Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, 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: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 68 of 74
Found at i:13451186 original size:88 final size:88
Alignment explanation
Indices: 13451080--13451265 Score: 241
Period size: 88 Copynumber: 2.1 Consensus size: 88
13451070 TATATTTTAT
* *
13451080 TTGCTTGATTATATATTTAATTACATGT-TTATTTGCATGATTATTAATATTATTATTTGCATGA
1 TTGCATGATTATATATTTAATTACATGTGTGA-TTGCATGATTATTAATATTATTATTTGCATGA
13451144 TTATATATTTAATCGCATGTCTAA
65 TTATATATTTAATCGCATGTCTAA
* * ** * *
13451168 TTGTATGATTAT-TAATTTATTTATTTGTGTGATTGTATGATTATTAATATTTTTATTTGCATGA
1 TTGCATGATTATAT-ATTTAATTACATGTGTGATTGCATGATTATTAATATTATTATTTGCATGA
* * *
13451232 TTATATATTTAATTGCATGTTTAT
65 TTATATATTTAATCGCATGTCTAA
13451256 TTGCATGATT
1 TTGCATGATT
13451266 TACATTATTA
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
87 1 0.01
88 81 0.96
89 2 0.02
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.54
Consensus pattern (88 bp):
TTGCATGATTATATATTTAATTACATGTGTGATTGCATGATTATTAATATTATTATTTGCATGAT
TATATATTTAATCGCATGTCTAA
Found at i:13451203 original size:32 final size:32
Alignment explanation
Indices: 13451167--13451355 Score: 129
Period size: 32 Copynumber: 5.9 Consensus size: 32
13451157 CGCATGTCTA
*
13451167 ATTGTATGATTATTAATTTATTTATTTGTGTG
1 ATTGTATGATTATTAATTTATTTATTTGTATG
*
13451199 ATTGTATGATTATTAATATT-TTTATTTGCATG
1 ATTGTATGATTATTAAT-TTATTTATTTGTATG
* * *
13451231 ATTATAT-A-T-TTAATTGCATGTTTATTTGCATG
1 ATTGTATGATTATTAATT---TATTTATTTGTATG
* * * * * *
13451263 ATT-TA-CATTATTAATTGCATGATTATATATTTA
1 ATTGTATGATTATTAATT-TAT--TTATTTGTATG
** * *
13451296 ATTACATGATTATTAATTTATTTGTTTGTGTG
1 ATTGTATGATTATTAATTTATTTATTTGTATG
*
13451328 ATTGTATGATTATTAATATATTTATTTG
1 ATTGTATGATTATTAATTTATTTATTTG
13451356 CATAGTTATT
Statistics
Matches: 122, Mismatches: 23, Indels: 24
0.72 0.14 0.14
Matches are distributed among these distances:
28 1 0.01
29 5 0.04
30 1 0.01
31 6 0.05
32 79 0.65
33 17 0.14
34 3 0.02
35 10 0.08
ACGTcount: A:0.29, C:0.03, G:0.12, T:0.56
Consensus pattern (32 bp):
ATTGTATGATTATTAATTTATTTATTTGTATG
Found at i:13451282 original size:33 final size:32
Alignment explanation
Indices: 13451219--13451288 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
13451209 TATTAATATT
*
13451219 TTTATTTGCATGATTATATATTTAATTGCATG
1 TTTATTTGCATGATTACATATTTAATTGCATG
13451251 TTTATTTGCATGATTTACAT-TATTAATTGCATG
1 TTTATTTGCATGA-TTACATAT-TTAATTGCATG
*
13451284 ATTAT
1 TTTAT
13451289 ATATTTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 14 0.41
33 20 0.59
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (32 bp):
TTTATTTGCATGATTACATATTTAATTGCATG
Found at i:13451416 original size:19 final size:19
Alignment explanation
Indices: 13451379--13451417 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
13451369 TTATTTATTA
* * *
13451379 TTATTGCATGATTTTATAT
1 TTATTACATGATATGATAT
13451398 TTATTACATGATATGATAT
1 TTATTACATGATATGATAT
13451417 T
1 T
13451418 ACATGTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (19 bp):
TTATTACATGATATGATAT
Found at i:13451588 original size:24 final size:22
Alignment explanation
Indices: 13451535--13451592 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
13451525 ATATTTGATT
13451535 TTTTGATTATATATTTGCATGAA
1 TTTT-ATTATATATTTGCATGAA
* *
13451558 TAGTTATTAATATATTTGCATGGTA
1 T-TTTATT-ATATATTTGCAT-GAA
13451583 TTTTA-TATAT
1 TTTTATTATAT
13451593 TACATGATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 4 0.14
23 5 0.17
24 17 0.59
25 3 0.10
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.53
Consensus pattern (22 bp):
TTTTATTATATATTTGCATGAA
Found at i:13451604 original size:35 final size:34
Alignment explanation
Indices: 13451565--13451630 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
13451555 GAATAGTTAT
* * *
13451565 TAATATATTTGCATGGTATTTTATATATTACATGA
1 TAATATATTTACATGATATTATATAT-TTACATGA
*
13451600 TAATATGTTTACATGATATTATATATTTACA
1 TAATATATTTACATGATATTATATATTTACA
13451631 CGATTGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 5 0.19
35 22 0.81
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (34 bp):
TAATATATTTACATGATATTATATATTTACATGA
Found at i:13451668 original size:20 final size:20
Alignment explanation
Indices: 13451543--13451670 Score: 60
Period size: 18 Copynumber: 6.7 Consensus size: 20
13451533 TTTTTTGATT
13451543 ATATATTTGCATGAATAGTTATTA
1 ATATATTTGCATG-ATA---ATTA
* * *
13451567 ATATATTTGCATGGTATTTT
1 ATATATTTGCATGATAATTA
*
13451587 ATATA-TTACATG---A-TA
1 ATATATTTGCATGATAATTA
* *
13451602 ATATGTTTACATGAT-ATT-
1 ATATATTTGCATGATAATTA
* * **
13451620 ATATATTTACACGATTGTT-
1 ATATATTTGCATGATAATTA
13451639 AT-TA-TTGCATGATAATTA
1 ATATATTTGCATGATAATTA
13451657 ATATATTTGCATGA
1 ATATATTTGCATGA
13451671 CATTCTTGCA
Statistics
Matches: 82, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
15 5 0.06
16 7 0.09
17 9 0.11
18 18 0.22
19 13 0.16
20 15 0.18
23 2 0.02
24 13 0.16
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (20 bp):
ATATATTTGCATGATAATTA
Found at i:13458901 original size:13 final size:13
Alignment explanation
Indices: 13458883--13458907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13458873 AGAATCTTTT
13458883 CATTCATTGCATG
1 CATTCATTGCATG
13458896 CATTCATTGCAT
1 CATTCATTGCAT
13458908 ATATTTGCAA
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:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
CATTCATTGCATG
Found at i:13459127 original size:43 final size:43
Alignment explanation
Indices: 13459080--13459509 Score: 356
Period size: 42 Copynumber: 10.2 Consensus size: 43
13459070 GAATGATCTT
* *
13459080 ATTTTATTTTTCAAAAGTTTCAAAGCCTCAGTTATAGGTGAGC
1 ATTTTATTTTTCAAAAGTTTCAAAGCCTCAGTTGTAGGGGAGC
* * * * * *
13459123 ATTTTTACTTTTCCAAAG-TTCTAAAGCTTTAATTGTGGGGGAGC
1 A-TTTTATTTTTCAAAAGTTTC-AAAGCCTCAGTTGTAGGGGAGC
* * * * *
13459167 ATTTTAGTTTTCTAAAG-TTCTAAAGCCTCAGTTAT-GTGAGAGT
1 ATTTTATTTTTCAAAAGTTTC-AAAGCCTCAGTTGTAG-GGGAGC
*
13459210 ATTTTATTTTTCAAAAGTTTCAAAGCCTTAGTTGT-GAGGGAGC
1 ATTTTATTTTTCAAAAGTTTCAAAGCCTCAGTTGTAG-GGGAGC
* * * *
13459253 ATTTGACTTTTCCAAAGTTCCAAAG-C-C--TT-T--GGGAGC
1 ATTTTATTTTTCAAAAGTTTCAAAGCCTCAGTTGTAGGGGAGC
* * ** *
13459289 ATTTTATTTTTCTAAAGTTCCAAAG-CTTTGATTGT-GGGGAAAC
1 ATTTTATTTTTCAAAAGTTTCAAAGCCTCAG-TTGTAGGGG-AGC
* *
13459332 ATTTTATTTTT-AAAAGTTTCAAAGCTTCAGTTGT-GGGAAAGC
1 ATTTTATTTTTCAAAAGTTTCAAAGCCTCAGTTGTAGGG-GAGC
* *
13459374 ATTTTATTTTT-AAAAGTTTCAAAGCCTCAATTGTAGGGGTGC
1 ATTTTATTTTTCAAAAGTTTCAAAGCCTCAGTTGTAGGGGAGC
* * *
13459416 ATTTTATTTTT-AAAAGTTTCAAAACCTCAGTTGTAGGAGAGT
1 ATTTTATTTTTCAAAAGTTTCAAAGCCTCAGTTGTAGGGGAGC
* * * *
13459458 ATTTTA-TTTCCAAAAGTTTCAAAGCCTCAGTTATGGGGGATC
1 ATTTTATTTTTCAAAAGTTTCAAAGCCTCAGTTGTAGGGGAGC
13459500 ATTTTATTTT
1 ATTTTATTTT
13459510 GAAATATGTC
Statistics
Matches: 315, Mismatches: 56, Indels: 32
0.78 0.14 0.08
Matches are distributed among these distances:
36 29 0.09
38 1 0.00
39 2 0.01
40 2 0.01
41 4 0.01
42 133 0.42
43 110 0.35
44 34 0.11
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (43 bp):
ATTTTATTTTTCAAAAGTTTCAAAGCCTCAGTTGTAGGGGAGC
Found at i:13459287 original size:36 final size:35
Alignment explanation
Indices: 13459247--13459318 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
13459237 TTAGTTGTGA
13459247 GGGAGCATTTGACTTTTCCAAAGTTCCAAAGCCTTT
1 GGGAGCATTTGACTTTTCCAAAGTTCCAAAG-CTTT
* * *
13459283 GGGAGCATTTTATTTTTCTAAAGTTCCAAAGCTTT
1 GGGAGCATTTGACTTTTCCAAAGTTCCAAAGCTTT
13459318 G
1 G
13459319 ATTGTGGGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 5 0.15
36 28 0.85
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (35 bp):
GGGAGCATTTGACTTTTCCAAAGTTCCAAAGCTTT
Found at i:13459643 original size:38 final size:40
Alignment explanation
Indices: 13459554--13459665 Score: 124
Period size: 39 Copynumber: 2.9 Consensus size: 40
13459544 TTTGAGATCA
* * *
13459554 AAAGTTGAAGCC-CAAGTGGAGGAGTTTTTTATTTTTTCC
1 AAAGTTGAAGCCTCGAGTGGAGGAGTATTTTATTTTCTCC
* *
13459593 AAAGTTGAAGCCTCGA-TTGAGGCGTATTTTATTTTCT-C
1 AAAGTTGAAGCCTCGAGTGGAGGAGTATTTTATTTTCTCC
**
13459631 AAAGTTGAAGCCTCG-GTGGAATAGTACTTTTATTT
1 AAAGTTGAAGCCTCGAGTGGAGGAGTA-TTTTATTT
13459666 AAAGTTTCAA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
38 22 0.36
39 37 0.61
40 2 0.03
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.38
Consensus pattern (40 bp):
AAAGTTGAAGCCTCGAGTGGAGGAGTATTTTATTTTCTCC
Found at i:13459985 original size:15 final size:15
Alignment explanation
Indices: 13459965--13460007 Score: 65
Period size: 13 Copynumber: 3.1 Consensus size: 15
13459955 TTATTTGTAT
13459965 TTTAATATTTTTTAG
1 TTTAATATTTTTTAG
13459980 TTT-A-ATTTTTTA-
1 TTTAATATTTTTTAG
13459992 TTTAATATTTTTTAG
1 TTTAATATTTTTTAG
13460007 T
1 T
13460008 CAAAAGAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.12
13 9 0.36
14 9 0.36
15 4 0.16
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (15 bp):
TTTAATATTTTTTAG
Found at i:13460634 original size:16 final size:17
Alignment explanation
Indices: 13460594--13460667 Score: 62
Period size: 17 Copynumber: 4.2 Consensus size: 17
13460584 ATTTGCATGA
13460594 ATTTGCATGATTAATATCAT
1 ATTTGCATGATTAAT-T--T
13460614 ATTTGCATGA-TAATTT
1 ATTTGCATGATTAATTT
* *
13460630 ATTTGCCT-AATATATTT
1 ATTTGCATGATTA-ATTT
* *
13460647 GTTTGCATGATTAATAT
1 ATTTGCATGATTAATTT
13460664 ATTT
1 ATTT
13460668 ATTTATGTGA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
15 1 0.02
16 10 0.22
17 16 0.36
18 4 0.09
19 4 0.09
20 10 0.22
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.50
Consensus pattern (17 bp):
ATTTGCATGATTAATTT
Found at i:13460717 original size:24 final size:24
Alignment explanation
Indices: 13460637--13460797 Score: 126
Period size: 24 Copynumber: 7.0 Consensus size: 24
13460627 TTTATTTGCC
*
13460637 TAATATATTTGTTTGCATG---AT
1 TAATATATTTATTTGCATGATTAT
*
13460658 TAATATATTTATTT--ATG-TGAT
1 TAATATATTTATTTGCATGATTAT
* *
13460679 TTAT-TAATATATTTGCATGATTAT
1 TAATAT-ATTTATTTGCATGATTAT
* *
13460703 TAATATATTTATTTGTACGATTA-
1 TAATATATTTATTTGCATGATTAT
*
13460726 TATTCA-ATTTGA-TTGCATGATTAT
1 TAAT-ATATTT-ATTTGCATGATTAT
* *
13460750 TAATATATTTAATTGCTTGATTAT
1 TAATATATTTATTTGCATGATTAT
* *
