Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002813.1 Hibiscus syriacus cultivar Beakdansim tig00005790_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: 65814
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:10887 original size:47 final size:44
Alignment explanation
Indices: 10801--10902 Score: 116
Period size: 47 Copynumber: 2.2 Consensus size: 44
10791 ATTCGACTCA
* *
10801 GTCATAATAATCTGCTCCACTCCTCAACAAAGAATGTTGGCTTG
1 GTCATAATAATCTGCTCAACTCCTCAACAAAGAATGTTGGATTG
* *
10845 GTCATAATAATCTGCTCAATTCTTCCATAGCAAAGTAA-GTTGGATTG
1 GTCATAATAATCTGCTCAACTCCT-CA-A-CAAAG-AATGTTGGATTG
*
10892 ATCATAATAAT
1 GTCATAATAAT
10903 GTACTTCACT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
44 21 0.43
45 2 0.04
46 1 0.02
47 23 0.47
48 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (44 bp):
GTCATAATAATCTGCTCAACTCCTCAACAAAGAATGTTGGATTG
Found at i:21113 original size:49 final size:49
Alignment explanation
Indices: 21057--21157 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
21047 TAAAGAACAT
21057 AAGAATAGTAATTTTACTATTTCCTTTACCTTGCAAATTAATGGATAAA
1 AAGAATAGTAATTTTACTATTTCCTTTACCTTGCAAATTAATGGATAAA
21106 AAGAATAGTAATTTTACTATTTCCTTTACCTTGCAAATTAATGGATAAA
1 AAGAATAGTAATTTTACTATTTCCTTTACCTTGCAAATTAATGGATAAA
21155 AAG
1 AAG
21158 TGTGTTAGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.38
Consensus pattern (49 bp):
AAGAATAGTAATTTTACTATTTCCTTTACCTTGCAAATTAATGGATAAA
Found at i:21211 original size:20 final size:22
Alignment explanation
Indices: 21166--21222 Score: 82
Period size: 20 Copynumber: 2.6 Consensus size: 22
21156 AGTGTGTTAG
21166 TTGCCAAACATTAACCGGACATGA
1 TTGCC-AACATTAACCGGA-ATGA
21190 TTGCCAACATTAACC-G-ATGA
1 TTGCCAACATTAACCGGAATGA
21210 TTGCCAACATTAA
1 TTGCCAACATTAA
21223 ACAAATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 10 0.30
24 5 0.15
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (22 bp):
TTGCCAACATTAACCGGAATGA
Found at i:21326 original size:23 final size:23
Alignment explanation
Indices: 21265--21326 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
21255 TTTGCGAAAG
** *
21265 TTAAACGAATATGTTGACAAGCA
1 TTAAACGAACGTGTTTACAAGCA
*
21288 TTAAACGAACGTGTTTACAAGCG
1 TTAAACGAACGTGTTTACAAGCA
*
21311 TTAAATGAACGTGTTT
1 TTAAACGAACGTGTTT
21327 GCGAATGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (23 bp):
TTAAACGAACGTGTTTACAAGCA
Found at i:25160 original size:32 final size:32
Alignment explanation
Indices: 25119--25224 Score: 160
Period size: 32 Copynumber: 3.3 Consensus size: 32
25109 AAAGCTCATG
* *
25119 TGCATTATCTGAATGCAACACCAACTCTGCTA
1 TGCATTATCTGAATGCAATACTAACTCTGCTA
25151 TGCATTATCTGAATGCAATACTAACTCTGCTA
1 TGCATTATCTGAATGCAATACTAACTCTGCTA
* *
25183 TACATTATCTGAATGCAATACTGACTCTGCTA
1 TGCATTATCTGAATGCAATACTAACTCTGCTA
*
25215 -GCACTATCTG
1 TGCATTATCTG
25225 GATGAAAGAC
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
31 8 0.12
32 60 0.88
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (32 bp):
TGCATTATCTGAATGCAATACTAACTCTGCTA
Found at i:31794 original size:21 final size:21
Alignment explanation
Indices: 31770--31819 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
31760 TAGTATTGAC
31770 ACTACTGTTCACGGTATCAAT
1 ACTACTGTTCACGGTATCAAT
*
31791 ACTACTGTTCATGGTATCAAT
