Locus 6541

Sequence ID	3L_DroMel_CAF1
Location	17,290,187 – 17,290,307
Length	120
Max. P	0.940722

overview

Window 7

Location	17,290,187 – 17,290,307
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.39
Mean single sequence MFE	-42.38
Consensus MFE	-36.67
Energy contribution	-36.68
Covariance contribution	0.00
Combinations/Pair	1.17
Mean z-score	-1.60
Structure conservation index	0.87
SVM decision value	0.45
SVM RNA-class probability	0.740617
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17290187 120 + 23771897
AAAGGACUUCGUGGAGUGGAACACAAAGUUGCAGAUCCGUGCGCUCAAAGAGCCUUCGAGCUCUCCAGCGAAACUGUUCCACUGCCUCGCCGCAGUCCUUGCGACUUUGCAGGAAGUCAU
.(((((((.((.(((((((((((....((((.(((.(((...((((...))))...)).).))).)))).....))))))))).))....)).)))))))..((((((....)))))).. ( -44.80)
>DroSec_CAF1 173918 120 + 1
AAAGGACUUCGUGGAGUGGAACGCAAAGUUGCAGAUCCGUGCGCUCAAAGAGCCUUCGUGCUCUCCAGCGAAACUGUUCCACUGCCUCGACGCAGUCCUUGUGUCCUUGCAGGAAGUCAU
....(((((((.(((((((((((((....))).........((((...(((((......)))))..)))).....)))))))).)).)(((((((...))))))).......)))))).. ( -44.50)
>DroSim_CAF1 170135 120 + 1
AAAGGACUUCGUGGAGUGGAACGCAAAGUUGCAGAUCCGUGCGCUCAAAGAGCCUUCGUGCUCUCCAGCGAAACUGUUCCACUGCCUCGACGCAGUCCUUGUGUGCUUGCAGGAAGUCAU
.((((((((((.(((((((((((((....))).........((((...(((((......)))))..)))).....)))))))).)).)))...)))))))(((.((((.....))))))) ( -43.20)
>DroYak_CAF1 182799 120 + 1
AGAGAACUUCGUGGAGUGGAAGGCAGAGUUGCAGAUCUGUGCGUUCGAAGAGCUUUCUUGCUCUCCAGCGAAACUCCUUCACUGCCUCGCCGCAGUCCUUGUGAUUUUGCAGGAAGUCAU
...((.((((..(((((.(((.(((.((........)).))).)))(.(((((......))))).)......)))))....((((.....(((((...))))).....)))))))))).. ( -37.00)
>consensus
AAAGGACUUCGUGGAGUGGAACGCAAAGUUGCAGAUCCGUGCGCUCAAAGAGCCUUCGUGCUCUCCAGCGAAACUGUUCCACUGCCUCGACGCAGUCCUUGUGACCUUGCAGGAAGUCAU
....(((((((.(((((((((((.......(((......)))(((...(((((......)))))..))).....))))))))).)).)(((((((...))))))).......)))))).. (-36.67 = -36.68 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	17,290,187 – 17,290,307
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.39
Mean single sequence MFE	-43.12
Consensus MFE	-39.17
Energy contribution	-39.17
Covariance contribution	0.00
Combinations/Pair	1.20
Mean z-score	-1.94
Structure conservation index	0.91
SVM decision value	1.31
SVM RNA-class probability	0.940722
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17290187 120 - 23771897
AUGACUUCCUGCAAAGUCGCAAGGACUGCGGCGAGGCAGUGGAACAGUUUCGCUGGAGAGCUCGAAGGCUCUUUGAGCGCACGGAUCUGCAACUUUGUGUUCCACUCCACGAAGUCCUUU
..((((((.......((((((.....))))))..((.(((((((((.....(((((((((((....)))))))).)))(((......))).......)))))))))))..)))))).... ( -48.50)
>DroSec_CAF1 173918 120 - 1
AUGACUUCCUGCAAGGACACAAGGACUGCGUCGAGGCAGUGGAACAGUUUCGCUGGAGAGCACGAAGGCUCUUUGAGCGCACGGAUCUGCAACUUUGCGUUCCACUCCACGAAGUCCUUU
......(((.....)))...(((((((...(((.((.((((((((......((((((((((......))))))).)))(((.((........)).))))))))))))).)))))))))). ( -45.50)
>DroSim_CAF1 170135 120 - 1
AUGACUUCCUGCAAGCACACAAGGACUGCGUCGAGGCAGUGGAACAGUUUCGCUGGAGAGCACGAAGGCUCUUUGAGCGCACGGAUCUGCAACUUUGCGUUCCACUCCACGAAGUCCUUU
....................(((((((...(((.((.((((((((......((((((((((......))))))).)))(((.((........)).))))))))))))).)))))))))). ( -43.50)
>DroYak_CAF1 182799 120 - 1
AUGACUUCCUGCAAAAUCACAAGGACUGCGGCGAGGCAGUGAAGGAGUUUCGCUGGAGAGCAAGAAAGCUCUUCGAACGCACAGAUCUGCAACUCUGCCUUCCACUCCACGAAGUUCUCU
..(((((((((((...((.....)).)))))...((.((((((((......((((((((((......))))))))...)).((((........)))))))).))))))..)))))).... ( -35.00)
>consensus
AUGACUUCCUGCAAAGACACAAGGACUGCGGCGAGGCAGUGGAACAGUUUCGCUGGAGAGCACGAAGGCUCUUUGAGCGCACGGAUCUGCAACUUUGCGUUCCACUCCACGAAGUCCUUU
.((((((......)))))).(((((((....((.((.((((((((......((((((((((......))))))).)))(((.((........)).))))))))))))).)).))))))). (-39.17 = -39.17 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:42 2006