Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold38
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: 2073527
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 11 of 15
Found at i:1476903 original size:3 final size:3
Alignment explanation
Indices: 1476895--1476919 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1476885 TAAAACCGTG
1476895 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1476920 GAAAACATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1477065 original size:2 final size:2
Alignment explanation
Indices: 1477058--1477088 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1477048 GTTTTTCTAA
1477058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1477089 ACTATTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1479043 original size:232 final size:232
Alignment explanation
Indices: 1478635--1479112 Score: 866
Period size: 232 Copynumber: 2.1 Consensus size: 232
1478625 AAAAGGTGTT
*
1478635 AGCTCCTTCATATTATGTTATACCATATAAGTACATAAAATAGACAGCAAGCTCCTTTATATTAG
1 AGCTCCTTCATATTATGTTATACCATATAAGTACATAAAATAGACAGCAAGCTCCTGTATATTAG
1478700 GTCATACCGTATAAGTATAAAAGAGACTGTAAACTTTATTATATTAGGTCGTGCTGTACAAGTGT
66 GTCATACCGTATAAGTATAAAAGAGACTGTAAACTTTATTATATTAGGTCGTGCTGTACAAGTGT
* *
1478765 GTGGAAAATATCATAAGCTCCTTTACATTAGGTCATACCAATAAGTACATAAAAACCCGTAAGCT
131 GTGGAAAATACCACAAGCTCCTTTACATTAGGTCATACCAATAAGTACATAAAAACCCGTAAGCT
1478830 TCTTTATATTAAGTATAAGTACGTAAAATAGTCCATA
196 TCTTTATATTAAGTATAAGTACGTAAAATAGTCCATA
* * * *
1478867 AGCTCCTCCATATTATGTTATGCCATGTAAGTACATAAAATAGACAGCAAGCTCCTGTCTATTAG
1 AGCTCCTTCATATTATGTTATACCATATAAGTACATAAAATAGACAGCAAGCTCCTGTATATTAG
*
1478932 GTCATACCGTATAAGTATAAAAGAGACTGTAAGCTTTATTATATTAGGTCGTGCTGTACAAGTGT
66 GTCATACCGTATAAGTATAAAAGAGACTGTAAACTTTATTATATTAGGTCGTGCTGTACAAGTGT
* *
1478997 GTGGAAAATACCACAAGCTTCTTTACATTAGGTCATACCTATAAGTACATAAAAACCCGTAAGCT
131 GTGGAAAATACCACAAGCTCCTTTACATTAGGTCATACCAATAAGTACATAAAAACCCGTAAGCT
1479062 TCTTTATATTAAGTATAAGTACGTAAAATAGTCCATA
196 TCTTTATATTAAGTATAAGTACGTAAAATAGTCCATA
1479099 AGCTCCTTCATATT
1 AGCTCCTTCATATT
1479113 GGATCTACCA
Statistics
Matches: 235, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
232 235 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (232 bp):
AGCTCCTTCATATTATGTTATACCATATAAGTACATAAAATAGACAGCAAGCTCCTGTATATTAG
GTCATACCGTATAAGTATAAAAGAGACTGTAAACTTTATTATATTAGGTCGTGCTGTACAAGTGT
GTGGAAAATACCACAAGCTCCTTTACATTAGGTCATACCAATAAGTACATAAAAACCCGTAAGCT
TCTTTATATTAAGTATAAGTACGTAAAATAGTCCATA
Found at i:1485013 original size:233 final size:233
Alignment explanation
Indices: 1484606--1485071 Score: 896
Period size: 233 Copynumber: 2.0 Consensus size: 233
1484596 TAACTGCTTC
*
1484606 GCTTGACGCAACATGGTGCTTTTATGATCTTTCCTCTGGCATATGCTTGACACAGGTCCTAACTC
1 GCTTGACGCAACATGGTGCTTTTATGATCTTTCCTCTAGCATATGCTTGACACAGGTCCTAACTC
*
1484671 TTCCTGATCTGTGAGGTTTCGATAACAACGAGCATCTTATTATCACTCATGAAGTAAATGAATTA
66 TTCCTGATCTGTGAGGTTTCCATAACAACGAGCATCTTATTATCACTCATGAAGTAAATGAATTA
1484736 ATTGGTCTCTTATTAATTAACAGCATCTTATGTTAGTATTTAATCTCTTTAATTGACCCTGAATT
131 ATTGGTCTCTTATTAATTAACAGCATCTTATGTTAGTATTTAATCTCTTTAATTGACCCTGAATT
1484801 CTGGGTTCTGACATTAAATATAACCCGTGTTTAACTGA
196 CTGGGTTCTGACATTAAATATAACCCGTGTTTAACTGA
1484839 GCTTGACGCAACATGGTGCTTTTATGATCTTTCCTCTAGCATATGCTTGACACAGGTCCTAACTC
1 GCTTGACGCAACATGGTGCTTTTATGATCTTTCCTCTAGCATATGCTTGACACAGGTCCTAACTC
*
1484904 TTCCTGATCTGTGAGGTTTCCATAACAATGAGCATCTTATTATCACTCATGAAGTAAATGAATTA
66 TTCCTGATCTGTGAGGTTTCCATAACAACGAGCATCTTATTATCACTCATGAAGTAAATGAATTA
*
1484969 ATTGGTCTCTTATTAATTAACAGCATCTTATGTTAGTTTTTAATCTCTTTAATTGACCCTGAATT
131 ATTGGTCTCTTATTAATTAACAGCATCTTATGTTAGTATTTAATCTCTTTAATTGACCCTGAATT
1485034 CTGGGTTCTGACATTAAATATAACCCGTGTTTAACTGA
196 CTGGGTTCTGACATTAAATATAACCCGTGTTTAACTGA
1485072 TTCATGAAGT
Statistics
Matches: 229, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
233 229 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (233 bp):
GCTTGACGCAACATGGTGCTTTTATGATCTTTCCTCTAGCATATGCTTGACACAGGTCCTAACTC
TTCCTGATCTGTGAGGTTTCCATAACAACGAGCATCTTATTATCACTCATGAAGTAAATGAATTA
ATTGGTCTCTTATTAATTAACAGCATCTTATGTTAGTATTTAATCTCTTTAATTGACCCTGAATT
CTGGGTTCTGACATTAAATATAACCCGTGTTTAACTGA
Found at i:1487561 original size:20 final size:20
Alignment explanation
Indices: 1487522--1487566 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1487512 AAATAATTTT
*
1487522 AATATTAAATAAATAGTAAA
1 AATATTAAATAAATAATAAA
* **
1487542 TATATTAAATACTTAATAAA
1 AATATTAAATAAATAATAAA
1487562 AATAT
1 AATAT
1487567 ATAATAGTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
AATATTAAATAAATAATAAA
Found at i:1489391 original size:2 final size:2
Alignment explanation
Indices: 1489384--1489428 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1489374 AATCATGAGA
1489384 AT AT AT 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
1489426 AT A
1 AT A
1489429 ATACTTTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1492485 original size:6 final size:6
Alignment explanation
Indices: 1492464--1492494 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
1492454 AAAGTGTTTG
1492464 AAAATA AAATATA AAAATA AAAATA AAAATA
1 AAAATA AAA-ATA AAAATA AAAATA AAAATA
1492495 TTTTATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:1492508 original size:40 final size:40
Alignment explanation
Indices: 1492464--1492545 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
1492454 AAAGTGTTTG
*
1492464 AAAATAAAATATAAAA-ATAAAAATAAAAATATTTTATTTA
1 AAAATAAAATA-AAAATATAAAAATAAAAATATTTTATATA
** ** *
1492504 AAAATATCATAAAAATATATTAATAAAAGTATTTTATATA
1 AAAATAAAATAAAAATATAAAAATAAAAATATTTTATATA
1492544 AA
1 AA
1492546 TTATTTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (40 bp):
AAAATAAAATAAAAATATAAAAATAAAAATATTTTATATA
Found at i:1493345 original size:33 final size:34
Alignment explanation
Indices: 1493292--1493382 Score: 89
Period size: 36 Copynumber: 2.6 Consensus size: 34
1493282 AATAATTATA
** *
1493292 ATTAATAAAAAATTAAAATAAATA-TTTTTATATT
1 ATTAATAATTAATTCAAATAAATATTTTTTA-ATT
*
1493326 -TT-ATAATTAATTTTAAATAAAAATATTTTTTAATT
1 ATTAATAATTAA-TTCAAAT--AAATATTTTTTAATT
1493361 ATTAATAATTAATTCAAATAAA
1 ATTAATAATTAATTCAAATAAA
1493383 GTCGATTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
32 6 0.13
33 8 0.17
34 3 0.06
35 8 0.17
36 14 0.30
37 8 0.17
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
ATTAATAATTAATTCAAATAAATATTTTTTAATT
Found at i:1493349 original size:39 final size:36
Alignment explanation
Indices: 1493279--1493382 Score: 95
Period size: 39 Copynumber: 2.8 Consensus size: 36
1493269 ATTATTTATA
* ** *
1493279 TTTAATAATTATAATTAATAAAAAATTAAAATAAATATT
1 TTTAATTATTATAATTAATTTAAAA-TAAAA-ATAT-TT
*
1493318 TTTATATT-TTATAATTAATTTTAAATAAAAATATTT
1 TTTA-ATTATTATAATTAATTTAAAATAAAAATATTT
*
1493354 TTTAATTATTAATAATTAA-TTCAAATAAA
1 TTTAATTATT-ATAATTAATTTAAAATAAA
1493383 GTCGATTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
35 3 0.05
36 17 0.30
37 11 0.20
38 5 0.09
39 18 0.32
40 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (36 bp):
TTTAATTATTATAATTAATTTAAAATAAAAATATTT
Found at i:1493380 original size:36 final size:35
Alignment explanation
Indices: 1493311--1493382 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 35
1493301 AAATTAAAAT
*
1493311 AAATATTTTTATATTTTATAATTAATTTTAAATAA
1 AAATATTTTTATATTTTATAATTAATTTCAAATAA
1493346 AAATATTTTT-TAATTATTAATAATTAA-TTCAAATAA
1 AAATATTTTTAT-ATT-TT-ATAATTAATTTCAAATAA
1493382 A
1 A
1493383 GTCGATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
34 1 0.03
35 13 0.39
36 11 0.33
37 8 0.24
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (35 bp):
AAATATTTTTATATTTTATAATTAATTTCAAATAA
Found at i:1493741 original size:26 final size:25
Alignment explanation
Indices: 1493699--1493759 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
1493689 CTTAATAAAA
* *
1493699 TTAAATTAAATTATTATAT-TTAATT
1 TTAAATTTAATTATTATATCTGAA-T
1493724 TTAAATTTAATTATTTATATCTGAAT
1 TTAAATTTAATTA-TTATATCTGAAT
1493750 TTAAATTTAA
1 TTAAATTTAA
1493760 ATATAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 12 0.38
26 17 0.53
27 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
TTAAATTTAATTATTATATCTGAAT
Found at i:1493778 original size:20 final size:20
Alignment explanation
Indices: 1493755--1493792 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1493745 TGAATTTAAA
1493755 TTTAAATATAAATTAAAATT
1 TTTAAATATAAATTAAAATT
*
