Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004364.1 Hibiscus syriacus cultivar Beakdansim tig00009561_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: 90523
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:5728 original size:20 final size:21
Alignment explanation
Indices: 5703--5741 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5693 AACTAGGGTA
5703 TTTAA-TTGTTTAAAAATATT
1 TTTAATTTGTTTAAAAATATT
*
5723 TTTAATTTTTTTAAAAATA
1 TTTAATTTGTTTAAAAATA
5742 AAATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TTTAATTTGTTTAAAAATATT
Found at i:15753 original size:24 final size:24
Alignment explanation
Indices: 15721--15777 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
15711 AACTTCCAGG
15721 TGAGGTATTCTTATTTGATTTGAT
1 TGAGGTATTCTTATTTGATTTGAT
*
15745 TGAGGTATTCTTATTTTATTTGAT
1 TGAGGTATTCTTATTTGATTTGAT
* *
15769 GGAGCTATT
1 TGAGGTATT
15778 AGTTCATGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (24 bp):
TGAGGTATTCTTATTTGATTTGAT
Found at i:23164 original size:2 final size:2
Alignment explanation
Indices: 23157--23197 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
23147 GTTAGTATGA
23157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
23198 GCTCGGTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33385 original size:23 final size:23
Alignment explanation
Indices: 33325--33388 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
33315 CAGCTCATAT
* *
33325 AATTGCACCGAAATTCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
33348 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
33371 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
33389 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:42814 original size:31 final size:31
Alignment explanation
Indices: 42779--42846 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
42769 GTACTGGTAC
42779 GCATTACCTAAATGCA-ACCTGAACATATTGT
1 GCATTACCTAAATGCACACCT-AACATATTGT
** * * *
42810 GCATTATTTGAATGCACCCCTAGCATATTGT
1 GCATTACCTAAATGCACACCTAACATATTGT
42841 GCATTA
1 GCATTA
42847 TCTGAATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (31 bp):
GCATTACCTAAATGCACACCTAACATATTGT
Found at i:49211 original size:14 final size:14
Alignment explanation
Indices: 49178--49210 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
49168 CACAGCTTCA
49178 TTTTTTCTTTTTCT
1 TTTTTTCTTTTTCT
49192 TTTTTTCTTTTT-T
1 TTTTTTCTTTTTCT
49205 TTTTTT
1 TTTTTT
49211 TACAAAGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTTTCTTTTTCT
Found at i:55431 original size:20 final size:19
Alignment explanation
Indices: 55374--55433 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
55364 AAGATAAGGA
*
55374 AAATAAAAAGTAAAACTATT
1 AAATAAAAAGTAAAA-TAAT
* * *
55394 TAA-AAAAATTAAATTAAT
1 AAATAAAAAGTAAAATAAT
55412 AAATAAACAAGTAAAATAAT
1 AAATAAA-AAGTAAAATAAT
55432 AA
1 AA
55434 TGCTATGACA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
18 5 0.16
19 12 0.39
20 14 0.45
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.25
Consensus pattern (19 bp):
AAATAAAAAGTAAAATAAT
Found at i:57145 original size:20 final size:20
Alignment explanation
Indices: 57116--57158 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
57106 ATTTCACCAT
*
57116 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
57136 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
57156 ATG
1 ATG
57159 GGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:58782 original size:19 final size:19
Alignment explanation
Indices: 58758--58799 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
58748 AGAATAAAAT
*
58758 TGTCTCGGTAATATTTTTC
1 TGTCTCGGCAATATTTTTC
58777 TGTCTCGGCAATATTTTTC
1 TGTCTCGGCAATATTTTTC
58796 TGTC
1 TGTC
58800 ATGCTATCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.17, T:0.50
