Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002021.1 Hibiscus syriacus cultivar Beakdansim tig00004130_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: 48373
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:2396 original size:31 final size:31
Alignment explanation
Indices: 2361--2420 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
2351 AAAATATAAT
2361 ATTTAGTCACTTT-TAAT-TTTATTTAATTAAG
1 ATTTAGTCACTTTCT--TCTTTATTTAATTAAG
2392 ATTTAGTCACTTTCTTCTTTATTTAATTA
1 ATTTAGTCACTTTCTTCTTTATTTAATTA
2421 GGATGTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 1 0.04
31 25 0.93
32 1 0.04
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (31 bp):
ATTTAGTCACTTTCTTCTTTATTTAATTAAG
Found at i:5792 original size:20 final size:20
Alignment explanation
Indices: 5764--5803 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5754 CTACTGCTTC
*
5764 AAAATTAGTTAACATTTATT
1 AAAAATAGTTAACATTTATT
*
5784 AAAAATAGTTAACTTTTATT
1 AAAAATAGTTAACATTTATT
5804 TTCTTGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
AAAAATAGTTAACATTTATT
Found at i:6344 original size:18 final size:17
Alignment explanation
Indices: 6321--6366 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
6311 TGTTTATGAG
6321 GGAATTGGAATATGTGAA
1 GGAATTGGAATATGT-AA
* * *
6339 GGAATTGAAATCTGTCA
1 GGAATTGGAATATGTAA
6356 GGAATTGGAAT
1 GGAATTGGAAT
6367 CCAATTTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.37, C:0.04, G:0.30, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATATGTAA
Found at i:7003 original size:31 final size:30
Alignment explanation
Indices: 6891--7005 Score: 108
Period size: 28 Copynumber: 3.6 Consensus size: 30
6881 TTTTCACCAT
* *
6891 AAAACCGAACCCGACCCAAATATCAAACTTA
1 AAAACCG-ACCCGACCCGAATATCACACTTA
*
6922 AAAA--GATCCGACCCGAATATCACACTTAAA
1 AAAACCGACCCGACCCGAATATCACACTT--A
6952 AAAACCGACCGACTCGACCCGAATATCACACTTA
1 AAAACCGA-C--C-CGACCCGAATATCACACTTA
*
6986 AAAACCCGACCCAACCCGAA
1 AAAA-CCGACCCGACCCGAA
7006 CAAAATAAAG
Statistics
Matches: 70, Mismatches: 5, Indels: 18
0.75 0.05 0.19
Matches are distributed among these distances:
28 19 0.27
29 1 0.01
30 5 0.07
31 12 0.17
32 3 0.04
34 6 0.09
35 5 0.07
36 19 0.27
ACGTcount: A:0.44, C:0.34, G:0.10, T:0.12
Consensus pattern (30 bp):
AAAACCGACCCGACCCGAATATCACACTTA
Found at i:7379 original size:22 final size:22
Alignment explanation
Indices: 7353--7397 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
7343 AATTCCCTCC
7353 AACAAATAAATTGAATTTCATT
1 AACAAATAAATTGAATTTCATT
7375 AACAAATAAATTGAATTTCATT
1 AACAAATAAATTGAATTTCATT
7397 A
1 A
7398 TTCTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (22 bp):
AACAAATAAATTGAATTTCATT
Found at i:14772 original size:2 final size:2
Alignment explanation
Indices: 14765--14793 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14755 TTATACATAC
14765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14794 GTGGATGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15225 original size:25 final size:25
Alignment explanation
Indices: 15197--15246 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
15187 GTGAGCACAG
*
15197 CTAATCTGGGGATTGAGTAAACTTA
1 CTAATCTGGGGATAGAGTAAACTTA
*
15222 CTAATCTGGTGATAGAGTAAACTTA
1 CTAATCTGGGGATAGAGTAAACTTA
15247 TTAACTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (25 bp):
CTAATCTGGGGATAGAGTAAACTTA
Found at i:17797 original size:46 final size:46
Alignment explanation
Indices: 17729--17819 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
17719 AATATTTTGT
* *