1493775 TTTAAATATTAATTAAAA
1 TTTAAATATAAATTAAAA
1493793 ATAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAATATAAATTAAAATT
Found at i:1493800 original size:20 final size:20
Alignment explanation
Indices: 1493757--1493800 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1493747 AATTTAAATT
* **
1493757 TAAATATAAATTAAAATTTT
1 TAAATATAAATTAAAAATAA
*
1493777 TAAATATTAATTAAAAATAA
1 TAAATATAAATTAAAAATAA
1493797 TAAA
1 TAAA
1493801 AATATTTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAATATAAATTAAAAATAA
Found at i:1497308 original size:14 final size:14
Alignment explanation
Indices: 1497289--1497315 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1497279 TATTTTTATG
1497289 ATAATATGATATTA
1 ATAATATGATATTA
1497303 ATAATATGATATT
1 ATAATATGATATT
1497316 TTATTTTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
ATAATATGATATTA
Found at i:1497840 original size:30 final size:32
Alignment explanation
Indices: 1497805--1497890 Score: 103
Period size: 28 Copynumber: 2.8 Consensus size: 32
1497795 ATTTTATAAC
1497805 ATAAATATTATATAAAAAATAAT-TAAAATAT
1 ATAAATATTATATAAAAAATAATATAAAATAT
*
1497836 -TAAATA--ATAT-AAAAATAATATTAAATAT
1 ATAAATATTATATAAAAAATAATATAAAATAT
*
1497864 ATAAATATTTATATAATAAA-AATATAA
1 ATAAATA-TTATATAAAAAATAATATAA
1497891 TAAATTATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
27 9 0.20
28 11 0.24
29 6 0.13
30 6 0.13
32 10 0.22
33 4 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (32 bp):
ATAAATATTATATAAAAAATAATATAAAATAT
Found at i:1497850 original size:28 final size:29
Alignment explanation
Indices: 1497805--1497920 Score: 82
Period size: 26 Copynumber: 4.0 Consensus size: 29
1497795 ATTTTATAAC
1497805 ATAAATATTATATAAAAAATAAT-TAAAATAT
1 ATAAATA--ATAT-AAAAATAATATAAAATAT
*
1497836 -TAAATAATATAAAAATAATATTAAATAT
1 ATAAATAATATAAAAATAATATAAAATAT
* *
1497864 ATAAAT-AT-T-TATATAATA-AAAATAT
1 ATAAATAATATAAAAATAATATAAAATAT
* * *
1497889 AATAAATTATAATAAATATAAATATATAATAT
1 -ATAAATAAT-ATAAAAAT-AATATAAAATAT
1497921 TTTAAATATA
Statistics
Matches: 70, Mismatches: 6, Indels: 17
0.75 0.06 0.18
Matches are distributed among these distances:
25 6 0.09
26 13 0.19
27 12 0.17
28 13 0.19
29 6 0.09
30 10 0.14
31 4 0.06
32 6 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
ATAAATAATATAAAAATAATATAAAATAT
Found at i:1497901 original size:10 final size:9
Alignment explanation
Indices: 1497841--1497919 Score: 60
Period size: 8 Copynumber: 9.0 Consensus size: 9
1497831 AATATTAAAT
1497841 AATATAA-A
1 AATATAATA
*
1497849 AATAATATTA
1 AAT-ATAATA
1497859 AATAT-ATA
1 AATATAATA
*
1497867 AATAT-TTA
1 AATATAATA
*
1497875 TATAATAA-A
1 AAT-ATAATA
1497884 AATATAATA
1 AATATAATA
1497893 AATTATAATA
1 AA-TATAATA
1497903 AATATAA-A
1 AATATAATA
*
1497911 TATATAATA
1 AATATAATA
1497920 TTTTAAATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
8 25 0.44
9 19 0.33
10 13 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
AATATAATA
Found at i:1497910 original size:62 final size:62
Alignment explanation
Indices: 1497805--1497930 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 62
1497795 ATTTTATAAC
1497805 ATAAATATTATATAAAAAATAATTAAAATATTAAATAATATAAA-A-ATAATA-TTAAATAT
1 ATAAATATTATATAAAAAATAATTAAAATATTAAATAATATAAATATATAATATTTAAATAT
*
1497864 ATAAATATTTATATAATAAA-AATATAATAA-ATTATAATAAATATAAATATATAATATTTTAAA
1 ATAAATA-TTATATAAAAAATAAT-TAA-AATATTA-AAT-AATATAAATATATAATA-TTTAAA
1497927 TAT
60 TAT
1497930 A
1 A
1497931 ATTATATATA
Statistics
Matches: 57, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
59 10 0.18
60 18 0.32
61 5 0.09
62 8 0.14
63 1 0.02
64 6 0.11
66 9 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (62 bp):
ATAAATATTATATAAAAAATAATTAAAATATTAAATAATATAAATATATAATATTTAAATAT
Found at i:1497926 original size:16 final size:16
Alignment explanation
Indices: 1497856--1497930 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 16
1497846 AAAAATAATA
1497856 TTAAATATATAAATATT
1 TTAAATATAT-AATATT
* *
1497873 TATATAATA-AAAATATA
1 T-TA-AATATATAATATT
* *
1497890 ATAAAT-TATAATAAAT
1 TTAAATATATAAT-ATT
*
1497906 ATAAATATATAATATT
1 TTAAATATATAATATT
1497922 TTAAATATA
1 TTAAATATA
1497931 ATTATATATA
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
15 7 0.16
16 19 0.42
17 12 0.27
18 3 0.07
19 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAATATATAATATT
Found at i:1497962 original size:19 final size:19
Alignment explanation
Indices: 1497926--1497962 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1497916 AATATTTTAA
* *
1497926 ATATAATTATATATAATAC
1 ATATAATTATACAAAATAC
1497945 ATATAATTATACAAAATA
1 ATATAATTATACAAAATA
1497963 AAATATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATAATTATACAAAATAC
Found at i:1499363 original size:22 final size:22
Alignment explanation
Indices: 1499335--1499379 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1499325 TGTGTTCTCA
1499335 TAGATTATATTATATATTTATG
1 TAGATTATATTATATATTTATG
*
1499357 TAGATTATATTTTATATTTATG
1 TAGATTATATTATATATTTATG
1499379 T
1 T
1499380 TTGAATATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (22 bp):
TAGATTATATTATATATTTATG
Found at i:1503295 original size:27 final size:25
Alignment explanation
Indices: 1503244--1503298 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 25
1503234 AATTTAATAA
1503244 TTTAAAAATATTTTAATATTCTATT
1 TTTAAAAATATTTTAATATTCTATT
*
1503269 TTTAAAATATAATTTTATTAGTT-TATT
1 TTTAAAA-AT-ATTTTAATA-TTCTATT
1503296 TTT
1 TTT
1503299 TATATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 7 0.27
26 2 0.08
27 15 0.58
28 2 0.08
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTAAAAATATTTTAATATTCTATT
Found at i:1510903 original size:3 final size:3
Alignment explanation
Indices: 1510895--1510923 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1510885 CTCAGGGGAG
1510895 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1510924 GCTTCAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1512164 original size:16 final size:16
Alignment explanation
Indices: 1512140--1512189 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
1512130 AAATATAATA
*
1512140 TAAAAATAATTAAAAT
1 TAAATATAATTAAAAT
1512156 TAAATATAATATAAAAT
1 TAAATATAAT-TAAAAT
*
1512173 T-AATATAATTTAAAT
1 TAAATATAATTAAAAT
1512188 TA
1 TA
1512190 TTAATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 6 0.20
16 17 0.57
17 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATATAATTAAAAT
Found at i:1512247 original size:25 final size:26
Alignment explanation
Indices: 1512219--1512277 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
1512209 ATAAATATAT
1512219 AATATTTTAAATA-AA-TTATATAAAA
1 AATA-TTTAAATAGAATTTATATAAAA
1512244 AATA--TAAATATGAATTTATATAAAA
1 AATATTTAAATA-GAATTTATATAAAA
1512269 AATAATTTA
1 AAT-ATTTA
1512278 TATATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
22 6 0.21
24 2 0.07
25 17 0.61
26 1 0.04
28 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
AATATTTAAATAGAATTTATATAAAA
Found at i:1518968 original size:22 final size:23
Alignment explanation
Indices: 1518943--1519002 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
1518933 AAAATTATTT
* *
1518943 TTATTTAAATTTAATTATAA-AA
1 TTATTTAAATTTAATAAAAATAA
*
1518965 TTATATAAATATTAATAAAAATAA
1 TTATTTAAAT-TTAATAAAAATAA
1518989 TT-TTTAATATTTAA
1 TTATTTAA-ATTTAA
1519003 ATACATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 9 0.29
23 16 0.52
24 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTATTTAAATTTAATAAAAATAA
Found at i:1519021 original size:18 final size:17
Alignment explanation
Indices: 1518978--1519024 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
1518968 TATAAATATT
*
1518978 AATAA-AAATAATTTTT
1 AATAATAAATAATTTTA
*
1518994 AATATTTAAATACATTTTA
1 AATA-ATAAATA-ATTTTA
1519013 AATAATAAATAA
1 AATAATAAATAA
1519025 AATTTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 4 0.16
17 1 0.04
18 11 0.44
19 9 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAATAAATAATTTTA
Found at i:1519029 original size:19 final size:19
Alignment explanation
Indices: 1518977--1519035 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
1518967 ATATAAATAT
*
1518977 TAATAAA-AATAATTTTTAA
1 TAATAAATAA-AATTTTAAA
* *
1518996 TATTTAAAT-ACATTTTAAA
1 TA-ATAAATAAAATTTTAAA
1519015 TAATAAATAAAATTTTTAAA
1 TAATAAATAAAA-TTTTAAA
1519035 T
1 T
1519036 TTACTGTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAATAAAATTTTAAA
