Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009391.1 Hibiscus syriacus cultivar Beakdansim tig00113290_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: 43194
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:305 original size:13 final size:13
Alignment explanation
Indices: 287--311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277 TTCCATTAGT
287 TTCATAAATAATA
1 TTCATAAATAATA
300 TTCATAAATAAT
1 TTCATAAATAAT
312 GTGATATGGC
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCATAAATAATA
Found at i:2404 original size:21 final size:21
Alignment explanation
Indices: 2378--2417 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2368 CAGAACCCCA
*
2378 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2399 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2418 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:6303 original size:22 final size:21
Alignment explanation
Indices: 6261--6300 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6251 GAGTTTGTTT
*
6261 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
6282 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
6301 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:14753 original size:21 final size:22
Alignment explanation
Indices: 14715--14756 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
14705 TTAAGATTAT
*
14715 TAAATTTTATTGAATTTTTTAA
1 TAAATTATATTGAATTTTTTAA
14737 TAAATTATATT-AATTTTTTA
1 TAAATTATATTGAATTTTTTA
14757 TTATAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TAAATTATATTGAATTTTTTAA
Found at i:14768 original size:22 final size:22
Alignment explanation
Indices: 14722--14768 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
14712 TATTAAATTT
*
14722 TATTGAATTTTTTAATAAATTA
1 TATTGAATTTTTTAATAAATAA
*
14744 TATT-AATTTTTTATTATAATAA
1 TATTGAATTTTTTAATA-AATAA
14766 TAT
1 TAT
14769 ATTCTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTGAATTTTTTAATAAATAA
Found at i:17852 original size:21 final size:20
Alignment explanation
Indices: 17814--17865 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
17804 ATAAATATAA
* *
17814 ATATTAA-TATTATTAAATT
1 ATATTAATTTTTAATAAATT
*
17833 TTATTGAATTTTTAATAAATT
1 ATATT-AATTTTTAATAAATT
17854 ATATTAATTTTT
1 ATATTAATTTTT
17866 TATTATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.15
20 9 0.33
21 14 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
ATATTAATTTTTAATAAATT
Found at i:17867 original size:21 final size:21
Alignment explanation
Indices: 17827--17865 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17817 TTAATATTAT
*
17827 TAAATTTTATTGAATTTTTAA
1 TAAATTATATTGAATTTTTAA
17848 TAAATTATATT-AATTTTT
1 TAAATTATATTGAATTTTT
17866 TATTATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (21 bp):
TAAATTATATTGAATTTTTAA
Found at i:20660 original size:17 final size:17
Alignment explanation
Indices: 20625--20672 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 17
20615 ATTAAGATTA
*
20625 TTAAATTTTATGAATTTTT
1 TTAAATTATAT-AA-TTTT
20644 TTAAATTATATAATTTT
1 TTAAATTATATAATTTT
20661 TT--ATTATATAAT
1 TTAAATTATATAAT
20673 ATATTCTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 10 0.36
17 6 0.21
18 2 0.07
19 10 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTAAATTATATAATTTT
Found at i:20660 original size:18 final size:19
Alignment explanation
Indices: 20625--20662 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
20615 ATTAAGATTA
*
20625 TTAAATTTTATGAATTTTT
1 TTAAATTATATGAATTTTT
20644 TTAAATTATAT-AATTTTT
1 TTAAATTATATGAATTTTT
20662 T
1 T
20663 ATTATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TTAAATTATATGAATTTTT
Found at i:20874 original size:28 final size:30
Alignment explanation
Indices: 20843--20914 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
20833 TTGAAAATCA
*
20843 TTATATATTATTA-AA-A-TAAAGTATAATA
1 TTATATATTATTATAATATTAAAGAAT-ATA
*
20871 TTATATATCATTATAATATTAAAGAATATA
1 TTATATATTATTATAATATTAAAGAATATA
*
20901 ATATCATATTATTA
1 TTAT-ATATTATTA
20915 GAATTATGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 12 0.33
29 2 0.06
30 7 0.19
31 15 0.42
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (30 bp):
TTATATATTATTATAATATTAAAGAATATA
Found at i:21323 original size:18 final size:17
