Locus 4013

Sequence ID	X_DroMel_CAF1
Location	10,629,786 – 10,629,881
Length	95
Max. P	0.989429

overview

Window 5

Location	10,629,786 – 10,629,881
Length	95
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	83.24
Mean single sequence MFE	-35.74
Consensus MFE	-25.60
Energy contribution	-26.92
Covariance contribution	1.32
Combinations/Pair	1.14
Mean z-score	-2.93
Structure conservation index	0.72
SVM decision value	2.16
SVM RNA-class probability	0.989429
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10629786 95 + 22224390
G-----------UUCUC--UCUCUAUAUGCAUAUGCAGAGUAUGCGAAAUUCGGAGAGAGCCGAAAAAAAACUAGCGGUUGGCAACAGCACGUGUGCGAGCGAGAGAG
.-----------..(((--((((....(((....)))..(((((((...(((((......)))))............((((....)))).)))))))....))))))) ( -32.90)
>DroSec_CAF1 11395 97 + 1
G-----------UUCUCUCUCUCUAUAUGCAUAUGCAGAGUAUGCGAAAUUCGAAGAGAGCCGAAAGAAAACUAGCGGUUGGCAACAGCACGUGUGCGAGAGAGAGAG
.-----------.((((((((((....(((....)))..(((((((...((((........))))............((((....)))).))))))))))))))))). ( -36.90)
>DroSim_CAF1 11458 97 + 1
G-----------UUCUCUCUCUCUAUAUGCAUAUGCAGAGUAUGCGAAAUUCGAAGAGAGCCGAAAGAAAACUAGCGGUUGGCAACAGCACGUGUGCGAGCGAGAGAG
.-----------.((((((.(((....(((....)))..(((((((...((((........))))............((((....)))).)))))))))).)))))). ( -32.40)
>DroEre_CAF1 11199 100 + 1
GC-GCU----CGUUCCCUCCCUCUCUAUGCAUAUGCA-AGUGUGCAAAAUUCGGA--GAGCCGAGAACCAACUAGCGGUUGGCAACAGCACAUCUGCGAGCGAGAGAG
..-...----..........((((((.(((...((((-..(((((....(((((.--...)))))..(((((.....))))).....)))))..)))).))))))))) ( -34.70)
>DroYak_CAF1 12036 108 + 1
GCCGCUCUCUCUCUCUCCCCCUUUCUAUGCAAAUGCAGAGUGUGCGAAAUUCGGAGAGAGCCGACCACCAACUGGCAGUUGGCAACAGCACGUGUGCGAGCGAGAGAG
....((((((((((((((.........(((....)))((((.......)))))))))))((((((..((....))..))))))....((.((....)).))))))))) ( -41.80)
>consensus
G___________UUCUCUCUCUCUAUAUGCAUAUGCAGAGUAUGCGAAAUUCGGAGAGAGCCGAAAAAAAACUAGCGGUUGGCAACAGCACGUGUGCGAGCGAGAGAG
............(((((((.(((....(((....)))..(((((((...(((((......)))))............((((....)))).)))))))))).))))))) (-25.60 = -26.92 +   1.32)

alignment

secondary structure

dotplot

Window 6

Location	10,629,786 – 10,629,881
Length	95
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	83.24
Mean single sequence MFE	-30.40
Consensus MFE	-21.56
Energy contribution	-21.40
Covariance contribution	-0.16
Combinations/Pair	1.18
Mean z-score	-1.83
Structure conservation index	0.71
SVM decision value	0.40
SVM RNA-class probability	0.720109
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10629786 95 - 22224390
CUCUCUCGCUCGCACACGUGCUGUUGCCAACCGCUAGUUUUUUUUCGGCUCUCUCCGAAUUUCGCAUACUCUGCAUAUGCAUAUAGAGA--GAGAA-----------C
(((((((((..(((....)))....)).....((.........(((((......)))))....(((.....)))....)).....))))--)))..-----------. ( -24.10)
>DroSec_CAF1 11395 97 - 1
CUCUCUCUCUCGCACACGUGCUGUUGCCAACCGCUAGUUUUCUUUCGGCUCUCUUCGAAUUUCGCAUACUCUGCAUAUGCAUAUAGAGAGAGAGAA-----------C
.(((((((((((((....)))...(((...(((..((....))..)))...............(((.....)))....)))....)))))))))).-----------. ( -28.70)
>DroSim_CAF1 11458 97 - 1
CUCUCUCGCUCGCACACGUGCUGUUGCCAACCGCUAGUUUUCUUUCGGCUCUCUUCGAAUUUCGCAUACUCUGCAUAUGCAUAUAGAGAGAGAGAA-----------C
.((((((.((((((....)))...(((...(((..((....))..)))...............(((.....)))....)))....))).)))))).-----------. ( -24.30)
>DroEre_CAF1 11199 100 - 1
CUCUCUCGCUCGCAGAUGUGCUGUUGCCAACCGCUAGUUGGUUCUCGGCUC--UCCGAAUUUUGCACACU-UGCAUAUGCAUAGAGAGGGAGGGAACG----AGC-GC
(((((((.(((((((.(((((....((((((.....))))))..((((...--.)))).....))))).)-))).((....))))).)))))))....----...-.. ( -33.70)
>DroYak_CAF1 12036 108 - 1
CUCUCUCGCUCGCACACGUGCUGUUGCCAACUGCCAGUUGGUGGUCGGCUCUCUCCGAAUUUCGCACACUCUGCAUUUGCAUAGAAAGGGGGAGAGAGAGAGAGCGGC
(((((((((.((....)).))....(((.((..((....))..)).)))((((((((.....).....((.(((....))).))......)))))))))))))).... ( -41.20)
>consensus
CUCUCUCGCUCGCACACGUGCUGUUGCCAACCGCUAGUUUUUUUUCGGCUCUCUCCGAAUUUCGCAUACUCUGCAUAUGCAUAUAGAGAGAGAGAA___________C
.((((((.(((......((((....((.....))..........((((......)))).....))))....(((....)))....))).))))))............. (-21.56 = -21.40 +  -0.16)

alignment

secondary structure

dotplot

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