Locus 9916

Sequence ID 3R_DroMel_CAF1
Location 26,495,354 – 26,495,462
Length 108
Max. P 0.994742
window15810 window15811

overview

Window 0

Location 26,495,354 – 26,495,462
Length 108
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 79.42
Mean single sequence MFE -31.20
Consensus MFE -26.82
Energy contribution -26.74
Covariance contribution -0.08
Combinations/Pair 1.12
Mean z-score -2.61
Structure conservation index 0.86
SVM decision value 2.51
SVM RNA-class probability 0.994742
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26495354 108 + 27905053
AGAACAGUUAAAGACGGCUAAGAUAAAUAUAUGUGCAUAUAUCCUCAUCUUUAAUAGAGGGUAUAUCUGCUUGAGACUGCCCCUUAUGAAGGGGGCGGUUCAUCAUUA
.....((((......))))..(((..........((((((((((((..........)))))))))..)))....(((((((((((....))))))))))).))).... ( -31.90)
>DroSec_CAF1 87237 96 + 1
UCAGCACUUUAU------------GUGUAUAUGCGCACACAUCCUCAUCUUUAAUAGAGGGUAUCUCUGUUUGAGACUGCCCCUUAUGAAGGGGGCGGUUCAUCAUGG
.(((.......(------------((((......))))).((((((..........))))))....)))..((((((((((((((....)))))))))))..)))... ( -30.00)
>DroSim_CAF1 87826 96 + 1
UCAGCACUUUAA------------GGGUACAUGUGCAUACAUCCUCAUCUUUAAUAGAGGGUAUCUCUGUUUGAGACUGCCCCUUAUGAAGGGGGCGGUUCAUCAUGG
...((((.....------------........))))...(((.....((((.(((((((.....))))))).))))(((((((((....)))))))))......))). ( -30.52)
>DroEre_CAF1 95156 94 + 1
UCAGCAUUUUAA------------GG--ACAAGUGCAUAUAUCCUCAUCUUCAAUAGAGGGUAUCUCUGUUUGAGACUGCCCCUUAUGAAGGGGGCGGUUCAUCAGGG
...((((((...------------..--..))))))..((((((((..........))))))))(((((..((((.(((((((((....))))))))))))).))))) ( -36.50)
>DroYak_CAF1 92376 83 + 1
GAAG---U----------------------UAGUGCACAUAUCCUCAUCUUCAAUAGAGGGUAUCUCUGUUUGAGGCUGCCCCUUAUGAGGGGGGCGGUUCAUCAUGG
....---.----------------------........((((((((..........))))))))(((.....)))((((((((((....))))))))))......... ( -27.10)
>consensus
UCAGCACUUUAA____________GG_UACAUGUGCAUAUAUCCUCAUCUUUAAUAGAGGGUAUCUCUGUUUGAGACUGCCCCUUAUGAAGGGGGCGGUUCAUCAUGG
..................................(((.((((((((..........))))))))...))).((((((((((((((....)))))))))))..)))... (-26.82 = -26.74 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 26,495,354 – 26,495,462
Length 108
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 79.42
Mean single sequence MFE -24.18
Consensus MFE -18.04
Energy contribution -18.44
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.75
SVM decision value 0.79
SVM RNA-class probability 0.852221
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26495354 108 - 27905053
UAAUGAUGAACCGCCCCCUUCAUAAGGGGCAGUCUCAAGCAGAUAUACCCUCUAUUAAAGAUGAGGAUAUAUGCACAUAUAUUUAUCUUAGCCGUCUUUAACUGUUCU
.......((((.(((((........))))).((((.....))))..........(((((((((((((((.(((......))).))))))...)))))))))..)))). ( -24.80)
>DroSec_CAF1 87237 96 - 1
CCAUGAUGAACCGCCCCCUUCAUAAGGGGCAGUCUCAAACAGAGAUACCCUCUAUUAAAGAUGAGGAUGUGUGCGCAUAUACAC------------AUAAAGUGCUGA
............(((((........))))).(((((.....)))))..((((..........))))(((((((......)))))------------)).......... ( -26.10)
>DroSim_CAF1 87826 96 - 1
CCAUGAUGAACCGCCCCCUUCAUAAGGGGCAGUCUCAAACAGAGAUACCCUCUAUUAAAGAUGAGGAUGUAUGCACAUGUACCC------------UUAAAGUGCUGA
............(((((........))))).(((((.....)))))..((((..........))))......((((........------------.....))))... ( -23.72)
>DroEre_CAF1 95156 94 - 1
CCCUGAUGAACCGCCCCCUUCAUAAGGGGCAGUCUCAAACAGAGAUACCCUCUAUUGAAGAUGAGGAUAUAUGCACUUGU--CC------------UUAAAAUGCUGA
............((...(((((..(((((..(((((.....)))))..)))))..))))).((((((((........)))--))------------)))....))... ( -26.60)
>DroYak_CAF1 92376 83 - 1
CCAUGAUGAACCGCCCCCCUCAUAAGGGGCAGCCUCAAACAGAGAUACCCUCUAUUGAAGAUGAGGAUAUGUGCACUA----------------------A---CUUC
.((((.......(((((........)))))..(((((((.((((.....)))).)).....))))).)))).......----------------------.---.... ( -19.70)
>consensus
CCAUGAUGAACCGCCCCCUUCAUAAGGGGCAGUCUCAAACAGAGAUACCCUCUAUUAAAGAUGAGGAUAUAUGCACAUAUA_CC____________UUAAAGUGCUGA
............(((((........))))).(((((.....)))))..((((..........)))).......................................... (-18.04 = -18.44 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:44:49 2006