Locus 6231

Sequence ID 3R_DroMel_CAF1
Location 16,282,373 – 16,282,569
Length 196
Max. P 0.812828
window10161 window10162 window10163 window10164

overview

Window 1

Location 16,282,373 – 16,282,489
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.03
Mean single sequence MFE -26.89
Consensus MFE -21.46
Energy contribution -21.47
Covariance contribution 0.01
Combinations/Pair 1.11
Mean z-score -1.76
Structure conservation index 0.80
SVM decision value 0.26
SVM RNA-class probability 0.657314
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16282373 116 + 27905053
GCGGGCAUGGCACUCGGAAUAGCAAGCAAGUUGUUGUCCUUCCUGGUAGCAAAAGAAAAA----AAAAACAGGAAAAACUUACUUGCGAUUGCAAAGUAAAAGAAAAGCAGGCGACGAAG
.((.((...((....(((.((((((.....)))))))))((((((...............----.....))))))....((((((((....)).)))))).......))..))..))... ( -24.35)
>DroSec_CAF1 3105 120 + 1
GCGGGCAUUGCAUUCGGAAUAGCAAGCAAGUUGUUGUCCUUCCUGGUAGCAAAAAAAAAAAAGAAAAAACAGGAAAAACAUACUUGCAAUUGCAAAGUAAAAGAAAAGCAGGCGACGAAG
.((.((.((((.(((......((((((((((...(((..((((((........................))))))..))).))))))..)))).........)))..))))))..))... ( -26.42)
>DroYak_CAF1 4198 106 + 1
GCGGGGUCUGCAUUCGGAAUAGCAAGCAAGUUUUUGUCCUUCCUGCUGG--------------AAAAAACGGGGAAAACUUACUUGCGAUUGCAAAGUAAAAGAAAAGCAGGCGGCGAAG
.((..((((((.(((......(((((.((((((((.((.((((....))--------------)).....)).)))))))).)))))..((((...))))..)))..))))))..))... ( -29.90)
>consensus
GCGGGCAUUGCAUUCGGAAUAGCAAGCAAGUUGUUGUCCUUCCUGGUAGCAAAA_AAAAA___AAAAAACAGGAAAAACUUACUUGCGAUUGCAAAGUAAAAGAAAAGCAGGCGACGAAG
((((...)))).((((.....((..((((((....((..((((((........................))))))..))..))))))..((((..............))))))..)))). (-21.46 = -21.47 +   0.01)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,282,373 – 16,282,489
Length 116
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 84.03
Mean single sequence MFE -25.12
Consensus MFE -18.77
Energy contribution -19.22
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -2.08
Structure conservation index 0.75
SVM decision value 0.52
SVM RNA-class probability 0.769266
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16282373 116 - 27905053
CUUCGUCGCCUGCUUUUCUUUUACUUUGCAAUCGCAAGUAAGUUUUUCCUGUUUUU----UUUUUCUUUUGCUACCAGGAAGGACAACAACUUGCUUGCUAUUCCGAGUGCCAUGCCCGC
.......((..((........(((((.(.(((.((((((((((((((((((.....----...............)))))))......))))))))))).)))).)))))....))..)) ( -23.75)
>DroSec_CAF1 3105 120 - 1
CUUCGUCGCCUGCUUUUCUUUUACUUUGCAAUUGCAAGUAUGUUUUUCCUGUUUUUUCUUUUUUUUUUUUGCUACCAGGAAGGACAACAACUUGCUUGCUAUUCCGAAUGCAAUGCCCGC
.......((.(((..(((.........((((..((((((.(((((((((((........................)))))))))))...))))))))))......))).)))..)).... ( -25.32)
>DroYak_CAF1 4198 106 - 1
CUUCGCCGCCUGCUUUUCUUUUACUUUGCAAUCGCAAGUAAGUUUUCCCCGUUUUUU--------------CCAGCAGGAAGGACAAAAACUUGCUUGCUAUUCCGAAUGCAGACCCCGC
.........((((...........((((.(((.(((((((((((((....(((((((--------------(.....)))))))).))))))))))))).))).)))).))))....... ( -26.30)
>consensus
CUUCGUCGCCUGCUUUUCUUUUACUUUGCAAUCGCAAGUAAGUUUUUCCUGUUUUUU___UUUUU_UUUUGCUACCAGGAAGGACAACAACUUGCUUGCUAUUCCGAAUGCAAUGCCCGC
