33
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTATTTTATTTTTAAATTAT
Found at i:18513929 original size:16 final size:16
Alignment explanation
Indices: 18513910--18513945 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
18513900 AAGCAAAAAT
18513910 AAAAAAATAAAAAAGG
1 AAAAAAATAAAAAAGG
* *
18513926 AAAAAAATGAGAAAGG
1 AAAAAAATAAAAAAGG
18513942 AAAA
1 AAAA
18513946 CTTAAACTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (16 bp):
AAAAAAATAAAAAAGG
Found at i:18515131 original size:86 final size:86
Alignment explanation
Indices: 18514994--18515255 Score: 272
Period size: 86 Copynumber: 3.0 Consensus size: 86
18514984 TAGGAGTCTA
* ** * * * * * * *
18514994 AAAGTCCTTGCAAATTTAAAAACCTTTACGAATCTAGGACCTCTGCAAAACTTGGAATCTTACGA
1 AAAGTCCTTACAAACCT-AAAACCTTTACAAATCTAAGACTTTTACGAAACTTGAAATCTTACGA
* * *
18515059 ATCTTTTATTCTTGAGAATGTG
65 ATCTTTCATTCTTGTGAATATG
* * * * *
18515081 AAAGTCTTTACAAACTTGAAACCTTTACAAATCTAAGACTTTTATGAAACTTGAAATCTTGCGAA
1 AAAGTCCTTACAAACCTAAAACCTTTACAAATCTAAGACTTTTACGAAACTTGAAATCTTACGAA
*
18515146 TCTTTCATTCTTGTGAATATA
66 TCTTTCATTCTTGTGAATATG
* *** * * *
18515167 AAAGTCCTTACGAACCTAAAACCTTTGTGAATCTAGGACTTTTACGAAATTTAAAATCTTACGAA
1 AAAGTCCTTACAAACCTAAAACCTTTACAAATCTAAGACTTTTACGAAACTTGAAATCTTACGAA
*
18515232 TCTTTCATTCTTGTGAATCTG
66 TCTTTCATTCTTGTGAATATG
18515253 AAA
1 AAA
18515256 ACCTATGCGA
Statistics
Matches: 144, Mismatches: 31, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
86 130 0.90
87 14 0.10
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (86 bp):
AAAGTCCTTACAAACCTAAAACCTTTACAAATCTAAGACTTTTACGAAACTTGAAATCTTACGAA
TCTTTCATTCTTGTGAATATG
Found at i:18515481 original size:55 final size:55
Alignment explanation
Indices: 18515412--18515647 Score: 199
Period size: 55 Copynumber: 4.3 Consensus size: 55
18515402 CTGATATGTA
* **
18515412 GTTCAATCCCAATCATTCGATCTTAGCTCAGTCCAGATCATTTTTTTTACTTGTG
1 GTTCAATCACAATCATTCGATCTTAGCTCAGTCCAGATCATTTTTTAAACTTGTG
* * * * * * *
18515467 GTTCAATCATAATCATTCGATCTTGGCTCAATCCAAATCATTTTTCCAGATTTGTG
1 GTTCAATCACAATCATTCGATCTTAGCTCAGTCCAGATCATTTTT-TAAACTTGTG
* * * * *
18515523 GTTTC-GTCCCGATCATTCGATCTTGGCTCAGTCCAGATCATTTTCTAAACTTGTG
1 G-TTCAATCACAATCATTCGATCTTAGCTCAGTCCAGATCATTTTTTAAACTTGTG
** * * * * * *
18515578 GTTTCGTTC-CAGTTA-TCTGATCTTAGCTCAGTCTAGATTATTTTTTTAACTTATG
1 G-TTCAATCACAATCATTC-GATCTTAGCTCAGTCCAGATCATTTTTTAAACTTGTG
*
18515633 GTTCAATCTCAATCA
1 GTTCAATCACAATCA
18515648 CCTATTTTGG
Statistics
Matches: 143, Mismatches: 33, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
54 7 0.05
55 91 0.64
56 42 0.29
57 3 0.02
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (55 bp):
GTTCAATCACAATCATTCGATCTTAGCTCAGTCCAGATCATTTTTTAAACTTGTG
Found at i:18515545 original size:56 final size:55
Alignment explanation
Indices: 18515478--18515584 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 55
18515468 TTCAATCATA
* *
18515478 ATCATTCGATCTTGGCTCAATCCAAATCATTTTTCCAGATTTGTGGTTTCGTCCCG
1 ATCATTCGATCTTGGCTCAATCCAAATCA-TTTTCCAAACTTGTGGTTTCGTCCCG
* * *
18515534 ATCATTCGATCTTGGCTCAGTCCAGATCATTTTCTAAACTTGTGGTTTCGT
1 ATCATTCGATCTTGGCTCAATCCAAATCATTTTCCAAACTTGTGGTTTCGT
18515585 TCCAGTTATC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
55 19 0.41
56 27 0.59
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (55 bp):
ATCATTCGATCTTGGCTCAATCCAAATCATTTTCCAAACTTGTGGTTTCGTCCCG
Found at i:18515937 original size:3 final size:3
Alignment explanation
Indices: 18515929--18516031 Score: 55
Period size: 3 Copynumber: 34.0 Consensus size: 3
18515919 TATTGTTACC
* ** * *
18515929 ATT ATT ATT TTT ATT ATT ATT ATT GGT ATT ATT ATTT GTT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
* * * * * * * * *
18515975 ATT ACT A-T AGT ATA ATAT GTT GTT GTT GTT GTT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
18516020 ATT ATT ATT ATT
1 ATT ATT ATT ATT
18516032 CATTCTTTCC
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
2 2 0.02
3 76 0.94
4 3 0.04
ACGTcount: A:0.27, C:0.01, G:0.10, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:18515944 original size:12 final size:12
Alignment explanation
Indices: 18515929--18515977 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
18515919 TATTGTTACC
18515929 ATTATTATTTTT
1 ATTATTATTTTT
18515941 ATTATTATTATTGGT
1 ATTATTATT-TT--T
18515956 ATTATTATTTGTT
1 ATTATTATTT-TT
*
18515969 AATATTATT
1 ATTATTATT
18515978 ACTATAGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 9 0.28
13 11 0.34
14 1 0.03
15 11 0.34
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (12 bp):
ATTATTATTTTT
Found at i:18516819 original size:22 final size:22
Alignment explanation
Indices: 18516794--18516864 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
18516784 AGGTTATTCT
18516794 TTTTTCATTTTATT-TTTATTTA
1 TTTTT-ATTTTATTATTTATTTA
18516816 TTTTATATTTTATTATTTATTT-
1 TTTT-TATTTTATTATTTATTTA
* *
18516838 TATTGACTTTTATTATTTATTTA
1 TTTTTA-TTTTATTATTTATTTA
18516861 TTTT
1 TTTT
18516865 ACTAAGTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.02
22 30 0.71
23 11 0.26
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (22 bp):
TTTTTATTTTATTATTTATTTA
Found at i:18516848 original size:29 final size:30
Alignment explanation
Indices: 18516802--18516863 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
18516792 CTTTTTTCAT
*
18516802 TTTATTTTTATTTATTTTA-TATTT-TATTA
1 TTTATTTTTATTGATTTTATTATTTAT-TTA
18516831 TTTA-TTTTATTGACTTTTATTATTTATTTA
1 TTTATTTTTATTGA-TTTTATTATTTATTTA
18516861 TTT
1 TTT
18516864 TACTAAGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.28
29 9 0.31
30 11 0.38
31 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (30 bp):
TTTATTTTTATTGATTTTATTATTTATTTA
Found at i:18516928 original size:15 final size:15
Alignment explanation
Indices: 18516910--18516945 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
18516900 AATTCTATTT
18516910 AAAAAAAAACAAACA
1 AAAAAAAAACAAACA
* *
18516925 AAAAAGAAACAAATA
1 AAAAAAAAACAAACA
18516940 AAAAAA
1 AAAAAA
18516946 TCATTTCAAA
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:0.86, C:0.08, G:0.03, T:0.03
Consensus pattern (15 bp):
AAAAAAAAACAAACA
Found at i:18521222 original size:1 final size:1
Alignment explanation
Indices: 18521216--18521240 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
18521206 GCCTCCTATG
18521216 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
18521241 CCTAGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18522866 original size:2 final size:2
Alignment explanation
Indices: 18522859--18522884 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18522849 GTAAAGTTAC
18522859 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
18522885 GCTGTGATTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:18523357 original size:12 final size:11
Alignment explanation
Indices: 18523335--18523362 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
18523325 GTTGAAACTC
18523335 TTTTTTCTTTT
1 TTTTTTCTTTT
18523346 TTTTTTCTTTT
1 TTTTTTCTTTT
18523357 TTTTTT
1 TTTTTT
18523363 AAATGTGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:18529783 original size:23 final size:24
Alignment explanation
