Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 84 of 130
Found at i:16687042 original size:16 final size:16
Alignment explanation
Indices: 16687001--16687043 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
16686991 GAGAAAAATG
16687001 AAATGGAAAAATGAAAA
1 AAAT-GAAAAATGAAAA
*
16687018 AGAA-AAAAAATGAAAA
1 A-AATGAAAAATGAAAA
16687034 AAATGAAAAA
1 AAATGAAAAA
16687044 AGTGAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
15 2 0.09
16 17 0.77
17 1 0.05
18 2 0.09
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (16 bp):
AAATGAAAAATGAAAA
Found at i:16688096 original size:41 final size:41
Alignment explanation
Indices: 16688051--16688180 Score: 152
Period size: 41 Copynumber: 3.1 Consensus size: 41
16688041 ATAATTGTCA
*
16688051 AGGAGCAATCTATTCTTCAAAGTTGTGATGCCTCTGATTAG
1 AGGAGCAATCTATTCTTAAAAGTTGTGATGCCTCTGATTAG
* ** *
16688092 AGGAGCAACCTATTCTTTGAAGTTGTGATGCCTCTGTTTAG
1 AGGAGCAATCTATTCTTAAAAGTTGTGATGCCTCTGATTAG
* * * * **
16688133 AGGAGCAATTTATTTTTTAAAAGTCGTTAAACCTCTGATTAG
1 AGGAGCAATCTA-TTCTTAAAAGTTGTGATGCCTCTGATTAG
16688175 AGGAGC
1 AGGAGC
16688181 TTTGTTTATT
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 47 0.64
42 27 0.36
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (41 bp):
AGGAGCAATCTATTCTTAAAAGTTGTGATGCCTCTGATTAG
Found at i:16688224 original size:85 final size:88
Alignment explanation
Indices: 16688119--16688287 Score: 263
Period size: 85 Copynumber: 2.0 Consensus size: 88
16688109 TGAAGTTGTG
* *
16688119 ATGCCTCTGTTTAGAGGAGCAATTTATTTTT-TAAAAGTCGTTAAACCTCTGATTAGAGGAGCTT
1 ATGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAAGTCGTTAAACCTCTGATTAGAAGAGCTT
16688183 TG-TT-TATTTTTCAAAGTTACA
66 TGTTTATATTTTTCAAAGTTACA
* ** *
16688204 ATGCCTCTGTTTAGATGAGCAATTTATTTTTCAAAAAGTCGTTAAGTCTCTGATTAGAAGTGCTT
1 ATGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAAGTCGTTAAACCTCTGATTAGAAGAGCTT
16688269 TGTTTATATTTTTCAAAGT
66 TGTTTATATTTTTCAAAGT
16688288 CATTGAGCCT
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
85 30 0.40
86 30 0.40
87 2 0.03
88 13 0.17
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (88 bp):
ATGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAAGTCGTTAAACCTCTGATTAGAAGAGCTT
TGTTTATATTTTTCAAAGTTACA
Found at i:16688242 original size:43 final size:42
Alignment explanation
Indices: 16688119--16688242 Score: 121
Period size: 43 Copynumber: 2.9 Consensus size: 42
16688109 TGAAGTTGTG
* *
16688119 ATGCCTCTGTTTAGAGGAGCAATTTATTTTTTAAAAGTCGTTAA
1 ATGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAA--AGTTAA
* **
16688163 A--CCTCTGATTAGAGGAGCTTTGTTTATTTTTC--AAAGTTACA
1 ATGCCTCTGTTTAGAGGAGC--AATTTATTTTTCAAAAAGTTA-A
*
16688204 ATGCCTCTGTTTAGATGAGCAATTTATTTTTCAAAAAGT
1 ATGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAAGT
16688243 CGTTAAGTCT
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
40 4 0.06
41 12 0.19
42 18 0.28
43 20 0.31
44 10 0.16
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (42 bp):
ATGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAAGTTAA
Found at i:16688255 original size:43 final size:42
Alignment explanation
Indices: 16688051--16688261 Score: 146
Period size: 41 Copynumber: 5.0 Consensus size: 42
16688041 ATAATTGTCA
* * * * *
16688051 AGGAGCAATCTATTCTTC-AAAGTTGTGATGCCTCTGATTAG
1 AGGAGCAATTTATTTTTCAAAAGTCGTTAAGCCTCTGATTAG
** * * * * *
16688092 AGGAGCAACCTATTCTTT--GAAGTTGTGATGCCTCTGTTTAG
1 AGGAGCAATTTATT-TTTCAAAAGTCGTTAAGCCTCTGATTAG
* *
16688133 AGGAGCAATTTATTTTTTAAAAGTCGTTAAACCTCTGATTAG
1 AGGAGCAATTTATTTTTCAAAAGTCGTTAAGCCTCTGATTAG
** * *
16688175 AGGAGCTTTGTTTATTTTTC-AAAGT--TACAATGCCTCTGTTTAG
1 AGGAGC--AATTTATTTTTCAAAAGTCGT-TAA-GCCTCTGATTAG
* *
16688218 ATGAGCAATTTATTTTTCAAAAAGTCGTTAAGTCTCTGATTAG
1 AGGAGCAATTTATTTTTC-AAAAGTCGTTAAGCCTCTGATTAG
16688261 A
1 A
16688262 AGTGCTTTGT
Statistics
Matches: 135, Mismatches: 24, Indels: 20
0.75 0.13 0.11
Matches are distributed among these distances:
40 3 0.02
41 57 0.42
42 27 0.20
43 36 0.27
44 11 0.08
45 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.38
Consensus pattern (42 bp):
AGGAGCAATTTATTTTTCAAAAGTCGTTAAGCCTCTGATTAG
Found at i:16688511 original size:19 final size:20
Alignment explanation
Indices: 16688487--16688562 Score: 93
Period size: 19 Copynumber: 3.8 Consensus size: 20
16688477 GGGTAGGCCC
*
16688487 ATTTTATTTTTTA-TTTTGT
1 ATTTTATTTATTATTTTTGT
16688506 ATTTTATATATATATATTTTTGT
1 ATTTTAT-T-TAT-TATTTTTGT
*
16688529 ATTTTATGTATTATTTTTGT
1 ATTTTATTTATTATTTTTGT
16688549 A-TTTATTTATTATT
1 ATTTTATTTATTATT
16688563 ACTATTTGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
19 19 0.38
20 11 0.22
21 5 0.10
22 2 0.04
23 13 0.26
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (20 bp):
ATTTTATTTATTATTTTTGT
Found at i:16688528 original size:23 final size:21
Alignment explanation
Indices: 16688500--16688552 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
16688490 TTATTTTTTA
16688500 TTTTGTATTTTATATATATATAT
1 TTTTGTATTTT-TATATAT-TAT
*
16688523 TTTTGTA-TTTTATGTATTAT
1 TTTTGTATTTTTATATATTAT
16688543 TTTTGTATTT
1 TTTTGTATTT
16688553 ATTTATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 10 0.36
21 8 0.29
22 3 0.11
23 7 0.25
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.70
Consensus pattern (21 bp):
TTTTGTATTTTTATATATTAT
Found at i:16688557 original size:4 final size:4
Alignment explanation
Indices: 16688489--16688720 Score: 53
Period size: 4 Copynumber: 58.8 Consensus size: 4
16688479 GTAGGCCCAT
* * * *
16688489 TTTA TTT- TTTA TTT- TGTA TTT- TATA TATA TATA TTT- TTGTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA -TTTA
* * *
16688535 TGTA -TTA TTT- TTGTA TTTA TTTA -TTA TTACTA TTTG TTAATA TATA
1 TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TT--TA TTTA TT--TA TTTA
* * * *
16688581 TATA TTTA TTT- TATTA TTTA TCTA TTAATA TATA TTTA -TTA TTTA TCTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TT--TA TTTA TTTA TTTA TTTA TTTA
* * * * *
16688630 TTTA TATA -TTA TTATA TATA TGTA TTTA -TTA -TTA TTTA TCTA CTTA
1 TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * *
16688676 TATA -TTA -TTG TTTA TCTA TTAA TATT- TTTA TTTA TCTA ATTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTT
16688721 TCTTTTAATT
Statistics
Matches: 166, Mismatches: 37, Indels: 50
0.66 0.15 0.20
Matches are distributed among these distances:
3 34 0.20
4 112 0.67
5 9 0.05
6 11 0.07
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:16688557 original size:23 final size:21
Alignment explanation
Indices: 16688500--16688563 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 21
16688490 TTATTTTTTA
*
16688500 TTTTGTATTTTATATATATATAT
1 TTTTGTATTTTTTAT-TAT-TAT
16688523 TTTTGTA--TTTTATGTATTAT
1 TTTTGTATTTTTTAT-TATTAT
16688543 TTTTGTATTTATTTATTATTA
1 TTTTGTATTT-TTTATTATTA
16688564 CTATTTGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 10 0.28
21 8 0.22
22 6 0.17
23 12 0.33
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTTGTATTTTTTATTATTAT
Found at i:16688619 original size:22 final size:21
Alignment explanation
Indices: 16688594--16688751 Score: 101
Period size: 22 Copynumber: 7.3 Consensus size: 21
16688584 ATTTATTTTA
16688594 TTATTTATCTATTAATATATATTT
1 TTATTTATCTATT-A-ATATA-TT
*
16688618 ATTATTTATCTATTTATATATT
1 -TTATTTATCTATTAATATATT
* *
16688640 ATTATATATATGTATT--TAT-TA
1 -TTAT-T-TATCTATTAATATATT
16688661 TTATTTATCTACTT-ATATATT
1 TTATTTATCTA-TTAATATATT
*
16688682 ATTGTTTATCTATTAATAT-TT
1 -TTATTTATCTATTAATATATT
* * *
16688703 TTATTTATCTAATTATTTTCTT
1 TTATTTATCT-ATTAATATATT
* * *
16688725 TTAATTATCTATTAACATTTT
1 TTATTTATCTATTAATATATT
16688746 TTATTT
1 TTATTT
16688752 GATTTGATTT
Statistics
Matches: 109, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
18 5 0.05
19 3 0.03
20 16 0.15
21 24 0.22
22 35 0.32
23 6 0.06
24 7 0.06
25 13 0.12
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (21 bp):
TTATTTATCTATTAATATATT
Found at i:16688624 original size:25 final size:23
Alignment explanation
Indices: 16688590--16688718 Score: 130
Period size: 20 Copynumber: 5.9 Consensus size: 23
16688580 ATATATTTAT
16688590 TTTATTATTTATCTATTAATATATA
1 TTTATTATTTATCTATT--TATATA
16688615 TTTATTATTTATCTATTTATATA
1 TTTATTATTTATCTATTTATATA
* * *
16688638 -TTATTA--TATATATGTATTTA
1 TTTATTATTTATCTATTTATATA
*
16688658 -TTATTATTTATCTACTTATATA
1 TTTATTATTTATCTATTTATATA
*
16688680 -TTATTGTTTATCTA-TTA-ATA
1 TTTATTATTTATCTATTTATATA
*
16688700 TTT-TTATTTATCTAATTAT
1 TTTATTATTTATCTATTTAT
16688719 TTTCTTTTAA
Statistics
Matches: 90, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
20 30 0.33
21 8 0.09
22 29 0.32
23 6 0.07
25 17 0.19
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTATTATTTATCTATTTATATA
Found at i:16688669 original size:42 final size:41
Alignment explanation
Indices: 16688611--16688718 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 41
16688601 TCTATTAATA
* *
16688611 TATATTTATTATTTATCTATTTATATATTATTATATATATGTAT
1 TATA-TTATTATTTATCTAATTATATATTATTAT-T-TATCTAT
* *
16688655 T-TATTATTATTTATCTACTTATATATTATTGTTTATCTAT
1 TATATTATTATTTATCTAATTATATATTATTATTTATCTAT
*
16688695 TAATATTTTTATTTATCTAATTAT
1 T-ATATTATTATTTATCTAATTAT
16688719 TTTCTTTTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
40 7 0.12
41 1 0.02
42 46 0.81
43 2 0.04
44 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (41 bp):
TATATTATTATTTATCTAATTATATATTATTATTTATCTAT
Found at i:16688682 original size:61 final size:58
Alignment explanation
Indices: 16688508--16688684 Score: 153
Period size: 59 Copynumber: 2.9 Consensus size: 58
16688498 TATTTTGTAT
* * * * *
16688508 TTTATATATATATATTTTTGTATTTTATGTATTATTTTTGTATTTATTTATTA-TTACTA
1 TTTATATATATATATATATGTATTTTAT-TATTATTTAT-TAATTATATATTATTTACTA
* * *
16688567 TTTGT-TAATATATATATATTTATTTTATTATTTATCTATTAATATATATTTATTATTTATCTA
1 TTTATAT-ATATATATATATGTATTTTATTA-TTATTTATTAAT-TATA--TATTATTTA-CTA
*
16688630 TTTATATATTATTATATATATGTA-TTTATTATTATTTATCTACTTATATATTATT
1 TTTATATA-TA-TATATATATGTATTTTATTATTATTTAT-TAATTATATATTATT
16688685 GTTTATCTAT
Statistics
Matches: 95, Mismatches: 12, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
58 6 0.06
59 31 0.33
61 12 0.13
62 3 0.03
63 19 0.20
64 13 0.14
65 11 0.12
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (58 bp):
TTTATATATATATATATATGTATTTTATTATTATTTATTAATTATATATTATTTACTA
Found at i:16688715 original size:17 final size:17
Alignment explanation
Indices: 16688591--16688721 Score: 65
Period size: 16 Copynumber: 7.4 Consensus size: 17
