Locus 1873

Sequence ID 3L_DroMel_CAF1
Location 5,238,491 – 5,238,596
Length 105
Max. P 0.973249
window2918 window2919

overview

Window 8

Location 5,238,491 – 5,238,596
Length 105
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 92.05
Mean single sequence MFE -25.00
Consensus MFE -21.07
Energy contribution -21.40
Covariance contribution 0.33
Combinations/Pair 1.18
Mean z-score -2.78
Structure conservation index 0.84
SVM decision value 1.71
SVM RNA-class probability 0.973249
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5238491 105 + 23771897
UGUGAGGGCAACCACACUAUAUCACUAUAUCAC-------AUCUCUUACAAAGAAAUCUUCGUAAUGCAACUCAGCAAUAAGCUAAGUAACUGCCAUCCUGUGGCAAGAGAA
(((((((....))....((((....))))))))-------)((((((((.(((....))).))).....(((.(((.....))).)))...((((((...))))))))))). ( -25.90)
>DroSec_CAF1 102902 105 + 1
UGUGAGGGCAACCACACUAUAUCACUAUAUCAC-------AUCUCUUUCAAAGAAAUCUUCGUAAUGCAACUCAGCAAUAAGCUAAGUAACUGCCAUCCUGUGGCAAGAGAA
(((((((....))....((((....))))))))-------)((((((......................(((.(((.....))).)))....(((((...))))))))))). ( -24.00)
>DroSim_CAF1 98970 105 + 1
UGUGAGGGCAACCACACUAUAUCACUAUAUCAC-------AUCUCUUACAAAGAAAUCUUCGUAAUGCAACUCAGCAAUAAGCUAAGUAACUGCCAUCCUGUGGCAAGAGAA
(((((((....))....((((....))))))))-------)((((((((.(((....))).))).....(((.(((.....))).)))...((((((...))))))))))). ( -25.90)
>DroEre_CAF1 105888 112 + 1
UGUGAGGGCAACCACACUAUAUCACUAUAUCUCUCUAACAAUCUCUUACAAAGAAAUCUUCGUAAUGCAACUCAGCAAUAAGCUAAGUAACUGCCAUCCUGUGGCGAGAGGA
.(((.((....)).)))............((((((..........((((.(((....))).))))....(((.(((.....))).)))....(((((...))))))))))). ( -28.50)
>DroYak_CAF1 105409 101 + 1
----AGGGCAACCACACUAUAUCACUAUAUCAC-------AUCUCUUACAAAGAAAUCUUCGUAAUGCAACUCAGCAAUAAGCUAAGUAACUGCCAUCCUGUGGCAAGAGAA
----.((....))....................-------.((((((((.(((....))).))).....(((.(((.....))).)))...((((((...))))))))))). ( -22.40)
>DroAna_CAF1 100309 104 + 1
UAUGAGGGCAACCGCACUAUAUCACUAUAUCAU-------AUCUAGGAUAAAGAAAUCUUUGUAAUGCAACUCGGCAAUAAGCUAAGUAACUGCCAUCCUGUGGCCAGAGA-
..((.((....)).))((.((((.(((......-------...))))))).))...((((((.......(((..((.....))..)))....(((((...)))))))))))- ( -23.30)
>consensus
UGUGAGGGCAACCACACUAUAUCACUAUAUCAC_______AUCUCUUACAAAGAAAUCUUCGUAAUGCAACUCAGCAAUAAGCUAAGUAACUGCCAUCCUGUGGCAAGAGAA
.(((.((....)).)))........................((((((......................(((.(((.....))).)))....(((((...))))))))))). (-21.07 = -21.40 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 5,238,491 – 5,238,596
Length 105
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 92.05
Mean single sequence MFE -32.20
Consensus MFE -27.02
Energy contribution -27.72
Covariance contribution 0.70
Combinations/Pair 1.12
Mean z-score -2.74
Structure conservation index 0.84
SVM decision value 1.56
SVM RNA-class probability 0.964215
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5238491 105 - 23771897
UUCUCUUGCCACAGGAUGGCAGUUACUUAGCUUAUUGCUGAGUUGCAUUACGAAGAUUUCUUUGUAAGAGAU-------GUGAUAUAGUGAUAUAGUGUGGUUGCCCUCACA
.((((.(((((.....)))))((.(((((((.....))))))).)).((((((((....)))))))))))).-------....((((....))))(((.((....)).))). ( -34.40)
>DroSec_CAF1 102902 105 - 1
UUCUCUUGCCACAGGAUGGCAGUUACUUAGCUUAUUGCUGAGUUGCAUUACGAAGAUUUCUUUGAAAGAGAU-------GUGAUAUAGUGAUAUAGUGUGGUUGCCCUCACA
.((((((((((.....)))).((.(((((((.....))))))).))....(((((....))))).)))))).-------....((((....))))(((.((....)).))). ( -32.20)
>DroSim_CAF1 98970 105 - 1
UUCUCUUGCCACAGGAUGGCAGUUACUUAGCUUAUUGCUGAGUUGCAUUACGAAGAUUUCUUUGUAAGAGAU-------GUGAUAUAGUGAUAUAGUGUGGUUGCCCUCACA
.((((.(((((.....)))))((.(((((((.....))))))).)).((((((((....)))))))))))).-------....((((....))))(((.((....)).))). ( -34.40)
>DroEre_CAF1 105888 112 - 1
UCCUCUCGCCACAGGAUGGCAGUUACUUAGCUUAUUGCUGAGUUGCAUUACGAAGAUUUCUUUGUAAGAGAUUGUUAGAGAGAUAUAGUGAUAUAGUGUGGUUGCCCUCACA
..(((((((((.....)))).((.(((((((.....))))))).)).((((((((....))))))))..........))))).((((....))))(((.((....)).))). ( -37.50)
>DroYak_CAF1 105409 101 - 1
UUCUCUUGCCACAGGAUGGCAGUUACUUAGCUUAUUGCUGAGUUGCAUUACGAAGAUUUCUUUGUAAGAGAU-------GUGAUAUAGUGAUAUAGUGUGGUUGCCCU----
...(((((...))))).(((((..((...((((((..(((.((..((((((((((....))))))....)))-------)..)).)))..))).)))))..)))))..---- ( -30.60)
>DroAna_CAF1 100309 104 - 1
-UCUCUGGCCACAGGAUGGCAGUUACUUAGCUUAUUGCCGAGUUGCAUUACAAAGAUUUCUUUAUCCUAGAU-------AUGAUAUAGUGAUAUAGUGCGGUUGCCCUCAUA
-...(((....)))((.(((((..(((..((.....))..)))(((((((.((((....))))((((((...-------......))).))).))))))).))))).))... ( -24.10)
>consensus
UUCUCUUGCCACAGGAUGGCAGUUACUUAGCUUAUUGCUGAGUUGCAUUACGAAGAUUUCUUUGUAAGAGAU_______GUGAUAUAGUGAUAUAGUGUGGUUGCCCUCACA
...((((((((.....)))).((.(((((((.....))))))).)).((((((((....))))))))))))............((((....))))(((.((....)).))). (-27.02 = -27.72 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:49 2006