Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 73 of 187
Found at i:21376634 original size:137 final size:137
Alignment explanation
Indices: 21376377--21376646 Score: 362
Period size: 137 Copynumber: 2.0 Consensus size: 137
21376367 TCGATTTAGG
* * *
21376377 GATGAAATGTATGCGATTGAATGGTTTATGATATATTTAAATTATTGAATGTTATGATGTTTGAA
1 GATGAAACGCATGCGATTGAATGATTTATGATATATTTAAATTATTGAATGTTATGATGTTTGAA
* * *
21376442 TATTTCTGATTGTACAGTAATACCCTGTAACCCTAATTCGACAATAGAGGTGGGTTAGGGGTGTT
66 TATTTCTGATTGTACAGTAATACCCTGTAACCCTAATTCGACAACAGAGGCGGGTTAGAGGTGTT
21376507 ACATTTA
131 ACATTTA
* * *
21376514 GATGAAACGCATGTGATTGGATGATTTATGATATATTTAAATTATTGAATGTTATGGTGTTTGAA
1 GATGAAACGCATGCGATTGAATGATTTATGATATATTTAAATTATTGAATGTTATGATGTTTGAA
* * * * * * * * *
21376579 TGTTTTTTATTGTACGGTAATGCTCC-GTAACCCTAATTTGGCGACAGATGCGGGTTAGAGGTGT
66 TATTTCTGATTGTACAGTAATAC-CCTGTAACCCTAATTCGACAACAGAGGCGGGTTAGAGGTGT
21376643 TACA
130 TACA
21376647 GTTCGAGTTT
Statistics
Matches: 114, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
137 112 0.98
138 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (137 bp):
GATGAAACGCATGCGATTGAATGATTTATGATATATTTAAATTATTGAATGTTATGATGTTTGAA
TATTTCTGATTGTACAGTAATACCCTGTAACCCTAATTCGACAACAGAGGCGGGTTAGAGGTGTT
ACATTTA
Found at i:21377162 original size:10 final size:10
Alignment explanation
Indices: 21377149--21377201 Score: 65
Period size: 10 Copynumber: 5.2 Consensus size: 10
21377139 TAAAAAGACA
21377149 AAGAGAAGAG
1 AAGAGAAGAG
21377159 AAGAGAAGAG
1 AAGAGAAGAG
21377169 AAGAG-AGAG
1 AAGAGAAGAG
21377178 -AGAGAAAGAG
1 AAGAG-AAGAG
21377188 AAAGAGAAAGAG
1 -AAGAG-AAGAG
21377200 AA
1 AA
21377202 TTGGAAATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 4 0.10
9 4 0.10
10 19 0.49
11 2 0.05
12 10 0.26
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
AAGAGAAGAG
Found at i:21377201 original size:6 final size:6
Alignment explanation
Indices: 21377142--21377201 Score: 72
Period size: 6 Copynumber: 10.3 Consensus size: 6
21377132 AAAGAAATAA
* *
21377142 AAAGAC AAAGAG -AAGAG -AAGAG -AAGAG AAGAGAG AGAGAG AAAGAG
1 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AA-AGAG AAAGAG AAAGAG
21377188 AAAGAG AAAGAG AA
1 AAAGAG AAAGAG AA
21377202 TTGGAAATGA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
5 15 0.31
6 29 0.59
7 5 0.10
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:21377358 original size:25 final size:25
Alignment explanation
Indices: 21377330--21377401 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 25
21377320 ATAGCTGGTA
*
21377330 TAAAAACCAAAACGCACCGTTTAA-
1 TAAAAACCAAAACACACCGTTTAAC
* * *
21377354 T-TAAATCAATACACACCGTTTAAC
1 TAAAAACCAAAACACACCGTTTAAC
* *
21377378 TAAAGACAAAAACACACCGTTTAA
1 TAAAAACCAAAACACACCGTTTAA
21377402 GCTAGCCAAC
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
23 18 0.49
24 2 0.05
25 17 0.46
ACGTcount: A:0.49, C:0.24, G:0.07, T:0.21
Consensus pattern (25 bp):
TAAAAACCAAAACACACCGTTTAAC
Found at i:21377370 original size:23 final size:25
Alignment explanation
Indices: 21377338--21377401 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 25
21377328 TATAAAAACC
* * *
21377338 AAAACGCACCGTTTAATTAAA-TC-
1 AAAACACACCGTTTAACTAAAGACA
*
21377361 AATACACACCGTTTAACTAAAGACA
1 AAAACACACCGTTTAACTAAAGACA
21377386 AAAACACACCGTTTAA
1 AAAACACACCGTTTAA
21377402 GCTAGCCAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 18 0.53
24 1 0.03
25 15 0.44
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.22
Consensus pattern (25 bp):
AAAACACACCGTTTAACTAAAGACA
Found at i:21378778 original size:14 final size:15
Alignment explanation
Indices: 21378759--21378792 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
21378749 ATGTAGCAGA
*
21378759 TTTTGT-TGTTTCTG
1 TTTTGTATGGTTCTG
21378773 TTTTGTATGGTTCTG
1 TTTTGTATGGTTCTG
21378788 TTTTG
1 TTTTG
21378793 GTGAACACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.03, C:0.06, G:0.24, T:0.68
Consensus pattern (15 bp):
TTTTGTATGGTTCTG
Found at i:21380015 original size:14 final size:14
Alignment explanation
Indices: 21379992--21380023 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
21379982 AAATTTTTTT
*
21379992 TATACCTATATATA
1 TATACATATATATA
21380006 TATACATATATATA
1 TATACATATATATA
21380020 TATA
1 TATA
21380024 TTACTTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (14 bp):
TATACATATATATA
Found at i:21380724 original size:15 final size:15
Alignment explanation
Indices: 21380704--21380739 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
21380694 CAAATACCAA
21380704 CAATTAATTTTAGGT
1 CAATTAATTTTAGGT
21380719 CAATTAATTTTAGGT
1 CAATTAATTTTAGGT
21380734 CAATTA
1 CAATTA
21380740 TACATATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (15 bp):
CAATTAATTTTAGGT
Found at i:21384369 original size:18 final size:17
Alignment explanation
Indices: 21384341--21384375 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21384331 ATTATTAAGA
*
21384341 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
21384358 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
21384376 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:21403926 original size:23 final size:23
Alignment explanation
Indices: 21403890--21403940 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
21403880 AGATCTCGTT
* *
21403890 TGTAATATCTCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
21403913 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
21403936 AGTAA
1 TGTAA
21403941 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:21406689 original size:23 final size:23
Alignment explanation
Indices: 21406664--21406706 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
21406654 TTAAGTTTTT
* *
21406664 TTTTTATTT-TTTTAATTTACCC
1 TTTTAATTTATTTTAAATTACCC
21406686 TTTTAATTTATTTTAAATTAC
1 TTTTAATTTATTTTAAATTAC
21406707 TATTTGGTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTAATTTATTTTAAATTACCC
Found at i:21419453 original size:44 final size:44
Alignment explanation
Indices: 21419388--21420094 Score: 621
Period size: 44 Copynumber: 16.0 Consensus size: 44
21419378 AAAAAGAAAA
* * *
21419388 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAG
1 CAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAG
* * * *
21419432 CAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGAT-G
1 CAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAGATAG
* * * * * *
21419476 CAGAGCTTATCTTCCCATGCTAGTGGC--GAAGTAGATCGAAGAAAA
1 CAGATCTTGTCTT-CC-T-ATATTGGCGTGAAGTAGATCGAAGATAG
* * *
21419521 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAATATAG
1 CAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAG
* * ** *
21419565 CAGGTCCTGTCTTCCTATATTAGTAG-GAAGTGGATCGAAGAT-G
1 CAGATCTTGTCTTCCTATATT-GGCGTGAAGTAGATCGAAGATAG
* * * * *
21419608 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAGATAG
* ** *
21419653 TAGATCTTGTCTTAATATATTGGCGTGAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAG
* * * *
21419697 CAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT-G
1 CAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAGATAG
* * * * *
21419740 CAGATCTTGTCTTCCCATACTGGTGGTAAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAGATAG
* * *
21419785 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAA
1 CAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAG
* * *
21419829 CAGGTCCTGTCTTCCTATATTGGCAG-GAAGTGGATCGAAGAT-G
1 CAGATCTTGTCTTCCTATATTGGC-GTGAAGTAGATCGAAGATAG
* * * * *
21419872 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA-AAAG
1 CAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAGATAG
* * *
21419916 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAAATCGAAGATAG
1 CAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAG
* * * *
21419960 CAGATCCTGTTTTCCTATATTGGTAGTGAAGTGGATCGAAGATA-
1 CAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAGATAG
* * *
21420004 CAGATCTTGTGTTCCCATACTAGTGGC--GAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTT-CC-TA-TATTGGCGTGAAGTAGATCGAAGATAG
* * * *
21420049 CAGATCTTGTCTTCATGTATTGGCGTGAAATAAATCGAAGATAG
1 CAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAG
21420093 CA
1 CA
21420095 AATTTTGTTC
Statistics
Matches: 523, Mismatches: 114, Indels: 52
0.76 0.17 0.08
Matches are distributed among these distances:
42 13 0.02
43 77 0.15
44 318 0.61
45 102 0.20
46 3 0.01
47 10 0.02
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (44 bp):
CAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAG
Found at i:21419674 original size:132 final size:132
Alignment explanation
Indices: 21419381--21420094 Score: 1169
Period size: 132 Copynumber: 5.4 Consensus size: 132
21419371 ATAGGTTAAA
* * *
21419381 AAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTGTCTTC
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTGTCTTC
* * * *
21419446 CTATATTGGTAGCGAAGTGGATCGAAGATGCAGAGCTTATCTTCCCATGCTAGTGGCGAAGTAGA
66 CTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
21419511 TCG
130 TCG
* *
21419514 AAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAATATAGCAGGTCCTGTCTTC
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTGTCTTC
*
21419579 CTATATTAGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
66 CTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
21419644 CG
131 CG
* * * *
21419646 AAGAAAGTAGATCTTGTCTTAATATATTGGCGTGAAGTAGATCAAAGATAGCAGGTCCTGTCTTC
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTGTCTTC
