Locus 3730

Sequence ID X_DroMel_CAF1
Location 9,936,573 – 9,936,761
Length 188
Max. P 0.908035
window6114 window6115 window6116 window6117

overview

Window 4

Location 9,936,573 – 9,936,687
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.14
Mean single sequence MFE -13.20
Consensus MFE -12.98
Energy contribution -12.85
Covariance contribution -0.13
Combinations/Pair 1.12
Mean z-score -1.12
Structure conservation index 0.98
SVM decision value 0.45
SVM RNA-class probability 0.739531
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9936573 114 - 22224390
---AAUAAAAAUACAAAAAAAAAAACCAUCCACAACCACAACAA---CAAGCGGGAGCGGCGAUAAAAUUGUUUUUCAUCUCAUUAUUGCACAAGCGGUCAAAGUAAUUCAUAACACACA
---.....................(((........((.(.....---...).))..((.(((((((...((.....)).....)))))))....)))))..................... ( -11.80)
>DroSec_CAF1 6349 114 - 1
AAAAAUAAAAAUACAAAA---ACAACCAUCCACAACCACAACAA---CAAGCGGGAGCGGCGAUAAAAUUGUUUUUCAUCUCAUUAUUGCACAAGUGGUCAAAGUAAUUCAUAACACACA
..................---.............(((((.....---...((....)).(((((((...((.....)).....)))))))....)))))..................... ( -15.50)
>DroEre_CAF1 6146 109 - 1
AAA---GAAAAUA--------AAAACAAUCCCCAACCACAACAACACCAAGCGGGAGCAGCGAUAAAAUUGUUUUUCAUCUCAUUAUUGCACAAGUGGUCAAAGUAAUUCAUAACACACA
...---.......--------.............(((((...........((....)).(((((((...((.....)).....)))))))....)))))..................... ( -15.70)
>DroYak_CAF1 6540 97 - 1
AAA------------------ACAACCAUACACAAUCACAACAA---CAAGUAGGAGCAGCGAUAAAAUUGUUUUUCAUCUCAUUAUUGCACAAGUGGUCAAAGUAAUUCAUAACA--CA
...------------------.......(((...(((((.....---...((....)).(((((((...((.....)).....)))))))....)))))....)))..........--.. (  -9.80)
>consensus
AAA___AAAAAUA________AAAACCAUCCACAACCACAACAA___CAAGCGGGAGCAGCGAUAAAAUUGUUUUUCAUCUCAUUAUUGCACAAGUGGUCAAAGUAAUUCAUAACACACA
..................................(((((...........((....)).(((((((...((.....)).....)))))))....)))))..................... (-12.98 = -12.85 +  -0.13)

