Locus 4248

Sequence ID 3L_DroMel_CAF1
Location 12,437,047 – 12,437,157
Length 110
Max. P 0.953394
window6573 window6574

overview

Window 3

Location 12,437,047 – 12,437,157
Length 110
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 93.94
Mean single sequence MFE -32.17
Consensus MFE -29.41
Energy contribution -28.97
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -2.66
Structure conservation index 0.91
SVM decision value 1.43
SVM RNA-class probability 0.953394
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12437047 110 + 23771897
GUUGCAAUUUCAAAUGCAAUUGCAAUUGCAUCAGUAGUUGCUGUUGCUUUUGCUGCUUUUGUUUUUGUUGCCACUGUCAAUCACAGAGGCGCGCACAACUCAGGUUUUCA
((((...........(((((.((((((((....)))))))).)))))...((((((((((((..(((..........)))..))))))))).)))))))........... ( -32.40)
>DroSec_CAF1 39912 104 + 1
GCUGCAAUUUCAAAUGCAAUUGCAAUUGCAUCAGUAGUUGUUGUUGC------UGCUUUUGUUUUUGUUGCCACUGUCAAUCACAGAGGCGCGCACAACUCAGGUUUUCA
((.((((...((((.(((((.((((((((....)))))))).)))))------....))))...)))).(((.((((.....)))).))))).................. ( -29.20)
>DroSim_CAF1 40654 109 + 1
GCUGCA-UUUCAAAUGCAAUUGCAAUUGCAUCAGUAGUUGCUGUUGCUGCUGCUGCUUUUGUUUUUGUUGCCACUGUCAAUCACAGAGGCGCGCACAACUCAGGUUUUCA
((.((.-........((((..((((..(((.(((((((.......))))))).)))..))))..)))).(((.((((.....)))).)))))))................ ( -34.90)
>consensus
GCUGCAAUUUCAAAUGCAAUUGCAAUUGCAUCAGUAGUUGCUGUUGCU__UGCUGCUUUUGUUUUUGUUGCCACUGUCAAUCACAGAGGCGCGCACAACUCAGGUUUUCA
((.((..........(((((.((((((((....)))))))).))))).......((((((((..(((..........)))..))))))))))))................ (-29.41 = -28.97 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,437,047 – 12,437,157
Length 110
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 93.94
Mean single sequence MFE -27.77
Consensus MFE -25.32
Energy contribution -25.43
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.05
Structure conservation index 0.91
SVM decision value 0.63
SVM RNA-class probability 0.806445
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12437047 110 - 23771897
UGAAAACCUGAGUUGUGCGCGCCUCUGUGAUUGACAGUGGCAACAAAAACAAAAGCAGCAAAAGCAACAGCAACUACUGAUGCAAUUGCAAUUGCAUUUGAAAUUGCAAC
...........(((((....(((.((((.....)))).)))........((((.(((((((..(((.(((......))).)))..))))...))).)))).....))))) ( -29.10)
>DroSec_CAF1 39912 104 - 1
UGAAAACCUGAGUUGUGCGCGCCUCUGUGAUUGACAGUGGCAACAAAAACAAAAGCA------GCAACAACAACUACUGAUGCAAUUGCAAUUGCAUUUGAAAUUGCAGC
.......(((.((((((((((((.((((.....)))).))).............)).------)).))))).....(.((((((((....)))))))).)......))). ( -25.11)
>DroSim_CAF1 40654 109 - 1
UGAAAACCUGAGUUGUGCGCGCCUCUGUGAUUGACAGUGGCAACAAAAACAAAAGCAGCAGCAGCAACAGCAACUACUGAUGCAAUUGCAAUUGCAUUUGAAA-UGCAGC
.......(((.(((((..(((((.((((.....)))).))).............((....)).)).))))).....(.((((((((....)))))))).)...-..))). ( -29.10)
>consensus
UGAAAACCUGAGUUGUGCGCGCCUCUGUGAUUGACAGUGGCAACAAAAACAAAAGCAGCA__AGCAACAGCAACUACUGAUGCAAUUGCAAUUGCAUUUGAAAUUGCAGC
..........((((((....(((.((((.....)))).))).............((.......))....)))))).....(((((((.(((......))).))))))).. (-25.32 = -25.43 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:43 2006