13460774 TAATATATTTGTTTGTATGATTAT
1 TAATATATTTATTTGCATGATTAT
13460798 ATATTTAATT
Statistics
Matches: 111, Mismatches: 17, Indels: 21
0.74 0.11 0.14
Matches are distributed among these distances:
19 3 0.03
20 1 0.01
21 25 0.23
23 21 0.19
24 60 0.54
25 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.54
Consensus pattern (24 bp):
TAATATATTTATTTGCATGATTAT
Found at i:13460753 original size:47 final size:45
Alignment explanation
Indices: 13460637--13460760 Score: 142
Period size: 47 Copynumber: 2.7 Consensus size: 45
13460627 TTTATTTGCC
** * **
13460637 TAATATATTTGTTTGCATGATTAATATATTTATTTATGTGATTTAT
1 TAATATATTTGCATG-ATTATTAATATATTTATTTATACGATTTAT
*
13460683 TAATATATTTGCATGATTATTAATATATTTATTTGTACGATTATAT
1 TAATATATTTGCATGATTATTAATATATTTATTTATACGATT-TAT
*
13460729 TCAATTTGA-TTGCATGATTATTAATATATTTA
1 T-AATAT-ATTTGCATGATTATTAATATATTTA
13460761 ATTGCTTGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
45 23 0.34
46 17 0.25
47 27 0.40
48 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (45 bp):
TAATATATTTGCATGATTATTAATATATTTATTTATACGATTTAT
Found at i:13460809 original size:24 final size:24
Alignment explanation
Indices: 13460752--13460862 Score: 63
Period size: 23 Copynumber: 4.5 Consensus size: 24
13460742 ATGATTATTA
* *
13460752 ATATATTTAATTGCTTG-ATTATT
1 ATATATTTAATTGTTTGTATGATT
*
13460775 A-ATA--TATTTGTTTGTATGATT
1 ATATATTTAATTGTTTGTATGATT
*
13460796 ATATATTTAATTGTATTTTTTTTGCATGATT
1 ATATATTTAATTG-------TTTGTATGATT
*
13460827 -TATATATT-ATTATTTGTATGATT
1 ATATAT-TTAATTGTTTGTATGATT
13460850 ATATATTTAATTG
1 ATATATTTAATTG
13460863 CATGTTTATT
Statistics
Matches: 66, Mismatches: 8, Indels: 27
0.65 0.08 0.27
Matches are distributed among these distances:
20 8 0.12
21 6 0.09
22 6 0.09
23 13 0.20
24 13 0.20
30 8 0.12
31 12 0.18
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.59
Consensus pattern (24 bp):
ATATATTTAATTGTTTGTATGATT
Found at i:13460843 original size:54 final size:54
Alignment explanation
Indices: 13460785--13460888 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 54
13460775 AATATATTTG
* *
13460785 TTTGTATGATTATATATTTAATTGTAT-TTTTTTTGCATGATTTATATATTATTA
1 TTTGTATGATTATATATTTAATTGCATGTTTATTTGCATGA-TTATATATTATTA
13460839 TTTGTATGATTATATATTTAATTGCATGTTTATTTGCATGATTATATATT
1 TTTGTATGATTATATATTTAATTGCATGTTTATTTGCATGATTATATATT
13460889 TAATTGCATA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
54 35 0.74
55 12 0.26
ACGTcount: A:0.28, C:0.03, G:0.11, T:0.59
Consensus pattern (54 bp):
TTTGTATGATTATATATTTAATTGCATGTTTATTTGCATGATTATATATTATTA
Found at i:13460873 original size:32 final size:32
Alignment explanation
Indices: 13460836--13460922 Score: 147
Period size: 32 Copynumber: 2.7 Consensus size: 32
13460826 TTATATATTA
* *
13460836 TTATTTGTATGATTATATATTTAATTGCATGT
1 TTATTTGCATGATTATATATTTAATTGCATAT
13460868 TTATTTGCATGATTATATATTTAATTGCATAT
1 TTATTTGCATGATTATATATTTAATTGCATAT
13460900 TTATTTGCATGATTTATATATTT
1 TTATTTGCATGA-TTATATATTT
13460923 TTATTTGCAT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
32 42 0.81
33 10 0.19
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (32 bp):
TTATTTGCATGATTATATATTTAATTGCATAT
Found at i:13460909 original size:87 final size:86
Alignment explanation
Indices: 13460785--13460970 Score: 309
Period size: 87 Copynumber: 2.2 Consensus size: 86
13460775 AATATATTTG
* * * *
13460785 TTTGTATGATTATATATTTAATTGTATTTTTTTTGCATGATTTATATATTATTATTTGTATGATT
1 TTTGCATGATTATATATTTAATTGCATTTTATTTGCATGATTTATATATTATTATTTGCATGATT
*
13460850 ATATATTTAATTGCATGTTTA
66 ATATATTTAATTACATGTTTA
*
13460871 TTTGCATGATTATATATTTAATTGCATATTTATTTGCATGATTTATATATTTTTATTTGCATGAT
1 TTTGCATGATTATATATTTAATTGCAT-TTTATTTGCATGATTTATATATTATTATTTGCATGAT
13460936 TATATATTTAATTACATGTTTA
65 TATATATTTAATTACATGTTTA
13460958 TTTGCATGATTAT
1 TTTGCATGATTAT
13460971 TAATATTATT
Statistics
Matches: 93, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
86 25 0.27
87 68 0.73
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.57
Consensus pattern (86 bp):
TTTGCATGATTATATATTTAATTGCATTTTATTTGCATGATTTATATATTATTATTTGCATGATT
ATATATTTAATTACATGTTTA
Found at i:13460941 original size:22 final size:23
Alignment explanation
Indices: 13460899--13460944 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
13460889 TAATTGCATA
13460899 TTTATTTGCATGATTTATATATT
1 TTTATTTGCATGATTTATATATT
13460922 TTTATTTGCATGA-TTATATATT
1 TTTATTTGCATGATTTATATATT
13460944 T
1 T
13460945 AATTACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (23 bp):
TTTATTTGCATGATTTATATATT
Found at i:13460953 original size:20 final size:20
Alignment explanation
Indices: 13460594--13460945 Score: 76
Period size: 20 Copynumber: 17.1 Consensus size: 20
13460584 ATTTGCATGA
*
13460594 ATTTGCATGATTA-ATATCAT
1 ATTTGCATGATTATATAT-TT
13460614 ATTTGCATG---ATA-ATTT
1 ATTTGCATGATTATATATTT
*
13460630 ATTTGCCT-A--ATATATTT
1 ATTTGCATGATTATATATTT
*
13460647 GTTTGCATGATTAATATATTT
1 ATTTGCATGATT-ATATATTT
*** *
13460668 ATTTATGTGATT-TATTAATAT
1 ATTTGCATGATTATA-T-ATTT
13460689 ATTTGCATGATTATTAATATATTT
1 ATTTGCATG---ATT-ATATATTT
* *
13460713 ATTTGTACGATTATATTCAATTT
1 ATTTGCATGATTATA-T--ATTT
13460736 GA-TTGCATGATTATTAATATATTT
1 -ATTTGCATG---ATT-ATATATTT
* *
13460760 AATTGCTTGATTATTAATATATTT
1 ATTTGC---ATGATT-ATATATTT
* *
13460784 GTTTGTATGATTATATATTT
1 ATTTGCATGATTATATATTT
*
13460804 A-AT---TG--TAT-T-TTT
1 ATTTGCATGATTATATATTT
13460816 -TTTGCATGATTTATATATTATT
1 ATTTGCATGA-TTATATA-T-TT
*
13460838 ATTTGTATGATTATATATTT
1 ATTTGCATGATTATATATTT
* * *
13460858 AATTGCATGTTTATTTGCATGATT
1 ATTTGCATGATTATAT--AT--TT
* *** * **
13460882 ATATATTTAATTGCATATTT
1 ATTTGCATGATTATATATTT
13460902 ATTTGCATGATTTATATATTTTT
1 ATTTGCATGA-TTATATA--TTT
13460925 ATTTGCATGATTATATATTT
1 ATTTGCATGATTATATATTT
13460945 A
1 A
13460946 ATTACATGTT
Statistics
Matches: 240, Mismatches: 47, Indels: 90
0.64 0.12 0.24
Matches are distributed among these distances:
12 4 0.02
13 1 0.00
14 3 0.01
15 2 0.01
16 13 0.05
17 13 0.05
18 5 0.02
19 4 0.02
20 46 0.19
21 41 0.17
22 20 0.08
23 31 0.13
24 45 0.19
25 1 0.00
26 6 0.03
27 5 0.02
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (20 bp):
ATTTGCATGATTATATATTT
Found at i:13460958 original size:20 final size:20
Alignment explanation
Indices: 13460896--13460958 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
13460886 ATTTAATTGC
13460896 ATATTTATTTGCATGATTTAT
1 ATATTTATTTGCATG-TTTAT
*
13460917 ATATTTTTATTTGCATGATTAT
1 ATA--TTTATTTGCATGTTTAT
* *
13460939 ATATTTAATTACATGTTTAT
1 ATATTTATTTGCATGTTTAT
13460959 TTGCATGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 14 0.39
21 3 0.08
22 7 0.19
23 12 0.33
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (20 bp):
ATATTTATTTGCATGTTTAT
Found at i:13460959 original size:32 final size:31
Alignment explanation
Indices: 13460922--13461107 Score: 123
Period size: 32 Copynumber: 6.4 Consensus size: 31
13460912 TTTATATATT
13460922 TTTATTTGCATGATTATATATTTAATTACATG
1 TTTATTTGCATGATTATATA-TTAATTACATG
*
13460954 TTTATTTGCATGATTAT-TAAT-ATT--A--
1 TTTATTTGCATGATTATATATTAATTACATG
* *
13460979 -TTATTTGCATAATTATATATTTAATTGCATG
1 TTTATTTGCATGATTATATA-TTAATTACATG
* *
13461010 TCTAATTGCAT-A--AT-TATTAATTA-A--
1 TTTATTTGCATGATTATATATTAATTACATG
* ** * *
13461034 TTTATTTGTATGATTGCATATT-ATTAATATT
1 TTTATTTGCATGATTATATATTAATT-ACATG
* *
13461065 TTTATTTGTATGATTATATATTTAATTGCATG
1 TTTATTTGCATGATTATATA-TTAATTACATG
13461097 TTTATTTGCAT
1 TTTATTTGCAT
13461108 AATTTACATT
Statistics
Matches: 119, Mismatches: 17, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
24 23 0.19
25 3 0.03
26 2 0.02
27 13 0.11
28 7 0.06
29 7 0.06
30 1 0.01
31 21 0.18
32 39 0.33
33 3 0.03
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.54
Consensus pattern (31 bp):
TTTATTTGCATGATTATATATTAATTACATG
Found at i:13461003 original size:56 final size:56
Alignment explanation
Indices: 13460868--13461048 Score: 242
Period size: 56 Copynumber: 3.2 Consensus size: 56
13460858 AATTGCATGT
* *
13460868 TTATTTGCATGATTATATATTTAATTGCATATTTATTTGCATGA-T-TTATATATTT
1 TTATTTGCATGATTATATATTTAATTGCATGTTTATTTGCATGATTATTA-ATATTA
*
13460923 TTATTTGCATGATTATATATTTAATTACATGTTTATTTGCATGATTATTAATATTA
1 TTATTTGCATGATTATATATTTAATTGCATGTTTATTTGCATGATTATTAATATTA
* * * * *
13460979 TTATTTGCATAATTATATATTTAATTGCATGTCTAATTGCATAATTATTAAT-TAA
1 TTATTTGCATGATTATATATTTAATTGCATGTTTATTTGCATGATTATTAATATTA
*
13461034 TTTATTTGTATGATT
1 -TTATTTGCATGATT
13461049 GCATATTATT
Statistics
Matches: 112, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
55 44 0.39
56 65 0.58
57 3 0.03
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (56 bp):
TTATTTGCATGATTATATATTTAATTGCATGTTTATTTGCATGATTATTAATATTA
Found at i:13461034 original size:87 final size:87
Alignment explanation
Indices: 13460927--13461111 Score: 241
Period size: 87 Copynumber: 2.1 Consensus size: 87
13460917 ATATTTTTAT
* *
13460927 TTGCATGATTATATATTTAATTACATGTT-TAT-TTGCATGATTATTAATATTATTATTTGCATA
1 TTGCATAATTATATAATTAATT-CAT-TTGTATATTGCAT-ATTATTAATATTATTATTTGCATA
13460990 ATTATATATTTAATTGCATGTCTAA
63 ATTATATATTTAATTGCATGTCTAA
* * * *
13461015 TTGCATAATTAT-TAATTAATTTATTTGTATGATTGCATATTATTAATATTTTTATTTGTATGAT
1 TTGCATAATTATATAATTAATTCATTTGTAT-ATTGCATATTATTAATATTATTATTTGCATAAT
* *
13461079 TATATATTTAATTGCATGTTTAT
65 TATATATTTAATTGCATGTCTAA
13461102 TTGCATAATT
1 TTGCATAATT
13461112 TACATTGTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
85 2 0.02
86 5 0.06
87 62 0.72
88 17 0.20
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.54
Consensus pattern (87 bp):
TTGCATAATTATATAATTAATTCATTTGTATATTGCATATTATTAATATTATTATTTGCATAATT
ATATATTTAATTGCATGTCTAA
Found at i:13461057 original size:31 final size:32
Alignment explanation
Indices: 13461014--13461079 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
13461004 TGCATGTCTA
13461014 ATTGCATAATTATTAAT-TAATTTATTTGTATG
1 ATTGCATAATTATTAATAT-ATTTATTTGTATG
*
13461046 ATTGCAT-ATTATTAATATTTTTATTTGTATG
1 ATTGCATAATTATTAATATATTTATTTGTATG
13461077 ATT
1 ATT
13461080 ATATATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 24 0.75
32 8 0.25
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (32 bp):
ATTGCATAATTATTAATATATTTATTTGTATG
Found at i:13461069 original size:111 final size:111
