Locus 8499

Sequence ID X_DroMel_CAF1
Location 21,067,127 – 21,067,352
Length 225
Max. P 0.932861
window13990 window13991 window13992 window13993 window13994

overview

Window 0

Location 21,067,127 – 21,067,240
Length 113
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 85.92
Mean single sequence MFE -37.63
Consensus MFE -23.28
Energy contribution -24.73
Covariance contribution 1.45
Combinations/Pair 1.09
Mean z-score -2.59
Structure conservation index 0.62
SVM decision value 0.09
SVM RNA-class probability 0.580830
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21067127 113 + 22224390
UGGA-------UGUAGGAGCCCUUGUUCCAUUUUUGGCCAUUACCUUUGGCAGUUGCGCCUGGAAAUGACAUUUUCACAUCAUUUGCUGAUGUGCCAAAUGUGUCGUCUGGCUAUCCAGC
((((-------(...(((((....)))))......(((((...((...(((......))).))..(((((((...(((((((.....)))))))......))))))).)))))))))).. ( -37.80)
>DroEre_CAF1 37632 115 + 1
UGCGUGUCCUGUGCAGCACCCCUUGGCCCGUUUUUGGCCAUUACCUUUGGCAGUUGCGCCUGGAAAUGACAUUUUCACAUCAUUUGCUGAUGUGGCAAAUG-----UCUGGCUCUCCAGC
.((...(((.(((((((...((.(((((.......)))))........))..)))))))..)))...(((((((((((((((.....)))))))).)))))-----))..))........ ( -38.90)
>DroYak_CAF1 40995 108 + 1
UGGC-------UGCAGGACCCCUUGUCCCGUUUUUGCCCAUUACCUUUGGCAGUUGCGCCUGGAAAUGACAUUUUCACAUCAUUUGCUGAUGUGGCAAAUG-----UCUGGCUAUCCAGU
.(((-------....((((.....)))).((..(((((.(......).)))))..)))))((((...(((((((((((((((.....)))))))).)))))-----))......)))).. ( -36.20)
>consensus
UGGA_______UGCAGGACCCCUUGUCCCGUUUUUGGCCAUUACCUUUGGCAGUUGCGCCUGGAAAUGACAUUUUCACAUCAUUUGCUGAUGUGGCAAAUG_____UCUGGCUAUCCAGC
((((........(((((.((....)).)).......((((.......))))...)))(((.(((.....(((((((((((((.....)))))))).))))).....))))))..)))).. (-23.28 = -24.73 +   1.45)

