Locus 5197

Sequence ID 2R_DroMel_CAF1
Location 16,913,156 – 16,913,292
Length 136
Max. P 0.986605
window8307 window8308

overview

Window 7

Location 16,913,156 – 16,913,263
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 91.23
Mean single sequence MFE -26.82
Consensus MFE -21.86
Energy contribution -22.98
Covariance contribution 1.12
Combinations/Pair 1.12
Mean z-score -2.32
Structure conservation index 0.82
SVM decision value 2.05
SVM RNA-class probability 0.986605
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16913156 107 + 20766785
GCUCAGUCAAUUGCGAAAGCUUAGAAAAUGGCAAGAAAAGCGACGUCGCAAAAUGUGGAACGGAAACCGAAAAGAGGUUUUGUGAAAACGCUUGCUAAAAGUUAGUG
((.((.((....((....))...))...)))).....(((((...(((((((((.(....(((...))).....).)))))))))...)))))((((.....)))). ( -26.20)
>DroSec_CAF1 10969 106 + 1
GCUCAAUAAAUUGCGAAAGCUUAGAAAAUGGCAAGAAAAGCGACGUCGCAAAAUGUGGAACGGAAACCGAU-AGAGGUUUUCUGAAAACGCUUGCUAAAAGUGGGCG
(((((.......((....))........(((((((....(((....))).....((.....(((((((...-...))))))).....)).)))))))....))))). ( -32.70)
>DroSim_CAF1 10975 106 + 1
GCUCAGUGAAUUGCGAAAGCUUAGAAAAUGGCAAGAAAAGCGACGUCGCAAAAUGUGGAACGGAAACCGAA-AGAGGUUUUCUGAAAACGCUUGCCAAAAGUGGGCG
(((((.(.....((....))........(((((((....(((....))).....((.....(((((((...-...))))))).....)).)))))))..).))))). ( -35.40)
>DroEre_CAF1 11186 102 + 1
GCUCAGUCAAUUGCAAAAGCUUAGAAAACGGCAAGAAAAGC---GUCGCAAAAUGUGGAACGGAAACCAAA-AGAGGUUUUCUGAAAACGGUUGCUAA-AGUGUACG
.....((((...((((..(.(((((((((..(.......(.---.((((.....))))..)(....)....-.)..)))))))))...)..))))...-..)).)). ( -18.80)
>DroYak_CAF1 11323 103 + 1
GCUCAGUCAAUUGCAAAAGCUUAGAAAACGGCAAGAAAAGC---GUCGCAAAAUGUGGAACGGAAACCAAA-AGAGGUUUUCUGAAAACGCUUGCUAAAAGUGUGUG
((.((.(.....((....(((........))).....((((---(((((.....)))....(((((((...-...))))))).....))))))))....).)).)). ( -21.00)
>consensus
GCUCAGUCAAUUGCGAAAGCUUAGAAAAUGGCAAGAAAAGCGACGUCGCAAAAUGUGGAACGGAAACCGAA_AGAGGUUUUCUGAAAACGCUUGCUAAAAGUGGGCG
(((((.......((....)).........((((((....(((....)))....(((.....(((((((.......))))))).....))))))))).....))))). (-21.86 = -22.98 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 16,913,191 – 16,913,292
Length 101
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 88.79
Mean single sequence MFE -29.64
Consensus MFE -22.34
Energy contribution -23.18
Covariance contribution 0.84
Combinations/Pair 1.12
Mean z-score -1.83
Structure conservation index 0.75
SVM decision value 0.47
SVM RNA-class probability 0.747581
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16913191 101 + 20766785
AAAAGCGACGUCGCAAAAUGUGGAACGGAAACCGAAAAGAGGUUUUGUGAAAACGCUUGCUAAAAGUUAGUGGAUGGG----UUGCAAGCUGCGAUCGCCUGUGC
....((((..(((((....((...(((.(((((.......))))))))....))((((((.....(((....)))...----..)))))))))))))))...... ( -27.90)
>DroSec_CAF1 11004 100 + 1
AAAAGCGACGUCGCAAAAUGUGGAACGGAAACCGAU-AGAGGUUUUCUGAAAACGCUUGCUAAAAGUGGGCGGAUGGG----UUGCAAGCUGCGAUCGCCUGUGC
....((((..(((((...((..(..((((((((...-...)))))))......((((..(.....)..))))...)..----)..))...)))))))))...... ( -34.60)
>DroSim_CAF1 11010 100 + 1
AAAAGCGACGUCGCAAAAUGUGGAACGGAAACCGAA-AGAGGUUUUCUGAAAACGCUUGCCAAAAGUGGGCGGAUGGG----UUGCAAGCUGCGAUCGCCUGUGC
....((((..(((((...((..(..((((((((...-...)))))))......((((..(.....)..))))...)..----)..))...)))))))))...... ( -33.90)
>DroEre_CAF1 11221 96 + 1
AAAAGC---GUCGCAAAAUGUGGAACGGAAACCAAA-AGAGGUUUUCUGAAAACGGUUGCUAA-AGUGUACGGAGGGA----UUCCAAACUGUGAUCGCCUGUGC
...(((---(((((.....))))...(((((((...-...)))))))..........))))..-...((((((.(.((----(..(.....)..))).))))))) ( -23.90)
>DroYak_CAF1 11358 101 + 1
AAAAGC---GUCGCAAAAUGUGGAACGGAAACCAAA-AGAGGUUUUCUGAAAACGCUUGCUAAAAGUGUGUGGAGGGGUUGUUUCCAAACUGUGAUCGCCUGUGC
....((---((((((...((.((((((((((((...-...))))))).....((((((.....))))))...........)))))))...))))).)))...... ( -27.90)
>consensus
AAAAGCGACGUCGCAAAAUGUGGAACGGAAACCGAA_AGAGGUUUUCUGAAAACGCUUGCUAAAAGUGGGCGGAUGGG____UUGCAAGCUGCGAUCGCCUGUGC
....(((..((((((...((..(...(((((((.......)))))))......(((((((.....)))))))..........)..))...)))))))))...... (-22.34 = -23.18 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:57 2006