Locus 4125

Sequence ID	X_DroMel_CAF1
Location	10,854,314 – 10,854,460
Length	146
Max. P	0.827233

overview

Window 6

Location	10,854,314 – 10,854,420
Length	106
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	90.60
Mean single sequence MFE	-31.50
Consensus MFE	-25.48
Energy contribution	-25.98
Covariance contribution	0.50
Combinations/Pair	1.11
Mean z-score	-1.91
Structure conservation index	0.81
SVM decision value	0.70
SVM RNA-class probability	0.827233
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10854314 106 + 22224390
UUGUGUGGGAGUGGGUUUUUUUUGUGGUU-UGGAGGGCUUGAAAGGGCGUCAUUAAAAAUCAUUAAAAAUCAGUGAAGCAUCGCAAAUGCGACCGCUGUCCCUU-UUG
......((((...(((((((...((((((-(.((.(.(((....)))).)).....))))))).))))))).....(((.((((....))))..))).))))..-... ( -28.00)
>DroSec_CAF1 8174 105 + 1
UUGUGUGGGAGUGGGAUU--UUUGUGGUUGUGGAGGGCUCGAAAGGGCGUCAUUAAAAAUCAUUAAAAAUCAGUGAAGCAUCGCAAAUGCGACCGCUGUCCCUU-UUG
......((((((((((((--(((((((((...((((((((....)))).)).))...))))).)))))))).........((((....))))))))..))))..-... ( -34.10)
>DroSim_CAF1 8291 105 + 1
UUGUAUGGGAGUGGGAUU--UUUGUGGUUGUGGAGGGCUCGAAAGGGCGUCAUUAAAAAUCAUUAAAAAUCAGUGAAGCAUCGCAAAUGCGACCGCUGUCCCUU-UUG
......((((((((((((--(((((((((...((((((((....)))).)).))...))))).)))))))).........((((....))))))))..))))..-... ( -34.10)
>DroYak_CAF1 8339 99 + 1
-----UAGGAGUGGGAUU--UUUGUGGUC--GGCGGACUCGAAAGGGCGUCAUUAAAAAUCAUUAAAAGUCAGUGAAGCAUCGCAAAUGCGACCGCUGUCCUUUUUUU
-----.(((((.(((((.--...((((((--((((..(((....)))))))........(((((.......))))).((((.....)))))))))).))))).))))) ( -29.80)
>consensus
UUGUGUGGGAGUGGGAUU__UUUGUGGUU_UGGAGGGCUCGAAAGGGCGUCAUUAAAAAUCAUUAAAAAUCAGUGAAGCAUCGCAAAUGCGACCGCUGUCCCUU_UUG
......((((((((((((.....((((((...((.(.(((....)))).))......))))))....)))).........((((....))))))))..))))...... (-25.48 = -25.98 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	10,854,343 – 10,854,460
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.83
Mean single sequence MFE	-36.45
Consensus MFE	-26.56
Energy contribution	-26.80
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.93
Structure conservation index	0.73
SVM decision value	0.11
SVM RNA-class probability	0.588904
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10854343 117 + 22224390
--UGGAGGGCUUGAAAGGGCGUCAUUAAAAAUCAUUAAAAAUCAGUGAAGCAUCGCAAAUGCGACCGCUGUCCCUU-UUGGCCAACCGUUUGAAAGGUUCAGCAUUUUUACGCCACUUGC
--..((((((.(((((((((.(((((.................))))).)).((((....))))))((((..((((-(..(.(....).)..)))))..))))..))))).))).))).. ( -35.13)
>DroSec_CAF1 8201 118 + 1
-GUGGAGGGCUCGAAAGGGCGUCAUUAAAAAUCAUUAAAAAUCAGUGAAGCAUCGCAAAUGCGACCGCUGUCCCUU-UUGGCCAACCGUUUGAAAGGUUCAGCAUUUUUACGCCACUUGC
-((((...((((....))))........................((((((..((((....))))..((((..((((-(..(.(....).)..)))))..))))..)))))).)))).... ( -37.20)
>DroSim_CAF1 8318 118 + 1
-GUGGAGGGCUCGAAAGGGCGUCAUUAAAAAUCAUUAAAAAUCAGUGAAGCAUCGCAAAUGCGACCGCUGUCCCUU-UUGGCCAACCGUUUGAAAGGUUCAGCAUUUUUACGCCACUUGC
-((((...((((....))))........................((((((..((((....))))..((((..((((-(..(.(....).)..)))))..))))..)))))).)))).... ( -37.20)
>DroYak_CAF1 8361 117 + 1
---GGCGGACUCGAAAGGGCGUCAUUAAAAAUCAUUAAAAGUCAGUGAAGCAUCGCAAAUGCGACCGCUGUCCUUUUUUUGGCAACCGUUUGAAAGGUUCAGCAUUUUUACGCCACUUGC
---(((((.(((....))))(((........(((((.......))))).((((.....))))))).((((.((((((..(((...)))...))))))..)))).......))))...... ( -33.40)
>DroAna_CAF1 2811 118 + 1
CAGGACGGGGUCGAAAGGGCGUCAUUAAAAAUCAUUAAAAACCAGUGAAGCGUCGCAAAUGCGACCGCUGUCCCUU--CGGCGCUGAGUUUGAAAGGUUCAGCAUUUUUACGCCACUUGC
..((.((..((((((.((((...........(((((.......)))))((((((((....)))).)))))))).))--))))((((((..(...)..)))))).......))))...... ( -39.30)
>consensus
__UGGAGGGCUCGAAAGGGCGUCAUUAAAAAUCAUUAAAAAUCAGUGAAGCAUCGCAAAUGCGACCGCUGUCCCUU_UUGGCCAACCGUUUGAAAGGUUCAGCAUUUUUACGCCACUUGC
..............((((((((.........(((((.......)))))....((((....))))..((((..((((...(((.....)))...))))..))))......))))).))).. (-26.56 = -26.80 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:56 2006