Alignment explanation
Indices: 13460868--13461081 Score: 265
Period size: 111 Copynumber: 1.9 Consensus size: 111
13460858 AATTGCATGT
* * * *
13460868 TTATTTGCATGATTATATATTTAATTGCATATTTATTTGCATGATTTATATATTTTTATTTGCAT
1 TTATTTGCATAATTATATATTTAATTGCATATCTAATTGCATAATTTATATATTTTTATTTGCAT
*
13460933 GATTATATATTTAATTACATGTTTATTTGCATGATTATTAATATTA
66 GATTACATATTTAATTACATGTTTATTTGCATGATTATTAATATTA
*
13460979 TTATTTGCATAATTATATATTTAATTGCATGTCTAATTGCATAA-TTAT-TAATTAATTTATTTG
1 TTATTTGCATAATTATATATTTAATTGCATATCTAATTGCATAATTTATAT-ATT--TTTATTTG
* * * * *
13461042 TATGATTGCATA-TT-ATTAATATTTTTATTTGTATGATTAT
63 CATGATTACATATTTAATT-ACATGTTTATTTGCATGATTAT
13461082 ATATTTAATT
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
109 1 0.01
110 10 0.11
111 60 0.68
112 17 0.19
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (111 bp):
TTATTTGCATAATTATATATTTAATTGCATATCTAATTGCATAATTTATATATTTTTATTTGCAT
GATTACATATTTAATTACATGTTTATTTGCATGATTATTAATATTA
Found at i:13461159 original size:143 final size:142
Alignment explanation
Indices: 13460754--13461149 Score: 475
Period size: 143 Copynumber: 2.8 Consensus size: 142
13460744 GATTATTAAT
* * * * * *
13460754 ATATTTAATTGCTTGATTATTAATATATTTGTTTGTATGATTATATATTTAATTGTAT-TTTTTT
1 ATATTTATTTGCATGATTATTAATATTTTTATTTGTATGATTATATATTTAATTGCATGTTTATT
* * *
13460818 TGCATGATTTATATATTATTATTTGTATGATTATATATTTAATTGCATGTTTATTTGCATGATTA
66 TGCATGAATT-TATATTATTATTTGTATGATTATATATTTAATTGCATGTTTAATTGCATAATTA
*
13460883 TATATTTAATTGC
130 TATAATTAATTGC
* *
13460896 ATATTTATTTGCATGA-T-TTATATATTTTTATTTGCATGATTATATATTTAATTACATGTTTAT
1 ATATTTATTTGCATGATTATTA-ATATTTTTATTTGTATGATTATATATTTAATTGCATGTTTAT
* * * *
13460959 TTGCATGATTATTAATATTATTATTTGCATAATTATATATTTAATTGCATGTCTAATTGCATAAT
65 TTGCATGA--ATTTATATTATTATTTGTATGATTATATATTTAATTGCATGTTTAATTGCATAAT
*
13461024 TAT-TAATTAATT-T
128 TATATAATTAATTGC
13461037 AT-TTGTATGATTGCAT-ATTATTAATATTTTTATTTGTATGATTATATATTTAATTGCATGTTT
1 ATATT-TAT--TTGCATGATTATTAATATTTTTATTTGTATGATTATATATTTAATTGCATGTTT
* * * * *
13461100 ATTTGCAT-AATTTACATTGTTAATTGTATGATTCTATATTTAATTACATG
63 ATTTGCATGAATTTATATTATTATTTGTATGATTATATATTTAATTGCATG
13461150 ATTATTAATT
Statistics
Matches: 218, Mismatches: 27, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
140 38 0.17
141 37 0.17
142 36 0.17
143 102 0.47
144 5 0.02
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.55
Consensus pattern (142 bp):
ATATTTATTTGCATGATTATTAATATTTTTATTTGTATGATTATATATTTAATTGCATGTTTATT
TGCATGAATTTATATTATTATTTGTATGATTATATATTTAATTGCATGTTTAATTGCATAATTAT
ATAATTAATTGC
Found at i:13461428 original size:35 final size:37
Alignment explanation
Indices: 13461375--13461445 Score: 103
Period size: 35 Copynumber: 2.0 Consensus size: 37
13461365 TGTATTATTG
13461375 CATAATTAATATATTTGCATGAT-ATT-ATATATTTA
1 CATAATTAATATATTTGCATGATAATTAATATATTTA
*
13461410 CATAATTATTAT-TATTGCATGATAATTAATATATTT
1 CATAATTAATATAT-TTGCATGATAATTAATATATTT
13461446 GCATGATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 1 0.03
35 20 0.62
36 3 0.09
37 8 0.25
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (37 bp):
CATAATTAATATATTTGCATGATAATTAATATATTTA
Found at i:13461436 original size:20 final size:20
Alignment explanation
Indices: 13461376--13461453 Score: 94
Period size: 18 Copynumber: 4.2 Consensus size: 20
13461366 GTATTATTGC
13461376 ATAATTAATATATTTGCATG
1 ATAATTAATATATTTGCATG
* *
13461396 AT-ATT-ATATATTTACATA
1 ATAATTAATATATTTGCATG
*
13461414 ATTATT-AT-TA-TTGCATG
1 ATAATTAATATATTTGCATG
13461431 ATAATTAATATATTTGCATG
1 ATAATTAATATATTTGCATG
13461451 ATA
1 ATA
13461454 TTCTTGCATG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
17 10 0.20
18 17 0.35
19 10 0.20
20 12 0.24
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (20 bp):
ATAATTAATATATTTGCATG
Found at i:13461470 original size:14 final size:14
Alignment explanation
Indices: 13461444--13461478 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
13461434 ATTAATATAT
13461444 TTGCATG-ATATTC
1 TTGCATGAATATTC
13461457 TTGCATGAATATTC
1 TTGCATGAATATTC
*
13461471 TAGCATGA
1 TTGCATGA
13461479 TCTAGGCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (14 bp):
TTGCATGAATATTC
Found at i:13464240 original size:22 final size:22
Alignment explanation
Indices: 13464215--13464256 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
13464205 GATTTATGGA
*
13464215 ATAAAATAACAATTATATTCTG
1 ATAAAAAAACAATTATATTCTG
*
13464237 ATAAAAAAACAATTTTATTC
1 ATAAAAAAACAATTATATTC
13464257 ACAAATCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAAAAAAACAATTATATTCTG
Found at i:13467616 original size:15 final size:16
Alignment explanation
Indices: 13467596--13467635 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
13467586 TAAAATTTTT
13467596 ATAATTTATTATAA-A
1 ATAATTTATTATAATA
13467611 ATAATTTGA-TATAATA
1 ATAATTT-ATTATAATA
13467627 AT-ATTTATT
1 ATAATTTATT
13467636 TATGATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.05
15 17 0.77
16 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATAATTTATTATAATA
Found at i:13475159 original size:108 final size:107
Alignment explanation
Indices: 13474954--13475166 Score: 372
Period size: 108 Copynumber: 2.0 Consensus size: 107
13474944 CGTGATCCAC
13474954 CCATTTTCATTCTTTTGAAACAAATTTTGCTTCTATTTAAAAACCAATCAATCCATACAAGGTAA
1 CCATTTTCATTCTTTTGAAACAAATTTTGCTTCTATTTAAAAACCAATCAATCCATACAAGGTAA
* * *
13475019 GGGATTGATCGGACCTTGAAACCCTTGTACCAATCGATCCCT
66 GGGATTAATCGAACCTTGAAACCCTTGTACCAATCAATCCCT
*
13475061 CCATTTTCATTCTTTTGAAACAAATTTTGCTTCTATTTAAAAAACCAATCAATCCATACAGGGTA
1 CCATTTTCATTCTTTTGAAACAAATTTTGCTTCTATTT-AAAAACCAATCAATCCATACAAGGTA
*
13475126 GGGGATTAATCGAACCTTGAAACCCTTGTACCAATCAATCC
65 AGGGATTAATCGAACCTTGAAACCCTTGTACCAATCAATCC
13475167 AATAAGAGAG
Statistics
Matches: 100, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
107 38 0.38
108 62 0.62
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (107 bp):
CCATTTTCATTCTTTTGAAACAAATTTTGCTTCTATTTAAAAACCAATCAATCCATACAAGGTAA
GGGATTAATCGAACCTTGAAACCCTTGTACCAATCAATCCCT
Found at i:13475517 original size:21 final size:21
Alignment explanation
Indices: 13475472--13475517 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
13475462 GCATGAAAAT
* *
13475472 GGATTGATCACCCAACCTAGG
1 GGATTGATCACCCAACATAGA
* *
13475493 GGATTGATCACCCTACATATA
1 GGATTGATCACCCAACATAGA
13475514 GGAT
1 GGAT
13475518 CAATCACGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
GGATTGATCACCCAACATAGA
Found at i:13480948 original size:59 final size:59
Alignment explanation
Indices: 13480876--13480992 Score: 180
Period size: 59 Copynumber: 2.0 Consensus size: 59
13480866 ACATGCAAAC
* * **
13480876 TCAACATAATAAACATTCACGATTAAACTTTTCTCTTGAAGACTTGAATAAGGCAACAT
1 TCAACATAATAAACACTCACAATTAAACTTTTCTCTTGAAGACTCAAATAAGGCAACAT
**
13480935 TCAACATAATAAACACTCACAATTGTACTTTTCTCTTGAAGACTCAAATAAGGCAACA
1 TCAACATAATAAACACTCACAATTAAACTTTTCTCTTGAAGACTCAAATAAGGCAACA
13480993 AAAGATTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (59 bp):
TCAACATAATAAACACTCACAATTAAACTTTTCTCTTGAAGACTCAAATAAGGCAACAT
Found at i:13482641 original size:42 final size:41
Alignment explanation
Indices: 13482566--13482650 Score: 95
Period size: 42 Copynumber: 2.0 Consensus size: 41
13482556 AATTTTTTTA
*
13482566 ATAAATAAATTATCTTATATTAATTTTTACATATATCA-AAT
1 ATAAATAAATTATCTTATATTAATTTATACATAT-TCATAAT
*
13482607 ATAAGATAAGATTATGTTAT-TTAATTTA-ATCATATTCATAAT
1 ATAA-ATAA-ATTATCTTATATTAATTTATA-CATATTCATAAT
13482649 AT
1 AT
13482651 CATTTTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
41 8 0.21
42 21 0.55
43 9 0.24
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (41 bp):
ATAAATAAATTATCTTATATTAATTTATACATATTCATAAT
Found at i:13485453 original size:28 final size:28
Alignment explanation
Indices: 13485412--13485469 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
13485402 ATTCTACCAA
13485412 ATCAGGGTGATTCCAAGATACAGGAAGC
1 ATCAGGGTGATTCCAAGATACAGGAAGC
*
13485440 ATCAGGGTGGTTCCAAGATACAGGAAGC
1 ATCAGGGTGATTCCAAGATACAGGAAGC
13485468 AT
1 AT
13485470 ATCTGATCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.19
Consensus pattern (28 bp):
ATCAGGGTGATTCCAAGATACAGGAAGC
Found at i:13487197 original size:2 final size:2
Alignment explanation
Indices: 13487190--13487224 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13487180 TCATGTTACA
13487190 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13487225 AACTTGTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13487786 original size:34 final size:34
Alignment explanation
Indices: 13487696--13487786 Score: 85
Period size: 34 Copynumber: 2.6 Consensus size: 34
13487686 TTTTGAAAGC
* * *
13487696 TTTAAGAAATTTTTGAATTTGTAAATTTAAAAATT
1 TTTAA-AAATTTTTGAATATGCAAATTCAAAAATT
* * * *
13487731 TTTTAAAGTTTTCGAAGATGCAAATTCAAAACA-T
1 TTTAAAAATTTTTGAATATGCAAATTCAAAA-ATT
*
13487765 TTTAAAACTTTTTGAATATGCA
1 TTTAAAAATTTTTGAATATGCA
13487787 TATCATAATA
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
34 39 0.89
35 5 0.11
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.43
Consensus pattern (34 bp):
TTTAAAAATTTTTGAATATGCAAATTCAAAAATT
Found at i:13489773 original size:13 final size:13
Alignment explanation
Indices: 13489755--13489785 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13489745 TTTAATTCGA
13489755 ATTAAATTTAAAT
1 ATTAAATTTAAAT
*
13489768 ATTAAATTTATAT
1 ATTAAATTTAAAT
13489781 ATTAA
1 ATTAA
13489786 GTTCAGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTAAATTTAAAT
Found at i:13495711 original size:14 final size:14
Alignment explanation
Indices: 13495692--13495720 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13495682 ATTTTACGAA
13495692 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
13495706 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
13495720 A
1 A
13495721 CATCACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:13497492 original size:3 final size:3
Alignment explanation
Indices: 13497484--13497510 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
13497474 TAATATAGTA
13497484 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
13497511 CTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:13499250 original size:10 final size:10
