Locus 4454

Sequence ID dm3.chr2R
Location 13,139,320 – 13,139,411
Length 91
Max. P 0.862000
window6100 window6101

overview

Window 0

Location 13,139,320 – 13,139,411
Length 91
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 86.72
Shannon entropy 0.22790
G+C content 0.47063
Mean single sequence MFE -28.86
Consensus MFE -22.24
Energy contribution -23.10
Covariance contribution 0.86
Combinations/Pair 1.04
Mean z-score -2.01
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.848990
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13139320 91 + 21146708
ACCUGCAGCUUAAUCCCAAAGCUUUGGCAUUGCUUUGGAUCAGC-CAGUACGUCGAGUACAUACAUAUAUAGAG-------------UGCAGUUCAGGUGCAGGU-
(((((((.((.(((.(((((((.........)))))))......-..((((.....))))..............-------------....))).)).)))))))- ( -27.60, z-score =  -1.74, R)
>droSim1.chr2R 11867470 87 + 19596830
ACCUGCAGCUUAAUCCCAAAGCUUUGGCAUUGCUUUGGAUCAGC-CAGUACGUCGAGUACAUA----UAUAGAG-------------UGCAGUUCAGGUGCAGGU-
(((((((.((.(((.(((((((.........)))))))......-..((((.....))))...----.......-------------....))).)).)))))))- ( -27.60, z-score =  -1.87, R)
>droSec1.super_1 10638121 87 + 14215200
ACCUGCAGCUUAAUCCCAAAGCUUUGGCAUUGCUUUGGAUCAGC-CAGUACGUCGAGUACAUA----UAUAGAG-------------UGCAGUUCAGGUGCAGGU-
(((((((.((.(((.(((((((.........)))))))......-..((((.....))))...----.......-------------....))).)).)))))))- ( -27.60, z-score =  -1.87, R)
>droYak2.chr2R 2803392 87 - 21139217
ACCUGCAGCUUAAUCCCAAAGCUUUGGCAUUGCUUUGGAUCAGC-CAGUACGUCGAGUACAUA----UAUAGAG-------------UGCAGUUGAGGUGCAGGU-
(((((((.((((((.(((((((.........)))))))......-..((((.....))))...----.......-------------....)))))).)))))))- ( -31.60, z-score =  -2.94, R)
>droEre2.scaffold_4845 9872631 86 - 22589142
ACCUGCAGCUUAAUCCCAAAGCUUUGGCAUUGCUUUGGAUCAGC-CAGUA-GUCGCGUACAUA----UAUAGAG-------------UGCAGUUCAGGUGCAGGU-
(((((((.((.(((.(((((((.........)))))))......-..(((-.((..(((....----))).)).-------------))).))).)).)))))))- ( -27.40, z-score =  -1.67, R)
>droAna3.scaffold_13266 6398295 106 - 19884421
AGCUGGAGCUUAAUCGCAAAGCUUUGGCAUUGCUUUGGAUCAGGACACUACAUAAAGUACACACACAUAGAGCGACUGCCAUUACACUGCACUUCGGGUGCAGGUA
.((..((((((.......))))))..)).((((((((.........(((......))).........)))))))).......(((.((((((.....))))))))) ( -31.37, z-score =  -1.96, R)
>consensus
ACCUGCAGCUUAAUCCCAAAGCUUUGGCAUUGCUUUGGAUCAGC_CAGUACGUCGAGUACAUA____UAUAGAG_____________UGCAGUUCAGGUGCAGGU_
(((((((.((.(((.(((((((.........))))))).........((((.....))))...............................))).)).))))))). (-22.24 = -23.10 +   0.86)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 13,139,320 – 13,139,411
Length 91
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 86.72
Shannon entropy 0.22790
G+C content 0.47063
Mean single sequence MFE -26.82
Consensus MFE -20.97
Energy contribution -21.80
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.96
SVM RNA-class probability 0.862000
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13139320 91 - 21146708
-ACCUGCACCUGAACUGCA-------------CUCUAUAUAUGUAUGUACUCGACGUACUG-GCUGAUCCAAAGCAAUGCCAAAGCUUUGGGAUUAAGCUGCAGGU
-((((((............-------------..........((((((.....)))))).(-(((((((((((((.........))))).))))).)))))))))) ( -28.40, z-score =  -2.53, R)
>droSim1.chr2R 11867470 87 - 19596830
-ACCUGCACCUGAACUGCA-------------CUCUAUA----UAUGUACUCGACGUACUG-GCUGAUCCAAAGCAAUGCCAAAGCUUUGGGAUUAAGCUGCAGGU
-((((((............-------------.......----...((((.....)))).(-(((((((((((((.........))))).))))).)))))))))) ( -26.40, z-score =  -2.23, R)
>droSec1.super_1 10638121 87 - 14215200
-ACCUGCACCUGAACUGCA-------------CUCUAUA----UAUGUACUCGACGUACUG-GCUGAUCCAAAGCAAUGCCAAAGCUUUGGGAUUAAGCUGCAGGU
-((((((............-------------.......----...((((.....)))).(-(((((((((((((.........))))).))))).)))))))))) ( -26.40, z-score =  -2.23, R)
>droYak2.chr2R 2803392 87 + 21139217
-ACCUGCACCUCAACUGCA-------------CUCUAUA----UAUGUACUCGACGUACUG-GCUGAUCCAAAGCAAUGCCAAAGCUUUGGGAUUAAGCUGCAGGU
-((((((............-------------.......----...((((.....)))).(-(((((((((((((.........))))).))))).)))))))))) ( -26.40, z-score =  -2.30, R)
>droEre2.scaffold_4845 9872631 86 + 22589142
-ACCUGCACCUGAACUGCA-------------CUCUAUA----UAUGUACGCGAC-UACUG-GCUGAUCCAAAGCAAUGCCAAAGCUUUGGGAUUAAGCUGCAGGU
-((((((........(((.-------------..(....----...)...)))..-....(-(((((((((((((.........))))).))))).)))))))))) ( -23.70, z-score =  -1.30, R)
>droAna3.scaffold_13266 6398295 106 + 19884421
UACCUGCACCCGAAGUGCAGUGUAAUGGCAGUCGCUCUAUGUGUGUGUACUUUAUGUAGUGUCCUGAUCCAAAGCAAUGCCAAAGCUUUGCGAUUAAGCUCCAGCU
(((((((((.....)))))).))).(((.(((.((.(((((((.........))))))).))..(((((((((((.........)))))).))))).))))))... ( -29.60, z-score =  -1.42, R)
>consensus
_ACCUGCACCUGAACUGCA_____________CUCUAUA____UAUGUACUCGACGUACUG_GCUGAUCCAAAGCAAUGCCAAAGCUUUGGGAUUAAGCUGCAGGU
.(((((((......................................((((.....))))...(((((((((((((.........)))))).)))).)))))))))) (-20.97 = -21.80 +   0.83)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:29:27 2011