Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002103.1 Hibiscus syriacus cultivar Beakdansim tig00004301_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: 39857
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1842 original size:18 final size:18
Alignment explanation
Indices: 1819--1853 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1809 AGCAAAAGGC
*
1819 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
1837 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1854 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:2056 original size:20 final size:20
Alignment explanation
Indices: 2031--2290 Score: 215
Period size: 20 Copynumber: 13.7 Consensus size: 20
2021 CACATTCATT
*
2031 TGACTATCGCAACGTGAATA
1 TGACTATCGCAACGCGAATA
2051 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* * *
2071 TGACTATCGCAATGTGAATT
1 TGACTATCGCAACGCGAATA
* *
2091 TGAATATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
2108 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
2125 TGACTATCACAACGCAAAT-
1 TGACTATCGCAACGCGAATA
*
2144 TGACTATCGCAATG-G---A
1 TGACTATCGCAACGCGAATA
* *
2160 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
2177 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
2197 TGACTATCGCAACGCAAATT
1 TGACTATCGCAACGCGAATA
* * *
2217 TAACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
*
2237 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
2257 TGATTATCGCAACGGGAATT
1 TGACTATCGCAACGCGAATA
2277 TGACTATCGCAACG
1 TGACTATCGCAACG
2291 AGAAATCGCA
Statistics
Matches: 197, Mismatches: 29, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
13 9 0.05
14 9 0.05
15 2 0.01
16 2 0.01
17 5 0.03
18 2 0.01
19 13 0.07
20 155 0.79
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:2170 original size:52 final size:53
Alignment explanation
Indices: 2056--2210 Score: 204
Period size: 52 Copynumber: 2.9 Consensus size: 53
2046 GAATATGACT
* * * * * *
2056 ATCGCAACGCGAATATGACTATCGCAATGTGAATTTGAATATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACG-CAAATTGACTATCGCAACGGGATA
* *
2110 ATCGCAATGCGAAAATGACTATCACAACGCAAATTGACTATCGCAA-TGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCAAATTGACTATCGCAACGGGATA
*
2162 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACG
1 ATCGCAATGCGAAAATGACTATCGCAACGC-AAATTGACTATCGCAACG
2211 CAAATTTAAC
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
52 34 0.39
53 29 0.33
54 25 0.28
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (53 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCAAATTGACTATCGCAACGGGATA
Found at i:2464 original size:36 final size:34
Alignment explanation
Indices: 2424--2503 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 34
2414 TCAACTTTTA
2424 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
2460 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
2490 ATCAATTAAACAAA
1 ATCAATTAAACAAA
2504 TCAACTCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 28 0.70
32 2 0.05
34 3 0.08
36 7 0.17
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:2473 original size:30 final size:30
Alignment explanation
Indices: 2439--2504 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
2429 TTAAACAAGC
2439 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
2469 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
2499 ACAAAT
1 ACAAAT
2505 CAACTCTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.29
