Locus 6070

Sequence ID 3L_DroMel_CAF1
Location 16,146,844 – 16,147,003
Length 159
Max. P 0.864045
window9741 window9742 window9743

overview

Window 1

Location 16,146,844 – 16,146,963
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.46
Mean single sequence MFE -30.30
Consensus MFE -25.36
Energy contribution -25.68
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -1.54
Structure conservation index 0.84
SVM decision value 0.29
SVM RNA-class probability 0.670408
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16146844 119 + 23771897
UUUAAAUU-UUAAACGAAUCCAAUAUCUAAAAUGAUUUCUCUCAGUGCACCCAGCAUAAGAGACACUCGUCGCAUGUGCAACGCAUGCCAUCUCGCUCUCGCCCACAGCUGCGUAUGCUG
........-....((((.......(((......))).(((((..((((.....)))).)))))...)))).(((((((...)))))))......((...(((........)))...)).. ( -24.30)
>DroSec_CAF1 8868 114 + 1
-----GCU-UAAGAUAAAUCAAAUAUUUAAAGUGAUUUCUCUCAGUGCAUCCAGCAUAAGAGACACUCGUCGCAUGUGCAACGCAUGCCAUCUCGCUCUCGCCCGCAGCUGCGUGUGCUG
-----...-..(((.((((((...........)))))).)))(((..(((.((((...((((((....)))(((((((...)))))))..))).((........)).)))).)))..))) ( -32.30)
>DroSim_CAF1 9624 114 + 1
-----GCU-UAAGAUAAAUCAAAUAUCUAAAGUGAUUUCUUUCAGUGCAUCCAGCAUAAGAGACACUCGUCGCAUGUGCAACGCAUGCCAUCUCGCUCUCGCCCACAGCUGCGUGUGCUG
-----(((-(.(((((.......))))).)))).........(((..(((.((((...((((((....)))(((((((...)))))))..))).((....)).....)))).)))..))) ( -32.90)
>DroEre_CAF1 8415 115 + 1
-----GUUCUUAGACUAGUCCUAUACUCAAAGUGCUUUCUCUCAGUGCAUCCAGCAUAAGAGACACUCGUCGCAUGUGCAACGCAUGCCAUCUCGCUCUCGCCCAUUGCUGCGAGUGCUG
-----.......(((.(((....(((.....)))...(((((..((((.....)))).))))).))).)))(((((((...)))))))......((.(((((........))))).)).. ( -31.70)
>consensus
_____GCU_UAAGACAAAUCAAAUAUCUAAAGUGAUUUCUCUCAGUGCAUCCAGCAUAAGAGACACUCGUCGCAUGUGCAACGCAUGCCAUCUCGCUCUCGCCCACAGCUGCGUGUGCUG
..........................................((((((((.((((...((((((....)))(((((((...)))))))..))).((....)).....)))).)))))))) (-25.36 = -25.68 +   0.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,146,844 – 16,146,963
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.46
Mean single sequence MFE -38.08
Consensus MFE -29.62
Energy contribution -29.62
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.78
SVM decision value 0.84
SVM RNA-class probability 0.864045
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16146844 119 - 23771897
CAGCAUACGCAGCUGUGGGCGAGAGCGAGAUGGCAUGCGUUGCACAUGCGACGAGUGUCUCUUAUGCUGGGUGCACUGAGAGAAAUCAUUUUAGAUAUUGGAUUCGUUUAA-AAUUUAAA
(((..(((.((((.....((....))((((.(((((.((((((....)))))).)))))))))..)))).)))..))).((....))..(((((((.(((((....)))))-.))))))) ( -39.00)
>DroSec_CAF1 8868 114 - 1
CAGCACACGCAGCUGCGGGCGAGAGCGAGAUGGCAUGCGUUGCACAUGCGACGAGUGUCUCUUAUGCUGGAUGCACUGAGAGAAAUCACUUUAAAUAUUUGAUUUAUCUUA-AGC-----
