Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007966.1 Hibiscus syriacus cultivar Beakdansim tig00110396_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: 85816
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:3906 original size:38 final size:42
Alignment explanation
Indices: 3852--3934 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 42
3842 TGGTTATTGG
*
3852 TTAATAAATGGTAAG-TAT-G-AAAATAAGCTTACGAGCTTA
1 TTAATAAATGGAAAGATATGGAAAAATAAGCTTACGAGCTTA
3891 TTAAT-AATGGAAAGTATATGGATAAAATAAGCTTACGAGCTTA
1 TTAATAAATGGAAAG-ATATGGA-AAAATAAGCTTACGAGCTTA
3934 T
1 T
3935 GGGATAAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
38 8 0.21
39 5 0.13
40 3 0.08
41 1 0.03
43 21 0.55
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.31
Consensus pattern (42 bp):
TTAATAAATGGAAAGATATGGAAAAATAAGCTTACGAGCTTA
Found at i:5170 original size:30 final size:30
Alignment explanation
Indices: 5136--5204 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
5126 TTATATGAGT
*
5136 TATGTGATAAAGGTATGG-AAATGATATGTC
1 TATGTGATAAAGGTA-GGAAAATAATATGTC
5166 TATGTGATAAAGGTAGGAAAATAATATGTC
1 TATGTGATAAAGGTAGGAAAATAATATGTC
*
5196 TACGTGATA
1 TATGTGATA
5205 CAAATTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 2 0.06
30 34 0.94
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGTGATAAAGGTAGGAAAATAATATGTC
Found at i:5453 original size:23 final size:23
Alignment explanation
Indices: 5423--5466 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
5413 ATGGTATTAC
5423 GGTGCAATTCTACGCGGCACTCT
1 GGTGCAATTCTACGCGGCACTCT
*
5446 GGTGCAATTCTACGTGGCACT
1 GGTGCAATTCTACGCGGCACT
5467 TCGGTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTCT
Found at i:5476 original size:23 final size:22
Alignment explanation
Indices: 5422--5477 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
5412 TATGGTATTA
5422 CGGTGCAATTCTACGCGGCACT
1 CGGTGCAATTCTACGCGGCACT
*
5444 CTGGTGCAATTCTACGTGGCACTT
1 C-GGTGCAATTCTACGCGGCAC-T
*
5468 CGGTTCAATT
1 CGGTGCAATT
5478 ATATGAGCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 1 0.03
23 27 0.90
24 2 0.07
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (22 bp):
CGGTGCAATTCTACGCGGCACT
Found at i:6270 original size:23 final size:23
Alignment explanation
Indices: 6239--6330 Score: 123
Period size: 23 Copynumber: 4.0 Consensus size: 23
6229 CAACACAGCT
*
6239 CGTATAAATGCACC-GAAGTGCCA
1 CGTAGAAATGCACCTG-AGTGCCA
* *
6262 CGTAGAAATACACCTGAGTGCCG
1 CGTAGAAATGCACCTGAGTGCCA
6285 CGTAGAAATGCACCTGAGTGCCA
1 CGTAGAAATGCACCTGAGTGCCA
* *
6308 TGTAGAAATGCACCGGAGTGCCA
1 CGTAGAAATGCACCTGAGTGCCA
6331 TATAAAATGT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 60 0.98
24 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCTGAGTGCCA
Found at i:6411 original size:21 final size:21
Alignment explanation
Indices: 6384--6463 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
6374 CATCTACATA
6384 TTCCAAAGGACCA-A-ATATG
1 TTCCAAAGGACCACATATATG
*
6403 TGTCTCAAAAGACCACATATATG
1 T-TC-CAAAGGACCACATATATG
**
6426 TTCCAAAGGATTACATATATG
1 TTCCAAAGGACCACATATATG
*
6447 -TCACGAAGGACCACATA
1 TTC-CAAAGGACCACATA
6464 CATCTTCGAC
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 1 0.02
20 4 0.08
21 35 0.71
22 3 0.06
23 6 0.12
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (21 bp):
TTCCAAAGGACCACATATATG
Found at i:8557 original size:13 final size:14
Alignment explanation
Indices: 8514--8560 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
8504 TTGATAATTT
8514 ATTTTCACAACTAAA
1 ATTTT-ACAACTAAA
*
8529 ATTTTACAAC-ATA
1 ATTTTACAACTAAA
*
8542 ATTTT-CCACTAAA
1 ATTTTACAACTAAA
8555 ATTTTA
1 ATTTTA
8561 TAAATACAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
12 3 0.11
13 14 0.52
14 5 0.19
15 5 0.19
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTTTACAACTAAA
Found at i:9880 original size:31 final size:31
Alignment explanation
Indices: 9842--9918 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
9832 TAAAAAAAAA
* *
9842 AAGTTTTGGTCACTTACGTTATTGTTTTGTT
