Locus 2497

Sequence ID 3R_DroMel_CAF1
Location 6,828,680 – 6,828,838
Length 158
Max. P 0.699111
window4093 window4094

overview

Window 3

Location 6,828,680 – 6,828,799
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 97.82
Mean single sequence MFE -34.90
Consensus MFE -29.81
Energy contribution -29.87
Covariance contribution 0.06
Combinations/Pair 1.06
Mean z-score -1.69
Structure conservation index 0.85
SVM decision value 0.31
SVM RNA-class probability 0.683271
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6828680 119 - 27905053
AAAUCAUUAAAAAUUUCCAGGGCAGAGACAUUGAGUUG-GGCCAGAGGCCAAUAUACCUGGACCUAGACUCUCAUCGCAUGCUGAGUAUUUAGCCGAGGUCAAAUUGAUAUGUCUGCCAG
....................((((((.(.((..(.(((-((((...)))).....((((((..(((((..((((........))))..))))))).))))))).)..)).).)))))).. ( -33.70)
>DroSec_CAF1 87789 119 - 1
AAAUCAUUAAAAAUUCCCAGAGCAGAGACAUUGAGUUG-GGCCAGAGGCCAAUAUACCUGGGCCUAGACUCUCAUCGCAUGCUGAGUAUUUAGCCGAGGUCAAAUUGAUAUGUCUGCCAG
...................(.(((((.(.((..(.(((-((((...)))).....((((.(((.((((..((((........))))..))))))).))))))).)..)).).)))))).. ( -35.20)
>DroSim_CAF1 93641 119 - 1
AAAUCAUUAAAAAUUCCCAGGGCAGAGACAUUGAGUUG-GGCCAGAGGCCAAUAUACCUGGCCCUAGACUCUCAUCGCAUGCUGAGUAUUUAGCCGAGGUCAAAUUGAUAUGUCUGCCAG
....................((((((.(.((..(...(-((((((.(.........))))))))..((((....(((...(((((....))))))))))))...)..)).).)))))).. ( -35.50)
>DroEre_CAF1 72711 119 - 1
AAAUCAUUAAAAAUUCCCAGGGCAGAGACAUUGAGUUG-GGCCAGAGGCCAAUAUACCUGGCCCUAGACUCUCAUCGCAUGCUGAGUAUUUAGCCGAGGUCAAAUUGAUAUGUCUGGCAG
.......((((.((((....((((..((....((((((-((((((.(.........))))))))..)))))...))...)))))))).))))(((((.(((.....)))...)).))).. ( -33.00)
>DroYak_CAF1 86082 119 - 1
AAAUCAUUAAAAAUUCCCAGGGCAGAGACAUUGAGUUG-GGCCAGAGGCCAAUAUACCUGGCCCUAGACUCUCAUCGCAUGCUGAGUAUUUAGCCGAGGUCAAAUUGAUAUGUCUGCCAG
....................((((((.(.((..(...(-((((((.(.........))))))))..((((....(((...(((((....))))))))))))...)..)).).)))))).. ( -35.50)
>DroAna_CAF1 44046 120 - 1
AAAUCAUUAAAAAUUCCCAGGGCAGAGACAUUGAGUUGGGGCCAGAGGCCAAUAUACCUGGCCCUAGACUUUCAUCGCAUGCUGAGUAUUUAGUCGAGGUCAAAUUGAUAUGUCUGCCAG
....................((((((.(.((..(..(((((((((.(.........))))))))))((((....(((...(((((....))))))))))))...)..)).).)))))).. ( -36.50)
>consensus
AAAUCAUUAAAAAUUCCCAGGGCAGAGACAUUGAGUUG_GGCCAGAGGCCAAUAUACCUGGCCCUAGACUCUCAUCGCAUGCUGAGUAUUUAGCCGAGGUCAAAUUGAUAUGUCUGCCAG
....................((((((.(.((..(.(((.((((...)))).....((((((..(((((..((((........))))..))))))).))))))).)..)).).)))))).. (-29.81 = -29.87 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,828,720 – 6,828,838
