Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002122.1 Hibiscus syriacus cultivar Beakdansim tig00004348_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: 61160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4607 original size:19 final size:19
Alignment explanation
Indices: 4583--4619 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4573 ATGACCAACA
*
4583 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
4602 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
4620 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:4772 original size:21 final size:21
Alignment explanation
Indices: 4746--4787 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4736 GATTCTGACT
4746 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
4767 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
4788 GCGTTTCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.14, T:0.14
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:4841 original size:16 final size:16
Alignment explanation
Indices: 4820--4853 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4810 AGTTCGCGTT
4820 GCGATTTTCCAAAATC
1 GCGATTTTCCAAAATC
*
4836 GCGATTTTCTAAAATC
1 GCGATTTTCCAAAATC
4852 GC
1 GC
4854 AACGACTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (16 bp):
GCGATTTTCCAAAATC
Found at i:6906 original size:28 final size:28
Alignment explanation
Indices: 6854--6908 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
6844 TGTTTAAGAA
* *
6854 TTTAGATTTTAAATTTTACAGTTTTAAG
1 TTTAGAATTTAAATTGTACAGTTTTAAG
6882 TTTAGAATTTAAATTGTA-AGATTTTAA
1 TTTAGAATTTAAATTGTACAG-TTTTAA
6909 ATATTAGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (28 bp):
TTTAGAATTTAAATTGTACAGTTTTAAG
Found at i:6909 original size:15 final size:14
Alignment explanation
Indices: 6852--6910 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 14
6842 TATGTTTAAG
6852 AATTT-AGATTTTA
1 AATTTAAGATTTTA
6865 AATTTTACAG-TTTTA
1 AA-TTTA-AGATTTTA
* *
6880 AGTTT-AGAATTTA
1 AATTTAAGATTTTA
6893 AATTGTAAGATTTTA
1 AATT-TAAGATTTTA
6908 AAT
1 AAT
6911 ATTAGGTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
12 2 0.06
13 9 0.25
14 7 0.19
15 16 0.44
16 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (14 bp):
AATTTAAGATTTTA
Found at i:11774 original size:6 final size:6
Alignment explanation
Indices: 11758--11790 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
11748 TCAGAGGCTC
*
11758 TCTCTT GCTCTT TCTCTT TCTCTT TCTCTT TCT
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCT
11791 AATGCTACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (6 bp):
TCTCTT
Found at i:16734 original size:17 final size:18
Alignment explanation
Indices: 16701--16734 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16691 AAGCATAAAG
*
16701 ATAAAATCTCTGTAAGTA
1 ATAAAATCTCTGAAAGTA
16719 ATAAAA-CTCTGAAAGT
1 ATAAAATCTCTGAAAGT
16735 CCTTACTCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (18 bp):
ATAAAATCTCTGAAAGTA
Found at i:25199 original size:23 final size:23
Alignment explanation
Indices: 25173--25224 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
25163 ATGGCAATTT
*
25173 GGTGCAATTCTACGCGGCACTTC
1 GGTGCAACTCTACGCGGCACTTC
* *
25196 GGTGCAACTCTACGTGGCACTTT
1 GGTGCAACTCTACGCGGCACTTC
