Locus 3743

Sequence ID X_DroMel_CAF1
Location 9,956,085 – 9,956,193
Length 108
Max. P 0.868750
window6149 window6150

overview

Window 9

Location 9,956,085 – 9,956,193
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.13
Mean single sequence MFE -16.44
Consensus MFE -13.14
Energy contribution -13.02
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -1.72
Structure conservation index 0.80
SVM decision value 0.45
SVM RNA-class probability 0.739381
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9956085 108 + 22224390
------UAGCCUUCAUUCGCAACCGAUUCAUUAUUGGGGUUUACGCCCAAUUGACUUUCGAUAAAGUCUACCCCCCUUCUU------UUUUUUUUUCAUUUUUUACCUUCUGAGAACUCU
------..((........))....(((((...(((((((....).)))))).((((((....)))))).............------..........................))).)). ( -12.80)
>DroSec_CAF1 24176 110 + 1
AUUCAUCAGCCUUCAUUCGCAACCGAUUCAUUAUCGGGGUUUACGCCCAAUUGACUUUCGAUAAAGUCUACCCCUCUUUU----------UUUUUUCAUUUUUUACCUUCUGAGAACUCU
.(((.((((...............(((.....)))(((((..((.....((((.....))))...))..)))))......----------...................))))))).... ( -16.70)
>DroSim_CAF1 5323 120 + 1
AUUCAUCAGCCUUCAUUCGCAACCGAUUCAUUAUCGGGGUUUACGCCCAAUUGACUUUCGAUAAAGUCUACCCCUCUUUUUUUUCAUUUUUUUUUUCAUUUUUUACCUUCUGAGAACUCU
.(((.((((...............(((.....)))(((((..((.....((((.....))))...))..)))))...................................))))))).... ( -16.70)
>DroEre_CAF1 18773 108 + 1
AUUCAUCAGCCUUCAAUCCCAACCGAUUCAAUAUCGGGGGCUACGCCCAAUUGACUUUCGAUAAAGUCU--UCUGCCCCU----------CUUUUUUAUUUUUUACCUUCUGAGAACUUU
.(((.((((.............(((((.....)))))((((...))))....((((((....)))))).--.........----------...................))))))).... ( -20.30)
>DroYak_CAF1 18522 108 + 1
AUUCAUCAGCCUUCAUUCGCAACCGAUUCAUUAUCGGGGUUUACGCCCAAUUGACUUUCGAUAAAGUCC--CCCUCUUGU----------UUUAUUUUUUUUUUACCUUCUGAGAACUUU
.(((.((((..............((((.....))))((((....))))....((((((....)))))).--.........----------...................))))))).... ( -15.70)
>consensus
AUUCAUCAGCCUUCAUUCGCAACCGAUUCAUUAUCGGGGUUUACGCCCAAUUGACUUUCGAUAAAGUCUACCCCUCUUCU__________UUUUUUCAUUUUUUACCUUCUGAGAACUCU
.....((((..............((((.....))))(((......)))....((((((....)))))).........................................))))....... (-13.14 = -13.02 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 9,956,085 – 9,956,193
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.13
Mean single sequence MFE -21.92
Consensus MFE -18.86
Energy contribution -18.90
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.81
Structure conservation index 0.86
SVM decision value 0.86
SVM RNA-class probability 0.868750
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9956085 108 - 22224390
AGAGUUCUCAGAAGGUAAAAAAUGAAAAAAAAA------AAGAAGGGGGGUAGACUUUAUCGAAAGUCAAUUGGGCGUAAACCCCAAUAAUGAAUCGGUUGCGAAUGAAGGCUA------
..(((..(((....((((....(((........------.............((((((....)))))).((((((.(....)))))))......))).))))...)))..))).------ ( -21.70)
>DroSec_CAF1 24176 110 - 1
AGAGUUCUCAGAAGGUAAAAAAUGAAAAAA----------AAAAGAGGGGUAGACUUUAUCGAAAGUCAAUUGGGCGUAAACCCCGAUAAUGAAUCGGUUGCGAAUGAAGGCUGAUGAAU
..(((..(((....((((....(((.....----------............((((((....)))))).((((((.(....)))))))......))).))))...)))..)))....... ( -21.40)
>DroSim_CAF1 5323 120 - 1
AGAGUUCUCAGAAGGUAAAAAAUGAAAAAAAAAAUGAAAAAAAAGAGGGGUAGACUUUAUCGAAAGUCAAUUGGGCGUAAACCCCGAUAAUGAAUCGGUUGCGAAUGAAGGCUGAUGAAU
..(((..(((....((((....(((...........................((((((....)))))).((((((.(....)))))))......))).))))...)))..)))....... ( -21.40)
>DroEre_CAF1 18773 108 - 1
AAAGUUCUCAGAAGGUAAAAAAUAAAAAAG----------AGGGGCAGA--AGACUUUAUCGAAAGUCAAUUGGGCGUAGCCCCCGAUAUUGAAUCGGUUGGGAUUGAAGGCUGAUGAAU
...((((((((..................(----------.(((((...--.((((((....)))))).((.....)).))))))....((.((((......)))).))..)))).)))) ( -22.40)
>DroYak_CAF1 18522 108 - 1
AAAGUUCUCAGAAGGUAAAAAAAAAAUAAA----------ACAAGAGGG--GGACUUUAUCGAAAGUCAAUUGGGCGUAAACCCCGAUAAUGAAUCGGUUGCGAAUGAAGGCUGAUGAAU
..(((..(((....((((............----------....((((.--...)))).((((...(((((((((.(....)))))))..))).))))))))...)))..)))....... ( -22.70)
>consensus
AGAGUUCUCAGAAGGUAAAAAAUGAAAAAA__________AAAAGAGGGGUAGACUUUAUCGAAAGUCAAUUGGGCGUAAACCCCGAUAAUGAAUCGGUUGCGAAUGAAGGCUGAUGAAU
..(((..(((....((((..................................((((((....)))))).((((((.(....)))))))..........))))...)))..)))....... (-18.86 = -18.90 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:20 2006