Locus 4947

Sequence ID	3R_DroMel_CAF1
Location	13,016,372 – 13,016,462
Length	90
Max. P	0.914648

overview

Window 5

Location	13,016,372 – 13,016,462
Length	90
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	81.60
Mean single sequence MFE	-24.24
Consensus MFE	-14.61
Energy contribution	-17.14
Covariance contribution	2.53
Combinations/Pair	1.15
Mean z-score	-2.40
Structure conservation index	0.60
SVM decision value	1.10
SVM RNA-class probability	0.914648
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13016372 90 + 27905053
AAUUUUAUCUGGUAAC-----UAUGAAGUGGAAACCACUUCAGAUGCAAACUCUUGGCCAAACUCUUGGCUCAAGUAAACGCCAGUGAAACAAAG
..(((((.(((((...-----..((((((((...))))))))..........(((((((((....))))).)))).....))))))))))..... ( -28.60)
>DroSec_CAF1 36441 85 + 1
AUUUUUUUCUGGUGAC-----UAUGAAGUGGAAACCACUUCGGAUGCAAACUUUUGGCCAAACUCUUGGCUCAAGUGAACGCCAGUGA-----AG
....(((.((((((..-----..((((((((...)))))))).......((((..((((((....)))))).))))...)))))).))-----). ( -28.00)
>DroSim_CAF1 28890 90 + 1
AUUUUUUUCUGGUGAC-----UAUGAAGUGGAAACCACUUCGGAUGCAAACUUUUGGCCAAACUCUUGGCUCAAGUGAACGCCAGUGAAACAAAG
...((((.((((((..-----..((((((((...)))))))).......((((..((((((....)))))).))))...)))))).))))..... ( -28.60)
>DroEre_CAF1 37014 83 + 1
AAUUUUCUCUGCUAACCAUAUUAUGACGUG------------GAUGCAAACUUUUGUCCAAACUCUUGGCUCAAGUAAGCGCCAGUGAAACAAAG
...((((.((((...((((........)))------------)..((..((((..(.((((....)))))..))))..))).))).))))..... ( -16.40)
>DroYak_CAF1 37682 95 + 1
GGUUUUUUCUAGUAACCAUAUUAUGUAGUGGAAACCACUUCGGAUGCAAACUUUUGGCCAAACUGUUGGUUCAAGUAAACGGCAGUGAAACAAAG
((((((..(((((((.....)))).)))..))))))..((((..(((.....(((((((((....)))).)))))......))).))))...... ( -19.60)
>consensus
AAUUUUUUCUGGUAAC_____UAUGAAGUGGAAACCACUUCGGAUGCAAACUUUUGGCCAAACUCUUGGCUCAAGUAAACGCCAGUGAAACAAAG
...((((.(((((..........((((((((...))))))))..........(((((((((....))))).)))).....))))).))))..... (-14.61 = -17.14 +   2.53)

alignment

secondary structure

dotplot

Window 6

Location	13,016,372 – 13,016,462
Length	90
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	81.60
Mean single sequence MFE	-21.48
Consensus MFE	-15.97
Energy contribution	-17.74
Covariance contribution	1.77
Combinations/Pair	1.14
Mean z-score	-1.58
Structure conservation index	0.74
SVM decision value	0.17
SVM RNA-class probability	0.617374
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13016372 90 - 27905053
CUUUGUUUCACUGGCGUUUACUUGAGCCAAGAGUUUGGCCAAGAGUUUGCAUCUGAAGUGGUUUCCACUUCAUA-----GUUACCAGAUAAAAUU
..........((((.((..((((..(((((....)))))...))))..))...((((((((...))))))))..-----....))))........ ( -26.00)
>DroSec_CAF1 36441 85 - 1
CU-----UCACUGGCGUUCACUUGAGCCAAGAGUUUGGCCAAAAGUUUGCAUCCGAAGUGGUUUCCACUUCAUA-----GUCACCAGAAAAAAAU
..-----...((((.((..((((..(((((....)))))...))))..))....(((((((...)))))))...-----....))))........ ( -24.50)
>DroSim_CAF1 28890 90 - 1
CUUUGUUUCACUGGCGUUCACUUGAGCCAAGAGUUUGGCCAAAAGUUUGCAUCCGAAGUGGUUUCCACUUCAUA-----GUCACCAGAAAAAAAU
..........((((.((..((((..(((((....)))))...))))..))....(((((((...)))))))...-----....))))........ ( -24.50)
>DroEre_CAF1 37014 83 - 1
CUUUGUUUCACUGGCGCUUACUUGAGCCAAGAGUUUGGACAAAAGUUUGCAUC------------CACGUCAUAAUAUGGUUAGCAGAGAAAAUU
(((((((..(((((.((..((((...((((....))))....))))..))..)------------))(((......))))).)))))))...... ( -16.00)
>DroYak_CAF1 37682 95 - 1
CUUUGUUUCACUGCCGUUUACUUGAACCAACAGUUUGGCCAAAAGUUUGCAUCCGAAGUGGUUUCCACUACAUAAUAUGGUUACUAGAAAAAACC
.....((((...(((((..((((...((((....))))....))))..))....(.(((((...))))).).......))).....))))..... ( -16.40)
>consensus
CUUUGUUUCACUGGCGUUUACUUGAGCCAAGAGUUUGGCCAAAAGUUUGCAUCCGAAGUGGUUUCCACUUCAUA_____GUUACCAGAAAAAAAU
..........((((.((..((((..(((((....)))))...))))..))....(((((((...)))))))............))))........ (-15.97 = -17.74 +   1.77)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:44 2006