Locus 5588

Sequence ID	2R_DroMel_CAF1
Location	17,859,212 – 17,859,433
Length	221
Max. P	0.919104

overview

Window 5

Location	17,859,212 – 17,859,313
Length	101
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	93.53
Mean single sequence MFE	-26.16
Consensus MFE	-20.20
Energy contribution	-21.28
Covariance contribution	1.08
Combinations/Pair	1.07
Mean z-score	-2.34
Structure conservation index	0.77
SVM decision value	1.13
SVM RNA-class probability	0.919104
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17859212 101 + 20766785
UAAAUGAAUUGGCCGAACAAAUGGCCAAUAAGUUUUGGCAUAUCGAUUGAAUGUCGGCCUACAGAAUGCAUGCAAAUUAAUGCAGUAUUUUGUGCUGAGCA
..........((((((.((....(((((......)))))...((....)).))))))))((((((((((.((((......))))))))))))))....... ( -31.70)
>DroSec_CAF1 24581 100 + 1
UAAAUGAAUUGGCCGAACAAAUGGCCAAUAAGUUUUGGCAUAUCGAUUGAGAGUCGGCCUACAAAAUGCAUGCAAAUUAAUGCAGUAUU-UGUGCUGAACA
.......((((((((......))))))))..((.(..((((.(((((.....)))))......((((((.((((......)))))))))-)))))..))). ( -28.50)
>DroSim_CAF1 25268 100 + 1
CAAAUGAAUUGGCCGAACAAAUGGCCAAUAAGUUUUGGCAUAUCGAUUGAGAGUCGGCCUACAAAAUGCAUGCAAAUUAAUGCAGUAUU-UGUGCUGAGCA
.......((((((((......))))))))..((.(..((((.(((((.....)))))......((((((.((((......)))))))))-)))))..))). ( -28.50)
>DroEre_CAF1 27237 99 + 1
UAAAUGAAUUUGCCGAACAAAUGGCCAAUAAGUUUUGGCAUAUCGAUUGAAAGGCGGCCUACA-AAUGCAUGCAAAUUAAUUCAGUAUU-UGUGCUGAGCC
...........(((...(((((((((((......))))).)))...)))...)))((((((((-(((((.((.((.....)))))))))-))))..).))) ( -21.60)
>DroYak_CAF1 24884 100 + 1
UAAAUGAAUUUGCCGUACAAAUGGCCAAUAAGUUUUGGCAUAUCGAUUGAAAAUCGGCCUACAAAAUGCAUGCAAAUUAAUUCCAUAUU-UGUGCUGAGCA
..........((((((((((((((((((......)))))...(((((.....)))))............................))))-))))).).))) ( -20.50)
>consensus
UAAAUGAAUUGGCCGAACAAAUGGCCAAUAAGUUUUGGCAUAUCGAUUGAAAGUCGGCCUACAAAAUGCAUGCAAAUUAAUGCAGUAUU_UGUGCUGAGCA
.......((((((((......))))))))..((.(..((...(((((.....)))))...(((.(((((.((((......))))))))).)))))..))). (-20.20 = -21.28 +   1.08)

alignment

secondary structure

dotplot

Window 6

Location	17,859,313 – 17,859,433
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.33
Mean single sequence MFE	-33.40
Consensus MFE	-27.90
Energy contribution	-28.14
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.55
Structure conservation index	0.84
SVM decision value	0.51
SVM RNA-class probability	0.764411
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17859313 120 + 20766785
AAACCAUUCGAACCGACUUGAUUGCACAAACCACAGACCAACGAGCACACCCCAAAGUGCCAUAAUGUCAAUGCCCGCCCUAGGGCGCCACAACUCGGUGACAAUUGACAUUGGCAGUGA
....................(((((.................(.((((........))))).((((((((((((((......))))(((.......)))....))))))))))))))).. ( -31.00)
>DroSec_CAF1 24681 120 + 1
AAACCAUUCGAAGCGACUUGAUUGCACAAACCACAGACCAACGAGCACGCCCCAAAGUGCCAUAAUGUCGAUGGCCGCCCUAGGGCGCCACAACUCGGUGACAAUUGACAUUGGCAGUGA
............((((.....))))......(((.(.((...(.((((........)))))..((((((((((((.(((....)))))).......(....).)))))))))))).))). ( -34.50)
>DroSim_CAF1 25368 120 + 1
AAACCAUUCGAAGCGACUUGAUUGCACAAACCACAGACCAACGAGCACGCCCCAAAGUGCCAUAAUGUCGAUGGCCGCCCUAGGGCGCCACAACUCGGUGACAAUUGACAUUGGCAGUGA
............((((.....))))......(((.(.((...(.((((........)))))..((((((((((((.(((....)))))).......(....).)))))))))))).))). ( -34.50)
>DroEre_CAF1 27336 120 + 1
AAAUCAUUUCAAGCGACUUGAUUGCACAAACCACAGACCAACGAGCACGCCCCAAAGUGCCAUAAUGUCGAGUUCCGCCCUAGGGCGCCACAACUCGGUGACAAUUGACAUUGGCAGUGG
.(((((..((....))..))))).......((((.(.((...(.((((........)))))..(((((((((((.((((....))))....)))))(....)....))))))))).)))) ( -36.70)
>DroYak_CAF1 24984 120 + 1
AAAUCAUUUGAAGCGACUUGAUUGCACAAACCACAGACCAACGAGCACGCCCCAAAGUGCCAUAAUGUCGAUGUCCACCCCAGGGCGCCACAACUCGGUGACAAUUGACAUUGGCAGUGA
............((((.....))))......(((........(.((((........)))))....((((((((((..((....))((((.......))))......))))))))))))). ( -30.30)
>consensus
AAACCAUUCGAAGCGACUUGAUUGCACAAACCACAGACCAACGAGCACGCCCCAAAGUGCCAUAAUGUCGAUGGCCGCCCUAGGGCGCCACAACUCGGUGACAAUUGACAUUGGCAGUGA
....................(((((.................(.((((........))))).((((((((((...((((....)))).(((......)))...))))))))))))))).. (-27.90 = -28.14 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:14 2006