Found at i:1519645 original size:45 final size:45
Alignment explanation
Indices: 1519556--1519664 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
1519546 CATTCCCAAT
* *
1519556 ACTGGAGCTCTAGGGATCCAGTGAGAAACTGAAGCTCCAATCCATG
1 ACTGGAGCTCT-GGGGTCCAATGAGAAACTGAAGCTCCAATCCATG
* * * * *
1519602 ACTGGAGCTCTGGGGTCCAATGAGAAATTGGAGTTCTAGTCCATG
1 ACTGGAGCTCTGGGGTCCAATGAGAAACTGAAGCTCCAATCCATG
* *
1519647 ACCGGTGCTCTGAGGGTC
1 ACTGGAGCTCTG-GGGTC
1519665 TAGTTACCAG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 37 0.70
46 16 0.30
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (45 bp):
ACTGGAGCTCTGGGGTCCAATGAGAAACTGAAGCTCCAATCCATG
Found at i:1519791 original size:28 final size:28
Alignment explanation
Indices: 1519757--1519914 Score: 100
Period size: 28 Copynumber: 5.2 Consensus size: 28
1519747 TTTGTTTGAT
1519757 ATATAAATATAATTTTAATAATTATTTA
1 ATATAAATATAATTTTAATAATTATTTA
*
1519785 ATATAAACATAATTTTTAATATAAACTTATATTTTA
1 ATATAAATATAA-TTTT-A-AT-AA--T-TA-TTTA
* * * * *
1519821 TTGTAGATATAATATTAATAATTTTTTA
1 ATATAAATATAATTTTAATAATTATTTA
* * * *
1519849 AAATAGATATAATTTTTAATTATTAGTTA
1 ATATAAATATAA-TTTTAATAATTATTTA
* * *
1519878 ATATAAAAATAATTTTATTATTTAATTTAA
1 ATATAAATATAATTTTAATAATT-ATTT-A
1519908 ATATAAA
1 ATATAAA
1519915 ATTTAATTAT
Statistics
Matches: 98, Mismatches: 21, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
28 32 0.33
29 29 0.30
30 10 0.10
31 2 0.02
32 4 0.04
33 2 0.02
34 2 0.02
35 5 0.05
36 12 0.12
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (28 bp):
ATATAAATATAATTTTAATAATTATTTA
Found at i:1519804 original size:18 final size:19
Alignment explanation
Indices: 1519774--1519810 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1519764 TATAATTTTA
1519774 ATAATTATTTAATATAAAC
1 ATAATTATTTAATATAAAC
1519793 ATAATT-TTTAATATAAAC
1 ATAATTATTTAATATAAAC
1519811 TTATATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAATTATTTAATATAAAC
Found at i:1519878 original size:29 final size:29
Alignment explanation
Indices: 1519824--1519893 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
1519814 TATTTTATTG
* **
1519824 TAGATATAA-TATTAATAATTTTTTAAAA
1 TAGATATAATTTTTAATAATTAGTTAAAA
* *
1519852 TAGATATAATTTTTAATTATTAGTTAATA
1 TAGATATAATTTTTAATAATTAGTTAAAA
* *
1519881 TAAAAATAATTTT
1 TAGATATAATTTT
1519894 ATTATTTAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 9 0.26
29 25 0.74
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TAGATATAATTTTTAATAATTAGTTAAAA
Found at i:1519897 original size:24 final size:24
Alignment explanation
Indices: 1519868--1519913 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1519858 TAATTTTTAA
1519868 TTATTAGTTAATATAAAAATAATT
1 TTATTAGTTAATATAAAAATAATT
* * *
1519892 TTATTATTTAATTTAAATATAA
1 TTATTAGTTAATATAAAAATAA
1519914 AATTTAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTATTAGTTAATATAAAAATAATT
Found at i:1520041 original size:21 final size:21
Alignment explanation
Indices: 1520015--1520078 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
1520005 AGCATATATT
1520015 TTATTAC-ATATTTTAATTTTA
1 TTATTACAATA-TTTAATTTTA
*
1520036 TTATTATAATATTTAATTTTA
1 TTATTACAATATTTAATTTTA
* *
1520057 TTATTAAAATAATTAATTTTA
1 TTATTACAATATTTAATTTTA
1520078 T
1 T
1520079 CGTCATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 36 0.92
22 3 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTACAATATTTAATTTTA
Found at i:1520060 original size:24 final size:21
Alignment explanation
Indices: 1520027--1520078 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1520017 ATTACATATT
* *
1520027 TTAATTTTATTATTATAATAT
1 TTAATTTTATTATTAAAATAA
1520048 TTAATTTTATTATTAAAATAA
1 TTAATTTTATTATTAAAATAA
1520069 TTAATTTTAT
1 TTAATTTTAT
1520079 CGTCATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAATTTTATTATTAAAATAA
Found at i:1521373 original size:3 final size:3
Alignment explanation
Indices: 1521365--1521393 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1521355 CTGATAATGG
1521365 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1521394 CTAGTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1521527 original size:33 final size:32
Alignment explanation
Indices: 1521448--1521527 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
1521438 TTATATTTAA
* ** *
1521448 AATAAATTATATTTATATTCATTTTGATATATT
1 AATAATTTATA-TTATATAAATTTTAATATATT
1521481 AATAATTTATATTATATAAATTTTAATATATT
1 AATAATTTATATTATATAAATTTTAATATATT
**
1521513 TTTATATTTATATTA
1 AATA-ATTTATATTA
1521528 AGTTTTAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
32 20 0.50
33 20 0.50
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (32 bp):
AATAATTTATATTATATAAATTTTAATATATT
Found at i:1521540 original size:28 final size:29
Alignment explanation
Indices: 1521486--1521554 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 29
1521476 ATATTAATAA
1521486 TTTATA-TTATA-TAAATTTTAATATATT
1 TTTATATTTATATTAAATTTTAATATATT
*
1521513 TTTATATTTATATTAAGTTTTAAT-TATT
1 TTTATATTTATATTAAATTTTAATATATT
1521541 TTT-TATATTATATT
1 TTTATAT-TTATATT
1521555 TATGTAATCG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
27 9 0.24
28 19 0.50
29 10 0.26
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (29 bp):
TTTATATTTATATTAAATTTTAATATATT
Found at i:1521543 original size:29 final size:28
Alignment explanation
Indices: 1521486--1521554 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 28
1521476 ATATTAATAA
1521486 TTTATATTATA-TAAATTTTAATATATT
1 TTTATATTATATTAAATTTTAATATATT
*
1521513 TTTATATTTATATTAAGTTTTAAT-TATTT
1 TTTATA-TTATATTAAATTTTAATATA-TT
1521542 TTTATATTATATT
1 TTTATATTATATT
1521555 TATGTAATCG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
27 6 0.16
28 14 0.37
29 18 0.47
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (28 bp):
TTTATATTATATTAAATTTTAATATATT
Found at i:1522737 original size:22 final size:22
Alignment explanation
Indices: 1522712--1522753 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1522702 ATTAAAATAT
1522712 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1522734 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1522754 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1523146 original size:2 final size:2
Alignment explanation
Indices: 1523139--1523187 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
1523129 GGCATCAAAT
* * *
1523139 TA TA TA TA TA TA TA TA TG TA TA TG TA TA CA 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
1523181 TA TA TA T
1 TA TA TA T
1523188 CAGTTCTGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1523577 original size:17 final size:17
Alignment explanation
Indices: 1523533--1523577 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1523523 TTATTTAAAA
1523533 TAATATTTAAAATTTTT
1 TAATATTTAAAATTTTT
* *
1523550 TAAAATATAAAATTTTT
1 TAATATTTAAAATTTTT
*
1523567 TATTATTTAAA
1 TAATATTTAAA
1523578 TAGTAATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATATTTAAAATTTTT
Found at i:1524945 original size:18 final size:18
Alignment explanation
Indices: 1524924--1524970 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1524914 TATATTAAAC
**
1524924 TATTAATAATTATTTTTA
1 TATTAATAATTATTTACA
1524942 TATTAAT-ATT-TTTACA
1 TATTAATAATTATTTACA
1524958 TATTACATAATTA
1 TATTA-ATAATTA
1524971 AATTTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 9 0.38
17 5 0.21
18 10 0.42
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTAATAATTATTTACA
Found at i:1526358 original size:3 final size:3
Alignment explanation
Indices: 1526341--1526387 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
1526331 GCTTTTCAAA
1526341 ATT A-T ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1526387 A
1 A
1526388 AAACATTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1526514 original size:16 final size:15
Alignment explanation
Indices: 1526496--1526620 Score: 55
Period size: 15 Copynumber: 8.3 Consensus size: 15
1526486 ATTTTTTATT
1526496 TATTAATATATTTTA
1 TATTAATATATTTTA
*
1526511 TTATATAATA-ATTATA
1 -TAT-TAATATATTTTA
*
1526527 T-TTAAAATATTTTA
1 TATTAATATATTTTA
**
1526541 TATT--TATA-TAAA
1 TATTAATATATTTTA
* *
1526553 TTTTAATATATTTAA
1 TATTAATATATTTTA
* * *
1526568 AATT-ATATTATATAA
1 TATTAATA-TATTTTA
* *
1526583 AATTTAAAATATTTTA
1 TA-TTAATATATTTTA
1526599 TATTAATATTATATTTA
1 TATTAATA-TAT-TTTA
1526616 TATTA
1 TATTA
1526621 TTTTTTATCT
Statistics
Matches: 82, Mismatches: 16, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
