Locus 413

Sequence ID	2L_DroMel_CAF1
Location	1,234,969 – 1,235,168
Length	199
Max. P	0.930256

overview

Window 7

Location	1,234,969 – 1,235,088
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.98
Mean single sequence MFE	-30.55
Consensus MFE	-27.05
Energy contribution	-28.05
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.24
Structure conservation index	0.89
SVM decision value	1.20
SVM RNA-class probability	0.930256
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1234969 119 - 22407834
GAGGAAAAACAUCUGAUCCUGAAGGAA-AAAAUCCGGGAUUUGGGUGAAAUGUUAAAUGGGCGACAUUUACACAUUCGUUACCCAGGUCCGAGCCCAAUUUGCUGACAAACAAAUUACAC
.((((...........))))...(((.-....))).(((((((((((((((((((((((.....)))))).)))))..))))))))))))......((((((........)))))).... ( -32.10)
>DroSec_CAF1 12288 119 - 1
GAAUAAAAACCUCUGAUCAUGAAGGAA-AAAAUCCGGGAUUUGGGUGAAAUGUUAAAUGGGCGACAUUUACACAUUCGUUACCCAGGUCCGAGCCCAAUUUGCUGACAAACAAAUUACAC
..........(((..........(((.-....))).(((((((((((((((((((((((.....)))))).)))))..)))))))))))))))...((((((........)))))).... ( -32.10)
>DroSim_CAF1 8105 119 - 1
GAAGAAAAACCUCUGAUCCUGAAGGAA-AAAAUCCGGGAUUUGGGGGAAAUGUUAAAUGGGCGACAUUUACACAUUCGUUACCCAGGUCCGAGCCCAAUUUGCUGACAAACAAAUUACAC
..........(((...(((....))).-........(((((((((..((((((((((((.....)))))).)))))..)..))))))))))))...((((((........)))))).... ( -28.60)
>DroYak_CAF1 8339 120 - 1
AAAGAAAAACCUCUGAUCCUGAGGCAAAAAAAUCCGGGAUUUUGGUGAAAUGUUAAAUGGGCAACAUUUACACAUUCGUUACCCAGGUCCGAGCCCAAUUUGUUGACAAACAAAUUACAC
.........((((.......))))............((((((.((((((((((((((((.....)))))).)))))..))))).))))))......((((((((....)))))))).... ( -29.40)
>consensus
GAAGAAAAACCUCUGAUCCUGAAGGAA_AAAAUCCGGGAUUUGGGUGAAAUGUUAAAUGGGCGACAUUUACACAUUCGUUACCCAGGUCCGAGCCCAAUUUGCUGACAAACAAAUUACAC
..........(((..........(((......))).(((((((((((((((((((((((.....)))))).)))))..)))))))))))))))...((((((........)))))).... (-27.05 = -28.05 +   1.00)

alignment

secondary structure

dotplot

Window 8

Location	1,235,049 – 1,235,168
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.05
Mean single sequence MFE	-36.01
Consensus MFE	-28.35
Energy contribution	-28.73
Covariance contribution	0.37
Combinations/Pair	1.09
Mean z-score	-1.85
Structure conservation index	0.79
SVM decision value	0.36
SVM RNA-class probability	0.702838
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1235049 119 + 22407834
AUCCCGGAUUUU-UUCCUUCAGGAUCAGAUGUUUUUCCUCUCUUUGACAUUGUCUAAUGAGUAAAUUAGGCUGGUGAUGCGGGUAGGUGGGUCCGUUCGGACUCCAUCAUGGGAACCAUU
.(((((......-..(((.((..((((((((((............))))))(((((((......)))))))))))..)).)))..(((((((((....)))).))))).)))))...... ( -37.20)
>DroSec_CAF1 12368 119 + 1
AUCCCGGAUUUU-UUCCUUCAUGAUCAGAGGUUUUUAUUCUCUGUGACAUUGUCUAAUGAGUAAAUUAGGCUGGUGAUGAGGGUAGGUGGGUCCGUUUGGAUUCCAUCAUCGGAAACAUU
...((((.....-..(((((((.(((((.....(((((((.....(((...)))....))))))).....))))).)))))))..(((((((((....))).)))))).))))....... ( -38.40)
>DroSim_CAF1 8185 119 + 1
AUCCCGGAUUUU-UUCCUUCAGGAUCAGAGGUUUUUCUUCUCUGCGACAUUGUCUAAUGAGUAAAUUAGGCUGGUGAUGCGGGUAGGUGGGUCCGUUCGGAUUCCAUCAUGGGAAACAUU
.((((((((...-.(((....((((((((((.....)))))(((((.(((((((((((......))))))).)))).))))).......)))))....)))....))).)))))...... ( -38.60)
>DroYak_CAF1 8419 120 + 1
AUCCCGGAUUUUUUUGCCUCAGGAUCAGAGGUUUUUCUUUUCUUUGACAUUGUCUAAUGAGUAAAUUAGGCUGGUGAUGCGGGUAGGUGGCUCCAUUCAGAUUCCAUCAUCGGAACCAUU
.(((.(((.......(((((.......))))).......))).........(((((((......))))))).(((((((.((((.((((....))))...))))))))))))))...... ( -29.84)
>consensus
AUCCCGGAUUUU_UUCCUUCAGGAUCAGAGGUUUUUCUUCUCUGUGACAUUGUCUAAUGAGUAAAUUAGGCUGGUGAUGCGGGUAGGUGGGUCCGUUCGGAUUCCAUCAUCGGAAACAUU
..((((((......)))....(.((((((((.......)))))...((...(((((((......)))))))..))))).))))..(((((((((....)))).)))))...(....)... (-28.35 = -28.73 +   0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:33 2006