Locus 4408

Sequence ID X_DroMel_CAF1
Location 11,629,016 – 11,629,142
Length 126
Max. P 0.818519
window7243 window7244

overview

Window 3

Location 11,629,016 – 11,629,111
Length 95
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 79.62
Mean single sequence MFE -23.04
Consensus MFE -19.67
Energy contribution -19.28
Covariance contribution -0.39
Combinations/Pair 1.27
Mean z-score -1.45
Structure conservation index 0.85
SVM decision value 0.67
SVM RNA-class probability 0.818519
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11629016 95 - 22224390
GCAUUUUAAAAUUGGCUGCUGCCUGCAGCUGAAUUUGAUAAGCUAAGCUGUGUAUUUUAAAUCCAUAUAGCCUAUGU-AUGUGAUGAUCA------------AGUUGA
((...(((((.(..(((((.....)))))..).)))))...))..((((.((.(((....(((((((((.....)))-))).))))))))------------)))).. ( -22.60)
>DroPse_CAF1 2930 91 - 1
GCAUUUUGAAAUUGGCUGCUGCCUGCAGCUGAAUUUGAUAAGCUAAGCUGUGAAUUUUAAAGCCAUACAGCCUGGUU-UU-U---GGUUC------------AUUGGU
((...(..((.(..(((((.....)))))..).))..)...))....(.(((((((..(((((((.......)))))-))-.---)))))------------)).).. ( -26.70)
>DroGri_CAF1 5144 107 - 1
GCAUUUUGAAAUUGGCUGCUGCCUGCAGCUGAAUUUGAUAAGCUAAGCUGUGAAUUUUAAAGCCGUACAGACUGAAUUAU-CGUUGUUUAUAUAGGUGCAACAGUUGU
((((((.(((.(..(((((.....)))))..).)))(((((....(((((((.............))))).))...))))-)...........))))))......... ( -24.82)
>DroEre_CAF1 1935 94 - 1
GCAUUUUAAAAUUGGCUGCUGCCUGCAGCUGAAUUUGAUAAGCUAAGCUGUGUAUUUUAAAGCCAUACAGCCUAUUU-GU-UGUUGUUUA------------AGUUGU
(((.((((((.(..(((((.....)))))..)....((((((.((.(((((((...........))))))).)))))-))-)....))))------------)).))) ( -23.70)
>DroWil_CAF1 9310 91 - 1
GCAUUUUGAAAUUAGCUGCUGCCUGUAGUUGAAUUUGAUAAGCUAAGCUGUGUAUUUUAAAGCCGUACAGCCUAACG-AA-G---GACGA------------AGAAGA
((...(..((.((((((((.....)))))))).))..)...))...((((((.............))))))....(.-..-.---)....------------...... ( -17.62)
>DroYak_CAF1 1642 86 - 1
GCAUUUUAAAAUUGGCUGCUGCCUGCAGCUGAAUUUGAUAAGCUAAGCUGUGUAUUUUAAAGCCAUACAGCCUAUUU-GU-UGUUGUU--------------------
((...(((((.(..(((((.....)))))..).)))))...))...(((((((...........)))))))......-..-.......-------------------- ( -22.80)
>consensus
GCAUUUUAAAAUUGGCUGCUGCCUGCAGCUGAAUUUGAUAAGCUAAGCUGUGUAUUUUAAAGCCAUACAGCCUAUUU_AU_UGUUGUUUA____________AGUUGU
((...(((((.((((((((.....)))))))).)))))...))...(((((((...........)))))))..................................... (-19.67 = -19.28 +  -0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,629,035 – 11,629,142
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.56
Mean single sequence MFE -28.89
Consensus MFE -19.85
Energy contribution -19.30
Covariance contribution -0.55
Combinations/Pair 1.14
Mean z-score -2.10
Structure conservation index 0.69
SVM decision value 0.15
SVM RNA-class probability 0.607484
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11629035 107 - 22224390
-----UUA---UU-AAGUUUUAAAUUUACCGCUCGUAGUGGCAUUUUAAAAUUG-GCUGCUGCCUGCAGCUGAAUUUGAUAAGCUA-AGCUGUGUAUUUUAAAUCCAUAUAGCCUAUG--
-----(((---((-((((((((((....((((.....))))...)))))).(..-(((((.....)))))..))))))))))....-.(((((((...........))))))).....-- ( -26.60)
>DroVir_CAF1 5404 107 - 1
-----AAA---UU-UCAUUUUAAAUUUACCGCUCGUAGUGGCAUUUUGAAAUUG-GCUGCUGCCUGCAGCUGAAUUUGAUAAGCUA-AGCUGUGAAUUUUAAAGCCGUACAGACUGCA--
-----...---..-...(((.((((((((.(((.....((((...(..((.(..-(((((.....)))))..).))..)...))))-))).)))))))).)))((.((....)).)).-- ( -28.60)
>DroPse_CAF1 2945 116 - 1
UUAAGUUAUAGUUAAGGUUUUAAAUUUACCGCUCGUAGUGGCAUUUUGAAAUUG-GCUGCUGCCUGCAGCUGAAUUUGAUAAGCUA-AGCUGUGAAUUUUAAAGCCAUACAGCCUGGU--
...............((((((((((((((.(((.....((((...(..((.(..-(((((.....)))))..).))..)...))))-))).))))).)))))))))............-- ( -33.50)
>DroWil_CAF1 9325 112 - 1
UUAUAUUA---GU-AGAUUUUAAAUUUACCGCUCGUAGUGGCAUUUUGAAAUUA-GCUGCUGCCUGUAGUUGAAUUUGAUAAGCUA-AGCUGUGUAUUUUAAAGCCGUACAGCCUAAC--
.....(((---((-.....((((((((((..(..((((..((............-))..))))..)..).)))))))))...))))-)((((((.............)))))).....-- ( -25.12)
>DroAna_CAF1 1631 109 - 1
-----UUA---AU-GAUUUUUAAAUUUACCGCUCGUAGUGGCAUUUUGAAAUUG-GCUGCUGCCUGCAGCUGAAUUUGAUAAGCUA-AGCUGUGUAUUUUAAAGCCAUACAGCCUGUUGU
-----...---..-...(((((((....((((.....))))...)))))))(..-(((((.....)))))..)........(((..-.(((((((...........)))))))..))).. ( -26.20)
>DroPer_CAF1 2018 118 - 1
UUAAGUUAUAGUUAAGGUUUUAAAUUUACCGCUCGUAGUGGCAUUUUGAAAUUGGGCUGCUGCCUGCAGCUGAAUUUGAUAAGCUAAAGCUGUGAAUUUUAAAGCCNNNNNNNNNNNN--
...............((((((((((((((.(((.....((((.((.(.(((((.((((((.....)))))).))))).).)))))).))).))))).)))))))))............-- ( -33.30)
>consensus
_____UUA___UU_AGGUUUUAAAUUUACCGCUCGUAGUGGCAUUUUGAAAUUG_GCUGCUGCCUGCAGCUGAAUUUGAUAAGCUA_AGCUGUGAAUUUUAAAGCCAUACAGCCUGUU__
..................((((((..(((.(((.....((((...(((((.(((.(((((.....)))))))).)))))...)))).))).)))...))))))................. (-19.85 = -19.30 +  -0.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:19 2006