Locus 2327

Sequence ID	2R_DroMel_CAF1
Location	8,534,017 – 8,534,137
Length	120
Max. P	0.978732

overview

Window 2

Location	8,534,017 – 8,534,137
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.56
Mean single sequence MFE	-35.38
Consensus MFE	-33.06
Energy contribution	-33.88
Covariance contribution	0.81
Combinations/Pair	1.03
Mean z-score	-2.52
Structure conservation index	0.93
SVM decision value	1.82
SVM RNA-class probability	0.978732
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8534017 120 + 20766785
CGCCUUUUACGUGGAGAGUCGCAUGAAAACCAGCUGCGGCCAUUUUGAGACGUUUUUUAUUGGUCAUAACUCUUGAGUUAUGACAAAUAUAGAAACCGAAAGCAUUCAAUUUGGCGACAG
..((........))...((((((((.....))..))).((((..(((((..((((((((((.(((((((((....))))))))).)))).))))))(....)..)))))..))))))).. ( -35.00)
>DroSec_CAF1 9519 120 + 1
CGCCUUUUACGUGAAGAGGCACACGAAAACCAGCUGCGGCCAUUUUGAGACGUUUUUUAUUGGUCAUAACUCUCGAGUUAUGACAAAUAUAGAAACCGAAAGCAUUCAAUUUGGCGACAG
.(((((((.....))))))).............(((..((((..(((((..((((((((((.(((((((((....))))))))).)))).))))))(....)..)))))..))))..))) ( -38.80)
>DroSim_CAF1 12983 120 + 1
CGCCUUUUACGUGAAGAGGCACACGAAAACCAGCUGCGGCCAUUUUGAGACGUUUUUUAUUGGUCAUAACUCUCGAGUUAUGACAAAUAUAGAAACCGAAAGCAUUCAAUUUGGCGACAG
.(((((((.....))))))).............(((..((((..(((((..((((((((((.(((((((((....))))))))).)))).))))))(....)..)))))..))))..))) ( -38.80)
>DroYak_CAF1 12747 120 + 1
CGCCUUUUUAGUGAAGACGCACAUGAAAACCAGCUGCGGCCAUUUUGAGACGUUUUUUAUUGGCCAUAACGCUUGAGUUAUGACAAAUAUAGAAACCGAAAGCAUUCAAUUUGGCGACAG
...((((.....)))).((((..((.....))..))))((((..(((((..((((((((((.(.((((((......)))))).).)))).))))))(....)..)))))..))))..... ( -28.90)
>consensus
CGCCUUUUACGUGAAGAGGCACACGAAAACCAGCUGCGGCCAUUUUGAGACGUUUUUUAUUGGUCAUAACUCUCGAGUUAUGACAAAUAUAGAAACCGAAAGCAUUCAAUUUGGCGACAG
.(((((((.....))))))).............(((..((((..(((((..((((((((((.(((((((((....))))))))).)))).))))))(....)..)))))..))))..))) (-33.06 = -33.88 +   0.81)

alignment

secondary structure

dotplot

Window 3

Location	8,534,017 – 8,534,137
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.56
Mean single sequence MFE	-31.15
Consensus MFE	-28.66
Energy contribution	-29.47
Covariance contribution	0.81
Combinations/Pair	1.03
Mean z-score	-1.55
Structure conservation index	0.92
SVM decision value	0.22
SVM RNA-class probability	0.640484
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8534017 120 - 20766785
CUGUCGCCAAAUUGAAUGCUUUCGGUUUCUAUAUUUGUCAUAACUCAAGAGUUAUGACCAAUAAAAAACGUCUCAAAAUGGCCGCAGCUGGUUUUCAUGCGACUCUCCACGUAAAAGGCG
((((.(((((((((((....)))))))....((((.(((((((((....))))))))).))))...............)))).))))...(((((..((((........)))).))))). ( -30.40)
>DroSec_CAF1 9519 120 - 1
CUGUCGCCAAAUUGAAUGCUUUCGGUUUCUAUAUUUGUCAUAACUCGAGAGUUAUGACCAAUAAAAAACGUCUCAAAAUGGCCGCAGCUGGUUUUCGUGUGCCUCUUCACGUAAAAGGCG
.(((.(((((((((((....)))))))....((((.(((((((((....))))))))).))))...............)))).)))(((..(((.((((........)))).))).))). ( -33.10)
>DroSim_CAF1 12983 120 - 1
CUGUCGCCAAAUUGAAUGCUUUCGGUUUCUAUAUUUGUCAUAACUCGAGAGUUAUGACCAAUAAAAAACGUCUCAAAAUGGCCGCAGCUGGUUUUCGUGUGCCUCUUCACGUAAAAGGCG
.(((.(((((((((((....)))))))....((((.(((((((((....))))))))).))))...............)))).)))(((..(((.((((........)))).))).))). ( -33.10)
>DroYak_CAF1 12747 120 - 1
CUGUCGCCAAAUUGAAUGCUUUCGGUUUCUAUAUUUGUCAUAACUCAAGCGUUAUGGCCAAUAAAAAACGUCUCAAAAUGGCCGCAGCUGGUUUUCAUGUGCGUCUUCACUAAAAAGGCG
((((.(((((((((((....)))))))....((((.((((((((......)))))))).))))...............)))).))))..............((((((.......)))))) ( -28.00)
>consensus
CUGUCGCCAAAUUGAAUGCUUUCGGUUUCUAUAUUUGUCAUAACUCAAGAGUUAUGACCAAUAAAAAACGUCUCAAAAUGGCCGCAGCUGGUUUUCAUGUGCCUCUUCACGUAAAAGGCG
.(((.(((((((((((....)))))))....((((.(((((((((....))))))))).))))...............)))).)))(((..(((.((((........)))).))).))). (-28.66 = -29.47 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:57 2006