Locus 6280

Sequence ID	X_DroMel_CAF1
Location	15,948,561 – 15,948,678
Length	117
Max. P	0.927681

overview

Window 1

Location	15,948,561 – 15,948,678
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.05
Mean single sequence MFE	-37.52
Consensus MFE	-28.23
Energy contribution	-31.85
Covariance contribution	3.62
Combinations/Pair	1.02
Mean z-score	-2.02
Structure conservation index	0.75
SVM decision value	0.83
SVM RNA-class probability	0.860567
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15948561 117 + 22224390
GGCAAAAUUGACCCACGGCAGAGGCGAUUCUCGGGGCAGAAG---UGUAUUGCCUUGGGGCGGAAAUCUACCUUUGCCGGGUCAAAGAAUCGGAAAUUGGAGAUCAUUUAAAUCGAUUAU
.......(((((((..((((((((.((((((((((((((...---....))))))))))).....)))..)))))))))))))))..((((((...(((((.....))))).)))))).. ( -40.50)
>DroSec_CAF1 16979 120 + 1
GGCAAAAUUGACCCACGGCAGAGGCGAUUCGCGGGGCAGAAGAUGAGUAUUGCCUUGGGGCGGAAAUCUACCUUUGCCGGGUCAAAGAAUCGGAAAUUUGAGAUCAUUUAAAUCGAUUAU
.......(((((((..((((((((.((((((((((((((..........)))))))...)))))..))..)))))))))))))))..((((((.....((....))......)))))).. ( -38.10)
>DroSim_CAF1 11477 120 + 1
GGCAAAAUUGACCCACGGCAGAGGCGAUUCUCGCGGCAGAAGAUGAGUAUUGCCUUGGGGCGGAAAUCUACCUUUGCCGGGUCAAAGAAUCGGAAAUUGGAGAUCAUUUAAAUCGAUUAU
.......(((((((..((((((((.((((..((((((((..........))))).....)))..))))..)))))))))))))))..((((((...(((((.....))))).)))))).. ( -39.60)
>DroEre_CAF1 16044 103 + 1
-GCCAGAUUGACCCGCGGCAGAGGCGAUUCCCGGGGCAAAA----------------GGGCGGAAAUCUCGCUUUGCCGGGUCAAGAAAUCGCAAAUUGCAGAUCACUUAAAUCGAUUAU
-....(((((((((..((((((((.((((.(((........----------------...))).)))).).))))))))))))(((..(((((.....)).)))..))).))))...... ( -31.90)
>consensus
GGCAAAAUUGACCCACGGCAGAGGCGAUUCUCGGGGCAGAAG___AGUAUUGCCUUGGGGCGGAAAUCUACCUUUGCCGGGUCAAAGAAUCGGAAAUUGGAGAUCAUUUAAAUCGAUUAU
.......(((((((..((((((((.((((((((((((((..........))))))))))).....)))..)))))))))))))))..((((((...(((((.....))))).)))))).. (-28.23 = -31.85 +   3.62)

alignment

secondary structure

dotplot

Window 2

Location	15,948,561 – 15,948,678
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.05
Mean single sequence MFE	-32.92
Consensus MFE	-25.36
Energy contribution	-26.67
Covariance contribution	1.31
Combinations/Pair	1.03
Mean z-score	-2.23
Structure conservation index	0.77
SVM decision value	1.18
SVM RNA-class probability	0.927681
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15948561 117 - 22224390
AUAAUCGAUUUAAAUGAUCUCCAAUUUCCGAUUCUUUGACCCGGCAAAGGUAGAUUUCCGCCCCAAGGCAAUACA---CUUCUGCCCCGAGAAUCGCCUCUGCCGUGGGUCAAUUUUGCC
......((((.....)))).........(((....(((((((((((.((((.((((..((......((((.....---....)))).))..)))))))).))))..)))))))..))).. ( -31.90)
>DroSec_CAF1 16979 120 - 1
AUAAUCGAUUUAAAUGAUCUCAAAUUUCCGAUUCUUUGACCCGGCAAAGGUAGAUUUCCGCCCCAAGGCAAUACUCAUCUUCUGCCCCGCGAAUCGCCUCUGCCGUGGGUCAAUUUUGCC
......((((.....)))).........(((....(((((((((((.((((.((((..(((.....((((............))))..))))))))))).))))..)))))))..))).. ( -31.70)
>DroSim_CAF1 11477 120 - 1
AUAAUCGAUUUAAAUGAUCUCCAAUUUCCGAUUCUUUGACCCGGCAAAGGUAGAUUUCCGCCCCAAGGCAAUACUCAUCUUCUGCCGCGAGAAUCGCCUCUGCCGUGGGUCAAUUUUGCC
......((((.....)))).........(((....(((((((((((.((((.((((..(((.....((((............)))))))..)))))))).))))..)))))))..))).. ( -35.70)
>DroEre_CAF1 16044 103 - 1
AUAAUCGAUUUAAGUGAUCUGCAAUUUGCGAUUUCUUGACCCGGCAAAGCGAGAUUUCCGCCC----------------UUUUGCCCCGGGAAUCGCCUCUGCCGCGGGUCAAUCUGGC-
......((((.(((.((((.((.....)))))).)))(((((((((.((.(.((((((((...----------------........)))))))).))).))))..)))))))))....- ( -32.40)
>consensus
AUAAUCGAUUUAAAUGAUCUCCAAUUUCCGAUUCUUUGACCCGGCAAAGGUAGAUUUCCGCCCCAAGGCAAUACU___CUUCUGCCCCGAGAAUCGCCUCUGCCGUGGGUCAAUUUUGCC
..(((((....((((........)))).)))))..(((((((((((.((((.(((((.((......((((............)))).)).))))))))).))))..)))))))....... (-25.36 = -26.67 +   1.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:25 2006