Locus 5261

Sequence ID 2R_DroMel_CAF1
Location 17,127,042 – 17,127,201
Length 159
Max. P 0.990630
window8401 window8402 window8403

overview

Window 1

Location 17,127,042 – 17,127,161
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.89
Mean single sequence MFE -40.88
Consensus MFE -34.44
Energy contribution -35.00
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -1.29
Structure conservation index 0.84
SVM decision value 0.06
SVM RNA-class probability 0.565993
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17127042 119 + 20766785
UCCGGCGGUCGAGCUGUCCGCUUGGGAUUGGAGAAAUUGGUGUU-UAGUCAGAAGGACCCAGGGAAGGAUCCAACUUGAGAAAGGUUUGAGCUUUCUCCGCCUCCAAGCAGGAUGCACAA
((((((((.....))))).(((((((..((((((((.....(((-((.......(((.((......)).)))(((((.....))))))))))))))))))..))))))).)))....... ( -38.90)
>DroSec_CAF1 62936 119 + 1
UCCGGCGGUCGAGCUGCCCGCUUGGGAUUGGAGAAAUUGGUGUU-UAGUCAGAAGGACCCAGGGUAGGAUCCAACUUGAGAAAGGUUUGAGCUUUCUCCGCCUCCAAGCAGGAUGCACAA
((((((((.....))))).(((((((..((((((((.....(((-((.......(((.((......)).)))(((((.....))))))))))))))))))..))))))).)))....... ( -41.60)
>DroSim_CAF1 53781 119 + 1
UCCGGCGGUCGAGCUGCCCGCUUGGGAUUGGAGAAAUUGGUGUU-UAGUCAGAAGGACCCAGGGUAGGAUCCGACUUGAGAAAGGUUUGAGCUUUCUCCGCCUCCAAGCAGGAUGCACAA
((((((((.....))))).(((((((..((((((((.....(((-((.......(((.((......)).)))(((((.....))))))))))))))))))..))))))).)))....... ( -42.00)
>DroEre_CAF1 68462 120 + 1
UCCGGCGGUCGAGCUGUCAGCUUGGGAUUGGAGAAAUUGGUGUUUUAGUCAGAAGGACCCCGCGAAGGGUCCAACUUGAAAAAGGUUUGAGCUUUCUCCGCACCCAAACAGGAUGCACAA
((((((((.....))))).(.(((((..((((((((((((....))))(((((.((((((......))))))..(((....))).)))))..))))))))..))))).).)))....... ( -41.10)
>DroYak_CAF1 70375 114 + 1
UCCGGCGGUCGAGCUGUCAGCUCGGGAUUGGAGAAAUUGGUGUUUUAGUCAGAAGGACCCUGGGAAGGGUCCAACUUGAAAAAGGUUUGAGCUUUCUCCGUACCCAAAC------CCAAA
....(.(((.((((.....))))(((..((((((((((((....))))(((((.(((((((....)))))))..(((....))).)))))..))))))))..)))..))------))... ( -40.80)
>consensus
UCCGGCGGUCGAGCUGUCCGCUUGGGAUUGGAGAAAUUGGUGUU_UAGUCAGAAGGACCCAGGGAAGGAUCCAACUUGAGAAAGGUUUGAGCUUUCUCCGCCUCCAAGCAGGAUGCACAA
((((((((.....))))).(((((((..((((((((..................(((.((......)).)))(((((.....))))).....))))))))..))))))).)))....... (-34.44 = -35.00 +   0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,127,042 – 17,127,161
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.89
Mean single sequence MFE -37.84
Consensus MFE -32.41
Energy contribution -32.77
Covariance contribution 0.36
Combinations/Pair 1.10
Mean z-score -2.10
Structure conservation index 0.86
SVM decision value 2.22
SVM RNA-class probability 0.990630
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17127042 119 - 20766785
UUGUGCAUCCUGCUUGGAGGCGGAGAAAGCUCAAACCUUUCUCAAGUUGGAUCCUUCCCUGGGUCCUUCUGACUA-AACACCAAUUUCUCCAAUCCCAAGCGGACAGCUCGACCGCCGGA
(((.((...((((((((.((.(((((((.............(((.(..((((((......))))))..))))...-........)))))))..))))))))))...)).)))........ ( -35.55)
>DroSec_CAF1 62936 119 - 1
UUGUGCAUCCUGCUUGGAGGCGGAGAAAGCUCAAACCUUUCUCAAGUUGGAUCCUACCCUGGGUCCUUCUGACUA-AACACCAAUUUCUCCAAUCCCAAGCGGGCAGCUCGACCGCCGGA
(((.((..(((((((((.((.(((((((.............(((.(..((((((......))))))..))))...-........)))))))..)))))))))))..)).)))........ ( -39.05)
>DroSim_CAF1 53781 119 - 1
