Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008600.1 Hibiscus syriacus cultivar Beakdansim tig00111551_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: 89497
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:14562 original size:21 final size:21
Alignment explanation
Indices: 14536--14596 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
14526 GGGATTTATG
14536 TTTTGGAAAAGGGATCGATCC
1 TTTTGGAAAAGGGATCGATCC
*** *
14557 TTTTGGTCGAGGGATCAATCC
1 TTTTGGAAAAGGGATCGATCC
14578 TTTT-GAAAAGGGATCGATC
1 TTTTGGAAAAGGGATCGATC
14597 ATTTGCTGGA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (21 bp):
TTTTGGAAAAGGGATCGATCC
Found at i:16594 original size:2 final size:2
Alignment explanation
Indices: 16587--16614 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16577 ATGTACATGC
16587 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
16615 GTTGGATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16895 original size:18 final size:18
Alignment explanation
Indices: 16872--16924 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
16862 AGGGATTATC
*
16872 AGTTGTCCTTCGGGACAT
1 AGTTGTCATTCGGGACAT
16890 AGTTGTCATTCGGGACAT
1 AGTTGTCATTCGGGACAT
* * *
16908 AGTGGTTATCCGGGACA
1 AGTTGTCATTCGGGACA
16925 AATATTCAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (18 bp):
AGTTGTCATTCGGGACAT
Found at i:17990 original size:15 final size:15
Alignment explanation
Indices: 17972--18010 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
17962 TTATTTTATA
17972 TATTGTTATATGGTC
1 TATTGTTATATGGTC
17987 TATTGTTATATGGTC
1 TATTGTTATATGGTC
18002 TATTGTTAT
1 TATTGTTAT
18011 CTATTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.56
Consensus pattern (15 bp):
TATTGTTATATGGTC
Found at i:18245 original size:30 final size:30
Alignment explanation
Indices: 18201--18265 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
18191 GAGTGTTGGA
*
18201 CCTTGAGCCCAAGCTAGTTA-TCTTATAGTT
1 CCTTGAGCCCAAGCTAGTTAGT-TTATAGTG
* *
18231 CCTTGTGCCTAAGCTAGTTAGTTTATAGTG
1 CCTTGAGCCCAAGCTAGTTAGTTTATAGTG
18261 CCTTG
1 CCTTG
18266 CGCACTCCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (30 bp):
CCTTGAGCCCAAGCTAGTTAGTTTATAGTG
Found at i:19691 original size:17 final size:17
Alignment explanation
Indices: 19657--19691 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19647 CATTTGTGAA
*
19657 ATGAAGAAGAAAATATG
1 ATGAAGAAGAAAAGATG
*
19674 ATGAAGAAGAAGAGATG
1 ATGAAGAAGAAAAGATG
19691 A
1 A
19692 GTGTTTGGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (17 bp):
ATGAAGAAGAAAAGATG
Found at i:33769 original size:14 final size:14
Alignment explanation
Indices: 33750--33777 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33740 TATTTCCTAA
33750 GAAATAACTGGTAG
1 GAAATAACTGGTAG
33764 GAAATAACTGGTAG
1 GAAATAACTGGTAG
33778 ACAATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.29, T:0.21
Consensus pattern (14 bp):
GAAATAACTGGTAG
Found at i:45436 original size:19 final size:19
Alignment explanation
Indices: 45412--45458 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
45402 GAAGAAGTTT
45412 GGAGAGCAATTGCTGATTC
1 GGAGAGCAATTGCTGATTC
45431 GGAGAGCAATTGCTGATTC
1 GGAGAGCAATTGCTGATTC
*
45450 GGATAGCAA
1 GGAGAGCAA
45459 CAAAGCTCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (19 bp):
GGAGAGCAATTGCTGATTC
Found at i:83800 original size:8 final size:8
Alignment explanation
Indices: 83789--83827 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
83779 ATATATATAT
*
83789 AGAGAGAG
1 AGAGAGGG
83797 AGAGAGGG
1 AGAGAGGG
83805 AGAGAGGG
1 AGAGAGGG
83813 AGAGAGGG
1 AGAGAGGG
83821 AGAGAGG
1 AGAGAGG
83828 TGAACTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (8 bp):
AGAGAGGG
Done.