Locus 5025

Sequence ID	2R_DroMel_CAF1
Location	16,326,953 – 16,327,073
Length	120
Max. P	0.701772

overview

Window 8

Location	16,326,953 – 16,327,073
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.36
Mean single sequence MFE	-30.51
Consensus MFE	-25.65
Energy contribution	-25.77
Covariance contribution	0.12
Combinations/Pair	1.07
Mean z-score	-1.71
Structure conservation index	0.84
SVM decision value	0.03
SVM RNA-class probability	0.549031
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16326953 120 + 20766785
UAGCGAGCACAUUUCAAAAACAUAAACGCACAAAAUGUGUCAACCGGAAUAUGCUCGCUGUGUAAACAGGGCCGAGGCGGCCACAUGCGGAAAUCACUAAAGGCACUUCCUGCACCACCA
.((((((((.(((((....(((((...........))))).....))))).))))))))(((((..((.(((((...)))))...)).((((....(....)....)))))))))..... ( -33.40)
>DroSec_CAF1 30128 117 + 1
UAGCGAGCACAUUUCAAAAACAUAAACGCACAAAAUGUGUCAACCGCAAUAUGCUCGCUGUGUAAACAGGGCCGAGGCGGCCACAUGCGGAAAUCACUAAAGGCACUUCCUGCAC---CA
(((.((((((((((..................))))))))...(((((.........((((....))))(((((...)))))...)))))...)).)))...(((.....)))..---.. ( -29.97)
>DroSim_CAF1 30612 117 + 1
UAGCGAGCACAUUUCAAAAACAUAAACGCACAAAAUGUGUCAACCGCAAUAUGCUCGCUGUGUAAACAGGGCCGAGGCGGCCACAUGCGGAAAUCACUAAAGGCACUUCCUGCAC---CA
(((.((((((((((..................))))))))...(((((.........((((....))))(((((...)))))...)))))...)).)))...(((.....)))..---.. ( -29.97)
>DroAna_CAF1 30880 117 + 1
AAGCGAACACAUUUCAAAAGCAUAAACGCACAAAAUGUGUCAACCGCAAUAUGCUCGCUGUGUAAACAGGACCGAGUUGGCCGCAUGCGGAAAUCACUAAAGGCACUUCCUGCAC---CA
.(((((((((((((.....((......))...)))))))).....((.....)))))))(((((...((..((.(((.(.(((....)))...).)))...))..))...)))))---.. ( -28.70)
>consensus
UAGCGAGCACAUUUCAAAAACAUAAACGCACAAAAUGUGUCAACCGCAAUAUGCUCGCUGUGUAAACAGGGCCGAGGCGGCCACAUGCGGAAAUCACUAAAGGCACUUCCUGCAC___CA
..((((((((((((..................))))))))...(((((.........((((....))))(((((...)))))...)))))...)).....(((.....)))))....... (-25.65 = -25.77 +   0.12)

alignment

secondary structure

dotplot

Window 9

Location	16,326,953 – 16,327,073
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.36
Mean single sequence MFE	-38.10
Consensus MFE	-36.00
Energy contribution	-35.75
Covariance contribution	-0.25
Combinations/Pair	1.08
Mean z-score	-1.55
Structure conservation index	0.94
SVM decision value	0.35
SVM RNA-class probability	0.701772
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16326953 120 - 20766785
UGGUGGUGCAGGAAGUGCCUUUAGUGAUUUCCGCAUGUGGCCGCCUCGGCCCUGUUUACACAGCGAGCAUAUUCCGGUUGACACAUUUUGUGCGUUUAUGUUUUUGAAAUGUGCUCGCUA
..(((((((.((((((..(....)..))))))))))..(((((...))))).......)))((((((((((((.(((..(((.(((...))).))).......))).)))))))))))). ( -40.60)
>DroSec_CAF1 30128 117 - 1
UG---GUGCAGGAAGUGCCUUUAGUGAUUUCCGCAUGUGGCCGCCUCGGCCCUGUUUACACAGCGAGCAUAUUGCGGUUGACACAUUUUGUGCGUUUAUGUUUUUGAAAUGUGCUCGCUA
..---((((.((((((..(....)..))))))))))..(((((...)))))..........(((((((((((((((...(((.(((...))).)))..)))......)))))))))))). ( -38.10)
>DroSim_CAF1 30612 117 - 1
UG---GUGCAGGAAGUGCCUUUAGUGAUUUCCGCAUGUGGCCGCCUCGGCCCUGUUUACACAGCGAGCAUAUUGCGGUUGACACAUUUUGUGCGUUUAUGUUUUUGAAAUGUGCUCGCUA
..---((((.((((((..(....)..))))))))))..(((((...)))))..........(((((((((((((((...(((.(((...))).)))..)))......)))))))))))). ( -38.10)
>DroAna_CAF1 30880 117 - 1
UG---GUGCAGGAAGUGCCUUUAGUGAUUUCCGCAUGCGGCCAACUCGGUCCUGUUUACACAGCGAGCAUAUUGCGGUUGACACAUUUUGUGCGUUUAUGCUUUUGAAAUGUGUUCGCUU
.(---(..(.....)..))...(((((...((((((((((((.....))))((((....))))...)))...)))))...((((((((((.(((....)))...))))))))))))))). ( -35.60)
>consensus
UG___GUGCAGGAAGUGCCUUUAGUGAUUUCCGCAUGUGGCCGCCUCGGCCCUGUUUACACAGCGAGCAUAUUGCGGUUGACACAUUUUGUGCGUUUAUGUUUUUGAAAUGUGCUCGCUA
.....((((.((((((..(....)..))))))))))..((((.....))))..........(((((((((((((((...(((.(((...))).)))..)))......)))))))))))). (-36.00 = -35.75 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:42 2006