Locus 4199

Sequence ID	3L_DroMel_CAF1
Location	12,263,722 – 12,263,813
Length	91
Max. P	0.630286

overview

Window 8

Location	12,263,722 – 12,263,813
Length	91
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	97.14
Mean single sequence MFE	-27.58
Consensus MFE	-25.20
Energy contribution	-26.60
Covariance contribution	1.40
Combinations/Pair	1.09
Mean z-score	-1.24
Structure conservation index	0.91
SVM decision value	0.20
SVM RNA-class probability	0.630286
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12263722 91 + 23771897
CGGUGGUUGAGUCCCGGCUCUUUGUUUGCCCACUUUUUCAGCGACCCCUACCACAAACAUCCCCUUCGAGGACCGUAAGGAUAUCCUUGGC
.(((.((((((....(((.........)))......)))))).)))...................(((((((((....))...))))))). ( -25.00)
>DroSec_CAF1 17244 91 + 1
CGGUGGUUGAGUCCGGGCUCUUUGUUUGCCCACUUUUCCAGCGACCCCUACCACAAACAUCCCCUUCGAGGACCGUAAGGAUAUCCUUGGC
((.(((..((((..((((.........))))))))..))).))......................(((((((((....))...))))))). ( -27.90)
>DroSim_CAF1 19670 91 + 1
CGGUGGUUGAGUCCGGGCUCUUUGUUUGCCCACUUUUCCAGCGACCCCUACCACAAACAUCCCCUUCGAGGACCGUAAGGAUAUCCUUGGC
((.(((..((((..((((.........))))))))..))).))......................(((((((((....))...))))))). ( -27.90)
>DroEre_CAF1 18119 91 + 1
CGGUGGUUGAGUCCGGGCUCUUUGUUUGCCCACUUUUCCAGCGACCCCUACCACAAACAUCCCCUUCGAGGGCCGUAAGGAUAUCCUUGGC
((.(((..((((..((((.........))))))))..))).))......................(((((((((....))...))))))). ( -27.00)
>DroYak_CAF1 18107 91 + 1
CGGUGGUUGAGUCCGGGCUCUUUGUUUGCCCACUUUGCCAGCGACCCCUACCACAAACCUCCCCUUCGAGGGCCGCAAGGAUAUCCUUGGC
((.((((.((((..((((.........)))))))).)))).))..............((((......))))....(((((....))))).. ( -30.10)
>consensus
CGGUGGUUGAGUCCGGGCUCUUUGUUUGCCCACUUUUCCAGCGACCCCUACCACAAACAUCCCCUUCGAGGACCGUAAGGAUAUCCUUGGC
((.(((..((((..((((.........))))))))..))).))......................(((((((((....))...))))))). (-25.20 = -26.60 +   1.40)

alignment

secondary structure

dotplot

Window 9

Location	12,263,722 – 12,263,813
Length	91
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	97.14
Mean single sequence MFE	-31.08
Consensus MFE	-29.38
Energy contribution	-29.34
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.14
Structure conservation index	0.95
SVM decision value	0.10
SVM RNA-class probability	0.585354
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12263722 91 - 23771897
GCCAAGGAUAUCCUUACGGUCCUCGAAGGGGAUGUUUGUGGUAGGGGUCGCUGAAAAAGUGGGCAAACAAAGAGCCGGGACUCAACCACCG
((((..(((((((((.((.....))..)))))))))..)))).(((((((((.....))))(((.........)))........))).)). ( -27.70)
>DroSec_CAF1 17244 91 - 1
GCCAAGGAUAUCCUUACGGUCCUCGAAGGGGAUGUUUGUGGUAGGGGUCGCUGGAAAAGUGGGCAAACAAAGAGCCCGGACUCAACCACCG
...((((....))))...(((((.....)))))....(((((..((((((((.....)))((((.........)))).))))).))))).. ( -30.40)
>DroSim_CAF1 19670 91 - 1
GCCAAGGAUAUCCUUACGGUCCUCGAAGGGGAUGUUUGUGGUAGGGGUCGCUGGAAAAGUGGGCAAACAAAGAGCCCGGACUCAACCACCG
...((((....))))...(((((.....)))))....(((((..((((((((.....)))((((.........)))).))))).))))).. ( -30.40)
>DroEre_CAF1 18119 91 - 1
GCCAAGGAUAUCCUUACGGCCCUCGAAGGGGAUGUUUGUGGUAGGGGUCGCUGGAAAAGUGGGCAAACAAAGAGCCCGGACUCAACCACCG
(((((((....))))..))).(((....)))......(((((..((((((((.....)))((((.........)))).))))).))))).. ( -31.70)
>DroYak_CAF1 18107 91 - 1
GCCAAGGAUAUCCUUGCGGCCCUCGAAGGGGAGGUUUGUGGUAGGGGUCGCUGGCAAAGUGGGCAAACAAAGAGCCCGGACUCAACCACCG
((.((((....))))))(((((((....))).)))).(((((..((((((((.....)))((((.........)))).))))).))))).. ( -35.20)
>consensus
GCCAAGGAUAUCCUUACGGUCCUCGAAGGGGAUGUUUGUGGUAGGGGUCGCUGGAAAAGUGGGCAAACAAAGAGCCCGGACUCAACCACCG
(((((((....))))..))).(((....)))......(((((..((((((((.....)))((((.........)))).))))).))))).. (-29.38 = -29.34 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:37 2006