Locus 2481

Sequence ID 2R_DroMel_CAF1
Location 8,888,528 – 8,888,782
Length 254
Max. P 0.929077
window4096 window4097 window4098

overview

Window 6

Location 8,888,528 – 8,888,636
Length 108
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 86.11
Mean single sequence MFE -26.90
Consensus MFE -19.48
Energy contribution -21.32
Covariance contribution 1.84
Combinations/Pair 1.14
Mean z-score -2.45
Structure conservation index 0.72
SVM decision value 1.20
SVM RNA-class probability 0.929077
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8888528 108 - 20766785
GUUGCUAAAAAUUGGCAGCUUAAAAUGAAGUAUAUAUUUUAUAUAACUUUAGGAUAUGUGCCACAAACAGCGGCUGUUGAUUCCAACAAAGGGCAAACAAAGGCCAAU
((((.....(((..((((((.....((..((((((((((((........))))))))))))..))......))))))..))).))))....(((........)))... ( -28.40)
>DroSec_CAF1 133304 108 - 1
GUUGCUAAAAAUUGGCAGCUCAACAUGAGGUAUAUAUAUUAUAUAUCUUUAGGUUAUGUACCACAAAAAGCGGCUGUUGAAUCCAAUUAAGGGCAAACAAAGGCCAUU
(((((((.....)))))))((((((.((((((((((...))))))))))..(((.....)))............))))))...........(((........)))... ( -26.10)
>DroSim_CAF1 133156 108 - 1
GUUGCUAAAAAUUGGCAGCUCAACAUGAGGUAUAACUUUUAUAUAUCUUUAGGAUAUGUGCCACAAAAAGCGGCUGUUGAUUCCAAUUAAGGGCAAACAAAGGCCAUU
(((((((.....)))))))((((((...............(((((((.....)))))))(((.(.....).)))))))))...........(((........)))... ( -26.40)
>DroEre_CAF1 136595 107 - 1
GUUGCUAAAAAUUGCCAACUUGACAUA-GGUAUAUAUUUGAUAUAUCUUUGGGAUAUGCGCCACAAAAAGCGGCCGUUGAUGCCAAUUAAGGGCAAACAAAGGCCGUA
(((((........).))))........-((..(((((((.(........).)))))))..)).......((((((.(((.((((.......))))..))).)))))). ( -29.50)
>DroYak_CAF1 138665 108 - 1
GUAGCUAAAAAUUGCCAGCUUAACAUAAGGUAUAUAUUUUAUAUAUCUUUAGGAUAUGUGCCACAAAAAGUAGCCGUUGAUUCUAAUCAAGAGCAAACUAAAGCGUUU
...((........))..((((.......(((((((((((((........)))))))))))))..........((..(((((....)))))..))......)))).... ( -24.10)
>consensus
GUUGCUAAAAAUUGGCAGCUUAACAUGAGGUAUAUAUUUUAUAUAUCUUUAGGAUAUGUGCCACAAAAAGCGGCUGUUGAUUCCAAUUAAGGGCAAACAAAGGCCAUU
(((((((.....))))))).........(((((((((((((........))))))))))))).........((((.(((...((.......))....))).))))... (-19.48 = -21.32 +   1.84)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,888,556 – 8,888,675
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.77
Mean single sequence MFE -26.72
Consensus MFE -21.44
Energy contribution -22.92
Covariance contribution 1.48
Combinations/Pair 1.16
Mean z-score -1.41
Structure conservation index 0.80
SVM decision value -0.04
SVM RNA-class probability 0.511457
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8888556 119 - 20766785
GCUAAUAUUCAUGAGUAUUUAUAUAGGGCGCGC-UUAAAAGUUGCUAAAAAUUGGCAGCUUAAAAUGAAGUAUAUAUUUUAUAUAACUUUAGGAUAUGUGCCACAAACAGCGGCUGUUGA
...((((((....)))))).......(((.(((-(...(((((((((.....)))))))))....((..((((((((((((........))))))))))))..))...)))))))..... ( -29.40)
>DroSec_CAF1 133332 119 - 1
ACCAAUAUUCAUGAGUAUUUAUUUAGGGCGCGC-UAAAAUGUUGCUAAAAAUUGGCAGCUCAACAUGAGGUAUAUAUAUUAUAUAUCUUUAGGUUAUGUACCACAAAAAGCGGCUGUUGA
..((((.....(((((....))))).(((.(((-(.....(((((((.....)))))))......((.((((((((..(((........)))..)))))))).))...))))))))))). ( -27.50)
>DroSim_CAF1 133184 119 - 1
ACCAAUAUUUAUGAGUAUUUAUUUAGGGCGCGC-UAAAAUGUUGCUAAAAAUUGGCAGCUCAACAUGAGGUAUAACUUUUAUAUAUCUUUAGGAUAUGUGCCACAAAAAGCGGCUGUUGA
