Locus 4474

Sequence ID X_DroMel_CAF1
Location 11,840,516 – 11,840,617
Length 101
Max. P 0.762863
window7353 window7354

overview

Window 3

Location 11,840,516 – 11,840,617
Length 101
Sequences 3
Columns 101
Reading direction forward
Mean pairwise identity 79.31
Mean single sequence MFE -16.33
Consensus MFE -11.94
Energy contribution -12.33
Covariance contribution 0.39
Combinations/Pair 1.10
Mean z-score -1.62
Structure conservation index 0.73
SVM decision value 0.46
SVM RNA-class probability 0.743732
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11840516 101 + 22224390
UCAAUGUAAAUGGUGUGAUAAAAAACGCAAUUAGGCGAUAAUUUCAUGAUAAUUUCAUGAGCGUUAUAAAAUAACACAAGACCAUAAUUGCAGAAAAUUUU
....(((((((((((((........(((......)))((((((((((((.....))))))).))))).......)))...)))))..)))))......... ( -21.20)
>DroSec_CAF1 16207 77 + 1
UCAAUGUAAAUGGUGUGAUAAAAAACGCAAUUAGGCGAUAAUUUC-----------AUG-------------AACAUAUGACCGUAAUUGCAGAAGAUAUU
....((((((((((...........(((......))).......(-----------(((-------------....)))))))))..)))))......... ( -10.60)
>DroSim_CAF1 16804 88 + 1
UCAAUGUAAAUGGUGUGAUAAAAAACGCAAUUAGGCGAUAAUUUCAUGAAAGUUUCAUG-------------AACAUAUGACCGUAAUUGCAGAAGAUAUU
....(((((((((((((........(((......))).....(((((((.....)))))-------------)))))...)))))..)))))......... ( -17.20)
>consensus
UCAAUGUAAAUGGUGUGAUAAAAAACGCAAUUAGGCGAUAAUUUCAUGA_A_UUUCAUG_____________AACAUAUGACCGUAAUUGCAGAAGAUAUU
....(((((((((((((........(((......))).......(((((.....)))))...............)))...)))))..)))))......... (-11.94 = -12.33 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,840,516 – 11,840,617
Length 101
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 79.31
Mean single sequence MFE -16.90
Consensus MFE -8.84
Energy contribution -8.95
Covariance contribution 0.11
Combinations/Pair 1.08
Mean z-score -2.80
Structure conservation index 0.52
SVM decision value 0.51
SVM RNA-class probability 0.762863
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11840516 101 - 22224390
AAAAUUUUCUGCAAUUAUGGUCUUGUGUUAUUUUAUAACGCUCAUGAAAUUAUCAUGAAAUUAUCGCCUAAUUGCGUUUUUUAUCACACCAUUUACAUUGA
..........(((((((.(((...(((((((...)))))))((((((.....)))))).......)))))))))).......................... ( -20.40)
>DroSec_CAF1 16207 77 - 1
AAUAUCUUCUGCAAUUACGGUCAUAUGUU-------------CAU-----------GAAAUUAUCGCCUAAUUGCGUUUUUUAUCACACCAUUUACAUUGA
..........(((((((.(((.(((....-------------...-----------.....))).)))))))))).......................... ( -10.60)
>DroSim_CAF1 16804 88 - 1
AAUAUCUUCUGCAAUUACGGUCAUAUGUU-------------CAUGAAACUUUCAUGAAAUUAUCGCCUAAUUGCGUUUUUUAUCACACCAUUUACAUUGA
..........(((((((.(((.(((..((-------------(((((.....)))))))..))).)))))))))).......................... ( -19.70)
>consensus
AAUAUCUUCUGCAAUUACGGUCAUAUGUU_____________CAUGAAA_U_UCAUGAAAUUAUCGCCUAAUUGCGUUUUUUAUCACACCAUUUACAUUGA
..........(((((((.(((.(((....................................))).)))))))))).......................... ( -8.84 =  -8.95 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:59 2006