Locus 4438

Sequence ID	dm3.chr2R
Location	13,042,729 – 13,042,792
Length	63
Max. P	0.986562

overview

Window 7

Location	13,042,729 – 13,042,792
Length	63
Sequences	11
Columns	66
Reading direction	forward
Mean pairwise identity	67.07
Shannon entropy	0.70344
G+C content	0.33456
Mean single sequence MFE	-10.77
Consensus MFE	-5.97
Energy contribution	-5.72
Covariance contribution	-0.25
Combinations/Pair	1.25
Mean z-score	-1.26
Structure conservation index	0.55
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.24
SVM RNA-class probability	0.986562
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13042729 63 + 21146708
AUCUGUGAAAAAUUAUU-CG-UUGUCUUGUCCUU-CUUUGGUUGCUAUCAAAGUUGAGUUCGCAGG
..(((((((...(((..-..-(((......((..-....)).......)))...))).))))))). ( -11.92, z-score =  -1.84, R)
>droSim1.chr2R 11776250 63 + 19596830
AUCUGUGAAAAAUUAUU-CG-UUGUCUUGUACUU-CUUUGGUUGUUAUCAAAGUUUAGUUCGCAGG
..(((((((........-.(-(........))..-(((((((....))))))).....))))))). ( -12.40, z-score =  -2.88, R)
>droSec1.super_1 10553008 63 + 14215200
AUCUGUGCAAUAUUAUU-CG-UUGUCUUGUGCUU-CUUUGGUUGUUAUCAAAGUUUAGUUCGCAGG
..(((((((((......-.)-))))...(.(((.-(((((((....)))))))...))).))))). ( -12.40, z-score =  -2.58, R)
>droYak2.chr2R 2711786 60 - 21139217
---UGUGAAAAAUUAUU-CG-UUGUCUUGUACUU-CUUUGGUUGUUAUCAAAGUGUAGUUAACAGG
---..............-..-....((((((((.-(((((((....)))))))...)))..))))) (  -9.70, z-score =  -1.44, R)
>droEre2.scaffold_4845 9783059 58 - 22589142
-----UGAAAAAUUAUG-CA-UUGUCUUGUACUU-CUUUGGUCGUUGUCAAAGUUUAGUUAACAGG
-----............-..-....((((((((.-((((((......))))))...)))..))))) (  -8.10, z-score =  -0.41, R)
>dp4.chr3 16639912 64 + 19779522
GUAAUUGAAAAUAUGUU-UG-UUGUCUUGCAUUUACUUUGGUAACCAUCAAAGUUUAUAGAACAGG
.............((((-((-(......))((..((((((((....))))))))..)).))))).. (  -8.90, z-score =  -0.02, R)
>droPer1.super_4 7031616 64 - 7162766
GUAAUUGAAAAAAUGUU-UG-UUGUCUUGCAUUUACUUUGGUAACCAUCAAAGUUUAUAGAACAGG
....(((...((((((.-.(-....)..))))))((((((((....))))))))........))). (  -9.50, z-score =  -0.28, R)
>droWil1.scaffold_181009 2764202 60 - 3585778
-----AGAAAAAUUACUGCA-UUGUCUUGUAUUUACUUUGAUUUAGAUCAAAGUAUUUGUCACAGG
-----...............-....(((((((.(((((((((....)))))))))...)).))))) ( -11.20, z-score =  -1.48, R)
>droVir3.scaffold_12875 7710806 58 + 20611582
-----AACUGUAAAAUUG---UUGUCUUGUAUUUUCUUUGAUAUACAUCAAAGGAUCUCGAACAGG
-----.............---((((.(((....(((((((((....)))))))))...))))))). ( -10.20, z-score =  -1.28, R)
>droMoj3.scaffold_6496 7264382 66 - 26866924
AACUGAAGGAAAUAACUGCACUUAUCUUGUGUGUUCUUUGGUGCACAUCAAAGGAUCUGCAACAGG
..(((..(((.......((((.......)))).(((((((((....))))))))))))....))). ( -14.80, z-score =  -0.89, R)
>droGri2.scaffold_15245 1229998 50 + 18325388
-------------GAUUG---UUGUCUUGUAUUUGCUUUGAUGAACAUCAAAGGAUCUGUAACAGG
-------------.....---....(((((((.(.(((((((....))))))).)...)).))))) (  -9.40, z-score =  -0.72, R)
>consensus
___UGUGAAAAAUUAUU_CG_UUGUCUUGUAUUU_CUUUGGUUGACAUCAAAGUUUAUUUAACAGG
.........................(((((.....(((((((....)))))))........))))) ( -5.97 =  -5.72 +  -0.25)