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:3361 original size:13 final size:13
Alignment explanation
Indices: 3343--3371 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3333 GGACGACTTT
3343 TGAGGGCTCTCGA
1 TGAGGGCTCTCGA
3356 TGAGGGCTCTCGA
1 TGAGGGCTCTCGA
3369 TGA
1 TGA
3372 TCCTTCTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.21, G:0.38, T:0.24
Consensus pattern (13 bp):
TGAGGGCTCTCGA
Found at i:9345 original size:27 final size:25
Alignment explanation
Indices: 9282--9345 Score: 58
Period size: 27 Copynumber: 2.5 Consensus size: 25
9272 ATAAATATTG
*
9282 TTTTTAAAAAATAATATTTTTAAAA
1 TTTTTAATAAATAATATTTTTAAAA
** *
9307 TCATT-ATAAAATAATACTTATTTATAA
1 TTTTTAAT-AAATAATA-TT-TTTAAAA
9334 TTTTTAATAAAT
1 TTTTTAATAAAT
9346 TACTAACAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
24 1 0.03
25 11 0.38
26 2 0.07
27 13 0.45
28 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTTTAATAAATAATATTTTTAAAA
Found at i:12725 original size:29 final size:28
Alignment explanation
Indices: 12674--12793 Score: 107
Period size: 29 Copynumber: 4.2 Consensus size: 28
12664 GACCGGGTGA
* *
12674 TATTTTGGGATTTAATTCGAAAATGTGC
1 TATTTTGGGAATTAATTCAAAAATGTGC
* *
12702 TATTTTGGGAATTTAATTCAAAAAAGTGA
1 TATTTTGGGAA-TTAATTCAAAAATGTGC
* * *
12731 TATTGTAGGAATTAACTCGAAAAGA-GTGC
1 TATTTTGGGAATTAATTC-AAAA-ATGTGC
* * *
12760 TATTTTGGTAATTATTTTAAAAATGGTGC
1 TATTTTGGGAATTAATTCAAAAAT-GTGC
12789 TATTT
1 TATTT
12794 CTGTAAAATG
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
27 1 0.01
28 20 0.27
29 51 0.70
30 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (28 bp):
TATTTTGGGAATTAATTCAAAAATGTGC
Found at i:17531 original size:13 final size:13
Alignment explanation
Indices: 17513--17542 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17503 GACTGGTTTC
*
17513 GACCCGACCTGTT
1 GACCCGACCCGTT
17526 GACCCGACCCGTT
1 GACCCGACCCGTT
17539 GACC
1 GACC
17543 GTTGACCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:17623 original size:29 final size:28
Alignment explanation
Indices: 17564--17693 Score: 143
Period size: 29 Copynumber: 4.5 Consensus size: 28
17554 ACCGGGTGAC
* *
17564 ATTTTGGGAATTAATTCGAAATTGGTACT
1 ATTTTGGGAATTAATTCGAAA-AGGTGCT
* * *
17593 ATTTTGTGAATTTAATTTGAAAATGTGCT
1 ATTTTGGGAA-TTAATTCGAAAAGGTGCT
* *
17622 ATTTTGGGAATTTAATTTGAAAAAGGCGCT
1 ATTTTGGGAA-TTAATTCG-AAAAGGTGCT
17652 ATTTTGGGAATTAATTCGAAAAGGGTGCT
1 ATTTTGGGAATTAATTCGAAAA-GGTGCT
*
17681 ATTTTGGTAATTA
1 ATTTTGGGAATTA
17694 TTTTAAAAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
28 4 0.05
29 55 0.63
30 28 0.32
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.42
Consensus pattern (28 bp):
ATTTTGGGAATTAATTCGAAAAGGTGCT
Found at i:17655 original size:59 final size:58
Alignment explanation
Indices: 17564--17704 Score: 160
Period size: 59 Copynumber: 2.4 Consensus size: 58
17554 ACCGGGTGAC
* ** * * * *
17564 ATTTTGGGAATTAATTCGAAATTGGTACTATTTTGTGAATTTAATTTGAAAA-TGTGCT
1 ATTTTGGGAATTAATTTGAAAAAGGCACTATTTTGGGAA-TTAATTCGAAAAGGGTGCT
*
17622 ATTTTGGGAATTTAATTTGAAAAAGGCGCTATTTTGGGAATTAATTCGAAAAGGGTGCT
1 ATTTTGGGAA-TTAATTTGAAAAAGGCACTATTTTGGGAATTAATTCGAAAAGGGTGCT
* *
17681 ATTTTGGTAATT-ATTTTAAAAAGG
1 ATTTTGGGAATTAATTTGAAAAAGG
17705 GTGATATTTC
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
57 11 0.15
58 23 0.32
59 37 0.52
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (58 bp):
ATTTTGGGAATTAATTTGAAAAAGGCACTATTTTGGGAATTAATTCGAAAAGGGTGCT
Found at i:17702 original size:29 final size:29
