Locus 3048

Sequence ID	X_DroMel_CAF1
Location	8,154,823 – 8,154,982
Length	159
Max. P	0.873725

overview

Window 7

Location	8,154,823 – 8,154,927
Length	104
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	89.50
Mean single sequence MFE	-32.63
Consensus MFE	-25.65
Energy contribution	-25.74
Covariance contribution	0.09
Combinations/Pair	1.21
Mean z-score	-2.30
Structure conservation index	0.79
SVM decision value	0.01
SVM RNA-class probability	0.540527
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8154823 104 + 22224390
AUCCAGUGACAUUACC----------AUCUGGUGUACUCACUUUUGGCCACCUAUUGCGGCUGGCCUAAACAUCUUAAACGAGCCUUGAGGCCGUUAAAUGGCGUCAAGUAAUU
....(((((...((((----------....))))...)))))...(((((((......)).)))))..................(((((.(((((...))))).)))))..... ( -32.40)
>DroSec_CAF1 58057 104 + 1
UUCCAGUGACAUUACC----------AUAUGGUUUACUCACUUUUGGCCACCUAUUGCGGUUGGCCUAAACAUCUUAAACGAGCCUUGAGGCCGUUAGACGGCGUCAAGUAAUU
....(((((....(((----------....)))....)))))...(((((((......)).)))))..................(((((.((((.....)))).)))))..... ( -33.20)
>DroSim_CAF1 39436 104 + 1
UUCCAGUGACAUUACC----------AUCUGGUUUACUCACUUUUGGCCACCUAUUGCGGUUGGCCUAAACAUCUUAAACGAGCCUUGAGGCCGUUAGACGGCGUCAAGUAAUU
....(((((....(((----------....)))....)))))...(((((((......)).)))))..................(((((.((((.....)))).)))))..... ( -33.20)
>DroEre_CAF1 48819 114 + 1
AUCCAGUGACAUUACCAUCUGCUACCAUCUGGUGUACUCACUUUUGGCCACCUAUUGCGGUUGGCCUAAACACCUUAAACGAGCCAUGAGGCCUUUAGACGGCGUCAAGUUAUU
....((((((..........(((.......(((((..........(((((((......)).)))))...))))).......)))..(((.(((.......))).))).)))))) ( -30.26)
>DroYak_CAF1 45884 104 + 1
AUCCAGUGGCAUUAGC----------AUCUGGUGUACUCACUUUUGGCCACCUAUUGCGGCUGGCCUAAACAUCUCAAACGAGCCUUGAGGCCGUUGGACGGCGUCAAGUAAUU
..((((..((....))----------..)))).............(((((((......)).))))).......(((....))).(((((.((((.....)))).)))))..... ( -33.30)
>DroAna_CAF1 66862 104 + 1
UUACGGUGGCAUUCCC----------AUCUGGUUUACUCACUUUUGGCCACAUCUUGCGGUUGGCCUAAACAUCUUAAACGAGCCUUGAGGCCGUUAGACGGUGUCGAGUAAUU
....(((((.....))----------)))....((((((......(((((.(((....))))))))...(((((((.((((.(((....))))))).)).))))).)))))).. ( -33.40)
>consensus
AUCCAGUGACAUUACC__________AUCUGGUGUACUCACUUUUGGCCACCUAUUGCGGUUGGCCUAAACAUCUUAAACGAGCCUUGAGGCCGUUAGACGGCGUCAAGUAAUU
....(((((....(((..............)))....)))))...(((((((......)).)))))..................(((((.((((.....)))).)))))..... (-25.65 = -25.74 +   0.09)

