Locus 4956

Sequence ID X_DroMel_CAF1
Location 12,948,791 – 12,948,904
Length 113
Max. P 0.814892
window8076 window8077

overview

Window 6

Location 12,948,791 – 12,948,904
Length 113
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 92.77
Mean single sequence MFE -40.03
Consensus MFE -33.94
Energy contribution -35.62
Covariance contribution 1.69
Combinations/Pair 1.06
Mean z-score -1.84
Structure conservation index 0.85
SVM decision value 0.66
SVM RNA-class probability 0.814892
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12948791 113 + 22224390
AGGGUAUCAACAGGUGCUCAAUUUCCACCUGUGCGCACUGCGCUGUUGUGAUUUUGUUGCCGCGACGGCGCAGCUUUUGCUUUUGACACAUUUUCGCGGCUGUCUCGCCGCCG
...((.((((((((((.........)))))))..((((((((((((((((..........)))))))))))))....)))...))).))......(((((......))))).. ( -44.60)
>DroSec_CAF1 7248 107 + 1
AGGGUAUCAACAGGUGCUCAAUUUCCACCUGUGCGCACAGCGCUGUUGUGAUUUUGUUGCCGCGACGGCGCAGCUUUUGCUUUUGACACAUUU------CUGUCUCGCCGCCG
..(((....(((((((.........)))))))(((....(((((((((((..........)))))))))))(((....)))...((((.....------.)))).))).))). ( -37.20)
>DroSim_CAF1 8005 113 + 1
AGGGUAUCAACAGGUGCUAAAUUUCCACCGGUGCGCACAGCGCUGUUGUGAUUUUGUUACCGCGACGGCGCAGCUUUUGCUUUUGACACAUUUUCGCGGCUGUCUCGCCGCCG
.(.(((((....((((.........))))))))).)...(((((((((((..........)))))))))))(((....)))..............(((((......))))).. ( -38.10)
>DroEre_CAF1 6488 112 + 1
AGGGUAUCAACAGGUGCUCAAUUUCCACCUGUGCCCUCUGCGUUGUUGUGA-UUUGCUGCCGCGACGGCGCAGCUUUUGCUUUUGACACAUUUUCGCGGCUGUCUCGUCGCCG
(((((....(((((((.........))))))))))))(((((((((((((.-........)))))))))))))......................(((((......))))).. ( -40.20)
>consensus
AGGGUAUCAACAGGUGCUCAAUUUCCACCUGUGCGCACAGCGCUGUUGUGAUUUUGUUGCCGCGACGGCGCAGCUUUUGCUUUUGACACAUUUUCGCGGCUGUCUCGCCGCCG
...((.((((((((((.........)))))))(((..(((((((((((((..........)))))))))))))....)))...))).))......(((((......))))).. (-33.94 = -35.62 +   1.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 12,948,791 – 12,948,904
Length 113
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 92.77
Mean single sequence MFE -37.71
Consensus MFE -29.00
Energy contribution -31.50
Covariance contribution 2.50
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.77
SVM decision value 0.29
SVM RNA-class probability 0.668732
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12948791 113 - 22224390
CGGCGGCGAGACAGCCGCGAAAAUGUGUCAAAAGCAAAAGCUGCGCCGUCGCGGCAACAAAAUCACAACAGCGCAGUGCGCACAGGUGGAAAUUGAGCACCUGUUGAUACCCU
..(((((......)))))......((((((...((....(((((((.((.(.((........)).).)).)))))))..))(((((((.........)))))))))))))... ( -41.40)
>DroSec_CAF1 7248 107 - 1
CGGCGGCGAGACAG------AAAUGUGUCAAAAGCAAAAGCUGCGCCGUCGCGGCAACAAAAUCACAACAGCGCUGUGCGCACAGGUGGAAAUUGAGCACCUGUUGAUACCCU
(((((((((.(((.------...))).))....(((.....)))))))))).(....)...((((.....((((...))))(((((((.........)))))))))))..... ( -39.50)
>DroSim_CAF1 8005 113 - 1
CGGCGGCGAGACAGCCGCGAAAAUGUGUCAAAAGCAAAAGCUGCGCCGUCGCGGUAACAAAAUCACAACAGCGCUGUGCGCACCGGUGGAAAUUUAGCACCUGUUGAUACCCU
..(((((......)))))......(((((((.(((....)))((((((.(((.((............)).))).)).))))...((((.........))))..)))))))... ( -35.40)
>DroEre_CAF1 6488 112 - 1
CGGCGACGAGACAGCCGCGAAAAUGUGUCAAAAGCAAAAGCUGCGCCGUCGCGGCAGCAAA-UCACAACAACGCAGAGGGCACAGGUGGAAAUUGAGCACCUGUUGAUACCCU
((....)).....(((((((....((((....(((....)))))))..))))))).((...-..........))..((((.(((((((.........))))))).....)))) ( -34.52)
>consensus
CGGCGGCGAGACAGCCGCGAAAAUGUGUCAAAAGCAAAAGCUGCGCCGUCGCGGCAACAAAAUCACAACAGCGCAGUGCGCACAGGUGGAAAUUGAGCACCUGUUGAUACCCU
..(((((......)))))......((((((...((....(((((((.((.(.((........)).).)).)))))))..))(((((((.........)))))))))))))... (-29.00 = -31.50 +   2.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:52 2006