Locus 1861

Sequence ID X_DroMel_CAF1
Location 5,132,692 – 5,132,842
Length 150
Max. P 0.594592
window3026 window3027 window3028

overview

Window 6

Location 5,132,692 – 5,132,804
Length 112
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 78.83
Mean single sequence MFE -29.54
Consensus MFE -15.84
Energy contribution -16.72
Covariance contribution 0.88
Combinations/Pair 1.05
Mean z-score -1.84
Structure conservation index 0.54
SVM decision value 0.10
SVM RNA-class probability 0.581113
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5132692 112 + 22224390
UUGUGCAGUUUAUCAAUCUCGAAUUUGAUUUCCUAGUGUGAAAUCUGACACGCGAUUCGCAUCAUUGCGAUUCGAUUGU-UGAGCACCAUGUGACAAAUUCGUCCAAUGGCAC
..((((.(((((.(((((.................(((((........)))))((.(((((....))))).))))))).-)))))..(((..(((......)))..))))))) ( -32.60)
>DroVir_CAF1 17416 86 + 1
UCAAUGAGUUUAUCAAUUU-AAAUUUGAUUCGGUUGUGUGAAAAUCGACACGCGGCU--------------------AU-UUGGCGCUGCGUGACAAAUUUGCACAG-----C
.....(((((((......)-))))))......((((((..((......((((((((.--------------------..-.....)))))))).....))..)))))-----) ( -25.80)
>DroSec_CAF1 8915 112 + 1
UUGUGCAGUUUAUCAAUCUCGAAUUUGAUUUCCUAGUGUGAAAUCUGACACGCGAUUCGCAUCAUUGCGAUUCGAUUGU-UGGGCACCAUGUGACAAAUUCGUCCAAUGGCAC
..((((.(((((.(((((.................(((((........)))))((.(((((....))))).))))))).-)))))..(((..(((......)))..))))))) ( -31.70)
>DroSim_CAF1 8684 112 + 1
UUGUGCAGUUUAUCAAUCUCGAAUUUGAUUUCCUAGUGUGAAAUCUGACACGCGAUUCGCAUCAUUGCGAUUCGAUUGU-UGGGCACCAUGUGACAAAUUCGUCCAAUGGCAC
..((((.(((((.(((((.................(((((........)))))((.(((((....))))).))))))).-)))))..(((..(((......)))..))))))) ( -31.70)
>DroYak_CAF1 9814 113 + 1
UUGAGCAGUUUAUCAAUCUGGAAUUUGAUUUCCUAGUGUGAAAUCUGACACGCGAUCCGCAUCAUUGCAAUUCGAUUGUUUGGGGACUAUGUGACAAAUUCGUCCUAUGGCAC
(..(((((((.(((.....((((......))))..(((((........))))))))..(((....))).....)))))))..).(.(((((.(((......))).)))))).. ( -25.90)
>consensus
UUGUGCAGUUUAUCAAUCUCGAAUUUGAUUUCCUAGUGUGAAAUCUGACACGCGAUUCGCAUCAUUGCGAUUCGAUUGU_UGGGCACCAUGUGACAAAUUCGUCCAAUGGCAC
....................(((((((........(((((........)))))((.(((((....))))).)).....................)))))))............ (-15.84 = -16.72 +   0.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,132,692 – 5,132,804
Length 112
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 78.83
Mean single sequence MFE -26.89
Consensus MFE -14.74
Energy contribution -17.34
Covariance contribution 2.60
Combinations/Pair 1.24
Mean z-score -1.77
Structure conservation index 0.55
SVM decision value -0.02
SVM RNA-class probability 0.522594
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5132692 112 - 22224390
GUGCCAUUGGACGAAUUUGUCACAUGGUGCUCA-ACAAUCGAAUCGCAAUGAUGCGAAUCGCGUGUCAGAUUUCACACUAGGAAAUCAAAUUCGAGAUUGAUAAACUGCACAA
(..((((..((((....))))..))))..)(((-(...((((((.....(((((((.....)))))))((((((.......))))))..))))))..))))............ ( -30.70)
>DroVir_CAF1 17416 86 - 1
G-----CUGUGCAAAUUUGUCACGCAGCGCCAA-AU--------------------AGCCGCGUGUCGAUUUUCACACAACCGAAUCAAAUUU-AAAUUGAUAAACUCAUUGA
.-----.((((.(((.(((.(((((.((.....-..--------------------.)).))))).))).))))))).......(((((....-...)))))........... ( -20.20)
>DroSec_CAF1 8915 112 - 1
