Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009416.1 Hibiscus syriacus cultivar Beakdansim tig00113368_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: 51085
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1970 original size:23 final size:22
Alignment explanation
Indices: 1918--1976 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 22
1908 TAATTTCATA
* *
1918 AACTCGATTAGACTTAAAAAATT
1 AACTCGATT-GAGTTAAAAAATG
* *
1941 AATTCGATTGAGTTATAAAATAG
1 AACTCGATTGAGTTAAAAAAT-G
*
1964 AACTCGAGTGAGT
1 AACTCGATTGAGT
1977 ACTCGAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (22 bp):
AACTCGATTGAGTTAAAAAATG
Found at i:3688 original size:31 final size:31
Alignment explanation
Indices: 3630--3688 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3620 ATACTTTTAG
*
3630 AATATTTAATGTGATACCTGCATTTTTACAA
1 AATATTTAATGTGATACCTGCACTTTTACAA
* *
3661 AATATTTAATGTGATACTTGTACTTTTA
1 AATATTTAATGTGATACCTGCACTTTTA
3689 AAAGGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (31 bp):
AATATTTAATGTGATACCTGCACTTTTACAA
Found at i:3953 original size:28 final size:29
Alignment explanation
Indices: 3903--3958 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 29
3893 ATTATATTAA
*
3903 ATATTTTAATGAAGTATAGATATTATATGG
1 ATATTTTAA-GAAGTATAAATATTATATGG
3933 ATATTTTAA-AAGTATAAATATTATAT
1 ATATTTTAAGAAGTATAAATATTATAT
3959 TAGACATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 16 0.64
30 9 0.36
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (29 bp):
ATATTTTAAGAAGTATAAATATTATATGG
Found at i:4061 original size:31 final size:30
Alignment explanation
Indices: 4026--4100 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
4016 ACAACAATTT
4026 TTTTATTAAAATATAAATAACACAATAGATA
1 TTTTA-TAAAATATAAATAACACAATAGATA
* * * *
4057 TTTTA-AAATTATATATAGCACATTAGATA
1 TTTTATAAAATATAAATAACACAATAGATA
*
4086 TTTTGTAAAAATATA
1 TTTTAT-AAAATATA
4101 CGTATCAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 24 0.67
31 12 0.33
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (30 bp):
TTTTATAAAATATAAATAACACAATAGATA
Found at i:4100 original size:29 final size:28
Alignment explanation
Indices: 4031--4089 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
4021 AATTTTTTTA
*
4031 TTAAAATATAAATAACACAATAGATATT
1 TTAAAATATATATAACACAATAGATATT
* *
4059 TTAAAATTATATATAGCACATTAGATATT
1 TTAAAA-TATATATAACACAATAGATATT
4088 TT
1 TT
4090 GTAAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (28 bp):
TTAAAATATATATAACACAATAGATATT
Found at i:4543 original size:60 final size:54
Alignment explanation
Indices: 4464--4630 Score: 178
Period size: 60 Copynumber: 3.0 Consensus size: 54
4454 ATCGATGACC
4464 AAAACATAAATT--ATATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAAA
1 AAAACAT-AATTAGATATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAAA
* * * **
4517 AATATATGATTATATTAGATAATATATAAGTGACCAAATAGGCAATTTACCCTAAAGTGACC
1 AA-A-A-CA-TA-ATTAGAT-ATATATAAGTGACCAAATAGGTAGTTTACCCTAAA-T-AAA
*
4579 AAAACATAATTAGATA-ATATAAGTGACCAAAGAGGTAGTTTACCCTAAATAA
1 AAAACATAATTAGATATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAA
4631 TAATCGAATG
Statistics