12 5 0.06
13 7 0.09
14 14 0.17
15 21 0.26
16 19 0.23
17 16 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTAATATATTTTA
Found at i:1526522 original size:20 final size:20
Alignment explanation
Indices: 1526486--1526529 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1526476 TATATATTTC
* *
1526486 ATTTTTTATTTATTAA-TAT
1 ATTTTTTATATAATAATTAT
1526505 ATTTTATTATATAATAATTAT
1 ATTTT-TTATATAATAATTAT
1526526 ATTT
1 ATTT
1526530 AAAATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTTTATATAATAATTAT
Found at i:1526544 original size:37 final size:38
Alignment explanation
Indices: 1526502--1526580 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 38
1526492 TATTTATTAA
* *
1526502 TATATTTTAT-TATATAATAATTATATTTAAAA-TATTT
1 TATATTTTATATAAATAATAA-TATATTTAAAATTATAT
**
1526539 TATA-TTTATATAAATTTTAATATATTTAAAATTATAT
1 TATATTTTATATAAATAATAATATATTTAAAATTATAT
1526576 TATAT
1 TATAT
1526581 AAAATTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
36 16 0.46
37 19 0.54
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (38 bp):
TATATTTTATATAAATAATAATATATTTAAAATTATAT
Found at i:1526582 original size:31 final size:31
Alignment explanation
Indices: 1526538--1526612 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
1526528 TTAAAATATT
* *
1526538 TTATATTTATATAAATTTTAATATATTTAAAA
1 TTATA-TTATATAAAATTTAAAATATTTAAAA
* *
1526570 TTATATTATATAAAATTTAAAATATTTTATA
1 TTATATTATATAAAATTTAAAATATTTAAAA
1526601 TTAATATTATAT
1 TT-ATATTATAT
1526613 TTATATTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TTATATTATATAAAATTTAAAATATTTAAAA
Found at i:1526586 original size:32 final size:32
Alignment explanation
Indices: 1526538--1526612 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
1526528 TTAAAATATT
*
1526538 TTATATT-TATATAAATTTTAATATATTTAAAA
1 TTATATTATATATAAA-TTTAAAATATTTAAAA
* *
1526570 TTATATTATATA-AAATTTAAAATATTTTATA
1 TTATATTATATATAAATTTAAAATATTTAAAA
1526601 TTAATATTATAT
1 TT-ATATTATAT
1526613 TTATATTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 15 0.39
32 19 0.50
33 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TTATATTATATATAAATTTAAAATATTTAAAA
Found at i:1526624 original size:27 final size:26
Alignment explanation
Indices: 1526526--1526603 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 26
1526516 TAATAATTAT
1526526 ATTTAAAATATTTTATATTTATATAAA
1 ATTTAAAATATTTTATA-TTATATAAA
* *
1526553 TTTTAATATATTTAAAATTATATTATATAAA
1 ATTTAAAATA-TT----TTATATTATATAAA
1526584 ATTTAAAATATTTTATATTA
1 ATTTAAAATATTTTATATTA
1526604 ATATTATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
26 8 0.19
27 8 0.19
28 2 0.05
30 2 0.05
31 17 0.40
32 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTTAAAATATTTTATATTATATAAA
Found at i:1527169 original size:20 final size:22
Alignment explanation
Indices: 1527144--1527196 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 22
1527134 ATCTCATGAG
1527144 TTTAATTAAATT-TTTTAT-TT
1 TTTAATTAAATTATTTTATATT
1527164 TTTAA-T--ATTATTTTATATT
1 TTTAATTAAATTATTTTATATT
1527183 TTTAATTAATATTA
1 TTTAATTAA-ATTA
1527197 AAGATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
17 3 0.11
18 6 0.22
19 8 0.30
20 6 0.22
23 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTAATTAAATTATTTTATATT
Found at i:1527492 original size:12 final size:12
Alignment explanation
Indices: 1527464--1527492 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1527454 TAATTTATCA
1527464 TATTTTAAAAAT
1 TATTTTAAAAAT
1527476 T-TTTTAAAAAT
1 TATTTTAAAAAT
1527487 TATTTT
1 TATTTT
1527493 TCTTATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTTTAAAAAT
Found at i:1528810 original size:30 final size:28
Alignment explanation
Indices: 1528767--1528836 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 28
1528757 TAAAAAACAA
1528767 AAAAAATTATATT-TTTAATTATT-TTTTTT
1 AAAAAA-TAT-TTATTTAA-TATTATTTTTT
1528796 AAAAAATATTTATTTAATATTAATTTTTT
1 AAAAAATATTTATTTAATATT-ATTTTTT
1528825 AAAAAATATTTA
1 AAAAAATATTTA
1528837 AAATTTTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.16
28 8 0.21
29 24 0.63
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AAAAAATATTTATTTAATATTATTTTTT
Found at i:1529532 original size:13 final size:13
Alignment explanation
Indices: 1529509--1529567 Score: 68
Period size: 13 Copynumber: 4.5 Consensus size: 13
1529499 AAAATAATTT
1529509 ATTTTAATATATTAA
1 ATTTT-ATA-ATTAA
1529524 TATTTTATAATTAA
1 -ATTTTATAATTAA
1529538 A-TTTA-AATTAA
1 ATTTTATAATTAA
*
1529549 TTTTTATAATTAA
1 ATTTTATAATTAA
1529562 ATTTTA
1 ATTTTA
1529568 GTTATTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
11 6 0.15
12 8 0.21
13 12 0.31
14 5 0.13
15 3 0.08
16 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTATAATTAA
Found at i:1529555 original size:24 final size:24
Alignment explanation
Indices: 1529519--1529595 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 24
1529509 ATTTTAATAT
1529519 ATTAATATTTTATAATTAAATTTAA
1 ATTAAT-TTTTATAATTAAATTTAA
*
1529544 ATTAATTTTTATAATTAAATTTTA
1 ATTAATTTTTATAATTAAATTTAA
* * * *
1529568 GTTATTTTTTATTATTTAATTTAA
1 ATTAATTTTTATAATTAAATTTAA
1529592 ATTA
1 ATTA
1529596 TTAAAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 39 0.87
25 6 0.13
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (24 bp):
ATTAATTTTTATAATTAAATTTAA
Found at i:1531120 original size:18 final size:17
Alignment explanation
Indices: 1531093--1531141 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1531083 TAACTTAAAG
*
1531093 GTTT-TTTTTTAAATAG
1 GTTTATTTTTTAAATAA
**
1531109 GTTTTATTTTTTATTTAA
1 G-TTTATTTTTTAAATAA
1531127 GTTTATTTTTTAAAT
1 GTTTATTTTTTAAAT
1531142 TTAATATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 1 0.04
17 15 0.58
18 10 0.38
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.67
Consensus pattern (17 bp):
GTTTATTTTTTAAATAA
Found at i:1531143 original size:19 final size:18
Alignment explanation
Indices: 1531111--1531162 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
1531101 TTAAATAGGT
1531111 TTTATTTTTT--ATTTAA
1 TTTATTTTTTAAATTTAA
1531127 GTTTATTTTTTAAATTTAA
1 -TTTATTTTTTAAATTTAA
1531146 TATT-TTTATTTAAATTT
1 T-TTATTT-TTTAAATTT
1531163 TTTTAACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 10 0.32
18 4 0.13
19 17 0.55
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTATTTTTTAAATTTAA
Found at i:1533994 original size:20 final size:20
Alignment explanation
Indices: 1533969--1534011 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1533959 TACTCTGCTG
*
1533969 TCTAAGAAAATGTTATGTGA
1 TCTAAGAAAATGTTATGTCA
1533989 TCTAAGAAAATGTTATGTCA
1 TCTAAGAAAATGTTATGTCA
1534009 TCT
1 TCT
1534012 TTTTAAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (20 bp):
TCTAAGAAAATGTTATGTCA
Found at i:1536376 original size:15 final size:15
Alignment explanation
Indices: 1536352--1536385 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1536342 TATCCGATAC
1536352 ATAT-TTAGACATAG
1 ATATATTAGACATAG
1536366 ATATATTAGACATAG
1 ATATATTAGACATAG
1536381 ATATA
1 ATATA
1536386 GTAAAATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (15 bp):
ATATATTAGACATAG
Found at i:1541173 original size:18 final size:18
Alignment explanation
Indices: 1541150--1541243 Score: 55
Period size: 19 Copynumber: 4.8 Consensus size: 18
1541140 CCTAATAGAC
1541150 TTATTTAAATTTAAATTT
1 TTATTTAAATTTAAATTT
*
1541168 TTATTTTATTATTTTATAATAATT
1 TTA-TTTA--AATTTA-AAT--TT
* *
1541192 TAATTTAAA-ATAATATTTT
1 TTATTTAAATTTAA-A-TTT
* *
1541211 TTATTAAAATATTATATTT
1 TTATTTAAAT-TTAAATTT
1541230 TTATTTAAATTTAA
1 TTATTTAAATTTAA
1541244 TTATAAAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 20
0.65 0.12 0.23
Matches are distributed among these distances:
18 6 0.11
19 26 0.46
20 4 0.07
21 9 0.16
22 3 0.05
23 4 0.07
24 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTTAAATTTAAATTT
Found at i:1541232 original size:19 final size:18
Alignment explanation
Indices: 1541196--1541239 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
1541186 ATAATTTAAT
1541196 TTAAAATAATATTTTTTA
1 TTAAAATAATATTTTTTA
*
1541214 TTAAAATATTATATTTTTA
1 TTAAAATAATAT-TTTTTA
*
1541233 TTTAAAT
1 TTAAAAT
1541240 TTAATTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAAATAATATTTTTTA
Found at i:1542350 original size:13 final size:13
Alignment explanation
Indices: 1542332--1542356 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1542322 CAAAGTTCTG
