Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006127.1 Hibiscus syriacus cultivar Beakdansim tig00014529_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: 52339
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:4404 original size:13 final size:15
Alignment explanation
Indices: 4386--4422 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
4376 GATCCTAACT
4386 TATCAC-TAAT-ACA
1 TATCACATAATCACA
4399 TATCACATAATCACA
1 TATCACATAATCACA
4414 TATCACATA
1 TATCACATA
4423 TACCATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 6 0.27
14 4 0.18
15 12 0.55
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (15 bp):
TATCACATAATCACA
Found at i:4613 original size:18 final size:18
Alignment explanation
Indices: 4590--4631 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4580 TTGTCTCGTA
*
4590 GACCACTATATCCCGAAG
1 GACCACTATATCACGAAG
* *
4608 GACCACTTTGTCACGAAG
1 GACCACTATATCACGAAG
4626 GACCAC
1 GACCAC
4632 GTAGACCCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
GACCACTATATCACGAAG
Found at i:10011 original size:21 final size:22
Alignment explanation
Indices: 9986--10039 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
9976 ATTGATTTCC
9986 CAAATTGGT-CATTT-AATATTT
1 CAAATTGGTCCATTTAAAT-TTT
10007 CAAATT-GTCCATTTAAATTTT
1 CAAATTGGTCCATTTAAATTTT
*
10028 CGAATTGG-CCAT
1 CAAATTGGTCCAT
10040 GCATTATAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 2 0.07
21 23 0.79
22 4 0.14
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (22 bp):
CAAATTGGTCCATTTAAATTTT
Found at i:15491 original size:15 final size:15
Alignment explanation
Indices: 15473--15514 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
15463 TTTTAGTGAC
*
15473 ATGATCTCTAATGAA
1 ATGATGTCTAATGAA
*
15488 ATGAAGTCTAATGAA
1 ATGATGTCTAATGAA
15503 ATGATGTCTAAT
1 ATGATGTCTAAT
15515 TTCAATGTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (15 bp):
ATGATGTCTAATGAA
Found at i:22367 original size:23 final size:23
Alignment explanation
Indices: 22341--22402 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 23
22331 GATAATTTAA
22341 AAATAATATTATTTTAAATAAA-T
1 AAATAATATTATTTTAAA-AAAGT
*
22364 AAATAATATGA-TTTAAAAAAGT
1 AAATAATATTATTTTAAAAAAGT
22386 AAATAA-A-TATTTTAAAA
1 AAATAATATTATTTTAAAA
22403 TATTTTCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.31
22 13 0.37
23 10 0.29
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (23 bp):
AAATAATATTATTTTAAAAAAGT
Found at i:24465 original size:22 final size:22
Alignment explanation
Indices: 24414--24457 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
24404 CTCAGATACC
* *
24414 ATATCGGAGAATTACTATACTT
1 ATATAGGAGAATTACTATAATT
24436 ATATAGGAGAATTACTATAATT
1 ATATAGGAGAATTACTATAATT
24458 TTTTAGGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
ATATAGGAGAATTACTATAATT
Found at i:25502 original size:36 final size:36
Alignment explanation
Indices: 25446--25543 Score: 133
Period size: 36 Copynumber: 2.7 Consensus size: 36
25436 CTTCCGTTAG
* * *
25446 TTTTTGTTGATGTGGCAGTTAACCCTCCACTAATAT
1 TTTTTGATGACGTGGAAGTTAACCCTCCACTAATAT
*
25482 TTTTTGATGACGTGGAAGTTAACCCTCTACTAATAT
1 TTTTTGATGACGTGGAAGTTAACCCTCCACTAATAT
* * *
25518 TTTTTGCTAACGTAGAAGTTAACCCT
1 TTTTTGATGACGTGGAAGTTAACCCT
25544 TCTTCTTCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (36 bp):
TTTTTGATGACGTGGAAGTTAACCCTCCACTAATAT
Found at i:25550 original size:3 final size:3
Alignment explanation
Indices: 25542--25577 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
25532 GAAGTTAACC
25542 CTT CTT CTT CTT CATT -TT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT
25578 GCTATTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:27280 original size:21 final size:22
Alignment explanation
Indices: 27255--27311 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
27245 TTCTCTTTTT
27255 TTATTTTTTATATAAA-ATATA
1 TTATTTTTTATATAAATATATA
* *
27276 TTATTTTATATGTGTAAATATATA
1 TTATTTT-T-TATATAAATATATA
27300 TGTATTTTTTAT
1 T-TATTTTTTAT
27312 TATTTATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 7 0.24
22 1 0.03
23 8 0.28
24 7 0.24
25 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TTATTTTTTATATAAATATATA
Found at i:27478 original size:17 final size:17
Alignment explanation
Indices: 27446--27496 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
27436 TATATATTGC
27446 CTTTATATTTATTTTAATT
1 CTTTAT-TTTA-TTTAATT
27465 CTTTATTTTATTT-ATT
1 CTTTATTTTATTTAATT
* *
27481 ATTATTTTTTATTTAA
1 CTT-TATTTTATTTAA
27497 GATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 5 0.18
17 12 0.43
18 5 0.18
19 6 0.21
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (17 bp):
CTTTATTTTATTTAATT
Found at i:27479 original size:22 final size:22
Alignment explanation