Matches: 94, Mismatches: 10, Indels: 20
0.76 0.08 0.16
Matches are distributed among these distances:
53 3 0.03
54 2 0.02
55 31 0.33
56 3 0.03
57 11 0.12
58 2 0.02
59 3 0.03
60 34 0.36
61 2 0.02
62 3 0.03
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (54 bp):
AAAACATAATTAGATATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAAA
Found at i:4663 original size:31 final size:30
Alignment explanation
Indices: 4627--4741 Score: 74
Period size: 31 Copynumber: 3.6 Consensus size: 30
4617 TTTACCCTAA
4627 ATAATAATCGAATGACCAAAACATAAATTAG
1 ATAATAATC-AATGACCAAAACATAAATTAG
* ***
4658 ATAAT-AT-AAGTGACCAATAGATAGTTTACCCTAG
1 ATAATAATCAA-TGACCAA-A-ACA---TAAATTAG
*
4692 ATAATAATCTAGTGACCAAAACATAAATTAG
1 ATAATAATC-AATGACCAAAACATAAATTAG
4723 ATAATATAT-AAGTGACCAA
1 ATAATA-ATCAA-TGACCAA
4742 TAGGTAGTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 22
0.66 0.11 0.23
Matches are distributed among these distances:
28 2 0.03
29 7 0.11
30 4 0.06
31 25 0.40
32 2 0.03
34 12 0.19
35 3 0.05
36 7 0.11
37 1 0.02
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (30 bp):
ATAATAATCAATGACCAAAACATAAATTAG
Found at i:4686 original size:65 final size:65
Alignment explanation
Indices: 4574--4759 Score: 277
Period size: 65 Copynumber: 2.8 Consensus size: 65
4564 TACCCTAAAG
4574 TGACCAAAACAT-AATTAGATAATATAAGTGACCAA-AGAGGTAGTTTACCCTAAATAATAATCG
1 TGACCAAAACATAAATTAGATAATATAAGTGACCAATAGA--TAGTTTACCCTAAATAATAATCG
4637 AA
64 AA
* * *
4639 TGACCAAAACATAAATTAGATAATATAAGTGACCAATAGATAGTTTACCCTAGATAATAATCTAG
1 TGACCAAAACATAAATTAGATAATATAAGTGACCAATAGATAGTTTACCCTAAATAATAATCGAA
* *
4704 TGACCAAAACATAAATTAGATAATATATAAGTGACCAATAGGTAGTTTACTCTAAA
1 TGACCAAAACATAAATTAGAT-A-ATATAAGTGACCAATAGATAGTTTACCCTAAA
4760 AAAATCCTAA
Statistics
Matches: 111, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
65 55 0.50
66 24 0.22
67 32 0.29
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (65 bp):
TGACCAAAACATAAATTAGATAATATAAGTGACCAATAGATAGTTTACCCTAAATAATAATCGAA
Found at i:6704 original size:24 final size:24
Alignment explanation
Indices: 6676--6739 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
6666 TGCATTGTAA
* **
6676 TATTTTGTTAAAGTTTGGTGGTTT
1 TATTTTGTTAAAGTATGGTGACTT
*
6700 TATTTTGTTAATGTATGGTGACTT
1 TATTTTGTTAAAGTATGGTGACTT
*
6724 TATTTTGTTCAAGTAT
1 TATTTTGTTAAAGTAT
6740 CAATACAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.20, C:0.03, G:0.20, T:0.56
Consensus pattern (24 bp):
TATTTTGTTAAAGTATGGTGACTT
Found at i:13688 original size:36 final size:36
Alignment explanation
Indices: 13573--13681 Score: 141
Period size: 35 Copynumber: 3.0 Consensus size: 36
13563 TCGTAATCAA
*
13573 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
13610 CTTTG-AAAATGATTTTCACAA-TTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCA-AAGTTTGGTAAATGTTT
* * *
13645 CTTTGAAAAATAGTTTTTTAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
13682 GTTGAAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
35 31 0.48
36 9 0.14
37 24 0.38
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:18194 original size:37 final size:37
Alignment explanation
Indices: 18141--18214 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
