Locus 7813

Sequence ID 3R_DroMel_CAF1
Location 20,938,313 – 20,938,459
Length 146
Max. P 0.939211
window12599 window12600 window12601

overview

Window 9

Location 20,938,313 – 20,938,419
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 88.11
Mean single sequence MFE -25.48
Consensus MFE -18.82
Energy contribution -18.58
Covariance contribution -0.24
Combinations/Pair 1.17
Mean z-score -1.80
Structure conservation index 0.74
SVM decision value 0.33
SVM RNA-class probability 0.690632
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20938313 106 - 27905053
UUGCAUAGCUUAGUAAGGAACGCUAGCGCAUUAGUGGGGGUACUUCUUUCCCCACCAAAAAGUGCUCAAUAAUGCAAAAUGGACAUAUGUACAAAUAUGGAAAAGC
((((((.(((.(((.......))))))(((((.(((((((........))))))).....)))))......))))))......(((((......)))))....... ( -28.60)
>DroSec_CAF1 1487 105 - 1
UGGCAUAGGUUAGUAAGGAAGACUAACGUAUUAAUGGGGGUACUUCUUCCCCCACCAA-AAGUGCUCAAUAAUGCAAAAUGGACAUAUGUACAAAUAUGGAAAAGC
....(((.((((((.......)))))).)))...((((((........))))))(((.-...(((........)))...))).(((((......)))))....... ( -27.50)
>DroSim_CAF1 1487 106 - 1
UGGCAUAGGUUAGUAAGGAACACUAACGUUUUAAUGGGGGCACUUCUUCCCCCACCAAAAAGUGCUCAAUAAUGCAAAAUGGACAUAUGUACAAAUAUGGAAAAGC
........((((((.......))))))(((((..((((((........))))))(((.....(((........)))...))).(((((......)))))..))))) ( -24.70)
>DroEre_CAF1 1344 106 - 1
GGGCGUCGCUUAGUAACAAACACUAACAUAUUAGUCGGGGCACUUCUUCCCCCACCAGAAAGUGCUCCGAAAUGCAAAAUGGACAUAUGUACAAAUAUGGAAAAGC
..((.(((((((((.......)))))........(((((((((((((.........)).)))))))))))...))........(((((......)))))))...)) ( -25.40)
>DroYak_CAF1 1483 106 - 1
GGGCAUCGCUUAGUAACAAACACUAACAUAAUAGUCGGGGUACUUGCUCCCCCACCGAAAAGUGCUCCAAAAUGCAAAAUGGACAUAUGUACAAAUAUGGAAAAGC
..((((.(.(((((.......)))))).........(((((((((..((.......)).)))))))))...))))........(((((......)))))....... ( -21.20)
>consensus
UGGCAUAGCUUAGUAAGGAACACUAACGUAUUAGUGGGGGUACUUCUUCCCCCACCAAAAAGUGCUCAAUAAUGCAAAAUGGACAUAUGUACAAAUAUGGAAAAGC
.......(.(((((.......)))))).......((((((........))))))(((.....(((........)))...))).(((((......)))))....... (-18.82 = -18.58 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,938,339 – 20,938,459
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.42
Mean single sequence MFE -33.78
Consensus MFE -23.18
Energy contribution -24.58
Covariance contribution 1.40
Combinations/Pair 1.08
Mean z-score -2.42
Structure conservation index 0.69
SVM decision value 1.22
SVM RNA-class probability 0.932426
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20938339 120 + 27905053
AUUUUGCAUUAUUGAGCACUUUUUGGUGGGGAAAGAAGUACCCCCACUAAUGCGCUAGCGUUCCUUACUAAGCUAUGCAAAAAUAAAGUACUCCAAAGCAUUUUCGUUCGCCAUAGCCCA
....(((......(((.((((((((((((((..........)))))))))((((.((((............)))))))).....))))).)))....))).................... ( -27.90)
>DroSec_CAF1 1513 118 + 1
AUUUUGCAUUAUUGAGCACUU-UUGGUGGGGGAAGAAGUACCCCCAUUAAUACGUUAGUCUUCCUUACUAACCUAUGCCAAA-AAAAGUGCUUCAAGGCAUUUUCGUUCGCCAUAGUCCA
...........((((((((((-((((((((((........)))))))).(((.((((((.......)))))).)))......-)))))))).))))(((..........)))........ ( -34.00)
>DroSim_CAF1 1513 120 + 1
AUUUUGCAUUAUUGAGCACUUUUUGGUGGGGGAAGAAGUGCCCCCAUUAAAACGUUAGUGUUCCUUACUAACCUAUGCCAAAAAAAAGUGCUCCAAGGCAUUUUUGUUCGCCAUAGUCCA
