Locus 5497

Sequence ID 3R_DroMel_CAF1
Location 14,467,120 – 14,467,337
Length 217
Max. P 0.711227
window8972 window8973 window8974

overview

Window 2

Location 14,467,120 – 14,467,218
Length 98
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 72.19
Mean single sequence MFE -25.43
Consensus MFE -17.69
Energy contribution -18.80
Covariance contribution 1.11
Combinations/Pair 1.04
Mean z-score -1.22
Structure conservation index 0.70
SVM decision value 0.38
SVM RNA-class probability 0.711227
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14467120 98 - 27905053
------CGCAUUCAACAACAAUUGCAGCCAGUUGAGGUUGAAGCGUCUGGUUGAACGGUUGUUGUACUUGUCUGGCGAUCAGAGAAGCCCAAGAAU----------------AACAAAAG
------(((.((((((..((((((....))))))..))))))))).(((......)))(((((((.((((...(((..........))))))).))----------------)))))... ( -28.80)
>DroSim_CAF1 25048 79 - 1
------CGUAUUCAACAACAAUUGCAGUCAGUUGAGGUUGAAGCGUCUGGUUGAAAGGUUGUUGU-------------------AAGCCCAAGAAU----------------AACUAAAG
------(((.((((((..((((((....))))))..)))))))))..((((((...((((.....-------------------.))))......)----------------)))))... ( -18.20)
>DroYak_CAF1 26833 120 - 1
CGUGUUCGUAUUCAACAACAAUUGCAGUCAGUUGAGGUUGAAGCGUCUGGUUGAAUGGUUGUUGUACUUGUCUGGCGAUCAGAAAAGCCCAAGAAUUACUACAGACCGUAAUAAUAAAAG
..((((((..((((((..((((((....))))))..))))))..(((((....(.(((((.(((..(((.((((.....)))).)))..))).))))).).))))))).))))....... ( -29.30)
>consensus
______CGUAUUCAACAACAAUUGCAGUCAGUUGAGGUUGAAGCGUCUGGUUGAAAGGUUGUUGUACUUGUCUGGCGAUCAGA_AAGCCCAAGAAU________________AACAAAAG
......(((.((((((..((((((....))))))..)))))))))............(((.(((..(((.((((.....)))).)))..))).)))........................ (-17.69 = -18.80 +   1.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,467,218 – 14,467,337
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.57
Mean single sequence MFE -33.90
Consensus MFE -21.55
Energy contribution -22.22
Covariance contribution 0.68
Combinations/Pair 1.19
Mean z-score -1.95
Structure conservation index 0.64
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14467218 119 + 27905053
AUUACUUGACGGUCUACGGUCUACCCAGAAACCAAAAGACUCACUCCAAUCUGGAAAAGCACUCCAGCUCAGAUUUGAGUGGGCCUUUUGAGUCAGA-CUUGAACUCGUUUGUUGUGCCU
..(((..((((((.((.(((((.....((...((((((.(((((((.((((((....(((......))))))))).))))))).))))))..)))))-)))).)).))))....)))... ( -33.50)
>DroSim_CAF1 25127 120 + 1
AUUACUUGGCGGUCUACGGUCUAUUCAGAAACCACAAGACUCACUCGAAUCUGAAAAAGCACUCCAGCUCAGAUUUGAGUGGGCCUUUUGAGCCAAGUUUCGAACUCGUUUGUUGUGCCU
...(((((((((.(....).))..........((.(((.(((((((((((((((....((......))))))))))))))))).))).)).)))))))....(((......)))...... ( -39.30)
>DroYak_CAF1 26953 112 + 1
AAUACUUGACGGU-------CUACUCAGAAACCACAAGACUCGCUCCACUCUGUAGAAACACUCCAUCUCAGAUUUGAGUGGGCUUUUUGAGCCAGG-CCUGAACUAGUUUGUCGUGCCU
.......((((((-------((.(((((((......((.(((((((...((((.(((.........)))))))...))))))))))))))))..)))-)).(((....))))))...... ( -28.90)
>consensus
AUUACUUGACGGUCUACGGUCUACUCAGAAACCACAAGACUCACUCCAAUCUGAAAAAGCACUCCAGCUCAGAUUUGAGUGGGCCUUUUGAGCCAGG_CUUGAACUCGUUUGUUGUGCCU
....(((((((((....((.....))....)))..(((.(((((((.((((((................)))))).))))))).)))....))))))....................... (-21.55 = -22.22 +   0.68)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,467,218 – 14,467,337
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.57
Mean single sequence MFE -36.50
Consensus MFE -23.99
Energy contribution -24.67
Covariance contribution 0.68
Combinations/Pair 1.17
Mean z-score -1.89
Structure conservation index 0.66
SVM decision value 0.00
SVM RNA-class probability 0.535979
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14467218 119 - 27905053
AGGCACAACAAACGAGUUCAAG-UCUGACUCAAAAGGCCCACUCAAAUCUGAGCUGGAGUGCUUUUCCAGAUUGGAGUGAGUCUUUUGGUUUCUGGGUAGACCGUAGACCGUCAAGUAAU
.(((.........((((.((..-..))))))(((((((.(((((.(((((((((......)))....)))))).))))).)))))))(((((.(((.....))).))))))))....... ( -39.40)
>DroSim_CAF1 25127 120 - 1
AGGCACAACAAACGAGUUCGAAACUUGGCUCAAAAGGCCCACUCAAAUCUGAGCUGGAGUGCUUUUUCAGAUUCGAGUGAGUCUUGUGGUUUCUGAAUAGACCGUAGACCGCCAAGUAAU
............((....))..(((((((....(((((.(((((.((((((((..((....))..)))))))).))))).)))))..(((((.((.......)).))))))))))))... ( -39.00)
>DroYak_CAF1 26953 112 - 1
AGGCACGACAAACUAGUUCAGG-CCUGGCUCAAAAAGCCCACUCAAAUCUGAGAUGGAGUGUUUCUACAGAGUGGAGCGAGUCUUGUGGUUUCUGAGUAG-------ACCGUCAAGUAUU
......(((...(((.((((((-((.(((((.....(((((((((....)))).))).))(((((........))))))))))....)))..))))))))-------...)))....... ( -31.10)
>consensus
AGGCACAACAAACGAGUUCAAG_CCUGGCUCAAAAGGCCCACUCAAAUCUGAGCUGGAGUGCUUUUACAGAUUGGAGUGAGUCUUGUGGUUUCUGAGUAGACCGUAGACCGUCAAGUAAU
.(((......................(((((.....(((((((((....)))).))).))(((((........))))))))))....(((((.((.......)).))))))))....... (-23.99 = -24.67 +   0.68)

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 11:56:39 2006