Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008116.1 Hibiscus syriacus cultivar Beakdansim tig00110655_pilon, 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: 363508
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:236917 original size:21 final size:19
Alignment explanation
Indices: 236872--236929 Score: 82
Period size: 18 Copynumber: 2.9 Consensus size: 19
236862 TGATGTTTTG
236872 ATATATTAAGATAATTATT
1 ATATATTAAGATAATTATT
236891 -TATATTAAGATAATATATTT
1 ATATATTAAGATAAT-TA-TT
236911 ATATATTAAGATATATTAT
1 ATATATTAAGATA-ATTAT
236930 CTTAATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 14 0.40
19 2 0.06
20 3 0.09
21 14 0.40
22 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (19 bp):
ATATATTAAGATAATTATT
Found at i:236937 original size:21 final size:19
Alignment explanation
Indices: 236874--236937 Score: 85
Period size: 21 Copynumber: 3.2 Consensus size: 19
236864 ATGTTTTGAT
236874 ATATTAAGATAATTATTT-
1 ATATTAAGATAATTATTTA
236892 ATATTAAGATAATATATTTA
1 ATATTAAGATAAT-TATTTA
236912 TATATTAAGATATATTATCTTA
1 -ATATTAAGATA-ATTAT-TTA
236934 ATAT
1 ATAT
236938 ATCAAAACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
18 13 0.32
19 5 0.12
21 18 0.44
22 5 0.12
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (19 bp):
ATATTAAGATAATTATTTA
Found at i:237450 original size:15 final size:15
Alignment explanation
Indices: 237430--237521 Score: 152
Period size: 15 Copynumber: 6.3 Consensus size: 15
237420 TTATTATTTT
237430 AATAATTTATTATAA
1 AATAATTTATTATAA
*
237445 AATAATTTATTTTAA
1 AATAATTTATTATAA
237460 AATAATTTATTATAA
1 AATAATTTATTATAA
237475 AATAATTTA-T-TAA
1 AATAATTTATTATAA
*
237488 AATAATTTATTTTAA
1 AATAATTTATTATAA
237503 AATAATTTATTATAA
1 AATAATTTATTATAA
237518 AATA
1 AATA
237522 TGGATTGATT
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
13 12 0.17
14 2 0.03
15 58 0.81
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAATTTATTATAA
Found at i:237490 original size:43 final size:45
Alignment explanation
Indices: 237430--237564 Score: 170
Period size: 43 Copynumber: 2.9 Consensus size: 45
237420 TTATTATTTT
237430 AATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAA
1 AATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAA
237475 AATAATTTA-T-TAAAATAATTTATTTTAAAATAATTTATTATAAA
1 AATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTAT-AA
*
237519 ATATGGATTGATTTATTTTAAAATAATTTATTTT-AAATAA-TTATTA
1 A-AT--A---ATTTATTATAAAATAATTTATTTTAAAATAATTTATTA
237565 GTATGGATTG
Statistics
Matches: 81, Mismatches: 0, Indels: 13
0.86 0.00 0.14
Matches are distributed among these distances:
43 31 0.38
44 4 0.05
45 11 0.14
47 1 0.01
50 11 0.14
51 7 0.09
52 16 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (45 bp):
AATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAA
Found at i:237514 original size:28 final size:28
Alignment explanation
Indices: 237430--237514 Score: 143
Period size: 28 Copynumber: 3.0 Consensus size: 28
237420 TTATTATTTT
237430 AATAATTTATTATAAAATAATTTATTTTAA
1 AATAATTTATTATAAAATAATTTA--TTAA
237460 AATAATTTATTATAAAATAATTTATTAA
1 AATAATTTATTATAAAATAATTTATTAA
*
237488 AATAATTTATTTTAAAATAATTTATTA
1 AATAATTTATTATAAAATAATTTATTA
237515 TAAAATATGG
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
28 30 0.56
30 24 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
AATAATTTATTATAAAATAATTTATTAA
Found at i:237532 original size:22 final size:22
Alignment explanation
Indices: 237507--237608 Score: 93
Period size: 22 Copynumber: 4.5 Consensus size: 22
237497 TTTTAAAATA
*
237507 ATTTATTATAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
237529 ATTTATTTTAAAATA---ATTT
1 ATTTATTTTAAAATATGGATTG
* * *
237548 ATTTTAAATAATTATTAGTATGGATTG
1 A-TTT--AT-TTTA-AAATATGGATTG
237575 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
237597 ATTTATTTTAAA
1 ATTTATTTTAAA
237609 TAATTTATTA
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
19 4 0.06
20 3 0.05
22 38 0.60
23 6 0.10
24 5 0.08
26 3 0.05
27 4 0.06
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:237558 original size:14 final size:15
Alignment explanation
Indices: 237430--237560 Score: 151
Period size: 15 Copynumber: 8.5 Consensus size: 15
237420 TTATTATTTT
*
237430 AATAATTTATTATAA
1 AATAATTTATTTTAA
237445 AATAATTTATTTTAA
1 AATAATTTATTTTAA
*
237460 AATAATTTATTATAA
1 AATAATTTATTTTAA
237475 AATAATTTA--TTAA
1 AATAATTTATTTTAA
237488 AATAATTTATTTTAA
1 AATAATTTATTTTAA
*
237503 AATAATTTATTATAAA
1 AATAATTTATT-TTAA
237519 ATATGGATTGATTTATTTTAA
1 A-AT--A---ATTTATTTTAA
237540 AATAATTTATTTT-A
1 AATAATTTATTTTAA
237554 AATAATT
1 AATAATT
237561 ATTAGTATGG
Statistics
Matches: 102, Mismatches: 5, Indels: 19
0.81 0.04 0.15
Matches are distributed among these distances:
13 12 0.12
14 8 0.08
15 61 0.60
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 7 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
AATAATTTATTTTAA
Found at i:237579 original size:31 final size:31
Alignment explanation
Indices: 237544--237692 Score: 156
Period size: 31 Copynumber: 5.4 Consensus size: 31
237534 TTTTAAAATA
237544 ATTTATTTTAAATAATTATTAGTATGGATTG
1 ATTTATTTTAAATAATTATTAGTATGGATTG
237575 ATTTA-TTT---TAA--A--A-TATGGATTG
1 ATTTATTTTAAATAATTATTAGTATGGATTG
237597 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAA-TTATTAGTATGGATTG
237629 ATTTA--TT---TAA--A--A-TATGGATTG
1 ATTTATTTTAAATAATTATTAGTATGGATTG
237650 ATTTATTTTAAATAATTATTAGTATGGATTG
1 ATTTATTTTAAATAATTATTAGTATGGATTG
237681 ATTTATTTTAAA
1 ATTTATTTTAAA
237693 ATATGGATTG
Statistics
Matches: 98, Mismatches: 0, Indels: 40
0.71 0.00 0.29
Matches are distributed among these distances:
21 14 0.14
22 15 0.15
23 6 0.06
24 1 0.01
25 1 0.01
26 6 0.06
27 6 0.06
28 1 0.01
29 1 0.01
30 6 0.06
31 27 0.28
32 14 0.14
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (31 bp):
ATTTATTTTAAATAATTATTAGTATGGATTG
Found at i:237607 original size:53 final size:53
Alignment explanation
Indices: 237544--237820 Score: 361
Period size: 53 Copynumber: 5.1 Consensus size: 53
237534 TTTTAAAATA
237544 ATTTATTTTAAATAATTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
