Locus 7548

Sequence ID	X_DroMel_CAF1
Location	18,819,372 – 18,819,487
Length	115
Max. P	0.969533

overview

Window 1

Location	18,819,372 – 18,819,487
Length	115
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	88.56
Mean single sequence MFE	-31.09
Consensus MFE	-24.43
Energy contribution	-24.23
Covariance contribution	-0.20
Combinations/Pair	1.08
Mean z-score	-2.36
Structure conservation index	0.79
SVM decision value	1.64
SVM RNA-class probability	0.969533
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18819372 115 + 22224390
GC----UCUGCCACCGGUUUUCCUUUAUCAUUCAUUAUUAUUAUUUUAUGCGAUCCGGCUGGUGGGUUGCACAACAACCCACACAAGAUGACAAAAAUCGAAGACCCAAAAGCAGCAAG
..----.((((....(((((((.........(((((.............((......))((((((((((.....)))))))).)).)))))........))))))).....)))).... ( -28.83)
>DroSec_CAF1 56440 105 + 1
GC----UCUGCCACCGGUUUUCCUUUAGCAUUCAUUAUUAUUAUUUUAUGCGAUCCGGCUGGUGGGUUGCACAACAACCCACACAAGAUGAGA-AAAUCGGAGACCCAAG---------
..----.......(((((((((.....((((....((....))....))))..((...((.((((((((.....))))))))...))..))))-))))))).........--------- ( -29.00)
>DroSim_CAF1 41687 105 + 1
GC----UCUGCCACCGGUUUUCCUUUAGCAUUCAUUAUUAUUAUUUUAUGCGAUCCGGCUGGUGGGUUGCACAACAACCCACACAAGAUGAGA-AAAUCGGAGACCCAAG---------
..----.......(((((((((.....((((....((....))....))))..((...((.((((((((.....))))))))...))..))))-))))))).........--------- ( -29.00)
>DroEre_CAF1 54566 100 + 1
GC----UCUGCCACCGGUUUUCCUUUA----UCAUUAUUAUUAUUUUAUGCGAUCCGGCUGGUGGGUUGCACAACAACCCACACAAGAUGGGA-AAAUCGGAGACCG-AG---------
.(----((.(.(.(((((((((((..(----((................((......))((((((((((.....)))))))).)).)))))))-))))))).).).)-))--------- ( -34.00)
>DroYak_CAF1 55377 104 + 1
GCUCGCUCAGCCACCGGUUUUCCUUUA----UCAUUAUUAUUAUUUUAUGCCAUCCGGCUGGUGGGUUGCACAACAACCCACACAAGACGGGA-AAAUCGGAGACCG-AA---------
..(((.((.....(((((((((((...----((................(((....)))((((((((((.....)))))))).)).)).))))-))))))).)).))-).--------- ( -34.60)
>consensus
GC____UCUGCCACCGGUUUUCCUUUA_CAUUCAUUAUUAUUAUUUUAUGCGAUCCGGCUGGUGGGUUGCACAACAACCCACACAAGAUGAGA_AAAUCGGAGACCCAAG_________
...............(((((((.........(((((.............((......))((((((((((.....)))))))).)).)))))........)))))))............. (-24.43 = -24.23 +  -0.20)

alignment

secondary structure

dotplot

Window 2

Location	18,819,372 – 18,819,487
Length	115
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	88.56
Mean single sequence MFE	-34.32
Consensus MFE	-24.78
Energy contribution	-24.58
Covariance contribution	-0.20
Combinations/Pair	1.08
Mean z-score	-2.36
Structure conservation index	0.72
SVM decision value	0.85
SVM RNA-class probability	0.866993
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18819372 115 - 22224390
CUUGCUGCUUUUGGGUCUUCGAUUUUUGUCAUCUUGUGUGGGUUGUUGUGCAACCCACCAGCCGGAUCGCAUAAAAUAAUAAUAAUGAAUGAUAAAGGAAAACCGGUGGCAGA----GC
....(((((..(.(((.(((...(((((((((..((.((((((((.....))))))))))((......))..................)))))))))))).))).).))))).----.. ( -34.00)
>DroSec_CAF1 56440 105 - 1
---------CUUGGGUCUCCGAUUU-UCUCAUCUUGUGUGGGUUGUUGUGCAACCCACCAGCCGGAUCGCAUAAAAUAAUAAUAAUGAAUGCUAAAGGAAAACCGGUGGCAGA----GC
---------(((..(((.(((.(((-(((.((((.((((((((((.....))))))))..)).)))).((((................))))....)))))).))).))).))----). ( -31.89)
>DroSim_CAF1 41687 105 - 1
---------CUUGGGUCUCCGAUUU-UCUCAUCUUGUGUGGGUUGUUGUGCAACCCACCAGCCGGAUCGCAUAAAAUAAUAAUAAUGAAUGCUAAAGGAAAACCGGUGGCAGA----GC
---------(((..(((.(((.(((-(((.((((.((((((((((.....))))))))..)).)))).((((................))))....)))))).))).))).))----). ( -31.89)
>DroEre_CAF1 54566 100 - 1
---------CU-CGGUCUCCGAUUU-UCCCAUCUUGUGUGGGUUGUUGUGCAACCCACCAGCCGGAUCGCAUAAAAUAAUAAUAAUGA----UAAAGGAAAACCGGUGGCAGA----GC
---------((-(.(((.(((.(((-(((.(((.((.((((((((.....))))))))))((......))................))----)...)))))).))).))).))----). ( -34.10)
>DroYak_CAF1 55377 104 - 1
---------UU-CGGUCUCCGAUUU-UCCCGUCUUGUGUGGGUUGUUGUGCAACCCACCAGCCGGAUGGCAUAAAAUAAUAAUAAUGA----UAAAGGAAAACCGGUGGCUGAGCGAGC
---------((-(((((.(((.(((-(((.(((.((.((((((((.....))))))))))(((....)))................))----)...)))))).))).)))))))..... ( -39.70)
>consensus
_________CUUGGGUCUCCGAUUU_UCUCAUCUUGUGUGGGUUGUUGUGCAACCCACCAGCCGGAUCGCAUAAAAUAAUAAUAAUGAAUG_UAAAGGAAAACCGGUGGCAGA____GC
..............(((.(((.(((.(((.....((.((((((((.....))))))))))((......))..........................)))))).))).)))......... (-24.78 = -24.58 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:38 2006