Locus 7694

Sequence ID	3L_DroMel_CAF1
Location	20,594,688 – 20,594,871
Length	183
Max. P	0.921265

overview

Window 9

Location	20,594,688 – 20,594,802
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.56
Mean single sequence MFE	-34.84
Consensus MFE	-31.60
Energy contribution	-32.40
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	0.91
SVM decision value	0.80
SVM RNA-class probability	0.854158
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20594688 114 - 23771897
UUUUAUGGCCCGGCCGUUUCAUUUUGUUUUGGAACGGUGCGAGGUUAUGUGUGCAAAACAAUUAUUCCGCAAUUAAACAGUUUGCACUUCGCCAA------GAGAGAGCGGGCAGGUCCA
.......((((((((((((((........)))))))))(((((((....(((.....)))........((((.........)))))))))))...------.......)))))....... ( -36.20)
>DroSec_CAF1 39406 114 - 1
UUUUAUGGCCCGGCCGUUUCAUUUUGUUUUGGAACGGUGCGAGGUUAUGUGUGCAAAACAAUUAUUCCGCAAUUAAACAGUUUGCACUUCGCCAA------GAGAGAGCGGGCAGGUCCA
.......((((((((((((((........)))))))))(((((((....(((.....)))........((((.........)))))))))))...------.......)))))....... ( -36.20)
>DroAna_CAF1 61882 120 - 1
UUUUAUGGCCAGGCCGUUUCAUUUUGUUUUGGAACGGUGCGAGGUUAUGUGUGCAAAACAAUUAUUCCGCAAUUAAACAGUUUGCACUUCGCCAAGAAAAAGAGAGAGCGACCAGGUCCA
......((((.((.(((((..((((.((((((...(((((((.(((...((((.((........)).))))....)))...)))))))...))))))..))))..))))).)).)))).. ( -32.60)
>DroSim_CAF1 32858 114 - 1
UUUUAUGGCCCGGCCGUUUCAUUUUGUUUUGGAACGGUGCGAGGUUAUGUGUGCAAAACAAUUAUUCCGCAAUUAAACAGUUUGCACUUCGCCAA------GAGAGAGCGGGCAGGUCCA
.......((((((((((((((........)))))))))(((((((....(((.....)))........((((.........)))))))))))...------.......)))))....... ( -36.20)
>DroEre_CAF1 32096 113 - 1
UUUUAUGGC-CGGCCGUUUCAUUUUGUUUUGGAACGGUGCGAGGUUAUGUGUGCAAAACAAUUAUUCCGCAAUUAAACAGUUUGCACUUCGCCAA------GAGAGAGCGGGCAGGUCCA
......(((-(.(((((((((........)))))))))(((..((....(((.....)))...))..))).........((((((.((((.....------)).)).)))))).)))).. ( -33.00)
>consensus
UUUUAUGGCCCGGCCGUUUCAUUUUGUUUUGGAACGGUGCGAGGUUAUGUGUGCAAAACAAUUAUUCCGCAAUUAAACAGUUUGCACUUCGCCAA______GAGAGAGCGGGCAGGUCCA
.......((((((((((((((........)))))))))(((((((....(((.....)))........((((.........)))))))))))................)))))....... (-31.60 = -32.40 +   0.80)

