Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004752.1 Hibiscus syriacus cultivar Beakdansim tig00010727_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: 54169
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:5214 original size:22 final size:22
Alignment explanation
Indices: 5189--5255 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
5179 CCATACTTAA
5189 TTAAATAAACGATGATATAAGT
1 TTAAATAAACGATGATATAAGT
**
5211 TTAATATATTC-AT-ACT-TAA--
1 TTAA-ATAAACGATGA-TATAAGT
5230 TTAAATAAACGATGATATAAGT
1 TTAAATAAACGATGATATAAGT
5252 TTAA
1 TTAA
5256 TATATTATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
18 4 0.12
19 7 0.21
20 4 0.12
21 4 0.12
22 11 0.32
23 4 0.12
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (22 bp):
TTAAATAAACGATGATATAAGT
Found at i:5216 original size:21 final size:21
Alignment explanation
Indices: 5192--5257 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
5182 TACTTAATTA
5192 AATAAACGATGATATAAGTTT
1 AATAAACGATGATATAAGTTT
* *
5213 AATATATTC-AT-ACT-TAA-TTA
1 AATA-A-ACGATGA-TATAAGTTT
5233 AATAAACGATGATATAAGTTT
1 AATAAACGATGATATAAGTTT
5254 AATA
1 AATA
5258 TATTATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
18 1 0.03
19 4 0.12
20 10 0.29
21 14 0.41
22 4 0.12
23 1 0.03
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (21 bp):
AATAAACGATGATATAAGTTT
Found at i:5231 original size:41 final size:41
Alignment explanation
Indices: 5175--5261 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 41
5165 ATTTCATATA
*
5175 ATATCCATACTTAATTAAATAAACGATGATATAAGTTTAAT
1 ATATTCATACTTAATTAAATAAACGATGATATAAGTTTAAT
5216 ATATTCATACTTAATTAAATAAACGATGATATAAGTTTAAT
1 ATATTCATACTTAATTAAATAAACGATGATATAAGTTTAAT
5257 ATATT
1 ATATT
5262 ATATTTTATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (41 bp):
ATATTCATACTTAATTAAATAAACGATGATATAAGTTTAAT
Found at i:9181 original size:19 final size:19
Alignment explanation
Indices: 9152--9201 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
9142 ACTTTATTTT
9152 TGTTT-TAAATTTTACTAG
1 TGTTTGTAAATTTTACTAG
9170 TGTTTGTAAATTTTACTAG
1 TGTTTGTAAATTTTACTAG
9189 TGTTTGTAAATTT
1 TGTTTGTAAATTT
9202 GTCGTGATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 5 0.16
19 26 0.84
ACGTcount: A:0.26, C:0.04, G:0.14, T:0.56
Consensus pattern (19 bp):
TGTTTGTAAATTTTACTAG
Found at i:14308 original size:23 final size:21
Alignment explanation
Indices: 14260--14336 Score: 111
Period size: 21 Copynumber: 3.6 Consensus size: 21
14250 TCGAAATAAT
14260 AAAAAAATATTATTTTTATTC
1 AAAAAAATATTATTTTTATTC
14281 AAAAAAATATTATTTTTATTC
1 AAAAAAATATTATTTTTATTC
* *
14302 AATAAAAATAATTA-TTTAATTG
1 AA-AAAAAT-ATTATTTTTATTC
14324 AAAAAAATATTAT
1 AAAAAAATATTAT
14337 ATAAAGGGTA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.08
21 29 0.57
22 14 0.27
23 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (21 bp):
AAAAAAATATTATTTTTATTC
Found at i:24768 original size:23 final size:21
Alignment explanation
Indices: 24714--24767 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
24704 TATTATATAT
24714 ATATATATATATTTAAAAATA
1 ATATATATATATTTAAAAATA
24735 ATATATATATATTTAAAAATA
1 ATATATATATATTTAAAAATA
* *
24756 ACATATAAATAT
