Locus 3075

Sequence ID 2R_DroMel_CAF1
Location 10,544,055 – 10,544,210
Length 155
Max. P 0.997646
window5075 window5076

overview

Window 5

Location 10,544,055 – 10,544,170
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.52
Mean single sequence MFE -25.87
Consensus MFE -23.48
Energy contribution -22.60
Covariance contribution -0.88
Combinations/Pair 1.24
Mean z-score -2.27
Structure conservation index 0.91
SVM decision value 2.90
SVM RNA-class probability 0.997646
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10544055 115 + 20766785
GGUGCCAAAACAAAUGGCACAAAAUACGAUCGCUUGUGUGUAUUGAUUAAAAUAGCAAA-AUA----UUUUUAAAAGAGGAAAUGGUAAUUUUCUUCAAAAAAGUCAUCAAACUAUGGCA
.((((((.......))))))...........(((...((....(((((((((((.....-.))----)))).....(((((((.......))))))).....)))))....))...))). ( -25.10)
>DroSec_CAF1 37175 119 + 1
GGUGCCAAAACAAAUGGCAUAAAAUACGAUCGCUUGUGUGUAUUGAUUUAAAUAGCAAA-AUAUGUAUUUUUAAAAGAGGAAAUGGUAAUUUUCUUCAAAAAAGCCAUCAAACUAUGGCA
.((((((.......))))))......(((((((....))).)))).((((((..(((..-...)))...)))))).(((((((.......)))))))......(((((......))))). ( -26.20)
>DroSim_CAF1 33736 119 + 1
GGUGCCAAAACAAAUGGCAUAAAAUACGAUCGCUUGUGCGUAUUGAUUAAAAUAGCAAA-AUAUGUAUUUUUAAAAGAGGAAAUGGUAAUUUUCUUCAAAAAAGCCAUCAAACUAUGGCA
.((((((.......))))))......(((((((....))).)))).((((((..(((..-...)))..))))))..(((((((.......)))))))......(((((......))))). ( -28.40)
>DroEre_CAF1 38564 117 + 1
GGUGGCAAAACAAAUGGCACAAAAUUCGAUCGCCUGUGCGAAUUGAUUAUAUUUGCAAA-AUAUUU--UUUGAAAAGAGGAAAUGCUAAUUUUCCCUAAAAAAGCCAUCAAACUAUGGCA
((((((....((((.(((.............)))..(((((((.......)))))))..-......--))))...((.(((((.......)))))))......))))))........... ( -24.92)
>DroYak_CAF1 38436 120 + 1
GGUGCCAAAACAAAUGGCAUAAACUGCGAUCGCUGGUGUGUAUUGAUUGUAUUUGCAAAAAUAUUUUGUUUGAAAAGAGGAAAUGGUAAUUUUCCUUAAAAAAGCUAUCAAACUAUGGCG
...((((......(((((.(((((..(((((((....))).))))...((((((....))))))...)))))....(((((((.......)))))))......))))).......)))). ( -24.72)
>consensus
GGUGCCAAAACAAAUGGCAUAAAAUACGAUCGCUUGUGUGUAUUGAUUAAAAUAGCAAA_AUAUGU_UUUUUAAAAGAGGAAAUGGUAAUUUUCUUCAAAAAAGCCAUCAAACUAUGGCA
.((((((.......))))))......(((((((....))).))))...............................(((((((.......)))))))......(((((......))))). (-23.48 = -22.60 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,544,095 – 10,544,210
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.80
Mean single sequence MFE -22.42
Consensus MFE -17.84
Energy contribution -18.12
Covariance contribution 0.28
Combinations/Pair 1.09
Mean z-score -1.43
Structure conservation index 0.80
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10544095 115 - 20766785
ACUCAUACAUACAUCGGAAAUGGAGAUUUUGGUUGGCAUAUGCCAUAGUUUGAUGACUUUUUUGAAGAAAAUUACCAUUUCCUCUUUUAAAAA----UAU-UUUGCUAUUUUAAUCAAUA
...............((((((((.((((((...((((....)))).((((....)))).........)))))).)))))))).......((((----((.-.....))))))........ ( -21.90)
>DroSec_CAF1 37215 119 - 1
ACUCAUACAUACAUCGGAAAUGGCGAUUUUGGUUGGCAUAUGCCAUAGUUUGAUGGCUUUUUUGAAGAAAAUUACCAUUUCCUCUUUUAAAAAUACAUAU-UUUGCUAUUUAAAUCAAUA
...............((((((((..(((((..(..(.....(((((......)))))....)..)..)))))..))))))))........(((((((...-..)).)))))......... ( -25.10)
>DroSim_CAF1 33776 119 - 1
ACUCAUACAUACAUCGGAAAUGGUGAUUUUGGUUGGCAUAUGCCAUAGUUUGAUGGCUUUUUUGAAGAAAAUUACCAUUUCCUCUUUUAAAAAUACAUAU-UUUGCUAUUUUAAUCAAUA
...............(((((((((((((((..(..(.....(((((......)))))....)..)..))))))))))))))).......((((((((...-..)).))))))........ ( -29.60)
>DroEre_CAF1 38604 113 - 1
CCUACU----ACAUCGGAAAUGGCGAUUUUGGUUGGCAUAUGCCAUAGUUUGAUGGCUUUUUUAGGGAAAAUUAGCAUUUCCUCUUUUCAAA--AAAUAU-UUUGCAAAUAUAAUCAAUU
......----.....(((((((..((((((..((((.....(((((......)))))....))))..))))))..)))))))..(((.((((--(....)-)))).)))........... ( -18.80)
>DroYak_CAF1 38476 116 - 1
AAUCAU----ACAUCGGAAAUUGCGAUUUUGGUUGGAAUACGCCAUAGUUUGAUAGCUUUUUUAAGGAAAAUUACCAUUUCCUCUUUUCAAACAAAAUAUUUUUGCAAAUACAAUCAAUA
......----..........((((((...((((........))))..((((((.((........((((((.......))))))))..)))))).........))))))............ ( -16.70)
>consensus
ACUCAUACAUACAUCGGAAAUGGCGAUUUUGGUUGGCAUAUGCCAUAGUUUGAUGGCUUUUUUGAAGAAAAUUACCAUUUCCUCUUUUAAAAA_AAAUAU_UUUGCUAUUUUAAUCAAUA
...............((((((((.((((((...((((....)))).((((....)))).........)))))).))))))))...................................... (-17.84 = -18.12 +   0.28)

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 10:46:53 2006