Alignment explanation
Indices: 13499235--13499259 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13499225 GCATCAAGGG
13499235 CTTTATTATT
1 CTTTATTATT
13499245 CTTTATTATT
1 CTTTATTATT
13499255 CTTTA
1 CTTTA
13499260 CTAATGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (10 bp):
CTTTATTATT
Found at i:13501154 original size:18 final size:17
Alignment explanation
Indices: 13501123--13501156 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
13501113 GTTTTGGTAG
*
13501123 ATTTTTTAATAAAAATT
1 ATTTTTTAAAAAAAATT
13501140 ATTTTTATAAAAAAAAT
1 ATTTTT-TAAAAAAAAT
13501157 CCAAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTTTTAAAAAAAATT
Found at i:13510487 original size:25 final size:25
Alignment explanation
Indices: 13510437--13510489 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
13510427 TTATTGTGTA
*
13510437 TTTATATGATTATTTTGTAATATAT
1 TTTATATGATTATGTTGTAATATAT
13510462 TTTATATTGA-TATGTT-TAATATTAT
1 TTTATA-TGATTATGTTGTAATA-TAT
13510487 TTT
1 TTT
13510490 TTAAATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 5 0.20
25 17 0.68
26 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (25 bp):
TTTATATGATTATGTTGTAATATAT
Found at i:13510586 original size:22 final size:22
Alignment explanation
Indices: 13510539--13510587 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
13510529 AAATGTATAT
* *
13510539 TAAATATTTCAAAATATTTTTA
1 TAAATATTTCAAAAGATTTTCA
13510561 TAAATATTTCAAAAGA-TTTCA
1 TAAATATTTCAAAAGATTTTCA
13510582 CTAAAT
1 -TAAAT
13510588 TTATCTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATATTTCAAAAGATTTTCA
Found at i:13511379 original size:89 final size:90
Alignment explanation
Indices: 13511253--13511420 Score: 221
Period size: 89 Copynumber: 1.9 Consensus size: 90
13511243 TATTTGGGAT
* * * * * *
13511253 AAGTGATTACTATGATGTGAGATGGTAATGGCGATAGAAGTTATTCCATGATTAGCCTTTCAATA
1 AAGTGATTACTATGATGCGAGATGGTAATGACAATAGAAGTTAGTCCACGATTAGCCTTTCAACA
13511318 CTTCTGCCTTTAAACAAATTGCGAC
66 CTTCTGCCTTTAAACAAATTGCGAC
* * * * *
13511343 AAGTGA-TGCTATGATGCGTGATGGTAATTACAATAGAAGTTAGTCTACGATTGGCCTTTCAACA
1 AAGTGATTACTATGATGCGAGATGGTAATGACAATAGAAGTTAGTCCACGATTAGCCTTTCAACA
*
13511407 CTTCTGTCTTTAAA
66 CTTCTGCCTTTAAA
13511421 TGACTTAGAT
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
89 60 0.91
90 6 0.09
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (90 bp):
AAGTGATTACTATGATGCGAGATGGTAATGACAATAGAAGTTAGTCCACGATTAGCCTTTCAACA
CTTCTGCCTTTAAACAAATTGCGAC
Found at i:13515408 original size:17 final size:17
Alignment explanation
Indices: 13515386--13515418 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13515376 GCACCGCGAA
*
13515386 AAAACTCTATTATAATT
1 AAAACTCTATCATAATT
13515403 AAAACTCTATCATAAT
1 AAAACTCTATCATAAT
13515419 ATTTATAGGC
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:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAACTCTATCATAATT
Found at i:13521401 original size:2 final size:2
Alignment explanation
Indices: 13521394--13521425 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
13521384 CTATTTGTAC
*
13521394 CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
13521426 TTTCACCCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:13526125 original size:2 final size:2
Alignment explanation
Indices: 13526118--13526145 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13526108 TTCATGATTT
13526118 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
13526146 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:13533997 original size:12 final size:12
Alignment explanation
Indices: 13533980--13534054 Score: 66
Period size: 12 Copynumber: 6.2 Consensus size: 12
13533970 TAAGGTTTTA
13533980 AATATTATAAAT
1 AATATTATAAAT
*
13533992 AATATTAAAAAT
1 AATATTATAAAT
13534004 -ATATATATAAAT
1 AATAT-TATAAAT
* *
13534016 -ATTTTATTAAT
1 AATATTATAAAT
13534027 ATATATT-TAAAAT
1 A-ATATTAT-AAAT
*
13534040 AATATTATTAAT
1 AATATTATAAAT
13534052 AAT
1 AAT
13534055 TATTTTTCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
11 10 0.20
12 32 0.63
13 9 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AATATTATAAAT
Found at i:13534004 original size:21 final size:21
Alignment explanation
Indices: 13533979--13534018 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13533969 TTAAGGTTTT
13533979 AAATATTATAAAT-AATATTAA
1 AAATA-TATAAATAAATATTAA
*
13534000 AAATATATATATAAATATT
1 AAATATATAAATAAATATT
13534019 TTATTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATATATAAATAAATATTAA
Found at i:13534047 original size:25 final size:24
Alignment explanation
Indices: 13533977--13534052 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 24
13533967 ATTTAAGGTT
13533977 TTAA-ATAT-TATAAATAATATTA
1 TTAATATATATATAAATAATATTA
** *
13533999 AAAATATATATATAAAT-ATTTTA
1 TTAATATATATATAAATAATATTA
*
13534022 TTAATATATATTTAAAATAATATTA
1 TTAATATATATAT-AAATAATATTA
13534047 TTAATA
1 TTAATA
13534053 ATTATTTTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
22 2 0.05
23 19 0.44
24 11 0.26
25 11 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAATATATATATAAATAATATTA
Found at i:13540589 original size:5 final size:5
Alignment explanation
Indices: 13540579--13540604 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
13540569 GCATGAGCAC
13540579 AAGAG AAGAG AAGAG AAGAG AAGAG A
1 AAGAG AAGAG AAGAG AAGAG AAGAG A
13540605 GACGTAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AAGAG
Found at i:13545367 original size:18 final size:18
Alignment explanation
Indices: 13545344--13545379 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
13545334 AAGGGTTTTA
*
13545344 AGGTTTGGTTTTAGGGTT
1 AGGTTTGATTTTAGGGTT
13545362 AGGTTTGATTTTAGGGTT
1 AGGTTTGATTTTAGGGTT
13545380 CAGAGGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (18 bp):
AGGTTTGATTTTAGGGTT
Found at i:13545433 original size:29 final size:29
Alignment explanation
Indices: 13545400--13545473 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 29
13545390 TAAGACTTGA
*
13545400 ATTTTAGGGTTTGGAGGTTTAGGGTTTAG
1 ATTTTAGGGTTTGGAGATTTAGGGTTTAG
* *
13545429 ATTTTAGGGTTTGAAAGATTTAGGGTTTTG
1 ATTTTAGGGTTTG-GAGATTTAGGGTTTAG
13545459 ATTTTAGGGTTTGGA
1 ATTTTAGGGTTTGGA
13545474 TTTTAGAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 14 0.35
30 26 0.65
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (29 bp):
ATTTTAGGGTTTGGAGATTTAGGGTTTAG
Found at i:13545470 original size:44 final size:45
Alignment explanation
Indices: 13545402--13545487 Score: 129
Period size: 44 Copynumber: 1.9 Consensus size: 45
13545392 AGACTTGAAT
*
13545402 TTTAGGGTTTGGAGGTTTAGGGTTTAGATTTTAGGGTTTGAAAGA
1 TTTAGGGTTTGGAGGTTTAGGGTTTAGATTTTAGAGTTTGAAAGA
* * *
13545447 TTTAGGGTTTTGA-TTTTAGGGTTTGGATTTTAGAGTTTGAA
1 TTTAGGGTTTGGAGGTTTAGGGTTTAGATTTTAGAGTTTGAA
13545488 TTTTAAGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 25 0.68
45 12 0.32
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.47
Consensus pattern (45 bp):
TTTAGGGTTTGGAGGTTTAGGGTTTAGATTTTAGAGTTTGAAAGA
Found at i:13545485 original size:14 final size:14
Alignment explanation
Indices: 13545400--13545534 Score: 103
Period size: 14 Copynumber: 9.4 Consensus size: 14
13545390 TAAGACTTGA
13545400 ATTTTAGGGTTTGG
1 ATTTTAGGGTTTGG
* *
13545414 AGGTTTAGGGTTTAG
1 A-TTTTAGGGTTTGG
13545429 ATTTTAGGGTTTGAAAG
1 ATTTTAGGGTTTG---G
*
13545446 A-TTTAGGGTTTTG
1 ATTTTAGGGTTTGG
13545459 ATTTTAGGGTTTGG
1 ATTTTAGGGTTTGG
* *
13545473 ATTTTAGAGTTTGA
1 ATTTTAGGGTTTGG
* * *
13545487 ATTTTAAGATTT-C
1 ATTTTAGGGTTTGG
* *
13545500 AGTTTGAGGGTTGTGA
1 A-TTTTAGGGTT-TGG
*
13545516 AGTTTAGGGTTTGG
1 ATTTTAGGGTTTGG
13545530 ATTTT
1 ATTTT
13545535 TTTTTTTTAA
Statistics
Matches: 93, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
13 3 0.03
14 56 0.60
15 21 0.23
16 11 0.12
17 2 0.02
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.47
Consensus pattern (14 bp):
ATTTTAGGGTTTGG
Found at i:13545633 original size:14 final size:14
Alignment explanation
Indices: 13545614--13545645 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
13545604 TTTTATGATT
13545614 TTTTAAAAAAATTA
1 TTTTAAAAAAATTA
*
13545628 TTTTAAAAAAATTC
1 TTTTAAAAAAATTA
13545642 TTTT
1 TTTT
13545646 TTTAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTAAAAAAATTA
Found at i:13548360 original size:29 final size:29
Alignment explanation
Indices: 13548328--13548390 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
13548318 TAAGGCTTGA
*
13548328 ATTTTAGGGTT-TGGAAGTTTAGGGTTTTG
1 ATTTTAGGGTTGT-GAAGTTTAGGGTTTGG
13548357 ATTTTAGGGTTGTGAAGTTTAGGGTTTGG
1 ATTTTAGGGTTGTGAAGTTTAGGGTTTGG
13548386 ATTTT
1 ATTTT
13548391 TTTAATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.49
Consensus pattern (29 bp):
ATTTTAGGGTTGTGAAGTTTAGGGTTTGG
Found at i:13548364 original size:14 final size:15
Alignment explanation
Indices: 13548326--13548390 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
13548316 TTTAAGGCTT
13548326 GAATTTTAGGGTTTG
1 GAATTTTAGGGTTTG
* *
13548341 GAAGTTTAGGGTTTT
1 GAATTTTAGGGTTTG
13548356 G-ATTTTAGGG-TTG
1 GAATTTTAGGGTTTG
*
13548369 TGAAGTTTAGGGTTTG
1 -GAATTTTAGGGTTTG
13548385 G-ATTTT
1 GAATTTT
13548391 TTTAATTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
13 2 0.05
14 13 0.32
15 23 0.56
16 3 0.07
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (15 bp):
GAATTTTAGGGTTTG
Found at i:13551736 original size:58 final size:60
Alignment explanation
Indices: 13551646--13551981 Score: 429
Period size: 58 Copynumber: 5.7 Consensus size: 60
13551636 TCTTGTGTAG
13551646 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATTATTTTTTTG-AAA-TTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTTGAAAATTTTGATTTTTAA
* * * *
13551704 GGAAAATTGATACTTTCAATTTTTCCCCAAAAATCTTTTTTTGAAAA-ATT-ATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTTGATTTTTAA
* * *
13551762 GGAAAATTGATACTTTCAACTTTTCCCTAAAAA-ATATTTTTTGCAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTTTGAAAATTTTGATTTTTAA
* * **
13551822 GGAAAATTGATACTTTCAACTTTTTCTCAAAAACCCTTTTTTTGAAAA-TTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTTGAAAATTTTGATTTTTAA
* *
13551881 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTTGATTTTTAA
* * * *