**
21419711 CTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGTAAAGTAGAT
66 CTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
21419776 CG
131 CG
*
21419778 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGGTCCTGTCTTC
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTGTCTTC
*
21419843 CTATATTGGCAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
66 CTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
21419908 CG
131 CG
* * *
21419910 AA-AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAAATCGAAGATAGCAGATCCTGTTTTC
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTGTCTTC
* * *
21419974 CTATATTGGTAGTGAAGTGGATCGAAGATACAGATCTTGTGTTCCCATACTAGTGGCGAAGTAGA
66 CTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
21420039 TCG
130 TCG
* *
21420042 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAATAAATCGAAGATAGCA
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCA
21420095 AATTTTGTTC
Statistics
Matches: 545, Mismatches: 34, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
131 69 0.13
132 354 0.65
133 122 0.22
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (132 bp):
AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTGTCTTC
CTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
CG
Found at i:21421502 original size:27 final size:27
Alignment explanation
Indices: 21421472--21421534 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
21421462 TATCTGTAAT
21421472 TATTTTTTATTTATATATACATATGTA
1 TATTTTTTATTTATATATACATATGTA
* * * *
21421499 TATTTGTTGTTTTTATATACATATTTA
1 TATTTTTTATTTATATATACATATGTA
21421526 T-TTTTTTAT
1 TATTTTTTAT
21421535 AAGTAATGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (27 bp):
TATTTTTTATTTATATATACATATGTA
Found at i:21427886 original size:13 final size:12
Alignment explanation
Indices: 21427868--21427909 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
21427858 ATTTCTAAAA
21427868 ATAAATAAATAAT
1 ATAAATAAAT-AT
21427881 ATAAATATAATAT
1 ATAAATA-AATAT
21427894 ATATAATAAA-AT
1 ATA-AATAAATAT
21427906 ATAA
1 ATAA
21427910 TAATAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 5 0.19
13 14 0.52
14 7 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAAATAAATAT
Found at i:21427905 original size:19 final size:19
Alignment explanation
Indices: 21427863--21427916 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
21427853 GTAAAATTTC
21427863 TAAAA-ATAA-ATAAATAA
1 TAAAATATAATATAAATAA
*
21427880 TATAAATATAATATATATAA
1 TA-AAATATAATATAAATAA
21427900 TAAAATATAATAATAAA
1 TAAAATATAAT-ATAAA
21427917 AAACCAGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 2 0.06
18 3 0.10
19 13 0.42
20 13 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAATATAATATAAATAA
Found at i:21427912 original size:13 final size:13
Alignment explanation
Indices: 21427865--21427917 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 13
21427855 AAAATTTCTA
21427865 AAAATA-AATAA-
1 AAAATATAATAAT
*
21427876 ATAATAT-A-AAT
1 AAAATATAATAAT
*
21427887 ATAATATATATAAT
1 AAAATATA-ATAAT
21427901 AAAATATAATAAT
1 AAAATATAATAAT
21427914 AAAA
1 AAAA
21427918 AACCAGTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 2 0.06
11 13 0.37
13 10 0.29
14 10 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATATAATAAT
Found at i:21427918 original size:14 final size:14
Alignment explanation
Indices: 21427874--21427917 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
21427864 AAAAATAAAT
21427874 AAATA-ATATAAATA
1 AAATATATAT-AATA
*
21427888 TAATATATATAATA
1 AAATATATATAATA
21427902 AAATATA-ATAATA
1 AAATATATATAATA
21427915 AAA
1 AAA
21427918 AACCAGTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 9 0.33
14 14 0.52
15 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATATATATAATA
Found at i:21428069 original size:14 final size:12
Alignment explanation
Indices: 21428025--21428077 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
21428015 ATGTAATAAC
21428025 AATAAAAA-TA-
1 AATAAAAATTAT
21428035 AATAAAAATTAT
1 AATAAAAATTAT
*
21428047 AAAAAAAATTATT
1 AATAAAAATTA-T
21428060 CAATAAAAA-TAT
1 -AATAAAAATTAT
21428072 AATAAA
1 AATAAA
21428078 TAATAAAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 8 0.22
11 8 0.22
12 11 0.30
13 3 0.08
14 7 0.19
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAAAAATTAT
Found at i:21428079 original size:15 final size:14
Alignment explanation
Indices: 21428031--21428080 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
21428021 TAACAATAAA
21428031 AATAAATAAAAATT
1 AATAAATAAAAATT
21428045 -ATAAA-AAAAATT
1 AATAAATAAAAATT
* *
21428057 ATTCAATAAAAATAT
1 AATAAATAAAAAT-T
21428072 AATAAATAA
1 AATAAATAA
21428081 TAAAAACTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
12 7 0.24
13 8 0.28
14 6 0.21
15 8 0.28
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAAATAAAAATT
Found at i:21428281 original size:7 final size:7
Alignment explanation
Indices: 21428269--21428298 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
21428259 AAACTGTTAC
21428269 AGCAGTT
1 AGCAGTT
21428276 AGCAGTT
1 AGCAGTT
21428283 AGCAGTT
1 AGCAGTT
21428290 AGCAGTT
1 AGCAGTT
21428297 AG
1 AG
21428299 TACTTGGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (7 bp):
AGCAGTT
Found at i:21431614 original size:24 final size:24
Alignment explanation
Indices: 21431565--21431617 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
21431555 GCTATCTGGT
* *
21431565 GCTACCCGTTAATTACTTTTCGGA
1 GCTACCAGTTAATTACTTTTCAGA
*
21431589 GCTACCAGTTAATTGCTCTTT-AGA
1 GCTACCAGTTAATTACT-TTTCAGA
21431613 GCTAC
1 GCTAC
21431618 TCGTTATAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (24 bp):
GCTACCAGTTAATTACTTTTCAGA
Found at i:21431623 original size:24 final size:23
Alignment explanation
Indices: 21431565--21431623 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 23
21431555 GCTATCTGGT
*
21431565 GCTACCCGTTAATTACTTTTCGGA
1 GCTA-CCGTTAATTACTTTTCAGA
*
21431589 GCTACCAGTTAATTGCTCTTT-AGA
1 GCTACC-GTTAATTACT-TTTCAGA
21431613 GCTACTCGTTA
1 GCTAC-CGTTA
21431624 TAGGCTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
23 2 0.07
24 24 0.80
25 4 0.13
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (23 bp):
GCTACCGTTAATTACTTTTCAGA
Found at i:21432319 original size:2 final size:2
Alignment explanation
Indices: 21432307--21432349 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
21432297 ATATTTTGAA
*
21432307 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21432349 A
1 A
21432350 GTCGTACTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21432511 original size:2 final size:2
Alignment explanation
Indices: 21432492--21432547 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
21432482 ACCTAATTAT
21432492 TA TA T- TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21432531 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
21432548 GGCCTTAACA
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 48 0.94
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21440048 original size:60 final size:60
Alignment explanation
Indices: 21439950--21440102 Score: 155
Period size: 60 Copynumber: 2.5 Consensus size: 60
21439940 TGGTATTTAA
* * * * *
21439950 TTTTTTTTAATTTAGTATCTAAACTATTTTTTGACTCAATTTAGTATCTGAACTT-GACAC
1 TTTTTTCTAATTTGGTATCT-AACTTTTTTTTGACTCAATTTAGTACCTAAACTTGGACAC
* * * ***
21440010 TTTTTTCTAATTTGGTATCTAATTTTTTTTTGGTCTCAATTTGGTACCTAAACTTGGATTT
1 TTTTTTCTAATTTGGTATCTAACTTTTTTTT-GACTCAATTTAGTACCTAAACTTGGACAC
* *
21440071 TTTTTTCTAATTTGGTACCTAAGGTTTTTTTT
1 TTTTTTCTAATTTGGTATCTAA-CTTTTTTTT
21440103 AGGTTTAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
59 9 0.12
60 37 0.48
61 23 0.30
62 8 0.10
ACGTcount: A:0.22, C:0.12, G:0.11, T:0.55
Consensus pattern (60 bp):
TTTTTTCTAATTTGGTATCTAACTTTTTTTTGACTCAATTTAGTACCTAAACTTGGACAC
Found at i:21440083 original size:32 final size:28
Alignment explanation
Indices: 21440010--21440126 Score: 94
Period size: 29 Copynumber: 3.9 Consensus size: 28
21440000 AACTTGACAC
*
21440010 TTTTTTCTAATTTGGTATCT-AATTTTT
1 TTTTTTCTAATTTGGTACCTAAATTTTT
*
21440037 TTTTGGTCTCAATTTGGTACCTAAACTTGGATTT
1 TTTT-TTCT-AATTTGGTACCTAAA-TT---TTT
*
21440071 TTTTTTCTAATTTGGTACCTAAGGTTTTT
1 TTTTTTCTAATTTGGTACCTAA-ATTTTT
* *
21440100 TTTAGGTT-TAATTTGGTTCCTAAATTT
1 TTT--TTTCTAATTTGGTACCTAAATTT
21440127 ATTAAATGTT
Statistics
Matches: 73, Mismatches: 7, Indels: 18
0.74 0.07 0.18
Matches are distributed among these distances:
27 4 0.05
28 3 0.04
29 20 0.27
30 16 0.22
31 4 0.05
32 16 0.22
33 3 0.04
34 7 0.10
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.56
Consensus pattern (28 bp):
TTTTTTCTAATTTGGTACCTAAATTTTT
Found at i:21440595 original size:31 final size:31
Alignment explanation
Indices: 21440557--21440703 Score: 141
Period size: 31 Copynumber: 4.9 Consensus size: 31
21440547 ATCAACTTAA
21440557 GAAAAAGTGTCAAGTTTAGGTACCAAATTAG
1 GAAAAAGTGTCAAGTTTAGGTACCAAATTAG
*
21440588 GAAAAAGTGTCAAGTTTAGGTGCC-AA--AG
1 GAAAAAGTGTCAAGTTTAGGTACCAAATTAG
* *
21440616 GAAAAAGGGTCAAGTTT-GAGTGCCAAATT-G
1 GAAAAAGTGTCAAGTTTAG-GTACCAAATTAG
*
21440646 GACCAAAA----AAAGGTTTAGGTACCAAATTAG
1 GA--AAAAGTGTCAA-GTTTAGGTACCAAATTAG
* *
21440676 GAAAAAGTGTCAAGTTCAGATACCAAAT
1 GAAAAAGTGTCAAGTTTAGGTACCAAAT
21440704 GTTATATTAA
Statistics
Matches: 96, Mismatches: 7, Indels: 26
0.74 0.05 0.20
Matches are distributed among these distances:
27 1 0.01
28 29 0.30
29 15 0.16
30 9 0.09
31 36 0.38
32 6 0.06
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (31 bp):
