Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006688.1 Hibiscus syriacus cultivar Beakdansim tig00016615_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: 63776
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1238 original size:15 final size:15
Alignment explanation
Indices: 1218--1248 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1208 GCAAGGATAG
1218 GAGGTACATTGCACT
1 GAGGTACATTGCACT
1233 GAGGTACATTGCACT
1 GAGGTACATTGCACT
1248 G
1 G
1249 TAAGAACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (15 bp):
GAGGTACATTGCACT
Found at i:25003 original size:25 final size:24
Alignment explanation
Indices: 24975--25043 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
24965 AACTCAAAAA
* * *
24975 AAAATTAGAAGTTCGATTGAAGCCT
1 AAAATTAG-AGCTCAATTGAAACCT
*
25000 AAAATTTGAGCTCAATTGAAACCT
1 AAAATTAGAGCTCAATTGAAACCT
*
25024 AAAATTTGAGCTCAATTGAA
1 AAAATTAGAGCTCAATTGAA
25044 GCGAAAGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 33 0.82
25 7 0.17
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (24 bp):
AAAATTAGAGCTCAATTGAAACCT
Found at i:25019 original size:24 final size:24
Alignment explanation
Indices: 24990--25045 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
24980 TAGAAGTTCG
24990 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
*
25014 ATTGAAACCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
25038 ATTGAAGC
1 ATTGAAGC
25046 GAAAGAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:30991 original size:63 final size:62
Alignment explanation
Indices: 30906--31094 Score: 216
Period size: 63 Copynumber: 3.0 Consensus size: 62
30896 TCCGATGGCG
* * * * * *
30906 GCAACGACTGATTCCACATTAGGTGGTGAAGATCAGAGTCCTCAGACACCTACGGTTCCGGGA
1 GCAACGACTGATTCAACATTAGGTGGTGAAGATCAGAGTCATCAGAC-CCGACGATGCCGGAA
* * *
30969 GCGACGACTGATTCAACGTTAGGTGGTGAAGATCAGAGTCATCAGACCCGATGATGCCGGAA
1 GCAACGACTGATTCAACATTAGGTGGTGAAGATCAGAGTCATCAGACCCGACGATGCCGGAA
* * * * * *
31031 GCAACAAGTGATTCGATATTAGGTGGTGAAGATCAGCGTCATCAGACGCCGAAGATGCCAGGAA
1 GCAACGACTGATTCAACATTAGGTGGTGAAGATCAGAGTCATCAGAC-CCGACGATGCC-GGAA
31095 TAATCGATGC
Statistics
Matches: 107, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
62 50 0.47
63 53 0.50
64 4 0.04
ACGTcount: A:0.30, C:0.22, G:0.29, T:0.20
Consensus pattern (62 bp):
GCAACGACTGATTCAACATTAGGTGGTGAAGATCAGAGTCATCAGACCCGACGATGCCGGAA
Found at i:36762 original size:20 final size:20
Alignment explanation
Indices: 36737--36779 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
36727 CGACATGACC
36737 TCATTTCTTGTTTTATACAA
1 TCATTTCTTGTTTTATACAA
36757 TCATTTCTTGTTTTATACAA
1 TCATTTCTTGTTTTATACAA
36777 TCA
1 TCA
36780 ACAAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (20 bp):
TCATTTCTTGTTTTATACAA
Found at i:46572 original size:14 final size:14
Alignment explanation
Indices: 46553--46580 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46543 TTAAAACTTA
46553 GAAGAAGGAATAAG
1 GAAGAAGGAATAAG
46567 GAAGAAGGAATAAG
1 GAAGAAGGAATAAG
46581 AAACAAATAA
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:0.57, C:0.00, G:0.36, T:0.07
Consensus pattern (14 bp):
GAAGAAGGAATAAG
Found at i:47136 original size:2 final size:2
Alignment explanation
Indices: 47129--47184 Score: 78
Period size: 2 Copynumber: 27.5 Consensus size: 2
47119 CATATTAAAC
*
47129 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAC AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT
47173 AT AT AT A- AT AT A
1 AT AT AT AT AT AT A
47185 ATAGGACGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
1 1 0.02
