Locus 1521

Sequence ID X_DroMel_CAF1
Location 4,437,500 – 4,437,699
Length 199
Max. P 0.955501
window2467 window2468 window2469 window2470

overview

Window 7

Location 4,437,500 – 4,437,619
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.43
Mean single sequence MFE -25.26
Consensus MFE -18.98
Energy contribution -21.04
Covariance contribution 2.06
Combinations/Pair 1.06
Mean z-score -2.04
Structure conservation index 0.75
SVM decision value 0.73
SVM RNA-class probability 0.835746
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4437500 119 + 22224390
GUUUUCAUUUCUUCUUUUUUUUUUUAGCCCCUUCCCCCAAUGGCAUGCUGCAUGUCUUCAUUAUCGUUUAUUGAAUACAAGCAUGCUUAUACACAUGUAUGUGUGCGUGUAGAGAGA-AU
...........((((((((......................((((((((...(((.((((.((.....)).)))).))))))))))).....(((((((....))))))))))))))-). ( -26.20)
>DroSec_CAF1 39332 115 + 1
GUUUUCAUUUCU-----UUUUUUUUAGCCCCUUCCCCCAAUGGCAUGCUGCAUGUCUUCAUUAUCGUUUAUUAAAUACAAGCAUGCUUAUGCACAUGUGUGUGUGCGUGUAGAGAGAAAU
......((((((-----((((....................((((((((..............................))))))))(((((((((....))))))))).)))))))))) ( -26.41)
>DroSim_CAF1 40764 115 + 1
GUUUUCAUUUCU-----UUUUUUUUAGCCCCUUCCCCCAAUGGCAUGCUGCAUGUCUUCAUUAUCGUUUAUUGAAUACAAGCAUGCUUAUGCACAUGUGUGUGUGCGUGUAGAGAGAAAU
......((((((-----((((....................((((((((...(((.((((.((.....)).)))).)))))))))))(((((((((....))))))))).)))))))))) ( -32.10)
>DroEre_CAF1 40937 103 + 1
GUUUUCAUUUCU-----UU-UUUUUAGCCCCUUCCCCCAAUGGCAUGCUGCAUGUCUUCAUUAUCGUUC----AAUACAAGCAUGCUUAUAC----AUAUG--UGUCUGUAGAGAGA-AU
........((((-----((-((..(((..............((((((((..(((....)))....((..----...)).)))))))).((((----....)--)))))).)))))))-). ( -16.80)
>DroYak_CAF1 39971 110 + 1
GUUUUCAUUUCU-----UU--UUUUAGCCCCUUCCCCCAAUGGCAUGCUGCAUGUCUUCAUUAUCGUUUAUUGAAUACAAGCAUGCUUAUACAUACAUAUG--UGUCUGUAGAGAGA-AU
........((((-----((--((.(((..............((((((((...(((.((((.((.....)).)))).))))))))))).((((((....)))--)))))).)))))))-). ( -24.80)
>consensus
GUUUUCAUUUCU_____UUUUUUUUAGCCCCUUCCCCCAAUGGCAUGCUGCAUGUCUUCAUUAUCGUUUAUUGAAUACAAGCAUGCUUAUACACAUGUAUGUGUGCGUGUAGAGAGA_AU
.(((((...................................((((((((...(((.((((.((.....)).)))).)))))))))))(((((((((....)))))))))..))))).... (-18.98 = -21.04 +   2.06)

