Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006812.1 Hibiscus syriacus cultivar Beakdansim tig00017291_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: 46392
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:5438 original size:18 final size:18
Alignment explanation
Indices: 5415--5450 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5405 CAGTGAACAT
5415 CTGATCAAACCTGTACCA
1 CTGATCAAACCTGTACCA
5433 CTGATCAAACCTGTACCA
1 CTGATCAAACCTGTACCA
5451 GCAATCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.22
Consensus pattern (18 bp):
CTGATCAAACCTGTACCA
Found at i:5457 original size:18 final size:18
Alignment explanation
Indices: 5418--5459 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5408 TGAACATCTG
*
5418 ATCAAACCTGTACCACTG
1 ATCAAACCTGTACCACTA
5436 ATCAAACCTGTACCAGC-A
1 ATCAAACCTGTACCA-CTA
5454 ATCAAA
1 ATCAAA
5460 AATCAAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.40, C:0.31, G:0.10, T:0.19
Consensus pattern (18 bp):
ATCAAACCTGTACCACTA
Found at i:7894 original size:11 final size:11
Alignment explanation
Indices: 7880--7906 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
7870 ATGATCCATG
7880 CAACTTTCTTA
1 CAACTTTCTTA
7891 CAACTTTCTTA
1 CAACTTTCTTA
7902 CAACT
1 CAACT
7907 CCCATATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (11 bp):
CAACTTTCTTA
Found at i:8761 original size:22 final size:21
Alignment explanation
Indices: 8727--8770 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
8717 GAGAGAGAGG
*
8727 GAAAAATATATAATAATAATA
1 GAAAAATAAATAATAATAATA
*
8748 GAAAAATTAAATAATAATTATA
1 GAAAAA-TAAATAATAATAATA
8770 G
1 G
8771 TAATACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
GAAAAATAAATAATAATAATA
Found at i:8762 original size:19 final size:21
Alignment explanation
Indices: 8727--8765 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
8717 GAGAGAGAGG
8727 GAAAAATATATAATAATAATA
1 GAAAAATATATAATAATAATA
8748 GAAAAAT-TA-AATAATAAT
1 GAAAAATATATAATAATAAT
8766 TATAGTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
GAAAAATATATAATAATAATA
Found at i:10973 original size:106 final size:106
Alignment explanation
Indices: 10752--11422 Score: 1073
Period size: 106 Copynumber: 6.4 Consensus size: 106
10742 GTATTGTTCA
* * * * * *
10752 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGGAACTGGG-AATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
* * * * *
10816 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTT--GTGCTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGT-C-GTCTG
*
10857 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
10922 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTG
*
10963 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
11028 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTG
* * * *
11069 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTCGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
*
11133 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTG
*
11174 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
11239 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTG
* * * *
11280 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTCGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
*
11344 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTG
11385 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
11423 TGGGTAAAAC
Statistics
Matches: 532, Mismatches: 30, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
105 231 0.43
106 298 0.56
107 1 0.00
108 2 0.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTG
Found at i:11152 original size:211 final size:211
Alignment explanation
Indices: 10752--11422 Score: 1123
Period size: 211 Copynumber: 3.2 Consensus size: 211
10742 GTATTGTTCA
* * * * * * *
10752 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGGAACTGGG-AATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
* * * * * *
10816 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTT--GTGCTGTCTTGAGTCCAATATCCTTCGCTGTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGT-C-GTCTGGAGTCCAATATCCTTCGTTGTG
* * * *
10879 AAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
129 AAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAA
*
10944 GTTGAACTTACGTCGTCTG
193 GTTGAACTTACGTTGTCTG
10963 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
11028 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTGGAGTCCAATATCCTTCGTTGTGAA
11093 GTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 GTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
11158 GAACTTACGTTGTCTG
196 GAACTTACGTTGTCTG
11174 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
11239 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTGGAGTCCAATATCCTTCGTTGTGAA
11304 GTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 GTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
11369 GAACTTACGTTGTCTG
196 GAACTTACGTTGTCTG
*
11385 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
11423 TGGGTAAAAC
Statistics
Matches: 438, Mismatches: 19, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
211 342 0.78
212 93 0.21
213 1 0.00
214 2 0.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (211 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTCGTCTGGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
GAACTTACGTTGTCTG
Found at i:12229 original size:1 final size:1
Alignment explanation
Indices: 12223--12247 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12213 ACCCCAAACG
