Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000038.1 Hibiscus syriacus cultivar Beakdansim tig00000059_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: 61363
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:584 original size:15 final size:15
Alignment explanation
Indices: 566--596 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
556 GACCGTAGAA
*
566 ATTATAAATTGTAAT
1 ATTATAAATTATAAT
581 ATTATAAATTATAAT
1 ATTATAAATTATAAT
596 A
1 A
597 CATTTACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
ATTATAAATTATAAT
Found at i:1865 original size:2 final size:2
Alignment explanation
Indices: 1858--1885 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1848 ATTAATATTC
1858 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
1886 TTATCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15524 original size:18 final size:18
Alignment explanation
Indices: 15497--15537 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
15487 CATGGATGGG
* * *
15497 TTCAGGGTCATCAGTCTC
1 TTCAGCGTCAGCAGACTC
15515 TTCAGCGTCAGCAGACTC
1 TTCAGCGTCAGCAGACTC
15533 TTCAG
1 TTCAG
15538 GTTCAGTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (18 bp):
TTCAGCGTCAGCAGACTC
Found at i:22364 original size:2 final size:2
Alignment explanation
Indices: 22357--22384 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22347 ATTAATATTC
22357 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
22385 CTTTTTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23482 original size:3 final size:3
Alignment explanation
Indices: 23474--23533 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
23464 TGTCATTGTA
23474 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
23522 AAT AAT AAT AAT
1 AAT AAT AAT AAT
23534 CCTATACTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:27927 original size:46 final size:46
Alignment explanation
Indices: 27855--27947 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
27845 TTCTGCCCTT
*
27855 ACTGATATTTTCTTTCAAAAAATTTCTAACAGAACTTATTGATATA
1 ACTGATATTTTCTTTCAAAAAATTTCTAACAGAACTTACTGATATA
*
27901 ACTGATATTTTCTTTCAAAAATTTTCTAACAGAACTTACTGATATA
1 ACTGATATTTTCTTTCAAAAAATTTCTAACAGAACTTACTGATATA
27947 A
1 A
27948 GAGGCTTCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (46 bp):
ACTGATATTTTCTTTCAAAAAATTTCTAACAGAACTTACTGATATA
Found at i:38272 original size:31 final size:31
Alignment explanation
Indices: 38235--38308 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 31
38225 AAAATCGAAT
*
38235 TAAACGGGGACGGAAAAAAAACTGTTTATGC
1 TAAACGGGGACGGAAAAAAAACCGTTTATGC
**
38266 TAAACGGGGAC-GAGGAAAAACCGTTTATGC
1 TAAACGGGGACGGAAAAAAAACCGTTTATGC
*
38296 TAAACTGGGACGG
1 TAAACGGGGACGG
38309 GGATGTGGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 26 0.68
31 12 0.32
ACGTcount: A:0.38, C:0.15, G:0.30, T:0.18
Consensus pattern (31 bp):
TAAACGGGGACGGAAAAAAAACCGTTTATGC
Found at i:38393 original size:2 final size:2
Alignment explanation
Indices: 38386--38468 Score: 54
Period size: 2 Copynumber: 45.0 Consensus size: 2
38376 AAATAATTAT
* * *
38386 TA TA TA TA TA TA TA TA TA TA T- TA -A TA AA TT TA -A TT TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
38424 T- TT TA -A AA TA TA -A TA TA TA TA TA TA TA TA TT TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38463 TA TA TA
1 TA TA TA
38469 CTCAGCCCGA
Statistics
Matches: 62, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
1 7 0.11
2 55 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39614 original size:12 final size:12
Alignment explanation
Indices: 39597--39646 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
39587 AAACATCCCG
39597 CCTCCCCTC-TCC
1 CCTCCCC-CATCC
39609 CCTCCCCCATCC
1 CCTCCCCCATCC
39621 CCAT-CCCCATCC
1 CC-TCCCCCATCC
39633 CCAT-CCCCATCC
1 CC-TCCCCCATCC
39645 CC
1 CC
39647 ATTTCCTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
11 1 0.03
12 34 0.94
13 1 0.03
ACGTcount: A:0.10, C:0.72, G:0.00, T:0.18
Consensus pattern (12 bp):
CCTCCCCCATCC
Found at i:39622 original size:6 final size:6
Alignment explanation
Indices: 39613--39648 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
39603 CTCTCCCCTC
39613 CCCCAT CCCCAT CCCCAT CCCCAT CCCCAT CCCCAT
1 CCCCAT CCCCAT CCCCAT CCCCAT CCCCAT CCCCAT
39649 TTCCTTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.67, G:0.00, T:0.17
Consensus pattern (6 bp):
CCCCAT
Found at i:40368 original size:15 final size:15
Alignment explanation
Indices: 40348--40382 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
40338 CCGTAGGACC
40348 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