237597 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTTAAAATATGGATTG
1 ATTTATTTTAAATAA-TTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
237650 ATTTATTTTAAATAATTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
237703 ATTTATTATT--GT-AGT-TT--TATGGATTGATTTATTTTAAATAATTTAGTATGGATTG
1 ATTTATT-TTAAATAATTATTAGTATGGATTGATTTATTTT--A-AA---A-TATGGATTG
* *
237758 ATTTATTTTAAATAATTTATTTGTATGGATTGATTGATTATTTAAAATATGGATTG
1 ATTTATTTTAAATAA-TTATTAGTATGGATTGATTTA-T-TTTAAAATATGGATTG
237814 ATTTATT
1 ATTTATT
237821 ATTGTAGTTG
Statistics
Matches: 200, Mismatches: 5, Indels: 35
0.83 0.02 0.15
Matches are distributed among these distances:
48 18 0.09
50 3 0.01
51 4 0.02
52 22 0.11
53 69 0.34
54 26 0.13
55 16 0.08
56 17 0.09
57 2 0.01
58 1 0.00
59 2 0.01
60 2 0.01
61 14 0.07
62 1 0.00
63 3 0.01
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (53 bp):
ATTTATTTTAAATAATTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:237646 original size:21 final size:21
Alignment explanation
Indices: 237620--237663 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
237610 AATTTATTAG
237620 TATGGATTGATTTATTTAAAA
1 TATGGATTGATTTATTTAAAA
*
237641 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTAAAA
237662 TA
1 TA
237664 ATTATTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (21 bp):
TATGGATTGATTTATTTAAAA
Found at i:237667 original size:106 final size:107
Alignment explanation
Indices: 237544--237883 Score: 421
Period size: 106 Copynumber: 3.1 Consensus size: 107
237534 TTTTAAAATA
237544 ATTTATTTTAAATAATTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAA
1 ATTTATTTTAAATAATTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTT--A
*
237609 TAATTTA-TTAGTATGGATTGATTTA-TTT-A-AA-A-TATGGATTG
64 T--TGTAGTT-GTATGGATTGATTTATTTTAATAATAGTATGGATTG
237650 ATTTATTTTAAATAATTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TTATT
1 ATTTATTTTAAATAATTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTATT
*
237713 GTAGTTTTATGGATTGATTTATTTTAAATAATTTAGTATGGATTG
66 GTAGTTGTATGGATTGATTTATTTT-AATAA--TAGTATGGATTG
* *
237758 ATTTATTTTAAATAATTTATTTGTATGGATTGATTGATTATTTAAAATATGGATTGATTTA--TT
1 ATTTATTTTAAATAA-TTATTAGTATGGATTGATTTA-T-TTTAAAATATGGATTGATTTATTTT
237821 ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
63 ATTGTAGTTGTATGGATTGATTTATTTT-AAT-A---A-TAGTATGGATTG
237872 ATTTATTTTAAA
1 ATTTATTTTAAA
237884 ATAGGATTGA
Statistics
Matches: 213, Mismatches: 5, Indels: 24
0.88 0.02 0.10
Matches are distributed among these distances:
100 17 0.08
101 5 0.02
102 2 0.01
103 1 0.00
104 4 0.02
106 58 0.27
107 1 0.00
108 24 0.11
109 19 0.09
110 1 0.00
111 54 0.25
112 1 0.00
114 25 0.12
115 1 0.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (107 bp):
ATTTATTTTAAATAATTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTATT
GTAGTTGTATGGATTGATTTATTTTAATAATAGTATGGATTG
Found at i:237723 original size:26 final size:25
Alignment explanation
Indices: 237694--237846 Score: 103
Period size: 26 Copynumber: 5.6 Consensus size: 25
237684 TATTTTAAAA
237694 TATGGATTGATTTATTATTGTAGTTT
1 TATGGATTGATTTATTATTGTA-TTT
*
237720 TATGGATTGATTTATT-TTAAATAATTT
1 TATGGATTGATTTATTATT--GT-ATTT
*
237747 AGTATGGATTGATTTATTTTAAATAATTTATTT
1 --TATGGATTGATTTA--TT--AT--TGTATTT
* ***
237780 GTATGGATTGATTGATTATT-TAAAA
1 -TATGGATTGATTTATTATTGTATTT
*
237805 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTATTGTA-TTT
237831 TATGGATTGATTTATT
1 TATGGATTGATTTATT
237847 TTAAATAATT
Statistics
Matches: 103, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
24 18 0.17
25 6 0.06
26 33 0.32
27 4 0.04
28 3 0.03
29 14 0.14
30 2 0.02
31 2 0.02
32 14 0.14
33 4 0.04
34 2 0.02
36 1 0.01
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (25 bp):
TATGGATTGATTTATTATTGTATTT
Found at i:237789 original size:32 final size:29
Alignment explanation
Indices: 237720--237911 Score: 150
Period size: 32 Copynumber: 7.0 Consensus size: 29
237710 ATTGTAGTTT
237720 TATGGATTGATTTATTTTAAATAATTTAG
1 TATGGATTGATTTATTTTAAATAATTTAG
237749 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTA---G
* *
237781 TATGGATTGATTGATTATT---TAA---AA
1 TATGGATTGATTTATT-TTAAATAATTTAG
* *
237805 TATGGATTGATTTATTATT--GT-AGTT-G
1 TATGGATTGATTTATT-TTAAATAATTTAG
237831 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAA--T-TTAG
237863 TATGGATTGATTTATTTT--A-AA---A-
1 TATGGATTGATTTATTTTAAATAATTTAG
237885 TA-GGATTGATTTATTTTAAATAATTTA
1 TATGGATTGATTTATTTTAAATAATTTA
237912 TTATTGTAGT
Statistics
Matches: 136, Mismatches: 6, Indels: 44
0.73 0.03 0.24
Matches are distributed among these distances:
21 15 0.11
22 2 0.01
23 2 0.01
24 21 0.15
25 3 0.02
26 16 0.12
27 3 0.02
28 1 0.01
29 30 0.22
30 4 0.03
31 2 0.01
32 35 0.26
33 2 0.01
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (29 bp):
TATGGATTGATTTATTTTAAATAATTTAG
Found at i:237934 original size:111 final size:108
Alignment explanation
Indices: 237641--237911 Score: 277
Period size: 111 Copynumber: 2.5 Consensus size: 108
237631 TTATTTAAAA
* * *
237641 TATGGATTGATTTATTTTAAATAATT-ATTAGTATGGATTGAT--TTATTTTAAAATATGGATTG
1 TATGGATTGATTTATTTTAAATAATTGATTTGTAT-G-TT-ATAAATAATTTAAAATATGGATTG
** *
237703 ATTTATTATTGTAGTTTTATGGATTGATTTATTTTAAATAATTTAG
63 ATGGATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTAG
* ** *
237749 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTGATTATTTAAAATATGGATTG
1 TATGGATTGATTTATTTTAAATAATTGATTTGTAT-G-TT-ATAAATAATTTAAAATATGGATTG
**
237814 ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
63 ATGGATTATTGTAGTTGTATGGATTGATTTATTTTAAATAA--T-TTAG
237863 TATGGATTGATTTATTTTAAAATAGGATTGA-TT-TAT-TT-TAAATAATTTA
1 TATGGATTGATTTATTTT-AAATA--ATTGATTTGTATGTTATAAATAATTTA
237912 TTATTGTAGT
Statistics
Matches: 145, Mismatches: 9, Indels: 16
0.85 0.05 0.09
Matches are distributed among these distances:
108 26 0.18
109 15 0.10
110 8 0.06
111 57 0.39
112 2 0.01
113 1 0.01
114 22 0.15
115 8 0.06
116 2 0.01
117 4 0.03
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (108 bp):
TATGGATTGATTTATTTTAAATAATTGATTTGTATGTTATAAATAATTTAAAATATGGATTGATG
GATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTAG
