Locus 4178

Sequence ID X_DroMel_CAF1
Location 10,982,869 – 10,982,985
Length 116
Max. P 0.808290
window6859 window6860

overview

Window 9

Location 10,982,869 – 10,982,985
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 71.33
Mean single sequence MFE -22.99
Consensus MFE -5.34
Energy contribution -5.62
Covariance contribution 0.28
Combinations/Pair 1.14
Mean z-score -1.85
Structure conservation index 0.23
SVM decision value 0.64
SVM RNA-class probability 0.808290
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10982869 116 + 22224390
CUU----GUAGUUUUAUGGUUGUUAAUUAUCUUUUUUUCAAAAACAUUUAGCCAUUUACCAAUUUGGACAAAGAGCUUUCCACAUGUAUACAAAUUGCUUGUACAGUGGAAACACCCACA
..(----(((((((((((((((..........................)))))))...((.....))....))))))((((((.((((((.........)))))))))))))))...... ( -19.77)
>DroSec_CAF1 6734 111 + 1
AUU----GU-GCUUAAUGGCUGUAAAUUAUCUCUUUUUCAAAAACAUUUAGCCAUUUAUCAAU--GGACAUAGAGCUGUCC--AUAUAUAAAAAUUGCUUGUACAGUGGAUACAUCCACA
..(----((-((..((((((((..........................)))))))).....((--(((((......)))))--))...............)))))(((((....))))). ( -27.37)
>DroSim_CAF1 6776 115 + 1
AUU----GU-GCUUAAUGGCUUUAAAUUAUCUCUUUUUCAAAAACAUUUAGCCAUUUAUCAAUUUGGACAUAGAGCUGUCUAAAUAUAUAAAAAUUCCUUGUACAGUGGAUACAUCCACA
..(----((-((..(((((((............................))))))).....(((((((((......)))))))))...............)))))(((((....))))). ( -25.49)
>DroEre_CAF1 7426 112 + 1
AUUUCCUUGAGAAACACGCAUUUAAGUUAUU-AUUUUUCGUAGGCAGUUAGCCAUUUAUCAAUUUGGACAAAGUGUUU---GC---UGUGUU-GUUGUUUGUUAAGUGGAAACACCCGCA
.(((((((((.(((((((((..(((....))-)......(((((((.((.((((..........))).).)).)))))---))---))))).-...)))).))))).))))......... ( -21.70)
>DroYak_CAF1 7066 118 + 1
AUUUCAUUCGGUUUUACACUUUUAAAUUUUG-GUUUUUUGGAAUCAUUUAACCAUUUAUCCAUUUGGACAAAGUUCUAUAUACAUAUGUGCAAAUUCUUUGU-CAGUGGAAACACCCUCA
.........(((.................((-(((...((....))...)))))....(((((...(((((((.......(((....)))......))))))-).)))))...))).... ( -20.62)
>consensus
AUU____GU_GCUUAAUGGCUUUAAAUUAUCUCUUUUUCAAAAACAUUUAGCCAUUUAUCAAUUUGGACAAAGAGCUGUCCACAUAUAUAAAAAUUGCUUGUACAGUGGAAACACCCACA
...................................................(((..........)))......................................((((......)))). ( -5.34 =  -5.62 +   0.28)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,982,869 – 10,982,985
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 71.33
Mean single sequence MFE -23.40
Consensus MFE -7.48
Energy contribution -8.56
Covariance contribution 1.08
Combinations/Pair 1.20
Mean z-score -1.82
Structure conservation index 0.32
SVM decision value 0.44
SVM RNA-class probability 0.738475
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10982869 116 - 22224390
UGUGGGUGUUUCCACUGUACAAGCAAUUUGUAUACAUGUGGAAAGCUCUUUGUCCAAAUUGGUAAAUGGCUAAAUGUUUUUGAAAAAAAGAUAAUUAACAACCAUAAAACUAC----AAG
(((((.(((((((((((((((((...))))))))...))))))((((.((((.((.....)))))).))))...(((((((.....)))))))....))).))))).......----... ( -27.10)
>DroSec_CAF1 6734 111 - 1
UGUGGAUGUAUCCACUGUACAAGCAAUUUUUAUAUAU--GGACAGCUCUAUGUCC--AUUGAUAAAUGGCUAAAUGUUUUUGAAAAAGAGAUAAUUUACAGCCAUUAAGC-AC----AAU
.(((((....))))).......((......(((..((--(((((......)))))--))..)))(((((((((((.(((((....)))))...))))..)))))))..))-..----... ( -28.90)
>DroSim_CAF1 6776 115 - 1
UGUGGAUGUAUCCACUGUACAAGGAAUUUUUAUAUAUUUAGACAGCUCUAUGUCCAAAUUGAUAAAUGGCUAAAUGUUUUUGAAAAAGAGAUAAUUUAAAGCCAUUAAGC-AC----AAU
.(((((....)))))(((.(..........(((..((((.((((......)))).))))..)))(((((((((((.(((((....)))))...))))..)))))))..).-))----).. ( -22.50)
>DroEre_CAF1 7426 112 - 1
UGCGGGUGUUUCCACUUAACAAACAAC-AACACA---GC---AAACACUUUGUCCAAAUUGAUAAAUGGCUAACUGCCUACGAAAAAU-AAUAACUUAAAUGCGUGUUUCUCAAGGAAAU
...(..((((.......))))..)...-(((((.---((---(.....((((((......)))))).(((.....)))..........-...........))))))))............ ( -17.10)
>DroYak_CAF1 7066 118 - 1
UGAGGGUGUUUCCACUG-ACAAAGAAUUUGCACAUAUGUAUAUAGAACUUUGUCCAAAUGGAUAAAUGGUUAAAUGAUUCCAAAAAAC-CAAAAUUUAAAAGUGUAAAACCGAAUGAAAU
...((.((((......)-))).....(((((((...............(((((((....)))))))(((((...((....))...)))-))..........))))))).))......... ( -21.40)
>consensus
UGUGGGUGUUUCCACUGUACAAGCAAUUUGUAUAUAUGUAGAAAGCUCUUUGUCCAAAUUGAUAAAUGGCUAAAUGUUUUUGAAAAAGAGAUAAUUUAAAACCAUAAAAC_AC____AAU
.(((((....)))))............................((((.((((((......)))))).))))................................................. ( -7.48 =  -8.56 +   1.08)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:19 2006