Locus 1928

Sequence ID	2R_DroMel_CAF1
Location	7,263,065 – 7,263,159
Length	94
Max. P	0.999768

overview

Window 5

Location	7,263,065 – 7,263,159
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	95.53
Mean single sequence MFE	-36.40
Consensus MFE	-29.92
Energy contribution	-29.88
Covariance contribution	-0.04
Combinations/Pair	1.09
Mean z-score	-1.90
Structure conservation index	0.82
SVM decision value	1.05
SVM RNA-class probability	0.907207
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7263065 94 + 20766785
GGUGGUUUCCUUGAUGGACAGGGACAGACCAACCGGCGCUGGUUGGACUGUGGCCAAUUGGAGUGGUGUUGAGUGGAUUGGCCCAGUUGGAGCC
(((((((((((((.....))))))..)))).)))(((.((.....(((((.((((((((.(..(......)..).))))))))))))))).))) ( -36.70)
>DroSec_CAF1 58638 94 + 1
GGUGUUUUCCUUGAUGGACACGGGCAGACCAACCGACGCUGGUUGGACUGUGGCCAAUUGGAGUGGUGUUGAGUGGAUUGGCCCAGUUGGAGCC
.((((((........)))))).(((...(((((((....)))))))((((.((((((((.(..(......)..).))))))))))))....))) ( -35.60)
>DroSim_CAF1 61689 94 + 1
GGUGGUUUCCUUGAUGGACAGGGGCAGACCAACCGGCGCUGGUUGGACUGAGGCCAAUUGGAGUGGUGUUGAGUGGAUUGGCCCAGUUGGAGCC
(((((((((((((.....))))))..)))).)))(((.((.....(((((.((((((((.(..(......)..).))))))))))))))).))) ( -35.80)
>DroEre_CAF1 58475 94 + 1
GGUGGUUUCCUUGAUGGACAGGGGCAGACCAACUGGCGCUGGUUGGACUGAAGCCAAUGGGAGUGGUGUUGAGUGGAUUGGCCCAGUUGGAGCC
...((((((((((.....))))))....((((((((.((..(((.(.((.((((((.......)))).)).))).)))..)))))))))))))) ( -35.40)
>DroYak_CAF1 60457 94 + 1
GGUGGUUUCCUUGAUGGACAGGGGCAGACCAACUGGCGCUGGUUGGACUGAAGCCAAUUGGAGUGGUGUUGAGUCGAUUGGCCCAGUUGGAGCC
...((((((((((.....))))))....((((((((.((..((((.(((.((((((.......)))).)).)))))))..)))))))))))))) ( -38.50)
>consensus
GGUGGUUUCCUUGAUGGACAGGGGCAGACCAACCGGCGCUGGUUGGACUGAGGCCAAUUGGAGUGGUGUUGAGUGGAUUGGCCCAGUUGGAGCC
(((((((((((((.....))))))(((.(((((((....))))))).))).))))..((.((.(((.((..(.....)..))))).)).))))) (-29.92 = -29.88 +  -0.04)

alignment

secondary structure

dotplot

Window 6

Location	7,263,065 – 7,263,159
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	95.53
Mean single sequence MFE	-27.74
Consensus MFE	-24.65
Energy contribution	-24.25
Covariance contribution	-0.40
Combinations/Pair	1.09
Mean z-score	-2.99
Structure conservation index	0.89
SVM decision value	4.04
SVM RNA-class probability	0.999768
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7263065 94 - 20766785
GGCUCCAACUGGGCCAAUCCACUCAACACCACUCCAAUUGGCCACAGUCCAACCAGCGCCGGUUGGUCUGUCCCUGUCCAUCAAGGAAACCACC
((.(((.....(((((((..................)))))))((((.((((((......)))))).)))).............)))..))... ( -28.67)
>DroSec_CAF1 58638 94 - 1
GGCUCCAACUGGGCCAAUCCACUCAACACCACUCCAAUUGGCCACAGUCCAACCAGCGUCGGUUGGUCUGCCCGUGUCCAUCAAGGAAAACACC
(((....(((((((((((..................))))))).))))((((((......))))))...))).((((((.....)))...))). ( -28.97)
>DroSim_CAF1 61689 94 - 1
GGCUCCAACUGGGCCAAUCCACUCAACACCACUCCAAUUGGCCUCAGUCCAACCAGCGCCGGUUGGUCUGCCCCUGUCCAUCAAGGAAACCACC
(((....(((((((((((..................))))))).))))((((((......))))))...)))(((........)))........ ( -28.27)
>DroEre_CAF1 58475 94 - 1
GGCUCCAACUGGGCCAAUCCACUCAACACCACUCCCAUUGGCUUCAGUCCAACCAGCGCCAGUUGGUCUGCCCCUGUCCAUCAAGGAAACCACC
(((.((((((((((((((..................))))))....((.......)).))))))))...)))(((........)))........ ( -25.37)
>DroYak_CAF1 60457 94 - 1
GGCUCCAACUGGGCCAAUCGACUCAACACCACUCCAAUUGGCUUCAGUCCAACCAGCGCCAGUUGGUCUGCCCCUGUCCAUCAAGGAAACCACC
(((.((((((((((.....((((.....(((.......)))....))))......)).))))))))...)))(((........)))........ ( -27.40)
>consensus
GGCUCCAACUGGGCCAAUCCACUCAACACCACUCCAAUUGGCCUCAGUCCAACCAGCGCCGGUUGGUCUGCCCCUGUCCAUCAAGGAAACCACC
(((....(((((((((((..................))))))).))))...((((((....))))))..)))....(((.....)))....... (-24.65 = -24.25 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:32 2006