Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, 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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 24 of 84
Found at i:5253047 original size:9 final size:9
Alignment explanation
Indices: 5253045--5253085 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
5253035 TTTTGAATTT
5253045 TTTTTTGAA
1 TTTTTTGAA
**
5253054 TTTTTT-TT
1 TTTTTTGAA
5253062 TTTTTTGAA
1 TTTTTTGAA
5253071 TTTTTTGAA
1 TTTTTTGAA
5253080 TTTTTT
1 TTTTTT
5253086 TTATTTGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 6 0.22
9 21 0.78
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (9 bp):
TTTTTTGAA
Found at i:5253064 original size:17 final size:17
Alignment explanation
Indices: 5253042--5253076 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5253032 TTTTTTTGAA
5253042 TTTTTTTTTGAATTTTT
1 TTTTTTTTTGAATTTTT
5253059 TTTTTTTTTGAATTTTT
1 TTTTTTTTTGAATTTTT
5253076 T
1 T
5253077 GAATTTTTTT
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:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTTTTTTTGAATTTTT
Found at i:5253064 original size:26 final size:26
Alignment explanation
Indices: 5253031--5253103 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 26
5253021 CCGCTCCAGG
5253031 TTTTTTTTGAATTT-TTTTTTGAATTT
1 TTTTTTTTG-ATTTATTTTTTGAATTT
5253057 TTTTTTTT--TTTGAATTTTTTGAATTT
1 TTTTTTTTGATTT--ATTTTTTGAATTT
5253083 TTTTTATTTGACTTTGATTTT
1 TTTTT-TTTGA-TTT-ATTTT
5253104 GATCTTGATT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
23 3 0.08
26 25 0.64
27 3 0.08
29 5 0.13
30 3 0.08
ACGTcount: A:0.15, C:0.01, G:0.08, T:0.75
Consensus pattern (26 bp):
TTTTTTTTGATTTATTTTTTGAATTT
Found at i:5253083 original size:17 final size:17
Alignment explanation
Indices: 5253046--5253084 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5253036 TTTGAATTTT
***
5253046 TTTTTGAATTTTTTTTT
1 TTTTTGAATTTTTTGAA
5253063 TTTTTGAATTTTTTGAA
1 TTTTTGAATTTTTTGAA
5253080 TTTTT
1 TTTTT
5253085 TTTATTTGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (17 bp):
TTTTTGAATTTTTTGAA
Found at i:5253087 original size:13 final size:12
Alignment explanation
Indices: 5253031--5253062 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
5253021 CCGCTCCAGG
5253031 TTTTTTTTGAAT
1 TTTTTTTTGAAT
5253043 TTTTTTTTGAAT
1 TTTTTTTTGAAT
5253055 TTTTTTTT
1 TTTTTTTT
5253063 TTTTTGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:5253730 original size:156 final size:156
Alignment explanation
Indices: 5253126--5253712 Score: 1019
Period size: 156 Copynumber: 3.8 Consensus size: 156
5253116 TTTTTCTTTA
* *
5253126 TTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACTCCT
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATACTCCT
* *
5253191 GAGGTGAGGGAATTTTCTC-ATTTTCTGCTAAAAGTATAAGAGTCAATTGAGAATAATTTCCGAT
65 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGAT
* * *
5253255 AATTAATTACTTGGCTGATTTTGA--T
130 AATTAATTAATTGGTTGATCTTGATTT
5253280 TT-TTT--TT--TCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
5253340 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
5253405 ATTAATTAATTGGTTGATCTTGATTT
131 ATTAATTAATTGGTTGATCTTGATTT
*
5253431 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAATAGTTTTTCTTGCATACTCCTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
5253496 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
5253561 ATTAATTAATTGGTTGATCTTGATTT
131 ATTAATTAATTGGTTGATCTTGATTT
* *
5253587 TTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCTTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
5253652 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
5253713 AACAACTAAC
Statistics
Matches: 414, Mismatches: 11, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
148 46 0.11
149 87 0.21
151 5 0.01
152 3 0.01
153 3 0.01
154 4 0.01
156 266 0.64
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (156 bp):
TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
ATTAATTAATTGGTTGATCTTGATTT
Found at i:5255497 original size:57 final size:57
Alignment explanation
Indices: 5255407--5255789 Score: 447
Period size: 58 Copynumber: 6.7 Consensus size: 57
5255397 TTTTGTGTAG
** * *
5255407 GAAAAATTGATACTTTCAAC--TTTTCCTCGAAATATTTTTTAGAAATTTTAATATCGA
1 GAAAAATTGATACTTTCAACTTTTTTCC-AAAAATATTTTTT-GAAACTTTAATTTCGA
* * *
5255464 GGAAAATTGATACTTTCAACTTTTTTCC-AAAATATCTTTTGAAACTTTAATTTCTA
1 GAAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGAAACTTTAATTTCGA
* * * **
5255520 GAAAAATTG-TACTTTCAA-TTTTTTCTCAAAAATTTTTTTTTGAAAATTTATTTTTTA
1 GAAAAATTGATACTTTCAACTTTTTTC-CAAAAA-TATTTTTTGAAACTTTAATTTCGA
*
5255577 AAAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTTGAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTTTCCAAAAATA-TTTTTTGAAACTTTAATTTCGA
* * * * * * * **
5255635 AAAAAATTGATACTTTCAA-TTTTTCCTCAAAAA-CTGTTTTAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTTC-CAAAAATATTTTTTGAAACTTTAATTTCGA
5255691 GAAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTG-AAACTTTAATTTCGA
*
5255749 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTT
1 GAAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTT
5255790 TTTGATTTTA
Statistics
Matches: 278, Mismatches: 36, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
54 7 0.03
55 10 0.04
56 65 0.23
57 74 0.27
58 109 0.39
59 13 0.05
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (57 bp):
GAAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGAAACTTTAATTTCGA
Found at i:5255565 original size:15 final size:15
Alignment explanation
Indices: 5255547--5255580 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5255537 ATTTTTTCTC
5255547 AAAAATTT-TTTTTT
1 AAAAATTTATTTTTT
*
5255561 GAAAATTTATTTTTT
1 AAAAATTTATTTTTT
5255576 AAAAA
1 AAAAA
5255581 AATTGATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
AAAAATTTATTTTTT
Found at i:5255704 original size:114 final size:112
Alignment explanation
Indices: 5255407--5255788 Score: 511
Period size: 114 Copynumber: 3.3 Consensus size: 112
5255397 TTTTGTGTAG
* * * * * ** *
5255407 GAAAAATTGATACTTTCAACTTTTCCTCGAAATATTTTTTAGAAATTTTAATATCGAGGAAAATT
1 GAAAAATTGATACTTTCAATTTTTCCTC-AAAAATTTTTTA-AAAATTTATTTTTAAGAAAAATT
* *
5255472 GATACTTTCAACTTTTTTCC-AAAATATCTTTTGAAACTTTAATTTCTA
64 GATACTTTCAACTTTTTTCCAAAAATATTTTTTGAAACTTTAATTTCGA
* *
5255520 GAAAAATTG-TACTTTCAATTTTTTCTCAAAAATTTTTTTTTGAAAATTTATTTTTTAA-AAAAA
1 GAAAAATTGATACTTTCAATTTTTCCTCAAAAA---TTTTTTAAAAATTTA-TTTTTAAGAAAAA
5255583 TTGATACTTTCAACTTTTTTCCAAAAATATTTTTTTGAAACTTTAATTTCGA
62 TTGATACTTTCAACTTTTTTCCAAAAATA-TTTTTTGAAACTTTAATTTCGA
* *
5255635 AAAAAATTGATACTTTCAATTTTTCCTCAAAAACTGTTTTAAAAATTTATTTTTAAGAAAAATTG
1 GAAAAATTGATACTTTCAATTTTTCCTCAAAAA-TTTTTTAAAAATTTATTTTTAAGAAAAATTG
5255700 ATACTTTCAACTTTTTTCCAAAAATATTTTTTGAAAACTTTAATTTCGA
65 ATACTTTCAACTTTTTTCCAAAAATATTTTTTG-AAACTTTAATTTCGA
5255749 GAAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTT
1 GAAAAATTGATACTTTCAA-TTTTTCCTCAAAAAT-TTTTT
5255789 TTTTGATTTT
Statistics
Matches: 239, Mismatches: 19, Indels: 21
0.86 0.07 0.08
Matches are distributed among these distances:
111 4 0.02
112 16 0.07
113 57 0.24
114 105 0.44
115 35 0.15
116 22 0.09
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (112 bp):
GAAAAATTGATACTTTCAATTTTTCCTCAAAAATTTTTTAAAAATTTATTTTTAAGAAAAATTGA
TACTTTCAACTTTTTTCCAAAAATATTTTTTGAAACTTTAATTTCGA
Found at i:5255722 original size:27 final size:27
Alignment explanation
Indices: 5255692--5255782 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 27
5255682 TATTTTTAAG
5255692 AAAAATTGATACTTTCAACTTTTTTCC
1 AAAAATTGATACTTTCAACTTTTTTCC
** * *
5255719 AAAAA-T-ATTTTTTGAAAACTTTAATTTCGAG
1 AAAAATTGATACTTT--CAACTTT--TTTC--C
*
5255750 AAAAATTGATACTTTCAACTTTTTCCC
1 AAAAATTGATACTTTCAACTTTTTTCC
5255777 AAAAAT
1 AAAAAT
5255783 ATTTTTTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 16
0.65 0.12 0.22
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 17 0.36
29 7 0.15
31 11 0.23
32 1 0.02
33 5 0.11
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (27 bp):
AAAAATTGATACTTTCAACTTTTTTCC
Found at i:5255815 original size:5 final size:5
Alignment explanation
Indices: 5255807--5255963 Score: 80
Period size: 5 Copynumber: 31.0 Consensus size: 5
5255797 TTATTTAAAG
*
5255807 AAAAT AAAAT --AAT AAAAT AAAAT AAAAGT GAAAAT -AAA- AAAAT -AAAG
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAAT
* *
5255854 AAAAT AAAGA- AAAGT AAAACA AAAAT AAAAAT AAAAT AAAGAT AAAA-
1 AAAAT AAA-AT AAAAT AAAA-T AAAAT -AAAAT AAAAT AAA-AT AAAAT
* * **
5255901 AAATAT TAAAT AAACCT AATCT AATAAT AAAAT -AAAT -AAAT AAAATT
1 AAA-AT AAAAT AAA-AT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAA-T
*
5255948 AAAAAT AAAAA AAAAT
1 -AAAAT AAAAT AAAAT
5255964 CTGGAGTGGC
Statistics
Matches: 119, Mismatches: 14, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
3 3 0.03
4 20 0.17
5 61 0.51
6 27 0.23
7 8 0.07
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:5255840 original size:17 final size:16
Alignment explanation
Indices: 5255807--5255963 Score: 84
Period size: 17 Copynumber: 9.3 Consensus size: 16
5255797 TTATTTAAAG
5255807 AAAATAAAATAATAAAAT
1 AAAAT-AAA-AATAAAAT
*
5255825 AAAATAAAAGTGAAAAT
1 AAAATAAAAAT-AAAAT
* *
5255842 AAAAAAATAAAGAAAAT
1 AAAATAA-AAATAAAAT
* * *
5255859 -AAAGAAAAGTAAAACA
1 AAAATAAAAATAAAA-T
5255875 AAAATAAAAATAAAAT
1 AAAATAAAAATAAAAT
*
5255891 AAAGATAAAAA-AATAT
1 AAA-ATAAAAATAAAAT
* ** **
5255907 TAAATAAACCTAATCT
1 AAAATAAAAATAAAAT
*
5255923 AATAATAAAATAAATAAAT
1 AA-AATAAAA-ATA-AAAT
*
5255942 AAAATTAAAAATAAAAA
1 AAAA-TAAAAATAAAAT
5255959 AAAAT
1 AAAAT
5255964 CTGGAGTGGC
Statistics
Matches: 105, Mismatches: 24, Indels: 22
0.70 0.16 0.15
Matches are distributed among these distances:
15 11 0.10
16 22 0.21
17 51 0.49
18 12 0.11
19 9 0.09
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.19
Consensus pattern (16 bp):
AAAATAAAAATAAAAT
