Locus 8905

Sequence ID 3R_DroMel_CAF1
Location 23,889,575 – 23,889,667
Length 92
Max. P 0.998736
window14285 window14286

overview

Window 5

Location 23,889,575 – 23,889,667
Length 92
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 76.67
Mean single sequence MFE -27.55
Consensus MFE -20.80
Energy contribution -20.55
Covariance contribution -0.25
Combinations/Pair 1.26
Mean z-score -2.59
Structure conservation index 0.75
SVM decision value 3.21
SVM RNA-class probability 0.998736
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23889575 92 + 27905053
CA-ACCCCCUGCGCCGGAUCCCAGC-----CCAA-UCCAACCCGUUCCACCCCCUUUGACAAACGCUUACAGCAGCGUUAAAUGUUCACCGGGGGUGGC
..-......((.((.((...)).))-----.)).-...........((((((((..(((((((((((......))))))...)).)))..)))))))). ( -28.60)
>DroSec_CAF1 95539 98 + 1
CA-UCCCCCUGCGCCGGAUCCCAGUCCAACCCAAGCCCAACCCGUUCCACCCCUUUUGACAAACGCUUACAGCAGCGUUAAAUGUUCACCGGGGGUGGC
..-............((((....))))...................((((((((..(((((((((((......))))))...)).)))..)))))))). ( -27.80)
>DroSim_CAF1 98100 97 + 1
CA-UCCCCCUGCGCCCAAUCCCAACGCAGCCCAA-CCCAACCCGUUCCACCCCCUUUGACAAACGCUUACAGCAGCGUUAAAUGUUCACCGGGGGUGGC
..-.....(((((...........))))).....-...........((((((((..(((((((((((......))))))...)).)))..)))))))). ( -31.20)
>DroAna_CAF1 103491 85 + 1
UGCUCCCCCU---CGGGACCU---------CUAA-UCUCUCCCUGCCCCCUUUUUUUGGCAAACGCUCACAGCAGCGUUAAAUGUUCAUUGGGG-UGAC
...((((((.---..((((..---------....-........((((..........))))((((((......))))))....))))...))))-.)). ( -22.60)
>consensus
CA_UCCCCCUGCGCCGGAUCCCAGC_____CCAA_CCCAACCCGUUCCACCCCCUUUGACAAACGCUUACAGCAGCGUUAAAUGUUCACCGGGGGUGGC
..............................................((((((((..(((((((((((......))))))...)).)))..)))))))). (-20.80 = -20.55 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 23,889,575 – 23,889,667
Length 92
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 76.67
Mean single sequence MFE -36.25
Consensus MFE -21.71
Energy contribution -24.27
Covariance contribution 2.56
Combinations/Pair 1.21
Mean z-score -2.07
Structure conservation index 0.60
SVM decision value 1.03
SVM RNA-class probability 0.902830
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23889575 92 - 27905053
GCCACCCCCGGUGAACAUUUAACGCUGCUGUAAGCGUUUGUCAAAGGGGGUGGAACGGGUUGGA-UUGG-----GCUGGGAUCCGGCGCAGGGGGU-UG
.((((((((..(((.((...((((((......)))))))))))..))))))))...(.((((((-((..-----.....)))))))).).......-.. ( -40.70)
>DroSec_CAF1 95539 98 - 1
GCCACCCCCGGUGAACAUUUAACGCUGCUGUAAGCGUUUGUCAAAAGGGGUGGAACGGGUUGGGCUUGGGUUGGACUGGGAUCCGGCGCAGGGGGA-UG
.(((((((...(((.((...((((((......)))))))))))...)))))))...(.((((((((..(......)..)).)))))).).......-.. ( -39.20)
>DroSim_CAF1 98100 97 - 1
GCCACCCCCGGUGAACAUUUAACGCUGCUGUAAGCGUUUGUCAAAGGGGGUGGAACGGGUUGGG-UUGGGCUGCGUUGGGAUUGGGCGCAGGGGGA-UG
.((((((((..(((.((...((((((......)))))))))))..))))))))...........-.....(((((((.......))))))).....-.. ( -39.00)
>DroAna_CAF1 103491 85 - 1
GUCA-CCCCAAUGAACAUUUAACGCUGCUGUGAGCGUUUGCCAAAAAAAGGGGGCAGGGAGAGA-UUAG---------AGGUCCCG---AGGGGGAGCA
((..-((((...........((((((......))))))((((..........))))((((....-....---------...)))).---.))))..)). ( -26.10)
>consensus
GCCACCCCCGGUGAACAUUUAACGCUGCUGUAAGCGUUUGUCAAAAGGGGUGGAACGGGUUGGA_UUGG_____GCUGGGAUCCGGCGCAGGGGGA_UG
.((((((((..(((......((((((......))))))..)))..))))))))...(.((((((.((.((.....)).)).)))))).).......... (-21.71 = -24.27 +   2.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:26 2006