Locus 3513

Sequence ID 3R_DroMel_CAF1
Location 9,502,560 – 9,502,701
Length 141
Max. P 0.996044
window5643 window5644

overview

Window 3

Location 9,502,560 – 9,502,662
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 97.84
Mean single sequence MFE -27.30
Consensus MFE -25.22
Energy contribution -25.42
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.92
SVM decision value 2.65
SVM RNA-class probability 0.996044
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9502560 102 - 27905053
CGAAAUACCUUUAUUUUUGUAAUCAAUUCGCACACACUCGAAUUGAUUGCCGUGCGAUUUUUCGAGGUCCCUCGUCGCCCGUCGUCUAUUCUGCGAUGUCCG
..................((((((((((((........))))))))))))...((((.....((((....)))))))).((((((.......)))))).... ( -27.20)
>DroSec_CAF1 132300 102 - 1
CGAAAUACCUUUAUUUUUGUAAUCAAUUCGCACACACUCGAAUUGAUUGCCGUGCGAUUUUUCGAGGUCCCUCGUCGCCCGUCGUCUAUUCUGCGAUGUCCG
..................((((((((((((........))))))))))))...((((.....((((....)))))))).((((((.......)))))).... ( -27.20)
>DroSim_CAF1 122465 102 - 1
CGAAAUACCUUUAUUUUUGUAAUCAAUUCGCACACACUCGAAUUGAUUGCCGUGCGAUUUUUCGAGGUCCCUCGUCGCCCGUCGUCUAUUCUGCGAUGUCCG
..................((((((((((((........))))))))))))...((((.....((((....)))))))).((((((.......)))))).... ( -27.20)
>DroEre_CAF1 140088 102 - 1
CGAAAUACCUUUAUUUUUGUAAUCAAUUCGCACACACUCGAAUUGAUUGCCGUGCGAUUUUUCGAGGUCCCUCGUCGCCCGUCGUUUAUUUUGCGAAGUCCG
(((((((...........((((((((((((........))))))))))))((.((((.....((((....)))))))).)).....)))))))......... ( -27.00)
>DroYak_CAF1 133850 102 - 1
CGAAAUACCUUUAUUUUUGUAAUCAAUUCGCACACACUCGAAUUGAUUGGCGUGCGAUUUUUCGAGGUCCCUCGUCGCCCGUCGUUUAUUUUGCGAAGUCCG
(((((((.............((((((((((........))))))))))((((.((((.....((((....)))))))).))))...)))))))......... ( -27.90)
>consensus
CGAAAUACCUUUAUUUUUGUAAUCAAUUCGCACACACUCGAAUUGAUUGCCGUGCGAUUUUUCGAGGUCCCUCGUCGCCCGUCGUCUAUUCUGCGAUGUCCG
..................((((((((((((........))))))))))))((.((((.....((((....)))))))).))((((.......))))...... (-25.22 = -25.42 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,502,595 – 9,502,701
Length 106
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 83.85
Mean single sequence MFE -23.27
Consensus MFE -14.86
Energy contribution -14.95
Covariance contribution 0.09
Combinations/Pair 1.18
Mean z-score -2.44
Structure conservation index 0.64
SVM decision value 0.04
SVM RNA-class probability 0.555167
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9502595 106 - 27905053
UCCUCACCAGGCACACACGCGCUUUUAUCGCUCACCUCUCGAAAUACCUUUAUUUUUGUAAUCAAUUCGCACA----CACUCGAAUUGAUUGCCGUGCGAUUUUUCGAGG
.((((...((((.(....).))))..(((((.(.......((((((....)))))).((((((((((((....----....)))))))))))).).))))).....)))) ( -27.80)
>DroPse_CAF1 135922 94 - 1
--------AGUG--CUACACGCUUUGGG-GCCUCUUUUUUGAA----UUUUAUUUUUUUACUAAAUUCGCACAAGCACAACCAAAUUGACAGA-UUCCGAUUUUUCGAAC
--------.(((--((....(((....)-)).........(((----(((............)))))).....))))).......((((.(((-(....)))).)))).. ( -13.10)
>DroSec_CAF1 132335 106 - 1
UCCUCACCAGACACACACGCGCUUUUAUCGCUCCCCUCUCGAAAUACCUUUAUUUUUGUAAUCAAUUCGCACA----CACUCGAAUUGAUUGCCGUGCGAUUUUUCGAGG
.((((.............((((..................((((((....)))))).((((((((((((....----....)))))))))))).))))((....)))))) ( -24.80)
>DroSim_CAF1 122500 106 - 1
UCCUCACCAGACACACACGCGCUUUUAUCGCUCACCUCUCGAAAUACCUUUAUUUUUGUAAUCAAUUCGCACA----CACUCGAAUUGAUUGCCGUGCGAUUUUUCGAGG
.((((.............((((..................((((((....)))))).((((((((((((....----....)))))))))))).))))((....)))))) ( -24.80)
>DroEre_CAF1 140123 106 - 1
UCCUCACCAGACAUACACGCGCUUUUAUCGCUCACCUCUCGAAAUACCUUUAUUUUUGUAAUCAAUUCGCACA----CACUCGAAUUGAUUGCCGUGCGAUUUUUCGAGG
.((((.............((((..................((((((....)))))).((((((((((((....----....)))))))))))).))))((....)))))) ( -24.80)
>DroYak_CAF1 133885 106 - 1
UCCUCACCAGACACACACGCGCUUUUAUCGCUCACCUCUCGAAAUACCUUUAUUUUUGUAAUCAAUUCGCACA----CACUCGAAUUGAUUGGCGUGCGAUUUUUCGAGG
.((((..........(((((((.......))...........................(((((((((((....----....)))))))))))))))).((....)))))) ( -24.30)
>consensus
UCCUCACCAGACACACACGCGCUUUUAUCGCUCACCUCUCGAAAUACCUUUAUUUUUGUAAUCAAUUCGCACA____CACUCGAAUUGAUUGCCGUGCGAUUUUUCGAGG
..................(.((.......)).)....(((((((.............((((((((((((............)))))))))))).........))))))). (-14.86 = -14.95 +   0.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:59 2006