Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007424.1 Hibiscus syriacus cultivar Beakdansim tig00020106_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: 62581
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:66 original size:13 final size:13
Alignment explanation
Indices: 48--72 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38 TCTGTTCATA
48 TATATATATATTT
1 TATATATATATTT
61 TATATATATATT
1 TATATATATATT
73 ACAATTTTAG
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATATATATTT
Found at i:2961 original size:16 final size:14
Alignment explanation
Indices: 2920--2960 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
2910 ATACTTCCAC
2920 TACAAATATATATT
1 TACAAATATATATT
2934 TACAAATATATATT
1 TACAAATATATATT
2948 TACAAATATATAT
1 TACAAATATATAT
2961 AGATCACGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
TACAAATATATATT
Found at i:3674 original size:15 final size:15
Alignment explanation
Indices: 3646--3860 Score: 322
Period size: 15 Copynumber: 14.3 Consensus size: 15
3636 GCTTTGATCT
*
3646 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
*
3661 TCTACAGGATTTTCA
1 TCTTCAGGATTTTCA
*
3676 TCTTTAGGATTTTCA
1 TCTTCAGGATTTTCA
*
3691 CCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
3706 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
3721 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
3736 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
*
3751 TCTTCAGGATTTCCA
1 TCTTCAGGATTTTCA
3766 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
*
3781 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
*
3796 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
* *
3811 CCTTCAGTATTTTCA
1 TCTTCAGGATTTTCA
*
3826 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
*
3841 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
*
3856 CCTTC
1 TCTTC
3861 CTCGATCATT
Statistics
Matches: 185, Mismatches: 15, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
15 185 1.00
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (15 bp):
TCTTCAGGATTTTCA
Found at i:5086 original size:31 final size:31
Alignment explanation
Indices: 5051--5145 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 31
5041 TAGAAAATAA
5051 AAGAAAACATAAAACCAAAAGAATTGAAGTT
1 AAGAAAACATAAAACCAAAAGAATTGAAGTT
* ***
5082 AAGAAAAAAT-ATTTCATAGAA-AA-T-AA---
1 AAGAAAACATAAAACCA-A-AAGAATTGAAGTT
5108 AAGAAAACATAAAACCAAAAGAATTGAAGTT
1 AAGAAAACATAAAACCAAAAGAATTGAAGTT
5139 AAGAAAA
1 AAGAAAA
5146 AACTTCTTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 18
0.64 0.11 0.25
Matches are distributed among these distances:
25 2 0.04
26 12 0.26
27 4 0.09
28 2 0.04
29 2 0.04
30 4 0.09
31 19 0.40
32 2 0.04
ACGTcount: A:0.64, C:0.07, G:0.12, T:0.17
Consensus pattern (31 bp):
AAGAAAACATAAAACCAAAAGAATTGAAGTT
Found at i:5101 original size:57 final size:57
Alignment explanation
Indices: 5028--5147 Score: 240
Period size: 57 Copynumber: 2.1 Consensus size: 57
5018 TCATACTGGA
5028 AAAAAATATTTCATAGAAAATAAAAGAAAACATAAAACCAAAAGAATTGAAGTTAAG
1 AAAAAATATTTCATAGAAAATAAAAGAAAACATAAAACCAAAAGAATTGAAGTTAAG
5085 AAAAAATATTTCATAGAAAATAAAAGAAAACATAAAACCAAAAGAATTGAAGTTAAG
1 AAAAAATATTTCATAGAAAATAAAAGAAAACATAAAACCAAAAGAATTGAAGTTAAG
5142 AAAAAA
1 AAAAAA
5148 CTTCTTTCAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 63 1.00
ACGTcount: A:0.65, C:0.07, G:0.10, T:0.18
Consensus pattern (57 bp):
AAAAAATATTTCATAGAAAATAAAAGAAAACATAAAACCAAAAGAATTGAAGTTAAG
Found at i:8499 original size:42 final size:42
Alignment explanation
Indices: 8391--8488 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
8381 TTGCAGCATC
* **
8391 CTCGGAGATCTTCTCATTGGCCTTTGTCTGCGTTGCTTCCAG
1 CTCGGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
* *
8433 CTTGGAGGTCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
1 CTCGGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
8475 CTCGGAGATCTTCT
1 CTCGGAGATCTTCT
8489 TATTCACCTC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.11, C:0.28, G:0.24, T:0.37
Consensus pattern (42 bp):
CTCGGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
