Locus 4270

Sequence ID 2R_DroMel_CAF1
Location 14,079,719 – 14,079,837
Length 118
Max. P 0.834892
window6855 window6856

overview

Window 5

Location 14,079,719 – 14,079,837
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.64
Mean single sequence MFE -37.60
Consensus MFE -25.76
Energy contribution -25.10
Covariance contribution -0.66
Combinations/Pair 1.06
Mean z-score -4.10
Structure conservation index 0.69
SVM decision value 0.73
SVM RNA-class probability 0.834892
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14079719 118 + 20766785
GAAGAACUGCAGGCAAUAAAAC--ACAGCUGAGCAACAAUGUUUCAACAAAGAUGGGGGAAAUUCCGAUCGAUAGGGAAACAUUUUGCUCGGUUGAGAAACUAAGAACUGUGUGCCUUCA
((((.((.((((..........--.(((((((((((.((((((((......(((.(((.....))).)))......)))))))))))))))))))............))))))..)))). ( -39.80)
>DroSim_CAF1 4270 117 + 1
GAAAAACUGCAGGCAAUAAAAC--ACAGCUGAACAACAAUGUUUCAACAAAGAUGG-GGAAAUUCCGAUCGAUAGGGAAACAUUUUGCUCGGUUGAGAAACUAAGAACUGUGUGCCUGCA
........(((((((.......--.(((((((.(((.((((((((......(((.(-((....))).)))......))))))))))).)))))))....((........)).))))))). ( -38.80)
>DroYak_CAF1 4942 119 + 1
GAAAAACUGCAGGCGAUAAAACACACAGCUGAACAACAAUGUUUUCACAGCGAUGG-GGAAAUUCCGAUCGAUAGGAAAACAUUUUGCUUGGUUGAGAAACUUCGAAGUGUAGGCCUCCA
........(.((((......((((.((((..(.(((.(((((((((....((((.(-((....))).))))....)))))))))))).)..)))).((....))...))))..)))).). ( -34.20)
>consensus
GAAAAACUGCAGGCAAUAAAAC__ACAGCUGAACAACAAUGUUUCAACAAAGAUGG_GGAAAUUCCGAUCGAUAGGGAAACAUUUUGCUCGGUUGAGAAACUAAGAACUGUGUGCCUCCA
........(.((((...........(((((((.(((.((((((((......(((.(.((....))).)))......))))))))))).)))))))....((........))..)))).). (-25.76 = -25.10 +  -0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 14,079,719 – 14,079,837
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.64
Mean single sequence MFE -33.34
Consensus MFE -22.50
Energy contribution -22.83
Covariance contribution 0.34
Combinations/Pair 1.05
Mean z-score -3.32
Structure conservation index 0.67
SVM decision value 0.44
SVM RNA-class probability 0.735410
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14079719 118 - 20766785
UGAAGGCACACAGUUCUUAGUUUCUCAACCGAGCAAAAUGUUUCCCUAUCGAUCGGAAUUUCCCCCAUCUUUGUUGAAACAUUGUUGCUCAGCUGU--GUUUUAUUGCCUGCAGUUCUUC
((.((((((((((((....(((....))).((((((((((((((..((..(((.((.......)).)))..))..)))))))).))))))))))))--))......)))).))....... ( -32.90)
>DroSim_CAF1 4270 117 - 1
UGCAGGCACACAGUUCUUAGUUUCUCAACCGAGCAAAAUGUUUCCCUAUCGAUCGGAAUUUCC-CCAUCUUUGUUGAAACAUUGUUGUUCAGCUGU--GUUUUAUUGCCUGCAGUUUUUC
(((((((((((((((....(((....))).((((((((((((((..((..(((.((......)-).)))..))..)))))))).))))))))))))--))......)))))))....... ( -37.60)
>DroYak_CAF1 4942 119 - 1
UGGAGGCCUACACUUCGAAGUUUCUCAACCAAGCAAAAUGUUUUCCUAUCGAUCGGAAUUUCC-CCAUCGCUGUGAAAACAUUGUUGUUCAGCUGUGUGUUUUAUCGCCUGCAGUUUUUC
((.((((..((((.....((((...((((.......(((((((((.((.((((.((......)-).)))).)).)))))))))))))...))))..))))......)))).))....... ( -29.51)
>consensus
UGAAGGCACACAGUUCUUAGUUUCUCAACCGAGCAAAAUGUUUCCCUAUCGAUCGGAAUUUCC_CCAUCUUUGUUGAAACAUUGUUGUUCAGCUGU__GUUUUAUUGCCUGCAGUUUUUC
((.(((((.((((((....(((....))).((((((((((((((..((..(((.((........)))))..))..)))))))).)))))))))))).........))))).))....... (-22.50 = -22.83 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:49 2006