Locus 1826

Sequence ID 3L_DroMel_CAF1
Location 5,118,380 – 5,118,483
Length 103
Max. P 0.863760
window2852 window2853

overview

Window 2

Location 5,118,380 – 5,118,483
Length 103
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 78.81
Mean single sequence MFE -41.17
Consensus MFE -24.10
Energy contribution -24.68
Covariance contribution 0.59
Combinations/Pair 1.27
Mean z-score -1.74
Structure conservation index 0.59
SVM decision value 0.33
SVM RNA-class probability 0.690542
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5118380 103 + 23771897
GUUUCUGCUGAUCGGACAUCAGCAAAUUGGCGGCUGCACUGGCCGCCUUGGGGCUGGUGAACAGCGGCAUUCCCAUAAACGUGGGUAUCUGCUGAUCCC-----------UUGG
((..((((((((.....)))))))....(((((((.....)))))))..)..)).((.((.((((((.((.(((((....))))).)))))))).))))-----------.... ( -45.90)
>DroVir_CAF1 4764 114 + 1
GCUUCUGCUGCUCCGCCUGCAGCAGGCUGGCCGCCGCACUCGCUGCCUUCACGUUGGUAAACAAGGGCAUGCCCAUGAAAGUAGGUAUUUGCUGCUGCGCCGACGACGACUGAC
((..(((((((.......))))))))).(((.((.......)).)))....(((((((...((.(((....))).))..(((((.......)))))..)))))))......... ( -39.30)
>DroSec_CAF1 4637 103 + 1
GUUUCUGCUGCUCGGUCAUCAGCAAAUUGGCCGCUGCACUGGCCGCCUUGGGGCUGGUGAACAGCGGCAUUCCCAUAAACGUGGGCAUCUGCUGAUCCC-----------UCGG
............(((..(((((((...((((((((((((..(((.(....))))..)))..)))))))...(((((....)))))))..)))))))..)-----------.)). ( -44.50)
>DroSim_CAF1 4627 103 + 1
GUUUCUGCUGCUCGGUCAUCAGCAAAUUGGCCGCUGCACUGGCCGCCUUGGGGCUGGUGAACAGCGGCAUUCCCAUAAACGUGGGCAUCUGCUGAUCCC-----------UCGG
............(((..(((((((...((((((((((((..(((.(....))))..)))..)))))))...(((((....)))))))..)))))))..)-----------.)). ( -44.50)
>DroEre_CAF1 4620 103 + 1
GUUUCUGCUGCUCGGAGAUCAGCAAACUGGCGGCCGCACUGGCCGCCUUUGGACUGGUGAACAGCGGCAUUCCCAUGAACGUAGGCAUCUGCUGAUCCC-----------UCGG
.....(((((((.(...((((((.....(((((((.....)))))))....).)))))...))))))))..........((.(((.(((....))).))-----------))). ( -38.60)
>DroAna_CAF1 5402 97 + 1
UUUUCUGUUGCUC------UAGCAGAUUGGCGGCCGCACUGGCAACCUUUGCACUGGUGAACAAUGGCAUUCCCAUAAAGGUGGGAAUCUGCUGAUCUC-----------UAGG
............(------(((.((((..(((((((((((.(((.....)))...)))).....))))((((((((....)))))))).)))..)))))-----------))). ( -34.20)
>consensus
GUUUCUGCUGCUCGGACAUCAGCAAAUUGGCCGCCGCACUGGCCGCCUUGGGGCUGGUGAACAGCGGCAUUCCCAUAAACGUGGGCAUCUGCUGAUCCC___________UCGG
..................((((((........(((((..((..((((........))))..)))))))...(((((....)))))....))))))................... (-24.10 = -24.68 +   0.59)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 5,118,380 – 5,118,483
Length 103
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 78.81
Mean single sequence MFE -39.58
Consensus MFE -25.41
Energy contribution -24.80
Covariance contribution -0.61
Combinations/Pair 1.42
Mean z-score -1.85
Structure conservation index 0.64
SVM decision value 0.84
SVM RNA-class probability 0.863760
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5118380 103 - 23771897
CCAA-----------GGGAUCAGCAGAUACCCACGUUUAUGGGAAUGCCGCUGUUCACCAGCCCCAAGGCGGCCAGUGCAGCCGCCAAUUUGCUGAUGUCCGAUCAGCAGAAAC
....-----------(((....(((....((((......))))..))).((((.....)))))))..((((((.......))))))..(((((((((.....)))))))))... ( -40.30)
>DroVir_CAF1 4764 114 - 1
GUCAGUCGUCGUCGGCGCAGCAGCAAAUACCUACUUUCAUGGGCAUGCCCUUGUUUACCAACGUGAAGGCAGCGAGUGCGGCGGCCAGCCUGCUGCAGGCGGAGCAGCAGAAGC
((..((((((((...(((.((................((.(((....))).))(((((....))))).)).)))...))))))))..))(((((((.......))))))).... ( -39.20)
>DroSec_CAF1 4637 103 - 1
CCGA-----------GGGAUCAGCAGAUGCCCACGUUUAUGGGAAUGCCGCUGUUCACCAGCCCCAAGGCGGCCAGUGCAGCGGCCAAUUUGCUGAUGACCGAGCAGCAGAAAC
.((.-----------(..((((((((((.((((......))))...(((((((..(((..((((....).)))..))))))))))..))))))))))..)))............ ( -42.00)
>DroSim_CAF1 4627 103 - 1
CCGA-----------GGGAUCAGCAGAUGCCCACGUUUAUGGGAAUGCCGCUGUUCACCAGCCCCAAGGCGGCCAGUGCAGCGGCCAAUUUGCUGAUGACCGAGCAGCAGAAAC
.((.-----------(..((((((((((.((((......))))...(((((((..(((..((((....).)))..))))))))))..))))))))))..)))............ ( -42.00)
>DroEre_CAF1 4620 103 - 1
CCGA-----------GGGAUCAGCAGAUGCCUACGUUCAUGGGAAUGCCGCUGUUCACCAGUCCAAAGGCGGCCAGUGCGGCCGCCAGUUUGCUGAUCUCCGAGCAGCAGAAAC
.((.-----------(((((((((((((......(..(.(((((((......)))).))))..)...(((((((.....))))))).)))))))))))))))............ ( -44.50)
>DroAna_CAF1 5402 97 - 1
CCUA-----------GAGAUCAGCAGAUUCCCACCUUUAUGGGAAUGCCAUUGUUCACCAGUGCAAAGGUUGCCAGUGCGGCCGCCAAUCUGCUA------GAGCAACAGAAAA
.(((-----------(((((..((..(((((((......)))))))((.((((.....))))))...((((((....))))))))..)))).)))------)............ ( -29.50)
>consensus
CCGA___________GGGAUCAGCAGAUGCCCACGUUUAUGGGAAUGCCGCUGUUCACCAGCCCCAAGGCGGCCAGUGCAGCCGCCAAUUUGCUGAUGACCGAGCAGCAGAAAC
...............((..(((((((((.((((......))))......((((.....)))).....(((.((.......)).))).)))))))))...))............. (-25.41 = -24.80 +  -0.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:45 2006