Locus 2335

Sequence ID X_DroMel_CAF1
Location 6,265,952 – 6,266,178
Length 226
Max. P 0.982093
window3789 window3790 window3791 window3792 window3793

overview

Window 9

Location 6,265,952 – 6,266,060
Length 108
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 76.23
Mean single sequence MFE -28.27
Consensus MFE -19.37
Energy contribution -20.03
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.29
Structure conservation index 0.69
SVM decision value -0.08
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6265952 108 - 22224390
UUGUUUGAAGUGCGUGUUGCAUCGUUCAACGCUGGCGUUAUUUAUGCAGCAACAGCAAUAGCAACAGCAACAUGAACGGAAGCGGCAACAACGUCUGCCAGUCGAUCU
(((.(((.((.(((((((((.(((((((..((((..(((((...(((.......))))))))..))))....))))))).....))))).))))))..))).)))... ( -30.90)
>DroSec_CAF1 8132 108 - 1
UUGUUUGAAGUGCGUGUUGCAUCGUUCAACGCUGGCGUUAUUUAUGCAGAAACAGCAAUAGCAACAGCAACAUGAACGGAAGCGGCAACAACGUCUGCCAGUCGAACU
..((((((.(((((((((((.(((((((..((((..(((((...(((.......))))))))..))))....))))))).....))))).))))..))...)))))). ( -33.90)
>DroSim_CAF1 9490 108 - 1
UUGUUUGAAGUGCGUGUUGCAUCGUUCAACGCUGGCGUUAUUUAUGCAGCAACAGCAAUAGCAACAGCAAGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
(((((((...(((.((((((((.....((((....))))....))))))))...)))....)))..))))...................................... ( -20.00)
>consensus
UUGUUUGAAGUGCGUGUUGCAUCGUUCAACGCUGGCGUUAUUUAUGCAGCAACAGCAAUAGCAACAGCAACAUGAACGGAAGCGGCAACAACGUCUGCCAGUCGA_CU
(((((((...(((.((((((((.....((((....))))....))))))))...)))....)))..)))).............((((........))))......... (-19.37 = -20.03 +   0.67)

alignment

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secondary structure

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Window 0

Location 6,265,992 – 6,266,100
Length 108
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 97.52
Mean single sequence MFE -26.81
Consensus MFE -25.27
Energy contribution -25.27
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.85
Structure conservation index 0.94
SVM decision value 1.91
SVM RNA-class probability 0.982093
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6265992 108 + 22224390
GCUGUUGCUAUUGCUGUUGCUGCAUAAAUAACGCCAGCGUUGAACGAUGCAACACGCACUUCAAACAACAAUAAAACAAGCAACAGCAACGCCCACAACAACAGAACU
.((((((...(((((((((((.......(((((....)))))...(((((.....)))..))................))))))))))).(....)..)))))).... ( -27.90)
>DroSec_CAF1 8172 107 + 1
GCUGUUGCUAUUGCUGUUUCUGCAUAAAUAACGCCAGCGUUGAACGAUGCAACACGCACUUCAAACAACAAUAACACAAGCAACAGCA-CACCCACAACAACAGAACU
(((((((((((((.(((((.(((((...(((((....)))))....)))))...........))))).))))......))))))))).-................... ( -25.60)
>DroSim_CAF1 9530 107 + 1
GCUGUUGCUAUUGCUGUUGCUGCAUAAAUAACGCCAGCGUUGAACGAUGCAACACGCACUUCAAACAACAAUAACACAAGCAACAGCA-CACCCACAACAACAGAACU
.((((((....((((((((((.......(((((....)))))...(((((.....)))..))................))))))))))-.........)))))).... ( -26.92)
>consensus
GCUGUUGCUAUUGCUGUUGCUGCAUAAAUAACGCCAGCGUUGAACGAUGCAACACGCACUUCAAACAACAAUAACACAAGCAACAGCA_CACCCACAACAACAGAACU
(((((((((((((.((((..(((((...(((((....)))))....)))))............)))).))))......)))))))))..................... (-25.27 = -25.27 +   0.00)

