Locus 1439

Sequence ID X_DroMel_CAF1
Location 4,338,886 – 4,338,977
Length 91
Max. P 0.997158
window2297 window2298

overview

Window 7

Location 4,338,886 – 4,338,977
Length 91
Sequences 5
Columns 91
Reading direction forward
Mean pairwise identity 70.48
Mean single sequence MFE -22.70
Consensus MFE -11.12
Energy contribution -12.72
Covariance contribution 1.60
Combinations/Pair 1.22
Mean z-score -1.76
Structure conservation index 0.49
SVM decision value 0.50
SVM RNA-class probability 0.758869
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4338886 91 + 22224390
AAUUAAGCGUGUGUGUCAUAUUUGACAUAAUGCUUUUUAUAGGAAACAGGCCACACUGGGCGAAUGAACAGUGUGACCUUGCUUAACAGCC
..((((((((((((((((....)))))).))))........(....)(((.(((((((..(....)..))))))).))).))))))..... ( -30.40)
>DroSec_CAF1 124761 81 + 1
AAUUAAGCUUGUGUGUCAUU----------UGCUUUUUAAAGGAAACAGACCACACUGGGCGAGUAAACAGUGUGACCCUGCUCAACAGCU
.....((((((.(((((.((----------(.(((....))).)))..)))(((((((..........))))))).....)).))..)))) ( -17.40)
>DroSim_CAF1 118141 81 + 1
AAUUAUGUUUGGGUGUCAUU----------UGCUUUUUAAAGGAAACAGACCACACUGGGCGAGUGAACAGUGUGACCCUGCUUAACAGCU
.....((((.(((((((.((----------(.(((....))).)))..)))(((((((..(....)..))))))))))).....))))... ( -21.90)
>DroEre_CAF1 132678 71 + 1
GAUUGAGCCUGG---------------UUAUGCUUUUUGUUGGAAGGCGGCCACACCUGGCGAGUAAAUAGUUUGACCCUGCUUAA-----
..((((((..((---------------(((.(((.(((((((..(((.(....).)))..))).)))).))).)))))..))))))----- ( -21.30)
>DroYak_CAF1 126635 89 + 1
AAUUGAGUCUGGGUAUCU-AUUAAACAUUAUCCUUUUUUUAGGAAACAGGCCACACCUGGCGCAUAAACGGUGUGACCCUGCCUAACC-CU
..........((((....-...........((((......))))..((((.((((((............))))))..))))....)))-). ( -22.50)
>consensus
AAUUAAGCCUGGGUGUCAUA_______U_AUGCUUUUUAUAGGAAACAGGCCACACUGGGCGAGUAAACAGUGUGACCCUGCUUAACAGCU
..((((((..((((...........................(....)....(((((((..........))))))))))).))))))..... (-11.12 = -12.72 +   1.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 4,338,886 – 4,338,977
Length 91
Sequences 5
Columns 91
Reading direction reverse
Mean pairwise identity 70.48
Mean single sequence MFE -22.80
Consensus MFE -13.78
Energy contribution -13.66
Covariance contribution -0.12
Combinations/Pair 1.40
Mean z-score -2.38
Structure conservation index 0.60
SVM decision value 2.81
SVM RNA-class probability 0.997158
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4338886 91 - 22224390
GGCUGUUAAGCAAGGUCACACUGUUCAUUCGCCCAGUGUGGCCUGUUUCCUAUAAAAAGCAUUAUGUCAAAUAUGACACACACGCUUAAUU
....(((((((.(((((((((((..(....)..)))))))))))....................(((((....))))).....))))))). ( -29.60)
>DroSec_CAF1 124761 81 - 1
AGCUGUUGAGCAGGGUCACACUGUUUACUCGCCCAGUGUGGUCUGUUUCCUUUAAAAAGCA----------AAUGACACACAAGCUUAAUU
....(((((((.((..(((((((..........)))))))..))((((........)))).----------............))))))). ( -21.50)
>DroSim_CAF1 118141 81 - 1
AGCUGUUAAGCAGGGUCACACUGUUCACUCGCCCAGUGUGGUCUGUUUCCUUUAAAAAGCA----------AAUGACACCCAAACAUAAUU
.(((....))).(((((((((((..(....)..)))))))(((.((((.(((....))).)----------)))))))))).......... ( -23.00)
>DroEre_CAF1 132678 71 - 1
-----UUAAGCAGGGUCAAACUAUUUACUCGCCAGGUGUGGCCGCCUUCCAACAAAAAGCAUAA---------------CCAGGCUCAAUC
-----.......((((.((....)).))))(((.(((...((................))...)---------------)).)))...... ( -11.09)
>DroYak_CAF1 126635 89 - 1
AG-GGUUAGGCAGGGUCACACCGUUUAUGCGCCAGGUGUGGCCUGUUUCCUAAAAAAAGGAUAAUGUUUAAU-AGAUACCCAGACUCAAUU
.(-(((((((((((((((((((............))))))))))...((((......))))...))))))..-....)))).......... ( -28.80)
>consensus
AGCUGUUAAGCAGGGUCACACUGUUUACUCGCCCAGUGUGGCCUGUUUCCUAUAAAAAGCAU_A_______AAUGACACCCAAGCUUAAUU
.......(((((.((((((((((..........)))))))))))))))........................................... (-13.78 = -13.66 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:29 2006