Locus 7048

Sequence ID 2L_DroMel_CAF1
Location 19,710,323 – 19,710,456
Length 133
Max. P 0.957813
window11241 window11242 window11243

overview

Window 1

Location 19,710,323 – 19,710,416
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 87.68
Mean single sequence MFE -21.45
Consensus MFE -16.77
Energy contribution -16.52
Covariance contribution -0.25
Combinations/Pair 1.17
Mean z-score -2.52
Structure conservation index 0.78
SVM decision value 1.48
SVM RNA-class probability 0.957813
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19710323 93 + 22407834
AAAUAAAGGUUGUGUGCAUUUAUAAAAGCUACAUUUAACACUUUGUGGCAAAGGAUGUAGCAUUUAAGUAAGCAACUUACAGGGAAAUUGUGG
......(((((((.(((.....((((.(((((((((..(((...))).....))))))))).)))).))).)))))))((((.....)))).. ( -19.90)
>DroSim_CAF1 3682 91 + 1
AAAUAAAGGUUGUGUGCAUUU--AAAAGCUACAUUUAACACUUUGUGGCAAAGGAUGUAGCAUUUAAGUAAGCAACUUACAGGGAAAUUGUGG
......(((((((....((((--(((.(((((((((..(((...))).....))))))))).)))))))..)))))))((((.....)))).. ( -22.40)
>DroEre_CAF1 3634 86 + 1
AAAUAAAGGUUGUAAGCAUUU--AAAAGCUACAUUCAACACCACGUGGCAAAGGAUGUGGCAUUUAAAUAAGCGACU-----GCAAAUUAUGG
.......((((((....((((--(((.(((((((((....((....))....))))))))).)))))))..))))))-----........... ( -22.40)
>DroYak_CAF1 3705 91 + 1
AAAUAAUGGUUGUAUGCAUUU--AAAAGCUACAUUUAACACUUUGUGGCGAAGAAUGUAGCAUUUAGGUAAGCAACUUACAGGGAAAUUAUGG
.......((((((.(((...(--(((.(((((((((..(.((....)).)..))))))))).)))).))).))))))................ ( -21.10)
>consensus
AAAUAAAGGUUGUAUGCAUUU__AAAAGCUACAUUUAACACUUUGUGGCAAAGGAUGUAGCAUUUAAGUAAGCAACUUACAGGGAAAUUAUGG
.......((((((.(((......(((.(((((((((..(((...))).....))))))))).)))..))).))))))................ (-16.77 = -16.52 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,710,323 – 19,710,416
Length 93
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 87.68
Mean single sequence MFE -15.18
Consensus MFE -11.39
Energy contribution -11.70
Covariance contribution 0.31
Combinations/Pair 1.06
Mean z-score -2.26
Structure conservation index 0.75
SVM decision value 1.01
SVM RNA-class probability 0.899517
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19710323 93 - 22407834
CCACAAUUUCCCUGUAAGUUGCUUACUUAAAUGCUACAUCCUUUGCCACAAAGUGUUAAAUGUAGCUUUUAUAAAUGCACACAACCUUUAUUU
.................(((((.....((((.(((((((((((((...))))).)....))))))).)))).....))).))........... ( -14.80)
>DroSim_CAF1 3682 91 - 1
CCACAAUUUCCCUGUAAGUUGCUUACUUAAAUGCUACAUCCUUUGCCACAAAGUGUUAAAUGUAGCUUUU--AAAUGCACACAACCUUUAUUU
.................(((((....(((((.(((((((((((((...))))).)....))))))).)))--))..))).))........... ( -14.50)
>DroEre_CAF1 3634 86 - 1
CCAUAAUUUGC-----AGUCGCUUAUUUAAAUGCCACAUCCUUUGCCACGUGGUGUUGAAUGUAGCUUUU--AAAUGCUUACAACCUUUAUUU
.........((-----....)).((((((((.((.((((.(..((((....))))..).)))).)).)))--)))))................ ( -14.80)
>DroYak_CAF1 3705 91 - 1
CCAUAAUUUCCCUGUAAGUUGCUUACCUAAAUGCUACAUUCUUCGCCACAAAGUGUUAAAUGUAGCUUUU--AAAUGCAUACAACCAUUAUUU
............((((...(((.....((((.((((((((...(((......)))...)))))))).)))--)...))))))).......... ( -16.60)
>consensus
CCACAAUUUCCCUGUAAGUUGCUUACUUAAAUGCUACAUCCUUUGCCACAAAGUGUUAAAUGUAGCUUUU__AAAUGCACACAACCUUUAUUU
.................(((((......(((.(((((((....(((......)))....))))))).)))......))).))........... (-11.39 = -11.70 +   0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,710,336 – 19,710,456
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.92
Mean single sequence MFE -29.68
Consensus MFE -17.06
Energy contribution -18.62
Covariance contribution 1.56
Combinations/Pair 1.22
Mean z-score -2.22
Structure conservation index 0.57
SVM decision value 0.40
SVM RNA-class probability 0.721026
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19710336 120 + 22407834
GUGCAUUUAUAAAAGCUACAUUUAACACUUUGUGGCAAAGGAUGUAGCAUUUAAGUAAGCAACUUACAGGGAAAUUGUGGCAGCUUUCAUGCUGGUGCAUGCUAUCAAUCUGUCUCUGUA
.(((.....((((.(((((((((..(((...))).....))))))))).)))).....)))...((((((((.(((((((((((..((.....)).)).))))).))))...)))))))) ( -33.00)
>DroSim_CAF1 3695 116 + 1
GUGCAUUU--AAAAGCUACAUUUAACACUUUGUGGCAAAGGAUGUAGCAUUUAAGUAAGCAACUUACAGGGAAAUUGUGGCAGCUUUCAU--UGGUGCAUGCCAUCAAUCUGUUUCUGUA
.(((((((--(((.(((((((((..(((...))).....))))))))).)))))))..)))...(((((..(.(((((((((((......--....)).))))).))))...)..))))) ( -35.40)
>DroEre_CAF1 3647 99 + 1
AAGCAUUU--AAAAGCUACAUUCAACACCACGUGGCAAAGGAUGUGGCAUUUAAAUAAGCGACU-----GCAAAUUAUGGCAGGUUUCA--------------AUCAAUCUAUUUCUGUU
..((((((--(((.(((((((((....((....))....))))))))).)))))))..))..((-----((........))))......--------------................. ( -24.00)
>DroYak_CAF1 3718 116 + 1
AUGCAUUU--AAAAGCUACAUUUAACACUUUGUGGCGAAGAAUGUAGCAUUUAGGUAAGCAACUUACAGGGAAAUUAUGGCAGUUUUCAU--UGGUGCAUGCUAUCCAUCUAUUUCUGUU
.(((((((--(((.(((((((((..(.((....)).)..))))))))).)))))))..)))....((((..(....((((((((......--....)).)))))).......)..)))). ( -26.30)
>consensus
AUGCAUUU__AAAAGCUACAUUUAACACUUUGUGGCAAAGGAUGUAGCAUUUAAGUAAGCAACUUACAGGGAAAUUAUGGCAGCUUUCAU__UGGUGCAUGCUAUCAAUCUAUUUCUGUA
..((......(((.(((((((((..(((...))).....))))))))).)))......)).....(((((((....((((((((............)).)))))).......))))))). (-17.06 = -18.62 +   1.56)

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 12:26:06 2006