Locus 5725

Sequence ID 3R_DroMel_CAF1
Location 14,943,421 – 14,943,535
Length 114
Max. P 0.870110
window9368 window9369

overview

Window 8

Location 14,943,421 – 14,943,535
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.26
Mean single sequence MFE -25.35
Consensus MFE -20.35
Energy contribution -20.85
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.04
Structure conservation index 0.80
SVM decision value 0.87
SVM RNA-class probability 0.870110
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14943421 114 + 27905053
AAAUUGCUCAAGCCAAAUGGGCAAGCUGUUCUCGUCUUGCCAAGU------AAGUCUUGAUUCAAGCUCAAAUUGCUUAAGUUUUGUAUUUGCUUUUAUUUGGUAUUUCAUAUUCUAAUU
...........((((((((((((((.((....)).))))))((((------(((((..((((.((((.......)))).))))..).)))))))).))))))))................ ( -29.60)
>DroSec_CAF1 79254 110 + 1
AAAUUGCUCAAGCCAAAUCGGCAAGUUGUUCUCGUCUUGCCAA----------GUCUUGAUUCAAGCUAAAAUUGCUUAUGUUUUGUAUUUGCUUUUAUUUGGUAUUUCAUAUUCUAAUU
...........(((((((.((((((.((....)).))))))((----------(((..(((..((((.......))))..)))..).))))......)))))))................ ( -21.50)
>DroSim_CAF1 72096 110 + 1
AAAUUGCUCAAGCCAAAUCGGCAAGUUGUUCUCGUCUUGCCAA----------GUCUUGAUUCAAGCUCAAAUUGCUUAAGUUUUGUAUUUGCUUUUAUUUGGUAUUUCAUAUUCUAAUU
...........(((((((.((((((.((....)).))))))((----------(((..((((.((((.......)))).))))..).))))......)))))))................ ( -22.30)
>DroYak_CAF1 76233 120 + 1
AAAUUGUGCAAGCCAAAUGGGCAAGUUGUUCUCGUCUUGCCAAGUCUUGCCAAGACUGGAUUCAAGCUCAAAUUGCUGAAGUUUUGCUUUUGCUUUUAUUUGGUAUUUCAUAUUCUAAUU
....((((.((((((((((((((((.((....)).))))))((((...((.((((((....(((.((.......)))))))))))))....)))).)))))))).)).))))........ ( -28.00)
>consensus
AAAUUGCUCAAGCCAAAUCGGCAAGUUGUUCUCGUCUUGCCAA__________GUCUUGAUUCAAGCUCAAAUUGCUUAAGUUUUGUAUUUGCUUUUAUUUGGUAUUUCAUAUUCUAAUU
...........(((((((.((((((.((....)).))))))..............(..((((.((((.......)))).))))..)...........)))))))................ (-20.35 = -20.85 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 14,943,421 – 14,943,535
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.26
Mean single sequence MFE -21.66
Consensus MFE -16.30
Energy contribution -16.80
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.75
SVM decision value 0.27
SVM RNA-class probability 0.662956
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14943421 114 - 27905053
AAUUAGAAUAUGAAAUACCAAAUAAAAGCAAAUACAAAACUUAAGCAAUUUGAGCUUGAAUCAAGACUU------ACUUGGCAAGACGAGAACAGCUUGCCCAUUUGGCUUGAGCAAUUU
...........................((...........((((((.......)))))).(((((.((.------....((((((.(.......))))))).....)))))))))..... ( -22.30)
>DroSec_CAF1 79254 110 - 1
AAUUAGAAUAUGAAAUACCAAAUAAAAGCAAAUACAAAACAUAAGCAAUUUUAGCUUGAAUCAAGAC----------UUGGCAAGACGAGAACAACUUGCCGAUUUGGCUUGAGCAAUUU
...((((((.((......)).......((...............)).))))))(((..(..((((..----------((((((((..(....)..))))))))))))..)..)))..... ( -20.56)
>DroSim_CAF1 72096 110 - 1
AAUUAGAAUAUGAAAUACCAAAUAAAAGCAAAUACAAAACUUAAGCAAUUUGAGCUUGAAUCAAGAC----------UUGGCAAGACGAGAACAACUUGCCGAUUUGGCUUGAGCAAUUU
...........................((...........((((((.......)))))).(((((..----------((((((((..(....)..)))))))).....)))))))..... ( -21.50)
>DroYak_CAF1 76233 120 - 1
AAUUAGAAUAUGAAAUACCAAAUAAAAGCAAAAGCAAAACUUCAGCAAUUUGAGCUUGAAUCCAGUCUUGGCAAGACUUGGCAAGACGAGAACAACUUGCCCAUUUGGCUUGCACAAUUU
.................((((((....((....)).........((((.(((..((((....).((((((.((.....)).)))))))))..))).))))..))))))............ ( -22.30)
>consensus
AAUUAGAAUAUGAAAUACCAAAUAAAAGCAAAUACAAAACUUAAGCAAUUUGAGCUUGAAUCAAGAC__________UUGGCAAGACGAGAACAACUUGCCCAUUUGGCUUGAGCAAUUU
.................((((((.................((((((.......))))))....................((((((..(....)..)))))).))))))............ (-16.30 = -16.80 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:56 2006