Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005622.1 Hibiscus syriacus cultivar Beakdansim tig00013084_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: 40427
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1871 original size:57 final size:59
Alignment explanation
Indices: 1737--1888 Score: 182
Period size: 57 Copynumber: 2.6 Consensus size: 59
1727 CAGGCTGCAC
* * * * *
1737 ATTCGGGATTGCACTAAAGTGTAACTAGTGCATATGTTAGGCACAACCTTATGTGTCAT
1 ATTCGGGACTACACTAAAGTATAACTAGTGCATATGTGAGGCACAACCTTATGTGCCAT
* * * *
1796 ATTCGGGATTGCACTAAAGTATAACT-GTGCATATG-GGGGCACAACTTTATGTGCCAT
1 ATTCGGGACTACACTAAAGTATAACTAGTGCATATGTGAGGCACAACCTTATGTGCCAT
* *
1853 ATTCTGGACTACAGTAAAGTATAACTAGTGTCATAT
1 ATTCGGGACTACACTAAAGTATAACTAGTG-CATAT
1889 TCGGGACTAC
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
57 40 0.49
58 12 0.15
59 30 0.37
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (59 bp):
ATTCGGGACTACACTAAAGTATAACTAGTGCATATGTGAGGCACAACCTTATGTGCCAT
Found at i:1896 original size:34 final size:32
Alignment explanation
Indices: 1850--1920 Score: 115
Period size: 34 Copynumber: 2.2 Consensus size: 32
1840 CTTTATGTGC
*
1850 CATATTCTGGACTACAGTAAAGTATAACTAGTG
1 CATATTCGGGACTACAGTAAAGTATAACTA-TG
1883 TCATATTCGGGACTACAGTAAAGTATAACTATG
1 -CATATTCGGGACTACAGTAAAGTATAACTATG
1916 CATAT
1 CATAT
1921 GGTTGGAACG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 5 0.14
33 2 0.06
34 29 0.81
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (32 bp):
CATATTCGGGACTACAGTAAAGTATAACTATG
Found at i:2777 original size:17 final size:18
Alignment explanation
Indices: 2744--2777 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2734 CAAGAAACTC
2744 ATACTTTTATATATTATA
1 ATACTTTTATATATTATA
2762 ATACTTTTAT-TATTAT
1 ATACTTTTATATATTAT
2778 CTACAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
ATACTTTTATATATTATA
Found at i:2785 original size:21 final size:18
Alignment explanation
Indices: 2744--2790 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
2734 CAAGAAACTC
*
2744 ATACTTTTATATATTATA
1 ATACTTTTATATATTACA
2762 ATACTTTTATTATTATCTACA
1 ATACTTTTA-TA-TAT-TACA
2783 ATA-TTTTA
1 ATACTTTTA
2791 AATTGTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 9 0.36
19 2 0.08
20 8 0.32
21 6 0.24
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (18 bp):
ATACTTTTATATATTACA
Found at i:4883 original size:13 final size:12
Alignment explanation
Indices: 4856--4893 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
4846 AATTTAATTC
4856 TTAATTCTT--T
1 TTAATTCTTAAT
4866 TTAATTCTTTAAT
1 TTAATTC-TTAAT
4879 TTAATTCTTAAT
1 TTAATTCTTAAT
4891 TTA
1 TTA
4894 GATAATAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 8 0.32
13 8 0.32
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (12 bp):
TTAATTCTTAAT
Found at i:4910 original size:26 final size:28
Alignment explanation
