Locus 8277

Sequence ID X_DroMel_CAF1
Location 20,584,134 – 20,584,275
Length 141
Max. P 0.986031
window13591 window13592 window13593

overview

Window 1

Location 20,584,134 – 20,584,241
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 88.76
Mean single sequence MFE -29.10
Consensus MFE -24.56
Energy contribution -24.53
Covariance contribution -0.03
Combinations/Pair 1.14
Mean z-score -1.81
Structure conservation index 0.84
SVM decision value 0.33
SVM RNA-class probability 0.691517
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20584134 107 - 22224390
--CUUUGCAGGUCAAAUGUUUCUUAUGAAUCGAUUUUUCGAUGGCGAAUUUAUAACAUUUGGCCUGAAAGUGAUAGAUUAUAUGGAGACCGAUCAGGAAGAUCGCAUGG-----------
--((((.(((((((((((((....((..(((((....))))).....))....))))))))))))))))).............(....)(((((.....))))).....----------- ( -30.00)
>DroVir_CAF1 203278 109 - 1
UGUUGCAUAGGUCAAAUGUUUCUUAUGAAUCGAUUUUUCGAUGGCGAAUUUAUGACAUUUGGCUUGGAUGUGAUAGAUUAUAUGGAGACCGAUCAGGAAGAUCGCAUGG-----------
(((..(((.(((((((((((....((..(((((....))))).....))....)))))))))))...)))..)))........(....)(((((.....))))).....----------- ( -28.70)
>DroPse_CAF1 188028 106 - 1
---UUUGCAGGUCAAAUGUUUCUUAUGAAUCGAUUUUUCGAUGGCGAAUUUAUGACAUUUGGCCUGGAUGUGAUAGAUUAUAUGGAGACCGAUCAAGAAGACCGCAUGG-----------
---..(((.((((....(.(((....))).)((((((((.(((...(((((((.((((((.....)))))).))))))).))).))))..)))).....)))))))...----------- ( -27.50)
>DroGri_CAF1 183205 109 - 1
CGUUGCAUAGGUCAAAUGUUUCUUAUGAAUAAAUUUUUCGAUGGCGAAUUUAUGACAUUUGGCUUGGAUGUGAUAGAUUAUAUGGAGACCGAUCAGGAAGAUCGCAUGG-----------
...(((...((((((((..(((....)))...)))).((.(((...(((((((.((((((.....)))))).))))))).))).))))))((((.....)))))))...----------- ( -27.80)
>DroSim_CAF1 168319 118 - 1
--CUUUGCAGGUCAAAUGUUUCUUAUGAAUCGAUUUUUCGAUGGCGAAUUUAUGACAUUUGGCCUGAAAGUGAUAGAUUAUAUGGAGACCGAUCAGGAAGAUCGCAUGGAUCCGNNNNNN
--((((.(((((((((((((....((..(((((....))))).....))....))))))))))))))))).............(((..((((((.....)))))...)..)))....... ( -34.40)
>DroWil_CAF1 189176 108 - 1
-CAAACGCAGGUCAAAUGUUUCUUAUGAAUCGAUUUUUCGAUGGCGAAUUUAUGACAUUUGGCUUAGAUGUGAUAGAUUAUAUGGAGACCGAUCAGGAAGAUCGUAUGG-----------
-((.((...((((............((.(((((....)))))..))(((((((.(((((((...))))))).))))))).......))))((((.....)))))).)).----------- ( -26.20)
>consensus
__CUUCGCAGGUCAAAUGUUUCUUAUGAAUCGAUUUUUCGAUGGCGAAUUUAUGACAUUUGGCCUGGAUGUGAUAGAUUAUAUGGAGACCGAUCAGGAAGAUCGCAUGG___________
.......(((((((((((((....((..(((((....))))).....))....)))))))))))))...(((...........(....)(((((.....))))))))............. (-24.56 = -24.53 +  -0.03)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,584,163 – 20,584,275
Length 112
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 75.98
Mean single sequence MFE -14.40
Consensus MFE -8.10
Energy contribution -8.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.65
Structure conservation index 0.56
SVM decision value 0.34
SVM RNA-class probability 0.697830
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20584163 112 + 22224390
UAAUCUAUCACUUUCAGGCCAAAUGUUAUAAAUUCGCCAUCGAAAAAUCGAUUCAUAAGAAACAUUUGACCUGCAAAG---GAACCACAAAAAAGAU--ACAAAUCAGCACCAAAGA-
...(((.((.((((((((.((((((((...........(((((....)))))((....)))))))))).)))).))))---))...........(((--....)))........)))- ( -20.40)
>DroVir_CAF1 203307 101 + 1
UAAUCUAUCACAUCCAAGCCAAAUGUCAUAAAUUCGCCAUCGAAAAAUCGAUUCAUAAGAAACAUUUGACCUAUGCAACAAGAACGACAUAUA-------C--A-------CACAGA-
.................((.....((((....(((...(((((....)))))......))).....))))....)).................-------.--.-------......- (  -8.30)
>DroPse_CAF1 188057 106 + 1
UAAUCUAUCACAUCCAGGCCAAAUGUCAUAAAUUCGCCAUCGAAAAAUCGAUUCAUAAGAAACAUUUGACCUGCAAA----GAAACACAAACAGAAU--UUAGAUC-----CAAUUC-
