Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004293.1 Hibiscus syriacus cultivar Beakdansim tig00009419_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: 101278
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:3000 original size:41 final size:41
Alignment explanation
Indices: 2943--3055 Score: 129
Period size: 41 Copynumber: 2.8 Consensus size: 41
2933 TTTCGAGTAG
* *
2943 TATCGATAC-CTATTCAAGTAGTATCGGTACTTCATGAACAA
1 TATCGATACTC-ATTCAAGTAGTATCGATACTGCATGAACAA
* * * *
2984 TATCGATACTCATTCAAGTAGTAACGATACTGGATGGACAG
1 TATCGATACTCATTCAAGTAGTATCGATACTGCATGAACAA
* * *
3025 TATCGATGCTAATTCTAGTAGTATCGATACT
1 TATCGATACTCATTCAAGTAGTATCGATACT
3056 ATGCTAGTAG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
41 60 0.98
42 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (41 bp):
TATCGATACTCATTCAAGTAGTATCGATACTGCATGAACAA
Found at i:3064 original size:20 final size:20
Alignment explanation
Indices: 3023--3116 Score: 93
Period size: 20 Copynumber: 4.5 Consensus size: 20
3013 CTGGATGGAC
* *
3023 AGTATCGATGCTAATTCTAGT
1 AGTATCGATACT-ATGCTAGT
3044 AGTATCGATACTATGCTAGT
1 AGTATCGATACTATGCTAGT
* *
3064 AGTTTCGATATCTA-GCAAGAGT
1 AGTATCGATA-CTATGC--TAGT
3086 AGTATCGATACTATG-TAAGT
1 AGTATCGATACTATGCT-AGT
3106 AGTATCGATAC
1 AGTATCGATAC
3117 CAAGTACACA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
20 32 0.52
21 17 0.27
22 13 0.21
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (20 bp):
AGTATCGATACTATGCTAGT
Found at i:3508 original size:15 final size:15
Alignment explanation
Indices: 3479--3518 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3469 TGCAAAGTAT
* *
3479 ATACATATTCTAGAA
1 ATACATCTTCCAGAA
*
3494 CTACATCTTCCAGAA
1 ATACATCTTCCAGAA
3509 ATACATCTTC
1 ATACATCTTC
3519 TTTTGTGACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.33
Consensus pattern (15 bp):
ATACATCTTCCAGAA
Found at i:6869 original size:33 final size:33
Alignment explanation
Indices: 6827--6895 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
6817 GTTGATGAAT
*
6827 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* *
6860 GAAGGATGATGTTATTGGCGTGATATGGTAATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
6893 GAA
1 GAA
6896 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:6936 original size:36 final size:36
Alignment explanation
Indices: 6866--6978 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
6856 AATGGAAGGA
* * *
6866 TGATGTTATTGGCGTGAT-ATGGTAATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
6901 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
6937 TGATGATATAGGCATGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
6973 TGATGA
1 TGATGA
6979 AAATAGTATC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:11292 original size:33 final size:35
Alignment explanation
Indices: 11254--11382 Score: 149
Period size: 36 Copynumber: 3.7 Consensus size: 35
11244 ATGGTGATGA
* *
11254 AATGGTAATGGA-A-GGATGATGTTATTGGCGTGAT
1 AATGGTAATGGATATGG-TGATGATATAGGCGTGAT
11288 -ATGGTAATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTAATGG-ATATGGTGATGATATAGGCGTGAT
* *
11323 AATGGTGATGGACTATGGTGATGATATAGGCATGAT
1 AATGGTAATGGA-TATGGTGATGATATAGGCGTGAT
11359 AATGG-AGATGGATTATGGTGATGA
1 AATGGTA-ATGGA-TATGGTGATGA
11383 AAATAGTATC
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
33 10 0.12
34 1 0.01
35 18 0.22
36 54 0.65
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (35 bp):
AATGGTAATGGATATGGTGATGATATAGGCGTGAT
Found at i:11340 original size:36 final size:36
Alignment explanation
Indices: 11270--11382 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
11260 AATGGAAGGA
* * *
11270 TGATGTTATTGGCGTGAT-ATGGTAATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
11305 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
11341 TGATGATATAGGCATGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
11377 TGATGA
1 TGATGA
11383 AAATAGTATC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:16229 original size:17 final size:17
Alignment explanation
Indices: 16204--16239 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
16194 TTGCGTCGGC
16204 TATAAAAATGGTTAGGG
1 TATAAAAATGGTTAGGG
* *
16221 TATAGAAATGGTTATGG
1 TATAAAAATGGTTAGGG
16238 TA
1 TA
