Locus 9923

Sequence ID 3R_DroMel_CAF1
Location 26,549,065 – 26,549,156
Length 91
Max. P 0.877663
window15820 window15821

overview

Window 0

Location 26,549,065 – 26,549,156
Length 91
Sequences 5
Columns 91
Reading direction forward
Mean pairwise identity 80.46
Mean single sequence MFE -17.92
Consensus MFE -12.84
Energy contribution -12.80
Covariance contribution -0.04
Combinations/Pair 1.19
Mean z-score -1.94
Structure conservation index 0.72
SVM decision value 0.90
SVM RNA-class probability 0.877663
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26549065 91 + 27905053
CGCUCCAUUCUAGACUCACACUUUGUGUGGGCUUUGUUCUUGGCCAUAACGUCGCCAAUAUGAAGUACCCGCGAACAUUUCUUUUUCCUUA
(((...........(((((((...)))))))(((..(..(((((.........))))).)..))).....))).................. ( -18.50)
>DroSec_CAF1 133191 74 + 1
CGCUCCAUUCUAGACCCACACUUUGUGUGGGCUUUGUUCUUGGCCAUAAUGUCGCCAAUA-----------------UUCCUUUUUCCUUA
...........((.(((((((...)))))))))......(((((.........)))))..-----------------.............. ( -15.40)
>DroSim_CAF1 134859 74 + 1
CGCUCCAUUCUAGACCCACACUUUGUGUGGGCUUUGUUCUUGGCCAUAAUGUCGCCAAUA-----------------UUCCUUUUUCCUUA
...........((.(((((((...)))))))))......(((((.........)))))..-----------------.............. ( -15.40)
>DroEre_CAF1 144024 91 + 1
CGCUUUAUUCUAGACGCACACUUUGUGUGGGCUUUGUUCAUGGCCAUAACGUCGCCAAUUUUGAGUACCCGCGAACAUUUCUUUUUCCUUA
(((..(((((..(((((((((...)))))((((........))))....)))).........)))))...))).................. ( -19.20)
>DroYak_CAF1 140663 82 + 1
AGCUUUAUUCUAAACCCACACUUUGUGUGGGCUUUGUUCUUGGUCAUAACGUCGCCAAUUUGGAGUAU---------UUGUUGUUUCCUUA
(((..((((((((((((((((...)))))))........(((((.........)))))))))))))).---------..)))......... ( -21.10)
>consensus
CGCUCCAUUCUAGACCCACACUUUGUGUGGGCUUUGUUCUUGGCCAUAACGUCGCCAAUAU__AGUA__________UUCCUUUUUCCUUA
..........(((((((((((...))))))).))))...(((((.........)))))................................. (-12.84 = -12.80 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 26,549,065 – 26,549,156
Length 91
Sequences 5
Columns 91
Reading direction reverse
Mean pairwise identity 80.46
Mean single sequence MFE -18.27
Consensus MFE -12.72
Energy contribution -12.96
Covariance contribution 0.24
Combinations/Pair 1.12
Mean z-score -1.63
Structure conservation index 0.70
SVM decision value 0.22
SVM RNA-class probability 0.637665
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26549065 91 - 27905053
UAAGGAAAAAGAAAUGUUCGCGGGUACUUCAUAUUGGCGACGUUAUGGCCAAGAACAAAGCCCACACAAAGUGUGAGUCUAGAAUGGAGCG
...............((((..((((........(((((.(.....).))))).......)))).(((.....)))...........)))). ( -18.96)
>DroSec_CAF1 133191 74 - 1
UAAGGAAAAAGGAA-----------------UAUUGGCGACAUUAUGGCCAAGAACAAAGCCCACACAAAGUGUGGGUCUAGAAUGGAGCG
..............-----------------.....((..((((.(((...........((((((((...))))))))))).))))..)). ( -18.80)
>DroSim_CAF1 134859 74 - 1
UAAGGAAAAAGGAA-----------------UAUUGGCGACAUUAUGGCCAAGAACAAAGCCCACACAAAGUGUGGGUCUAGAAUGGAGCG
..............-----------------.....((..((((.(((...........((((((((...))))))))))).))))..)). ( -18.80)
>DroEre_CAF1 144024 91 - 1
UAAGGAAAAAGAAAUGUUCGCGGGUACUCAAAAUUGGCGACGUUAUGGCCAUGAACAAAGCCCACACAAAGUGUGCGUCUAGAAUAAAGCG
..............(((((((.(((.......))).))((((....(((..........)))(((((...)))))))))..)))))..... ( -16.80)
>DroYak_CAF1 140663 82 - 1
UAAGGAAACAACAA---------AUACUCCAAAUUGGCGACGUUAUGACCAAGAACAAAGCCCACACAAAGUGUGGGUUUAGAAUAAAGCU
...(....).....---------..........((((((......)).)))).....((((((((((...))))))))))........... ( -18.00)
>consensus
UAAGGAAAAAGAAA__________UACU__AUAUUGGCGACGUUAUGGCCAAGAACAAAGCCCACACAAAGUGUGGGUCUAGAAUGGAGCG
....................................((..((((.(((...........((((((((...))))))))))).))))..)). (-12.72 = -12.96 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:44:58 2006