Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005204.1 Hibiscus syriacus cultivar Beakdansim tig00011765_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: 51766
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:90 original size:14 final size:14
Alignment explanation
Indices: 71--100 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
61 TTCAAAGGGA
*
71 TAATTGTGATTGGG
1 TAATTGTAATTGGG
85 TAATTGTAATTGGG
1 TAATTGTAATTGGG
99 TA
1 TA
101 GGATCGGCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (14 bp):
TAATTGTAATTGGG
Found at i:12145 original size:12 final size:12
Alignment explanation
Indices: 12112--12164 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
12102 ATATACAAAT
*
12112 ACCTAACTC-TC
1 ACCTAAATCTTC
*
12123 ACCTAACTCTTC
1 ACCTAAATCTTC
12135 ACC-AAATTCTTC
1 ACCTAAA-TCTTC
12147 ACCTAAATCTTC
1 ACCTAAATCTTC
12159 ACCTAA
1 ACCTAA
12165 CTAAATTGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
11 11 0.29
12 24 0.63
13 3 0.08
ACGTcount: A:0.32, C:0.38, G:0.00, T:0.30
Consensus pattern (12 bp):
ACCTAAATCTTC
Found at i:15771 original size:31 final size:31
Alignment explanation
Indices: 15734--15798 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
15724 AAGTCTTTAG
* *
15734 TTTCTTCAATCGTCACGACTATGTGCTCAAA
1 TTTCTTCAATCGCCACGACTATATGCTCAAA
15765 TTTCTTCAATCGCCACGACTATATGCTCAAA
1 TTTCTTCAATCGCCACGACTATATGCTCAAA
15796 TTT
1 TTT
15799 GGGATCCAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (31 bp):
TTTCTTCAATCGCCACGACTATATGCTCAAA
Found at i:16766 original size:12 final size:12
Alignment explanation
Indices: 16733--16787 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
16723 ATATAAAAAT
16733 ACCTAACTC-TC
1 ACCTAACTCTTC
16744 ACCTAACTCTTC
1 ACCTAACTCTTC
* *
16756 ATCTAATTCTTC
1 ACCTAACTCTTC
*
16768 ACCTAACTCTTT
1 ACCTAACTCTTC
16780 ACCTAACT
1 ACCTAACT
16788 AAATTGATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
11 9 0.24
12 29 0.76
ACGTcount: A:0.27, C:0.36, G:0.00, T:0.36
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:19947 original size:19 final size:19
Alignment explanation
Indices: 19923--19976 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
19913 AATGGATTTG
19923 ATGCATCGATGCACTAGCC
1 ATGCATCGATGCACTAGCC
19942 ATGCATCGATGCACTAGCC
1 ATGCATCGATGCACTAGCC
19961 ATGCATCGATGCACTA
1 ATGCATCGATGCACTA
19977 TGGCTATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (19 bp):
ATGCATCGATGCACTAGCC
Found at i:28285 original size:65 final size:64
Alignment explanation
Indices: 28211--28370 Score: 182
Period size: 65 Copynumber: 2.5 Consensus size: 64
28201 GAATAAATTG
* * * *
28211 AACATCGAATGCATTCCATGCATCGATGCA-GATACTATTCATCGATGCACTCAGAG-T-TTTAT
1 AACATCGAATGCATTTCATGCATCGATGCACCA-ACCATGCATCGATGCACTCAG-GCTATTT-T
28273 GAA
63 G-A
* * * **
28276 AACATCGAATGAATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTTTGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCACCAACCATGCATCGATGCACTCAGGCTATTTTGA
28340 AACATCGAATGCATTTCATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
28371 TAAGGGTCCA
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
64 31 0.38
65 46 0.57
66 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACCAACCATGCATCGATGCACTCAGGCTATTTTGA
Found at i:32173 original size:2 final size:2
Alignment explanation
Indices: 32166--32190 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32156 ATTGAAATTT
32166 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
32191 TAAAAAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45919 original size:21 final size:22
Alignment explanation
Indices: 45880--45920 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
45870 AACTAGGGTT
*
45880 TATTCTCTACCCAATATTAGGG
1 TATTCTCTACCCAAGATTAGGG
45902 TATTCTCTA-CCAAGATTAG
1 TATTCTCTACCCAAGATTAG
45921 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (22 bp):
TATTCTCTACCCAAGATTAGGG
Done.