18131 TGGCAACCAA
18141 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
18178 CTTTG-AAAAATGGGTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
18215 GTTGAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 6 0.17
37 29 0.83
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (37 bp):
CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:20798 original size:12 final size:12
Alignment explanation
Indices: 20783--20837 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
20773 GTTATTTAAA
20783 CGGGTATTGGGC
1 CGGGTATTGGGC
*
20795 CGGGTATTGGGT
1 CGGGTATTGGGC
20807 CGGGTATTGGGC
1 CGGGTATTGGGC
* * *
20819 CGAGAATCGGGC
1 CGGGTATTGGGC
20831 CGGGTAT
1 CGGGTAT
20838 ATATATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.13, C:0.16, G:0.47, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:20874 original size:31 final size:31
Alignment explanation
Indices: 20836--20916 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
20826 CGGGCCGGGT
20836 ATATATATATATATTTAAATTAAATATATAA
1 ATATATATATATATTTAAATTAAATATATAA
* * * *
20867 ATATATATTTTTATTTAAATTAAATTTATTA
1 ATATATATATATATTTAAATTAAATATATAA
*
20898 ATAT-TATATATATATAAAT
1 ATATATATATATATTTAAAT
20917 AATTATTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 12 0.28
31 31 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
ATATATATATATATTTAAATTAAATATATAA
Found at i:20964 original size:13 final size:13
Alignment explanation
Indices: 20934--20976 Score: 63
Period size: 12 Copynumber: 3.5 Consensus size: 13
20924 TTTAATATTT
*
20934 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
20946 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
20959 ATCGGGGC-GGTA
1 ATCGGGGCGGGTA
20971 ATCGGG
1 ATCGGG
20977 TAATCGGGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 21 0.72
13 8 0.28
ACGTcount: A:0.14, C:0.16, G:0.51, T:0.19
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:21400 original size:18 final size:17
Alignment explanation
Indices: 21377--21419 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
21367 AGAAAAGAAA
21377 AAAATAAATAAATAAAAT
1 AAAATAAAT-AATAAAAT
*
21395 AAAATAGATAATAAAAT
1 AAAATAAATAATAAAAT
21412 AATAATAA
1 AA-AATAA
21420 TATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (17 bp):
AAAATAAATAATAAAAT
Found at i:21409 original size:12 final size:11
Alignment explanation
Indices: 21386--21419 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
21376 AAAAATAAAT
21386 AAATAA-AATA
1 AAATAATAATA
21396 AAATAGATAATA
1 AAATA-ATAATA
21408 AAATAATAATA
1 AAATAATAATA
21419 A
1 A
21420 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.23
11 8 0.36
12 9 0.41
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (11 bp):
AAATAATAATA
Found at i:21493 original size:38 final size:38
Alignment explanation
Indices: 21450--21884 Score: 514
Period size: 38 Copynumber: 11.8 Consensus size: 38
21440 AAAGAAATTG
* *
21450 AAAACTATATATTATATATATAATTTTTAAAAAGTTTT-
1 AAAACTATATATTATATATAT-ATTTTCAAAATGTTTTA
* *
21488 CAAACTATATA-T-TATATA-GTTTTCAAAATGTTTT-
1 AAAACTATATATTATATATATATTTTCAAAATGTTTTA
* *
21522 --AA--A-A-ATCATATATATATTTTCAAAATGCTTTTTT
