Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001550.1 Hibiscus syriacus cultivar Beakdansim tig00003052_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: 52882
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3797 original size:20 final size:21
Alignment explanation
Indices: 3772--3831 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
3762 TTTTGGTGCA
3772 GAGGGAATCGATACCCCC-AT
1 GAGGGAATCGATACCCCCTAT
* * *
3792 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATACCCCCTAT
3813 GAAGGGGAATCGATACCCC
1 G-A-GGGAATCGATACCCC
3832 TGGGGTTCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 16 0.50
21 2 0.06
22 1 0.03
23 13 0.41
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.17
Consensus pattern (21 bp):
GAGGGAATCGATACCCCCTAT
Found at i:7929 original size:17 final size:19
Alignment explanation
Indices: 7902--7950 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
7892 TATTTTGAAA
7902 CATCGAATGCACT-TGA-TG
1 CATC-AATGCACTCTGAGTG
*
7920 CATCAATGCACTCTTAGTG
1 CATCAATGCACTCTGAGTG
*
7939 CACCAATGCACT
1 CATCAATGCACT
7951 AAGGGTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 8 0.30
18 6 0.22
19 13 0.48
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (19 bp):
CATCAATGCACTCTGAGTG
Found at i:12204 original size:49 final size:48
Alignment explanation
Indices: 12016--12205 Score: 258
Period size: 49 Copynumber: 3.9 Consensus size: 48
12006 TACCATGAGT
* *
12016 GGCACCTTTTATACCGAAAATGCACCGTTATGCATTTGAA--TTCATTATT
1 GGCACCTTTTATGCC-AAAATGCACCGTTATGCATTT-AACTTTCATTA-C
* *
12065 GGCATCTTTTATGCCAAAATACACCGTTATGCATTTAACTTTCATTAC
1 GGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATTAC
* *
12113 TGGCACCTTTAATGCCAAAATGCACGGTTATGCATTTAACTTTCATTAC
1 -GGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATTAC
*
12162 GAGCACCTTTTATGCCAAAATGCACCGTTATGCATGTAACTTTC
1 G-GCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTC
12206 TTTATTCATT
Statistics
Matches: 126, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
47 2 0.02
48 21 0.17
49 103 0.82
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (48 bp):
GGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATTAC
Found at i:30492 original size:20 final size:20
Alignment explanation
Indices: 30467--30508 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
30457 GAAAGTCTCA
30467 TTACTTTTCTTTTCCATATT
1 TTACTTTTCTTTTCCATATT
30487 TTACTTTTCTTTTCCATATT
1 TTACTTTTCTTTTCCATATT
30507 TT
1 TT
30509 GAAGAGTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (20 bp):
TTACTTTTCTTTTCCATATT
Found at i:43448 original size:8 final size:8
Alignment explanation
Indices: 43435--43477 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
43425 TTTGTTTTGT
43435 TTTTAATA
1 TTTTAATA
43443 TTTTAATA
1 TTTTAATA
43451 TATTTAATAA
1 T-TTTAAT-A
*
43461 TTATAATA
1 TTTTAATA
43469 TTATTAATA
1 TT-TTAATA
43478 ATAATGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 12 0.40
9 16 0.53
10 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTTAATA
Found at i:43469 original size:18 final size:17
Alignment explanation
Indices: 43435--43479 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
43425 TTTGTTTTGT
*
43435 TTTTAAT-ATTTTAATA
1 TTTTAATAATTATAATA
43451 TATTTAATAATTATAATA
1 T-TTTAATAATTATAATA
43469 TTATTAATAAT
1 TT-TTAATAAT
43480 AATGAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 7 0.28
18 17 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAATAATTATAATA
Found at i:43706 original size:14 final size:16
Alignment explanation
Indices: 43687--43723 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
43677 CATTATGGAT
43687 ATCCAT-CAATCA-AC
1 ATCCATACAATCACAC
43701 ATCCATACAATCACAC
1 ATCCATACAATCACAC
*
43717 ATGCATA
1 ATCCATA
43724 AAACGGTGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 6 0.30
15 6 0.30
16 8 0.40
ACGTcount: A:0.43, C:0.32, G:0.03, T:0.22
Consensus pattern (16 bp):
ATCCATACAATCACAC
Done.