2 45 0.92
3 3 0.06
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:48356 original size:9 final size:8
Alignment explanation
Indices: 48341--48446 Score: 52
Period size: 8 Copynumber: 12.2 Consensus size: 8
48331 TAGAAATTAC
48341 AATAAAAA
1 AATAAAAA
48349 ACATAAAAGA
1 A-ATAAAA-A
*
48359 TATAATAAA
1 AATAA-AAA
48368 AATAAAATA
1 AATAAAA-A
*
48377 ATGTAACAAA
1 A-ATAA-AAA
*
48387 GA-AAAAA
1 AATAAAAA
* *
48394 AAGAAAAT
1 AATAAAAA
48402 AATAAAAGA
1 AATAAAA-A
48411 AAGTAAAAA
1 AA-TAAAAA
*
48420 AATCAAAA
1 AATAAAAA
*
48428 ATTAAAAA
1 AATAAAAA
*
48436 TATAACAAA
1 AATAA-AAA
48445 AA
1 AA
48447 ATATATATAT
Statistics
Matches: 73, Mismatches: 15, Indels: 19
0.68 0.14 0.18
Matches are distributed among these distances:
7 4 0.05
8 29 0.40
9 26 0.36
10 12 0.16
11 2 0.03
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.16
Consensus pattern (8 bp):
AATAAAAA
Found at i:48394 original size:26 final size:26
Alignment explanation
Indices: 48365--48427 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
48355 AAGATATAAT
**
48365 AAAAATAAAATAATGTAACAAAGAAA
1 AAAAATAAAATAATAAAACAAAGAAA
* * *
48391 AAAAAGAAAATAATAAAAGAAAGTAA
1 AAAAATAAAATAATAAAACAAAGAAA
48417 AAAAATCAAAA
1 AAAAAT-AAAA
48428 ATTAAAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (26 bp):
AAAAATAAAATAATAAAACAAAGAAA
Found at i:48940 original size:28 final size:27
Alignment explanation
Indices: 48887--48939 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
48877 ATAAATTAAG
* *
48887 TATTTTTTATTTCTAAAATTTATTTTA
1 TATTTTTAATTTCTAAAATATATTTTA
48914 TATTTTTAATTTTCTAAAATA-ATTTT
1 TATTTTTAA-TTTCTAAAATATATTTT
48940 TTAAATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (27 bp):
TATTTTTAATTTCTAAAATATATTTTA
Found at i:58622 original size:27 final size:27
Alignment explanation
Indices: 58592--58650 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
58582 AACTTTAATT
58592 GTTCCATCATACATCTTCAATTTGATG
1 GTTCCATCATACATCTTCAATTTGATG
58619 GTTCCATCATACATCTTCAATTTGATG
1 GTTCCATCATACATCTTCAATTTGATG
58646 GTTCC
1 GTTCC
58651 CACGCCAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (27 bp):
GTTCCATCATACATCTTCAATTTGATG
Found at i:59918 original size:46 final size:46
Alignment explanation
Indices: 59865--59995 Score: 183
Period size: 46 Copynumber: 2.8 Consensus size: 46
59855 AGAGTACTAA
* *
59865 CTAAAATGTTACTTTTTTTACTGGAAATATTAATATCGGGCGCTAC
1 CTAAAATGTTACTTTTTTTACTGAAAATATTAATATCGAGCGCTAC
*
59911 CTAAAATGTTACTTTTTCTACTGAAAATATTAATATCGAGCGCTAC
1 CTAAAATGTTACTTTTTTTACTGAAAATATTAATATCGAGCGCTAC
* *
59957 TTAAAATGTTA-TTTTTTCTACCGAAAATATATTAATATC
1 CTAAAATGTTACTTTTTT-TACTG-AAA-ATATTAATATC
59996 AGAAATATTT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
45 5 0.07
46 57 0.75
47 3 0.04
48 11 0.14
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (46 bp):
CTAAAATGTTACTTTTTTTACTGAAAATATTAATATCGAGCGCTAC
Found at i:62964 original size:46 final size:46
Alignment explanation
Indices: 62912--63033 Score: 171
Period size: 44 Copynumber: 2.7 Consensus size: 46
62902 AGAGTACTAG
62912 CTAAAATGTTACTTTTTCTACTGGAAATATTAATATC-GGACGCTAC
1 CTAAAATGTTACTTTTTCTACTGGAAATATTAATATCTGG-CGCTAC
*
62958 CTAAAATG-TACTTTTT-TACTGAAAATATTAATATCTGGCGCTAC
1 CTAAAATGTTACTTTTTCTACTGGAAATATTAATATCTGGCGCTAC
* * *
63002 TTAAAATGTTATTTTTTCTAC-CGAAATATTAA
1 CTAAAATGTTACTTTTTCTACTGGAAATATTAA
63034 CATCAGAAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
44 31 0.46
45 26 0.38
46 11 0.16
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (46 bp):
CTAAAATGTTACTTTTTCTACTGGAAATATTAATATCTGGCGCTAC
Done.