Locus 1606

Sequence ID 2R_DroMel_CAF1
Location 6,026,148 – 6,026,284
Length 136
Max. P 0.999962
window2689 window2690 window2691 window2692

overview

Window 9

Location 6,026,148 – 6,026,257
Length 109
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 92.12
Mean single sequence MFE -29.38
Consensus MFE -23.34
Energy contribution -23.34
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.79
SVM decision value 0.27
SVM RNA-class probability 0.663688
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6026148 109 + 20766785
AGUUGACUCUAUGAGACUUAAAGUGUAUUAUUUACUGGCUACAUACAGUGGGGCCUCUAUAUCUGGACACUGGUUUCAUUCAUCCAGAAGUUUCACUGUACGUAAGCAG
..((((.((.....)).))))((((.......)))).(((((.(((((((..((.......((((((...(((......))))))))).))..))))))).)).))).. ( -26.70)
>DroSec_CAF1 44500 107 + 1
AGUUGACUCUAUGAGACUUAACGUGUAUCAUUUACUGGCUACAUACAGUGGGGCCUCU--AUCUGGACACUGGCUUCUUCAAUCCAGAAGUUUCACUGUACGUAAGCAG
.(((((.((.....)).)))))..(((.....)))..(((((.(((((((..((....--.((((((...(((.....))).)))))).))..))))))).)).))).. ( -29.80)
>DroSim_CAF1 44235 107 + 1
AGUUGACUCUAUGAGACUUAACGUGUAUCAUUUACUGGCUACAUACAGUGGGGCCUCU--AUCUGGACACGGGUUUCUUCAAUCCAGAAGUUUCACUGUACGUAGGCAG
.(((((.((.....)).)))))............(((.((((.(((((((..((....--.((((((....((.....))..)))))).))..))))))).)))).))) ( -35.40)
>DroEre_CAF1 44648 106 + 1
AGUUGACUCUAUGAGACUUAAAGUGUAUUACUUGCUGGAUACAUACAGUGGGGCCUCU--AUCUGGACACUGGUUGCUC-AAUCCAGAAGUUUCACUGUACGUAGGCAG
...((.(.(((((.........(((((((........)))))))((((((..((....--.((((((...(((....))-).)))))).))..)))))).)))))))). ( -28.70)
>DroYak_CAF1 44133 107 + 1
AGUUGACUCUAUGAGACUUAAAGUGUAUUACUUGCUGGAUACAUACAGUGGGGCCUCU--AUCUGGACAAUAGUUUCUUAAAUCCAGAAGUUUCACUGUACGUAAGCAG
(((..((.((.(((...))).)).))...)))((((...(((.(((((((..((....--.((((((....((...))....)))))).))..))))))).))))))). ( -26.30)
>consensus
AGUUGACUCUAUGAGACUUAAAGUGUAUUAUUUACUGGCUACAUACAGUGGGGCCUCU__AUCUGGACACUGGUUUCUUCAAUCCAGAAGUUUCACUGUACGUAAGCAG
......(((...)))...................(((..(((.(((((((..((.......((((((...............)))))).))..))))))).)))..))) (-23.34 = -23.34 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,026,148 – 6,026,257
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 92.12
Mean single sequence MFE -29.17
Consensus MFE -27.00
Energy contribution -27.32
Covariance contribution 0.32
Combinations/Pair 1.04
Mean z-score -2.28
Structure conservation index 0.93
SVM decision value 3.75
SVM RNA-class probability 0.999587
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6026148 109 - 20766785
CUGCUUACGUACAGUGAAACUUCUGGAUGAAUGAAACCAGUGUCCAGAUAUAGAGGCCCCACUGUAUGUAGCCAGUAAAUAAUACACUUUAAGUCUCAUAGAGUCAACU
(((.((((((((((((...(((((((((...((....))..))))))).....))....)))))))))))).)))..........((((((.......))))))..... ( -29.00)
