Locus 2412

Sequence ID	3R_DroMel_CAF1
Location	6,757,659 – 6,757,858
Length	199
Max. P	0.997512

overview

Window 1

Location	6,757,659 – 6,757,779
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.00
Mean single sequence MFE	-27.86
Consensus MFE	-25.02
Energy contribution	-25.42
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.33
Structure conservation index	0.90
SVM decision value	0.12
SVM RNA-class probability	0.593740
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6757659 120 + 27905053
GGCUUUUGUAAUAAUUCAAUGAGCGCUGCUUCAUUUGUCACAUUGCUCAUACGCCAUGUGCAACGGAAACGGAAACCUCGGCGACCAAGUGAAAGUAUUCAUUAUACUUACAUUACUUCC
.(((((((........))).))))((((.(((..(((.(((((.((......)).))))))))((....)))))....)))).....((((.((((((.....)))))).))))...... ( -28.40)
>DroSec_CAF1 21829 120 + 1
GGCUUUUGUAAUAAUUCAAUGAGCGCUGCUUCAUUUGUCACAUUGCUCAUACGCCAUGUGCAACGGAAUCAUAAACCUCGGCGUCCAAGGGAAAGUAUUCAUUAUACUUACAUUACUUCC
.......(((((..(((..((..(((((......(((.(((((.((......)).)))))))).((.........)).)))))..))..)))((((((.....))))))..))))).... ( -25.70)
>DroSim_CAF1 26202 120 + 1
GGCUUUUGUAAUAAUUCAAUGAGCGCUGCUUCAUUUGUCACAUUGCUCAUACGCCAUGUGCAACGGAAACGGAAACCUCGGCGACCAAGUGAAAGUAUUCAUUAUACUUACAUUACUUCC
.(((((((........))).))))((((.(((..(((.(((((.((......)).))))))))((....)))))....)))).....((((.((((((.....)))))).))))...... ( -28.40)
>DroEre_CAF1 6294 120 + 1
GGCUUUUGUAAUAAUUCAAUGAGCGCUGCUUCAUUUGUCACAUUGCUCAUACGCCAUGUGCAACGGAAACGGAAACCUCGGCGACCAAGUGAAAGUAUUCAUUAUACUUACAUUAUUUCC
.(((((((........))).))))((((.(((..(((.(((((.((......)).))))))))((....)))))....)))).....((((.((((((.....)))))).))))...... ( -28.40)
>DroYak_CAF1 18284 120 + 1
GGCUUUUGUAAUAAUUCAAUGAGCGCUGCUUCAUUUGUCACAUUGCUCAUACGCCAUGUGCAACGGAAACGGAAACCUCGGCGACCAAGUGAAAGUAUUCAUUAUACUUACAUUACUUCC
.(((((((........))).))))((((.(((..(((.(((((.((......)).))))))))((....)))))....)))).....((((.((((((.....)))))).))))...... ( -28.40)
>consensus
GGCUUUUGUAAUAAUUCAAUGAGCGCUGCUUCAUUUGUCACAUUGCUCAUACGCCAUGUGCAACGGAAACGGAAACCUCGGCGACCAAGUGAAAGUAUUCAUUAUACUUACAUUACUUCC
.(((((((........))).))))((((......(((.(((((.((......)).))))))))((....)).......)))).....((((.((((((.....)))))).))))...... (-25.02 = -25.42 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	6,757,739 – 6,757,858
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.05
Mean single sequence MFE	-19.18
Consensus MFE	-15.15
Energy contribution	-15.40
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-3.01
Structure conservation index	0.79
SVM decision value	2.87
SVM RNA-class probability	0.997512
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6757739 119 + 27905053
GCGACCAAGUGAAAGUAUUCAUUAUACUUACAUUACUUCCC-CAGCUUCCUUUACUUCGCCUUCGUCCUUCAACGACCGCUUUCCCUCCCCUUUCUCCCAUUUUCUUGGUCGUCAUUUCG
(((((((((((.((((((.....)))))).)).........-................((..((((......))))..))........................)))))))))....... ( -22.50)
>DroSec_CAF1 21909 119 + 1
GCGUCCAAGGGAAAGUAUUCAUUAUACUUACAUUACUUCCC-CAGCUUCCUUUACUUCUCCUUCGUCGUUCAACAACCGCUCUCCCUCCCCUUCCUCCCAUUUUCUUGGUCGUCAUUUCG
(((.(((((..(((((((.....))))))............-......................((.(((....))).)).....................)..))))).)))....... ( -16.80)
>DroEre_CAF1 6374 101 + 1
GCGACCAAGUGAAAGUAUUCAUUAUACUUACAUUAUUUCCA-CAGCUUCCUUGCC---------------CAAC---CGCUUUCUCUCCCAUUUCUUGCAUUUUCUUGGUCGUCAUUUCG
(((((((((((.((((((.....)))))).)).........-..((......)).---------------....---...........................)))))))))....... ( -18.70)
>DroYak_CAF1 18364 105 + 1
GCGACCAAGUGAAAGUAUUCAUUAUACUUACAUUACUUCCUCCAGCUUCCUUGCC---------------CAACCACCGCUUUCUCUACCAUCUCUCGCAUUUUCUUGGUCGUCAUUUCG
(((((((((((.((((((.....)))))).))............((......)).---------------..................................)))))))))....... ( -18.70)
>consensus
GCGACCAAGUGAAAGUAUUCAUUAUACUUACAUUACUUCCC_CAGCUUCCUUGAC_______________CAAC_ACCGCUUUCCCUCCCAUUUCUCCCAUUUUCUUGGUCGUCAUUUCG
(((((((((..(((((((.....))))))..............(((................................)))....................)..)))))))))....... (-15.15 = -15.40 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:10 2006