Locus 4211

Sequence ID 3L_DroMel_CAF1
Location 12,319,542 – 12,319,644
Length 102
Max. P 0.948578
window6526 window6527

overview

Window 6

Location 12,319,542 – 12,319,644
Length 102
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 71.10
Mean single sequence MFE -29.10
Consensus MFE -5.04
Energy contribution -5.50
Covariance contribution 0.46
Combinations/Pair 1.10
Mean z-score -2.15
Structure conservation index 0.17
SVM decision value 1.38
SVM RNA-class probability 0.948578
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12319542 102 + 23771897
CGGGCGAGCAGUGGGGAAAGUGUGCUAGUUGCAUAACUUGCGUGCGGGAAAUCCACUUACCAUCCACUUAGGAGGAAAUUUCCCUUUG-GUUCUUUU--UCAUCU
.....((((...((((((((..(((.((((....)))).)))..).((....)).....((.(((.....)))))...)))))))...-))))....--...... ( -29.80)
>DroSec_CAF1 4954 88 + 1
CGGGCGAGCAGU--GGAAAGUGUGCUAGUUGCAUAACUAGCGUG-GGUAAAUCCACUUACCAUCCACU-----------UUCCCUUUG-GUUCUUUU--CCAUCU
.(((.((((((.--((((((((.(((((((....)))))))(((-((....)))))........))))-----------))))))...-))))...)--)).... ( -30.60)
>DroSim_CAF1 5434 90 + 1
CGGGCGAGCAGG--GGAAAGUGUGCUAGUUGCAUAACUAGCGUG-GGUAAAUCCACUUACCAUCCACU-----------UUCCCUUUG-GUUCUUUUAUUCAUCU
.....((((.((--((((((((.(((((((....)))))))(((-((....)))))........))))-----------))))))...-))))............ ( -33.90)
>DroEre_CAF1 5359 84 + 1
CGUGCGAGCUGG--GGAAAAUGUGCUAGUUGCAUAACUUG-----------------CACCAUCCCGUGGCGAGGAAACCUCCCAUUUUGUUCUUUA--UCCUCU
.....((((..(--(((....((((.((((....)))).)-----------------)))..))))((((.((((...))))))))...))))....--...... ( -25.30)
>DroYak_CAF1 5342 95 + 1
CGGGCAAGCUGG---AAUAAUUUGCUAGUUGCAUAGCUUGAGUG-UGGAG---GACAUACCAUCCACUUGCGUGGAAACUUCCCAUUG-CUGCUUUU--CCAUCU
.(((((((.(((---(.......((((......)))).((.(((-((...---..))))))))))))))))((((.......))))..-........--)).... ( -25.90)
>consensus
CGGGCGAGCAGG__GGAAAGUGUGCUAGUUGCAUAACUUGCGUG_GGGAAAUCCACUUACCAUCCACU___G_GGAAA_UUCCCUUUG_GUUCUUUU__UCAUCU
.(((................(((((.....)))))..........((.....))...........................)))..................... ( -5.04 =  -5.50 +   0.46)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,319,542 – 12,319,644
Length 102
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 71.10
Mean single sequence MFE -27.03
Consensus MFE -5.20
Energy contribution -6.38
Covariance contribution 1.18
Combinations/Pair 1.12
Mean z-score -2.04
Structure conservation index 0.19
SVM decision value 1.14
SVM RNA-class probability 0.920600
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12319542 102 - 23771897
AGAUGA--AAAAGAAC-CAAAGGGAAAUUUCCUCCUAAGUGGAUGGUAAGUGGAUUUCCCGCACGCAAGUUAUGCAACUAGCACACUUUCCCCACUGCUCGCCCG
......--........-....(((.............(((((..((.(((((..........((....))..(((.....)))))))).))))))).....))). ( -20.87)
>DroSec_CAF1 4954 88 - 1
AGAUGG--AAAAGAAC-CAAAGGGAA-----------AGUGGAUGGUAAGUGGAUUUACC-CACGCUAGUUAUGCAACUAGCACACUUUCC--ACUGCUCGCCCG
...(((--.......)-))..(((..-----------((((((.(((..((((......)-)))(((((((....)))))))..))).)))--))).....))). ( -32.40)
>DroSim_CAF1 5434 90 - 1
AGAUGAAUAAAAGAAC-CAAAGGGAA-----------AGUGGAUGGUAAGUGGAUUUACC-CACGCUAGUUAUGCAACUAGCACACUUUCC--CCUGCUCGCCCG
................-....(((((-----------((((........((((......)-)))(((((((....))))))).))))))))--)........... ( -29.70)
>DroEre_CAF1 5359 84 - 1
AGAGGA--UAAAGAACAAAAUGGGAGGUUUCCUCGCCACGGGAUGGUG-----------------CAAGUUAUGCAACUAGCACAUUUUCC--CCAGCUCGCACG
.(((..--............(((((((...)))).))).((((..(((-----------------(.((((....)))).))))....)))--)...)))..... ( -25.30)
>DroYak_CAF1 5342 95 - 1
AGAUGG--AAAAGCAG-CAAUGGGAAGUUUCCACGCAAGUGGAUGGUAUGUC---CUCCA-CACUCAAGCUAUGCAACUAGCAAAUUAUU---CCAGCUUGCCCG
....((--..((((((-(..((((.....(((((....)))))(((......---..)))-..)))).))).(((.....))).......---...))))..)). ( -26.90)
>consensus
AGAUGA__AAAAGAAC_CAAAGGGAA_UUUCC_C___AGUGGAUGGUAAGUGGAUUUACC_CACGCAAGUUAUGCAACUAGCACACUUUCC__CCUGCUCGCCCG
.....................(((...............((.((((..((((...........))))..)))).))...(((..............)))..))). ( -5.20 =  -6.38 +   1.18)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:56 2006