Locus 1469

Sequence ID 3L_DroMel_CAF1
Location 4,264,317 – 4,264,413
Length 96
Max. P 0.959259
window2288 window2289

overview

Window 8

Location 4,264,317 – 4,264,413
Length 96
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 76.69
Mean single sequence MFE -21.00
Consensus MFE -17.16
Energy contribution -16.88
Covariance contribution -0.28
Combinations/Pair 1.15
Mean z-score -1.73
Structure conservation index 0.82
SVM decision value 1.50
SVM RNA-class probability 0.959259
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4264317 96 + 23771897
AUCCCAUAAAUGUUGAAUGUUUGAAAUUUAUAAAUUUU---UAUUUCUUUCUAGGCUUGGAAUGCCAUGGCCACGAAUGUCCUGCAAGUGGCCACCAUU
.....((((((.(..(....)..).)))))).......---............(((.......))).(((((((...((.....)).)))))))..... ( -19.50)
>DroSec_CAF1 28665 96 + 1
AUCCCACAAGUUUUGAAUGCUCUAAAUUUACAAAUUUA---UGUUACUUUCUAGGCUUGGAAUGCCAUGGCCACGAAUGUCCUGCAAGUGGCCACCAUU
......(((((((.(((.((..((((((....))))))---.))....))).))))))).((((...(((((((...((.....)).))))))).)))) ( -22.60)
>DroSim_CAF1 28526 96 + 1
AUCCCACAAGUUUUGAAUGUUCGAAAUUCACAAAUUUA---UAUUACUUUCUAGGCUUGGAAUGCCAUGGCCACGAAUGUCCUGCAAGUGGCCACCAUU
......(((((((.(((.((...(((((....))))).---....)).))).))))))).((((...(((((((...((.....)).))))))).)))) ( -22.70)
>DroEre_CAF1 29409 88 + 1
AUCACACAAAUG--------UUUCAAAUUAAAAAUGCA---UAUUUCUUUUUAGGCUUGGAAUGCCAUGGCCACGAAUGUUUUGCAAGUGGCCACCAUU
...........(--------((((((.(((((((....---......)))))))..)))))))....(((((((...((.....)).)))))))..... ( -18.80)
>DroYak_CAF1 31273 96 + 1
AUCACACAAAUUUUGUAUUUUUCCAAACUAAAAAUGUU---UAUUUUUUUUUAGGCAUGGAAUGCCAUGGCCACGAAUGUUUUGCAAGUGGCCACCAUU
....................(((((..(((((((....---......)))))))...))))).....(((((((...((.....)).)))))))..... ( -21.80)
>DroMoj_CAF1 25861 87 + 1
AUGUA-UA---------UAUUCA--GCUUAUAAAUAUAUUUUUUUAUCUUUUAGGCCUGGAAUGCUAUGGCCACCAAUGCGCUGCAAGUGGCCACGAUU
..(((-(.---------..((((--(((((.(((.(((......))).))))))).)))))))))..(((((((...(((...))).)))))))..... ( -20.60)
>consensus
AUCCCACAAAUUUUGAAUGUUCGAAAUUUAAAAAUUUA___UAUUACUUUCUAGGCUUGGAAUGCCAUGGCCACGAAUGUCCUGCAAGUGGCCACCAUU
.....................................................(((.......))).(((((((...(((...))).)))))))..... (-17.16 = -16.88 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,264,317 – 4,264,413
Length 96
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 76.69
Mean single sequence MFE -20.67
Consensus MFE -16.03
Energy contribution -16.20
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.41
Structure conservation index 0.78
SVM decision value 1.10
SVM RNA-class probability 0.915192
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4264317 96 - 23771897
AAUGGUGGCCACUUGCAGGACAUUCGUGGCCAUGGCAUUCCAAGCCUAGAAAGAAAUA---AAAAUUUAUAAAUUUCAAACAUUCAACAUUUAUGGGAU
((((((((((((.((.....))...))))))))(((.......)))..((((...(((---(....))))...))))...))))............... ( -19.10)
>DroSec_CAF1 28665 96 - 1
AAUGGUGGCCACUUGCAGGACAUUCGUGGCCAUGGCAUUCCAAGCCUAGAAAGUAACA---UAAAUUUGUAAAUUUAGAGCAUUCAAAACUUGUGGGAU
..(.((((((((.((.....))...)))))))).).((((((.(((((((...(.(((---......))).).))))).))...((.....)))))))) ( -21.30)
>DroSim_CAF1 28526 96 - 1
AAUGGUGGCCACUUGCAGGACAUUCGUGGCCAUGGCAUUCCAAGCCUAGAAAGUAAUA---UAAAUUUGUGAAUUUCGAACAUUCAAAACUUGUGGGAU
..(.((((((((.((.....))...)))))))).).((((((......((((...(((---......)))...))))((....))........)))))) ( -20.50)
>DroEre_CAF1 29409 88 - 1
AAUGGUGGCCACUUGCAAAACAUUCGUGGCCAUGGCAUUCCAAGCCUAAAAAGAAAUA---UGCAUUUUUAAUUUGAAA--------CAUUUGUGUGAU
....((((((((.((.....))...))))))))(((.......)))..........((---((((.((((.....))))--------....)))))).. ( -18.10)
>DroYak_CAF1 31273 96 - 1
AAUGGUGGCCACUUGCAAAACAUUCGUGGCCAUGGCAUUCCAUGCCUAAAAAAAAAUA---AACAUUUUUAGUUUGGAAAAAUACAAAAUUUGUGUGAU
..(.((((((((.((.....))...)))))))).)..(((((...(((((((......---....)))))))..)))))..(((((.....)))))... ( -23.10)
>DroMoj_CAF1 25861 87 - 1
AAUCGUGGCCACUUGCAGCGCAUUGGUGGCCAUAGCAUUCCAGGCCUAAAAGAUAAAAAAAUAUAUUUAUAAGC--UGAAUA---------UA-UACAU
.(((((((((((((((...)))..))))))))).((.......))......)))......(((((((((.....--))))))---------))-).... ( -21.90)
>consensus
AAUGGUGGCCACUUGCAGGACAUUCGUGGCCAUGGCAUUCCAAGCCUAAAAAGAAAUA___UAAAUUUAUAAAUUUAAAACAUUCAAAAUUUGUGGGAU
....((((((((.((.....))...))))))))(((.......)))..................................................... (-16.03 = -16.20 +   0.17)

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 10:08:30 2006