16688581 TATATTTATT
16688591 TTATTATTTATCTATTAA
1 TTATT-TTTATCTATTAA
* *
16688609 TATATATTTAT-TATTTA
1 T-TATTTTTATCTATTAA
*
16688626 TCTA--TTTATATATT-A
1 T-TATTTTTATCTATTAA
* * * *
16688641 TTATATATATGTATTTA
1 TTATTTTTATCTATTAA
16688658 TTATTATTTATCTACTTATATA
1 TTATT-TTTATCTA--T-TA-A
16688680 TTATTGTTTATCTATTAA
1 TTATT-TTTATCTATTAA
*
16688698 -TATTTTTATTTATCTAA
1 TTATTTTTATCTAT-TAA
16688715 TTATTTT
1 TTATTTT
16688722 CTTTTAATTA
Statistics
Matches: 90, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
14 2 0.02
15 7 0.08
16 20 0.22
17 20 0.22
18 19 0.21
19 5 0.06
20 2 0.02
21 1 0.01
22 14 0.16
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (17 bp):
TTATTTTTATCTATTAA
Found at i:16688720 original size:64 final size:66
Alignment explanation
Indices: 16688551--16688700 Score: 182
Period size: 69 Copynumber: 2.3 Consensus size: 66
16688541 ATTTTTGTAT
* * * *
16688551 TTATTTAT-TATTACTAT-TTGTTAATATATATATATTTATTTTATTATTTATCTATTAATATAT
1 TTATTTATCTATTAATATATTATT-ATATATATGTATTTA--TTATTATTTATCTACT-ATATAT
16688614 ATTTA
62 ATTTA
*
16688619 TTATTTATCTATTTATATATTATTATATATATGTATTTATTATTATTTATCTACT-TATATA-TT
1 TTATTTATCTATTAATATATTATTATATATATGTATTTATTATTATTTATCTACTATATATATTT
16688682 A
66 A
*
16688683 TTGTTTATCTATTAATAT
1 TTATTTATCTATTAATAT
16688701 TTTTATTTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
64 19 0.26
65 6 0.08
67 15 0.21
68 8 0.11
69 21 0.29
70 4 0.05
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (66 bp):
TTATTTATCTATTAATATATTATTATATATATGTATTTATTATTATTTATCTACTATATATATTT
A
Found at i:16689540 original size:4 final size:4
Alignment explanation
Indices: 16689531--16689636 Score: 53
Period size: 4 Copynumber: 25.8 Consensus size: 4
16689521 TTCCTATGTT
*
16689531 TTTA TTTA TTTA TTTA -TTA -TTA -TTA TTTA TTT- TTTAGA TTTG TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT--A TTTA TTTA
* * *
16689577 GTTT- TTT- TTTA TTGTTA TTTT TTTC TTTA CTTTTA TTTTA TTTTA TTTT
1 -TTTA TTTA TTTA -T-TTA TTTA TTTA TTTA --TTTA -TTTA -TTTA TTTA
16689626 TTTA TTTA TTT
1 TTTA TTTA TTT
16689637 TTGTTATTAT
Statistics
Matches: 85, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
3 18 0.21
4 42 0.49
5 15 0.18
6 10 0.12
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:16689591 original size:18 final size:17
Alignment explanation
Indices: 16689529--16689638 Score: 55
Period size: 17 Copynumber: 6.2 Consensus size: 17
16689519 TGTTCCTATG
* *
16689529 TTTTTATTTATTTATTTA
1 TTTTTA-TTGTTTATTTT
* *
16689547 TTATTATTATTTA-TTT
1 TTTTTATTGTTTATTTT
**
16689563 TTTAGATTTGTTTAGTTTT
1 TTTTTA-TTGTTTA-TTTT
16689582 TTTTTATTG-TTATTTTT
1 TTTTTATTGTTTA-TTTT
*
16689599 TTCTTTACT-TTTATTTT
1 TT-TTTATTGTTTATTTT
* *
16689616 ATTTTATTTTTTTATTTAT
1 TTTTTA-TTGTTTATTT-T
16689635 TTTT
1 TTTT
16689639 GTTATTATTT
Statistics
Matches: 71, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
16 9 0.13
17 28 0.39
18 23 0.32
19 11 0.15
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTTATTGTTTATTTT
Found at i:16689598 original size:17 final size:17
Alignment explanation
Indices: 16689536--16689644 Score: 60
Period size: 18 Copynumber: 5.9 Consensus size: 17
16689526 ATGTTTTTAT
* * *
16689536 TTATTTATTTATTATTA
1 TTATTTTTTTTTTATTG
*
16689553 TTATTTATTTTTTAGATTTG
1 TTATTT-TTTTTT-TA-TTG
*
16689573 TTTAGTTTTTTTTTATTG
1 -TTATTTTTTTTTTATTG
16689591 TTATTTTTTTCTTTACTT-
1 TTATTTTTTT-TTTA-TTG
*
16689609 TTATTTTATTTTATT-TTT
1 TTATTTT-TTTT-TTATTG
16689627 TTATTTATTTTTGTTATT
1 TTATTT-TTTTT-TTATT
16689645 ATTTTCTTTA
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
17 17 0.23
18 31 0.42
19 12 0.16
20 8 0.11
21 5 0.07
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (17 bp):
TTATTTTTTTTTTATTG
Found at i:16689610 original size:28 final size:26
Alignment explanation
Indices: 16689579--16689644 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 26
16689569 TTTGTTTAGT
*
16689579 TTTTTTTTATTGTTATTTTTTTCTTTA
1 TTTTTTTTATT-TTATTTTTTTATTTA
16689606 CTTTTATTTTATTTTATTTTTTTATTTA
1 -TTTT-TTTTATTTTATTTTTTTATTTA
*
16689634 TTTTTGTTATT
1 TTTTTTTTATT
16689645 ATTTTCTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 6 0.17
27 4 0.11
28 18 0.51
29 7 0.20
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (26 bp):
TTTTTTTTATTTTATTTTTTTATTTA
Found at i:16689801 original size:28 final size:28
Alignment explanation
Indices: 16689765--16689863 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 28
16689755 TCAATTTTCC
16689765 TTGAAAAAAAGTTTTCTAAAAAATATTT
1 TTGAAAAAAAGTTTTCTAAAAAATATTT
* *
16689793 TTGAGAAAAAG--TT-GAAAGTATCAAT-TTT
1 TTGAAAAAAAGTTTTCTAAA--A--AATATTT
16689821 CCTTGAAAAAAAGTTTTCTAAAAAATATTT
1 --TTGAAAAAAAGTTTTCTAAAAAATATTT
*
16689851 TTGAGAAAAAGTT
1 TTGAAAAAAAGTT
16689864 GAAAGTATCA
Statistics
Matches: 56, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
25 3 0.05
26 2 0.04
27 1 0.02
28 25 0.45
29 6 0.11
30 13 0.23
31 1 0.02
32 2 0.04
33 3 0.05
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.36
Consensus pattern (28 bp):
TTGAAAAAAAGTTTTCTAAAAAATATTT
Found at i:16689938 original size:58 final size:57
Alignment explanation
Indices: 16689661--16689941 Score: 420
Period size: 58 Copynumber: 4.8 Consensus size: 57
16689651 TTTAAATAAA
* * * *
16689661 TTTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTT-CTTTAAAAATAATT
1 TTTCTAAAAAATATTTTTGA-GAAAAGTTGAAAGTATCAATTTTCCTTGAAAAA-AAGT
* *
16689719 TTTCTAAAACATATTTTTGAGGGAAAGTTGAAAGTATCAATTTTCCTTGAAAAAAAGT
1 TTTCTAAAAAATATTTTTGA-GAAAAGTTGAAAGTATCAATTTTCCTTGAAAAAAAGT
16689777 TTTCTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAAAAGT
1 TTTCTAAAAAATATTTTTGAG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAAAAAGT
**
16689835 TTTCTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAATTT
1 TTTCTAAAAAATATTTTTGAG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAA-AAAGT
*
16689894 TTTCTAAAAAATATTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTG
1 TTTCTAAAAAATATTTTTGAGAAAAGTTGAAAGTATCAATTTTCCTTG
16689942 TATAAAAGCA
Statistics
Matches: 209, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
57 1 0.00
58 177 0.85
59 31 0.15
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.38
Consensus pattern (57 bp):
TTTCTAAAAAATATTTTTGAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAAAAGT
Found at i:16691235 original size:3 final size:3
Alignment explanation
Indices: 16691227--16691264 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
16691217 TTTATAATAT
16691227 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16691265 GTGACTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16692843 original size:41 final size:40
Alignment explanation
Indices: 16692758--16692858 Score: 114
Period size: 41 Copynumber: 2.5 Consensus size: 40
16692748 CATAGACTCG
*
16692758 ACAACTTTTGAAAATTAAAAGCTCTTTCAAGCAAAGGCTTA
1 ACAA-TTTTGAAAATTAAAAGCTCTTTCAAGCAAAGGCTGA
* * **
16692799 ACAATTTTTAAAAATTAAAAGCTC-TTCTAAGTAGGGGCTGA
1 ACAA-TTTTGAAAATTAAAAGCTCTTTC-AAGCAAAGGCTGA
*
16692840 ACAACTTTGAAAATTAAAA
1 ACAATTTTGAAAATTAAAA
16692859 ACTCCTTTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 16 0.31
41 35 0.69
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.30
Consensus pattern (40 bp):
ACAATTTTGAAAATTAAAAGCTCTTTCAAGCAAAGGCTGA
Found at i:16692883 original size:40 final size:42
Alignment explanation
Indices: 16692839--16692934 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
16692829 GTAGGGGCTG
*
16692839 AACAACTTTGAAAATTAAA-AA-CTCCTTTAAAC-GGAGACTT
1 AACAACTTTGAAAATTAAAGAAGCTCCTTTAAACAGAAG-CTT
*
16692879 AACAACTTTGAAAATTAAAGAAGCTCCTTTAAGCAGAAGCTT
1 AACAACTTTGAAAATTAAAGAAGCTCCTTTAAACAGAAGCTT
*
16692921 AACAACTTTAAAAA
1 AACAACTTTGAAAA
16692935 GCTCATCGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
40 19 0.38
41 2 0.04
42 26 0.52
43 3 0.06
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (42 bp):
AACAACTTTGAAAATTAAAGAAGCTCCTTTAAACAGAAGCTT
Found at i:16693189 original size:42 final size:40
Alignment explanation
Indices: 16693106--16693198 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 40
16693096 TACCTGGAGG
* *
16693106 ACTTATGAAAATTAAAAACTTCTCTAAGCGGAGACTTAACA
1 ACTT-TGAAAATTAAAAACTTCTCTAAGCGAAGACTCAACA
16693147 ACTTTGAAAATTAAAAAAGC-TCTTCTAAGCAGAAG-CTCAACA
1 ACTTTGAAAATT-AAAAA-CTTC-TCTAAGC-GAAGACTCAACA
*
16693189 ACTTTAAAAA
1 ACTTTGAAAA
16693199 GTTCATATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
40 8 0.18
41 11 0.24
42 23 0.51
43 3 0.07
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (40 bp):
ACTTTGAAAATTAAAAACTTCTCTAAGCGAAGACTCAACA
Found at i:16693329 original size:113 final size:114
Alignment explanation
Indices: 16693165--16693424 Score: 281
Period size: 114 Copynumber: 2.3 Consensus size: 114
16693155 AATTAAAAAA
* * **
16693165 GCTCTTCTAAGCAGAAGCTCAACAACTTTAAAAAGTTCATATAAGTAGAGG-TTCACAACTTTTG
1 GCTCCTCTAAGCAGAAGCTCAACAACTTTAAAAAGCTCATATAAGTAGAGGTTTCACAACTTTCA
* *
16693229 AAATTTTAGCATATTCTACC-AAGAGGACTTACAAATCTTAATAATGAAT
66 AAAATTTAGAATATTCTACCTAA-AGGACTTACAAATCTTAATAATGAAT
* * * * * *
16693278 GCTCCTCTAAGTAGAGGGTCAATAACTTTAAAAAGCTCTTTTAAGTAGAGGTTTCACAACTTTCA
1 GCTCCTCTAAGCAGAAGCTCAACAACTTTAAAAAGCTCATATAAGTAGAGGTTTCACAACTTTCA
* * * * ** *
16693343 AAAATTTATAATATTTTACCTAAAGGACTTATAAATCTTGATAGCGATT
66 AAAATTTAGAATATTCTACCTAAAGGACTTACAAATCTTAATAATGAAT
* * * * *
16693392 ACTCCTATAAGCAAAAGCTTAATAACTTTAAAA
1 GCTCCTCTAAGCAGAAGCTCAACAACTTTAAAA
16693425 TTTTAAAAAG
Statistics
Matches: 119, Mismatches: 26, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
113 43 0.36
114 74 0.62
115 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (114 bp):
GCTCCTCTAAGCAGAAGCTCAACAACTTTAAAAAGCTCATATAAGTAGAGGTTTCACAACTTTCA
AAAATTTAGAATATTCTACCTAAAGGACTTACAAATCTTAATAATGAAT
Found at i:16693338 original size:263 final size:264
Alignment explanation
Indices: 16692843--16693374 Score: 732
Period size: 263 Copynumber: 2.0 Consensus size: 264
16692833 GGGCTGAACA
* *
16692843 ACTT-TGAAAATTAAAAACTCCTTTAAACGGAGACTTAACAACTTTGAAAATTAAAGAAGCTCCT
1 ACTTATGAAAATTAAAAACTCCTCTAAACGGAGACTTAACAACTTTGAAAATTAAAAAAGCTCCT
* *
16692907 TTAAGCAGAAGCTTAACAACTTTAAAAAGCTCATCGAAGTAAAGACTCCACAACTTTTGACAATT
66 TTAAGCAGAAGCTCAACAACTTTAAAAAGCTCATAGAAGTAAAGACTCCACAACTTTTGACAATT
* * * *
16692972 TAAAGTATTTTGCCAAAAGGACTTACGAATCTTGATAATGAATGCTCCTCTAAGCAAAGGCTCAA
131 TAAAGTATTCTACCAAAAGGACTTACAAATCTTAATAATGAATGCTCCTCTAAGCAAAGGCTCAA
* ** *
16693037 TAACTTTAAAAAGTTCTTCTAAGCAGAGGTTCCACAACTTTTGAAAATTTAAAATATTCTACCTG
