Locus 3157

Sequence ID 3L_DroMel_CAF1
Location 9,184,985 – 9,185,118
Length 133
Max. P 0.999323
window4925 window4926 window4927

overview

Window 5

Location 9,184,985 – 9,185,086
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 92.28
Mean single sequence MFE -19.36
Consensus MFE -16.34
Energy contribution -16.54
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.98
Structure conservation index 0.84
SVM decision value 3.51
SVM RNA-class probability 0.999323
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9184985 101 - 23771897
GCAAAUGGAAGCAGUUCAUCCAAAAUAUUGCUCCCAUAAAGCCAUAUAUGACCCAUAAUUGUCAUAUCUCAAAAACACUUUUUACUGCGGCUAAUCAAACA
....((((.((((((...........)))))).))))..((((..(((((((........)))))))...((((.....)))).....))))......... ( -19.50)
>DroSec_CAF1 39700 101 - 1
GCAAAUGGAAGCAGUUCAUCCAAAAUAUUGCUCCCAUAAAGCGAAAUAUGACCCAUAAUUGUCAUAUCUCAAAAACACUUUUUACUGCGGCUAAUCAAACG
(((.((((.((((((...........)))))).)))).....((.(((((((........))))))).))...............)))............. ( -20.80)
>DroSim_CAF1 40016 101 - 1
GCAAAUGGAAGCAGUUCAUCCAAAAUAUUGCUCCCAUAAAGCCAUAUAUGACCCAUUAUUGUCAUAUCUCAAAAACACUUUUUACUGCGGCUAUUCAAACG
....((((.((((((...........)))))).))))..((((..(((((((........)))))))...((((.....)))).....))))......... ( -19.50)
>DroEre_CAF1 54905 101 - 1
GCAAAUGGAAGCAGUUCAUCCGAAAAAUUGCUCCCCUAAAACCACAUAUGACCCAUAAUAGUCAUAUCUCACAAGCACUUUUUACAGCGGCUAAUCAAACA
((....((.(((((((.........))))))).))..........(((((((........))))))).......))......................... ( -15.20)
>DroYak_CAF1 55040 101 - 1
GCAAAUGGAAGCAGUUCAUCCAAAAUAUUGCUUCCAUAAAAGCACAUAUGACCCAUAAUUGUCAUAUCUCAAAAACACUUUUUACAGCGACUGAUCAAACA
((..(((((((((((...........)))))))))))........(((((((........)))))))...................))............. ( -21.80)
>consensus
GCAAAUGGAAGCAGUUCAUCCAAAAUAUUGCUCCCAUAAAGCCACAUAUGACCCAUAAUUGUCAUAUCUCAAAAACACUUUUUACUGCGGCUAAUCAAACA
((..((((.((((((...........)))))).))))........(((((((........)))))))...................))............. (-16.34 = -16.54 +   0.20)