16240 GAGGTAGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (17 bp):
TATAAAAATGGTTAGGG
Found at i:21911 original size:26 final size:26
Alignment explanation
Indices: 21882--21962 Score: 108
Period size: 26 Copynumber: 3.1 Consensus size: 26
21872 GCTAAGAGCA
*
21882 TATGGTGTGCACGACCTTATGTGTAT
1 TATGGTGAGCACGACCTTATGTGTAT
*
21908 TATGGTGAGCATGACCTTATGTGTAT
1 TATGGTGAGCACGACCTTATGTGTAT
* * * *
21934 GATGGTGGGTACAACCTTATGTGTAT
1 TATGGTGAGCACGACCTTATGTGTAT
21960 TAT
1 TAT
21963 CACTTCGGTG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.38
Consensus pattern (26 bp):
TATGGTGAGCACGACCTTATGTGTAT
Found at i:28922 original size:14 final size:15
Alignment explanation
Indices: 28903--28933 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
28893 AATACTCTGT
28903 TTCATTCTG-ACTTG
1 TTCATTCTGAACTTG
28917 TTCATTCTGAACTTG
1 TTCATTCTGAACTTG
28932 TT
1 TT
28934 TAGGCATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.16, C:0.19, G:0.13, T:0.52
Consensus pattern (15 bp):
TTCATTCTGAACTTG
Found at i:31083 original size:12 final size:12
Alignment explanation
Indices: 31055--31097 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
31045 TATATGAGTC
31055 TTTTTCTTTTCT
1 TTTTTCTTTTCT
* *
31067 CTTTTATTTTCT
1 TTTTTCTTTTCT
31079 TTTTTCTTGTTGCT
1 TTTTTCTT-TT-CT
31093 TTTTT
1 TTTTT
31098 TTTGTAGCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 16 0.64
13 2 0.08
14 7 0.28
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:34433 original size:77 final size:79
Alignment explanation
Indices: 34350--34502 Score: 195
Period size: 77 Copynumber: 2.0 Consensus size: 79
34340 GAATTAAATA
* **
34350 AAAATCTTATTTAATTAATTCAAATTAGATAT-ACATT-AAAGACTTATAATCTGAATTACAATC
1 AAAATCTTATTTAATTAATTCAAATTAAATATCA-ATTAAAAGACTTATAATCAAAATTACAATC
34413 -TTTAATGTTTATTT
65 ATTTAATGTTTATTT
* ** * * *
34427 AAAATCTTATTTAATTATTTTGAATTAAATATCAATTAAAAGAGTTGTAATCAAAATTACATTCA
1 AAAATCTTATTTAATTAATTCAAATTAAATATCAATTAAAAGACTTATAATCAAAATTACAATCA
34492 TTTAATGTTTA
66 TTTAATGTTTA
34503 CTTTCTATAT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
77 31 0.48
78 22 0.34
79 11 0.17
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (79 bp):
AAAATCTTATTTAATTAATTCAAATTAAATATCAATTAAAAGACTTATAATCAAAATTACAATCA
TTTAATGTTTATTT
Found at i:36626 original size:16 final size:16
Alignment explanation
Indices: 36581--36634 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
36571 AAATTATTTA
36581 ATTTATTTTTAATAATT
1 ATTTATTTTTAAT-ATT
**
36598 ATTTAAATTTAATATT
1 ATTTATTTTTAATATT
36614 CA-TTATTTTTAATAGTT
1 -ATTTATTTTTAATA-TT
36631 ATTT
1 ATTT
36635 TAAATTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (16 bp):
ATTTATTTTTAATATT
Found at i:36657 original size:20 final size:20
Alignment explanation
Indices: 36556--36669 Score: 70
Period size: 22 Copynumber: 5.3 Consensus size: 20
36546 TACATATAAA
36556 TAAATATATTTATCTAAATTATT
1 TAAAT-TATTT-T-TAAATTATT
*
36579 TAATTTATTTTTAATAATTATT
1 TAAATTATTTTT-A-AATTATT
* * *
36601 TAAATTTAATATT-CATTATTTT
1 TAAA-TTATTTTTAAATTA--TT
36623 TAATAGTTA-TTTTAAATTATT
1 TAA-A-TTATTTTTAAATTATT
* *
36644 TAAATTATTTTTAATTTATC
1 TAAATTATTTTTAAATTATT
36664 TAAATT
1 TAAATT
36670 TTCTGTTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 19
0.72 0.10 0.19
Matches are distributed among these distances:
19 3 0.04
20 22 0.30
21 7 0.10
22 23 0.32
23 18 0.25
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.58
Consensus pattern (20 bp):
TAAATTATTTTTAAATTATT
Found at i:37093 original size:21 final size:20
Alignment explanation
Indices: 37047--37096 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
37037 TGCATGTAAT
* * *
37047 TGTTTTTTTTCTTTTAAATT
1 TGTTTTTTTGCTGTTAAATA
*
37067 TATTTTCTTTGCTGTTAAATA
1 TGTTTT-TTTGCTGTTAAATA
37088 TGTTTTTTT
1 TGTTTTTTT
37097 TTCGATATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.16, C:0.06, G:0.08, T:0.70
Consensus pattern (20 bp):
TGTTTTTTTGCTGTTAAATA
Found at i:42883 original size:35 final size:36
Alignment explanation
Indices: 42832--42905 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 36
42822 ATAAGATACT
*
42832 ATCTGTCCATCACCATTTCATGCCTATATCATCACC
1 ATCTGTCCATCACCATTTCACGCCTATATCATCACC
42868 ATCT-TCCATCACCATTTCACGCCTATATCATCACC
1 ATCTGTCCATCACCATTTCACGCCTATATCATCACC
