Locus 3739

Sequence ID 2L_DroMel_CAF1
Location 10,887,298 – 10,887,414
Length 116
Max. P 0.993808
window5888 window5889

overview

Window 8

Location 10,887,298 – 10,887,414
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.17
Mean single sequence MFE -38.90
Consensus MFE -34.49
Energy contribution -35.32
Covariance contribution 0.84
Combinations/Pair 1.17
Mean z-score -2.70
Structure conservation index 0.89
SVM decision value 2.43
SVM RNA-class probability 0.993808
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10887298 116 + 22407834
UUCACUGGCCAGAAUGGUCGAGAUGAUUGACUUCAUGCAAAUGUUCUUGUUAAGACCCA-UGUCUGGUUGGGAAAUUUGCAUUUGG--CUUGUUUGACCAGUCUGGCUGGC-ACGGGAAU
....(..((((((.((((((((......(.((..((((((((.((((((...((((...-.))))...))))))))))))))..))--)...)))))))).))))))..).-........ ( -41.60)
>DroSec_CAF1 26951 116 + 1
UUCACUGGCCAGAAUGGUCGAGAUGAUUGACUUCAUGCAAAUGCUCUUGUUAAGACCCA-UGUCUGGUUGGGAAAUUUGCAUUUGG--CUUGUUUGACCAGUCUGGCUGGC-ACGGGAAU
....(..((((((.((((((((......(.((..((((((((..(((((...((((...-.))))...))))).))))))))..))--)...)))))))).))))))..).-........ ( -41.50)
>DroSim_CAF1 27326 116 + 1
UUCACUGGCCAGAAUGGUCGAGAUGAUUGACUUCAUGCAAAUGCUCUUGUUAAGACCCA-UGUCUGGUUGGGAAAUUUGCAUUUGG--CUUGUUUGACCAGUCUGGCUGGC-ACGGGAAU
....(..((((((.((((((((......(.((..((((((((..(((((...((((...-.))))...))))).))))))))..))--)...)))))))).))))))..).-........ ( -41.50)
>DroEre_CAF1 27265 116 + 1
UUCACUGGCCUGAAUGGUCAAGAUGAUUGACUUCAUGCAAAUGUUCUUGUUAAGACCCA-UGUCUGGUCGGAGAAUUUGCAUUUGG--CUUGUUUGACCAGUCUGGCUGGC-ACUGGAAU
(((((..(((.((.((((((((......(.((..((((((((.((((.....((((...-.))))....)))).))))))))..))--)...)))))))).)).)))..).-..)))).. ( -37.00)
>DroYak_CAF1 27829 116 + 1
UUCACUGGCCAGAAUGGUCGAGAUGAUUGACUUCAUGCAAAUGUUCUUGUUAAGACCCA-UGUCUGGUUUGAAAAUUUGCAUUUGG--CUUGUUUGACCAGUCUGGCUGGC-ACUGGAAU
(((((..((((((.((((((((......(.((..((((((((.(((......((((...-.)))).....))).))))))))..))--)...)))))))).))))))..).-..)))).. ( -40.70)
>DroAna_CAF1 28970 115 + 1
UUCAGUGACCAG-----CCGAGAUGAUUGACUUCAUGCAAAUUUUCUUGUUAAGCCCGAUUGUCUGGUCAGAAAAUUUGCAUUUGGUUCUUGUUUGACCAGACUGGCUAUCGACUAUCUC
............-----..((((((.((((......((((......))))..((((.....(((((((((((......((.....)).....))))))))))).)))).)))).)))))) ( -31.10)
>consensus
UUCACUGGCCAGAAUGGUCGAGAUGAUUGACUUCAUGCAAAUGUUCUUGUUAAGACCCA_UGUCUGGUUGGAAAAUUUGCAUUUGG__CUUGUUUGACCAGUCUGGCUGGC_ACGGGAAU
....(((((((((.((((((((........((..((((((((.((((.....((((.....))))....)))).))))))))..))......)))))))).))))))))).......... (-34.49 = -35.32 +   0.84)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,887,298 – 10,887,414