>DroSec_CAF1 44500 107 - 1
CUGCUUACGUACAGUGAAACUUCUGGAUUGAAGAAGCCAGUGUCCAGAU--AGAGGCCCCACUGUAUGUAGCCAGUAAAUGAUACACGUUAAGUCUCAUAGAGUCAACU
(((.((((((((((((...((((......))))..(((..(((....))--)..)))..)))))))))))).)))...((((.((.......)).)))).......... ( -29.60)
>DroSim_CAF1 44235 107 - 1
CUGCCUACGUACAGUGAAACUUCUGGAUUGAAGAAACCCGUGUCCAGAU--AGAGGCCCCACUGUAUGUAGCCAGUAAAUGAUACACGUUAAGUCUCAUAGAGUCAACU
(((.((((((((((((...(((((((((.............))))))).--..))....)))))))))))).)))...((((.((.......)).)))).......... ( -31.02)
>DroEre_CAF1 44648 106 - 1
CUGCCUACGUACAGUGAAACUUCUGGAUU-GAGCAACCAGUGUCCAGAU--AGAGGCCCCACUGUAUGUAUCCAGCAAGUAAUACACUUUAAGUCUCAUAGAGUCAACU
(((..(((((((((((...((((((..((-(..((.....))..))).)--)))))...)))))))))))..)))..........((((((.......))))))..... ( -28.30)
>DroYak_CAF1 44133 107 - 1
CUGCUUACGUACAGUGAAACUUCUGGAUUUAAGAAACUAUUGUCCAGAU--AGAGGCCCCACUGUAUGUAUCCAGCAAGUAAUACACUUUAAGUCUCAUAGAGUCAACU
(((..(((((((((((...(((((((((.............))))))).--..))....)))))))))))..)))..........((((((.......))))))..... ( -27.92)
>consensus
CUGCUUACGUACAGUGAAACUUCUGGAUUGAAGAAACCAGUGUCCAGAU__AGAGGCCCCACUGUAUGUAGCCAGUAAAUAAUACACUUUAAGUCUCAUAGAGUCAACU
(((.((((((((((((...(((((((((.............))))))).....))....)))))))))))).))).................(.(((...))).).... (-27.00 = -27.32 +   0.32)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,026,178 – 6,026,284
Length 106
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 89.74
Mean single sequence MFE -32.66
Consensus MFE -27.48
Energy contribution -27.24
Covariance contribution -0.24
Combinations/Pair 1.04
Mean z-score -1.38
Structure conservation index 0.84
SVM decision value 0.21
SVM RNA-class probability 0.635353
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6026178 106 + 20766785
UUUACUGGCUACAUACAGUGGGGCCUCUAUAUCUGGACACUGGUUUCAUUCAUCCAGAAGUUUCACUGUACGUAAGCAGCGUGUGUGUUGGUGUGUC-----UAUGUACCU--
..(((..((.((((((((((..((.......((((((...(((......))))))))).))..))))))((((.....))))))))))..)))....-----.........-- ( -30.20)
>DroSec_CAF1 44530 106 + 1
UUUACUGGCUACAUACAGUGGGGCCUCU--AUCUGGACACUGGCUUCUUCAAUCCAGAAGUUUCACUGUACGUAAGCAGCGUGUGUGUUGGUGUGUC-----UAUGUACCUGC
..(((..((.((((((((((..((....--.((((((...(((.....))).)))))).))..))))))((((.....))))))))))..)))....-----........... ( -30.50)
>DroSim_CAF1 44265 106 + 1
UUUACUGGCUACAUACAGUGGGGCCUCU--AUCUGGACACGGGUUUCUUCAAUCCAGAAGUUUCACUGUACGUAGGCAGCGUGUGUGUUGGUGUGUC-----UGUGUACCUGC
....(((.((((.(((((((..((....--.((((((....((.....))..)))))).))..))))))).)))).))).......((.((((....-----....)))).)) ( -34.40)
>DroEre_CAF1 44678 108 + 1
CUUGCUGGAUACAUACAGUGGGGCCUCU--AUCUGGACACUGGUUGCUC-AAUCCAGAAGUUUCACUGUACGUAGGCAGCGUGUGUGUUGGUGUGUCAUACAUAUGUACCU--
