Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006914.1 Hibiscus syriacus cultivar Beakdansim tig00017712_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: 45799
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3451 original size:10 final size:10
Alignment explanation
Indices: 3433--3466 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3423 TAAGAGTATC
3433 AATATTTTAA
1 AATATTTTAA
*
3443 AATAATTT-A
1 AATATTTTAA
3452 AATATTTTAA
1 AATATTTTAA
3462 AATAT
1 AATAT
3467 AAAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AATATTTTAA
Found at i:3474 original size:19 final size:19
Alignment explanation
Indices: 3433--3471 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3423 TAAGAGTATC
**
3433 AATATTTTAAAATAATTTA
1 AATATTTTAAAATAATAAA
3452 AATATTTTAAAAT-ATAAA
1 AATATTTTAAAATAATAAA
3470 AA
1 AA
3472 ATAAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATTTTAAAATAATAAA
Found at i:4312 original size:2 final size:2
Alignment explanation
Indices: 4300--4334 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4290 AATAAATAAA
*
4300 AT AT AT A- AT AT AT AT AT AT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4335 GTAGAATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4923 original size:29 final size:31
Alignment explanation
Indices: 4891--4958 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
4881 TATAAAAAGA
4891 AATAAAAT-AC-ATACATATATACATATA-AT
1 AATAAAATAACAATA-ATATATACATATATAT
*
4920 AATAATAATAACAATAATATATATATATATAT
1 AATAA-AATAACAATAATATATACATATATAT
4952 AATAAAA
1 AATAAAA
4959 ACGTAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
29 5 0.15
30 3 0.09
31 16 0.47
32 10 0.29
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (31 bp):
AATAAAATAACAATAATATATACATATATAT
Found at i:6595 original size:105 final size:105
Alignment explanation
Indices: 6413--6966 Score: 937
Period size: 105 Copynumber: 5.3 Consensus size: 105
6403 TTGTGTTTTT
*
6413 GAGTCCAATATCCTTCGTTGTGAAGTT-AAATTGGCTCTGAAATTGAGAAATATTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAAT-GTTTGTTGACAA
*
6477 CCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
6518 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
6583 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
6623 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGATAAATGTTCG-TGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
6687 CAGCGGTCCCTTCGTCGTGAAGTTGAA--TGCGTTGTCCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
6725 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
6790 CAGCGGT-CC--CGTCGTGAAGTTGAACTTGCG-TGTCCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
6826 GAGTCCAATATCCTTCGTTGTGTGAAGTTGAAA-TGGCTCTGAAATTGAGAAATGTTTGTTGACA
1 GAGTCCAATATCCTTCG-T-TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACA
6890 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
6932 GAGTCCAATATCCTTCGTTGGGAAGTTGAAATTGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
6967 GCTGGGTAAA
Statistics
Matches: 427, Mismatches: 11, Indels: 22
0.93 0.02 0.05
Matches are distributed among these distances:
100 15 0.04
101 23 0.05
102 111 0.26
103 29 0.07
104 46 0.11
105 157 0.37
106 46 0.11
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:6771 original size:207 final size:205
Alignment explanation
Indices: 6413--6966 Score: 918
Period size: 207 Copynumber: 2.7 Consensus size: 205
6403 TTGTGTTTTT
*
6413 GAGTCCAATATCCTTCGTTGTGAAGTT-AAATTGGCTCTGAAATTGAGAAATATTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAAT-GTTTGTTGACAA
*
6477 CCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAAC-TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
6542 GTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
129 GTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGT-CC--CGTCGTGAAGTT
*
6607 GAACTTACGTTGTCTG
191 GAACTTACG-TGTCCG
* *
6623 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGATAAATGTTCG-TGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