Indices: 27398--27530 Score: 71
Period size: 22 Copynumber: 5.8 Consensus size: 22
27388 CTACCTTTTT
*
27398 TTTATTTTACTTCTATTTTTATTC
1 TTTATTTTA-TT-TATTATTATTC
*
27422 TTTATTCTTACTT-TTATATATTGCC
1 TTTATT-TTATTTATTAT-TATT--C
27447 TTTA---TATTTATT-TTAATTC
1 TTTATTTTATTTATTATT-ATTC
*
27466 TTTATTTTATTTATTATTATTT
1 TTTATTTTATTTATTATTATTC
* *
27488 TTTATTTAAGATATATATATTATT-
1 TTTATTT--TATTTAT-TATTATTC
*
27512 ATTATTTTATTATATTATT
1 TTTATTTTATT-TATTATT
27531 TCATCGTATT
Statistics
Matches: 86, Mismatches: 9, Indels: 30
0.69 0.07 0.24
Matches are distributed among these distances:
19 5 0.06
20 1 0.01
21 8 0.09
22 29 0.34
23 10 0.12
24 18 0.21
25 15 0.17
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTATTTTATTTATTATTATTC
Found at i:27647 original size:2 final size:2
Alignment explanation
Indices: 27640--27668 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27630 TTATTTCATT
27640 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
27669 CTTATTCATT
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:37853 original size:13 final size:12
Alignment explanation
Indices: 37830--37877 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
37820 CTAAATTGAA
37830 AAAATAGAAAAAG
1 AAAA-AGAAAAAG
37843 AACAAAG-AAAAG
1 AA-AAAGAAAAAG
37855 AAAAAGAGAAAAG
1 AAAAAGA-AAAAG
*
37868 AAAAGGAAAA
1 AAAAAGAAAA
37878 TAAGATGGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 4 0.13
12 10 0.32
13 15 0.48
14 2 0.06
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:37858 original size:18 final size:18
Alignment explanation
Indices: 37835--37877 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
37825 TTGAAAAAAT
37835 AGAAAAAGA-ACAAAGAAA
1 AGAAAAAGAGA-AAAGAAA
37853 AGAAAAAGAGAAAAGAAA
1 AGAAAAAGAGAAAAGAAA
*
37871 AGGAAAA
1 AGAAAAA
37878 TAAGATGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (18 bp):
AGAAAAAGAGAAAAGAAA
Found at i:37859 original size:6 final size:6
Alignment explanation
Indices: 37830--37877 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
37820 CTAAATTGAA
*
37830 AAAATAG AAAAAG AACAAAG -AAAAG AAAAAG AGAAAAG AAAAGG AAAA
1 AAAA-AG AAAAAG AA-AAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAA
37878 TAAGATGGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
5 4 0.11
6 19 0.51
7 14 0.38
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:38873 original size:43 final size:43
Alignment explanation
Indices: 38808--38923 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
38798 CGAATGAGCC
* *
38808 ATCCACGATTTCATCTCCACGATGGAGGATATCGTACCCATAA
1 ATCCACAATTTCAACTCCACGATGGAGGATATCGTACCCATAA
* * * *
38851 ATCCACAATTTTAACTCTACGATGGAGGATATTGTGCCCAT--
1 ATCCACAATTTCAACTCCACGATGGAGGATATCGTACCCATAA
* * * *
38892 ATCCACGATTTCAACTTCACGACGAAGGATAT
1 ATCCACAATTTCAACTCCACGATGGAGGATAT
38924 TGTGCCAACT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 26 0.43
43 35 0.57
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (43 bp):
ATCCACAATTTCAACTCCACGATGGAGGATATCGTACCCATAA
Found at i:39740 original size:21 final size:20
Alignment explanation
Indices: 39711--39761 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
39701 ATTTTTTATA
* * *
39711 ATATGTATTATATGATATAC
1 ATATATATTATATAATAAAC
39731 ATACTATATTATATAATAAAC
1 ATA-TATATTATATAATAAAC
*
39752 GTATATATTA
1 ATATATATTA
39762 ATTTTCTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (20 bp):
ATATATATTATATAATAAAC
Found at i:41150 original size:19 final size:18
Alignment explanation
Indices: 41128--41177 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
41118 TATATATTGC
41128 CTTTATATTTATTTTAATT
1 CTTTAT-TTTATTTTAATT
*
41147 CTTTATTTTATTCTTTATT
1 CTTTATTTTATT-TTAATT
41166 CTTT-TTTTATTT
1 CTTTATTTTATTT
41178 AAGATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 1 0.03
18 13 0.45
19 15 0.52
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (18 bp):
CTTTATTTTATTTTAATT
Found at i:41161 original size:12 final size:12
Alignment explanation
Indices: 41135--41177 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
41125 TGCCTTTATA
41135 TTTATTTTAATTC
1 TTTATTTT-ATTC
41148 TTTATTTTATTC
1 TTTATTTTATTC
41160 TTTATTCTT-TT-
1 TTTATT-TTATTC
41171 TTTATTT
1 TTTATTT
41178 AAGATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.03
11 6 0.21
12 12 0.41
13 10 0.34
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTTTATTC
Found at i:51910 original size:19 final size:19
Alignment explanation
Indices: 51886--51927 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
51876 TGTTGTAACA
51886 GTAGCATTCAAACTATCTG
1 GTAGCATTCAAACTATCTG
*
51905 GTAGCATTCCAACTATCTG
1 GTAGCATTCAAACTATCTG
51924 GTAG
1 GTAG
51928 AGATGATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (19 bp):
GTAGCATTCAAACTATCTG
Done.