Locus 664

Sequence ID 3L_DroMel_CAF1
Location 1,977,111 – 1,977,328
Length 217
Max. P 0.704833
window1014 window1015

overview

Window 4

Location 1,977,111 – 1,977,228
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.45
Mean single sequence MFE -24.50
Consensus MFE -16.80
Energy contribution -16.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.69
SVM decision value 0.36
SVM RNA-class probability 0.704833
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1977111 117 + 23771897
--GACUUGGGACUUAAUGUGUAAUGUGUAAGCCGCAAACAUAAUAAAUAAGCUUAAGUU-UGGUCAAUUUGACAAAAUUGUUUGAGCUUAGCACAGUAUGGUGGUGGUCUUCAAGGUGAG
--..(((((((((......(((.(((((((((..((((((.......(((((....)))-))(((.....))).....)))))).)))).))))).)))......)))).)))))..... ( -30.00)
>DroPse_CAF1 36251 103 + 1
----CCAGGGACUUAAUGUGUAAUGUGUAAGCCGCAAACAUAAUAAAUAAGCUUAAGUUUUGGUCAAUUUGACAAAAUUGUUUGAGCUUAGUGCCA-------------CGAAAGGUGAG
----...((.(((((.(((((..((((.....)))).))))).))).(((((((((((((((.((.....))))))))...))))))))))).)).-------------(....)..... ( -24.30)
>DroWil_CAF1 43141 109 + 1
CUGGCCCAGGUCUUAAUGUGUAAUGUGUAAGCCGCAAACAUAAUAAAUAAGCUUAAGUU-UGGUCAAUUUGACAAAAUUGUUUGAGCUUAGCGAAAAGCUUUCGUUUUCU----------
..(((....)))(((.(((((..((((.....)))).))))).)))....(((.(((((-..(.((((((....)))))).)..))))))))(((((.......))))).---------- ( -23.00)
>DroYak_CAF1 28902 104 + 1
--GACUUGGGACUUAAUGUGUAAUGUGUAAGCCGCAAACAUAAUAAAUAAGCUUAAGUU-UGGUCAAUUUGACAAAAUUGUUUGAGCUUAGCCAAG-------------UUUAAGGUGAG
--(((((((...(((.(((((..((((.....)))).))))).))).((((((((((((-(.(((.....))).))))...))))))))).)))))-------------))......... ( -25.80)
>DroAna_CAF1 24564 96 + 1
--GACUAUGGACUUAAUGUGUAAUGUGUAAGCCGCAAACAUAAUAAAUAAGCUUAAGUU-UGGUCAAUUUGACAAAAUUGUUUGAGCUUAGCGAAAUAU---------------------
--..........(((.(((((..((((.....)))).))))).)))....(((.(((((-..(.((((((....)))))).)..)))))))).......--------------------- ( -19.60)
>DroPer_CAF1 35780 103 + 1
----CCAGGGACUUAAUGUGUAAUGUGUAAGCCGCAAACAUAAUAAAUAAGCUUAAGUUUUGGUCAAUUUGACAAAAUUGUUUGAGCUUAGUGCCA-------------CGAAAGGUGAG
----...((.(((((.(((((..((((.....)))).))))).))).(((((((((((((((.((.....))))))))...))))))))))).)).-------------(....)..... ( -24.30)
>consensus
__GACCAGGGACUUAAUGUGUAAUGUGUAAGCCGCAAACAUAAUAAAUAAGCUUAAGUU_UGGUCAAUUUGACAAAAUUGUUUGAGCUUAGCGAAA_____________U__AAGGUGAG
............(((.(((((..((((.....)))).))))).))).((((((((((.....(((.....))).......)))))))))).............................. (-16.80 = -16.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,977,228 – 1,977,328
Length 100
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 75.46
Mean single sequence MFE -27.88
Consensus MFE -18.44
Energy contribution -18.25
Covariance contribution -0.19
Combinations/Pair 1.18
Mean z-score -1.13
Structure conservation index 0.66
SVM decision value 0.12
SVM RNA-class probability 0.592803
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1977228 100 + 23771897
GGUGGUG--GAGGGGUGGUCAAG-------------CGGAAGGGCAGUUAGGGUGGCUCAAAUAAAUCAGCUGCCAUUUAAGCUGCCAGCGUUAGCCCCAUAAGCGAAUUUAUUA
.......--..(((((......(-------------(.....(((((((..((((((...............))))))..))))))).))....)))))................ ( -32.66)
>DroSec_CAF1 28274 100 + 1
GAUGAGGAUGAGGGGCGGUCCAG-------------CGGAAGGGCAGUUAGGGUGGCUCAAAUAAAUCAGCUGCCAUUUAAUCUGCCAGCGUUAGC--CAUAAGCGAAUUUAUCA
((((((..((...(((......(-------------(.....((((((((.((..(((..........)))..))...))).))))).))....))--).....))..)))))). ( -29.90)
>DroSim_CAF1 42442 100 + 1
GAUGGGGAUGAGGGGCGGUCAAG-------------CGGAAGGGCAGUUAGGGUGGCUCAAAUAAAUCAGCUGCCAUUUAAUCUGCCAGCGUUAGC--CAUAAGCGAAUUUAUUA
.((((.((((...(((((.....-------------(....)((((((...(((...........))).)))))).......)))))..))))..)--))).............. ( -27.40)
>DroEre_CAF1 33866 102 + 1
GG----------GUGUGGUCAAGUUGAAUGGGGAG-GGGAGAGGCAGUUAGGGCGGCUCAAAUAAAUCAGCUGCCAUUUAAUCUGCCAGCGUUAGC--CAUAAGCGAAUUUAUUA
..----------..........(((..((((..((-.(....((((((((.(((((((..........)))))))...))).)))))..).))..)--))).))).......... ( -25.40)
>DroYak_CAF1 29006 101 + 1
GG----------G--UGGUCAAGUUGGCUGAGGCGGGGGAAAGGCAGUUAGGGCGGCUCAAAUAAAUCAGCUGCCAUUUAAUCUGCCAGCGUUAGC--CAUAAGCGAAUUUAUUA
..----------.--.....(((((.(((..(((..(.(...((((((((.(((((((..........)))))))...))).)))))..).)..))--)...))).))))).... ( -33.90)
>DroPer_CAF1 35883 75 + 1
G--------------------------------------AGAGGCGUGCAGGGCAGAUCCUAUAAAUCAGCUGCCAUUUAAUCUGCCAGCGUUAGC--CAUAAGCGAAUUUAUUA
.--------------------------------------...(((.(((..(((((((....(((((........)))))))))))).)))...))--)................ ( -18.00)
>consensus
GG__________GGGUGGUCAAG_____________CGGAAAGGCAGUUAGGGCGGCUCAAAUAAAUCAGCUGCCAUUUAAUCUGCCAGCGUUAGC__CAUAAGCGAAUUUAUUA
..........................................(((((....(((((((..........))))))).......))))).((.(((......))))).......... (-18.44 = -18.25 +  -0.19)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:58 2006