Locus 4236

Sequence ID 2R_DroMel_CAF1
Location 13,979,589 – 13,979,683
Length 94
Max. P 0.882040
window6798 window6799

overview

Window 8

Location 13,979,589 – 13,979,683
Length 94
Sequences 4
Columns 94
Reading direction forward
Mean pairwise identity 89.89
Mean single sequence MFE -27.96
Consensus MFE -21.20
Energy contribution -21.45
Covariance contribution 0.25
Combinations/Pair 1.17
Mean z-score -1.93
Structure conservation index 0.76
SVM decision value 0.50
SVM RNA-class probability 0.760690
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13979589 94 + 20766785
UGAGAAGCCACAUAAAGUGCAAGUGUGAGUGCAUGGGGAAUUCGCACACGAUGCACUUGCCGCGCAUGGGAAUAUCCUUAAAAUAAAAUGUCUC
.((((...........((((..(.(..(((((((.(............).)))))))..))..))))(((.....)))............)))) ( -24.40)
>DroSec_CAF1 17877 94 + 1
UGAGAAGCCACAUAAAGUGCAAGUGUGAGUGCGUGGGGAAUUCACUCACGAUGCACUUGCCGCGCAUGGGAAUAUCCUUUAAAUAAUAUGUCUC
.((((.((......(((((((..((((((((.((.....)).)))))))).))))))).....))..(((.....)))............)))) ( -27.40)
>DroSim_CAF1 16961 94 + 1
UGAGAAGCCACAUAAAGUGCAAGUGUGAGUGCGUGGGGAAUUCACUCACGAUGCACUUGCCGCGCACGGGAAUAUCCUUAAGAUAAUAUGUCUC
.((((.....((((..((((..(.(..((((((((((.......)))))...)))))..))..))))(((.....)))........)))))))) ( -28.10)
>DroEre_CAF1 17985 94 + 1
UGCGAAGCCACAUAAAGUGCAAGUGCGAGAGCCUGGGGAAUUCACCCAGGAUGCACUUGCCGCGCAAGGCUAAAUCCUUAAAAUAAUAUUUAUU
.....((((.......(.(((((((((....((((((.......)))))).))))))))))......))))....................... ( -31.92)
>consensus
UGAGAAGCCACAUAAAGUGCAAGUGUGAGUGCGUGGGGAAUUCACUCACGAUGCACUUGCCGCGCAUGGGAAUAUCCUUAAAAUAAUAUGUCUC
.((((...........(((((((((((....((((((.......)))))).)))))))).)))....((......)).............)))) (-21.20 = -21.45 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 13,979,589 – 13,979,683
Length 94
Sequences 4
Columns 94
Reading direction reverse
Mean pairwise identity 89.89
Mean single sequence MFE -28.48
Consensus MFE -20.94
Energy contribution -22.38
Covariance contribution 1.44
Combinations/Pair 1.08
Mean z-score -2.65
Structure conservation index 0.74
SVM decision value 0.92
SVM RNA-class probability 0.882040
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13979589 94 - 20766785
GAGACAUUUUAUUUUAAGGAUAUUCCCAUGCGCGGCAAGUGCAUCGUGUGCGAAUUCCCCAUGCACUCACACUUGCACUUUAUGUGGCUUCUCA
((((.............((......))....((.(((((((((..(((((.(.............).))))).))))))...))).)).)))). ( -24.12)
>DroSec_CAF1 17877 94 - 1
GAGACAUAUUAUUUAAAGGAUAUUCCCAUGCGCGGCAAGUGCAUCGUGAGUGAAUUCCCCACGCACUCACACUUGCACUUUAUGUGGCUUCUCA
((((.............((......))....((.(((((((((..(((((((...........)))))))...))))))...))).)).)))). ( -29.20)
>DroSim_CAF1 16961 94 - 1
GAGACAUAUUAUCUUAAGGAUAUUCCCGUGCGCGGCAAGUGCAUCGUGAGUGAAUUCCCCACGCACUCACACUUGCACUUUAUGUGGCUUCUCA
((((.....((((.....)))).........((.(((((((((..(((((((...........)))))))...))))))...))).)).)))). ( -29.20)
>DroEre_CAF1 17985 94 - 1
AAUAAAUAUUAUUUUAAGGAUUUAGCCUUGCGCGGCAAGUGCAUCCUGGGUGAAUUCCCCAGGCUCUCGCACUUGCACUUUAUGUGGCUUCGCA
..............(((((......))))).(((((((((((..((((((.(....))))))).....))))))))((.....)).....))). ( -31.40)
>consensus
GAGACAUAUUAUUUUAAGGAUAUUCCCAUGCGCGGCAAGUGCAUCGUGAGUGAAUUCCCCACGCACUCACACUUGCACUUUAUGUGGCUUCUCA
((((.............((......))....((.(((((((((..(((((((...........)))))))...))))))...))).)).)))). (-20.94 = -22.38 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:55 2006