Locus 4528

Sequence ID	X_DroMel_CAF1
Location	11,935,487 – 11,935,638
Length	151
Max. P	0.837622

overview

Window 3

Location	11,935,487 – 11,935,599
Length	112
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	86.39
Mean single sequence MFE	-42.86
Consensus MFE	-31.56
Energy contribution	-32.52
Covariance contribution	0.96
Combinations/Pair	1.14
Mean z-score	-2.07
Structure conservation index	0.74
SVM decision value	0.74
SVM RNA-class probability	0.837622
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11935487 112 - 22224390
ACACUGACAUCGAUUCGCACCCACUUCCCUGUUUUCGAAUAACAGGGAUGAUGAGGUGGAUGCAGGA-------UUCAGGAUUCAGUACUCCGGAUUCGGGUUGGUGGCACGGAGAGAU
...(((.((((((((((((.(((((((((((((.......))))))))......))))).))).(((-------(((.(((........))))))))))))))))))...)))...... ( -41.50)
>DroSec_CAF1 18658 118 - 1
ACACUGACAUCGAUUCGCACCCACUUCCCUGUUUUCGAAUAACAGGGAUGAUGAGGUGGAUGCAGGAUGCAGGAUUCAGUAUUCAGUACUCCGGAUUCGGGUUGGUGG-ACGGAGAGAU
.(((..((.((((.(((((.(((((((((((((.......))))))))......))))).))).((((((.((((.....)))).))).))).)).))))))..))).-.......... ( -43.00)
>DroSim_CAF1 9349 119 - 1
ACACUGACAUCGAUUCGCACCCACUUCCCUGUUUUCGAAUAACAGGGAUGAUGAGGUGGAUGCAGGAUGCAGGAUUCAGUAUUCAGUACUCCGGAUUCGGGUUGGUGGCACGGAGAGAU
.(((..((.((((.(((((.(((((((((((((.......))))))))......))))).))).((((((.((((.....)))).))).))).)).))))))..)))............ ( -43.00)
>DroEre_CAF1 3384 119 - 1
ACACCGACAUCGAAUCGCACCCACUUCCAAGUUUCCGAAGGGCAGGGACGACGAGGUGGGUGCAGGAUGCAGGAUUCGGGAUACAGUACUCCGGAACCGGGUUGGUGGAACGGAGAGCU
.(((((((.((((((((((((((((((...((((((....))...))))...))))))))))).(....)..)))))))...........(((....))))))))))............ ( -48.80)
>DroYak_CAF1 2876 112 - 1
ACACUGACAUCGAUUCGCACCCACCUCGCAGUUUUCGAAGGGCAGGGAUGAUGAGGUUGGUGCAGGAUUCAGGAUU-------CAGAACUCCGGAUUCGGCUUGGUGGCACGGAGAGAU
...((((.(((((((((((((.((((((..((((..(.....)..))))..)))))).))))).)))))...))))-------)))..(((((......(((....))).))))).... ( -38.00)
>consensus
ACACUGACAUCGAUUCGCACCCACUUCCCUGUUUUCGAAUAACAGGGAUGAUGAGGUGGAUGCAGGAUGCAGGAUUCAGGAUUCAGUACUCCGGAUUCGGGUUGGUGGCACGGAGAGAU
.(((((((.((((.(((((.(((((((((((((.......))))))))......))))).))).((((((...............))).))).)).)))))))))))............ (-31.56 = -32.52 +   0.96)

alignment

secondary structure

dotplot

Window 4

Location	11,935,526 – 11,935,638
Length	112
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	85.88
Mean single sequence MFE	-34.46
Consensus MFE	-23.14
Energy contribution	-24.78
Covariance contribution	1.64
Combinations/Pair	1.04
Mean z-score	-2.19
Structure conservation index	0.67
SVM decision value	0.48
SVM RNA-class probability	0.751719
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11935526 112 + 22224390
CCUGAA-------UCCUGCAUCCACCUCAUCAUCCCUGUUAUUCGAAAACAGGGAAGUGGGUGCGAAUCGAUGUCAGUGUAUUAGUAAUUGUUUGAUUUCACCCGCCUCCUGGUAACAC
......-------..........(((......((((((((.......)))))))).(((((((.(((((((...((((.........)))).)))))))))))))).....)))..... ( -33.10)
>DroSec_CAF1 18696 119 + 1
ACUGAAUCCUGCAUCCUGCAUCCACCUCAUCAUCCCUGUUAUUCGAAAACAGGGAAGUGGGUGCGAAUCGAUGUCAGUGUAUUAGUAAUUGUUUGAUUUCACCCGCCUCCUGGAAUCAC
((((((..(((((((.(((((((((.......((((((((.......)))))))).)))))))))....)))).)))..).))))).......((((((((.........)))))))). ( -37.50)
>DroSim_CAF1 9388 119 + 1
ACUGAAUCCUGCAUCCUGCAUCCACCUCAUCAUCCCUGUUAUUCGAAAACAGGGAAGUGGGUGCGAAUCGAUGUCAGUGUAUUAGUAAUUGUUUGAUUUCACCCGCCUCCUGGAAUCAC
((((((..(((((((.(((((((((.......((((((((.......)))))))).)))))))))....)))).)))..).))))).......((((((((.........)))))))). ( -37.50)
>DroEre_CAF1 3423 110 + 1
CCCGAAUCCUGCAUCCUGCACCCACCUCGUCGUCCCUGCCCUUCGGAAACUUGGAAGUGGGUGCGAUUCGAUGUCGGUGUAUUAGUAAUUGUUUGAUUUCACCCGCCUCC---------
..((((((.........((((((((.((...((..(((.....)))..))...)).))))))))))))))..((.((((.(((((.......)))))..)))).))....--------- ( -29.90)
>DroYak_CAF1 2912 115 + 1
----AAUCCUGAAUCCUGCACCAACCUCAUCAUCCCUGCCCUUCGAAAACUGCGAGGUGGGUGCGAAUCGAUGUCAGUGUAUUAGUAAUUGUUUGAUUUCACCCGCCUCCGGGAGUCAC
----.....(((.(((((...................((............))((((((((((.(((((((...((((.........)))).)))))))))))))))))))))).))). ( -34.30)
>consensus
ACUGAAUCCUGCAUCCUGCAUCCACCUCAUCAUCCCUGUUAUUCGAAAACAGGGAAGUGGGUGCGAAUCGAUGUCAGUGUAUUAGUAAUUGUUUGAUUUCACCCGCCUCCUGGAAUCAC
................................((((((((.......)))))))).(((((((.(((((((...((((.........)))).))))))))))))))............. (-23.14 = -24.78 +   1.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:20 2006