Locus 1716

Sequence ID X_DroMel_CAF1
Location 4,780,178 – 4,780,286
Length 108
Max. P 0.919304
window2814 window2815

overview

Window 4

Location 4,780,178 – 4,780,286
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.43
Mean single sequence MFE -26.13
Consensus MFE -19.24
Energy contribution -20.13
Covariance contribution 0.89
Combinations/Pair 1.08
Mean z-score -1.84
Structure conservation index 0.74
SVM decision value 1.13
SVM RNA-class probability 0.919304
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4780178 108 + 22224390
GAGGUGGUGGAGA---------AACAUCGAUGCCAAACAUCGAUAUUUUCGAAAAAUCACAUAAAUUGGUG---UUUUUUGAUGAAUAUUCAUUUUUGAUGUAUAUUCAAAUUUCUGAUG
(((((..((((..---------.(((((((((.....))))(((((((((((((((.(((........)))---)))))))).))))))).......)))))...)))).)))))..... ( -25.70)
>DroSec_CAF1 19184 117 + 1
GAGGUGGAGAAAAAUUGAUGCCAACAUCGAUGUCAAACAUCGAUAUUUUCGAAGAAUCACAAACAUCGGUG---UUUUUCGAGGAAUCAUCGUAUAAAUUGUAAGUACAAAUUAAUUUUG
((((((..((...(((((((....))))))).))...))))(((.(((((((((((.(((........)))---)))))))))))))).))...(((.((((....)))).)))...... ( -26.80)
>DroSim_CAF1 13919 120 + 1
GAGGUGGAGAAAAAUUGAUGCCAACAUCGAUGUCAAACAUCGAUAUUUUCGAAGAAUCACACACAUCGGUUUGUUUUUUCGAGGAAUCAUCGUAUAAAUUGUAAGUACAAAUUAAUUUUG
((((((..((...(((((((....))))))).))...))))(((.(((((((((((.((.((......)).)).)))))))))))))).))...(((.((((....)))).)))...... ( -25.90)
>consensus
GAGGUGGAGAAAAAUUGAUGCCAACAUCGAUGUCAAACAUCGAUAUUUUCGAAGAAUCACAAACAUCGGUG___UUUUUCGAGGAAUCAUCGUAUAAAUUGUAAGUACAAAUUAAUUUUG
..(((((..................(((((((.....))))))).(((((((((((.(((........)))...))))))))))).)))))............................. (-19.24 = -20.13 +   0.89)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 5

Location 4,780,178 – 4,780,286
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.43
Mean single sequence MFE -22.73
Consensus MFE -12.53
Energy contribution -13.20
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.55
SVM decision value 0.58
SVM RNA-class probability 0.790103
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4780178 108 - 22224390
CAUCAGAAAUUUGAAUAUACAUCAAAAAUGAAUAUUCAUCAAAAAA---CACCAAUUUAUGUGAUUUUUCGAAAAUAUCGAUGUUUGGCAUCGAUGUU---------UCUCCACCACCUC
.....((((..(((((((.(((.....))).)))))))........---(((........)))...))))(((((((((((((.....))))))))))---------).))......... ( -21.70)
>DroSec_CAF1 19184 117 - 1
CAAAAUUAAUUUGUACUUACAAUUUAUACGAUGAUUCCUCGAAAAA---CACCGAUGUUUGUGAUUCUUCGAAAAUAUCGAUGUUUGACAUCGAUGUUGGCAUCAAUUUUUCUCCACCUC
......(((.((((....)))).))).....((((.(((((((.((---(((........))).)).))))).((((((((((.....)))))))))))).))))............... ( -23.60)
>DroSim_CAF1 13919 120 - 1
CAAAAUUAAUUUGUACUUACAAUUUAUACGAUGAUUCCUCGAAAAAACAAACCGAUGUGUGUGAUUCUUCGAAAAUAUCGAUGUUUGACAUCGAUGUUGGCAUCAAUUUUUCUCCACCUC
......(((.((((....)))).))).....((((.(((((((...(((.((....)).))).....))))).((((((((((.....)))))))))))).))))............... ( -22.90)
>consensus
CAAAAUUAAUUUGUACUUACAAUUUAUACGAUGAUUCCUCGAAAAA___CACCGAUGUAUGUGAUUCUUCGAAAAUAUCGAUGUUUGACAUCGAUGUUGGCAUCAAUUUUUCUCCACCUC
......................................(((((.((...(((........))).)).))))).((((((((((.....))))))))))...................... (-12.53 = -13.20 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:19 2006