Indices: 4878--4931 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
4868 AATTCTTTAA
4878 TTTAA-TTC-TTAATTTAGATAATAAAG
1 TTTAATTTCATTAATTTAGATAATAAAG
4904 TTTAATTTTCATTTAATTTAGATAATAA
1 TTTAA-TTTCA-TTAATTTAGATAATAA
4932 TTTGTGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 5 0.21
28 3 0.12
30 16 0.67
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (28 bp):
TTTAATTTCATTAATTTAGATAATAAAG
Found at i:5149 original size:6 final size:6
Alignment explanation
Indices: 5140--5999 Score: 771
Period size: 6 Copynumber: 143.7 Consensus size: 6
5130 GATCTCCGGA
* *
5140 AGAAGA AGAAGA AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
5188 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
*
5236 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAATG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * *
5284 AGAATG AGAATG AGAATG AGAATG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
*
5332 AGAAGG AGAAGG AGAAGG AGAATG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * *
5380 AGAAGG AGAAGG AGAAGG AGCAGC AGAAGG AGCAGC AGAAGG AGCAGA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * * *
5428 AGGAGC AGAAGG AGAAGA AGAGAGA AGAA-G AGAAGA AGGAGA AGAAGG
1 AGAAGG AGAAGG AGAAGG AGA-AGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * *
5476 AGAA-G AGGAGA AGAAGC AGAA-- ACAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * *
5521 AGAAGG AGAAGG A-AAGA AGGAGA AGAAGG AGAAGA AGGAGA AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * * * * *
5568 AGAAGA AGGAGG AGAAGG AGGAGA AGGAGG AGAAGC AGGAGA AGGAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * *
5616 AGAAGG AGGAGA AGGAGG AGAAGG AGGAGA AGGAGG AGAA-G AGAGAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGA-AGG
* * * *
5664 AGAAAGG AGAAAAGG AGGA-G AAAAGG AGAAGG AGGAGAGG AGGAGA AGAAGG
1 AG-AAGG AG--AAGG AGAAGG AGAAGG AGAAGG A-GA-AGG AGAAGG AGAAGG
* * *
5716 AGAAGAG AAGAAGG A-AAGAA AGAAGG AGAAGG AGAA-G AGGAGA AGAAGAG
1 AGAAG-G -AGAAGG AGAAG-G AGAAGG AGAAGG AGAAGG AGAAGG AGAAG-G
* * * * * * *
5766 AGAAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
*
5814 AGGAGG AGAAGG AGAAGG AGAA-G -G-AGG AGAAGG AGAAGG AG-A--
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * * *
5856 AGAAGG AAAAGG AGAAGA AGAAGA AGGAGA AGAAGA AGAAGG AGAAGA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * *
5904 AGAAGA AGGAGA AGAAGA AGAAGG AGAAGAG AAGAAGG AAGAAGG AGAAGA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAG-G -AGAAGG -AGAAGG AGAAGG
* * * * * *
5955 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAA-G AGAAGA AGAA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAA
6000 AGAAGAACCC
Statistics
Matches: 737, Mismatches: 89, Indels: 56
0.84 0.10 0.06
Matches are distributed among these distances:
3 3 0.00
4 6 0.01
5 33 0.04
6 637 0.86
7 36 0.05
