Locus 15

Sequence ID	3R_DroMel_CAF1
Location	174,845 – 174,980
Length	135
Max. P	0.921959

overview

Window 8

Location	174,845 – 174,955
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.47
Mean single sequence MFE	-33.32
Consensus MFE	-17.98
Energy contribution	-18.58
Covariance contribution	0.60
Combinations/Pair	1.17
Mean z-score	-1.89
Structure conservation index	0.54
SVM decision value	0.01
SVM RNA-class probability	0.537972
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 174845 110 + 27905053
AUAGAGU----CUUCACGAGCACAUAGAUUACGACUGGACUAGGGGUAGGGGGUUUCAAUAAGCCCCCAGCUCACUAUUUGGUGAUCC----UG-GACGAA-GAUUGAAAGUUCGAACAA
....(((----((((.(.(((...........).)).).((((((((.((((((((....)))))))).))(((((....))))))))----))-)..)))-)))).............. ( -32.70)
>DroSec_CAF1 11609 109 + 1
AUAGAGU----GUUCACGAGCACGUAGAUUACGAAUGGACUAAGGAUAGGGGGUUUCAAUAAGCC-CCAGCUCACUCUUUCGUGAUCC----UG-GCCGAA-GAUUCUAAGUUCGAACGA
.((((((----.((((((....))).(((((((((.(((.....((...(((((((....)))))-))...))..)))))))))))).----..-...)))-.))))))........... ( -31.90)
>DroSim_CAF1 10973 110 + 1
AUAGAGU----GUUCACGAGCACGUAGAUUACGAAUGGACUAAGGAUAGGGGGUUUCAAUAAGCCCCCAGCUCACUCUUUGGUGAUCC----UG-GCCGAA-GAUUCUAAGUUCGAACGA
.....((----(((....)))))........((..((((((.((((..((((((((....)))))))).......((((((((.....----..-))))))-)))))).))))))..)). ( -36.30)
>DroEre_CAF1 11845 116 + 1
AUAGAAGUGUGUUCAACGAUCACAUAGAUUACGA---GAUUAA-GAUAGGGGGUUUCAAUAAACCUCCAGCUCACGGUUUGGUGAUCCUUCCUCUGCCGAAGGAUUGUAAGUUCGAGAGA
......(((((.((...)).))))).........---......-....((((((((....))))))))..(((.(((....(..(((((((.......)))))))..)....))).))). ( -31.60)
>DroYak_CAF1 12410 108 + 1
AUAGAGU----UUCCACGAUCACAUAGAUUACGG---GAUUAA-GAUAGGAGGUUUUAAUAAGCCUCCAGCCCACUGUUUGGUGAUCC----CGUGCCGAAAAAUUGAAACUACGUGAGA
....(((----(((...((((.....))))((((---(((((.-....((((((((....))))))))...(((.....)))))))))----)))...........)))))).(....). ( -34.10)
>consensus
AUAGAGU____GUUCACGAGCACAUAGAUUACGA_UGGACUAAGGAUAGGGGGUUUCAAUAAGCCCCCAGCUCACUCUUUGGUGAUCC____UG_GCCGAA_GAUUGUAAGUUCGAACGA
................(((((.....((((.((...............((((((((....))))))))...((((......))))............))...))))....)))))..... (-17.98 = -18.58 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	174,881 – 174,980
Length	99
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	73.94
Mean single sequence MFE	-30.26
Consensus MFE	-17.26
Energy contribution	-17.06
Covariance contribution	-0.20
Combinations/Pair	1.33
Mean z-score	-1.93
Structure conservation index	0.57
SVM decision value	1.14
SVM RNA-class probability	0.921959
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 174881 99 + 27905053
UAGGGGUAGGGGGUUUCAAUAAGCCCCCAGCUCACUAUUUGGUGAUCC----UG-GACGAA-GAUUGAAAGUUCGAACAAUUUCGAAAUGGUU-------UUCCUGAUUGAA
(((((((.((((((((....)))))))).))(((((....))))))))----))-...(((-(((((....((((((....)))))).)))))-------)))......... ( -30.20)
>DroSec_CAF1 11645 97 + 1
UAAGGAUAGGGGGUUUCAAUAAGCC-CCAGCUCACUCUUUCGUGAUCC----UG-GCCGAA-GAUUCUAAGUUCGAACGAUUUCGAAGUAGUU------UUUCCCGACCG--
..((((...(((((((....)))))-))...((((......)))))))----)(-(.((.(-((..(((..((((((....)))))).)))..------)))..)).)).-- ( -28.10)
>DroSim_CAF1 11009 98 + 1
UAAGGAUAGGGGGUUUCAAUAAGCCCCCAGCUCACUCUUUGGUGAUCC----UG-GCCGAA-GAUUCUAAGUUCGAACGAUUUCGAAGUAGUU------UUUCCCGACCG--
..((((..((((((((....))))))))...(((((....))))))))----)(-(.((.(-((..(((..((((((....)))))).)))..------)))..)).)).-- ( -32.10)
>DroEre_CAF1 11882 105 + 1
UAA-GAUAGGGGGUUUCAAUAAACCUCCAGCUCACGGUUUGGUGAUCCUUCCUCUGCCGAAGGAUUGUAAGUUCGAGAGAUUACGGAAUAGCCUACCAAUCAC--UG--U--
...-(((.((((((((....)))))))).......(((..(((((((((((.......))))))))((((..((....))))))......))).))).)))..--..--.-- ( -31.20)
>DroYak_CAF1 12443 105 + 1
UAA-GAUAGGAGGUUUUAAUAAGCCUCCAGCCCACUGUUUGGUGAUCC----CGUGCCGAAAAAUUGAAACUACGUGAGAUUACGGAAUAGCCAACCAAUCUCACGACUC--
...-....((((((((....)))))))).........((((((.....----...))))))............(((((((((..((.....))....)))))))))....-- ( -29.70)
>consensus
UAAGGAUAGGGGGUUUCAAUAAGCCCCCAGCUCACUCUUUGGUGAUCC____UG_GCCGAA_GAUUGUAAGUUCGAACGAUUUCGAAAUAGUU______UUUCCCGACCG__
...((((.((((((((....))))))))....(((......))))))).......................((((((....))))))......................... (-17.26 = -17.06 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:16 2006