Locus 1394

Sequence ID	X_DroMel_CAF1
Location	4,192,284 – 4,192,377
Length	93
Max. P	0.842756

overview

Window 4

Location	4,192,284 – 4,192,377
Length	93
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	77.35
Mean single sequence MFE	-20.98
Consensus MFE	-13.18
Energy contribution	-12.98
Covariance contribution	-0.19
Combinations/Pair	1.10
Mean z-score	-1.49
Structure conservation index	0.63
SVM decision value	0.39
SVM RNA-class probability	0.716966
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4192284 93 + 22224390
UGUGU--UUGUAUUUGUGUGUCGUCUGGCUAACAAGCUCUCCAAGUUUAACAAUGAGCGAA-AUUUCGCAGCUCAUUGAAUUUGAAGUCAUGUGUA
.....--........(..((.(....((((....))))...((((((...((((((((...-........))))))))))))))..).))..)... ( -18.20)
>DroVir_CAF1 43671 85 + 1
UGGCUGGCUGGCUUUG---------GCGCUAACGAGCU--UCAAGUUUAACAAUGAGCGAACAUUUUGCAGCUCAUUGAAUUUGAAGUCAUGUGAA
((((..(((......)---------))))))(((.(((--(((((((...((((((((............))))))))))))))))))..)))... ( -25.00)
>DroGri_CAF1 32725 80 + 1
U-----ACUGACAUCG---------GCUCUAACGAGCU--UCAAGUUUAACAAUGAGCGAACAUUUUGCAGCUCAUUGAAUUUGAAGUCAUGUGAA
(-----((((((....---------((((....))))(--(((((((...((((((((............)))))))))))))))))))).))).. ( -28.20)
>DroEre_CAF1 26106 79 + 1
-------------UUGUGU---GUCUGGCUAACAAGCUCUCCAAGUUUAACAAUGAGCGAA-AUUUCGCAGCUCAUUGAAUUUGAAGUCAUGUGUA
-------------..(..(---(.((((((....))))...((((((...((((((((...-........)))))))))))))).)).))..)... ( -18.90)
>DroWil_CAF1 31922 83 + 1
------------UGUGUGUGUUGACUGGCUAACGAGCU-UCUAAGUUUAACAAUGAACGAAAAUUUUGCAGCUCAUUGAAUUUGAAGUCAUGUGAA
------------.........(((((((((....))))-...........((((((.(............).)))))).......)))))...... ( -12.00)
>DroMoj_CAF1 42759 83 + 1
UGGCU--UUGGCUUUG---------GCGCUAACGAGCU--UCAAGUUUAACAAUGAGCGAACAUUUUGCAGCUCAUUGAAUUUGAAGUCAUGUGAA
.....--(((((....---------..))))).((.((--(((((((...((((((((............)))))))))))))))))))....... ( -23.60)
>consensus
U_______UG_CUUUG_________GCGCUAACGAGCU__CCAAGUUUAACAAUGAGCGAACAUUUUGCAGCUCAUUGAAUUUGAAGUCAUGUGAA
...............................(((.(((...((((((...((((((((............)))))))))))))).)))..)))... (-13.18 = -12.98 +  -0.19)

alignment

secondary structure

dotplot

Window 5

Location	4,192,284 – 4,192,377
Length	93
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	77.35
Mean single sequence MFE	-18.03
Consensus MFE	-10.16
Energy contribution	-9.72
Covariance contribution	-0.44
Combinations/Pair	1.17
Mean z-score	-1.94
Structure conservation index	0.56
SVM decision value	0.76
SVM RNA-class probability	0.842756
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4192284 93 - 22224390
UACACAUGACUUCAAAUUCAAUGAGCUGCGAAAU-UUCGCUCAUUGUUAAACUUGGAGAGCUUGUUAGCCAGACGACACACAAAUACAA--ACACA
.........((((((...((((((((........-...))))))))......)))))).(((....)))....................--..... ( -16.20)
>DroVir_CAF1 43671 85 - 1
UUCACAUGACUUCAAAUUCAAUGAGCUGCAAAAUGUUCGCUCAUUGUUAAACUUGA--AGCUCGUUAGCGC---------CAAAGCCAGCCAGCCA
..........(((((...((((((((.((.....))..))))))))......))))--)(((.(((.((..---------....)).))).))).. ( -20.70)
>DroGri_CAF1 32725 80 - 1
UUCACAUGACUUCAAAUUCAAUGAGCUGCAAAAUGUUCGCUCAUUGUUAAACUUGA--AGCUCGUUAGAGC---------CGAUGUCAGU-----A
...((.((((.((.....((((((((.((.....))..))))))))..........--.((((....))))---------.)).))))))-----. ( -22.90)
>DroEre_CAF1 26106 79 - 1
UACACAUGACUUCAAAUUCAAUGAGCUGCGAAAU-UUCGCUCAUUGUUAAACUUGGAGAGCUUGUUAGCCAGAC---ACACAA-------------
.........((((((...((((((((........-...))))))))......)))))).(((....))).....---......------------- ( -16.20)
>DroWil_CAF1 31922 83 - 1
UUCACAUGACUUCAAAUUCAAUGAGCUGCAAAAUUUUCGUUCAUUGUUAAACUUAGA-AGCUCGUUAGCCAGUCAACACACACA------------
......(((((.......((((((((............))))))))...........-.(((....))).))))).........------------ ( -12.70)
>DroMoj_CAF1 42759 83 - 1
UUCACAUGACUUCAAAUUCAAUGAGCUGCAAAAUGUUCGCUCAUUGUUAAACUUGA--AGCUCGUUAGCGC---------CAAAGCCAA--AGCCA
.....((((((((((...((((((((.((.....))..))))))))......))))--)).))))..((..---------....))...--..... ( -19.50)
>consensus
UUCACAUGACUUCAAAUUCAAUGAGCUGCAAAAUGUUCGCUCAUUGUUAAACUUGA__AGCUCGUUAGCCA_________CAAAG_CA_______A
.....((((((((((...((((((((............))))))))......))))..)).))))............................... (-10.16 =  -9.72 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:19 2006