196 TAACTTTAAAAAGCTCTTCTAAGCAGAGGTTCCACAACTTTCAAAAATTTAAAATATTCTACCTA
*
16693102 GAGG
261 AAGG
* *
16693106 ACTTATGAAAATTAAAAACTTCTCTAAGCGGAGACTTAACAACTTTGAAAATTAAAAAAGCT-CT
1 ACTTATGAAAATTAAAAACTCCTCTAAACGGAGACTTAACAACTTTGAAAATTAAAAAAGCTCCT
* * * * *
16693170 TCTAAGCAGAAGCTCAACAACTTTAAAAAGTTCATATAAGTAGAG-GTTCACAACTTTTGA-AAT
66 T-TAAGCAGAAGCTCAACAACTTTAAAAAGCTCATAGAAGTAAAGACTCCACAACTTTTGACAAT
* * * * *
16693233 TT-TAGCATATTCTACCAAGAGGACTTACAAATCTTAATAATGAATGCTCCTCTAAGTAGAGGGT
130 TTAAAG--TATTCTACCAAAAGGACTTACAAATCTTAATAATGAATGCTCCTCTAAGCAAAGGCT
* * * * *
16693297 CAATAACTTTAAAAAGCTCTTTTAAGTAGAGGTTTCACAACTTTCAAAAATTTATAATATTTTAC
193 CAATAACTTTAAAAAGCTCTTCTAAGCAGAGGTTCCACAACTTTCAAAAATTTAAAATATTCTAC
16693362 CTAAAGG
258 CTAAAGG
16693369 ACTTAT
1 ACTTAT
16693375 AAATCTTGAT
Statistics
Matches: 235, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
261 2 0.01
262 5 0.02
263 137 0.58
264 91 0.39
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (264 bp):
ACTTATGAAAATTAAAAACTCCTCTAAACGGAGACTTAACAACTTTGAAAATTAAAAAAGCTCCT
TTAAGCAGAAGCTCAACAACTTTAAAAAGCTCATAGAAGTAAAGACTCCACAACTTTTGACAATT
TAAAGTATTCTACCAAAAGGACTTACAAATCTTAATAATGAATGCTCCTCTAAGCAAAGGCTCAA
TAACTTTAAAAAGCTCTTCTAAGCAGAGGTTCCACAACTTTCAAAAATTTAAAATATTCTACCTA
AAGG
Found at i:16704327 original size:15 final size:15
Alignment explanation
Indices: 16704309--16704338 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16704299 CAAGAAAACA
*
16704309 AAAATGAAAAGAAAT
1 AAAATGAAAAAAAAT
16704324 AAAATGAAAAAAAAT
1 AAAATGAAAAAAAAT
16704339 GATTTAGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (15 bp):
AAAATGAAAAAAAAT
Found at i:16704462 original size:57 final size:57
Alignment explanation
Indices: 16704392--16704666 Score: 394
Period size: 57 Copynumber: 4.8 Consensus size: 57
16704382 TGCTTTTATA
* *
16704392 CAAGAAAAATTGATACTTTCAACTTTTCC-CCAAAATATTTTTCTG-AAACTTTAATTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTT-TGAAAAC-TTATTTT
* *
16704449 CGAGAAAAATTGATACTTTCAACTTTTCCTCGAAAATATTTTTTCTGAAAACTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTT-TGAAAACTTATTTT
* * * *
16704508 CAAGGAAAATTGATACTTTTAACTTTTCCTTAAAAATATTTTTAGAAAACTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTATTTT
16704565 CAA-AGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATTTT
1 CAAGA-AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-GAAAACTTATTTT
*
16704623 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
16704667 TTGAATTTTA
Statistics
Matches: 198, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
57 80 0.40
58 67 0.34
59 47 0.24
60 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (57 bp):
CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTATTTT
Found at i:16704589 original size:30 final size:30
Alignment explanation
Indices: 16704555--16704647 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
16704545 ATTTTTAGAA
16704555 AACTTATTTTCAAAGAAAATTGATACTTTC
1 AACTTATTTTCAAAGAAAATTGATACTTTC
* * *
16704585 AACTT-TTCCTCAAA-AATATT--T--TTTAGAA
1 AACTTATT-TTCAAAGAAAATTGATACTTT---C
*
16704613 AACTTATTTTCAAGGAAAATTGATACTTTC
1 AACTTATTTTCAAAGAAAATTGATACTTTC
16704643 AACTT
1 AACTT
16704648 TTCCTCAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 20
0.63 0.10 0.27
Matches are distributed among these distances:
25 3 0.07
27 1 0.02
28 9 0.20
29 14 0.30
30 15 0.33
31 1 0.02
33 3 0.07
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (30 bp):
AACTTATTTTCAAAGAAAATTGATACTTTC
Found at i:16704679 original size:58 final size:58
Alignment explanation
Indices: 16704392--16704667 Score: 405
Period size: 58 Copynumber: 4.8 Consensus size: 58
16704382 TGCTTTTATA
* * * *
16704392 CAAGAAAAATTGATACTTTCAACTTTTCC-CCAAAATATTTTTCTG-AAACTTTAATTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAAC-TTATTTT
* * *
16704449 CGAGAAAAATTGATACTTTCAACTTTTCCTCGAAAATATTTTTTCTGAAAACTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-TGAAAACTTATTTT
* * *
16704508 CAAGGAAAATTGATACTTTTAACTTTTCCTTAAAAATA-TTTTTAGAAAACTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTT
* *
16704565 CAAAGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTT
16704623 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
16704668 TGAATTTTAT
Statistics
Matches: 200, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
57 76 0.38
58 79 0.40
59 41 0.20
60 4 0.02
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (58 bp):
CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTT
Found at i:16704743 original size:25 final size:23
Alignment explanation
Indices: 16704715--16704783 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 23
16704705 TAAAATAAGG
*
16704715 AATACTAAATAATTATAATCTAATA
1 AATA-TAAATAATAATAAT-TAATA
*
16704740 AATAAATAATAATAATAATTAATAA
1 AATATA-AATAATAATAATTAAT-A
16704765 ATATATAAATAAATAATAA
1 A-ATATAAAT-AATAATAA
16704784 AAAAACCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 5 0.14
25 20 0.54
26 12 0.32
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (23 bp):
AATATAAATAATAATAATTAATA
Found at i:16705627 original size:28 final size:26
Alignment explanation
Indices: 16705602--16705759 Score: 136
Period size: 24 Copynumber: 6.3 Consensus size: 26
16705592 AAAAAGATAA
16705602 AAATAAAAATATATATATTAATAGAT
1 AAATAAAAATATATATATTAATAGAT
**
16705628 AAAT---AATA-ATATATGGATAGAT
1 AAATAAAAATATATATATTAATAGAT
16705650 AAATAATTAAATATATATATTAATAGAT
1 AAATAA--AAATATATATATTAATAGAT
* *
16705678 AAATAATAA-A-ATATGTTAATAGAT
1 AAATAAAAATATATATATTAATAGAT
* *
16705702 AAATAAATAAAATATATATTAATAAAT
1 AAATAAA-AATATATATATTAATAGAT
* * * *
16705729 -AATAATAGTA-ATA-ATAAATAAAT
1 AAATAAAAATATATATATTAATAGAT
16705752 AAATAAAA
1 AAATAAAA
16705760 TAAAATACAA
Statistics
Matches: 108, Mismatches: 14, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
22 16 0.15
23 13 0.12
24 28 0.26
25 5 0.05
26 12 0.11
27 16 0.15
28 18 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
AAATAAAAATATATATATTAATAGAT
Found at i:16705655 original size:4 final size:4
Alignment explanation
Indices: 16705648--16705763 Score: 53
Period size: 4 Copynumber: 29.2 Consensus size: 4
16705638 ATATGGATAG
* * * * * * * *
16705648 ATAA ATAA TTAA ATAT ATAT ATTA ATAG ATAA AT-A ATAAA ATAT GTTA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA
* * * *
16705696 ATAG ATAA ATAA ATAA A-AT ATAT ATTA ATAA AT-A AT-A ATAGTA AT-A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA
16705742 ATAA ATAA ATAA ATAAA ATAA A
1 ATAA ATAA ATAA AT-AA ATAA A
16705764 ATACAAATGG
Statistics
Matches: 84, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
3 14 0.17
4 60 0.71
5 7 0.08
6 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (4 bp):
ATAA
Found at i:16705671 original size:50 final size:51
Alignment explanation
Indices: 16705608--16705756 Score: 192
Period size: 50 Copynumber: 3.1 Consensus size: 51
16705598 ATAAAAATAA
* * *
16705608 AAATATATATATTAATAGATAAATAATAATATATG-GATAGATAAATAATT
1 AAATATATATATTAATAGATAAATAATAAAATATGTAATAGATAAATAAAT
16705658 AAATATATATATTAATAGATAAATAATAAAATATGTTAATAGATAAATAAAT
1 AAATATATATATTAATAGATAAATAATAAAATATG-TAATAGATAAATAAAT
16705710 AAA-ATATATA-T--TA-ATAAATAAT--AATA-GTAATA-ATAAATAAAT
1 AAATATATATATTAATAGATAAATAATAAAATATGTAATAGATAAATAAAT
16705752 AAATA
1 AAATA
16705757 AAATAAAATA
Statistics
Matches: 93, Mismatches: 3, Indels: 13
0.85 0.03 0.12
Matches are distributed among these distances:
42 13 0.14
43 6 0.06
44 1 0.01
45 4 0.04
47 9 0.10
48 2 0.02
50 35 0.38
51 7 0.08
52 16 0.17
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.34
Consensus pattern (51 bp):
AAATATATATATTAATAGATAAATAATAAAATATGTAATAGATAAATAAAT
Found at i:16705727 original size:19 final size:18
Alignment explanation
Indices: 16705703--16705750 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
16705693 TTAATAGATA
16705703 AATAAATAAAATA-TATATT
1 AATAAATAAAATAGTA-A-T
16705722 AATAAATAATAATAGTAAT
1 AATAAATAA-AATAGTAAT
16705741 AATAAATAAA
1 AATAAATAAA
16705751 TAAATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.04
19 19 0.70
20 5 0.19
21 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AATAAATAAAATAGTAAT
Found at i:16705752 original size:20 final size:20
Alignment explanation
Indices: 16705651--16705753 Score: 68
Period size: 20 Copynumber: 4.8 Consensus size: 20
16705641 TGGATAGATA
* *
16705651 AATAATTAAATATAT-ATATT
1 AATAA-TAAATAAATAATAGT
*
16705671 AATAGATAAATAATAAAATATGTT
1 AATA-ATAAATAA-ATAATA-G-T
16705695 AATAGATAAATAAATAAAATA-T
1 AATA-ATAAATAAAT--AATAGT
16705717 ATATTAATAAAT-AATAATAGT
1 A-A-TAATAAATAAATAATAGT
16705738 AATAATAAATAAATAA
1 AATAATAAATAAATAA
16705754 ATAAAATAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 22
0.72 0.04 0.23
Matches are distributed among these distances:
19 8 0.12
20 20 0.29
21 4 0.06
22 8 0.12
23 8 0.12
24 16 0.24
25 4 0.06
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
AATAATAAATAAATAATAGT
Found at i:16706746 original size:19 final size:19
Alignment explanation
Indices: 16706695--16706747 Score: 88
Period size: 20 Copynumber: 2.7 Consensus size: 19
16706685 TTAAACAACC
16706695 GATCGATCCTTTTAAGAGGG
1 GATCGATCC-TTTAAGAGGG
16706715 GATCGATTCCTTTAAGAGGG
1 GATCGA-TCCTTTAAGAGGG
16706735 GATCGATCCTTTA
1 GATCGATCCTTTA
16706748 CCTTAGGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.22
20 22 0.69
21 3 0.09
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (19 bp):
GATCGATCCTTTAAGAGGG
Found at i:16707340 original size:18 final size:18
Alignment explanation
Indices: 16707317--16707354 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16707307 CAATATCAAA
* *
16707317 ACATTATCAGATTTTCAT
1 ACATTAACAAATTTTCAT
16707335 ACATTAACAAATTTTCAT
1 ACATTAACAAATTTTCAT
16707353 AC
1 AC
16707355 CAATATTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (18 bp):
ACATTAACAAATTTTCAT
Found at i:16707613 original size:6 final size:6
Alignment explanation
Indices: 16707602--16707634 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
16707592 AGGCTTTAGT
*
16707602 GAGGTG GAGGTG GAGGTG GAGGTG GAGGAG GAG
1 GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG GAG
16707635 AATAAGGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.67, T:0.12
Consensus pattern (6 bp):
GAGGTG
Found at i:16709287 original size:73 final size:73
Alignment explanation
Indices: 16709158--16709302 Score: 236
Period size: 73 Copynumber: 2.0 Consensus size: 73
16709148 GATCAATCAG
*
16709158 TTCTTCCTAGGTTCAGCAAAATTGGCTACTACCTTCACACCCGATCGATCCTGTCCCAAAAAGGA
