Locus 5576

Sequence ID	3R_DroMel_CAF1
Location	14,741,672 – 14,741,777
Length	105
Max. P	0.996607

overview

Window 7

Location	14,741,672 – 14,741,777
Length	105
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	69.16
Mean single sequence MFE	-30.52
Consensus MFE	-18.23
Energy contribution	-19.35
Covariance contribution	1.11
Combinations/Pair	1.16
Mean z-score	-2.69
Structure conservation index	0.60
SVM decision value	2.72
SVM RNA-class probability	0.996607
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14741672 105 + 27905053
CAUUUUCCCAAAGCCAGCAACAUUUGUUGCCACAAC-UUUGUUGCUGGCG-GUGUCAUUGACACUGGGUACACUUCACGUCGAGUAUACAUAGAUAGAUGAGGCCAC
............((((((((((...((((...))))-..))))))))))(-((.(((((....(((.(((.((((......)))).))).)))...))))).))).. ( -38.30)
>DroPse_CAF1 524 83 + 1
U---------AAAUCCCCAACAUUC---UCUAGACACAUUGUUGCCGGCAAAUGUCAAUGACAUUGGCCCUAA------------AAAAAUACUUUGACGAGCCCUC
.---------.......(((((...---...........)))))..(((.((((((...)))))).)))....------------...................... ( -11.94)
>DroSec_CAF1 541 97 + 1
CAUUUUCCCAAUGCCAGCAACAUUUGUUGCCAGACU-CUUGUUGCUGGCG-GUGUCAUUGACACUGGGUACACUUUACGUCGAGUAUUUGUAGAUACUU--------
......(((...((((((((((...(((....))).-..))))))))))(-(((((...))))))))).............(((((((....)))))))-------- ( -35.00)
>DroSim_CAF1 562 105 + 1
CAUUUUCCAGAUGCCAGCAACAUUUGUUGCCAGACU-CUUGUUGCUGGCG-GUGUCAUUGACACUGGGUACACUUAACGUCGAGUAUUUGUAGAUAGAUGAGGCCAC
............((((((((((...(((....))).-..))))))))))(-((.((((((((..((((....))))..)))...((((....))))))))).))).. ( -34.90)
>DroEre_CAF1 406 99 + 1
CUCUCUCCCGAUGCCCGCAACAUUUGUUGCCAGACC-CUUGUUGCUGGCA-GUGUCAUUGACACUGGGUACACUUCACGUCGAGUAUAAAUAG------GAGGGCUU
(((((((((...(((.((((((...(((....))).-..)))))).)))(-(((((...)))))))))...((((......)))).......)------)))))... ( -32.30)
>DroYak_CAF1 410 97 + 1
CACUUUCCCGAAGCCAGCAACAUUUGUUGCCAGACU-AUUGUUGCUGACA-GUGUCAUUGACACUGGGUACACUUUUCGUCGAGUAUAGAC--------GAGCCCUU
.......((.....((((((((...(((....))).-..)))))))).((-(((((...))))))))).......((((((.......)))--------)))..... ( -30.70)
>consensus
CAUUUUCCCGAAGCCAGCAACAUUUGUUGCCAGACU_CUUGUUGCUGGCA_GUGUCAUUGACACUGGGUACACUUCACGUCGAGUAUAAAUAGAUAGAUGAGGCCUC
......((((..((((((((((.................))))))))))..(((((...)))))))))....................................... (-18.23 = -19.35 +   1.11)

alignment

secondary structure

dotplot

Window 8

Location	14,741,672 – 14,741,777
Length	105
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	69.16
Mean single sequence MFE	-30.07
Consensus MFE	-19.32
Energy contribution	-20.37
Covariance contribution	1.05
Combinations/Pair	1.27
Mean z-score	-2.23
Structure conservation index	0.64
SVM decision value	2.29
SVM RNA-class probability	0.991838
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14741672 105 - 27905053
GUGGCCUCAUCUAUCUAUGUAUACUCGACGUGAAGUGUACCCAGUGUCAAUGACAC-CGCCAGCAACAAA-GUUGUGGCAACAAAUGUUGCUGGCUUUGGGAAAAUG
...................((((((........))))))(((((((((...)))))-.((((((((((..-.((((....)))).))))))))))..))))...... ( -34.30)
>DroPse_CAF1 524 83 - 1
GAGGGCUCGUCAAAGUAUUUUU------------UUAGGGCCAAUGUCAUUGACAUUUGCCGGCAACAAUGUGUCUAGA---GAAUGUUGGGGAUUU---------A
......((.((((.....((((------------(((((((.((((((...)))))).)))(....).......)))))---)))..)))).))...---------. ( -21.30)
>DroSec_CAF1 541 97 - 1
--------AAGUAUCUACAAAUACUCGACGUAAAGUGUACCCAGUGUCAAUGACAC-CGCCAGCAACAAG-AGUCUGGCAACAAAUGUUGCUGGCAUUGGGAAAAUG
--------.......((((..(((.....)))...))))(((((((((...)))))-.((((((((((..-....((....))..))))))))))..))))...... ( -32.10)
>DroSim_CAF1 562 105 - 1
GUGGCCUCAUCUAUCUACAAAUACUCGACGUUAAGUGUACCCAGUGUCAAUGACAC-CGCCAGCAACAAG-AGUCUGGCAACAAAUGUUGCUGGCAUCUGGAAAAUG
((((..........))))..(((((........)))))..((((((((...)))))-.((((((((((..-....((....))..))))))))))...)))...... ( -28.90)
>DroEre_CAF1 406 99 - 1
AAGCCCUC------CUAUUUAUACUCGACGUGAAGUGUACCCAGUGUCAAUGACAC-UGCCAGCAACAAG-GGUCUGGCAACAAAUGUUGCGGGCAUCGGGAGAGAG
..((((..------............(((.(....(((...(((((((...)))))-))...)))....)-.)))..(((((....))))))))).((....))... ( -31.30)
>DroYak_CAF1 410 97 - 1
AAGGGCUC--------GUCUAUACUCGACGAAAAGUGUACCCAGUGUCAAUGACAC-UGUCAGCAACAAU-AGUCUGGCAACAAAUGUUGCUGGCUUCGGGAAAGUG
......((--------(((.......)))))........(((((((((...)))))-)((((((((((..-....((....))..))))))))))...)))...... ( -32.50)
>consensus
GAGGCCUCAUCUAUCUAUAUAUACUCGACGUAAAGUGUACCCAGUGUCAAUGACAC_CGCCAGCAACAAG_AGUCUGGCAACAAAUGUUGCUGGCAUCGGGAAAAUG
...................((((((........))))))(((.(((((...)))))..((((((((((.......((....))..))))))))))...)))...... (-19.32 = -20.37 +   1.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:28 2006