Locus 5828

Sequence ID 2R_DroMel_CAF1
Location 18,464,128 – 18,464,228
Length 100
Max. P 0.826755
window9334 window9335

overview

Window 4

Location 18,464,128 – 18,464,228
Length 100
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 77.24
Mean single sequence MFE -33.87
Consensus MFE -15.53
Energy contribution -17.37
Covariance contribution 1.84
Combinations/Pair 1.18
Mean z-score -2.26
Structure conservation index 0.46
SVM decision value 0.66
SVM RNA-class probability 0.815352
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18464128 100 + 20766785
GCUAAAGCGGGCCAAAAGUGU--GGU-----UU-GGGGGAGAGGUCAAACUUUGACAAGGUUCAAAGCCACUAGAGU--CCGCAAUGGACACCAUCGCAUUGGCCCAAUU
((....))(((((((....((--(((-----((-..(((....((((.....))))....))).)))))))....((--((.....)))).........))))))).... ( -35.00)
>DroSec_CAF1 26152 100 + 1
GCUAAAGCGGGCCAAAAGUGA--GGU-----GG-GGGGUGGAGGUCAAACUUUGACAAGGUUCAAAGCCACUAGAGU--GCGCAAUGGACACCAUCGCAUUGGCCCAAUU
((....))((((((...(((.--(((-----((-...((.((((.....)))).))...(((((..(((((....))--).))..))))).))))).))))))))).... ( -38.20)
>DroSim_CAF1 26392 98 + 1
GCUAAAGCGGGCCAAAAGUGG--GGU-----GG-GGG--GGAGGUCAAACUUUGACAAGGUUCAAAGCCACUAGAGU--GCGCAAUGGACACCAUCGCAUUGGCCCAAUU
((....))((((((...(((.--(((-----((-...--....((((.....))))...(((((..(((((....))--).))..))))).))))).))))))))).... ( -38.30)
>DroEre_CAF1 26214 83 + 1
GCUAAA------------------------GGG-GGGAGGGAGGUCAAACUUUGACAAGGUUCAAAGCCACUAGAGU--CCGCAAUGGACACCAUCGCAUUGGCCCAAUU
......------------------------(((-(((....((((((.....))))..(((.....))).))....)--))((.((((...)))).)).....))).... ( -20.60)
>DroYak_CAF1 27035 107 + 1
GCUAAAUCGGGCUAAGAGUGGAUGGUAGCGGAG-GGGGGAGAGGUCAAACUUUGACAAGGUUCAAAGCCACUAGAGU--GCGCAAUGGACACCAUCGCAUUGGCCCAAUU
........(((((((..(((.(((((.((((((-....((....))...))))).)...(((((..(((((....))--).))..))))))))))))).))))))).... ( -34.70)
>DroAna_CAF1 24059 95 + 1
U--------GGCCAGGAGGGG--GUC-----GCGGCGGGUGAGGUCAAAGUUUGACAGAGCUCAGAGCCACUGGAGUUGGAGCUUUGGAGAUACUCUCAUUGGCACAAUU
(--------(((((((((((.--.((-----..(((((((...((((.....))))...))))...))).(..((((....))))..).))..))))).))))).))... ( -36.40)
>consensus
GCUAAAGCGGGCCAAAAGUGG__GGU_____GG_GGGGGGGAGGUCAAACUUUGACAAGGUUCAAAGCCACUAGAGU__GCGCAAUGGACACCAUCGCAUUGGCCCAAUU
........(((((((..........................((((((.....))))..(((.....))).)).........((.((((...)))).)).))))))).... (-15.53 = -17.37 +   1.84)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,464,128 – 18,464,228
Length 100
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 77.24
Mean single sequence MFE -27.37
Consensus MFE -16.05
Energy contribution -18.72
Covariance contribution 2.67
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.59
SVM decision value 0.70
SVM RNA-class probability 0.826755
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18464128 100 - 20766785
AAUUGGGCCAAUGCGAUGGUGUCCAUUGCGG--ACUCUAGUGGCUUUGAACCUUGUCAAAGUUUGACCUCUCCCCC-AA-----ACC--ACACUUUUGGCCCGCUUUAGC
....(((((((((((((((...)))))))).--......((((.((((......((((.....))))........)-))-----)))--))....)))))))........ ( -31.94)
>DroSec_CAF1 26152 100 - 1
AAUUGGGCCAAUGCGAUGGUGUCCAUUGCGC--ACUCUAGUGGCUUUGAACCUUGUCAAAGUUUGACCUCCACCCC-CC-----ACC--UCACUUUUGGCCCGCUUUAGC
....(((((((.(.((.((((..((..((.(--((....)))))..))......((((.....)))).........-.)-----)))--)).)..)))))))........ ( -29.90)
>DroSim_CAF1 26392 98 - 1
AAUUGGGCCAAUGCGAUGGUGUCCAUUGCGC--ACUCUAGUGGCUUUGAACCUUGUCAAAGUUUGACCUCC--CCC-CC-----ACC--CCACUUUUGGCCCGCUUUAGC
....(((((((.(((((((...))))))).(--((....)))(((((((......))))))).........--...-..-----...--......)))))))........ ( -29.60)
>DroEre_CAF1 26214 83 - 1
AAUUGGGCCAAUGCGAUGGUGUCCAUUGCGG--ACUCUAGUGGCUUUGAACCUUGUCAAAGUUUGACCUCCCUCCC-CCC------------------------UUUAGC
....(((.....(((((((...)))))))((--(.((....((((((((......)))))))).))..))).....-)))------------------------...... ( -21.40)
>DroYak_CAF1 27035 107 - 1
AAUUGGGCCAAUGCGAUGGUGUCCAUUGCGC--ACUCUAGUGGCUUUGAACCUUGUCAAAGUUUGACCUCUCCCCC-CUCCGCUACCAUCCACUCUUAGCCCGAUUUAGC
((((((((.((((.(((((((......((((--((....)))(((((((......)))))))..............-...))))))))))))...)).)))))))).... ( -28.30)
>DroAna_CAF1 24059 95 - 1
AAUUGUGCCAAUGAGAGUAUCUCCAAAGCUCCAACUCCAGUGGCUCUGAGCUCUGUCAAACUUUGACCUCACCCGCCGC-----GAC--CCCCUCCUGGCC--------A
...((.((((.((.((((.........))))))......(((((..((((....((((.....))))))))...)))))-----...--.......)))))--------) ( -23.10)
>consensus
AAUUGGGCCAAUGCGAUGGUGUCCAUUGCGC__ACUCUAGUGGCUUUGAACCUUGUCAAAGUUUGACCUCCCCCCC_CC_____ACC__CCACUUUUGGCCCGCUUUAGC
....((((((..((((((.....))))))............((((((((......)))))))).................................))))))........ (-16.05 = -18.72 +   2.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:27 2006