Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005124.1 Hibiscus syriacus cultivar Beakdansim tig00011523_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: 59304
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:7609 original size:3 final size:3
Alignment explanation
Indices: 7603--7670 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
7593 TCATTTAAAT
** * *
7603 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7651 TTA TTA -TA TT- TTA TTTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA
7671 AATATTACAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:16980 original size:114 final size:114
Alignment explanation
Indices: 16780--17002 Score: 347
Period size: 114 Copynumber: 2.0 Consensus size: 114
16770 TGCTATATGA
* * *
16780 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAACTGTTCTTTGAGTTATCTGATTTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAACTGTTCTTTGAGTTATCTGATCTGG
* * * *
16845 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTGC
* *
16894 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAACTGTTCTTTGAGTTATCTGATCTGG
* *
16959 TTCGGTAGGAATCCCATAACCAATCATTGAAATTGAAAGATGAA
66 TTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAA
17003 CTGCATGATC
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 98 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAACTGTTCTTTGAGTTATCTGATCTGG
TTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTGC
Found at i:19035 original size:54 final size:54
Alignment explanation
Indices: 18953--19107 Score: 256
Period size: 54 Copynumber: 2.9 Consensus size: 54
18943 GAAATCTTGG
*
18953 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATTTGAA
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
* *
19007 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAG
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
***
19061 CAGAAGCCACAGGAAAGGATGAATGCACTGTCAAATGTTTTACGAAC
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
19108 CTGCTATTCT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 94 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.23
Consensus pattern (54 bp):
CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
Found at i:19500 original size:22 final size:22
Alignment explanation
Indices: 19474--19572 Score: 180
Period size: 22 Copynumber: 4.5 Consensus size: 22
19464 ATCTACACTC
19474 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
19496 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
19518 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
19540 TTTAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
19562 TTCAAAGATGA
1 TTCAAAGATGA
19573 AAGCTTTATG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:20556 original size:76 final size:76
Alignment explanation
Indices: 20246--20960 Score: 1299
Period size: 76 Copynumber: 9.4 Consensus size: 76
20236 CTATTTCTCA
*
20246 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
20311 AGCCTTAGGGT
66 AGCCTTAGGGT
20322 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
20386 AGCCTTAGGGT
66 AGCCTTAGGGT
20397 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
20462 AAGCCTTAGGGT
65 AAGCCTTAGGGT
20474 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
20539 AGCCTTAGGGT
66 AGCCTTAGGGT
20550 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
20615 AATCCTTAGGGT
65 AAGCCTTAGGGT
20627 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
20692 AGCCTTAGGGT
66 AGCCTTAGGGT
20703 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
20768 AGCCTTAGGGT
66 AGCCTTAGGGT
*
20779 CATCTGTAAGTCCTACAGTGCATGGTGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
20844 A-CCTTCGGGT
66 AGCCTTAGGGT
*
20854 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
20919 AAACCTTCGGGT
65 AAGCCTTAGGGT
* * *
20931 CATTTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
20961 TCAACATTTC
Statistics
Matches: 623, Mismatches: 11, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
75 144 0.23
76 294 0.47
77 185 0.30
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:20591 original size:153 final size:152
Alignment explanation
Indices: 20246--20960 Score: 1299
Period size: 153 Copynumber: 4.7 Consensus size: 152
20236 CTATTTCTCA
*
20246 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
20311 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
20375 GATGTTTTCAAAGCCTTAGGGT
131 GATGTTTTCAAAGCCTTAGGGT
20397 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
20462 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
65 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
20527 TGATGTTTTCAAAGCCTTAGGGT
130 TGATGTTTTCAAAGCCTTAGGGT
20550 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
20615 AATCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
65 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
20680 TGATGTTTTCAAAGCCTTAGGGT
130 TGATGTTTTCAAAGCCTTAGGGT
20703 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
20768 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGGTGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
20833 GATGTTTTCAAA-CCTTCGGGT
131 GATGTTTTCAAAGCCTTAGGGT
*
20854 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* * * * *
20919 AAACCTTCGGGTCATTTGTAAGCCCTTCAGTGCATGATGTTT
65 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTT
20961 TCAACATTTC
Statistics
Matches: 549, Mismatches: 12, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
151 101 0.18
152 221 0.40
153 227 0.41
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (152 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTAGGGT
Found at i:21099 original size:3 final size:3
Alignment explanation
Indices: 21091--21158 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
21081 TCATTTAAAT
** * *
21091 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21139 TTA TTA TATA TTA TTTA TTA
1 TTA TTA T-TA TTA -TTA TTA
21159 AATATTACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:39573 original size:60 final size:60
Alignment explanation
Indices: 39478--39595 Score: 191
Period size: 60 Copynumber: 2.0 Consensus size: 60
39468 TCTCGAAGAC
** *
39478 TAGGAAGGAGCCTGATGATGGTGGGTTGGATGGAGAAGGGGATACTGGGAACAGAAGAAA
1 TAGGAAGGAGCCTGATGATGGTGCATTGGAAGGAGAAGGGGATACTGGGAACAGAAGAAA
* *
39538 TAGGAAGGAGCCTGATGATGGTGCATTGGAAGGAGAAGTGGATACTGGGAATAGAAGA
1 TAGGAAGGAGCCTGATGATGGTGCATTGGAAGGAGAAGGGGATACTGGGAACAGAAGA
39596 TCTAATTTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.34, C:0.07, G:0.42, T:0.18
Consensus pattern (60 bp):
TAGGAAGGAGCCTGATGATGGTGCATTGGAAGGAGAAGGGGATACTGGGAACAGAAGAAA
Found at i:43737 original size:20 final size:20
Alignment explanation
Indices: 43712--43751 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
43702 TATTTTTGGT
43712 TATAATCGAAATTATTATCA
1 TATAATCGAAATTATTATCA
*
43732 TATAATTGAAATTATTATCA
1 TATAATCGAAATTATTATCA
43752 ATGATAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (20 bp):
TATAATCGAAATTATTATCA
Found at i:44959 original size:33 final size:33
Alignment explanation
Indices: 44917--45016 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
44907 AGTTTATGAT
* * *
44917 AATTGAAATACTTAAATACTTACAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
44950 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
44983 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
45016 A
1 A
45017 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:54180 original size:21 final size:21
Alignment explanation
Indices: 54139--54181 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
54129 TTTTGTTGGT
*
54139 TTTGGAACTAGCGCAGTTGGA
1 TTTGGAACTAGCGCAGATGGA
**
54160 TTTGGAACTAGTTCAGATGGA
1 TTTGGAACTAGCGCAGATGGA
54181 T
1 T
54182 GTAAAATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.33
Consensus pattern (21 bp):
TTTGGAACTAGCGCAGATGGA
Done.