Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000988.1 Hibiscus syriacus cultivar Beakdansim tig00001978_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: 32698
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:549 original size:60 final size:59
Alignment explanation
Indices: 423--540 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 59
413 AAATTATGTT
* * *
423 TCTCATTCTAAATTGATCTCTAAACTTTTGAATATTCAAATTTCATCCCTAAACTATGAC
1 TCTCATTCTAAATTGATCTCTAAACTTTTAAACATTCAAA-TTCATCCCCAAACTATGAC
*
483 TCTCATTCTAAATTGGTCTCTAAACTTTTAAACATTCCAAA-TCACTCCCCAAACTATG
1 TCTCATTCTAAATTGATCTCTAAACTTTTAAACATT-CAAATTCA-TCCCCAAACTATG
541 GTCCTCATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
59 3 0.06
60 45 0.87
61 4 0.08
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (59 bp):
TCTCATTCTAAATTGATCTCTAAACTTTTAAACATTCAAATTCATCCCCAAACTATGAC
Found at i:4357 original size:421 final size:421
Alignment explanation
Indices: 3571--4413 Score: 1542
Period size: 421 Copynumber: 2.0 Consensus size: 421
3561 GACTATATAC
*
3571 ATGATCATAACAAGAATTCAAGAAAGAAAACGCTTCTTAAAGATAAGAGATAAAGAAGACATGTT
1 ATGATCATAACAAGAATTCAAGAAAGAAAACGCTTCTTAAAGATAAGAGATAAAGAAGACATGAT
* *
3636 GACAAAAGATGATCAGAGTGTTCTCCAGAAGATGCAAGCCTGAAATATAAAGTTCTCACGCTGAT
66 GACAAAAGATGATCAGAGTGTTCTCCAGAAGATGCAAGCCTAAAATATAAAGTTCTCACGCTGAC
*
3701 ATTGGGGCAAGCTTTATTCCAGAATGGTCAAGTGAAGGAAGATCAAGTTCTCTAACCTTTAAAGT
131 ATTGGGGCAAGCTTTATTCCAGAATGGTCAAGTGAAGGAAGATCAAGTTCTATAACCTTTAAAGT
*
3766 CAGAAGAAGATTAATGATCGACATTTTTGCATATAAGAACATCATGCGATGAATTTAATTGCATT
196 CAGAAGAAGATTAATGATCGACATTTTTGCATATAAGAACATCATGCAATGAATTTAATTGCATT
* *
3831 CATATTTTCATACATAGATGTACAATTCTTATAGCTCTTCTAAGAAAAGAAGAGAAAGAAAAGAA
261 CATATTTTCATACATAGATATACAATTCTTATAGATCTTCTAAGAAAAGAAGAGAAAGAAAAGAA
*
3896 AATTAGAATTCATGCTTCAAATGGAGGGAAATACATTTAGAGTGGTAGAACTTTAAGAATTGAGG
326 AATTAGAATTCATGCTTCAAATGGAGGGAAATACATTTAGAGTGGTAGAACTTTAAGAATCGAGG
3961 AGCCCAAACCACATAACAATCATTACTTTAA
391 AGCCCAAACCACATAACAATCATTACTTTAA
3992 ATGATCATAACAAGAATTCAAGAAAGAAAACGCTTCTTAAAGATAAGAGATAAAGAAGACATGAT
1 ATGATCATAACAAGAATTCAAGAAAGAAAACGCTTCTTAAAGATAAGAGATAAAGAAGACATGAT
* * * *
4057 GACAAAAGATGATCAGAGTGTTCTCCTGAAGATGCAAGCCTAAAATATCAAGTTGTCATGCTGAC
66 GACAAAAGATGATCAGAGTGTTCTCCAGAAGATGCAAGCCTAAAATATAAAGTTCTCACGCTGAC
4122 ATTGGGGCAAGCTTTATTCCAGAATGGTCAAGTGAAGGAAGATCAAGTTCTATAACCTTTAAAGT
131 ATTGGGGCAAGCTTTATTCCAGAATGGTCAAGTGAAGGAAGATCAAGTTCTATAACCTTTAAAGT
*
4187 CAGAAGAAGATTAATGATCGACATTTTTGCATATAAGAACATCATGCAATGCATTTAATTGCATT
196 CAGAAGAAGATTAATGATCGACATTTTTGCATATAAGAACATCATGCAATGAATTTAATTGCATT
* *
4252 CATATTTTCATACATAGATATACAATTCTTATATATCTTCTAAGAAAAGAAGAGAAAGAAAAGCA
261 CATATTTTCATACATAGATATACAATTCTTATAGATCTTCTAAGAAAAGAAGAGAAAGAAAAGAA
