Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003829.1 Hibiscus syriacus cultivar Beakdansim tig00008208_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: 65837
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:14606 original size:27 final size:27
Alignment explanation
Indices: 14546--14607 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
14536 TAAAATTTAC
* *
14546 AAAAAATTTAGGTTTTTTATTAAAAAT
1 AAAAATTTTAAGTTTTTTATTAAAAAT
* * **
14573 TATAATTTTAAGTTTTTTATTTTAAAT
1 AAAAATTTTAAGTTTTTTATTAAAAAT
14600 AAAAATTT
1 AAAAATTT
14608 ATATTACCAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (27 bp):
AAAAATTTTAAGTTTTTTATTAAAAAT
Found at i:15462 original size:16 final size:16
Alignment explanation
Indices: 15413--15464 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 16
15403 ATTCCAGACA
*
15413 ACCTCTCCACAAGTGTC
1 ACCTCT-CAAAAGTGTC
* *
15430 ACCCCTAATACAAGTGTC
1 ACCTCTCA-A-AAGTGTC
15448 ACCTCTCAAAAGTGTC
1 ACCTCTCAAAAGTGTC
15464 A
1 A
15465 TCCTGAGGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 9 0.32
17 6 0.21
18 13 0.46
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.23
Consensus pattern (16 bp):
ACCTCTCAAAAGTGTC
Found at i:26816 original size:13 final size:12
Alignment explanation
Indices: 26791--26828 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
26781 TTGCTTCGAA
26791 AATAAAT-AAAT
1 AATAAATAAAAT
26802 AATAAATAGAAAT
1 AATAAATA-AAAT
26815 AAATAAATAAAAT
1 -AATAAATAAAAT
26828 A
1 A
26829 CCTCTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.29
12 1 0.04
13 8 0.33
14 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AATAAATAAAAT
Found at i:27919 original size:2 final size:2
Alignment explanation
Indices: 27912--27954 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
27902 AATAAAGACG
27912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27954 A
1 A
27955 ATAGTTTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35906 original size:3 final size:3
Alignment explanation
Indices: 35893--35929 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
35883 GATAGAAGGG
35893 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35930 TTAAAATCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:40420 original size:25 final size:25
Alignment explanation
Indices: 40385--40444 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
40375 CAAATAAGCA
40385 AGTTAAACTTCAATATGCTATGCTT
1 AGTTAAACTTCAATATGCTATGCTT
* *
40410 CGTTAAACTTCGATATGCTATGCTT
1 AGTTAAACTTCAATATGCTATGCTT
40435 AGTTAAACTT
1 AGTTAAACTT
40445 ACCGCGGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (25 bp):
AGTTAAACTTCAATATGCTATGCTT
Found at i:42849 original size:13 final size:13
Alignment explanation
Indices: 42802--42838 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
42792 AACCCGACCC
42802 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
42815 TACCCGACCAGTT
1 GACCCGACCCGTT
42828 GACCCGACCCG
1 GACCCGACCCG
42839 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.46, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:42853 original size:7 final size:7
Alignment explanation
Indices: 42841--42871 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
42831 CCGACCCGAC
42841 CCGTTGA
1 CCGTTGA
42848 CCGTTGA
1 CCGTTGA
42855 CCCGTTGA
1 -CCGTTGA
42863 CCGTTGA
1 CCGTTGA
42870 CC
1 CC
42872 CACGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.13, C:0.35, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:42858 original size:15 final size:15
Alignment explanation
Indices: 42838--42872 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
42828 GACCCGACCC
42838 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
42853 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
42868 GACCC
1 GACCC
42873 ACGTTGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.37, G:0.26, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:42892 original size:10 final size:9
Alignment explanation
Indices: 42838--42892 Score: 50
Period size: 7 Copynumber: 6.6 Consensus size: 9
42828 GACCCGACCC
42838 GACC-CGTT
1 GACCACGTT
42846 GA-C-CGTT
1 GACCACGTT
42853 GACC-CGTT
1 GACCACGTT
42861 GA-C-CGTT
1 GACCACGTT
42868 GACCCACGTT
1 GA-CCACGTT
42878 GACCACTGTT
1 GACCAC-GTT
42888 GACCA
1 GACCA
42893 AAACTTTGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
7 14 0.33
8 9 0.21
9 5 0.12
10 14 0.33
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (9 bp):
GACCACGTT
Found at i:44193 original size:18 final size:18
Alignment explanation
Indices: 44167--44202 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
44157 TCGAAAGGAC
*
44167 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
44185 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
44203 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:45383 original size:23 final size:23
Alignment explanation
Indices: 45357--45430 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
45347 AATTCTATTA
*
45357 TGATCCTGACCTGGATTCTGATC
1 TGATCATGACCTGGATTCTGATC
*
45380 TGAT-ATTGACATGGATTCTGATC
1 TGATCA-TGACCTGGATTCTGATC
*
45403 TGATACATGACCTGGATTCTGATA
1 TGAT-CATGACCTGGATTCTGATC
45427 TGAT
1 TGAT
45431 ACTTGACTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
23 24 0.55
24 19 0.43
25 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (23 bp):
TGATCATGACCTGGATTCTGATC
Found at i:45418 original size:24 final size:24
Alignment explanation
Indices: 45363--45437 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
45353 ATTATGATCC
45363 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
45386 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
45410 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
45434 TGAC
1 TGAC
45438 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:47170 original size:22 final size:22
Alignment explanation
