Locus 4007

Sequence ID	2L_DroMel_CAF1
Location	11,640,918 – 11,641,030
Length	112
Max. P	0.854993

overview

Window 6

Location	11,640,918 – 11,641,030
Length	112
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	95.55
Mean single sequence MFE	-31.72
Consensus MFE	-26.58
Energy contribution	-26.86
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-1.58
Structure conservation index	0.84
SVM decision value	0.58
SVM RNA-class probability	0.788786
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11640918 112 + 22407834
GCUGGUCCGGCUUGUUAUUUACAGCCGGUUUUCAGAACUUGUGGCAUAAUUUAAGCACCUUGUUUAGCCACUGUUUAUGGUC-UCUCAUGUCACUGGUCCAUCUGCCAGAGUG
.((((.((((((.((.....))))))))....(((((((.(((((((....(((((.....)))))((((.......)))).-....))))))).)))...)))))))).... ( -33.40)
>DroSec_CAF1 94249 112 + 1
GCUGGUCCGGCUUGUUAUUUACAGCCGGUUUUCAGAACUUGUGGCAUAAUUUAAGCACCUUGUUUAGCCACUGUUUAUGGUC-UCUCAUGUCACUGGUCCAUCUGCCAGAGUG
.((((.((((((.((.....))))))))....(((((((.(((((((....(((((.....)))))((((.......)))).-....))))))).)))...)))))))).... ( -33.40)
>DroEre_CAF1 124327 112 + 1
GCUGGUCCGGCUUGUUAUUUACAGCCGGUUUUCAGAAUUUGUGGCAUAAUUUAAGCACCUUGUUUAGCCACUGUUUAUGAUC-UCUCAUGUCACUGUUCCAUCUGCAAGAGUG
.((((.((((((.((.....))))))))...)))).....(((((......(((((.....))))))))))....(((((..-..))))).((((.((.(....).)).)))) ( -28.50)
>DroYak_CAF1 97848 112 + 1
GCUGGUCCGGCUUGUUAUUUACAGCCGGUUUUCAGAAUUUGUGGCAUAAUUUAAGCACCUUGUUUAGCCACUGUUUAUGGUC-UCUCAUGUCACUGGUCCAUCUGCCAGAGUG
.((((.((((((.((.....))))))))...))))...((.(((((.....(((((.....)))))((((.((..(((((..-..))))).)).)))).....))))).)).. ( -31.60)
>DroAna_CAF1 108271 112 + 1
GCCGGUCCAGCUUGUUAUUUACAACCGGUUUUCAGAUCUUGUGGCAUAAUUUAAGCACCUUGUUUAGCCACUGUUUAUGGUCGUCUCAUGUCAGUGGUCCAUCUGCCAGAGG-
((((((......(((.....)))))))))........(((.(((((.....(((((.....)))))(((((((..(((((.....))))).))))))).....))))).)))- ( -31.70)
>consensus
GCUGGUCCGGCUUGUUAUUUACAGCCGGUUUUCAGAACUUGUGGCAUAAUUUAAGCACCUUGUUUAGCCACUGUUUAUGGUC_UCUCAUGUCACUGGUCCAUCUGCCAGAGUG
.((((.((((((.((.....))))))))...)))).((((.(((((.....(((((.....)))))((((.((..(((((.....))))).)).)))).....))))))))). (-26.58 = -26.86 +   0.28)

alignment

secondary structure

dotplot

Window 7

Location	11,640,918 – 11,641,030
Length	112
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	95.55
Mean single sequence MFE	-27.74
Consensus MFE	-24.58
Energy contribution	-24.30
Covariance contribution	-0.28
Combinations/Pair	1.12
Mean z-score	-1.43
Structure conservation index	0.89
SVM decision value	0.80
SVM RNA-class probability	0.854993
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11640918 112 - 22407834
CACUCUGGCAGAUGGACCAGUGACAUGAGA-GACCAUAAACAGUGGCUAAACAAGGUGCUUAAAUUAUGCCACAAGUUCUGAAAACCGGCUGUAAAUAACAAGCCGGACCAGC
....(((((((((((.(((.((..(((...-...)))...)).)))))).....(((...........)))......))))....((((((((.....)).)))))).)))). ( -28.70)
>DroSec_CAF1 94249 112 - 1
CACUCUGGCAGAUGGACCAGUGACAUGAGA-GACCAUAAACAGUGGCUAAACAAGGUGCUUAAAUUAUGCCACAAGUUCUGAAAACCGGCUGUAAAUAACAAGCCGGACCAGC
....(((((((((((.(((.((..(((...-...)))...)).)))))).....(((...........)))......))))....((((((((.....)).)))))).)))). ( -28.70)
>DroEre_CAF1 124327 112 - 1
CACUCUUGCAGAUGGAACAGUGACAUGAGA-GAUCAUAAACAGUGGCUAAACAAGGUGCUUAAAUUAUGCCACAAAUUCUGAAAACCGGCUGUAAAUAACAAGCCGGACCAGC
............(((..(((....((((..-..)))).....(((((.....................))))).....)))....((((((((.....)).)))))).))).. ( -25.60)
>DroYak_CAF1 97848 112 - 1
CACUCUGGCAGAUGGACCAGUGACAUGAGA-GACCAUAAACAGUGGCUAAACAAGGUGCUUAAAUUAUGCCACAAAUUCUGAAAACCGGCUGUAAAUAACAAGCCGGACCAGC
....(((((((((((.(((.((..(((...-...)))...)).)))))).....(((...........)))......))))....((((((((.....)).)))))).)))). ( -28.70)
>DroAna_CAF1 108271 112 - 1
-CCUCUGGCAGAUGGACCACUGACAUGAGACGACCAUAAACAGUGGCUAAACAAGGUGCUUAAAUUAUGCCACAAGAUCUGAAAACCGGUUGUAAAUAACAAGCUGGACCGGC
-...(((((((((((.((((((..(((.......)))...))))))))......(((...........))).....)))))....((((((((.....)).)))))).)))). ( -27.00)
>consensus
CACUCUGGCAGAUGGACCAGUGACAUGAGA_GACCAUAAACAGUGGCUAAACAAGGUGCUUAAAUUAUGCCACAAGUUCUGAAAACCGGCUGUAAAUAACAAGCCGGACCAGC
....((((((((............(((.......))).....(((((.....................)))))....))))....((((((((.....)).)))))).)))). (-24.58 = -24.30 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:00 2006