alignment

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secondary structure

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Window 8

Location 4,437,500 – 4,437,619
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.43
Mean single sequence MFE -24.63
Consensus MFE -20.44
Energy contribution -20.98
Covariance contribution 0.54
Combinations/Pair 1.15
Mean z-score -1.96
Structure conservation index 0.83
SVM decision value 1.46
SVM RNA-class probability 0.955501
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4437500 119 - 22224390
AU-UCUCUCUACACGCACACAUACAUGUGUAUAAGCAUGCUUGUAUUCAAUAAACGAUAAUGAAGACAUGCAGCAUGCCAUUGGGGGAAGGGGCUAAAAAAAAAAAGAAGAAAUGAAAAC
.(-((((((.....(((((......)))))....((((((((((.((((.((.....)).)))).)))...)))))))....)))))))............................... ( -25.10)
>DroSec_CAF1 39332 115 - 1
AUUUCUCUCUACACGCACACACACAUGUGCAUAAGCAUGCUUGUAUUUAAUAAACGAUAAUGAAGACAUGCAGCAUGCCAUUGGGGGAAGGGGCUAAAAAAAA-----AGAAAUGAAAAC
.((((((((.....(((((......)))))....((((((((((.((((.((.....)).)))).)))...)))))))....)))))))).............-----............ ( -25.90)
>DroSim_CAF1 40764 115 - 1
AUUUCUCUCUACACGCACACACACAUGUGCAUAAGCAUGCUUGUAUUCAAUAAACGAUAAUGAAGACAUGCAGCAUGCCAUUGGGGGAAGGGGCUAAAAAAAA-----AGAAAUGAAAAC
.((((((((.....(((((......)))))....((((((((((.((((.((.....)).)))).)))...)))))))....)))))))).............-----............ ( -28.10)
>DroEre_CAF1 40937 103 - 1
AU-UCUCUCUACAGACA--CAUAU----GUAUAAGCAUGCUUGUAUU----GAACGAUAAUGAAGACAUGCAGCAUGCCAUUGGGGGAAGGGGCUAAAAA-AA-----AGAAAUGAAAAC
.(-((((((((((....--....)----)))...(((((((.((((.----................)))))))))))....)))))))...........-..-----............ ( -20.13)
>DroYak_CAF1 39971 110 - 1
AU-UCUCUCUACAGACA--CAUAUGUAUGUAUAAGCAUGCUUGUAUUCAAUAAACGAUAAUGAAGACAUGCAGCAUGCCAUUGGGGGAAGGGGCUAAAA--AA-----AGAAAUGAAAAC
.(-((((((((((.(((--....))).))))...((((((((((.((((.((.....)).)))).)))...)))))))....)))))))..........--..-----............ ( -23.90)
>consensus
AU_UCUCUCUACACGCACACAUACAUGUGUAUAAGCAUGCUUGUAUUCAAUAAACGAUAAUGAAGACAUGCAGCAUGCCAUUGGGGGAAGGGGCUAAAAAAAA_____AGAAAUGAAAAC
...((((((.....(((((......)))))....((((((((((.((((.((.....)).)))).)))...)))))))....))))))................................ (-20.44 = -20.98 +   0.54)

