Locus 4685

Sequence ID	2R_DroMel_CAF1
Location	15,328,780 – 15,328,908
Length	128
Max. P	0.936890

overview

Window 3

Location	15,328,780 – 15,328,873
Length	93
Sequences	6
Columns	93
Reading direction	reverse
Mean pairwise identity	90.61
Mean single sequence MFE	-27.20
Consensus MFE	-22.12
Energy contribution	-23.65
Covariance contribution	1.53
Combinations/Pair	1.08
Mean z-score	-2.29
Structure conservation index	0.81
SVM decision value	0.41
SVM RNA-class probability	0.726928
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15328780 93 - 20766785
GCCCGAACAGGGACACUUGCUCAGACACAAGGUGUGUCUCUGUGUUCUCUGAAUGAAUUGCUGAGUAACCAGUAAUGAAGUAAAACUGUUCAA
....((((((((((((......((((((.....))))))..)))))).........(((((((......))))))).........)))))).. ( -28.60)
>DroSec_CAF1 134772 93 - 1
GCCCGAGCAGGGACACUUGCUCAGACACAAGGUGUGUCUCUGUGUUCUCUGAAUGAAUUGCUGAGUAACCAGUAAUGAAGUAAAACUGUUCAA
....((((((((((((......((((((.....))))))..)))))).........(((((((......))))))).........)))))).. ( -28.60)
>DroSim_CAF1 112516 93 - 1
GCCCGAGCAGGGACACUUGCUCAGACACAAGGUGUGUCUCUGUGUUCUCUGAAUGAAUUGCUGAGUAACCAGUAAUGAAGUAAAACUGUUCAA
....((((((((((((......((((((.....))))))..)))))).........(((((((......))))))).........)))))).. ( -28.60)
>DroEre_CAF1 121368 93 - 1
GCCCGAGCAGGGACACUUGCUCAGACACAAGGUGUGUCUCUGUGUUCUCCGAAUGAAUUGCUGAGUAACCAGUAAUGAAGUAAAACUGUUCAA
....((((((((((((......((((((.....))))))..)))))).........(((((((......))))))).........)))))).. ( -28.60)
>DroYak_CAF1 125682 93 - 1
GCCCGAACAGGGACACUUGCUCAGACACAAGGUGUGUCUCUGUGUUCUCUGAAUGGAUUGCUGAGUAACCAGUAAUGAAGUAAAACUGUUCAA
....((((((((((((......((((((.....))))))..)))))).........(((((((......))))))).........)))))).. ( -28.70)
>DroAna_CAF1 108490 78 - 1
-------GAGGGACACAUCUACAGAUACAAGGUGUGUC--------CUCUGAAUGAAUUGCUGAGUAACCAAUAAUGAAGUAAAACUGUUCGA
-------.((((((((((((.........)))))))))--------).))(((((..(((((..((........))..)))))...))))).. ( -20.10)
>consensus
GCCCGAGCAGGGACACUUGCUCAGACACAAGGUGUGUCUCUGUGUUCUCUGAAUGAAUUGCUGAGUAACCAGUAAUGAAGUAAAACUGUUCAA
....((((((((((((......((((((.....))))))..)))))).........(((((((......))))))).........)))))).. (-22.12 = -23.65 +   1.53)

alignment

secondary structure

dotplot

Window 4

Location	15,328,818 – 15,328,908
Length	90
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	72.12
Mean single sequence MFE	-26.18
Consensus MFE	-8.53
Energy contribution	-8.67
Covariance contribution	0.14
Combinations/Pair	1.25
Mean z-score	-2.43
Structure conservation index	0.33
SVM decision value	1.26
SVM RNA-class probability	0.936890
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15328818 90 - 20766785
AAAGGACAUGGCCAUAAAAAGGGCAAUGCGAUGGCGCCCGAACA--GGGACACUUGCUCAGACACAAGGUGUGUCUCUGUGUUCUCU--GAAUG
..(((((((((.........((((((.((....))((((.....--))).)..))))))((((((.....)))))))))))))))..--..... ( -28.70)
>DroVir_CAF1 169040 76 - 1
AAAGGACAUGGCCAUAAAAAGGGCAAUGCGAGCGAGG-CAAGUGCUGGC---------CAACUACAAGGUGUGUC--------CUCUGUGAAUG
..((((((((((((........(((.(((.......)-))..)))))))---------).(((....))))))))--------))......... ( -21.10)
>DroGri_CAF1 141430 72 - 1
AAAGGACAUGGCCAUAAAAAGGGCAAUGCGAGAGCAG-CAGCAGC--AG---------CAACUAUAAGGUGUGUC--------CUGU--GAAUG
..((((((((.((.........((..(((....))))-).((...--.)---------)........))))))))--------))..--..... ( -20.10)
>DroEre_CAF1 121406 90 - 1
AAAGGACAUGGCCAUAAAAAGGGCAAUGCGAUGGCGCCCGAGCA--GGGACACUUGCUCAGACACAAGGUGUGUCUCUGUGUUCUCC--GAAUG
..(((((((((.........((((...((....))))))(((((--((....)))))))((((((.....)))))))))))))))..--..... ( -34.50)
>DroYak_CAF1 125720 90 - 1
AAAGGACAUGGCCAUAAAAAGGGCAAUGCGAUGGCGCCCGAACA--GGGACACUUGCUCAGACACAAGGUGUGUCUCUGUGUUCUCU--GAAUG
..(((((((((.........((((((.((....))((((.....--))).)..))))))((((((.....)))))))))))))))..--..... ( -28.70)
>DroAna_CAF1 108528 69 - 1
A-AGGACAUGGCCAUAAAAAGGGCAAUGUG------------GA--GGGACACAUCUACAGAUACAAGGUGUGUC--------CUCU--GAAUG
.-...((((.(((........))).))))(------------((--((.((((((((.........)))))))))--------))))--..... ( -24.00)
>consensus
AAAGGACAUGGCCAUAAAAAGGGCAAUGCGAUGGCGC_CGAACA__GGGACACUUGCUCAGACACAAGGUGUGUC________CUCU__GAAUG
....(.(((.(((........))).))))...............................(((((.....)))))................... ( -8.53 =  -8.67 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:49 2006