Locus 3936

Sequence ID	X_DroMel_CAF1
Location	10,493,219 – 10,493,362
Length	143
Max. P	0.998263

overview

Window 7

Location	10,493,219 – 10,493,331
Length	112
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	91.45
Mean single sequence MFE	-24.40
Consensus MFE	-19.30
Energy contribution	-20.05
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-2.14
Structure conservation index	0.79
SVM decision value	0.78
SVM RNA-class probability	0.849735
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10493219 112 + 22224390
CCCUCAUUUUUUCUUUUU--UUUUUUUUUUGCCACCCAACGUGUAGUUUCUGUGCACUUGUUGUCAUUUGUUCGGCGGCAACAGCAAGAACAAAACUGACAAUACCAGACUUUU
..................--.......((((.........(((((.......))))).(((((((((((((((.(((....).))..)))))))..)))))))).))))..... ( -21.40)
>DroSec_CAF1 24437 111 + 1
CCGUCAUUUUUUCUUUUUCUUUUUUUUUUUGCCACUCAACGUGUAGUUUCUGUGCACUU---GUCAUUUGUUCGGCGGCAACAGCAAGAACAAAACUGACAAUACCAGACUUUU
..(((........................(((.((..(((.....)))...))))).((---(((((((((((.(((....).))..)))))))..)))))).....))).... ( -22.10)
>DroSim_CAF1 24931 107 + 1
CCGUCAUUUUUUCUUU-------UUUUUUUGCCACUCAACGUGUAGUUUCUGUGCACUUGUUGUCAUUUGUUCGGCGGCAACAGCAAGAACAAAACUGACAAUACCAGACUUUU
..(((...........-------......(((.((..(((.....)))...)))))..(((((((((((((((.(((....).))..)))))))..))))))))...))).... ( -24.50)
>DroYak_CAF1 26243 108 + 1
CC--CAUUUUU-GUU-UU--UCGUUUUUUUGCCGCCCAACGUGUAGUUUCUGUGCACUUGUUGUCAUUUGUUCGGCGGCAACAGCAAGAACAAAACUGACAAUACCAGACUUUU
..--((.((((-(((-((--(.(((...((((((((.((((((((.......))))).((....))...))).)))))))).))))))))))))).))................ ( -29.60)
>consensus
CCGUCAUUUUUUCUUUUU__UUUUUUUUUUGCCACCCAACGUGUAGUUUCUGUGCACUUGUUGUCAUUUGUUCGGCGGCAACAGCAAGAACAAAACUGACAAUACCAGACUUUU
...........................((((.........(((((.......))))).(((((((((((((((.(((....).))..)))))))..)))))))).))))..... (-19.30 = -20.05 +   0.75)

alignment

secondary structure

dotplot

Window 8

Location	10,493,257 – 10,493,362
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	96.49
Mean single sequence MFE	-26.06
Consensus MFE	-23.74
Energy contribution	-24.54
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.20
Structure conservation index	0.91
SVM decision value	3.05
SVM RNA-class probability	0.998263
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10493257 105 + 22224390
GUGUAGUUUCUGUGCACUUGUUGUCAUUUGUUCGGCGGCAACAGCAAGAACAAAACUGACAAUACCAGACUUUUAUCCAUUGAAUGCAUACACACGCACUCACUC
((((.((.(.((((((..(((((((((((((((.(((....).))..)))))))..)))))))).......((((.....)))))))))).).))))))...... ( -26.60)
>DroSec_CAF1 24477 98 + 1
GUGUAGUUUCUGUGCACUU---GUCAUUUGUUCGGCGGCAACAGCAAGAACAAAACUGACAAUACCAGACUUUUAUCCAUUGAAUGCAUACACACGCAC----UA
((((.((.(.((((((.((---(((((((((((.(((....).))..)))))))..)))))).........((((.....)))))))))).).))))))----.. ( -24.20)
>DroSim_CAF1 24964 101 + 1
GUGUAGUUUCUGUGCACUUGUUGUCAUUUGUUCGGCGGCAACAGCAAGAACAAAACUGACAAUACCAGACUUUUAUCCAUUGAAUGCAUACACACGCAC----UC
((((.((.(.((((((..(((((((((((((((.(((....).))..)))))))..)))))))).......((((.....)))))))))).).))))))----.. ( -26.60)
>DroEre_CAF1 26066 101 + 1
GAGUAGUUUCUGUGCACUUGUUGUCAUUUGUUCGGCGGCAACAGCAAGAACAAAACUGACAAUACCAGACUUUUAUCCAUUGAAUGCAUACACACGCAC----UC
((((.((.(.((((((..(((((((((((((((.(((....).))..)))))))..)))))))).......((((.....)))))))))).).))..))----)) ( -26.30)
>DroYak_CAF1 26277 101 + 1
GUGUAGUUUCUGUGCACUUGUUGUCAUUUGUUCGGCGGCAACAGCAAGAACAAAACUGACAAUACCAGACUUUUAUCCAUUGAAUGCAUACACACGCAC----UC
((((.((.(.((((((..(((((((((((((((.(((....).))..)))))))..)))))))).......((((.....)))))))))).).))))))----.. ( -26.60)
>consensus
GUGUAGUUUCUGUGCACUUGUUGUCAUUUGUUCGGCGGCAACAGCAAGAACAAAACUGACAAUACCAGACUUUUAUCCAUUGAAUGCAUACACACGCAC____UC
((((.((...((((((..(((((((((((((((.(((....).))..)))))))..)))))))).......((((.....)))))))))).))))))........ (-23.74 = -24.54 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:16 2006