Locus 4018

Sequence ID	X_DroMel_CAF1
Location	10,632,141 – 10,632,238
Length	97
Max. P	0.991685

overview

Window 2

Location	10,632,141 – 10,632,238
Length	97
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	79.10
Mean single sequence MFE	-26.85
Consensus MFE	-20.53
Energy contribution	-22.97
Covariance contribution	2.44
Combinations/Pair	1.14
Mean z-score	-1.60
Structure conservation index	0.76
SVM decision value	0.36
SVM RNA-class probability	0.705435
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10632141 97 + 22224390
CAGUGACUUGGGGAUGAAAGCUGCAAAAAUACCGCAUAUCGAUAGUUGCUUU---------------------AACUGGUAUUUAUUCGGCGAUCUAUCGAUAUUCAGCUAGAUUUCG
..........(..((...((((((.........))(((((((((((((((.(---------------------((.......)))...))))).))))))))))..))))..))..). ( -21.10)
>DroSec_CAF1 13748 118 + 1
NNNNNNNNNNNNGAUGAAAGCUGCAAAAAUACCGCAUAUCGAUAGUUGCUUAGAAAAAUAAAUAUAUUUUUCAAGCUGGUAUUUAUUCGGCGAUCUAUCGAUAUUCAGCUAGAUUUUG
..................((((((.........))((((((((((...(...((((((((....))))))))..(((((.......))))))..))))))))))..))))........ ( -26.20)
>DroSim_CAF1 13833 118 + 1
CAGUGACUUGGGGAUGAAAGCUGCAAAAAUACCGCAUAUCGAUAGUUGCUUAGAAAAAUAAAUAUAUUUUUCAAGCUGGUAUUUAUUUGGCGAUCUAUCGAUAUACAGCUAGAUUUCG
..........(..((...((((((.........))((((((((((...(...((((((((....))))))))..((..(.......)..)))..))))))))))..))))..))..). ( -27.40)
>DroYak_CAF1 14468 118 + 1
CUGUGACUUGGGGAUGAAAGCUGCAAAAAUACCGCAUAUCGAUAGUUGCCUGAAGAAAUAAAUGCUUAUUUUUAACUGGUAUUUAUUUGGUGAACUAUCGAUAUUCGGCUAGAUUUCG
.(((..(((........)))..)))......(((.(((((((((((((((.....(((((((((((...........)))))))))))))).)))))))))))).))).......... ( -32.70)
>consensus
CAGUGACUUGGGGAUGAAAGCUGCAAAAAUACCGCAUAUCGAUAGUUGCUUAGAAAAAUAAAUAUAUUUUUCAAACUGGUAUUUAUUCGGCGAUCUAUCGAUAUUCAGCUAGAUUUCG
..........(((((...((((((.........))(((((((((((((((.....((((((((((.............))))))))))))))).))))))))))..))))..))))). (-20.53 = -22.97 +   2.44)

alignment

secondary structure

dotplot

Window 3

Location	10,632,141 – 10,632,238
Length	97
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	79.10
Mean single sequence MFE	-24.67
Consensus MFE	-17.24
Energy contribution	-18.05
Covariance contribution	0.81
Combinations/Pair	1.18
Mean z-score	-2.49
Structure conservation index	0.70
SVM decision value	2.28
SVM RNA-class probability	0.991685
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10632141 97 - 22224390
CGAAAUCUAGCUGAAUAUCGAUAGAUCGCCGAAUAAAUACCAGUU---------------------AAAGCAACUAUCGAUAUGCGGUAUUUUUGCAGCUUUCAUCCCCAAGUCACUG
.(((....((((..((((((((((...((..(((........)))---------------------...))..))))))))))((((.....)))))))))))............... ( -18.80)
>DroSec_CAF1 13748 118 - 1
CAAAAUCUAGCUGAAUAUCGAUAGAUCGCCGAAUAAAUACCAGCUUGAAAAAUAUAUUUAUUUUUCUAAGCAACUAUCGAUAUGCGGUAUUUUUGCAGCUUUCAUCNNNNNNNNNNNN
(((((....((((.((((((((((.((...))..........((((((((((((....)))))))).))))..)))))))))).))))..)))))....................... ( -26.40)
>DroSim_CAF1 13833 118 - 1
CGAAAUCUAGCUGUAUAUCGAUAGAUCGCCAAAUAAAUACCAGCUUGAAAAAUAUAUUUAUUUUUCUAAGCAACUAUCGAUAUGCGGUAUUUUUGCAGCUUUCAUCCCCAAGUCACUG
(((((....(((((((((((((((((......))........((((((((((((....)))))))).))))..)))))))))))))))..)))))....................... ( -29.90)
>DroYak_CAF1 14468 118 - 1
CGAAAUCUAGCCGAAUAUCGAUAGUUCACCAAAUAAAUACCAGUUAAAAAUAAGCAUUUAUUUCUUCAGGCAACUAUCGAUAUGCGGUAUUUUUGCAGCUUUCAUCCCCAAGUCACAG
.........((((.((((((((((((..((((((((((....(((.......))))))))))).....)).)))))))))))).)))).....((..((((........))))..)). ( -23.60)
>consensus
CGAAAUCUAGCUGAAUAUCGAUAGAUCGCCAAAUAAAUACCAGCUUGAAAAAUAUAUUUAUUUUUCUAAGCAACUAUCGAUAUGCGGUAUUUUUGCAGCUUUCAUCCCCAAGUCACUG
(((((....((((.((((((((((((......))........((((((((((((....)))))))).))))..)))))))))).))))..)))))....................... (-17.24 = -18.05 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:20 2006