alignment

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secondary structure

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Window 1

Location 21,067,127 – 21,067,240
Length 113
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.92
Mean single sequence MFE -38.77
Consensus MFE -24.63
Energy contribution -24.63
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.49
Structure conservation index 0.64
SVM decision value 0.97
SVM RNA-class probability 0.891643
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21067127 113 - 22224390
GCUGGAUAGCCAGACGACACAUUUGGCACAUCAGCAAAUGAUGUGAAAAUGUCAUUUCCAGGCGCAACUGCCAAAGGUAAUGGCCAAAAAUGGAACAAGGGCUCCUACA-------UCCA
...((((((((.......((((((..(((((((.....))))))).))))))...(((((((((....))))...(((....))).....)))))....)))).....)-------))). ( -35.00)
>DroEre_CAF1 37632 115 - 1
GCUGGAGAGCCAGA-----CAUUUGCCACAUCAGCAAAUGAUGUGAAAAUGUCAUUUCCAGGCGCAACUGCCAAAGGUAAUGGCCAAAAACGGGCCAAGGGGUGCUGCACAGGACACGCA
.(((((((....((-----(((((..(((((((.....))))))).))))))).)))))))((((..(((((...)))..(((((.......)))))))..)))).((.........)). ( -43.10)
>DroYak_CAF1 40995 108 - 1
ACUGGAUAGCCAGA-----CAUUUGCCACAUCAGCAAAUGAUGUGAAAAUGUCAUUUCCAGGCGCAACUGCCAAAGGUAAUGGGCAAAAACGGGACAAGGGGUCCUGCA-------GCCA
..((((......((-----(((((..(((((((.....))))))).)))))))...))))(((((...((((...))))....)).....((((((.....))))))..-------))). ( -38.20)
>consensus
GCUGGAUAGCCAGA_____CAUUUGCCACAUCAGCAAAUGAUGUGAAAAUGUCAUUUCCAGGCGCAACUGCCAAAGGUAAUGGCCAAAAACGGGACAAGGGGUCCUGCA_______CCCA
.((((....))))......(((((..(((((((.....))))))).)))))(((((.((.((((....))))...)).)))))..................................... (-24.63 = -24.63 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,067,160 – 21,067,272
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.94
Mean single sequence MFE -34.43
Consensus MFE -25.55
Energy contribution -25.00
Covariance contribution -0.55
Combinations/Pair 1.12
Mean z-score -2.20
Structure conservation index 0.74
SVM decision value 0.68
SVM RNA-class probability 0.822266
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21067160 112 + 22224390
UUACCUUUGGCAGUUGCGCCUGGAAAUGACAUUUUCACAUCAUUUGCUGAUGUGCCAAAUGUGUCGUCUGGCUAUCCAGCUAUCCAGCUAUCCAUCU--------CGUUAGCUCUCGAGC
.........((....))((.((((.(((((((...(((((((.....)))))))......))))))).(((((....))))))))))).......((--------((........)))). ( -28.70)
>DroEre_CAF1 37672 115 + 1
UUACCUUUGGCAGUUGCGCCUGGAAAUGACAUUUUCACAUCAUUUGCUGAUGUGGCAAAUG-----UCUGGCUCUCCAGCUCUUCGGCUCUUCGGCUCUUCAGCUGUUUAGCUCUGGGGC
...((...(((......))).))....(((((((((((((((.....)))))))).)))))-----))(((....)))(((((..((((...(((((....)))))...))))..))))) ( -40.10)
>DroYak_CAF1 41028 115 + 1
UUACCUUUGGCAGUUGCGCCUGGAAAUGACAUUUUCACAUCAUUUGCUGAUGUGGCAAAUG-----UCUGGCUAUCCAGUUCUCCAGCUCUUCAGCUCUUCAGCGCUUCAGCUCUCGAGC
.....(((((.(((((((((((((...(((((((((((((((.....)))))))).)))))-----))......)))))......((((....)))).....))))...)))).))))). ( -34.50)
>consensus
UUACCUUUGGCAGUUGCGCCUGGAAAUGACAUUUUCACAUCAUUUGCUGAUGUGGCAAAUG_____UCUGGCUAUCCAGCUCUCCAGCUCUUCAGCUCUUCAGC_CUUUAGCUCUCGAGC
....((..((.(((((.(((.(((.....(((((((((((((.....)))))))).))))).....)))))).....((((....))))...................)))))))..)). (-25.55 = -25.00 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,067,160 – 21,067,272
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.94
Mean single sequence MFE -36.43
Consensus MFE -26.29
Energy contribution -27.07
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -2.68
Structure conservation index 0.72
SVM decision value 1.22
SVM RNA-class probability 0.932861
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21067160 112 - 22224390
GCUCGAGAGCUAACG--------AGAUGGAUAGCUGGAUAGCUGGAUAGCCAGACGACACAUUUGGCACAUCAGCAAAUGAUGUGAAAAUGUCAUUUCCAGGCGCAACUGCCAAAGGUAA
.((((........))--------)).(((.((((((((..(((((...((((((.......))))))...))))).((((((((....)))))))))))))......))))))....... ( -32.10)
>DroEre_CAF1 37672 115 - 1
GCCCCAGAGCUAAACAGCUGAAGAGCCGAAGAGCCGAAGAGCUGGAGAGCCAGA-----CAUUUGCCACAUCAGCAAAUGAUGUGAAAAUGUCAUUUCCAGGCGCAACUGCCAAAGGUAA
((.((.(.(((...(((((...(.((......)))....)))))...)))).((-----(((((..(((((((.....))))))).))))))).......)).))...((((...)))). ( -36.60)
>DroYak_CAF1 41028 115 - 1
GCUCGAGAGCUGAAGCGCUGAAGAGCUGAAGAGCUGGAGAACUGGAUAGCCAGA-----CAUUUGCCACAUCAGCAAAUGAUGUGAAAAUGUCAUUUCCAGGCGCAACUGCCAAAGGUAA
(((....)))....(((((....((((....))))(((((..(((....)))((-----(((((..(((((((.....))))))).))))))).))))).)))))...((((...)))). ( -40.60)
>consensus
GCUCGAGAGCUAAAG_GCUGAAGAGCUGAAGAGCUGGAGAGCUGGAUAGCCAGA_____CAUUUGCCACAUCAGCAAAUGAUGUGAAAAUGUCAUUUCCAGGCGCAACUGCCAAAGGUAA
(((....)))......................((((((((.((((....))))......(((((..(((((((.....))))))).)))))...))))).((((....))))...))).. (-26.29 = -27.07 +   0.78)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,067,240 – 21,067,352
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 76.88
Mean single sequence MFE -33.20
Consensus MFE -23.73
Energy contribution -24.30
Covariance contribution 0.57
Combinations/Pair 1.21
Mean z-score -1.42
Structure conservation index 0.71
SVM decision value 0.33
SVM RNA-class probability 0.691289
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21067240 112 - 22224390
UUUUGGGAGUGGCAUUUUGGGCGUUUUUGUAAAUUUCUGGCUACACAGAGAGAAGCGAUACGGGGAGACACUGGCAAAAAGCUCGAGAGCUAACG--------AGAUGGAUAGCUGGAUA
(((((....((((.((((((((.(((((((...((((((......)))))).........((((....).)))))))))))))))))))))).))--------))).............. ( -32.50)
>DroEre_CAF1 37747 109 - 1
-----------GCGAUUUGGGCGUUUUUGUGAGUUUCUGGCUACACAGAGAGAAGCGAUACAGGGACACACUGGCAAAAGGCCCCAGAGCUAAACAGCUGAAGAGCCGAAGAGCCGAAGA
-----------....(((.((((((((((((.((((((..((....))..))))))..)))))))))............(((.(...((((....))))...).))).....))).))). ( -30.80)
>DroYak_CAF1 41103 119 - 1
UU-UGGGGGUGGCAUUUUGGGUGUUUUUGUGAAUUUCUGGCUACACAGAGAGAAGCGAUACCGGGAGACACUGGCGAAAAGCUCGAGAGCUGAAGCGCUGAAGAGCUGAAGAGCUGGAGA
((-((..((((...((((.((((((...((...((((((......))))))...)))))))).)))).))))..))))...(((.((..((..(((........)))..))..)).))). ( -36.30)
>consensus
UU_UGGG_GUGGCAUUUUGGGCGUUUUUGUGAAUUUCUGGCUACACAGAGAGAAGCGAUACAGGGAGACACUGGCAAAAAGCUCGAGAGCUAAAG_GCUGAAGAGCUGAAGAGCUGGAGA
.........((((.((((((((.(((((((...((((((......)))))).........((((....).))))))))))))))))))))))............................ (-23.73 = -24.30 +   0.57)

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 13:05:57 2006