Locus 6908

Sequence ID X_DroMel_CAF1
Location 17,288,254 – 17,288,461
Length 207
Max. P 0.998617
window11296 window11297 window11298 window11299

overview

Window 6

Location 17,288,254 – 17,288,365
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.16
Mean single sequence MFE -35.87
Consensus MFE -35.11
Energy contribution -34.67
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -2.41
Structure conservation index 0.98
SVM decision value 1.85
SVM RNA-class probability 0.980046
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17288254 111 - 22224390
GCCAGACAUUAUGCAAUAUUGGGGCCCUAAGGCGAUUGGGACCGGUACCCGAAAUAGCCACCGAAAUACGCUGCCAUUCAAAUGCAGUGAUGCCCCAAUAGUUUGAAAU---------AU
..(((((.........(((((((((.....(((..(((((.......)))))....))).........((((((.........))))))..))))))))))))))....---------.. ( -35.20)
>DroSim_CAF1 7126 111 - 1
GCCAGACAUUAUGCAAUAUUGGGGUCCUAAGGCGAUUGGGACCGGUACCCGAAAUAGCCACCGAAAUACGCUGCCAUUCAAAUGCAGUGAUGCCCCAAUAGUUUGAAAU---------AU
..(((((.........(((((((((.....(((..(((((.......)))))....))).........((((((.........))))))..))))))))))))))....---------.. ( -33.30)
>DroYak_CAF1 8694 120 - 1
GCCAGACAUUAUGCAAUAUUGGGGCCCUAAGGCGAUUGGGACCGGUACCCAAAAUAGCCACCGAAAUACGCUGCCAUUCAAAUGCAGUGAUGCCCCAAUAGUUUGAAAUCGAAUAGGUGU
(((.............(((((((((.....(((..(((((.......)))))....))).........((((((.........))))))..)))))))))(((((....))))).))).. ( -39.10)
>consensus
GCCAGACAUUAUGCAAUAUUGGGGCCCUAAGGCGAUUGGGACCGGUACCCGAAAUAGCCACCGAAAUACGCUGCCAUUCAAAUGCAGUGAUGCCCCAAUAGUUUGAAAU_________AU
..(((((.........(((((((((.....(((..(((((.......)))))....))).........((((((.........))))))..))))))))))))))............... (-35.11 = -34.67 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,288,325 – 17,288,428
Length 103
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.09
Mean single sequence MFE -41.70
Consensus MFE -30.87
Energy contribution -31.10
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -1.62
Structure conservation index 0.74
SVM decision value -0.00
SVM RNA-class probability 0.533315
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17288325 103 - 22224390
UUGGUCAUC-----------------GGCCAUUGGCCAUUGGCCAUCGGACACCGGCCACCGGCUGAUAAAUGAGUCUGGGCCAGACAUUAUGCAAUAUUGGGGCCCUAAGGCGAUUGGG
(..((((((-----------------((((..(((((..((.((...)).))..)))))..)))))))......(((((((((...((.(((...))).)).)))))..)))))))..). ( -40.40)
>DroSim_CAF1 7197 103 - 1
UUGGUCAUC-----------------GGCCAUUGGCCAUUGGCCAUCGGACACCGGCCACCGGCUGACAAAUGAGUCUGGGCCAGACAUUAUGCAAUAUUGGGGUCCUAAGGCGAUUGGG
(..(((.((-----------------((((..(((((..((.((...)).))..)))))..)))))).......(((((((((...((.(((...))).)).)))))..)))))))..). ( -36.40)
>DroYak_CAF1 8774 120 - 1
UUGGUCAUCAUCGGCCACCAGCCACCAGCCACCGGCCAUCGGGCAUUGGCCAUUGGCCAUCGGCUGAUAAAUGAGUCUGGGCCAGACAUUAUGCAAUAUUGGGGCCCUAAGGCGAUUGGG
(..(((.((((.(((.....)))..(((((...(((((...(((....)))..)))))...)))))....))))(((((((((...((.(((...))).)).)))))..)))))))..). ( -48.30)
>consensus
UUGGUCAUC_________________GGCCAUUGGCCAUUGGCCAUCGGACACCGGCCACCGGCUGAUAAAUGAGUCUGGGCCAGACAUUAUGCAAUAUUGGGGCCCUAAGGCGAUUGGG
(..(((....................((((..(((((..((.........))..)))))..)))).........(((((((((...((.(((...))).)).)))))..)))))))..). (-30.87 = -31.10 +   0.23)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,288,365 – 17,288,461
