Locus 1788

Sequence ID X_DroMel_CAF1
Location 4,937,156 – 4,937,250
Length 94
Max. P 0.834128
window2921 window2922

overview

Window 1

Location 4,937,156 – 4,937,250
Length 94
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 85.19
Mean single sequence MFE -26.05
Consensus MFE -19.36
Energy contribution -19.68
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -1.94
Structure conservation index 0.74
SVM decision value 0.73
SVM RNA-class probability 0.834128
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4937156 94 + 22224390
GCCAAA--CCGGCAGAUAAAUUGUAGAUACAGACAGGUACACAGGUGCACACACCC--AUAUAGCGUAUAGCAAAAGG-----CGGAAUGUGUGCCAAGUGGG
......--((.((.......((((....))))...((((((((((((....)))).--.....((.....))......-----.....))))))))..)).)) ( -24.30)
>DroSim_CAF1 2412 94 + 1
GCCAAA--CCGGCAGAUAAAUUGUAGAUACAGACAGGUACACAGGUGCACACACCU--AUAUAGCAUAUAGCAAAAGG-----CGGAAUGUGUGCCAAGUGGG
......--((.((.......((((....))))...((((((((((((....)))))--.....((.....))......-----......)))))))..)).)) ( -24.20)
>DroEre_CAF1 11465 94 + 1
GCCAAA--CCGGCAGAUAAAUUGUAGAUACAGACAGGUACACAGGUGCACACAUCCACAUAUA-------GCAAUAGCGGUAUGGGAAUGUGUGCCAAGUGGG
(((...--..))).......((((........))))...(((..(.((((((((((.(((((.-------((....)).))))))).)))))))))..))).. ( -30.80)
>DroYak_CAF1 10928 94 + 1
GGCAAACACCGGCAGAUAAAUUGUAGAUACAGGCAGGUACACAGGUGCACACACCC--AUAUA-------GCAAAAGCGGAAUGGAAAUGUGUGCCAAGUGGG
........((.((.......((((....))))...((((((((((((....))))(--((...-------((....))...)))....))))))))..)).)) ( -24.90)
>consensus
GCCAAA__CCGGCAGAUAAAUUGUAGAUACAGACAGGUACACAGGUGCACACACCC__AUAUA_______GCAAAAGC_____CGGAAUGUGUGCCAAGUGGG
........((.((.......((((....))))...((((((((((((....))))...............((....))..........))))))))..)).)) (-19.36 = -19.68 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 4,937,156 – 4,937,250
Length 94
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 85.19
Mean single sequence MFE -24.00
Consensus MFE -15.90
Energy contribution -15.65
Covariance contribution -0.25
Combinations/Pair 1.15
Mean z-score -1.64
Structure conservation index 0.66
SVM decision value 0.08
SVM RNA-class probability 0.573650
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4937156 94 - 22224390
CCCACUUGGCACACAUUCCG-----CCUUUUGCUAUACGCUAUAU--GGGUGUGUGCACCUGUGUACCUGUCUGUAUCUACAAUUUAUCUGCCGG--UUUGGC
.(((.((((((........(-----(.....))((((.(((((((--(((((....))))))))))...)).)))).............))))))--..))). ( -20.80)
>DroSim_CAF1 2412 94 - 1
CCCACUUGGCACACAUUCCG-----CCUUUUGCUAUAUGCUAUAU--AGGUGUGUGCACCUGUGUACCUGUCUGUAUCUACAAUUUAUCUGCCGG--UUUGGC
.(((.((((((........(-----(.....))((((.(((((((--(((((....))))))))))...)).)))).............))))))--..))). ( -22.10)
>DroEre_CAF1 11465 94 - 1
CCCACUUGGCACACAUUCCCAUACCGCUAUUGC-------UAUAUGUGGAUGUGUGCACCUGUGUACCUGUCUGUAUCUACAAUUUAUCUGCCGG--UUUGGC
..(((...((((((((((.((((..((....))-------..)))).))))))))))....))).(((.((..(((.........)))..)).))--)..... ( -26.90)
>DroYak_CAF1 10928 94 - 1
CCCACUUGGCACACAUUUCCAUUCCGCUUUUGC-------UAUAU--GGGUGUGUGCACCUGUGUACCUGCCUGUAUCUACAAUUUAUCUGCCGGUGUUUGCC
..(((...((((((((..((((...((....))-------...))--))))))))))....)))((((.((..(((.........)))..)).))))...... ( -26.20)
>consensus
CCCACUUGGCACACAUUCCC_____CCUUUUGC_______UAUAU__GGGUGUGUGCACCUGUGUACCUGUCUGUAUCUACAAUUUAUCUGCCGG__UUUGGC
..(((...((((((((((.............................))))))))))....)))..((.((..(((.........)))..)).))........ (-15.90 = -15.65 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:55 2006