Locus 3214

Sequence ID	3R_DroMel_CAF1
Location	8,574,138 – 8,574,233
Length	95
Max. P	0.819442

overview

Window 2

Location	8,574,138 – 8,574,233
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	97.64
Mean single sequence MFE	-14.40
Consensus MFE	-12.44
Energy contribution	-12.44
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.86
SVM decision value	0.68
SVM RNA-class probability	0.819442
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8574138 95 + 27905053
GCAAAAAUGAAAAUUCAACGAAAACAAAGCAAUCAACUAGGGUAAAUAAACCAAAAAUGGCUAUGUUGUAUACCCGAGUAUAGCCAGUAAAGCAC
............................((..........(((......))).....(((((((((((......))).)))))))).....)).. ( -15.70)
>DroSec_CAF1 1812 92 + 1
GCAAAAAUGAAAAUUCAACGAAAACAAAGCAAUCAACUAGGGUAAAUAAACCAAAAAUGGCUAUGUUGUAUACCCGAGU---GCCAGUAAAGCAC
((.....(((....)))..................(((.(((((.((((.(((....))).....)))).))))).)))---.........)).. ( -14.10)
>DroSim_CAF1 13570 92 + 1
GCAAAAAUGAAAAUUCAACGAAAACAAAGCAAUCAACUAGGGUAAAUAAACCAAAAAUGGCUAUGUUGUAUACCCGAGU---GCCAGUAAAGCAC
((.....(((....)))..................(((.(((((.((((.(((....))).....)))).))))).)))---.........)).. ( -14.10)
>DroEre_CAF1 13113 92 + 1
UCAAAAAUGAAAAUUCAACGAAAACAAAGCAAUCAACUAGGGUAAAUAAACCAAAAAUGGCUAUGUUGUAUACCCGAGU---GCUAGUAAAGCAC
.......................................(((((.((((.(((....))).....)))).)))))..((---(((.....))))) ( -15.00)
>DroYak_CAF1 3605 92 + 1
UCAAAAAUGAAAAUUCAACGAAAACAAAGCAAUCAACUAGGGUAAAUAAACCAAAAAUGGCUAUGUUGUAUACCCGAGU---GCCAGUAAAGCAC
.......................................(((((.((((.(((....))).....)))).)))))..((---((.......)))) ( -13.10)
>consensus
GCAAAAAUGAAAAUUCAACGAAAACAAAGCAAUCAACUAGGGUAAAUAAACCAAAAAUGGCUAUGUUGUAUACCCGAGU___GCCAGUAAAGCAC
............................((.....(((.(((((.((((.(((....))).....)))).))))).)))...))........... (-12.44 = -12.44 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	8,574,138 – 8,574,233
Length	95
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	97.64
Mean single sequence MFE	-17.34
Consensus MFE	-15.10
Energy contribution	-14.94
Covariance contribution	-0.16
Combinations/Pair	1.06
Mean z-score	-1.34
Structure conservation index	0.87
SVM decision value	-0.04
SVM RNA-class probability	0.512340
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8574138 95 - 27905053
GUGCUUUACUGGCUAUACUCGGGUAUACAACAUAGCCAUUUUUGGUUUAUUUACCCUAGUUGAUUGCUUUGUUUUCGUUGAAUUUUCAUUUUUGC
.......((.(((...(((.(((((........(((((....)))))....))))).))).....)))..))....................... ( -15.50)
>DroSec_CAF1 1812 92 - 1
GUGCUUUACUGGC---ACUCGGGUAUACAACAUAGCCAUUUUUGGUUUAUUUACCCUAGUUGAUUGCUUUGUUUUCGUUGAAUUUUCAUUUUUGC
(((((.....)))---))..(((((........(((((....)))))....)))))..(..((((.(..((....))..)))))..)........ ( -17.80)
>DroSim_CAF1 13570 92 - 1
GUGCUUUACUGGC---ACUCGGGUAUACAACAUAGCCAUUUUUGGUUUAUUUACCCUAGUUGAUUGCUUUGUUUUCGUUGAAUUUUCAUUUUUGC
(((((.....)))---))..(((((........(((((....)))))....)))))..(..((((.(..((....))..)))))..)........ ( -17.80)
>DroEre_CAF1 13113 92 - 1
GUGCUUUACUAGC---ACUCGGGUAUACAACAUAGCCAUUUUUGGUUUAUUUACCCUAGUUGAUUGCUUUGUUUUCGUUGAAUUUUCAUUUUUGA
(((((.....)))---))..(((((........(((((....)))))....)))))..(..((((.(..((....))..)))))..)........ ( -17.80)
>DroYak_CAF1 3605 92 - 1
GUGCUUUACUGGC---ACUCGGGUAUACAACAUAGCCAUUUUUGGUUUAUUUACCCUAGUUGAUUGCUUUGUUUUCGUUGAAUUUUCAUUUUUGA
(((((.....)))---))..(((((........(((((....)))))....)))))..(..((((.(..((....))..)))))..)........ ( -17.80)
>consensus
GUGCUUUACUGGC___ACUCGGGUAUACAACAUAGCCAUUUUUGGUUUAUUUACCCUAGUUGAUUGCUUUGUUUUCGUUGAAUUUUCAUUUUUGC
.......((.(((...(((.(((((........(((((....)))))....))))).))).....)))..))....................... (-15.10 = -14.94 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:51 2006