Locus 13453

Sequence ID dm3.chrX
Location 6,632,529 – 6,632,604
Length 75
Max. P 0.898072
window18525 window18526

overview

Window 5

Location 6,632,529 – 6,632,604
Length 75
Sequences 7
Columns 82
Reading direction forward
Mean pairwise identity 73.19
Shannon entropy 0.46981
G+C content 0.47109
Mean single sequence MFE -20.43
Consensus MFE -8.99
Energy contribution -9.77
Covariance contribution 0.78
Combinations/Pair 1.22
Mean z-score -2.25
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.14
SVM RNA-class probability 0.898072
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6632529 75 + 22422827
UAUUGCAAAAUUUUCCUUUAGCCCAAGCGGGUAAAGUUCCCGA-------UACCCGUUGCAACUGGUUAUACCGGUUCGUCU
....................((...((((((((..(....)..-------))))))))))((((((.....))))))..... ( -17.70, z-score =  -1.22, R)
>droSim1.chrX 5224333 68 + 17042790
UAUUGCAAAAUUUUCCUUUAGCCCAAGCGGGUAAAGUUC--------------CCGUUGCAACCGGUUAUACCGGUUCGUCU
...(((((.......(((((.(((....))))))))...--------------...)))))(((((.....)))))...... ( -19.62, z-score =  -2.66, R)
>droSec1.super_4 6017385 75 - 6179234
UAUUGCAAAAUUUUCCUUUAGCCCAAGCGGGUAAAGCUCCCGA-------UACCCGUUGCAACCGGUUAUACCGGUUCGUCU
....................((...((((((((..(....)..-------))))))))))((((((.....))))))..... ( -19.60, z-score =  -1.71, R)
>droYak2.chrX 2595210 75 + 21770863
UAUUGCAAAAUUUUCCUUUAGCCCAAGCGGGUAAAGUUCCCAA-------UACCCGUUGCAACCGGUUAUACCGGUUCAUCU
....................((...((((((((..........-------))))))))))((((((.....))))))..... ( -19.30, z-score =  -2.67, R)
>droEre2.scaffold_4690 15558397 82 + 18748788
UAUUUCAAAAUUUUCCUUUAGCCCAAGCGGGUAAAGUUUCCAACCGGUUAUACCGGUUGCAACCGGCUAUACCGCUUCAUCU
........................((((((.((.((((..(((((((.....))))))).....)))).))))))))..... ( -21.20, z-score =  -2.48, R)
>dp4.chrXL_group1a 6447589 68 + 9151740
--UGGCAGACCUCUGUCGGAGCCAUUUCCAAUACAGUGUUC------------CCGUUGCAACCGGUUAAACCGGUUGUACU
--.(((((....)))))(((((.(((........)))))))------------)...(((((((((.....))))))))).. ( -25.30, z-score =  -3.44, R)
>droPer1.super_25 575371 68 - 1448063
--UGGCAGACCUCUGUCGAAGCCAUUUCCAAUACAGUGUUC------------CCGUUGCAACCGGUUAAACCGGUUGGACU
--((((.(((....)))...)))).................------------..(((.(((((((.....)))))))))). ( -20.30, z-score =  -1.59, R)
>consensus
UAUUGCAAAAUUUUCCUUUAGCCCAAGCGGGUAAAGUUCCC_A_______UACCCGUUGCAACCGGUUAUACCGGUUCGUCU
....((((.......(((((.(((....))))))))....................))))((((((.....))))))..... ( -8.99 =  -9.77 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 6,632,529 – 6,632,604
Length 75
Sequences 7
Columns 82
Reading direction reverse
Mean pairwise identity 73.19
Shannon entropy 0.46981
G+C content 0.47109
Mean single sequence MFE -22.46
Consensus MFE -11.58
Energy contribution -11.01
Covariance contribution -0.57
Combinations/Pair 1.36
Mean z-score -1.72
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.80
SVM RNA-class probability 0.821120
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6632529 75 - 22422827
AGACGAACCGGUAUAACCAGUUGCAACGGGUA-------UCGGGAACUUUACCCGCUUGGGCUAAAGGAAAAUUUUGCAAUA
.........((.....)).(((((((((((((-------..(....)..))))))(((......))).......))))))). ( -19.70, z-score =  -0.99, R)
>droSim1.chrX 5224333 68 - 17042790
AGACGAACCGGUAUAACCGGUUGCAACGG--------------GAACUUUACCCGCUUGGGCUAAAGGAAAAUUUUGCAAUA
.....((((((.....))))))((((...--------------...((((((((....))).))))).......)))).... ( -19.92, z-score =  -1.93, R)
>droSec1.super_4 6017385 75 + 6179234
AGACGAACCGGUAUAACCGGUUGCAACGGGUA-------UCGGGAGCUUUACCCGCUUGGGCUAAAGGAAAAUUUUGCAAUA
.....((((((.....))))))((((((((((-------..(....)..))))))(((......))).......)))).... ( -22.90, z-score =  -1.43, R)
>droYak2.chrX 2595210 75 - 21770863
AGAUGAACCGGUAUAACCGGUUGCAACGGGUA-------UUGGGAACUUUACCCGCUUGGGCUAAAGGAAAAUUUUGCAAUA
.....((((((.....))))))((((((((((-------..(....)..))))))(((......))).......)))).... ( -24.80, z-score =  -2.77, R)
>droEre2.scaffold_4690 15558397 82 - 18748788
AGAUGAAGCGGUAUAGCCGGUUGCAACCGGUAUAACCGGUUGGAAACUUUACCCGCUUGGGCUAAAGGAAAAUUUUGAAAUA
.....((.(((.....))).)).(((((((.....)))))))....((((((((....))).)))))............... ( -24.30, z-score =  -1.67, R)
>dp4.chrXL_group1a 6447589 68 - 9151740
AGUACAACCGGUUUAACCGGUUGCAACGG------------GAACACUGUAUUGGAAAUGGCUCCGACAGAGGUCUGCCA--
....(((((((.....)))))))..((((------------.....))))........((((.((......))...))))-- ( -21.80, z-score =  -1.32, R)
>droPer1.super_25 575371 68 + 1448063
AGUCCAACCGGUUUAACCGGUUGCAACGG------------GAACACUGUAUUGGAAAUGGCUUCGACAGAGGUCUGCCA--
....(((((((.....)))))))..((((------------.....))))..(((....((((((....))))))..)))-- ( -23.80, z-score =  -1.91, R)
>consensus
AGACGAACCGGUAUAACCGGUUGCAACGGGUA_______U_GGGAACUUUACCCGCUUGGGCUAAAGGAAAAUUUUGCAAUA
.....((((((.....))))))........................((((((((....))).)))))............... (-11.58 = -11.01 +  -0.57)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:21:42 2011