Locus 33

Sequence ID 2R_DroMel_CAF1
Location 1,243,772 – 1,243,948
Length 176
Max. P 0.975231
window56 window57 window58 window59

overview

Window 6

Location 1,243,772 – 1,243,880
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.01
Mean single sequence MFE -39.34
Consensus MFE -26.76
Energy contribution -27.10
Covariance contribution 0.34
Combinations/Pair 1.07
Mean z-score -1.86
Structure conservation index 0.68
SVM decision value 1.00
SVM RNA-class probability 0.898145
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1243772 108 + 20766785
GGAGGCAAACAUAGUCCUGGAAGGGCGAGCACUUGAGAUAAUCGCCUUAGGGUUGUUUUGGCAGCGGGUGCUACCAGGAGACUGCUACCAGGC------------GGUUGCCAUAAACGA
...(((........((((((.((.((..((..(..((((((((.......))))))))..)..))..)).)).))))))(((((((....)))------------)))))))........ ( -39.60)
>DroSim_CAF1 1 104 + 1
----------------CUGGAAGGGCGAGCACUUGAGAUAAUCGCCUUAGGGUUGUUUUGGCAGCGGGUGCUACCAGGAGACUGCUACCAGGCCCGGGUUGCCCCGCUCGCCAUAAACGA
----------------.....(((((((.............)))))))....((((((((((((((((.((.(((.((.(.(((....))).))).))).)))))))).)))).)))))) ( -42.72)
>DroYak_CAF1 1 97 + 1
--------------------AAGGGCGAGCACUUGAGAUAAUCGCCUUAGGGUUGUUUUGGUAGCGGGUGCUACCAGGAGACUACUACCAGGC---GGUUGCCCCGUUCACCAUAAACGA
--------------------..((((((.(....((.....))(((((((((((.((((((((((....)))))))))))))).)))..))))---).))))))((((.......)))). ( -35.70)
>consensus
________________CUGGAAGGGCGAGCACUUGAGAUAAUCGCCUUAGGGUUGUUUUGGCAGCGGGUGCUACCAGGAGACUGCUACCAGGC___GGUUGCCCCGCUCGCCAUAAACGA
.......................(((((((....((.....))(((((((((((.((((((.(((....))).)))))))))).)))..))))............)))))))........ (-26.76 = -27.10 +   0.34)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,243,772 – 1,243,880
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.01
Mean single sequence MFE -35.27
Consensus MFE -25.26
Energy contribution -25.40
Covariance contribution 0.14
Combinations/Pair 1.07
Mean z-score -2.10
Structure conservation index 0.72
SVM decision value 1.75
SVM RNA-class probability 0.975231
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1243772 108 - 20766785
UCGUUUAUGGCAACC------------GCCUGGUAGCAGUCUCCUGGUAGCACCCGCUGCCAAAACAACCCUAAGGCGAUUAUCUCAAGUGCUCGCCCUUCCAGGACUAUGUUUGCCUCC
........(((((.(------------((((((.((........(((((((....)))))))............(((((.(((.....))).))))))).)))))....)).)))))... ( -33.50)
>DroSim_CAF1 1 104 - 1
UCGUUUAUGGCGAGCGGGGCAACCCGGGCCUGGUAGCAGUCUCCUGGUAGCACCCGCUGCCAAAACAACCCUAAGGCGAUUAUCUCAAGUGCUCGCCCUUCCAG----------------
..((((.((((.((((((((.(((.(((.(((....))).).)).))).)).))))))))))))))........(((((.(((.....))).))))).......---------------- ( -41.80)
>DroYak_CAF1 1 97 - 1
UCGUUUAUGGUGAACGGGGCAACC---GCCUGGUAGUAGUCUCCUGGUAGCACCCGCUACCAAAACAACCCUAAGGCGAUUAUCUCAAGUGCUCGCCCUU--------------------
..((((..((.((((.((((....---)))).)).....)).))(((((((....)))))))))))........(((((.(((.....))).)))))...-------------------- ( -30.50)
>consensus
UCGUUUAUGGCGAACGGGGCAACC___GCCUGGUAGCAGUCUCCUGGUAGCACCCGCUGCCAAAACAACCCUAAGGCGAUUAUCUCAAGUGCUCGCCCUUCCAG________________
..((((..(((....(((....)))..))).((.((....))))(((((((....)))))))))))........(((((.(((.....))).)))))....................... (-25.26 = -25.40 +   0.14)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,243,812 – 1,243,920