1542332 TTTTTTATTTTTA
1 TTTTTTATTTTTA
1542345 TTTTTTATTTTT
1 TTTTTTATTTTT
1542357 TAACGTGTCT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:1542972 original size:25 final size:26
Alignment explanation
Indices: 1542906--1542975 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
1542896 TTTAATTTTT
1542906 TTTATTTTT-ATAATTATAATTAATA
1 TTTATTTTTAATAATTATAATTAATA
* *
1542931 TTTA-TTATAATTTATTATAA-TAATA
1 TTTATTTTTAA-TAATTATAATTAATA
*
1542956 TTTATTTTTAATCATTATAA
1 TTTATTTTTAATAATTATAA
1542976 ATTATAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
24 3 0.08
25 22 0.58
26 13 0.34
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTATTTTTAATAATTATAATTAATA
Found at i:1543150 original size:18 final size:18
Alignment explanation
Indices: 1543127--1543161 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1543117 AATGGCTCAA
1543127 AGCTAACTGCTGGTTAAG
1 AGCTAACTGCTGGTTAAG
1543145 AGCTAACTGCTGGTTAA
1 AGCTAACTGCTGGTTAA
1543162 TATGGTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
AGCTAACTGCTGGTTAAG
Found at i:1547868 original size:18 final size:17
Alignment explanation
Indices: 1547847--1547896 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
1547837 GAAAAATAAT
1547847 TAAATTACATAAAAAATA
1 TAAA-TACATAAAAAATA
*
1547865 TAAATATCATATAAATATA
1 TAAATA-CATA-AAAAATA
1547884 TAAATACATAAAA
1 TAAATACATAAAA
1547897 TTTTATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 12 0.41
19 12 0.41
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAATACATAAAAAATA
Found at i:1547903 original size:18 final size:18
Alignment explanation
Indices: 1547863--1547935 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 18
1547853 ACATAAAAAA
*
1547863 TATAAATATCATATAAATA
1 TATAAATA-CATATAAATT
1547882 TATAAATACATA-AAATT
1 TATAAATACATATAAATT
*
1547899 T-TATATA-ATATAAA-T
1 TATAAATACATATAAATT
*
1547914 TATAAATATATCA-AAATT
1 TATAAATACAT-ATAAATT
1547932 TATA
1 TATA
1547936 TAAATATAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
15 5 0.11
16 13 0.28
17 10 0.22
18 10 0.22
19 8 0.17
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
TATAAATACATATAAATT
Found at i:1547930 original size:17 final size:16
Alignment explanation
Indices: 1547858--1547944 Score: 61
Period size: 16 Copynumber: 5.1 Consensus size: 16
1547848 AAATTACATA
*
1547858 AAAAATATAAATATCAT
1 AAAATTATAAATAT-AT
*
1547875 ATAAATATATAAATACAT
1 A-AAAT-TATAAATATAT
* *
1547893 AAAATTTTATATA-AT
1 AAAATTATAAATATAT
1547908 ATAAATTATAAATATAT
1 A-AAATTATAAATATAT
1547925 CAAAATTTATATAA-ATAT
1 -AAAA-TTATA-AATATAT
1547943 AA
1 AA
1547945 CACTTTAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
15 3 0.05
16 16 0.28
17 12 0.21
18 16 0.28
19 10 0.18
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATTATAAATATAT
Found at i:1547934 original size:32 final size:33
Alignment explanation
Indices: 1547868--1547944 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 33
1547858 AAAAATATAA
*
1547868 ATATCATATAAATATATAAATACATAAAATTTT
1 ATATAATATAAATATATAAATACATAAAATTTT
*
1547901 ATATAATATAAAT-TATAAATATATCAAAA-TTT
1 ATATAATATAAATATATAAATACAT-AAAATTTT
1547933 ATATAAATATAA
1 ATAT-AATATAA
1547945 CACTTTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 17 0.43
33 23 0.57
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (33 bp):
ATATAATATAAATATATAAATACATAAAATTTT
Found at i:1548630 original size:197 final size:198
Alignment explanation
Indices: 1548200--1548986 Score: 1154
Period size: 197 Copynumber: 4.0 Consensus size: 198
1548190 AGTATTATAA
* * *** * * *
1548200 TTCTCGATATCCTATAAGACTTTCATTACATTTGTTGGTTTAGTCTTACGACAATGAGATTTTGC
1 TTCTCGATATCCTAAAAGACTTTTATTGTGTTTGTTGATTTAGTCTTACGACAATGAAATCTTGC
* * * * *
1548265 TTGAGTTGTATTTGATATTTTCATTTATGATATTTTAACTTTTAATTTTTTT--AAAAATATTAT
66 TTGAGTTGTATTTGATATTTTTATCTATAATATTTTAACTCTTAATTTTTTTAAAAAAATATTTT
* *
1548328 ATATTTAATTTAAAATAAATTTAAATATGAATATGAAAAATTGTAACCTTAAACAGGTCATCGCA
131 ATATTTAATTTAAAATAAATTTAAATATGAATATGAAAAATTGTAACCTTAAGCAGGTCATAGCA
1548393 TTT
196 TTT
* * *
1548396 TTCTCGATATCCTAAAAGACTTTTATTGCGTTTGTTGATTTAGTCTTACGACAATGAGACCTTGC
1 TTCTCGATATCCTAAAAGACTTTTATTGTGTTTGTTGATTTAGTCTTACGACAATGAAATCTTGC
* *
1548461 TTGAGTTGTATTTGATATTTTTATCTATGATATTTTAACTCTTAATTTTTTT-AAGAAATATTTT
66 TTGAGTTGTATTTGATATTTTTATCTATAATATTTTAACTCTTAATTTTTTTAAAAAAATATTTT
* * * *
1548525 ATACTTAATTTAAAATATATTTAAATATGAATAT-AAAAAGTTGTAACTTTAAGCAGGTCATGGC
131 ATATTTAATTTAAAATAAATTTAAATATGAATATGAAAAA-TTGTAACCTTAAGCAGGTCATAGC
1548589 ATTT
195 ATTT
** * * *
1548593 TTCTCGATATCCTCGAAGGCTTCTATTGTGCTTGTTGATTTAGTCTTACGACAATGAAATCTTGC
1 TTCTCGATATCCTAAAAGACTTTTATTGTGTTTGTTGATTTAGTCTTACGACAATGAAATCTTGC
* *
1548658 TTGAGTTGTATTTGATATTTTTATCTATAATATTTT-ATTCTTAATTTTTTTCAAAAAATATTTT
66 TTGAGTTGTATTTGATATTTTTATCTATAATATTTTAACTCTTAATTTTTTTAAAAAAATATTTT
* *
1548722 ATATTTAATTTAAAATAAATTTAAATATGAATATGAAAAATTATAACCTTAAGCAGGTCATAACA
131 ATATTTAATTTAAAATAAATTTAAATATGAATATGAAAAATTGTAACCTTAAGCAGGTCATAGCA
1548787 TTT
196 TTT
* * * *
1548790 TTCTCGATATCCTAAAAGACTTTTATTATGTTTGTTGGTTTAGTTTTACGACAATGAAATCTTAC
1 TTCTCGATATCCTAAAAGACTTTTATTGTGTTTGTTGATTTAGTCTTACGACAATGAAATCTTGC
* *
1548855 TTGAGTTGTATTTGATATTTTTATTTATAATATTTTAATTCTTAATTTTTTTAAAAAAATATTTT
66 TTGAGTTGTATTTGATATTTTTATCTATAATATTTTAACTCTTAATTTTTTTAAAAAAATATTTT
* *
1548920 ATATTTAATTTAAAATAAATTTAAATATGAATATGAAAAATCGTAACC-TAAGTAGGTCATAGCA
131 ATATTTAATTTAAAATAAATTTAAATATGAATATGAAAAATTGTAACCTTAAGCAGGTCATAGCA
1548984 TTT
196 TTT
1548987 AGCCATAAGG
Statistics
Matches: 537, Mismatches: 49, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
196 126 0.23
197 333 0.62
198 78 0.15
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.46
Consensus pattern (198 bp):
TTCTCGATATCCTAAAAGACTTTTATTGTGTTTGTTGATTTAGTCTTACGACAATGAAATCTTGC
TTGAGTTGTATTTGATATTTTTATCTATAATATTTTAACTCTTAATTTTTTTAAAAAAATATTTT
ATATTTAATTTAAAATAAATTTAAATATGAATATGAAAAATTGTAACCTTAAGCAGGTCATAGCA
TTT
Found at i:1550809 original size:2 final size:2
Alignment explanation
Indices: 1550802--1550853 Score: 63
Period size: 2 Copynumber: 26.0 Consensus size: 2
1550792 ACATAAGTCA
*
1550802 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A- AT AT CA-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
1550843 AT AT AT CAT AT
1 AT AT AT -AT AT
1550854 GTCTATCCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 2 0.05
2 39 0.89
3 3 0.07
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1551534 original size:14 final size:13
Alignment explanation
Indices: 1551512--1551559 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
1551502 AGAATTTTTC
1551512 ATAAACAATTAAT
1 ATAAACAATTAAT
*
1551525 ATAAATCAATTTAT
1 ATAAA-CAATTAAT
*
1551539 AT-AACACTATAAT
1 ATAAACAAT-TAAT
1551552 ATAAACAA
1 ATAAACAA
1551560 AGAAAAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
12 3 0.11
13 12 0.43
14 13 0.46
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAACAATTAAT
Found at i:1553349 original size:189 final size:189
Alignment explanation
Indices: 1553139--1553524 Score: 754
Period size: 189 Copynumber: 2.0 Consensus size: 189
1553129 TTATTACATA
1553139 ATATATATTAATTAATTACTAAATCTCAATAATGAAAGAAATTTTAAAAATTTATTACTTATATT
1 ATATATATTAATTAATTACTAAATCTCAATAATGAAAGAAATTTTAAAAATTTATTACTTATATT
1553204 TTAAGCTGTTAAAATTTTATATATTCTTTTAATATTGACAAATGCTTTAAAAAAGTGCAAATATT
66 TTAAGCTGTTAAAATTTTATATATTCTTTTAATATTGACAAATGCTTTAAAAAAGTGCAAATATT
1553269 ATTAGTTTTGCTTGATAATAGCTTTTTTCGACATTTAAAATTGATTTAATGATTCGTAT
131 ATTAGTTTTGCTTGATAATAGCTTTTTTCGACATTTAAAATTGATTTAATGATTCGTAT
1553328 ATATATATTAATTAATTACTAAATCTCAATAATGAAAGAAATTTTAAAAATTTATTACTTATATT
1 ATATATATTAATTAATTACTAAATCTCAATAATGAAAGAAATTTTAAAAATTTATTACTTATATT
1553393 TTAAGCTGTTAAAATTTTATATATTCTTTTAATATTGACAAATGCTTTAAAAAAGTGCAAATATT
66 TTAAGCTGTTAAAATTTTATATATTCTTTTAATATTGACAAATGCTTTAAAAAAGTGCAAATATT
*
1553458 ATTAGTTTTGCTTGATAATAGCTTTTTTCGATATTTAAAATTGATTTAATGATTCGTAT
131 ATTAGTTTTGCTTGATAATAGCTTTTTTCGACATTTAAAATTGATTTAATGATTCGTAT
*
1553517 ATTTATAT
1 ATATATAT
1553525 ATTATATATA
Statistics
Matches: 195, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
189 195 1.00
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (189 bp):
ATATATATTAATTAATTACTAAATCTCAATAATGAAAGAAATTTTAAAAATTTATTACTTATATT
TTAAGCTGTTAAAATTTTATATATTCTTTTAATATTGACAAATGCTTTAAAAAAGTGCAAATATT
ATTAGTTTTGCTTGATAATAGCTTTTTTCGACATTTAAAATTGATTTAATGATTCGTAT
Found at i:1553566 original size:30 final size:31
