Locus 5117

Sequence ID X_DroMel_CAF1
Location 13,363,586 – 13,363,777
Length 191
Max. P 0.993496
window8318 window8319

overview

Window 8

Location 13,363,586 – 13,363,686
Length 100
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 90.34
Mean single sequence MFE -13.00
Consensus MFE -10.12
Energy contribution -9.38
Covariance contribution -0.75
Combinations/Pair 1.25
Mean z-score -1.80
Structure conservation index 0.78
SVM decision value 0.42
SVM RNA-class probability 0.727958
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13363586 100 - 22224390
AAAGACAAUAAAAACAAAUAAAAAGUAUUUUAAAAUGCCAUUUGAAUUAAACUUGAAACCGAGAACC---AACCGAAGGC----AACU--GAAACACAGUGGCAAAAAU
...................................(((((((((.......((((....))))....---......((..----..))--....)).)))))))..... ( -13.90)
>DroSec_CAF1 9298 98 - 1
AAAGACAAUAAAAACAAAUAAAAAGUAUUUUGAAAUGCCAUUUGAAUUAAACUUGAAACCAAGAACC---AACCGAAGGC----AACU--GAAA--CAGUGGCAAAAAU
..............((((..........))))...(((((((.(.......((((....))))....---......((..----..))--....--))))))))..... ( -13.40)
>DroSim_CAF1 9315 98 - 1
AAAGACAAUAAAAACAAAUAAAAAGUAUUUUGAAAUGCCAUUUGAAUUAAACUUGAAACCGAGAACC---AACCGAAGGC----AACU--GAAA--CAGUGGCAAAAAU
..............((((..........))))...(((((((.(.......((((....))))....---......((..----..))--....--))))))))..... ( -13.10)
>DroYak_CAF1 11054 107 - 1
AAAGACAAUAAAAACAAAUAAAAAGUAUUUCGAAAUGCCAUUUGAAUUAAACUUGAAACCGAGAACUGAGAACUGAGAACCAAAAACUGAGAAA--CAGUGGCGAAAAU
...................................((((............((((....)))).((((....((.((.........)).))...--))))))))..... ( -11.60)
>consensus
AAAGACAAUAAAAACAAAUAAAAAGUAUUUUGAAAUGCCAUUUGAAUUAAACUUGAAACCGAGAACC___AACCGAAGGC____AACU__GAAA__CAGUGGCAAAAAU
...................................(((((((.........((((....))))..........(....)..................)))))))..... (-10.12 =  -9.38 +  -0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 13,363,686 – 13,363,777
Length 91
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 69.48
Mean single sequence MFE -25.08
Consensus MFE -11.75
Energy contribution -13.00
Covariance contribution 1.25
Combinations/Pair 1.24
Mean z-score -2.70
Structure conservation index 0.47
SVM decision value 2.40
SVM RNA-class probability 0.993496
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13363686 91 + 22224390
UAUUUUCGCUCGCCUC---CUCGGUACUCCAGUUCGCUCUACUACACAGAGAGA--AACUGUAGAUC-------ACUA-----AUC-----ACAGUU---UCAUUAAAUCUUUAAC
........((((((..---...))).....(((.......))).....))).((--((((((.(((.-------....-----)))-----))))))---)).............. ( -16.00)
>DroSec_CAF1 9396 103 + 1
UAUUUUCGCUCGCCUC---CUCGGUACUCCGGUUCUCUCUGCUACAGAGAGAAAAAAAAUGUAGAGCGGACUUGGCAA-----AUC-----UAUAUUUACUAAUCAAAUAUUAAGC
....(((((((.....---.((((....))))(((((((((...)))))))))..........))))))).((((.((-----((.-----...)))).))))............. ( -25.60)
>DroSim_CAF1 9413 103 + 1
UAUUUUCGCUCGCCUC---CGCGCUACUCCGGUUCCCUCUGCUACAGAGAGAAAAAAAAUGUAGGGCGGACUUGGCAA-----AUC-----UAUAUUUACUAAUCAAAUAUUAAGC
.......(((.(((((---(((.((((.....(((.(((((...))))).))).......)))).)))))...)))..-----...-----.((((((.......))))))..))) ( -27.80)
>DroYak_CAF1 11161 111 + 1
UAUUUUCGCUCGACUCCUUCUCGGUGCUCUUAUUCUCUCUACUACAGAGAGAGA--AAAUGUUGAGCGGGCUUGUUAAUAUUAAUGUUAAUACAGCU---CCAUUAAAACAUCAAU
.......(((((((.((.....))........((((((((.......)))))))--)...)))))))(((((((((((((....)))))))).))).---)).............. ( -30.90)
>consensus
UAUUUUCGCUCGCCUC___CUCGGUACUCCGGUUCUCUCUACUACAGAGAGAAA__AAAUGUAGAGCGGACUUGGCAA_____AUC_____AAAAUU___UAAUCAAAUAUUAAAC
....(((((((...........((....))..((((((((.....))))))))..........))))))).............................................. (-11.75 = -13.00 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:29 2006