Locus 5889

Sequence ID	3R_DroMel_CAF1
Location	15,468,100 – 15,468,204
Length	104
Max. P	0.978413

overview

Window 7

Location	15,468,100 – 15,468,204
Length	104
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	76.87
Mean single sequence MFE	-27.33
Consensus MFE	-22.02
Energy contribution	-22.05
Covariance contribution	0.03
Combinations/Pair	1.32
Mean z-score	-3.45
Structure conservation index	0.81
SVM decision value	1.81
SVM RNA-class probability	0.978413
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15468100 104 + 27905053
CCAGAGCGCCAACUUUGGCACUGCCUAAAUUUAGCAUCUUGUUUCUGAGAAAUUCCUAAAUUUAGUCAGUUUCGCUAAAUCGCAUUCUCUCUUCUUUUUCGCUC
...((((((((....))))((((.((((((((((..((((......)))).....)))))))))).))))...((......)).................)))) ( -26.10)
>DroPse_CAF1 26261 90 + 1
----AGACGCUUCUUCGGCGCCGUCUAAAUUUAGCAUUUUGCUUAGUGGCAACUUUUAAAUUUGGCCAAUC-GGCGGAGUCUUGCU---------GCUUCCCCC
----(((((((.....)))((((.((((((((((.(..(((((....)))))..))))))))))).....)-)))...))))....---------......... ( -22.90)
>DroSec_CAF1 23604 104 + 1
CCAGAGCGCCAACUUUGGCACUGCCUAAAUUUAGCAUCUUGUUUCUGAGAAAUUCCUAAAUUUAGCCAGUUUCGCUAAAUCGCGCUCUCUCUUCUCCUUCGCUC
..(((((((....((((((((((.((((((((((..((((......)))).....)))))))))).))))...))))))..)))))))................ ( -30.80)
>DroSim_CAF1 25006 104 + 1
CCAGAGCGCCAACUUUGGCGCUGCCUAAAUUUAGCAUCUUGUUUCUGAGAAAUUCUUAAAUUUAGCCAGUUUCGCUAAAUCGCGCUCUCUCUUCUCUUCCGCUC
..(((((((....((((((((((.((((((((((..((((......)))).....)))))))))).)))...)))))))..)))))))................ ( -29.30)
>DroEre_CAF1 25269 101 + 1
CCAGAGCGUCGACUCUGGCGCUGCCUAAAUUUAGCAUCUUGUUGAUGAGAAAUUCUUAAAUUUAGCCAGUUUUGCUAAAUUGCGCUCUCUCU---CUUCCUCUC
..((((((.(((...((((((((.(((((((((.((((.....))))((.....))))))))))).))))...))))..)))))))))....---......... ( -27.20)
>DroYak_CAF1 24618 91 + 1
CCAGAGCGGCAACUUUGGCGCUGCCUAAAUUUAGCAUCUUGUUGCUGAGAAAUUCUUAAAUUUAGUCAGUUUUGCUAAAUCGCGCUCUC-------------UC
..((((((.(...((((((((((.((((((((((((......))))(((.....))))))))))).))))...))))))..))))))).-------------.. ( -27.70)
>consensus
CCAGAGCGCCAACUUUGGCGCUGCCUAAAUUUAGCAUCUUGUUUCUGAGAAAUUCUUAAAUUUAGCCAGUUUCGCUAAAUCGCGCUCUCUCU___CUUUCGCUC
..(((((((....((((((((((.((((((((((..((((......)))).....)))))))))).))))...))))))..)))))))................ (-22.02 = -22.05 +   0.03)

alignment

secondary structure

dotplot

Window 8

Location	15,468,100 – 15,468,204
Length	104
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	76.87
Mean single sequence MFE	-27.27
Consensus MFE	-16.98
Energy contribution	-17.65
Covariance contribution	0.67
Combinations/Pair	1.24
Mean z-score	-2.29
Structure conservation index	0.62
SVM decision value	1.72
SVM RNA-class probability	0.973916
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15468100 104 - 27905053
GAGCGAAAAAGAAGAGAGAAUGCGAUUUAGCGAAACUGACUAAAUUUAGGAAUUUCUCAGAAACAAGAUGCUAAAUUUAGGCAGUGCCAAAGUUGGCGCUCUGG
((((................(((......)))..((((.((((((((((.(...(((........)))).)))))))))).))))((((....))))))))... ( -27.40)
>DroPse_CAF1 26261 90 - 1
GGGGGAAGC---------AGCAAGACUCCGCC-GAUUGGCCAAAUUUAAAAGUUGCCACUAAGCAAAAUGCUAAAUUUAGACGGCGCCGAAGAAGCGUCU----
((.(((..(---------.....)..))).))-...((((..((((....))))))))...(((.....)))..........(((((.......))))).---- ( -19.60)
>DroSec_CAF1 23604 104 - 1
GAGCGAAGGAGAAGAGAGAGCGCGAUUUAGCGAAACUGGCUAAAUUUAGGAAUUUCUCAGAAACAAGAUGCUAAAUUUAGGCAGUGCCAAAGUUGGCGCUCUGG
((((................(((......)))..((((.((((((((((.(...(((........)))).)))))))))).))))((((....))))))))... ( -31.60)
>DroSim_CAF1 25006 104 - 1
GAGCGGAAGAGAAGAGAGAGCGCGAUUUAGCGAAACUGGCUAAAUUUAAGAAUUUCUCAGAAACAAGAUGCUAAAUUUAGGCAGCGCCAAAGUUGGCGCUCUGG
...(....).......((((((((((((.(((...(((.(((((((((.(....(((........)))..)))))))))).))))))..))))).))))))).. ( -30.00)
>DroEre_CAF1 25269 101 - 1
GAGAGGAAG---AGAGAGAGCGCAAUUUAGCAAAACUGGCUAAAUUUAAGAAUUUCUCAUCAACAAGAUGCUAAAUUUAGGCAGCGCCAGAGUCGACGCUCUGG
..(..((.(---(((((...(..((((((((.......))))))))...)..)))))).))..)..(.((((.......)))).).(((((((....))))))) ( -27.60)
>DroYak_CAF1 24618 91 - 1
GA-------------GAGAGCGCGAUUUAGCAAAACUGACUAAAUUUAAGAAUUUCUCAGCAACAAGAUGCUAAAUUUAGGCAGCGCCAAAGUUGCCGCUCUGG
..-------------.(((((..(((((((((...((((..(((((....))))).))))........)))))))))..((((((......))))))))))).. ( -27.40)
>consensus
GAGCGAAAG___AGAGAGAGCGCGAUUUAGCGAAACUGGCUAAAUUUAAGAAUUUCUCAGAAACAAGAUGCUAAAUUUAGGCAGCGCCAAAGUUGGCGCUCUGG
................((((((((((((.((....(((.(((((((((...(((............)))..))))))))).))).))..)))))).)))))).. (-16.98 = -17.65 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:58 2006