17729 TTTAATTTATATATAGTTAAATAAGACACTATATTTCTTAAGATCC
1 TTTAATTTATATATAGTGAAATAAGACACTATATCTCTTAAGATCC
17775 TTTAATTTATATATAGTGAAATAAGACACTATATCTCTTAAGATC
1 TTTAATTTATATATAGTGAAATAAGACACTATATCTCTTAAGATC
17820 TCTTAAGATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (46 bp):
TTTAATTTATATATAGTGAAATAAGACACTATATCTCTTAAGATCC
Found at i:21608 original size:19 final size:19
Alignment explanation
Indices: 21576--21615 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21566 TTATTTAGAT
*
21576 TTTATGATAATCTTATTAA
1 TTTATGATAATCTTAATAA
* *
21595 TTTATTATAGTCTTAATAA
1 TTTATGATAATCTTAATAA
21614 TT
1 TT
21616 AAAATTGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTATGATAATCTTAATAA
Found at i:27907 original size:23 final size:22
Alignment explanation
Indices: 27881--27924 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
27871 GATAATAATG
27881 TTTCTTAT-TATTGTATTCATTAT
1 TTTCTTATAT-TTGTATT-ATTAT
27904 TTTCTTATATTTGTATTATTA
1 TTTCTTATATTTGTATTATTA
27925 ATATATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 15 0.75
24 1 0.05
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTCTTATATTTGTATTATTAT
Found at i:34176 original size:18 final size:19
Alignment explanation
Indices: 34153--34204 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
34143 TACTTACTCA
* *
34153 TCATGGGCATGGGT-ATGG
1 TCATGGTCATGGATGATGG
34171 TCATGGTCAT-GATGATGG
1 TCATGGTCATGGATGATGG
34189 TCATGGTCAT-GATGAT
1 TCATGGTCATGGATGAT
34205 CGCTGGAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 2 0.06
18 29 0.94
ACGTcount: A:0.21, C:0.12, G:0.35, T:0.33
Consensus pattern (19 bp):
TCATGGTCATGGATGATGG
Found at i:34194 original size:6 final size:6
Alignment explanation
Indices: 34153--34199 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
34143 TACTTACTCA
* * *
34153 TCATGG GCATGGG T-ATGG TCATGG TCATGA TGATGG TCATGG TCATG
1 TCATGG TCAT-GG TCATGG TCATGG TCATGG TCATGG TCATGG TCATG
34200 ATGATCGCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 3 0.09
6 28 0.85
7 2 0.06
ACGTcount: A:0.19, C:0.13, G:0.36, T:0.32
Consensus pattern (6 bp):
TCATGG
Found at i:34287 original size:7 final size:7
Alignment explanation
Indices: 34275--34310 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
34265 AGAGGGAATT
34275 GAGTGAG
1 GAGTGAG
34282 GAGTGAG
1 GAGTGAG
34289 GAGTGAG
1 GAGTGAG
34296 GAGTGAG
1 GAGTGAG
34303 GAGTGAG
1 GAGTGAG
34310 G
1 G
34311 GAATTCACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.58, T:0.14
Consensus pattern (7 bp):
GAGTGAG
Found at i:39981 original size:127 final size:127
Alignment explanation
Indices: 39755--40001 Score: 458
Period size: 127 Copynumber: 1.9 Consensus size: 127
39745 TTATCTCTAA
* *
39755 CTATATAAATATCCTTTAACTATATGAAGGTCAGTTATACCATTATTCCCCAATTCAATCTTGAA
1 CTATATAAATATCCTTTAACTATATGAAGGCCAATTATACCATTATTCCCCAATTCAATCTTGAA
39820 TTTTCCACCCTAAACCTAGACCCTATCTTCTCCTTCAAAAATTCCAACTCAACCCGAACCTG
66 TTTTCCACCCTAAACCTAGACCCTATCTTCTCCTTCAAAAATTCCAACTCAACCCGAACCTG
*
39882 CTATATAAATATCCTTTAACTATATGAAGGCCAATTATACCATTATTCCCCAATTCAATCTTGTA
1 CTATATAAATATCCTTTAACTATATGAAGGCCAATTATACCATTATTCCCCAATTCAATCTTGAA
*
39947 TTTTCCACCCTAAACCTAGACCCTATCTTCTCCTTCAAAACTTCCAACTCAACCC
66 TTTTCCACCCTAAACCTAGACCCTATCTTCTCCTTCAAAAATTCCAACTCAACCC
40002 ACTGAATTTT
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 116 1.00
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (127 bp):
CTATATAAATATCCTTTAACTATATGAAGGCCAATTATACCATTATTCCCCAATTCAATCTTGAA
TTTTCCACCCTAAACCTAGACCCTATCTTCTCCTTCAAAAATTCCAACTCAACCCGAACCTG
Done.