Locus 4209

Sequence ID 3R_DroMel_CAF1
Location 11,354,677 – 11,354,913
Length 236
Max. P 0.889533
window6793 window6794 window6795 window6796

overview

Window 3

Location 11,354,677 – 11,354,797
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.17
Mean single sequence MFE -43.94
Consensus MFE -41.34
Energy contribution -41.74
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.94
SVM decision value 0.96
SVM RNA-class probability 0.889533
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11354677 120 + 27905053
AGCCAUUGAAAUGGUUGCCCGGGAAACUGGAGCAGUUGGAGUCCGCCAAGCAGACGUUUGCUGGUCAUAUCUGGCUCGCUGCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACA
((((((....))))))...(((....)))((((((.....((((((...((((.((...((..(......)..)).))))))...)))))).(((.(((...)))..))).))))))... ( -47.00)
>DroSec_CAF1 102245 120 + 1
AGCCAUUGAAAUGGUUGCCCUGGAAACUGGAGCAGUUGGAGUCCGCCAAGCAGACGUUUGCUGGUCAUAUCUGGCUCGCUGCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACA
((((((....)))))).....(....)..((((((.....((((((...((((.((...((..(......)..)).))))))...)))))).(((.(((...)))..))).))))))... ( -43.10)
>DroSim_CAF1 93020 120 + 1
AGCCAUUGAAAUGGUUGCCCUGGAAACUGGAGCAGUUGGAGUCCGCCAAGCAGACGUUUGCUGGUCAUAUCUGGCUCGCUGCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACA
((((((....)))))).....(....)..((((((.....((((((...((((.((...((..(......)..)).))))))...)))))).(((.(((...)))..))).))))))... ( -43.10)
>DroEre_CAF1 89782 120 + 1
AGCCAUUGAAAAGGUUUCCCUGGAAACUGGAGCAGUUGGAGUCCGCCAAGCAGACGUUUGCUGGUCAUAUCUGGCUCGCUGCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACA
............((((((....)))))).((((((.....((((((...((((.((...((..(......)..)).))))))...)))))).(((.(((...)))..))).))))))... ( -43.90)
>DroYak_CAF1 92279 120 + 1
AGCCAUUGAAAAGGUUGCACUGGAAACUGGAGCAGUUGGAGUCCGCCGAGCAGACGUUUGCUGGUCAUAUCUGGCUCGCUGCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACA
((((........))))...(.(....).)((((((.....((((((.((((((.((...((..(......)..)).)))))).)))))))).(((.(((...)))..))).))))))... ( -42.60)
>consensus
AGCCAUUGAAAUGGUUGCCCUGGAAACUGGAGCAGUUGGAGUCCGCCAAGCAGACGUUUGCUGGUCAUAUCUGGCUCGCUGCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACA
((((((....))))))...(.(....).)((((((.....((((((...((((.((...((..(......)..)).))))))...)))))).(((.(((...)))..))).))))))... (-41.34 = -41.74 +   0.40)