Indices: 18529735--18529802 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
18529725 ACTTATTAAT
*
18529735 TTTTTTCAACTTTGAAAATTATAAA
1 TTTTTT-AATTTTGAAAATTATAAA
*
18529760 TTTTTTAATTTTTAAAATTA-AAA
1 TTTTTTAATTTTGAAAATTATAAA
**
18529783 TTAATTATATTTTGAAAATT
1 TTTTTTA-ATTTTGAAAATT
18529803 CTTTTCAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 8 0.22
24 23 0.62
25 6 0.16
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (24 bp):
TTTTTTAATTTTGAAAATTATAAA
Found at i:18529937 original size:2 final size:2
Alignment explanation
Indices: 18529924--18529965 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
18529914 AAACATCCAT
*
18529924 TC TC TA TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18529966 CTACCATTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:18530442 original size:27 final size:29
Alignment explanation
Indices: 18530389--18530442 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 29
18530379 TATTACTATT
***
18530389 ATTTATAATTTTTATTTTTACTGTAATTC
1 ATTTATAATTTTTATTTTTAAAATAATTC
18530418 ATTTA-AATTTTTA-TTTTAAAATAAT
1 ATTTATAATTTTTATTTTTAAAATAAT
18530443 AATTTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 9 0.41
28 8 0.36
29 5 0.23
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (29 bp):
ATTTATAATTTTTATTTTTAAAATAATTC
Found at i:18530479 original size:22 final size:22
Alignment explanation
Indices: 18530427--18530479 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
18530417 CATTTAAATT
18530427 TTTATTTTAAAATAATAATTTTA
1 TTTATTTT-AAATAATAATTTTA
* *
18530450 TTTA-TTTAAATCATATTTTTA
1 TTTATTTTAAATAATAATTTTA
18530471 TTTATTTTA
1 TTTATTTTA
18530480 TTTTGCAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 16 0.59
22 7 0.26
23 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTATTTTAAATAATAATTTTA
Found at i:18530644 original size:20 final size:20
Alignment explanation
Indices: 18530621--18530661 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18530611 GTGAAATTGC
* *
18530621 TGATAAGATTGTTAAATTAT
1 TGATAAGATTATGAAATTAT
*
18530641 TGATGAGATTATGAAATTAT
1 TGATAAGATTATGAAATTAT
18530661 T
1 T
18530662 TTTAAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (20 bp):
TGATAAGATTATGAAATTAT
Found at i:18530657 original size:51 final size:51
Alignment explanation
Indices: 18530601--18530707 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 51
18530591 GGATTACATG
* * * *
18530601 TGAAATTGTTGTGAAATTGCTGATAAGATTGTTAAATTATTGATGAGATTA
1 TGAAATTATTGTGAAAATACTGATAAGATTGTAAAATTATTGATGAGATTA
* * * * * *
18530652 TGAAATTATTTTTAAAATATTGATGAGATTGTAAAATTGTTGATGAGATTG
1 TGAAATTATTGTGAAAATACTGATAAGATTGTAAAATTATTGATGAGATTA
18530703 TGAAA
1 TGAAA
18530708 CCATAATTAC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (51 bp):
TGAAATTATTGTGAAAATACTGATAAGATTGTAAAATTATTGATGAGATTA
Found at i:18530688 original size:19 final size:20
Alignment explanation
Indices: 18530664--18530703 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
18530654 AAATTATTTT
18530664 TAAAA-TATTGATGAGATTG
1 TAAAATTATTGATGAGATTG
*
18530683 TAAAATTGTTGATGAGATTG
1 TAAAATTATTGATGAGATTG
18530703 T
1 T
18530704 GAAACCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.40
Consensus pattern (20 bp):
TAAAATTATTGATGAGATTG
Found at i:18535213 original size:12 final size:13
Alignment explanation
Indices: 18535194--18535231 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
18535184 GTGCTCATAC
18535194 ACACCATTCAGCA
1 ACACCATTCAGCA
*
18535207 A-ACCATTCAGAA
1 ACACCATTCAGCA
18535219 ACACCATTCAGCA
1 ACACCATTCAGCA
18535232 TACAATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.42, C:0.34, G:0.08, T:0.16
Consensus pattern (13 bp):
ACACCATTCAGCA
Found at i:18544751 original size:22 final size:22
Alignment explanation
Indices: 18544709--18544751 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18544699 TGTAGTTAAT
* **
18544709 AAATGTCACTAAACAGTAAAAA
1 AAATGTCACTAAAAACCAAAAA
18544731 AAATGTCACTAAAAACCAAAA
1 AAATGTCACTAAAAACCAAAA
18544752 CCCCTGTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.16, G:0.07, T:0.16
Consensus pattern (22 bp):
AAATGTCACTAAAAACCAAAAA
Found at i:18546040 original size:2 final size:2
Alignment explanation
Indices: 18546035--18546084 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
18546025 TTTTTGGTAA
18546035 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
18546077 CT CT CT CT
1 CT CT CT CT
18546085 ATATATATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:18549034 original size:3 final size:3
Alignment explanation
Indices: 18549026--18549061 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
18549016 CATCACACCA
18549026 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18549062 GCAATAATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:18550161 original size:11 final size:12
Alignment explanation
Indices: 18550129--18550162 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
18550119 ACTTTTGATC
*
18550129 AAATAAAAAAAT
1 AAATAATAAAAT
18550141 AAATAATAAAAT
1 AAATAATAAAAT
18550153 AAA-AATAAAA
1 AAATAATAAAA
18550163 AATTAAGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
AAATAATAAAAT
Found at i:18553736 original size:1 final size:1
Alignment explanation
Indices: 18553730--18553756 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
18553720 AAAGATTTAG
18553730 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
18553757 GGAATTTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:18560746 original size:86 final size:85
Alignment explanation
Indices: 18560602--18560769 Score: 237
Period size: 86 Copynumber: 2.0 Consensus size: 85
18560592 TATTTCTAGC
* * * *
18560602 ATTTACTATGACATCATTACAGTTATTTTAGTCCATAGCAGTAATCCAGAATAAAATTCAGTACA
1 ATTTACTATGACATCATTACAGTAATGTTAGTCCATAACAATAATCCAGAATAAAATTCAGTACA
*
18560667 CATTCTTGTTATTGCATAAT
66 CATTCTTGTTATAGCATAAT
* * *
18560687 ATTTACTATGATATCATTACAGTAAATGTTAGTCCATAATAATATTCCAGAATAAAATTCAGTAC
1 ATTTACTATGACATCATTACAGT-AATGTTAGTCCATAACAATAATCCAGAATAAAATTCAGTAC
* *
18560752 GCATTGTTGTTATAGCAT
65 ACATTCTTGTTATAGCAT
18560770 TATTATGTGT
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 22 0.31
86 50 0.69
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (85 bp):
ATTTACTATGACATCATTACAGTAATGTTAGTCCATAACAATAATCCAGAATAAAATTCAGTACA
CATTCTTGTTATAGCATAAT
Found at i:18562699 original size:2 final size:2
Alignment explanation
Indices: 18562692--18562721 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18562682 CTTATCAAGA
18562692 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
18562722 TTGCCTTCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18566219 original size:14 final size:12
Alignment explanation
Indices: 18566194--18566229 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
18566184 TTTTTTTATT
18566194 ATATTTTTAAAA
1 ATATTTTTAAAA
18566206 ATATTTTTAAAA
1 ATATTTTTAAAA
*
18566218 AAATTATTTAAA
1 ATATT-TTTAAA
18566230 CATCTTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATTTTTAAAA
Found at i:18566299 original size:33 final size:32
Alignment explanation
Indices: 18566257--18566318 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
18566247 AGATATTTAA
