Locus 1131

Sequence ID 3R_DroMel_CAF1
Location 3,393,926 – 3,394,158
Length 232
Max. P 0.721085
window1857 window1858 window1859 window1860

overview

Window 7

Location 3,393,926 – 3,394,046
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.61
Mean single sequence MFE -23.63
Consensus MFE -23.48
Energy contribution -23.10
Covariance contribution -0.38
Combinations/Pair 1.11
Mean z-score -1.29
Structure conservation index 0.99
SVM decision value 0.12
SVM RNA-class probability 0.593683
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3393926 120 - 27905053
GGUGAGCAAAAAAUGCUAUACGCAUUAUAGCAGUUUUUCGUUGGGUAAACUUUAUUUGGCCGGCAAUUAGUUUGUAUUAUUUUUCAGUUUACUUUGCCAUUUAUAUUUGUUCUUUUUGCC
((((((((((...(((((((.....))))))).......((..((((((((...........((((.....))))..........))))))))..))........))))))).....))) ( -24.50)
>DroSim_CAF1 2848 120 - 1
GCUGAGCAAAAAAUGCUAUACACAUUAUAGCAGUUUUUCGUUGGGUAAACUUUAUUUGGCCGGCAAUUAGUUUGUAUUAUUUUUCAGUUUACUUUGCCAUUUAUAUUUGUUCUUUUAGCC
((((((((((...(((((((.....))))))).......((..((((((((...........((((.....))))..........))))))))..))........)))))))....))). ( -25.40)
>DroEre_CAF1 1006 120 - 1
GCUGAGCAAAAAAUGUUUUAUACACUAUAGCAGUUUUUCGUUGGGUAAACUUUAUUUGGAUGGCAAUUAGUUUGUAUUAUUUUUCAGUUUACCUUGCCAUUUAUAUUUGUUCUUGUUGUC
...(((((((...((((.((.....)).)))).......((.(((((((((.......((((.(((.....))))))).......))))))))).))........)))))))........ ( -21.24)
>DroYak_CAF1 6511 120 - 1
GCUGAGCAAAAAAUGUUAUAUACACUAUAACAGUUUUUCGUUGGGUAAACUUUAUUUGGACGGCAAUUAGUUUGUAUUAUUUUUCAGUUUACUUUGCCAUUUAUAUUUGUUCUUUUUGCA
((.(((((((...(((((((.....))))))).......((..((((((((...........((((.....))))..........))))))))..))........))))))).....)). ( -23.40)
>consensus
GCUGAGCAAAAAAUGCUAUACACACUAUAGCAGUUUUUCGUUGGGUAAACUUUAUUUGGACGGCAAUUAGUUUGUAUUAUUUUUCAGUUUACUUUGCCAUUUAUAUUUGUUCUUUUUGCC
...(((((((...(((((((.....))))))).......((..((((((((...........((((.....))))..........))))))))..))........)))))))........ (-23.48 = -23.10 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,393,966 – 3,394,080
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.59
Mean single sequence MFE -16.77
Consensus MFE -13.05
Energy contribution -12.18
Covariance contribution -0.88
Combinations/Pair 1.17
Mean z-score -1.71
Structure conservation index 0.78
SVM decision value 0.04
SVM RNA-class probability 0.554752
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3393966 114 + 27905053
AUAAUACAAACUAAUUGCCGGCCAAAUAAAGUUUACCCAACGAAAAACUGCUAUAAUGCGUAUAGCAUUUUUUGCUCACCCACUUUUCUUCGAUUUCGUUUAAACUUUUCCAAC------
...................((......((((((((...(((((((....((......))....((((.....)))).................))))))))))))))).))...------ ( -15.90)
>DroSim_CAF1 2888 120 + 1
AUAAUACAAACUAAUUGCCGGCCAAAUAAAGUUUACCCAACGAAAAACUGCUAUAAUGUGUAUAGCAUUUUUUGCUCAGCCACUUUUCUUCGAUUUCGUUUAAACUUUUCCAACGGCAAA
..............((((((.......((((((((...(((((((...(((((((.....)))))))......((...)).............))))))))))))))).....)))))). ( -25.50)
>DroEre_CAF1 1046 114 + 1
AUAAUACAAACUAAUUGCCAUCCAAAUAAAGUUUACCCAACGAAAAACUGCUAUAGUGUAUAAAACAUUUUUUGCUCAGCCACUUUUCUUCGAUUUCGUUUAAACUUUUCCAAC------
...........................((((((((...(((((((....((...(((((.....)))))....)).......(........).)))))))))))))))......------ ( -11.70)
>DroYak_CAF1 6551 114 + 1
AUAAUACAAACUAAUUGCCGUCCAAAUAAAGUUUACCCAACGAAAAACUGUUAUAGUGUAUAUAACAUUUUUUGCUCAGCUACUUUUCUUCGAUUUCGUUUAAACUUUUCCAAC------
...........................((((((((...(((((((...(((((((.....)))))))......((...)).............)))))))))))))))......------ ( -14.00)
>consensus
AUAAUACAAACUAAUUGCCGGCCAAAUAAAGUUUACCCAACGAAAAACUGCUAUAAUGUAUAUAACAUUUUUUGCUCAGCCACUUUUCUUCGAUUUCGUUUAAACUUUUCCAAC______
