Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000365.1 Hibiscus syriacus cultivar Beakdansim tig00000665_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: 83057
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:552 original size:43 final size:43
Alignment explanation
Indices: 491--576 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
481 CCAGTAAGAC
491 TTTGCATATCCTTCAAAGTCATGCACATCACAAAAGCTCCTAA
1 TTTGCATATCCTTCAAAGTCATGCACATCACAAAAGCTCCTAA
*
534 TTTGCATATCCTTCAAAGTCTTGCACATCACAAAAGCTCCTAA
1 TTTGCATATCCTTCAAAGTCATGCACATCACAAAAGCTCCTAA
577 AAGAATCTCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.29
Consensus pattern (43 bp):
TTTGCATATCCTTCAAAGTCATGCACATCACAAAAGCTCCTAA
Found at i:13069 original size:36 final size:36
Alignment explanation
Indices: 13028--13135 Score: 175
Period size: 35 Copynumber: 3.0 Consensus size: 36
13018 ATATTTCAAC
*
13028 AAACATCTACCAAAC-TTGAAAAACCATTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAACCATTTTTCAAAG
13064 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
13099 AAACATTTACCAAACTTTGAAAACCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TTTTTCAAAG
13136 TTGGTTGCCA
Statistics
Matches: 68, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
35 35 0.51
36 21 0.31
37 12 0.18
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
Found at i:13091 original size:21 final size:21
Alignment explanation
Indices: 13067--13127 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
13057 TTCAAAGAAA
13067 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
13088 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
13102 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
13123 CATTT
1 CATTT
13128 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:17694 original size:37 final size:37
Alignment explanation
Indices: 17652--17725 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
17642 ATATTTCAAC
*
17652 AAACATCTATCAAACTTTGAAAATCAATTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAATCAATTTTTCAAAG
* *
17689 AAACATTTACCAAACTTTGAAAATCATTTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAATCAATTTTTCAAAG
17726 TTGATTGCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (37 bp):
AAACATCTACCAAACTTTGAAAATCAATTTTTCAAAG
Found at i:17884 original size:21 final size:21
Alignment explanation
Indices: 17858--17899 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
17848 GTGGTGTCTG
17858 GGGTTTTTACGTTGCGAATTC
1 GGGTTTTTACGTTGCGAATTC
17879 GGGTTTTTACGTTGCGAATTC
1 GGGTTTTTACGTTGCGAATTC
17900 TGATAAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (21 bp):
GGGTTTTTACGTTGCGAATTC
Found at i:31194 original size:36 final size:36
Alignment explanation
Indices: 31152--31227 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
31142 TTATAGCTAA
* *
31152 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCATATTTATTCGAATTTTGCCAAAAATAGC
31188 AAAAATCATATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCATATTTATTCGAATTTTGCCAAAAATAGC
31224 AAAA
1 AAAA
31228 TCCCGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (36 bp):
AAAAATCATATTTATTCGAATTTTGCCAAAAATAGC
Found at i:35721 original size:15 final size:15
Alignment explanation
Indices: 35703--35732 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
35693 CCACGGTGCT
35703 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
35718 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
35733 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:36196 original size:36 final size:36
Alignment explanation
Indices: 36154--36229 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
36144 TTATAGCTAA
*
36154 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
36190 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
