Locus 7328

Sequence ID X_DroMel_CAF1
Location 18,286,963 – 18,287,176
Length 213
Max. P 0.670637
window11999 window12000

overview

Window 9

Location 18,286,963 – 18,287,076
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.29
Mean single sequence MFE -25.74
Consensus MFE -20.23
Energy contribution -19.85
Covariance contribution -0.38
Combinations/Pair 1.11
Mean z-score -1.49
Structure conservation index 0.79
SVM decision value 0.05
SVM RNA-class probability 0.558149
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18286963 113 - 22224390
CUUU--CACCCCGUGGAAUACCCAAUUCACCCAUC-----ACAAGAGUUCAGCCAGGUCGGUGGUUCCUAUGCUCCAGCGAAUUCCUGGUAAACGUUUUACAUAUUGUAAAAUAACAAUA
....--......(((((........))))).....-----......(((..(((((((((.(((..........))).)))...)))))).)))(((((((.....)))))))....... ( -24.40)
>DroSec_CAF1 77 117 - 1
CUUU--CGCCCC-UGGAAUACCCAAAACACCCGCCUCCCCUCGAGAGUUCAGCCAGGUCGGUGGUUCCUAUGCUCCAGCGAAUUCCUGGUAAACGUUUUACAUAUUGUAAAAUAACAAUA
((((--((....-.(((..................)))...))))))....(((((((((.(((..........))).)))...))))))....(((((((.....)))))))....... ( -25.77)
>DroSim_CAF1 120 117 - 1
CUUU--CGCCCC-UGGAAUACCCAAAACACCCGCCUCCCCUCGAGAGUUCAGCCAGGUCGGUGGUUCCUAUGCUCCAGCGAAUUCCUGGUAAACGUUUUACAUAUUGUAAAAUAACAAUA
((((--((....-.(((..................)))...))))))....(((((((((.(((..........))).)))...))))))....(((((((.....)))))))....... ( -25.77)
>DroYak_CAF1 120 101 - 1
CUUUUCCGCCCC-UU---UUCCCAAA---------------CGGCAGCUCGACCAGGUCGCUGGUUUCUACGCUCCGGCGAAUUCCUGGUAAACGUUUUACAUAUUGUAAAAUAACAAUA
.......(((..-..---........---------------.)))......(((((((((((((..........)))))))...))))))....(((((((.....)))))))....... ( -27.02)
>consensus
CUUU__CGCCCC_UGGAAUACCCAAAACACCCGCC_____UCGAGAGUUCAGCCAGGUCGGUGGUUCCUAUGCUCCAGCGAAUUCCUGGUAAACGUUUUACAUAUUGUAAAAUAACAAUA
...................................................(((((((((.(((..........))).)))...))))))....(((((((.....)))))))....... (-20.23 = -19.85 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 18,287,076 – 18,287,176
Length 100
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.38
Mean single sequence MFE -34.80
Consensus MFE -22.30
Energy contribution -22.30
Covariance contribution 0.00
Combinations/Pair 1.12
Mean z-score -1.87
Structure conservation index 0.64
SVM decision value 0.29
SVM RNA-class probability 0.670637
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18287076 100 - 22224390
AGCGAUGGC-GAAUUGAAGGGGUUAGCAAAUGGCAAACGACUUUGACAAAUACCCCAAUGCAGGGAGG--UGGUGAAAGCAGCCUUUCAGCC-----------------AGCCGCCACAC
.(((.((((-........(((((...((((.(........)))))......)))))......(..(((--(.((....)).))))..).)))-----------------)..)))..... ( -33.60)
>DroSec_CAF1 194 104 - 1
AGCGAUGGG-GAAUUGAAGGGGUUAGCAAAUGGCAAACGACUUUGACAAAUACCCCAAUGCAGGGAGG--UGGUGAAAGCAGCCUUUCAGCCAGC-------------CAGCCGCCCCAC
.(((.((((-(..(..(((..(((.((.....)).)))..)))..)......))))).)))..((.((--((((....((.((......))..))-------------..)))))))).. ( -35.20)
>DroSim_CAF1 237 100 - 1
AGCGAUGGG-GAAUUGAAGGGGUUAGCAAAUGGCAAACGACUUUGACAAAUACCCCAAUGCAGGGAGG--UGGUGAAAGCAGCCUUUCAGCC-----------------AGCCGCCCCAC
.(((.((((-(..(..(((..(((.((.....)).)))..)))..)......))))).))).(((.((--(((((((((....)))))).))-----------------).))..))).. ( -36.90)
>DroYak_CAF1 221 120 - 1
GGAGAUGGGUUUAUUGAAGGGGUUAGCAAAUGGCAAACGACUUUGACAAAUACCCCAAUGCAGUAAGGUGUGGUGAAAGCAGCCUUUCAACUUGUCCCGCCCCUCAUCCUCCUUCCCCAU
(((((((((.((((((..(((((...((((.(........)))))......)))))....))))))((((.((((((((....))))))......)))))).))))).))))........ ( -33.50)
>consensus
AGCGAUGGG_GAAUUGAAGGGGUUAGCAAAUGGCAAACGACUUUGACAAAUACCCCAAUGCAGGGAGG__UGGUGAAAGCAGCCUUUCAGCC_________________AGCCGCCCCAC
.(((.((((....(..(((..(((.((.....)).)))..)))..).......))))..((.((((((....((....))..)))))).)).....................)))..... (-22.30 = -22.30 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:05 2006