Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006436.1 Hibiscus syriacus cultivar Beakdansim tig00015542_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: 78459
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3800 original size:7 final size:7
Alignment explanation
Indices: 3788--3813 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3778 GTAATGATGT
3788 ATTTTAA
1 ATTTTAA
3795 ATTTTAA
1 ATTTTAA
3802 ATTTTAA
1 ATTTTAA
3809 ATTTT
1 ATTTT
3814 GATTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTAA
Found at i:6451 original size:44 final size:44
Alignment explanation
Indices: 6388--6476 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
6378 CTCTCTGGTC
6388 TTTCTTTCTGGGTTAAATTATGATATTAATCCCTCTACTCGAAG
1 TTTCTTTCTGGGTTAAATTATGATATTAATCCCTCTACTCGAAG
6432 TTTCTTTCTGGGTTAAATTATGATATTAATCCCTCTACTCGAAG
1 TTTCTTTCTGGGTTAAATTATGATATTAATCCCTCTACTCGAAG
6476 T
1 T
6477 AAATTAGCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (44 bp):
TTTCTTTCTGGGTTAAATTATGATATTAATCCCTCTACTCGAAG
Found at i:12218 original size:2 final size:2
Alignment explanation
Indices: 12211--12243 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12201 TAGTGGGAAC
*
12211 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12244 CTCGTGGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15811 original size:18 final size:18
Alignment explanation
Indices: 15788--15825 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
15778 AGCATGAATG
15788 GAGACTCAGTGAGTGAGT
1 GAGACTCAGTGAGTGAGT
*
15806 GAGACTCAGTGAGTGGGT
1 GAGACTCAGTGAGTGAGT
15824 GA
1 GA
15826 AGAGATTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.42, T:0.21
Consensus pattern (18 bp):
GAGACTCAGTGAGTGAGT
Found at i:18742 original size:23 final size:22
Alignment explanation
Indices: 18691--18744 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
18681 TTTATTCCAT
*
18691 TCGATTAA-TAATTTTAAAAAA
1 TCGATTAATTAATATTAAAAAA
*
18712 T-AATTTAATTAATAATTAAAAAA
1 TCGA-TTAATTAAT-ATTAAAAAA
18735 TCGATTAATT
1 TCGATTAATT
18745 CAATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.04
21 5 0.19
22 4 0.15
23 15 0.58
24 1 0.04
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (22 bp):
TCGATTAATTAATATTAAAAAA
Found at i:22294 original size:303 final size:302
Alignment explanation
Indices: 21743--22352 Score: 1157
Period size: 303 Copynumber: 2.0 Consensus size: 302
21733 TAGAATAAAA
*
21743 TATTGTTGGGTAAATTACATGTTTAGTACCTAAAGTATTCATTTTTGTTCATTTTAGTACTTAAA
1 TATTTTTGGGTAAATTACATGTTTAGTACCTAAAGTATTCATTTTTGTTCATTTTAGTACTTAAA
*
21808 TTTTTAATTTTTCAAATCATACATAACGTTTAGTTTTTGTTTCAGCTTAATACTCCGTCGTTAAA
66 TTTTTAATTTTTCAAATCATACATAACATTTAGTTTTTGTTTCAGCTTAATACTCCGTCGTTAAA
*
21873 AACTTAATTGGTGGCCTTATTGACTGTCGCATTTGTCGGCCGATGAAGGCCAAACTTTCCATCCC
131 AACTTAATTGGTGGCCTTATCGACTGTCGCATTTGTCGGCCGATGAAGGCCAAACTTTCCATCCC
*
21938 ACACCTTTTCGACCACCTGAACATGATTTAGGCCTTCGTTTCACCTACAAATGCATGAATCTCCT
196 ACACCTTTTCGACCACCTGAACATGATTTAGGCCTTCGTTTCACCTACAAATGCATGAATCTCCC
*
22003 CAAATTGACTTCTTCATCCTCCGATCTTGACGTCTGAAGGGG
261 CAAATTGACTTCTTCATCCTCCGATCTTGACATCTGAAGGGG
*
22045 TATTTTTGGGTAAATTACATGTTTAGTACCTAAAGTATTCATTTTTGTTCGTTTTAGTACTTAAA
1 TATTTTTGGGTAAATTACATGTTTAGTACCTAAAGTATTCATTTTTGTTCATTTTAGTACTTAAA
22110 TTTTTAATTTTTTCAAATCATACATAACATTTAGTTTTTGTTTCAGCTTAATACTCCGTCGTTAA
66 TTTTTAA-TTTTTCAAATCATACATAACATTTAGTTTTTGTTTCAGCTTAATACTCCGTCGTTAA
22175 AAACTTAATTGGTGGCCTTATCGACTGTCGCATTTGTCGGCCGATGAAGGCCAAACTTTCCATCC
130 AAACTTAATTGGTGGCCTTATCGACTGTCGCATTTGTCGGCCGATGAAGGCCAAACTTTCCATCC
22240 CACACCTTTTCGACCACCTGAACATGATTTAGGCCTTCGTTTCACCTACAAATGCATGAATCTCC
195 CACACCTTTTCGACCACCTGAACATGATTTAGGCCTTCGTTTCACCTACAAATGCATGAATCTCC
22305 CCAAATTGACTTCTTCATCCTCCGATCTTGACATCTGAAGGGG
260 CCAAATTGACTTCTTCATCCTCCGATCTTGACATCTGAAGGGG
22348 TATTT
1 TATTT
22353 AAGTGTTCGT
Statistics
Matches: 301, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
302 70 0.23
303 231 0.77
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (302 bp):
TATTTTTGGGTAAATTACATGTTTAGTACCTAAAGTATTCATTTTTGTTCATTTTAGTACTTAAA
TTTTTAATTTTTCAAATCATACATAACATTTAGTTTTTGTTTCAGCTTAATACTCCGTCGTTAAA
AACTTAATTGGTGGCCTTATCGACTGTCGCATTTGTCGGCCGATGAAGGCCAAACTTTCCATCCC
ACACCTTTTCGACCACCTGAACATGATTTAGGCCTTCGTTTCACCTACAAATGCATGAATCTCCC
CAAATTGACTTCTTCATCCTCCGATCTTGACATCTGAAGGGG
Found at i:24529 original size:14 final size:14
Alignment explanation
Indices: 24512--24542 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
24502 ATTAATATTT
24512 TTAAAATAATTATA
1 TTAAAATAATTATA
*
24526 TTAAAATAATTTTA
1 TTAAAATAATTATA
24540 TTA
1 TTA