Alignment explanation
Indices: 1553514--1553590 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 31
1553504 TAATGATTCG
* *
1553514 TATATTTATATA-TTAT-ATATAAATTTTGA
1 TATATTAATATATTTATAATATAAATTTTAA
1553543 TATATTAATA-ATTTATAATATAAATTTTAA
1 TATATTAATATATTTATAATATAAATTTTAA
*
1553573 TATATTTATATATTTATA
1 TATATTAATATATTTATA
1553591 TTATTTTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 1 0.02
29 13 0.31
30 21 0.50
31 7 0.17
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (31 bp):
TATATTAATATATTTATAATATAAATTTTAA
Found at i:1553577 original size:14 final size:13
Alignment explanation
Indices: 1553526--1553576 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
1553516 TATTTATATA
1553526 TTATATATAAATT
1 TTATATATAAATT
*
1553539 TTGATATATTAATAAT
1 TT-ATATA-TAA-ATT
1553555 TTATAATATAAATT
1 TTAT-ATATAAATT
1553569 TTA-ATATA
1 TTATATATA
1553577 TTTATATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
12 5 0.16
13 2 0.06
14 10 0.31
15 8 0.25
16 7 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
TTATATATAAATT
Found at i:1554391 original size:20 final size:18
Alignment explanation
Indices: 1554361--1554405 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1554351 AATTAATAAA
1554361 TTTAA-ATTA-AAATATTT
1 TTTAATATTATAAA-ATTT
*
1554378 TTAAATATTATAAAATTT
1 TTTAATATTATAAAATTT
1554396 TTTAATATTA
1 TTTAATATTA
1554406 AATAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 17 0.71
19 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATATTATAAAATTT
Found at i:1554410 original size:20 final size:22
Alignment explanation
Indices: 1554357--1554411 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
1554347 ATTAAATTAA
1554357 TAAAT-TTAAATTAAAATATTTT
1 TAAATATTAAA-TAAAATATTTT
1554379 TAAATATT--ATAAAAT-TTTT
1 TAAATATTAAATAAAATATTTT
1554398 T-AATATTAAATAAA
1 TAAATATTAAATAAA
1554412 TAATTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 6 0.20
19 5 0.17
20 11 0.37
21 1 0.03
22 5 0.17
23 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAATATTAAATAAAATATTTT
Found at i:1554701 original size:23 final size:21
Alignment explanation
Indices: 1554659--1554701 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1554649 TTTATTTATT
*
1554659 ATAATTTTTATTTTTAAAATC
1 ATAATTTTTAATTTTAAAATC
1554680 ATAATTTTTAAATTTTATAAAT
1 ATAATTTTT-AATTTTA-AAAT
1554702 AAAATAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 6 0.32
23 4 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATAATTTTTAATTTTAAAATC
Found at i:1558504 original size:11 final size:11
Alignment explanation
Indices: 1558478--1558535 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
1558468 TATTTGTATT
1558478 TAAT-TATAAA
1 TAATATATAAA
*
1558488 -AATATATGAA
1 TAATATATAAA
*
1558498 TAATATAAAAA
1 TAATATATAAA
* *
1558509 TAATATTTTAA
1 TAATATATAAA
1558520 TAATATAATAAA
1 TAATAT-ATAAA
1558532 TAAT
1 TAAT
1558536 TAAATAAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
9 3 0.08
10 5 0.14
11 22 0.59
12 7 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TAATATATAAA
Found at i:1558506 original size:19 final size:20
Alignment explanation
Indices: 1558482--1558542 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 20
1558472 TGTATTTAAT
1558482 TATAAAAATATA-TGAATAA
1 TATAAAAATATATTGAATAA
*
1558501 TATAAAAATAATATTTTAATAA
1 TATAAAAAT-ATA-TTGAATAA
*
1558523 TATAATAAATA-ATTAAATAA
1 TATAA-AAATATATTGAATAA
1558543 ATTTTCAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 9 0.25
20 10 0.28
21 1 0.03
22 12 0.33
23 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
TATAAAAATATATTGAATAA
Found at i:1558513 original size:22 final size:23
Alignment explanation
Indices: 1558483--1558535 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
1558473 GTATTTAATT
1558483 ATAAA-AATATATGAATAATATA
1 ATAAATAATATATGAATAATATA
* *
1558505 A-AAATAATATTTTAATAATATA
1 ATAAATAATATATGAATAATATA
1558527 ATAAATAAT
1 ATAAATAAT
1558536 TAAATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 17 0.63
23 7 0.26
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAAATAATATATGAATAATATA
Found at i:1558648 original size:2 final size:2
Alignment explanation
Indices: 1558641--1558668 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1558631 GCTTGCTGAA
1558641 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
1558669 CAATAGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1564612 original size:30 final size:30
Alignment explanation
Indices: 1564556--1564617 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
1564546 ATCAAATCAA
1564556 AAATTAAATATGTAAAATTTTAATATTTAAAT
1 AAATTAAATA-GTAAAATTTTAATA-TTAAAT
* *
1564588 AAATTAAATA-TATAATTTTGATATTAAAT
1 AAATTAAATAGTAAAATTTTAATATTAAAT
1564617 A
1 A
1564618 TAATATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 7 0.25
30 11 0.39
32 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTAAATAGTAAAATTTTAATATTAAAT
Found at i:1564722 original size:41 final size:42
Alignment explanation
Indices: 1564632--1564731 Score: 98
Period size: 41 Copynumber: 2.4 Consensus size: 42
1564622 ATTTATTTAA
* * * *
1564632 AATTTTTTATTTTTTAATATATAATTAAAAAGATACAAATTT
1 AATTTTTTATTATTTAAAAAATAATTAAAAAGATACAAATAT
* *
1564674 AA-ATTTTATTATTTAAAAAATAA-TAAAAATA-ACAAAATAT
1 AATTTTTTATTATTTAAAAAATAATTAAAAAGATAC-AAATAT
*
1564714 AATTTTTTACCTATTTAA
1 AATTTTTTA-TTATTTAA
1564732 TTTAAATTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
39 2 0.04
40 14 0.30
41 22 0.47
42 9 0.19
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (42 bp):
AATTTTTTATTATTTAAAAAATAATTAAAAAGATACAAATAT
Found at i:1564914 original size:17 final size:18
Alignment explanation
Indices: 1564887--1564924 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1564877 CTTGATAAAT
*
1564887 TAATATTTAATAAATTTA
1 TAATATTTAATAAATTAA
*
1564905 TAAT-TTTAATTAATTAA
1 TAATATTTAATAAATTAA
1564922 TAA
1 TAA
1564925 AATATCAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATATTTAATAAATTAA
Found at i:1565031 original size:22 final size:22
Alignment explanation
Indices: 1564991--1565048 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1564981 GATCTAATAA
*
1564991 ATATATAAAT-TAATAAT-TTTT
1 ATATAAAAATATAA-AATATTTT
1565012 AT-TAAAAATATAAAATATTTT
1 ATATAAAAATATAAAATATTTT
*
1565033 ATATAATAATATAAAA
1 ATATAAAAATATAAAA
1565049 AACTAACTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 9 0.28
21 11 0.34
22 12 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATAAAAATATAAAATATTTT
Found at i:1572398 original size:16 final size:17
Alignment explanation
Indices: 1572371--1572402 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1572361 AAAATAATAA
1572371 AAATTATTAAATATATT
1 AAATTATTAAATATATT
1572388 AAATT-TTAAATATAT
1 AAATTATTAAATATAT
1572403 ATAAGATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTATTAAATATATT
Found at i:1572434 original size:14 final size:14
Alignment explanation
Indices: 1572375--1572445 Score: 60
Period size: 14 Copynumber: 5.2 Consensus size: 14
1572365 TAATAAAAAT
1572375 TATTAAATATATTAAA
1 TATTAAATATATT--A
*
1572391 TTTTAAATATA-TA
1 TATTAAATATATTA
*
1572404 TA--AGATATATT-
1 TATTAAATATATTA
*
1572415 TATTAAATATGTTA
1 TATTAAATATATTA
*
1572429 TATTAATTATATTA
1 TATTAAATATATTA
1572443 TAT
1 TAT
1572446 CATATTTGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
11 8 0.18
12 1 0.02
13 9 0.20
14 15 0.34
15 1 0.02
16 10 0.23
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
TATTAAATATATTA
Found at i:1572472 original size:8 final size:9
Alignment explanation
Indices: 1572409--1572512 Score: 50
Period size: 9 Copynumber: 11.1 Consensus size: 9
1572399 ATATATAAGA
1572409 TATATTTAT
1 TATATTTAT
* * *
1572418 TAAATATGT
1 TATATTTAT
*
1572427 TATATTAAT
1 TATATTTAT
1572436 TATATTATAT
1 TATATT-TAT
*
1572446 CATATTTGTAAT
1 TATA-TT-T-AT
*
1572458 AATATTT-T
1 TATATTTAT
1572466 TATATTTAT
1 TATATTTAT
**
1572475 TATACATAT
1 TATATTTAT
*
1572484 TATATCAATAT
1 TATAT--TTAT
*
1572495 CATATTT-T
1 TATATTTAT
1572503 TATATTTAT
1 TATATTTAT
1572512 T
1 T
1572513 TAAAGTTATA
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
8 14 0.20
9 32 0.46
10 6 0.09
11 13 0.19
12 5 0.07
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (9 bp):
TATATTTAT
Found at i:1573679 original size:154 final size:154
Alignment explanation
Indices: 1573399--1573941 Score: 585
Period size: 154 Copynumber: 3.5 Consensus size: 154
