Locus 6900

Sequence ID 3R_DroMel_CAF1
Location 18,227,637 – 18,227,757
Length 120
Max. P 0.556305
window11202 window11203

overview

Window 2

Location 18,227,637 – 18,227,757
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.28
Mean single sequence MFE -20.57
Consensus MFE -16.50
Energy contribution -17.25
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.80
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18227637 120 + 27905053
AAUCUAAAAUUCACAAAUUGAUUUGUAAACAUUAUUCAAUCCGUGUUAUCAAAACAAACGGAGAAAAGAUUCAAAUAUAUGCUAAUACAUACAGUUGUAUAUCUGAAAUUUGUACCAAUU
............(((((((....................((((((((.....)))..)))))....((((.(((...((((......))))...)))...))))..)))))))....... ( -15.10)
>DroSec_CAF1 29811 120 + 1
AAUCUAAAAUUCACAAAUUGAUUUGUAAACAUUAUUCAAUCCGUGUUACCAAAACAAACGGAGAAAAGAUGCAAAUGUAUGCAAAUACAUACAGUUGUAUAUCUGAAAUUUGUACCAAUU
............(((((((..((((..(((((..........)))))..)))).....((((......((((((.((((((......)))))).)))))).)))).)))))))....... ( -21.70)
>DroSim_CAF1 30931 120 + 1
AAUCUAAAAUUCACAAAUUGAUUUGUAAACAUUAUUCAAUCCGUGUUAUCAAAACAAACGGAGAAAAGAUGCAAAUGUAUGCAAAUACAUACAGUUGUAUAUCUGAAAUUUGUACCAAUU
............(((((....)))))..(((...((((.((((((((.....)))..)))))......((((((.((((((......)))))).))))))...))))...)))....... ( -21.20)
>DroYak_CAF1 25391 120 + 1
AGACGAAAAUUCCCAAAUUGAUUUGUAAACAUUAUUCAAUCCGUGUUAUCAAAACAAACGGAGAAAAGAUUCAAAUGUAUGCAAAUAUAUACAGUUGUAUAUCGGAAAUUUGUUCCAAUU
.((((((..((((.......(((((((.(((((......((((((((.....)))..)))))(((....))).))))).)))))))((((((....)))))).)))).))))))...... ( -24.30)
>consensus
AAUCUAAAAUUCACAAAUUGAUUUGUAAACAUUAUUCAAUCCGUGUUAUCAAAACAAACGGAGAAAAGAUGCAAAUGUAUGCAAAUACAUACAGUUGUAUAUCUGAAAUUUGUACCAAUU
............(((((((.(((((((.(((((..((..((((((((.....)))..))))).....))....))))).)))))))..((((....))))......)))))))....... (-16.50 = -17.25 +   0.75)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,227,637 – 18,227,757
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.28
Mean single sequence MFE -23.43
Consensus MFE -20.62
Energy contribution -21.00
Covariance contribution 0.38
Combinations/Pair 1.06
Mean z-score -1.55
Structure conservation index 0.88
SVM decision value 0.05
SVM RNA-class probability 0.556305
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18227637 120 - 27905053
AAUUGGUACAAAUUUCAGAUAUACAACUGUAUGUAUUAGCAUAUAUUUGAAUCUUUUCUCCGUUUGUUUUGAUAACACGGAUUGAAUAAUGUUUACAAAUCAAUUUGUGAAUUUUAGAUU
.((..(.((((((...(((.((.(((.(((((((....))))))).))).))....)))..)))))).)..))..((((((((((....((....))..))))))))))........... ( -22.30)
>DroSec_CAF1 29811 120 - 1
AAUUGGUACAAAUUUCAGAUAUACAACUGUAUGUAUUUGCAUACAUUUGCAUCUUUUCUCCGUUUGUUUUGGUAACACGGAUUGAAUAAUGUUUACAAAUCAAUUUGUGAAUUUUAGAUU
.((..(.((((((...(((.((.(((.(((((((....))))))).))).))....)))..)))))).)..))..((((((((((....((....))..))))))))))........... ( -24.50)
>DroSim_CAF1 30931 120 - 1
AAUUGGUACAAAUUUCAGAUAUACAACUGUAUGUAUUUGCAUACAUUUGCAUCUUUUCUCCGUUUGUUUUGAUAACACGGAUUGAAUAAUGUUUACAAAUCAAUUUGUGAAUUUUAGAUU
.((..(.((((((...(((.((.(((.(((((((....))))))).))).))....)))..)))))).)..))..((((((((((....((....))..))))))))))........... ( -24.20)
>DroYak_CAF1 25391 120 - 1
AAUUGGAACAAAUUUCCGAUAUACAACUGUAUAUAUUUGCAUACAUUUGAAUCUUUUCUCCGUUUGUUUUGAUAACACGGAUUGAAUAAUGUUUACAAAUCAAUUUGGGAAUUUUCGUCU
....(((..(((((((((((((((....))))))(((((...(((((.(((....)))(((((((((....)))).)))))......)))))...))))).....)))))))))...))) ( -22.70)
>consensus
AAUUGGUACAAAUUUCAGAUAUACAACUGUAUGUAUUUGCAUACAUUUGAAUCUUUUCUCCGUUUGUUUUGAUAACACGGAUUGAAUAAUGUUUACAAAUCAAUUUGUGAAUUUUAGAUU
.((..(.((((((...(((.((.(((.(((((((....))))))).))).))....)))..)))))).)..))..((((((((((....((....))..))))))))))........... (-20.62 = -21.00 +   0.38)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:52 2006