Locus 3440

Sequence ID 3R_DroMel_CAF1
Location 9,329,450 – 9,329,566
Length 116
Max. P 0.805463
window5519 window5520

overview

Window 9

Location 9,329,450 – 9,329,566
Length 116
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 80.83
Mean single sequence MFE -38.26
Consensus MFE -21.38
Energy contribution -21.47
Covariance contribution 0.09
Combinations/Pair 1.33
Mean z-score -1.86
Structure conservation index 0.56
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9329450 116 + 27905053
GGUUUUUUGGGUGGUUUUCGGGUGAUUUUCUGGAGGUGGUACUGGCGGA--CUGGUGUCUCACUCGCCCCACCAGGGAGUUGGCCACCGAAAAUUCAAUGAUUAAUGUGCGUUGGUGG
....((((.(((((((.......((((..((((.((.(((...(..(((--(....))))..)..))))).))))..))))))))))).)))).((((((((....)).))))))... ( -37.31)
>DroSec_CAF1 100191 102 + 1
GGUUUU------------UGGGUGAUUUUUUGGAGGUGGUA--AGCGGA--CUGGUGUCUCACUCGCCCCACCAGGGAGUUGGCCACCGAAAAUUCAAUGAUUAAUGUGCGUUGGUGG
(((...------------.((.(((((((((((.((.((..--((.(((--(....))).).))..)))).))))))))))).)))))......((((((((....)).))))))... ( -31.70)
>DroSim_CAF1 102485 102 + 1
GGUUUU------------UGGGUGAUUUUCUGGAGGUGGUA--AGCGGA--CUGGUGUCUCACUCGCCCCACCAGGGAGUUGGCCACCGAAAAUUCAAUGAUUAAUGUGCGUUGGUGG
(((...------------.((.(((((..((((.((.((..--((.(((--(....))).).))..)))).))))..))))).)))))......((((((((....)).))))))... ( -34.40)
>DroEre_CAF1 101660 113 + 1
GGUUUU-UGGGUGGCUUUCGGGUGAUUUUCUGGUGGUGGCA--AGCGGC--CUGGUGUCUCGCUCGCCCCAUCAGGGAGUUGGCCACCGAAAAUUCAAUGAUUAAUGUGCGUUGGUGG
...(((-(.(((((((.......((((..(((((((.(((.--(((((.--(....).).)))).))))))))))..))))))))))).)))).((((((((....)).))))))... ( -45.41)
>DroYak_CAF1 101915 113 + 1
GGUUUU-UGGGUGGCUUUUGGGUGAUUUUCUGGUGGUGGUA--AGCGGA--CUGGUGUCUCACUCGCCCCACCAGGGAGUUGGCCACCGAAAAUUCAAUGAUUAAUGUGCGUUGGUGG
...(((-(.(((((((.......((((..(((((((.((..--((.(((--(....))).).))..)))))))))..))))))))))).)))).((((((((....)).))))))... ( -46.81)
>DroAna_CAF1 98246 95 + 1
--------GGGUGGC----GAGGGGU-------UGGCGGUA--AGCGGUGAACGGUG--GAGUUGACCUCUCCUGGGAGUUGGCCACCAAAAAUUCAAUGAUUAAUGUGCGUUGGUGG
--------.((((((----(((((((-------..((....--.((.(....).)).--..))..)))))))(........)))))))......((((((((....)).))))))... ( -33.90)
>consensus
GGUUUU__GGGUGGC___UGGGUGAUUUUCUGGAGGUGGUA__AGCGGA__CUGGUGUCUCACUCGCCCCACCAGGGAGUUGGCCACCGAAAAUUCAAUGAUUAAUGUGCGUUGGUGG
.......................((((((((((.((.(((.....(((...)))(((...)))..))))).))))))))))..(((((((.....((........))....))))))) (-21.38 = -21.47 +   0.09)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,329,450 – 9,329,566
Length 116
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 80.83
Mean single sequence MFE -27.84
Consensus MFE -13.06
Energy contribution -13.45
Covariance contribution 0.39
Combinations/Pair 1.12
Mean z-score -2.89
Structure conservation index 0.47
SVM decision value 0.63
SVM RNA-class probability 0.805463
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9329450 116 - 27905053
CCACCAACGCACAUUAAUCAUUGAAUUUUCGGUGGCCAACUCCCUGGUGGGGCGAGUGAGACACCAG--UCCGCCAGUACCACCUCCAGAAAAUCACCCGAAAACCACCCAAAAAACC
.........................((((((((((....((....(((((..(..(((.(((....)--)))))..)..)))))...))....))).))))))).............. ( -26.00)
>DroSec_CAF1 100191 102 - 1
CCACCAACGCACAUUAAUCAUUGAAUUUUCGGUGGCCAACUCCCUGGUGGGGCGAGUGAGACACCAG--UCCGCU--UACCACCUCCAAAAAAUCACCCA------------AAAACC
(((((......((........)).......))))).........(((.((((..((((.(((....)--))))))--..)).)).)))............------------...... ( -24.72)
>DroSim_CAF1 102485 102 - 1
CCACCAACGCACAUUAAUCAUUGAAUUUUCGGUGGCCAACUCCCUGGUGGGGCGAGUGAGACACCAG--UCCGCU--UACCACCUCCAGAAAAUCACCCA------------AAAACC
(((((......((........)).......)))))........((((.((((..((((.(((....)--))))))--..)).)).))))...........------------...... ( -27.82)
>DroEre_CAF1 101660 113 - 1
CCACCAACGCACAUUAAUCAUUGAAUUUUCGGUGGCCAACUCCCUGAUGGGGCGAGCGAGACACCAG--GCCGCU--UGCCACCACCAGAAAAUCACCCGAAAGCCACCCA-AAAACC
.........................((((.((((((.......(((.(((((((((((.(.......--.)))))--)))).))).)))....((....))..)))))).)-)))... ( -33.70)
>DroYak_CAF1 101915 113 - 1
CCACCAACGCACAUUAAUCAUUGAAUUUUCGGUGGCCAACUCCCUGGUGGGGCGAGUGAGACACCAG--UCCGCU--UACCACCACCAGAAAAUCACCCAAAAGCCACCCA-AAAACC
.........................((((.((((((.......(((((((((..((((.(((....)--))))))--..)).)))))))..............)))))).)-)))... ( -35.00)
>DroAna_CAF1 98246 95 - 1
CCACCAACGCACAUUAAUCAUUGAAUUUUUGGUGGCCAACUCCCAGGAGAGGUCAACUC--CACCGUUCACCGCU--UACCGCCA-------ACCCCUC----GCCACCC--------
..............................((((((...(((....))).(((.(((..--....))).)))...--........-------.......----)))))).-------- ( -19.80)
>consensus
CCACCAACGCACAUUAAUCAUUGAAUUUUCGGUGGCCAACUCCCUGGUGGGGCGAGUGAGACACCAG__UCCGCU__UACCACCACCAGAAAAUCACCCA___GCCACCC__AAAACC
(((((......((........)).......)))))..........(((((((((.................))))....))))).................................. (-13.06 = -13.45 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:03 2006