Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005437.1 Hibiscus syriacus cultivar Beakdansim tig00012464_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: 74830
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4399 original size:2 final size:2
Alignment explanation
Indices: 4392--4435 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4382 AACACTGTTC
4392 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
4434 AT
1 AT
4436 GATTTTATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9476 original size:36 final size:36
Alignment explanation
Indices: 9435--9510 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
9425 ATTTTCGGGA
*
9435 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
9471 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
9507 TTTT
1 TTTT
9511 TTTGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:10948 original size:23 final size:21
Alignment explanation
Indices: 10922--10988 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
10912 TTTATATATA
10922 TTATATTTAATATTTTAAGAAT
1 TTATATTTAATATTTTAA-AAT
*
10944 TT-TATTTTTATATTATTAAAAT
1 TTATA-TTTAATATT-TTAAAAT
*
10966 ATATCAATTTAATATTTTAAAAT
1 TTAT--ATTTAATATTTTAAAAT
10989 ATAATAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.05
22 14 0.38
23 12 0.32
24 8 0.22
25 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (21 bp):
TTATATTTAATATTTTAAAAT
Found at i:10989 original size:23 final size:23
Alignment explanation
Indices: 10917--10991 Score: 82
Period size: 23 Copynumber: 3.2 Consensus size: 23
10907 ATTAATTTAT
10917 ATATATTATATTTAATATTTTAAGA
1 ATATATTA-ATTTAATATTTTAA-A
* *
10942 AT-T-TTATTTTTATATTATTAAA
1 ATATATTAATTTAATATT-TTAAA
*
10964 ATATATCAATTTAATATTTTAAA
1 ATATATTAATTTAATATTTTAAA
10987 ATATA
1 ATATA
10992 ATAAATAGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 11 0.26
23 18 0.43
24 11 0.26
25 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (23 bp):
ATATATTAATTTAATATTTTAAA
Found at i:11454 original size:3 final size:3
Alignment explanation
Indices: 11446--11485 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
11436 GGTTTCACTT
11446 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11486 GTTCATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12121 original size:2 final size:2
Alignment explanation
Indices: 12116--12145 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12106 TTTTTTACAA
12116 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
12146 TATTTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17120 original size:7 final size:7
Alignment explanation
Indices: 17108--17138 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
17098 AAAAGGTCAG
17108 GGGAGGA
1 GGGAGGA
17115 GGGAGGA
1 GGGAGGA
17122 GGGAGGA
1 GGGAGGA
*
17129 AGGAGGA
1 GGGAGGA
17136 GGG
1 GGG
17139 GAGTTGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.71, T:0.00
Consensus pattern (7 bp):
GGGAGGA
Found at i:17374 original size:15 final size:15
Alignment explanation
Indices: 17356--17436 Score: 60
Period size: 15 Copynumber: 5.5 Consensus size: 15
17346 TTATTTAATT
17356 TAATTTTAATTTCAG
1 TAATTTTAATTTCAG
* * *
17371 TAATCTAAATTTCTG
1 TAATTTTAATTTCAG
* *
17386 TAATTTAAATTTTA-
1 TAATTTTAATTTCAG
* *
17400 TAATTTT-ATTTTAA
1 TAATTTTAATTTCAG
17414 TAATATTTAATTT-AG
1 TAAT-TTTAATTTCAG
*
17429 TCATTTTA
1 TAATTTTA
17437 GGGTAAGTTG
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
13 6 0.11
14 14 0.26
15 30 0.56
16 4 0.07
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.56
Consensus pattern (15 bp):
TAATTTTAATTTCAG
Found at i:19519 original size:31 final size:31
Alignment explanation
Indices: 19481--19635 Score: 267
Period size: 31 Copynumber: 5.0 Consensus size: 31
19471 ATCCCGAAGG
*
19481 ATCAGTCCATATGTTCCGAAGAACATAGGTA
1 ATCAGTCCATATGTCCCGAAGAACATAGGTA
*
19512 ATCAGTCCATATGTCCCGAAGAACATAAGTA
1 ATCAGTCCATATGTCCCGAAGAACATAGGTA
*
19543 ATCAGTCCATATGTCCTGAAGAACATAGGTA
1 ATCAGTCCATATGTCCCGAAGAACATAGGTA
*
19574 ATTAGTCCATATGTCCCGAAGAACATAGGTA
1 ATCAGTCCATATGTCCCGAAGAACATAGGTA
19605 ATCAGT-CATATGTCCCGAAGAACATAGGTA