..((((.....(((((....))))).(((.(((-(.....(((((((.....)))))))......((.((((((..(((((........)))))..)))))).))...))))))))))). ( -26.00)
>DroEre_CAF1 136623 118 - 1
AGCAAUAUUCAUGAGCACUUAUUUAGGGCGCGC-UAAAAUGUUGCUAAAAAUUGCCAACUUGACAUA-GGUAUAUAUUUGAUAUAUCUUUGGGAUAUGCGCCACAAAAAGCGGCCGUUGA
(((((((((...(.((.(((.....))).)).)-...))))))))).........((((....((.(-(((((((.....)))))))).))((...(((..........))).)))))). ( -27.50)
>DroYak_CAF1 138693 120 - 1
ACCAAUAUUCAUGAGCAUUUAUUUAGGGCGCGAACAAAAUGUAGCUAAAAAUUGCCAGCUUAACAUAAGGUAUAUAUUUUAUAUAUCUUUAGGAUAUGUGCCACAAAAAGUAGCCGUUGA
..((((.....(((((....((((..(((....((.....)).)))..)))).....)))))......(((((((((((((........))))))))))))).............)))). ( -23.20)
>consensus
ACCAAUAUUCAUGAGUAUUUAUUUAGGGCGCGC_UAAAAUGUUGCUAAAAAUUGGCAGCUUAACAUGAGGUAUAUAUUUUAUAUAUCUUUAGGAUAUGUGCCACAAAAAGCGGCUGUUGA
.........................((.(((.........(((((((.....))))))).........(((((((((((((........))))))))))))).......))).))..... (-21.44 = -22.92 +   1.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,888,675 – 8,888,782
Length 107
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 87.12
Mean single sequence MFE -24.64
Consensus MFE -18.15
Energy contribution -17.55
Covariance contribution -0.60
Combinations/Pair 1.24
Mean z-score -1.92
Structure conservation index 0.74
SVM decision value 0.51
SVM RNA-class probability 0.763191
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8888675 107 + 20766785
GGAGAGCUAUAAAUCCCCUUUGAAAAGGCAUAUAU----AUAUAUUCACCUGUGCCCCAUCCA------CAUCCACUCCAUUAACGUGGGUUUUAUGGCCCACUGGCGCCACACCA-U
((...((((.................((((((...----...........)))))).......------................(((((((....))))))))))).))......-. ( -22.84)
>DroSec_CAF1 133451 107 + 1
GGAUAGCUAUAAAUCCCCUUUGGAAAGGCAUAUAU----AUAUAUUCACCUGUGCCCCACCCA------CAUCCACUCCAUUAACGUGGAUUUUAUGGCCUACUGGCGCCACACCA-U
((...((((((((.......(((...((((((...----...........))))))....)))------.((((((.........))))))))))))))....((....))..)).-. ( -22.44)
>DroSim_CAF1 133303 111 + 1
GGAUAGCUAUAAAUCCCCUUUGGAAAGGCAUAUAUAUAUAUAUAUUCACCUGUGCCCCACCCA------CAUCCACUCCAUUAACGUGGAUUUUAUGGCCUACUGGCGCCACACCA-U
((((........))))....(((...(((((((((....))))))...((.(((..(((....------.((((((.........))))))....)))..))).)).)))...)))-. ( -23.60)
>DroEre_CAF1 136741 104 + 1
GUAUAGCUGUAAAUCCCCUUUGGAGAGGCAUAU--------ACAUUCACCUGUGCCACAUCCA------CACCCACUCCAUUAACGUGGGUUUUAUGGCCUACUGGCGCCCCACCACU
((((((((.....(((.....)))..))).)))--------))........((((((...(((------.((((((.........))))))....))).....))))))......... ( -27.70)
>DroYak_CAF1 138813 109 + 1
GGAUAGCUAUAAAUCCCCUUUGGAAAGGCAUAU--------AUAUUUAGCUGUGCCACACCCACAUCCACAGCUACUCCAUUAACCUGGGUUUUAUGGCCUACUGGCGCCCCACCA-U
((((........))))....(((...(((....--------.....((((((((.............))))))))...(((.(((....)))..)))(((....))))))...)))-. ( -26.62)
>consensus
GGAUAGCUAUAAAUCCCCUUUGGAAAGGCAUAUAU____AUAUAUUCACCUGUGCCCCACCCA______CAUCCACUCCAUUAACGUGGGUUUUAUGGCCUACUGGCGCCACACCA_U
.....((((((((........((...((((((..................))))))...)).........((((((.........))))))))))))))....(((.......))).. (-18.15 = -17.55 +  -0.60)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:09 2006