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.72
Mean single sequence MFE -32.05
Consensus MFE -27.49
Energy contribution -27.66
Covariance contribution 0.17
Combinations/Pair 1.18
Mean z-score -1.62
Structure conservation index 0.86
SVM decision value 0.35
SVM RNA-class probability 0.699111
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6828720 118 + 27905053
AUGCGAUGAGAGUCUAGGUCCAGGUAUAUUGGCCUCUGGCC-CAACUCAAUGUCUCUGCCCUGGAAAUUUUUAAUGAUUUUCUCACAAUUUCUUAAGGCCCUUUCAUUCGUUCG-UUCGU
..((((((((((((((((..(((..(((((((((...))))-......)))))..))).))))))...((((((.((..((.....))..))))))))..)))))).))))...-..... ( -26.50)
>DroSec_CAF1 87829 118 + 1
AUGCGAUGAGAGUCUAGGCCCAGGUAUAUUGGCCUCUGGCC-CAACUCAAUGUCUCUGCUCUGGGAAUUUUUAAUGAUUUUCUCACAAUUUCUUGAGGCCCUUUCAUUCGUUCG-UUCGU
..((((((((((....((((((((...(((((((...))).-...................((((((..((....))..))))))))))..)))).)))))))))).))))...-..... ( -30.10)
>DroSim_CAF1 93681 118 + 1
AUGCGAUGAGAGUCUAGGGCCAGGUAUAUUGGCCUCUGGCC-CAACUCAAUGUCUCUGCCCUGGGAAUUUUUAAUGAUUUUCUCACAAUUUCUUGAGGCCCUUUCAUUCGUUCG-UUCGU
..((((((((((....(((((((((......)))..)))))-)........(((((.....((((((..((....))..)))))).........))))).)))))).))))...-..... ( -33.54)
>DroEre_CAF1 72751 118 + 1
AUGCGAUGAGAGUCUAGGGCCAGGUAUAUUGGCCUCUGGCC-CAACUCAAUGUCUCUGCCCUGGGAAUUUUUAAUGAUUUUCUCACAAUUUCUUGAGGCCCUUUCAUUCGUUCA-UUCGU
..((((((((((....(((((((((......)))..)))))-)........(((((.....((((((..((....))..)))))).........))))).)))))).))))...-..... ( -33.54)
>DroYak_CAF1 86122 118 + 1
AUGCGAUGAGAGUCUAGGGCCAGGUAUAUUGGCCUCUGGCC-CAACUCAAUGUCUCUGCCCUGGGAAUUUUUAAUGAUUUUCUCACAAUUUCUUGAGGUCCUUUCAUUCGUUGG-UUCGU
..((((((((((((((((((.((..(((((((((...))))-......)))))..))))))))))...............(((((........)))))..)))))).))))...-..... ( -33.50)
>DroAna_CAF1 44086 120 + 1
AUGCGAUGAAAGUCUAGGGCCAGGUAUAUUGGCCUCUGGCCCCAACUCAAUGUCUCUGCCCUGGGAAUUUUUAAUGAUUUUCUCACAAUUUCUUGGGGCCUUUCUUUCCAUUCGAAUCGU
...(((.(((((....(((((((.....)))))))..(((((((((.....))........((((((..((....))..))))))........)))))))...)))))...)))...... ( -35.10)
>consensus
AUGCGAUGAGAGUCUAGGGCCAGGUAUAUUGGCCUCUGGCC_CAACUCAAUGUCUCUGCCCUGGGAAUUUUUAAUGAUUUUCUCACAAUUUCUUGAGGCCCUUUCAUUCGUUCG_UUCGU
..((((((((((((((((((.((..(((((((((...)))).......)))))..))))))))))...............(((((........)))))..))))))).)))......... (-27.49 = -27.66 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:57 2006