Locus 972

Sequence ID 2R_DroMel_CAF1
Location 4,117,498 – 4,117,602
Length 104
Max. P 0.600827
window1731 window1732

overview

Window 1

Location 4,117,498 – 4,117,602
Length 104
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 89.26
Mean single sequence MFE -28.61
Consensus MFE -18.85
Energy contribution -19.60
Covariance contribution 0.75
Combinations/Pair 1.09
Mean z-score -2.31
Structure conservation index 0.66
SVM decision value 0.14
SVM RNA-class probability 0.600827
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4117498 104 + 20766785
CACGUCG------CUGUUGUUGUUUAUUGAAUUUCUAUGCAAUUUUGUUAACUGGAUCAAUUAUUUCAAUUGCGUGUUCGGUAAACACAACUAGUGACGCAGUCCAUGGA--
..(((((------(((((((.(((((((((((....((((((((....(((.((...)).)))....)))))))))))))))))))))))).)))))))...........-- ( -31.70)
>DroSim_CAF1 30564 104 + 1
CACGUCG------CUGUUGUUGUUUAUUGAAUUUCUAUGCAAUUUUGUUAACUGGAUCAAUUAUUUCAAUUGCGUGUUCGGUAAACACAACUAGUGACGCAGUCCAUGGA--
..(((((------(((((((.(((((((((((....((((((((....(((.((...)).)))....)))))))))))))))))))))))).)))))))...........-- ( -31.70)
>DroEre_CAF1 7979 103 + 1
UACGGCG---------CUCUUGUUUAUUGAAUUUCUAUGCAGUUUUGUUAACUGGAUCAAUUACUUCAAUUGCGUGUUCGGUAAACACAACUUGUGACGCAGUCCACGGAGA
.......---------((((((((((((((((....((((((((..((..............))...))))))))))))))))))))......(((........))))))). ( -21.14)
>DroYak_CAF1 14521 112 + 1
UACGCUGCCUACGCUGUUGUUGUUUAUUGAAUUUCUAUGCAAUUUUGUUAACUGGAUCAAUUAUUUCAAUUGCGUGUUCGGUAAACACAACUUGUGACGCAGUCCACAGAGA
...(((((...(((.(((((.(((((((((((....((((((((....(((.((...)).)))....))))))))))))))))))))))))..)))..)))))......... ( -29.90)
>consensus
CACGUCG______CUGUUGUUGUUUAUUGAAUUUCUAUGCAAUUUUGUUAACUGGAUCAAUUAUUUCAAUUGCGUGUUCGGUAAACACAACUAGUGACGCAGUCCACGGA__
...............(((((.(((((((((((....((((((((....(((.((...)).)))....))))))))))))))))))))))))(((((........)))))... (-18.85 = -19.60 +   0.75)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 4,117,498 – 4,117,602
Length 104
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 89.26
Mean single sequence MFE -22.35
Consensus MFE -16.75
Energy contribution -17.38
Covariance contribution 0.62
Combinations/Pair 1.04
Mean z-score -1.50
Structure conservation index 0.75
SVM decision value 0.03
SVM RNA-class probability 0.549585
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4117498 104 - 20766785
--UCCAUGGACUGCGUCACUAGUUGUGUUUACCGAACACGCAAUUGAAAUAAUUGAUCCAGUUAACAAAAUUGCAUAGAAAUUCAAUAAACAACAACAG------CGACGUG
--..........(((((.((.((((((((((........((((((....((((((...))))))....))))))...(.....)..))))).)))))))------.))))). ( -24.20)
>DroSim_CAF1 30564 104 - 1
--UCCAUGGACUGCGUCACUAGUUGUGUUUACCGAACACGCAAUUGAAAUAAUUGAUCCAGUUAACAAAAUUGCAUAGAAAUUCAAUAAACAACAACAG------CGACGUG
--..........(((((.((.((((((((((........((((((....((((((...))))))....))))))...(.....)..))))).)))))))------.))))). ( -24.20)
>DroEre_CAF1 7979 103 - 1
UCUCCGUGGACUGCGUCACAAGUUGUGUUUACCGAACACGCAAUUGAAGUAAUUGAUCCAGUUAACAAAACUGCAUAGAAAUUCAAUAAACAAGAG---------CGCCGUA
.........((.(((((....((.((((((...)))))))).((((((.......((.(((((.....))))).)).....))))))......)).---------))).)). ( -18.00)
>DroYak_CAF1 14521 112 - 1
UCUCUGUGGACUGCGUCACAAGUUGUGUUUACCGAACACGCAAUUGAAAUAAUUGAUCCAGUUAACAAAAUUGCAUAGAAAUUCAAUAAACAACAACAGCGUAGGCAGCGUA
.....((...((((((.....((((((((((........((((((....((((((...))))))....))))))...(.....)..))))).))))).))))))...))... ( -23.00)
>consensus
__UCCAUGGACUGCGUCACAAGUUGUGUUUACCGAACACGCAAUUGAAAUAAUUGAUCCAGUUAACAAAAUUGCAUAGAAAUUCAAUAAACAACAACAG______CGACGUA
............(((((.......((((((...))))))((((((....((((((...))))))....))))))................................))))). (-16.75 = -17.38 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:07 2006