Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004531.1 Hibiscus syriacus cultivar Beakdansim tig00010007_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: 47421
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6185 original size:21 final size:22
Alignment explanation
Indices: 6161--6207 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
6151 TAACTTTTTC
6161 TTTTATATTTCAT-TATTAACTT
1 TTTTATATTTCATCT-TTAACTT
* *
6183 TTTTCTCTTTCATCTTTAACTT
1 TTTTATATTTCATCTTTAACTT
6205 TTT
1 TTT
6208 CTCTCTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATATTTCATCTTTAACTT
Found at i:6212 original size:23 final size:22
Alignment explanation
Indices: 6168--6217 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
6158 TTCTTTTATA
6168 TTTCATTATTAACTTTTTTCTC
1 TTTCATTATTAACTTTTTTCTC
6190 TTTCATCT-TTAAC-TTTTTCTC
1 TTTCAT-TATTAACTTTTTTCTC
*
6211 TCTCATT
1 TTTCATT
6218 TCTTCATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 13 0.50
22 11 0.42
23 1 0.04
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTCATTATTAACTTTTTTCTC
Found at i:13454 original size:19 final size:18
Alignment explanation
Indices: 13420--13467 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 18
13410 TCGAAAAAAT
13420 AGAAAAAAATGAAAAGGAAA
1 AGAAAAAAAT-AAAA-GAAA
13440 CAGAAAAAAAT-AAAGAAA
1 -AGAAAAAAATAAAAGAAA
13458 ATGAAAAAAA
1 A-GAAAAAAA
13468 ATAACAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 1 0.04
18 12 0.46
19 3 0.12
21 10 0.38
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (18 bp):
AGAAAAAAATAAAAGAAA
Found at i:16740 original size:21 final size:21
Alignment explanation
Indices: 16690--16750 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
16680 ATTATCCAAT
* *
16690 AAACATGATATCCATAA-AAC
1 AAACTTGAAATCCATAATAAC
16710 AAACTTGAAATCCATAATAACC
1 AAACTTGAAATCCATAATAA-C
16732 AAA-TTGAAATCCATAATAA
1 AAACTTGAAATCCATAATAA
16751 TAAATCAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 15 0.41
21 18 0.49
22 4 0.11
ACGTcount: A:0.54, C:0.18, G:0.05, T:0.23
Consensus pattern (21 bp):
AAACTTGAAATCCATAATAAC
Found at i:21956 original size:20 final size:20
Alignment explanation
Indices: 21930--21983 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
21920 TAGTATTGTC
* *
21930 CTGTATGAATAGTATCGATG
1 CTGTATGAATAATATCGATA
*
21950 GTGTATGAATAATATCGATA
1 CTGTATGAATAATATCGATA
*
21970 CTGTATGAACAATA
1 CTGTATGAATAATA
21984 ATGAACAGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.33
Consensus pattern (20 bp):
CTGTATGAATAATATCGATA
Found at i:24744 original size:20 final size:20
Alignment explanation
Indices: 24719--24789 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
24709 AAAATGTTTT
24719 TATGAATAGTATTGATATTG
1 TATGAATAGTATTGATATTG
24739 TATGAATAGTATTGATATTG
1 TATGAATAGTATTGATATTG
** *
24759 TATGAATAGTACCGATACTG
1 TATGAATAGTATTGATATTG
*
24779 TGTGAATAGTA
1 TATGAATAGTA
24790 CCGATACTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.39
Consensus pattern (20 bp):
TATGAATAGTATTGATATTG
Found at i:24790 original size:20 final size:20
Alignment explanation
Indices: 24719--24814 Score: 102
Period size: 20 Copynumber: 4.8 Consensus size: 20
24709 AAAATGTTTT
** *
24719 TATGAATAGTATTGATATTG
1 TATGAATAGTACCGATACTG
** *
24739 TATGAATAGTATTGATATTG
1 TATGAATAGTACCGATACTG
24759 TATGAATAGTACCGATACTG
1 TATGAATAGTACCGATACTG
*
24779 TGTGAATAGTACCGATACTG
1 TATGAATAGTACCGATACTG
* * *
24799 TGTGAACAATACCGAT
1 TATGAATAGTACCGAT
24815 GCTCAAAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.35
Consensus pattern (20 bp):
TATGAATAGTACCGATACTG
Found at i:24867 original size:20 final size:20
Alignment explanation
Indices: 24842--24881 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
