Locus 4236

Sequence ID 3L_DroMel_CAF1
Location 12,399,416 – 12,399,507
Length 91
Max. P 0.932423
window6556 window6557

overview

Window 6

Location 12,399,416 – 12,399,507
Length 91
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 79.37
Mean single sequence MFE -31.71
Consensus MFE -26.14
Energy contribution -26.37
Covariance contribution 0.22
Combinations/Pair 1.11
Mean z-score -1.22
Structure conservation index 0.82
SVM decision value 0.41
SVM RNA-class probability 0.723917
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12399416 91 + 23771897
GGGUGGCCACCUUCGGCUUGGAGCCGCCAAUUAGGCCAGGUGGUCGCAGGGUGCCUGCAAGAUGGAUA-----AAUUGGGGUUUCAACAA--UGUAC----U
.(((((((......)))((((((((.((((((.((((....))))(((((...)))))..........-----))))))))))))))...--..)))----) ( -33.70)
>DroSec_CAF1 2029 93 + 1
GGGUGGCCACCUUCGGCUUGGAGCCGCCAAUUAGGCCAGGUGGUCGCAGGGUGCCUGUAAGAUGGAUA-----AAUUGGGGGUUAAACUAUAUAUAC----U
..((((((((((..(((.....)))(((.....))).))))))))))((...((((.(((........-----..))).))))....))........----. ( -32.20)
>DroSim_CAF1 2008 91 + 1
GGGUGGCCACCUUCGGCUUGGAGCCGCCAAUUAGGCCAGGUGGUCGCAGGGUGCCUGCAAGAUGGAUA-----AAUUGGGGGUUAAGCAU--UGUAC----U
..((((((((((..(((.....)))(((.....))).))))))))))...((((((.(((........-----..))).))))...))..--.....----. ( -32.90)
>DroEre_CAF1 1958 70 + 1
GGGUGGCCACCUUCGGCUUGGAGCCGCCAAUUAGGCCAGGUGGUCGCAGGGUGCCUGCAAGAUGGAUA-----AA---------------------------
....((((((((..(((.....)))(((.....))).))))))))(((((...)))))..........-----..--------------------------- ( -29.70)
>DroYak_CAF1 2055 100 + 1
GGGUGGCCACCUUCGGCUUGGAGCCGCCAAUUAGGCCAGGUGGUCGCAGGGUGCCUGCAAGAUGGAUAUGGUAAAUUGCGGGUUAGACAU--GGUACAUGGU
..((((((((((..(((.....)))(((.....))).)))))))))).....((((((((...............))))))))....(((--(...)))).. ( -37.46)
>DroAna_CAF1 1683 91 + 1
GGGUGGCCACUUUGGGCUUGGAGCCUCCUAUUAGGCCCGGAGGUCGCAGCGUGCCUGCAAAGAAAAGA-----GAUUGUGGAUUGAAACU--UGUAU----U
..((((((..(((((((((((((....)).))))))))))))))))).......(..(((........-----..)))..).........--.....----. ( -24.30)
>consensus
GGGUGGCCACCUUCGGCUUGGAGCCGCCAAUUAGGCCAGGUGGUCGCAGGGUGCCUGCAAGAUGGAUA_____AAUUGGGGGUUAAACAU__UGUAC____U
....((((((((..(((.....)))(((.....))).))))))))((((.....))))............................................ (-26.14 = -26.37 +   0.22)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,399,416 – 12,399,507
Length 91
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 79.37
Mean single sequence MFE -25.62
Consensus MFE -22.30
Energy contribution -23.13
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.87
SVM decision value 1.22
SVM RNA-class probability 0.932423
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12399416 91 - 23771897
A----GUACA--UUGUUGAAACCCCAAUU-----UAUCCAUCUUGCAGGCACCCUGCGACCACCUGGCCUAAUUGGCGGCUCCAAGCCGAAGGUGGCCACCC
.----.....--..((((......)))).-----........(((((((...)))))))((((((.(((.....)))(((.....)))..))))))...... ( -27.70)
>DroSec_CAF1 2029 93 - 1
A----GUAUAUAUAGUUUAACCCCCAAUU-----UAUCCAUCUUACAGGCACCCUGCGACCACCUGGCCUAAUUGGCGGCUCCAAGCCGAAGGUGGCCACCC
.----........................-----...........((((...)))).(.((((((.(((.....)))(((.....)))..)))))).).... ( -22.80)
>DroSim_CAF1 2008 91 - 1
A----GUACA--AUGCUUAACCCCCAAUU-----UAUCCAUCUUGCAGGCACCCUGCGACCACCUGGCCUAAUUGGCGGCUCCAAGCCGAAGGUGGCCACCC
.----.....--.................-----........(((((((...)))))))((((((.(((.....)))(((.....)))..))))))...... ( -27.40)
>DroEre_CAF1 1958 70 - 1
---------------------------UU-----UAUCCAUCUUGCAGGCACCCUGCGACCACCUGGCCUAAUUGGCGGCUCCAAGCCGAAGGUGGCCACCC
---------------------------..-----........(((((((...)))))))((((((.(((.....)))(((.....)))..))))))...... ( -27.40)
>DroYak_CAF1 2055 100 - 1
ACCAUGUACC--AUGUCUAACCCGCAAUUUACCAUAUCCAUCUUGCAGGCACCCUGCGACCACCUGGCCUAAUUGGCGGCUCCAAGCCGAAGGUGGCCACCC
..((((...)--)))...........................(((((((...)))))))((((((.(((.....)))(((.....)))..))))))...... ( -27.90)
>DroAna_CAF1 1683 91 - 1
A----AUACA--AGUUUCAAUCCACAAUC-----UCUUUUCUUUGCAGGCACGCUGCGACCUCCGGGCCUAAUAGGAGGCUCCAAGCCCAAAGUGGCCACCC
.----.....--.........((((....-----........((((((.....)))))).....((((((......)))).)).........))))...... ( -20.50)
>consensus
A____GUACA__AUGUUUAACCCCCAAUU_____UAUCCAUCUUGCAGGCACCCUGCGACCACCUGGCCUAAUUGGCGGCUCCAAGCCGAAGGUGGCCACCC
..........................................((((((.....))))))((((((.(((.....)))(((.....)))..))))))...... (-22.30 = -23.13 +   0.83)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:27 2006