Locus 5643

Sequence ID	3R_DroMel_CAF1
Location	14,831,195 – 14,831,315
Length	120
Max. P	0.934880

overview

Window 1

Location	14,831,195 – 14,831,315
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.56
Mean single sequence MFE	-34.53
Consensus MFE	-31.28
Energy contribution	-31.83
Covariance contribution	0.56
Combinations/Pair	1.02
Mean z-score	-1.92
Structure conservation index	0.91
SVM decision value	0.33
SVM RNA-class probability	0.692151
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14831195 120 + 27905053
UCUUUAAUUUGCCUGGCUGCGCCUGCAAUUGUUUUCGCUUUAAAUAAUUAAAUUAAAGUGGUCAGUCAACUGAUUGAAGGAGCCUCCAGUCUCUGAACCAUGGAGCAACUUACUCCCGAC
.(((((((((((..(((...))).))((((((((.......)))))))))))))))))(((((((......(((((.((....)).))))).))).)))).((((.......)))).... ( -28.80)
>DroSec_CAF1 9388 120 + 1
UCUUUAAUUUGCCUGGCUGCGCCUGCAAUUGUUUUCGCUUUAAAUAAUUAAAUUAAAGUGGGCAGCCAACUGAUUGAAGGAGCCUCCAGUCUCUGCCCAAUGGAGCAGCUUGCUCGCGAC
.(((((((((((..(((...))).))((((((((.......)))))))))))))))))(((((((......(((((.((....)).))))).)))))))...((((.....))))..... ( -36.20)
>DroSim_CAF1 9551 120 + 1
UCUUUAAUUUGCCUGGCUGCGCCUGCAAUUGUUUUCGCUUUAAAUAAUUAAAUUAAAGUGGGCAGCCAACUGAUUGAAGGAGCCUCCAGUCUCUGCCCAAUGGAGCAGCUUGCUCCCGAC
.(((((((((((..(((...))).))((((((((.......)))))))))))))))))(((((((......(((((.((....)).))))).)))))))..(((((.....))))).... ( -38.60)
>consensus
UCUUUAAUUUGCCUGGCUGCGCCUGCAAUUGUUUUCGCUUUAAAUAAUUAAAUUAAAGUGGGCAGCCAACUGAUUGAAGGAGCCUCCAGUCUCUGCCCAAUGGAGCAGCUUGCUCCCGAC
.(((((((((((..(((...))).))((((((((.......))))))))))))))))).((((((......(((((.((....)).))))).))))))...(((((.....))))).... (-31.28 = -31.83 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	14,831,195 – 14,831,315
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	95.56
Mean single sequence MFE	-37.20
Consensus MFE	-35.10
Energy contribution	-35.10
Covariance contribution	0.00
Combinations/Pair	1.06
Mean z-score	-2.33
Structure conservation index	0.94
SVM decision value	1.24
SVM RNA-class probability	0.934880
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14831195 120 - 27905053
GUCGGGAGUAAGUUGCUCCAUGGUUCAGAGACUGGAGGCUCCUUCAAUCAGUUGACUGACCACUUUAAUUUAAUUAUUUAAAGCGAAAACAAUUGCAGGCGCAGCCAGGCAAAUUAAAGA
....(((((.....))))).((((.(((.((((((((....)))....)))))..)))))))(((((((((...........((((......)))).(((...)))....))))))))). ( -32.40)
>DroSec_CAF1 9388 120 - 1
GUCGCGAGCAAGCUGCUCCAUUGGGCAGAGACUGGAGGCUCCUUCAAUCAGUUGGCUGCCCACUUUAAUUUAAUUAUUUAAAGCGAAAACAAUUGCAGGCGCAGCCAGGCAAAUUAAAGA
.......((..(((((.((..(((((((.((((((((....)))....)))))..)))))))....................((((......)))).)).)))))...)).......... ( -38.20)
>DroSim_CAF1 9551 120 - 1
GUCGGGAGCAAGCUGCUCCAUUGGGCAGAGACUGGAGGCUCCUUCAAUCAGUUGGCUGCCCACUUUAAUUUAAUUAUUUAAAGCGAAAACAAUUGCAGGCGCAGCCAGGCAAAUUAAAGA
....(((((.....)))))..(((((((.((((((((....)))....)))))..)))))))(((((((((...........((((......)))).(((...)))....))))))))). ( -41.00)
>consensus
GUCGGGAGCAAGCUGCUCCAUUGGGCAGAGACUGGAGGCUCCUUCAAUCAGUUGGCUGCCCACUUUAAUUUAAUUAUUUAAAGCGAAAACAAUUGCAGGCGCAGCCAGGCAAAUUAAAGA
....(((((.....)))))...((((((.((((((((....)))....)))))..)))))).(((((((((...........((((......)))).(((...)))....))))))))). (-35.10 = -35.10 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:16 2006