Locus 5244

Sequence ID 3L_DroMel_CAF1
Location 14,474,198 – 14,474,318
Length 120
Max. P 0.978833
window8294 window8295

overview

Window 4

Location 14,474,198 – 14,474,318
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.69
Mean single sequence MFE -31.19
Consensus MFE -28.83
Energy contribution -28.89
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.66
Structure conservation index 0.92
SVM decision value 1.82
SVM RNA-class probability 0.978833
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14474198 120 + 23771897
UCUCCGCUUCUUUCUUGACUUUCUGAUAGCUUUCGAUCAGCUUUUGGGCCUCCUGCUCAAGACGUCGCUCCUCAUCGGUCUUCUUAAGGAGCUUGGCACCCUUUUUGCCAGCAAUUUCCU
.....((.........(((...(((((........))))).((((((((.....)))))))).)))((((((....((....))..)))))).(((((.......)))))))........ ( -29.50)
>DroSec_CAF1 70754 120 + 1
UCUCCGCUUCUUUCUUGACUUUCUGAUAGCUCUCGAUCAGCUUUUGGGCCUCCUGCUCAAGACGUCGCUCCUCAUCGGUCUUUUUAAGGAGCUUGGCACCCUUUUUGCCAGCAAUUUCCU
.....((.........(((...(((((........))))).((((((((.....)))))))).)))((((((..............)))))).(((((.......)))))))........ ( -29.24)
>DroSim_CAF1 86315 120 + 1
UCUCCGCUUCUUUCUUGACUUUCUGAUAGCUUUCGAUCAGCUUUUGGGCCUCCUGCUCAAGACGUCGCUCCUCAUCGGUCUUUUUAAGGAGCUUGGCACCCUUUUUGCCAGCAAUUUCCU
.....((.........(((...(((((........))))).((((((((.....)))))))).)))((((((..............)))))).(((((.......)))))))........ ( -29.24)
>DroYak_CAF1 77963 120 + 1
UCUCCGCUUCCUUCUUGACCUUCUGAUAGCUUUCGAUCAGCUUCUGGGCCUCCUGCUCGAGAAGUCGCUCCUCAUCGGUCUUCUUGAGGAGCUUGGCACCCUUCUUGCCAGCGAUUUCCU
....(((...((((((((((..(((((........))))).....))((.....))))))))))..((((((((..........)))))))).(((((.......))))))))....... ( -36.80)
>consensus
UCUCCGCUUCUUUCUUGACUUUCUGAUAGCUUUCGAUCAGCUUUUGGGCCUCCUGCUCAAGACGUCGCUCCUCAUCGGUCUUCUUAAGGAGCUUGGCACCCUUUUUGCCAGCAAUUUCCU
.....((.........(((...(((((........))))).((((((((.....)))))))).)))((((((..............)))))).(((((.......)))))))........ (-28.83 = -28.89 +   0.06)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 14,474,198 – 14,474,318
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.69
Mean single sequence MFE -34.00
Consensus MFE -32.81
Energy contribution -32.50
Covariance contribution -0.31
Combinations/Pair 1.10
Mean z-score -2.24
Structure conservation index 0.97
SVM decision value 1.67
SVM RNA-class probability 0.971105
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14474198 120 - 23771897
AGGAAAUUGCUGGCAAAAAGGGUGCCAAGCUCCUUAAGAAGACCGAUGAGGAGCGACGUCUUGAGCAGGAGGCCCAAAAGCUGAUCGAAAGCUAUCAGAAAGUCAAGAAAGAAGCGGAGA
......(((((((((.......))))..((((((((.(.....)..))))))))....((((((...((....)).....((((((....)..)))))....))))))....)))))... ( -32.70)
>DroSec_CAF1 70754 120 - 1
AGGAAAUUGCUGGCAAAAAGGGUGCCAAGCUCCUUAAAAAGACCGAUGAGGAGCGACGUCUUGAGCAGGAGGCCCAAAAGCUGAUCGAGAGCUAUCAGAAAGUCAAGAAAGAAGCGGAGA
......(((((((((.......))))..((((((((..........))))))))....((((((...((....)).....((((((....)..)))))....))))))....)))))... ( -31.40)
>DroSim_CAF1 86315 120 - 1
AGGAAAUUGCUGGCAAAAAGGGUGCCAAGCUCCUUAAAAAGACCGAUGAGGAGCGACGUCUUGAGCAGGAGGCCCAAAAGCUGAUCGAAAGCUAUCAGAAAGUCAAGAAAGAAGCGGAGA
......(((((((((.......))))..((((((((..........))))))))....((((((...((....)).....((((((....)..)))))....))))))....)))))... ( -32.40)
>DroYak_CAF1 77963 120 - 1
AGGAAAUCGCUGGCAAGAAGGGUGCCAAGCUCCUCAAGAAGACCGAUGAGGAGCGACUUCUCGAGCAGGAGGCCCAGAAGCUGAUCGAAAGCUAUCAGAAGGUCAAGAAGGAAGCGGAGA
......(((((((((.......))))..((((((((.(.....)..))))))))..(((((.((.(.((....)).....((((((....)..)))))..).)).)))))..)))))... ( -39.50)
>consensus
AGGAAAUUGCUGGCAAAAAGGGUGCCAAGCUCCUUAAAAAGACCGAUGAGGAGCGACGUCUUGAGCAGGAGGCCCAAAAGCUGAUCGAAAGCUAUCAGAAAGUCAAGAAAGAAGCGGAGA
......(((((((((.......))))..((((((((..........))))))))((((((((......))))).......((((((....)..)))))...)))........)))))... (-32.81 = -32.50 +  -0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:23 2006