Locus 3798

Sequence ID	2R_DroMel_CAF1
Location	12,544,461 – 12,544,612
Length	151
Max. P	0.946784

overview

Window 3

Location	12,544,461 – 12,544,579
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	96.44
Mean single sequence MFE	-31.48
Consensus MFE	-28.30
Energy contribution	-28.30
Covariance contribution	0.00
Combinations/Pair	1.06
Mean z-score	-1.56
Structure conservation index	0.90
SVM decision value	1.19
SVM RNA-class probability	0.928836
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12544461 118 + 20766785
AUUCAUUUGACCCGUGAUUAGUCAGCAAACGUUGUUUGAAAAUAGCCAAUUGACGAGGUGAAACUUUGCGCCGUCUCACAGUUCUGAAACGCACUGUGUUUGCUGAUUGUUUAUACCA
.............((((.((((((((((((((((((....)))))).....((((..(..(....)..)..))))..(((((.(......).))))))))))))))))).)))).... ( -30.50)
>DroSec_CAF1 5929 118 + 1
AUUCAUUUGACCCGUGAUUAGUCAGCAAACGUUGUUUGAAAAUCGCCAAUUGACGAGGUGAAACUUUGCGCCGUCUCACAGUUCUGAAACGCACUGUGUUUGCUGAUUGUUUAUACCA
.............((((.(((((((((((((((..(((........)))..)))).((((........))))....((((((.(......).))))))))))))))))).)))).... ( -30.20)
>DroSim_CAF1 5946 118 + 1
AUUCAUUUGACCCGUGAUUAGUCAGCAAACGUUGUUUGAAAAUCGCCAAUUGACGAGGUGAAACUUUGCGCCGUCUCACAGUUCUGAAACGCACUGUGUUUGCUGAUUGUUUAUACCA
.............((((.(((((((((((((((..(((........)))..)))).((((........))))....((((((.(......).))))))))))))))))).)))).... ( -30.20)
>DroEre_CAF1 5935 118 + 1
AUUCAUUUGACCCGUGAUUAGUCACCAAACGUUGUUUGAAAAAUUCCAAUUGGCGAGGUGAAACUUUUCGCCGUCUCACAGUUCUGAAACGCACUGUGUUUGCUGAUUGUUUAUACCA
.((((..((((..((((....)))).....))))..))))......((((..((((((((((....))))))....((((((.(......).)))))).))))..))))......... ( -30.50)
>DroYak_CAF1 6018 118 + 1
AUUCAUUUGACCCGUGAUUAGUCAGCGAACGUUGUUUGAAAAAUGCCAAUUGGCGAGGUGAAACUUUUCGCCGUCUCACAGUUCUGAAACGCACUGCGUUUGCUGAUUGUUUAUACCA
.............((((.((((((((((((((.((.((......(((....)))((((((((....)))))).))..............)).)).)))))))))))))).)))).... ( -36.00)
>consensus
AUUCAUUUGACCCGUGAUUAGUCAGCAAACGUUGUUUGAAAAUCGCCAAUUGACGAGGUGAAACUUUGCGCCGUCUCACAGUUCUGAAACGCACUGUGUUUGCUGAUUGUUUAUACCA
.............((((.(((((((((((((((..(((........)))..)))).((((........))))....((((((.(......).))))))))))))))))).)))).... (-28.30 = -28.30 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	12,544,501 – 12,544,612
Length	111
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	96.94
Mean single sequence MFE	-28.98
Consensus MFE	-26.64
Energy contribution	-26.60
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.57
Structure conservation index	0.92
SVM decision value	1.37
SVM RNA-class probability	0.946784
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12544501 111 - 20766785
GCACAAAAACAACCCCAAGCUUGGGGGAACUAUUGGUAUAAACAAUCAGCAAACACAGUGCGUUUCAGAACUGUGAGACGGCGCAAAGUUUCACCUCGUCAAUUGGCUAUU
((((........(((((....)))))...((((((.......)))).))........))))......((...(((((((........))))))).))(((....))).... ( -26.30)
>DroSec_CAF1 5969 111 - 1
GCACAAAAACAACCCCAAGCUUGGGGGAACUAUUGGUAUAAACAAUCAGCAAACACAGUGCGUUUCAGAACUGUGAGACGGCGCAAAGUUUCACCUCGUCAAUUGGCGAUU
((((........(((((....)))))...((((((.......)))).))........))))...........(((((((........))))))).(((((....))))).. ( -29.70)
>DroSim_CAF1 5986 111 - 1
GCACAAAAACAACCCCAAGCUUGGGGGAACUAUUGGUAUAAACAAUCAGCAAACACAGUGCGUUUCAGAACUGUGAGACGGCGCAAAGUUUCACCUCGUCAAUUGGCGAUU
((((........(((((....)))))...((((((.......)))).))........))))...........(((((((........))))))).(((((....))))).. ( -29.70)
>DroEre_CAF1 5975 111 - 1
GCACAAAAACAACCCCAAGCUUGGGGGAACUAUUGGUAUAAACAAUCAGCAAACACAGUGCGUUUCAGAACUGUGAGACGGCGAAAAGUUUCACCUCGCCAAUUGGAAUUU
((((........(((((....)))))...((((((.......)))).))........))))((((((......))))))(((((...........)))))........... ( -29.10)
>DroYak_CAF1 6058 111 - 1
GCACAAAAACAACCCCAAGCUUGGGGGAACUAUUGGUAUAAACAAUCAGCAAACGCAGUGCGUUUCAGAACUGUGAGACGGCGAAAAGUUUCACCUCGCCAAUUGGCAUUU
((.(((......(((((....)))))......(((((...........(.((((((...))))))).((...(((((((........))))))).)))))))))))).... ( -30.10)
>consensus
GCACAAAAACAACCCCAAGCUUGGGGGAACUAUUGGUAUAAACAAUCAGCAAACACAGUGCGUUUCAGAACUGUGAGACGGCGCAAAGUUUCACCUCGUCAAUUGGCAAUU
((((........(((((....)))))...((((((.......)))).))........))))......((...(((((((........))))))).))(((....))).... (-26.64 = -26.60 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:19 2006