Locus 6554

Sequence ID 3L_DroMel_CAF1
Location 17,309,705 – 17,309,859
Length 154
Max. P 0.694079
window10671 window10672

overview

Window 1

Location 17,309,705 – 17,309,819
Length 114
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 85.15
Mean single sequence MFE -36.42
Consensus MFE -27.28
Energy contribution -26.65
Covariance contribution -0.63
Combinations/Pair 1.32
Mean z-score -2.28
Structure conservation index 0.75
SVM decision value 0.20
SVM RNA-class probability 0.628995
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17309705 114 + 23771897
GCCAGGUGGCAUAAUCGAUGCUCUGAAUGAAGAAACGAAUGGGCUCCAGGAUAAGAUAUUGGAAAAAGAAGACCAGGACGAUGGUUACCAACAUCGUCUUGAAUCUCUGGGGCU
.(((..((((((.....))))(((......)))..))..)))((((((((((......((....)).......((((((((((........)))))))))).))).))))))). ( -37.90)
>DroPse_CAF1 7632 114 + 1
GCCAGGUGGCCGAGUCGAUGGACAGCACAAUGAAUCUGAUAGGAUCGAGGACGAUGAACUGGAACAGCAAUACUAGCACAAUCGUCACCACCAUGGUCUUGAACUUCUUGGUCU
((((((.(..((((.(.((((..........((.(((....)))))(..((((((...((((..........))))....))))))..).)))).).))))..)..)))))).. ( -31.90)
>DroSec_CAF1 8622 114 + 1
GCCAGGUGGCAUAAUCGAUGCUCAGAAUGAAGAAACGAAUGGGCUCCAGGAUGAGGUAUUGGAAAAAGAAGACCAGGACGAUGGUUACCAACAUCGUCUUGAGUCUCUGGGGCU
.(((..((((((.....))))((.....)).....))..)))(((((((.........((....))...((((((((((((((........)))))))))).))))))))))). ( -38.60)
>DroSim_CAF1 7517 114 + 1
GCCAGGUGGCAUAAUCGAUGCUCAGAAUGAAGAAACGAAUGGGCUCCAGGAUGAGGUAUUGGAAAAAGAAGACCAGGACGAUGGUUACCAACAUCGUCUUGAGUCUCUGGGGCU
.(((..((((((.....))))((.....)).....))..)))(((((((.........((....))...((((((((((((((........)))))))))).))))))))))). ( -38.60)
>DroEre_CAF1 6929 114 + 1
GCCAGGUGGCAUAGUCGAUGCCCAGAACGAAGAAACGAAAGGGCUCUAGGACGAGAUAUUGGAAAAAGAACACCAGGACGAUGGUCACCAACAUCGUCUUGAAUCUCUGCGGCU
(((....)))..(((((..((((....((......))...))))........(((((.((....)).......((((((((((........)))))))))).)))))..))))) ( -35.90)
>DroYak_CAF1 8963 114 + 1
GCCAGGUGGCAUAAUCGAUGCCCAGAAUGAGGAAACGGAUGGGUUCUAGAAUGAGAUAUUGGAAAAAGAACACCAGGACGAUGGUCACCAACAUCGUCUUGAAUCUCUGGGGCU
(((....)))..........((((((....(....).(((..(((((...................)))))..((((((((((........)))))))))).)))))))))... ( -35.61)
>consensus
GCCAGGUGGCAUAAUCGAUGCUCAGAAUGAAGAAACGAAUGGGCUCCAGGAUGAGAUAUUGGAAAAAGAAGACCAGGACGAUGGUCACCAACAUCGUCUUGAAUCUCUGGGGCU
(((....)))...............................(((((((((.(((....)))............((((((((((........))))))))))....))))))))) (-27.28 = -26.65 +  -0.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 17,309,745 – 17,309,859
Length 114
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 82.81
Mean single sequence MFE -34.84
Consensus MFE -26.58
Energy contribution -26.00
Covariance contribution -0.58
Combinations/Pair 1.40
Mean z-score -1.76
Structure conservation index 0.76
SVM decision value 0.34
SVM RNA-class probability 0.694079
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17309745 114 + 23771897
GGGCUCCAGGAUAAGAUAUUGGAAAAAGAAGACCAGGACGAUGGUUACCAACAUCGUCUUGAAUCUCUGGGGCUCGUGCAUGAAUCCCGAGAAGAUUGAGACCAGAACGAAGCA
((((((((((((......((....)).......((((((((((........)))))))))).))).)))))))))((...((..((.(((.....))).)).))..))...... ( -35.10)
>DroPse_CAF1 7672 114 + 1
AGGAUCGAGGACGAUGAACUGGAACAGCAAUACUAGCACAAUCGUCACCACCAUGGUCUUGAACUUCUUGGUCUCGUGUUGGAAGCCUGUGAUCACGGCUAUUAGGGUGAAACU
..(((((((((((((...((((..........))))....))))))(((.....))).........)))))))(((..((((.((((.((....)))))).))))..))).... ( -28.50)
>DroSec_CAF1 8662 114 + 1
GGGCUCCAGGAUGAGGUAUUGGAAAAAGAAGACCAGGACGAUGGUUACCAACAUCGUCUUGAGUCUCUGGGGCUCGUGCAUAAAUCCCGAGAAGAUUGCGACCAGGAUGAAGCA
(((((((((.........((....))...((((((((((((((........)))))))))).))))))))))))).(((....((((.(.(..(....)..)).))))...))) ( -40.40)
>DroSim_CAF1 7557 114 + 1
GGGCUCCAGGAUGAGGUAUUGGAAAAAGAAGACCAGGACGAUGGUUACCAACAUCGUCUUGAGUCUCUGGGGCUCGUGCAUAAAUCCCGAAAAGAUUGCGACCAGGAUGAAGCA
(((((((((.........((....))...((((((((((((((........)))))))))).))))))))))))).(((....((((.(.............).))))...))) ( -39.72)
>DroEre_CAF1 6969 114 + 1
GGGCUCUAGGACGAGAUAUUGGAAAAAGAACACCAGGACGAUGGUCACCAACAUCGUCUUGAAUCUCUGCGGCUCGUGCAUGAAUCCAGAGAACAUUGAUACCAGGAUGAAGCA
((.(((......))).(((..(...........((((((((((........))))))))))..((((((.(..(((....)))..)))))))...)..)))))........... ( -31.70)
>DroYak_CAF1 9003 114 + 1
GGGUUCUAGAAUGAGAUAUUGGAAAAAGAACACCAGGACGAUGGUCACCAACAUCGUCUUGAAUCUCUGGGGCUCGUGUAUGAAUCCCGAGAAGAUUGAUACCAGGGUGAAGCA
((((((((((........((....)).......((((((((((........))))))))))....))))))))))(.((((.((((.......)))).)))))........... ( -33.60)
>consensus
GGGCUCCAGGAUGAGAUAUUGGAAAAAGAAGACCAGGACGAUGGUCACCAACAUCGUCUUGAAUCUCUGGGGCUCGUGCAUGAAUCCCGAGAAGAUUGAGACCAGGAUGAAGCA
((((((((((.(((....)))............((((((((((........))))))))))....))))))))))..((....((((.(.............).))))...)). (-26.58 = -26.00 +  -0.58)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:13 2006