Locus 8205

Sequence ID	3L_DroMel_CAF1
Location	21,569,347 – 21,569,467
Length	120
Max. P	0.948411

overview

Window 4

Location	21,569,347 – 21,569,467
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	94.44
Mean single sequence MFE	-42.33
Consensus MFE	-39.24
Energy contribution	-39.80
Covariance contribution	0.56
Combinations/Pair	1.07
Mean z-score	-2.11
Structure conservation index	0.93
SVM decision value	0.84
SVM RNA-class probability	0.862971
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21569347 120 + 23771897
GCCCUUCGUUAGCAUUCCAUGGGCCUGGACGGCUACCAACCUGCUUCACAAUGCAGUGAGUGCUCAUGGCGCCGUUGAGGAGUCAGUCCUUAUCCUAAUCCCUCUUGCCAGGCCCACCUG
...................((((((((((((((..(((....(((((((......))))).))...))).))))).((((..(.((........)).)..))))...))))))))).... ( -41.90)
>DroSec_CAF1 16845 120 + 1
GCCCUUCGUCAGCAUUCCGUGGGCCUGGACGGCCACCAAUCUGCUUCACAAUGCAGUGAGUGGUCAUGGCGUCGAUGAGAAGUCAGUCUUUAUCCUAAUCCCUCUUCCCAGGCCCACCUG
..................((((((((((..((((((((..((((........)))))).)))))).((((.((.....)).))))......................))))))))))... ( -43.50)
>DroSim_CAF1 17063 120 + 1
GCCCUUCGUCAGCAUUCCGUGGGCCUGGACGGCCACCAAUCUGCUUCACAAUGCAGUGAGUGGUCAUGGCGCCGAUGAGAAGUCAGUCUUUAUCCUAAUCCCUCUUCCCAGGCCCACCUG
..................((((((((((..((((((((..((((........)))))).))))))........((.(((..((.((........)).))..))).))))))))))))... ( -41.60)
>consensus
GCCCUUCGUCAGCAUUCCGUGGGCCUGGACGGCCACCAAUCUGCUUCACAAUGCAGUGAGUGGUCAUGGCGCCGAUGAGAAGUCAGUCUUUAUCCUAAUCCCUCUUCCCAGGCCCACCUG
..................((((((((((..((((((((..((((........)))))).)))))).((((.((.....)).))))......................))))))))))... (-39.24 = -39.80 +   0.56)

alignment

secondary structure

dotplot

Window 5

Location	21,569,347 – 21,569,467
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	94.44
Mean single sequence MFE	-48.17
Consensus MFE	-46.14
Energy contribution	-46.03
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-2.29
Structure conservation index	0.96
SVM decision value	1.38
SVM RNA-class probability	0.948411
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21569347 120 - 23771897
CAGGUGGGCCUGGCAAGAGGGAUUAGGAUAAGGACUGACUCCUCAACGGCGCCAUGAGCACUCACUGCAUUGUGAAGCAGGUUGGUAGCCGUCCAGGCCCAUGGAAUGCUAACGAAGGGC
...((((((((((...((((..((((........))))..)))).((((((((((((....)))((((........))))..)))).)))))))))))))))..........(....).. ( -51.00)
>DroSec_CAF1 16845 120 - 1
CAGGUGGGCCUGGGAAGAGGGAUUAGGAUAAAGACUGACUUCUCAUCGACGCCAUGACCACUCACUGCAUUGUGAAGCAGAUUGGUGGCCGUCCAGGCCCACGGAAUGCUGACGAAGGGC
...((((((((((((.((((..((((........))))..)))).))......(((.(((((..((((........))))...))))).)))))))))))))..........(....).. ( -45.50)
>DroSim_CAF1 17063 120 - 1
CAGGUGGGCCUGGGAAGAGGGAUUAGGAUAAAGACUGACUUCUCAUCGGCGCCAUGACCACUCACUGCAUUGUGAAGCAGAUUGGUGGCCGUCCAGGCCCACGGAAUGCUGACGAAGGGC
...(((((((((((..((((..((((........))))..))))..(((((((((((....)))((((........))))..)))).)))))))))))))))..........(....).. ( -48.00)
>consensus
CAGGUGGGCCUGGGAAGAGGGAUUAGGAUAAAGACUGACUUCUCAUCGGCGCCAUGACCACUCACUGCAUUGUGAAGCAGAUUGGUGGCCGUCCAGGCCCACGGAAUGCUGACGAAGGGC
...((((((((((...((((..((((........))))..))))..(((((((((((....)))((((........))))..)))).)))).))))))))))..........(....).. (-46.14 = -46.03 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:23 2006