Alignment explanation
Indices: 17564--17713 Score: 108
Period size: 29 Copynumber: 5.1 Consensus size: 29
17554 ACCGGGTGAC
* * ** *
17564 ATTTTGGGAATTAATTCGAAATTGGTACT
1 ATTTTGGGAATTATTTCAAAAAGGGTGCT
* * *
17593 ATTTTGTGAATTTAATTT-GAAAA-TGTGCT
1 ATTTTGGGAA-TT-ATTTCAAAAAGGGTGCT
* *
17622 ATTTTGGGAATTTAATTTGAAAAA-GGCGCT
1 ATTTTGGGAA-TT-ATTTCAAAAAGGGTGCT
* *
17652 ATTTTGGGAATTAATTCGAAAAGGGTGCT
1 ATTTTGGGAATTATTTCAAAAAGGGTGCT
* * *
17681 ATTTTGGTAATTATTTTAAAAAGGGTGAT
1 ATTTTGGGAATTATTTCAAAAAGGGTGCT
17710 ATTT
1 ATTT
17714 CTGTAAAATG
Statistics
Matches: 99, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
28 7 0.07
29 65 0.66
30 24 0.24
31 3 0.03
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (29 bp):
ATTTTGGGAATTATTTCAAAAAGGGTGCT
Found at i:18057 original size:8 final size:8
Alignment explanation
Indices: 18044--18069 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
18034 CCAAAAAAGC
18044 TTAGTATT
1 TTAGTATT
18052 TTAGTATT
1 TTAGTATT
18060 TTAGTATT
1 TTAGTATT
18068 TT
1 TT
18070 GATTATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (8 bp):
TTAGTATT
Found at i:19927 original size:40 final size:40
Alignment explanation
Indices: 19870--19952 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
19860 ACATCTGAGA
19870 GAGATACTTACAAGAGCGACGTCAGGAGTTTCAGGATCTG
1 GAGATACTTACAAGAGCGACGTCAGGAGTTTCAGGATCTG
* *
19910 GAGATACTTGCAGGAGCGACGTCAGGAGTTTCAGGATCTG
1 GAGATACTTACAAGAGCGACGTCAGGAGTTTCAGGATCTG
19950 GAG
1 GAG
19953 CAGGGTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.22
Consensus pattern (40 bp):
GAGATACTTACAAGAGCGACGTCAGGAGTTTCAGGATCTG
Found at i:24853 original size:30 final size:29
Alignment explanation
Indices: 24807--24932 Score: 120
Period size: 29 Copynumber: 4.4 Consensus size: 29
24797 ATCGGGTGAC
*
24807 ATTTTGGGAA-TTAATTCG-AAATGGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAT--ATGCT
24836 ATTTTGGGAATTTAATTCGAAAATATGCT
1 ATTTTGGGAATTTAATTCGAAAATATGCT
* *
24865 ATTTTGGGAATTTAATT-AAAAAAATGCT
1 ATTTTGGGAATTTAATTCGAAAATATGCT
* *
24893 ATTTAT--GAA-TTAATTCGAAAAGAGTGCA
1 ATTT-TGGGAATTTAATTCGAAAATA-TGCT
*
24921 ATTTTGGTAATT
1 ATTTTGGGAATT
24933 ATTTAAAAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
26 6 0.07
27 9 0.11
28 20 0.24
29 34 0.41
30 9 0.11
31 4 0.05
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.40
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCGAAAATATGCT
Found at i:24913 original size:28 final size:29
Alignment explanation
Indices: 24832--24932 Score: 95
Period size: 28 Copynumber: 3.5 Consensus size: 29
24822 TCGAAATGGG
*
24832 TGCTATTTTGGGAATTTAATTCG-AAAATA
1 TGCTATTTT-GGAATTTAATTCGAAAAAAA
24861 TGCTATTTTGGGAATTTAATT--AAAAAAA
1 TGCTATTTT-GGAATTTAATTCGAAAAAAA
* *
24889 TGCTATTTAT-GAA-TTAATTCGAAAAGAG
1 TGCTATTT-TGGAATTTAATTCGAAAAAAA
*
24917 TGCAATTTTGGTAATT
1 TGCTATTTTGG-AATT
24933 ATTTAAAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
26 6 0.10
27 4 0.07
28 26 0.43
29 24 0.39
30 1 0.02
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.41
Consensus pattern (29 bp):
TGCTATTTTGGAATTTAATTCGAAAAAAA
Found at i:33661 original size:2 final size:2
Alignment explanation
Indices: 33656--33713 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
33646 AATTAGGGTT
33656 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33698 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
33714 ATTTTTTTTA
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):
TA
Done.