Locus 2280

Sequence ID	2R_DroMel_CAF1
Location	8,401,662 – 8,401,754
Length	92
Max. P	0.999862

overview

Window 2

Location	8,401,662 – 8,401,754
Length	92
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	75.50
Mean single sequence MFE	-19.98
Consensus MFE	-11.49
Energy contribution	-11.69
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.27
Structure conservation index	0.58
SVM decision value	1.91
SVM RNA-class probability	0.982297
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8401662 92 + 20766785
UUUGUGUUUUCAUGUCCCGACGGAGGUUUAUUUAAAAAUGAUUCCUAUUGCCGUCGGACCUUAGCUAU-----AUUUUCA----UUUCAAUAGCUUUUACU
...(((.......((((.((((((((.(((((....)))))..)))....)))))))))...((((((-----.......----.....))))))..))). ( -19.60)
>DroSec_CAF1 12632 96 + 1
UUGUUAUUCCCAUGUCCCGACGGAGUUUAACUUAAAAAUGAUUCCUGUUGCCGUCGGAACUUAAAUAU-----AUUUUCAUAUAUUUCAGUAGCUUUGAUU
..((((((.....((.(((((((....((((...............))))))))))).))..((((((-----((....)))))))).))))))....... ( -18.26)
>DroSim_CAF1 12577 96 + 1
UUGUAAUUCGCAUGUCCCGACGGAGUUUAAUUUAAAAAUAAUUCCUGUUGCCGUCGGAACUUAAAUAU-----AUUUUCAUAUAUUUCAGUAGCUUUUACU
..((((...((.....(((((((.....((((.......)))).......))))))).(((.((((((-----((....)))))))).))).))..)))). ( -21.20)
>DroEre_CAF1 14809 101 + 1
CUUUGAGUUCGAUGUCCCGACGGAUCCUAACUUAAGAAUUAUUUCUUUUGCCGUCGGAACUUAUAAAAUUUUAAUUUUCAUAUAUUUGAGUUGCUCUCUCU
....(((..((((((.(((((((..........(((((....)))))...))))))).)).................(((......)))))))..)))... ( -21.52)
>DroYak_CAF1 12763 98 + 1
UUUUGAUUUUUAUGUCCCGACGGAUCCUAACUUAAG-UUUAUUUCUUAUGCCGUCGGAACAUACAAAUUUUU--UUUUUAUAUAUUCGAGUUGCUUUUACU
....(((((.(((((.(((((((.........((((-.......))))..))))))).))))).)))))...--........................... ( -19.30)
>consensus
UUUUGAUUUCCAUGUCCCGACGGAGCUUAACUUAAAAAUGAUUCCUGUUGCCGUCGGAACUUAAAUAU_____AUUUUCAUAUAUUUCAGUAGCUUUUACU
.............((.(((((((...........................))))))).))......................................... (-11.49 = -11.69 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	8,401,662 – 8,401,754
Length	92
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	75.50
Mean single sequence MFE	-23.05
Consensus MFE	-14.89
Energy contribution	-15.09
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-3.68
Structure conservation index	0.65
SVM decision value	4.29
SVM RNA-class probability	0.999862
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8401662 92 - 20766785
AGUAAAAGCUAUUGAAA----UGAAAAU-----AUAGCUAAGGUCCGACGGCAAUAGGAAUCAUUUUUAAAUAAACCUCCGUCGGGACAUGAAAACACAAA
......((((((.....----.......-----))))))..(..(((((((....(((.................))))))))))..)............. ( -19.33)
>DroSec_CAF1 12632 96 - 1
AAUCAAAGCUACUGAAAUAUAUGAAAAU-----AUAUUUAAGUUCCGACGGCAACAGGAAUCAUUUUUAAGUUAAACUCCGUCGGGACAUGGGAAUAACAA
........(((...((((((((....))-----))))))..((((((((((.(((..(((.....)))..))).....)))))))))).)))......... ( -23.90)
>DroSim_CAF1 12577 96 - 1
AGUAAAAGCUACUGAAAUAUAUGAAAAU-----AUAUUUAAGUUCCGACGGCAACAGGAAUUAUUUUUAAAUUAAACUCCGUCGGGACAUGCGAAUUACAA
.((((..((.....((((((((....))-----))))))..((((((((((......((.(((....))).)).....))))))))))..))...)))).. ( -27.50)
>DroEre_CAF1 14809 101 - 1
AGAGAGAGCAACUCAAAUAUAUGAAAAUUAAAAUUUUAUAAGUUCCGACGGCAAAAGAAAUAAUUCUUAAGUUAGGAUCCGUCGGGACAUCGAACUCAAAG
...(((..(..........(((((((.......))))))).((((((((((...........(((((......)))))))))))))))...)..))).... ( -24.00)
>DroYak_CAF1 12763 98 - 1
AGUAAAAGCAACUCGAAUAUAUAAAAA--AAAAAUUUGUAUGUUCCGACGGCAUAAGAAAUAAA-CUUAAGUUAGGAUCCGUCGGGACAUAAAAAUCAAAA
...........................--....((((.(((((((((((((.((....(((...-.....)))...))))))))))))))).))))..... ( -20.50)
>consensus
AGUAAAAGCUACUGAAAUAUAUGAAAAU_____AUAUUUAAGUUCCGACGGCAAAAGGAAUAAUUUUUAAGUUAAACUCCGUCGGGACAUGAAAAUAAAAA
.........................................((((((((((...........................))))))))))............. (-14.89 = -15.09 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:32 2006