Locus 3435

Sequence ID 3R_DroMel_CAF1
Location 9,321,111 – 9,321,203
Length 92
Max. P 0.671329
window5512 window5513

overview

Window 2

Location 9,321,111 – 9,321,203
Length 92
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 85.79
Mean single sequence MFE -30.85
Consensus MFE -22.82
Energy contribution -23.68
Covariance contribution 0.86
Combinations/Pair 1.11
Mean z-score -2.74
Structure conservation index 0.74
SVM decision value 0.29
SVM RNA-class probability 0.671329
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9321111 92 + 27905053
AACACAAGUGUACAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUACAGAGA-CAUCUCUGUCUCCGACU------CCGACUC----------AGAGUCGCAGUUGCA
..(((.(((((....))))).)))((....((((((....(((...((((((.-...)))))).)))((((------(......----------.))))))))))))). ( -29.60)
>DroSec_CAF1 92053 92 + 1
AACACAAGUGUACAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUGCAGAGA-CAUCUCUGUCUCCGACU------CCGACUC----------AGAGUCGCAGUUGCA
..(((.(((((....))))).)))((....((((((....(((...((((((.-...)))))).)))((((------(......----------.))))))))))))). ( -29.90)
>DroSim_CAF1 94164 92 + 1
AACACAAGUGUACAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUGCAGAGA-CAUCUCUGUCUCCGACU------CCGACUC----------AGAGUCGCAGUUGCA
..(((.(((((....))))).)))((....((((((....(((...((((((.-...)))))).)))((((------(......----------.))))))))))))). ( -29.90)
>DroEre_CAF1 93533 97 + 1
AACACAAGUGUGCAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUACAGAGA-CAUCUCUGUCUCCGACUCCGACUCCGACUC----------AGAGUCGCAGUUGC-
..(((.(((((....))))).)))..((.(((.(((((((.......))).))-))..))).))..(((((.((((((......----------.)))))).))))).- ( -33.00)
>DroYak_CAF1 93560 85 + 1
AACACAAGUGUACAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUACAGAGA-CAUCUCUGUCUCCG------------ACUC----------AGAGUCGCAGUCGC-
..(((.(((((....))))).)))......((((((....(((...((((((.-...)))))).)))(------------((..----------...)))))))))..- ( -28.10)
>DroAna_CAF1 90042 103 + 1
AACACGAGUGUACAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUACAGACAUCUUCUCUGUUUCUGUCU------CAGUCUCCAUCGCCGCCACCGCCGCCGCAGCA
..(((((((((....)))))))))(((...(((.(..((((((...(((((.......))))).....)))------)))...).)))((.((....)).))))).... ( -34.60)
>consensus
AACACAAGUGUACAAACACUCGUGGCGAAAGAUUGUCCUGGGAAAUACAGAGA_CAUCUCUGUCUCCGACU______CCGACUC__________AGAGUCGCAGUUGCA
..(((.(((((....))))).)))......((((((....(((...((((((.....)))))).)))............(((((...........)))))))))))... (-22.82 = -23.68 +   0.86)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,321,111 – 9,321,203
Length 92
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 85.79
Mean single sequence MFE -35.98
Consensus MFE -25.23
Energy contribution -26.28
Covariance contribution 1.06
Combinations/Pair 1.07
Mean z-score -3.17
Structure conservation index 0.70
SVM decision value 0.28
SVM RNA-class probability 0.665649
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9321111 92 - 27905053
UGCAACUGCGACUCU----------GAGUCGG------AGUCGGAGACAGAGAUG-UCUCUGUAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGUACACUUGUGUU
.((..((.(((((((----------(...)))------))))).))..(((((((-((.(((.......)))))).)))))).))(((((((((....))))))))).. ( -36.40)
>DroSec_CAF1 92053 92 - 1
UGCAACUGCGACUCU----------GAGUCGG------AGUCGGAGACAGAGAUG-UCUCUGCAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGUACACUUGUGUU
.((..((.(((((((----------(...)))------))))).))..(((((((-((.(((.......)))))).)))))).))(((((((((....))))))))).. ( -36.10)
>DroSim_CAF1 94164 92 - 1
UGCAACUGCGACUCU----------GAGUCGG------AGUCGGAGACAGAGAUG-UCUCUGCAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGUACACUUGUGUU
.((..((.(((((((----------(...)))------))))).))..(((((((-((.(((.......)))))).)))))).))(((((((((....))))))))).. ( -36.10)
>DroEre_CAF1 93533 97 - 1
-GCAACUGCGACUCU----------GAGUCGGAGUCGGAGUCGGAGACAGAGAUG-UCUCUGUAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGCACACUUGUGUU
-((.(((.(((((((----------(...)))))))).))).(((.((((((...-.))))))...)))..............))(((((((((....))))))))).. ( -38.30)
>DroYak_CAF1 93560 85 - 1
-GCGACUGCGACUCU----------GAGU------------CGGAGACAGAGAUG-UCUCUGUAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGUACACUUGUGUU
-((((((.((((...----------..))------------)).))...((((((-((.(((.......)))))).)))))))))(((((((((....))))))))).. ( -32.60)
>DroAna_CAF1 90042 103 - 1
UGCUGCGGCGGCGGUGGCGGCGAUGGAGACUG------AGACAGAAACAGAGAAGAUGUCUGUAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGUACACUCGUGUU
.(((((....)))))...(((((.(((..(((------.((..((.(((((.......))))).)))).))).....))).)))))((((((((....))))))))... ( -36.40)
>consensus
UGCAACUGCGACUCU__________GAGUCGG______AGUCGGAGACAGAGAUG_UCUCUGUAUUUCCCAGGACAAUCUUUCGCCACGAGUGUUUGUACACUUGUGUU
.((.....((((((...........))))))...........((((((((((.....)))))..)))))..............))(((((((((....))))))))).. (-25.23 = -26.28 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:56 2006