Locus 3998

Sequence ID	2R_DroMel_CAF1
Location	13,224,807 – 13,225,030
Length	223
Max. P	0.968218

overview

Window 3

Location	13,224,807 – 13,224,914
Length	107
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	83.61
Mean single sequence MFE	-26.60
Consensus MFE	-20.95
Energy contribution	-22.40
Covariance contribution	1.45
Combinations/Pair	1.10
Mean z-score	-2.06
Structure conservation index	0.79
SVM decision value	0.70
SVM RNA-class probability	0.827319
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13224807 107 - 20766785
GUUUGCAGCACUAUAACGGCAGUCUCAUAGGAUUUAUUUGAAAUGGAGUGUGUAUUUCAAAUACUUAUU-------------AUUACUUGCUUUCUGAGUGUAUAAUAUUGCAAAUAUAU
((((((((((((.....((((((...(((((...(((((((((((.......)))))))))))))))).-------------...)).)))).....))))).......))))))).... ( -23.91)
>DroSec_CAF1 5421 120 - 1
GUUUGCAGCAUUAUAACGGCAGUCUGUUAAGAUUUAUUUGAAAUGGAGUGUGUAUUUCAAAUAGAUUUCGAACUCAAAGGAACUUAUGUAUUUUCUGAGUGCAUAAUAUUGUAAAUAUAU
((((((((.((((((((((....))))))((((((((((((((((.......)))))))))))))))).(.(((((.((((((....)).)))).))))).).)))).)))))))).... ( -27.90)
>DroSim_CAF1 6359 120 - 1
GUUUGCAGCAUUGUAACGGCAGUCUGUUAAGAUUUAUUUGAAAUGGAGUGUGUAUUUCAAAUAGAUUUCGAACUCAAAAGAACUUAUGUAUUUUCUGAGUGCAUAAUAUUGUAAAUAUAU
((((((((.((((((((((....))))).((((((((((((((((.......)))))))))))))))).(.(((((.((((((....)).)))).))))).)))))).)))))))).... ( -28.00)
>consensus
GUUUGCAGCAUUAUAACGGCAGUCUGUUAAGAUUUAUUUGAAAUGGAGUGUGUAUUUCAAAUAGAUUUCGAACUCAAA_GAACUUAUGUAUUUUCUGAGUGCAUAAUAUUGUAAAUAUAU
((((((((.....((((((....))))))((((((((((((((((.......))))))))))))))))...............((((((((((...))))))))))..)))))))).... (-20.95 = -22.40 +   1.45)

alignment

secondary structure

dotplot

Window 4

Location	13,224,914 – 13,225,030
Length	116
Sequences	3
Columns	116
Reading direction	forward
Mean pairwise identity	82.76
Mean single sequence MFE	-23.10
Consensus MFE	-18.04
Energy contribution	-18.27
Covariance contribution	0.23
Combinations/Pair	1.10
Mean z-score	-2.63
Structure conservation index	0.78
SVM decision value	1.62
SVM RNA-class probability	0.968218
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13224914 116 + 20766785
AUUUAUAUUAAGCAUCCACCCACAGUUUUUGAAUCAUGUAAAAUGUUAAAAGCAACACGGCGUAUGCGUGAUACACUUUACAGCCACCAAUUGGCAGUCGUAUUAAUGCCAAAUAC
.....((((..((((.........((((((((..(((.....)))))))))))...(((((......((((......)))).((((.....)))).)))))....))))..)))). ( -23.20)
>DroSec_CAF1 5541 94 + 1
AUUUAUAUUA----------------------UACAUGUAAAAUGUAAAAAACAACACGGCGUAUGCGUGAUAAAUUUUACAGCCACCAAUUGGCAGUCGCAUUAAAGCCAAAUAC
.((((((((.----------------------((....)).)))))))).........(((..((((((((......)))).((((.....))))....))))....)))...... ( -21.90)
>DroSim_CAF1 6479 116 + 1
AUUUAUAUUAAGCAUCCACCCACAGUUUUUGAAACAUGUAAAAUGUAAAAAACAACACGGCGUAUGCGUGAUAAAUUUUACAGCCACCAAUUGGCAGUCGCAUUAAAGCCAAAUAC
........................((((((...((((.....)))).)))))).....(((..((((((((......)))).((((.....))))....))))....)))...... ( -24.20)
>consensus
AUUUAUAUUAAGCAUCCACCCACAGUUUUUGAAACAUGUAAAAUGUAAAAAACAACACGGCGUAUGCGUGAUAAAUUUUACAGCCACCAAUUGGCAGUCGCAUUAAAGCCAAAUAC
................................(((((.....)))))...........(((..((((((((......)))).((((.....))))....))))....)))...... (-18.04 = -18.27 +   0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:19 2006