Locus 5559

Sequence ID	2L_DroMel_CAF1
Location	15,827,479 – 15,827,690
Length	211
Max. P	0.851519

overview

Window 8

Location	15,827,479 – 15,827,599
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.22
Mean single sequence MFE	-45.50
Consensus MFE	-41.69
Energy contribution	-42.13
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-2.12
Structure conservation index	0.92
SVM decision value	0.64
SVM RNA-class probability	0.808768
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15827479 120 + 22407834
ACAGACUGAGAACGGGUGGGUGGGCGCUAGAUGGCGAGGUGGCAAGGACAUCCUUUUCCAUGGCAGCCGGCAAAUAUCGAGAGGUAAACACGUGCAUUGCCAGCUUCCGUUAUCAGUCAG
...((((((.((((((..((..(((((..(.(((((..((((.((((....))))..))))..).)))).)...((((....)))).....)))).)..))....)))))).)))))).. ( -46.90)
>DroSec_CAF1 15 119 + 1
ACAGACUGAGAACGGGUGGGUG-GCGCUAGAAGGCGAGGUGGCGAGGACAUCCUUUUCCAUGGCAGCCGGCAAAUAUCGAGAGGUAAACACGAGCAUUGCCAGCUUCCGUUAUCAGUCAG
...((((((.((((((.((.((-(((((.(..((((..((((.((((....))))..))))..).)))..)...((((....))))......)))...)))).)))))))).)))))).. ( -46.60)
>DroSim_CAF1 201 120 + 1
ACAUACUGAGAACGGGUGGGUGGGCGCUAGAAGGCGAGGUGGCGAGGACAUCCUUUUCCAUGGCAGCCGGCAAAUAUCGAGAGGUAAACACGUGCAUUGCCAGCUUCCGUUAUCAGUCAG
....(((((.((((((..((..(((((..(..((((..((((.((((....))))..))))..).)))..)...((((....)))).....)))).)..))....)))))).)))))... ( -43.00)
>consensus
ACAGACUGAGAACGGGUGGGUGGGCGCUAGAAGGCGAGGUGGCGAGGACAUCCUUUUCCAUGGCAGCCGGCAAAUAUCGAGAGGUAAACACGUGCAUUGCCAGCUUCCGUUAUCAGUCAG
...((((((.((((((..(((..((((..(..((((..((((.((((....))))..))))..).)))..)...((((....)))).....))))...)))....)))))).)))))).. (-41.69 = -42.13 +   0.45)

alignment

secondary structure

dotplot

Window 9

Location	15,827,479 – 15,827,599
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.22
Mean single sequence MFE	-38.67
Consensus MFE	-37.00
Energy contribution	-37.33
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.96
SVM decision value	0.79
SVM RNA-class probability	0.851519
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15827479 120 - 22407834
CUGACUGAUAACGGAAGCUGGCAAUGCACGUGUUUACCUCUCGAUAUUUGCCGGCUGCCAUGGAAAAGGAUGUCCUUGCCACCUCGCCAUCUAGCGCCCACCCACCCGUUCUCAGUCUGU
..((((((.(((((.(((((((((....((.(.......).))....)))))))))((..(((..((((....)))).)))....((......))))........))))).))))))... ( -39.20)
>DroSec_CAF1 15 119 - 1
CUGACUGAUAACGGAAGCUGGCAAUGCUCGUGUUUACCUCUCGAUAUUUGCCGGCUGCCAUGGAAAAGGAUGUCCUCGCCACCUCGCCUUCUAGCGC-CACCCACCCGUUCUCAGUCUGU
..((((((.(((((.(((((((((...(((.(.......).)))...)))))))))((..(((...(((....)))..)))....((......))))-.......))))).))))))... ( -40.90)
>DroSim_CAF1 201 120 - 1
CUGACUGAUAACGGAAGCUGGCAAUGCACGUGUUUACCUCUCGAUAUUUGCCGGCUGCCAUGGAAAAGGAUGUCCUCGCCACCUCGCCUUCUAGCGCCCACCCACCCGUUCUCAGUAUGU
...(((((.(((((.(((((((((....((.(.......).))....)))))))))((..(((...(((....)))..)))....((......))))........))))).))))).... ( -35.90)
>consensus
CUGACUGAUAACGGAAGCUGGCAAUGCACGUGUUUACCUCUCGAUAUUUGCCGGCUGCCAUGGAAAAGGAUGUCCUCGCCACCUCGCCUUCUAGCGCCCACCCACCCGUUCUCAGUCUGU
..((((((.(((((.(((((((((....((.(.......).))....)))))))))....(((...(((....)))..)))...(((......))).........))))).))))))... (-37.00 = -37.33 +   0.33)

alignment

secondary structure

dotplot

Window 0

Location	15,827,599 – 15,827,690
Length	91
Sequences	3
Columns	91
Reading direction	forward
Mean pairwise identity	98.53
Mean single sequence MFE	-25.40
Consensus MFE	-25.62
Energy contribution	-25.40
Covariance contribution	-0.22
Combinations/Pair	1.05
Mean z-score	-1.60
Structure conservation index	1.01
SVM decision value	0.49
SVM RNA-class probability	0.755504
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15827599 91 + 22407834
CUUGUUUGCCAGACAGCCGGGCCAUUUCCAUUGGACGCGCCCACCCGGUUUACCUGGCCAACAUCGCUCCCCCAUCGCCGUUCGUCUAUAU
..((((.(((((..(((((((..........(((......))))))))))...))))).))))............................ ( -23.80)
>DroSec_CAF1 134 91 + 1
CUUGUUUGCCAGACAGCCGGGCCAUUUCCAUUGGACGCGCCCACCCGGCUUACCUGGCCAACAUCGCUCCCCCAUCGCUGUUCGUCUAUAU
..((((.(((((..(((((((..........(((......))))))))))...))))).))))............................ ( -26.20)
>DroSim_CAF1 321 91 + 1
CUUGUUUGCCAGACAGCCGGGCCAUUUCCAUUGGACGCGCCCACCCGGCUUACCUGGCCAACAUCGCUCCCCCAUCGCUGUUCGUCUAUAU
..((((.(((((..(((((((..........(((......))))))))))...))))).))))............................ ( -26.20)
>consensus
CUUGUUUGCCAGACAGCCGGGCCAUUUCCAUUGGACGCGCCCACCCGGCUUACCUGGCCAACAUCGCUCCCCCAUCGCUGUUCGUCUAUAU
..((((.(((((..(((((((..........(((......))))))))))...))))).))))............................ (-25.62 = -25.40 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:09 2006