Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 115 of 121
Found at i:19778607 original size:39 final size:38
Alignment explanation
Indices: 19778548--19778833 Score: 252
Period size: 39 Copynumber: 7.4 Consensus size: 38
19778538 CTCTAAGATC
**
19778548 TTTAATTTAAAGTTTGTTGCCTTTGGTTAAATAAGCCTT
1 TTTAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAG-CTT
* *
19778587 TTTAATTTAAAGTTTATTGCCTTTGGTTAAAAGAGCTT
1 TTTAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTT
* *
19778625 TTGGAATTTAAAGTTTATTGCCTTTGGTTAAAGGAGC-T
1 TT-TAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTT
* * * * *
19778663 TTTAGATTTAAAGTTTGTTACCTCTAGTGAGAGGAGCTT
1 TTTA-ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTT
* * * * *
19778702 TTTGAATTTAAAGTTTGTTGCCTCTGATGAGATGAGCCTT
1 TTT-AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAG-CTT
* *** * *
19778742 TTGAATTTAAAGTCCATTGCCTTTGGTTAAATGAGCAT
1 TTTAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTT
* * * * *
19778780 TTGAATTTAAAGTTCGTTGTCTCTGG-TAAGAGAAGCTT
1 TTTAATTTAAAGTTTGTTGCCTTTGGTTAA-AGGAGCTT
19778818 TTTGAATTTAAAGTTT
1 TTT-AATTTAAAGTTT
19778834 TATAGCCTCT
Statistics
Matches: 206, Mismatches: 34, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
37 4 0.02
38 65 0.32
39 131 0.64
40 6 0.03
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.44
Consensus pattern (38 bp):
TTTAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTT
Found at i:19778711 original size:77 final size:78
Alignment explanation
Indices: 19778551--19778833 Score: 245
Period size: 77 Copynumber: 3.7 Consensus size: 78
19778541 TAAGATCTTT
* * * * *
19778551 AATTTAAAGTTTGTTGCCTTTGGTTAAATAAGCCTTTTTAATTTAAAGTTTATTGCCTTTGGTTA
1 AATTTAAAGTTTGTTGCCTTTGGTTAAAGAAGCCTTTTTAATTTAAAGTTTATTACCTCTAGTGA
19778616 AAAGAGCTTTTGG
66 AAAGAGCTTTTGG
* * *
19778629 AATTTAAAGTTTATTGCCTTTGGTTAAAGGAG-C-TTTTAGATTTAAAGTTTGTTACCTCTAGTG
1 AATTTAAAGTTTGTTGCCTTTGGTTAAAGAAGCCTTTTTA-ATTTAAAGTTTATTACCTCTAGTG
* * *
19778692 AGAGGAGCTTTTTG
65 AAAAGAGCTTTTGG
* * * * * ** * * * *
19778706 AATTTAAAGTTTGTTGCCTCTGATGAGATG-AGCCTTTTGAATTTAAAGTCCATTGCCTTTGGTT
1 AATTTAAAGTTTGTTGCCTTTGGTTA-AAGAAGCCTTTTTAATTTAAAGTTTATTACCTCTAGTG
* *
19778770 AAATGAGCATTT-G
65 AAAAGAGCTTTTGG
* * *
19778783 AATTTAAAGTTCGTTGTCTCTGG-TAAGAGAAG-CTTTTTGAATTTAAAGTTT
1 AATTTAAAGTTTGTTGCCTTTGGTTAA-AGAAGCCTTTTT-AATTTAAAGTTT
19778834 TATAGCCTCT
Statistics
Matches: 163, Mismatches: 35, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
75 1 0.01
76 12 0.07
77 88 0.54
78 58 0.36
79 4 0.02
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (78 bp):
AATTTAAAGTTTGTTGCCTTTGGTTAAAGAAGCCTTTTTAATTTAAAGTTTATTACCTCTAGTGA
AAAGAGCTTTTGG
Found at i:19778761 original size:116 final size:116
Alignment explanation
Indices: 19778584--19778843 Score: 319
Period size: 116 Copynumber: 2.2 Consensus size: 116
19778574 TTAAATAAGC
* * * **
19778584 CTTTTT-AATTTAAAGTTTATTGCCTTTGGTTAAAAGAGCTTTTGGAATTTAAAGTTTATTGCCT
1 CTTTTTGAATTTAAAGTTTATTGCCTCTGATGAAAAGAGCTTTTGGAATTTAAAGTCCATTGCCT
* * * *
19778648 TTGGTTAAAGGAGC-TTTTAGATTTAAAGTTTGTTACCTCTAGTGAGAGGAG
66 TTGGTTAAAGGAGCATTTGA-ATTTAAAGTTCGTTACCTCTAGTAAGAGAAG
* * *
19778699 CTTTTTGAATTTAAAGTTTGTTGCCTCTGATGAGATGAGCCTTTT-GAATTTAAAGTCCATTGCC
1 CTTTTTGAATTTAAAGTTTATTGCCTCTGATGAAAAGAG-CTTTTGGAATTTAAAGTCCATTGCC
* ** *
19778763 TTTGGTTAAATGAGCATTTGAATTTAAAGTTCGTTGTCTCTGGTAAGAGAAG
65 TTTGGTTAAAGGAGCATTTGAATTTAAAGTTCGTTACCTCTAGTAAGAGAAG
*
19778815 CTTTTTGAATTTAAAGTTTTATAGCCTCT
1 CTTTTTGAATTTAAAG-TTTATTGCCTCT
19778844 ACTTAGAGGA
Statistics
Matches: 123, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
115 6 0.05
116 98 0.80
117 19 0.15
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (116 bp):
CTTTTTGAATTTAAAGTTTATTGCCTCTGATGAAAAGAGCTTTTGGAATTTAAAGTCCATTGCCT
TTGGTTAAAGGAGCATTTGAATTTAAAGTTCGTTACCTCTAGTAAGAGAAG
Found at i:19779905 original size:12 final size:12
Alignment explanation
Indices: 19779888--19779941 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
19779878 GTTTCGTAAG
*
19779888 TTTTTCCTTTTC
1 TTTTTCCTTTTA
*
19779900 TTTTTCTTTTTA
1 TTTTTCCTTTTA
*
19779912 TTTTTCGTTTTGA
1 TTTTTCCTTTT-A
*
19779925 TTTTTACTTTTA
1 TTTTTCCTTTTA
19779937 TTTTT
1 TTTTT
19779942 TTATGTTGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
12 26 0.72
13 10 0.28
ACGTcount: A:0.07, C:0.11, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTTCCTTTTA
Found at i:19779941 original size:26 final size:25
Alignment explanation
Indices: 19779907--19779967 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
19779897 TTCTTTTTCT
* *
19779907 TTTTA-TTTTTCGTTTTGATTTTTA
1 TTTTATTTTTTCATGTTGATTTTTA
*
19779931 CTTTTATTTTTTTATGTTGATTTTTA
1 -TTTTATTTTTTCATGTTGATTTTTA
*
19779957 TGTTATTTTTT
1 TTTTATTTTTT
19779968 ATGATGCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 15 0.48
26 16 0.52
ACGTcount: A:0.13, C:0.03, G:0.08, T:0.75
Consensus pattern (25 bp):
TTTTATTTTTTCATGTTGATTTTTA
Found at i:19779967 original size:12 final size:13
Alignment explanation
Indices: 19779938--19779970 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
19779928 TTACTTTTAT
19779938 TTTTTTATGTTGA
1 TTTTTTATGTTGA
19779951 -TTTTTATGTT-A
1 TTTTTTATGTTGA
19779962 TTTTTTATG
1 TTTTTTATG
19779971 ATGCTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.05
12 18 0.95
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (13 bp):
TTTTTTATGTTGA
Found at i:19780083 original size:17 final size:17
Alignment explanation
Indices: 19780053--19780085 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19780043 AATAGAATAA
19780053 AAAATGAAAACTAAAAT
1 AAAATGAAAACTAAAAT
19780070 AAAAT-AAAACCTAAAA
1 AAAATGAAAA-CTAAAA
19780086 AAATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.09, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAATGAAAACTAAAAT
Found at i:19780090 original size:15 final size:15
Alignment explanation
Indices: 19780051--19780105 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
19780041 TAAATAGAAT
19780051 AAAAAATGAAAACTAA
1 AAAAAAT-AAAACTAA
19780067 AATAAAATAAAACCT-A
1 AA-AAAATAAAA-CTAA
19780083 AAAAAAT-AAA-TAA
1 AAAAAATAAAACTAA
19780096 AAAATAATAA
1 AAAA-AATAA
19780106 TAATAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
12 1 0.03
13 5 0.15
14 6 0.18
15 6 0.18
16 9 0.26
17 7 0.21
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.16
Consensus pattern (15 bp):
AAAAAATAAAACTAA
Found at i:19781239 original size:16 final size:16
Alignment explanation
Indices: 19781218--19781248 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19781208 TGTAAGAATT
*
19781218 TTCAGATTCATAAGAA
1 TTCAGATTCACAAGAA
19781234 TTCAGATTCACAAGA
1 TTCAGATTCACAAGA
19781249 CCTCAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (16 bp):
TTCAGATTCACAAGAA
Found at i:19781385 original size:17 final size:17
Alignment explanation
Indices: 19781312--19781386 Score: 53
Period size: 17 Copynumber: 4.4 Consensus size: 17
19781302 CTTTAGATTC
*
19781312 GCAACAACTTCAAGTTT
1 GCAAGAACTTCAAGTTT
* * *
19781329 GTAAGAGCTTTAAGTTCT
1 GCAAGAACTTCAAGTT-T
* * * *
19781347 -CAAGAATTTTAGGTTA
1 GCAAGAACTTCAAGTTT
*
19781363 GTAAGAACTTCAAGTTT
1 GCAAGAACTTCAAGTTT
19781380 GCAAGAA
1 GCAAGAA
19781387 TCTAAAGTCC
Statistics
Matches: 41, Mismatches: 15, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
17 40 0.98
18 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (17 bp):
GCAAGAACTTCAAGTTT
Found at i:19785186 original size:61 final size:60
Alignment explanation
Indices: 19785016--19785264 Score: 335
Period size: 61 Copynumber: 4.2 Consensus size: 60
19785006 TTGTGCAGTA
* ** * *
19785016 AAAATTGATACTTTCAACTTTTTCCC-AAAATA--TCTTTTAGAAATTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTAGAAAACTTATTTTCAAGG
* *
19785073 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAAACTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTAGAAAACTTATTTTCAAGG
** * * *
19785133 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTAAAAAAAAACTTATTTCCAAGA
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTT-TTAGAAAACTTATTTTCAAGG
19785194 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTTTAGAAAACTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTTCC-CAAAAATA-TTTTTTTTAGAAAACTTATTTTCAAGG
