Locus 562

Sequence ID	3R_DroMel_CAF1
Location	2,094,895 – 2,095,003
Length	108
Max. P	0.968525

overview

Window 3

Location	2,094,895 – 2,095,003
Length	108
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	91.80
Mean single sequence MFE	-35.40
Consensus MFE	-27.26
Energy contribution	-28.14
Covariance contribution	0.88
Combinations/Pair	1.07
Mean z-score	-1.90
Structure conservation index	0.77
SVM decision value	0.64
SVM RNA-class probability	0.808550
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2094895 108 + 27905053
UGGUGUUUUUCUCCCAGUACAACAA-AGCUGUUGGCUAUUCAGAGCGUAGUAUGCAUGAUGAGUGCAUGCGGCAGUUGAAAACUACCAGCAAGCUGCAGCACUAAAGCA
(((.(.......))))...(((((.-...)))))(((..(((..((((...)))).)))..(((((.((((((.((((........))))..)))))))))))..))). ( -30.70)
>DroSec_CAF1 237772 108 + 1
UGUGGUUUUUCUCCCAGUGCAACAA-AGCUGUUGGCUAUUCAGAGCGUAGUAUGCAUGAUGAGUGCAUGCGGCAGCUGGAAACUGCCUGCAAGCUGCAGCACUAAAGCA
....(((((......(((((.....-((((((.(((..(((..(((((.((((((((.....)))))))).)).))).)))...))).)).))))...)))))))))). ( -35.80)
>DroSim_CAF1 240879 108 + 1
UGUGGUUUUUCUCCCAGUGCAACAA-AGCUGUUGGCUAUUCAGAGCGUAGUAUGCAUGAUGAGUGCAUGCGGCAGCUGGAAACUGCCUGCAAGCUGCAGCACUAAAGCA
....(((((......(((((.....-((((((.(((..(((..(((((.((((((((.....)))))))).)).))).)))...))).)).))))...)))))))))). ( -35.80)
>DroEre_CAF1 239197 107 + 1
GGCUGU-UUUCUCCCAGUGCAACAAUAGCUGUUGGCUAUUCAGAGCGUAGUAUGCAUGAUGAGUGCAUGCGGCAGCUGGAAACUGCCUGCA-GAUAAAGCUAUAAAGCA
((((..-..(((..(((.(((....((((((((.(((......)))...((((((((.....)))))))))))))))).....)))))).)-))...))))........ ( -35.40)
>DroYak_CAF1 241890 108 + 1
UGUGGU-UUUCUCGCAGUGCAAUAAUAGCUGUUGGCUAUUCAGAGCGUAGUAUGCAUGAUGAGUGCAUGCGGCAGCUGGCAACUGCCUGCAAGCUAAAGCACUAAAGCA
.(((.(-((.((.((((.(((....((((((((.(((......)))...((((((((.....)))))))))))))))).....))))))).))..))).)))....... ( -39.30)
>consensus
UGUGGUUUUUCUCCCAGUGCAACAA_AGCUGUUGGCUAUUCAGAGCGUAGUAUGCAUGAUGAGUGCAUGCGGCAGCUGGAAACUGCCUGCAAGCUGCAGCACUAAAGCA
...............(((((......((((((.(((..(((((...((.((((((((.....)))))))).))..)))))....))).))).)))...)))))...... (-27.26 = -28.14 +   0.88)

alignment

secondary structure

dotplot

Window 4

Location	2,094,895 – 2,095,003
Length	108
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	91.80
Mean single sequence MFE	-30.34
Consensus MFE	-28.08
Energy contribution	-27.80
Covariance contribution	-0.28
Combinations/Pair	1.18
Mean z-score	-1.56
Structure conservation index	0.93
SVM decision value	1.63
SVM RNA-class probability	0.968525
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2094895 108 - 27905053
UGCUUUAGUGCUGCAGCUUGCUGGUAGUUUUCAACUGCCGCAUGCACUCAUCAUGCAUACUACGCUCUGAAUAGCCAACAGCU-UUGUUGUACUGGGAGAAAAACACCA
...((((((((.((((...(((((((((.....))))))(((((.......))))).......(((......)))....))).-)))).))))))))............ ( -26.60)
>DroSec_CAF1 237772 108 - 1
UGCUUUAGUGCUGCAGCUUGCAGGCAGUUUCCAGCUGCCGCAUGCACUCAUCAUGCAUACUACGCUCUGAAUAGCCAACAGCU-UUGUUGCACUGGGAGAAAAACCACA
(((..(((.((((..(((..((((((((.....))))))(((((.......)))))...........))...)))...)))).-)))..))).(((........))).. ( -31.30)
>DroSim_CAF1 240879 108 - 1
UGCUUUAGUGCUGCAGCUUGCAGGCAGUUUCCAGCUGCCGCAUGCACUCAUCAUGCAUACUACGCUCUGAAUAGCCAACAGCU-UUGUUGCACUGGGAGAAAAACCACA
(((..(((.((((..(((..((((((((.....))))))(((((.......)))))...........))...)))...)))).-)))..))).(((........))).. ( -31.30)
>DroEre_CAF1 239197 107 - 1
UGCUUUAUAGCUUUAUC-UGCAGGCAGUUUCCAGCUGCCGCAUGCACUCAUCAUGCAUACUACGCUCUGAAUAGCCAACAGCUAUUGUUGCACUGGGAGAAA-ACAGCC
.(((......((((...-((((((((((.....))))))(((((.......))))).............((((((.....))))))..))))...))))...-..))). ( -28.70)
>DroYak_CAF1 241890 108 - 1
UGCUUUAGUGCUUUAGCUUGCAGGCAGUUGCCAGCUGCCGCAUGCACUCAUCAUGCAUACUACGCUCUGAAUAGCCAACAGCUAUUAUUGCACUGCGAGAAA-ACCACA
.......(((.(((..((((((((((((.....))))))(((((.......))))).......((....((((((.....))))))...))..)))))).))-).))). ( -33.80)
>consensus
UGCUUUAGUGCUGCAGCUUGCAGGCAGUUUCCAGCUGCCGCAUGCACUCAUCAUGCAUACUACGCUCUGAAUAGCCAACAGCU_UUGUUGCACUGGGAGAAAAACCACA
..(((((((((..(((...((.((((((.....))))))(((((.......))))).......(((......))).....))..)))..)))))).))).......... (-28.08 = -27.80 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:08 2006