*
4317 AATTAGAATTCATGCTTCAAATGGAGGGAAATATATTTAGAGTGGTAGAACTTTAAGAATCGAGG
326 AATTAGAATTCATGCTTCAAATGGAGGGAAATACATTTAGAGTGGTAGAACTTTAAGAATCGAGG
4382 AGCCCAAACCACATAACAATCATTACTTTAA
391 AGCCCAAACCACATAACAATCATTACTTTAA
4413 A
1 A
4414 GCGGGGCATG
Statistics
Matches: 406, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
421 406 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (421 bp):
ATGATCATAACAAGAATTCAAGAAAGAAAACGCTTCTTAAAGATAAGAGATAAAGAAGACATGAT
GACAAAAGATGATCAGAGTGTTCTCCAGAAGATGCAAGCCTAAAATATAAAGTTCTCACGCTGAC
ATTGGGGCAAGCTTTATTCCAGAATGGTCAAGTGAAGGAAGATCAAGTTCTATAACCTTTAAAGT
CAGAAGAAGATTAATGATCGACATTTTTGCATATAAGAACATCATGCAATGAATTTAATTGCATT
CATATTTTCATACATAGATATACAATTCTTATAGATCTTCTAAGAAAAGAAGAGAAAGAAAAGAA
AATTAGAATTCATGCTTCAAATGGAGGGAAATACATTTAGAGTGGTAGAACTTTAAGAATCGAGG
AGCCCAAACCACATAACAATCATTACTTTAA
Found at i:5121 original size:71 final size:68
Alignment explanation
Indices: 4996--5129 Score: 171
Period size: 71 Copynumber: 1.9 Consensus size: 68
4986 CATTTCACTA
* * *
4996 AGATTTTATCTAACTTGAGATTATTTTTCTTAAAAAGATATCTCATTTGAGATTATTTTTCTTTA
1 AGATTTCATCTAACTAGAGATTATTTTTCTTAAAAAGATATCTCATTTGAGATTATTGTTCTTTA
5061 AAT
66 AAT
* * *
5064 AGATTTCATCTAACTAGATATT-TTTTTCTTAAAACATATTTTATCTCATTTGTGATTATTGTTC
1 AGATTTCATCTAACTAGAGATTATTTTTCTTAAAA-AGA---TATCTCATTTGAGATTATTGTTC
5128 TT
62 TT
5130 AAAACAAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
67 12 0.21
68 21 0.38
71 23 0.41
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.51
Consensus pattern (68 bp):
AGATTTCATCTAACTAGAGATTATTTTTCTTAAAAAGATATCTCATTTGAGATTATTGTTCTTTA
AAT
Found at i:7705 original size:18 final size:18
Alignment explanation
Indices: 7682--7724 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
7672 TAGGATTATT
*
7682 TTTAGGTGTTTTATTTCC
1 TTTAGGTATTTTATTTCC
*
7700 TTTAGGTATTTTATTTTC
1 TTTAGGTATTTTATTTCC
7718 TTTAGGT
1 TTTAGGT
7725 TATCTCAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.07, G:0.16, T:0.63
Consensus pattern (18 bp):
TTTAGGTATTTTATTTCC
Found at i:7854 original size:19 final size:22
Alignment explanation
Indices: 7816--7860 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
7806 CTTATAAAGG
*
7816 TTATTTTCTTCTTCATCTTTGT
1 TTATTTTCTTCTTCATCTTTCT
7838 TTATTTTCTTC-T-A-CTTTCT
1 TTATTTTCTTCTTCATCTTTCT
7857 TTAT
1 TTAT
7861 AAGGTAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 1 0.05
21 1 0.05
22 11 0.50
ACGTcount: A:0.11, C:0.18, G:0.02, T:0.69
Consensus pattern (22 bp):
TTATTTTCTTCTTCATCTTTCT
Found at i:10779 original size:18 final size:18
Alignment explanation
Indices: 10756--10799 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
10746 CCTTCCGTCC
10756 GATCTTATTATTTAATTT
1 GATCTTATTATTTAATTT
10774 GATCTTATTATTTAATTT