GAAAAAGTGTCAAGTTTAGGTACCAAATTAG
Found at i:21440627 original size:28 final size:28
Alignment explanation
Indices: 21440557--21440642 Score: 111
Period size: 28 Copynumber: 3.0 Consensus size: 28
21440547 ATCAACTTAA
*
21440557 GAAAAAGTGTCAAGTTTAGGTACCAAATTAG
1 GAAAAAGTGTCAAGTTTAGGTGCC-AA--AG
21440588 GAAAAAGTGTCAAGTTTAGGTGCCAAAG
1 GAAAAAGTGTCAAGTTTAGGTGCCAAAG
*
21440616 GAAAAAGGGTCAAGTTT-GAGTGCCAAA
1 GAAAAAGTGTCAAGTTTAG-GTGCCAAA
21440643 TTGGACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
27 1 0.02
28 26 0.50
30 2 0.04
31 23 0.44
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.22
Consensus pattern (28 bp):
GAAAAAGTGTCAAGTTTAGGTGCCAAAG
Found at i:21440813 original size:6 final size:6
Alignment explanation
Indices: 21440804--21440839 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
21440794 TTGAATTTGA
21440804 ATTTAG ATTTAG ATTTAG ATTTTAG ATTTTAG ATTT
1 ATTTAG ATTTAG ATTTAG A-TTTAG A-TTTAG ATTT
21440840 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 16 0.55
7 13 0.45
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.56
Consensus pattern (6 bp):
ATTTAG
Found at i:21440849 original size:15 final size:15
Alignment explanation
Indices: 21440817--21440890 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
21440807 TAGATTTAGA
*
21440817 TTTAGATTTT-AGAT
1 TTTAGATTTTAAAAT
21440831 TTTAGATTTTAAAAT
1 TTTAGATTTTAAAAT
* * *
21440846 TTTATATTTGAAACT
1 TTTAGATTTTAAAAT
21440861 TTT-G-TTTTATAAAT
1 TTTAGATTTTA-AAAT
*
21440875 TTATA-ATTTTCAAAT
1 TT-TAGATTTTAAAAT
21440890 T
1 T
21440891 CTCTGTCAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
13 4 0.09
14 15 0.32
15 24 0.51
16 4 0.09
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTAGATTTTAAAAT
Found at i:21440854 original size:7 final size:7
Alignment explanation
Indices: 21440805--21440841 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
21440795 TGAATTTGAA
21440805 TTTAGA-
1 TTTAGAT
21440811 TTTAGA-
1 TTTAGAT
21440817 TTTAGAT
1 TTTAGAT
21440824 TTTAGAT
1 TTTAGAT
21440831 TTTAGAT
1 TTTAGAT
21440838 TTTA
1 TTTA
21440842 AAATTTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (7 bp):
TTTAGAT
Found at i:21442248 original size:29 final size:29
Alignment explanation
Indices: 21442166--21442248 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
21442156 ATTTTTAAAT
*
21442166 GATAGTCGCTGTCAGACTCTTG-TTTGGTA
1 GATAGTCACTGT-AGACTCTTGATTTGGTA
* *
21442195 GATAGTCATTGCTAGACTCTT-ATTTGGTG
1 GATAGTCACTG-TAGACTCTTGATTTGGTA
*
21442224 GATAGTCACTGTGGACTCTTGATTT
1 GATAGTCACTGTAGACTCTTGATTT
21442249 AATATAGTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
28 8 0.17
29 37 0.80
30 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (29 bp):
GATAGTCACTGTAGACTCTTGATTTGGTA
Found at i:21444014 original size:22 final size:22
Alignment explanation
Indices: 21443982--21444065 Score: 114
Period size: 22 Copynumber: 3.8 Consensus size: 22
21443972 GGAGGTCCTT
*
21443982 ATGTTTCACGTACTAAGCTCTC
1 ATGTTTAACGTACTAAGCTCTC
21444004 ATGTTTAACGTACTAAGCTCTC
1 ATGTTTAACGTACTAAGCTCTC
* * *
21444026 ATGTTTAACGAACTAAACCCTC
1 ATGTTTAACGTACTAAGCTCTC
**
21444048 ATGGCTAACGTACTAAGC
1 ATGTTTAACGTACTAAGC
21444066 AGCATTACTG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (22 bp):
ATGTTTAACGTACTAAGCTCTC
Found at i:21445486 original size:42 final size:42
Alignment explanation
Indices: 21445386--21445489 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 42
21445376 ATGCTGCATA
* * * * * *
21445386 GAAGCACATAAGTGCTAAACAGAAACCCATAAGAGTTGAACG
1 GAAGCTCATAAGAGCTGAACAAAAACCCAGAAGAGTTAAACG
* *
21445428 GAAGCTCATAAGAGCTGAACAAAAACCCAGAAGGGTTAAACT
1 GAAGCTCATAAGAGCTGAACAAAAACCCAGAAGAGTTAAACG
21445470 GAAGCTCGA-AAGAGCTGAAC
1 GAAGCTC-ATAAGAGCTGAAC
21445490 TGAAACTCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 52 0.98
43 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.13
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTGAACAAAAACCCAGAAGAGTTAAACG
Found at i:21452262 original size:3 final size:3
Alignment explanation
Indices: 21452254--21452281 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
21452244 CTGCATACCG
21452254 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
21452282 ATATCTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:21453937 original size:25 final size:25
Alignment explanation
Indices: 21453902--21453968 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
21453892 AAGTTAATGA
*
21453902 AAACGGGGAGTTTTGGGTATTAGTT
1 AAACGGTGAGTTTTGGGTATTAGTT
* *
21453927 AAACGGTGAGTTTTGGATGTTAGTT
1 AAACGGTGAGTTTTGGGTATTAGTT
*
21453952 AGACGGTGAGTTTTGGG
1 AAACGGTGAGTTTTGGG
21453969 GTGTTAATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.22, C:0.04, G:0.37, T:0.36
Consensus pattern (25 bp):
AAACGGTGAGTTTTGGGTATTAGTT
Found at i:21456037 original size:25 final size:25
Alignment explanation
Indices: 21455967--21456039 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
21455957 GTTTTTCAGT
*
21455967 TAACACCCCAAAACTCACCGTCTAAC
1 TAACA-CCCAAAACTCACCGTTTAAC
*
21455993 TAACATCCAAAACTCACCGTTTAAC
1 TAACACCCAAAACTCACCGTTTAAC
*
21456018 TAATACCCAAAACTTC-CCGTTT
1 TAACACCCAAAAC-TCACCGTTT
21456040 TCATTAACTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 35 0.83
26 7 0.17
ACGTcount: A:0.37, C:0.36, G:0.04, T:0.23
Consensus pattern (25 bp):
TAACACCCAAAACTCACCGTTTAAC
Found at i:21462231 original size:2 final size:2
Alignment explanation
Indices: 21462224--21462248 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21462214 AAAACGTTAC
21462224 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 A
21462249 CACAGTAGAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21464914 original size:3 final size:3
Alignment explanation
Indices: 21464803--21464899 Score: 169
Period size: 3 Copynumber: 32.3 Consensus size: 3
21464793 ATTAATTGGT
*
21464803 TTA TTA TTA TTA -TA TTTA TTA TTA TTA TTA GTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21464848 TTA 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
21464896 TTA T
1 TTA T
21464900 ATGTACATTA
Statistics
Matches: 90, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.02
3 86 0.96
4 2 0.02
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:21476360 original size:48 final size:49
Alignment explanation
Indices: 21476270--21476366 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 49
21476260 AAGGAGAAGG
* * * *
21476270 GACCAAGGTGAAAACCCGCAAAGGGCACTTTGATTTCTAAAAAA-AAAA
1 GACCAAGGTAAAAACCCGCAAAGGGCACTTTGAGTCCAAAAAAATAAAA
* **
21476318 GACCAAGGTAAAAACCCGCAAATGGTGCTTTGAGTCCAAAAAAATAAAA
1 GACCAAGGTAAAAACCCGCAAAGGGCACTTTGAGTCCAAAAAAATAAAA
21476367 AATAAACCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
48 37 0.90
49 4 0.10
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.16
Consensus pattern (49 bp):
GACCAAGGTAAAAACCCGCAAAGGGCACTTTGAGTCCAAAAAAATAAAA
Found at i:21477753 original size:44 final size:44
Alignment explanation
Indices: 21477691--21478182 Score: 204
Period size: 44 Copynumber: 11.2 Consensus size: 44
21477681 AGTTGCAGTA
* * *
21477691 GAGTGGATTGAAGATAACCAACCTTATCTCCCTAAGCAGTAGTG
1 GAGTAGATTAAAGATAACCAATCTTATCTCCCTAAGCAGTAGTG
* * *
21477735 GAGTAGATTAAAGATAACCAACCTTATCTCCCTGAGCAGCAGTG
1 GAGTAGATTAAAGATAACCAATCTTATCTCCCTAAGCAGTAGTG
* * * * * * *
21477779 GAGTAGGTTGAAGAT-AGCAGATCTTGTCTTCCTATA-CTAGCAGCG
1 GAGTAGATTAAAGATAACCA-ATCTTATCTCCCTA-AGC-AGTAGTG
* * ** * * * *
21477824 AAGTAGATCAAAGAT-ACCAGCCTTATCTCCCTGAGCAGCAATA
1 GAGTAGATTAAAGATAACCAATCTTATCTCCCTAAGCAGTAGTG
* * * *
21477867 GAGTGGGTTGAAA-ATTA-CAGACCTTATCTCCCTAAGCAGTAGTG
1 GAGTAGATT-AAAGATAACCA-ATCTTATCTCCCTAAGCAGTAGTG
* * * *** *
21477911 GAGCAGATCAAAGACAGTAAATTTTATCTTCCC-AAGGCAGTAG-G
1 GAGTAGATTAAAGATAACCAATCTTATC-TCCCTAA-GCAGTAGTG
* ** ** * * *
21477955 GAAGTAGATTTAAG-CCACCAGCCTTATCTTCCTGAGCAGCAGTG
1 G-AGTAGATTAAAGATAACCAATCTTATCTCCCTAAGCAGTAGTG
* * * *
21477999 GAGTAGGTTGAAA-ATTA-TAGATCTTATCTCCCTAAGCAGTAGTA
1 GAGTAGATT-AAAGATAACCA-ATCTTATCTCCCTAAGCAGTAGTG
* * * * * *
21478043 GAGCAGATCAAAGACAGCAAATTTTATCTTCCC-AAGGCAGTAG-G
1 GAGTAGATTAAAGATAACCAATCTTATC-TCCCTAA-GCAGTAGTG
* * * * * *
21478087 GAAGTAGATTTAAG-TCACTAGTCTTATCTCCCTGAGCAGCAGTG
1 G-AGTAGATTAAAGATAACCAATCTTATCTCCCTAAGCAGTAGTG
* * *
21478131 GAGTAG-GTAGAAAATTA-CAGATCTTATCTCCCTAAGCAGTAGTG
1 GAGTAGATTA-AAGATAACCA-ATCTTATCTCCCTAAGCAGTAGTG
*
21478175 GAGCAGAT
1 GAGTAGAT
21478183 AGAAGACGAC
Statistics
Matches: 322, Mismatches: 98, Indels: 55
0.68 0.21 0.12
Matches are distributed among these distances:
42 1 0.00
43 58 0.18
44 200 0.62
45 63 0.20
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (44 bp):
GAGTAGATTAAAGATAACCAATCTTATCTCCCTAAGCAGTAGTG
Found at i:21477939 original size:88 final size:88
Alignment explanation
Indices: 21477670--21477924 Score: 284
Period size: 88 Copynumber: 2.9 Consensus size: 88
21477660 CCACAAATCC
** * *
21477670 TATCTCCCTGAAGTTGCAGTAGAGTGGATTGAAGATAACCA-ACCTTATCTCCCTAAGCAGTAGT
1 TATCTCCCTG-AGCAGCAGTAGAGTGGGTTGAAGATTACCAGACCTTATCTCCCTAAGCAGTAGT
*
21477734 GGAGTAGATTAAAGATAACCAACCT
65 GGAGTAGATCAAAGAT-ACCAACCT
* * * * * * *
21477759 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGA-TAGCAGATCTTGTCTTCCTATA-CTAGCAG
1 TATCTCCCTGAGCAGCAGTAGAGTGGGTTGAAGATTACCAGACCTTATCTCCCTA-AGC-AGTAG
* * *
21477822 CGAAGTAGATCAAAGATACCAGCCT
64 TGGAGTAGATCAAAGATACCAACCT
* *
21477847 TATCTCCCTGAGCAGCAATAGAGTGGGTTGAAAATTA-CAGACCTTATCTCCCTAAGCAGTAGTG