(((((..(((....))).((....))((((.(((((.((((((....)))))).))))))))).))))).......(((((.((((((..(.....)..)))))).)))))-...----- ( -38.40)
>DroSim_CAF1 9624 114 - 1
CAGCACACGCAGCUGUGGGCGAGAGCGAGAUGGCAUGCGUUGCACAUGCGACGAGUGUCUCUUAUGCUGGAUGCACUGAAAGAAAUCACUUUAGAUAUUUGAUUUAUCUUA-AGC-----
(((..((..((((.....((....))((((.(((((.((((((....)))))).)))))))))..))))..))..)))..........(((.(((((.......))))).)-)).----- ( -34.90)
>DroEre_CAF1 8415 115 - 1
CAGCACUCGCAGCAAUGGGCGAGAGCGAGAUGGCAUGCGUUGCACAUGCGACGAGUGUCUCUUAUGCUGGAUGCACUGAGAGAAAGCACUUUGAGUAUAGGACUAGUCUAAGAAC-----
..((.(((((........))))).)).....(((((.((((((....)))))).)))))(((((.(((((.((.(((.((((......)))).))).))...))))).)))))..----- ( -40.00)
>consensus
CAGCACACGCAGCUGUGGGCGAGAGCGAGAUGGCAUGCGUUGCACAUGCGACGAGUGUCUCUUAUGCUGGAUGCACUGAGAGAAAUCACUUUAAAUAUUGGAUUUAUCUAA_AAC_____
..(((....((((.....((....))((((.(((((.((((((....)))))).)))))))))..))))..))).............................................. (-29.62 = -29.62 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,146,883 – 16,147,003
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.25
Mean single sequence MFE -41.30
Consensus MFE -39.89
Energy contribution -39.70
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -1.48
Structure conservation index 0.97
SVM decision value 0.14
SVM RNA-class probability 0.604167
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16146883 120 - 23771897
AAAGUCAUAAACUUUAUUUUCUGUUGCCUGCACAAAGGCGCAGCAUACGCAGCUGUGGGCGAGAGCGAGAUGGCAUGCGUUGCACAUGCGACGAGUGUCUCUUAUGCUGGGUGCACUGAG
(((((.....)))))..........((((......)))).(((..(((.((((.....((....))((((.(((((.((((((....)))))).)))))))))..)))).)))..))).. ( -42.00)
>DroSec_CAF1 8902 120 - 1
AAAGUCAUAAACUUUAUUUUCUGUUGCCUGCACAAAGGCGCAGCACACGCAGCUGCGGGCGAGAGCGAGAUGGCAUGCGUUGCACAUGCGACGAGUGUCUCUUAUGCUGGAUGCACUGAG
(((((.....))))).....((.((((((((......))(((((.......))))))))))).)).((((.(((((.((((((....)))))).))))))))).(((.....)))..... ( -41.10)
>DroSim_CAF1 9658 120 - 1
AAAGUCAUAAACUUUAUUUUCUGUUGCCUGCACAAAGGCGCAGCACACGCAGCUGUGGGCGAGAGCGAGAUGGCAUGCGUUGCACAUGCGACGAGUGUCUCUUAUGCUGGAUGCACUGAA
..((((((............((((.((((......))))))))......((((.....((....))((((.(((((.((((((....)))))).)))))))))..)))).))).)))... ( -39.50)
>DroEre_CAF1 8450 120 - 1
GAAGUCAUAAACUUUAUUUUCUGUUGCCUGCAUAAAGGCGCAGCACUCGCAGCAAUGGGCGAGAGCGAGAUGGCAUGCGUUGCACAUGCGACGAGUGUCUCUUAUGCUGGAUGCACUGAG
(((((.....)))))......(((.((((......)))))))(((.((.(((((....((....))((((.(((((.((((((....)))))).))))))))).))))))))))...... ( -42.60)
>consensus
AAAGUCAUAAACUUUAUUUUCUGUUGCCUGCACAAAGGCGCAGCACACGCAGCUGUGGGCGAGAGCGAGAUGGCAUGCGUUGCACAUGCGACGAGUGUCUCUUAUGCUGGAUGCACUGAG
..((((((............((((.((((......))))))))......((((.....((....))((((.(((((.((((((....)))))).)))))))))..)))).))).)))... (-39.89 = -39.70 +  -0.19)

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 12:09:08 2006