Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 85 of 113
Found at i:17770829 original size:20 final size:20
Alignment explanation
Indices: 17770801--17770849 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
17770791 GGATTAGATT
*
17770801 AAAAGGGAAAAAATAAAGAG
1 AAAAGGGAAAAAAGAAAGAG
*
17770821 AAAATGGAAAAAAGAAAG-G
1 AAAAGGGAAAAAAGAAAGAG
*
17770840 GAAAGGGAAA
1 AAAAGGGAAA
17770850 TAGATATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (20 bp):
AAAAGGGAAAAAAGAAAGAG
Found at i:17773126 original size:20 final size:20
Alignment explanation
Indices: 17773069--17773127 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
17773059 TCACATGATT
* * *
17773069 GTTAACTTTGTTAACGTGGC
1 GTTAACTTTGATAACATGGA
* *
17773089 GTTAACTTTGACAGCATGGA
1 GTTAACTTTGATAACATGGA
17773109 GTTAACTTTGATAACATGG
1 GTTAACTTTGATAACATGG
17773128 TAACATGGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.36
Consensus pattern (20 bp):
GTTAACTTTGATAACATGGA
Found at i:17773542 original size:30 final size:30
Alignment explanation
Indices: 17773487--17773543 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
17773477 ATTTTAAAAA
*
17773487 TTTTATTATTTTTTAAATATTACATTTATT
1 TTTTATTATTTTTAAAATATTACATTTATT
17773517 TTTTA-TATATTTTAAAAT-TTAACATTT
1 TTTTATTAT-TTTTAAAATATT-ACATTT
17773544 TTAGAATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTATTATTTTTAAAATATTACATTTATT
Found at i:17773798 original size:21 final size:21
Alignment explanation
Indices: 17773740--17773799 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
17773730 ATATTGATTT
** **
17773740 TTTTTAAAAAGCAAAATTTGA
1 TTTTTAAAAATTAAAATAGGA
*
17773761 TTTTAAAATAATT-AAATAGGA
1 TTTTTAAA-AATTAAAATAGGA
17773782 TTTTTAAAAATTAAAATA
1 TTTTTAAAAATTAAAATA
17773800 TTTAGAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 4 0.13
21 25 0.81
22 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTTTAAAAATTAAAATAGGA
Found at i:17774441 original size:39 final size:39
Alignment explanation
Indices: 17774356--17774441 Score: 120
Period size: 39 Copynumber: 2.2 Consensus size: 39
17774346 ACTATTTTGA
* * *
17774356 TATC-ATTTATGAAAATTTACACCTAACTTATGAGACAT
1 TATCTATTTATGAAAATTTACACCCAACCTACGAGACAT
* *
17774394 TGTTTATTTATGAAAATTTACACCCAACCTACGAGACAT
1 TATCTATTTATGAAAATTTACACCCAACCTACGAGACAT
17774433 TATCTATTT
1 TATCTATTT
17774442 TAATCTGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
38 2 0.05
39 38 0.95
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.38
Consensus pattern (39 bp):
TATCTATTTATGAAAATTTACACCCAACCTACGAGACAT
Found at i:17775235 original size:15 final size:16
Alignment explanation
Indices: 17775215--17775247 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17775205 TTGTGAACGC
17775215 CAAAAGAACTAA-AAA
1 CAAAAGAACTAAGAAA
*
17775230 CAAAAGCACTAAGAAA
1 CAAAAGAACTAAGAAA
17775246 CA
1 CA
17775248 TAAAAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.67, C:0.18, G:0.09, T:0.06
Consensus pattern (16 bp):
CAAAAGAACTAAGAAA
Found at i:17776213 original size:2 final size:2
Alignment explanation
Indices: 17776206--17776261 Score: 78
Period size: 2 Copynumber: 28.5 Consensus size: 2
17776196 ACGACTTGGT
* * *
17776206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17776248 TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA T
17776262 GTCAATTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17777808 original size:15 final size:15
Alignment explanation
Indices: 17777768--17777810 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
17777758 CTTTTAGCAT
17777768 TAAAAATTAAAAAAAA
1 TAAAAATT-AAAAAAA
* * *
17777784 TAACATTTAAAAAAC
1 TAAAAATTAAAAAAA
17777799 TAAAAATTAAAA
1 TAAAAATTAAAA
17777811 TAGAAATTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAAAATTAAAAAAA
Found at i:17778606 original size:29 final size:29
Alignment explanation
Indices: 17778573--17778635 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
17778563 AGTTATCAAA
*
17778573 CAATATATTTATATTTAACATTTAATTTT
1 CAATATATTTATATTCAACATTTAATTTT
*
17778602 CAATATATTTATATTCAACATTTTATTTT
1 CAATATATTTATATTCAACATTTAATTTT
17778631 CAATA
1 CAATA
17778636 AAAATACCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (29 bp):
CAATATATTTATATTCAACATTTAATTTT
Found at i:17778632 original size:14 final size:14
Alignment explanation
Indices: 17778580--17778633 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
17778570 AAACAATATA
17778580 TTTATATTT-AACAT
1 TTTAT-TTTCAACAT
* *
17778594 TTAATTTTCAATAT
1 TTTATTTTCAACAT
*
17778608 ATTTATATTCAACAT
1 -TTTATTTTCAACAT
17778623 TTTATTTTCAA
1 TTTATTTTCAA
17778634 TAAAAATACC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 3 0.09
14 18 0.56
15 11 0.34
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTATTTTCAACAT
Found at i:17783305 original size:14 final size:14
Alignment explanation
Indices: 17783278--17783317 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
17783268 AAAGCTAAAG
*
17783278 AAAAAATAGTAAAAA
1 AAAAAAAAG-AAAAA
17783293 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
*
17783307 AAGAAAAAGAA
1 AAAAAAAAGAA
17783318 GAAGTGGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (14 bp):
AAAAAAAAGAAAAA
Found at i:17783319 original size:9 final size:8
Alignment explanation
Indices: 17783274--17783320 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
17783264 AAGAAAAGCT
17783274 AAAGAAAA
1 AAAGAAAA
*
17783282 AATAGTAAA
1 AA-AGAAAA
17783291 AAA-AAAA
1 AAAGAAAA
17783298 AAAGAAAA
1 AAAGAAAA
17783306 AAAGAAAA
1 AAAGAAAA
17783314 AGAAGAA
1 A-AAGAA
17783321 GTGGATTCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
7 6 0.18
8 16 0.47
9 12 0.35
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (8 bp):
AAAGAAAA
Found at i:17787236 original size:14 final size:14
Alignment explanation
Indices: 17787217--17787271 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
17787207 TAATTTTGAT
17787217 TATTATTTTTAAAA
1 TATTATTTTTAAAA
* *
17787231 TATTA-TATTAAAT
1 TATTATTTTTAAAA
**
17787244 TAAAATTTTTACAAA
1 TATTATTTTTA-AAA
17787259 TA-TATTTTTAAAA
1 TATTATTTTTAAAA
17787272 ATCTGAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
13 12 0.38
14 16 0.50
15 4 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTATTTTTAAAA
Found at i:17788695 original size:25 final size:24
Alignment explanation
Indices: 17788648--17788695 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
17788638 TTTATAAATA
* *
17788648 TAAAATTATAAATATGAAGACTCG
1 TAAAATTATAAATATAAAAACTCG
17788672 TAAAGATTATAAATATAAAAACTC
1 TAAA-ATTATAAATATAAAAACTC
17788696 AGCATGAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.29
Consensus pattern (24 bp):
TAAAATTATAAATATAAAAACTCG
Found at i:17789951 original size:11 final size:11
Alignment explanation
Indices: 17789937--17789966 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
17789927 TTTTATATTA
17789937 ATAATATAAAT
1 ATAATATAAAT
17789948 ATAATATAAAT
1 ATAATATAAAT
17789959 ATTAATAT
1 A-TAATAT
17789967 TAGTCCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:17790238 original size:29 final size:28
Alignment explanation
Indices: 17790191--17790278 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 28
17790181 ATTTATTATT
17790191 TTAATCATATT-TTTATATATATTCATA
1 TTAATCATATTATTTATATATATTCATA
* *
17790218 TTAATCATATCTATTCATATATA-TCTATT
1 TTAATCATAT-TATTTATATATATTC-ATA
* *
17790247 TTAATTATATTCATTTATATATATTTATA
1 TTAATCATATT-ATTTATATATATTCATA
17790276 TTA
1 TTA
17790279 TTCGTAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
27 10 0.20
28 4 0.08
29 35 0.70
30 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (28 bp):
TTAATCATATTATTTATATATATTCATA
Found at i:17790266 original size:10 final size:9
Alignment explanation
Indices: 17790197--17790280 Score: 53
Period size: 10 Copynumber: 8.9 Consensus size: 9
17790187 TATTTTAATC
17790197 ATATT-TTT
1 ATATTATTT
*
17790205 ATATATATTC
1 ATAT-TATTT
* *
17790215 ATATTAATC
1 ATATTATTT
*
17790224 ATATCTATTC
1 ATAT-TATTT
*
17790234 ATATATATCT
1 ATAT-TATTT
* *
17790244 ATTTTAATT
1 ATATTATTT
17790253 ATATTCATTT
1 ATATT-ATTT
17790263 ATATATATTT
1 ATAT-TATTT
17790273 ATATTATT
1 ATATTATT
17790281 CGTAATTTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
8 4 0.07
9 20 0.33
10 35 0.58
11 1 0.02
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (9 bp):
ATATTATTT
Found at i:17790985 original size:6 final size:6
Alignment explanation
Indices: 17790974--17791008 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
17790964 TCTTCATCAT
* *
17790974 CCTCAC CCTCAC CCTCAA CCTCAA CCTCAA CCTCA
1 CCTCAA CCTCAA CCTCAA CCTCAA CCTCAA CCTCA
17791009 TCTTTAAGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.26, C:0.57, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTCAA
Found at i:17796620 original size:14 final size:14
Alignment explanation
Indices: 17796588--17796614 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17796578 CATGTTTACT
17796588 AAATTTCTTTCTCA
1 AAATTTCTTTCTCA
17796602 AAATTTCTTTCTC
1 AAATTTCTTTCTC
17796615 CTAATTATTA
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:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATTTCTTTCTCA
Found at i:17799175 original size:30 final size:30
Alignment explanation
Indices: 17799122--17799188 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
17799112 CATCAAGTAA
* * *
17799122 AAAAAATATTATTTTAAATAATTAATAATTT
1 AAAAAATACTATTTTAAACAATTAATAA-AT
* *
17799153 AAAAAATACTA-TTTAGACAATTACTAAAT
1 AAAAAATACTATTTTAAACAATTAATAAAT
17799182 AAAAAAT
1 AAAAAAT
17799189 GTTAGCAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 8 0.26
30 13 0.42
31 10 0.32
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAAAATACTATTTTAAACAATTAATAAAT
Found at i:17799837 original size:17 final size:19
Alignment explanation
Indices: 17799800--17799837 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
17799790 TACTGGAATT
*
17799800 TATTTTTATTAATTTTATA
1 TATTTTTATAAATTTTATA
17799819 TATTTTT-TAAATTTT-TA
1 TATTTTTATAAATTTTATA
17799836 TA
1 TA