19785255 AAAATTGATA
1 AAAATTGATA
19785265 GCCCATATCA
Statistics
Matches: 167, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
57 25 0.15
58 6 0.04
60 63 0.38
61 67 0.40
62 6 0.04
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (60 bp):
AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTAGAAAACTTATTTTCAAGG
Found at i:19785429 original size:26 final size:26
Alignment explanation
Indices: 19785395--19785449 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
19785385 ATTCCTATGA
19785395 AACAAATATAACT-CAAAAACATAGAC
1 AACAAATATAA-TGCAAAAACATAGAC
*
19785421 AACAAATATAATGCAAAATCATAGAC
1 AACAAATATAATGCAAAAACATAGAC
19785447 AAC
1 AAC
19785450 CATTGAGTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.60, C:0.18, G:0.05, T:0.16
Consensus pattern (26 bp):
AACAAATATAATGCAAAAACATAGAC
Found at i:19785612 original size:43 final size:43
Alignment explanation
Indices: 19785543--19785787 Score: 253
Period size: 43 Copynumber: 5.7 Consensus size: 43
19785533 ACAAATTAAA
* *
19785543 CTCCTCTATATAGAGGC-AAACAAATTTAAATTAAGAAATTGG
1 CTCCTCTATATAGAGGCTAAACAACTTTAAATTAAGAAATGGG
* * * * *
19785585 CTCCTTTATATAGAGGCTAAATAAATTTAAACTAGGAAATGGG
1 CTCCTCTATATAGAGGCTAAACAACTTTAAATTAAGAAATGGG
* * * * *
19785628 CTCATCTAT-TCAAAGGCAAAACAACTTTAAAATAGGAAATGGG
1 CTCCTCTATAT-AGAGGCTAAACAACTTTAAATTAAGAAATGGG
*
19785671 CTCCTCTATATAGAGGCTAAACAACTTTAAAATTAAGAAATGAG
1 CTCCTCTATATAGAGGCTAAACAACTTT-AAATTAAGAAATGGG
** * * *
19785715 CTTTTCTATACAGAGACTAAACAACTTTAAATTAAGAAA-CGG
1 CTCCTCTATATAGAGGCTAAACAACTTTAAATTAAGAAATGGG
* * * *
19785757 ATTCTCTATACAGAGGTTAAACAACTTTAAA
1 CTCCTCTATATAGAGGCTAAACAACTTTAAA
19785788 AACTTTAAAT
Statistics
Matches: 171, Mismatches: 28, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
42 45 0.26
43 89 0.52
44 37 0.22
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (43 bp):
CTCCTCTATATAGAGGCTAAACAACTTTAAATTAAGAAATGGG
Found at i:19786077 original size:17 final size:17
Alignment explanation
Indices: 19786049--19786121 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 17
19786039 GTTTGTAAAT
* *
19786049 GATTCAAGATTCTCAAA
1 GATTCCAGATTCACAAA
*
19786066 GGTTCCAGATTCACAAA
1 GATTCCAGATTCACAAA
* ** *
19786083 GATTCCAAGTTTCGTAGA
1 GATTCC-AGATTCACAAA
* *
19786101 GATTCTAGATTTACAAA
1 GATTCCAGATTCACAAA
19786118 GATT
1 GATT
19786122 TCAAGTTTCG
Statistics
Matches: 41, Mismatches: 14, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
17 29 0.71
18 12 0.29
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (17 bp):
GATTCCAGATTCACAAA
Found at i:19786105 original size:18 final size:18
Alignment explanation
Indices: 19786080--19786143 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
19786070 CCAGATTCAC
19786080 AAAGATTCCAAGTTTCGT
1 AAAGATTCCAAGTTTCGT
* *
19786098 AGAGATT-CTAGATTTAC--
1 AAAGATTCCAAG-TTT-CGT
*
19786115 AAAGATTTCAAGTTTCGT
1 AAAGATTCCAAGTTTCGT
19786133 AAAGATTCCAA
1 AAAGATTCCAA
19786144 AGTCGTAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
16 1 0.03
17 12 0.33
18 22 0.61
19 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (18 bp):
AAAGATTCCAAGTTTCGT
Found at i:19786111 original size:35 final size:35
Alignment explanation
Indices: 19786063--19786140 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
19786053 CAAGATTCTC
* *
19786063 AAAGGTTCCAGATTCACAAAGATTCCAAGTTTCGT
1 AAAGATTCTAGATTCACAAAGATTCCAAGTTTCGT
* * *
19786098 AGAGATTCTAGATTTACAAAGATTTCAAGTTTCGT
1 AAAGATTCTAGATTCACAAAGATTCCAAGTTTCGT
19786133 AAAGATTC
1 AAAGATTC
19786141 CAAAGTCGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (35 bp):
AAAGATTCTAGATTCACAAAGATTCCAAGTTTCGT
Found at i:19786763 original size:11 final size:11
Alignment explanation
Indices: 19786747--19786795 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
19786737 AATTTTCTAA
19786747 AGAGAAAGAAG
1 AGAGAAAGAAG
19786758 AGAG-AA-AAG
1 AGAGAAAGAAG
*
19786767 AAAG-AAGAGAG
1 AGAGAAAGA-AG
19786778 AGAGAAAGAAG
1 AGAGAAAGAAG
*
19786789 GGAGAAA
1 AGAGAAA
19786796 TCTGAAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
9 8 0.25
10 3 0.09
11 17 0.53
12 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (11 bp):
AGAGAAAGAAG
Found at i:19787070 original size:13 final size:13
Alignment explanation
Indices: 19787054--19787078 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19787044 TCTTTTTGGT
19787054 ATTTTTTTAATTA
1 ATTTTTTTAATTA
19787067 ATTTTTTTAATT
1 ATTTTTTTAATT
19787079 TTTTTCTTTT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTTTAATTA
Found at i:19787340 original size:8 final size:8
Alignment explanation
Indices: 19787323--19787360 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
19787313 TTCAAACCAA
19787323 AAAAAT-T
1 AAAAATAT
19787330 AAAAATAT
1 AAAAATAT
*
19787338 AAAAAACAT
1 -AAAAATAT
19787347 AAAAATAT
1 AAAAATAT
19787355 AAAAAT
1 AAAAAT
19787361 TTTTGGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 6 0.22
8 14 0.52
9 7 0.26
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAT
Found at i:19788856 original size:16 final size:15
Alignment explanation
Indices: 19788830--19788862 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
19788820 TCTGCAATGT
19788830 TTCCATATCATTTCA
1 TTCCATATCATTTCA
19788845 TTCCATTATCATTTCA
1 TTCCA-TATCATTTCA
19788861 TT
1 TT
19788863 ATATGCATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (15 bp):
TTCCATATCATTTCA
Found at i:19799334 original size:62 final size:62
Alignment explanation
Indices: 19799238--19799358 Score: 199
Period size: 62 Copynumber: 2.0 Consensus size: 62
19799228 TGTTAAGGAA
*
19799238 CAATTTATTTTTCCAAAGTTCTGTTACCTCTATTTAGAGGAGCAATTTATTTTT-TCAAGAG
1 CAATTTATTTTTCCAAAGTTCTGTTACCTCTATTTAAAGGAGCAATTTATTTTTCTCAAGAG
* *
19799299 CAATTTATTTTTTCCAAAGTTTTGTTGCCTCTATTTAAAGGAGCAATTTATTTTTCTCAA
1 CAATTTA-TTTTTCCAAAGTTCTGTTACCTCTATTTAAAGGAGCAATTTATTTTTCTCAA
19799359 AGTCGTTGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 7 0.13
62 44 0.80
63 4 0.07
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (62 bp):
CAATTTATTTTTCCAAAGTTCTGTTACCTCTATTTAAAGGAGCAATTTATTTTTCTCAAGAG
Found at i:19799348 original size:43 final size:43
Alignment explanation
Indices: 19799296--19799385 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
19799286 ATTTTTTCAA
* *
19799296 GAGCAATTTATTTTT-TCCAAAGT-TTTGTTGCCTCTATTTAAAG
1 GAGCAATTTATTTTTCT-CAAAGTCGTTG-AGCCTCTATTTAAAG
*
19799339 GAGCAATTTATTTTTCTCAAAGTCGTTGAGCCTCTATTTAGAG
1 GAGCAATTTATTTTTCTCAAAGTCGTTGAGCCTCTATTTAAAG
19799382 GAGC
1 GAGC
19799386 TTTGTTTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 38 0.90
44 4 0.10
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.41
Consensus pattern (43 bp):
GAGCAATTTATTTTTCTCAAAGTCGTTGAGCCTCTATTTAAAG
Found at i:19801055 original size:54 final size:56
Alignment explanation
Indices: 19800973--19801081 Score: 136
Period size: 54 Copynumber: 2.0 Consensus size: 56
19800963 AGAAATAATA
* *
19800973 AAAAAGAAGAATTTCTAAATAGGCCCAAATTGTGGAAA-ATTTAGA-A-ATTTTCAG
1 AAAAAGAAAAATTTCTAAATAGGCCCAAATGGTGGAAATA-TTAGATATATTTTCAG
* *
19801027 AAAAAGAAAATATTTCTAATTTGG-CCAAATGGTGGAAATATTAGATATATTTTCA
1 AAAAAGAAAA-ATTTCTAAATAGGCCCAAATGGTGGAAATATTAGATATATTTTCA
19801082 ACAAAAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
54 27 0.57
55 13 0.28
56 7 0.15
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (56 bp):
AAAAAGAAAAATTTCTAAATAGGCCCAAATGGTGGAAATATTAGATATATTTTCAG
Found at i:19801718 original size:17 final size:17
Alignment explanation
Indices: 19801698--19801767 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
19801688 TCGTAAAGGC
*
19801698 TTCAGGTTCACAAGAGT
1 TTCAGGTTCACAAGAAT
*
19801715 TTCAGGTTCTCAAGAAT
1 TTCAGGTTCACAAGAAT
*
19801732 TTCAGGTT-AGCAAGAAC
1 TTCAGGTTCA-CAAGAAT
**
19801749 TTCAGGTTCGTAAGAAT
1 TTCAGGTTCACAAGAAT
19801766 TT
1 TT
19801768 AATATTCGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (17 bp):
TTCAGGTTCACAAGAAT
Found at i:19801736 original size:34 final size:34
Alignment explanation
Indices: 19801673--19801767 Score: 97
Period size: 34 Copynumber: 2.8 Consensus size: 34
19801663 ACTAAGTTTT
* **
19801673 GCAAGAACTTCAAGTTCGTAA-AGGCTTCAGGTTCA
1 GCAAGAACTTCAGGTTCGTAAGA-ATTTCAGGTT-A
**
19801708 -CAAGAGTTTCAGGTTC-TCAAGAATTTCAGGTTA
1 GCAAGAACTTCAGGTTCGT-AAGAATTTCAGGTTA
