Locus 3280

Sequence ID X_DroMel_CAF1
Location 8,719,875 – 8,719,995
Length 120
Max. P 0.988363
window5374 window5375

overview

Window 4

Location 8,719,875 – 8,719,995
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.83
Mean single sequence MFE -45.40
Consensus MFE -38.27
Energy contribution -38.63
Covariance contribution 0.36
Combinations/Pair 1.19
Mean z-score -3.00
Structure conservation index 0.84
SVM decision value 1.90
SVM RNA-class probability 0.981719
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8719875 120 + 22224390
UCUCGACGGCCUCCAUAUUCUUGGCCUCCUCGAGGCGCUGCAGCAUCGCCUGCAGCUCCUUCUGGCGCAGCUCCAGCUCAUCCUUGGCGGCCUGCAGCUGCUUCAGCUGCUCCUCCAGCC
((((((.((((...........))))...)))))).(((((((......))))))).......((((.(((....)))).....(((.((...(((((((...))))))).)).)))))) ( -47.70)
>DroVir_CAF1 1353 120 + 1
UCUCGACGGCCUCCAUGUUCUUGGCCUCCUCGAGGCGCUGCAGCAUAGACUGCAGCUCCUUUUGGCGCAGCUCAAGCUCAUCCUUGGCGGCCUGCAGCUGCUUCAGCUGCUCCUCCAAUC
.......((((.(((((..(((((((.((..((((.(((((((......))))))).))))..)).)..)).))))..))....))).)))).(((((((...))))))).......... ( -49.70)
>DroGri_CAF1 4414 120 + 1
UCUCAACGGCCUCCAUGUUCUUGGCCUCCUCGAGGCGCUGCAGCAUAGACUGCAGCUCCUUCUGGCGCAGCUCGAGCUCAUCCUUGGCGGCCUGCAGCUGCUUCAGCUGCUCCUCCAAUC
.......((((.(((((..(((((((.((..((((.(((((((......))))))).))))..)).)..)).))))..))....))).)))).(((((((...))))))).......... ( -49.40)
>DroWil_CAF1 815 120 + 1
UCUCAGCAGCCUCCAUGUUUUUGGCCUCUUCGAGACGCUGCAACAUGGCCUGCAAUUCCUUUUGACGCAACUCGAGCUCAUCCUUGGCGGCCUGCAGUUGUUUAAGUUGCUCCUCCAGUC
.....((((...(((((((...(((.((.....)).)))..))))))).)))).............((((((..(((.((....))((.....))....)))..)))))).......... ( -29.70)
>DroMoj_CAF1 1342 120 + 1
UCUCGACGGCCUCCAUAUUCUUGGCCUCCUCCAAGCGCUGCAGCAUCGAUUGCAGCUCCUUCUGGCGCAGCUCAAGCUCAUCCUUGGCGGCCUGCAGCUGCUUCAGCUGCUCCUCCAAUC
.......((((.(((....(((((......))))).(((((.(((.....))).(((......)))))))).............))).)))).(((((((...))))))).......... ( -42.10)
>DroAna_CAF1 651 120 + 1
UCUCGACGGCCUCCAUGUUCUUGGCCUCCUCGAGGCGCUGCAGCAUCGACUGCAGCUCCUUCUGGCGCAGCUCGAGCUCGUCCUUGGCGGCCUGCAGCUGCUUGAGCUGCUCCUCCAGCC
.(((((.((((...........))))...)))))(((((((((......))))))).......((.(((((((((((.(((.....)))((.....)).))))))))))).))....)). ( -53.80)
>consensus
UCUCGACGGCCUCCAUGUUCUUGGCCUCCUCGAGGCGCUGCAGCAUCGACUGCAGCUCCUUCUGGCGCAGCUCGAGCUCAUCCUUGGCGGCCUGCAGCUGCUUCAGCUGCUCCUCCAAUC
.......((((...........)))).....((((.(((((((......))))))).))))..((.((((((((((......))))(((((.....)))))...)))))).))....... (-38.27 = -38.63 +   0.36)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,719,875 – 8,719,995
