Locus 5419

Sequence ID	2R_DroMel_CAF1
Location	17,469,049 – 17,469,289
Length	240
Max. P	0.985588

overview

Window 4

Location	17,469,049 – 17,469,169
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.89
Mean single sequence MFE	-39.53
Consensus MFE	-39.03
Energy contribution	-39.03
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.91
Structure conservation index	0.99
SVM decision value	2.01
SVM RNA-class probability	0.985588
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17469049 120 + 20766785
GGCAUGGCCCAUGAAUAUUCAUGGCGUUUGCCGGGCCAGUCAUUCAUUCAUUCGUGAUUUCACGCAAAAGGGGGAAAUGCGAAGAAGCUGUGGAAAACAAUGAAGAGGAAUGGCACAAGA
....((((((((((....))))(((....)))))))))(((((((.(((((((((.(((((.(.(....).).)))))))))).....(((.....))).))))...)))))))...... ( -39.50)
>DroSim_CAF1 4990 120 + 1
GGCAUGGCCCAUGAAUAUUCAUGGCGUUUGCCGGGCCAGUCAUUCAUUCAUUCGUGAUUUCACGCAAAAGAGGGAAAUGCGAAGAAGCUGUGGAAAACAAUGAAGAGGAAUGGCACAAGA
....((((((((((....))))(((....)))))))))(((((((.((((((.((..((((((((.....................)).)))))).))))))))...)))))))...... ( -38.90)
>DroYak_CAF1 5277 120 + 1
GGCAUGGCCCAUGAAUAUUCAUGGCGUUUGCCGGGCCAGUCAUUCAUUCAUUCGUGAUUUCACGCUAAAGGGGGAAAUGCGAAGAAGCUGUGGAAAACAAUGAAGAGGAAUGGCACAAGA
....((((((((((....))))(((....)))))))))(((((((.((((((.((..(((((((((...(.(.....).).....))).)))))).))))))))...)))))))...... ( -40.20)
>consensus
GGCAUGGCCCAUGAAUAUUCAUGGCGUUUGCCGGGCCAGUCAUUCAUUCAUUCGUGAUUUCACGCAAAAGGGGGAAAUGCGAAGAAGCUGUGGAAAACAAUGAAGAGGAAUGGCACAAGA
....((((((((((....))))(((....)))))))))(((((((.(((((((((.(((((.(.(....).).)))))))))).....(((.....))).))))...)))))))...... (-39.03 = -39.03 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	17,469,049 – 17,469,169
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.89
Mean single sequence MFE	-32.20
Consensus MFE	-32.20
Energy contribution	-32.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.51
Structure conservation index	1.00
SVM decision value	1.75
SVM RNA-class probability	0.975576
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17469049 120 - 20766785
UCUUGUGCCAUUCCUCUUCAUUGUUUUCCACAGCUUCUUCGCAUUUCCCCCUUUUGCGUGAAAUCACGAAUGAAUGAAUGACUGGCCCGGCAAACGCCAUGAAUAUUCAUGGGCCAUGCC
......(((((((...((((((..........((......))..............((((....)))))))))).)))))..(((((((((....)))((((....)))))))))).)). ( -32.20)
>DroSim_CAF1 4990 120 - 1
UCUUGUGCCAUUCCUCUUCAUUGUUUUCCACAGCUUCUUCGCAUUUCCCUCUUUUGCGUGAAAUCACGAAUGAAUGAAUGACUGGCCCGGCAAACGCCAUGAAUAUUCAUGGGCCAUGCC
......(((((((...((((((..........((......))..............((((....)))))))))).)))))..(((((((((....)))((((....)))))))))).)). ( -32.20)
>DroYak_CAF1 5277 120 - 1
UCUUGUGCCAUUCCUCUUCAUUGUUUUCCACAGCUUCUUCGCAUUUCCCCCUUUAGCGUGAAAUCACGAAUGAAUGAAUGACUGGCCCGGCAAACGCCAUGAAUAUUCAUGGGCCAUGCC
......(((((((...((((((..........((......))..............((((....)))))))))).)))))..(((((((((....)))((((....)))))))))).)). ( -32.20)
>consensus
UCUUGUGCCAUUCCUCUUCAUUGUUUUCCACAGCUUCUUCGCAUUUCCCCCUUUUGCGUGAAAUCACGAAUGAAUGAAUGACUGGCCCGGCAAACGCCAUGAAUAUUCAUGGGCCAUGCC
......(((((((...((((((..........((......))..............((((....)))))))))).)))))..(((((((((....)))((((....)))))))))).)). (-32.20 = -32.20 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	17,469,169 – 17,469,289
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-23.70
Consensus MFE	-20.92
Energy contribution	-22.20
Covariance contribution	1.28
Combinations/Pair	1.04
Mean z-score	-2.87
Structure conservation index	0.88
SVM decision value	1.02
SVM RNA-class probability	0.901663
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17469169 120 + 20766785
CAAAACAUGAAGCCAAAUAAAUAAACAAAUGUCAAGCCAUGUUGCUGAGGGCGGACACAAAAGCCAAGAAAUUGGCGUGAAAAUAAAUCAAGAAAUAAAUUGGAAAAUUUGUUAUUUCAA
.......(((((.................((((..(((...........))).))))((...(((((....))))).))..............((((((((....)))))))).))))). ( -23.30)
>DroSim_CAF1 5110 120 + 1
CAAAACAUGAAGCCAAAUAAAUAAACAAAUGUCAAGCCAUGUUGCUGAGGGCGGACACAAAAGCCAAGAAAUUGGCGUGAGAAUAAAUCAAGAAAUAAAUUGGAAAAUUUGUUAUUUCAA
.......(((((.................((((..(((...........))).))))((...(((((....))))).))..............((((((((....)))))))).))))). ( -23.30)
>DroYak_CAF1 5397 120 + 1
CAAAACAUGAAACCAAAUAAAUAAACAAAUGUCAGGCCAUGUUGCUGAGGGCGGACACAAAAGCCAAGAAAUUGGCGUGAAAAUAAAUCAAGAAAUAAAUUGGAAAAUUUGUUAUUUCAA
.......(((((.................((((..(((...........))).))))((...(((((....))))).))..............((((((((....)))))))).))))). ( -24.50)
>consensus
CAAAACAUGAAGCCAAAUAAAUAAACAAAUGUCAAGCCAUGUUGCUGAGGGCGGACACAAAAGCCAAGAAAUUGGCGUGAAAAUAAAUCAAGAAAUAAAUUGGAAAAUUUGUUAUUUCAA
.......(((((...................(((.((((.....((...(((..........))).))....)))).))).............((((((((....)))))))).))))). (-20.92 = -22.20 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:21 2006