Locus 1978

Sequence ID	2L_DroMel_CAF1
Location	5,362,617 – 5,362,777
Length	160
Max. P	0.922197

overview

Window 6

Location	5,362,617 – 5,362,737
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.22
Mean single sequence MFE	-32.88
Consensus MFE	-29.33
Energy contribution	-29.25
Covariance contribution	-0.08
Combinations/Pair	1.10
Mean z-score	-1.66
Structure conservation index	0.89
SVM decision value	1.15
SVM RNA-class probability	0.922197
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5362617 120 + 22407834
UUCUUCGCCGUGUUCGGACAAACGACGACCGAGCAAACGCAAGUUGACAAAAUCAAAAAUGUAGCCACGCCCACUCAACCGUAUUGGGUUGAGUACCUGUUCAAAAUUGUCUUUGGCAUU
......(((((((((((.(.......).)))))))(((....)))(((((.............((...))..((((((((......))))))))............)))))..))))... ( -32.60)
>DroVir_CAF1 43783 120 + 1
UUCUUCGCCGUGUUUGGCCAGACGACGACGGAGCAAACGCAAGUUGAUAAAAUCAAAAAUUUAGCCACGCCCACUCAACCGUAUUGGGUUGAGUAUCUGUUCAAAAUUGUCUUUGGCAUA
................((((((.(((((..((((((((....)))...........................((((((((......))))))))...)))))....)))))))))))... ( -33.90)
>DroGri_CAF1 38376 120 + 1
UUCUUCGCCGUGUUUGGUCAGACGACGACGGAGCAAACGCAAGUUGAUAAAAUCAAAAAUUUAGCCACGCCCACUCAACCGUAUUGGGUUGAGUAUCUAUUCAAAAUUGUCUUUGGCAUA
......((((.((((....))))(((((.((.((.(((....)))(((...)))..............))))((((((((......))))))))............)))))..))))... ( -31.40)
>DroWil_CAF1 43499 120 + 1
UUCUUCGCCGUGUUUGGUCAGACGACGACCGAACAGACGCAAGUUGAUAAAAUCAAAAAUGUAGCCACGCCCACUCAACCAUACUGGGUUGAGUAUCUGUUCAAAAUUGUCUUUGGCAUU
......((((.....((((.......))))(((((((.(((..(((((...)))))...)))..........((((((((......)))))))).)))))))...........))))... ( -35.30)
>DroMoj_CAF1 39353 120 + 1
UUCUUCGCCGUGUUUGGCCAGACGACGACGGAGCAAACGCAAGUUGAUAAAAUCAAAAAUUUAGCCACGCCCACUCAACCGUAUUGGGUUGAGUAUCUGUUCAAAAUUGUCUUUGGCAUA
................((((((.(((((..((((((((....)))...........................((((((((......))))))))...)))))....)))))))))))... ( -33.90)
>DroAna_CAF1 26550 120 + 1
UUCUUCGCCGUGUUCGGACAAACGACGACCGAGCAGACCCAAGUUGACAAAAUCAAAAAUGUAGCCACGCCCACUCAACCGUAUUGGGUUGAGUACCUGUUCAAAAUUGUCUUUGGCAUU
......(((((((((((.(.......).)))))))(((.....((((((..............((...))..((((((((......))))))))...)).))))....)))..))))... ( -30.20)
>consensus
UUCUUCGCCGUGUUUGGACAGACGACGACCGAGCAAACGCAAGUUGAUAAAAUCAAAAAUGUAGCCACGCCCACUCAACCGUAUUGGGUUGAGUAUCUGUUCAAAAUUGUCUUUGGCAUA
......((((.((((....))))(((((..((((((((....)))...........................((((((((......))))))))...)))))....)))))..))))... (-29.33 = -29.25 +  -0.08)

alignment

secondary structure

dotplot

Window 7

Location	5,362,657 – 5,362,777
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.89
Mean single sequence MFE	-28.95
Consensus MFE	-27.25
Energy contribution	-26.62
Covariance contribution	-0.64
Combinations/Pair	1.10
Mean z-score	-0.83
Structure conservation index	0.94
SVM decision value	-0.06
SVM RNA-class probability	0.505337
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5362657 120 + 22407834
AAGUUGACAAAAUCAAAAAUGUAGCCACGCCCACUCAACCGUAUUGGGUUGAGUACCUGUUCAAAAUUGUCUUUGGCAUUUACAUGUUGGUGUCGGUGGUUGUGCUCAUUAACCUGCUGA
...((((.....)))).((((.(((.(((.((((((((((......))))))))...........((((.(.(..((((....))))..).).)))))).)))))))))).......... ( -28.70)
>DroVir_CAF1 43823 120 + 1
AAGUUGAUAAAAUCAAAAAUUUAGCCACGCCCACUCAACCGUAUUGGGUUGAGUAUCUGUUCAAAAUUGUCUUUGGCAUAUACAUGCUGGUAUCGGUGGUUGUACUCAUUAACCUGCUGA
...(((((...))))).......((((.((....((((((......))))))((((.(((.((((......))))))).))))..)))))).((((((((((.......))))).))))) ( -29.10)
>DroPse_CAF1 35968 120 + 1
AAGUUGACAAAAUCAAAAAUGUAGCCACGCCCACUCAACCGUACUGGGUUGAGUAUCUGUUCAAAAUUGUCUUUGGCAUAUACAUGCUGGUGUCGGUGGUUGUCCUAAUUAACCUGCUGA
...((((.....))))....(((((((((((.((((((((......))))))))....................(((((....)))))))))).)))(((((.......))))))))... ( -30.60)
>DroGri_CAF1 38416 120 + 1
AAGUUGAUAAAAUCAAAAAUUUAGCCACGCCCACUCAACCGUAUUGGGUUGAGUAUCUAUUCAAAAUUGUCUUUGGCAUAUACAUGUUGGUAUCGGUGGUUGUACUCAUUAACCUGCUGA
...(((((...)))))....(((((...(((.((((((((......))))))))..............(...(..((((....))))..)...))))(((((.......))))).))))) ( -26.70)
>DroWil_CAF1 43539 120 + 1
AAGUUGAUAAAAUCAAAAAUGUAGCCACGCCCACUCAACCAUACUGGGUUGAGUAUCUGUUCAAAAUUGUCUUUGGCAUUUACAUGUUGGUAUCGGUGGUUGUGCUCAUUAAUCUGCUGA
...(((((...))))).((((.(((.(((.((((((((((......))))))))...........((((...(..((((....))))..)...)))))).)))))))))).......... ( -28.00)
>DroPer_CAF1 35752 120 + 1
AAGUUGACAAAAUCAAAAAUGUAGCCACGCCCACUCAACCGUACUGGGUUGAGUAUCUGUUCAAAAUUGUCUUUGGCAUAUACAUGCUGGUGUCGGUGGUUGUCCUAAUUAACCUGCUGA
...((((.....))))....(((((((((((.((((((((......))))))))....................(((((....)))))))))).)))(((((.......))))))))... ( -30.60)
>consensus
AAGUUGACAAAAUCAAAAAUGUAGCCACGCCCACUCAACCGUACUGGGUUGAGUAUCUGUUCAAAAUUGUCUUUGGCAUAUACAUGCUGGUAUCGGUGGUUGUACUCAUUAACCUGCUGA
.....(((((.............((...))..((((((((......))))))))............))))).(..((((....))))..)..((((((((((.......))))).))))) (-27.25 = -26.62 +  -0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:25 2006