Locus 4477

Sequence ID X_DroMel_CAF1
Location 11,848,003 – 11,848,228
Length 225
Max. P 0.992413
window7358 window7359 window7360 window7361 window7362

overview

Window 8

Location 11,848,003 – 11,848,122
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 57.38
Mean single sequence MFE -20.07
Consensus MFE -13.39
Energy contribution -12.40
Covariance contribution -0.99
Combinations/Pair 1.24
Mean z-score -0.80
Structure conservation index 0.67
SVM decision value 0.70
SVM RNA-class probability 0.828017
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11848003 119 - 22224390
UCCAAAACAGAUUGCGAAAGUGCAGCAUUACAGUUUUGAAAAGCGUAAUGAGAAGUUUUCGAGUU-UAAGCAGCUCAAAGUUUGAACACUUUUUGAACAGAAAACAGAAACUGAAGCCUA
.......(((...((....))....((((((.((((....))))))))))....(((((((((((-.....)))))...(((..((.....))..))).)))))).....)))....... ( -25.10)
>DroSim_CAF1 3671 118 - 1
UCCAAAACAGAUUGCGA-AGCGCAGCAUCGCAGUUUUGAAAAGCGUAAUGAGAAGUUUUCAAGUU-UAAGCACCUCAAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
..((((((....(((((-.((...)).)))))))))))..........((((..((((.......-.))))..))))........................................... ( -16.50)
>DroEre_CAF1 4112 94 - 1
UUCAAGGCAGAUUGCGAAAGCGCAGCAUCACAGUUUCGAAAACACCAACGAGGCGUUUUCAAAUUAUAAGCAACUCGAGGUUUUAAG--------------------------AAGUCAA
.....(((.....((....))...((.....(((((.((((((.((.....)).)))))))))))....))................--------------------------..))).. ( -18.60)
>consensus
UCCAAAACAGAUUGCGAAAGCGCAGCAUCACAGUUUUGAAAAGCGUAAUGAGAAGUUUUCAAGUU_UAAGCAACUCAAAGUUU_AA___________________________AAG_C_A
..((((((.(((((((....))))..)))...))))))..........((((..((((.........))))..))))........................................... (-13.39 = -12.40 +  -0.99)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,848,082 – 11,848,188
Length 106
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.48
Mean single sequence MFE -27.45
Consensus MFE -18.55
Energy contribution -20.30
Covariance contribution 1.75
Combinations/Pair 1.17
Mean z-score -2.37
Structure conservation index 0.68
SVM decision value 1.65
SVM RNA-class probability 0.969679
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11848082 106 + 22224390
UUCAAAACUGUAAUGCUGCACUUUCGCAAUCUGUUUUGGAAUAUUUUUUUUUUUGCAAUUUGCCAUCGGGUUAAUU--------------UGCCCGUUGGCGACUUCUGUUGCUCUGUUA
((((((((.(...(((.........)))..).))))))))..............(((((((((((.(((((.....--------------.))))).)))))).....)))))....... ( -29.30)
>DroSim_CAF1 3750 100 + 1
UUCAAAACUGCGAUGCUGCGCU-UCGCAAUCUGUUUUGGAAUAUUU-----UUUGCAAUUUGCCAUCGGGUUAAUU--------------UGCCCGUUGGCGACUUCUGUUGCUCUGUUA
(((((((((((((.((...)).-)))))....))))))))......-----...(((((((((((.(((((.....--------------.))))).)))))).....)))))....... ( -34.30)
>DroEre_CAF1 4166 100 + 1
UUCGAAACUGUGAUGCUGCGCUUUCGCAAUCUGCCUUGAAAU--AU----UUUUGCAAUUUGCCAUCGGGUUAAUU--------------UGCCCGUUGCCGGCUACUGUAACUCUGUUA
......((.(((..((((.((....((((..(((...(((..--..----))).)))..))))...(((((.....--------------.)))))..))))))))).)).......... ( -21.90)
>DroYak_CAF1 4056 114 + 1