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.20
Mean single sequence MFE -47.37
Consensus MFE -37.59
Energy contribution -40.37
Covariance contribution 2.78
Combinations/Pair 1.05
Mean z-score -2.44
Structure conservation index 0.79
SVM decision value 0.45
SVM RNA-class probability 0.742217
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1243812 108 + 20766785
AUCGCCUUAGGGUUGUUUUGGCAGCGGGUGCUACCAGGAGACUGCUACCAGGC------------GGUUGCCAUAAACGAUCCUGUAAUUCUCGUUGGGCGCGCGCUCGCGAUUGUUCUU
(((((..((((((((((((((((((.(.(..((.(((....))).))...).)------------.))))))).)))))))))))...........((((....)))))))))....... ( -41.90)
>DroSim_CAF1 25 120 + 1
AUCGCCUUAGGGUUGUUUUGGCAGCGGGUGCUACCAGGAGACUGCUACCAGGCCCGGGUUGCCCCGCUCGCCAUAAACGAUCCUGUAAUUCUCGUUGGGCGCGCGCUCGCGAUUGUUCUU
(((((..(((((((((((((((((((((.((.(((.((.(.(((....))).))).))).)))))))).)))).)))))))))))...........((((....)))))))))....... ( -54.10)
>DroYak_CAF1 21 117 + 1
AUCGCCUUAGGGUUGUUUUGGUAGCGGGUGCUACCAGGAGACUACUACCAGGC---GGUUGCCCCGUUCACCAUAAACGAUCCUGUAAUUCUCGUUGGGCGCGCGCUCGCGAUUGUUCUU
(((((..(((((((((((((((((((((.((.(((((....)).(.....)..---))).)))))))).)))).)))))))))))...........((((....)))))))))....... ( -46.10)
>consensus
AUCGCCUUAGGGUUGUUUUGGCAGCGGGUGCUACCAGGAGACUGCUACCAGGC___GGUUGCCCCGCUCGCCAUAAACGAUCCUGUAAUUCUCGUUGGGCGCGCGCUCGCGAUUGUUCUU
(((((..(((((((((((((((((((((.((.(((((....))(((....)))...))).)))))))).)))).)))))))))))...........((((....)))))))))....... (-37.59 = -40.37 +   2.78)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,243,852 – 1,243,948
Length 96
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.32
Mean single sequence MFE -39.00
Consensus MFE -32.89
Energy contribution -33.03
Covariance contribution 0.14
Combinations/Pair 1.07
Mean z-score -1.21
Structure conservation index 0.84
SVM decision value -0.02
SVM RNA-class probability 0.521601
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1243852 96 - 20766785
AUGCUC------------CUGCUGCCUGGGUGCCCACAUAAAGAACAAUCGCGAGCGCGCGCCCAACGAGAAUUACAGGAUCGUUUAUGGCAACC------------GCCUGGUAGCAGU
......------------((((((((.((((((.........((....))((....))))))))(((((...........)))))...(((....------------))).)))))))). ( -32.60)
>DroSim_CAF1 65 108 - 1
AUGCUC------------CUGCUGCCUGGGUGCCCACAUGAAGAACAAUCGCGAGCGCGCGCCCAACGAGAAUUACAGGAUCGUUUAUGGCGAGCGGGGCAACCCGGGCCUGGUAGCAGU
.(((((------------(....((((((((((((..............(....)(((.((((.(((((...........)))))...)))).))))))).))))))))..)).)))).. ( -47.30)
>DroYak_CAF1 61 117 - 1
AUGCUCCUGCUCCUGCUCCUGCUGCCUGGGUGCUCACAUAAAGAACAAUCGCGAGCGCGCGCCCAACGAGAAUUACAGGAUCGUUUAUGGUGAACGGGGCAACC---GCCUGGUAGUAGU
..((....))........(((((((((((((((.........((....))((....)))))))))...........(((..(((((.....)))))((....))---.))))))))))). ( -37.10)
>consensus
AUGCUC____________CUGCUGCCUGGGUGCCCACAUAAAGAACAAUCGCGAGCGCGCGCCCAACGAGAAUUACAGGAUCGUUUAUGGCGAACGGGGCAACC___GCCUGGUAGCAGU
..................((((((((.((((((.........((....))((....))))))))(((((...........)))))...(((....(((....)))..))).)))))))). (-32.89 = -33.03 +   0.14)

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 09:24:02 2006