Locus 4806

Sequence ID 3L_DroMel_CAF1
Location 13,433,685 – 13,433,882
Length 197
Max. P 0.988250
window7573 window7574 window7575 window7576

overview

Window 3

Location 13,433,685 – 13,433,802
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.00
Mean single sequence MFE -39.10
Consensus MFE -35.53
Energy contribution -36.52
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.28
Structure conservation index 0.91
SVM decision value 1.62
SVM RNA-class probability 0.967751
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13433685 117 + 23771897
UCAUUACGGCAGCCAUCUUUUAUGGUGCCUCCGCCAAAGUAUCCAGCAUUAGUUUAUGUGUUAUUUGCCCACCCAUAUGGAUGUUGGCUUUUGGGGAGGCAGGGCGUAC---UACAUCAC
....((((.(.(((((.....)))))((((((.((((((...((((((((....((((.((.........)).))))..)))))))).))))))))))))..).)))).---........ ( -39.60)
>DroSim_CAF1 32755 117 + 1
UCAUUACGGCAGCCAUCUUUUAUGGUGCCUCCGCCAAAGUAUCCAGCAUUAGUUUAUGUGUUAUUUGCCCACCCAUAUGGAUGUUGGCUUUUGGGGAGGCAGGGCGUAC---UACACACC
....((((.(.(((((.....)))))((((((.((((((...((((((((....((((.((.........)).))))..)))))))).))))))))))))..).)))).---........ ( -39.60)
>DroEre_CAF1 31967 114 + 1
UCAUUACGGCAGCCAUCUUUUAUGGUGCCUCCGCCAAAGUAUCCAGCAUUAGUUUAUGUGUUAUUUGCCCACCCAUAUGGAUGUUGGCUUUUGGGGAGGCAGG------GCGUACAUACC
....((((.(.(((((.....)))))((((((.((((((...((((((((....((((.((.........)).))))..)))))))).))))))))))))..)------.))))...... ( -39.60)
>DroYak_CAF1 31226 120 + 1
UCAUUACGGCAGCCAUCUUUUAUGGUGCCUCCGCCAAAGUAUCCAGCAUUAGUUUAUGUGUUAUUUGCCCACCCAUAUGGAUGUUGGCUUUUGGGGAGGCAGGACGUACGCGUACAUAGC
....((((...(((((.....)))))((((((.((((((...((((((((....((((.((.........)).))))..)))))))).))))))))))))....))))............ ( -37.60)
>consensus
UCAUUACGGCAGCCAUCUUUUAUGGUGCCUCCGCCAAAGUAUCCAGCAUUAGUUUAUGUGUUAUUUGCCCACCCAUAUGGAUGUUGGCUUUUGGGGAGGCAGGGCGUAC___UACAUACC
....((((.(.(((((.....)))))((((((.((((((...((((((((....((((.((.........)).))))..)))))))).))))))))))))..).))))............ (-35.53 = -36.52 +   1.00)

alignment

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secondary structure

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Window 4

Location 13,433,685 – 13,433,802
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.00
Mean single sequence MFE -36.65
Consensus MFE -32.56
Energy contribution -33.12
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -2.33
Structure conservation index 0.89
SVM decision value 1.51
SVM RNA-class probability 0.959891
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13433685 117 - 23771897
GUGAUGUA---GUACGCCCUGCCUCCCCAAAAGCCAACAUCCAUAUGGGUGGGCAAAUAACACAUAAACUAAUGCUGGAUACUUUGGCGGAGGCACCAUAAAAGAUGGCUGCCGUAAUGA
.....(((---(.......((((((((((((.(((..(((((....))))))))......(((((......))).)).....))))).)))))))((((.....))))))))........ ( -35.10)
>DroSim_CAF1 32755 117 - 1
GGUGUGUA---GUACGCCCUGCCUCCCCAAAAGCCAACAUCCAUAUGGGUGGGCAAAUAACACAUAAACUAAUGCUGGAUACUUUGGCGGAGGCACCAUAAAAGAUGGCUGCCGUAAUGA
((((((..---.)))))).((((((((((((.(((..(((((....))))))))......(((((......))).)).....))))).)))))))((((.....))))............ ( -37.50)
>DroEre_CAF1 31967 114 - 1
GGUAUGUACGC------CCUGCCUCCCCAAAAGCCAACAUCCAUAUGGGUGGGCAAAUAACACAUAAACUAAUGCUGGAUACUUUGGCGGAGGCACCAUAAAAGAUGGCUGCCGUAAUGA
((((.......------..((((((((((((.(((..(((((....))))))))......(((((......))).)).....))))).)))))))((((.....)))).))))....... ( -36.60)
>DroYak_CAF1 31226 120 - 1
GCUAUGUACGCGUACGUCCUGCCUCCCCAAAAGCCAACAUCCAUAUGGGUGGGCAAAUAACACAUAAACUAAUGCUGGAUACUUUGGCGGAGGCACCAUAAAAGAUGGCUGCCGUAAUGA
......((((.(((.....((((((((((((.(((..(((((....))))))))......(((((......))).)).....))))).)))))))((((.....)))).))))))).... ( -37.40)
>consensus
GGUAUGUA___GUACGCCCUGCCUCCCCAAAAGCCAACAUCCAUAUGGGUGGGCAAAUAACACAUAAACUAAUGCUGGAUACUUUGGCGGAGGCACCAUAAAAGAUGGCUGCCGUAAUGA
((((...............((((((((((((.(((..(((((....))))))))......(((((......))).)).....))))).)))))))((((.....)))).))))....... (-32.56 = -33.12 +   0.56)

