Locus 8096

Sequence ID	3R_DroMel_CAF1
Location	21,739,153 – 21,739,275
Length	122
Max. P	0.985661

overview

Window 3

Location	21,739,153 – 21,739,258
Length	105
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	86.75
Mean single sequence MFE	-41.26
Consensus MFE	-33.44
Energy contribution	-33.84
Covariance contribution	0.40
Combinations/Pair	1.12
Mean z-score	-2.47
Structure conservation index	0.81
SVM decision value	2.01
SVM RNA-class probability	0.985661
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21739153 105 + 27905053
GGAGUGGCCUGAGUGGGUGAAAACUGUUUACUAGGGCAGGUACCACACAUGGCAUGUAAUCCUGCCAGGAUGUGUGGUGCAUGGGCUCCGCUCGCUGGUCUAUA-------U
(((.((((..((((((((.....((((((....))))))(((((((((((((((.(....).)))))...))))))))))....)).)))))))))).)))...-------. ( -44.50)
>DroSec_CAF1 5856 105 + 1
GGAGUGGCCUGAGUGGGUGAAAACUGUUUACUAGGGCAGGUACCACACAUGGCAAGUAAUCCUGCCAGAAUGUGGGGUGCAUGGGCUCGGCUCACUGGUCUAUA-------U
..(((((((..(((((((....)))...)))).((((..(((((.(((((((((........)))))...)))).)))))....))))))).))))........-------. ( -38.10)
>DroSim_CAF1 6040 105 + 1
GGAGUGGCCUGAGUGGGUGAAAACUGUUUACUAGGGCAGGUACCACACAUGGCAUGUAAUCCUGCCAGAAUGUGGGGUGCACACGCUCGGCUCGCUGGUCUAUA-------U
..(((((((.(((((.((.....((((((....))))))(((((.(((((((((.(....).)))))...)))).))))))).)))))))).))))........-------. ( -40.10)
>DroEre_CAF1 14233 107 + 1
GGAGUGGCCUGAGUGGGUGAAAACGGUUUACUAGAGCAGGUACCACACAUGGCAUGUAAUCCGGCCAGGAUGUGGGGUGCAUUGG-----CUCGCUGGCCUAUUCAUAAUGU
.((((((((..(((.((((((.....)))))).((((..(((((.((((((((.((.....))))))...)))).)))))....)-----)))))))))).))))....... ( -38.10)
>DroYak_CAF1 5957 107 + 1
GGAGUGGCCUGAGUGGGUGAAAACGGUUUACUAGAGCAGGCACCACACAUGGCAUGUAAUCCAGCCAGGAUGUGUGGUGCAUGGG-----CUCGCUGGCCUAUUCAUGAUGU
.((((((((..(((.((((((.....)))))).((((..((((((((((((((.((.....))))))...))))))))))....)-----)))))))))).))))....... ( -45.50)
>consensus
GGAGUGGCCUGAGUGGGUGAAAACUGUUUACUAGGGCAGGUACCACACAUGGCAUGUAAUCCUGCCAGGAUGUGGGGUGCAUGGGCUC_GCUCGCUGGUCUAUA_______U
.....((((..(((((((.....((((((....))))))(((((.(((((((((.(....).)))))...)))).))))).........)))))))))))............ (-33.44 = -33.84 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	21,739,185 – 21,739,275
Length	90
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	79.87
Mean single sequence MFE	-31.34
Consensus MFE	-21.38
Energy contribution	-22.40
Covariance contribution	1.02
Combinations/Pair	1.12
Mean z-score	-2.05
Structure conservation index	0.68
SVM decision value	1.07
SVM RNA-class probability	0.911025
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21739185 90 + 27905053
AGGGCAGGUACCACACAUGGCAUGUAAUCCUGCCAGGAUGUGUGGUGCAUGGGCUCCGCUCGCUGGUCUAUA-------UGGUAUAAUAUGGUACAU
..(((..(((((((((((((((.(....).)))))...))))))))))..((((...))))))).(((((((-------(......)))))).)).. ( -34.50)
>DroSec_CAF1 5888 90 + 1
AGGGCAGGUACCACACAUGGCAAGUAAUCCUGCCAGAAUGUGGGGUGCAUGGGCUCGGCUCACUGGUCUAUA-------UGGUAUAAUAUGGUACAU
(((.((((((((.(((((((((........)))))...)))).))))).(((((...)))))))).)))...-------..((((......)))).. ( -30.00)
>DroSim_CAF1 6072 90 + 1
AGGGCAGGUACCACACAUGGCAUGUAAUCCUGCCAGAAUGUGGGGUGCACACGCUCGGCUCGCUGGUCUAUA-------UGGUAUAAUAUGGUACAC
.......((((((...(((.((((((.....(((((...((.(((((....))))).))...))))).))))-------)).)))....)))))).. ( -29.60)
>DroEre_CAF1 14265 87 + 1
AGAGCAGGUACCACACAUGGCAUGUAAUCCGGCCAGGAUGUGGGGUGCAUUGG-----CUCGCUGGCCUAUUCAUAAUGUGGUACAUUUUCG-----
.(((...((((((((.(((((((.(.((((.....))))...).))))...((-----((....))))....)))..))))))))...))).----- ( -29.80)
>DroYak_CAF1 5989 92 + 1
AGAGCAGGCACCACACAUGGCAUGUAAUCCAGCCAGGAUGUGUGGUGCAUGGG-----CUCGCUGGCCUAUUCAUGAUGUGUUACAUUUUCGUACAU
..((((.((((((((((((((.((.....))))))...))))))))))(((((-----((....)))))))........)))).............. ( -32.80)
>consensus
AGGGCAGGUACCACACAUGGCAUGUAAUCCUGCCAGGAUGUGGGGUGCAUGGGCUC_GCUCGCUGGUCUAUA_______UGGUAUAAUAUGGUACAU
(((.((((((((.(((((((((.(....).)))))...)))).))))).(((((...)))))))).)))............................ (-21.38 = -22.40 +   1.02)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:02:32 2006