Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005288.1 Hibiscus syriacus cultivar Beakdansim tig00011964_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: 47186
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2486 original size:25 final size:25
Alignment explanation
Indices: 2457--2526 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
2447 TACTGCTAAA
2457 ATAATTTAATATGTTTTAAAAGATAT
1 ATAATTTAATAT-TTTTAAAAGATAT
* * *
2483 -TAATTTATTAAATTTTAAAATATAT
1 ATAATTTAAT-ATTTTTAAAAGATAT
2508 ATAGATTTAATTATTTTTA
1 ATA-ATTTAA-TATTTTTA
2527 TTATTGATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
25 20 0.57
26 3 0.09
27 11 0.31
28 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
ATAATTTAATATTTTTAAAAGATAT
Found at i:7231 original size:15 final size:15
Alignment explanation
Indices: 7211--7241 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7201 TTGTACATAA
7211 AAAATTATTCAATAG
1 AAAATTATTCAATAG
*
7226 AAAATTGTTCAATAG
1 AAAATTATTCAATAG
7241 A
1 A
7242 TGTATGACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (15 bp):
AAAATTATTCAATAG
Found at i:7930 original size:19 final size:19
Alignment explanation
Indices: 7869--7931 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
7859 AAACTTTATT
* *
7869 TATTTATTTAATATAATTTTC
1 TATTTA-TTAATTTAA-TATC
7890 TATTT-TTAATTTAATAAT-
1 TATTTATTAATTTAAT-ATC
7908 TATTTATTAATTTAATATC
1 TATTTATTAATTTAATATC
7927 TATTT
1 TATTT
7932 TAAATTACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 8 0.22
19 24 0.65
21 5 0.14
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTATTAATTTAATATC
Found at i:12306 original size:19 final size:19
Alignment explanation
Indices: 12282--12353 Score: 144
Period size: 19 Copynumber: 3.8 Consensus size: 19
12272 GAATGTATTT
12282 CATGCATCGATGCACATAC
1 CATGCATCGATGCACATAC
12301 CATGCATCGATGCACATAC
1 CATGCATCGATGCACATAC
12320 CATGCATCGATGCACATAC
1 CATGCATCGATGCACATAC
12339 CATGCATCGATGCAC
1 CATGCATCGATGCAC
12354 TGAGGATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.21
Consensus pattern (19 bp):
CATGCATCGATGCACATAC
Found at i:12397 original size:65 final size:63
Alignment explanation
Indices: 12321--12463 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 63
12311 TGCACATACC
* *
12321 ATGCATCGATGCACATACCATGCATCGATGCACT-GAGGAT-TTTATGAAAACATAGAATGCATT
1 ATGCATCGATGCACA-ACCATGCATCAATGCACTCGA-GATATTT-TG-AAACATAGAATGCACT
12384 TG
62 TG
* * * *
12386 ATGCATCGATGCACCAGCCATGCATCAATGCACTCTAGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCA-CAACCATGCATCAATGCACTCGAGATATTTTGAAACATAGAATGCACTTG
12450 ATGCATCGATGCAC
1 ATGCATCGATGCAC
12464 TCTTAGTGCA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
63 1 0.01
64 29 0.42
65 33 0.48
66 6 0.09
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCAATGCACTCGAGATATTTTGAAACATAGAATGCACTTG
Found at i:12463 original size:17 final size:19
Alignment explanation
Indices: 12435--12483 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
12425 TATTTTGAAA
12435 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
12453 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
12472 CACCGATGCACT
1 CATCGATGCACT
12484 AACGGTCCAT
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:14590 original size:20 final size:21
Alignment explanation
Indices: 14565--14620 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
14555 TTGTGCTTCA
14565 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-AG
*
14585 TGCATCGATACATCCTTGAATG
1 TGCATCGATACA-CCTTGAAAG
14607 TGCATCGATACACC
1 TGCATCGATACACC
14621 ATAAAGGTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 12 0.38
21 4 0.12
22 14 0.44
23 2 0.06
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACCTTGAAAG
Found at i:14658 original size:44 final size:42
Alignment explanation
Indices: 14567--14659 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 42
14557 GTGCTTCATG
* *