Consensus pattern (19 bp):
TGTCTCGGCAATATTTTTC
Found at i:62630 original size:20 final size:21
Alignment explanation
Indices: 62592--62630 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
62582 CATCAAGGTC
* *
62592 TTTGTGGAGGCCATGAAATCT
1 TTTGTCGAGGCCATCAAATCT
62613 TTTGTCGAGGCCA-CAAAT
1 TTTGTCGAGGCCATCAAAT
62631 TCCTTCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (21 bp):
TTTGTCGAGGCCATCAAATCT
Found at i:62772 original size:21 final size:21
Alignment explanation
Indices: 62742--62781 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
62732 TGGCCTGTAA
*
62742 TTTGTTGAGGCCATGAAATCT
1 TTTGTCGAGGCCATGAAATCT
62763 TTTGTCGAGGCCATGAAAT
1 TTTGTCGAGGCCATGAAAT
62782 GTTGATAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (21 bp):
TTTGTCGAGGCCATGAAATCT
Found at i:68269 original size:21 final size:23
Alignment explanation
Indices: 68245--68286 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
68235 CTTAACTTTA
68245 AAATCAAT-ATTTT-ATTTTTCC
1 AAATCAATGATTTTAATTTTTCC
*
68266 AAATCATTGATTTTAATTTTT
1 AAATCAATGATTTTAATTTTT
68287 GAAAGCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (23 bp):
AAATCAATGATTTTAATTTTTCC
Found at i:68328 original size:20 final size:20
Alignment explanation
Indices: 68303--68345 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
68293 TCAAAATCAT
*
68303 TTTTCAAAATTTC-ATTTTGC
1 TTTTCAAAA-TCCAATTTTGC
68323 TTTTCAAAATCCAATTTTGC
1 TTTTCAAAATCCAATTTTGC
68343 TTT
1 TTT
68346 CAGAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTCAAAATCCAATTTTGC
Found at i:71966 original size:102 final size:101
Alignment explanation
Indices: 71851--72054 Score: 327
Period size: 102 Copynumber: 2.0 Consensus size: 101
71841 AACTTCAACT
*
71851 TTTTTTTTACATACTTCAAGGAGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTAAAAGG
1 TTTTTTTAACATACTTCAAGGAGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTAAAAGG
*
71916 GAGCATACCTTCCACCCTCGAGCTAGTCAAGTAGAG
66 GAGCATACCTTCCACCCCCGAGCTAGTCAAGTAGAG
* * * *
71952 TTTTTTTAAGCATACTTTAAGGGGAGTCAGCTCATCACACTACCATTCCACACTCTAAGTGAAAG
1 TTTTTTTAA-CATACTTCAAGGAGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTAAAAG
* *
72017 GGAGCATACCTTCCACCCCCGATCTAGTCAGGTAGAG
65 GGAGCATACCTTCCACCCCCGAGCTAGTCAAGTAGAG
72054 T
1 T
72055 CATCCTGTGA
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 8 0.09
102 86 0.91
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (101 bp):
TTTTTTTAACATACTTCAAGGAGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTAAAAGG
GAGCATACCTTCCACCCCCGAGCTAGTCAAGTAGAG
Found at i:72877 original size:9 final size:9
Alignment explanation
Indices: 72860--72889 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
72850 ACTAATATTA
*
72860 AAAGAAAAT
1 AAAGCAAAT
72869 AAAGCAAAT
1 AAAGCAAAT
72878 AAAGCAAAT
1 AAAGCAAAT
72887 AAA
1 AAA
72890 AACATAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.73, C:0.07, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAGCAAAT
Found at i:86162 original size:21 final size:21
Alignment explanation
Indices: 86138--86184 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
86128 TGTTTTGGCA
86138 AAGCCCACACAATATCGATCG
1 AAGCCCACACAATATCGATCG
*
86159 AAGCCCACACAATTTCGATCG
1 AAGCCCACACAATATCGATCG
86180 AAGCC
1 AAGCC
86185 TTAACGGGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.34, G:0.15, T:0.15
Consensus pattern (21 bp):
AAGCCCACACAATATCGATCG
Found at i:87031 original size:16 final size:16
Alignment explanation
Indices: 87007--87037 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
86997 CACAGATTAT
87007 AAAAAAACATATTAAC
1 AAAAAAACATATTAAC
*
87023 AAAATAACATATTAA
1 AAAAAAACATATTAA
87038 TCGTTTCGGT
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:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAAACATATTAAC
Done.