Locus 1086

Sequence ID	3R_DroMel_CAF1
Location	3,305,230 – 3,305,428
Length	198
Max. P	0.553571

overview

Window 0

Location	3,305,230 – 3,305,348
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.23
Mean single sequence MFE	-29.89
Consensus MFE	-25.67
Energy contribution	-26.05
Covariance contribution	0.38
Combinations/Pair	1.07
Mean z-score	-1.42
Structure conservation index	0.86
SVM decision value	0.04
SVM RNA-class probability	0.552982
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3305230 118 + 27905053
CUCGUCUUUAAUUAAUUUCCCUACUCGUUUCUAGCAGAUUGAGGACAAAACCCGAAAACUUUCACAAUUUGCGCACG--CACAUCGCAACAGAUGUGAUGUGGCGGGCGAUAAAGUUGCC
...((((((((((.......................))))))))))..................((((((.(((.((--(((((((((.....)))))))).))).)))...)))))).. ( -31.60)
>DroSec_CAF1 9290 116 + 1
GUCGUCUUUAAUUAAUUUCCCAGCUCGUUUCUAGCAGAUUGAAGACAAAACCCGAAAACUUUCACAAUUUGCGCACG--CACAUCGCAGCAGAUGUGAUGU--CGGGCGAUAAAGUUGCC
...((((((((((.........(((.......))).))))))))))..................((((((.(((.((--.((((((((.....))))))))--)).)))...)))))).. ( -29.90)
>DroSim_CAF1 12899 116 + 1
GUCGUCUUUAAUUAAUUUCCCAGCUCGUUUCUAGCAGAUUGAAGACAAAACCCGAAAACUUUCACAAUUUGCGCACG--CACAUCGCAGCAGAUGUGAUGU--CGGGCGAUAAAGUUGCC
...((((((((((.........(((.......))).))))))))))..................((((((.(((.((--.((((((((.....))))))))--)).)))...)))))).. ( -29.90)
>DroYak_CAF1 19497 118 + 1
GCCGUCUUUAAUUAAUCUCCCUGCUCGUUUCUAGCAGAUUGAAGACGAACCCCGAAAACUUUCACAAUUUGCGCACAUUCACAUUGCAGCAGAUGUGAUGU--CAUGCGAUAAACUUGCC
((((((((((((........(((((.......))))))))))))))).....((.......(((((.((((((((.........))).))))))))))...--....))........)). ( -28.14)
>consensus
GUCGUCUUUAAUUAAUUUCCCAGCUCGUUUCUAGCAGAUUGAAGACAAAACCCGAAAACUUUCACAAUUUGCGCACG__CACAUCGCAGCAGAUGUGAUGU__CGGGCGAUAAAGUUGCC
...((((((((((.......................))))))))))..................((((((.(((.((...((((((((.....))))))))..)).)))...)))))).. (-25.67 = -26.05 +   0.38)

alignment

secondary structure

dotplot

Window 1

Location	3,305,308 – 3,305,428
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.70
Mean single sequence MFE	-30.88
Consensus MFE	-24.27
Energy contribution	-25.40
Covariance contribution	1.13
Combinations/Pair	1.06
Mean z-score	-1.81
Structure conservation index	0.79
SVM decision value	0.04
SVM RNA-class probability	0.553571
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3305308 120 + 27905053
ACAUCGCAACAGAUGUGAUGUGGCGGGCGAUAAAGUUGCCGGGGCGGAGUUCAACUAUUAAUUACGUAACGGAAAUGCAAAUAUUUCAACCAAUUUGUGCCCGCAACAAGACACAGCUAC
((((((((.....)))))))).(((((((...((((((.((..(((.((((........)))).)))..))((((((....))))))...)))))).)))))))................ ( -36.20)
>DroSec_CAF1 9368 118 + 1
ACAUCGCAGCAGAUGUGAUGU--CGGGCGAUAAAGUUGCCGUAGCGGAGUUCAACUAUUAAUUACGUAACGGAAAUGCAAAUAUUUCAACCAAUUUGUGUCCGCAACAAAACACAGAUAC
((((((((.....))))))))--((((((...((((((.(((.(((.((((........)))).))).)))((((((....))))))...)))))).))))))................. ( -28.70)
>DroSim_CAF1 12977 118 + 1
ACAUCGCAGCAGAUGUGAUGU--CGGGCGAUAAAGUUGCCGUUGCGGAGUUCAACUAUUAAUUACGUAACGGAAAUGCAAAUAUUUCAACCAAUUUGUGCCCGCAACAAAACACAGCUAC
((((((((.....))))))))--((((((...((((((.(((((((.((((........)))).)))))))((((((....))))))...)))))).))))))................. ( -35.00)
>DroYak_CAF1 19577 118 + 1
ACAUUGCAGCAGAUGUGAUGU--CAUGCGAUAAACUUGCCAGGGCGGAGUUCAACUAUUAAUUACGUAACGGAAAUGCAAAUAUUUCAACCAAUUUGUGCCCGCAACAAAACACAUCUAC
..........(((((((.(((--(....))))...((((..(((((.((...............((...))((((((....)))))).......)).))))))))).....))))))).. ( -23.60)
>consensus
ACAUCGCAGCAGAUGUGAUGU__CGGGCGAUAAAGUUGCCGGGGCGGAGUUCAACUAUUAAUUACGUAACGGAAAUGCAAAUAUUUCAACCAAUUUGUGCCCGCAACAAAACACAGCUAC
((((((((.....))))))))..((((((...((((((.(((.(((.((((........)))).))).)))((((((....))))))...)))))).))))))................. (-24.27 = -25.40 +   1.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:17 2006