Locus 12888

Sequence ID dm3.chrX
Location 3,008,875 – 3,008,938
Length 63
Max. P 0.927731
window17721 window17722

overview

Window 1

Location 3,008,875 – 3,008,938
Length 63
Sequences 6
Columns 65
Reading direction forward
Mean pairwise identity 80.17
Shannon entropy 0.38703
G+C content 0.39241
Mean single sequence MFE -13.78
Consensus MFE -8.11
Energy contribution -8.25
Covariance contribution 0.14
Combinations/Pair 1.47
Mean z-score -1.84
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.73
SVM RNA-class probability 0.801965
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3008875 63 + 22422827
AGUCAAAUGGCAAAUAAUCGGAG-CCCCAAGGCUCCAAA-UAAUUCCAUUAACUGGCAAAUAGAA
.(((((((((.........((((-((....))))))...-.....)))))...))))........ ( -17.53, z-score =  -3.05, R)
>droSim1.chrX 2134348 63 + 17042790
AGUCAAAUGGCAAAUAAGCGGAG-CCCCAAGGCUCCAAA-UAAUUCCAUUAACUGGCAAAUAGAA
.((((((((((......))((((-((....))))))...-......))))...))))........ ( -18.00, z-score =  -2.83, R)
>droSec1.super_10 2739479 61 + 3036183
AGUCAAAUGGCAAAUAAUCGGAG-CCCCA-GGCUCCAAA-UAAUUCCAUUAACUGGCAA-UAGAA
.(((((((((.........((((-((...-))))))...-.....)))))...))))..-..... ( -16.43, z-score =  -2.57, R)
>droYak2.chrX 16409183 64 - 21770863
AGUCAAAUGGCAAAUAAUCGCAGGCCCCAAGGCUCCAAA-UAAUUCCAUUAACUGGCAAAUAGAA
.(((((((((............((((....)))).....-.....)))))...))))........ ( -10.35, z-score =   0.06, R)
>droEre2.scaffold_4690 433021 64 + 18748788
AGUCAAAUGGCAAAUAAUCGGAG-CCCCAAGGCACCAAAAUAAUUCCAUUAACUGACAAAUAGAA
.(((((((((.........((.(-((....))).)).........)))))...))))........ ( -13.67, z-score =  -2.70, R)
>droAna3.scaffold_12613 97160 65 - 519072
AGCUGAAUGAAAAACACACAAGCUGCGAAAAUUUCUGCAUAAAUUCCACGAAUCGGAAAAUCAAA
((((...((.......))..))))(((........))).....((((.......))))....... (  -6.70, z-score =   0.07, R)
>consensus
AGUCAAAUGGCAAAUAAUCGGAG_CCCCAAGGCUCCAAA_UAAUUCCAUUAACUGGCAAAUAGAA
.(((((((((.........((((.((....)))))).........)))))...))))........ ( -8.11 =  -8.25 +   0.14)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 3,008,875 – 3,008,938
Length 63
Sequences 6
Columns 65
Reading direction reverse
Mean pairwise identity 80.17
Shannon entropy 0.38703
G+C content 0.39241
Mean single sequence MFE -17.17
Consensus MFE -11.73
Energy contribution -11.49
Covariance contribution -0.24
Combinations/Pair 1.59
Mean z-score -1.85
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.33
SVM RNA-class probability 0.927731
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3008875 63 - 22422827
UUCUAUUUGCCAGUUAAUGGAAUUA-UUUGGAGCCUUGGGG-CUCCGAUUAUUUGCCAUUUGACU
...........(((((((((...((-.((((((((....))-)))))).))....))).)))))) ( -21.90, z-score =  -3.52, R)
>droSim1.chrX 2134348 63 - 17042790
UUCUAUUUGCCAGUUAAUGGAAUUA-UUUGGAGCCUUGGGG-CUCCGCUUAUUUGCCAUUUGACU
...........(((((((((...((-..(((((((....))-)))))..))....))).)))))) ( -20.40, z-score =  -2.72, R)
>droSec1.super_10 2739479 61 - 3036183
UUCUA-UUGCCAGUUAAUGGAAUUA-UUUGGAGCC-UGGGG-CUCCGAUUAUUUGCCAUUUGACU
.....-.....(((((((((...((-.((((((((-...))-)))))).))....))).)))))) ( -20.00, z-score =  -2.84, R)
>droYak2.chrX 16409183 64 + 21770863
UUCUAUUUGCCAGUUAAUGGAAUUA-UUUGGAGCCUUGGGGCCUGCGAUUAUUUGCCAUUUGACU
...........(((((((((...((-.(((.((((....)).)).))).))....))).)))))) ( -13.40, z-score =  -0.06, R)
>droEre2.scaffold_4690 433021 64 - 18748788
UUCUAUUUGUCAGUUAAUGGAAUUAUUUUGGUGCCUUGGGG-CUCCGAUUAUUUGCCAUUUGACU
........((((...(((((.......((((.(((....))-).)))).......))))))))). ( -18.54, z-score =  -2.79, R)
>droAna3.scaffold_12613 97160 65 + 519072
UUUGAUUUUCCGAUUCGUGGAAUUUAUGCAGAAAUUUUCGCAGCUUGUGUGUUUUUCAUUCAGCU
.((((..(((((.....)))))...(((.((((((...(((.....))).))))))))))))).. (  -8.80, z-score =   0.82, R)
>consensus
UUCUAUUUGCCAGUUAAUGGAAUUA_UUUGGAGCCUUGGGG_CUCCGAUUAUUUGCCAUUUGACU
...........(((((((((.......((((((((....)).)))))).......))).)))))) (-11.73 = -11.49 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:10:44 2011