Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000389.1 Hibiscus syriacus cultivar Beakdansim tig00000715_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: 2672246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 15
Found at i:2665350 original size:17 final size:16
Alignment explanation
Indices: 2665319--2665356 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
2665309 TGTCATGCAC
2665319 TTTTAATAAATATAT-
1 TTTTAATAAATATATA
2665334 TTTTAATATAATAATATA
1 TTTTAATA-AAT-ATATA
2665352 TTTTA
1 TTTTA
2665357 CTTTATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 3 0.15
17 4 0.20
18 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTAATAAATATATA
Found at i:2666134 original size:14 final size:15
Alignment explanation
Indices: 2666115--2666152 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
2666105 TTGACTCTAC
2666115 ATTTAAAA-AAAAAT
1 ATTTAAAATAAAAAT
2666129 ATTTAACAATAAAAAT
1 ATTTAA-AATAAAAAT
2666145 -TTTAAAAT
1 ATTTAAAAT
2666153 TTATTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.41
15 7 0.32
16 6 0.27
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
ATTTAAAATAAAAAT
Found at i:2666563 original size:23 final size:23
Alignment explanation
Indices: 2666537--2666584 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2666527 TATAAAGTAC
*
2666537 ATAACATACTAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
** *
2666560 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
2666583 AT
1 AT
2666585 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:2667352 original size:23 final size:23
Alignment explanation
Indices: 2667326--2667388 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2667316 ATATAACCAC
2667326 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2667349 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2667372 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2667389 GTTTGCCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2667848 original size:38 final size:38
Alignment explanation
Indices: 2667780--2667864 Score: 136
Period size: 38 Copynumber: 2.2 Consensus size: 38
2667770 TCAAGTTGTA
* *
2667780 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAG-CTTG
2667819 GATTTTGATTTCC-TTTGCTTGGCACCATATGAGCTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTG
2667856 GATTTTGAT
1 GATTTTGAT
2667865 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 12 0.27
38 19 0.43
39 13 0.30
ACGTcount: A:0.18, C:0.14, G:0.21, T:0.47
Consensus pattern (38 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTG
Found at i:2668140 original size:18 final size:18
Alignment explanation
Indices: 2668117--2668153 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2668107 GCCGAAATAT
2668117 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2668135 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2668153 A
1 A
2668154 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2668801 original size:23 final size:23
Alignment explanation
Indices: 2668775--2668835 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
2668765 ATATAACCAC
2668775 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
2668798 TACC--TTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
2668819 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2668836 GTTTACCTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 18 0.56
23 14 0.44
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2672047 original size:178 final size:180
Alignment explanation
Indices: 2671601--2672246 Score: 1053
Period size: 177 Copynumber: 3.6 Consensus size: 180
2671591 AATTACCGAC
*
2671601 ACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTA
1 ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACC-ACACAATATTA
2671666 AAAAGTGTCGATATAGGTTGTAGACCTATT--CGCATAAAACCGGTATATTTATA-CGGTTATAT
65 AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATAT
2671728 TACAAA-ATCTATTTACATTATAAATATGGGTTCCGATGTGTAAATGTCGAT
130 TACAAATATCTA-TTACATTATAAATATGGGTTCCGATGTGTAAATGTCGAT
2671779 ACTTTTTTAAATCGTATCGACACA-TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTA
1 ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACC-ACACAATATTA
* *
2671843 TAAAGTGTCGAGATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTTTAT
65 AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGG--TTAT
*
2671908 ATTACAACATATCTATTACATTATAAATCTGGGTTCCGATGTGT-AATGTCGAT
128 ATTACAA-ATATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTCGAT
*
2671961 AC-TTTTTAAATCGTATCGACACATTTTT-TTTCAATATGGAC-TAAAGTACC-CACAATATTAA
1 ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCACACAATATTAA
*
2672022 AAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGATATATTTATACCGGTTATATT
66 AAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATT
* * *
2672087 ATAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGAC
131 A-CAAA-TATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTCGAT
2672139 ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTA
1 ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACC-ACACAATATTA
2672204 AAAAGTGTCGATATAGGTTGTAGACCTATTCG-GCATAAAACCG
65 AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCG
Statistics
Matches: 439, Mismatches: 13, Indels: 28
0.91 0.03 0.06
Matches are distributed among these distances:
176 9 0.02
177 103 0.23
178 99 0.23
179 49 0.11
180 24 0.05
181 42 0.10
182 37 0.08
183 71 0.16
184 5 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (180 bp):
ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCACACAATATTAA
AAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATT
ACAAATATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTCGAT
Done.