Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003384.1 Hibiscus syriacus cultivar Beakdansim tig00007121_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: 79164
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:155 original size:24 final size:24
Alignment explanation
Indices: 110--155 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
100 GGTTTTGGAT
*
110 TGGGTTTAGAGAGGAAGGAGAGAG
1 TGGGTTTAGAGAGGAAGAAGAGAG
*
134 TGGGTTTTAGAG-GGGAGAAGAG
1 TGGG-TTTAGAGAGGAAGAAGAG
156 GAGGCGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.30, C:0.00, G:0.50, T:0.20
Consensus pattern (24 bp):
TGGGTTTAGAGAGGAAGAAGAGAG
Found at i:5118 original size:33 final size:33
Alignment explanation
Indices: 5077--5165 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
5067 TTAAGAAAAT
5077 AAACCAATGTATTTGAGTCCAATTGAAACACTA
1 AAACCAATGTATTTGAGTCCAATTGAAACACTA
* * *
5110 AAATCAATGTATTTGAATCCTATTGAAACACTA
1 AAACCAATGTATTTGAGTCCAATTGAAACACTA
5143 AAACCGAA-GTATTTTGAGTCCAA
1 AAACC-AATGTA-TTTGAGTCCAA
5166 GTCTCTAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 37 0.77
34 11 0.23
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (33 bp):
AAACCAATGTATTTGAGTCCAATTGAAACACTA
Found at i:5539 original size:13 final size:14
Alignment explanation
Indices: 5516--5544 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5506 ATTGTTATAT
5516 ATATATATATATTA
1 ATATATATATATTA
5530 ATAT-TATATATTA
1 ATATATATATATTA
5543 AT
1 AT
5545 TTTTTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATATATATATTA
Found at i:11118 original size:16 final size:17
Alignment explanation
Indices: 11091--11125 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
11081 TATCGCCGAC
11091 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
11108 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
11124 CG
1 CG
11126 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:25561 original size:31 final size:31
Alignment explanation
Indices: 25496--25563 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
25486 GGGTGTACAC
* *
25496 ATCTTAATTAAATAAAAACGAAAGTGATCAT
1 ATCTTAATTAAATAAAAACGAAAGAGACCAT
*
25527 ATCTTAATTAAATAAAAAC-AAGAGAGACCCT
1 ATCTTAATTAAATAAAAACGAA-AGAGACCAT
25558 ATCTTA
1 ATCTTA
25564 TATTTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACGAAAGAGACCAT
Found at i:37373 original size:14 final size:14
Alignment explanation
Indices: 37326--37376 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
37316 AAAAACCGAT
37326 AAACCGAACCGAAA
1 AAACCGAACCGAAA
* *
37340 AATCCAAACCGTTAAAA
1 AAACCGAACCG---AAA
37357 AAACCGAACCGAAA
1 AAACCGAACCGAAA
37371 AAACCG
1 AAACCG
37377 GTTTCGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 18 0.60
17 12 0.40
ACGTcount: A:0.55, C:0.27, G:0.12, T:0.06
Consensus pattern (14 bp):
AAACCGAACCGAAA
Found at i:50493 original size:18 final size:19
Alignment explanation
Indices: 50470--50508 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
50460 ATTTATAACT
50470 ATATGA-GGTAAAAAAATA
1 ATATGATGGTAAAAAAATA
* *
50488 ATATGATTGTAAAAATATA
1 ATATGATGGTAAAAAAATA
50507 AT
1 AT
50509 TATTTAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (19 bp):
ATATGATGGTAAAAAAATA
Found at i:50631 original size:10 final size:10
Alignment explanation
Indices: 50598--50634 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
50588 ATCATAATAT
50598 TATTTT-TTA
1 TATTTTATTA
*
50607 TATTATATTA
1 TATTTTATTA
50617 TATTTTATTA
1 TATTTTATTA
