Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001460.1 Hibiscus syriacus cultivar Beakdansim tig00002822_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: 66199
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1017 original size:27 final size:27
Alignment explanation
Indices: 983--1037 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
973 TAAACTAAAA
*
983 ACTAAATTTTAAATTTTAAAAGATTGG
1 ACTAAATTATAAATTTTAAAAGATTGG
*
1010 ACTAAATTATAGATTTTAAAAGATTGG
1 ACTAAATTATAAATTTTAAAAGATTGG
1037 A
1 A
1038 GGAAGTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (27 bp):
ACTAAATTATAAATTTTAAAAGATTGG
Found at i:4955 original size:18 final size:18
Alignment explanation
Indices: 4928--4963 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4918 CCAGAACCCA
*
4928 AGGGGTATCGATTCCCCT
1 AGGGGGATCGATTCCCCT
*
4946 AGGGGGATCGGTTCCCCT
1 AGGGGGATCGATTCCCCT
4964 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.25
Consensus pattern (18 bp):
AGGGGGATCGATTCCCCT
Found at i:11149 original size:12 final size:12
Alignment explanation
Indices: 11132--11156 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11122 TACACCACAT
11132 GATGGAAAATGG
1 GATGGAAAATGG
11144 GATGGAAAATGG
1 GATGGAAAATGG
11156 G
1 G
11157 TATAATCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.44, T:0.16
Consensus pattern (12 bp):
GATGGAAAATGG
Found at i:15711 original size:21 final size:20
Alignment explanation
Indices: 15678--15723 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
15668 ATCATTAAAT
15678 TTATAAAACTTATAAAATTAA
1 TTATAAAACTTATAAAATT-A
* * *
15699 TTATTAAATTTATGAAATTA
1 TTATAAAACTTATAAAATTA
15719 TTATA
1 TTATA
15724 GATAATTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
TTATAAAACTTATAAAATTA
Found at i:19752 original size:31 final size:30
Alignment explanation
Indices: 19714--19792 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 30
19704 GGTTTCAAAA
* *
19714 GTAATAAATCGGTCACTAATGATATCGATTT
1 GTAATAAAT-GGTCACTAATGATATCAATCT
*
19745 GTAATAAAATGGTCACTAATGTTATCAATCT
1 GTAAT-AAATGGTCACTAATGATATCAATCT
*
19776 GTAACAAAATGGTCACT
1 GTAA-TAAATGGTCACT
19793 CGACCAACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 38 0.90
32 4 0.10
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (30 bp):
GTAATAAATGGTCACTAATGATATCAATCT
Found at i:21530 original size:32 final size:34
Alignment explanation
Indices: 21489--21568 Score: 101
Period size: 35 Copynumber: 2.4 Consensus size: 34
21479 TTTAAATAGT
*
21489 TATTATTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTTATATTAAATAATATTTATATAAA
* *
21521 TATTATTTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATATT-AAATAATATTTATATAAA
21556 TATTATTTATTTA
1 TATTATTT-TTTA
21569 GAATTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
32 15 0.38
34 3 0.08
35 19 0.47
36 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTATATTAAATAATATTTATATAAA
Found at i:21532 original size:34 final size:33
Alignment explanation
Indices: 21456--21563 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 33
21446 GTGGTAAGAA
* *
21456 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
21490 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
21525 ATTTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
21560 ATTT
1 ATTT
21564 ATTTAGAATT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
33 1 0.02
34 27 0.43
35 28 0.44
36 7 0.11
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:21729 original size:17 final size:17
Alignment explanation
Indices: 21707--21760 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
21697 AATGTTAATA
21707 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
21724 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
21741 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
21758 TTT
1 TTT
21761 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:23352 original size:21 final size:21
Alignment explanation
Indices: 23328--23455 Score: 116
Period size: 21 Copynumber: 6.1 Consensus size: 21
23318 GCCCACCAGT
*
23328 TTATATGCC-ATCTCCGCAGGG
1 TTATATGCCGAGC-CCGCAGGG
*
23349 TTATATTCCGAGCCCGCAGGG
1 TTATATGCCGAGCCCGCAGGG
* *
23370 TTACATTCCGAGCCCGCAGGG
1 TTATATGCCGAGCCCGCAGGG
* *
23391 TTACATTCCGAGCCCGCAGGG
1 TTATATGCCGAGCCCGCAGGG
* * * *
23412 TTACATTCCTAGCCCGCCA-AG
1 TTATATGCCGAGCCCG-CAGGG
* *
23433 TTACATGCCTAGCCCGCAGGG
1 TTATATGCCGAGCCCGCAGGG
23454 TT
1 TT
23456 TTATACCATA
Statistics
Matches: 97, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
20 2 0.02
21 91 0.94
22 4 0.04
ACGTcount: A:0.20, C:0.32, G:0.25, T:0.23
Consensus pattern (21 bp):
TTATATGCCGAGCCCGCAGGG
Found at i:23388 original size:42 final size:42
Alignment explanation
Indices: 23341--23455 Score: 169
Period size: 42 Copynumber: 2.7 Consensus size: 42
23331 TATGCCATCT
*
23341 CCGCAGGGTTATATTCCGAGCCCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGCCCGCAGGGTTACATTCCGAGC
*
23383 CCGCAGGGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGCCCGCAGGGTTACATTCCGAGC
* * *
23425 CCGCCA-AGTTACATGCCTAGCCCGCAGGGTT
1 CCG-CAGGGTTACATTCCGAGCCCGCAGGGTT
