Locus 2477

Sequence ID	3R_DroMel_CAF1
Location	6,808,282 – 6,808,387
Length	105
Max. P	0.983366

overview

Window 8

Location	6,808,282 – 6,808,387
Length	105
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	87.01
Mean single sequence MFE	-32.81
Consensus MFE	-26.06
Energy contribution	-26.50
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-2.51
Structure conservation index	0.79
SVM decision value	1.94
SVM RNA-class probability	0.983366
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6808282 105 + 27905053
------------CGAAACGGACGAAAGUCGGA--AAAGCGAAAACGAGAAGCUGGGCCAAAAGAGUGCCAACUGGCUGAUGGGUUUGUCAGUUGGCAUCAAAGCGCAUUAGUUUGUAUG
------------.....(.(((....))).).--............(.(((((((((.......((((((((((((..........))))))))))))......)).))))))).)... ( -32.62)
>DroSec_CAF1 66540 105 + 1
------------CGAAAUGGCGGCAAAUCGGA--AAAGCGAAAACGAGAAGCUGCGCCAAAAGAGUGCCAACUGGCUGAUGGGUUUGUCAGUUGGCAUCAAAGCGCAUUAGUUUGUAUG
------------...(((((((((...(((..--..........)))...)))))((.......((((((((((((..........))))))))))))....)).)))).......... ( -32.10)
>DroSim_CAF1 72111 105 + 1
------------CGAAAGGGCCGCAAAUCGGA--AAAGCGAAAACGAGAAGCUGCGCCAAAAGAGUGCCAACUGGCUGAUGGGUUUGUCAGUUGGCAUCAAAGCGCAUUAGUUUGUAUG
------------(....)....((((((..(.--..(((...........)))((((.......((((((((((((..........))))))))))))....)))).)..))))))... ( -32.50)
>DroEre_CAF1 52274 117 + 1
AAAGCGAAAAAGCGGGAAAGCGGAAAAUCGGA--AAAGCGAAAACGGGAAGCUGCUCCAAAGGAGUGCCAACUGGCUGAUGGGUUUGUCAGUUGGCAUCAAAGCGCAUUAGUUUGUAUC
...(((((...((((((..((((....(((..--..........)))....)))))))....((.(((((((((((..........)))))))))))))....))).....)))))... ( -35.30)
>DroYak_CAF1 65160 113 + 1
------AAAAAGCGGAAAUGCGGAAAAUCGAAAAAAAGCGAAAACGAGAAGCUGCUCCAAAGAAGUGCCAACUGGCUGAUGGGUUUGUCAGUUGGCAUCAAAGCGCAUUAGUUUGUAUG
------.....(((((...((((....(((..............)))....)))))))......((((((((((((..........))))))))))))....))(((......)))... ( -31.54)
>consensus
____________CGAAAAGGCGGAAAAUCGGA__AAAGCGAAAACGAGAAGCUGCGCCAAAAGAGUGCCAACUGGCUGAUGGGUUUGUCAGUUGGCAUCAAAGCGCAUUAGUUUGUAUG
...........................(((........)))..(((((....(((((.......((((((((((((..........))))))))))))....)))))....)))))... (-26.06 = -26.50 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	6,808,282 – 6,808,387
Length	105
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	87.01
Mean single sequence MFE	-24.88
Consensus MFE	-19.82
Energy contribution	-20.26
Covariance contribution	0.44
Combinations/Pair	1.05
Mean z-score	-1.79
Structure conservation index	0.80
SVM decision value	0.65
SVM RNA-class probability	0.812530
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6808282 105 - 27905053
CAUACAAACUAAUGCGCUUUGAUGCCAACUGACAAACCCAUCAGCCAGUUGGCACUCUUUUGGCCCAGCUUCUCGUUUUCGCUUU--UCCGACUUUCGUCCGUUUCG------------
.....((((...((.(((..(((((((((((..............))))))))).))....))).))..................--...(((....))).))))..------------ ( -20.24)
>DroSec_CAF1 66540 105 - 1
CAUACAAACUAAUGCGCUUUGAUGCCAACUGACAAACCCAUCAGCCAGUUGGCACUCUUUUGGCGCAGCUUCUCGUUUUCGCUUU--UCCGAUUUGCCGCCAUUUCG------------
............((((((..(((((((((((..............))))))))).))....))))))..................--..(((..((....))..)))------------ ( -25.94)
>DroSim_CAF1 72111 105 - 1
CAUACAAACUAAUGCGCUUUGAUGCCAACUGACAAACCCAUCAGCCAGUUGGCACUCUUUUGGCGCAGCUUCUCGUUUUCGCUUU--UCCGAUUUGCGGCCCUUUCG------------
............((((((..(((((((((((..............))))))))).))....)))))).....((((..(((....--..)))...))))........------------ ( -28.54)
>DroEre_CAF1 52274 117 - 1
GAUACAAACUAAUGCGCUUUGAUGCCAACUGACAAACCCAUCAGCCAGUUGGCACUCCUUUGGAGCAGCUUCCCGUUUUCGCUUU--UCCGAUUUUCCGCUUUCCCGCUUUUUCGCUUU
.............(((....(((((((((((..............))))))))).))..((((((.(((...........))).)--))))).....)))......((......))... ( -25.24)
>DroYak_CAF1 65160 113 - 1
CAUACAAACUAAUGCGCUUUGAUGCCAACUGACAAACCCAUCAGCCAGUUGGCACUUCUUUGGAGCAGCUUCUCGUUUUCGCUUUUUUUCGAUUUUCCGCAUUUCCGCUUUUU------
..........(((((((((..((((((((((..............))))))))).....)..))))(((...........)))...............)))))..........------ ( -24.44)
>consensus
CAUACAAACUAAUGCGCUUUGAUGCCAACUGACAAACCCAUCAGCCAGUUGGCACUCUUUUGGCGCAGCUUCUCGUUUUCGCUUU__UCCGAUUUUCCGCCUUUUCG____________
............((((((..(((((((((((..............))))))))).))....))))))...........(((........)))........................... (-19.82 = -20.26 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:22 2006