GUGCCAUUGGACGAAUUUGUCACAUGGUGCCCA-ACAAUCGAAUCGCAAUGAUGCGAAUCGCGUGUCAGAUUUCACACUAGGAAAUCAAAUUCGAGAUUGAUAAACUGCACAA
(..((((..((((....))))..))))..)...-.(((((((.(((((....))))).)).((.((..((((((.......))))))..)).)).)))))............. ( -29.60)
>DroSim_CAF1 8684 112 - 1
GUGCCAUUGGACGAAUUUGUCACAUGGUGCCCA-ACAAUCGAAUCGCAAUGAUGCGAAUCGCGUGUCAGAUUUCACACUAGGAAAUCAAAUUCGAGAUUGAUAAACUGCACAA
(..((((..((((....))))..))))..)...-.(((((((.(((((....))))).)).((.((..((((((.......))))))..)).)).)))))............. ( -29.60)
>DroYak_CAF1 9814 113 - 1
GUGCCAUAGGACGAAUUUGUCACAUAGUCCCCAAACAAUCGAAUUGCAAUGAUGCGGAUCGCGUGUCAGAUUUCACACUAGGAAAUCAAAUUCCAGAUUGAUAAACUGCUCAA
(.((....((((..............)))).....((((((((((....(((((((.....)))))))((((((.......)))))).)))))..))))).......)).).. ( -24.34)
>consensus
GUGCCAUUGGACGAAUUUGUCACAUGGUGCCCA_ACAAUCGAAUCGCAAUGAUGCGAAUCGCGUGUCAGAUUUCACACUAGGAAAUCAAAUUCGAGAUUGAUAAACUGCACAA
(((((((..((((....))))..))))))).....(((((((.(((((....))))).))........((((((.......))))))........)))))............. (-14.74 = -17.34 +   2.60)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,132,727 – 5,132,842
Length 115
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 75.22
Mean single sequence MFE -33.55
Consensus MFE -11.30
Energy contribution -12.86
Covariance contribution 1.56
Combinations/Pair 1.27
Mean z-score -1.77
Structure conservation index 0.34
SVM decision value 0.12
SVM RNA-class probability 0.594592
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5132727 115 + 22224390
GUGUGAAAUCUGACACGCGAUUCGCAUCAUUGCGAUUCGAUUGU-UGAGCACCAUGUGACAAAUUCGUCCAAUGGCACGAAUAAUACCACCAUUUUUGC-UGGCAACAU-GCCACGCC
(((((...((.((((..(((.(((((....))))).)))..)))-)))....(((((.....((((((((...)).))))))....(((.((....)).-)))..))))-).))))). ( -32.60)
>DroVir_CAF1 17450 91 + 1
GUGUGAAAAUCGACACGCGGCU--------------------AU-UUGGCGCUGCGUGACAAAUUUGCACAG-----CCAGCGAGAUCGGAAUUCGGUCGGGGCGCCAC-GCGGUGCC
(((..((......((((((((.--------------------..-.....)))))))).....))..)))..-----.......(((((.....)))))..((((((..-..)))))) ( -34.80)
>DroSec_CAF1 8950 115 + 1
GUGUGAAAUCUGACACGCGAUUCGCAUCAUUGCGAUUCGAUUGU-UGGGCACCAUGUGACAAAUUCGUCCAAUGGCACGAAUAAUACCUCCAUUUUUGC-UGCCAACAU-GCUACGCC
(((((...((..(((..(((.(((((....))))).)))..)))-..))...((((((((......)))...(((((((((.............)))).-)))))))))-).))))). ( -34.72)
>DroSim_CAF1 8719 115 + 1
GUGUGAAAUCUGACACGCGAUUCGCAUCAUUGCGAUUCGAUUGU-UGGGCACCAUGUGACAAAUUCGUCCAAUGGCACGAAUAAUACCUCCAUUUUUGC-UGCCAACAU-GCCACGCC
(((((...((..(((..(((.(((((....))))).)))..)))-..))...((((((((......)))...(((((((((.............)))).-)))))))))-).))))). ( -36.82)
>DroYak_CAF1 9849 117 + 1
GUGUGAAAUCUGACACGCGAUCCGCAUCAUUGCAAUUCGAUUGUUUGGGGACUAUGUGACAAAUUCGUCCUAUGGCACGAAUAAUACCUCCAUUUCUGC-UGCCAACAUAGCCACGCC
((((....((.((((..(((...(((....)))...)))..)))).))((.(((((((((......)))...(((((((((............))).).-))))))))))))))))). ( -28.80)
>consensus
GUGUGAAAUCUGACACGCGAUUCGCAUCAUUGCGAUUCGAUUGU_UGGGCACCAUGUGACAAAUUCGUCCAAUGGCACGAAUAAUACCUCCAUUUUUGC_UGCCAACAU_GCCACGCC
(((((........(((((((.(((((....))))).)))......((.....))))))....(((((((.....).))))))..............................))))). (-11.30 = -12.86 +   1.56)

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 10:20:29 2006