Locus 5323

Sequence ID	2R_DroMel_CAF1
Location	17,245,060 – 17,245,272
Length	212
Max. P	0.999620

overview

Window 3

Location	17,245,060 – 17,245,169
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	97.80
Mean single sequence MFE	-23.66
Consensus MFE	-21.00
Energy contribution	-21.40
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.78
Structure conservation index	0.89
SVM decision value	1.34
SVM RNA-class probability	0.944299
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17245060 109 + 20766785
AAAAAUUUGUGCUUUCCUCAUUUGAUUCAAUUACACCUUUGGGUGUUGUAAUUUUAUUUUUGCCCUCCUCUUUCACAAAACAAAUGGCUUCAGAUGGAGCACAAUGGAU
......((((((((....(((((((.(((...(((((....))))).((((........)))).....................)))..)))))))))))))))..... ( -23.20)
>DroSec_CAF1 48980 109 + 1
AAAAAUUUGUGCUUUCCUCAUUUGAUUCAAUUACACCUUUGGGUGUUGUAAUUUUAUUUUUGCCCUCCUCUUUCACAAAACAAAUGGCUUCAGAUGGAGCACAAUGGAU
......((((((((....(((((((.(((...(((((....))))).((((........)))).....................)))..)))))))))))))))..... ( -23.20)
>DroSim_CAF1 47706 109 + 1
AAAAAUUUGUGCUUUCCUCAUUUGAUUCAAUUACACCUUUGGGUGUUGUAAUUUUAUUUUGGCCCUCCUCUUUCACAAAACAAAUGGCUUCAGAUGGAGCACAAUGGAU
......((((((((....(((((((....((.(((((....))))).))...........((((.....................)))))))))))))))))))..... ( -23.90)
>DroEre_CAF1 47075 108 + 1
AA-AAUUUGUGCUUUCCUCAUUUGAUUCAAUUACACCUUUGGGUGUUGUAAUUUUUUUUGUGCCCUCCUCUUUCACAAAACAAAUGGCUUGAGAUGGAGCACAAUGGAU
..-...(((((((((.((((............(((((....))))).((.((((.(((((((...........))))))).)))).)).))))..)))))))))..... ( -26.20)
>DroYak_CAF1 46370 108 + 1
AA-AAUUUGUGCUUUCCUCAUUUGAUUCAAUUACACCUUUGGGUGUUGUAAUUUUAUUUUUGCCCUCCUCUUUCACAAAACAAAUGGCUUGAGAUGGAGCACAAUGGAU
..-...(((((((((.((((.........((.(((((....))))).))............(((.....................))).))))..)))))))))..... ( -21.80)
>consensus
AAAAAUUUGUGCUUUCCUCAUUUGAUUCAAUUACACCUUUGGGUGUUGUAAUUUUAUUUUUGCCCUCCUCUUUCACAAAACAAAUGGCUUCAGAUGGAGCACAAUGGAU
......((((((((....(((((((....((.(((((....))))).))............(((.....................))).)))))))))))))))..... (-21.00 = -21.40 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	17,245,060 – 17,245,169
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	97.80
Mean single sequence MFE	-25.56
Consensus MFE	-24.32
Energy contribution	-24.32
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.50
Structure conservation index	0.95
SVM decision value	3.79
SVM RNA-class probability	0.999620
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17245060 109 - 20766785
AUCCAUUGUGCUCCAUCUGAAGCCAUUUGUUUUGUGAAAGAGGAGGGCAAAAAUAAAAUUACAACACCCAAAGGUGUAAUUGAAUCAAAUGAGGAAAGCACAAAUUUUU
.....(((((((((((.(((.(((.(((.((((....)))).))))))...............(((((....))))).......))).))).)...)))))))...... ( -24.70)
>DroSec_CAF1 48980 109 - 1
AUCCAUUGUGCUCCAUCUGAAGCCAUUUGUUUUGUGAAAGAGGAGGGCAAAAAUAAAAUUACAACACCCAAAGGUGUAAUUGAAUCAAAUGAGGAAAGCACAAAUUUUU
.....(((((((((((.(((.(((.(((.((((....)))).))))))...............(((((....))))).......))).))).)...)))))))...... ( -24.70)
>DroSim_CAF1 47706 109 - 1
