Locus 933

Sequence ID	2R_DroMel_CAF1
Location	4,068,738 – 4,068,853
Length	115
Max. P	0.718159

overview

Window 7

Location	4,068,738 – 4,068,853
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.43
Mean single sequence MFE	-41.46
Consensus MFE	-30.88
Energy contribution	-31.12
Covariance contribution	0.24
Combinations/Pair	1.12
Mean z-score	-1.80
Structure conservation index	0.74
SVM decision value	0.39
SVM RNA-class probability	0.718159
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4068738 115 + 20766785
GCUGCUCCUGUAAGUUUCACGAGCAGCAGAUGCAAGAUUGUUUCACCACUCGAUGCAAAUGCGUUGGCGCUGAAAGCAGCGCUCUAAUGUGAGGGGGGGGGGG-----UGUGAGGUGCUG
(((((((.((.......)).)))))))((.(((.(.(((.(..(.((.((((((((....)))))(((((((....))))))).......))).)))..).))-----).)...))))). ( -41.50)
>DroSec_CAF1 51381 108 + 1
GCAGCUCCUGUAAGUUUCACGAGCAGCAGCUGCAAGAUUGUUUCACCACUCGAUGCAAAUGCGUUGGCGCUGAAAGUUGCGCUCUAAUGUGGGUGU------------GGUGAGGUGGAG
((((((.((((..(.....)..)))).))))))....(..(((((((((.((((((....))))))((((........))))............))------------)))))))..).. ( -44.10)
>DroSim_CAF1 59572 106 + 1
GCAGCUCCUGUAAGUUUCACGAGCAGCAGCUGCAAGAUUGUUUCACCACUCGAUGCAAAUGCGUUGGCGCUGAAAGUUGCGCUCUAAUGUGGG--G------------GGUGAGGUGGGG
((((((.((((..(.....)..)))).))))))....(..(((((((.((((((((....)))))(((((........))))).......)))--.------------)))))))..).. ( -41.90)
>DroEre_CAF1 52835 108 + 1
GCUGCUCCUGUAAGUUUCACGAGCAGCAGCUGCAAGAUUGUUUCACCACUCAAUGCAAAUGCGUUGGCGCUGAAAGUUGCGCUCUAAUGUGGC--AAGGG--------GGUGGGGUGG--
(((((((.((.......)).)))))))..........(..(..((((.(((..(((....((((((((((........)))))..))))).))--).)))--------))))..)..)-- ( -39.80)
>DroYak_CAF1 55466 117 + 1
GCUGCUCCUGUAAGUUUCACGAGCAGCAGCUGCAAGAUUGUUUCACCACUCGAUGCAAAUGCGUUGGCGCUGAAAGUAGCGUUCUAGUGUGGGGGAAGGGCGGAGUAUGGCGGGGA-G--
(((((((.((.......)).)))))))..((((....((.(..(((.(((((((((....))))))((((((....))))))...))))))..).))..)))).............-.-- ( -40.00)
>consensus
GCUGCUCCUGUAAGUUUCACGAGCAGCAGCUGCAAGAUUGUUUCACCACUCGAUGCAAAUGCGUUGGCGCUGAAAGUUGCGCUCUAAUGUGGG_GA_GGG________GGUGAGGUGG_G
(((((((.((.......)).))))))).............(((((((...((((((....))))))((((........))))..........................)))))))..... (-30.88 = -31.12 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	4,068,738 – 4,068,853
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.43
Mean single sequence MFE	-30.41
Consensus MFE	-23.80
Energy contribution	-24.24
Covariance contribution	0.44
Combinations/Pair	1.05
Mean z-score	-1.62
Structure conservation index	0.78
SVM decision value	0.21
SVM RNA-class probability	0.636630
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4068738 115 - 20766785
CAGCACCUCACA-----CCCCCCCCCCCUCACAUUAGAGCGCUGCUUUCAGCGCCAACGCAUUUGCAUCGAGUGGUGAAACAAUCUUGCAUCUGCUGCUCGUGAAACUUACAGGAGCAGC
..(((.......-----........(((((......(.((((((....)))))))...((....))...))).)).((.....)).)))....(((((((.((.......)).))))))) ( -32.00)
>DroSec_CAF1 51381 108 - 1
CUCCACCUCACC------------ACACCCACAUUAGAGCGCAACUUUCAGCGCCAACGCAUUUGCAUCGAGUGGUGAAACAAUCUUGCAGCUGCUGCUCGUGAAACUUACAGGAGCUGC
.......(((((------------((..........(.((((........)))))...((....)).....))))))).........((((((.(((.............))).)))))) ( -32.72)
>DroSim_CAF1 59572 106 - 1
CCCCACCUCACC------------C--CCCACAUUAGAGCGCAACUUUCAGCGCCAACGCAUUUGCAUCGAGUGGUGAAACAAUCUUGCAGCUGCUGCUCGUGAAACUUACAGGAGCUGC
.......(((((------------.--(.(......(.((((........)))))...((....))...).).))))).........((((((.(((.............))).)))))) ( -27.72)
>DroEre_CAF1 52835 108 - 1
--CCACCCCACC--------CCCUU--GCCACAUUAGAGCGCAACUUUCAGCGCCAACGCAUUUGCAUUGAGUGGUGAAACAAUCUUGCAGCUGCUGCUCGUGAAACUUACAGGAGCAGC
--..........--------...(.--.((((......((((........))))(((.((....)).))).))))..)...............(((((((.((.......)).))))))) ( -32.00)
>DroYak_CAF1 55466 117 - 1
--C-UCCCCGCCAUACUCCGCCCUUCCCCCACACUAGAACGCUACUUUCAGCGCCAACGCAUUUGCAUCGAGUGGUGAAACAAUCUUGCAGCUGCUGCUCGUGAAACUUACAGGAGCAGC
--.-....((((..((((.....................((((......)))).....((....))...))))))))................(((((((.((.......)).))))))) ( -27.60)
>consensus
C_CCACCUCACC________CCC_CC_CCCACAUUAGAGCGCAACUUUCAGCGCCAACGCAUUUGCAUCGAGUGGUGAAACAAUCUUGCAGCUGCUGCUCGUGAAACUUACAGGAGCAGC
............................((((....(.((((........)))))...((....)).....))))..................(((((((.((.......)).))))))) (-23.80 = -24.24 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:47 2006