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.17
Mean single sequence MFE -31.75
Consensus MFE -25.28
Energy contribution -25.70
Covariance contribution 0.42
Combinations/Pair 1.14
Mean z-score -2.88
Structure conservation index 0.80
SVM decision value 0.76
SVM RNA-class probability 0.842389
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10887298 116 - 22407834
AUUCCCGU-GCCAGCCAGACUGGUCAAACAAG--CCAAAUGCAAAUUUCCCAACCAGACA-UGGGUCUUAACAAGAACAUUUGCAUGAAGUCAAUCAUCUCGACCAUUCUGGCCAGUGAA
........-((..((((((.(((((.......--....(((((((((((......((((.-...))))......))).))))))))((......)).....))))).))))))..))... ( -31.40)
>DroSec_CAF1 26951 116 - 1
AUUCCCGU-GCCAGCCAGACUGGUCAAACAAG--CCAAAUGCAAAUUUCCCAACCAGACA-UGGGUCUUAACAAGAGCAUUUGCAUGAAGUCAAUCAUCUCGACCAUUCUGGCCAGUGAA
........-((..((((((.(((((......(--(.((((((......((((........-))))(((.....)))))))))))((((......))))...))))).))))))..))... ( -34.30)
>DroSim_CAF1 27326 116 - 1
AUUCCCGU-GCCAGCCAGACUGGUCAAACAAG--CCAAAUGCAAAUUUCCCAACCAGACA-UGGGUCUUAACAAGAGCAUUUGCAUGAAGUCAAUCAUCUCGACCAUUCUGGCCAGUGAA
........-((..((((((.(((((......(--(.((((((......((((........-))))(((.....)))))))))))((((......))))...))))).))))))..))... ( -34.30)
>DroEre_CAF1 27265 116 - 1
AUUCCAGU-GCCAGCCAGACUGGUCAAACAAG--CCAAAUGCAAAUUCUCCGACCAGACA-UGGGUCUUAACAAGAACAUUUGCAUGAAGUCAAUCAUCUUGACCAUUCAGGCCAGUGAA
....((.(-(...(((.((.(((((((.....--....(((((((((((..((((.....-..))))......)))..))))))))((......))...))))))).)).))))).)).. ( -28.10)
>DroYak_CAF1 27829 116 - 1
AUUCCAGU-GCCAGCCAGACUGGUCAAACAAG--CCAAAUGCAAAUUUUCAAACCAGACA-UGGGUCUUAACAAGAACAUUUGCAUGAAGUCAAUCAUCUCGACCAUUCUGGCCAGUGAA
....((.(-(...((((((.(((((.......--....((((((((.(((.....((((.-...))))......))).))))))))((......)).....))))).)))))))).)).. ( -33.20)
>DroAna_CAF1 28970 115 - 1
GAGAUAGUCGAUAGCCAGUCUGGUCAAACAAGAACCAAAUGCAAAUUUUCUGACCAGACAAUCGGGCUUAACAAGAAAAUUUGCAUGAAGUCAAUCAUCUCGG-----CUGGUCACUGAA
.......(((.(..(((((((((((......).)))).(((((((((((((..((........))........)))))))))))))...............))-----))))..).))). ( -29.20)
>consensus
AUUCCAGU_GCCAGCCAGACUGGUCAAACAAG__CCAAAUGCAAAUUUCCCAACCAGACA_UGGGUCUUAACAAGAACAUUUGCAUGAAGUCAAUCAUCUCGACCAUUCUGGCCAGUGAA
.............((((((.(((((.............(((((((((((......((((.....))))......))).))))))))((......)).....))))).))))))....... (-25.28 = -25.70 +   0.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:51 2006