Locus 5820

Sequence ID 2L_DroMel_CAF1
Location 16,490,237 – 16,490,349
Length 112
Max. P 0.733735
window9238 window9239

overview

Window 8

Location 16,490,237 – 16,490,349
Length 112
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 80.91
Mean single sequence MFE -27.08
Consensus MFE -14.00
Energy contribution -14.88
Covariance contribution 0.88
Combinations/Pair 1.19
Mean z-score -1.96
Structure conservation index 0.52
SVM decision value -0.01
SVM RNA-class probability 0.528062
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16490237 112 + 22407834
AGUUUGAGCUUAAGUUUUGUGAUUAGAUUAAAGCCUUAUCACAUCUGUUAGGCAUUACAGCACUUUUGUUUUAGUUUUGCUUGGAAUAAG----AAGAAAA-AAGAAAAAGAGCUCG
.....((((((......((((((.((........)).))))))(((.(((((((..((((((....))))...))..)))))))....))----)......-........)))))). ( -25.10)
>DroSec_CAF1 2294 117 + 1
AGUUUGAGCUUAAGUUUUGUGAUAAGAUUAAAGCCUUAUCACAUCUGUUAGGCAUUACAGCACUUUUGUUUUAGUUUUGCUUGGAAUAGGCGAUAAGAAAAUAAUGAACAUAGCUCG
.....(((((...(((((((((((((........))))))))).((((........)))).....(((((((....(((((((...)))))))....))))))).))))..))))). ( -29.10)
>DroSim_CAF1 2277 117 + 1
AGUUUGAGCUUAAGUUUUGUGAUUAGAUUAAAGCCUUAUCACAUCUGUUAGGCAUUACAGCACUUUUGUUUUAGUUUUGCUUGGAAUAGGCGAUAAGAAAAUAAUGAACAUAGCUCG
.....(((((...((((((((((.((........)).)))))).((((........)))).....(((((((....(((((((...)))))))....))))))).))))..))))). ( -25.10)
>DroEre_CAF1 15082 112 + 1
AGUUUGAGCUUAUGUUUUGUGAUUAGAUGU---UAUGAUCACA--UGUUGAGCAUUACAGCUCUUAAAAAGCACUUUUGCUUGGAAUAGCUGAUAAGUAAAUAAUGAACAUAGCUAA
......((((.((((((((((((((.....---..))))))))--((((..((.((((((((.((...(((((....)))))..)).))))).))))).))))..)))))))))).. ( -29.50)
>DroYak_CAF1 3024 115 + 1
AGCAUGAUCUUAGGUUUUGUGAUUAGAAUAAAGCCUUAUCACA--UGUUAUGCAUUACAGCACUUAAAAUAACUUUAUGCUUGUAAUGGCUAAUAAGAAAAUAAUGAACAUGGCUUG
(((.((((...(((((((((.......))))))))).))))((--((((...((((((((((..((((.....))))))).))))))).((....)).........))))))))).. ( -26.60)
>consensus
AGUUUGAGCUUAAGUUUUGUGAUUAGAUUAAAGCCUUAUCACAUCUGUUAGGCAUUACAGCACUUUUGUUUUAGUUUUGCUUGGAAUAGGCGAUAAGAAAAUAAUGAACAUAGCUCG
.....(((((...((((((((((.((........)).))))))....(((((((..((...............))..))))))).....................))))..))))). (-14.00 = -14.88 +   0.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,490,237 – 16,490,349
Length 112
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 80.91
Mean single sequence MFE -20.88
Consensus MFE -10.88
Energy contribution -11.76
Covariance contribution 0.88
Combinations/Pair 1.09
Mean z-score -2.17
Structure conservation index 0.52
SVM decision value 0.43
SVM RNA-class probability 0.733735
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16490237 112 - 22407834
CGAGCUCUUUUUCUU-UUUUCUU----CUUAUUCCAAGCAAAACUAAAACAAAAGUGCUGUAAUGCCUAACAGAUGUGAUAAGGCUUUAAUCUAAUCACAAAACUUAAGCUCAAACU
.(((((..((((..(-(((.(((----........))).))))..))))...((((.((((........)))).((((((.(((......))).))))))..)))).)))))..... ( -18.40)
>DroSec_CAF1 2294 117 - 1
CGAGCUAUGUUCAUUAUUUUCUUAUCGCCUAUUCCAAGCAAAACUAAAACAAAAGUGCUGUAAUGCCUAACAGAUGUGAUAAGGCUUUAAUCUUAUCACAAAACUUAAGCUCAAACU
.(((((....................((.........)).............((((.((((........)))).((((((((((......))))))))))..)))).)))))..... ( -23.10)
>DroSim_CAF1 2277 117 - 1
CGAGCUAUGUUCAUUAUUUUCUUAUCGCCUAUUCCAAGCAAAACUAAAACAAAAGUGCUGUAAUGCCUAACAGAUGUGAUAAGGCUUUAAUCUAAUCACAAAACUUAAGCUCAAACU
.(((((....................((.........)).............((((.((((........)))).((((((.(((......))).))))))..)))).)))))..... ( -19.20)
>DroEre_CAF1 15082 112 - 1
UUAGCUAUGUUCAUUAUUUACUUAUCAGCUAUUCCAAGCAAAAGUGCUUUUUAAGAGCUGUAAUGCUCAACA--UGUGAUCAUA---ACAUCUAAUCACAAAACAUAAGCUCAAACU
..(((((((((..........(((.(((((.....(((((....)))))......)))))))).........--((((((....---.......)))))).))))).))))...... ( -20.90)
>DroYak_CAF1 3024 115 - 1
CAAGCCAUGUUCAUUAUUUUCUUAUUAGCCAUUACAAGCAUAAAGUUAUUUUAAGUGCUGUAAUGCAUAACA--UGUGAUAAGGCUUUAUUCUAAUCACAAAACCUAAGAUCAUGCU
..(((.(((.((...............((.((((((.((((.............))))))))))))......--((((((.(((......))).))))))........)).)))))) ( -22.82)
>consensus
CGAGCUAUGUUCAUUAUUUUCUUAUCACCUAUUCCAAGCAAAACUAAAACAAAAGUGCUGUAAUGCCUAACAGAUGUGAUAAGGCUUUAAUCUAAUCACAAAACUUAAGCUCAAACU
.(((((.......................((((...((((...............))))..)))).........((((((.(((......))).)))))).......)))))..... (-10.88 = -11.76 +   0.88)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:50 2006