Locus 1444

Sequence ID 3L_DroMel_CAF1
Location 4,178,714 – 4,178,807
Length 93
Max. P 0.998987
window2250 window2251

overview

Window 0

Location 4,178,714 – 4,178,807
Length 93
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 71.27
Mean single sequence MFE -26.97
Consensus MFE -15.30
Energy contribution -15.26
Covariance contribution -0.04
Combinations/Pair 1.22
Mean z-score -2.65
Structure conservation index 0.57
SVM decision value 3.31
SVM RNA-class probability 0.998987
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4178714 93 + 23771897
A----GAGGCAGUGAUGGAGUGUAACUAACUAC--------------UGAUGAGU-CUGAUCCCAGUUUAAGUUUAAGUGACCCAUCACUGCCCCAUAACAGUUUGGCCCAC
.----..(((((((((((.((...(((((((((--------------((..((..-....)).))))...))))..))).)))))))))))))(((........)))..... ( -29.20)
>DroSec_CAF1 24400 93 + 1
A----GAGGCAGUGAUGGAGUGAAACUAACUGC--------------UGAUGAAU-CAGAUCCCAACUUAAGUUUAACUGACCCAUCACUGCCCUAUAACUGUUUGGCCUAC
(----(.(((((((((((.((.(....((((.(--------------(((....)-)))...........))))....).)))))))))))))))................. ( -27.30)
>DroSim_CAF1 28931 93 + 1
A----AAGGCAGUGAUGGAGUGUAACUAACUGC--------------UGAUAAAU-CAGAUCCCAACUUAAGUUUAACUGACCCAUCACUGCCCCAUAAUUGUGUGGCCCAC
.----..(((((((((((.((......((((.(--------------(((....)-)))...........))))......)))))))))))))(((((....)))))..... ( -28.90)
>DroEre_CAF1 24797 112 + 1
GGACUGAGCCAGUGAUGGAGUGUAACUACCAACCGCCGUAACAAGCCUAAUGUAACAGAUUUCCCACCUAAGUUUAUUACUCCAAUCACUGCCCCAUAAUUGUUUGGCCCAC
((.(..((((((((((((((((.((((..........((.(((.......))).)).(......).....))))...)))))).)))))))..........)))..).)).. ( -25.20)
>DroYak_CAF1 28837 86 + 1
A----AGGGCAGUGAUGGAGUGUAACUACUAGU------------------U----CAAUUUCCUACCUAUGUUCAAUUCUCCAAUCGCUGCCCCAUAAUUGUUUGGCCCAC
.----.((((((((((((((.......(((((.------------------.----...........))).))......)))).)))))))))).................. ( -24.24)
>consensus
A____GAGGCAGUGAUGGAGUGUAACUAACUGC______________UGAUGAAU_CAGAUCCCAACUUAAGUUUAACUGACCCAUCACUGCCCCAUAAUUGUUUGGCCCAC
.......(((((((((((((.....))......................................((....)).........)))))))))))(((........)))..... (-15.30 = -15.26 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,178,714 – 4,178,807
Length 93
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 71.27
Mean single sequence MFE -29.78
Consensus MFE -16.84
Energy contribution -16.72
Covariance contribution -0.12
Combinations/Pair 1.39
Mean z-score -2.24
Structure conservation index 0.57
SVM decision value 2.30
SVM RNA-class probability 0.991968
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4178714 93 - 23771897
GUGGGCCAAACUGUUAUGGGGCAGUGAUGGGUCACUUAAACUUAAACUGGGAUCAG-ACUCAUCA--------------GUAGUUAGUUACACUCCAUCACUGCCUC----U
.................(((((((((((((((.(((..((((...(((((((....-..)).)))--------------)))))))))...)).)))))))))))))----. ( -31.50)
>DroSec_CAF1 24400 93 - 1
GUAGGCCAAACAGUUAUAGGGCAGUGAUGGGUCAGUUAAACUUAAGUUGGGAUCUG-AUUCAUCA--------------GCAGUUAGUUUCACUCCAUCACUGCCUC----U
..................((((((((((((...(((.(((((...(((((((....-..)).)))--------------))....))))).))))))))))))))).----. ( -31.50)
>DroSim_CAF1 28931 93 - 1
GUGGGCCACACAAUUAUGGGGCAGUGAUGGGUCAGUUAAACUUAAGUUGGGAUCUG-AUUUAUCA--------------GCAGUUAGUUACACUCCAUCACUGCCUU----U
(((.....)))......((((((((((((((((((((.(((....)))..)).)))-)).....(--------------((.....))).....)))))))))))))----. ( -30.60)
>DroEre_CAF1 24797 112 - 1
GUGGGCCAAACAAUUAUGGGGCAGUGAUUGGAGUAAUAAACUUAGGUGGGAAAUCUGUUACAUUAGGCUUGUUACGGCGGUUGGUAGUUACACUCCAUCACUGGCUCAGUCC
..((((..........((((.(((((((.(((((...........((((.((..(((......)))..)).))))(((........)))..)))))))))))).)))))))) ( -32.30)
>DroYak_CAF1 28837 86 - 1
GUGGGCCAAACAAUUAUGGGGCAGCGAUUGGAGAAUUGAACAUAGGUAGGAAAUUG----A------------------ACUAGUAGUUACACUCCAUCACUGCCCU----U
.................(((((((.(((.((((.....(((.(((...........----.------------------.)))...)))...))))))).)))))))----. ( -23.02)
>consensus
GUGGGCCAAACAAUUAUGGGGCAGUGAUGGGUCAAUUAAACUUAAGUUGGGAUCUG_AUUCAUCA______________GCAGUUAGUUACACUCCAUCACUGCCUC____U
.................((((((((((((((.......((((..(((((...............................)))))))))....))))))))))))))..... (-16.84 = -16.72 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:52 2006