Locus 5088

Sequence ID	3L_DroMel_CAF1
Location	13,957,233 – 13,957,323
Length	90
Max. P	0.990463

overview

Window 1

Location	13,957,233 – 13,957,323
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	80.80
Mean single sequence MFE	-32.80
Consensus MFE	-18.22
Energy contribution	-20.38
Covariance contribution	2.16
Combinations/Pair	1.19
Mean z-score	-3.05
Structure conservation index	0.56
SVM decision value	2.21
SVM RNA-class probability	0.990463
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13957233 90 + 23771897
ACACACACACGCGCGCGCGCCUAUGAGUGUUUGUGUGUGUGUGUUUGGCUUUUGUCUUUCACUGGGGGCCCAAGUCAGCUGGGCCUUACA
(((((((((((((.((((........)))).)))))))))))))..(((....)))........((((((((.(....)))))))))... ( -40.70)
>DroSec_CAF1 12764 80 + 1
ACACAAACACACG--CGCGCCUAUUCGUGU--------GUGUGCAUGGCUUUUGUCUUUCACUGGGGGCCCAAGUCAGCUGGGCCUUACA
.......((((((--((((......)))))--------)))))...(((....)))........((((((((.(....)))))))))... ( -29.90)
>DroSim_CAF1 12856 88 + 1
ACACACACACGCG--CGCGCCUAUUUGUGUGUGUGUGUGUGUGCUUGGCUUUUGUCUUUCACUGGGAGCCCAAGUCAGCUGGGCCUUACA
(((((((((((((--((((......)))))))))))))))))(((..(((((((..((((....))))..))))..)))..)))...... ( -41.20)
>DroEre_CAF1 13044 88 + 1
AUACACAC--AAACACCUAGCUAUGCGUGUGUGUGUGUGUGUAUUUGGCUUUUGUCUUUCACUGGGGGCUUCAGUCAGCUGGGCCUUACA
((((((((--(.((((...((...))..)))).)))))))))....(((....)))........((((((.(((....)))))))))... ( -28.90)
>DroYak_CAF1 13269 88 + 1
AUACACACACACACACCUAUCUAUAUGUGUUC--GCGUGUGUGUUUGGCUUUUGUCUUUCACUGGGCUCCCAAGUCAGCUGGGCCUUACA
..((((((((.(((((.((....)).))))..--).))))))))..((((((((.((.....(((....))))).)))..)))))..... ( -23.30)
>consensus
ACACACACACACGC_CGCGCCUAUGCGUGUGUGUGUGUGUGUGUUUGGCUUUUGUCUUUCACUGGGGGCCCAAGUCAGCUGGGCCUUACA
((((((((..((((............))))..))))))))(((...(((....)))...)))..(((((((.((....)))))))))... (-18.22 = -20.38 +   2.16)

alignment

secondary structure

dotplot

Window 2

Location	13,957,233 – 13,957,323
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	80.80
Mean single sequence MFE	-26.18
Consensus MFE	-16.68
Energy contribution	-17.44
Covariance contribution	0.76
Combinations/Pair	1.39
Mean z-score	-1.79
Structure conservation index	0.64
SVM decision value	0.25
SVM RNA-class probability	0.654212
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13957233 90 - 23771897
UGUAAGGCCCAGCUGACUUGGGCCCCCAGUGAAAGACAAAAGCCAAACACACACACACAAACACUCAUAGGCGCGCGCGCGUGUGUGUGU
.....(((((((.....)))))))........................((((((((((.....(.....)(((....))))))))))))) ( -30.40)
>DroSec_CAF1 12764 80 - 1
UGUAAGGCCCAGCUGACUUGGGCCCCCAGUGAAAGACAAAAGCCAUGCACAC--------ACACGAAUAGGCGCG--CGUGUGUUUGUGU
.....(((((((.....)))))))....(((...(........)...)))..--------(((((((((.((...--.)).))))))))) ( -24.40)
>DroSim_CAF1 12856 88 - 1
UGUAAGGCCCAGCUGACUUGGGCUCCCAGUGAAAGACAAAAGCCAAGCACACACACACACACACAAAUAGGCGCG--CGCGUGUGUGUGU
.....(((((((.....)))))))......................((((((((((.(.(.(.(......).).)--.).)))))))))) ( -26.40)
>DroEre_CAF1 13044 88 - 1
UGUAAGGCCCAGCUGACUGAAGCCCCCAGUGAAAGACAAAAGCCAAAUACACACACACACACACGCAUAGCUAGGUGUUU--GUGUGUAU
.....(((....((.((((.......))))...))......)))..(((((((((.((((....((...))...)))).)--)))))))) ( -23.30)
>DroYak_CAF1 13269 88 - 1
UGUAAGGCCCAGCUGACUUGGGAGCCCAGUGAAAGACAAAAGCCAAACACACACGC--GAACACAUAUAGAUAGGUGUGUGUGUGUGUAU
.....(((....((..(((((....)))).)..))......)))..((((((((((--..((((..........)))))))))))))).. ( -26.40)
>consensus
UGUAAGGCCCAGCUGACUUGGGCCCCCAGUGAAAGACAAAAGCCAAACACACACACACAAACACAAAUAGGCGCG_GCGUGUGUGUGUGU
.....(((((((.....)))))))....(((...(........)...)))..........(((((((((.(((....))).))))))))) (-16.68 = -17.44 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:41 2006