Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005514.1 Hibiscus syriacus cultivar Beakdansim tig00012735_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: 52520
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Found at i:3036 original size:16 final size:15
Alignment explanation
Indices: 3011--3051 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
3001 TAAAAACCCC
3011 TTTT-ATATTTATTA
1 TTTTAATATTTATTA
3025 TTATTAATATTTATTA
1 TT-TTAATATTTATTA
*
3041 TTTTATTATTT
1 TTTTAATATTT
3052 TTTCCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 2 0.08
15 10 0.42
16 12 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTAATATTTATTA
Found at i:3793 original size:21 final size:21
Alignment explanation
Indices: 3767--3806 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3757 CCTTTTGATA
3767 AGTTAAATTGCATGAAAGATC
1 AGTTAAATTGCATGAAAGATC
3788 AGTTAAATTGCATGAAAGA
1 AGTTAAATTGCATGAAAGA
3807 ATGTTTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (21 bp):
AGTTAAATTGCATGAAAGATC
Found at i:4414 original size:20 final size:21
Alignment explanation
Indices: 4391--4433 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4381 AGGTTGCAAT
4391 CTGATTT-TTCATATGAAAAC
1 CTGATTTATTCATATGAAAAC
*
4411 CTGATTTCATTCTTATGAAAAC
1 CTGATTT-ATTCATATGAAAAC
4433 C
1 C
4434 ATATTTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (21 bp):
CTGATTTATTCATATGAAAAC
Found at i:16882 original size:21 final size:21
Alignment explanation
Indices: 16858--16899 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16848 ATACATGGAT
*
16858 AATCCTCTACACAACAATCTG
1 AATCATCTACACAACAATCTG
* *
16879 AATCATCTGCACAATAATCTG
1 AATCATCTACACAACAATCTG
16900 TTAATCTGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.29, G:0.07, T:0.26
Consensus pattern (21 bp):
AATCATCTACACAACAATCTG
Found at i:17793 original size:17 final size:17
Alignment explanation
Indices: 17760--17793 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17750 TAATTCATTA
**
17760 TAGTTTATTTAGTATTT
1 TAGTTTATTTAAAATTT
17777 TAGTTTATTTAAAATTT
1 TAGTTTATTTAAAATTT
17794 ATATTATTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (17 bp):
TAGTTTATTTAAAATTT
Found at i:27727 original size:23 final size:23
Alignment explanation
Indices: 27689--27746 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
27679 TAGTTATAAT
27689 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
27710 TTTTACATAATATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
27733 TTTTACATAATATA
1 TTTTACATAATATA
27747 TATTAATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Found at i:29048 original size:42 final size:42
Alignment explanation
Indices: 28940--29295 Score: 478
Period size: 42 Copynumber: 8.6 Consensus size: 42
28930 CGTAATATAA
* *
28940 TGGCGTTTTTATA-CAAACGCCGCTATAAACTA-GTA-TTTTAG
1 TGGCGTTTTAATACCAAACGCCGCTATAGAC-ACGTACTTTT-G
* * *
28981 TGGCGTTTTTATA-CAAATGCTGCTATAGACACGTACTTTTG
1 TGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTTG
* * *
29022 TGGTGTTTTAATACCAAACGCCGCTATAGACTCGTACTTTAG
1 TGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTTG
* *
29064 TAGCATTTT--TACACAAACGCCGCTATAGACACGTACTTTTG
1 TGGCGTTTTAATAC-CAAACGCCGCTATAGACACGTACTTTTG
29105 TGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTTG
1 TGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTTG
*
29147 TGGCGTTTTAATATCAAACGCCGCTATAGACACGTACTTTTG
1 TGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTTG
* * *
29189 TGGCGTTTTAATACCAAACACCGCTATAGATTA-GTACTTTAG
1 TGGCGTTTTAATACCAAACGCCGCTATAGA-CACGTACTTTTG
29231 TGGCGTTTT--TACACAAACGCCGCTATAGACACGTACTTTTG
1 TGGCGTTTTAATAC-CAAACGCCGCTATAGACACGTACTTTTG
29272 TGGCGTTTTAATACCAAACGCCGC
1 TGGCGTTTTAATACCAAACGCCGC
