Locus 1370

Sequence ID dm3.chr2L
Location 10,637,988 – 10,638,049
Length 61
Max. P 0.964506
window1866 window1867

overview

Window 6

Location 10,637,988 – 10,638,049
Length 61
Sequences 6
Columns 62
Reading direction forward
Mean pairwise identity 68.04
Shannon entropy 0.62924
G+C content 0.39648
Mean single sequence MFE -12.08
Consensus MFE -6.39
Energy contribution -6.75
Covariance contribution 0.36
Combinations/Pair 1.36
Mean z-score -1.38
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.74
SVM RNA-class probability 0.964506
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 10637988 61 + 23011544
GCUGUACUUGUGUGAACAUGGAAAACGCUCACAUAACCAGGCAAAAAA-UACACUCAGAAAA
(((....((((((((...((.....)).))))))))...)))......-............. ( -10.40, z-score =  -1.04, R)
>droSim1.chr2L 10435141 61 + 22036055
CCGGUACUUGUGUGAACAUGGAAAAUGCUCACAUAACCAUGCACAAAA-UACACUGAGAAAA
..(((...(((((((.(((.....))).))))))))))..........-............. ( -12.40, z-score =  -1.75, R)
>droSec1.super_3 6056119 61 + 7220098
GCGGUACUUGUGUGAACAUGGAAAAUGCUCACAUAACCAUGCAAAAAA-UACACUGAGAGAA
(((....((((((((.(((.....))).))))))))...)))......-............. ( -13.50, z-score =  -2.09, R)
>droYak2.chr2L 7040839 62 + 22324452
GCUGUACUUGUGUGAACAUGGAAAACGCUCACAUAACCAUGCAAAAGAGUGCACUGAGAAAA
..(((((((...((..(((((...............)))))))...)))))))......... ( -12.16, z-score =  -0.59, R)
>droAna3.scaffold_12916 14479891 61 + 16180835
UGUGUGCCUGUGUGAAAAUGCAAAAUACUCACAUACGAAGACGGCUAA-UGCACUUGGAGAA
.((((((((((((((..((.....))..))))))).......)))...-.))))........ ( -11.01, z-score =  -0.20, R)
>droVir3.scaffold_12963 9854807 51 - 20206255
GCAGUGGACAUGUAAGUGUUGAUAACUAUAA-AUGUCUAAGGCAAAAG-UUCA---------
((..(((((((...(((.......)))....-)))))))..)).....-....--------- ( -13.00, z-score =  -2.59, R)
>consensus
GCUGUACUUGUGUGAACAUGGAAAACGCUCACAUAACCAUGCAAAAAA_UACACUGAGAAAA
.......((((((((.(((.....))).)))))))).......................... ( -6.39 =  -6.75 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 10,637,988 – 10,638,049
Length 61
Sequences 6
Columns 62
Reading direction reverse
Mean pairwise identity 68.04
Shannon entropy 0.62924
G+C content 0.39648
Mean single sequence MFE -11.85
Consensus MFE -6.45
Energy contribution -6.90
Covariance contribution 0.45
Combinations/Pair 1.22
Mean z-score -1.25
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.57
SVM RNA-class probability 0.950919
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 10637988 61 - 23011544
UUUUCUGAGUGUA-UUUUUUGCCUGGUUAUGUGAGCGUUUUCCAUGUUCACACAAGUACAGC
....(((((.(((-.....))))).....(((((((((.....)))))))))......))). ( -12.40, z-score =  -1.00, R)
>droSim1.chr2L 10435141 61 - 22036055
UUUUCUCAGUGUA-UUUUGUGCAUGGUUAUGUGAGCAUUUUCCAUGUUCACACAAGUACCGG
........(.(((-((((((((((((..(((....)))...)))))..)))).))))))).. ( -15.30, z-score =  -2.15, R)
>droSec1.super_3 6056119 61 - 7220098
UUCUCUCAGUGUA-UUUUUUGCAUGGUUAUGUGAGCAUUUUCCAUGUUCACACAAGUACCGC
........(((((-.....)))))(((..(((((((((.....))))))))).....))).. ( -15.40, z-score =  -2.72, R)
>droYak2.chr2L 7040839 62 - 22324452
UUUUCUCAGUGCACUCUUUUGCAUGGUUAUGUGAGCGUUUUCCAUGUUCACACAAGUACAGC
........(((((......))))).....(((((((((.....))))))))).......... ( -13.80, z-score =  -1.21, R)
>droAna3.scaffold_12916 14479891 61 - 16180835
UUCUCCAAGUGCA-UUAGCCGUCUUCGUAUGUGAGUAUUUUGCAUUUUCACACAGGCACACA
........((((.-.....((....))..((((((...........))))))...))))... ( -10.10, z-score =  -0.47, R)
>droVir3.scaffold_12963 9854807 51 + 20206255
---------UGAA-CUUUUGCCUUAGACAU-UUAUAGUUAUCAACACUUACAUGUCCACUGC
---------....-.....((....(((((-.((.(((.......))))).)))))....)) (  -4.10, z-score =   0.07, R)
>consensus
UUUUCUCAGUGUA_UUUUUUGCAUGGUUAUGUGAGCAUUUUCCAUGUUCACACAAGUACAGC
.............................(((((((((.....))))))))).......... ( -6.45 =  -6.90 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:30:38 2011