alignment

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secondary structure

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Window 6

Location 9,185,019 – 9,185,118
Length 99
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 78.65
Mean single sequence MFE -27.39
Consensus MFE -17.10
Energy contribution -18.69
Covariance contribution 1.59
Combinations/Pair 1.24
Mean z-score -1.97
Structure conservation index 0.62
SVM decision value 0.95
SVM RNA-class probability 0.887482
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9185019 99 + 23771897
AUAUGACAAUUAUGGGUCAUAUAUGGCUUUAUGGGAGCAAUAUUUUGGAUGA----ACUGCUUCCAUUUGC----------GAUUGCCGCUGCAGAAAGUCGUGCCAAUAUGA
(((((((........))))))).((((...(((((((((.............----..)))))))))..((----------((((..(......)..))))))))))...... ( -28.16)
>DroSec_CAF1 39734 99 + 1
AUAUGACAAUUAUGGGUCAUAUUUCGCUUUAUGGGAGCAAUAUUUUGGAUGA----ACUGCUUCCAUUUGC----------GAUAGGCGCUGCAGAAAGUCGUGCCAAUUUGA
(((((((........))))))).((((...(((((((((.............----..)))))))))..))----------))..(((((.((.....)).)))))....... ( -32.76)
>DroSim_CAF1 40050 99 + 1
AUAUGACAAUAAUGGGUCAUAUAUGGCUUUAUGGGAGCAAUAUUUUGGAUGA----ACUGCUUCCAUUUGC----------GAUAGGUGCUGCAGAAAGUCGUGCCAAUUUGA
.((((((........))))))(((.((...(((((((((.............----..)))))))))..))----------.)))((..(.((.....)).)..))....... ( -28.96)
>DroEre_CAF1 54939 99 + 1
AUAUGACUAUUAUGGGUCAUAUGUGGUUUUAGGGGAGCAAUUUUUCGGAUGA----ACUGCUUCCAUUUGC----------GAUAGGCGGUGCAGAAAGUCGUGCCAAAUUGA
.(((((((......)))))))(((.((.....(((((((.(((.......))----).)))))))....))----------.)))...((..(........)..))....... ( -26.70)
>DroYak_CAF1 55074 99 + 1
AUAUGACAAUUAUGGGUCAUAUGUGCUUUUAUGGAAGCAAUAUUUUGGAUGA----ACUGCUUCCAUUUGC----------GAUAGGCGUUGCAGAAAGUCGAGCUAAAUUGA
(((((((........)))))))..((((...((((((((.............----..))))))))(((((----------(((....)))))))).....))))........ ( -26.56)
>DroAna_CAF1 41568 100 + 1
--AUGAUAAC-----CUC------AGCUGUUUGUUUGCAAUGAGCUGGAUGAGUUUAAUGCUUUUACUUGCUUCAUAUUCAUAUAGAAGCUGCAGAAAGUCGUGCCAAUUUGA
--........-----.((------((((..(((....)))..))))))..(((((..((((((((....(((((.(((....))))))))....))))).)))...))))).. ( -21.20)
>consensus
AUAUGACAAUUAUGGGUCAUAUAUGGCUUUAUGGGAGCAAUAUUUUGGAUGA____ACUGCUUCCAUUUGC__________GAUAGGCGCUGCAGAAAGUCGUGCCAAUUUGA
(((((((........)))))))...((...(((((((((...................)))))))))..))..............(((((.((.....)).)))))....... (-17.10 = -18.69 +   1.59)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,185,019 – 9,185,118
Length 99
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 78.65
Mean single sequence MFE -21.01
Consensus MFE -9.46
Energy contribution -11.21
Covariance contribution 1.75
Combinations/Pair 1.00
Mean z-score -2.39
Structure conservation index 0.45
SVM decision value 0.48
SVM RNA-class probability 0.753180
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9185019 99 - 23771897
UCAUAUUGGCACGACUUUCUGCAGCGGCAAUC----------GCAAAUGGAAGCAGU----UCAUCCAAAAUAUUGCUCCCAUAAAGCCAUAUAUGACCCAUAAUUGUCAUAU
......((((.............(((.....)----------))..((((.((((((----...........)))))).))))...)))).(((((((........))))))) ( -24.50)
>DroSec_CAF1 39734 99 - 1
UCAAAUUGGCACGACUUUCUGCAGCGCCUAUC----------GCAAAUGGAAGCAGU----UCAUCCAAAAUAUUGCUCCCAUAAAGCGAAAUAUGACCCAUAAUUGUCAUAU
.......(((.(..(.....)..).)))..((----------((..((((.((((((----...........)))))).))))...)))).(((((((........))))))) ( -25.30)
>DroSim_CAF1 40050 99 - 1
UCAAAUUGGCACGACUUUCUGCAGCACCUAUC----------GCAAAUGGAAGCAGU----UCAUCCAAAAUAUUGCUCCCAUAAAGCCAUAUAUGACCCAUUAUUGUCAUAU
......((((.............((.......----------))..((((.((((((----...........)))))).))))...)))).(((((((........))))))) ( -22.10)
>DroEre_CAF1 54939 99 - 1
UCAAUUUGGCACGACUUUCUGCACCGCCUAUC----------GCAAAUGGAAGCAGU----UCAUCCGAAAAAUUGCUCCCCUAAAACCACAUAUGACCCAUAAUAGUCAUAU
......(((..........(((..........----------)))...((.((((((----(.........))))))).))......))).(((((((........))))))) ( -15.50)
>DroYak_CAF1 55074 99 - 1
UCAAUUUAGCUCGACUUUCUGCAACGCCUAUC----------GCAAAUGGAAGCAGU----UCAUCCAAAAUAUUGCUUCCAUAAAAGCACAUAUGACCCAUAAUUGUCAUAU
........(((........(((..........----------))).(((((((((((----...........)))))))))))...)))..(((((((........))))))) ( -22.90)
>DroAna_CAF1 41568 100 - 1
UCAAAUUGGCACGACUUUCUGCAGCUUCUAUAUGAAUAUGAAGCAAGUAAAAGCAUUAAACUCAUCCAGCUCAUUGCAAACAAACAGCU------GAG-----GUUAUCAU--
............((((((..((.((((((((....))).)))))..((((.(((..............)))..)))).........)).------)))-----))).....-- ( -15.74)
>consensus
UCAAAUUGGCACGACUUUCUGCAGCGCCUAUC__________GCAAAUGGAAGCAGU____UCAUCCAAAAUAUUGCUCCCAUAAAGCCACAUAUGACCCAUAAUUGUCAUAU
........(((........)))........................((((.((((((...............)))))).))))........(((((((........))))))) ( -9.46 = -11.21 +   1.75)

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 10:50:59 2006