Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008829.1 Hibiscus syriacus cultivar Beakdansim tig00112011_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: 58518
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5951 original size:62 final size:63
Alignment explanation
Indices: 5854--5985 Score: 239
Period size: 62 Copynumber: 2.1 Consensus size: 63
5844 ATCATTAATG
5854 GATTTAAAAGAAATTCGCTTTTGTTTTCCTTTAGCACAAGCATCACAGATTTTACCATTA-CA
1 GATTTAAAAGAAATTCGCTTTTGTTTTCCTTTAGCACAAGCATCACAGATTTTACCATTATCA
*
5916 GATTTAAAAGAAATTCGCTTTTGTTTTCCTTTAGCACAAGCATCACAGATTTTATCATTATCA
1 GATTTAAAAGAAATTCGCTTTTGTTTTCCTTTAGCACAAGCATCACAGATTTTACCATTATCA
*
5979 AATTTAA
1 GATTTAA
5986 GCTTAGGCAA
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 59 0.88
63 8 0.12
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (63 bp):
GATTTAAAAGAAATTCGCTTTTGTTTTCCTTTAGCACAAGCATCACAGATTTTACCATTATCA
Found at i:6861 original size:21 final size:22
Alignment explanation
Indices: 6837--6877 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6827 TAAGTTATGC
6837 AAATCAGT-ATTTTTCTTTTCA
1 AAATCAGTAATTTTTCTTTTCA
* *
6858 AAATCATTAATTTTTTTTTT
1 AAATCAGTAATTTTTCTTTT
6878 TGCAATTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.59
Consensus pattern (22 bp):
AAATCAGTAATTTTTCTTTTCA
Found at i:9015 original size:64 final size:64
Alignment explanation
Indices: 8901--9043 Score: 168
Period size: 64 Copynumber: 2.2 Consensus size: 64
8891 TGGACCCTTA
** *
8901 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGG-TAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTAAGAAAAA-CCTGAGTGCATCGATACATGGAT-T
8965 -
64 G
*
8965 GTGCATCGATGCATAAAATGCATTCGATGTTCAAGAAATTAA-TTGA-TGCATCGATACATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTT-AAGAAA--AACCTGAGTGCATCGATACATGGAT
9028 TG
63 TG
*
9030 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
9044 GCCCTTGAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
64 46 0.67
65 21 0.30
67 2 0.03
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTAAGAAAAACCTGAGTGCATCGATACATGGATTG
Found at i:9955 original size:34 final size:32
Alignment explanation
Indices: 9888--9984 Score: 151
Period size: 33 Copynumber: 3.0 Consensus size: 32
9878 TTTATTTTGT
*
9888 TCGGGTCGGGTTTTTTAAGTGTGATATTC-GG
1 TCGGGTCGGGTTTTTTAAGTGTGGTATTCGGG
9919 TCGGGTCGGGGTTTTTTTAAGTGTGGTATTCGGG
1 TCGGGTC-GGG-TTTTTTAAGTGTGGTATTCGGG
9953 TCGGGTCGGGATTTTTTAAGTGTGGTATTCGG
1 TCGGGTCGGG-TTTTTTAAGTGTGGTATTCGG
9985 ACCGACCCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
31 7 0.11
32 3 0.05
33 42 0.69
34 9 0.15
ACGTcount: A:0.11, C:0.09, G:0.38, T:0.41
Consensus pattern (32 bp):
TCGGGTCGGGTTTTTTAAGTGTGGTATTCGGG
Found at i:28130 original size:140 final size:139
Alignment explanation
Indices: 27660--28142 Score: 533
Period size: 136 Copynumber: 3.5 Consensus size: 139
27650 AAACAAGTTA
* * * * *
27660 AGGTTGAACAAGTTCTTCTCATTACGAACTTCTT-T-CCTCTCATCGGATAAGTTCTTCTCATTA
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCT-TTATCGGATGAGTTCTTCTCATTA
* * * * * *
27723 TGAACTCTCCA-CTGAAAATATTGATCCTTCAAGCGAGGTATTGTTGATTCGAAGTGT-T--G-T
65 TGAACTCTCCATATG-AAATGTTGATCCCTCAAGCGAGGTGTTGTTGATTC-AACTATATGCGAT
*
27783 GAATCGAGCAAT
128 GAATCGAGCTAT
* * *
27795 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTATCGGATGAGTTCTTCTCATTAT
* * *** **
27860 GAACTCTCCATATGAAATG-TCATTCCCTCAAGCGAGGCGTCACTGATTCAA--A-ATGTAATGA
66 GAACTCTCCATATGAAATGTTGA-TCCCTCAAGCGAGGTGTTGTTGATTCAACTATATGCGATGA
*
27921 ATCCAG-TGAT
130 ATCGAGCT-AT
27931 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTATCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTATCGGATGAGTTCTTCTCATTAT
* * *
27996 GAACTCTCCATTTGAAGTGTTGATCCCTCAAGTGAGGTGTTGTTGATTCAACTCCATATGCGATG
66 GAACTCTCCATATGAAATGTTGATCCCTCAAGCGAGGTGTTGTTGATTCAACT--ATATGCGATG
28061 AATCGAGCTA-
129 AATCGAGCTAT
* * * * *
28071 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTTTGTTGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTATCGGATGAGTTCTTCTCATTAT
28136 GAACTCT
66 GAACTCT
28143 TCTGGAAATG
Statistics
Matches: 292, Mismatches: 40, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
133 1 0.00
135 35 0.12
136 167 0.57
137 7 0.02
140 68 0.23
141 13 0.04
142 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (139 bp):
AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTATCGGATGAGTTCTTCTCATTAT
GAACTCTCCATATGAAATGTTGATCCCTCAAGCGAGGTGTTGTTGATTCAACTATATGCGATGAA
TCGAGCTAT
Found at i:28256 original size:105 final size:105
Alignment explanation
Indices: 28076--28484 Score: 622
Period size: 105 Copynumber: 3.9 Consensus size: 105
28066 AGCTAAGGTT
* * * *
28076 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTTTGTTGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTACGAAC--CTTCTCC--TT-TAGGACGAGTTCTTCTCATTATGAACT
*
28141 CTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATTTGAAAG
61 CTTCTGGAAATGTTGGTTCACCTCCTTCTGGGGTGAATTTGAAAG
* *
28186 GAACAAGTTCTTCTCATTACAAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
1 GAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