....((.(((((.(((((((((((((((((((........)))))))).....(((((((.....)))))))..........)))))))))))...(((..........)))))))).)) ( -38.20)
>DroEre_CAF1 1370 120 + 1
AUUUUGCAUUUCGGAGCACUUUCUGGUGGGGGAAGAAGUGCCCCGACUAAUAUGUUAGUGUUUGUUACUAAGCGACGCCCAAAUAAAGUGCUCCAUAUUAGUUUUAUUCGCCAUAGUCCA
............((((((((((.((((.((((........)))).))))........(((((.(((....))))))))......)))))))))).......................... ( -32.90)
>DroYak_CAF1 1509 120 + 1
AUUUUGCAUUUUGGAGCACUUUUCGGUGGGGGAGCAAGUACCCCGACUAUUAUGUUAGUGUUUGUUACUAAGCGAUGCCCAAACAAAGUGCUCCAAAUAAGUUUUAUGCGCCAUAUUCCA
.....(((((((((((((((((..(((.((((........)))).)))......((((((.....)))))).............)))))))))))))........))))........... ( -35.90)
>consensus
AUUUUGCAUUAUUGAGCACUUUUUGGUGGGGGAAGAAGUACCCCCACUAAUACGUUAGUGUUCCUUACUAAGCUAUGCCAAAAAAAAGUGCUCCAAAGCAUUUUUGUUCGCCAUAGUCCA
.............(((((((((.(((((((((........))))))))).....((((((.....)))))).............)))))))))........................... (-23.18 = -24.58 +   1.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,938,339 – 20,938,459
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.42
Mean single sequence MFE -34.00
Consensus MFE -23.10
Energy contribution -23.78
Covariance contribution 0.68
Combinations/Pair 1.21
Mean z-score -2.50
Structure conservation index 0.68
SVM decision value 1.30
SVM RNA-class probability 0.939211
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20938339 120 - 27905053
UGGGCUAUGGCGAACGAAAAUGCUUUGGAGUACUUUAUUUUUGCAUAGCUUAGUAAGGAACGCUAGCGCAUUAGUGGGGGUACUUCUUUCCCCACCAAAAAGUGCUCAAUAAUGCAAAAU
...((....)).........(((....(((((((((.....(((.((((............))))..)))...(((((((........)))))))...)))))))))......))).... ( -33.80)
>DroSec_CAF1 1513 118 - 1
UGGACUAUGGCGAACGAAAAUGCCUUGAAGCACUUUU-UUUGGCAUAGGUUAGUAAGGAAGACUAACGUAUUAAUGGGGGUACUUCUUCCCCCACCAA-AAGUGCUCAAUAAUGCAAAAU
........((((........))))((((.(((((((.-..(((.(((.((((((.......)))))).)))...((((((........))))))))))-))))))))))........... ( -34.70)
>DroSim_CAF1 1513 120 - 1
UGGACUAUGGCGAACAAAAAUGCCUUGGAGCACUUUUUUUUGGCAUAGGUUAGUAAGGAACACUAACGUUUUAAUGGGGGCACUUCUUCCCCCACCAAAAAGUGCUCAAUAAUGCAAAAU
........((((........))))...((((((((((...(((.....((((((.......)))))).......((((((........)))))))))))))))))))............. ( -35.00)
>DroEre_CAF1 1370 120 - 1
UGGACUAUGGCGAAUAAAACUAAUAUGGAGCACUUUAUUUGGGCGUCGCUUAGUAACAAACACUAACAUAUUAGUCGGGGCACUUCUUCCCCCACCAGAAAGUGCUCCGAAAUGCAAAAU
.........(((.......((((((((((((.((......)))).))..(((((.......)))))))))))))(((((((((((((.........)).)))))))))))..)))..... ( -31.80)
>DroYak_CAF1 1509 120 - 1
UGGAAUAUGGCGCAUAAAACUUAUUUGGAGCACUUUGUUUGGGCAUCGCUUAGUAACAAACACUAACAUAAUAGUCGGGGUACUUGCUCCCCCACCGAAAAGUGCUCCAAAAUGCAAAAU
...........((((........(((((((((((((...((((....(.(((((.......)))))).........(((((....)))))))))....)))))))))))))))))..... ( -34.70)
>consensus
UGGACUAUGGCGAACAAAAAUGCUUUGGAGCACUUUAUUUUGGCAUAGCUUAGUAAGGAACACUAACGUAUUAGUGGGGGUACUUCUUCCCCCACCAAAAAGUGCUCAAUAAUGCAAAAU
.........(((..((((.....))))(((((((((...........(.(((((.......))))))......(((((((........)))))))...))))))))).....)))..... (-23.10 = -23.78 +   0.68)

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 12:55:23 2006