Length 96
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.38
Mean single sequence MFE -41.40
Consensus MFE -26.92
Energy contribution -25.59
Covariance contribution -1.32
Combinations/Pair 1.24
Mean z-score -1.84
Structure conservation index 0.65
SVM decision value 0.87
SVM RNA-class probability 0.871943
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17288365 96 + 22224390
CCAGACUCAUUUAUCAGCCGGUGGCCGGUGUCCGAUGGCCAAUGGCCAAUGGCC-----------------GAUGACCAAAGGCCAGCGGA-------GGAGAGUCAGCCGAACUGCAAU
...(((((.....((..(((.(((((..((..((.((((((........)))))-----------------).))..))..))))).))).-------.))))))).((......))... ( -39.30)
>DroSim_CAF1 7237 96 + 1
CCAGACUCAUUUGUCAGCCGGUGGCCGGUGUCCGAUGGCCAAUGGCCAAUGGCC-----------------GAUGACCAAAGGCCAGCGGA-------GGAGAGCCAGCCGAACUGCAAU
...(((......))).(((((((((...(.((((.(((((...((((...))))-----------------(.....)...))))).))))-------.)...)))).)))....))... ( -36.80)
>DroYak_CAF1 8814 120 + 1
CCAGACUCAUUUAUCAGCCGAUGGCCAAUGGCCAAUGCCCGAUGGCCGGUGGCUGGUGGCUGGUGGCCGAUGAUGACCAAAGGCCAGCGGAGAGGAGAGAAGAGCCAGUCGAACUGCAAU
.....(((..((((((((((.((((((..(((....)))...)))))).))))))))))(((.(((((..((.....))..))))).))).))).........((.((.....))))... ( -48.10)
>consensus
CCAGACUCAUUUAUCAGCCGGUGGCCGGUGUCCGAUGGCCAAUGGCCAAUGGCC_________________GAUGACCAAAGGCCAGCGGA_______GGAGAGCCAGCCGAACUGCAAU
.(((............((((.((((((..(((....)))...)))))).))))............................(((..((...............))..)))...))).... (-26.92 = -25.59 +  -1.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,288,365 – 17,288,461
Length 96
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 77.38
Mean single sequence MFE -42.67
Consensus MFE -31.65
Energy contribution -31.43
Covariance contribution -0.22
Combinations/Pair 1.11
Mean z-score -2.61
Structure conservation index 0.74
SVM decision value 3.16
SVM RNA-class probability 0.998617
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17288365 96 - 22224390
AUUGCAGUUCGGCUGACUCUCC-------UCCGCUGGCCUUUGGUCAUC-----------------GGCCAUUGGCCAUUGGCCAUCGGACACCGGCCACCGGCUGAUAAAUGAGUCUGG
...((......)).(((((...-------((((.(((((..((((((..-----------------......))))))..))))).))))...(((((...)))))......)))))... ( -39.50)
>DroSim_CAF1 7237 96 - 1
AUUGCAGUUCGGCUGGCUCUCC-------UCCGCUGGCCUUUGGUCAUC-----------------GGCCAUUGGCCAUUGGCCAUCGGACACCGGCCACCGGCUGACAAAUGAGUCUGG
.(((((((.(((.(((((....-------((((.(((((..((((((..-----------------......))))))..))))).))))....)))))))))))).))).......... ( -44.90)
>DroYak_CAF1 8814 120 - 1
AUUGCAGUUCGACUGGCUCUUCUCUCCUCUCCGCUGGCCUUUGGUCAUCAUCGGCCACCAGCCACCAGCCACCGGCCAUCGGGCAUUGGCCAUUGGCCAUCGGCUGAUAAAUGAGUCUGG
............(.(((((.............(((((....(((((......))))))))))...(((((...(((((...(((....)))..)))))...)))))......))))).). ( -43.60)
>consensus
AUUGCAGUUCGGCUGGCUCUCC_______UCCGCUGGCCUUUGGUCAUC_________________GGCCAUUGGCCAUUGGCCAUCGGACACCGGCCACCGGCUGAUAAAUGAGUCUGG
.(((((((.(((.(((((............(((.(((((..(((((....................)))))..))))).)))............)))))))))))).))).......... (-31.65 = -31.43 +  -0.22)

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 12:25:41 2006