Locus 3894

Sequence ID 2R_DroMel_CAF1
Location 12,864,354 – 12,864,552
Length 198
Max. P 0.720995
window6288 window6289

overview

Window 8

Location 12,864,354 – 12,864,473
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.36
Mean single sequence MFE -25.95
Consensus MFE -20.23
Energy contribution -20.73
Covariance contribution 0.50
Combinations/Pair 1.11
Mean z-score -1.73
Structure conservation index 0.78
SVM decision value 0.40
SVM RNA-class probability 0.720995
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12864354 119 - 20766785
CAACAUUUGUGUUUAUUUUUAUUUGCUUUGUUAUGAUUCUC-CAAAUUAUUUGCUAGCAUAUUGACAAAUGCGAUGGCAAAGUGUGUGGGGCAAGUUUUUAAUAAACUUUAAACUAUGUA
..((((....(((((((...((((((((..(..(((((...-..)))))(((((((((((........))))..)))))))....)..))))))))....)))))))........)))). ( -23.70)
>DroSim_CAF1 219642 118 - 1
CAACAUUUGUGUUUAUUUUUAUUUGCUUUGUUAUGAUUCUC-CAAAUUAUUUGCUAGCAUAUUGACAGAUGUGA-GGCAAGUUGGGUGGGGAAAGUUUUUAAUAAACUUUAAACUAUGUA
..((((....(((((..((((((.((((.........((((-((....(((((((..((((((....)))))).-)))))))....))))))))))....))))))...))))).)))). ( -26.80)
>DroEre_CAF1 211785 115 - 1
CAACAUUUGUGUUUAUUUUUAUUUGCUUUGUUAUGAUUUUC-GAAAUAAUUUGCUAGCAUAUUGACAAAUGCGA-GGCGA---GGAUAGAGCAAGUUUUUAAUAAACUUAAAACUAUGUU
.....((((.(((((((...((((((((((((.((.....)-)......((((((.((((........))))..-)))))---)))))))))))))....))))))).))))........ ( -26.60)
>DroYak_CAF1 217764 119 - 1
CAACAUUUGUGUUUAUUUUUAUUUGCUUUGUUAUGAUUCUCCAAAAUUAUACGCUAGCAUAUUGACAAAUGCGG-GGCCAACUGGGUGGAGCAAGUUUUUAAUAAACUUUCAACUAUGUA
..(((((((.(((((((...((((((((..((((((((......))))))..(((.((((........))))..-)))......))..))))))))....)))))))...)))..)))). ( -26.70)
>consensus
CAACAUUUGUGUUUAUUUUUAUUUGCUUUGUUAUGAUUCUC_CAAAUUAUUUGCUAGCAUAUUGACAAAUGCGA_GGCAAA_UGGGUGGAGCAAGUUUUUAAUAAACUUUAAACUAUGUA
..((((....(((((((...((((((((..((((((((......))))))(((((.((((........))))...)))))....))..))))))))....)))))))........)))). (-20.23 = -20.73 +   0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,864,433 – 12,864,552
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.77
Mean single sequence MFE -25.95
Consensus MFE -23.88
Energy contribution -24.12
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.65
Structure conservation index 0.92
SVM decision value -0.01
SVM RNA-class probability 0.526928
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12864433 119 - 20766785
AAUUUAUGACGCCCCGAAAGCUGUACAAGAUUUAUGGCGCCCAACAACUGGCGCUAACUCACAAAUAAUUGUUGCCG-AACAACAUUUGUGUUUAUUUUUAUUUGCUUUGUUAUGAUUCU
...((((((((......((((.(((.(((((...(((((((........)))))))...(((((((..(((((....-))))).)))))))...))))))))..)))))))))))).... ( -26.30)
>DroSim_CAF1 219720 120 - 1
AAUUUAUGACGCCCCGAAAGCUGUACAAGAUUUAUGGCGCCCAACAACUGGCGCUAACUCACAAAUAAUUGUUGCCAAAACAACAUUUGUGUUUAUUUUUAUUUGCUUUGUUAUGAUUCU
...((((((((......((((.(((.(((((...(((((((........)))))))...(((((((..(((((.....))))).)))))))...))))))))..)))))))))))).... ( -27.00)
>DroEre_CAF1 211860 119 - 1
AAUUUAUGACGCCCCGAAAACUGUACAAGAUUUAUGGCGCCCAACAACUGGCGCUAACUCAGAAAUAAUUGUUGCCG-AACAACAUUUGUGUUUAUUUUUAUUUGCUUUGUUAUGAUUUU
...((((((((...((((................(((((((........)))))))....(((.((((.(((((...-..))))).)))).))).......))))...)))))))).... ( -23.50)
>DroYak_CAF1 217843 119 - 1
AAUUUAUGACGCCCCGAAAGCUGUACAAGAUUUAUGGCGCCCAACAACUGGCGCUAACUCACAAAUAAUUGUUGCCA-AACAACAUUUGUGUUUAUUUUUAUUUGCUUUGUUAUGAUUCU
...((((((((......((((.(((.(((((...(((((((........)))))))...(((((((..(((((....-))))).)))))))...))))))))..)))))))))))).... ( -27.00)
>consensus
AAUUUAUGACGCCCCGAAAGCUGUACAAGAUUUAUGGCGCCCAACAACUGGCGCUAACUCACAAAUAAUUGUUGCCA_AACAACAUUUGUGUUUAUUUUUAUUUGCUUUGUUAUGAUUCU
...((((((((...((((................(((((((........)))))))...((((((....(((((......)))))))))))..........))))...)))))))).... (-23.88 = -24.12 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:40 2006