Locus 7805

Sequence ID	3R_DroMel_CAF1
Location	20,918,826 – 20,918,984
Length	158
Max. P	0.954093

overview

Window 6

Location	20,918,826 – 20,918,944
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.98
Mean single sequence MFE	-22.78
Consensus MFE	-17.56
Energy contribution	-17.40
Covariance contribution	-0.16
Combinations/Pair	1.22
Mean z-score	-1.79
Structure conservation index	0.77
SVM decision value	0.55
SVM RNA-class probability	0.778291
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20918826 118 + 27905053
UAGCAUGCACGCCUAAACGCUGAGAUUAACUAAGGAAGCUAGACACCAAGUUCGUUAAUUAACGAACGAAUAAAAAGAAGACC-CCUUCUU-AUUCUCUGCUCACACCUCAAUUAUCUCA
.(((..............)))(((((......(((.(((.(((......(((((((....)))))))(((((...(((((...-.))))))-))))))))))....))).....))))). ( -25.84)
>DroSec_CAF1 2161 118 + 1
UAGCAUGCACGCCUAAACGCUGGGAUUAACUAAGGAAGCUAGACACCAAGUUCGUUAAUUAACGAACGAAUAAAAAGAAGACC-CCUUCUU-AUUCUCUGCUCACACCUCAAUUAUCUCA
.(((..............)))(((((......(((.(((.(((......(((((((....)))))))(((((...(((((...-.))))))-))))))))))....))).....))))). ( -24.94)
>DroSim_CAF1 10559 119 + 1
UAGCAUGCACGCCUAAACGCUGGGAUUAACUAAGGAAGCUAGACACCAAGUUCGUUAAUUAACGAACGAAUAAAAAGAAGACCCCCUUCUU-AUUCUCUGCUCACACCUCAAUUAUCUCA
.(((..............)))(((((......(((.(((.(((......(((((((....)))))))(((((...(((((.....))))))-))))))))))....))).....))))). ( -24.94)
>DroEre_CAF1 10394 112 + 1
------GCACACCUAAACGCUGGGAUUAACUAAGGAAACUAGACACCAGGUUCGUUAAUUAGCGAGUGAAUAAAAAGAAGACC-CCUACUU-ACUUUCUGCUCACACCUCAAUUAUCUCA
------...............(((((...(((.(....)))).....(((((((((....)))))((((.((.(((((((...-....)))-.)))).)).)))))))).....))))). ( -20.10)
>DroYak_CAF1 8568 119 + 1
UAGCCCGCACUUCUAAACGCUGGGAUUAACUAGGGAAACUAGAUACCAAGUUCUCUAAUUAACGAACGAAUAAAAAGAAGACC-CCUUCUUCUCCUUCUGCUCACACCUUAAUUAUCUCA
...(((((..........)).))).((((.(((((((.((........))))))))).)))).((.((((..(.((((((...-.)))))).)..))).).))................. ( -18.10)
>consensus
UAGCAUGCACGCCUAAACGCUGGGAUUAACUAAGGAAGCUAGACACCAAGUUCGUUAAUUAACGAACGAAUAAAAAGAAGACC_CCUUCUU_AUUCUCUGCUCACACCUCAAUUAUCUCA
.....................(((((......(((..............(((((((....)))))))((.....((((((.....)))))).....))........))).....))))). (-17.56 = -17.40 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	20,918,866 – 20,918,984
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.54
Mean single sequence MFE	-29.11
Consensus MFE	-25.42
Energy contribution	-25.42
Covariance contribution	-0.00
Combinations/Pair	1.12
Mean z-score	-1.65
Structure conservation index	0.87
SVM decision value	1.44
SVM RNA-class probability	0.954093
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20918866 118 + 27905053
AGACACCAAGUUCGUUAAUUAACGAACGAAUAAAAAGAAGACC-CCUUCUU-AUUCUCUGCUCACACCUCAAUUAUCUCAUUGGCAGUCUGGAGAGGGAUCUUUGAGUUAGUAGAGCGUU
.(((.....(((((((....)))))))(((((...(((((...-.))))))-))))...((((((..(((((..(((((.((..(.....)..)))))))..)))))...)).))))))) ( -30.60)
>DroSec_CAF1 2201 116 + 1
AGACACCAAGUUCGUUAAUUAACGAACGAAUAAAAAGAAGACC-CCUUCUU-AUUCUCUGCUCACACCUCAAUUAUCUCAUUGGCAGUCUGGA--GGGAUCUUUGAGUUAGUAGAGCGUU
.(((.....(((((((....)))))))(((((...(((((...-.))))))-))))...((((((..(((((..(((((.(..(....)..).--)))))..)))))...)).))))))) ( -32.80)
>DroSim_CAF1 10599 117 + 1
AGACACCAAGUUCGUUAAUUAACGAACGAAUAAAAAGAAGACCCCCUUCUU-AUUCUCUGCUCACACCUCAAUUAUCUCAUUGGCAGUCUGGA--GGGAUCUUUGAGUUAGUAGAGCGUU
.(((.....(((((((....)))))))(((((...(((((.....))))))-))))...((((((..(((((..(((((.(..(....)..).--)))))..)))))...)).))))))) ( -32.80)
>DroEre_CAF1 10428 116 + 1
AGACACCAGGUUCGUUAAUUAGCGAGUGAAUAAAAAGAAGACC-CCUACUU-ACUUUCUGCUCACACCUCAAUUAUCUCAUUGGCAGUCUGGA--GGGAUCUUUGAGUUAGUAGAGCGUU
.........((((....((((((..((((.((.(((((((...-....)))-.)))).)).))))...((((..(((((.(..(....)..).--)))))..)))))))))).))))... ( -23.70)
>DroYak_CAF1 8608 117 + 1
AGAUACCAAGUUCUCUAAUUAACGAACGAAUAAAAAGAAGACC-CCUUCUUCUCCUUCUGCUCACACCUUAAUUAUCUCAUUGGCAGCCUGGA--GGGAUCUUUGAGUUAGUAGAGCGUU
.........(((((((((((..((((.((.....((((((...-.))))))((((..(((((....................)))))...)))--)...)))))))))))).)))))... ( -25.65)
>consensus
AGACACCAAGUUCGUUAAUUAACGAACGAAUAAAAAGAAGACC_CCUUCUU_AUUCUCUGCUCACACCUCAAUUAUCUCAUUGGCAGUCUGGA__GGGAUCUUUGAGUUAGUAGAGCGUU
.........(((((((....)))))))((.....((((((.....)))))).....)).((((((..(((((..(((((.(..(....)..)...)))))..)))))...)).))))... (-25.42 = -25.42 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:09 2006