Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007354.1 Hibiscus syriacus cultivar Beakdansim tig00019709_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: 58464
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:8805 original size:9 final size:9
Alignment explanation
Indices: 8791--8840 Score: 59
Period size: 10 Copynumber: 5.6 Consensus size: 9
8781 TCATTTTTTT
8791 ATTTTTTCAA
1 ATTTTTTC-A
8801 ATTTTTTCA
1 ATTTTTTCA
8810 ATTTTTTTC-
1 A-TTTTTTCA
8819 ATTTTTTCA
1 ATTTTTTCA
*
8828 TTTTTTTC-
1 ATTTTTTCA
8836 ATTTT
1 ATTTT
8841 AGTGGGTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 11 0.31
9 10 0.28
10 15 0.42
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (9 bp):
ATTTTTTCA
Found at i:8806 original size:18 final size:16
Alignment explanation
Indices: 8780--8840 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 16
8770 TATTCATAAC
*
8780 TTCATTTTTTTATTTT
1 TTCATTTTTTAATTTT
8796 TTCAAATTTTTTCAATTTTT
1 TTC--ATTTTTT-AA-TTTT
*
8816 TTCATTTTTTCATTTTT
1 TTCATTTTTT-AATTTT
8833 TTCATTTT
1 TTCATTTT
8841 AGTGGGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.08
17 12 0.31
18 16 0.41
19 1 0.03
20 7 0.18
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCATTTTTTAATTTT
Found at i:8823 original size:7 final size:8
Alignment explanation
Indices: 8780--8840 Score: 68
Period size: 8 Copynumber: 7.0 Consensus size: 8
8770 TATTCATAAC
8780 TTCATTTT
1 TTCATTTT
*
8788 TTTATTTT
1 TTCATTTT
8796 TTCAAATTTT
1 TTC--ATTTT
8806 TTCAATTTTT
1 TTC-A-TTTT
8816 TTCATTTT
1 TTCATTTT
8824 TTCATTTTT
1 TTCA-TTTT
8833 TTCATTTT
1 TTCATTTT
8841 AGTGGGTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
8 21 0.45
9 11 0.23
10 15 0.32
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (8 bp):
TTCATTTT
Found at i:16799 original size:17 final size:17
Alignment explanation
Indices: 16779--16811 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16769 AACAAGCTTC
16779 TATTTTAAGATTATGTG
1 TATTTTAAGATTATGTG
*
16796 TATTTTAATATTATGT
1 TATTTTAAGATTATGT
16812 TTTTTACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (17 bp):
TATTTTAAGATTATGTG
Found at i:18381 original size:24 final size:24
Alignment explanation
Indices: 18354--18400 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
18344 GAACTTGATA
* *
18354 TTGCTATAGTGTCTCGAGTTGAAG
1 TTGCTACAATGTCTCGAGTTGAAG
*
18378 TTGCTACAATGTTTCGAGTTGAA
1 TTGCTACAATGTCTCGAGTTGAA
18401 ATCCTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (24 bp):
TTGCTACAATGTCTCGAGTTGAAG
Found at i:20735 original size:23 final size:23
Alignment explanation
Indices: 20709--20753 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
20699 TGGAGTTTAG
*
20709 ATTTTGAAATTCTTTTACACATT
1 ATTTTGAAATTCTTTTAAACATT
* *
20732 ATTTTGATATTTTTTTAAACAT
1 ATTTTGAAATTCTTTTAAACAT
20754 GTCAATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (23 bp):
ATTTTGAAATTCTTTTAAACATT
Found at i:30794 original size:19 final size:19
Alignment explanation
Indices: 30762--30804 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
30752 CTTTCTTTTC
*
30762 TTTTCTTTTCAAGTTTTCAT
1 TTTTATTTTCAAGTTTT-AT
30782 TTTTATTTT-AAGTTTTAT
1 TTTTATTTTCAAGTTTTAT
30800 TTTTA
1 TTTTA
30805 AACATGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTTCAAGTTTTAT
Found at i:31390 original size:17 final size:17
Alignment explanation
Indices: 31367--31408 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
31357 TACATTCTTT
31367 ATTTTTACT-TTAAATC
1 ATTTTTACTATTAAATC
* *
31383 ACTTTTTATTATTTAATC
1 A-TTTTTACTATTAAATC
31401 ATTTTTAC
1 ATTTTTAC
31409 CAAAACCCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 7 0.33
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTACTATTAAATC
Found at i:34694 original size:69 final size:68
Alignment explanation
Indices: 34589--34834 Score: 156
Period size: 69 Copynumber: 3.5 Consensus size: 68
34579 AAGTCTCCAT
* * *
34589 CTCCTCTCAA-GAAGCCATACAAGTACAAAT-ATCCACTTCCACCTTCTCCAGTGTACAAGTCTC
1 CTCCTCCCAAGGAA-CCATACAAATACAAGTCA-CCACTTCCACC-TCTCCAGTGTACAAGTCTC
34652 TTCCTC
63 TTCCTC
* * * * * * *
34658 CTCCTCCCAAGGAACCATACAAATACAAGTCACCACTGCCCACCCCACCGGTCTACAAGTATAAG
