Locus 5948

Sequence ID 2L_DroMel_CAF1
Location 16,772,781 – 16,772,941
Length 160
Max. P 0.998076
window9451 window9452 window9453

overview

Window 1

Location 16,772,781 – 16,772,901
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.33
Mean single sequence MFE -46.28
Consensus MFE -42.35
Energy contribution -42.13
Covariance contribution -0.22
Combinations/Pair 1.10
Mean z-score -2.29
Structure conservation index 0.92
SVM decision value 3.00
SVM RNA-class probability 0.998076
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16772781 120 - 22407834
CUUGGGCUUCUGGAAUGGAGCCGACUUGCCCAAAUGGGUGUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGGGGAACAUAGACUCUUCCUCCAGGAUGGACAAGAUACCCAU
..((((((((((((..(((((.((((.((((....))))...)))).)))))))).)))))((((..((.((..(((.((((((.........)))))).))))).))..)))).)))). ( -46.30)
>DroVir_CAF1 2617 120 - 1
CUUGGGCUUCUGGAAUGGAGCCGACUUGCCCAAAUGGGUGUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGGGGAACAUAGACUCUUCCUCAAGAAUCGACAAGAUACCCAU
..((((((((((((..(((((.((((.((((....))))...)))).)))))))).)))))((((..(((((...(((((((((.........))))))))).)))))..)))).)))). ( -51.00)
>DroPse_CAF1 2613 120 - 1
CUUUGGCUUCUGGAAUGGAGCGGACUUGCCCAAAUGGGUAUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGGGGAACAUAGACUCUUCCUCCAGGAUGGACAGGAUACCCAU
...(((((((((((..(((((.(((((((((....)))))..)))).)))))))).)))))((((..((.((..(((.((((((.........)))))).))))).))..))))..))). ( -43.40)
>DroGri_CAF1 2573 120 - 1
CUUUGGCUUCUGGAAUGGAGCCGACUUGCCCAAAUGGGUGUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGGGGAACAUAGACUCUUCCUCCAGGAUGGACAAGAUACCCAU
..((((((((......)))))))).........(((((((((.(((.(((...((((..(....)..)))).)))(((((((((.........)))).)))))...)))..))))))))) ( -42.90)
>DroWil_CAF1 2392 120 - 1
CUUGGGCUUCUGGAAUGGAGCUGAUUUACCCAAAUGGGUGUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGGGGAACAUAGACUCUUCUUCCAGGAUGGACAAGAUACCCAU
((((..((((((((..(((((((((((((((....)))))..))))))))))....((((((((((....((..((....)).)).))))).)))))))))))).)..))))........ ( -46.50)
>DroAna_CAF1 2435 120 - 1
CUUGGGCUUCUGGAAUGGAGCCGACUUGCCCAAAUGGGUGUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGGGGAACAUAGACUCUUCUUCAAGGAUGGACAGGAUACCCAU
..((((((((((((..(((((.((((.((((....))))...)))).)))))))).)))))((((..((.((..((((((((((.........)))))))))))).))..)))).)))). ( -47.60)
>consensus
CUUGGGCUUCUGGAAUGGAGCCGACUUGCCCAAAUGGGUGUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGGGGAACAUAGACUCUUCCUCCAGGAUGGACAAGAUACCCAU
..((((((((((((..(((((.((((.((((....))))...)))).)))))))).)))))((((..((.((..(((.((((((.........)))))).))))).))..)))).)))). (-42.35 = -42.13 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,772,821 – 16,772,941
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.72
Mean single sequence MFE -34.85
Consensus MFE -32.37
Energy contribution -32.32
Covariance contribution -0.05
Combinations/Pair 1.11
Mean z-score -1.31
Structure conservation index 0.93
SVM decision value 1.07
SVM RNA-class probability 0.910922
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16772821 120 + 22407834
CCAAGGCCACCGAUCAGACCUUCUCGGAGAAGCUGACCAACACCCAUUUGGGCAAGUCGGCUCCAUUCCAGAAGCCCAAGCCUCCAAAGCCCGGUCAGCAGGCUGCCCACUUCGCCAUUG
....((((.((((..........))))....(((((((.........((((((...((((.......)).)).))))))((.......))..))))))).))))................ ( -34.50)
>DroVir_CAF1 2657 120 + 1
CCAAGGCCACCGAUCAGACCUUCUCGGAGAAGCUGACCAACACCCAUUUGGGCAAGUCGGCUCCAUUCCAGAAGCCCAAGCCACCAAAGCCCGGCCAGCAGGCAGCUCACUUUGCCAUCG
....((((........(..(((((.((((.(((((((.....(((....)))...)))))))...)))))))))..)..((.......))..))))....(((((......))))).... ( -37.00)
>DroPse_CAF1 2653 120 + 1
CCAAGGCCACCGAUCAGACCUUCUCGGAGAAGCUGACCAAUACCCAUUUGGGCAAGUCCGCUCCAUUCCAGAAGCCAAAGCCCCCAAAGCCUGGCCAGCAGGCUGCCCACUUCGCCAUCG
