Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007896.1 Hibiscus syriacus cultivar Beakdansim tig00110281_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: 73830
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10050 original size:4 final size:4
Alignment explanation
Indices: 10043--10072 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
10033 ATTCCCTCTT
10043 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
10073 CTCTTGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:10326 original size:18 final size:19
Alignment explanation
Indices: 10303--10340 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
10293 TTTTCATCTA
10303 ATAATACAAATTT-ATTTT
1 ATAATACAAATTTCATTTT
* *
10321 ATAATATATATTTCATTTT
1 ATAATACAAATTTCATTTT
10340 A
1 A
10341 GAAGAGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
ATAATACAAATTTCATTTT
Found at i:10693 original size:28 final size:27
Alignment explanation
Indices: 10639--10696 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
10629 AATTTTTTCT
*
10639 TCTCAAATTTTAATAAATTCGTATTATA
1 TCTCAAATTTTAAAAAATTC-TATTATA
10667 TCTCAAAATTTTAAAAAATT-TAGTTATA
1 TCTC-AAATTTTAAAAAATTCTA-TTATA
10695 TC
1 TC
10697 CTTTTTTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 2 0.07
28 11 0.41
29 14 0.52
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.45
Consensus pattern (27 bp):
TCTCAAATTTTAAAAAATTCTATTATA
Found at i:14961 original size:35 final size:35
Alignment explanation
Indices: 14906--14975 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
14896 TATTATTTTG
* *
14906 ATTATTTTAGAATTTAGGGTTTAGAAT-ATAATTGA
1 ATTATTTTAGAATGTAGGGTTAAGAATGA-AATTGA
* *
14941 ATTATTTTGGAATGTGGGGTTAAGAATGAAATTGA
1 ATTATTTTAGAATGTAGGGTTAAGAATGAAATTGA
14976 GGATTACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (35 bp):
ATTATTTTAGAATGTAGGGTTAAGAATGAAATTGA
Found at i:20443 original size:21 final size:23
Alignment explanation
Indices: 20419--20468 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
20409 TACAACATTA
*
20419 ATTATTAT-TTATACAATATAT-
1 ATTATTATATTATACAATAGATC
*
20440 ATTA-TATATTATATAATAGATC
1 ATTATTATATTATACAATAGATC
20462 ATTATTA
1 ATTATTA
20469 CATAATAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.12
21 15 0.62
22 4 0.17
23 2 0.08
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTATTATATTATACAATAGATC
Found at i:34312 original size:18 final size:18
Alignment explanation
Indices: 34273--34306 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34263 AAGTATTATC
*
34273 ATTATAAATCTAAAATAA
1 ATTATAAATCAAAAATAA
34291 ATTATAAAT-AAAAATA
1 ATTATAAATCAAAAATA
34307 CTATTAACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTATAAATCAAAAATAA
Found at i:36438 original size:40 final size:40
Alignment explanation
Indices: 36383--36469 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 40
36373 AATATTTGAA
* * *
36383 TATTTACACTAGTCAAAGTTATTGCCGAGTGTGGTTTATG
1 TATTTACACTAGTCAAAGTTATTGCCAAGTGCGGTATATG
*
36423 TATTTACACTAGTCAAAGTTATTGCTAAGTGCGGTATATG
1 TATTTACACTAGTCAAAGTTATTGCCAAGTGCGGTATATG
36463 TATTTAC
1 TATTTAC
36470 GATCGATGCG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.40
Consensus pattern (40 bp):
TATTTACACTAGTCAAAGTTATTGCCAAGTGCGGTATATG
Found at i:45362 original size:22 final size:22
Alignment explanation
Indices: 45321--45387 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
45311 CTCGTATAAA
*
45321 TGCACCGAAGTTCCCCGTAGAAT
1 TGCACCGAAG-TGCCCGTAGAAT
45344 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
45366 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