29296 AATTGTCATA
Statistics
Matches: 280, Mismatches: 24, Indels: 21
0.86 0.07 0.06
Matches are distributed among these distances:
40 8 0.03
41 107 0.38
42 158 0.56
43 7 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (42 bp):
TGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTTG
Found at i:29092 original size:83 final size:83
Alignment explanation
Indices: 28894--29295 Score: 549
Period size: 83 Copynumber: 4.8 Consensus size: 83
28884 AATACTATAT
* * * * * * ** *
28894 TTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGA-ATCGTAATATAATGGCGTTTTTATA-CAAA
1 TTTAGTGGCGTTTTTACACAAACGCCGCTATAGACA-CGTACTTTTGTGGCGTTTTAATACCAAA
* *
28957 CGCCGCTATAAACTAGTAT
65 CGCCGCTATAGACTAGTAC
* * * *
28976 TTTAGTGGCGTTTTTATACAAATGCTGCTATAGACACGTACTTTTGTGGTGTTTTAATACCAAAC
1 TTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAAC
*
29041 GCCGCTATAGACTCGTAC
66 GCCGCTATAGACTAGTAC
* *
29059 TTTAGTAGCATTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAAC
1 TTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAAC
29124 GCCGCTATAGAC-ACGTAC
66 GCCGCTATAGACTA-GTAC
* * *
29142 TTTTGTGGCGTTTTAATATCAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAA
1 TTTAGTGGCGTTTTTACA-CAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAA
* *
29207 CACCGCTATAGATTAGTAC
65 CGCCGCTATAGACTAGTAC
29226 TTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAAC
1 TTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAAC
29291 GCCGC
66 GCCGC
29296 AATTGTCATA
Statistics
Matches: 283, Mismatches: 32, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
82 46 0.16
83 160 0.57
84 76 0.27
85 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (83 bp):
TTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAAC
GCCGCTATAGACTAGTAC
Found at i:29199 original size:167 final size:166
Alignment explanation
Indices: 28940--29295 Score: 565
Period size: 167 Copynumber: 2.1 Consensus size: 166
28930 CGTAATATAA
* * * *
28940 TGGCGTTTTTATA-CAAACGCCGCTATAAACTAGTATTTTAGTGGCGTTTTTATACAAATGCTGC
1 TGGCGTTTTAATACCAAACGCCGCTATAAACTAGTATTTTAGTGGCGTTTTAATACAAACGCCGC
* * *
29004 TATAGACACGTACTTTTGTGGTGTTTTAATACCAAACGCCGCTATAGACTCGTACTTTAGTAGCA
66 TATAGACACGTACTTTTGTGGCGTTTTAATACCAAACACCGCTATAGACTAGTACTTTAGTAGCA
29069 TTTTTACACAAACGCCGCTATAGACACGTACTTTTG
131 TTTTTACACAAACGCCGCTATAGACACGTACTTTTG
*
29105 TGGCGTTTTAATACCAAACGCCGCTATAGAC-ACGTACTTTT-GTGGCGTTTTAATATCAAACGC
1 TGGCGTTTTAATACCAAACGCCGCTATAAACTA-GTA-TTTTAGTGGCGTTTTAATA-CAAACGC
* *
29168 CGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACACCGCTATAGATTAGTACTTTAGTG
63 CGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACACCGCTATAGACTAGTACTTTAGTA
*
29233 GCGTTTTTACACAAACGCCGCTATAGACACGTACTTTTG
128 GCATTTTTACACAAACGCCGCTATAGACACGTACTTTTG
29272 TGGCGTTTTAATACCAAACGCCGC
1 TGGCGTTTTAATACCAAACGCCGC
29296 AATTGTCATA
Statistics
Matches: 176, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
165 13 0.07
166 32 0.18
167 131 0.74
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (166 bp):
TGGCGTTTTAATACCAAACGCCGCTATAAACTAGTATTTTAGTGGCGTTTTAATACAAACGCCGC
TATAGACACGTACTTTTGTGGCGTTTTAATACCAAACACCGCTATAGACTAGTACTTTAGTAGCA
TTTTTACACAAACGCCGCTATAGACACGTACTTTTG
Found at i:29438 original size:58 final size:58
Alignment explanation
Indices: 29348--29458 Score: 204
Period size: 58 Copynumber: 1.9 Consensus size: 58
29338 TTTTATATGT
*
29348 GGTACGACTGTAAATAATGCGAATATTGTGGTTAACAATTGAATGAGTAGGGTGAGAG
1 GGTACGACTGTAAATAATGCGAATACTGTGGTTAACAATTGAATGAGTAGGGTGAGAG
*
29406 GGTACGACTGTAAATAATGCGAATGCTGTGGTTAACAATTGAATGAGTAGGGT
1 GGTACGACTGTAAATAATGCGAATACTGTGGTTAACAATTGAATGAGTAGGGT
29459 TTTGCTTTAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (58 bp):
