Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000068.1 Hibiscus syriacus cultivar Beakdansim tig00000117_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: 65825
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2397 original size:41 final size:41
Alignment explanation
Indices: 2298--2468 Score: 146
Period size: 41 Copynumber: 4.2 Consensus size: 41
2288 GTAAACAAAT
* * ** *
2298 GCCACTAAAGTATGAGTCTTTAGCGGCGTTTGT-TTAAAAC
1 GCCACTAAAGTACGAGTCTATAGCAACGTTTGTATAAAAAC
* * * * **
2338 GACACTAAAATACAAGTCTATTGCAATTTTTGTATAAAAAC
1 GCCACTAAAGTACGAGTCTATAGCAACGTTTGTATAAAAAC
** * * *
2379 GCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATACAGAT
1 GCCACTAAAGTACGAGTCTATAGCAACGTTTGTATAAAAAC
** * *
2420 GCCACTAAAGTACGAGTCTATAGCGGCGTTTGTCAAAAAAAT
1 GCCACTAAAGTACGAGTCTATAGCAACGTTTGT-ATAAAAAC
2462 GCCACTA
1 GCCACTA
2469 TACATTATCT
Statistics
Matches: 104, Mismatches: 25, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 23 0.22
41 69 0.66
42 12 0.12
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
GCCACTAAAGTACGAGTCTATAGCAACGTTTGTATAAAAAC
Found at i:2458 original size:81 final size:81
Alignment explanation
Indices: 2298--2468 Score: 180
Period size: 81 Copynumber: 2.1 Consensus size: 81
2288 GTAAACAAAT
* * * *
2298 GCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTTTAAAACGACACTAAAATACAAGTCTATTGCA
1 GCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAACGACACTAAAATACAAGTCTATAGCA
** *
2363 ATTTTTGTATAAAAAC
66 ACGTTTGTACAAAAAC
* * * * *
2379 GCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATACAGATGCCACTAAAGTACGAGTCTATAGC
1 GCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA-AAACGACACTAAAATACAAGTCTATAGC
** * *
2444 GGCGTTTGTCAAAAAAAT
65 AACGTTTGT-ACAAAAAC
2462 GCCACTA
1 GCCACTA
2469 TACATTATCT
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
81 33 0.45
82 27 0.37
83 13 0.18
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (81 bp):
GCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAACGACACTAAAATACAAGTCTATAGCA
ACGTTTGTACAAAAAC
Found at i:15715 original size:19 final size:21
Alignment explanation
Indices: 15691--15745 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
15681 TGCAGAAATG
*
15691 GTATCGATACCATG-ATTG-A
1 GTATCGATACCATGTATAGTA
*
15710 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCAT-GTATAGTA
15732 GTATCGATACCATG
1 GTATCGATACCATG
15746 GTAGGGGTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 12 0.40
20 1 0.03
21 4 0.13
22 13 0.43
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (21 bp):
GTATCGATACCATGTATAGTA
Found at i:16193 original size:20 final size:20
Alignment explanation
Indices: 16168--16311 Score: 83
Period size: 20 Copynumber: 6.6 Consensus size: 20
16158 ACTAAATATC
16168 CATGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
*
16188 CATGAAAGGATGCCATAAATGAAATG
1 CATGAAAGGATG-CAT---T--AAGG
*
16214 CATGAAAGGATGCATTAAGA
1 CATGAAAGGATGCATTAAGG
** * *
16234 CATGAAATAATGCATGAAGA
1 CATGAAAGGATGCATTAAGG
*
16254 TATGAAAGGATGCCA-TAAGTG
1 CATGAAAGGATG-CATTAAG-G
*
16275 AAATGTATAAAAGGATGCATTAAGG
1 -CATG----AAAGGATGCATTAAGG
*
16300 CATGAAATGATG
1 CATGAAAGGATG
16312 TTGTAAATGA
Statistics
Matches: 96, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
20 50 0.52
21 5 0.05
22 4 0.04
24 4 0.04
25 6 0.06
26 27 0.28
ACGTcount: A:0.44, C:0.09, G:0.25, T:0.22
Consensus pattern (20 bp):
CATGAAAGGATGCATTAAGG
Found at i:16224 original size:46 final size:45
Alignment explanation
Indices: 16169--16396 Score: 140
Period size: 46 Copynumber: 5.0 Consensus size: 45
16159 CTAAATATCC
16169 ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATG
1 ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATG
* ** *
16214 CATGAAAGGATGCATTAAGACATGAAATAATG-CATGAA-G--AT-
1 -ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATG
*
