Locus 5445

Sequence ID X_DroMel_CAF1
Location 14,179,988 – 14,180,083
Length 95
Max. P 0.934957
window8828 window8829

overview

Window 8

Location 14,179,988 – 14,180,083
Length 95
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 92.46
Mean single sequence MFE -32.12
Consensus MFE -25.71
Energy contribution -25.77
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.23
Structure conservation index 0.80
SVM decision value 0.81
SVM RNA-class probability 0.857304
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14179988 95 + 22224390
GGAAAGAAGGAGAAGAUGAAAAACCGGGGAAGCCCACUCAGCCACCCAAUCUCCUUAUGGGUUCUCAGGUUCUUAGGACCUCAGGACCUCGUCCU
(((...(((((((...(....)...(((....)))..............)))))))..(((((((.(((((.....))))).)))))))..))). ( -32.00)
>DroSec_CAF1 90429 95 + 1
GGAAAGGACGAGAAGAUGAAAAACCGGGGAAGCCCACUCAGCCACCCAAUCUCCUUAUGGGUUCUCAGGUUCUCAGGACCCCAGAACCUCGUCCU
....(((((((((............(((....)))........(((((.........)))))))))(((((((..((...))))))))).))))) ( -29.80)
>DroSim_CAF1 67942 95 + 1
GGAAAGGACGAGAAGAUGAAAAACCGGGGAAGCCCACUCAGCCACCCAAUCUCCUUAUGGGUUCUCAGGUUCUCAGGACCUCAGGACCUCGUCCU
....((((((((.............(((....))).................((....))(((((.(((((.....))))).))))))))))))) ( -31.30)
>DroEre_CAF1 80112 94 + 1
GGAAAAAACGAGAAGAUGGAAGA-GGGGGAGGCCCACUCAGCCACCCAAUCUUCUUAUGGGUUCUCAGGUUUUCAAGACCUCAGGACCUCGUCCU
(((......((((((((((..((-((((....))).)))..))).....)))))))..(((((((.(((((.....))))).)))))))..))). ( -35.40)
>consensus
GGAAAGAACGAGAAGAUGAAAAACCGGGGAAGCCCACUCAGCCACCCAAUCUCCUUAUGGGUUCUCAGGUUCUCAGGACCUCAGGACCUCGUCCU
(((......(((.((((.........(((..((.......))..))).)))).)))..(((((((.(((((.....))))).)))))))..))). (-25.71 = -25.77 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 14,179,988 – 14,180,083
Length 95
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 92.46
Mean single sequence MFE -34.35
Consensus MFE -31.67
Energy contribution -31.05
Covariance contribution -0.62
Combinations/Pair 1.23
Mean z-score -1.89
Structure conservation index 0.92
SVM decision value 1.24
SVM RNA-class probability 0.934957
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14179988 95 - 22224390
AGGACGAGGUCCUGAGGUCCUAAGAACCUGAGAACCCAUAAGGAGAUUGGGUGGCUGAGUGGGCUUCCCCGGUUUUUCAUCUUCUCCUUCUUUCC
.(((.(.(((.((.((((.......)))).)).))))..(((((((..((((((..((.((((....)))).))..)))))))))))))...))) ( -32.80)
>DroSec_CAF1 90429 95 - 1
AGGACGAGGUUCUGGGGUCCUGAGAACCUGAGAACCCAUAAGGAGAUUGGGUGGCUGAGUGGGCUUCCCCGGUUUUUCAUCUUCUCGUCCUUUCC
((((((.((((((.((((.......)))).))))))).....((((..((((((..((.((((....)))).))..))))))))))))))).... ( -38.30)
>DroSim_CAF1 67942 95 - 1
AGGACGAGGUCCUGAGGUCCUGAGAACCUGAGAACCCAUAAGGAGAUUGGGUGGCUGAGUGGGCUUCCCCGGUUUUUCAUCUUCUCGUCCUUUCC
(((((((((((((..(((.((.((...)).)).)))....))))....((((((..((.((((....)))).))..))))))))))))))).... ( -34.30)
>DroEre_CAF1 80112 94 - 1
AGGACGAGGUCCUGAGGUCUUGAAAACCUGAGAACCCAUAAGAAGAUUGGGUGGCUGAGUGGGCCUCCCCC-UCUUCCAUCUUCUCGUUUUUUCC
((((((((((.((.((((.......)))).)).))).....(((((..(((.((((.....)))).)))..-))))).......))))))).... ( -32.00)
>consensus
AGGACGAGGUCCUGAGGUCCUGAGAACCUGAGAACCCAUAAGGAGAUUGGGUGGCUGAGUGGGCUUCCCCGGUUUUUCAUCUUCUCGUCCUUUCC
((((((((((.((.((((.......)))).)).))).....((((((((((.((((.....))))..)))))))))).......))))))).... (-31.67 = -31.05 +  -0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:03 2006