1 AAGTTTTGGTCACTTACGTTATCGTTTTATT
*
9873 AAGTTTTGGTCACTTATGTTATCGTTTTATT
1 AAGTTTTGGTCACTTACGTTATCGTTTTATT
*
9904 AAATTTTGGTCACTT
1 AAGTTTTGGTCACTT
9919 GGACGTTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.53
Consensus pattern (31 bp):
AAGTTTTGGTCACTTACGTTATCGTTTTATT
Found at i:33725 original size:25 final size:25
Alignment explanation
Indices: 33691--33739 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
33681 CTTCAAGATG
33691 CAGAAACCTCAGCCGCACCATGATA
1 CAGAAACCTCAGCCGCACCATGATA
* *
33716 CAGAACCCTCAGTCGCACCATGAT
1 CAGAAACCTCAGCCGCACCATGAT
33740 GCCAACACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.37, G:0.16, T:0.14
Consensus pattern (25 bp):
CAGAAACCTCAGCCGCACCATGATA
Found at i:34653 original size:23 final size:23
Alignment explanation
Indices: 34622--34686 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 23
34612 CACCACAGCT
* *
34622 CGTATAAATGCACC-ATAGTTCCG
1 CGTAGAAATGCACCGA-AGTACCG
34645 CGTAGAAATGCACCGAAGTACCG
1 CGTAGAAATGCACCGAAGTACCG
34668 CGTAGAAATGCACCGAAGT
1 CGTAGAAATGCACCGAAGT
34687 GCCATATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTACCG
Found at i:35089 original size:2 final size:2
Alignment explanation
Indices: 35077--35132 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
35067 TTTTATGTCT
35077 TA TA T- TA TA TA TA TA TA TA TA 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 TA TA TA
35118 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
35133 CACCTAGATC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35835 original size:17 final size:17
Alignment explanation
Indices: 35804--35841 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
35794 ACTCACACAC
35804 TCATAACAAACACATGT
1 TCATAACAAACACATGT
35821 TCATAACAAACACATGT
1 TCATAACAAACACATGT
35838 TCAT
1 TCAT
35842 GTTCATACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (17 bp):
TCATAACAAACACATGT
Found at i:72733 original size:19 final size:19
Alignment explanation
Indices: 72704--72747 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
72694 GAAAGATTCG
72704 AAATT-GGTGGAATATCGT
1 AAATTAGGTGGAATATCGT
72722 AAATTAGGTGGAATATCGT
1 AAATTAGGTGGAATATCGT
72741 AAATTAG
1 AAATTAG
72748 TTCTAAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (19 bp):
AAATTAGGTGGAATATCGT
Found at i:75526 original size:55 final size:55
Alignment explanation
Indices: 75460--75876 Score: 353
Period size: 55 Copynumber: 7.8 Consensus size: 55
75450 GTGAAGCAAA
* *
75460 TGAAGATTGTTCGAGTCTTATACTCTCTGAACAAATAGAGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * * * *
75515 TGAAGATTGTTCAAGTCTCATACTCTCTTAAGCAATAGGGAGCAGACATGAATAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* *
75570 TGAAAATTGTTCGAGTC-TATACTCTCTGAAGAAATAGGGAGCAGACACGAATGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * * *
75624 TGAAAATTATTTGAGTCTTATACTCTTTGAAGGAATA-GG-G-AGACACGTTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * * *
75676 TGAAGGTTGTTCAAGTCATATACTCTCTGAAAAAATAGGGAGCGGACACGTTTGAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG-T
* * * *
75732 TGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATGGGGAGCGGACAC-ATTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGT
* * * * ** *
75783 TGAAGA-T-TT--AGTCCTATACTCTCTGAAGGAATAGAGAACAGACTTG-TTTT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * *
75833 ATGAAGATTGTTTGAGT-TTTTACTCCCTGAAGCAAA-AGGGAGCA
1 -TGAAGATTGTTCGAGTCTTATACTCTCTGAAG-AAATAGGGAGCA
75877 AACCCAGTGG
Statistics
Matches: 296, Mismatches: 52, Indels: 29
0.79 0.14 0.08
Matches are distributed among these distances:
50 3 0.01
51 43 0.15
52 76 0.26
53 7 0.02
54 68 0.23
55 93 0.31
56 6 0.02
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
Found at i:75841 original size:51 final size:51
Alignment explanation
Indices: 75582--75825 Score: 165
Period size: 52 Copynumber: 4.7 Consensus size: 51
75572 AAAATTGTTC
* * * * *
75582 GAGT-CTATACTCTCTGAAGAAATAGGGAGCAGACACGA-ATGTTGAAAATTATTT
1 GAGTCCTATACTCTCTGAAGGAATAGAGAACAGACAC-ATTTGTTG--AA-GA-TT
