Locus 6898

Sequence ID X_DroMel_CAF1
Location 17,260,985 – 17,261,216
Length 231
Max. P 0.934715
window11283 window11284

overview

Window 3

Location 17,260,985 – 17,261,097
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.28
Mean single sequence MFE -32.72
Consensus MFE -20.06
Energy contribution -21.98
Covariance contribution 1.92
Combinations/Pair 1.12
Mean z-score -1.95
Structure conservation index 0.61
SVM decision value 0.27
SVM RNA-class probability 0.662829
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17260985 112 - 22224390
GCUCGUUUUGCUUUUGACAGUUCAUGAUAGAUUGAAUUGCAGA-AGCUGUUGAUAAAUUGGACAGCUGAUACAAGGCCAAAGUUUGCUCCUA-------UGGCGAAUUGGUUGCAAGAGG
...(.((((((.((((.(((((((........)))))))))))-(((((((.(.....).))))))).......(((((..(((((((....-------.)))))))))))))))))).) ( -34.30)
>DroSec_CAF1 106514 109 - 1
GCUCGUUUUGCGUUUGACAGUUCA---UAGAUUGAAUUGCAGA-AGCUGUUGAUAAAUUGGACAGCUGAUGCGAGACCAAAGUUUGCUCCUA-------UGGCGAAUUGGUUGCAAGAGG
.(((((((((((((((.(((((((---.....)))))))))..-(((((((.(.....).)))))))))))))))))...((((((((....-------.))))))))........))). ( -36.70)
>DroSim_CAF1 110085 112 - 1
GCUCGUUUUGCUUUUGACAGUCCAUGAUAGAUUGAAUUGCAGA-AGCUGUUGAUAAAUUGGACAGCUGAUGCGAGACCAAAGUUAGCUCCUA-------UGGCGAAUUGGUUGCAAGAGG
...(.((((((......(((((.......)))))..(((((..-(((((((.(.....).)))))))..)))))((((((.....(((....-------.)))...)))))))))))).) ( -33.50)
>DroEre_CAF1 112025 99 - 1
GCUCGUUGUGCCUUCGACAGCUCAUGAUAGAUUGAAUUGGAGA-AGCUGUUGAUGAAUUGGGCAGCUG--GCA-----GAAGUUUGCUUCUA-------UGGCGAAUUUGAUGU------
..((((..((((.((..(((.(((........))).)))..))-(((((((.(.....).))))))))--))(-----((((....))))))-------..)))).........------ ( -30.30)
>DroYak_CAF1 116472 119 - 1
GCUCGUUGUGCUUUUGACAGUUCAUGAUAGAUGGAAUUGAAGAAAGCUGUUGAUAAAUUGGACAGCUGAGGCAAGAGCAAAGUUGGCUUCCAUCAAACAUGUCAAAUUUGUUGCAA-AGG
((((....((((((...((((((..........)))))).....(((((((.(.....).))))))))))))).))))(((.(((((.............))))).))).......-... ( -28.82)
>consensus
GCUCGUUUUGCUUUUGACAGUUCAUGAUAGAUUGAAUUGCAGA_AGCUGUUGAUAAAUUGGACAGCUGAUGCAAGACCAAAGUUUGCUCCUA_______UGGCGAAUUGGUUGCAAGAGG
((..(((((((......(((((((........))))))).....(((((((.(.....).)))))))...)))))))...((((((((............))))))))....))...... (-20.06 = -21.98 +   1.92)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,261,097 – 17,261,216
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.97
Mean single sequence MFE -25.84
Consensus MFE -9.68
Energy contribution -9.84
Covariance contribution 0.16
Combinations/Pair 1.26
Mean z-score -2.05
Structure conservation index 0.37
SVM decision value 1.24
SVM RNA-class probability 0.934715
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17261097 119 + 22224390
UUUUCUAUUUUCACACUACAAUCAAGUUGACUUAUUGCACUUUGCACAAGUCAAUGGAACGCAUAAGUUCGAUUGCACAUAAGAUAACAUCCGCAUGGAAUUUAAAAAA-UUCGGAAUAA
.....((((((.......(((((..((((((((..(((.....))).)))))))).((((......))))))))).....))))))...((((.((............)-).)))).... ( -23.00)
>DroSec_CAF1 106623 119 + 1
UCUUCUAUUUUCACACUACGAGUAAGUUGACUUAUUGCACUUUGCUCAAGUCAGUGGAACGCAUAAGUUGGCUUGCACAUAAGAUAACAUCCGCAUGGAAUUUCAAUAA-UUCCGAAUAA
.........(((.........((((((..((((((.((..((..((......))..))..))))))))..))))))....................((((((.....))-)))))))... ( -29.40)
>DroSim_CAF1 110197 119 + 1
UCUUCUAUUUUCACACUACGAGCAAGUUGACUUAUUGCACUUUGCACAAGUCAGUGGAACGCAUAAGUUGGCUUGCACAUAAGAUAACAUCCGCAUGGAAUUUCAAUAA-UUCCGAAUAA
.........(((.........((((((..((((((.((..((..(........)..))..))))))))..))))))....................((((((.....))-)))))))... ( -30.50)
>DroEre_CAF1 112124 96 + 1
UCUUUUAUACUCACACCACCAGCAAGUUGACCUAUUGCACUUUGCACAAGUCAGCGGAGCACAGAAGA---CACACAUC------------CGUGUGAAAUUUCAAUACAU---------
..........((((((.........((((((....(((.....)))...))))))(((..........---......))------------))))))).............--------- ( -19.69)
>DroYak_CAF1 116591 101 + 1
UCUUCUAUCUUCACGCCACAAGGAGGUUGACUCAUUGCACUUAGCACCAGUCAAUGGAACGCACAAGUUGGCCUGCAUGCAGGAUAAGAUAAGAGUGAAGA-------------------
.......((((((((((........(((((((...(((.....)))..)))))))..(((......))))))(((....)))............)))))))------------------- ( -26.60)
>consensus
UCUUCUAUUUUCACACUACAAGCAAGUUGACUUAUUGCACUUUGCACAAGUCAGUGGAACGCAUAAGUUGGCUUGCACAUAAGAUAACAUCCGCAUGGAAUUUCAAUAA_UUC_GAAUAA
..((((((.................(((((((...(((.....)))..))))))).....(((..........)))..................)))))).................... ( -9.68 =  -9.84 +   0.16)

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 12:25:28 2006