Locus 1082

Sequence ID	dm3.chr2L
Location	8,128,946 – 8,129,104
Length	158
Max. P	0.975148

overview

Window 9

Location	8,128,946 – 8,129,064
Length	118
Sequences	3
Columns	121
Reading direction	forward
Mean pairwise identity	66.57
Shannon entropy	0.45940
G+C content	0.34226
Mean single sequence MFE	-26.63
Consensus MFE	-13.59
Energy contribution	-12.93
Covariance contribution	-0.66
Combinations/Pair	1.21
Mean z-score	-2.41
Structure conservation index	0.51
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.92
SVM RNA-class probability	0.975148
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8128946 118 + 23011544
UUUAUUUUUUUUAUAUGACUUGCUAGAAUAGAACCU---UUAGUUCAUAGCAUAUUCAACAUGUAUGUUUAAUGUUUAUAUCCCGCAAGGGAAAUGAAAGUCUGAUAAGAAACGGGUCGCG
......((((((((..(((((((((((((.((....---)).)))).))))(((((.((((....)))).)))))((((.((((....)))).)))))))))..))))))))......... ( -27.50, z-score =  -2.31, R)
>droSim1.chr2L 7908428 98 + 22036055
-------------------UUGCUAGAAGGGAACCU---UUAGUUCAUAGCAUAUUUAACAUAUGUUUUUAA-GUUUAUAUCCCGCAAGGGAAAUGAAAGUCUGAUAAGAAACGAGUUGCG
-------------------.(((((.....((((..---...)))).)))))....((((...(((((((.(-((((((.((((....)))).)))))...))....))))))).)))).. ( -21.80, z-score =  -1.79, R)
>droYak2.chr2L 10759912 109 + 22324452
----------UUUCUUUUUUUACUCAUUCCUUGCUUGAAUAGAGCUAAAGCAUGUUCAACAUAUA--UUUAAUGUUCAUAUUCCGCAAGGGAAAUGAAAGAGUGAUAAGAAGCGGGUCGCG
----------.(((((...((((((......((.(((((((..((....)).)))))))))....--.......(((((.((((....)))).))))).)))))).)))))(((...))). ( -30.60, z-score =  -3.14, R)
>consensus
__________UU___U___UUGCUAGAACAGAACCU___UUAGUUCAUAGCAUAUUCAACAUAUAU_UUUAAUGUUUAUAUCCCGCAAGGGAAAUGAAAGUCUGAUAAGAAACGGGUCGCG
.................................................((.......................(((((.((((....)))).))))).....(((.........))))). (-13.59 = -12.93 +  -0.66)

alignment

secondary structure

dotplot

Window 0

Location	8,128,985 – 8,129,104
Length	119
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	77.50
Shannon entropy	0.37204
G+C content	0.32840
Mean single sequence MFE	-23.33
Consensus MFE	-13.54
Energy contribution	-12.97
Covariance contribution	-0.56
Combinations/Pair	1.21
Mean z-score	-1.98
Structure conservation index	0.58
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.79
SVM RNA-class probability	0.817481
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8128985 119 + 23011544
GUUCAUAGCAUAUUCAACAUGUAUGUUUAAUGUUUAUAUCCCGCAAGGGAAAUGAAAGUCUGAUAAGAAACGGGUCGCGAUUAUUACAGAAAUUCAAAGUAAAAUGCACAUAUACUAAA
((.((((((((((.......))))))).....(((((.((((....))))..((((..((((.(((.((.((.....)).)).)))))))..))))..)))))))).)).......... ( -23.70, z-score =  -1.64, R)
>droSim1.chr2L 7908448 118 + 22036055
GUUCAUAGCAUAUUUAACAUAUGU-UUUUAAGUUUAUAUCCCGCAAGGGAAAUGAAAGUCUGAUAAGAAACGAGUUGCGAUUAUUGCAGAAAUUCAAAGUAAGAUGCAUACAUAUUCAG
.......((((.((((......((-((((.(((((((.((((....)))).)))))...))....))))))(((((((((...)))))...))))....))))))))............ ( -22.50, z-score =  -1.39, R)
>droSec1.super_3 3625329 117 + 7220098
GUUCAUAGCAUAUUUAACAUAUGU-UUU-AUGUUUAUAUCCCGCAAGGGAAAUGAAAGCCUGAUAAGAAACGAGUCGCCAUUAUUGCAGAAAUUCAAAGUAAGAUGCAUACAUAUACAG
.......((((.((((......((-(((-...(((((.((((....)))).))))).((.((((..((......))...))))..)).)))))......))))))))............ ( -19.70, z-score =  -0.56, R)
>droYak2.chr2L 10759949 95 + 22324452
-----AAGCAUGUUCAACAUAUAU--UUAAUGUUCAUAUUCCGCAAGGGAAAUGAAAGAGUGAUAAGAAGCGGGUCGCGAUUAUUACAGAAAAUGCGAAUUA-----------------
-----..((((.(((.........--......(((((.((((....)))).)))))...(((((((...(((...)))..))))))).))).))))......----------------- ( -27.40, z-score =  -4.35, R)
>consensus
GUUCAUAGCAUAUUCAACAUAUAU_UUUAAUGUUUAUAUCCCGCAAGGGAAAUGAAAGUCUGAUAAGAAACGAGUCGCGAUUAUUACAGAAAUUCAAAGUAAGAUGCAUACAUAUUCAG
.......((.......................(((((.((((....)))).))))).....(((.........)))))......................................... (-13.54 = -12.97 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:25:16 2011