alignment

secondary structure

dotplot

Window 8

Location	13,042,729 – 13,042,792
Length	63
Sequences	11
Columns	66
Reading direction	reverse
Mean pairwise identity	67.07
Shannon entropy	0.70344
G+C content	0.33456
Mean single sequence MFE	-6.55
Consensus MFE	-2.91
Energy contribution	-2.91
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-0.72
Structure conservation index	0.44
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.18
SVM RNA-class probability	0.579285
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13042729 63 - 21146708
CCUGCGAACUCAACUUUGAUAGCAACCAAAG-AAGGACAAGACAA-CG-AAUAAUUUUUCACAGAU
.(((.(((.....(((((........)))))-..(.......)..-..-........))).))).. (  -6.80, z-score =  -0.97, R)
>droSim1.chr2R 11776250 63 - 19596830
CCUGCGAACUAAACUUUGAUAACAACCAAAG-AAGUACAAGACAA-CG-AAUAAUUUUUCACAGAU
.(((.(((.....(((((........)))))-..((.....))..-..-........))).))).. (  -7.50, z-score =  -2.59, R)
>droSec1.super_1 10553008 63 - 14215200
CCUGCGAACUAAACUUUGAUAACAACCAAAG-AAGCACAAGACAA-CG-AAUAAUAUUGCACAGAU
.(((.........(((((........)))))-..(((........-..-........))).))).. (  -5.87, z-score =  -2.18, R)
>droYak2.chr2R 2711786 60 + 21139217
CCUGUUAACUACACUUUGAUAACAACCAAAG-AAGUACAAGACAA-CG-AAUAAUUUUUCACA---
..((((...(((.(((((........)))))-..)))...)))).-.(-((......)))...--- (  -6.70, z-score =  -1.55, R)
>droEre2.scaffold_4845 9783059 58 + 22589142
CCUGUUAACUAAACUUUGACAACGACCAAAG-AAGUACAAGACAA-UG-CAUAAUUUUUCA-----
..((((.(((...(((((........)))))-.)))....)))).-..-............----- (  -4.10, z-score =   0.21, R)
>dp4.chr3 16639912 64 - 19779522
CCUGUUCUAUAAACUUUGAUGGUUACCAAAGUAAAUGCAAGACAA-CA-AACAUAUUUUCAAUUAC
..((((.(((..((((((........))))))..)))...)))).-..-................. (  -5.30, z-score =   0.49, R)
>droPer1.super_4 7031616 64 + 7162766
CCUGUUCUAUAAACUUUGAUGGUUACCAAAGUAAAUGCAAGACAA-CA-AACAUUUUUUCAAUUAC
..((((.(((..((((((........))))))..)))...)))).-..-................. (  -5.30, z-score =   0.61, R)
>droWil1.scaffold_181009 2764202 60 + 3585778
CCUGUGACAAAUACUUUGAUCUAAAUCAAAGUAAAUACAAGACAA-UGCAGUAAUUUUUCU-----
...........(((((((((....)))))))))............-...............----- (  -8.20, z-score =  -1.20, R)
>droVir3.scaffold_12875 7710806 58 - 20611582
CCUGUUCGAGAUCCUUUGAUGUAUAUCAAAGAAAAUACAAGACAA---CAAUUUUACAGUU-----
.((((........(((((((....)))))))(((((.........---..)))))))))..----- (  -6.30, z-score =  -0.20, R)
>droMoj3.scaffold_6496 7264382 66 + 26866924
CCUGUUGCAGAUCCUUUGAUGUGCACCAAAGAACACACAAGAUAAGUGCAGUUAUUUCCUUCAGUU
..((.((((.(((....))).)))).))...(((.(((.......)))..)))............. (  -9.60, z-score =   0.38, R)
>droGri2.scaffold_15245 1229998 50 - 18325388
CCUGUUACAGAUCCUUUGAUGUUCAUCAAAGCAAAUACAAGACAA---CAAUC-------------
..((((.......(((((((....))))))).........)))).---.....------------- (  -6.39, z-score =  -0.93, R)
>consensus
CCUGUUAAAUAAACUUUGAUAACAACCAAAG_AAAUACAAGACAA_CG_AAUAAUUUUUCACA___
.............(((((........)))))................................... ( -2.91 =  -2.91 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:29:09 2011