40363 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
40378 ACTAC
1 ACTAC
40383 AGAACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:47213 original size:15 final size:15
Alignment explanation
Indices: 47193--47242 Score: 100
Period size: 15 Copynumber: 3.3 Consensus size: 15
47183 CCGTAGGACC
47193 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
47208 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
47223 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
47238 ACTAC
1 ACTAC
47243 AGAACCCTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.28, C:0.34, G:0.24, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:48953 original size:13 final size:13
Alignment explanation
Indices: 48935--48959 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48925 ATATTTTAGT
48935 TTTTTATAATTTA
1 TTTTTATAATTTA
48948 TTTTTATAATTT
1 TTTTTATAATTT
48960 CATTAAAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTATAATTTA
Found at i:49728 original size:17 final size:17
Alignment explanation
Indices: 49703--49747 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
49693 TGATAGAAAA
* *
49703 TAAACAAATTATTTGTT
1 TAAATAAATTATTTATT
49720 TAAATAAATTA-TTATT
1 TAAATAAATTATTTATT
*
49736 TAAATGAATTAT
1 TAAATAAATTAT
49748 AAACTGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (17 bp):
TAAATAAATTATTTATT
Found at i:50063 original size:19 final size:19
Alignment explanation
Indices: 50039--50075 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
50029 GTTAATAATT
*
50039 TTTAAATAAATTTTGGTTG
1 TTTAAACAAATTTTGGTTG
50058 TTTAAACAAATTTTGGTT
1 TTTAAACAAATTTTGGTT
50076 AATAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (19 bp):
TTTAAACAAATTTTGGTTG
Found at i:50086 original size:122 final size:123
Alignment explanation
Indices: 49899--50184 Score: 441
Period size: 122 Copynumber: 2.3 Consensus size: 123
49889 ATTTGGTTAA
*
49899 TTCGGTTCGGTTAATAATTTTCAAATAAA-TTTGGTTGTTTAAACAAATTTCGGTTAATAATTAT
1 TTCGGTTCGGTTAATAATTTTTAAATAAATTTTGGTTGTTTAAACAAATTTCGGTTAATAATTAT
* * * *
49963 TAATTGAACCGAAGAAATTTTGGTTAATTCAAAAATTGACCGAATTTACCGAAA-TTG
66 TAACTGAACCGAACAAATTTCGGTTAATTCAAAAATTGACCGAATTAACCGAAATTTG
*
50020 TTCGGTTCGGTTAATAATTTTTAAATAAATTTTGGTTGTTTAAACAAATTTTGGTTAATAATTAT
1 TTCGGTTCGGTTAATAATTTTTAAATAAATTTTGGTTGTTTAAACAAATTTCGGTTAATAATTAT
50085 TAACTGAACCGAACAAATTTCGGTTAATTCAAAAATTGACCGAATTAACCGAAATTTG
66 TAACTGAACCGAACAAATTTCGGTTAATTCAAAAATTGACCGAATTAACCGAAATTTG
* *
50143 TTTGGTTCGATTCGTTTAATAATTTTTAAATAAATTTCGGTT
1 TTCGGTTCG----G-TTAATAATTTTTAAATAAATTTTGGTT
50185 CGATTAATGG
Statistics
Matches: 150, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
121 28 0.19
122 84 0.56
123 11 0.07
127 1 0.01
128 26 0.17
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (123 bp):
TTCGGTTCGGTTAATAATTTTTAAATAAATTTTGGTTGTTTAAACAAATTTCGGTTAATAATTAT
TAACTGAACCGAACAAATTTCGGTTAATTCAAAAATTGACCGAATTAACCGAAATTTG
Found at i:50334 original size:17 final size:17
Alignment explanation
Indices: 50312--50378 Score: 107
Period size: 17 Copynumber: 3.8 Consensus size: 17
50302 TAATTTAAAT
50312 AATAATTTGTTTAAACA
1 AATAATTTGTTTAAACA
50329 AATAATTTGTTGTAAGACA
1 AATAATTTGTT-TAA-ACA
*
50348 AATAATTTATTTAAACA
1 AATAATTTGTTTAAACA
50365 AATAATTTGTTTAA
1 AATAATTTGTTTAA
50379 TTTTTTATCA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 27 0.59
18 6 0.13
19 13 0.28
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (17 bp):
AATAATTTGTTTAAACA
Found at i:57004 original size:21 final size:22
Alignment explanation
Indices: 56959--57004 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
56949 GGGAATTTAT
*
56959 AAAATTTAAAAAAATTATCAATA
1 AAAATGTAAAAAAATTATC-ATA
*
56982 AAAATGTAAAAATATTATC-TA
1 AAAATGTAAAAAAATTATCATA
57003 AA
1 AA
57005 TTAAATGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
23 17 0.81
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAATGTAAAAAAATTATCATA
Found at i:57278 original size:2 final size:2
Alignment explanation
Indices: 57271--57305 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
57261 TATCATCTAA
57271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57306 ATTTTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57439 original size:22 final size:21
Alignment explanation
Indices: 57411--57460 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
57401 CATTTGGAGG
57411 ATTAAATTA-AATAAAATATAGA
1 ATTAAATTATAA-AAAATAT-GA
57433 ATTAAATTATTAAAAAATATGA
1 ATTAAATTA-TAAAAAATATGA
57455 ATTAAA
1 ATTAAA
57461 ATTACATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 17 0.65
23 7 0.27
24 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
ATTAAATTATAAAAAATATGA
Done.