42903 ATC
1 ATC
42906 CCTTAACCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 33 0.89
36 4 0.11
ACGTcount: A:0.26, C:0.38, G:0.04, T:0.32
Consensus pattern (36 bp):
ATCTGTCCATCACCATTTCACGCCTATATCATCACC
Found at i:43285 original size:20 final size:18
Alignment explanation
Indices: 43256--43295 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
43246 CAAGTGGTGC
*
43256 AACAAGAAGAAAATGAAAAA
1 AACAAAAAG-AAA-GAAAAA
43276 AACAAAAAGAAAGAAAAA
1 AACAAAAAGAAAGAAAAA
43294 AA
1 AA
43296 AAGAATCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 3 0.16
20 8 0.42
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.03
Consensus pattern (18 bp):
AACAAAAAGAAAGAAAAA
Found at i:43343 original size:15 final size:15
Alignment explanation
Indices: 43323--43371 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
43313 TTTGTAGTGC
43323 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
43338 AAAAG-AAGAAAA-A
1 AAAAGAAAGAAAAGA
*
43351 TTCAAAGAAA-AAAAGA
1 --AAAAGAAAGAAAAGA
43367 AAAAG
1 AAAAG
43372 TGAAGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
13 1 0.04
14 11 0.39
15 13 0.46
16 3 0.11
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:43380 original size:31 final size:30
Alignment explanation
Indices: 43324--43388 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 30
43314 TTGTAGTGCA
43324 AAAGAAAGAAAAGAAAAAGAAGAAAAATT-C
1 AAAGAAAGAAAAGAAAAAGAAG-AAAATTGC
43354 AAAGAAA-AAAAGAAAAAGTGAAGAAAATTGC
1 AAAGAAAGAAAAGAAAAA--GAAGAAAATTGC
43385 AAAG
1 AAAG
43389 TACAAAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 10 0.31
30 13 0.41
31 9 0.28
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.08
Consensus pattern (30 bp):
AAAGAAAGAAAAGAAAAAGAAGAAAATTGC
Found at i:47328 original size:13 final size:12
Alignment explanation
Indices: 47310--47372 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
47300 ATACTATATG
47310 TCCATCACCATCT
1 TCCATCACCAT-T
47323 TCCATCACCATT
1 TCCATCACCATT
* *
47335 T-CA-CGCCTATA
1 TCCATCACC-ATT
47346 T-CATCACCATCT
1 TCCATCACCAT-T
47358 TCCATCACCATT
1 TCCATCACCATT
47370 TCC
1 TCC
47373 CGGCTATATC
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
10 3 0.07
11 9 0.21
12 10 0.24
13 20 0.48
ACGTcount: A:0.24, C:0.43, G:0.02, T:0.32
Consensus pattern (12 bp):
TCCATCACCATT
Found at i:47352 original size:35 final size:35
Alignment explanation
Indices: 47312--47391 Score: 142
Period size: 35 Copynumber: 2.3 Consensus size: 35
47302 ACTATATGTC
47312 CATCACCATCTTCCATCACCATTTCACGCCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAT
* *
47347 CATCACCATCTTCCATCACCATTTCCCGGCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAT
47382 CATCACCATC
1 CATCACCATC
47392 CCTTAACCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.25, C:0.41, G:0.04, T:0.30
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATTTCACGCCTATAT
Found at i:64148 original size:36 final size:36
Alignment explanation
Indices: 64071--64174 Score: 147
Period size: 36 Copynumber: 2.9 Consensus size: 36
64061 ATTTATAAGT
* * *
64071 TGGTGATAATATAGGCGTGAT-TTAGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* **
64106 TAGTGATGATATAGGCGTGATAATGGTGATGGGCTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
64142 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
64175 CAAATTGTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 19 0.32
36 41 0.68
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:85973 original size:19 final size:19
Alignment explanation
Indices: 85935--85973 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
85925 GTTCAAAGAC
**
85935 AAAAAGAAGAAAAATTAGA
1 AAAAAGAAGAAAAAAGAGA
*
85954 AAAAAGATGAAAAAAGAGA
1 AAAAAGAAGAAAAAAGAGA
85973 A
1 A
85974 TTTCAACAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (19 bp):
AAAAAGAAGAAAAAAGAGA
Found at i:97824 original size:35 final size:37
Alignment explanation
Indices: 97778--97857 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
97768 TTTGAGAATT
* *
97778 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
*
97813 TGGTGATGATATAGGCATGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
97850 TGGTGATG
1 TGGTGATG
97858 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
Done.