Locus 4831

Sequence ID X_DroMel_CAF1
Location 12,545,887 – 12,546,083
Length 196
Max. P 0.986820
window7894 window7895 window7896 window7897

overview

Window 4

Location 12,545,887 – 12,546,005
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.80
Mean single sequence MFE -53.50
Consensus MFE -39.43
Energy contribution -39.22
Covariance contribution -0.21
Combinations/Pair 1.19
Mean z-score -1.66
Structure conservation index 0.74
SVM decision value -0.03
SVM RNA-class probability 0.518777
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12545887 118 + 22224390
GCAGCCGCUUUGGCCACCUUUUCACCGGCAGCCGUUGCUUCGACAGCCUUAGUGGCGGCGCUUGCCUUUUCGGCGGCACUUUCAGCCGCUUUG-GCAGCAUCAGCUGCCGCUUUCUCU-G
(((((.(((...(((...........)))))).))))).....(((....((((((((((((.(((.....((((((.......))))))..)-)))))....)))))))))....))-) ( -48.20)
>DroPse_CAF1 55268 118 + 1
GCGGCUGCCUUGGCCACCUUCUCGCUGACGACAAUGGCCUCGACCGCCUUGGUGACGGCGCUGGCCUUCUCAGCGGCACUUUCGGCCGCCUUG-GCGGCAUCGGCGGCAGCCUUCUCG-G
..(((((((...(((......(((((((.((....((((.....((((..(....)))))..)))).)))))))))........(((((....-)))))...))))))))))......-. ( -56.00)
>DroPer_CAF1 54577 120 + 1
GCGGCUGCCUUGGCCACCUUCUCGCUGACGACAAUGGCCUCGACCGCCUUGGUGACGGCGCUGGCCUUCUCAGCGGCACUUUCGGCCGCCUUGGGCGGCAUCGGCGGCAGCCUUCUCGGG
..(((((((...(((......(((((((.((....((((.....((((..(....)))))..)))).)))))))))........((((((...))))))...))))))))))........ ( -56.30)
>consensus
GCGGCUGCCUUGGCCACCUUCUCGCUGACGACAAUGGCCUCGACCGCCUUGGUGACGGCGCUGGCCUUCUCAGCGGCACUUUCGGCCGCCUUG_GCGGCAUCGGCGGCAGCCUUCUCG_G
((.((((((..((((......(((((((.((....((((.....((((........))))..)))).))))))))).......))))(((......)))...)))))).))......... (-39.43 = -39.22 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,545,887 – 12,546,005
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.80
Mean single sequence MFE -59.80
Consensus MFE -47.91
Energy contribution -47.03
Covariance contribution -0.87
Combinations/Pair 1.25
Mean z-score -3.27
Structure conservation index 0.80
SVM decision value 2.06
SVM RNA-class probability 0.986820
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12545887 118 - 22224390
C-AGAGAAAGCGGCAGCUGAUGCUGC-CAAAGCGGCUGAAAGUGCCGCCGAAAAGGCAAGCGCCGCCACUAAGGCUGUCGAAGCAACGGCUGCCGGUGAAAAGGUGGCCAAAGCGGCUGC
.-.........((((((....)))))-)...(((((((.....((((((.....(((....)))..((((..(((.((((......)))).)))))))....)))))).....))))))) ( -53.90)
>DroPse_CAF1 55268 118 - 1
C-CGAGAAGGCUGCCGCCGAUGCCGC-CAAGGCGGCCGAAAGUGCCGCUGAGAAGGCCAGCGCCGUCACCAAGGCGGUCGAGGCCAUUGUCGUCAGCGAGAAGGUGGCCAAGGCAGCCGC
.-......(((((((..((..(((((-(..(((((((....).))))))..((.(((....))).)).....)))))))).(((((((.(((....)))...)))))))..))))))).. ( -63.20)
>DroPer_CAF1 54577 120 - 1
CCCGAGAAGGCUGCCGCCGAUGCCGCCCAAGGCGGCCGAAAGUGCCGCUGAGAAGGCCAGCGCCGUCACCAAGGCGGUCGAGGCCAUUGUCGUCAGCGAGAAGGUGGCCAAGGCAGCCGC
........(((((((..((..((((((...(((((((....).))))))..((.(((....))).)).....)))))))).(((((((.(((....)))...)))))))..))))))).. ( -62.30)
>consensus
C_CGAGAAGGCUGCCGCCGAUGCCGC_CAAGGCGGCCGAAAGUGCCGCUGAGAAGGCCAGCGCCGUCACCAAGGCGGUCGAGGCCAUUGUCGUCAGCGAGAAGGUGGCCAAGGCAGCCGC
........((((((((((...(((......(((((((....).)))))).....)))...(((((((.....))))).)).))).......((((.(.....).))))...))))))).. (-47.91 = -47.03 +  -0.87)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,545,927 – 12,546,044
Length 117
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 82.62
Mean single sequence MFE -57.23
Consensus MFE -40.93
Energy contribution -41.83
Covariance contribution 0.90
Combinations/Pair 1.18
Mean z-score -2.12
Structure conservation index 0.72
SVM decision value 0.71