36226 AAAA
1 AAAA
36230 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:37956 original size:19 final size:19
Alignment explanation
Indices: 37932--37982 Score: 93
Period size: 19 Copynumber: 2.6 Consensus size: 19
37922 TTACAGACGC
37932 GCATATGATATTAATGACT
1 GCATATGATATTAATGACT
37951 GCATATGATATTAATGACT
1 GCATATGATATTAATGACT
37970 GCATATGAATATT
1 GCATATG-ATATT
37983 GTTCAACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 26 0.84
20 5 0.16
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (19 bp):
GCATATGATATTAATGACT
Found at i:39060 original size:31 final size:31
Alignment explanation
Indices: 39022--39133 Score: 206
Period size: 31 Copynumber: 3.6 Consensus size: 31
39012 ATTATAATAT
39022 TACAGTGACCATTTTGTAACAATTTAAAAGA
1 TACAGTGACCATTTTGTAACAATTTAAAAGA
39053 TACAGTGACCATTTTGTAACAATTTAAAAGA
1 TACAGTGACCATTTTGTAACAATTTAAAAGA
39084 TACAGTGACCATTTTGTAACAATTTAAAAGA
1 TACAGTGACCATTTTGTAACAATTTAAAAGA
* *
39115 TACAATGATCATTTTGTAA
1 TACAGTGACCATTTTGTAA
39134 ACTTTAGAAT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (31 bp):
TACAGTGACCATTTTGTAACAATTTAAAAGA
Found at i:43584 original size:17 final size:17
Alignment explanation
Indices: 43562--43621 Score: 52
Period size: 20 Copynumber: 3.4 Consensus size: 17
43552 AAATTAATGA
43562 AAATAAATGAATAAAAT
1 AAATAAATGAATAAAAT
*
43579 AAATAAATATTGAATAAAAA
1 AAAT-AA-A-TGAATAAAAT
*
43599 ATAAT-AATG-AGAAAAT
1 A-AATAAATGAATAAAAT
43615 AAATAAA
1 AAATAAA
43622 GTAAAAGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
15 3 0.09
16 8 0.23
17 6 0.17
18 3 0.09
19 2 0.06
20 10 0.29
21 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
AAATAAATGAATAAAAT
Found at i:46774 original size:23 final size:24
Alignment explanation
Indices: 46746--46807 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 24
46736 CCTGATTATA
46746 TATATATATTAAGAAT-TTTTATTTT
1 TATAT-TATTAA-AATATTTTATTTT
*
46771 TATATTGTTAAAATATTTTA--TT
1 TATATTATTAAAATATTTTATTTT
46793 TA-ATTATTAAAATAT
1 TATATTATTAAAATAT
46808 AAAAATGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 12 0.35
22 4 0.12
23 3 0.09
24 10 0.29
25 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (24 bp):
TATATTATTAAAATATTTTATTTT
Found at i:46845 original size:42 final size:43
Alignment explanation
Indices: 46799--46889 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
46789 TATTTAATTA
46799 TTAAAATATAA-AAAT-GATAATAAAATATATTAATTTAACCAT
1 TTAAAATATAATAAATAG-TAATAAAATATATTAATTTAACCAT
* * **
46841 TTAAAATATAATAAATAGTTATAAAATATATTATTTTAATTAT
1 TTAAAATATAATAAATAGTAATAAAATATATTAATTTAACCAT
46884 TTAAAA
1 TTAAAA
46890 AAATTAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 11 0.26
43 31 0.72
44 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (43 bp):
TTAAAATATAATAAATAGTAATAAAATATATTAATTTAACCAT
Found at i:50871 original size:3 final size:3
Alignment explanation
Indices: 50863--50889 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
50853 TTATGGGTAA
50863 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
50890 CACTTCGGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:52046 original size:2 final size:2
Alignment explanation
Indices: 52039--52068 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52029 CACCAACATA
52039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52069 GATGTATCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52372 original size:38 final size:38
Alignment explanation
Indices: 52296--52372 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 38
52286 CTTAATCTGA
* *
52296 CTAAAAAATTATACATCCTCCACTCAATTCGACCCGAT
1 CTAAAAAATTATACATCCTCCACTCAACTCGACACGAT
*
52334 CTAAAAAA-TATACA-CTCTTCACTCAACTCGAACACGAT
1 CTAAAAAATTATACATC-CTCCACTCAACTCG-ACACGAT
52372 C
1 C