Found at i:5255841 original size:30 final size:29
Alignment explanation
Indices: 5255806--5255905 Score: 88
Period size: 28 Copynumber: 3.5 Consensus size: 29
5255796 TTTATTTAAA
* *
5255806 GAAAATAAAATAATAAAATAAAATAAAAGT
1 GAAAATAAAAAAAT-AAAGAAAATAAAAGT
5255836 GAAAATAAAAAAATAAAGAAAAT-AAA--
1 GAAAATAAAAAAATAAAGAAAATAAAAGT
5255862 GAAAAGTAAAACAAA-AATA-AAAATAAAA-T
1 GAAAA-TAAAA-AAATAA-AGAAAATAAAAGT
5255891 -AAAGATAAAAAAATA
1 GAAA-ATAAAAAAATA
5255906 TTAAATAAAC
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
26 5 0.08
27 15 0.25
28 19 0.31
29 9 0.15
30 13 0.21
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.15
Consensus pattern (29 bp):
GAAAATAAAAAAATAAAGAAAATAAAAGT
Found at i:5255867 original size:33 final size:32
Alignment explanation
Indices: 5255812--5255895 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 32
5255802 TAAAGAAAAT
* *
5255812 AAAAT-AATAAAATAAAATAAAAGTGAAAATAAA
1 AAAATAAATAAAAT-AAAGAAAAGT-AAAACAAA
*
5255845 AAAATAAAGAAAATAAAGAAAAGTAAAACAAA
1 AAAATAAATAAAATAAAGAAAAGTAAAACAAA
5255877 AATAA-AAATAAAATAAAGA
1 AA-AATAAATAAAATAAAGA
5255896 TAAAAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
32 22 0.49
33 16 0.36
34 7 0.16
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.14
Consensus pattern (32 bp):
AAAATAAATAAAATAAAGAAAAGTAAAACAAA
Found at i:5255934 original size:8 final size:9
Alignment explanation
Indices: 5255808--5255944 Score: 58
Period size: 8 Copynumber: 15.3 Consensus size: 9
5255798 TATTTAAAGA
5255808 AAATAAAAT
1 AAATAAAAT
5255817 -AATAAAAT
1 AAATAAAAT
*
5255825 AAA-ATAA-
1 AAATAAAAT
*
5255832 AAGTGAAAAT
1 AAAT-AAAAT
5255842 AAA-AAAAT
1 AAATAAAAT
*
5255850 AAAGAAAAT
1 AAATAAAAT
*
5255859 AAAGAAAAGT
1 AAATAAAA-T
*
5255869 AAA-ACAA-
1 AAATAAAAT
5255876 AAATAAAAAT
1 AAAT-AAAAT
5255886 AAAATAAAGAT
1 -AAATAAA-AT
*
5255897 AAAAAAATATT
1 AAATAAA-A-T
*
5255908 AAATAAACCT
1 AAATAAA-AT
**
5255918 -AATCTAAT
1 AAATAAAAT
5255926 -AATAAAAT
1 AAATAAAAT
5255934 AAAT-AAAT
1 AAATAAAAT
5255942 AAA
1 AAA
5255945 ATTAAAAATA
Statistics
Matches: 99, Mismatches: 16, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
7 5 0.05
8 33 0.33
9 31 0.31
10 17 0.17
11 13 0.13
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:5256829 original size:20 final size:21
Alignment explanation
Indices: 5256806--5256865 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
5256796 AAATCAAATG
5256806 AAAATAAATCAGATAAATAAA
1 AAAATAAATCAGATAAATAAA
*
5256827 AAAATTAA-CAGATAAATTAAA
1 AAAATAAATCAGATAAA-TAAA
5256848 ATTAAAT-AA-CAGATAAAT
1 A--AAATAAATCAGATAAAT
5256866 TATAACATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 8 0.23
21 13 0.37
22 10 0.29
23 4 0.11
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (21 bp):
AAAATAAATCAGATAAATAAA
Found at i:5256845 original size:12 final size:12
Alignment explanation
Indices: 5256828--5256867 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
5256818 ATAAATAAAA
5256828 AAATTAACAGAT
1 AAATTAACAGAT
5256840 AAATTAA-A-ATT
1 AAATTAACAGA-T
5256851 AAA-TAACAGAT
1 AAATTAACAGAT
5256862 AAATTA
1 AAATTA
5256868 TAACATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 10 0.42
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (12 bp):
AAATTAACAGAT
Found at i:5256860 original size:22 final size:21
Alignment explanation
Indices: 5256806--5256867 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 21
5256796 AAATCAAATG
*
5256806 AAAATAAATCAGATAAA-TAAA
1 AAAATTAA-CAGATAAATTAAA
5256827 AAAATTAACAGATAAATTAAA
1 AAAATTAACAGATAAATTAAA
5256848 ATTAAA-TAACAGATAAATTA
1 A--AAATTAACAGATAAATTA
5256868 TAACATATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 8 0.22
21 12 0.32
22 14 0.38
23 3 0.08
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (21 bp):
AAAATTAACAGATAAATTAAA
Found at i:5256969 original size:15 final size:14
Alignment explanation
Indices: 5256951--5257097 Score: 64
Period size: 15 Copynumber: 10.6 Consensus size: 14
5256941 TAGTAGTGAT
5256951 AAATAAATAAATAA
1 AAATAAATAAATAA
**
5256965 TAAATACCTAAGATAA
1 -AAATAAATAA-ATAA
*
5256981 AAATAAA-AGGAAAAA
1 AAATAAATA--AATAA
*
5256996 AAATATATAAA-AA
1 AAATAAATAAATAA
5257009 ACAAT-AAT-AATAA
1 A-AATAAATAAATAA
*
5257022 TAAT-AATAAATAA
1 AAATAAATAAATAA
5257035 AAAT--A-AAATAA
1 AAATAAATAAATAA
*
5257046 AAATGTAAAATACA-AA
1 AAA--T-AAATAAATAA
5257062 AAAT-AA-AAATAA
1 AAATAAATAAATAA
*
5257074 AAATAACAATAAAAAA
1 AAAT-A-AATAAATAA
5257090 AAATAAAT
1 AAATAAAT
5257098 TTACCTATTT
Statistics
Matches: 102, Mismatches: 12, Indels: 37
0.68 0.08 0.25
Matches are distributed among these distances:
11 11 0.11
12 17 0.17
13 16 0.16
14 10 0.10
15 25 0.25
16 21 0.21
17 2 0.02
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:5257007 original size:10 final size:10
Alignment explanation
Indices: 5256981--5257097 Score: 71
Period size: 10 Copynumber: 11.4 Consensus size: 10
5256971 CCTAAGATAA
**
5256981 AAATAAAAGG
1 AAATAAAAAT
5256991 AAA-AAAAAT
1 AAATAAAAAT
*
5257000 ATATAAAAA-
1 AAATAAAAAT
*
5257009 ACAATAATAAT
1 A-AATAAAAAT
*
5257020 -AATAATAAT
1 AAATAAAAAT
5257029 AAATAAAAAT
1 AAATAAAAAT
5257039 AAAATAAAAATGT
1 -AAATAAAAA--T
*
5257052 AAAATACAAA-
1 -AAATAAAAAT
5257062 AAATAAAAAT
1 AAATAAAAAT
*
5257072 AAAAATAACAAT
1 --AAATAAAAAT
*
5257084 AAAAAAAAAT
1 AAATAAAAAT
5257094 AAAT
1 AAAT
5257098 TTACCTATTT
Statistics
Matches: 85, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
9 24 0.28
10 33 0.39
11 9 0.11
12 9 0.11
13 10 0.12
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:5257039 original size:22 final size:21
Alignment explanation
Indices: 5257014--5257096 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 21
5257004 AAAAAACAAT
*
5257014 AATAATAATAATAATAAATAAA
1 AATAA-AATAAAAATAAATAAA
*
5257036 AATAAAATAAAAAT--GT-AA
1 AATAAAATAAAAATAAATAAA
5257054 AATACAAA-AAATAA-AAATAAA
1 AATA-AAATAAA-AATAAATAAA
*
5257075 AATAACAATAAAAAAAAATAAA
1 AATAA-AATAAAAATAAATAAA
5257097 TTTACCTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
18 9 0.18
19 6 0.12
20 2 0.04
21 18 0.36
22 15 0.30
ACGTcount: A:0.77, C:0.02, G:0.01, T:0.19
Consensus pattern (21 bp):
AATAAAATAAAAATAAATAAA
Found at i:5257048 original size:12 final size:12
Alignment explanation
Indices: 5256993--5257089 Score: 58
Period size: 13 Copynumber: 7.5 Consensus size: 12
5256983 ATAAAAGGAA
5256993 AAAAAATATATAA-
1 AAAAAATA-A-AAT
5257006 AAAACAATAATAAT
1 AAAA-AATAA-AAT
5257020 AATAATAAT-AAAT
1 AA-AA-AATAAAAT
5257033 -AAAAATAAAAT
1 AAAAAATAAAAT
*
5257044 AAAAATGTAAAAT
1 AAAAA-ATAAAAT
5257057 ACAAAAAATAAAA-
1 --AAAAAATAAAAT
5257070 ATAAAAATAACAAT
1 A-AAAAATAA-AAT
5257084 AAAAAA
1 AAAAAA
5257090 AAATAAATTT
Statistics
Matches: 70, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
10 3 0.04
11 7 0.10
12 13 0.19
13 24 0.34
14 13 0.19
15 10 0.14
ACGTcount: A:0.76, C:0.03, G:0.01, T:0.20
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:5257062 original size:7 final size:6
Alignment explanation
Indices: 5256977--5257096 Score: 79
Period size: 6 Copynumber: 19.8 Consensus size: 6
5256967 AATACCTAAG
** * * * *
5256977 ATAAAA ATAAAA GGAAAA A-AAAT ATATAAA A-AACA ATAATA ATAATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATA-AAA ATAAAA ATAAAA ATAAAA
*
5257024 ATAATAA ATAAAA AT-AAA ATAAAA ATGTAAAA TACAAAAA ATAAAA ATAAAA
1 ATAA-AA ATAAAA ATAAAA ATAAAA A--TAAAA -A-TAAAA ATAAAA ATAAAA
*
5257076 ATAACA AT-AAA A-AAAA ATAAA
1 ATAAAA ATAAAA ATAAAA ATAAA
5257097 TTTACCTATT
Statistics
Matches: 91, Mismatches: 13, Indels: 20
0.73 0.10 0.16
Matches are distributed among these distances:
5 19 0.21
6 53 0.58
7 9 0.10
8 9 0.10
9 1 0.01
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:5283732 original size:82 final size:82
Alignment explanation
Indices: 5283595--5283762 Score: 336
Period size: 82 Copynumber: 2.0 Consensus size: 82
5283585 TTCGTTTCTT
5283595 ATATATACATTTCTTATAGTCTTTTGACTCCCTAATGGTTGACTCATTTTGAGGTTATTGTAACT
1 ATATATACATTTCTTATAGTCTTTTGACTCCCTAATGGTTGACTCATTTTGAGGTTATTGTAACT
5283660 ATTTTATATAGATGGTG
66 ATTTTATATAGATGGTG
5283677 ATATATACATTTCTTATAGTCTTTTGACTCCCTAATGGTTGACTCATTTTGAGGTTATTGTAACT
1 ATATATACATTTCTTATAGTCTTTTGACTCCCTAATGGTTGACTCATTTTGAGGTTATTGTAACT
5283742 ATTTTATATAGATGGTG
66 ATTTTATATAGATGGTG
5283759 ATAT
1 ATAT
5283763 TGTCATTGAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 86 1.00
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.46
Consensus pattern (82 bp):
ATATATACATTTCTTATAGTCTTTTGACTCCCTAATGGTTGACTCATTTTGAGGTTATTGTAACT
ATTTTATATAGATGGTG
Found at i:5290648 original size:13 final size:14
Alignment explanation
Indices: 5290625--5290656 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
5290615 AGATTTGATT
5290625 GACACGCTTAGAGA
1 GACACGCTTAGAGA
5290639 GACA-GCTTAGAGA
1 GACACGCTTAGAGA
5290652 GACAC
1 GACAC
5290657 AATTACAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.38, C:0.22, G:0.28, T:0.12
Consensus pattern (14 bp):
GACACGCTTAGAGA
Found at i:5294845 original size:22 final size:22
Alignment explanation
Indices: 5294817--5294860 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5294807 CTAAATCTTC
*
5294817 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
5294839 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
5294861 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:5298556 original size:23 final size:25
Alignment explanation
Indices: 5298501--5298559 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
5298491 AAAGGGTTCG
* * *
5298501 GCAATGAAGGCCTAAACAGGATTCG
1 GCAATGAAGGCCTAAACAGAAGTCA
5298526 GCAATGAAGGCCTAAA-A-AAGTCA
1 GCAATGAAGGCCTAAACAGAAGTCA
5298549 GCAATGAAGGC
1 GCAATGAAGGC
5298560 TGAAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 14 0.45
24 1 0.03
25 16 0.52
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.14
Consensus pattern (25 bp):
GCAATGAAGGCCTAAACAGAAGTCA
Found at i:5298735 original size:22 final size:22
Alignment explanation