SVM RNA-class probability 0.829438
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12545927 117 - 22224390
GUGAGCGUGCGGAACGUGCCGCCGAGCGUGAGCGUGUGGCAGAGAAAGCGGCAGCUGAUGCUGCCAAAGCGGCUGAAAGUGCCGCCGAAAAGGCAAGCGCCGCCACUAAGGCUGUCG
(((.(((.(((.....((((((((.((....))...)))).........((((((....))))))...(((((.......)))))......))))..)))))))))........... ( -52.70)
>DroYak_CAF1 1156 117 - 1
GUGAGCGUGCCGAGCGUGCUGCCGAGCGGGAACGGGUGGCGGAGAAGGCGGCUGCGGAUGCUGCCAAGGCGGCCGAAAGUGCCGCCGAGAAGGCAAGCGCCGCUAGCAAGGCUGUCG
..((.((.(((..((.(.((((((..((....))..))))))...).)).(((((((.(((((((..(((((((....).)))))).....))).)))))))).)))..))))))). ( -60.60)
>DroMoj_CAF1 1054 117 - 1
GCGAACGGGCCGAGCGUGCCGCCGAACGGGAACGCGUCGCCGAGAAGGCAGCCGCUGAUGCCGCCAAGGCGGCCGAGUGUGCCGCCGAGAAGGCGAGCGCCGUUAGCAAAGCUGCCG
.......(((.((((((.(((.....)))..)))).))))).....((((((.(((((((((((....)))))...(.((((((((.....)))).)))))))))))...)))))). ( -58.40)
>consensus
GUGAGCGUGCCGAGCGUGCCGCCGAGCGGGAACGCGUGGCAGAGAAGGCGGCAGCUGAUGCUGCCAAGGCGGCCGAAAGUGCCGCCGAGAAGGCAAGCGCCGCUAGCAAGGCUGUCG
((.((((.((...((.((((((((..((....))..))))......((((((.......))))))..(((((((....).)))))).....)))).)))))))).)).......... (-40.93 = -41.83 +   0.90)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,545,967 – 12,546,083
Length 116
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 83.22
Mean single sequence MFE -55.10
Consensus MFE -37.35
Energy contribution -37.30
Covariance contribution -0.05
Combinations/Pair 1.29
Mean z-score -1.91
Structure conservation index 0.68
SVM decision value 0.09
SVM RNA-class probability 0.577054
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12545967 116 - 22224390
AACAAAAGUCCGGCGGUCGUUCAUCCGCCGUUGCUGAGCGUGAGCGUGCGGAACGUGCCGCCGAGCGUGAGCGUGUGGCAGAGAAAGCGGCAGCUGAUGCUGCCAAAGCGGCUGAA
......((((((((((........))))))..(((..((....))..((......((((((...((....))..))))))......))((((((....))))))..)))))))... ( -52.30)
>DroVir_CAF1 1247 116 - 1
AACAGAAAUCCGGCAAUCGUUCCAGCGCCGUCGCUGAACGCGAACGUGCCGAACGCGCCGCCGAACGGGAGCGUGUCGCCGAAAAGGCCGCCGCCGAUGCGGCCAAGGCGGCCGAA
..........(((((.((((..(((((....)))))...))))...)))))..((.((((((...(((((.....)).)))....((((((.......))))))..)))))))).. ( -51.80)
>DroSec_CAF1 9843 116 - 1
AGCAAAAGUCCGGCGGUCGUUCAUCCGCCGUUGCCGAGCGUGAGCGUGCGGAACGGGCCGCCGAGCGGGAGCGCGUGGCGGAGAAAGCGGCAGCGGAUGCCGCCAAGGCGGCAGAA
.......(((((((((........)))))((((((..((....))..((........((((((.(((....))).)))))).....))))))))))))(((((....))))).... ( -61.82)
>DroSim_CAF1 8101 116 - 1
AGCAAAAGUCCGGCGGUCGUUCAUCCGCCGUUUUCGAGCGUGAGCGUGCGGAACGGGCCGCCGAGCGGGAGCGUGUGGCGGAGAAAGCGGCAGCGGAUGCCGCCAAGGCGGCAGAA
.......(((((.(.((((((..(((.((((((.((.((....))...))))))))(((((...((....))..))))))))...)))))).))))))(((((....))))).... ( -57.50)
>DroYak_CAF1 1196 116 - 1
AGCAAAAGUCCGGCGGUCGCUCAUCCGCCGUUGCCGAGCGUGAGCGUGCCGAGCGUGCUGCCGAGCGGGAACGGGUGGCGGAGAAGGCGGCUGCGGAUGCUGCCAAGGCGGCCGAA
.......(((((.((((((((..(((((((((.(((..((..(((((((...)))))))..))..))).)))....))))))...)))))))))))))(((((....))))).... ( -59.40)
>DroMoj_CAF1 1094 116 - 1
AACAAAAGUCCGGUAAUCGCUCCAGCGCCGUGGCGGAACGCGAACGGGCCGAGCGUGCCGCCGAACGGGAACGCGUCGCCGAGAAGGCAGCCGCUGAUGCCGCCAAGGCGGCCGAG
..........((((....((..((((((((((((((.((((...........)))).)))))..))))....((...(((.....))).)))))))..))(((....))))))).. ( -47.80)
>consensus
AACAAAAGUCCGGCGGUCGUUCAUCCGCCGUUGCCGAGCGUGAGCGUGCCGAACGUGCCGCCGAGCGGGAGCGUGUGGCGGAGAAAGCGGCAGCGGAUGCCGCCAAGGCGGCCGAA
.......(((((((((((((((....((((((((.....)))).)).)).))))).))))))).(((....)))((.((.......)).))....)))(((((....))))).... (-37.35 = -37.30 +  -0.05)

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 11:34:07 2006