Locus 5886

Sequence ID	2L_DroMel_CAF1
Location	16,635,827 – 16,635,939
Length	112
Max. P	0.956861

overview

Window 1

Location	16,635,827 – 16,635,939
Length	112
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	92.05
Mean single sequence MFE	-28.84
Consensus MFE	-23.64
Energy contribution	-23.80
Covariance contribution	0.16
Combinations/Pair	1.11
Mean z-score	-1.83
Structure conservation index	0.82
SVM decision value	1.19
SVM RNA-class probability	0.928770
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16635827 112 + 22407834
UCGCUGAAUGAGAUCAGACGGUGCAUUUUAUAGGAAAAGUUGAGCAGAUAAAAGGAAUUCUUUUGUUGGAAGUGCU---GGCAAAAUUUGAAAGCUCAACUUGUUAUUGCAUCUU
..(((((......)))).)((((((....((((...(((((((((.((..........))((((((..(.....).---.)))))).......))))))))).)))))))))).. ( -29.00)
>DroSec_CAF1 90603 112 + 1
UCGCUGAAUGAGAUCAGACGGUGCGUUUUAUAGGAAAAGUUGAGCAGAUAAAAGGAAUUCUUUUGUUGGAAGUGCU---GGCGAAAUUUGAAAGCUCAACUUGUUAUUGCAUCUC
..(((((......)))).)((((((....((((...(((((((((.....(((((....)))))((..(.....).---.))...........))))))))).)))))))))).. ( -28.10)
>DroSim_CAF1 92800 112 + 1
UCGCUGAAUGAGAUCAGACGGUGCGUUUUAUAGGAAAAGUUGAGCAGAUAAAAGGAAUUCUUUUGUUGGAAGUGCU---GGCGAAAUUUGAAAGCUCAACUUGUUAUUGCAUCUC
..(((((......)))).)((((((....((((...(((((((((.....(((((....)))))((..(.....).---.))...........))))))))).)))))))))).. ( -28.10)
>DroEre_CAF1 91783 115 + 1
UCGCCGAAUGAGAUCAGACAUUGAGUUUUAUGGCAAAAGUUGAGCAGAUAAAAGGAAUUCUUUUGUUGGCAGUGCUAUUUGCGAAAUUUGAAAGCUCAACUUAUUAUUGCAUCUA
..(((..((((((((((...)))).)))))))))..(((((((((.((((((((.....)))))))).((((......))))...........)))))))))............. ( -28.90)
>DroYak_CAF1 89656 112 + 1
UCGCUGAAUGAGAUCAGACAGUGAGUUUUAUAGGAAAAGUUGAGCUGAUAAAAGGAAUUCCUUUGUUGGAAGUGCU---GGCGAAAUUUGAAAGUUCAACUUAUUAUGGUAUCUA
((((((..((....))..))))))...((((((...((((((((((..((((.((....))(((((..(.....).---.))))).))))..)))))))))).))))))...... ( -30.10)
>consensus
UCGCUGAAUGAGAUCAGACGGUGCGUUUUAUAGGAAAAGUUGAGCAGAUAAAAGGAAUUCUUUUGUUGGAAGUGCU___GGCGAAAUUUGAAAGCUCAACUUGUUAUUGCAUCUA
.(((((..((....))..))))).............(((((((((.((((((((.....)))))))).....(((.....)))..........)))))))))............. (-23.64 = -23.80 +   0.16)

alignment

secondary structure

dotplot

Window 2

Location	16,635,827 – 16,635,939
Length	112
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	92.05
Mean single sequence MFE	-18.26
Consensus MFE	-18.64
Energy contribution	-18.28
Covariance contribution	-0.36
Combinations/Pair	1.14
Mean z-score	-1.33
Structure conservation index	1.02
SVM decision value	1.47
SVM RNA-class probability	0.956861
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16635827 112 - 22407834
AAGAUGCAAUAACAAGUUGAGCUUUCAAAUUUUGCC---AGCACUUCCAACAAAAGAAUUCCUUUUAUCUGCUCAACUUUUCCUAUAAAAUGCACCGUCUGAUCUCAUUCAGCGA
....(((((((..(((((((((..........((..---..))........(((((.....)))))....)))))))))....)))....)))).((.((((......)))))). ( -20.00)
>DroSec_CAF1 90603 112 - 1
GAGAUGCAAUAACAAGUUGAGCUUUCAAAUUUCGCC---AGCACUUCCAACAAAAGAAUUCCUUUUAUCUGCUCAACUUUUCCUAUAAAACGCACCGUCUGAUCUCAUUCAGCGA
.............(((((((((...........(..---..).........(((((.....)))))....)))))))))................((.((((......)))))). ( -18.30)
>DroSim_CAF1 92800 112 - 1
GAGAUGCAAUAACAAGUUGAGCUUUCAAAUUUCGCC---AGCACUUCCAACAAAAGAAUUCCUUUUAUCUGCUCAACUUUUCCUAUAAAACGCACCGUCUGAUCUCAUUCAGCGA
.............(((((((((...........(..---..).........(((((.....)))))....)))))))))................((.((((......)))))). ( -18.30)
>DroEre_CAF1 91783 115 - 1
UAGAUGCAAUAAUAAGUUGAGCUUUCAAAUUUCGCAAAUAGCACUGCCAACAAAAGAAUUCCUUUUAUCUGCUCAACUUUUGCCAUAAAACUCAAUGUCUGAUCUCAUUCGGCGA
.....((((....(((((((((...........(((........)))....(((((.....)))))....)))))))))))))............((.((((......)))))). ( -21.20)
>DroYak_CAF1 89656 112 - 1
UAGAUACCAUAAUAAGUUGAACUUUCAAAUUUCGCC---AGCACUUCCAACAAAGGAAUUCCUUUUAUCAGCUCAACUUUUCCUAUAAAACUCACUGUCUGAUCUCAUUCAGCGA
.............(((((((.((..........(..---..).........(((((....)))))....)).)))))))............((.(((..((....))..))).)) ( -13.50)
>consensus
GAGAUGCAAUAACAAGUUGAGCUUUCAAAUUUCGCC___AGCACUUCCAACAAAAGAAUUCCUUUUAUCUGCUCAACUUUUCCUAUAAAACGCACCGUCUGAUCUCAUUCAGCGA
.............(((((((((...........((.....)).........(((((.....)))))....)))))))))................((.((((......)))))). (-18.64 = -18.28 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:29 2006