Locus 3390

Sequence ID	2R_DroMel_CAF1
Location	11,456,218 – 11,456,329
Length	111
Max. P	0.695591

overview

Window 1

Location	11,456,218 – 11,456,329
Length	111
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	81.98
Mean single sequence MFE	-37.41
Consensus MFE	-25.39
Energy contribution	-26.95
Covariance contribution	1.56
Combinations/Pair	1.33
Mean z-score	-1.86
Structure conservation index	0.68
SVM decision value	0.34
SVM RNA-class probability	0.695591
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11456218 111 + 20766785
ACCUGGUACGGAAAGUCAGCGAUGUCCGCCUGAUCGCCACCAACAAUGUGGGUGCUUAUGGAGGCGGAAUCCGUGAGAAUUACCACACCAAGUGCAGCCAAAAGAAACAAA
.....((((((...(((((((.....)).)))))..))........(((((...((((((((.......)))))))).....)))))....))))................ ( -31.00)
>DroVir_CAF1 14690 111 + 1
ACCUGAUACGGAUAGUUCACAAUAUCCGUCUCGAUGCCGCCCACAAUGUGGGUGCUAAUGGAGGCGCCACUGUUCAAGGCCGUUAGCGAAAGCAGGCCCAAAACUAUUAAU
...(((.(((((((........)))))(((((.((..(((((((...)))))))...)).)))))......))))).((((....((....)).))))............. ( -38.50)
>DroSec_CAF1 6358 111 + 1
ACCUGGUACGGAUAGUCAGCGAUGUCCGCCUGAUCGCCACCAACAAUGUGGGUGCUUAUGGAGGCGGAAUCCGUGGGGAUUACCACACCAAGUGCAGCCAAAAGACACAAA
...((((..((.(((((.(((...(((((((((.((((..((....))..)))).))....)))))))...)))...)))))))..)))).((((........).)))... ( -33.10)
>DroSim_CAF1 6356 111 + 1
ACCUGGUACGGAUAGUCAGCGAUGUCCGCCUGAUCGCCACCCACAAUGUGGGUGCUUAUGGAGGCGGAAUCCGUGGGGAUUACCACACCAAGUGCAGCCAAAAGACACAAA
...((((..((.(((((.(((...(((((((......(((((((...))))))).......)))))))...)))...)))))))..)))).((((........).)))... ( -39.22)
>DroEre_CAF1 6253 111 + 1
ACCUGGUACGGAUACUCGGCGAUGUCCGCCUGAUCGCCACCCACAAUGUGGGUGCUUAUGGAGGCGGAAUCCGAGAGGAUAACCAGGCCAAGUAGACCCAAAAGACAUAAG
...(((...(..((((.(((....(((((((......(((((((...))))))).......)))))))((((....))))......))).))))..))))........... ( -40.82)
>DroYak_CAF1 6348 111 + 1
ACCUGGUACGGAUAGUCGGCGAUGUCCGCCUGAUCGCCACCCACAAUGUGGGGGCUUAUGGAGGCGGAAUCCGUGUGGAUUACCAGGCCAAGUAGACCCAAAAAACACAAA
((.((((..((.(((((.(((...(((((((....(((.(((((...))))))))......))))))).....))).)))))))..)))).)).................. ( -41.80)
>consensus
ACCUGGUACGGAUAGUCAGCGAUGUCCGCCUGAUCGCCACCCACAAUGUGGGUGCUUAUGGAGGCGGAAUCCGUGAGGAUUACCACACCAAGUACACCCAAAAGACACAAA
((.((((..((.(((((.(((...(((((((......(((((((...))))))).......)))))))...)))...)))))))..)))).)).................. (-25.39 = -26.95 +   1.56)

alignment

secondary structure

dotplot

Window 2

Location	11,456,218 – 11,456,329
Length	111
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	81.98
Mean single sequence MFE	-38.62
Consensus MFE	-23.93
Energy contribution	-25.43
Covariance contribution	1.50
Combinations/Pair	1.14
Mean z-score	-1.70
Structure conservation index	0.62
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11456218 111 - 20766785
UUUGUUUCUUUUGGCUGCACUUGGUGUGGUAAUUCUCACGGAUUCCGCCUCCAUAAGCACCCACAUUGUUGGUGGCGAUCAGGCGGACAUCGCUGACUUUCCGUACCAGGU
..................(((((((((((.((...((((((..(((((((......((..(((......)))..))....)))))))..))).)))..))))))))))))) ( -34.10)
>DroVir_CAF1 14690 111 - 1
AUUAAUAGUUUUGGGCCUGCUUUCGCUAACGGCCUUGAACAGUGGCGCCUCCAUUAGCACCCACAUUGUGGGCGGCAUCGAGACGGAUAUUGUGAACUAUCCGUAUCAGGU
.......((((.(((((.((....))....))))).)))).(((.((((..((.............))..)))).))).((.(((((((........))))))).)).... ( -36.02)
>DroSec_CAF1 6358 111 - 1
UUUGUGUCUUUUGGCUGCACUUGGUGUGGUAAUCCCCACGGAUUCCGCCUCCAUAAGCACCCACAUUGUUGGUGGCGAUCAGGCGGACAUCGCUGACUAUCCGUACCAGGU
...(((((....))).))(((((((((((......))))(((((((((((......((..(((......)))..))....)))))))...........))))..))))))) ( -35.20)
>DroSim_CAF1 6356 111 - 1
UUUGUGUCUUUUGGCUGCACUUGGUGUGGUAAUCCCCACGGAUUCCGCCUCCAUAAGCACCCACAUUGUGGGUGGCGAUCAGGCGGACAUCGCUGACUAUCCGUACCAGGU
...(((((....))).))(((((((((((......))))(((((((((((......((((((((...)))))).))....)))))))...........))))..))))))) ( -40.90)
>DroEre_CAF1 6253 111 - 1
CUUAUGUCUUUUGGGUCUACUUGGCCUGGUUAUCCUCUCGGAUUCCGCCUCCAUAAGCACCCACAUUGUGGGUGGCGAUCAGGCGGACAUCGCCGAGUAUCCGUACCAGGU
.......................(((((((......(((((..(((((((......((((((((...)))))).))....))))))).....))))).......))))))) ( -42.62)
>DroYak_CAF1 6348 111 - 1
UUUGUGUUUUUUGGGUCUACUUGGCCUGGUAAUCCACACGGAUUCCGCCUCCAUAAGCCCCCACAUUGUGGGUGGCGAUCAGGCGGACAUCGCCGACUAUCCGUACCAGGU
...(((..(((..((((.....))))..).))..)))(((((((((((((......((((((((...))))).)))....)))))))...........))))))....... ( -42.90)
>consensus
UUUGUGUCUUUUGGCUCCACUUGGUCUGGUAAUCCUCACGGAUUCCGCCUCCAUAAGCACCCACAUUGUGGGUGGCGAUCAGGCGGACAUCGCUGACUAUCCGUACCAGGU
..................((((((..(((..((((....))))(((((((......((((((((...)))))).))....))))))).............)))..)))))) (-23.93 = -25.43 +   1.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:24 2006