Indices: 5298707--5298750 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5298697 CTAAATCTTC
*
5298707 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
5298729 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
5298751 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:5317965 original size:2 final size:2
Alignment explanation
Indices: 5317958--5317983 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5317948 CATTATGAAT
5317958 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
5317984 GAGGAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5319299 original size:34 final size:33
Alignment explanation
Indices: 5319224--5319287 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
5319214 ATTTAAATAG
5319224 ATAATAAAATTGATTATGATATGATTAAAAACA
1 ATAATAAAATTGATTATGATATGATTAAAAACA
*
5319257 ATAATAAAATT-ATTATAGTTATGATTAAAAA
1 ATAATAAAATTGATTAT-GATATGATTAAAAA
5319288 AATTTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 5 0.17
33 24 0.83
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.36
Consensus pattern (33 bp):
ATAATAAAATTGATTATGATATGATTAAAAACA
Found at i:5320920 original size:16 final size:16
Alignment explanation
Indices: 5320901--5320934 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5320891 ATTATAGATA
5320901 AATGTAAT-TAATGTTT
1 AATGTAATGTAA-GTTT
5320917 AATGTAATGTAAGTTT
1 AATGTAATGTAAGTTT
5320933 AA
1 AA
5320935 CATATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (16 bp):
AATGTAATGTAAGTTT
Found at i:5322981 original size:17 final size:17
Alignment explanation
Indices: 5322937--5322982 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
5322927 TTTTTATAAG
*
5322937 TTAAA-TAATTTAAATT
1 TTAAATTAATATAAATT
*
5322953 TT-TATTACATATAAATT
1 TTAAATTA-ATATAAATT
5322970 TTAAATTAATATA
1 TTAAATTAATATA
5322983 TTTAATAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 1 0.04
16 4 0.17
17 15 0.62
18 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAATTAATATAAATT
Found at i:5325313 original size:2 final size:2
Alignment explanation
Indices: 5325308--5325349 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5325298 AGAAGTAACT
5325308 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5325350 TTGTCTGTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5332873 original size:18 final size:18
Alignment explanation
Indices: 5332842--5332880 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5332832 CAATAATTGT
*
5332842 AAAAAAAATTGCAA-TAA
1 AAAAAAAATGGCAATTAA
5332859 AAAATAAAATGGCAATTAA
1 AAAA-AAAATGGCAATTAA
5332878 AAA
1 AAA
5332881 CATTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 9 0.47
19 6 0.32
ACGTcount: A:0.69, C:0.05, G:0.08, T:0.18
Consensus pattern (18 bp):
AAAAAAAATGGCAATTAA
Found at i:5336015 original size:32 final size:32
Alignment explanation
Indices: 5335978--5336038 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
5335968 GGGTGCATAA
* *
5335978 AGAATAATTGTGACTGG-TTAATAGTTAGATTC
1 AGAATAACTCTGAC-GGATTAATAGTTAGATTC
*
5336010 AGAATAACTCTGACGGATTAATTGTTAGA
1 AGAATAACTCTGACGGATTAATAGTTAGA
5336039 CTTTGCTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 2 0.08
32 23 0.92
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.34
Consensus pattern (32 bp):
AGAATAACTCTGACGGATTAATAGTTAGATTC
Found at i:5339982 original size:3 final size:3
Alignment explanation
Indices: 5339974--5340014 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
5339964 GTGTTGATAC
5339974 CAT CAT CAT CAT CAT CAT CAT CAT -AT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
5340015 GAGTAATTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
CAT
Found at i:5344576 original size:36 final size:35
Alignment explanation
Indices: 5344528--5344636 Score: 96
Period size: 42 Copynumber: 2.9 Consensus size: 35
5344518 AGTATATTAA
5344528 ATAAT-TTTTAAAAATAAAATAATTTATTATTTAT
1 ATAATATTTTAAAAATAAAATAATTTATTATTTAT
*
5344562 ATTAATATTTTAAAATATAAAAAATAAAATATTTTTATTTAT
1 A-TAATATTTTAAAA-AT--AAAAT--AAT-TTATTATTTAT
* *
5344604 ATAATAATATTAAAAATAGTAAT-ATTTATTATT
1 ATAAT-ATTTTAAAAATA-AAATAATTTATTATT
5344637 AGAGTATTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
34 1 0.02
35 4 0.07
36 15 0.25
37 4 0.07
39 6 0.10
40 3 0.05
41 9 0.15
42 19 0.31
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (35 bp):
ATAATATTTTAAAAATAAAATAATTTATTATTTAT
Found at i:5344617 original size:42 final size:44
Alignment explanation
Indices: 5344537--5344618 Score: 125
Period size: 42 Copynumber: 1.9 Consensus size: 44
5344527 AATAATTTTT
*
5344537 AAAAATAAAATAATTTATTATTTATATTAATATTTTAAAATATA
1 AAAAATAAAATAATTTATTATTTATATTAATATATTAAAATATA
5344581 AAAAATAAAAT-ATTT-TTATTTATA-TAATAATATTAAAA
1 AAAAATAAAATAATTTATTATTTATATTAAT-ATATTAAAA
5344619 ATAGTAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
41 4 0.11
42 17 0.47
43 4 0.11
44 11 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (44 bp):
AAAAATAAAATAATTTATTATTTATATTAATATATTAAAATATA
Found at i:5344619 original size:29 final size:30
Alignment explanation
Indices: 5344587--5344657 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
5344577 TATAAAAAAT
*
5344587 AAAATATTTTTATTTATATAATA-A-TATTA
1 AAAATATTTATATTTAT-TAATAGAGTATTA
* * *
5344616 AAAATAGTAATATTTATTATTAGAGTATTA
1 AAAATATTTATATTTATTAATAGAGTATTA
5344646 AAAATATTTATA
1 AAAATATTTATA
5344658 CTATTAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 4 0.12
29 15 0.44
30 15 0.44
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (30 bp):
AAAATATTTATATTTATTAATAGAGTATTA
Found at i:5344940 original size:23 final size:23
Alignment explanation
Indices: 5344914--5344957 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
5344904 TTAAAAGAAT
*
5344914 AATA-CAATAATATTTACTATTGA
1 AATATCAAAAATATTTA-TATTGA
*
5344937 AATATTAAAAATATTTATATT
1 AATATCAAAAATATTTATATT
5344958 TAATAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (23 bp):
AATATCAAAAATATTTATATTGA
Found at i:5344941 original size:44 final size:41
Alignment explanation
Indices: 5344854--5344944 Score: 103
Period size: 41 Copynumber: 2.1 Consensus size: 41
5344844 TATTAAAAAT
* * *
5344854 TATTAATTATTAAAATAATAAAAAACTATTTACTATATTAA
1 TATTAATTATTAAAAGAATAAAAAAATATTTACTATATAAA
*
5344895 TATTTATTATTAAAAGAATAATACAATAATATTTACTAT-TGAAA
1 TATTAATTATTAAAAGAATAA-A-AA-AATATTTACTATAT-AAA
5344939 TATTAA
1 TATTAA
5344945 AAATATTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
41 19 0.46
42 1 0.02
43 3 0.07
44 18 0.44
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (41 bp):
TATTAATTATTAAAAGAATAAAAAAATATTTACTATATAAA
Found at i:5345412 original size:17 final size:19
Alignment explanation
Indices: 5345368--5345413 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
5345358 TTTTTATTAA
5345368 TTAA-TAAATAATTTTTTG
1 TTAACTAAATAATTTTTTG
*
5345386 TTAAGT-AATAATTTTTT-
1 TTAACTAAATAATTTTTTG
5345403 TT-ACTAAATAA
1 TTAACTAAATAA
5345414 ATATAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 7 0.28
18 15 0.60
19 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (19 bp):
TTAACTAAATAATTTTTTG
Found at i:5355966 original size:26 final size:27
Alignment explanation
Indices: 5355937--5355997 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
5355927 TATATCACCT
5355937 TATTAATAAATA-AAATTTTTAAAATA
1 TATTAATAAATATAAATTTTTAAAATA
** **
5355963 TATTAATTTTATATAGTTTTTTAAAATA
1 TATTAA-TAAATATAAATTTTTAAAATA
5355991 TATTAAT
1 TATTAAT
5355998 CTTTATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 6 0.21
27 5 0.17
28 18 0.62
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
TATTAATAAATATAAATTTTTAAAATA
Found at i:5355990 original size:28 final size:29
Alignment explanation
Indices: 5355951--5356015 Score: 107
Period size: 28 Copynumber: 2.3 Consensus size: 29
5355941 AATAAATAAA
5355951 ATTTTTAAAATATATTAAT-TTTATATAGT
1 ATTTTTAAAATATATTAATCTTTATATA-T
5355980 -TTTTTAAAATATATTAATCTTTATATAT
1 ATTTTTAAAATATATTAATCTTTATATAT
5356008 ATTTTTAA
1 ATTTTTAA
5356016 GGGTTAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 19 0.56
29 15 0.44
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (29 bp):
ATTTTTAAAATATATTAATCTTTATATAT
Found at i:5359063 original size:3 final size:3
Alignment explanation
Indices: 5359051--5359086 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
5359041 TTCATTTAAG
5359051 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5359087 ATTTAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:5359203 original size:30 final size:29
Alignment explanation
Indices: 5359169--5359240 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
5359159 ATTGATATCA
** *
5359169 AAATAAATTTTTAGTGTTTAATTTGTATTC
1 AAATAAATTTTTA-CATTTAATTTATATTC
* *
5359199 AAATAAAATTTTACATTTAATTTATATTT
1 AAATAAATTTTTACATTTAATTTATATTC
*
5359228 AAATAAATCTTTA
1 AAATAAATTTTTA
5359241 ATATAAATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (29 bp):
AAATAAATTTTTACATTTAATTTATATTC
Found at i:5359969 original size:22 final size:21
Alignment explanation
Indices: 5359935--5359978 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
5359925 AAGTCAATAT
5359935 ATTAATAGAATTTAATATAAAA
1 ATTAATAGAATTT-ATATAAAA
*
5359957 ATTAATA-ATATTTATTTAAAA
1 ATTAATAGA-ATTTATATAAAA
5359978 A
1 A
5359979 ACATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTAATAGAATTTATATAAAA
Found at i:5362381 original size:28 final size:29
Alignment explanation
Indices: 5362329--5362387 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
5362319 AAGACTGCTT
* * *
5362329 AAAAAAGGTTTATAAAGGATAAATCCTTC
1 AAAAAACGATTATAAAAGATAAATCCTTC
5362358 AAAAAACGATTATAAAAGAT-AATCCTTC
1 AAAAAACGATTATAAAAGATAAATCCTTC
5362386 AA
1 AA
5362388 TCACATGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.25
Consensus pattern (29 bp):
AAAAAACGATTATAAAAGATAAATCCTTC
Found at i:5362776 original size:87 final size:87
Alignment explanation
Indices: 5362671--5362845 Score: 287
Period size: 87 Copynumber: 2.0 Consensus size: 87
