Locus 408

Sequence ID 3R_DroMel_CAF1
Location 1,521,269 – 1,521,393
Length 124
Max. P 0.999544
window666 window667 window668 window669

overview

Window 6

Location 1,521,269 – 1,521,362
Length 93
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 74.85
Mean single sequence MFE -26.70
Consensus MFE -16.55
Energy contribution -16.67
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -1.81
Structure conservation index 0.62
SVM decision value 1.04
SVM RNA-class probability 0.904386
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1521269 93 + 27905053
UAU----------ACCAGAAAG-------------AACAGAUUGCAAGAAGUAAGAAGUAAGUCGUCUGCAAUCUUUAAAGCAGUAGACUGCUUGUUAGUGCAGUGGAUUUCUGCG
...----------..((((((.-------------.((((((((((.((..((.....))..))...))))))))...((((((....)))))).........))...)))))).. ( -24.30)
>DroSec_CAF1 23216 110 + 1
UAUCUUUCCGCGCGCUAGAAAGU-AACGUUUAUUGAAAGGAUAGCAAGAA-----AAGUAGCUCGUCUGCAAUCUUUAAAGCAGUAUACUGCUUGUUAUUGCAGUGGAUUUCUGCU
......(((((..((.....(((-(((.........((((((.(((.((.-----.((...))..))))).)))))).((((((....)))))))))))))).)))))........ ( -27.10)
>DroSim_CAF1 21388 111 + 1
UAUCUUUCCGCGCGCUAGAAAGUCAAAAUUUAUUGAAAGGAUAGCAAGAA-----AAGUAGCUCGUCUGCAAUCUUUAAAGCAGUAUACUGCUUGUUAUUGCAGUGGAACUAUACU
.....((((((..((((.....((((......)))).....)))).....-----............((((((.....((((((....))))))...))))))))))))....... ( -28.70)
>consensus
UAUCUUUCCGCGCGCUAGAAAGU_AA__UUUAUUGAAAGGAUAGCAAGAA_____AAGUAGCUCGUCUGCAAUCUUUAAAGCAGUAUACUGCUUGUUAUUGCAGUGGAUUUCUGCU
.........................................................(((..((..(((((((.....((((((....))))))...)))))))..))....))). (-16.55 = -16.67 +   0.11) 

alignment

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secondary structure

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Window 7

Location 1,521,269 – 1,521,362
Length 93
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 74.85
Mean single sequence MFE -26.97
Consensus MFE -15.71
Energy contribution -16.05
Covariance contribution 0.34
Combinations/Pair 1.13
Mean z-score -3.12
Structure conservation index 0.58
SVM decision value 3.71
SVM RNA-class probability 0.999544
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1521269 93 - 27905053
CGCAGAAAUCCACUGCACUAACAAGCAGUCUACUGCUUUAAAGAUUGCAGACGACUUACUUCUUACUUCUUGCAAUCUGUU-------------CUUUCUGGU----------AUA
.((((.......))))((((..((((((....))))))...((((((((((.(............).)).))))))))...-------------.....))))----------... ( -21.80)
>DroSec_CAF1 23216 110 - 1
AGCAGAAAUCCACUGCAAUAACAAGCAGUAUACUGCUUUAAAGAUUGCAGACGAGCUACUU-----UUCUUGCUAUCCUUUCAAUAAACGUU-ACUUUCUAGCGCGCGGAAAGAUA
(((((.......(((((((...((((((....)))))).....)))))))..(((......-----))))))))...(((((......((((-(.....)))))....)))))... ( -26.80)
>DroSim_CAF1 21388 111 - 1
AGUAUAGUUCCACUGCAAUAACAAGCAGUAUACUGCUUUAAAGAUUGCAGACGAGCUACUU-----UUCUUGCUAUCCUUUCAAUAAAUUUUGACUUUCUAGCGCGCGGAAAGAUA
....((((((..(((((((...((((((....)))))).....)))))))..))))))(((-----(((.(((((.....((((......)))).....)))))...))))))... ( -32.30)
>consensus
AGCAGAAAUCCACUGCAAUAACAAGCAGUAUACUGCUUUAAAGAUUGCAGACGAGCUACUU_____UUCUUGCUAUCCUUUCAAUAAA__UU_ACUUUCUAGCGCGCGGAAAGAUA
.((((((.....(((((((...((((((....)))))).....))))))).((((.............))))........................)))).))............. (-15.71 = -16.05 +   0.34) 

