Locus 4209

Sequence ID 3L_DroMel_CAF1
Location 12,313,338 – 12,313,472
Length 134
Max. P 0.638449
window6523 window6524

overview

Window 3

Location 12,313,338 – 12,313,433
Length 95
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 90.70
Mean single sequence MFE -20.78
Consensus MFE -18.67
Energy contribution -18.18
Covariance contribution -0.50
Combinations/Pair 1.18
Mean z-score -1.41
Structure conservation index 0.90
SVM decision value 0.22
SVM RNA-class probability 0.638449
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12313338 95 + 23771897
GUCAUAUAAUUGUAAAUUGUAACUGACUCUGAUUGCACAUUGAUUAUAAUUGUAAUUAUUGUUGCUUAUAUCGGAUUACACGCUGGCGAAUUGGC
((((((((((.....))))))..))))((((((.(((((.(((((((....))))))).)).)))....))))))......((..(....)..)) ( -19.90)
>DroSec_CAF1 48463 95 + 1
GUAAUUUAAGCUGAAAUUGUAAGUGACUCUGAUUGCACAUUGAUUAUAAUUGUAAUUAUUGUUGCUUAUAUCGGAUUACACGCUGGCGAAUUCGC
(((((.....((((...((((((..((..((((((((.((((....))))))))))))..))..)))))))))))))))......(((....))) ( -22.80)
>DroSim_CAF1 48342 95 + 1
GUCAUUUAAGCUGAAAUUGUAAGUGACUCUGAUUGCACAUUGAUUAUAAUUGUAAUUAUUGUUGCUUAUAUCGGGUUACACGCUGGCGAAUUCGC
((((..(((.((((...((((((..((..((((((((.((((....))))))))))))..))..)))))))))).))).....))))........ ( -23.70)
>DroYak_CAF1 52075 94 + 1
GUCAUUUAAGCUGAAAUUGUAAGUGACUCUGAUUGCACACUGAUUAUAAUUGUAUUUAUUGUAGCUUAUAUCAGAUUACAUA-UAGCGAAUUUGC
.........((((....(((((.....((((((.(((((.(((.(((....))).))).))).))....)))))))))))..-))))........ ( -16.70)
>consensus
GUCAUUUAAGCUGAAAUUGUAAGUGACUCUGAUUGCACAUUGAUUAUAAUUGUAAUUAUUGUUGCUUAUAUCGGAUUACACGCUGGCGAAUUCGC
............(((.((((..(((..((((((.(((((.(((((((....))))))).))).))....))))))...)))....)))).))).. (-18.67 = -18.18 +  -0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,313,354 – 12,313,472
Length 118
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 88.28
Mean single sequence MFE -24.30
Consensus MFE -19.10
Energy contribution -19.48
Covariance contribution 0.37
Combinations/Pair 1.15
Mean z-score -1.54
Structure conservation index 0.79
SVM decision value 0.19
SVM RNA-class probability 0.627470
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12313354 118 + 23771897
UUGUAACUGACUCUGAUUGCACAUUGAUUAUAAUUGUAAUUAUUGUUGCUUAUAUCGGAUUACACGCUGGCGAAUUGGCAACAUUUGAAACAUUCAGAAGUUAAAUCUAUUUUUUUCA
.(((((.....((((((.(((((.(((((((....))))))).)).)))....))))))))))).((..(....)..))(((.(((((.....))))).)))................ ( -22.20)
>DroSec_CAF1 48479 118 + 1
UUGUAAGUGACUCUGAUUGCACAUUGAUUAUAAUUGUAAUUAUUGUUGCUUAUAUCGGAUUACACGCUGGCGAAUUCGCAACAUUUGAAACAUUAUAAAGUUAAAUCUAUUUUCUUCA
((((((((((.((((((.(((((.(((((((....))))))).)).)))....))))))))))......(((....))).............)))))).................... ( -23.00)
>DroSim_CAF1 48358 118 + 1
UUGUAAGUGACUCUGAUUGCACAUUGAUUAUAAUUGUAAUUAUUGUUGCUUAUAUCGGGUUACACGCUGGCGAAUUCGCAACAUUUGAAACAUUCAAAAGUGAAAUCUAUUUUCUUCA
.((((((..((..((((((((.((((....))))))))))))..))..))))))..(((((.(((....(((....)))....(((((.....))))).))).))))).......... ( -28.90)
>DroYak_CAF1 52091 114 + 1
UUGUAAGUGACUCUGAUUGCACACUGAUUAUAAUUGUAUUUAUUGUAGCUUAUAUCAGAUUACAUA-UAGCGAAUUUGCAACAUUUGUAAUUUGCAGACGUUAAACCUAUAC---UCA
..(((.((((.((((((.(((((.(((.(((....))).))).))).))....))))))))))...-(((((..(((((((..........))))))))))))......)))---... ( -23.10)
>consensus
UUGUAAGUGACUCUGAUUGCACAUUGAUUAUAAUUGUAAUUAUUGUUGCUUAUAUCGGAUUACACGCUGGCGAAUUCGCAACAUUUGAAACAUUCAAAAGUUAAAUCUAUUUUCUUCA
......((((.((((((.(((((.(((((((....))))))).))).))....))))))))))......(((....)))(((.(((((.....))))).)))................ (-19.10 = -19.48 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:51 2006