Locus 5313

Sequence ID	2R_DroMel_CAF1
Location	17,234,751 – 17,234,842
Length	91
Max. P	0.809648

overview

Window 7

Location	17,234,751 – 17,234,842
Length	91
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	81.34
Mean single sequence MFE	-23.52
Consensus MFE	-12.97
Energy contribution	-13.72
Covariance contribution	0.75
Combinations/Pair	1.20
Mean z-score	-2.19
Structure conservation index	0.55
SVM decision value	0.15
SVM RNA-class probability	0.609559
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17234751 91 + 20766785
GAGACUCACGUCCUUCAAUCGAAGGAUGCCAAUUGAAUGUAAAUAAGAAAGUG----------ACAGCCAAAAAUGGCGGGAAUGAAUGGGGAAAUUCAUU
....(((.((((((((....)))))))).........................----------...((((....)))))))(((((((......))))))) ( -23.10)
>DroPse_CAF1 33682 94 + 1
GACUCUCUCUCUCCUCCAAUGAACGCUGCCAAUUGAAUGUAAAUGAGAGAAUGGGUGGCGCUGUCAGCUAAA-CGGAUAGGAAUGGAUUG-A-GAG----U
.((((((..(((..(((......(((..((..((..((....))..)).....))..)))((((.......)-)))...)))..)))..)-)-)))----) ( -26.40)
>DroSec_CAF1 34421 90 + 1
GAGACUCACGUCCUUCCAUCGAAGGAUGCCAAUUGAAUGUAAAUAAGGAAGUG----------ACAGCCAAAAAUGGCGGGAAUGAAUGG-GAAAUUCAUU
....(((..(((((((((((....)))....(((.......)))..))))).)----------)).((((....)))))))(((((((..-...))))))) ( -24.80)
>DroSim_CAF1 37008 90 + 1
GAGACUCACGUCCUUCCAUCGAAGGAUGCCAAUUGAAUGUAAAUAAGGAAGUG----------ACAGCCAAAAAUGGCGGGAAUGAAUGG-GAAAUUCAUU
....(((..(((((((((((....)))....(((.......)))..))))).)----------)).((((....)))))))(((((((..-...))))))) ( -24.80)
>DroEre_CAF1 36390 86 + 1
AGGACUCACGUCCUUCCAUCGAAGGAUGCCAAUUGAAUGUAAAUAAGGAAGUG----------ACAGCCAAAAAUGGCGGGAAUGAAUGG-GAAAU----U
....((((.(((((((((((....)))....(((.......)))..))))).)----------)).((((....)))).........)))-)....----. ( -21.00)
>DroYak_CAF1 35214 86 + 1
AGGACUCACGUCCUUCCAUCGAAGGAUGCCAAUUGAAUGUAAAUAAGGAAGUG----------ACAGCCAAAAAUGGCGGGAAUGAAUGG-GAAAU----U
....((((.(((((((((((....)))....(((.......)))..))))).)----------)).((((....)))).........)))-)....----. ( -21.00)
>consensus
GAGACUCACGUCCUUCCAUCGAAGGAUGCCAAUUGAAUGUAAAUAAGGAAGUG__________ACAGCCAAAAAUGGCGGGAAUGAAUGG_GAAAU____U
....(((.((((((((....))))))))......................................((((....))))))).................... (-12.97 = -13.72 +   0.75)

alignment

secondary structure

dotplot

Window 8

Location	17,234,751 – 17,234,842
Length	91
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	81.34
Mean single sequence MFE	-21.39
Consensus MFE	-11.98
Energy contribution	-11.82
Covariance contribution	-0.16
Combinations/Pair	1.39
Mean z-score	-2.61
Structure conservation index	0.56
SVM decision value	0.64
SVM RNA-class probability	0.809648
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17234751 91 - 20766785
AAUGAAUUUCCCCAUUCAUUCCCGCCAUUUUUGGCUGU----------CACUUUCUUAUUUACAUUCAAUUGGCAUCCUUCGAUUGAAGGACGUGAGUCUC
(((((((......)))))))...((((....))))...----------................(((((((((......)))))))))((((....)))). ( -21.80)
>DroPse_CAF1 33682 94 - 1
A----CUC-U-CAAUCCAUUCCUAUCCG-UUUAGCUGACAGCGCCACCCAUUCUCUCAUUUACAUUCAAUUGGCAGCGUUCAUUGGAGGAGAGAGAGAGUC
(----(((-(-(..((..((((.....(-((.....)))(((((...(((....................)))..)))))....))))..))..)))))). ( -21.05)
>DroSec_CAF1 34421 90 - 1
AAUGAAUUUC-CCAUUCAUUCCCGCCAUUUUUGGCUGU----------CACUUCCUUAUUUACAUUCAAUUGGCAUCCUUCGAUGGAAGGACGUGAGUCUC
(((((((...-..)))))))...((((....))))..(----------(((.(((((.....((......)).((((....)))).))))).))))..... ( -21.20)
>DroSim_CAF1 37008 90 - 1
AAUGAAUUUC-CCAUUCAUUCCCGCCAUUUUUGGCUGU----------CACUUCCUUAUUUACAUUCAAUUGGCAUCCUUCGAUGGAAGGACGUGAGUCUC
(((((((...-..)))))))...((((....))))..(----------(((.(((((.....((......)).((((....)))).))))).))))..... ( -21.20)
>DroEre_CAF1 36390 86 - 1
A----AUUUC-CCAUUCAUUCCCGCCAUUUUUGGCUGU----------CACUUCCUUAUUUACAUUCAAUUGGCAUCCUUCGAUGGAAGGACGUGAGUCCU
.----.....-(((((.......((((...(((..(((----------.............)))..))).)))).......))))).(((((....))))) ( -21.56)
>DroYak_CAF1 35214 86 - 1
A----AUUUC-CCAUUCAUUCCCGCCAUUUUUGGCUGU----------CACUUCCUUAUUUACAUUCAAUUGGCAUCCUUCGAUGGAAGGACGUGAGUCCU
.----.....-(((((.......((((...(((..(((----------.............)))..))).)))).......))))).(((((....))))) ( -21.56)
>consensus
A____AUUUC_CCAUUCAUUCCCGCCAUUUUUGGCUGU__________CACUUCCUUAUUUACAUUCAAUUGGCAUCCUUCGAUGGAAGGACGUGAGUCUC
.......................((((....)))).............(((.(((((.....((......)).((((....)))).))))).)))...... (-11.98 = -11.82 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:50 2006