Found at i:237964 original size:31 final size:31
Alignment explanation
Indices: 237929--237987 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
237919 AGTTGTATGG
* *
237929 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
237960 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
237988 CTTTAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:239034 original size:2 final size:2
Alignment explanation
Indices: 239027--239068 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
239017 GTTTTCTATT
239027 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
239069 ATTTATGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:242538 original size:41 final size:41
Alignment explanation
Indices: 242483--242560 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
242473 CTTTAATTCT
242483 AAAAAACCCTGATTTCACTTTAAACCTAATTAGATAAATTA
1 AAAAAACCCTGATTTCACTTTAAACCTAATTAGATAAATTA
242524 AAAAAACCCTGATTTCACTTTAAACCTAATTAGATAA
1 AAAAAACCCTGATTTCACTTTAAACCTAATTAGATAA
242561 TAATAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (41 bp):
AAAAAACCCTGATTTCACTTTAAACCTAATTAGATAAATTA
Found at i:242989 original size:19 final size:20
Alignment explanation
Indices: 242961--243008 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
242951 TTTGAGTTAA
*
242961 TTAAACATGTTTAAAG-TGT
1 TTAAATATGTTTAAAGATGT
*
242980 TTAAATATGTTTAAAGATTT
1 TTAAATATGTTTAAAGATGT
243000 TTAAATATG
1 TTAAATATG
243009 AAAATACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (20 bp):
TTAAATATGTTTAAAGATGT
Found at i:242990 original size:10 final size:10
Alignment explanation
Indices: 242961--243008 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
242951 TTTGAGTTAA
*
242961 TTAAACATGT
1 TTAAATATGT
*
242971 TTAAA-GTGT
1 TTAAATATGT
242980 TTAAATATGT
1 TTAAATATGT
* *
242990 TTAAAGATTT
1 TTAAATATGT
243000 TTAAATATG
1 TTAAATATG
243009 AAAATACTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
9 8 0.26
10 23 0.74
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (10 bp):
TTAAATATGT
Found at i:243211 original size:20 final size:20
Alignment explanation
Indices: 243185--243240 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
243175 ATTTTTAAGT
243185 AAAAGTTTCGAAACTGTCATC
1 AAAAGTTTCGAAACTGTC-TC
* * *
243206 -AAAGTTTCAAAATTTTCTC
1 AAAAGTTTCGAAACTGTCTC
*
243225 AAAAGTTTTGAAACTG
1 AAAAGTTTCGAAACTG
243241 CATGTGCATG
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (20 bp):
AAAAGTTTCGAAACTGTCTC
Found at i:244928 original size:7 final size:7
Alignment explanation
Indices: 244916--244959 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
244906 TATTAAACCC
244916 CTAACTT
1 CTAACTT
244923 CTAACTT
1 CTAACTT
244930 CTAACTT
1 CTAACTT
**
244937 ACTAACCC
1 -CTAACTT
244945 CTAACTT
1 CTAACTT
244952 ACTAACTT
1 -CTAACTT
244960 TATTTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
7 19 0.61
8 12 0.39
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (7 bp):
CTAACTT
Found at i:244948 original size:15 final size:15
Alignment explanation
Indices: 244911--244957 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
244901 TTCATTATTA
244911 AACCCCTAACTT-CT
1 AACCCCTAACTTACT
**
244925 AACTTCTAACTTACT
1 AACCCCTAACTTACT
244940 AACCCCTAACTTACT
1 AACCCCTAACTTACT
244955 AAC
1 AAC
244958 TTTATTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.34, C:0.36, G:0.00, T:0.30
Consensus pattern (15 bp):
AACCCCTAACTTACT
Found at i:245290 original size:15 final size:15
Alignment explanation
Indices: 245253--245286 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
245243 ATTTCTATAA
245253 TTTAATTTTATGTAC
1 TTTAATTTTATGTAC
*
245268 TTTAATTTT-TGTCC
1 TTTAATTTTATGTAC
245282 TTTAA
1 TTTAA
245287 ATTTCTAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTAATTTTATGTAC
Found at i:245300 original size:44 final size:45
Alignment explanation
Indices: 245207--245305 Score: 105
Period size: 44 Copynumber: 2.2 Consensus size: 45
245197 CTTAATTTTT
* * * *
245207 CATTTACA-TTTATGCACTTTATTTTTTTCTGTTTACATTTCTAT
1 CATTTACATTTTATGCACTTTATTTTTGTCTCTTTAAATTTCTAG
* *
245251 AATTTA-ATTTTATGTACTTTAATTTTTGTC-CTTTAAATTTCTAG
1 CATTTACATTTTATGCACTTT-ATTTTTGTCTCTTTAAATTTCTAG
*
245295 CATTTATATTT
1 CATTTACATTT
245306 GAGTTCTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
43 1 0.02
44 32 0.71
45 12 0.27
ACGTcount: A:0.24, C:0.12, G:0.05, T:0.59
Consensus pattern (45 bp):
CATTTACATTTTATGCACTTTATTTTTGTCTCTTTAAATTTCTAG
Found at i:246852 original size:14 final size:15
Alignment explanation
Indices: 246819--246857 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
246809 AAATTGGGAA
246819 TTAGGGATTTGAATT
1 TTAGGGATTTGAATT
246834 TTAGGGATTT-AGA-T
1 TTAGGGATTTGA-ATT
246848 TTAGGGATTT
1 TTAGGGATTT
246858 TGGGTGACGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (15 bp):
TTAGGGATTTGAATT
Found at i:258768 original size:25 final size:26
Alignment explanation
Indices: 258733--258824 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 26
258723 TTTAAGGATA
258733 AAATTGATATTTGATGTAAAGTTTAG
1 AAATTGATATTTGATGTAAAGTTTAG
* *
258759 AAATT-ATATTATAAAT-T-AA-TTAATG
1 AAATTGATATT-T-GATGTAAAGTTTA-G
258784 AAAATTTGATATTTGATGTAAAGTTTAG
1 -AAA-TTGATATTTGATGTAAAGTTTAG
*
258812 AAGTT-ATATTTGA
1 AAATTGATATTTGA
258825 AATTAATAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 19
0.68 0.07 0.25
Matches are distributed among these distances:
24 3 0.06
25 16 0.31
26 14 0.27
27 8 0.15
28 8 0.15
29 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.43
Consensus pattern (26 bp):
AAATTGATATTTGATGTAAAGTTTAG
Found at i:258811 original size:53 final size:52
Alignment explanation
Indices: 258732--258831 Score: 166
Period size: 53 Copynumber: 1.9 Consensus size: 52
258722 GTTTAAGGAT
258732 AAAATTGATATTTGATGTAAAGTTTAGAAATTATATTAT-AAATTAATTAATG
1 AAAATTGATATTTGATGTAAAGTTTAGAAATTATATT-TGAAATTAATTAATG
*
258784 AAAATTTGATATTTGATGTAAAGTTTAGAAGTTATATTTGAAATTAAT
1 AAAA-TTGATATTTGATGTAAAGTTTAGAAATTATATTTGAAATTAAT
258832 AGATCAATGA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
52 5 0.11
53 40 0.89
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.43
Consensus pattern (52 bp):