19801741 GCAAGAACTTCAGGTTCGTAAGAATTT
1 GCAAGAACTTCAGGTTCGTAAGAATTT
19801768 AATATTCGCA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
33 2 0.04
34 45 0.92
35 2 0.04
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (34 bp):
GCAAGAACTTCAGGTTCGTAAGAATTTCAGGTTA
Found at i:19801779 original size:34 final size:34
Alignment explanation
Indices: 19801715--19801781 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
19801705 TCACAAGAGT
* *
19801715 TTCAGGTTCTCAAGAATTTCAGGTTAGCAAGAAC
1 TTCAGGTTCTCAAGAATTTAAGATTAGCAAGAAC
* *
19801749 TTCAGGTTCGT-AAGAATTTAATATTCGCAAGAA
1 TTCAGGTTC-TCAAGAATTTAAGATTAGCAAGAA
19801782 TCTAAGGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (34 bp):
TTCAGGTTCTCAAGAATTTAAGATTAGCAAGAAC
Found at i:19808103 original size:73 final size:73
Alignment explanation
Indices: 19807997--19808149 Score: 272
Period size: 73 Copynumber: 2.1 Consensus size: 73
19807987 AAACCTTTAC
*
19807997 TTATATAAAGATTTAATTTTTACATGATTAAAGAGAACTAAAAA-AAGTTGCAATAGAAATTTGA
1 TTATTTAAAGATTTAATTTTTACATGATTAAAGAGAACTAAAAACAA-TTGCAATAGAAATTTGA
19808061 AATAAAAAT
65 AATAAAAAT
19808070 TTATTTAAAGATTTAATTTTTACATGATTAAAGAGAACTAAAAACAATTGCAATAGAAATTTGAA
1 TTATTTAAAGATTTAATTTTTACATGATTAAAGAGAACTAAAAACAATTGCAATAGAAATTTGAA
*
19808135 ATAAAAGT
66 ATAAAAAT
19808143 TTATTTA
1 TTATTTA
19808150 GCTGTAAATC
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
73 75 0.97
74 2 0.03
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (73 bp):
TTATTTAAAGATTTAATTTTTACATGATTAAAGAGAACTAAAAACAATTGCAATAGAAATTTGAA
ATAAAAAT
Found at i:19808198 original size:30 final size:29
Alignment explanation
Indices: 19808160--19808216 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
19808150 GCTGTAAATC
* *
19808160 AAAATATAAAAGTTTATTTAAGTAAAAGA
1 AAAATATAAAAGTCTATTTAAATAAAAGA
*
19808189 AAAATTATAAGAGTCTATTTAAATAAAA
1 AAAA-TATAAAAGTCTATTTAAATAAAA
19808217 TAATAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.32
Consensus pattern (29 bp):
AAAATATAAAAGTCTATTTAAATAAAAGA
Found at i:19809298 original size:18 final size:20
Alignment explanation
Indices: 19809266--19809303 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
19809256 ATTGAAATTT
*
19809266 AAATAAATAACATAAGATAA
1 AAATAAATAACATAAAATAA
19809286 AAATAAA-AA-ATAAAATAA
1 AAATAAATAACATAAAATAA
19809304 TTACCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (20 bp):
AAATAAATAACATAAAATAA
Found at i:19810836 original size:2 final size:2
Alignment explanation
Indices: 19810831--19810857 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19810821 TGTGTGTGTC
19810831 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19810858 TCCTGCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19814677 original size:87 final size:88
Alignment explanation
Indices: 19814565--19814726 Score: 220
Period size: 88 Copynumber: 1.9 Consensus size: 88
19814555 CAAAGAAATC
* *
19814565 TAAATTAAGAAATGTGCTCTTCTATACATAAGCT-AAACAACTTTAAAATAAAAAACGGGCTCCT
1 TAAATTAAGAAATGAGCTCTTCTATACAAAAGCTAAAACAACTTTAAAATAAAAAACGGGCTCCT
19814629 TTATACAGAGACTGAGCAACTTT
66 TTATACAGAGACTGAGCAACTTT
* * * * * *
19814652 TAAATTAAGAAATGAG-TTTCTCTATATAAAAGCTAAAACAACTTTAAATTAAGAAATGGGTTCC
1 TAAATTAAGAAATGAGCTCT-TCTATACAAAAGCTAAAACAACTTTAAAATAAAAAACGGGCTCC
*
19814716 TTTATATAGAG
65 TTTATACAGAG
19814727 GTTAAACAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
86 2 0.03
87 27 0.42
88 35 0.55
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.31
Consensus pattern (88 bp):
TAAATTAAGAAATGAGCTCTTCTATACAAAAGCTAAAACAACTTTAAAATAAAAAACGGGCTCCT
TTATACAGAGACTGAGCAACTTT
Found at i:19815031 original size:17 final size:17
Alignment explanation
Indices: 19815005--19815047 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
19814995 GTTTGTAAAT
*
19815005 GATTCAAGATTCTCAAA
1 GATTCAAGATTCACAAA
*
19815022 GATTCTAGATTCACAAA
1 GATTCAAGATTCACAAA
19815039 GATTTCAAG
1 GA-TTCAAG
19815048 TTTCGCATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (17 bp):
GATTCAAGATTCACAAA
Found at i:19815263 original size:3 final size:3
Alignment explanation
Indices: 19815257--19815316 Score: 88
Period size: 3 Copynumber: 20.7 Consensus size: 3
19815247 CTTCTTGTTA
* *
19815257 TAT TAT TA- TAT AAT TCT -AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19815303 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
19815317 ATCTTTAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 3 0.06
3 48 0.94
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:19815874 original size:52 final size:52
Alignment explanation
Indices: 19815754--19815881 Score: 138
Period size: 51 Copynumber: 2.5 Consensus size: 52
19815744 TGGGTCGTCG
* *
19815754 AAAA-CTGGAAAAGTTTGAATTTTT-AGATGACCATTGAATTTTTCAGCACC
1 AAAATCTGGAAAACTTTGAATTTTTCAGATGACCATTGAATTTTTCACCACC
* * * *
19815804 AGAATCTGGAAAAGTTTGAATTTTTCA-ATTACCATTGAATTTTTTGACCACC
1 AAAATCTGGAAAACTTTGAATTTTTCAGATGACCATTGAA-TTTTTCACCACC
* *
19815856 AAAATCTAGG-GATCTTTGAATTTTTC
1 AAAATCT-GGAAAACTTTGAATTTTTC
19815882 TGTGTCATTG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
50 3 0.05
51 31 0.47
52 30 0.45
53 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (52 bp):
AAAATCTGGAAAACTTTGAATTTTTCAGATGACCATTGAATTTTTCACCACC
Found at i:19817159 original size:18 final size:18
Alignment explanation
Indices: 19817136--19817171 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19817126 ATGCAAGAAA
**
19817136 TTCAAATTTGTAAGAATT
1 TTCAAATTCATAAGAATT
19817154 TTCAAATTCATAAGAATT
1 TTCAAATTCATAAGAATT
19817172 CAGATTTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (18 bp):
TTCAAATTCATAAGAATT
Found at i:19817297 original size:34 final size:34
Alignment explanation
Indices: 19817248--19817325 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
19817238 CTTTAGATTC
* * *
19817248 GCAACAATTTCAGGTTTGTAAGAGCTTCAAGTTCT
1 GCAAGAATTTCAGGTTAGTAAGAACTTCAAGTT-T
*
19817283 -CAAGAATTTTAGGTTAGTAAGAACTTCAAGTTT
1 GCAAGAATTTCAGGTTAGTAAGAACTTCAAGTTT
19817316 GCAAGAATTT
1 GCAAGAATTT
19817326 AAAGTCCGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 1 0.03
34 37 0.97
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (34 bp):
GCAAGAATTTCAGGTTAGTAAGAACTTCAAGTTT
Found at i:19824110 original size:2 final size:2
Alignment explanation
Indices: 19824103--19824127 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19824093 AGAATATGTG
19824103 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
19824128 TCCTGCCATT
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:19824219 original size:6 final size:6
Alignment explanation
Indices: 19824199--19824233 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
19824189 AATTTAGTGT
*
19824199 ATTTAA TATTAAA ATTTAA ATTTAA ATTTAA ATTT
1 ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA ATTT
19824234 CATTCAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:19827961 original size:52 final size:50
Alignment explanation
Indices: 19827810--19827964 Score: 184
Period size: 52 Copynumber: 3.0 Consensus size: 50
19827800 ATAACCATAT
* * * * *
19827810 AAACTTACCTATTAAGAATCCTTTTCATCTTCGAATTCTTCTCCTACAAGTC
1 AAACTTGCCTATTAAGAAT-CTTTTC-CCTTAGAATTCTTCTCTTGCAAGTC
* *
19827862 AAACTTGCCTATTAAAAATCTATTTCCTCTTAAAATTCTTCTCTTGCAAGTC
1 AAACTTGCCTATTAAGAATCT-TTTCC-CTTAGAATTCTTCTCTTGCAAGTC
*
19827914 AAACTTGCCTATTAAGAATCTTCTTTCCCTTAGAATTCTTCTTTTGCAAGT
1 AAACTTGCCTATTAAGAATC-T-TTTCCCTTAGAATTCTTCTCTTGCAAGT
19827965 TTTCTTGTCC
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
51 2 0.02
52 81 0.91
53 6 0.07
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (50 bp):
AAACTTGCCTATTAAGAATCTTTTCCCTTAGAATTCTTCTCTTGCAAGTC
Found at i:19829004 original size:30 final size:30
Alignment explanation
Indices: 19828970--19829030 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
19828960 AGTTTTAGCT
19828970 TTTAATTTACA-TTCAAATAAG-CTCTTAATA
1 TTTAATTTACACTT-AAATAAGTCT-TTAATA
*
19829000 TTTAATTTATACTTAAATAAGTCTTTAATA
1 TTTAATTTACACTTAAATAAGTCTTTAATA
19829030 T
1 T
19829031 AATACATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTAATTTACACTTAAATAAGTCTTTAATA
Found at i:19829784 original size:22 final size:22
Alignment explanation
Indices: 19829758--19829801 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19829748 TGATTTTAAT
