Locus 1218

Sequence ID	2L_DroMel_CAF1
Location	3,259,064 – 3,259,224
Length	160
Max. P	0.844400

overview

Window 3

Location	3,259,064 – 3,259,184
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.17
Mean single sequence MFE	-21.76
Consensus MFE	-21.36
Energy contribution	-21.12
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-1.41
Structure conservation index	0.98
SVM decision value	0.76
SVM RNA-class probability	0.844400
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3259064 120 + 22407834
CAUGCCCUGUUGUUUAAGCAAAUAAUUUCCGAAACUUCUCUCGAAAUCAAACAAAAGAACAUGCAGUUGAAGGGCCACAAGCGACUUCAUUAACAAAACAAACAGCAGCCGCAUUUCUCA
.((((.(((((((((..(((.........(((........)))...((........))...)))...(((((.((.....))..)))))..........)))))))))..))))...... ( -22.50)
>DroSec_CAF1 85640 120 + 1
CAUGCCCUGUUGUUUAAGCAAAUAAUUUCCGAAACUUCUCUCGAAAUCAAACAAAAGAACAUGCAGUUGAAGGGCCACAAGCGACUUCAUUAACAAAACAAACAGCAGCCGCAUUUCUCA
.((((.(((((((((..(((.........(((........)))...((........))...)))...(((((.((.....))..)))))..........)))))))))..))))...... ( -22.50)
>DroSim_CAF1 88762 120 + 1
CAUGCCUUGUUGUUUAAGCAAAUAAUUUCCGAAACUUCUCUCGAAAUCAAACAAAAGAACAUGCAGUUGAAGGGCCACAAGCGACUUCAUUAACAAAACAAACAGCAGCCGCAUUUCUCA
.((((.(((((((((..(((.........(((........)))...((........))...)))...(((((.((.....))..)))))..........)))))))))..))))...... ( -20.20)
>DroEre_CAF1 82501 120 + 1
CAUGCCUUGUUGUUUAAGCAAAUAAUUUCCGAAACUUCUCUCGAAAUCAAACAAAAGAACAUGCAGUUGAAGGGCCACAAGCGACUUCAUUAACAAAACAAACAGCAGCCGCAUUUCUCA
.((((.(((((((((..(((.........(((........)))...((........))...)))...(((((.((.....))..)))))..........)))))))))..))))...... ( -20.20)
>DroYak_CAF1 81831 120 + 1
CAUGCCUUGUUGUUUGAGCAAAUAAUUUCCGAAACUUCUCUCGAAAUCAAACAAAAGAACAUGCAGUUGAAGGGCCACAAGCGACUUCAUUAACAAAACAAACAGCAGCCGCAUUUCUCA
.((((.((((((((((.(((.........(((........)))...((........))...)))...(((((.((.....))..))))).........))))))))))..))))...... ( -23.40)
>consensus
CAUGCCUUGUUGUUUAAGCAAAUAAUUUCCGAAACUUCUCUCGAAAUCAAACAAAAGAACAUGCAGUUGAAGGGCCACAAGCGACUUCAUUAACAAAACAAACAGCAGCCGCAUUUCUCA
.((((.(((((((((..(((.........(((........)))...((........))...)))...(((((.((.....))..)))))..........)))))))))..))))...... (-21.36 = -21.12 +  -0.24)

alignment

secondary structure

dotplot

Window 4

Location	3,259,104 – 3,259,224
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.17
Mean single sequence MFE	-32.02
Consensus MFE	-31.02
Energy contribution	-30.38
Covariance contribution	-0.64
Combinations/Pair	1.07
Mean z-score	-1.21
Structure conservation index	0.97
SVM decision value	0.26
SVM RNA-class probability	0.656421
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3259104 120 - 22407834
GUUGAGGUCCAGUUGGGGGCAAAAUAAAUUGUUGUUGAAAUGAGAAAUGCGGCUGCUGUUUGUUUUGUUAAUGAAGUCGCUUGUGGCCCUUCAACUGCAUGUUCUUUUGUUUGAUUUCGA
.((((((((((((((((((((((((((((.((.((((............)))).)).))))))))))........((((....))))))))))))))((........))...)))))))) ( -30.70)
>DroSec_CAF1 85680 120 - 1
GUUGGGGUCCAGUUGGAGGCAAAAUAAAUUGUUGUUGAAAUGAGAAAUGCGGCUGCUGUUUGUUUUGUUAAUGAAGUCGCUUGUGGCCCUUCAACUGCAUGUUCUUUUGUUUGAUUUCGA
.(((..(((((((((((((((((((((((.((.((((............)))).)).))))))))))........((((....))))))))))))))((........))...)))..))) ( -31.50)
>DroSim_CAF1 88802 120 - 1
GUUGGGGUCCAGUUGGAGGCAAAAUAAAUUGUUGUUGAAAUGAGAAAUGCGGCUGCUGUUUGUUUUGUUAAUGAAGUCGCUUGUGGCCCUUCAACUGCAUGUUCUUUUGUUUGAUUUCGA
.(((..(((((((((((((((((((((((.((.((((............)))).)).))))))))))........((((....))))))))))))))((........))...)))..))) ( -31.50)
>DroEre_CAF1 82541 120 - 1
GUUGGGGUCAAGUUGGGGGCAAAAUAAACUGUUGUUGAAAUGAGAAAUGCGGCUGCUGUUUGUUUUGUUAAUGAAGUCGCUUGUGGCCCUUCAACUGCAUGUUCUUUUGUUUGAUUUCGA
.(((..(((((((((((((((((((((((.((.((((............)))).)).))))))))))........((((....)))))))))))))(((........))).))))..))) ( -33.20)
>DroYak_CAF1 81871 120 - 1
GUUGGGGUCAAGUUGGGGGCAAAAUAAACUGUUGUUGAAAUGAGAAAUGCGGCUGCUGUUUGUUUUGUUAAUGAAGUCGCUUGUGGCCCUUCAACUGCAUGUUCUUUUGUUUGAUUUCGA
.(((..(((((((((((((((((((((((.((.((((............)))).)).))))))))))........((((....)))))))))))))(((........))).))))..))) ( -33.20)
>consensus
GUUGGGGUCCAGUUGGGGGCAAAAUAAAUUGUUGUUGAAAUGAGAAAUGCGGCUGCUGUUUGUUUUGUUAAUGAAGUCGCUUGUGGCCCUUCAACUGCAUGUUCUUUUGUUUGAUUUCGA
.((((((((.(((((((((((((((((((.((.((((............)))).)).))))))))))........((((....)))))))))))))(((........)))..)))))))) (-31.02 = -30.38 +  -0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:54 2006