alignment

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secondary structure

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Window 9

Location 4,437,540 – 4,437,659
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.67
Mean single sequence MFE -20.09
Consensus MFE -16.06
Energy contribution -16.60
Covariance contribution 0.54
Combinations/Pair 1.15
Mean z-score -2.01
Structure conservation index 0.80
SVM decision value 1.06
SVM RNA-class probability 0.908081
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4437540 119 - 22224390
CGGUAGAAUACCCCCCCCCCCCCCACCACCACUUUUAUAUAU-UCUCUCUACACGCACACAUACAUGUGUAUAAGCAUGCUUGUAUUCAAUAAACGAUAAUGAAGACAUGCAGCAUGCCA
(((((((...................................-....))))).)).(((((....)))))....((((((((((.((((.((.....)).)))).)))...))))))).. ( -19.93)
>DroSec_CAF1 39367 105 - 1
CGGUAGAAUACCCCCCAC---------------UUUAUAUAUUUCUCUCUACACGCACACACACAUGUGCAUAAGCAUGCUUGUAUUUAAUAAACGAUAAUGAAGACAUGCAGCAUGCCA
..(((((...........---------------..............)))))..(((((......)))))....((((((((((.((((.((.....)).)))).)))...))))))).. ( -20.31)
>DroSim_CAF1 40799 105 - 1
CGGUAGAAUACCCCCCAC---------------UUUAUAUAUUUCUCUCUACACGCACACACACAUGUGCAUAAGCAUGCUUGUAUUCAAUAAACGAUAAUGAAGACAUGCAGCAUGCCA
..(((((...........---------------..............)))))..(((((......)))))....((((((((((.((((.((.....)).)))).)))...))))))).. ( -22.51)
>DroEre_CAF1 40971 95 - 1
CGGUAGAAUACCCCCCUC--------------UUUUAUAUAU-UCUCUCUACAGACA--CAUAU----GUAUAAGCAUGCUUGUAUU----GAACGAUAAUGAAGACAUGCAGCAUGCCA
.((((.............--------------..((((((((-....((....))..--...))----))))))((((((((.((((----....))))...))).)))))....)))). ( -17.80)
>DroYak_CAF1 40004 96 - 1
CGGUAGAAUACCCCCU---------------------CAUAU-UCUCUCUACAGACA--CAUAUGUAUGUAUAAGCAUGCUUGUAUUCAAUAAACGAUAAUGAAGACAUGCAGCAUGCCA
.(..((((((......---------------------..)))-)))..)((((.(((--....))).))))...((((((((((.((((.((.....)).)))).)))...))))))).. ( -19.90)
>consensus
CGGUAGAAUACCCCCCAC_______________UUUAUAUAU_UCUCUCUACACGCACACAUACAUGUGUAUAAGCAUGCUUGUAUUCAAUAAACGAUAAUGAAGACAUGCAGCAUGCCA
..(((((........................................)))))..(((((......)))))....((((((((((.((((.((.....)).)))).)))...))))))).. (-16.06 = -16.60 +   0.54)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,437,580 – 4,437,699
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.03
Mean single sequence MFE -23.24
Consensus MFE -19.58
Energy contribution -19.80
Covariance contribution 0.22
Combinations/Pair 1.10
Mean z-score -2.05
Structure conservation index 0.84
SVM decision value 1.27
SVM RNA-class probability 0.938111
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4437580 119 - 22224390
UCGGCAACGCGUGCAAUACUCAGGGAUUACCUUUGUCUCCCGGUAGAAUACCCCCCCCCCCCCCACCACCACUUUUAUAUAU-UCUCUCUACACGCACACAUACAUGUGUAUAAGCAUGC
..(....)((((((..((((..(((((.......)))))..)))).....................................-...........(((((......)))))....)))))) ( -21.30)
>DroSec_CAF1 39407 105 - 1
UCGGCAACGCGUGCAAUACUCAGGGAUUACCUUUGUCUCCCGGUAGAAUACCCCCCAC---------------UUUAUAUAUUUCUCUCUACACGCACACACACAUGUGCAUAAGCAUGC
..(....)((((((........((((...........)))).(((((...........---------------..............)))))..(((((......)))))....)))))) ( -24.01)
>DroSim_CAF1 40839 105 - 1
UCGGCAACGCGUGCAAUACUCAGGGAUUACCUUUGUCUCCCGGUAGAAUACCCCCCAC---------------UUUAUAUAUUUCUCUCUACACGCACACACACAUGUGCAUAAGCAUGC
..(....)((((((........((((...........)))).(((((...........---------------..............)))))..(((((......)))))....)))))) ( -24.01)
>DroEre_CAF1 41007 99 - 1
UCGGCAACGCGUGCAAUACUGAGGGAUUACCUUUGUCUCCCGGUAGAAUACCCCCCUC--------------UUUUAUAUAU-UCUCUCUACAGACA--CAUAU----GUAUAAGCAUGC
..(....)((((((..(((((.(((((.......))))).))))).............--------------..((((((((-....((....))..--...))----)))))))))))) ( -23.70)
>DroYak_CAF1 40044 96 - 1
UCGGCAACGCGUGCAAUACUCAGGGAUUACCUUUGCCUCCCGGUAGAAUACCCCCU---------------------CAUAU-UCUCUCUACAGACA--CAUAUGUAUGUAUAAGCAUGC
..(....)((((((.......((((..((..((((((....)))))).))..))))---------------------.....-......((((.(((--....))).))))...)))))) ( -23.20)
>consensus
UCGGCAACGCGUGCAAUACUCAGGGAUUACCUUUGUCUCCCGGUAGAAUACCCCCCAC_______________UUUAUAUAU_UCUCUCUACACGCACACAUACAUGUGUAUAAGCAUGC
..(....)((((((........((((...........)))).(((((........................................)))))..(((((......)))))....)))))) (-19.58 = -19.80 +   0.22)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:05 2006