*
19829758 TTCGATTTAACTACAATTACAA
1 TTCGATTTAACTACAATCACAA
19829780 TTCGATTTAACTACAATCACAA
1 TTCGATTTAACTACAATCACAA
19829802 AATTCTAACT
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:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (22 bp):
TTCGATTTAACTACAATCACAA
Found at i:19833270 original size:43 final size:42
Alignment explanation
Indices: 19833210--19833410 Score: 181
Period size: 43 Copynumber: 4.7 Consensus size: 42
19833200 AATTAAATCC
* *
19833210 CTCTATACAGAGG-TAAACAAATCTAAATTAAGAAATTGGTTT
1 CTCTATACAGAGGCTAAACAACTTTAAATTAAGAAATTGG-TT
* * * *
19833252 CTCTATACATAGGCTAAACAACTTTAAAATAAGAAATTAGCT
1 CTCTATACAGAGGCTAAACAACTTTAAATTAAGAAATTGGTT
*
19833294 CATCTATACAGAGGCTAAACAACTTTAAAATTAAGAAA-TGAGCTC
1 C-TCTATACAGAGGCTAAACAACTTT-AAATTAAGAAATTG-G-TT
* * * * * * *
19833339 CTCTATACAAAGGCTAAAATAATTTTACATTAAGAAATAGACTC
1 CTCTATACAGAGGCT-AAACAACTTTAAATTAAGAAATTG-GTT
* *
19833383 CTCTATACAGAAGTTAAACAACTTTAAA
1 CTCTATACAGAGGCTAAACAACTTTAAA
19833411 AACTTTAAAA
Statistics
Matches: 129, Mismatches: 23, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
42 14 0.11
43 56 0.43
44 48 0.37
45 11 0.09
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (42 bp):
CTCTATACAGAGGCTAAACAACTTTAAATTAAGAAATTGGTT
Found at i:19833344 original size:44 final size:44
Alignment explanation
Indices: 19833209--19833411 Score: 220
Period size: 44 Copynumber: 4.7 Consensus size: 44
19833199 AAATTAAATC
* * *
19833209 CCTCTATACAGAGG-TAAACAAATCT-AAATTAAGAAATTG-GTT
1 CCTCTATACAGAGGCTAAACAACTTTAAAATTAAGAAA-TGAGCT
* * *
19833251 TCTCTATACATAGGCTAAACAACTTTAAAA-TAAGAAATTAGCT
1 CCTCTATACAGAGGCTAAACAACTTTAAAATTAAGAAATGAGCT
*
19833294 CATCTATACAGAGGCTAAACAACTTTAAAATTAAGAAATGAGCT
1 CCTCTATACAGAGGCTAAACAACTTTAAAATTAAGAAATGAGCT
* * * *
19833338 CCTCTATACAAAGGCTAAA-ATAATTTTACATTAAGAAAT-AGACT
1 CCTCTATACAGAGGCTAAACA-ACTTTAAAATTAAGAAATGAG-CT
* *
19833382 CCTCTATACAGAAGTTAAACAACTTTAAAA
1 CCTCTATACAGAGGCTAAACAACTTTAAAA
19833412 ACTTTAAAAG
Statistics
Matches: 133, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
42 13 0.10
43 48 0.36
44 71 0.53
45 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (44 bp):
CCTCTATACAGAGGCTAAACAACTTTAAAATTAAGAAATGAGCT
Found at i:19833684 original size:17 final size:17
Alignment explanation
Indices: 19833659--19833698 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
19833649 TTTGTAAATG
* *
19833659 ATTCAAGATTCTCAAAA
1 ATTCTAGATTCGCAAAA
*
19833676 ATTCTAGATTCGCAAAG
1 ATTCTAGATTCGCAAAA
19833693 ATTCTA
1 ATTCTA
19833699 AGTTTCGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (17 bp):
ATTCTAGATTCGCAAAA
Found at i:19833764 original size:17 final size:17
Alignment explanation
Indices: 19833742--19833790 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
19833732 AAATTTTTAG
19833742 AGGTTTCAGATTCACAA
1 AGGTTTCAGATTCACAA
* *
19833759 ATGTTTCAAGTTTCACAA
1 AGGTTTC-AGATTCACAA
*
19833777 AGGTTTCAAATTCA
1 AGGTTTCAGATTCA
19833791 TAAGAATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (17 bp):
AGGTTTCAGATTCACAA
Found at i:19833790 original size:35 final size:35
Alignment explanation
Indices: 19833742--19833850 Score: 89
Period size: 35 Copynumber: 3.1 Consensus size: 35
19833732 AAATTTTTAG
*
19833742 AGGTTTCAGATTCACAAATGTTTCAAGTTTCACAA
1 AGGTTTCAAATTCACAAATGTTTCAAGTTTCACAA
* **
19833777 AGGTTTCAAATTCATAAGAAT-TTT--AGTTTTTCAA
1 AGGTTTCAAATTCA-CA-AATGTTTCAAGTTTCACAA
* ** * * *
19833811 AGGTTCCAAATTTGCAAAGGTTTCAAGTTTCGCAG
1 AGGTTTCAAATTCACAAATGTTTCAAGTTTCACAA
19833846 AGGTT
1 AGGTT
19833851 CTAGATTTGC
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
32 2 0.04
33 4 0.07
34 19 0.33
35 25 0.44
36 4 0.07
37 3 0.05
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (35 bp):
AGGTTTCAAATTCACAAATGTTTCAAGTTTCACAA
Found at i:19833812 original size:34 final size:35
Alignment explanation
Indices: 19833707--19833822 Score: 100
Period size: 34 Copynumber: 3.4 Consensus size: 35
19833697 TAAGTTTCGT
*
19833707 AAAGGTTTC-AATTCATAAG-ATTTTCAAATTTTT-
1 AAAGGTTTCAAATTCATAAGAATTTT-AAGTTTTTC
* * * **
19833740 AGAGGTTTCAGATTCA-CA-AATGTTTCAAGTTTCAC
1 AAAGGTTTCAAATTCATAAGAAT-TTT-AAGTTTTTC
19833775 AAAGGTTTCAAATTCATAAGAATTTT-AGTTTTTC
1 AAAGGTTTCAAATTCATAAGAATTTTAAGTTTTTC
*
19833809 AAAGGTTCCAAATT
1 AAAGGTTTCAAATT
19833823 TGCAAAGGTT
Statistics
Matches: 65, Mismatches: 12, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
33 11 0.17
34 33 0.51
35 14 0.22
36 4 0.06
37 3 0.05
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (35 bp):
AAAGGTTTCAAATTCATAAGAATTTTAAGTTTTTC
Found at i:19833830 original size:17 final size:17
Alignment explanation
Indices: 19833808--19833862 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
19833798 TTTAGTTTTT
19833808 CAAAGGTTCCAAATTTG
1 CAAAGGTTCCAAATTTG
* *
19833825 CAAAGGTTTCAAGTTTCG
1 CAAAGGTTCCAAATTT-G
* * *
19833843 CAGAGGTTCTAGATTTG
1 CAAAGGTTCCAAATTTG
19833860 CAA
1 CAA
19833863 GAATTTTCAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (17 bp):
CAAAGGTTCCAAATTTG
Found at i:19833836 original size:69 final size:67
Alignment explanation
Indices: 19833698--19833850 Score: 173
Period size: 69 Copynumber: 2.2 Consensus size: 67
19833688 CAAAGATTCT
* * * * *
19833698 AAGTTTCGTAAAGGTTTCAATTCATAAGATTTTCAAATTTTTAGAGGTTTCAGATTCACAAATGT
1 AAGTTTCGCAAAGGTTTCAATTCATAAGATTTT-AAATTTTTAAAGGTTCCAAATTCACAAAGGT
19833763 TTC
65 TTC
* * **
19833766 AAGTTTCACAAAGGTTTCAAATTCATAAGAATTTT-AGTTTTTCAAAGGTTCCAAATTTGCAAAG
1 AAGTTTCGCAAAGGTTTC-AATTCATAAG-ATTTTAAATTTTT-AAAGGTTCCAAATTCACAAAG
19833830 GTTTC
63 GTTTC
*
19833835 AAGTTTCGCAGAGGTT
1 AAGTTTCGCAAAGGTT
19833851 CTAGATTTGC
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
68 22 0.31
69 44 0.62
70 5 0.07
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (67 bp):
AAGTTTCGCAAAGGTTTCAATTCATAAGATTTTAAATTTTTAAAGGTTCCAAATTCACAAAGGTT
TC
Found at i:19833972 original size:34 final size:34
Alignment explanation
Indices: 19833929--19834069 Score: 115
Period size: 34 Copynumber: 4.1 Consensus size: 34
19833919 TAAGTTTCGT
* *
19833929 AAGAACTTCAGATTTACAAGAACTTCAGGTTTGC
1 AAGAACTTCAGATTTACAAGAATTTAAGGTTTGC
* * * * *
19833963 AAGAGCTTCAGGTTCT-CAAGAATTTTAGATTAGC
1 AAGAACTTCAGATT-TACAAGAATTTAAGGTTTGC
* *
19833997 TAGAACTTCAGA-TTATCAAGAATTTAAAGTTTGC
1 AAGAACTTCAGATTTA-CAAGAATTTAAGGTTTGC
* * * * * *
19834031 AAGAATTTAAGGTTCACAAGAATATAAGGTTTGT
1 AAGAACTTCAGATTTACAAGAATTTAAGGTTTGC
19834065 AAGAA
1 AAGAA
19834070 TTTTTAGATT
Statistics
Matches: 82, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
32 1 0.01
33 1 0.01
34 77 0.94
35 3 0.04
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (34 bp):
AAGAACTTCAGATTTACAAGAATTTAAGGTTTGC
Found at i:19834011 original size:17 final size:17
Alignment explanation
Indices: 19833929--19834018 Score: 74
Period size: 17 Copynumber: 5.3 Consensus size: 17
19833919 TAAGTTTCGT
19833929 AAGAACTTCAGATTTA-C
1 AAGAACTTCAGA-TTAGC
* *
19833946 AAGAACTTCAGGTTTGC
1 AAGAACTTCAGATTAGC
* * **
19833963 AAGAGCTTCAGGTTCTC
1 AAGAACTTCAGATTAGC
* *
19833980 AAGAATTTTAGATTAGC
1 AAGAACTTCAGATTAGC
* *
19833997 TAGAACTTCAGATTATC
1 AAGAACTTCAGATTAGC
19834014 AAGAA
1 AAGAA
19834019 TTTAAAGTTT
Statistics
Matches: 56, Mismatches: 16, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
16 2 0.04
17 54 0.96
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (17 bp):
AAGAACTTCAGATTAGC
Found at i:19834033 original size:17 final size:17
Alignment explanation
Indices: 19834013--19834072 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
19834003 TTCAGATTAT
*
19834013 CAAGAATTTAAAGTTTG
1 CAAGAATTTAAGGTTTG
**
19834030 CAAGAATTTAAGGTTCA
1 CAAGAATTTAAGGTTTG
*
19834047 CAAGAATATAAGGTTTG
1 CAAGAATTTAAGGTTTG
*
19834064 TAAGAATTT
1 CAAGAATTT
19834073 TTAGATTTGC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (17 bp):
CAAGAATTTAAGGTTTG
Found at i:19836782 original size:22 final size:22
Alignment explanation
Indices: 19836757--19836824 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
19836747 TGAGCTCATA
19836757 TGTTAGTGCTTGAAAAGCTAGT
1 TGTTAGTGCTTGAAAAGCTAGT
*
19836779 TGTTAATGCTTGAAAAGCTAGT
1 TGTTAGTGCTTGAAAAGCTAGT
19836801 TGTTAGTGCTTGAAAAGCTAGT
1 TGTTAGTGCTTGAAAAGCTAGT
19836823 TG
1 TG
