Locus 3662

Sequence ID	3L_DroMel_CAF1
Location	10,723,486 – 10,723,594
Length	108
Max. P	0.827332

overview

Window 3

Location	10,723,486 – 10,723,594
Length	108
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	92.16
Mean single sequence MFE	-23.54
Consensus MFE	-19.84
Energy contribution	-20.28
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.51
Structure conservation index	0.84
SVM decision value	0.70
SVM RNA-class probability	0.827332
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10723486 108 + 23771897
UCUAAAAAUGUGACAAAAAAUGAUUUCGUUAAUGUCAGCAGAAAAUAAGUUUGCCCAAAGUCCAAG-CCUUUGGGAAACUUUUUGCUUCGUUUCAUUUUU-UUUUUUUAG
.(((((((..(((((...((((....))))..)))))((((((....(((((.(((((((......-.))))))))))))))))))..............-..))))))) ( -26.10)
>DroSec_CAF1 57438 108 + 1
UCUAC-AAUGUGACGAAAAAUGAUUUCGUUAAUGUCAGCAGAAAAUAAGUUGGCCCAAAGUCCAAG-CCUUUGGGAAACUUUUUGCUUCGUUUCAGUUUUUUUUUUUUAG
...((-(...((((((((.....)))))))).))).(((((((....((((..(((((((......-.))))))).)))))))))))....................... ( -24.30)
>DroSim_CAF1 59603 104 + 1
UCUAC-AAUGUGACGAAAAAUGAUUUCGUUAAUGCCAGCAGAAAAUAAGUUGGCCCAAAGUCCAAG-CCUUUGGGAAACUUUUUGCUUCGUUUCAGUUUU----UUUUAG
.....-..((.((((((.((((....)))).......((((((....((((..(((((((......-.))))))).)))))))))))))))).)).....----...... ( -24.10)
>DroEre_CAF1 62083 102 + 1
UCUAC-AAUGUGACGAUAAAUGAUUUCGUUAAUGUCAGCACAAAAUAAGUUGGCCUAAAGUCCAAGUCCAUUGGGAAACUUUUUGCUUCGUUUCAGUUU-------UUAG
....(-((((.(((....((((....))))...((((((.........))))))...........)))))))).(((((..........))))).....-------.... ( -18.20)
>DroYak_CAF1 71634 102 + 1
UCUAC-AAUGUGACGAAAAAUGAUUUCGUUAAUGUCAGCAGAAAAUAAGUUUGCCCAAAGUCCAAG-CCUUUGGGAAACUUUUUGCUUCGUUUCAGUUU------UUUAG
...((-(...((((((((.....)))))))).))).(((((((....(((((.(((((((......-.)))))))))))))))))))............------..... ( -25.00)
>consensus
UCUAC_AAUGUGACGAAAAAUGAUUUCGUUAAUGUCAGCAGAAAAUAAGUUGGCCCAAAGUCCAAG_CCUUUGGGAAACUUUUUGCUUCGUUUCAGUUUU____UUUUAG
........((.(((((..((((....))))......(((((((....((((..(((((((........))))))).)))))))))))))))).))............... (-19.84 = -20.28 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	10,723,486 – 10,723,594
Length	108
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	92.16
Mean single sequence MFE	-21.20
Consensus MFE	-16.40
Energy contribution	-16.84
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.64
Structure conservation index	0.77
SVM decision value	0.23
SVM RNA-class probability	0.643484
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10723486 108 - 23771897
CUAAAAAAA-AAAAAUGAAACGAAGCAAAAAGUUUCCCAAAGG-CUUGGACUUUGGGCAAACUUAUUUUCUGCUGACAUUAACGAAAUCAUUUUUUGUCACAUUUUUAGA
(((((((.(-((((((((..((.((((..(((((((((((((.-......))))))).))))))......))))........))...)))))))))......))))))). ( -24.20)
>DroSec_CAF1 57438 108 - 1
CUAAAAAAAAAAAACUGAAACGAAGCAAAAAGUUUCCCAAAGG-CUUGGACUUUGGGCCAACUUAUUUUCUGCUGACAUUAACGAAAUCAUUUUUCGUCACAUU-GUAGA
.............................(((((.(((((((.-......)))))))..)))))....(((((........((((((.....))))))......-))))) ( -20.84)
>DroSim_CAF1 59603 104 - 1
CUAAAA----AAAACUGAAACGAAGCAAAAAGUUUCCCAAAGG-CUUGGACUUUGGGCCAACUUAUUUUCUGCUGGCAUUAACGAAAUCAUUUUUCGUCACAUU-GUAGA
......----...................(((((.(((((((.-......)))))))..)))))....(((((........((((((.....))))))......-))))) ( -20.84)
>DroEre_CAF1 62083 102 - 1
CUAA-------AAACUGAAACGAAGCAAAAAGUUUCCCAAUGGACUUGGACUUUAGGCCAACUUAUUUUGUGCUGACAUUAACGAAAUCAUUUAUCGUCACAUU-GUAGA
....-------...(((....(((((.....))))).((((((((((((.(.....)))))...(((((((..........)))))))........))).))))-)))). ( -16.80)
>DroYak_CAF1 71634 102 - 1
CUAAA------AAACUGAAACGAAGCAAAAAGUUUCCCAAAGG-CUUGGACUUUGGGCAAACUUAUUUUCUGCUGACAUUAACGAAAUCAUUUUUCGUCACAUU-GUAGA
.....------..................(((((((((((((.-......))))))).))))))....(((((........((((((.....))))))......-))))) ( -23.34)
>consensus
CUAAAA____AAAACUGAAACGAAGCAAAAAGUUUCCCAAAGG_CUUGGACUUUGGGCCAACUUAUUUUCUGCUGACAUUAACGAAAUCAUUUUUCGUCACAUU_GUAGA
(((....................((((.(((((..(((((((........))))))).......))))).)))).......((((((.....))))))........))). (-16.40 = -16.84 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:34 2006