Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006704.1 Hibiscus syriacus cultivar Beakdansim tig00016697_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: 43596
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:617 original size:16 final size:17
Alignment explanation
Indices: 591--622 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
581 GGCAACATCT
591 TTTTCTTTCTTTTCTTG
1 TTTTCTTTCTTTTCTTG
608 TTTT-TTTCTTTTCTT
1 TTTTCTTTCTTTTCTT
623 CTTGTTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTTCTTTCTTTTCTTG
Found at i:624 original size:19 final size:20
Alignment explanation
Indices: 590--628 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
580 AGGCAACATC
*
590 TTTTTCTTTCTTTTCTTGTT
1 TTTTTCTTTCTCTTCTTGTT
610 TTTTTCTTT-TCTTCTTGTT
1 TTTTTCTTTCTCTTCTTGTT
629 CTTGTTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTCTCTTCTTGTT
Found at i:640 original size:25 final size:25
Alignment explanation
Indices: 591--640 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
581 GGCAACATCT
**
591 TTTTCTTTCTTTTCTTGTTTTTTTC
1 TTTTCTTTCTTTTCTTGTTCCTTTC
616 TTTTC-TTCTTGTTCTTGTTCCTTTC
1 TTTTCTTTCTT-TTCTTGTTCCTTTC
641 CATTATCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.00, C:0.20, G:0.06, T:0.74
Consensus pattern (25 bp):
TTTTCTTTCTTTTCTTGTTCCTTTC
Found at i:2975 original size:103 final size:103
Alignment explanation
Indices: 2796--3000 Score: 374
Period size: 103 Copynumber: 2.0 Consensus size: 103
2786 CAAGTACTTT
*
2796 GGGTGAGTCCTAAATCACCGTTAACATCAAGAATGTACACCCGACTAGTCTACTCCGTTCTAGTA
1 GGGTGAGTCCTAAATCACCGTTAACATCAAGAATGTACACCCGACTAGTCTACTCCGTTCGAGTA
2861 TTTTAGATCATATAACGTTAGAAAAAACATTCAACTGG
66 TTTTAGATCATATAACGTTAGAAAAAACATTCAACTGG
* * *
2899 GGGTGAGTCTTGAATCACCGTTAACATCAAGAATGTACACCCGACTAGTCTACTTCGTTCGAGTA
1 GGGTGAGTCCTAAATCACCGTTAACATCAAGAATGTACACCCGACTAGTCTACTCCGTTCGAGTA
2964 TTTTAGATCATATAACGTTAGAAAAAACATTCAACTG
66 TTTTAGATCATATAACGTTAGAAAAAACATTCAACTG
3001 ACATTTTCAA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (103 bp):
GGGTGAGTCCTAAATCACCGTTAACATCAAGAATGTACACCCGACTAGTCTACTCCGTTCGAGTA
TTTTAGATCATATAACGTTAGAAAAAACATTCAACTGG
Found at i:3496 original size:20 final size:19
Alignment explanation
Indices: 3462--3499 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3452 GTTGAATTAA
*
3462 AACACCTCGGTATTGATAT
1 AACACCTCAGTATTGATAT
3481 AACACACTCAGTATTGATA
1 AACAC-CTCAGTATTGATA
3500 CCAAAAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (19 bp):
AACACCTCAGTATTGATAT
Found at i:9197 original size:24 final size:24
Alignment explanation
Indices: 9165--9211 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
9155 AGTCTTACTG
9165 ATGATGTATAAAACATCTATGTAT
1 ATGATGTATAAAACATCTATGTAT
9189 ATGATGTATAAAACATCTATGTA
1 ATGATGTATAAAACATCTATGTA
9212 CAATGTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAT
Found at i:10550 original size:31 final size:31
Alignment explanation
Indices: 10507--10600 Score: 152
Period size: 31 Copynumber: 3.0 Consensus size: 31
10497 AATTAGCATT
*
10507 AAACCAAGACACCTAAACCTTATCATCTTCC
1 AAACCAAGACACCTCAACCTTATCATCTTCC
*
10538 AAACCAATACACCTCAACCTTATCATCTTCC
1 AAACCAAGACACCTCAACCTTATCATCTTCC
* *
10569 AACCCAAGACACTTCAACCTTATCATCTTCC
1 AAACCAAGACACCTCAACCTTATCATCTTCC
10600 A
1 A
10601 TATGTCAAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.36, C:0.37, G:0.02, T:0.24
Consensus pattern (31 bp):
AAACCAAGACACCTCAACCTTATCATCTTCC
Found at i:16672 original size:24 final size:24
Alignment explanation
Indices: 16639--16685 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
16629 AGTCTTCCTG
*
16639 ATGATGTATAAAACATCAATGTAT
1 ATGATATATAAAACATCAATGTAT
*
16663 ATGATATATAAAACATCTATGTA
1 ATGATATATAAAACATCAATGTA
16686 CAATGTCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.34
Consensus pattern (24 bp):
ATGATATATAAAACATCAATGTAT
Found at i:18009 original size:31 final size:31
Alignment explanation
Indices: 17971--18033 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
17961 AATGACCATT
*
17971 AAACCAAGACTCCTAAACCTTATCATCTTCC
1 AAACCAAGACACCTAAACCTTATCATCTTCC
* *
18002 AAACCAAGACACCTCAACCTTATCATTTTCC
1 AAACCAAGACACCTAAACCTTATCATCTTCC
18033 A
1 A
18034 TAAGTCAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.35, G:0.03, T:0.25
Consensus pattern (31 bp):
AAACCAAGACACCTAAACCTTATCATCTTCC
Found at i:24343 original size:17 final size:17
Alignment explanation
Indices: 24321--24354 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
24311 GGAAGAGTGT
* *
24321 ACTTATTCTTTACCATC
1 ACTTATTATTTAACATC
24338 ACTTATTATTTAACATC
1 ACTTATTATTTAACATC
24355 TTTCTTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (17 bp):
ACTTATTATTTAACATC
Done.