Locus 6117

Sequence ID 2L_DroMel_CAF1
Location 17,117,572 – 17,117,730
Length 158
Max. P 0.808955
window9746 window9747 window9748 window9749

overview

Window 6

Location 17,117,572 – 17,117,690
Length 118
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 86.38
Mean single sequence MFE -29.20
Consensus MFE -20.33
Energy contribution -20.45
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -1.60
Structure conservation index 0.70
SVM decision value 0.13
SVM RNA-class probability 0.598711
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17117572 118 + 22407834
CCUAAGCGCAUUAGCUUUAGUUUCUAGAAUUUUUUCUUAGCUUCCACUUGGCCGGCGAGGCCAAAGUUGGUUUUACCAAAGGAGCAAAGUGGUAAAAAAUGGAAAAAAAAAAUUGGCA
.((((((......)).))))((((((...(((((.(((.(((((...((((((.....))))))..((((.....)))).))))).)))....))))).))))))............. ( -29.20)
>DroSec_CAF1 81361 118 + 1
CCUAAGCGCAUUAGCUUUAGUUUCUAGCUUUUUUUCUUAGCUUCCACUUGGCCAGCUAGGCCAAAGUUGGUUUUACCAGAAGAGCAAAGUGGUAAAAAAAAUGAAAAAAAAAUUGGCA
.((((((......)).))))......((((((((((.......((((((((((.....)))).))).)))((((((((...........)))))))).....))))))).....))). ( -27.00)
>DroEre_CAF1 83444 115 + 1
ACUAAGCGCAUUAGCCUUAGUUUCUAGCAUUUUUUCGCAGCUUCCACUUGGCCAGCGAGGCCAAAGUUGGUCUAACCAGAAGAGCAAAGUGGUAAAAAGGGU---AAAAAAAUUGGCA
((((((.((....)))))))).....(((((((((..(..(((((((((((((.....))))...(((..(((....)))..))).))))))....))).).---.)))))))..)). ( -31.60)
>DroYak_CAF1 83297 113 + 1
ACUAAGCGAAUUAGCUUCAGGUUCUAGCAUUUUUUUGAAGCUUCCACUUGGCCAGCGAGGCCAAAGUUGGUUUUACAAGAAGAGCAAAGUGGUAAAAAAG-U----ACAAAAUUGCAA
.....((((...(((((((((............))))))))).((((((((((.....))))))..(((.((((.....)))).))).))))........-.----......)))).. ( -29.00)
>consensus
ACUAAGCGCAUUAGCUUUAGUUUCUAGCAUUUUUUCGUAGCUUCCACUUGGCCAGCGAGGCCAAAGUUGGUUUUACCAGAAGAGCAAAGUGGUAAAAAAGGU___AAAAAAAUUGGCA
.((((((......)).)))).......................((((((((((.....))))))..(((.((((.....)))).))).)))).......................... (-20.33 = -20.45 +   0.12)