5362661 GCAATCATAA
* * **
5362671 TCATAACACTTAATTACAAGTATAATGACTTGATGTGAAAATATTAAATAATAATGGATTAAGAA
1 TCATAAAACTTAATTACAAGTATAACGACTTGATGCAAAAATATTAAATAATAATGGATTAAGAA
5362736 ATATTTAATATTAAATATGCAT
66 ATATTTAATATTAAATATGCAT
* *
5362758 TCATAAAACTTAATTACAAGTGTAACGACTTGATGCAAAAATATTAAATAATAATGGATTAATAA
1 TCATAAAACTTAATTACAAGTATAACGACTTGATGCAAAAATATTAAATAATAATGGATTAAGAA
*
5362823 ATATTTAATATTAACTATGCAT
66 ATATTTAATATTAAATATGCAT
5362845 T
1 T
5362846 AATTACAGGT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (87 bp):
TCATAAAACTTAATTACAAGTATAACGACTTGATGCAAAAATATTAAATAATAATGGATTAAGAA
ATATTTAATATTAAATATGCAT
Found at i:5367921 original size:70 final size:70
Alignment explanation
Indices: 5367808--5367946 Score: 260
Period size: 70 Copynumber: 2.0 Consensus size: 70
5367798 GTACTCCTTG
*
5367808 ATGAAAAGCTTTTGACGAAGTAAGTTCCATATCCCCTCTCATGAATCCATATATATATATATTTA
1 ATGAAAAGCTTTTGACGAAGTAAGTTCCATATCCCCTCTCATGAATCCATATATATATATATATA
5367873 TATAT
66 TATAT
*
5367878 ATGAAAAGCTTTTGACGAAGTAAGTTCTATATCCCCTCTCATGAATCCATATATATATATATATA
1 ATGAAAAGCTTTTGACGAAGTAAGTTCCATATCCCCTCTCATGAATCCATATATATATATATATA
5367943 TATA
66 TATA
5367947 CTAATATTAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (70 bp):
ATGAAAAGCTTTTGACGAAGTAAGTTCCATATCCCCTCTCATGAATCCATATATATATATATATA
TATAT
Found at i:5373205 original size:19 final size:17
Alignment explanation
Indices: 5373171--5373207 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
5373161 TTTTATGATA
5373171 AATTATATCAAATTTAC
1 AATTATATCAAATTTAC
5373188 AATTATTATCACAATTTAC
1 AATTA-TATCA-AATTTAC
5373207 A
1 A
5373208 TAACAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 8 0.44
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTATATCAAATTTAC
Found at i:5374735 original size:20 final size:21
Alignment explanation
Indices: 5374710--5374881 Score: 81
Period size: 20 Copynumber: 8.1 Consensus size: 21
5374700 AGCTCATTTA
5374710 TATTTATAT-TTA-TATTTATT
1 TATTTATATATTATTA-TTATT
5374730 TATTTAT-TATTATTATTATT
1 TATTTATATATTATTATTATT
* * * *
5374750 TATTAATATATAAATATTTTT
1 TATTTATATATTATTATTATT
* * *
5374771 TAGTTATTTATCTATTAACATATT
1 TATTTATATAT-TATT-A-TTATT
* * *
5374795 T-TATTATTTATCTATTAATATA
1 TAT-TTATATAT-TATTATTATT
*
5374817 TATTT-T-TATTATTATTTATC
1 TATTTATATATTATTA-TTATT
* *
5374837 TATTCATATATTATTATTTATC
1 TATTTATATATTATTA-TTATT
*
5374859 TATTAATATA-TATTACTT-TT
1 TATTTATATATTATTA-TTATT
5374879 TAT
1 TAT
5374882 CTTTTTCTTG
Statistics
Matches: 122, Mismatches: 19, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
19 6 0.05
20 35 0.29
21 29 0.24
22 32 0.26
23 3 0.02
24 17 0.14
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (21 bp):
TATTTATATATTATTATTATT
Found at i:5374743 original size:24 final size:24
Alignment explanation
Indices: 5374710--5374867 Score: 81
Period size: 24 Copynumber: 6.4 Consensus size: 24
5374700 AGCTCATTTA
*
5374710 TATTTATATTTATATTTATTTATT
1 TATTAATATTTATATTTATTTATT
* * *
5374734 TATTATTA-TTATTATTTATTAATA
1 TATTAATATTTA-TATTTATTTATT
* * * *
5374758 TATAAATATTTTTTAGTTATTTATC
1 TATTAATA-TTTATATTTATTTATT
*
5374783 TATTAACATATTT-TA-TTATTTATC
1 TATT-A-ATATTTATATTTATTTATT
* *
5374807 TATTAATATATATTTTTATTATTATT
1 TATTAATATTTATATTTA-T-TTATT
* * *
5374833 TATCTATTCATATAT-TATTATTTATC
1 TAT-TAAT-ATTTATAT-TTATTTATT
5374859 TATTAATAT
1 TATTAATAT
5374868 ATATTACTTT
Statistics
Matches: 105, Mismatches: 17, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
22 5 0.05
23 5 0.05
24 40 0.38
25 18 0.17
26 20 0.19
27 8 0.08
28 9 0.09
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.62
Consensus pattern (24 bp):
TATTAATATTTATATTTATTTATT
Found at i:5374848 original size:22 final size:22
Alignment explanation
Indices: 5374823--5374873 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
5374813 TATATATTTT
*
5374823 TATTATTATTTATCTATTCATA
1 TATTATTATTTATCTATTAATA
5374845 TATTATTATTTATCTATTAATA
1 TATTATTATTTATCTATTAATA
5374867 TA-TATTA
1 TATTATTA
5374874 CTTTTTATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTATTATTTATCTATTAATA
Found at i:5374880 original size:24 final size:24
Alignment explanation
Indices: 5374780--5374883 Score: 111
Period size: 24 Copynumber: 4.2 Consensus size: 24
5374770 TTAGTTATTT
* *
5374780 ATCTATTAACATATTTTATTATTT
1 ATCTATTAATATATATTATTATTT
*
5374804 ATCTATTAATATATATTTTTATTATT
1 ATCTATTAATATATATTATTA-T-TT
* *
5374830 ATTTATCTATTCATATATTATTATTT
1 ATCTAT-TAAT-ATATATTATTATTT
5374856 ATCTATTAATATATATTACTT-TTT
1 ATCTATTAATATATATTA-TTATTT
5374880 ATCT
1 ATCT
5374884 TTTTCTTGAT
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
24 33 0.49
25 6 0.09
26 14 0.21
27 4 0.06
28 10 0.15
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.60
Consensus pattern (24 bp):
ATCTATTAATATATATTATTATTT
Found at i:5375760 original size:6 final size:6
Alignment explanation
Indices: 5375749--5375873 Score: 67
Period size: 6 Copynumber: 22.3 Consensus size: 6
5375739 ATTTATTTAT
* * *
5375749 TTATTA TTATTA TT-TCTT TTATTA TTAGTA TTATTGA -TGTTA TTATTA
1 TTATTA TTATTA TTAT-TA TTATTA TTATTA TTATT-A TTATTA TTATTA
* ** *
5375797 TTATTA TTA-GA TTAAAA TTATTTA GTATT- TT-TTA TT-TTA TT-TTA
1 TTATTA TTATTA TTATTA TTA-TTA TTATTA TTATTA TTATTA TTATTA
*
5375841 TTTTTA TT-TTA TT-TTA TT-TTA TT-TTA TT-TTA TT
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TT
5375874 TTTTGATTTT
Statistics
Matches: 99, Mismatches: 12, Indels: 17
0.77 0.09 0.13
Matches are distributed among these distances:
4 2 0.02
5 44 0.44
6 48 0.48
7 5 0.05
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.69
Consensus pattern (6 bp):
TTATTA
Found at i:5375762 original size:21 final size:21
Alignment explanation
Indices: 5375737--5375804 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
5375727 CCAAAGGGTT
5375737 TTATTTATTTATTTATTATTA
1 TTATTTATTTATTTATTATTA
* *
5375758 TTATTTCTTT-TATTATTAGTA
1 TTATTTATTTAT-TTATTATTA
*
5375779 TTATTGATGTTA-TTATTATTA
1 TTATTTAT-TTATTTATTATTA
5375800 TTATT
1 TTATT
5375805 AGATTAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 36 0.92
22 2 0.05
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.68
Consensus pattern (21 bp):
TTATTTATTTATTTATTATTA
Found at i:5375836 original size:5 final size:5
Alignment explanation
Indices: 5375826--5375875 Score: 91
Period size: 5 Copynumber: 9.8 Consensus size: 5
5375816 ATTTAGTATT
5375826 TTTTA TTTTA TTTTA TTTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5375876 TTGATTTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 39 0.89
6 5 0.11
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:5375846 original size:16 final size:16
Alignment explanation
Indices: 5375825--5375876 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
5375815 TATTTAGTAT
5375825 TTTTTATTTTATTTTA
1 TTTTTATTTTATTTTA
5375841 TTTTTATTTTATTTTA
1 TTTTTATTTTATTTTA
5375857 -TTTTATTTTATTTTA
1 TTTTTATTTTATTTTA
5375872 TTTTT
1 TTTTT
5375877 TGATTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.43
16 20 0.57
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTATTTTATTTTA
Found at i:5375885 original size:10 final size:9
Alignment explanation
Indices: 5375824--5375886 Score: 65
Period size: 10 Copynumber: 6.6 Consensus size: 9
5375814 TTATTTAGTA
5375824 TTTTTTATT
1 TTTTTTATT
5375833 TTATTTTATTT
1 TT-TTTTA-TT
5375844 TTATTTTATT
1 TT-TTTTATT
5375854 TTATTTTATT
1 TT-TTTTATT
5375864 TTATTTTA-T
1 TT-TTTTATT
*
5375873 TTTTTGATT
1 TTTTTTATT
5375882 TTTTT
1 TTTTT
5375887 AAATAAAATT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
8 4 0.08
9 11 0.22
10 25 0.50
11 10 0.20
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTATT
Found at i:5375886 original size:16 final size:15
Alignment explanation
Indices: 5375822--5375887 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 15
5375812 AATTATTTAG
5375822 TATTTTTTATTTTATT
1 TATTTTTTATTTT-TT
5375838 T-TATTTTTATTTTATTT
1 TAT-TTTTTA-TTT-TTT
*
5375855 TATTTTATT-TTATTT
1 TATTTT-TTATTTTTT
5375870 TATTTTTTGATTTTTT
1 TATTTTTT-ATTTTTT
5375886 TA
1 TA
5375888 AATAAAATTC
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
14 2 0.05
15 10 0.24
16 16 0.39
17 9 0.22
18 4 0.10
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (15 bp):
TATTTTTTATTTTTT
Found at i:5375964 original size:57 final size:57
Alignment explanation
Indices: 5375909--5376021 Score: 190
Period size: 58 Copynumber: 2.0 Consensus size: 57
5375899 AAAAAAAAAT
* *
5375909 ATTTTCGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAATTTTTTAAAAAGC
1 ATTTTCGAGGAAAAGTTAAAAATATCAATTTTCTTTGAAAAT-AATTTTTTAAAAAGC
*
5375967 ATTTTCGAGGAAAAGTTAAAAATATCGATTTTCTTTGAAAATAATTTTTTAAAAA
1 ATTTTCGAGGAAAAGTTAAAAATATCAATTTTCTTTGAAAATAATTTTTTAAAAA
5376022 AAGGTTTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 13 0.25
58 39 0.75
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (57 bp):
ATTTTCGAGGAAAAGTTAAAAATATCAATTTTCTTTGAAAATAATTTTTTAAAAAGC
Found at i:5377717 original size:9 final size:9
Alignment explanation
Indices: 5377703--5377807 Score: 88
Period size: 9 Copynumber: 11.0 Consensus size: 9
5377693 TACTATGCTT
5377703 GAAAAAAAA
1 GAAAAAAAA
*
5377712 G-AAAAAAT
1 GAAAAAAAA
5377720 GAAATGAAAAA
1 GAAA--AAAAA
*
5377731 TGAAAAAAAT
1 -GAAAAAAAA
5377741 GAAAAAAAA
1 GAAAAAAAA
*
5377750 TGAAAAAAAT
1 -GAAAAAAAA
*
5377760 GAAAAAAAT
1 GAAAAAAAA
5377769 GAAAAAAAA
1 GAAAAAAAA
5377778 -ATGAAAAAAA
1 GA--AAAAAAA
5377788 GAAAAAAAAA
1 G-AAAAAAAA
5377798 GAAAAGAAAA
1 GAAAA-AAAA
5377808 AGTGAATGAA
Statistics
Matches: 80, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
8 8 0.10
9 32 0.40
10 31 0.39
11 4 0.05
12 5 0.06
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:5377736 original size:19 final size:18
Alignment explanation
Indices: 5377714--5377820 Score: 57
Period size: 19 Copynumber: 5.9 Consensus size: 18
5377704 AAAAAAAAGA
5377714 AAAAATGAAATGAAAAATG
1 AAAAA-GAAATGAAAAATG
