Locus 7506

Sequence ID 3R_DroMel_CAF1
Location 20,057,200 – 20,057,305
Length 105
Max. P 0.987175
window12122 window12123

overview

Window 2

Location 20,057,200 – 20,057,305
Length 105
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 91.27
Mean single sequence MFE -26.38
Consensus MFE -22.52
Energy contribution -23.52
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.85
SVM decision value 1.43
SVM RNA-class probability 0.953020
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20057200 105 + 27905053
UUGUUGAUGUGUUUCUGUGCCGCCGCCGUCACCGCCGUGACCCUACACACCUUUGAAAAACACAUCAACAAAGUUGUUAAAUUCACUUGUAGUGAAAUUUAUUUG
((((((((((((((..(.((....)))(((((....)))))................))))))))))))))......(((((((((.....))).)))))).... ( -27.30)
>DroSec_CAF1 45669 105 + 1
UUGUUGAUGUGUUUCUGUGCCGCCGCCGUCACUGCCGUGCCCCUACACACCUUUGAAAAACACAUCAACAAAGUUGUUAAAUUCACUUGUAGUGAAAUUUAUUUU
((((((((((((((..(((.((....)).)))....(((......))).........))))))))))))))......(((((((((.....))).)))))).... ( -26.70)
>DroSim_CAF1 47931 105 + 1
UUGUUGAUGUGUUUCUGUGCCGCCGCCGUCACCGCCGUGCCCCUACACUCCUUUGAAAAACACAUCAACAAAGUUGUUAAAUUCACUUGUAGUGAAAUUUAUUUG
((((((((((((((..(((.((....)).)))....(((......))).........))))))))))))))......(((((((((.....))).)))))).... ( -25.80)
>DroYak_CAF1 48709 98 + 1
UUGUUGAUGUGUUUUUGUGCCGCCGCCG---CCGACGUGCCCC----CUCCCUUGAAAAACACAUCAACAAAGUUGUUAAAUUCACUUAGAGUGACAUUUACUUG
((((((((((((((((..((((.((...---.)).)).))...----(......)))))))))))))))))......(((((((((.....)))).))))).... ( -25.70)
>consensus
UUGUUGAUGUGUUUCUGUGCCGCCGCCGUCACCGCCGUGCCCCUACACACCUUUGAAAAACACAUCAACAAAGUUGUUAAAUUCACUUGUAGUGAAAUUUAUUUG
((((((((((((((..(((.((....)).)))....(((......))).........))))))))))))))......(((((((((.....)))).))))).... (-22.52 = -23.52 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 20,057,200 – 20,057,305
Length 105
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 91.27
Mean single sequence MFE -34.08
Consensus MFE -28.85
Energy contribution -29.91
Covariance contribution 1.06
Combinations/Pair 1.03
Mean z-score -3.65
Structure conservation index 0.85
SVM decision value 2.07
SVM RNA-class probability 0.987175
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20057200 105 - 27905053
CAAAUAAAUUUCACUACAAGUGAAUUUAACAACUUUGUUGAUGUGUUUUUCAAAGGUGUGUAGGGUCACGGCGGUGACGGCGGCGGCACAGAAACACAUCAACAA
....((((((.(((.....)))))))))......(((((((((((((((.......(((((.......((.((....)).))...)))))))))))))))))))) ( -34.81)
>DroSec_CAF1 45669 105 - 1
AAAAUAAAUUUCACUACAAGUGAAUUUAACAACUUUGUUGAUGUGUUUUUCAAAGGUGUGUAGGGGCACGGCAGUGACGGCGGCGGCACAGAAACACAUCAACAA
....((((((.(((.....)))))))))......((((((((((((((((....(.(((((....))))).).(((.((....)).))))))))))))))))))) ( -33.80)
>DroSim_CAF1 47931 105 - 1
CAAAUAAAUUUCACUACAAGUGAAUUUAACAACUUUGUUGAUGUGUUUUUCAAAGGAGUGUAGGGGCACGGCGGUGACGGCGGCGGCACAGAAACACAUCAACAA
....((((((.(((.....)))))))))......(((((((((((((((((....))((((....((.((.((....)).)))).)))).))))))))))))))) ( -37.20)
>DroYak_CAF1 48709 98 - 1
CAAGUAAAUGUCACUCUAAGUGAAUUUAACAACUUUGUUGAUGUGUUUUUCAAGGGAG----GGGGCACGUCGG---CGGCGGCGGCACAAAAACACAUCAACAA
....(((((.((((.....)))))))))......(((((((((((((((((....)).----...((.(((((.---...)))))))...))))))))))))))) ( -30.50)
>consensus
CAAAUAAAUUUCACUACAAGUGAAUUUAACAACUUUGUUGAUGUGUUUUUCAAAGGAGUGUAGGGGCACGGCGGUGACGGCGGCGGCACAGAAACACAUCAACAA
....(((((.((((.....)))))))))......((((((((((((((((.......((((....((.((.((....)).)))).)))))))))))))))))))) (-28.85 = -29.91 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:47:36 2006