17799838 AAATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 7 0.39
19 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTTTATAAATTTTATA
Found at i:17800033 original size:15 final size:15
Alignment explanation
Indices: 17799990--17800038 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
17799980 AACTAGACCA
17799990 AAAAAATTCAA-TTT
1 AAAAAATTCAATTTT
* *
17800004 AGATCAAATTAAATTTT
1 A-A-AAAATTCAATTTT
17800021 AAAAAATTCAATTTT
1 AAAAAATTCAATTTT
17800036 AAA
1 AAA
17800039 TTTTAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 1 0.04
15 15 0.54
16 8 0.29
17 4 0.14
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (15 bp):
AAAAAATTCAATTTT
Found at i:17800524 original size:58 final size:59
Alignment explanation
Indices: 17800460--17800570 Score: 179
Period size: 58 Copynumber: 1.9 Consensus size: 59
17800450 CAAAATAAAA
* *
17800460 CAAAATAACATTATTCTCAACTCTTTGATAAAAAG-TAAGACATAGAAATAAGCATAAG
1 CAAAATAACAGTAATCTCAACTCTTTGATAAAAAGTTAAGACATAGAAATAAGCATAAG
* *
17800518 CAAAATAACAGTAATCTTAACTCTTTGATAAAAAGTTAAGAGATAGAAATAAG
1 CAAAATAACAGTAATCTCAACTCTTTGATAAAAAGTTAAGACATAGAAATAAG
17800571 TACAAGATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
58 32 0.67
59 16 0.33
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (59 bp):
CAAAATAACAGTAATCTCAACTCTTTGATAAAAAGTTAAGACATAGAAATAAGCATAAG
Found at i:17801360 original size:24 final size:24
Alignment explanation
Indices: 17801332--17801378 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
17801322 ACTAATTATC
17801332 CAAAGGTAAAATTTT-TAGAAATTA
1 CAAAGGTAAAATTTTATA-AAATTA
*
17801356 CAAAGGTTAAATTTTATAAAATT
1 CAAAGGTAAAATTTTATAAAATT
17801379 CCTAAGTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (24 bp):
CAAAGGTAAAATTTTATAAAATTA
Found at i:17801640 original size:11 final size:11
Alignment explanation
Indices: 17801626--17801661 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
17801616 AATTTAGATG
17801626 AAATTTCAATA
1 AAATTTCAATA
*
17801637 AAATTTCAATG
1 AAATTTCAATA
17801648 AAATTTCAATA
1 AAATTTCAATA
17801659 AAA
1 AAA
17801662 GTAATTGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (11 bp):
AAATTTCAATA
Found at i:17801978 original size:13 final size:13
Alignment explanation
Indices: 17801962--17801987 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17801952 AAATTTAGAA
17801962 ATAAAAATAAATT
1 ATAAAAATAAATT
17801975 ATAAAAATAAATT
1 ATAAAAATAAATT
17801988 TCGATGATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAAAATAAATT
Found at i:17802604 original size:23 final size:25
Alignment explanation
Indices: 17802566--17802612 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
17802556 ACTAATTATC
17802566 CAAAGGTGAAATTTTTA-AAAATTA
1 CAAAGGTGAAATTTTTATAAAATTA
*
17802590 CAAAGGT-TAATTTTTATAAAATT
1 CAAAGGTGAAATTTTTATAAAATT
17802613 CCTAGGTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (25 bp):
CAAAGGTGAAATTTTTATAAAATTA
Found at i:17803022 original size:21 final size:21
Alignment explanation
Indices: 17802948--17803025 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
17802938 TAAGTTTTAA
17802948 TAAAAGGGATCGATCCCCTAAG
1 TAAAAGGGATCGATCCCCT-AG
** **
17802970 -GGAAGGGATCGATCCCCTTCT
1 TAAAAGGGATCGATCCCC-TAG
**
17802991 TATCA--GATCGATCCCCTAG
1 TAAAAGGGATCGATCCCCTAG
17803010 TAAAAGGGATCGATCC
1 TAAAAGGGATCGATCC
17803026 TGTTTTCTTC
Statistics
Matches: 41, Mismatches: 11, Indels: 9
0.67 0.18 0.15
Matches are distributed among these distances:
19 4 0.10
20 11 0.27
21 24 0.59
22 2 0.05
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (21 bp):
TAAAAGGGATCGATCCCCTAG
Found at i:17808957 original size:73 final size:74
Alignment explanation
Indices: 17808880--17809025 Score: 204
Period size: 74 Copynumber: 2.0 Consensus size: 74
17808870 TGCAGAACTG
* * * *
17808880 ATCGATCTCC-TTGGGATAGGATCGATTGGGTATTCAACCAGTAACTAAAAGAAGTTGGAAACGT
1 ATCGATCCCCTTTGGGATAGGATCGATCGGGTATTCAACCAATAACTAAAAAAAGTTGGAAACGT
17808944 GCAAAATCA
66 GCAAAATCA
* ** *
17808953 ATCGATCCCCTTTTGGATAGGATCGATCGGGTATTCAACCAATAGTTAAAAAAAGTTGGAAATGT
1 ATCGATCCCCTTTGGGATAGGATCGATCGGGTATTCAACCAATAACTAAAAAAAGTTGGAAACGT
*
17809018 GTAAAATC
66 GCAAAATC
17809026 GATTGAGCCC
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
73 9 0.14
74 54 0.86
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (74 bp):
ATCGATCCCCTTTGGGATAGGATCGATCGGGTATTCAACCAATAACTAAAAAAAGTTGGAAACGT
GCAAAATCA
Found at i:17811599 original size:20 final size:20
Alignment explanation
Indices: 17811574--17811625 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
17811564 CACCTAAGGC
17811574 AAGGGATCGATCCCCTCTTA
1 AAGGGATCGATCCCCTCTTA
17811594 AAGGGATCGATCCCCTCTTA
1 AAGGGATCGATCCCCTCTTA
17811614 AAGGGATCGATC
1 AAGGGATCGATC
17811626 GGTTGCTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (20 bp):
AAGGGATCGATCCCCTCTTA
Found at i:17814750 original size:32 final size:35
Alignment explanation
Indices: 17814693--17814774 Score: 98
Period size: 33 Copynumber: 2.4 Consensus size: 35
17814683 ATTTTTTTTA
*
17814693 TTTTTTATTATTTTGAAAACTTTATTT-ACAAAGAT
1 TTTTTTATTATTTT-AAAACTTTATTTGAAAAAGAT
* *
17814728 TTTTTTATTCTTTT-AAAC-TTATTTGAAAAAGGT
1 TTTTTTATTATTTTAAAACTTTATTTGAAAAAGAT
17814761 TTTTTTATTTATTT
1 TTTTTTA-TTATTT
17814775 CATAAATAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 6 0.15
33 17 0.41
34 5 0.12
35 13 0.32
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.60
Consensus pattern (35 bp):
TTTTTTATTATTTTAAAACTTTATTTGAAAAAGAT
Found at i:17814793 original size:3 final size:3
Alignment explanation
Indices: 17814779--17814822 Score: 70
Period size: 3 Copynumber: 14.0 Consensus size: 3
17814769 TTATTTCATA
17814779 AAT AAGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAGT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
17814823 GTATTTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17815553 original size:47 final size:50
Alignment explanation
Indices: 17815440--17815557 Score: 134
Period size: 50 Copynumber: 2.4 Consensus size: 50
17815430 TTTTAATGAG
* ** *
17815440 AATTGATTTTGAAATTAAATCCCAAAAATCTCTCCTATCATTGTAATGTG
1 AATTGATTATGAAATTAAATCCCAAAAATCTCTCCTATCATTCAAATGTC
* * * *
17815490 GATTGATTATGGAATTAAATCCCGACAATCTCTCC-A-CA-TCAAATGTC
1 AATTGATTATGAAATTAAATCCCAAAAATCTCTCCTATCATTCAAATGTC
*
17815537 AATTGATTCTGAAATTAAATC
1 AATTGATTATGAAATTAAATC
17815558 TTAAAATCTC
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
47 24 0.42
48 2 0.04
49 1 0.02
50 30 0.53
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (50 bp):
AATTGATTATGAAATTAAATCCCAAAAATCTCTCCTATCATTCAAATGTC
Found at i:17816384 original size:86 final size:86
Alignment explanation
Indices: 17816251--17816462 Score: 223
Period size: 86 Copynumber: 2.5 Consensus size: 86
17816241 TCAAATTTGC
* * * *
17816251 AAGAATGAAAGATTCTCAAGATTTCAAACTTCACAGAGGTTTTAGATTCACAAAGGTTCCAA-GT
1 AAGAAAGAAAGATTCTCAAGATTTCAAACTTCACAAAGGTTCTAGATTCACAAA-GATCCAAGGT
* *
17816315 TCATAAGGACTTTCAGATTGGT
65 TCACAAGGACTTTCAGATTCGT
* ** * *
17816337 AAGAAAGAAAGATT-TGCAAGATTTTAAGTTTCATAAAGGTTCTAGATTCACAAAGATGCAAGGT
1 AAGAAAGAAAGATTCT-CAAGATTTCAAACTTCACAAAGGTTCTAGATTCACAAAGATCCAAGGT
* *
17816401 TCGCAAGGACTTTTAGATTCGT
65 TCACAAGGACTTTCAGATTCGT
* * **
17816423 AAAAAAGAAAGATTCAT-AAAATTTCAAGTTTCACAAAGGT
1 AAGAAAGAAAGATTC-TCAAGATTTCAAACTTCACAAAGGT
17816463 GCAAGGTTCG
Statistics
Matches: 105, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
85 6 0.06
86 98 0.93
88 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (86 bp):
AAGAAAGAAAGATTCTCAAGATTTCAAACTTCACAAAGGTTCTAGATTCACAAAGATCCAAGGTT
CACAAGGACTTTCAGATTCGT
Found at i:17816466 original size:69 final size:69
Alignment explanation
Indices: 17816383--17816701 Score: 347
Period size: 69 Copynumber: 4.6 Consensus size: 69
17816373 AGGTTCTAGA
* * *
17816383 TTCACAAAGATGCAAGGTTCGCAAGGACTTTTAGATTCGTAAAAAAGAAAGATTCATAAAATTTC
1 TTCACAAAGATGCAAGGTTCGCAAGGACTTTTAGATTCATAAAAAAGAAAGATTCACAAGATTTC
17816448 AAGT
66 AAGT
* * * ** * *
17816452 TTCACAAAGGTGCAAGGTTCGTAAGGACTTTCAGATTCGCAAGAAAGAAAGATTCATAAGATTTC
1 TTCACAAAGATGCAAGGTTCGCAAGGACTTTTAGATTCATAAAAAAGAAAGATTCACAAGATTTC
17816517 AAGT
66 AAGT
** * * * * ** *
17816521 TTCGTAAAAATGTAAGGTTCGCAAAGGATTTTTAGATTCACAAAAAAG-AAGATTTGCAAGATTC
1 TTCACAAAGATGCAAGGTTCGC-AAGGACTTTTAGATTCATAAAAAAGAAAGATTCACAAGATTT
17816585 CAAGT
65 CAAGT
* * * *
17816590 TTCACAAAGGTGCAAGGTTCACAAGGATTTTTAGATTCATAAGAAAA-AAAGATTCGCAAGATTT
1 TTCACAAAGATGCAAGGTTCGCAAGGACTTTTAGATTCATAA-AAAAGAAAGATTCACAAGATTT
17816654 CAAGT
65 CAAGT
** * *
17816659 TTCGTAAAAATGCAAGGTTCACAAGGA-TTTTCAGATTCATAAA
1 TTCACAAAGATGCAAGGTTCGCAAGGACTTTT-AGATTCATAAA
17816702 GATTTTCAAA
Statistics
Matches: 213, Mismatches: 33, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
68 24 0.11
69 168 0.79
70 21 0.10
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (69 bp):
TTCACAAAGATGCAAGGTTCGCAAGGACTTTTAGATTCATAAAAAAGAAAGATTCACAAGATTTC
AAGT
Found at i:17816566 original size:138 final size:136
Alignment explanation
Indices: 17816392--17816697 Score: 405
Period size: 138 Copynumber: 2.2 Consensus size: 136
17816382 ATTCACAAAG
* * * *
17816392 ATGCAAGGTTCGCAAGGACTTTTAGATTCGTAAAAAAGAAAGATTCATAAAATTTCAAGTTTCAC
1 ATGCAAGGTTCGCAAGGATTTTTAGATTC-AAAAAAAG-AAGATTCACAAAATTCCAAGTTTCAC
** * * *
17816457 AAAGGTGCAAGGTTCGTAAGGACTTTCAGATTCGCAAGAAAGAAAGATTCATAAGATTTCAAGTT
64 AAAGGTGCAAGGTTCACAAGGACTTTCAGATTCACAAGAAAAAAAGATTCACAAGATTTCAAGTT
17816522 TCGTAAAA
129 TCGTAAAA
* ** *
17816530 ATGTAAGGTTCGCAAAGGATTTTTAGATTCACAAAAAAGAAGATTTGCAAGATTCCAAGTTTCAC
1 ATGCAAGGTTCGC-AAGGATTTTTAGATTCA-AAAAAAGAAGATTCACAAAATTCCAAGTTTCAC
* * * *
17816595 AAAGGTGCAAGGTTCACAAGGATTTTTAGATTCATAAGAAAAAAAGATTCGCAAGATTTCAAGTT
64 AAAGGTGCAAGGTTCACAAGGACTTTCAGATTCACAAGAAAAAAAGATTCACAAGATTTCAAGTT
17816660 TCGTAAAA
129 TCGTAAAA
* *
17816668 ATGCAAGGTTCACAAGGATTTTCAGATTCA
1 ATGCAAGGTTCGCAAGGATTTTTAGATTCA
17816698 TAAAGATTTT
Statistics
Matches: 146, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
137 16 0.11
138 108 0.74
139 22 0.15
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (136 bp):
