Locus 4538

Sequence ID 2R_DroMel_CAF1
Location 14,837,610 – 14,837,708
Length 98
Max. P 0.992808
window7275 window7276

overview

Window 5

Location 14,837,610 – 14,837,708
Length 98
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 79.07
Mean single sequence MFE -38.02
Consensus MFE -21.43
Energy contribution -24.16
Covariance contribution 2.72
Combinations/Pair 1.07
Mean z-score -4.17
Structure conservation index 0.56
SVM decision value 2.35
SVM RNA-class probability 0.992808
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14837610 98 + 20766785
GUUGCUGUUUAUUUAUAGCAAAGGUUUAUUUAUGGCUGUGCUGCAGAAAGUGCAGUUGCCGA------UGCAGACGCAGCUGCAGA---------------UGCUGAUGCAGCAAAUGC
.(((((((......)))))))............((((((((((((....(.((....)))..------))))).)))))))(((..---------------(((((...)))))..))) ( -35.70)
>DroSec_CAF1 10028 104 + 1
GUUGCUGUUUAUUUAUAGCAAAGGUUUAUUUAUGGCUGUGCUGCAGAAAGUGCAGUUGCAGAUGCAGAUGCAGACGCAGCUGCAGA---------------UGCUGAUGCAGCAAAUGC
.(((((((......))))))).............((..(((((((...(((((((((((...(((....)))...))))))))...---------------.)))..)))))))...)) ( -39.50)
>DroSim_CAF1 10157 104 + 1
GUUGCUGUUUAUUUAUAGCAAAGGUUUAUUUAUGGCUGUGCUGCAGAAAGUGCAGUUGCAGAUGCAGAUGCAGACGCAGCUGCAGA---------------UGCUGAUGCAGCAAAUGC
.(((((((......))))))).............((..(((((((...(((((((((((...(((....)))...))))))))...---------------.)))..)))))))...)) ( -39.50)
>DroEre_CAF1 10091 98 + 1
GUUGCUGUUUAUUUAUAGCAAAGGUUUAUUUAUGGCUGUGCUGCAGAAAGUGCAGUUGCAGAUGCAGAGGCUGAUGCAGCUGCAUC---------------------UGCAGCAAAUGC
.(((((((......))))))).............((..(((((((((...((((((((((...((....))...))))))))))))---------------------)))))))...)) ( -43.20)
>DroYak_CAF1 10326 119 + 1
GUUGCUGUUUAUUUAUAGCAAAGGUUUAUUUAUGGCUGUGCUGCAGCAAGUGCAGUUGCAGAUGCUGAUGCUGAUGCAGCUGUAUCUGUAUCUGUAUCUGCUGUUUCUGCAGCAAAUGC
.(((((((......))))))).............((((((..((((((..(((((.(((((((((...(((....)))...))))))))).)))))..))))))...))))))...... ( -49.70)
>DroAna_CAF1 12883 85 + 1
GU--AUGUUUAUUUAUAGCAGAGGUUUAUUUAUGGC-----------AACUGCAGAUUCUGA------AUCAGAUUCAGAUGCAUC---------------UGUGGAUGCAGCAAAUGC
..--.(((.........((((..(((.......)))-----------..))))....(((((------((...)))))))((((((---------------....)))))))))..... ( -20.50)
>consensus
GUUGCUGUUUAUUUAUAGCAAAGGUUUAUUUAUGGCUGUGCUGCAGAAAGUGCAGUUGCAGAUGCAGAUGCAGACGCAGCUGCAGA_______________UGCUGAUGCAGCAAAUGC
.(((((((......))))))).............((..(((((((.....(((((((((....((....))....))))))))).......................)))))))...)) (-21.43 = -24.16 +   2.72)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,837,610 – 14,837,708
Length 98
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 79.07
Mean single sequence MFE -27.80
Consensus MFE -11.33
Energy contribution -14.22
Covariance contribution 2.89
Combinations/Pair 1.04
Mean z-score -3.89
Structure conservation index 0.41
SVM decision value 1.98
SVM RNA-class probability 0.984667
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14837610 98 - 20766785
GCAUUUGCUGCAUCAGCA---------------UCUGCAGCUGCGUCUGCA------UCGGCAACUGCACUUUCUGCAGCACAGCCAUAAAUAAACCUUUGCUAUAAAUAAACAGCAAC
(((..(((((...)))))---------------..))).((((.(.(((((------...((....))......)))))).)))).............(((((..........))))). ( -26.70)
>DroSec_CAF1 10028 104 - 1
GCAUUUGCUGCAUCAGCA---------------UCUGCAGCUGCGUCUGCAUCUGCAUCUGCAACUGCACUUUCUGCAGCACAGCCAUAAAUAAACCUUUGCUAUAAAUAAACAGCAAC
(((..(((((...)))))---------------..))).((((((..((((..(((....)))..)))).....))))))..................(((((..........))))). ( -28.50)
>DroSim_CAF1 10157 104 - 1
GCAUUUGCUGCAUCAGCA---------------UCUGCAGCUGCGUCUGCAUCUGCAUCUGCAACUGCACUUUCUGCAGCACAGCCAUAAAUAAACCUUUGCUAUAAAUAAACAGCAAC
(((..(((((...)))))---------------..))).((((((..((((..(((....)))..)))).....))))))..................(((((..........))))). ( -28.50)
>DroEre_CAF1 10091 98 - 1
GCAUUUGCUGCA---------------------GAUGCAGCUGCAUCAGCCUCUGCAUCUGCAACUGCACUUUCUGCAGCACAGCCAUAAAUAAACCUUUGCUAUAAAUAAACAGCAAC
((...(((((((---------------------(((((((.((((...((....))...)))).)))))...)))))))))..)).............(((((..........))))). ( -31.30)
>DroYak_CAF1 10326 119 - 1
GCAUUUGCUGCAGAAACAGCAGAUACAGAUACAGAUACAGCUGCAUCAGCAUCAGCAUCUGCAACUGCACUUGCUGCAGCACAGCCAUAAAUAAACCUUUGCUAUAAAUAAACAGCAAC
((...((((((((.....((((...(((((.(.(((...((((...))))))).).)))))...)))).....))))))))..)).............(((((..........))))). ( -32.40)
>DroAna_CAF1 12883 85 - 1
GCAUUUGCUGCAUCCACA---------------GAUGCAUCUGAAUCUGAU------UCAGAAUCUGCAGUU-----------GCCAUAAAUAAACCUCUGCUAUAAAUAAACAU--AC
(((.((((((((((....---------------))))))(((((((...))------)))))....)))).)-----------))..............................--.. ( -19.40)
>consensus
GCAUUUGCUGCAUCAGCA_______________GAUGCAGCUGCAUCUGCAUCUGCAUCUGCAACUGCACUUUCUGCAGCACAGCCAUAAAUAAACCUUUGCUAUAAAUAAACAGCAAC
....((((((.........................(((((.((((...((....))...)))).)))))........((((.((............)).)))).........)))))). (-11.33 = -14.22 +   2.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:33 2006