Locus 4534

Sequence ID	2R_DroMel_CAF1
Location	14,833,563 – 14,833,655
Length	92
Max. P	0.879322

overview

Window 0

Location	14,833,563 – 14,833,655
Length	92
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	77.99
Mean single sequence MFE	-34.23
Consensus MFE	-16.98
Energy contribution	-17.23
Covariance contribution	0.25
Combinations/Pair	1.32
Mean z-score	-2.34
Structure conservation index	0.50
SVM decision value	0.91
SVM RNA-class probability	0.879322
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14833563 92 + 20766785
CAGUCGCUUCACUGCG-UUCACCUGCCAUGUCCUUGGAAACUGUGAAUGCCAACAGGCC-----------AAAGGACAUAUGCAUAGUGUCCUUGGGCGUCGAU
..(((((......(((-(((((...(((......))).....))))))))......(((-----------.((((((((.......)))))))).)))).)))) ( -32.30)
>DroSec_CAF1 6031 92 + 1
CAGUCGCCUCACUGGG-UUCACCUGCCAUGUCCUUGGAAACUGUGAAUGCCAUCAGGCC-----------AAAGGACAUAUGCAAAGUGUCCUUGGGCGUCGAU
..(.(((((....(((-..(((.(((.((((((((((...(((((.....)).))).))-----------.))))))))..)))..))).))).))))).)... ( -33.50)
>DroSim_CAF1 6126 92 + 1
CAGUCGGCUCACUGGG-UUCACCUGCCAUGUCCUUGGAAACUGUGAAUGCCAUCAGGCC-----------AAAGGACAUAUGCAUAGUGUUCUUGGGCGUCGAU
..((((((.(.(..((-..(((.(((.((((((((((...(((((.....)).))).))-----------.))))))))..)))..)))..))..)).)))))) ( -34.90)
>DroEre_CAF1 6043 92 + 1
CAGCCGUUUCACUGGG-UUCACCUGCCAUGUCCUUGGAAACUGUGAGUGCCAACAGGCC-----------AAAGGACAUGUGCAUGGUGUCCUUGGGCGUCGAU
....((.....(..((-..((((((((((((((((((...((((........)))).))-----------.))))))))).))).))))..))..)....)).. ( -39.40)
>DroYak_CAF1 6222 92 + 1
CAGCCGCUUCACUGGG-CUCACCUGCCAUGUCCUUGGAAACUGUGAGUGCCAACGGGGC-----------AAAGGACAUGUGCAUGGUGUCCUUGGGCGUCGAU
..(.(((((....(((-..(((((((((((((((((....)......((((.....)))-----------)))))))))).))).)))).))).))))).)... ( -39.10)
>DroAna_CAF1 9063 90 + 1
CAAAUUUUACCUUCCGUUGCACCUGG-AUGCC-CCGGCAACAGUGAAUGCUAAAAGACCAUGUGGGCGCCCAAGGACA-------AGUGUCCUUGGC-----AU
..............((((.(((.(((-.(((.-...)))..(((....)))......))).))))))).((((((((.-------...)))))))).-----.. ( -26.20)
>consensus
CAGUCGCUUCACUGGG_UUCACCUGCCAUGUCCUUGGAAACUGUGAAUGCCAACAGGCC___________AAAGGACAUAUGCAUAGUGUCCUUGGGCGUCGAU
..(((......(((...(((((...(((......))).....)))))......)))...............((((((((.......)))))))).)))...... (-16.98 = -17.23 +   0.25)

alignment

secondary structure

dotplot

Window 1

Location	14,833,563 – 14,833,655
Length	92
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	77.99
Mean single sequence MFE	-30.17
Consensus MFE	-21.62
Energy contribution	-21.34
Covariance contribution	-0.29
Combinations/Pair	1.39
Mean z-score	-1.37
Structure conservation index	0.72
SVM decision value	0.64
SVM RNA-class probability	0.809647
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14833563 92 - 20766785
AUCGACGCCCAAGGACACUAUGCAUAUGUCCUUU-----------GGCCUGUUGGCAUUCACAGUUUCCAAGGACAUGGCAGGUGAA-CGCAGUGAAGCGACUG
.(((.(((....(..((((.(((.(((((((((.-----------((.((((........))))...))))))))))))))))))..-)...)))...)))... ( -28.20)
>DroSec_CAF1 6031 92 - 1
AUCGACGCCCAAGGACACUUUGCAUAUGUCCUUU-----------GGCCUGAUGGCAUUCACAGUUUCCAAGGACAUGGCAGGUGAA-CCCAGUGAGGCGACUG
.....((((((.((.(((((.((.(((((((((.-----------((.(((.((.....)))))...))))))))))))))))))..-))...)).)))).... ( -32.20)
>DroSim_CAF1 6126 92 - 1
AUCGACGCCCAAGAACACUAUGCAUAUGUCCUUU-----------GGCCUGAUGGCAUUCACAGUUUCCAAGGACAUGGCAGGUGAA-CCCAGUGAGCCGACUG
.(((..((.((....((((.(((.(((((((((.-----------((.(((.((.....)))))...))))))))))))))))))..-.....)).)))))... ( -25.10)
>DroEre_CAF1 6043 92 - 1
AUCGACGCCCAAGGACACCAUGCACAUGUCCUUU-----------GGCCUGUUGGCACUCACAGUUUCCAAGGACAUGGCAGGUGAA-CCCAGUGAAACGGCUG
......(((...((.((((.(((.(((((((((.-----------((.((((........))))...))))))))))))))))))..-.)).(.....)))).. ( -32.30)
>DroYak_CAF1 6222 92 - 1
AUCGACGCCCAAGGACACCAUGCACAUGUCCUUU-----------GCCCCGUUGGCACUCACAGUUUCCAAGGACAUGGCAGGUGAG-CCCAGUGAAGCGGCUG
......(((......((((.(((.((((((((((-----------(((.....))))............)))))))))))))))).(-(........))))).. ( -32.00)
>DroAna_CAF1 9063 90 - 1
AU-----GCCAAGGACACU-------UGUCCUUGGGCGCCCACAUGGUCUUUUAGCAUUCACUGUUGCCGG-GGCAU-CCAGGUGCAACGGAAGGUAAAAUUUG
..-----.((((((((...-------.))))))))(((((...(((.(((..(((((.....)))))..))-).)))-...)))))..(....).......... ( -31.20)
>consensus
AUCGACGCCCAAGGACACUAUGCAUAUGUCCUUU___________GGCCUGUUGGCAUUCACAGUUUCCAAGGACAUGGCAGGUGAA_CCCAGUGAAGCGACUG
...............((((.(((.(((((((((.............(((....))).............)))))))))))))))).....((((......)))) (-21.62 = -21.34 +  -0.29)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:29 2006