Locus 1093

Sequence ID	X_DroMel_CAF1
Location	3,217,766 – 3,217,875
Length	109
Max. P	0.903189

overview

Window 1

Location	3,217,766 – 3,217,875
Length	109
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	89.29
Mean single sequence MFE	-21.10
Consensus MFE	-15.02
Energy contribution	-15.52
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.90
Structure conservation index	0.71
SVM decision value	0.27
SVM RNA-class probability	0.663629
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3217766 109 + 22224390
GAAAAUUUUCCACAAACAUGGAAACAAGUUCCUCAGAUAUAUCUCUGAAUUAUGUAUAAGCAUAC--AUAUUAUA--UAUGCCAUGCCAUUUGCCUUU-UUUUUAUUGACUUGA
......((((((......))))))((((((..(((((......))))).....(((...((((.(--((((...)--))))..))))....)))....-........)))))). ( -19.30)
>DroSec_CAF1 26852 110 + 1
GAAAAUUUUCCACAAACUUGGAAACAAGUUCCCCAGAUAUAUCUCUGAAUUAUGUAUAAGCAUACACAUAUUAUA--UAUGCCAUGCCAUUUGCCUUU--UUUUAUUGACUUGA
......((((((......))))))((((((...((((......))))......(((...((((...(((((...)--))))..))))....)))....--.......)))))). ( -17.50)
>DroEre_CAF1 28630 108 + 1
GAAA--UGUCCACAAACGUGGAAACAAGUUCGCCAGAU--AUCUCUGAAUUAUGUAUAAGCAUACAUGUAUUAUA--UAUGCCAUGCCAUUUGCUUUUUUUUUUAUUGACUUGA
....--..(((((....)))))..((((((...((((.--...))))......(((...((((.((((((...))--))))..))))....))).............)))))). ( -21.30)
>DroYak_CAF1 32023 110 + 1
GAAAAUUUUCCACAAACUUGGAAACAAGUUCGCCAGAU--AUCUCUGAAUUAUGUAUAAGCAUACAUAUUAUAUAUGUAUGCCAUGGCAUUUGAUUUU--UUUUAUCGACUUGA
......((((((......))))))((((((.....(((--(.....(((((((((....((((((((((...))))))))))....))))..))))).--...)))))))))). ( -26.30)
>consensus
GAAAAUUUUCCACAAACUUGGAAACAAGUUCCCCAGAU__AUCUCUGAAUUAUGUAUAAGCAUACAUAUAUUAUA__UAUGCCAUGCCAUUUGCCUUU__UUUUAUUGACUUGA
......((((((......))))))((((((...((((......))))......((((..(((((.............))))).))))....................)))))). (-15.02 = -15.52 +   0.50)

alignment

secondary structure

dotplot

Window 2

Location	3,217,766 – 3,217,875
Length	109
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	89.29
Mean single sequence MFE	-25.62
Consensus MFE	-18.75
Energy contribution	-19.25
Covariance contribution	0.50
Combinations/Pair	1.07
Mean z-score	-2.71
Structure conservation index	0.73
SVM decision value	1.03
SVM RNA-class probability	0.903189
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3217766 109 - 22224390
UCAAGUCAAUAAAAA-AAAGGCAAAUGGCAUGGCAUA--UAUAAUAU--GUAUGCUUAUACAUAAUUCAGAGAUAUAUCUGAGGAACUUGUUUCCAUGUUUGUGGAAAAUUUUC
.((((((........-........(((....((((((--(((...))--)))))))....)))..((((((......))))))).)))))(((((((....)))))))...... ( -26.00)
>DroSec_CAF1 26852 110 - 1
UCAAGUCAAUAAAA--AAAGGCAAAUGGCAUGGCAUA--UAUAAUAUGUGUAUGCUUAUACAUAAUUCAGAGAUAUAUCUGGGGAACUUGUUUCCAAGUUUGUGGAAAAUUUUC
.((((((.......--........(((....((((((--(((.....)))))))))....)))..((((((......))))))).)))))((((((......))))))...... ( -24.80)
>DroEre_CAF1 28630 108 - 1
UCAAGUCAAUAAAAAAAAAAGCAAAUGGCAUGGCAUA--UAUAAUACAUGUAUGCUUAUACAUAAUUCAGAGAU--AUCUGGCGAACUUGUUUCCACGUUUGUGGACA--UUUC
.((((((.................(((....((((((--(((.....)))))))))....)))...(((((...--.))))).).)))))..(((((....)))))..--.... ( -24.20)
>DroYak_CAF1 32023 110 - 1
UCAAGUCGAUAAAA--AAAAUCAAAUGCCAUGGCAUACAUAUAUAAUAUGUAUGCUUAUACAUAAUUCAGAGAU--AUCUGGCGAACUUGUUUCCAAGUUUGUGGAAAAUUUUC
.(((((((......--........(((....(((((((((((...)))))))))))....)))...(((((...--.))))))).)))))((((((......))))))...... ( -27.50)
>consensus
UCAAGUCAAUAAAA__AAAAGCAAAUGGCAUGGCAUA__UAUAAUAUAUGUAUGCUUAUACAUAAUUCAGAGAU__AUCUGGCGAACUUGUUUCCAAGUUUGUGGAAAAUUUUC
.((((((.................(((....((((((.............))))))....)))...(((((......))))).).)))))(((((((....)))))))...... (-18.75 = -19.25 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:23 2006