Locus 14248

Sequence ID dm3.chrX
Location 12,132,450 – 12,132,589
Length 139
Max. P 0.649445
window19622 window19623

overview

Window 2

Location 12,132,450 – 12,132,550
Length 100
Sequences 6
Columns 121
Reading direction reverse
Mean pairwise identity 68.91
Shannon entropy 0.51427
G+C content 0.52544
Mean single sequence MFE -24.32
Consensus MFE -14.38
Energy contribution -14.93
Covariance contribution 0.56
Combinations/Pair 1.24
Mean z-score -0.87
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.540102
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12132450 100 - 22422827
------------------CUCCACCUCCACCUCCGUCGAUUCGGAUUUGCUUUCAUUUGUUCUGGCCAUCACACCUGGCCUCCGGGGAAGUCCCAA---UGAAAUCGAAUCGAAUACACUG
------------------.................(((((((((......(((((((......(((((.......)))))....(((....)))))---))))))))))))))........ ( -26.70, z-score =  -1.72, R)
>droSim1.chrX_random 3302805 88 - 5698898
------------------------------CUCCGUCGACUCGGAUUUGCUUUCAUUUGUUCUGGUCAUCACACCUGGCCUCCGGGGAAGUCCCAA---UGAAAUCGAAUCGAAUACACUG
------------------------------...((......))((((((.(((((((......(((((.......)))))....(((....)))))---))))).)))))).......... ( -21.20, z-score =  -0.24, R)
>droSec1.super_45 150454 88 - 245362
------------------------------CUCCGUCGACUCGGAUUUGCUUUCAUUUGUUCUGGCCAUCACACCUGGCCUCCGGGGAAGUCCCAA---UGAAAUCGAAUCGAAUACACUG
------------------------------...((......))((((((.(((((((......(((((.......)))))....(((....)))))---))))).)))))).......... ( -23.90, z-score =  -1.25, R)
>droYak2.chrX 20042615 96 + 21770863
----------------------CUCUCAACCUCCGCCGACUUGGAUUUGCUUUCAUUUGUUCUGGCCAUCACACCUGGCCUCCGGGGAAGACCCAA---UGAAAUCGAAUCGAAUACACUG
----------------------..................((.((((((.(((((((......(((((.......)))))...(((.....)))))---))))).)))))).))....... ( -24.80, z-score =  -1.84, R)
>droEre2.scaffold_4690 4038673 118 + 18748788
CUCCACCUCCAAAUCCUCAUCCACAUCCACCUCCUCCGAUUCGGAUUUGCUUUCAUUUGUUCUGGCCAUCACACCUGGCCUCCGGGGAAGUCGCAA---UGAAAUCGAAUCGAAUACACUG
....................................((((((((..((((....((((.(((.(((((.......)))))...))).)))).))))---.....))))))))......... ( -22.30, z-score =  -0.01, R)
>droAna3.scaffold_13335 2111863 83 + 3335858
------------------------------------UUGCUCGAACUUGGUCGCUGGCCCACCUGGCCUUAGACUCAUCCUCAGCCUUAGCCCCGAGGGGGAAAUCGGUUCGAACACGG--
------------------------------------.((.(((((((..(((...((((.....))))...)))((..((((.((....))...))))..))....))))))).))...-- ( -27.00, z-score =  -0.16, R)
>consensus
______________________________CUCCGUCGACUCGGAUUUGCUUUCAUUUGUUCUGGCCAUCACACCUGGCCUCCGGGGAAGUCCCAA___UGAAAUCGAAUCGAAUACACUG
........................................(((.(((((.(((((........(((((.......)))))...(((.....))).....))))).))))))))........ (-14.38 = -14.93 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 12,132,490 – 12,132,589
Length 99
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 71.73
Shannon entropy 0.47541
G+C content 0.47717
Mean single sequence MFE -24.78
Consensus MFE -13.13
Energy contribution -13.80
Covariance contribution 0.67
Combinations/Pair 1.24
Mean z-score -1.42
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.33
SVM RNA-class probability 0.649445
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12132490 99 + 22422827
CCAGGUGUGAUGGCCAGAACAAAUGAAAGCAAAUCCGAAUCGACGGAGGUGGA------------------GGUGGAGGUGGAAAACCAAACGAACUACAUGACAUCUGGAGUACUA
((((((((.(((.....................((((..((.((....)).))------------------..))))(((.....)))..........))).))))))))....... ( -28.80, z-score =  -2.29, R)
>droSim1.chrX_random 3302845 87 + 5698898
CCAGGUGUGAUGACCAGAACAAAUGAAAGCAAAUCCGAGUCGACGGAGGUGGA------------------------------AAACCAAACGAACUACAUGACAUCUGGAGUACUA
((((((((.(((.....................((((......))))(((...------------------------------..)))..........))).))))))))....... ( -24.00, z-score =  -2.55, R)
>droSec1.super_45 150494 87 + 245362
CCAGGUGUGAUGGCCAGAACAAAUGAAAGCAAAUCCGAGUCGACGGAGGUGGA------------------------------AAACCAAACGAACUACAUGACAUCUGGAGUACUA
((((((((.(((.....................((((......))))(((...------------------------------..)))..........))).))))))))....... ( -24.20, z-score =  -2.24, R)
>droYak2.chrX 20042655 95 - 21770863
CCAGGUGUGAUGGCCAGAACAAAUGAAAGCAAAUCCAAGUCGGCGGAGGUUGA----------------------GAGGUGGAAAACCAAACGAACUACAUAACAUCUGGAGUACUA
((((((((.(((...............(((...(((........))).)))..----------------------..(((.....)))..........))).))))))))....... ( -21.70, z-score =  -0.57, R)
>droEre2.scaffold_4690 4038713 117 - 18748788
CCAGGUGUGAUGGCCAGAACAAAUGAAAGCAAAUCCGAAUCGGAGGAGGUGGAUGUGGAUGAGGAUUUGGAGGUGGAGGUGGAAAACCAAACGAACUACAUGACAUCUGGAGUACUA
((((((((.(((.(((((.(........(((..((((..((....))..))))))).......).))))).(((.....(((....))).....))).))).))))))))....... ( -32.16, z-score =  -2.17, R)
>droAna3.scaffold_13335 2111892 93 - 3335858
CUAAGGCUGAGGAUGAGUCUAAGGCCAGGUGGGCCAG---CGACCAAGUUCGA---------------------GCAAAUGGAAGAGAACAUAAACUACACGGGAUCUGAGGAACUA
....((((..(((....)))..)))).(((.(.....---).))).(((((..---------------------....(((........)))........(((...)))..))))). ( -17.80, z-score =   1.29, R)
>consensus
CCAGGUGUGAUGGCCAGAACAAAUGAAAGCAAAUCCGAGUCGACGGAGGUGGA______________________GAGGUGGAAAACCAAACGAACUACAUGACAUCUGGAGUACUA
((((((((.(((.....................(((........)))(((...................................)))..........))).))))))))....... (-13.13 = -13.80 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:36:44 2011