Locus 2239

Sequence ID 3R_DroMel_CAF1
Location 6,363,692 – 6,363,805
Length 113
Max. P 0.833569
window3633 window3634

overview

Window 3

Location 6,363,692 – 6,363,805
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.95
Mean single sequence MFE -26.24
Consensus MFE -22.14
Energy contribution -21.89
Covariance contribution -0.25
Combinations/Pair 1.03
Mean z-score -1.56
Structure conservation index 0.84
SVM decision value -0.05
SVM RNA-class probability 0.506498
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6363692 113 + 27905053
------CCAUGCGAGCUAAUUUAAAAAUUGUUGUAAUUUUUUCGCUUUGCUCUUUUGGAAUUUUUGCAAUGCGCGACAA-AAUGAUUUAUGUCGCUGCCUGGGCGAAAUUAAAAAUAUUA
------(((...((((......((((((((...)))))))).......))))...)))...((((((...((((((((.-((....)).)))))).))....))))))............ ( -26.02)
>DroVir_CAF1 136267 119 + 1
UGUGUGCGCUGCGAGCUAAUUUAAAAAUUUUUGUAAUUUUUUCGCCUUGCUCUUUUGGAAUUUUUGCAAUGCGCGACAA-AAUGAUUUAUGUCGCUGCCUGCGCAAAAUUAAAAAUAUUA
....(((((.((((((......(((((((.....))))))).......))))....................((((((.-((....)).)))))).))..)))))............... ( -27.32)
>DroPse_CAF1 125962 113 + 1
------CCAUGCGAGCUAAUUUAAAAAUUUUUGUAAUUUUUUCGCUUUGCUCUUUUGGAAUUUUUGCAAUGCGCGACAA-AAUGAUUUAUGUCGCUGCCUGGGCGAAAUUAAAAAUAUUA
------(((...((((......(((((((.....))))))).......))))...)))...((((((...((((((((.-((....)).)))))).))....))))))............ ( -26.42)
>DroGri_CAF1 163031 119 + 1
UGUGUGUGUUGCGAGCUAAUUUAAAAAUUUUUGUAAUUUUUUCGCCUUGCUCUUUUGGAAUUUUUGCAAUGCGCGACAA-AAUGAUUUAUGUCGCUGCCUGCGCAAAAUUAAAAAUAUUA
((((((((((((((((......(((((((.....))))))).......)))).....((....)))))))))((((((.-((....)).)))))).....)))))............... ( -26.32)
>DroMoj_CAF1 181816 119 + 1
UGUGUGUGCUGCGAGCUAAUUUAAAAAUUUUUGUAAUUUUUUCGCCUUGCUCUUUUGGAAUUUUUGCAAUGCGCGACAA-AAUGAUUUAUGUCGCUGCCUGCGCAAAAUUAAAAAUAUUA
....(((((.((((((......(((((((.....))))))).......))))....................((((((.-((....)).)))))).))..)))))............... ( -25.42)
>DroPer_CAF1 133052 114 + 1
-----CCCAUGCGAGCUAAUUUAAAAAUU-UUGUAAUUUUUUCGCUUUGCUCUUUUGGAAUUUUUGCAAUGCGCGACAAAAAUGAUUUAUGUCGCUGCCUGGGCGAAAUUAAAAAUAUUA
-----.(((...((((......(((((((-....))))))).......))))...)))...((((((...((((((((.((.....)).)))))).))....))))))............ ( -25.92)
>consensus
_____GCCAUGCGAGCUAAUUUAAAAAUUUUUGUAAUUUUUUCGCCUUGCUCUUUUGGAAUUUUUGCAAUGCGCGACAA_AAUGAUUUAUGUCGCUGCCUGCGCAAAAUUAAAAAUAUUA
............((((......(((((((.....))))))).......))))((((((...((((((...((((((((...........)))))).))....))))))))))))...... (-22.14 = -21.89 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,363,692 – 6,363,805
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.95
Mean single sequence MFE -24.53
Consensus MFE -19.98
Energy contribution -19.73
Covariance contribution -0.25
Combinations/Pair 1.04
Mean z-score -2.52
Structure conservation index 0.81
SVM decision value 0.72
SVM RNA-class probability 0.833569
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6363692 113 - 27905053
UAAUAUUUUUAAUUUCGCCCAGGCAGCGACAUAAAUCAUU-UUGUCGCGCAUUGCAAAAAUUCCAAAAGAGCAAAGCGAAAAAAUUACAACAAUUUUUAAAUUAGCUCGCAUGG------
................((....((.((((((.........-.))))))))...)).......(((...((((.((....(((((((.....)))))))...)).))))...)))------ ( -21.80)
>DroVir_CAF1 136267 119 - 1
UAAUAUUUUUAAUUUUGCGCAGGCAGCGACAUAAAUCAUU-UUGUCGCGCAUUGCAAAAAUUCCAAAAGAGCAAGGCGAAAAAAUUACAAAAAUUUUUAAAUUAGCUCGCAGCGCACACA
...............(((((..((.((((((.........-.))))))....................((((.((....(((((((.....)))))))...)).)))))).))))).... ( -26.50)
>DroPse_CAF1 125962 113 - 1
UAAUAUUUUUAAUUUCGCCCAGGCAGCGACAUAAAUCAUU-UUGUCGCGCAUUGCAAAAAUUCCAAAAGAGCAAAGCGAAAAAAUUACAAAAAUUUUUAAAUUAGCUCGCAUGG------
................((....((.((((((.........-.))))))))...)).......(((...((((.((....(((((((.....)))))))...)).))))...)))------ ( -22.00)
>DroGri_CAF1 163031 119 - 1
UAAUAUUUUUAAUUUUGCGCAGGCAGCGACAUAAAUCAUU-UUGUCGCGCAUUGCAAAAAUUCCAAAAGAGCAAGGCGAAAAAAUUACAAAAAUUUUUAAAUUAGCUCGCAACACACACA
..............((((((((((.((((((.........-.)))))))).)))).............((((.((....(((((((.....)))))))...)).))))))))........ ( -26.30)
>DroMoj_CAF1 181816 119 - 1
UAAUAUUUUUAAUUUUGCGCAGGCAGCGACAUAAAUCAUU-UUGUCGCGCAUUGCAAAAAUUCCAAAAGAGCAAGGCGAAAAAAUUACAAAAAUUUUUAAAUUAGCUCGCAGCACACACA
..............((((((((((.((((((.........-.)))))))).)))).............((((.((....(((((((.....)))))))...)).))))))))........ ( -26.00)
>DroPer_CAF1 133052 114 - 1
UAAUAUUUUUAAUUUCGCCCAGGCAGCGACAUAAAUCAUUUUUGUCGCGCAUUGCAAAAAUUCCAAAAGAGCAAAGCGAAAAAAUUACAA-AAUUUUUAAAUUAGCUCGCAUGGG-----
.................((((.((.((((((...........))))))....................((((.((....(((((((....-)))))))...)).)))))).))))----- ( -24.60)
>consensus
UAAUAUUUUUAAUUUCGCCCAGGCAGCGACAUAAAUCAUU_UUGUCGCGCAUUGCAAAAAUUCCAAAAGAGCAAAGCGAAAAAAUUACAAAAAUUUUUAAAUUAGCUCGCAUCGC_____
................((....((.((((((...........))))))))..................((((.((....(((((((.....)))))))...)).)))))).......... (-19.98 = -19.73 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:38 2006