Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002018.1 Hibiscus syriacus cultivar Beakdansim tig00004122_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: 52754
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4928 original size:14 final size:14
Alignment explanation
Indices: 4909--4938 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4899 CTAATTAGCA
4909 TATTTATTTAGAAT
1 TATTTATTTAGAAT
4923 TATTTATTTAGAAT
1 TATTTATTTAGAAT
4937 TA
1 TA
4939 GAAGAAATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TATTTATTTAGAAT
Found at i:12675 original size:23 final size:23
Alignment explanation
Indices: 12649--12709 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
12639 CACCATAGCT
* *
12649 CGTATAATTGCACCGAAGTGTCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
12672 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
12695 CGTAGAATTGCACCG
1 CGTAGAATTGCACCG
12710 TAGTATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:12960 original size:30 final size:30
Alignment explanation
Indices: 12919--12987 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
12909 ACATAATTTG
* * *
12919 TATCACGTAGACATATTATTTTCATACCTT
1 TATCACATAGACATATCATTTCCATACCTT
*
12949 TATCACATAGACATATCATTTCCATACTTT
1 TATCACATAGACATATCATTTCCATACCTT
12979 TATCACATA
1 TATCACATA
12988 ACTCATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (30 bp):
TATCACATAGACATATCATTTCCATACCTT
Found at i:13352 original size:20 final size:20
Alignment explanation
Indices: 13329--13421 Score: 168
Period size: 20 Copynumber: 4.7 Consensus size: 20
13319 TAATGGAGAT
*
13329 ATGCATCGATGCATTACACC
1 ATGCATCGATGCACTACACC
*
13349 ATGCATCGGTGCACTACACC
1 ATGCATCGATGCACTACACC
13369 ATGCATCGATGCACTACACC
1 ATGCATCGATGCACTACACC
13389 ATGCATCGATGCACTACACC
1 ATGCATCGATGCACTACACC
13409 ATGCATCGATGCA
1 ATGCATCGATGCA
13422 TAAATCTTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (20 bp):
ATGCATCGATGCACTACACC
Found at i:13533 original size:56 final size:55
Alignment explanation
Indices: 13430--13535 Score: 140
Period size: 56 Copynumber: 1.9 Consensus size: 55
13420 CATAAATCTT
** * * *
13430 ATTCGATGTTTGTATTTAATGGGGTGCATCGATGCACTCCTTATGCATCGATGGC
1 ATTCGATGTTTGTATTTAAAAGAGTGCATCAATGCACTCCATATGCATCGATGGC
* *
13485 ATTCGATGTTTGTATTTTAAAAGAGTGCATCAATGCACTTCATGTGCATCG
1 ATTCGATGTTTGTA-TTTAAAAGAGTGCATCAATGCACTCCATATGCATCG
13536 GTACACCTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
55 14 0.33
56 29 0.67
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (55 bp):
ATTCGATGTTTGTATTTAAAAGAGTGCATCAATGCACTCCATATGCATCGATGGC
Found at i:21130 original size:24 final size:22
Alignment explanation
Indices: 21081--21130 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
21071 ACAGAATGTC
21081 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
21102 CAGGAGGGAACCGATTCCCTCCTA
1 AAGGAGGGAACCGATACCC-CC-A
21126 AAGGA
1 AAGGA
21131 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 3 0.13
22 13 0.57
23 2 0.09
24 5 0.22
ACGTcount: A:0.32, C:0.30, G:0.28, T:0.10
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:21526 original size:20 final size:22
Alignment explanation
Indices: 21486--21542 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
21476 TGAATATGTG
*
21486 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
21508 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
21528 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
21543 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:22113 original size:31 final size:31
Alignment explanation
Indices: 22075--22167 Score: 179
Period size: 31 Copynumber: 3.0 Consensus size: 31
22065 AGGGTCGAGG
22075 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
22106 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
22137 GTTTACCTATGTTCTTCGGGACA-ATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
22167 G
1 G
22168 GTCCTTCGGG
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 8 0.13
31 54 0.87
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:34544 original size:2 final size:2
Alignment explanation
Indices: 34537--34571 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
34527 TATGTTGTTG
34537 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 A
34572 CATAAAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39121 original size:17 final size:17
Alignment explanation
Indices: 39099--39131 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39089 AGAATAAAGA
39099 TTAAAT-TGATAGAATTT
1 TTAAATATGA-AGAATTT
39116 TTAAATATGAAGAATT
1 TTAAATATGAAGAATT
39132 AAATTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (17 bp):
TTAAATATGAAGAATTT
Found at i:44945 original size:40 final size:40
Alignment explanation
Indices: 44901--45000 Score: 164
Period size: 40 Copynumber: 2.5 Consensus size: 40
44891 GGGGTTTGCA
* *
44901 TTGAACAAAAGATTATGATTATCATAAATGTTTGATTCTT
1 TTGAATAAAAGATAATGATTATCATAAATGTTTGATTCTT
*
44941 TTGAATAAAAGATAATAATTATCATAAATGTTTGATTCTT
1 TTGAATAAAAGATAATGATTATCATAAATGTTTGATTCTT
*
44981 TTGAATAAAAGATGATGATT
1 TTGAATAAAAGATAATGATT
45001 TGCAACAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (40 bp):
TTGAATAAAAGATAATGATTATCATAAATGTTTGATTCTT
Found at i:46350 original size:28 final size:28
Alignment explanation
Indices: 46276--46348 Score: 132
Period size: 28 Copynumber: 2.7 Consensus size: 28
46266 TCAAGTAGAG
46276 TAAA-GAAACAAAAGAAAATCAAAAGGC
1 TAAAGGAAACAAAAGAAAATCAAAAGGC
46303 TAAAGGAAACAAAAGAAAATCAAAAGGC
1 TAAAGGAAACAAAAGAAAATCAAAAGGC
46331 TAAAGGAAAC-AAAGAAAA
1 TAAAGGAAACAAAAGAAAA
46349 ATACCATGCA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
27 12 0.27
28 33 0.73
ACGTcount: A:0.67, C:0.10, G:0.16, T:0.07
Consensus pattern (28 bp):
TAAAGGAAACAAAAGAAAATCAAAAGGC
Found at i:49857 original size:21 final size:22
Alignment explanation
Indices: 49815--49858 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
49805 AGTTTATATA
*
49815 TATTTATTTAAATTTTAAAATC
1 TATTTATTTAAATCTTAAAATC
49837 TATTT-TTTAAATCTTAAAATC
1 TATTTATTTAAATCTTAAAATC
49858 T
1 T
49859 TAAACGGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTATTTAAATCTTAAAATC
Found at i:51658 original size:33 final size:34
Alignment explanation
Indices: 51616--51684 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 34
51606 CATTTGATGT
51616 AGGTGACAAGAGA-TGGTCTTGAACTCTCTGAAG
1 AGGTGACAAGAGATTGGTCTTGAACTCTCTGAAG
51649 AGGTGACAAGAGATTTGGTCTTGAACTCTCTGAAG
1 AGGTGACAAGAGA-TTGGTCTTGAACTCTCTGAAG
51684 A
1 A
51685 ATCAACCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 13 0.38
35 21 0.62
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.26
Consensus pattern (34 bp):
AGGTGACAAGAGATTGGTCTTGAACTCTCTGAAG
Done.