50627 TATTTTAT
1 TATTTTAT
50635 GTAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 5 0.20
10 20 0.80
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTTATTA
Found at i:51088 original size:16 final size:16
Alignment explanation
Indices: 51067--51099 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
51057 ATACTACTCG
51067 AAAGCATTATTTAGGT
1 AAAGCATTATTTAGGT
51083 AAAGCATTATTTAGGT
1 AAAGCATTATTTAGGT
51099 A
1 A
51100 TATTGTCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (16 bp):
AAAGCATTATTTAGGT
Found at i:53926 original size:5 final size:5
Alignment explanation
Indices: 53918--53968 Score: 102
Period size: 5 Copynumber: 10.2 Consensus size: 5
53908 CGTCTCGTCT
53918 CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA
1 CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA
53968 C
1 C
53969 AATTCACTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.20, C:0.41, G:0.39, T:0.00
Consensus pattern (5 bp):
CGGCA
Found at i:55203 original size:40 final size:40
Alignment explanation
Indices: 55159--55244 Score: 172
Period size: 40 Copynumber: 2.1 Consensus size: 40
55149 ATAATGCTAT
55159 TCTCAAATATAATATTATATTTCGTGAACCAAAAGCTAAC
1 TCTCAAATATAATATTATATTTCGTGAACCAAAAGCTAAC
55199 TCTCAAATATAATATTATATTTCGTGAACCAAAAGCTAAC
1 TCTCAAATATAATATTATATTTCGTGAACCAAAAGCTAAC
55239 TCTCAA
1 TCTCAA
55245 TACTCTCCAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.33
Consensus pattern (40 bp):
TCTCAAATATAATATTATATTTCGTGAACCAAAAGCTAAC
Found at i:61541 original size:32 final size:32
Alignment explanation
Indices: 61505--61594 Score: 180
Period size: 32 Copynumber: 2.8 Consensus size: 32
61495 GATCGATCGC
61505 TGACCTCATTCTCCCTCTCATCGATCAATCAT
1 TGACCTCATTCTCCCTCTCATCGATCAATCAT
61537 TGACCTCATTCTCCCTCTCATCGATCAATCAT
1 TGACCTCATTCTCCCTCTCATCGATCAATCAT
61569 TGACCTCATTCTCCCTCTCATCGATC
1 TGACCTCATTCTCCCTCTCATCGATC
61595 GATGGGTGAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.20, C:0.39, G:0.07, T:0.34
Consensus pattern (32 bp):
TGACCTCATTCTCCCTCTCATCGATCAATCAT
Found at i:63707 original size:28 final size:28
Alignment explanation
Indices: 63667--63735 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
63657 AAATCTAGGC
* *
63667 AACTTTCAAAAATC-ATCGTGTTCCAAAT
1 AACTTTTAGAAATCTAT-GTGTTCCAAAT
*
63695 AACTTTTAGAAATCGTTATGTGTTCTAAAT
1 AACTTTTAGAAATC--TATGTGTTCCAAAT
63725 AACTTTTAGAA
1 AACTTTTAGAA
63736 GTCGTTGTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.34
30 21 0.60
31 2 0.06
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (28 bp):
AACTTTTAGAAATCTATGTGTTCCAAAT
Found at i:63725 original size:30 final size:30
Alignment explanation
Indices: 63684--63753 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
63674 AAAAATCATC
63684 GTGTTCCAAATAACTTTTAGAAATCGTTAT
1 GTGTTCCAAATAACTTTTAGAAATCGTTAT
* * *
63714 GTGTTCTAAATAACTTTTAGAAGTCGTTGT
1 GTGTTCCAAATAACTTTTAGAAATCGTTAT
*
63744 GTGATCCAAA
1 GTGTTCCAAA
63754 CGACTGCCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (30 bp):
GTGTTCCAAATAACTTTTAGAAATCGTTAT
Found at i:71021 original size:23 final size:23
Alignment explanation
Indices: 70995--71045 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
70985 GAAGGGGCCA
70995 ATTCCATTAATGAGGAATTTGGT
1 ATTCCATTAATGAGGAATTTGGT
71018 ATTCCATTAATGAGGAATTTGGT
1 ATTCCATTAATGAGGAATTTGGT
71041 ATTCC
1 ATTCC
71046 TCAGATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (23 bp):
ATTCCATTAATGAGGAATTTGGT
Done.