Locus 7742

Sequence ID 3R_DroMel_CAF1
Location 20,784,244 – 20,784,423
Length 179
Max. P 0.686597
window12479 window12480 window12481

overview

Window 9

Location 20,784,244 – 20,784,343
Length 99
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.67
Mean single sequence MFE -31.23
Consensus MFE -27.52
Energy contribution -28.93
Covariance contribution 1.42
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.88
SVM decision value 0.12
SVM RNA-class probability 0.591071
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20784244 99 + 27905053
---------------------UCACUCUCGAAGCUCCUUUCCCGAUGUCAUUAAAGGCUUAAGGAAUUCGAAUUUGAAUAGCCGUGAACUGCAGGCGACUGCACUCGGUAUCAUCUUCCC
---------------------(((...(((((..(((((..((............))...))))).)))))...)))...((((.(...(((((....)))))).))))........... ( -25.90)
>DroSec_CAF1 1 120 + 1
CUAAUGGAUGUGCUCGUAUAUCCAGACUCGAAGCUCCUUUCCCGAUGUCAUUAAAGGCUUAAGGAAUUCGAAUUUGAAUAGCCGUGAACUGCAGGCGACUGCACUCGGUAUCAUCUUCCC
....((((((((....))))))))...(((((..(((((..((............))...))))).)))))...(((...((((.(...(((((....)))))).)))).)))....... ( -33.90)
>DroSim_CAF1 1 120 + 1
CUAAUGGAUGUGCUCGUAUAUCCAGACUCGAAGCUCCUUUCCCGAUGUCAUUAAAGGCUUAAGGAAUUCGAAUUUGAAUAGCCGUGAACUGCAGGCGACUGCACUCGGUAUCAUCUUCCC
....((((((((....))))))))...(((((..(((((..((............))...))))).)))))...(((...((((.(...(((((....)))))).)))).)))....... ( -33.90)
>consensus
CUAAUGGAUGUGCUCGUAUAUCCAGACUCGAAGCUCCUUUCCCGAUGUCAUUAAAGGCUUAAGGAAUUCGAAUUUGAAUAGCCGUGAACUGCAGGCGACUGCACUCGGUAUCAUCUUCCC
....((((((((....))))))))...(((((..(((((..((............))...))))).)))))...(((...((((.(...(((((....)))))).)))).)))....... (-27.52 = -28.93 +   1.42)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,784,263 – 20,784,383
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -27.70
Consensus MFE -27.70
Energy contribution -27.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 1.00
SVM decision value 0.32
SVM RNA-class probability 0.686597
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20784263 120 + 27905053
CCCGAUGUCAUUAAAGGCUUAAGGAAUUCGAAUUUGAAUAGCCGUGAACUGCAGGCGACUGCACUCGGUAUCAUCUUCCCACUACCAUUCCCGGCACUCAAUCCGUAUCCAAAUCCUCCU
...((((((......)))....(((...((...((((...((((.(((.(((((....)))))...((((............)))).))).))))..))))..))..)))..)))..... ( -27.70)
>DroSec_CAF1 41 120 + 1
CCCGAUGUCAUUAAAGGCUUAAGGAAUUCGAAUUUGAAUAGCCGUGAACUGCAGGCGACUGCACUCGGUAUCAUCUUCCCACUACCAUUCCCGGCACUCAAUCCGUAUCCAAAUCCUCCU
...((((((......)))....(((...((...((((...((((.(((.(((((....)))))...((((............)))).))).))))..))))..))..)))..)))..... ( -27.70)
>DroSim_CAF1 41 120 + 1
CCCGAUGUCAUUAAAGGCUUAAGGAAUUCGAAUUUGAAUAGCCGUGAACUGCAGGCGACUGCACUCGGUAUCAUCUUCCCACUACCAUUCCCGGCACUCAAUCCGUAUCCAAAUCCUCCU
...((((((......)))....(((...((...((((...((((.(((.(((((....)))))...((((............)))).))).))))..))))..))..)))..)))..... ( -27.70)
>consensus
CCCGAUGUCAUUAAAGGCUUAAGGAAUUCGAAUUUGAAUAGCCGUGAACUGCAGGCGACUGCACUCGGUAUCAUCUUCCCACUACCAUUCCCGGCACUCAAUCCGUAUCCAAAUCCUCCU
...((((((......)))....(((...((...((((...((((.(((.(((((....)))))...((((............)))).))).))))..))))..))..)))..)))..... (-27.70 = -27.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,784,303 – 20,784,423
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.32
Mean single sequence MFE -34.97
Consensus MFE -34.10
Energy contribution -34.43
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.98
SVM decision value 0.12
SVM RNA-class probability 0.591809
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20784303 120 + 27905053
GCCGUGAACUGCAGGCGACUGCACUCGGUAUCAUCUUCCCACUACCAUUCCCGGCACUCAAUCCGUAUCCAAAUCCUCCUGAAGUGCCGCCGUCAAAAGUUCGGGAUGAUGGGCCAUCUU
((((.(...(((((....)))))).)))).(((((.(((((((........(((((((((...................)).)))))))........)))..)))).)))))........ ( -35.40)
>DroSec_CAF1 81 118 + 1
GCCGUGAACUGCAGGCGACUGCACUCGGUAUCAUCUUCCCACUACCAUUCCCGGCACUCAAUCCGUAUCCAAAUCCUCCUGAAGUGCCGCCGUCA--AUUUCGGGAUGAUGGGCCAUCUU
((((.(...(((((....)))))).)))).(((((.((((...........(((((((((...................)).)))))))......--.....)))).)))))........ ( -34.76)
>DroSim_CAF1 81 118 + 1
GCCGUGAACUGCAGGCGACUGCACUCGGUAUCAUCUUCCCACUACCAUUCCCGGCACUCAAUCCGUAUCCAAAUCCUCCUGAAGUGCCGCCGUCA--AGUUCGGGAUGAUGGGCCAUCUU
((((.(...(((((....)))))).)))).(((((.((((...........(((((((((...................)).)))))))......--.....)))).)))))........ ( -34.76)
>consensus
GCCGUGAACUGCAGGCGACUGCACUCGGUAUCAUCUUCCCACUACCAUUCCCGGCACUCAAUCCGUAUCCAAAUCCUCCUGAAGUGCCGCCGUCA__AGUUCGGGAUGAUGGGCCAUCUU
((((.(...(((((....)))))).)))).(((((.(((((((........(((((((((...................)).)))))))........)))..)))).)))))........ (-34.10 = -34.43 +   0.33)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:23 2006