Locus 4270

Sequence ID X_DroMel_CAF1
Location 11,230,845 – 11,231,059
Length 214
Max. P 0.943761
window7015 window7016 window7017 window7018 window7019

overview

Window 5

Location 11,230,845 – 11,230,947
Length 102
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 97.55
Mean single sequence MFE -26.27
Consensus MFE -25.98
Energy contribution -26.22
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.99
SVM decision value 0.99
SVM RNA-class probability 0.896182
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11230845 102 + 22224390
AGGUGAACAACGGGGCGGAUGAGCAACAUCAGGCAUGCUUCCAAAUAUUACGUAUACGCCCCACGUGCCCAACAGCAAUCGCUCACCAAUUAAAAGCACCAC
.(((((.(...((((((((((.....)))).((.......))..............))))))...(((......)))...).)))))............... ( -27.30)
>DroSim_CAF1 9609 102 + 1
AGGUGAACAACGGGGCGGAUGAGCAACAUCAGGCAUGAUUCCAAAUAUUACGUAUACGCCCCACGUGCCCAACAGCAAUCGCUCACCAAUUAAAAGCACCAC
.(((((.(...((((((((((.....))))..((.((((.......)))).))...))))))...(((......)))...).)))))............... ( -27.80)
>DroEre_CAF1 17543 102 + 1
AGGAGAACAACGGGGCGGAUGAGCAACAUCAGGCAUGCUUCCAAAUAUUACGUAUACGCCCCACGUGCCCAACAGCAAUCGCUCACCAAUUAAAAGCACCAC
.((.((.....((((((((((.....)))).((.......))..............))))))...(((......))).))(((...........))).)).. ( -22.70)
>DroYak_CAF1 9645 102 + 1
AGGUGAACAACGGGGCGGAUGAACGACAUCAGGCAUGCUUCCAAAUAUUACGUAUACGCCCCACGUGCCAAACAGCAAUCGCUCACCAAUUAAAAGCACCAC
.(((((.(...((((((((((.....)))).((.......))..............))))))...(((......)))...).)))))............... ( -27.30)
>consensus
AGGUGAACAACGGGGCGGAUGAGCAACAUCAGGCAUGCUUCCAAAUAUUACGUAUACGCCCCACGUGCCCAACAGCAAUCGCUCACCAAUUAAAAGCACCAC
.(((((.(...((((((((((.....)))).((.......))..............))))))...(((......)))...).)))))............... (-25.98 = -26.22 +   0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,230,845 – 11,230,947
Length 102
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 97.55
Mean single sequence MFE -36.32
Consensus MFE -35.41
Energy contribution -35.73
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.21
Structure conservation index 0.97
SVM decision value 1.22
SVM RNA-class probability 0.932866
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11230845 102 - 22224390
GUGGUGCUUUUAAUUGGUGAGCGAUUGCUGUUGGGCACGUGGGGCGUAUACGUAAUAUUUGGAAGCAUGCCUGAUGUUGCUCAUCCGCCCCGUUGUUCACCU
...............((((((((((((((....))))...((((((.((..((((((((.((.......)).))))))))..)).)))))))))))))))). ( -38.30)
>DroSim_CAF1 9609 102 - 1
GUGGUGCUUUUAAUUGGUGAGCGAUUGCUGUUGGGCACGUGGGGCGUAUACGUAAUAUUUGGAAUCAUGCCUGAUGUUGCUCAUCCGCCCCGUUGUUCACCU
...............((((((((((((((....))))...((((((.((..((((((((.((.......)).))))))))..)).)))))))))))))))). ( -38.30)
>DroEre_CAF1 17543 102 - 1
GUGGUGCUUUUAAUUGGUGAGCGAUUGCUGUUGGGCACGUGGGGCGUAUACGUAAUAUUUGGAAGCAUGCCUGAUGUUGCUCAUCCGCCCCGUUGUUCUCCU
...............((.(((((((((((....))))...((((((.((..((((((((.((.......)).))))))))..)).))))))))))))).)). ( -34.30)
>DroYak_CAF1 9645 102 - 1
