Locus 2911

Sequence ID 3L_DroMel_CAF1
Location 8,293,827 – 8,293,966
Length 139
Max. P 0.996478
window4545 window4546 window4547

overview

Window 5

Location 8,293,827 – 8,293,939
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.61
Mean single sequence MFE -29.61
Consensus MFE -24.87
Energy contribution -24.68
Covariance contribution -0.19
Combinations/Pair 1.08
Mean z-score -2.54
Structure conservation index 0.84
SVM decision value 1.92
SVM RNA-class probability 0.982463
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8293827 112 + 23771897
AUGAUAUAUGCAUUUUUCAAGCAUCGCAUCGCAUCGCCAACAAAGACUGCCUC--------UUGCUUAUAAAUUAGAAGCAACCGAAAUAAUAGCCAUAUUUUGGUUGCUUUUCGCCAGU
.........((.......(((((..(((((..............)).)))...--------.))))).......((((((((((((((((.......)))))))))))))))).)).... ( -26.04)
>DroSim_CAF1 15313 112 + 1
AUGAUAUAUGCAUUUUUCAAGCAUCGCAUCGCAUCGCCAACAAAGGCUGCCUC--------UUGCUUAUAAAUUAGAAGCAACCGAAAUAAUAGCCAUAUUUUGGUUGCUUUUCGCCAGU
.........((.......(((((.......(((..(((......))))))...--------.))))).......((((((((((((((((.......)))))))))))))))).)).... ( -29.40)
>DroEre_CAF1 15804 110 + 1
AUGAUAUAUGCAUUUUUCAAGCAU----------CGCCAACAAUGGCUGCCUCUGCGCGCUUUGCUUGUAAAUUGGAAGCAGCCGAAAUAAAAGCCAUAUUUUGGUUGCUUUUCGCCAGU
..........((.(((.((((((.----------.((((....)))).((......))....)))))).))).))(((((((((((((((.......)))))))))))))))........ ( -32.50)
>DroYak_CAF1 15341 110 + 1
AUGAUAUAUGCAUUUUUCAAGCAU----------CGCCAACAAUGGCUGCCUCUGCGCGCGUUGCUUAUAAAUUAGAAGCAGCCGAAAUAAAAGCCAUAUUUUGGUUGCUUUUCGCCAGU
.........((.......(((((.----------(((((....))((.((....))))))).))))).......((((((((((((((((.......)))))))))))))))).)).... ( -30.50)
>consensus
AUGAUAUAUGCAUUUUUCAAGCAU__________CGCCAACAAAGGCUGCCUC________UUGCUUAUAAAUUAGAAGCAACCGAAAUAAAAGCCAUAUUUUGGUUGCUUUUCGCCAGU
.........((.......(((((............(((......)))...............))))).......((((((((((((((((.......)))))))))))))))).)).... (-24.87 = -24.68 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,293,867 – 8,293,966
Length 99
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.12
Mean single sequence MFE -27.80
Consensus MFE -20.58
Energy contribution -19.95
Covariance contribution -0.63
Combinations/Pair 1.11
Mean z-score -2.73
Structure conservation index 0.74
SVM decision value 2.70
SVM RNA-class probability 0.996478
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8293867 99 + 23771897
CAAAGACUGCCUC--------UUGCUUAUAAAUUAGAAGCAACCGAAAUAAUAGCCAUAUUUUGGUUGCUUUUCGCCAGUUUUGGUUUUU-------------GCUUUUCCAACACAUAU
(((((((((...(--------(.((.........((((((((((((((((.......)))))))))))))))).)).))...))))))))-------------)................ ( -24.50)
>DroSim_CAF1 15353 97 + 1
CAAAGGCUGCCUC--------UUGCUUAUAAAUUAGAAGCAACCGAAAUAAUAGCCAUAUUUUGGUUGCUUUUCGCCAGUUUUGGUUUUU-------------GCUUUUCCAACAUAU--