1573389 ATTTATCGTG
* * * * * * * * *
1573399 AAAGTCATTGAATCATTAAGGACAAATGGGAATTGGTAGGAATATATCTAGATGTGAATTCCATA
1 AAAGTCATTGAATCTTTAAGAAAAAAAGGAAATTGGTAAGTATATATCTAGATGTAAATTCTATA
** * *
1573464 AATATTTTAGTAAATTAAAGTTGCTCAT-ACAAGCCAAAGTACGGTAAAAATGCATTCTCACCAC
66 AATATTTTAGTAAATTAAAGTTATTCATAACAAGCTAAAGTGCGGTAAAAATGCATTCTCACCAC
*
1573528 AATATCGGAGCCATGTTTAATCCTA
131 AATATCAGAGCCATGTTTAATCC-A
* * *
1573553 AAAGTCCTTGAATCTTTAAGAAAAAAAGGAAATTGGTAGGTATATATCTTGATGTAAATTCTATA
1 AAAGTCATTGAATCTTTAAGAAAAAAAGGAAATTGGTAAGTATATATCTAGATGTAAATTCTATA
* * * * *
1573618 AATATTTTAGTAAATTAAAGTTATTCATAAAAAGCTATAGTGC-GTAAAAATGTAATCTCACCTC
66 AATATTTTAGTAAATTAAAGTTATTCATAACAAGCTAAAGTGCGGTAAAAATGCATTCTCACCAC
* * *
1573682 AATATCAAAGTCAAT-TTTGATCCA
131 AATATCAGAG-CCATGTTTAATCCA
* * * *
1573706 AAAGTCATTGAATCCTTAAGAGAAAAAGGGGAATTGGTAAGTATATATCTAAATGTAAATTCTAT
1 AAAGTCATTGAATCTTTAAGA-AAAAAAGGAAATTGGTAAGTATATATCTAGATGTAAATTCTAT
* * * *
1573771 AAAAAATTTTAGTAAATTAAAGTTATTTATAACAAG-TCAAAGTGCGGTAAAAATACATTCTCAT
65 -AAATATTTTAGTAAATTAAAGTTATTCATAACAAGCT-AAAGTGCGGTAAAAATGCATTCTCAC
* * *
1573835 CATAGTATCAGAGCCATGTTTACTACCA
128 CACAATATCAGAGCCATGTTTAAT-CCA
* * * * *
1573863 AAAATCATTGAATCCTTAAAGGAAAAAAA--AAGATTGATAAGTATATATCAAGATGTACATTCT
1 AAAGTCATTGAAT-CTTTAA-GAAAAAAAGGAA-ATTGGTAAGTATATATCTAGATGTAAATTCT
*
1573926 TTAAATATTTTAGTAA
63 ATAAATATTTTAGTAA
1573942 TTCATAACAA
Statistics
Matches: 322, Mismatches: 56, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
153 20 0.06
154 153 0.48
155 54 0.17
156 41 0.13
157 43 0.13
158 9 0.03
159 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (154 bp):
AAAGTCATTGAATCTTTAAGAAAAAAAGGAAATTGGTAAGTATATATCTAGATGTAAATTCTATA
AATATTTTAGTAAATTAAAGTTATTCATAACAAGCTAAAGTGCGGTAAAAATGCATTCTCACCAC
AATATCAGAGCCATGTTTAATCCA
Found at i:1578205 original size:2 final size:2
Alignment explanation
Indices: 1578198--1578228 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1578188 TTGAAATCAA
1578198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1578229 AACTGTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1579072 original size:30 final size:30
Alignment explanation
Indices: 1578984--1579078 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
1578974 AAATATTGAT
* * * * *
1578984 TTAAAGATTTGTTTAGGAATAAATTAAAGG
1 TTAAAAATTTATTTCGGTATAAATTAAAAG
*
1579014 TTAAGAATTTATTTCGGTA-AAAGTTAAAAG
1 TTAAAAATTTATTTCGGTATAAA-TTAAAAG
*
1579044 TTAAAAATTTATTT-GAGTATAAAATAAAAG
1 TTAAAAATTTATTTCG-GTATAAATTAAAAG
1579074 TTAAA
1 TTAAA
1579079 GGCTTATCGA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
29 4 0.07
30 47 0.87
31 3 0.06
ACGTcount: A:0.47, C:0.01, G:0.15, T:0.37
Consensus pattern (30 bp):
TTAAAAATTTATTTCGGTATAAATTAAAAG
Found at i:1581050 original size:23 final size:23
Alignment explanation
Indices: 1581024--1581092 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 23
1581014 TAAAAATTTT
1581024 ATTTTTAT-ATTAATATTTATATA
1 ATTTTTATAATTAA-ATTTATATA
1581047 A-TTTTATAATTAAAATTTATAT-
1 ATTTTTATAATT-AAATTTATATA
*
1581069 ATTTTTATAATTAAATTTAAATA
1 ATTTTTATAATTAAATTTATATA
1581092 A
1 A
1581093 AAATTTTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
22 16 0.39
23 23 0.56
24 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTTTATAATTAAATTTATATA
Found at i:1582556 original size:19 final size:18
Alignment explanation
Indices: 1582519--1582566 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1582509 ACTTCACGCA
1582519 TGTAATTTATAAATTTTT
1 TGTAATTTATAAATTTTT
* *
1582537 TGTAGTTTATACATTTTT
1 TGTAATTTATAAATTTTT
1582555 T-TAATATTATAA
1 TGTAAT-TTATAA
1582567 TAAATATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.58
Consensus pattern (18 bp):
TGTAATTTATAAATTTTT
Found at i:1585661 original size:18 final size:18
Alignment explanation
Indices: 1585638--1585673 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1585628 TTTGTAATCC
1585638 TAAACTTAAAATTCATTT
1 TAAACTTAAAATTCATTT
1585656 TAAACTTAAAATTCATTT
1 TAAACTTAAAATTCATTT
1585674 GGTATAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAACTTAAAATTCATTT
Found at i:1586251 original size:19 final size:21
Alignment explanation
Indices: 1586204--1586252 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
1586194 TTTTTAAAAA
1586204 TTTAATTATAAAATATATAAAT
1 TTTAA-TATAAAATATATAAAT
* *
1586226 ATTAATATAAAA-ATA-ATAT
1 TTTAATATAAAATATATAAAT
1586245 TTTAATAT
1 TTTAATAT
1586253 TATTATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.42
20 3 0.12
21 7 0.29
22 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAATATAAAATATATAAAT
Found at i:1587753 original size:26 final size:26
Alignment explanation
Indices: 1587724--1587821 Score: 87
Period size: 26 Copynumber: 3.7 Consensus size: 26
1587714 ATATAATTAT
1587724 ATTTAAAATATTTTATATTTATTTAA
1 ATTTAAAATATTTTATATTTATTTAA
* *
1587750 ATTTAATATATTATTAATTTATATTATATAA
1 ATTTAAAATATT-TT-A--TAT-TTATTTAA
*
1587781 ATTTAAAATA---TATATTTATTTAT
1 ATTTAAAATATTTTATATTTATTTAA
1587804 ATATT-AAATATTTTATAT
1 AT-TTAAAATATTTTATAT
1587822 ATATATTATA
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
23 13 0.22
24 5 0.09
26 17 0.29
27 3 0.05
28 1 0.02
30 3 0.05
31 16 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTAAAATATTTTATATTTATTTAA
Found at i:1587785 original size:31 final size:31
Alignment explanation
Indices: 1587735--1587852 Score: 98
Period size: 32 Copynumber: 3.7 Consensus size: 31
1587725 TTTAAAATAT
*
1587735 TTTATATTTATTTAAATTTAATATAT-TATTAA
1 TTTATA-TTA-TTAAATTTAAAATATATATTAA
*
1587767 TTTATATTATATAAATTTAAAATATATATTTA
1 TTTATATTAT-TAAATTTAAAATATATATTAA
* *
1587799 TTTATA-TATTAAATATTTTATATATATATTATA
1 TTTATATTATT-AA-ATTTAAAATATATATTA-A
* * *
1587832 TTCATATAATT-TATTTAAAAT
1 TTTATATTATTAAATTTAAAAT
1587853 TAATTATAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
30 2 0.03
31 28 0.40
32 31 0.44
33 6 0.09
34 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (31 bp):
TTTATATTATTAAATTTAAAATATATATTAA
Found at i:1587802 original size:32 final size:30
Alignment explanation
Indices: 1587735--1587812 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 30
1587725 TTTAAAATAT
*
1587735 TTTATATTTATTTAAATTTAATATATTATTAA
1 TTTATA-TTA-TTAAATTTAAAATATTATTAA
*
1587767 TTTATATTATATAAATTTAAAATATATATTTA
1 TTTATATTAT-TAAATTTAAAATAT-TATTAA
1587799 TTTATA-TATTAAAT
1 TTTATATTATTAAAT
1587813 ATTTTATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 6 0.14
31 19 0.45
32 17 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TTTATATTATTAAATTTAAAATATTATTAA
Found at i:1587845 original size:15 final size:14
Alignment explanation
Indices: 1587756--1587845 Score: 62
Period size: 15 Copynumber: 6.2 Consensus size: 14
1587746 TTAAATTTAA
1587756 TATATTAT-TAATT
1 TATATTATATAATT
1587769 TATATTATATAAATT
1 TATATTATAT-AATT
* *
1587784 TAAAATATAT-ATT
1 TATATTATATAATT
1587797 TAT-TTATAT-ATT
1 TATATTATATAATT
*
1587809 AAATATTTTATATATATAT
1 ---TATATTATATA-AT-T
1587828 TATATTCATATAATT
1 TATATT-ATATAATT
1587843 TAT
1 TAT
1587846 TTAAAATTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
12 8 0.13
13 13 0.21
14 1 0.02
15 19 0.31
16 13 0.21
17 5 0.08
18 2 0.03
19 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (14 bp):
TATATTATATAATT
Found at i:1589173 original size:13 final size:13
Alignment explanation
Indices: 1589135--1589173 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
1589125 AAAATTACTA
1589135 TTATACTTTAATT
1 TTATACTTTAATT
*
1589148 TAATA-TTTAATT
1 TTATACTTTAATT
*
1589160 TTATACTTTTATT
1 TTATACTTTAATT
1589173 T
1 T
1589174 GATTGAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATACTTTAATT
Found at i:1589674 original size:31 final size:31
Alignment explanation
Indices: 1589620--1589696 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
1589610 ATGGTAACTG
*
1589620 ATAAAATTCAA-TAAAAATCAAAATTTAGTA
1 ATAAAATTTAATTAAAAATCAAAATTTAGTA
* *
1589650 ATAAAATTTAATTAAAAATTAAAATTTAGTT
1 ATAAAATTTAATTAAAAATCAAAATTTAGTA
*
1589681 GTAAAATTTAATTAAA
1 ATAAAATTTAATTAAA
1589697 TAAAATTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 10 0.24
31 32 0.76
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (31 bp):
ATAAAATTTAATTAAAAATCAAAATTTAGTA
Found at i:1589763 original size:60 final size:60
Alignment explanation
Indices: 1589690--1589806 Score: 141
Period size: 60 Copynumber: 1.9 Consensus size: 60
1589680 TGTAAAATTT
*
1589690 AATTAAATAAAATTAAAATAGTAAA-TTTACCTA-TAATCTTAAAATATAATAATAAATATA