5377733 -AAAA-AAATGAAAAAAAATG
1 AAAAAGAAATG---AAAAATG
5377752 -AAAA-AAATGAAAAAAATG
1 AAAAAGAAATG--AAAAATG
* *
5377770 AAAAAAAAATGAAAAAAAG
1 AAAAAGAAATG-AAAAATG
*
5377789 AAAAA-AAAAG-AAAA-G
1 AAAAAGAAATGAAAAATG
*
5377804 AAAAAGTGAATGAAAAA
1 AAAAAG-AAATGAAAAA
5377821 GGAGGACCTA
Statistics
Matches: 76, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
15 6 0.08
16 9 0.12
17 3 0.04
18 21 0.28
19 32 0.42
20 5 0.07
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (18 bp):
AAAAAGAAATGAAAAATG
Found at i:5377745 original size:28 final size:27
Alignment explanation
Indices: 5377702--5377795 Score: 118
Period size: 28 Copynumber: 3.3 Consensus size: 27
5377692 GTACTATGCT
*
5377702 TGAAAAAAAAGAAAAAATGAAATG-AAAAA
1 TGAAAAAAATG-AAAAA--AAATGAAAAAA
5377731 TGAAAAAAATGAAAAAAAATGAAAAAAA
1 TGAAAAAAATGAAAAAAAATG-AAAAAA
5377759 TGAAAAAAATGAAAAAAAAATGAAAAAA
1 TGAAAAAAATG-AAAAAAAATGAAAAAA
*
5377787 AGAAAAAAA
1 TGAAAAAAA
5377796 AAGAAAAGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
26 5 0.08
28 35 0.58
29 20 0.33
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (27 bp):
TGAAAAAAATGAAAAAAAATGAAAAAA
Found at i:5377802 original size:28 final size:28
Alignment explanation
Indices: 5377703--5377813 Score: 127
Period size: 29 Copynumber: 3.8 Consensus size: 28
5377693 TACTATGCTT
*
5377703 GAAAAAAAAGAAAAAATGAAATG-AAAAAT
1 GAAAAAAAAGAAAAAA--AAATGAAAAAAA
*
5377732 GAAAAAAATG-AAAAAAAATGAAAAAAA
1 GAAAAAAAAGAAAAAAAAATGAAAAAAA
*
5377759 TGAAAAAAATGAAAAAAAAATGAAAAAAA
1 -GAAAAAAAAGAAAAAAAAATGAAAAAAA
5377788 GAAAAAAAAAGAAAAGAAAAAGTGAA
1 G-AAAAAAAAGAAAA-AAAAA-TGAA
5377814 TGAAAAAGGA
Statistics
Matches: 73, Mismatches: 3, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
26 5 0.07
27 5 0.07
28 16 0.22
29 38 0.52
30 5 0.07
31 4 0.05
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (28 bp):
GAAAAAAAAGAAAAAAAAATGAAAAAAA
Found at i:5377821 original size:23 final size:24
Alignment explanation
Indices: 5377736--5377821 Score: 66
Period size: 23 Copynumber: 4.0 Consensus size: 24
5377726 AAAAATGAAA
5377736 AAAATG-AAAAAA-AATG--AAA-
1 AAAATGAAAAAAAGAATGAAAAAG
5377755 AAAATG--AAAAA-AATGAAAAA-
1 AAAATGAAAAAAAGAATGAAAAAG
**
5377775 AAAATGAAAAAAAGAAAAAAAAAG
1 AAAATGAAAAAAAGAATGAAAAAG
**
5377799 AAAA-GAAAAAGTGAATGAAAAAG
1 AAAATGAAAAAAAGAATGAAAAAG
5377822 GAGGACCTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
18 9 0.16
19 6 0.11
20 9 0.16
22 5 0.09
23 22 0.40
24 4 0.07
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (24 bp):
AAAATGAAAAAAAGAATGAAAAAG
Found at i:5378932 original size:43 final size:43
Alignment explanation
Indices: 5378842--5378939 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
5378832 AGTTATGGTG
* * * *
5378842 CCTCTGTTTAGATGAGTAATTTATTTTTCAAAAGTCGTGGGTG
1 CCTCTGTTTAGAGGAGTAATTTATTTTCCAAAAGTCGTGGATA
*
5378885 CCTCTGTTTAGAGGAGTAATTTATTGTTCCCAAAA-TTGT-GATA
1 CCTCTGTTTAGAGGAGTAATTTATT-TT-CCAAAAGTCGTGGATA
*
5378928 CCTCTGATTAGA
1 CCTCTGTTTAGA
5378940 TGAGCTTTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 37 0.79
44 5 0.11
45 5 0.11
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (43 bp):
CCTCTGTTTAGAGGAGTAATTTATTTTCCAAAAGTCGTGGATA
Found at i:5379004 original size:41 final size:41
Alignment explanation
Indices: 5378951--5379285 Score: 345
Period size: 41 Copynumber: 8.0 Consensus size: 41
5378941 GAGCTTTGTT
* *
5378951 TTTATTTCTCAAAGTCGTTGAGCCTCTTATTAGAGGAGCCA
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
*
5378992 TTTATTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCCA
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
* * **
5379033 TTTATTTTTCAAAGTTG-TAATGCCTCTGATTAGAGGAGCTTTG
1 TTTATTTTTCAAAGTCGTTGA-GCCTCTGATTAGAGGAGC--CA
* *
5379076 TTTTTGTTTCTCAAAGTCGTTGAGCCTCTGATTAGAAGAGCCA
1 TTTAT-TTT-TCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
* * * **
5379119 TTTATTTTTCAAAGTTG-TGATGCCTTTGATTAGAAGAGCTTTG
1 TTTATTTTTCAAAGTCGTTGA-GCCTCTGATTAGAGGAGC--CA
* *
5379162 TTTATGTTTCTCAAAAGTCGTTGAGCCTTTGATTAGATGAGCCA
1 TTTAT-TTT-TC-AAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
*
5379206 TTTA-CTTTCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
1 TTTATTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
* * *
5379247 TTTATTTTTCAAAATTG-TGATGCCTATGATTAGAGGAGC
1 TTTATTTTTCAAAGTCGTTGA-GCCTCTGATTAGAGGAGC
5379286 TTTGTTTATA
Statistics
Matches: 249, Mismatches: 30, Indels: 30
0.81 0.10 0.10
Matches are distributed among these distances:
40 8 0.03
41 154 0.62
42 9 0.04
43 13 0.05
44 10 0.04
45 27 0.11
46 25 0.10
47 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (41 bp):
TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
Found at i:5379088 original size:127 final size:128
Alignment explanation
Indices: 5378841--5379285 Score: 476
Period size: 127 Copynumber: 3.5 Consensus size: 128
5378831 AAGTTATGGT
* * ** * * * *
5378841 GCCTCTGTTTAGATGAGTAATTTATTTTTCAAAAGTCGTGGGTGCCTCTGTTTAGAGGAGTAATT
1 GCCTCTGATTAGAGGAGCCATTTATTTTTC-AAAGTTGT-GATGCCTCTGATTAGAGGAGCAATT
* * *
5378906 TATTGTTCCCAAAATTGTGATACCTCTGATTAGATGAGCTTTGTTTTTATTTCTCAAAGTCGTTG
64 TATT-TTCTCAAAGTTGTGATGCCTCTGATTAGATGAGCTTTGTTTTTATTTCTCAAAGTCGTTG
5378971 A
128 A
* *
5378972 GCCTCTTATTAGAGGAGCCATTTATTTTTCAAAGTCAT-TGA-GCCTCTGATTAGAGGAGCCATT
1 GCCTCTGATTAGAGGAGCCATTTATTTTTCAAAGT--TGTGATGCCTCTGATTAGAGGAGCAATT
* * *
5379035 TATTTT-TCAAAGTTGTAATGCCTCTGATTAGAGGAGCTTTGTTTTTGTTTCTCAAAGTCGTTGA
64 TATTTTCTCAAAGTTGTGATGCCTCTGATTAGATGAGCTTTGTTTTTATTTCTCAAAGTCGTTGA
* * * **
5379099 GCCTCTGATTAGAAGAGCCATTTATTTTTCAAAGTTGTGATGCCTTTGATTAGAAGAGCTTTGTT
1 GCCTCTGATTAGAGGAGCCATTTATTTTTCAAAGTTGTGATGCCTCTGATTAGAGGAGC--AATT
* * ** *
5379164 TATGTTTCTCAAAAGTCGTTGA-GCCTTTGATTAGATGAGC----CATTTACTTTC-AAAAGTCG
64 TAT-TTTCTC-AAAGTTG-TGATGCCTCTGATTAGATGAGCTTTGTTTTTA-TTTCTCAAAGTCG
5379223 TTGA
125 TTGA
* *
5379227 GCCTCTGATTAGAGGAGCCATTTATTTTTCAAAATTGTGATGCCTATGATTAGAGGAGC
1 GCCTCTGATTAGAGGAGCCATTTATTTTTCAAAGTTGTGATGCCTCTGATTAGAGGAGC
5379286 TTTGTTTATA
Statistics
Matches: 269, Mismatches: 34, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
125 1 0.00
126 3 0.01
127 101 0.38
128 71 0.26
129 32 0.12
130 9 0.03
131 28 0.10
132 22 0.08
133 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (128 bp):
GCCTCTGATTAGAGGAGCCATTTATTTTTCAAAGTTGTGATGCCTCTGATTAGAGGAGCAATTTA
TTTTCTCAAAGTTGTGATGCCTCTGATTAGATGAGCTTTGTTTTTATTTCTCAAAGTCGTTGA
Found at i:5379105 original size:86 final size:86
Alignment explanation
Indices: 5378951--5379244 Score: 368
Period size: 86 Copynumber: 3.5 Consensus size: 86
5378941 GAGCTTTGTT
* * * ** *
5378951 TTTATTTCTCAAAGTCGTTGA-GCCTCTTATTAGAGGAGC--CATTTAT-TTT-TCAAAGTCATT
1 TTTATTTTTCAAAGTTG-TGATGCCTCTGATTAGAGGAGCTTTGTTTATGTTTCTCAAAGTCGTT
*
5379011 GAGCCTCTGATTAGAGGAGCCA
65 GAGCCTCTGATTAGAAGAGCCA
* *
5379033 TTTATTTTTCAAAGTTGTAATGCCTCTGATTAGAGGAGCTTTGTTTTTGTTTCTCAAAGTCGTTG
1 TTTATTTTTCAAAGTTGTGATGCCTCTGATTAGAGGAGCTTTGTTTATGTTTCTCAAAGTCGTTG
5379098 AGCCTCTGATTAGAAGAGCCA
66 AGCCTCTGATTAGAAGAGCCA
* *
5379119 TTTATTTTTCAAAGTTGTGATGCCTTTGATTAGAAGAGCTTTGTTTATGTTTCTCAAAAGTCGTT
1 TTTATTTTTCAAAGTTGTGATGCCTCTGATTAGAGGAGCTTTGTTTATGTTTCTC-AAAGTCGTT
* *
5379184 GAGCCTTTGATTAGATGAGCCA
65 GAGCCTCTGATTAGAAGAGCCA
* *
5379206 TTTA-CTTTCAAAAGTCGTTGA-GCCTCTGATTAGAGGAGC
1 TTTATTTTTC-AAAGTTG-TGATGCCTCTGATTAGAGGAGC
5379245 CATTTATTTT
Statistics
Matches: 185, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
81 2 0.01
82 32 0.17
84 4 0.02
85 3 0.02
86 86 0.46
87 55 0.30
88 3 0.02
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (86 bp):
TTTATTTTTCAAAGTTGTGATGCCTCTGATTAGAGGAGCTTTGTTTATGTTTCTCAAAGTCGTTG
AGCCTCTGATTAGAAGAGCCA
Found at i:5379257 original size:214 final size:213
Alignment explanation
Indices: 5378915--5379310 Score: 616
Period size: 214 Copynumber: 1.9 Consensus size: 213
5378905 TTATTGTTCC
* *
5378915 CAAAATTGTGATACCTCTGATTAGATGAGCTTTGTTTTTATTTCTCAAAGTCGTTGAGCCTCTTA
1 CAAAATTGTGATACCTCTGATTAGAAGAGCTTTGTTTATATTTCTCAAAGTCGTTGAGCCTCTTA
*
5378980 TTAGAGGAGCCATTTATTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCAA
66 TTAGAGGAGCCATTTATCTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCAA
* * * * *
5379045 AGTTGTAATGCCTCTGATTAGAGGAGCTTTGTTTTTGTTTCTCAAAGTCGTTGAGCCTCTGATTA
131 AATTGTAATGCCTATGATTAGAGGAGCTTTGTTTATATTTCTCAAAATCGTTGAGCCTCTGATTA
5379110 GAAGAGCCATTTATTTTT
196 GAAGAGCCATTTATTTTT
* * * *
5379128 CAAAGTTGTGATGCCTTTGATTAGAAGAGCTTTGTTTATGTTTCTCAAAAGTCGTTGAGCCT-TT
1 CAAAATTGTGATACCTCTGATTAGAAGAGCTTTGTTTATATTTCTC-AAAGTCGTTGAGCCTCTT
* *
5379192 GATTAGATGAGCCATTTA-CTTTCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTT
65 -ATTAGAGGAGCCATTTATCTTTC-AAAGTCATTGAGCCTCTGATTAGAGGAGCCATTTATTTTT
*
5379256 CAAAATTGTGATGCCTATGATTAGAGGAGCTTTGTTTATATTTCTCAAAATCGTT
128 CAAAATTGTAATGCCTATGATTAGAGGAGCTTTGTTTATATTTCTCAAAATCGTT
5379311 AAACCTCATC
Statistics
Matches: 165, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
213 46 0.28
214 119 0.72
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (213 bp):
CAAAATTGTGATACCTCTGATTAGAAGAGCTTTGTTTATATTTCTCAAAGTCGTTGAGCCTCTTA
TTAGAGGAGCCATTTATCTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCAA
AATTGTAATGCCTATGATTAGAGGAGCTTTGTTTATATTTCTCAAAATCGTTGAGCCTCTGATTA
GAAGAGCCATTTATTTTT
Found at i:5379530 original size:6 final size:6
Alignment explanation
Indices: 5379513--5379574 Score: 52
Period size: 6 Copynumber: 9.5 Consensus size: 6
5379503 GGGTAAGCCC
* * *
5379513 ATTTTGT ATTTTT ATTTTT ATTTGT ATTTGT ATTTTT AATATTT ATTTATTT
1 ATTTT-T ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT -ATTTTT A-TT-TTT
5379565 ATTTATT ATT
1 ATTT-TT ATT
5379575 ACTATTATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
6 25 0.53
7 18 0.38
8 4 0.09
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (6 bp):
ATTTTT
Found at i:5379538 original size:18 final size:18
Alignment explanation
Indices: 5379515--5379550 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5379505 GTAAGCCCAT
