Locus 1966

Sequence ID	3R_DroMel_CAF1
Location	5,550,585 – 5,550,731
Length	146
Max. P	0.843343

overview

Window 6

Location	5,550,585 – 5,550,702
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.05
Mean single sequence MFE	-31.63
Consensus MFE	-19.40
Energy contribution	-20.82
Covariance contribution	1.42
Combinations/Pair	1.29
Mean z-score	-1.95
Structure conservation index	0.61
SVM decision value	0.06
SVM RNA-class probability	0.564883
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5550585 117 + 27905053
UUAUUUGGCGUUUAAAGGUUUUGGGUUAUGGAAAACGCUGAACGAUUUCAUGCCAUGUGCUGAAAGAGCGACAUUCG-GCGAAAUAUAAUGUACAAAUC--AAGCAUGUGAAAACAUGUU
................(((((((.((((((.....(((((((((.(((((.((.....)))))))...))...))))-)))...)))))).)).)))))--.(((((((....))))))) ( -28.90)
>DroSec_CAF1 9719 118 + 1
UAAUUUGGUGUUUAAAGGUUUUGGGUUAUGGAAAACGCUGAACGUUUUGAUGCCAUGUGCUGAAAGAGCGGCAUUCGCGCGAAAUAUAAUGUACAAAUC--GGGCAUGUGAAAACAUGUU
.....(((((((.(((.((((.(.(((......))).).)))).))).)))))))(((((........((((....)).)).........)))))....--.(((((((....))))))) ( -30.43)
>DroSim_CAF1 9783 118 + 1
UAAUUUGGUGUUUAAAGGUUUUGGGUUAUGGAAAACGCUGAACGUUUUGAUGCCAUGUGCUGAAAGAGCGGCAUUCGCGCGAAAUAUAAUGUACAAAUC--GGGCAUGUGAAAACAUGUU
.....(((((((.(((.((((.(.(((......))).).)))).))).)))))))(((((........((((....)).)).........)))))....--.(((((((....))))))) ( -30.43)
>DroEre_CAF1 8863 117 + 1
UUUUUUGGCAAUUAAGGUUUAUGGGUUAUGGAAAACACUCAACGUUUUGAUGCCAUGUGCUGGAAGACUGGCUUCCA-GCGAAACAUAAUGUUCAAAUU--GUGUUUGUAAAAGCAUUUU
.....(((((.((((..(...(((((..(....)..)))))..)..)))))))))(((((((((((.....))))))-)).(((((((((......)))--))))))......))).... ( -32.60)
>DroYak_CAF1 8915 118 + 1
UUAGUCGGCGUUUAAUGUUUAUGGGUUAUGGAAAACGCUCAACGUUUUGAUGCCAUGUGCUGGAAGACUGGCUUUCA-GCAACAUAUAUUGUG-AAAUAGGGAGCAUGUGAAAGCAUGUU
......((((((.((((((...(.(((......))).)..))))))..))))))((((((((((((.....))))))-)).))))........-........(((((((....))))))) ( -35.80)
>consensus
UUAUUUGGCGUUUAAAGGUUUUGGGUUAUGGAAAACGCUGAACGUUUUGAUGCCAUGUGCUGAAAGAGCGGCAUUCG_GCGAAAUAUAAUGUACAAAUC__GAGCAUGUGAAAACAUGUU
......((((((.(((.(((..(.(((......))).)..))).))).))))))...(((((((.(.....).)))).))).....................(((((((....))))))) (-19.40 = -20.82 +   1.42)

alignment

secondary structure

dotplot

Window 7

Location	5,550,625 – 5,550,731
Length	106
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	83.80
Mean single sequence MFE	-31.96
Consensus MFE	-15.18
Energy contribution	-18.12
Covariance contribution	2.94
Combinations/Pair	1.23
Mean z-score	-3.13
Structure conservation index	0.47
SVM decision value	0.76
SVM RNA-class probability	0.843343
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5550625 106 + 27905053
AACGAUUUCAUGCCAUGUGCUGAAAGAGCGACAUUCG-GCGAAAUAUAAUGUACAAAUC--AAGCAUGUGAAAACAUGUUUGUAACAUUGUACAUUUUAGUCGGAAGCA
..((((....(((((((((((.....))).))))..)-)))...((.(((((((((..(--((((((((....))))))))).....))))))))).))))))...... ( -33.40)
>DroSec_CAF1 9759 106 + 1
AACGUUUUGAUGCCAUGUGCUGAAAGAGCGGCAUUCGCGCGAAAUAUAAUGUACAAAUC--GGGCAUGUGAAAACAUGUUUGUAAC-AUGUAUAUUUUAGCCGGAAGCA
..((((((...((.....))....))))))((.((((.((((((((((((((......(--((((((((....)))))))))..))-)).)))))))).)))))).)). ( -31.70)
>DroSim_CAF1 9823 107 + 1
AACGUUUUGAUGCCAUGUGCUGAAAGAGCGGCAUUCGCGCGAAAUAUAAUGUACAAAUC--GGGCAUGUGAAAACAUGUUUGUAACAAUGUAUAUUUUAGCCGGAAGCA
..((((((...((.....))....))))))((.((((.((.......((((((((...(--((((((((....)))))))))......))))))))...)))))).)). ( -30.70)
>DroEre_CAF1 8903 104 + 1
AACGUUUUGAUGCCAUGUGCUGGAAGACUGGCUUCCA-GCGAAACAUAAUGUUCAAAUU--GUGUUUGUAAAAGCAUUUUGGUUGCAAUGUAU--UUAAGCCGGAAGCA
...((((((((((....(((((((((.....))))))-)))(((((((((......)))--))))))......))))).(((((.........--...)))))))))). ( -31.40)
>DroYak_CAF1 8955 106 + 1
AACGUUUUGAUGCCAUGUGCUGGAAGACUGGCUUUCA-GCAACAUAUAUUGUG-AAAUAGGGAGCAUGUGAAAGCAUGUUGGUUACAAUGUAUA-UUUAGCCGGAAGCA
...(((((...((....(((((((((.....))))))-)))..((((((((((-(.......(((((((....)))))))..))))))))))).-....))..))))). ( -32.60)
>consensus
AACGUUUUGAUGCCAUGUGCUGAAAGAGCGGCAUUCG_GCGAAAUAUAAUGUACAAAUC__GAGCAUGUGAAAACAUGUUUGUAACAAUGUAUAUUUUAGCCGGAAGCA
...(((((..(((...((((((......))))))....)))......((((((((......((((((((....)))))))).......)))))))).......))))). (-15.18 = -18.12 +   2.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:03 2006