Locus 4712

Sequence ID X_DroMel_CAF1
Location 12,250,260 – 12,250,359
Length 99
Max. P 0.834141
window7733 window7734

overview

Window 3

Location 12,250,260 – 12,250,359
Length 99
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 80.67
Mean single sequence MFE -35.27
Consensus MFE -19.65
Energy contribution -20.43
Covariance contribution 0.78
Combinations/Pair 1.12
Mean z-score -2.79
Structure conservation index 0.56
SVM decision value 0.73
SVM RNA-class probability 0.834141
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12250260 99 + 22224390
CCAGGCCCCAAGAAAAAAUGGGGAAUCUUUUCUCUGUUUUUUUUU----UGCACUUCUU----------UUUUUUUUGGUGGGGUGAUGGGGUAGGUGGGGCGCCGCACUUGC
(((.(((((((((((((((((((((....))))))))))))))))----...(((....----------........))))))))..))).(((((((.(....).))))))) ( -35.10)
>DroSec_CAF1 18292 99 + 1
CCAG-CCCCAAGAAAAAAUGGGGAAUCUUUUCUCUGCUUCUUUUU----U-UACUUCUU--------CUUUUUUUUUGGUGGGGUGAAGGGGUAGGUGGGGCGCUGCACUUGC
...(-(((((((((((.((.....)).))))))((((((((....----(-((((((..--------((........)).))))))))))))))).))))))........... ( -28.80)
>DroEre_CAF1 13520 110 + 1
CCAG-CCCCAAGAAAAAAUGGGGAAUCUUUCCUCUGCUCUUUUUUCACUUCCACUUCCACUUCCCCCCUUUUUUUUUGGUGGGU--GAGGGGUAGGUGGUGGGCUGCACUUGC
.(((-(((...(((((((.(((((.....))))).....)))))))....((((((((.(((((((((.........)).))).--)))))).)))))).))))))....... ( -41.90)
>consensus
CCAG_CCCCAAGAAAAAAUGGGGAAUCUUUUCUCUGCUUUUUUUU____U_CACUUCUU________CUUUUUUUUUGGUGGGGUGAAGGGGUAGGUGGGGCGCUGCACUUGC
((...(((((........)))))...((((.(((..((.......................................))..))).))))))(((((((.(....).))))))) (-19.65 = -20.43 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,250,260 – 12,250,359
Length 99
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 80.67
Mean single sequence MFE -26.12
Consensus MFE -15.20
Energy contribution -14.76
Covariance contribution -0.44
Combinations/Pair 1.10
Mean z-score -2.04
Structure conservation index 0.58
SVM decision value -0.05
SVM RNA-class probability 0.506460
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12250260 99 - 22224390
GCAAGUGCGGCGCCCCACCUACCCCAUCACCCCACCAAAAAAAA----------AAGAAGUGCA----AAAAAAAAACAGAGAAAAGAUUCCCCAUUUUUUCUUGGGGCCUGG
.......(((.(((((................(((.........----------.....)))..----...........((((((((((.....)))))))))))))))))). ( -20.54)
>DroSec_CAF1 18292 99 - 1
GCAAGUGCAGCGCCCCACCUACCCCUUCACCCCACCAAAAAAAAAG--------AAGAAGUA-A----AAAAAGAAGCAGAGAAAAGAUUCCCCAUUUUUUCUUGGGG-CUGG
((....))...(((((...(((..((((.................)--------)))..)))-.----...........((((((((((.....))))))))))))))-)... ( -22.43)
>DroEre_CAF1 13520 110 - 1
GCAAGUGCAGCCCACCACCUACCCCUC--ACCCACCAAAAAAAAAGGGGGGAAGUGGAAGUGGAAGUGAAAAAAGAGCAGAGGAAAGAUUCCCCAUUUUUUCUUGGGG-CUGG
.......((((((.((((...((.((.--.(((.((.........)))))..)).))..))))................((((((((((.....)))))))))).)))-))). ( -35.40)
>consensus
GCAAGUGCAGCGCCCCACCUACCCCUUCACCCCACCAAAAAAAAAG________AAGAAGUG_A____AAAAAAAAGCAGAGAAAAGAUUCCCCAUUUUUUCUUGGGG_CUGG
((....)).........((..((((..................................((...............)).((((((((((.....))))))))))))))...)) (-15.20 = -14.76 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:38 2006