1 TTCTTCCTAGGTTCAACAAAATTGGCTACTACCTTCACACCCGATCGATCCTGTCCCAAAAAGGA
16709223 TCGATCGA
66 TCGATCGA
* ** **
16709231 TTCTTCCTGGGTTCAACAAAATTGGCTACTACCTTTGCACCCGATCGATCCTGTCCCAAAGGGGA
1 TTCTTCCTAGGTTCAACAAAATTGGCTACTACCTTCACACCCGATCGATCCTGTCCCAAAAAGGA
16709296 TCGATCG
66 TCGATCG
16709303 GTTCCCTATG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (73 bp):
TTCTTCCTAGGTTCAACAAAATTGGCTACTACCTTCACACCCGATCGATCCTGTCCCAAAAAGGA
TCGATCGA
Found at i:16713100 original size:440 final size:440
Alignment explanation
Indices: 16712274--16713150 Score: 1479
Period size: 440 Copynumber: 2.0 Consensus size: 440
16712264 AAGAAAGCTC
16712274 TTATGTTTCTAGCATGTCATTGAGCTTTTGATGACCCATATAAAATCTAGAAAATAAATTATGTA
1 TTATGTTTCTAGCATGTCATTGAGCTTTTGATGACCCATATAAAATCTAGAAAATAAATTATGTA
* * *
16712339 GATTTTCATTTTTCTTAATCAAGTCATTAAGATTTACCTTTAAGAGCTCAACTTCCTTTTCTAAG
66 AATTTTCATTTTTCTTAATCAAGTCATTAACATTTACCTTCAAGAGCTCAACTTCCTTTTCTAAG
*
16712404 TCTTCTTTTGCTTTAGTCAATGACTCATTTTTTAGTTTTAATTTACTGATCATTTTTTTATATTT
131 TCTTCTTTTGCTTTAGTCAATGACTCATTTTTTAGTTTCAATTTACTGATCATTTTTTTATATTT
* * *
16712469 CATGCTCATATTTTCAAATTCTATAGCTAATTCATCATAGGCATCTTGTAGTTCATCAAATTATT
196 CATGCTCATATTCTCAAATTCTATAGCTAATTCATCATAGGCATCTTGTAGTTCATCAAATGAGT
* * *
16712534 ATGAATTTAAATCACATGGATTAGAGGTTACCTTAGGCTCATTAAGAGCCATGAGATATAGGTTG
261 ATGAATTTAAATCACATGGATTAGAGGTTACCTTAGGCTCATCAAGAGCCATGAGACATAAGTTG
* *
16712599 GCTACTTCTCTCTTATTTGATTCATCATCGAAAAAGTCGCTATCACTTCATGTTGCTACCATAGC
326 GCTACTTCTCTCTTATTTAATTCATCATCGAAAAAGTCGCTATCACTTCATGTTACTACCATAGC
16712664 TTTCTTCTTTGGGTTGGTCATGTTCTGCTTTTTCCACAAAGGACAATGAA
391 TTTCTTCTTTGGGTTGGTCATGTTCTGCTTTTTCCACAAAGGACAATGAA
*
16712714 TTATGTTTCTAGCATGTCATTGAGCTTTTGATGACCCATATAAAATCTAGAAAATGAATTATGTA
1 TTATGTTTCTAGCATGTCATTGAGCTTTTGATGACCCATATAAAATCTAGAAAATAAATTATGTA
* * *
16712779 AATTTTCATTTTTCTTAGTCAAGTCATTTACATTTACCTTCAAGAGCTCAACTTTCTTTTCTAAG
66 AATTTTCATTTTTCTTAATCAAGTCATTAACATTTACCTTCAAGAGCTCAACTTCCTTTTCTAAG
16712844 TCTTCTTTTGCTTTAGTCAATGACTCATTTTTTAGTTTCAATTTACTGATCATTTTTTTATATTT
131 TCTTCTTTTGCTTTAGTCAATGACTCATTTTTTAGTTTCAATTTACTGATCATTTTTTTATATTT
16712909 CATGCTCATATTCTCAAATTCTATAGCTAATTCATCATAGGCATCTTGTAGTTCATCAAATGAGT
196 CATGCTCATATTCTCAAATTCTATAGCTAATTCATCATAGGCATCTTGTAGTTCATCAAATGAGT
* *
16712974 ATGAATTTGAATCACATGGATTAGAGGTTACCTTGGGCTCATCAAGAGCCATGAGACATAAGTTG
261 ATGAATTTAAATCACATGGATTAGAGGTTACCTTAGGCTCATCAAGAGCCATGAGACATAAGTTG
* * * * * *
16713039 GTTATTTCTCT-TTCATTTAATTCATCATTGGAGAAGTCGTTATCAC-TCAATGTTACTACCATA
326 GCTACTTCTCTCTT-ATTTAATTCATCATCGAAAAAGTCGCTATCACTTC-ATGTTACTACCATA
* * *
16713102 GCTTTCTTCTTTGGGTTGGTCATGTTTTGCTTTTTTCATAAAGGACAAT
389 GCTTTCTTCTTTGGGTTGGTCATGTTCTGCTTTTTCCACAAAGGACAAT
16713151 CAAGTTTAAT
Statistics
Matches: 408, Mismatches: 27, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
439 4 0.01
440 404 0.99
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (440 bp):
TTATGTTTCTAGCATGTCATTGAGCTTTTGATGACCCATATAAAATCTAGAAAATAAATTATGTA
AATTTTCATTTTTCTTAATCAAGTCATTAACATTTACCTTCAAGAGCTCAACTTCCTTTTCTAAG
TCTTCTTTTGCTTTAGTCAATGACTCATTTTTTAGTTTCAATTTACTGATCATTTTTTTATATTT
CATGCTCATATTCTCAAATTCTATAGCTAATTCATCATAGGCATCTTGTAGTTCATCAAATGAGT
ATGAATTTAAATCACATGGATTAGAGGTTACCTTAGGCTCATCAAGAGCCATGAGACATAAGTTG
GCTACTTCTCTCTTATTTAATTCATCATCGAAAAAGTCGCTATCACTTCATGTTACTACCATAGC
TTTCTTCTTTGGGTTGGTCATGTTCTGCTTTTTCCACAAAGGACAATGAA
Found at i:16714356 original size:14 final size:14
Alignment explanation
Indices: 16714332--16714365 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
16714322 GAGTTAGAGA
16714332 ATTTA-ACACCAAG
1 ATTTATACACCAAG
16714345 ATTTATACACCAAG
1 ATTTATACACCAAG
16714359 ATTTATA
1 ATTTATA
16714366 GAGGTTCGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (14 bp):
ATTTATACACCAAG
Found at i:16715628 original size:9 final size:9
Alignment explanation
Indices: 16715614--16715647 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
16715604 CCACTCGACC
16715614 TTTTTTCTT
1 TTTTTTCTT
*
16715623 TTTTTTCACT
1 TTTTTTC-TT
16715633 TTTTTTCTT
1 TTTTTTCTT
16715642 TTTTTT
1 TTTTTT
16715648 GTGTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:16715767 original size:42 final size:40
Alignment explanation
Indices: 16715668--16716013 Score: 198
Period size: 41 Copynumber: 8.1 Consensus size: 40
16715658 TTTGATTAAA
* **
16715668 GCTCCTCTAAGT-AGAGGCTCACCGACTTTGAGAAACATAAACAAA
1 GCTCCTCTAA-TCAGAGGCTCA-CAACTTTGA-AAA-AT-AA-ATG
16715713 GCTCCTCTAATCAGAGGCATCACAACTTTGAAAAAATAAATG
1 GCTCCTCTAATCAGAGGC-TCACAACTTTG-AAAAATAAATG
* * * *
16715755 GCTCCTCTAATCAGAGGCTCAACGACTGTGGAAATTAAATG
1 GCTCCTCTAATCAGAGGCTC-ACAACTTTGAAAAATAAATG
**
16715796 GCTAATCTAATCAGAGGCTCA-ATGACTTTTG-AAAATAAATG
1 GCTCCTCTAATCAGAGGCTCACA--AC-TTTGAAAAATAAATG
* * * *
16715837 GCTCATCTAATCAGAGGCTCAACAACTTTTGGAAAGTAAATT
1 GCTCCTCTAATCAGAGGCTC-ACAAC-TTTGAAAAATAAATG
* * * **
16715879 GCTTCTCTAATTAGAGGCTCA-ATGACTTTTAAAAATATAAACAAA
1 GCTCCTCTAATCAGAGGCTCACA--AC-TTTGAAAA-AT-AA-ATG
* *
16715924 GCTCCTCTAATCA-ACGGCATCACAACTTTGGGAACAATAAATT
1 GCTCCTCTAATCAGA-GGC-TCACAACTTT--GAAAAATAAATG
* * * *
16715967 GCTCCTCTAAACAGAGGCACCCACAACTTTTAAAAAATAAATT
1 GCTCCTCTAATCAGAGG--CTCACAAC-TTTGAAAAATAAATG
16716010 GCTC
1 GCTC
16716014 ATTGACAATT
Statistics
Matches: 244, Mismatches: 33, Indels: 50
0.75 0.10 0.15
Matches are distributed among these distances:
40 2 0.01
41 67 0.27
42 64 0.26
43 33 0.14
44 18 0.07
45 49 0.20
46 10 0.04
47 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (40 bp):
GCTCCTCTAATCAGAGGCTCACAACTTTGAAAAATAAATG
Found at i:16715806 original size:41 final size:41
Alignment explanation
Indices: 16715680--16715907 Score: 217
Period size: 41 Copynumber: 5.4 Consensus size: 41
16715670 TCCTCTAAGT
* ** *
16715680 AGAGGCTCACCGACTTTGAGAAACATAAACAAAGCTCCTCTAATC
1 AGAGGCTCAACGACTTTG-GAAA-AT-AA-ATGGCTCATCTAATC
* * *
16715725 AGAGGCATC-ACAACTTTGAAAAAATAAATGGCTCCTCTAATC
1 AGAGGC-TCAACGACTTTG-GAAAATAAATGGCTCATCTAATC
* * *
16715767 AGAGGCTCAACGACTGTGGAAATTAAATGGCTAATCTAATC
1 AGAGGCTCAACGACTTTGGAAAATAAATGGCTCATCTAATC
* *
16715808 AGAGGCTCAATGACTTTTGAAAATAAATGGCTCATCTAATC
1 AGAGGCTCAACGACTTTGGAAAATAAATGGCTCATCTAATC
* * * *
16715849 AGAGGCTCAACAACTTTTGGAAAGTAAATTGCTTC-TCTAATT
1 AGAGGCTCAACGAC-TTTGGAAAATAAATGGC-TCATCTAATC
*
16715891 AGAGGCTCAATGACTTT
1 AGAGGCTCAACGACTTT
16715908 TAAAAATATA
Statistics
Matches: 155, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
41 72 0.46
42 58 0.37
43 4 0.03
44 2 0.01
45 17 0.11
46 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (41 bp):
AGAGGCTCAACGACTTTGGAAAATAAATGGCTCATCTAATC
Found at i:16715851 original size:82 final size:83
Alignment explanation
Indices: 16715718--16715915 Score: 258
Period size: 83 Copynumber: 2.4 Consensus size: 83
16715708 ACAAAGCTCC
* * *
16715718 TCTAATCAGAGGCATCACA--ACTTTGAAAAAATAAATGGCTCCTCTAATCAGAGGCTCAACGAC
1 TCTAATCAGAGGC-TCA-ATGACTTT-TAAAAATAAATGGCTCATCTAATCAGAGGCTCAACAAC
*
16715781 -TGTGGAAATTAAATGGCTAA
63 TTGTGGAAAGTAAATGGCTAA
* *
16715801 TCTAATCAGAGGCTCAATGACTTTTGAAAATAAATGGCTCATCTAATCAGAGGCTCAACAACTTT
1 TCTAATCAGAGGCTCAATGACTTTTAAAAATAAATGGCTCATCTAATCAGAGGCTCAACAACTTG
* **
16715866 TGGAAAGTAAATTGCTTC
66 TGGAAAGTAAATGGCTAA
*
16715884 TCTAATTAGAGGCTCAATGACTTTTAAAAATA
1 TCTAATCAGAGGCTCAATGACTTTTAAAAATA
16715916 TAAACAAAGC
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
81 1 0.01
82 37 0.37
83 63 0.62
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (83 bp):
TCTAATCAGAGGCTCAATGACTTTTAAAAATAAATGGCTCATCTAATCAGAGGCTCAACAACTTG
TGGAAAGTAAATGGCTAA
Found at i:16727746 original size:8 final size:7
Alignment explanation
Indices: 16727712--16727762 Score: 59
Period size: 8 Copynumber: 7.0 Consensus size: 7
16727702 TAATCTAATC
16727712 AATAAAT
1 AATAAAT
16727719 AAT-AAT
1 AATAAAT
*
16727725 AATAATT
1 AATAAAT
16727732 AATAAAT
1 AATAAAT
16727739 ATATAAAT
1 A-ATAAAT
16727747 ATATAAAT
1 A-ATAAAT
16727755 AAATAAAT
1 -AATAAAT
16727763 CTTTGGAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
6 6 0.15
7 12 0.31
8 20 0.51
9 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
AATAAAT
Found at i:16728682 original size:53 final size:51
Alignment explanation
Indices: 16728584--16728719 Score: 177
Period size: 51 Copynumber: 2.6 Consensus size: 51
16728574 AAAGAAGATA
* * * *
16728584 AAATAAAAAATATATATTAATAGATAGATAATAATATATGGATAGATAAAT
1 AAATAAATAATATATATTAATAGATAAATAATAAAATATGAATAGATAAAT
*
16728635 -AATTAATATATATATATTAATAGATAAATAATAAAATATGTTAATAGATAAAT
1 AAATAAATA-ATATATATTAATAGATAAATAATAAAATATG--AATAGATAAAT
*
16728688 AAATAAATAATATATATTAATAAAT-AATAATA
1 AAATAAATAATATATATTAATAGATAAATAATA
16728720 GTAATAATAA
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
50 6 0.08
51 29 0.39
52 7 0.09
53 25 0.34
54 7 0.09
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.35
Consensus pattern (51 bp):
AAATAAATAATATATATTAATAGATAAATAATAAAATATGAATAGATAAAT
Found at i:16728707 original size:29 final size:28
Alignment explanation
Indices: 16728602--16728728 Score: 111
Period size: 29 Copynumber: 4.5 Consensus size: 28
16728592 AATATATATT
* **
16728602 AATAGATAGATAATAATATATGGATAGATA
1 AATA-ATAAATAAT-ATATATTAATAGATA
*
16728632 AATAATTAATATATATATATTAATAGATA
1 AATAATAAATA-ATATATATTAATAGATA
*
16728661 AATAAT--A-AA-ATATGTTAATAGATA
1 AATAATAAATAATATATATTAATAGATA
*
16728685 AATAAATAAATAATATATATTAATAAAT-
1 AAT-AATAAATAATATATATTAATAGATA
16728713 AATAATAGTAATAATA
1 AATAATA--AATAATA
16728729 ATTAAAAATA
Statistics
Matches: 82, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
24 17 0.21
25 4 0.05
26 1 0.01
27 6 0.07
28 5 0.06
29 43 0.52
30 6 0.07
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (28 bp):
AATAATAAATAATATATATTAATAGATA
Found at i:16728711 original size:17 final size:16
Alignment explanation
Indices: 16728689--16728730 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
16728679 TAGATAAATA
*
16728689 AATAAATAATATATATT
1 AATAAATAATA-ATAGT
16728706 AATAAATAATAATAGT
1 AATAAATAATAATAGT
16728722 AAT-AATAAT
1 AATAAATAAT
16728731 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 6 0.25
16 7 0.29
17 11 0.46
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AATAAATAATAATAGT
Found at i:16729237 original size:12 final size:12
Alignment explanation
Indices: 16729220--16729244 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16729210 TTAAAATATT
16729220 AAATAATAACAA
1 AAATAATAACAA
16729232 AAATAATAACAA
1 AAATAATAACAA
16729244 A
1 A
16729245 TTAGGTCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATAATAACAA
