Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001536.1 Hibiscus syriacus cultivar Beakdansim tig00003017_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: 53898
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:186 original size:27 final size:28
Alignment explanation
Indices: 155--207 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
145 TATTCATTTT
155 TTAAAAATAAATAAATGC-ATAAAAAAA
1 TTAAAAATAAATAAATGCAATAAAAAAA
* * *
182 TTAAAAGTGAATAAATTCAATAAAAA
1 TTAAAAATAAATAAATGCAATAAAAA
208 TATAATGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.25
Consensus pattern (28 bp):
TTAAAAATAAATAAATGCAATAAAAAAA
Found at i:3122 original size:2 final size:2
Alignment explanation
Indices: 3060--3113 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
3050 ATTACTCCAC
3060 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3102 TA GA TA TA TA TA
1 TA TA TA TA TA TA
3114 AAGTATATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4176 original size:18 final size:18
Alignment explanation
Indices: 4153--4198 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 18
4143 AATAAAGATG
4153 AAATAAAACAAAATGATT
1 AAATAAAACAAAATGATT
*
4171 AAAT--AA-AAAATTATT
1 AAATAAAACAAAATGATT
4186 AAATAAAACAAAA
1 AAATAAAACAAAA
4199 GAAAAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 12 0.50
16 2 0.08
17 2 0.08
18 8 0.33
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (18 bp):
AAATAAAACAAAATGATT
Found at i:5456 original size:13 final size:13
Alignment explanation
Indices: 5409--5445 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5399 AACCCGACCC
5409 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
5422 TACCTGACCCGTT
1 GACCCGACCCGTT
5435 GACCCGACCCG
1 GACCCGACCCG
5446 ACCTGTTGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:7968 original size:12 final size:12
Alignment explanation
Indices: 7931--7969 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
7921 ATCTGATACT
7931 TGACATGGATTC
1 TGACATGGATTC
*
7943 TGATAT-GATATC
1 TGACATGGAT-TC
7955 TGACATGGATTC
1 TGACATGGATTC
7967 TGA
1 TGA
7970 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:8037 original size:24 final size:24
Alignment explanation
Indices: 7915--8030 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
7905 TTCGATTTGA
7915 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
7939 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
7963 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* * *
7987 ATTCTGATCTGTTACTTGACCT-T
1 ATTCTGATCTGATACTTGACATGG
*
8010 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
8031 CTGATTTATG
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
23 2 0.02
24 78 0.96
25 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:12155 original size:25 final size:23
Alignment explanation
Indices: 12119--12165 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
12109 TGGTTGGTTA
*
12119 AATGGTTGTTTAAACTTTATTTTT
1 AATGGTTATTT-AACTTTATTTTT
*
12143 AATGGTATATTTAAGTTTATTTT
1 AATGGT-TATTTAACTTTATTTT
12166 GGTTCTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (23 bp):
AATGGTTATTTAACTTTATTTTT
Found at i:31578 original size:2 final size:2
Alignment explanation
Indices: 31571--31648 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
31561 AATGCATACT
31571 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31649 ATTTTATAGC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31964 original size:18 final size:18
Alignment explanation
Indices: 31892--31963 Score: 83
Period size: 18 Copynumber: 4.0 Consensus size: 18
31882 CGAGGGATTA
31892 TCAGTGGTCCTTCGAGAC
1 TCAGTGGTCCTTCGAGAC
* *
31910 TCAGTGGTCCTACGGGAC
1 TCAGTGGTCCTTCGAGAC
* *
31928 TCAGTGGTCTTTCGGGAC
1 TCAGTGGTCCTTCGAGAC
*
31946 AT-AGTGGTCATTCGAGAC
1 -TCAGTGGTCCTTCGAGAC
31964 AAATATTCAG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
18 46 0.98
19 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.28
Consensus pattern (18 bp):
TCAGTGGTCCTTCGAGAC
Found at i:38520 original size:2 final size:2
Alignment explanation
Indices: 38513--38539 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38503 CATGCATACT
38513 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
38540 GTGTGTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38821 original size:22 final size:22
Alignment explanation
Indices: 38796--38837 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
38786 GAGGGATTAT
*
38796 CAGTGGTCCTTCGGGACATATA
1 CAGTGGTCCTTCGAGACATATA
38818 CAGTGGTCCTTCGAGACATA
1 CAGTGGTCCTTCGAGACATA
38838 GTGGTCCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
CAGTGGTCCTTCGAGACATATA
