Locus 968

Sequence ID 2R_DroMel_CAF1
Location 4,113,705 – 4,113,822
Length 117
Max. P 0.847314
window1722 window1723

overview

Window 2

Location 4,113,705 – 4,113,822
Length 117
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 91.60
Mean single sequence MFE -28.68
Consensus MFE -21.83
Energy contribution -22.32
Covariance contribution 0.50
Combinations/Pair 1.14
Mean z-score -2.48
Structure conservation index 0.76
SVM decision value 0.77
SVM RNA-class probability 0.847314
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4113705 117 + 20766785
CAUUGUUUUUUUUUUCCCGAAGCGACGCAACUUUUCAGCUUUUUCUUCAGGUUUUCACUUUUGUUUUGUUCCAUUU-UUUGUGGACAUGAAAAUGUCUGGGUCGUGGAAAA-AAAAACA
...(((((((((((((.....(((((.((((((((((..........((((........))))...(((.((((..-...))))))))))))).)).)).)))))))))))-))))))) ( -28.20)
>DroSim_CAF1 25254 117 + 1
CAUUGUUUUUUUU--UCCGAAGCGACGCAACUUUUCAGCUUUUUCUUCAGGUUUUCACUUUUGUUUUGUUCCAUUUUUUUGUGGACAUGAAAAUGUCUGGGUCGGGGAAAAAAAAAACA
.....((((((((--(((....((((.((((((((((..........((((........))))...(((.((((......))))))))))))).)).)).)))).)))))))))))... ( -26.50)
>DroEre_CAF1 4444 110 + 1
CAUUGUUUU--UU--UCCGAAGCGACGCAGGUUUUCAGCUUUUUCUUCAGGUUUUCACUUCUGUUUUGUUCCACUU-UUUGUGGACAUGGAAAUGUCUGGGUCGG---AAGA-AAAACA
.....((((--((--((((((((((.(((((.....(((((.......)))))......))))).)))))((((..-...))((((((....)))))))).))))---))))-)))... ( -29.30)
>DroYak_CAF1 10917 113 + 1
CAUUGUUUUUUUU--UCCGAAGCGACGCAAUUUUUCAGCUUUUUCUUCAGGUUUUCACUUUUGUUUUGUUCCAUUU-UUUGUGGACAUGAAAAUGUCUGGGUCGG---AAAAAAAAACA
...((((((((((--((((((((((.((((......(((((.......))))).......)))).)))))......-.....((((((....))))))...))))---))))))))))) ( -30.72)
>consensus
CAUUGUUUUUUUU__UCCGAAGCGACGCAACUUUUCAGCUUUUUCUUCAGGUUUUCACUUUUGUUUUGUUCCAUUU_UUUGUGGACAUGAAAAUGUCUGGGUCGG___AAAAAAAAACA
...((((((((((..(((((..(((((....((((((..........((((........))))...(((.((((......))))))))))))))))).)..)))))...)))))))))) (-21.83 = -22.32 +   0.50) 

alignment

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secondary structure

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dotplot

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Window 3

Location 4,113,705 – 4,113,822
Length 117
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 91.60
Mean single sequence MFE -28.02
Consensus MFE -19.94
Energy contribution -21.25
Covariance contribution 1.31
Combinations/Pair 1.00
Mean z-score -3.90
Structure conservation index 0.71
SVM decision value 0.35
SVM RNA-class probability 0.699138
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4113705 117 - 20766785
UGUUUUU-UUUUCCACGACCCAGACAUUUUCAUGUCCACAAA-AAAUGGAACAAAACAAAAGUGAAAACCUGAAGAAAAAGCUGAAAAGUUGCGUCGCUUCGGGAAAAAAAAAACAAUG
(((((((-((((((.(((....(((.((((((((((((....-...))).)))........((....)).))))))...((((....))))..)))...))))).)))))))))))... ( -27.80)
>DroSim_CAF1 25254 117 - 1
UGUUUUUUUUUUCCCCGACCCAGACAUUUUCAUGUCCACAAAAAAAUGGAACAAAACAAAAGUGAAAACCUGAAGAAAAAGCUGAAAAGUUGCGUCGCUUCGGA--AAAAAAAACAAUG
(((((((((((((..((((.(((...(((((((.((((........))))...........))))))).))).......((((....))))..))))....)))--))))))))))... ( -26.30)
>DroEre_CAF1 4444 110 - 1
UGUUUU-UCUU---CCGACCCAGACAUUUCCAUGUCCACAAA-AAGUGGAACAAAACAGAAGUGAAAACCUGAAGAAAAAGCUGAAAACCUGCGUCGCUUCGGA--AA--AAAACAAUG
((((((-(.((---((((....(((.((((..(((((((...-..)))).)))...(((..((....)))))..))))..((.........)))))...)))))--))--))))))... ( -28.00)
>DroYak_CAF1 10917 113 - 1
UGUUUUUUUUU---CCGACCCAGACAUUUUCAUGUCCACAAA-AAAUGGAACAAAACAAAAGUGAAAACCUGAAGAAAAAGCUGAAAAAUUGCGUCGCUUCGGA--AAAAAAAACAAUG
(((((((((((---((((....(((.((((((((((((....-...))).)))........((....)).))))))....((.........)))))...)))))--))))))))))... ( -30.00)
>consensus
UGUUUUUUUUU___CCGACCCAGACAUUUUCAUGUCCACAAA_AAAUGGAACAAAACAAAAGUGAAAACCUGAAGAAAAAGCUGAAAAGUUGCGUCGCUUCGGA__AAAAAAAACAAUG
((((((((((....((((....(((.((((((((((((........))).)))........((....)).))))))....((.........)))))...))))...))))))))))... (-19.94 = -21.25 +   1.31) 

alignment

Postscript

secondary structure

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dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:59 2006