Locus 8977

Sequence ID	3R_DroMel_CAF1
Location	24,084,247 – 24,084,381
Length	134
Max. P	0.830934

overview

Window 7

Location	24,084,247 – 24,084,345
Length	98
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	80.67
Mean single sequence MFE	-31.88
Consensus MFE	-14.45
Energy contribution	-14.78
Covariance contribution	0.33
Combinations/Pair	1.06
Mean z-score	-2.74
Structure conservation index	0.45
SVM decision value	0.38
SVM RNA-class probability	0.713445
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24084247 98 - 27905053
GCAA----------------AACGCGACUCGCUGCUCC-CUCAAAUAUUUGUGCAGAGCCAAAAACGGGCACACAAAUGUGUAACCAACACGCUAUUUGCUUGAGGCAAACUC-AC
((((----------------(..(((.......((((.-(.(((....))).)..)))).......((..((((....))))..))....)))..))))).((((.....)))-). ( -24.60)
>DroVir_CAF1 295203 100 - 1
GCAA---AUGUUGUAAUGUAAGCGC----CGUUGCUCAAGUCAAAUAUUUGAGCAG---------CGGGCACACAAAUGUGUAACCAACACGCUAUUUGCUUGAGGCAACCUCUAC
((((---(((.(((.......((.(----((((((((((((.....))))))))))---------)))))((((....)))).......))).)))))))..((((...))))... ( -37.90)
>DroPse_CAF1 292151 113 - 1
GCAA---AUGUUGUAAUGGAAGCGCGAUUCUCUGCUCCACUCAAAUAUUUGUGCAGAGCCAAAAACGGGCACACAAAUGUGUAACCAACACGCUAUUUGCUUGAGGCACACUGGGC
((((---(((((....((((.(((.(.....))))))))....))))))))).(((.(((......((..((((....))))..))..((.((.....)).)).)))...)))... ( -31.40)
>DroGri_CAF1 252715 100 - 1
GCAA---AUGUUGUAAUGUAAGCGC----CGUUGCUCAAGCCAAAUAUUUGAGCAG---------CGGGCACACAAAUGUGUAACCAACACGCUAUUUGCUUGAGGCAACCUAUAC
((((---(((.(((.......((.(----(((((((((((.......)))))))))---------)))))((((....)))).......))).)))))))....(....)...... ( -33.30)
>DroWil_CAF1 328281 110 - 1
GCUACAAAUGUUGUAAUGUAAGCGCGA-----UGCUCGAGUCAAAUAUUUGAGCAGAGCCAAAAACGGGCACACAAAUGUGUAACCAACACGAUAUUUGCUUGAGGCAAACAC-AC
(((.((((((((((.......(.((..-----(((((((((.....)))))))))..)))......((..((((....))))..))...)))))))))).....)))......-.. ( -32.70)
>DroPer_CAF1 293820 113 - 1
GCAA---AUGUUGUAAUGGAAGCGCGAUUCUCUGCUCCACUCAAAUAUUUGUGCAGAGCCAAAAACGGGCACACAAAUGUGUAACCAACACGCUAUUUGCUUGAGGCACACUGGGC
((((---(((((....((((.(((.(.....))))))))....))))))))).(((.(((......((..((((....))))..))..((.((.....)).)).)))...)))... ( -31.40)
>consensus
GCAA___AUGUUGUAAUGUAAGCGCGA__CGCUGCUCCACUCAAAUAUUUGAGCAGAGCCAAAAACGGGCACACAAAUGUGUAACCAACACGCUAUUUGCUUGAGGCAAACUC_AC
....................((((.......((((.................))))..........((..((((....))))..))....))))...(((.....)))........ (-14.45 = -14.78 +   0.33)

alignment

secondary structure

dotplot

Window 8

Location	24,084,284 – 24,084,381
Length	97
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	79.15
Mean single sequence MFE	-28.23
Consensus MFE	-16.24
Energy contribution	-17.63
Covariance contribution	1.39
Combinations/Pair	1.08
Mean z-score	-2.08
Structure conservation index	0.58
SVM decision value	0.71
SVM RNA-class probability	0.830934
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24084284 97 + 27905053
AUUUGUGUGCCCGUUUUUGGCUCUGCACAAAUAUUUGAG-G-GAGCAGCGA-GUCGCGUU----------------UUGCAGCAGCUGAAAAUAUAACGUAUACGCAACAUUAGCA
..(((((((..((((((..(((((((.(((....)))..-(-((((.(((.-..))))))----------------)))))).)))..)).....))))..)))))))........ ( -26.90)
>DroVir_CAF1 295241 98 + 1
AUUUGUGUGCCCG---------CUGCUCAAAUAUUUGACUU-GAGCAACG-----GCGCUUACAUUACAACAU---UUGCAGCAGCUGAAAAUAUAAAGUAUACGCAGCAUUAAUA
...((((.(((((---------.(((((((.........))-))))).))-----).)).)))).........---........((((...((((...))))...))))....... ( -24.60)
>DroPse_CAF1 292189 111 + 1
AUUUGUGUGCCCGUUUUUGGCUCUGCACAAAUAUUUGAGUG-GAGCAGAGA-AUCGCGCUUCCAUUACAACAU---UUGCAGCAGCUGAAAAUAUAACGUAUACGCAGCAUUAGCA
...((((((..((((((..((((((((..(((..(((((((-((((.(...-..)..)).)))))).))).))---)))))).)))..)).....))))..))))))((....)). ( -32.50)
>DroWil_CAF1 328318 109 + 1
AUUUGUGUGCCCGUUUUUGGCUCUGCUCAAAUAUUUGACUC-GAGCA------UCGCGCUUACAUUACAACAUUUGUAGCAGCAGCUGAAAAUAUAACGUAUACGCAGCAUUAGCA
...((((((..((((((..(((((((((((((.(((((...-((((.------....))))...))).)).))))).))))).)))..)).....))))..))))))((....)). ( -30.50)
>DroAna_CAF1 283215 98 + 1
AUUUGUGUGC-CGUUUUUGGCCCUGCACAAAUAUUUGAG-UCGCGCUACAUUACAGCAUU----------------UUGCAGCAGCUGAAAAUAUAACAUAUACGCAGCAUUAGCA
((((((((((-((....))))...)))))))).......-....((((.......((...----------------..))....((((...((((...))))...))))..)))). ( -23.00)
>DroPer_CAF1 293858 111 + 1
AUUUGUGUGCCCGUUUUUGGCUCUGCACAAAUAUUUGAGUG-GAGCAGAGA-AUCGCGCUUCCAUUACAACAU---UUGCAGCAGCUGAAAAUAUAACGUAUACGCAACAUUAGCA
..(((((((..((((((..((((((((..(((..(((((((-((((.(...-..)..)).)))))).))).))---)))))).)))..)).....))))..)))))))........ ( -31.90)
>consensus
AUUUGUGUGCCCGUUUUUGGCUCUGCACAAAUAUUUGAGUG_GAGCAGCGA_AUCGCGCUU_CAUUACAACAU___UUGCAGCAGCUGAAAAUAUAACGUAUACGCAGCAUUAGCA
..(((((((..((((((..(((((((((((....))).......((.........))....................))))).)))..)).....))))..)))))))........ (-16.24 = -17.63 +   1.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:24:01 2006