UUCGAA--UGUGAUGCUGCACUUUCGCCAUCUGUUUUGCAAUAUAU----UUUAGCAAUUCGCCAUCGGGUUAAUUUUCCCAAUGCCCAUUGCCUGUUGCCGGCUUCUGUUGCUCUGUUA
..((((--.(((......))).))))...........((((((.(.----.(..(((((..((.((.((((.............)))))).))..)))))..)..).))))))....... ( -24.32)
>consensus
UUCAAAACUGUGAUGCUGCACUUUCGCAAUCUGUUUUGGAAUAUAU____UUUUGCAAUUUGCCAUCGGGUUAAUU______________UGCCCGUUGCCGACUUCUGUUGCUCUGUUA
((((((((...(((..(((......)))))).))))))))..............(((((((((((.(((((....................))))).)))))).....)))))....... (-18.55 = -20.30 +   1.75)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,848,082 – 11,848,188
Length 106
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.48
Mean single sequence MFE -25.57
Consensus MFE -12.95
Energy contribution -13.07
Covariance contribution 0.13
Combinations/Pair 1.17
Mean z-score -2.45
Structure conservation index 0.51
SVM decision value 0.21
SVM RNA-class probability 0.636546
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11848082 106 - 22224390
UAACAGAGCAACAGAAGUCGCCAACGGGCA--------------AAUUAACCCGAUGGCAAAUUGCAAAAAAAAAAAUAUUCCAAAACAGAUUGCGAAAGUGCAGCAUUACAGUUUUGAA
...((((((..........((((.((((..--------------......)))).))))...((((..............((.......))..((....)))))).......)))))).. ( -24.00)
>DroSim_CAF1 3750 100 - 1
UAACAGAGCAACAGAAGUCGCCAACGGGCA--------------AAUUAACCCGAUGGCAAAUUGCAAA-----AAAUAUUCCAAAACAGAUUGCGA-AGCGCAGCAUCGCAGUUUUGAA
.......((((..(....)((((.((((..--------------......)))).))))...))))...-----........((((((....(((((-.((...)).))))))))))).. ( -27.80)
>DroEre_CAF1 4166 100 - 1
UAACAGAGUUACAGUAGCCGGCAACGGGCA--------------AAUUAACCCGAUGGCAAAUUGCAAAA----AU--AUUUCAAGGCAGAUUGCGAAAGCGCAGCAUCACAGUUUCGAA
.....(((((.(....(((..((.((((..--------------......)))).))((.....))....----..--.......))).....((....))).))).))........... ( -20.90)
>DroYak_CAF1 4056 114 - 1
UAACAGAGCAACAGAAGCCGGCAACAGGCAAUGGGCAUUGGGAAAAUUAACCCGAUGGCGAAUUGCUAAA----AUAUAUUGCAAAACAGAUGGCGAAAGUGCAGCAUCACA--UUCGAA
.....((((((........(....).((((((.(.(((((((........))))))).)..))))))...----.....))))......((((((....))....))))...--.))... ( -29.60)
>consensus
UAACAGAGCAACAGAAGCCGCCAACGGGCA______________AAUUAACCCGAUGGCAAAUUGCAAAA____AAAUAUUCCAAAACAGAUUGCGAAAGCGCAGCAUCACAGUUUCGAA
.....((((..........((((.((((......................)))).))))....(((................(......)...((....))))))).))........... (-12.95 = -13.07 +   0.13)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,848,122 – 11,848,228
Length 106
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.08
Mean single sequence MFE -29.05
Consensus MFE -25.19
Energy contribution -24.50
Covariance contribution -0.69
Combinations/Pair 1.22
Mean z-score -2.65
Structure conservation index 0.87
SVM decision value 2.33
SVM RNA-class probability 0.992413
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11848122 106 + 22224390
AUAUUUUUUUUUUUGCAAUUUGCCAUCGGGUUAAUU--------------UGCCCGUUGGCGACUUCUGUUGCUCUGUUAUCAGGCCGGGCUAUCCAGCCCUCCAAUUCUCCGCUUAUCA
..............(((((((((((.(((((.....--------------.))))).)))))).....)))))((((....))))..(((((....)))))................... ( -31.40)
