Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007347.1 Hibiscus syriacus cultivar Beakdansim tig00019684_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: 62972
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7873 original size:53 final size:53
Alignment explanation
Indices: 7815--7930 Score: 232
Period size: 53 Copynumber: 2.2 Consensus size: 53
7805 TCATTCGATA
7815 CAAATTCCATGTCACAACATAAATGTTGACAATAAAACTTCTAATTGACCAAT
1 CAAATTCCATGTCACAACATAAATGTTGACAATAAAACTTCTAATTGACCAAT
7868 CAAATTCCATGTCACAACATAAATGTTGACAATAAAACTTCTAATTGACCAAT
1 CAAATTCCATGTCACAACATAAATGTTGACAATAAAACTTCTAATTGACCAAT
7921 CAAATTCCAT
1 CAAATTCCAT
7931 TTTATCCAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 63 1.00
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (53 bp):
CAAATTCCATGTCACAACATAAATGTTGACAATAAAACTTCTAATTGACCAAT
Found at i:10666 original size:45 final size:45
Alignment explanation
Indices: 10602--10688 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
10592 TAAAAAAATG
*
10602 AGTCTTAGGGAATAAGTTGGGTAATGCTGCTAATAGCTCCAACAT
1 AGTCTTAGGGAATAAGTTGGGCAATGCTGCTAATAGCTCCAACAT
* *
10647 AGTCTTAGGGAATAAGTTGGGCAATGTTGGTAATAGCTCCAA
1 AGTCTTAGGGAATAAGTTGGGCAATGCTGCTAATAGCTCCAA
10689 AAATAGTGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (45 bp):
AGTCTTAGGGAATAAGTTGGGCAATGCTGCTAATAGCTCCAACAT
Found at i:10706 original size:45 final size:45
Alignment explanation
Indices: 10596--10711 Score: 126
Period size: 45 Copynumber: 2.6 Consensus size: 45
10586 TATTTCTAAA
* * *
10596 AAAATGAGTCTTAGGGAATAAGTTGGGTAATGCTGCTAATAGCTCC
1 AAAAT-AGTCGTAGGAAATAAGTTGGGCAATGCTGCTAATAGCTCC
* * * * *
10642 AACATAGTCTTAGGGAATAAGTTGGGCAATGTTGGTAATAGCTCC
1 AAAATAGTCGTAGGAAATAAGTTGGGCAATGCTGCTAATAGCTCC
*
10687 AAAAATAGTGGTA-GAAATAAGTTGG
1 -AAAATAGTCGTAGGAAATAAGTTGG
10712 AATTCCAACA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
45 48 0.79
46 13 0.21
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (45 bp):
AAAATAGTCGTAGGAAATAAGTTGGGCAATGCTGCTAATAGCTCC
Found at i:13570 original size:26 final size:26
Alignment explanation
Indices: 13540--13592 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
13530 TCTCTCAACG
*
13540 TTGGTGTTAATTTTCTAGATTTTTAA
1 TTGGTATTAATTTTCTAGATTTTTAA
13566 TTGGTATTAATTTTCTAGATTTTTAA
1 TTGGTATTAATTTTCTAGATTTTTAA
13592 T
1 T
13593 GCAAAACTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.04, G:0.13, T:0.58
Consensus pattern (26 bp):
TTGGTATTAATTTTCTAGATTTTTAA
Found at i:13788 original size:5 final size:5
Alignment explanation
Indices: 13778--13807 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
13768 AACCATTTGT
*
13778 CGACC CAACC CGACC CGACC CGACC CGACC
1 CGACC CGACC CGACC CGACC CGACC CGACC
13808 AGTTGATCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.23, C:0.60, G:0.17, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:14483 original size:29 final size:29
Alignment explanation
Indices: 14440--14545 Score: 90
Period size: 29 Copynumber: 3.7 Consensus size: 29
14430 ATATTTATGC
* * **
14440 TTCTGCATGGAATTAAATCTCTGTT-TTGT
1 TTCTGCATGGGATTAAATCCCCATTATT-T
*
14469 TTCTGCATGGGATTAAACCCCCATTATTT
1 TTCTGCATGGGATTAAATCCCCATTATTT
* * * *
14498 TTCTTCATGGGATTAAATCCCCGTCCA-AT
1 TTCTGCATGGGATTAAATCCCCAT-TATTT
*
14527 TTCTACATGGGATTAAATC
1 TTCTGCATGGGATTAAATC
14546 ATCGTCCTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 61 0.95
30 3 0.05
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (29 bp):
TTCTGCATGGGATTAAATCCCCATTATTT
Found at i:14551 original size:29 final size:29
Alignment explanation
Indices: 14497--14571 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
14487 CCCCATTATT
* *
14497 TTTCTTCATGGGATTAAATCCCCGTCCAA
1 TTTCTACATGGGATTAAATCACCGTCCAA
* *
14526 TTTCTACATGGGATTAAATCATCGTCCTA
1 TTTCTACATGGGATTAAATCACCGTCCAA
* **
14555 TTTTTGTATGGGATTAA
1 TTTCTACATGGGATTAA
14572 GTCTTCATCT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (29 bp):
TTTCTACATGGGATTAAATCACCGTCCAA
Found at i:17229 original size:14 final size:14
