Locus 1850

Sequence ID X_DroMel_CAF1
Location 5,103,653 – 5,103,749
Length 96
Max. P 0.574827
window3006 window3007

overview

Window 6

Location 5,103,653 – 5,103,749
Length 96
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 88.92
Mean single sequence MFE -23.83
Consensus MFE -17.24
Energy contribution -17.64
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.68
Structure conservation index 0.72
SVM decision value 0.02
SVM RNA-class probability 0.542766
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5103653 96 + 22224390
GAAACACUAUUUCUGU--------UUUUUUAUGCUUUUUGGGCAACUGUCAACGCCCGCAAAUUGUCAUUGUCCUGCGG-GACUUUGGCUCAGUUCCCAUUGUUC
((((((.......)))--------)))...........((((.(((((((((.(((((((..............)))))-).).)))))..))))))))...... ( -24.44)
>DroSec_CAF1 14894 96 + 1
GAAACACUACUUCUUU--------CUUUUUAUGCUUUUUGGGCAACUGUCAACGCCCGCAAAUUGUCAUUGUCCUGCGG-GACUUUGGCUCAGUUCCCAUUGUUC
................--------..............((((.(((((((((.(((((((..............)))))-).).)))))..))))))))...... ( -23.14)
>DroEre_CAF1 14867 93 + 1
GAAACACUAUUUCU-----------UUUUUAUGCUUUUUGGGCAACUGUCAACGCCCGCAAAUUGUCAUUGUCCUGCGG-GACUUUGGCUGAGUUCCCAUUGUUC
..............-----------.............((((.(((((((((.(((((((..............)))))-).).)))))..))))))))...... ( -23.14)
>DroYak_CAF1 14879 93 + 1
GAAACACUAUUUCU-----------UUUUUAUGCUUUUUGGGGAACUGUCAACGCCCGCAAAUUGUCAUUGUCCUGCGG-GAGUUUGGCUCAGUUCCCAUUGUUC
..............-----------...............(((((((((((((.((((((..............)))))-).).)))))..)))))))....... ( -26.24)
>DroAna_CAF1 23967 105 + 1
GGGACACUAUUUCUUUUCUCGUUUUUUUUUUUUGUAUUUCGGCAACUGUCAACGCCCGCAAAUUGUCAUUGUCCUGCGGGGACUCUGGCUCAGUUCCCAUUGUGC
((((.(((......................(((((.....(((..........))).)))))..((((..((((.....))))..))))..)))))))....... ( -22.20)
>consensus
GAAACACUAUUUCU_U_________UUUUUAUGCUUUUUGGGCAACUGUCAACGCCCGCAAAUUGUCAUUGUCCUGCGG_GACUUUGGCUCAGUUCCCAUUGUUC
......................................((((.(((((((((..((((((..............))))).)...)))))..))))))))...... (-17.24 = -17.64 +   0.40)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 7

Location 5,103,653 – 5,103,749
Length 96
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 88.92
Mean single sequence MFE -23.54
Consensus MFE -16.72
Energy contribution -16.96
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -1.82
Structure conservation index 0.71
SVM decision value 0.08
SVM RNA-class probability 0.574827
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5103653 96 - 22224390
GAACAAUGGGAACUGAGCCAAAGUC-CCGCAGGACAAUGACAAUUUGCGGGCGUUGACAGUUGCCCAAAAAGCAUAAAAAA--------ACAGAAAUAGUGUUUC
......(((((((((...(((.(.(-(((((((..........))))))))).))).))))).))))..((((((......--------.........)))))). ( -23.86)
>DroSec_CAF1 14894 96 - 1
GAACAAUGGGAACUGAGCCAAAGUC-CCGCAGGACAAUGACAAUUUGCGGGCGUUGACAGUUGCCCAAAAAGCAUAAAAAG--------AAAGAAGUAGUGUUUC
......(((((((((...(((.(.(-(((((((..........))))))))).))).))))).))))..((((((......--------.........)))))). ( -23.86)
>DroEre_CAF1 14867 93 - 1
GAACAAUGGGAACUCAGCCAAAGUC-CCGCAGGACAAUGACAAUUUGCGGGCGUUGACAGUUGCCCAAAAAGCAUAAAAA-----------AGAAAUAGUGUUUC
......((((((((((((....(.(-(((((((..........))))))))))))))..))).))))..((((((.....-----------.......)))))). ( -21.40)
>DroYak_CAF1 14879 93 - 1
GAACAAUGGGAACUGAGCCAAACUC-CCGCAGGACAAUGACAAUUUGCGGGCGUUGACAGUUCCCCAAAAAGCAUAAAAA-----------AGAAAUAGUGUUUC
.......((((((((.....(((.(-(((((((..........)))))))).)))..))))))))....((((((.....-----------.......)))))). ( -27.00)
>DroAna_CAF1 23967 105 - 1
GCACAAUGGGAACUGAGCCAGAGUCCCCGCAGGACAAUGACAAUUUGCGGGCGUUGACAGUUGCCGAAAUACAAAAAAAAAAAACGAGAAAAGAAAUAGUGUCCC
((((..(((.(((((...(((....((((((((..........))))))))..))).))))).))).........................(....).))))... ( -21.60)
>consensus
GAACAAUGGGAACUGAGCCAAAGUC_CCGCAGGACAAUGACAAUUUGCGGGCGUUGACAGUUGCCCAAAAAGCAUAAAAA_________A_AGAAAUAGUGUUUC
......(((((((((...(((...(.(((((((..........))))))))..))).))))).))))...................................... (-16.72 = -16.96 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:11 2006