1 GATCTTATTATTTAATTT
10792 GATCTTAT
1 GATCTTAT
10800 CACTTACTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (18 bp):
GATCTTATTATTTAATTT
Found at i:14596 original size:27 final size:25
Alignment explanation
Indices: 14547--14626 Score: 76
Period size: 25 Copynumber: 3.1 Consensus size: 25
14537 ATTATATATA
14547 TATATATTAACTTA--AAAAGTATTT
1 TATATATTAACTTATTAAAA-TATTT
*
14571 GTTTATATTAACTTATTAAATATATTT
1 -TATATATTAACTTATTAAA-ATATTT
14598 TAT-TATTAACTTAATTTAAAAATATTT
1 TATATATTAACTT-A-TT-AAAATATTT
14625 TA
1 TA
14627 ATTTTATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
25 22 0.47
26 3 0.06
27 18 0.38
28 4 0.09
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (25 bp):
TATATATTAACTTATTAAAATATTT
Found at i:19479 original size:42 final size:41
Alignment explanation
Indices: 19433--19580 Score: 135
Period size: 41 Copynumber: 3.6 Consensus size: 41
19423 TAAACAATAA
*
19433 CGGCGTTTATAGTAAAAACGCCGCAATATAGTAG-ACATTTAG
1 CGGCGTTTATAGTAAAAACGCCGCAATATAGT-GTA-ATATAG
19475 CGGCGTTT-TAGCT-AAAACGCCGCAATATAGTGTAATATAG
1 CGGCGTTTATAG-TAAAAACGCCGCAATATAGTGTAATATAG
* * * * * * * *
19515 CGACGTTTATTGTATAAACGTCGCAAAAAACATGTGATATAG
1 CGGCGTTTATAGTAAAAACGCCGCAATATA-GTGTAATATAG
*
19557 TGGCGTTT-T-GTAAAAACGCCGCAA
1 CGGCGTTTATAGTAAAAACGCCGCAA
19581 AATGTTAAAT
Statistics
Matches: 88, Mismatches: 13, Indels: 12
0.78 0.12 0.11
Matches are distributed among these distances:
40 27 0.31
41 37 0.42
42 24 0.27
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (41 bp):
CGGCGTTTATAGTAAAAACGCCGCAATATAGTGTAATATAG
Found at i:20614 original size:57 final size:57
Alignment explanation
Indices: 20547--20734 Score: 367
Period size: 57 Copynumber: 3.3 Consensus size: 57
20537 GTGAAGACTG
*
20547 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTTTTAAGTAGT
1 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
20604 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
1 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
20661 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
1 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
20718 TTTATGCATAAGTACTT
1 TTTATGCATAAGTACTT
20735 CTGTTTTAAT
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
57 130 1.00
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (57 bp):
TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
Found at i:21018 original size:41 final size:41
Alignment explanation
Indices: 20969--21085 Score: 119
Period size: 41 Copynumber: 2.9 Consensus size: 41
20959 CGGCGTTTTT
* * * * *
20969 AAACGCCGCAAAATATTTGTATTTTAGTGGCGTTTGTATGA
1 AAACGCCGCAAAAGACTTCTACTTTAGTGGCGTTTGTATAA
* * *
21010 ACACGCCGCTATAGACTTCTACTTTAGTGGCGTTTGTATAA
1 AAACGCCGCAAAAGACTTCTACTTTAGTGGCGTTTGTATAA
