Locus 4250

Sequence ID X_DroMel_CAF1
Location 11,168,374 – 11,168,472
Length 98
Max. P 0.884747
window6983 window6984

overview

Window 3

Location 11,168,374 – 11,168,472
Length 98
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 55.59
Mean single sequence MFE -22.94
Consensus MFE -11.53
Energy contribution -9.99
Covariance contribution -1.54
Combinations/Pair 1.50
Mean z-score -1.32
Structure conservation index 0.50
SVM decision value 0.67
SVM RNA-class probability 0.818400
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11168374 98 + 22224390
AGGGGUUCAGCGACCUGCUUAGCAGGCCUCAAAGGGUUAAACCAGAAAUCCCUUUGGCUGAGAAUAAUAUGUAAUAGAGUUUGGUGGACCAAACUCAA--------------
.....(((((((.(((((...))))).).(((((((.............)))))))))))))..............((((((((....))))))))..-------------- ( -35.32)
>DroSim_CAF1 27912 98 + 1
AGGGGUUCAGCGACCUGGUUAGUAAGCCUCAAAGGGUUAAACCAGAAAUCUUUUUGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--------------
..(((((....)))))........(((((....)))))...((((((....)))))).........................................-------------- ( -11.00)
>DroYak_CAF1 77736 112 + 1
AGGGGUUCAGCGACCUGCUUAGCAGACCUUAAAGGGUUAAACCAGCAAUUCCUUUGGCUAAGAAUAAAAUGUAAUAGAGUUUUACAAAGAAUUCAAUUUACUUUGAAUAUAA
..(((((....))))).((((((.(((((....))))).......(((.....))))))))).......(((((.......)))))....((((((......)))))).... ( -22.50)
>consensus
AGGGGUUCAGCGACCUGCUUAGCAGGCCUCAAAGGGUUAAACCAGAAAUCCCUUUGGCU_AGAAUAA_AUGUAAUAGAGUUU_____A__A__C__________________
.((((((..((..........)).))))))((((((.............))))))......................................................... (-11.53 =  -9.99 +  -1.54)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,168,374 – 11,168,472
Length 98
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 55.59
Mean single sequence MFE -22.49
Consensus MFE -8.70
Energy contribution -11.49
Covariance contribution 2.78
Combinations/Pair 1.16
Mean z-score -2.12
Structure conservation index 0.39
SVM decision value 0.93
SVM RNA-class probability 0.884747
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11168374 98 - 22224390
--------------UUGAGUUUGGUCCACCAAACUCUAUUACAUAUUAUUCUCAGCCAAAGGGAUUUCUGGUUUAACCCUUUGAGGCCUGCUAAGCAGGUCGCUGAACCCCU
--------------..((((((((....))))))))...............((((((((((((.((........))))))))).(((((((...))))))))))))...... ( -37.90)
>DroSim_CAF1 27912 98 - 1
--------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCAAAAAGAUUUCUGGUUUAACCCUUUGAGGCUUACUAACCAGGUCGCUGAACCCCU
--------------...............................................((...((((((((((.((.....)).)))..)))))))...))........ ( -10.50)
>DroYak_CAF1 77736 112 - 1
UUAUAUUCAAAGUAAAUUGAAUUCUUUGUAAAACUCUAUUACAUUUUAUUCUUAGCCAAAGGAAUUGCUGGUUUAACCCUUUAAGGUCUGCUAAGCAGGUCGCUGAACCCCU
..................((((....(((((.......)))))....))))(((((.(((((...............)))))..(..((((...))))..))))))...... ( -19.06)
>consensus
__________________G__U__U_____AAACUCUAUUACAU_UUAUUCU_AGCCAAAGGGAUUUCUGGUUUAACCCUUUGAGGCCUGCUAAGCAGGUCGCUGAACCCCU
...................................................((((((((((((.............))))))).(((((((...))))))))))))...... ( -8.70 = -11.49 +   2.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:15 2006