ATGCAAGGTTCGCAAGGATTTTTAGATTCAAAAAAAGAAGATTCACAAAATTCCAAGTTTCACAA
AGGTGCAAGGTTCACAAGGACTTTCAGATTCACAAGAAAAAAAGATTCACAAGATTTCAAGTTTC
GTAAAA
Found at i:17816736 original size:86 final size:87
Alignment explanation
Indices: 17816615--17816781 Score: 214
Period size: 86 Copynumber: 1.9 Consensus size: 87
17816605 GGTTCACAAG
* * *
17816615 GATTTTTAGATTCATAAGAAAAAAAGATTCGCAAGATTTC-AAGTTTCGTAAAAATGCAAGGTTC
1 GATTTTCAAATTCATAAGAAAAAAAGATTCGCAAGA-TTCAAAGTTTCATAAAAATGCAAGGTTC
17816679 ACAAGGA-TTTTCAGATTCATAAA
65 ACAAGGACTTTT-AGATTCATAAA
* * * * *
17816702 GATTTTCAAATTCGTAAG-AAATAAGATTTGCAAGATTCAAAGTTTCATAAAAGTGCAAGGTTCG
1 GATTTTCAAATTCATAAGAAAAAAAGATTCGCAAGATTCAAAGTTTCATAAAAATGCAAGGTTCA
*
17816766 TAAGGACTTTTAGATT
66 CAAGGACTTTTAGATT
17816782 TGCAAAGGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
85 3 0.04
86 47 0.68
87 19 0.28
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (87 bp):
GATTTTCAAATTCATAAGAAAAAAAGATTCGCAAGATTCAAAGTTTCATAAAAATGCAAGGTTCA
CAAGGACTTTTAGATTCATAAA
Found at i:17816839 original size:17 final size:17
Alignment explanation
Indices: 17816797--17816867 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 17
17816787 AGGTTCTAGA
*
17816797 TTCGCAAAGATGCAAAG
1 TTCGCAAAGATGCAAGG
*
17816814 TTTGCAAAGATGCAAGG
1 TTCGCAAAGATGCAAGG
* * *
17816831 TTCGTAAAGATACAAGA
1 TTCGCAAAGATGCAAGG
* *
17816848 TTCGTAAAGGTGCAAGG
1 TTCGCAAAGATGCAAGG
17816865 TTC
1 TTC
17816868 ACAAGGACTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (17 bp):
TTCGCAAAGATGCAAGG
Found at i:17817885 original size:24 final size:23
Alignment explanation
Indices: 17817833--17817878 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
17817823 TCTTTTTCAT
*
17817833 TTTTTTCATTTTTTTTTGTTTTC
1 TTTTTTCATTTTTTATTGTTTTC
*
17817856 TATTTTCTATTTTTTATTGTTTT
1 TTTTTTC-ATTTTTTATTGTTTT
17817879 TGTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.80
Consensus pattern (23 bp):
TTTTTTCATTTTTTATTGTTTTC
Found at i:17818233 original size:8 final size:8
Alignment explanation
Indices: 17818216--17818247 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
17818206 GCCCCATCAA
17818216 TTTTTC-T
1 TTTTTCAT
17818223 TTTTTCA-
1 TTTTTCAT
17818230 TTTTTCAT
1 TTTTTCAT
17818238 TTTTTCAT
1 TTTTTCAT
17818246 TT
1 TT
17818248 GTCAGGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 13 0.57
8 10 0.43
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTCAT
Found at i:17818234 original size:15 final size:15
Alignment explanation
Indices: 17818215--17818247 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
17818205 TGCCCCATCA
17818215 ATTTTTC-TTTTTTC
1 ATTTTTCATTTTTTC
17818229 ATTTTTCATTTTTTC
1 ATTTTTCATTTTTTC
17818244 ATTT
1 ATTT
17818248 GTCAGGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTTCATTTTTTC
Found at i:17821885 original size:20 final size:17
Alignment explanation
Indices: 17821842--17821891 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 17
17821832 AAGAAATAAT
17821842 AAAAGTAAATAAAATAAAC
1 AAAA-TAAA-AAAATAAAC
17821861 AAAATAAGAAAAATAGAATC
1 AAAATAA-AAAAATA-AA-C
17821881 AAAATAAAAAA
1 AAAATAAAAAA
17821892 CAGAGTGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.32
19 11 0.39
20 8 0.29
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAATAAAAAAATAAAC
Found at i:17822547 original size:47 final size:48
Alignment explanation
Indices: 17822420--17822550 Score: 131
Period size: 47 Copynumber: 2.7 Consensus size: 48
17822410 TTTTAATGAG
* * * * *
17822420 AATTGATTTTGAAATCAAATCC-CAAAATCTCTCCCTATCATTTTAATGTG
1 AATTGATTTTGGAATTAAATCCTAAAAATCTCTCCATATCA---TAATGTC
* * * * *
17822470 GATTGATTATGGAATTAAATCTTGACAATCTCTCCATATCA-AATGTC
1 AATTGATTTTGGAATTAAATCCTAAAAATCTCTCCATATCATAATGTC
17822517 AATTGATTTTGGAATTAAATCCTAAAAATCTCTC
1 AATTGATTTTGGAATTAAATCCTAAAAATCTCTC
17822551 AACCATGGTT
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
47 34 0.52
50 17 0.26
51 15 0.23
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (48 bp):
AATTGATTTTGGAATTAAATCCTAAAAATCTCTCCATATCATAATGTC
Found at i:17830999 original size:44 final size:44
Alignment explanation
Indices: 17830917--17831397 Score: 291
Period size: 43 Copynumber: 11.1 Consensus size: 44
17830907 GATTATTGAT
* ** * * *
17830917 GAGCTTTATTTATTTTTC-AAAGTTGTTGAGCCTCTGTTTAGAG
1 GAGCCTTATTTATTTTTCAAAAGTCATTAAGCCTTTATTTAGAG
* * ** * *
17830960 AAGCCTTAGTTATTTTTCAAAAGTGGTTAAGCCTTTGTTTAAAG
1 GAGCCTTATTTATTTTTCAAAAGTCATTAAGCCTTTATTTAGAG
* * * * * *
17831004 GAGCCTTATTTATTTTTGAAAA-TCGTTAAGCATCTACTTAGAA
1 GAGCCTTATTTATTTTTCAAAAGTCATTAAGCCTTTATTTAGAG
* * * *
17831047 GAGCCTTATTTACTTTTCAAAAGTCATTGAGCCATTGTTT-GAAG
1 GAGCCTTATTTATTTTTCAAAAGTCATTAAGCCTTTATTTAG-AG
* * * * * *
17831091 GAGTCTTATTTACTTTTAAAAAATTATTAAGCTTTTATTTAGAG
1 GAGCCTTATTTATTTTTCAAAAGTCATTAAGCCTTTATTTAGAG
* * * *
17831135 GAGCTTTATTTTTTTTTCAAAAGTCATTGAGCCTCTATTTAGAG
1 GAGCCTTATTTATTTTTCAAAAGTCATTAAGCCTTTATTTAGAG
* * * *
17831179 GAGTCTTTTTTACTTTTT--AAAGTCATTAATCCTTTATTTATAG
1 GAGCCTTATTTA-TTTTTCAAAAGTCATTAAGCCTTTATTTAGAG
* ** *
17831222 GAGCTTTATTTATTTTGT--AAAGTTGTTAAGCTTTTATTTAGAG
1 GAGCCTTATTTATTTT-TCAAAAGTCATTAAGCCTTTATTTAGAG
* * ** * * ** *
17831265 AAGCCTTATTTATTTTTC-AATGTTGTTGAGCCTATGCTTATAG
1 GAGCCTTATTTATTTTTCAAAAGTCATTAAGCCTTTATTTAGAG
* * * * *
17831308 GAGCTTTATTTA-TTTTCTAAAGTCATTGAA-ACTCTACTTAGAG
1 GAGCCTTATTTATTTTTCAAAAGTCATT-AAGCCTTTATTTAGAG
* * ** * * *
17831351 GAGCTTTGTTT-TCTTTTCAAAAACCATTGAGCCTCTATTTAAAG
1 GAGCCTTATTTAT-TTTTCAAAAGTCATTAAGCCTTTATTTAGAG
17831395 GAG
1 GAG
17831398 TTTTATGTTA
Statistics
Matches: 338, Mismatches: 88, Indels: 23
0.75 0.20 0.05
Matches are distributed among these distances:
42 10 0.03
43 169 0.50
44 153 0.45
45 6 0.02
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.44
Consensus pattern (44 bp):
GAGCCTTATTTATTTTTCAAAAGTCATTAAGCCTTTATTTAGAG
Found at i:17831068 original size:87 final size:86
Alignment explanation
Indices: 17830917--17831281 Score: 268
Period size: 87 Copynumber: 4.2 Consensus size: 86
17830907 GATTATTGAT
* * ** * * *
17830917 GAGCTTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAG-AGAAGCCTTAGTTATTTTTCAAA
1 GAGCCTTATTTATTTTT-AAAATCATTAAGCCTCTATTTAGAAG-AGCCTTATTTATTTTTCAAA
** *
17830981 AGTGGTTAAGCCTTTGTTTAAAG
64 AGTCATTAAGCCTTTATTTAAAG
* * * *
17831004 GAGCCTTATTTATTTTTGAAAATCGTTAAGCATCTACTTAGAAGAGCCTTATTTACTTTTCAAAA
1 GAGCCTTATTTATTTTT-AAAATCATTAAGCCTCTATTTAGAAGAGCCTTATTTATTTTTCAAAA
* * * *
17831069 GTCATTGAGCCATTGTTTGAAG
65 GTCATTAAGCCTTTATTTAAAG
* * * * * * * *
17831091 GAGTCTTATTTACTTTTAAAAAATTATTAAGCTTTTATTTAGAGGAGCTTTATTTTTTTTTCAAA
1 GAGCCTTATTTA-TTTT-TAAAATCATTAAGCCTCTATTTAGAAGAGCCTTATTTATTTTTCAAA
* * *
17831156 AGTCATTGAGCCTCTATTTAGAG
64 AGTCATTAAGCCTTTATTTAAAG
* * * * * * * *
17831179 GAGTCTTTTTTACTTTTTAAAGTCATTAATCCTTTATTTATAGGAGCTTTATTTATTTTGT--AA
1 GAGCCTTATTTA-TTTTTAAAATCATTAAGCCTCTATTTAGAAGAGCCTTATTTATTTT-TCAAA
** * *
17831242 AGTTGTTAAGCTTTTATTTAGAG
64 AGTCATTAAGCCTTTATTTAAAG
*
17831265 AAGCCTTATTTATTTTT
1 GAGCCTTATTTATTTTT
17831282 CAATGTTGTT
Statistics
Matches: 227, Mismatches: 47, Indels: 10
0.80 0.17 0.04
Matches are distributed among these distances:
85 5 0.02
86 29 0.13
87 115 0.51
88 78 0.34
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.46
Consensus pattern (86 bp):
GAGCCTTATTTATTTTTAAAATCATTAAGCCTCTATTTAGAAGAGCCTTATTTATTTTTCAAAAG
TCATTAAGCCTTTATTTAAAG
Found at i:17831156 original size:88 final size:85
Alignment explanation
Indices: 17830953--17831237 Score: 282
Period size: 87 Copynumber: 3.3 Consensus size: 85
17830943 TGAGCCTCTG
* * ** * * *
17830953 TTTAGAGAAGCCTTAGTTATTTTTCAAAAGTGGTTAAGCCTTTGTTTAAAGGAGCCTTATTTATT
1 TTTAGAGGAGCCTTATTTATTTTTCAAAAGTCATTGAGCC-TTGTTT-AAGGAGTCTTATTTACT
* * *
17831018 TTTGAAAATCGTTAAGCATCTA
64 TTTAAAAATCATTAAGCATTTA
* * *
17831040 CTTAGAAGAGCCTTATTTACTTTTCAAAAGTCATTGAGCCATTGTTTGAAGGAGTCTTATTTACT
1 TTTAGAGGAGCCTTATTTATTTTTCAAAAGTCATTGAGCC-TTGTTT-AAGGAGTCTTATTTACT
* *
17831105 TTTAAAAAATTATTAAGCTTTTA
64 TTT-AAAAATCATTAAGCATTTA
* * * *
17831128 TTTAGAGGAGCTTTATTTTTTTTTCAAAAGTCATTGAGCCTCTATTTAGAGGAGTCTTTTTTACT
1 TTTAGAGGAGCCTTATTTATTTTTCAAAAGTCATTGAGCCT-TGTTTA-AGGAGTCTTATTTACT
* * * *
17831193 TTTTAAAGTCATTAATCCTTTA
64 TTTAAAAATCATTAAGCATTTA
* *
17831215 TTTATAGGAGCTTTATTTATTTT
1 TTTAGAGGAGCCTTATTTATTTT
17831238 GTAAAGTTGT
Statistics
Matches: 164, Mismatches: 31, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
87 93 0.57
88 71 0.43
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (85 bp):
TTTAGAGGAGCCTTATTTATTTTTCAAAAGTCATTGAGCCTTGTTTAAGGAGTCTTATTTACTTT
TAAAAATCATTAAGCATTTA
Found at i:17833586 original size:21 final size:20
Alignment explanation
Indices: 17833525--17833609 Score: 70
Period size: 20 Copynumber: 4.2 Consensus size: 20
17833515 AGTTACTCAG
*
17833525 TAAAA-TAAAAT-AAATAAA
1 TAAAATTAAAATGAAAAAAA
* * *
17833543 TAAAACTGAAAAT-CAAAATA
1 TAAAA-TTAAAATGAAAAAAA
17833563 TAAAA-TAAATATGTAAAAAAA
1 TAAAATTAAA-ATG-AAAAAAA
17833584 TAAAATTAAAATGAAAAAAA
1 TAAAATTAAAATGAAAAAAA
17833604 TGAAAA
1 T-AAAA
17833610 CTTGCGATTG
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
18 8 0.15
19 2 0.04
20 22 0.42
21 17 0.32
22 4 0.08
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (20 bp):
TAAAATTAAAATGAAAAAAA
Found at i:17834428 original size:3 final size:3
Alignment explanation
Indices: 17834415--17834542 Score: 91
Period size: 3 Copynumber: 45.3 Consensus size: 3
17834405 GAAAATAGAA
17834415 AAT AAT AAAT AAT AAAT AAT AA- ATAT AAT -AT AAT -AT AAT AAT -AT
1 AAT AAT -AAT AAT -AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* * * *
17834459 AGT TAT ACT -AT AAT AAT AAT AAT AAT -AT ACAT -AT TAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
*
17834501 AAT AAT -AT AAT -AT AAT AAT AAT -AT AAT GAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17834543 TGCTATACTA
Statistics
Matches: 100, Mismatches: 9, Indels: 32
0.71 0.06 0.23
Matches are distributed among these distances:
2 22 0.22
3 69 0.69
4 9 0.09
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:17834431 original size:14 final size:15