alignment

secondary structure

dotplot

Window 8

Location	8,154,887 – 8,154,982
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	90.78
Mean single sequence MFE	-27.72
Consensus MFE	-21.42
Energy contribution	-21.50
Covariance contribution	0.08
Combinations/Pair	1.15
Mean z-score	-1.87
Structure conservation index	0.77
SVM decision value	0.68
SVM RNA-class probability	0.819791
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8154887 95 + 22224390
UUAAACGAGCCUUGAGGCCGUUAAAUGGCGUCAAGUAAUUUGGGCAAGCACAUGGCUGCUGGAUUCUGAAUUCCGAGUACACUCAUAAAAAGAUG
.....((((.(((((.(((((...))))).)))))...))))((((.((.....))))))(((........)))(((....)))........... ( -24.90)
>DroSec_CAF1 58121 94 + 1
UUAAACGAGCCUUGAGGCCGUUAGACGGCGUCAAGUAAUUUG-GCCAGCACAUGGCUGCUGGAUUCGGAAUUCCAAAUACACUCAUAAAAAGAUG
......(((.(((((.((((.....)))).)))))..(((((-(((((((......))))))..........))))))...)))........... ( -29.30)
>DroSim_CAF1 39500 93 + 1
UUAAACGAGCCUUGAGGCCGUUAGACGGCGUCAAGUAAUUU--GCCAGCACAUGGCUGCUGGAUUCGGAAUUCCGAGUACACUCAUAAAAAGAUG
......(((.(((((.((((.....)))).)))))......--.((((((......))))))((((((....))))))...)))........... ( -33.50)
>DroEre_CAF1 48893 94 + 1
UUAAACGAGCCAUGAGGCCUUUAGACGGCGUCAAGUUAUUUG-GACAGCACAUGGCUGCUGGAUUCCGAAUUCCGAGUACACUCAUAAAAAGAUG
............(((.(((.......))).))).(..(((((-(((((((......)))))...)))))))..)(((....)))........... ( -24.20)
>DroYak_CAF1 45948 94 + 1
UCAAACGAGCCUUGAGGCCGUUGGACGGCGUCAAGUAAUUUG-GACAGCACAUGGCUGCUGGAUUCUGGAUUCCAACUGCACUUAUAAAAAAAUA
............((((((.((((((....(((.((.((((..-(.((((.....)))))..)))))).))))))))).)).)))).......... ( -26.70)
>consensus
UUAAACGAGCCUUGAGGCCGUUAGACGGCGUCAAGUAAUUUG_GCCAGCACAUGGCUGCUGGAUUCGGAAUUCCGAGUACACUCAUAAAAAGAUG
......(((.(((((.((((.....)))).)))))..........((((.....)))).((((........))))......)))........... (-21.42 = -21.50 +   0.08)

alignment

secondary structure

dotplot

Window 9

Location	8,154,887 – 8,154,982
Length	95
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	90.78
Mean single sequence MFE	-26.68
Consensus MFE	-20.22
Energy contribution	-21.62
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-2.13
Structure conservation index	0.76
SVM decision value	0.88
SVM RNA-class probability	0.873725
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8154887 95 - 22224390
CAUCUUUUUAUGAGUGUACUCGGAAUUCAGAAUCCAGCAGCCAUGUGCUUGCCCAAAUUACUUGACGCCAUUUAACGGCCUCAAGGCUCGUUUAA
.........((((((......(((........))).(((((.....)).)))........(((((.(((.......))).))))))))))).... ( -21.50)
>DroSec_CAF1 58121 94 - 1
CAUCUUUUUAUGAGUGUAUUUGGAAUUCCGAAUCCAGCAGCCAUGUGCUGGC-CAAAUUACUUGACGCCGUCUAACGGCCUCAAGGCUCGUUUAA
.........((((((..((((((....))))))((((((......)))))).-.......(((((.((((.....)))).))))))))))).... ( -31.40)
>DroSim_CAF1 39500 93 - 1
CAUCUUUUUAUGAGUGUACUCGGAAUUCCGAAUCCAGCAGCCAUGUGCUGGC--AAAUUACUUGACGCCGUCUAACGGCCUCAAGGCUCGUUUAA
.........((((((....((((....))))..((((((......)))))).--......(((((.((((.....)))).))))))))))).... ( -32.10)
>DroEre_CAF1 48893 94 - 1
CAUCUUUUUAUGAGUGUACUCGGAAUUCGGAAUCCAGCAGCCAUGUGCUGUC-CAAAUAACUUGACGCCGUCUAAAGGCCUCAUGGCUCGUUUAA
...((((..(((.((((.(..(..(((.(((...(((((......)))))))-).)))..)..))))))))..))))(((....)))........ ( -21.80)
>DroYak_CAF1 45948 94 - 1
UAUUUUUUUAUAAGUGCAGUUGGAAUCCAGAAUCCAGCAGCCAUGUGCUGUC-CAAAUUACUUGACGCCGUCCAACGGCCUCAAGGCUCGUUUGA
............((..((((((((........)))))).....))..))...-(((((..(((((.((((.....)))).)))))....))))). ( -26.60)
>consensus
CAUCUUUUUAUGAGUGUACUCGGAAUUCAGAAUCCAGCAGCCAUGUGCUGGC_CAAAUUACUUGACGCCGUCUAACGGCCUCAAGGCUCGUUUAA
.........((((((..................((((((......)))))).........(((((.((((.....)))).))))))))))).... (-20.22 = -21.62 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:45 2006