Locus 2778

Sequence ID	X_DroMel_CAF1
Location	7,468,458 – 7,468,652
Length	194
Max. P	0.981477

overview

Window 4

Location	7,468,458 – 7,468,578
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.50
Mean single sequence MFE	-40.60
Consensus MFE	-37.76
Energy contribution	-37.80
Covariance contribution	0.04
Combinations/Pair	1.02
Mean z-score	-1.44
Structure conservation index	0.93
SVM decision value	0.68
SVM RNA-class probability	0.820717
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7468458 120 - 22224390
CAAUUGCCCGGGCAGCGAGCAGAAAAAGUGUUGCGUUUAACUGGUAAAUCAGUUCGACUACCGGCUGAGUCCGUAUCUGAGAUAUGAGAUCCACCGCCGGACGUUGGCGGCGGAAAGACA
.....(((.((((((((...........))))))(((.((((((....)))))).)))..)))))...(((((((((...))))))...(((.((((((.....)))))).)))..))). ( -40.30)
>DroSec_CAF1 1763 120 - 1
CAAUUGCCCGGGCAGCGAGCAGAAAAAGUGUUGCGUUUAACUGGUAAAUAAGUUCGACUACCGGCUGAGUCCGUAUCUGAGAUAUGAGAUUCACCGCCGGACGUUGGCGGCGGAAAGACA
...(((((..(.(((((.((((........))))(((.((((........)))).)))..(((((((((((((((((...)))))).))))))..))))).))))).))))))....... ( -40.70)
>DroSim_CAF1 3465 120 - 1
CAAUUGCCCGGGCAGCGAGCAGAAAAAGUGUUGCGUUUAACUGGUAAAUCAGUUCGACUACCGGCUGAGUCCGUAUCUGAGAUAUGAGAUUCACCGCCGGACGUUGGCGGCGGAAAGACA
...(((((..(.(((((.((((........))))(((.((((((....)))))).)))..(((((((((((((((((...)))))).))))))..))))).))))).))))))....... ( -43.20)
>DroEre_CAF1 2003 120 - 1
CAAUUGCCCGGGCAGCGAGCAGAAAAAGUGUUGCGUUUAACUGGUAAAUCAGUUCGACUACCGGCUGAGUCCGUAUCUGAGAUAUGAGAUCCACCGCCGGACGUUGGCGGCGGAAAGACA
.....(((.((((((((...........))))))(((.((((((....)))))).)))..)))))...(((((((((...))))))...(((.((((((.....)))))).)))..))). ( -40.30)
>DroYak_CAF1 3981 120 - 1
CAAUUGCCCGGGCAGCGAGCAGAAAAAGUGUUGCGUUUAACUGGUAAAUCAGUUCGACUACCGGCUGAGUUCGUAUCUGAGAUAUGAGAUCCAACGCCGGACGUUGGCGGCGGAAAGACA
...(((((..(.(((((.((((........))))(((.((((((....)))))).)))..(((((.((.((((((((...)))))))).))....))))).))))).))))))....... ( -38.50)
>consensus
CAAUUGCCCGGGCAGCGAGCAGAAAAAGUGUUGCGUUUAACUGGUAAAUCAGUUCGACUACCGGCUGAGUCCGUAUCUGAGAUAUGAGAUCCACCGCCGGACGUUGGCGGCGGAAAGACA
...(((((..(.(((((.((((........))))(((.((((((....)))))).)))..(((((((.(((((((((...)))))).))).))..))))).))))).))))))....... (-37.76 = -37.80 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	7,468,538 – 7,468,652
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.18
Mean single sequence MFE	-19.92
Consensus MFE	-18.50
Energy contribution	-18.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.93
SVM decision value	1.89
SVM RNA-class probability	0.981477
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7468538 114 + 22224390
UUAAACGCAACACUUUUUCUGCUCGCUGCCCGGGCAAUUGAUCAUACUAAUGAUUAUUAUCUGGCCGCCGGACGAGACAAUCCCAAUCCCAUUCC------AUCAUUCCCCAUCCCCCAU
...................(((((((((..(((.((..(((((((....))))))).....)).))).))).)))).))................------................... ( -19.00)
>DroSec_CAF1 1843 107 + 1
UUAAACGCAACACUUUUUCUGCUCGCUGCCCGGGCAAUUGAUCAUACUAAUGAUUAUUAUCUGGCCGCCGGACGAGACAAUCCCAAUCCCAUUCC------AUCAUUCCCCAU-------
...................(((((((((..(((.((..(((((((....))))))).....)).))).))).)))).))................------............------- ( -19.00)
>DroSim_CAF1 3545 107 + 1
UUAAACGCAACACUUUUUCUGCUCGCUGCCCGGGCAAUUGAUCAUACUAAUGAUUAUUAUCUGGCCGCCGGACGAGACAAUCCCAAUCCCAUUCC------AUCAUUCCCCAU-------
...................(((((((((..(((.((..(((((((....))))))).....)).))).))).)))).))................------............------- ( -19.00)
>DroEre_CAF1 2083 113 + 1
UUAAACGCAACACUUUUUCUGCUCGCUGCCCGGGCAAUUGAUCAUACUAAUGAUUAUUAUCUGCCCGCCGGACGAGACAAUCCCAAUCCCAUUCCCCAUCCCCCAUUCCCCAU-------
...................(((((((((..((((((..(((((((....))))))).....)))))).))).)))).))..................................------- ( -23.60)
>DroYak_CAF1 4061 106 + 1
UUAAACGCAACACUUUUUCUGCUCGCUGCCCGGGCAAUUGAUCAUACUAAUGAUUAUUAUCUGGCCGCCGGACGAGACAAUCCCAAACCCAUUCCCC--CCAUCAUUU------------
...................(((((((((..(((.((..(((((((....))))))).....)).))).))).)))).))..................--.........------------ ( -19.00)
>consensus
UUAAACGCAACACUUUUUCUGCUCGCUGCCCGGGCAAUUGAUCAUACUAAUGAUUAUUAUCUGGCCGCCGGACGAGACAAUCCCAAUCCCAUUCC______AUCAUUCCCCAU_______
...................(((((((((..(((.((..(((((((....))))))).....)).))).))).)))).))......................................... (-18.50 = -18.50 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:57 2006