..............((((.(((((((......(((...(((((....)))))......)))))))))).))))....----................--.......-----......- ( -14.50)
>DroWil_CAF1 189205 102 + 1
UAAUCUAUCACAUCUAAGCCAAAUGUCAUAAAUUCGCCAUCGAAAAAUCGAUUCAUAAGAAACAUUUGACCUGCGUUUG--AAAGAACAAAGAAGAC--------------CAGAGAA
...(((......(((..(((((((((......(((...(((((....)))))......))))))))))....))((((.--...))))..)))....--------------...))). ( -13.92)
>DroMoj_CAF1 252474 94 + 1
UAAUCUAUCACAUCCAAGCCAAAUGUCAUAAAUUCACCAUCGAAAAAUCGAUUCAUAAGAAACAUUUGACCUGCGAAACGAAAACAACAAAUU-----------------------A-
............((((.(.(((((((.............((((....))))(((....)))))))))).).)).)).................-----------------------.- (  -9.80)
>DroAna_CAF1 160954 117 + 1
UAAUCUAUCACAUCCAGGCCAAAUGUCAUAAAUUCGCCAUCGAAAAAUCGAUUCAUAAGAAACAUUUGACCUGAAAAAGGUGAAACAAAAACAAAAUGUAGCAAUUAGCAAGUCAGC-
.......((((...((((.(((((((......(((...(((((....)))))......)))))))))).))))......)))).................((.....))........- ( -19.50)
>consensus
UAAUCUAUCACAUCCAAGCCAAAUGUCAUAAAUUCGCCAUCGAAAAAUCGAUUCAUAAGAAACAUUUGACCUGCAAAA___GAACCACAAACAA_AU______A_______CAAAGA_
...................(((((((.............((((....))))(((....)))))))))).................................................. ( -8.10 =  -8.10 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,584,163 – 20,584,275
Length 112
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 75.98
Mean single sequence MFE -26.48
Consensus MFE -21.15
Energy contribution -20.82
Covariance contribution -0.33
Combinations/Pair 1.15
Mean z-score -2.56
Structure conservation index 0.80
SVM decision value 2.03
SVM RNA-class probability 0.986031
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20584163 112 - 22224390
-UCUUUGGUGCUGAUUUGU--AUCUUUUUUGUGGUUC---CUUUGCAGGUCAAAUGUUUCUUAUGAAUCGAUUUUUCGAUGGCGAAUUUAUAACAUUUGGCCUGAAAGUGAUAGAUUA
-.....(((((......))--))).........((..---((((.(((((((((((((....((..(((((....))))).....))....)))))))))))))))))..))...... ( -31.00)
>DroVir_CAF1 203307 101 - 1
-UCUGUG-------U--G-------UAUAUGUCGUUCUUGUUGCAUAGGUCAAAUGUUUCUUAUGAAUCGAUUUUUCGAUGGCGAAUUUAUGACAUUUGGCUUGGAUGUGAUAGAUUA
-......-------.--.-------............((((..(((.(((((((((((....((..(((((....))))).....))....)))))))))))...)))..)))).... ( -23.90)
>DroPse_CAF1 188057 106 - 1
-GAAUUG-----GAUCUAA--AUUCUGUUUGUGUUUC----UUUGCAGGUCAAAUGUUUCUUAUGAAUCGAUUUUUCGAUGGCGAAUUUAUGACAUUUGGCCUGGAUGUGAUAGAUUA
-(((((.-----......)--))))....(.((((..----..(.(((((((((((((....((..(((((....))))).....))....))))))))))))).)...)))).)... ( -26.50)
>DroWil_CAF1 189205 102 - 1
UUCUCUG--------------GUCUUCUUUGUUCUUU--CAAACGCAGGUCAAAUGUUUCUUAUGAAUCGAUUUUUCGAUGGCGAAUUUAUGACAUUUGGCUUAGAUGUGAUAGAUUA
.......--------------...........(((.(--((.....((((((((((((....((..(((((....))))).....))....)))))))))))).....))).)))... ( -22.00)
>DroMoj_CAF1 252474 94 - 1
-U-----------------------AAUUUGUUGUUUUCGUUUCGCAGGUCAAAUGUUUCUUAUGAAUCGAUUUUUCGAUGGUGAAUUUAUGACAUUUGGCUUGGAUGUGAUAGAUUA
-(-----------------------(((((((..(.......((.(((((((((((((..((((..(((((....))))).))))......))))))))))))))).)..)))))))) ( -25.80)
>DroAna_CAF1 160954 117 - 1
-GCUGACUUGCUAAUUGCUACAUUUUGUUUUUGUUUCACCUUUUUCAGGUCAAAUGUUUCUUAUGAAUCGAUUUUUCGAUGGCGAAUUUAUGACAUUUGGCCUGGAUGUGAUAGAUUA
-((......))(((..((........))..)))..((((....(((((((((((((((....((..(((((....))))).....))....))))))))))))))).))))....... ( -29.70)
>consensus
_UCUGUG_______U______AU_UUAUUUGUGGUUC___UUUCGCAGGUCAAAUGUUUCUUAUGAAUCGAUUUUUCGAUGGCGAAUUUAUGACAUUUGGCCUGGAUGUGAUAGAUUA
.............................................(((((((((((((....((..(((((....))))).....))....))))))))))))).............. (-21.15 = -20.82 +  -0.33)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:59 2006