1 TATCTCCCTGAGCAGCAGTAGAGTGGGTTGAAGATTACCAGACCTTATCTCCCTAAGCAGTAGTG
*
21477911 GAGCAGATCAAAGA
66 GAGTAGATCAAAGA
21477925 CAGTAAATTT
Statistics
Matches: 135, Mismatches: 26, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
87 21 0.16
88 83 0.61
89 31 0.23
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (88 bp):
TATCTCCCTGAGCAGCAGTAGAGTGGGTTGAAGATTACCAGACCTTATCTCCCTAAGCAGTAGTG
GAGTAGATCAAAGATACCAACCT
Found at i:21477959 original size:132 final size:131
Alignment explanation
Indices: 21477839--21478291 Score: 640
Period size: 132 Copynumber: 3.4 Consensus size: 131
21477829 GATCAAAGAT
* * * *
21477839 ACCAGCCTTATCTCCCTGAGCAGCAATAGAGTGGGTTGAAAATTACAGACCTTATCTCCCTAAGC
1 ACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGC
21477904 AGTAGTGGAGCAGATCAAAGACAGTAAATTTTATCTTCCCAAGGCAGTAGGGAAGTAGATTTAAG
66 AGTAGTGGAGCAGATCAAAGACAG-AAATTTTATCTTCCCAAGGCAGTAGGGAAGTAGATTTAAG
21477969 CC
130 CC
* *
21477971 ACCAGCCTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAAATTATAGATCTTATCTCCCTAAGC
1 ACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGC
*
21478036 AGTAGTAGAGCAGATCAAAGACAGCAAATTTTATCTTCCCAAGGCAGTAGGGAAGTAGATTTAAG
66 AGTAGTGGAGCAGATCAAAGACAG-AAATTTTATCTTCCCAAGGCAGTAGGGAAGTAGATTTAAG
*
21478101 TC
130 CC
* * *
21478103 ACTAGTCTTATCTCCCTGAGCAGCAGTGGAGTAGGTAGAAAATTACAGATCTTATCTCCCTAAGC
1 ACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGC
* *** * *
21478168 AGTAGTGGAGCAGAT-AGAAGAC-GACGAATCTTATCTTTAAAAGACAGTAAGGAAGTAGATTTA
66 AGTAGTGGAGCAGATCA-AAGACAGA--AATTTTATCTTCCCAAGGCAGTAGGGAAGTAGATTTA
21478231 AGCC
128 AGCC
* * * * **
21478235 ACTAGCCTTATCTCCCTGAGCAACAGTGGAGTAGGTCGAAGATTGTAGATCTTATCT
1 ACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCT
21478292 TCTTGTACTG
Statistics
Matches: 290, Mismatches: 28, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
130 1 0.00
131 2 0.01
132 287 0.99
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (131 bp):
ACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGC
AGTAGTGGAGCAGATCAAAGACAGAAATTTTATCTTCCCAAGGCAGTAGGGAAGTAGATTTAAGC
C
Found at i:21478373 original size:88 final size:87
Alignment explanation
Indices: 21478238--21478409 Score: 200
Period size: 88 Copynumber: 2.0 Consensus size: 87
21478228 TTAAGCCACT
* * * * * * * * *
21478238 AGCCTTATCTCCCTGAGCAACAGTGGAGTAGGTCGAAGATTGTAGATCTTATCTTCTTGTACTGG
1 AGCCTTATCTCCCTGAGCAACAGCGAAGCAGGTCAAAAATAGCAGATCTTACCTTCTTGTACTGC
*
21478303 CAGTAAAGCAGATCGGAAGCACC
66 CAATAAAGCAGATC-GAAGCACC
* * * *
21478326 AGCCTTATCTCCCTGAGCAGCAGCGAAGCAGGTTAAAAATAGCAGATCTTGCCTTCTTGTATTGC
1 AGCCTTATCTCCCTGAGCAACAGCGAAGCAGGTCAAAAATAGCAGATCTTACCTTCTTGTACTGC
*
21478391 CAATGAAGCAGATCGAAGC
66 CAATAAAGCAGATCGAAGC
21478410 CAATAATCTT
Statistics
Matches: 69, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
87 5 0.07
88 64 0.93
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (87 bp):
AGCCTTATCTCCCTGAGCAACAGCGAAGCAGGTCAAAAATAGCAGATCTTACCTTCTTGTACTGC
CAATAAAGCAGATCGAAGCACC
Found at i:21479224 original size:7 final size:7
Alignment explanation
Indices: 21479212--21479236 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21479202 CAGTATTTTA
21479212 TTTTATT
1 TTTTATT
21479219 TTTTATT
1 TTTTATT
21479226 TTTTATT
1 TTTTATT
21479233 TTTT
1 TTTT
21479237 GATTATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:21480020 original size:27 final size:26
Alignment explanation
Indices: 21479990--21480076 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 26
21479980 TTACTATTAA
21479990 ATTAATAGGTTTATTATTATTATAT-TT
1 ATTAATA--TTTATTATTATTATATATT
21480017 ATT-ATATTTATTA-TATT-TATTATT
1 ATTAATATTTATTATTATTATA-TATT
21480041 ATTATTATATTTATTATTATTAT-TATT
1 ATTA--ATATTTATTATTATTATATATT
*
21480068 ATTATTATT
1 ATTAATATT
21480077 ATATGTACAT
Statistics
Matches: 52, Mismatches: 1, Indels: 16
0.75 0.01 0.23
Matches are distributed among these distances:
22 2 0.04
23 5 0.10
24 12 0.23
25 4 0.08
26 3 0.06
27 21 0.40
28 4 0.08
29 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
ATTAATATTTATTATTATTATATATT
Found at i:21480021 original size:18 final size:18
Alignment explanation
Indices: 21480000--21480078 Score: 126
Period size: 18 Copynumber: 4.4 Consensus size: 18
21479990 ATTAATAGGT
21480000 TTATTATTATTATATTTA
1 TTATTATTATTATATTTA
21480018 TTA-TATTTATTATATTTA
1 TTATTA-TTATTATATTTA
21480036 TTATTATTATTATATTTA
1 TTATTATTATTATATTTA
21480054 TTATTATTATTAT-TATTA
1 TTATTATTATTATAT-TTA
21480072 TTATTAT
1 TTATTAT
21480079 ATGTACATTA
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
17 3 0.05
18 53 0.91
19 2 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTATTATTATATTTA
Found at i:21480093 original size:3 final size:3
Alignment explanation
Indices: 21480000--21480078 Score: 94
Period size: 3 Copynumber: 26.3 Consensus size: 3
21479990 ATTAATAGGT
21480000 TTA TTA TTA TTA -TA TTTA TTA -TA TTTA TTA -TA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA
21480045 TTA -TA TTTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T
21480079 ATGTACATTA
Statistics
Matches: 68, Mismatches: 0, Indels: 16
0.81 0.00 0.19
Matches are distributed among these distances:
2 8 0.12
3 52 0.76
4 8 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21483310 original size:61 final size:61
Alignment explanation
Indices: 21483196--21483310 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 61
21483186 ATTACTTTTA
* *
21483196 TGACTCCAATTTCGCGACATTGAAGGTCGGATGTCGCAACACCAAAGATAGATTACTCTAT
1 TGACTCCAATTTCGCGACACTGAAGGTCGGATGTCGCAACACCAAAGACAGATTACTCTAT
* ** * *
21483257 TGACTCTAATGTT-GCGACACTGAAGGTCGGATGTCGTGACACTAAAGGCAGATT
1 TGACTCCAAT-TTCGCGACACTGAAGGTCGGATGTCGCAACACCAAAGACAGATT
21483311 GCCCAAAACA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
61 44 0.96
62 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (61 bp):
TGACTCCAATTTCGCGACACTGAAGGTCGGATGTCGCAACACCAAAGACAGATTACTCTAT
Found at i:21486292 original size:25 final size:25
Alignment explanation
Indices: 21486263--21486353 Score: 137
Period size: 25 Copynumber: 3.6 Consensus size: 25
21486253 GGACACACCA
* * *
21486263 CAGCTCGCATGAGCTTCCTGATACT
1 CAGCTCGCATGAGCTTCCCGTTATT
21486288 CAGCTCGCATGAGCTTCCCGTTATT
1 CAGCTCGCATGAGCTTCCCGTTATT
21486313 CAGCTCGCATGAGCTTCCCGTTATT
1 CAGCTCGCATGAGCTTCCCGTTATT
* *
21486338 CAGCTCGGAAGAGCTT
1 CAGCTCGCATGAGCTT
21486354 ACTATTTACA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.19, C:0.31, G:0.22, T:0.29
Consensus pattern (25 bp):
CAGCTCGCATGAGCTTCCCGTTATT
Found at i:21495486 original size:363 final size:362
Alignment explanation
Indices: 21494852--21495582 Score: 1426
Period size: 363 Copynumber: 2.0 Consensus size: 362
21494842 ATTCGGGTTG
21494852 ATCCGAGTAAAATTTCAGCTATACTTGATTTGAGACCTCTAAAAAATGTCTCTGAAGTTCGAAGC
1 ATCCGAGTAAAATTTCAGCTATACTTGATTTGAGACCTCTAAAAAATGTCTCTGAAGTTCGAAGC
21494917 TTTCTAGGGCTCACTGGTTATTATAGACAGTTTATAAAAGGGTTCTATATGATTACTACCCTGAT
66 TTTCTAGGGCTCACTGGTTATTATAGACAGTTTATAAAAGGGTTCTATATGATTACTACCCTGAT
21494982 GACAAGTTACTACAAAAAGATGTTATGTTTGAGTGGTCAGAAAAGTGCCAAAAAAGTTTTGATCA
131 GACAAGTTACTACAAAAAGATGTTATGTTTGAGTGGTCAGAAAAGTGCCAAAAAAGTTTTGATCA
21495047 GTTGAAAGTTCTTTTGACCGAAGCTCTAGTCTTAGTTCAGCCAGAATCGGGTAAAGAGTTTTTTA
196 GTTGAAAGTTCTTTTGACCGAAGCTCTAGTCTTAGTTCAGCCAGAATCGGGTAAAGAGTTTTTTA
21495112 TTTATAGTGATGCATCTTTAAATGGTTTGGGCTGTGTTTTGATACAGGAAGGCAAAGTTGTAGCC
261 TTTATAGTGATGCATCTTTAAATGGTTTGGGCTGTGTTTTGATACAGGAAGGCAAAGTTGTAGCC
21495177 TATGCCTCGAGACAGTTAAAGCCGCACAAAAAGAACT
326 TATGCCTCGAGACAGTTAAAGCCGCACAAAAAGAACT
* *
21495214 ATCCGAGTAAAATTTCAGCTATATTTGATTTGAGACCTCTGAAAAATGTCTCTGAAGTTCGAAGC
1 ATCCGAGTAAAATTTCAGCTATACTTGATTTGAGACCTCTAAAAAATGTCTCTGAAGTTCGAAGC
*
21495279 TTTCTAGGGCTCGCTGGTTATTATAGACAGTTTATAAAAGGGTTCTATATGATTACTACCCTGAT
66 TTTCTAGGGCTCACTGGTTATTATAGACAGTTTATAAAAGGGTTCTATATGATTACTACCCTGAT
21495344 GACAAAGTTACTACAAAAAGATGTTATGTTTGAGTGGTCAGAAAAGTGCCAAAAAAGTTTTGATC
131 GAC-AAGTTACTACAAAAAGATGTTATGTTTGAGTGGTCAGAAAAGTGCCAAAAAAGTTTTGATC
21495409 AGTTGAAAGTTCTTTTGACCGAAGCTCTAGTCTTAGTTCAGCCAGAATCGGGTAAAGAGTTTTTT
195 AGTTGAAAGTTCTTTTGACCGAAGCTCTAGTCTTAGTTCAGCCAGAATCGGGTAAAGAGTTTTTT
21495474 ATTTATAGTGATGCATCTTTAAATGGTTTGGGCTGTGTTTTGATACAGGAAGGCAAAGTTGTAGC
260 ATTTATAGTGATGCATCTTTAAATGGTTTGGGCTGTGTTTTGATACAGGAAGGCAAAGTTGTAGC
21495539 CTATGCCTCGAGACAGTTAAAGCCGCACAAAAAGAACT
325 CTATGCCTCGAGACAGTTAAAGCCGCACAAAAAGAACT
21495577 ATCCGA
1 ATCCGA
21495583 CGCACAATCT
Statistics
Matches: 365, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
362 130 0.36
363 235 0.64
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.32
Consensus pattern (362 bp):
ATCCGAGTAAAATTTCAGCTATACTTGATTTGAGACCTCTAAAAAATGTCTCTGAAGTTCGAAGC
TTTCTAGGGCTCACTGGTTATTATAGACAGTTTATAAAAGGGTTCTATATGATTACTACCCTGAT
GACAAGTTACTACAAAAAGATGTTATGTTTGAGTGGTCAGAAAAGTGCCAAAAAAGTTTTGATCA
GTTGAAAGTTCTTTTGACCGAAGCTCTAGTCTTAGTTCAGCCAGAATCGGGTAAAGAGTTTTTTA
TTTATAGTGATGCATCTTTAAATGGTTTGGGCTGTGTTTTGATACAGGAAGGCAAAGTTGTAGCC
TATGCCTCGAGACAGTTAAAGCCGCACAAAAAGAACT
Found at i:21499599 original size:2 final size:2
Alignment explanation
Indices: 21499592--21499622 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21499582 ATATGACTTT
*
21499592 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21499623 TTAGTTATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:21499605 original size:10 final size:10
Alignment explanation
Indices: 21499590--21499625 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 10
21499580 TTATATGACT
21499590 TTTATATATA