Alignment explanation
Indices: 17834416--17834542 Score: 113
Period size: 14 Copynumber: 8.4 Consensus size: 15
17834406 AAAATAGAAA
17834416 ATAATAAATAATAA-
1 ATAATAAATAATAAT
17834430 ATAATAAAT-ATAAT
1 ATAATAAATAATAAT
17834444 ATAATATAATAAT-AT
1 ATAATA-AATAATAAT
* *
17834459 AGTTATACTATAATAAT
1 A-TAATA-AATAATAAT
17834476 AATAAT-AAT-ATACAT
1 -ATAATAAATAATA-AT
*
17834491 ATTATAATATAATAAT
1 ATAATAA-ATAATAAT
17834507 ATAATATAATAATAAT
1 ATAATA-AATAATAAT
*
17834523 ATAAT-GATAATAAT
1 ATAATAAATAATAAT
17834537 ATAATA
1 ATAATA
17834543 TGCTATACTA
Statistics
Matches: 93, Mismatches: 8, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
13 4 0.04
14 35 0.38
15 11 0.12
16 33 0.35
17 9 0.10
18 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
ATAATAAATAATAAT
Found at i:17834446 original size:5 final size:5
Alignment explanation
Indices: 17834416--17834567 Score: 110
Period size: 5 Copynumber: 31.2 Consensus size: 5
17834406 AAAATAGAAA
*
17834416 ATAAT A-AAT AATAA- ATAAT A-AAT ATAAT ATAAT AT-A- ATAAT ATAGTT
1 ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
*
17834463 ATACT ATAAT AATAAT AATAAT ATACAT AT--T ATAAT AT-A- ATAAT
1 ATAAT ATAAT -ATAAT -ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT
** * *
17834507 ATAAT ATAAT AATAAT ATAAT GAT-A- ATAAT ATAAT ATGCT ATACT ATATT
1 ATAAT ATAAT -ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
17834557 ATAAT ATAAT A
1 ATAAT ATAAT A
17834568 CGGGTAATAA
Statistics
Matches: 122, Mismatches: 8, Indels: 34
0.74 0.05 0.21
Matches are distributed among these distances:
3 9 0.07
4 16 0.13
5 69 0.57
6 28 0.23
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:17834497 original size:55 final size:55
Alignment explanation
Indices: 17834415--17834567 Score: 159
Period size: 55 Copynumber: 2.7 Consensus size: 55
17834405 GAAAATAGAA
* * *
17834415 AATAATAAATAATAA-ATA-ATAAATATAATATAATATAATAATATAGTTATACTAT
1 AATAAT-AATAATAATATACAT-AATATAATATAATATAATAATATAATAATAATAT
*
17834470 AATAATAATAATAATATACATATTATAATATAATA-ATATAATATAATAATAATAT
1 AATAATAATAATAATATACATAATATAATATAATATA-ATAATATAATAATAATAT
* * * *
17834525 AATGATAATAATATAATATGCTATACTATATTATAATATAATA
1 AATAATAAT-A-ATAATATAC-ATAATATAATATAATATAATA
17834568 CGGGTAATAA
Statistics
Matches: 83, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
54 9 0.11
55 45 0.54
56 3 0.04
57 8 0.10
58 17 0.20
59 1 0.01
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (55 bp):
AATAATAATAATAATATACATAATATAATATAATATAATAATATAATAATAATAT
Found at i:17842145 original size:7 final size:6
Alignment explanation
Indices: 17842111--17842146 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
17842101 TATTCTTTGA
17842111 ATCAAT ATCAAT ATCAAT ATCATAT ATCAATT ATCA
1 ATCAAT ATCAAT ATCAAT ATCA-AT ATCAA-T ATCA
17842147 TTCCAACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 17 0.61
7 11 0.39
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (6 bp):
ATCAAT
Found at i:17842195 original size:19 final size:19
Alignment explanation
Indices: 17842171--17842207 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
17842161 GAACCAAGAC
17842171 ATAGACATGTTTAGCTAGT
1 ATAGACATGTTTAGCTAGT
17842190 ATAGACATGTTTAGCTAG
1 ATAGACATGTTTAGCTAG
17842208 CATGGCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (19 bp):
ATAGACATGTTTAGCTAGT
Found at i:17848972 original size:186 final size:185
Alignment explanation
Indices: 17848674--17849282 Score: 780
Period size: 186 Copynumber: 3.3 Consensus size: 185
17848664 ATAGTCCCGT
* * ***
17848674 AAATTTTAAAAGAAAATTATTGAAGGCGTTTGCTCTAAAAAAATGCCTTCAATTATTATGTATGC
1 AAATTTTAAAAGAAAATTATTGAAGGCGTTTGTTCTCAAAAAATGCCTTCAATTATTATGTACAT
*
17848739 AAATTAGAGGGAATTAGTGAAGGCATTTTTCTAGAATAAACGCCTTCACTAACAATCTTAAAATT
66 AAATTAGAAGGAATTAGTGAAGGCATTTTTCTAGAATAAACGCCTTCACTAACAATCTTAAAATT
* * * *
17848804 AGAGTTGTCGAAAATTAAATGTGTTTTTCACTGGAAAACGCCTTTAATAATCTCAA
131 AGAGTTGTCGAAAATTGAAGGAGTTTTTCATTGGAAAACGCCTTTAATAATC-CAA
* * *
17848860 AAATTTTAAAA-AGGAATTATTGAAGGTGTTTGTTCTCAAAAAATGCCTTCAATCATTATGTACA
1 AAATTTTAAAAGA-AAATTATTGAAGGCGTTTGTTCTCAAAAAATGCCTTCAATTATTATGTACA
* * *
17848924 TAAATTAGAAGAAATTAGTGAAGGCATTTCTCTAGAATAAACGCCTTCACTAACCATCTTAAAAT
65 TAAATTAGAAGGAATTAGTGAAGGCATTTTTCTAGAATAAACGCCTTCACTAACAATCTTAAAAT
* * * *
17848989 TAGAGTTGTCGAAAATTGAAGGCA-TTTTTCATTAGAAGATGTCTTTAATAATCCTAA
130 TAGAGTTGTCGAAAATTGAAGG-AGTTTTTCATTGGAAAACGCCTTTAATAATCC-AA
* * * *
17849046 AAATTTTAAAAGGAAATTATTGAAGGCATTTGTTCTCAAAAAATACCCAT-AATTATTATGTACA
1 AAATTTTAAAAGAAAATTATTGAAGGCGTTTGTTCTCAAAAAAT-GCCTTCAATTATTATGTACA
* * * **
17849110 TAAATTGGAAGGAATTAGTGAAGGCATTTTTCTAGAATAAATGCCTTTACTAACTGTCTTAAAAT
65 TAAATTAGAAGGAATTAGTGAAGGCATTTTTCTAGAATAAACGCCTTCACTAACAATCTTAAAAT
* * * *
17849175 TAGAGTTGTGGAAAATTGGAGGCAG-TTTTCATTGAAAAACGCCTTTAATAATCCCAT
130 TAGAGTTGTCGAAAATTGAAGG-AGTTTTTCATTGGAAAACGCCTTTAATAAT-CCAA
* *
17849232 AAATTTTAAAAGAAAATTATTGAATGTGTTT-TTCT-AGAATAAATGCCTTCA
1 AAATTTTAAAAGAAAATTATTGAAGGCGTTTGTTCTCA-AA-AAATGCCTTCA
17849283 TTAACTATCT
Statistics
Matches: 365, Mismatches: 48, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
184 1 0.00
185 11 0.03
186 348 0.95
187 5 0.01
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (185 bp):
AAATTTTAAAAGAAAATTATTGAAGGCGTTTGTTCTCAAAAAATGCCTTCAATTATTATGTACAT
AAATTAGAAGGAATTAGTGAAGGCATTTTTCTAGAATAAACGCCTTCACTAACAATCTTAAAATT
AGAGTTGTCGAAAATTGAAGGAGTTTTTCATTGGAAAACGCCTTTAATAATCCAA
Found at i:17849270 original size:124 final size:124
Alignment explanation
Indices: 17849136--17849379 Score: 371
Period size: 124 Copynumber: 2.0 Consensus size: 124
17849126 AGTGAAGGCA
* * ** **
17849136 TTTTTCTAGAATAAATGCCTTTACTAACTGTCTTAAAATTAGAGTTGTGGAAAATTGGAGGCAGT
1 TTTTTCTAGAATAAATGCCTTCACTAACTATCTTAAAATTAGAGTTGTCAAAAATTAAAGGCAGT
*
17849201 TTTCATTGAAAAACGCCTTTAATAATCCCATAAATTTTAAAAGAAAATTATTGAATGTG
66 TTTCATTGAAAAACGCCTTTAATAATCCCAAAAATTTTAAAAGAAAATTATTGAATGTG
* *
17849260 TTTTTCTAGAATAAATGCCTTCATTAACTATCTTAAAATTAGAGTTGTCAAAAATTAAAGGCATT
1 TTTTTCTAGAATAAATGCCTTCACTAACTATCTTAAAATTAGAGTTGTCAAAAATTAAAGGCAGT
* * **
17849325 TTTCATTGAAAAACGCCTTTAATAATCTCAAAAATTTTAAGAGGGAATTATTGAA
66 TTTCATTGAAAAACGCCTTTAATAATCCCAAAAATTTTAAAAGAAAATTATTGAA
17849380 AGCGTTTGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
124 107 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (124 bp):
TTTTTCTAGAATAAATGCCTTCACTAACTATCTTAAAATTAGAGTTGTCAAAAATTAAAGGCAGT
TTTCATTGAAAAACGCCTTTAATAATCCCAAAAATTTTAAAAGAAAATTATTGAATGTG
Found at i:17849363 original size:310 final size:311
Alignment explanation
Indices: 17848954--17849598 Score: 921
Period size: 310 Copynumber: 2.1 Consensus size: 311
17848944 AAGGCATTTC
* * *
17848954 TCTAGAATAAACGCCTTCACTAACCATCTTAAAATTAGAGTTGTCGAAAATTGAAGGCATTTTTC
1 TCTAGAATAAACGCCTTCACTAACTATCTTAAAATTAGAGTTGTCAAAAATTAAAGGCATTTTTC
* * * *
17849019 ATTAGAAGATGTCTTTAATAATCCTAAAAATTTTAAAAGGAAATTATTGAAGGCATTTGTTCTCA
66 ATTAGAAAACGCCTTTAATAATCCTAAAAATTTTAAAAGGAAATTATTGAAAGCATTTGTTCTCA
*
17849084 AAAAATACCCAT-AATTATTATGTACATAAATTGGAAGGAATTAGTGAAGGCAT-TTTTCTAGAA
131 AAAAATA-CCATCAATTATTATGTACATAAATTAGAAGGAATTAGTGAAGGCATGTTTTCTAGAA
* ** * **
17849147 TAAATGCCTTTACTAACTGTCTTAAAATTAGAGTTGTGGAAAATTGGAGGCAG-TTTTCA-TTGA
195 -AAATGCCTTCACTAACTGTCTTAAAATTAGAGTTGTAAAAAATTGAAGGC-GTTTTTCACCAG-
* *
17849210 AAAACGCCTTTAATAATCCCATAAATTTTAAAAGAAAATTATTGAATGTGTTT-T
257 AAAACACCTTTAATAATCCCATAAATTTTAAAAGAAAATTATTGAAGGTGTTTGT
* *
17849264 TCTAGAATAAATGCCTTCATTAACTATCTTAAAATTAGAGTTGTCAAAAATTAAAGGCATTTTTC
1 TCTAGAATAAACGCCTTCACTAACTATCTTAAAATTAGAGTTGTCAAAAATTAAAGGCATTTTTC
* * *
17849329 ATT-GAAAAACGCCTTTAATAAT-CTCAAAAATTTTAAGAGGGAATTATTGAAAGCGTTTGTTCT
66 ATTAG-AAAACGCCTTTAATAATCCT-AAAAATTTTAAAAGGAAATTATTGAAAGCATTTGTTCT
* * *
17849392 CAAAAAATACCTTCAATTATTATGTACGTAAATTAGAAGGAATTAGTGAAGGCATGTTTTTTAGA
129 CAAAAAATACCATCAATTATTATGTACATAAATTAGAAGGAATTAGTGAAGGCATGTTTTCTAGA
17849457 AAAATGCCTTCACTAACTGTCTTAAAATTAGAGTTGTAAAAAATTGAAGGCGTTTTTCACCAGAA
194 AAAATGCCTTCACTAACTGTCTTAAAATTAGAGTTGTAAAAAATTGAAGGCGTTTTTCACCAGAA
* * *
17849522 GACACCTTTAATAATCCCGTAAATTTTAAAAGGAAATTATTGAAGGTGTTTGT
259 AACACCTTTAATAATCCCATAAATTTTAAAAGAAAATTATTGAAGGTGTTTGT
17849575 TCTCA-AA-AAACGCCTTCACTAACT
1 TCT-AGAATAAACGCCTTCACTAACT
17849599 GTCGTAAAGT
Statistics
Matches: 298, Mismatches: 29, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
309 7 0.02
310 274 0.92
311 16 0.05
312 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (311 bp):
TCTAGAATAAACGCCTTCACTAACTATCTTAAAATTAGAGTTGTCAAAAATTAAAGGCATTTTTC
ATTAGAAAACGCCTTTAATAATCCTAAAAATTTTAAAAGGAAATTATTGAAAGCATTTGTTCTCA
AAAAATACCATCAATTATTATGTACATAAATTAGAAGGAATTAGTGAAGGCATGTTTTCTAGAAA
AATGCCTTCACTAACTGTCTTAAAATTAGAGTTGTAAAAAATTGAAGGCGTTTTTCACCAGAAAA
CACCTTTAATAATCCCATAAATTTTAAAAGAAAATTATTGAAGGTGTTTGT
Found at i:17849405 original size:124 final size:124
Alignment explanation
Indices: 17849122--17849406 Score: 358
Period size: 124 Copynumber: 2.3 Consensus size: 124
17849112 AATTGGAAGG
* * * * * * * **
17849122 AATTAGTGAAGGCATTTTTCTAGAATAAATGCCTTTACTAACTGTCTTAAAATTAGAGTTGTGGA
1 AATTATTGAAAGCGTTTTTCTAGAATAAATACCTTCATTAACTATCTTAAAATTAGAGTTGTCAA
** *
17849187 AAATTGGAGGCAGTTTTCATTGAAAAACGCCTTTAATAATCCCATAAATTTTAAAAGAA
66 AAATTAAAGGCAGTTTTCATTGAAAAACGCCTTTAATAATCCCAAAAATTTTAAAAGAA
* * *
17849246 AATTATTGAATGTGTTTTTCTAGAATAAATGCCTTCATTAACTATCTTAAAATTAGAGTTGTCAA
1 AATTATTGAAAGCGTTTTTCTAGAATAAATACCTTCATTAACTATCTTAAAATTAGAGTTGTCAA
* * * **
17849311 AAATTAAAGGCATTTTTCATTGAAAAACGCCTTTAATAATCTCAAAAATTTTAAGAGGG
66 AAATTAAAGGCAGTTTTCATTGAAAAACGCCTTTAATAATCCCAAAAATTTTAAAAGAA
17849370 AATTATTGAAAGCGTTTGTTCTCA-AA-AAATACCTTCA
1 AATTATTGAAAGCGTTT-TTCT-AGAATAAATACCTTCA
17849407 ATTATTATGT
Statistics
Matches: 139, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
124 132 0.95
125 6 0.04
126 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (124 bp):
AATTATTGAAAGCGTTTTTCTAGAATAAATACCTTCATTAACTATCTTAAAATTAGAGTTGTCAA
AAATTAAAGGCAGTTTTCATTGAAAAACGCCTTTAATAATCCCAAAAATTTTAAAAGAA
Found at i:17851955 original size:22 final size:21
Alignment explanation
