Locus 28

Sequence ID	3L_DroMel_CAF1
Location	109,335 – 109,429
Length	94
Max. P	0.992054

overview

Window 4

Location	109,335 – 109,429
Length	94
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	75.00
Mean single sequence MFE	-19.69
Consensus MFE	-4.72
Energy contribution	-6.28
Covariance contribution	1.56
Combinations/Pair	1.18
Mean z-score	-1.82
Structure conservation index	0.24
SVM decision value	0.61
SVM RNA-class probability	0.799938
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 109335 94 + 23771897
AAUAGCGUCGCACCACGCAAUACCGUGCACCAAAAAAGCACAGGUGUAGCAAAAUGUUCCC-------CAAAAAUGGGAAAAUGCAAAAUGUUAUAAAGGC
.(((((((.(((....((.(((((((((.........)))).))))).))......(((((-------.......)))))..)))...)))))))...... ( -25.50)
>DroSec_CAF1 44970 81 + 1
GAUAGCGCUGCACAAUGCAAUACCGUGCACCGAAGAAGCACAGGGGUCGCAAAAUGUUCGC-------GC-------------ACAAAAAGUUAUAAAGGC
....((((.(((...(((.(..((((((.........)))).))..).)))...)))..))-------))-------------.................. ( -19.40)
>DroSim_CAF1 50675 81 + 1
GAUAGCGCUGCACCAUGCAAUACCGUGCACCGAAGAAGCACAGGGGUCGCAAAAUGUUCGC-------GC-------------ACAAAAAGUUAUAAAGGC
....((((.(((...(((.(..((((((.........)))).))..).)))...)))..))-------))-------------.................. ( -19.40)
>DroEre_CAF1 67012 87 + 1
GAUAGCAUCGCACCCUGCAAUACCGUGCACCAAAAAAU-GCAGGGAUAGCAAAAUGUUUGCAAAAUGUGC-------------ACAAAAAUUUAGAAAGGC
....((((....(((((((..................)-))))))...((((.....)))).....))))-------------.................. ( -18.07)
>DroYak_CAF1 62446 81 + 1
GAUAACAUCGCACCCAGCAAUACCGUGCACCAAAAAAG-UGACGGAUUGCAAAAAGUUUCC------CGC-------------ACAAAAAGUUAGAAAGGC
.............((.(((((.((((.(((.......)-)))))))))))......((((.------.((-------------.......))..)))))). ( -16.10)
>consensus
GAUAGCGUCGCACCAUGCAAUACCGUGCACCAAAAAAGCACAGGGGUAGCAAAAUGUUCGC_______GC_____________ACAAAAAGUUAUAAAGGC
....(((..(((...(((.((.((((((.........)))).)).)).)))...))).)))........................................ ( -4.72 =  -6.28 +   1.56)

alignment

secondary structure

dotplot

Window 5

Location	109,335 – 109,429
Length	94
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	75.00
Mean single sequence MFE	-25.04
Consensus MFE	-10.18
Energy contribution	-11.62
Covariance contribution	1.44
Combinations/Pair	1.26
Mean z-score	-2.48
Structure conservation index	0.41
SVM decision value	2.30
SVM RNA-class probability	0.992054
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 109335 94 - 23771897
GCCUUUAUAACAUUUUGCAUUUUCCCAUUUUUG-------GGGAACAUUUUGCUACACCUGUGCUUUUUUGGUGCACGGUAUUGCGUGGUGCGACGCUAUU
................((..(((((((....))-------)))))(((..(((...(((((..((.....))..)).)))...)))..)))....)).... ( -24.70)
>DroSec_CAF1 44970 81 - 1
GCCUUUAUAACUUUUUGU-------------GC-------GCGAACAUUUUGCGACCCCUGUGCUUCUUCGGUGCACGGUAUUGCAUUGUGCAGCGCUAUC
..................-------------((-------((...(((..(((((..((.((((..(....).))))))..)))))..)))..)))).... ( -27.10)
>DroSim_CAF1 50675 81 - 1
GCCUUUAUAACUUUUUGU-------------GC-------GCGAACAUUUUGCGACCCCUGUGCUUCUUCGGUGCACGGUAUUGCAUGGUGCAGCGCUAUC
..................-------------((-------((...(((..(((((..((.((((..(....).))))))..)))))..)))..)))).... ( -27.20)
>DroEre_CAF1 67012 87 - 1
GCCUUUCUAAAUUUUUGU-------------GCACAUUUUGCAAACAUUUUGCUAUCCCUGC-AUUUUUUGGUGCACGGUAUUGCAGGGUGCGAUGCUAUC
................((-------------((((.....((((.....))))........(-(.....))))))))((((((((.....))))))))... ( -21.70)
>DroYak_CAF1 62446 81 - 1
GCCUUUCUAACUUUUUGU-------------GCG------GGAAACUUUUUGCAAUCCGUCA-CUUUUUUGGUGCACGGUAUUGCUGGGUGCGAUGUUAUC
.......((((...(((.-------------.((------(....))....(((((((((((-((.....)))).)))).)))))...)..))).)))).. ( -24.50)
>consensus
GCCUUUAUAACUUUUUGU_____________GC_______GCGAACAUUUUGCGACCCCUGUGCUUUUUUGGUGCACGGUAUUGCAUGGUGCGACGCUAUC
........................................(((..(((..(((((..((((((((.....)))))).))..)))))..)))...))).... (-10.18 = -11.62 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:15 2006