AAAATTGATATTTGATGTAAAGTTTAGAAATTATATTTGAAATTAATTAATG
Found at i:263105 original size:22 final size:22
Alignment explanation
Indices: 263080--263122 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
263070 GATGTACCGA
*
263080 ATCGCGATTTTGAAACGATCCG
1 ATCGCGATTTTAAAACGATCCG
263102 ATCGCGATTTTAAAACGATCC
1 ATCGCGATTTTAAAACGATCC
263123 AAACGCGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (22 bp):
ATCGCGATTTTAAAACGATCCG
Found at i:263129 original size:22 final size:22
Alignment explanation
Indices: 263082--263129 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
263072 TGTACCGAAT
* * *
263082 CGCGATTTTGAAACGATCCGAT
1 CGCGATTTTAAAACGATCCAAA
263104 CGCGATTTTAAAACGATCCAAA
1 CGCGATTTTAAAACGATCCAAA
263126 CGCG
1 CGCG
263130 TTCGTACCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (22 bp):
CGCGATTTTAAAACGATCCAAA
Found at i:271160 original size:2 final size:2
Alignment explanation
Indices: 271153--271178 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
271143 GTTTTATGAT
271153 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
271179 GTTTTGCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:274118 original size:31 final size:31
Alignment explanation
Indices: 274082--274159 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
274072 TCAAAAAACA
* *
274082 TAAGTTTTAGTCACTTACGTTAT-TGTTTTCT
1 TAAGTTTTGGTCACTTACGTTATAT-TTTTAT
274113 TAAGTTTTGGTCACTTACGTTATATTTTTAT
1 TAAGTTTTGGTCACTTACGTTATATTTTTAT
274144 TAAGTTTTGGTCACTT
1 TAAGTTTTGGTCACTT
274160 GGATATTGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 43 0.98
32 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.54
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGTTATATTTTTAT
Found at i:275496 original size:31 final size:31
Alignment explanation
Indices: 275461--275538 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
275451 TTCAACGTCC
*
275461 AAGTGACCAAAACTTAATAAAACGATAACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
*
275492 AAGTGACAAAAACTTAATAAAACAATAACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
*
275523 GAGTGACCAAAACTTA
1 AAGTGACCAAAACTTA
275539 TGTTTTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.19
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACAT
Found at i:282693 original size:12 final size:12
Alignment explanation
Indices: 282672--282701 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
282662 CAAAATTATA
282672 ATTTAGTAAATT
1 ATTTAGTAAATT
*
282684 ATTTATTAAATT
1 ATTTAGTAAATT
282696 ATTTAG
1 ATTTAG
282702 ATTTTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (12 bp):
ATTTAGTAAATT
Found at i:284206 original size:18 final size:18
Alignment explanation
Indices: 284185--284221 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
284175 TTCTTTTTAA
*
284185 ATTTTATAATTTTTAAAT
1 ATTTTATAATTTTGAAAT
*
284203 ATTTTATTATTTTGAAAT
1 ATTTTATAATTTTGAAAT
284221 A
1 A
284222 ATATTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
ATTTTATAATTTTGAAAT
Found at i:284877 original size:32 final size:32
Alignment explanation
Indices: 284841--284917 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
284831 TAACTGTTAC
*
284841 GCATTATCTAAATGCGACAC-TGATACTCA-TGT
1 GCATTATCTAAATGC-AAACTTGATACT-ATTGT
* **
284873 GCATTATCTGAATGCAAACTTGATTGTATTGT
1 GCATTATCTAAATGCAAACTTGATACTATTGT
284905 GCATTATCTAAAT
1 GCATTATCTAAAT
284918 ACAATACTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
31 4 0.11
32 34 0.89
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (32 bp):
GCATTATCTAAATGCAAACTTGATACTATTGT
Found at i:288189 original size:22 final size:22
Alignment explanation
Indices: 288161--288216 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
288151 TCTACGCATT
*
288161 CTTCGGGACATACTCATAGGTC
1 CTTCGGGACATACTCACAGGTC
*
288183 CTTCGGGACATACTCGCAGGTC
1 CTTCGGGACATACTCACAGGTC
288205 CTTCGGGACATA
1 CTTCGGGACATA
288217 TTTCACATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (22 bp):
CTTCGGGACATACTCACAGGTC
Found at i:290736 original size:263 final size:263
Alignment explanation
Indices: 290233--290767 Score: 853
Period size: 262 Copynumber: 2.0 Consensus size: 263
290223 GTTTTTCTAC
* * *
290233 AATAAA-AAAATCTCATTTTTATTGCTAATTGGGCCCGATTCCAAATCTAATTAAGCCCAACGAC
1 AATAAAGATAATCTCATTTTTATTGCTAATTGGGCCCGATTCCAAACCCAATTAAGCCCAACGAC
290297 TTAAATTAGAATTTTCGCGGGATACACTTACCCTCTCGGATAAACTCGAAACTACTAACCTCAAA
66 TTAAATTAGAATTTTCGCGGGATACACTTACCCTCTCGGATAAACTCGAAACTACTAACCTCAAA
* ** *
290362 TTTGACATGTTACAAATGACAAAAACATTTATAGTAATATAAAATAGTTAACATCAGTTTAATAA
131 TTTGACATGTTACAAATGACAAAAACATTGATAACAATATAAAATAGTTAACATCAATTTAATAA
290427 TTTTGTTAATTTTTTGTCAATTGACTCAATTTAATAAAAATGTTTAAGAATGAAAACAGAAAAAA
196 TTTTGTTAATTTTTTGTCAATTGACTCAATTTAATAAAAATGTTTAAGAATGAAAACAGAAAAAA
290492 TAA
261 TAA
*
290495 AATAAAGATAATCTCATTTTTATTGCTAATTGGGCCCGATTTCAAACCCAATTAAGCCCAAC-AC
1 AATAAAGATAATCTCATTTTTATTGCTAATTGGGCCCGATTCCAAACCCAATTAAGCCCAACGAC
* *
290559 TTAAATTAGAATTTTTGCGGGATACACTTACCCTCTCGGATAAAC-CTGAAACTATTAACC-CGA
66 TTAAATTAGAATTTTCGCGGGATACACTTACCCTCTCGGATAAACTC-GAAACTACTAACCTC-A
* * ** *
290622 ATTTTGGCATGTTACAGCTGACATAAACATTGATAACAATATAAAATAGTTAACATCAATTTAAT
129 AATTTGACATGTTACAAATGACAAAAACATTGATAACAATATAAAATAGTTAACATCAATTTAAT
* * *
290687 AGTTTTGTTAATTTTTTTGTCAGTTGACTCAATTTAATAAAAATGTTTAAGAATGAGAACAGAAA
194 AATTTTGTTAA-TTTTTTGTCAATTGACTCAATTTAATAAAAATGTTTAAGAATGAAAACAGAAA
290752 AAATAA
258 AAATAA
290758 AATAAAGATA
1 AATAAAGATA
290768 GATATAATAT
Statistics
Matches: 251, Mismatches: 18, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
261 2 0.01
262 131 0.52
263 118 0.47
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (263 bp):
AATAAAGATAATCTCATTTTTATTGCTAATTGGGCCCGATTCCAAACCCAATTAAGCCCAACGAC
TTAAATTAGAATTTTCGCGGGATACACTTACCCTCTCGGATAAACTCGAAACTACTAACCTCAAA
TTTGACATGTTACAAATGACAAAAACATTGATAACAATATAAAATAGTTAACATCAATTTAATAA
TTTTGTTAATTTTTTGTCAATTGACTCAATTTAATAAAAATGTTTAAGAATGAAAACAGAAAAAA
TAA
Found at i:291498 original size:17 final size:17
Alignment explanation
Indices: 291478--291525 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
291468 GGTAAAACAT
291478 ATTAAATAATAAATATA
1 ATTAAATAATAAATATA
* *
