Locus 5310

Sequence ID	X_DroMel_CAF1
Location	13,896,137 – 13,896,255
Length	118
Max. P	0.804810

overview

Window 3

Location	13,896,137 – 13,896,255
Length	118
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	93.30
Mean single sequence MFE	-32.34
Consensus MFE	-25.77
Energy contribution	-26.33
Covariance contribution	0.56
Combinations/Pair	1.06
Mean z-score	-2.34
Structure conservation index	0.80
SVM decision value	0.16
SVM RNA-class probability	0.610207
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13896137 118 + 22224390
GCAAC-CGUUUUACUUUCCUGCACUUCCCUAACCACCAUUAAUAACAAUUAAUUUGUAUUUAUGGCUGGGCAUC-CGUGGCGCACAGGGUGCCCAUCGCGAAAACGCAAUUGCACAAGUA
((((.-((((((.......(((.............((((.((((.(((.....))))))).)))).((((((((-((((...))).)))))))))..)))))))))...))))....... ( -32.21)
>DroSec_CAF1 32097 120 + 1
GGAACCCAUUUUACUUUCCUGCACUUCCCUAACCACCAUUAAUAACAAUUAAUUUGUAUUUACGGCUGGGCAUCCCGUGGCGCACAGGGUGCCCACCGCGAAAAUGCAAUUGCACAAGUA
...........(((((...((((..............((((((....))))))((((((((.(((.(((((((((.(((...))).))))))))))))...)))))))).)))).))))) ( -34.40)
>DroEre_CAF1 25181 118 + 1
GCACC-CGUUUUACUGUCCUGCACUUCCUUAACCACCAUUAAUAACAAUUAAUUUGUAUUUAUGGCUGGGCAUU-UGUGGCGCACAGGGUGCCCACCGCGAAAAUGCAAUUGCACAAGUA
.....-.....((((....((((.........(((((((.((((.(((.....))))))).)))).)))(((((-(((((.((((...)))))))).....))))))...))))..)))) ( -30.40)
>consensus
GCAAC_CGUUUUACUUUCCUGCACUUCCCUAACCACCAUUAAUAACAAUUAAUUUGUAUUUAUGGCUGGGCAUC_CGUGGCGCACAGGGUGCCCACCGCGAAAAUGCAAUUGCACAAGUA
...........(((((...((((.........(((((((.((((.(((.....))))))).)))).)))((((..(((((.((((...))))...)))))...))))...)))).))))) (-25.77 = -26.33 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	13,896,137 – 13,896,255
Length	118
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	93.30
Mean single sequence MFE	-39.23
Consensus MFE	-33.31
Energy contribution	-33.20
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-2.43
Structure conservation index	0.85
SVM decision value	0.63
SVM RNA-class probability	0.804810
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13896137 118 - 22224390
UACUUGUGCAAUUGCGUUUUCGCGAUGGGCACCCUGUGCGCCACG-GAUGCCCAGCCAUAAAUACAAAUUAAUUGUUAUUAAUGGUGGUUAGGGAAGUGCAGGAAAGUAAAACG-GUUGC
(((((((((.((((((....))))))..))))((((..(.((.(.-...(((..(((((.(((((((.....))).)))).))))))))..)))..)..)))).))))).....-..... ( -37.70)
>DroSec_CAF1 32097 120 - 1
UACUUGUGCAAUUGCAUUUUCGCGGUGGGCACCCUGUGCGCCACGGGAUGCCCAGCCGUAAAUACAAAUUAAUUGUUAUUAAUGGUGGUUAGGGAAGUGCAGGAAAGUAAAAUGGGUUCC
(((((......((((((((((((((((((((.((((((...)))))).)))))).)))).........(((((..(((....)))..)))))))))))))))..)))))........... ( -43.40)
>DroEre_CAF1 25181 118 - 1
UACUUGUGCAAUUGCAUUUUCGCGGUGGGCACCCUGUGCGCCACA-AAUGCCCAGCCAUAAAUACAAAUUAAUUGUUAUUAAUGGUGGUUAAGGAAGUGCAGGACAGUAAAACG-GGUGC
(((((((((..((((((((((((.((((((((...)))).)))).-...))(((.((((.(((((((.....))).)))).)))))))....))))))))))....))...)))-)))). ( -36.60)
>consensus
UACUUGUGCAAUUGCAUUUUCGCGGUGGGCACCCUGUGCGCCACG_GAUGCCCAGCCAUAAAUACAAAUUAAUUGUUAUUAAUGGUGGUUAGGGAAGUGCAGGAAAGUAAAACG_GUUGC
(((((((((.(((((......)))))..))))((((..(.((.......(((..(((((.(((((((.....))).)))).))))))))...))..)..)))).)))))........... (-33.31 = -33.20 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:33 2006