Locus 5401

Sequence ID	3L_DroMel_CAF1
Location	14,816,798 – 14,816,898
Length	100
Max. P	0.857183

overview

Window 3

Location	14,816,798 – 14,816,898
Length	100
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.51
Mean single sequence MFE	-27.33
Consensus MFE	-18.23
Energy contribution	-18.62
Covariance contribution	0.39
Combinations/Pair	1.08
Mean z-score	-2.40
Structure conservation index	0.67
SVM decision value	0.81
SVM RNA-class probability	0.857183
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14816798 100 + 23771897
UUUCU------------CUGCGUAUUUUAUGCUGAUUUUGCCUCAGCUCUUGGGGCCAUCUAUUGUGUGUUUGGAUUUGCACAUUUCCAG--------AUUUUCUGGGGGCAAACACACA
....(------------(.(((((...))))).))....(((((((...))))))).......((((((((((..........(..((((--------.....))))..))))))))))) ( -29.70)
>DroSec_CAF1 51696 100 + 1
UUUCU------------CUGCGUAUUUUAUGCUGAUUUUGCCUCAGCUCUUGGGGCCAUCUAUUGUGUGUUUGGAUUUGCACAUUUGCAG--------AUUUUCUGGGCCCAAACACACA
....(------------(.(((((...))))).))....(((((((...))))))).......((((((((((((((((((....)))))--------)).........))))))))))) ( -30.80)
>DroSim_CAF1 44810 100 + 1
UUUCU------------CUGCGUAUUUUAUGCUGAUUUUGCCUCAGCUCUUGGGGCCAUCUAUUGUGUGUUUGGAUUUGCACAUUUGCAG--------AUUUUCUGGGGGCAAACACACA
....(------------(.(((((...))))).))....(((((((...))))))).......((((((((((((((((((....)))))--------))).((....)))))))))))) ( -28.90)
>DroEre_CAF1 52222 106 + 1
CUUCA------------CUGCGUAUUUUAUGCUGAUUUUGCCUCAACUCUUGGGGCCGUCUAUUGUGUGUUUGGACUUGCACAUUUCCAGAUU--CGGAUUUUCUGUGGGCAAACACACA
.....------------..(((((...))))).(((...((((((.....)))))).)))...((((((((((..((..((....(((.....--.))).....))..)))))))))))) ( -31.20)
>DroYak_CAF1 54894 108 + 1
CUUCU------------UUGCGUAUUUUAUGCUGAUUUCGCCUCAACUCUUGGGGCCAUCUAUUGUGUGUUUGGAUUUGCACAUUUCCAGAUUUCCAGAUUUUCUGUGGGCAAACACACA
..((.------------..(((((...))))).))....((((((.....)))))).......((((((((((((((((........))))))(((((.....))).)).)))))))))) ( -28.00)
>DroAna_CAF1 49262 112 + 1
UUCCUCUUCCUUAUCCUUUGCACAUUUUAUGCCGAUUUUGCUUCAACUCGUGGUGCCAUCUAUUGU--GUUUGGAUUUUCAAAUUUUCGC-CA--CCAACUAACUG---GCAAACAUACA
............((((...(((((.(..(((.((...(..(........)..))).)))..).)))--))..))))............((-((--.........))---))......... ( -15.40)
>consensus
UUUCU____________CUGCGUAUUUUAUGCUGAUUUUGCCUCAACUCUUGGGGCCAUCUAUUGUGUGUUUGGAUUUGCACAUUUCCAG________AUUUUCUGGGGGCAAACACACA
...................(((((...))))).(((...((((((.....)))))).)))...((((((((((.....................................)))))))))) (-18.23 = -18.62 +   0.39)

alignment

secondary structure

dotplot

Window 4

Location	14,816,798 – 14,816,898
Length	100
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.51
Mean single sequence MFE	-24.19
Consensus MFE	-15.34
Energy contribution	-16.01
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	0.63
SVM decision value	0.36
SVM RNA-class probability	0.705893
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14816798 100 - 23771897
UGUGUGUUUGCCCCCAGAAAAU--------CUGGAAAUGUGCAAAUCCAAACACACAAUAGAUGGCCCCAAGAGCUGAGGCAAAAUCAGCAUAAAAUACGCAG------------AGAAA
((((((((((((.((((.....--------))))...((((............))))......))).......(((((.......)))))...))))))))).------------..... ( -26.20)
>DroSec_CAF1 51696 100 - 1
UGUGUGUUUGGGCCCAGAAAAU--------CUGCAAAUGUGCAAAUCCAAACACACAAUAGAUGGCCCCAAGAGCUGAGGCAAAAUCAGCAUAAAAUACGCAG------------AGAAA
(((((((((((((((((.....--------)))....((((............))))......))))).....(((((.......)))))...))))))))).------------..... ( -28.80)
>DroSim_CAF1 44810 100 - 1
UGUGUGUUUGCCCCCAGAAAAU--------CUGCAAAUGUGCAAAUCCAAACACACAAUAGAUGGCCCCAAGAGCUGAGGCAAAAUCAGCAUAAAAUACGCAG------------AGAAA
((((((((((.....((.....--------))(((....))).....))))))))))...(((.(((.((.....)).)))...))).((.........))..------------..... ( -22.20)
>DroEre_CAF1 52222 106 - 1
UGUGUGUUUGCCCACAGAAAAUCCG--AAUCUGGAAAUGUGCAAGUCCAAACACACAAUAGACGGCCCCAAGAGUUGAGGCAAAAUCAGCAUAAAAUACGCAG------------UGAAG
((((((((((((((((.....((((--....))))..))))...(((.............)))))).......(((((.......)))))...))))))))).------------..... ( -23.12)
>DroYak_CAF1 54894 108 - 1
UGUGUGUUUGCCCACAGAAAAUCUGGAAAUCUGGAAAUGUGCAAAUCCAAACACACAAUAGAUGGCCCCAAGAGUUGAGGCGAAAUCAGCAUAAAAUACGCAA------------AGAAG
((((((((((..((((.....((..(....)..))..))))......))))))))))...(((.(((.((.....)).)))...))).((.........))..------------..... ( -25.00)
>DroAna_CAF1 49262 112 - 1
UGUAUGUUUGC---CAGUUAGUUGG--UG-GCGAAAAUUUGAAAAUCCAAAC--ACAAUAGAUGGCACCACGAGUUGAAGCAAAAUCGGCAUAAAAUGUGCAAAGGAUAAGGAAGAGGAA
......(((((---((.(.....).--))-))))).........((((....--......(((.((..((.....))..))...))).((((.....))))...))))............ ( -19.80)
>consensus
UGUGUGUUUGCCCCCAGAAAAU________CUGGAAAUGUGCAAAUCCAAACACACAAUAGAUGGCCCCAAGAGCUGAGGCAAAAUCAGCAUAAAAUACGCAG____________AGAAA
((((((((((.....................................))))))))))...(((.(((.((.....)).)))...))).((.........))................... (-15.34 = -16.01 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:23 2006