Found at i:16729836 original size:13 final size:14
Alignment explanation
Indices: 16729818--16729850 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16729808 CTTTTTATAA
16729818 TTTTATT-AAAATT
1 TTTTATTCAAAATT
*
16729831 TTTTATTCTAAATT
1 TTTTATTCAAAATT
16729845 TTTTAT
1 TTTTAT
16729851 CATTATGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATTCAAAATT
Found at i:16731267 original size:6 final size:6
Alignment explanation
Indices: 16731251--16731329 Score: 51
Period size: 6 Copynumber: 13.7 Consensus size: 6
16731241 AAAAAAATTG
* * * *
16731251 AAAAT- AAAATA AAAATA AAAAT- --AATA AAAATA TATATG AAAAGA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* *
16731295 AAAATG AAATTGA AAAAT- AAAATA AAAATA GAAAA
1 AAAATA AAAAT-A AAAATA AAAATA AAAATA -AAAA
16731330 GGAAAACCTA
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
3 3 0.05
5 10 0.18
6 34 0.62
7 8 0.15
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:16731276 original size:15 final size:15
Alignment explanation
Indices: 16731236--16731282 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
16731226 CAAAACTAGT
16731236 AAAATAA-AAAAATTGA
1 AAAATAATAAAAA-T-A
*
16731252 AAATAAAATAAAAATA
1 AAA-ATAATAAAAATA
16731268 AAAATAATAAAAATA
1 AAAATAATAAAAATA
16731283 TATATGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 11 0.41
16 7 0.26
17 4 0.15
18 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAATAATAAAAATA
Found at i:16732123 original size:3 final size:3
Alignment explanation
Indices: 16732108--16732174 Score: 50
Period size: 3 Copynumber: 23.3 Consensus size: 3
16732098 AAAGAAAGAA
* * * * * * *
16732108 AAT AAT AAA AAT AAT AAA AAT ATT ATT ATT ATT AAT -AG AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16732154 AAT AAT AAT AAT -AT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
16732175 TACAATATCA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 5 0.09
3 48 0.91
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:16732169 original size:8 final size:8
Alignment explanation
Indices: 16732146--16732176 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
16732136 TTATTAATAG
16732146 AATATAAT
1 AATATAAT
16732154 AATAATAAT
1 AAT-ATAAT
16732163 AATATAAT
1 AATATAAT
16732171 AATATA
1 AATATA
16732177 CAATATCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AATATAAT
Found at i:16732209 original size:3 final size:3
Alignment explanation
Indices: 16732203--16732234 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
16732193 TACAATAATA
16732203 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
16732235 AATAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:16732239 original size:3 final size:3
Alignment explanation
Indices: 16732233--16732302 Score: 108
Period size: 3 Copynumber: 24.0 Consensus size: 3
16732223 GATGATGATG
*
16732233 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
16732281 ATA ATA AT- ATA ACA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
16732303 TAGTGTACCA
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
2 4 0.06
3 58 0.94
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:16732902 original size:176 final size:176
Alignment explanation
Indices: 16732582--16732913 Score: 389
Period size: 176 Copynumber: 1.9 Consensus size: 176
16732572 TTGAGTCAAG
* * * * *
16732582 ATCAAAAGACTATGACAAAACCACCACTCTAAAAGATAAAGTGACTAGGATCGAGTCAAGGTCAA
1 ATCAAAAGACTATGACAAAACCACCACTCTAAAAGATAAAGCGACCAAGATCAAGTCAAAGTCAA
* * ** * *
16732647 AGATAAATATTCGGGACAAAATCGTGAATCAGAAAAAATAATCTGGACAGAGCTGAGATCGAATG
66 AAATAAATATTCGAGACAAAATCACGAATCAGAAAAAATAATCTGAACAGAGCTAAGATCGAATG
* *
16732712 ATCAAGACAAATCACGAGTCTAAAAAATGATCTAAACTAAGCCAAA
131 ACCAAGACAAATCACAAGTCTAAAAAATGATCTAAACTAAGCCAAA
* * ** *
16732758 ATCAAATGACTATGACAAAATCATGAGTCTAAAAGATAAAGCGACCAAGATCAAGTCAAAGTCAA
1 ATCAAAAGACTATGACAAAACCACCACTCTAAAAGATAAAGCGACCAAGATCAAGTCAAAGTCAA
* * * * ** *
16732823 AAATGAATGTTCGAGACAAAATTACGAGTCA-AAAAAATAATCTGAATTGAG-TCAAGATCGGAT
66 AAATAAATATTCGAGACAAAATCACGAATCAGAAAAAATAATCTGAACAGAGCT-AAGATCGAAT
* *
16732886 GACCGAGATGAAATCACAAGTCTAAAAA
130 GACCAAGA-CAAATCACAAGTCTAAAAA
16732914 TGAAGTGATC
Statistics
Matches: 127, Mismatches: 27, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
174 1 0.01
175 31 0.24
176 95 0.75
ACGTcount: A:0.48, C:0.16, G:0.17, T:0.19
Consensus pattern (176 bp):
ATCAAAAGACTATGACAAAACCACCACTCTAAAAGATAAAGCGACCAAGATCAAGTCAAAGTCAA
AAATAAATATTCGAGACAAAATCACGAATCAGAAAAAATAATCTGAACAGAGCTAAGATCGAATG
ACCAAGACAAATCACAAGTCTAAAAAATGATCTAAACTAAGCCAAA
Found at i:16732994 original size:66 final size:66
Alignment explanation
Indices: 16732891--16733046 Score: 181
Period size: 66 Copynumber: 2.4 Consensus size: 66
16732881 CGGATGACCG
* * * *
16732891 AGATGAAATCACAAGTC-TAAAAATGAAGTGATCAGGACCGAGTCGAAGTCAAAAATAAATGATC
1 AGATGAAATCACGAGTCAGAAAAATAAAGTGATCAGGACCAAGTCGAAGTCAAAAATAAATGATC
16732955 A
66 A
* * * *
16732956 AGATGAAATCATGAGTCAGAAAAATAAAGTGAAT-AGGACCAAGTCGAGGTCGAAAATAAATTAT
1 AGATGAAATCACGAGTCAGAAAAATAAAGTG-ATCAGGACCAAGTCGAAGTCAAAAATAAATGAT
16733020 CA
65 CA
* ** *
16733022 GGACAAAATCGCGAGTCAGAAAAAT
1 AGATGAAATCACGAGTCAGAAAAAT
16733047 GATTTGGACT
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
65 15 0.20
66 59 0.78
67 2 0.03
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.18
Consensus pattern (66 bp):
AGATGAAATCACGAGTCAGAAAAATAAAGTGATCAGGACCAAGTCGAAGTCAAAAATAAATGATC
A
Found at i:16733293 original size:66 final size:66
Alignment explanation
Indices: 16733152--16733298 Score: 172
Period size: 66 Copynumber: 2.2 Consensus size: 66
16733142 GACAAAATTG
* * * * *
16733152 CGAGTT-AAGAAATGAAGCGACTAAGATTGAGTCGAGATCGAAAATGAATGACTGAGATGAAATC
1 CGAGTTAAAAAAATGAAGCGACCAAGATTGAGTCAAGATCAAAAATGAATAACTGAGATGAAATC
16733216 A
66 A
* * * *
16733217 CAAGTCAAAAAAATGAAGCGACCAAGATTGAGTCAAGGTCAAAAATGTATAACT-AGAATGAAAT
1 CGAGTTAAAAAAATGAAGCGACCAAGATTGAGTCAAGATCAAAAATGAATAACTGAG-ATGAAAT
*
16733281 CG
65 CA
*
16733283 TGAGTTAAAAAAATGA
1 CGAGTTAAAAAAATGA
16733299 TCTGGACTAA
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
65 6 0.09
66 61 0.91
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.20
Consensus pattern (66 bp):
CGAGTTAAAAAAATGAAGCGACCAAGATTGAGTCAAGATCAAAAATGAATAACTGAGATGAAATC
A
Found at i:16738868 original size:17 final size:16
Alignment explanation
Indices: 16738843--16738874 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
16738833 TATACAAAGA
16738843 TTTTTTTATTTTTATT
1 TTTTTTTATTTTTATT
16738859 TTTTTATTATTTTTAT
1 TTTTT-TTATTTTTAT
16738875 CATTTTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTATTTTTATT
Found at i:16738873 original size:9 final size:9
Alignment explanation
Indices: 16738842--16738881 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
16738832 TTATACAAAG
16738842 ATTTTT-TT
1 ATTTTTATT
16738850 ATTTTTATT
1 ATTTTTATT
16738859 -TTTTTATT
1 ATTTTTATT
*
16738867 ATTTTTATC
1 ATTTTTATT
16738876 ATTTTT
1 ATTTTT
16738882 CAGAAAGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 14 0.48
9 15 0.52
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (9 bp):
ATTTTTATT
Found at i:16738880 original size:17 final size:17
Alignment explanation
Indices: 16738842--16738880 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
16738832 TTATACAAAG
* *
16738842 ATTTTTTTATTTTTATT
1 ATTTTATTATTTTTATC
*
16738859 TTTTTATTATTTTTATC
1 ATTTTATTATTTTTATC
16738876 ATTTT
1 ATTTT
16738881 TCAGAAAGGA
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:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (17 bp):
ATTTTATTATTTTTATC
Found at i:16738964 original size:22 final size:21
Alignment explanation
Indices: 16738939--16738979 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
16738929 TTACTTAAAG
16738939 AAAATAA-ATAAATAATAAAACA
1 AAAATAATA-AAATAA-AAAACA
16738961 AAAATAATAAAATAAAAAA
1 AAAATAATAAAATAAAAAA
16738980 TTGAAAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 13 0.72
23 1 0.06
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAATAATAAAATAAAAAACA
Found at i:16738967 original size:14 final size:14
Alignment explanation
Indices: 16738948--16738978 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
16738938 GAAAATAAAT
16738948 AAATAATAAAACAA
1 AAATAATAAAACAA
*
16738962 AAATAATAAAATAA
1 AAATAATAAAACAA
16738976 AAA
1 AAA
16738979 ATTGAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (14 bp):
AAATAATAAAACAA
Found at i:16740860 original size:23 final size:25
Alignment explanation
Indices: 16740834--16740881 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
16740824 AGGTTTCTGC
*
16740834 CAAAGGTTT-TTTT-TTTTTTTTTG
1 CAAAGCTTTCTTTTCTTTTTTTTTG
16740857 CAAAGCTTTCTTTTCCTTTTTTTTT
1 CAAAGCTTTCTTTT-CTTTTTTTTT
16740882 TTTAATGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 4 0.19
26 9 0.43
ACGTcount: A:0.12, C:0.12, G:0.08, T:0.67
Consensus pattern (25 bp):
CAAAGCTTTCTTTTCTTTTTTTTTG
Found at i:16742321 original size:18 final size:17
Alignment explanation
Indices: 16742297--16742354 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
16742287 AGGCCCGAAA
16742297 ATTTTAATTTTGGTTTT
1 ATTTTAATTTTGGTTTT
*
16742314 AGTTTTAATATTGGTTTTT
1 A-TTTTAATTTTGG-TTTT
*
16742333 ATTTT-ATTTTAGTTTT
1 ATTTTAATTTTGGTTTT
16742349 AATTTT
1 -ATTTT
16742355 TGGTTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
16 4 0.11
17 11 0.31
18 15 0.43
19 5 0.14
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (17 bp):
ATTTTAATTTTGGTTTT
Found at i:16742355 original size:18 final size:18
Alignment explanation
Indices: 16742296--16742378 Score: 51
Period size: 18 Copynumber: 4.6 Consensus size: 18
16742286 TAGGCCCGAA
* *
16742296 AATTTTAATTTTGGTTTT
1 AATTTTTATTTTAGTTTT
* * * *
16742314 AGTTTTAATATTGGTTTT
1 AATTTTTATTTTAGTTTT
*
16742332 TA-TTTTATTTTAGTTTT
1 AATTTTTATTTTAGTTTT
* *
16742349 AATTTTTGGTTTTTAATTTT
1 AATTTTT--ATTTTAGTTTT
*
16742369 AGTTTTTATT
1 AATTTTTATT
16742379 CTTTTTAGTC
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
17 13 0.26
18 22 0.44
20 15 0.30
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (18 bp):
AATTTTTATTTTAGTTTT
Found at i:16742373 original size:13 final size:13
Alignment explanation
Indices: 16742334--16742376 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
16742324 TTGGTTTTTA
16742334 TTTT-ATTTTAG-
1 TTTTAATTTTAGT
*
16742345 TTTTAATTTTTGGT
1 TTTTAA-TTTTAGT
16742359 TTTTAATTTTAGT
1 TTTTAATTTTAGT
16742372 TTTTA
1 TTTTA