52373 CGATTTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 1 0.03
37 18 0.53
38 15 0.44
ACGTcount: A:0.39, C:0.31, G:0.05, T:0.25
Consensus pattern (38 bp):
CTAAAAAATTATACATCCTCCACTCAACTCGACACGAT
Found at i:52480 original size:23 final size:21
Alignment explanation
Indices: 52416--52484 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 21
52406 ACCTGAAATA
*
52416 ATATATTTATTAAAAAATATT
1 ATATATTTATTAAAAAATAAT
* *
52437 AT-TCTTTATTCAATAAA-AAT
1 ATATATTTATT-AAAAAATAAT
52457 ATATATTTAATTGAAAAAATAAT
1 ATATATTT-ATT-AAAAAATAAT
52480 ATATA
1 ATATA
52485 CATGGATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 11 0.29
21 11 0.29
22 8 0.21
23 8 0.21
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (21 bp):
ATATATTTATTAAAAAATAAT
Found at i:53110 original size:3 final size:3
Alignment explanation
Indices: 53097--53130 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
53087 TTCGTCCCAC
53097 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
53131 CTTTTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:54721 original size:5 final size:6
Alignment explanation
Indices: 54704--54728 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
54694 GTTTTAGTCC
54704 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
54729 GCATGTTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:55532 original size:129 final size:130
Alignment explanation
Indices: 55221--55546 Score: 352
Period size: 131 Copynumber: 2.5 Consensus size: 130
55211 TTCCGGTCGA
* * * *
55221 AGTAATAAATGAATGTTTTAAGGCATGATAGGTCATTTATTCTCGATTGGAAATAATTCGATATT
1 AGTAATAAATGAATGTCTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATT
** ** * * * *
55286 ACTGTTTTTTCTCAAATCAATATTGATTTTTAAGATAGAATGATGATATCTCTTCGTTTCAATTG
66 ACCATTTTCCCTCAAATCAATATTGAATTTTAAGAGAGAATAATGA-ATCTCTTCATTTCAATTG
55351 G
130 G
* * * * * * *
55352 AGCAATTAATGACTG-CTTTAAGGTATGAGAGGTCATTTATTATCAAATGGAAATTATTAGATAT
1 AGTAATAAATGAATGTC-TTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
* * * *
55416 TACCATTTTCCCTCGAATCGATATTGAATTTTAAGACGA-AATAATG-ATCTCTTTATTTCGATT
65 TACCATTTTCCCTCAAATCAATATTGAATTTTAAGA-GAGAATAATGAATCTCTTCATTTCAATT
55479 GG
129 GG
* * * * *
55481 GGTAATAAATGATTGTCTTAAGGTACGAGAGATCATTTATTCTTGATTGGAAATAATTAGATATT
1 AGTAATAAATGAATGTCTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATT
55546 A
66 A
55547 TCGTTTTCAC
Statistics
Matches: 158, Mismatches: 34, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
129 69 0.44
130 1 0.01
131 87 0.55
132 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (130 bp):
AGTAATAAATGAATGTCTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATT
ACCATTTTCCCTCAAATCAATATTGAATTTTAAGAGAGAATAATGAATCTCTTCATTTCAATTGG
Found at i:58913 original size:24 final size:27
Alignment explanation
Indices: 58885--58937 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
58875 ATTTGAGGAT
*
58885 TTTAAG-GATATGAGG-TTTTTT-TAA
1 TTTAAGAGAAATGAGGATTTTTTATAA
*
58909 TTTAAGAGAAATTAGGATTTTTTATAA
1 TTTAAGAGAAATGAGGATTTTTTATAA
58936 TT
1 TT
58938 ATTATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.25
25 7 0.29
26 6 0.25
27 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (27 bp):
TTTAAGAGAAATGAGGATTTTTTATAA
Found at i:59823 original size:2 final size:2
Alignment explanation
Indices: 59816--59862 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
59806 ACACCTCAAC
59816 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59858 TA TA T
1 TA TA T
59863 TATTTTTTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61915 original size:19 final size:19
Alignment explanation
Indices: 61891--61955 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
61881 AAAATCGCAA
61891 TGCGATTTTTCAAATTCGT
1 TGCGATTTTTCAAATTCGT
** *
61910 TGCGA-TAGTCGAAGTTAGCGT
1 TGCGATTTTTC-AAATT--CGT
*
