Locus 1916

Sequence ID 2R_DroMel_CAF1
Location 7,204,528 – 7,204,663
Length 135
Max. P 0.955891
window3169 window3170 window3171

overview

Window 9

Location 7,204,528 – 7,204,629
Length 101
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 78.08
Mean single sequence MFE -20.78
Consensus MFE -12.86
Energy contribution -13.94
Covariance contribution 1.08
Combinations/Pair 1.15
Mean z-score -2.04
Structure conservation index 0.62
SVM decision value 1.06
SVM RNA-class probability 0.909164
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7204528 101 + 20766785
UUUCACAUUUUCACACUUUUUAAAAAAGUUCGCAAUUGGCGAGAAAGCUUUUUGAUGCUUUUAGCUACAAUUUGUUU-UGGCUUGAUCAGCUUUCUAGUAUA
..............(((((.....)))))((((.....))))(((((((..(..(.(((...(((........))).-.))))..)..)))))))....... ( -20.60)
>DroSec_CAF1 4185 93 + 1
UUUCACAUUUUCACACUUUUCUAA-AAGUAUGCA-------AGAAAGCUUUUUGAUGCUUUUAUAUACAAUUUGUUU-UAGCUUGAUCAGCGUUCUAGUAUA
..............(((((....)-))))((((.-------((((.(((..(..(.(((...(((.......)))..-.))))..)..))).)))).)))). ( -15.60)
>DroSim_CAF1 7045 100 + 1
UUUCACAUUUUCACACUUUUUGAA-AAGUUCGCAAUUGGCGAGAAAGCUUUUUGAUGCUUUUAGCUACAAUUUGUUU-UAGCUUGAUCAGCUUUCUAGUAUA
.......((((((.......))))-))..((((.....))))(((((((..(..(.(((...(((........))).-.))))..)..)))))))....... ( -22.00)
>DroEre_CAF1 6147 100 + 1
CAUCGAUAUCCCGCACGUU-UUAAAUGUUUUGCAAAUGGCUAGAAAGCUUUUUGAUGCUUUUAGCUAAAAUUUGCUU-CAACUCGAUCAGCUUUCUAGUAUU
............((((((.-....))))...)).....(((((((((((..((((.(.((..(((........))).-.)))))))..)))))))))))... ( -22.80)
>DroYak_CAF1 7590 96 + 1
------AAUCCCGCACUUUUUUAAAAAAUUGGCAAGUGGCUAGAAAGCUUUUUGAUGCUUUUUGCUAACAAUUUUUUAAGGCUUGAUCAGCUUUCUAGUAUU
------.......(((((..((((....)))).)))))(((((((((((..(..(.(((((................))))))..)..)))))))))))... ( -22.89)
>consensus
UUUCACAUUUUCACACUUUUUUAAAAAGUUCGCAAUUGGCGAGAAAGCUUUUUGAUGCUUUUAGCUACAAUUUGUUU_UAGCUUGAUCAGCUUUCUAGUAUA
......................................((.((((((((..((((.(((...(((........)))...)))))))..)))))))).))... (-12.86 = -13.94 +   1.08)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,204,553 – 7,204,663
Length 110
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 81.07
Mean single sequence MFE -23.96
Consensus MFE -15.62
Energy contribution -17.10
Covariance contribution 1.48
Combinations/Pair 1.11
Mean z-score -2.41
Structure conservation index 0.65
SVM decision value 1.46
SVM RNA-class probability 0.955891
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7204553 110 + 20766785
AAGUUCGCAAUUGGCGAGAAAGCUUUUUGAUGCUUUUAGCUACAAUUUGUUU-UGGCUUGAUCAGCUUUCUAGUAUAACUAAUUUAAUUAAUAAAGCUCUCAUAAAAGCUU
.(((((((.....)))((((((((..(..(.(((...(((........))).-.))))..)..)))))))).....)))).............(((((........))))) ( -23.30)
>DroSec_CAF1 4209 91 + 1
AAGUAUGCA-------AGAAAGCUUUUUGAUGCUUUUAUAUACAAUUUGUUU-UAGCUUGAUCAGCGUUCUAGUAUAACUACUUUAACUAAAAAAG------------CUU
.(((((((.-------((((.(((..(..(.(((...(((.......)))..-.))))..)..))).)))).)))).)))................------------... ( -16.20)
>DroSim_CAF1 7069 110 + 1
