Locus 2942

Sequence ID	X_DroMel_CAF1
Location	7,887,038 – 7,887,194
Length	156
Max. P	0.869936

overview

Window 5

Location	7,887,038 – 7,887,154
Length	116
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	97.13
Mean single sequence MFE	-48.30
Consensus MFE	-44.54
Energy contribution	-44.79
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.82
Structure conservation index	0.92
SVM decision value	0.44
SVM RNA-class probability	0.736396
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7887038 116 - 22224390
AGGCAAUCACUGGCGAUCGCGACCGUGACAGGGAUCGCGAGCGGGAACGUGAACGUUCCGGCAGCGGUGGCGGUCAGUCUGGCAAUGGGAACAACAGCAGCAAUUCGGCCAACAGC
.(((........((((((((.(((((((......))))..((.((((((....)))))).))...))).)))))).(.(((....((....)).)))).))......)))...... ( -46.54)
>DroSec_CAF1 935 116 - 1
AGGCAAUCACUGGCGAUCGCGACCGUGACAGGGAUCGCGAGCGGGAACGUGAGCGAUCCGGCAGCGGUGGCGGUCAGUCCGGCAAUGGGAACAACAGCAGCAAUUCGGCCAACAGC
.(((.....(((((((((((.(((((..(..(((((((..(((....)))..))))))).)..))))).)))))).).))))...((....))..............)))...... ( -51.70)
>DroEre_CAF1 981 116 - 1
AGGCAAUCACUGGCGAUCGCGACCGUGACAGGGAUCGCGAGCGGGAACGUGAGCGUUCCGGCAGCGGUGGCGGUCAGUCCGGCAAUGGAAACAACAGCAGCAAUUCGGCCAACAGC
.(((.....(((((((((((.(((((....((((.(((..(((....)))..)))))))....))))).)))))).).))))...((....))..............)))...... ( -49.30)
>DroYak_CAF1 1003 116 - 1
AGGCAAUCACUGGCGAUCGCGACCGUGACAGAGAUCGCGAGCGGGAACGUGAGCGUUCCGGCAGCGGUGGCGGUCAUUCCGGCAAUGGCAACAACAGCAGCAAUUCGGCCAACAGC
.(((........((((((((.(((((((......))))..((.((((((....)))))).))...))).))))))......((..((....))...)).))......)))...... ( -45.64)
>consensus
AGGCAAUCACUGGCGAUCGCGACCGUGACAGGGAUCGCGAGCGGGAACGUGAGCGUUCCGGCAGCGGUGGCGGUCAGUCCGGCAAUGGGAACAACAGCAGCAAUUCGGCCAACAGC
.(((........((((((((.(((((((......))))..((.((((((....)))))).))...))).))))))......((..((....))...)).))......)))...... (-44.54 = -44.79 +   0.25)

alignment

secondary structure

dotplot

Window 6

Location	7,887,078 – 7,887,194
Length	116
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	96.41
Mean single sequence MFE	-56.85
Consensus MFE	-51.47
Energy contribution	-51.10
Covariance contribution	-0.37
Combinations/Pair	1.08
Mean z-score	-2.07
Structure conservation index	0.91
SVM decision value	0.87
SVM RNA-class probability	0.869936
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7887078 116 - 22224390
GGCGGCAGCAGUAGUGGCGGUGCCGGUUCGACCAGCCAACAGGCAAUCACUGGCGAUCGCGACCGUGACAGGGAUCGCGAGCGGGAACGUGAACGUUCCGGCAGCGGUGGCGGUCA
..(((((.(.((....))).)))))....((((.(((....)))..((((((.(..((((((((.......)).))))))((.((((((....)))))).)).))))))).)))). ( -54.80)
>DroSec_CAF1 975 116 - 1
GGCGGCGGCAGUAGUGGUGGUGCCGGUUCGACCAGCCAACAGGCAAUCACUGGCGAUCGCGACCGUGACAGGGAUCGCGAGCGGGAACGUGAGCGAUCCGGCAGCGGUGGCGGUCA
.(((((((((.((....)).))))((.....)).)))..(((.......)))))((((((.(((((..(..(((((((..(((....)))..))))))).)..))))).)))))). ( -60.20)
>DroEre_CAF1 1021 116 - 1
GGCGGCGGCAGUAGUAGCGGUGCCGGUUCGGCCAGCCAACAGGCAAUCACUGGCGAUCGCGACCGUGACAGGGAUCGCGAGCGGGAACGUGAGCGUUCCGGCAGCGGUGGCGGUCA
.((.((.((....)).)).))((((((...(((........)))....))))))((((((.(((((....((((.(((..(((....)))..)))))))....))))).)))))). ( -56.80)
>DroYak_CAF1 1043 116 - 1
GGCGGCGGUAGUAGUGGCGGUGCCGGUUCGGCCAGCCAACAGGCAAUCACUGGCGAUCGCGACCGUGACAGAGAUCGCGAGCGGGAACGUGAGCGUUCCGGCAGCGGUGGCGGUCA
(.(((.(((.((..((((.(.((((...))))).))))....)).))).))).)((((((.(((((((......))))..((.((((((....)))))).))...))).)))))). ( -55.60)
>consensus
GGCGGCGGCAGUAGUGGCGGUGCCGGUUCGACCAGCCAACAGGCAAUCACUGGCGAUCGCGACCGUGACAGGGAUCGCGAGCGGGAACGUGAGCGUUCCGGCAGCGGUGGCGGUCA
.((.((.((....)).)).))((((((..((...(((....)))..))))))))((((((.(((((((......))))..((.((((((....)))))).))...))).)))))). (-51.47 = -51.10 +  -0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:17 2006