61931 TGCGATTTTCCAAATTCGT
1 TGCGATTTTTCAAATTCGT
61950 TGCGAT
1 TGCGAT
61956 AGTCCAAGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
18 3 0.09
19 18 0.51
21 12 0.34
22 2 0.06
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (19 bp):
TGCGATTTTTCAAATTCGT
Found at i:61933 original size:21 final size:20
Alignment explanation
Indices: 61907--61976 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 20
61897 TTTTCAAATT
*
61907 CGTTGCGATAGTCGAAGTTAG
1 CGTTGCGATAGTCCAAGTT-G
** *
61928 CGTTGCGATTTTCCAAATT-
1 CGTTGCGATAGTCCAAGTTG
61947 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTT-G
61968 CGTTGCGAT
1 CGTTGCGAT
61977 TTTCTCTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 16 0.40
21 24 0.60
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCCAAGTTG
Found at i:61935 original size:40 final size:40
Alignment explanation
Indices: 61891--61980 Score: 153
Period size: 40 Copynumber: 2.2 Consensus size: 40
61881 AAAATCGCAA
* *
61891 TGCGATTTTTCAAATTCGTTGCGATAGTCGAAGTTAGCGT
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTAGCGT
*
61931 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTAGCGT
61971 TGCGATTTTC
1 TGCGATTTTC
61981 TCTAAATAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTAGCGT
Found at i:61961 original size:19 final size:19
Alignment explanation
Indices: 61901--61967 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
61891 TGCGATTTTT
61901 CAAATTCGTTGCGATAGTC
1 CAAATTCGTTGCGATAGTC
* * **
61920 GAAGTTAGCGTTGCGATTTTC
1 CAAATT--CGTTGCGATAGTC
61941 CAAATTCGTTGCGATAGTC
1 CAAATTCGTTGCGATAGTC
*
61960 CAAGTTCG
1 CAAATTCG
61968 CGTTGCGATT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 22 0.59
21 15 0.41
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (19 bp):
CAAATTCGTTGCGATAGTC
Found at i:69334 original size:16 final size:16
Alignment explanation
Indices: 69313--69364 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
69303 TACAGATTTT
69313 TTTAAAACAGTAACAG
1 TTTAAAACAGTAACAG
* **
69329 TTTAAAA-TGT-A-TT
1 TTTAAAACAGTAACAG
69342 TTTAAAACAGTAACAG
1 TTTAAAACAGTAACAG
69358 TTTAAAA
1 TTTAAAA
69365 TGTATTTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 7 0.26
14 3 0.11
15 3 0.11
16 14 0.52
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.35
Consensus pattern (16 bp):
TTTAAAACAGTAACAG
Found at i:69343 original size:29 final size:29
Alignment explanation
Indices: 69311--69378 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
69301 AGTACAGATT
69311 TTTTTAAAACAGTAACAGTTTAAAATGTA
1 TTTTTAAAACAGTAACAGTTTAAAATGTA
69340 TTTTTAAAACAGTAACAGTTTAAAATGTA
1 TTTTTAAAACAGTAACAGTTTAAAATGTA
69369 TTTTTAAAAC
1 TTTTTAAAAC
69379 CATGGTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (29 bp):
TTTTTAAAACAGTAACAGTTTAAAATGTA
Found at i:69720 original size:35 final size:35
Alignment explanation
Indices: 69674--69846 Score: 233
Period size: 35 Copynumber: 4.9 Consensus size: 35
69664 CTTAGATATG
69674 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
1 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
69709 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
1 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
** * * *
69744 TAAGGAATTACCAGTTTAATCAAG-CTGAACCTGTCG
1 TAAGGAATTACCAGTTCGATC-GGTCTGAACCTAT-A
*
69780 TAAGGAATTACCAGTTCGATCAGTCTGAACCTATA
1 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
* *
69815 TAAGGAATTACCAATTTGATCGAG-CTGAACCT
1 TAAGGAATTACCAGTTCGATCG-GTCTGAACCT
69847 GTAGAGACTA
Statistics
Matches: 122, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
35 92 0.75
36 30 0.25
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (35 bp):
TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
Found at i:69806 original size:71 final size:69
Alignment explanation