* *
18566257 ATTTCAT-AAATTTTATAATTTTTATAAAATCT
1 ATTTCATAAAATTATA-AAATTTTATAAAATCT
18566289 ATTTCGATAAAATTATAAAATTTTATAAAA
1 ATTTC-ATAAAATTATAAAATTTTATAAAA
18566319 ATTCATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 5 0.19
33 14 0.54
34 7 0.27
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (32 bp):
ATTTCATAAAATTATAAAATTTTATAAAATCT
Found at i:18566415 original size:17 final size:17
Alignment explanation
Indices: 18566395--18566428 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18566385 AAATTTTATT
*
18566395 AATTAGTGTAATAAAAA
1 AATTAGTATAATAAAAA
*
18566412 AATTATTATAATAAAAA
1 AATTAGTATAATAAAAA
18566429 TTATAAATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
AATTAGTATAATAAAAA
Found at i:18566443 original size:15 final size:16
Alignment explanation
Indices: 18566425--18566457 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18566415 TATTATAATA
*
18566425 AAAATT-ATAAATGTT
1 AAAATTAATAAAAGTT
18566440 AAAATTAATAAAAGTT
1 AAAATTAATAAAAGTT
18566456 AA
1 AA
18566458 TTTTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
AAAATTAATAAAAGTT
Found at i:18566749 original size:27 final size:27
Alignment explanation
Indices: 18566719--18566772 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
18566709 AAATTTTAAT
*
18566719 AATTGATACAAAAAATTACATTTATTA
1 AATTGATAAAAAAAATTACATTTATTA
* **
18566746 AATTTATAAAAAAAATTATTTTTATTA
1 AATTGATAAAAAAAATTACATTTATTA
18566773 TTTTATCCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (27 bp):
AATTGATAAAAAAAATTACATTTATTA
Found at i:18566860 original size:23 final size:24
Alignment explanation
Indices: 18566834--18566879 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
18566824 CTCAAAATAG
*
18566834 TAAAATTA-ATTTTTTATTAATTT
1 TAAAATTAGATTTTTTAATAATTT
18566857 TAAAATTATGATTTTTTAATAAT
1 TAAAATTA-GATTTTTTAATAAT
18566880 AATTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
25 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TAAAATTAGATTTTTTAATAATTT
Found at i:18567519 original size:19 final size:19
Alignment explanation
Indices: 18567438--18567526 Score: 97
Period size: 20 Copynumber: 4.6 Consensus size: 19
18567428 GTAAAAAAAT
*
18567438 ATCATGCAAATATTTAATGA
1 ATCATGCAAATAATTAAT-A
*
18567458 ATCATGCAAATAAATAATA
1 ATCATGCAAATAATTAATA
* * *
18567477 GTTATGCAAATACATTAGTA
1 ATCATGCAAATA-ATTAATA
* *
18567497 ATCATGCAAATAGTGAATA
1 ATCATGCAAATAATTAATA
18567516 ATCATGCAAAT
1 ATCATGCAAAT
18567527 GCAAATATAT
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
19 26 0.46
20 31 0.54
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.30
Consensus pattern (19 bp):
ATCATGCAAATAATTAATA
Found at i:18567523 original size:39 final size:39
Alignment explanation
Indices: 18567438--18567526 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
18567428 GTAAAAAAAT
*
18567438 ATCATGCAAATATTTAATGAATCATGCAAATAAATAATA
1 ATCATGCAAATAATTAATGAATCATGCAAATAAATAATA
* * * *
18567477 GTTATGCAAATACATTAGT-AATCATGCAAAT-AGTGAATA
1 ATCATGCAAATA-ATTAATGAATCATGCAAATAAAT-AATA
18567516 ATCATGCAAAT
1 ATCATGCAAAT
18567527 GCAAATATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.05
39 35 0.85
40 4 0.10
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.30
Consensus pattern (39 bp):
ATCATGCAAATAATTAATGAATCATGCAAATAAATAATA
Found at i:18569294 original size:21 final size:22
Alignment explanation
Indices: 18569259--18569299 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18569249 CTAAAGCAAT
18569259 AAAAATTAAAAAAAT-TAAACA
1 AAAAATTAAAAAAATCTAAACA
* *
18569280 AAAAATTGAATAAATCTAAA
1 AAAAATTAAAAAAATCTAAA
18569300 AATACAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAAATTAAAAAAATCTAAACA
Found at i:18570231 original size:26 final size:26
Alignment explanation
Indices: 18570193--18570277 Score: 147
Period size: 26 Copynumber: 3.3 Consensus size: 26
18570183 GTGAAAGGTA
*
18570193 ATATATATGTACATATATATATATAC
1 ATATATATATACATATATATATATAC
18570219 ATATATATATACATATATATATATAC
1 ATATATATATACATATATATATATAC
18570245 ATATATATATAC--ATATATATATAC
1 ATATATATATACATATATATATATAC
18570269 ATATATATA
1 ATATATATA
18570278 AACACATAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
24 21 0.36
26 37 0.64
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (26 bp):
ATATATATATACATATATATATATAC
Found at i:18570285 original size:14 final size:12
Alignment explanation
Indices: 18570193--18570277 Score: 125
Period size: 12 Copynumber: 6.8 Consensus size: 12
18570183 GTGAAAGGTA
*
18570193 ATATATATGTAC
1 ATATATATATAC
18570205 ATATATATATATAC
1 --ATATATATATAC
18570219 ATATATATATAC
1 ATATATATATAC
18570231 ATATATATATATAC
1 --ATATATATATAC
18570245 ATATATATATAC
1 ATATATATATAC
18570257 ATATATATATAC
1 ATATATATATAC
18570269 ATATATATA
1 ATATATATA
18570278 AACACATAGA
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
12 45 0.66
14 23 0.34
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (12 bp):
ATATATATATAC
Found at i:18570783 original size:20 final size:20
Alignment explanation
Indices: 18570749--18570800 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
18570739 ATCACTTTGT
*
18570749 TATTACTATAGTATAGTAT-G
1 TATTA-TATATTATAGTATAG
18570769 CTATTATATATTATAGTATAG
1 -TATTATATATTATAGTATAG
18570790 TATTAT-TATTA
1 TATTATATATTA
18570801 GAATTATTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.17
20 18 0.62
21 6 0.21
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (20 bp):
TATTATATATTATAGTATAG
Found at i:18570806 original size:25 final size:24
Alignment explanation
Indices: 18570755--18570807 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
18570745 TTGTTATTAC
*
18570755 TATAGTATAGTATGCTATTATATAT
1 TATAGTATAGTAT-CTATTATAAAT
18570780 TATAGTATAGTAT-TATTATTAGAAT
1 TATAGTATAGTATCTATTA-TA-AAT
18570805 TAT
1 TAT
18570808 TACAGTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 5 0.20
24 2 0.08
25 18 0.72
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (24 bp):
TATAGTATAGTATCTATTATAAAT
Found at i:18570856 original size:3 final size:3
Alignment explanation
Indices: 18570843--18570946 Score: 112
Period size: 3 Copynumber: 36.3 Consensus size: 3
18570833 ATCATTTGTC
18570843 TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
18570890 TAT TAT CAT TA- CAC TA- TATT TAT TA- TAC TA- TAG TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
18570931 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
18570947 TATTCGTTTT
Statistics
Matches: 90, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
2 11 0.12
3 77 0.86
4 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:18571835 original size:13 final size:14
Alignment explanation
Indices: 18571819--18571885 Score: 73
Period size: 15 Copynumber: 4.7 Consensus size: 14
18571809 TCTTTTTCTA
18571819 TTTTTA-TTTCATT
1 TTTTTATTTTCATT
*
18571832 TTTTTATTTTGATT
1 TTTTTATTTTCATT
*
18571846 TTATTTATTTTCATA
1 TT-TTTATTTTCATT
* *
18571861 TTTTAAGTTTCTATT
1 TTTTTATTTTC-ATT
18571876 TTTTTATTTT
1 TTTTTATTTT
18571886 TGATTTTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
13 6 0.14
14 15 0.35
15 22 0.51
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.75
Consensus pattern (14 bp):
TTTTTATTTTCATT
