Locus 2965

Sequence ID X_DroMel_CAF1
Location 7,903,750 – 7,903,947
Length 197
Max. P 0.953878
window4865 window4866 window4867 window4868

overview

Window 5

Location 7,903,750 – 7,903,867
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.04
Mean single sequence MFE -44.83
Consensus MFE -36.47
Energy contribution -36.92
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.26
Structure conservation index 0.81
SVM decision value 0.33
SVM RNA-class probability 0.690218
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7903750 117 + 22224390
CUCGACUGAAAGUUGCAGCUGCUCAGGCGUGCGGUAGAGCGAGACAACAGUAGGGGGCUACGUAAUACGUAGCCAAAUGCAAAUAUGGCGGCAUGUCGCCGUCCAUGUGUGUU---UGCG
(((.((((....((((.(((((........)))))...)))).....)))).)))(((((((.....)))))))....((((((((((((((.....)))))).....)))))---))). ( -45.10)
>DroSec_CAF1 4355 120 + 1
CUCCGUUGAAAGUUGCAGCUGCUCAGGCGUGCGGUAGAGCGAGACAACAGUAGGGGGCUACGUAAUACGUAGCCAAAUGCAAAUAUGGCGGCAUGUCGCCGUCCAUGUGUGUUGUGUGCG
((((((........((....))........)))).)).(((..(((((((((...(((((((.....)))))))...)))..((((((((((.....)))).)))))).)))))).))). ( -46.99)
>DroYak_CAF1 7582 112 + 1
CUCGGCUGAAAGUUGCAGCUGCUCAGGCGUGCGAUAGAACGAGACAACGGUAGGGGCCUACGUAA-ACGUAGCCAAAUGCAAAUAUGGCGGCAUGUCGCCG-CCAUGUGUAUU---U---
((((..(....(((((((((.....))).)))))).)..))))......(((..(((.((((...-.)))))))...)))..((((((((((.....))))-)))))).....---.--- ( -42.40)
>consensus
CUCGGCUGAAAGUUGCAGCUGCUCAGGCGUGCGGUAGAGCGAGACAACAGUAGGGGGCUACGUAAUACGUAGCCAAAUGCAAAUAUGGCGGCAUGUCGCCGUCCAUGUGUGUU___UGCG
((((........((((((((.....))).))))).....))))......(((...(((((((.....)))))))...)))..((((((((((.....)))).))))))............ (-36.47 = -36.92 +   0.45)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,903,790 – 7,903,907
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 85.71
Mean single sequence MFE -43.21
Consensus MFE -32.84
Energy contribution -33.07
Covariance contribution 0.23
Combinations/Pair 1.06
Mean z-score -3.13
Structure conservation index 0.76
SVM decision value 1.44
SVM RNA-class probability 0.953878
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7903790 117 + 22224390
GAGACAACAGUAGGGGGCUACGUAAUACGUAGCCAAAUGCAAAUAUGGCGGCAUGUCGCCGUCCAUGUGUGUU---UGCGUUCGAGUGUGUGUGUGUGAAGUGGCAUUCGGACGAGGAGA
.(((((...(((...(((((((.....)))))))...)))..((((((((((.....)))).)))))).))))---).(((((((((((..............)))))))))))...... ( -46.14)
>DroSec_CAF1 4395 117 + 1
GAGACAACAGUAGGGGGCUACGUAAUACGUAGCCAAAUGCAAAUAUGGCGGCAUGUCGCCGUCCAUGUGUGUUGUGUGCGGGUGCGUGUGUGUGUGCGAAGUGGCAUUCGGACG---AGA
...(((((((((...(((((((.....)))))))...)))..((((((((((.....)))).)))))).))))))((.(((((((...(((....))).....))))))).)).---... ( -48.20)
>DroYak_CAF1 7622 107 + 1
GAGACAACGGUAGGGGCCUACGUAA-ACGUAGCCAAAUGCAAAUAUGGCGGCAUGUCGCCG-CCAUGUGUAUU---U--------GUGAGUGUGUGUGAAGUGGCAUUCGAACAGGGAGA
...((((..(((..(((.((((...-.)))))))...)))..((((((((((.....))))-))))))....)---)--------))((((((..........))))))........... ( -35.30)
>consensus
GAGACAACAGUAGGGGGCUACGUAAUACGUAGCCAAAUGCAAAUAUGGCGGCAUGUCGCCGUCCAUGUGUGUU___UGCG___G_GUGUGUGUGUGUGAAGUGGCAUUCGGACG_GGAGA
...(((((((((...(((((((.....)))))))...)))..((((((((((.....)))).))))))..................))).)))((.((((......)))).))....... (-32.84 = -33.07 +   0.23)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,903,790 – 7,903,907