14567 CATCGATACACCTAACAGTGCATCGATACATCCTTGAATGTG
1 CATCGATACACCTAACAGTGCACCGATACATCCTTGAATGTA
*
14609 CATCGATACACCATAA-AGGTGCACCGATGCA-CGCGTTGAATGTA
1 CATCGATACACC-TAACA-GTGCACCGATACATC-C-TTGAATGTA
14653 CATCGAT
1 CATCGAT
14660 GCACAATGCC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
42 14 0.32
43 15 0.34
44 15 0.34
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (42 bp):
CATCGATACACCTAACAGTGCACCGATACATCCTTGAATGTA
Found at i:17406 original size:65 final size:63
Alignment explanation
Indices: 17316--17475 Score: 171
Period size: 65 Copynumber: 2.5 Consensus size: 63
17306 AATCAAATTG
* * *
17316 AACATCGAGTGCGTTTCATGCATCGATGCACATACCATGCATCGATGCACT-GAGGAT-TTTATG
1 AACATCGAATGCATTTAATGCATCGATGCACAT-CCATGCATCGATGCACTCGA-GATATTT-TG
17379 AA
63 -A
* * * * *
17381 AACATCGAATGCATTTGATGTATCGATGCACCATCTATGCATCGATGCACTCTAGCTATTTTGA
1 AACATCGAATGCATTTAATGCATCGATGCA-CATCCATGCATCGATGCACTCGAGATATTTTGA
* *
17445 AACATCGAATGCACTTAATGGATCGATGCAC
1 AACATCGAATGCATTTAATGCATCGATGCAC
17476 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
63 1 0.01
64 28 0.34
65 46 0.56
66 7 0.09
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTAATGCATCGATGCACATCCATGCATCGATGCACTCGAGATATTTTGA
Found at i:23310 original size:22 final size:21
Alignment explanation
Indices: 23284--23359 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
23274 ACACCTAACA
23284 GTGCATCGATACATCCTTGAAT
1 GTGCATCGATACA-CCTTGAAT
* *
23306 GTGCATCGATACACCATGAAG
1 GTGCATCGATACACCTTGAAT
* *
23327 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGAT--ACACCTTGAAT
* *
23350 ATACATCGAT
1 GTGCATCGAT
23360 GCACAATGGC
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
21 15 0.35
22 13 0.30
23 15 0.35
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (21 bp):
GTGCATCGATACACCTTGAAT
Found at i:23330 original size:21 final size:22
Alignment explanation
Indices: 23284--23336 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
23274 ACACCTAACA
* *
23284 GTGCATCGATACATCCTTGAAT
1 GTGCATCGATACATCCATGAAG
23306 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATACATCCATGAAG
*
23327 GTGCACCGAT
1 GTGCATCGAT
23337 GCACGCCTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (22 bp):
GTGCATCGATACATCCATGAAG
Found at i:26145 original size:17 final size:19
Alignment explanation
Indices: 26117--26165 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
26107 TTTATGAAAA
26117 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
26135 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
26154 CACCGATGCACT
1 CATCGATGCACT
26166 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:26161 original size:65 final size:65
Alignment explanation
Indices: 26050--26171 Score: 158
Period size: 65 Copynumber: 1.9 Consensus size: 65
26040 AATCAAATTG
* * * *
26050 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCATCGATGTACTGAGGGTTTTATGAA
1 AACATCGAATGCACTTCATGCATCGATGCACATACCATGCACCGATGCACTAAGGGTTTTATGAA
* *
26115 AACATCGAATGCACTTGATGCATCGATGCAC-T-CTTAGTGCACCGATGCACTAAGGGT
1 AACATCGAATGCACTTCATGCATCGATGCACATAC-CA-TGCACCGATGCACTAAGGGT
26172 CCAACGGTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
63 1 0.02
64 2 0.04
65 46 0.94
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCACTTCATGCATCGATGCACATACCATGCACCGATGCACTAAGGGTTTTATGAA
Found at i:28075 original size:44 final size:43
Alignment explanation
Indices: 27961--28105 Score: 191
Period size: 44 Copynumber: 3.3 Consensus size: 43
27951 CTTTTACCAT
* *
27961 TTATCCCATAAGCTCATAAGCTTATTTTACCAATATACTTACAA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTAC-A
* *
28005 TTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATATTTATCA
1 -TT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA-CA
* *
28051 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATACACTTGCCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTT-ACA
28095 TTATTCCATAA
1 TTATTCCATAA
