Locus 995

Sequence ID 3R_DroMel_CAF1
Location 3,174,867 – 3,175,008
Length 141
Max. P 0.650047
window1611 window1612

overview

Window 1

Location 3,174,867 – 3,174,983
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.50
Mean single sequence MFE -27.20
Consensus MFE -14.45
Energy contribution -14.70
Covariance contribution 0.25
Combinations/Pair 1.20
Mean z-score -2.01
Structure conservation index 0.53
SVM decision value 0.20
SVM RNA-class probability 0.629082
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3174867 116 + 27905053
CAGGUCUAAAAACUUUUGAAUUGUAGCUUGCAAAUUUUUAAGCUUCCGUUGAGUUUCCUUUUGUAGGUUCUAAUGAAAGGAGA----UCAACGAUCGAGUUAGUUCUGGUUAAGUCUUAC
.(((.((...((((...((((((.((((((........))))))..((((((.((((((((..(........)..))))))))----)))))).......)))))).)))).)).))).. ( -28.60)
>DroSec_CAF1 119 106 + 1
CAGGUCUAAAAACUUUUGAAUUGUAUCUUUCAAAUUUUUAAGCUUCCGUUGAGUUUCCUUUUGUAGGUUCUAAUAAGAGGAGA----UCAACGAUCGAGUUAGA----------CCUUAC
.(((((((.(((..((((((........))))))..)))..((((.((((((.(((((((((((........)))))))))))----))))))...))))))))----------)))... ( -32.30)
>DroSim_CAF1 6106 97 + 1
CAGGUCUAAAAACUUUUGAAUUGUAUCUUGCAAAUUUUUUAGCUUCCGUUGAGUUUCCUUUUGUAGGUUCUAGUGAAAGGAGA----UCAACGAUCG-------------------UUAC
.(((.(((((((..((((............)))).)))))))))).((((((.((((((((..(........)..))))))))----))))))....-------------------.... ( -22.50)
>DroEre_CAF1 1000 120 + 1
GAAGUCUAGAAAUUUUUGAAUGGUAGCUUGCAGAUUCUCAAGCUUGCGUUGAGUUUCAUUUUGUAGGCUCUGAAUAAAGGAGAGAAAUCAUAGGUCGAGUUAAGCUAAGUCAAAUCUUAA
..............(((((....((((((...((((((((((((((((.((.....))...)))))))).)))........((....)).......)))))))))))..)))))...... ( -25.40)
>consensus
CAGGUCUAAAAACUUUUGAAUUGUAGCUUGCAAAUUUUUAAGCUUCCGUUGAGUUUCCUUUUGUAGGUUCUAAUGAAAGGAGA____UCAACGAUCGAGUUAG___________UCUUAC
.(((.((.((((..((((............)))).)))).))))).((((((.(((((((((((........)))))))))))....))))))........................... (-14.45 = -14.70 +   0.25)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 3,174,907 – 3,175,008
Length 101
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 66.57
Mean single sequence MFE -19.89
Consensus MFE -13.30
Energy contribution -14.63
Covariance contribution 1.34
Combinations/Pair 1.09
Mean z-score -1.00
Structure conservation index 0.67
SVM decision value 0.24
SVM RNA-class probability 0.650047
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3174907 101 + 27905053
AGCUUCCGUUGAGUUUCCUUUUGUAGGUUCUAAUGAAAGGAGA----UCAACGAUCGAGUUAGUUCUGGUUAAGUCUUACAUAAAAUA----------AAAUCGAGACAAAAACU-----
(((((.((((((.((((((((..(........)..))))))))----))))))...)))))............(((((..........----------.....))))).......----- ( -22.76)
>DroSec_CAF1 159 91 + 1
AGCUUCCGUUGAGUUUCCUUUUGUAGGUUCUAAUAAGAGGAGA----UCAACGAUCGAGUUAGA----------CCUUACAUAAAUUA----------AAAAAGGAACAAAAACU-----
(((((.((((((.(((((((((((........)))))))))))----))))))...)))))...----------((((..........----------...))))..........----- ( -22.02)
>DroEre_CAF1 1040 120 + 1
AGCUUGCGUUGAGUUUCAUUUUGUAGGCUCUGAAUAAAGGAGAGAAAUCAUAGGUCGAGUUAAGCUAAGUCAAAUCUUAAAUACAAUAUUUGUUAAAAAAAAAUGAACGAAAAUAAUUGC
((((((..((((.((..(((((.....((((.......)))).)))))...)).))))..))))))......................((((((...........))))))......... ( -14.90)
>consensus
AGCUUCCGUUGAGUUUCCUUUUGUAGGUUCUAAUAAAAGGAGA____UCAACGAUCGAGUUAGA____GU_AA_UCUUACAUAAAAUA__________AAAAAGGAACAAAAACU_____
(((((.((((((.(((((((((((........)))))))))))....))))))...)))))........................................................... (-13.30 = -14.63 +   1.34)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:54 2006