Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005058.1 Hibiscus syriacus cultivar Beakdansim tig00011353_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: 44814
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:3256 original size:13 final size:13
Alignment explanation
Indices: 3238--3265 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3228 GGATTGCCTT
3238 TTCTTCAATCTTA
1 TTCTTCAATCTTA
3251 TTCTTCAATCTTA
1 TTCTTCAATCTTA
3264 TT
1 TT
3266 AATGCATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.57
Consensus pattern (13 bp):
TTCTTCAATCTTA
Found at i:11594 original size:59 final size:59
Alignment explanation
Indices: 11532--11934 Score: 501
Period size: 59 Copynumber: 6.9 Consensus size: 59
11522 TGACACTAAA
* *
11532 TGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGATAGGGCACTTCA
1 TGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTCG
* * * *
11591 TGTGTTAAAATGGTAAGGAAATCATACTAAGTGTATCAATTTCCAGTTTGGGCACTTCG
1 TGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTCG
* *
11650 TGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATAAATTTCTAGATAGGGCACTTCG
1 TGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTCG
* * *
11709 TGTGCAAAAATGGTAAGGAAATCATATTAAGTGTAT-AATTTTCAGATAGGGCAC-TCTG
1 TGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC-G
* * *
11767 TGTGCTAAAATGGTAAGGAAATCATACTAAGCGTATGAATTTCTATATAGGGCACTTCG
1 TGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTCG
* * * * * * *
11826 TGTGCTAAACTGTTAAGTAATTCATACTAAGTGTATAAATTTCCGGA-ATGGGCACTTTG
1 TGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATA-GGGCACTTCG
* * * * * *
11885 TGTGC--AAATTGTTATGAGAGTCATACTAAATGTATGAATTTCCATATAGG
1 TGTGCTAAAATGGTAAGGA-AATCATACTAAGTGTATGAATTTCCAGATAGG
11935 AAATGTGAGT
Statistics
Matches: 296, Mismatches: 42, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
57 8 0.03
58 76 0.26
59 210 0.71
60 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.32
Consensus pattern (59 bp):
TGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTCG
Found at i:11719 original size:118 final size:117
Alignment explanation
Indices: 11532--11926 Score: 517
Period size: 117 Copynumber: 3.4 Consensus size: 117
11522 TGACACTAAA
* * * *
11532 TGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGATAGGGCACTTCATGTGTT
1 TGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGCACTTCGTGTGCT
*
11597 AAAATGGTAAGGAAATCATACTAAGTGTATCAATTTCCAGTTTGGGCACTTCG
66 AAAATGGTAAGGAAATCATACTAAGTGTAT-AATTTCCAGATTGGGCACTTCG
* *
11650 TGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATAAATTTCTAGATAGGGCACTTCGTGTGCA
1 TGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGCACTTCGTGTGCT
* * *
11715 AAAATGGTAAGGAAATCATATTAAGTGTATAATTTTCAGATAGGGCAC-TCTG
66 AAAATGGTAAGGAAATCATACTAAGTGTATAATTTCCAGATTGGGCACTTC-G
* *
11767 TGTGCTAAAATGGTAAGGAAATCATACTAAGCGTATGAATTTCTATATAGGGCACTTCGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGCACTTCGTGTGCT
* * * * * * *
11832 AAACTGTTAAGTAATTCATACTAAGTGTATAAATTTCCGGAATGGGCACTTTG
66 AAAATGGTAAGGAAATCATACTAAGTGTAT-AATTTCCAGATTGGGCACTTCG
* * * * *
11885 TGTGC--AAATTGTTATGAGAGTCATACTAAATGTATGAATTTC
1 TGTGCTAAAATGGTAAGGA-AATCATACTAAGTGTATGAATTTC
11927 CATATAGGAA
Statistics
Matches: 243, Mismatches: 30, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
116 11 0.05
117 123 0.51
118 108 0.44
119 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.32
Consensus pattern (117 bp):
TGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGCACTTCGTGTGCT
AAAATGGTAAGGAAATCATACTAAGTGTATAATTTCCAGATTGGGCACTTCG
Found at i:11780 original size:176 final size:177
Alignment explanation
Indices: 11532--11934 Score: 532
Period size: 176 Copynumber: 2.3 Consensus size: 177
11522 TGACACTAAA
*
11532 TGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGATAGGGCACTTCATGTGTT
1 TGTGCAAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGATAGGGCACTTCATGTGTT
* *
11597 AAAATGGTAAGGAAATCATACTAAGTGTATCAATTTCCAGT-TTGGGCACTTCGTGTGCTAAAAT
66 AAAATGGTAAGGAAATCATACTAAGCGTATCAATTTCCA-TATAGGGCACTTCGTGTGCTAAAAT
*
11661 GGTAAGGAAATCATACTAAGTGTATAAATTTCTAG-ATAGGGCACTTCG
130 GGTAAGGAAATCATACTAAGTGTATAAATTTCCAGAAT-GGGCACTTCG
* * *
11709 TGTGCAAAAATGGTAAGGAAATCATATTAAGTGTAT-AATTTTCAGATAGGGCAC-TC-TGTGTG
1 TGTGCAAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGATAGGGCACTTCATGTGT-
* * *
11771 CTAAAATGGTAAGGAAATCATACTAAGCGTATGAATTTCTATATAGGGCACTTCGTGTGCTAAAC
65 -TAAAATGGTAAGGAAATCATACTAAGCGTATCAATTTCCATATAGGGCACTTCGTGTGCTAAAA
* * * * *
11836 TGTTAAGTAATTCATACTAAGTGTATAAATTTCCGGAATGGGCACTTTG
129 TGGTAAGGAAATCATACTAAGTGTATAAATTTCCAGAATGGGCACTTCG
* * * * *
11885 TGTGC--AAATTGTTATGAGAGTCATACTAAATGTATGAATTTCCATATAGG
1 TGTGCAAAAATGGTAAGGA-AATCATACTAAATGTATGAATTTCCAGATAGG
11935 AAATGTGAGT
Statistics
Matches: 197, Mismatches: 23, Indels: 13
0.85 0.10 0.06
Matches are distributed among these distances:
174 14 0.07
175 17 0.09
176 131 0.66
177 35 0.18
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.32
Consensus pattern (177 bp):
TGTGCAAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGATAGGGCACTTCATGTGTT
AAAATGGTAAGGAAATCATACTAAGCGTATCAATTTCCATATAGGGCACTTCGTGTGCTAAAATG
GTAAGGAAATCATACTAAGTGTATAAATTTCCAGAATGGGCACTTCG
Done.