Locus 3041

Sequence ID	dm3.chr2R
Location	1,727,958 – 1,728,110
Length	152
Max. P	0.977075

overview

Window 2

Location	1,727,958 – 1,728,070
Length	112
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	88.83
Shannon entropy	0.15305
G+C content	0.34573
Mean single sequence MFE	-26.43
Consensus MFE	-22.20
Energy contribution	-22.53
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.62
Structure conservation index	0.84
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.28
SVM RNA-class probability	0.624954
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 1727958 112 + 21146708
--UCGGCCAAGUUGGUUUAACCUUUAACUAAUAA------CUCCUAAAUUUGCUCAUAAGUGUAAGGAUUUCUGCACCCAAUGGUGUAGAAUACAUUUAUUAAGUCGGUGCACUUAAAAA
--..((....(((((((........)))))))..------..))............((((((((..((((((((((((....)))))))))............)))..)))))))).... ( -27.10, z-score =  -2.26, R)
>droSec1.super_26 384624 118 + 826190
--UCGGCCAAGUUGGUUUAACCUUUAACUAAUAAUUGAAACUCCUAAAUUUGCUCAUAAGUGUGAGGAUUUCUGCACCAGUUGGUGUAGAAUAUAUUUAUUAGAUCGGUGUACUUCAAAA
--...(((.....((.....)).....(((((((.((....((((..(((((....)))))...)))).(((((((((....)))))))))..)).)))))))...)))........... ( -27.50, z-score =  -1.72, R)
>droSim1.chr2R 641792 120 + 19596830
UCACGGCCAAGUUGGUUUAACCUUUAACUAAUAAUUGAAACUCCUAAAUUUGCUCAUAAGUGUGAGGAUUUCUGCACCCGUUGGUGUAGAAUAUAUUUCUUAGAUCAGUGUACUUCAAAA
.((((..(..(((((((........)))))))....((((.((((..(((((....)))))...)))).(((((((((....)))))))))....))))...)..).))).......... ( -24.70, z-score =  -0.89, R)
>consensus
__UCGGCCAAGUUGGUUUAACCUUUAACUAAUAAUUGAAACUCCUAAAUUUGCUCAUAAGUGUGAGGAUUUCUGCACCCGUUGGUGUAGAAUAUAUUUAUUAGAUCGGUGUACUUCAAAA
.....(((..(((((((........))))))).........((((..(((((....)))))...)))).(((((((((....)))))))))...............)))........... (-22.20 = -22.53 +   0.33)

alignment

secondary structure

dotplot

Window 3

Location	1,727,990 – 1,728,110
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	86.78
Shannon entropy	0.17601
G+C content	0.34815
Mean single sequence MFE	-27.97
Consensus MFE	-23.46
Energy contribution	-23.36
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-2.58
Structure conservation index	0.84
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.97
SVM RNA-class probability	0.977075
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 1727990 120 + 21146708
CUCCUAAAUUUGCUCAUAAGUGUAAGGAUUUCUGCACCCAAUGGUGUAGAAUACAUUUAUUAAGUCGGUGCACUUAAAAAUGGUUUCCAUCCCCAUAUAUGUACCGAUAUUUGUUGUAUU
..........(((..(((((((((.....(((((((((....))))))))))))))))))...(((((((((..((...((((...)))).....))..))))))))).......))).. ( -31.70, z-score =  -3.34, R)
>droSec1.super_26 384662 108 + 826190
CUCCUAAAUUUGCUCAUAAGUGUGAGGAUUUCUGCACCAGUUGGUGUAGAAUAUAUUUAUUAGAUCGGUGUACUUCAAAAUGGUUUCCAU------------ACCGAUAUUUGUUGUAUU
...((((.....(((((....)))))...(((((((((....)))))))))........))))(((((((((((.......)))....))------------))))))............ ( -28.10, z-score =  -2.67, R)
>droSim1.chr2R 641832 108 + 19596830
CUCCUAAAUUUGCUCAUAAGUGUGAGGAUUUCUGCACCCGUUGGUGUAGAAUAUAUUUCUUAGAUCAGUGUACUUCAAAAUGGUUUCCAU------------ACCGAUAUUUGUUGUAUU
...((((.....(((((....)))))...(((((((((....)))))))))........))))......((((..((((.((((......------------))))...))))..)))). ( -24.10, z-score =  -1.71, R)
>consensus
CUCCUAAAUUUGCUCAUAAGUGUGAGGAUUUCUGCACCCGUUGGUGUAGAAUAUAUUUAUUAGAUCGGUGUACUUCAAAAUGGUUUCCAU____________ACCGAUAUUUGUUGUAUU
.((((..(((((....)))))...)))).(((((((((....)))))))))((((........((((((..........((((...))))............))))))......)))).. (-23.46 = -23.36 +  -0.11)

alignment

secondary structure

dotplot

Window 4

Location	1,727,990 – 1,728,110
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	86.78
Shannon entropy	0.17601
G+C content	0.34815
Mean single sequence MFE	-20.53
Consensus MFE	-18.70
Energy contribution	-17.82
Covariance contribution	-0.88
Combinations/Pair	1.15
Mean z-score	-1.18
Structure conservation index	0.91
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.30
SVM RNA-class probability	0.632878
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 1727990 120 - 21146708
AAUACAACAAAUAUCGGUACAUAUAUGGGGAUGGAAACCAUUUUUAAGUGCACCGACUUAAUAAAUGUAUUCUACACCAUUGGGUGCAGAAAUCCUUACACUUAUGAGCAAAUUUAGGAG
.............(((((.(((...(((((((((...))))))))).))).)))))((((.(((.((((((((.((((....)))).)))).....)))).)))))))............ ( -24.90, z-score =  -1.28, R)
>droSec1.super_26 384662 108 - 826190
AAUACAACAAAUAUCGGU------------AUGGAAACCAUUUUGAAGUACACCGAUCUAAUAAAUAUAUUCUACACCAACUGGUGCAGAAAUCCUCACACUUAUGAGCAAAUUUAGGAG
............((((((------------((((...))))..........))))))((..(((((...((((.((((....)))).))))...((((......))))...)))))..)) ( -18.60, z-score =  -1.43, R)
>droSim1.chr2R 641832 108 - 19596830
AAUACAACAAAUAUCGGU------------AUGGAAACCAUUUUGAAGUACACUGAUCUAAGAAAUAUAUUCUACACCAACGGGUGCAGAAAUCCUCACACUUAUGAGCAAAUUUAGGAG
..(((..((((....(((------------......)))..))))..)))......((((((.......((((.((((....)))).))))...((((......))))....)))))).. ( -18.10, z-score =  -0.84, R)
>consensus
AAUACAACAAAUAUCGGU____________AUGGAAACCAUUUUGAAGUACACCGAUCUAAUAAAUAUAUUCUACACCAACGGGUGCAGAAAUCCUCACACUUAUGAGCAAAUUUAGGAG
.............(((((............((((...))))..........)))))(((((........((((.((((....)))).))))...((((......)))).....))))).. (-18.70 = -17.82 +  -0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:02:32 2011