Locus 1762

Sequence ID X_DroMel_CAF1
Location 4,880,033 – 4,880,176
Length 143
Max. P 0.706457
window2882 window2883

overview

Window 2

Location 4,880,033 – 4,880,141
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.73
Mean single sequence MFE -24.08
Consensus MFE -17.01
Energy contribution -17.84
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -2.87
Structure conservation index 0.71
SVM decision value 0.36
SVM RNA-class probability 0.706457
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4880033 108 + 22224390
UCAUUCACUUAGUCAGCAGACACUGGCGACUUGGUUU-------UUGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCAGCCAAAAGCAAAAAAAAAAAAA-----GAAAAUAAACA
...(((.....(((....))).(((((((((.((((.-------..)))).)))).......(((((......)))))))))).....................-----)))........ ( -24.60)
>DroSec_CAF1 31313 104 + 1
UCAUUCACUUAGUCAGCAGACACUGGCGACUUGGUUU-------UUGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCAGCCAAAAGCAAAAA-AA---AA-----CAAGAUAAAUA
.......(((.(((....))).(((((((((.((((.-------..)))).)))).......(((((......)))))))))).............-..---..-----.)))....... ( -23.90)
>DroSim_CAF1 32566 105 + 1
UCAUUCACUUAGUCAGCAGACACUGGCGACUUGGUUU-------UUGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCAGCCAAAAGCAAAAAAAA---AA-----CAAGAUAAAUA
.......(((.(((....))).(((((((((.((((.-------..)))).)))).......(((((......))))))))))................---..-----.)))....... ( -23.90)
>DroEre_CAF1 34227 97 + 1
UCAUUCACUUAGUCAGCAGACACAGGCGACUUGGAUU-------UUGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCAGCCAAAAGAAAAA----------------AGAUAAGUA
......((((((((....)))...(((...(((((((-------.......)))))))((..(((((......)))))..)))))..........----------------...))))). ( -24.70)
>DroYak_CAF1 32014 97 + 1
UCAUUCACUUAGUCAGCAGACACUGGCGACUUGGAUU-------UUGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCAGCCAAAAGGAAAA----------------AGAUAAAUA
...(((.(((.(((....))).(((((...(((((((-------.......)))))))....(((((......))))))))))....))))))..----------------......... ( -25.30)
>DroAna_CAF1 84521 114 + 1
UCACUCACUUAGUCAGCAGACA--AGCGAAUUGGAUUUUUUUUUUCGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCGACCAAAAAAAUCAA-AA---AACCUCAGACACUAAAUA
...........(((.((.....--.))......(((((((((..(((..(((......))).(((((......)))))..)))..)))))))))..-..---.......)))........ ( -22.10)
>consensus
UCAUUCACUUAGUCAGCAGACACUGGCGACUUGGAUU_______UUGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCAGCCAAAAGCAAAAA_AA___AA______AAGAUAAAUA
...........(((....))).(((((((((.((..............)).)))).......(((((......))))))))))..................................... (-17.01 = -17.84 +   0.83)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,880,070 – 4,880,176
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.84
Mean single sequence MFE -15.50
Consensus MFE -8.32
Energy contribution -8.18
Covariance contribution -0.14
Combinations/Pair 1.14
Mean z-score -1.85
Structure conservation index 0.54
SVM decision value 0.30
SVM RNA-class probability 0.677819
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4880070 106 + 22224390
----UUGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCAGCCAAAAGCAAAAAAAAAAAAA-----GAAAAUAAACACAAAUAAUCUGUGCAAAAA-AAAACUUCGGUGAUA----U
----(((.(.(((.....((..(((((......)))))..))((.....)).............-----...................))).))))...-...((....))....----. ( -14.40)
>DroSec_CAF1 31350 99 + 1
----UUGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCAGCCAAAAGCAAAAA-AA---AA-----CAAGAUAAAUACAAAUAAUCUGUGCAAA----AAACUUCUGUGAGA----U
----....((((......((..(((((......)))))..)).......(((....-..---..-----..((((...........)))).)))...----.........)))).----. ( -14.50)
>DroSim_CAF1 32603 100 + 1
----UUGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCAGCCAAAAGCAAAAAAAA---AA-----CAAGAUAAAUACAAAUAAUCUGUGCAAA----AAACUUCGGUGAGA----U
----....((((..((..((..(((((......)))))..)).......(((.......---..-----..((((...........)))).)))...----.......)))))).----. ( -15.90)
>DroEre_CAF1 34264 91 + 1
----UUGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCAGCCAAAAGAAAAA----------------AGAUAAGUAUAAAUAAACUGUGCAAAA----AACAUUGGUGAAA-----
----.....(((..((((((..(((((......))))).................----------------......(((((.......)))))....----..)))))))))..----- ( -17.10)
>DroYak_CAF1 32051 100 + 1
----UUGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCAGCCAAAAGGAAAA----------------AGAUAAAUAAAAAUAAUCUGUGCAAAAAAAAAACUUUGGAGAAAACCUC
----.........(((((.(..(((((......)))))(((((((....))....----------------.................))).))..........).)))))......... ( -13.99)
>DroAna_CAF1 84559 106 + 1
UUUUUCGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCGACCAAAAAAAUCAA-AA---AACCUCAGACACUAAAUAAAAACAAUUUGUU--AA----GAGUUUCGGUUAGA----U
....(((..(((......))).(((((......)))))..))).............-..---((((..((((.((.((((((.....))))))--.)----).)))).))))...----. ( -17.10)
>consensus
____UUGACUCAGUCCAAUGAACUGCAAAAAUCUGCAGGCCAGCCAAAAGCAAAAA_AA___AA______AAGAUAAAUACAAAUAAUCUGUGCAAA____AAACUUCGGUGAGA____U
..................((..(((((......)))))..)).............................................................................. ( -8.32 =  -8.18 +  -0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:20 2006