Found at i:18571854 original size:15 final size:14
Alignment explanation
Indices: 18571819--18571894 Score: 66
Period size: 15 Copynumber: 5.3 Consensus size: 14
18571809 TCTTTTTCTA
*
18571819 TTTTTA-TTTCATT
1 TTTTTATTTTGATT
18571832 TTTTTATTTTGATT
1 TTTTTATTTTGATT
* *
18571846 TTATTTATTTTCATA
1 TT-TTTATTTTGATT
*
18571861 TTTTAAGTTTCT-ATT
1 TTTTTA-TTT-TGATT
18571876 TTTTTATTTTTGATT
1 TTTTTA-TTTTGATT
18571891 TTTT
1 TTTT
18571895 ATTCCATTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
13 6 0.12
14 12 0.24
15 32 0.63
16 1 0.02
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (14 bp):
TTTTTATTTTGATT
Found at i:18571857 original size:29 final size:29
Alignment explanation
Indices: 18571819--18571895 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
18571809 TCTTTTTCTA
*
18571819 TTTTTA-TTTCATTTTTTTA-TTT-TGATT
1 TTTTTATTTTCATTTTTTAAGTTTCT-ATT
*
18571846 TTATTTATTTTCATATTTTAAGTTTCTATT
1 TT-TTTATTTTCATTTTTTAAGTTTCTATT
*
18571876 TTTTTATTTTTGATTTTTTA
1 TTTTTA-TTTTCATTTTTTA
18571896 TTCCATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 2 0.05
28 4 0.10
29 15 0.37
30 19 0.46
31 1 0.02
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (29 bp):
TTTTTATTTTCATTTTTTAAGTTTCTATT
Found at i:18574300 original size:23 final size:23
Alignment explanation
Indices: 18574274--18574322 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
18574264 TTGCTCTATA
18574274 AAATAGCACTAATATTTAGTAAG
1 AAATAGCACTAATATTTAGTAAG
***
18574297 AAATAGTTTTAATATTTAGTAAG
1 AAATAGCACTAATATTTAGTAAG
18574320 AAA
1 AAA
18574323 ACATAGCTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.35
Consensus pattern (23 bp):
AAATAGCACTAATATTTAGTAAG
Found at i:18582023 original size:39 final size:39
Alignment explanation
Indices: 18581954--18582030 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
18581944 TCTCTTCTTC
*
18581954 TCTTCAATATATACATTAATACCCTCATTCACAAGATTT
1 TCTTCAATATATACAGTAATACCCTCATTCACAAGATTT
* * * *
18581993 TCTTCAATATGTACAGTATTATCCTTATTCACAAGATT
1 TCTTCAATATATACAGTAATACCCTCATTCACAAGATT
18582031 ATCCTTAGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (39 bp):
TCTTCAATATATACAGTAATACCCTCATTCACAAGATTT
Found at i:18582056 original size:21 final size:21
Alignment explanation
Indices: 18582030--18582096 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
18582020 TTCACAAGAT
18582030 TATCCTTAGCATGTACATTAC
1 TATCCTTAGCATGTACATTAC
* *
18582051 TATCCTTACCTAT-TATATT-C
1 TATCCTTAGC-ATGTACATTAC
*
18582071 --T-CTTAGCATGTACATTAT
1 TATCCTTAGCATGTACATTAC
18582089 TATCCTTA
1 TATCCTTA
18582097 CCCCTTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
16 2 0.06
17 10 0.29
18 1 0.03
20 2 0.06
21 18 0.51
22 2 0.06
ACGTcount: A:0.27, C:0.22, G:0.06, T:0.45
Consensus pattern (21 bp):
TATCCTTAGCATGTACATTAC
Found at i:18582085 original size:38 final size:38
Alignment explanation
Indices: 18582033--18582129 Score: 140
Period size: 38 Copynumber: 2.5 Consensus size: 38
18582023 ACAAGATTAT
*
18582033 CCTTAGCATGTACATTACTATCCTTACCTATTATATTC
1 CCTTAGCATGTACATTACTATCCTTACCCATTATATTC
* * *
18582071 TCTTAGCATGTACATTATTATCCTTACCCCTTATATTC
1 CCTTAGCATGTACATTACTATCCTTACCCATTATATTC
*
18582109 CCTTCAACATGTACATTACTA
1 CCTT-AGCATGTACATTACTA
18582130 CATTTAGCCT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 37 0.73
39 14 0.27
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.41
Consensus pattern (38 bp):
CCTTAGCATGTACATTACTATCCTTACCCATTATATTC
Found at i:18588842 original size:34 final size:33
Alignment explanation
Indices: 18588804--18588870 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 33
18588794 ATATTTTTTT
*
18588804 GTTTTTATTTTTTATTTTCATT-TTTTAAAAAATA
1 GTTTTTACTTTTTATTTT--TTATTTTAAAAAATA
18588838 GTTTTTACTTTTTATTTTTTATTTTAAAAAATA
1 GTTTTTACTTTTTATTTTTTATTTTAAAAAATA
18588871 TGTTCGGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 2 0.06
33 12 0.39
34 17 0.55
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (33 bp):
GTTTTTACTTTTTATTTTTTATTTTAAAAAATA
Found at i:18589376 original size:12 final size:13
Alignment explanation
Indices: 18589359--18589387 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18589349 ATGGATTTTT
18589359 AAAAAAT-CTTTA
1 AAAAAATCCTTTA
18589371 AAAAAATCCTTTA
1 AAAAAATCCTTTA
18589384 AAAA
1 AAAA
18589388 TCTAAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAATCCTTTA
Found at i:18589423 original size:18 final size:18
Alignment explanation
Indices: 18589391--18589427 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
18589381 TTAAAAATCT
*
18589391 AAAAAGTTAAAAAATTTC
1 AAAAAATTAAAAAATTTC
18589409 AAAAAATTAAAAAATTTC
1 AAAAAATTAAAAAATTTC
18589427 A
1 A
18589428 TTTTTAAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAAAATTAAAAAATTTC
Found at i:18589716 original size:29 final size:31
Alignment explanation
Indices: 18589654--18589716 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
18589644 AAATAATCAA
*
18589654 ATTT-CATTTTTAAAAAAGTAATTTTCAATT
1 ATTTACATTTTTAAAAAAGTAATTTCCAATT
*
18589684 -TTTACATTTTTTAAAAAG-AA-TTCCAATT
1 ATTTACATTTTTAAAAAAGTAATTTCCAATT
18589712 ATTTA
1 ATTTA
18589717 AAATATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 7 0.24
29 9 0.31
30 13 0.45
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (31 bp):
ATTTACATTTTTAAAAAAGTAATTTCCAATT
Found at i:18593107 original size:14 final size:14
Alignment explanation
Indices: 18593079--18593116 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
18593069 ATTCTTCTAG
*
18593079 TATTT-TTTATTTT
1 TATTTATTTATGTT
18593092 TATTTATTTATGTT
1 TATTTATTTATGTT
*
18593106 TAGTTATTTAT
1 TATTTATTTAT
18593117 TCATTTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (14 bp):
TATTTATTTATGTT
Found at i:18593182 original size:15 final size:13
Alignment explanation
Indices: 18593124--18593186 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 13
18593114 TATTCATTTG
18593124 TTTATTTGTTTTCCA
1 TTTATTTG-TTT-CA
*
18593139 TTTATGTT-TTTTA
1 TTTAT-TTGTTTCA
18593152 TTTATTTG-TTCA
1 TTTATTTGTTTCA
18593164 -TTATTTGTTATCCA
1 TTTATTTGTT-T-CA
18593178 TTTATTTGT
1 TTTATTTGT
18593187 AAATATTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
11 7 0.17
12 6 0.15
13 7 0.17
14 5 0.12
15 13 0.32
16 2 0.05
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (13 bp):
TTTATTTGTTTCA
Found at i:18597055 original size:51 final size:52
Alignment explanation
Indices: 18596936--18597072 Score: 136
Period size: 51 Copynumber: 2.7 Consensus size: 52
18596926 ACTGTAATTA
* * **
18596936 AGAGATTTTTAGGATTTAATTCCAAAATCAATTGGCATTAAAAATGATATGG
1 AGAGATTTTTGGGATTTAATTCTAAAATCAATTCACATTAAAAATGATATGG
* * * * * *
18596988 AGAGATTGTCGAGATTTAATTCTATAATCAATTCACGTT-AGAATGATA-GAG
1 AGAGATTTTTGGGATTTAATTCTAAAATCAATTCACATTAAAAATGATATG-G
*
18597039 AGAGATTTTTGGGATTTGATT-TCAAAATCAATTC
1 AGAGATTTTTGGGATTTAATTCT-AAAATCAATTC
18597073 TTATTAAACG
Statistics
Matches: 68, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
50 2 0.03
51 36 0.53
52 30 0.44
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (52 bp):
AGAGATTTTTGGGATTTAATTCTAAAATCAATTCACATTAAAAATGATATGG
Found at i:18597609 original size:14 final size:14
Alignment explanation