8 22 0.03
ACGTcount: A:0.52, C:0.01, G:0.46, T:0.01
Consensus pattern (6 bp):
AGAAGG
Found at i:6002 original size:15 final size:14
Alignment explanation
Indices: 5138--6006 Score: 261
Period size: 15 Copynumber: 60.4 Consensus size: 14
5128 ATGATCTCCG
5138 GAAGAAGAAGAAGAA
1 GAAGAAGAAG-AGAA
*
5153 GAAGGAGAAG-G-A
1 GAAGAAGAAGAGAA
*
5165 GAAGGAGAAGGAGAA
1 GAAGAAGAA-GAGAA
* * *
5180 GGAGAAGGAGAAGGA
1 GAAGAAGAAG-AGAA
*
5195 GAAGGAGAAGGAGAA
1 GAAGAAGAA-GAGAA
* * *
5210 GGAGAAGGAGAAGGA
1 GAAGAAGAAG-AGAA
*
5225 GAAGGAGAAGGAGAA
1 GAAGAAGAA-GAGAA
* * *
5240 GGAGAAGGAGAAGGA
1 GAAGAAGAAG-AGAA
*
5255 GAAGGAGAAGGAGAA
1 GAAGAAGAA-GAGAA
* *
5270 GGAGAAGGAGA-ATGA
1 GAAGAAGAAGAGA--A
5285 GAATG-AGAATGAGAA
1 GAA-GAAGAA-GAGAA
*
5300 TG-AGAATG-AGAAGGA
1 -GAAGAA-GAAG-AGAA
*
5315 GAAGGAGAAGGAGAA
1 GAAGAAGAA-GAGAA
* * *
5330 GGAGAAGGAGAAGGA
1 GAAGAAGAAG-AGAA
*
5345 GAAGGAGAATGAGAA
1 GAAGAAGAA-GAGAA
*
5360 GGAGAAG--GAGAA
1 GAAGAAGAAGAGAA
*
5372 GGAGAAG--GAGAA
1 GAAGAAGAAGAGAA
* * *
5384 GGAGAAGGAGAAGGA
1 GAAGAAGAAG-AGAA
* * *
5399 GCAGCAGAAGGAGCA
1 GAAGAAGAA-GAGAA
* *
5414 GCAGAAGGAGCAGAA
1 GAAGAAGAAG-AGAA
* *
5429 GGAGCAGAAG-G-A
1 GAAGAAGAAGAGAA
5441 GAAGAAG-AGAGAA
1 GAAGAAGAAGAGAA
5454 GAAGAGAAGAAGGAGAA
1 G-A-AGAAGAA-GAGAA
* *
5471 GAAGGAGAAGAGGA
1 GAAGAAGAAGAGAA
*
5485 GAAGAAGCAGA-AA
1 GAAGAAGAAGAGAA
* *
5498 CAAGGAGAAG-G-A
1 GAAGAAGAAGAGAA
*
5510 GAAGGAGAAGGAGAA
1 GAAGAAGAA-GAGAA
*
5525 GGAGAAGGAA-AGAA
1 GAAGAA-GAAGAGAA
*
5539 GGAGAAGAAGGAGAA
1 GAAGAAGAA-GAGAA
* *
5554 GAAGGAGAAGAAGGA
1 GAAGAAGAAG-AGAA
*
5569 GAAGAAGGAGGAGAA
1 GAAGAA-GAAGAGAA
* *
5584 GGAGGAGAAG-G-A
1 GAAGAAGAAGAGAA
* *
5596 GGAGAAGCAGGAGAA
1 GAAGAAG-AAGAGAA
* *
5611 GGAGGAGAAG-G-A
1 GAAGAAGAAGAGAA
* *
5623 GGAGAAGGAGGAGAA
1 GAAGAA-GAAGAGAA
* * *
5638 GGAGGAGAAGGAGGA
1 GAAGAAGAA-GAGAA
*
5653 GAAGAGAGAGGAGAAA
1 GAAGA-AGAAGAG-AA
* *
5669 GGAGAA-AAGGAGGA
1 GAAGAAGAA-GAGAA
* *
5683 GAA-AAGGAGAAGGA
1 GAAGAAGAAG-AGAA
* * *
5697 GGAGAGGAGGAGAA
1 GAAGAAGAAGAGAA
*
5711 GAAGGAGAAGAGAA
1 GAAGAAGAAGAGAA
*
5725 GAAGGA-AAGA-AA
1 GAAGAAGAAGAGAA
*
5737 GAAGGAGAAGGAGAA
1 GAAGAAGAA-GAGAA
5752 GAGGAGAAGAAGAG-A
1 GA--AGAAGAAGAGAA
* * *
5767 GAAGGAGGAGGAGGAG
1 GAA-GAAGAAGA-GAA
* * * *
5783 GAGGAGGAGGAGGAG
1 GAAGAAGAAGA-GAA
* * * *
5798 GAGGAGGAGGAGGA
1 GAAGAAGAAGAGAA
* * * *
5812 GGAGGAGGAGAAGGA
1 GAAGAAGAAG-AGAA
* *
5827 GAAGGAGAAGGAGGA
1 GAAGAAGAA-GAGAA
*
5842 GAAGGAGAAGGAGAA
1 GAAGAAGAA-GAGAA
5857 GAAGGAA-AAGGAGAA
1 GAA-GAAGAA-GAGAA
5872 GAAGAAGAAGGAGAA
1 GAAGAAGAA-GAGAA
5887 GAAGAAGAAGGAGAA
1 GAAGAAGAA-GAGAA
5902 GAAGAAGAAGGAGAA
1 GAAGAAGAA-GAGAA
5917 GAAGAAGAAGGAGAA
1 GAAGAAGAA-GAGAA
5932 G-AGAAGAAG-GAA
1 GAAGAAGAAGAGAA
*
5944 GAAGGAGAAGAAGAA
1 GAAGAAGAAG-AGAA
5959 GAAGAAGAAGAAGAA
1 GAAGAAGAAG-AGAA
5974 GAAGAAGAAGAAGAA
1 GAAGAAGAAG-AGAA
5989 G-AGAAGAAGA-AA
1 GAAGAAGAAGAGAA
6001 GAAGAA
1 GAAGAA
6007 CCCAAACACT
