Locus 4268

Sequence ID 2R_DroMel_CAF1
Location 14,078,476 – 14,078,633
Length 157
Max. P 0.863282
window6849 window6850 window6851

overview

Window 9

Location 14,078,476 – 14,078,595
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.87
Mean single sequence MFE -42.73
Consensus MFE -39.25
Energy contribution -39.03
Covariance contribution -0.22
Combinations/Pair 1.09
Mean z-score -2.09
Structure conservation index 0.92
SVM decision value 0.76
SVM RNA-class probability 0.842661
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14078476 119 + 20766785
CUUUAAUGCCCCGGCGACAAAGUGUCUUAUGUCCACAGACAUAGCCGUAAUUU-UCUGCAGCGGCUUCAGGUGUCCGCUUCGCACCUGGGGCAAGCAGCAAAAGCCGGCAAUUUAUGGCC
......((((.(((((((.....))).((((((....))))))))))...(((-(((((....(((((((((((.......)))))))))))..)))).))))...)))).......... ( -44.10)
>DroSim_CAF1 3027 119 + 1
CUUUAAUGCCCCGGCGACAAAGUGUCUUAUGUCCACAGACAUAGCCGUAAUUU-UCUGCAGCGACUUCAGGUGUCCGCUUCGCACCUGGGGCAAGCACCCAAAGCCGCCCAUUUAUGGCC
.......(((.(((((((.....))).((((((....))))))))))......-......(((.(((..(((((..((((((....))))))..)))))..))).)))........))). ( -37.90)
>DroYak_CAF1 3667 120 + 1
CUUUAAUGCCCCGGCGACAAAGUGUCUUGUGUCCACAGACGCAGCCGUAAUUUUUGUGCAGCGGCUUCAGGUGUCCGCUUCGCACCUGGGGCAAGCACCCAAAGCCGGCAAUUUAUGGCG
.......(((.(((((((.....))).((((((....)))))))))).........(((..((((((..(((((..((((((....))))))..)))))..)))))))))......))). ( -46.20)
>consensus
CUUUAAUGCCCCGGCGACAAAGUGUCUUAUGUCCACAGACAUAGCCGUAAUUU_UCUGCAGCGGCUUCAGGUGUCCGCUUCGCACCUGGGGCAAGCACCCAAAGCCGGCAAUUUAUGGCC
...........(((((((.....))).((((((....))))))))))........((((....(((((((((((.......)))))))))))..)))).....((((........)))). (-39.25 = -39.03 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,078,476 – 14,078,595
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.87
Mean single sequence MFE -46.10
Consensus MFE -40.53
Energy contribution -40.53
Covariance contribution 0.00
Combinations/Pair 1.06
Mean z-score -2.15
Structure conservation index 0.88
SVM decision value 0.52
SVM RNA-class probability 0.766261
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14078476 119 - 20766785
GGCCAUAAAUUGCCGGCUUUUGCUGCUUGCCCCAGGUGCGAAGCGGACACCUGAAGCCGCUGCAGA-AAAUUACGGCUAUGUCUGUGGACAUAAGACACUUUGUCGCCGGGGCAUUAAAG
.(((.....((((((((((((((((((((((....).)).)))))).))...)))))))..)))).-......((((((((((....)))))).(((.....))))))).)))....... ( -44.90)
>DroSim_CAF1 3027 119 - 1
GGCCAUAAAUGGGCGGCUUUGGGUGCUUGCCCCAGGUGCGAAGCGGACACCUGAAGUCGCUGCAGA-AAAUUACGGCUAUGUCUGUGGACAUAAGACACUUUGUCGCCGGGGCAUUAAAG
.(((.......((((((((..((((..(((..(......)..)))..))))..)))))))).....-......((((((((((....)))))).(((.....))))))).)))....... ( -47.80)
>DroYak_CAF1 3667 120 - 1
CGCCAUAAAUUGCCGGCUUUGGGUGCUUGCCCCAGGUGCGAAGCGGACACCUGAAGCCGCUGCACAAAAAUUACGGCUGCGUCUGUGGACACAAGACACUUUGUCGCCGGGGCAUUAAAG
.(((......(((((((((..((((..(((..(......)..)))..))))..))))))..))).........((((((.(((....))).)).(((.....))))))).)))....... ( -45.60)
>consensus
GGCCAUAAAUUGCCGGCUUUGGGUGCUUGCCCCAGGUGCGAAGCGGACACCUGAAGCCGCUGCAGA_AAAUUACGGCUAUGUCUGUGGACAUAAGACACUUUGUCGCCGGGGCAUUAAAG
.(((.......(.((((((..((((..(((..(......)..)))..))))..))))))).............((((((((((....)))))).(((.....))))))).)))....... (-40.53 = -40.53 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,078,516 – 14,078,633
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 92.72
Mean single sequence MFE -42.97
Consensus MFE -36.66
Energy contribution -37.11
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -2.56
Structure conservation index 0.85
SVM decision value 0.84
SVM RNA-class probability 0.863282
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14078516 117 + 20766785
AUAGCCGUAAUUU-UCUGCAGCGGCUUCAGGUGUCCGCUUCGCACCUGGGGCAAGCAGCAAAAGCCGGCAAUUUAUGGCCGGCCUGACACAAUUUCAUAAGGCCCC-AAAAGGCUC-CAU
...((((...(((-(((((....(((((((((((.......)))))))))))..)))).))))..)))).......(((((((((..............)))))..-....)))).-... ( -42.94)
>DroSim_CAF1 3067 116 + 1
AUAGCCGUAAUUU-UCUGCAGCGACUUCAGGUGUCCGCUUCGCACCUGGGGCAAGCACCCAAAGCCGCCCAUUUAUGGCCGGCCUGACACAAUUUCAUAAGGCCCC-A-AAGGCUC-CAU
..(((((((....-..))).(((.(((..(((((..((((((....))))))..)))))..))).))).......(((..(((((..............)))))))-)-..)))).-... ( -35.54)
>DroYak_CAF1 3707 120 + 1
GCAGCCGUAAUUUUUGUGCAGCGGCUUCAGGUGUCCGCUUCGCACCUGGGGCAAGCACCCAAAGCCGGCAAUUUAUGGCGGGCCUGACACAAUUUCAUAAGGCCCCCAAAAGGCUCGCAU
((((((..........(((..((((((..(((((..((((((....))))))..)))))..))))))))).....(((.((((((..............)))))))))...)))).)).. ( -50.44)
>consensus
AUAGCCGUAAUUU_UCUGCAGCGGCUUCAGGUGUCCGCUUCGCACCUGGGGCAAGCACCCAAAGCCGGCAAUUUAUGGCCGGCCUGACACAAUUUCAUAAGGCCCC_AAAAGGCUC_CAU
..((((.........((((....(((((((((((.......)))))))))))..)))).....((((........)))).(((((..............))))).......))))..... (-36.66 = -37.11 +   0.45)

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 11:15:45 2006