>DroSim_CAF1 3789 101 + 1
AUAUUU-----UUUGCAAUUUGCCAUCGGGUUAAUU--------------UGCCCGUUGGCGACUUCUGUUGCUCUGUUAUCAGGCCGGGCUAUCCAGCCCUCCAAUUGUCCGCUUAUCA
......-----...((.....((((.(((((.....--------------.))))).))))(((.......((.(((....))))).(((((....))))).......))).))...... ( -32.80)
>DroEre_CAF1 4206 100 + 1
AU--AU----UUUUGCAAUUUGCCAUCGGGUUAAUU--------------UGCCCGUUGCCGGCUACUGUAACUCUGUUAUCAGGUCGGGCUAUCCAGCCCUCCAAUUGUUCGCUUAUCA
..--..----....((((((.(((..(((((.....--------------.))))).....)))..(((((((...)))).)))...(((((....)))))...)))))).......... ( -25.40)
>DroYak_CAF1 4094 116 + 1
AUAUAU----UUUAGCAAUUCGCCAUCGGGUUAAUUUUCCCAAUGCCCAUUGCCUGUUGCCGGCUUCUGUUGCUCUGUUAUCAGGCCGGGCUAUCCAGUCCUCCAAUUGUUCGCUUAUCA
......----...(((((((.......(((........)))...((((...(((((..((.(((.......)).).))...))))).)))).............)))))))......... ( -26.60)
>consensus
AUAUAU____UUUUGCAAUUUGCCAUCGGGUUAAUU______________UGCCCGUUGCCGACUUCUGUUGCUCUGUUAUCAGGCCGGGCUAUCCAGCCCUCCAAUUGUCCGCUUAUCA
..............((...((((((.(((((....................))))).))))))........((.(((....))))).(((((....)))))...........))...... (-25.19 = -24.50 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,848,122 – 11,848,228
Length 106
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.08
Mean single sequence MFE -31.53
Consensus MFE -21.92
Energy contribution -22.05
Covariance contribution 0.13
Combinations/Pair 1.12
Mean z-score -3.01
Structure conservation index 0.70
SVM decision value 2.03
SVM RNA-class probability 0.986104
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11848122 106 - 22224390
UGAUAAGCGGAGAAUUGGAGGGCUGGAUAGCCCGGCCUGAUAACAGAGCAACAGAAGUCGCCAACGGGCA--------------AAUUAACCCGAUGGCAAAUUGCAAAAAAAAAAAUAU
......((((.((.(((..(((((....))))).(((((....))).))..)))...))((((.((((..--------------......)))).))))...)))).............. ( -31.50)
>DroSim_CAF1 3789 101 - 1
UGAUAAGCGGACAAUUGGAGGGCUGGAUAGCCCGGCCUGAUAACAGAGCAACAGAAGUCGCCAACGGGCA--------------AAUUAACCCGAUGGCAAAUUGCAAA-----AAAUAU
......((((((..(((..(((((....))))).(((((....))).))..)))..)))((((.((((..--------------......)))).))))....)))...-----...... ( -33.90)
>DroEre_CAF1 4206 100 - 1
UGAUAAGCGAACAAUUGGAGGGCUGGAUAGCCCGACCUGAUAACAGAGUUACAGUAGCCGGCAACGGGCA--------------AAUUAACCCGAUGGCAAAUUGCAAAA----AU--AU
......((((...((((..(((((....)))))((((((....))).))).)))).((((....((((..--------------......)))).))))...))))....----..--.. ( -29.20)
>DroYak_CAF1 4094 116 - 1
UGAUAAGCGAACAAUUGGAGGACUGGAUAGCCCGGCCUGAUAACAGAGCAACAGAAGCCGGCAACAGGCAAUGGGCAUUGGGAAAAUUAACCCGAUGGCGAAUUGCUAAA----AUAUAU
..................(((.((((.....)))))))........(((((((...((((....).)))..))(.(((((((........))))))).)...)))))...----...... ( -31.50)
>consensus
UGAUAAGCGAACAAUUGGAGGGCUGGAUAGCCCGGCCUGAUAACAGAGCAACAGAAGCCGCCAACGGGCA______________AAUUAACCCGAUGGCAAAUUGCAAAA____AAAUAU
......((((......((.(((((....))))).(((((....))).))........))((((.((((......................)))).))))...)))).............. (-21.92 = -22.05 +   0.13)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:05 2006