Locus 3370

Sequence ID 2L_DroMel_CAF1
Location 9,770,540 – 9,770,672
Length 132
Max. P 0.885334
window5335 window5336

overview

Window 5

Location 9,770,540 – 9,770,652
Length 112
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 77.22
Mean single sequence MFE -25.27
Consensus MFE -15.55
Energy contribution -16.08
Covariance contribution 0.53
Combinations/Pair 1.33
Mean z-score -1.83
Structure conservation index 0.62
SVM decision value 0.94
SVM RNA-class probability 0.885334
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9770540 112 - 22407834
AGUUGGCCUUAUCCCAUUACC-UUUAGC-U---ACCUAUCUCCCACUUGCAGAGCUAUCUGGCUGGCUUUCCUCACCGCCAUUAUGAUUUACACCCACAUCGUGAUCGCUGACCUCA
(((..(((.............-....((-.---...............))(((....))))))..))).........((.((((((((..........)))))))).))........ ( -18.89)
>DroSec_CAF1 52586 113 - 1
AGUUGGCCUCAUACCAUUACCAUUCAGC-U---ACCUAUCUCCCACUUGCAGAGCUAUCUGGCUGGCUCUGCUCACCGGCAUCAUGAUUUACACCCACAUCGUGAUCGCUGACCUCA
((((((.................)))))-)---...............(((((((((......)))))))))....((((((((((((..........)))))))).))))...... ( -28.93)
>DroSim_CAF1 52038 113 - 1
AGUUGGCCUUAUAUCAUUACCAUUUAGC-U---ACCUAUCUCCCACUUGCAGAGCUAUCUGGCUGGCUCUGCUCACCGCCAUCAUGAUCUACACCCACAUCGUGAUCGCUGACCUCA
.((..((.....................-.---...............(((((((((......)))))))))........((((((((..........)))))))).))..)).... ( -26.70)
>DroEre_CAF1 52031 112 - 1
AGUUGGCCUUAUAGUUUUAAC-UGGAGC-U---ACCCAUCUGCCAUUUGCAGAGCUGCCUGGCUGGCUCUGCUCACCGCCAUUAUGAUUUACACCCACAUAGUGAUCGCUGACCUCA
.((..((....(((((((...-.)))))-)---).......((.....((((((((((...)).)))))))).....))(((((((...........)))))))...))..)).... ( -29.50)
>DroYak_CAF1 54192 95 - 1
-----------------UAUC-CUGAGC-U---ACCUAUCUCCCACUUGCAGAGCUGUCUGGCUGGCUCUGCUCACCGCCAUUGUGAUAUACACCCACAUCGUGAUCGCUGACCUCA
-----------------....-..(((.-.---...............((((((((........)))))))).....((.((..((((..........))))..)).))....))). ( -22.30)
>DroAna_CAF1 59949 115 - 1
AGUUCACUUU-GCUGAUUAAC-UUGAGACUAAAACUUAAAUAACUAUUUCAGAGCUAUUUGGCUGGCCUUUCUAACUAGCCUUGUGAUCUACACCCAUUUAGUGAUUGUGAACCUGA
.((((((.(.-.((((.....-(((((.......)))))...........(((..(((..((((((.........))))))..))).)))........))))..)..)))))).... ( -25.30)
>consensus
AGUUGGCCUUAUACCAUUACC_UUGAGC_U___ACCUAUCUCCCACUUGCAGAGCUAUCUGGCUGGCUCUGCUCACCGCCAUUAUGAUUUACACCCACAUCGUGAUCGCUGACCUCA
.((((((.........................................(((((((((......))))))))).............((((.((.........)))))))))))).... (-15.55 = -16.08 +   0.53)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 9,770,580 – 9,770,672
Length 92
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 63.38
Mean single sequence MFE -18.44
Consensus MFE -9.76
Energy contribution -10.16
Covariance contribution 0.40
Combinations/Pair 1.22
Mean z-score -1.56
Structure conservation index 0.53
SVM decision value 0.52
SVM RNA-class probability 0.769424
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9770580 92 - 22407834
UCCAACUCAA-------UG------------UUUAAAAAAGUUGGCCUUAUCCCAUUACC-UUUAGC-U---ACCUAUCUCCCACUUGCAGAGCUAUCUGGCUGGCUUUCCUCACC
..........-------..------------......(((((..(((.............-....((-.---...............))(((....))))))..)))))....... ( -13.89)
>DroSec_CAF1 52626 100 - 1
CCUAACAUAAAGAUACCUG------------CUUAAAAAAGUUGGCCUCAUACCAUUACCAUUCAGC-U---ACCUAUCUCCCACUUGCAGAGCUAUCUGGCUGGCUCUGCUCACC
..........(((((...(------------((.........(((.......))).........)))-.---...))))).......(((((((((......)))))))))..... ( -21.07)
>DroSim_CAF1 52078 100 - 1
CCUAACAUAAAGAUACCUG------------UUUAAAACAGUUGGCCUUAUAUCAUUACCAUUUAGC-U---ACCUAUCUCCCACUUGCAGAGCUAUCUGGCUGGCUCUGCUCACC
..........(((((.(((------------(.....)))).((((...................))-)---)..))))).......(((((((((......)))))))))..... ( -19.51)
>DroEre_CAF1 52071 111 - 1
CUCAUUGGUCACAUUCCUACUGCUCCUAUUCUGUAAACCAGUUGGCCUUAUAGUUUUAAC-UGGAGC-U---ACCCAUCUGCCAUUUGCAGAGCUGCCUGGCUGGCUCUGCUCACC
.....((((............(((((.(..((((((.((....))..))))))..)....-.)))))-.---........))))...((((((((((...)).))))))))..... ( -29.10)
>DroAna_CAF1 59989 80 - 1
----------------------------------AUAGUAGUUCACUUU-GCUGAUUAAC-UUGAGACUAAAACUUAAAUAACUAUUUCAGAGCUAUUUGGCUGGCCUUUCUAACU
----------------------------------.(((.((..(.....-.((((.....-(((((.......))))).........))))((((....)))))..))..)))... (  -8.64)
>consensus
CCCAACAUAAA_AU_CCUG____________UUUAAAAAAGUUGGCCUUAUACCAUUACC_UUGAGC_U___ACCUAUCUCCCACUUGCAGAGCUAUCUGGCUGGCUCUGCUCACC
.......................................................................................(((((((((......)))))))))..... ( -9.76 = -10.16 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:49 2006