Statistics
Matches: 660, Mismatches: 122, Indels: 146
0.71 0.13 0.16
Matches are distributed among these distances:
11 2 0.00
12 78 0.12
13 48 0.07
14 109 0.17
15 375 0.57
16 35 0.05
17 13 0.02
ACGTcount: A:0.52, C:0.01, G:0.46, T:0.01
Consensus pattern (14 bp):
GAAGAAGAAGAGAA
Found at i:7201 original size:14 final size:14
Alignment explanation
Indices: 7182--7212 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
7172 TTTTTATATT
7182 ATTTACAAAAAGAA
1 ATTTACAAAAAGAA
7196 ATTTACAAAAAGAA
1 ATTTACAAAAAGAA
7210 ATT
1 ATT
7213 GAAGGTAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (14 bp):
ATTTACAAAAAGAA
Found at i:11847 original size:2 final size:2
Alignment explanation
Indices: 11840--11884 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
11830 TCAATCTACA
11840 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11882 AT A
1 AT A
11885 ATACAATACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17806 original size:21 final size:21
Alignment explanation
Indices: 17780--17821 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17770 TTAAACCTTC
17780 CAACAACAT-TTTTTAGTGATT
1 CAACAACATGTTTTTA-TGATT
*
17801 CAACAACTTGTTTTTATGATT
1 CAACAACATGTTTTTATGATT
17822 TGAGTAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (21 bp):
CAACAACATGTTTTTATGATT
Found at i:28621 original size:45 final size:45
Alignment explanation
Indices: 28350--28609 Score: 396
Period size: 45 Copynumber: 5.8 Consensus size: 45
28340 TAAAAATAAT
* *
28350 AAATGCATATGGGTGCATTATCGGTATGAAAAGATGCCATAATTG
1 AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAATTG
28395 AAATGCATATGGGTGCATTATCGGCATGAAA-GATGCCATAATTG
1 AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAATTG
* * *
28439 AAATGGATATGGGTGCATTATTGGCATGAAAGGATACCATAATTG
1 AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAATTG
* *
28484 AAATTCATATGGATGCATTATCGGCATGAAAGGATGCCATAATTG
1 AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAATTG
* *
28529 AAATGCATATGGGTGCGTTATCGGCATTAAAGGATGCCATAATTG
1 AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAATTG
* ** *
28574 AAATACATATGGGTGCATTATATGCATGAATGGATG
1 AAATGCATATGGGTGCATTATCGGCATGAAAGGATG
28610 TTATTAATGA
Statistics
Matches: 195, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
44 42 0.22
45 153 0.78
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.29
Consensus pattern (45 bp):
AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAATTG
Found at i:35833 original size:21 final size:21
Alignment explanation
Indices: 35794--35833 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35784 CAATGGGATT
* *
35794 AGGATTAGGAATTGGATTTTG
1 AGGATTAGGAAGTGAATTTTG
*
35815 AGGATTTGGAAGTGAATTT
1 AGGATTAGGAAGTGAATTT
35834 GGTTGACGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.38
Consensus pattern (21 bp):
AGGATTAGGAAGTGAATTTTG
Done.