Locus 1464

Sequence ID	X_DroMel_CAF1
Location	4,402,918 – 4,403,072
Length	154
Max. P	0.824168

overview

Window 5

Location	4,402,918 – 4,403,038
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.17
Mean single sequence MFE	-30.94
Consensus MFE	-27.40
Energy contribution	-27.96
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.39
Structure conservation index	0.89
SVM decision value	0.69
SVM RNA-class probability	0.824168
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4402918 120 + 22224390
ACCCACAAAUGGCCCUUUUGGCAGAAACUUUCAUCCGCAUCGAUUCGGGGUUAUUAAUGAUCGGUCGAUCCAUUGACCCCGACAGAAAGUCAAAGAAGAAAUAGUAAUAAAACGGGUUCU
((((.......(((.....)))....(((((((((......)))(((((((((.....((((....))))...)))))))))..)))))).......................))))... ( -32.40)
>DroSec_CAF1 5528 120 + 1
ACCCACAAAUGGCCCUUUUGGCAGAAACUUUCAUCCACAUCGAUGCGGGGUUAUUAAUGAUCGGUCGAUCCAUUGACCCCGACAGAAAGCCAAAGAAGAAAUAGUAAUCAAACGGGUUCU
..........((((((((((((.........((((......))))((((((((.....((((....))))...)))))))).......)))))))........((......))))))).. ( -33.10)
>DroSim_CAF1 5611 120 + 1
ACCCACAAAUGGCCCUUUUGGCAGAAACUUUCAUCCGCAUCGAUGCGGGGUUAUUAAUGAUCGGUCGAUCCAUUGAACCCGACAGAAAGCCAAAGAAGAAAUAGUAAUCAAACGGGUUCU
..........((((((((((((.............((((....))))((((..(((((((((....))).))))))))))........)))))))........((......))))))).. ( -30.20)
>DroEre_CAF1 6277 120 + 1
ACCCACAAAGGGCCCUUUUGGCAGAAACUUUCAUCCGCAUCGAUGCGGGGUUAUUAAUGAUCGGCCGAUCCAUUGACCCCGACAGAAAGUCAAAGAAGAAAUAGUCAUAAAACGGGUUCC
.........(((((((((((...((...((((.((.(((....)))(((((((.....((((....))))...)))))))(((.....)))...)).))))...)).))))).)))))). ( -33.50)
>DroYak_CAF1 5749 120 + 1
ACACACAAUGGGCCCUUUUGGCAGAAACUUUCAUCCGCAUCGAUGCUUGGUUAUUAAUGAUCGGUCGAUCCAUUGACCCCGACAGAAAGUCAAAGAAGAAAUAGUAAUAAAACGGGUUCU
.........(((((((((((((...((((..((((......))))...))))..........((((((....))))))..........)))))))........((......)))))))). ( -25.50)
>consensus
ACCCACAAAUGGCCCUUUUGGCAGAAACUUUCAUCCGCAUCGAUGCGGGGUUAUUAAUGAUCGGUCGAUCCAUUGACCCCGACAGAAAGUCAAAGAAGAAAUAGUAAUAAAACGGGUUCU
..........((((((((((((.........((((......))))((((((((.....((((....))))...)))))))).......)))))))........((......))))))).. (-27.40 = -27.96 +   0.56)

alignment

secondary structure

dotplot

Window 6

Location	4,402,958 – 4,403,072
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.05
Mean single sequence MFE	-31.56
Consensus MFE	-23.04
Energy contribution	-23.84
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.72
Structure conservation index	0.73
SVM decision value	0.05
SVM RNA-class probability	0.560589
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4402958 114 + 22224390
CGAUUCGGGGUUAUUAAUGAUCGGUCGAUCCAUUGACCCCGACAGAAAGUCAAAGAAGAAAUAGUAAUAAAACGGGUUCUCGGAAGAAGAAAGCCCAACGAUGCUAGCCAAGCU------
((.((((((((((.....((((....))))...)))))))(((.....)))...)))................((((((((....).)))..))))..))..(((.....))).------ ( -31.20)
>DroSec_CAF1 5568 114 + 1
CGAUGCGGGGUUAUUAAUGAUCGGUCGAUCCAUUGACCCCGACAGAAAGCCAAAGAAGAAAUAGUAAUCAAACGGGUUCUCGGAAGAAGAAAGCCCAACGAUGCUGGCCAAGCU------
...((((((((((.....((((....))))...)))))))).))....((((...........((......))((((((((....).)))..))))........))))......------ ( -32.90)
>DroSim_CAF1 5651 114 + 1
CGAUGCGGGGUUAUUAAUGAUCGGUCGAUCCAUUGAACCCGACAGAAAGCCAAAGAAGAAAUAGUAAUCAAACGGGUUCUCGGAAGAAGAAAGCCCAACGAUGCUGGCCAAGCU------
....((.((((..(((((((((....))).))))))))))........((((...........((......))((((((((....).)))..))))........))))...)).------ ( -28.30)
>DroEre_CAF1 6317 116 + 1
CGAUGCGGGGUUAUUAAUGAUCGGCCGAUCCAUUGACCCCGACAGAAAGUCAAAGAAGAAAUAGUCAUAAAACGGGUUCCCGGAA---GAAAGCCCAAAGAUGCUAGCCAAGCUGG-GAU
.(((..(((((((.....((((....))))...)))))))(((.....)))............))).......(((((..(....---)..)))))....((.(((((...)))))-.)) ( -34.40)
>DroYak_CAF1 5789 117 + 1
CGAUGCUUGGUUAUUAAUGAUCGGUCGAUCCAUUGACCCCGACAGAAAGUCAAAGAAGAAAUAGUAAUAAAACGGGUUCUCCAAA---GAAAGCCCAAUGGUGCUAGCCAAGCUGGAGAU
....(((((((((.........((((((....))))))(((((.....)))......................(((((.((....---)).)))))...))...)))))))))....... ( -31.00)
>consensus
CGAUGCGGGGUUAUUAAUGAUCGGUCGAUCCAUUGACCCCGACAGAAAGUCAAAGAAGAAAUAGUAAUAAAACGGGUUCUCGGAAGAAGAAAGCCCAACGAUGCUAGCCAAGCU______
.....((((((((.....((((....))))...))))))))................................(((((.((.......)).)))))......(((.....)))....... (-23.04 = -23.84 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:03 2006