Locus 2380

Sequence ID	2R_DroMel_CAF1
Location	8,615,094 – 8,615,327
Length	233
Max. P	0.930058

overview

Window 8

Location	8,615,094 – 8,615,207
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.80
Mean single sequence MFE	-33.26
Consensus MFE	-23.09
Energy contribution	-23.73
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-2.16
Structure conservation index	0.69
SVM decision value	0.71
SVM RNA-class probability	0.828550
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8615094 113 + 20766785
---GGCAGGCCAAG-GGGUGAGAUGCCAAAAAGCGACUGUGAAAUAUUCGCAGCUGACAGUUUUGAAAAAUGAAAGCUGAGUGGGCGGUGCACUGGGU---UGGUGGGCGGAGGGCGGAG
---.((..(((((.-.((((...((((......((.((((((.....)))))).)).(((((((........)))))))....))))...))))...)---))))..))........... ( -33.50)
>DroSec_CAF1 17434 106 + 1
---GGCAGGCCAAG-GGGUGAGAUGCCAAAAAGCGACUGUGAAAUAUUCGCAGCUGACAGUUUUGAAAAAUGAAAGCUGUGUGGGCGGUGCACUGCGU---UG-------GAGGGCGGAG
---.((...(((((-.((((...((((......((.((((((.....)))))).))((((((((........))))))))...))))...)))).).)---))-------)...)).... ( -35.80)
>DroSim_CAF1 14033 106 + 1
---GGCAGGCCAAG-GGGUGAGAUGCCAAAAAGCGACUGUGAAAUAUUCGCAGCUGACAGUUUUGAAAAAUGAAAGCUGUGUGGGCGGUGCACUGCGU---UG-------GAGGGCGGAG
---.((...(((((-.((((...((((......((.((((((.....)))))).))((((((((........))))))))...))))...)))).).)---))-------)...)).... ( -35.80)
>DroEre_CAF1 15263 100 + 1
---GGCGGGCCAGG-GGCUGAGAUGCCAAAAAGCGACUGUGAAAUAUUCGCAGCUGACAGUUUUGAAAAAUGAAAGCUGAGAGGGCGGUG----------------GGCGGUGGGUGGUG
---.((.(.(((..-(.(((...((((......((.((((((.....)))))).)).(((((((........)))))))....)))).))----------------).)..))).).)). ( -29.20)
>DroYak_CAF1 10831 120 + 1
AAUGGAAGGCCAGGGGGGUGAGAUGCCAAAAAGCGACUGUGAAAUAUUCGCAGCUGACAGUUUUGAAAAAUGAAAGCUGAGAGGGCGGUGCACUUGGAGCACGGAGGACGGAGGGCGGUA
........(((....(((((...((((......((.((((((.....)))))).)).(((((((........)))))))....))))...)))))...((.((.....))....))))). ( -32.00)
>consensus
___GGCAGGCCAAG_GGGUGAGAUGCCAAAAAGCGACUGUGAAAUAUUCGCAGCUGACAGUUUUGAAAAAUGAAAGCUGAGUGGGCGGUGCACUGCGU___UG___G_CGGAGGGCGGAG
........(((.....((((...((((......((.((((((.....)))))).)).(((((((........)))))))....))))...))))...................))).... (-23.09 = -23.73 +   0.64)

alignment

secondary structure

dotplot

Window 9

Location	8,615,207 – 8,615,327
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.83
Mean single sequence MFE	-41.52
Consensus MFE	-37.70
Energy contribution	-38.34
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.55
Structure conservation index	0.91
SVM decision value	1.20
SVM RNA-class probability	0.930058
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8615207 120 + 20766785
GGCGUGGCACAAGCCAUAAAGAUCCAGUGGCAGCUUCAGCGGAAGCGGAAGCGUUCGGCUCGUGCGAAUAUUGCAAAUGUGGCGGAAAAUAUGGCGUCAGUCAAAAGUCAGCGCAGCGCG
(((.((((....((((((....(((.((.((((((((.((....)).)))))(((((.(....))))))........))).)))))...))))))....))))...))).(((...))). ( -43.20)
>DroSec_CAF1 17540 120 + 1
GGCGUGGCACAAGCCAUAAAGAUCCAGUGGCAGUUUCAGCGGAAGCGGAAGCGUUCGGCUCGUGCGAAUAUUGCAAAUAUGGCGGAAAAUAUGGCGUCAGUCAAAAGUCAGCGCAGCGCG
.((((.((.(..((((((..((.((...(((.(((((.((....)).)))))))).)).)).(((((...)))))..)))))).((.....((((....))))....)).).)).)))). ( -38.90)
>DroSim_CAF1 14139 120 + 1
GGCGUGGCACAAGCCAUAAAGAUCCAGUGGCAGUUUCAGCGGAAGCGGAAGCGUUCGGCUCGUGCGAAUAUUGCAAAUGUGGCGGAAAAUAUGGCGUCAGUCAAAAGUCAGCGCAGCGCG
(((.((((....((((((....(((.((.((((((((.((....)).)))))(((((.(....))))))........))).)))))...))))))....))))...))).(((...))). ( -40.80)
>DroEre_CAF1 15363 114 + 1
GGCGUGGCGCAAGCCAUAAAGAUCCAGUGGCAGUUUCAGCGG------AAGCGUUCGGCUCGUGCGAAUAUUGCAAAUGUGGCGGAAAAUAUGGCGUCAGUCAAAAGUCAGCGCAGCGCG
.((((.((((..((((((....(((.((.(((.((.((((..------..))(((((.(....))))))..)).)).))).)))))...))))))(.(........).).)))).)))). ( -39.40)
>DroYak_CAF1 10951 120 + 1
GGCGUGGCGCAAGCCAUAAAGAUCCAGUGGCAGUUUCAGCGGAAGCGGAAGCGUUCGGCUCGUGCGAAUAUUGCAAAUGUGGCGGAAAAUAUGGCGUCAGUCAAAAGUCAGCGCAGCGCG
.((((.((((..((((((....(((.((.((((((((.((....)).)))))(((((.(....))))))........))).)))))...))))))(.(........).).)))).)))). ( -45.30)
>consensus
GGCGUGGCACAAGCCAUAAAGAUCCAGUGGCAGUUUCAGCGGAAGCGGAAGCGUUCGGCUCGUGCGAAUAUUGCAAAUGUGGCGGAAAAUAUGGCGUCAGUCAAAAGUCAGCGCAGCGCG
(((.((((....((((((....(((.((.((((((((.((....)).)))))(((((.(....))))))........))).)))))...))))))....))))...))).(((...))). (-37.70 = -38.34 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:38 2006