Locus 1418

Sequence ID	3L_DroMel_CAF1
Location	4,121,617 – 4,121,857
Length	240
Max. P	0.783055

overview

Window 5

Location	4,121,617 – 4,121,737
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.56
Mean single sequence MFE	-51.15
Consensus MFE	-46.69
Energy contribution	-46.50
Covariance contribution	-0.19
Combinations/Pair	1.11
Mean z-score	-1.61
Structure conservation index	0.91
SVM decision value	0.30
SVM RNA-class probability	0.679288
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4121617 120 - 23771897
AGCGACUGGGACAGGAACAUCGAUUUGGCCGCGUCGGUGCAGCAGAAGCUGGACGCCUACAAGGCCGACGAUGCCACCAUGGGCGAGGGCCCCGAGAAGGCACGAUCCCAGCUGCUGAUC
((((.((((((..((....(((...((((..(((((((.((((....)))).))(((.....))))))))..))))....((((....))))))).....).)..)))))).)))).... ( -51.60)
>DroSec_CAF1 3236 120 - 1
AGCGAUUGGGACAGGAACAUCGAUCUGGCCGCGUCUGUGCAGCAGAAGCUGGACGCCUACAAGGCCGACGAUGCCACCAUGGGCGAGGGCCCUGAGAAGGCACGAUCCCAGCUGCUGAUU
((((.((((((..(....((((.((.(((((((((....((((....)))))))))......))))))))))(((.(((.((((....)))))).)..))).)..)))))).)))).... ( -47.20)
>DroEre_CAF1 3432 120 - 1
AGCGACUGGGACAGGAACAUCGAUUUGGCCGCGUCGGUGCAGCAGAAGCUGGACGCCUACAAGGCCGACGAUGCCACCAUGGGCGAGGGUCCCGAGAAGGCCCGAUCCCAGCUGCUGAUC
((((.((((((..((..(.(((...((((..(((((((.((((....)))).))(((.....))))))))..))))....((((....)))))))...)..))..)))))).)))).... ( -52.60)
>DroYak_CAF1 3882 120 - 1
AGCGACUGGGACAGGAACAUCGAUCUGGCGGCGUCGGUGCAGCAGAAGCUGGACGCCUACAAGGCCGACGAUGCCACCAUGGGCGAGGGACCCGAGAAGGCUCGAUCUCAGCUGCUGAUC
((((.((((((..((..(.(((..((((.(((((((((.((((....)))).))(((.....)))...))))))).))).)..))).)..))((((....)))).)))))).)))).... ( -53.20)
>consensus
AGCGACUGGGACAGGAACAUCGAUCUGGCCGCGUCGGUGCAGCAGAAGCUGGACGCCUACAAGGCCGACGAUGCCACCAUGGGCGAGGGCCCCGAGAAGGCACGAUCCCAGCUGCUGAUC
((((.((((((..((....(((...((((..(((((((.((((....)))).))(((.....))))))))..))))....((((....))))))).....).)..)))))).)))).... (-46.69 = -46.50 +  -0.19)

alignment

secondary structure

dotplot

Window 6

Location	4,121,737 – 4,121,857
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.50
Mean single sequence MFE	-48.75
Consensus MFE	-47.34
Energy contribution	-47.52
Covariance contribution	0.19
Combinations/Pair	1.05
Mean z-score	-1.80
Structure conservation index	0.97
SVM decision value	0.56
SVM RNA-class probability	0.783055
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4121737 120 + 23771897
GCGGUAGCGCACAUUUGGGUACUCCCCAAGGGUAGCGCACAGUGUGGCUAUUUGCUCGGCAAUUCGCUCGAUGUGCUUGCUCCGAAUGGAGGCAAAGGCCGGCGAGUAGAGGCAUUGGAA
......((((((.((((((.....)))))).)).)))).((((((..((((((((.((((.....((.......))(((((((....))).))))..))))))))))))..))))))... ( -51.00)
>DroSec_CAF1 3356 120 + 1
GCGGUAGCGCACAUUUGGGUAUUCCCCAAGGGUAGCGCACAGUGUGGCUAUUUGCUCGGCAAUCCGCUCGAUGUGCUUGCUCCGAAUGGAGGCAAAGGCCGGCGAGUAGAGGCAUUGGAA
......((((((.((((((.....)))))).)).)))).((((((..((((((((.((((....(((.....))).(((((((....))).))))..))))))))))))..))))))... ( -51.00)
>DroEre_CAF1 3552 120 + 1
GCGGUAGCGCACAUUUGGGUAUUCCCCGAGGGUAGCGCACAGUGUGGCUAUUUGCUCGGCAAUCCGCUCGAUGUGCUUGCUCCGAAUGGAGGCAAAGGCCGGCGAGUAUAGGCAUUGGAA
......((((((.((((((.....)))))).)).)))).((((((...(((((((.((((....(((.....))).(((((((....))).))))..)))))))))))...))))))... ( -45.30)
>DroYak_CAF1 4002 120 + 1
GCGGUAGCGCACAUUCGGGUAUUCCCCAAGGGUAGCGCACAGUGUGGCUAUUUGCUCGGCAAUCCGCUCGAUGUGCUUGCUGCGAAUGGAGGCAAAGGCCGGCGAGUAGAGGCAUUGGAA
......((((((.((.(((....))).))..)).)))).((((((..((((((((.((((......(((.((.(((.....))).)).)))......))))))))))))..))))))... ( -47.70)
>consensus
GCGGUAGCGCACAUUUGGGUAUUCCCCAAGGGUAGCGCACAGUGUGGCUAUUUGCUCGGCAAUCCGCUCGAUGUGCUUGCUCCGAAUGGAGGCAAAGGCCGGCGAGUAGAGGCAUUGGAA
......((((((.((((((.....)))))).)).)))).((((((..((((((((.((((..((((.(((..((....))..))).)))).......))))))))))))..))))))... (-47.34 = -47.52 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:02 2006