Locus 8010

Sequence ID X_DroMel_CAF1
Location 19,916,478 – 19,916,577
Length 99
Max. P 0.963128
window13148 window13149

overview

Window 8

Location 19,916,478 – 19,916,577
Length 99
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 93.72
Mean single sequence MFE -38.80
Consensus MFE -34.38
Energy contribution -36.88
Covariance contribution 2.50
Combinations/Pair 1.00
Mean z-score -2.35
Structure conservation index 0.89
SVM decision value 1.55
SVM RNA-class probability 0.963128
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19916478 99 + 22224390
GGCUCAAUCAAGGCGAUGUGUCGCCGGUCUGAUUGGAAGCA---------GCAGCUGAGAAGCCGCAAGGAUCGUGCCUGGGUGAGCCAUAACACAUAGUGGUGACAC
((((((..((.(((((....)))))(((.((((((....).---------((.(((....))).))...))))).)))))..))))))..........(((....))) ( -38.70)
>DroSec_CAF1 30551 99 + 1
GGCUCAAUCAAGGCGAUGUGUCGCCGGUCUGAUUGGAAACA---------GCAGCUGAGAAGCCGCAAGGAUCGUGCCUGGGUGAGCCAUAACACAAAGUGGUGACAC
((((((..((.(((((....)))))(((.((((((....).---------((.(((....))).))...))))).)))))..))))))..........(((....))) ( -41.20)
>DroEre_CAF1 28042 99 + 1
GGCUCAAUCAAGGCGAUGUGUCGCCCGUCUGAUUGGAAGCA---------GCAGCUGAGAAGCCGCAAGGAUCGUGCCUGGGUGAGCCAUAACACAAAGUGGUAACAC
((((((..((.(((.(((.((((((((......)))..)).---------((.(((....))).))...)))))))))))..))))))..........(((....))) ( -32.40)
>DroYak_CAF1 29828 108 + 1
GGCUCAAUCAAGGCGAUGUGUCGCCGGUCUGAUUGGAAGCAGCAGCAGCAGCAGCUGAGAAGCCGCAAGGAUCGUGCCUGGGUGAGCCAUAACACAAAGUGGUGACAC
((((((..((.(((((....)))))(((.((((......((((.((....)).)))).....((....)))))).)))))..))))))..........(((....))) ( -42.90)
>consensus
GGCUCAAUCAAGGCGAUGUGUCGCCGGUCUGAUUGGAAGCA_________GCAGCUGAGAAGCCGCAAGGAUCGUGCCUGGGUGAGCCAUAACACAAAGUGGUGACAC
((((((..((.(((((....)))))(((.((((((....)..........((.(((....))).))...))))).)))))..))))))..........(((....))) (-34.38 = -36.88 +   2.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 19,916,478 – 19,916,577
Length 99
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 93.72
Mean single sequence MFE -31.98
Consensus MFE -30.16
Energy contribution -29.78
Covariance contribution -0.38
Combinations/Pair 1.06
Mean z-score -1.43
Structure conservation index 0.94
SVM decision value 0.28
SVM RNA-class probability 0.666240
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19916478 99 - 22224390
GUGUCACCACUAUGUGUUAUGGCUCACCCAGGCACGAUCCUUGCGGCUUCUCAGCUGC---------UGCUUCCAAUCAGACCGGCGACACAUCGCCUUGAUUGAGCC
(((((..(((...)))...(((.....)))))))).......((((((....))))))---------.(((..(((((((...(((((....))))))))))))))). ( -30.50)
>DroSec_CAF1 30551 99 - 1
GUGUCACCACUUUGUGUUAUGGCUCACCCAGGCACGAUCCUUGCGGCUUCUCAGCUGC---------UGUUUCCAAUCAGACCGGCGACACAUCGCCUUGAUUGAGCC
(.((((..((.....))..)))).).....(((..((..(..((((((....))))))---------.)..))(((((((...(((((....)))))))))))).))) ( -30.70)
>DroEre_CAF1 28042 99 - 1
GUGUUACCACUUUGUGUUAUGGCUCACCCAGGCACGAUCCUUGCGGCUUCUCAGCUGC---------UGCUUCCAAUCAGACGGGCGACACAUCGCCUUGAUUGAGCC
(((....))).(((((((.(((.....)))))))))).....((((((....))))))---------.(((..((((((...((((((....))))))))))))))). ( -32.10)
>DroYak_CAF1 29828 108 - 1
GUGUCACCACUUUGUGUUAUGGCUCACCCAGGCACGAUCCUUGCGGCUUCUCAGCUGCUGCUGCUGCUGCUUCCAAUCAGACCGGCGACACAUCGCCUUGAUUGAGCC
(((....))).(((((((.(((.....)))))))))).....(((((....((((....))))..)))))...(((((((...(((((....)))))))))))).... ( -34.60)
>consensus
GUGUCACCACUUUGUGUUAUGGCUCACCCAGGCACGAUCCUUGCGGCUUCUCAGCUGC_________UGCUUCCAAUCAGACCGGCGACACAUCGCCUUGAUUGAGCC
(((.(((......))).)))(((((....(((((........((((((....)))))).........)))))..((((((...(((((....)))))))))))))))) (-30.16 = -29.78 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:12 2006