Locus 6918

Sequence ID 3R_DroMel_CAF1
Location 18,264,003 – 18,264,148
Length 145
Max. P 0.909692
window11225 window11226

overview

Window 5

Location 18,264,003 – 18,264,122
Length 119
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 90.64
Mean single sequence MFE -25.68
Consensus MFE -21.52
Energy contribution -22.05
Covariance contribution 0.53
Combinations/Pair 1.15
Mean z-score -2.42
Structure conservation index 0.84
SVM decision value 1.07
SVM RNA-class probability 0.909692
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18264003 119 + 27905053
AGAAAUUUGUUUAUAAAUAAAUUUGUAUAAAUUGCAUAGAUUUGACAUAAGACAAAGGCCUUUGUGCCCCACGAAAUAAACGUGUCAAUGAGGGCCGCGGUAAUAAUUUAAAAUGCAAA
..(((((((((....))))))))).......((((((...(((((......((...((((((..(....((((.......))))...)..))))))...))......))))))))))). ( -27.60)
>DroPse_CAF1 25157 119 + 1
AGAAAUUUGUUUGAAAAUAAAUUUGUAUAAAUUGUAGAUAUUCGAUAUAAGACAAAGGCCUUUGUGCCACAUGAAAUACACAUGUCAAUGAGGGCCGCAGUAAUAAUUUAAAAUGCAAA
..(((((((((....))))))))).......((((..((((...))))...)))).((((((..(...(((((.......)))))..)..))))))(((.(((....)))...)))... ( -25.40)
>DroSec_CAF1 20205 119 + 1
AGAAAUUUGUUUAUAAAUAAAUUUGUAUAAAUUGCAUAGAUUUGACAUAAGACAAAGGCCUUUGUGCCCCACAAAAUAAACGUGUCAAUGAGGGCCGCGGUAAUAAUUUAAAAUGCAAA
..(((((((((....))))))))).......((((((...(((((......((...((((((..(....(((.........)))...)..))))))...))......))))))))))). ( -25.10)
>DroSim_CAF1 20990 119 + 1
GGAAAUUUGUUUAUAAAUAAAUUUGUAUAAAUUGCAUAGAUUUGACAUAAGACAAAGGCCUUUGUGCCCCACGAAAUAAACGUGUCAAUGAGGGCCGCGGUAAUAAUUUAAAAUGCAAA
..(((((((((....))))))))).......((((((...(((((......((...((((((..(....((((.......))))...)..))))))...))......))))))))))). ( -27.60)
>DroAna_CAF1 21468 118 + 1
AGAAAUUUGUUUAAAAAUAAAUUUGUAUAAAUUGCAUACAUUUGACAUAAGACAAUGGCA-UUGUGAGCUAUGAAAUCAACGUGUCAAUGAGGGCCAGACCAAUAAUUUAAAAUGCAAA
..(((((((((....))))))))).......((((((.((((.(((((..((..(((((.-......)))))....))...))))))))).((......))...........)))))). ( -23.00)
>DroPer_CAF1 25362 119 + 1
AGAAAUUUGUUUGAAAAUAAAUUUGUAUAAAUUGUAGAUAUUCGAUAUAAGACAAAGGCCUUUGUGCCACAUGAAAUACACAUGUCAAUGAGGGCCGCAGUAAUAAUUUAAAAUGCAAA
..(((((((((....))))))))).......((((..((((...))))...)))).((((((..(...(((((.......)))))..)..))))))(((.(((....)))...)))... ( -25.40)
>consensus
AGAAAUUUGUUUAAAAAUAAAUUUGUAUAAAUUGCAUAGAUUUGACAUAAGACAAAGGCCUUUGUGCCCCACGAAAUAAACGUGUCAAUGAGGGCCGCAGUAAUAAUUUAAAAUGCAAA
(.(((((((((....))))))))).).....((((((...(((((......((...((((((..(....((((.......))))...)..))))))...))......))))))))))). (-21.52 = -22.05 +   0.53)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,264,042 – 18,264,148
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.65
Mean single sequence MFE -24.40
Consensus MFE -17.02
Energy contribution -16.80
Covariance contribution -0.22
Combinations/Pair 1.24
Mean z-score -1.82
Structure conservation index 0.70
SVM decision value 0.66
SVM RNA-class probability 0.813533
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18264042 106 + 27905053
AUUUGACAUAAGACAAAGGCCUUUGUGCCCCACGAAAUAAACGUGUCAAUGAGGGCCGCGGUAAUAAUUUAAAAUGCAAAUAG-----UCGAAA---------AAGGCAAUCGCAGGCCG
.((((((..........((((((..(....((((.......))))...)..))))))(((.(((....)))...))).....)-----))))).---------..(((........))). ( -29.80)
>DroPse_CAF1 25196 120 + 1
AUUCGAUAUAAGACAAAGGCCUUUGUGCCACAUGAAAUACACAUGUCAAUGAGGGCCGCAGUAAUAAUUUAAAAUGCAAAUAAAUAAACCGAAUAAACUCGACAAGAAAUUCAUGGAUUG
(((((............((((((..(...(((((.......)))))..)..))))))(((.(((....)))...)))............))))).......................... ( -24.30)
>DroEre_CAF1 20891 106 + 1
AUUUGACAUAAGACAAAGGCCUUUGUGCCCCAUGAAAUAAACGUGUCAAUGAGGGCCGCGGUAAUAAUUUAAAAUGCAAAUAG-----UCGAAA---------AAGGCAAUCGAAGACCG
.((((((..........((((((..(....((((.......))))...)..))))))(((.(((....)))...))).....)-----))))).---------..(((.......).)). ( -24.00)
>DroYak_CAF1 20758 106 + 1
AUUUGACAUAAGACAAAGGCCUUUGUGCCCCACGAAAUAAACGUGUCAAUGAGGGCCGCGGUAAUAAUUUAAAAUGCAAAUAG-----UCGAAA---------GAGGCAAUCGCAGACCG
.((((((..........((((((..(....((((.......))))...)..))))))(((.(((....)))...))).....)-----))))).---------...((....))...... ( -26.40)
>DroAna_CAF1 21507 105 + 1
AUUUGACAUAAGACAAUGGCA-UUGUGAGCUAUGAAAUCAACGUGUCAAUGAGGGCCAGACCAAUAAUUUAAAAUGCAAAUAG-----UCGAAA---------AAAGCAAUCGUAGAUUG
.((((((......((.(((((-(..(((.........)))..)))))).)).((......))....................)-----))))).---------....(((((...))))) ( -17.60)
>DroPer_CAF1 25401 120 + 1
AUUCGAUAUAAGACAAAGGCCUUUGUGCCACAUGAAAUACACAUGUCAAUGAGGGCCGCAGUAAUAAUUUAAAAUGCAAAUAAAUAAACCGAAUAAACUCGACAAGAAAUUCAUGGAUUG
(((((............((((((..(...(((((.......)))))..)..))))))(((.(((....)))...)))............))))).......................... ( -24.30)
>consensus
AUUUGACAUAAGACAAAGGCCUUUGUGCCCCAUGAAAUAAACGUGUCAAUGAGGGCCGCAGUAAUAAUUUAAAAUGCAAAUAG_____UCGAAA_________AAGGCAAUCGUAGACCG
.((((............((((((..(....((((.......))))...)..))))))(((.(((....)))...)))............))))........................... (-17.02 = -16.80 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:14 2006