*
5379515 TTTGTATTTTTATTTTTA
1 TTTGTATTTGTATTTTTA
5379533 TTTGTATTTGTATTTTTA
1 TTTGTATTTGTATTTTTA
5379551 ATATTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (18 bp):
TTTGTATTTGTATTTTTA
Found at i:5379569 original size:19 final size:19
Alignment explanation
Indices: 5379547--5379623 Score: 50
Period size: 19 Copynumber: 3.9 Consensus size: 19
5379537 TATTTGTATT
5379547 TTTAATATTTATTTATTTA
1 TTTAATATTTATTTATTTA
*
5379566 TTTATTATTACTATTATTATTTA
1 TTTAATATT--TA-T-TTATTTA
* **
5379589 -TTAATATATAAATATTT-
1 TTTAATATTTATTTATTTA
*
5379606 TTTAATTATTTATCTATT
1 TTTAA-TATTTATTTATT
5379624 ATCATATTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
18 9 0.20
19 17 0.39
20 2 0.05
21 2 0.05
22 7 0.16
23 7 0.16
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTAATATTTATTTATTTA
Found at i:5379616 original size:52 final size:52
Alignment explanation
Indices: 5379554--5379722 Score: 143
Period size: 52 Copynumber: 3.2 Consensus size: 52
5379544 ATTTTTAATA
* *
5379554 TTTATTTATTTATTTATTAT-TACTATTATTATTTATTAATATATAAATATTT
1 TTTAATTATTTATTTATTATATA-TATTATTATTTATTAATATATAAATATAT
* * * *
5379606 TTTAATTATTTATCTATTATCATATTTTATTATTTATCTATTAATATATATATAT
1 TTTAATTATTTATTTATTAT-ATATATTATTATTTAT-TAAT-ATATAAATATAT
* * * *
5379661 ATT-ATTATTT-TTCTATT-CATATATTATTATTTATCTATTA-ATATATATAT
1 TTTAATTATTTATT-TATTATATATATTATTATTTAT-TAATATATAAATATAT
*
5379711 TTT-ATTTTTTAT
1 TTTAATTATTTAT
5379723 CTTTTTCTTA
Statistics
Matches: 99, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
50 18 0.18
51 2 0.02
52 38 0.38
53 13 0.13
54 16 0.16
55 12 0.12
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (52 bp):
TTTAATTATTTATTTATTATATATATTATTATTTATTAATATATAAATATAT
Found at i:5379623 original size:8 final size:8
Alignment explanation
Indices: 5379612--5379699 Score: 53
Period size: 8 Copynumber: 11.5 Consensus size: 8
5379602 ATTTTTTAAT
5379612 TATTTATC
1 TATTTATC
5379620 TA-TTATC
1 TATTTATC
5379627 ATATTTTAT-
1 -TA-TTTATC
5379636 TATTTATC
1 TATTTATC
* *
5379644 TATTAATA
1 TATTTATC
* *
5379652 TATATATA
1 TATTTATC
5379660 TA-TTAT-
1 TATTTATC
*
5379666 TATTTTTC
1 TATTTATC
* *
5379674 TATTCATA
1 TATTTATC
5379682 TA-TTAT-
1 TATTTATC
5379688 TATTTATC
1 TATTTATC
5379696 TATT
1 TATT
5379700 AATATATATA
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
6 4 0.06
7 23 0.37
8 31 0.50
10 4 0.06
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTTATC
Found at i:5379640 original size:24 final size:24
Alignment explanation
Indices: 5379605--5379700 Score: 88
Period size: 24 Copynumber: 3.8 Consensus size: 24
5379595 TATAAATATT
5379605 TTTTAATTATTTATCTATTATCATA
1 TTTT-ATTATTTATCTATTATCATA
5379630 TTTTATTATTTATCTATTAAT-ATA
1 TTTTATTATTTATCTATT-ATCATA
* *
5379654 TATATATATTA-TTATTTTTCTATTCATA
1 T-T-T-TATTATTTATCTAT-TA-TCATA
*
5379682 TATTATTATTTATCTATTA
1 TTTTATTATTTATCTATTA
5379701 ATATATATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
24 18 0.31
25 14 0.24
26 15 0.26
27 7 0.12
28 4 0.07
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTATTATTTATCTATTATCATA
Found at i:5379668 original size:30 final size:30
Alignment explanation
Indices: 5379627--5379724 Score: 90
Period size: 28 Copynumber: 3.6 Consensus size: 30
5379617 ATCTATTATC
*
5379627 ATATTTTATTATTTATCTATTAATATATAT
1 ATATATTATTATTTATCTATTAATATATAT
* *
5379657 ATATATTATTA--T-T-T-TT-CTAT-T-C
1 ATATATTATTATTTATCTATTAATATATAT
5379679 ATATATTATTATTTATCTATTAATATATAT
1 ATATATTATTATTTATCTATTAATATATAT
*
5379709 AT-T-TTATTTTTTATCT
1 ATATATTATTATTTATCT
5379725 TTTTCTTAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
22 11 0.20
23 1 0.02
24 4 0.07
25 3 0.06
26 2 0.04
27 3 0.06
28 16 0.30
29 2 0.04
30 12 0.22
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (30 bp):
ATATATTATTATTTATCTATTAATATATAT
Found at i:5379669 original size:22 final size:22
Alignment explanation
Indices: 5379639--5379711 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
5379629 ATTTTATTAT
5379639 TTATCTATTAATATATAT-ATATA
1 TTAT-TATTAATATAT-TCATATA
** *
5379662 TTATTATTTTTCTATTCATATA
1 TTATTATTAATATATTCATATA
* * *
5379684 TTATTATTTATCTATTAATATA
1 TTATTATTAATATATTCATATA
5379706 TATATT
1 T-TATT
5379712 TTATTTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
21 1 0.02
22 34 0.79
23 8 0.19
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATTATTAATATATTCATATA
Found at i:5380524 original size:3 final size:3
Alignment explanation
Indices: 5380516--5380589 Score: 89
Period size: 3 Copynumber: 24.7 Consensus size: 3
5380506 CAAAGGTTTT
5380516 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * *
5380562 GTA TTTC TTA TT- TTA TTT TTA TT- TTA TT
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
5380590 TTTTTGATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 4 0.07
3 53 0.87
4 4 0.07
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:5387258 original size:77 final size:77
Alignment explanation
Indices: 5387125--5387269 Score: 245
Period size: 77 Copynumber: 1.9 Consensus size: 77
5387115 TTTTTACAAT
* * * *
5387125 ATTTTAATTTGGCTTTCTTTGTTTGTCCTTGTTAATTTCAAATAAACAAATGGATGTATGCCAAA
1 ATTTTAATTTGGCTTTCTTTGTTTGTCCCTGTTAATTTCAAATAAACAAATAGATGTATACAAAA
5387190 AAATAAAAAAGC
66 AAATAAAAAAGC
*
5387202 ATTTTAATTTGGCTTTCTTTGTTTGTCCCTGTTAATTTCAAATAAACATATAGATGTATACAAAA
1 ATTTTAATTTGGCTTTCTTTGTTTGTCCCTGTTAATTTCAAATAAACAAATAGATGTATACAAAA
5387267 AAA
66 AAA
5387270 AAGCATTCAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 63 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (77 bp):
ATTTTAATTTGGCTTTCTTTGTTTGTCCCTGTTAATTTCAAATAAACAAATAGATGTATACAAAA
AAATAAAAAAGC
Found at i:5393442 original size:13 final size:13
Alignment explanation
Indices: 5393424--5393453 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5393414 GTTGGATACC
5393424 TCTAAAATTTTTT
1 TCTAAAATTTTTT
*
5393437 TCTAAACTTTTTT
1 TCTAAAATTTTTT
5393450 TCTA
1 TCTA
5393454 TTGATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (13 bp):
TCTAAAATTTTTT
Found at i:5400916 original size:52 final size:52
Alignment explanation
Indices: 5400826--5400930 Score: 124
Period size: 52 Copynumber: 2.0 Consensus size: 52
5400816 TATAACCATA
* *
5400826 CAAACTTGCCCATTAAGAATCCCTCTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCCATTAAGAATCCCTCTCCTTTGAGAATTCTTCTCTTGCAAGT
* * * *
5400878 CAAACTTACCTATTAAGAAT-CCTCTTTCTCTTGA-AATTCTTCTTTTGTAAGT
1 CAAACTTACCCATTAAGAATCCCTC-TCCT-TTGAGAATTCTTCTCTTGCAAGT
5400930 C
1 C
5400931 TTCTTGTCCA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 4 0.09
52 38 0.84
53 3 0.07
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.40
Consensus pattern (52 bp):
CAAACTTACCCATTAAGAATCCCTCTCCTTTGAGAATTCTTCTCTTGCAAGT
Found at i:5400971 original size:11 final size:11
Alignment explanation
Indices: 5400955--5400994 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
5400945 ACAATATCTG
5400955 ACAAATCCCAA
1 ACAAATCCCAA
* *
5400966 ACAAATCTCTA
1 ACAAATCCCAA
5400977 ACAAATCCCAA
1 ACAAATCCCAA
5400988 ACAAATC
1 ACAAATC
5400995 TCTTATGGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.15
Consensus pattern (11 bp):
ACAAATCCCAA
Found at i:5400983 original size:22 final size:22
Alignment explanation
Indices: 5400942--5400997 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
5400932 TCTTGTCCAT
* *
5400942 CAAAC-AATATCTGACAAATCC
1 CAAACAAATCTCTAACAAATCC
5400963 CAAACAAATCTCTAACAAATCC
1 CAAACAAATCTCTAACAAATCC
5400985 CAAACAAATCTCT
1 CAAACAAATCTCT
5400998 TATGGGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 5 0.16
22 27 0.84
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.20
Consensus pattern (22 bp):
CAAACAAATCTCTAACAAATCC
Found at i:5402100 original size:12 final size:12
Alignment explanation
Indices: 5402083--5402107 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5402073 TCAACACTTG
5402083 ATCAACATGGCC
1 ATCAACATGGCC
5402095 ATCAACATGGCC
1 ATCAACATGGCC
5402107 A
1 A
5402108 ACCCTTTGAG
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:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (12 bp):
ATCAACATGGCC
Found at i:5406369 original size:58 final size:58
Alignment explanation
Indices: 5406307--5406473 Score: 266
Period size: 58 Copynumber: 2.9 Consensus size: 58
5406297 TTTTGAAAAT
5406307 TTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTAAAAAGC
1 TTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTAAAAAGC
* * * *
5406365 TTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAGC
1 TTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTAAAAAGC
5406423 TTATTTTTAA-AGAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTT
1 TTATTTTTAAGA-AAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTT
5406474 TTGAATTTTA
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
57 5 0.05
58 95 0.95
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (58 bp):
TTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTAAAAAGC
Found at i:5406510 original size:13 final size:13
Alignment explanation
Indices: 5406492--5406537 Score: 53
Period size: 12 Copynumber: 3.6 Consensus size: 13
5406482 TATTTAATGG
5406492 AAATAAAATAATA
1 AAATAAAATAATA
5406505 AAAT-AAA-AATAA
1 AAATAAAATAAT-A
5406517 AAATAAAAATAA-A
1 AAAT-AAAATAATA
5406530 AAATAAAA
1 AAATAAAA
5406538 ATAAAAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
11 3 0.10
12 12 0.41
13 9 0.31
14 3 0.10
15 2 0.07
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:5406532 original size:25 final size:25
Alignment explanation
Indices: 5406492--5406551 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
5406482 TATTTAATGG
5406492 AAATAAAATAATAAAATAAAAATAA
1 AAATAAAATAATAAAATAAAAATAA
5406517 AAATAAAAATAA-AAAATAAAAATAA
1 AAAT-AAAATAATAAAATAAAAATAA
5406542 AAATGAAAAT
1 AAAT-AAAAT
5406552 GAAATTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
25 26 0.79
26 7 0.21
