Locus 7562

Sequence ID dm3.chr3L
Location 15,588,802 – 15,588,859
Length 57
Max. P 0.901862
window10410 window10411

overview

Window 0

Location 15,588,802 – 15,588,859
Length 57
Sequences 5
Columns 61
Reading direction forward
Mean pairwise identity 68.07
Shannon entropy 0.56540
G+C content 0.27158
Mean single sequence MFE -10.16
Consensus MFE -5.41
Energy contribution -4.85
Covariance contribution -0.56
Combinations/Pair 1.43
Mean z-score -1.38
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.16
SVM RNA-class probability 0.901862
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 15588802 57 + 24543557
UAAAACAUUGUUCUGGUGAAAUUCUUA-CAUCAGAGAAG---UAAAUUUAUUAUCUGAUGU
.....((((.....))))........(-(((((((..((---((....)))).)))))))) ( -10.30, z-score =  -1.31, R)
>droSim1.chr3L 14928751 57 + 22553184
UAAAUAAUUGUUCUGGUGAAAUUCUUA-CAUCAGAGCAG---UAAAUUUAUUAUCUGAUGU
......((((((((((((.........-)))))))))))---).................. ( -14.00, z-score =  -3.23, R)
>droYak2.chr3L 18136565 60 + 24197627
UAAAACGUUGUUCUGGUGAAAUUUUUA-CAUCAGAGAAGAAUUGAAUUUAUUGUCUGAUGU
..........(((....)))......(-(((((((.((.((......)).)).)))))))) ( -10.50, z-score =  -0.88, R)
>droEre2.scaffold_4784 17847193 57 + 25762168
---UACAACCUUCUGGUAAAAUUCUUA-CAUCAGAGUAGAAGUAAAUGUAUUAUCUGAUGU
---....(((....))).........(-((((((((((.(......).)))..)))))))) ( -10.70, z-score =  -1.41, R)
>droVir3.scaffold_13049 2766615 52 - 25233164
UAAUAUAUCAUU----UGGACUUCUUGGUGUCAAUGAA----UUAACCUAAAAAUUGUAA-
.......(((((----.(.(((....))).).))))).----..................- (  -5.30, z-score =  -0.06, R)
>consensus
UAAAACAUUGUUCUGGUGAAAUUCUUA_CAUCAGAGAAG___UAAAUUUAUUAUCUGAUGU
............................(((((((..................))))))). ( -5.41 =  -4.85 +  -0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 15,588,802 – 15,588,859
Length 57
Sequences 5
Columns 61
Reading direction reverse
Mean pairwise identity 68.07
Shannon entropy 0.56540
G+C content 0.27158
Mean single sequence MFE -7.36
Consensus MFE -4.65
Energy contribution -4.09
Covariance contribution -0.56
Combinations/Pair 1.43
Mean z-score -0.99
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.10
SVM RNA-class probability 0.890767
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 15588802 57 - 24543557
ACAUCAGAUAAUAAAUUUA---CUUCUCUGAUG-UAAGAAUUUCACCAGAACAAUGUUUUA
((((((((...........---....)))))))-).......................... (  -7.96, z-score =  -1.04, R)
>droSim1.chr3L 14928751 57 - 22553184
ACAUCAGAUAAUAAAUUUA---CUGCUCUGAUG-UAAGAAUUUCACCAGAACAAUUAUUUA
((((((((...........---....)))))))-).......................... (  -7.96, z-score =  -1.67, R)
>droYak2.chr3L 18136565 60 - 24197627
ACAUCAGACAAUAAAUUCAAUUCUUCUCUGAUG-UAAAAAUUUCACCAGAACAACGUUUUA
((((((((.((.((......)).)).)))))))-).......................... (  -7.90, z-score =  -1.82, R)
>droEre2.scaffold_4784 17847193 57 - 25762168
ACAUCAGAUAAUACAUUUACUUCUACUCUGAUG-UAAGAAUUUUACCAGAAGGUUGUA---
((((((((..................)))))))-).........(((....)))....--- (  -8.97, z-score =  -0.65, R)
>droVir3.scaffold_13049 2766615 52 + 25233164
-UUACAAUUUUUAGGUUAA----UUCAUUGACACCAAGAAGUCCA----AAUGAUAUAUUA
-..................----.((((((((........)))..----)))))....... (  -4.00, z-score =   0.23, R)
>consensus
ACAUCAGAUAAUAAAUUUA___CUUCUCUGAUG_UAAGAAUUUCACCAGAACAAUGUUUUA
.(((((((..................)))))))............................ ( -4.65 =  -4.09 +  -0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:29:15 2011