* * *
21051 AAACGCCACTATAGAC-TCGTACTTTAGTGGCGTTT
1 AAACGCCGCAAAAGACTTC-TACTTTAGTGGCGTTT
21086 TCGTAGAAAC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 2 0.03
41 63 0.97
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (41 bp):
AAACGCCGCAAAAGACTTCTACTTTAGTGGCGTTTGTATAA
Found at i:21096 original size:41 final size:40
Alignment explanation
Indices: 20991--21098 Score: 130
Period size: 41 Copynumber: 2.6 Consensus size: 40
20981 ATATTTGTAT
*
20991 TTTAGTGGCG-TTTGTATGAACACGCCGCTATAGACTTCTAC
1 TTTAGTGGCGTTTTGTA-GAA-ACGCCACTATAGACTTCTAC
* *
21032 TTTAGTGGCGTTTGTATAAAAACGCCACTATAGAC-TCGTAC
1 TTTAGTGGCGTTT-TGTAGAAACGCCACTATAGACTTC-TAC
21073 TTTAGTGGCGTTTTCGTAGAAACGCC
1 TTTAGTGGCGTTTT-GTAGAAACGCC
21099 GTAAAGTATT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
40 3 0.05
41 48 0.83
42 4 0.07
43 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (40 bp):
TTTAGTGGCGTTTTGTAGAAACGCCACTATAGACTTCTAC
Found at i:22081 original size:46 final size:46
Alignment explanation
Indices: 22011--22101 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
22001 CTAAGGTACT
*
22011 TACTTGCCTTCGTTCCTCTTTCTTGTTTGACCATGTAGTTATTTCG
1 TACTTGCCTTCGTTCCTCTGTCTTGTTTGACCATGTAGTTATTTCG
22057 TACTTGCCTTCGTTCCTCTGTCTTGTTTGACCATGTAGTTATTTC
1 TACTTGCCTTCGTTCCTCTGTCTTGTTTGACCATGTAGTTATTTC
22102 AGAATCGCTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.11, C:0.24, G:0.15, T:0.49
Consensus pattern (46 bp):
TACTTGCCTTCGTTCCTCTGTCTTGTTTGACCATGTAGTTATTTCG
Found at i:29301 original size:21 final size:21
Alignment explanation
Indices: 29283--29338 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
29273 ATGAAGCAAG
29283 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
29304 GGAAGCAGCCAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
29325 GGAAGCAGAGAGAG
1 GGAAGCAGAGAGAG
29339 AAACAGTGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.20, G:0.43, T:0.00
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:29359 original size:21 final size:21
Alignment explanation
Indices: 29314--29406 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
29304 GGAAGCAGCC
* * * *
29314 AGAGCAGCAGCGGAAGCAGAG
1 AGAGAAGCAGCGGCAGCACAA
* *
29335 AGAGAAACAGTGGCAGCACAA
1 AGAGAAGCAGCGGCAGCACAA
*
29356 AGAGAGGCAGCGGCAGCACAA
1 AGAGAAGCAGCGGCAGCACAA
*
29377 AGAGAGGCAGCGGCAGCACAA
1 AGAGAAGCAGCGGCAGCACAA
29398 AGAGAAGCA
1 AGAGAAGCA
29407 ACATATCAGC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.42, C:0.20, G:0.37, T:0.01
Consensus pattern (21 bp):
AGAGAAGCAGCGGCAGCACAA
Found at i:29872 original size:43 final size:43
Alignment explanation
Indices: 29802--29906 Score: 106
Period size: 43 Copynumber: 2.4 Consensus size: 43
29792 CGCCAAATCA
* * * *