* * * * *
75636 GAGTCTTATACTCTTTGAAGGAATAG-G--GAGACACGTTTGTTGAAGGTT
1 GAGTCCTATACTCTCTGAAGGAATAGAGAACAGACACATTTGTTGAAGATT
* ** * * * *
75684 GTTCAAGTCATATACTCTCTGAAAAAATAGGGAGCGGACACGTTTGATTGAAGATT
1 G----AGTCCTATACTCTCTGAAGGAATAGAGAACAGACACATTTG-TTGAAGATT
* * * *
75740 GAGTCCTATACTCTCTGAAGGAATGGGGAGCGGACACATTTGTTGAAGATT
1 GAGTCCTATACTCTCTGAAGGAATAGAGAACAGACACATTTGTTGAAGATT
*
75791 TAGTCCTATACTCTCTGAAGGAATAGAGAACAGAC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAACAGAC
75826 TTGTTTTATG
Statistics
Matches: 155, Mismatches: 25, Indels: 23
0.76 0.12 0.11
Matches are distributed among these distances:
48 3 0.02
50 2 0.01
51 39 0.25
52 68 0.44
53 1 0.01
54 5 0.03
55 28 0.18
56 9 0.06
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.28
Consensus pattern (51 bp):
GAGTCCTATACTCTCTGAAGGAATAGAGAACAGACACATTTGTTGAAGATT
Found at i:79375 original size:146 final size:142
Alignment explanation
Indices: 79086--79368 Score: 385
Period size: 145 Copynumber: 2.0 Consensus size: 142
79076 ATATATATTA
* * *
79086 TATAGATGAAACTTATGATTTTAAGACTTGTAAGAAAAATAATTTTCTTTTATCTTTGAGATAGA
1 TATAGATGAAACTGATGATTTTAAAACTTATAAGAAAAATAATTTTCTTTTATCTTTGAGATAGA
* * *
79151 TGGGTTTAATATTCTAATTATTTAAAATGCAATAAAAATATAAATTTTATGAAAATTATATTATA
66 TGAGTTTAATATTCTAATTATTTAAAA-GAAATAAAAATATAAAGTTTA-GAAAATTATATTATA
79216 ACAACCTCTATACT
129 ACAACCTCTATACT
*
79230 TATAGATGTAACTGATTGATTTTAAAACTTATAAGAAAAATAATTTTTCTTTTA-CTATTGAGAT
1 TATAGATGAAACTGA-TGATTTTAAAACTTATAAGAAAAATAA-TTTTCTTTTATCT-TTGAGAT
* *
79294 AGATGAGTTTAATATTTCTAATTTTTTAAAA-AAATAAAAATAT-AAGTTTA-CAAATTATTATT
63 AGATGAGTTTAATA-TTCTAATTATTTAAAAGAAATAAAAATATAAAGTTTAGAAAATTA-TATT
*
79356 ATAAGAACCTCTA
126 ATAACAACCTCTA
79369 ATATACTAAA
Statistics
Matches: 124, Mismatches: 10, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
142 6 0.05
143 16 0.13
144 19 0.15
145 38 0.31
146 30 0.24
147 15 0.12
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.41
Consensus pattern (142 bp):
TATAGATGAAACTGATGATTTTAAAACTTATAAGAAAAATAATTTTCTTTTATCTTTGAGATAGA
TGAGTTTAATATTCTAATTATTTAAAAGAAATAAAAATATAAAGTTTAGAAAATTATATTATAAC
AACCTCTATACT
Found at i:79821 original size:6 final size:6
Alignment explanation
Indices: 79810--79915 Score: 108
Period size: 6 Copynumber: 18.0 Consensus size: 6
79800 ATTATTGCAT
79810 GGGTTG GGGTTG GGGTTG GGGTT- GGGTTG GGGTTG GGGTTG GGGTTG
1 GGGTTG GGGTTG GGGTTG GGGTTG GGGTTG GGGTTG GGGTTG GGGTTG
* * * * * * * *
79857 GGGCTG GGGCT- GGGCTG AGGTTG AGGTTG AGGTTG AGGTTG AGGTTG
1 GGGTTG GGGTTG GGGTTG GGGTTG GGGTTG GGGTTG GGGTTG GGGTTG
* *
79904 AGGTTG AGGTTG
1 GGGTTG GGGTTG
79916 AGAAATGATA
Statistics
Matches: 95, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
5 10 0.11
6 85 0.89
ACGTcount: A:0.07, C:0.03, G:0.59, T:0.31
Consensus pattern (6 bp):
GGGTTG
Found at i:80112 original size:24 final size:22
Alignment explanation
Indices: 80080--80143 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 22
80070 ACTACAAGAT
*
80080 TAATAATTTTGTTTAAATTTTATA
1 TAATTATTTT-TTTAAATTTTA-A
*
80104 TAATTATTTTTACTAAATTTTAA
1 TAATTATTTTT-TTAAATTTTAA
*
80127 AAATATATTTTATTTAA
1 TAAT-TATTTT-TTTAA
80144 TTAAAATTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 5 0.15
24 27 0.82
25 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TAATTATTTTTTTAAATTTTAA
Found at i:84717 original size:15 final size:15
Alignment explanation
Indices: 84697--84729 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
84687 TAATATCTTT
84697 AATATCTTTAATTAA
1 AATATCTTTAATTAA
84712 AATATCTTTAATTAA
1 AATATCTTTAATTAA
84727 AAT
1 AAT
84730 GCAAATGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATCTTTAATTAA
Found at i:85770 original size:4 final size:4
Alignment explanation
Indices: 85761--85796 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
85751 CGCTCATGTT
*
85761 TATG TATG TATG TATG TATG TATG TATG TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
85797 AATTTTTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
TATG
Done.