Locus 3854

Sequence ID X_DroMel_CAF1
Location 10,257,761 – 10,257,860
Length 99
Max. P 0.999990
window6341 window6342

overview

Window 1

Location 10,257,761 – 10,257,860
Length 99
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 72.64
Mean single sequence MFE -22.05
Consensus MFE -13.30
Energy contribution -14.08
Covariance contribution 0.78
Combinations/Pair 1.18
Mean z-score -3.78
Structure conservation index 0.60
SVM decision value 5.58
SVM RNA-class probability 0.999990
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10257761 99 + 22224390
A--------UUGCUAGAGCACAAAACUGUUUAACAGUCUUAAAU-----AAGAACAGGAAACUGCUCUAGA-AAUGUAACCAAAAUAUAAAUAACUAUAUAUCGGUUGAUCGG
.--------...((((((((.....((((((.............-----..)))))).....)))))))).-....(((((...(((((......)))))...)))))..... ( -21.96)
>DroSec_CAF1 24543 97 + 1
A--------UUUCUAGAGCACAAAACUGUUUAACAGUCUUAAAAAAG--AAGAACAGGAAACUGCUCUAGAAAAUGUAACCAAAAUAUAAAUAA------AAUAGUUGAUCGG
.--------(((((((((((.....((((((.....((((....)))--).)))))).....))))))))))).....................------............. ( -22.80)
>DroYak_CAF1 25213 109 + 1
AUUUGCGUAUUGCUAAAGCGCAAAACAGUUUAACAUUCUCAAAUAAAAAAAGAACAGGAAACUGCUUGAACAAAUU-GAUCAAAACAUAAACAAUUAUAU---AUUUGAUCGA
.(((((((.........)))))))...((((((..((((...........))))(((....))).))))))...((-(((((((..((((....))))..---.))))))))) ( -21.40)
>consensus
A________UUGCUAGAGCACAAAACUGUUUAACAGUCUUAAAUAA___AAGAACAGGAAACUGCUCUAGAAAAUGUAACCAAAAUAUAAAUAA_UAUAUA__AGUUGAUCGG
.........(((((((((((.....((((((....................)))))).....)))))))))))........................................ (-13.30 = -14.08 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 10,257,761 – 10,257,860
Length 99
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 72.64
Mean single sequence MFE -24.70
Consensus MFE -14.89
Energy contribution -15.02
Covariance contribution 0.12
Combinations/Pair 1.23
Mean z-score -3.70
Structure conservation index 0.60
SVM decision value 5.55
SVM RNA-class probability 0.999989
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10257761 99 - 22224390
CCGAUCAACCGAUAUAUAGUUAUUUAUAUUUUGGUUACAUU-UCUAGAGCAGUUUCCUGUUCUU-----AUUUAAGACUGUUAAACAGUUUUGUGCUCUAGCAA--------U
......((((((.((((((....)))))).))))))..(((-.((((((((.............-----...((((((((.....)))))))))))))))).))--------) ( -25.29)
>DroSec_CAF1 24543 97 - 1
CCGAUCAACUAUU------UUAUUUAUAUUUUGGUUACAUUUUCUAGAGCAGUUUCCUGUUCUU--CUUUUUUAAGACUGUUAAACAGUUUUGUGCUCUAGAAA--------U
..((((((.(((.------......)))..))))))....(((((((((((.............--......((((((((.....)))))))))))))))))))--------. ( -21.20)
>DroYak_CAF1 25213 109 - 1
UCGAUCAAAU---AUAUAAUUGUUUAUGUUUUGAUC-AAUUUGUUCAAGCAGUUUCCUGUUCUUUUUUUAUUUGAGAAUGUUAAACUGUUUUGCGCUUUAGCAAUACGCAAAU
..(((((((.---((((((....)))))))))))))-.((((((..(((((((((..(((((((.........)))))))..)))))))))(((......)))....)))))) ( -27.60)
>consensus
CCGAUCAACU__UAUAUA_UUAUUUAUAUUUUGGUUACAUUUUCUAGAGCAGUUUCCUGUUCUU___UUAUUUAAGACUGUUAAACAGUUUUGUGCUCUAGCAA________U
..((((((......................))))))....((((((((((((....))..............((((((((.....)))))))).))))))))))......... (-14.89 = -15.02 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:21 2006