Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006542.1 Hibiscus syriacus cultivar Beakdansim tig00015970_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: 60484
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1716 original size:5 final size:5
Alignment explanation
Indices: 1704--1780 Score: 52
Period size: 5 Copynumber: 15.8 Consensus size: 5
1694 CGACACGACA
* * * *
1704 CGAG- CGAGC CGAG- CGAGC CGAGC CGAGC CAAGC CAAGC CGTA-C CGTGT
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CG-AGC CGAGC
* * * *
1752 CGTGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
1781 ACGGACGGAC
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
4 8 0.13
5 53 0.85
6 1 0.02
ACGTcount: A:0.22, C:0.34, G:0.38, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:3370 original size:6 final size:6
Alignment explanation
Indices: 3359--3389 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3349 TCCATTGCTC
3359 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
3390 GCCGAGCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3397 original size:5 final size:5
Alignment explanation
Indices: 3387--3425 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
3377 ACCACGACCA
* * *
3387 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
3426 ATGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:11298 original size:21 final size:22
Alignment explanation
Indices: 11274--11315 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11264 AGTGAAAAAA
*
11274 CCGGATTG-GTTTTTATCCGAT
1 CCGGATCGAGTTTTTATCCGAT
*
11295 CCGGATCGATTTTTTATCCGA
1 CCGGATCGAGTTTTTATCCGA
11316 CTTTGTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.40
Consensus pattern (22 bp):
CCGGATCGAGTTTTTATCCGAT
Found at i:13127 original size:24 final size:24
Alignment explanation
Indices: 13081--13129 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
13071 AGAAAAGAGG
13081 AGTAAACGATATGAAGAGAGAATA
1 AGTAAACGATATGAAGAGAGAATA
*
13105 AGTAAACGATATGAATAGAGAATA
1 AGTAAACGATATGAAGAGAGAATA
13129 A
1 A
13130 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.04, G:0.22, T:0.18
Consensus pattern (24 bp):
AGTAAACGATATGAAGAGAGAATA
Found at i:25382 original size:21 final size:21
Alignment explanation
Indices: 25353--25392 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25343 CTTTAGACTT
* *
25353 AGAAAGAATCGAAAGTAAATC
1 AGAAAGAATAGAAAATAAATC
*
25374 AGAATGAATAGAAAATAAA
1 AGAAAGAATAGAAAATAAA
25393 GTTTCCAACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.05, G:0.17, T:0.15
Consensus pattern (21 bp):
AGAAAGAATAGAAAATAAATC
Found at i:30943 original size:21 final size:20
Alignment explanation
Indices: 30915--30953 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
30905 CACTGCAGGA
*
30915 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
30935 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
30954 GACTTTTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:35587 original size:14 final size:15
Alignment explanation
Indices: 35568--35596 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
35558 AGTTTCTTTT
35568 CCTTAAAA-TTTTCC
1 CCTTAAAAGTTTTCC
35582 CCTTAAAAGTTTTCC
1 CCTTAAAAGTTTTCC
35597 ATATTGCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (15 bp):
CCTTAAAAGTTTTCC
Found at i:40076 original size:13 final size:13
Alignment explanation
Indices: 40058--40088 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
40048 TGCAACCTCT
40058 TAACTTCACTATC
1 TAACTTCACTATC
40071 TAACTTCACTATC
1 TAACTTCACTATC
40084 TAACT
1 TAACT
40089 CAGACACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (13 bp):
TAACTTCACTATC
Found at i:45355 original size:23 final size:25
Alignment explanation
Indices: 45324--45370 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
45314 GGGATTAAAA
* *
45324 GTAAGAAATTTAGGTGAAA-ATGTG
1 GTAAGAAATTGAAGTGAAATATGTG
45348 GTAA-AAATTGAAGTGAAATATGT
1 GTAAGAAATTGAAGTGAAATATGT
45371 AAAACTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.30
Consensus pattern (25 bp):
GTAAGAAATTGAAGTGAAATATGTG
Done.