19836825 ATAAGAACTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (22 bp):
TGTTAGTGCTTGAAAAGCTAGT
Found at i:19840871 original size:2 final size:2
Alignment explanation
Indices: 19840866--19840891 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19840856 GTGTGTGTAA
19840866 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
19840892 TCTCTTTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19842804 original size:30 final size:30
Alignment explanation
Indices: 19842698--19842805 Score: 126
Period size: 30 Copynumber: 3.6 Consensus size: 30
19842688 TTTGATTTAC
* *
19842698 ATTAAAAGTTTATTTAAATACAAATTAAAA
1 ATTAAAAATTTATTTGAATACAAATTAAAA
* * *
19842728 GTTAAAAATTTATTTTAATATAAATTAAAA
1 ATTAAAAATTTATTTGAATACAAATTAAAA
* * *
19842758 AGCTAAAAACTTATTTGAATGCAAATTAAAA
1 A-TTAAAAATTTATTTGAATACAAATTAAAA
*
19842789 ATTAAAAATGTATTTGA
1 ATTAAAAATTTATTTGA
19842806 TTATAATAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 39 0.61
31 25 0.39
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (30 bp):
ATTAAAAATTTATTTGAATACAAATTAAAA
Found at i:19845263 original size:30 final size:30
Alignment explanation
Indices: 19845229--19845286 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
19845219 TATATGAACA
19845229 TTTAATTTAAACTCAAATAAACCCTTAATT
1 TTTAATTTAAACTCAAATAAACCCTTAATT
* * * *
19845259 TTTAATTTATATTTAAATAAACTCTTAA
1 TTTAATTTAAACTCAAATAAACCCTTAA
19845287 CATAATACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTAATTTAAACTCAAATAAACCCTTAATT
Found at i:19846252 original size:24 final size:24
Alignment explanation
Indices: 19846185--19846253 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
19846175 AATAATAATT
* *
19846185 TAAAATATGACACAATAAAATGATA
1 TAAAA-ATGATACAATAAAATGACA
* *
19846210 TAAAAATCATATAAATAAAAT-ACA
1 TAAAAATGATA-CAATAAAATGACA
19846234 TAAAAATGATACAATTAAAA
1 TAAAAATGATACAA-TAAAA
19846254 ATTTTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
23 2 0.06
24 21 0.58
25 13 0.36
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.25
Consensus pattern (24 bp):
TAAAAATGATACAATAAAATGACA
Found at i:19847052 original size:31 final size:31
Alignment explanation
Indices: 19847010--19847068 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
19847000 TTATTTTAAA
19847010 TAAAAAATTATTTA-AGTACAAATTAAAATTT
1 TAAAAAATTATTTAGA-TACAAATTAAAATTT
* *
19847041 TAAAAATTTATTTGGATACAAATTAAAA
1 TAAAAAATTATTTAGATACAAATTAAAA
19847069 ATTAAGTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.37
Consensus pattern (31 bp):
TAAAAAATTATTTAGATACAAATTAAAATTT
Found at i:19847109 original size:29 final size:30
Alignment explanation
Indices: 19847017--19847123 Score: 87
Period size: 29 Copynumber: 3.6 Consensus size: 30
19847007 AAATAAAAAA
* *
19847017 TTATTT-AAGTACAAATTAAAATTTTAAAAAT
1 TTATTTGAA-TACAAATTAAAA-ATTAAATAT
* * *
19847048 TTATTTGGATACAAATTAAAAATTAAGTGT
1 TTATTTGAATACAAATTAAAAATTAAATAT
*
19847078 TTATTTGAATA-TAA-TAAAAATATAAATAT
1 TTATTTGAATACAAATTAAAAAT-TAAATAT
* *
19847107 TTATCTAAATA-AAATTA
1 TTATTTGAATACAAATTA
19847124 TAAAGTTCAA
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
28 7 0.11
29 18 0.30
30 17 0.28
31 18 0.30
32 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (30 bp):
TTATTTGAATACAAATTAAAAATTAAATAT
Found at i:19850580 original size:4 final size:4
Alignment explanation
Indices: 19850571--19850610 Score: 62
Period size: 4 Copynumber: 9.8 Consensus size: 4
19850561 ATAGATAATC
*
19850571 AAAT AAAT AAAT AAAT AAATT AAAT AATT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAA
19850611 AATAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:19850595 original size:21 final size:21
Alignment explanation
Indices: 19850571--19850610 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
19850561 ATAGATAATC
19850571 AAATAAATAAATAAATAAATT
1 AAATAAATAAATAAATAAATT
*
19850592 AAATAATTAAATAAATAAA
1 AAATAAATAAATAAATAAA
19850611 AATAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATAAATAAATAAATAAATT
Found at i:19850596 original size:17 final size:18
Alignment explanation
Indices: 19850573--19850621 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
19850563 AGATAATCAA
19850573 ATAAATAAATAAATAAAT
1 ATAAATAAATAAATAAAT
*
19850591 -TAAATAATTAAATAAAT
1 ATAAATAAATAAATAAAT
*
19850608 AAAAATAAAATAAA
1 ATAAAT-AAATAAA
19850622 ATAATACTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
ATAAATAAATAAATAAAT
Found at i:19853792 original size:27 final size:27
Alignment explanation
Indices: 19853762--19853816 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
19853752 ATGAGGATAG
19853762 AAAAAAAAAATTAAA-AAATAAAAAAT
1 AAAAAAAAAATTAAATAAATAAAAAAT
* *
19853788 AAAAAAAACATTAAATAAATAAATAAT
1 AAAAAAAAAATTAAATAAATAAAAAAT
19853815 AA
1 AA
19853817 TAATAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (27 bp):
AAAAAAAAAATTAAATAAATAAAAAAT
Found at i:19853794 original size:15 final size:14
Alignment explanation
Indices: 19853762--19853795 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19853752 ATGAGGATAG
*
19853762 AAAAAAAAAATTAA
1 AAAAAAAAAAATAA
*
19853776 AAAATAAAAAATAA
1 AAAAAAAAAAATAA
19853790 AAAAAA
1 AAAAAA
19853796 CATTAAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAAAAAAATAA
Found at i:19853817 original size:3 final size:3
Alignment explanation
Indices: 19853809--19853838 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
19853799 TAAATAAATA
19853809 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19853839 GGTGTTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19865347 original size:8 final size:8
Alignment explanation
Indices: 19865334--19865363 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
19865324 TTTGCTTGAG
19865334 AAAAAATA
1 AAAAAATA
19865342 AAAAAATA
1 AAAAAATA
19865350 AAAAAATA
1 AAAAAATA
19865358 AAAAAA
1 AAAAAA
19865364 AAACTCAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAATA
Found at i:19866444 original size:62 final size:62
Alignment explanation
Indices: 19866348--19866468 Score: 199
Period size: 62 Copynumber: 2.0 Consensus size: 62
19866338 TGTTAAGGAA
* *
19866348 CAATTTATTTTTCCAAAGTTCTGTTACCTCTATTTAGATGAGCAATTTATTTTT-TCAAGAG
1 CAATTTATTTTTCCAAAGTTCTGTTACCTCTATTTAAAGGAGCAATTTATTTTTCTCAAGAG
*
19866409 CAATTTATTTTTCCCAAAGTTCTGTTGCCTCTATTTAAAGGAGCAATTTATTTTTCTCAA
1 CAATTTATTTTT-CCAAAGTTCTGTTACCTCTATTTAAAGGAGCAATTTATTTTTCTCAA
19866469 AGTTGTTGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 12 0.22
62 39 0.71
63 4 0.07
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.45
Consensus pattern (62 bp):
CAATTTATTTTTCCAAAGTTCTGTTACCTCTATTTAAAGGAGCAATTTATTTTTCTCAAGAG
Found at i:19866458 original size:43 final size:42
Alignment explanation
Indices: 19866406--19866495 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 42
19866396 ATTTTTTCAA
19866406 GAGCAATTTATTTTTCCCAAAGTTCTGTT-GCCTCTATTTAAAG
1 GAGCAATTTATTTTTCCCAAAG-T-TGTTAGCCTCTATTTAAAG
* *
19866449 GAGCAATTTATTTTTCTCAAAGTTGTTGAGCCTCTATTTAGAG
1 GAGCAATTTATTTTTCCCAAAGTTGTT-AGCCTCTATTTAAAG
19866492 GAGC
1 GAGC
19866496 TTTGTTTACT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 1 0.02
43 38 0.88
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (42 bp):
GAGCAATTTATTTTTCCCAAAGTTGTTAGCCTCTATTTAAAG
Found at i:19867462 original size:13 final size:13
Alignment explanation
Indices: 19867444--19867468 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19867434 TCTTTTTAGT
19867444 ATTTTTTTAATTA
1 ATTTTTTTAATTA
19867457 ATTTTTTTAATT
1 ATTTTTTTAATT
19867469 TTTTTCTTTT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTTTAATTA
Found at i:19867734 original size:17 final size:18
Alignment explanation
Indices: 19867712--19867753 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
19867702 TTTCAAACCA
19867712 AAAAAATTA-AAAAATAT
1 AAAAAATTATAAAAATAT
*
19867729 AAAAAA-CATAAAAATAT
1 AAAAAATTATAAAAATAT
19867746 AAAAAATT
1 AAAAAATT
19867754 TTAGAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAAATTATAAAAATAT
Found at i:19867752 original size:9 final size:9
Alignment explanation
Indices: 19867712--19867752 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
19867702 TTTCAAACCA
19867712 AAAAAAT-T
1 AAAAAATAT
19867720 AAAAAATAT
1 AAAAAATAT
*
19867729 AAAAAACAT