13551940 GAAAAATTGATACTTTCAATTTTTCCTCAAAAATTTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
13551982 TTTGAAACTT
Statistics
Matches: 241, Mismatches: 28, Indels: 16
0.85 0.10 0.06
Matches are distributed among these distances:
57 21 0.09
58 88 0.37
59 76 0.32
60 45 0.19
61 10 0.04
62 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTTGATTTTTAA
Found at i:13551982 original size:118 final size:116
Alignment explanation
Indices: 13551646--13551981 Score: 516
Period size: 118 Copynumber: 2.9 Consensus size: 116
13551636 TCTTGTGTAG
* *
13551646 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATTATTTTTTTGAAA-TTT-ATTTTTAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAA-TA-TTTTTTGAAATTTTGATTTTCAAGGAAA
* * *
13551709 ATTGATACTTTCAATTTTTCCCCAAAAATCTTTTTTTGAAAAATTATTTCTAA
64 ATTGATACTTTCAATTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAA
13551762 GGAAAATTGATACTTTCAACTTTTCCCTAAAAAATATTTTTTGCAAATTTTGATTTTCAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTG-AAATTTTGATTTTCAAGGAAA
*
13551827 ATTGATACTTTCAACTTTTT-CTCAAAAACCCTTTTTTTGAAAATTTATTTTTAA
64 ATTGATACTTTCAA-TTTTTCCTCAAAAA-TCTTTTTTTGAAAATTTATTTTTAA
*
13551881 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTTGATTTTCAAGAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTG-AAATTTTGATTTTCAAGGAAAA
*
13551946 TTGATACTTTCAATTTTTCCTCAAAAATTTTTTTTT
65 TTGATACTTTCAATTTTTCCTCAAAAATCTTTTTTT
13551982 TTTGAAACTT
Statistics
Matches: 203, Mismatches: 10, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
115 7 0.03
116 32 0.16
117 20 0.10
118 89 0.44
119 55 0.27
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (116 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAATTTTGATTTTCAAGGAAAAT
TGATACTTTCAATTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAA
Found at i:13552042 original size:18 final size:18
Alignment explanation
Indices: 13552021--13552060 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
13552011 ATAGAATAAC
*
13552021 AAAAAAATAAAGAAAATT
1 AAAAAAATAAAGAAAAGT
13552039 AAAAAAATAAAGAAAAGT
1 AAAAAAATAAAGAAAAGT
13552057 AAAA
1 AAAA
13552061 CAAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (18 bp):
AAAAAAATAAAGAAAAGT
Found at i:13552045 original size:9 final size:8
Alignment explanation
Indices: 13552021--13552158 Score: 55
Period size: 8 Copynumber: 15.9 Consensus size: 8
13552011 ATAGAATAAC
13552021 AAAAAAAT
1 AAAAAAAT
13552029 AAAGAAAATT
1 AAA-AAAA-T
13552039 AAAAAAAT
1 AAAAAAAT
13552047 AAAGAAAAGT
1 AAA-AAAA-T
13552057 AAAACAAA-
1 AAAA-AAAT
*
13552065 AATAAAGAT
1 AA-AAAAAT
13552074 AAAATAAAGAT
1 -AAA-AAA-AT
13552085 AAAAAGAAT
1 AAAAA-AAT
**
13552094 -ATTAAAT
1 AAAAAAAT
**
13552101 AAATCTAAT
1 AAA-AAAAT
*
13552110 CAAATAAAT
1 -AAAAAAAT
13552119 AAAAAAAT
1 AAAAAAAT
*
13552127 AAAAAAAC
1 AAAAAAAT
* *
13552135 AAATAAAC
1 AAAAAAAT
*
13552143 AAATAAAT
1 AAAAAAAT
13552151 GAAAAAAA
1 -AAAAAAA
13552159 AAATGGAATG
Statistics
Matches: 101, Mismatches: 14, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
7 3 0.03
8 42 0.42
9 32 0.32
10 22 0.22
11 2 0.02
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (8 bp):
AAAAAAAT
Found at i:13552141 original size:24 final size:25
Alignment explanation
Indices: 13552110--13552162 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
13552100 TAAATCTAAT
*
13552110 CAAATAAATAAAAAAAT-AAAAAAA
1 CAAATAAACAAAAAAATGAAAAAAA
*
13552134 CAAATAAACAAATAAATGAAAAAAA
1 CAAATAAACAAAAAAATGAAAAAAA
13552159 -AAAT
1 CAAAT
13552163 GGAATGGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.13
Consensus pattern (25 bp):
CAAATAAACAAAAAAATGAAAAAAA
Found at i:13552163 original size:12 final size:11
Alignment explanation
Indices: 13552111--13552162 Score: 59
Period size: 12 Copynumber: 4.4 Consensus size: 11
13552101 AAATCTAATC
13552111 AAATAAATAAAA
1 AAATAAA-AAAA
13552123 AAATAAAAAAA
1 AAATAAAAAAA
*
13552134 CAAATAAACAAAT
1 -AAATAAA-AAAA
13552147 AAATGAAAAAAA
1 AAAT-AAAAAAA
13552159 AAAT
1 AAAT
13552163 GGAATGGCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 4 0.11
12 25 0.71
13 6 0.17
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (11 bp):
AAATAAAAAAA
Found at i:13553170 original size:8 final size:8
Alignment explanation
Indices: 13553151--13553243 Score: 50
Period size: 8 Copynumber: 11.8 Consensus size: 8
13553141 TACAAAAAAA
13553151 ATAT-AAT
1 ATATAAAT
13553158 A-ATAAAT
1 ATATAAAT
*
13553165 ATATAACT
1 ATATAAAT
13553173 ATATAAAT
1 ATATAAAT
*
13553181 A-A-AATAC
1 ATATAA-AT
13553188 ATATAAAT
1 ATATAAAT
* *
13553196 CTAATCTAAT
1 AT-AT-AAAT
*
13553206 AAATAAAT
1 ATATAAAT
*
13553214 AAATAAAT
1 ATATAAAT
*
13553222 ATATACAT
1 ATATAAAT
*
13553230 ATATTAAT
1 ATATAAAT
*
13553238 ACATAA
1 ATATAA
13553244 TAATAATAAA
Statistics
Matches: 64, Mismatches: 15, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
6 4 0.06
7 8 0.12
8 43 0.67
9 6 0.09
10 3 0.05
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (8 bp):
ATATAAAT
Found at i:13554666 original size:15 final size:16
Alignment explanation
Indices: 13554648--13554700 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
13554638 ATTTTTTCCA
13554648 TTTTTTCTTC-TTTCT
1 TTTTTTCTTCATTTCT
13554663 TTTTTT-TTCCATTT-T
1 TTTTTTCTT-CATTTCT
*
13554678 TTTTTTCATCATTTTCT
1 TTTTTTCTTCA-TTTCT
13554695 TTTTTT
1 TTTTTT
13554701 TCTCATTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 2 0.06
15 16 0.50
16 7 0.22
17 7 0.22
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTCTTCATTTCT
Found at i:13554709 original size:15 final size:16
Alignment explanation
Indices: 13554648--13554710 Score: 53
Period size: 15 Copynumber: 4.0 Consensus size: 16
13554638 ATTTTTTCCA
* *
13554648 TTTTTTCTTCTTTCTT
1 TTTTTTCATCATTCTT
13554664 TTTTTT--TCCATT-TT
1 TTTTTTCAT-CATTCTT
13554678 TTTTTTCATCATTTTCTT
1 TTTTTTCATCA--TTCTT
13554696 TTTTTTC-TCATTCTT
1 TTTTTTCATCATTCTT
13554711 CACCTATTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
14 9 0.22
15 10 0.25
16 7 0.17
17 5 0.12
18 9 0.22
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTCATCATTCTT
Found at i:13554929 original size:21 final size:21
Alignment explanation
Indices: 13554886--13554929 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13554876 AGGGTCATAA
*
13554886 AAAAATGGATATAATAGGCTC
1 AAAAATGGATATAAAAGGCTC
*
13554907 AAAAATGG-TATTAAAAGGTTC
1 AAAAATGGATA-TAAAAGGCTC
13554928 AA
1 AA
13554930 GACCGAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (21 bp):
AAAAATGGATATAAAAGGCTC
Found at i:13558674 original size:58 final size:57
Alignment explanation
Indices: 13558609--13558881 Score: 374
Period size: 58 Copynumber: 4.7 Consensus size: 57
13558599 TTGTGTAGGA
13558609 AAAATTGATACTTTCAACTTTTTCCTAAAAATTATTTTTTTGAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCCTAAAAA-TATTTTTTTGAAATTTATTTTTAAGG
* *
13558667 AAAATTGATACTTTCAACTTTTTTCC-AAAAATATTTTTTTGAAACTTATTTCTAAGG
1 AAAATTGATACTTTCAAC-TTTTTCCTAAAAATATTTTTTTGAAATTTATTTTTAAGG
* *
13558724 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTTCCTAAAAATA-TTTTTTTG-AAATTTATTTTTAAGG
* *
13558783 AAAATTGATACTTTCAAC-TTTTCCTTAAAAATATTTTTTGGAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTTCC-TAAAAATATTTTTTTGAAA-TTT-ATTTTTAAGG
*
13558842 -AAATTGATACTTTCAAC-TTTTCCTCAAAAATCCTTTTTTT
1 AAAATTGATACTTTCAACTTTTTCCT-AAAAAT-ATTTTTTT
13558882 TTTGAAACTT
Statistics
Matches: 195, Mismatches: 11, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
56 7 0.04
57 53 0.27
58 76 0.39
59 59 0.30
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTGAAATTTATTTTTAAGG
Found at i:13558697 original size:27 final size:27
Alignment explanation
Indices: 13558667--13558755 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
13558657 ATTTTTAAGG
13558667 AAAATTGATACTTTCAACTTTTTTCCA
1 AAAATTGATACTTTCAACTTTTTTCCA
** * * *
13558694 AAAA-T-ATTTTTTTGAAACTTATTTCTAA
1 AAAATTGA-TACTTT-CAACTTTTTTC-CA
*
13558722 GGAAAATTGATACTTTCAACTTTTTCCCA
1 --AAAATTGATACTTTCAACTTTTTTCCA
13558751 AAAAT
1 AAAAT
13558756 ATTTTTTTTG
Statistics
Matches: 44, Mismatches: 11, Indels: 14
0.64 0.16 0.20
Matches are distributed among these distances:
25 1 0.02
26 5 0.11
27 18 0.41
28 1 0.02
29 1 0.02
30 12 0.27
31 5 0.11
32 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTTTCCA
Found at i:13558942 original size:10 final size:9
Alignment explanation
Indices: 13558918--13559040 Score: 50
Period size: 9 Copynumber: 12.2 Consensus size: 9
13558908 AAAATAGAAT
13558918 AATAAAAAA
1 AATAAAAAA
13558927 AATAAAGAAA
1 AATAAA-AAA
* *
13558937 AGTAAAACA
1 AATAAAAAA
*
13558946 AA-AATAAA
1 AATAAAAAA
*
13558954 GATAAAAAGA
1 AATAAAAA-A
13558964 ATATTAAATAAA
1 A-A-TAAA-AAA
* *
13558976 TCTAATCAAATA
1 ---AATAAAAAA
13558988 AATAAAAAA
1 AATAAAAAA
*
13558997 ATAAAAAAATA
1 A-ATAAAAA-A
13559008 AATAAACAAATA
1 AAT-AA-AAA-A
13559020 AATGAAAAAA
1 AAT-AAAAAA
13559030 AATAAAAAA
1 AATAAAAAA
13559039 AA
1 AA
13559041 ACCTGGAGCG
Statistics
Matches: 86, Mismatches: 15, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
8 5 0.06
9 29 0.34
10 20 0.23
11 8 0.09
12 17 0.20
13 5 0.06
14 1 0.01
15 1 0.01
ACGTcount: A:0.76, C:0.03, G:0.04, T:0.16
Consensus pattern (9 bp):
AATAAAAAA
Found at i:13558990 original size:4 final size:4
Alignment explanation
Indices: 13558968--13559035 Score: 59
Period size: 4 Copynumber: 17.0 Consensus size: 4
13558958 AAAAGAATAT
* * * *
13558968 TAAA TAAA TCTAA TCAAA TAAA TAAA AAAA TAAA AAAA TAAA TAAA CAAA
1 TAAA TAAA T-AAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
*
13559018 TAAA TGAA -AAA -AAA TAAA
1 TAAA TAAA TAAA TAAA TAAA
13559036 AAAAAACCTG
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
3 5 0.10
4 40 0.77
5 7 0.13
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.19
Consensus pattern (4 bp):
TAAA
Found at i:13559000 original size:12 final size:12
Alignment explanation
Indices: 13558983--13559041 Score: 68
Period size: 12 Copynumber: 4.8 Consensus size: 12
13558973 AAATCTAATC
13558983 AAATAAATAAAA-
1 AAATAAA-AAAAT
13558995 AAATAAAAAAAT
1 AAATAAAAAAAT
*
13559007 AAATAAACAAAT
1 AAATAAAAAAAT
13559019 AAATGAAAAAAAAT
1 AAAT--AAAAAAAT
13559033 AAA-AAAAAA
1 AAATAAAAAA
13559042 CCTGGAGCGG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
11 10 0.24
12 22 0.52
