Locus 1164

Sequence ID 2R_DroMel_CAF1
Location 4,628,679 – 4,628,814
Length 135
Max. P 0.852667
window2041 window2042

overview

Window 1

Location 4,628,679 – 4,628,775
Length 96
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 88.37
Mean single sequence MFE -24.60
Consensus MFE -17.93
Energy contribution -18.87
Covariance contribution 0.94
Combinations/Pair 1.12
Mean z-score -1.82
Structure conservation index 0.73
SVM decision value 0.38
SVM RNA-class probability 0.711640
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4628679 96 - 20766785
AUUAUAUGCCAAGUGAUUGCUUGACAGUCGGACAAAAGCCUGGCUUCCACAUUUUUCCCAUCUGUGGAUAAUUUACUGGUCCGAAACUGCCGCAUG
....((((((((((....))))).(((((((((...((.......((((((...........)))))).......)).))))))..)))..))))) ( -26.34)
>DroSec_CAF1 5210 96 - 1
AUUAUAUGCCAAGCAAUUGCUUGACAGGCGCACAAAAGCCAGGCUUCCACAUUUUUCCCAUCUGUGGAUCAUUUACUGGUCCGAAACUGCCGCAUG
....((((((((((....)))))...((((.......(((((...((((((...........)))))).......))))).......))))))))) ( -28.14)
>DroSim_CAF1 5212 96 - 1
AUUAUAUGCCAAGCAAUUGCUUGACAGCCGCACAAAAGCCAGGCUUCCACAUUUUUCCCAUCUGUGGAUCAUUUACUGGUCCGAAACUGCCGCAUG
......((.(((((....))))).))((.(((.....(((((...((((((...........)))))).......))))).......))).))... ( -24.70)
>DroYak_CAF1 5254 96 - 1
AGAUUAUGUCAAGCAAUGGUUUGACAGUCGGACAAAAGCCUUCGUUCCACAUUUUUCUCAUCUGUCAAACAUUUACAGGUCCGAAACUCCCGCAUG
......((((((((....)))))))).((((((...(((....)))...............((((.........))))))))))............ ( -19.20)
>consensus
AUUAUAUGCCAAGCAAUUGCUUGACAGUCGCACAAAAGCCAGGCUUCCACAUUUUUCCCAUCUGUGGAUCAUUUACUGGUCCGAAACUGCCGCAUG
....((((((((((....))))).(((.(((((...((.......((((((...........)))))).......)).)))))...)))..))))) (-17.93 = -18.87 +   0.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 4,628,719 – 4,628,814
Length 95
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 85.34
Mean single sequence MFE -25.90
Consensus MFE -18.75
Energy contribution -18.81
Covariance contribution 0.06
Combinations/Pair 1.10
Mean z-score -2.04
Structure conservation index 0.72
SVM decision value 0.79
SVM RNA-class probability 0.852667
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4628719 95 + 20766785
AAAAAUGUGGAAGCCAGGCUUUUGUCCGACUGUCAAGCAAUCACUUGGCAUAUAAUGUAGAGCGAAUUUAUGAU-UUUUUCUGCAUAAAGCCGCAC
.....(((((..((((((...((((..(.....)..))))...)))))).....((((((((.(((((...)))-)).))))))))....))))). ( -26.80)
>DroSec_CAF1 5250 91 + 1
AAAAAUGUGGAAGCCUGGCUUUUGUGCGCCUGUCAAGCAAUUGCUUGGCAUAUAAUGUAAAGCGAAUUUCUGAU-----UCUGCAUAAAGCCGCAC
............((..((((((.((((...((((((((....)))))))).............(((((...)))-----)).)))))))))))).. ( -26.30)
>DroSim_CAF1 5252 96 + 1
AAAAAUGUGGAAGCCUGGCUUUUGUGCGGCUGUCAAGCAAUUGCUUGGCAUAUAAUGUAAAGCGAAUUUCUGAUAUUUUUCAGCAUAAAGCCGCAC
........((((((...))))))(((((((((((((((....)))))))....................((((......)))).....)))))))) ( -30.90)
>DroYak_CAF1 5294 94 + 1
AAAAAUGUGGAACGAAGGCUUUUGUCCGACUGUCAAACCAUUGCUUGACAUAAUCUGUAGAGCGAUUAUCUGAUG--UUUCUGUAUAAAGCCGCAC
................((((((...(.((..((((....(((((((.(((.....))).)))))))....)))).--..)).)...)))))).... ( -19.60)
>consensus
AAAAAUGUGGAAGCCAGGCUUUUGUCCGACUGUCAAGCAAUUGCUUGGCAUAUAAUGUAAAGCGAAUUUCUGAU___UUUCUGCAUAAAGCCGCAC
.....(((((.......(((((........((((((((....))))))))........)))))........((......)).........))))). (-18.75 = -18.81 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:03 2006