...........((..(((.........((((..((((((..((((((((((........................))))))))))....))))))))))......))).))......... (-18.77 = -19.22 +   0.45)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,282,449 – 16,282,569
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -33.29
Consensus MFE -31.75
Energy contribution -31.53
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.88
Structure conservation index 0.95
SVM decision value 0.61
SVM RNA-class probability 0.799685
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16282449 120 + 27905053
UACUUGCGAUUGCAAAGUAAAAGAAAAGCAGGCGACGAAGAAGGAAGCCUCGAAUUGCUGCGGGAUUUCAUCUUCUUUCUUCUCGCACUUACUUUUCUUGUUUGCCACGUUUUUCAUGCU
.....(((...(((((....((((((((.((((((.(((((((((((....(((((.(...).)))))...))))))))))))))).))..)))))))).)))))..))).......... ( -34.40)
>DroSec_CAF1 3185 120 + 1
UACUUGCAAUUGCAAAGUAAAAGAAAAGCAGGCGACGAAGAAGGAAGCCUCGAAUUGCUGCGGGAUUUCAUCUUCUUUCUUCUCGCACUUACUUUUCUUGUUUGCCACGUUUUUCCUGCU
(((((((....)).))))).((((((((.((((((.(((((((((((....(((((.(...).)))))...))))))))))))))).))..))))))))..................... ( -33.50)
>DroYak_CAF1 4264 120 + 1
UACUUGCGAUUGCAAAGUAAAAGAAAAGCAGGCGGCGAAGAAGGAAGCCUCGAAUUGCUGCGGGAUUUUAUCUUCUUUCUUCUCGCACUUACUUUUCCUGUUUGCCACGUUUUUCCAGCU
(((((((....)).)))))...(((((((.(..((((((..(((((((........))(((((((...............))))))).......))))).)))))).))))))))..... ( -31.96)
>consensus
UACUUGCGAUUGCAAAGUAAAAGAAAAGCAGGCGACGAAGAAGGAAGCCUCGAAUUGCUGCGGGAUUUCAUCUUCUUUCUUCUCGCACUUACUUUUCUUGUUUGCCACGUUUUUCCUGCU
...((((....)))).(((((.((((((.((((((.(((((((((((....(((((.(...).)))))...))))))))))))))).))..))))))...)))))............... (-31.75 = -31.53 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,282,449 – 16,282,569
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -33.14
Consensus MFE -30.85
Energy contribution -30.74
Covariance contribution -0.11
Combinations/Pair 1.05
Mean z-score -2.03
Structure conservation index 0.93
SVM decision value 0.65
SVM RNA-class probability 0.812828
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16282449 120 - 27905053
AGCAUGAAAAACGUGGCAAACAAGAAAAGUAAGUGCGAGAAGAAAGAAGAUGAAAUCCCGCAGCAAUUCGAGGCUUCCUUCUUCGUCGCCUGCUUUUCUUUUACUUUGCAAUCGCAAGUA
..((((.....))))(((((.((((((((((.(.((((((((((.((((.......((((.(....).)).)))))).)))))).)))))))))))))))....)))))...(....).. ( -34.01)
>DroSec_CAF1 3185 120 - 1
AGCAGGAAAAACGUGGCAAACAAGAAAAGUAAGUGCGAGAAGAAAGAAGAUGAAAUCCCGCAGCAAUUCGAGGCUUCCUUCUUCGUCGCCUGCUUUUCUUUUACUUUGCAAUUGCAAGUA
.((((......)...(((((.((((((((((.(.((((((((((.((((.......((((.(....).)).)))))).)))))).)))))))))))))))....)))))...)))..... ( -34.01)
>DroYak_CAF1 4264 120 - 1
AGCUGGAAAAACGUGGCAAACAGGAAAAGUAAGUGCGAGAAGAAAGAAGAUAAAAUCCCGCAGCAAUUCGAGGCUUCCUUCUUCGCCGCCUGCUUUUCUUUUACUUUGCAAUCGCAAGUA
.((((........))))....((((((((((.(.(((.((((((.((((.......((((.(....).)).)))))).))))))..)))))))))))))).(((((.((....))))))) ( -31.41)
>consensus
AGCAGGAAAAACGUGGCAAACAAGAAAAGUAAGUGCGAGAAGAAAGAAGAUGAAAUCCCGCAGCAAUUCGAGGCUUCCUUCUUCGUCGCCUGCUUUUCUUUUACUUUGCAAUCGCAAGUA
...........((..(((((.((((((((((.(.((((((((((.((((.......((((.(....).)).)))))).)))))).)))))))))))))))....)))))...))...... (-30.85 = -30.74 +  -0.11)

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 12:16:13 2006