1 ATATATATATAT
24768 AAATATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATATATATATTTAAAAATA
Found at i:27698 original size:44 final size:43
Alignment explanation
Indices: 27616--27703 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 43
27606 AAAGAAAGGT
*
27616 GCAACCGAAGATGTTGAATTTTTTTTAACATTTCCGGTTGAGC
1 GCAACCGAAGATGTTGAATTTTTTTTAACATTTCCGGTTAAGC
** *
27659 GCAACCGAAGATGTTGAACTTTTTTTTAATGTTTTCGGTTAAGC
1 GCAACCGAAGATGTTGAA-TTTTTTTTAACATTTCCGGTTAAGC
27703 G
1 G
27704 TAATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 18 0.45
44 22 0.55
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.39
Consensus pattern (43 bp):
GCAACCGAAGATGTTGAATTTTTTTTAACATTTCCGGTTAAGC
Found at i:27746 original size:33 final size:37
Alignment explanation
Indices: 27709--27788 Score: 96
Period size: 37 Copynumber: 2.3 Consensus size: 37
27699 AAGCGTAATT
27709 TAAAATATTA-ATTTTTTAA-ATA-TTT-TTACAACC
1 TAAAATATTACATTTTTTAACATATTTTATTACAACC
* * *
27742 TAAAATGTTACTTTTTTTAACATATTTTATTGCAACC
1 TAAAATATTACATTTTTTAACATATTTTATTACAACC
*
27779 GAAAATATTA
1 TAAAATATTA
27789 TGAAGAATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
33 9 0.24
34 8 0.21
35 3 0.08
36 3 0.08
37 15 0.39
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (37 bp):
TAAAATATTACATTTTTTAACATATTTTATTACAACC
Found at i:28719 original size:15 final size:15
Alignment explanation
Indices: 28695--28730 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
28685 GTGTCATTAA
*
28695 ATTAATTTATAAAAC
1 ATTAAATTATAAAAC
*
28710 ATTAAATTATAAAAT
1 ATTAAATTATAAAAC
28725 ATTAAA
1 ATTAAA
28731 CGTATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATTATAAAAC
Found at i:30345 original size:13 final size:13
Alignment explanation
Indices: 30329--30353 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30319 ATAAATAGAT
30329 ATTAGAAATTAGG
1 ATTAGAAATTAGG
30342 ATTAGAAATTAG
1 ATTAGAAATTAG
30354 TTCATTTGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (13 bp):
ATTAGAAATTAGG
Found at i:38297 original size:22 final size:22
Alignment explanation
Indices: 38272--38321 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
38262 CAAGATTTAA
*
38272 ATAATTATACGTTTATTACTTT
1 ATAATTATACATTTATTACTTT
*
38294 ATAAGTATACATTTATTACTTT
1 ATAATTATACATTTATTACTTT
38316 ATAATT
1 ATAATT
38322 TAATGTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (22 bp):
ATAATTATACATTTATTACTTT
Found at i:42499 original size:13 final size:14
Alignment explanation
Indices: 42475--42504 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
42465 TTTAGTAATT
42475 TTAAGATTTTGAAA
1 TTAAGATTTTGAAA
42489 TTAAG-TTTTGAAA
1 TTAAGATTTTGAAA
42502 TTA
1 TTA
42505 CTCCCCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TTAAGATTTTGAAA
Found at i:54019 original size:22 final size:22
Alignment explanation
Indices: 53994--54051 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
53984 GGATCGCTTC
53994 GGTACGATGTACCATATAAATT
1 GGTACGATGTACCATATAAATT
54016 GGTACGATGTACCATATAAATT
1 GGTACGATGTACCATATAAATT
54038 GGTACGATGTACCA
1 GGTACGATGTACCA
54052 GTTTCTTAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (22 bp):
GGTACGATGTACCATATAAATT
Done.