1 AAAAAATAT
19867738 -AAAAATAT
1 AAAAAATAT
19867746 AAAAAAT
1 AAAAAAT
19867753 TTTAGAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 14 0.48
9 15 0.52
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATAT
Found at i:19868209 original size:56 final size:57
Alignment explanation
Indices: 19868108--19868227 Score: 138
Period size: 56 Copynumber: 2.1 Consensus size: 57
19868098 CAGAAATAAT
* * *
19868108 AAAAAAGAATAATTTCTAAATAGGCCCAAATTGTGAAAAATTTAGA-A-ATTTTCGA
1 AAAAAAGAAAAATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGATATATTTTCAA
* * *
19868163 AAAAAAGAAAATATTTCTAATTTGGCCCAAATGGTGGAATAA-TTAGATATATTTTCAA
1 AAAAAAGAAAA-ATTTCTAAATAGGCCCAAATGGT-GAAAAATTTAGATATATTTTCAA
19868221 ACAAAAA
1 A-AAAAA
19868228 TAAACTAACA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
55 10 0.19
56 25 0.46
57 6 0.11
58 8 0.15
59 5 0.09
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.29
Consensus pattern (57 bp):
AAAAAAGAAAAATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGATATATTTTCAA
Found at i:19868707 original size:35 final size:35
Alignment explanation
Indices: 19868668--19868780 Score: 97
Period size: 35 Copynumber: 3.3 Consensus size: 35
19868658 TTATGACACC
*
19868668 AGATTCGCAAAGGTTTCAAGTTTCGCAGAGGTTCT
1 AGATTCGCAAAGGTTTCAAGTTTCACAGAGGTTCT
* * * **
19868703 AGATTTGC-AAGAATTT-TAGTTT-TTAGAGGTTCT
1 AGATTCGCAAAG-GTTTCAAGTTTCACAGAGGTTCT
* ** *
19868736 AAATTCGCAAAGGTACCAAGTTTCACAAAGGTTCT
1 AGATTCGCAAAGGTTTCAAGTTTCACAGAGGTTCT
*
19868771 AGATTAGCAA
1 AGATTCGCAA
19868781 GACTTTTAGA
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
33 16 0.28
34 16 0.28
35 26 0.45
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (35 bp):
AGATTCGCAAAGGTTTCAAGTTTCACAGAGGTTCT
Found at i:19868856 original size:17 final size:17
Alignment explanation
Indices: 19868836--19868905 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
19868826 TCGTAAAGGC
*
19868836 TTCAGGTTCACAAGAGT
1 TTCAGGTTCACAAGAAT
*
19868853 TTCAGGTTCTCAAGAAT
1 TTCAGGTTCACAAGAAT
*
19868870 TTCAGGTT-AGCAAGAAC
1 TTCAGGTTCA-CAAGAAT
**
19868887 TTCAGGTTCGTAAGAAT
1 TTCAGGTTCACAAGAAT
19868904 TT
1 TT
19868906 AATATTCGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (17 bp):
TTCAGGTTCACAAGAAT
Found at i:19868874 original size:34 final size:34
Alignment explanation
Indices: 19868811--19868905 Score: 97
Period size: 34 Copynumber: 2.8 Consensus size: 34
19868801 ACTAAGTTTT
* **
19868811 GCAAGAACTTCAAGTTCGTAA-AGGCTTCAGGTTCA
1 GCAAGAACTTCAGGTTCGTAAGA-ATTTCAGGTT-A
**
19868846 -CAAGAGTTTCAGGTTC-TCAAGAATTTCAGGTTA
1 GCAAGAACTTCAGGTTCGT-AAGAATTTCAGGTTA
19868879 GCAAGAACTTCAGGTTCGTAAGAATTT
1 GCAAGAACTTCAGGTTCGTAAGAATTT
19868906 AATATTCGCA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
33 2 0.04
34 45 0.92
35 2 0.04
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (34 bp):
GCAAGAACTTCAGGTTCGTAAGAATTTCAGGTTA
Found at i:19868917 original size:34 final size:34
Alignment explanation
Indices: 19868853--19868919 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
19868843 TCACAAGAGT
* *
19868853 TTCAGGTTCTCAAGAATTTCAGGTTAGCAAGAAC
1 TTCAGGTTCTCAAGAATTTAAGATTAGCAAGAAC
* *
19868887 TTCAGGTTCGT-AAGAATTTAATATTCGCAAGAA
1 TTCAGGTTC-TCAAGAATTTAAGATTAGCAAGAA
19868920 TCTAAGGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (34 bp):
TTCAGGTTCTCAAGAATTTAAGATTAGCAAGAAC
Found at i:19875264 original size:73 final size:73
Alignment explanation
Indices: 19875158--19875310 Score: 288
Period size: 73 Copynumber: 2.1 Consensus size: 73
19875148 AAACCTTTAC
19875158 TTATTTAAAGATTTAATTTTTACATGATTAAAGAGAACTAAAAAAAATTGCAATAGAAATTTGAA
1 TTATTTAAAGATTTAATTTTTACATGATTAAAGAGAACTAAAAAAAATTGCAATAGAAATTTGAA
19875223 ATAAAAAT
66 ATAAAAAT
*
19875231 TTATTTAAAGATTTAATTTTTACATGATTAAAGAGAACTAAAAACAATTGCAATAGAAATTTGAA
1 TTATTTAAAGATTTAATTTTTACATGATTAAAGAGAACTAAAAAAAATTGCAATAGAAATTTGAA
*
19875296 ATAAAAGT
66 ATAAAAAT
19875304 TTATTTA
1 TTATTTA
19875311 GCTGTAAATC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
73 78 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.36
Consensus pattern (73 bp):
TTATTTAAAGATTTAATTTTTACATGATTAAAGAGAACTAAAAAAAATTGCAATAGAAATTTGAA
ATAAAAAT
Found at i:19875359 original size:30 final size:29
Alignment explanation
Indices: 19875321--19875377 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
19875311 GCTGTAAATC
*
19875321 AAAATATAAAAGAT-TATTTAAGTAAAAGA
1 AAAATATAAAAG-TCTATTTAAATAAAAGA
*
19875350 AAAATTATAAGAGTCTATTTAAATAAAA
1 AAAA-TATAAAAGTCTATTTAAATAAAA
19875378 TAATAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (29 bp):
AAAATATAAAAGTCTATTTAAATAAAAGA
Found at i:19876380 original size:24 final size:24
Alignment explanation
Indices: 19876353--19876444 Score: 73
Period size: 25 Copynumber: 3.8 Consensus size: 24
19876343 ATTTTCTTTT
*
19876353 TTTAAAATAAATAAATAAATAGAA
1 TTTAAAATAAATAAATAAATTGAA
* *
19876377 TTTACAAGTAAAATAAA-AAATTCAA
1 TTTA-AAAT-AAATAAATAAATTGAA
* *
19876402 TTATAAATTAAAAAAAT-AATTGAAA
1 TT-TAAAATAAATAAATAAATTG-AA
19876427 TTT-AAATAAATAACATAA
1 TTTAAAATAAATAA-ATAA
19876445 GATAAAAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
23 8 0.15
24 17 0.32
25 19 0.36
26 9 0.17
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (24 bp):
TTTAAAATAAATAAATAAATTGAA
Found at i:19876422 original size:19 final size:20
Alignment explanation
Indices: 19876385--19876422 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19876375 AATTTACAAG
*
19876385 TAAAATAAAAAATTCAATTA
1 TAAAATAAAAAAATCAATTA
*
19876405 TAAATTAAAAAAAT-AATT
1 TAAAATAAAAAAATCAATT
19876423 GAAATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAATAAAAAAATCAATTA
Found at i:19876462 original size:18 final size:20
Alignment explanation
Indices: 19876430--19876467 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
19876420 ATTGAAATTT
*
19876430 AAATAAATAACATAAGATAA
1 AAATAAATAACATAAAATAA
19876450 AAATAAA-AA-ATAAAATAA
1 AAATAAATAACATAAAATAA
19876468 TTACCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (20 bp):
AAATAAATAACATAAAATAA
Found at i:19878002 original size:2 final size:2
Alignment explanation
Indices: 19877997--19878031 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
19877987 TGTGTGTGTC
*
19877997 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19878032 TCCTGCCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19878122 original size:6 final size:6
Alignment explanation
Indices: 19878102--19878136 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
19878092 GAATTAGTGT
*
19878102 ATTTAA TATTAAA ATTTAA ATTTAA ATTTAA ATTT
1 ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA ATTT
19878137 CATTCAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:19881370 original size:5 final size:5
Alignment explanation
Indices: 19881360--19881398 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
19881350 TTTTGTTTGA
19881360 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
19881399 TTATTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:19881896 original size:44 final size:44
Alignment explanation
Indices: 19881758--19881961 Score: 172
Period size: 44 Copynumber: 4.7 Consensus size: 44
19881748 CAAATTAAAC
* * * *
19881758 TCTTCTATATAGAGGC-AAAGAAATCT-AAATTAAGAAATGTGC-
1 TCTTCTATATAGAGACTAAACAACTTTAAAATTAAGAAATG-GCT
* * *
19881800 TCTTCTATACATAGGCTAAACAACTTTAAAA-TAAGAAATGGACT
1 TCTTCTATATAGAGACTAAACAACTTTAAAATTAAGAAATGG-CT
* **
19881844 CCTT-TATATAGAGACTAAGTAACTTTAAAATTAAGAAATGAGCT
1 TCTTCTATATAGAGACTAAACAACTTTAAAATTAAGAAATG-GCT
*
19881888 TC-TCTATATAGA-AGCTAAAACAACTTT-AAATTAAGAAATGGGT
1 TCTTCTATATAGAGA-CT-AAACAACTTTAAAATTAAGAAATGGCT
* ** *
19881931 TCTTTTATATAGAGGTTAAACAATTTTAAAA
1 TCTTCTATATAGAGACTAAACAACTTTAAAA
19881962 ACTTTAAATA
Statistics
Matches: 131, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
42 15 0.11
43 53 0.40
44 54 0.41
45 9 0.07
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (44 bp):
TCTTCTATATAGAGACTAAACAACTTTAAAATTAAGAAATGGCT
Found at i:19881938 original size:88 final size:87
Alignment explanation
Indices: 19881784--19881944 Score: 225
Period size: 88 Copynumber: 1.8 Consensus size: 87
19881774 AAAGAAATCT
* * *
19881784 AAATTAAGAAATGTGCTCTTCTATACATAGGCTAAACAACTTTAAAATAAGAAATGGACTCCTTT
