Locus 718

Sequence ID X_DroMel_CAF1
Location 1,977,465 – 1,977,705
Length 240
Max. P 0.726733
window1154 window1155 window1156

overview

Window 4

Location 1,977,465 – 1,977,585
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 92.22
Mean single sequence MFE -51.27
Consensus MFE -48.98
Energy contribution -49.21
Covariance contribution 0.23
Combinations/Pair 1.09
Mean z-score -1.51
Structure conservation index 0.96
SVM decision value 0.27
SVM RNA-class probability 0.660309
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1977465 120 + 22224390
AGUUUGCGGCCGGUUGUCUUUGAGUCGGGUGCGCUUGGCGAUCUGCUGCUGAGCGGUAGUAGUGGGUGGCGCCGUCUGAUUGAUGGCGUUCCGACUGACCCACGUGCUGCCUUAGAGCUG
((((((((.(((..(.......)..))).)))(((..(((......)))..)))((((((((((((((((((((((.....))))))))).......)))))).)))))))...))))). ( -56.61)
>DroSec_CAF1 10490 120 + 1
AGUUUGCGGCCGGUUGUCCUUGAGUCGCGUGUACUUGGCGAUCUGCUGCUGAGCGGCAGUAGUGGGUGGCGCCGUCUGAUUGAUGGCGUUCCGACUGACCCACGUGCUACCUUAGAGCUG
(((((((((((((......))).)))))((((((.(((.(..(((((((...)))))))((((.((.(((((((((.....))))))))))).)))).)))).)))).))....))))). ( -49.50)
>DroYak_CAF1 10566 120 + 1
AGUUUGCGGCCGGUUGUCUUCGAGUUGGGUGUGCUUGGCGAUCUGCAGCUGAGCGGCAGUAGUGGGUGGCGCCGUCUGAUGGAUGGCGUUCCGGCUGAUCCACGUGCAGCCUUAGAACUG
(((((((.(((((((((......((..((....))..)).....))))))).)).)).......((.(((((((((.....)))))))))))(((((.........)))))...))))). ( -47.70)
>consensus
AGUUUGCGGCCGGUUGUCUUUGAGUCGGGUGUGCUUGGCGAUCUGCUGCUGAGCGGCAGUAGUGGGUGGCGCCGUCUGAUUGAUGGCGUUCCGACUGACCCACGUGCUGCCUUAGAGCUG
((((((((((.(((((((...((((.......))))))))))).))))).....((((((((((((((((((((((.....))))))))).......)))))).)))))))...))))). (-48.98 = -49.21 +   0.23) 

alignment

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secondary structure

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dotplot

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Window 5

Location 1,977,545 – 1,977,665
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -43.10
Consensus MFE -38.89
Energy contribution -38.90
Covariance contribution 0.01
Combinations/Pair 1.09
Mean z-score -1.81
Structure conservation index 0.90
SVM decision value 0.14
SVM RNA-class probability 0.603794
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1977545 120 - 22224390
CUAAGGUGCCUGGAAACACUCGCCCAGAAGGCAGGCAUCAGCUUCGACGAGGACUUUGCCAAGAGUCCAUCCCAAUCGCCCAGCUCUAAGGCAGCACGUGGGUCAGUCGGAACGCCAUCA
....((((((((....)....(((.....)))))))))).((((((((..(((((((....)))))))..((((...((...(((....))).))...))))...))))))..))..... ( -43.60)
>DroSec_CAF1 10570 120 - 1
CUAAGGUGCCUGGAAACACUCGCCCAGAAGGCAGGCAUCAGCUUCGACGAGGACUUUGCCAAGAGUCCAUCCCAAUCGCCCAGCUCUAAGGUAGCACGUGGGUCAGUCGGAACGCCAUCA
....((((((((....)....(((.....)))))))))).((((((((..(((((((....))))))).........(((((((((....).)))...)))))..))))))..))..... ( -42.70)
>DroYak_CAF1 10646 120 - 1
CUAAGGUGCCUGGAAACACUCGCCCAGAAGGCGGGCAUCAGCUUCGACGAGGACUUUACCAAGAGUCCAUCCCAAUCGCCCAGUUCUAAGGCUGCACGUGGAUCAGCCGGAACGCCAUCC
....((((..((....))..))))..((.(((((((.((......))...(((((((....))))))).........)))).(((((..(((((.........))))))))))))).)). ( -43.00)
>consensus
CUAAGGUGCCUGGAAACACUCGCCCAGAAGGCAGGCAUCAGCUUCGACGAGGACUUUGCCAAGAGUCCAUCCCAAUCGCCCAGCUCUAAGGCAGCACGUGGGUCAGUCGGAACGCCAUCA
....((((((((....)....(((.....)))))))))).((((((((..(((((((....)))))))..((((...((...(((....))).))...))))...))))))..))..... (-38.89 = -38.90 +   0.01) 

alignment

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secondary structure

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dotplot

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Window 6

Location 1,977,585 – 1,977,705
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -40.20
Consensus MFE -39.02
Energy contribution -39.13
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.67
Structure conservation index 0.97
SVM decision value 0.41
SVM RNA-class probability 0.726733
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1977585 120 - 22224390
AAAGGUCAACUCCACCACUCGCGUGGACCCCCAGCGGCCACUAAGGUGCCUGGAAACACUCGCCCAGAAGGCAGGCAUCAGCUUCGACGAGGACUUUGCCAAGAGUCCAUCCCAAUCGCC
...(((.......)))....((((((.((......))))))...((((((((....)....(((.....)))))))))).))..(((.(((((((((....))))))).))....))).. ( -38.20)
>DroSec_CAF1 10610 120 - 1
AAAGGGCAACUACAACACUGGCGUGGACCCCCAGCGGCCACUAAGGUGCCUGGAAACACUCGCCCAGAAGGCAGGCAUCAGCUUCGACGAGGACUUUGCCAAGAGUCCAUCCCAAUCGCC
...(((.............(((((((.((......))))))...((((((((....)....(((.....)))))))))).))).......(((((((....)))))))..)))....... ( -41.30)
>DroYak_CAF1 10686 120 - 1
AAAGGGUAACUCCAACACUCGCGUGGACCCCCAGCGGCCACUAAGGUGCCUGGAAACACUCGCCCAGAAGGCGGGCAUCAGCUUCGACGAGGACUUUACCAAGAGUCCAUCCCAAUCGCC
...(((..............((((((.((......))))))...((((((((....))..((((.....)))))))))).))........(((((((....)))))))..)))....... ( -41.10)
>consensus
AAAGGGCAACUCCAACACUCGCGUGGACCCCCAGCGGCCACUAAGGUGCCUGGAAACACUCGCCCAGAAGGCAGGCAUCAGCUUCGACGAGGACUUUGCCAAGAGUCCAUCCCAAUCGCC
...(((..............((((((.((......))))))...((((((((....)....(((.....)))))))))).))........(((((((....)))))))..)))....... (-39.02 = -39.13 +   0.11) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:58 2006