14 10 0.24
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.14
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:13559582 original size:26 final size:24
Alignment explanation
Indices: 13559544--13559593 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
13559534 AATCTGGAAA
*
13559544 TTTCCCAGAAATTTCCAAAACAATT
1 TTTCCCAAAAATTTCCAAAA-AATT
*
13559569 TTTCGCCAAAAATTTCTAAAAAATT
1 TTTC-CCAAAAATTTCCAAAAAATT
13559594 ATTTTCGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.34
Consensus pattern (24 bp):
TTTCCCAAAAATTTCCAAAAAATT
Found at i:13560165 original size:16 final size:15
Alignment explanation
Indices: 13560146--13560184 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
13560136 ATACATATAT
*
13560146 TAATACATAATAATAA
1 TAATAAATAATAA-AA
13560162 TAATAAATAATAAAA
1 TAATAAATAATAAAA
13560177 TACATAAA
1 TA-ATAAA
13560185 ATACAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (15 bp):
TAATAAATAATAAAA
Found at i:13560166 original size:9 final size:10
Alignment explanation
Indices: 13560131--13560189 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 10
13560121 CTAATAAATA
13560131 AATATATACAT
1 AATA-ATACAT
13560142 ATATTAATACAT
1 A-A-TAATACAT
13560154 AATAATA-AT
1 AATAATACAT
13560163 AATAAATA-AT
1 AAT-AATACAT
13560173 AA-AATACAT
1 AATAATACAT
13560182 AA-AATACA
1 AATAATACA
13560190 AAAGAAAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
8 4 0.09
9 15 0.34
10 13 0.30
11 2 0.05
12 8 0.18
13 2 0.05
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.31
Consensus pattern (10 bp):
AATAATACAT
Found at i:13560820 original size:41 final size:41
Alignment explanation
Indices: 13560775--13560856 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
13560765 AGGATTATGG
*
13560775 TTGCTGAGTCAAATCATTTGAGTGATTAGGAAAATGAAAGT
1 TTGCTAAGTCAAATCATTTGAGTGATTAGGAAAATGAAAGT
* *
13560816 TTGCTAAGTCAAATCATTTGAGTGATTAGGGACATGAAAGT
1 TTGCTAAGTCAAATCATTTGAGTGATTAGGAAAATGAAAGT
13560857 ATTCAAAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (41 bp):
TTGCTAAGTCAAATCATTTGAGTGATTAGGAAAATGAAAGT
Found at i:13563879 original size:26 final size:26
Alignment explanation
Indices: 13563832--13563882 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
13563822 TATATTTTTG
***
13563832 AAATATAAAATAAAAGGGATTAAATT
1 AAATATAAAATAAAACCCATTAAATT
*
13563858 AAATATCAAATAAAACCCATTAAAT
1 AAATATAAAATAAAACCCATTAAAT
13563883 CCAATCATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.25
Consensus pattern (26 bp):
AAATATAAAATAAAACCCATTAAATT
Found at i:13565047 original size:15 final size:15
Alignment explanation
Indices: 13565011--13565048 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
13565001 TAAAGGTTAT
*
13565011 AGTTTTAGATTTTGG
1 AGTTTTGGATTTTGG
13565026 AGTTTTGGATTTTGG
1 AGTTTTGGATTTTGG
*
13565041 GGTTTTGG
1 AGTTTTGG
13565049 TTTGAGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.34, T:0.53
Consensus pattern (15 bp):
AGTTTTGGATTTTGG
Found at i:13565120 original size:14 final size:14
Alignment explanation
Indices: 13565094--13565149 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
13565084 GTTTAGAGAG
*
13565094 TTTTAAGGCTTGAA
1 TTTTAAGGTTTGAA
*
13565108 TTTTAGGGTTTGAAAA
1 TTTTAAGGTTTG--AA
* *
13565124 GTTTAAGGTTTTAA
1 TTTTAAGGTTTGAA
13565138 TTTTAAGGTTTG
1 TTTTAAGGTTTG
13565150 GGGATTAGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
14 22 0.67
16 11 0.33
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.48
Consensus pattern (14 bp):
TTTTAAGGTTTGAA
Found at i:13565131 original size:30 final size:32
Alignment explanation
Indices: 13565077--13565149 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 32
13565067 TAGGATTTGG
*
13565077 TTTTAGGGTTT-AGAGAGTTTTAAGGCTTGAA
1 TTTTAGGGTTTGAGAAAGTTTTAAGGCTTGAA
* *
13565108 TTTTAGGGTTTGA-AAAG-TTTAAGGTTTTAA
1 TTTTAGGGTTTGAGAAAGTTTTAAGGCTTGAA
*
13565138 TTTTAAGGTTTG
1 TTTTAGGGTTTG
13565150 GGGATTAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 22 0.59
31 14 0.38
32 1 0.03
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.47
Consensus pattern (32 bp):
TTTTAGGGTTTGAGAAAGTTTTAAGGCTTGAA
Found at i:13565375 original size:3 final size:3
Alignment explanation
Indices: 13565369--13565429 Score: 88
Period size: 3 Copynumber: 20.3 Consensus size: 3
13565359 TTTATAAAAC
* *
13565369 TTA TTA TTA TTA CTTA TCA AT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13565414 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
13565430 GTTTTTTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
2 1 0.02
3 48 0.92
4 3 0.06
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:13568310 original size:25 final size:25
Alignment explanation
Indices: 13568278--13568331 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
13568268 AAAATTTTTT
*
13568278 ATAATTTTTTT-AATTATAATTATA
1 ATAATTTTTTTAAATCATAATTATA
13568302 ATAATTTTTTTAAATCATAATTATA
1 ATAATTTTTTTAAATCATAATTATA
13568327 ATAAT
1 ATAAT
13568332 AATAATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 11 0.39
25 17 0.61
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
ATAATTTTTTTAAATCATAATTATA
Found at i:13573958 original size:27 final size:27
Alignment explanation
Indices: 13573927--13574016 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 27
13573917 TTTGTGCAGG
13573927 AAAAATTGATACTTTCAACTTTTCTCA
1 AAAAATTGATACTTTCAACTTTTCTCA
* * *
13573954 AAAAA-T-ATTCTTTTGAAACTTTAATTTCGA
1 AAAAATTGATAC-TTT-CAACTTT--TCTC-A
13573984 GAAAAATTGATACTTTCAACTTTTCCTCA
1 -AAAAATTGATACTTTCAACTTTT-CTCA
13574013 AAAA
1 AAAA
13574017 TTTATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
25 3 0.06
26 4 0.08
27 11 0.23
28 4 0.08
29 5 0.10
30 3 0.06
31 11 0.23
32 4 0.08
33 3 0.06
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.39
Consensus pattern (27 bp):
AAAAATTGATACTTTCAACTTTTCTCA
Found at i:13574048 original size:17 final size:16
Alignment explanation
Indices: 13574013--13574051 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
13574003 CTTTTCCTCA
**
13574013 AAAATTTATTTTTTTG
1 AAAATTTATTTTTAGG
13574029 AAAATTTATTTTTAAGG
1 AAAATTTATTTTT-AGG
13574046 AAAATT
1 AAAATT
13574052 AATACTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (16 bp):
AAAATTTATTTTTAGG
Found at i:13574063 original size:118 final size:114
Alignment explanation
Indices: 13573928--13574320 Score: 520
Period size: 118 Copynumber: 3.3 Consensus size: 114
13573918 TTGTGCAGGA
* * *
13573928 AAAATTGATACTTTCAACTTTTCTCAAAAAATATTCTTTTGAAACTTTAATTTCGAGAAAAATTG
1 AAAATTGATACTTTCAACTTTTCTC-AAAAATATTTTTTTGAAACTTTATTTTCGAGGAAAATTG
*
13573993 ATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTGAAAATTTATTTTTAAGG
65 ATACTTTCAACTTTTCC-CAAAAA--TATTTTTTGGAAAATTTATTTTTAAGG
* *
13574046 AAAATTAATACTTTCAACTTTTTCTCAAAAATA-TTATTTGAAAACTTTGATTTTCGAGGAAAAT
1 AAAATTGATACTTTCAAC-TTTTCTCAAAAATATTTTTTTG-AAACTTT-ATTTTCGAGGAAAAT
* * **
13574110 TGATACGTTCAACTTTTCCCAAAAAATATTTTTTGGAAACTTTGATTTTCGAGG
63 TGATACTTTCAACTTTTCCC-AAAAATATTTTTTGGAAAATTT-ATTTTTAAGG
* * **
13574164 AAAATTGATACATTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGGAAAATT
1 AAAATTGATACTTTCAACTTTT-CTCAAAAATA-TTTTTTTGAAACTTTATTTTCGAGGAAAATT
13574229 GATACTTTCAACTTTTTCCCAAAAATA-TTTTTGGAAAAATTTATTTTTAAGG
64 GATACTTTCAAC-TTTTCCCAAAAATATTTTTTGG-AAAATTTATTTTTAAGG
13574281 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTCT-CAAAAATATTTTTTT
13574321 TTGGATTTTA
Statistics
Matches: 243, Mismatches: 21, Indels: 24
0.84 0.07 0.08
Matches are distributed among these distances:
116 9 0.04
117 68 0.28
118 104 0.43
119 56 0.23
120 6 0.02
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (114 bp):
AAAATTGATACTTTCAACTTTTCTCAAAAATATTTTTTTGAAACTTTATTTTCGAGGAAAATTGA
TACTTTCAACTTTTCCCAAAAATATTTTTTGGAAAATTTATTTTTAAGG
Found at i:13574126 original size:59 final size:58
Alignment explanation
Indices: 13573928--13574319 Score: 472
Period size: 59 Copynumber: 6.7 Consensus size: 58
13573918 TTGTGCAGGA
* * *
13573928 AAAATTGATACTTTCAAC-TTTTCTCAAAAAATATTCTTTTG-AAACTTTAATTTCGAGA
1 AAAATTGATACTTTCAACTTTTTCTC-AAAAATATT-TTTTGAAAACTTTATTTTCAAGG
* *
13573986 AAAATTGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTGAAAA-TTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAA--TA-TTTTTTGAAAACTTTATTTTCAAGG
* * *
13574046 AAAATTAATACTTTCAACTTTTTCTCAAAAATATTATTTGAAAACTTTGATTTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAACTTT-ATTTTCAAGG
* * * *
13574105 AAAATTGATACGTTCAAC-TTTTCCCAAAAAATATTTTTTGGAAACTTTGATTTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCTC-AAAAATATTTTTTGAAAACTTT-ATTTTCAAGG
* * *
13574164 AAAATTGATACATTCAACTTTTCCTCAAAAATATTTTTTTTGAAAA-TTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATA--TTTTTTGAAAACTTTATTTTCAAGG
* * * *
13574223 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTGGAAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAACTTTATTTTCAAGG
13574281 AAAATTGATACTTTCAAC-TTTTCTCCAAAAATATTTTTT
1 AAAATTGATACTTTCAACTTTTTCT-CAAAAATATTTTTT
13574320 TTTGGATTTT
Statistics
Matches: 294, Mismatches: 27, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
57 25 0.09
58 78 0.27
59 123 0.42
60 53 0.18
61 15 0.05
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAACTTTATTTTCAAGG
Found at i:13574204 original size:177 final size:175
Alignment explanation
Indices: 13573928--13574319 Score: 610
Period size: 177 Copynumber: 2.2 Consensus size: 175
13573918 TTGTGCAGGA
*
13573928 AAAATTGATACTTTCAACTTTTCTCAAAAAATATTCTTTTGAAACTTTAATTTCGAGAAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCAAAAAATATT-TTTTGAAACTTTAATTTCGAGAAAAATTG
* *
13573993 ATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTGAAAATTTATTTTTAAGGAAAATTAATACT
65 ATACATTCAACTTTTCCTCAAAAATATATTTTTTTGAAAATTTATTTTTAAGGAAAATTAATACT
* * *
13574058 TTCAACTTTTTCTCAAAAATATTATTT-GAAAACTTTGATTTTCGAGG
130 TTCAACTTTTTCCCAAAAATATT-TTTGGAAAAATTT-ATTTTCAAGG
* * *
13574105 AAAATTGATACGTTCAACTTTTCCCAAAAAATATTTTTTGGAAACTTTGATTTTCGAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTT-GAAACTTT-AATTTCGAGAAAAATT
*
13574170 GATACATTCAACTTTTCCTCAAAAATAT-TTTTTTTGAAAATTTATTTTTAAGGAAAATTGATAC
64 GATACATTCAACTTTTCCTCAAAAATATATTTTTTTGAAAATTTATTTTTAAGGAAAATTAATAC
*
13574234 TTTCAACTTTTTCCCAAAAATATTTTTGGAAAAATTTATTTTTAAGG
