Locus 3732

Sequence ID	X_DroMel_CAF1
Location	9,938,911 – 9,939,070
Length	159
Max. P	0.801075

overview

Window 9

Location	9,938,911 – 9,939,030
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.28
Mean single sequence MFE	-42.00
Consensus MFE	-35.12
Energy contribution	-35.00
Covariance contribution	-0.12
Combinations/Pair	1.10
Mean z-score	-2.02
Structure conservation index	0.84
SVM decision value	0.62
SVM RNA-class probability	0.801075
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9938911 119 - 22224390
AACAACUAGGUGGAGGUGGUUUGGAUGCCUGGUUGGGCAAUUUCCAAAUGAAAGAACUGUGUCGCCAUGGGUCACCAG-UUGGGCAGUAAAUCUUCGCCAGCUUGUGGCUUUUACUUGGC
.....(((((((((((((((((((((((((....)))))...))))))).............))))...((((((.((-(((((.((.....)).).)))))).))))))))))))))). ( -40.11)
>DroSec_CAF1 8686 120 - 1
AACAACUAGGUGGAGGUGGUUUGGAUGCCUGGUUGGGCAAUUUCCAAAUGGAAGAAUUGUGUCGCCAUGGGUCACCAACUUGGGCAGUAAAUCUUCGCCAGCUUGUGGCUUUUACUUGGC
.....((((((((((((((((((..((((((((.(.(((((((((....)))..)))))).).))).(((....)))....))))).))))))..(((......))))))))))))))). ( -39.50)
>DroEre_CAF1 8385 119 - 1
AAUAACUAGGUGGAGGUGGUUUGGAUGCCUGGUUGGCCAAUUUCCAAAUGGAAGAACUGUGUCGCCAUGGGUCACCAG-CUGGGCAGUAAAUCUUCGCCAGCUUGUGGCUUUUACUUGGG
.....((((((((((((((((((..((((..(((((.....((((....))))((.(((((....))))).)).))))-)..)))).))))))..(((......))))))))))))))). ( -44.10)
>DroYak_CAF1 8797 119 - 1
AAUAACAAGGUGGAGGUGGUUUCAAUGCCUGGUUGGGCAAUUUCCAAAUGGAAGAAUUGUGUCGCCAUGGGUCACCAG-CCGGGCAGUAAAUCUUCGCCAGCUUGUGGCUUUUACUUGGA
....(((((.(((.((.(((((...((((((((((((((((((((....)))..))))))...(((...)))..))))-)))))))..))))).)).))).))))).............. ( -44.30)
>consensus
AACAACUAGGUGGAGGUGGUUUGGAUGCCUGGUUGGGCAAUUUCCAAAUGGAAGAACUGUGUCGCCAUGGGUCACCAG_CUGGGCAGUAAAUCUUCGCCAGCUUGUGGCUUUUACUUGGC
.....((((((((((((((((((..(((((((((((.....((((....))))((.(..((....))..).)).)))).))))))).))))))..(((......))))))))))))))). (-35.12 = -35.00 +  -0.12)

alignment

secondary structure

dotplot

Window 0

Location	9,938,951 – 9,939,070
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.98
Mean single sequence MFE	-31.10
Consensus MFE	-27.05
Energy contribution	-27.80
Covariance contribution	0.75
Combinations/Pair	1.03
Mean z-score	-1.89
Structure conservation index	0.87
SVM decision value	0.59
SVM RNA-class probability	0.792475
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9938951 119 - 22224390
CGACAAACAAUUGCAACAUUGAAAAAUGUUAAAUUAAAUAAACAACUAGGUGGAGGUGGUUUGGAUGCCUGGUUGGGCAAUUUCCAAAUGAAAGAACUGUGUCGCCAUGGGUCACCAG-U
.(((....((((..((((((....)))))).))))..........((((((((.(((.((((((((((((....)))))...)))))))......)))...))))).)))))).....-. ( -31.60)
>DroSec_CAF1 8726 120 - 1
CGACAAACAAUUGCAACAUUGAAAAAUGUUAAAUUAAAUAAACAACUAGGUGGAGGUGGUUUGGAUGCCUGGUUGGGCAAUUUCCAAAUGGAAGAAUUGUGUCGCCAUGGGUCACCAACU
((((..((((((((((((((....))))))............((((((((((..((....))...)))))))))).))..(((((....)))))))))))))))...(((....)))... ( -33.50)
>DroEre_CAF1 8425 119 - 1
CGACAAACAAUUGCAACAUUGAAAAAUGUAAAAUUAAAUAAAUAACUAGGUGGAGGUGGUUUGGAUGCCUGGUUGGCCAAUUUCCAAAUGGAAGAACUGUGUCGCCAUGGGUCACCAG-C
.(((....((((...(((((....)))))..))))..........((((((((..(..((((....(((.....)))....((((....))))))))..).))))).)))))).....-. ( -28.30)
>DroYak_CAF1 8837 119 - 1
CGACAAACAAUUGCAACAUUGAAAAAUGUUAAAUUAAAUAAAUAACAAGGUGGAGGUGGUUUCAAUGCCUGGUUGGGCAAUUUCCAAAUGGAAGAAUUGUGUCGCCAUGGGUCACCAG-C
........((((..((((((....)))))).)))).............(((((..(((((..((.(((((....))))).(((((....))))).....))..)))))...)))))..-. ( -31.00)
>consensus
CGACAAACAAUUGCAACAUUGAAAAAUGUUAAAUUAAAUAAACAACUAGGUGGAGGUGGUUUGGAUGCCUGGUUGGGCAAUUUCCAAAUGGAAGAACUGUGUCGCCAUGGGUCACCAG_C
(((((.....((((((((((....))))))............((((((((((..((....))...)))))))))).))))(((((....))))).....)))))...(((....)))... (-27.05 = -27.80 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:53 2006