Locus 197

Sequence ID	3R_DroMel_CAF1
Location	856,891 – 857,003
Length	112
Max. P	0.962945

overview

Window 0

Location	856,891 – 857,003
Length	112
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.19
Mean single sequence MFE	-42.70
Consensus MFE	-30.58
Energy contribution	-32.83
Covariance contribution	2.25
Combinations/Pair	1.00
Mean z-score	-2.18
Structure conservation index	0.72
SVM decision value	0.02
SVM RNA-class probability	0.542699
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 856891 112 + 27905053
AGCACAAUAUAUUUAUAUUGUAUUUAGGUGGCUUGUCAGCCGGUGAUUGAUGUGGCAGCGG-CUGCU-------GGCUGCCGGCUUUGGACUUUCUGCCAUAUUCGGCGCACAAAGCCGG
...(((((((....))))))).....((..(((.(.((((((.((..........)).)))-)))).-------)))..))(((((((.......((((......))))..))))))).. ( -43.30)
>DroSec_CAF1 31701 115 + 1
AGCACAAUAUAUUUAUAUUGUAUUUAGGUGGCUUGUCAGCCGGUGAUUGAUGUGGCAGCGG-CUGCUGGCUGCUGGCUGCCGGCUUUGGACUUUCUGCCAUAUUCGGCGCACAAAG----
.(((((((((....)))))))......(((((..(((((((((((........(.((((((-(.....))))))).)))))))))...))).....))))).......))......---- ( -40.50)
>DroSim_CAF1 30859 119 + 1
AGCACAAUAUAUUUAUAUUGUAUUUAGGUGGCUUGUCAGCCGGUGAUUGAUGUGGCAGUGG-CUGCUGGCUGCUGGCUGCCGGCUUUGGACUUUCUGCCAUAUUCGGCGCACAAAGCCGG
((((((((((....))))))).....((..(((.(.((((((.((..........)).)))-)))).)))..)).))).(((((((((.......((((......))))..))))))))) ( -45.80)
>DroEre_CAF1 31927 120 + 1
AGCACAAUAUAUUUAUAUUGUAUUUAGGUGGCUUGUCAGCCGGUGAUUGAUGUGGCUGCUGCCUGCUGCCUGCUGGCUGCCGACUUUGGAUUUUCUGCCGUAUUCGGCGCACAAAGCCGG
((((((((((....)))))))....(((..((..(.((((.(((.((....)).))))))))..))..))))))(((((((((...(((........)))...)))))......)))).. ( -41.20)
>consensus
AGCACAAUAUAUUUAUAUUGUAUUUAGGUGGCUUGUCAGCCGGUGAUUGAUGUGGCAGCGG_CUGCUGGCUGCUGGCUGCCGGCUUUGGACUUUCUGCCAUAUUCGGCGCACAAAGCCGG
...(((((((....))))))).....((..(((...((((((((....................))))))))..)))..))(((((((.......((((......))))..))))))).. (-30.58 = -32.83 +   2.25)

alignment

secondary structure

dotplot

Window 1

Location	856,891 – 857,003
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.19
Mean single sequence MFE	-36.47
Consensus MFE	-29.90
Energy contribution	-30.84
Covariance contribution	0.94
Combinations/Pair	1.06
Mean z-score	-2.95
Structure conservation index	0.82
SVM decision value	1.55
SVM RNA-class probability	0.962945
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 856891 112 - 27905053
CCGGCUUUGUGCGCCGAAUAUGGCAGAAAGUCCAAAGCCGGCAGCC-------AGCAG-CCGCUGCCACAUCAAUCACCGGCUGACAAGCCACCUAAAUACAAUAUAAAUAUAUUGUGCU
..(((((((..((((......))).....)..)))))))((((((.-------.....-..))))))............((((....)))).......((((((((....)))))))).. ( -38.10)
>DroSec_CAF1 31701 115 - 1
----CUUUGUGCGCCGAAUAUGGCAGAAAGUCCAAAGCCGGCAGCCAGCAGCCAGCAG-CCGCUGCCACAUCAAUCACCGGCUGACAAGCCACCUAAAUACAAUAUAAAUAUAUUGUGCU
----(((((..((((......))).....)..)))))..((((((..((........)-).))))))............((((....)))).......((((((((....)))))))).. ( -31.60)
>DroSim_CAF1 30859 119 - 1
CCGGCUUUGUGCGCCGAAUAUGGCAGAAAGUCCAAAGCCGGCAGCCAGCAGCCAGCAG-CCACUGCCACAUCAAUCACCGGCUGACAAGCCACCUAAAUACAAUAUAAAUAUAUUGUGCU
..(((((((..((((......))).....)..)))))))(((((...((........)-)..)))))............((((....)))).......((((((((....)))))))).. ( -36.40)
>DroEre_CAF1 31927 120 - 1
CCGGCUUUGUGCGCCGAAUACGGCAGAAAAUCCAAAGUCGGCAGCCAGCAGGCAGCAGGCAGCAGCCACAUCAAUCACCGGCUGACAAGCCACCUAAAUACAAUAUAAAUAUAUUGUGCU
(((((((((...((((....)))).(.....))))))))))..(((....)))(((.(((..(((((............)))))....)))........(((((((....)))))))))) ( -39.80)
>consensus
CCGGCUUUGUGCGCCGAAUAUGGCAGAAAGUCCAAAGCCGGCAGCCAGCAGCCAGCAG_CCGCUGCCACAUCAAUCACCGGCUGACAAGCCACCUAAAUACAAUAUAAAUAUAUUGUGCU
..(((((((.((((((....)))).....)).)))))))((((((................))))))............((((....)))).......((((((((....)))))))).. (-29.90 = -30.84 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:03 2006