.((((((.(((..--------..(((........((((((((((((((((.......))))))))))))))))....)))...)))....-------------)))))).........-- ( -25.60)
>DroEre_CAF1 15834 120 + 1
CAAUGGCUGCCUCUGCGCGCUUUGCUUGUAAAUUGGAAGCAGCCGAAAUAAAAGCCAUAUUUUGGUUGCUUUUCGCCAGUUUUGGUUUUUGGUUUUGGUUUUCGGUUUUCCAGCUCUUUU
....((((((....))).)))..(((.(.(((((((((...((((((((((((((((....(((((........)))))...)))))))).))))))))))))))))).).)))...... ( -33.10)
>DroYak_CAF1 15371 108 + 1
CAAUGGCUGCCUCUGCGCGCGUUGCUUAUAAAUUAGAAGCAGCCGAAAUAAAAGCCAUAUUUUGGUUGCUUUUCGCCAGUUUUGGUUU------------UUCGAUUUACCAUCUUUUUU
(((((((.((....)))).)))))....((((((((((((((((((((((.......)))))))))))))))).(((......)))..------------...))))))........... ( -28.00)
>consensus
CAAAGGCUGCCUC________UUGCUUAUAAAUUAGAAGCAACCGAAAUAAAAGCCAUAUUUUGGUUGCUUUUCGCCAGUUUUGGUUUUU_____________GCUUUUCCAACACAUUU
(((.(((((.(..........(((....)))...((((((((((((((((.......)))))))))))))))).).)))))))).................................... (-20.58 = -19.95 +  -0.63)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,293,867 – 8,293,966
Length 99
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.12
Mean single sequence MFE -23.08
Consensus MFE -16.89
Energy contribution -17.20
Covariance contribution 0.31
Combinations/Pair 1.09
Mean z-score -1.81
Structure conservation index 0.73
SVM decision value 0.67
SVM RNA-class probability 0.818801
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8293867 99 - 23771897
AUAUGUGUUGGAAAAGC-------------AAAAACCAAAACUGGCGAAAAGCAACCAAAAUAUGGCUAUUAUUUCGGUUGCUUCUAAUUUAUAAGCAA--------GAGGCAGUCUUUG
.((((.(((((((....-------------.....(((....)))......((((((.(((((.......))))).))))))))))))).)))).((..--------...))........ ( -20.70)
>DroSim_CAF1 15353 97 - 1
--AUAUGUUGGAAAAGC-------------AAAAACCAAAACUGGCGAAAAGCAACCAAAAUAUGGCUAUUAUUUCGGUUGCUUCUAAUUUAUAAGCAA--------GAGGCAGCCUUUG
--...((((.....)))-------------)............(((...((((((((.(((((.......))))).))))))))...........((..--------...)).))).... ( -21.00)
>DroEre_CAF1 15834 120 - 1
AAAAGAGCUGGAAAACCGAAAACCAAAACCAAAAACCAAAACUGGCGAAAAGCAACCAAAAUAUGGCUUUUAUUUCGGCUGCUUCCAAUUUACAAGCAAAGCGCGCAGAGGCAGCCAUUG
..(((((((((....))...........................((.....))...........))))))).....(((((((((..........((.....))...))))))))).... ( -24.92)
>DroYak_CAF1 15371 108 - 1
AAAAAAGAUGGUAAAUCGAA------------AAACCAAAACUGGCGAAAAGCAACCAAAAUAUGGCUUUUAUUUCGGCUGCUUCUAAUUUAUAAGCAACGCGCGCAGAGGCAGCCAUUG
......(((.....)))(((------------(..(((....)))..((((((............)))))).))))((((((((((.........((.....))..)))))))))).... ( -25.70)
>consensus
AAAAAAGUUGGAAAAGC_____________AAAAACCAAAACUGGCGAAAAGCAACCAAAAUAUGGCUAUUAUUUCGGCUGCUUCUAAUUUAUAAGCAA________GAGGCAGCCAUUG
..........((((.....................(((....)))..((((((............)))))).))))(((((((((......................))))))))).... (-16.89 = -17.20 +   0.31)

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 10:44:51 2006