Locus 4093

Sequence ID	2L_DroMel_CAF1
Location	11,783,233 – 11,783,346
Length	113
Max. P	0.920503

overview

Window 9

Location	11,783,233 – 11,783,346
Length	113
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	93.83
Mean single sequence MFE	-40.18
Consensus MFE	-34.74
Energy contribution	-34.78
Covariance contribution	0.04
Combinations/Pair	1.07
Mean z-score	-1.53
Structure conservation index	0.86
SVM decision value	0.97
SVM RNA-class probability	0.891715
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11783233 113 + 22407834
CUCCUCGACUUUUCCCCAGGCGACUUGCCUUUG------CCUUUGCGUUUGACACUUUUCCACAGUAACGGAAGUGGGACUGCUGGGGAACUAUCAAAGUGCACCUAGGCGAGGGGGAC
...........((((((((((.....))))(((------(((.(((((((((.(.((..(((((((.((....))...)))).)))..)).).))))).))))...)))))))))))). ( -44.90)
>DroSec_CAF1 40973 110 + 1
CUCCUCGACUUUUCCCCAGGCGACUUGCCUUUG------CCUUUGCGUUUGACACUUUUCCACAGUAACGGAAGUGGGGCUGCUGGGGAACUAUCAAAGUGCACCUAGAC---GGGGAC
............(((((((((((.......)))------))).(((((((((.(.((..(((((((.((....))...)))).)))..)).).))))).)))).......---))))). ( -38.00)
>DroSim_CAF1 40067 110 + 1
CUCCUCGACUUUUCCCCAGGCGACUUGCCUUUG------CCUUUGCGUUUGACACUUUUCCACAGUAACGGAAGUGGGGCUGCUGGGGAACUAUCAAAGUGCACCUAGAC---GGGGAC
............(((((((((((.......)))------))).(((((((((.(.((..(((((((.((....))...)))).)))..)).).))))).)))).......---))))). ( -38.00)
>DroEre_CAF1 51343 109 + 1
CUCCUCGACUUUUCCCCAGGCGACUUGCCUUUG------CGUUUGCGUUUGACACUUUUCCGCAGUAACGGAAGUGG-GCUGCUGGGGAACUAUCAAAGUGCACCUAGAC---GGGGAC
............(((((((((.....))))...------.((((((((((((.(.((..(((((((.((....))..-))))).))..)).).))))).))))....)))---))))). ( -38.70)
>DroYak_CAF1 42856 115 + 1
CUCCUCGACUUUUCCCCAGGCGACUUGCCUUUGCGAGUGCGUUUGCGUUUGACACUUUUCCGCAGAAACGGAAGUGG-GCUGCUGGGGAACUAUCAUAGUGCACCUAGAC---GGGGAC
.((((((....((((((((((.((((((....))))))))(((..((.....)....(((((......))))))..)-))..))))))))...((.(((.....))))))---))))). ( -41.30)
>consensus
CUCCUCGACUUUUCCCCAGGCGACUUGCCUUUG______CCUUUGCGUUUGACACUUUUCCACAGUAACGGAAGUGGGGCUGCUGGGGAACUAUCAAAGUGCACCUAGAC___GGGGAC
............(((((((((.....)))).............(((((((((.(.((..(((((((.((....))...)))).)))..)).).))))).))))..........))))). (-34.74 = -34.78 +   0.04)

alignment

secondary structure

dotplot

Window 0

Location	11,783,233 – 11,783,346
Length	113
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	93.83
Mean single sequence MFE	-38.56
Consensus MFE	-33.98
Energy contribution	-33.94
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.52
Structure conservation index	0.88
SVM decision value	1.13
SVM RNA-class probability	0.920503
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11783233 113 - 22407834
GUCCCCCUCGCCUAGGUGCACUUUGAUAGUUCCCCAGCAGUCCCACUUCCGUUACUGUGGAAAAGUGUCAAACGCAAAGG------CAAAGGCAAGUCGCCUGGGGAAAAGUCGAGGAG
.(((((...((((...(((..(((((((.((..(((.((((..(......)..)))))))..)).))))))).))).)))------)..((((.....)))))))))............ ( -38.80)
>DroSec_CAF1 40973 110 - 1
GUCCCC---GUCUAGGUGCACUUUGAUAGUUCCCCAGCAGCCCCACUUCCGUUACUGUGGAAAAGUGUCAAACGCAAAGG------CAAAGGCAAGUCGCCUGGGGAAAAGUCGAGGAG
(..((.---.....))..).(((((((..((((((....(((((((..........))))....(((.....)))...))------)..((((.....))))))))))..))))))).. ( -38.90)
>DroSim_CAF1 40067 110 - 1
GUCCCC---GUCUAGGUGCACUUUGAUAGUUCCCCAGCAGCCCCACUUCCGUUACUGUGGAAAAGUGUCAAACGCAAAGG------CAAAGGCAAGUCGCCUGGGGAAAAGUCGAGGAG
(..((.---.....))..).(((((((..((((((....(((((((..........))))....(((.....)))...))------)..((((.....))))))))))..))))))).. ( -38.90)
>DroEre_CAF1 51343 109 - 1
GUCCCC---GUCUAGGUGCACUUUGAUAGUUCCCCAGCAGC-CCACUUCCGUUACUGCGGAAAAGUGUCAAACGCAAACG------CAAAGGCAAGUCGCCUGGGGAAAAGUCGAGGAG
(..((.---.....))..).(((((((..((((((.((...-....((((((....))))))..(((.....)))....)------)..((((.....))))))))))..))))))).. ( -39.20)
>DroYak_CAF1 42856 115 - 1
GUCCCC---GUCUAGGUGCACUAUGAUAGUUCCCCAGCAGC-CCACUUCCGUUUCUGCGGAAAAGUGUCAAACGCAAACGCACUCGCAAAGGCAAGUCGCCUGGGGAAAAGUCGAGGAG
(..((.---.....))..).((.((((..((((((.((...-.(((((((((....)))))..))))......((....))....))..((((.....))))))))))..)))).)).. ( -37.00)
>consensus
GUCCCC___GUCUAGGUGCACUUUGAUAGUUCCCCAGCAGCCCCACUUCCGUUACUGUGGAAAAGUGUCAAACGCAAAGG______CAAAGGCAAGUCGCCUGGGGAAAAGUCGAGGAG
(..((.........))..).(((((((..((((((.((.....((((((((......))))..))))......))..............((((.....))))))))))..))))))).. (-33.98 = -33.94 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:10 2006