Alignment explanation
Indices: 17210--17237 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17200 CACTAGTGTG
17210 TAAGGACATTTAGT
1 TAAGGACATTTAGT
17224 TAAGGACATTTAGT
1 TAAGGACATTTAGT
17238 GCAGCACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
TAAGGACATTTAGT
Found at i:30393 original size:21 final size:21
Alignment explanation
Indices: 30367--30421 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
30357 TGATGAGTTA
*
30367 TGGCTTTGTAATAGAGCAGCC
1 TGGCTTTGTAATAGAGCAGAC
*
30388 TGGCTTTGTAATAGAGCAGAT
1 TGGCTTTGTAATAGAGCAGAC
*
30409 TAGCTTTGTAATA
1 TGGCTTTGTAATA
30422 AAACACCTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (21 bp):
TGGCTTTGTAATAGAGCAGAC
Found at i:37815 original size:26 final size:26
Alignment explanation
Indices: 37779--37833 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
37769 ATGCACCCAA
37779 ATTGGAATGTAAAACTTTGCCATCGC
1 ATTGGAATGTAAAACTTTGCCATCGC
37805 ATTGGAATGTAAAACTTTGCCATCGC
1 ATTGGAATGTAAAACTTTGCCATCGC
37831 ATT
1 ATT
37834 TAATGAACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (26 bp):
ATTGGAATGTAAAACTTTGCCATCGC
Found at i:40703 original size:90 final size:89
Alignment explanation
Indices: 40583--40757 Score: 296
Period size: 90 Copynumber: 2.0 Consensus size: 89
40573 TAATCTCGAA
* *
40583 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAA-CCCTAATATGAT
*
40648 TAGGGTAACTTGGATATAAAATTAT
65 TAGGATAACTTGGATATAAAATTAT
*
40673 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
*
40738 AGGATAACTTGGCTATAAAA
66 AGGATAACTTGGATATAAAA
40758 GGGTGTGTTA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 31 0.39
90 49 0.61
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
AGGATAACTTGGATATAAAATTAT
Found at i:42083 original size:17 final size:17
Alignment explanation
Indices: 42061--42102 Score: 77
Period size: 16 Copynumber: 2.5 Consensus size: 17
42051 CATTTTCTCT
42061 CCTTCAAAAAAATTTTC
1 CCTTCAAAAAAATTTTC
42078 CCTTC-AAAAAATTTTC
1 CCTTCAAAAAAATTTTC
42094 CCTTCAAAA
1 CCTTCAAAA
42103 TTTCCCCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.33
Consensus pattern (17 bp):
CCTTCAAAAAAATTTTC
Found at i:46677 original size:21 final size:21
Alignment explanation
Indices: 46653--46692 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
46643 CACCACAAGA
46653 AAATATGACCT-AAATGCAACT
1 AAATATGA-CTAAAATGCAACT
*
46674 AAATGTGACTAAAATGCAA
1 AAATATGACTAAAATGCAA
46693 TGACAACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.23
Consensus pattern (21 bp):
AAATATGACTAAAATGCAACT
Found at i:47147 original size:17 final size:19
Alignment explanation
Indices: 47119--47167 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
47109 TATTTTGAAA
47119 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
47137 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
47156 CACCGATGCACT
1 CATCGATGCACT
47168 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:49114 original size:22 final size:21
Alignment explanation
Indices: 49090--49129 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
49080 GAGAAATTGT
49090 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
49111 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
49130 AAATAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:55293 original size:16 final size:16
Alignment explanation
Indices: 55272--55311 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
55262 GAGAAATATT
55272 AAGTGTTAAAGGGGAG
1 AAGTGTTAAAGGGGAG
55288 AAGTGTTAAAGGGGAG
1 AAGTGTTAAAGGGGAG
55304 AAGTGTTA
1 AAGTGTTA
55312 TAGTAAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.23
Consensus pattern (16 bp):
AAGTGTTAAAGGGGAG
Found at i:55820 original size:17 final size:19
Alignment explanation
Indices: 55792--55840 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
55782 ATTTTTGAAA
55792 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
55810 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
55829 CACCGATGCACT
1 CATCGATGCACT
55841 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Done.