Locus 4871

Sequence ID 2L_DroMel_CAF1
Location 13,867,467 – 13,867,560
Length 93
Max. P 0.708562
window7725 window7726

overview

Window 5

Location 13,867,467 – 13,867,560
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.85
Mean single sequence MFE -29.07
Consensus MFE -12.50
Energy contribution -12.45
Covariance contribution -0.05
Combinations/Pair 1.26
Mean z-score -2.30
Structure conservation index 0.43
SVM decision value 0.37
SVM RNA-class probability 0.708562
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13867467 93 + 22407834
-----------AAG-----AGGAGCAGCUC----UGCAUCGACUUCAAUGUAGAGCAAAACUCAUUUAGUAGCUGCUGC---UGUUGCUGAUGUUUACUAUGUUAUCCUUUUU--AUG--
-----------(((-----(((((((((((----(((((.(....).))))))))).((((....((((((((......---.)))))))).))))....)))..))))))).--...-- ( -30.00)
>DroSec_CAF1 11535 96 + 1
-----------AAG-----AGGAGCAGCAC----UGCAUCGACUUCAAUGUGGAGCAAAACUCAUUUAGUAGCUGCUGCUCCUGCUGCUGAUGUUUACUAUGUUAUCCUUUUU--AUG--
-----------.((-----(((((((((((----(((....((......)).(((.....))).....)))).)))))))))).))..((((((.....))))))........--...-- ( -26.80)
>DroSim_CAF1 13046 96 + 1
-----------AAG-----AGGAGCAGUUC----UGCAUCGACUUCAAUGUAGAGCAAAACUCAUUUAGUAGCUGCUGCUCCUGCUGCUGAUGUUUACUAUGUUAUCCUUUUU--AUG--
-----------(((-----(((((((((((----(((((.(....).))))))))).((((....((((((((..........)))))))).))))....)))..))))))).--...-- ( -29.40)
>DroEre_CAF1 11842 98 + 1
GAUGCAGGAUAAAG-----AGGAGCAGCUC----UGCAUCGACUUCAAUGUAGAGCAAAACUCAUUUAGUAGCUGCC---------GCUGAUGUUUACUAUGUUAUCCUUUUU--AUG--
.....(((((((..-----(((((((((((----(((((.(....).))))))))).............((((....---------)))).))))).))...)))))))....--...-- ( -28.60)
>DroYak_CAF1 13210 105 + 1
GAUGCAGGAUAAAGAGAAGAGGAGCAGCUC----UGCAUCGGCUUCAAUGUAGAGCAAAACUCAUUUAGUAGCUGCU---------GCUGAUGUUUACUAUGUUAUUCUUUUU--AUGUG
......(.((((((((((....((((((((----(((((........))))))))).((((....(((((((...))---------))))).))))....)))).))))))))--)).). ( -30.50)
>DroAna_CAF1 10584 108 + 1
GAGG-------GCGCGGAGAGGAGUGCCUCCUGCAGCAGCAGCUUCAAUGUAGAGCAAAACUCAUUUAGUAGCUCCUGU---UGAUGUUGAUAUUUACUGUGUUAUUCCUUUUAUAUG--
((((-------((((((.((((....)))))))).))..((((.(((((...((((...(((.....))).))))..))---))).)))).................)))).......-- ( -29.10)
>consensus
___________AAG_____AGGAGCAGCUC____UGCAUCGACUUCAAUGUAGAGCAAAACUCAUUUAGUAGCUGCUGC___UG_UGCUGAUGUUUACUAUGUUAUCCUUUUU__AUG__
....................((((((((......(((((.(....).)))))(((.....)))........)))))............((((((.....)))))))))............ (-12.50 = -12.45 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,867,467 – 13,867,560
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.85
Mean single sequence MFE -23.95
Consensus MFE -11.48
Energy contribution -12.20
Covariance contribution 0.72
Combinations/Pair 1.13
Mean z-score -2.10
Structure conservation index 0.48
SVM decision value 0.34
SVM RNA-class probability 0.695564
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13867467 93 - 22407834
--CAU--AAAAAGGAUAACAUAGUAAACAUCAGCAACA---GCAGCAGCUACUAAAUGAGUUUUGCUCUACAUUGAAGUCGAUGCA----GAGCUGCUCCU-----CUU-----------
--...--....((((.................((....---)).((((((.((....(((.....)))..(((((....))))).)----)))))))))))-----...----------- ( -21.20)
>DroSec_CAF1 11535 96 - 1
--CAU--AAAAAGGAUAACAUAGUAAACAUCAGCAGCAGGAGCAGCAGCUACUAAAUGAGUUUUGCUCCACAUUGAAGUCGAUGCA----GUGCUGCUCCU-----CUU-----------
--...--....((((.......(....)....(((((((((((((.((((........))))))))))).(((((....)))))..----.))))))))))-----...----------- ( -28.70)
>DroSim_CAF1 13046 96 - 1
--CAU--AAAAAGGAUAACAUAGUAAACAUCAGCAGCAGGAGCAGCAGCUACUAAAUGAGUUUUGCUCUACAUUGAAGUCGAUGCA----GAACUGCUCCU-----CUU-----------
--...--...........................((.((((((((..((.(((.....)))...))(((.(((((....))))).)----)).))))))))-----)).----------- ( -22.70)
>DroEre_CAF1 11842 98 - 1
--CAU--AAAAAGGAUAACAUAGUAAACAUCAGC---------GGCAGCUACUAAAUGAGUUUUGCUCUACAUUGAAGUCGAUGCA----GAGCUGCUCCU-----CUUUAUCCUGCAUC
--...--....(((((((..((((.......(((---------....)))))))...((((...(((((.(((((....))))).)----)))).))))..-----..)))))))..... ( -27.01)
>DroYak_CAF1 13210 105 - 1
CACAU--AAAAAGAAUAACAUAGUAAACAUCAGC---------AGCAGCUACUAAAUGAGUUUUGCUCUACAUUGAAGCCGAUGCA----GAGCUGCUCCUCUUCUCUUUAUCCUGCAUC
...((--(((.((((.....((((.......(((---------....)))))))...((((...(((((.(((((....))))).)----)))).))))...)))).)))))........ ( -21.91)
>DroAna_CAF1 10584 108 - 1
--CAUAUAAAAGGAAUAACACAGUAAAUAUCAACAUCA---ACAGGAGCUACUAAAUGAGUUUUGCUCUACAUUGAAGCUGCUGCUGCAGGAGGCACUCCUCUCCGCGC-------CCUC
--........(((......................(((---(..(((((.(((.....)))...)))))...)))).(((((....)))(((((......)))))))..-------))). ( -22.20)
>consensus
__CAU__AAAAAGGAUAACAUAGUAAACAUCAGCA_CA___GCAGCAGCUACUAAAUGAGUUUUGCUCUACAUUGAAGUCGAUGCA____GAGCUGCUCCU_____CUU___________
...........................................(((((((.......(((.....)))..(((((....))))).......)))))))...................... (-11.48 = -12.20 +   0.72)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:48 2006