Locus 10064

Sequence ID 3R_DroMel_CAF1
Location 26,959,552 – 26,959,682
Length 130
Max. P 0.934978
window16029 window16030

overview

Window 9

Location 26,959,552 – 26,959,648
Length 96
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 80.79
Mean single sequence MFE -22.89
Consensus MFE -12.54
Energy contribution -12.77
Covariance contribution 0.22
Combinations/Pair 1.17
Mean z-score -2.23
Structure conservation index 0.55
SVM decision value 0.33
SVM RNA-class probability 0.691706
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26959552 96 + 27905053
UAAAUAAGAAUGGCAAUAAAUAACGCCGAAAACGGAA-GUU-GGUGCGAGGUGACGCUGGAA------------AAUUGUAUGCAAAGUAAACACUUGCCGGUAAAAAUU
.......................(((....(((....-)))-...))).(....)(((((..------------...(((.(((...))).)))....)))))....... ( -17.20)
>DroSec_CAF1 7156 98 + 1
UAAAUAAGAAUGGCAAUAAAUAACGCCGGAAACGGAAAGUUGGGUGCGAGGUGGCGCUGGAA------------GAGCGAAUGCAAAGCAAACACUUGCCGGGGAAAAUU
..........((((((.....(((.(((....)))...)))(..(((...((..((((....------------.))))...))...)))..)..))))))......... ( -27.90)
>DroSim_CAF1 7447 96 + 1
UAAAUAAGAAUGGCAAUAAAUAACGCCGGAAACGGAA-GUU-GGUGCGAGGUGGCGCUGGAA------------AAGCGAAUGCAAAGCAAACACUUGCCGGGGAAAAUU
..........((((((....((((.(((....)))..-)))-).(((...((..((((....------------.))))...))...))).....))))))......... ( -26.30)
>DroEre_CAF1 9369 85 + 1
UAAAUAAGAAUGGCAAUAAAUAACGCCGGAAACGGAA-GUU-GGUGCGAGGUGGCGCUGGAA------------A-----------UGUAAACACUUGCAGGGGAAAAUU
............((((.........(((....)))..-.(.-.((((......))))..)..------------.-----------.........))))........... ( -18.00)
>DroYak_CAF1 7190 96 + 1
UAAAUAAGAAUGGCAAUAAAUAACGCCGGAAACGGAA-GUU-GGUGCGAGGUGGCGCUGGAG------------AAGCGAAUGCAGAGUAAACACUUGCAGGGGGAAAUU
............(((.....((((.(((....)))..-)))-).))).......((((....------------.))))..((((.(((....))))))).......... ( -21.20)
>DroAna_CAF1 7290 106 + 1
UAAAUAAAGCCGGCAAUAAAUAACGCCGGAAACGGAA-GUG-GGCCC--GGUGGUGUUGGCAGUGGUGAGGGCUAAGUGAAUGCAAAGCAAAUAAAUGCAAACGAAAAUU
........(((((((........((((((..((....-)).-...))--)))).))))))).(((......(((..((....))..))).......)))........... ( -26.72)
>consensus
UAAAUAAGAAUGGCAAUAAAUAACGCCGGAAACGGAA_GUU_GGUGCGAGGUGGCGCUGGAA____________AAGCGAAUGCAAAGCAAACACUUGCAGGGGAAAAUU
............((((.........(((....))).......(((((......))))).....................................))))........... (-12.54 = -12.77 +   0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 26,959,588 – 26,959,682
Length 94
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 77.73
Mean single sequence MFE -27.05
Consensus MFE -14.16
Energy contribution -14.72
Covariance contribution 0.56
Combinations/Pair 1.26
Mean z-score -2.39
Structure conservation index 0.52
SVM decision value 1.24
SVM RNA-class probability 0.934978
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26959588 94 + 27905053
A-GUU-GGUGCGAGGUGACGCUGGAAAAUUGUAUGCAAAGUAAACACUUGCCGG-----UAAAAA-UUCAGCGGGUGAUUUG-AUCCGCAUCCAACAAAUCAA
.-(((-(((((..(....)...(((...(((....)))..(((((((((((.((-----......-.)).))))))).))))-.)))))).)))))....... ( -26.70)
>DroPse_CAF1 7081 98 + 1
A-GUU-GA-GCGA--UUAGGGAGAUGAAGUGAAUGCAGAGCAAACAAUAGCAGAAAGAAGGAAAAUUCGAGCGAAUGAUUAACAGGCGCUUCUGGAAAAUGGA
.-(((-..-(((.--(((...........))).)))..))).........(((((.(((......)))..(((..((.....))..))))))))......... ( -13.60)
>DroSec_CAF1 7192 96 + 1
AAGUUGGGUGCGAGGUGGCGCUGGAAGAGCGAAUGCAAAGCAAACACUUGCCGG-----GGAAAA-UUGAGCGGGUGAUUUG-AUCCGCAUCCAACAAAUCAA
..((((((((((.(((..((((.....)))).........((((((((((((((-----......-))).))))))).))))-)))))))))))))....... ( -36.10)
>DroSim_CAF1 7483 94 + 1
A-GUU-GGUGCGAGGUGGCGCUGGAAAAGCGAAUGCAAAGCAAACACUUGCCGG-----GGAAAA-UUGAGCGGGUGAUUUG-AUCCGCAUCCAACAAAUCAA
.-(((-((((((.(((..((((.....)))).........((((((((((((((-----......-))).))))))).))))-))))))).)))))....... ( -32.30)
>DroEre_CAF1 9405 83 + 1
A-GUU-GGUGCGAGGUGGCGCUGGAAA-----------UGUAAACACUUGCAGG-----GGAAAA-UUGAGCGGGUGAUUUG-AUCCGCAUCCAACAAAUCAA
.-(((-((((((((((...((......-----------.))..)).))))))..-----......-....((((((......-))))))..)))))....... ( -24.20)
>DroYak_CAF1 7226 94 + 1
A-GUU-GGUGCGAGGUGGCGCUGGAGAAGCGAAUGCAGAGUAAACACUUGCAGG-----GGGAAA-UUGAGCGGGUGAUUUG-AUCCGCAACCAACAAAUCAA
.-(((-((((((((((.((.(((.(........).))).))..)).)))))...-----......-....((((((......-)))))).))))))....... ( -29.40)
>consensus
A_GUU_GGUGCGAGGUGGCGCUGGAAAAGCGAAUGCAAAGCAAACACUUGCAGG_____GGAAAA_UUGAGCGGGUGAUUUG_AUCCGCAUCCAACAAAUCAA
..(((.((((((.......(((................)))...(((((((...................))))))).........)))))).)))....... (-14.16 = -14.72 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:48:07 2006