Locus 3134

Sequence ID	3L_DroMel_CAF1
Location	9,129,448 – 9,129,555
Length	107
Max. P	0.999729

overview

Window 1

Location	9,129,448 – 9,129,555
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.06
Mean single sequence MFE	-34.06
Consensus MFE	-24.94
Energy contribution	-24.38
Covariance contribution	-0.56
Combinations/Pair	1.16
Mean z-score	-4.21
Structure conservation index	0.73
SVM decision value	3.96
SVM RNA-class probability	0.999729
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9129448 107 + 23771897
AUAUUGGCACUAGAGCUGGCAAGUAAUCAAUGGCAUUAUAAGUUAUAAUAU---UCUGAAAUUUGUUGAAAUUUUACUUUAAG----------UAGAUGCCUGUGAUUCCUUGUCAGCUC
............(((((((((((.(((((..((((((..(((((.(((((.---.........))))).)))))(((.....)----------))))))))..))))).))))))))))) ( -33.00)
>DroSec_CAF1 4486 107 + 1
AUUUUGGCACUAGAGCUGGCAAGUAGUCAAUGGCAUUGUAUGUUCUAAUAU---UCUGAUUUUUGUAGAUAUUUUACUUUAAG----------UAGAAGCCUCUGAUUGCUUGUCAGCUC
............(((((((((((((((((..(((....(((......)))(---((((......(((((...)))))......----------))))))))..))))))))))))))))) ( -37.70)
>DroSim_CAF1 4486 107 + 1
AUAUUGGCACUAGAGCUGGCAAGUAAUCAAUGGCAUUGUAAGUUCUAAUAU---UCAGAUUAUUGUAGAUAUUUAACUUUAAG----------UGGAAGCCUCUGAUUUCUUGUCAGCUC
............(((((((((((.(((((..((((((..(((((..(((((---..(.(....).)..))))).)))))..))----------)....)))..))))).))))))))))) ( -31.30)
>DroEre_CAF1 4565 117 + 1
AUAUUGGCAAUAGAGCUGGCAAGUAAUCAAAGGCAUUCUAAGUUCGGAUAUAGUUUUUACAUUUUUGA--UUUUAAGU-UAAGUUUGAUUUGAUUUAAGCCCCUGAUUGCUUGUCGGCUC
............(((((((((((((((((..(((.........(((((.((.((....)))).)))))--..((((((-(((((...))))))))))))))..))))))))))))))))) ( -38.70)
>DroYak_CAF1 4631 108 + 1
AUAUUGGCAAUAGAGCUGGCAAGUAAUCAAAGGUAUUCGAGGUUGUUAUAUAUAUUUAAGAUUUCUAG--GUUGCAGUUUAAG----------UUAAAGCCUCUGAUUUCUUGUCGGCUC
............(((((((((((.(((((.((((....((((((.(((........)))))))))(((--.(((.....))).----------)))..)))).))))).))))))))))) ( -29.60)
>consensus
AUAUUGGCACUAGAGCUGGCAAGUAAUCAAUGGCAUUCUAAGUUCUAAUAU___UCUGAUAUUUGUAGA_AUUUAACUUUAAG__________UAGAAGCCUCUGAUUGCUUGUCAGCUC
............(((((((((((.(((((..(((................................................................)))..))))).))))))))))) (-24.94 = -24.38 +  -0.56)

alignment

secondary structure

dotplot

Window 2

Location	9,129,448 – 9,129,555
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	77.06
Mean single sequence MFE	-23.19
Consensus MFE	-18.78
Energy contribution	-19.78
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.97
Structure conservation index	0.81
SVM decision value	3.21
SVM RNA-class probability	0.998745
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9129448 107 - 23771897
GAGCUGACAAGGAAUCACAGGCAUCUA----------CUUAAAGUAAAAUUUCAACAAAUUUCAGA---AUAUUAUAACUUAUAAUGCCAUUGAUUACUUGCCAGCUCUAGUGCCAAUAU
((((((.((((.(((((..(((((.((----------(.....)))((((((....))))))....---...............)))))..))))).)))).))))))............ ( -25.40)
>DroSec_CAF1 4486 107 - 1
GAGCUGACAAGCAAUCAGAGGCUUCUA----------CUUAAAGUAAAAUAUCUACAAAAAUCAGA---AUAUUAGAACAUACAAUGCCAUUGACUACUUGCCAGCUCUAGUGCCAAAAU
((((((.((((...((((.(((...((----------(.....))).....((((...........---....)))).........))).))))...)))).))))))............ ( -22.26)
>DroSim_CAF1 4486 107 - 1
GAGCUGACAAGAAAUCAGAGGCUUCCA----------CUUAAAGUUAAAUAUCUACAAUAAUCUGA---AUAUUAGAACUUACAAUGCCAUUGAUUACUUGCCAGCUCUAGUGCCAAUAU
((((((.((((.((((((.(((.....----------....(((((.((((((...........).---)))))..))))).....))).)))))).)))).))))))............ ( -26.14)
>DroEre_CAF1 4565 117 - 1
GAGCCGACAAGCAAUCAGGGGCUUAAAUCAAAUCAAACUUA-ACUUAAAA--UCAAAAAUGUAAAAACUAUAUCCGAACUUAGAAUGCCUUUGAUUACUUGCCAGCUCUAUUGCCAAUAU
((((.(.((((.((((((((((...................-((......--........)).....(((..........)))...)))))))))).)))).).))))............ ( -22.74)
>DroYak_CAF1 4631 108 - 1
GAGCCGACAAGAAAUCAGAGGCUUUAA----------CUUAAACUGCAAC--CUAGAAAUCUUAAAUAUAUAUAACAACCUCGAAUACCUUUGAUUACUUGCCAGCUCUAUUGCCAAUAU
((((.(.((((.(((((((((......----------......(((....--.)))...................(......)....))))))))).)))).).))))............ ( -19.40)
>consensus
GAGCUGACAAGAAAUCAGAGGCUUCAA__________CUUAAAGUAAAAU_UCUACAAAUAUCAGA___AUAUUAGAACUUACAAUGCCAUUGAUUACUUGCCAGCUCUAGUGCCAAUAU
((((((.((((.((((((.(((................................................................))).)))))).)))).))))))............ (-18.78 = -19.78 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:27 2006