Locus 3152

Sequence ID	dm3.chr2R
Location	2,889,709 – 2,889,837
Length	128
Max. P	0.763228

overview

Window 6

Location	2,889,709 – 2,889,810
Length	101
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	70.87
Shannon entropy	0.46781
G+C content	0.48296
Mean single sequence MFE	-27.75
Consensus MFE	-15.60
Energy contribution	-17.47
Covariance contribution	1.87
Combinations/Pair	1.18
Mean z-score	-1.47
Structure conservation index	0.56
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.60
SVM RNA-class probability	0.757269
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2889709 101 + 21146708
CUUCUGAUCGGAUGCGAUGCUAACUAUUCUGAUCCCACGAACCGCUGAGCUCGGCGGCUGAGUCAUGCUGCAGUUUGGCGCAAUCCUACGAAUUUAUGAAC----
.(((.(((((((...............)))))))........(((..((((..(((((........)))))))))..))).........))).........---- ( -25.76, z-score =  -0.06, R)
>droAna3.scaffold_13266 9193150 102 + 19884421
CAUCUGUUCCGAUCUGAU--CUGCUCCAUUGAACUGAUGAACUCGUCAGUCUCUCCAUU-AGUCAUGGCGCUAUUAGAUCGAAUUAGUUUAUCUCUCUAAUUAAA
.........(((((((((--..((.((((.(((((((((....))))))).........-..)))))).)).)))))))))((((((.........))))))... ( -27.80, z-score =  -3.79, R)
>droSec1.super_1 555717 100 + 14215200
-CUCUGAUCGGAUGCGAUGCUAACUAAUCUGAUCCCAUGAACCGCUGAGCUCGGCGGCUGAGUCAUGCUGCAGUUUGGCGCAAUCCUACGAAUUUAUGAAC----
-....((((((((.............)))))))).((((((.(((..((((..(((((........)))))))))..)))...((....)).))))))...---- ( -28.72, z-score =  -1.12, R)
>droSim1.chr2R 1690469 101 + 19596830
CUUCUGAUCGGAUGCGAUGCUAACUAAUCUGAUCCCAUGAACCGCUGAGCUCGGCGGCUGAGUCAUGCUGCAGUUUGGCGCAAUCCCACGAAUUUAUGAAC----
.....((((((((.............)))))))).((((((.(((..((((..(((((........)))))))))..)))...((....)).))))))...---- ( -28.72, z-score =  -0.89, R)
>consensus
CUUCUGAUCGGAUGCGAUGCUAACUAAUCUGAUCCCAUGAACCGCUGAGCUCGGCGGCUGAGUCAUGCUGCAGUUUGGCGCAAUCCUACGAAUUUAUGAAC____
.....((((((((.............))))))))........(((((((((..(((((........))))))))))))))......................... (-15.60 = -17.47 +   1.87)

alignment

secondary structure

dotplot

Window 7

Location	2,889,735 – 2,889,837
Length	102
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	72.25
Shannon entropy	0.43361
G+C content	0.46744
Mean single sequence MFE	-31.65
Consensus MFE	-19.36
Energy contribution	-20.23
Covariance contribution	0.87
Combinations/Pair	1.24
Mean z-score	-1.47
Structure conservation index	0.61
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.62
SVM RNA-class probability	0.763228
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2889735 102 + 21146708
UUCUGAUCCCACGAACCGCUGAGCUCGGCGGC-------UGAGUCAUGCUGCAGUUUGGCGCAAUC---CUACGAAUUUA-UGAACUAUAGUUUGGCUGGGGGUGGAUCUAAU
....(((((.((...((((((....))))))(-------(.(((((.((((.((((((.((.....---...))......-)))))).)))).))))).)).))))))).... ( -33.30, z-score =  -1.17, R)
>droAna3.scaffold_13266 9193166 113 + 19884421
AUCUGCUCCAUUGAACUGAUGAACUCGUCAGUCUCUCCAUUAGUCAUGGCGCUAUUAGAUCGAAUUAGUUUAUCUCUCUAAUUAAAUAGAGCAUGACGCAGGGCGAUAAAAAU
.(((((......(((((((((....))))))).)).......((((((.(.(((((......((((((.........)))))).))))).))))))))))))........... ( -28.70, z-score =  -1.77, R)
>droSec1.super_1 555742 102 + 14215200
AUCUGAUCCCAUGAACCGCUGAGCUCGGCGGC-------UGAGUCAUGCUGCAGUUUGGCGCAAUC---CUACGAAUUUA-UGAACUGUAGUUUGACAUGAGGAGCAUCUAAU
...((.((((((...((((((....)))))).-------...((((.(((((((((((.((.....---...))......-))))))))))).))))))).))).))...... ( -33.50, z-score =  -1.97, R)
>droSim1.chr2R 1690495 102 + 19596830
AUCUGAUCCCAUGAACCGCUGAGCUCGGCGGC-------UGAGUCAUGCUGCAGUUUGGCGCAAUC---CCACGAAUUUA-UGAACUAUAGUUUGACAUGGGGAGCAUCUAAU
......(((((((...(((..((((..(((((-------........)))))))))..))).....---...((((((..-........)))))).))))))).......... ( -31.10, z-score =  -0.99, R)
>consensus
AUCUGAUCCCAUGAACCGCUGAGCUCGGCGGC_______UGAGUCAUGCUGCAGUUUGGCGCAAUC___CUACGAAUUUA_UGAACUAUAGUUUGACAUGGGGAGCAUCUAAU
......((((((...((((((....))))))...........((((.((((.(((((.........................))))).)))).)))))))))).......... (-19.36 = -20.23 +   0.87)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:04:46 2011