....(((............(((((.((((.(((.(((.....(((....)))...))).)))...))))))))).............((((((.....)))))).........))).... ( -32.30)
>DroGri_CAF1 2613 120 + 1
CCAAGGCCACCGAUCAGACCUUCUCGGAGAAGCUGACCAACACCCAUUUGGGCAAGUCGGCUCCAUUCCAGAAGCCAAAGCCCCCAAAGCCCGGCCAGCAGGCCGCUCACUUUGCCAUUG
....(((............(((((.((((.(((((((.....(((....)))...)))))))...)))))))))...........((((..(((((....)))))....))))))).... ( -36.30)
>DroWil_CAF1 2432 120 + 1
CCAAGGCCACCGAUCAGACCUUCUCGGAGAAGCUGACCAACACCCAUUUGGGUAAAUCAGCUCCAUUCCAGAAGCCCAAGCCUCCAAAGCCCGGCCAGCAGGCUGCCCACUUUGCCAUUG
....((((........(..(((((.((((.((((((.....((((....))))...))))))...)))))))))..)..((.......))..))))....(((..........))).... ( -34.30)
>DroMoj_CAF1 2678 120 + 1
CCAAGGCCACCGAUCAGACCUUCUCGGAGAAGCUGACCAACACCCAUUUGGGCAAGUCGGCUCCAUUCCAGAAGCCCAAGCCACCAAAGCCCGGCCAGCAGGCAGCUCACUUUGCUAUUG
....((((........(..(((((.((((.(((((((.....(((....)))...)))))))...)))))))))..)..((.......))..))))((((((........)))))).... ( -34.70)
>consensus
CCAAGGCCACCGAUCAGACCUUCUCGGAGAAGCUGACCAACACCCAUUUGGGCAAGUCGGCUCCAUUCCAGAAGCCCAAGCCACCAAAGCCCGGCCAGCAGGCUGCCCACUUUGCCAUUG
....((((...........(((((.((((.(((((((.....(((....)))...)))))))...))))))))).....((.......))..))))....(((..........))).... (-32.37 = -32.32 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,772,821 – 16,772,941
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.72
Mean single sequence MFE -49.63
Consensus MFE -46.23
Energy contribution -45.82
Covariance contribution -0.41
Combinations/Pair 1.12
Mean z-score -1.48
Structure conservation index 0.93
SVM decision value 1.58
SVM RNA-class probability 0.965662
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16772821 120 - 22407834
CAAUGGCGAAGUGGGCAGCCUGCUGACCGGGCUUUGGAGGCUUGGGCUUCUGGAAUGGAGCCGACUUGCCCAAAUGGGUGUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGG
(((.(((.((((.(((.(((((.....)))))((..(((((....)))))..)).....))).))))((((....)))).((((((((((((.....))))..))))))))..)))))). ( -49.50)
>DroVir_CAF1 2657 120 - 1
CGAUGGCAAAGUGAGCUGCCUGCUGGCCGGGCUUUGGUGGCUUGGGCUUCUGGAAUGGAGCCGACUUGCCCAAAUGGGUGUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGG
(((.(((.....((((..((.(((.....)))...))..))))((.((((((((..(((((.((((.((((....))))...)))).)))))))).))))).)).........)))))). ( -48.30)
>DroPse_CAF1 2653 120 - 1
CGAUGGCGAAGUGGGCAGCCUGCUGGCCAGGCUUUGGGGGCUUUGGCUUCUGGAAUGGAGCGGACUUGCCCAAAUGGGUAUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGG
(((.(((.....((....)).((((..((((((((((((((....))))))(((..(((((.(((((((((....)))))..)))).))))))))...))))))))..)))).)))))). ( -49.60)
>DroGri_CAF1 2613 120 - 1
CAAUGGCAAAGUGAGCGGCCUGCUGGCCGGGCUUUGGGGGCUUUGGCUUCUGGAAUGGAGCCGACUUGCCCAAAUGGGUGUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGG
.....((.......))((((.((((..((((((((((((((....))))))(((..(((((.((((.((((....))))...)))).))))))))...))))))))..)))))))).... ( -51.30)
>DroWil_CAF1 2432 120 - 1
CAAUGGCAAAGUGGGCAGCCUGCUGGCCGGGCUUUGGAGGCUUGGGCUUCUGGAAUGGAGCUGAUUUACCCAAAUGGGUGUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGG
(((.(((.....((....)).((((..((((((((((((((....))))))(((..(((((((((((((((....)))))..)))))))))))))...))))))))..)))).)))))). ( -52.10)
>DroMoj_CAF1 2678 120 - 1
CAAUAGCAAAGUGAGCUGCCUGCUGGCCGGGCUUUGGUGGCUUGGGCUUCUGGAAUGGAGCCGACUUGCCCAAAUGGGUGUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGG
....(((.......)))(((.((((..((((((((((.((((..((((((......))))))((((.((((....))))...))))))))...))))...))))))..)))))))..... ( -47.00)
>consensus
CAAUGGCAAAGUGAGCAGCCUGCUGGCCGGGCUUUGGAGGCUUGGGCUUCUGGAAUGGAGCCGACUUGCCCAAAUGGGUGUUGGUCAGCUUCUCCGAGAAGGUCUGAUCGGUGGCCUUGG
(((..((.......)).(((.((((..((((((((((((((....))))))(((..(((((.((((.((((....))))...)))).))))))))...))))))))..))))))).))). (-46.23 = -45.82 +  -0.41)

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 11:57:16 2006