Locus 8508

Sequence ID 3L_DroMel_CAF1
Location 22,299,161 – 22,299,272
Length 111
Max. P 0.999705
window13925 window13926

overview

Window 5

Location 22,299,161 – 22,299,272
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.06
Mean single sequence MFE -26.96
Consensus MFE -24.94
Energy contribution -24.86
Covariance contribution -0.08
Combinations/Pair 1.09
Mean z-score -2.36
Structure conservation index 0.93
SVM decision value 3.92
SVM RNA-class probability 0.999705
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22299161 111 + 23771897
CUUGUAAAUCUCUUGCUUUCAACACGGCGGCCACUACACCUAC---AUA------CAUGUGGCUGCCCCGUUUCCCCAACUUUUCUGCCUGGUCAUGGCUUUUAAGAGAAUUCUUUAAGC
........(((((((.....(((..(((((((((.........---...------...)))))))))..)))..............(((.......)))...)))))))........... ( -28.56)
>DroSec_CAF1 57720 111 + 1
CUUGUAAAUCUCCUGCUUUCAACACGGCGGCCACUACACCUAC---AUA------CAUGUGGCUGCCCCGCUUUACCAACUUUUCUGCCUGGUCAUGGCUUUUAAGAGAAUUCUUUAAGC
........((((.............(((((((((.........---...------...)))))))))..(((..((((.(......)..))))...)))......))))........... ( -26.96)
>DroSim_CAF1 39794 111 + 1
CUUGUAAAUCUCCUGCUUUCAACACGGCGGCCACUACACCUAC---AUA------CAUGUGGCUGCCCCGCUUUACCAACUUUUCUGCCUGGUCAUGGCUUUUAAGAGAAUUCUUUAAGC
........((((.............(((((((((.........---...------...)))))))))..(((..((((.(......)..))))...)))......))))........... ( -26.96)
>DroEre_CAF1 56251 120 + 1
CUUGUAAAUCUCUUGCUUUCAACACGGCGGCCACCACACCUACUACCUACUGCCCCGUGUGGCUGCCCCGUUUUCCCAACUUUUCUGCCUGGUCAUAGCUUUUAAGAGAAUUCUUUAAGC
........(((((((((.....((.((((((..((((((.................))))))..)))..(((.....)))......))))).....)))....))))))........... ( -26.13)
>DroYak_CAF1 22534 107 + 1
CUUGUAAAUCUCUUGCUUUCAACACGGCGGCCACUACACCUAC-------------AUGUGGCUGCCCCGUUUUCCCAACUUUUCUGCCUGGUCAUAGCUUUUAAGAGAAUUCUUUAAGC
........(((((((..........(((((((((.........-------------..)))))))))..(((...(((.(......)..)))....)))...)))))))........... ( -26.20)
>consensus
CUUGUAAAUCUCUUGCUUUCAACACGGCGGCCACUACACCUAC___AUA______CAUGUGGCUGCCCCGUUUUCCCAACUUUUCUGCCUGGUCAUGGCUUUUAAGAGAAUUCUUUAAGC
........(((((((..........(((((((((........................)))))))))..(((...(((.(......)..)))....)))...)))))))........... (-24.94 = -24.86 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 22,299,161 – 22,299,272
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.06
Mean single sequence MFE -31.54
Consensus MFE -29.36
Energy contribution -28.64
Covariance contribution -0.72
Combinations/Pair 1.12
Mean z-score -1.67
Structure conservation index 0.93
SVM decision value 2.05
SVM RNA-class probability 0.986791
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22299161 111 - 23771897
GCUUAAAGAAUUCUCUUAAAAGCCAUGACCAGGCAGAAAAGUUGGGGAAACGGGGCAGCCACAUG------UAU---GUAGGUGUAGUGGCCGCCGUGUUGAAAGCAAGAGAUUUACAAG
...........((((((....(((.......)))......(((.....((((.(((.((((((..------(..---....)..).))))).))).))))...)))))))))........ ( -31.20)
>DroSec_CAF1 57720 111 - 1
GCUUAAAGAAUUCUCUUAAAAGCCAUGACCAGGCAGAAAAGUUGGUAAAGCGGGGCAGCCACAUG------UAU---GUAGGUGUAGUGGCCGCCGUGUUGAAAGCAGGAGAUUUACAAG
...........((((((....(((.......)))......(((.....((((.(((.((((((..------(..---....)..).))))).))).))))...)))))))))........ ( -30.90)
>DroSim_CAF1 39794 111 - 1
GCUUAAAGAAUUCUCUUAAAAGCCAUGACCAGGCAGAAAAGUUGGUAAAGCGGGGCAGCCACAUG------UAU---GUAGGUGUAGUGGCCGCCGUGUUGAAAGCAGGAGAUUUACAAG
...........((((((....(((.......)))......(((.....((((.(((.((((((..------(..---....)..).))))).))).))))...)))))))))........ ( -30.90)
>DroEre_CAF1 56251 120 - 1
GCUUAAAGAAUUCUCUUAAAAGCUAUGACCAGGCAGAAAAGUUGGGAAAACGGGGCAGCCACACGGGGCAGUAGGUAGUAGGUGUGGUGGCCGCCGUGUUGAAAGCAAGAGAUUUACAAG
...........((((((....(((....((..((......))..))...(((((((.(((((((...((........))..))))))).))).))))......)))))))))........ ( -35.40)
>DroYak_CAF1 22534 107 - 1
GCUUAAAGAAUUCUCUUAAAAGCUAUGACCAGGCAGAAAAGUUGGGAAAACGGGGCAGCCACAU-------------GUAGGUGUAGUGGCCGCCGUGUUGAAAGCAAGAGAUUUACAAG
...........((((((....(((....((..((......))..))..((((.(((.(((((((-------------......)).))))).))).))))...)))))))))........ ( -29.30)
>consensus
GCUUAAAGAAUUCUCUUAAAAGCCAUGACCAGGCAGAAAAGUUGGGAAAACGGGGCAGCCACAUG______UAU___GUAGGUGUAGUGGCCGCCGUGUUGAAAGCAAGAGAUUUACAAG
...........((((((....(((.......)))......(((.....((((.(((.(((((........................))))).))).))))...)))))))))........ (-29.36 = -28.64 +  -0.72)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:25 2006