alignment

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secondary structure

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Window 5

Location 9,936,613 – 9,936,724
Length 111
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 82.69
Mean single sequence MFE -26.30
Consensus MFE -17.88
Energy contribution -18.31
Covariance contribution 0.44
Combinations/Pair 1.11
Mean z-score -2.20
Structure conservation index 0.68
SVM decision value 1.06
SVM RNA-class probability 0.908035
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9936613 111 + 22224390
GAUGAAAAACAAUUUUAUCGCCGCUCCCGCUUG---UUGUUGUGGUUGUGGAUGGUUUUUUUUUUUGUAUUUUUAUU---UUUGCAGCUACCAAAUUGGAAUUCCAAUUAAAUGGGU
((((((((((((....((((((((..((((...---.....))))..)))).))))........)))).))))))))---..........(((((((((....))))))...))).. ( -26.10)
>DroSec_CAF1 6389 111 + 1
GAUGAAAAACAAUUUUAUCGCCGCUCCCGCUUG---UUGUUGUGGUUGUGGAUGGUUGU---UUUUGUAUUUUUAUUUUUUUUGCAGCUAUCAAAUUGGAAUUCCAAUUAAAUGGCU
((((((((((((....((((((((..((((...---.....))))..)))).))))...---..)))).))))))))........((((((..((((((....))))))..)))))) ( -32.10)
>DroEre_CAF1 6186 106 + 1
GAUGAAAAACAAUUUUAUCGCUGCUCCCGCUUGGUGUUGUUGUGGUUGGGGAUUGUUUU--------UAUUUUC---UUUUUUGCAGCUACAAAAUUGGAAUUCCAAUUAAAUGGGU
(((((((.....)))))))......((((.....(((.((((..(..(((((.......--------....)))---))..)..)))).))).((((((....))))))...)))). ( -25.60)
>DroYak_CAF1 6578 96 + 1
GAUGAAAAACAAUUUUAUCGCUGCUCCUACUUG---UUGUUGUGAUUGUGUAUGGUUGU------------------UUUUUUGCAGCUACCAAAUUGGAAUUCCAAUUAAAUGGGU
(((((((.....)))))))(((((.(((((..(---((.....)))...))).))....------------------......)))))..(((((((((....))))))...))).. ( -21.40)
>consensus
GAUGAAAAACAAUUUUAUCGCCGCUCCCGCUUG___UUGUUGUGGUUGUGGAUGGUUGU________UAUUUUU___UUUUUUGCAGCUACCAAAUUGGAAUUCCAAUUAAAUGGGU
(((((((.....)))))))......((((............(((((((((((............................)))))))))))..((((((....))))))...)))). (-17.88 = -18.31 +   0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,936,613 – 9,936,724
Length 111
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 82.69
Mean single sequence MFE -16.38
Consensus MFE -12.61
Energy contribution -12.37
Covariance contribution -0.25
Combinations/Pair 1.06
Mean z-score -1.73
Structure conservation index 0.77
SVM decision value 0.47
SVM RNA-class probability 0.748749
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9936613 111 - 22224390
ACCCAUUUAAUUGGAAUUCCAAUUUGGUAGCUGCAAA---AAUAAAAAUACAAAAAAAAAAACCAUCCACAACCACAACAA---CAAGCGGGAGCGGCGAUAAAAUUGUUUUUCAUC
...........(((((...((((((....(((((...---.((....)).......................((.(.....---...).))..)))))....))))))..))))).. ( -14.40)
>DroSec_CAF1 6389 111 - 1
AGCCAUUUAAUUGGAAUUCCAAUUUGAUAGCUGCAAAAAAAAUAAAAAUACAAAA---ACAACCAUCCACAACCACAACAA---CAAGCGGGAGCGGCGAUAAAAUUGUUUUUCAUC
(((.(((.((((((....)))))).))).)))...................((((---((((....((.(..((.(.....---...).))..).))........)))))))).... ( -17.00)
>DroEre_CAF1 6186 106 - 1
ACCCAUUUAAUUGGAAUUCCAAUUUUGUAGCUGCAAAAAA---GAAAAUA--------AAAACAAUCCCCAACCACAACAACACCAAGCGGGAGCAGCGAUAAAAUUGUUUUUCAUC
...........(((((...(((((((((.(((((......---(......--------....)..(((((.................).))))))))).)))))))))..))))).. ( -20.23)
>DroYak_CAF1 6578 96 - 1
ACCCAUUUAAUUGGAAUUCCAAUUUGGUAGCUGCAAAAAA------------------ACAACCAUACACAAUCACAACAA---CAAGUAGGAGCAGCGAUAAAAUUGUUUUUCAUC
...........(((((...((((((....(((((......------------------....((.(((.............---...))))).)))))....))))))..))))).. ( -13.89)
>consensus
ACCCAUUUAAUUGGAAUUCCAAUUUGGUAGCUGCAAAAAA___AAAAAUA________AAAACCAUCCACAACCACAACAA___CAAGCGGGAGCAGCGAUAAAAUUGUUUUUCAUC
...........(((((...((((((....(((((...........................................................)))))....))))))..))))).. (-12.61 = -12.37 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,936,650 – 9,936,761
Length 111
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 69.01
Mean single sequence MFE -18.38
Consensus MFE -6.72
Energy contribution -8.24
Covariance contribution 1.52
Combinations/Pair 1.27
Mean z-score -1.90
Structure conservation index 0.37
SVM decision value 0.60
SVM RNA-class probability 0.795162
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9936650 111 - 22224390
UGUCGCUGGGAUUUUAAUGCAAUUUUCCCAGUCCAAGACCCAUUUAAUUGGAAUUCCAAUUUGGUAGCUG---CAAA---AAUAAAAAUACAAAAAAAAAAACCAUCCACAACCACA
.((((((((((..............)))))))....)))(((...((((((....)))))))))......---....---..................................... ( -18.14)
>DroSec_CAF1 6426 111 - 1
UGUCGCUGGGAUUUUAAUGCAAUUUUCCCAGUCCAAGAGCCAUUUAAUUGGAAUUCCAAUUUGAUAGCUG---CAAAAAAAAUAAAAAUACAAAA---ACAACCAUCCACAACCACA
(((.(((((((..............))))))).....(((.(((.((((((....)))))).))).))))---))....................---................... ( -20.44)
>DroEre_CAF1 6226 103 - 1
UGUCGCGGGGAUUUUAAUGCAAUUUUCCCAGUCCAAGACCCAUUUAAUUGGAAUUCCAAUUUUGUAGCUG---CAAAAAA---GAAAAUA--------AAAACAAUCCCCAACCACA
......(((((((........((((((....(((((...........))))).......((((((....)---)))))..---)))))).--------.....)))))))....... ( -20.14)
>DroYak_CAF1 6615 96 - 1
UGUCGCGGGGAUUUUAAUGCAAUUUUCCCAGUCCAAGACCCAUUUAAUUGGAAUUCCAAUUUGGUAGCUG---CAAAAAA------------------ACAACCAUACACAAUCACA
(((.(((((((..((.....))..)))))..........(((...((((((....)))))))))..)).)---)).....------------------................... ( -17.80)
>DroMoj_CAF1 823 98 - 1
AGUCGCUU---------GUCAAUUGCAGCAACGCAAAGCCGGUUUCAUGCCAAUUCGGCAUUCAUCGCCAAAUCCAAAGAGAUAACAAAACAAAU---A-------CAACAAACACA
....(.((---------(((..((((......))))....(((...(((((.....))))).....)))...........)))))).........---.-------........... ( -15.40)
>consensus
UGUCGCUGGGAUUUUAAUGCAAUUUUCCCAGUCCAAGACCCAUUUAAUUGGAAUUCCAAUUUGGUAGCUG___CAAAAAA_AUAAAAAUACAAA____AAAACCAUCCACAACCACA
....(((((((..............))))))).........((..((((((....))))))..)).................................................... ( -6.72 =  -8.24 +   1.52)

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 11:06:50 2006