Locus 5851

Sequence ID 3L_DroMel_CAF1
Location 15,770,315 – 15,770,424
Length 109
Max. P 0.996539
window9332 window9333

overview

Window 2

Location 15,770,315 – 15,770,424
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.30
Mean single sequence MFE -34.72
Consensus MFE -24.04
Energy contribution -26.88
Covariance contribution 2.84
Combinations/Pair 1.09
Mean z-score -3.86
Structure conservation index 0.69
SVM decision value 2.71
SVM RNA-class probability 0.996539
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15770315 109 + 23771897
AAGGAGCAGCAGAUCCUAAACACAAUGGCAUUU----GGCAGAAAGGAGGGGUA-----AAAGCGGAAGCAAAGUCUUAAGACUUUUACUCGCUGCUCGAUUUGAAA--AAUCUCGAAUU
...(((((((...((((.....(((......))----)......)))).(((((-----(((((....))...(((....))))))))))))))))))(((((((..--....))))))) ( -36.60)
>DroSec_CAF1 21919 109 + 1
AAGGAGCAGCAGAUCCCGAACACAAUGCCAUUU----GGCAGAAAGGAUGGGUA-----AAAGCGGAAGCAAAGUCUUAAGACUUUUACUCGCUGCUCGAUUUGAAA--AAUCUCGAAUU
...(((((((..((((.........((((....----))))....))))(((((-----(((((....))...(((....))))))))))))))))))(((((((..--....))))))) ( -39.72)
>DroSim_CAF1 22989 109 + 1
AAGGAGCAGCAGAUCCUGAACACAAUGCCAUUU----GGCAGAAAGGAGGGGUA-----AAAGCGGAAGCAAAGUCUUAAGACUUUUACUCGCUGCUCGAUUUGAAA--AAUCUCGAAUU
...(((((((...((((........((((....----))))...)))).(((((-----(((((....))...(((....))))))))))))))))))(((((((..--....))))))) ( -41.30)
>DroEre_CAF1 22210 109 + 1
AAGGAGCAGCAGAUCCUGAAUACAAUGCCAUUU----GGCAGAAAGGAGGGUUA-----GAAGCGGAAGCAAAGUCUUAAGGCUUUUACUCGCUACUCGAUUUAAAA--AAUCUCAAAUU
...(((.(((...((((........((((....----))))...))))((((..-----...((....))((((((....)))))).))))))).)))((((.....--))))....... ( -29.40)
>DroAna_CAF1 18188 117 + 1
AAGGAGCAGCAGAUACGGACAACAAUA--AACGGGCCGUAAGAAAGGAUGAGGAGCUCGAAAGCGGAAGCAAAGUCUUAAGACCU-AGCUCGCUUCUCGAUUUAAAAAAAAACUAAAUUU
...(((.(((...(((((....(....--...)..)))))............(((((.(...((....))...(((....)))).-)))))))).)))...................... ( -26.60)
>consensus
AAGGAGCAGCAGAUCCUGAACACAAUGCCAUUU____GGCAGAAAGGAGGGGUA_____AAAGCGGAAGCAAAGUCUUAAGACUUUUACUCGCUGCUCGAUUUGAAA__AAUCUCGAAUU
...(((((((...((((........((((........))))...)))).(((((........((....))((((((....))))))))))))))))))(((((((........))))))) (-24.04 = -26.88 +   2.84)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,770,315 – 15,770,424
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.30
Mean single sequence MFE -26.95
Consensus MFE -17.96
Energy contribution -18.92
Covariance contribution 0.96
Combinations/Pair 1.14
Mean z-score -2.06
Structure conservation index 0.67
SVM decision value 0.47
SVM RNA-class probability 0.748806
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15770315 109 - 23771897
AAUUCGAGAUU--UUUCAAAUCGAGCAGCGAGUAAAAGUCUUAAGACUUUGCUUCCGCUUU-----UACCCCUCCUUUCUGCC----AAAUGCCAUUGUGUUUAGGAUCUGCUGCUCCUU
.......((((--.....))))((((((((((((((.(((....)))))))))).......-----......((((....(((----((......))).))..))))...)))))))... ( -27.20)
>DroSec_CAF1 21919 109 - 1
AAUUCGAGAUU--UUUCAAAUCGAGCAGCGAGUAAAAGUCUUAAGACUUUGCUUCCGCUUU-----UACCCAUCCUUUCUGCC----AAAUGGCAUUGUGUUCGGGAUCUGCUGCUCCUU
.......((((--.....))))((((((((((((((.(((....)))))))))).......-----..(((........((((----....))))........)))....)))))))... ( -31.79)
>DroSim_CAF1 22989 109 - 1
AAUUCGAGAUU--UUUCAAAUCGAGCAGCGAGUAAAAGUCUUAAGACUUUGCUUCCGCUUU-----UACCCCUCCUUUCUGCC----AAAUGGCAUUGUGUUCAGGAUCUGCUGCUCCUU
.......((((--.....))))((((((((((((((.(((....)))))))))).......-----......((((..(((((----....))))....)...))))...)))))))... ( -28.90)
>DroEre_CAF1 22210 109 - 1
AAUUUGAGAUU--UUUUAAAUCGAGUAGCGAGUAAAAGCCUUAAGACUUUGCUUCCGCUUC-----UAACCCUCCUUUCUGCC----AAAUGGCAUUGUAUUCAGGAUCUGCUGCUCCUU
.......((((--.....))))(((((((((((..((((...........))))..)))).-----....(((......((((----....))))........)))....)))))))... ( -23.34)
>DroAna_CAF1 18188 117 - 1
AAAUUUAGUUUUUUUUUAAAUCGAGAAGCGAGCU-AGGUCUUAAGACUUUGCUUCCGCUUUCGAGCUCCUCAUCCUUUCUUACGGCCCGUU--UAUUGUUGUCCGUAUCUGCUGCUCCUU
.....((((...........((((((.((((((.-(((((....))))).)))..)))))))))................(((((..((..--......)).)))))...))))...... ( -23.50)
>consensus
AAUUCGAGAUU__UUUCAAAUCGAGCAGCGAGUAAAAGUCUUAAGACUUUGCUUCCGCUUU_____UACCCCUCCUUUCUGCC____AAAUGGCAUUGUGUUCAGGAUCUGCUGCUCCUU
......................((((((((((((.(((((....)))))))))).........................((((........))))...............)))))))... (-17.96 = -18.92 +   0.96)

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 12:02:07 2006