Locus 7810

Sequence ID dm3.chr3L
Location 17,492,622 – 17,492,720
Length 98
Max. P 0.983838
window10743 window10744

overview

Window 3

Location 17,492,622 – 17,492,720
Length 98
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 72.66
Shannon entropy 0.45693
G+C content 0.56473
Mean single sequence MFE -31.33
Consensus MFE -15.04
Energy contribution -15.96
Covariance contribution 0.92
Combinations/Pair 1.33
Mean z-score -1.96
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.80
SVM RNA-class probability 0.822303
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17492622 98 + 24543557
CGCCAGCACACACACAAAUACACACAUGCACGAGCGCUGGGAAAA-----CAAGAGAGGAAGAGCGCGAGAGCCACCGUUAGUCGCAUGUCUGUGUGCGUGCU
....(((((.((((((.......((((((....(((((.......-----............)))))((.(((....)))..)))))))).)))))).))))) ( -29.51, z-score =  -0.37, R)
>droSim1.chr2L 658062 90 + 22036055
--------CGCCAGCACACACACACAUGUAUGCGCGCUGGGAAAA-----CCAGAGAGGAAGAGCGAGAGAGCCACCGUUAGUCGCAUGUCUGUGUGCGUGCC
--------.....((((...((((((..(((((((.((((.....-----))))...((..(..(....)..)..))....).))))))..)))))).)))). ( -32.00, z-score =  -1.58, R)
>droSec1.super_0 9545149 90 + 21120651
--------CGCCAGCACACACACACAUGCAUGCGCGCUGGGUAAA-----CCAGAGAGGAAGAGCGAGAGAGCCACCGUUAGUCGCAUGUCUGUGUGCGUGCC
--------.....((((.((((((...((((((((.((((.....-----))))...((..(..(....)..)..))....).))))))).)))))).)))). ( -35.60, z-score =  -2.19, R)
>droEre2.scaffold_4784 9405319 88 - 25762168
----------CGCCAGCACACACACAUACAUGCGCACUGGGAAAA-----CCAGAGAGGAAGAGCGAGAGAGCCACCGUUAGUCGAAUGUCUGUGUGCGUGCC
----------.....((((.((((((.((((.(((.((((.....-----))))...((..(..(....)..)..))....).)).)))).)))))).)))). ( -31.40, z-score =  -2.79, R)
>droAna3.scaffold_13337 14202845 93 + 23293914
---------ACCAACACACAUGCAUGCGGAUACGAAAUAAAAGAGAGCGCCUACAGUCGAAGAGAGUUA-AGAGACCGUUAGGCGCCCGAAUGUGUGCGUGCU
---------.....(((.(((((((.(((...(.........)...((((((((.(((...........-...))).).)))))))))).))))))).))).. ( -28.14, z-score =  -2.89, R)
>consensus
________CACCAACACACACACACAUGCAUGCGCGCUGGGAAAA_____CCAGAGAGGAAGAGCGAGAGAGCCACCGUUAGUCGCAUGUCUGUGUGCGUGCC
.............((.((((((.((((((.......((((..........))))....((..((((..........))))..)))))))).)))))).))... (-15.04 = -15.96 +   0.92)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 4

Location 17,492,622 – 17,492,720
Length 98
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 72.66
Shannon entropy 0.45693
G+C content 0.56473
Mean single sequence MFE -34.35
Consensus MFE -18.72
Energy contribution -20.64
Covariance contribution 1.92
Combinations/Pair 1.27
Mean z-score -2.43
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.15
SVM RNA-class probability 0.983838
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17492622 98 - 24543557
AGCACGCACACAGACAUGCGACUAACGGUGGCUCUCGCGCUCUUCCUCUCUUG-----UUUUCCCAGCGCUCGUGCAUGUGUGUAUUUGUGUGUGUGCUGGCG
((((((((((((.(((((((.(....)...((.(..(((((......(....)-----.......)))))..).)).)))))))...)))))))))))).... ( -34.92, z-score =  -1.36, R)
>droSim1.chr2L 658062 90 - 22036055
GGCACGCACACAGACAUGCGACUAACGGUGGCUCUCUCGCUCUUCCUCUCUGG-----UUUUCCCAGCGCGCAUACAUGUGUGUGUGUGCUGGCG--------
((((((((((((.(.(((((......((.(((......)))...))...((((-----.....))))..)))))...).))))))))))))....-------- ( -33.60, z-score =  -1.79, R)
>droSec1.super_0 9545149 90 - 21120651
GGCACGCACACAGACAUGCGACUAACGGUGGCUCUCUCGCUCUUCCUCUCUGG-----UUUACCCAGCGCGCAUGCAUGUGUGUGUGUGCUGGCG--------
((((((((((((.(((((((......((.(((......)))...))...((((-----.....))))..))))))..).))))))))))))....-------- ( -36.50, z-score =  -1.99, R)
>droEre2.scaffold_4784 9405319 88 + 25762168
GGCACGCACACAGACAUUCGACUAACGGUGGCUCUCUCGCUCUUCCUCUCUGG-----UUUUCCCAGUGCGCAUGUAUGUGUGUGUGCUGGCG----------
((((((((((((.((((.((......((.(((......)))...)).(.((((-----.....)))).))).)))).))))))))))))....---------- ( -33.60, z-score =  -2.70, R)
>droAna3.scaffold_13337 14202845 93 - 23293914
AGCACGCACACAUUCGGGCGCCUAACGGUCUCU-UAACUCUCUUCGACUGUAGGCGCUCUCUUUUAUUUCGUAUCCGCAUGCAUGUGUGUUGGU---------
..((.((((((((..(((((((((.(((((...-...........))))))))))))))...........((((....))))))))))))))..--------- ( -33.14, z-score =  -4.32, R)
>consensus
GGCACGCACACAGACAUGCGACUAACGGUGGCUCUCUCGCUCUUCCUCUCUGG_____UUUUCCCAGCGCGCAUGCAUGUGUGUGUGUGCUGGCG________
.(((((((((((..((((((......((.(((......)))...))...((((..........))))..))))))..)))))))))))............... (-18.72 = -20.64 +   1.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:33:52 2011