Locus 5103

Sequence ID	3L_DroMel_CAF1
Location	13,994,232 – 13,994,392
Length	160
Max. P	0.999863

overview

Window 5

Location	13,994,232 – 13,994,352
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.83
Mean single sequence MFE	-31.64
Consensus MFE	-27.22
Energy contribution	-27.94
Covariance contribution	0.72
Combinations/Pair	1.09
Mean z-score	-2.03
Structure conservation index	0.86
SVM decision value	2.19
SVM RNA-class probability	0.989939
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13994232 120 + 23771897
AUCUUGGCCAUUUGCGAACUUCGAAAAACGGUGUGCGAUGCGGUGCUUAUCGCGUAGCACAUAACAAAUGCAAUUUGGAACCGAAAAAUUGCAUUUAAAGAUCACUUUUUCUCUUUUAUC
...((.((.....)).))....((((((.(((((((.(((((((....))))))).))))))...(((((((((((.........)))))))))))........)))))))......... ( -30.20)
>DroSec_CAF1 7651 120 + 1
AUCUUGGCCGUUCGCGAACUUCGAAAAACGGUGUGCGACGCGGUGCUUAUCGCGUAGCACAUACCAAAUGCAAUUUGGAACCGAAAAAUUGCAUUUAAAGAUCACUUUUUCUCUUUUAUC
((((((((((((..((.....))...)))))(((((.(((((((....))))))).)))))..))(((((((((((.........))))))))))).))))).................. ( -36.60)
>DroSim_CAF1 5379 120 + 1
AUCUUGGUCGUUCGCGAACUUCGAAAAACGGUUUGCGAUGCGGUGCUUAUCGCGUAGCACAUACCAAAUGCAAUUUGGAACCGAAAAAUUGCAUUUAAAGAUCACUUUUUCUCUUUUAUC
((((((((((((((((((((.........))))))))).)))(((((........)))))..)))(((((((((((.........))))))))))).))))).................. ( -33.80)
>DroEre_CAF1 6430 119 + 1
AUCUUAGCCGUUCGCGAACUUCGGAAAACGGUGGGCGAUGCGGUGCUUAUCGCGUAGCACAUACCAAAUGCAAUUUACAACAGAAAAAUUGCAUUUAUAGAUCACUUUUU-UCUUUUAUC
......((.....)).......((((((.(((((((.(((((((....))))))).)).......(((((((((((.........))))))))))).....))))).)))-)))...... ( -28.90)
>DroYak_CAF1 6995 120 + 1
AUCUUAGCCGUUCGCGAACUUCGGAAAACGGUGGGCGAUGAGGUGCUUAUCGCGUAGCACAUACCAGAUGCAAUUUACAACCGAAAAAUUGCAUUUAAAGAUCACUUUUUCUCUUUUAUC
(((((.(((((((.((.....))))..)))))((((((((((...))))))))(.....)...))(((((((((((.........))))))))))).))))).................. ( -28.70)
>consensus
AUCUUGGCCGUUCGCGAACUUCGAAAAACGGUGUGCGAUGCGGUGCUUAUCGCGUAGCACAUACCAAAUGCAAUUUGGAACCGAAAAAUUGCAUUUAAAGAUCACUUUUUCUCUUUUAUC
(((((.((((((..((.....))...))))))((((.(((((((....))))))).)))).....(((((((((((.........))))))))))).))))).................. (-27.22 = -27.94 +   0.72)

alignment

secondary structure

dotplot

Window 6

Location	13,994,272 – 13,994,392
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.67
Mean single sequence MFE	-31.00
Consensus MFE	-27.98
Energy contribution	-29.02
Covariance contribution	1.04
Combinations/Pair	1.03
Mean z-score	-2.82
Structure conservation index	0.90
SVM decision value	4.29
SVM RNA-class probability	0.999863
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13994272 120 + 23771897
CGGUGCUUAUCGCGUAGCACAUAACAAAUGCAAUUUGGAACCGAAAAAUUGCAUUUAAAGAUCACUUUUUCUCUUUUAUCACCGCUGCGCCUUCCGCCUAGAGUUGGUACAAAACACUGU
(((((......(((((((.......(((((((((((.........)))))))))))..(((........)))...........))))))).....(((.......)))......))))). ( -30.10)
>DroSec_CAF1 7691 120 + 1
CGGUGCUUAUCGCGUAGCACAUACCAAAUGCAAUUUGGAACCGAAAAAUUGCAUUUAAAGAUCACUUUUUCUCUUUUAUCACCGCUGCGCCUUCCGCCUAGAGUUGGAACAAAACUCUGU
.((((......(((((((.......(((((((((((.........)))))))))))..(((........)))...........)))))))....))))(((((((.......))))))). ( -33.50)
>DroSim_CAF1 5419 120 + 1
CGGUGCUUAUCGCGUAGCACAUACCAAAUGCAAUUUGGAACCGAAAAAUUGCAUUUAAAGAUCACUUUUUCUCUUUUAUCACCGCUGCGCCUUCCGCCUAGAGUUGGAACAAAACUCUGU
.((((......(((((((.......(((((((((((.........)))))))))))..(((........)))...........)))))))....))))(((((((.......))))))). ( -33.50)
>DroEre_CAF1 6470 119 + 1
CGGUGCUUAUCGCGUAGCACAUACCAAAUGCAAUUUACAACAGAAAAAUUGCAUUUAUAGAUCACUUUUU-UCUUUUAUCACCGCUCCGCCUUCCGCAUAGAGUUGGAACAAAACUCAGU
..((((.....(((.(((.......(((((((((((.........)))))))))))..(((.........-))).........))).))).....)))).(((((.......)))))... ( -25.50)
>DroYak_CAF1 7035 120 + 1
AGGUGCUUAUCGCGUAGCACAUACCAGAUGCAAUUUACAACCGAAAAAUUGCAUUUAAAGAUCACUUUUUCUCUUUUAUCACCGCUGCGCCUUCCGCCUAGAGUGGAAACAAAACUCUGU
(((((......(((((((.......(((((((((((.........)))))))))))..(((........)))...........)))))))....)))))((((((....)...))))).. ( -32.40)
>consensus
CGGUGCUUAUCGCGUAGCACAUACCAAAUGCAAUUUGGAACCGAAAAAUUGCAUUUAAAGAUCACUUUUUCUCUUUUAUCACCGCUGCGCCUUCCGCCUAGAGUUGGAACAAAACUCUGU
.((((......(((((((.......(((((((((((.........)))))))))))(((((..........))))).......)))))))....))))(((((((.......))))))). (-27.98 = -29.02 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:04 2006