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (25 bp):
AAATAAAATAATAAAATAAAAATAA
Found at i:5406538 original size:13 final size:13
Alignment explanation
Indices: 5406492--5406544 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
5406482 TATTTAATGG
5406492 AAAT-AAAATAATA
1 AAATAAAAATAA-A
5406505 AAATAAAAAT-AA
1 AAATAAAAATAAA
5406517 AAATAAAAATAAA
1 AAATAAAAATAAA
5406530 AAATAAAAATAAA
1 AAATAAAAATAAA
5406543 AA
1 AA
5406545 TGAAAATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.29
13 22 0.58
14 5 0.13
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:5406538 original size:19 final size:19
Alignment explanation
Indices: 5406504--5406550 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
5406494 ATAAAATAAT
5406504 AAAAT-AAAAATAAAAATA
1 AAAATAAAAAATAAAAATA
5406522 AAAATAAAAAATAAAAATA
1 AAAATAAAAAATAAAAATA
5406541 AAAATGAAAA
1 AAAAT-AAAA
5406551 TGAAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 5 0.19
19 18 0.67
20 4 0.15
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (19 bp):
AAAATAAAAAATAAAAATA
Found at i:5406555 original size:6 final size:6
Alignment explanation
Indices: 5406504--5406551 Score: 78
Period size: 6 Copynumber: 7.8 Consensus size: 6
5406494 ATAAAATAAT
*
5406504 AAAATA AAAATA AAAATA AAAATAA AAAATA AAAATA AAAATG AAAAT
1 AAAATA AAAATA AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAAT
5406552 GAAATTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
6 34 0.85
7 6 0.15
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:5408345 original size:5 final size:6
Alignment explanation
Indices: 5408330--5408378 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
5408320 ATAGATATAA
* *
5408330 AAAAAT AAAAAT AAAAAAT ATATATT AAATAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT -AAAAAT A-AAAAT AAA-AAT AAAAAT AAAAAT AAAA
5408379 GCCAATTGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 21 0.58
7 15 0.42
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:5408349 original size:27 final size:27
Alignment explanation
Indices: 5408319--5408373 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
5408309 AAAAAATATT
5408319 AATAGATATAAAAAAATAAAAATAAAA
1 AATAGATATAAAAAAATAAAAATAAAA
* * *
5408346 AATATATATTAAATAATAAAAATAAAA
1 AATAGATATAAAAAAATAAAAATAAAA
5408373 A
1 A
5408374 TAAAAGCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (27 bp):
AATAGATATAAAAAAATAAAAATAAAA
Found at i:5408349 original size:33 final size:33
Alignment explanation
Indices: 5408309--5408378 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 33
5408299 ATAGAAATTA
5408309 AAAAAATAT-TAATAGATATAA-AAAAATAAAAAT
1 AAAAAATATATAATA-A-ATAATAAAAATAAAAAT
*
5408342 AAAAAATATATATTAAATAATAAAAATAAAAAT
1 AAAAAATATATAATAAATAATAAAAATAAAAAT
5408375 AAAA
1 AAAA
5408379 GCCAATTGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
32 4 0.12
33 26 0.76
34 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.24
Consensus pattern (33 bp):
AAAAAATATATAATAAATAATAAAAATAAAAAT
Found at i:5410981 original size:2 final size:2
Alignment explanation
Indices: 5410974--5410998 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5410964 TAATTGGTTT
5410974 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
5410999 TCGGGTTCTT
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:5415617 original size:21 final size:21
Alignment explanation
Indices: 5415579--5415620 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5415569 ATAAAGATTA
* *
5415579 TTTTAATTTTAATTTTTAATT
1 TTTTAATTATAATATTTAATT
*
5415600 TTTTAATTATGATATTTAATT
1 TTTTAATTATAATATTTAATT
5415621 AGCTATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTAATTATAATATTTAATT
Found at i:5416014 original size:29 final size:29
Alignment explanation
Indices: 5415977--5416044 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
5415967 TATGTTAATC
*
5415977 ATATCTATTCATGTATATCCATATTAGTT
1 ATATTTATTCATGTATATCCATATTAGTT
* ** *
5416006 ATGTTTATTCATGTATATCTTTATTATTT
1 ATATTTATTCATGTATATCCATATTAGTT
5416035 ATATTTATTC
1 ATATTTATTC
5416045 GTATCATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.28, C:0.10, G:0.06, T:0.56
Consensus pattern (29 bp):
ATATTTATTCATGTATATCCATATTAGTT
Found at i:5416030 original size:16 final size:16
Alignment explanation
Indices: 5415982--5416030 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
5415972 TAATCATATC
**
5415982 TATTCATGTATATCCA
1 TATTCATGTATATCTT
*
5415998 TATT-A-GT-TATGTT
1 TATTCATGTATATCTT
5416011 TATTCATGTATATCTT
1 TATTCATGTATATCTT
5416027 TATT
1 TATT
5416031 ATTTATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
13 7 0.27
14 3 0.12
15 3 0.12
16 13 0.50
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.55
Consensus pattern (16 bp):
TATTCATGTATATCTT
Found at i:5432042 original size:32 final size:32
Alignment explanation
Indices: 5432005--5432090 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 32
5431995 TATATATTAA
*
5432005 TATAAATGTTTTATTATTTTATTTGTATATTC
1 TATAAATATTTTATTATTTTATTTGTATATTC
* *
5432037 TATAAATATTTTATTCTTTTATTTGTATAATC
1 TATAAATATTTTATTATTTTATTTGTATATTC
** *
5432069 T-T-TTTATTTTAATATTTTATTT
1 TATAAATATTTTATTATTTTATTT
5432091 AAGGTTTCCT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 16 0.34
31 1 0.02
32 30 0.64
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (32 bp):
TATAAATATTTTATTATTTTATTTGTATATTC
Found at i:5437230 original size:12 final size:12
Alignment explanation
Indices: 5437213--5437237 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5437203 CATTATTTAA
5437213 TATAATTTTATT
1 TATAATTTTATT
5437225 TATAATTTTATT
1 TATAATTTTATT
5437237 T
1 T
5437238 TATTTTACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATAATTTTATT
Found at i:5439506 original size:2 final size:2
Alignment explanation
Indices: 5439501--5439529 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5439491 TGTGTGTGTA
5439501 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5439530 CAGAACATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5441695 original size:29 final size:28
Alignment explanation
Indices: 5441662--5441728 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
5441652 AAACAACGAT
*
5441662 TTTTCTCAGATACCGAAC-AAACCCACAAA
1 TTTTCTCAGA-A-AGAACAAAACCCACAAA
* *
5441691 TTTTCTCGAGAAATAACAAAACCCAGAAA
1 TTTTCTC-AGAAAGAACAAAACCCACAAA
5441720 TTTTCTCAG
1 TTTTCTCAG
5441729 CACCCAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 5 0.15
29 25 0.76
30 3 0.09
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.25
Consensus pattern (28 bp):
TTTTCTCAGAAAGAACAAAACCCACAAA
Found at i:5441819 original size:23 final size:23
Alignment explanation
Indices: 5441776--5441819 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5441766 ATTTTTCCAT
**
5441776 TAAAAAAAACCAGTAAATTTCTC
1 TAAAAAAAACCAACAAATTTCTC
*
5441799 TAAAAAAAACCAACAATTTTC
1 TAAAAAAAACCAACAAATTTC
5441820 ACAGCACAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (23 bp):
TAAAAAAAACCAACAAATTTCTC
Found at i:5442752 original size:13 final size:14
Alignment explanation
Indices: 5442734--5442768 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
5442724 TAGTTTAGAT
5442734 TTTTTTAATT-TTA
1 TTTTTTAATTATTA
5442747 TTTTTTAATTATTA
1 TTTTTTAATTATTA
*
5442761 ATTTTTAA
1 TTTTTTAA
5442769 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTAATTATTA
Found at i:5446632 original size:21 final size:22
Alignment explanation
Indices: 5446594--5446634 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5446584 TAAAAATAGA
*
5446594 TATTTGATAATTAATCAATTTT
1 TATTTGATAATAAATCAATTTT
5446616 TATTTGATAA-AAATCAATT
1 TATTTGATAATAAATCAATT
5446635 GATGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (22 bp):
TATTTGATAATAAATCAATTTT
Found at i:5453032 original size:2 final size:2
Alignment explanation
Indices: 5453025--5453055 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5453015 CATCTGTCTG
5453025 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5453056 TTGGCCTTAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5454362 original size:13 final size:13
Alignment explanation
Indices: 5454344--5454368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5454334 GTTGTTACAG
5454344 ACTTTTATTAATA
1 ACTTTTATTAATA
5454357 ACTTTTATTAAT
1 ACTTTTATTAAT
5454369 TTATCTCCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ACTTTTATTAATA
Found at i:5456309 original size:1 final size:1
Alignment explanation
Indices: 5456303--5456327 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
5456293 TTAAACAATC
5456303 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
5456328 GAGGATAAGA
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:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5457865 original size:23 final size:23
Alignment explanation
Indices: 5457839--5457890 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
5457829 TATTTATTTA
**
5457839 TTTTTAAAAT-ATTTAAAATATAT
1 TTTTTAAAATCATAAAAAAT-TAT
*
5457862 TTTTTTAAATCATAAAAAATTAT
1 TTTTTAAAATCATAAAAAATTAT
5457885 TTTTTA
1 TTTTTA
5457891 TGTATAGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTTAAAATCATAAAAAATTAT
Found at i:5460325 original size:2 final size:2
Alignment explanation
Indices: 5460320--5460352 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5460310 AAAAACATCA
*
5460320 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5460353 CATGTATCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 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):
AT
Found at i:5465446 original size:8 final size:8
Alignment explanation
Indices: 5465426--5465474 Score: 64
Period size: 8 Copynumber: 6.2 Consensus size: 8
5465416 TATTTTTTTA
5465426 AAATATA-
1 AAATATAT
*
5465433 AAATATTT
1 AAATATAT
5465441 AAATATAT
1 AAATATAT
*
5465449 AATTATAT
1 AAATATAT
5465457 AAATATAT
1 AAATATAT
*
5465465 AAATAAAT
1 AAATATAT
5465473 AA
1 AA
5465475 TTAATTAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
