Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006744.1 Hibiscus syriacus cultivar Beakdansim tig00016937_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: 89317
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:43 original size:20 final size:20
Alignment explanation
Indices: 20--169 Score: 176
Period size: 20 Copynumber: 7.5 Consensus size: 20
10 TATGTATTAT
20 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
40 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACG
* **
60 CATTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACG
* *
80 CATTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
100 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
120 CGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACG-GATACG
* ** *
140 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGGATACG
160 CGTTGCGATT
1 CGTTGCGATT
170 ATGGAAAATC
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
20 111 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:164 original size:60 final size:60
Alignment explanation
Indices: 1--169 Score: 194
Period size: 60 Copynumber: 2.8 Consensus size: 60
** *
1 TTGCGATTTTATGTATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGCA
1 TTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCA
*** * * * *
62 TTGCGATTTACCCATACGCATTGCGATTTACGGATACACGTTGCGATTTACGGATACGCG
1 TTGCGATTTATGTATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCA
* * ** *
122 TTGCGATTTATGTGTTCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TTGCGATTTATGTATTCGCGTTGCGATTTACGGATACGCGTTGCGATT
170 ATGGAAAATC
Statistics
Matches: 87, Mismatches: 21, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
60 81 0.93
61 6 0.07
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (60 bp):
TTGCGATTTATGTATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCA
Found at i:250 original size:20 final size:20
Alignment explanation
Indices: 225--276 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
215 AAGAATCACG
*
225 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
245 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
265 TTGCGATTCTGG
1 TTGCGATTCTGG
277 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:2198 original size:48 final size:48
Alignment explanation
Indices: 2107--2198 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
2097 TCATTAAAAA
* * * *
2107 CTTAACGCATTTAATACCTAAATCATCGATTTTAATGTGTTTTATTAC
1 CTTAACGCATTTAATACATAAATCATCAATTTTAATATATTTTATTAC
*
2155 CTTAACGCATTTAATACATAAATTATCAATTTTAATATATTTTA
1 CTTAACGCATTTAATACATAAATCATCAATTTTAATATATTTTA
2199 ATACTGAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (48 bp):
CTTAACGCATTTAATACATAAATCATCAATTTTAATATATTTTATTAC
Found at i:4476 original size:8 final size:8
Alignment explanation
Indices: 4463--5024 Score: 324
Period size: 8 Copynumber: 74.8 Consensus size: 8
4453 AAGATTTAAC
4463 TTTAATGA
1 TTTAATGA
4471 TTTAATGA
1 TTTAATGA
4479 TTTAATGA
1 TTTAATGA
4487 TTTAAT-A
1 TTTAATGA
* *
4494 -ATAATTA
1 TTTAATGA
4501 CTTTAATGA
1 -TTTAATGA
*
4510 TTTAA--C
1 TTTAATGA
4516 TTTAATGA
1 TTTAATGA
4524 TTTAAT-A
1 TTTAATGA
* *
4531 -ATAATTA
1 TTTAATGA
*
4538 TTTAACTTTA
1 TTTAA--TGA
4548 CTTTAATGA
1 -TTTAATGA
4557 TTTAAT-A
1 TTTAATGA
* *
4564 -ATAATTA
1 TTTAATGA
4571 CTTTAATGA
1 -TTTAATGA
4580 TTTAAT--
1 TTTAATGA
4586 TTTAATGA
1 TTTAATGA
4594 TTTAAT-A
1 TTTAATGA
* *
4601 -ATAATTA
1 TTTAATGA
4608 CTTTAATGA
1 -TTTAATGA
4617 TTTAAT--
1 TTTAATGA
4623 TTTAATGA
1 TTTAATGA
4631 TTTAATGA
1 TTTAATGA
*
4639 TTTAA--C
1 TTTAATGA
4645 TTTAATGA
1 TTTAATGA
4653 TTTAAT-A
1 TTTAATGA
* *
4660 -ATAATTA
1 TTTAATGA
4667 CTTTAATGA
1 -TTTAATGA
4676 TTTAAT--
1 TTTAATGA
4682 TTTAATGA
1 TTTAATGA
4690 TTTAAT-A
1 TTTAATGA
* *
4697 -ATAATTA
1 TTTAATGA
4704 CTTTAATGA
1 -TTTAATGA
4713 TTTAAT--
1 TTTAATGA
4719 TTTAATGA
1 TTTAATGA
4727 TTTAATGA
1 TTTAATGA
*
4735 TTTAA--C
1 TTTAATGA
4741 TTTAATGA
1 TTTAATGA
4749 TTTAAT-A
1 TTTAATGA
* *
4756 -ATAATTA
1 TTTAATGA
4763 CTTTAATGA
1 -TTTAATGA
4772 TTTAAT-A
1 TTTAATGA
* *
4779 -ATAATTA
1 TTTAATGA
4786 CTTTAATGA
1 -TTTAATGA
*
4795 TTTAA--C
1 TTTAATGA
*
4801 TTTAATGC
1 TTTAATGA
4809 TTTAAT-A
1 TTTAATGA
* *
4816 -ATAATTA
1 TTTAATGA
4823 CTTTAATGA
1 -TTTAATGA
4832 TTTAATGA
1 TTTAATGA
4840 TTTAATGA
1 TTTAATGA
4848 TTTAATGA
1 TTTAATGA
4856 TTTAATGA
1 TTTAATGA
4864 TTTAAT-A
1 TTTAATGA
* *
4871 -ATAATTA
1 TTTAATGA
4878 CTTTAATGA
1 -TTTAATGA
*
4887 TTTAA--C
1 TTTAATGA
*
4893 TTTAATGC
1 TTTAATGA
4901 TTTAAT-A
1 TTTAATGA
* *
4908 -ATAATTA
1 TTTAATGA
4915 CTTTAATGA
1 -TTTAATGA
4924 TTTAATGA
1 TTTAATGA
4932 TTTAATGA
1 TTTAATGA
4940 TTTAAT-A
1 TTTAATGA
* *
4947 -ATAATTA
1 TTTAATGA
4954 CTTTAATGA
1 -TTTAATGA
4963 TTTAAT--
1 TTTAATGA
*
4969 TTTAATAA
1 TTTAATGA
4977 TTTAAT-A
1 TTTAATGA
* *
4984 -ATAATTA
1 TTTAATGA
*
4991 CTTAAT--
1 TTTAATGA
4997 TTTAATGA
1 TTTAATGA
5005 TTTAAT--
1 TTTAATGA
5011 TTTAATGA
1 TTTAATGA
5019 TTTAAT
1 TTTAAT
