Locus 2153

Sequence ID	3L_DroMel_CAF1
Location	5,856,058 – 5,856,188
Length	130
Max. P	0.560929

overview

Window 8

Location	5,856,058 – 5,856,149
Length	91
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	87.37
Mean single sequence MFE	-35.62
Consensus MFE	-25.03
Energy contribution	-24.70
Covariance contribution	-0.33
Combinations/Pair	1.11
Mean z-score	-3.29
Structure conservation index	0.70
SVM decision value	0.05
SVM RNA-class probability	0.560929
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5856058 91 - 23771897
AGCAACUCUCCGCA------CUCGCGGCACUUGGCCCAUCUGUCCUGAUUCUGCUCGGAGUCUGUUCAGAUUCAGGUCCUGC-AGAGAGCAC---CACCCU
...........((.------(((((((.((((((...(((((..(.((((((....)))))).)..))))))))))).))))-.))).))..---...... ( -30.70)
>DroPse_CAF1 68647 93 - 1
----GUUCUCCGCACU----CUCGCGGCACUCGGCCCAUCUGUCCAGAUUCUGCACGGAGUCUGUUCAGAUUCUGCCUCUGCCGGAGAGCACGGACACCCU
----....((((..((----(((.(((((...(((..(((((..((((((((....))))))))..)))))...)))..))))))))))..))))...... ( -44.70)
>DroSim_CAF1 46810 91 - 1
AGCAACUCUCCGCA------CUCGCGGCACUUGGCCCAUCUGUCCUGAUUCUGCUCGGAGUCUGUUCAGAUUCAGGUCCUGC-AGAGAGCAC---CACCCU
...........((.------(((((((.((((((...(((((..(.((((((....)))))).)..))))))))))).))))-.))).))..---...... ( -30.70)
>DroEre_CAF1 66728 91 - 1
AGCAACUCUCCGCA------CUCGCGGCACUUGGCCCAUCUGUCCUGAUUCUGCUCGGAGUCUGUUCAGAUUCAGGUCCUGC-AGAGAGCAC---CACCCU
...........((.------(((((((.((((((...(((((..(.((((((....)))))).)..))))))))))).))))-.))).))..---...... ( -30.70)
>DroYak_CAF1 69353 97 - 1
AGCAACUCUCCGCACUCGCACUCGCGGCACUUGGCCCAUCUGUCCUGAUUCUGCUCGGAGUCUGUUCAGAUUCAGGUCCUGC-AGAGAGCAC---CACCCU
.....(((((.((....))....((((.((((((...(((((..(.((((((....)))))).)..))))))))))).))))-.)))))...---...... ( -32.20)
>DroPer_CAF1 67666 93 - 1
----GUUCUCCGCACU----CUCGCGGCACUCGGCCCAUCUGUCCAGAUUCUGCACGGAGUCUGUUCAGAUUCUGCCUCUGCCGGAGAGCACGGACACCCU
----....((((..((----(((.(((((...(((..(((((..((((((((....))))))))..)))))...)))..))))))))))..))))...... ( -44.70)
>consensus
AGCAACUCUCCGCA______CUCGCGGCACUUGGCCCAUCUGUCCUGAUUCUGCUCGGAGUCUGUUCAGAUUCAGGUCCUGC_AGAGAGCAC___CACCCU
.....((((((((..........)))(((...((((.(((((..(.((((((....)))))).)..)))))...)))).)))..)))))............ (-25.03 = -24.70 +  -0.33)

alignment

secondary structure

dotplot

Window 9

Location	5,856,077 – 5,856,188
Length	111
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	89.43
Mean single sequence MFE	-32.08
Consensus MFE	-25.04
Energy contribution	-25.10
Covariance contribution	0.06
Combinations/Pair	1.08
Mean z-score	-2.42
Structure conservation index	0.78
SVM decision value	0.04
SVM RNA-class probability	0.553128
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5856077 111 - 23771897
AUUCUCGUAUUCUCAUAUUGUCCCAUUCA-AUUGGGAAAAAGCAACUCUCCGCA------CUCGCGGCACUUGGCCCAUCUGUCCUGAUUCUGCUCGGAGUCUGUUCAGAUUCAGGUC
....................(((((....-..)))))............((((.------...)))).((((((...(((((..(.((((((....)))))).)..))))))))))). ( -29.50)
>DroPse_CAF1 68670 109 - 1
AUUCUCGUAUUCUCAUAUUGUCCCAUUCAGAUUGGGAGA-----GUUCUCCGCACU----CUCGCGGCACUCGGCCCAUCUGUCCAGAUUCUGCACGGAGUCUGUUCAGAUUCUGCCU
....................(((((.......)))))((-----((...((((...----...)))).))))(((..(((((..((((((((....))))))))..)))))...))). ( -39.50)
>DroSec_CAF1 63268 111 - 1
ACUCUCGUAUUCUCAUAUUGUCCCAUUCA-AUUUGGAAAAAGCAACUCUCCGCA------CUCGCGGCACUUGGCCCAUCUGUCCUGAUUCUGCUCGGAGUCUGUUCAGAUUCAGGUC
.........(((.((.((((.......))-)).)))))...........((((.------...)))).((((((...(((((..(.((((((....)))))).)..))))))))))). ( -25.90)
>DroEre_CAF1 66747 111 - 1
AUUUUCGUAUUCUCAUAUUGUCCCAUUCA-AUUGGGAAAAAGCAACUCUCCGCA------CUCGCGGCACUUGGCCCAUCUGUCCUGAUUCUGCUCGGAGUCUGUUCAGAUUCAGGUC
....................(((((....-..)))))............((((.------...)))).((((((...(((((..(.((((((....)))))).)..))))))))))). ( -29.50)
>DroYak_CAF1 69372 117 - 1
AUUCUCGUAUUCUCAUAUUGUCCCAUUCA-AUUGGGAAAAAGCAACUCUCCGCACUCGCACUCGCGGCACUUGGCCCAUCUGUCCUGAUUCUGCUCGGAGUCUGUUCAGAUUCAGGUC
....................(((((....-..)))))............((((..........)))).((((((...(((((..(.((((((....)))))).)..))))))))))). ( -28.60)
>DroPer_CAF1 67689 109 - 1
AUUCUCGUAUUCUCAUAUUGUCCCAUUCAGAUUGGGAGA-----GUUCUCCGCACU----CUCGCGGCACUCGGCCCAUCUGUCCAGAUUCUGCACGGAGUCUGUUCAGAUUCUGCCU
....................(((((.......)))))((-----((...((((...----...)))).))))(((..(((((..((((((((....))))))))..)))))...))). ( -39.50)
>consensus
AUUCUCGUAUUCUCAUAUUGUCCCAUUCA_AUUGGGAAAAAGCAACUCUCCGCA______CUCGCGGCACUUGGCCCAUCUGUCCUGAUUCUGCUCGGAGUCUGUUCAGAUUCAGGUC
....................(((((.......)))))............((((..........)))).....((((.(((((..(.((((((....)))))).)..)))))...)))) (-25.04 = -25.10 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:39 2006