Locus 3398

Sequence ID	X_DroMel_CAF1
Location	9,096,333 – 9,096,438
Length	105
Max. P	0.709982

overview

Window 1

Location	9,096,333 – 9,096,438
Length	105
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	87.31
Mean single sequence MFE	-29.32
Consensus MFE	-21.90
Energy contribution	-22.38
Covariance contribution	0.48
Combinations/Pair	1.15
Mean z-score	-1.79
Structure conservation index	0.75
SVM decision value	0.37
SVM RNA-class probability	0.709982
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9096333 105 + 22224390
AGCAGCGGGGAUCGGGAUCAUGGAACUCCUAGUUUCCAAUGCCAAUUCCCCAUACCCUUUCCACGGAGACAAAGGAAUGGAAU---AUGGCAUUUCAAAUUGGAAAGU
......(((((...((....(((((........)))))...))...))))).....(((((((.(....)...((((((....---....))))))....))))))). ( -32.30)
>DroSec_CAF1 3421 105 + 1
AGCAGCGGGGAUCGGGAUCAUGGAACCUCUAGUUUCCAAUGCCAAUUUCCCAUACCCUUUCCACGGAGACAAAGGAAUGGAAU---AUGGCAUUUCAAAUUGGAAAGU
......(((((...((....(((((.(....).)))))...))...))))).....(((((((.(....)...((((((....---....))))))....))))))). ( -29.80)
>DroSim_CAF1 2068 105 + 1
AGCAGCGGGGAUCGGGAUCAUGGAACCUCUAGUUUCCAAUGCCAAUUUCCCAUGCCCUUUCCACGGAGACAAAGGAAUGGAAU---AUGGCAUUUCAAAUUGGAAAGU
.(((..(((((...((....(((((.(....).)))))...))...))))).))).(((((((.(....)...((((((....---....))))))....))))))). ( -32.90)
>DroEre_CAF1 3361 102 + 1
AGCAGUGGGGA------UCGUGGAACUCCUAGUUCUCAAUUCCCAUUUCCCAUACCCUUUUCAUGAAGAAAAAGGAAUGGAAUGGAAUGGCAUUUCGAAUUGGAAAGU
.((((((((((------(.(.(((((.....)))))).)))))))))..((((.((.(((((.....))))).)).)))).........)).((((......)))).. ( -28.20)
>DroYak_CAF1 3528 99 + 1
AUUAGUGGGGA------UCAUGGAACUCCAAGUGCCCAAUGCCAAUUUCCCAUACCCUUUCCACGAAGACAAAGGAAUGGAAU---AUGGCAUUUCAAAUUGGAAAGU
.....((((.(------(..(((....))).)).))))...(((((((.(((((.((.((((...........)))).))..)---))))......)))))))..... ( -23.40)
>consensus
AGCAGCGGGGAUCGGGAUCAUGGAACUCCUAGUUUCCAAUGCCAAUUUCCCAUACCCUUUCCACGGAGACAAAGGAAUGGAAU___AUGGCAUUUCAAAUUGGAAAGU
......(((((...((.....(((((.....))))).....))...))))).....(((((((.(....)...((((((...........))))))....))))))). (-21.90 = -22.38 +   0.48)

alignment

secondary structure

dotplot

Window 2

Location	9,096,333 – 9,096,438
Length	105
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	87.31
Mean single sequence MFE	-27.62
Consensus MFE	-21.76
Energy contribution	-21.16
Covariance contribution	-0.60
Combinations/Pair	1.21
Mean z-score	-1.45
Structure conservation index	0.79
SVM decision value	-0.02
SVM RNA-class probability	0.524702
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9096333 105 - 22224390
ACUUUCCAAUUUGAAAUGCCAU---AUUCCAUUCCUUUGUCUCCGUGGAAAGGGUAUGGGGAAUUGGCAUUGGAAACUAGGAGUUCCAUGAUCCCGAUCCCCGCUGCU
.(((((((....((((((....---....))))......))....)))))))((((((((((.((((...(((((........))))).....)))))))))).)))) ( -28.70)
>DroSec_CAF1 3421 105 - 1
ACUUUCCAAUUUGAAAUGCCAU---AUUCCAUUCCUUUGUCUCCGUGGAAAGGGUAUGGGAAAUUGGCAUUGGAAACUAGAGGUUCCAUGAUCCCGAUCCCCGCUGCU
..((((((.......((((((.---.((((((.(((((..(.....)..))))).))))))...)))))))))))).(((.((......(((....))).)).))).. ( -25.51)
>DroSim_CAF1 2068 105 - 1
ACUUUCCAAUUUGAAAUGCCAU---AUUCCAUUCCUUUGUCUCCGUGGAAAGGGCAUGGGAAAUUGGCAUUGGAAACUAGAGGUUCCAUGAUCCCGAUCCCCGCUGCU
.(((((((....((((((....---....))))......))....)))))))((((((((..(((((...(((((.(....).))))).....))))).)))).)))) ( -26.00)
>DroEre_CAF1 3361 102 - 1
ACUUUCCAAUUCGAAAUGCCAUUCCAUUCCAUUCCUUUUUCUUCAUGAAAAGGGUAUGGGAAAUGGGAAUUGAGAACUAGGAGUUCCACGA------UCCCCACUGCU
.................((.......((((((.((((((((.....)))))))).))))))..((((.((((.((((.....))))..)))------).))))..)). ( -28.30)
>DroYak_CAF1 3528 99 - 1
ACUUUCCAAUUUGAAAUGCCAU---AUUCCAUUCCUUUGUCUUCGUGGAAAGGGUAUGGGAAAUUGGCAUUGGGCACUUGGAGUUCCAUGA------UCCCCACUAAU
..............(((((((.---.((((((.(((((.(((....)))))))).))))))...)))))))(((....(((....)))...------..)))...... ( -29.60)
>consensus
ACUUUCCAAUUUGAAAUGCCAU___AUUCCAUUCCUUUGUCUCCGUGGAAAGGGUAUGGGAAAUUGGCAUUGGAAACUAGGAGUUCCAUGAUCCCGAUCCCCGCUGCU
(((((....(((..(((((((.....((((((.(((((.((.....)).))))).))))))...)))))))..)))...)))))........................ (-21.76 = -21.16 +  -0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:24 2006