25219 GGTGCA
1 GGTGCA
25225 TTTATATGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (23 bp):
GGTGCAACTCTACGCGGCACTTC
Found at i:26637 original size:45 final size:45
Alignment explanation
Indices: 26573--26697 Score: 205
Period size: 45 Copynumber: 2.8 Consensus size: 45
26563 TGTGATCCTA
* *
26573 CACTTGCCACGACAACGTCATTAACTATACTTGCCTTGGCAACTT
1 CACTTGCCATGACAACGTCATTAACTATACTTGCCTTGACAACTT
* *
26618 CACTTGCCATGACAACGTCATTAACTCTACTTGCCTTTACAACTT
1 CACTTGCCATGACAACGTCATTAACTATACTTGCCTTGACAACTT
*
26663 CACTTGCCATGACAACGTCATTAACTTTACTTGCC
1 CACTTGCCATGACAACGTCATTAACTATACTTGCC
26698 ACGATAACGT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.26, C:0.31, G:0.11, T:0.31
Consensus pattern (45 bp):
CACTTGCCATGACAACGTCATTAACTATACTTGCCTTGACAACTT
Found at i:26651 original size:27 final size:27
Alignment explanation
Indices: 26619--26715 Score: 86
Period size: 27 Copynumber: 3.9 Consensus size: 27
26609 TGGCAACTTC
26619 ACTTGCCATGACAACGTCATTAACTCT
1 ACTTGCCATGACAACGTCATTAACTCT
* *
26646 ACTTGCCTTTACAA---C--T---TC-
1 ACTTGCCATGACAACGTCATTAACTCT
*
26664 ACTTGCCATGACAACGTCATTAACTTT
1 ACTTGCCATGACAACGTCATTAACTCT
* *
26691 ACTTGCCACGATAACGTCATTAACT
1 ACTTGCCATGACAACGTCATTAACT
26716 TTCAAACCAG
Statistics
Matches: 54, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
18 12 0.22
19 2 0.04
21 1 0.02
22 1 0.02
23 1 0.02
24 1 0.02
26 1 0.02
27 35 0.65
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (27 bp):
ACTTGCCATGACAACGTCATTAACTCT
Found at i:26716 original size:27 final size:27
Alignment explanation
Indices: 26658--26717 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
26648 TTGCCTTTAC
* *
26658 AACTTCACTTGCCATGACAACGTCATT
1 AACTTTACTTGCCACGACAACGTCATT
*
26685 AACTTTACTTGCCACGATAACGTCATT
1 AACTTTACTTGCCACGACAACGTCATT
26712 AACTTT
1 AACTTT
26718 CAAACCAGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (27 bp):
AACTTTACTTGCCACGACAACGTCATT
Found at i:26894 original size:37 final size:35
Alignment explanation
Indices: 26808--26907 Score: 146
Period size: 36 Copynumber: 2.7 Consensus size: 35
26798 CTTCAATGAG
*
26808 AAAATACCCAAATTTCTTATGAAACCTTTAATAAGA
1 AAAATA-CCAAATTTCTTATGAAACCTTTAACAAGA
*
26844 AAAACACTCAAATTTCTTATGAAACCTTTAACAAGAA
1 AAAATAC-CAAATTTCTTATGAAACCTTTAACAAG-A
26881 AAAATACCAAAATTTCTTATGAAACCT
1 AAAATACC-AAATTTCTTATGAAACCT
26908 AAATTGATGA
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
35 1 0.02
36 32 0.55
37 25 0.43
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.29
Consensus pattern (35 bp):
AAAATACCAAATTTCTTATGAAACCTTTAACAAGA
Found at i:29088 original size:26 final size:29
Alignment explanation
Indices: 29056--29114 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 29
29046 CTCGTTAAAT
29056 TCGTT-AAAA-TT-TTGCTCGACTCATGC
1 TCGTTAAAAATTTATTGCTCGACTCATGC
29082 TCGTTAAGAAAATTTATTGCTCGACTCATGC
1 TCGTT-A-AAAATTTATTGCTCGACTCATGC
29113 TC
1 TC
29115 ATATTGAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 5 0.18
29 4 0.14
30 2 0.07
31 17 0.61
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (29 bp):
TCGTTAAAAATTTATTGCTCGACTCATGC
Found at i:37285 original size:2 final size:2
Alignment explanation
Indices: 37278--37347 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
