Locus 4971

Sequence ID X_DroMel_CAF1
Location 12,971,710 – 12,971,844
Length 134
Max. P 0.848604
window8105 window8106

overview

Window 5

Location 12,971,710 – 12,971,808
Length 98
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.03
Mean single sequence MFE -24.02
Consensus MFE -14.64
Energy contribution -15.45
Covariance contribution 0.81
Combinations/Pair 1.12
Mean z-score -2.00
Structure conservation index 0.61
SVM decision value 0.34
SVM RNA-class probability 0.696068
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12971710 98 + 22224390
AAUUGAAAAGCAUUGCACGAG-----CGUCGUCGACGCUUGGGAUAUUGCACAAUAUAUGGCAAUAUAU--------------AGAUGUGGAACCAAA---CAGACGUACGUAAUUUACA
...........(((((.((((-----((((...))))))))((...((.((((.((((((....)))))--------------)..)))).))))...---.........)))))..... ( -22.30)
>DroSim_CAF1 6713 101 + 1
AAUUGAAAAGCAUUGCACGAG-----CGACGUCGACGUUUGGGAUAUUGCACAAUAUAUGGCAAUAUAU--------------AGAUGGGGAACCAAACAACAGACGUACGUAAUUUACA
.........((.((((....)-----))).))(((((((((..(((((((.((.....)))))))))..--------------...(((....))).....))))))).))......... ( -24.10)
>DroEre_CAF1 5949 94 + 1
AAUUGAAAAGCAUUGCACGAG-----CGACGUCAACGUUUGGUAUAUUGCACAAUAUAUGGCAAUAUAU--------------AGUUGGGGAACCAA-------ACAAACGUAAUUUACA
.........((.((((....)-----))).))..((((((((((((((((.((.....)))))))))))--------------..((((....))))-------.)))))))........ ( -26.30)
>DroYak_CAF1 6289 114 + 1
AAUUGAAAAGCAUUGCACGAACGGAACGACGUCAACGUUUGAGAUAUUGCACAAUAUAUGGCAAUAUAUCUAUGUAUAUGUACAGUUGGGGAACCAAA------ACCGACGUAAUUUACA
.......................(((..(((((.((((..((.(((((((.((.....))))))))).)).))))..........((((....)))).------...)))))..)))... ( -23.40)
>consensus
AAUUGAAAAGCAUUGCACGAG_____CGACGUCAACGUUUGGGAUAUUGCACAAUAUAUGGCAAUAUAU______________AGAUGGGGAACCAAA______ACGUACGUAAUUUACA
.............((.(((..........)))))(((((((..(((((((.((.....)))))))))...................(((....))).........)))))))........ (-14.64 = -15.45 +   0.81)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 12,971,745 – 12,971,844
Length 99
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 80.62
Mean single sequence MFE -24.30
Consensus MFE -14.88
Energy contribution -15.50
Covariance contribution 0.62
Combinations/Pair 1.12
Mean z-score -2.15
Structure conservation index 0.61
SVM decision value 0.78
SVM RNA-class probability 0.848604
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12971745 99 + 22224390
GGGAUAUUGCACAAUAUAUGGCAAUAUAU--------------AGAUGUGGAACCAAA---CAGACGUACGUAAUUUACAACUUCUUU-UUUCGAGAAAUGCUUGAGAAAGGAGUGA
.((...((.((((.((((((....)))))--------------)..)))).))))...---...................(((.((((-(((((((.....)))))))))))))).. ( -20.90)
>DroSim_CAF1 6748 102 + 1
GGGAUAUUGCACAAUAUAUGGCAAUAUAU--------------AGAUGGGGAACCAAACAACAGACGUACGUAAUUUACAACUUCUUU-UUUCGAGAAAUGCUUGAGAAAGGAGCGA
...(((((((.((.....)))))))))..--------------...(((....))).........(((..(((...)))....(((((-(((((((.....))))))))))))))). ( -25.00)
>DroEre_CAF1 5984 95 + 1
GGUAUAUUGCACAAUAUAUGGCAAUAUAU--------------AGUUGGGGAACCAA-------ACAAACGUAAUUUACAACUUCUUU-UUUCGAGAAAUGCUUGAGUUAAGUAGGU
.(((((((((.((.....)))))))))))--------------..((((....))))-------................(((((((.-.((((((.....))))))..))).)))) ( -23.60)
>DroYak_CAF1 6329 111 + 1
GAGAUAUUGCACAAUAUAUGGCAAUAUAUCUAUGUAUAUGUACAGUUGGGGAACCAAA------ACCGACGUAAUUUACAACUUCUUUUUUUCGAGAAAUGCUUAAGUUAAGGAGGU
((.(((((((.((.....))))))))).))..(((((((((....((((....)))).------....)))))...))))((((((((..((..((.....))..))..)))))))) ( -27.70)
>consensus
GGGAUAUUGCACAAUAUAUGGCAAUAUAU______________AGAUGGGGAACCAAA______ACGUACGUAAUUUACAACUUCUUU_UUUCGAGAAAUGCUUGAGAAAAGAAGGA
...(((((((.((.....)))))))))...................(((....))).........................((((((...((((((.....))))))..)))))).. (-14.88 = -15.50 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:17 2006