Locus 345

Sequence ID 3R_DroMel_CAF1
Location 1,327,212 – 1,327,307
Length 95
Max. P 0.999953
window572 window573

overview

Window 2

Location 1,327,212 – 1,327,307
Length 95
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 76.10
Mean single sequence MFE -25.93
Consensus MFE -17.17
Energy contribution -18.30
Covariance contribution 1.13
Combinations/Pair 1.15
Mean z-score -3.58
Structure conservation index 0.66
SVM decision value 4.82
SVM RNA-class probability 0.999953
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1327212 95 + 27905053
GUUGAAAAUGAAAAUUUAUUUUCAACACGCUAACCGCUGAGAAAACAGAAGAGAUUGUGUCUUUUAUAUUUUCUCUUAAUUUACAUCUUAA------------------ACAA
(((((((((((....)))))))))))..((.....)).(((((((...(((((((...)))))))...)))))))................------------------.... ( -21.80)
>DroSec_CAF1 15821 113 + 1
GUUGAAAAUGAAAAUUCAUUUUCGACACGCUAAUCGCUGAGAAAACAGAAGAGAUUAUGUCUUUUAUAUUUUUUCUUAAUUUACAUCUUAAUUAAGGGGGGAAUAUGAAACAA
(((((((((((....)))))))))))(((.(((((.(((......)))....)))))))).(((((((((((..(((((((........)))))).)..)))))))))))... ( -30.10)
>DroSim_CAF1 17520 109 + 1
GUUGAAAAUGAAAAUUCAUUUUCGACACGCUAAUCGCUGAGAAAACAGAAGAGAUUGUGUCUUUUAUAUUUUCUCUUAAUUUACAUCUUAAUUAAGAGGGGAACAUGAA----
(((((((((((....)))))))))))((((.((((.(((......)))....))))))))........((..(((((((((........)))))))))..)).......---- ( -31.80)
>DroYak_CAF1 16703 84 + 1
GUAGGAA-GGAAAAU-----UUGGACACGCUAAUCGCUGAGAAAACAGCAGAGAAUGUGUCUUUAA--UUUUUUCGUAAUAUACAUCUUAAG---------------------
.(((((.-((((((.-----..(((((((....((((((......)))).))...)))))))....--.))))))(((...))).)))))..--------------------- ( -20.00)
>consensus
GUUGAAAAUGAAAAUUCAUUUUCGACACGCUAAUCGCUGAGAAAACAGAAGAGAUUGUGUCUUUUAUAUUUUCUCUUAAUUUACAUCUUAAU_____________________
(((((((((((....)))))))))))..((.....)).(((((((...((((((.....))))))...)))))))...................................... (-17.17 = -18.30 +   1.13)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,327,212 – 1,327,307
Length 95
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 76.10
Mean single sequence MFE -18.55
Consensus MFE -11.62
Energy contribution -13.62
Covariance contribution 2.00
Combinations/Pair 1.08
Mean z-score -1.91
Structure conservation index 0.63
SVM decision value 0.86
SVM RNA-class probability 0.868730
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1327212 95 - 27905053
UUGU------------------UUAAGAUGUAAAUUAAGAGAAAAUAUAAAAGACACAAUCUCUUCUGUUUUCUCAGCGGUUAGCGUGUUGAAAAUAAAUUUUCAUUUUCAAC
....------------------.....((((.((((..(((((((((.((.(((.....))).)).)))))))))...)))).))))(((((((((........))))))))) ( -18.60)
>DroSec_CAF1 15821 113 - 1
UUGUUUCAUAUUCCCCCCUUAAUUAAGAUGUAAAUUAAGAAAAAAUAUAAAAGACAUAAUCUCUUCUGUUUUCUCAGCGAUUAGCGUGUCGAAAAUGAAUUUUCAUUUUCAAC
.................(((((((........))))))).............(((((((((....(((......))).))))...)))))((((((((....))))))))... ( -18.10)
>DroSim_CAF1 17520 109 - 1
----UUCAUGUUCCCCUCUUAAUUAAGAUGUAAAUUAAGAGAAAAUAUAAAAGACACAAUCUCUUCUGUUUUCUCAGCGAUUAGCGUGUCGAAAAUGAAUUUUCAUUUUCAAC
----...(((((...(((((((((........)))))))))..)))))....(((((.........((......))((.....)))))))((((((((....))))))))... ( -24.60)
>DroYak_CAF1 16703 84 - 1
---------------------CUUAAGAUGUAUAUUACGAAAAAA--UUAAAGACACAUUCUCUGCUGUUUUCUCAGCGAUUAGCGUGUCCAA-----AUUUUCC-UUCCUAC
---------------------.................(((((((--((...(((((.(..((.((((......))))))..)..)))))..)-----)))))..-))).... ( -12.90)
>consensus
_____________________AUUAAGAUGUAAAUUAAGAAAAAAUAUAAAAGACACAAUCUCUUCUGUUUUCUCAGCGAUUAGCGUGUCGAAAAUGAAUUUUCAUUUUCAAC
..........................((..(.......(((((((((.((.(((.....))).)).))))))))).((.....)))..))(((((((......)))))))... (-11.62 = -13.62 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:54 2006