Locus 2184

Sequence ID 2L_DroMel_CAF1
Location 5,902,080 – 5,902,220
Length 140
Max. P 0.991585
window3523 window3524

overview

Window 3

Location 5,902,080 – 5,902,188
Length 108
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 74.68
Mean single sequence MFE -32.04
Consensus MFE -18.29
Energy contribution -22.42
Covariance contribution 4.13
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 0.57
SVM decision value 2.28
SVM RNA-class probability 0.991585
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5902080 108 - 22407834
CCCCUGCCUCAAAGUUCAAUUGUUUGCGGCGAAGUCGCCAGUUUUUCCAU--GGGUCAGUCCCC-GUGGAAAAGCGUU-CCUCAAAAAUCCGACAAUUGCUCCGCGA-AAUCA
.............(..((((((((...((((....)))).((((((((((--(((......)))-))))))))))...-............))))))))..).....-..... ( -34.70)
>DroSim_CAF1 93033 103 - 1
--------UCAAAGUUCAAUUGUUCGCGGCGAAGUCGCCAGUUUUUCCAUGAGGGUCAGUUCCCGGUGGAAAAGCGUU-CCUCAAAAAUCCGACAAUUGCUGCGCGA-AAUCA
--------.....((.(((((((.((.((((....)))).((((((((((..(((......))).))))))))))...-...........)))))))))..))....-..... ( -34.30)
>DroEre_CAF1 116947 97 - 1
CAACCGCUUCAAAGUUCAAUUGUUGGCCGC-----------UUUUUCCAU--GGGUCAGUCCCC-GCGGAAAAGCGUU-CCUCAAAAAUCCGACAAUUGCUGCGCGA-AAUCA
....(((.....((..((((((((((.(((-----------((((.((.(--(((......)))-).)))))))))..-..........))))))))))))..))).-..... ( -27.72)
>DroYak_CAF1 117875 108 - 1
CACCCGCUUCAAAGUUCAAUUGUUGGCGGCGAAGUCGCCAGUUUUUCCAU--GGGUCAGUCCCC-GUGGAAAAGCGUU-CCUCAAAAAUCCGACAAUUGCUGCGCGA-AAUCA
....(((.....((..((((((((((.((((....)))).((((((((((--(((......)))-))))))))))...-..........))))))))))))..))).-..... ( -42.50)
>DroAna_CAF1 92846 89 - 1
GACAUACUUGAGAGUUCAAUUGUGGGCUGAGAAGC-------UGUUGCA-----------------UGGCAAAGCGUUUUCACAAAAUACCGCCAAUUGCCUGGCGAAAAUCA
..((((.(((......))).))))...((((((((-------(.((((.-----------------..))))))).))))))........(((((......)))))....... ( -21.00)
>consensus
CACCCGCUUCAAAGUUCAAUUGUUGGCGGCGAAGUCGCCAGUUUUUCCAU__GGGUCAGUCCCC_GUGGAAAAGCGUU_CCUCAAAAAUCCGACAAUUGCUGCGCGA_AAUCA
................((((((((((.((((....)))).(((((((((((.(((.....))).)))))))))))..............)))))))))).............. (-18.29 = -22.42 +   4.13)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,902,112 – 5,902,220
Length 108
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 83.73
Mean single sequence MFE -39.00
Consensus MFE -28.96
Energy contribution -30.02
Covariance contribution 1.06
Combinations/Pair 1.09
Mean z-score -2.26
Structure conservation index 0.74
SVM decision value 0.80
SVM RNA-class probability 0.852967
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5902112 108 - 22407834
GGUGGCUGCUAGAGCUUU-UGCAUGAGACUUUUCCCCUGCCUCAAAGUUCAAUUGUUUGCGGCGAAGUCGCCAGUUUUUCCAU--GGGUCAGUCCCC-GUGGAAAAGCGUUC
(((((((....(((((((-.(((.(.((....)).).)))...)))))))..((((.....))))))))))).((((((((((--(((......)))-)))))))))).... ( -41.20)
>DroSim_CAF1 93065 99 - 1
GUUGGCUGCUAGAGCUUU-UGCAUGAGAC------------UCAAAGUUCAAUUGUUCGCGGCGAAGUCGCCAGUUUUUCCAUGAGGGUCAGUUCCCGGUGGAAAAGCGUUC
..((((.(((.((((((.-.....))).)------------)).........((((.....))))))).))))((((((((((..(((......))).)))))))))).... ( -32.30)
>DroYak_CAF1 117907 109 - 1
GGCUGCUGCCAGAGGUUCCAGCAUGAGACUUUUCACCCGCUUCAAAGUUCAAUUGUUGGCGGCGAAGUCGCCAGUUUUUCCAU--GGGUCAGUCCCC-GUGGAAAAGCGUUC
((((((((((...))...)))))...((((((....(((((.(((.......)))..))))).))))))))).((((((((((--(((......)))-)))))))))).... ( -43.50)
>consensus
GGUGGCUGCUAGAGCUUU_UGCAUGAGACUUUUC_CC_GC_UCAAAGUUCAAUUGUUCGCGGCGAAGUCGCCAGUUUUUCCAU__GGGUCAGUCCCC_GUGGAAAAGCGUUC
((((((((((.((((((......((((.............))))))))))....(....))))..))))))).(((((((((((.(((.....))).))))))))))).... (-28.96 = -30.02 +   1.06)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:42 2006