Locus 371

Sequence ID	3R_DroMel_CAF1
Location	1,422,256 – 1,422,374
Length	118
Max. P	0.882369

overview

Window 6

Location	1,422,256 – 1,422,374
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.54
Mean single sequence MFE	-28.07
Consensus MFE	-24.65
Energy contribution	-24.52
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-2.02
Structure conservation index	0.88
SVM decision value	0.92
SVM RNA-class probability	0.882369
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1422256 118 + 27905053
AGUUUUCAUUGGCCUUUGAUGCUCGGAUUUUGUGAGGCAACAAGGCAAGCAAA-AACUCAAAUGCUCUUGCAAUUUUGUACAAUGAAAAUGUCAUCCAGGACAAGACCAUUCUCAAAAA-
.(((((((((((((((.(.((((((.......))).))).))))))..(((((-(...(((......)))...)))))).))))))))))(((......))).................- ( -26.50)
>DroSec_CAF1 4151 118 + 1
AGUUUUCAUUGGCCUUUGAUGCUCGGGUUUUGUGAGGCAACAAGGCAAGCAAA-AACUCAAAUGCUCUUGCAAUUUUGUACAAUGAAAAUGUCAUCCAGGACAAGACCAUUCUCAAAAA-
.((((((((((((.(((((((((...(((((((......))))))).))))..-...))))).))...((((....))))))))))))))(((......))).................- ( -28.10)
>DroEre_CAF1 4351 119 + 1
AGUUUUCAUUGGCCUUUGAUGCUCGGACUUUGUGAAGCAACAAGGCAAGCAAAAAACUAAUAUGCUCUUGCAAUUUUGUACAAUGAAAAUGUCAUCCAGGACAAGACCAUUCUCAAAAA-
.(((((((((((((((.(.((((((.......)).)))).))))))..((((((........(((....))).)))))).))))))))))(((......))).................- ( -26.20)
>DroYak_CAF1 4745 119 + 1
AGUUUUCAUUGGCCAUUGGUGCUCAGACUUUGUGAAGCACCAAGGCAAGCAAA-AACUCAUAUGCUCUUGCAAUUUUGUACAAUGAAAAUCUCAUCCAGGACAAGACCAUUCUCAAAAAU
.(((((((((((((.((((((((((.......)).)))))))))))..(((((-(.......(((....))).)))))).))))))))))........((......))............ ( -31.50)
>consensus
AGUUUUCAUUGGCCUUUGAUGCUCGGACUUUGUGAAGCAACAAGGCAAGCAAA_AACUCAAAUGCUCUUGCAAUUUUGUACAAUGAAAAUGUCAUCCAGGACAAGACCAUUCUCAAAAA_
.(((((((((((((.(((.((((((.(...).))).))).))))))................(((....)))........))))))))))(((......))).................. (-24.65 = -24.52 +  -0.12)

alignment

secondary structure

dotplot

Window 7

Location	1,422,256 – 1,422,374
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.54
Mean single sequence MFE	-30.75
Consensus MFE	-24.02
Energy contribution	-24.03
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.92
Structure conservation index	0.78
SVM decision value	-0.04
SVM RNA-class probability	0.512713
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1422256 118 - 27905053
-UUUUUGAGAAUGGUCUUGUCCUGGAUGACAUUUUCAUUGUACAAAAUUGCAAGAGCAUUUGAGUU-UUUGCUUGCCUUGUUGCCUCACAAAAUCCGAGCAUCAAAGGCCAAUGAAAACU
-.....((((....))))(((......))).(((((((((.........((((((((......)))-)))))..(((((..(((.((.........)))))...)))))))))))))).. ( -29.10)
>DroSec_CAF1 4151 118 - 1
-UUUUUGAGAAUGGUCUUGUCCUGGAUGACAUUUUCAUUGUACAAAAUUGCAAGAGCAUUUGAGUU-UUUGCUUGCCUUGUUGCCUCACAAAACCCGAGCAUCAAAGGCCAAUGAAAACU
-.....((((....))))(((......))).(((((((((.........((((((((......)))-)))))..(((((..(((.((.........)))))...)))))))))))))).. ( -29.10)
>DroEre_CAF1 4351 119 - 1
-UUUUUGAGAAUGGUCUUGUCCUGGAUGACAUUUUCAUUGUACAAAAUUGCAAGAGCAUAUUAGUUUUUUGCUUGCCUUGUUGCUUCACAAAGUCCGAGCAUCAAAGGCCAAUGAAAACU
-.((((((.(((((...((((......))))...))))).).))))).(((....)))....(((((((.....(((((..(((((..........)))))...)))))....))))))) ( -26.90)
>DroYak_CAF1 4745 119 - 1
AUUUUUGAGAAUGGUCUUGUCCUGGAUGAGAUUUUCAUUGUACAAAAUUGCAAGAGCAUAUGAGUU-UUUGCUUGCCUUGGUGCUUCACAAAGUCUGAGCACCAAUGGCCAAUGAAAACU
.............((((..((...))..))))((((((((.........((((((((......)))-)))))..(((((((((((.((.......)))))))))).)))))))))))... ( -37.90)
>consensus
_UUUUUGAGAAUGGUCUUGUCCUGGAUGACAUUUUCAUUGUACAAAAUUGCAAGAGCAUAUGAGUU_UUUGCUUGCCUUGUUGCCUCACAAAAUCCGAGCAUCAAAGGCCAAUGAAAACU
...........(.((((......)))).)..(((((((((.........((((((((......))).)))))..((((((.(((.((.........))))).))).)))))))))))).. (-24.02 = -24.03 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:37 2006