Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001640.1 Hibiscus syriacus cultivar Beakdansim tig00003280_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: 51650
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:15903 original size:18 final size:18
Alignment explanation
Indices: 15880--15922 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
15870 ATTGAACGTC
15880 GTTCTAATATAAAGAGTT
1 GTTCTAATATAAAGAGTT
15898 GTTCTAATATAAAGAGTT
1 GTTCTAATATAAAGAGTT
15916 GTTCTAA
1 GTTCTAA
15923 GGAGTCGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (18 bp):
GTTCTAATATAAAGAGTT
Found at i:23209 original size:7 final size:6
Alignment explanation
Indices: 23163--23363 Score: 63
Period size: 6 Copynumber: 31.0 Consensus size: 6
23153 ATTTTGCTTG
23163 AAGAATA AATGAAA AAGAAA AAGAGAA AAG-AA AAGAAA AAGGAAA AA-AATGA
1 AAGAA-A AA-GAAA AAGAAA AAGA-AA AAGAAA AAGAAA AA-GAAA AAGAA--A
* * *
23215 AATGAAAA AATGAAA ATGATGAA AAGAAA AAGAAA AATGAAAA AACGGAG
1 AA-G-AAA AA-GAAA AAGA--AA AAGAAA AAGAAA AA-G-AAA AA-GAAA
* * * * *
23265 AA-AAA TAGAAA ATGGGAAA ATGAAAAA AATGAAA AA-AAA ATGACA AAGAAA
1 AAGAAA AAGAAA A--AGAAA A--AGAAA AA-GAAA AAGAAA AAGAAA AAGAAA
* * * *
23316 AAGAAAA AAGGAA AAGAAA AATG-AT GA-AAA AAGAAA AAGAGA AAGAAA
1 AAG-AAA AAGAAA AAGAAA AA-GAAA AAGAAA AAGAAA AAGAAA AAGAAA
23364 TTAAAGGGGG
Statistics
Matches: 147, Mismatches: 25, Indels: 45
0.68 0.12 0.21
Matches are distributed among these distances:
5 15 0.10
6 61 0.41
7 39 0.27
8 30 0.20
10 2 0.01
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (6 bp):
AAGAAA
Found at i:23225 original size:8 final size:8
Alignment explanation
Indices: 23214--23301 Score: 52
Period size: 8 Copynumber: 10.4 Consensus size: 8
23204 GAAAAAAATG
23214 AAATGAAA
1 AAATGAAA
23222 AAATGAAA
1 AAATGAAA
*
23230 ATGATGAAA
1 A-AATGAAA
**
23239 AGAAAAAGAA
1 A-AATGA-AA
23249 AAATGAAA
1 AAATGAAA
*
23257 AAACGGAGAA
1 AAA-TGA-AA
*
23267 AAAT-AGA
1 AAATGAAA
**
23274 AAATGGGA
1 AAATGAAA
23282 AAATGAAAA
1 AAATG-AAA
23291 AAATGAAA
1 AAATGAAA
23299 AAA
1 AAA
23302 AAATGACAAA
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
7 5 0.08
8 28 0.46
9 20 0.33
10 8 0.13
ACGTcount: A:0.70, C:0.01, G:0.18, T:0.10
Consensus pattern (8 bp):
AAATGAAA
Found at i:23229 original size:22 final size:22
Alignment explanation
Indices: 23188--23245 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
23178 AGAAAAAGAG
23188 AAAA-GAAAAG-AAAAAGGAAA
1 AAAATGAAAAGAAAAAAGGAAA
* *
23208 AAAATGAAATGAAAAAATGAAA
1 AAAATGAAAAGAAAAAAGGAAA
**
23230 ATGATGAAAAGAAAAA
1 AAAATGAAAAGAAAAA
23246 GAAAAATGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 4 0.13
21 5 0.16
22 22 0.71
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (22 bp):
AAAATGAAAAGAAAAAAGGAAA
Found at i:23286 original size:60 final size:56
Alignment explanation
Indices: 23169--23363 Score: 158
Period size: 55 Copynumber: 3.5 Consensus size: 56
23159 CTTGAAGAAT
23169 AAATGAAAAAGA--AAAAGAGAAAAG-AAAAG-AAAAAGGAAAAAAATGAAATGAAA
1 AAATGAAAAAGATGAAAAGA-AAAAGAAAAAGAAAAAAGGAAAAAAATGAAATGAAA
* * **
23222 AAATGAAAATGATGAAAAGAAAAAGAAAAATGAAAAAACGGAGAAAAATAGAAAATGGGA
1 AAATGAAAAAGATGAAAAGAAAAAGAAAAA-GAAAAAA-GGAAAAAAAT-G-AAATGAAA
* * * *
23282 AAATGAAAAAAATGAAAA-AAAAATGACAAAG-AAAAA-G-AAAAAAGGAAAAGAAA
1 AAATGAAAAAGATGAAAAGAAAAA-GAAAAAGAAAAAAGGAAAAAAATGAAATGAAA
*
23335 AATGATGAAAAA-A-GAAAAAGAGAAAGAAA
