Locus 3467

Sequence ID dm3.chr2R
Location 5,556,239 – 5,556,329
Length 90
Max. P 0.999177
window4760 window4761

overview

Window 0

Location 5,556,239 – 5,556,329
Length 90
Sequences 7
Columns 111
Reading direction forward
Mean pairwise identity 64.76
Shannon entropy 0.61062
G+C content 0.41564
Mean single sequence MFE -14.15
Consensus MFE -10.38
Energy contribution -10.52
Covariance contribution 0.14
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.69
SVM RNA-class probability 0.999177
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5556239 90 + 21146708
CGUGACCUGCAAAUUUAAUUUUCUCUUUCAUUUUCCACACAUACGAGAAAAUUGUCACACUCGCACCACGAUUUUCACGCUUUCCCUCCG---------------------
(((((..........((((((((((...................))))))))))......(((.....)))...)))))...........--------------------- ( -12.71, z-score =  -2.76, R)
>droYak2.chr2L 18187924 78 + 22324452
CGUGACCUGCAAAUUUAAUUUUCUCUUUCAUUUUCC-CACAUAUGAGAAAAUUGUCACACUCGCACCACGUUUUCCCCU--------------------------------
((((...(((.....((((((((((...........-.......))))))))))........))).)))).........-------------------------------- ( -12.59, z-score =  -3.45, R)
>droEre2.scaffold_4929 17842233 80 - 26641161
CGUGACCUGAAAAUUUAAUUUUCUCUUUCGUUUUCCCCACAU--GAGAAAAUUGUCACACUCGCACCACGCUUUCCAUCCCC-----------------------------
.(((((..........(((((((((.................--))))))))))))))....((.....))...........----------------------------- ( -12.83, z-score =  -2.82, R)
>droWil1.scaffold_180701 3500210 71 + 3904529
CAUGACCUGCAAAUUAAAUUUUCUCUUUCAUAU-----------GAGAAAAUUGUCACACUCUAACAUUGCUUUUUUUCACA-----------------------------
........((((....(((((((((........-----------)))))))))((.........)).))))...........----------------------------- (  -9.80, z-score =  -2.01, R)
>droGri2.scaffold_15112 780117 111 + 5172618
CGUGACCUGCAAAUUAAAUUUUCUCUUUCAUUUCGGAUAUAUAUGAGAAAAUUGUCACACACUGCCACACGGCCACGCCUCCACCCUUUGCAGCACCAACCACCCGCGCUG
.(((..(((((((...(((((((((...................)))))))))..........(((....))).............))))))))))............... ( -20.01, z-score =  -1.57, R)
>droMoj3.scaffold_6496 2664759 78 - 26866924
CGUGACCUGCAAAUUAAAUUUUCUCUUUCAUUUCGGAUAUAU--GAGAAAAUUGUCACACACA--CUCUCUGGCACGCCUCC-----------------------------
.(((((..........(((((((((.(((.....))).....--)))))))))))))).....--......((....))...----------------------------- ( -13.80, z-score =  -1.65, R)
>droVir3.scaffold_12875 5855212 87 + 20611582
CGUGACCUGCAAAUUAAAUUUUCUCUUUCAUUUCGGAUAUAU--GAGAAAAUUGUCACACACUGCCACGCCUCC-CACAGAGACCGGCCG---------------------
.(((((..........(((((((((.(((.....))).....--)))))))))))))).....(((..(.(((.-....))).).)))..--------------------- ( -17.30, z-score =  -1.60, R)
>consensus
CGUGACCUGCAAAUUAAAUUUUCUCUUUCAUUUCCCACACAU__GAGAAAAUUGUCACACUCGCACAACGCUUUACACCCCC_____________________________
.(((((..........(((((((((...................))))))))))))))..................................................... (-10.38 = -10.52 +   0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 5,556,239 – 5,556,329
Length 90
Sequences 7
Columns 111
Reading direction reverse
Mean pairwise identity 64.76
Shannon entropy 0.61062
G+C content 0.41564
Mean single sequence MFE -18.75
Consensus MFE -10.55
Energy contribution -10.57
Covariance contribution 0.02
Combinations/Pair 1.18
Mean z-score -0.87
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.81
SVM RNA-class probability 0.824464
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5556239 90 - 21146708
---------------------CGGAGGGAAAGCGUGAAAAUCGUGGUGCGAGUGUGACAAUUUUCUCGUAUGUGUGGAAAAUGAAAGAGAAAAUUAAAUUUGCAGGUCACG
---------------------....................((((((((((((.....(((((((((.(((.........)))...)))))))))..)))))))..))))) ( -18.20, z-score =  -0.80, R)
>droYak2.chr2L 18187924 78 - 22324452
--------------------------------AGGGGAAAACGUGGUGCGAGUGUGACAAUUUUCUCAUAUGUG-GGAAAAUGAAAGAGAAAAUUAAAUUUGCAGGUCACG
--------------------------------.........((((((((((((.....(((((((((.(((...-.....)))...)))))))))..)))))))..))))) ( -17.20, z-score =  -2.10, R)
>droEre2.scaffold_4929 17842233 80 + 26641161
-----------------------------GGGGAUGGAAAGCGUGGUGCGAGUGUGACAAUUUUCUC--AUGUGGGGAAAACGAAAGAGAAAAUUAAAUUUUCAGGUCACG
-----------------------------...........((.....))....(((((..(((((((--....))))))).(....).((((((...))))))..))))). ( -16.20, z-score =  -0.80, R)
>droWil1.scaffold_180701 3500210 71 - 3904529
-----------------------------UGUGAAAAAAAGCAAUGUUAGAGUGUGACAAUUUUCUC-----------AUAUGAAAGAGAAAAUUUAAUUUGCAGGUCAUG
-----------------------------.((((......(((((((((.....)))))((((((((-----------........)))))))).....))))...)))). ( -13.20, z-score =  -1.41, R)
>droGri2.scaffold_15112 780117 111 - 5172618
CAGCGCGGGUGGUUGGUGCUGCAAAGGGUGGAGGCGUGGCCGUGUGGCAGUGUGUGACAAUUUUCUCAUAUAUAUCCGAAAUGAAAGAGAAAAUUUAAUUUGCAGGUCACG
((((((.(.....).)))))).............(((((((..((.((.....)).))(((((((((...................))))))))).........))))))) ( -27.61, z-score =   0.44, R)
>droMoj3.scaffold_6496 2664759 78 + 26866924
-----------------------------GGAGGCGUGCCAGAGAG--UGUGUGUGACAAUUUUCUC--AUAUAUCCGAAAUGAAAGAGAAAAUUUAAUUUGCAGGUCACG
-----------------------------....(((..(......)--..)))((((((((((((((--.................)))))))))..........))))). ( -14.83, z-score =  -0.07, R)
>droVir3.scaffold_12875 5855212 87 - 20611582
---------------------CGGCCGGUCUCUGUG-GGAGGCGUGGCAGUGUGUGACAAUUUUCUC--AUAUAUCCGAAAUGAAAGAGAAAAUUUAAUUUGCAGGUCACG
---------------------..(((((((((....-.))))).)))).....((((((((((((((--.................)))))))))..........))))). ( -24.03, z-score =  -1.35, R)
>consensus
_____________________________GGAGGUGAAAAGCGGGGUGAGAGUGUGACAAUUUUCUC__AUAUAUCCAAAAUGAAAGAGAAAAUUUAAUUUGCAGGUCACG
.....................................................((((((((((((((...(((.......)))...)))))))))..........))))). (-10.55 = -10.57 +   0.02)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:10:46 2011