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.71
Mean single sequence MFE -29.10
Consensus MFE -22.65
Energy contribution -22.93
Covariance contribution 0.28
Combinations/Pair 1.04
Mean z-score -2.48
Structure conservation index 0.78
SVM decision value 0.89
SVM RNA-class probability 0.875374
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7903790 117 - 22224390
UCUCCUCGUCCGAAUGCCACUUCACACACACACACUCGAACGCA---AACACACAUGGACGGCGACAUGCCGCCAUAUUUGCAUUUGGCUACGUAUUACGUAGCCCCCUACUGUUGUCUC
.......((.(((.((................)).))).))(((---((.....((((.((((.....)))))))).)))))....(((((((.....)))))))............... ( -28.79)
>DroSec_CAF1 4395 117 - 1
UCU---CGUCCGAAUGCCACUUCGCACACACACACGCACCCGCACACAACACACAUGGACGGCGACAUGCCGCCAUAUUUGCAUUUGGCUACGUAUUACGUAGCCCCCUACUGUUGUCUC
...---.((.((((......)))).))........((....))..((((((...((((.((((.....))))))))..........(((((((.....)))))))......))))))... ( -32.90)
>DroYak_CAF1 7622 107 - 1
UCUCCCUGUUCGAAUGCCACUUCACACACACUCAC--------A---AAUACACAUGG-CGGCGACAUGCCGCCAUAUUUGCAUUUGGCUACGU-UUACGUAGGCCCCUACCGUUGUCUC
...............(((................(--------(---(((.((.((((-((((.....))))))))...)).)))))..((((.-...)))))))............... ( -25.60)
>consensus
UCUCC_CGUCCGAAUGCCACUUCACACACACACAC_C___CGCA___AACACACAUGGACGGCGACAUGCCGCCAUAUUUGCAUUUGGCUACGUAUUACGUAGCCCCCUACUGUUGUCUC
.........((((((((..................((....))...........((((.((((.....))))))))....))))))))(((((.....)))))................. (-22.65 = -22.93 +   0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,903,830 – 7,903,947
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.39
Mean single sequence MFE -36.88
Consensus MFE -33.37
Energy contribution -32.93
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.90
Structure conservation index 0.90
SVM decision value 0.83
SVM RNA-class probability 0.862581
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7903830 117 + 22224390
AAAUAUGGCGGCAUGUCGCCGUCCAUGUGUGUU---UGCGUUCGAGUGUGUGUGUGUGAAGUGGCAUUCGGACGAGGAGAGCAUUUGUUGUUGUAGGUUUUAGUGCCAUCGUUGUGUAUC
..((((((((((.....)))).))))))(((((---(.(((((((((((..............)))))))))))....))))))...........(((......)))............. ( -35.24)
>DroSec_CAF1 4435 117 + 1
AAAUAUGGCGGCAUGUCGCCGUCCAUGUGUGUUGUGUGCGGGUGCGUGUGUGUGUGCGAAGUGGCAUUCGGACG---AGAGCAUUUGUUGUUGUAGGUUUUAGUGCCAUCGUUGUGUAUC
..((((((((((.....)))).)))))).....(..((((....))))..)(((..(((.((((((((..(((.---(.((((.....)))).)..)))..))))))))..)))..))). ( -38.80)
>DroYak_CAF1 7661 108 + 1
AAAUAUGGCGGCAUGUCGCCG-CCAUGUGUAUU---U--------GUGAGUGUGUGUGAAGUGGCAUUCGAACAGGGAGAGCAUUUGUUGUUGUAGGUUUUAGUGCCAUCGUUGUGUAUC
..((((((((((.....))))-)))))).....---.--------......(((..(((.((((((((.((((....(.((((.....)))).)..)))).))))))))..)))..))). ( -36.60)
>consensus
AAAUAUGGCGGCAUGUCGCCGUCCAUGUGUGUU___UGCG___G_GUGUGUGUGUGUGAAGUGGCAUUCGGACG_GGAGAGCAUUUGUUGUUGUAGGUUUUAGUGCCAUCGUUGUGUAUC
..((((((((((.....)))).)))))).......................(((..(((.((((((((..(((....(.((((.....)))).)..)))..))))))))..)))..))). (-33.37 = -32.93 +  -0.44)

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 10:47:55 2006