5025 AATAATTACT
Statistics
Matches: 441, Mismatches: 49, Indels: 128
0.71 0.08 0.21
Matches are distributed among these distances:
6 118 0.27
7 24 0.05
8 234 0.53
9 57 0.13
10 3 0.01
11 5 0.01
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (8 bp):
TTTAATGA
Found at i:4507 original size:23 final size:23
Alignment explanation
Indices: 4479--5035 Score: 239
Period size: 23 Copynumber: 24.1 Consensus size: 23
4469 GATTTAATGA
*
4479 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATATTAATTAC
*
4502 TTTAATGATTTAACT-TTAATGA-
1 TTTAATGATTTAA-TATTAATTAC
*
4524 TTTAAT-A-ATAATTATTTAACTTTAC
1 TTTAATGATTTAA-TA-TTAA--TTAC
*
4549 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATATTAATTAC
* *
4572 TTTAATGATTTAATTTTAATGA-
1 TTTAATGATTTAATATTAATTAC
* * *
4594 TTTAATAATAATTACT-TTAATGA-
1 TTTAATGAT--TTAATATTAATTAC
4617 TTTAAT--TTTAATGATTTAATGATTTAAC
1 TTTAATGATTTAAT-A-TT-A--A-TT-AC
*
4645 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATATTAATTAC
* *
4668 TTTAATGATTTAATTTTAATGA-
1 TTTAATGATTTAATATTAATTAC
* * *
4690 TTTAATAATAATTACT-TTAATGA-
1 TTTAATGAT--TTAATATTAATTAC
4713 TTTAAT--TTTAATGATTTAATGATTTAAC
1 TTTAATGATTTAAT-A-TT-A--A-TT-AC
*
4741 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATATTAATTAC
*
4764 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATATTAATTAC
*
4787 TTTAATGATTTAACT-TTAA-TGC
1 TTTAATGATTTAA-TATTAATTAC
* * *
4809 TTTAATAATAATTACT-TTAATGA-
1 TTTAATGAT--TTAATATTAATTAC
*
4832 TTTAATGATTTAATGATTTAATGA-
1 TTTAATGATTTAAT-A-TTAATTAC
*
4856 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATATTAATTAC
*
4879 TTTAATGATTTAACT-TTAA-TGC
1 TTTAATGATTTAA-TATTAATTAC
* * *
4901 TTTAATAATAATTACT-TTAATGA-
1 TTTAATGAT--TTAATATTAATTAC
4924 TTTAATGATTTAATGATTTAA-TA-
1 TTTAATGATTTAAT-A-TTAATTAC
* *
4947 -ATAATTACTTTAATGATTTAA-T--
1 TTTAATGA-TTTAAT-A-TTAATTAC
* *
4969 TTTAATAATTTAATAATAATTAC
1 TTTAATGATTTAATATTAATTAC
4992 -TTAAT--TTTAATGATTTAA-T--
1 TTTAATGATTTAAT-A-TTAATTAC
*
5011 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATATTAATTAC
5034 TT
1 TT
5036 GACTTTAATG
Statistics
Matches: 423, Mismatches: 49, Indels: 124
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.02
20 21 0.05
21 17 0.04
22 80 0.19
23 196 0.46
24 48 0.11
25 13 0.03
26 5 0.01
27 7 0.02
28 14 0.03
29 2 0.00
30 12 0.03
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (23 bp):
TTTAATGATTTAATATTAATTAC
Found at i:4529 original size:37 final size:37
Alignment explanation
Indices: 4461--5035 Score: 548
Period size: 37 Copynumber: 15.1 Consensus size: 37
4451 AAAAGATTTA
*
4461 ACTTTAATGATTTAATGATTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAA--CTTTAATGATTTAATAATAATT
4500 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
*
4537 A-TTTAA--CTTT-ACTTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
*
4570 ACTTTAATGATTTAATTTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
* *
4607 ACTTTAATGATTTAATTTTAATGATTTAATGAT--TT
1 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
** *
4642 AACTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATG
1 -ACTTTAATGA--T--T--T-A--ACTTTAATGATTTAATAATAATT
* ** *
4689 A-TTTAATAATAATT-ACTTTAATGATTTAATTTTAATG
1 ACTTTAATGAT--TTAACTTTAATGATTTAATAATAATT
4726 A-TTTAATGATTTAACTTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
* * *
4762 ACTTTAATGATTTAA-TAATAATTACTTTAATGAT--TT
1 ACTTTAATGATTTAACT-TTAATGA-TTTAATAATAATT
* * * * *
4798 AACTTTAATGCTTTAA-TAATAATTACTTTAATGATTTAATG
1 -ACTTTAATGATTTAACT-TTAATGA-TTTAAT-A-ATAATT
*
4839 A-TTTAATGATTTAATGATTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAA--CTTTAATGATTTAATAATAATT
*
4877 ACTTTAATGATTTAACTTTAATGCTTTAATAATAATT
1 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
*
4914 ACTTTAATGATTTAATGATTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAA--CTTTAATGATTTAATAATAATT
* *
4953 ACTTTAATGATTTAATTTTAATAATTTAATAATAATT
1 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
*
4990 ACTTAATTTTAATGATTTAATTTTAATGATTTAATAATAATT
1 AC-----TTTAATGATTTAACTTTAATGATTTAATAATAATT
5032 ACTT
1 ACTT
5036 GACTTTAATG
Statistics
Matches: 467, Mismatches: 33, Indels: 74
0.81 0.06 0.13
Matches are distributed among these distances:
33 24 0.05
34 8 0.02
35 4 0.01
36 42 0.09
37 215 0.46
38 14 0.03
39 77 0.16
40 8 0.02
41 7 0.01
42 38 0.08
43 5 0.01
45 23 0.05
46 1 0.00
47 1 0.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (37 bp):
ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
Found at i:5044 original size:76 final size:73
Alignment explanation
Indices: 4461--5035 Score: 451
Period size: 76 Copynumber: 7.6 Consensus size: 73
4451 AAAAGATTTA
* *
4461 ACTTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATT
1 ACTTTAATGATTTAAT-ATTTAATGATTTAATAATAATTAC-TT-ATGATTTAATTTTAATAATT
4526 TAATAATAATT
63 TAATAATAATT
* * *
4537 A-TTTAA--CTTT-A-CTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTT
1 ACTTTAATGATTTAATATTTAATGATTTAATAATAATTAC-TT-ATGATTTAATTTTAATAATTT
4597 AATAATAATT
64 AATAATAATT
* ** *
4607 ACTTTAATGATTTAAT-TTTAATGATTTAATGAT--TTAACTTTAATGATTTAATAATAATTACT
1 ACTTTAATGATTTAATATTTAATGATTTAATAATAATT-AC-TT-ATGATTTAATTTTAA-TAAT
*
4669 TTAATGAT--TT
62 TTAATAATAATT
* ** * * *
4679 AATTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATGATTTAACTTT
1 -ACTTTAATGA--T--T--TAA-TA-TTTAATGATTTAATAATAATTACTT-ATGATTTAATTTT
*
4744 AATGATTTAATAATAATT
56 AATAATTTAATAATAATT
* * * * ** *
4762 ACTTTAATGATTTAATA-ATAATTACTTTAATGAT--TTAACTTTAATGCTTTAATAATAATTAC
1 ACTTTAATGATTTAATATTTAATGA-TTTAATAATAATT-AC-TT-ATGATTTAATTTTAA-TAA
* *
4824 TTTAATGATTTAATG
61 TTTAAT-A-ATAATT
* **
4839 A-TTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGCTT
1 ACTTTAATGATTTAAT-ATTTAATGATTTAATAATAATTAC-TT-ATGATTTAATTTTAATAATT
4903 TAATAATAATT
63 TAATAATAATT
4914 ACTTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATAATT
1 ACTTTAATGATTTAAT-ATTTAATGATTTAATAATAATTAC-TT-ATGATTTAATTTTAATAATT
4979 TAATAATAATT
63 TAATAATAATT
4990 ACTTAATTTTAATGATTTAAT-TTTAATGATTTAATAATAATTACTT
1 AC-----TTTAATGATTTAATATTTAATGATTTAATAATAATTACTT
5036 GACTTTAATG
Statistics
Matches: 413, Mismatches: 49, Indels: 72
0.77 0.09 0.13
Matches are distributed among these distances:
70 58 0.14
71 5 0.01
72 6 0.01
73 40 0.10
74 47 0.11
75 20 0.05
76 93 0.23
77 23 0.06
78 25 0.06
79 28 0.07
80 2 0.00
81 23 0.06
82 39 0.09
83 3 0.01
84 1 0.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (73 bp):
ACTTTAATGATTTAATATTTAATGATTTAATAATAATTACTTATGATTTAATTTTAATAATTTAA
TAATAATT
Found at i:5056 original size:14 final size:13
Alignment explanation
Indices: 4455--5061 Score: 286
Period size: 14 Copynumber: 48.2 Consensus size: 13
4445 AGGAAAAAAA
4455 GATTTAACTTTAAT
1 GATTTAA-TTTAAT
4469 GATTTAATGATTTAAT
1 GATTT-A--ATTTAAT
4485 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
4496 -AATTACTTTAAT
1 GATTTAATTTAAT
4508 GATTTAACTTTAAT
1 GATTTAA-TTTAAT
4522 GATTTAA--TAAT
1 GATTTAATTTAAT
*
4533 -AATT-ATTTAA-
1 GATTTAATTTAAT
* *
4543 -CTTTACTTTAAT
1 GATTTAATTTAAT
4555 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
4566 -AATTACTTTAAT
1 GATTTAATTTAAT
4578 GATTTAATTTTAAT
1 GATTTAA-TTTAAT
4592 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
4603 -AATTACTTTAAT
1 GATTTAATTTAAT
4615 GATTTAATTTTAAT
1 GATTTAA-TTTAAT
4629 G-----ATTTAAT
1 GATTTAATTTAAT
4637 GATTTAACTTTAAT
1 GATTTAA-TTTAAT
4651 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
4662 -AATTACTTTAAT
1 GATTTAATTTAAT
4674 GATTTAATTTTAAT
1 GATTTAA-TTTAAT
4688 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
4699 -AATTACTTTAAT
1 GATTTAATTTAAT
4711 GATTTAATTTTAAT
1 GATTTAA-TTTAAT
4725 G-----ATTTAAT
1 GATTTAATTTAAT
4733 GATTTAACTTTAAT
1 GATTTAA-TTTAAT
4747 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
4758 -AATTACTTTAAT
1 GATTTAATTTAAT
4770 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
4781 -AATTACTTTAAT
1 GATTTAATTTAAT
4793 GATTTAACTTTAAT
1 GATTTAA-TTTAAT
*
4807 GCTTTAA--TAAT
1 GATTTAATTTAAT
* *
4818 -AATTACTTTAAT
1 GATTTAATTTAAT
4830 GATTTAATGATTTAAT
1 GATTT-A--ATTTAAT
4846 GATTTAATGATTTAAT
1 GATTT-A--ATTTAAT
4862 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
4873 -AATTACTTTAAT
1 GATTTAATTTAAT
4885 GATTTAACTTTAAT
1 GATTTAA-TTTAAT
*
4899 GCTTTAA--TAAT
1 GATTTAATTTAAT
* *
4910 -AATTACTTTAAT
1 GATTTAATTTAAT
4922 GATTTAATGATTTAAT
1 GATTT-A--ATTTAAT
4938 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
4949 -AATTACTTTAAT
1 GATTTAATTTAAT
4961 GATTTAATTTTAAT
1 GATTTAA-TTTAAT
* *
4975 AATTTAATAATAAT
1 GATTTAAT-TTAAT
* *
4989 TACTTAATTTTAAT
1 GATTTAA-TTTAAT
5003 GATTTAATTTTAAT
1 GATTTAA-TTTAAT
*
5017 GATTTAATAATAAT
1 GATTTAAT-TTAAT
* * *
5031 TACTTGACTTTAAT
1 GA-TTTAATTTAAT
*
5045 GATTTATATTTACT
1 GATTTA-ATTTAAT
5059 GAT
1 GAT
5062 AATAATAGTA
Statistics
Matches: 451, Mismatches: 70, Indels: 144
0.68 0.11 0.22
Matches are distributed among these distances:
8 14 0.03
9 3 0.01
10 47 0.10
11 56 0.12
12 44 0.10
13 56 0.12
14 172 0.38
15 9 0.02
16 49 0.11
17 1 0.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (13 bp):
GATTTAATTTAAT
Found at i:5064 original size:76 final size:77
Alignment explanation
Indices: 4908--5065 Score: 173
Period size: 79 Copynumber: 2.0 Consensus size: 77
4898 TGCTTTAATA
4908 ATAATTACTTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGA-TTTAAT--T
1 ATAATTACTTTAATGATTTAAT-ATTTAATGATTTAATAATAATTAC--T--TGACTTTAATGAT
*
4970 TTAATAATTTAATAATAAT
61 TT-AT-ATTTAATGATAAT
* *
4989 -TACTTAATTTTAATGATTTAAT-TTTAATGATTTAATAATAATTACTTGACTTTAATGATTTAT
1 ATAATT-ACTTTAATGATTTAATATTTAATGATTTAATAATAATTACTTGACTTTAATGATTTAT
*
5052 ATTTACTGATAAT
65 ATTTAATGATAAT
5065 A
1 A
5066 ATAGTAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
75 3 0.04
76 17 0.25
77 3 0.04
78 3 0.04
79 23 0.34
80 4 0.06
81 15 0.22
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (77 bp):