...((((..(((.(((((((..((....--.((((((...(((....))-).)))))).))..))))))).)))..))))(((((((.........)))))))........-- ( -36.80)
>DroYak_CAF1 44163 104 + 1
CUUGCUGGAUACAUACAGUGGGGCCUCU--AUCUGGACAAUAGUUUCUUAAAUCCAGAAGUUUCACUGUACGUAAGCAGCGUGUGUGUUGGUGUGUC-----UGUGUACCU--
...((((..(((.(((((((..((....--.((((((....((...))....)))))).))..))))))).)))..)))).........((((....-----....)))).-- ( -31.40)
>consensus
UUUACUGGCUACAUACAGUGGGGCCUCU__AUCUGGACACUGGUUUCUUCAAUCCAGAAGUUUCACUGUACGUAAGCAGCGUGUGUGUUGGUGUGUC_____UAUGUACCU__
....(((..(((.(((((((..((.......((((((...............)))))).))..))))))).)))..)))..........((((..(.......)..))))... (-27.48 = -27.24 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,026,178 – 6,026,284
Length 106
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 89.74
Mean single sequence MFE -31.95
Consensus MFE -30.04
Energy contribution -30.12
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -3.01
Structure conservation index 0.94
SVM decision value 4.92
SVM RNA-class probability 0.999962
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6026178 106 - 20766785
--AGGUACAUA-----GACACACCAACACACACGCUGCUUACGUACAGUGAAACUUCUGGAUGAAUGAAACCAGUGUCCAGAUAUAGAGGCCCCACUGUAUGUAGCCAGUAAA
--.(((.....-----.....))).........((((.((((((((((((...(((((((((...((....))..))))))).....))....)))))))))))).))))... ( -30.80)
>DroSec_CAF1 44530 106 - 1
GCAGGUACAUA-----GACACACCAACACACACGCUGCUUACGUACAGUGAAACUUCUGGAUUGAAGAAGCCAGUGUCCAGAU--AGAGGCCCCACUGUAUGUAGCCAGUAAA
...(((.....-----.....))).........((((.((((((((((((...((((......))))..(((..(((....))--)..)))..)))))))))))).))))... ( -31.00)
>DroSim_CAF1 44265 106 - 1
GCAGGUACACA-----GACACACCAACACACACGCUGCCUACGUACAGUGAAACUUCUGGAUUGAAGAAACCCGUGUCCAGAU--AGAGGCCCCACUGUAUGUAGCCAGUAAA
...(((.....-----.....))).........((((.((((((((((((...(((((((((.............))))))).--..))....)))))))))))).))))... ( -32.42)
>DroEre_CAF1 44678 108 - 1
--AGGUACAUAUGUAUGACACACCAACACACACGCUGCCUACGUACAGUGAAACUUCUGGAUU-GAGCAACCAGUGUCCAGAU--AGAGGCCCCACUGUAUGUAUCCAGCAAG
--..((((....)))).................((((..(((((((((((...((((((..((-(..((.....))..))).)--)))))...)))))))))))..))))... ( -33.20)
>DroYak_CAF1 44163 104 - 1
--AGGUACACA-----GACACACCAACACACACGCUGCUUACGUACAGUGAAACUUCUGGAUUUAAGAAACUAUUGUCCAGAU--AGAGGCCCCACUGUAUGUAUCCAGCAAG
--.(((.....-----.....))).........((((..(((((((((((...(((((((((.............))))))).--..))....)))))))))))..))))... ( -32.32)
>consensus
__AGGUACAUA_____GACACACCAACACACACGCUGCUUACGUACAGUGAAACUUCUGGAUUGAAGAAACCAGUGUCCAGAU__AGAGGCCCCACUGUAUGUAGCCAGUAAA
...(((...............))).........((((.((((((((((((...(((((((((.............))))))).....))....)))))))))))).))))... (-30.04 = -30.12 +   0.08)

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 10:08:43 2006