Locus 3748

Sequence ID 3R_DroMel_CAF1
Location 10,169,570 – 10,169,707
Length 137
Max. P 0.893243
window6007 window6008 window6009

overview

Window 7

Location 10,169,570 – 10,169,683
Length 113
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 87.10
Mean single sequence MFE -45.98
Consensus MFE -38.04
Energy contribution -38.27
Covariance contribution 0.22
Combinations/Pair 1.13
Mean z-score -2.55
Structure conservation index 0.83
SVM decision value 0.98
SVM RNA-class probability 0.893243
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10169570 113 - 27905053
CGU------GUGGCAACGCUCGACGAGCCUGCCAAUUGAGCGGAGCGUGGAGCUCUCAACACGCUUCAGCGAAGCGUGCGGCGGGCAACACGGCGUAUGCGUGUUAUGCCAACUUAAAU
.((------.(((((..((((.(((..((.(((....).))))..))).))))....(((((((....))...(((((((.(((....).)).)))))))))))).)))))))...... ( -49.10)
>DroVir_CAF1 28781 111 - 1
--U------GCAGCAACGCUUGACGAGCCUGCCAAUUGAGCGCAGCGCGAAGCUCUCAACACGCUUCAGCGAAGCGUGCGGCGGGUAACGCUGCGUAUGCGUGUUAUGCCAAAUUAAAU
--.------(((((..((.....)).(((((((..(((((.((........)).)))))((((((((...)))))))).)))))))...)))))(((((.....))))).......... ( -42.60)
>DroGri_CAF1 31217 111 - 1
--U------GCGGCAACGCUUGAUGAGCCUCUCAAUUGAGUGUAGCGCGAAGCUCUCAACACGCUUCACCGAAGCGUGCGGCGGGCAACGCGGCGUAUGCGUGUUAUGCUAACUUAAAU
--.------(((....)))....((((...)))).((((((.(((((((..((((.(..((((((((...))))))))..).))))..))).(((....))).....)))))))))).. ( -43.80)
>DroWil_CAF1 33250 110 - 1
---------GGCGCAACGCUCGACAAGCCUGCCAAUUGAGCGAAGCGCUGAGCUCUCAACACGCUUCAUCGAAGCGUACCGCAGGCAACGCGGCGUAUGCGUGUUCUGCCAAAUUAAAU
---------.(((((((((.((....((((((...(((((...(((.....)))))))).(((((((...)))))))...))))))....)))))).)))))................. ( -42.00)
>DroMoj_CAF1 32354 111 - 1
--U------GCAGCAACGCUUGACGAGCCUGCCAAUUGAGCGCAGCGCGAAGCUCUCAACACGCUUCAGCGAAGCGUUCGGCAGGCAACGCGGCGUAUGCGUGUUAUGCCAAAUUAAAU
--.------(((((((((((.(.((.(((((((....((((((..((((((((.........))))).)))..)))))))))))))..)))))))).))).)))............... ( -45.60)
>DroAna_CAF1 25966 119 - 1
CGAGUGCCCGCGGCAACGCUCGACGAGCCUGCCAAUUGAGCGGAGCGCGGAGCUCUCAACACGCUUCAGCGAAGCGUGCGGCGGGCAACACAGCGUAUGCGUGUUCUGCCAACUCAAAU
.(((.(((((((.(..(((((((...(....)...)))))))..)))))).)).)))..((((((((...)))))))).((((((..((((.((....))))))))))))......... ( -52.80)
>consensus
__U______GCGGCAACGCUCGACGAGCCUGCCAAUUGAGCGCAGCGCGAAGCUCUCAACACGCUUCAGCGAAGCGUGCGGCGGGCAACGCGGCGUAUGCGUGUUAUGCCAAAUUAAAU
............((((((((......(((((((..(((((...(((.....))))))))((((((((...)))))))).))))))).....))))).)))................... (-38.04 = -38.27 +   0.22)

