Locus 7412

Sequence ID 3L_DroMel_CAF1
Location 19,944,471 – 19,944,631
Length 160
Max. P 0.775362
window12041 window12042

overview

Window 1

Location 19,944,471 – 19,944,591
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -39.05
Consensus MFE -36.04
Energy contribution -36.48
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -1.66
Structure conservation index 0.92
SVM decision value 0.54
SVM RNA-class probability 0.775362
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19944471 120 + 23771897
CGUCAAGGAUAUCAACGAUAAUCGGCCGCAGUUUGAACGUGUGAACUGCUAUGGCAAAGUGACCAAAUCGGCGCCGAUGGGCACCGAGGUAUUCGUUACCUCAGCCAUUGACUUUGAUGC
((((((((.......((.....))...(((((((........))))))).(((((...(((.((..((((....)))).))))).((((((.....)))))).)))))...)))))))). ( -41.90)
>DroSec_CAF1 9878 120 + 1
CGUCAAGGAUAUCAACGAUAAUCGGCCACAGUUUGAACGUGUGAACUGCUAUGGCAAAGUGACCAAAUCGGCGCCGAUGGGCACCGAGGUAUUCGUUACCUCAGCCAUUGACUUUGAUGC
((((((((...(((.((.....))((((((((((........))))))...))))....))).......((((((....)))...((((((.....)))))).))).....)))))))). ( -39.70)
>DroSim_CAF1 9424 120 + 1
CGUCAAGGAUAUCAACGAUUAUCGGCCGCAGUUUGAACGUGUGAACUGCUAUGGCAAAGUGACCAAAUCGGCGCCGAUGGGCACCGAGGUAUUCGUUACCUCAGCCAUUGACUUUGAUGC
((((((((...((((....(((((((((((((((........)))))))..((((.....).))).....).)))))))(((...((((((.....)))))).))).)))))))))))). ( -42.30)
>DroYak_CAF1 10008 120 + 1
CGUCAAGGAUAUUAACGAUAAUCGACCGCAGUUUGAACGAGUGAACUGCUAUGGAAAAGUGACCAAAUCGGCCCCGAUGGGUACCGAAGUUUUCGUUACCUCAGCUAUUGACUUUGACGC
((((((((....((((((.(((.....(((((((........)))))))..(((........)))..((((..((....))..)))).))).))))))..((((...)))))))))))). ( -32.30)
>consensus
CGUCAAGGAUAUCAACGAUAAUCGGCCGCAGUUUGAACGUGUGAACUGCUAUGGCAAAGUGACCAAAUCGGCGCCGAUGGGCACCGAGGUAUUCGUUACCUCAGCCAUUGACUUUGAUGC
((((((((.......((.....))...(((((((........))))))).(((((...(((.((..((((....)))).))))).((((((.....)))))).)))))...)))))))). (-36.04 = -36.48 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 19,944,511 – 19,944,631
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.42
Mean single sequence MFE -33.35
Consensus MFE -26.66
Energy contribution -26.98
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -1.59
Structure conservation index 0.80
SVM decision value 0.35
SVM RNA-class probability 0.698240
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19944511 120 - 23771897
CUCGUUGCCGUCGCUCAACCUAUAGGAUAUUAUAUCGCCUGCAUCAAAGUCAAUGGCUGAGGUAACGAAUACCUCGGUGCCCAUCGGCGCCGAUUUGGUCACUUUGCCAUAGCAGUUCAC
.((((((((.((......((....))..........(((.((......))....))).))))))))))..(((((((((((....))))))))...)))....((((....))))..... ( -34.80)
>DroSec_CAF1 9918 120 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCUGCAUCAAAGUCAAUGGCUGAGGUAACGAAUACCUCGGUGCCCAUCGGCGCCGAUUUGGUCACUUUGCCAUAGCAGUUCAC
......................................((((....(((((.......((((((.....))))))((((((....)))))))))))(((......)))...))))..... ( -29.70)
>DroSim_CAF1 9464 120 - 1
CUCGUUGCCAUCGCUCAACCUAUAGGAUAUUAUAUCGCCUGCAUCAAAGUCAAUGGCUGAGGUAACGAAUACCUCGGUGCCCAUCGGCGCCGAUUUGGUCACUUUGCCAUAGCAGUUCAC
.((((((((.((......((....))..........(((.((......))....))).))))))))))..(((((((((((....))))))))...)))....((((....))))..... ( -34.80)
>DroYak_CAF1 10048 120 - 1
CUCGUUGCCAUCGCUCAAGCGAUAGGAUAUUAUAUCGCCUGCGUCAAAGUCAAUAGCUGAGGUAACGAAAACUUCGGUACCCAUCGGGGCCGAUUUGGUCACUUUUCCAUAGCAGUUCAC
.((((((((..(((....((((((........))))))..)))......(((.....))))))))))).(((((((((.(((...))))))))..(((........)))....))))... ( -34.10)
>consensus
CUCGUUGCCAUCGCUCAACCUAUAGGAUAUUAUAUCGCCUGCAUCAAAGUCAAUGGCUGAGGUAACGAAUACCUCGGUGCCCAUCGGCGCCGAUUUGGUCACUUUGCCAUAGCAGUUCAC
......................................((((....(((((.......((((((.....))))))((((((....)))))))))))((........))...))))..... (-26.66 = -26.98 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:22 2006