Locus 2204

Sequence ID 3L_DroMel_CAF1
Location 6,084,616 – 6,084,753
Length 137
Max. P 0.942791
window3411 window3412

overview

Window 1

Location 6,084,616 – 6,084,721
Length 105
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 78.94
Mean single sequence MFE -15.78
Consensus MFE -12.86
Energy contribution -12.72
Covariance contribution -0.14
Combinations/Pair 1.07
Mean z-score -1.33
Structure conservation index 0.82
SVM decision value 0.63
SVM RNA-class probability 0.805825
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6084616 105 - 23771897
CAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUCGU----UCGCCUACAAC-----GG--CACCACCCCUCCCUCCACC-UAACA-
...(((.(((.(((.(((((............................))))).)))......(((((----(.......)))-----))--)........))).)))...-.....- ( -18.59)
>DroVir_CAF1 53215 96 - 1
CAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUCGU----UCGCCCACAUU-----GC--GACUACACCCAC---A----UC----
....((((((.(((.(((((............................))))).)))...))))))((----((((.......-----))--))..))......---.----..---- ( -16.59)
>DroPse_CAF1 39063 102 - 1
CAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUCGU----UCGCCUACAAC-----AC--CCCCAGCUCCUCCCCC----GUGCA-
.((.((((((.(((.(((((............................))))).)))...)))))).)----)..........-----..--.....((.........----..)).- ( -13.89)
>DroGri_CAF1 43664 107 - 1
CAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUCGUUCGUUCGCCUACAUAUUUUAGCCAAGCUACACCCAC---A----AA----
.((.((((((.(((.(((((............................))))).)))...)))))).)).................((((...)))).......---.----..---- ( -14.49)
>DroWil_CAF1 54577 105 - 1
CAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUUGU-----CGUCGUCGUC-----GU--UGCAACUACUCCCACA-CAUACACAU
.(((((.(((((...)))))...)))))..(((((...........)))))............(((((-----...((....)-----).--.)))))..........-......... ( -14.50)
>DroMoj_CAF1 42793 99 - 1
CAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUCGC----UCGCCCACAUU-----GC--GACUACACCCAC---A-AAUCC----
.(((((.(((((...)))))...)))))..(((((...........)))))............(((((----...........-----))--))).........---.-.....---- ( -16.60)
>consensus
CAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUCGU____UCGCCUACAUC_____GC__CACUACACCCAC___A____AC____
....((((((.(((.(((((............................))))).)))...)))))).................................................... (-12.86 = -12.72 +  -0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 6,084,645 – 6,084,753
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.08
Mean single sequence MFE -30.02
Consensus MFE -25.94
Energy contribution -26.00
Covariance contribution 0.06
Combinations/Pair 1.10
Mean z-score -2.15
Structure conservation index 0.86
SVM decision value 1.33
SVM RNA-class probability 0.942791
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6084645 108 - 23771897
---GCAUCG---CCUUUUUAGUGGGUGAC--ACGAAGCAACAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUCGU----UCGCCUAC
---......---........(((((((((--(((((((...(((((.(((((...)))))...)))))..(((((...........))))).......))))))).).----)))))))) ( -29.50)
>DroVir_CAF1 53235 108 - 1
---GCGUUG---CCUUUUUAGUGGGUGAC--ACGAAGCAACAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUCGU----UCGCCCAC
---......---........(((((((((--(((((((...(((((.(((((...)))))...)))))..(((((...........))))).......))))))).).----)))))))) ( -31.80)
>DroGri_CAF1 43691 114 - 1
---GCGCUG---CCUUUUUAGUGGGUGACACACGAAGCAACAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUCGUUCGUUCGCCUAC
---......---........((((((((.(((((((((...(((((.(((((...)))))...)))))..(((((...........))))).......))))))).))....)))))))) ( -28.60)
>DroSim_CAF1 34327 108 - 1
---GCAUCG---CCUUUUUAGUGGGUGAC--ACGAAGCAACAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUCGU----UCGCUUAC
---......---........(((((((((--(((((((...(((((.(((((...)))))...)))))..(((((...........))))).......))))))).).----)))))))) ( -26.70)
>DroWil_CAF1 54607 113 - 1
AAGGCAGCGAUUCGUUUUUAGUGGGUGAC--ACGAAGCAACAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUUGU-----CGUCGUC
..((((((((..(((.(((.((((....)--..((((.((.(((((.(((((...)))))...))))).)).))))))).))).))..((......)))..)))))))-----)...... ( -31.70)
>DroMoj_CAF1 42816 108 - 1
---GCGUUG---CCUUUUUAGUGGGUGAC--ACGAAGCAACAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUCGC----UCGCCCAC
---......---........(((((((((--(((((((...(((((.(((((...)))))...)))))..(((((...........))))).......))))))).).----)))))))) ( -31.80)
>consensus
___GCAUCG___CCUUUUUAGUGGGUGAC__ACGAAGCAACAAGGACGGAUGUAUUAUCCACUUCCUUUUUCCUUCCACCAAACACAAGGAUAUUACCGUUUCGUCGU____UCGCCUAC
....................((((((((...(((((((...(((((.(((((...)))))...)))))..(((((...........))))).......))))))).......)))))))) (-25.94 = -26.00 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:43 2006