Locus 684

Sequence ID 3L_DroMel_CAF1
Location 2,024,126 – 2,024,253
Length 127
Max. P 0.981602
window1045 window1046 window1047 window1048

overview

Window 5

Location 2,024,126 – 2,024,220
Length 94
Sequences 3
Columns 95
Reading direction forward
Mean pairwise identity 94.39
Mean single sequence MFE -23.83
Consensus MFE -23.66
Energy contribution -23.00
Covariance contribution -0.66
Combinations/Pair 1.08
Mean z-score -1.93
Structure conservation index 0.99
SVM decision value 1.15
SVM RNA-class probability 0.923423
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2024126 94 + 23771897
GAAUGUAAGUUUUGAGUAAUUGUCAGGAUCACAGGUGGUCCUGCAAUGG-AGGAUAGGUGGUGUAACUCAGUCGAAGAAUUAAUCGACACUAAAA
.......(((..(((((.((((.((((((((....))))))))))))..-...(((.....))).)))))(((((........)))))))).... ( -23.90)
>DroSec_CAF1 74585 95 + 1
GUAUUUAAGUUUUGAGUAUUUGUCAGGACCACAGGUGGUCCUGCAAGGGAAGGAUAGGUGGUGUAACUCAGUCAAAGAAUUAAUCGAUACUAAAA
.......(((.((((...((((.((((((((....)))))))))))).....(((.(((......)))..)))..........)))).))).... ( -23.80)
>DroSim_CAF1 89736 95 + 1
GUAUUUAAGUUUUGAGUAUUUGUCAGGACCACAGGUGGUCCUGCAAGGGAAGGAUAGGUGGUGUAACUCAGUCAAAGAAUUAAUCGAUACUAAAA
.......(((.((((...((((.((((((((....)))))))))))).....(((.(((......)))..)))..........)))).))).... ( -23.80)
>consensus
GUAUUUAAGUUUUGAGUAUUUGUCAGGACCACAGGUGGUCCUGCAAGGGAAGGAUAGGUGGUGUAACUCAGUCAAAGAAUUAAUCGAUACUAAAA
.......(((.((((...((((.((((((((....)))))))))))).....(((.(((......)))..)))..........)))).))).... (-23.66 = -23.00 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,024,126 – 2,024,220
Length 94
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 94.39
Mean single sequence MFE -20.79
Consensus MFE -19.02
Energy contribution -19.13
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -3.66
Structure conservation index 0.91
SVM decision value 1.89
SVM RNA-class probability 0.981602
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2024126 94 - 23771897
UUUUAGUGUCGAUUAAUUCUUCGACUGAGUUACACCACCUAUCCU-CCAUUGCAGGACCACCUGUGAUCCUGACAAUUACUCAAAACUUACAUUC
.......(((((........)))))(((((...............-..(((((((((.((....)).))))).)))).)))))............ ( -18.97)
>DroSec_CAF1 74585 95 - 1
UUUUAGUAUCGAUUAAUUCUUUGACUGAGUUACACCACCUAUCCUUCCCUUGCAGGACCACCUGUGGUCCUGACAAAUACUCAAAACUUAAAUAC
(((.(((((....((((((.......)))))).................(((((((((((....)))))))).)))))))).))).......... ( -21.70)
>DroSim_CAF1 89736 95 - 1
UUUUAGUAUCGAUUAAUUCUUUGACUGAGUUACACCACCUAUCCUUCCCUUGCAGGACCACCUGUGGUCCUGACAAAUACUCAAAACUUAAAUAC
(((.(((((....((((((.......)))))).................(((((((((((....)))))))).)))))))).))).......... ( -21.70)
>consensus
UUUUAGUAUCGAUUAAUUCUUUGACUGAGUUACACCACCUAUCCUUCCCUUGCAGGACCACCUGUGGUCCUGACAAAUACUCAAAACUUAAAUAC
(((.((((.....((((((.......)))))).................(((((((((((....)))))))).))).)))).))).......... (-19.02 = -19.13 +   0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,024,156 – 2,024,253
