Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008757.1 Hibiscus syriacus cultivar Beakdansim tig00111849_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: 497375
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 3
Found at i:477584 original size:126 final size:126
Alignment explanation
Indices: 477263--477740 Score: 904
Period size: 126 Copynumber: 3.8 Consensus size: 126
477253 TTTAAGTTAT
*
477263 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
477328 GCGTCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
477389 -ACCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
477453 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
477514 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
477579 ACGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
477640 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
477705 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
477741 CCGATTATAG
Statistics
Matches: 343, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
125 121 0.35
126 222 0.65
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:477821 original size:8 final size:8
Alignment explanation
Indices: 477808--477848 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
477798 TCACAATCTT
477808 TCAAATTC
1 TCAAATTC
477816 TCAAATTC
1 TCAAATTC
* *
477824 CCAAACTC
1 TCAAATTC
477832 T-AAATTC
1 TCAAATTC
477839 TCAAATTC
1 TCAAATTC
477847 TC
1 TC
477849 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:480874 original size:12 final size:13
Alignment explanation
Indices: 480841--480878 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
480831 AAATACATAA
480841 ATATATTTAATAT
1 ATATATTTAATAT
*
480854 ATTTATTTAATAT
1 ATATATTTAATAT
480867 A-ATATTTAATAT
1 ATATATTTAATAT
480879 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:480930 original size:23 final size:23
Alignment explanation
Indices: 480891--480949 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
480881 TTAGTTATAA
480891 ATTTTACAT--TATAATCGAAAC
1 ATTTTACATAATATAATCGAAAC
480912 ATTTTACATAATATAATCGAAAC
1 ATTTTACATAATATAATCGAAAC
480935 ATTTTACATAATATA
1 ATTTTACATAATATA
480950 TTATTAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.25
23 27 0.75
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.39
Consensus pattern (23 bp):
ATTTTACATAATATAATCGAAAC
Found at i:482044 original size:13 final size:13
Alignment explanation
Indices: 482023--482082 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
482013 ATTTTGTTAG
482023 TATTTTATTTAAT
1 TATTTTATTTAAT
*
482036 TATTGTA-TT-AT
1 TATTTTATTTAAT
* *
482047 TTTATTTAATT-AT
1 TAT-TTTATTTAAT
482060 TATTTTATTTAAT
1 TATTTTATTTAAT
482073 TATTTTATTT
1 TATTTTATTT
482083 TTTTGCAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 4 0.10
12 11 0.28
13 24 0.62
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:482048 original size:21 final size:21
Alignment explanation
Indices: 482023--482069 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
482013 ATTTTGTTAG
*
482023 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATTATAT
*
482044 TATTTTATTTAATTATTATTT
1 TATTTTATTTAATTATTATAT
482065 TATTT
1 TATTT
482070 AATTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TATTTTATTTAATTATTATAT
Found at i:482060 original size:16 final size:16
Alignment explanation
Indices: 482041--482076 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
482031 TTAATTATTG
482041 TATTATTTTATTTAAT
1 TATTATTTTATTTAAT
482057 TATTATTTTATTTAAT
1 TATTATTTTATTTAAT
482073 TATT
1 TATT
482077 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTATTTTATTTAAT
Found at i:482080 original size:21 final size:21
Alignment explanation
Indices: 482023--482086 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
482013 ATTTTGTTAG
*
482023 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATTTTAT
482044 TATTTTATTT-A--A--TTAT
1 TATTTTATTTAATTATTTTAT
482060 TATTTTATTTAATTATTTTAT
1 TATTTTATTTAATTATTTTAT
*
482081 TTTTTT
1 TATTTT
482087 GCAGTTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
16 13 0.36
17 1 0.03
18 1 0.03
19 1 0.03
20 1 0.03
21 19 0.53
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
TATTTTATTTAATTATTTTAT
Found at i:482400 original size:12 final size:13
Alignment explanation
Indices: 482336--482405 Score: 54
Period size: 13 Copynumber: 5.4 Consensus size: 13
482326 ATAACTGCAA
*
482336 AAAATAAAATAAT
1 AAAATAATATAAT
* *
482349 TAAATAAAATAAT
1 AAAATAATATAAT
*
482362 AAGAAATAAAATAAT
1 -A-AAATAATATAAT
482377 AAAATAAT-TAAT
1 AAAATAATATAAT
*
482389 ACAA-AATATAAT
1 AAAATAATATAAT
*
482401 TAAAT
1 AAAAT
482406 TTATAGAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
11 3 0.06
12 13 0.28
13 18 0.38
14 1 0.02
15 12 0.26
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (13 bp):
AAAATAATATAAT
Found at i:493016 original size:18 final size:19
Alignment explanation
Indices: 492993--493028 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
492983 AAAGTTCAAT
492993 TTTAAAGA-AATTTAAAAA
1 TTTAAAGATAATTTAAAAA
*
493011 TTTAAAGATTATTTAAAA
1 TTTAAAGATAATTTAAAA
493029 TGTGTCGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (19 bp):
TTTAAAGATAATTTAAAAA
Found at i:495728 original size:21 final size:22
Alignment explanation
Indices: 495703--495749 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
495693 TATTTTTTAA
495703 ATAATTAATTGC-ATATAAATT
1 ATAATTAATTGCAATATAAATT
* *
495724 ATAA-TATTTTCAATATAAATT
1 ATAATTAATTGCAATATAAATT
495745 ATAAT
1 ATAAT
495750 ATTTGATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (22 bp):
ATAATTAATTGCAATATAAATT
Done.