AAGUUCGCAAUUGGCGAGAAAGCUUUUUGAUGCUUUUAGCUACAAUUUGUUU-UAGCUUGAUCAGCUUUCUAGUAUAACUAUUUUAACUAAAAAAGCUUUAAUAAAAGCUU
.(((((((.....)))((((((((..(..(.(((...(((........))).-.))))..)..)))))))).....)))).............(((((((....))))))) ( -25.40)
>DroEre_CAF1 6171 110 + 1
UGUUUUGCAAAUGGCUAGAAAGCUUUUUGAUGCUUUUAGCUAAAAUUUGCUU-CAACUCGAUCAGCUUUCUAGUAUUACUACUUUAAUUAAUAAAGCUUUGAUAAAAGCUU
.............(((((((((((..((((.(.((..(((........))).-.)))))))..)))))))))))...................(((((((....))))))) ( -27.30)
>DroYak_CAF1 7609 111 + 1
AAAUUGGCAAGUGGCUAGAAAGCUUUUUGAUGCUUUUUGCUAACAAUUUUUUAAGGCUUGAUCAGCUUUCUAGUAUUACUACUUUAAUUAAUAAAGCUUUUAUAAAAGCUU
.((((((..(((((((((((((((..(..(.(((((................))))))..)..)))))))))))..))))...))))))....(((((((....))))))) ( -27.59)
>consensus
AAGUUCGCAAUUGGCGAGAAAGCUUUUUGAUGCUUUUAGCUACAAUUUGUUU_UAGCUUGAUCAGCUUUCUAGUAUAACUACUUUAAUUAAUAAAGCUUU_AUAAAAGCUU
.............((.((((((((..((((.(((...(((........)))...)))))))..)))))))).))...................(((((((....))))))) (-15.62 = -17.10 +   1.48)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,204,553 – 7,204,663
Length 110
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 81.07
Mean single sequence MFE -21.19
Consensus MFE -10.67
Energy contribution -11.19
Covariance contribution 0.52
Combinations/Pair 1.10
Mean z-score -2.44
Structure conservation index 0.50
SVM decision value 0.86
SVM RNA-class probability 0.867812
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7204553 110 - 20766785
AAGCUUUUAUGAGAGCUUUAUUAAUUAAAUUAGUUAUACUAGAAAGCUGAUCAAGCCA-AAACAAAUUGUAGCUAAAAGCAUCAAAAAGCUUUCUCGCCAAUUGCGAACUU
((((((((.(((..(((((...........((((((((.......(((.....)))..-........))))))))))))).)))))))))))..((((.....)))).... ( -21.93)
>DroSec_CAF1 4209 91 - 1
AAG------------CUUUUUUAGUUAAAGUAGUUAUACUAGAACGCUGAUCAAGCUA-AAACAAAUUGUAUAUAAAAGCAUCAAAAAGCUUUCU-------UGCAUACUU
.((------------(((..(((((...((((....)))).....)))))..))))).-........((((....(((((........)))))..-------))))..... ( -16.00)
>DroSim_CAF1 7069 110 - 1
AAGCUUUUAUUAAAGCUUUUUUAGUUAAAAUAGUUAUACUAGAAAGCUGAUCAAGCUA-AAACAAAUUGUAGCUAAAAGCAUCAAAAAGCUUUCUCGCCAAUUGCGAACUU
((((((((.....(((((..((((((....(((.....)))...))))))..))))).-............((.....))....))))))))..((((.....)))).... ( -23.40)
>DroEre_CAF1 6171 110 - 1
AAGCUUUUAUCAAAGCUUUAUUAAUUAAAGUAGUAAUACUAGAAAGCUGAUCGAGUUG-AAGCAAAUUUUAGCUAAAAGCAUCAAAAAGCUUUCUAGCCAUUUGCAAAACA
(((((((....)))))))..............((((..((((((((((....(((((.-.(((........)))...))).))....))))))))))....))))...... ( -25.70)
>DroYak_CAF1 7609 111 - 1
AAGCUUUUAUAAAAGCUUUAUUAAUUAAAGUAGUAAUACUAGAAAGCUGAUCAAGCCUUAAAAAAUUGUUAGCAAAAAGCAUCAAAAAGCUUUCUAGCCACUUGCCAAUUU
(((((((....)))))))..............((((..((((((((((...(((...........)))...((.....)).......))))))))))....))))...... ( -18.90)
>consensus
AAGCUUUUAU_AAAGCUUUAUUAAUUAAAGUAGUUAUACUAGAAAGCUGAUCAAGCUA_AAACAAAUUGUAGCUAAAAGCAUCAAAAAGCUUUCUAGCCAAUUGCAAACUU
(((((((....)))))))..........((((....))))((((((((......((......................)).......))))))))................ (-10.67 = -11.19 +   0.52)

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 10:16:18 2006