12223 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
12248 CCAACTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:23011 original size:22 final size:21
Alignment explanation
Indices: 22977--23020 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
22967 GAGAGAGAGG
*
22977 GAAAAATATATAATAATAATA
1 GAAAAATAAATAATAATAATA
*
22998 GAAAAATTAAATAATAATTATA
1 GAAAAA-TAAATAATAATAATA
23020 G
1 G
23021 TAATACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
GAAAAATAAATAATAATAATA
Found at i:23012 original size:19 final size:21
Alignment explanation
Indices: 22977--23015 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
22967 GAGAGAGAGG
22977 GAAAAATATATAATAATAATA
1 GAAAAATATATAATAATAATA
22998 GAAAAAT-TA-AATAATAAT
1 GAAAAATATATAATAATAAT
23016 TATAGTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
GAAAAATATATAATAATAATA
Found at i:30538 original size:28 final size:28
Alignment explanation
Indices: 30498--30556 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
30488 TGTATCTTTC
*
30498 CTTGCTAATATATATGTTTTATT-ATTTA
1 CTTGCTAATATATATATTTTATTGA-TTA
* *
30526 CTTGCTATTATATTTATTTTATTGATTA
1 CTTGCTAATATATATATTTTATTGATTA
30554 CTT
1 CTT
30557 TTAAATATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.25, C:0.08, G:0.07, T:0.59
Consensus pattern (28 bp):
CTTGCTAATATATATATTTTATTGATTA
Found at i:32320 original size:2 final size:2
Alignment explanation
Indices: 32313--32412 Score: 191
Period size: 2 Copynumber: 50.0 Consensus size: 2
32303 TAGTATTTGG
32313 AT AT AT 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 AT AT AT
32355 AT AT AT 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 AT AT AT
*
32397 AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT
32413 CTTTGGGTTT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 96 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32870 original size:2 final size:2
Alignment explanation
Indices: 32863--32888 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32853 TTGCTGTAAG
32863 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
32889 ATCACCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:35801 original size:22 final size:21
Alignment explanation
Indices: 35775--35834 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
35765 GTTTTAAAAT
35775 ATAAATTTATTTATTATTCATA
1 ATAAATTTATTTATTATT-ATA
* **
35797 TTAAATTTAAATATTATTATA
1 ATAAATTTATTTATTATTATA
*
35818 ATAAATTTTATTGATTA
1 ATAAA-TTTATTTATTA
35835 GACTGTCAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
ATAAATTTATTTATTATTATA
Found at i:39358 original size:22 final size:22
Alignment explanation
Indices: 39315--39355 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39305 AAAAAATTAT
39315 TTTTTATTAAATATTTTTAATA
1 TTTTTATTAAATATTTTTAATA
*
39337 TTTTTATTTAAT-TTTTTAA
1 TTTTTATTAAATATTTTTAA
39356 ATAATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTATTAAATATTTTTAATA
Found at i:40559 original size:22 final size:21
Alignment explanation
Indices: 40529--40594 Score: 81
Period size: 17 Copynumber: 3.4 Consensus size: 21
40519 TGAAAAACCG
40529 AAAAACCGAACCGAACCGTTA
1 AAAAACCGAACCGAACCGTTA
40550 AAAAA-C---CCGAACCGTTA
1 AAAAACCGAACCGAACCGTTA
40567 AAAAACCCGAACCGAACCG--A
1 AAAAA-CCGAACCGAACCGTTA
40587 AAAAACCG
1 AAAAACCG
40595 GTTTCGGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
17 16 0.40
19 4 0.10
20 7 0.17
21 5 0.12
22 8 0.20
ACGTcount: A:0.50, C:0.30, G:0.14, T:0.06
Consensus pattern (21 bp):
AAAAACCGAACCGAACCGTTA
Found at i:40561 original size:17 final size:17
Alignment explanation
Indices: 40539--40580 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
40529 AAAAACCGAA
40539 CCGAACCGTTAAAAAAC
1 CCGAACCGTTAAAAAAC
40556 CCGAACCGTTAAAAAAC
1 CCGAACCGTTAAAAAAC
40573 CCGAACCG
1 CCGAACCG
40581 AACCGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.33, G:0.14, T:0.10
Consensus pattern (17 bp):
CCGAACCGTTAAAAAAC
Found at i:40700 original size:5 final size:5
Alignment explanation
Indices: 40690--40716 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
40680 TTTGGTAAAA
40690 AACCG AACCG AACCG AACCG AACCG AA
1 AACCG AACCG AACCG AACCG AACCG AA
40717 TACACCCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.37, G:0.19, T:0.00
Consensus pattern (5 bp):
AACCG
Found at i:42933 original size:15 final size:15
Alignment explanation
Indices: 42915--42954 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
42905 TAGCGTTTAT
*
42915 ATAATTCATGCTTAA
1 ATAATTCATACTTAA
*
42930 ATAATTAATACTTAA
1 ATAATTCATACTTAA
42945 ATAATTCATA
1 ATAATTCATA
42955 ATGTTGTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (15 bp):
ATAATTCATACTTAA
Found at i:44009 original size:18 final size:18
Alignment explanation
Indices: 43963--44010 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
43953 GAAGGACTGG
*
43963 CTTCATCGCCAATGAATC
1 CTTCATCGCCGATGAATC
*
43981 CGTCATCGCCGATGAATC
1 CTTCATCGCCGATGAATC
43999 CTTCATCGCCGA
1 CTTCATCGCCGA
44011 GGAGTAGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (18 bp):
CTTCATCGCCGATGAATC
Found at i:45225 original size:22 final size:22
Alignment explanation
Indices: 45197--45242 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
45187 CCACCAGCAA
45197 CTACATCCCTACGGCATTCCAT
1 CTACATCCCTACGGCATTCCAT
45219 CTACATCCCTACGGCATTCCAT
1 CTACATCCCTACGGCATTCCAT
45241 CT
1 CT
45243 CCGAGAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.41, G:0.09, T:0.28
Consensus pattern (22 bp):
CTACATCCCTACGGCATTCCAT
Done.