Locus 1951

Sequence ID X_DroMel_CAF1
Location 5,343,309 – 5,343,420
Length 111
Max. P 0.970505
window3172 window3173

overview

Window 2

Location 5,343,309 – 5,343,420
Length 111
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 66.06
Mean single sequence MFE -23.17
Consensus MFE -11.48
Energy contribution -12.35
Covariance contribution 0.87
Combinations/Pair 1.23
Mean z-score -1.64
Structure conservation index 0.50
SVM decision value 0.48
SVM RNA-class probability 0.752936
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5343309 111 + 22224390
UCUAAGAAAACGAAAUAUUCUUGCUUGUAACGAAUUACUAUAUAUGUAUGUACAUACAUUGCAU-UCCUUGCAAUCCACGAAGUGCUUGCAAAUGCAAGGAUAGCAGUUGAU--
........(((....(((((((((..((((....))))......((((.((((....((((((.-....)))))).......)))).))))...)))))))))...)))...-- ( -23.90)
>DroSec_CAF1 18811 96 + 1
---------ACUAAAUGUUCUUGCUUGUAACGAAUUAUUAUAUAUGUGGG--------UUGCAU-UCCUUGCAACCAACGAUGGGUUUGUAAAUGCAAGGAUAGCAGUUGAUAA
---------(((...(((((((((...(.(((((((....(((.(((.((--------(((((.-....))))))).))))))))))))).)..)))))))))..)))...... ( -26.80)
>DroSim_CAF1 16262 87 + 1
UCUAAGAAAACUAAAUGUUCUUGCUUGUAAGGAAAUAUUAUACAUGUGGG--------UUGCAU-UCCCUGCA------------------AAUGCAAGGAUAGCAGUUGAUAA
........((((...((((((((((((((.(((..........((((...--------..))))-))).))))------------------)..)))))))))..))))..... ( -19.50)
>DroYak_CAF1 19375 102 + 1
UUCUAGAAAACGAAAUAUUCUUGCUACUGGCGAGUUACUAUACUA----G--------UUGCAUAUACUAGCAGCCCACGAAUUUUGUGCAAGUGCAAGGGGAGCAGUUUAGAA
.((((((..........(((((((.(((.((((((......))).----(--------((((........)))))............))).))))))))))......)))))). ( -22.49)
>consensus
UCUAAGAAAACGAAAUAUUCUUGCUUGUAACGAAUUACUAUACAUGUGGG________UUGCAU_UCCUUGCAACCCACGAAGUGUUUGCAAAUGCAAGGAUAGCAGUUGAUAA
........(((....(((((((((.(((((.......)))))................(((((......)))))....................)))))))))...)))..... (-11.48 = -12.35 +   0.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 5,343,309 – 5,343,420
Length 111
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 66.06
Mean single sequence MFE -20.11
Consensus MFE -11.98
Energy contribution -13.10
Covariance contribution 1.12
Combinations/Pair 1.25
Mean z-score -1.68
Structure conservation index 0.60
SVM decision value 1.66
SVM RNA-class probability 0.970505
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5343309 111 - 22224390
--AUCAACUGCUAUCCUUGCAUUUGCAAGCACUUCGUGGAUUGCAAGGA-AUGCAAUGUAUGUACAUACAUAUAUAGUAAUUCGUUACAAGCAAGAAUAUUUCGUUUUCUUAGA
--.......(((.((((((((((..(.........)..)).))))))))-.(((.((((((((....)))))))).)))..........)))(((((.........)))))... ( -27.20)
>DroSec_CAF1 18811 96 - 1
UUAUCAACUGCUAUCCUUGCAUUUACAAACCCAUCGUUGGUUGCAAGGA-AUGCAA--------CCCACAUAUAUAAUAAUUCGUUACAAGCAAGAACAUUUAGU---------
...............(((((...............((.(((((((....-.)))))--------)).)).....((((.....))))...)))))..........--------- ( -17.60)
>DroSim_CAF1 16262 87 - 1
UUAUCAACUGCUAUCCUUGCAUU------------------UGCAGGGA-AUGCAA--------CCCACAUGUAUAAUAUUUCCUUACAAGCAAGAACAUUUAGUUUUCUUAGA
........((((.(((((((...------------------.)))))))-(((((.--------......)))))..............))))(((((.....)))))...... ( -17.00)
>DroYak_CAF1 19375 102 - 1
UUCUAAACUGCUCCCCUUGCACUUGCACAAAAUUCGUGGGCUGCUAGUAUAUGCAA--------C----UAGUAUAGUAACUCGCCAGUAGCAAGAAUAUUUCGUUUUCUAGAA
.(((((((.......((((((((..(((.......)))((((((((((.......)--------)----)))))..(.....))))))).)))))........)))...)))). ( -18.66)
>consensus
UUAUCAACUGCUAUCCUUGCAUUUGCAAACACUUCGUGGGUUGCAAGGA_AUGCAA________CCCACAUAUAUAAUAAUUCGUUACAAGCAAGAACAUUUAGUUUUCUUAGA
........(((..(((((((((((((.........))))).))))))))...)))........................................................... (-11.98 = -13.10 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:39 2006