Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005807.1 Hibiscus syriacus cultivar Beakdansim tig00013615_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: 44419
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:17990 original size:19 final size:18
Alignment explanation
Indices: 17953--17997 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
17943 ACAGATGTTT
*
17953 TCTCTTATCCTGTTCTGA
1 TCTCTGATCCTGTTCTGA
*
17971 TCTCTGATCACTGTTTTGA
1 TCTCTGATC-CTGTTCTGA
*
17990 TTTCTGAT
1 TCTCTGAT
17998 ATCTCTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.13, C:0.22, G:0.13, T:0.51
Consensus pattern (18 bp):
TCTCTGATCCTGTTCTGA
Found at i:18164 original size:66 final size:66
Alignment explanation
Indices: 18058--18187 Score: 197
Period size: 66 Copynumber: 2.0 Consensus size: 66
18048 GGTATGAAGA
** *
18058 CTCTGGCAGGTTCAGTCGTTGCGGGTAATTCCTTGTATAGGTTTTGTACCGACTGGTAATTCCTA
1 CTCTGGCAGGTTCAGTCGTTGCGGGTAATTCCTTGTATAGGTTCAGCACCGACTGGTAATTCCTA
18123 T
66 T
** * *
18124 CTCTGGCAGGTTCAGTCGTTGTTGGTAATTCCTTTTATAGGTTCAGCACTGACTGGTAATTCCT
1 CTCTGGCAGGTTCAGTCGTTGCGGGTAATTCCTTGTATAGGTTCAGCACCGACTGGTAATTCCT
18188 TATGGACCTA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (66 bp):
CTCTGGCAGGTTCAGTCGTTGCGGGTAATTCCTTGTATAGGTTCAGCACCGACTGGTAATTCCTA
T
Found at i:27910 original size:19 final size:18
Alignment explanation
Indices: 27877--27921 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
27867 ACAGATGTTT
*
27877 TCTCTTATCCTGTTCTGA
1 TCTCTGATCCTGTTCTGA
27895 TCTCTGATCACTGTTCTGA
1 TCTCTGATC-CTGTTCTGA
*
27914 TTTCTGAT
1 TCTCTGAT
27922 ATCTCTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.13, C:0.24, G:0.13, T:0.49
Consensus pattern (18 bp):
TCTCTGATCCTGTTCTGA
Found at i:28102 original size:66 final size:66
Alignment explanation
Indices: 27982--28111 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
27972 GGTATGAAGA
* *
27982 CTCTGGCAGGTTCAGTCGTTGCGGGTAATTCTTTGTATAGGTTTTATACCGACTGGTAATTCCTA
1 CTCTGGCAGGTTCAGTCGTTGCGGGTAATTCTTTGTATAGGTTTCACACCGACTGGTAATTCCTA
28047 T
66 T
** *
28048 CTCTGGCAGGTTCAGTCGTTGTTGGTAATTCCTTT-TATAGG-TTCAGCACTGACTGGTAATTCC
1 CTCTGGCAGGTTCAGTCGTTGCGGGTAATT-CTTTGTATAGGTTTCA-CACCGACTGGTAATTCC
28111 T
64 T
28112 TATGGACCTA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
65 3 0.05
66 50 0.88
67 4 0.07
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (66 bp):
CTCTGGCAGGTTCAGTCGTTGCGGGTAATTCTTTGTATAGGTTTCACACCGACTGGTAATTCCTA
T
Found at i:32942 original size:115 final size:115
Alignment explanation
Indices: 32730--32944 Score: 394
Period size: 115 Copynumber: 1.9 Consensus size: 115
32720 TAATTTATCA
* *
32730 TGAATTTTTAAATATTATCATTTCACTGTATCTATGCATCAAGTTATGATTAAATATTAAAATAA
1 TGAATTTTTAAATATTATCATTTCACTATATCTATGCATCAAGTTATAATTAAATATTAAAATAA
*
32795 AATTAATAACTATATTTTTTGTCTCATAAAAAATAGTTAACAATAATAGT
66 AATTAATAACTAGATTTTTTGTCTCATAAAAAATAGTTAACAATAATAGT
32845 TGAATTTTTAAATATTATCATTTCACTATATCTATGCATCAAGTTATAATTAAATATTAAAATAA
1 TGAATTTTTAAATATTATCATTTCACTATATCTATGCATCAAGTTATAATTAAATATTAAAATAA
32910 AATTAATAACTAGAGTTTTTTGTCTCATAAAAAAT
66 AATTAATAACTAGA-TTTTTTGTCTCATAAAAAAT
32945 TTAATTATAA
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
115 76 0.79
116 20 0.21
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.42
Consensus pattern (115 bp):
TGAATTTTTAAATATTATCATTTCACTATATCTATGCATCAAGTTATAATTAAATATTAAAATAA
AATTAATAACTAGATTTTTTGTCTCATAAAAAATAGTTAACAATAATAGT
Found at i:41002 original size:87 final size:87
Alignment explanation
Indices: 40856--41018 Score: 229
Period size: 87 Copynumber: 1.9 Consensus size: 87
40846 TATGTTATAT
* * * *
40856 CATTTAATCGGAAATATTATCAAGCACAACTACATATTAAGTAACGTTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAACACAACTACAAATTAAGTAACGTTTATATAATGTAATAGGT
*
40921 ATCGCTTATATAATAAAATAGA
66 AACGCTTATATAATAAAATAGA
* * * *
40943 CATTTAACCGAAAATATTATCAAATAGAA-TAACAAATTAGGTAGCGTTTATATAATGTAATAGG
1 CATTTAACCGAAAATATTATCAAACACAACT-ACAAATTAAGTAACGTTTATATAATGTAATAGG
41007 TAACGCTTATAT
65 TAACGCTTATAT
41019 TGATATATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
86 1 0.02
87 65 0.98
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAACACAACTACAAATTAAGTAACGTTTATATAATGTAATAGGT
AACGCTTATATAATAAAATAGA
Done.