Locus 10298

Sequence ID	3R_DroMel_CAF1
Location	27,608,599 – 27,608,698
Length	99
Max. P	0.901326

overview

Window 6

Location	27,608,599 – 27,608,698
Length	99
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	73.87
Mean single sequence MFE	-22.33
Consensus MFE	-11.25
Energy contribution	-10.83
Covariance contribution	-0.41
Combinations/Pair	1.25
Mean z-score	-1.71
Structure conservation index	0.50
SVM decision value	0.28
SVM RNA-class probability	0.665193
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27608599 99 + 27905053
AUUGUUUU-----------CUGUAUCAAUCUCUUAAUAUC---UCUUCUUUUUAGGAACACUGCACGCCAGAGCAAAUGUUUUUGCACCCCACACCUGCUCAAGUGCUAUACA
........-----------..((((.....((((((....---........)))))).....((((....(((((..(((...........)))..)))))..)))).)))). ( -16.00)
>DroPse_CAF1 12771 106 + 1
AGAUUGAU--CUGC-----AUACGUCAGCCUUUUCACGGGGCAUCUUUCCAGCAGGAGAGCUGCACCCCCGAACAGAUGUUCCUGCAUCCGACGCCCGCCCAAGUGCUCUACA
........--..((-----...((((......(((..((((((.((((((....)))))).))).)))..)))..(((((....))))).))))...)).............. ( -28.70)
>DroSec_CAF1 10403 99 + 1
AUUUUAUU-----------GUAUAUUAAUCUCUUAAUAUC---UCUUCUUUUUAGGAACACUGCACUCCAGAGCAAAUGUUUUUGCACCCCACGCCUGCUCAAGUGCUAUACA
.......(-----------(((((......((((((....---........)))))).....(((((...(((((..(((...........)))..))))).))))))))))) ( -17.70)
>DroSim_CAF1 10467 99 + 1
AGUUUAUU-----------GUAUAUUAAUCUCUUAAUAUC---UCUUCCCUUUAGGAACACUGCACUCCAGAGCAAAUGUUUUUGCACCCCACGCCUGCUCAAGUGCUAUACA
.......(-----------(((((......((((((....---........)))))).....(((((...(((((..(((...........)))..))))).))))))))))) ( -17.70)
>DroEre_CAF1 10537 110 + 1
AGUUCAUUAUGUGCAUUGUCUACAUUAAUCUCUAAUUAAC---UCUUCCUUCUAGGAACAUUGCACGCCGGAGCAGAUGUUUUUGCAUCCCACACCUGCUCAAGUGCUGUACA
.........((((((.........................---..((((.....))))....((((....((((((.(((...........))).))))))..)))))))))) ( -25.00)
>DroYak_CAF1 10454 110 + 1
AUUUUGUCAUGUGCACCGCCUAAAUUAAUGUCUUAUUAAC---UCUUUCUUUUAGGAGCACUGCACGCCGGAGCAGAUGUUUUUGCACCCCACACCUGCUCAGGUGCUGUACA
..........((((....((((((..((.((.......))---...))..)))))).))))((((((((.((((((.(((...........))).)))))).)))).)))).. ( -28.90)
>consensus
AGUUUAUU___________CUAUAUUAAUCUCUUAAUAUC___UCUUCCUUUUAGGAACACUGCACGCCAGAGCAAAUGUUUUUGCACCCCACACCUGCUCAAGUGCUAUACA
.............................................((((.....))))....((((....(((((..(((...........)))..)))))..))))...... (-11.25 = -10.83 +  -0.41)

alignment

secondary structure

dotplot

Window 7

Location	27,608,599 – 27,608,698
Length	99
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	73.87
Mean single sequence MFE	-28.94
Consensus MFE	-14.98
Energy contribution	-14.32
Covariance contribution	-0.66
Combinations/Pair	1.31
Mean z-score	-1.95
Structure conservation index	0.52
SVM decision value	1.02
SVM RNA-class probability	0.901326
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27608599 99 - 27905053
UGUAUAGCACUUGAGCAGGUGUGGGGUGCAAAAACAUUUGCUCUGGCGUGCAGUGUUCCUAAAAAGAAGA---GAUAUUAAGAGAUUGAUACAG-----------AAAACAAU
(((((.((((..((((((((((...........))))))))))....))))(((((..((.......)).---.))))).........))))).-----------........ ( -24.50)
>DroPse_CAF1 12771 106 - 1
UGUAGAGCACUUGGGCGGGCGUCGGAUGCAGGAACAUCUGUUCGGGGGUGCAGCUCUCCUGCUGGAAAGAUGCCCCGUGAAAAGGCUGACGUAU-----GCAG--AUCAAUCU
...(((........(((.(((((((..((((......))))(((.(((.(((.((.(((....))).)).)))))).))).....))))))).)-----))..--.....))) ( -35.66)
>DroSec_CAF1 10403 99 - 1
UGUAUAGCACUUGAGCAGGCGUGGGGUGCAAAAACAUUUGCUCUGGAGUGCAGUGUUCCUAAAAAGAAGA---GAUAUUAAGAGAUUAAUAUAC-----------AAUAAAAU
(((((((((((((((((((.((...........)).)))))))..))))))(((((..((.......)).---.)))))..........)))))-----------)....... ( -23.60)
>DroSim_CAF1 10467 99 - 1
UGUAUAGCACUUGAGCAGGCGUGGGGUGCAAAAACAUUUGCUCUGGAGUGCAGUGUUCCUAAAGGGAAGA---GAUAUUAAGAGAUUAAUAUAC-----------AAUAAACU
(((((((((((((((((((.((...........)).)))))))..))))))..(.((((.....)))).)---................)))))-----------)....... ( -24.70)
>DroEre_CAF1 10537 110 - 1
UGUACAGCACUUGAGCAGGUGUGGGAUGCAAAAACAUCUGCUCCGGCGUGCAAUGUUCCUAGAAGGAAGA---GUUAAUUAGAGAUUAAUGUAGACAAUGCACAUAAUGAACU
.((.((((....((((((((((...........))))))))))..))(((((.((((((.....)))...---(((((((...)))))))....))).)))))....)).)). ( -31.20)
>DroYak_CAF1 10454 110 - 1
UGUACAGCACCUGAGCAGGUGUGGGGUGCAAAAACAUCUGCUCCGGCGUGCAGUGCUCCUAAAAGAAAGA---GUUAAUAAGACAUUAAUUUAGGCGGUGCACAUGACAAAAU
(((.((((((((((((((((((...........))))))))).))).)))).((((.((.....(...((---((((((.....))))))))...))).)))).))))).... ( -34.00)
>consensus
UGUAUAGCACUUGAGCAGGCGUGGGGUGCAAAAACAUCUGCUCUGGCGUGCAGUGUUCCUAAAAGGAAGA___GAUAUUAAGAGAUUAAUAUAG___________AAUAAAAU
......((((..(((((((.((...........)).)))))))....)))).............................................................. (-14.98 = -14.32 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:53:32 2006