291495 ATT-ATTATATAACTATA
1 ATTAAATA-ATAAATATA
*
291512 ATTAAAAAATAAAT
1 ATTAAATAATAAAT
291526 TTGGGGCTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
16 3 0.12
17 19 0.79
18 2 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTAAATAATAAATATA
Found at i:301326 original size:26 final size:26
Alignment explanation
Indices: 301296--301350 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
301286 TCTTTTCAAG
301296 GAGTTTGATGTGTTAGATATTGAGGA
1 GAGTTTGATGTGTTAGATATTGAGGA
301322 GAGTTTGATGTGTTAGATATTGAGGA
1 GAGTTTGATGTGTTAGATATTGAGGA
301348 GAG
1 GAG
301351 GTTGTGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.36, T:0.36
Consensus pattern (26 bp):
GAGTTTGATGTGTTAGATATTGAGGA
Found at i:301593 original size:13 final size:13
Alignment explanation
Indices: 301575--301602 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
301565 ACATAAATCG
301575 GAAATGTGAATGT
1 GAAATGTGAATGT
301588 GAAATGTGAATGT
1 GAAATGTGAATGT
301601 GA
1 GA
301603 TGTGTAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (13 bp):
GAAATGTGAATGT
Found at i:311572 original size:28 final size:29
Alignment explanation
Indices: 311536--311595 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
311526 AATTTAATCC
311536 TTTTATTAT-TATTATATTTTATTA-TTTA
1 TTTTATTATATA-TATATTTTATTATTTTA
* *
311564 TTTTGTTATATATATATTTTTTTATTTTA
1 TTTTATTATATATATATTTTATTATTTTA
311593 TTT
1 TTT
311596 ATTTAACCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (29 bp):
TTTTATTATATATATATTTTATTATTTTA
Found at i:311661 original size:68 final size:69
Alignment explanation
Indices: 311511--311668 Score: 187
Period size: 68 Copynumber: 2.3 Consensus size: 69
311501 GACCACCCAA
* * * * *
311511 TTTGCTTTTTATTTCAATTTAATCCTTTTATTATTATTATATTTTATTATTTATTTTGTTATATA
1 TTTG-TTTTTATTT--ATTTAACCCTTTTATTATTATTATATATAATTATATATTTTATTATATA
311576 TATATTT
63 TATATTT
*
311583 TTT-TATTTTATTTATTTAACCCTTCTTATTATTATTATATATAATTATAT-TTTTATT-TATTT
1 TTTGT-TTTTATTTATTTAACCCTT-TTATTATTATTATATATAATTATATATTTTATTATATAT
*
311645 CTATTT
64 ATATTT
311651 TTTGTTTTTATTTATTTA
1 TTTGTTTTTATTTATTTA
311669 TTTATATATA
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
68 25 0.33
69 17 0.22
70 23 0.30
71 8 0.11
72 3 0.04
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.68
Consensus pattern (69 bp):
TTTGTTTTTATTTATTTAACCCTTTTATTATTATTATATATAATTATATATTTTATTATATATAT
ATTT
Found at i:311911 original size:15 final size:15
Alignment explanation
Indices: 311891--311921 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
311881 ACCAAACTTA
*
311891 TATTTTCTTTTGTTT
1 TATTTTCTTTTCTTT
311906 TATTTTCTTTTCTTT
1 TATTTTCTTTTCTTT
311921 T
1 T
311922 CGGTGGAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.10, G:0.03, T:0.81
Consensus pattern (15 bp):
TATTTTCTTTTCTTT
Found at i:312037 original size:4 final size:4
Alignment explanation
Indices: 312028--312216 Score: 82
Period size: 4 Copynumber: 47.8 Consensus size: 4
312018 TATATTTTTG
* *
312028 TTTA TTTA TTTA TTTA TTTA -TT- TTTA TTTA TTTCA TTTTC TTTA TTTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A -TTTA TTTA TTTA
* * * **
312076 TTGTA GTTT- TATA TTT- TTATA TTTA CTTA TTT- TCTA TTCCC TTTA
1 TT-TA -TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TT-TA TTTA
312121 --TA TTTA TTT- TGTT- TCTTA TTTA TTTA TTTA TTTA -TT- TTTA TTTA
1 TTTA TTTA TTTA T-TTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
312165 TTTA -TTA TATTA -TTA -TTA TATTC TTTA TTTTA CTTA TTTTT TTTA
1 TTTA TTTA T-TTA TTTA TTTA T-TTA TTTA -TTTA TTTA -TTTA TTTA
312210 TTTA TTT
1 TTTA TTT
312217 TTACTTTTAC
Statistics
Matches: 141, Mismatches: 21, Indels: 46
0.68 0.10 0.22
Matches are distributed among these distances:
2 2 0.01
3 24 0.17
4 90 0.64
5 20 0.14
6 5 0.04
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:312037 original size:14 final size:14
Alignment explanation
Indices: 311987--312243 Score: 127
Period size: 14 Copynumber: 18.8 Consensus size: 14
311977 TACATAATAG
* *
311987 TTATATATTTTTGT
1 TTATTTATTTTTAT
*
312001 TT-TTAATTTTTCA-
1 TTATTTATTTTT-AT
*
312014 TTATTATATTTTTGT
1 TTATT-TATTTTTAT
312029 TTATTTA--TTTAT
1 TTATTTATTTTTAT
312041 TTATTTATTTTTAT
1 TTATTTATTTTTAT
*
312055 TTATTTCA-TTTTCT
1 TTATTT-ATTTTTAT
*
312069 TTATTT-TTTGTAGT
1 TTATTTATTTTTA-T
*
312083 TT-TATATTTTTA-
1 TTATTTATTTTTAT
312095 -TATTTACTTATTT-T
1 TTATTTA-TT-TTTAT
* ** *
312109 CTATTCCCTTTATAT
1 TTATT-TATTTTTAT
* *
312124 TTATTT-TGTTT-C
1 TTATTTATTTTTAT
312136 TTATTTA--TTTAT
1 TTATTTATTTTTAT
312148 TTATTTATTTTTAT
1 TTATTTATTTTTAT
312162 TTATTTATTATATTA-
1 TTATTTATT-T-TTAT
312177 TTATTATATTCTTTATT
1 TTATT-TATT-TTTA-T
*
312194 TTACTTATTTTT-T
1 TTATTTATTTTTAT
312207 TTATTTATTTTTA-
1 TTATTTATTTTTAT
* *
312220 CT-TTTACTTTTAT
1 TTATTTATTTTTAT
*
312233 TTTTTTATTTT
1 TTATTTATTTT
312244 CTTATCTTTA
Statistics
Matches: 186, Mismatches: 28, Indels: 58
0.68 0.10 0.21
Matches are distributed among these distances:
11 4 0.02
12 36 0.19
13 33 0.18
14 62 0.33
15 35 0.19
16 12 0.06
17 4 0.02
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (14 bp):
TTATTTATTTTTAT
Found at i:312048 original size:28 final size:27
Alignment explanation
Indices: 311990--312066 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 27
311980 ATAATAGTTA
* *
311990 TATATTTTTGTTT-TTAATTTTTCATTAT
1 TATATTTTTGTTTATTTATTTTTTA-T-T
312018 TATATTTTTGTTTATTTATTTATTTA-T
1 TATATTTTTGTTTATTTATTT-TTTATT
*
312045 T-TATTTTTATTTATTTCATTTT
1 TATATTTTTGTTTATTT-ATTTT
312067 CTTTATTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
26 15 0.35
27 6 0.14
28 13 0.30
29 6 0.14
30 3 0.07
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (27 bp):
TATATTTTTGTTTATTTATTTTTTATT
Found at i:312053 original size:18 final size:18
Alignment explanation
Indices: 312032--312243 Score: 100
Period size: 18 Copynumber: 11.1 Consensus size: 18
312022 TTTTTGTTTA
312032 TTTATTTATTTATTTATT
1 TTTATTTATTTATTTATT
*
312050 TTTATTTATTTCATTT-TC
1 TTTATTTATTT-ATTTATT
*
312068 TTTATTTTTTGTAGTTTTATAT
1 TTTATTTATT-TA--TTTAT-T
* *
312090 TTT-TATATTTACTTATT
1 TTTATTTATTTATTTATT
312107 TTCTATTCCCT-TTATATTTATT
1 TT-TATT---TATT-TATTTATT
*
312129 TTGTTTCTTATTTATTTA--
