Locus 1580

Sequence ID 2R_DroMel_CAF1
Location 5,941,395 – 5,941,555
Length 160
Max. P 0.885783
window2646 window2647

overview

Window 6

Location 5,941,395 – 5,941,515
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.91
Mean single sequence MFE -27.34
Consensus MFE -13.18
Energy contribution -13.78
Covariance contribution 0.60
Combinations/Pair 1.19
Mean z-score -2.15
Structure conservation index 0.48
SVM decision value 0.87
SVM RNA-class probability 0.871190
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5941395 120 - 20766785
UCGAUGAUAUCGAUAUCUAUUCCGACACCUGACAACAUCAGAGUGCGCUCGGCAGCUAUCGAUUAUUCUUAUCGAAUAAAUCUCUUUAGGCGCCUAAAUUCAAAAUUUGAUAAGCAGUAA
........(((((((.((...(((((((((((.....)))).)))...)))).)).)))))))((((((((((((((.......(((((....)))))......)))))))))).)))). ( -30.12)
>DroSec_CAF1 83476 120 - 1
UCGAUGCUAUCGAUAUUUAUUCCGACACCUGACAACAUCCGAGUGCGCUCGCUAGCCAUCGAUUAUUCUUAUCGAAUAAAUCUCUUUAGGCGCCUAAGUGUGAAAUUUGAUAAGCAAUAA
(((((((((.(((....(((((.((............)).)))))...))).))).))))))(((((((((((((((...((.((((((....))))).).)).)))))))))).))))) ( -28.10)
>DroSim_CAF1 81324 120 - 1
UCGAUGCUAUCGAUAUUUAUUCCGACACCUGACAACAUCCGAGUGCGCUCCCUAGCUAUCGAUUAUUCUUAUCGAAUAAAUCUAUUUAGGCGCCUAAAUGUGAAAUUUGAUAAGCAAUAA
((((((((((((..........)))...............(((....)))..)))).)))))(((((((((((((((...(((((((((....))))))).)).)))))))))).))))) ( -27.70)
>DroEre_CAF1 68622 106 - 1
UCGAUGCUAUCGAU--UCUAU------------CAGACACUAGUCUGCUCGGCAGCUAUCGAUUAUUCAUAUCGAUUAAAUUCCUCUUGGCGCCUAAAUUCAAAAUCUGAUAAGCAAUAG
....((((((((((--(....------------(((((....)))))...(((.(((((((((.......))))))............)))))).........)))).))).)))).... ( -23.20)
>DroYak_CAF1 86245 106 - 1
UCGACGCUAUCGAU--UGAUU------------AACAUCAGAGUGUGCUUGGCAGCUAUCGAUAAUUCUUAUCGAUUAAGUCCCUCUUGGCGCUGAAAUGCAAAAUCUGAUAAGCAAUAC
.....((((((...--.))).------------...((((((...(((....((((.(((((((.....)))))))...(((......)))))))....)))...)))))).)))..... ( -27.60)
>consensus
UCGAUGCUAUCGAUAUUUAUUCCGACACCUGACAACAUCCGAGUGCGCUCGGCAGCUAUCGAUUAUUCUUAUCGAAUAAAUCUCUUUAGGCGCCUAAAUGCAAAAUUUGAUAAGCAAUAA
........((((((.....................(((....))).(((....))).))))))((((((((((((((.......(((((....)))))......)))))))))).)))). (-13.18 = -13.78 +   0.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,941,435 – 5,941,555
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.38
Mean single sequence MFE -31.38
Consensus MFE -19.42
Energy contribution -22.42
Covariance contribution 3.00
Combinations/Pair 1.12
Mean z-score -2.35
Structure conservation index 0.62
SVM decision value 0.94
SVM RNA-class probability 0.885783
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5941435 120 + 20766785
UUUAUUCGAUAAGAAUAAUCGAUAGCUGCCGAGCGCACUCUGAUGUUGUCAGGUGUCGGAAUAGAUAUCGAUAUCAUCGAAUGAACAUCGGCUUUUGUUCCAGCUCUAUAGCAUAAAGUC
.((((((.....))))))......((((..((((((((.(((((...))))))))).((((((((..(((((.((((...))))..)))))..)))))))).))))..))))........ ( -37.90)
>DroSec_CAF1 83516 120 + 1
UUUAUUCGAUAAGAAUAAUCGAUGGCUAGCGAGCGCACUCGGAUGUUGUCAGGUGUCGGAAUAAAUAUCGAUAGCAUCGAAUGAACAUCGGUUUUUGUUCCAGCUCUAUAGCAUAAAGUC
.((((((.....))))))......((((..((((((((..((......))..)))).((((((((.((((((..(((...)))...)))))).)))))))).))))..))))........ ( -34.80)
>DroSim_CAF1 81364 120 + 1
UUUAUUCGAUAAGAAUAAUCGAUAGCUAGGGAGCGCACUCGGAUGUUGUCAGGUGUCGGAAUAAAUAUCGAUAGCAUCGAAUGAACAUCGGUUUUUGUUCCAGCUCUAUAGCAUAAAGUC
.((((((.....))))))......((((.(((((((((..((......))..)))).((((((((.((((((..(((...)))...)))))).)))))))).))))).))))........ ( -37.20)
>DroEre_CAF1 68662 106 + 1
UUUAAUCGAUAUGAAUAAUCGAUAGCUGCCGAGCAGACUAGUGUCUG------------AUAGA--AUCGAUAGCAUCGAAUAAACAUCGGUUUUUGUUCCACCUCUAUAGCAUAAAGUC
...(((((((.(...((.(((((.((((.(((.(((((....)))))------------.....--.))).))))))))).)).).)))))))........................... ( -23.20)
>DroYak_CAF1 86285 106 + 1
CUUAAUCGAUAAGAAUUAUCGAUAGCUGCCAAGCACACUCUGAUGUU------------AAUCA--AUCGAUAGCGUCGAAUAAACAUCGCCUUUUGUUCCAGCUCUAUAGCAUAAAGUC
....(((((((.....))))))).((((...(((.......((((((------------(.((.--...)))))))))(((((((........)))))))..)))...))))........ ( -23.80)
>consensus
UUUAUUCGAUAAGAAUAAUCGAUAGCUGCCGAGCGCACUCGGAUGUUGUCAGGUGUCGGAAUAAAUAUCGAUAGCAUCGAAUGAACAUCGGUUUUUGUUCCAGCUCUAUAGCAUAAAGUC
.....(((((.......)))))..((((..((((.......(((((((((.(((((........))))))))))))))(((((((........)))))))..))))..))))........ (-19.42 = -22.42 +   3.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:00 2006