Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001336.1 Hibiscus syriacus cultivar Beakdansim tig00002610_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: 57127
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:19871 original size:24 final size:24
Alignment explanation
Indices: 19831--19876 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
19821 TTTTAATTTC
*
19831 TTTTGTTATTCTTTTTTCTCTTTT
1 TTTTGTTATTCTATTTTCTCTTTT
*
19855 TTTTGTTATAT-TATTTTTTCTT
1 TTTTGTTAT-TCTATTTTCTCTT
19877 ATTCTATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTTGTTATTCTATTTTCTCTTTT
Found at i:20224 original size:21 final size:22
Alignment explanation
Indices: 20166--20228 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 22
20156 GTTTCATCTT
* * *
20166 TAGAATAGAGATAAAGATATTG
1 TAGAGTAGAGATAGAGATGTTG
20188 TAGAGTA-AGATAGAGATGTTG
1 TAGAGTAGAGATAGAGATGTTG
20209 TAGAGTAGAGAT-GAGA-GTTG
1 TAGAGTAGAGATAGAGATGTTG
20229 GAGATTACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 4 0.11
21 23 0.62
22 10 0.27
ACGTcount: A:0.41, C:0.00, G:0.32, T:0.27
Consensus pattern (22 bp):
TAGAGTAGAGATAGAGATGTTG
Found at i:20967 original size:10 final size:10
Alignment explanation
Indices: 20952--20994 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 10
20942 GAATAGATGT
20952 AAACGAACAC
1 AAACGAACAC
20962 AAACGAACAAAC
1 AAACGAAC--AC
20974 TTAAACGAACAC
1 --AAACGAACAC
20986 AAACGAACA
1 AAACGAACA
20995 AACTTAAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 17 0.59
12 4 0.14
14 8 0.28
ACGTcount: A:0.60, C:0.26, G:0.09, T:0.05
Consensus pattern (10 bp):
AAACGAACAC
Found at i:20978 original size:24 final size:24
Alignment explanation
Indices: 20951--21011 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
20941 CGAATAGATG
20951 TAAACGAACACAAACGAACAAACT
1 TAAACGAACACAAACGAACAAACT
20975 TAAACGAACACAAACGAACAAACT
1 TAAACGAACACAAACGAACAAACT
20999 TAAACGAACACAA
1 TAAACGAACACAA
21012 TAAACGAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.59, C:0.25, G:0.08, T:0.08
Consensus pattern (24 bp):
TAAACGAACACAAACGAACAAACT
Found at i:20981 original size:14 final size:13
Alignment explanation
Indices: 20951--21021 Score: 66
Period size: 14 Copynumber: 5.8 Consensus size: 13
20941 CGAATAGATG
20951 TAAACGAAC--AC
1 TAAACGAACAAAC
20962 -AAACGAACAAAC
1 TAAACGAACAAAC
20974 TTAAACGAAC--AC
1 -TAAACGAACAAAC
20986 -AAACGAACAAAC
1 TAAACGAACAAAC
20998 TTAAACGAACACAA-
1 -TAAACGAACA-AAC
21012 TAAACGAACA
1 TAAACGAACA
21022 TAAATGAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
10 16 0.31
12 6 0.12
13 10 0.20
14 17 0.33
15 2 0.04
ACGTcount: A:0.59, C:0.24, G:0.08, T:0.08
Consensus pattern (13 bp):
TAAACGAACAAAC
Found at i:21514 original size:27 final size:25
Alignment explanation
Indices: 21455--21510 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
21445 CCAACACTTC
21455 AGTCCAAGAGGACCCATGCATATAT
1 AGTCCAAGAGGACCCATGCATATAT
21480 AGTCCAAGAGGACCCATGCATATAT
1 AGTCCAAGAGGACCCATGCATATAT
21505 AGTCCA
1 AGTCCA
21511 CAAGCGTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (25 bp):
AGTCCAAGAGGACCCATGCATATAT
Found at i:22104 original size:2 final size:2
Alignment explanation
Indices: 22097--22126 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22087 ATTTGACGTG
22097 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
22127 TAAAATATTT
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:23235 original size:15 final size:15
Alignment explanation
Indices: 23212--23247 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
23202 CGCACCGCAT
*
23212 CCGCACCGCATCCAC
1 CCGCCCCGCATCCAC
*
23227 CCGCCCCGCATCCGC
1 CCGCCCCGCATCCAC
23242 CCGCCC
1 CCGCCC
23248 AACTAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.67, G:0.17, T:0.06
Consensus pattern (15 bp):
CCGCCCCGCATCCAC
Found at i:28883 original size:12 final size:12
Alignment explanation
Indices: 28855--28891 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
28845 TTTGGTAATC
28855 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
28868 CCCGCCCCGATA
1 CCCGCCCCGATA
*
28880 CCCGACCCGATA
1 CCCGCCCCGATA
28892 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.19, C:0.54, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:28947 original size:24 final size:26
Alignment explanation
Indices: 28920--28976 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
28910 ATATATATAT
*
28920 ATAATATTAATA-A-ATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
28944 ATAA-A-AAATATATATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
28968 ATATATATA
1 ATA-ATATA
28977 TACCCGGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 4 0.15
23 2 0.07
24 18 0.67
25 1 0.04
26 1 0.04
27 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATATAAATATATATTTAATTTAA
Found at i:28962 original size:19 final size:19
Alignment explanation
Indices: 28938--28977 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28928 AATAAATTTA
28938 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
28957 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
28976 AT
1 AT
28978 ACCCGGCCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:29024 original size:12 final size:12
Alignment explanation
Indices: 28976--29029 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
28966 AAATATATAT
*
28976 ATACCCGGCCCG
1 ATACCCGGCCCA
*
28988 ATTCCCGGCCCA
1 ATACCCGGCCCA
**
29000 ATA-CCAACCCA
1 ATACCCGGCCCA
29011 ATACCCGGCCCA
1 ATACCCGGCCCA
29023 ATACCCG
1 ATACCCG
29030 TTTAAATAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
11 9 0.26
12 25 0.74
ACGTcount: A:0.26, C:0.48, G:0.15, T:0.11
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:29729 original size:76 final size:75
Alignment explanation
Indices: 29596--29742 Score: 199
Period size: 76 Copynumber: 1.9 Consensus size: 75
29586 GGGTAGTATG
* * * * *
29596 CCTGAAATCTAATTTTTTTTATGTTAGTTGTTTATTTTATTAAATGTGTCTATCCTAAAATTTTA
1 CCTGAAATCTAATTTTTTTTATGTTAGTCGTTTATTTGATGAAATGCG-CTACCCTAAAATTTTA
29661 TTTGTGTTCAT
65 TTTGTGTTCAT
29672 CCTGAAATCT-ATATTTTTTTATGTTAGTCGTTTATTTGACTGAAGATGCG-TACCCTAAAATTT
1 CCTGAAATCTAAT-TTTTTTTATGTTAGTCGTTTATTTGA-TGAA-ATGCGCTACCCTAAAATTT
29735 TATTTGTG
63 TATTTGTG
29743 CCCACCCATA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
75 2 0.03
76 54 0.86
77 3 0.05
78 4 0.06
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (75 bp):
CCTGAAATCTAATTTTTTTTATGTTAGTCGTTTATTTGATGAAATGCGCTACCCTAAAATTTTAT
TTGTGTTCAT
Found at i:52929 original size:16 final size:16
Alignment explanation
Indices: 52899--52929 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52889 TAATATTGAA
*
52899 ACTTGAACTCGAAAAG
1 ACTTGAACTCAAAAAG
52915 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
52930 AAAAATTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Done.