1 TT-TAT-TTATTTATTTATT
312147 TTTATTTATTTTTATTTATT
1 TTTATTTA--TTTATTTATT
312167 TATTATATTA-TTATTATATT
1 T-TTAT-TTATTTATT-TATT
*
312187 CTTTATTTTACTTATTT-TT
1 -TTTA-TTTATTTATTTATT
*
312206 TTTATTTA-TT-TTTACT
1 TTTATTTATTTATTTATT
*
312222 TTTACTTTTATTTTTTTATT
1 TTTA--TTTATTTATTTATT
312242 TT
1 TT
312244 CTTATCTTTA
Statistics
Matches: 152, Mismatches: 13, Indels: 56
0.69 0.06 0.25
Matches are distributed among these distances:
15 3 0.02
16 10 0.07
17 9 0.06
18 45 0.30
19 15 0.10
20 31 0.20
21 20 0.13
22 18 0.12
23 1 0.01
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73
Consensus pattern (18 bp):
TTTATTTATTTATTTATT
Found at i:312086 original size:129 final size:136
Alignment explanation
Indices: 311953--312245 Score: 292
Period size: 133 Copynumber: 2.2 Consensus size: 136
311943 TTTTTTTATT
311953 TTTTACTATTTATTATTATTATTTTACATAAT-AGTTATATAT-TTTTGTTT-TTAATTT-TTCA
1 TTTTACTATTTATTATTATTATTTT-C-TAATCAGTTATATATATTTTGTTTCTT-ATTTATTCA
* *
312014 -TTATTATATTTTTGTTTATTTATT-TA-T-TTATT-TATT-TTTA-TTTATTTCATTTTCTTTA
63 TTTATT-TATTTTTATTTATTTATTATATTATTATTATATTCTTTATTTTACTT-ATTTTCTTTA
*
312072 TTT-TTTGTAG
126 TTTATTTGTAC
* * ** * *
312082 TTTTA-TATTTTTATATTTACTTATTTTCTATTCCCTTTATATTTATTTTGTTTCTTATTTATTT
1 TTTTACTATTTAT-TA-TTA-TTATTTTCTAAT-CAGTTATATATATTTTGTTTCTTATTTATTC
*
312146 ATTTATTTATTTTTATTTATTTATTATATTATTATTATATTCTTTATTTTACTTATTTTTTTTAT
62 ATTTATTTATTTTTATTTATTTATTATATTATTATTATATTCTTTATTTTACTTATTTTCTTTAT
*
312211 TTATTTTTAC
127 TTATTTGTAC
*
312221 TTTTACT-TTTATT-TTTTTATTTTCT
1 TTTTACTATTTATTATTATTATTTTCT
312246 TATCTTTATT
Statistics
Matches: 134, Mismatches: 13, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
128 6 0.04
129 10 0.07
130 4 0.03
131 14 0.10
132 12 0.09
133 22 0.16
134 7 0.05
135 10 0.07
136 7 0.05
137 4 0.03
138 17 0.13
139 20 0.15
140 1 0.01
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (136 bp):
TTTTACTATTTATTATTATTATTTTCTAATCAGTTATATATATTTTGTTTCTTATTTATTCATTT
ATTTATTTTTATTTATTTATTATATTATTATTATATTCTTTATTTTACTTATTTTCTTTATTTAT
TTGTAC
Found at i:312180 original size:29 final size:29
Alignment explanation
Indices: 312139--312344 Score: 75
Period size: 29 Copynumber: 7.3 Consensus size: 29
312129 TTGTTTCTTA
*
312139 TTTA-TTTATTTATTTATTTTTATTTATT
1 TTTACTTTATTTATTTATTATTATTTATT
*
312167 TATTA-TATTA-TTA-TTA-TATTCTTTA-T
1 T-TTACT-TTATTTATTTATTATTATTTATT
* *
312193 TTTAC-TTATTTTTTTTATTTATT-TTTACT
1 TTTACTTTA-TTTATTTA-TTATTATTTATT
* * *
312222 TTTACTTTTATTTTTTTATT-TT-CTTATC
1 TTTAC-TTTATTTATTTATTATTATTTATT
* * * *
312250 TTTATTTTA-TTATTTTATTATTCTTTGTC
1 TTTACTTTATTTA-TTTATTATTATTTATT
*
312279 TTTACTTTATTT-TCTT-TT-TTATCTCA-T
1 TTTACTTTATTTAT-TTATTATTAT-TTATT
* *
312306 TTTACTTT-TTTCTTTTATTATTTTTTATT
1 TTTACTTTATTT-ATTTATTATTATTTATT
312335 TATGTACTTT
1 T-T-TACTTT
312345 CATTATCTTT
Statistics
Matches: 137, Mismatches: 17, Indels: 45
0.69 0.09 0.23
Matches are distributed among these distances:
24 3 0.02
25 3 0.02
26 9 0.07
27 33 0.24
28 28 0.20
29 38 0.28
30 14 0.10
31 9 0.07
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.73
Consensus pattern (29 bp):
TTTACTTTATTTATTTATTATTATTTATT
Found at i:312186 original size:11 final size:10
Alignment explanation
Indices: 312136--312183 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 10
312126 ATTTTGTTTC
312136 TTATTTATTTA
1 TTATTTA-TTA
*
312147 TTTATTTATTT
1 -TTATTTATTA
312158 TTATTTATTTA
1 TTATTTA-TTA
312169 TTATATTATTA
1 TTAT-TTATTA
312180 TTAT
1 TTAT
312184 ATTCTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 7 0.22
11 15 0.47
12 10 0.31
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTATTTATTA
Found at i:312217 original size:22 final size:23
Alignment explanation
Indices: 312020--312329 Score: 114
Period size: 22 Copynumber: 13.9 Consensus size: 23
312010 TTCATTATTA
*
312020 TATTTT-TGTTTATTTA-TTTATT
1 TATTTTAT-TTTATTTATTTTACT
*
312042 TA-TTTATTTTTATTTATTTCA-T
1 TATTTTA-TTTTATTTATTTTACT
*
312064 TTTCTTTATTTT-TTGTAGTTTTA--
1 TAT-TTTATTTTATT-TA-TTTTACT
*
312087 TATTTTTATATTTACTTATTTT-C-
1 TA-TTTTAT-TTTATTTATTTTACT
*** *
312110 TATTCCCTTTATATTTATTTT-GT
1 TATTTTATTT-TATTTATTTTACT
* *
312133 T-TCTTA-TTTATTTA-TTTATT
1 TATTTTATTTTATTTATTTTACT
*
312153 TATTTT-TATTTATTTATTATA-T
1 TATTTTAT-TTTATTTATTTTACT
* *
312175 TATTATTATATTCTTTATTTTACT
1 TATT-TTATTTTATTTATTTTACT
312199 TATTTT-TTTTATTTATTTTTACTTT
1 TATTTTATTTTATTTA-TTTTAC--T
312224 TACTTTTATTTT-TTTATTTT-CT
1 TA-TTTTATTTTATTTATTTTACT
312246 TATCTTTATTTTA-TTATTTTA-T
1 TAT-TTTATTTTATTTATTTTACT
* * * *
312268 TATTCT-TTGTCTTTACTTTA-T
1 TATTTTATTTTATTTATTTTACT
*
312289 T-TTCTT-TTTTATCTCATTTTACT
1 TATT-TTATTTTAT-TTATTTTACT
*
312312 T-TTTTCTTTTA-TTATTTT
1 TATTTTATTTTATTTATTTT
312330 TTATTTATGT
Statistics
Matches: 222, Mismatches: 32, Indels: 69
0.69 0.10 0.21
Matches are distributed among these distances:
19 3 0.01
20 13 0.06
21 33 0.15
22 77 0.35
23 55 0.25
24 21 0.09
25 8 0.04
26 8 0.04
27 4 0.02
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (23 bp):
TATTTTATTTTATTTATTTTACT
Found at i:312240 original size:8 final size:8
Alignment explanation
Indices: 312000--312271 Score: 70
Period size: 8 Copynumber: 32.0 Consensus size: 8
311990 TATATTTTTG
*
312000 TTTTTAAT
1 TTTTTATT
*
312008 TTTTCATT
1 TTTTTATT
* *
312016 ATTATATTT
1 TTTTTA-TT
312025 TTGTTTATT
1 TT-TTTATT
*
312034 TATTTATT
1 TTTTTATT
*
312042 TATTTA--
1 TTTTTATT
312048 TTTTTATT
1 TTTTTATT
*
312056 TATTTCATT
1 T-TTTTATT
312065 TTCTTTATT
1 TT-TTTATT
*
312074 TTTTGTAGT
1 TTTT-TATT
*
312083 TTTATATT
1 TTTTTATT
*
312091 TTTATATT
1 TTTTTATT
**
312099 TACTTA-T
1 TTTTTATT
*
312106 TTTCTATT
1 TTTTTATT
*
312114 CCCTTTATATT
1 ---TTTTTATT
*
312125 TATTTT-GT
1 T-TTTTATT
*
312133 TTCTTATT
1 TTTTTATT
*
312141 TATTTATT
1 TTTTTATT
*
312149 TATTTATTT
1 TTTTTA-TT
312158 TTATTTATT
1 TT-TTTATT
*
312167 TATTATATT
1 T-TTTTATT
*
312176 ATTATTATAT
1 -TTTTTAT-T
*
312186 TCTTTATT
1 TTTTTATT
*
312194 TTACTTATTT
1 TT-TTTA-TT
312204 TTTTTATTT
1 TTTTTA-TT
312213 ATTTTTACTTT
1 -TTTTTA--TT
312224 TACTTTTATT
1 T--TTTTATT
312234 TTTTTATT
1 TTTTTATT
*
312242 TTCTTA--
1 TTTTTATT
*
312248 TCTTTATT
1 TTTTTATT
*
312256 TTATTATT