16742377 TTCTTTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 1 0.04
13 16 0.59
14 6 0.22
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (13 bp):
TTTTAATTTTAGT
Found at i:16742421 original size:16 final size:15
Alignment explanation
Indices: 16742396--16742434 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
16742386 GTCAAAGGTT
16742396 AAAAAAAAAGGAAAA
1 AAAAAAAAAGGAAAA
16742411 AAAAAAGAAAGGAAAA
1 AAAAAA-AAAGGAAAA
16742427 ATAAAAAA
1 A-AAAAAA
16742435 TGAGAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.27
16 11 0.50
17 5 0.23
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAGGAAAA
Found at i:16743365 original size:12 final size:12
Alignment explanation
Indices: 16743348--16743393 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
16743338 CCAACGCAGG
*
16743348 TTTTTCTTTTTT
1 TTTTTCTTTTAT
*
16743360 TTTTTCATTTAT
1 TTTTTCTTTTAT
* *
16743372 TTTTTGTTTTAA
1 TTTTTCTTTTAT
16743384 TTTTTCTTTT
1 TTTTTCTTTT
16743394 CTCTATGTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.09, C:0.07, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTTCTTTTAT
Found at i:16743916 original size:40 final size:40
Alignment explanation
Indices: 16743859--16743934 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
16743849 TAAATTTATA
* * * *
16743859 TATTTTTTGTATGTATTATTTGTATACTAACCCTTTATGT
1 TATTTTTTATATATATTATATGCATACTAACCCTTTATGT
*
16743899 TATTTTTTATATATATTATATGCATACTAATCCTTT
1 TATTTTTTATATATATTATATGCATACTAACCCTTT
16743935 TCTTTTACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.57
Consensus pattern (40 bp):
TATTTTTTATATATATTATATGCATACTAACCCTTTATGT
Found at i:16747516 original size:11 final size:10
Alignment explanation
Indices: 16747465--16747532 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
16747455 TGAGATGTGT
16747465 AAAAAAAACA
1 AAAAAAAACA
* * *
16747475 TAAAAATATA
1 AAAAAAAACA
*
16747485 TAAAAAAA-A
1 AAAAAAAACA
**
16747494 AAGTAAAACA
1 AAAAAAAACA
16747504 AAAAAAAACCA
1 AAAAAAAA-CA
16747515 AAAAAAAA-A
1 AAAAAAAACA
16747524 GAAAAAAAA
1 -AAAAAAAA
16747533 GGAAAAATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
9 7 0.15
10 29 0.63
11 10 0.22
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.07
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:16747518 original size:12 final size:11
Alignment explanation
Indices: 16747498--16747532 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
16747488 AAAAAAAAGT
16747498 AAAACAAAAAA
1 AAAACAAAAAA
*
16747509 AAACCAAAAAA
1 AAAACAAAAAA
*
16747520 AAAAGAAAAAA
1 AAAACAAAAAA
16747531 AA
1 AA
16747533 GGAAAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.89, C:0.09, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:16748509 original size:22 final size:22
Alignment explanation
Indices: 16748482--16748587 Score: 65
Period size: 22 Copynumber: 4.9 Consensus size: 22
16748472 CCTTTGAAAC
16748482 TTTGGATGTAAATCTCTAACTT
1 TTTGGATGTAAATCTCTAACTT
* * * * **
16748504 TTTGGATTTGAATATTTAAAAT
1 TTTGGATGTAAATCTCTAACTT
* *
16748526 TTTGGATGTGAATC-CTTAAATTT
1 TTTGGATGTAAATCTC-T-AACTT
* * *
16748549 TTTGAATGAAAATCTTTAAC-T
1 TTTGGATGTAAATCTCTAACTT
*
16748570 TTTGG-TATAAATCTCTAA
1 TTTGGATGTAAATCTCTAA
16748588 AATTTTTCGA
Statistics
Matches: 61, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
20 10 0.16
21 5 0.08
22 31 0.51
23 15 0.25
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.46
Consensus pattern (22 bp):
TTTGGATGTAAATCTCTAACTT
Found at i:16748871 original size:17 final size:17
Alignment explanation
Indices: 16748815--16748873 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
16748805 AGATTCCTAC
16748815 AATTCTTGC-AAATCTAAA
1 AATTCTTGCAAAAT-T-AA
* *
16748833 AATTCTTACAAATATT-T
1 AATTCTTGCAAA-ATTAA
*
16748850 GATTCTTGCAAAATTAA
1 AATTCTTGCAAAATTAA
16748867 AATTCTT
1 AATTCTT
16748874 ACGAATATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
16 3 0.09
17 16 0.50
18 8 0.25
19 3 0.09
20 2 0.06
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (17 bp):
AATTCTTGCAAAATTAA
Found at i:16748874 original size:34 final size:35
Alignment explanation
Indices: 16748816--16748881 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
16748806 GATTCCTACA
16748816 ATTCTTGCAAATCTAAAAATTCTTACAAATATTTG
1 ATTCTTGCAAATCTAAAAATTCTTACAAATATTTG
*
16748851 ATTCTTGCAAAAT-T-AAAATTCTTACGAATAT
1 ATTCTTGC-AAATCTAAAAATTCTTACAAATAT
16748882 GAAAATCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 16 0.55
35 9 0.31
36 4 0.14
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (35 bp):
ATTCTTGCAAATCTAAAAATTCTTACAAATATTTG
Found at i:16748890 original size:17 final size:18
Alignment explanation
Indices: 16748865--16748898 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16748855 TTGCAAAATT
16748865 AAAATTCTTACGAATATG
1 AAAATTCTTACGAATATG
*
16748883 AAAA-TCTTGCGAATAT
1 AAAATTCTTACGAATAT
16748899 TTGAGTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (18 bp):
AAAATTCTTACGAATATG
Found at i:16748891 original size:34 final size:35
Alignment explanation
Indices: 16748818--16748892 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 35
16748808 TTCCTACAAT
*** *
16748818 TCTTGCAAATCTAAAAATTCTTACAAATATTTGAT
1 TCTTGCAAATCTAAAAATTCTTACAAATATGAAAA
*
16748853 TCTTGCAAAAT-T-AAAATTCTTACGAATATGAAAA
1 TCTTGC-AAATCTAAAAATTCTTACAAATATGAAAA
16748887 TCTTGC
1 TCTTGC
16748893 GAATATTTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 23 0.68
35 7 0.21
36 4 0.12
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (35 bp):
TCTTGCAAATCTAAAAATTCTTACAAATATGAAAA
Found at i:16749045 original size:18 final size:18
Alignment explanation
Indices: 16749022--16749086 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
16749012 GTAAATCAAG
* *
16749022 AATCTTTGTAAAACTTGA
1 AATCTTTGTGAATCTTGA
16749040 AATCTTTGTGAATCTT-A
1 AATCTTTGTGAATCTTGA
*
16749057 ACAT-TTTGTGAATTTTGA
1 A-ATCTTTGTGAATCTTGA
16749075 AATCTTTGTGAA
1 AATCTTTGTGAA
16749087 ATTTTTGCGA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 15 0.37
18 26 0.63
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (18 bp):
AATCTTTGTGAATCTTGA
Found at i:16749585 original size:6 final size:6
Alignment explanation
Indices: 16749569--16749633 Score: 60
Period size: 6 Copynumber: 10.8 Consensus size: 6
16749559 TTTACTTTCG
* * * * *
16749569 ATTTTA GTTTTA ATTTTG ATTTTG ATTTT- ATTTTA GTTTTA GTTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
*
16749616 ATTTTTA ATTTTA GTTTT
1 A-TTTTA ATTTTA ATTTT
16749634 TATTATTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
5 5 0.10
6 40 0.78
7 6 0.12
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (6 bp):
ATTTTA
Found at i:16749589 original size:18 final size:18
Alignment explanation
Indices: 16749558--16749633 Score: 77
Period size: 18 Copynumber: 4.2 Consensus size: 18
16749548 GGCCCAAACA
* *
16749558 TTTTACTTTCGATTTTAG
1 TTTTAATTTTGATTTTAG
16749576 TTTTAATTTTGATTTT-G
1 TTTTAATTTTGATTTTAG
16749593 ATTTT-ATTTT-AGTTTTAG
1 -TTTTAATTTTGA-TTTTAG
*
16749611 TTTTAATTTTTAATTTTAG
1 TTTTAA-TTTTGATTTTAG
16749630 TTTT
1 TTTT
16749634 TATTATTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
16 1 0.02
17 14 0.28
18 20 0.40
19 14 0.28
20 1 0.02
ACGTcount: A:0.20, C:0.03, G:0.09, T:0.68
Consensus pattern (18 bp):
TTTTAATTTTGATTTTAG
Found at i:16749644 original size:35 final size:35
Alignment explanation
Indices: 16749570--16749646 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
16749560 TTACTTTCGA
* *
16749570 TTTTAGTTTTAATTTTGATTTTGATTTTATTTTAG
1 TTTTAGTTTTAATTTTAATTTTGATTTTATATTAG
*
16749605 TTTTAGTTTTAATTTTTAATTTT-AGTTTT-TATTAT
1 TTTTAGTTTTAA-TTTTAATTTTGA-TTTTATATTAG
16749640 TTTTAGT
1 TTTTAGT
16749647 CAAAGGTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 24 0.65
36 13 0.35
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (35 bp):
TTTTAGTTTTAATTTTAATTTTGATTTTATATTAG
Found at i:16750642 original size:17 final size:15
Alignment explanation
Indices: 16750616--16750658 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
16750606 ACAGCACAAG
16750616 TTTTTTTTTTCATTT
1 TTTTTTTTTTCATTT
*
16750631 ATTTTTTATTTTGATTT
1 -TTTTTT-TTTTCATTT
16750648 TTTTTCTTTTT
1 TTTTT-TTTTT
16750659 TCTATGTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.09, C:0.05, G:0.02, T:0.84
Consensus pattern (15 bp):
TTTTTTTTTTCATTT
Found at i:16750659 original size:17 final size:17
Alignment explanation
Indices: 16750616--16750660 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
16750606 ACAGCACAAG
16750616 TTTTTTTTTTCATTTAT
1 TTTTTTTTTTCATTTAT
* *
16750633 TTTTTATTTTGATTT-T
1 TTTTTTTTTTCATTTAT
16750649 TTTTCTTTTTTC
1 TTTT-TTTTTTC
16750661 TATGTTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.09, C:0.07, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTCATTTAT
Found at i:16750702 original size:14 final size:14
Alignment explanation
Indices: 16750685--16750732 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
16750675 TTTTTCTGTT
16750685 TTTTATATATATTA
1 TTTTATATATATTA
*
16750699 TTTT-TATATTTATA
1 TTTTATATATAT-TA
*
16750713 TTTTAATATTTATTA
1 TTTT-ATATATATTA
16750728 TTTTA
1 TTTTA
16750733 GATGGTTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 6 0.21
14 11 0.39
15 6 0.21
16 5 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATATATATTA
Found at i:16750702 original size:15 final size:15
Alignment explanation
Indices: 16750684--16750731 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
16750674 ATTTTTCTGT
*
16750684 TTTTTATATATATTA
1 TTTTTATATTTATTA
16750699 TTTTTATATTTA-TA
1 TTTTTATATTTATTA
*
16750713 TTTTAATATTTATTA
1 TTTTTATATTTATTA
16750728 TTTT
1 TTTT
16750732 AGATGGTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 13 0.43
15 17 0.57
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTATATTTATTA
Found at i:16750861 original size:21 final size:24
Alignment explanation
Indices: 16750837--16750880 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
16750827 ATATATTTGT
16750837 ATGAT-ATTT-TATATTA-ATTAC
1 ATGATAATTTATATATTATATTAC
16750858 ATGATAATTTATATATTATATTA
1 ATGATAATTTATATATTATATTA
16750881 TTATATGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 4 0.20
23 7 0.35
24 4 0.20
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (24 bp):
ATGATAATTTATATATTATATTAC
Found at i:16750896 original size:27 final size:28
Alignment explanation
Indices: 16750840--16750896 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
16750830 TATTTGTATG
* *
