Locus 3675

Sequence ID X_DroMel_CAF1
Location 9,821,469 – 9,821,627
Length 158
Max. P 0.837996
window6023 window6024

overview

Window 3

Location 9,821,469 – 9,821,587
Length 118
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 81.92
Mean single sequence MFE -39.80
Consensus MFE -30.48
Energy contribution -32.40
Covariance contribution 1.92
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.77
SVM decision value 0.74
SVM RNA-class probability 0.837996
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9821469 118 + 22224390
GCCUUAGAGUUGAUGGCUGAUAGCUUUUAGCUUUUGGCCCAAAGCGCGUUGAUGGCUAAACUGGCUGCUGUAUCUUGGGCUAAGGCUUAUCUGGCCAGAGCCAUCGAUUCGACGAACG
(((..((((((((.(((.....))).)))))))).))).....(((.((((((((((...((((((...(.....(((((....))))).).)))))))))))))))).)).)..... ( -42.60)
>DroSec_CAF1 22902 117 + 1
GCCUUAGAGUUGAUGGCUGAUAGAUUUUAGCUUUUGGCCCAAAGCGCGUUGAUGGCUGAACUGGCUGCUGUAUCUUGGGCUAAGGCUUAUCUGGCCAGAGCCAUCGAUCCG-CGAACG
......(.((..(.((((((......)))))).)..)).)...(((.((((((((((...((((((...(.....(((((....))))).).)))))))))))))))).))-)..... ( -42.50)
>DroEre_CAF1 14243 93 + 1
GGCUUAGAGCUGAUGGC-------UUUUAGCUUUCGGCCCA------------------ACUGGCUGCUGUAUCUUGGGCUAAGGCUUAUCUGGCCAGAGCCAUCGAUUCGACAAACG
......(((.(((((((-------(((........((((((------------------(...((....))...)))))))..((((.....)))))))))))))).)))........ ( -34.30)
>consensus
GCCUUAGAGUUGAUGGCUGAUAG_UUUUAGCUUUUGGCCCAAAGCGCGUUGAUGGCU_AACUGGCUGCUGUAUCUUGGGCUAAGGCUUAUCUGGCCAGAGCCAUCGAUUCGACGAACG
......((((((((((((...............((((((((((((.........)))......((....))...)))))))))((((.....))))..))))))))))))........ (-30.48 = -32.40 +   1.92)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 9,821,509 – 9,821,627
Length 118
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 87.01
Mean single sequence MFE -39.27
Consensus MFE -35.22
Energy contribution -35.00
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.36
Structure conservation index 0.90
SVM decision value 0.07
SVM RNA-class probability 0.568437
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9821509 118 + 22224390
AAAGCGCGUUGAUGGCUAAACUGGCUGCUGUAUCUUGGGCUAAGGCUUAUCUGGCCAGAGCCAUCGAUUCGACGAACGACCUUGAGACCGUUACCGGUUUCUUUGGGCCAGGCCACUC
...(((.((((((((((...((((((...(.....(((((....))))).).)))))))))))))))).)).)....(.(((.(((((((....)))))))...))).)......... ( -40.40)
>DroSec_CAF1 22942 117 + 1
AAAGCGCGUUGAUGGCUGAACUGGCUGCUGUAUCUUGGGCUAAGGCUUAUCUGGCCAGAGCCAUCGAUCCG-CGAACGACCUUGAGACCCUUACCGGUUUCUUUGGGCCAGGCCACUC
...(((.((((((((((...((((((...(.....(((((....))))).).)))))))))))))))).))-)....(.(((.((((((......))))))...))).)......... ( -41.90)
>DroEre_CAF1 14276 100 + 1
A------------------ACUGGCUGCUGUAUCUUGGGCUAAGGCUUAUCUGGCCAGAGCCAUCGAUUCGACAAACGACCUUGAGACCAUUACCGGUUUCUUUGGGCCAGGCCACUC
.------------------.(((((((.((.(((...((((..((((.....))))..))))...))).)).)).....((..((((((......))))))...)))))))....... ( -35.50)
>consensus
AAAGCGCGUUGAUGGCU_AACUGGCUGCUGUAUCUUGGGCUAAGGCUUAUCUGGCCAGAGCCAUCGAUUCGACGAACGACCUUGAGACCAUUACCGGUUUCUUUGGGCCAGGCCACUC
....................(((((((.((.(((...((((..((((.....))))..))))...))).)).)).....((..((((((......))))))...)))))))....... (-35.22 = -35.00 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:25 2006