Indices: 17851930--17851971 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17851920 AAGAAGTTCT
*
17851930 GTTATATGAGACATCATCGATG
1 GTTAGATGAGA-ATCATCGATG
*
17851952 GTTAGATGATAATCATCGAT
1 GTTAGATGAGAATCATCGAT
17851972 TTAGATTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (21 bp):
GTTAGATGAGAATCATCGATG
Found at i:17853590 original size:17 final size:17
Alignment explanation
Indices: 17853565--17853597 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17853555 AATTACGGAC
17853565 TTTTAGATTCACAAAGG
1 TTTTAGATTCACAAAGG
*
17853582 TTTTGGATTCACAAAG
1 TTTTAGATTCACAAAG
17853598 ATGCAAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (17 bp):
TTTTAGATTCACAAAGG
Found at i:17853638 original size:17 final size:17
Alignment explanation
Indices: 17853594--17853659 Score: 87
Period size: 17 Copynumber: 3.9 Consensus size: 17
17853584 TTGGATTCAC
* *
17853594 AAAGATGCAAAGTTCGC
1 AAAGATGCAAGGTTCGT
17853611 AAAGATGCAAGGTTCGT
1 AAAGATGCAAGGTTCGT
* *
17853628 AAAGATACAAGATTCGT
1 AAAGATGCAAGGTTCGT
*
17853645 AAAGGTGCAAGGTTC
1 AAAGATGCAAGGTTC
17853660 ACAATGACTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.21
Consensus pattern (17 bp):
AAAGATGCAAGGTTCGT
Found at i:17854940 original size:11 final size:10
Alignment explanation
Indices: 17854923--17854961 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
17854913 CCCCATCAAA
17854923 TTTTTTTTCT
1 TTTTTTTTCT
17854933 TATTTTTTTCT
1 T-TTTTTTTCT
*
17854944 TTTTTGCTTCT
1 TTTTT-TTTCT
17854955 TTTTTTT
1 TTTTTTT
17854962 GGGTAGCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.85
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:17854946 original size:19 final size:19
Alignment explanation
Indices: 17854924--17854960 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17854914 CCCATCAAAT
*
17854924 TTTTTTTCTTATTTTTTTC
1 TTTTTTGCTTATTTTTTTC
*
17854943 TTTTTTGCTTCTTTTTTT
1 TTTTTTGCTTATTTTTTT
17854961 TGGGTAGCAC
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:0.03, C:0.11, G:0.03, T:0.84
Consensus pattern (19 bp):
TTTTTTGCTTATTTTTTTC
Found at i:17858694 original size:20 final size:17
Alignment explanation
Indices: 17858651--17858700 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 17
17858641 AAGAAATAAT
17858651 AAAAGTAAATAAAATAAAC
1 AAAA-TAAA-AAAATAAAC
17858670 AAAATAAGAAAAATAGAATC
1 AAAATAA-AAAAATA-AA-C
17858690 AAAATAAAAAA
1 AAAATAAAAAA
17858701 CGGAATGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.32
19 11 0.39
20 8 0.29
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAATAAAAAAATAAAC
Found at i:17859296 original size:51 final size:51
Alignment explanation
Indices: 17859213--17859355 Score: 150
Period size: 51 Copynumber: 2.9 Consensus size: 51
17859203 GTTTGATTTC
* * * * *
17859213 CATTTTAATGAGAATTGATTTTGCAATCAAATCCCAAAAATCTCTCCCTAT
1 CATTTTAATGTGAATTGATTATGCAATTAAATCCTAAAAATCTCTCCATAT
* * * *
17859264 CATTTTAATGTGGATTGATTATGGAATTAAATCCTGACAATCTCTCCATAT
1 CATTTTAATGTGAATTGATTATGCAATTAAATCCTAAAAATCTCTCCATAT
* * *
17859315 CA----AATGTCAATTGATTCTGTAATTAAATCCTAAAAATCTCT
1 CATTTTAATGTGAATTGATTATGCAATTAAATCCTAAAAATCTCT
17859356 TAACCATGGT
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
47 33 0.43
51 44 0.57
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (51 bp):
CATTTTAATGTGAATTGATTATGCAATTAAATCCTAAAAATCTCTCCATAT
Found at i:17866643 original size:13 final size:13
Alignment explanation
Indices: 17866625--17866651 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17866615 TACTATGTTT
17866625 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
17866638 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
17866651 A
1 A
17866652 CTCAAATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:17867748 original size:44 final size:44
Alignment explanation
Indices: 17867666--17868147 Score: 294
Period size: 44 Copynumber: 11.1 Consensus size: 44
17867656 GATTATTGAT
* * * *
17867666 GAGCTTTATTTATTTTTC-AAAGTTGTTAAGCCTCTATTTAGAT
1 GAGCCTTATTTACTTTTCAAAAGTCGTTAAGCCTCTATTTAGAG
* * * * *
17867709 GAGCCTTAGTTACTTTTCAAAAGTGGTTAAGCTTTTATTTAAAG
1 GAGCCTTATTTACTTTTCAAAAGTCGTTAAGCCTCTATTTAGAG
* * ** *
17867753 GAGCCTTATTTATTTTTC-CAAGTCGTTAAGCCTCTACCTAGAA
1 GAGCCTTATTTACTTTTCAAAAGTCGTTAAGCCTCTATTTAGAG
* * * * *
17867796 GAGTCTTATGTACTTTTCAAAAGTCGTTGAGCCTTTGTTTAGAG
1 GAGCCTTATTTACTTTTCAAAAGTCGTTAAGCCTCTATTTAGAG
* * ** * * * *
17867840 GAGTCTTATTTACTTTTCAAAAATTATTAAGCTTTTATTTAAAA
1 GAGCCTTATTTACTTTTCAAAAGTCGTTAAGCCTCTATTTAGAG
* ** * *
17867884 GAGCTTTATTTTTTTTTCAAAAGTCATTGAGCCTCTATTTAGAG
1 GAGCCTTATTTACTTTTCAAAAGTCGTTAAGCCTCTATTTAGAG
* * * * *
17867928 GAGTCTTATTTACTTTTTC--AAGTCATTAATCCTTTATTTATAG
1 GAGCCTTATTTAC-TTTTCAAAAGTCGTTAAGCCTCTATTTAGAG
* * * ** * *
17867971 GAGCTTTATTTTA-TTTTCAAAAATTGTTAAGTTTTTGTTTAGAG
1 GAGCCTTA-TTTACTTTTCAAAAGTCGTTAAGCCTCTATTTAGAG
* * * * * * ** *
17868015 GAGCTTTATTTATTTTTC-AATGTTGTTGAGCCTATGCTTATAG
1 GAGCCTTATTTACTTTTCAAAAGTCGTTAAGCCTCTATTTAGAG
* * * * * ***
17868058 GAGCTTTATTTAC-TTTCTAAAGTCATTGAGACTCGGCTTAGAG
1 GAGCCTTATTTACTTTTCAAAAGTCGTTAAGCCTCTATTTAGAG
* * * * * *
17868101 GAGCTTTATTTTCTTTTCAAAAGCCATTGAGCCTCTATTTAAAG
1 GAGCCTTATTTACTTTTCAAAAGTCGTTAAGCCTCTATTTAGAG
17868145 GAG
1 GAG
17868148 TTTTATGTTA
Statistics
Matches: 340, Mismatches: 90, Indels: 17
0.76 0.20 0.04
Matches are distributed among these distances:
42 9 0.03
43 136 0.40
44 190 0.56
45 5 0.01
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (44 bp):
GAGCCTTATTTACTTTTCAAAAGTCGTTAAGCCTCTATTTAGAG
Found at i:17867817 original size:87 final size:87
Alignment explanation
Indices: 17867666--17868034 Score: 258
Period size: 87 Copynumber: 4.2 Consensus size: 87
17867656 GATTATTGAT
* * ** *
17867666 GAGCTTTATTTATTTTTCAAAGTTGTTAAGCCTCTATTTAGATGAGCCTTAGTTACTTTTCAAAA
1 GAGCCTTATTTATTTTTCAAAGTCGTTAAGCCTCTACCTAGAAGAGCCTTAGTTACTTTTCAAAA
* *
17867731 GTGGTTAAGCTTTTATTTAAAG
66 GTCGTTAAGCCTTTATTTAAAG
* *
17867753 GAGCCTTATTTATTTTTCCAAGTCGTTAAGCCTCTACCTAGAAGAGTCTTA-TGTACTTTTCAAA
1 GAGCCTTATTTATTTTTCAAAGTCGTTAAGCCTCTACCTAGAAGAGCCTTAGT-TACTTTTCAAA
* * *
17867817 AGTCGTTGAGCCTTTGTTTAGAG
65 AGTCGTTAAGCCTTTATTTAAAG
* * * ** * * ** * * * **
17867840 GAGTCTTATTTACTTTTCAAAAATTATTAAGCTTTTATTTAAAAGAGCTTTATTTTTTTTTCAAA
1 GAGCCTTATTTATTTTTC-AAAGTCGTTAAGCCTCTACCTAGAAGAGCCTTAGTTACTTTTCAAA
* * * *
17867905 AGTCATTGAGCCTCTATTTAGAG
65 AGTCGTTAAGCCTTTATTTAAAG
* * * * ** * * * *
17867928 GAGTCTTATTTACTTTTTC-AAGTCATTAATCCTTTATTTATAGGAGCTTTATTTTA-TTTTCAA
1 GAGCCTTATTTA-TTTTTCAAAGTCGTTAAGCCTCTACCTAGAAGAGCCTTA-GTTACTTTTCAA
* * ** * *
17867991 AAATTGTTAAGTTTTTGTTTAGAG
64 AAGTCGTTAAGCCTTTATTTAAAG
*
17868015 GAGCTTTATTTATTTTTCAA
1 GAGCCTTATTTATTTTTCAA
17868035 TGTTGTTGAG
Statistics
Matches: 228, Mismatches: 48, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
86 7 0.03
87 149 0.65
88 66 0.29
89 6 0.03
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.46
Consensus pattern (87 bp):
GAGCCTTATTTATTTTTCAAAGTCGTTAAGCCTCTACCTAGAAGAGCCTTAGTTACTTTTCAAAA
GTCGTTAAGCCTTTATTTAAAG
Found at i:17868087 original size:43 final size:43
Alignment explanation
Indices: 17868009--17868134 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
17867999 AAGTTTTTGT
* * ** *
17868009 TTAGAGGAGCTTTATTTA-TTTTTCAATGTTGTTGAGCCTATGC
1 TTAGAGGAGCTTTATTTACTTTCT-AAAGTCATTGAGCCTAGGC
* * *
17868052 TTATAGGAGCTTTATTTACTTTCTAAAGTCATTGAGACTCGGC
1 TTAGAGGAGCTTTATTTACTTTCTAAAGTCATTGAGCCTAGGC
* * *
17868095 TTAGAGGAGCTTTATTTTCTTTTCAAAAGCCATTGAGCCT
1 TTAGAGGAGCTTTATTTAC-TTTCTAAAGTCATTGAGCCT
17868135 CTATTTAAAG
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 47 0.69
44 21 0.31
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (43 bp):
TTAGAGGAGCTTTATTTACTTTCTAAAGTCATTGAGCCTAGGC
Found at i:17870330 original size:13 final size:12
Alignment explanation
Indices: 17870261--17870342 Score: 58
Period size: 13 Copynumber: 6.2 Consensus size: 12
17870251 GTTACTCAGT
*
17870261 AAAATAAAATAA
1 AAAATAAAATTA
* *
17870273 ATAAATAAAACTG
1 A-AAATAAAATTA
17870286 AAAATCAAAA-TA
1 AAAAT-AAAATTA
17870298 CAAAATAAATATGTAAA
1 -AAAATAAA-AT-T--A
17870315 AAAATAAAATTGA
1 AAAATAAAATT-A
17870328 AAAATAAAATTA
1 AAAATAAAATTA
17870340 AAA
1 AAA
17870343 TGAAAAAATG
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
12 13 0.23
13 31 0.54
14 1 0.02
15 3 0.05
16 8 0.14
17 1 0.02
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.21
Consensus pattern (12 bp):
AAAATAAAATTA
Found at i:17870350 original size:19 final size:20
Alignment explanation
Indices: 17870314--17870356 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
17870304 AAATATGTAA
17870314 AAAAATAAAATTGAAAAAT-
1 AAAAATAAAATTGAAAAATG
*
17870333 AAAATTAAAA-TGAAAAAATG
1 AAAAATAAAATTG-AAAAATG
17870353 AAAA
1 AAAA
17870357 CCTGCGATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 15 0.71
20 4 0.19
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (20 bp):
AAAAATAAAATTGAAAAATG
Found at i:17871156 original size:3 final size:3
Alignment explanation
Indices: 17871143--17871253 Score: 76
Period size: 3 Copynumber: 38.3 Consensus size: 3
17871133 GAAAATAGAA
* *
17871143 AAT AAT AAAT AAT AA- ATAT AAT -AT AAT -AT AAT AAT -AT AGT TAT
1 AAT AAT -AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
17871186 ACT -AT AAT AAT AAT AAT AAT AAT ATAC AGAT TAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT
*
17871231 AAT -AT AAT GAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
17871254 TGCTATACTA
Statistics
Matches: 84, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
2 14 0.17
3 63 0.75
4 7 0.08
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:17871159 original size:14 final size:14
Alignment explanation
Indices: 17871142--17871253 Score: 52
Period size: 14 Copynumber: 7.6 Consensus size: 14
17871132 AGAAAATAGA
17871142 AAATAATAAATAAT
1 AAATAATAAATAAT
17871156 AAAT-ATAATATAAT
1 AAATAATAA-ATAAT
* *
17871170 ATAATAATATAGTTAT
1 A-AATAATA-AATAAT
*
17871186 ACTATAAT-AATAAT
1 A-AATAATAAATAAT
*
17871200 -AATAATAATATACAG
1 AAATAATAA-ATA-AT
*
17871215 ATTATAATATAATAAT