6687 CAGCGGTCCCTTCGTCGTGAAGTTGAA-TGCGTTGTCCGGAGTCCAATATCCTTCGTTGTGAAGT
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
6751 TGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCGTCGTGAAGTTGAACT
131 TGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCGTCGTGAAGTTGAACT
*
6816 TGCGTGTCCG
196 TACGTGTCCG
6826 GAGTCCAATATCCTTCGTTGTGTGAAGTTGAAA-TGGCTCTGAAATTGAGAAATGTTTGTTGACA
1 GAGTCCAATATCCTTCG-T-TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACA
*
6890 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGGGA
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAAC-TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
6955 AGTTGAAATTGG
128 AGTTGAAATTGG
6967 GCTGGGTAAA
Statistics
Matches: 326, Mismatches: 12, Indels: 15
0.92 0.03 0.04
Matches are distributed among these distances:
203 22 0.07
204 44 0.13
205 47 0.14
206 2 0.01
207 125 0.38
209 33 0.10
210 30 0.09
211 23 0.07
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (205 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCGTCGTGAAGTTGAACT
TACGTGTCCG
Found at i:17161 original size:10 final size:10
Alignment explanation
Indices: 17136--17197 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
17126 AAGGTTAGTA
*
17136 AAATAGAAAT
1 AAATAAAAAT
*
17146 AGATAAAAAT
1 AAATAAAAAT
17156 AAATAAAAAT
1 AAATAAAAAT
**
17166 AAATGGTAAAT
1 AAAT-AAAAAT
*
17177 AAA-AAACAT
1 AAATAAAAAT
17186 AAA-AAAAAT
1 AAATAAAAAT
17195 AAA
1 AAA
17198 AAGGTTAGGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
9 14 0.33
10 21 0.50
11 7 0.17
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:18479 original size:16 final size:16
Alignment explanation
Indices: 18458--18507 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
18448 TATACATACG
18458 TATATAATAATAAAAA
1 TATATAATAATAAAAA
** *
18474 TATATAATAGCATAAA
1 TATATAATAATAAAAA
* *
18490 TAAATAATAATAATAA
1 TATATAATAATAAAAA
18506 TA
1 TA
18508 GTAAAAAGTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (16 bp):
TATATAATAATAAAAA
Found at i:20629 original size:31 final size:27
Alignment explanation
Indices: 20582--20637 Score: 76
Period size: 31 Copynumber: 1.9 Consensus size: 27
20572 TTAAAATGAT
20582 TATTTTGTCTTTCATTTTATATTTAGAA
1 TATTTTGTCTTTCATTTTAT-TTTAGAA
20610 TATTTTAGTCATTATCATTTTATTTTAG
1 TATTTT-GTC-TT-TCATTTTATTTTAG
20638 GGCAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 6 0.24
29 3 0.12
30 7 0.28
31 9 0.36
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.61
Consensus pattern (27 bp):
TATTTTGTCTTTCATTTTATTTTAGAA
Found at i:21389 original size:11 final size:11
Alignment explanation
Indices: 21373--21414 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
21363 TTTAATTGAA
21373 TTATTTATATT
1 TTATTTATATT
21384 TTATTTATATT
1 TTATTTATATT
*
21395 TTATCTTAT-TA
1 TTAT-TTATATT
21406 TTATTTATA
1 TTATTTATA
21415 AATAGTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 4 0.14
11 20 0.71
12 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTTATATT
Found at i:21410 original size:16 final size:17
Alignment explanation
Indices: 21372--21414 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
21362 TTTTAATTGA
*
21372 ATTATTTATATTTTATT
1 ATTATTTATATCTTATT
21389 -TATATTT-TATCTTATT
1 AT-TATTTATATCTTATT
21405 ATTATTTATA
1 ATTATTTATA
21415 AATAGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATTTATATCTTATT
Found at i:21594 original size:66 final size:61
Alignment explanation
Indices: 21477--21614 Score: 168
Period size: 66 Copynumber: 2.2 Consensus size: 61
21467 AACATGTGGC
* * **
21477 TTTCATTCAACAATTATTTCTCATCTATCCCATCCGACTTTCGAAAATAAAGGGCGACAAACATT
1 TTTCATTCAACAATTATTTATCATCTATCACATCCGACTACCGAAAATAAA--G-G--AAACATT
21542 G
61 G
* * *
21543 TTTCATTCAACAATTATTTATGATCTATCACATCCGACTACCTAAATTAAAGGAAACATTG
1 TTTCATTCAACAATTATTTATCATCTATCACATCCGACTACCGAAAATAAAGGAAACATTG
21604 TTTCATTCAAC
1 TTTCATTCAAC
21615 TTAGCTTTCT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
61 19 0.29
63 1 0.02
64 1 0.02
66 44 0.68
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (61 bp):