1 AA--ATGAAAAAGATG-AAAAGAAAAAGAAA
23364 TTAAAGGGGG
Statistics
Matches: 115, Mismatches: 14, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
53 19 0.17
54 14 0.12
55 27 0.23
56 2 0.02
57 5 0.04
58 14 0.12
59 7 0.06
60 27 0.23
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (56 bp):
AAATGAAAAAGATGAAAAGAAAAAGAAAAAGAAAAAAGGAAAAAAATGAAATGAAA
Found at i:23303 original size:11 final size:11
Alignment explanation
Indices: 23287--23324 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
23277 TGGGAAAATG
23287 AAAAAAATGAA
1 AAAAAAATGAA
23298 AAAAAAATGACA
1 AAAAAAATGA-A
23310 AAGAAAAA-GAA
1 AA-AAAAATGAA
23321 AAAA
1 AAAA
23325 GGAAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 13 0.52
12 5 0.20
13 5 0.20
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.05
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:23322 original size:19 final size:18
Alignment explanation
Indices: 23296--23336 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
23286 GAAAAAAATG
*
23296 AAAAAAAAATGACAAAGAA
1 AAAAAAAAAGGA-AAAGAA
23315 AAAGAAAAAAGGAAAAGAA
1 AAA-AAAAAAGGAAAAGAA
23334 AAA
1 AAA
23337 TGATGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAGGAAAAGAA
Found at i:23430 original size:45 final size:44
Alignment explanation
Indices: 23366--23450 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
23356 GAAAGAAATT
* * *
23366 AAAGGGGGTTCAAGATGAAAATCCGCAAAGGACGTCTTGAAACC
1 AAAGGAGGTTCAAGATGAAAACCCGCAAAGGACGGCTTGAAACC
* *
23410 AAAGGAGGTCTCAAGTTGAAAACCCGCAAAGGGCGGCTTGA
1 AAAGGAGGT-TCAAGATGAAAACCCGCAAAGGACGGCTTGA
23451 GTTTTGTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 8 0.23
45 27 0.77
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.15
Consensus pattern (44 bp):
AAAGGAGGTTCAAGATGAAAACCCGCAAAGGACGGCTTGAAACC
Found at i:24654 original size:37 final size:36
Alignment explanation
Indices: 24605--24676 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
24595 CAAAACAAGT
24605 CCATCTTAAGCCTTCACGAAAGAGCAGTGAAGCAAA
1 CCATCTTAAGCCTTCACGAAAGAGCAGTGAAGCAAA
* *
24641 CCATCTATAAGCCTTCACGGAAGAGTAGTGAAGCAA
1 CCATCT-TAAGCCTTCACGAAAGAGCAGTGAAGCAA
24677 GCTCATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 6 0.18
37 27 0.82
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (36 bp):
CCATCTTAAGCCTTCACGAAAGAGCAGTGAAGCAAA
Found at i:24825 original size:55 final size:53
Alignment explanation
Indices: 24693--24946 Score: 214
Period size: 55 Copynumber: 4.7 Consensus size: 53
24683 TTTATAAAGA
* * * * * *
24693 TCGAGTCATATACTCTCTGAATGAATAGGGAGCGGATACGTTTTTTGAAGA----
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGC--AGACCTTTTATGAAGATTGT
* * * *
24744 TCGAGTCTTATACTCTCTGAAGGAATATGGAGCATACTCGTTTTATAAAGATTGT
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGAC-C-TTTTATGAAGATTGT
* * * * * * *
24799 TCGAGTTTTATACTCTCTGAAAGAATAGAGAGCGGGCCCATTTTCTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGC-AGACC-TTTTATGAAGATTGT
*
24854 TCGAGT-TCTATACTCCCTGAACGAATAGGGAG-AGGACCTATTTATTGAAGATTGT
1 TCGAGTCT-TATACTCCCTGAAGGAATAGGGAGCA-GACCT-TTTA-TGAAGATTGT
24909 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACC
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACC
24947 CGTCATTCAA
Statistics
Matches: 167, Mismatches: 23, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
49 4 0.02
51 39 0.23
53 1 0.01
54 7 0.04
55 113 0.68