1 ACTACTGTTCACGGTATCAAT
*
31812 ATTACTGT
1 ACTACTGT
31820 AGTAGTATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (21 bp):
ACTACTGTTCACGGTATCAAT
Found at i:31896 original size:21 final size:21
Alignment explanation
Indices: 31872--31911 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31862 TCGGTACTGT
*
31872 TCATGGTATCGATACTACTAG
1 TCATGGTATCAATACTACTAG
31893 TCATGGTATCAATACTACT
1 TCATGGTATCAATACTACT
31912 GTTCACATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (21 bp):
TCATGGTATCAATACTACTAG
Found at i:31941 original size:20 final size:20
Alignment explanation
Indices: 31898--31973 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
31888 ACTAGTCATG
*
31898 GTATCAATACTACTGTTCACATA
1 GTATCAATACTA---TTCATATA
*
31921 GTATCAATATTATTCATATA
1 GTATCAATACTATTCATATA
*
31941 GTATCAATACTATTCATACA
1 GTATCAATACTATTCATATA
*
31961 GTAT-AGTACTATT
1 GTATCAATACTATT
31974 AAAAAACAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 8 0.17
20 29 0.60
23 11 0.23
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (20 bp):
GTATCAATACTATTCATATA
Found at i:32265 original size:23 final size:23
Alignment explanation
Indices: 32237--32280 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
32227 AAAAGCCTTG
*
32237 TTTACCAAAACCATAAAACTCCA
1 TTTACCAAAACCAAAAAACTCCA
*
32260 TTTACCATAACCAAAAAACTC
1 TTTACCAAAACCAAAAAACTC
32281 TGTTTCTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (23 bp):
TTTACCAAAACCAAAAAACTCCA
Found at i:41427 original size:13 final size:13
Alignment explanation
Indices: 41398--41440 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
41388 GCAAGCACTC
*
41398 AAAAGAAGAAAACA
1 AAAAGAAG-AAAGA
41412 AAAAGAAGAAAGA
1 AAAAGAAGAAAGA
* *
41425 AAAAAAAGCAAGA
1 AAAAGAAGAAAGA
41438 AAA
1 AAA
41441 GTTGAAAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 18 0.69
14 8 0.31
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAAGA
Found at i:41428 original size:14 final size:14
Alignment explanation
Indices: 41398--41440 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
41388 GCAAGCACTC
41398 AAAAGAAGAAA-ACA
1 AAAAGAAGAAAGA-A
41412 AAAAGAAGAAAGAA
1 AAAAGAAGAAAGAA
*
41426 AAAA-AAGCAAGAA
1 AAAAGAAGAAAGAA
41439 AA
1 AA
41441 GTTGAAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 10 0.37
14 16 0.59
15 1 0.04
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAGAA
Found at i:52610 original size:17 final size:16
Alignment explanation
Indices: 52572--52604 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
52562 TATCGCCAAC
*
52572 CAAATTTTACTATTCA
1 CAAAATTTACTATTCA
52588 CAAAATTTACTATTCA
1 CAAAATTTACTATTCA
52604 C
1 C
52605 GTAAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (16 bp):
CAAAATTTACTATTCA
Found at i:54542 original size:22 final size:23
Alignment explanation
Indices: 54517--54568 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
54507 GTAATAGTAG
* * *
54517 ATTAATATGATTA-TAATTATAT
1 ATTAATATAAATATTAACTATAT
54539 ATT-ATATAAATATTAACTATAT
1 ATTAATATAAATATTAACTATAT
*
54561 ACTAATAT
1 ATTAATAT
54569 TAGGGATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 7 0.29
22 13 0.54
23 4 0.17
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTAATATAAATATTAACTATAT
Done.