1 TTTATATATA
21499600 TTTATATATA
1 TTTATATATA
21499610 TATATATATATA
1 T-T-TATATATA
21499622 TTTA
1 TTTA
21499626 GTTATGCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 13 0.54
11 2 0.08
12 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTATATATA
Found at i:21501550 original size:25 final size:25
Alignment explanation
Indices: 21501483--21501554 Score: 99
Period size: 25 Copynumber: 2.9 Consensus size: 25
21501473 CACACCACAG
* * * *
21501483 CTCGCATGAGCTTCCTGATACTCAG
1 CTCGCATGAGCTTCCCGTTATTCAA
21501508 CTCGCATGAGCTTCCCGTTATTCAA
1 CTCGCATGAGCTTCCCGTTATTCAA
*
21501533 CTCGCATGACCTTCCCGTTATT
1 CTCGCATGAGCTTCCCGTTATT
21501555 TATTTCAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.18, C:0.33, G:0.17, T:0.32
Consensus pattern (25 bp):
CTCGCATGAGCTTCCCGTTATTCAA
Found at i:21502579 original size:43 final size:43
Alignment explanation
Indices: 21502493--21502582 Score: 135
Period size: 43 Copynumber: 2.1 Consensus size: 43
21502483 CACGGGCATA
* * **
21502493 TGTCTCATCCGTGTGTGACACACGGCTAGGTGACACGGCCGTG
1 TGTCTCAGCCGTGTGTGACACACGGCCAGGTGACACAACCGTG
*
21502536 TGTCTCAGCCGTGTGTGACACACGGCCAGGTGACACAATCGTG
1 TGTCTCAGCCGTGTGTGACACACGGCCAGGTGACACAACCGTG
21502579 TGTC
1 TGTC
21502583 CTATGTATCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.18, C:0.28, G:0.31, T:0.23
Consensus pattern (43 bp):
TGTCTCAGCCGTGTGTGACACACGGCCAGGTGACACAACCGTG
Found at i:21503757 original size:76 final size:76
Alignment explanation
Indices: 21503623--21503765 Score: 189
Period size: 76 Copynumber: 1.9 Consensus size: 76
21503613 TCGGGAAATC
* * * * *
21503623 CAGGGTGGCAGATCATTATTGCCGGGCAACCTGGGATAACATAAATGAGCTGAAAAACCATTGTT
1 CAGGGTGGCAAATCATCATTGCCAGACAACCTGGGATAACATAAATGAGATGAAAAACCATTGTT
21503688 GCCGAACAATT
66 GCCGAACAATT
* * * *
21503699 CAGGGTGGCAAATCATCATTGTCAGACAACTTGGGATAACATAAATGA-ATTAAGAAACCATTTT
1 CAGGGTGGCAAATCATCATTGCCAGACAACCTGGGATAACATAAATGAGATGAA-AAACCATTGT
21503763 TGC
65 TGC
21503766 TAAGCAATCC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
75 3 0.05
76 54 0.95
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (76 bp):
CAGGGTGGCAAATCATCATTGCCAGACAACCTGGGATAACATAAATGAGATGAAAAACCATTGTT
GCCGAACAATT
Found at i:21508598 original size:33 final size:36
Alignment explanation
Indices: 21508561--21508636 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 36
21508551 TAACCTAGTT
*
21508561 ATGGTCTTTTCA-TTAAA-ATGC-CATAGCCCAACC
1 ATGGTCTTTACATTTAAACATGCTCATAGCCCAACC
* * *
21508594 ATGGTC-TTACATTTAAACATTCTCATAGTCCAACG
1 ATGGTCTTTACATTTAAACATGCTCATAGCCCAACC
21508629 ATGGTCTT
1 ATGGTCTT
21508637 ATTCGTCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 4 0.11
33 11 0.31
34 3 0.09
35 16 0.46
36 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (36 bp):
ATGGTCTTTACATTTAAACATGCTCATAGCCCAACC
Found at i:21523499 original size:39 final size:40
Alignment explanation
Indices: 21523414--21523501 Score: 99
Period size: 39 Copynumber: 2.2 Consensus size: 40
21523404 AAAAGTATTT
*
21523414 ATATTAAAAAAATCAACCATAAATATAATAAATGTCTTATT
1 ATATTAAAAAAATCAA-CATAAATATAATAAATGTCTTATG
* * *
21523455 ATATTAAAAAACAT-AA-ATAAATATAATAACTTTTTTATG
1 ATATTAAAAAA-ATCAACATAAATATAATAAATGTCTTATG
*
21523494 GTATTAAA
1 ATATTAAA
21523502 TATAATTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 26 0.63
41 13 0.32
42 2 0.05
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.36
Consensus pattern (40 bp):
ATATTAAAAAAATCAACATAAATATAATAAATGTCTTATG
Found at i:21524483 original size:6 final size:7
Alignment explanation
Indices: 21524467--21524492 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
21524457 AATAAAACGA
21524467 TTTTTCT
1 TTTTTCT
21524474 TTTTTCT
1 TTTTTCT
21524481 TTTTTCT
1 TTTTTCT
21524488 TTTTT
1 TTTTT
21524493 TGTTTCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:21526779 original size:9 final size:9
Alignment explanation
Indices: 21526765--21526813 Score: 73
Period size: 9 Copynumber: 5.4 Consensus size: 9
21526755 TTAATTTTAT
*
21526765 TTTTTATAA
1 TTTTTACAA
21526774 TTTTTACAA
1 TTTTTACAA
21526783 TTTTTTACAA
1 -TTTTTACAA
21526793 -TTTTACAA
1 TTTTTACAA
21526801 TTTTTACAA
1 TTTTTACAA
21526810 TTTT
1 TTTT
21526814 AAATTATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 8 0.22
9 20 0.54
10 9 0.24
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTTACAA
Found at i:21526785 original size:19 final size:18
Alignment explanation
Indices: 21526763--21526818 Score: 80
Period size: 17 Copynumber: 3.2 Consensus size: 18
21526753 TTTTAATTTT
*
21526763 ATTTTTTATAATTTTTACA
1 ATTTTTTACAA-TTTTACA
21526782 ATTTTTTACAATTTTACA
1 ATTTTTTACAATTTTACA
21526800 A-TTTTTACAATTTTA-A
1 ATTTTTTACAATTTTACA
21526816 ATT
1 ATT
21526819 ATTATATTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
16 2 0.06
17 15 0.43
18 8 0.23
19 10 0.29
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTTTACAATTTTACA
Found at i:21526786 original size:8 final size:8
Alignment explanation
Indices: 21526775--21526818 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
21526765 TTTTTATAAT
21526775 TTTTACAA
1 TTTTACAA
21526783 TTTTTTACAA
1 --TTTTACAA
21526793 TTTTACAA
1 TTTTACAA
21526801 TTTTTACAA
1 -TTTTACAA
21526810 TTTTA-AA
1 TTTTACAA
21526817 TT
1 TT
21526819 ATTATATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 4 0.12
8 13 0.39
9 8 0.24
10 8 0.24
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTTACAA
Found at i:21526832 original size:21 final size:20
Alignment explanation
Indices: 21526807--21526861 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
21526797 ACAATTTTTA
21526807 CAATTTTAAATTATT-ATATT
1 CAATTTTAAATTATTCATA-T
*
21526827 CAAATTATTATA-TATTGCATAT
1 C-AATT-TTAAATTATT-CATAT
21526849 CAATTTTAAATTA
1 CAATTTTAAATTA
21526862 ATAATCCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
20 5 0.18
21 14 0.50
22 6 0.21
23 3 0.11
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (20 bp):
CAATTTTAAATTATTCATAT
Found at i:21527052 original size:75 final size:79
Alignment explanation
Indices: 21526910--21527059 Score: 209
Period size: 82 Copynumber: 1.9 Consensus size: 79
21526900 TATAAAGAAC
* * *
21526910 TTATTTAATATATAAATTAAAAAGCACTAATTAATCCAAATCTTAAACCCTAACCCGACCCCAAA
1 TTATTTAATATATAAATTAAAAAGCACTAATTAATCCAAACCCTAAACCATAA--C-ACCCCAAA
21526975 TCCCTAACCCCTAAACT
63 TCCCTAACCCCTAAACT
*
21526992 TTATTTAATATATAAATTAAAAAGCACTAATTAATCTAAACCCTAAACCAT-A-A-CCC-AATCC
1 TTATTTAATATATAAATTAAAAAGCACTAATTAATCCAAACCCTAAACCATAACACCCCAAATCC
21527053 CTAACCC
66 CTAACCC
21527060 TTAACCCTTA
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
75 12 0.19
76 3 0.05
77 1 0.02
81 1 0.02
82 47 0.73
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.27
Consensus pattern (79 bp):
TTATTTAATATATAAATTAAAAAGCACTAATTAATCCAAACCCTAAACCATAACACCCCAAATCC
CTAACCCCTAAACT
Found at i:21527073 original size:14 final size:14
Alignment explanation
Indices: 21527051--21527090 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
21527041 ATAACCCAAT
21527051 CCCTAACCCTTAAC
1 CCCTAACCCTTAAC
* *
21527065 CCTTAACCCCTAAC
1 CCCTAACCCTTAAC
*
21527079 CCCTAAACCTTA
1 CCCTAACCCTTA
21527091 TTTAATATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.47, G:0.00, T:0.23
Consensus pattern (14 bp):
CCCTAACCCTTAAC
Found at i:21527077 original size:21 final size:21
Alignment explanation
Indices: 21527051--21527090 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21527041 ATAACCCAAT
* *
21527051 CCCTAACCCTTAACCCTTAAC
1 CCCTAACCCCTAAACCTTAAC
21527072 CCCTAACCCCTAAACCTTA
1 CCCTAACCCCTAAACCTTA
21527091 TTTAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.47, G:0.00, T:0.23
Consensus pattern (21 bp):
CCCTAACCCCTAAACCTTAAC
Found at i:21527087 original size:8 final size:7
Alignment explanation
Indices: 21527051--21527084 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
21527041 ATAACCCAAT
21527051 CCCTAAC
1 CCCTAAC
*
21527058 CCTTAAC
1 CCCTAAC
*
21527065 CCTTAAC
1 CCCTAAC
21527072 CCCTAAC
1 CCCTAAC
21527079 CCCTAA
1 CCCTAA
21527085 ACCTTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.29, C:0.50, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCTAAC
Found at i:21527194 original size:7 final size:7
Alignment explanation
Indices: 21527184--21527221 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
21527174 CTCTTAACAT
21527184 CTAACCC
1 CTAACCC
21527191 CTAA--C
1 CTAACCC
21527196 CTAACCC
1 CTAACCC
21527203 CTAACCC
1 CTAACCC
21527210 CTAACCC
1 CTAACCC
21527217 CTAAC
1 CTAAC
21527222 TCTTAACCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
7 24 0.83
ACGTcount: A:0.32, C:0.53, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAACCC
Found at i:21527195 original size:14 final size:13
Alignment explanation
Indices: 21527178--21527230 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 13
21527168 CCCTAACTCT
21527178 TAACATCTAACCCC
1 TAAC-TCTAACCCC
21527192 TAAC-CTAACCCC
1 TAACTCTAACCCC
*
21527204 TAACCCCTAACCCC
1 TAA-CTCTAACCCC
21527218 TAACTCTTAACCC
1 TAACTC-TAACCC
21527231 ATAAACCTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
12 11 0.31
13 3 0.09
14 21 0.60
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (13 bp):
TAACTCTAACCCC
Found at i:21527207 original size:26 final size:26
Alignment explanation
Indices: 21527169--21527238 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
21527159 ACCCTAAATC
* * *
21527169 CCTAACTCTTAACATCTAACCCCTAA
1 CCTAACCCCTAACACCTAACCCCTAA
*