1 CTCCTCCCAAGGAACCATACAAATACAAGTCACCACT-TCCACCTCTCCAGTGTACAAGTCT--C
34723 TCTCCTC
63 T-TCCTC
* * ** * * * * * * *
34730 TTCCTCCTAAGGAGTCATACAAATACAAGTCTCCACCTCCTCCAGTGTACA-AGTACAAGTCTCC
1 CTCCTCCCAAGGAACCATACAAATACAAGTCACCACTTCCACC--TCTCCAGTGTACAAGTCTCT
34794 TCCTC
64 TCCTC
** * * *
34799 CTCCTCTTAAGGAGCCATACAAGTATAAGTCACCAC
1 CTCCTCCCAAGGAACCATACAAATACAAGTCACCAC
34835 GGCCACCCCT
Statistics
Matches: 135, Mismatches: 34, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
69 76 0.56
70 9 0.07
71 5 0.04
72 44 0.33
73 1 0.01
ACGTcount: A:0.29, C:0.36, G:0.11, T:0.24
Consensus pattern (68 bp):
CTCCTCCCAAGGAACCATACAAATACAAGTCACCACTTCCACCTCTCCAGTGTACAAGTCTCTTC
CTC
Found at i:37670 original size:21 final size:21
Alignment explanation
Indices: 37646--37709 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
37636 TGGTTAAGAT
37646 CTTTTGTTGAAAGGACTTAAC
1 CTTTTGTTGAAAGGACTTAAC
* * * *
37667 CTTTCGATT-AAATGACTCATC
1 CTTTTG-TTGAAAGGACTTAAC
*
37688 CTTTTGATGAAAGTG-CTTAAC
1 CTTTTGTTGAAAG-GACTTAAC
37709 C
1 C
37710 ATTTCATGAA
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
20 1 0.03
21 27 0.87
22 3 0.10
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (21 bp):
CTTTTGTTGAAAGGACTTAAC
Found at i:39071 original size:17 final size:17
Alignment explanation
Indices: 39039--39088 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
39029 TAAGAGTTAA
* *
39039 TTTAATAAACGAACTAG
1 TTTAATGAATGAACTAG
*
39056 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
*
39073 TTTAATTAATGAACTA
1 TTTAATGAATGAACTA
39089 ATTCCCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:40975 original size:12 final size:12
Alignment explanation
Indices: 40958--40986 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
40948 ATGGGTGAAT
40958 GTATACCGGTTG
1 GTATACCGGTTG
40970 GTATACCGGTTG
1 GTATACCGGTTG
40982 GTATA
1 GTATA
40987 ACCGTCATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (12 bp):
GTATACCGGTTG
Found at i:41495 original size:19 final size:19
Alignment explanation
Indices: 41468--41512 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
41458 AAGCATGGTT
*
41468 TTGCGATTTGGACATTGGC
1 TTGCAATTTGGACATTGGC
41487 TTGCAATTTGGACATTGGC
1 TTGCAATTTGGACATTGGC
*
41506 TTACAAT
1 TTGCAAT
41513 GTGTTCATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (19 bp):
TTGCAATTTGGACATTGGC
Found at i:42567 original size:15 final size:15
Alignment explanation
Indices: 42535--42563 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42525 TTAGTAATAA
42535 AAAAAATAACCTCAC
1 AAAAAATAACCTCAC
42550 AAAAAA-AACCTCAC
1 AAAAAATAACCTCAC
42564 CAAACACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAATAACCTCAC
Found at i:42893 original size:45 final size:46
Alignment explanation
Indices: 42829--42929 Score: 177
Period size: 45 Copynumber: 2.2 Consensus size: 46
42819 ACGTAAATAT
* *
42829 TTTTTTCTTTAAAGATGAAAAGAATTACTCCCTCCCTCTTTAAA-C
1 TTTTTTCTTTAAAGATGAAAAGAATTACGCCCTCCCCCTTTAAACC
42874 TTTTTTCTTTAAAGATGAAAAGAATTACGCCCTCCCCCTTTAAACC
1 TTTTTTCTTTAAAGATGAAAAGAATTACGCCCTCCCCCTTTAAACC
42920 TTTTTTCTTT
1 TTTTTTCTTT
42930 CTTTTATTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
45 42 0.79
46 11 0.21
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.43
Consensus pattern (46 bp):
TTTTTTCTTTAAAGATGAAAAGAATTACGCCCTCCCCCTTTAAACC
Found at i:53173 original size:22 final size:22
Alignment explanation
Indices: 53143--53187 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53133 AATAAGTAAG
**
53143 TGCTGGTTCATTTTGCCGCCCA
1 TGCTGGTTCACATTGCCGCCCA
*
53165 TGCTTGTTCACATTGCCGCCCA
1 TGCTGGTTCACATTGCCGCCCA
53187 T
1 T
53188 TTTGATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.11, C:0.33, G:0.20, T:0.36
Consensus pattern (22 bp):
TGCTGGTTCACATTGCCGCCCA
Found at i:54826 original size:19 final size:21
Alignment explanation
Indices: 54802--54853 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
54792 CGGCCAAGAG
*
54802 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
54821 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
54842 CATGTATTTTCA
1 CATGTATTTTCA
54854 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Done.