Locus 4422

Sequence ID	3L_DroMel_CAF1
Location	12,912,987 – 12,913,080
Length	93
Max. P	0.999751

overview

Window 4

Location	12,912,987 – 12,913,080
Length	93
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	76.29
Mean single sequence MFE	-22.30
Consensus MFE	-14.68
Energy contribution	-15.74
Covariance contribution	1.06
Combinations/Pair	1.04
Mean z-score	-2.68
Structure conservation index	0.66
SVM decision value	3.17
SVM RNA-class probability	0.998654
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12912987 93 + 23771897
UGAGCAAUAAAAACACCUGCUAGUGUUAUUUUCACAUACUUCGAUUUAAG-UAUCGCUCACAAAAAUCGA----UGUAUGUGAAAAUUAUUCAUUACC----------------------
..((((...........))))((((..((((((((((((.(((((((..(-(.......))..)))))))----.))))))))))))....))))...---------------------- ( -25.10)
>DroSec_CAF1 33717 93 + 1
UGAGCAAUAAAAACACCUGCUAGUGCUAUUUUCACAUACUUCGAUUUAAG-UAUCGUUCACAAAAAUCGA----UGUAUGUGAAAAUUAUCCAUUAAC----------------------
..((((...........))))((((..((((((((((((.(((((((..(-(.......))..)))))))----.))))))))))))....))))...---------------------- ( -24.40)
>DroEre_CAF1 39007 98 + 1
UGAGCGAUAAAAACACCUGCUUGUGCCAUUGGCACAUACUUCGAUUUAAGCUAUCGUUCACAUAAAACGACGUUUGUAUGUGAAAAUUAUCCGUAAGC----------------------
...(((((((........(..((((((...))))))..)..((((.......))))((((((((((((...)))).))))))))..)))).)))....---------------------- ( -20.20)
>DroYak_CAF1 36335 114 + 1
UGAGCAAUAAAAACACCUGCUAUCGCUAUUUGCACAUACUUCGAAUUUGGGUAUCGUUCACAUAAAUCGA----UGUAUGUGAAAAUUAU--GUAAUUAUUUGCCAUUUUUCGCCAAUUG
((.(((((((..(((...((....)).((((.(((((((.((((.((((.((.......)).))))))))----.))))))).))))..)--))..))).)))))).............. ( -19.50)
>consensus
UGAGCAAUAAAAACACCUGCUAGUGCUAUUUGCACAUACUUCGAUUUAAG_UAUCGUUCACAAAAAUCGA____UGUAUGUGAAAAUUAUCCAUAAAC______________________
..((((...........))))......((((((((((((.(((((((................))))))).....))))))))))))................................. (-14.68 = -15.74 +   1.06)

alignment

secondary structure

dotplot

Window 5

Location	12,912,987 – 12,913,080
Length	93
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	76.29
Mean single sequence MFE	-27.85
Consensus MFE	-15.84
Energy contribution	-16.77
Covariance contribution	0.94
Combinations/Pair	1.16
Mean z-score	-3.58
Structure conservation index	0.57
SVM decision value	4.00
SVM RNA-class probability	0.999751
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12912987 93 - 23771897
----------------------GGUAAUGAAUAAUUUUCACAUACA----UCGAUUUUUGUGAGCGAUA-CUUAAAUCGAAGUAUGUGAAAAUAACACUAGCAGGUGUUUUUAUUGCUCA
----------------------(((((((((..((((((((((((.----(((((((..(((.....))-)..))))))).))))))))))))((((((....))))))))))))))).. ( -34.10)
>DroSec_CAF1 33717 93 - 1
----------------------GUUAAUGGAUAAUUUUCACAUACA----UCGAUUUUUGUGAACGAUA-CUUAAAUCGAAGUAUGUGAAAAUAGCACUAGCAGGUGUUUUUAUUGCUCA
----------------------..(((((((..((((((((((((.----(((((((..(((.....))-)..))))))).))))))))))))((((((....))))))))))))).... ( -29.70)
>DroEre_CAF1 39007 98 - 1
----------------------GCUUACGGAUAAUUUUCACAUACAAACGUCGUUUUAUGUGAACGAUAGCUUAAAUCGAAGUAUGUGCCAAUGGCACAAGCAGGUGUUUUUAUCGCUCA
----------------------.......(((((....(((........(((((((.....))))))).............((.((((((...)))))).))..)))...)))))..... ( -23.20)
>DroYak_CAF1 36335 114 - 1
CAAUUGGCGAAAAAUGGCAAAUAAUUAC--AUAAUUUUCACAUACA----UCGAUUUAUGUGAACGAUACCCAAAUUCGAAGUAUGUGCAAAUAGCGAUAGCAGGUGUUUUUAUUGCUCA
...............(((((.(((..((--((.((((.(((((((.----(((((((..(((.....)))..))).)))).))))))).)))).((....))..))))..)))))))).. ( -24.40)
>consensus
______________________GAUAACGGAUAAUUUUCACAUACA____UCGAUUUAUGUGAACGAUA_CUUAAAUCGAAGUAUGUGAAAAUAGCACUAGCAGGUGUUUUUAUUGCUCA
.............................((((((((((((((((.....(((((((.(((.....)))....))))))).))))))))))))(((((......)))))..))))..... (-15.84 = -16.77 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:13 2006