Locus 4482

Sequence ID	3L_DroMel_CAF1
Location	12,972,932 – 12,973,120
Length	188
Max. P	0.879449

overview

Window 3

Location	12,972,932 – 12,973,045
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.56
Mean single sequence MFE	-31.44
Consensus MFE	-25.00
Energy contribution	-25.08
Covariance contribution	0.08
Combinations/Pair	1.18
Mean z-score	-1.94
Structure conservation index	0.80
SVM decision value	0.91
SVM RNA-class probability	0.879449
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12972932 113 + 23771897
UA----UAACGUAAUAUAUAUGGGCAGGU---GUACUUGCAUUAUAUUUUUGCCAACUCUGUUGAGGCUAAAAGAACACUAGUUACCAGGUUACGCGAAAGCGUCACGUUGGCAUCGCGU
..----..((((...(((((...(((((.---...)))))..)))))...(((((((.(((..(..((((.........))))..))))((.((((....)))).)))))))))..)))) ( -34.20)
>DroSec_CAF1 90315 113 + 1
UA----UAACGUAAUAUAUAUGGGCAGGU---GUACUUGCAUUAUAUUUAUGCCAACUCUAUUGAGGCUAAAAGAACACUAGUUACCAGGUUACGCGAAAGCGUCACGUUGGCAUCGCGU
..----..((((...(((((...(((((.---...)))))..)))))..((((((((........(((((.........))))).....((.((((....)))).)))))))))).)))) ( -33.30)
>DroSim_CAF1 100009 113 + 1
UA----UAACGUAAUAUAUAUGGGCAAGU---GUACUUGCAUUAUAUUUAUGCCAACUCUAUUGAGGCUAAAAGAACACUAGUUACCAGGUUACGCGAAAGCGUCACGUUGGCAUCGCGU
..----..((((...(((((...(((((.---...)))))..)))))..((((((((........(((((.........))))).....((.((((....)))).)))))))))).)))) ( -33.60)
>DroEre_CAF1 95690 119 + 1
UAGUAAUUUCUCUAUAUAUGUGUGUAAUUUCCUUACUUGCAUGAUCACCUUGCCAACUCUAUUGAGGCCAGAAGAACUCGCGUUACCAGGUUACGCGA-AGCGUCACGUUGGCAUCGCGU
..((............((((((.((((.....)))).)))))).......((((((((((.(((....))).)))..((((((.((...)).))))))-........)))))))..)).. ( -26.20)
>DroYak_CAF1 94264 101 + 1
UA----CAUCGCUAUAUAUGUGA---------------GCAUGAUCACUUUGCCAACUCUAUUGAGGCUAGAAGAAUACUCGUUACCAGGUUACGCGAAAGCGUCACGUUGGCAUCGCGU
..----...(((.......((((---------------......))))..(((((((......(((............)))........((.((((....)))).)))))))))..))). ( -29.90)
>consensus
UA____UAACGUAAUAUAUAUGGGCAAGU___GUACUUGCAUUAUAUUUUUGCCAACUCUAUUGAGGCUAAAAGAACACUAGUUACCAGGUUACGCGAAAGCGUCACGUUGGCAUCGCGU
.........(((...........((((((.....))))))..........((((((((((.(((....))).)))..............((.((((....)))).)))))))))..))). (-25.00 = -25.08 +   0.08)

alignment

secondary structure

dotplot

Window 4

Location	12,973,005 – 12,973,120
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.84
Mean single sequence MFE	-32.73
Consensus MFE	-29.44
Energy contribution	-29.12
Covariance contribution	-0.32
Combinations/Pair	1.07
Mean z-score	-1.19
Structure conservation index	0.90
SVM decision value	0.25
SVM RNA-class probability	0.653571
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12973005 115 + 23771897
AGUUACCAGGUUACGCGAAAGCGUCACGUUGGCAUCGCGUGCUGGGCAACGUGUGCUGGAUAAU-----AUAACGUAUACGCCAAGGCGGCCAAAUGUGUAGAAAUGAAACAUUAAAUUA
.(((.((((((.((((....)))).)).))))...(((((..(((.(...((((((........-----.....))))))((....))).))).))))).........)))......... ( -31.82)
>DroSec_CAF1 90388 115 + 1
AGUUACCAGGUUACGCGAAAGCGUCACGUUGGCAUCGCGUGCUGGGCAACGUGUGCUGGAUAAU-----AUAACGUAUAUGCCAAGGCGGCCAAAUGUGUAGAAAUGAAACAUUAAAUUA
.((..((..((.((((....)))).)).(((((((.((((....(....)((((........))-----)).))))..)))))))))..))..(((((.((....))..)))))...... ( -30.70)
>DroSim_CAF1 100082 115 + 1
AGUUACCAGGUUACGCGAAAGCGUCACGUUGGCAUCGCGUGCUGGGCAACGUGUGCUGGAUAAU-----AUAACGUAUACGCCAAGGCGGCCAAAUGUGUAGAAAUGAAACAUUAAAUUA
.(((.((((((.((((....)))).)).))))...(((((..(((.(...((((((........-----.....))))))((....))).))).))))).........)))......... ( -31.82)
>DroEre_CAF1 95770 113 + 1
CGUUACCAGGUUACGCGA-AGCGUCACGUUGGCAUCGCGUGCUU-ACAACGUGUGCUGGGUAGU-----AUAACGUAUACGCCAAGGUGGCCAAAUGUGUAGAAAUGAAACAUUAAAUUA
.(((..((..(((((((.-...(((((.(((((...(((..(..-.....)..)))......((-----(((...)))))))))).)))))....)))))))...)).)))......... ( -32.40)
>DroYak_CAF1 94325 119 + 1
CGUUACCAGGUUACGCGAAAGCGUCACGUUGGCAUCGCGUGCUU-ACAACGUGUGCUGGGUAGUGCGAUAUAACGUAUACGCCAAGGCGGCCAAAUGUGCAGAAAUGAAACAUUAAAUUA
...((((..((.((((....)))).))...((((.(((((....-...))))))))).))))(((((......))))).(((....)))....(((((.((....))..)))))...... ( -36.90)
>consensus
AGUUACCAGGUUACGCGAAAGCGUCACGUUGGCAUCGCGUGCUGGGCAACGUGUGCUGGAUAAU_____AUAACGUAUACGCCAAGGCGGCCAAAUGUGUAGAAAUGAAACAUUAAAUUA
.((((....((.((((....)))).)).(..(((.(((((........))))))))..)...........)))).....(((....)))....(((((...........)))))...... (-29.44 = -29.12 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:29 2006