24543 TTACGCCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAAAATAATTATA
Found at i:34694 original size:10 final size:10
Alignment explanation
Indices: 34676--34705 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
34666 AAATTGGATG
34676 ATAAATATCA
1 ATAAATATCA
*
34686 ATGAATATCA
1 ATAAATATCA
34696 ATAAATATCA
1 ATAAATATCA
34706 CGACTAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (10 bp):
ATAAATATCA
Found at i:37484 original size:3 final size:3
Alignment explanation
Indices: 37476--37529 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
37466 ACCCTATATT
37476 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
37524 TAA TAA
1 TAA TAA
37530 AAGCTAGCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:47947 original size:30 final size:31
Alignment explanation
Indices: 47903--47964 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
47893 CAAATGGTCT
*
47903 CCGATTATACGGTGTTGTTTTATTGAGTCCC
1 CCGATTATACGGTGTTGCTTTATTGAGTCCC
* *
47934 CCGA-TATAGGGTGTTGCTTTGTTGAGTCCC
1 CCGATTATACGGTGTTGCTTTATTGAGTCCC
47964 C
1 C
47965 GGCTATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.39
Consensus pattern (31 bp):
CCGATTATACGGTGTTGCTTTATTGAGTCCC
Found at i:53805 original size:2 final size:2
Alignment explanation
Indices: 53792--53827 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
53782 GATAGACGAG
* *
53792 TA TA TA TG TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53828 GGGTAAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:54071 original size:2 final size:2
Alignment explanation
Indices: 54064--54093 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54054 TTCCTGCGCC
54064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54094 TATTTTCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55956 original size:29 final size:28
Alignment explanation
Indices: 55897--55975 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
55887 TTTTTTTATT
* * *
55897 TAAATATTTAAAGTATTTTTTATTAAGA
1 TAAATATCTAAAATATTTTTTATTAAAA
*
55925 TAAATATCTAAAATATTTTTTTTTCAAAA
1 TAAATATCTAAAATATTTTTTATT-AAAA
* *
55954 TAAGTACCTAAAATATTTTTTA
1 TAAATATCTAAAATATTTTTTA
55976 AATCAAAAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 21 0.49
29 22 0.51
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (28 bp):
TAAATATCTAAAATATTTTTTATTAAAA
Found at i:56157 original size:30 final size:31
Alignment explanation
Indices: 56106--56177 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
56096 GTTTTGACAT
*
56106 AAAAT-ATTTTAGATACATATTTT-AACTAA
1 AAAATAATTTTAAATACATATTTTGAACTAA
* **
56135 AAAATAATTTTAAATACTTATTTTGATTTAA
1 AAAATAATTTTAAATACATATTTTGAACTAA
*
56166 AAAATACTTTTA
1 AAAATAATTTTA
56178 CGTACTTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 5 0.14
30 16 0.44
31 15 0.42
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (31 bp):
AAAATAATTTTAAATACATATTTTGAACTAA
Found at i:56479 original size:3 final size:3
Alignment explanation
Indices: 56471--56512 Score: 66
Period size: 3 Copynumber: 13.3 Consensus size: 3
56461 ATAAAACGTC
56471 TAA TAA TAA TAAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA TAA TAA T
56513 TTTTTTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 31 0.82
4 7 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:62958 original size:27 final size:28
Alignment explanation
Indices: 62901--62964 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
62891 AATAATGTAT
* *
62901 TTATAATTATTTATTATATTTTAAACGA
1 TTATAATAATTTATTATATTTTAAACAA
* *
62929 TTATAATAATTT-TTATATTTTTAATAA
1 TTATAATAATTTATTATATTTTAAACAA
62956 TTA-AATAAT
1 TTATAATAAT
62965 ATACTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 6 0.19
27 15 0.47
28 11 0.34
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
TTATAATAATTTATTATATTTTAAACAA
Found at i:65142 original size:15 final size:15
Alignment explanation
Indices: 65122--65150 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
65112 ATATATCTCT
65122 TCTCATTTACATTTA
1 TCTCATTTACATTTA
65137 TCTCATTTACATTT
1 TCTCATTTACATTT
65151 CTAAGCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTCATTTACATTTA
Found at i:73160 original size:30 final size:28
Alignment explanation
Indices: 73126--73183 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
73116 AATTCGGTGA
73126 ATTCAATATGTCCTTCTCACTAGGAACTCC
1 ATTCAATATGTCC-T-TCACTAGGAACTCC
*
73156 ATTCAATATGTCCTTCATTAGGAACTCC
1 ATTCAATATGTCCTTCACTAGGAACTCC
73184 CAAACTCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 13 0.48
29 1 0.04
30 13 0.48
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (28 bp):
ATTCAATATGTCCTTCACTAGGAACTCC
Done.