Locus 3349

Sequence ID	2R_DroMel_CAF1
Location	11,369,516 – 11,369,609
Length	93
Max. P	0.996056

overview

Window 4

Location	11,369,516 – 11,369,609
Length	93
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	71.14
Mean single sequence MFE	-20.93
Consensus MFE	-9.87
Energy contribution	-11.31
Covariance contribution	1.45
Combinations/Pair	1.11
Mean z-score	-2.11
Structure conservation index	0.47
SVM decision value	1.50
SVM RNA-class probability	0.958972
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11369516 93 + 20766785
UAUCUGCGA-AUAGAUAGAUACUUAUACA------UAUAUUUA------------UGAGUUUUACUUAUCGAUGGCAAUCUUUCGUCCAUCGACAAUUGUUUAUCGCUAAAA
.....((((-.(((((((..(((((((..------......))------------)))))........((((((((........).)))))))...)))))))))))..... ( -21.80)
>DroSec_CAF1 2271 87 + 1
UAUCGGCGA-UUAGAUAGAUACUUA------------UAUUUA------------UGAGUUGUAUUUAUCGAUGGCAAUCUUUCGUCCAUCGACAAUUGUUUAUCGCUAAAA
....(((((-(((((((.(.(((((------------(....)------------)))))).))))))((((((((........).))))))).........)))))).... ( -22.60)
>DroSim_CAF1 2265 87 + 1
UAUCUGCGA-UUAGAUAGAUACUUA------------UAUUUA------------UGAGUUGUAUUUAUCGAUGGCAAUCUUUCGUCCAUCGACAAUUGUUUAUCGCUAAAA
.....((((-(((((((.(.(((((------------(....)------------)))))).))))))((((((((........).))))))).........)))))..... ( -21.20)
>DroEre_CAF1 2286 105 + 1
UAUCUGCGA-UUAGAUAGAUACCUAUAAA------GAUAUUUAUACGAUUACCCCUGAGUUGUAUUUAUCGAUGGCAAACUAUCGUCCAUCGACAAUUGUUUAUCGCUAAAA
.....((((-(.((((((...........------((((...((((((((.......)))))))).))))((((((........).))))).....)))))))))))..... ( -23.30)
>DroYak_CAF1 2372 111 + 1
UAUCUGCGA-UUAGAUAGAUACCUAUACAUACGAGUAUAUUUAUACGAUUACCCCUGAGUUGUAUUUAUCGAUGGCAAACUAUCGUCCAUCGACAAUUGUUUAUCGCUAAAU
.....((((-(.((((((.....(((((......)))))...((((((((.......))))))))...((((((((........).)))))))...)))))))))))..... ( -24.00)
>DroPer_CAF1 2281 92 + 1
CAUCUGCAUACAAUAUAGAU--UG--AAAGAUGGG--CAUUAA-AC-----------GCAUGUAUUCUUCAAUGUUUCACUUUUAUAGUUCGCUCAUGGUUUAUCGCAUU--
(((((.....((((....))--))--..))))).(--(..(((-((-----------.((((...........((...(((.....)))..)).)))))))))..))...-- ( -12.70)
>consensus
UAUCUGCGA_UUAGAUAGAUACUUA_A_A________UAUUUA____________UGAGUUGUAUUUAUCGAUGGCAAACUUUCGUCCAUCGACAAUUGUUUAUCGCUAAAA
.....((((....(((((((((.......................................)))))))))((((((........).)))))............))))..... ( -9.87 = -11.31 +   1.45)

alignment

secondary structure

dotplot

Window 5

Location	11,369,516 – 11,369,609
Length	93
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	71.14
Mean single sequence MFE	-21.92
Consensus MFE	-13.37
Energy contribution	-13.82
Covariance contribution	0.45
Combinations/Pair	1.26
Mean z-score	-2.56
Structure conservation index	0.61
SVM decision value	2.65
SVM RNA-class probability	0.996056
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11369516 93 - 20766785
UUUUAGCGAUAAACAAUUGUCGAUGGACGAAAGAUUGCCAUCGAUAAGUAAAACUCA------------UAAAUAUA------UGUAUAAGUAUCUAUCUAU-UCGCAGAUA
.....((((.......((((((((((.(....)....)))))))))).....(((.(------------((......------..))).)))..........-))))..... ( -21.00)
>DroSec_CAF1 2271 87 - 1
UUUUAGCGAUAAACAAUUGUCGAUGGACGAAAGAUUGCCAUCGAUAAAUACAACUCA------------UAAAUA------------UAAGUAUCUAUCUAA-UCGCCGAUA
..(..(((((......((((((((((.(....)....)))))))))).....(((.(------------(....)------------).))).........)-))))..).. ( -20.50)
>DroSim_CAF1 2265 87 - 1
UUUUAGCGAUAAACAAUUGUCGAUGGACGAAAGAUUGCCAUCGAUAAAUACAACUCA------------UAAAUA------------UAAGUAUCUAUCUAA-UCGCAGAUA
.....(((((......((((((((((.(....)....)))))))))).....(((.(------------(....)------------).))).........)-))))..... ( -21.20)
>DroEre_CAF1 2286 105 - 1
UUUUAGCGAUAAACAAUUGUCGAUGGACGAUAGUUUGCCAUCGAUAAAUACAACUCAGGGGUAAUCGUAUAAAUAUC------UUUAUAGGUAUCUAUCUAA-UCGCAGAUA
.....(((((......((((((((((.(((....)))))))))))))...........(((((..(.((((((....------)))))).)....))))).)-))))..... ( -27.60)
>DroYak_CAF1 2372 111 - 1
AUUUAGCGAUAAACAAUUGUCGAUGGACGAUAGUUUGCCAUCGAUAAAUACAACUCAGGGGUAAUCGUAUAAAUAUACUCGUAUGUAUAGGUAUCUAUCUAA-UCGCAGAUA
.....(((((......((((((((((.(((....)))))))))))))...........(((((...((((...(((((......))))).)))).))))).)-))))..... ( -30.00)
>DroPer_CAF1 2281 92 - 1
--AAUGCGAUAAACCAUGAGCGAACUAUAAAAGUGAAACAUUGAAGAAUACAUGC-----------GU-UUAAUG--CCCAUCUUU--CA--AUCUAUAUUGUAUGCAGAUG
--...(((.(((((((((.....(((.....)))....(......)....)))).-----------))-))).))--).(((((..--((--((....)))).....))))) ( -11.20)
>consensus
UUUUAGCGAUAAACAAUUGUCGAUGGACGAAAGAUUGCCAUCGAUAAAUACAACUCA____________UAAAUA________U_U_UAAGUAUCUAUCUAA_UCGCAGAUA
.....((((.......((((((((((.(((....)))))))))))))..........................................((.......))...))))..... (-13.37 = -13.82 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:20 2006