alignment

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secondary structure

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Window 5

Location 13,433,725 – 13,433,842
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.58
Mean single sequence MFE -38.80
Consensus MFE -37.83
Energy contribution -37.45
Covariance contribution -0.38
Combinations/Pair 1.06
Mean z-score -2.26
Structure conservation index 0.97
SVM decision value 2.11
SVM RNA-class probability 0.988250
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13433725 117 - 23771897
AUGCAGGAGUGCCUCUGAUUUAUGCGGGGGCACAUACAUGGUGAUGUA---GUACGCCCUGCCUCCCCAAAAGCCAACAUCCAUAUGGGUGGGCAAAUAACACAUAAACUAAUGCUGGAU
..(((((.(((((((((.......))))))))).(((((....)))))---......)))))....(((...(((..(((((....))))))))........(((......))).))).. ( -38.40)
>DroSim_CAF1 32795 117 - 1
AUGCAGGAGUGCCUCUGAUUUAUGCGGGGGCACAUACAUGGGUGUGUA---GUACGCCCUGCCUCCCCAAAAGCCAACAUCCAUAUGGGUGGGCAAAUAACACAUAAACUAAUGCUGGAU
..(((((((((((((((.......)))))))))...((.(((((((..---.)))))))))..)))......(((..(((((....))))))))..................)))..... ( -39.70)
>DroEre_CAF1 32007 114 - 1
AUGCAGGAGUGCCUCUGAUUUAUGCGGGGGCACAUACGUGGGUAUGUACGC------CCUGCCUCCCCAAAAGCCAACAUCCAUAUGGGUGGGCAAAUAACACAUAAACUAAUGCUGGAU
..(((((.(((((((((.......)))))))((((((....))))))..))------)))))....(((...(((..(((((....))))))))........(((......))).))).. ( -38.00)
>DroYak_CAF1 31266 120 - 1
AUGCAGGAGUGCCUCUGAUUUAUGCGGGGGCACAUACAUGGCUAUGUACGCGUACGUCCUGCCUCCCCAAAAGCCAACAUCCAUAUGGGUGGGCAAAUAACACAUAAACUAAUGCUGGAU
..(((((((((((((((.......))))))))).(((((....)))))........))))))....(((...(((..(((((....))))))))........(((......))).))).. ( -39.10)
>consensus
AUGCAGGAGUGCCUCUGAUUUAUGCGGGGGCACAUACAUGGGUAUGUA___GUACGCCCUGCCUCCCCAAAAGCCAACAUCCAUAUGGGUGGGCAAAUAACACAUAAACUAAUGCUGGAU
..(((((.(((((((((.......))))))))).(((((....))))).........)))))....(((...(((..(((((....))))))))........(((......))).))).. (-37.83 = -37.45 +  -0.38)

alignment

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secondary structure

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Window 6

Location 13,433,765 – 13,433,882
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.66
Mean single sequence MFE -40.45
Consensus MFE -38.03
Energy contribution -38.65
Covariance contribution 0.62
Combinations/Pair 1.06
Mean z-score -1.82
Structure conservation index 0.94
SVM decision value 1.28
SVM RNA-class probability 0.939461
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13433765 117 - 23771897
CUCAAGACUUGUGAGAACAACCCAAGGACAAGGCUGGGUCAUGCAGGAGUGCCUCUGAUUUAUGCGGGGGCACAUACAUGGUGAUGUA---GUACGCCCUGCCUCCCCAAAAGCCAACAU
.......((((.(........))))).....(((((((....(((((.(((((((((.......))))))))).(((((....)))))---......)))))...)))...))))..... ( -38.70)
>DroSim_CAF1 32835 116 - 1
CUCAAGACUUGUGA-AACAACACAAGGACAAGGCUGGGUCAUGCAGGAGUGCCUCUGAUUUAUGCGGGGGCACAUACAUGGGUGUGUA---GUACGCCCUGCCUCCCCAAAAGCCAACAU
.......((((((.-.....)))))).....(((((((....(((((.(((((((((.......))))))))).(((((....)))))---......)))))...)))...))))..... ( -43.60)
>DroEre_CAF1 32047 114 - 1
CUUAAGACUUGUGAGAACAACACAAGGACGAGGCCGGGUCAUGCAGGAGUGCCUCUGAUUUAUGCGGGGGCACAUACGUGGGUAUGUACGC------CCUGCCUCCCCAAAAGCCAACAU
.......((((((.......))))))...(((((.(((((((((.(..(((((((((.......)))))))))...)....)))))...))------)).)))))............... ( -41.60)
>DroYak_CAF1 31306 120 - 1
CUUAAGACUUGCGAGAACAACACAAGGACGAGGCCGGGUCAUGCAGGAGUGCCUCUGAUUUAUGCGGGGGCACAUACAUGGCUAUGUACGCGUACGUCCUGCCUCCCCAAAAGCCAACAU
.......((((.(.......).)))).....(((.(((....(((((((((((((((.......))))))))).(((((....)))))........))))))...)))....)))..... ( -37.90)
>consensus
CUCAAGACUUGUGAGAACAACACAAGGACAAGGCCGGGUCAUGCAGGAGUGCCUCUGAUUUAUGCGGGGGCACAUACAUGGGUAUGUA___GUACGCCCUGCCUCCCCAAAAGCCAACAU
.......((((((.......)))))).....(((((((....(((((.(((((((((.......))))))))).(((((....))))).........)))))...)))...))))..... (-38.03 = -38.65 +   0.62)

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 11:33:54 2006