16255 ATGAAAGGATGCCA-TAAGTGAAATGTATAAAAGGATG-CATTAAGGCATGAAATG
1 ATGAAAGGATG-CATTAAG-G-CATG----AAAGGATGCCA-TAA---ATGAAATG
* *
16309 ATGTTGTAA--ATG-A--AATGCATGAAAGGATGCCA-AGAATGAAATG
1 A---TGAAAGGATGCATTAAGGCATGAAAGGATGCCATA-AATGAAATG
*
16352 AATGAAAGGATGCATTAAGGCATGAAAGGGTGCCATAAATGAAAT
1 -ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAAT
16397 TAACGAATAA
Statistics
Matches: 140, Mismatches: 15, Indels: 54
0.67 0.07 0.26
Matches are distributed among these distances:
40 15 0.11
41 6 0.04
42 5 0.04
43 11 0.08
44 3 0.02
45 6 0.04
46 70 0.50
47 5 0.04
50 4 0.03
51 2 0.01
52 2 0.01
53 3 0.02
54 1 0.01
55 3 0.02
57 4 0.03
ACGTcount: A:0.45, C:0.08, G:0.25, T:0.21
Consensus pattern (45 bp):
ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATG
Found at i:16429 original size:12 final size:12
Alignment explanation
Indices: 16412--16445 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
16402 AATAATTACT
16412 AAGAAAAATGAA
1 AAGAAAAATGAA
16424 AAGAAAAATGAA
1 AAGAAAAATGAA
16436 AAGAAAAATG
1 AAGAAAAATG
16446 TATAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (12 bp):
AAGAAAAATGAA
Found at i:16907 original size:81 final size:81
Alignment explanation
Indices: 16759--17248 Score: 629
Period size: 81 Copynumber: 6.0 Consensus size: 81
16749 AGTATAAAAC
* * *
16759 TTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATTCTAGTTAGATGAAAGGTTAAAT
1 TTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
16824 ACCTTTGAGTAAAAGA
66 ACCTTTGAGTAAAAGA
* * * *
16840 TTAGTGGCTTAGTTGTGCATTTGGTAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
1 TTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
*
16905 ACCTTTGAATAAAAGA
66 ACCTTTGAGTAAAAGA
* * * * * * *
16921 TTAATGACCTAGCAGTGCATTTGGCATAAAAGTGTTAATTATGTCAGTTAGATGCAATGTTAAAT
1 TTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
* *
16986 AGCTTTGAGTAAAAAA
66 ACCTTTGAGTAAAAGA
* * * * * * * * *
17002 TTAATAGCCTAGATGTGTATTTGGTAGAAATGTGTTAGTTATTCTAGTTAGATGAAAGGTTAAAT
1 TTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
* *
17067 ACTTTTGAGTAAAATA
66 ACCTTTGAGTAAAAGA
* * * *
17083 TTAATGGCCTAGATGTGCATTTGGCAGAAAAGTGTCAATCATGCAAGTTAGTTGAAAGGTTAAAT
1 TTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
17148 ACCTTTGAGTAAAAGA
66 ACCTTTGAGTAAAAGA
* * * * *
17164 TTAATGGCCTAGCTATGTATTTGGCAGAAAGGTGTCAATTATGCCAGTTATATGAAAGGTTAAAC
1 TTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
* *
17229 ACCTTCGACTAAAAGA
66 ACCTTTGAGTAAAAGA
17245 TTAA
1 TTAA
17249 AGGCTAAAAG
Statistics
Matches: 347, Mismatches: 62, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 347 1.00
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (81 bp):
TTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
ACCTTTGAGTAAAAGA
Found at i:27688 original size:36 final size:36
Alignment explanation
Indices: 27647--27722 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
27637 ATTTTCGGGA
*
27647 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
27683 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
27719 TTTT
1 TTTT
27723 TTTAGCTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:43139 original size:20 final size:20
Alignment explanation
Indices: 43110--43148 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
43100 TATCCACCAC
43110 ATGCAACTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
*
43130 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
43149 TATAGGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:62767 original size:23 final size:23
Alignment explanation
Indices: 62740--62792 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
62730 GCTGAACTTG
62740 TGTGAATCACCATCAAAACAAAT
1 TGTGAATCACCATCAAAACAAAT
62763 TGTGAATCACCATCAAAACAAAT
1 TGTGAATCACCATCAAAACAAAT
62786 TGTGAAT
1 TGTGAAT
62793 ATGCTCATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (23 bp):
TGTGAATCACCATCAAAACAAAT
Done.