16750840 ATATTTTATATTAATTACATGATAATTT
1 ATATATTATATTAATTACATGATAACTT
* *
16750868 ATATATTATATT-ATTATATGATAGCTT
1 ATATATTATATTAATTACATGATAACTT
16750895 AT
1 AT
16750897 GTTTATTGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.53
Consensus pattern (28 bp):
ATATATTATATTAATTACATGATAACTT
Found at i:16751199 original size:17 final size:17
Alignment explanation
Indices: 16751177--16751220 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
16751167 TATTAGAAGA
*
16751177 TATTTTTAAAAATAAAT
1 TATTTTCAAAAATAAAT
*
16751194 TATTTTCACAAATAAAT
1 TATTTTCAAAAATAAAT
*
16751211 AAATTTTCAA
1 -TATTTTCAA
16751221 CCCTATCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (17 bp):
TATTTTCAAAAATAAAT
Found at i:16751751 original size:2 final size:2
Alignment explanation
Indices: 16751739--16751773 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
16751729 TATGTCTAAT
*
16751739 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16751774 TTATGCTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16752452 original size:15 final size:15
Alignment explanation
Indices: 16752434--16752470 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
16752424 TTTAAAAGAA
*
16752434 TTTAATTAATTTAAT
1 TTTAAATAATTTAAT
16752449 TTTAAATAATTTAAT
1 TTTAAATAATTTAAT
*
16752464 TTAAAAT
1 TTTAAAT
16752471 TAAGCGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAAATAATTTAAT
Found at i:16756113 original size:15 final size:16
Alignment explanation
Indices: 16756088--16756120 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
16756078 ATCATGAATG
16756088 TATTAAAATTTATTTA
1 TATTAAAATTTATTTA
*
16756104 TATT-AAATTTGTTTA
1 TATTAAAATTTATTTA
16756119 TA
1 TA
16756121 ACATGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TATTAAAATTTATTTA
Found at i:16758088 original size:13 final size:13
Alignment explanation
Indices: 16758045--16758093 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
16758035 CAAAATATCA
16758045 ATTA-TTTTTATT
1 ATTATTTTTTATT
*
16758057 TTTATTTTTTATT
1 ATTATTTTTTATT
16758070 A--ATTTTTTATT
1 ATTATTTTTTATT
* *
16758081 ATTGTTTTATATT
1 ATTATTTTTTATT
16758094 GTTTAAATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
11 11 0.37
12 3 0.10
13 16 0.53
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (13 bp):
ATTATTTTTTATT
Found at i:16758093 original size:10 final size:11
Alignment explanation
Indices: 16758058--16758097 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
16758048 ATTTTTATTT
16758058 TTATT-TTTTA
1 TTATTGTTTTA
16758068 TTAATT-TTTTA
1 TT-ATTGTTTTA
16758079 TTATTGTTTTA
1 TTATTGTTTTA
16758090 -TATTGTTT
1 TTATTGTTT
16758098 AAATCAATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 13 0.46
11 15 0.54
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (11 bp):
TTATTGTTTTA
Found at i:16759418 original size:3 final size:3
Alignment explanation
Indices: 16759360--16759398 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
16759350 TTTTAAAGAT
16759360 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16759399 ACAAAATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16759429 original size:29 final size:29
Alignment explanation
Indices: 16759380--16759435 Score: 53
Period size: 29 Copynumber: 1.9 Consensus size: 29
16759370 AATAATAATA
* * *
16759380 ATAATAATAATAATAATAAACAAAATTATAT
1 ATAATAATAAAAAAAAAAAACAAAA-T-TAT
16759411 A-A-TAATAAAAAAAAAAAACAAAATT
1 ATAATAATAAAAAAAAAAAACAAAATT
16759436 GGTGCCTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.05
28 1 0.05
29 18 0.82
30 1 0.05
31 1 0.05
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (29 bp):
ATAATAATAAAAAAAAAAAACAAAATTAT
Found at i:16759728 original size:39 final size:39
Alignment explanation
Indices: 16759604--16760107 Score: 439
Period size: 39 Copynumber: 13.3 Consensus size: 39
16759594 AGAGGCTATA
* * * * * *
16759604 AAACTTTAAATTCAAAAAGCTCATTTCACCAGAGGTAAT
1 AAACTTTAAATTCAAAAGGCTCCTTTAACCAAAGGCAAC
* * *
16759643 GAACTTTAAATTTAAAA-GCTCATTTAACCAAAGGCAAC
1 AAACTTTAAATTCAAAAGGCTCCTTTAACCAAAGGCAAC
* * * * *
16759681 GAACTTTAAATTCAAAAGGATCCTCTCACCAGAGGCAAC
1 AAACTTTAAATTCAAAAGGCTCCTTTAACCAAAGGCAAC
* *
16759720 AAACTTTAAATCCAAAA-GCTCATTTAACCAAAGGCAAC
1 AAACTTTAAATTCAAAAGGCTCCTTTAACCAAAGGCAAC
* **
16759758 AAATTTTAAATTCAAAA-GCTTTTTTAACCAAAGGCAAC
1 AAACTTTAAATTCAAAAGGCTCCTTTAACCAAAGGCAAC
*
16759796 AAACTTTAAATTCCAAAA-GCTCTTTTAACCAAAGGCAAC
1 AAACTTTAAATT-CAAAAGGCTCCTTTAACCAAAGGCAAC
* * *
16759835 AAACTTTAAATGTTAAAAGGCTCCTTTCACCAGAGGCAAC
1 AAACTTTAAAT-TCAAAAGGCTCCTTTAACCAAAGGCAAC
* * * * * *
16759875 GAACTTTAGA-T-----GGCTCTTTTAACTAAAAGTAAC
1 AAACTTTAAATTCAAAAGGCTCCTTTAACCAAAGGCAAC
* * * *
16759908 AAACTTTAAATTCAAAAGGCTCCTCTCACTAGAGGCAAC
1 AAACTTTAAATTCAAAAGGCTCCTTTAACCAAAGGCAAC
* * *
16759947 AAACTTTAAATCCAAAA-GCTCTTTTAACCAAAGGTAAC
1 AAACTTTAAATTCAAAAGGCTCCTTTAACCAAAGGCAAC
* * * * *
16759985 AAACTTTAAATGTTAAAAGGCTCCTCTGACCAGAGACAAC
1 AAACTTTAAAT-TCAAAAGGCTCCTTTAACCAAAGGCAAC
*
16760025 GAACTTTAAA-T-----GGCTCCTTTAACCAAAGGCAAC
1 AAACTTTAAATTCAAAAGGCTCCTTTAACCAAAGGCAAC
* * * * *
16760058 AAACTTTAAATTCAAAAGGCTCCTCTCACTAGAGGCAAT
1 AAACTTTAAATTCAAAAGGCTCCTTTAACCAAAGGCAAC
16760097 AAACTTTAAAT
1 AAACTTTAAAT
16760108 CTAAAAATCT
Statistics
Matches: 376, Mismatches: 71, Indels: 36
0.78 0.15 0.07
Matches are distributed among these distances:
33 51 0.14
34 2 0.01
38 122 0.32
39 150 0.40
40 51 0.14
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (39 bp):
AAACTTTAAATTCAAAAGGCTCCTTTAACCAAAGGCAAC
Found at i:16759737 original size:77 final size:77
Alignment explanation
Indices: 16759604--16760113 Score: 583
Period size: 77 Copynumber: 6.7 Consensus size: 77
16759594 AGAGGCTATA
* * * * ** ** *
16759604 AAACTTTAAATTCAAAAAGCTCATTTCACCAGAGGTAATGAACTTTAAATTTAAAAGCTCATTTA
1 AAACTTTAAATTCAAAAGGCTCCTCTCACCAGAGGCAACAAACTTTAAATCCAAAAGCTCTTTTA
16759669 ACCAAAGGCAAC
66 ACCAAAGGCAAC
* * *
16759681 GAACTTTAAATTCAAAAGGATCCTCTCACCAGAGGCAACAAACTTTAAATCCAAAAGCTCATTTA
1 AAACTTTAAATTCAAAAGGCTCCTCTCACCAGAGGCAACAAACTTTAAATCCAAAAGCTCTTTTA
16759746 ACCAAAGGCAAC
66 ACCAAAGGCAAC
* ** * * *
16759758 AAATTTTAAATTCAAAA-GCTTTTTTAACCAAAGGCAACAAACTTTAAATTCCAAAAGCTCTTTT
1 AAACTTTAAATTCAAAAGGCTCCTCTCACCAGAGGCAACAAACTTTAAA-TCCAAAAGCTCTTTT
16759822 AACCAAAGGCAAC
65 AACCAAAGGCAAC
* * * * *
16759835 AAACTTTAAATGTTAAAAGGCTCCTTTCACCAGAGGCAACGAACTTTAGAT-----GGCTCTTTT
1 AAACTTTAAAT-TCAAAAGGCTCCTCTCACCAGAGGCAACAAACTTTAAATCCAAAAGCTCTTTT
* * *
16759895 AACTAAAAGTAAC
65 AACCAAAGGCAAC
*
16759908 AAACTTTAAATTCAAAAGGCTCCTCTCACTAGAGGCAACAAACTTTAAATCCAAAAGCTCTTTTA
1 AAACTTTAAATTCAAAAGGCTCCTCTCACCAGAGGCAACAAACTTTAAATCCAAAAGCTCTTTTA
*
16759973 ACCAAAGGTAAC
66 ACCAAAGGCAAC
* * * * * *
16759985 AAACTTTAAATGTTAAAAGGCTCCTCTGACCAGAGACAACGAACTTTAAAT-----GGCTCCTTT
1 AAACTTTAAAT-TCAAAAGGCTCCTCTCACCAGAGGCAACAAACTTTAAATCCAAAAGCTCTTTT
16760045 AACCAAAGGCAAC
65 AACCAAAGGCAAC
* * *
16760058 AAACTTTAAATTCAAAAGGCTCCTCTCACTAGAGGCAATAAACTTTAAATCTAAAA
1 AAACTTTAAATTCAAAAGGCTCCTCTCACCAGAGGCAACAAACTTTAAATCCAAAA
16760114 ATCTGAGAGG
Statistics
Matches: 365, Mismatches: 54, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
72 67 0.18
73 59 0.16
76 25 0.07
77 149 0.41
78 40 0.11
79 25 0.07
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (77 bp):
AAACTTTAAATTCAAAAGGCTCCTCTCACCAGAGGCAACAAACTTTAAATCCAAAAGCTCTTTTA
ACCAAAGGCAAC
Found at i:16759964 original size:150 final size:150
Alignment explanation
Indices: 16759604--16760113 Score: 646
Period size: 150 Copynumber: 3.4 Consensus size: 150
16759594 AGAGGCTATA
* * * * ** ** *
16759604 AAACTTTAAATTCAAAAAGCTCATTTCACCAGAGGTAATGAACTTTAAATTTAAAAGCTCATTTA
1 AAACTTTAAATTCAAAAGGCTCCTCTCACCAGAGGCAACAAACTTTAAATCCAAAAGCTCTTTTA
* * * *
16759669 ACCAAAGGCAACGAACTTTAAAT-TCAAAAGGATCCTCTCACCAGAGGCAACAAACTTTAAATCC
66 ACCAAAGGCAACAAACTTTAAATGTTAAAAGGCTCCTCTCACCAGAGGCAACGAACTTTAAAT--
*
16759733 AAAAGCTCATTTAACCAAAGGCAAC
129 ---GGCTCATTTAACCAAAGGCAAC
* ** * * *
16759758 AAATTTTAAATTCAAAA-GCTTTTTTAACCAAAGGCAACAAACTTTAAATTCCAAAAGCTCTTTT
1 AAACTTTAAATTCAAAAGGCTCCTCTCACCAGAGGCAACAAACTTTAAA-TCCAAAAGCTCTTTT
* *
16759822 AACCAAAGGCAACAAACTTTAAATGTTAAAAGGCTCCTTTCACCAGAGGCAACGAACTTTAGATG
65 AACCAAAGGCAACAAACTTTAAATGTTAAAAGGCTCCTCTCACCAGAGGCAACGAACTTTAAATG
* * * *
16759887 GCTCTTTTAACTAAAAGTAAC
130 GCTCATTTAACCAAAGGCAAC
*
16759908 AAACTTTAAATTCAAAAGGCTCCTCTCACTAGAGGCAACAAACTTTAAATCCAAAAGCTCTTTTA
1 AAACTTTAAATTCAAAAGGCTCCTCTCACCAGAGGCAACAAACTTTAAATCCAAAAGCTCTTTTA
* * *
16759973 ACCAAAGGTAACAAACTTTAAATGTTAAAAGGCTCCTCTGACCAGAGACAACGAACTTTAAATGG
66 ACCAAAGGCAACAAACTTTAAATGTTAAAAGGCTCCTCTCACCAGAGGCAACGAACTTTAAATGG
*
16760038 CTCCTTTAACCAAAGGCAAC
131 CTCATTTAACCAAAGGCAAC
* * *
16760058 AAACTTTAAATTCAAAAGGCTCCTCTCACTAGAGGCAATAAACTTTAAATCTAAAA
1 AAACTTTAAATTCAAAAGGCTCCTCTCACCAGAGGCAACAAACTTTAAATCCAAAA
16760114 ATCTGAGAGG
Statistics
Matches: 313, Mismatches: 40, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
150 179 0.57
151 25 0.08
153 24 0.08
154 51 0.16
155 34 0.11
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (150 bp):
AAACTTTAAATTCAAAAGGCTCCTCTCACCAGAGGCAACAAACTTTAAATCCAAAAGCTCTTTTA
ACCAAAGGCAACAAACTTTAAATGTTAAAAGGCTCCTCTCACCAGAGGCAACGAACTTTAAATGG
CTCATTTAACCAAAGGCAAC
Found at i:16760040 original size:33 final size:33
Alignment explanation
Indices: 16759997--16760068 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
16759987 ACTTTAAATG
* * * *
16759997 TTAAAAGGCTCCTCTGACCAGAGACAACGAACT
1 TTAAATGGCTCCTCTAACCAAAGACAACAAACT
* *
16760030 TTAAATGGCTCCTTTAACCAAAGGCAACAAACT
1 TTAAATGGCTCCTCTAACCAAAGACAACAAACT
16760063 TTAAAT
1 TTAAAT
16760069 TCAAAAGGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (33 bp):
TTAAATGGCTCCTCTAACCAAAGACAACAAACT
Found at i:16760505 original size:19 final size:19
Alignment explanation
Indices: 16760481--16760525 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
16760471 TCCATGTTGA
16760481 CCACTTTATGGCTTATAAG
1 CCACTTTATGGCTTATAAG
16760500 CCACTTTATGGCTTATAAG
1 CCACTTTATGGCTTATAAG
16760519 CCACTTT
1 CCACTTT
16760526 TCCCATTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.38
Consensus pattern (19 bp):
CCACTTTATGGCTTATAAG
Found at i:16772248 original size:17 final size:17
Alignment explanation
Indices: 16772209--16772257 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
16772199 ATTCATTTAA
16772209 ATAATTTATT-TTTTATT
1 ATAATTTATTATTTT-TT
*
16772226 -TTATTTATTATTTTTT
1 ATAATTTATTATTTTTT
16772242 ATAATTTATTATTTTT
1 ATAATTTATTATTTTT
16772258 AGCAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 10 0.36