Found at i:41252 original size:31 final size:31
Alignment explanation
Indices: 41211--41428 Score: 348
Period size: 31 Copynumber: 7.0 Consensus size: 31
41201 AGGGTCGAGG
* *
41211 GTTTATCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
41242 GTTTACCTATGTTCTTCGGGACATATGTACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
41273 GTTTACCTATGTTCTTCAGGACAAATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
41304 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
41335 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
41366 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
41397 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
41428 G
1 G
41429 GTCCTTCGGG
Statistics
Matches: 175, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
31 174 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:44366 original size:6 final size:6
Alignment explanation
Indices: 44355--44384 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
44345 TATTTAAAAT
*
44355 AAATAA AAATAA AGATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA
44385 GACAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:44392 original size:38 final size:38
Alignment explanation
Indices: 44321--44395 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
44311 AATAAAAGGA
***
44321 AAAAATAAAGATAAAAAGGAAAAATATTTAAAATAAAT
1 AAAAATAAAGATAAAAAGGAAAAATAGACAAAATAAAT
*
44359 AAAAATAAAGATAAAAA-TAAAAATAAGACAAAATAAA
1 AAAAATAAAGATAAAAAGGAAAAAT-AGACAAAATAAA
44396 ATAATAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 6 0.19
38 26 0.81
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (38 bp):
AAAAATAAAGATAAAAAGGAAAAATAGACAAAATAAAT
Found at i:44404 original size:18 final size:16
Alignment explanation
Indices: 44355--44396 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
44345 TATTTAAAAT
*
44355 AAATAAAAATAAAGATAA
1 AAATAAAAAT-AAGA-CA
44373 AAATAAAAATAAGACA
1 AAATAAAAATAAGACA
44389 AAATAAAA
1 AAATAAAA
44397 TAATAAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 4 0.17
18 10 0.43
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (16 bp):
AAATAAAAATAAGACA
Found at i:44440 original size:38 final size:33
Alignment explanation
Indices: 44379--44466 Score: 81
Period size: 33 Copynumber: 2.5 Consensus size: 33
44369 ATAAAAATAA
*
44379 AAATAAGACAAAATAAAATAATAAGATGAATAAAGATG
1 AAATAAAACAAAATAAAATAAT-A-A--AAT-AAGATG
* *
44417 AAATAAAACAAAAT-GAATAAATAAAATAAGATT
1 AAATAAAACAAAATAAAAT-AATAAAATAAGATG
44450 AAATAAAACAAAA-AAAA
1 AAATAAAACAAAATAAAA
44467 GGAAAAAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
33 20 0.45
34 3 0.07
36 1 0.02
37 4 0.09
38 16 0.36
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (33 bp):
AAATAAAACAAAATAAAATAATAAAATAAGATG
Found at i:44518 original size:17 final size:18
Alignment explanation
Indices: 44488--44521 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44478 AATGGAATTA
44488 AAAAACAGAAACAAAAAT
1 AAAAACAGAAACAAAAAT
*
44506 AAAAACA-ATACAAAAA
1 AAAAACAGAAACAAAAA
44522 CAATATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.12, G:0.03, T:0.06
Consensus pattern (18 bp):
AAAAACAGAAACAAAAAT
Found at i:44602 original size:8 final size:8
Alignment explanation
Indices: 44591--44662 Score: 53
Period size: 8 Copynumber: 9.2 Consensus size: 8
44581 AAAAAGGAAA
44591 AAATATAT
1 AAATATAT
44599 AAATATAT
1 AAATATAT
44607 AAAT-T-T
1 AAATATAT
* *
44613 TAATGT-T
1 AAATATAT
*
44620 AAATTAAAT
1 AAA-TATAT
44629 AAATAATAT
1 AAAT-ATAT
*
44638 ATATATAT
1 AAATATAT
*
44646 ATATATAT
1 AAATATAT
44654 AAATA-AT
1 AAATATAT
44661 AA
1 AA
44663 TAATAATACT
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
6 4 0.08
7 9 0.17
8 30 0.57
9 10 0.19
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (8 bp):
AAATATAT
Found at i:51549 original size:14 final size:15
Alignment explanation
Indices: 51413--51550 Score: 76
Period size: 14 Copynumber: 9.3 Consensus size: 15
51403 ATTTTGTTGT
51413 TTTTAATATTTT-AA
1 TTTTAATATTTTAAA
*
51427 TTGTAATATTTTAAAA
1 TTTTAATATTTT-AAA
*
51443 TTTTAGAAATTTT--A
1 TTTTA-ATATTTTAAA
*
51457 TTTT-ATATTTTTAA
1 TTTTAATATTTTAAA
* *
51471 -TAT-ATGTTTTTAAA
1 TTTTAAT-ATTTTAAA
*
51485 TTTTAATAATTTTAAT
1 TTTTAAT-ATTTTAAA
51501 TTTTAATATATTT-AA
1 TTTTAATAT-TTTAAA
* **
51516 TTGTTGATTATTTTTTA
1 TT-TT-AATATTTTAAA
51533 TTTT-ATATTTTAAA
1 TTTTAATATTTTAAA
51547 TTTT
1 TTTT
51551 TAAAATATTC
Statistics
Matches: 95, Mismatches: 17, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
12 6 0.06
13 4 0.04
14 34 0.36
15 7 0.07
16 31 0.33
17 13 0.14
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (15 bp):
TTTTAATATTTTAAA
Done.