Locus 4991

Sequence ID	3L_DroMel_CAF1
Location	13,750,560 – 13,750,680
Length	120
Max. P	0.979407

overview

Window 3

Location	13,750,560 – 13,750,680
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.67
Mean single sequence MFE	-28.47
Consensus MFE	-26.02
Energy contribution	-25.98
Covariance contribution	-0.04
Combinations/Pair	1.13
Mean z-score	-1.39
Structure conservation index	0.91
SVM decision value	1.02
SVM RNA-class probability	0.901183
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13750560 120 + 23771897
AUAAGCCACCAGUUUUUAUUUAUAUUAUAAAACUUCGUAAUGAAGUGGGCAAAAACAAAGAGUGUCCAGCAAACUUAAAGUUCUUAAACCGAAUUGAGCUGGUCAUGUCCAGCGCUGAUG
....(((.......(((((.......)))))(((((.....))))).)))................((((........(((((.......)))))..(((((......)))))))))... ( -25.50)
>DroSec_CAF1 157302 120 + 1
AUAAGCCAGCAGUUUUUAUUUAUAUUUUAAAACUUCGUAAUGAAGUGGGCAAAAACAAAGAGUGUCCAGCAAAUUUAAAGUUCUUAAACCGAAUUGAGCUGGUCAUGUCCAGCGCUGCUG
......(((((((.....((((.(((((((((((((.....)))))(((((...........)))))......))))))))...)))).........(((((......)))))))))))) ( -30.80)
>DroSim_CAF1 169544 120 + 1
AUAAGCCAGCAGUUUUUAUUUAUAUUUUAAAACUUCGUAAUGAAGUGGGCAAAAACAAAGAGUGUCCAGCAAAUUUAAAGUUCUUAAACCGAAUUGAGCUGGUCAUGUCCAGCGCUGCUG
......(((((((.....((((.(((((((((((((.....)))))(((((...........)))))......))))))))...)))).........(((((......)))))))))))) ( -30.80)
>DroEre_CAF1 164158 120 + 1
AUAAGCCAGCAGUUCUCAUUUAUAUUAUAAAACUUCGUAAUGAAGUGGGCAAGAACAAAGAGUGUCCAGCGAACUUAAAGUCCUUAAACCGAAUUGAGCUGGUCAUGUCCAGCACUGCUG
......(((((((.((...............(((((.....)))))(((((...((.....))(.(((((...........................))))).).))))))).))))))) ( -27.83)
>DroYak_CAF1 168487 120 + 1
AUAAGCCAGCAGCUCUCAUUUAUAUUAUAAAACUUCGUAAUGAAGUGGGCGAAAACAAAGAGUGUCCGGCAAACUUAAAGUUCUUAAACCGAAUUGAGCUGGUCAUGUCCAGCGCUGCCG
........(((((.(((((((.((((((........))))))))))))).(((....(((..((.....))..)))....)))..............(((((......)))))))))).. ( -27.40)
>consensus
AUAAGCCAGCAGUUUUUAUUUAUAUUAUAAAACUUCGUAAUGAAGUGGGCAAAAACAAAGAGUGUCCAGCAAACUUAAAGUUCUUAAACCGAAUUGAGCUGGUCAUGUCCAGCGCUGCUG
......(((((((..................(((((.....)))))(((((...((.....))(.(((((........(((((.......)))))..))))).).)))))...))))))) (-26.02 = -25.98 +  -0.04)

alignment

secondary structure

dotplot

Window 4

Location	13,750,560 – 13,750,680
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.67
Mean single sequence MFE	-29.17
Consensus MFE	-25.88
Energy contribution	-24.36
Covariance contribution	-1.52
Combinations/Pair	1.27
Mean z-score	-1.75
Structure conservation index	0.89
SVM decision value	1.84
SVM RNA-class probability	0.979407
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13750560 120 - 23771897
CAUCAGCGCUGGACAUGACCAGCUCAAUUCGGUUUAAGAACUUUAAGUUUGCUGGACACUCUUUGUUUUUGCCCACUUCAUUACGAAGUUUUAUAAUAUAAAUAAAAACUGGUGGCUUAU
..((((((((((......)))))..............((((.....))))))))).((((....(((((((...(((((.....)))))(((((...)))))))))))).))))...... ( -25.00)
>DroSec_CAF1 157302 120 - 1
CAGCAGCGCUGGACAUGACCAGCUCAAUUCGGUUUAAGAACUUUAAAUUUGCUGGACACUCUUUGUUUUUGCCCACUUCAUUACGAAGUUUUAAAAUAUAAAUAAAAACUGCUGGCUUAU
((((((.(((((......)))))....((((((.................)))))).....(((((.(((....(((((.....)))))....))).)))))......))))))...... ( -25.53)
>DroSim_CAF1 169544 120 - 1
CAGCAGCGCUGGACAUGACCAGCUCAAUUCGGUUUAAGAACUUUAAAUUUGCUGGACACUCUUUGUUUUUGCCCACUUCAUUACGAAGUUUUAAAAUAUAAAUAAAAACUGCUGGCUUAU
((((((.(((((......)))))....((((((.................)))))).....(((((.(((....(((((.....)))))....))).)))))......))))))...... ( -25.53)
>DroEre_CAF1 164158 120 - 1
CAGCAGUGCUGGACAUGACCAGCUCAAUUCGGUUUAAGGACUUUAAGUUCGCUGGACACUCUUUGUUCUUGCCCACUUCAUUACGAAGUUUUAUAAUAUAAAUGAGAACUGCUGGCUUAU
((((((((((((......)))))........(((((.((((.....))))..))))).((((((((........(((((.....)))))........))))).))).)))))))...... ( -33.39)
>DroYak_CAF1 168487 120 - 1
CGGCAGCGCUGGACAUGACCAGCUCAAUUCGGUUUAAGAACUUUAAGUUUGCCGGACACUCUUUGUUUUCGCCCACUUCAUUACGAAGUUUUAUAAUAUAAAUGAGAGCUGCUGGCUUAU
((((((((((((......)))))....((((((....((((.....))))))))))..((((((((........(((((.....)))))........))))).))).)))))))...... ( -36.39)
>consensus
CAGCAGCGCUGGACAUGACCAGCUCAAUUCGGUUUAAGAACUUUAAGUUUGCUGGACACUCUUUGUUUUUGCCCACUUCAUUACGAAGUUUUAUAAUAUAAAUAAAAACUGCUGGCUUAU
((((((.(((((......))))).)..((((((....((((.....))))))))))........(((((((...(((((.....)))))((((.....))))))))))))))))...... (-25.88 = -24.36 +  -1.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:52 2006