Locus 3518

Sequence ID X_DroMel_CAF1
Location 9,436,452 – 9,436,571
Length 119
Max. P 0.807600
window5763 window5764

overview

Window 3

Location 9,436,452 – 9,436,571
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.84
Mean single sequence MFE -30.90
Consensus MFE -16.73
Energy contribution -18.29
Covariance contribution 1.56
Combinations/Pair 1.04
Mean z-score -2.25
Structure conservation index 0.54
SVM decision value 0.09
SVM RNA-class probability 0.577109
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9436452 119 + 22224390
UGCCCUUGAUUGUGGCAUUUCUGAACCAUCUGAAUGCCACACAGCUAGUCUUAUCUGCCUUAGCUGCCACUUGCAGCUAAUCAGCAGCUUACGCACUCUCGAUGCAAUCGCAGUGCAUU-
..........((((((((((..((....)).)))))))))).............((((.((((((((.....))))))))...)))).....(((((..((((...)))).)))))...- ( -37.40)
>DroSec_CAF1 18056 118 + 1
UGCCCUUGAUUGUGGCACUUCC--ACCCCCUGAAUGCCACCCGGCUAGUCUUAUCUGCCUUAGCUGCCACUUGCAGCUUAUCAGCAGCUCACGCACUCUCGAUGCAAUCGCAGUGCAUCG
.((..(((((.((((((.(((.--.......)))))))))..(((.((......)))))..((((((.....)))))).)))))..))....(((((..((((...)))).))))).... ( -35.00)
>DroEre_CAF1 18431 97 + 1
UGCCCUUGAUUGUGGCAUUUCC----------------AUCCAGCCAUUCUUAUCAGCC------UCCACUUGCAGCUUAUCAGCAGCUCACGCACUCUCGAUGCAAUCGCAGUGCAUC-
.....(((((.(((((......----------------.....)))))....)))))..------.......((.(((....))).))....(((((..((((...)))).)))))...- ( -20.10)
>DroYak_CAF1 18981 111 + 1
UGCCCUUGAUUGUGGCAUUUCC--AGCCCCUGAAAGCCACCCAGCUACUCUUAUCAGCC------GCCACUUGCGGCUUAUCAGCAGCUCACGCCCUCUCGAUGCAAUCGCAGUGCAUC-
(((.((((((((((((.((((.--.......)))))))....((((.((..((..((((------((.....))))))))..)).))))..............))))))).)).)))..- ( -31.10)
>consensus
UGCCCUUGAUUGUGGCAUUUCC__ACCCCCUGAAUGCCACCCAGCUAGUCUUAUCAGCC______GCCACUUGCAGCUUAUCAGCAGCUCACGCACUCUCGAUGCAAUCGCAGUGCAUC_
(((.(((((((((((((..............((..((......))...))..............))))))..((((((....))).((....))........)))))))).)).)))... (-16.73 = -18.29 +   1.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,436,452 – 9,436,571
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.84
Mean single sequence MFE -39.27
Consensus MFE -23.11
Energy contribution -25.55
Covariance contribution 2.44
Combinations/Pair 1.11
Mean z-score -2.28
Structure conservation index 0.59
SVM decision value 0.64
SVM RNA-class probability 0.807600
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9436452 119 - 22224390
-AAUGCACUGCGAUUGCAUCGAGAGUGCGUAAGCUGCUGAUUAGCUGCAAGUGGCAGCUAAGGCAGAUAAGACUAGCUGUGUGGCAUUCAGAUGGUUCAGAAAUGCCACAAUCAAGGGCA
-.(((((((.((((...))))..)))))))...(((((..((((((((.....))))))))))))).........(((.((((((((((.((....)).).)))))))))......))). ( -44.50)
>DroSec_CAF1 18056 118 - 1
CGAUGCACUGCGAUUGCAUCGAGAGUGCGUGAGCUGCUGAUAAGCUGCAAGUGGCAGCUAAGGCAGAUAAGACUAGCCGGGUGGCAUUCAGGGGGU--GGAAGUGCCACAAUCAAGGGCA
..(((((((.((((...))))..)))))))..(((..((((.((((((.....))))))..(((((......)).)))..(((((((((.......--.).)))))))).))))..))). ( -43.10)
>DroEre_CAF1 18431 97 - 1
-GAUGCACUGCGAUUGCAUCGAGAGUGCGUGAGCUGCUGAUAAGCUGCAAGUGGA------GGCUGAUAAGAAUGGCUGGAU----------------GGAAAUGCCACAAUCAAGGGCA
-((((((.......))))))....((.(.(((((.(((....))).))..((((.------((((.........))))..((----------------....)).))))..))).).)). ( -25.70)
>DroYak_CAF1 18981 111 - 1
-GAUGCACUGCGAUUGCAUCGAGAGGGCGUGAGCUGCUGAUAAGCCGCAAGUGGC------GGCUGAUAAGAGUAGCUGGGUGGCUUUCAGGGGCU--GGAAAUGCCACAAUCAAGGGCA
-((((((.......))))))((...(((((.((((.((((.(((((((.(((.((------..((....)).)).)))..))))))))))).))))--....)))))....))....... ( -43.80)
>consensus
_GAUGCACUGCGAUUGCAUCGAGAGUGCGUGAGCUGCUGAUAAGCUGCAAGUGGC______GGCAGAUAAGACUAGCUGGGUGGCAUUCAGGGGGU__GGAAAUGCCACAAUCAAGGGCA
..(((((((.((((...))))..)))))))..(((..((((..((((....))))......(((((.......)))))..((((((((.............)))))))).))))..))). (-23.11 = -25.55 +   2.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:27 2006