GUGGUGCUUUUAAUUGGUGAGCGAUUGCUGUUUGGCACGUGGGGCGUAUACGUAAUAUUUGGAAGCAUGCCUGAUGUCGUUCAUCCGCCCCGUUGUUCACCU
...............((((((((((((((....))))...((((((...(((..(((((.((.......)).)))))))).....)))))))))))))))). ( -34.40)
>consensus
GUGGUGCUUUUAAUUGGUGAGCGAUUGCUGUUGGGCACGUGGGGCGUAUACGUAAUAUUUGGAAGCAUGCCUGAUGUUGCUCAUCCGCCCCGUUGUUCACCU
...............((((((((((((((....))))...((((((.((..((((((((.((.......)).))))))))..)).)))))))))))))))). (-35.41 = -35.73 +   0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,230,909 – 11,231,026
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 94.73
Mean single sequence MFE -25.88
Consensus MFE -25.91
Energy contribution -26.23
Covariance contribution 0.31
Combinations/Pair 1.07
Mean z-score -1.65
Structure conservation index 1.00
SVM decision value 0.91
SVM RNA-class probability 0.879371
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11230909 117 + 22224390
GUGCCCAACAGCAAUCGCUCACCAAUUAAAAGCACCACCAGGUGGCGCAAAUUAAAAGUGAUUAAACCUGCACAGCAGUUAAUUGAGCCAUUACUUUAAUUAAUUGCUGGAAUUCUU
((((......((....))((((...((((..((.((((...)))).))...))))..))))........))))((((((((((((((.......))))))))))))))......... ( -28.40)
>DroSim_CAF1 9673 117 + 1
GUGCCCAACAGCAAUCGCUCACCAAUUAAAAGCACCACCAGGUGGCGCAAAUUAAAAGUGAUUAAAACCGCACAGCAGUUAAUUGAGCCAUUACUUUAAUUAAUCGCUGGAAUUCGU
(((((....(((....)))..............(((....)))))))).........(((........))).((((.((((((((((.......)))))))))).))))........ ( -25.40)
>DroEre_CAF1 17607 117 + 1
GUGCCCAACAGCAAUCGCUCACCAAUUAAAAGCACCACCAGGUGGCACAAAUGAAAAGUGAUUAAGCCCGCACAGCCGUUAAUUGAGCCAUUACUUUAAUUAAUUGCUGGAAUUUGU
(((((....(((....)))..............(((....)))))))).........(((........))).((((.((((((((((.......)))))))))).))))........ ( -25.80)
>DroYak_CAF1 9709 117 + 1
GUGCCAAACAGCAAUCGCUCACCAAUUAAAAGCACCACCAGGUGGCACAAAUGAAAAGUGAUUAAAACCGCACAGCAGUUAAUUGAGCCAUUACUUUAAUUAAUUACUGGAAUUUGU
(((((....(((....)))..............(((....)))))))).........(((........))).(((.(((((((((((.......))))))))))).)))........ ( -23.90)
>consensus
GUGCCCAACAGCAAUCGCUCACCAAUUAAAAGCACCACCAGGUGGCACAAAUGAAAAGUGAUUAAAACCGCACAGCAGUUAAUUGAGCCAUUACUUUAAUUAAUUGCUGGAAUUCGU
(((((....(((....)))..............(((....)))))))).........(((........))).(((((((((((((((.......)))))))))))))))........ (-25.91 = -26.23 +   0.31)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,230,909 – 11,231,026
Length 117
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 94.73
Mean single sequence MFE -32.72
Consensus MFE -28.49
Energy contribution -27.86
Covariance contribution -0.62
Combinations/Pair 1.11
Mean z-score -1.72
Structure conservation index 0.87
SVM decision value 0.37
SVM RNA-class probability 0.710706
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11230909 117 - 22224390
AAGAAUUCCAGCAAUUAAUUAAAGUAAUGGCUCAAUUAACUGCUGUGCAGGUUUAAUCACUUUUAAUUUGCGCCACCUGGUGGUGCUUUUAAUUGGUGAGCGAUUGCUGUUGGGCAC
......(((((((..........(((((.(((((.....((((...)))).........(..((((...(((((((...)))))))..))))..).))))).))))))))))))... ( -35.40)
