Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006800.1 Hibiscus syriacus cultivar Beakdansim tig00017257_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: 48622
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:377 original size:31 final size:31
Alignment explanation
Indices: 270--379 Score: 102
Period size: 31 Copynumber: 3.6 Consensus size: 31
260 AGTACCTTGA
* * *
270 GGCCTTAGAGCCTACCCAA-GAA-ATATCTTG
1 GGCCTAAGAGCCTACCCAATGAACATCTC-GG
* * * *
300 GGCCTTA-ATCCTA-CCAATGAAGCACCTTGG
1 GGCCTAAGAGCCTACCCAATGAA-CATCTCGG
*
330 GGCCTAAGAACCTACCCAATGAACATCTCGG
1 GGCCTAAGAGCCTACCCAATGAACATCTCGG
361 GGCCTAAGAGCCTACCCAA
1 GGCCTAAGAGCCTACCCAA
380 GGTCACCTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
28 4 0.06
29 8 0.12
30 14 0.22
31 31 0.48
32 8 0.12
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (31 bp):
GGCCTAAGAGCCTACCCAATGAACATCTCGG
Found at i:3279 original size:12 final size:11
Alignment explanation
Indices: 3232--3280 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
3222 GATAAAGAAA
3232 TAATTTTTTAT
1 TAATTTTTTAT
3243 TAATTTTTT-T
1 TAATTTTTTAT
* *
3253 TAATTATTAATT
1 TAATTTTTTA-T
3265 TAATATTTTTAT
1 TAAT-TTTTTAT
3277 TAAT
1 TAAT
3281 CATTTTTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 8 0.26
11 9 0.29
12 10 0.32
13 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TAATTTTTTAT
Found at i:3287 original size:13 final size:12
Alignment explanation
Indices: 3232--3288 Score: 50
Period size: 13 Copynumber: 4.9 Consensus size: 12
3222 GATAAAGAAA
3232 TAAT-TTTTTAT
1 TAATATTTTTAT
3243 TAAT-TTTTT-T
1 TAATATTTTTAT
* *
3253 TAAT-TATTAATT
1 TAATATTTTTA-T
3265 TAATATTTTTAT
1 TAATATTTTTAT
3277 TAATCATTTTTA
1 TAAT-ATTTTTA
3289 CATTGATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
10 8 0.21
11 9 0.24
12 10 0.26
13 11 0.29
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (12 bp):
TAATATTTTTAT
Found at i:9632 original size:19 final size:19
Alignment explanation
Indices: 9608--9655 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
9598 CAATTGGTGC
9608 ATCGATGCATAAGGAGTGT
1 ATCGATGCATAAGGAGTGT
9627 ATCGATGCATAAGGAGTGT
1 ATCGATGCATAAGGAGTGT
9646 ATCGATGCAT
1 ATCGATGCAT
9656 CACAACAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.27
Consensus pattern (19 bp):
ATCGATGCATAAGGAGTGT
Found at i:10224 original size:15 final size:15
Alignment explanation
Indices: 10206--10238 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
10196 GAGGGTATAA
10206 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
10221 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
10236 TAG
1 TAG
10239 GAGTCCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:21998 original size:9 final size:9
Alignment explanation
Indices: 21984--22008 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21974 CATATATCGA
21984 GAGACTGAC
1 GAGACTGAC
21993 GAGACTGAC
1 GAGACTGAC
22002 GAGACTG
1 GAGACTG
22009 TCGCTTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.20, G:0.36, T:0.12
Consensus pattern (9 bp):
GAGACTGAC
Found at i:31967 original size:13 final size:14
Alignment explanation
Indices: 31934--31967 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
31924 CGGTAAACTA
31934 AACATGTAATTATG
1 AACATGTAATTATG
31948 AACATGTAATTATG
1 AACATGTAATTATG
31962 -ACATGT
1 AACATGT
31968 TTCCTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (14 bp):
AACATGTAATTATG
Found at i:32379 original size:21 final size:22
Alignment explanation
Indices: 32337--32379 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
32327 AAAGGAAAAC
32337 ATGTCATAAAGACATAAAATTAT
1 ATGTCATAAAGA-ATAAAATTAT
*
32360 ATGTCATAAAG-ATCAAATTA
1 ATGTCATAAAGAATAAAATTA
32380 CTACAAACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (22 bp):
ATGTCATAAAGAATAAAATTAT
Found at i:37996 original size:23 final size:22
Alignment explanation
Indices: 37965--38015 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
37955 TCCCACTGAG
* *
37965 TGACATATGAAATTTGTCCCGAA
1 TGACCTATG-AATTTATCCCGAA
* *
37988 TGACCTATGTATTTATCTCGAA
1 TGACCTATGAATTTATCCCGAA
38010 TGACCT
1 TGACCT
38016 TTGTATACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (22 bp):
TGACCTATGAATTTATCCCGAA
Done.