1 A-AATAATA-AATAAT
*
17871231 AATATAAT-GATAAT
1 AA-ATAATAAATAAT
17871245 AATATAATA
1 AA-ATAATA
17871254 TGCTATACTA
Statistics
Matches: 74, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
12 5 0.07
13 5 0.07
14 30 0.41
15 4 0.05
16 19 0.26
17 10 0.14
18 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.36
Consensus pattern (14 bp):
AAATAATAAATAAT
Found at i:17871167 original size:5 final size:5
Alignment explanation
Indices: 17871147--17871276 Score: 76
Period size: 5 Copynumber: 25.8 Consensus size: 5
17871137 ATAGAAAATA
* *
17871147 ATAA- ATAAT A-AAT ATAAT ATAAT AT-A- ATAAT ATAGTT ATACT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT
*
17871194 AATAAT AATAAT A-ATAT ACAGATT ATAAT ATAAT AATAAT ATAAT GAT-A-
1 -ATAAT -ATAAT ATA-AT ATA-A-T ATAAT ATAAT -ATAAT ATAAT -ATAAT
** * *
17871243 ATAAT ATAAT ATGCT ATACT ATATT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
17871277 CATGGGTAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 25
0.75 0.07 0.18
Matches are distributed among these distances:
3 4 0.04
4 12 0.12
5 59 0.57
6 25 0.24
7 3 0.03
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:17871208 original size:31 final size:32
Alignment explanation
Indices: 17871157--17871238 Score: 116
Period size: 34 Copynumber: 2.6 Consensus size: 32
17871147 ATAAATAATA
17871157 AATATAAT-ATAATATAATAATAT-AG-TTAT
1 AATATAATAATAATATAATAATATAAGATTAT
*
17871186 ACTATAATAATAATAATAATAATATACAGATTAT
1 AATATAATAATAAT-ATAATAATATA-AGATTAT
17871220 AATATAATAATAATATAAT
1 AATATAATAATAATATAAT
17871239 GATAATAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
29 7 0.15
30 5 0.11
31 10 0.22
33 7 0.15
34 17 0.37
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (32 bp):
AATATAATAATAATATAATAATATAAGATTAT
Found at i:17871211 original size:25 final size:25
Alignment explanation
Indices: 17871143--17871253 Score: 113
Period size: 25 Copynumber: 4.4 Consensus size: 25
17871133 GAAAATAGAA
17871143 AATAATAAATAATAAATATAATATAAT
1 AATAAT-AATAAT-AATATAATATAAT
* *
17871170 -ATAATAAT-ATAGTTATACTATAAT
1 AATAATAATAATA-ATATAATATAAT
* *
17871194 AATAATAATAATAATATACAGATTAT
1 AATAATAATAATAATATA-ATATAAT
17871220 AAT-ATAATAATAATATAATGATAAT
1 AATAATAATAATAATATAAT-ATAAT
17871245 AAT-ATAATA
1 AATAATAATA
17871254 TGCTATACTA
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
23 1 0.01
24 13 0.18
25 42 0.59
26 15 0.21
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (25 bp):
AATAATAATAATAATATAATATAAT
Found at i:17871234 original size:11 final size:11
Alignment explanation
Indices: 17871143--17871245 Score: 85
Period size: 11 Copynumber: 9.6 Consensus size: 11
17871133 GAAAATAGAA
17871143 AATAATA-AAT
1 AATAATATAAT
17871153 AATAAATATAAT
1 AAT-AATATAAT
17871165 -ATAATATAAT
1 AATAATATAAT
17871175 AAT-ATAGT--T
1 AATAATA-TAAT
*
17871184 -ATACTATAAT
1 AATAATATAAT
17871194 AATAATAATAAT
1 AATAAT-ATAAT
*
17871206 AAT-ATACAGAT
1 AATAATATA-AT
*
17871217 TATAATATAAT
1 AATAATATAAT
17871228 AATAATATAAT
1 AATAATATAAT
*
17871239 GATAATA
1 AATAATA
17871246 ATATAATATG
Statistics
Matches: 75, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
8 3 0.04
9 3 0.04
10 17 0.23
11 37 0.49
12 15 0.20
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (11 bp):
AATAATATAAT
Found at i:17871270 original size:10 final size:10
Alignment explanation
Indices: 17871157--17871275 Score: 51
Period size: 11 Copynumber: 12.6 Consensus size: 10
17871147 ATAAATAATA
*
17871157 AATATAATAT
1 AATATATTAT
17871167 AATATA--AT
1 AATATATTAT
17871175 AATATAGTTAT
1 AATATA-TTAT
*
17871186 ACTATA--AT
1 AATATATTAT
*
17871194 AATA-ATAAT
1 AATATATTAT
17871203 AATA-A-TAT
1 AATATATTAT
* *
17871211 -ACAGATTAT
1 AATATATTAT
*
17871220 AATATAATAAT
1 AATAT-ATTAT
*
17871231 AATATAATGAT
1 AATAT-ATTAT
17871242 AATA-A-TAT
1 AATATATTAT
**
17871250 AATATGCTAT
1 AATATATTAT
*
17871260 ACTATATTAT
1 AATATATTAT
17871270 AATATA
1 AATATA
17871276 ACATGGGTAA
Statistics
Matches: 84, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
7 3 0.04
8 22 0.26
9 11 0.13
10 23 0.27
11 25 0.30
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (10 bp):
AATATATTAT
Found at i:17878483 original size:16 final size:16
Alignment explanation
Indices: 17878462--17878494 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17878452 GCTTGTTAGC
17878462 ATCAAGTATGCTATGA
1 ATCAAGTATGCTATGA
17878478 ATCAAGTATGCTATGA
1 ATCAAGTATGCTATGA
17878494 A
1 A
17878495 ACGATAAGTT
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:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (16 bp):
ATCAAGTATGCTATGA
Found at i:17879334 original size:19 final size:19
Alignment explanation
Indices: 17879310--17879350 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
17879300 TGAAGCAAGA
*
17879310 CATAGACATGTTTAGCTAG
1 CATAGACATGTTTAACTAG
17879329 CATAGACATGTTTAACTAG
1 CATAGACATGTTTAACTAG
17879348 CAT
1 CAT
17879351 GGCCAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (19 bp):
CATAGACATGTTTAACTAG
Found at i:17885360 original size:35 final size:35
Alignment explanation
Indices: 17885314--17885383 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
17885304 TGTATATGTC
* * *
17885314 AAGTCAATTGTAGGTTTATGCCCAGAAAACGTTTA
1 AAGTCAATTGTAGATTTATGCCCACAAAACATTTA
*
17885349 AAGTCAATTGTATATTTATGCCCACAAAACATTTA
1 AAGTCAATTGTAGATTTATGCCCACAAAACATTTA
17885384 GTTTATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (35 bp):
AAGTCAATTGTAGATTTATGCCCACAAAACATTTA
Found at i:17886240 original size:186 final size:186
Alignment explanation
Indices: 17885709--17886501 Score: 897
Period size: 186 Copynumber: 4.4 Consensus size: 186
17885699 TCTAACCTCA
* * **
17885709 GAAAACTCCTTTAATAGTCCTGTAAATTTTAAAAGGGAATTATTGAAGGCGTTTGTTCTCAAAAA
1 GAAAACGCCTTTAATAATCCCATAAATTTTAAAAGGGAATTATTGAAGGCGTTTGTTCTCAAAAA
* * * * * *
17885774 ATGCCTTCAATCATTATGTACGTAAATTAGAGGAAATTAGTGAAGGCGTTTCTCTAGAATAAACG
66 ATGCCTTCAATTATTATGTACATAAATTAGAAGAAATTAGTGAAAGTGTTTTTCTAGAATAAACG
* * * *
17885839 CCTTCACTAACCATCTTAAAATTAGAGTTGTCG-AAAATTAAAGGCTTTTTTCATTA
131 CCTTCATTAACCGTCTTAAAATTAGAGTTGT-GAAAAATTAAAGGCATTTTTCATTG
* * * * * *
17885895 GAAGATGTCTTTAATAATCCCAAAAATTTTAAGAGGGAATTATTGAAGGCGTTTGTTCTAAAAAA
1 GAAAACGCCTTTAATAATCCCATAAATTTTAAAAGGGAATTATTGAAGGCGTTTGTTCT-CAAAA
* * * * *
17885960 AATGCCTTCAATTATTATGAACATAAATTGGAAGGAATTAGTGAAGGTATTTTTCTAGAATAAAC
65 AATGCCTTCAATTATTATGTACATAAATTAGAAGAAATTAGTGAAAGTGTTTTTCTAGAATAAAC
* * * *
17886025 GTCTTTATTAACTGCCTTAAAATTAGAGTTGTGAAAAATTAAAGGCATTTTTCATTG
130 GCCTTCATTAACCGTCTTAAAATTAGAGTTGTGAAAAATTAAAGGCATTTTTCATTG
* ** * * *
17886082 GAAAACGCTTTTAATAATCCCATAAATTTTAAAAGAAAATTTTTGAAGGTGTTTATTCTCAAAAA
1 GAAAACGCCTTTAATAATCCCATAAATTTTAAAAGGGAATTATTGAAGGCGTTTGTTCTCAAAAA
* * * *
17886147 ATGCCTTCAATTATTATGTACATAAATTAGAGGGAATTAGTGAAAGTGTTTTTCTAAAATAAATG
66 ATGCCTTCAATTATTATGTACATAAATTAGAAGAAATTAGTGAAAGTGTTTTTCTAGAATAAACG
*
17886212 CCTTCATTAACCGTCTTAAAATTAGAGTTGTCAAAAATTAAAGGCATTTTTCATT-
131 CCTTCATTAACCGTCTTAAAATTAGAGTTGTGAAAAATTAAAGGCATTTTTCATTG
** * * *
17886267 GAAATACGCCTTTAATAATCTTAAAAAATTTAAGAGGGAATTATTGAAGGCGTTTGTTCTCAAAA
1 GAAA-ACGCCTTTAATAATCCCATAAATTTTAAAAGGGAATTATTGAAGGCGTTTGTTCTCAAAA
* **
17886332 AATGCCTTCAATTATTATGTACGTAAATTAGAAGAAATTAGTG-AAG-GCATTT-T----T----
65 AATGCCTTCAATTATTATGTACATAAATTAGAAGAAATTAGTGAAAGTGTTTTTCTAGAATAAAC
* * *
17886386 --C-TAATT----GTCTTAAAATTAGAGTTGTGAAAAATTGAAGGCATTTTTCATCG
130 GCCTTCATTAACCGTCTTAAAATTAGAGTTGTGAAAAATTAAAGGCATTTTTCATTG
* * * ** * *
17886436 GAAGATGCCTTTAATAATCCCGTAAATTTTAAAAGAAAATTATTGAAGGTGTTTGTTCTAAAAAA
1 GAAAACGCCTTTAATAATCCCATAAATTTTAAAAGGGAATTATTGAAGGCGTTTGTTCTCAAAAA
17886501 A
66 A
17886502 CACCTTCACT
Statistics
Matches: 520, Mismatches: 83, Indels: 26
0.83 0.13 0.04
Matches are distributed among these distances:
168 91 0.17
169 3 0.01
172 4 0.01
173 1 0.00
179 1 0.00
183 1 0.00
184 4 0.01
185 7 0.01
186 253 0.49
187 155 0.30
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (186 bp):
GAAAACGCCTTTAATAATCCCATAAATTTTAAAAGGGAATTATTGAAGGCGTTTGTTCTCAAAAA
ATGCCTTCAATTATTATGTACATAAATTAGAAGAAATTAGTGAAAGTGTTTTTCTAGAATAAACG
CCTTCATTAACCGTCTTAAAATTAGAGTTGTGAAAAATTAAAGGCATTTTTCATTG
Found at i:17890895 original size:28 final size:28
Alignment explanation
Indices: 17890863--17890922 Score: 113
Period size: 27 Copynumber: 2.2 Consensus size: 28
17890853 GTATGGATTT
17890863 ACACTTGTAAATTTTTCTTGATTAATTC
1 ACACTTGTAAATTTTTCTTGATTAATTC
17890891 ACAC-TGTAAATTTTTCTTGATTAATTC
1 ACACTTGTAAATTTTTCTTGATTAATTC
17890918 ACACT
1 ACACT
17890923 ACACAACAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.47
Consensus pattern (28 bp):
ACACTTGTAAATTTTTCTTGATTAATTC
Found at i:17894540 original size:1 final size:1
Alignment explanation
Indices: 17894496--17894528 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
17894486 CGCTAAACGT
17894496 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17894529 CACTACTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17894862 original size:19 final size:20
Alignment explanation
Indices: 17894813--17894862 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
17894803 AATTTAATCA
*
17894813 TCACT-ATAAAATATTATTG
1 TCACTAATAAAATAATATTG
*
17894832 TGAC-AA-AAAATAAT-TTG
1 TCACTAATAAAATAATATTG
17894849 TCACTAATAAAATA
1 TCACTAATAAAATA
17894863 CACAAATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
17 6 0.24
18 9 0.36
19 10 0.40
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (20 bp):
TCACTAATAAAATAATATTG
Found at i:17897820 original size:20 final size:20
Alignment explanation
Indices: 17897795--17897837 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
17897785 AATAATTATG
17897795 TAAAATATTTATATAATTTA
1 TAAAATATTTATATAATTTA
17897815 TAAAATATTTATATAATTTA
1 TAAAATATTTATATAATTTA
17897835 TAA
1 TAA
17897838 TATTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATATTTATATAATTTA
Found at i:17897839 original size:18 final size:19
Alignment explanation
Indices: 17897797--17897842 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
17897787 TAATTATGTA