1 AAATTAAGAAATGAGCTCTTCTATACAGAAGCTAAACAACTTTAAAATAAGAAATGGACTCCTTT
19881849 ATATAGAGACTAAGTAACTTTA
66 ATATAGAGACTAAGTAACTTTA
* * ** *
19881871 AAATTAAGAAATGAGCT-TCTCTATATAGAAGCTAAAACAACTTTAAATTAAGAAATGGGTTCTT
1 AAATTAAGAAATGAGCTCT-TCTATACAGAAGCT-AAACAACTTTAAAATAAGAAATGGACTCCT
19881935 TTATATAGAG
64 TTATATAGAG
19881945 GTTAAACAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
86 1 0.02
87 27 0.42
88 36 0.56
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.32
Consensus pattern (87 bp):
AAATTAAGAAATGAGCTCTTCTATACAGAAGCTAAACAACTTTAAAATAAGAAATGGACTCCTTT
ATATAGAGACTAAGTAACTTTA
Found at i:19882259 original size:17 final size:17
Alignment explanation
Indices: 19882223--19882265 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
19882213 GTTTGTAAAT
* *
19882223 GATTCAAGATTCTCAGA
1 GATTCAAGATTCACAAA
*
19882240 GATTCTAGATTCACAAA
1 GATTCAAGATTCACAAA
19882257 GATTTCAAG
1 GA-TTCAAG
19882266 TTTCGCATAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (17 bp):
GATTCAAGATTCACAAA
Found at i:19882481 original size:3 final size:3
Alignment explanation
Indices: 19882475--19882541 Score: 93
Period size: 3 Copynumber: 22.7 Consensus size: 3
19882465 CTTCTTGTTA
* *
19882475 TAT TAT TA- TAT AAT TCT -AT TTAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
19882519 TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
19882542 ATCTTTAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 3 0.05
3 51 0.89
4 3 0.05
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:19884517 original size:34 final size:34
Alignment explanation
Indices: 19884468--19884545 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
19884458 CTTTAGATTC
* * *
19884468 GCAACAATTTCAGGTTTGTAAGAGCTTCAAGTTCT
1 GCAAGAATTTCAGGTTAGTAAGAACTTCAAGTT-T
* *
19884503 -CAAGAATTTTAGGTTAGTAAGAACTTTAAGTTT
1 GCAAGAATTTCAGGTTAGTAAGAACTTCAAGTTT
19884536 GCAAGAATTT
1 GCAAGAATTT
19884546 AAAGTCCGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 1 0.03
34 36 0.97
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (34 bp):
GCAAGAATTTCAGGTTAGTAAGAACTTCAAGTTT
Found at i:19884524 original size:17 final size:17
Alignment explanation
Indices: 19884503--19884550 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
19884493 TTCAAGTTCT
*
19884503 CAAGAATTTTAGGTTAG
1 CAAGAATTTTAAGTTAG
* * *
19884520 TAAGAACTTTAAGTTTG
1 CAAGAATTTTAAGTTAG
*
19884537 CAAGAATTTAAAGT
1 CAAGAATTTTAAGT
19884551 CCGCAATAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (17 bp):
CAAGAATTTTAAGTTAG
Found at i:19884710 original size:11 final size:11
Alignment explanation
Indices: 19884691--19884730 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
19884681 AATCCCATAA
19884691 GAGATTTGTTT
1 GAGATTTGTTT
* *
19884702 GAAATTTGTTA
1 GAGATTTGTTT
19884713 GAGATTTGTTT
1 GAGATTTGTTT
19884724 GAGATTT
1 GAGATTT
19884731 TTCAGATATT
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:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:19889037 original size:22 final size:22
Alignment explanation
Indices: 19889012--19889058 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
19889002 CAATTAGATA
*
19889012 AAATTTAATATATTATAATATT
1 AAATTTAATATATTATAAAATT
* * *
19889034 AAATTTATTTTTTTATAAAATT
1 AAATTTAATATATTATAAAATT
19889056 AAA
1 AAA
19889059 GTTTCCTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTTAATATATTATAAAATT
Found at i:19889495 original size:16 final size:16
Alignment explanation
Indices: 19889474--19889504 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19889464 AAAATTTTTT
19889474 ATTAAAAGTAATAAAA
1 ATTAAAAGTAATAAAA
*
19889490 ATTAAAATTAATAAA
1 ATTAAAAGTAATAAA
19889505 TTTAAAGATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
ATTAAAAGTAATAAAA
Found at i:19889656 original size:12 final size:12
Alignment explanation
Indices: 19889639--19889663 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19889629 TTAAATTATA
19889639 AATAATTTTTTT
1 AATAATTTTTTT
19889651 AATAATTTTTTT
1 AATAATTTTTTT
19889663 A
1 A
19889664 CATATTATTA
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:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATAATTTTTTT
Found at i:19890972 original size:19 final size:20
Alignment explanation
Indices: 19890948--19890992 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
19890938 ATTTTTATTT
*
19890948 TATAAAAATT-TAAAATATA
1 TATAAAAATTATAAAAAATA
*
19890967 TATAAAATTTGATAAAAAATA
1 TATAAAAATT-ATAAAAAATA
19890988 TATAA
1 TATAA
19890993 TTCAATTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
21 13 0.59
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
TATAAAAATTATAAAAAATA
Found at i:19890993 original size:57 final size:57
Alignment explanation
Indices: 19890885--19890994 Score: 127
Period size: 55 Copynumber: 1.9 Consensus size: 57
19890875 ATTATATATA
* * * *
19890885 TTATTTTAATAAAATTTTAAATATATTTAAATAAATTTATATATAAAATAATTATTT
1 TTATTTTAATAAAAATTTAAATATATATAAATAAATTTATAAAAAAAATAATTATTT
*
19890942 TTATTTT-ATAAAAATTTAAA-ATATATATA-AAATTTGATAAAAAATATATAATT
1 TTATTTTAATAAAAATTTAAATATATATAAATAAATTT-ATAAAAAA-A-ATAATT
19890995 CAATTTAGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
54 6 0.13
55 13 0.29
56 13 0.29
57 13 0.29
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (57 bp):
TTATTTTAATAAAAATTTAAATATATATAAATAAATTTATAAAAAAAATAATTATTT
Found at i:19891156 original size:12 final size:12
Alignment explanation
Indices: 19891141--19891166 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19891131 TAATTTTTAA
19891141 TTTTCTCTTTTT
1 TTTTCTCTTTTT
19891153 TTTTCTCTTTTT
1 TTTTCTCTTTTT
19891165 TT
1 TT
19891167 CTCACCTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:19893916 original size:23 final size:23
Alignment explanation
Indices: 19893884--19893934 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
19893874 TATAATATGA
*
19893884 ATAAATAAATTATTATATCTAATT
1 ATAAATAAATGATTATAT-TAATT
* *
19893908 ATAAA-AAATGATTTTATTTATT
1 ATAAATAAATGATTATATTAATT
19893930 ATAAA
1 ATAAA
19893935 GATAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.38
23 10 0.42
24 5 0.21
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAATAAATGATTATATTAATT
Found at i:19894520 original size:17 final size:19
Alignment explanation
Indices: 19894498--19894538 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
19894488 AAGTAAGTTT
19894498 TTATTTTA-AATAAAAAA-
1 TTATTTTACAATAAAAAAC
*
19894515 TTA-TTTACATTAAAAAAC
1 TTATTTTACAATAAAAAAC
19894533 TTATTT
1 TTATTT
19894539 AAGTACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 4 0.20
17 11 0.55
18 3 0.15
19 2 0.10
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATTTTACAATAAAAAAC
Found at i:19895315 original size:29 final size:29
Alignment explanation
Indices: 19895248--19895323 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
19895238 CTAAAATTTA
*
19895248 ATAATTATTTAAATTTTTTATTTTTAATT
1 ATAATTAATTAAATTTTTTATTTTTAATT
*
19895277 ATAATCAATTAAATTTTTTATTTTT-ATT
1 ATAATTAATTAAATTTTTTATTTTTAATT
* *
19895305 TTAAATTAATTACATTTTT
1 AT-AATTAATTAAATTTTT
19895324 AAATTAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
28 4 0.10
29 37 0.90
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (29 bp):
ATAATTAATTAAATTTTTTATTTTTAATT
Found at i:19896292 original size:2 final size:2
Alignment explanation
Indices: 19896287--19896311 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19896277 CGTTTGTGTG
19896287 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
19896312 TTACCTTCCT
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:19896783 original size:13 final size:13
Alignment explanation
Indices: 19896765--19896794 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19896755 TTTAGTAAGC
*
19896765 AAATAATATATAT
1 AAATAAAATATAT
19896778 AAATAAAATATAT
1 AAATAAAATATAT
19896791 AAAT
1 AAAT
19896795 TTATAAGCTG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATAAAATATAT
Found at i:19897170 original size:17 final size:16
Alignment explanation
Indices: 19897144--19897178 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
19897134 TGTGCAAATT
*
19897144 AATGATAAATATATAA
1 AATGATAAATAAATAA
19897160 AATGAATAAATAAATAA
1 AATG-ATAAATAAATAA
19897177 AA
1 AA
19897179 CAAATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
