Locus 5505

Sequence ID 2R_DroMel_CAF1
Location 17,655,548 – 17,655,708
Length 160
Max. P 0.999841
window8807 window8808 window8809

overview

Window 7

Location 17,655,548 – 17,655,668
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.17
Mean single sequence MFE -44.81
Consensus MFE -39.88
Energy contribution -39.60
Covariance contribution -0.28
Combinations/Pair 1.11
Mean z-score -2.53
Structure conservation index 0.89
SVM decision value 3.75
SVM RNA-class probability 0.999586
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17655548 120 - 20766785
AACAAUUUCCACGUCAGGGAAGCGUAGGCAGAGUUCGACUAUAUCGCAGGUCUAUUGACGUUUGUCUGAGCUCUGUCUACGCAGCUGGAUGUCUGUUAACCCCUCCGAGGCCCCACGAAU
...........(((..(((..(((((((((((((((((((........))))....(((....))).))))))))))))))).((((((.(..(....)..).)))..)))))))))... ( -42.30)
>DroSec_CAF1 9112 120 - 1
GACAAUUUCCACGUCAGGGUAGCGUAGGCAGAGUUCGACUAUAUCGCAGCUCUAUUGACGUUUGUCUGAGCUCUGUCUACGCAGCUGGAUGCCUGUUAACCCCUCCGAGGCCCCACAAAU
(((.........))).(((..((((((((((((((((((.....(((((.....))).))...))).)))))))))))))))........((((.............)))))))...... ( -41.72)
>DroSim_CAF1 15048 120 - 1
GACAAUUUCCACGUCAGGGUAGCGUAGGCAGAGUUCGACUAUAUCGCAGCUCUAUUGACGUUUGUCUGAGCUCUGUCUACGCAGCUGGAUGCCUGUUAACCCCUCCGAGGCCCCACGAAU
(((.........))).(((..((((((((((((((((((.....(((((.....))).))...))).)))))))))))))))........((((.............)))))))...... ( -41.72)
>DroEre_CAF1 9330 120 - 1
GGCCAUUUUCUGGCCAGGGAAGCGUAGGCAGAGUUCGACUAUAUCGCAGGUCUAUUGACGUUUGUCUGAGCUCUGUCUACGCAGCUGGAUGUCUGGUAACCCCUCCGAAGCCCCACGGAU
(((((.....))))).(((..(((((((((((((((((((........))))....(((....))).))))))))))))))).((..(....)..))...)))((((........)))). ( -53.80)
>DroYak_CAF1 20777 120 - 1
GAUAAUUUCCACGUCAGGGAAGCGUAGGCAGAGUUCGACUAUAUUGCUGGUCUAUUGACGUUUGUCUGAGCUCUGUCUACGCAGCUGGAUGUCUGGUAACCCCGCCGAAGCCCCACGAAU
...........((.(.(((..((((((((((((((((((((......)))))....(((....))).))))))))))))))).((..(....)..))..))).).))............. ( -44.50)
>consensus
GACAAUUUCCACGUCAGGGAAGCGUAGGCAGAGUUCGACUAUAUCGCAGGUCUAUUGACGUUUGUCUGAGCUCUGUCUACGCAGCUGGAUGUCUGUUAACCCCUCCGAGGCCCCACGAAU
(((.........))).(((..((((((((((((((((((.....(((((.....))).))...))).))))))))))))))).((((((.(..(....)..).)))..))))))...... (-39.88 = -39.60 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,655,588 – 17,655,708
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.17
Mean single sequence MFE -35.26
Consensus MFE -33.50
Energy contribution -33.38
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -1.79
Structure conservation index 0.95
SVM decision value 2.74
SVM RNA-class probability 0.996745
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17655588 120 + 20766785
GUAGACAGAGCUCAGACAAACGUCAAUAGACCUGCGAUAUAGUCGAACUCUGCCUACGCUUCCCUGACGUGGAAAUUGUUGGGAAAUUACCGGGAAGUGGCAAACGAAAGCAGUUUGAAC
((((.(((((.((.(((....)))....(((..........))))).))))).))))(((((((.((((.......))))((.......)))))))))..(((((.......)))))... ( -35.30)
>DroSec_CAF1 9152 120 + 1
GUAGACAGAGCUCAGACAAACGUCAAUAGAGCUGCGAUAUAGUCGAACUCUGCCUACGCUACCCUGACGUGGAAAUUGUCGGGAAAUUACCGGGAAGUGGCAAACGAAAGCAGUUUGAAC
((((.((((((((.(((....)))....))))..((((...))))...)))).))))(((.(((.((((.......))))((.......))))).)))..(((((.......)))))... ( -33.00)
>DroSim_CAF1 15088 120 + 1