129 TTTCAACTTTTTCCCAAAAATATTTTTGGAAAAATTTATTTTCAAGG
13574281 AAAATTGATACTTTCAACTTTTCTCC-AAAAATATTTTTT
1 AAAATTGATACTTTCAACTTTTC-CCAAAAAATATTTTTT
13574320 TTTGGATTTT
Statistics
Matches: 199, Mismatches: 12, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
176 50 0.25
177 109 0.55
178 40 0.20
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (175 bp):
AAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTGAAACTTTAATTTCGAGAAAAATTGA
TACATTCAACTTTTCCTCAAAAATATATTTTTTTGAAAATTTATTTTTAAGGAAAATTAATACTT
TCAACTTTTTCCCAAAAATATTTTTGGAAAAATTTATTTTCAAGG
Found at i:13574346 original size:5 final size:5
Alignment explanation
Indices: 13574338--13574443 Score: 58
Period size: 5 Copynumber: 20.6 Consensus size: 5
13574328 TTATTTAAAG
* *
13574338 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAGAAAT AAAAA AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -A-AAAT AAAAT AAAAT
* * *
13574384 -AAAT AAAGA- AAAGT AAAACA AAAAT AAAAAT AAAAT AAAGAT AAAAG
1 AAAAT AAA-AT AAAAT AAAA-T AAAAT -AAAAT AAAAT AAA-AT AAAAT
* *
13574431 AACAT TAAAT AAA
1 AAAAT AAAAT AAA
13574444 CCTAATCTAA
Statistics
Matches: 76, Mismatches: 14, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
3 3 0.04
4 4 0.05
5 47 0.62
6 17 0.22
7 2 0.03
8 3 0.04
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:13574374 original size:23 final size:22
Alignment explanation
Indices: 13574348--13574422 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
13574338 AAAATAAAAT
**
13574348 AATAAAACAAAATAAAAGTGAGA
1 AATAAAACAAAATAAAAAAGA-A
*
13574371 AATAAAAAAAAATAAATAAAGAA
1 AATAAAACAAAATAAA-AAAGAA
*
13574394 AAGTAAAACAAAA-ATAAAAATAA
1 AA-TAAAACAAAATA-AAAAAGAA
13574417 AATAAA
1 AATAAA
13574423 GATAAAAGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.09
23 26 0.59
24 14 0.32
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (22 bp):
AATAAAACAAAATAAAAAAGAA
Found at i:13574412 original size:17 final size:17
Alignment explanation
Indices: 13574392--13574430 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
13574382 ATAAATAAAG
13574392 AAAAGTAAAACAAAAAT
1 AAAAGTAAAACAAAAAT
* * *
13574409 AAAAATAAAATAAAGAT
1 AAAAGTAAAACAAAAAT
13574426 AAAAG
1 AAAAG
13574431 AACATTAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (17 bp):
AAAAGTAAAACAAAAAT
Found at i:13574427 original size:11 final size:11
Alignment explanation
Indices: 13574338--13574429 Score: 62
Period size: 11 Copynumber: 7.8 Consensus size: 11
13574328 TTATTTAAAG
13574338 AAAATAAAATAA
1 AAAATAAAAT-A
*
13574350 TAAAACAAAATA
1 -AAAATAAAATA
*
13574362 AAAGTGAGAAATA
1 AAAAT-A-AAATA
13574375 AAAA-AAAATAA
1 AAAATAAAAT-A
*
13574386 ATAAAGAAAAGTA
1 A-AAATAAAA-TA
13574399 AAACA-AAAATA
1 AAA-ATAAAATA
13574410 AAAATAAAATA
1 AAAATAAAATA
*
13574421 AAGATAAAA
1 AAAATAAAA
13574430 GAACATTAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
10 5 0.08
11 25 0.38
12 11 0.17
13 24 0.36
14 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:13574429 original size:23 final size:21
Alignment explanation
Indices: 13574338--13574422 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 21
13574328 TTATTTAAAG
13574338 AAAATAAAATAATAAAACAAAATA
1 AAAATAAAAT-A-AAAA-AAAATA
*
13574362 AAAGTGAGAAATAAAAAAAAATAA
1 AAAAT-A-AAATAAAAAAAAAT-A
*
13574386 ATAAAGAAAAGTAAAACAAAAATA
1 A-AAATAAAA-TAAAA-AAAAATA
13574410 AAAATAAAATAAA
1 AAAATAAAATAAA
13574423 GATAAAAGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
22 4 0.08
23 15 0.29
24 18 0.35
25 10 0.20
26 4 0.08
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (21 bp):
AAAATAAAATAAAAAAAAATA
Found at i:13575350 original size:22 final size:21
Alignment explanation
Indices: 13575322--13575372 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
13575312 AAAAAAAAGG
*
13575322 AAAAAAAATCTGATAAACGAA
1 AAAAAAAATCAGATAAACGAA
13575343 AAAAAAAATCAGATAAACGAA
1 AAAAAAAATCAGATAAACGAA
13575364 AAAGAAAAA
1 AAA-AAAAA
13575373 AAATATAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.73, C:0.08, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAAAAAATCAGATAAACGAA
Found at i:13575406 original size:21 final size:20
Alignment explanation
Indices: 13575391--13575461 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
13575381 CAGATAATTA
13575391 AAAATAATAATAAGATAAAT
1 AAAATAATAATAAGATAAAT
*
13575411 AAAA-AATATTACAAGATAAAT
1 AAAATAATA--ATAAGATAAAT
*
13575432 AAAACAATAATAA-ATAAATT
1 AAAATAATAATAAGATAAA-T
*
13575452 ATAATAATAA
1 AAAATAATAA
13575462 ATATATAACT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 9 0.21
20 16 0.37
21 14 0.33
22 4 0.09
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAATAATAATAAGATAAAT
Found at i:13575441 original size:41 final size:40
Alignment explanation
Indices: 13575370--13575450 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 40
13575360 CGAAAAAGAA
* *
13575370 AAAAAATATAACAGATAATTAAAAATAATAATAAGATAAAT
1 AAAAAATATAACAGATAAATAAAAACAATAATAA-ATAAAT
*
13575411 AAAAAATATTACAAGATAAAT-AAAACAATAATAAATAAAT
1 AAAAAATATAAC-AGATAAATAAAAACAATAATAAATAAAT
13575451 TATAATAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 6 0.17
41 23 0.64
42 7 0.19
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (40 bp):
AAAAAATATAACAGATAAATAAAAACAATAATAAATAAAT
Found at i:13575455 original size:14 final size:15
Alignment explanation
Indices: 13575438--13575480 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
13575428 AAATAAAACA
13575438 ATAATAAATAAAT-T
1 ATAATAAATAAATAT
13575452 ATAAT-AATAAATAT
1 ATAATAAATAAATAT
*
13575466 ATAACTAGATAAATA
1 ATAA-TAAATAAATA
13575481 AAATACATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 7 0.28
14 10 0.40
15 1 0.04
16 7 0.28
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
ATAATAAATAAATAT
Found at i:13575477 original size:48 final size:42
Alignment explanation
Indices: 13575370--13575483 Score: 124
Period size: 48 Copynumber: 2.6 Consensus size: 42
13575360 CGAAAAAGAA
*
13575370 AAAAAATATAACAGAT-AATTAAAAATAATAATAAGATAAAT
1 AAAAAATATAACAGATAAATAAAAAATAATAATAAGATAAAT
*
13575411 AAAAAATATTACAAGATAAATAAAACAATAATAAATAA-ATTATAAT
1 AAAAAATATAAC-AGATAAATAAAA-AATAAT-AATAAGA-TA-AAT
13575457 AATAAATATATAACTAGATAAATAAAA
1 AA-AAA-ATATAAC-AGATAAATAAAA
13575484 TACATATATA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
41 11 0.18
42 4 0.07
43 6 0.10
44 7 0.11
45 7 0.11
46 5 0.08
47 3 0.05
48 18 0.30
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (42 bp):
AAAAAATATAACAGATAAATAAAAAATAATAATAAGATAAAT
Found at i:13575485 original size:21 final size:20
Alignment explanation
Indices: 13575370--13575483 Score: 77
Period size: 21 Copynumber: 5.2 Consensus size: 20
13575360 CGAAAAAGAA
13575370 AAAAAATATAACAGAT-AAT
1 AAAAAATATAACAGATAAAT
* *
13575389 TAAAAATAATAATAAGATAAAT
1 AAAAAAT-ATAA-CAGATAAAT
*
13575411 AAAAAATATTACAAGATAAAT
1 AAAAAATATAAC-AGATAAAT
* *
13575432 AAAACAATAATAAATAAATTATAAT
1 AAAA-AAT-AT-AACAGA-TA-AAT
13575457 AATAAATATATAACTAGATAAAT
1 AA-AAA-ATATAAC-AGATAAAT
13575480 AAAA
1 AAAA
13575484 TACATATATA
Statistics
Matches: 73, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
19 6 0.08
20 4 0.05
21 19 0.26
22 14 0.19
23 9 0.12
24 7 0.10
25 10 0.14
26 4 0.05
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (20 bp):
AAAAAATATAACAGATAAAT
Found at i:13575485 original size:25 final size:24
Alignment explanation
Indices: 13575368--13575493 Score: 76
Period size: 22 Copynumber: 5.5 Consensus size: 24
13575358 AACGAAAAAG
13575368 AAAAAAA-ATATAAC-AGAT-AAT
1 AAAAAAATATATAACTAGATAAAT
*
13575389 -TAAAAATA-ATAA-TAAGATAAAT
1 AAAAAAATATATAACT-AGATAAAT
*
13575411 -AAAAAATAT-T-ACAAGATAAAT
1 AAAAAAATATATAACTAGATAAAT
* * *
13575432 AAAACAATA-ATAAATAAATTATAAT
1 AAAAAAATATATAACTAGA-TA-AAT
*
13575457 -AATAAATATATAACTAGATAAAT
1 AAAAAAATATATAACTAGATAAAT
*
13575480 AAAATACATATATA
1 AAAA-AAATATATA
13575494 GATATTAACA
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
20 9 0.12
21 14 0.18
22 19 0.24
23 6 0.08
24 12 0.15
25 18 0.23
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (24 bp):
AAAAAAATATATAACTAGATAAAT
Found at i:13585192 original size:18 final size:17
Alignment explanation
Indices: 13585161--13585204 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
13585151 TATAAAATAC
*
13585161 GAAATATAATAAAAAATAT
1 GAAATACAA-AAAAAA-AT
*
13585180 GAATTACAAAAAAAAAT
1 GAAATACAAAAAAAAAT
13585197 GAAATACA
1 GAAATACA
13585205 TAATAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 9 0.41
18 6 0.27
19 7 0.32
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (17 bp):
GAAATACAAAAAAAAAT
Found at i:13587162 original size:192 final size:193
Alignment explanation
Indices: 13586912--13587260 Score: 628
Period size: 192 Copynumber: 1.8 Consensus size: 193
13586902 CTTAGACCTC
*
13586912 CCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGA
1 CCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTTTAAGAAATCTATAGGTGAGAAAGA
*
13586977 GTTCTTTTAATATTACCAACGTACTGAAATATGTTAAGAATTATTTCAATAAAAAGGTTTTAATT
66 GTTCTTTTAATATTACCAACGTACTGAAACATGTTAAGAATTATTTCAATAAAAAGGTTTTAATT
13587042 TATTTTT-TCGAGAATAAATTTTTTTAACATGACATTGTCTTACGAAAAATAAATTCGAGTCT
131 TATTTTTCTCGAGAATAAATTTTTTTAACATGACATTGTCTTACGAAAAATAAATTCGAGTCT
13587104 CCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTTTAAGAAATCTATAGGTGAGAAAGA
1 CCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTTTAAGAAATCTATAGGTGAGAAAGA
* * * *
13587169 GTTCTTTTAATGTTACCAACGTACTGAAACATTTTAAGAATTATTTCAATAAAAATGTTTTGATT
66 GTTCTTTTAATATTACCAACGTACTGAAACATGTTAAGAATTATTTCAATAAAAAGGTTTTAATT
*
13587234 TATTTTTCTCGAGAATAATTTTTTTTA
131 TATTTTTCTCGAGAATAAATTTTTTTA
13587261 TATAAATAAA
Statistics
Matches: 149, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
192 131 0.88
193 18 0.12
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (193 bp):
CCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTTTAAGAAATCTATAGGTGAGAAAGA
GTTCTTTTAATATTACCAACGTACTGAAACATGTTAAGAATTATTTCAATAAAAAGGTTTTAATT
TATTTTTCTCGAGAATAAATTTTTTTAACATGACATTGTCTTACGAAAAATAAATTCGAGTCT
Found at i:13588345 original size:43 final size:43
Alignment explanation
Indices: 13588284--13588369 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
13588274 ATTCTGTAAG
