Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001496.1 Hibiscus syriacus cultivar Beakdansim tig00002911_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: 71611
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:4514 original size:24 final size:22
Alignment explanation
Indices: 4479--4522 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
4469 TCCACAAGAC
* *
4479 ATGTTCCTTTGACATTTCAAAGG
1 ATGTACCTTTGA-AATTCAAAGG
4502 ATGTACCTCTTGAAATTCAAA
1 ATGTACCT-TTGAAATTCAAA
4523 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (22 bp):
ATGTACCTTTGAAATTCAAAGG
Found at i:6489 original size:19 final size:20
Alignment explanation
Indices: 6465--6514 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
6455 CGGCGAAGAG
*
6465 CATGTATTTTCATT-AAAGT
1 CATGTATTTTCATTAAAAAT
6484 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
6504 CATGTAATTTT
1 CATGT-ATTTT
6515 AGGAAGGTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 14 0.50
20 9 0.32
21 5 0.18
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:14874 original size:12 final size:12
Alignment explanation
Indices: 14852--14937 Score: 53
Period size: 12 Copynumber: 7.6 Consensus size: 12
14842 TATTATGCTT
14852 AGAAG-AAAAGA
1 AGAAGAAAAAGA
14863 AGAAGAAAAAGA
1 AGAAGAAAAAGA
*
14875 A-AA-AAGAA-A
1 AGAAGAAAAAGA
*
14884 AG--GAAAGAGA
1 AGAAGAAAAAGA
14894 A-AAGAAAAAAGA
1 AGAAG-AAAAAGA
* *
14906 GAGAA-AATAAGC
1 -AGAAGAAAAAGA
14918 AGAAGAAAAAGAA
1 AGAAGAAAAAG-A
14931 AGAAGAA
1 AGAAGAA
14938 TAGAAAATGA
Statistics
Matches: 56, Mismatches: 8, Indels: 20
0.67 0.10 0.24
Matches are distributed among these distances:
9 5 0.09
10 6 0.11
11 12 0.21
12 23 0.41
13 8 0.14
14 2 0.04
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.01
Consensus pattern (12 bp):
AGAAGAAAAAGA
Found at i:14882 original size:24 final size:24
Alignment explanation
Indices: 14854--14905 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
14844 TTATGCTTAG
14854 AAGAAAAGAAGAAGA-AAAAGAAAA
1 AAGAAAAGAA-AAGAGAAAAGAAAA
*
14878 AAGAAAAGGAAAGAGAAAAGAAAA
1 AAGAAAAGAAAAGAGAAAAGAAAA
14902 AAGA
1 AAGA
14906 GAGAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (24 bp):
AAGAAAAGAAAAGAGAAAAGAAAA
Found at i:14924 original size:14 final size:12
Alignment explanation
Indices: 14871--14937 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
14861 GAAGAAGAAA
*
14871 AAGAAAAAAGAA
1 AAGAAAAAAGAG
* * *
14883 AAGGAAAGAGAA
1 AAGAAAAAAGAG
14895 AAGAAAAAAGAG
1 AAGAAAAAAGAG
14907 -AGAAAATAAGCAG
1 AAGAAAA-AAG-AG
*
14920 AAGAAAAAGAAAG
1 AAGAAAAA-AGAG
14933 AAGAA
1 AAGAA
14938 TAGAAAATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
11 6 0.13
12 22 0.49
13 10 0.22
14 7 0.16
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.01
Consensus pattern (12 bp):
AAGAAAAAAGAG
Found at i:31028 original size:33 final size:33
Alignment explanation
Indices: 30986--31054 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
30976 GTTGATGAAT
*
30986 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
31019 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
31052 GAA
1 GAA
31055 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:35496 original size:33 final size:33
Alignment explanation
Indices: 35454--35522 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
35444 GTTGATGAAT
*
35454 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
35487 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
35520 GAA
1 GAA
35523 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:45246 original size:22 final size:22
Alignment explanation
Indices: 45220--45261 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
45210 TATTTATAGC
45220 TATGATGATGA-TATTATGAATG
1 TATGATG-TGATTATTATGAATG
*
45242 TATGATGTTATTATTATGAA
1 TATGATGTGATTATTATGAA
45262 CCACATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (22 bp):
TATGATGTGATTATTATGAATG
Found at i:65887 original size:6 final size:6
Alignment explanation
Indices: 65876--65919 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
65866 CAAAAGCAAC
* *
65876 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG AGAAAG AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
65920 CTCCTACAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:65901 original size:25 final size:24
Alignment explanation
Indices: 65873--65919 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
65863 TAACAAAAGC
65873 AACAAAAAGAAAAAGAAAGAAGAAA
1 AACAAAAAGAAAAAGAAA-AAGAAA
*
65898 AACAAAAAGAGAAAGAAAAAGA
1 AACAAAAAGAAAAAGAAAAAGA
65920 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGAAAAAGAAAAAGAAA
Found at i:65904 original size:19 final size:18
Alignment explanation
Indices: 65876--65917 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
65866 CAAAAGCAAC
*
65876 AAAAAGAAAAAGAAAGAAG
1 AAAAACAAAAAGAAA-AAG
*
65895 AAAAACAAAAAGAGAAAG
1 AAAAACAAAAAGAAAAAG
65913 AAAAA
1 AAAAA
65918 GACTCCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAACAAAAAGAAAAAG
Found at i:65953 original size:5 final size:5
Alignment explanation
Indices: 65943--65985 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
65933 TTTGGAGTGC
*
65943 AAAAG AAAAG AAAA- AGAAG AAAACG AAAAG AAAATG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAA-G AAAAG AAAA-G AAAAG AA
65986 GCAATTTGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 20 0.61
6 10 0.30
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:65959 original size:11 final size:11
Alignment explanation
Indices: 65943--65985 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
65933 TTTGGAGTGC
65943 AAAAGAAAAGA
1 AAAAGAAAAGA
65954 AAAAG--AAGA
1 AAAAGAAAAGA
*
65963 AAACGAAAAGA
1 AAAAGAAAAGA
*
65974 AAATGAAAAGA
1 AAAAGAAAAGA
65985 A
1 A
65986 GCAATTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 8 0.29
11 20 0.71
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:69222 original size:18 final size:18
Alignment explanation
Indices: 69186--69231 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
69176 CGACCAAGAG
**
69186 CATGTATCTTCATTTAAAT
1 CATGTAT-TTCATCAAAAT
69205 CATGTATTTCATCAAAAT
1 CATGTATTTCATCAAAAT
69223 CATGTATTT
1 CATGTATTT
69232 TCAAAGGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (18 bp):
CATGTATTTCATCAAAAT
Done.