ATAATTACTTTAATGATTTAATATTTAATGATTTAATAATAATTACTTGACTTTAATGATTTATA
TTTAATGATAAT
Found at i:5532 original size:6 final size:6
Alignment explanation
Indices: 5517--5547 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5507 GGTGAGAAGA
*
5517 ACTCCT ACTCCC ACTCCC ACTCCC ACTCCC A
1 ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC A
5548 GTCCTTCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.61, G:0.00, T:0.19
Consensus pattern (6 bp):
ACTCCC
Found at i:7587 original size:172 final size:173
Alignment explanation
Indices: 7274--7632 Score: 569
Period size: 172 Copynumber: 2.1 Consensus size: 173
7264 CATCAAATAT
* *
7274 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
*
7339 TATAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAAC
66 TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
* *
7404 TTTTTATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTGC
131 TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
* *
7447 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAAAGTTAGCAATTTAATC-CATAAAT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* * * *
7511 TT-TAAATTCTTTCTAATTTAACCAATTAAGCATACTAATACTAAATTCTAGCATATTATAGCAA
65 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAA
* *
7575 CTTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
130 CTTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
*
7619 AAAACGGTCCCTAA
1 AAAACGATCCCTAA
7633 AACTTTACAA
Statistics
Matches: 171, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
172 111 0.65
173 60 0.35
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (173 bp):
AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
Found at i:7935 original size:41 final size:41
Alignment explanation
Indices: 7875--7952 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
7865 CCCTCTCAGG
*
7875 CTCTCACTGCTTCTGTAATTGTGAATTGCCTCAGCCCCAAA
1 CTCTCACTGCTTCTATAATTGTGAATTGCCTCAGCCCCAAA
7916 CTCTCACTGCTTCTATAATTGTGAATTGCCTCAGCCC
1 CTCTCACTGCTTCTATAATTGTGAATTGCCTCAGCCC
7953 GAGCAGTCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.21, C:0.32, G:0.14, T:0.33
Consensus pattern (41 bp):
CTCTCACTGCTTCTATAATTGTGAATTGCCTCAGCCCCAAA
Found at i:8131 original size:23 final size:23
Alignment explanation
Indices: 8105--8148 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
8095 AGTTGCATGC
8105 CCCCCACATGCAGACGTGCAGGA
1 CCCCCACATGCAGACGTGCAGGA
8128 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGCAGACGTGCAG
8149 CCCTGCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGCAGACGTGCAGGA
Found at i:8267 original size:34 final size:34
Alignment explanation
Indices: 8224--8308 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
8214 CATGCACAGC
*
8224 ACTGAAGACGCCGAGATTTCCTACGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
*
8258 ACTGAAGACGCCGAGAGTTCCTATGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
8292 ACTGAAGACGCCGAGAG
1 ACTGAAGACGCCGAGAG
8309 ATCAATCATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (34 bp):
ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
Found at i:19576 original size:31 final size:31
Alignment explanation
Indices: 19541--19626 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
19531 ATGATTTTAA
* *
19541 AAAATTGAAAGCTTAGGTACTAAAAAGGACC
1 AAAATTGATAGTTTAGGTACTAAAAAGGACC
*
19572 AAAATTGATAGTTTAGGTACTAAAAAGGATC
1 AAAATTGATAGTTTAGGTACTAAAAAGGACC
*
19603 AAAACTGATAGTTTAGGTACTAAA
1 AAAATTGATAGTTTAGGTACTAAA
19627 CATGTAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.26
Consensus pattern (31 bp):
AAAATTGATAGTTTAGGTACTAAAAAGGACC
Found at i:23535 original size:10 final size:10
Alignment explanation
Indices: 23520--23544 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
23510 AAATATAAAA
23520 ATATTGAATT
1 ATATTGAATT
23530 ATATTGAATT
1 ATATTGAATT
23540 ATATT
1 ATATT
23545 TGTACATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (10 bp):
ATATTGAATT
Found at i:27294 original size:17 final size:17
Alignment explanation
Indices: 27272--27311 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
27262 TCTATAATTT
*
27272 ATTTTATA-ATTTTATAA
1 ATTTTATATACTTTA-AA
27289 ATTTTATATACTTTAAA
1 ATTTTATATACTTTAAA
27306 ATTTTA
1 ATTTTA
27312 AAAGAGTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTATATACTTTAAA
Found at i:29634 original size:14 final size:14
Alignment explanation
Indices: 29615--29644 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29605 CAACCCTTTG
*
29615 ATCATAAACCCTAA
1 ATCATAAAACCTAA
29629 ATCATAAAACCTAA
1 ATCATAAAACCTAA
29643 AT
1 AT
29645 TTTAGACCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (14 bp):
ATCATAAAACCTAA
Found at i:30691 original size:17 final size:18
Alignment explanation
Indices: 30659--30698 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
30649 TTCGTCTAAA
30659 ATTTTAAAATTATTATAT
1 ATTTTAAAATTATTATAT
*
30677 ATTTT-AAATTTTTATAT
1 ATTTTAAAATTATTATAT
30694 ATTTT
1 ATTTT
