Locus 8927

Sequence ID 3R_DroMel_CAF1
Location 23,942,191 – 23,942,315
Length 124
Max. P 0.812998
window14313 window14314

overview

Window 3

Location 23,942,191 – 23,942,281
Length 90
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.96
Mean single sequence MFE -33.32
Consensus MFE -20.56
Energy contribution -19.78
Covariance contribution -0.77
Combinations/Pair 1.26
Mean z-score -2.23
Structure conservation index 0.62
SVM decision value 0.65
SVM RNA-class probability 0.812998
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23942191 90 + 27905053
---------------GCCAUGAUAUCAGCGCUGUAAUUAAUUGCGGCCGCUGCAUUUCUGGGUGGCCAUGGCAAUUGUGGCGUGCAAAUUAAAAGCCAGCAGG--------------CA-
---------------(((..((.(((((((((((((....)))))).))))).)).))..(.((((((((.((....)).))))..........)))).).))--------------).- ( -30.10)
>DroPse_CAF1 155582 105 + 1
GUACUGCGGCAGUGUGGCAUGAUAUCAGCGCCGUAAUUAAUUGCGGCCGCUGCAUUUCAGGGUGGCCAUGGCAAUUGUGGCGUGCAAAUUAAAAACCAGCAAG--------------AG-
((((.((.((((((((((.(((.(((((((((((((....)))))).))))).)).))).....)))))....))))).))))))..................--------------..- ( -37.20)
>DroGri_CAF1 116128 91 + 1
---------------GGCAUGAUAUCAGGGCUGUAAUUAAUUGUGGCCGCUGCAUUUCGGGGCGGCCAUGGUAAUUGUGGCGUGCAAAUUAAAAGCCAGCAAG--------------CAG
---------------(((.((((....(.((..((((((.(..((((((((.(.....).))))))))..)))))))..)).)....))))...)))......--------------... ( -35.50)
>DroWil_CAF1 186592 90 + 1
---------------GGCAUGAUAUCAGCGCUGUAAUUAAUUGCGGCCGCUGCAUUUUGGGGUGGCCAUGGUAAUUGUGGCAUGGAAAUUAAAAGCCAGCAAA--------------GA-
---------------(((.((((.((...((..((((((.....(((((((.(.....).)))))))....))))))..))...)).))))...)))......--------------..- ( -30.60)
>DroMoj_CAF1 161149 105 + 1
---------------GGCAUGAUAUCAGGACUGUAAUUAAUUGUGGCCGCUGCAUUUCGGGGUGGCCAUGGUAAUUGUGGCGUGCAAAUUAAAAGCCAGCAAGCCAGCGCGAAGGAACAG
---------------(((.((((..((.(.(..((((((.(..((((((((.(.....).))))))))..)))))))..)).))...))))...))).((......))............ ( -32.90)
>DroPer_CAF1 156116 100 + 1
-----GCGGCAGUGUGGCAUGAUAUCAGCGCCGUAAUUAAUUGCGGCCGCUGCAUUUCAGGGUGGCCAUGGCAAUUGUGGCGUGCAAAUUAAAAACCAGCAAG--------------AG-
-----((.((((((((((.(((.(((((((((((((....)))))).))))).)).))).....)))))....))))).)).(((.............)))..--------------..- ( -33.62)
>consensus
_______________GGCAUGAUAUCAGCGCUGUAAUUAAUUGCGGCCGCUGCAUUUCGGGGUGGCCAUGGCAAUUGUGGCGUGCAAAUUAAAAGCCAGCAAG______________CA_
................(((((.(((.(..(((((((....))))(((((((.........)))))))..)))..).))).)))))................................... (-20.56 = -19.78 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 4

Location 23,942,216 – 23,942,315
Length 99
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 80.54
Mean single sequence MFE -27.88
Consensus MFE -17.33
Energy contribution -17.34
Covariance contribution 0.00
Combinations/Pair 1.22
Mean z-score -1.46
Structure conservation index 0.62
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23942216 99 + 27905053
UUGCGGCCGCUGCAUUUCUGGGUGGCCAUGGCAAUUGUGGCGUGCAAAUUAAAAGCCAGCAGG--------------CA-----AAAGCUUGUUCUGCGAAAAAGUUGAGUAAAACAA
(((((((((((.((....)))))))))....(((((.((((.............))))(((((--------------((-----(....))).))))).....))))).))))..... ( -29.02)
>DroVir_CAF1 161239 100 + 1
UUGUGGCCGCUGCAUUUCGGGGUGGCCAUGGUAAUUGUGGCGUGCAAAUUAAAAGCCAGCCAG--------------CAGAAAGAAAGCGUGUG----GAAAAAGUUGCGGAAAACAA
..(((((((((.(.....).))))))))).((((((.((((..((.........))..))))(--------------(.........)).....----.....))))))......... ( -27.70)
>DroPse_CAF1 155622 99 + 1
UUGCGGCCGCUGCAUUUCAGGGUGGCCAUGGCAAUUGUGGCGUGCAAAUUAAAAACCAGCAAG--------------AG-----AGCGGUUGUUCUACGAAAAAGUUGUAAAAAACAA
..(((((((((((((.(((.(((.((....)).))).))).))))...........(.....)--------------..-----)))))))))..(((((.....)))))........ ( -24.90)
>DroGri_CAF1 116153 100 + 1
UUGUGGCCGCUGCAUUUCGGGGCGGCCAUGGUAAUUGUGGCGUGCAAAUUAAAAGCCAGCAAG--------------CAGAAAGAAAGCGUGUG----GAAAAAGUUGAGAAGAGCAA
(..((((((((.(.....).))))))))..)...(((((((.............)))).)))(--------------(........(((...(.----...)..))).......)).. ( -27.58)
>DroMoj_CAF1 161174 113 + 1
UUGUGGCCGCUGCAUUUCGGGGUGGCCAUGGUAAUUGUGGCGUGCAAAUUAAAAGCCAGCAAGCCAGCGCGAAGGAACAGAAAGAAAGCGUGUG----GAA-AAGUUGCGAAAAAAAA
..(((((((((.(.....).))))))))).((((((.((((.(((.............))).))))((((.................))))...----...-.))))))......... ( -33.15)
>DroPer_CAF1 156151 99 + 1
UUGCGGCCGCUGCAUUUCAGGGUGGCCAUGGCAAUUGUGGCGUGCAAAUUAAAAACCAGCAAG--------------AG-----AGCGGUUGUUCUACGAAAAAGUUGUAAAAAACAA
..(((((((((((((.(((.(((.((....)).))).))).))))...........(.....)--------------..-----)))))))))..(((((.....)))))........ ( -24.90)
>consensus
UUGCGGCCGCUGCAUUUCGGGGUGGCCAUGGCAAUUGUGGCGUGCAAAUUAAAAGCCAGCAAG______________CA_____AAAGCGUGUG____GAAAAAGUUGAGAAAAACAA
(((((((((((.........)))))))..........((((.............))))))))..........................................(((......))).. (-17.33 = -17.34 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:52 2006