Locus 5747

Sequence ID	2R_DroMel_CAF1
Location	18,200,682 – 18,200,774
Length	92
Max. P	0.992439

overview

Window 3

Location	18,200,682 – 18,200,774
Length	92
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	80.04
Mean single sequence MFE	-26.86
Consensus MFE	-14.83
Energy contribution	-16.71
Covariance contribution	1.88
Combinations/Pair	1.11
Mean z-score	-2.62
Structure conservation index	0.55
SVM decision value	1.69
SVM RNA-class probability	0.972363
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18200682 92 + 20766785
AUCCACAGCUCGUAUGCCCAACCACUUCUCGCGAGC----CCCCUUUUUU----CCCAAUUCAACUCACGAUCCGGGGUUUAGUGGAAAAGUGUCUGGGC
...............(((((..(((((.((((((((----(((.......----....................))))))).))))..)))))..))))) ( -25.53)
>DroSec_CAF1 25780 91 + 1
AUCCACAGCUCGUACGCCCAACCACU-CUCCCGAGC----CCCCUGUUUU----CCCAAUUCAACUCACGAUCCGGGGUUUAGUGGAAAAGUGGCUGGGC
...............(((((.(((((-.((((((((----(((..(((..----...............)))..))))))).).)))..))))).))))) ( -28.13)
>DroSim_CAF1 27500 92 + 1
AUCCACAGCUCGUACGCCCAACCACUUCUCCCGAGC----CCCCUUUUUU----UCCAAUUCAACUCACGAUCCGGGGUUUAGUGGAAAAGUGGCUGGGC
...............(((((.((((((.((((((((----(((.......----....................))))))).).))).)))))).))))) ( -30.63)
>DroEre_CAF1 26444 96 + 1
AUCCACAGCUCGUACUCCCAAGCACUUCUCCCUAUCCAUUCCCCCUUUUU----CCGGAUUCAACUCACGAUCCGUGGUUUAGUGGAAAAGUGCCUGGGC
................((((.((((((.((((((.(((............----.((((((........)))))))))..))).))).)))))).)))). ( -28.41)
>DroYak_CAF1 27251 83 + 1
-------------ACUCCCAAGCUUAUAACACUAUA----CCCCUUCUUUCUAUUCCGAUUCAACUCACGAUCCGGGGUUUAGUGGAAAAGUGGAUGGGC
-------------...((((.((((....(((((.(----((((.....((......)).((.......))...))))).)))))...))))...)))). ( -21.60)
>consensus
AUCCACAGCUCGUACGCCCAACCACUUCUCCCGAGC____CCCCUUUUUU____CCCAAUUCAACUCACGAUCCGGGGUUUAGUGGAAAAGUGGCUGGGC
...............(((((.((((((.(((.........((((..............................))))......))).)))))).))))) (-14.83 = -16.71 +   1.88)

alignment

secondary structure

dotplot

Window 4

Location	18,200,682 – 18,200,774
Length	92
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	80.04
Mean single sequence MFE	-33.64
Consensus MFE	-22.81
Energy contribution	-25.45
Covariance contribution	2.64
Combinations/Pair	1.05
Mean z-score	-2.74
Structure conservation index	0.68
SVM decision value	2.33
SVM RNA-class probability	0.992439
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18200682 92 - 20766785
GCCCAGACACUUUUCCACUAAACCCCGGAUCGUGAGUUGAAUUGGG----AAAAAAGGGG----GCUCGCGAGAAGUGGUUGGGCAUACGAGCUGUGGAU
((((((.((((((((.......((((...((.(((......))).)----).....))))----......)))))))).))))))............... ( -29.82)
>DroSec_CAF1 25780 91 - 1
GCCCAGCCACUUUUCCACUAAACCCCGGAUCGUGAGUUGAAUUGGG----AAAACAGGGG----GCUCGGGAG-AGUGGUUGGGCGUACGAGCUGUGGAU
((((((((((((((((......((((...((.(((......))).)----).....))))----....)))))-)))))))))))............... ( -39.30)
>DroSim_CAF1 27500 92 - 1
GCCCAGCCACUUUUCCACUAAACCCCGGAUCGUGAGUUGAAUUGGA----AAAAAAGGGG----GCUCGGGAGAAGUGGUUGGGCGUACGAGCUGUGGAU
((((((((((((((((......((((....(....).....((...----.))...))))----.....))))))))))))))))............... ( -40.50)
>DroEre_CAF1 26444 96 - 1
GCCCAGGCACUUUUCCACUAAACCACGGAUCGUGAGUUGAAUCCGG----AAAAAGGGGGAAUGGAUAGGGAGAAGUGCUUGGGAGUACGAGCUGUGGAU
.(((((((((((((((.((((((((((...)))).)))...(((..----.....)))........))))))))))))))))))(((....)))...... ( -35.80)
>DroYak_CAF1 27251 83 - 1
GCCCAUCCACUUUUCCACUAAACCCCGGAUCGUGAGUUGAAUCGGAAUAGAAAGAAGGGG----UAUAGUGUUAUAAGCUUGGGAGU-------------
.((((....(((...(((((.(((((....(....).....((......)).....))))----).)))))....)))..))))...------------- ( -22.80)
>consensus
GCCCAGCCACUUUUCCACUAAACCCCGGAUCGUGAGUUGAAUUGGG____AAAAAAGGGG____GCUCGGGAGAAGUGGUUGGGCGUACGAGCUGUGGAU
((((((((((((((((......((((....(....)....................)))).........))))))))))))))))............... (-22.81 = -25.45 +   2.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:21 2006