Alignment explanation
Indices: 21289--21324 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21279 AGCTTCTATT
*
21289 TTTTAATTTTATTTATA
1 TTTTAATTTTATATATA
21306 TTTTAATTTTGATATATA
1 TTTTAATTTT-ATATATA
21324 T
1 T
21325 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTAATTTTATATATA
Found at i:21324 original size:2 final size:2
Alignment explanation
Indices: 21317--21355 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
21307 TTTAATTTTG
21317 AT AT 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 AT AT A
21356 AAAATTATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21756 original size:38 final size:39
Alignment explanation
Indices: 21705--21781 Score: 147
Period size: 38 Copynumber: 2.0 Consensus size: 39
21695 TTAGAAAAAG
21705 TTTTGTGATTATGAATGACTCC-TTTAACTTAAATTTTT
1 TTTTGTGATTATGAATGACTCCTTTTAACTTAAATTTTT
21743 TTTTGTGATTATGAATGACTCCTTTTAACTTAAATTTTT
1 TTTTGTGATTATGAATGACTCCTTTTAACTTAAATTTTT
21782 ATTTCATAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 22 0.58
39 16 0.42
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.53
Consensus pattern (39 bp):
TTTTGTGATTATGAATGACTCCTTTTAACTTAAATTTTT
Found at i:29207 original size:16 final size:16
Alignment explanation
Indices: 29186--29218 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29176 TTTTATTGAA
29186 ACTTTTAATAAATTAT
1 ACTTTTAATAAATTAT
29202 ACTTTTAATAAATTAT
1 ACTTTTAATAAATTAT
29218 A
1 A
29219 TTAATTTTTT
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:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
ACTTTTAATAAATTAT
Found at i:29821 original size:18 final size:18
Alignment explanation
Indices: 29794--29833 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
29784 ATATATATAT
29794 ATATTATTTTTATGAAA-A
1 ATATTATTTTTAT-AAATA
*
29812 ATATTTTTTTTATAAATA
1 ATATTATTTTTATAAATA
29830 ATAT
1 ATAT
29834 AAAAGTCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
ATATTATTTTTATAAATA
Found at i:33013 original size:18 final size:17
Alignment explanation
Indices: 32986--33023 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
32976 ATATATATTT
32986 TATTTTTTTATGAAA-AA
1 TATTTTTTTAT-AAATAA
33003 TATTATTTTTATAAATAA
1 TATT-TTTTTATAAATAA
33021 TAT
1 TAT
33024 AAAAGTCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TATTTTTTTATAAATAA
Found at i:36179 original size:18 final size:19
Alignment explanation
Indices: 36149--36189 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
36139 ATATATATAT
36149 ATATTATTTTTTATGAAA-A
1 ATATTATTTTTTAT-AAATA
36168 ATATTA-TTTTTATAAATA
1 ATATTATTTTTTATAAATA
36186 ATAT
1 ATAT
36190 AAAAGTCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 12 0.57
19 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATATTATTTTTTATAAATA
Found at i:37546 original size:2 final size:2
Alignment explanation
Indices: 37541--37567 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37531 AAAAATATCT
37541 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
37568 TTCCAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41670 original size:140 final size:141
Alignment explanation
Indices: 41514--41795 Score: 521
Period size: 140 Copynumber: 2.0 Consensus size: 141
41504 CTCTAACAAT
*
41514 TCAAAAAAATTATATTTTTAGTCTCTAAACCATTTTTGCTCACAATTTAGCCCTTAAATAAAATA
1 TCAAAAAAA-TATATTTTTAGTCTCTAAACCATTTTTACTCACAATTTAGCCCTTAAATAAAATA
41579 TAATTATAATGTCCCATTGCTCGATACTTACAAGGTGATCCTAAATGTGGAGATGGAAGTTCAAA
65 TAATTATAATGTCCCATTGCTCGATACTTACAAGGTGATCCTAAATGTGGAGATGGAAGTTCAAA
41644 GTGTTAATGTAG
130 GTGTTAATGTAG
41656 TCAAAAAAA-ATATTTTTAGTCTCTAAACCATTTTTACTCACAATTTAGCCCTTAAATAAAATAT
1 TCAAAAAAATATATTTTTAGTCTCTAAACCATTTTTACTCACAATTTAGCCCTTAAATAAAATAT
* *
41720 AATTATCATGTCCCATTGCTCGATACTTACAAGGTGATTCTAAATGTGGAGATGGAAGTTCAAAG
66 AATTATAATGTCCCATTGCTCGATACTTACAAGGTGATCCTAAATGTGGAGATGGAAGTTCAAAG
41785 TGTTAATGTAG
131 TGTTAATGTAG
41796 CTATCATAGG
Statistics
Matches: 137, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
140 128 0.93
142 9 0.07
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (141 bp):
TCAAAAAAATATATTTTTAGTCTCTAAACCATTTTTACTCACAATTTAGCCCTTAAATAAAATAT
AATTATAATGTCCCATTGCTCGATACTTACAAGGTGATCCTAAATGTGGAGATGGAAGTTCAAAG
TGTTAATGTAG
Done.