30699 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTAAAATTATTATAT
Found at i:30763 original size:29 final size:29
Alignment explanation
Indices: 30726--30787 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
30716 TTTTAATCTC
* *
30726 TTAACATTTTATAAATTTAAGTTTATTTT
1 TTAAAATTTTATAAATTTAAATTTATTTT
30755 TTAAAATTTTATAAATTTAAATTTATTTT
1 TTAAAATTTTATAAATTTAAATTTATTTT
30784 TTAA
1 TTAA
30788 CTTAAAATCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
TTAAAATTTTATAAATTTAAATTTATTTT
Found at i:31367 original size:16 final size:16
Alignment explanation
Indices: 31340--31385 Score: 83
Period size: 16 Copynumber: 2.8 Consensus size: 16
31330 ACCCATTAAT
31340 ATTTTAAAACTCAATTA
1 ATTTT-AAACTCAATTA
31357 ATTTTAAACTCAATTA
1 ATTTTAAACTCAATTA
31373 ATTTTAAACTCAA
1 ATTTTAAACTCAA
31386 ATAAAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 24 0.83
17 5 0.17
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTTTAAACTCAATTA
Found at i:48532 original size:23 final size:24
Alignment explanation
Indices: 48483--48532 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
48473 GTTAGTGGAC
*
48483 GAACATATAAAATTTTGAGGGAGT
1 GAACATATAAAATTTTGAGGGAAT
* *
48507 GAACTTATAACATTTT-AGGGAAT
1 GAACATATAAAATTTTGAGGGAAT
48530 GAA
1 GAA
48533 AACGGGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (24 bp):
GAACATATAAAATTTTGAGGGAAT
Found at i:59561 original size:16 final size:17
Alignment explanation
Indices: 59526--59559 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
59516 ATTTATAACA
59526 TTATTGTTAAATTATTT
1 TTATTGTTAAATTATTT
59543 TTATT-TTAAA-TATTT
1 TTATTGTTAAATTATTT
59558 TT
1 TT
59560 TAAATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 5 0.29
17 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTATTGTTAAATTATTT
Found at i:59564 original size:27 final size:29
Alignment explanation
Indices: 59532--59595 Score: 89
Period size: 27 Copynumber: 2.3 Consensus size: 29
59522 AACATTATTG
*
59532 TTAAATTATTTTTA-TTTT-AAATATTTT
1 TTAAATTATTTTAATTTTTAAAATATTTT
*
59559 TTAAATAATTTTAATTTTTAAAATATTTT
1 TTAAATTATTTTAATTTTTAAAATATTTT
59588 TT-AATTAT
1 TTAAATTAT
59596 ATGTTTTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 12 0.38
28 9 0.28
29 11 0.34
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TTAAATTATTTTAATTTTTAAAATATTTT
Found at i:59577 original size:18 final size:19
Alignment explanation
Indices: 59554--59593 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
59544 TATTTTAAAT
*
59554 ATTTTTTAAATA-ATTTTA
1 ATTTTTAAAATATATTTTA
*
59572 ATTTTTAAAATATTTTTTA
1 ATTTTTAAAATATATTTTA
59591 ATT
1 ATT
59594 ATATGTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTAAAATATATTTTA
Found at i:59669 original size:15 final size:16
Alignment explanation
Indices: 59638--59683 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
59628 TAAAAATATT
59638 TTTAAAATAATTAAAA
1 TTTAAAATAATTAAAA
* *
59654 TTTAGAATAATAAAATA
1 TTTAAAATAATTAAA-A
59671 TTTAAAA-AATTAA
1 TTTAAAATAATTAA
59684 TTAGAACTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
TTTAAAATAATTAAAA
Found at i:63403 original size:21 final size:20
Alignment explanation
Indices: 63318--63474 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
63308 AATGACCAAT
** *
63318 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
63337 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
63357 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
63377 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
63398 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
63419 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
63440 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
63460 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
63475 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:63503 original size:20 final size:20
Alignment explanation
Indices: 63441--63665 Score: 240
Period size: 20 Copynumber: 11.2 Consensus size: 20
63431 CGATTTTCCA
* ** *
63441 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
63461 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
63481 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
63501 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
63521 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
63541 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
63561 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
63581 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
*
63601 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
63621 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
63641 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
63661 AAATC
1 AAATC
63666 CGGTAGGGCA
Statistics
Matches: 177, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
19 1 0.01
20 174 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:64416 original size:24 final size:24
Alignment explanation