alignment

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secondary structure

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dotplot

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Window 8

Location 1,521,282 – 1,521,393
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.25
Mean single sequence MFE -30.23
Consensus MFE -19.97
Energy contribution -21.17
Covariance contribution 1.20
Combinations/Pair 1.04
Mean z-score -2.02
Structure conservation index 0.66
SVM decision value 0.38
SVM RNA-class probability 0.711375
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1521282 111 + 27905053
ACAGAUUGCAAGAAGUAAGAAGUAAGUCGUCUGCAAUCUUUAAAGCAGUAGACUGCUUGUUAGUGCAGUGGAUUUCUGCGUGAAAAGUGC---UU------CUGCAUCUCUCUCGCACUU
..((((((((.((..((.....))..))...))))))))...((((((....))))))...(((((.(..(....)..)(.((.(..(((---..------..)))..).)).)))))). ( -31.70)
>DroSec_CAF1 23251 115 + 1
AAGGAUAGCAAGAA-----AAGUAGCUCGUCUGCAAUCUUUAAAGCAGUAUACUGCUUGUUAUUGCAGUGGAUUUCUGCUUGAAAAAUUCAGCUUGCAUAGCUUCAUCUCUCUCGCACUU
.......((.(((.-----((((((.((..(((((((.....((((((....))))))...)))))))..))...)))))).........((((.....)))).......))).)).... ( -29.20)
>DroSim_CAF1 21424 115 + 1
AAGGAUAGCAAGAA-----AAGUAGCUCGUCUGCAAUCUUUAAAGCAGUAUACUGCUUGUUAUUGCAGUGGAACUAUACUUGAAAAAUCCUGCUUGUAUAGCUUCUUCUCUCUCGCACUU
.(((((..((((..-----..((((.((..(((((((.....((((((....))))))...)))))))..)).)))).))))....)))))(((.....))).................. ( -29.80)
>consensus
AAGGAUAGCAAGAA_____AAGUAGCUCGUCUGCAAUCUUUAAAGCAGUAUACUGCUUGUUAUUGCAGUGGAUUUCUGCUUGAAAAAUCC_GCUUG_AUAGCUUCAUCUCUCUCGCACUU
.......((.(((......(((((..((..(((((((.....((((((....))))))...)))))))..))....)))))..........(((.....)))........))).)).... (-19.97 = -21.17 +   1.20) 

alignment

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secondary structure

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dotplot

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Window 9

Location 1,521,282 – 1,521,393
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.25
Mean single sequence MFE -32.30
Consensus MFE -23.28
Energy contribution -24.37
Covariance contribution 1.08
Combinations/Pair 1.00
Mean z-score -3.03
Structure conservation index 0.72
SVM decision value 2.05
SVM RNA-class probability 0.986624
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1521282 111 - 27905053
AAGUGCGAGAGAGAUGCAG------AA---GCACUUUUCACGCAGAAAUCCACUGCACUAACAAGCAGUCUACUGCUUUAAAGAUUGCAGACGACUUACUUCUUACUUCUUGCAAUCUGU
...((((.(((((.(((..------..---))).))))).))))..................((((((....))))))...((((((((((.(............).)).)))))))).. ( -28.00)
>DroSec_CAF1 23251 115 - 1
AAGUGCGAGAGAGAUGAAGCUAUGCAAGCUGAAUUUUUCAAGCAGAAAUCCACUGCAAUAACAAGCAGUAUACUGCUUUAAAGAUUGCAGACGAGCUACUU-----UUCUUGCUAUCCUU
....(((((((((..(.((((.......((((((((((.((((((......(((((........)))))...)))))).))))))).)))...)))).)))-----)))))))....... ( -33.00)
>DroSim_CAF1 21424 115 - 1
AAGUGCGAGAGAGAAGAAGCUAUACAAGCAGGAUUUUUCAAGUAUAGUUCCACUGCAAUAACAAGCAGUAUACUGCUUUAAAGAUUGCAGACGAGCUACUU-----UUCUUGCUAUCCUU
....(((((((((((((((((.....)))....)))))).....((((((..(((((((...((((((....)))))).....)))))))..))))))..)-----)))))))....... ( -35.90)
>consensus
AAGUGCGAGAGAGAUGAAGCUAU_CAAGC_GAAUUUUUCAAGCAGAAAUCCACUGCAAUAACAAGCAGUAUACUGCUUUAAAGAUUGCAGACGAGCUACUU_____UUCUUGCUAUCCUU
....((((((((((....(((.....)))......)))).............(((((((...((((((....)))))).....))))))).................))))))....... (-23.28 = -24.37 +   1.08) 

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 09:42:28 2006