29802 AACACATATTGCGGCG-TTTAAGCTAAAAATGCCGCGAAACCTT
1 AACACATATTGCGGCGTTTTAA-CTAAAAACGCCACGAAACATC
* *
29845 AACACTTATTGCGGCGTTTGTAA-TAAAAACGCCACTAAACATC
1 AACACATATTGCGGCGTTT-TAACTAAAAACGCCACGAAACATC
* *
29888 AACACCTACTGCGGCGTTT
1 AACACATATTGCGGCGTTT
29907 CTGGGAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
43 47 0.90
44 2 0.04
45 3 0.06
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (43 bp):
AACACATATTGCGGCGTTTTAACTAAAAACGCCACGAAACATC
Found at i:29962 original size:129 final size:129
Alignment explanation
Indices: 29828--30078 Score: 281
Period size: 129 Copynumber: 1.9 Consensus size: 129
29818 TTTAAGCTAA
* *
29828 AAATGCCGCGAAACCTTAACA-CTTATTGCGGCGTTTGTAATAAAAACGCCACTAAACATCAACA
1 AAATGCCGCGAAACATCAACATC-TATTGCGGCGTTTGTAATAAAAACGCCACTAAACATCAACA
*
29892 CCTACTGCGGCGTTTCTGGGAAAAACGCCGCTAAAAATCGAA-ACCTACTGCGGCGTTTGTCTTC
65 CCTACTGCGGCGTTTCTCGGAAAAACGCCGCTAAAAATC-AACACCTACTGCGGCGTTTGTCTTC
29956 C
129 C
* * * ** ** * * *
29957 AAATGCCGCTAAATATCAATATCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATCAACAT
1 AAATGCCGCGAAACATCAACATCTATTGCGGCGTTTGTAATAAAAACGCCACTAAACATCAACAC
* * * * ** * *
30022 CTATTGTGGCGTTTGTCTGTCAAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
66 CTACTGCGGCGTTTCTCGGAAAAACGCCGCTAAAAATCAACACCTACTGCGGCGTTT
30079 TTTCATGAAA
Statistics
Matches: 99, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
128 2 0.02
129 96 0.97
130 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (129 bp):
AAATGCCGCGAAACATCAACATCTATTGCGGCGTTTGTAATAAAAACGCCACTAAACATCAACAC
CTACTGCGGCGTTTCTCGGAAAAACGCCGCTAAAAATCAACACCTACTGCGGCGTTTGTCTTCC
Found at i:29965 original size:43 final size:43
Alignment explanation
Indices: 29845--30078 Score: 247
Period size: 43 Copynumber: 5.4 Consensus size: 43
29835 GCGAAACCTT
* ** ** * *
29845 AACACTTATTGCGGCGTTTGTAATAAAAACGCCACTAAACATC
1 AACACCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATC
* * ***** *
29888 AACACCTACTGCGGCGTTTCTGGGAAAAACGCCGCTAAAAATC
1 AACACCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATC
* *
29931 GAA-ACCTACTGCGGCGTTTGTCTTCCAAATGCCGCTAAATATC
1 -AACACCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATC
* *
29974 AATATCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATC
1 AACACCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATC
* *
30017 AACATCTATTGTGGCGTTTGTCTGT-CAAACGCCGCTAAATATC
1 AACACCTATTGCGGCGTTTGTCT-TCCAAACGCCGCTAAATATC
30060 AACACCTATTGCGGCGTTT
1 AACACCTATTGCGGCGTTT
30079 TTTCATGAAA
Statistics
Matches: 165, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
42 2 0.01
43 160 0.97
44 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (43 bp):
AACACCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATC
Done.