Locus 8578

Sequence ID 3R_DroMel_CAF1
Location 22,941,434 – 22,941,554
Length 120
Max. P 0.565346
window13778 window13779

overview

Window 8

Location 22,941,434 – 22,941,554
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.44
Mean single sequence MFE -27.28
Consensus MFE -23.21
Energy contribution -24.02
Covariance contribution 0.81
Combinations/Pair 1.07
Mean z-score -1.59
Structure conservation index 0.85
SVM decision value 0.06
SVM RNA-class probability 0.565346
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22941434 120 + 27905053
ACUUUUUGUCCUUUUUGCUAGUGGAGGACUUCUUCUUUUUAGGCUUCUUGAUACCGUCGGCUGUCUUUUCCAGCCAAACAUCUUCCUCCUCGGACUCAUCUUCGCUGUCAGAACUGGAAC
........(((.(((((.((((((((((.............(((...........)))(((((.......)))))........))))))..(((......))))))).)))))..))).. ( -28.00)
>DroSec_CAF1 3055 120 + 1
ACUUUUUGUCCUGUUUGCUGGCGGAGGACUUCUUCUUUUUAGGCUUCUUGAUACCGUCGGCUGUCUUUUCCAGCCAAACAUCUUCCUCCUCGGACUCAUCUUCGCUGUCAGAACUGGAAC
........(((.((...(((((((((((.............(((...........)))(((((.......)))))........)))))).((((......))))..))))).)).))).. ( -30.80)
>DroSim_CAF1 3074 120 + 1
ACUUUUUGUCCUUUUUGCUAGCGGAGGACUUCUUCUUUUUAGGCUUCUUGAUACCGUCGGCUGUCUUUUCCAGCCAAACAUCUUCCUCCUCGGACUCAUCUUCGCUGUCAGAACUGGAAC
........(((.(((((.((((((((((.............(((...........)))(((((.......)))))........))))))..(((......))))))).)))))..))).. ( -30.70)
>DroYak_CAF1 3105 118 + 1
ACUUUUUGUCCUUUUUGCUGGCAGACGACUUUUUCUUUUUAGGCUUCUUGAUACCGUCGGCAGUCUUUUCCAGCCACACAUCUUCAUCCUCGGACUCAUCUUCGCUUUCCGAACUGGA--
........(((.....(((((.(((.((((....((....))(((...((....))..))))))).))))))))...............(((((.............)))))...)))-- ( -19.62)
>consensus
ACUUUUUGUCCUUUUUGCUAGCGGAGGACUUCUUCUUUUUAGGCUUCUUGAUACCGUCGGCUGUCUUUUCCAGCCAAACAUCUUCCUCCUCGGACUCAUCUUCGCUGUCAGAACUGGAAC
........(((..((((.((((((((((.............(((...........)))(((((.......)))))........))))))..(((......))))))).))))...))).. (-23.21 = -24.02 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 22,941,434 – 22,941,554
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -29.50
Consensus MFE -26.76
Energy contribution -26.70
Covariance contribution -0.06
Combinations/Pair 1.08
Mean z-score -1.43
Structure conservation index 0.91
SVM decision value 0.06
SVM RNA-class probability 0.563271
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22941434 120 - 27905053
GUUCCAGUUCUGACAGCGAAGAUGAGUCCGAGGAGGAAGAUGUUUGGCUGGAAAAGACAGCCGACGGUAUCAAGAAGCCUAAAAAGAAGAAGUCCUCCACUAGCAAAAAGGACAAAAAGU
......(((((....((...((....))...((((((......(((((((.......))))))).(((........))).............))))))....))....)))))....... ( -30.00)
>DroSec_CAF1 3055 120 - 1
GUUCCAGUUCUGACAGCGAAGAUGAGUCCGAGGAGGAAGAUGUUUGGCUGGAAAAGACAGCCGACGGUAUCAAGAAGCCUAAAAAGAAGAAGUCCUCCGCCAGCAAACAGGACAAAAAGU
......((((((...((...((....))...((((((......(((((((.......))))))).(((........))).............))))))....))...))))))....... ( -32.00)
>DroSim_CAF1 3074 120 - 1
GUUCCAGUUCUGACAGCGAAGAUGAGUCCGAGGAGGAAGAUGUUUGGCUGGAAAAGACAGCCGACGGUAUCAAGAAGCCUAAAAAGAAGAAGUCCUCCGCUAGCAAAAAGGACAAAAAGU
........(((........)))...((((..((((((......(((((((.......))))))).(((........))).............))))))(....).....))))....... ( -30.30)
>DroYak_CAF1 3105 118 - 1
--UCCAGUUCGGAAAGCGAAGAUGAGUCCGAGGAUGAAGAUGUGUGGCUGGAAAAGACUGCCGACGGUAUCAAGAAGCCUAAAAAGAAAAAGUCGUCUGCCAGCAAAAAGGACAAAAAGU
--(((..((((((...(......)..))))))..............(((((...((((.......(((........)))......((.....)))))).))))).....)))........ ( -25.70)
>consensus
GUUCCAGUUCUGACAGCGAAGAUGAGUCCGAGGAGGAAGAUGUUUGGCUGGAAAAGACAGCCGACGGUAUCAAGAAGCCUAAAAAGAAGAAGUCCUCCGCCAGCAAAAAGGACAAAAAGU
......(((((....((...((....))...((((((....((.((((((.......))))))))(((........))).............))))))....))....)))))....... (-26.76 = -26.70 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:14:30 2006