1 AAAACTATATATTATATATATATTTTCAAAATG--TTTTA
* * *
21556 AAAACTATATATTATATA-A-ATTTTCAGAATGATTTC
1 AAAACTATATATTATATATATATTTTCAAAATGTTTTA
*
21592 AAAACTATATATTATATA-AGT-TTTTTAAAATGTTTTA
1 AAAACTATATATTATATATA-TATTTTCAAAATGTTTTA
21629 AAAACTATATATTATATATATATTTTCAAAATGTTTTA
1 AAAACTATATATTATATATATATTTTCAAAATGTTTTA
*
21667 AAAACTATATATTATATATATATATTTCAAAATATTTTA
1 AAAACTATATATTATATATATAT-TTTCAAAATGTTTTA
21706 AAAACTATATATTATATATATATTTTTCAAAATGTTTTA
1 AAAACTATATATTATATATATA-TTTTCAAAATGTTTTA
*
21745 AAAACTATAT-TT-TATATATATATTCAAAATGTTTTA
1 AAAACTATATATTATATATATATTTTCAAAATGTTTTA
*
21781 AAAACTATATATTATATATGTATTTTCAAAATGTTTTA
1 AAAACTATATATTATATATATATTTTCAAAATGTTTTA
** *
21819 AAAACTATATATTATATA-A-GCTTTCAAAATATTTTA
1 AAAACTATATATTATATATATATTTTCAAAATGTTTTA
* *
21855 AAAATTACATATTATATATATA-TTTCAAAA
1 AAAACTATATATTATATATATATTTTCAAAA
21885 ATCATTTGCA
Statistics
Matches: 348, Mismatches: 27, Indels: 45
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.00
29 1 0.00
30 7 0.02
31 11 0.03
32 2 0.01
33 4 0.01
34 13 0.04
36 85 0.24
37 51 0.15
38 103 0.30
39 62 0.18
40 8 0.02
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (38 bp):
AAAACTATATATTATATATATATTTTCAAAATGTTTTA
Found at i:21498 original size:75 final size:73
Alignment explanation
Indices: 21419--21914 Score: 400
Period size: 75 Copynumber: 6.7 Consensus size: 73
21409 AATAATAATA
* * * *
21419 ATATATATATATATATTTAAAAAAGAAATTGAAAACTATATATTATATATATAATTTTTAAAAAG
1 ATATATATATATATATTTCAAAATG--ATTTAAAACTATATATTATATATAT-ATTTTCAAAAAG
*
21484 TTTT-CAAACT
63 TTTTAAAAACT
* * *
21494 ATATAT-TATATAGT-TTTCAAAATG-TTT-TAA--A-A-ATCATATATATATTTTCAAAATGCT
1 ATATATATATATA-TATTTCAAAATGATTTAAAACTATATATTATATATATATTTTCAAAAAG--
*
21551 TTTTTAAAACT
63 TTTTAAAAACT
* * * *
21562 ATATAT-TATATAAATTTTCAGAATGATTTCAAAACTATATATTATATA-AGT-TTTTTAAAATG
1 ATATATATATATATA-TTTCAAAATGATTT-AAAACTATATATTATATATA-TATTTTCAAAAAG
21624 TTTTAAAAACT
63 TTTTAAAAACT
*
21635 ATATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATATATATTTCAAAAT
1 ATATA-TATATATATA-TTTCAAAATGATTT-AAAACTATATATTATATATATAT-TTTCAAAA-
21700 A-TTTTAAAAACT
61 AGTTTTAAAAACT
* * *
21712 ATATATTATATATATATTTTTCAAAATGTTTTAAAAACTATAT-TT-TATATATATATTCAAAAT
1 ATATA-TATATATATA--TTTCAAAATGATTT-AAAACTATATATTATATATATATTTTCAAAAA
21775 GTTTTAAAAACT
62 GTTTTAAAAACT
* * **
21787 ATATATTATATATGTATTTTCAAAATGTTTTAAAAACTATATATTATATA-A-GCTTTCAAAATA
1 ATATA-TATATATATA-TTTCAAAATGATTT-AAAACTATATATTATATATATATTTTCAAAA-A
*
21850 -TTTTAAAAATT
62 GTTTTAAAAACT
* * **
21861 ACATATTATATATATATTTCAAAAATCATTTGCAA-TATATATATATATATATAT
1 ATATA-TATATATATATTTC-AAAATGATTTAAAACTATATAT-TATATATATAT
21915 AATAAATACG
Statistics
Matches: 356, Mismatches: 36, Indels: 58
0.79 0.08 0.13
Matches are distributed among these distances:
65 10 0.03
66 10 0.03
67 5 0.01
68 18 0.05
69 9 0.03
70 5 0.01
71 2 0.01
72 9 0.03
73 27 0.08
74 82 0.23
75 94 0.26
76 23 0.06
77 36 0.10
78 26 0.07
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (73 bp):
ATATATATATATATATTTCAAAATGATTTAAAACTATATATTATATATATATTTTCAAAAAGTTT
TAAAAACT
Found at i:21844 original size:36 final size:36
Alignment explanation
Indices: 21450--21872 Score: 439