GGTACGACTGTAAATAATGCGAATACTGTGGTTAACAATTGAATGAGTAGGGTGAGAG
Found at i:33896 original size:21 final size:20
Alignment explanation
Indices: 33872--33921 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
33862 TGATTTATTA
*
33872 TTATGGATTTAATTTTTCTTG
1 TTATGGATTTAA-GTTTCTTG
*
33893 TTATGGATTTTAAGTTTGTTG
1 TTATGGA-TTTAAGTTTCTTG
33914 TTATGGAT
1 TTATGGAT
33922 GTCAAGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.77
22 5 0.19
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.58
Consensus pattern (20 bp):
TTATGGATTTAAGTTTCTTG
Found at i:33928 original size:21 final size:21
Alignment explanation
Indices: 33890--33930 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33880 TTAATTTTTC
* *
33890 TTGTTATGGATTTTAAGTTTG
1 TTGTTATGGATGTCAAGTTTG
33911 TTGTTATGGATGTCAAGTTT
1 TTGTTATGGATGTCAAGTTT
33931 ATTGGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.02, G:0.24, T:0.54
Consensus pattern (21 bp):
TTGTTATGGATGTCAAGTTTG
Found at i:34264 original size:43 final size:43
Alignment explanation
Indices: 34129--34310 Score: 172
Period size: 43 Copynumber: 4.3 Consensus size: 43
34119 ACCAGATCTT
* * *
34129 TTGCGGTGTTTG-TGGAAAAACGCCACTAAATCTCAATACCTA
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATCTCAACACCTA
* *
34171 TTGCGGCATTT-TTGGGAAAAACGTCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTT-GGAAAAACGCCGCTAAATCTCAACACCTA
* * * * *
34214 TTGCGGCGTTTGTTAGAAAAATGCCGCCAAATATCAACACTTA
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATCTCAACACCTA
** * * ***
34257 TTGCGGCGTTTG-TCCAACAAACGCCGCTATATATCGTTACCTA
1 TTGCGGCGTTTGTTGGAA-AAACGCCGCTAAATCTCAACACCTA
34300 TTGCGGCGTTT
1 TTGCGGCGTTT
34311 TTTGTTACCA
Statistics
Matches: 115, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
42 13 0.11
43 100 0.87
44 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (43 bp):
TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATCTCAACACCTA
Found at i:38792 original size:20 final size:19
Alignment explanation
Indices: 38728--38796 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
38718 AGAAGCCCAA
*
38728 AAAGTTTCGATACTTT-TCT
1 AAAGTTTCGAAACTTTCT-T
* * *
38747 ATAGTTTCGAAACTATCTC
1 AAAGTTTCGAAACTTTCTT
38766 AAGAGTTTCGAAACTTTCATT
1 AA-AGTTTCGAAACTTTC-TT
38787 AAAGTTTCGA
1 AAAGTTTCGA
38797 TGCTTTGGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
19 14 0.35
20 23 0.57
21 3 0.08
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (19 bp):
AAAGTTTCGAAACTTTCTT
Found at i:46970 original size:20 final size:19
Alignment explanation
Indices: 46897--46971 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 19
46887 AAAAACCCAA
* *
46897 AAAGTTTCGATACTTTTTT
1 AAAGTTTCGAAACTTTCTT
* *
46916 ATAGTTTCGAAACTATCTT
1 AAAGTTTCGAAACTTTCTT
* *
46935 AAGTGTTTCAAAACTTTCATT
1 AA-AGTTTCGAAACTTTC-TT
*
46956 AAAGTTTCGATACTTT
1 AAAGTTTCGAAACTTT
46972 GGGTCCAACA
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
19 16 0.37
20 23 0.53
21 4 0.09
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (19 bp):
AAAGTTTCGAAACTTTCTT
Found at i:50026 original size:54 final size:54
Alignment explanation
Indices: 49968--50087 Score: 170
Period size: 54 Copynumber: 2.2 Consensus size: 54
49958 AAATGACTAG
*
49968 GGGTATCGGTACCTC-TAGGGAATTCTGTTTTTCTCGGAGCCAAAATTGGCACAA
1 GGGTATCGGTACC-CATAGGGAATTCAGTTTTTCTCGGAGCCAAAATTGGCACAA
* * * *
50022 GGGTATCGGTACCCATTGGGCATTCAGTTTTTCTCGGAGCCAAAATTGGCATAG
1 GGGTATCGGTACCCATAGGGAATTCAGTTTTTCTCGGAGCCAAAATTGGCACAA
*
50076 GGGTATTGGTAC
1 GGGTATCGGTAC
50088 ACCCTATGAG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.02
54 58 0.98
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (54 bp):
GGGTATCGGTACCCATAGGGAATTCAGTTTTTCTCGGAGCCAAAATTGGCACAA
Done.