1 TTTTTATT
*
312264 TTATTATT
1 TTTTTATT
312272 CTTTGTCTTT
Statistics
Matches: 197, Mismatches: 41, Indels: 52
0.68 0.14 0.18
Matches are distributed among these distances:
6 9 0.05
7 7 0.04
8 84 0.43
9 58 0.29
10 24 0.12
11 10 0.05
12 5 0.03
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73
Consensus pattern (8 bp):
TTTTTATT
Found at i:312240 original size:85 final size:83
Alignment explanation
Indices: 312143--312337 Score: 218
Period size: 85 Copynumber: 2.3 Consensus size: 83
312133 TTCTTATTTA
*
312143 TTTATTTATTTATTTTTATTTATTTATTATATTATTATTA-TATTCTTTAT-TTTAC-TTATTTT
1 TTTATTTTTTTATTTTT-TTTATTTATTATATTATT-TTATTATTCTTTATCTTTACTTTATTTT
* * *
312205 TTTTATTTATTTTTACTTTTACT
64 CTTT-TTTA-TCTCA-TTTTACT
* * * *
312228 TTTATTTTTTTATTTTCTTATCTTTATTTTATTATTTTATTATTCTTTGTCTTTACTTTATTTTC
1 TTTATTTTTTTATTTT-TTTTATTTATTATATTATTTTATTATTCTTTATCTTTACTTTATTTTC
312293 TTTTTTATCTCATTTTACT
65 TTTTTTATCTCATTTTACT
*
312312 TTT-TTCTTTTATTATTTTTTATTTAT
1 TTTATTTTTTTATT-TTTTTTATTTAT
312338 GTACTTTCAT
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
83 17 0.18
84 15 0.16
85 42 0.45
86 10 0.11
87 10 0.11
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (83 bp):
TTTATTTTTTTATTTTTTTTATTTATTATATTATTTTATTATTCTTTATCTTTACTTTATTTTCT
TTTTTATCTCATTTTACT
Found at i:312253 original size:14 final size:13
Alignment explanation
Indices: 312132--312274 Score: 55
Period size: 14 Copynumber: 10.5 Consensus size: 13
312122 ATTTATTTTG
312132 TTTCTTA-TTTAT
1 TTTCTTATTTTAT
312144 TTAT-TTA-TTTAT
1 TT-TCTTATTTTAT
*
312156 TTT-TATTTATTTAT
1 TTTCT-TAT-TTTAT
* *
312170 TATATTATTATTAT
1 TTTCTTATT-TTAT
*
312184 ATTCTTTATTTTACT
1 TTTC-TTATTTTA-T
312199 TATT-TT-TTTTATT
1 T-TTCTTATTTTA-T
*
312212 TATTTTTACTTTTACT
1 T-TTCTTA-TTTTA-T
* *
312228 TTTATTTTTTTAT
1 TTTCTTATTTTAT
312241 TTTCTTATCTTTAT
1 TTTCTTAT-TTTAT
*
312255 TTTATTATTTTAT
1 TTTCTTATTTTAT
312268 TATTCTT
1 T-TTCTT
312275 TGTCTTTACT
Statistics
Matches: 102, Mismatches: 15, Indels: 26
0.71 0.10 0.18
Matches are distributed among these distances:
11 2 0.02
12 13 0.13
13 25 0.25
14 42 0.41
15 11 0.11
16 9 0.09
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCTTATTTTAT
Found at i:312258 original size:49 final size:49
Alignment explanation
Indices: 312139--312265 Score: 133
Period size: 49 Copynumber: 2.6 Consensus size: 49
312129 TTGTTTCTTA
*
312139 TTTA-TTTATTTA-TTTATTTTTATTTATTTATTATATTATTATTATATTC
1 TTTATTTTACTTATTTTA-TTTTATTTATTT-TTATATTATTATTATATTC
* *
312188 TTTATTTTACTTATTTT-TTTTATTTATTTTTACTTTTACTT-TTAT-TTT
1 TTTATTTTACTTATTTTATTTTATTTATTTTTA-TATTA-TTATTATATTC
312236 TTTATTTT-CTTATCTTTATTTTA-TTATTTT
1 TTTATTTTACTTAT-TTTATTTTATTTATTTT
312266 ATTATTCTTT
Statistics
Matches: 69, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
47 5 0.07
48 23 0.33
49 29 0.42
50 9 0.13
51 3 0.04
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (49 bp):
TTTATTTTACTTATTTTATTTTATTTATTTTTATATTATTATTATATTC
Found at i:312322 original size:56 final size:54
Alignment explanation
Indices: 312191--312330 Score: 144
Period size: 56 Copynumber: 2.5 Consensus size: 54
312181 TATATTCTTT
*
312191 ATTTTACTTATTTTTTTTATTTATTTTTACTTTTACTTTTATTTTTTTATTTTCTT
1 ATTTTACTT-TTTTTTTTA-TTATTTTTACTTTTACTTTTATTTTTTTATTTTCTC
*
312247 ATCTTTA-TTTTATTATTTTATTATTCTTT-GTCTTTAC-TTTATTTTCTTT-TTTATCTC
1 AT-TTTACTTTT-TT-TTTTATTATT-TTTACT-TTTACTTTTATTTT-TTTATTT-TCTC
312304 ATTTTACTTTTTTCTTTTATTATTTTT
1 ATTTTACTTTTTT-TTTTATTATTTTT
312331 TATTTATGTA
Statistics
Matches: 73, Mismatches: 3, Indels: 17
0.78 0.03 0.18
Matches are distributed among these distances:
55 5 0.07
56 39 0.53
57 29 0.40
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.74
Consensus pattern (54 bp):
ATTTTACTTTTTTTTTTATTATTTTTACTTTTACTTTTATTTTTTTATTTTCTC
Found at i:313109 original size:40 final size:40
Alignment explanation
Indices: 313064--313145 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 40
313054 CTAATCGAAT
* *
313064 TTATAAA-ATTTA-AATTATTTTGATTTTTATTTAAATTTAA
1 TTATAAATATTTATAA-TATTATGA-TATTATTTAAATTTAA
*
313104 TTATAAATATTTATAATATTATGATATTATTTAATTTTAA
1 TTATAAATATTTATAATATTATGATATTATTTAAATTTAA
313144 TT
1 TT
313146 TAGACCATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 23 0.62
41 12 0.32
42 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (40 bp):
TTATAAATATTTATAATATTATGATATTATTTAAATTTAA
Found at i:319597 original size:30 final size:31
Alignment explanation
Indices: 319561--319649 Score: 126
Period size: 32 Copynumber: 2.9 Consensus size: 31
319551 AGGACCTATT
* *
319561 CATATGTTCCGAAGAACATAGGTAA-CTGTC
1 CATATGTCCCGAAGGACATAGGTAACCTGTC
319591 CATATGTCCCGAAGGACATAGGTAATCCTGTC
1 CATATGTCCCGAAGGACATAGGTAA-CCTGTC
* *
319623 TATATGTCCCGAAGGACATAGGCAACC
1 CATATGTCCCGAAGGACATAGGTAACC
319650 CTCGACTCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
30 23 0.43
31 2 0.04
32 28 0.53
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (31 bp):
CATATGTCCCGAAGGACATAGGTAACCTGTC
Found at i:325195 original size:33 final size:33
Alignment explanation
Indices: 325153--325217 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
325143 ATCAGTGAAA
* *
325153 ACAAACCCAATCCCTAGAAGTAGCTGGAGAGCG
1 ACAAACCCAATCCCAAGAAGTAGATGGAGAGCG
325186 ACAAACCCAATCCCAAGAAGTAGATGGAGAGC
1 ACAAACCCAATCCCAAGAAGTAGATGGAGAGC
325218 TCCAGCGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
ACAAACCCAATCCCAAGAAGTAGATGGAGAGCG
Found at i:327324 original size:19 final size:20
Alignment explanation
Indices: 327300--327339 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
327290 CCATCCCCGA
*
327300 ACCCGACCCG-AAATATTAT
1 ACCCGAACCGAAAATATTAT
327319 ACCCGAACCGAAAATATTAT
1 ACCCGAACCGAAAATATTAT
327339 A
1 A
327340 TATAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (20 bp):
ACCCGAACCGAAAATATTAT
Found at i:327429 original size:11 final size:12
Alignment explanation
Indices: 327410--327440 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
327400 CCGAACCCGA
327410 CCCGAAAAAATC
1 CCCGAAAAAATC
327422 CCCGAAAAAATC
1 CCCGAAAAAATC
327434 CCCGAAA
1 CCCGAAA
327441 CCGAACCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.48, C:0.35, G:0.10, T:0.06