...........................((((((((...(((((((....((...(((((.....)))))....)).......(........).)))))))))))))))............ (-13.05 = -12.18 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,393,966 – 3,394,080
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.59
Mean single sequence MFE -25.85
Consensus MFE -22.24
Energy contribution -22.55
Covariance contribution 0.31
Combinations/Pair 1.06
Mean z-score -1.63
Structure conservation index 0.86
SVM decision value 0.40
SVM RNA-class probability 0.721085
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3393966 114 - 27905053
------GUUGGAAAAGUUUAAACGAAAUCGAAGAAAAGUGGGUGAGCAAAAAAUGCUAUACGCAUUAUAGCAGUUUUUCGUUGGGUAAACUUUAUUUGGCCGGCAAUUAGUUUGUAUUAU
------((..((((((((((..(((...(((((((.((((.(((((((.....)))).))).)))).......))))))))))..)))))))).))..))..((((.....))))..... ( -27.20)
>DroSim_CAF1 2888 120 - 1
UUUGCCGUUGGAAAAGUUUAAACGAAAUCGAAGAAAAGUGGCUGAGCAAAAAAUGCUAUACACAUUAUAGCAGUUUUUCGUUGGGUAAACUUUAUUUGGCCGGCAAUUAGUUUGUAUUAU
.(((((((..((((((((((..(((...(((((((..((......))......(((((((.....))))))).))))))))))..)))))))).))..).)))))).............. ( -32.40)
>DroEre_CAF1 1046 114 - 1
------GUUGGAAAAGUUUAAACGAAAUCGAAGAAAAGUGGCUGAGCAAAAAAUGUUUUAUACACUAUAGCAGUUUUUCGUUGGGUAAACUUUAUUUGGAUGGCAAUUAGUUUGUAUUAU
------.(..((((((((((..(((...(((((((.((((...(((((.....)))))....)))).......))))))))))..)))))))).))..)...((((.....))))..... ( -21.60)
>DroYak_CAF1 6551 114 - 1
------GUUGGAAAAGUUUAAACGAAAUCGAAGAAAAGUAGCUGAGCAAAAAAUGUUAUAUACACUAUAACAGUUUUUCGUUGGGUAAACUUUAUUUGGACGGCAAUUAGUUUGUAUUAU
------(((.((((((((((..(((...(((((((.....((...))......(((((((.....))))))).))))))))))..)))))))..))).))).((((.....))))..... ( -22.20)
>consensus
______GUUGGAAAAGUUUAAACGAAAUCGAAGAAAAGUGGCUGAGCAAAAAAUGCUAUACACACUAUAGCAGUUUUUCGUUGGGUAAACUUUAUUUGGACGGCAAUUAGUUUGUAUUAU
......((..((((((((((..(((...(((((((..((......))......(((((((.....))))))).))))))))))..)))))))).))..))..((((.....))))..... (-22.24 = -22.55 +   0.31)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,394,046 – 3,394,158
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.33
Mean single sequence MFE -23.23
Consensus MFE -16.83
Energy contribution -17.09
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.72
SVM decision value 0.04
SVM RNA-class probability 0.552300
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3394046 112 - 27905053
UGAACUAAAAAUUGGUCGACAUACAAAAAAAAAAUCGCACAAUUUGCGGAAAGUUCGUUAAUGUUU-UUUCCAGAAGCC-------GUUGGAAAAGUUUAAACGAAAUCGAAGAAAAGUG
...........((..((((...............(((((.....)))))....((((((.....((-(((((((.....-------.)))))))))....)))))).))))..))..... ( -20.40)
>DroSim_CAF1 2968 118 - 1
UCAACUAAAAAUUGGUCGACAUACAAAA--AAAUUCGCACAAUUUGCGGAAAGUUCGUUAAUGUUUUUUUCCAGAAGCCGUUUGCCGUUGGAAAAGUUUAAACGAAAUCGAAGAAAAGUG
...........((..((((.........--...((((((.....))))))...((((((..((..(((((((((..((.....))..)))))))))..)))))))).))))..))..... ( -24.90)
>DroEre_CAF1 1126 108 - 1
UCAAC-AGAAAUUGGUCGACGAACAA---AAAAUUCGCACAAUUUGCGGAAAGUUCGUUAAUGUUU-UUUCCAGAAGCC-------GUUGGAAAAGUUUAAACGAAAUCGAAGAAAAGUG
.....-....(((..((..(((....---....((((((.....))))))...((((((.....((-(((((((.....-------.)))))))))....)))))).)))..))..))). ( -23.60)
>DroYak_CAF1 6631 110 - 1
UUAAC-AAAAAUUGGUCGACGACCAA-AAAAAAUUCGCACAAUUUGCGGAAAGUUCGUUAAUGUUU-UUUCCAGAAGCC-------GUUGGAAAAGUUUAAACGAAAUCGAAGAAAAGUA
.....-.....((((((...))))))-......((((((.....))))))...((((((.....((-(((((((.....-------.)))))))))....)))))).............. ( -24.00)
>consensus
UCAAC_AAAAAUUGGUCGACAAACAA_A_AAAAUUCGCACAAUUUGCGGAAAGUUCGUUAAUGUUU_UUUCCAGAAGCC_______GUUGGAAAAGUUUAAACGAAAUCGAAGAAAAGUG
...........((..((((..............((((((.....))))))...((((((........(((((((.............)))))))......)))))).))))..))..... (-16.83 = -17.09 +   0.25)

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 10:01:50 2006