37268 CTTTCTGCTT
37278 TA TA TA 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
37320 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
37348 GCCACTCTCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39149 original size:31 final size:31
Alignment explanation
Indices: 39088--39150 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
39078 AAATACGTGG
*
39088 ATTAAGTTTTGGTCACTTACATTATTGTTTT
1 ATTAAGTTTTGGTCACTTACATTATCGTTTT
* * **
39119 ATTAATTTTTTGTCACTTATGTTATCGTTTT
1 ATTAAGTTTTGGTCACTTACATTATCGTTTT
39150 A
1 A
39151 AGTTTTAGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.22, C:0.10, G:0.11, T:0.57
Consensus pattern (31 bp):
ATTAAGTTTTGGTCACTTACATTATCGTTTT
Found at i:42781 original size:12 final size:12
Alignment explanation
Indices: 42764--42788 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42754 GTGGCCGGTG
42764 AGGATCATTATT
1 AGGATCATTATT
42776 AGGATCATTATT
1 AGGATCATTATT
42788 A
1 A
42789 TAGGTAATAC
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
AGGATCATTATT
Found at i:47902 original size:11 final size:11
Alignment explanation
Indices: 47886--47996 Score: 59
Period size: 11 Copynumber: 9.5 Consensus size: 11
47876 AAAATTCAGG
47886 AGCTCGATTGA
1 AGCTCGATTGA
*
47897 AGCTCGAGACTCG-
1 AGCTC--GA-TTGA
47910 AGCTCGATTGA
1 AGCTCGATTGA
*
47921 AGCTCGAGACTCG-
1 AGCTC--GA-TTGA
47934 AGCTCGATTGA
1 AGCTCGATTGA
*
47945 AGCTCGAGACTCG-
1 AGCTC--GA-TTGA
47958 AGCTCGATTGA
1 AGCTCGATTGA
47969 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
47981 AGCTCGATTCA
1 AGCTCGATTGA
47992 AGCTC
1 AGCTC
47997 AAACTCAAAC
Statistics
Matches: 78, Mismatches: 7, Indels: 30
0.68 0.06 0.26
Matches are distributed among these distances:
10 8 0.10
11 33 0.42
12 7 0.09
13 24 0.31
14 6 0.08
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:47912 original size:24 final size:24
Alignment explanation
Indices: 47885--47975 Score: 182
Period size: 24 Copynumber: 3.8 Consensus size: 24
47875 AAAAATTCAG
47885 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTGAAGCTCGAGACTC
47909 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTGAAGCTCGAGACTC
47933 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTGAAGCTCGAGACTC
47957 GAGCTCGATTGAAGCTCGA
1 GAGCTCGATTGAAGCTCGA
47976 TTTTGAGCTC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.25, C:0.24, G:0.30, T:0.21
Consensus pattern (24 bp):
GAGCTCGATTGAAGCTCGAGACTC
Found at i:47915 original size:13 final size:13
Alignment explanation
Indices: 47897--47964 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
47887 GCTCGATTGA
47897 AGCTCGAGACTCG
1 AGCTCGAGACTCG
*
47910 AGCTC--GA-TTG
1 AGCTCGAGACTCG
47920 AAGCTCGAGACTCG
1 -AGCTCGAGACTCG
*
47934 AGCTC--GA-TTG
1 AGCTCGAGACTCG
47944 AAGCTCGAGACTCG
1 -AGCTCGAGACTCG
47958 AGCTCGA
1 AGCTCGA
47965 TTGAAGCTCG
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
10 4 0.09
11 14 0.33
13 21 0.49
14 4 0.09
ACGTcount: A:0.25, C:0.26, G:0.29, T:0.19
Consensus pattern (13 bp):
AGCTCGAGACTCG
Found at i:48009 original size:23 final size:23
Alignment explanation
Indices: 47995--48039 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
47985 CGATTCAAGC
*
47995 TCAAACTCAAACTCGAACTCGAT
1 TCAAACTCAAACTCAAACTCGAT
* *
