Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003146.1 Hibiscus syriacus cultivar Beakdansim tig00006618_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: 66618
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:13620 original size:2 final size:2
Alignment explanation
Indices: 13613--13641 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13603 GTCCGTGCTT
13613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13642 TTGGTTGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16900 original size:6 final size:6
Alignment explanation
Indices: 16891--16920 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
16881 GAGAGTTATA
16891 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
16921 CCATCATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:20254 original size:183 final size:182
Alignment explanation
Indices: 19869--20254 Score: 634
Period size: 183 Copynumber: 2.1 Consensus size: 182
19859 ATTAATTTTT
*
19869 AAATATTAAATATATTATATATAACATATGGCTCAACCCAAATCATTTAAAACCCAATTAATAAT
1 AAATATTAAATATATTATATATAACATATGGCTCAACCCAAACCATTTAAAACCCAATTAATAAT
*
19934 TTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTTACATAAATTTTTT
66 TTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTTACATAAAATTTTT
* *
19999 ATTTTATAATTATATATTATTTAAATTATTTGTAAACTGTTTTTAAATTAAA
131 ATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTAAATTAAA
*
20051 AAATATTAAATATATTATATATAATATATGGGCT-AAGCCCAAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATAT-GGCTCAA-CCCAAACCATTTAAAACCCAATTAATA
20115 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATC-TAAAAT
64 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATT-AAAAATTTA-CATAAAAT
* *
20179 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
127 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTAAATTAAA
* *
20235 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
20255 AATTAGAAAA
Statistics
Matches: 191, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
182 30 0.16
183 84 0.44
184 76 0.40
185 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (182 bp):
AAATATTAAATATATTATATATAACATATGGCTCAACCCAAACCATTTAAAACCCAATTAATAAT
TTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTTACATAAAATTTTT
ATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTAAATTAAA
Found at i:23168 original size:39 final size:39
Alignment explanation
Indices: 23123--23223 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
23113 TTGAACGGGT
23123 GTACTAGAATGAAACAAAAACTATAATGCTTAACAACGG
1 GTACTAGAATGAAACAAAAACTATAATGCTTAACAACGG
**
23162 GTACTAGAATGAAACAAAAACTATAATTTTTAACAACGG
1 GTACTAGAATGAAACAAAAACTATAATGCTTAACAACGG
* *
23201 GTATTATAATGAAACAAAAACTA
1 GTACTAGAATGAAACAAAAACTA
23224 AACTTTAGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (39 bp):
GTACTAGAATGAAACAAAAACTATAATGCTTAACAACGG
Found at i:25610 original size:36 final size:37
Alignment explanation
Indices: 25551--25622 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 37
25541 ATAATTTTTA
* *
25551 TTTTAAAATAAATATTGATTTATTATATTGT-GTACC
1 TTTTAAAATAAATACTGACTTATTATATTGTAGTACC
*
25587 TTTTAAAATAATTACTGACTTATTATATTGTAGTAC
1 TTTTAAAATAAATACTGACTTATTATATTGTAGTAC
25623 ACAATATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 28 0.88
37 4 0.12
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (37 bp):
TTTTAAAATAAATACTGACTTATTATATTGTAGTACC
Found at i:34891 original size:19 final size:18
Alignment explanation
Indices: 34862--34898 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
34852 CTATATGGTT
34862 ATGTATTTGTAATGAGTG
1 ATGTATTTGTAATGAGTG
*
34880 ATGTAGTTTGTAATTAGTG
