Locus 336

Sequence ID 2L_DroMel_CAF1
Location 1,010,667 – 1,010,780
Length 113
Max. P 0.975037
window535 window536

overview

Window 5

Location 1,010,667 – 1,010,780
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.88
Mean single sequence MFE -27.49
Consensus MFE -21.68
Energy contribution -22.24
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.06
Structure conservation index 0.79
SVM decision value 0.95
SVM RNA-class probability 0.887775
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1010667 113 + 22407834
UUAUUUGUAUUUGUAUAUUAUCAUCCGCGGCUACCAAACUCAAUCCUUCUGAAAGAAAACAGUGCGAAAACAGUG-GAUUCAAGUUUGGUCGCCUCUCCGAUAACUUUGUACGC------
............((((((((((....(.(((.((((((((.(((((..(((...................))).)-))))..)))))))).))).)...)))))...)))))..------ ( -26.61)
>DroSec_CAF1 122391 111 + 1
UUAUUUGUAUUUGUAUAUUAUCAUCCGCGGCCACCAAACUGAAUCCUUUUGAAAGAAGACAGUGCGU--UCAUUG-GAUUCAAGUUUGGUUGCCUCUCCGAUAACUUUGUACGC------
............((((((((((....(.(((.((((((((((((((...((((....(......).)--)))..)-))))).)))))))).))).)...)))))...)))))..------ ( -32.00)
>DroSim_CAF1 122953 110 + 1
UUAUUUGUAUUUGUAUAUUAUCAUCCGCGGCCACCAAACUGAAUCCUUUUGAAAGAAAACAGUGCGU--UCAUUG-GAUUCAAGU-UGGUUGCCUCUCCGAUAACUUUGUACGC------
............((((((((((....(.(((.(((((..(((((((...((((.(.........).)--)))..)-))))))..)-)))).))).)...)))))...)))))..------ ( -28.90)
>DroYak_CAF1 129635 118 + 1
UUAUUUGUAUUUGUAUAUUAUCAUCCGCGGUUACCAAACUGAAUCCUUUCGAAAAAAAACUGCUAGA--ACAUUGAGACUCAAGUUUGGUUGCCUCUCUGAUAACUUUGUACGCCAGACU
......((...((((((((((((...(.(((.((((((((......((((((...............--...))))))....)))))))).))).)..))))))...))))))....)). ( -22.47)
>consensus
UUAUUUGUAUUUGUAUAUUAUCAUCCGCGGCCACCAAACUGAAUCCUUUUGAAAGAAAACAGUGCGA__ACAUUG_GAUUCAAGUUUGGUUGCCUCUCCGAUAACUUUGUACGC______
............((((((((((....(.(((.((((((((((((((............................).))))).)))))))).))).)...)))))...)))))........ (-21.68 = -22.24 +   0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,010,667 – 1,010,780
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.88
Mean single sequence MFE -31.31
Consensus MFE -24.43
Energy contribution -24.81
Covariance contribution 0.38
Combinations/Pair 1.07
Mean z-score -2.83
Structure conservation index 0.78
SVM decision value 1.74
SVM RNA-class probability 0.975037
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1010667 113 - 22407834
------GCGUACAAAGUUAUCGGAGAGGCGACCAAACUUGAAUC-CACUGUUUUCGCACUGUUUUCUUUCAGAAGGAUUGAGUUUGGUAGCCGCGGAUGAUAAUAUACAAAUACAAAUAA
------..(((....((((((.(...(((.(((((((((.((((-(..(((....)))(((........)))..)))))))))))))).))).).))))))....)))............ ( -33.60)
>DroSec_CAF1 122391 111 - 1
------GCGUACAAAGUUAUCGGAGAGGCAACCAAACUUGAAUC-CAAUGA--ACGCACUGUCUUCUUUCAAAAGGAUUCAGUUUGGUGGCCGCGGAUGAUAAUAUACAAAUACAAAUAA
------..(((....((((((.(...(((.((((((((.(((((-(..(((--(.............))))...)))))))))))))).))).).))))))....)))............ ( -33.42)
>DroSim_CAF1 122953 110 - 1
------GCGUACAAAGUUAUCGGAGAGGCAACCA-ACUUGAAUC-CAAUGA--ACGCACUGUUUUCUUUCAAAAGGAUUCAGUUUGGUGGCCGCGGAUGAUAAUAUACAAAUACAAAUAA
------..(((....((((((.(...(((.((((-(.(((((((-(..(((--(.............))))...)))))))).))))).))).).))))))....)))............ ( -30.92)
>DroYak_CAF1 129635 118 - 1
AGUCUGGCGUACAAAGUUAUCAGAGAGGCAACCAAACUUGAGUCUCAAUGU--UCUAGCAGUUUUUUUUCGAAAGGAUUCAGUUUGGUAACCGCGGAUGAUAAUAUACAAAUACAAAUAA
........(((....(((((((..(.((..((((((((.(((((....(((--....))).........(....))))))))))))))..)).)...))))))).)))............ ( -27.30)
>consensus
______GCGUACAAAGUUAUCGGAGAGGCAACCAAACUUGAAUC_CAAUGA__ACGCACUGUUUUCUUUCAAAAGGAUUCAGUUUGGUAGCCGCGGAUGAUAAUAUACAAAUACAAAUAA
........(((....((((((.(...(((.((((((((.(((((....((...................))....))))))))))))).))).).))))))....)))............ (-24.43 = -24.81 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:33:21 2006