Locus 1299

Sequence ID	3L_DroMel_CAF1
Location	3,776,009 – 3,776,104
Length	95
Max. P	0.962194

overview

Window 3

Location	3,776,009 – 3,776,104
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	92.63
Mean single sequence MFE	-38.80
Consensus MFE	-28.80
Energy contribution	-29.64
Covariance contribution	0.84
Combinations/Pair	1.10
Mean z-score	-3.32
Structure conservation index	0.74
SVM decision value	1.54
SVM RNA-class probability	0.962194
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3776009 95 + 23771897
GCUUCAGUGUCGCCAUUUGCAUAAUGCGUGUGUGUUAGUGAGCUGCUGUGCUGGUGUUUGCAGCAUCCUUUCAGUCGCAUUGUGCACCGUGGUGC
..........((((((.(((((((((((....((..((.(((((((...((....))..))))).))))..))..)))))))))))..)))))). ( -36.80)
>DroSec_CAF1 173674 95 + 1
GCUUCAGUGUCGCCAUUUGCAUAAUGCGUGUGUGUUAGUGAGCUGCUGUGCUGGUGUUUGCAGCAUCCUUUCAGGCGCAUUGUGCACCGUGGUGC
..........((((((.((((((((((((.((....((.(((((((...((....))..))))).))))..)).))))))))))))..)))))). ( -40.70)
>DroSim_CAF1 168021 95 + 1
GCUUCAGUGUCGCCAUUUGCAUAAUGCGUGUGUGUUAGUGAGCUGCUGUGCUGGUGUUUGCAGCAUCCUUUCAGUCGCAUUGUGCACCGUGGUGC
..........((((((.(((((((((((....((..((.(((((((...((....))..))))).))))..))..)))))))))))..)))))). ( -36.80)
>DroEre_CAF1 166458 95 + 1
GCUUCAGUGUCGCCAUUUGCAUAAUGCAUGUGUGUGCGUGUGCUGGUGUGCUGGUGUUUGUAGCAGCCUUUCAGGCGCAUUGUGCACCGUGGGGC
(((((((((.(((((...(((((.(((((....)))))))))))))))))))(((((.....((.(((.....))))).....)))))..))))) ( -36.70)
>DroYak_CAF1 158262 95 + 1
GCUUCAGUGUCGCCAUUUGCAUAAUGCAAGUGUGUUAGUGUGCUGCUGCGUUGCCGUUUGCAGCAUACUUUCAGGAGCAUUGUGCACCGUGGUGC
..........((((((.((((((((((...(.((..((((((((((.(((....)))..))))))))))..)).).))))))))))..)))))). ( -43.00)
>consensus
GCUUCAGUGUCGCCAUUUGCAUAAUGCGUGUGUGUUAGUGAGCUGCUGUGCUGGUGUUUGCAGCAUCCUUUCAGGCGCAUUGUGCACCGUGGUGC
..........((((((.(((((((((((..((....((.(((((((...((....))..))))).))))..))..)))))))))))..)))))). (-28.80 = -29.64 +   0.84)

alignment

secondary structure

dotplot

Window 4

Location	3,776,009 – 3,776,104
Length	95
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	92.63
Mean single sequence MFE	-25.71
Consensus MFE	-20.50
Energy contribution	-21.18
Covariance contribution	0.68
Combinations/Pair	1.05
Mean z-score	-2.12
Structure conservation index	0.80
SVM decision value	1.37
SVM RNA-class probability	0.947392
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3776009 95 - 23771897
GCACCACGGUGCACAAUGCGACUGAAAGGAUGCUGCAAACACCAGCACAGCAGCUCACUAACACACACGCAUUAUGCAAAUGGCGACACUGAAGC
.(.(((...((((.((((((.((....))..(((((.............))))).............)))))).))))..))).).......... ( -25.12)
>DroSec_CAF1 173674 95 - 1
GCACCACGGUGCACAAUGCGCCUGAAAGGAUGCUGCAAACACCAGCACAGCAGCUCACUAACACACACGCAUUAUGCAAAUGGCGACACUGAAGC
((((....)))).((.((((((....((((.(((((.............))))))).)).........((.....))....)))).)).)).... ( -26.22)
>DroSim_CAF1 168021 95 - 1
GCACCACGGUGCACAAUGCGACUGAAAGGAUGCUGCAAACACCAGCACAGCAGCUCACUAACACACACGCAUUAUGCAAAUGGCGACACUGAAGC
.(.(((...((((.((((((.((....))..(((((.............))))).............)))))).))))..))).).......... ( -25.12)
>DroEre_CAF1 166458 95 - 1
GCCCCACGGUGCACAAUGCGCCUGAAAGGCUGCUACAAACACCAGCACACCAGCACACGCACACACAUGCAUUAUGCAAAUGGCGACACUGAAGC
(((.((.(((((.....)))))))...))).(((.((.......((......))...(((.((....(((.....)))..)))))....)).))) ( -22.40)
>DroYak_CAF1 158262 95 - 1
GCACCACGGUGCACAAUGCUCCUGAAAGUAUGCUGCAAACGGCAACGCAGCAGCACACUAACACACUUGCAUUAUGCAAAUGGCGACACUGAAGC
.(.(((...((((.(((((...((..(((.((((((...((....))..)))))).)))..)).....))))).))))..))).).......... ( -29.70)
>consensus
GCACCACGGUGCACAAUGCGCCUGAAAGGAUGCUGCAAACACCAGCACAGCAGCUCACUAACACACACGCAUUAUGCAAAUGGCGACACUGAAGC
.(.(((...((((.((((((.((....))..(((((.............))))).............)))))).))))..))).).......... (-20.50 = -21.18 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:16 2006