Locus 3602

Sequence ID 2R_DroMel_CAF1
Location 11,979,194 – 11,979,328
Length 134
Max. P 0.879725
window5868 window5869

overview

Window 8

Location 11,979,194 – 11,979,288
Length 94
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.55
Mean single sequence MFE -18.30
Consensus MFE -12.60
Energy contribution -12.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.71
Structure conservation index 0.69
SVM decision value 0.91
SVM RNA-class probability 0.879725
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11979194 94 + 20766785
AAUUAC-GUC-------------------------UACAAAUACACAUAAAAGGGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAAGGAAUUAAUUGUCCACGAAAU
.....(-(((-------------------------..........(......).....((((((((....))))))))))))...((((((((.((.......)).))))))))...... ( -16.00)
>DroVir_CAF1 35801 112 + 1
AAUUAC-GGGCGAA-----GGCAGCGCAGCAAACGGACACAAACACAC--AAAAGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAAGAAAUUAAUUGUCCACGAAAU
.....(-(.((...-----.))..)).......((.............--........((((((((....)))))))).......((((((((.((.......)).)))))))))).... ( -18.20)
>DroGri_CAF1 33632 113 + 1
AAUUACUGGGCAAA-----GUCAGUGUGGCAAAUGGACACACAAACAC--AAAAGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAAGAAAUUAAUUGUCCACGAAAU
..............-----(((.(((((.........)))))......--........((((((((....)))))))))))....((((((((.((.......)).))))))))...... ( -23.00)
>DroEre_CAF1 30669 94 + 1
AAUUAC-GUC-------------------------UACAAAUACACAUAAAAGGGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAGGGAAUUAAUUGUCCACGAAAU
.....(-(((-------------------------..........(......).....((((((((....))))))))))))...((((((((.((.......)).))))))))...... ( -16.00)
>DroAna_CAF1 31584 94 + 1
AAUUAC-GUC-------------------------UACAAAUACACAUAAAAGGGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAGGGAAUUAAUUGUCCACGAAAU
.....(-(((-------------------------..........(......).....((((((((....))))))))))))...((((((((.((.......)).))))))))...... ( -16.00)
>DroMoj_CAF1 40455 115 + 1
AAUUGC-GAACGAGCAGCGAGCAGCGCAGCAAACGGACACAAACA--C--AAAAGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAAGAAAUUAAUUGUCCACGAAAU
..(((.-(..((.((.(((.....))).))...))..).)))...--.--........((((((((....)))))))).......((((((((.((.......)).))))))))...... ( -20.60)
>consensus
AAUUAC_GUC_________________________GACAAAUACACAC__AAAAGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAAGAAAUUAAUUGUCCACGAAAU
..........................................................((((((((....)))))))).......((((((((.((.......)).))))))))...... (-12.60 = -12.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,979,208 – 11,979,328
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.31
Mean single sequence MFE -20.12
Consensus MFE -14.00
Energy contribution -14.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.70
SVM decision value 0.79
SVM RNA-class probability 0.852542
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11979208 120 + 20766785
AUACACAUAAAAGGGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAAGGAAUUAAUUGUCCACGAAAUGCAAUUAUGCUUUCCCCUCUCUUUUUCCGCCUUUUCUUUU
........((((((((((((((((((....))))))))((.((..((((((((.((.......)).)))))))).((((.(((....)))))))...))))...)))).))))))..... ( -26.70)
>DroVir_CAF1 35835 92 + 1
AAACACAC--AAAAGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAAGAAAUUAAUUGUCCACGAAAUGCAAUUAUGCU-CCG-------------------------
........--....(((.((((((((....)))))))).......((((((((.((.......)).))))))))......(((....))))-)).------------------------- ( -17.00)
>DroGri_CAF1 33667 92 + 1
ACAAACAC--AAAAGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAAGAAAUUAAUUGUCCACGAAAUGCAAUUAUGCU-CCG-------------------------
........--....(((.((((((((....)))))))).......((((((((.((.......)).))))))))......(((....))))-)).------------------------- ( -17.00)
>DroSec_CAF1 30398 117 + 1
AUACACAUAAAAGGGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAAGGAAUUAAUUGUCCACGAAAUGCAAUUAUGCU-UCCCGUCGCUUAUUCCGCAUUUC--UUU
............(.((((((((((((....))))))))((((...((((((((.((.......)).))))))))......(((....))).-...)))).....)))).).....--... ( -26.00)
>DroAna_CAF1 31598 104 + 1
AUACACAUAAAAGGGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAGGGAAUUAAUUGUCCACGAAAUGCAAUUAUGCU-CAGC-UUUCUUACU--------------
..........(((..(..((((((((....))))))))...((..((((((((.((.......)).))))))))......(((....))))-)...-)..)))...-------------- ( -17.00)
>DroMoj_CAF1 40494 90 + 1
AAACA--C--AAAAGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAAGAAAUUAAUUGUCCACGAAAUGCAAUUAUGCU-CCG-------------------------
.....--.--....(((.((((((((....)))))))).......((((((((.((.......)).))))))))......(((....))))-)).------------------------- ( -17.00)
>consensus
AUACACAC__AAAAGGAAGUAAUUUGCAAUUAAAUUACGACGAAAUGGGCAAUAGAAAAGAAAUUAAUUGUCCACGAAAUGCAAUUAUGCU_CCG_________________________
..................((((((((....)))))))).......((((((((.((.......)).))))))))......(((....))).............................. (-14.00 = -14.00 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:40 2006