Indices: 64377--64423 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
64367 AAATTTGGTC
64377 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
64401 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
64424 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:64615 original size:12 final size:12
Alignment explanation
Indices: 64598--64622 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64588 ATATAATCCT
64598 GAAGAAGAAAAA
1 GAAGAAGAAAAA
64610 GAAGAAGAAAAA
1 GAAGAAGAAAAA
64622 G
1 G
64623 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:66980 original size:33 final size:34
Alignment explanation
Indices: 66929--67164 Score: 229
Period size: 33 Copynumber: 6.8 Consensus size: 34
66919 CGGAAATTAC
*
66929 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
* *
66962 AATCCCAAC-ATGAAAATCGCAATGCGGAAATAAA
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAA
66996 AATCGCAACGA-GAAAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
67029 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
67062 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
* *
67100 AATCGCAACGA-GATAATTGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
67133 AATCGCAATGCGAAATGAAAATCGCATTGCGA
1 AATCGCAA--CG--ATGAAAATCGCAATGCGA
67165 TTCTCTCGTT
Statistics
Matches: 173, Mismatches: 12, Indels: 31
0.80 0.06 0.14
Matches are distributed among these distances:
32 1 0.01
33 93 0.54
34 31 0.18
35 7 0.04
36 4 0.02
37 3 0.02
38 34 0.20
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (34 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:67057 original size:52 final size:52
Alignment explanation
Indices: 66971--67158 Score: 331
Period size: 52 Copynumber: 3.6 Consensus size: 52
66961 AAATCCCAAC
*
66971 ATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
*
67024 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
* *
67076 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATTGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
67128 ATGAAAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCA
67159 TTGCGATTCT
Statistics
Matches: 131, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 115 0.88
53 16 0.12
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
Found at i:67099 original size:71 final size:71
Alignment explanation
Indices: 66943--67164 Score: 228
Period size: 71 Copynumber: 3.2 Consensus size: 71
66933 GCAACGAGAG
* * * * **
66943 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATAAAAATCGCAA--C
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GATAATTGAAATGC-GAAACGAAAATCGCAATGC
67005 G--A-GAA
64 GAAATGAA
* * *
67010 AATCGCAATGCGAAATGAAAATCGCAATGCGA-AA-TGAAAAT-CGCAACGAGAGAATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATTG-AAATGCGAAACGA-A-AATCGCAATG
67072 CGAAATGAA
63 CGAAATGAA
* *
67081 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATTGCAATGCGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATTGAAATGCGAAACGAAAATCGCAATGCGA
67146 AATGAA
66 AATGAA
*
67152 AATCGCATTGCGA
1 AATCGCAATGCGA
67165 TTCTCTCGTT
Statistics
Matches: 129, Mismatches: 14, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
64 4 0.03
65 3 0.02
66 13 0.10
67 28 0.22
68 2 0.02
70 1 0.01
71 64 0.50
72 6 0.05
73 8 0.06
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGATAATTGAAATGCGAAACGAAAATCGCAATGCGA
AATGAA
Found at i:67163 original size:19 final size:19
Alignment explanation
Indices: 66943--67164 Score: 241
Period size: 19 Copynumber: 12.7 Consensus size: 19
66933 GCAACGAGAG
66943 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
66962 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
66976 AATCGCAATGCGGAAATAAA
1 AATCGCAATGC-GAAATGAA
66996 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
67010 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
67029 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
67048 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
67062 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
67081 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
67100 AATCGCAA--CG--A-GAT
1 AATCGCAATGCGAAATGAA
*
67114 AATTGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
67133 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
67152 AATCGCATTGCGA
1 AATCGCAATGCGA
67165 TTCTCTCGTT
Statistics
Matches: 171, Mismatches: 11, Indels: 42
0.76 0.05 0.19
Matches are distributed among these distances:
14 41 0.24
15 3 0.02
16 7 0.04
17 6 0.04
18 4 0.02
19 98 0.57
20 12 0.07
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:67267 original size:52 final size:53
Alignment explanation
Indices: 67154--67270 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
67144 GAAATGAAAA
67154 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
67207 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
67259 TCGCATTGCGAT
1 TCGCATTGCGAT