AUCCAUUGUGCUCCAUCUGAAGCCAUUUGUUUUGUGAAAGAGGAGGGCCAAAAUAAAAUUACAACACCCAAAGGUGUAAUUGAAUCAAAUGAGGAAAGCACAAAUUUUU
.....(((((((((((.(((.(((.(((.((((....)))).))))))...............(((((....))))).......))).))).)...)))))))...... ( -23.80)
>DroEre_CAF1 47075 108 - 1
AUCCAUUGUGCUCCAUCUCAAGCCAUUUGUUUUGUGAAAGAGGAGGGCACAAAAAAAAUUACAACACCCAAAGGUGUAAUUGAAUCAAAUGAGGAAAGCACAAAUU-UU
.....(((((((...(((((.(((.(((.((((....)))).))))))...............(((((....)))))............)))))..)))))))...-.. ( -27.30)
>DroYak_CAF1 46370 108 - 1
AUCCAUUGUGCUCCAUCUCAAGCCAUUUGUUUUGUGAAAGAGGAGGGCAAAAAUAAAAUUACAACACCCAAAGGUGUAAUUGAAUCAAAUGAGGAAAGCACAAAUU-UU
.....(((((((...(((((.(((.(((.((((....)))).))))))...............(((((....)))))............)))))..)))))))...-.. ( -27.30)
>consensus
AUCCAUUGUGCUCCAUCUGAAGCCAUUUGUUUUGUGAAAGAGGAGGGCAAAAAUAAAAUUACAACACCCAAAGGUGUAAUUGAAUCAAAUGAGGAAAGCACAAAUUUUU
.....(((((((((.((....(((.(((.((((....)))).))))))...............(((((....))))).............)))))..))))))...... (-24.32 = -24.32 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	17,245,169 – 17,245,272
Length	103
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	93.52
Mean single sequence MFE	-26.90
Consensus MFE	-19.92
Energy contribution	-19.80
Covariance contribution	-0.12
Combinations/Pair	1.09
Mean z-score	-2.42
Structure conservation index	0.74
SVM decision value	0.59
SVM RNA-class probability	0.790676
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17245169 103 + 20766785
AGCAAACGGAAACGAACAUAAAAGGGAGGAAAAUUCAGGACGAA---AGAAACAAGUGCAGCUGUUUU-CACCAAAAGAUGCGGAUGCGUCCGUUCUUUAAGCUGAA
(((...((....)).........((...((((((...(.((...---........)).)....)))))-).)).(((((.(((((....))))))))))..)))... ( -22.90)
>DroSec_CAF1 49089 104 + 1
AGCAAACGGAAACGAACAUAAAAGGGAGGAAAAUUCAGGACGAA---GGAAACAAGUGCAGCUGUUUUGCACCAAAAGAUGCGGAUGCGUCUGCUCUUUAAGCUGAA
(((...((....))......((((((.((........(.((...---(....)..)).).((......)).))...((((((....)))))).))))))..)))... ( -26.00)
>DroSim_CAF1 47815 104 + 1
AGCAAACGGAAACGAACAUAAAAGGGAGGAAAAUUCAGGACGAA---AGAAACAAGUGCAGCUGUUUUGCACCAAAAGAUGCGGAUGCGUCUGCUCUUUAAGCUGAA
(((...((....))........((((((............(...---.)......((((((.....))))))....((((((....)))))).))))))..)))... ( -25.40)
>DroEre_CAF1 47183 106 + 1
AGCAAACGGAAACGAAAAUAAAAGGGAGGAAAAUUCAGGGCGAAACAAGAAACAAGUGCAGCUGUUUU-CAGAAAAAGAUGCGGCUGCGUCUGCUCUUUAAGCUGAA
(((...((....))........((((((.....(((..(......)..))).((..(((((((((..(-(.......)).)))))))))..))))))))..)))... ( -29.00)
>DroYak_CAF1 46478 103 + 1
AGCAAACGGAAACGGACAUAAAAGGGAGGAAAAUUCAGGACGAA---GGAAACGAUUGCAGCUGUUUU-CAGCAAAAGAUGCGGCUGCGUCUGCUCUUUAAGCUGAA
(((...((....))........((((((((....)).((((...---(....)....((((((((..(-(.......)).)))))))))))).))))))..)))... ( -31.20)
>consensus
AGCAAACGGAAACGAACAUAAAAGGGAGGAAAAUUCAGGACGAA___AGAAACAAGUGCAGCUGUUUU_CACCAAAAGAUGCGGAUGCGUCUGCUCUUUAAGCUGAA
(((...((....))........((((((....................((((((........))))))........((((((....)))))).))))))..)))... (-19.92 = -19.80 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:06 2006