Locus 3830

Sequence ID 3L_DroMel_CAF1
Location 11,059,873 – 11,059,972
Length 99
Max. P 0.895442
window5965 window5966

overview

Window 5

Location 11,059,873 – 11,059,972
Length 99
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 89.97
Mean single sequence MFE -28.80
Consensus MFE -22.89
Energy contribution -22.75
Covariance contribution -0.14
Combinations/Pair 1.16
Mean z-score -3.12
Structure conservation index 0.79
SVM decision value 0.99
SVM RNA-class probability 0.895442
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11059873 99 + 23771897
GGUGGGCGAUAAAAAUAGUU--CUUCGCAUUGUUU----ACUUAACCACAUGUGAAACGAAUUAUCACAUUUUAUUUUUAUCGCCAGCGCAGCACGUGCCAGACA
....((((((((((((((..--.(((((((.(((.----....)))...)))))))..((....)).....)))))))))))))).((((.....))))...... ( -26.90)
>DroSec_CAF1 3875 98 + 1
GGUGGGCGAUAAAAAUAGUU--CUUCGCAUUGUGU----ACUUAA-CACAUGUGAAACGAAUUAUCACAUUUUAUUUUUAUCGCCAGCGCAGCACGUGCCAGACA
....((((((((((((((..--.(((((((.((((----.....)-))))))))))..((....)).....)))))))))))))).((((.....))))...... ( -31.70)
>DroSim_CAF1 3809 98 + 1
GGUGGGCGAUAAAAAUAGUU--CUUCGCAUUGUUU----ACUUAA-CACAUGUGAAACGAAUUAUCACAUUUUAUUUUUAUCGCCAGCGCAGCACGUGCCAGACA
....((((((((((((((..--.(((((((((((.----....))-)).)))))))..((....)).....)))))))))))))).((((.....))))...... ( -29.50)
>DroEre_CAF1 3879 98 + 1
GGUAGGCGAUAAAAAUAGUU--UUUCGCAUUGUUU----ACUUGA-CACAUGUGAAACGAAUUAUCACAUUUUAUUUUUAUCGCCAGUGCAGCACGUGCCAGACU
((((((((((((((((((..--((((((((((((.----....))-)).)))))))).((....)).....)))))))))))))).(((...))).))))..... ( -31.50)
>DroYak_CAF1 3733 97 + 1
GGUAGGCGAUAAAAAUAGUU---UUCGCAUUGUUU----ACUUGA-CACAUGUGAAACGAAUUAUCACAUUUUAUUUUUAUCGCCAGCGCAGCACGUGCCAGACA
....((((((((((((((.(---(((((((((((.----....))-)).)))))))).((....)).....)))))))))))))).((((.....))))...... ( -30.80)
>DroAna_CAF1 3464 104 + 1
CGAUGGCGAUAAAAAUAGUUGUUUUUGCAUUCUUCUGCCCCCCGA-CACAUGUGAAUCGAAUUAUCGCGUUUUAUUUUUAUCACCAGCCUAGCACGUGCCAGACA
...(((.((((((((((((((.....(((......)))....)))-)..((((((.........))))))..)))))))))).)))(.((.((....)).)).). ( -22.40)
>consensus
GGUGGGCGAUAAAAAUAGUU__CUUCGCAUUGUUU____ACUUAA_CACAUGUGAAACGAAUUAUCACAUUUUAUUUUUAUCGCCAGCGCAGCACGUGCCAGACA
....((((((((((((((.....(((((((((.((........)).)).)))))))..((....)).....)))))))))))))).((((.....))))...... (-22.89 = -22.75 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,059,873 – 11,059,972
Length 99
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 89.97
Mean single sequence MFE -27.66
Consensus MFE -21.71
Energy contribution -21.63
Covariance contribution -0.08
Combinations/Pair 1.11
Mean z-score -2.54
Structure conservation index 0.78
SVM decision value 0.20
SVM RNA-class probability 0.629350
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11059873 99 - 23771897
UGUCUGGCACGUGCUGCGCUGGCGAUAAAAAUAAAAUGUGAUAAUUCGUUUCACAUGUGGUUAAGU----AAACAAUGCGAAG--AACUAUUUUUAUCGCCCACC
.((.((((....)))).)).(((((((((((((..((((((.........))))))...(((..((----(.....)))....--)))))))))))))))).... ( -26.00)
>DroSec_CAF1 3875 98 - 1
UGUCUGGCACGUGCUGCGCUGGCGAUAAAAAUAAAAUGUGAUAAUUCGUUUCACAUGUG-UUAAGU----ACACAAUGCGAAG--AACUAUUUUUAUCGCCCACC
.((.((((....)))).)).(((((((((((((..((((((.........))))))(((-(.....----)))).........--...))))))))))))).... ( -28.40)
>DroSim_CAF1 3809 98 - 1
UGUCUGGCACGUGCUGCGCUGGCGAUAAAAAUAAAAUGUGAUAAUUCGUUUCACAUGUG-UUAAGU----AAACAAUGCGAAG--AACUAUUUUUAUCGCCCACC
.((.((((....)))).)).(((((((((((((..((((((.........))))))..(-((..((----(.....)))....--)))))))))))))))).... ( -26.00)
>DroEre_CAF1 3879 98 - 1
AGUCUGGCACGUGCUGCACUGGCGAUAAAAAUAAAAUGUGAUAAUUCGUUUCACAUGUG-UCAAGU----AAACAAUGCGAAA--AACUAUUUUUAUCGCCUACC
(((.((((....)))).)))(((((((((((((..((((((.........))))))((.-....((----(.....)))....--.))))))))))))))).... ( -26.80)
>DroYak_CAF1 3733 97 - 1
UGUCUGGCACGUGCUGCGCUGGCGAUAAAAAUAAAAUGUGAUAAUUCGUUUCACAUGUG-UCAAGU----AAACAAUGCGAA---AACUAUUUUUAUCGCCUACC
.((.((((....)))).)).(((((((((((((..((((((.........))))))((.-....((----(.....)))...---.))))))))))))))).... ( -25.60)
>DroAna_CAF1 3464 104 - 1
UGUCUGGCACGUGCUAGGCUGGUGAUAAAAAUAAAACGCGAUAAUUCGAUUCACAUGUG-UCGGGGGGCAGAAGAAUGCAAAAACAACUAUUUUUAUCGCCAUCG
.(((((((....)))))))((((((((((((((...(.(((((..............))-))).)..(((......))).........))))))))))))))... ( -33.14)
>consensus
UGUCUGGCACGUGCUGCGCUGGCGAUAAAAAUAAAAUGUGAUAAUUCGUUUCACAUGUG_UCAAGU____AAACAAUGCGAAG__AACUAUUUUUAUCGCCCACC
.((.((((....)))).)).(((((((((((((..((((((.........))))))((...................)).........))))))))))))).... (-21.71 = -21.63 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:45 2006