alignment

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secondary structure

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Window 4

Location 11,354,717 – 11,354,837
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.49
Mean single sequence MFE -33.89
Consensus MFE -33.44
Energy contribution -33.20
Covariance contribution -0.24
Combinations/Pair 1.04
Mean z-score -1.08
Structure conservation index 0.99
SVM decision value 0.30
SVM RNA-class probability 0.680461
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11354717 120 + 27905053
GUCCGCCAAGCAGACGUUUGCUGGUCAUAUCUGGCUCGCUGCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACACCCAGGAAUCAGAUCCUGCAACUCCACUCCACUAUCCCUC
((((((...((((.((...((..(......)..)).))))))...)))))).............((((((((((........))))..........)))))).................. ( -33.20)
>DroSec_CAF1 102285 120 + 1
GUCCGCCAAGCAGACGUUUGCUGGUCAUAUCUGGCUCGCUGCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACACCCAGGAAUCAGAUCCUGCAACUCCACUCCAACACCCAUC
((((((...((((.((...((..(......)..)).))))))...))))))............(((((.(..((........(((((......)))))......))..))))))...... ( -33.34)
>DroSim_CAF1 93060 120 + 1
GUCCGCCAAGCAGACGUUUGCUGGUCAUAUCUGGCUCGCUGCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACACCCAGGAAUCGGAUCCUGCAACUCCACUCCACCACCCAUC
((((((...((((.((...((..(......)..)).))))))...)))))).............(((((.((((........))))....(....).))))).................. ( -34.40)
>DroEre_CAF1 89822 107 + 1
GUCCGCCAAGCAGACGUUUGCUGGUCAUAUCUGGCUCGCUGCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACACCCAGGAAUCAGAUCCUGCAGCUCCUC-------------
((((((...((((.((...((..(......)..)).))))))...))))))..(((.......(((.((....))..)))..(((((......))))).))).....------------- ( -33.60)
>DroYak_CAF1 92319 118 + 1
GUCCGCCGAGCAGACGUUUGCUGGUCAUAUCUGGCUCGCUGCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACACCCAGGAAUCAGAUCCUGCAGCUCCACUCCU--UCCCAUC
((((((.((((((.((...((..(......)..)).)))))).))))))))..(((.......(((.((....))..)))..(((((......))))).))).........--....... ( -34.90)
>consensus
GUCCGCCAAGCAGACGUUUGCUGGUCAUAUCUGGCUCGCUGCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACACCCAGGAAUCAGAUCCUGCAACUCCACUCCA__ACCCAUC
((((((...((((.((...((..(......)..)).))))))...)))))).............((((((((((........))))..........)))))).................. (-33.44 = -33.20 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,354,757 – 11,354,875
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.83
Mean single sequence MFE -27.02
Consensus MFE -22.32
Energy contribution -23.56
Covariance contribution 1.24
Combinations/Pair 1.04
Mean z-score -1.60
Structure conservation index 0.83
SVM decision value 0.27
SVM RNA-class probability 0.662197
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11354757 118 + 27905053
GCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACACCCAGGAAUCAGAUCCUGCAACUCCACUCCACUAUCCCUC-CCCAUCUCCAUCCCCU-CUCUUGGGUCCUGGGUCGACAA
...(((.(((((.((.((........)).)).)))))..((((((((..(((...)))......................-............(((.-.....))))))))))))))... ( -29.60)
>DroSec_CAF1 102325 118 + 1
GCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACACCCAGGAAUCAGAUCCUGCAACUCCACUCCAACACCCAUC-CCCAUCUCCAUCCCCU-CUCUUGGGUCCUGGGUCGACAA
...(((.(((((.((.((........)).)).)))))..((((((((..(((...)))......................-............(((.-.....))))))))))))))... ( -29.60)
>DroSim_CAF1 93100 118 + 1
GCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACACCCAGGAAUCGGAUCCUGCAACUCCACUCCACCACCCAUC-CCCAUCUCCAUCCCCU-CUCUUGGGUCCUGGGUCGACAA
...(((.(((((.((.((........)).)).)))))..((((((((...(((.........)))...............-............(((.-.....))))))))))))))... ( -32.20)
>DroEre_CAF1 89862 91 + 1
GCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACACCCAGGAAUCAGAUCCUGCAGCUCCUC-------------------------CCCACCCCUC----UCCUGGGUCGACAA
...(((.(((((.((.((........)).)).)))))..((((((((....................-------------------------..........----)))))))))))... ( -23.41)
>DroYak_CAF1 92359 113 + 1
GCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACACCCAGGAAUCAGAUCCUGCAGCUCCACUCCU--UCCCAUCUCUCAUAUCCACCCCAC-CCCC----UCCUGAGUCGACAA
((...((((((.((..(((...))).)).)))))).......(((((......)))))..))((.((((..--........................-....----....)))).))... ( -20.28)
>consensus
GCAUCGCGGGCACGCUCAUAAAAUGUUGCGCCUGCUCACACCCAGGAAUCAGAUCCUGCAACUCCACUCCA__ACCCAUC_CCCAUCUCCAUCCCCU_CUCUUGGGUCCUGGGUCGACAA
...(((.(((((.((.((........)).)).)))))..((((((((..(((...)))...................................(((.......))))))))))))))... (-22.32 = -23.56 +   1.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,354,797 – 11,354,913
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.97
Mean single sequence MFE -23.69
Consensus MFE -17.68
Energy contribution -18.92
Covariance contribution 1.24
Combinations/Pair 1.04
Mean z-score -1.75
Structure conservation index 0.75
SVM decision value 0.46
SVM RNA-class probability 0.745004
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11354797 116 + 27905053
CCCAGGAAUCAGAUCCUGCAACUCCACUCCACUAUCCCUC-CCCAUCUCCAUCCCCU-CUCUUGGGUCCUGGGUCGACAAAUUUGCUUAGAAUUUGAAAUGCAAGCCAG-ACAAUGGC-C
(((((((..(((...)))......................-............(((.-.....))))))))))....(((((((.....)))))))........((((.-....))))-. ( -25.40)
>DroSec_CAF1 102365 118 + 1
CCCAGGAAUCAGAUCCUGCAACUCCACUCCAACACCCAUC-CCCAUCUCCAUCCCCU-CUCUUGGGUCCUGGGUCGACAAAUUUGCUUAGAAUUUGAAAUGCAAGCCAGCACAAUGGCCC
...((((......))))(((.............(((((..-((((............-....))))...)))))...(((((((.....)))))))...)))..((((......)))).. ( -26.49)
>DroSim_CAF1 93140 116 + 1
CCCAGGAAUCGGAUCCUGCAACUCCACUCCACCACCCAUC-CCCAUCUCCAUCCCCU-CUCUUGGGUCCUGGGUCGACAAAUUUGCUUAGAAUUUGAAAUGCAAGCCAG-ACAAUGGC-C
(((((((...(((.........)))...............-............(((.-.....))))))))))....(((((((.....)))))))........((((.-....))))-. ( -28.00)
>DroEre_CAF1 89902 89 + 1
CCCAGGAAUCAGAUCCUGCAGCUCCUC-------------------------CCCACCCCUC----UCCUGGGUCGACAAAUUUGCUUAGAAUUUGAAAUGCAAGCCAG-ACAAUGGC-C
..(((((......)))))..((.....-------------------------.....(((..----....)))....(((((((.....)))))))....))..((((.-....))))-. ( -20.80)
>DroYak_CAF1 92399 111 + 1
CCCAGGAAUCAGAUCCUGCAGCUCCACUCCU--UCCCAUCUCUCAUAUCCACCCCAC-CCCC----UCCUGAGUCGACAAAUUUGCUUAGAAUUUGAAAUGCAAGCCAG-ACAAUGGC-C
..(((((......)))))..((((.((((..--........................-....----....)))).))(((((((.....)))))))....))..((((.-....))))-. ( -17.78)
>consensus
CCCAGGAAUCAGAUCCUGCAACUCCACUCCA__ACCCAUC_CCCAUCUCCAUCCCCU_CUCUUGGGUCCUGGGUCGACAAAUUUGCUUAGAAUUUGAAAUGCAAGCCAG_ACAAUGGC_C
(((((((..(((...)))...................................(((.......))))))))))....(((((((.....)))))))........((((......)))).. (-17.68 = -18.92 +   1.24)

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 11:21:49 2006