Found at i:16934 original size:83 final size:84
Alignment explanation
Indices: 16842--16998 Score: 264
Period size: 84 Copynumber: 1.9 Consensus size: 84
16832 GTATCTACCG
* * *
16842 GCACCAATACCACATAA-AATGGCGGGGGAAAATAG-TAAAAATCTCAACTGCCCTGGGAAGGAG
1 GCACCAATACCACATAATAA-GGCGGGGCAAAATAGAAAAAAATCTCAACTACCCTGGGAAGGAG
16905 GGCAATAATTATAACTACTA
65 GGCAATAATTATAACTACTA
16925 GCACCAATACCACATAATAAGGCGGGGCAAAATAGAAAAAAATCTCAACTACCCTGGGAAGGAGG
1 GCACCAATACCACATAATAAGGCGGGGCAAAATAGAAAAAAATCTCAACTACCCTGGGAAGGAGG
16990 GCAATAATT
66 GCAATAATT
16999 CAAAGGCAGA
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
83 31 0.45
84 38 0.55
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (84 bp):
GCACCAATACCACATAATAAGGCGGGGCAAAATAGAAAAAAATCTCAACTACCCTGGGAAGGAGG
GCAATAATTATAACTACTA
Found at i:18764 original size:2 final size:2
Alignment explanation
Indices: 18757--18793 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
18747 AAGGTGTTTG
18757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18794 ACGACGTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21940 original size:16 final size:16
Alignment explanation
Indices: 21905--21940 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
21895 TCATACTGGA
*
21905 AAAAAATATTTCATGG
1 AAAAAATATTTCATAG
*
21921 AAAAAATATTTCATAT
1 AAAAAATATTTCATAG
21937 AAAA
1 AAAA
21941 TAAAAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAAAATATTTCATAG
Found at i:28628 original size:111 final size:111
Alignment explanation
Indices: 28501--28716 Score: 432
Period size: 111 Copynumber: 1.9 Consensus size: 111
28491 TAAATTGAAA
28501 ATGCAATAATTGGTACGAGTAATAACTATTACCAACCCGGTAATCCATCAACAGCAGATTGCAAC
1 ATGCAATAATTGGTACGAGTAATAACTATTACCAACCCGGTAATCCATCAACAGCAGATTGCAAC
28566 ATGCAAAAAAATAAGTAGTTTTCCAGCTCTTTTACCAAAAGTGGAT
66 ATGCAAAAAAATAAGTAGTTTTCCAGCTCTTTTACCAAAAGTGGAT
28612 ATGCAATAATTGGTACGAGTAATAACTATTACCAACCCGGTAATCCATCAACAGCAGATTGCAAC
1 ATGCAATAATTGGTACGAGTAATAACTATTACCAACCCGGTAATCCATCAACAGCAGATTGCAAC
28677 ATGCAAAAAAATAAGTAGTTTTCCAGCTCTTTTACCAAAA
66 ATGCAAAAAAATAAGTAGTTTTCCAGCTCTTTTACCAAAA
28717 ACTGGAAAAA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (111 bp):
ATGCAATAATTGGTACGAGTAATAACTATTACCAACCCGGTAATCCATCAACAGCAGATTGCAAC
ATGCAAAAAAATAAGTAGTTTTCCAGCTCTTTTACCAAAAGTGGAT
Found at i:30189 original size:29 final size:29
Alignment explanation
Indices: 30154--30235 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
30144 AAACTAAATT
*
30154 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
30183 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
30212 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
30236 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:34957 original size:29 final size:29
Alignment explanation
Indices: 34922--35003 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
34912 AAACTAAATT
*
34922 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
34951 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
34980 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
35004 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:40082 original size:31 final size:31
Alignment explanation
Indices: 40047--40131 Score: 170
Period size: 31 Copynumber: 2.7 Consensus size: 31
40037 AAGTGAAAAC
40047 TTCTTACATATTAAATAAATTTCAATATATA
1 TTCTTACATATTAAATAAATTTCAATATATA
40078 TTCTTACATATTAAATAAATTTCAATATATA
1 TTCTTACATATTAAATAAATTTCAATATATA
40109 TTCTTACATATTAAATAAATTTC
1 TTCTTACATATTAAATAAATTTC
40132 TCTAAAAGTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.46
Consensus pattern (31 bp):
TTCTTACATATTAAATAAATTTCAATATATA
Found at i:40805 original size:20 final size:22
Alignment explanation
Indices: 40765--40805 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
40755 TTATTATCAT
*
40765 TCAAAAATATTTTTTTAGAATG
1 TCAAAAATATCTTTTTAGAATG
40787 TCAAAAAT-TCTTTTT-GAAT
1 TCAAAAATATCTTTTTAGAAT
40806 ATTATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (22 bp):
TCAAAAATATCTTTTTAGAATG
Found at i:45149 original size:12 final size:14
Alignment explanation
Indices: 45125--45164 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