21527195 CCTAACCCCTAACCCCTAACCCCTAA
1 CCTAACCCCTAACACCTAACCCCTAA
*
21527221 CTCTTAACCCATAA-ACCT
1 C-C-TAACCCCTAACACCT
21527239 TAAATCACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 23 0.64
27 4 0.11
28 9 0.25
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.23
Consensus pattern (26 bp):
CCTAACCCCTAACACCTAACCCCTAA
Found at i:21527240 original size:14 final size:14
Alignment explanation
Indices: 21527185--21527241 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
21527175 TCTTAACATC
21527185 TAACCCCT-AACC-
1 TAACCCCTAAACCT
* *
21527197 TAACCCCTAACCCC
1 TAACCCCTAAACCT
21527211 TAACCCCT-AACTCT
1 TAACCCCTAAAC-CT
*
21527225 TAACCCATAAACCT
1 TAACCCCTAAACCT
21527239 TAA
1 TAA
21527242 ATCACATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 8 0.22
13 5 0.14
14 21 0.57
15 3 0.08
ACGTcount: A:0.35, C:0.44, G:0.00, T:0.21
Consensus pattern (14 bp):
TAACCCCTAAACCT
Found at i:21527286 original size:14 final size:15
Alignment explanation
Indices: 21527264--21527297 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
21527254 CTTAAACCAG
*
21527264 AATCCCTAA-TCCAT
1 AATCTCTAATTCCAT
21527278 AATCTCTAATTCCAT
1 AATCTCTAATTCCAT
21527293 AATCT
1 AATCT
21527298 ATAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Found at i:21527373 original size:20 final size:21
Alignment explanation
Indices: 21527348--21527391 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
21527338 CTAATTAATT
*
21527348 AACCATATATA-TATACCCTA
1 AACCATATATATTAAACCCTA
*
21527368 AACCATATTTATTAAACCCTA
1 AACCATATATATTAAACCCTA
21527389 AAC
1 AAC
21527392 TATAATGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (21 bp):
AACCATATATATTAAACCCTA
Found at i:21528815 original size:18 final size:18
Alignment explanation
Indices: 21528794--21528860 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 18
21528784 TGTCATAAAA
21528794 ATATTATATTAATTATAT
1 ATATTATATTAATTATAT
*
21528812 ATATTAAATAATAATTATAT
1 ATATT--ATATTAATTATAT
21528832 ATATTTATATTTATATT-TAT
1 ATA-TTATA-TTA-ATTATAT
21528852 AT-TTATATT
1 ATATTATATT
21528861 TATATTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
17 2 0.05
18 10 0.24
19 3 0.07
20 22 0.52
21 5 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTATATTAATTATAT
Found at i:21528842 original size:6 final size:6
Alignment explanation
Indices: 21528831--21528866 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
21528821 AATAATTATA
21528831 TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT
21528867 AAATTACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:21539127 original size:2 final size:2
Alignment explanation
Indices: 21539120--21539149 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21539110 AATTTCTTAA
*
21539120 AT AT AT AT AC 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
21539150 TTGTAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21539842 original size:15 final size:15
Alignment explanation
Indices: 21539822--21539887 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
21539812 ACTACAAAAC
21539822 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
21539837 ATTTATAATTGCAATAAAT
1 ATTTATTATT--AAT--AT
*
21539856 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
21539871 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
21539884 ATTT
1 ATTT
21539888 TCAATAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 12 0.29
17 5 0.12
19 11 0.26
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:21540064 original size:33 final size:31
Alignment explanation
Indices: 21540004--21540065 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 31
21539994 AATCATATTG
*
21540004 AAAAATAAAATATTTTAAATATTTTAATAAT
1 AAAAATAAAATATTTTAAATATATTAATAAT
21540035 AAAAATAAAAT-TTATTATTAATATATTAATA
1 AAAAATAAAATATT-TTA--AATATATTAATA
21540066 TTAAGCTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 2 0.07
31 14 0.52
33 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
AAAAATAAAATATTTTAAATATATTAATAAT
Found at i:21541362 original size:2 final size:2
Alignment explanation
Indices: 21541355--21541434 Score: 108
Period size: 2 Copynumber: 40.0 Consensus size: 2
21541345 TTGAGTATTT
21541355 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
21541397 TA TA TA TA TGA -A TG GA TT TA TA TT TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21541435 AGGTTATCAT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.01
2 66 0.97
3 1 0.01
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21547752 original size:63 final size:63
Alignment explanation
Indices: 21547653--21547789 Score: 265
Period size: 63 Copynumber: 2.2 Consensus size: 63
21547643 GACTTCAGGT
*
21547653 ATTATTTTGTAAAATATCTATGCCCTCAAGCAAGCTTCCAATCATTCAAAAGTTAACTGAGGA
1 ATTATTTTGTAAAATATCTATGCCCTCAAGCAAGCTTCCAATCATTCAAAAGTTAACAGAGGA
21547716 ATTATTTTGTAAAATATCTATGCCCTCAAGCAAGCTTCCAATCATTCAAAAGTTAACAGAGGA
1 ATTATTTTGTAAAATATCTATGCCCTCAAGCAAGCTTCCAATCATTCAAAAGTTAACAGAGGA
21547779 ATTATTTTGTA
1 ATTATTTTGTA
21547790 GTTTTCTCCT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 73 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (63 bp):
ATTATTTTGTAAAATATCTATGCCCTCAAGCAAGCTTCCAATCATTCAAAAGTTAACAGAGGA
Found at i:21553487 original size:20 final size:19
Alignment explanation
Indices: 21553464--21553505 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
21553454 ATTTTTAGTG
21553464 TATA-TAAAATTGATTTTGAT
1 TATACTAAAATT-ATTTTG-T
*
21553484 TATACTAACATTATTTTGT
1 TATACTAAAATTATTTTGT
21553503 TAT
1 TAT
21553506 TGTTGTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 10 0.50
21 6 0.30
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (19 bp):
TATACTAAAATTATTTTGT
Found at i:21556793 original size:13 final size:11
Alignment explanation
Indices: 21556764--21556829 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
21556754 TATTTTTTAA
21556764 TTTTAAAATAC
1 TTTTAAAATAC
21556775 TTTTAAAATAC
1 TTTTAAAATAC
21556786 TTTTTTAAAAT--
1 --TTTTAAAATAC
*
21556797 TTCT-AAA-A-
1 TTTTAAAATAC
*
21556805 TTTTAAAAT-T
1 TTTTAAAATAC
21556815 TTTTAAAATAC
1 TTTTAAAATAC
21556826 TTTT
1 TTTT
21556830 TTAATTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
8 6 0.13
9 6 0.13
10 9 0.20
11 15 0.33
13 9 0.20
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:21556836 original size:29 final size:27
Alignment explanation
Indices: 21556803--21556865 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
21556793 AAATTTCTAA
21556803 AATTTTAAAATTTTTTAAAATACTTTTTT
1 AATTTTAAAA--TTTTAAAATACTTTTTT
** *
21556832 AATTTTTTTAATTTTAAATTACTTTTTT
1 AA-TTTTAAAATTTTAAAATACTTTTTT
21556860 AATTTT
1 AATTTT
21556866 TGTTTTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 4 0.13
28 18 0.60
29 2 0.07
30 6 0.20
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (27 bp):
AATTTTAAAATTTTAAAATACTTTTTT
Found at i:21556854 original size:28 final size:30
Alignment explanation
Indices: 21556815--21556883 Score: 106
Period size: 28 Copynumber: 2.3 Consensus size: 30
21556805 TTTTAAAATT
21556815 TTTTAAAATACTTTTTTAA-TTT-TTTTAA
1 TTTTAAAATACTTTTTTAATTTTGTTTTAA
*
21556843 TTTTAAATTACTTTTTTAATTTTTGTTTTAA
1 TTTTAAAATACTTTTTTAA-TTTTGTTTTAA
21556874 TTTTAAAATA
1 TTTTAAAATA
21556884 AAATTTTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 18 0.50
30 3 0.08
31 15 0.42
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (30 bp):
TTTTAAAATACTTTTTTAATTTTGTTTTAA
Found at i:21556858 original size:40 final size:39
Alignment explanation
Indices: 21556749--21556858 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 39
21556739 ATTTTTATTA
21556749 TTTTTT-A-TTTTTTAATTTTAAAATAC-TTTTAAAATAC
1 TTTTTTAATTTTTTTAATTTT-AAATACTTTTTAAAATAC
* ** *
21556786 TTTTTTAAAATTTCTAAAATTTTAAA-ATTTTTTAAAATAC
1 TTTTTT--AATTTTTTTAATTTTAAATACTTTTTAAAATAC
21556826 TTTTTTAATTTTTTTAATTTTAAATTACTTTTT
1 TTTTTTAATTTTTTTAATTTTAAA-TACTTTTT
21556859 TAATTTTTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
37 6 0.10
38 15 0.26
39 1 0.02
40 27 0.47
41 9 0.16
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.61
Consensus pattern (39 bp):
TTTTTTAATTTTTTTAATTTTAAATACTTTTTAAAATAC
Found at i:21565252 original size:42 final size:43
Alignment explanation
Indices: 21565200--21565280 Score: 146
Period size: 42 Copynumber: 1.9 Consensus size: 43
21565190 TTTACAAGTC
*
21565200 ACACGGCTTGGACACATGCCCGTGTCCT-TGCTCGTGTGGTTT
1 ACACGACTTGGACACATGCCCGTGTCCTCTGCTCGTGTGGTTT
21565242 ACACGACTTGGACACATGCCCGTGTCCTCTGCTCGTGTG
1 ACACGACTTGGACACATGCCCGTGTCCTCTGCTCGTGTG
21565281 TCTCACACGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
42 27 0.73
43 10 0.27
ACGTcount: A:0.14, C:0.31, G:0.27, T:0.28
Consensus pattern (43 bp):
ACACGACTTGGACACATGCCCGTGTCCTCTGCTCGTGTGGTTT
Found at i:21565311 original size:43 final size:42
Alignment explanation
Indices: 21565198--21565291 Score: 145
Period size: 42 Copynumber: 2.2 Consensus size: 42
21565188 AATTTACAAG
21565198 TCACACGGCTTGGACACATGCCCGTGTCCTTGCTCGTGTGGT
1 TCACACGGCTTGGACACATGCCCGTGTCCTTGCTCGTGTGGT
* *
21565240 TTACACGACTTGGACACATGCCCGTGTCCTCTGCTCGTGT-GT
1 TCACACGGCTTGGACACATGCCCGTGTCCT-TGCTCGTGTGGT
21565282 CTCACACGGC
1 -TCACACGGC
21565292 CTAGGCACAC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
42 30 0.65
43 16 0.35
ACGTcount: A:0.14, C:0.33, G:0.26, T:0.28
Consensus pattern (42 bp):
TCACACGGCTTGGACACATGCCCGTGTCCTTGCTCGTGTGGT
Found at i:21571266 original size:24 final size:25
Alignment explanation