28106 CCATATACCA
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
44 48 0.53
45 4 0.04
46 37 0.41
47 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (43 bp):
TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACA
Found at i:28127 original size:20 final size:20
Alignment explanation
Indices: 28102--28144 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
28092 CCATTATTCC
* *
28102 ATAACCATATACCATAGACA
1 ATAACCATACACAATAGACA
28122 ATAACCATACACAATAGACA
1 ATAACCATACACAATAGACA
28142 ATA
1 ATA
28145 GCCCAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.23, G:0.05, T:0.19
Consensus pattern (20 bp):
ATAACCATACACAATAGACA
Found at i:28286 original size:42 final size:39
Alignment explanation
Indices: 28204--28281 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
28194 GAAGTGCTAC
28204 ACATAAGGTCGTACCACCATATACACCGAAGTGTATTAA
1 ACATAAGGTCGTACCACCATATACACCGAAGTGTATTAA
* * *
28243 ACATAAGGTTGTGCTCACCATATATACCGAAGTGTATTA
1 ACATAAGGTCGTAC-CACCATATACACCGAAGTGTATTA
28282 TAAACCTGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 12 0.34
40 23 0.66
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27
Consensus pattern (39 bp):
ACATAAGGTCGTACCACCATATACACCGAAGTGTATTAA
Found at i:33163 original size:89 final size:88
Alignment explanation
Indices: 33012--33281 Score: 404
Period size: 89 Copynumber: 3.1 Consensus size: 88
33002 CAGAACTGTA
* * * *
33012 TCCGTAGGGCTTA-CCTA-GCACATAGCAAAAGGGAGCCAACCTAAGGATATCCTTGGGGCCTAT
1 TCCGTAGGG-TTACCCTATGCACACAGC-AAATGAAACCAACCTAAGGATATCCTTGGGGCCTAT
33075 GGGCCTACCCAAGGGTATCCTTAGG
64 GGGCCTACCCAAGGGTATCCTTAGG
33100 TCCGTAGGGTTACCCTATGCACACAGCAAATGAAACCAACCTAAGGATATACCTTGGGGCCTATG
1 TCCGTAGGGTTACCCTATGCACACAGCAAATGAAACCAACCTAAGGATAT-CCTTGGGGCCTATG
33165 GGCCTACCCAAGGGTATCCTTAGG
65 GGCCTACCCAAGGGTATCCTTAGG
* **
33189 TCCGTAGGGTTACCCTATGCATACAATAAATGAAACCAACCTAAGGATATGCCTTGGGGCCTAT-
1 TCCGTAGGGTTACCCTATGCACACAGCAAATGAAACCAACCTAAGGATAT-CCTTGGGGCCTATG
*
33253 AGCCTACCCAA-GGTATCCTTAGG
65 GGCCTACCCAAGGGTATCCTTAGG
33276 TCCGTA
1 TCCGTA
33282 AGGTCTTACC
Statistics
Matches: 170, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
87 21 0.12
88 43 0.25
89 106 0.62
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (88 bp):
TCCGTAGGGTTACCCTATGCACACAGCAAATGAAACCAACCTAAGGATATCCTTGGGGCCTATGG
GCCTACCCAAGGGTATCCTTAGG
Found at i:42777 original size:15 final size:16
Alignment explanation
Indices: 42757--42802 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
42747 TTTGATATCA
42757 TTTCTTTCCATTTCC-
1 TTTCTTTCCATTTCCT
42772 TTTCTTAT-CATTTCCT
1 TTTCTT-TCCATTTCCT
42788 TCTTCTTTCCATTTC
1 T-TTCTTTCCATTTC
42803 TTATTTCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 13 0.48
16 3 0.11
17 11 0.41
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTCTTTCCATTTCCT
Found at i:43027 original size:11 final size:11
Alignment explanation
Indices: 43005--43038 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
42995 TGCAACAAGC
*
43005 AAAAGAAGAAG
1 AAAAGAAAAAG
*
43016 AAAAGCAAAAG
1 AAAAGAAAAAG
43027 AAAAGAAAAAG
1 AAAAGAAAAAG
43038 A
1 A
43039 CTCTTACTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:43037 original size:17 final size:17
Alignment explanation
Indices: 43001--43035 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
42991 GTGATGCAAC
43001 AAGCAAAAGAAGAAGAA
1 AAGCAAAAGAAGAAGAA
43018 AAGCAAAAGAA-AAGAA
1 AAGCAAAAGAAGAAGAA
43034 AA
1 AA
43036 AGACTCTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.74, C:0.06, G:0.20, T:0.00
Consensus pattern (17 bp):
AAGCAAAAGAAGAAGAA
Found at i:43090 original size:20 final size:20
Alignment explanation
Indices: 43062--43099 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43052 ATTGGAGTGC
*
43062 AAAAGAAAG-AAACGAAAAAG
1 AAAAAAAAGCAAA-GAAAAAG
43082 AAAAAAAAGCAAAGAAAA
1 AAAAAAAAGCAAAGAAAA
43100 GTGAAGCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGCAAAGAAAAAG
Done.