Length 97
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 94.56
Mean single sequence MFE -26.73
Consensus MFE -22.17
Energy contribution -22.07
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -2.65
Structure conservation index 0.83
SVM decision value 0.61
SVM RNA-class probability 0.797875
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2024156 97 + 23771897
ACAGGUGGUCCUGCAAUGG-AGGAUAGGUGGUGUAACUCAGUCGAAGAAUUAAUCGACACUAAAAACUGUUAAAUAAUACAACCUCUAUCCUUAGCCA
.((((....)))).....(-((((((((.((((((.....(((((........)))))((........)).......))).))))))))))))..... ( -26.10)
>DroSec_CAF1 74615 98 + 1
ACAGGUGGUCCUGCAAGGGAAGGAUAGGUGGUGUAACUCAGUCAAAGAAUUAAUCGAUACUAAAAACUGUCAAGUAAUACAACCUCUAUCCUUAGCCA
.((((....))))...((.(((((((((.(((((((((((((...((.(((....))).))....))))...)))..))).))))))))))))..)). ( -25.40)
>DroSim_CAF1 89766 98 + 1
ACAGGUGGUCCUGCAAGGGAAGGAUAGGUGGUGUAACUCAGUCAAAGAAUUAAUCGAUACUAAAAAGUGUCAAGUAAGACAACCUCUAUCCUUAGCCA
.((((....))))...((.(((((((((.((((.....).(((...((.....))((((((....))))))......))).))))))))))))..)). ( -28.70)
>consensus
ACAGGUGGUCCUGCAAGGGAAGGAUAGGUGGUGUAACUCAGUCAAAGAAUUAAUCGAUACUAAAAACUGUCAAGUAAUACAACCUCUAUCCUUAGCCA
.((((....))))....((.((((((((.((((((...........((.....))((((........))))......))).)))))))))))...)). (-22.17 = -22.07 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,024,156 – 2,024,253
Length 97
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 94.56
Mean single sequence MFE -25.13
Consensus MFE -21.46
Energy contribution -21.47
Covariance contribution 0.01
Combinations/Pair 1.10
Mean z-score -2.15
Structure conservation index 0.85
SVM decision value 0.28
SVM RNA-class probability 0.666805
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2024156 97 - 23771897
UGGCUAAGGAUAGAGGUUGUAUUAUUUAACAGUUUUUAGUGUCGAUUAAUUCUUCGACUGAGUUACACCACCUAUCCU-CCAUUGCAGGACCACCUGU
(((...(((((((..(.((((..(((((((........))(((((........)))))))))))))).)..)))))))-)))..(((((....))))) ( -25.80)
>DroSec_CAF1 74615 98 - 1
UGGCUAAGGAUAGAGGUUGUAUUACUUGACAGUUUUUAGUAUCGAUUAAUUCUUUGACUGAGUUACACCACCUAUCCUUCCCUUGCAGGACCACCUGU
.((..((((((((..(.((((..(((...(((((...((............))..)))))))))))).)..)))))))).))..(((((....))))) ( -24.50)
>DroSim_CAF1 89766 98 - 1
UGGCUAAGGAUAGAGGUUGUCUUACUUGACACUUUUUAGUAUCGAUUAAUUCUUUGACUGAGUUACACCACCUAUCCUUCCCUUGCAGGACCACCUGU
.((..((((((((.(((((((......))))...((((((...((.....))....))))))....)))..)))))))).))..(((((....))))) ( -25.10)
>consensus
UGGCUAAGGAUAGAGGUUGUAUUACUUGACAGUUUUUAGUAUCGAUUAAUUCUUUGACUGAGUUACACCACCUAUCCUUCCCUUGCAGGACCACCUGU
.((..((((((((..(.((((..(((((((........)).((((........)))).))))))))).)..))))))))))...(((((....))))) (-21.46 = -21.47 +   0.01)

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 09:48:29 2006