Locus 4819

Sequence ID 3L_DroMel_CAF1
Location 13,514,489 – 13,514,605
Length 116
Max. P 0.999554
window7595 window7596

overview

Window 5

Location 13,514,489 – 13,514,605
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 95.51
Mean single sequence MFE -35.07
Consensus MFE -33.77
Energy contribution -33.97
Covariance contribution 0.19
Combinations/Pair 1.06
Mean z-score -2.08
Structure conservation index 0.96
SVM decision value 3.72
SVM RNA-class probability 0.999554
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13514489 116 + 23771897
----AAAUUAUAAAGAAAAGCUUACCUUCACGCUGAGUGGGUGCAACCGCCGCUAGGGGAGGUGGUAAAGCUUGUGGAAACUGUCCAUAGACGGCGGGAAAGGCUGCAUUAUAUAUAAAU
----....(((((.(...(((((...(((.(((((....(((...((((((.(.....).))))))...)))((((((.....))))))..))))).)))))))).).)))))....... ( -32.50)
>DroPse_CAF1 1944 116 + 1
----AAAUAAUAAUGAAAAGCUUACCUUCACGCUGAGUGGGUGCAACCGCCGCUAGGGGAGGUGGUAAAGCUUGUGGAAACUGUCCAUAGACGGCGGGGAAGGCUGCAUUAUAUAUAGAU
----.....((((((...(((((.(((...(((((....(((...((((((.(.....).))))))...)))((((((.....))))))..)))))))).))))).))))))........ ( -37.60)
>DroWil_CAF1 2903 120 + 1
AAAUCAAAAAUAAUAUAAAGCUUACCUUCACGCUGAGUGGGUGCAACCGCCGCUAGGGGGGGUGGUAAAGCUUGUGGAAACUGUCCAUAGACGGCGGGAAAGGCUGCAUUAUAUAUAAAU
............((((((.((...(((((.(((((....(((...((((((.(.....).))))))...)))((((((.....))))))..))))).).))))..)).))))))...... ( -36.00)
>DroMoj_CAF1 1843 116 + 1
----AAAUAAUAAUGAAAAGCUUACCUUCACGCUGAGUGGGUGCAACCGCCGCUAGGGGAGGUGGUAAAGCUUGUGGAAACUGUCCAUAGACGGCGGGAAAGGCUGCGUUAUAUAUAAAU
----.....((((((...(((((...(((.(((((....(((...((((((.(.....).))))))...)))((((((.....))))))..))))).)))))))).))))))........ ( -35.30)
>DroAna_CAF1 1764 116 + 1
----AAAUAAUAAAGAAAAGCUUACCUUCACGCUGAGUGGGUGCAACCGCCGCUAGGGGAGGUGGUAAAGCUUGUGGAAACUGUCCAUAGACGGCGGGAAAGGCUGCAUUAUAUAUAAAU
----.....((((.(...(((((...(((.(((((....(((...((((((.(.....).))))))...)))((((((.....))))))..))))).)))))))).).))))........ ( -31.40)
>DroPer_CAF1 2036 116 + 1
----AAAUAAUAAUGAAAAGCUUACCUUCACGCUGAGUGGGUGCAACCGCCGCUAGGGGAGGUGGUAAAGCUUGUGGAAACUGUCCAUAGACGGCGGGGAAGGCUGCAUUAUAUAUAGAU
----.....((((((...(((((.(((...(((((....(((...((((((.(.....).))))))...)))((((((.....))))))..)))))))).))))).))))))........ ( -37.60)
>consensus
____AAAUAAUAAUGAAAAGCUUACCUUCACGCUGAGUGGGUGCAACCGCCGCUAGGGGAGGUGGUAAAGCUUGUGGAAACUGUCCAUAGACGGCGGGAAAGGCUGCAUUAUAUAUAAAU
.........((((((...(((((...(((.(((((....(((...((((((.(.....).))))))...)))((((((.....))))))..))))).)))))))).))))))........ (-33.77 = -33.97 +   0.19)

alignment

Postscript

secondary structure

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dotplot

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Window 6

Location 13,514,489 – 13,514,605
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 95.51
Mean single sequence MFE -24.64
Consensus MFE -23.98
Energy contribution -23.76
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -0.98
Structure conservation index 0.97
SVM decision value 0.94
SVM RNA-class probability 0.886209
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13514489 116 - 23771897
AUUUAUAUAUAAUGCAGCCUUUCCCGCCGUCUAUGGACAGUUUCCACAAGCUUUACCACCUCCCCUAGCGGCGGUUGCACCCACUCAGCGUGAAGGUAAGCUUUUCUUUAUAAUUU----
..(((((......((.(((((..((((((.((((((..(((((....)))))...))).......))))))))).......(((.....))))))))..)).......)))))...---- ( -24.33)
>DroPse_CAF1 1944 116 - 1
AUCUAUAUAUAAUGCAGCCUUCCCCGCCGUCUAUGGACAGUUUCCACAAGCUUUACCACCUCCCCUAGCGGCGGUUGCACCCACUCAGCGUGAAGGUAAGCUUUUCAUUAUUAUUU----
.............((.((((((.((((((.((((((..(((((....)))))...))).......)))))))))..((.........))..))))))..))...............---- ( -25.11)
>DroWil_CAF1 2903 120 - 1
AUUUAUAUAUAAUGCAGCCUUUCCCGCCGUCUAUGGACAGUUUCCACAAGCUUUACCACCCCCCCUAGCGGCGGUUGCACCCACUCAGCGUGAAGGUAAGCUUUAUAUUAUUUUUGAUUU
......((((((.((.(((((..((((((.((((((..(((((....)))))...))).......))))))))).......(((.....))))))))..)).))))))............ ( -26.41)
>DroMoj_CAF1 1843 116 - 1
AUUUAUAUAUAACGCAGCCUUUCCCGCCGUCUAUGGACAGUUUCCACAAGCUUUACCACCUCCCCUAGCGGCGGUUGCACCCACUCAGCGUGAAGGUAAGCUUUUCAUUAUUAUUU----
.............((.(((((..((((((.((((((..(((((....)))))...))).......))))))))).......(((.....))))))))..))...............---- ( -23.51)
>DroAna_CAF1 1764 116 - 1
AUUUAUAUAUAAUGCAGCCUUUCCCGCCGUCUAUGGACAGUUUCCACAAGCUUUACCACCUCCCCUAGCGGCGGUUGCACCCACUCAGCGUGAAGGUAAGCUUUUCUUUAUUAUUU----
............(((((((....((((.(((....)))(((((....)))))...............)))).)))))))..........(((((((........))))))).....---- ( -23.40)
>DroPer_CAF1 2036 116 - 1
AUCUAUAUAUAAUGCAGCCUUCCCCGCCGUCUAUGGACAGUUUCCACAAGCUUUACCACCUCCCCUAGCGGCGGUUGCACCCACUCAGCGUGAAGGUAAGCUUUUCAUUAUUAUUU----
.............((.((((((.((((((.((((((..(((((....)))))...))).......)))))))))..((.........))..))))))..))...............---- ( -25.11)
>consensus
AUUUAUAUAUAAUGCAGCCUUUCCCGCCGUCUAUGGACAGUUUCCACAAGCUUUACCACCUCCCCUAGCGGCGGUUGCACCCACUCAGCGUGAAGGUAAGCUUUUCAUUAUUAUUU____
.............((.((((((.((((((.((((((..(((((....)))))...))).......)))))))))..((.........))..))))))..))................... (-23.98 = -23.76 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:18 2006