AATGATAAATAAATAA
Found at i:19897184 original size:17 final size:17
Alignment explanation
Indices: 19897148--19897186 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
19897138 CAAATTAATG
* **
19897148 ATAAATATATAAAATGA
1 ATAAATAAATAAAACAA
19897165 ATAAATAAATAAAACAA
1 ATAAATAAATAAAACAA
19897182 ATAAA
1 ATAAA
19897187 ATACAAACAA
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:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (17 bp):
ATAAATAAATAAAACAA
Found at i:19899764 original size:12 final size:12
Alignment explanation
Indices: 19899747--19899777 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19899737 TTTTCAAAAA
19899747 TTTTATTAATTG
1 TTTTATTAATTG
*
19899759 TTTTATTAATTT
1 TTTTATTAATTG
19899771 TTTTATT
1 TTTTATT
19899778 TTTAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTTATTAATTG
Found at i:19901375 original size:27 final size:27
Alignment explanation
Indices: 19901317--19901386 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
19901307 AAGAAGGAAA
* *
19901317 AAATAAATAAATAGAAAATGAAAAAAT
1 AAATAAATAAATATATAATGAAAAAAT
19901344 AAATAAATAAATATATAAT-AATAATAAT
1 AAATAAATAAATATATAATGAA-AA-AAT
19901372 -AAT-AATAAATTATAT
1 AAATAAATAAA-TATAT
19901387 TTACAGCAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 8 0.21
27 27 0.71
28 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (27 bp):
AAATAAATAAATATATAATGAAAAAAT
Found at i:19903011 original size:15 final size:14
Alignment explanation
Indices: 19902986--19903018 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
19902976 CACTGAAGAC
19902986 CTTGGATTCAAGTG
1 CTTGGATTCAAGTG
19903000 CTTGGCATTCAAGTG
1 CTTGG-ATTCAAGTG
19903015 CTTG
1 CTTG
19903019 ACCTATTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (14 bp):
CTTGGATTCAAGTG
Found at i:19903776 original size:30 final size:30
Alignment explanation
Indices: 19903725--19903791 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
19903715 TTTAAATAAG
19903725 TTTATATATTTTTATTATATTCAAATAAATC
1 TTTAT-TATTTTTATTATATTCAAATAAATC
*
19903756 TTTATTA-TTTTATTCGTATTCAAATAAATC
1 TTTATTATTTTTATT-ATATTCAAATAAATC
*
19903786 ATTATT
1 TTTATT
19903792 TCAAACGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 7 0.21
30 21 0.64
31 5 0.15
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.55
Consensus pattern (30 bp):
TTTATTATTTTTATTATATTCAAATAAATC
Found at i:19903919 original size:30 final size:30
Alignment explanation
Indices: 19903813--19903920 Score: 126
Period size: 30 Copynumber: 3.6 Consensus size: 30
19903803 TTTGATTTAC
* *
19903813 ATTAAAAATTTATTTAAATACAAATTAAAG
1 ATTAAAAATTTATTTGAATACAAATTAAAA
* * * *
19903843 GTTAATAATTTATTTTAATATAAATTAAAA
1 ATTAAAAATTTATTTGAATACAAATTAAAA
* *
19903873 AGTTAAAAACTTATTTGAATGCAAATTAAAA
1 A-TTAAAAATTTATTTGAATACAAATTAAAA
*
19903904 ATTAAAAAATTATTTGA
1 ATTAAAAATTTATTTGA
19903921 TTATAATAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 40 0.62
31 25 0.38
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (30 bp):
ATTAAAAATTTATTTGAATACAAATTAAAA
Found at i:19904914 original size:20 final size:20
Alignment explanation
Indices: 19904891--19904937 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19904881 TGTACTCAAA
19904891 TAAATTTTTAATTTTTAATT
1 TAAATTTTTAATTTTTAATT
**
19904911 TAAACCTTTAATTTTTAATT
1 TAAATTTTTAATTTTTAATT
*
19904931 TATATTT
1 TAAATTT
19904938 AAATAAACTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TAAATTTTTAATTTTTAATT
Found at i:19905488 original size:23 final size:23
Alignment explanation
Indices: 19905462--19905510 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
19905452 AATTAAGATA
*
19905462 AAAATTTAATATATTATAATATT
1 AAAATTTAATATATTATAAAATT
* * *
19905485 AAAATTTATTTTTTTATAAAATT
1 AAAATTTAATATATTATAAAATT
19905508 AAA
1 AAA
19905511 GTTTCCTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATTTAATATATTATAAAATT
Found at i:19905604 original size:21 final size:20
Alignment explanation
Indices: 19905548--19905605 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
19905538 AAAATATCAT
19905548 AAAAATAATTTTAAACTATA
1 AAAAATAATTTTAAACTATA
* *
19905568 AAAGTAAGAGTTTTAAA-TATTTA
1 AAA--AATAATTTTAAACTA--TA
19905591 AAAAATAATTTTAAA
1 AAAAATAATTTTAAA
19905606 ACATCTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 3 0.10
21 12 0.40
22 10 0.33
23 5 0.17
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAAATAATTTTAAACTATA
Found at i:19906039 original size:36 final size:37
Alignment explanation
Indices: 19905974--19906056 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 37
19905964 TTATGAAATT
19905974 TTTTATTAAAAAAATTAAAATCAATAAA-TTAAAAAA
1 TTTTATTAAAAAAATTAAAATCAATAAATTTAAAAAA
* *
19906010 TTTTATTATATAAATT-AAAT-ATATAAAATTTAAAAAA
1 TTTTATTAAAAAAATTAAAATCA-AT-AAATTTAAAAAA
* *
19906047 TCTTAATAAA
1 TTTTATTAAA
19906057 TTTTGATCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
34 1 0.03
35 6 0.15
36 17 0.44
37 15 0.38
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (37 bp):
TTTTATTAAAAAAATTAAAATCAATAAATTTAAAAAA
Found at i:19906237 original size:25 final size:26
Alignment explanation
Indices: 19906186--19906236 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
19906176 TTGATATTCA
19906186 TATT-AAATTTTATCAATTTATTTTT
1 TATTAAAATTTTATCAATTTATTTTT
**
19906211 TATTAAAATTTTATTTATTTATTTTT
1 TATTAAAATTTTATCAATTTATTTTT
19906237 AATAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
TATTAAAATTTTATCAATTTATTTTT
Found at i:19906244 original size:26 final size:26
Alignment explanation
Indices: 19906190--19906244 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
19906180 TATTCATATT
* *
19906190 AAATTTTATCAATTTATTTTTTATTA
1 AAATTTTATCAATTTATTTTTAATAA
**
19906216 AAATTTTATTTATTTATTTTTAATAA
1 AAATTTTATCAATTTATTTTTAATAA
19906242 AAA
1 AAA
19906245 ATTTCATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
AAATTTTATCAATTTATTTTTAATAA
Found at i:19906257 original size:27 final size:26
Alignment explanation
Indices: 19906190--19906257 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
19906180 TATTCATATT
* * *
19906190 AAATTTTATCAATTTATTTTTTATTA
1 AAATTTTATAAATTTATTTTTAATAA
**
19906216 AAATTTTATTTATTTATTTTTAATAAA
1 AAATTTTATAAATTTATTTTTAAT-AA
*
19906243 AAATTTCATAAATTT
1 AAATTTTATAAATTT
19906258 TATCTACGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 21 0.62
27 13 0.38
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (26 bp):
AAATTTTATAAATTTATTTTTAATAA
Found at i:19906843 original size:6 final size:6
Alignment explanation
Indices: 19906832--19906857 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19906822 ATTATAAATT
19906832 TTTAAA TTTAAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TT
19906858 ATTTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:19909936 original size:25 final size:25
Alignment explanation
Indices: 19909890--19909938 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
19909880 TAATATAAAT
19909890 ATATGAATTATCAATATTTTATATA
1 ATATGAATTATCAATATTTTATATA
19909915 ATATGAATATAT-AA-ATTATTATAT
1 ATATGAAT-TATCAATATT-TTATAT
19909939 CTAATTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.14
25 16 0.73
26 3 0.14
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (25 bp):
ATATGAATTATCAATATTTTATATA
Found at i:19909948 original size:33 final size:33
Alignment explanation
Indices: 19909876--19909948 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
19909866 TTTTATATAA
* *
19909876 AATATAATATAAATATATGAATTATCAATATTT
1 AATATAATATAAATATATAAATTATCAATATCT
* * *
19909909 TATATAATATGAATATATAAATTAT-TATATCT
1 AATATAATATAAATATATAAATTATCAATATCT
19909941 AATTATAA
1 AA-TATAA
19909949 AAAATGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
32 6 0.18
33 27 0.82
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (33 bp):
AATATAATATAAATATATAAATTATCAATATCT
Found at i:19909953 original size:23 final size:22
Alignment explanation
Indices: 19909927--19909971 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
19909917 ATGAATATAT
*
19909927 AAATTATTATATCTAATTATAAA
1 AAATGATTATAT-TAATTATAAA
* *
19909950 AAATGATTTTATTTATTATAAA
1 AAATGATTATATTAATTATAAA
19909972 GATAACAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATGATTATATTAATTATAAA
Done.