GUAGACAGAGCUCAGACAAACGUCAAUAGAGCUGCGAUAUAGUCGAACUCUGCCUACGCUACCCUGACGUGGAAAUUGUCGGGAAAUUACCGGGAAGUGGCAAACGAAAGCAGUUUGAAC
((((.((((((((.(((....)))....))))..((((...))))...)))).))))(((.(((.((((.......))))((.......))))).)))..(((((.......)))))... ( -33.00)
>DroEre_CAF1 9370 120 + 1
GUAGACAGAGCUCAGACAAACGUCAAUAGACCUGCGAUAUAGUCGAACUCUGCCUACGCUUCCCUGGCCAGAAAAUGGCCGGGAAAUUACCGGGAAGUGGCAAGCGAAAGCAGUUUGAAU
((((.(((((.((.(((....)))....(((..........))))).))))).))))(((((((.(((((.....)))))((.......))))))))).....((....))......... ( -45.60)
>DroYak_CAF1 20817 119 + 1
GUAGACAGAGCUCAGACAAACGUCAAUAGACCAGCAAUAUAGUCGAACUCUGCCUACGCUUCCCUGACGUGGAAAUUAUCGAGAAAUUACCGGGAAGUG-CAAAUAAAAGCGGUUUGAAU
((((.(((((.((.(((....)))....(((.(......).))))).))))).))))(((((((......((.((((.......)))).))))))))).-(((((.......)))))... ( -29.40)
>consensus
GUAGACAGAGCUCAGACAAACGUCAAUAGACCUGCGAUAUAGUCGAACUCUGCCUACGCUUCCCUGACGUGGAAAUUGUCGGGAAAUUACCGGGAAGUGGCAAACGAAAGCAGUUUGAAC
((((.(((((.((.(((....)))....((.(((.....))))))).))))).))))(((((((.((((.......))))((.......)))))))))..(((((.......)))))... (-33.50 = -33.38 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,655,588 – 17,655,708
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.17
Mean single sequence MFE -38.48
Consensus MFE -34.50
Energy contribution -34.70
Covariance contribution 0.20
Combinations/Pair 1.11
Mean z-score -2.76
Structure conservation index 0.90
SVM decision value 4.22
SVM RNA-class probability 0.999841
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17655588 120 - 20766785
GUUCAAACUGCUUUCGUUUGCCACUUCCCGGUAAUUUCCCAACAAUUUCCACGUCAGGGAAGCGUAGGCAGAGUUCGACUAUAUCGCAGGUCUAUUGACGUUUGUCUGAGCUCUGUCUAC
.........((......(((((.......))))).(((((................)))))))(((((((((((((((((........))))....(((....))).))))))))))))) ( -35.99)
>DroSec_CAF1 9152 120 - 1
GUUCAAACUGCUUUCGUUUGCCACUUCCCGGUAAUUUCCCGACAAUUUCCACGUCAGGGUAGCGUAGGCAGAGUUCGACUAUAUCGCAGCUCUAUUGACGUUUGUCUGAGCUCUGUCUAC
.........(((.....(((((.......)))))...((((((.........))).))).)))((((((((((((((((.....(((((.....))).))...))).))))))))))))) ( -36.20)
>DroSim_CAF1 15088 120 - 1
GUUCAAACUGCUUUCGUUUGCCACUUCCCGGUAAUUUCCCGACAAUUUCCACGUCAGGGUAGCGUAGGCAGAGUUCGACUAUAUCGCAGCUCUAUUGACGUUUGUCUGAGCUCUGUCUAC
.........(((.....(((((.......)))))...((((((.........))).))).)))((((((((((((((((.....(((((.....))).))...))).))))))))))))) ( -36.20)
>DroEre_CAF1 9370 120 - 1
AUUCAAACUGCUUUCGCUUGCCACUUCCCGGUAAUUUCCCGGCCAUUUUCUGGCCAGGGAAGCGUAGGCAGAGUUCGACUAUAUCGCAGGUCUAUUGACGUUUGUCUGAGCUCUGUCUAC
...............(((((((.......))))).((((((((((.....))))).)))))))(((((((((((((((((........))))....(((....))).))))))))))))) ( -47.10)
>DroYak_CAF1 20817 119 - 1
AUUCAAACCGCUUUUAUUUG-CACUUCCCGGUAAUUUCUCGAUAAUUUCCACGUCAGGGAAGCGUAGGCAGAGUUCGACUAUAUUGCUGGUCUAUUGACGUUUGUCUGAGCUCUGUCUAC
.........((........)-).((((((((.((((.......)))).))......)))))).((((((((((((((((((......)))))....(((....))).))))))))))))) ( -36.90)
>consensus
GUUCAAACUGCUUUCGUUUGCCACUUCCCGGUAAUUUCCCGACAAUUUCCACGUCAGGGAAGCGUAGGCAGAGUUCGACUAUAUCGCAGGUCUAUUGACGUUUGUCUGAGCUCUGUCUAC
.........((......(((((.......))))).((((((((.........))).)))))))((((((((((((((((.....(((((.....))).))...))).))))))))))))) (-34.50 = -34.70 +   0.20)

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 11:46:59 2006