* *
28251 GGAAATGTCGGTTCACCTCCTTCT-GGGTGAATTCGAAAG
66 GGAAATGTTGGTTCACCTCCTTCTGGGGTGAATTTGAAAG
* * *
28290 GAACAGGCTCTTCTCATTACGAACCTTTTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCT
1 GAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
* * *
28355 GGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAAG
66 GGAAATGTTGGTTCACCTCCTTCTGGGGTGAATTTGAAAG
*
28395 GAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
1 GAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
28460 GGAAATGTTGGTTCACCTCCTTCTG
66 GGAAATGTTGGTTCACCTCCTTCTG
28485 CAGTGGATTT
Statistics
Matches: 277, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
104 96 0.35
105 150 0.54
106 2 0.01
108 7 0.03
110 22 0.08
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (105 bp):
GAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
GGAAATGTTGGTTCACCTCCTTCTGGGGTGAATTTGAAAG
Found at i:33863 original size:12 final size:12
Alignment explanation
Indices: 33846--33870 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33836 CTGCCCTGCA
33846 GAATGAATCCAT
1 GAATGAATCCAT
33858 GAATGAATCCAT
1 GAATGAATCCAT
33870 G
1 G
33871 GTCTCCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (12 bp):
GAATGAATCCAT
Found at i:41575 original size:24 final size:24
Alignment explanation
Indices: 41526--41576 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
41516 TATATTATAT
* *
41526 ACAAAGTAATATATAATAATACAA
1 ACAAAATAATATATAAAAATACAA
41550 ACAAAATAATATATAAAACATA-AA
1 ACAAAATAATATATAAAA-ATACAA
41574 ACA
1 ACA
41577 TACTTTAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.22
Consensus pattern (24 bp):
ACAAAATAATATATAAAAATACAA
Found at i:43297 original size:22 final size:18
Alignment explanation
Indices: 43252--43287 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43242 TTAATAAATA
43252 AAATAAATATTATTTATT
1 AAATAAATATTATTTATT
*
43270 ATATAAATATATATTTAT
1 AAATAAATAT-TATTTAT
43288 GGCTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATAAATATTATTTATT
Found at i:43396 original size:21 final size:20
Alignment explanation
Indices: 43370--43410 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
43360 TATATATTTA
*
43370 AAATAAATAAAACTTGTAAAT
1 AAATAAATAAAAATTG-AAAT
43391 AAATAAATAAAAATTGAAAT
1 AAATAAATAAAAATTGAAAT
43411 TAGTGACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (20 bp):
AAATAAATAAAAATTGAAAT
Found at i:44861 original size:3 final size:3
Alignment explanation
Indices: 44853--44898 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
44843 ATTTTTTATT
* *
44853 TAA TAA TAA TAT TATA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
44899 ATATGATGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 36 0.95
4 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:56904 original size:20 final size:20
Alignment explanation
Indices: 56810--57178 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
56800 GATTTTCCAT
* ** *
56810 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
56830 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
56850 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
56870 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
56890 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
56910 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
56930 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
56950 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
56970 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
56990 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
57010 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
57030 AATCACAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
57050 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
57070 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
57090 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
57110 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
57130 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
57150 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
57170 AATCACAAC
1 AATCGCAAC
57179 ACTTAAATTT
Statistics
Matches: 303, Mismatches: 36, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.01
20 295 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:57897 original size:22 final size:23
Alignment explanation
Indices: 57855--57899 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
57845 AAATTTGGTC
57855 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATA-CCGGACTTTGATA
*
57879 TTGGTCAATA-CGGATTTTGAT
1 TTGGTCAATACCGGACTTTGAT
57900 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
24 10 0.50
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.40
Consensus pattern (23 bp):
TTGGTCAATACCGGACTTTGATA
Found at i:58084 original size:12 final size:12
Alignment explanation
Indices: 58067--58091 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58057 ATATAATCCT
58067 GAAGAAGAAAAA
1 GAAGAAGAAAAA
58079 GAAGAAGAAAAA
1 GAAGAAGAAAAA
58091 G
1 G
58092 TCCCGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Done.