Period size: 36 Copynumber: 11.5 Consensus size: 36
21440 AAAGAAATTG
* * *
21450 AAAACTATATATTATATATATAATTTTTAAAAAGTTTT-
1 AAAACTATATA-T-TATATA-AGTTTTCAAAATGTTTTA
*
21488 CAAACTATATATTATAT-AGTTTTCAAAATGTTTTA
1 AAAACTATATATTATATAAGTTTTCAAAATGTTTTA
* *
21523 AAAA-T-CATA-TATAT-A-TTTTCAAAATGCTTTTTT
1 AAAACTATATATTATATAAGTTTTCAAAATG--TTTTA
* * * *
21556 AAAACTATATATTATATAAATTTTCAGAATGATTTC
1 AAAACTATATATTATATAAGTTTTCAAAATGTTTTA
*
21592 AAAACTATATATTATATAAGTTTTTTAAAATGTTTTA
1 AAAACTATATATTATATAAG-TTTTCAAAATGTTTTA
*
21629 AAAACTATATATTATATATATATTTTCAAAATGTTTTA
1 AAAACTATATATTATATA-A-GTTTTCAAAATGTTTTA
* *
21667 AAAACTATATATTATATATATATATTTCAAAATATTTTA
1 AAAACTATATATTATATA-A-GT-TTTCAAAATGTTTTA
*
21706 AAAACTATATATTATATATATATTTTTCAAAATGTTTTA
1 AAAACTATATA-T-TATATA-AGTTTTCAAAATGTTTTA
* *
21745 AAAACTATATTTTATATATA-TATTCAAAATGTTTTA
1 AAAACTATATATTATATA-AGTTTTCAAAATGTTTTA
*
21781 AAAACTATATATTATATATGTATTTTCAAAATGTTTTA
1 AAAACTATATATTATATAAG--TTTTCAAAATGTTTTA
* *
21819 AAAACTATATATTATATAAGCTTTCAAAATATTTTA
1 AAAACTATATATTATATAAGTTTTCAAAATGTTTTA
* *
21855 AAAATTACATATTATATA
1 AAAACTATATATTATATA
21873 TATATTTCAA
Statistics
Matches: 337, Mismatches: 31, Indels: 36
0.83 0.08 0.09
Matches are distributed among these distances:
31 11 0.03
32 6 0.02
33 11 0.03
34 16 0.05
35 6 0.02
36 94 0.28
37 40 0.12
38 94 0.28
39 49 0.15
40 2 0.01
41 8 0.02
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (36 bp):
AAAACTATATATTATATAAGTTTTCAAAATGTTTTA
Found at i:23291 original size:16 final size:15
Alignment explanation
Indices: 23267--23305 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
23257 GATTTCGACC
*
23267 ATATCATATAATGAAT
1 ATATTATATAAT-AAT
23283 ATATTATATAATAAT
1 ATATTATATAATAAT
23298 ATA-TATAT
1 ATATTATAT
23306 TTATACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 6 0.27
16 11 0.50
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (15 bp):
ATATTATATAATAAT
Found at i:24776 original size:10 final size:9
Alignment explanation
Indices: 24739--24795 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
24729 TTTTTACTAT
24739 TTTATTTT-
1 TTTATTTTC
24747 TTT-TTCTTC
1 TTTATT-TTC
*
24756 TTT-TGTT-
1 TTTATTTTC
24763 TTTATTCTTC
1 TTTATT-TTC
24773 TTTATTTTC
1 TTTATTTTC
*
24782 TTTATTTTT
1 TTTATTTTC
24791 TTTAT
1 TTTAT
24796 CTTCATGTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
7 5 0.12
8 8 0.20
9 22 0.54
10 6 0.15
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTATTTTC
Found at i:35273 original size:52 final size:54
Alignment explanation
Indices: 35192--35294 Score: 147
Period size: 52 Copynumber: 1.9 Consensus size: 54
35182 AATACTTCGC
* * * *
35192 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAA-AAAAA-AAAAACAT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAGAAAAAGAAAAACAT
*
35244 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAGAAAAAGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAGAAAAAGAAAAA
35295 AGAAGAGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 34 0.77
53 5 0.11
54 5 0.11
ACGTcount: A:0.51, C:0.14, G:0.21, T:0.14
Consensus pattern (54 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAGAAAAAGAAAAACAT
Found at i:36242 original size:105 final size:105
Alignment explanation
Indices: 36060--36940 Score: 1496
Period size: 105 Copynumber: 8.4 Consensus size: 105
36050 AGGTTTTACC
**
36060 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTATAGACAACGAAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGAAAGTTCAACTTCACG
*
36125 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
36165 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGAAAGTTCAACTTCACG
*
36230 ACGAAGGGACCGCTGGTTGTCAACAAACGTTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
36270 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCCCAGACAACAAAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGAAAGTTCAACTTCACG
36335 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
36375 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCCCAGACAACGAAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGAAAGTTCAACTTCACG
36440 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
36480 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGAAAGTTCAACTTCACG
36545 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
36585 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGAAAGTTCAACTTCACG
36650 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
36690 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGAAAGTTCAACTTCACG
36755 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
36795 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGAC-A-GTATAAGTTTAACTTCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG-A-AAGTTCAACTTCA
* ** ** * * *
36858 CGACGAAGGGGCCGCTGACTGTCAACCGACGATTTCCCAGTTC
64 CGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * **
36901 CAGAACCAATTTCAACTTCACAGCGGGGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
36941 GGAACAATAT
Statistics
Matches: 745, Mismatches: 28, Indels: 5
0.96 0.04 0.01
Matches are distributed among these distances:
103 1 0.00
104 1 0.00
105 698 0.94
106 45 0.06
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGAAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:37426 original size:16 final size:15
Alignment explanation
Indices: 37402--37440 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
37392 GATTTCGACC
*
37402 ATATCATATAATGAAT
1 ATATTATATAAT-AAT
37418 ATATTATATAATAAT
1 ATATTATATAATAAT
37433 ATA-TATAT
1 ATATTATAT
37441 TTATACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 6 0.27
16 11 0.50
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (15 bp):
ATATTATATAATAAT
Found at i:38885 original size:16 final size:16
Alignment explanation
Indices: 38861--38901 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
38851 TTTTTACTAT
*
38861 TTTATTTTTTTTTCTTC
1 TTTA-TTTTTATTCTTC
*
38878 TTTGTTTTTATTCTTC
1 TTTATTTTTATTCTTC
38894 TTTATTTT
1 TTTATTTT
38902 CTTTATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTATTTTTATTCTTC
Found at i:41054 original size:18 final size:19
Alignment explanation
Indices: 41025--41067 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
41015 ATTTGAATTA
41025 AAAAAATCAGAAAAAATAC
1 AAAAAATCAGAAAAAATAC
**
41044 AAAAAAT-AGAAAATTTAC