Indices: 18597590--18597628 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
18597580 TTTTGTTTTG
*
18597590 ATTTTATTTTTCAT
1 ATTTTATTTATCAT
*
18597604 ATTTTATTTATGAT
1 ATTTTATTTATCAT
*
18597618 ATTTTGTTTAT
1 ATTTTATTTAT
18597629 TTGTATTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (14 bp):
ATTTTATTTATCAT
Found at i:18615157 original size:39 final size:39
Alignment explanation
Indices: 18615057--18615261 Score: 189
Period size: 39 Copynumber: 5.2 Consensus size: 39
18615047 GGGTTTTACC
* *
18615057 TTATCTTTTAAAGTTGTGTGCCTCTATTGATGGGGGGCCT
1 TTAT-TTTTAAAGTTGTGTGCCTCTATTGATGAGGAGCCT
* * * *
18615097 TTA-GTCTAAAGTTGAGTGCCTCTATTGATGATGAGCCT
1 TTATTTTTAAAGTTGTGTGCCTCTATTGATGAGGAGCCT
* * *
18615135 TTATTTTTAAAGTTATGTGCCTCTATTGATAAGGAGTCT
1 TTATTTTTAAAGTTGTGTGCCTCTATTGATGAGGAGCCT
* * * * *
18615174 TTA-TTTCACAAGTTGTGTGCCTTTATTGATTAGAAGTCTT
1 TTATTTTTA-AAGTTGTGTGCCTCTATTGATGAGGAG-CCT
* * * * *
18615214 TTATTATTAAAAGTTGTATGCCTTTATTGATGATGAGTCT
1 TTATT-TTTAAAGTTGTGTGCCTCTATTGATGAGGAGCCT
18615254 TTATTTTT
1 TTATTTTT
18615262 TAAAAAAAGT
Statistics
Matches: 132, Mismatches: 28, Indels: 11
0.77 0.16 0.06
Matches are distributed among these distances:
38 36 0.27
39 56 0.42
40 13 0.10
41 24 0.18
42 3 0.02
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.46
Consensus pattern (39 bp):
TTATTTTTAAAGTTGTGTGCCTCTATTGATGAGGAGCCT
Found at i:18617241 original size:35 final size:36
Alignment explanation
Indices: 18617201--18617276 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 36
18617191 CTTTAAAAAA
* * *
18617201 ATAATTTC-CATAAAATCCTACCAATGTATTGGAGG
1 ATAATTTCACAAAAAATCCTACCAATATATTGGAAG
*
18617236 ATAATTTCTAGCAAAAAATCTTACCAATATATTGGAAG
1 ATAATTTC-A-CAAAAAATCCTACCAATATATTGGAAG
18617274 ATA
1 ATA
18617277 TTTTAAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 8 0.24
38 26 0.76
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (36 bp):
ATAATTTCACAAAAAATCCTACCAATATATTGGAAG
Found at i:18617292 original size:38 final size:39
Alignment explanation
Indices: 18617210--18617292 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 39
18617200 AATAATTTCC
* * *
18617210 ATAAAATCCTACCAATGTATTGGAGGATAATTTCTAGCA
1 ATAAAATCCTACCAATATATTGGAAGATAATTTCTAGAA
*
18617249 A-AAAATCTTACCAATATATTGGAAGAT-ATTT-TAAGAA
1 ATAAAATCCTACCAATATATTGGAAGATAATTTCT-AGAA
18617286 ATAAAAT
1 ATAAAAT
18617293 ATTTTTATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
36 1 0.03
37 8 0.21
38 28 0.74
39 1 0.03
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (39 bp):
ATAAAATCCTACCAATATATTGGAAGATAATTTCTAGAA
Found at i:18619274 original size:21 final size:21
Alignment explanation
Indices: 18619248--18619289 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
18619238 AACGTAGTCC
18619248 TTGTTAAATAACAAAAATCAT
1 TTGTTAAATAACAAAAATCAT
* *
18619269 TTGTTAAATAATAAAGATCAT
1 TTGTTAAATAACAAAAATCAT
18619290 GTTTGTTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (21 bp):
TTGTTAAATAACAAAAATCAT
Found at i:18619503 original size:21 final size:20
Alignment explanation
Indices: 18619479--18619521 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
18619469 TAACATCAAT
18619479 TTCAACCT-TTGCGATTTTATC
1 TTCAACCTGTT-C-ATTTTATC
*
18619500 TTCATCCTGTTCATTTTATC
1 TTCAACCTGTTCATTTTATC
18619520 TT
1 TT
18619522 ATCTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 8 0.40
22 2 0.10
ACGTcount: A:0.16, C:0.23, G:0.07, T:0.53
Consensus pattern (20 bp):
TTCAACCTGTTCATTTTATC
Found at i:18635165 original size:28 final size:28
Alignment explanation
Indices: 18635133--18635189 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
18635123 AATTTTTAAC
**
18635133 TCAATATATCTACCTTGTGGGGTAAGAA
1 TCAATATATCTACCTTGTGGCATAAGAA
18635161 TCAATATATCTACCTTGTGGCATAAGAA
1 TCAATATATCTACCTTGTGGCATAAGAA
18635189 T
1 T
18635190 TTAGATAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (28 bp):
TCAATATATCTACCTTGTGGCATAAGAA
Found at i:18641602 original size:356 final size:354
Alignment explanation
Indices: 18640940--18641832 Score: 1136
Period size: 356 Copynumber: 2.5 Consensus size: 354
18640930 TTGAACATAT
* * *
18640940 CGCCACACAAATTTTAACCTGGTTATTGAAGGCGTATATCCAAGAAAGACGCCTTTAATAATTTC
1 CGCCACACAAATTTTAACATGGTTATTAAAGGCGTATATCCAAGAAAGACGCCTTTAATAATTCC
* ** * * * * **
18641005 TATCATAATTTGTAGATAATTAGTGAAGGTGTTTTCTACGTTAAC--GGCTTCAATAATTTGCTT
66 TATCATAGTTTGTAGATAATTAGTGAAGAAGATTAC-A-GATAACAACGCTTCAATAATTTTTTT
* * * *
18641068 AACAAAAGTTTTTTGGATTATTAAAGGTGTCTTTTATTATGAAACGCCTTCAATATACTACGATG
129 AA-AAAAATTTTTTGGATTATTAAAGGCGTCTTTTATTATGAAACGCCTTCAATATACCACCATG
* *
18641133 GTTATGGAAGGCATTTATTCGAAAAGCCGCATTCAATATACCTTTAAACTTAATAATCCATTACT
193 CTTATGGAAGGCATTTATTCAAAAAGCCGCATTCAATATACCTTTAAACTTAATAATCCATTACT
* * * * *
18641198 AAAGGCGTTTGTTAATAACATATGCCTTCAAAATTTTTTCACTAAAAATTTTAAGAATCATTAAA
258 AAAGGCGTTTATTAATAACAAACGCCTTCAAAATTTTCTCACTAAAAATTTTAAAAATCATTAAA
* * ** *
18641263 GGTGTCTTCTACTATAAAATATGTTTTATATAC
323 -GCGTCTTCTAATATAAAATACCTTCTATATAC
* * * * *
18641296 CGTCATACAAATTTTAATATTGTTATTAAAGGTGTATATCCAAGAAATG-CGCCTTTAATAATTC
1 CGCCACACAAATTTTAACATGGTTATTAAAGGCGTATATCCAAGAAA-GACGCCTTTAATAATTC
* *
18641360 CTATCACAGTTTGTAGATAATTAGTGAAGACGATTACAGATAACAACGCTTTCAATAATTTTTTT
65 CTATCATAGTTTGTAGATAATTAGTGAAGAAGATTACAGATAACAACGC-TTCAATAATTTTTTT
18641425 AAAAAAATTTTTTGGATTATTAAAGGCGTCTTTTATTATGAAACGCCTTCAATATACCACCATGC
129 AAAAAAATTTTTTGGATTATTAAAGGCGTCTTTTATTATGAAACGCCTTCAATATACCACCATGC
*
18641490 TTATGGAAGGCGTTTATTCAAAAAAGCAC-C-TTCAATATACCTTTAAACTTAATAATCCATTAC
194 TTATGGAAGGCATTTATTC-AAAAAGC-CGCATTCAATATACCTTTAAACTTAATAATCCATTAC
* * *
18641553 TGAAGGCGTTTATTAATAACAAACGCCTTCAAAATTTTCTCATTAAAAATTTTAAAAATTATTAA
257 TAAAGGCGTTTATTAATAACAAACGCCTTCAAAATTTTCTCACTAAAAATTTTAAAAATCATTAA
*
18641618 AGCGTCTTCTAATGTAAAATACCTTCTATATAC
322 AGCGTCTTCTAATATAAAATACCTTCTATATAC
* * * * *
18641651 CGCCACACAAATTCTAACATGGTTATTAAAGACGTATATCTAAGAAAGACTCATTTAATAATTCC
1 CGCCACACAAATTTTAACATGGTTATTAAAGGCGTATATCCAAGAAAGACGCCTTTAATAATTCC
* * *
18641716 TATCATAGTTTATAGATAATTAGT-AA-AAGCAGTTGCAGATAACAATGCCTTCAATAA-TTTTT
66 TATCATAGTTTGTAGATAATTAGTGAAGAAG-A-TTACAGATAACAACG-CTTCAATAATTTTTT
* *** * * *
18641778 CAAAAAAAAAATTTGGATTATTAAAGACGTCTTTTATTATAAAATGCCTTCAATA
128 TAAAAAAATTTTTTGGATTATTAAAGGCGTCTTTTATTATGAAACGCCTTCAATA
18641833 ATTTGCTATA
Statistics
Matches: 466, Mismatches: 61, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
353 2 0.00
354 62 0.13
355 123 0.26
356 255 0.55
357 23 0.05
358 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (354 bp):
CGCCACACAAATTTTAACATGGTTATTAAAGGCGTATATCCAAGAAAGACGCCTTTAATAATTCC
TATCATAGTTTGTAGATAATTAGTGAAGAAGATTACAGATAACAACGCTTCAATAATTTTTTTAA
AAAAATTTTTTGGATTATTAAAGGCGTCTTTTATTATGAAACGCCTTCAATATACCACCATGCTT
ATGGAAGGCATTTATTCAAAAAGCCGCATTCAATATACCTTTAAACTTAATAATCCATTACTAAA
GGCGTTTATTAATAACAAACGCCTTCAAAATTTTCTCACTAAAAATTTTAAAAATCATTAAAGCG
TCTTCTAATATAAAATACCTTCTATATAC
Found at i:18645900 original size:35 final size:35
Alignment explanation
Indices: 18645846--18645913 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
18645836 ATATATAAAC
* *
18645846 CAAATATTTTTTGGGCATAAA-TATACAACTGACAG
