Locus 5566

Sequence ID	3L_DroMel_CAF1
Location	15,254,266 – 15,254,400
Length	134
Max. P	0.814052

overview

Window 3

Location	15,254,266 – 15,254,362
Length	96
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	90.29
Mean single sequence MFE	-25.14
Consensus MFE	-20.18
Energy contribution	-20.62
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.68
Structure conservation index	0.80
SVM decision value	0.66
SVM RNA-class probability	0.814052
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15254266 96 - 23771897
CAGUAUUUGGAGGCGGAUAAGUACUCGAUACUUGUUCGGUUUUCAAGUGCUCGGAACAGGGAUAACCAAG--------GAAUUGAAAACUUCAACAAGUAUUCU---
.((((((((((((((((((((((.....))))))))).))))))))))))).......((((((......--------(((.(....).)))......))))))--- ( -26.50)
>DroSec_CAF1 143447 92 - 1
----AUUUGGAGGCGGAUAAGUACUCGAUACUUGUUCGGUUUUCAAGUGCUCGGAACAGGGAUAACCAAG--------GAAUUGAAAACUUCAACAAGUAUUCU---
----.....(((((......)).)))((((((((((.(((((((((.(.((.((...........)).))--------.).)))))))))..))))))))))..--- ( -24.30)
>DroSim_CAF1 151659 92 - 1
----AUUUGGAGGCGGAUAAGUACUCGAUACUUGUUCGGUUUUCAAGUGCUCGGAACAGGGAUAACCAAG--------GAAUUGAGAACUUCAACAAGUAUUCU---
----.....(((((......)).)))((((((((((.(((((((((.(.((.((...........)).))--------.).)))))))))..))))))))))..--- ( -24.40)
>DroEre_CAF1 143802 103 - 1
----AUUUGGAGGCGGAUAAGUACUCGAUACUUGUUGGGUUUUCAAGUGCUCGGAACAGGGAUAACCAAGGAACCAAGGAACUGAAAACUUCUACAAGUAUUCUUCU
----.....(((((......)).)))(((((((((.(((((((((..(.((.((..(..((....))..)...)).)).)..)))))))))..)))))))))..... ( -26.70)
>DroYak_CAF1 149855 95 - 1
----AUUUGGAGGCGGAUAAGUACUCGAUACUUGUUGGGUUUUCAAGUGCUCGGAACAAGGAUAACCAAA--------GAAUGGAAAACUUCAACAAGUAUUCUUCU
----.....(((((......)).)))((((((((((((((((((..((.......))..((....))...--------.....)))))).))))))))))))..... ( -23.80)
>consensus
____AUUUGGAGGCGGAUAAGUACUCGAUACUUGUUCGGUUUUCAAGUGCUCGGAACAGGGAUAACCAAG________GAAUUGAAAACUUCAACAAGUAUUCU___
.........(((((......)).)))(((((((((..(((((((((((.......)).((.....))..............)))))))))...)))))))))..... (-20.18 = -20.62 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	15,254,290 – 15,254,400
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.80
Mean single sequence MFE	-28.06
Consensus MFE	-19.85
Energy contribution	-20.25
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.71
Structure conservation index	0.71
SVM decision value	0.50
SVM RNA-class probability	0.761307
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15254290 110 - 23771897
GUAAUAAAGAA--UAACAAGGAUAAUCCAGUGAAAGUAUCCAGUAUUUGGAGGCGGAUAAGUACUCGAUACUUGUUCGGUUUUCAAGUGCUCGGAACAGGGAUAACCAAG--------GA
...........--............(((.......((.(((((((((((((((((((((((((.....))))))))).))))))))))))).))))).((.....))..)--------)) ( -31.80)
>DroSec_CAF1 143471 105 - 1
GUAAUAAAGAAUAUAACAAGGAUAAUCCGGUGAAAGU-------AUUUGGAGGCGGAUAAGUACUCGAUACUUGUUCGGUUUUCAAGUGCUCGGAACAGGGAUAACCAAG--------GA
...................((...((((.((...(((-------(((((((((((((((((((.....))))))))).)))))))))))))....))..))))..))...--------.. ( -29.20)
>DroSim_CAF1 151683 103 - 1
GUAAUAAAGAA--UAACAAGGAUAAUCCAGUGAAAGU-------AUUUGGAGGCGGAUAAGUACUCGAUACUUGUUCGGUUUUCAAGUGCUCGGAACAGGGAUAACCAAG--------GA
...........--......((.((.(((.((...(((-------(((((((((((((((((((.....))))))))).)))))))))))))....)).))).)).))...--------.. ( -28.40)
>DroEre_CAF1 143829 111 - 1
GUAAUAAAGAA--UAACAAGGAUAAUCCAGUGAAAGU-------AUUUGGAGGCGGAUAAGUACUCGAUACUUGUUGGGUUUUCAAGUGCUCGGAACAGGGAUAACCAAGGAACCAAGGA
...........--......((....(((.((...(((-------((((((((((.((((((((.....)))))))).).))))))))))))....)).((.....))..))).))..... ( -26.20)
>DroYak_CAF1 149882 103 - 1
GUAAUAAGGAA--UAACAAGGAUAAUCCAGUGAAAGU-------AUUUGGAGGCGGAUAAGUACUCGAUACUUGUUGGGUUUUCAAGUGCUCGGAACAAGGAUAACCAAA--------GA
...........--......((...((((.((...(((-------((((((((((.((((((((.....)))))))).).))))))))))))....))..))))..))...--------.. ( -24.70)
>consensus
GUAAUAAAGAA__UAACAAGGAUAAUCCAGUGAAAGU_______AUUUGGAGGCGGAUAAGUACUCGAUACUUGUUCGGUUUUCAAGUGCUCGGAACAGGGAUAACCAAG________GA
...................((...((((.((...(((.......(((((((((((((((((((.....))))))))).)))))))))))))....))..))))..))............. (-19.85 = -20.25 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:33 2006