Locus 2660

Sequence ID	X_DroMel_CAF1
Location	7,140,013 – 7,140,134
Length	121
Max. P	0.997466

overview

Window 6

Location	7,140,013 – 7,140,121
Length	108
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	96.03
Mean single sequence MFE	-33.58
Consensus MFE	-30.24
Energy contribution	-30.64
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.15
Structure conservation index	0.90
SVM decision value	2.86
SVM RNA-class probability	0.997466
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7140013 108 + 22224390
AGUGGGCACAUUUUGUAGAGCUUGAACUUUACCUUUGAAAGGGUUGCUCUUGCUCC-CUUUUGAAACUCUGACCUUCAGAAGGAAAAGGAAACCCGGUGCUCAAGUCCC
..(((((((.....((((((......))))))........(((((..((((....(-((((((((.........)))))))))..)))).))))).)))))))...... ( -34.10)
>DroSec_CAF1 7790 108 + 1
AGUGGGCACAUUUUGUCGAGCUUGAACUUUACCUUUCAAAGGGUUGCUCUUGCUCC-CUUUUGAAACUCUGACCUUCAGAAGGAAAAGGAAACCCGGUGCUCAAGUCCC
..(((((((......((((((..((.(...(((((....))))).).))..))))(-((((((((.........))))))))).....))......)))))))...... ( -32.90)
>DroSim_CAF1 2157 108 + 1
AGUGGGCACAUUUUGUAGAGCUUGAACUUUACCUUUCAAAGGGUUGCUCUUGCUCC-CUUUUGAAACUCUGACCUUCAGAAGGAAAAGGAAACCCGGUGCUCAAGUCCC
..(((((((.....((((((......))))))........(((((..((((....(-((((((((.........)))))))))..)))).))))).)))))))...... ( -34.10)
>DroEre_CAF1 8012 107 + 1
AGUGGGCACUU-UUGUAGAGCUUGAACUUUACCUUACAAAGGGUUGCUCUUGCUCC-CUUUUGAAACUCUGACCUUCAGAAGGAAAAGGAAACCCGGUGCUCAAGUCCC
..((((((((.-..((((((......))))))........(((((..((((....(-((((((((.........)))))))))..)))).)))))))))))))...... ( -34.40)
>DroYak_CAF1 7585 109 + 1
AGUGGGCACUCGUUGUAGAGCUUGAACUUAACCAUUGAAAGGGUUGCUCUUGCUCCCCUUUUGAAACUCUGACCUUCAGAAGGAAAAGGAAACCCGGUGCUCAAGUCCC
..(((((((.((.....((((..((...(((((........))))).))..)))).(((((((((.........)))))))))....(....).)))))))))...... ( -32.40)
>consensus
AGUGGGCACAUUUUGUAGAGCUUGAACUUUACCUUUCAAAGGGUUGCUCUUGCUCC_CUUUUGAAACUCUGACCUUCAGAAGGAAAAGGAAACCCGGUGCUCAAGUCCC
..(((((((.....((((((......))))))........(((((..((((..(((..(((((((.........)))))))))).)))).))))).)))))))...... (-30.24 = -30.64 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	7,140,013 – 7,140,121
Length	108
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	96.03
Mean single sequence MFE	-31.82
Consensus MFE	-26.77
Energy contribution	-26.97
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.47
Structure conservation index	0.84
SVM decision value	0.27
SVM RNA-class probability	0.663293
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7140013 108 - 22224390
GGGACUUGAGCACCGGGUUUCCUUUUCCUUCUGAAGGUCAGAGUUUCAAAAG-GGAGCAAGAGCAACCCUUUCAAAGGUAAAGUUCAAGCUCUACAAAAUGUGCCCACU
(((....((((.....((((((((((..(((((.....)))))....)))))-)))))..((((.(((........)))...))))..))))(((.....))))))... ( -30.80)
>DroSec_CAF1 7790 108 - 1
GGGACUUGAGCACCGGGUUUCCUUUUCCUUCUGAAGGUCAGAGUUUCAAAAG-GGAGCAAGAGCAACCCUUUGAAAGGUAAAGUUCAAGCUCGACAAAAUGUGCCCACU