* *
13588284 AAATAAAAAAGGCTCACATATAACAG-GTATTTATCCCCCAAAC
1 AAATAAAAAAAGCTCACATATAAC-GCATATTTATCCCCCAAAC
13588327 AAATAAAAAAAGCTCACATATAACGCATATTTATCCCCCAAAC
1 AAATAAAAAAAGCTCACATATAACGCATATTTATCCCCCAAAC
13588370 TGTTTTCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 1 0.03
43 39 0.98
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.21
Consensus pattern (43 bp):
AAATAAAAAAAGCTCACATATAACGCATATTTATCCCCCAAAC
Found at i:13589627 original size:3 final size:3
Alignment explanation
Indices: 13589619--13589664 Score: 65
Period size: 3 Copynumber: 14.3 Consensus size: 3
13589609 AGATGTAATT
13589619 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTTA TTA GTTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA -TTA T
13589665 CAATTCATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 31 0.76
4 10 0.24
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13589986 original size:21 final size:22
Alignment explanation
Indices: 13589949--13590029 Score: 69
Period size: 22 Copynumber: 3.6 Consensus size: 22
13589939 TTTTGGTTCG
*
13589949 GGTTTTAAGGGTTTGAAGGTTT-
1 GGTTTT-AGGATTTGAAGGTTTA
13589971 GGTTTTAGGATTTGAAAGGTTTA
1 GGTTTTAGGATTTG-AAGGTTTA
*
13589994 GGGTTTT--GATTTTAAGGTTTAAA
1 -GGTTTTAGGATTTGAAGGTTT--A
*
13590017 GGTTTTAAGATTT
1 GGTTTTAGGATTT
13590030 TGATTTTAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
21 14 0.28
22 24 0.48
23 1 0.02
24 11 0.22
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (22 bp):
GGTTTTAGGATTTGAAGGTTTA
Found at i:13590038 original size:60 final size:60
Alignment explanation
Indices: 13589950--13590254 Score: 180
Period size: 60 Copynumber: 5.1 Consensus size: 60
13589940 TTTGGTTCGG
* * *
13589950 GTTTTAAGGGTTT-GAAGGTTTGGTTTTAGGATTTGAAA-GGTTTAGGGTTTTGATTTTA-A
1 GTTTAAAGGGTTTAG-AGTTTTGATTTTAGGATTT-AAAGGGTTTAGGGTTTTGATTTTAGA
* * **
13590009 GGTTTAAAGGTTTTA-AGATTTTGATTTTAGGATTCAAAGGGTTTAGTATTTTGATTTTAGA
1 -GTTTAAAGGGTTTAGAG-TTTTGATTTTAGGATTTAAAGGGTTTAGGGTTTTGATTTTAGA
** * * **
13590070 GTTTGGAGGGTTTAGAGTTTTGATTTTAGAATTTAAAGGGTTTTAGGGTTTAAAGGGTTTATG-
1 GTTTAAAGGGTTTAGAGTTTTGATTTTAGGATTTAAAGGG-TTTAGGGTTT--TGATTTTA-GA
* * * ** * ** *
13590133 GTTTGGAA-GGTTTAGAGCTTT-AGTTTTAGGGTTTGGAGGATTTAAAGTTTTGATTTTAGG
1 GTTT-AAAGGGTTTAGAGTTTTGA-TTTTAGGATTTAAAGGGTTTAGGGTTTTGATTTTAGA
* * * * * * *
13590193 GTTTGGAA-GGTTTAGGGTTTAG-TTTTAGGGTTTAGAGGGTTTAGGGTTTAG-TTTTAGG
1 GTTT-AAAGGGTTTAGAGTTTTGATTTTAGGATTTAAAGGGTTTAGGGTTTTGATTTTAGA
13590251 GTTT
1 GTTT
13590255 TGATTTTAAG
Statistics
Matches: 195, Mismatches: 37, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
58 11 0.06
59 30 0.15
60 98 0.50
61 11 0.06
62 9 0.05
63 33 0.17
64 3 0.02
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.46
Consensus pattern (60 bp):
GTTTAAAGGGTTTAGAGTTTTGATTTTAGGATTTAAAGGGTTTAGGGTTTTGATTTTAGA
Found at i:13590115 original size:17 final size:17
Alignment explanation
Indices: 13590093--13590129 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
13590083 AGAGTTTTGA
13590093 TTTTAGAATTTAAAGGG
1 TTTTAGAATTTAAAGGG
**
13590110 TTTTAGGGTTTAAAGGG
1 TTTTAGAATTTAAAGGG
13590127 TTT
1 TTT
13590130 ATGGTTTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (17 bp):
TTTTAGAATTTAAAGGG
Found at i:13590197 original size:13 final size:14
Alignment explanation
Indices: 13590181--13590295 Score: 78
Period size: 13 Copynumber: 8.0 Consensus size: 14
13590171 GATTTAAAGT
13590181 TTTGA-TTTTAGGG
1 TTTGAGTTTTAGGG
*
13590194 TTTGGAAGGTTTAGGG
1 TTT-G-AGTTTTAGGG
13590210 TTT-AGTTTTAGGG
1 TTTGAGTTTTAGGG
*
13590223 TTTAGAGGGTTTAGGG
1 TTT-GA-GTTTTAGGG
13590239 TTT-AGTTTTAGGG
1 TTTGAGTTTTAGGG
13590252 TTTTGA-TTTTAAGGG
1 -TTTGAGTTTT-AGGG
* * *
13590267 TTAGAGGGTTTAAGGT
1 TTTGA--GTTTTAGGG
13590283 TTTGA-TTTTAGGG
1 TTTGAGTTTTAGGG
13590296 GTTAGAGGGT
Statistics
Matches: 80, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
13 29 0.36
14 13 0.16
15 7 0.09
16 28 0.35
17 3 0.04
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (14 bp):
TTTGAGTTTTAGGG
Found at i:13590208 original size:16 final size:14
Alignment explanation
Indices: 13590111--13590311 Score: 72
Period size: 16 Copynumber: 13.5 Consensus size: 14
13590101 TTTAAAGGGT
*
13590111 TTTAGGGTTTAAAGGG
1 TTTAGGGTTT-GA-GG
*
13590127 TTTATGGTTTGGAAGG
1 TTTAGGGTTT-G-AGG
* *
13590143 TTTAGAGCTTT-AGT
1 TTTAG-GGTTTGAGG
13590157 TTTAGGGTTTGGAGG
1 TTTAGGGTTT-GAGG
* * *
13590172 ATTTAAAGTTTTGA-T
1 -TTT-AGGGTTTGAGG
13590187 TTTAGGGTTTGGAAGG
1 TTTAGGGTTT-G-AGG
*
13590203 TTTAGGGTTT-AGT
1 TTTAGGGTTTGAGG
13590216 TTTAGGGTTTAGAGGG
1 TTTAGGGTTT-GA-GG
*
13590232 TTTAGGGTTT-AGT
1 TTTAGGGTTTGAGG
*
13590245 TTTAGGGTTTTGA-T
1 TTTAGGG-TTTGAGG
*
13590259 TTTAAGGGTTAGAGGG
1 TTT-AGGGTTTGA-GG
* *
13590275 TTTAAGGTTTTGA-T
1 TTT-AGGGTTTGAGG
*
13590289 TTTAGGGGTTAGAGGG
1 TTTA-GGGTTTGA-GG
13590305 TTTAGGG
1 TTTAGGG
13590312 CTTAGTTTTT
Statistics
Matches: 140, Mismatches: 25, Indels: 41
0.68 0.12 0.20
Matches are distributed among these distances:
13 30 0.21
14 32 0.23
15 12 0.09
16 56 0.40
17 10 0.07
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.44
Consensus pattern (14 bp):
TTTAGGGTTTGAGG
Found at i:13590213 original size:7 final size:7
Alignment explanation
Indices: 13590187--13590254 Score: 59
Period size: 7 Copynumber: 9.4 Consensus size: 7
13590177 AAGTTTTGAT
13590187 TTTAGGG
1 TTTAGGG
*
13590194 TTTGGAAGG
1 TTT--AGGG
13590203 TTTAGGG
1 TTTAGGG
*
13590210 TTTA-GT
1 TTTAGGG
13590216 TTTAGGG
1 TTTAGGG
13590223 TTTAGAGGG
1 TTT--AGGG
13590232 TTTAGGG
1 TTTAGGG
*
13590239 TTTA-GT
1 TTTAGGG
13590245 TTTAGGG
1 TTTAGGG
13590252 TTT
1 TTT
13590255 TGATTTTAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
6 10 0.20
7 26 0.53
9 13 0.27
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:13590225 original size:59 final size:59
Alignment explanation
Indices: 13590127--13590254 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
13590117 GTTTAAAGGG
* * *
13590127 TTTATGGTTTGGAAGGTTTAGAGCTTTAGTTTTAGGGTTTGGAGGATTTAAAGTTTTGAT
1 TTTAGGGTTTGGAAGGTTTAGAGCTTTAGTTTTAGGGTTTAGAGGATTTAAAGTTTAG-T
* * **
13590187 TTTAGGGTTTGGAAGGTTTAG-GGTTTAGTTTTAGGGTTTAGAGGGTTTAGGGTTTAGT
1 TTTAGGGTTTGGAAGGTTTAGAGCTTTAGTTTTAGGGTTTAGAGGATTTAAAGTTTAGT
13590245 TTTAGGGTTT
1 TTTAGGGTTT
13590255 TGATTTTAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 11 0.18
59 30 0.49
60 20 0.33
ACGTcount: A:0.19, C:0.01, G:0.34, T:0.47
Consensus pattern (59 bp):
TTTAGGGTTTGGAAGGTTTAGAGCTTTAGTTTTAGGGTTTAGAGGATTTAAAGTTTAGT
Found at i:13590251 original size:29 final size:30
Alignment explanation
Indices: 13589988--13590254 Score: 189
Period size: 30 Copynumber: 8.9 Consensus size: 30
13589978 GGATTTGAAA
* *
13589988 GGTTTAGGGTTTTGATTTTAAGGTTTAAAG
1 GGTTTAGGGTTTTGATTTTAGGGTTTAGAG
* * * * * *
13590018 GTTTTAAGATTTTGATTTTAGGATTCAAAG
1 GGTTTAGGGTTTTGATTTTAGGGTTTAGAG
** * *
13590048 GGTTTAGTATTTTGATTTTAGAGTTTGGAG
1 GGTTTAGGGTTTTGATTTTAGGGTTTAGAG
* ** *
13590078 GGTTTAGAGTTTTGATTTTAGAATTTAAAG
1 GGTTTAGGGTTTTGATTTTAGGGTTTAGAG
* ** * * *
13590108 GGTTTTAGGGTTTAAAGGGTTTATGGTTTGGAA
1 GG-TTTAGGGTTT--TGATTTTAGGGTTTAGAG
* * *
13590141 GGTTTAGAGCTTT-AGTTTTAGGGTTTGGAG
1 GGTTTAGGGTTTTGA-TTTTAGGGTTTAGAG
* ** * *
13590171 GATTTAAAGTTTTGATTTTAGGGTTTGGAA
1 GGTTTAGGGTTTTGATTTTAGGGTTTAGAG
*
13590201 GGTTTAGGGTTTAG-TTTTAGGGTTTAGAG
1 GGTTTAGGGTTTTGATTTTAGGGTTTAGAG
*
13590230 GGTTTAGGGTTTAG-TTTTAGGGTTT
1 GGTTTAGGGTTTTGATTTTAGGGTTT
13590255 TGATTTTAAG
Statistics
Matches: 186, Mismatches: 46, Indels: 11
0.77 0.19 0.05
Matches are distributed among these distances:
29 38 0.20
30 119 0.64
31 10 0.05
32 8 0.04
33 11 0.06
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.46
Consensus pattern (30 bp):
GGTTTAGGGTTTTGATTTTAGGGTTTAGAG
Found at i:13590271 original size:43 final size:43
Alignment explanation
Indices: 13590203--13590300 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 43
13590193 GTTTGGAAGG
*
13590203 TTTAGGGTTTAGTTTTAGGGTTTAGAGGGTTTAGGGTTTAG-T
1 TTTAGGGTTTAGTTTTAGGGTTTAGAGGGTTTAAGGTTTAGAT
* *
13590245 TTTAGGGTTTTGATTTTAAGGG-TTAGAGGGTTTAAGGTTTTGAT
1 TTTAGGGTTTAG-TTTT-AGGGTTTAGAGGGTTTAAGGTTTAGAT
*
13590289 TTTAGGGGTTAG
1 TTTAGGGTTTAG
13590301 AGGGTTTAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 11 0.23
43 22 0.46
44 15 0.31
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (43 bp):
TTTAGGGTTTAGTTTTAGGGTTTAGAGGGTTTAAGGTTTAGAT
Found at i:13590286 original size:30 final size:30
Alignment explanation
Indices: 13590245--13590308 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
13590235 AGGGTTTAGT
*
13590245 TTTAGGGTTTTGATTTTAAGGGTTAGAGGG
1 TTTAAGGTTTTGATTTTAAGGGTTAGAGGG
*
13590275 TTTAAGGTTTTGATTTTAGGGGTTAGAGGG
1 TTTAAGGTTTTGATTTTAAGGGTTAGAGGG
13590305 TTTA
1 TTTA
13590309 GGGCTTAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.45
Consensus pattern (30 bp):
TTTAAGGTTTTGATTTTAAGGGTTAGAGGG
Found at i:13590305 original size:73 final size:72
Alignment explanation
Indices: 13590179--13590320 Score: 205
Period size: 73 Copynumber: 2.0 Consensus size: 72
13590169 AGGATTTAAA
* * * *
13590179 GTTTTGATTTTAGGGTTTGGAAGGTTTAGGGTTTAGTTTTAGGGTTTAGAGGGTTTAGGGTTTAG
1 GTTTTGATTTTAGGGTTTAGAAGGTTTAAGGTTTAGTTTTAGGGGTTAGAGGGTTTAGGGCTTAG
13590244 TTTTAGG
66 TTTTAGG
* *
13590251 GTTTTGATTTTAAGGG-TTAGAGGGTTTAAGGTTTTGATTTTAGGGGTTAGAGGGTTTAGGGCTT
1 GTTTTGATTTT-AGGGTTTAGAAGGTTTAAGGTTTAG-TTTTAGGGGTTAGAGGGTTTAGGGCTT
13590315 AGTTTT
64 AGTTTT
13590321 TTTTTTAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
72 27 0.44
73 35 0.56
ACGTcount: A:0.18, C:0.01, G:0.35, T:0.46
Consensus pattern (72 bp):
GTTTTGATTTTAGGGTTTAGAAGGTTTAAGGTTTAGTTTTAGGGGTTAGAGGGTTTAGGGCTTAG
TTTTAGG
Found at i:13590743 original size:12 final size:12
Alignment explanation
Indices: 13590696--13590755 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
13590686 AAGTTTTAAA
*
13590696 ATCATTTTTATT
1 ATCATTATTATT
**
13590708 ATGGTTATTATT
1 ATCATTATTATT
13590720 ATCATTATTATT
1 ATCATTATTATT
* *
13590732 GTTATTATTATT
1 ATCATTATTATT
*
13590744 AATCACTATTAT
1 -ATCATTATTAT
13590756 GAAACAACAA
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
12 29 0.78
13 8 0.22
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (12 bp):
ATCATTATTATT
Done.