23456 TTATACCATA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
42 65 0.97
43 2 0.03
ACGTcount: A:0.19, C:0.33, G:0.27, T:0.21
Consensus pattern (42 bp):
CCGCAGGGTTACATTCCGAGCCCGCAGGGTTACATTCCGAGC
Found at i:24036 original size:33 final size:34
Alignment explanation
Indices: 23977--24073 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
23967 AAATGTTTTT
*
23977 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
24011 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
24044 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
24074 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:24080 original size:34 final size:32
Alignment explanation
Indices: 23975--24080 Score: 122
Period size: 34 Copynumber: 3.2 Consensus size: 32
23965 ATAAATGTTT
*
23975 TTAAAATACAAATTATATTATTCAAAATTTAAAA
1 TTAAAATAAAAATTATATTATTC-AAATTT-AAA
* *
24009 TAAAAATAAAAATAATATTATTCAAATTTAAA
1 TTAAAATAAAAATTATATTATTCAAATTTAAA
* *
24041 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTC-AAATTTAA-A
24076 TTAAA
1 TTAAA
24081 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (32 bp):
TTAAAATAAAAATTATATTATTCAAATTTAAA
Found at i:24846 original size:128 final size:128
Alignment explanation
Indices: 24474--24846 Score: 622
Period size: 128 Copynumber: 2.9 Consensus size: 128
24464 TTACCTGATT
* *
24474 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * * *** *
24539 TGACAAAATAATGGAAGACGCGCCCCCGGGAACGCGTCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
24602 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
24667 TGATGAAATAATGGAAGGCGCGCCCCCAGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
24730 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
24795 TGACGAAATAATGGAAGGCGCGCCCCTGGGAACGCGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
24847 ACTCCGATTA
Statistics
Matches: 230, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
127 1 0.00
128 229 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:24930 original size:8 final size:8
Alignment explanation
Indices: 24917--24957 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
24907 TCACAATCTT
24917 TCAAATTC
1 TCAAATTC
24925 TCAAATTC
1 TCAAATTC
* *
24933 CCAAACTC
1 TCAAATTC
24941 T-AAATTC
1 TCAAATTC
24948 TCAAATTC
1 TCAAATTC
24956 TC
1 TC
24958 TGAAATGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:30304 original size:7 final size:7
Alignment explanation
Indices: 30294--30328 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
30284 CTACAAACAC
30294 TGTCGAT
1 TGTCGAT
30301 TGTCGAT
1 TGTCGAT
30308 TGTCGAT
1 TGTCGAT
*
30315 TGTCAAT
1 TGTCGAT
30322 TGTCGAT
1 TGTCGAT
30329 CTTTTAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (7 bp):
TGTCGAT
Found at i:36220 original size:25 final size:25
Alignment explanation
Indices: 36191--36238 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
36181 TTTAATTAGT
36191 AATGAACAAAACAGTGAACAGTAAC
1 AATGAACAAAACAGTGAACAGTAAC
** *
36216 AATGAACAGTACCGTGAACAGTA
1 AATGAACAAAACAGTGAACAGTA
36239 GGGGAATCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.15
Consensus pattern (25 bp):
AATGAACAAAACAGTGAACAGTAAC
Found at i:36967 original size:40 final size:40
Alignment explanation
Indices: 36923--37004 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
36913 ACCGTAGTGC
* *
36923 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAACTGTAT
36963 TACACATAAGGTCGTGCCCACCATATACACCAAACTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAACTGTAT
37003 TA
1 TA
37005 TAAACCTACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAACTGTAT
Found at i:43598 original size:12 final size:12
Alignment explanation
Indices: 43581--43617 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
43571 TTACTATTCA
*
43581 TGCTACAATAGC
1 TGCTACAATAAC
*
43593 TGCTACAGTAAC
1 TGCTACAATAAC
43605 TGCTACAATAAC
1 TGCTACAATAAC
43617 T
1 T
43618 TCCAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (12 bp):
TGCTACAATAAC
Found at i:43786 original size:22 final size:22
Alignment explanation
Indices: 43758--43801 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
43748 TGTCTTACTG
43758 TTATTGAAATATACCTTTCGAT
1 TTATTGAAATATACCTTTCGAT
43780 TTATTGAAATATACCTTTCGAT
1 TTATTGAAATATACCTTTCGAT
43802 GCTTGATGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (22 bp):
TTATTGAAATATACCTTTCGAT
Found at i:44065 original size:44 final size:44
Alignment explanation
Indices: 44009--44140 Score: 142
Period size: 44 Copynumber: 2.9 Consensus size: 44
43999 AAAATAATAT
*
44009 AAAATATCTTACCATTTA-TCCTATAAGCTCGTAAGCTTATTTACC
1 AAAATA-CTTACCATTTATTCC-ATAAGCTCATAAGCTTATTTACC
* * *
44054 AAAATACTTACCATTTAAATTCCATAAACTCATAAGCTTATTTTTCT
1 AAAATACTTACCATTT--ATTCCATAAGCTCATAAGCTTA-TTTACC
* * *
44101 AATATACTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 AAAATACTTACCATTTATTCCATAAGCTCATAAGCTTATTT
44141 GCATGGTTAC
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
43 3 0.04
44 30 0.40
45 6 0.08
46 18 0.24
47 18 0.24
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.39
Consensus pattern (44 bp):
AAAATACTTACCATTTATTCCATAAGCTCATAAGCTTATTTACC
Done.