Indices: 69674--69849 Score: 253
Period size: 71 Copynumber: 2.5 Consensus size: 69
69664 CTTAGATATG
* * * *
69674 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATATAAGGAATTACCAGTTCGATCGGTCTGAAC
1 TAAGGAATTACCAGTTTGATCAG-CTGAACCTGTATAAGGAATTACCAGTTCGATCAGTCTGAAC
69739 CTATA
65 CTATA
* *
69744 TAAGGAATTACCAGTTTAATCAAGCTGAACCTGTCGTAAGGAATTACCAGTTCGATCAGTCTGAA
1 TAAGGAATTACCAGTTTGATC-AGCTGAACCTGT-ATAAGGAATTACCAGTTCGATCAGTCTGAA
69809 CCTATA
64 CCTATA
*
69815 TAAGGAATTACCAATTTGATCGAGCTGAACCTGTA
1 TAAGGAATTACCAGTTTGATC-AGCTGAACCTGTA
69850 GAGACTACAT
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
70 28 0.30
71 66 0.70
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (69 bp):
TAAGGAATTACCAGTTTGATCAGCTGAACCTGTATAAGGAATTACCAGTTCGATCAGTCTGAACC
TATA
Found at i:70040 original size:78 final size:78
Alignment explanation
Indices: 69911--70067 Score: 242
Period size: 78 Copynumber: 2.0 Consensus size: 78
69901 TACAGTAATC
* * * *
69911 AGTGGTAGCAGGAAATCATAGTTTAAACATAACAATTCAGTAGAAAAGGTATCCAGAGATCATGA
1 AGTGGTAACAGAAAATCAGAGTTCAAACATAACAATTCAGTAGAAAAGGTATCCAGAGATCATGA
*
69976 ATCAAACATGCAG
66 ATCAAACAAGCAG
* *
69989 AGTGGTAACAGAAAATCAGAGTTCAAACATATCAATTCAGTAGAAACGGTATCCAGAGATCATGA
1 AGTGGTAACAGAAAATCAGAGTTCAAACATAACAATTCAGTAGAAAAGGTATCCAGAGATCATGA
*
70054 ATCAGACAAGCAG
66 ATCAAACAAGCAG
70067 A
1 A
70068 CTTAAAACTT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.20
Consensus pattern (78 bp):
AGTGGTAACAGAAAATCAGAGTTCAAACATAACAATTCAGTAGAAAAGGTATCCAGAGATCATGA
ATCAAACAAGCAG
Found at i:72473 original size:16 final size:16
Alignment explanation
Indices: 72443--72482 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
72433 TAAATTATTT
*
72443 ATTAACATTATTTTAAA
1 ATTAA-ATTAATTTAAA
72460 ATTAAATTAATTTAAA
1 ATTAAATTAATTTAAA
*
72476 TTTAAAT
1 ATTAAAT
72483 AGAATTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAAATTAATTTAAA
Found at i:72681 original size:26 final size:28
Alignment explanation
Indices: 72632--72693 Score: 101
Period size: 26 Copynumber: 2.3 Consensus size: 28
72622 TAGTATATGT
*
72632 ATTTTATCTATTTACTATTTATTATAAA
1 ATTTTATCTATATACTATTTATTATAAA
72660 ATTTTATCTA-AT-CTATTTATTATAAA
1 ATTTTATCTATATACTATTTATTATAAA
72686 ATTTTATC
1 ATTTTATC
72694 ATACAACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 22 0.67
27 1 0.03
28 10 0.30
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTTATCTATATACTATTTATTATAAA
Found at i:73071 original size:19 final size:20
Alignment explanation
Indices: 73027--73071 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
73017 ATTTGTTTTT
*
73027 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
73047 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTATCAA
73066 AATAAA
1 AATAAA
73072 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:80039 original size:12 final size:13
Alignment explanation
Indices: 80011--80053 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
80001 TATTTTATTC
* *
80011 TCATTTTCCACTT
1 TCATATTCCATTT
80024 TCATATT-CATTT
1 TCATATTCCATTT
*
80036 TCATATTCCATGT
1 TCATATTCCATTT
80049 TCATA
1 TCATA
80054 ATAAATACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.23, C:0.23, G:0.02, T:0.51
Consensus pattern (13 bp):
TCATATTCCATTT
Found at i:80130 original size:19 final size:19
Alignment explanation
Indices: 80094--80161 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
80084 TCTGAATTAG
*
80094 AACTTATTTCCAG-TTCAT
1 AACTTATTTTCAGATTCAT
*
80112 AACTTATTTTCAGACTCAT
1 AACTTATTTTCAGATTCAT
* *
80131 AACTTACTGTCAGATTCAT
1 AACTTATTTTCAGATTCAT
*
80150 ATCTTATTTTCA
1 AACTTATTTTCA
80162 AATTTATAGC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
18 12 0.29
19 29 0.71
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (19 bp):
AACTTATTTTCAGATTCAT
Done.