alignment

secondary structure

dotplot

Window 0

Location	20,594,722 – 20,594,842
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.00
Mean single sequence MFE	-30.38
Consensus MFE	-29.24
Energy contribution	-29.24
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.55
Structure conservation index	0.96
SVM decision value	1.14
SVM RNA-class probability	0.921265
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20594722 120 - 23771897
AGAAUACCUUUUGUGGUCAUUAAUUCGCACUUAAUAUGCUUUUUAUGGCCCGGCCGUUUCAUUUUGUUUUGGAACGGUGCGAGGUUAUGUGUGCAAAACAAUUAUUCCGCAAUUAAACAG
..........((((((....(((((.((((.............((((((((((((((((((........))))))))).)).))))))).)))).....)))))..))))))........ ( -30.94)
>DroSec_CAF1 39440 120 - 1
AGAAUACCUUUUGUGGUCAUUAAUUCGCACUUAAUAUGCUUUUUAUGGCCCGGCCGUUUCAUUUUGUUUUGGAACGGUGCGAGGUUAUGUGUGCAAAACAAUUAUUCCGCAAUUAAACAG
..........((((((....(((((.((((.............((((((((((((((((((........))))))))).)).))))))).)))).....)))))..))))))........ ( -30.94)
>DroAna_CAF1 61922 120 - 1
AGAAAACCUUUUGUGGUCAUUAAUUCGCACUUAAUAUGCUUUUUAUGGCCAGGCCGUUUCAUUUUGUUUUGGAACGGUGCGAGGUUAUGUGUGCAAAACAAUUAUUCCGCAAUUAAACAG
.............(((((((......(((.......))).....))))))).(((((((((........)))))))))(((..((....(((.....)))...))..))).......... ( -29.70)
>DroSim_CAF1 32892 120 - 1
AGAAUACCUUUUGUGGUCAUUAAUUCGCACUUAAUAUGCUUUUUAUGGCCCGGCCGUUUCAUUUUGUUUUGGAACGGUGCGAGGUUAUGUGUGCAAAACAAUUAUUCCGCAAUUAAACAG
..........((((((....(((((.((((.............((((((((((((((((((........))))))))).)).))))))).)))).....)))))..))))))........ ( -30.94)
>DroEre_CAF1 32130 119 - 1
AGAAUACCUUUUGUGGUCAUUAAUUCGCACUUAAUAUGCUUUUUAUGGC-CGGCCGUUUCAUUUUGUUUUGGAACGGUGCGAGGUUAUGUGUGCAAAACAAUUAUUCCGCAAUUAAACAG
.(((((..(((((((..(((...(((((.........(((......)))-..(((((((((........))))))))))))))...)))..)))))))....)))))............. ( -29.40)
>consensus
AGAAUACCUUUUGUGGUCAUUAAUUCGCACUUAAUAUGCUUUUUAUGGCCCGGCCGUUUCAUUUUGUUUUGGAACGGUGCGAGGUUAUGUGUGCAAAACAAUUAUUCCGCAAUUAAACAG
..........((((((.(((...(((((.........(((......)))...(((((((((........))))))))))))))...)))(((.....)))......))))))........ (-29.24 = -29.24 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	20,594,762 – 20,594,871
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.12
Mean single sequence MFE	-27.72
Consensus MFE	-19.54
Energy contribution	-19.74
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.31
Structure conservation index	0.70
SVM decision value	0.39
SVM RNA-class probability	0.716484
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20594762 109 - 23771897
CGUUUUUG-----------CAGCGCUCUUUUUUCGCUCAAAGAAUACCUUUUGUGGUCAUUAAUUCGCACUUAAUAUGCUUUUUAUGGCCCGGCCGUUUCAUUUUGUUUUGGAACGGUGC
..((((((-----------.((((.........))))))))))........((.((((((......(((.......))).....))))))))(((((((((........))))))))).. ( -27.70)
>DroSec_CAF1 39480 109 - 1
CGUUUUUG-----------CAGCGCUCUUUUUUCGCUCAAAGAAUACCUUUUGUGGUCAUUAAUUCGCACUUAAUAUGCUUUUUAUGGCCCGGCCGUUUCAUUUUGUUUUGGAACGGUGC
..((((((-----------.((((.........))))))))))........((.((((((......(((.......))).....))))))))(((((((((........))))))))).. ( -27.70)
>DroAna_CAF1 61962 110 - 1
CGUUUUUCUUCCUCAACGGCUGAGCU----------UUAAAGAAAACCUUUUGUGGUCAUUAAUUCGCACUUAAUAUGCUUUUUAUGGCCAGGCCGUUUCAUUUUGUUUUGGAACGGUGC
.(.(((((((.((((.....))))..----------...))))))).).....(((((((......(((.......))).....))))))).(((((((((........))))))))).. ( -27.30)
>DroSim_CAF1 32932 109 - 1
CGUUUUUG-----------CAGCGCUCUUUUUUCGCUCAAAGAAUACCUUUUGUGGUCAUUAAUUCGCACUUAAUAUGCUUUUUAUGGCCCGGCCGUUUCAUUUUGUUUUGGAACGGUGC
..((((((-----------.((((.........))))))))))........((.((((((......(((.......))).....))))))))(((((((((........))))))))).. ( -27.70)
>DroEre_CAF1 32170 108 - 1
CGUUUUUG-----------CAGCGCUCUUUUUUCGCUCAAAGAAUACCUUUUGUGGUCAUUAAUUCGCACUUAAUAUGCUUUUUAUGGC-CGGCCGUUUCAUUUUGUUUUGGAACGGUGC
..((((((-----------.((((.........))))))))))..........(((((((......(((.......))).....)))))-))(((((((((........))))))))).. ( -28.20)
>consensus
CGUUUUUG___________CAGCGCUCUUUUUUCGCUCAAAGAAUACCUUUUGUGGUCAUUAAUUCGCACUUAAUAUGCUUUUUAUGGCCCGGCCGUUUCAUUUUGUUUUGGAACGGUGC
.......................((.............................((((((......(((.......))).....))))))..(((((((((........))))))))))) (-19.54 = -19.74 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:08 2006