Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004039.1 Hibiscus syriacus cultivar Beakdansim tig00008823_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: 60414
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2808 original size:16 final size:17
Alignment explanation
Indices: 2787--2828 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2777 AGAATTTATT
2787 AAATATTATG-TACAAA
1 AAATATTATGTTACAAA
* *
2803 AAATATTATGTTTCAAT
1 AAATATTATGTTACAAA
2820 AAATATTAT
1 AAATATTAT
2829 TTTATTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (17 bp):
AAATATTATGTTACAAA
Found at i:13857 original size:31 final size:31
Alignment explanation
Indices: 13818--13909 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 31
13808 AATTAAAAAA
13818 ATTTTGATCCTTAAACTTCAGATAAAATATT
1 ATTTTGATCCTTAAACTTCAGATAAAATATT
*
13849 TTTTTGATCCTTAAACTTCAGATAAAATATT
1 ATTTTGATCCTTAAACTTCAGATAAAATATT
* * * * *
13880 AATTTAATTCTTAAATTTTAGATAAAATAT
1 ATTTTGATCCTTAAACTTCAGATAAAATAT
13910 CAAATGAATC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (31 bp):
ATTTTGATCCTTAAACTTCAGATAAAATATT
Found at i:13924 original size:21 final size:21
Alignment explanation
Indices: 13900--13939 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13890 TTAAATTTTA
* *
13900 GATAAAATATCAAATGAATCT
1 GATAAAAAATAAAATGAATCT
13921 GATAAAAAATAAAATGAAT
1 GATAAAAAATAAAATGAAT
13940 TAAAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.05, G:0.10, T:0.25
Consensus pattern (21 bp):
GATAAAAAATAAAATGAATCT
Found at i:24556 original size:17 final size:17
Alignment explanation
Indices: 24519--24556 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
24509 TAATTTTTAA
24519 AAATATTAAAAAAAATT
1 AAATATTAAAAAAAATT
24536 -AATATTAAAAAAAATT
1 AAATATTAAAAAAAATT
24552 AAATA
1 AAATA
24557 ATACAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATATTAAAAAAAATT
Found at i:24564 original size:17 final size:16
Alignment explanation
Indices: 24520--24564 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
24510 AATTTTTAAA
*
24520 AATATTAAAAAAAATT
1 AATAATAAAAAAAATT
*
24536 AATATTAAAAAAAATT
1 AATAATAAAAAAAATT
24552 AAATAATACAAAA
1 -AATAATA-AAAA
24565 TAATATAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 16 0.62
17 6 0.23
18 4 0.15
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAATAAAAAAAATT
Found at i:27046 original size:29 final size:29
Alignment explanation
Indices: 27004--27074 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
26994 CCCTATTGGT
27004 GTATTGGGCCAAATAATTTACCCACTTTA
1 GTATTGGGCCAAATAATTTACCCACTTTA
27033 GTATTGGGCCAAATAATTTACCCACTTTA
1 GTATTGGGCCAAATAATTTACCCACTTTA
27062 GTATTGGGCCAAA
1 GTATTGGGCCAAA
27075 ACCCCCGAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (29 bp):
GTATTGGGCCAAATAATTTACCCACTTTA
Found at i:29955 original size:17 final size:19
Alignment explanation
Indices: 29933--29967 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
29923 GCTTTTGTTC
29933 AGTTTG-AGAGGG-AATCT
1 AGTTTGAAGAGGGCAATCT
29950 AGTTTGAAGAGGGCAATC
1 AGTTTGAAGAGGGCAATC
29968 GAGATGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTTTGAAGAGGGCAATCT
Found at i:44237 original size:23 final size:22
Alignment explanation
Indices: 44209--44268 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
44199 GTACTCAACG
44209 TATAATTATAAATTAGTTAAAAA
1 TATAATTATAAATTA-TTAAAAA
* *
44232 TATAATTGTAAATTATTTAAAA
1 TATAATTATAAATTATTAAAAA
*
44254 TA-AAATATAAATTAT
1 TATAATTATAAATTAT
44269 ATTATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.33
22 8 0.24
23 14 0.42
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (22 bp):
TATAATTATAAATTATTAAAAA
Found at i:44397 original size:21 final size:21
Alignment explanation
Indices: 44381--44420 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44371 TTGCCATTGT
*
44381 CTCTTTCACCGTCGCCACTGC
1 CTCTGTCACCGTCGCCACTGC
*
44402 CTCTGTCACCGTCACCACT
1 CTCTGTCACCGTCGCCACT
44421 ATCTCTACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.47, G:0.12, T:0.28
Consensus pattern (21 bp):
CTCTGTCACCGTCGCCACTGC
Found at i:44426 original size:21 final size:21
Alignment explanation
Indices: 44380--44426 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
44370 GTTGCCATTG
* * *
44380 TCTCTTTCACCGTCGCCACTG
1 TCTCTGTCACCGTCACCACTA
*
44401 CCTCTGTCACCGTCACCACTA
1 TCTCTGTCACCGTCACCACTA
44422 TCTCT
1 TCTCT
44427 ACCACCGTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.45, G:0.11, T:0.32
Consensus pattern (21 bp):
TCTCTGTCACCGTCACCACTA
Found at i:46470 original size:15 final size:15
Alignment explanation
Indices: 46450--46483 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
46440 TTTAGCTGGG
46450 CGGGCGGATGCGGGA
1 CGGGCGGATGCGGGA
*
46465 CGGGCGGATGCGGGG
1 CGGGCGGATGCGGGA
46480 CGGG
1 CGGG
46484 TAATGTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.21, G:0.65, T:0.06
Consensus pattern (15 bp):
CGGGCGGATGCGGGA
Found at i:46711 original size:2 final size:2
Alignment explanation
Indices: 46704--46739 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
46694 TAAAATGATA
46704 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
46740 TCTGTTGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.