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.83
Mean single sequence MFE -49.15
Consensus MFE -43.75
Energy contribution -43.20
Covariance contribution -0.55
Combinations/Pair 1.28
Mean z-score -2.36
Structure conservation index 0.89
SVM decision value 2.12
SVM RNA-class probability 0.988363
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8719875 120 - 22224390
GGCUGGAGGAGCAGCUGAAGCAGCUGCAGGCCGCCAAGGAUGAGCUGGAGCUGCGCCAGAAGGAGCUGCAGGCGAUGCUGCAGCGCCUCGAGGAGGCCAAGAAUAUGGAGGCCGUCGAGA
((((......(((((((...))))))).((((.((..((.(((((....))).)))).((.((.(((((((......))))))).))))..)).))))...........))))....... ( -53.10)
>DroVir_CAF1 1353 120 - 1
GAUUGGAGGAGCAGCUGAAGCAGCUGCAGGCCGCCAAGGAUGAGCUUGAGCUGCGCCAAAAGGAGCUGCAGUCUAUGCUGCAGCGCCUCGAGGAGGCCAAGAACAUGGAGGCCGUCGAGA
(((.......(((((((...))))))).((((.(((....((..((((.(((...((...(((.((((((((....)))))))).)))...)).)))))))..))))).))))))).... ( -54.10)
>DroGri_CAF1 4414 120 - 1
GAUUGGAGGAGCAGCUGAAGCAGCUGCAGGCCGCCAAGGAUGAGCUCGAGCUGCGCCAGAAGGAGCUGCAGUCUAUGCUGCAGCGCCUCGAGGAGGCCAAGAACAUGGAGGCCGUUGAGA
..........(((((((...))))))).((((.(((.((.(((((....))).)))).......((((((((....))))))))(((((...)))))........))).))))....... ( -50.50)
>DroWil_CAF1 815 120 - 1
GACUGGAGGAGCAACUUAAACAACUGCAGGCCGCCAAGGAUGAGCUCGAGUUGCGUCAAAAGGAAUUGCAGGCCAUGUUGCAGCGUCUCGAAGAGGCCAAAAACAUGGAGGCUGCUGAGA
......((.(((...........((((((....((...(((((((....))).))))....))..)))))).(((((((...(.(((((...))))))...)))))))..))).)).... ( -35.30)
>DroMoj_CAF1 1342 120 - 1
GAUUGGAGGAGCAGCUGAAGCAGCUGCAGGCCGCCAAGGAUGAGCUUGAGCUGCGCCAGAAGGAGCUGCAAUCGAUGCUGCAGCGCUUGGAGGAGGCCAAGAAUAUGGAGGCCGUCGAGA
(((.......(((((((...))))))).((((.(((...((...((((.(((...((...(((.((((((........)))))).)))...)).))))))).)).))).))))))).... ( -47.90)
>DroAna_CAF1 651 120 - 1
GGCUGGAGGAGCAGCUCAAGCAGCUGCAGGCCGCCAAGGACGAGCUCGAGCUGCGCCAGAAGGAGCUGCAGUCGAUGCUGCAGCGCCUCGAGGAGGCCAAGAACAUGGAGGCCGUCGAGA
((((......((((((.....)))))).((((.((..((.(((((....))).)))).((.((.((((((((....)))))))).))))..)).))))...........))))....... ( -54.00)
>consensus
GACUGGAGGAGCAGCUGAAGCAGCUGCAGGCCGCCAAGGAUGAGCUCGAGCUGCGCCAGAAGGAGCUGCAGUCGAUGCUGCAGCGCCUCGAGGAGGCCAAGAACAUGGAGGCCGUCGAGA
..((.((...((((((.....)))))).((((.(((.((.(((((....))).)))).......(((((((......)))))))(((((...)))))........))).)))).)).)). (-43.75 = -43.20 +  -0.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:31 2006