Locus 3339

Sequence ID 2R_DroMel_CAF1
Location 11,349,473 – 11,349,565
Length 92
Max. P 0.823299
window5462 window5463

overview

Window 2

Location 11,349,473 – 11,349,565
Length 92
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 86.99
Mean single sequence MFE -19.27
Consensus MFE -13.71
Energy contribution -13.78
Covariance contribution 0.06
Combinations/Pair 1.06
Mean z-score -2.09
Structure conservation index 0.71
SVM decision value 0.69
SVM RNA-class probability 0.823299
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11349473 92 + 20766785
UAAUCUUCCAUGA---AUAGUAUCUUUCCUAGAUGGUUAUACUUUUGAAAUAUAUAAUUCAAAAGAUGUGCUCACCUUAAACUUAGAGCACUGAA
(((((.((...((---(........)))...)).)))))..((((((((........))))))))..((((((............)))))).... ( -18.00)
>DroSec_CAF1 7655 91 + 1
UAAUCUUCCAUGA---AUAGUAGCUUUCCUAUAUGGUUAUACUUUUGAAAUAUAUAAUUCAAAAGGUGUGCUCACCUUAAACUUAGAGCACUG-A
.......((((..---((((........)))))))).....((((((((........))))))))..((((((............))))))..-. ( -18.20)
>DroSim_CAF1 7479 91 + 1
UAAUCUUCCAUGA---AUAGUAGCUUUCCUAGAUGGUUAUACUUUUGAAAUAUAUAAUUCAAAAGGUG-GCUCACCUUAAACUUAGAGCACUGUA
.............---(((((.(((((...((.(((((((.((((((((........)))))))))))-)).)).)).......)))))))))). ( -18.30)
>DroYak_CAF1 7545 95 + 1
UAAUAACUCACUAAAGAGGGUAUUUUUCCUAGAUGGUUCUACUUUUGAAGUACAUCAUUUAAAAGAUGUGCUCACCUCAAACUUAGAGCACUGUA
................((((......)))).....((((((..(((((((((((((........))))))))....)))))..))))))...... ( -22.60)
>consensus
UAAUCUUCCAUGA___AUAGUAGCUUUCCUAGAUGGUUAUACUUUUGAAAUAUAUAAUUCAAAAGAUGUGCUCACCUUAAACUUAGAGCACUGUA
...........................((.....)).....((((((((........))))))))..((((((............)))))).... (-13.71 = -13.78 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 11,349,473 – 11,349,565
Length 92
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 86.99
Mean single sequence MFE -19.15
Consensus MFE -13.80
Energy contribution -14.30
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.72
SVM decision value 0.29
SVM RNA-class probability 0.669951
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11349473 92 - 20766785
UUCAGUGCUCUAAGUUUAAGGUGAGCACAUCUUUUGAAUUAUAUAUUUCAAAAGUAUAACCAUCUAGGAAAGAUACUAU---UCAUGGAAGAUUA
....((((((............))))))..((((((((........)))))))).....((((.(((........))).---..))))....... ( -20.00)
>DroSec_CAF1 7655 91 - 1
U-CAGUGCUCUAAGUUUAAGGUGAGCACACCUUUUGAAUUAUAUAUUUCAAAAGUAUAACCAUAUAGGAAAGCUACUAU---UCAUGGAAGAUUA
.-..((((((............))))))..((((((((........)))))))).....((((((((........))))---..))))....... ( -21.60)
>DroSim_CAF1 7479 91 - 1
UACAGUGCUCUAAGUUUAAGGUGAGC-CACCUUUUGAAUUAUAUAUUUCAAAAGUAUAACCAUCUAGGAAAGCUACUAU---UCAUGGAAGAUUA
....((((((............))).-)))((((((((........)))))))).....((((.(((........))).---..))))....... ( -15.50)
>DroYak_CAF1 7545 95 - 1
UACAGUGCUCUAAGUUUGAGGUGAGCACAUCUUUUAAAUGAUGUACUUCAAAAGUAGAACCAUCUAGGAAAAAUACCCUCUUUAGUGAGUUAUUA
........((((..((((((((....(((((........)))))))))))))..)))).((.....)).........(((......)))...... ( -19.50)
>consensus
UACAGUGCUCUAAGUUUAAGGUGAGCACACCUUUUGAAUUAUAUAUUUCAAAAGUAUAACCAUCUAGGAAAGAUACUAU___UCAUGGAAGAUUA
....((((((............))))))..((((((((........)))))))).....((.....))........................... (-13.80 = -14.30 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:08 2006