48018 TCAAGCTCGAACTCAAACTCGA
1 TCAAACTCAAACTCAAACTCGA
48040 ATTTGAACTT
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:0.38, C:0.31, G:0.11, T:0.20
Consensus pattern (23 bp):
TCAAACTCAAACTCAAACTCGAT
Found at i:48015 original size:29 final size:29
Alignment explanation
Indices: 47983--48040 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
47973 CGATTTTGAG
47983 CTCGATTCAAGCTCAAACTCAAACTCGAA
1 CTCGATTCAAGCTCAAACTCAAACTCGAA
*
48012 CTCGATTCAAGCTCGAACTCAAACTCGAA
1 CTCGATTCAAGCTCAAACTCAAACTCGAA
48041 TTTGAACTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.31, G:0.12, T:0.21
Consensus pattern (29 bp):
CTCGATTCAAGCTCAAACTCAAACTCGAA
Found at i:50513 original size:14 final size:15
Alignment explanation
Indices: 50458--50513 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 15
50448 CACATAATTG
* *
50458 GGTTTAGGGGTTA-A
1 GGTTTAGAGTTTAGA
*
50472 GGTTTAGTGTTTA-A
1 GGTTTAGAGTTTAGA
*
50486 GGTTTATAGTTTAGA
1 GGTTTAGAGTTTAGA
50501 -GTTTAGAGTTTAG
1 GGTTTAGAGTTTAG
50514 GATTTATGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
14 35 0.97
15 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (15 bp):
GGTTTAGAGTTTAGA
Found at i:50604 original size:7 final size:7
Alignment explanation
Indices: 50592--50652 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
50582 GGTAAGTATA
50592 ATTTAGG
1 ATTTAGG
50599 ATTTAGG
1 ATTTAGG
50606 ATTTAGG
1 ATTTAGG
*
50613 GTTTAGG
1 ATTTAGG
*
50620 GTTTA-G
1 ATTTAGG
*
50626 ATTTTATG
1 A-TTTAGG
*
50634 ATTTATG
1 ATTTAGG
*
50641 TTTTAGG
1 ATTTAGG
*
50648 GTTTA
1 ATTTA
50653 TAGTTAGGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
6 1 0.02
7 44 0.94
8 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (7 bp):
ATTTAGG
Found at i:55120 original size:35 final size:36
Alignment explanation
Indices: 55081--55155 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
55071 TTCATGTTCA
55081 AAATTTC-AAAACACTTCAATTACATTCTAAACCCC
1 AAATTTCTAAAACACTTCAATTACATTCTAAACCCC
* * * *
55116 AAA-TTCTAAAATATTTTAATTACATTCTAAACCCT
1 AAATTTCTAAAACACTTCAATTACATTCTAAACCCC
55151 AAATT
1 AAATT
55156 AAAGTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 3 0.09
35 30 0.88
36 1 0.03
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (36 bp):
AAATTTCTAAAACACTTCAATTACATTCTAAACCCC
Found at i:55206 original size:35 final size:35
Alignment explanation
Indices: 55151--55227 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
55141 TCTAAACCCT
* *
55151 AAATTAAAGTATTTTAGAATTTGGAGTTTAAAATG
1 AAATTGAATTATTTTAGAATTTGGAGTTTAAAATG
* * * *
55186 TAATTGAATTATTTTGGAATTTGGTGTTTAGAATG
1 AAATTGAATTATTTTAGAATTTGGAGTTTAAAATG
55221 AAATTGA
1 AAATTGA
55228 GGACTGTGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTGGAGTTTAAAATG
Found at i:55673 original size:33 final size:33
Alignment explanation
Indices: 55629--55698 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
55619 TTCTATCTGC
*
55629 ATTTGAATTTCTGGATTTGCTTTAGACGGCTTT
1 ATTTGAATTTCTGGATTTGCTTGAGACGGCTTT
* *
55662 ATTTGAGTTTCTGGATTTTCTTGAGACGGCTTT
1 ATTTGAATTTCTGGATTTGCTTGAGACGGCTTT
55695 ATTT
1 ATTT
55699 TCTAGTTACA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.17, C:0.11, G:0.21, T:0.50
Consensus pattern (33 bp):
ATTTGAATTTCTGGATTTGCTTGAGACGGCTTT
Done.