>DroSim_CAF1 9673 117 - 1
ACGAAUUCCAGCGAUUAAUUAAAGUAAUGGCUCAAUUAACUGCUGUGCGGUUUUAAUCACUUUUAAUUUGCGCCACCUGGUGGUGCUUUUAAUUGGUGAGCGAUUGCUGUUGGGCAC
......((((((..........((((((.(((((...((((((...)))))).......(..((((...(((((((...)))))))..))))..).))))).))))))))))))... ( -35.80)
>DroEre_CAF1 17607 117 - 1
ACAAAUUCCAGCAAUUAAUUAAAGUAAUGGCUCAAUUAACGGCUGUGCGGGCUUAAUCACUUUUCAUUUGUGCCACCUGGUGGUGCUUUUAAUUGGUGAGCGAUUGCUGUUGGGCAC
........((((((((.....((((.((((((........))))))....))))..(((((........(..((((...))))..)........)))))..))))))))........ ( -30.39)
>DroYak_CAF1 9709 117 - 1
ACAAAUUCCAGUAAUUAAUUAAAGUAAUGGCUCAAUUAACUGCUGUGCGGUUUUAAUCACUUUUCAUUUGUGCCACCUGGUGGUGCUUUUAAUUGGUGAGCGAUUGCUGUUUGGCAC
.(((((..(((((.((((((..(((....))).)))))).))))).((((((....(((((........(..((((...))))..)........)))))..)))))).))))).... ( -29.29)
>consensus
ACAAAUUCCAGCAAUUAAUUAAAGUAAUGGCUCAAUUAACUGCUGUGCGGGUUUAAUCACUUUUAAUUUGCGCCACCUGGUGGUGCUUUUAAUUGGUGAGCGAUUGCUGUUGGGCAC
........((((((((.......(((.((((..........)))))))........(((((........(((((((...)))))))........)))))..))))))))........ (-28.49 = -27.86 +  -0.62)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,230,947 – 11,231,059
Length 112
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 92.10
Mean single sequence MFE -27.57
Consensus MFE -24.01
Energy contribution -25.57
Covariance contribution 1.56
Combinations/Pair 1.06
Mean z-score -2.14
Structure conservation index 0.87
SVM decision value 1.34
SVM RNA-class probability 0.943761
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11230947 112 + 22224390
CAGGUGGCGCAAAUUAAAAGUGAUUAAACCUGCACAGCAGUUAAUUGAGCCAUUACUUUAAUUAAUUGCUGGAAUUCUUAAUAAAUUCACAGCCAUACGGUUGACACGUUUA
(((((..(((.........))).....)))))..(((((((((((((((.......)))))))))))))))(((((.......))))).(((((....)))))......... ( -30.00)
>DroSim_CAF1 9711 112 + 1
CAGGUGGCGCAAAUUAAAAGUGAUUAAAACCGCACAGCAGUUAAUUGAGCCAUUACUUUAAUUAAUCGCUGGAAUUCGUAAUAAAUUCACAGCCAUACGGUUGACACGUUUA
...((((((..........(((........))).((((.((((((((((.......)))))))))).)))).....)))..........(((((....))))).)))..... ( -24.30)
>DroEre_CAF1 17645 110 + 1
CAGGUGGCACAAAUGAAAAGUGAUUAAGCCCGCACAGCCGUUAAUUGAGCCAUUACUUUAAUUAAUUGCUGGAAUUUGUGAUA--UUCACAGCCAUACGGUUGACACGUUUA
...(((.(((((((.....(((........))).((((.((((((((((.......)))))))))).))))..)))))))...--....(((((....))))).)))..... ( -29.40)
>DroYak_CAF1 9747 111 + 1
CAGGUGGCACAAAUGAAAAGUGAUUAAAACCGCACAGCAGUUAAUUGAGCCAUUACUUUAAUUAAUUACUGGAAUUUGUGAUA-GUUCACAGCCAUACGGUUGACACAUUUU
...(((.(((((((.....(((........))).(((.(((((((((((.......))))))))))).)))..)))))))...-.....(((((....))))).)))..... ( -26.60)
>consensus
CAGGUGGCACAAAUGAAAAGUGAUUAAAACCGCACAGCAGUUAAUUGAGCCAUUACUUUAAUUAAUUGCUGGAAUUCGUAAUA_AUUCACAGCCAUACGGUUGACACGUUUA
...(((.(((((((.....(((........))).(((((((((((((((.......)))))))))))))))..))))))).........(((((....))))).)))..... (-24.01 = -25.57 +   1.56)

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 11:20:49 2006