Locus 5828

Sequence ID 2L_DroMel_CAF1
Location 16,532,850 – 16,532,991
Length 141
Max. P 0.841196
window9249 window9250

overview

Window 9

Location 16,532,850 – 16,532,959
Length 109
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 95.54
Mean single sequence MFE -17.27
Consensus MFE -16.26
Energy contribution -16.26
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.18
Structure conservation index 0.94
SVM decision value 0.44
SVM RNA-class probability 0.738120
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16532850 109 + 22407834
UUUUGUUGUCGAGCUUCCACUGCAAAAAAUAUGCAAAGCAGCAGCAACAAUAACUAAAACAACAGUAAAACAGCAGCAGCAGAAAAUGGCAAGAAAACAU---UACAUAUAC
((((.((((((...(((..((((........(((......)))((.......(((........)))......)).))))..)))..)))))).))))...---......... ( -17.52)
>DroSec_CAF1 44451 112 + 1
UUUUGUUGUCGAGCUUCCACUGCAAAAAAUAUGCAAAGCAGCAGCAACAAUAACUAAAACAACAGUAAAACAGCAGCAACUGAAAAUGGCAAGAAAACAUUCUUAUGUAUAC
.(((.((((((.((((....((((.......)))))))).((.((.......(((........)))......)).)).........)))))).)))((((....)))).... ( -16.52)
>DroSim_CAF1 30960 112 + 1
UUUUGUUGUCGAGCUUCCACUGCAAAAAAUAUGCAAAGCAGCAGCAACAAUAACUAAAACAACAGUAAAACAGCAGCAACUGAAAAUGGCAAGAAAACAUUCUUAUGUAUAC
.(((.((((((.((((....((((.......)))))))).((.((.......(((........)))......)).)).........)))))).)))((((....)))).... ( -16.52)
>DroEre_CAF1 50386 112 + 1
UUUUGUUGUCGAGCUUCCACUGCAAAAAAUAUGCAAAGCAGCAGCAACAAUAACUAAAACAACAGUGAAACAGCAGCAACAGAAAAUGGCAAGAAAACAUUCUUAUGUAUAU
(((((((((...(((..(((((((.......)))...((....))..................))))....))).)))))))))......(((((....)))))........ ( -17.90)
>DroYak_CAF1 38369 112 + 1
UUUUGUUGUCGAGCUUCCACUGCAAAAAAUAUGCAAAGCAGCAGCAACAACAACUAAAACAACAGUGAAACAGCAGCAACAGAAAAUGGCAAGAAAACAUUCUUAUGUAUGU
(((((((((...(((..(((((((.......)))...((....))..................))))....))).)))))))))......(((((....)))))........ ( -17.90)
>consensus
UUUUGUUGUCGAGCUUCCACUGCAAAAAAUAUGCAAAGCAGCAGCAACAAUAACUAAAACAACAGUAAAACAGCAGCAACAGAAAAUGGCAAGAAAACAUUCUUAUGUAUAC
((((.((((((.((((....((((.......)))))))).((.((.......(((........)))......)).)).........)))))).))))............... (-16.26 = -16.26 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,532,888 – 16,532,991
Length 103
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 89.47
Mean single sequence MFE -19.31
Consensus MFE -15.47
Energy contribution -16.92
Covariance contribution 1.45
Combinations/Pair 1.03
Mean z-score -2.63
Structure conservation index 0.80
SVM decision value 0.75
SVM RNA-class probability 0.841196
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16532888 103 + 22407834
CAGCAGCAACAAUAACUAAAACAACAGUAAAACAGCAGCAGCAGAAAAUGGCAAGAAAACAU---UACAUAUACAUAUGUAUGUA--------UAUGUAUGUAAAUAUACAUGG
..((.((.......(((........)))......)).)).((........))......((((---.((((((((((....)))))--------)))))))))............ ( -16.52)
>DroSec_CAF1 44489 114 + 1
CAGCAGCAACAAUAACUAAAACAACAGUAAAACAGCAGCAACUGAAAAUGGCAAGAAAACAUUCUUAUGUAUACAUAUGUACAUACAUUCAUGUAUGUAUGUAAAUAUAAAUGG
.....((.......(((........)))....(((......)))......)).......((((..(((((.(((((((((((((......))))))))))))).))))))))). ( -20.70)
>DroSim_CAF1 30998 114 + 1
CAGCAGCAACAAUAACUAAAACAACAGUAAAACAGCAGCAACUGAAAAUGGCAAGAAAACAUUCUUAUGUAUACAUAUGUACAUACAUUCAUGUAUGUAUGUAAAUAUAAAUGG
.....((.......(((........)))....(((......)))......)).......((((..(((((.(((((((((((((......))))))))))))).))))))))). ( -20.70)
>consensus
CAGCAGCAACAAUAACUAAAACAACAGUAAAACAGCAGCAACUGAAAAUGGCAAGAAAACAUUCUUAUGUAUACAUAUGUACAUACAUUCAUGUAUGUAUGUAAAUAUAAAUGG
..((.((.......(((........)))......)).))....................((((..(((((.(((((((((((((......))))))))))))).))))))))). (-15.47 = -16.92 +   1.45)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:01 2006