UUGUGCAUCCUGCUUGGAGGCGGAGAAAGCUCAAACCUUUCUCAAGUCGGAUCCUACCCUGGGUCCUUCUGACUA-AACACCAAUUUCUCCAAUCCCAAGCGGGCAGCUCGACCGCCGGA
(((.((..(((((((((.(((.(((((((.......)))))))..)))((((((......)))))).........-...................)))))))))..)).)))........ ( -39.80)
>DroEre_CAF1 68462 120 - 1
UUGUGCAUCCUGUUUGGGUGCGGAGAAAGCUCAAACCUUUUUCAAGUUGGACCCUUCGCGGGGUCCUUCUGACUAAAACACCAAUUUCUCCAAUCCCAAGCUGACAGCUCGACCGCCGGA
(((.((.((..(((((((...(((((((.............(((.(..(((((((....)))))))..))))............)))))))...))))))).))..)).)))........ ( -37.01)
>DroYak_CAF1 70375 114 - 1
UUUGG------GUUUGGGUACGGAGAAAGCUCAAACCUUUUUCAAGUUGGACCCUUCCCAGGGUCCUUCUGACUAAAACACCAAUUUCUCCAAUCCCGAGCUGACAGCUCGACCGCCGGA
....(------(((.(((...(((((((.............(((.(..(((((((....)))))))..))))............)))))))...)))((((.....))))))))...... ( -37.81)
>consensus
UUGUGCAUCCUGCUUGGAGGCGGAGAAAGCUCAAACCUUUCUCAAGUUGGAUCCUUCCCUGGGUCCUUCUGACUA_AACACCAAUUUCUCCAAUCCCAAGCGGACAGCUCGACCGCCGGA
(((.((...((((((((....(((((((.............(((.(..((((((......))))))..))))............)))))))....))))))))...)).)))........ (-32.41 = -32.77 +   0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,127,082 – 17,127,201
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.22
Mean single sequence MFE -38.20
Consensus MFE -33.04
Energy contribution -32.12
Covariance contribution -0.92
Combinations/Pair 1.26
Mean z-score -1.42
Structure conservation index 0.86
SVM decision value 0.38
SVM RNA-class probability 0.712581
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17127082 119 - 20766785
UAUAUAUGACUCGCGACGUUCGUCGACGCCCCUCGGUGAGUUGUGCAUCCUGCUUGGAGGCGGAGAAAGCUCAAACCUUUCUCAAGUUGGAUCCUUCCCUGGGUCCUUCUGACUA-AACA
.....(..(((((((((....)))).)(((....)))))))..)((.(((.....))).)).(((((((.......))))))).((..((((((......))))))..)).....-.... ( -37.20)
>DroSec_CAF1 62976 119 - 1
UAUACAUGACUCGCGACGUUCGUCGACGUCCCUUGGUGAGUUGUGCAUCCUGCUUGGAGGCGGAGAAAGCUCAAACCUUUCUCAAGUUGGAUCCUACCCUGGGUCCUUCUGACUA-AACA
.....(..((((((((((((....)))))).....))))))..)((.(((.....))).)).(((((((.......))))))).((..((((((......))))))..)).....-.... ( -38.50)
>DroSim_CAF1 53821 119 - 1
UAUACAUGACUCGCGACGUUCGUCGACGUCCCUCGGUGAGUUGUGCAUCCUGCUUGGAGGCGGAGAAAGCUCAAACCUUUCUCAAGUCGGAUCCUACCCUGGGUCCUUCUGACUA-AACA
.....(..((((((((((((....)))))).....))))))..)((.(((.....))).)).(((((((.......))))))).((((((((((......))))))....)))).-.... ( -40.10)
>DroEre_CAF1 68502 120 - 1
UAUACAAAACUCGAGACGUUCGUCGGCGUCCCUCGGUGAGUUGUGCAUCCUGUUUGGGUGCGGAGAAAGCUCAAACCUUUUUCAAGUUGGACCCUUCGCGGGGUCCUUCUGACUAAAACA
...((((.((.((((((((......)))))..)))))...))))((((((.....)))))).(((((((.......))))))).((..(((((((....)))))))..)).......... ( -39.20)
>DroYak_CAF1 70415 114 - 1
UAUACAAAACUCGAGACGUUCGUCGGCGUCCCUCGGUGAGUUUGG------GUUUGGGUACGGAGAAAGCUCAAACCUUUUUCAAGUUGGACCCUUCCCAGGGUCCUUCUGACUAAAACA
..........(((((((((......)))))..))))((((...((------((((((((.........))))))))))..))))((..(((((((....)))))))..)).......... ( -36.00)
>consensus
UAUACAUGACUCGCGACGUUCGUCGACGUCCCUCGGUGAGUUGUGCAUCCUGCUUGGAGGCGGAGAAAGCUCAAACCUUUCUCAAGUUGGAUCCUUCCCUGGGUCCUUCUGACUA_AACA
....((((((((((((((((....)))))).....))))))))))......((......)).(((((((.......))))))).((((((((((......))))))....))))...... (-33.04 = -32.12 +  -0.92)

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 11:40:27 2006