56 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (53 bp):
TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACCTTTTATGAAGATTGT
Found at i:27020 original size:21 final size:21
Alignment explanation
Indices: 26994--27038 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
26984 GATTTCTGGG
* *
26994 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
27015 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
27036 CAA
1 CAA
27039 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:28779 original size:149 final size:149
Alignment explanation
Indices: 28601--28915 Score: 567
Period size: 149 Copynumber: 2.1 Consensus size: 149
28591 GAGTCGACGG
* *
28601 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
28666 ACTTGATCCCTAGTATATGTATATGATTCTTAATGAATAATATGTGGTCCTTAGGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTGAGGGACATTATTA
28731 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
28750 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
28815 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTGATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTGAGGGACATTATTA
28880 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
28899 TCTACGCGGTACTTCGG
1 TCTACGCGGTCCTTCGG
28916 TGTAATTATA
Statistics
Matches: 159, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 159 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTGAGGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:32196 original size:76 final size:76
Alignment explanation
Indices: 32059--32206 Score: 192
Period size: 76 Copynumber: 1.9 Consensus size: 76
32049 ATTAATCCAA
* ** *
32059 TAGGATGAGACATTAGATATCTCAAGTAAAGTCATGAGTTTGAATCCGGACGTTTGCGGATAGAT
1 TAGGATGAGACATTAGATATCTCAAGCAAAGTCATGAGTTTGAATCCGGAAATTTGCGGATAGAG
32124 CAAACTATTGG
66 CAAACTATTGG
* * * *
32135 TAGGATGAGGCATTAGA-ACTCTCAAGCAAGGTCATGAGTTTGAATCAC-TAAATTTGTGGATAG
1 TAGGATGAGACATTAGATA-TCTCAAGCAAAGTCATGAGTTTGAATC-CGGAAATTTGCGGATAG
32198 AGCAAACTA
64 AGCAAACTA
32207 AGTTTTGAGA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
75 1 0.02
76 60 0.97
77 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (76 bp):
TAGGATGAGACATTAGATATCTCAAGCAAAGTCATGAGTTTGAATCCGGAAATTTGCGGATAGAG
CAAACTATTGG
Found at i:33141 original size:2 final size:2
Alignment explanation
Indices: 33134--33169 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
33124 ATACCTCTAC
33134 TA TA TA TA TA TA TA -A 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 TA TA TA TA TA T
33170 TTAATTACTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35221 original size:3 final size:3
Alignment explanation
Indices: 35199--35266 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
35189 GAAAACAAAT
* * * *
35199 TAA TAAA TAA -AA TAAA TAA TAA TAG TAA TAC TAT TAA TAT TAA TAA
1 TAA T-AA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
35245 CAA TAA AAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
35267 GGTATTCGGA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:45461 original size:19 final size:18
Alignment explanation
Indices: 45433--45472 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
45423 AATAACACTA
45433 TAATTTAAACACTTATTT
1 TAATTTAAACACTTATTT
*
45451 TAATATTAAACATTTATTT
1 TAAT-TTAAACACTTATTT
45470 TAA
1 TAA
45473 ATGCCCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTTAAACACTTATTT
Done.