alignment

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secondary structure

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Window 1

Location 6,265,992 – 6,266,100
Length 108
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 97.52
Mean single sequence MFE -35.43
Consensus MFE -34.53
Energy contribution -34.87
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.74
Structure conservation index 0.97
SVM decision value 1.87
SVM RNA-class probability 0.980926
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6265992 108 - 22224390
AGUUCUGUUGUUGUGGGCGUUGCUGUUGCUUGUUUUAUUGUUGUUUGAAGUGCGUGUUGCAUCGUUCAACGCUGGCGUUAUUUAUGCAGCAACAGCAAUAGCAACAGC
......((((((((....((((((((((((.........((((..(((..(((.....))))))..))))....((((.....)))))))))))))))).)))))))) ( -38.30)
>DroSec_CAF1 8172 107 - 1
AGUUCUGUUGUUGUGGGUG-UGCUGUUGCUUGUGUUAUUGUUGUUUGAAGUGCGUGUUGCAUCGUUCAACGCUGGCGUUAUUUAUGCAGAAACAGCAAUAGCAACAGC
....((((((((((.....-(((((((..((((((((.(((((..(((..(((.....))))))..))))).)))).........)))).))))))))))))))))). ( -30.90)
>DroSim_CAF1 9530 107 - 1
AGUUCUGUUGUUGUGGGUG-UGCUGUUGCUUGUGUUAUUGUUGUUUGAAGUGCGUGUUGCAUCGUUCAACGCUGGCGUUAUUUAUGCAGCAACAGCAAUAGCAACAGC
....((((((((((.....-((((((((((.........((((..(((..(((.....))))))..))))....((((.....)))))))))))))))))))))))). ( -37.10)
>consensus
AGUUCUGUUGUUGUGGGUG_UGCUGUUGCUUGUGUUAUUGUUGUUUGAAGUGCGUGUUGCAUCGUUCAACGCUGGCGUUAUUUAUGCAGCAACAGCAAUAGCAACAGC
....((((((((((......((((((((((.........((((..(((..(((.....))))))..))))....((((.....)))))))))))))))))))))))). (-34.53 = -34.87 +   0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,266,060 – 6,266,178
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.88
Mean single sequence MFE -24.26
Consensus MFE -21.14
Energy contribution -21.14
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.87
SVM decision value 0.59
SVM RNA-class probability 0.791037
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6266060 118 + 22224390
CAAUAAAACAAGCAACAGCAACGCCCACAACAACAGAACUUUGCACGUUUUGCAUACAAAGCAGAAUAACCCGCAAAAAAAAAGUAUCUGGCGGGUGAGGG--AGCCGGCAAGAAAUAUU
.................((....(((....................(((((((.......))))))).((((((................))))))..)))--.....)).......... ( -23.79)
>DroSec_CAF1 8240 114 + 1
CAAUAACACAAGCAACAGCA-CACCCACAACAACAGAACUUUGCACGUUUUGCAUACAAAGCAGAAUAACCCGCAAA---AAAGUAUCUGGCGGGUGAGGG--AGCCAGCAAGAAAUAUU
...........((....((.-..(((....................(((((((.......))))))).((((((...---..........))))))..)))--.))..)).......... ( -22.42)
>DroSim_CAF1 9598 114 + 1
CAAUAACACAAGCAACAGCA-CACCCACAACAACAGAACUUUGCACGUUUUGCAUACAAAGCAGAAUAACCCGCAAA---AAAGUAUCUGGCGGGUGAGGG--AGCCAGCAAGAAAUAUU
...........((....((.-..(((....................(((((((.......))))))).((((((...---..........))))))..)))--.))..)).......... ( -22.42)
>DroYak_CAF1 5380 116 + 1
CACUAACAGUAGCAACAGCA-CACCCACAACAACAAAACGUUGCACGUUUUGCAUACAAAGCAGAAUAACCCGCAAA---AAAGUAUCUGGCGGGUGAGGGGAAAGCUGCAAGAAAUAUU
..((..((((.((....)).-..(((....((((.....))))...(((((((.......))))))).((((((...---..........))))))..)))....))))..))....... ( -28.42)
>consensus
CAAUAACACAAGCAACAGCA_CACCCACAACAACAGAACUUUGCACGUUUUGCAUACAAAGCAGAAUAACCCGCAAA___AAAGUAUCUGGCGGGUGAGGG__AGCCAGCAAGAAAUAUU
...........((....))....(((....................(((((((.......))))))).((((((................))))))..)))................... (-21.14 = -21.14 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,266,060 – 6,266,178
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.88
Mean single sequence MFE -32.40
Consensus MFE -25.39
Energy contribution -25.70
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -2.02
Structure conservation index 0.78
SVM decision value 0.39
SVM RNA-class probability 0.715809
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6266060 118 - 22224390
AAUAUUUCUUGCCGGCU--CCCUCACCCGCCAGAUACUUUUUUUUUGCGGGUUAUUCUGCUUUGUAUGCAAAACGUGCAAAGUUCUGUUGUUGUGGGCGUUGCUGUUGCUUGUUUUAUUG
((((...(..((((((.--(((.(((((((.(((........))).))))))......((((((((((.....)))))))))).........).)))....))))..))..)...)))). ( -32.40)
>DroSec_CAF1 8240 114 - 1
AAUAUUUCUUGCUGGCU--CCCUCACCCGCCAGAUACUUU---UUUGCGGGUUAUUCUGCUUUGUAUGCAAAACGUGCAAAGUUCUGUUGUUGUGGGUG-UGCUGUUGCUUGUGUUAUUG
((((...(..((.(((.--(((.(((((((.(((.....)---)).))))))......((((((((((.....)))))))))).........).)))..-.)))...))..)...)))). ( -32.40)
>DroSim_CAF1 9598 114 - 1
AAUAUUUCUUGCUGGCU--CCCUCACCCGCCAGAUACUUU---UUUGCGGGUUAUUCUGCUUUGUAUGCAAAACGUGCAAAGUUCUGUUGUUGUGGGUG-UGCUGUUGCUUGUGUUAUUG
((((...(..((.(((.--(((.(((((((.(((.....)---)).))))))......((((((((((.....)))))))))).........).)))..-.)))...))..)...)))). ( -32.40)
>DroYak_CAF1 5380 116 - 1
AAUAUUUCUUGCAGCUUUCCCCUCACCCGCCAGAUACUUU---UUUGCGGGUUAUUCUGCUUUGUAUGCAAAACGUGCAACGUUUUGUUGUUGUGGGUG-UGCUGUUGCUACUGUUAGUG
..........(((((........(((((((...((((...---...(((((....)))))...))))((((((((.....))))))))....)))))))-.))))).((((....)))). ( -32.40)
>consensus
AAUAUUUCUUGCUGGCU__CCCUCACCCGCCAGAUACUUU___UUUGCGGGUUAUUCUGCUUUGUAUGCAAAACGUGCAAAGUUCUGUUGUUGUGGGUG_UGCUGUUGCUUGUGUUAUUG
..........((.(((...(((.(((((((.(((.........)))))))))......((((((((((.....)))))))))).........).)))....)))...))........... (-25.39 = -25.70 +   0.31)

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 10:31:58 2006