Locus 5101

Sequence ID 3R_DroMel_CAF1
Location 13,443,793 – 13,443,943
Length 150
Max. P 0.985225
window8314 window8315 window8316

overview

Window 4

Location 13,443,793 – 13,443,910
Length 117
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 82.71
Mean single sequence MFE -33.90
Consensus MFE -30.30
Energy contribution -30.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.44
Structure conservation index 0.89
SVM decision value 2.00
SVM RNA-class probability 0.985225
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13443793 117 + 27905053
ACGUGCAGUUGACCGUUGAACAAC-AAAAUAACACAGCUGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCAUAAC
.....((((((....(((.....)-)).......))))))((((((((((((.......)))))((..((((((.......)))))).))..............)))))))....... ( -35.30)
>DroPse_CAF1 22865 102 + 1
AUAUU----------------GAUAAAAAAAGGUUAGCUGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCUUGCC
.....----------------..........(((.((..(((((((((((((.......)))))((..((((((.......)))))).))..............)))))))))).))) ( -33.60)
>DroSec_CAF1 12937 98 + 1
-----------------AAAAAAA---AAUAAUACAGCUGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCAUAAC
-----------------.......---............(((((((((((((.......)))))((..((((((.......)))))).))..............))))))))...... ( -30.30)
>DroSim_CAF1 12606 100 + 1
-----------------AAAAAAA-AAAGUAAUACAGCUGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCAUAAA
-----------------.......-..(((......)))(((((((((((((.......)))))((..((((((.......)))))).))..............))))))))...... ( -30.50)
>DroEre_CAF1 12940 114 + 1
AUGUG--GUUGAACG--GAACGACAAAAGUAAUACAGCUGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCAUGCA
.(((.--(((.....--.))).)))...........((((((((((((((((.......)))))((..((((((.......)))))).))..............))))))).)).)). ( -37.90)
>DroYak_CAF1 17169 109 + 1
AUGUG--GUUGAA-------CGACAAAAGUAAUAUAGCUGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCAUGCA
.(((.--(.....-------).)))...........((((((((((((((((.......)))))((..((((((.......)))))).))..............))))))).)).)). ( -35.80)
>consensus
AUGUG_____________AACAAC_AAAAUAAUACAGCUGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCAUAAA
.......................................(((((((((((((.......)))))((..((((((.......)))))).))..............))))))))...... (-30.30 = -30.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,443,793 – 13,443,910
Length 117
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 82.71
Mean single sequence MFE -35.17
Consensus MFE -32.40
Energy contribution -32.57
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.92
SVM decision value 0.44
SVM RNA-class probability 0.737435
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13443793 117 - 27905053
GUUAUGAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCAGCUGUGUUAUUUU-GUUGUUCAACGGUCAACUGCACGU
....((.((((((((.......(((.....(((((((.......)))))))..)))(((.......))).))))))))))...((((....((-(((....)))))......)))).. ( -38.70)
>DroPse_CAF1 22865 102 - 1
GGCAAGAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCAGCUAACCUUUUUUUAUC----------------AAUAU
((..((.((((((((.......(((.....(((((((.......)))))))..)))(((.......))).))))))))...))..))..........----------------..... ( -34.00)
>DroSec_CAF1 12937 98 - 1
GUUAUGAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCAGCUGUAUUAUU---UUUUUUU-----------------
....((.((((((((.......(((.....(((((((.......)))))))..)))(((.......))).))))))))))...........---.......----------------- ( -33.10)
>DroSim_CAF1 12606 100 - 1
UUUAUGAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCAGCUGUAUUACUUU-UUUUUUU-----------------
....((.((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))))).............-.......----------------- ( -33.10)
>DroEre_CAF1 12940 114 - 1
UGCAUGAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCAGCUGUAUUACUUUUGUCGUUC--CGUUCAAC--CACAU
.((.((.((((((((.......(((.....(((((((.......)))))))..)))(((.......))).))))))))))))...........(((.(((.--.....)))--.))). ( -36.70)
>DroYak_CAF1 17169 109 - 1
UGCAUGAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCAGCUAUAUUACUUUUGUCG-------UUCAAC--CACAU
.((.((.((((((((.......(((.....(((((((.......)))))))..)))(((.......))).))))))))))))................-------......--..... ( -35.40)
>consensus
GGCAUGAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCAGCUGUAUUACUUU_GUCGUU_____________CACAU
....((.((((((((.......(((.....(((((((.......)))))))..)))(((.......))).))))))))))...................................... (-32.40 = -32.57 +   0.17)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,443,830 – 13,443,943
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.94
Mean single sequence MFE -36.58
Consensus MFE -29.75
Energy contribution -29.92
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 0.81
SVM decision value 0.75
SVM RNA-class probability 0.841961
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13443830 113 + 27905053
UGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCAUAACGAGUA-------GGCAGCUGUUCGCCAGUUUCCAACUAGG
.(((((((((((((.......)))))((..((((((.......)))))).))..............)))))))).....(.(((.-------((.(((((.....))))).)).))).). ( -39.10)
>DroPse_CAF1 22887 120 + 1
UGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCUUGCCGAGUCAUGCCCAGAUAACAGUUUUCUAUAUGUGAGCCAAA
.(((((((((((((.......)))))((..((((((.......)))))).))..............)))))))).............((.((.(((..((....)).))).)).)).... ( -33.40)
>DroEre_CAF1 12974 113 + 1
UGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCAUGCAAGAAU-------CGCCGCUGCUUGCAAGUUUCGAUCUAUG
.(((((((((((((.......)))))((..((((((.......)))))).))..............))))))))..((((((...-------........)))))).............. ( -36.20)
>DroYak_CAF1 17198 113 + 1
UGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCAUGCAGAGUU-------CGCGGCUGUUAGCCUCUUUCGAACUGAG
.(((((((((((((.......)))))((..((((((.......)))))).))..............)))))))).......((((-------((.(((.....))).....))))))... ( -39.70)
>DroAna_CAF1 9852 112 + 1
CGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCGCAUGGAC-GUC-------UGCUGCAUUUUUUCAGUUUUGUGCCAGA
..((((((((((((.......)))))((..((((((.......)))))).))..............)))))))...(((((-(..-------.((((........))))..))).))).. ( -37.60)
>DroPer_CAF1 16383 120 + 1
CGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCUUGCCGAGUCAUGCCCAGAUAACAGUUUUCUAUAUGUGAGCCAAA
.(((((((((((((.......)))))((..((((((.......)))))).))..............)))))))).............((.((.(((..((....)).))).)).)).... ( -33.50)
>consensus
UGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCAUGCAGAGUC_______GGCAGCAGUUUGCCAGUUUCGAGCCAAA
.(((((((((((((.......)))))((..((((((.......)))))).))..............)))))))).............................................. (-29.75 = -29.92 +   0.17)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:13 2006