Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003734.1 Hibiscus syriacus cultivar Beakdansim tig00007984_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: 80072
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:8174 original size:12 final size:13
Alignment explanation
Indices: 8147--8179 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
8137 GTGCAAAAAG
8147 AAAAGAAAAGACA
1 AAAAGAAAAGACA
8160 AAAAGAAAAGTA-A
1 AAAAGAAAAG-ACA
8173 AAAAGAA
1 AAAAGAA
8180 CTCAAGCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 18 0.95
14 1 0.05
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAGACA
Found at i:9325 original size:18 final size:16
Alignment explanation
Indices: 9263--9319 Score: 114
Period size: 16 Copynumber: 3.6 Consensus size: 16
9253 AAGACGTTGC
9263 AGTTGAAAAATGAGAG
1 AGTTGAAAAATGAGAG
9279 AGTTGAAAAATGAGAG
1 AGTTGAAAAATGAGAG
9295 AGTTGAAAAATGAGAG
1 AGTTGAAAAATGAGAG
9311 AGTTGAAAA
1 AGTTGAAAA
9320 GAATGAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.30, T:0.19
Consensus pattern (16 bp):
AGTTGAAAAATGAGAG
Found at i:13412 original size:7 final size:7
Alignment explanation
Indices: 13400--13439 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
13390 TGCTATTTAA
13400 AAAAAAC
1 AAAAAAC
*
13407 AAAAAAG
1 AAAAAAC
*
13414 GAAAAA-
1 AAAAAAC
13420 AAAAAAC
1 AAAAAAC
13427 AAAAAAC
1 AAAAAAC
13434 AAAAAA
1 AAAAAA
13440 GCCAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:13438 original size:20 final size:20
Alignment explanation
Indices: 13398--13439 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
13388 TTTGCTATTT
**
13398 AAAAAAAACAAAAAAGGAAA
1 AAAAAAAACAAAAAACAAAA
13418 AAAAAAAACAAAAAACAAAA
1 AAAAAAAACAAAAAACAAAA
13438 AA
1 AA
13440 GCCAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAAAACAAAAAACAAAA
Found at i:18593 original size:24 final size:21
Alignment explanation
Indices: 18559--18601 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
18549 TCCACAAGAC
*
18559 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
18581 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
18602 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:22531 original size:24 final size:21
Alignment explanation
Indices: 22497--22539 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
22487 TCCACAAGAT
*
22497 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
22519 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
22540 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:28038 original size:5 final size:5
Alignment explanation
Indices: 28024--28076 Score: 58
Period size: 6 Copynumber: 10.6 Consensus size: 5
28014 AACATCTCTA
28024 TTCA- TTCAT TTCATT TTCATT TTCATT TTCAT TTCAT TTC-T TTCA-
1 TTCAT TTCAT TTCA-T TTCA-T TTCA-T TTCAT TTCAT TTCAT TTCAT
28069 TTCAT TTC
1 TTCAT TTC
28077 TTATTCCATT
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
4 12 0.27
5 16 0.36
6 17 0.38
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (5 bp):
TTCAT
Found at i:28302 original size:20 final size:19
Alignment explanation
Indices: 28265--28302 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
28255 GTGTTGTAAC
*
28265 AAAAACAAAAAGGAAGAAG
1 AAAAACAAAAAGAAAGAAG
28284 AAAAACAAAAAGAATAGAA
1 AAAAACAAAAAGAA-AGAA
28303 AACGAACCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.03
Consensus pattern (19 bp):
AAAAACAAAAAGAAAGAAG
Found at i:31091 original size:24 final size:24
Alignment explanation
Indices: 31051--31097 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
31041 AAAGTGCTAC
31051 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
31076 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
31098 CTCCTACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:31163 original size:20 final size:17
Alignment explanation
Indices: 31119--31166 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 17
31109 AATTTGGAGT
31119 GCAAAAGAAAAAAAAAA
1 GCAAAAGAAAAAAAAAA
31136 G-AAGAAGAAGAAAAGCAAAA
1 GCAA-AAGAA-AAAA--AAAA
31156 GCAAAAGAAAA
1 GCAAAAGAAAA
31167 GTGAAGCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.08
17 6 0.23
18 4 0.15
19 2 0.08
20 10 0.38
21 2 0.08
ACGTcount: A:0.75, C:0.06, G:0.19, T:0.00
Consensus pattern (17 bp):
GCAAAAGAAAAAAAAAA
Found at i:39519 original size:24 final size:24
Alignment explanation
Indices: 39487--39535 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
39477 CTAGAGGGTT
39487 CAAGTCCCAACTTACCACCCCTTA
1 CAAGTCCCAACTTACCACCCCTTA
39511 CAAGTCCCAACTTACCACCCCTTA
1 CAAGTCCCAACTTACCACCCCTTA
39535 C
1 C
39536 TTAAGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.47, G:0.04, T:0.20
Consensus pattern (24 bp):
CAAGTCCCAACTTACCACCCCTTA
Found at i:43521 original size:24 final size:25
Alignment explanation
Indices: 43475--43521 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
43465 CACCATGATC
* * *
43475 TGCATTTTCTTCAGTTTCTTCATCT
1 TGCATTGTCTTCAGGTTCCTCATCT
43500 TGCATTGT-TTCAGGTTCCTCAT
1 TGCATTGTCTTCAGGTTCCTCAT
43522 AAAAAATAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.51
Consensus pattern (25 bp):
TGCATTGTCTTCAGGTTCCTCATCT
Found at i:44516 original size:19 final size:21
Alignment explanation
Indices: 44473--44524 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
44463 GAAACCCCTT
44473 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
*
44494 TGAAAATATATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
44513 TGAAGATACATG
1 TGAAAATACATG
44525 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:56448 original size:16 final size:17
Alignment explanation
Indices: 56421--56452 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
56411 TTGGAGTGCA
56421 AAAAGAAAGAGAAAAAC
1 AAAAGAAAGAGAAAAAC
56438 AAAAG-AAGAGAAAAA
1 AAAAGAAAGAGAAAAA
56453 TCAGAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAGAAAGAGAAAAAC
Found at i:66759 original size:19 final size:21
Alignment explanation
Indices: 66735--66786 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
66725 CTGCCAAGAG
*
66735 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
66754 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
66775 CATGTATTTTCA
1 CATGTATTTTCA
66787 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Done.