Indices: 21571213--21571260 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
21571203 TTGGCCCTCT
* *
21571213 CGAGCTTCCTGTTATATAGTTCTTG
1 CGAGCTTCCCGTTATATAGCTCTTG
21571238 CGAGCTTCCCGTTA-ATAGCTCTT
1 CGAGCTTCCCGTTATATAGCTCTT
21571261 CGGAGCATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.40
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATAGCTCTTG
Found at i:21573858 original size:26 final size:26
Alignment explanation
Indices: 21573829--21573886 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
21573819 CCTGTTATTT
21573829 GGCTCTTCGTGAGCTT-CTCAATTAAA
1 GGCTCTTCGTGAGCTTCCT-AATTAAA
* *
21573855 GGCTCTTTGTGAGCTTCCTAATTAAT
1 GGCTCTTCGTGAGCTTCCTAATTAAA
21573881 GGCTCT
1 GGCTCT
21573887 CCGAAGCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 27 0.93
27 2 0.07
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCTAATTAAA
Found at i:21574017 original size:73 final size:73
Alignment explanation
Indices: 21573865--21574002 Score: 188
Period size: 73 Copynumber: 1.9 Consensus size: 73
21573855 GGCTCTTTGT
* * *
21573865 GAGCTTCCTAATTAATGGCTCTCCGAAGCTTCCCGATATGACTTGCTTGAACTTCCCGATATATG
1 GAGCTTCCTAATTAATGGCTCTCCGAAGCTACCCGATATGACTCGCATGAACTTCCCGATATATG
21573930 ACTATTCA
66 ACTATTCA
** * * *
21573938 GAGCTTCCTAATTAATGGCTCTTTGAAGCTACCCGTTATTGGCTCGCATGAGCTTCCCGAT-TAT
1 GAGCTTCCTAATTAATGGCTCTCCGAAGCTACCCGATA-TGACTCGCATGAACTTCCCGATATAT
21574002 G
65 G
21574003 GCTTTTATTA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 38 0.68
74 18 0.32
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.33
Consensus pattern (73 bp):
GAGCTTCCTAATTAATGGCTCTCCGAAGCTACCCGATATGACTCGCATGAACTTCCCGATATATG
ACTATTCA
Found at i:21581495 original size:23 final size:22
Alignment explanation
Indices: 21581452--21581496 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
21581442 GTTAAATTGA
* **
21581452 ATTGTATGTATGTGATTGTATT
1 ATTGTATGTATATGAAAGTATT
21581474 ATTGTCATGTATATGAAAGTATT
1 ATTGT-ATGTATATGAAAGTATT
21581497 CACATATCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (22 bp):
ATTGTATGTATATGAAAGTATT
Found at i:21581689 original size:24 final size:25
Alignment explanation
Indices: 21581643--21581689 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
21581633 TAGCCTTTTT
** *
21581643 GAGCTTCTTGTTATATAGTTCTTGC
1 GAGCTTCCCGTTATATAGCTCTTGC
21581668 GAGCTTCCCGTTA-ATAGCTCTT
1 GAGCTTCCCGTTATATAGCTCTT
21581690 TGGAGCATCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTGC
Found at i:21581695 original size:24 final size:24
Alignment explanation
Indices: 21581619--21581695 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
21581609 CAGCTCGAAA
* * *
21581619 GAGCGTCCCGTTACTAGC-CTTTTT
1 GAGCTTCCCGTTAATAGCTC-TTTG
** *
21581643 GAGCTTCTTGTTATATAGTTC-TTG
1 GAGCTTCCCGTTA-ATAGCTCTTTG
21581667 CGAGCTTCCCGTTAATAGCTCTTTG
1 -GAGCTTCCCGTTAATAGCTCTTTG
21581692 GAGC
1 GAGC
21581696 ATCCTAATTA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
24 22 0.55
25 17 0.43
26 1 0.03
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.39
Consensus pattern (24 bp):
GAGCTTCCCGTTAATAGCTCTTTG
Found at i:21581837 original size:25 final size:25
Alignment explanation
Indices: 21581800--21581847 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
21581790 GGATTTTTGT
*
21581800 GAGCTTCCTAATTAATGGCTCTTCA
1 GAGCTTCCCAATTAATGGCTCTTCA
21581825 GAGCTTCCCAATTAATGGCTCTT
1 GAGCTTCCCAATTAATGGCTCTT
21581848 AGGATCTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (25 bp):
GAGCTTCCCAATTAATGGCTCTTCA
Found at i:21590894 original size:3 final size:3
Alignment explanation
Indices: 21590886--21590913 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
21590876 TACTATTGCT
21590886 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
21590914 CTGCTGCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:21604020 original size:32 final size:32
Alignment explanation
Indices: 21603973--21604041 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
21603963 ATATTAAAAA
* * * * *
21603973 TGAACCTAGACAAATGGTTGTCTAGATATATC
1 TGAATCTAGACAAATGATTATCCAAATATATC
*
21604005 TGAATCTAGATAAATGATTATCCAAATATATC
1 TGAATCTAGACAAATGATTATCCAAATATATC
21604037 TGAAT
1 TGAAT
21604042 TTGGACACTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (32 bp):
TGAATCTAGACAAATGATTATCCAAATATATC
Found at i:21604739 original size:23 final size:23
Alignment explanation
Indices: 21604713--21604781 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
21604703 TGATTTTTAA
21604713 ATTTTGAATTATTTAGTGATAAT
1 ATTTTGAATTATTTAGTGATAAT
*
21604736 ATTTAGAATTATTTAGTGATAAT
1 ATTTTGAATTATTTAGTGATAAT
*
21604759 A-TTTAAGATTATTTAGTGATAAT
1 ATTTTGA-ATTATTTAGTGATAAT
21604782 CTTAGAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
22 3 0.07
23 39 0.93
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (23 bp):
ATTTTGAATTATTTAGTGATAAT
Found at i:21605688 original size:25 final size:23
Alignment explanation
Indices: 21605643--21605707 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
21605633 TTATTTATCC
* *
21605643 ATTTATTTTATTTTCTATTTTTGA
1 ATTT-TTTTATTTTATTTTTTTGA
*
21605667 ATTTGTTTTTATTTTATTTTTTTGT
1 A-TT-TTTTTATTTTATTTTTTTGA
*
21605692 ATTTTCTTATTTTATT
1 ATTTTTTTATTTTATT
21605708 ATCTTAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 12 0.34
24 3 0.09
25 19 0.54
26 1 0.03
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (23 bp):
ATTTTTTTATTTTATTTTTTTGA
Found at i:21609279 original size:44 final size:44
Alignment explanation
Indices: 21609096--21609289 Score: 161
Period size: 43 Copynumber: 4.5 Consensus size: 44
21609086 ATATCTCGGA
* ** * *
21609096 TATGGTCTTACATGTTATCAC-ATATCGGTGCCAATAGCCCA-AC
1 TATGGTCTTACACGAAATCACTATAACGATGCC-ATAGCCCAGAC
21609139 TATGGTCTTACACGAAATCAC-ATAACGATGCCA-ATGTCCCAGAC
1 TATGGTCTTACACGAAATCACTATAACGATGCCATA-G-CCCAGAC
* * * * *
21609183 -ATGGTCTTACACGTAATCACATATATCAATGTCATATCCCAGA-
1 TATGGTCTTACACGAAATCAC-TATAACGATGCCATAGCCCAGAC
*
21609226 TATGGTCTTACAC-AAAGTCTCGTATAACGATGCCATAGCCCA-AC
1 TATGGTCTTACACGAAA-TCAC-TATAACGATGCCATAGCCCAGAC
* *
21609270 TATGATCTTATACGAAATCA
1 TATGGTCTTACACGAAATCA
21609290 TGTAATGCCA
Statistics
Matches: 121, Mismatches: 20, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 53 0.44
44 52 0.43
45 12 0.10
46 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (44 bp):
TATGGTCTTACACGAAATCACTATAACGATGCCATAGCCCAGAC
Found at i:21620154 original size:24 final size:24
Alignment explanation
Indices: 21620122--21620170 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
21620112 TTTGATTTTG
21620122 TAAGTGTCGAAATCCAAGACTGCC
1 TAAGTGTCGAAATCCAAGACTGCC
21620146 TAAGTGTCGAAATCCAAGACTGCC
1 TAAGTGTCGAAATCCAAGACTGCC
21620170 T
1 T
21620171 TGAAACTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (24 bp):
TAAGTGTCGAAATCCAAGACTGCC
Found at i:21626499 original size:15 final size:16
Alignment explanation
Indices: 21626479--21626512 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21626469 TCTTATGAAT
21626479 TTTATA-ATTTTAAAA
1 TTTATATATTTTAAAA
*
21626494 TTTATATATTTTAATA
1 TTTATATATTTTAAAA
21626510 TTT
1 TTT
21626513 CAAATAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATATATTTTAAAA
Found at i:21633351 original size:29 final size:29
Alignment explanation
Indices: 21633290--21633351 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 29
21633280 TAACAAGGGT
* **
21633290 TCAAAAGGACACTCTCACTATCAGTTCTA
1 TCAAAAAGACACTCTCACTATCAGTTAAA
21633319 -CAAAAAGACACTCTCACTATCAGTTAAA
1 TCAAAAAGACACTCTCACTATCAGTTAAA
21633347 TCAAA
1 TCAAA
21633352 TAATACTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.24
Consensus pattern (29 bp):
TCAAAAAGACACTCTCACTATCAGTTAAA
Found at i:21633908 original size:6 final size:6
Alignment explanation
Indices: 21633869--21633907 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
21633859 ATTAACAACA
21633869 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT- AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
21633908 AAGCAACAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.72, C:0.13, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:21634162 original size:7 final size:7
Alignment explanation
Indices: 21634150--21634191 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
21634140 CAGATGCACG
21634150 GGGAAAT
1 GGGAAAT
21634157 GGGAAAT
1 GGGAAAT
*
21634164 GGGGAA-
1 GGGAAAT
21634170 GGGAAAT
1 GGGAAAT
21634177 GGGAAAT
1 GGGAAAT
21634184 GGGAAAT
1 GGGAAAT
21634191 G
1 G
21634192 TATTTTAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.40, C:0.00, G:0.48, T:0.12
Consensus pattern (7 bp):
GGGAAAT
Found at i:21635901 original size:26 final size:26
Alignment explanation
Indices: 21635871--21635928 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
21635861 TTTACATGAA
21635871 AGAATATCTAATGGTTACCATGAGAT
1 AGAATATCTAATGGTTACCATGAGAT
21635897 AGAATATCTAATGGTTACCATGAGAT
1 AGAATATCTAATGGTTACCATGAGAT
*
21635923 AAAATA
1 AGAATA
21635929 GAATCATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.29
Consensus pattern (26 bp):
AGAATATCTAATGGTTACCATGAGAT
Found at i:21641172 original size:68 final size:70
Alignment explanation
Indices: 21641098--21641229 Score: 214
Period size: 68 Copynumber: 1.9 Consensus size: 70
21641088 TATTAAAAAA
* * * *
21641098 TATATTAAAATTTTAAATTTGGTTATACTTAA-ATTTT-TTTAATATGTTTAAAATTTTAATATA
1 TATATTAAAAATTTAAAATTGGTTATACTCAACATTTTCTTTAACATGTTTAAAATTTTAATATA
21641161 TTAAG
66 TTAAG
21641166 TATATTAAAAATTTAAAATTGGTTATACTCAACATTTTCTTTAACATGTTTAAAATTTTAATAT