67271 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:67278 original size:19 final size:19
Alignment explanation
Indices: 67173--67270 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
67163 GATTCTCTCG
67173 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
67193 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
67212 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
67226 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
67245 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
67264 TTGCGAT
1 TTGCGAT
67271 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:67392 original size:14 final size:14
Alignment explanation
Indices: 67373--67409 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
67363 CATCAATTAC
67373 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
67387 ACAAATCATCTTTT
1 ACAAATCAACTTTT
67401 ACAAATCAA
1 ACAAATCAA
67410 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:69374 original size:19 final size:19
Alignment explanation
Indices: 69334--69431 Score: 91
Period size: 19 Copynumber: 5.4 Consensus size: 19
69324 TAGTTTACTT
* *
69334 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
69354 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
69373 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
**
69392 TCGCAA--C----TTAAAA
1 TCGCAACGCGAAACCAAAA
69405 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
69424 TCGCAACG
1 TCGCAACG
69432 AAAGAATCGC
Statistics
Matches: 65, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
13 11 0.17
15 1 0.02
17 1 0.02
19 39 0.60
20 13 0.20
ACGTcount: A:0.46, C:0.28, G:0.15, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:69410 original size:32 final size:32
Alignment explanation
Indices: 69369--69446 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
69359 ACGCGAAACC
** **
69369 AAAATCGCAACGCGAAATGAAAATCGCAACTT
1 AAAATCGCAACGCGAAACCAAAATCGCAACGA
69401 AAAATCGCAACGCGAAACCAAAATCGCAACGA
1 AAAATCGCAACGCGAAACCAAAATCGCAACGA
69433 AAGAATCGCAACGC
1 AA-AATCGCAACGC
69447 TGTGAAGATA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 30 0.73
33 11 0.27
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.10
Consensus pattern (32 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGA
Found at i:69582 original size:19 final size:19
Alignment explanation
Indices: 69558--69641 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
69548 GCAACGAGAG
*
69558 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
69577 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
69596 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
69610 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
69629 AATCGCAATGCGA
1 AATCGCAACGCGA
69642 TTTTGGTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 40 0.71
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:69598 original size:52 final size:52
Alignment explanation
Indices: 69536--69641 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
69526 TCTTTGGGTT
*
69536 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGACAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
*
69588 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
69640 GA
1 GA
69642 TTTTGGTTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (52 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:69672 original size:14 final size:14
Alignment explanation
Indices: 69653--69709 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
69643 TTTGGTTTCG
69653 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
69667 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
69686 CGTTGCGATTATCT
1 CGTTGCGATTCTCT
69700 CGTTGCGATT
1 CGTTGCGATT
69710 GTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 2 0.06
19 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:69685 original size:33 final size:33
Alignment explanation
Indices: 69637--69726 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
69627 AAAATCGCAA
** *
69637 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
69670 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
69703 TGCGATTGTCATTTCGCGTTGCGA
1 TGCGATTTTCATTTCGCGTTGCGA
69727 CTCTTCTGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.10, C:0.21, G:0.26, T:0.43
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:69691 original size:19 final size:19
Alignment explanation
Indices: 69667--69726 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
69657 GCGATTCTCT
69667 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
69686 CGTTGCGA--TT-A--TCT
1 CGTTGCGATTTTCATTTCG
*
69700 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
69719 CGTTGCGA
1 CGTTGCGA
69727 CTCTTCTGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 10 0.30
16 2 0.06
17 3 0.09
19 18 0.55
ACGTcount: A:0.12, C:0.22, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:70079 original size:22 final size:22
Alignment explanation
