Locus 4986

Sequence ID	3L_DroMel_CAF1
Location	13,746,456 – 13,746,656
Length	200
Max. P	0.988673

overview

Window 2

Location	13,746,456 – 13,746,549
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	98.71
Mean single sequence MFE	-20.48
Consensus MFE	-18.64
Energy contribution	-19.04
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.32
Structure conservation index	0.91
SVM decision value	0.02
SVM RNA-class probability	0.543568
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13746456 93 + 23771897
GGAAACGAACAAAUAAAAGGCUCAGCCCGCAAUCAUUGCGGUAAACAAAAGACAACAGCAGGGUUCACGAGGACACAUGUUUAUCAAUGUCCU
(....)((((........(((...)))((((.....))))......................))))...((((((..((.....)).)))))) ( -18.70)
>DroSec_CAF1 153214 93 + 1
GGAAACGAACAAAUAAAAGGCUCAGCCCGCAAUCAUUGCGGUAAACAAAAGACAACUGCAGGGUUCACGAGGACACAUGUUUAUCAAUGUCCU
(....)((((........(((...)))........(((((((............))))))).))))...((((((..((.....)).)))))) ( -20.70)
>DroSim_CAF1 164354 93 + 1
GGAAACGAACAAAUAAAAGGCUCAGCCCGCAAUCAUUGCGGUAAACAAAAGACAACUGCAGGGUUCACGAGGACACAUGUUUAUCAAUGUCCU
(....)((((........(((...)))........(((((((............))))))).))))...((((((..((.....)).)))))) ( -20.70)
>DroEre_CAF1 160058 92 + 1
GGAAACGAACAAAUAAAAGGCUCAGC-CGCAAUCAUUGCGGUAAACAAAAGACAACUGCAGGGUUCACGAGGACACAUGUUUAUCAAUGUCCU
(....)((((........(((...))-).......(((((((............))))))).))))...((((((..((.....)).)))))) ( -21.60)
>DroYak_CAF1 164303 93 + 1
GGAGACGAACAAAUAAAAGGCUCAGCCCGCAAUCAUUGCGGUAAACAAAAGACAACUGCAGGGUUCACGAGGACACAUGUUUAUCAAUGUCCU
(....)((((........(((...)))........(((((((............))))))).))))...((((((..((.....)).)))))) ( -20.70)
>consensus
GGAAACGAACAAAUAAAAGGCUCAGCCCGCAAUCAUUGCGGUAAACAAAAGACAACUGCAGGGUUCACGAGGACACAUGUUUAUCAAUGUCCU
(....)((((........(((...)))........(((((((............))))))).))))...((((((..((.....)).)))))) (-18.64 = -19.04 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	13,746,549 – 13,746,656
Length	107
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	93.13
Mean single sequence MFE	-25.33
Consensus MFE	-20.90
Energy contribution	-22.12
Covariance contribution	1.22
Combinations/Pair	1.09
Mean z-score	-2.29
Structure conservation index	0.82
SVM decision value	2.13
SVM RNA-class probability	0.988673
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13746549 107 + 23771897
CAGCAAAAAAUUAGUUCAAAGCGGAAUAGAAAUAUCGGAAGCAAA-AAAUAGCACGGUAUUCCGAUAGCUGGUUGAAAAAGCAGCAAAACCACAGGCGCAGAUGCUGA
(((((........((.....))((........((((((((((...-.....))......))))))))((((.((....)).))))....))...........))))). ( -26.00)
>DroSec_CAF1 153307 107 + 1
CAGCAAAAAAUUAGUUCAAAGCGGAAUAGAAAUAUCGGGGGCAAA-AAAUUGCACGUUAUUCCGAUAGCUGAUUGAAAAAGCAGCAAAACCACAGGCGCAGAUGCUGA
(((((...((((((((.....((((((((......((...((((.-...)))).))))))))))..))))))))......((.((..........))))...))))). ( -25.80)
>DroSim_CAF1 164447 107 + 1
CAGCAAAAAAUUAGUUCAAAGCGGAAUAGAAAUAUCGGGGGCAAA-AAAUUGCACGUUAUUCCGAUAGCUGGUUGAAAAAGCAGCAAAACCACAGGCGCAGAUGCUGA
(((((................((((((((......((...((((.-...)))).))))))))))...((((.((....)).)))).................))))). ( -26.90)
>DroEre_CAF1 160150 108 + 1
CGGCAAAAAAUUAGUUCAAAGCGGAAUAGAAACAUCGGGAGCAAAAAAAUAGCACGUUAUUGCGAUAGCUGGUUGAAAAAGCAGCAAAGCCACAGACGCAGAUGCUGA
(((((........((((......)))).......((.(..((.........(((......)))....((((.((....)).))))...))..).))......))))). ( -21.90)
>DroYak_CAF1 164396 108 + 1
CAGCAAAAAAUUAGUUCAAAGCGGAAUAGAAGCAUCGAGAGCAAAAAAAUAGCACGUUAUUCCGAUAGCUGGCUGAAAAGGCAGCCAAACCACAGACGCAGAUGCUGA
(((((................((((((((..((..................))...))))))))...((((.((....)).)))).................))))). ( -26.07)
>consensus
CAGCAAAAAAUUAGUUCAAAGCGGAAUAGAAAUAUCGGGAGCAAA_AAAUAGCACGUUAUUCCGAUAGCUGGUUGAAAAAGCAGCAAAACCACAGGCGCAGAUGCUGA
(((((................(((((((((....))....((.........))....)))))))...((((.((....)).)))).................))))). (-20.90 = -22.12 +   1.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:42 2006