Locus 3519

Sequence ID 2L_DroMel_CAF1
Location 10,282,861 – 10,283,021
Length 160
Max. P 0.967163
window5556 window5557 window5558 window5559

overview

Window 6

Location 10,282,861 – 10,282,981
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.94
Mean single sequence MFE -34.90
Consensus MFE -29.30
Energy contribution -31.97
Covariance contribution 2.67
Combinations/Pair 1.05
Mean z-score -2.58
Structure conservation index 0.84
SVM decision value 0.48
SVM RNA-class probability 0.752559
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10282861 120 + 22407834
UACCCCCGAAUGCAUUCGACUUGUUGGAAUCAGUUCGCAGCAAUUUAGUGCAGGUUUCUACUAUAUCAGAGUCUUCUGAUACGACUGAAAGGUCGCCAUUUCGUCUAUCCGAAAUGACCU
..........((((((.((.(((((((((....))).)))))))).))))))(((........((((((......))))))(((((....))))).(((((((......)))))))))). ( -35.00)
>DroSec_CAF1 3070 120 + 1
UACCCCCGAAUGCAUUCGACUUGUUGGAAUCAGUUCGCAGCAGUUUGGUGCAGGUUUCUACUAUAUCAGAUUCUUCUGAUACGACUGAAAGGUCGCCAUUUCGUCUAUCCGAAAUGACUU
..........(((((..((((.(((((((....))).))))))))..)))))...........(((((((....)))))))(((((....))))).(((((((......))))))).... ( -36.70)
>DroSim_CAF1 2837 120 + 1
UACCCCCGAAUGCAUUCGACUUGUUGGAAUCAGUUCGCAGCAUUUUGGUACAGGUUUCUACUAUAUCAGAUUCUUCUGAUACGACUGAAAGGUCGCCAUUUCGUCUAUCCGAAAUGACUU
.(((((.((((((...(((.(((.......))).)))..)))))).))....)))........(((((((....)))))))(((((....))))).(((((((......))))))).... ( -33.00)
>consensus
UACCCCCGAAUGCAUUCGACUUGUUGGAAUCAGUUCGCAGCAAUUUGGUGCAGGUUUCUACUAUAUCAGAUUCUUCUGAUACGACUGAAAGGUCGCCAUUUCGUCUAUCCGAAAUGACUU
..........(((((.(((.(((((((((....))).)))))).))))))))(((........(((((((....)))))))(((((....))))).(((((((......)))))))))). (-29.30 = -31.97 +   2.67)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,282,861 – 10,282,981
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.94
Mean single sequence MFE -36.60
Consensus MFE -34.52
Energy contribution -34.30
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.65
Structure conservation index 0.94
SVM decision value 1.53
SVM RNA-class probability 0.961529
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10282861 120 - 22407834
AGGUCAUUUCGGAUAGACGAAAUGGCGACCUUUCAGUCGUAUCAGAAGACUCUGAUAUAGUAGAAACCUGCACUAAAUUGCUGCGAACUGAUUCCAACAAGUCGAAUGCAUUCGGGGGUA
..(((((((((......))))))))).((((.((((((((((((((....))))))...((((....))))...........))).)))))..........(((((....))))))))). ( -35.70)
>DroSec_CAF1 3070 120 - 1
AAGUCAUUUCGGAUAGACGAAAUGGCGACCUUUCAGUCGUAUCAGAAGAAUCUGAUAUAGUAGAAACCUGCACCAAACUGCUGCGAACUGAUUCCAACAAGUCGAAUGCAUUCGGGGGUA
..(((((((((......)))))))))(((......)))((((((((....)))))))).((((....))))(((...(((.((((...(((((......)))))..))))..))).))). ( -36.10)
>DroSim_CAF1 2837 120 - 1
AAGUCAUUUCGGAUAGACGAAAUGGCGACCUUUCAGUCGUAUCAGAAGAAUCUGAUAUAGUAGAAACCUGUACCAAAAUGCUGCGAACUGAUUCCAACAAGUCGAAUGCAUUCGGGGGUA
..(((((((((......))))))))).(((((((.(..((((((((....))))))))..).))))......((..(((((..(((..((.......))..)))...)))))..))))). ( -38.00)
>consensus
AAGUCAUUUCGGAUAGACGAAAUGGCGACCUUUCAGUCGUAUCAGAAGAAUCUGAUAUAGUAGAAACCUGCACCAAAAUGCUGCGAACUGAUUCCAACAAGUCGAAUGCAUUCGGGGGUA
