Locus 307

Sequence ID 2R_DroMel_CAF1
Location 2,047,666 – 2,047,764
Length 98
Max. P 0.964728
window628 window629

overview

Window 8

Location 2,047,666 – 2,047,764
Length 98
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 75.36
Mean single sequence MFE -23.38
Consensus MFE -13.89
Energy contribution -15.45
Covariance contribution 1.56
Combinations/Pair 1.05
Mean z-score -2.20
Structure conservation index 0.59
SVM decision value 1.57
SVM RNA-class probability 0.964728
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2047666 98 + 20766785
GUUUGCCAACCAGCCACACACACAUACUCGUGUAUACAUACAUAUGUGUCUAUAUAGUAUCUUUAUAUGGGAGUGCAGUAUAGAGAGUAAGGCAAACA
(((((((.............((((((...(((....)))...))))))(((((((.(((((((.....)))).))).)))))))......))))))). ( -28.10)
>DroSec_CAF1 32435 81 + 1
GUUUGCCAACCAGCCUGCCACACAUACCCAU----------------GUCUAUAUAGUAUCGUU-UAAGGGAGUGCAGUAUAGAGAGUAAGGCAAACA
(((((((...............(((....))----------------)(((((((.(((((...-.....)).))).)))))))......))))))). ( -19.00)
>DroSim_CAF1 33031 82 + 1
GUUUGCCAACCAGCCUGCCACACAUACUCAU----------------GUCUAUAUAGUAUCUUUAUAGGGGAGUGCAGUAUAGAGAGUAAGGCAAACA
(((((((.....(....)......(((((..----------------.(((((((.(((((((.....)))).))).)))))))))))).))))))). ( -23.80)
>DroYak_CAF1 35149 81 + 1
GUUUGCCAGCCAGCCA----CACAUAUAUGU--------AUGUAUGUAUCUAU-----AUCUGGAUAGGGGAGUGCAGUGCAGAGAGUAAGGCAAACA
(((((((.((...((.----.(((((((...--------.))))))).(((((-----......)))))))...))..(((.....))).))))))). ( -22.60)
>consensus
GUUUGCCAACCAGCCAGCCACACAUACUCAU________________GUCUAUAUAGUAUCUUUAUAGGGGAGUGCAGUAUAGAGAGUAAGGCAAACA
(((((((.....(.......)...........................(((((((.(((((((.....)))).))).)))))))......))))))). (-13.89 = -15.45 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 2,047,666 – 2,047,764
Length 98
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 75.36
Mean single sequence MFE -22.52
Consensus MFE -10.54
Energy contribution -11.79
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.14
Structure conservation index 0.47
SVM decision value -0.04
SVM RNA-class probability 0.512782
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2047666 98 - 20766785
UGUUUGCCUUACUCUCUAUACUGCACUCCCAUAUAAAGAUACUAUAUAGACACAUAUGUAUGUAUACACGAGUAUGUGUGUGUGGCUGGUUGGCAAAC
.(((((((..(((..((((((.((((............((((((((((......)))))).))))..........))))))))))..))).))))))) ( -27.05)
>DroSec_CAF1 32435 81 - 1
UGUUUGCCUUACUCUCUAUACUGCACUCCCUUA-AACGAUACUAUAUAGAC----------------AUGGGUAUGUGUGGCAGGCUGGUUGGCAAAC
.(((((((..(((..((...(..(((.(((...-.................----------------..)))...)))..)..))..))).))))))) ( -21.25)
>DroSim_CAF1 33031 82 - 1
UGUUUGCCUUACUCUCUAUACUGCACUCCCCUAUAAAGAUACUAUAUAGAC----------------AUGAGUAUGUGUGGCAGGCUGGUUGGCAAAC
.(((((((..(((((((((((...((((..(((((.((...)).)))))..----------------..))))..)))))).))...))).))))))) ( -21.70)
>DroYak_CAF1 35149 81 - 1
UGUUUGCCUUACUCUCUGCACUGCACUCCCCUAUCCAGAU-----AUAGAUACAUACAU--------ACAUAUAUGUG----UGGCUGGCUGGCAAAC
.(((((((.........((...((......((((......-----))))...(((((((--------(....))))))----))))..)).))))))) ( -20.10)
>consensus
UGUUUGCCUUACUCUCUAUACUGCACUCCCCUAUAAAGAUACUAUAUAGAC________________ACGAGUAUGUGUGGCAGGCUGGUUGGCAAAC
.(((((((..(((..((...((((((.................................................))))))..))..))).))))))) (-10.54 = -11.79 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:04 2006