1 AATTAAATAAAATTAAAATAATAAACTTTA-CTATTAA-CTTAAAATATAATAATAAATATA
* * * *
1589750 AATTAAA-ATAAATTATAATAATAAACTTTATTATTCACTTACAATATAATAATAAAT
1 AATTAAATA-AAATTAAAATAATAAACTTTACTATTAACTTAAAATATAATAATAAAT
1589807 TTATATTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
59 1 0.02
60 42 0.86
61 6 0.12
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.37
Consensus pattern (60 bp):
AATTAAATAAAATTAAAATAATAAACTTTACTATTAACTTAAAATATAATAATAAATATA
Found at i:1590012 original size:21 final size:19
Alignment explanation
Indices: 1589986--1590037 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
1589976 ATTATAAAAT
1589986 TATTTTATATTAATATTTATA
1 TATTTTATATTAA-ATTTA-A
1590007 TATTTTATAATTAAATTTAA
1 TATTTTAT-ATTAAATTTAA
*
1590027 -ATTTCATATTA
1 TATTTTATATTA
1590038 TTAAAAGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.14
19 6 0.21
20 1 0.03
21 13 0.45
22 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTTATATTAAATTTAA
Found at i:1592424 original size:23 final size:23
Alignment explanation
Indices: 1592396--1592440 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1592386 ACCGTAAAAC
*
1592396 TATATTACTTAAATTCGAGTGTA
1 TATATTACTCAAATTCGAGTGTA
1592419 TATATTACTCAAATTCGAGTGT
1 TATATTACTCAAATTCGAGTGT
1592441 GAACATTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.42
Consensus pattern (23 bp):
TATATTACTCAAATTCGAGTGTA
Found at i:1592448 original size:23 final size:23
Alignment explanation
Indices: 1592399--1592448 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1592389 GTAAAACTAT
* *
1592399 ATTACTTAAATTCGAGTGTATAT
1 ATTACTCAAATTCGAGTGTATAC
1592422 ATTACTCAAATTCGAGTGTGA-AC
1 ATTACTCAAATTCGAGTGT-ATAC
1592445 ATTA
1 ATTA
1592449 GATATGGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (23 bp):
ATTACTCAAATTCGAGTGTATAC
Found at i:1596324 original size:16 final size:16
Alignment explanation
Indices: 1596303--1596334 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1596293 TAAATTTTTA
1596303 TTTTTTAAATTTAAAT
1 TTTTTTAAATTTAAAT
1596319 TTTTTTAAATTTAAAT
1 TTTTTTAAATTTAAAT
1596335 AGTTTTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTTAAATTTAAAT
Found at i:1596340 original size:16 final size:16
Alignment explanation
Indices: 1596305--1596341 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1596295 AATTTTTATT
**
1596305 TTTTAAATTTAAATTT
1 TTTTAAATTTAAATAG
1596321 TTTTAAATTTAAATAG
1 TTTTAAATTTAAATAG
1596337 TTTTA
1 TTTTA
1596342 TGTTTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTAAATTTAAATAG
Found at i:1597536 original size:18 final size:18
Alignment explanation
Indices: 1597515--1597564 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1597505 ATCATCAAAA
1597515 TATATAAAATTATTTTAT
1 TATATAAAATTATTTTAT
* * *
1597533 TATATAAAATCAATTTGT
1 TATATAAAATTATTTTAT
*
1597551 TAAAT-AAATTATTT
1 TATATAAAATTATTT
1597565 AAAAAATAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TATATAAAATTATTTTAT
Found at i:1598180 original size:25 final size:25
Alignment explanation
Indices: 1598152--1598204 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
1598142 AAAATTGTCT
1598152 TTAAATTT-A-ATTATATATATATATA
1 TTAAATTTGAGATTA-ATATAT-TATA
*
1598177 TTAACTTTGAGATTAATATATTATA
1 TTAAATTTGAGATTAATATATTATA
1598202 TTA
1 TTA
1598205 TTTTTATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 14 0.56
26 7 0.28
27 4 0.16
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (25 bp):
TTAAATTTGAGATTAATATATTATA
Found at i:1598464 original size:23 final size:23
Alignment explanation
Indices: 1598436--1598480 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1598426 CTAAATTTTT
1598436 AAATAATAATA-ATTAATAAATTA
1 AAATAA-AATATATTAATAAATTA
*
1598459 AAATAAAATATTTTAATAAATT
1 AAATAAAATATATTAATAAATT
1598481 CATTTCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATAAAATATATTAATAAATTA
Found at i:1599404 original size:3 final size:3
Alignment explanation
Indices: 1599396--1599434 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1599386 GTTAATATAT
*
1599396 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1599435 AATTTATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1599590 original size:33 final size:32
Alignment explanation
Indices: 1599489--1599595 Score: 112
Period size: 33 Copynumber: 3.3 Consensus size: 32
1599479 TTATTAAATT
*
1599489 TTTTTAATTAATTTTAAGTTTAAATTATTTTAGA
1 TTTTTAATTAA-TTTGAGTTTAAATTATTTTA-A
* *
1599523 TTTAT-ATTATTTTGAGTTTAAAATTATTTT-A
1 TTTTTAATTAATTTGAGTTT-AAATTATTTTAA
1599554 TTTTTGAATTAATTTGA-TTTCAAATTATTTTAA
1 TTTTT-AATTAATTTGAGTTT-AAATTATTTTAA
*
1599587 TTTTAAATT
1 TTTTTAATT
1599596 TTTTTATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
31 5 0.08
32 25 0.40
33 28 0.45
34 4 0.06
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.60
Consensus pattern (32 bp):
TTTTTAATTAATTTGAGTTTAAATTATTTTAA
Found at i:1599600 original size:16 final size:16
Alignment explanation
Indices: 1599489--1599614 Score: 110
Period size: 16 Copynumber: 7.8 Consensus size: 16
1599479 TTATTAAATT
*
1599489 TTTTTAATTAATTTTAA
1 TTTTAAATT-ATTTTAA
*
1599506 GTTTAAATTATTTTAGA
1 TTTTAAATTATTTTA-A
* *
1599523 -TTTATATTATTTTGAG
1 TTTTAAATTATTTT-AA
* *
1599539 TTTAAAATTATTTTAT
1 TTTTAAATTATTTTAA
* * *
1599555 TTTTGAATTAATTTGA
1 TTTTAAATTATTTTAA
*
1599571 TTTCAAATTATTTTAA
1 TTTTAAATTATTTTAA
* *
1599587 TTTTAAATTTTTTTAT
1 TTTTAAATTATTTTAA
1599603 TTTTAAATTATT
1 TTTTAAATTATT
1599615 AATTTTTTTA
Statistics
Matches: 86, Mismatches: 20, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
16 66 0.77
17 20 0.23
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTAAATTATTTTAA
Found at i:1599611 original size:23 final size:22
Alignment explanation
Indices: 1599581--1599624 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1599571 TTTCAAATTA
1599581 TTTTAATT-TTAAATTTTTTTAT
1 TTTTAATTATT-AATTTTTTTAT
1599603 TTTTAAATTATTAATTTTTTTA
1 TTTT-AATTATTAATTTTTTTA
1599625 ATTAAATCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 14 0.70
24 2 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTAATTATTAATTTTTTTAT
Found at i:1599968 original size:16 final size:16
Alignment explanation
Indices: 1599947--1599979 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1599937 AATCACCCTT
1599947 TGATTAAAGATTTAAA
1 TGATTAAAGATTTAAA
1599963 TGATTAAAGATTTAAA
1 TGATTAAAGATTTAAA
1599979 T
1 T
1599980 TATAGTTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (16 bp):
TGATTAAAGATTTAAA
Found at i:1601033 original size:25 final size:25
Alignment explanation
Indices: 1601005--1601052 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
1600995 ATAGAAGAAA
1601005 AAAAAT-AAATTATTAAAAATTAAAT
1 AAAAATAAAATT-TTAAAAATTAAAT
1601030 AAAAATAAAATTTTAAAAATTAA
1 AAAAATAAAATTTTAAAAATTAA
1601053 TAATATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAAATAAAATTTTAAAAATTAAAT
Found at i:1603039 original size:21 final size:23
Alignment explanation
Indices: 1603015--1603058 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1603005 TTACACCATA
1603015 TAAA-TACGATACAAAA-ATAAT
1 TAAATTACGATACAAAATATAAT
* *
1603036 TAAATTATGATATAAAATATAAT
1 TAAATTACGATACAAAATATAAT
1603059 ATGATATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (23 bp):
TAAATTACGATACAAAATATAAT
Found at i:1603322 original size:14 final size:15
Alignment explanation
Indices: 1603297--1603325 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1603287 GAATTAACTC
1603297 AAATTATTATTTAAA
1 AAATTATTATTTAAA
1603312 AAATT-TTATTTAAA
1 AAATTATTATTTAAA
1603326 TTTAATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTATTATTTAAA
Found at i:1603691 original size:8 final size:8
Alignment explanation
Indices: 1603649--1603743 Score: 59
Period size: 8 Copynumber: 10.9 Consensus size: 8
1603639 AAATTTAACT
1603649 TATAAAT-
1 TATAAATA
*
1603656 TATTAATA
1 TATAAATA
1603664 TATCAAATA
1 TAT-AAATA
1603673 TATACATATA
1 TATA-A-ATA
1603683 TATAAATA
1 TATAAATA
1603691 TAT-AATA
1 TATAAATA
*
1603698 TTTTAAATA
1 -TATAAATA
*
1603707 TAATTTTAATA
1 T-A--TAAATA
1603718 TATAAATA
1 TATAAATA
1603726 TAAGATAAATA
1 T---ATAAATA
1603737 TATAAAT
1 TATAAAT
1603744 TATCATATCA
Statistics
Matches: 70, Mismatches: 6, Indels: 23
0.71 0.06 0.23
Matches are distributed among these distances:
7 10 0.14
8 25 0.36
9 13 0.19
10 8 0.11
11 14 0.20
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (8 bp):
TATAAATA
Done.