(((((((((((.....((((((((((..(((((.....)))))....)))))-)))))..((((.(((........)))...))))..))))))......)).)))... ( -32.00)
>DroSim_CAF1 2157 108 - 1
GGGACUUGAGCACCGGGUUUCCUUUUCCUUCUGAAGGUCAGAGUUUCAAAAG-GGAGCAAGAGCAACCCUUUGAAAGGUAAAGUUCAAGCUCUACAAAAUGUGCCCACU
(((.(((((((((((((........)))(((((.....)))))(((((((.(-(..((....))..)).))))))))))...)))))))...(((.....))))))... ( -30.80)
>DroEre_CAF1 8012 107 - 1
GGGACUUGAGCACCGGGUUUCCUUUUCCUUCUGAAGGUCAGAGUUUCAAAAG-GGAGCAAGAGCAACCCUUUGUAAGGUAAAGUUCAAGCUCUACAA-AAGUGCCCACU
(((((((((((.....((((((((((..(((((.....)))))....)))))-)))))..((((.(((........)))...))))..)))).....-)))).)))... ( -32.70)
>DroYak_CAF1 7585 109 - 1
GGGACUUGAGCACCGGGUUUCCUUUUCCUUCUGAAGGUCAGAGUUUCAAAAGGGGAGCAAGAGCAACCCUUUCAAUGGUUAAGUUCAAGCUCUACAACGAGUGCCCACU
((((((((............((((((..(((((.....)))))....))))))(((((..((((((((........))))..))))..)))))....))))).)))... ( -32.80)
>consensus
GGGACUUGAGCACCGGGUUUCCUUUUCCUUCUGAAGGUCAGAGUUUCAAAAG_GGAGCAAGAGCAACCCUUUGAAAGGUAAAGUUCAAGCUCUACAAAAUGUGCCCACU
(((.(((((((((((((((..(((((...((((.....))))(((((......)))))))))).))))).......)))...)))))))...(((.....))))))... (-26.77 = -26.97 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	7,140,042 – 7,140,134
Length	92
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	97.62
Mean single sequence MFE	-32.56
Consensus MFE	-26.60
Energy contribution	-26.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-3.63
Structure conservation index	0.82
SVM decision value	2.14
SVM RNA-class probability	0.988853
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7140042 92 + 22224390
UACCUUUGAAAGGGUUGCUCUUGCUCC-CUUUUGAAACUCUGACCUUCAGAAGGAAAAGGAAACCCGGUGCUCAAGUCCCGGAGUGCCUUUAA
..((((..((((((..((....)).))-))))..))..((((.....)))).)).(((((..((((((..(....)..)))).)).))))).. ( -32.40)
>DroSec_CAF1 7819 92 + 1
UACCUUUCAAAGGGUUGCUCUUGCUCC-CUUUUGAAACUCUGACCUUCAGAAGGAAAAGGAAACCCGGUGCUCAAGUCCCGGAGUGCCUUUAA
..((((((((((((..((....))..)-))))))))..((((.....))))))).(((((..((((((..(....)..)))).)).))))).. ( -33.10)
>DroSim_CAF1 2186 92 + 1
UACCUUUCAAAGGGUUGCUCUUGCUCC-CUUUUGAAACUCUGACCUUCAGAAGGAAAAGGAAACCCGGUGCUCAAGUCCCGGAGUGCCUUUAA
..((((((((((((..((....))..)-))))))))..((((.....))))))).(((((..((((((..(....)..)))).)).))))).. ( -33.10)
>DroEre_CAF1 8040 92 + 1
UACCUUACAAAGGGUUGCUCUUGCUCC-CUUUUGAAACUCUGACCUUCAGAAGGAAAAGGAAACCCGGUGCUCAAGUCCCGGAGUGCCUUUAA
..((((.(((((((..((....))..)-)))))).....(((.....))))))).(((((..((((((..(....)..)))).)).))))).. ( -30.90)
>DroYak_CAF1 7614 93 + 1
AACCAUUGAAAGGGUUGCUCUUGCUCCCCUUUUGAAACUCUGACCUUCAGAAGGAAAAGGAAACCCGGUGCUCAAGUCCCGGAGUGCCUUUAA
..((.(..((((((..((....))..))))))..)...((((.....)))).)).(((((..((((((..(....)..)))).)).))))).. ( -33.30)
>consensus
UACCUUUCAAAGGGUUGCUCUUGCUCC_CUUUUGAAACUCUGACCUUCAGAAGGAAAAGGAAACCCGGUGCUCAAGUCCCGGAGUGCCUUUAA
...........(((((..((((..(((..(((((((.........)))))))))).)))).)))))((..(((........)))..))..... (-26.60 = -26.60 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:20 2006