Locus 5789

Sequence ID	X_DroMel_CAF1
Location	15,021,451 – 15,021,569
Length	118
Max. P	0.794272

overview

Window 4

Location	15,021,451 – 15,021,541
Length	90
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	61.68
Mean single sequence MFE	-38.80
Consensus MFE	-10.38
Energy contribution	-10.30
Covariance contribution	-0.08
Combinations/Pair	1.44
Mean z-score	-2.21
Structure conservation index	0.27
SVM decision value	0.40
SVM RNA-class probability	0.720444
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15021451 90 - 22224390
GGCGAGGCGGGUGGUGUCAGGGUGGAGGGCUCCUCGGCCCCACCACCAA---------CUAGUCCACCGCCGGUGAUCACCACCGACACCUUGCCAGUC
(((((((.((((((......(((((.(((((....)))))..)))))..---------.....)))))..(((((.....))))).).))))))).... ( -47.92)
>DroPse_CAF1 46872 69 - 1
GGUGAAGCGGGCGGCGUUAGGGUGGCCGGCUCCUCUGGACCACUA---------------------UUGUCGGAGG---------AGACCUUAACCAUC
(((......(((.((......)).)))((((((((((.((.....---------------------..))))))))---------)).))...)))... ( -27.10)
>DroEre_CAF1 40039 90 - 1
GGCGAGGCGGGUGGUGUCAGGGUGGAGGGCUCCUCGGCCCCACCACCAA---------CUCCUCCGGCGCCGGUGGUCACCACCGUGACCUUGCCAAUC
((((((((((((((((....(((((.(((((....)))))..)))))..---------..((.(((....))).)).))))))).)).))))))).... ( -51.50)
>DroYak_CAF1 40238 99 - 1
GGCGAGGCAGGUGGUGUCAGGGUGGAGGGCUCCUCGGCCACACCACCAACUCCACCAACUCCACCGCCGCCGGUGGUCACCACCGUUACCUUGCCAAUC
(((((((..(((((((....(((((((((((....))))..........)))))))....((((((....)))))).)))))))....))))))).... ( -50.50)
>DroAna_CAF1 34538 69 - 1
GGGGAGGCGGGCGGCGUCAGGGUGGUGGGUUCGCCGGCGUC-----------------------CAG--GUCGAGGUCCU-----UGCCGUUGCCAAUG
((.((((((((.(((.((..(((((.....)))))(((...-----------------------...--))))).)))))-----)))).)).)).... ( -28.70)
>DroPer_CAF1 47425 69 - 1
GGUGAAGCGGGCGGCGUUAGGGUGGCCGGCUCCUCUGGACCACUA---------------------UUGUCGGAGG---------AGACCUUAACCAUC
(((......(((.((......)).)))((((((((((.((.....---------------------..))))))))---------)).))...)))... ( -27.10)
>consensus
GGCGAGGCGGGCGGCGUCAGGGUGGAGGGCUCCUCGGCCCCACCA___________________C_CCGCCGGAGGUCAC_____AGACCUUGCCAAUC
(((((((((.....))))..(((((...((......)).)))))..............................................))))).... (-10.38 = -10.30 +  -0.08)

alignment

secondary structure

dotplot

Window 5

Location	15,021,474 – 15,021,569
Length	95
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	72.36
Mean single sequence MFE	-48.25
Consensus MFE	-29.81
Energy contribution	-31.62
Covariance contribution	1.81
Combinations/Pair	1.38
Mean z-score	-1.64
Structure conservation index	0.62
SVM decision value	0.60
SVM RNA-class probability	0.794272
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15021474 95 - 22224390
UGUCUGCGACGGUGGUGGAGUGGCGGGCGGCGAGGCGGGUGGUGUCAGGGUGGAGGGCUCCUCGGCCCCACCACCAA---------CUAGUCCACCGCCGGUGA
.........((((((((((.(((...((......)).(((((((...((((.((((...)))).)))))))))))..---------))).)))))))))).... ( -51.70)
>DroEre_CAF1 40062 95 - 1
UGUCUGCGAUGGCGGAGGAGUGGCGGGCGGCGAGGCGGGUGGUGUCAGGGUGGAGGGCUCCUCGGCCCCACCACCAA---------CUCCUCCGGCGCCGGUGG
(.(((((....))))).)....((.((((.(((((..(((((((...((((.((((...)))).)))))))))))..---------..))).)).)))).)).. ( -50.40)
>DroWil_CAF1 43842 95 - 1
UGGUGGUUGUGGCGGCGGUGUUGCUGGCGGCGAGGCGGGGGGCGUUAAAGUGGUUGGCUCAUCGCUUGGCUGAGUGA---------CGCAAACAGAGACGGAGG
..((..((((.......((((..((..((((.(((((..((((.............))))..))))).))))))..)---------)))..))))..))..... ( -32.12)
>DroYak_CAF1 40261 104 - 1
UGUCUGCGAUGGCGGUGGAGUGGCGGGCGGCGAGGCAGGUGGUGUCAGGGUGGAGGGCUCCUCGGCCACACCACCAACUCCACCAACUCCACCGCCGCCGGUGG
......((.((((((((((((((.((((......)).((((((((...(((.((((...)))).)))))))))))....)).)).)))))))))))).)).... ( -58.80)
>consensus
UGUCUGCGAUGGCGGUGGAGUGGCGGGCGGCGAGGCGGGUGGUGUCAGGGUGGAGGGCUCCUCGGCCCCACCACCAA_________CUCCACCACCGCCGGUGG
......((.(((((((((((.((...((......)).(((((((...((((.((((...)))).)))))))))))...........)).))))))))))).)). (-29.81 = -31.62 +   1.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:26 2006