1 ATCAGTCCATATGTCCCGAAGAACATAGGTA
19635 A
1 A
19636 CCCTCGACTC
Statistics
Matches: 117, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
30 25 0.21
31 92 0.79
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (31 bp):
ATCAGTCCATATGTCCCGAAGAACATAGGTA
Found at i:29137 original size:44 final size:44
Alignment explanation
Indices: 29074--29166 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 44
29064 GGTTCCTGTA
*
29074 ACGTGTCTTCCCTCCATGCATGTATGAAAGGCGCGCTCCCTGCC
1 ACGTGTCTTCCCTCCATGCATGTATGAAAGGCGCGCTCCCTACC
29118 ACGTGTCTTCCCTCCATGCATGTATGAAAGGCGCGCTCCCTACC
1 ACGTGTCTTCCCTCCATGCATGTATGAAAGGCGCGCTCCCTACC
29162 ACGTG
1 ACGTG
29167 CTTTATTATC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.17, C:0.35, G:0.23, T:0.25
Consensus pattern (44 bp):
ACGTGTCTTCCCTCCATGCATGTATGAAAGGCGCGCTCCCTACC
Found at i:37666 original size:3 final size:3
Alignment explanation
Indices: 37658--37686 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
37648 TTTGACTGTC
37658 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
37687 ACATATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:38462 original size:18 final size:19
Alignment explanation
Indices: 38436--38471 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
38426 ATTATGTATG
*
38436 ATTTTGATA-AAAATAAAA
1 ATTTAGATATAAAATAAAA
38454 ATTTAGATATAAAATAAA
1 ATTTAGATATAAAATAAA
38472 TTAAAATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (19 bp):
ATTTAGATATAAAATAAAA
Found at i:39825 original size:27 final size:28
Alignment explanation
Indices: 39778--39841 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
39768 TATTTTTCTC
39778 AAATAATATTATTAAATTA-TTAATAAT
1 AAATAATATTATTAAATTATTTAATAAT
* *
39805 AAATAATATTATT-TATGTATTTAATATT
1 AAATAATATTATTAAAT-TATTTAATAAT
39833 AATATAATA
1 AA-ATAATA
39842 ATCTAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.06
27 15 0.47
28 9 0.28
29 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
AAATAATATTATTAAATTATTTAATAAT
Found at i:40236 original size:20 final size:20
Alignment explanation
Indices: 40211--40268 Score: 100
Period size: 20 Copynumber: 2.9 Consensus size: 20
40201 TCTACGAAAA
40211 ATATTTTTCAAAAAATATCT
1 ATATTTTTCAAAAAATATCT
40231 ATATTTTTCAAAAAATATCT
1 ATATTTTTCAAAAAATATCT
40251 ATA-TTTTCTAAAAAATAT
1 ATATTTTTC-AAAAAATAT
40269 TTTAAGTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.14
20 32 0.86
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTTTTCAAAAAATATCT
Found at i:48466 original size:13 final size:13
Alignment explanation
Indices: 48431--48466 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
48421 TATTTTTTCC
*
48431 TAAAAATAGTTTT
1 TAAAAATATTTTT
48444 TAAATAATATTTTT
1 TAAA-AATATTTTT
48458 TAAAAATAT
1 TAAAAATAT
48467 ATCAACATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
TAAAAATATTTTT
Found at i:52881 original size:15 final size:16
Alignment explanation
Indices: 52849--52882 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
52839 TTTGTTAGAA
52849 TTAAGAGTTGAATATT
1 TTAAGAGTTGAATATT
*
52865 TTAAGAGTT-AGTATT
1 TTAAGAGTTGAATATT
52880 TTA
1 TTA
52883 TTTTCATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (16 bp):
TTAAGAGTTGAATATT
Found at i:54467 original size:15 final size:15
Alignment explanation
Indices: 54447--54478 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54437 CCTTAGGCAG
54447 GTTAGTAGAAGAACA
1 GTTAGTAGAAGAACA
*
54462 GTTAGTAGAAGAGCA
1 GTTAGTAGAAGAACA
54477 GT
1 GT
54479 CAATGAAGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.06, G:0.31, T:0.22
Consensus pattern (15 bp):
GTTAGTAGAAGAACA
Found at i:55362 original size:155 final size:156
Alignment explanation
Indices: 55049--55485 Score: 616
Period size: 155 Copynumber: 2.8 Consensus size: 156
55039 CAAGTGGTTT
* *
55049 AAATTTGGTAAAAAAACAAACTTAAAATGAATGACAAATTGAATG-AATAAGGAGATTATAAAAA
1 AAATTTGGT-AAAAAA-AAACTTAAAATAAATGACAAATTGAA-GAAATAAGGAGATTATGAAAA
* * * *
55113 ATTGAATGACTAAATTGAAATAA-AAAAA-TTGTTATCTAAAAGAGGAATTGAATGT-TCATATG
63 ATTGAAGGACTAAATTGAAA-AATAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAT-ACATG
*
