Locus 6629

Sequence ID	2L_DroMel_CAF1
Location	18,623,989 – 18,624,138
Length	149
Max. P	0.734719

overview

Window 3

Location	18,623,989 – 18,624,099
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.10
Mean single sequence MFE	-34.42
Consensus MFE	-25.58
Energy contribution	-25.32
Covariance contribution	-0.25
Combinations/Pair	1.11
Mean z-score	-1.61
Structure conservation index	0.74
SVM decision value	0.24
SVM RNA-class probability	0.647314
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18623989 110 + 22407834
GCUGUCCGCUCCUCUGG----------UCCUCCGAGUUGCAAAACCGCGACUCCCCGCACCCCUUUUGGAACCGCUCCCGGACUUCCAACUGACUGCCAAUUGUGGCAGCGGUAAAGAUU
...(((((.......((----------(.(...(((((((......)))))))...).)))......(((.....)))))))).....((((.((((((....))))))))))....... ( -34.60)
>DroSec_CAF1 101535 110 + 1
GCUGUCCGCUCCUCUGG----------UCCUCCGAGCUGCAAAACCGCGAAUCCCCGCUCCCCUUUUGGAACCGCUCGCGGACUUCCAACUGCCUGCCAAUUGUGGCAGCGGUAAAGAUU
...((((((......((----------....))((((.........(((......)))(((......)))...)))))))))).....(((((.(((((....))))))))))....... ( -37.90)
>DroEre_CAF1 100527 120 + 1
GUUCUCCGCUCCUCUGGUAUUCUCUAGUACUCCGAGCCCCAAAACCGCGACUCCCCGCUGCCCCUUUGGAACCGCUCCCGGACUUCCAACUGGCUGCCAAUUGUGGCAGCGGUAAAGAUU
.......((((....(((((......)))))..)))).........(((......)))((((...(((((((((....)))..))))))...(((((((....)))))))))))...... ( -34.70)
>DroYak_CAF1 101981 109 + 1
GUUCUCCGCUCCUCUGG----------AACUCCAAGCCCCAAAACCGCUACUCUCCGCUCCCCC-UUGGAACCGCUCCCGGACUUCCAACUGGCUGCCAAUUGUGGCAGCGGUAAAGAUU
..((((((((....(((----------....)))............(((((.....((..((..-(((((((((....)))..))))))..))..)).....))))))))))...))).. ( -30.50)
>consensus
GCUCUCCGCUCCUCUGG__________UACUCCGAGCCCCAAAACCGCGACUCCCCGCUCCCCCUUUGGAACCGCUCCCGGACUUCCAACUGGCUGCCAAUUGUGGCAGCGGUAAAGAUU
.((..(((((........................((((........(((......))).......(((((((((....)))..))))))..))))((((....)))))))))...))... (-25.58 = -25.32 +  -0.25)

alignment

secondary structure

dotplot

Window 4

Location	18,624,019 – 18,624,138
Length	119
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	95.38
Mean single sequence MFE	-47.90
Consensus MFE	-43.91
Energy contribution	-44.10
Covariance contribution	0.19
Combinations/Pair	1.08
Mean z-score	-1.65
Structure conservation index	0.92
SVM decision value	0.43
SVM RNA-class probability	0.734719
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18624019 119 - 22407834
CUGCGGGUCUCAGCUGCGGUCACACACAACAGCGAACGAAAUCUUUACCGCUGCCACAAUUGGCAGUCAGUUGGAAGUCCGGGAGCGGUUCCAAAAGGGGUGCGGGGAGUCGCGGUUUU
((((((.((((.((((..((.....))..))))...((...(((((...(((((((....)))))))...((((((..(((....))))))))))))))...)))))).)))))).... ( -46.30)
>DroSec_CAF1 101565 119 - 1
CUGCGGGUCUCAGCUGCGGUCACACACAACAGCGAACGAAAUCUUUACCGCUGCCACAAUUGGCAGGCAGUUGGAAGUCCGCGAGCGGUUCCAAAAGGGGAGCGGGGAUUCGCGGUUUU
(((((((((((.(((((((.(.....((((.((((......)).......((((((....)))))))).))))...).)))).))).(((((......))))).))))))))))).... ( -48.70)
>DroEre_CAF1 100567 119 - 1
CUGCGGGUCUCGGCUGCGGUCACACACAACAGCGAACGAAAUCUUUACCGCUGCCACAAUUGGCAGCCAGUUGGAAGUCCGGGAGCGGUUCCAAAGGGGCAGCGGGGAGUCGCGGUUUU
((((((.((((.((((((.((.(........).)).)..........(((((((((....)))))))...((((((..(((....))))))))).)).))))).)))).)))))).... ( -51.20)
>DroYak_CAF1 102011 118 - 1
CUGCGGGUCUCAGCUGCGGUCACACACAACAGCGAACGAAAUCUUUACCGCUGCCACAAUUGGCAGCCAGUUGGAAGUCCGGGAGCGGUUCCAA-GGGGGAGCGGAGAGUAGCGGUUUU
((((.(.((((.((((..((.....))..))))...((...(((...(((((((((....)))))))...((((((..(((....)))))))))-)).))).)))))).).)))).... ( -45.40)
>consensus
CUGCGGGUCUCAGCUGCGGUCACACACAACAGCGAACGAAAUCUUUACCGCUGCCACAAUUGGCAGCCAGUUGGAAGUCCGGGAGCGGUUCCAAAAGGGGAGCGGGGAGUCGCGGUUUU
((((((.((((.((((..((.....))..))))...((...(((((...(((((((....)))))))...((((((..(((....))))))))))))))...)))))).)))))).... (-43.91 = -44.10 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:55 2006