7 6 0.17
8 30 0.83
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
AAATATAT
Found at i:5465467 original size:24 final size:24
Alignment explanation
Indices: 5465428--5465498 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
5465418 TTTTTTTAAA
* *
5465428 ATATAAAATATTTAAATATATAATT
1 ATAT-AAATATATAAATAAATAATT
5465453 ATATAAATATATAAATAAATAATT
1 ATATAAATATATAAATAAATAATT
*
5465477 A-ATTAAATA-ATTAA-AAATAATT
1 ATA-TAAATATATAAATAAATAATT
5465499 TTTATATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.19
23 5 0.12
24 25 0.60
25 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATAAATATATAAATAAATAATT
Found at i:5485169 original size:3 final size:3
Alignment explanation
Indices: 5485161--5485185 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5485151 GCTATAGTTA
5485161 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
5485186 TAATAATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5486538 original size:2 final size:2
Alignment explanation
Indices: 5486531--5486563 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5486521 ATAGATTTAA
5486531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5486564 CACTTTCTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5487705 original size:13 final size:13
Alignment explanation
Indices: 5487687--5487711 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5487677 TTTCATGTGT
5487687 AAATATATAAAAC
1 AAATATATAAAAC
5487700 AAATATATAAAA
1 AAATATATAAAA
5487712 TTAATTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATATATAAAAC
Found at i:5488028 original size:799 final size:792
Alignment explanation
Indices: 5487014--5489011 Score: 2712
Period size: 799 Copynumber: 2.5 Consensus size: 792
5487004 ATCATATCTA
** * * *
5487014 ATATAAATATATAAAAG-TTAAAGTTTTTGACAAAAAAGAAAAAAAAATC-TATGTGGATAGCTT
1 ATATAAATATATAAAAGCCAAAACTTTTAG-CAAAAATG--AAAAAAATCTTATGTGGAT-GCTT
** * * *
5487077 AAAATATTGACATGTAAATA-ATTTTAAAAATCATCATGTGACATCTAATAAATGTATTTTATTT
62 AAAATATTGACATGTGGATAGA-CTTAAAAATCA-CACGTGACATCTAATAAATATATTTTATTT
* *
5487141 TATTTTATATATTTTTAATTTAAAAATAATTCAAAAAATTAAATTGATTATATTTAAGTTTTATT
125 TATTTTATATATTTTTAATTTAAAAATAATT-AAAAAAATAAATTGATTATATTTAATTTTTATT
* *
5487206 ATTAACCATAAATCAATCTCAATTCAATTCATATTAAAAGTACTAAAATTTT-AAAATTTTTTAA
189 ATTAACCTTAAATCACTCTCAATTCAATTCATATTAAAAGTACTAAAATTTTAAAAATTTTTT-A
5487270 ATTTGACAAATTAAATCAATCAATATATAATTAATAAATTAATAAATACTATAATTACAATTATA
253 ATTTGACAAATTAAATCAATCAATATATAATTAATAAATTAATAAATACTATAATTACAATTATA
*
5487335 AAATAATTGATTCTCTAATCAATTATTTGATATATTTATATTTGATTAAATATAGTATCCAGTAA
318 AAATAGTTGATTCTCTAATCAATTATTTGATATATTTATATTTGATTAAATATAGTATCCAGTAA
* * * *
5487400 TTAATGTATTTCATATGTAAATATATAAAGTAAATATAATTTTAAAAAA-TAAATTGATTATATT
383 TTAATGCATTTCATATGTAAATATAGAAAGTAAATATAA-TTTAAAAAACCAAATTCATTATATT
* * * *
5487464 TA-TATTATTTATTTTAAATCACTCTCAATTCAATTTATATTAAAAGTATTAAAATTTTAAAAAT
447 TATTATTATTAATTTTAAATCACTCTCAACTCAATTCATATTAAAAATATTAAAATTTT--AAAT
* * * * *
5487528 TT-CTT-AATTTAACAGATTTAATCAATCAATATATAATTAGTAAATTAATAAACACTACTATTA
510 TTGCTTAAATTGAAAAAATTAAATCAATCAATATATAA-T--T-AA-TAATAAACACTACAATTA
* *
5487591 CAATAATAAAATAGTTGATTCTCTAATTAATTATTTGATACATTTATATTTGATTAAATGTAGTA
570 CAATAATAAAATAGTTGATTCTCTAATTAATTATTTGAAACATTTATATTTGATTAAATATAGTA
5487656 TCCATTTAAGTAATTGATGTATTTC-ATGTGTAAATATATAAAACAAATATATAAAATTAATTCT
635 TCCATTTAAGTAATTGATGTATTTCTATGTGTAAATATATAAAACAAATATATAAAATTAATTCT
* * *
5487720 CCATAATTAAATTTATGAAATAAAATATTTTATTAATTTATATTTGATTGATACATTTTATATTT
700 CCATAAGTAAATTAATGAAATAAAATATTTTATTAATTTATATTTGATTGATAC-CTTTATATTT
* * *
5487785 TATTAAATATTATTTCATTTTATTTTATT
764 CATTAAATATGATTTCATTTGATTTTATT
*
5487814 TTATAAATATATAAAAGCCAAAACTTTTAGCAAAAATGAAAAAAATCTTATGTGGATGCCTTAAA
1 ATATAAATATATAAAAGCCAAAACTTTTAGCAAAAATGAAAAAAATCTTATGTGGATG-CTTAAA
*
5487879 ATATTGATATGTGGATAGACTTAAAAATCACCACGTGACATCTAATAAATATATTTTATTTTATT
65 ATATTGACATGTGGATAGACTTAAAAATCA-CACGTGACATCTAATAAATATATTTTATTTTATT
5487944 TTATATATTTTTAATTTAAAAATAATTAAAAAAATAAATTGATTATATTTATATTTTTATTATTA
129 TTATATATTTTTAATTTAAAAATAATTAAAAAAATAAATTGATTATATTTA-ATTTTTATTATTA
* **
5488009 ACCTTAAATCACTCTCAATTCAATTCATATTAAAAGTATTAAAATTTTAAAAAAATTTTAATTTG
193 ACCTTAAATCACTCTCAATTCAATTCATATTAAAAGTACTAAAATTTTAAAAATTTTTTAATTTG
* *
5488074 ACAAATTAAATAAATCAATATATAATTAATAAATTAATAAATACTACAATTACAATTATAAAATA
258 ACAAATTAAATCAATCAATATATAATTAATAAATTAATAAATACTATAATTACAATTATAAAATA
* * * *
5488139 GCTGATTATCTAATCAATCAATTATTTGATATATTTATATTTTATTAAATATAGTATCCAATAAT
323 GTTGA-T-TCT-CT-AATCAATTATTTGATATATTTATATTTGATTAAATATAGTATCCAGTAAT
* * *
5488204 TAATGCATTTCATGTGTAAATATAGAAAGTAAATATCATTTAAAAAACCAACTTCATTATATTTA
384 TAATGCATTTCATATGTAAATATAGAAAGTAAATATAATTTAAAAAACCAAATTCATTATATTTA
5488269 TGTTTTTATTATTAATTTTAAATCACTCTCAACTCAATTCATATTAAAAATATTAAAATTTTAAA
449 -----TTATTATTAATTTTAAATCACTCTCAACTCAATTCATATTAAAAATATTAAAATTTTAAA
* *
5488334 TTTGTTTAAATTGAAAAAATTAAATCAATCAATATATAATTAATAATAAATACTACAATTACAAT
509 TTTGCTTAAATTGAAAAAATTAAATCAATCAATATATAATTAATAATAAACACTACAATTACAAT
* *
5488399 TATAAAATAGTTGATTCTCTAATTAATTATTTGAAACATTTATATTTGATTAAATATAGTATCTA
574 AATAAAATAGTTGATTCTCTAATTAATTATTTGAAACATTTATATTTGATTAAATATAGTATCCA
* * *
5488464 TTTGAGTAATTGATGTATTTCATAATGTATTTTTATGTGTAAATATATAAAGCAAATATATCAAA
639 TTTAAGTAATTGATGTATTTC------------TATGTGTAAATATATAAAACAAATATATAAAA
* *
5488529 TTAATTCTTCATAAGTAAATTAATGGAATAAAATATTTTATTAATTTATATTTGATTGATACCTT
692 TTAATTCTCCATAAGTAAATTAATGAAATAAAATATTTTATTAATTTATATTTGATTGATACCTT
5488594 TATATTTCATTAAATATGATTTCATTTGATTTTATT
757 TATATTTCATTAAATATGATTTCATTTGATTTTATT
* * * * *
5488630 ATATAAATATATAAAAGCTAAAGCTTTTGGCAAAAATG-AAAAAAT-TATATATAGG-TGGGTTA
1 ATATAAATATATAAAAGCCAAAACTTTTAGCAAAAATGAAAAAAATCT-TATGT-GGAT-GCTTA
* * * * * *
5488692 AAATGTTAAGATGTGGATAGTCTTAAAAATTAC-CG-GACATCTAATAAATACATTTTATTTTAT
63 AAATATTGACATGTGGATAGACTTAAAAATCACACGTGACATCTAATAAATATATTTTATTTTAT
* * * * * *
5488755 TTAATACATATTTAATTTAAATATAATTCAAAATATAAATTGATTATATTTAAGTTTTTATTATT
128 TTTATATATTTTTAATTTAAAAATAATTAAAAAAATAAATTGATTATATTTAA-TTTTTATTATT
* * **
5488820 AACTTTAAATCACTTTCAATTCAATTCATATTAAAAGTACTAAAATTTTAAAAATTGCTTAATTT
192 AACCTTAAATCACTCTCAATTCAATTCATATTAAAAGTACTAAAATTTTAAAAATTTTTTAATTT
* *
5488885 AACAAATTAAATCAATCAATATATAATTAATAAATTAATAAATACTATAATTATAATTATAAAAT
257 GACAAATTAAATCAATCAATATATAATTAATAAATTAATAAATACTATAATTACAATTATAAAAT
* * *
5488950 AGTTGATTCTCTAATTAATTATTTAATACATTTATATTTGATTAAATATAGTAAT-CAGTAAT
322 AGTTGATTCTCTAATCAATTATTTGATATATTTATATTTGATTAAATATAGT-ATCCAGTAAT
5489012 ACATTTATAT
Statistics
Matches: 1065, Mismatches: 96, Indels: 66
0.87 0.08 0.05
Matches are distributed among these distances:
798 33 0.03
799 227 0.21
800 33 0.03
801 11 0.01
802 10 0.01
803 96 0.09
804 101 0.09
805 2 0.00
806 1 0.00
807 6 0.01
808 45 0.04
809 82 0.08
810 3 0.00
811 2 0.00
812 208 0.20
813 2 0.00
814 2 0.00
815 42 0.04
816 72 0.07
817 87 0.08
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.42
Consensus pattern (792 bp):
ATATAAATATATAAAAGCCAAAACTTTTAGCAAAAATGAAAAAAATCTTATGTGGATGCTTAAAA
TATTGACATGTGGATAGACTTAAAAATCACACGTGACATCTAATAAATATATTTTATTTTATTTT
ATATATTTTTAATTTAAAAATAATTAAAAAAATAAATTGATTATATTTAATTTTTATTATTAACC
TTAAATCACTCTCAATTCAATTCATATTAAAAGTACTAAAATTTTAAAAATTTTTTAATTTGACA
AATTAAATCAATCAATATATAATTAATAAATTAATAAATACTATAATTACAATTATAAAATAGTT
GATTCTCTAATCAATTATTTGATATATTTATATTTGATTAAATATAGTATCCAGTAATTAATGCA
TTTCATATGTAAATATAGAAAGTAAATATAATTTAAAAAACCAAATTCATTATATTTATTATTAT
TAATTTTAAATCACTCTCAACTCAATTCATATTAAAAATATTAAAATTTTAAATTTGCTTAAATT
GAAAAAATTAAATCAATCAATATATAATTAATAATAAACACTACAATTACAATAATAAAATAGTT
GATTCTCTAATTAATTATTTGAAACATTTATATTTGATTAAATATAGTATCCATTTAAGTAATTG
ATGTATTTCTATGTGTAAATATATAAAACAAATATATAAAATTAATTCTCCATAAGTAAATTAAT
GAAATAAAATATTTTATTAATTTATATTTGATTGATACCTTTATATTTCATTAAATATGATTTCA
TTTGATTTTATT
Found at i:5489119 original size:209 final size:215
Alignment explanation
Indices: 5488798--5489212 Score: 583
Period size: 209 Copynumber: 1.9 Consensus size: 215
5488788 TATAAATTGA
* *
5488798 TTATATTTAAGTTTTTATTATTAACTTTAAATCACTTTCAATTCAATTCATATTAAAAGTACTAA
1 TTATATTTAAGTTTTTATTATTAACTTTAAATAACTCTCAATTCAATTCATATTAAAAGTACTAA
*
5488863 AATTTTAAAAATTGCTTAATTTAACAAATTAAATCAATCAATATATAATTAATAAATTAATAAAT
66 AA--TT---AATTGCTTAATTTAAAAAATTAAATCAATCAATATATAATTAATAAATTAATAAAT
* * *
5488928 ACTATAATTATAATTATAAAATAGTTGATTCTCTAATTAATT-A-TTTAATACATTTATATTTGA
126 ACTATAATTACAATTATAAAATAATTGATTCTCTAATTAATTAATTTTAATACATTTATATTTAA
*
5488991 TTAAATATAGTAATCAGTAATACAT
191 ATAAATATAGTAATCAGTAATACAT
* * *
5489016 TTATATTTATA-TTTTTATTATTGATTTTAAATAACTCTCAA-TCAATTCATATTAAAAGTATTA
1 TTATATTTA-AGTTTTTATTATTAACTTTAAATAACTCTCAATTCAATTCATATTAAAAGTACTA
* *
5489079 AAA-T-ATT-CTTAATTTAAAAAATTAAATCAATCAATATATAATTAATAAATTAATGAATATTA
65 AAATTAATTGCTTAATTTAAAAAATTAAATCAATCAATATATAATTAATAAATTAATAAATACTA
* *
5489141 TAATTACAATTATAAAATAATTTATTCTCTAATTAATTAATTTTTTGATACATTTATATTTAAAT
130 TAATTACAATTATAAAATAATTGATTCTCTAATTAATTAA--TTTTAATACATTTATATTTAAAT
5489206 AAATATA
193 AAATATA
5489213 ATATTCATTT
Statistics
Matches: 178, Mismatches: 14, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
209 87 0.49
210 4 0.02
213 26 0.15
214 1 0.01
217 24 0.13
218 35 0.20
219 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (215 bp):
TTATATTTAAGTTTTTATTATTAACTTTAAATAACTCTCAATTCAATTCATATTAAAAGTACTAA
AATTAATTGCTTAATTTAAAAAATTAAATCAATCAATATATAATTAATAAATTAATAAATACTAT
AATTACAATTATAAAATAATTGATTCTCTAATTAATTAATTTTAATACATTTATATTTAAATAAA
TATAGTAATCAGTAATACAT
Found at i:5489127 original size:23 final size:24
Alignment explanation
Indices: 5489101--5489146 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
5489091 TTTAAAAAAT
5489101 TAAATCAATCAATA-TATAATTAA
1 TAAATCAATCAATATTATAATTAA
* *
5489124 TAAATTAATGAATATTATAATTA
1 TAAATCAATCAATATTATAATTA
5489147 CAATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (24 bp):
TAAATCAATCAATATTATAATTAA
Done.