Locus 3729

Sequence ID	X_DroMel_CAF1
Location	9,935,533 – 9,935,693
Length	160
Max. P	0.921498

overview

Window 2

Location	9,935,533 – 9,935,653
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.67
Mean single sequence MFE	-26.05
Consensus MFE	-26.58
Energy contribution	-25.95
Covariance contribution	-0.63
Combinations/Pair	1.12
Mean z-score	-1.59
Structure conservation index	1.02
SVM decision value	1.14
SVM RNA-class probability	0.921498
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9935533 120 - 22224390
CCAACUAAAAAAUAAAACAAAAACAAAGUGGAAGAGGGGUGCAUUACAUAUGCCACGAGUGCGUUUGGGCAUAAAUCCCAAUUUAAUCCAUCCGGCUUUUAGUUUUGUACAUUUUCCAUC
...........................((((((((...(((((..((....((((((....)))(((((.......)))))............))).....))..))))).)))))))). ( -26.50)
>DroSec_CAF1 5303 120 - 1
ACAACUAAAAAAUAAAACAAAAACAAAGUGGAAGAGGGGUGCAUUACAUAUGCCACGAGUGCGUUUGGGCAUAAAUCCCAAUUUAAUCCAUCCGGCUUUUAGUUUUGUACAUUUUCCAUC
...........................((((((((...(((((..((....((((((....)))(((((.......)))))............))).....))..))))).)))))))). ( -26.50)
>DroEre_CAF1 5187 119 - 1
CCUACUAAAGAAUAAAACAAAAACAAAAUGGAAGA-GGGUGCAUUACAUAUGCCACGAGUGCGUUUGGGCAUAAAUCCCAAUUUAAUCCAUCCGGCUUUUAGUUUUGUACAUUUUCCAUC
...........................((((((((-..(((((..((....((((((....)))(((((.......)))))............))).....))..))))).)))))))). ( -26.20)
>DroYak_CAF1 5484 109 - 1
CUAACUAA-----------AAAACAAAAUGGAGGGGGGGUGCAUUACAUAUGCCACGAGUGCGUUUGGGCAUAAAUCCCAAUUUAAUACAUCCGGCUUUUAGUUUUGUACAUUUUCCAUC
........-----------........((((((((...(((((..((....((((((....)))(((((.......)))))............))).....))..))))).)))))))). ( -25.00)
>consensus
CCAACUAAAAAAUAAAACAAAAACAAAAUGGAAGAGGGGUGCAUUACAUAUGCCACGAGUGCGUUUGGGCAUAAAUCCCAAUUUAAUCCAUCCGGCUUUUAGUUUUGUACAUUUUCCAUC
...........................((((((((...(((((..((....((((((....)))(((((.......)))))............))).....))..))))).)))))))). (-26.58 = -25.95 +  -0.63)

alignment

secondary structure

dotplot

Window 3

Location	9,935,573 – 9,935,693
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.40
Mean single sequence MFE	-27.58
Consensus MFE	-19.20
Energy contribution	-19.70
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.49
Structure conservation index	0.70
SVM decision value	-0.04
SVM RNA-class probability	0.514292
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9935573 120 - 22224390
AAAAAAAAACAUUGGGUGGGGGCUCUAGGAGCUUAGGAGCCCAACUAAAAAAUAAAACAAAAACAAAGUGGAAGAGGGGUGCAUUACAUAUGCCACGAGUGCGUUUGGGCAUAAAUCCCA
...........((((((..((((((...))))))....))))))...............................(((((........((((((.((((....)))))))))).))))). ( -29.50)
>DroSec_CAF1 5343 116 - 1
A----AAAACAGUGGGUGGGGGGUCUCGGGGCUUAGGAGCACAACUAAAAAAUAAAACAAAAACAAAGUGGAAGAGGGGUGCAUUACAUAUGCCACGAGUGCGUUUGGGCAUAAAUCCCA
.----..............(((((((((.(((.((.((((((..((.....((..............)).....))..)))).))...)).))).))))(((......)))...))))). ( -25.04)
>DroEre_CAF1 5227 112 - 1
AAA-----A--AUGGGUAGCGAGUCUAGGGGCUUAGGACCCCUACUAAAGAAUAAAACAAAAACAAAAUGGAAGA-GGGUGCAUUACAUAUGCCACGAGUGCGUUUGGGCAUAAAUCCCA
...-----.--.((((..(((((((....)))))...((((((.(((.....................))).)).-))))))......((((((.((((....))))))))))...)))) ( -26.50)
>DroYak_CAF1 5524 104 - 1
AAA-----AGAGUGGGUGGUGGGUCUAGGGGCUUAGGACCCUAACUAA-----------AAAACAAAAUGGAGGGGGGGUGCAUUACAUAUGCCACGAGUGCGUUUGGGCAUAAAUCCCA
...-----..(((((((..((((((....))))))..))))..)))..-----------.............((((..((((....((.(((((....).)))).)).))))...)))). ( -29.30)
>consensus
AAA_____ACAGUGGGUGGGGGGUCUAGGGGCUUAGGACCCCAACUAAAAAAUAAAACAAAAACAAAAUGGAAGAGGGGUGCAUUACAUAUGCCACGAGUGCGUUUGGGCAUAAAUCCCA
............((((......(((((((.((((((........))))..............................((((((.....))).)))....)).)))))))......)))) (-19.20 = -19.70 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:47 2006