Locus 4238

Sequence ID 2L_DroMel_CAF1
Location 12,116,462 – 12,116,560
Length 98
Max. P 0.737467
window6691 window6692

overview

Window 1

Location 12,116,462 – 12,116,560
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.30
Mean single sequence MFE -30.18
Consensus MFE -18.34
Energy contribution -19.18
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -2.32
Structure conservation index 0.61
SVM decision value 0.44
SVM RNA-class probability 0.737467
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12116462 98 + 22407834
ACUGCUUCUUCUUGCCACUUCUUGGAGCUUGACGUGACGACAUGCAAUCGCAAAGAAGGUA--------GAAAGAAGA------A----GCU----AUAAGAAGCGGUAGAACAACACCA
...((((((((((....((((((...(.(((.((((....))))))).)...))))))...--------..)))))))------)----)).----.........(((........))). ( -29.00)
>DroSec_CAF1 18580 91 + 1
UCUGCUUCUUCUUGCCACUUCUUGGAGCUUGACGUGACGACAUGCAAUCGCAAAGAAGGUA--------GAAAGAAGAAG---------------------AAGCGGUAGAACAACACCA
.((((((((((((.(..((((((...(.(((.((((....))))))).)...))))))...--------)....))))))---------------------))))))............. ( -27.10)
>DroSim_CAF1 18413 101 + 1
UCUGCUUCUUCUUGCCACUUCUUGGAGCUUGACGUGACGACAUGCAAUCGCAAAGAAGGUA--------GAAAGAAGAAGA---A----GCU----AUAAGAAGCGGUAGAACAACACCA
....(((((((((....((((((...(.(((.((((....))))))).)...))))))...--------..))))))))).---.----(((----......)))(((........))). ( -28.20)
>DroEre_CAF1 18849 116 + 1
UCUGCUUCUUCUUGCCACUUCUUAGAGCUUGACGUGACGACAUGCAAUCGCAAAGAAGGUAAGAAGGUAGGAAGAAGAAGAUGAAGCGGGCU----AUAACAAGCGGUAGAACAACACCA
(((.((((((((((((.((((((.(.(.(((.((((....))))))).).).)))))).......)))))))))))).)))........(((----......)))(((........))). ( -33.40)
>DroYak_CAF1 18763 115 + 1
UCUGCUUCUUCUUGCCACUUCUUAGAGCUUCACGUGACGACAUGCAAUCGCAAAGAAGGUA-----GUUGGAAGAAGAAGAUGAAGCUGGCUACAUAUAAGAAGCGGCAGAACAACACCA
((((((.((((((((((((((......((((......((((.(((..((.....))..)))-----))))......))))..)))).)))).......)))))).))))))......... ( -33.21)
>consensus
UCUGCUUCUUCUUGCCACUUCUUGGAGCUUGACGUGACGACAUGCAAUCGCAAAGAAGGUA________GAAAGAAGAAGA___A____GCU____AUAAGAAGCGGUAGAACAACACCA
(((((((((((((.(..((((((...(.(((.((((....))))))).)...))))))...........).)))))))...........(((..........)))))))))......... (-18.34 = -19.18 +   0.84)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,116,462 – 12,116,560
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.30
Mean single sequence MFE -28.69
Consensus MFE -18.46
Energy contribution -18.90
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.84
Structure conservation index 0.64
SVM decision value 0.05
SVM RNA-class probability 0.561163
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12116462 98 - 22407834
UGGUGUUGUUCUACCGCUUCUUAU----AGC----U------UCUUCUUUC--------UACCUUCUUUGCGAUUGCAUGUCGUCACGUCAAGCUCCAAGAAGUGGCAAGAAGAAGCAGU
.((((......)))).........----.((----(------(((((((.(--------(((.(((((.(.(.(((.((((....))))))).).).))))))))).))))))))))... ( -29.90)
>DroSec_CAF1 18580 91 - 1
UGGUGUUGUUCUACCGCUU---------------------CUUCUUCUUUC--------UACCUUCUUUGCGAUUGCAUGUCGUCACGUCAAGCUCCAAGAAGUGGCAAGAAGAAGCAGA
.((((......))))((((---------------------((((((....(--------(((.(((((.(.(.(((.((((....))))))).).).))))))))).))))))))))... ( -27.10)
>DroSim_CAF1 18413 101 - 1
UGGUGUUGUUCUACCGCUUCUUAU----AGC----U---UCUUCUUCUUUC--------UACCUUCUUUGCGAUUGCAUGUCGUCACGUCAAGCUCCAAGAAGUGGCAAGAAGAAGCAGA
.((((......))))(((......----)))----.---.(((((((((.(--------(((.(((((.(.(.(((.((((....))))))).).).))))))))).))))))))).... ( -27.50)
>DroEre_CAF1 18849 116 - 1
UGGUGUUGUUCUACCGCUUGUUAU----AGCCCGCUUCAUCUUCUUCUUCCUACCUUCUUACCUUCUUUGCGAUUGCAUGUCGUCACGUCAAGCUCUAAGAAGUGGCAAGAAGAAGCAGA
.((((......))))(((......----))).........(((((((((.((((.((((((.(((...((((((.....)))).))....)))...)))))))))).))))))))).... ( -28.10)
>DroYak_CAF1 18763 115 - 1
UGGUGUUGUUCUGCCGCUUCUUAUAUGUAGCCAGCUUCAUCUUCUUCUUCCAAC-----UACCUUCUUUGCGAUUGCAUGUCGUCACGUGAAGCUCUAAGAAGUGGCAAGAAGAAGCAGA
...((((.(((((((((((((((.........((((((((..............-----..........(((((.....)))))...)))))))).))))))))))).))))..)))).. ( -30.83)
>consensus
UGGUGUUGUUCUACCGCUUCUUAU____AGC____U___UCUUCUUCUUUC________UACCUUCUUUGCGAUUGCAUGUCGUCACGUCAAGCUCCAAGAAGUGGCAAGAAGAAGCAGA
.((((......)))).........................(((((((((...................(((....)))....(((((.((.........)).)))))))))))))).... (-18.46 = -18.90 +   0.44)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:09 2006