Consensus pattern (12 bp):
CCCGAAAAAATC
Found at i:328945 original size:17 final size:17
Alignment explanation
Indices: 328919--328953 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
328909 TTTTGGTTCG
328919 GTCTGACCTGTTTAAAA
1 GTCTGACCTGTTTAAAA
*
328936 GTCTGGCCTGTTTAAAA
1 GTCTGACCTGTTTAAAA
328953 G
1 G
328954 CTTGTTTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (17 bp):
GTCTGACCTGTTTAAAA
Found at i:336523 original size:17 final size:17
Alignment explanation
Indices: 336503--336544 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
336493 TTCATATTTT
336503 AAATAAATTTTAACAT-A
1 AAATAAATTTTAA-ATGA
*
336520 AAATATATTTTTAAATGA
1 AAATA-AATTTTAAATGA
336538 AAATAAA
1 AAATAAA
336545 ATAAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
AAATAAATTTTAAATGA
Found at i:336642 original size:25 final size:25
Alignment explanation
Indices: 336588--336651 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
336578 CATATTTAAT
* * *
336588 AATTTAATAGA-A-AAAATATTTTT
1 AATTTAATATATATAAAATATTATG
*
336611 AAGTTAATATATATAAAATATTATG
1 AATTTAATATATATAAAATATTATG
*
336636 AATTTAAGTATTTATA
1 AATTTAA-TATATATA
336652 CACTAAGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 9 0.28
24 1 0.03
25 15 0.47
26 7 0.22
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (25 bp):
AATTTAATATATATAAAATATTATG
Found at i:340727 original size:22 final size:19
Alignment explanation
Indices: 340681--340729 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
340671 AGTCATCATG
340681 TATCATCATTTTCGTCCAC
1 TATCATCATTTTCGTCCAC
340700 TATCATCATTTTCGTCCAC
1 TATCATCATTTTCGTCCAC
*
340719 TATCGTCATTT
1 TATCATCATTT
340730 ATCTTATTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.20, C:0.29, G:0.06, T:0.45
Consensus pattern (19 bp):
TATCATCATTTTCGTCCAC
Found at i:346014 original size:2 final size:2
Alignment explanation
Indices: 346007--346040 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
345997 TTACCAACTA
346007 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
346041 GCAATGTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:347275 original size:3 final size:3
Alignment explanation
Indices: 347264--347324 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
347254 TTTTTTTCCG
*
347264 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCA TTA -TA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
347309 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
347325 CAATTTTTGC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 6 0.12
3 43 0.83
4 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:347455 original size:26 final size:25
Alignment explanation
Indices: 347402--347600 Score: 371
Period size: 25 Copynumber: 7.9 Consensus size: 25
347392 ACCCACCAGA
347402 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
347427 TTAGGGTTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCT-AAATCAGT
*
347453 TTAGGGGTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCT-AAATCAGT
347479 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
347504 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
347529 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
347554 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
347579 TTAGGGTTTCAAACCCTAAATC
1 TTAGGGTTTCAAACCCTAAATC
347601 CCCAACTGCA
Statistics
Matches: 171, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
25 122 0.71
26 49 0.29
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (25 bp):
TTAGGGTTTCAAACCCTAAATCAGT
Found at i:349551 original size:15 final size:16
Alignment explanation
Indices: 349528--349561 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
349518 TAGAAATTAT
*
349528 TTTTATTGTTATTTTA
1 TTTTATTGTTAATTTA
349544 TTTT-TTGTTAATTTA
1 TTTTATTGTTAATTTA
349559 TTT
1 TTT
349562 GATGTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTATTGTTAATTTA
Found at i:362679 original size:3 final size:3
Alignment explanation
Indices: 362673--362724 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
362663 TTTTTTTCCG
362673 TTA TTA TTA TT- TTA TTA TT- TTCA TTA -TA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
362715 TTTA TTA TTA
1 -TTA TTA TTA
362725 CAATTTTTGC
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
2 8 0.19
3 30 0.70
4 5 0.12
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:362709 original size:22 final size:23
Alignment explanation
Indices: 362677--362722 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
362667 TTTCCGTTAT
*
362677 TATTATTTTATTATT-TTCATTA
1 TATTATATTATTATTATTCATTA
*
362699 TATTATATTATTATTATTTATTA
1 TATTATATTATTATTATTCATTA
362722 T
1 T
362723 TACAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTATATTATTATTATTCATTA
Found at i:362843 original size:25 final size:25
Alignment explanation
Indices: 362798--362965 Score: 276
Period size: 25 Copynumber: 6.9 Consensus size: 25
362788 ACAACCCAGA
362798 TTAGGGTTTCAAAACCCTAAATCAGT
1 TTAGGGTTTC-AAACCCTAAATCAGT
362824 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
362849 TTAGGGTTTC-AACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCT-AAATCAGT
362874 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
362899 TTAGGGTTTCAAACCCTAAATC---
1 TTAGGGTTTCAAACCCTAAATCAGT
362921 -TAGGGTTTCAAACCCT-AATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
362944 TTAGGGTTTCAAACCCTAAATC
1 TTAGGGTTTCAAACCCTAAATC
362966 CCCAACTCAC
Statistics
Matches: 135, Mismatches: 0, Indels: 15
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.03
21 16 0.12
24 22 0.16
25 77 0.57
26 16 0.12
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (25 bp):
TTAGGGTTTCAAACCCTAAATCAGT
Found at i:363326 original size:30 final size:30
Alignment explanation
Indices: 363270--363327 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
363260 AAGCAAAAAG
* * *
363270 GAAACAAAAAATAAAGAGGGACGAAAAATC
1 GAAACAAAAAAAAAAAAGAGACGAAAAATC
363300 GAAACAGAAAAAAAAAAAGAGA-GAAAAA
1 GAAACA-AAAAAAAAAAAGAGACGAAAAA
363328 AGAAAGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.71, C:0.07, G:0.19, T:0.03
Consensus pattern (30 bp):
GAAACAAAAAAAAAAAAGAGACGAAAAATC
Done.