Locus 4246

Sequence ID	3L_DroMel_CAF1
Location	12,434,611 – 12,434,709
Length	98
Max. P	0.562810

overview

Window 0

Location	12,434,611 – 12,434,709
Length	98
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	77.69
Mean single sequence MFE	-23.90
Consensus MFE	-14.42
Energy contribution	-14.78
Covariance contribution	0.37
Combinations/Pair	1.27
Mean z-score	-1.39
Structure conservation index	0.60
SVM decision value	-0.03
SVM RNA-class probability	0.517902
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12434611 98 + 23771897
------------------GGGAAGGGCCCAAGAACAACAUUGUUGUCAUAUUAGUAAACGUAACUAACUUUAGUUAUUGCUGGUGUUGCGACUUCGCACGUUUAUGGUCCAUUUAG
------------------.....(((((...((((......(((((.(((((((((...(((((((....)))))))))))))))).))))).......))))..)))))...... ( -27.62)
>DroVir_CAF1 36949 89 + 1
-----------------------GGGU----UGGCAACAAUGUUGUUGUAUUAGUUAACGUUACUAACUUUAGUUAUUGCGCGUGUUGCGAUUUCGCGCUUUUAUGGUCCAUUUAA
-----------------------(((.----.(((((((....)))))).(((((.......)))))...........(((((...........))))).....)..)))...... ( -17.80)
>DroPse_CAF1 37414 110 + 1
CUGUUGCUGAUGCUGAUGCUG--GAGC----CGACAACAUUGUUGUCAUAUUAGUAAACGUAACUAACUUUAGUUAUUGCUAGUGUUGCGACUUCGCACGUUUAUGGUCCAUUUAG
......((((.((....))((--((.(----(((((((...))))))......((((((((....(((.(((((....))))).)))(((....))))))))))))))))).)))) ( -30.00)
>DroYak_CAF1 39699 91 + 1
---------------AUGGUG----------GAACAACAUUGUUGUCAUAUUAGUAAACGUAACUAACUUUAGUUAUUGCUGGUGUUGCGACUUCGCACGUUUAUGGUCCAUUUAG
---------------..((((----------(((((((...))))).......((((((((....(((.(((((....))))).)))(((....)))))))))))..))))))... ( -22.40)
>DroMoj_CAF1 32921 89 + 1
-----------------------GAAU----CGGCAACAAUGUUGUCGUAUUAGUUAUCGUAACUAACUUUAGUUAUUGCGCGUGUUGUGAUUUCGUGCUUUUAUGGUCCAUUUAA
-----------------------.(((----(((((((...))))))).)))....(((((((.((((....))))..(((((...........)))))..)))))))........ ( -16.90)
>DroPer_CAF1 37879 98 + 1
CUGUUG------------CUG--GAGC----CGACAACAUUGUUGUCAUAUUAGUAAACGUAACUAACUUUAGUUAUUGCUAGUGUUGCGACUUCGCACGUUUAUGGUCCAUUUAG
......------------.((--((.(----(((((((...))))))......((((((((....(((.(((((....))))).)))(((....)))))))))))))))))..... ( -28.70)
>consensus
___________________UG__GAGC____CGACAACAUUGUUGUCAUAUUAGUAAACGUAACUAACUUUAGUUAUUGCUAGUGUUGCGACUUCGCACGUUUAUGGUCCAUUUAG
................................((((((...))))))(((((((((...(((((((....))))))))))))))))((((....)))).................. (-14.42 = -14.78 +   0.37)

alignment

secondary structure

dotplot

Window 1

Location	12,434,611 – 12,434,709
Length	98
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	77.69
Mean single sequence MFE	-20.12
Consensus MFE	-8.88
Energy contribution	-10.22
Covariance contribution	1.33
Combinations/Pair	1.05
Mean z-score	-2.10
Structure conservation index	0.44
SVM decision value	0.06
SVM RNA-class probability	0.562810
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12434611 98 - 23771897
CUAAAUGGACCAUAAACGUGCGAAGUCGCAACACCAGCAAUAACUAAAGUUAGUUACGUUUACUAAUAUGACAACAAUGUUGUUCUUGGGCCCUUCCC------------------
......((.(((((((((((((....))))..........((((((....)))))))))))).......((((((...))))))..)))..)).....------------------ ( -20.00)
>DroVir_CAF1 36949 89 - 1
UUAAAUGGACCAUAAAAGCGCGAAAUCGCAACACGCGCAAUAACUAAAGUUAGUAACGUUAACUAAUACAACAACAUUGUUGCCA----ACCC-----------------------
.....(((.........(((((...........)))))..........((((((.......)))))).(((((....))))))))----....----------------------- ( -16.20)
>DroPse_CAF1 37414 110 - 1
CUAAAUGGACCAUAAACGUGCGAAGUCGCAACACUAGCAAUAACUAAAGUUAGUUACGUUUACUAAUAUGACAACAAUGUUGUCG----GCUC--CAGCAUCAGCAUCAGCAACAG
.....((((((.((((((((((....)))...((((((..........)))))).))))))).......((((((...)))))))----).))--))((....))........... ( -28.10)
>DroYak_CAF1 39699 91 - 1
CUAAAUGGACCAUAAACGUGCGAAGUCGCAACACCAGCAAUAACUAAAGUUAGUUACGUUUACUAAUAUGACAACAAUGUUGUUC----------CACCAU---------------
....((((....((((((((((....))))..........((((((....)))))))))))).......((((((...)))))).----------..))))--------------- ( -18.30)
>DroMoj_CAF1 32921 89 - 1
UUAAAUGGACCAUAAAAGCACGAAAUCACAACACGCGCAAUAACUAAAGUUAGUUACGAUAACUAAUACGACAACAUUGUUGCCG----AUUC-----------------------
.....(((.........((.((...........)).))..........((((((((...)))))))).(((((....))))))))----....----------------------- ( -11.20)
>DroPer_CAF1 37879 98 - 1
CUAAAUGGACCAUAAACGUGCGAAGUCGCAACACUAGCAAUAACUAAAGUUAGUUACGUUUACUAAUAUGACAACAAUGUUGUCG----GCUC--CAG------------CAACAG
.....((((((.((((((((((....)))...((((((..........)))))).))))))).......((((((...)))))))----).))--)).------------...... ( -26.90)
>consensus
CUAAAUGGACCAUAAACGUGCGAAGUCGCAACACCAGCAAUAACUAAAGUUAGUUACGUUUACUAAUAUGACAACAAUGUUGUCG____GCUC__CA___________________
.((((((............(((....)))...........((((((....)))))))))))).......((((((...))))))................................ ( -8.88 = -10.22 +   1.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:40 2006