Locus 8180

Sequence ID 3R_DroMel_CAF1
Location 21,994,019 – 21,994,211
Length 192
Max. P 0.847642
window13153 window13154

overview

Window 3

Location 21,994,019 – 21,994,131
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.79
Mean single sequence MFE -32.12
Consensus MFE -22.75
Energy contribution -23.12
Covariance contribution 0.37
Combinations/Pair 1.08
Mean z-score -1.48
Structure conservation index 0.71
SVM decision value -0.01
SVM RNA-class probability 0.529688
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21994019 112 + 27905053
AAAU--------AAAUAUAUGUCAGCGGGCAUUAUGCUUUACGGUUUUCUCAUUGCUGCAGACCUGGCCUCGUCCUCGGAAAAUGGCAGCCAACAGGGAAUAAAUGUUGGUUGCAGACUG
....--------........(((.(.((((.....(((....(((((.(........).))))).)))...)))).)........((((((((((.........)))))))))).))).. ( -29.50)
>DroSim_CAF1 30308 111 + 1
AAA---------AAAUAUAUGUCAGCGGGCAUUAUCCUUUACGGUUUUCUCAUUGCGGAAGACCUGGCCUCGUCCGCGGAAAAUGGCAGCCAACAGGGAAUAAAUGUUGGUUGCAGACUG
...---------........(((.((((((.....((.....((((((((......)))))))).))....))))))........((((((((((.........)))))))))).))).. ( -38.30)
>DroEre_CAF1 35970 112 + 1
AACA--------AAAUAUAUGUCAGGGGGCAUUAUACUUUAAUGUUUUCUCAUUGCGCCAGACUUGGCUUCGUCCGCAGAAAAUGGCAGCCAACAGGGAAUAAAUGUUGGUUGCAGACUG
....--------........(((((..(((((((.....)))))))..))..(((((...(((........))))))))......((((((((((.........)))))))))).))).. ( -34.00)
>DroYak_CAF1 34596 120 + 1
AAAAAAUAAGCGAAAUAUAUGUCAGCAGCCAUUAUACUUUAAUGUUUUCUCAUUGCGGCAGACUUGGCCACGUCCGUGGAAAAUGACAGCCAACAGGGAAUAAAUGUUGGUUGCAGACUG
.........(((.......(((((....((((...((..(((((......))))).(((.......)))..))..))))....)))))(((((((.........))))))))))...... ( -26.70)
>consensus
AAAA________AAAUAUAUGUCAGCGGGCAUUAUACUUUAAGGUUUUCUCAUUGCGGCAGACCUGGCCUCGUCCGCGGAAAAUGGCAGCCAACAGGGAAUAAAUGUUGGUUGCAGACUG
....................(((....................(((((((....(((...(((........))))))))))))).((((((((((.........)))))))))).))).. (-22.75 = -23.12 +   0.37)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,994,091 – 21,994,211
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -37.30
Consensus MFE -31.99
Energy contribution -31.86
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -2.48
Structure conservation index 0.86
SVM decision value 0.78
SVM RNA-class probability 0.847642
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21994091 120 + 27905053
AAAUGGCAGCCAACAGGGAAUAAAUGUUGGUUGCAGACUGGCAGGGAUUACUCAUCAAACCAAGUGCAGUCAGUUCAACGUGGCGGAAACCGCACAUAAAGCCACUAGAGACCUGCAUUU
.....((((((((((.........))))))))))......((((((((.....))).......((((.((((........))))(....).))))................))))).... ( -35.60)
>DroSim_CAF1 30379 120 + 1
AAAUGGCAGCCAACAGGGAAUAAAUGUUGGUUGCAGACUGUCAGGGAUUACUCAUCAAACCAAGUGCAGGCAGUCCAACGUGGCGGAAACCGCACAGAAAGCCACUAGAGACCUGCAUUU
.....((((((((((.........)))))))))).........(((....)))........((((((((((.(.....)((((((....)(.....)...)))))....).))))))))) ( -36.10)
>DroEre_CAF1 36042 120 + 1
AAAUGGCAGCCAACAGGGAAUAAAUGUUGGUUGCAGACUGGCAGGGAUUACUCAUCAAACCAAGUGCAGUCUGUCCAACGUGGUGGAAACCGCACAGAAAGCCACUAGAGACCUGCAUUU
.....((((((((((.........))))))))))......((((((((.....)))......(((((..(((((.....(((((....))))))))))..).)))).....))))).... ( -41.80)
>DroYak_CAF1 34676 120 + 1
AAAUGACAGCCAACAGGGAAUAAAUGUUGGUUGCAGACUGGCAGGGAUUACUCAUCAAACCAAGUGCAGUAAGUCCAACGUGGCGGAAACCGCACAGAAAGCCACUAGAGACCUGCAUUU
...((.(((((((((.........))))))))))).....(((((((((((((((........))).))).)))))...((((((....)(.....)...))))).......)))).... ( -35.70)
>consensus
AAAUGGCAGCCAACAGGGAAUAAAUGUUGGUUGCAGACUGGCAGGGAUUACUCAUCAAACCAAGUGCAGUCAGUCCAACGUGGCGGAAACCGCACAGAAAGCCACUAGAGACCUGCAUUU
.....((((((((((.........)))))))))).........(((....)))........((((((((...(((....(((((................)))))....))))))))))) (-31.99 = -31.86 +  -0.12)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:04:28 2006