Locus 6332

Sequence ID 3R_DroMel_CAF1
Location 16,573,968 – 16,574,112
Length 144
Max. P 0.934823
window10325 window10326

overview

Window 5

Location 16,573,968 – 16,574,072
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.09
Mean single sequence MFE -25.41
Consensus MFE -13.90
Energy contribution -14.30
Covariance contribution 0.40
Combinations/Pair 1.28
Mean z-score -2.05
Structure conservation index 0.55
SVM decision value 1.24
SVM RNA-class probability 0.934823
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16573968 104 - 27905053
CAGUGUAGUAAUUUCGGAAAUAGUCAAGAUCGUUCAGAACGAAAAGG------AGCUCCAAGCGAAGGCACAUAAAAUGAAGAGAUGAAUUGCUA-CACCUAC--AGAUCGUU-------
..(((((((((((.((....(..(((...((((.....))))...((------....))..((....))........)))..)..))))))))))-)))....--........------- ( -22.50)
>DroSec_CAF1 130174 113 - 1
CAGCUGUGUUAUUUCGGAAAUAGUUAAGAUCUUUCAGAAGGAAAAGGAGCAGGAGCUCCAAGCGAAGGCACAUAAAAUGAAGAGAUGAAAUGCUGUUAUCUACACAAAUAGUU-------
....(((((......(((((((((....((((((((.........(((((....)))))..((....))........)).)))))).....)))))).)))))))).......------- ( -26.50)
>DroSim_CAF1 134524 113 - 1
CAGCUGUGUAAUUUCGGAAAUAGUUAAGAUCCUUCAGAAGGAAAAGGAGCAGGAGCUCCAAGCGAAGGCACAUAAAAUGAAGAGAUGAAAUGCUGUUAUCUACACCAAUAGUU-------
.((((((........(((((((((....((((((((.........(((((....)))))..((....))........))))).))).....)))))).)))......))))))------- ( -28.44)
>DroEre_CAF1 134281 120 - 1
CGGCAGUGUAAUUGCCGAAAUACUUAAGAUCCUGCAGAGCGAAAAGGAGCAGGAGCUCCAAAGGAAGACACAUAAAAUGAACAAAUGAAAUACGGUUAUCUAAACCAACAGAUCGUUUAC
(((((((...)))))))...................((((((...(((((....)))))..................................((((.....))))......)))))).. ( -26.10)
>DroYak_CAF1 130300 104 - 1
CGGCAGUGUAAUUGCCGAAAUAGUUAAGAUCCUUCAAAAGGAAAAGGAGCAGGAGCUCCAAAGGAAGACACAUAAAAUGAACAAAUAA--------------AACCUACAGAUUAUUU--
(((((((...)))))))((((((((....((((.....))))...(((((....))))).............................--------------........))))))))-- ( -23.50)
>consensus
CAGCAGUGUAAUUUCGGAAAUAGUUAAGAUCCUUCAGAAGGAAAAGGAGCAGGAGCUCCAAGCGAAGGCACAUAAAAUGAAGAGAUGAAAUGCUGUUAUCUACACCAAUAGUU_______
.....((((..(((((.............((((.....))))...(((((....)))))...)))))))))................................................. (-13.90 = -14.30 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,573,998 – 16,574,112
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.25
Mean single sequence MFE -30.32
Consensus MFE -22.38
Energy contribution -22.66
Covariance contribution 0.28
Combinations/Pair 1.32
Mean z-score -1.92
Structure conservation index 0.74
SVM decision value 0.51
SVM RNA-class probability 0.762313
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16573998 114 - 27905053
UGGCCGUAUUGGAGAAUGGCAAGCCAAUGAAAAUGCUGGACAGUGUAGUAAUUUCGGAAAUAGUCAAGAUCGUUCAGAACGAAAAGG------AGCUCCAAGCGAAGGCACAUAAAAUGA
..(((...((((((..((((.......(((((.(((((.......))))).)))))......))))...((((.....)))).....------..)))))).....)))........... ( -25.12)
>DroSec_CAF1 130207 120 - 1
UGGCCGUUUUGGAGAAUGGCAAGCCAAUGAAGAUGCUGGACAGCUGUGUUAUUUCGGAAAUAGUUAAGAUCUUUCAGAAGGAAAAGGAGCAGGAGCUCCAAGCGAAGGCACAUAAAAUGA
..(((((((....)))))))...((..(((((((.((....((((((.((......)).)))))).))))).))))...))....(((((....)))))..((....))........... ( -30.60)
>DroSim_CAF1 134557 120 - 1
UGGCUGUUUUGGAGAAUGGCAAGCCAAUGAAGAUGCUGGACAGCUGUGUAAUUUCGGAAAUAGUUAAGAUCCUUCAGAAGGAAAAGGAGCAGGAGCUCCAAGCGAAGGCACAUAAAAUGA
((((((((((.((((.(((....)))........(((....))).......)))).))))))))))...((((.....))))...(((((....)))))..((....))........... ( -34.20)
>DroEre_CAF1 134321 120 - 1
UAGCCGUUUUGGAGAAGGGCAAGCCGAUGAAAAUGCUGGACGGCAGUGUAAUUGCCGAAAUACUUAAGAUCCUGCAGAGCGAAAAGGAGCAGGAGCUCCAAAGGAAGACACAUAAAAUGA
..(((.(((....))).)))...((..((....(((.((((((((((...))))))).....(....).))).)))...))....(((((....)))))...))................ ( -31.30)
>DroYak_CAF1 130324 120 - 1
UAGCCGUUUUGGAAAAGGGCAAGCCAAUGAAUAUGCUGGACGGCAGUGUAAUUGCCGAAAUAGUUAAGAUCCUUCAAAAGGAAAAGGAGCAGGAGCUCCAAAGGAAGACACAUAAAAUGA
..((((((..(.(....((....))........).)..)))))).((((.....((.............((((.....))))...(((((....)))))...))...))))......... ( -30.40)
>consensus
UGGCCGUUUUGGAGAAUGGCAAGCCAAUGAAAAUGCUGGACAGCAGUGUAAUUUCGGAAAUAGUUAAGAUCCUUCAGAAGGAAAAGGAGCAGGAGCUCCAAGCGAAGGCACAUAAAAUGA
..(((((((....)))))))..............(((....))).((((..(((((.............((((.....))))...(((((....)))))...)))))))))......... (-22.38 = -22.66 +   0.28)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:53 2006