Locus 4998

Sequence ID 3L_DroMel_CAF1
Location 13,755,615 – 13,755,786
Length 171
Max. P 0.920452
window7898 window7899 window7900

overview

Window 8

Location 13,755,615 – 13,755,711
Length 96
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 97.24
Mean single sequence MFE -26.15
Consensus MFE -26.39
Energy contribution -26.17
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.73
Structure conservation index 1.01
SVM decision value 0.75
SVM RNA-class probability 0.841986
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13755615 96 + 23771897
UGCCAGUUGCCAUGAAAAGUUGAGCGGUGUUUUCAGGCUUUUUU-CAUGACCGCCGCCUUGUACGGCCACAGCUUGACUUUUUAUUUUUAUGCUAAA
....(((....(((((((((..(((.(((......(((..((..-...))..)))(((......)))))).)))..)))))))))......)))... ( -27.00)
>DroSim_CAF1 174612 96 + 1
UGCCAGUUGCCAUGAAAAGUUGAGCGGUGUUUUCAGGCUUUUUU-CAUGACCGCCGCCUUGUACGGCCACAGCUUGACUUUUUAUUUUUAUGCUAAA
....(((....(((((((((..(((.(((......(((..((..-...))..)))(((......)))))).)))..)))))))))......)))... ( -27.00)
>DroYak_CAF1 173571 97 + 1
UGCCAGUUGCCAUGAAAAGUUGAGCGGUGUUUUCAGGCUUUUUUCCACGACCGCCGCCUUGCACGGCCACAGUUUGACUUUUUAUUUUUAUGCUAAA
....(((....(((((((((..(((.(((......(((..............)))(((......)))))).)))..)))))))))......)))... ( -24.44)
>consensus
UGCCAGUUGCCAUGAAAAGUUGAGCGGUGUUUUCAGGCUUUUUU_CAUGACCGCCGCCUUGUACGGCCACAGCUUGACUUUUUAUUUUUAUGCUAAA
....(((....(((((((((..(((.(((......(((..((......))..)))(((......)))))).)))..)))))))))......)))... (-26.39 = -26.17 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,755,615 – 13,755,711
Length 96
Sequences 3
Columns 97
Reading direction reverse
Mean pairwise identity 97.24
Mean single sequence MFE -25.50
Consensus MFE -24.52
Energy contribution -24.30
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -2.20
Structure conservation index 0.96
SVM decision value 1.13
SVM RNA-class probability 0.920452
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13755615 96 - 23771897
UUUAGCAUAAAAAUAAAAAGUCAAGCUGUGGCCGUACAAGGCGGCGGUCAUG-AAAAAAGCCUGAAAACACCGCUCAACUUUUCAUGGCAACUGGCA
....((.........((((((..(((.((((((((.....)))))(((..(.-...)..)))......))).)))..))))))((.(....))))). ( -25.70)
>DroSim_CAF1 174612 96 - 1
UUUAGCAUAAAAAUAAAAAGUCAAGCUGUGGCCGUACAAGGCGGCGGUCAUG-AAAAAAGCCUGAAAACACCGCUCAACUUUUCAUGGCAACUGGCA
....((.........((((((..(((.((((((((.....)))))(((..(.-...)..)))......))).)))..))))))((.(....))))). ( -25.70)
>DroYak_CAF1 173571 97 - 1
UUUAGCAUAAAAAUAAAAAGUCAAACUGUGGCCGUGCAAGGCGGCGGUCGUGGAAAAAAGCCUGAAAACACCGCUCAACUUUUCAUGGCAACUGGCA
...................((((..(..(((((((((...)).)))))))..)......(((((((((...........)))))).)))...)))). ( -25.10)
>consensus
UUUAGCAUAAAAAUAAAAAGUCAAGCUGUGGCCGUACAAGGCGGCGGUCAUG_AAAAAAGCCUGAAAACACCGCUCAACUUUUCAUGGCAACUGGCA
...................((((.(((((.(((......))).)))))...........(((((((((...........)))))).)))...)))). (-24.52 = -24.30 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,755,671 – 13,755,786
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.66
Mean single sequence MFE -31.97
Consensus MFE -15.16
Energy contribution -17.56
Covariance contribution 2.40
Combinations/Pair 1.17
Mean z-score -2.10
Structure conservation index 0.47
SVM decision value 0.35
SVM RNA-class probability 0.700824
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13755671 115 - 23771897
UUUCCUCUUUGUGCCUCAGUUUGGCAG----CCAGUUUUUUGCGCAAACGAAAUACGGCCUU-UUGCAAAGAGGAAACAGUUUAGCAUAAAAAUAAAAAGUCAAGCUGUGGCCGUACAAG
.((((((((((((((.......))).(----((.((.(((((......))))).)))))...-..)))))))))))(((((((..(.............)..)))))))........... ( -34.22)
>DroPse_CAF1 168839 115 - 1
UUUCCGCUUCAGAACAUGGUUCGGAUGGGGCUAAGUUUUUUGUGCAAGUGAAAUGCGGCCUGUCCGCAGAGAGGAAACAGUUUAGCAUAAAAAUGAAAAGUCAAAUA-----AGUAGAAG
..((((..(((.....)))..))))...((((....(((((((((........(((((.....)))))....(....)......))))))))).....)))).....-----........ ( -28.10)
>DroSim_CAF1 174668 115 - 1
UUUCCUCUUUGUGCCUCAGUUUGGCAG----CCAGUUUUUUGCGCAAACGAAAUACGGCCUU-UUGCAAAGAGGAAACAGUUUAGCAUAAAAAUAAAAAGUCAAGCUGUGGCCGUACAAG
.((((((((((((((.......))).(----((.((.(((((......))))).)))))...-..)))))))))))(((((((..(.............)..)))))))........... ( -34.22)
>DroYak_CAF1 173628 115 - 1
UUUCCUCUUUGUGCCUCAGUUUGGCUG----CCAGUUUUUUGCGCAAACGAAAUACAGGCUU-UUGCAAAGAGGAAACAGUUUAGCAUAAAAAUAAAAAGUCAAACUGUGGCCGUGCAAG
.(((((((((((((((...((((..((----((((....))).)))..))))....))))..-..)))))))))))(((((((..(.............)..)))))))........... ( -35.22)
>DroPer_CAF1 169012 115 - 1
UUUCCGCUUCAGAACAUGGUUCGGAUGGGGCUAAGUUUUUUGUGCAAGUGAAAUGCGGCCUGUCCGCAGAGAGGAAACAGUUUAGCAUAAAAAUGAAAAGUCAAAUA-----AGUAGAAG
..((((..(((.....)))..))))...((((....(((((((((........(((((.....)))))....(....)......))))))))).....)))).....-----........ ( -28.10)
>consensus
UUUCCUCUUUGUGCCUCAGUUUGGCUG____CCAGUUUUUUGCGCAAACGAAAUACGGCCUU_UUGCAAAGAGGAAACAGUUUAGCAUAAAAAUAAAAAGUCAAACUGUGGCCGUACAAG
.((((((((((((((.......))).........((.(((((......))))).)).........)))))))))))(((((((..(.............)..)))))))........... (-15.16 = -17.56 +   2.40)

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 11:39:06 2006