17 18 0.64
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATAATTTATTATTTTTT
Found at i:16772536 original size:21 final size:22
Alignment explanation
Indices: 16772492--16772538 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
16772482 ACATTATAAA
** *
16772492 AAAATAACATAAAAATCAATAG
1 AAAATAACATAAAAAGAAAAAG
16772514 AAAATAA-ATAAAAAGAAAAAG
1 AAAATAACATAAAAAGAAAAAG
16772535 AAAA
1 AAAA
16772539 AAAACCTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.13
Consensus pattern (22 bp):
AAAATAACATAAAAAGAAAAAG
Found at i:16772685 original size:11 final size:11
Alignment explanation
Indices: 16772669--16772693 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16772659 GCTTTTCTTT
16772669 TTTATTTTTTC
1 TTTATTTTTTC
16772680 TTTATTTTTTC
1 TTTATTTTTTC
16772691 TTT
1 TTT
16772694 CCCCCTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTTTC
Found at i:16775107 original size:5 final size:5
Alignment explanation
Indices: 16775097--16775125 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
16775087 CGGTTGTTAA
16775097 GGAAG GGAAG GGAAG GGAAG GGAAG GGAA
1 GGAAG GGAAG GGAAG GGAAG GGAAG GGAA
16775126 ATTAAAGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (5 bp):
GGAAG
Found at i:16781103 original size:15 final size:15
Alignment explanation
Indices: 16781081--16781114 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16781071 AAATTAATTT
16781081 TATA-ATAATTCAAA
1 TATATATAATTCAAA
*
16781095 TATATATAATTTAAA
1 TATATATAATTCAAA
16781110 TATAT
1 TATAT
16781115 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
TATATATAATTCAAA
Found at i:16781246 original size:61 final size:61
Alignment explanation
Indices: 16781177--16781382 Score: 193
Period size: 61 Copynumber: 3.2 Consensus size: 61
16781167 TATCCAGCAC
16781177 TAATTTTCTAATAGTTTACATATATATAATTTAAATATATATATTTTTTATCTTCTAAAAT
1 TAATTTTCTAATAGTTTACATATATATAATTTAAATATATATATTTTTTATCTTCTAAAAT
* * ** * * *
16781238 TAATTTTCTACTAATTTTATGTTATTTATCAA-ATAAATA-AAAGTATTTAAAAATGATTAGT-T
1 TAATTTTCTAAT-AGTTTA-CATATATAT-AATTTAAATATATA-TATTT-----T--TTA-TCT
*
16781300 ATCCAAAAT
54 -TCTAAAAT
*
16781309 TAATTTTCTAATAGTTTACATATATATAATTTAAATATATATCTTTTTTATCTTCTAAAAT
1 TAATTTTCTAATAGTTTACATATATATAATTTAAATATATATATTTTTTATCTTCTAAAAT
16781370 TAATTTTCTAATA
1 TAATTTTCTAATA
16781383 ATTTTATGTT
Statistics
Matches: 112, Mismatches: 17, Indels: 32
0.70 0.11 0.20
Matches are distributed among these distances:
61 32 0.29
62 11 0.10
63 17 0.15
64 3 0.03
68 3 0.03
69 16 0.14
70 11 0.10
71 19 0.17
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (61 bp):
TAATTTTCTAATAGTTTACATATATATAATTTAAATATATATATTTTTTATCTTCTAAAAT
Found at i:16781312 original size:71 final size:70
Alignment explanation
Indices: 16781233--16781455 Score: 227
Period size: 71 Copynumber: 3.3 Consensus size: 70
16781223 TTTATCTTCT
*
16781233 AAAATTAATTTTCTACTAATTTTATGTTATTTATCAAATAAATAAAAGTATTTAAAAATGATTAG
1 AAAATTAATTTTCTAATAATTTTATGTTATTTATCAAATAAATAAAAGTATTTAAAAAT-ATTAG
16781298 TTATCC
65 TTATCC
* ** * * * *
16781304 AAAATTAATTTTCTAAT-AGTTTA-CATATATAT-AATTTAAAT-ATA-TATCTT-----TTTTA
1 AAAATTAATTTTCTAATAATTTTATGTTATTTATCAA-ATAAATAAAAGTAT-TTAAAAATATTA
*
16781359 -TCT-TCT
64 GT-TATCC
*
16781365 AAAATTAATTTTCTAATAATTTTATGTTATTTATCAAATAAATAAAAGTATTTAAAAACAATTAG
1 AAAATTAATTTTCTAATAATTTTATGTTATTTATCAAATAAATAAAAGTATTTAAAAA-TATTAG
16781430 TTATCC
65 TTATCC
16781436 AAAATTAATTTTCTAATAAT
1 AAAATTAATTTTCTAATAAT
16781456 ATATAATTTA
Statistics
Matches: 118, Mismatches: 18, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
61 20 0.17
62 9 0.08
63 12 0.10
64 6 0.05
65 3 0.03
67 3 0.03
68 6 0.05
69 11 0.09
70 9 0.08
71 39 0.33
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (70 bp):
AAAATTAATTTTCTAATAATTTTATGTTATTTATCAAATAAATAAAAGTATTTAAAAATATTAGT
TATCC
Found at i:16781356 original size:132 final size:132
Alignment explanation
Indices: 16781134--16781453 Score: 543
Period size: 132 Copynumber: 2.4 Consensus size: 132
16781124 TTTAAAATCA
* * * ** *
16781134 ATCAAATAAGTAAAAATATTT-AAAATTATTAGTTATCCAGCACTAATTTTCTAATAGTTTACAT
1 ATCAAATAAATAAAAGTATTTAAAAATAATTAGTTATCCAAAATTAATTTTCTAATAGTTTACAT
*
16781198 ATATATAATTTAAATATATATATTTTTTATCTTCTAAAATTAATTTTCTACTAATTTTATGTTAT
66 ATATATAATTTAAATATATATATTTTTTATCTTCTAAAATTAATTTTCTAATAATTTTATGTTAT
16781263 TT
131 TT
*
16781265 ATCAAATAAATAAAAGTATTTAAAAATGATTAGTTATCCAAAATTAATTTTCTAATAGTTTACAT
1 ATCAAATAAATAAAAGTATTTAAAAATAATTAGTTATCCAAAATTAATTTTCTAATAGTTTACAT
*
16781330 ATATATAATTTAAATATATATCTTTTTTATCTTCTAAAATTAATTTTCTAATAATTTTATGTTAT
66 ATATATAATTTAAATATATATATTTTTTATCTTCTAAAATTAATTTTCTAATAATTTTATGTTAT
16781395 TT
131 TT
*
16781397 ATCAAATAAATAAAAGTATTTAAAAACAATTAGTTATCCAAAATTAATTTTCTAATA
1 ATCAAATAAATAAAAGTATTTAAAAATAATTAGTTATCCAAAATTAATTTTCTAATA
16781454 ATATATAATT
Statistics
Matches: 178, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
131 19 0.11
132 159 0.89
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.46
Consensus pattern (132 bp):
ATCAAATAAATAAAAGTATTTAAAAATAATTAGTTATCCAAAATTAATTTTCTAATAGTTTACAT
ATATATAATTTAAATATATATATTTTTTATCTTCTAAAATTAATTTTCTAATAATTTTATGTTAT
TT
Found at i:16781529 original size:132 final size:128
Alignment explanation
Indices: 16781134--16781507 Score: 496
Period size: 132 Copynumber: 2.9 Consensus size: 128
16781124 TTTAAAATCA
* * ** ** *
16781134 ATCAAATAAGTAAAAATATTT-AAAATTATTAGTTATCCAGCACTAATTTTCTAATAGTTTACAT
1 ATCAAATAAATAAAAGTATTTAAAAACAATTAGTTATCCAAAATTAATTTTCTAATA--TTA-AT
* *
16781198 ATATATAATTTAAATATATATATTTTTTATCTTCTAAAATTAATTTTCTACTAATTTTATGTTAT
63 ATATATAATTTAAATATATAT-CTTTTTATCTTCTAAAATTAATTTTCTAATAATTTTATGTTAT
16781263 TT
127 TT
**
16781265 ATCAAATAAATAAAAGTATTTAAAAATGATTAGTTATCCAAAATTAATTTTCTAATAGTTTACAT
1 ATCAAATAAATAAAAGTATTTAAAAACAATTAGTTATCCAAAATTAATTTTCTAATA--TTA-AT
16781330 ATATATAATTTAAATATATATCTTTTTTATCTTCTAAAATTAATTTTCTAATAATTTTATGTTAT
63 ATATATAATTTAAATATATATC-TTTTTATCTTCTAAAATTAATTTTCTAATAATTTTATGTTAT
16781395 TT
127 TT
16781397 ATCAAATAAATAAAAGTATTTAAAAACAATTAGTTATCCAAAATTAATTTTCT-A-A-T-A-ATA
1 ATCAAATAAATAAAAGTATTTAAAAACAATTAGTTATCCAAAATTAATTTTCTAATATTAATATA
*
16781457 TATAATTTAAATATATATC-TTTTATCTT-TCGAAATTAATTTT-TAATAATTT
66 TATAATTTAAATATATATCTTTTTATCTTCT-AAAATTAATTTTCTAATAATTT
16781508 AGATAATATC
Statistics
Matches: 229, Mismatches: 11, Indels: 16
0.89 0.04 0.06
Matches are distributed among these distances:
121 10 0.04
122 20 0.09
124 22 0.10
125 1 0.00
127 1 0.00
130 1 0.00
131 20 0.09
132 154 0.67
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (128 bp):
ATCAAATAAATAAAAGTATTTAAAAACAATTAGTTATCCAAAATTAATTTTCTAATATTAATATA
TATAATTTAAATATATATCTTTTTATCTTCTAAAATTAATTTTCTAATAATTTTATGTTATTT
Found at i:16783696 original size:13 final size:13
Alignment explanation
Indices: 16783671--16783710 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
16783661 TGATTTTGTT
16783671 AATAAAAATAAAAA
1 AATAAAAA-AAAAA
*
16783685 ACTAAAAAAAAAA
1 AATAAAAAAAAAA
*
16783698 AAGAAAAAAAAAA
1 AATAAAAAAAAAA
16783711 CAAATGGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.88, C:0.03, G:0.03, T:0.07
Consensus pattern (13 bp):
AATAAAAAAAAAA
Found at i:16784060 original size:19 final size:19
Alignment explanation
Indices: 16784032--16784077 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
16784022 TAGATTCTGG
*
16784032 TGAAGATTCCAACAAAATT
1 TGAAGTTTCCAACAAAATT
**
16784051 TGAAGTTTCCAATGAAATT
1 TGAAGTTTCCAACAAAATT
16784070 TGAAGTTT
1 TGAAGTTT
16784078 TCGATGAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (19 bp):
TGAAGTTTCCAACAAAATT
Found at i:16784084 original size:19 final size:19
Alignment explanation
Indices: 16784046--16784098 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
16784036 GATTCCAACA
*
16784046 AAATTTGAAGTTTCCAATG
1 AAATTTGAAGTTTTCAATG
*
16784065 AAATTTGAAGTTTTCGATG
1 AAATTTGAAGTTTTCAATG
*
16784084 AAACTTGAAGATTTT
1 AAATTTGAAG-TTTT
16784099 GACAACTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.40
Consensus pattern (19 bp):
AAATTTGAAGTTTTCAATG
Found at i:16791127 original size:10 final size:10
Alignment explanation
Indices: 16791114--16791142 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
16791104 ATAAAAAAAT
16791114 AAAAAATG-A
1 AAAAAATGAA
16791123 AAAAAATGAA
1 AAAAAATGAA
16791133 AAAAAATGAA
1 AAAAAATGAA
16791143 GGAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:16791148 original size:10 final size:9
Alignment explanation
Indices: 16791106--16791142 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
16791096 AATAATGGAT
16791106 AAAAAAAT-
1 AAAAAAATG
16791114 -AAAAAATG
1 AAAAAAATG
16791122 AAAAAAATG
1 AAAAAAATG
16791131 AAAAAAAATG
1 -AAAAAAATG
16791141 AA
1 AA
16791143 GGAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.27
9 10 0.38
10 9 0.35
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (9 bp):
AAAAAAATG
Found at i:16792351 original size:33 final size:33
Alignment explanation
Indices: 16792308--16792378 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
16792298 ACTTGATATT
* ** *
16792308 TGCATGGCATGCATTGCATTTCTGAATGTTTAG
1 TGCATAGCATGCATTGCATTTAAGAATGTTTAA
16792341 TGCATAGCATGCATTGCATTTAAGAATGTTTAA
1 TGCATAGCATGCATTGCATTTAAGAATGTTTAA
16792374 TGCAT
1 TGCAT
16792379 GAATCTAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCATAGCATGCATTGCATTTAAGAATGTTTAA
Found at i:16792713 original size:43 final size:43
Alignment explanation
Indices: 16792665--16792922 Score: 214
Period size: 43 Copynumber: 6.0 Consensus size: 43
16792655 TGTCGAAGAG
* *
16792665 CTTATTTATTTTTTCAAAATC-TTGAGCCTCTGTTTAGGGGTGC
1 CTTATTTA-TTTTTCAAAATCATTGAGCCTCTGTTTAGAGGAGC
* * * * *
16792708 CTTATTTATTTTTCAAAGTTATTGAGCTTTTGTATAGAGGAGC
1 CTTATTTATTTTTCAAAATCATTGAGCCTCTGTTTAGAGGAGC
* * * * * *
16792751 CTTATTTATTTATCAAAGTCATTGAGCATTTATTTAGAGAAGC
1 CTTATTTATTTTTCAAAATCATTGAGCCTCTGTTTAGAGGAGC
* * ** * *
16792794 CTTATTTATTTTTCAAAATCGTTGAACCTCTAATTAGATGAGT
1 CTTATTTATTTTTCAAAATCATTGAGCCTCTGTTTAGAGGAGC
* * * *
16792837 CTTTTTTATTTTTCCAAAGTCA-TGAGCCTCTATTTCGAGGAGC
1 CTTATTTATTTTT-CAAAATCATTGAGCCTCTGTTTAGAGGAGC
* * ** * *
16792880 TTTATTTATTTCTCAAAAGTTGTAGAGCTTCTGTTTAGAGGAG
1 CTTATTTATTTTTCAAAA-TCATTGAGCCTCTGTTTAGAGGAG
16792923 TTTTTATATT
Statistics
Matches: 170, Mismatches: 41, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
42 14 0.08
43 134 0.79
44 22 0.13
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.44
Consensus pattern (43 bp):
CTTATTTATTTTTCAAAATCATTGAGCCTCTGTTTAGAGGAGC
Done.