Locus 8394

Sequence ID	3R_DroMel_CAF1
Location	22,362,305 – 22,362,425
Length	120
Max. P	0.854333

overview

Window 0

Location	22,362,305 – 22,362,425
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.58
Mean single sequence MFE	-33.90
Consensus MFE	-31.31
Energy contribution	-31.50
Covariance contribution	0.19
Combinations/Pair	1.06
Mean z-score	-1.41
Structure conservation index	0.92
SVM decision value	0.05
SVM RNA-class probability	0.560329
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22362305 120 + 27905053
GUGGCCCCUGUAACUACAGUAAAUACUCGUGCAAAUAACGCGUCAAAGCGUGCGAAAAACGCAGGGAGAACGCCAGCUAGCGCCUUCUCUUUCACUUUUUCGCUGAUUCCUCGCCGCCUU
(((((..((((....)))).......((.........((((......))))((((((((...(((((((((((......)))..))))))))...)))))))).))......)))))... ( -33.80)
>DroSim_CAF1 73997 120 + 1
GUGGCUCCUGUAACUACAGUAAAUACUCGUGCGAAUAACGCGUCAAAGCGUGCGAAAAACGCAAGGAGAACGCCAGAUAGCGCCCUCUCUUUCACUUUUUCGCUGAUUCCUCGCCGCCUU
(((((..((((....)))).........(.(.((((.((((......))))((((((((...(((((((.(((......)))...)))))))...))))))))..))))).))))))... ( -36.10)
>DroEre_CAF1 72815 117 + 1
GUGGCCCCUGUAA---CAGUAAAUACUCGUGCGAAUAACGCGUCAAAGCGUGCGAAAAACGCAAGGAGAACACCAGAUAGCGCCCUCUCUUUCACUUUUUCGCUUACUCCUUGCCGCCUU
(((((...((((.---.(((....)))..))))....((((......))))((((((((...(((((((................)))))))...)))))))).........)))))... ( -28.09)
>DroYak_CAF1 72341 120 + 1
GCGGCCCCUGUAACUACAGUAAAUACUCGUGCGAAUAACGCGUCAAAGCGUGCGAAAAACGCAAGGAGAACGCCAGAUAGCGCCCUCUCUUUCACUUUUUCGCUGAUUCCUCGCCGCCUU
(((((..((((....)))).........(.(.((((.((((......))))((((((((...(((((((.(((......)))...)))))))...))))))))..))))).))))))... ( -37.60)
>consensus
GUGGCCCCUGUAACUACAGUAAAUACUCGUGCGAAUAACGCGUCAAAGCGUGCGAAAAACGCAAGGAGAACGCCAGAUAGCGCCCUCUCUUUCACUUUUUCGCUGAUUCCUCGCCGCCUU
..(((..(((......))).........(.((((...((((......))))((((((((...(((((((.(((......)))...)))))))...)))))))).......)))))))).. (-31.31 = -31.50 +   0.19)

alignment

secondary structure

dotplot

Window 1

Location	22,362,305 – 22,362,425
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.58
Mean single sequence MFE	-41.98
Consensus MFE	-39.94
Energy contribution	-40.62
Covariance contribution	0.69
Combinations/Pair	1.05
Mean z-score	-1.69
Structure conservation index	0.95
SVM decision value	0.80
SVM RNA-class probability	0.854333
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22362305 120 - 27905053
AAGGCGGCGAGGAAUCAGCGAAAAAGUGAAAGAGAAGGCGCUAGCUGGCGUUCUCCCUGCGUUUUUCGCACGCUUUGACGCGUUAUUUGCACGAGUAUUUACUGUAGUUACAGGGGCCAC
..(((.(((((......(((..((((((..((.((..(((((....)))))..)).))(((.....))).))))))..)))....)))))...........((((....))))..))).. ( -38.30)
>DroSim_CAF1 73997 120 - 1
AAGGCGGCGAGGAAUCAGCGAAAAAGUGAAAGAGAGGGCGCUAUCUGGCGUUCUCCUUGCGUUUUUCGCACGCUUUGACGCGUUAUUCGCACGAGUAUUUACUGUAGUUACAGGAGCCAC
..(((.(((((......((((((((.((.(((.(((((((((....)))))))))))).))))))))))((((......))))..)))))...........((((....))))..))).. ( -45.30)
>DroEre_CAF1 72815 117 - 1
AAGGCGGCAAGGAGUAAGCGAAAAAGUGAAAGAGAGGGCGCUAUCUGGUGUUCUCCUUGCGUUUUUCGCACGCUUUGACGCGUUAUUCGCACGAGUAUUUACUG---UUACAGGGGCCAC
..(((.((...(((((((((..((((((.(((.(((((((((....))))))))))))(((.....))).))))))..))).))))))))....(((.......---.)))....))).. ( -39.20)
>DroYak_CAF1 72341 120 - 1
AAGGCGGCGAGGAAUCAGCGAAAAAGUGAAAGAGAGGGCGCUAUCUGGCGUUCUCCUUGCGUUUUUCGCACGCUUUGACGCGUUAUUCGCACGAGUAUUUACUGUAGUUACAGGGGCCGC
..(((.(((((......((((((((.((.(((.(((((((((....)))))))))))).))))))))))((((......))))..)))))...........((((....))))..))).. ( -45.10)
>consensus
AAGGCGGCGAGGAAUCAGCGAAAAAGUGAAAGAGAGGGCGCUAUCUGGCGUUCUCCUUGCGUUUUUCGCACGCUUUGACGCGUUAUUCGCACGAGUAUUUACUGUAGUUACAGGGGCCAC
..(((.(((((......((((((((.((.(((.(((((((((....)))))))))))).))))))))))((((......))))..)))))...........((((....))))..))).. (-39.94 = -40.62 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:28 2006