1 ATGTA-TTTGTAATGAGTG
34899 CTTTTGTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (18 bp):
ATGTATTTGTAATGAGTG
Found at i:37790 original size:13 final size:14
Alignment explanation
Indices: 37772--37803 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
37762 TATTGTTTAG
37772 AGGTTATGGG-TTA
1 AGGTTATGGGCTTA
37785 AGGTTATGGGCTTA
1 AGGTTATGGGCTTA
37799 AGGTT
1 AGGTT
37804 TTAAGTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.22, C:0.03, G:0.38, T:0.38
Consensus pattern (14 bp):
AGGTTATGGGCTTA
Found at i:39523 original size:2 final size:2
Alignment explanation
Indices: 39512--39543 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
39502 CTTCCTTCGG
39512 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39544 CACAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50198 original size:42 final size:42
Alignment explanation
Indices: 50163--50250 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
50153 ATTTGGTTTG
*
50163 GGTCATTTCAGGTCTAGATTATATTC-GATTTAATTTTATTCA
1 GGTCATTTCAGGTCTAGATTATATTCAG-TTTAATTTGATTCA
* * *
50205 GGTCATTTCATGTCTAGATTATATTCAGTTTAATTTTATTCG
1 GGTCATTTCAGGTCTAGATTATATTCAGTTTAATTTGATTCA
50247 GGTC
1 GGTC
50251 TGGTTTGGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 42 0.98
43 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (42 bp):
GGTCATTTCAGGTCTAGATTATATTCAGTTTAATTTGATTCA
Found at i:50945 original size:28 final size:28
Alignment explanation
Indices: 50914--50970 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
50904 ATAAGAAGAT
* *
50914 ATGAATCAAGTGATATCGGTCATAAAAG
1 ATGAATCAAGTGACATCGGTAATAAAAG
*
50942 ATGAATCAAGTGACATCTGTAATAAAAG
1 ATGAATCAAGTGACATCGGTAATAAAAG
50970 A
1 A
50971 GTCGTGGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.25
Consensus pattern (28 bp):
ATGAATCAAGTGACATCGGTAATAAAAG
Found at i:54888 original size:32 final size:32
Alignment explanation
Indices: 54788--54888 Score: 109
Period size: 32 Copynumber: 3.2 Consensus size: 32
54778 AAACAGTTGT
*
54788 TTTTCGGTTCG-GATCAATATCAGATCGATTGA
1 TTTTCGGGTCGAG-TCAATATCAGATCGATTGA
* * * *
54820 TTTT-GGGTCGAGTTAATACCAGACCAATTAGA
1 TTTTCGGGTCGAGTCAATATCAGATCGATT-GA
*
54852 -TTTCGGGTCGAGTCAATATTAGATCGATTGA
1 TTTTCGGGTCGAGTCAATATCAGATCGATTGA
54883 TTTTCG
1 TTTTCG
54889 ATTTGAGTCA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
31 23 0.42
32 32 0.58
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (32 bp):
TTTTCGGGTCGAGTCAATATCAGATCGATTGA
Found at i:55754 original size:31 final size:29
Alignment explanation
Indices: 55719--55790 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 29
55709 AAATTATGCG
55719 TTTAGTACCTAAACTATCA-TATCTGGTCTGT
1 TTTAGTACCTAAACTATCAGT-T-T-GTCTGT
* *
55750 TTTAGTACATAAACTATCAGTTTGTTTGT
1 TTTAGTACCTAAACTATCAGTTTGTCTGT
55779 TTTAGTACCTAA
1 TTTAGTACCTAA
55791 GTTTTTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 16 0.43
30 1 0.03
31 19 0.51
32 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (29 bp):
TTTAGTACCTAAACTATCAGTTTGTCTGT
Found at i:60567 original size:36 final size:35
Alignment explanation
Indices: 60507--60586 Score: 117
Period size: 36 Copynumber: 2.3 Consensus size: 35
60497 TGACAATCAA
*
60507 TTTTGAAAAATATTTTTTCAAAGTTTGGTAAATGTT
1 TTTTGAAAAATAGTTTTTCAAAGTTTGGTAAA-GTT
60543 TCTTTGAAAAAT-GTTTTTCAAAGTTTGGTAAAGTT
1 T-TTTGAAAAATAGTTTTTCAAAGTTTGGTAAAGTT
*
60578 TGTTGAAAA
1 TTTTGAAAA
60587 TAGGAATGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
34 7 0.17
35 4 0.10
36 20 0.49
37 10 0.24
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (35 bp):
TTTTGAAAAATAGTTTTTCAAAGTTTGGTAAAGTT
Done.