17897797 AAATATTTATATAATTTAT
1 AAATATTTATATAATTTAT
17897816 AAAATATTTATATAATTTAT
1 -AAATATTTATATAATTTAT
17897836 -AATATTT
1 AAATATTT
17897843 TAAAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 7 0.27
20 19 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATATTTATATAATTTAT
Found at i:17900922 original size:16 final size:18
Alignment explanation
Indices: 17900893--17900929 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
17900883 CGTATTTATG
*
17900893 TTTATATATATTTTTAGA
1 TTTATATATATTTTTAAA
17900911 TTTAT-TAT-TTTTTAAA
1 TTTATATATATTTTTAAA
17900927 TTT
1 TTT
17900930 TGTCACTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTATATATATTTTTAAA
Found at i:17903186 original size:24 final size:23
Alignment explanation
Indices: 17903154--17903201 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
17903144 CACTATTTGA
*
17903154 ATTAAAATTAAAGTAAAAATAAAT
1 ATTAAAATT-AACTAAAAATAAAT
* *
17903178 ATTATAATTGACTAAAAATAAAT
1 ATTAAAATTAACTAAAAATAAAT
17903201 A
1 A
17903202 AATACTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (23 bp):
ATTAAAATTAACTAAAAATAAAT
Found at i:17903439 original size:34 final size:35
Alignment explanation
Indices: 17903401--17903467 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
17903391 GGCATTTACA
* * * *
17903401 TTTTTAATCTTTTTGAAATTGCATATTC-AAAATG
1 TTTTTAACCTTTTCGAAAATACATATTCTAAAATG
17903435 TTTTTAACCTTTTCGAAAATACATATTCTAAAA
1 TTTTTAACCTTTTCGAAAATACATATTCTAAAA
17903468 GGCTAAAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (35 bp):
TTTTTAACCTTTTCGAAAATACATATTCTAAAATG
Found at i:17903661 original size:12 final size:12
Alignment explanation
Indices: 17903644--17903670 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17903634 AAGTATCGAA
17903644 AAATACATATCC
1 AAATACATATCC
17903656 AAATACATATCC
1 AAATACATATCC
17903668 AAA
1 AAA
17903671 ATGTGTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (12 bp):
AAATACATATCC
Found at i:17905196 original size:24 final size:24
Alignment explanation
Indices: 17905169--17905227 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
17905159 CAAAAATTTT
*
17905169 ATGCAATAAATATAAAATCACACC
1 ATGCAATAAATAGAAAATCACACC
*
17905193 ATGCAATAAATAGAAAATCATACC
1 ATGCAATAAATAGAAAATCACACC
* *
17905217 CTGTAATAAAT
1 ATGCAATAAAT
17905228 TATGCAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.53, C:0.17, G:0.07, T:0.24
Consensus pattern (24 bp):
ATGCAATAAATAGAAAATCACACC
Found at i:17905300 original size:13 final size:14
Alignment explanation
Indices: 17905275--17905304 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
17905265 GGATTACACC
17905275 AAAATATCAATGCA
1 AAAATATCAATGCA
17905289 AAAATATC-ATGCA
1 AAAATATCAATGCA
17905302 AAA
1 AAA
17905305 TATTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (14 bp):
AAAATATCAATGCA
Found at i:17905306 original size:12 final size:13
Alignment explanation
Indices: 17905274--17905307 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
17905264 AGGATTACAC
17905274 CAAAATATCAATG
1 CAAAATATCAATG
17905287 CAAAAATATC-ATG
1 C-AAAATATCAATG
17905300 CAAAATAT
1 CAAAATAT
17905308 TAATTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 5 0.25
14 8 0.40
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (13 bp):
CAAAATATCAATG
Found at i:17905357 original size:20 final size:20
Alignment explanation
Indices: 17905294--17905383 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
17905284 ATGCAAAAAT
17905294 ATCATGCAAA-ATATTAATT-
1 ATCATGCAAATATATT-ATTA
*
17905313 ATTATGCAAATA-A--ATTA
1 ATCATGCAAATATATTATTA
* *
17905330 ACCATGCAAATATATTATTC
1 ATCATGCAAATATATTATTA
17905350 ATCATGCAAATATATTATTA
1 ATCATGCAAATATATTATTA
17905370 ATCATGCAAATATA
1 ATCATGCAAATATA
17905384 AATCACACAT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
16 3 0.05
17 10 0.17
18 1 0.02
19 10 0.17
20 36 0.60
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.36
Consensus pattern (20 bp):
ATCATGCAAATATATTATTA
Found at i:17905606 original size:18 final size:18
Alignment explanation
Indices: 17905563--17905609 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
17905553 CAATTAAATT
17905563 ATAAAAAATAAAAAATAAA
1 ATAAAAAAT-AAAAATAAA
**
17905582 ACCAAAAATAAAAATAAA
1 ATAAAAAATAAAAATAAA
17905600 ATAAAAAATA
1 ATAAAAAATA
17905610 GAAACGTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (18 bp):
ATAAAAAATAAAAATAAA
Found at i:17905621 original size:30 final size:30
Alignment explanation
Indices: 17905567--17905630 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
17905557 TAAATTATAA
*
17905567 AAAATAAAAAATAAAACCAAAAATAAAAAT
1 AAAATAAAAAATAAAACCAAAAATAAAAAG
**
17905597 AAAATAAAAAATAGAAA-CGTAAATAAAAAG
1 AAAATAAAAAATA-AAACCAAAAATAAAAAG
17905627 AAAA
1 AAAA
17905631 AGAAATACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (30 bp):
AAAATAAAAAATAAAACCAAAAATAAAAAG
Found at i:17907387 original size:77 final size:77
Alignment explanation
Indices: 17907269--17907424 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 77
17907259 GCTTTCACAT
17907269 GTTAGTTTAAGTTTATCCAAACTTCAACCTATGAGATTGGTTACTTACTTCATAAGTAAAAGTAT
1 GTTAGTTTAAGTTTATCCAAACTTCAACCTATGAGATTGGTTACTTACTTCATAAGTAAAAGTAT
*
17907334 AACCATGTGCTA
66 AACCATATGCTA
17907346 GTTAGTTTAAGTTTATCCAAACTTCAACCTATGAGATTGGTTACTTACTTCATAAGTAAAAGTAT
1 GTTAGTTTAAGTTTATCCAAACTTCAACCTATGAGATTGGTTACTTACTTCATAAGTAAAAGTAT
17907411 AACCATATGCTA
66 AACCATATGCTA
17907423 GT
1 GT
17907425 CTCAATGGTT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (77 bp):
GTTAGTTTAAGTTTATCCAAACTTCAACCTATGAGATTGGTTACTTACTTCATAAGTAAAAGTAT
AACCATATGCTA
Found at i:17907815 original size:39 final size:38
Alignment explanation
Indices: 17907771--17907862 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 38
17907761 AGTTTGCTTG
* *
17907771 AAAATTCAACA-CAAATCCAGAAAAA-CCTAGATAATCCC
1 AAAATTCAA-ATCAAACCCAGAAAAATCCTAG-CAATCCC
17907809 ATAAATTCAAATTCAAACCCAGAAAAATCCTAGCAATCCC
1 A-AAATTCAAA-TCAAACCCAGAAAAATCCTAGCAATCCC
*
17907849 AAAACTCAAATCAA
1 AAAATTCAAATCAA
17907863 CCTTAGAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
38 6 0.13
39 16 0.34
40 20 0.43
41 5 0.11
ACGTcount: A:0.52, C:0.26, G:0.04, T:0.17
Consensus pattern (38 bp):
AAAATTCAAATCAAACCCAGAAAAATCCTAGCAATCCC
Found at i:17908405 original size:20 final size:19
Alignment explanation
Indices: 17908352--17908405 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
17908342 TTTTTCTTTT
* **
17908352 TTTTTTTTTGGTTTTTTGA
1 TTTTTTTTTGCTTTTTAAA
**
17908371 TTTTTTTTTATTTTTTAAA
1 TTTTTTTTTGCTTTTTAAA
17908390 CTTTTTTTTTGCTTTT
1 -TTTTTTTTTGCTTTT
17908406 GACAAAATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.09, C:0.04, G:0.07, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTGCTTTTTAAA
Found at i:17908852 original size:76 final size:77
Alignment explanation
Indices: 17908720--17909006 Score: 237
Period size: 76 Copynumber: 3.7 Consensus size: 77
17908710 GTTTGAGAAA
* * *
17908720 TTTGAAAAACAAAATACTCATCCATTAAGGCTTTAACTTTTGAAAAATAAAGTACTCTGCCATCG
1 TTTGAAAAACAAAATACTCATCCATCAAGGCTTCAACTTTTGAAAAATAAAGTACTCTGCCACCG
*
17908785 AGGCTTTGA-TT
66 AGACTTTGATTT
* * * * * *
17908796 TTTGAAAAACAAAATACTCCTCTATCGAGGCTTCGACTTTTGAAAAATAGAA-TACTCTTCTACC
1 TTTGAAAAACAAAATACTCATCCATCAAGGCTTCAACTTTTGAAAAATA-AAGTACTCTGCCACC
17908860 GAGACTTTGATTT
65 GAGACTTTGATTT
* * ** * * * * *
17908873 TTTGAAACATAAAATACTTTTCCACCAAGGC-TCTAATTTTTAAAAAAATAAAGTAGTCTTCCAC
1 TTTGAAAAACAAAATACTCATCCATCAAGGCTTC-AACTTTT-GAAAAATAAAGTACTCTGCCAC
* * **
17908937 CAAGGCTTT-AACT
64 CGAGACTTTGATTT
* * *
17908950 TTCGAAAAA-ATAAAGTACT-ACTCCACCAAGACTTCAAC-TTTGAAAAATAAAGTACTC
1 TTTGAAAAACA-AAA-TACTCA-TCCATCAAGGCTTCAACTTTTGAAAAATAAAGTACTC
17909007 CTCCAATGAA
Statistics
Matches: 169, Mismatches: 33, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
76 78 0.46
77 50 0.30
78 39 0.23
79 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.31
Consensus pattern (77 bp):
TTTGAAAAACAAAATACTCATCCATCAAGGCTTCAACTTTTGAAAAATAAAGTACTCTGCCACCG
AGACTTTGATTT
Found at i:17908889 original size:39 final size:38
Alignment explanation
Indices: 17908720--17908890 Score: 171
Period size: 38 Copynumber: 4.5 Consensus size: 38
17908710 GTTTGAGAAA
* * * ** * *
17908720 TTTGAAAAACAAAATACTCATCCATTAAGGCTTTAACT
1 TTTGAAAAATAAAATACTCTTCTATCGAGGCTTTGATT
* * *
17908758 TTTGAAAAATAAAGTACTCTGCCATCGAGGCTTTGATT
1 TTTGAAAAATAAAATACTCTTCTATCGAGGCTTTGATT
* * * *
17908796 TTTGAAAAACAAAATACTCCTCTATCGAGGCTTCGACT
1 TTTGAAAAATAAAATACTCTTCTATCGAGGCTTTGATT
* * *
17908834 TTTGAAAAATAGAATACTCTTCTACCGAGACTTTGATTT
1 TTTGAAAAATAAAATACTCTTCTATCGAGGCTTTGA-TT
*
17908873 TTTGAAACATAAAATACT
1 TTTGAAAAATAAAATACT
17908891 TTTCCACCAA
Statistics
Matches: 108, Mismatches: 24, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
38 91 0.84
39 17 0.16
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (38 bp):
TTTGAAAAATAAAATACTCTTCTATCGAGGCTTTGATT
Found at i:17908912 original size:39 final size:39
Alignment explanation
Indices: 17908720--17908979 Score: 136
Period size: 38 Copynumber: 6.7 Consensus size: 39
17908710 GTTTGAGAAA
* * ** * *
17908720 TTTGAAAAACAAAATACTCATCCATTAAGGCTTTAA-CT
1 TTTGAAAAATAAAATACTCTTCCACCAAGGCTCTAATTT
* * * * * *
17908758 TTTGAAAAATAAAGTACTCTGCCATCGAGGCTTTGA-TT
1 TTTGAAAAATAAAATACTCTTCCACCAAGGCTCTAATTT
* * * * * * *
17908796 TTTGAAAAACAAAATACTCCTCTATCGAGGCT-TCGA-CT
1 TTTGAAAAATAAAATACTCTTCCACCAAGGCTCT-AATTT
* * * * * *
17908834 TTTGAAAAATAGAATACTCTTCTACCGAGACTTTGATTT
1 TTTGAAAAATAAAATACTCTTCCACCAAGGCTCTAATTT
* *
17908873 TTTGAAACATAAAATACTTTTCCACCAAGGCTCTAATTT
1 TTTGAAAAATAAAATACTCTTCCACCAAGGCTCTAATTT
** * * * *
17908912 TTAAAAAAATAAAGTAGTCTTCCACCAAGGCTTTAA-CT
1 TTTGAAAAATAAAATACTCTTCCACCAAGGCTCTAATTT
* *
17908950 TTCGAAAAAATAAAGTACTAC-TCCACCAAG
1 TTTG-AAAAATAAAATACT-CTTCCACCAAG
17908980 ACTTCAACTT
Statistics
Matches: 178, Mismatches: 39, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
37 1 0.01
38 92 0.52
39 84 0.47
40 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.32
Consensus pattern (39 bp):
