Locus 6248

Sequence ID 2L_DroMel_CAF1
Location 17,354,179 – 17,354,306
Length 127
Max. P 0.956040
window9982 window9983

overview

Window 2

Location 17,354,179 – 17,354,275
Length 96
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 82.69
Mean single sequence MFE -17.14
Consensus MFE -12.73
Energy contribution -12.86
Covariance contribution 0.13
Combinations/Pair 1.14
Mean z-score -1.51
Structure conservation index 0.74
SVM decision value 0.03
SVM RNA-class probability 0.550670
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17354179 96 - 22407834
CCAGGAUGUCCUGACAUCUGCACCCAGAACAAUCAACCAACAAAAAAAAAUAAAUAAAUAACCUGAUAUAAACUGGGGCCCUCGCUCUGAUGCUGG
(((((((((....))))).((.(((((....((((............................)))).....))))))).............)))) ( -18.39)
>DroSec_CAF1 56058 81 - 1
CCGGGAUGUCCUGACAUCUGCACCCAGAACAAUCAACCAAAAAAAA---------AAAUAACCUGAUAUAAACUGGGG------CUCUGAUGCUGG
.((((....)))).((((.((.(((((....((((...........---------........)))).....))))))------)...)))).... ( -18.91)
>DroSim_CAF1 52412 80 - 1
CCGGGAUGUCCUGACAUCUGCACCCAGAACAAUCAACCAAAAA-AA---------AAAUAACCAGAUAUAAACUGGGG------CUCUGAUGCUGG
.((((....)))).((((.((.(((((....(((.........-..---------.........))).....))))))------)...)))).... ( -17.75)
>DroEre_CAF1 53849 85 - 1
CCGGGAUGUCCUGACAUCUGCACCCAGAACAAUCAACGAAAAGAAA---------AAAAAA--UUAAAUAAAAUGGGGCCCUCACUCUGAUGCCGC
.((((((((....))))).((.((((....................---------......--..........)))))).............))). ( -13.52)
>consensus
CCGGGAUGUCCUGACAUCUGCACCCAGAACAAUCAACCAAAAAAAA_________AAAUAACCUGAUAUAAACUGGGG______CUCUGAUGCUGG
(((((((((....)))))....(((((.............................................)))))...............)))) (-12.73 = -12.86 +   0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 17,354,207 – 17,354,306
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 85.71
Mean single sequence MFE -20.98
Consensus MFE -19.20
Energy contribution -19.57
Covariance contribution 0.37
Combinations/Pair 1.06
Mean z-score -2.02
Structure conservation index 0.92
SVM decision value 1.46
SVM RNA-class probability 0.956040
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17354207 99 - 22407834
GGGUGGAAUCUCUGCAACGAGAGGAGCAAAACCAGGAUGUCCUGACAUCUGCACCCAGAACAAUCAACCAACAAAAAAAAAUAAAUAAAUAACCUGAUA
(((((.......(((..(....)..)))......((((((....)))))).)))))........................................... ( -20.30)
>DroSec_CAF1 56080 90 - 1
GGGUGGAAUCUAGGCAACGAGAGGAGCGACACCGGGAUGUCCUGACAUCUGCACCCAGAACAAUCAACCAAAAAAAA---------AAAUAACCUGAUA
(((((........((..(....)..)).......((((((....)))))).))))).....................---------............. ( -19.60)
>DroSim_CAF1 52434 89 - 1
GGGUGGAAUCUCGGCAAUGAGAGGAGCGACACCGGGAUGUCCUGACAUCUGCACCCAGAACAAUCAACCAAAAA-AA---------AAAUAACCAGAUA
(((((...(((((....)))))............((((((....)))))).)))))..................-..---------............. ( -19.80)
>DroEre_CAF1 53877 88 - 1
GGGUGGAAUCUCGGCUUCGAGAGGAGCGACACCGGGAUGUCCUGACAUCUGCACCCAGAACAAUCAACGAAAAGAAA---------AAAAAA--UUAAA
(((((........(((((....))))).......((((((....)))))).))))).....................---------......--..... ( -24.20)
>consensus
GGGUGGAAUCUCGGCAACGAGAGGAGCGACACCGGGAUGUCCUGACAUCUGCACCCAGAACAAUCAACCAAAAAAAA_________AAAUAACCUGAUA
(((((...(((((....)))))............((((((....)))))).)))))........................................... (-19.20 = -19.57 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:18 2006