1 CAAACATTTTTTGGACATAAACT-TACAACTGACAG
18645881 CAAACATTTTTTGGACATAAACTTACAACTGAC
1 CAAACATTTTTTGGACATAAACTTACAACTGAC
18645914 TTCACATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.31
Consensus pattern (35 bp):
CAAACATTTTTTGGACATAAACTTACAACTGACAG
Found at i:18648890 original size:15 final size:15
Alignment explanation
Indices: 18648870--18648902 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
18648860 GTCGAGGAGC
18648870 GTGATTAAACAAGGG
1 GTGATTAAACAAGGG
18648885 GTGATTAAACAAGGG
1 GTGATTAAACAAGGG
18648900 GTG
1 GTG
18648903 CGTTTCGGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (15 bp):
GTGATTAAACAAGGG
Found at i:18656678 original size:2 final size:2
Alignment explanation
Indices: 18656671--18656695 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18656661 AAAATTTCTT
18656671 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
18656696 TACAATATAC
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:18656697 original size:120 final size:121
Alignment explanation
Indices: 18656555--18656807 Score: 422
Period size: 120 Copynumber: 2.1 Consensus size: 121
18656545 ACATCTAATT
18656555 TATATATATATATATATATATTACAATATACATAGTTAT-AAGATAAGATTTGTTGATATGGATA
1 TATATATATATATATATATATTACAATATACATAGTTATCAA-ATAAGATTTGTTGATATGGATA
*
18656619 CTTGCATGGACAA-TTTTTTTTTTGACACAAAAGAAAATTGCTAAAATTTCTTTATA
65 CTTACATGGACAATTTTTTTTTTTGACACAAAAGAAAATTGCTAAAATTTCTTTATA
18656675 TATATATATATATATATATATTACAATATACATAGTTATCAAATAAGATTTGTTGATATGGATAC
1 TATATATATATATATATATATTACAATATACATAGTTATCAAATAAGATTTGTTGATATGGATAC
* * * *
18656740 TTACATGGATAATTTTTTTTTTTGACACATAAGAAAATTGTTAAAATTTCTTTTTA
66 TTACATGGACAATTTTTTTTTTTGACACAAAAGAAAATTGCTAAAATTTCTTTATA
18656796 TA-ATGATATATA
1 TATAT-ATATATA
18656808 AGATATTTTT
Statistics
Matches: 125, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
120 74 0.59
121 51 0.41
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (121 bp):
TATATATATATATATATATATTACAATATACATAGTTATCAAATAAGATTTGTTGATATGGATAC
TTACATGGACAATTTTTTTTTTTGACACAAAAGAAAATTGCTAAAATTTCTTTATA
Found at i:18657690 original size:2 final size:2
Alignment explanation
Indices: 18657683--18657707 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18657673 ACTTTGACTT
18657683 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
18657708 TACTAGATAT
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:18657831 original size:20 final size:21
Alignment explanation
Indices: 18657795--18657836 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
18657785 GATTATTCAC
18657795 TCAATTAGTTATTTTTT-TTT
1 TCAATTAGTTATTTTTTATTT
*
18657815 TCAATTGGTT-TTCTTTTATTT
1 TCAATTAGTTATT-TTTTATTT
18657836 T
1 T
18657837 ATATATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 2 0.11
20 13 0.68
21 4 0.21
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.69
Consensus pattern (21 bp):
TCAATTAGTTATTTTTTATTT
Found at i:18659842 original size:20 final size:19
Alignment explanation
Indices: 18659783--18659842 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
18659773 TTTAATTTGA
*
18659783 ATTTAAATTAATAAATTAT
1 ATTTAAAATAATAAATTAT
* *
18659802 A--TAAAATAATAATTTTTT
1 ATTTAAAATAATAA-ATTAT
18659820 ATTTAAAATAATAAATATAT
1 ATTTAAAATAATAAAT-TAT
18659840 ATT
1 ATT
18659843 AATTCGATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
17 10 0.31
18 4 0.12
19 2 0.06
20 16 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAAATAATAAATTAT
Found at i:18660266 original size:20 final size:20
Alignment explanation
Indices: 18660221--18660276 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 20
18660211 TAATAAGTGA
*
18660221 ATAATATATAATTTTTTTATT
1 ATAA-ATATAATTTTTTTATC
*
18660242 TTAAATAT-ATTTTTTTAATC
1 ATAAATATAATTTTTTT-ATC
*
18660262 ATAAAAATACATTTT
1 ATAAATATA-ATTTT
18660277 AAAGAGCTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 8 0.29
20 12 0.43
21 3 0.11
22 5 0.18
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAAATATAATTTTTTTATC
Found at i:18664528 original size:29 final size:31
Alignment explanation
Indices: 18664496--18664554 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
18664486 AAATAAAACG
*
18664496 TTAAAAATTTT-TTA-AATTTCAAAATCATA
1 TTAAAAATTTTATTATAATTTAAAAATCATA
*
18664525 TTAAATATTTTATTATAATTTAAAAATCAT
1 TTAAAAATTTTATTATAATTTAAAAATCAT
18664555 CCTTAACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 10 0.38
30 3 0.12
31 13 0.50
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (31 bp):
TTAAAAATTTTATTATAATTTAAAAATCATA
Found at i:18673791 original size:17 final size:17
Alignment explanation
Indices: 18673769--18673819 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
18673759 TAATGTTATC
18673769 ATATCATATATATATAT
1 ATATCATATATATATAT
18673786 ATATCATATATCATAT-T
1 ATATCATATAT-ATATAT
18673803 ATATTACA-ATATATATA
1 ATA-T-CATATATATATA
18673820 AAAAATCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 19 0.63
18 9 0.30
19 2 0.07
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATCATATATATATAT
Found at i:18674851 original size:10 final size:11
Alignment explanation
Indices: 18674829--18674858 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
18674819 AAATTATGAT
18674829 ATAATATAAAA
1 ATAATATAAAA
18674840 ATAATA-AAAA
1 ATAATATAAAA
18674850 ATAATATAA
1 ATAATATAA
18674859 TTCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:18684950 original size:61 final size:60
Alignment explanation
Indices: 18684809--18684950 Score: 146
Period size: 62 Copynumber: 2.3 Consensus size: 60
18684799 TTTTTATAAG
** * * *
18684809 GGATTATTCAAGGTATTTTTAGACAAAAATACTTGAGTAATTTCATTCAATTTTTTGTAAT
1 GGATTATTCAAGGTA-TTTTAGACAAAAATACTCCAATAATATCATTCAATTTTTTGCAAT
* *
18684870 GTATTATTCAAGGAGATTTTAG-CTAAAAATACCTCCAATAATCAT-ATTCAATTTTTTGCAA-
1 GGATTATTCAAGG-TATTTTAGAC-AAAAATA-CTCCAATAAT-ATCATTCAATTTTTTGCAAT
18684931 GAGATTATTCAAGGTATTTT
1 G-GATTATTCAAGGTATTTT
18684951 TGAGATAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
60 1 0.01
61 31 0.46
62 34 0.51
63 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.42
Consensus pattern (60 bp):
GGATTATTCAAGGTATTTTAGACAAAAATACTCCAATAATATCATTCAATTTTTTGCAAT
Found at i:18686433 original size:33 final size:34
Alignment explanation
Indices: 18686337--18686462 Score: 97
Period size: 32 Copynumber: 3.8 Consensus size: 34
18686327 TTAAAATTTT
*
18686337 AATA-AATCATATATATTTGATAAAAA-TA-AAA
1 AATATAATCATATATATTTGATAAAAATTATATA
* * * *
18686368 AAT-TATATAATTTGTATTTGAT--ATATTAATATA
1 AATATA-ATCATATATATTTGATAAAAATT-ATATA
* *
18686401 AAT-T-GTGATACTATATTTGATAAAAATTATATA
1 AATATAATCATA-TATATTTGATAAAAATTATATA
18686434 AATATAAATCATATATATTTGATAAAAAT
1 AATAT-AATCATATATATTTGATAAAAAT
18686463 AAAAAATCAT
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
30 2 0.03
31 8 0.11
32 23 0.32
33 14 0.19
34 5 0.07
35 16 0.22
36 4 0.06
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (34 bp):
AATATAATCATATATATTTGATAAAAATTATATA
Found at i:18688223 original size:30 final size:30
Alignment explanation
Indices: 18688187--18688254 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
18688177 CTACAAGTCT
* *
18688187 CCACCACCTCCTTATATTTACAAATCTCCA
1 CCACCACCTCCATATATCTACAAATCTCCA