1 AAAAAATCAGAAAAAATAC
41062 AAAAAA
1 AAAAAA
41068 AATTAGTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.74, C:0.07, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAAAATCAGAAAAAATAC
Found at i:41153 original size:9 final size:9
Alignment explanation
Indices: 41139--41171 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
41129 TTGAATTTAA
41139 AAAAATCAG
1 AAAAATCAG
41148 AAAAATACA-
1 AAAAAT-CAG
41157 AAAAATCAG
1 AAAAATCAG
41166 AAAAAT
1 AAAAAT
41172 TACAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 18 0.82
10 2 0.09
ACGTcount: A:0.73, C:0.09, G:0.06, T:0.12
Consensus pattern (9 bp):
AAAAATCAG
Found at i:41161 original size:18 final size:19
Alignment explanation
Indices: 41138--41180 Score: 79
Period size: 18 Copynumber: 2.3 Consensus size: 19
41128 CTTGAATTTA
41138 AAAAAATCAGAAAAA-TAC
1 AAAAAATCAGAAAAATTAC
41156 AAAAAATCAGAAAAATTAC
1 AAAAAATCAGAAAAATTAC
41175 AAAAAA
1 AAAAAA
41181 ATTACTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.74, C:0.09, G:0.05, T:0.12
Consensus pattern (19 bp):
AAAAAATCAGAAAAATTAC
Found at i:41208 original size:112 final size:111
Alignment explanation
Indices: 41011--41261 Score: 371
Period size: 112 Copynumber: 2.3 Consensus size: 111
41001 TCTAATAAAT
* *
41011 ATCTATTTGAATTAAAAAAATCAGAAAAAATACAAAAAATAGAAAATTTACAAAAAAAATTAGTA
1 ATCTATTTGAATTAAAAAAATCAG-AAAAATACAAAAAATAGAAAAATTACAAAAAAAATTACTA
* * *
41076 TGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAAATTA
65 TATTTATATATCTAATTTCAATGTATTTTTATATATCTTGCAAATTA
*
41123 ATCTACTTGAATTTAAAAAAATCAGAAAAATACAAAAAATCAGAAAAATTAC-AAAAAAATTACT
1 ATCTATTTGAA-TTAAAAAAATCAGAAAAATACAAAAAAT-AGAAAAATTACAAAAAAAATTACT
** *
41187 ATATTTATATATCTAATTTCAATGTATTTTTATATATCTTTTAATTTA
64 ATATTTATATATCTAATTTCAATGTATTTTTATATATCTTGCAAATTA
*
41235 ATATATTTGAATTAAAAAAA-CAGAAAA
1 ATCTATTTGAATTAAAAAAATCAGAAAA
41262 TTGTAGCGTT
Statistics
Matches: 126, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
110 7 0.06
111 9 0.07
112 87 0.69
113 23 0.18
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (111 bp):
ATCTATTTGAATTAAAAAAATCAGAAAAATACAAAAAATAGAAAAATTACAAAAAAAATTACTAT
ATTTATATATCTAATTTCAATGTATTTTTATATATCTTGCAAATTA
Found at i:45140 original size:20 final size:20
Alignment explanation
Indices: 45077--45146 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
45067 CTTACCTTTG
* *
45077 GTATCGATACTGCAAGAACA
1 GTATCGATACTGTAATAACA
* * * * *
45097 ATATCGATATTGTTCAT-GCG
1 GTATCGATACTG-TAATAACA
45117 GTATCGATACTGTAATAACA
1 GTATCGATACTGTAATAACA
45137 GTATCGATAC
1 GTATCGATAC
45147 GACTCACCTA
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
19 3 0.08
20 32 0.89
21 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (20 bp):
GTATCGATACTGTAATAACA
Found at i:46368 original size:28 final size:28
Alignment explanation
Indices: 46313--46369 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
46303 CATTAATTGA
46313 TTTAAATAGTAAAAGAGAATATTATTTT
1 TTTAAATAGTAAAAGAGAATATTATTTT
* * *
46341 TTTAATTA-TAAAATAGAATGTTATTTT
1 TTTAAATAGTAAAAGAGAATATTATTTT
46368 TT
1 TT
46370 CTAGTGGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (28 bp):
TTTAAATAGTAAAAGAGAATATTATTTT
Done.