alignment

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secondary structure

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Window 7

Location 17,117,572 – 17,117,690
Length 118
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 86.38
Mean single sequence MFE -28.32
Consensus MFE -20.56
Energy contribution -21.25
Covariance contribution 0.69
Combinations/Pair 1.10
Mean z-score -1.96
Structure conservation index 0.73
SVM decision value 0.64
SVM RNA-class probability 0.808955
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17117572 118 - 22407834
UGCCAAUUUUUUUUUUCCAUUUUUUACCACUUUGCUCCUUUGGUAAAACCAACUUUGGCCUCGCCGGCCAAGUGGAAGCUAAGAAAAAAUUCUAGAAACUAAAGCUAAUGCGCUUAGG
....((((((((((((((((.((((((((...........))))))))......((((((.....)))))))))))....))))))))))).......((((.((....))..)))). ( -28.30)
>DroSec_CAF1 81361 118 - 1
UGCCAAUUUUUUUUUCAUUUUUUUUACCACUUUGCUCUUCUGGUAAAACCAACUUUGGCCUAGCUGGCCAAGUGGAAGCUAAGAAAAAAAGCUAGAAACUAAAGCUAAUGCGCUUAGG
.......(((((((((.....((((((((...........))))))))(((...((((((.....)))))).))).......))))))))).......((((.((....))..)))). ( -29.20)
>DroEre_CAF1 83444 115 - 1
UGCCAAUUUUUUU---ACCCUUUUUACCACUUUGCUCUUCUGGUUAGACCAACUUUGGCCUCGCUGGCCAAGUGGAAGCUGCGAAAAAAUGCUAGAAACUAAGGCUAAUGCGCUUAGU
.............---.....(((((.((.(((((.(((((((.....)).((((.((((.....)))))))))))))..)))))....)).)))))((((((((....)).)))))) ( -29.10)
>DroYak_CAF1 83297 113 - 1
UUGCAAUUUUGU----A-CUUUUUUACCACUUUGCUCUUCUUGUAAAACCAACUUUGGCCUCGCUGGCCAAGUGGAAGCUUCAAAAAAAUGCUAGAACCUGAAGCUAAUUCGCUUAGU
..((........----.-........(((((((((.......))))).......((((((.....)))))))))).(((((((................))))))).....))..... ( -26.69)
>consensus
UGCCAAUUUUUUU___ACCUUUUUUACCACUUUGCUCUUCUGGUAAAACCAACUUUGGCCUCGCUGGCCAAGUGGAAGCUAAGAAAAAAUGCUAGAAACUAAAGCUAAUGCGCUUAGG
.....((((((((........((((((((...........))))))))(((...((((((.....)))))).))).......))))))))........(((.(((......)))))). (-20.56 = -21.25 +   0.69)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,117,612 – 17,117,730
Length 118
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 89.79
Mean single sequence MFE -33.92
Consensus MFE -31.73
Energy contribution -31.47
Covariance contribution -0.25
Combinations/Pair 1.17
Mean z-score -1.30
Structure conservation index 0.94
SVM decision value 0.13
SVM RNA-class probability 0.597357
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17117612 118 + 22407834
CUUCCACUUGGCCGGCGAGGCCAAAGUUGGUUUUACCAAAGGAGCAAAGUGGUAAAAAAUGGAAAAAAAAAAUUGGCAGAAGGUCGCUUCUCUGCAUUAGCUGGUCUGCAAGCGGCUC
.(((((.((((((.....))))))......((((((((...........))))))))..)))))...........(((((.((.....)))))))...(((((.(.....).))))). ( -32.00)
>DroSec_CAF1 81401 118 + 1
CUUCCACUUGGCCAGCUAGGCCAAAGUUGGUUUUACCAGAAGAGCAAAGUGGUAAAAAAAAUGAAAAAAAAAUUGGCAGAAGGUCGCUUCUCUGCAUUAGCUGGCCUGCAAGCGGCUC
...((.(((((((((((((((((...(((.((((.....)))).)))..))))......................(((((.((.....))))))).))))))))))...))).))... ( -36.90)
>DroEre_CAF1 83484 115 + 1
CUUCCACUUGGCCAGCGAGGCCAAAGUUGGUCUAACCAGAAGAGCAAAGUGGUAAAAAGGGU---AAAAAAAUUGGCAGAAGGUCGCUCCUCUGCAUUAGCUGGUCUGCAAGCGGCUC
...((.((((((((((...((((...(((.(((.......))).)))..)))).........---..........(((((.((.....)))))))....))))))...)))).))... ( -35.60)
>DroYak_CAF1 83337 113 + 1
CUUCCACUUGGCCAGCGAGGCCAAAGUUGGUUUUACAAGAAGAGCAAAGUGGUAAAAAAG-U----ACAAAAUUGCAAGAAGGUCGCUCCUCUGCAUUAGCUGGUCCGCAAGCGGCUC
...((.((((((((((...((((...(((.((((.....)))).)))..)))).......-.----.......((((.((.((.....))))))))...))))))...)))).))... ( -31.20)
>consensus
CUUCCACUUGGCCAGCGAGGCCAAAGUUGGUUUUACCAGAAGAGCAAAGUGGUAAAAAAGGU___AAAAAAAUUGGCAGAAGGUCGCUCCUCUGCAUUAGCUGGUCUGCAAGCGGCUC
...((.((((((((((...((((...(((.((((.....)))).)))..))))......................(((((.((.....)))))))....))))))...)))).))... (-31.73 = -31.47 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,117,612 – 17,117,730
Length 118
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 89.79
Mean single sequence MFE -33.05
Consensus MFE -27.67
Energy contribution -28.29
Covariance contribution 0.62
Combinations/Pair 1.07
Mean z-score -1.47
Structure conservation index 0.84
SVM decision value 0.15
SVM RNA-class probability 0.609726
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17117612 118 - 22407834
GAGCCGCUUGCAGACCAGCUAAUGCAGAGAAGCGACCUUCUGCCAAUUUUUUUUUUCCAUUUUUUACCACUUUGCUCCUUUGGUAAAACCAACUUUGGCCUCGCCGGCCAAGUGGAAG
.....(((........)))....((((((........))))))...........((((((.((((((((...........))))))))......((((((.....)))))))))))). ( -28.40)
>DroSec_CAF1 81401 118 - 1
GAGCCGCUUGCAGGCCAGCUAAUGCAGAGAAGCGACCUUCUGCCAAUUUUUUUUUCAUUUUUUUUACCACUUUGCUCUUCUGGUAAAACCAACUUUGGCCUAGCUGGCCAAGUGGAAG
...((((((...(((((((((..((((((........))))))..................((((((((...........))))))))(((....)))..)))))))))))))))... ( -36.90)
>DroEre_CAF1 83484 115 - 1
GAGCCGCUUGCAGACCAGCUAAUGCAGAGGAGCGACCUUCUGCCAAUUUUUUU---ACCCUUUUUACCACUUUGCUCUUCUGGUUAGACCAACUUUGGCCUCGCUGGCCAAGUGGAAG
...(((((((..(.(((((......((((((((((..................---...............))))))))))(((((((.....)))))))..)))))))))))))... ( -33.91)
>DroYak_CAF1 83337 113 - 1
GAGCCGCUUGCGGACCAGCUAAUGCAGAGGAGCGACCUUCUUGCAAUUUUGU----A-CUUUUUUACCACUUUGCUCUUCUUGUAAAACCAACUUUGGCCUCGCUGGCCAAGUGGAAG
...((((((..((.(((((...((((((((((((.....).((((....)))----)-...............))))))).))))...(((....)))....)))))))))))))... ( -33.00)
>consensus
GAGCCGCUUGCAGACCAGCUAAUGCAGAGAAGCGACCUUCUGCCAAUUUUUUU___ACCUUUUUUACCACUUUGCUCUUCUGGUAAAACCAACUUUGGCCUCGCUGGCCAAGUGGAAG
...(((((((..(.(((((.....(((((((((((....................................)))))))))))......(((....)))....)))))))))))))... (-27.67 = -28.29 +   0.62)

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 12:02:24 2006