* *
18688217 CCACCACCTCCATATGTCTACAAGTCTCCA
1 CCACCACCTCCATATATCTACAAATCTCCA
18688247 CCACCACC
1 CCACCACC
18688255 ATCACCCTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.28, C:0.46, G:0.03, T:0.24
Consensus pattern (30 bp):
CCACCACCTCCATATATCTACAAATCTCCA
Found at i:18688256 original size:27 final size:27
Alignment explanation
Indices: 18688172--18688256 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 27
18688162 TCTCTCTCCT
* *
18688172 TATGTCTACAAGTCTCCACCACCTCCT
1 TATGTCTACAAGTCTCCACCACCACCA
* * *
18688199 TATATTTACAAATCTCCACCACCACCTCCA
1 TATGTCTACAAGTCTCCACCACCA---CCA
18688229 TATGTCTACAAGTCTCCACCACCACCA
1 TATGTCTACAAGTCTCCACCACCACCA
18688256 T
1 T
18688257 CACCCTCTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
27 24 0.51
30 23 0.49
ACGTcount: A:0.28, C:0.40, G:0.05, T:0.27
Consensus pattern (27 bp):
TATGTCTACAAGTCTCCACCACCACCA
Found at i:18688292 original size:48 final size:48
Alignment explanation
Indices: 18688217--18689135 Score: 686
Period size: 48 Copynumber: 19.1 Consensus size: 48
18688207 CAAATCTCCA
*
18688217 CCACCACCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
* * * * * *
18688265 CCACCTCCTCCATATGTCTATATGTCTCCACCACCTCCATCTCCATCA
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
* * * ** * * * **
18688313 CCTCCTCTTCCTTACATTTACAAGTCTCCACCACCTCCATCTCTATCT
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
** * * *
18688361 CCACGACCTCCTTATGTTTACAAATCTCCACCACCA-C--CA------
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
* *
18688400 CCA---CCTCCATACGTCTACAAGTCTCCACCACCACCATCACCCTAT
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
* * * *
18688445 CCACCTCCTCCATATGTCTATAAGTCTCAACCACCTCCAT---CTTCAT
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTC-T
* * * *
18688491 -CACCTCCCCCAT-TTTACATTTACAAGTCTCCACCACCACCATCACCTTCA
1 CCACCTCCTCCATATGT-C---TACAAGTCTCCACCACCACCATCACCCTCT
* *
18688541 CCACCTCCTCCATATGTATACAAGTCTCCACCACCACCACCACCATCACCCTTT
1 CCACCTCCTCCATATGTCTACAAGTCT------CCACCACCACCATCACCCTCT
* * * * * *
18688595 CCACCTCTTCCTTATGTTTATAAGTCTCCACCACCACCATCACCGTCAC
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTC-T
* ** * * *
18688644 CATCACCTTCTCCTCCTTACATTTACAAGTCTCCACCTCCACCATCACCCTTT
1 C--CA-C--CTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
* * *
18688697 CCACCACCTCCATATGTGTACAAGTATCCACCACCACCATCACCCTCT
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
*
18688745 CCACCTCCTCCATATGTCTATAAGTCTCCACCACCACCATCACCCT-T
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
* * * * ** * *
18688792 ACCACCTCCTCCATATGTGTACAATTCACCACCACCTCTGTCTCCATCT
1 -CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
* ** * * * * *
18688841 CCACCACCTCTTTATATTTATAAGTCTCCACCACCACCATCACCTTCA
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
*
18688889 CCACCACCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
* * ** * * *
18688937 CCACCTCCTCCATATGTTTATAAGTCTCCACCACCTTCATCTCCATCA
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
* ** ** * * *
18688985 CCTCCTCCTCTTTACCTTTACAAGTCTCCACCAGCACCATCACCCTCA
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
* * * * *
18689033 CCATCTCCTCCATATGTGTACAAGTCTCCACCACCTCCATCTCCATCT
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
* * ** * * * * *
18689081 CCACCACCTCCTTACATTTACAAATCTCCACCACCACCGTCACCTTCA
1 CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
18689129 CCACCTC
1 CCACCTC
18689136 TTTCATACAT
Statistics
Matches: 686, Mismatches: 149, Indels: 72
0.76 0.16 0.08
Matches are distributed among these distances:
36 26 0.04
37 1 0.00
39 5 0.01
44 2 0.00
45 18 0.03
46 1 0.00
47 2 0.00
48 528 0.77
49 2 0.00
50 1 0.00
51 19 0.03
52 3 0.00
53 1 0.00
54 77 0.11
ACGTcount: A:0.24, C:0.46, G:0.04, T:0.26
Consensus pattern (48 bp):
CCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCT
Found at i:18688339 original size:96 final size:96
Alignment explanation
Indices: 18688215--18689135 Score: 761
Period size: 96 Copynumber: 9.6 Consensus size: 96
18688205 TACAAATCTC
* * * *
18688215 CACCACCACCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCTCCACCTCCTCCATAT
1 CACCACCTCCTCCTTACGTTTACAAGTCTCCACCACCACCATCACCCTCTCCACCTCCTCCATAT
* * * *
18688280 GTCTATATGTCTCCACCACCTCCATCTCCAT
66 GTTTATAAGTCTCCACCACCACCATCACCAT
* * * * * ** ** *
18688311 CACCTCCTCTTCCTTACATTTACAAGTCTCCACCACCTCCATCTCTATCTCCACGACCTCCTTAT
1 CACCACCTCCTCCTTACGTTTACAAGTCTCCACCACCACCATCACCCTCTCCACCTCCTCCATAT
* *
18688376 GTTTACAAATCT---CCACCA-C--CA-C--
66 GTTTATAAGTCTCCACCACCACCATCACCAT
* * *
18688398 CACCA---CCTCCATACGTCTACAAGTCTCCACCACCACCATCACCCTATCCACCTCCTCCATAT
1 CACCACCTCCTCCTTACGTTTACAAGTCTCCACCACCACCATCACCCTCTCCACCTCCTCCATAT
* * * **
18688460 GTCTATAAGTCTCAACCACCTCCATCTTCAT
66 GTTTATAAGTCTCCACCACCACCATCACCAT
* * * * * *
18688491 CACCTCCCCCAT-TTTACATTTACAAGTCTCCACCACCACCATCACCTTCACCACCTCCTCCATA
1 CACCACCTCC-TCCTTACGTTTACAAGTCTCCACCACCACCATCACCCTCTCCACCTCCTCCATA
* * *
18688555 TGTATACAAGTCTCCACCACCACCACCACCAT
65 TGTTTATAAGTCTCCACCACCACCATCACCAT
* * * * *
18688587 CACCCTTTCCACCTCTTCCTTATGTTTATAAGTCTCCACCACCACCATCACCGTCACCATCACCT
1 CA------CCACCTCCTCCTTACGTTTACAAGTCTCCACCACCACCATCACCCTC-TC--CA-C-
* ** * * *
18688652 TCTCCTCCTTACATTTACAAGTCTCCACCTCCACCATCACCCT
55 -CTCCTCCATATGTTTATAAGTCTCCACCACCACCATCACCAT
** * * * * *
18688695 TTCCACCACCTCCATATGTGTACAAGTATCCACCACCACCATCACCCTCTCCACCTCCTCCATAT
1 CACCACCTCCTCCTTACGTTTACAAGTCTCCACCACCACCATCACCCTCTCCACCTCCTCCATAT
* *
18688760 GTCTATAAGTCTCCACCACCACCATCACCCT
66 GTTTATAAGTCTCCACCACCACCATCACCAT
* * * * * * * ** * * * **
18688791 TACCACCTCCTCCATATGTGTACAATTCACCACCACCTCTGTCTCCATCTCCACCACCTCTTTAT
1 CACCACCTCCTCCTTACGTTTACAAGTCTCCACCACCACCATCACCCTCTCCACCTCCTCCATAT
* *
18688856 ATTTATAAGTCTCCACCACCACCATCACCTT
66 GTTTATAAGTCTCCACCACCACCATCACCAT
* * * *
18688887 CACCACCACCTCCATATGTCTACAAGTCTCCACCACCACCATCACCCTCTCCACCTCCTCCATAT
1 CACCACCTCCTCCTTACGTTTACAAGTCTCCACCACCACCATCACCCTCTCCACCTCCTCCATAT
** *
18688952 GTTTATAAGTCTCCACCACCTTCATCTCCAT
66 GTTTATAAGTCTCCACCACCACCATCACCAT
* * * * * *
18688983 CACCTCCTCCTCTTTACCTTTACAAGTCTCCACCAGCACCATCACCCTCACCATCTCCTCCATAT
1 CACCACCTCCTCCTTACGTTTACAAGTCTCCACCACCACCATCACCCTCTCCACCTCCTCCATAT
* * * *
18689048 GTGTACAAGTCTCCACCACCTCCATCTCCAT
66 GTTTATAAGTCTCCACCACCACCATCACCAT
* * * * * * *
18689079 CTCCACCACCTCCTTACATTTACAAATCTCCACCACCACCGTCACCTTCACCACCTC
1 CACCACCTCCTCCTTACGTTTACAAGTCTCCACCACCACCATCACCCTCTCCACCTC
18689136 TTTCATACAT
Statistics
Matches: 657, Mismatches: 142, Indels: 52
0.77 0.17 0.06
Matches are distributed among these distances:
84 54 0.08
87 9 0.01
88 1 0.00
89 1 0.00
90 2 0.00
91 1 0.00
92 1 0.00
93 9 0.01
96 457 0.70
97 1 0.00
98 1 0.00
99 2 0.00
101 2 0.00
102 77 0.12
103 1 0.00
105 2 0.00
106 1 0.00
108 35 0.05
ACGTcount: A:0.24, C:0.46, G:0.04, T:0.26
Consensus pattern (96 bp):
CACCACCTCCTCCTTACGTTTACAAGTCTCCACCACCACCATCACCCTCTCCACCTCCTCCATAT
GTTTATAAGTCTCCACCACCACCATCACCAT
Found at i:18688406 original size:36 final size:36
Alignment explanation
Indices: 18688361--18688440 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
18688351 ATCTCTATCT
* * * *
18688361 CCACGACCTCCTTATGTTTACAAATCTCCACCACCA