24832 TACAAAATGG
24842 GTATCGATACCT-CTACAGTA
1 GTATCGATA-CTGCTACAGTA
24862 GTATCGATACTGCTACAGTA
1 GTATCGATACTGCTACAGTA
24882 AAATCAAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (20 bp):
GTATCGATACTGCTACAGTA
Found at i:25267 original size:34 final size:34
Alignment explanation
Indices: 25224--25290 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
25214 TGTAAAATGA
* *
25224 AAGGTTCTAGCTGAGCCCTTGAAAAGCTAGGGAT
1 AAGGTTCTAGCTGAGCCCGTGAAAAACTAGGGAT
* *
25258 AAGGTTCTAGTTTAGCCCGTGAAAAACTAGGGA
1 AAGGTTCTAGCTGAGCCCGTGAAAAACTAGGGA
25291 GTTGTAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.24
Consensus pattern (34 bp):
AAGGTTCTAGCTGAGCCCGTGAAAAACTAGGGAT
Found at i:26478 original size:8 final size:8
Alignment explanation
Indices: 26465--26494 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
26455 GATAAGGCAA
26465 GGAGAGAG
1 GGAGAGAG
26473 GGAGAGAG
1 GGAGAGAG
26481 GGAGAGAG
1 GGAGAGAG
26489 GGAGAG
1 GGAGAG
26495 TCATATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (8 bp):
GGAGAGAG
Found at i:28785 original size:42 final size:42
Alignment explanation
Indices: 28660--28811 Score: 155
Period size: 42 Copynumber: 3.6 Consensus size: 42
28650 CAATCGTGGT
* *
28660 GTTTA-TAATAAAAACGCCACTAAGGTACATGACTATTGCGGC
1 GTTTATTAA-AAAAACGCCACTAAAGTACATGATTATTGCGGC
** *
28702 GTTTATTAAAAAAATACCACTAAATTACATGATTATTGCGGC
1 GTTTATTAAAAAAACGCCACTAAAGTACATGATTATTGCGGC
* * * * *
28744 ATTTATTACAAAAACGCCACTAAAGTACAAGTTTATAGCGGC
1 GTTTATTAAAAAAACGCCACTAAAGTACATGATTATTGCGGC
* * * *
28786 GTTT-GTATAAAAATGTCACTAAAGTA
1 GTTTATTAAAAAAACGCCACTAAAGTA
28812 TGAGTCTATA
Statistics
Matches: 91, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
41 18 0.20
42 70 0.77
43 3 0.03
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (42 bp):
GTTTATTAAAAAAACGCCACTAAAGTACATGATTATTGCGGC
Found at i:28822 original size:41 final size:41
Alignment explanation
Indices: 28753--28933 Score: 146
Period size: 41 Copynumber: 4.4 Consensus size: 41
28743 CATTTATTAC
** *
28753 AAAAACGCCACTAAAGTACAAGTTTATAGCGGCGTTTGTAT
1 AAAAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTAT
* * * * *
28794 AAAAATGTCACTAAAGTATGAGTCTATAGTGGTGTTTATAT
1 AAAAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTAT
* * * * * * *
28835 ACAAACCCCACGAAAGTCTGAGTCTTTAGCGGTGTTTGTAC
1 AAAAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTAT
* * * * * *
28876 ACAAACGCCAATAAAGTAAGAGTCTTTTGCGGCGTTTGATCAA
1 AAAAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTG-T-AT
*
28919 AAAAAGGCCACTAAA
1 AAAAACGCCACTAAA
28934 AAATGCCACT
Statistics
Matches: 109, Mismatches: 29, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
41 95 0.87
42 1 0.01
43 13 0.12
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTAT
Found at i:29354 original size:83 final size:83
Alignment explanation
Indices: 29153--29369 Score: 274
Period size: 85 Copynumber: 2.6 Consensus size: 83
29143 GGTGTGAAGC
* * *
29153 CACTATAGATGAACCCTATTGCGACGTTTGTATAAAAATGCCGCGTAAATACTACTCTATTACGT
1 CACTATAGATGAACCCTATTGCGGCGTTTGTATAAAAATGCTGC-TAAATACTACTCTATTACGG
29218 CGTTTGTTGAAAAAAAATGT
65 CGTTTGTT-AAAAAAAATGT
* * ** * * * *
29238 CATTATATATGAACCCTATTGCGGTTTTTGTATAACAACGCTGCTAAAGTACTACTCTGTTGCGG
1 CACTATAGATGAACCCTATTGCGGCGTTTGTATAAAAATGCTGCTAAA-TACTACTCTATTACGG
*
29303 CGTTTGTT-CAAAAAATGT
65 CGTTTGTTAAAAAAAATGT
* *
29321 CACTATAGATGAATCATATTGCGGCGTTTGTATAAAAATGCTGCTAAAT
1 CACTATAGATGAACCCTATTGCGGCGTTTGTATAAAAATGCTGCTAAAT
29370 TTACCATTTT
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
82 1 0.01
83 49 0.44
84 4 0.04
85 57 0.51
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (83 bp):
CACTATAGATGAACCCTATTGCGGCGTTTGTATAAAAATGCTGCTAAATACTACTCTATTACGGC
GTTTGTTAAAAAAAATGT
Done.