Locus 8185

Sequence ID	3R_DroMel_CAF1
Location	22,000,777 – 22,000,933
Length	156
Max. P	0.935957

overview

Window 3

Location	22,000,777 – 22,000,893
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.66
Mean single sequence MFE	-42.22
Consensus MFE	-33.43
Energy contribution	-33.99
Covariance contribution	0.56
Combinations/Pair	1.11
Mean z-score	-1.90
Structure conservation index	0.79
SVM decision value	0.49
SVM RNA-class probability	0.757671
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22000777 116 - 27905053
AAUCGCCAGGUGAACAGGCC---GGA-GCACUUGCUACUGUUUACCUGCCAGUUAAUUUGCAUAAUGCUCGGCAGUGGACAAGCCUGGGCACUUAUUUGCCGAACGCUUCUGCUUGGGCA
.......(((((..(((((.---..(-((....)))..(((((((.(((((((.............))).))))))))))).)))))..)))))...((((.((.((....)))).)))) ( -41.22)
>DroSim_CAF1 37155 119 - 1
AAUCGCCAGGUGAACAGGCCAGUGGA-GCACUUGCUACUGUUUACCUGCCAGUUAAUUUGCAUAAUGCUCGGCAGUGGACGAGCCUGGGCACUUAUUUGCCGAACGCUUCUGCCUGGGCA
..(((((((((((((((((.((((..-.)))).))..)))))))))(((((((.............))).)))).))).)))(((..((((.......((.....))...))))..))). ( -44.92)
>DroEre_CAF1 42809 120 - 1
AAUAGCAGGGUGAACAGGCCAGUGAAGGCACUUUCUACUGUUUACCUGCCAGUUAAUUUGCAUAAUGCUCGGCAGUGGAAGAGCCUAGGCACUUAUUUGCCGAACGCUUCUGCCUGUGCA
....(((((.(((((((...((((....)))).....)))))))))))).........((((((..(.(((((((...(((.((....)).)))..))))))).)((....)).)))))) ( -41.70)
>DroYak_CAF1 41436 120 - 1
AAUCGCCAGGUGAACAGGCCAGUGAAGGCACUUUCUGCUGUUUACCUGCCAGUUAAUUUGCAUAAUGCUGGCCAUUGGACGAGCAUGGGCACUUAUUUGCCGAACGCUUCUGCCUGGGCA
....((((((((((((((((......))).(.....)))))))))))((((((.............))))))....((..((((.(.((((......)))).)..))))...))..))). ( -41.02)
>consensus
AAUCGCCAGGUGAACAGGCCAGUGAA_GCACUUGCUACUGUUUACCUGCCAGUUAAUUUGCAUAAUGCUCGGCAGUGGACGAGCCUGGGCACUUAUUUGCCGAACGCUUCUGCCUGGGCA
....(((((((((((((((.((((....)))).))..))))))))))((((((.............))).)))...((..((((...((((......))))....))))...))..))). (-33.43 = -33.99 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	22,000,817 – 22,000,933
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.13
Mean single sequence MFE	-36.73
Consensus MFE	-29.45
Energy contribution	-31.07
Covariance contribution	1.62
Combinations/Pair	1.06
Mean z-score	-2.37
Structure conservation index	0.80
SVM decision value	1.25
SVM RNA-class probability	0.935957
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22000817 116 - 27905053
AAAAACAAACAUAGCUAGUGAGGAGCCUAAAAGCUUCUUAAAUCGCCAGGUGAACAGGCC---GGA-GCACUUGCUACUGUUUACCUGCCAGUUAAUUUGCAUAAUGCUCGGCAGUGGAC
.........(((.(((((((((((((......))))))).....(.(((((((((((...---..(-((....))).))))))))))).)................))).))).)))... ( -35.10)
>DroSim_CAF1 37195 119 - 1
AAAAACAAACAUAGCUAGUGAGGAGCCUAAAAGCUUCUUAAAUCGCCAGGUGAACAGGCCAGUGGA-GCACUUGCUACUGUUUACCUGCCAGUUAAUUUGCAUAAUGCUCGGCAGUGGAC
.........(((.(((((((((((((......))))))).....(.(((((((((((((.((((..-.)))).))..))))))))))).)................))).))).)))... ( -36.10)
>DroEre_CAF1 42849 120 - 1
UUUAACAAACAUGGCUAGUGAGGAGUCCAUAAGCUUCUUAAAUAGCAGGGUGAACAGGCCAGUGAAGGCACUUUCUACUGUUUACCUGCCAGUUAAUUUGCAUAAUGCUCGGCAGUGGAA
.........(((.((((.((((((((......))))))))..)))).((((((((((...((((....)))).....))))))))))((((((.............))).))).)))... ( -34.92)
>DroYak_CAF1 41476 120 - 1
UUUAACAAACAUGGCUAGUGAGGAGCCUAUAAGCUUCUUAAAUCGCCAGGUGAACAGGCCAGUGAAGGCACUUUCUGCUGUUUACCUGCCAGUUAAUUUGCAUAAUGCUGGCCAUUGGAC
.........(((((((((((((((((......))))))).....(.((((((((((((((......))).(.....)))))))))))).)................)))))))).))... ( -40.80)
>consensus
AAAAACAAACAUAGCUAGUGAGGAGCCUAAAAGCUUCUUAAAUCGCCAGGUGAACAGGCCAGUGAA_GCACUUGCUACUGUUUACCUGCCAGUUAAUUUGCAUAAUGCUCGGCAGUGGAC
.........(((.(((((((((((((......))))))).....(.(((((((((((((.((((....)))).))..))))))))))).)................))).))).)))... (-29.45 = -31.07 +   1.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:04:46 2006