45388 GATGTCCATA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
22 32 0.76
23 10 0.24
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.21
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:47104 original size:21 final size:21
Alignment explanation
Indices: 47080--47124 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
47070 TCTTGTTCGT
* *
47080 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
47101 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
47122 TTG
1 TTG
47125 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:55983 original size:32 final size:31
Alignment explanation
Indices: 55942--56043 Score: 109
Period size: 32 Copynumber: 3.3 Consensus size: 31
55932 TTAGCTTAAT
*
55942 AATTATAATGACTATTTTGTAATAATTTGGTA
1 AATT-TAATGACTATTTTGTAATAATTTGATA
* *
55974 GAATTTAATGATTATTTTGTAATAATGTGATA
1 -AATTTAATGACTATTTTGTAATAATTTGATA
* *
56006 ACATTTAATGAGTATTTTATAAT-ATTTGA-A
1 A-ATTTAATGACTATTTTGTAATAATTTGATA
*
56036 AAGTTAAT
1 AATTTAAT
56044 AGGCAAAAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
29 6 0.10
30 2 0.03
31 6 0.10
32 43 0.70
33 4 0.07
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (31 bp):
AATTTAATGACTATTTTGTAATAATTTGATA
Found at i:58881 original size:20 final size:21
Alignment explanation
Indices: 58845--58884 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
58835 TGGTTGATAT
58845 AAAACATTTTAAAATTTAAAC
1 AAAACATTTTAAAATTTAAAC
*
58866 AAAATATTTT-AAATTTAAA
1 AAAACATTTTAAAATTTAAA
58885 GATTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAACATTTTAAAATTTAAAC
Found at i:69031 original size:34 final size:34
Alignment explanation
Indices: 68993--69064 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
68983 GGACTCGACT
68993 CGAAAACTTTAAAATTGATTTCGTCGAAAACTCG
1 CGAAAACTTTAAAATTGATTTCGTCGAAAACTCG
69027 CGAAAACTTTAAAATTGATTTCGTCGAAAACTCG
1 CGAAAACTTTAAAATTGATTTCGTCGAAAACTCG
69061 CGAA
1 CGAA
69065 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (34 bp):
CGAAAACTTTAAAATTGATTTCGTCGAAAACTCG
Found at i:71279 original size:16 final size:16
Alignment explanation
Indices: 71258--71292 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
71248 GGTATTACCC
71258 GACCTGTTATCAACCT
1 GACCTGTTATCAACCT
*
71274 GACCTGTTATGAACCT
1 GACCTGTTATCAACCT
71290 GAC
1 GAC
71293 ATGTAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (16 bp):
GACCTGTTATCAACCT
Found at i:71882 original size:22 final size:23
Alignment explanation
Indices: 71850--71894 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
71840 TCTGTAAGGT
71850 GTGTGTTTATTAACATGTTAAGA
1 GTGTGTTTATTAACATGTTAAGA
71873 GTGT-TTTATTAACATGTTAAGA
1 GTGTGTTTATTAACATGTTAAGA
71895 AAATTCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.44
Consensus pattern (23 bp):
GTGTGTTTATTAACATGTTAAGA
Found at i:72882 original size:14 final size:13
Alignment explanation
Indices: 72857--72889 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
72847 ATAATGTATA
72857 ATGTAT-AATGAT
1 ATGTATGAATGAT
72869 ATGTATGAATTGAT
1 ATGTATGAA-TGAT
72883 ATGTATG
1 ATGTATG
72890 TAAAGTGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 2 0.11
14 11 0.58
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (13 bp):
ATGTATGAATGAT
Found at i:73756 original size:18 final size:19
Alignment explanation
Indices: 73728--73765 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
73718 TACCAGGGTA
73728 ATCGATACCAATAAGGAGT
1 ATCGATACCAATAAGGAGT
73747 ATCG-TACCAATAAGGAGT
1 ATCGATACCAATAAGGAGT
73765 A
1 A
73766 CAGTACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (19 bp):
ATCGATACCAATAAGGAGT
Done.