TTTCATTCAACAATTATTTATCATCTATCACATCCGACTACCGAAAATAAAGGAAACATTG
Found at i:22696 original size:25 final size:26
Alignment explanation
Indices: 22668--22727 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
22658 GATTAATATT
* *
22668 AATTTTATAAAAAT-GAAAAACACTA
1 AATTTTATAAAAATAAAAAAAAACTA
**
22693 AA-TTTATAAATTTAAAAAAAAACTA
1 AATTTTATAAAAATAAAAAAAAACTA
22718 AATTTTATAA
1 AATTTTATAA
22728 TTTCTCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 9 0.31
25 13 0.45
26 7 0.24
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (26 bp):
AATTTTATAAAAATAAAAAAAAACTA
Found at i:22724 original size:26 final size:28
Alignment explanation
Indices: 22683--22750 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 28
22673 TATAAAAATG
*
22683 AAAAACACTAAA-TTTATAAATT-T-AA
1 AAAAAAACTAAATTTTATAAATTCTCAA
*
22708 AAAAAAACTAAATTTTATAATTTCTCAA
1 AAAAAAACTAAATTTTATAAATTCTCAA
22736 AAAAGAAACGTAAAT
1 AAAA-AAAC-TAAAT
22751 CCTTAAATCC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 11 0.31
26 9 0.25
27 1 0.03
28 6 0.17
29 4 0.11
30 5 0.14
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (28 bp):
AAAAAAACTAAATTTTATAAATTCTCAA
Found at i:25343 original size:18 final size:18
Alignment explanation
Indices: 25320--25354 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25310 TTCCATCCGG
*
25320 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
25338 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
25355 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:26679 original size:13 final size:13
Alignment explanation
Indices: 26661--26685 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26651 CAGTCAACGG
26661 GTCAACGGGTCGA
1 GTCAACGGGTCGA
26674 GTCAACGGGTCG
1 GTCAACGGGTCG
26686 GGTCGGGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:26689 original size:18 final size:18
Alignment explanation
Indices: 26652--26702 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
26642 GACGGTCAAC
26652 AGTCAACGGGTCAACGGGTCG
1 AGTCAACGGGT---CGGGTCG
26673 AGTCAACGGGTCGGGTCG
1 AGTCAACGGGTCGGGTCG
*
26691 GGTCAACGGGTC
1 AGTCAACGGGTC
26703 AGGTAAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 18 0.62
21 11 0.38
ACGTcount: A:0.20, C:0.24, G:0.41, T:0.16
Consensus pattern (18 bp):
AGTCAACGGGTCGGGTCG
Found at i:26695 original size:31 final size:31
Alignment explanation
Indices: 26658--26724 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
26648 CAACAGTCAA
*
26658 CGGGTCAACGGGTC-GAGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCAG-GTAAACGGGTCGGGT
26689 CGGGTCAACGGGTCAGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCAGGTAAACGGGTCGGGT
26720 CGGGT
1 CGGGT
26725 TGTGACCGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCAGGTAAACGGGTCGGGT
Found at i:26700 original size:13 final size:13
Alignment explanation
Indices: 26684--26720 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
26674 GTCAACGGGT
26684 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
* *
26697 CGGGTCAGGTAAA
1 CGGGTCGGGTCAA
26710 CGGGTCGGGTC
1 CGGGTCGGGTC
26721 GGGTTGTGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.46, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:40704 original size:21 final size:21
Alignment explanation
Indices: 40662--40704 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
40652 GTTTTAAATG
* *
40662 ATAAATGGGAGAATTGTTAAA
1 ATAAAGGGGAGAATTGTCAAA
40683 ATAAAGGGGAGTAATT-TCAAA
1 ATAAAGGGGAG-AATTGTCAAA
40704 A
1 A
40705 CTTGATTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.23, T:0.26
Consensus pattern (21 bp):
ATAAAGGGGAGAATTGTCAAA
Found at i:44855 original size:27 final size:27
Alignment explanation
Indices: 44825--44879 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
44815 GCAAAGTGAA
44825 TGTGTCTTTTGTCGAGAAAAAGGGCAC
1 TGTGTCTTTTGTCGAGAAAAAGGGCAC
44852 TGTGTCTTTTGTCGAGAAAAAGGGCAC
1 TGTGTCTTTTGTCGAGAAAAAGGGCAC
44879 T
1 T
44880 AGAAGAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (27 bp):
TGTGTCTTTTGTCGAGAAAAAGGGCAC
Done.