1 CCACCACCTCCATACGTCTACAAATCTCCACCACCA
*
18688397 CCACCACCTCCATACGTCTACAAGTCTCCACCACCA
1 CCACCACCTCCATACGTCTACAAATCTCCACCACCA
*
18688433 CCATCACC
1 CCACCACC
18688441 CTATCCACCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.47, G:0.05, T:0.20
Consensus pattern (36 bp):
CCACCACCTCCATACGTCTACAAATCTCCACCACCA
Found at i:18688440 original size:180 final size:180
Alignment explanation
Indices: 18688184--18688584 Score: 577
Period size: 180 Copynumber: 2.3 Consensus size: 180
18688174 TGTCTACAAG
* *
18688184 TCTCCACCACCTCCTTATATTTACAAATCT------CCACCACCACCTCCATATGTCTACAAGTC
1 TCTCCACCACCTCCTTATGTTTACAAATCTCCACCACCACCACCACCTCCATACGTCTACAAGTC
* * *
18688243 TCCACCACCACCATCACCCTCTCCACCTCCTCCATATGTCTATATGTCTCCACCACCTCCATCTC
66 TCCACCACCACCATCACCCTATCCACCTCCTCCATATGTCTATAAGTCTCAACCACCTCCATCTC
* * *
18688308 CATCACCT-CCTC-TTCCTTACATTTACAAGTCTCCACCACCTCCATC-TCT
131 CATCACCTCCCCCATT--TTACATTTACAAGTCTCCACCACCACCATCACCT
*
18688357 ATCTCCACGACCTCCTTATGTTTACAAATCTCCACCACCACCACCACCTCCATACGTCTACAAGT
1 -TCTCCACCACCTCCTTATGTTTACAAATCTCCACCACCACCACCACCTCCATACGTCTACAAGT
18688422 CTCCACCACCACCATCACCCTATCCACCTCCTCCATATGTCTATAAGTCTCAACCACCTCCATCT
65 CTCCACCACCACCATCACCCTATCCACCTCCTCCATATGTCTATAAGTCTCAACCACCTCCATCT
*
18688487 TCATCACCTCCCCCATTTTACATTTACAAGTCTCCACCACCACCATCACCT
130 CCATCACCTCCCCCATTTTACATTTACAAGTCTCCACCACCACCATCACCT
* * * * *
18688538 TCACCACCTCCTCCATATGTATACAAGTCTCCACCACCACCACCACC
1 TCTCCACCACCTCCTTATGTTTACAAATCTCCACCACCACCACCACC
18688585 ATCACCCTTT
Statistics
Matches: 202, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
174 28 0.14
180 167 0.83
181 5 0.02
182 2 0.01
ACGTcount: A:0.25, C:0.46, G:0.03, T:0.26
Consensus pattern (180 bp):
TCTCCACCACCTCCTTATGTTTACAAATCTCCACCACCACCACCACCTCCATACGTCTACAAGTC
TCCACCACCACCATCACCCTATCCACCTCCTCCATATGTCTATAAGTCTCAACCACCTCCATCTC
CATCACCTCCCCCATTTTACATTTACAAGTCTCCACCACCACCATCACCT
Found at i:18688920 original size:27 final size:27
Alignment explanation
Indices: 18688889--18688972 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
18688879 ATCACCTTCA
18688889 CCACCACCTCCATATGTCTACAAGTCT
1 CCACCACCTCCATATGTCTACAAGTCT
* **
18688916 CCACCACCACC--A--TC-AC-CCTCT
1 CCACCACCTCCATATGTCTACAAGTCT
* * *
18688937 CCACCTCCTCCATATGTTTATAAGTCT
1 CCACCACCTCCATATGTCTACAAGTCT
18688964 CCACCACCT
1 CCACCACCT
18688973 TCATCTCCAT
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
21 12 0.29
22 2 0.05
23 3 0.07
25 2 0.05
26 1 0.02
27 21 0.51
ACGTcount: A:0.24, C:0.46, G:0.05, T:0.25
Consensus pattern (27 bp):
CCACCACCTCCATATGTCTACAAGTCT
Found at i:18697646 original size:56 final size:55
Alignment explanation
Indices: 18697556--18697745 Score: 215
Period size: 56 Copynumber: 3.5 Consensus size: 55
18697546 GAACCCAAAA
** *
18697556 AAAAAAAAAAGAAAGAAAAAGTTCAAGTTGAAAACCCGAAAGGGCAGTTTGAATCT
1 AAAAAAAAAA-AAAGAAAAAGTTCAAGTTGAAAACCCGAAAGGGCAACTTGAACCT
18697612 AAACAAAAAAAAAAGAAAAAGTTCAAGTTGAAAACCCGAAAGGGCAACTTGAACCT
1 AAA-AAAAAAAAAAGAAAAAGTTCAAGTTGAAAACCCGAAAGGGCAACTTGAACCT
* * * ** * * *
18697668 AAAAAAAAGAGAGAGAAAAAGTTCAAATTGAAAACCTAAAAGGGTAGCTTGGACC-
1 AAAAAAAA-AAAAAGAAAAAGTTCAAGTTGAAAACCCGAAAGGGCAACTTGAACCT
* *
18697723 -AAAAAACAAGAA-AAAAAGTTCAA
1 AAAAAAAAAAAAAGAAAAAGTTCAA
18697746 AACCTAAAAA
Statistics
Matches: 117, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
52 11 0.09
53 2 0.02
54 6 0.05
55 5 0.04
56 86 0.74
57 7 0.06
ACGTcount: A:0.56, C:0.12, G:0.18, T:0.14
Consensus pattern (55 bp):
AAAAAAAAAAAAAGAAAAAGTTCAAGTTGAAAACCCGAAAGGGCAACTTGAACCT
Found at i:18698728 original size:83 final size:83
Alignment explanation
Indices: 18698572--18698728 Score: 188
Period size: 83 Copynumber: 1.9 Consensus size: 83
18698562 TTACGACCTT
* * * ** * *
18698572 GACTCGATCTTGATCTCTTTCAGACTCGTGACATTGTCCCAGTCATTTGATCTTGACTCAGGTCA
1 GACTCGATCTTGATCGCCTTCAGACTCATGACATCATCCCAGTCATCTGATCTCGACTCAGGTCA
*
18698637 AATTATCTTCACGCCCTC
66 AATCATCTTCACGCCCTC
* * * * *
18698655 GACTCGGTCTTGGTCGCCTTCAGACTCATGACATCATCCTAGTCATCTGATCTCGACTTAGTTCA
1 GACTCGATCTTGATCGCCTTCAGACTCATGACATCATCCCAGTCATCTGATCTCGACTCAGGTCA
*
18698720 GATCATCTT
66 AATCATCTT
18698729 TAGACTTACG
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
83 60 1.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (83 bp):
GACTCGATCTTGATCGCCTTCAGACTCATGACATCATCCCAGTCATCTGATCTCGACTCAGGTCA
AATCATCTTCACGCCCTC
Found at i:18698757 original size:197 final size:197
Alignment explanation
Indices: 18698410--18698767 Score: 491
Period size: 197 Copynumber: 1.8 Consensus size: 197
18698400 TCATGGCATA
* * *
18698410 GTCCCAATCATTTGATCTAGACTCAGGTCAGATTATCATCATGACATCGACTTGATCTTGGTCAC
1 GTCCCAATCATTTGATCTAGACTCAGGTCAAATTATCATCACGACATCGACTCGATCTTGGTCAC
* ** * *
18698475 CTTCAGACTCGCGGGATCATCCTAGTCATTTGATATTGACTCAGGTCAGATCATCTTTAGACTTA
66 CTTCAGACTCACGACATCATCCTAGTCATCTGATATCGACTCAGGTCAGATCATCTTTAGACTTA
* * *
18698540 CAACATTAGTTCGATCATTTATTTACGACCTTGACTCGATCTTGATCTCTTTCAGACTCGTGACA
131 CAACATCAATTCGATCATTTATCTACGACCTTGACTCGATCTTGATCTCTTTCAGACTCGTGACA
18698605 TT
196 TT
* * * * * * *
18698607 GTCCCAGTCATTTGATCTTGACTCAGGTCAAATTATCTTCACGCCCTCGACTCGGTCTTGGTCGC
1 GTCCCAATCATTTGATCTAGACTCAGGTCAAATTATCATCACGACATCGACTCGATCTTGGTCAC
* * * *
18698672 CTTCAGACTCATGACATCATCCTAGTCATCTGATCTCGACTTAGTTCAGATCATCTTTAGACTTA
66 CTTCAGACTCACGACATCATCCTAGTCATCTGATATCGACTCAGGTCAGATCATCTTTAGACTTA
* * *
18698737 CGACATCAATTCGGTCATTTATCTATGACCT
131 CAACATCAATTCGATCATTTATCTACGACCT
18698768 CAATTCAGTC
Statistics
Matches: 136, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
197 136 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.35
Consensus pattern (197 bp):
GTCCCAATCATTTGATCTAGACTCAGGTCAAATTATCATCACGACATCGACTCGATCTTGGTCAC
CTTCAGACTCACGACATCATCCTAGTCATCTGATATCGACTCAGGTCAGATCATCTTTAGACTTA
CAACATCAATTCGATCATTTATCTACGACCTTGACTCGATCTTGATCTCTTTCAGACTCGTGACA
TT
Found at i:18699050 original size:3 final size:3
Alignment explanation
Indices: 18699042--18699118 Score: 93
Period size: 3 Copynumber: 25.3 Consensus size: 3
18699032 TATACTATAG
* * * *
18699042 TAT TAT TAT ATAT TA- TAT TAT ACAC TAT AAT TAT TAG TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
18699088 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18699119 TACGATGATT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 2 0.03
3 57 0.90
4 4 0.06
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:18699768 original size:19 final size:19
Alignment explanation
Indices: 18699718--18699768 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
18699708 CAAATTATGG
*
18699718 TAAAATTTTCAAAATCCGA
1 TAAAATTTTCAGAATCCGA
* * **
18699737 TGAGATTCCCAGAATCCGA
1 TAAAATTTTCAGAATCCGA
18699756 TAAAATTTTCAGA
1 TAAAATTTTCAGA
18699769 TTTCGTTTGA
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (19 bp):
TAAAATTTTCAGAATCCGA
Found at i:18700140 original size:9 final size:9
Alignment explanation
Indices: 18700126--18700154 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
18700116 TTTTCAAATG
18700126 AAAATAAAA
1 AAAATAAAA
18700135 AAAAT-AAA
1 AAAATAAAA
18700143 AAAATAAAA
1 AAAATAAAA
18700152 AAA
1 AAA
18700155 TCTTTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAATAAAA
Done.