Locus 7033

Sequence ID	3R_DroMel_CAF1
Location	18,543,757 – 18,543,849
Length	92
Max. P	0.995859

overview

Window 3

Location	18,543,757 – 18,543,849
Length	92
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	70.63
Mean single sequence MFE	-24.64
Consensus MFE	-5.77
Energy contribution	-6.45
Covariance contribution	0.68
Combinations/Pair	1.24
Mean z-score	-2.67
Structure conservation index	0.23
SVM decision value	2.62
SVM RNA-class probability	0.995859
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18543757 92 + 27905053
UA-CCCAGUUCCCCUUUA------GUUUCC-CAUCCCCGGAGAACCACUCAUGCAUCCGAGCAU-------CCAGCUCGAGCAUCCCUU--AUAGGU------GAUGCCUUACUU
..-...............------(((..(-(......))..)))............(((((..-------...))))).(((((((..--...)).------)))))....... ( -21.00)
>DroSec_CAF1 13713 92 + 1
UA-CCCAGUUCCCCUUUA------GUUUCC-CAUCCCCGGAGAAUCACUCAUGCAUCCAAGCAU-------CCAGCUCAAGCAUCCCUU--AUAGGU------GAUGCCUUACUU
..-...((((........------.(((((-.......))))).......((((......))))-------..))))...(((((((..--...)).------)))))....... ( -15.00)
>DroEre_CAF1 13497 92 + 1
AA-CACAGUUGC-CUCUA------GAUUCC-CAUCCCCGGAAAUCCACUCAUGCAUC-GAGCAU-------CCAGCUCGAGCAUCCCUUAUAGAGGU------GAUGCCUUACUU
..-....((..(-(((((------((((.(-(......)).)))).....((((.((-((((..-------...))))))))))......)))))).------.))......... ( -30.10)
>DroYak_CAF1 13572 97 + 1
UA-CCCAGUUGC-CUCUA------GUUUCC-CAUCCCCGGAAACUCACUCAUGCAUC-GAGCAUCCAGCAUCCAGCUCGAGCAUCCCUU--AGAGGU------GAUGCCUUACUU
..-....((..(-(((((------((((((-.......))))))......((((.((-((((............))))))))))....)--))))).------.))......... ( -31.30)
>DroAna_CAF1 13838 101 + 1
GGUUCUAGUCCUCUGUUAGAUCCGGUUUCCACAACUCCGUGAAACCAGUCGAGCG---CAGCAU-------C-ACCGUUAGCAUCCCUU--GCGGCUACAGGAGC-CCCGCAGCU
((.(((((.......))))).))((((((.((......)))))))).....((((---(.....-------.-.......(((.....)--))((((.....)))-)..)).))) ( -25.80)
>consensus
UA_CCCAGUUCCCCUUUA______GUUUCC_CAUCCCCGGAAAACCACUCAUGCAUC_GAGCAU_______CCAGCUCGAGCAUCCCUU__AGAGGU______GAUGCCUUACUU
.........................(((((........))))).......((((......))))................((((((((.....))).......)))))....... ( -5.77 =  -6.45 +   0.68)

alignment

secondary structure

dotplot

Window 4

Location	18,543,757 – 18,543,849
Length	92
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	70.63
Mean single sequence MFE	-31.06
Consensus MFE	-6.53
Energy contribution	-7.45
Covariance contribution	0.92
Combinations/Pair	1.12
Mean z-score	-1.99
Structure conservation index	0.21
SVM decision value	0.92
SVM RNA-class probability	0.881462
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18543757 92 - 27905053
AAGUAAGGCAUC------ACCUAU--AAGGGAUGCUCGAGCUGG-------AUGCUCGGAUGCAUGAGUGGUUCUCCGGGGAUG-GGAAAC------UAAAGGGGAACUGGG-UA
..(((.((((((------.((...--..))))))))(((((...-------..)))))..)))......((((((((.....((-(....)------))..))))))))...-.. ( -33.90)
>DroSec_CAF1 13713 92 - 1
AAGUAAGGCAUC------ACCUAU--AAGGGAUGCUUGAGCUGG-------AUGCUUGGAUGCAUGAGUGAUUCUCCGGGGAUG-GGAAAC------UAAAGGGGAACUGGG-UA
.(((.(((((((------.((...--..)))))))))..)))..-------.((((..(..((....))..((((((.....((-(....)------))..)))))))..))-)) ( -28.00)
>DroEre_CAF1 13497 92 - 1
AAGUAAGGCAUC------ACCUCUAUAAGGGAUGCUCGAGCUGG-------AUGCUC-GAUGCAUGAGUGGAUUUCCGGGGAUG-GGAAUC------UAGAG-GCAACUGUG-UU
.......(((((------.(((.....))))))))((((((...-------..))))-)).((((...((((((((((....))-))))))------)).((-....)))))-). ( -33.40)
>DroYak_CAF1 13572 97 - 1
AAGUAAGGCAUC------ACCUCU--AAGGGAUGCUCGAGCUGGAUGCUGGAUGCUC-GAUGCAUGAGUGAGUUUCCGGGGAUG-GGAAAC------UAGAG-GCAACUGGG-UA
......((((((------.((...--..))))))))..(.(..(.((((..((((..-...)))).....(((((((.......-))))))------)...)-))).)..).-). ( -29.80)
>DroAna_CAF1 13838 101 - 1
AGCUGCGGG-GCUCCUGUAGCCGC--AAGGGAUGCUAACGGU-G-------AUGCUG---CGCUCGACUGGUUUCACGGAGUUGUGGAAACCGGAUCUAACAGAGGACUAGAACC
....(((.(-((((((((((((..--..)....))).)))).-)-------).))).---)))..(((((((((((((....))).)))))))).)).................. ( -30.20)
>consensus
AAGUAAGGCAUC______ACCUAU__AAGGGAUGCUCGAGCUGG_______AUGCUC_GAUGCAUGAGUGGUUUUCCGGGGAUG_GGAAAC______UAAAGGGGAACUGGG_UA
.(((..((((((.......(((.....)))))))))...))).........((((......)))).................................................. ( -6.53 =  -7.45 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:57 2006