alignment

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secondary structure

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Window 8

Location 10,169,609 – 10,169,707
Length 98
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 76.74
Mean single sequence MFE -34.03
Consensus MFE -23.78
Energy contribution -24.08
Covariance contribution 0.31
Combinations/Pair 1.17
Mean z-score -1.32
Structure conservation index 0.70
SVM decision value 0.65
SVM RNA-class probability 0.811907
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10169609 98 + 27905053
CGCACGCUUCGCUGAAGCGUGUUGAGAGCUCCACGCUCCGCUCAAUUGGCAGGCUCGUCGAGCGUUGCCACACGGCACACACAUCCUACC-----UAUG-----CUCG
.(((((((((...))))))))).(((.((((.(((..(((((.....))).))..))).))))((((((....)))).))..........-----....-----))). ( -35.10)
>DroVir_CAF1 28820 84 + 1
CGCACGCUUCGCUGAAGCGUGUUGAGAGCUUCGCGCUGCGCUCAAUUGGCAGGCUCGUCAAGCGUUGCUGCA-------UAAA------------UUUG-----CUCG
.(((((((((...)))))))))...((((...((((.(((((....((((......))))))))).)).)).-------....------------...)-----))). ( -29.90)
>DroPse_CAF1 31380 101 + 1
CGCACGCUUCGCUGAAGCGUGUUGAGAGCUCUGCGCUCCGCUCAAUUGGCAGGCUCGUCGAGCGUUGCCACA-------GAUAUGUUGCCACGAGUAUGGCAGCCACG
.(((((((((...)))))))))(((((((.....))))...)))..((((((((((...)))).))))))..-------.....(((((((......))))))).... ( -38.90)
>DroWil_CAF1 33289 87 + 1
GGUACGCUUCGAUGAAGCGUGUUGAGAGCUCAGCGCUUCGCUCAAUUGGCAGGCUUGUCGAGCGUUGCGCC------UAAA-AUU----C-----UCAA-----CUUG
...(((((((...)))))))((((((((....((((..(((((.((.((....)).)).)))))..)))).------....-.))----)-----))))-----)... ( -34.20)
>DroMoj_CAF1 32393 84 + 1
CGAACGCUUCGCUGAAGCGUGUUGAGAGCUUCGCGCUGCGCUCAAUUGGCAGGCUCGUCAAGCGUUGCUGCA-------UAAA------------UUUG-----CUCG
.((.(((..(((.(((((.........))))))))..))).))....((((((((.....))).)))))(((-------....------------..))-----)... ( -27.20)
>DroPer_CAF1 31606 101 + 1
CGCACGCUUCGCUGAAGCGUGUUGAGAGCUCUGCGCUCCGCUCAAUUGGCAGGCUCGUCGAGCGUUGCCACA-------GAUAUGUUGCCACGAGUAUGGCAGCCACG
.(((((((((...)))))))))(((((((.....))))...)))..((((((((((...)))).))))))..-------.....(((((((......))))))).... ( -38.90)
>consensus
CGCACGCUUCGCUGAAGCGUGUUGAGAGCUCCGCGCUCCGCUCAAUUGGCAGGCUCGUCGAGCGUUGCCACA_______GAAAU_____C_____UAUG_____CUCG
.(((((((((...)))))))))...((((..........))))...((((((((((...)))).))))))...................................... (-23.78 = -24.08 +   0.31)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,169,609 – 10,169,707
Length 98
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 76.74
Mean single sequence MFE -34.63
Consensus MFE -20.50
Energy contribution -20.62
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -1.85
Structure conservation index 0.59
SVM decision value 0.89
SVM RNA-class probability 0.875417
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10169609 98 - 27905053
CGAG-----CAUA-----GGUAGGAUGUGUGUGCCGUGUGGCAACGCUCGACGAGCCUGCCAAUUGAGCGGAGCGUGGAGCUCUCAACACGCUUCAGCGAAGCGUGCG
...(-----(((.-----((((((.((.(((((((....))).)))).)).....))))))......((((((((((..........)))))))).)).....)))). ( -38.30)
>DroVir_CAF1 28820 84 - 1
CGAG-----CAAA------------UUUA-------UGCAGCAACGCUUGACGAGCCUGCCAAUUGAGCGCAGCGCGAAGCUCUCAACACGCUUCAGCGAAGCGUGCG
...(-----((..------------....-------))).(((.(((((..(..(((((((......).)))).))(((((.........))))).)..)))))))). ( -26.80)
>DroPse_CAF1 31380 101 - 1
CGUGGCUGCCAUACUCGUGGCAACAUAUC-------UGUGGCAACGCUCGACGAGCCUGCCAAUUGAGCGGAGCGCAGAGCUCUCAACACGCUUCAGCGAAGCGUGCG
..(((((((((((...(((....)))...-------)))))))..((((...))))..)))).......(((((.....)))))...((((((((...)))))))).. ( -39.50)
>DroWil_CAF1 33289 87 - 1
CAAG-----UUGA-----G----AAU-UUUA------GGCGCAACGCUCGACAAGCCUGCCAAUUGAGCGAAGCGCUGAGCUCUCAACACGCUUCAUCGAAGCGUACC
...(-----((((-----(----(.(-((..------(((((..(((((((...(....)...)))))))..)))))))).)))))))(((((((...)))))))... ( -36.50)
>DroMoj_CAF1 32393 84 - 1
CGAG-----CAAA------------UUUA-------UGCAGCAACGCUUGACGAGCCUGCCAAUUGAGCGCAGCGCGAAGCUCUCAACACGCUUCAGCGAAGCGUUCG
...(-----((..------------....-------))).(((..((((...)))).))).....((((((..((((((((.........))))).)))..)))))). ( -27.20)
>DroPer_CAF1 31606 101 - 1
CGUGGCUGCCAUACUCGUGGCAACAUAUC-------UGUGGCAACGCUCGACGAGCCUGCCAAUUGAGCGGAGCGCAGAGCUCUCAACACGCUUCAGCGAAGCGUGCG
..(((((((((((...(((....)))...-------)))))))..((((...))))..)))).......(((((.....)))))...((((((((...)))))))).. ( -39.50)
>consensus
CGAG_____CAUA_____G_____AUAUA_______UGUGGCAACGCUCGACGAGCCUGCCAAUUGAGCGGAGCGCGGAGCUCUCAACACGCUUCAGCGAAGCGUGCG
........................................((..(((((((...(....)...)))))))..)).............((((((((...)))))))).. (-20.50 = -20.62 +   0.11)

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 11:09:07 2006