1 TATATTAAAAATTTAAAATTGGTTATACTCAACATTTTCTTTAACATGTTTAAAATTTTAATAT
21641230 TTTTACATAT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 29 0.50
69 5 0.09
70 24 0.41
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (70 bp):
TATATTAAAAATTTAAAATTGGTTATACTCAACATTTTCTTTAACATGTTTAAAATTTTAATATA
TTAAG
Found at i:21641243 original size:18 final size:18
Alignment explanation
Indices: 21641217--21641263 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
21641207 TAACATGTTT
*
21641217 AAAATTTTAATATTTTTA
1 AAAATTTTAAAATTTTTA
* *
21641235 CATATTTTAAAATTTTTA
1 AAAATTTTAAAATTTTTA
21641253 AAAATTTTAAA
1 AAAATTTTAAA
21641264 TATATTAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATTTTAAAATTTTTA
Found at i:21641247 original size:70 final size:66
Alignment explanation
Indices: 21641096--21641249 Score: 191
Period size: 70 Copynumber: 2.2 Consensus size: 66
21641086 CCTATTAAAA
* * * *
21641096 AATATATTAAAATTTTAAATTTGGTTATACTTAAATTTTTTTAATATGTTTAAAATTTTAATATA
1 AATATTTTAAAA-TTTAAAATTGGTTATACTCAAATTTTTTTAACATGTTTAAAATTTTAATATA
21641161 TT
65 TT
*
21641163 AAGTATATTAAAAATTTAAAATTGGTTATACTCAACATTTTCTTTAACATGTTTAAAATTTTAAT
1 AA-TAT-TTTAAAATTTAAAATTGGTTATACTCAA-ATTTT-TTTAACATGTTTAAAATTTTAAT
*
21641228 ATTTTT
62 A-TATT
21641234 ACATATTTTAAAATTT
1 A-ATATTTTAAAATTT
21641250 TTAAAAATTT
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
67 2 0.03
68 22 0.30
69 10 0.14
70 32 0.43
71 7 0.09
72 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (66 bp):
AATATTTTAAAATTTAAAATTGGTTATACTCAAATTTTTTTAACATGTTTAAAATTTTAATATAT
T
Found at i:21641256 original size:10 final size:9
Alignment explanation
Indices: 21641214--21641263 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
21641204 CTTTAACATG
21641214 TTTAAAA-T
1 TTTAAAATT
*
21641222 TTTAATATT
1 TTTAAAATT
*
21641231 TTT-ACATAT
1 TTTAAAAT-T
21641240 TTTAAAATT
1 TTTAAAATT
*
21641249 TTTAAAAAT
1 TTTAAAATT
21641258 TTTAAA
1 TTTAAA
21641264 TATATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 9 0.26
9 23 0.66
10 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (9 bp):
TTTAAAATT
Found at i:21641260 original size:27 final size:26
Alignment explanation
Indices: 21641214--21641273 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
21641204 CTTTAACATG
* * *
21641214 TTTAAAATTTTAATATTTTTACATAT
1 TTTAAAATTTTAAAAATTTTAAATAT
21641240 TTTAAAATTTTTAAAAATTTTAAATAT
1 TTTAAAA-TTTTAAAAATTTTAAATAT
*
21641267 ATTAAAA
1 TTTAAAA
21641274 AAATTTCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTAAAATTTTAAAAATTTTAAATAT
Found at i:21641404 original size:18 final size:18
Alignment explanation
Indices: 21641381--21641432 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
21641371 TATACTTAAC
21641381 ATTTTTTAAATATATTTA
1 ATTTTTTAAATATATTTA
* *
21641399 ATTTTTTTAAGT-TTTTTA
1 A-TTTTTTAAATATATTTA
**
21641417 AAATTTTAAATATATT
1 ATTTTTTAAATATATT
21641433 AAGAAAACCT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
17 7 0.27
18 10 0.38
19 9 0.35
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTTTTAAATATATTTA
Found at i:21641518 original size:18 final size:17
Alignment explanation
Indices: 21641472--21641510 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
21641462 AAAATATATA
*
21641472 TTAAGTATATTAAAATT
1 TTAAATATATTAAAATT
21641489 TTAAATATATTAAAATT
1 TTAAATATATTAAAATT
21641506 TTAAA
1 TTAAA
21641511 ATGAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAATATATTAAAATT
Found at i:21642701 original size:19 final size:19
Alignment explanation
Indices: 21642677--21642735 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
21642667 TCTAATTAAG
*
21642677 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTCATT
* *
21642696 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTCATT
21642714 TAATAACTCTATTTTCATT
1 TAATAACTCTATTTTCATT
21642733 TAA
1 TAA
21642736 AATATAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAACTCTATTTTCATT
Found at i:21642986 original size:29 final size:28
Alignment explanation
Indices: 21642921--21642989 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
21642911 TAAGGGAATA
*
21642921 TATTAAA-TTTATAAAATTAAAATAGTT
1 TATTAAATTTTATAAAATTAAAATAGGT
* * *
21642948 TAATTTAATTTTTTTAAATTAAAATAGAGT
1 T-ATTAAATTTTATAAAATTAAAATAG-GT
21642978 TATTAAATTTTA
1 TATTAAATTTTA
21642990 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 1 0.03
28 5 0.15
29 25 0.76
30 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
TATTAAATTTTATAAAATTAAAATAGGT
Found at i:21650505 original size:106 final size:106
Alignment explanation
Indices: 21650313--21650525 Score: 374
Period size: 106 Copynumber: 2.0 Consensus size: 106
21650303 AAAAAAAGAG
21650313 ACAGAATTTGAGCTTTTGAATGAATGAAACAAAAATGACAGTTTAATGATACACTCATAAACTCT
1 ACAGAATTTGAGCTTTTGAATGAATGAAACAAAAATGACAGTTTAATGATACACTCATAAACTCT
*
21650378 ATACAAGATGGAAACCCCCCCCCCCCCCCCCCCAAGAAAAT
66 ATACAAGATGGAAACCCCCCCCCCCCTCCCCCCAAGAAAAT
21650419 ACAGAATTTGAGCTTTTGAATGAATGAAACAAAAATGACAAAGTTTAATGATACACTCATAAACT
1 ACAGAATTTGAGCTTTTGAATGAATGAAACAAAAATGAC--AGTTTAATGATACACTCATAAACT
* *
21650484 GTATACAAGATGGAAA-TCCCCCCCCCCTCCCCCCAAGAAAAT
64 CTATACAAGATGGAAACCCCCCCCCCCCTCCCCCCAAGAAAAT
21650526 TTGGGCACAG
Statistics
Matches: 102, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
106 39 0.38
107 24 0.24
108 39 0.38
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.22
Consensus pattern (106 bp):
ACAGAATTTGAGCTTTTGAATGAATGAAACAAAAATGACAGTTTAATGATACACTCATAAACTCT
ATACAAGATGGAAACCCCCCCCCCCCTCCCCCCAAGAAAAT
Found at i:21652967 original size:29 final size:30
Alignment explanation
Indices: 21652921--21652995 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
21652911 TGTAATTTTT
* *
21652921 TATATTTTTATAATTTTTAG-AGGATT-AAA
1 TATAATTTTATCATTTTT-GTAGGATTAAAA
* * *
21652950 TCTAATTTTATCATTTTTGTGGGGTTAAAA
1 TATAATTTTATCATTTTTGTAGGATTAAAA
21652980 TATAATTTTATCATTT
1 TATAATTTTATCATTT
21652996 CTAATTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 1 0.03
29 19 0.50
30 18 0.47
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (30 bp):
TATAATTTTATCATTTTTGTAGGATTAAAA
Found at i:21654420 original size:3 final size:3
Alignment explanation
Indices: 21654414--21654450 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
21654404 ACTTAAATTT
21654414 ATA ATA 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
21654451 ACCTTCCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:21655330 original size:109 final size:109
Alignment explanation
Indices: 21654964--21655395 Score: 663
Period size: 109 Copynumber: 4.0 Consensus size: 109
21654954 GAAATTCGAG
* * * * * *
21654964 AGGATATTTGGCTATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGTACG-TTCCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* *
21655026 AAATTTCCAAACGCAAAACATTGGCTTATTTTGAAAATTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTTAAA
* * *
21655070 AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTT
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* *
21655135 GAATTTCTCAAACGTAAAACATTGCCTTATTTTAAAAAATTTTAAA
66 GAATTTC-CAAACGCAAAACATTGCCTTATTTT-GAAAATTTTAAA
* *
21655181 AGGATATTAAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
*
21655246 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTTAAA
* *
21655290 AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
21655355 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTT
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTT
21655396 CCTTTTGAAG
Statistics
Matches: 297, Mismatches: 24, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
106 24 0.08
108 25 0.08
109 121 0.41
110 47 0.16
111 80 0.27
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (109 bp):
AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTTAAA
Found at i:21655344 original size:220 final size:215
Alignment explanation
Indices: 21654977--21655395 Score: 676
Period size: 220 Copynumber: 1.9 Consensus size: 215
21654967 ATATTTGGCT
*
21654977 ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGTACGTTCCTCAAATTTCCAAACGCAA
1 ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCAAATTTCCAAACGCAA
*
21655042 AACATTGGCTTATTTTGAAAATTTTAAAAGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGA
66 AACATTGCCTTATTTTGAAAATTTTAAAAGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGA
* * * *
21655107 CACCCAGCACCTTAGGGCATGTTTTCTTGAATTTCTCAAACGTAAAACATTGCCTTATTTTAAAA
131 CACCCAGCACATTAGGGCACGTTTTCTCGAATTTC-CAAACGCAAAACATTGCCTTATTTT-AAA
21655172 AATTTTAAAAGGATATTAAGCC
194 AATTTTAAAAGGATATTAAGCC
* * * * *
21655194 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTCAAATTTCCAAACG
*
21655259 CAAAACATTGCCTTATTTTGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAATGAGAAAAAT
63 CAAAACATTGCCTTATTTTGAAAATTTTAAAAGGATATTTAGCCATTTGGTTGAATGAGAAAAAT
*
21655324 CGACACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGA
128 CGACACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAA
21655389 AAATTTT
193 AAATTTT
21655396 CCTTTTGAAG
Statistics
Matches: 186, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
217 14 0.08
218 8 0.04
219 49 0.26
220 115 0.62
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (215 bp):
ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCAAATTTCCAAACGCAA
AACATTGCCTTATTTTGAAAATTTTAAAAGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGA
CACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAAA
TTTTAAAAGGATATTAAGCC
Done.