Locus 6480

Sequence ID 3R_DroMel_CAF1
Location 17,044,729 – 17,044,846
Length 117
Max. P 0.999755
window10545 window10546

overview

Window 5

Location 17,044,729 – 17,044,846
Length 117
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 75.84
Mean single sequence MFE -33.13
Consensus MFE -21.48
Energy contribution -21.60
Covariance contribution 0.12
Combinations/Pair 1.19
Mean z-score -3.01
Structure conservation index 0.65
SVM decision value 4.01
SVM RNA-class probability 0.999755
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17044729 117 + 27905053
ACAGGGUGCACCUUGUGUAUUUAUAAAACCAAU-UCUAACCGAAAUU-GACUGAACAUGGUUAUUGCGAUGUCAGUAUAUCGAUGUCUUGAGCUAUCGAUAGCACAAGGUGCAAUUGUC
((((..((((((((((((...........((((-(........))))-)(((((.(((.((....)).)))))))).((((((((.(....).)))))))))))))))))))).)))). ( -41.10)
>DroSim_CAF1 1254 118 + 1
UCAGGGUGCACCUUGUUUAUUUAUAAAACCAAU-UCUUAUCGAAAUUCGAUUUAACAUGGCUAUUGGCUCGUCAGUGUAUCGAUGUCUUGAGCUAUCGAUAGCACAAGGUGCAAUUGUC
.(((..((((((((((.............((..-....((((.....))))......))((((((((((((.((.........))...)))))...))))))))))))))))).))).. ( -33.10)
>DroYak_CAF1 1253 110 + 1
UCAGGGUGCACCUUGUUUAUUUAUAAAACUAAAUUUAUAUCGAUAAUAGAUUCGACAUGGCUAUCUAUCCACGCAUCUAUCGAU---------UGUCGAUAGCAUACGGUGCAAUUGUC
.(((..((((((..((((.......))))........((((((((((((((.((...(((........))))).))))))....---------))))))))......)))))).))).. ( -25.20)
>consensus
UCAGGGUGCACCUUGUUUAUUUAUAAAACCAAU_UCUUAUCGAAAUU_GAUUCAACAUGGCUAUUGACACGUCAGUAUAUCGAUGUCUUGAGCUAUCGAUAGCACAAGGUGCAAUUGUC
.(((..((((((((((.............................................(((((......)))))((((((((........))))))))..)))))))))).))).. (-21.48 = -21.60 +   0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,044,729 – 17,044,846
Length 117
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 75.84
Mean single sequence MFE -31.07
Consensus MFE -17.96
Energy contribution -18.72
Covariance contribution 0.76
Combinations/Pair 1.12
Mean z-score -3.04
Structure conservation index 0.58
SVM decision value 3.11
SVM RNA-class probability 0.998460
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17044729 117 - 27905053
GACAAUUGCACCUUGUGCUAUCGAUAGCUCAAGACAUCGAUAUACUGACAUCGCAAUAACCAUGUUCAGUC-AAUUUCGGUUAGA-AUUGGUUUUAUAAAUACACAAGGUGCACCCUGU
.(((..(((((((((((.(((((((..(....)..))))))).((((((((.(......).))).)))))(-(((((......))-))))............)))))))))))...))) ( -32.50)
>DroSim_CAF1 1254 118 - 1
GACAAUUGCACCUUGUGCUAUCGAUAGCUCAAGACAUCGAUACACUGACGAGCCAAUAGCCAUGUUAAAUCGAAUUUCGAUAAGA-AUUGGUUUUAUAAAUAAACAAGGUGCACCCUGA
......((((((((((..(((((((..(....)..))))))).......(((((((((((...)))).((((.....))))....-.))))))).........))))))))))...... ( -31.30)
>DroYak_CAF1 1253 110 - 1
GACAAUUGCACCGUAUGCUAUCGACA---------AUCGAUAGAUGCGUGGAUAGAUAGCCAUGUCGAAUCUAUUAUCGAUAUAAAUUUAGUUUUAUAAAUAAACAAGGUGCACCCUGA
......((((((((((.((((((...---------..))))))))))((((((.((((....))))..))))))......((((((......)))))).........))))))...... ( -29.40)
>consensus
GACAAUUGCACCUUGUGCUAUCGAUAGCUCAAGACAUCGAUACACUGACGAACCAAUAGCCAUGUUAAAUC_AAUUUCGAUAAGA_AUUGGUUUUAUAAAUAAACAAGGUGCACCCUGA
......((((((((((..(((((((..(....)..)))))))...............(((((......(((.......))).......)))))..........))))))))))...... (-17.96 = -18.72 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:25 2006