..(((((((((......))))))))).(((((((.(..((((((((....))))))))..).))))......((....(((..(((..((.......))..)))...)))....))))). (-34.52 = -34.30 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,282,901 – 10,283,021
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -33.27
Consensus MFE -28.49
Energy contribution -30.27
Covariance contribution 1.78
Combinations/Pair 1.03
Mean z-score -2.10
Structure conservation index 0.86
SVM decision value 0.18
SVM RNA-class probability 0.620276
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10282901 120 + 22407834
CAAUUUAGUGCAGGUUUCUACUAUAUCAGAGUCUUCUGAUACGACUGAAAGGUCGCCAUUUCGUCUAUCCGAAAUGACCUUCUGGAGAUUACGUGAUAACACUUUGUUGUGACAAAGCAG
........(((.((((((((...((((((......))))))(((((....))))).(((((((......)))))))......))))))))..((.(((((.....))))).))...))). ( -34.50)
>DroSec_CAF1 3110 120 + 1
CAGUUUGGUGCAGGUUUCUACUAUAUCAGAUUCUUCUGAUACGACUGAAAGGUCGCCAUUUCGUCUAUCCGAAAUGACUUUCUGGAGAUUGCGUGAUAAAACUUUGUUGUGACAAAGCAG
..((((...((((.((((((...(((((((....)))))))(((((....))))).(((((((......)))))))......))))))))))((.((((.......)))).)).)))).. ( -33.20)
>DroSim_CAF1 2877 120 + 1
CAUUUUGGUACAGGUUUCUACUAUAUCAGAUUCUUCUGAUACGACUGAAAGGUCGCCAUUUCGUCUAUCCGAAAUGACUUUCUGGAGAUUACGUGAUAAAACUUUGUUGUGACAAAGCAG
..(((((.(((.((((((((...(((((((....)))))))(((((....))))).(((((((......)))))))......))))))))..))).)))))((((((....))))))... ( -32.10)
>consensus
CAAUUUGGUGCAGGUUUCUACUAUAUCAGAUUCUUCUGAUACGACUGAAAGGUCGCCAUUUCGUCUAUCCGAAAUGACUUUCUGGAGAUUACGUGAUAAAACUUUGUUGUGACAAAGCAG
..........((.((.(((.((((((((((....)))))))(((((....))))).(((((((......)))))))......))))))..)).))......((((((....))))))... (-28.49 = -30.27 +   1.78)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,282,901 – 10,283,021
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -31.40
Consensus MFE -30.17
Energy contribution -30.17
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.50
Structure conservation index 0.96
SVM decision value 1.61
SVM RNA-class probability 0.967163
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10282901 120 - 22407834
CUGCUUUGUCACAACAAAGUGUUAUCACGUAAUCUCCAGAAGGUCAUUUCGGAUAGACGAAAUGGCGACCUUUCAGUCGUAUCAGAAGACUCUGAUAUAGUAGAAACCUGCACUAAAUUG
..(((((((....)))))))......................(((((((((......)))))))))(((......)))((((((((....)))))))).((((....))))......... ( -32.00)
>DroSec_CAF1 3110 120 - 1
CUGCUUUGUCACAACAAAGUUUUAUCACGCAAUCUCCAGAAAGUCAUUUCGGAUAGACGAAAUGGCGACCUUUCAGUCGUAUCAGAAGAAUCUGAUAUAGUAGAAACCUGCACCAAACUG
..(((((((....)))))))................(((...(((((((((......)))))))))(((......)))((((((((....)))))))).((((....))))......))) ( -32.10)
>DroSim_CAF1 2877 120 - 1
CUGCUUUGUCACAACAAAGUUUUAUCACGUAAUCUCCAGAAAGUCAUUUCGGAUAGACGAAAUGGCGACCUUUCAGUCGUAUCAGAAGAAUCUGAUAUAGUAGAAACCUGUACCAAAAUG
..(((((((....)))))))................(((...(((((((((......)))))))))....((((.(..((((((((....))))))))..).)))).))).......... ( -30.10)
>consensus
CUGCUUUGUCACAACAAAGUUUUAUCACGUAAUCUCCAGAAAGUCAUUUCGGAUAGACGAAAUGGCGACCUUUCAGUCGUAUCAGAAGAAUCUGAUAUAGUAGAAACCUGCACCAAAAUG
..(((((((....)))))))................(((...(((((((((......)))))))))....((((.(..((((((((....))))))))..).)))).))).......... (-30.17 = -30.17 +   0.00)

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 10:54:28 2006