Locus 5006

Sequence ID X_DroMel_CAF1
Location 13,090,496 – 13,090,602
Length 106
Max. P 0.999577
window8153 window8154

overview

Window 3

Location 13,090,496 – 13,090,602
Length 106
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 72.57
Mean single sequence MFE -29.20
Consensus MFE -20.14
Energy contribution -20.57
Covariance contribution 0.44
Combinations/Pair 1.15
Mean z-score -2.53
Structure conservation index 0.69
SVM decision value 3.74
SVM RNA-class probability 0.999577
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13090496 106 + 22224390
-CGCAUACUUUGGACGCAUCUUU-CAGAU-----ACUUAUCUAUCCACUUAACUAUCCACUUACCAGUUGGUCUUGUUGGGCCCAUUGGCCUCGCCAAUAGUGUGGGUGGCCA
-.........(((..........-.((((-----....))))..............(((((((((.((((((......(((((....))))).)))))).).))))))))))) ( -26.50)
>DroSec_CAF1 41010 82 + 1
-CGC-------------AUCUUU-UAGAU-----AC-UAUCUAUCCAC----------ACUUACCAGUUGGUCUUGUUGGGCCCAUUGGCCUCGCCAAUAGUGUGGGUGGCUA
-...-------------(((...-..)))-----..-...((((((((----------(((.....((((((......(((((....))))).)))))))))))))))))... ( -27.00)
>DroSim_CAF1 34275 82 + 1
-CGC-------------AUCUUU-UAGAU-----AC-UAUCUAUCCAC----------ACUUACCAGUUGGUCUUGUUGGGCCCAUUGGCCUCGCCAAUAGUGUGGGUGGCUA
-...-------------(((...-..)))-----..-...((((((((----------(((.....((((((......(((((....))))).)))))))))))))))))... ( -27.00)
>DroYak_CAF1 47757 110 + 1
AUGUAUAUUUUGGAUCCUUCUUCGAUGAUCAAUGAUAUAUGUAUGAAUG---UUAGCCACUUACCAAUUGGUCUUGUUGGGCCCAUUGGCCUCACCAAUCGUGUGAGUGGCCA
(((((((((...((((.((....)).))))...))))))))).......---...((((((((((.((((((......(((((....))))).)))))).).))))))))).. ( -36.30)
>consensus
_CGC_____________AUCUUU_UAGAU_____AC_UAUCUAUCCAC__________ACUUACCAGUUGGUCUUGUUGGGCCCAUUGGCCUCGCCAAUAGUGUGGGUGGCCA
........................................................(((((((((.((((((......(((((....))))).)))))).).))))))))... (-20.14 = -20.57 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,090,496 – 13,090,602
Length 106
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 72.57
Mean single sequence MFE -29.42
Consensus MFE -13.80
Energy contribution -14.18
Covariance contribution 0.37
Combinations/Pair 1.07
Mean z-score -2.84
Structure conservation index 0.47
SVM decision value 2.27
SVM RNA-class probability 0.991553
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13090496 106 - 22224390
UGGCCACCCACACUAUUGGCGAGGCCAAUGGGCCCAACAAGACCAACUGGUAAGUGGAUAGUUAAGUGGAUAGAUAAGU-----AUCUG-AAAGAUGCGUCCAAAGUAUGCG-
(((.(..((((((((((.(((.((((....)))))......(((....)))..)).))))))...))))........((-----(((..-...)))))).))).........- ( -30.80)
>DroSec_CAF1 41010 82 - 1
UAGCCACCCACACUAUUGGCGAGGCCAAUGGGCCCAACAAGACCAACUGGUAAGU----------GUGGAUAGAUA-GU-----AUCUA-AAAGAU-------------GCG-
.......(((((((.(((..(.((((....)))))..))).(((....))).)))----------)))).......-((-----(((..-...)))-------------)).- ( -27.40)
>DroSim_CAF1 34275 82 - 1
UAGCCACCCACACUAUUGGCGAGGCCAAUGGGCCCAACAAGACCAACUGGUAAGU----------GUGGAUAGAUA-GU-----AUCUA-AAAGAU-------------GCG-
.......(((((((.(((..(.((((....)))))..))).(((....))).)))----------)))).......-((-----(((..-...)))-------------)).- ( -27.40)
>DroYak_CAF1 47757 110 - 1
UGGCCACUCACACGAUUGGUGAGGCCAAUGGGCCCAACAAGACCAAUUGGUAAGUGGCUAA---CAUUCAUACAUAUAUCAUUGAUCAUCGAAGAAGGAUCCAAAAUAUACAU
((((((((.((.(((((((((.((((....)))))......)))))))))).)))))))).---..........(((((....((((..........))))....)))))... ( -32.10)
>consensus
UAGCCACCCACACUAUUGGCGAGGCCAAUGGGCCCAACAAGACCAACUGGUAAGU__________GUGGAUAGAUA_GU_____AUCUA_AAAGAU_____________GCG_
............(((((.(((.((((....)))))......(((....)))..............)).)))))........................................ (-13.80 = -14.18 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:59 2006