Locus 3408

Sequence ID 2R_DroMel_CAF1
Location 11,540,955 – 11,541,055
Length 100
Max. P 0.666814
window5563 window5564

overview

Window 3

Location 11,540,955 – 11,541,055
Length 100
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 76.99
Mean single sequence MFE -22.33
Consensus MFE -15.70
Energy contribution -15.62
Covariance contribution -0.08
Combinations/Pair 1.33
Mean z-score -1.12
Structure conservation index 0.70
SVM decision value 0.28
SVM RNA-class probability 0.666814
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11540955 100 + 20766785
AUAAUUUAUAAGAGAAAUUGAAAUGAAUUAGCCA--AAAU----UUACCUCCUUGGCGGAUCGAAGGCAGGCCAGCUGCUUGGCGUUUUCAAGGCUGCCCACAAAA
.((((((((..((....))...))))))))(((.--..((----(..((.....))..)))....))).((.((((..(((((.....))))))))).))...... ( -23.40)
>DroGri_CAF1 1156 94 + 1
AUAGUU-UUAAAAA----------A-AUUUACUUUUCAAAUGCCUUACCUCCUUGGCGGGCUUGUGACAGGCCAGCCUCAAGGCGCUCUCUAAGCUGCCCACAAAA
......-.......----------.-...............((((..((.....)).))))(((((...(((..(((....)))(((.....))).)))))))).. ( -20.10)
>DroSec_CAF1 1122 90 + 1
AUAAUUUAUAAGAC----------GAAUUAGUCA--AAAU----UUACCUCCUUGGCGGAUCGAAGGCAGGCCAGCUGCUUGGCGUUUUCAAGGCUGCCCACAAAA
...........(((----------......))).--....----..........(((((...((((((..(((((....)))))))))))....)))))....... ( -20.80)
>DroSim_CAF1 1120 90 + 1
AUAAUUUAUAAGAG----------GAAUUUGCCA--AAAU----UUACCUCCUUGGCGGAUCGAAGGCAGGCCAGCUGCUUGGCGUUUUCAAGGCUGCCCACAAAA
...........(((----------((((((....--))))----)..))))...(((((...((((((..(((((....)))))))))))....)))))....... ( -22.60)
>DroEre_CAF1 1120 88 + 1
A--ACUUACAAGAG----------GAAUAAGCCA--AAUA----UUACCUCCUUGGCGGGUCUAAGGCAGGCCAGCUGCUUGGCGCUUUCAAGACUGCCCACAAAA
.--........(((----------(((((.....--..))----)).))))...(((((.((((((((..(((((....))))))))))..))))))))....... ( -23.40)
>DroYak_CAF1 1121 90 + 1
AAGACUUUGUAAAG----------UAAUAAACUA--AAAA----UUACCUCCUUGGCAGGUCGAAGGCAGGCCAGCUGCUUGGCGCUUUCAAGACUGCCCACAAAA
.....(((((...(----------((((......--...)----))))......(((((...((((((..(((((....)))))))))))....))))).))))). ( -23.70)
>consensus
AUAAUUUAUAAGAG__________GAAUUAGCCA__AAAA____UUACCUCCUUGGCGGAUCGAAGGCAGGCCAGCUGCUUGGCGCUUUCAAGGCUGCCCACAAAA
......................................................(((((.((((((((..(((((....)))))))))))..)))))))....... (-15.70 = -15.62 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,540,955 – 11,541,055
Length 100
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 76.99
Mean single sequence MFE -24.00
Consensus MFE -16.36
Energy contribution -16.12
Covariance contribution -0.25
Combinations/Pair 1.29
Mean z-score -1.01
Structure conservation index 0.68
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11540955 100 - 20766785
UUUUGUGGGCAGCCUUGAAAACGCCAAGCAGCUGGCCUGCCUUCGAUCCGCCAAGGAGGUAA----AUUU--UGGCUAAUUCAUUUCAAUUUCUCUUAUAAAUUAU
.((((((((.((..((((((..((......))((((((((((((..........))))))).----....--.))))).....))))))...)))))))))).... ( -22.20)
>DroGri_CAF1 1156 94 - 1
UUUUGUGGGCAGCUUAGAGAGCGCCUUGAGGCUGGCCUGUCACAAGCCCGCCAAGGAGGUAAGGCAUUUGAAAAGUAAAU-U----------UUUUUAA-AACUAU
..(((((((((((((.(((.....))).))))).)))...)))))(((.(((.....)))..))).(((((((((.....-)----------)))))))-)..... ( -26.10)
>DroSec_CAF1 1122 90 - 1
UUUUGUGGGCAGCCUUGAAAACGCCAAGCAGCUGGCCUGCCUUCGAUCCGCCAAGGAGGUAA----AUUU--UGACUAAUUC----------GUCUUAUAAAUUAU
......((.((((((((.......))))..)))).))(((((((..........)))))))(----((((--.(((......----------)))....))))).. ( -22.20)
>DroSim_CAF1 1120 90 - 1
UUUUGUGGGCAGCCUUGAAAACGCCAAGCAGCUGGCCUGCCUUCGAUCCGCCAAGGAGGUAA----AUUU--UGGCAAAUUC----------CUCUUAUAAAUUAU
.(((((((.((((((((.......))))..)))).))(((((((..........))))))).----....--..)))))...----------.............. ( -22.60)
>DroEre_CAF1 1120 88 - 1
UUUUGUGGGCAGUCUUGAAAGCGCCAAGCAGCUGGCCUGCCUUAGACCCGCCAAGGAGGUAA----UAUU--UGGCUUAUUC----------CUCUUGUAAGU--U
.......(((.((((....((.((((......)))))).....))))..))).((((((.((----((..--.....)))))----------)))))......--. ( -24.50)
>DroYak_CAF1 1121 90 - 1
UUUUGUGGGCAGUCUUGAAAGCGCCAAGCAGCUGGCCUGCCUUCGACCUGCCAAGGAGGUAA----UUUU--UAGUUUAUUA----------CUUUACAAAGUCUU
((((((.(((((..(((((.((((((......))))..)).))))).)))))...(((((((----(...--......))))----------)))))))))).... ( -26.40)
>consensus
UUUUGUGGGCAGCCUUGAAAACGCCAAGCAGCUGGCCUGCCUUCGACCCGCCAAGGAGGUAA____AUUU__UGGCUAAUUC__________CUCUUAUAAAUUAU
......((.((((((((.......))))..)))).))(((((((..........)))))))............................................. (-16.36 = -16.12 +  -0.25)

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 10:54:46 2006