Indices: 70025--70079 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
70015 TGGTTGTGAG
**
70025 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
** *
70047 GGAAATATTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
70069 GGATTTCTTCG
1 GGATTTCTTCG
70080 CCGTAGAGAG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.15, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:70253 original size:20 final size:20
Alignment explanation
Indices: 70226--70418 Score: 228
Period size: 20 Copynumber: 9.7 Consensus size: 20
70216 CTTTAAATAT
*
70226 CGCGTTGCGATTTACGGATT
1 CGCGTTGCGATTTACGGATA
*
70246 CTCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
*
70267 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
70286 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
70306 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
70326 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
70346 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
70366 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
70386 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
70406 CGCGTTGCGATTT
1 CGCGTTGCGATTT
70419 TGGAAAATCG
Statistics
Matches: 150, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 146 0.97
21 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:70435 original size:21 final size:21
Alignment explanation
Indices: 70405--70487 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
70395 ATTTTCATAT
*
70405 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
70426 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
70447 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
70468 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
70488 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:70478 original size:42 final size:43
Alignment explanation
Indices: 70385--70483 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
70375 ATTTATGTGT
* *
70385 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
70426 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
70468 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
70484 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:70833 original size:20 final size:19
Alignment explanation
Indices: 70803--70840 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
70793 TTAATTTAAA
70803 GTTTTTTATTGAAAAAATT
1 GTTTTTTATTGAAAAAATT
70822 GTTTTATTATTGAAAAAAT
1 GTTTT-TTATTGAAAAAAT
70841 CATGGCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (19 bp):
GTTTTTTATTGAAAAAATT
Found at i:75465 original size:32 final size:32
Alignment explanation
Indices: 75429--75497 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
75419 TTTTACCTTA
75429 TATATTTAGGAATAATTACAATAATACCCCTC
1 TATATTTAGGAATAATTACAATAATACCCCTC
75461 TATATTTAGGAATAATTACAATAATACCCCTC
1 TATATTTAGGAATAATTACAATAATACCCCTC
75493 TATAT
1 TATAT
75498 ATATTTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (32 bp):
TATATTTAGGAATAATTACAATAATACCCCTC
Found at i:76591 original size:13 final size:13
Alignment explanation
Indices: 76560--76592 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
76550 ATATTTTTAA
76560 TTAAAATAAATAT
1 TTAAAATAAATAT
*
76573 TT-AAATAGATAT
1 TTAAAATAAATAT
76585 TTAAAATA
1 TTAAAATA
76593 TTTTTTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
TTAAAATAAATAT
Found at i:76608 original size:40 final size:40
Alignment explanation
Indices: 76541--76617 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
76531 TTTTATTTAA
*
76541 ATATATAAAATATTTTTAATTAAAATAAATATTTAAATAG
1 ATATATAAAATATTTTTAATCAAAATAAATATTTAAATAG
* * * * *
76581 ATATTTAAAATATTTTTTATCATAATAAGTGTTTAAA
1 ATATATAAAATATTTTTAATCAAAATAAATATTTAAA
76618 ACTTTAATCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (40 bp):
ATATATAAAATATTTTTAATCAAAATAAATATTTAAATAG
Found at i:76902 original size:15 final size:15
Alignment explanation
Indices: 76851--76904 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
76841 CTTTAAATAC
76851 TTATTTATAATATAT
1 TTATTTATAATATAT
* *
76866 TTTTTAGTATAACTAGAT
1 TTATT--TATAA-TATAT
*
76884 TTATTTATAATATAA
1 TTATTTATAATATAT
76899 TTATTT
1 TTATTT
76905 TTAAAGTGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 13 0.42
16 5 0.16
17 5 0.16
18 8 0.26
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (15 bp):
TTATTTATAATATAT
Found at i:82233 original size:28 final size:28
Alignment explanation
Indices: 82181--82246 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
82171 CTTAATTATG
*
82181 AATATTAAAA-AATTGAACTCATAATA-
1 AATATTAAAATAATTGAAATCATAATAT
82207 AATATTGAAAATAATT-AAATCGATAATAT
1 AATATT-AAAATAATTGAAATC-ATAATAT
82236 AAGTATTAAAA
1 AA-TATTAAAA
82247 ATAGTTAGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
26 6 0.18
27 8 0.24
28 10 0.29
29 6 0.18
30 4 0.12
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.32
Consensus pattern (28 bp):
AATATTAAAATAATTGAAATCATAATAT
Done.