Locus 14115

Sequence ID	dm3.chrX
Location	11,277,676 – 11,277,809
Length	133
Max. P	0.642737

overview

Window 7

Location	11,277,676 – 11,277,809
Length	133
Sequences	3
Columns	137
Reading direction	forward
Mean pairwise identity	81.77
Shannon entropy	0.24130
G+C content	0.38820
Mean single sequence MFE	-28.77
Consensus MFE	-17.75
Energy contribution	-17.53
Covariance contribution	-0.21
Combinations/Pair	1.17
Mean z-score	-2.23
Structure conservation index	0.62
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.32
SVM RNA-class probability	0.642737
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11277676 133 + 22422827
GUAUGUACAUCAUACAUGUGCUGGAAUGCAAUACCCCUUCAAGUGAUACCCCUUCUAUAGGGUAUGUUUUAAAUACCCGUUCCAAUUGUUCCAAGAACAGCUACACAAGUUUGAGUUCCUUCAACCAAA----CAUA
(((((.....))))).((((.(((((((...(((........)))((((((........))))))............))))))).((((((...))))))...)))).(((((.(((.....)))))))----)... ( -29.90, z-score =  -2.24, R)
>droSim1.chrX 8707851 122 + 17042790
----------CAUACAUGUGCGGGGACGCAAUACCCCUUCAAGUGAUACCCCU-CUAUAGGGUAUCAGUUAAAUAGGC----CAAAUAAACCAAGAACAACUAUACAAGUUUGAGUUUCUUCAACCAAAACAUCAUA
----------........((((....)))).....(((..((.((((((((..-.....)))))))).))....))).----..........................((((..(((.....)))..))))...... ( -25.30, z-score =  -1.30, R)
>droSec1.super_36 1105 121 + 449511
----------CAUAUAUGUGCGGGGACGCAAUACCCCUUUAAGUGAUACCCCU-CUAUAGGGUAUCAGUUAAAUAGGC----CAAAUAAACCAAGAACAACUAUACAAGUUUGAGUUUCUUCAACCAAA-CAUCAUA
----------........((((....))))...((..(((((.((((((((..-.....)))))))).)))))..)).----..........................(((((.(((.....)))))))-)...... ( -31.10, z-score =  -3.14, R)
>consensus
__________CAUACAUGUGCGGGGACGCAAUACCCCUUCAAGUGAUACCCCU_CUAUAGGGUAUCAGUUAAAUAGGC____CAAAUAAACCAAGAACAACUAUACAAGUUUGAGUUUCUUCAACCAAA_CAUCAUA
..................((..(((((.((..........((.((((((((........)))))))).))............................((((.....)))))).)))))..)).............. (-17.75 = -17.53 +  -0.21)

alignment

secondary structure

dotplot

Window 8

Location	11,277,676 – 11,277,809
Length	133
Sequences	3
Columns	137
Reading direction	reverse
Mean pairwise identity	81.77
Shannon entropy	0.24130
G+C content	0.38820
Mean single sequence MFE	-35.13
Consensus MFE	-23.65
Energy contribution	-23.77
Covariance contribution	0.12
Combinations/Pair	1.12
Mean z-score	-1.89
Structure conservation index	0.67
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.03
SVM RNA-class probability	0.507747
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11277676 133 - 22422827
UAUG----UUUGGUUGAAGGAACUCAAACUUGUGUAGCUGUUCUUGGAACAAUUGGAACGGGUAUUUAAAACAUACCCUAUAGAAGGGGUAUCACUUGAAGGGGUAUUGCAUUCCAGCACAUGUAUGAUGUACAUAC
...(----(((((((.....))).))))).(((((...(((((...)))))..(((((.((((((.......)))))).......(.((((((.((....)))))))).).)))))))))).(((((.....))))) ( -32.00, z-score =  -0.39, R)
>droSim1.chrX 8707851 122 - 17042790
UAUGAUGUUUUGGUUGAAGAAACUCAAACUUGUAUAGUUGUUCUUGGUUUAUUUG----GCCUAUUUAACUGAUACCCUAUAG-AGGGGUAUCACUUGAAGGGGUAUUGCGUCCCCGCACAUGUAUG----------
((((.(((...(((..((.(((((..((((.....))))......))))).))..----)))..(((((.(((((((((....-.))))))))).)))))((((........)))))))))))....---------- ( -36.60, z-score =  -2.46, R)
>droSec1.super_36 1105 121 - 449511
UAUGAUG-UUUGGUUGAAGAAACUCAAACUUGUAUAGUUGUUCUUGGUUUAUUUG----GCCUAUUUAACUGAUACCCUAUAG-AGGGGUAUCACUUAAAGGGGUAUUGCGUCCCCGCACAUAUAUG----------
((((.((-(..(((..((.(((((..((((.....))))......))))).))..----)))..(((((.(((((((((....-.))))))))).)))))((((........)))))))))))....---------- ( -36.80, z-score =  -2.81, R)
>consensus
UAUGAUG_UUUGGUUGAAGAAACUCAAACUUGUAUAGUUGUUCUUGGUUUAUUUG____GCCUAUUUAACUGAUACCCUAUAG_AGGGGUAUCACUUGAAGGGGUAUUGCGUCCCCGCACAUGUAUG__________
........(((((((.....))).))))...(((((..(((.......................(((((.(((((((((......))))))))).)))))((((........)))))))..)))))........... (-23.65 = -23.77 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:33:58 2011