Locus 2455

Sequence ID	3L_DroMel_CAF1
Location	6,942,489 – 6,942,649
Length	160
Max. P	0.999264

overview

Window 4

Location	6,942,489 – 6,942,609
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.83
Mean single sequence MFE	-40.06
Consensus MFE	-34.13
Energy contribution	-34.45
Covariance contribution	0.32
Combinations/Pair	1.09
Mean z-score	-1.57
Structure conservation index	0.85
SVM decision value	0.95
SVM RNA-class probability	0.888354
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6942489 120 - 23771897
CCUAAAAGCCCUCAGGGAACUGGACAGCAAAGUGUUCCACGUUCCACCGCAUGUGCUGCAUCCGGAGCACAUGUUCGUCGAGAAUCAGUAUACCAGCGAAGAGGAGGAGCAGAAGACAGC
.......((((((..(((((((((((......)).)))).)))))..((((((((((.(....).)))))))((((.....))))..........))).....)))).)).......... ( -37.60)
>DroSec_CAF1 11943 120 - 1
CCUGAAAGCCCUCAGGCAACUGGACAGCAAAGUAUUCCACGUUCCACCGCAUGUGCUGCAUCCGGAGCACAUGUUCUUCGAGAAUCAGUAUACCAGCGAGGAGGAGGAGCAGAAAACAGC
.(((...((..((((....))))...))............(((((.(((((((((((.(....).)))))))))((((((................)))))))).)))))......))). ( -39.29)
>DroSim_CAF1 12634 120 - 1
CCUAAAAGCCCUCAGGCAACUGGACAGCAAAGUGUUCCACGUUCCACCGCAUGUGCUGCAUCCGGAGCACAUGUUCUUCGAGAAUCAGUAUACCAGCGAGGAGGAGGAGCAGAAGACAGC
.......((..((((....))))...))...((.(((...(((((.(((((((((((.(....).)))))))))((((((................)))))))).))))).))).))... ( -40.49)
>DroEre_CAF1 12446 120 - 1
CCUAAAAGCCCUGAGGGAACUGGACAGGAAGGUGUUCCACGUUCCAUCGCAUGUGCUGCAUCCGGAGCACAUGUUCUUCGCAAAUCAGUUUACCAGCGAGGAGGAGGAGCAGAAAGUAGC
.......(((((((.(((((((((((......)).)))).))))).))(((((((((.(....).)))))))))(((((((..............)))))))..))).)).......... ( -41.84)
>DroYak_CAF1 12321 120 - 1
CCUAAAAGCUCUGAGGGAACUGGACAGCCGGGUGUUCCACGUUCCACCGCAUGUGCUGCAUCCGGAGCACAUGUUCUUCGAAAAUCAGUACACCAGCGAGGAGGAGGAGCAGAAGACAGC
..........(((.((((.((((....))))...))))..(((((.(((((((((((.(....).)))))))))((((((................)))))))).)))))......))). ( -41.09)
>consensus
CCUAAAAGCCCUCAGGGAACUGGACAGCAAAGUGUUCCACGUUCCACCGCAUGUGCUGCAUCCGGAGCACAUGUUCUUCGAGAAUCAGUAUACCAGCGAGGAGGAGGAGCAGAAGACAGC
.......((..((((....))))...))...((.(((...(((((.(((((((((((.(....).)))))))))((((((................)))))))).))))).))).))... (-34.13 = -34.45 +   0.32)

alignment

secondary structure

dotplot

Window 5

Location	6,942,529 – 6,942,649
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.67
Mean single sequence MFE	-49.60
Consensus MFE	-42.92
Energy contribution	-44.00
Covariance contribution	1.08
Combinations/Pair	1.05
Mean z-score	-2.64
Structure conservation index	0.87
SVM decision value	3.47
SVM RNA-class probability	0.999264
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6942529 120 - 23771897
AGACCGUUGAGCGUCGUUUCCAGGCAUCCGCCUCCAAGGGCCUAAAAGCCCUCAGGGAACUGGACAGCAAAGUGUUCCACGUUCCACCGCAUGUGCUGCAUCCGGAGCACAUGUUCGUCG
.(((.((.((((((.((((((((((....))))...(((((......)))))..)))))).(((((......))))).)))))).)).(((((((((.(....).)))))))))..))). ( -47.90)
>DroSec_CAF1 11983 120 - 1
AGAACGUGGAGCGUCGUUUCCAGGCAUCCGCCUCCAAGGGCCUGAAAGCCCUCAGGCAACUGGACAGCAAAGUAUUCCACGUUCCACCGCAUGUGCUGCAUCCGGAGCACAUGUUCUUCG
.(((((((((((...((((((((......((((...(((((......))))).))))..))))).)))...))..)))))))))....(((((((((.(....).)))))))))...... ( -50.40)
>DroSim_CAF1 12674 120 - 1
AGACCGUGGAGCGUCGUUUCGAGGCAUCCGCCUCCAAGGGCCUAAAAGCCCUCAGGCAACUGGACAGCAAAGUGUUCCACGUUCCACCGCAUGUGCUGCAUCCGGAGCACAUGUUCUUCG
.((.(((((((((((.....(((((....)))))..(((((......)))))(((....)))))).((...)))))))))).))....(((((((((.(....).)))))))))...... ( -50.60)
>DroEre_CAF1 12486 120 - 1
AAAACGUGGAGCGUCGGUUCCAGGCCGCCGCCGGCAAAGGCCUAAAAGCCCUGAGGGAACUGGACAGGAAGGUGUUCCACGUUCCAUCGCAUGUGCUGCAUCCGGAGCACAUGUUCUUCG
.....((((((((((((((((..((((....))))...(((......))).....)))))))....((((....))))))))))))).(((((((((.(....).)))))))))...... ( -49.60)
>DroYak_CAF1 12361 120 - 1
AAACCGUGGAGCGUCGUUUCCAGGCCGCCGCCUGCAAGGGCCUAAAAGCUCUGAGGGAACUGGACAGCCGGGUGUUCCACGUUCCACCGCAUGUGCUGCAUCCGGAGCACAUGUUCUUCG
.....(((((((((......(((((....)))))..(((((......)))))..((((.((((....))))...))))))))))))).(((((((((.(....).)))))))))...... ( -49.50)
>consensus
AGACCGUGGAGCGUCGUUUCCAGGCAUCCGCCUCCAAGGGCCUAAAAGCCCUCAGGGAACUGGACAGCAAAGUGUUCCACGUUCCACCGCAUGUGCUGCAUCCGGAGCACAUGUUCUUCG
.....(((((((((.((((((.(((....)))....(((((......)))))..)))))).(((((......))))).))))))))).(((((((((.(....).)))))))))...... (-42.92 = -44.00 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:42 2006