55175 TATTATACTATGGTTTAGGAGCATGCGGCTC
126 TATTATACTATGGTTTAGGAGCATGCGACTC
* * * *
55206 AAATTTGGT-TAAAATAACTTAAAATAAATGACAAATTGAAGAAATAGGGAGATTAGGAAAAATT
1 AAATTTGGTAAAAAAAAACTTAAAATAAATGACAAATTGAAGAAATAAGGAGATTATGAAAAATT
*
55270 GAAGGACTAAATTGAAAAATAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTATACATGTATTC
66 GAAGGACTAAATTGAAAAATAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTATACATGTATTA
*
55335 TACTATGGTTTAGGAGCATGTGACTC
131 TACTATGGTTTAGGAGCATGCGACTC
** * * *
55361 AAATTTGGTAAAAAAAAAGGT-GACTAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATT
1 AAATTTGGTAAAAAAAAACTTAAAATAAATGACAAATTGAAGAAATAAGGAGATTATGAAAAATT
*
55425 GAAGGACTAAATTGAAAAATAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAAACATGT
66 GAAGGACTAAATTGAAAAATAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTATACATGT
55486 GAATCAAATT
Statistics
Matches: 252, Mismatches: 23, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
153 3 0.01
154 64 0.25
155 168 0.67
156 8 0.03
157 9 0.04
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27
Consensus pattern (156 bp):
AAATTTGGTAAAAAAAAACTTAAAATAAATGACAAATTGAAGAAATAAGGAGATTATGAAAAATT
GAAGGACTAAATTGAAAAATAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTATACATGTATTA
TACTATGGTTTAGGAGCATGCGACTC
Found at i:59996 original size:103 final size:103
Alignment explanation
Indices: 59812--60029 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
59802 GTCGAGGGTC
* *
59812 TATGTGGTCATTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAT
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
59877 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
59915 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
59980 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
60018 TATGTGGTCCTT
1 TATGTGGTCCTT
60030 ATGGGCATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:60112 original size:23 final size:23
Alignment explanation
Indices: 60053--60113 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
60043 TATGGTACTA
* *
60053 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTATATGCGGCACTC
* *
60076 CGGTGCAATTATATGTGGCACTT
1 CGGTGCAATTATATGCGGCACTC
60099 CGGTGCAATTATATG
1 CGGTGCAATTATATG
60114 AGTTGTGGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (23 bp):
CGGTGCAATTATATGCGGCACTC
Found at i:68675 original size:23 final size:23
Alignment explanation
Indices: 68631--68679 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
68621 ATAAAGAACC
*
68631 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
68654 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
68677 AAA
1 AAA
68680 CCAACACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:73162 original size:101 final size:99
Alignment explanation
Indices: 72983--73184 Score: 332
Period size: 101 Copynumber: 2.0 Consensus size: 99
72973 TCGAGGGTCT
*
72983 ATGTGGTCCTTCGGGACATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATACTTG
1 ATGTGGTCCTTCGGGACATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTG
** *
73048 ATCTTTGGCATATGTATATGATTCTTAAGGAATG
66 ATCCCTAGCATATGTATATGATTCTTAAGGAATG
*
73082 ATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
1 ATGTGGTCCTTCGGGAC--ATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
*
73147 TGATCCCTAGTATATGTATATGATTCTTAAGGAATG
64 TGATCCCTAGCATATGTATATGATTCTTAAGGAATG
73183 AT
1 AT
73185 ATGTGGTACT
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
99 16 0.17
101 79 0.83
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.37
Consensus pattern (99 bp):
ATGTGGTCCTTCGGGACATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTG
ATCCCTAGCATATGTATATGATTCTTAAGGAATG
Found at i:73243 original size:22 final size:22
Alignment explanation
Indices: 73218--73270 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
73208 ATATGGCATA
*
73218 CGGTGCAATCTACGCGGCACTC
1 CGGTGCAATATACGCGGCACTC
* * *
73240 CGGTGCAATATATGTGGCACTT
1 CGGTGCAATATACGCGGCACTC
73262 CGGTGCAAT
1 CGGTGCAAT
73271 TATATGAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.25
Consensus pattern (22 bp):
CGGTGCAATATACGCGGCACTC
Done.