Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002043.1 Hibiscus syriacus cultivar Beakdansim tig00004164_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: 71997
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6180 original size:120 final size:120
Alignment explanation
Indices: 5967--6208 Score: 484
Period size: 120 Copynumber: 2.0 Consensus size: 120
5957 ATCAAAATCA
5967 CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
1 CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
6032 ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
66 ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
6087 CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
1 CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
6152 ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
66 ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
6207 CA
1 CA
6209 ATAGGAAGGT
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 122 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (120 bp):
CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
Found at i:10006 original size:26 final size:26
Alignment explanation
Indices: 9970--10021 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
9960 TATATAAAAG
9970 TTAAATTTGATTAAATTCGAGTATGT
1 TTAAATTTGATTAAATTCGAGTATGT
9996 TTAAATTTGATTAAATTCGAGTATGT
1 TTAAATTTGATTAAATTCGAGTATGT
10022 GAACTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (26 bp):
TTAAATTTGATTAAATTCGAGTATGT
Found at i:11699 original size:16 final size:15
Alignment explanation
Indices: 11674--11703 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
11664 TGAGAGGCTG
11674 AATTAAGCTTAACTA
1 AATTAAGCTTAACTA
11689 AATTGAAGCTTAACT
1 AATT-AAGCTTAACT
11704 GGTTTCATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (15 bp):
AATTAAGCTTAACTA
Found at i:19741 original size:43 final size:43
Alignment explanation
Indices: 19680--19768 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
19670 AATCGGTATC
19680 TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
1 TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
19723 TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
1 TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
19766 TCT
1 TCT
19769 CCTGAACTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (43 bp):
TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
Found at i:23515 original size:24 final size:24
Alignment explanation
Indices: 23461--23515 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
23451 AATGTGCCAT
*
23461 GGATTTACGTAGATGAAACCATCA
1 GGATTTTCGTAGATGAAACCATCA
23485 GGATTTTCGTAGATGAAACCATCA
1 GGATTTTCGTAGATGAAACCATCA
23509 GGATTTT
1 GGATTTT
23516 GTATGTGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (24 bp):
GGATTTTCGTAGATGAAACCATCA
Found at i:29117 original size:29 final size:29
Alignment explanation
Indices: 29057--29117 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
29047 TACCCCGTTA
*
29057 CATATTACATACGGAAAACAAGGGCATTT
1 CATATTACATACGGAAAACAAGGGCATGT
*
29086 CATATTACATACGGAGAACAAGGGACA-GT
1 CATATTACATACGGAAAACAAGGG-CATGT
29115 CAT
1 CAT
29118 TAAGGTGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.93
30 2 0.07
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (29 bp):
CATATTACATACGGAAAACAAGGGCATGT
Found at i:30135 original size:23 final size:23
Alignment explanation
Indices: 30109--30169 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
30099 TTCATGAAAG
* * *
30109 TTAAATAAACATATTTGCGAACA
1 TTAAACAAATATATTTACGAACA
* *
30132 TTAAACGAATATATTTACGAACG
1 TTAAACAAATATATTTACGAACA
30155 TTAAACAAATATATT
1 TTAAACAAATATATT
30170 CGCAAACTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (23 bp):
TTAAACAAATATATTTACGAACA
Found at i:30258 original size:21 final size:19
Alignment explanation
Indices: 30212--30259 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
30202 TCAAAAACAA
30212 ACAAACAAAATATTAAAAAT
1 ACAAAC-AAATATTAAAAAT
**
30232 TTAAACAAATATTAATTAAAT
1 ACAAACAAATATTAA--AAAT
30253 ACAAACA
1 ACAAACA
30260 CTTCAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 9 0.41
20 4 0.18
21 9 0.41
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (19 bp):
ACAAACAAATATTAAAAAT
Found at i:31327 original size:24 final size:24
Alignment explanation
Indices: 31300--31345 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
31290 TAAAATTAGA
31300 AATTGAAGGTACATAAATATTTGG
1 AATTGAAGGTACATAAATATTTGG
* *
31324 AATTGAAGTTATATAAATATTT
1 AATTGAAGGTACATAAATATTT
31346 TATAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.15, T:0.39
Consensus pattern (24 bp):
AATTGAAGGTACATAAATATTTGG
Found at i:33404 original size:16 final size:16
Alignment explanation
Indices: 33380--33416 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
33370 AATATGTGAA
*
33380 AAACTGAAAAAATTTC
1 AAACCGAAAAAATTTC
33396 AAACCGAAAAAATTTC
1 AAACCGAAAAAATTTC
33412 AAACC
1 AAACC
33417 TGAATAGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.57, C:0.19, G:0.05, T:0.19
Consensus pattern (16 bp):
AAACCGAAAAAATTTC
Found at i:37394 original size:2 final size:2
Alignment explanation
Indices: 37387--37416 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
37377 TCCAGACCAT
37387 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
37417 CATGTATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47797 original size:35 final size:35
Alignment explanation
Indices: 47751--47826 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
47741 AAAACAGTCC
* *
47751 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* **
47786 TCAATTTCATTCTCAACCTTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
47821 TCAATT
1 TCAATT
47827 AAATTCAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:48369 original size:130 final size:130
Alignment explanation
Indices: 48223--48470 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
48213 TATTTATATA
* ** *
48223 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* *
48288 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
48353 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
48418 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
48471 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:48443 original size:23 final size:21
Alignment explanation
Indices: 48397--48443 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
48387 AATTAATCAT
48397 TTAACCAGGATCTGACATATG
1 TTAACCAGGATCTGACATATG
* *
48418 TTAACACATGATCATGATATATG
1 TTAAC-CAGGATC-TGACATATG
48441 TTA
1 TTA
48444 TTGGTGACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (21 bp):
TTAACCAGGATCTGACATATG
Found at i:48501 original size:130 final size:129
Alignment explanation
Indices: 48237--48501 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
48227 ATTTGGTCCT
* ** * *
48237 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* *** * * **** *
48302 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
48367 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* * * *
48432 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
48496 -A
128 CA
48497 AAATT
1 AAATT
48502 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:48956 original size:16 final size:18
Alignment explanation
Indices: 48935--48968 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
48925 ATTTCTTATT
48935 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
48951 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
48969 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:51831 original size:21 final size:21
Alignment explanation
Indices: 51807--51850 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
51797 TGTCCTGGAG
51807 CTGTCACCATTTTCCCTGCAC
1 CTGTCACCATTTTCCCTGCAC
51828 CTGTCACCATTTTCCCTGCAC
1 CTGTCACCATTTTCCCTGCAC
51849 CT
1 CT
51851 CACTGCACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.43, G:0.09, T:0.34
Consensus pattern (21 bp):
CTGTCACCATTTTCCCTGCAC
Found at i:52080 original size:22 final size:23
Alignment explanation
Indices: 52036--52080 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
52026 ATATATCAAA
* *
52036 TTTATGGAATCCTTTTTACGGTT
1 TTTATGGAATCCTTTCTAAGGTT
*
52059 TTTA-GGATTCCTTTCTAAGGTT
1 TTTATGGAATCCTTTCTAAGGTT
52081 AAAGGTTGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (23 bp):
TTTATGGAATCCTTTCTAAGGTT
Done.