TTTGAAAAATAAAATACTCTTCCACCAAGGCTCTAATTT
Found at i:17908989 original size:39 final size:37
Alignment explanation
Indices: 17908915--17909028 Score: 124
Period size: 39 Copynumber: 3.0 Consensus size: 37
17908905 CTAATTTTTA
* * *
17908915 AAAAAATAAAGTAGTCTTCCACCAAGGCTTTAACTTTCG
1 AAAAAATAAAGTACTC-TCCACCAAGACTTCAACTTT-G
17908954 AAAAAATAAAGTACTACTCCACCAAGACTTCAACTTTG
1 AAAAAATAAAGTACT-CTCCACCAAGACTTCAACTTTG
**
17908992 -AAAAATAAAGTACTCCTCCAATGAA-ACTTCAACTTTG
1 AAAAAATAAAGTACT-CTCC-ACCAAGACTTCAACTTTG
17909029 GAAGATAAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
37 30 0.45
38 4 0.06
39 32 0.48
40 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (37 bp):
AAAAAATAAAGTACTCTCCACCAAGACTTCAACTTTG
Found at i:17909005 original size:37 final size:36
Alignment explanation
Indices: 17908916--17909038 Score: 122
Period size: 37 Copynumber: 3.3 Consensus size: 36
17908906 TAATTTTTAA
* * *
17908916 AAAAATAAAGTAGTCTTCCACCAAGGCTTTAACTTTCG
1 AAAAATAAAGTACTC-TCCACCAAGACTTCAACTTT-G
17908954 AAAAAATAAAGTACTACTCCACCAAGACTTCAACTTTG
1 -AAAAATAAAGTACT-CTCCACCAAGACTTCAACTTTG
**
17908992 AAAAATAAAGTACTCCTCCAATGAA-ACTTCAACTTTG
1 AAAAATAAAGTACT-CTCC-ACCAAGACTTCAACTTTG
* *
17909029 GAAGATAAAG
1 AAAAATAAAG
17909039 ACTTATATGA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
37 38 0.51
38 4 0.05
39 31 0.42
40 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.25
Consensus pattern (36 bp):
AAAAATAAAGTACTCTCCACCAAGACTTCAACTTTG
Found at i:17915846 original size:16 final size:16
Alignment explanation
Indices: 17915825--17915855 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17915815 TCCTATCTTT
17915825 TGTATGAATGAATGCA
1 TGTATGAATGAATGCA
*
17915841 TGTATGCATGAATGC
1 TGTATGAATGAATGC
17915856 CCCAAAAAGA
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:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (16 bp):
TGTATGAATGAATGCA
Found at i:17915950 original size:39 final size:40
Alignment explanation
Indices: 17915902--17915979 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
17915892 ATAGTAAAAG
* * *
17915902 AAAATGGTTAGTA-AACATAATATGTACAAGGAACAATAT
1 AAAAGGGTTAGTAGAACATAATATATACAACGAACAATAT
*
17915941 AAAAGGGTTAGTATGCACATAATATATACAACGAACAAT
1 AAAAGGGTTAGTA-GAACATAATATATACAACGAACAAT
17915980 TTATAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 12 0.36
41 21 0.64
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.24
Consensus pattern (40 bp):
AAAAGGGTTAGTAGAACATAATATATACAACGAACAATAT
Found at i:17917026 original size:32 final size:32
Alignment explanation
Indices: 17916984--17917076 Score: 123
Period size: 32 Copynumber: 2.8 Consensus size: 32
17916974 TCATGTAATA
* *
17916984 AATATAAAATCATACCATGCAATAAATCATGC
1 AATATGAAATCATACCATGCAATAAATCATAC
*
17917016 AATATGAAATCATACCATGCAATGAATCATAC
1 AATATGAAATCATACCATGCAATAAATCATAC
17917048 AATAAGTAGAAAATCATACCATGCAATAA
1 AAT-A-T-G-AAATCATACCATGCAATAA
17917077 TATATCATGC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
32 32 0.60
33 1 0.02
34 1 0.02
35 1 0.02
36 18 0.34
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.24
Consensus pattern (32 bp):
AATATGAAATCATACCATGCAATAAATCATAC
Found at i:17917036 original size:68 final size:68
Alignment explanation
Indices: 17916948--17917076 Score: 177
Period size: 68 Copynumber: 1.9 Consensus size: 68
17916938 TCATGCAATA
* ** *
17916948 AATATAAAAACATACTATGCAACAAATCATGTAATAAATATAAAATCATACCATGCAATAAATCA
1 AATATAAAAACATACCATGCAACAAATCATACAATAAATAGAAAATCATACCATGCAATAAATCA
17917013 TGC
66 TGC
* * ** *
17917016 AATATGAAATCATACCATGCAATGAATCATACAATAAGTAGAAAATCATACCATGCAATAA
1 AATATAAAAACATACCATGCAACAAATCATACAATAAATAGAAAATCATACCATGCAATAA
17917077 TATATCATGC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 52 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (68 bp):
AATATAAAAACATACCATGCAACAAATCATACAATAAATAGAAAATCATACCATGCAATAAATCA
TGC
Found at i:17917074 original size:36 final size:36
Alignment explanation
Indices: 17916937--17917076 Score: 171
Period size: 36 Copynumber: 4.0 Consensus size: 36
17916927 AATCAGAAAT
* * * *
17916937 ATCATGCAATAAATATAAAAACATACTATGCAACAA
1 ATCATGCAATAAATAGAAAATCATACCATGCAATAA
* *
17916973 ATCATGTAATAAATATAAAATCATACCATGCAATAA
1 ATCATGCAATAAATAGAAAATCATACCATGCAATAA
*
17917009 ATCATGCAAT--AT-G-AAATCATACCATGCAATGA
1 ATCATGCAATAAATAGAAAATCATACCATGCAATAA
* *
17917041 ATCATACAATAAGTAGAAAATCATACCATGCAATAA
1 ATCATGCAATAAATAGAAAATCATACCATGCAATAA
17917077 TATATCATGC
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
32 27 0.30
34 3 0.03
35 1 0.01
36 59 0.66
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.24
Consensus pattern (36 bp):
ATCATGCAATAAATAGAAAATCATACCATGCAATAA
Found at i:17917188 original size:19 final size:19
Alignment explanation
Indices: 17917161--17917241 Score: 63
Period size: 20 Copynumber: 4.2 Consensus size: 19
17917151 TATAATGCAA
*
17917161 ATAGATTAACCATGCAAAT
1 ATAGATTAACCATACAAAT
* *
17917180 ATAGGTTAATCATACAAAT
1 ATAGATTAACCATACAAAT
* * * *
17917199 ATATTACTAATCATGCAAAT
1 ATA-GATTAACCATACAAAT
* *
17917219 ATATTATTAATCATACAAAT
1 ATA-GATTAACCATACAAAT
17917239 ATA
1 ATA
17917242 AATAATACAA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
19 19 0.37
20 33 0.63
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (19 bp):
ATAGATTAACCATACAAAT
Found at i:17917211 original size:20 final size:20
Alignment explanation
Indices: 17917186--17917241 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
17917176 AAATATAGGT
17917186 TAATCATACAAATATATTAC
1 TAATCATACAAATATATTAC
* *
17917206 TAATCATGCAAATATATTAT
1 TAATCATACAAATATATTAC
17917226 TAATCATACAAATATA
1 TAATCATACAAATATA
17917242 AATAATACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (20 bp):
TAATCATACAAATATATTAC
Found at i:17917308 original size:20 final size:20
Alignment explanation
Indices: 17917283--17917320 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17917273 TAAATTATAA
17917283 ATATTAATAATCATGCAATT
1 ATATTAATAATCATGCAATT
*
17917303 ATATTAGTAATCATGCAA
1 ATATTAATAATCATGCAA
17917321 ATAATAATAT
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:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (20 bp):
ATATTAATAATCATGCAATT
Found at i:17917400 original size:47 final size:43
Alignment explanation
Indices: 17917310--17917400 Score: 103
Period size: 43 Copynumber: 2.0 Consensus size: 43
17917300 ATTATATTAG
* * *
17917310 TAATCATGCAAATAATAATATATCATGTGAATAAATATATTTA
1 TAATCATGCAAATAATAATATATAATATGAATAAATAAATTTA
17917353 TAATCATGCAAATAATAA-ATAATAAATATGCAAGTAAACTAAATTTA
1 TAATCATGCAAATAATAATAT-AT-AATATG-AA-TAAA-TAAATTTA
17917400 T
1 T
17917401 GCAAATAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
42 2 0.05
43 20 0.50
44 4 0.10
45 2 0.05
46 4 0.10
47 8 0.20
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.34
Consensus pattern (43 bp):
TAATCATGCAAATAATAATATATAATATGAATAAATAAATTTA
Found at i:17917475 original size:18 final size:18
Alignment explanation
Indices: 17917442--17917476 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17917432 TCATCAAAAT
**
17917442 TAAATAACAACTAAATAA
1 TAAATAACAAAAAAATAA
17917460 TAAATAACAAAAAAATA
1 TAAATAACAAAAAAATA
17917477 GAAAATCATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (18 bp):
TAAATAACAAAAAAATAA
Found at i:17917482 original size:18 final size:17
Alignment explanation
Indices: 17917443--17917499 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
17917433 CATCAAAATT
**
17917443 AAATAACAACTAAATAA
1 AAATAACAAAAAAATAA
17917460 TAAATAACAAAAAAATAGA
1 -AAATAACAAAAAAATA-A
* *
17917479 AAATCATAAATAAAATAA
1 AAATAACAAA-AAAATAA
17917497 AAA
1 AAA
17917500 ATCATAAACG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 26 0.79
19 7 0.21
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.18
Consensus pattern (17 bp):
AAATAACAAAAAAATAA
Found at i:17917515 original size:20 final size:19
Alignment explanation
Indices: 17917471--17917519 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
17917461 AAATAACAAA
* *
17917471 AAAATAGAAAATCATAAAT
1 AAAATAAAAAATCATAAAG
17917490 AAAATAAAAAATCATAAACG
1 AAAATAAAAAATCATAAA-G
17917510 AAAATAAAAA
1 AAAATAAAAA
17917520 GAAAAAGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.16
Consensus pattern (19 bp):
AAAATAAAAAATCATAAAG
Found at i:17918441 original size:11 final size:11
Alignment explanation
Indices: 17918425--17918450 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17918415 CAAAATCTCA
17918425 TTTTTTTTGTT
1 TTTTTTTTGTT
17918436 TTTTTTTTGTT
1 TTTTTTTTGTT
17918447 TTTT
1 TTTT
17918451 GACTTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:17918457 original size:16 final size:17
Alignment explanation
Indices: 17918438--17918479 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
17918428 TTTTTGTTTT
17918438 TTTTTTGTTTTTTG-AC
1 TTTTTTGTTTTTTGAAC
*
17918454 TTTTTT-ATTTTTGAAC
1 TTTTTTGTTTTTTGAAC
17918470 TTTTTTGTTT
1 TTTTTTGTTT
17918480 ACTTTTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 6 0.27
16 14 0.64
17 2 0.09
ACGTcount: A:0.10, C:0.05, G:0.10, T:0.76
Consensus pattern (17 bp):
TTTTTTGTTTTTTGAAC
Found at i:17918556 original size:9 final size:9
Alignment explanation
Indices: 17918537--17918570 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
17918527 ATCCAAATCT
17918537 AAATT-AAA
1 AAATTAAAA
17918545 AAATTAAAA
1 AAATTAAAA
17918554 AAATTAAAA
1 AAATTAAAA
17918563 AAATTAAA
1 AAATTAAA
17918571 GTTAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.20
9 20 0.80
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATTAAAA
Found at i:17919639 original size:21 final size:20
Alignment explanation
Indices: 17919615--17919658 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
17919605 CAGTTTATTC
17919615 AATTTG-GTTATTGTATTAGTT
1 AATTTGTGTT-TTGT-TTAGTT
17919636 AATTTGTTGTTTTGTTTAGTT
1 AATTTG-TGTTTTGTTTAGTT
17919657 AA
1 AA
17919659 ATAATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 14 0.67
22 4 0.19
23 3 0.14
ACGTcount: A:0.23, C:0.00, G:0.18, T:0.59
Consensus pattern (20 bp):
AATTTGTGTTTTGTTTAGTT
Done.