Indices: 47142--47196 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
47132 GGTATGAATT
*
47142 TTATTTATTGTAAATAATAATG
1 TTATTTATTGTAAATAAAAATG
47164 TTATTTATTGTAAATAAAAATG
1 TTATTTATTGTAAATAAAAATG
47186 TTATTTATTGT
1 TTATTTATTGT
47197 CAACGTGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (22 bp):
TTATTTATTGTAAATAAAAATG
Found at i:50547 original size:26 final size:26
Alignment explanation
Indices: 50517--50567 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
50507 CAATATCTTA
*
50517 TGTAAAATATCGATATATTGTAGTTT
1 TGTAAAATATCGATATATTATAGTTT
50543 TGTAAAATATCGATATATTATAGTT
1 TGTAAAATATCGATATATTATAGTT
50568 CAACTGTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (26 bp):
TGTAAAATATCGATATATTATAGTTT
Found at i:51176 original size:44 final size:45
Alignment explanation
Indices: 51118--51202 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
51108 TTTTCCCATG
* *
51118 CAACCACCCTTTGGAAATCCCAACGTCTTTAGGCTTAATGGCATA
1 CAACCACCCTTTGGAAATACCAACGTCCTTAGGCTTAATGGCATA
* * *
51163 CAACCA-CCTTTGGAAGTATCGACGTCCTTAGGCTTAATGG
1 CAACCACCCTTTGGAAATACCAACGTCCTTAGGCTTAATGG
51203 GGGGTTGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 29 0.83
45 6 0.17
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (45 bp):
CAACCACCCTTTGGAAATACCAACGTCCTTAGGCTTAATGGCATA
Found at i:52043 original size:4 final size:4
Alignment explanation
Indices: 52034--52062 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
52024 TTAGCCTATC
52034 AATT AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT A
52063 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:53899 original size:2 final size:2
Alignment explanation
Indices: 53892--53949 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
53882 ATATTTATGC
53892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53934 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
53950 TATTGTATTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55309 original size:65 final size:65
Alignment explanation
Indices: 55115--55314 Score: 207
Period size: 65 Copynumber: 3.1 Consensus size: 65
55105 CTAAGAGTGA
* * * * ** * *
55115 ATCGATGCATGAAGTGCATTCTATGTTTCA-AACCAGCCTGAGTGCATCGATGCATGG-TCTGTA
1 ATCGATGCATAAAATGCATTCGATGTTTCATAA-AATTCTGAGTGCATCGATGCATGGATATGTG
55178 C
65 C
55179 ATCGATGCATAAAATGCATTCGATGTTTTCATAAAATTCTGAGTGCATCGATGCAT-GATATGTG
1 ATCGATGCATAAAATGCATTCGATG-TTTCATAAAATTCTGAGTGCATCGATGCATGGATATGTG
55243 C
65 C
**
55244 ATCGATGCATAAAATGCATTCGATG-TTCA-ATTTATTCAATG-GTGCATCGATGCATGGAT-TG
1 ATCGATGCATAAAATGCATTCGATGTTTCATA-AAATTC--TGAGTGCATCGATGCATGGATAT-
55305 GTGC
62 GTGC
55309 ATCGAT
1 ATCGAT
55315 ACACTCTTTT
Statistics
Matches: 118, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
62 1 0.01
63 8 0.07
64 38 0.32
65 69 0.58
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (65 bp):
ATCGATGCATAAAATGCATTCGATGTTTCATAAAATTCTGAGTGCATCGATGCATGGATATGTGC
Found at i:55898 original size:2 final size:2
Alignment explanation
Indices: 55891--55915 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55881 ACCAAACCAA
55891 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 A
55916 ATAAGTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56233 original size:31 final size:31
Alignment explanation
Indices: 56166--56225 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
56156 CAATTTAAGG
*
56166 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
56197 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
56226 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:56317 original size:19 final size:19
Alignment explanation
Indices: 56290--56355 Score: 105
Period size: 19 Copynumber: 3.5 Consensus size: 19
56280 AATGTTTTTA
* *
56290 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
56309 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
*
56328 TGAACAGTAAATCACTATT
1 TGAACAGTAAATTACTATT
56347 TGAACAGTA
1 TGAACAGTA
56356 CCCAGAGGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:58914 original size:21 final size:22
Alignment explanation
Indices: 58852--58933 Score: 60
Period size: 23 Copynumber: 3.6 Consensus size: 22
58842 GCATGGCATT
*
58852 GTGCACCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTC-AGGA
* * * *
58875 GTGCATCGGTGTACCTTCA-TA
1 GTGCATCGATGCACATTCAGGA
*
58896 GTGTATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC--AGGA
58919 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
58934 TGTTAAGTGT
Statistics
Matches: 44, Mismatches: 11, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
21 15 0.34
22 1 0.02
23 16 0.36
24 12 0.27
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGA
Found at i:62769 original size:22 final size:21
Alignment explanation
Indices: 62727--62766 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
62717 GAGTTTATTT
*
62727 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
62748 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
62767 ATAATTTCTC
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:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:64848 original size:65 final size:65
Alignment explanation
Indices: 64716--64875 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 65
64706 TGCACTAAGA
* * * * * * * * *
64716 GTGCACCGATGCATGAAGTGCATTTGATG-TTTCAAACAAGCATGAGTGCATCGATGCATGGTCT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAACAACCACGAGTGCATCAATGCATAGTAT
*
64780 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AACCCCGAGTGCATCAATGCATAGTA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AACAACCACGAGTGCATCAATGCATAGTA
64844 T
65 T
64845 GTGCATCGATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
64876 CAATTTATTC
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 25 0.30
65 57 0.68
66 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAACAACCACGAGTGCATCAATGCATAGTAT
Done.