45115 ATACTTCCAC
45125 TACAAATATATATT
1 TACAAATATATATT
45139 TACAAATATATATT
1 TACAAATATATATT
45153 TACAAATATATA
1 TACAAATATATA
45165 GATCACGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (14 bp):
TACAAATATATATT
Found at i:45877 original size:15 final size:15
Alignment explanation
Indices: 45849--46063 Score: 322
Period size: 15 Copynumber: 14.3 Consensus size: 15
45839 GCTTTGATCT
*
45849 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
*
45864 TCTACAGGATTTTCA
1 TCTTCAGGATTTTCA
*
45879 TCTTTAGGATTTTCA
1 TCTTCAGGATTTTCA
*
45894 CCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
45909 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
45924 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
45939 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
*
45954 TCTTCAGGATTTCCA
1 TCTTCAGGATTTTCA
45969 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
*
45984 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
*
45999 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
* *
46014 CCTTCAGTATTTTCA
1 TCTTCAGGATTTTCA
*
46029 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
*
46044 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
*
46059 CCTTC
1 TCTTC
46064 CTCGATCATT
Statistics
Matches: 185, Mismatches: 15, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
15 185 1.00
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (15 bp):
TCTTCAGGATTTTCA
Found at i:47296 original size:58 final size:58
Alignment explanation
Indices: 47234--47356 Score: 246
Period size: 58 Copynumber: 2.1 Consensus size: 58
47224 ATTCATACTG
47234 GAAAAAAATATTTCATAGAAAATAAAAGAAAACATAAAACCAAAAGAATTGAAGTTAA
1 GAAAAAAATATTTCATAGAAAATAAAAGAAAACATAAAACCAAAAGAATTGAAGTTAA
47292 GAAAAAAATATTTCATAGAAAATAAAAGAAAACATAAAACCAAAAGAATTGAAGTTAA
1 GAAAAAAATATTTCATAGAAAATAAAAGAAAACATAAAACCAAAAGAATTGAAGTTAA
47350 GAAAAAA
1 GAAAAAA
47357 CTTCTTTCAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 65 1.00
ACGTcount: A:0.65, C:0.07, G:0.11, T:0.18
Consensus pattern (58 bp):
GAAAAAAATATTTCATAGAAAATAAAAGAAAACATAAAACCAAAAGAATTGAAGTTAA
Found at i:50715 original size:42 final size:42
Alignment explanation
Indices: 50607--50704 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
50597 TTGCAGCATC
* **
50607 CTCGGAGATCTTCTCATTGGCCTTTGTCTGCGTTGCTTCCAG
1 CTCGGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
* *
50649 CTTGGAGGTCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
1 CTCGGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
50691 CTCGGAGATCTTCT
1 CTCGGAGATCTTCT
50705 TATTCACCTC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.11, C:0.28, G:0.24, T:0.37
Consensus pattern (42 bp):
CTCGGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
Found at i:59130 original size:83 final size:84
Alignment explanation
Indices: 59038--59194 Score: 264
Period size: 84 Copynumber: 1.9 Consensus size: 84
59028 GTATCTACCG
* * *
59038 GCACCAATACCACATAA-AATGGCGGGGGAAAATAG-TAAAAATCTCAACTGCCCTGGGAAGGAG
1 GCACCAATACCACATAATAA-GGCGGGGCAAAATAGAAAAAAATCTCAACTACCCTGGGAAGGAG
59101 GGCAATAATTATAACTACTA
65 GGCAATAATTATAACTACTA
59121 GCACCAATACCACATAATAAGGCGGGGCAAAATAGAAAAAAATCTCAACTACCCTGGGAAGGAGG
1 GCACCAATACCACATAATAAGGCGGGGCAAAATAGAAAAAAATCTCAACTACCCTGGGAAGGAGG
59186 GCAATAATT
66 GCAATAATT
59195 CAAAGGCAGA
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
83 31 0.45
84 38 0.55
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (84 bp):
GCACCAATACCACATAATAAGGCGGGGCAAAATAGAAAAAAATCTCAACTACCCTGGGAAGGAGG
GCAATAATTATAACTACTA
Found at i:59959 original size:2 final size:2
Alignment explanation
Indices: 59952--59979 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59942 TATTTTTAAA
59952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59980 TTCAATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60950 original size:2 final size:2
Alignment explanation
Indices: 60943--60983 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
60933 AGGTGTTTTG
60943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60984 ACGACGTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.