Locus 6422

Sequence ID X_DroMel_CAF1
Location 16,111,255 – 16,111,433
Length 178
Max. P 0.975843
window10483 window10484 window10485 window10486 window10487

overview

Window 3

Location 16,111,255 – 16,111,358
Length 103
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 86.98
Mean single sequence MFE -35.65
Consensus MFE -26.17
Energy contribution -26.93
Covariance contribution 0.75
Combinations/Pair 1.13
Mean z-score -2.36
Structure conservation index 0.73
SVM decision value 1.10
SVM RNA-class probability 0.914863
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16111255 103 + 22224390
GCUGGGACACUUCUUCGAUGGAAGGCCGUUGCAUUGAAUCGCUUUCCA--UGCAUUCGGCGACACUAUCUGGUGUCGCCGCCCACAUUCUGUCUGCUCAUUGUAG
..((((...........(((((((((.(((......))).))))))))--).....((((((((((....))))))))))))))........((((.....)))) ( -38.50)
>DroSim_CAF1 13755 105 + 1
GCUGGGACACUUCUUCGAUAGAAGGCCUUUGCAUUGAAUCGUUUUCCAAAUGCAUUCGGCGACACUAUCGUGUGUCGCCGCCCACAUUCUGUCUGCUCAUUGUGG
((.(((...(((((.....))))).)))..))...((((((((.....)))).))))((((((((......))))))))..(((((....(....)....))))) ( -35.40)
>DroEre_CAF1 25827 105 + 1
GCUGGGAUACUUCUUCGAUGGAAGGCCUUGGUAUUGAAUUGUUUUCCAAAUGUAUCCGGCGACACCAUACGGUAUCGCCGCCCACAUUGUGUCUGCUCAUUGUUG
((..((((((........((((((((..(........)..))))))))(((((...((((((.(((....))).))))))...)))))))))))))......... ( -32.40)
>DroYak_CAF1 12279 105 + 1
GCUGGGAAACUUCUUCGAUGGAAGGCCUUCGCAUUGAACUGUUUUCCAAAUGUAUCCGGCGAACCAAUCUGGUAUCGCCGCCCACAUUUUGUCUGCUCCUUGUGG
..((((((((...((((((((((....))).)))))))..))))))))........(((((((((.....))).)))))).(((((....(....)....))))) ( -36.30)
>consensus
GCUGGGACACUUCUUCGAUGGAAGGCCUUUGCAUUGAAUCGUUUUCCAAAUGCAUCCGGCGACACUAUCUGGUAUCGCCGCCCACAUUCUGUCUGCUCAUUGUGG
..((((...(((((.....)))))......((((((((.....)))..)))))...(((((((((......)))))))))))))........((((.....)))) (-26.17 = -26.93 +   0.75)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,111,255 – 16,111,358
Length 103
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 86.98
Mean single sequence MFE -33.44
Consensus MFE -26.16
Energy contribution -26.85
Covariance contribution 0.69
Combinations/Pair 1.11
Mean z-score -2.10
Structure conservation index 0.78
SVM decision value 1.01
SVM RNA-class probability 0.900691
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16111255 103 - 22224390
CUACAAUGAGCAGACAGAAUGUGGGCGGCGACACCAGAUAGUGUCGCCGAAUGCA--UGGAAAGCGAUUCAAUGCAACGGCCUUCCAUCGAAGAAGUGUCCCAGC
(((((.((......))...))))).(((((((((......)))))))))..((((--(.(((.....))).)))))..(((((((.......)))).)))..... ( -32.10)
>DroSim_CAF1 13755 105 - 1
CCACAAUGAGCAGACAGAAUGUGGGCGGCGACACACGAUAGUGUCGCCGAAUGCAUUUGGAAAACGAUUCAAUGCAAAGGCCUUCUAUCGAAGAAGUGUCCCAGC
(((((.((......))...))))).(((((((((......)))))))))..((((((.(((......)))))))))..((((((((.....))))).)))..... ( -36.70)
>DroEre_CAF1 25827 105 - 1
CAACAAUGAGCAGACACAAUGUGGGCGGCGAUACCGUAUGGUGUCGCCGGAUACAUUUGGAAAACAAUUCAAUACCAAGGCCUUCCAUCGAAGAAGUAUCCCAGC
.........((...(((...))).))(((((((((....)))))))))((((((.(((((..............)))))..((((....))))..)))))).... ( -32.84)
>DroYak_CAF1 12279 105 - 1
CCACAAGGAGCAGACAAAAUGUGGGCGGCGAUACCAGAUUGGUUCGCCGGAUACAUUUGGAAAACAGUUCAAUGCGAAGGCCUUCCAUCGAAGAAGUUUCCCAGC
((....)).((.....(((((((..((((((.(((.....)))))))))..)))))))((.((((........((....))((((....))))..)))).)).)) ( -32.10)
>consensus
CCACAAUGAGCAGACAGAAUGUGGGCGGCGACACCAGAUAGUGUCGCCGAAUACAUUUGGAAAACAAUUCAAUGCAAAGGCCUUCCAUCGAAGAAGUGUCCCAGC
.........((......((((((..(((((((((......)))))))))..))))))(((...((........((....))((((....))))..))...))))) (-26.16 = -26.85 +   0.69)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,111,286 – 16,111,396
Length 110
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 85.71
Mean single sequence MFE -43.92
Consensus MFE -40.51
Energy contribution -42.33
Covariance contribution 1.81
Combinations/Pair 1.08
Mean z-score -6.12
Structure conservation index 0.92
SVM decision value 1.76
SVM RNA-class probability 0.975843
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16111286 110 + 22224390
CAUUGAAUCGCUUUCCA--UGCAUUCGGCGACACUAUCUGGUGUCGCCGCCCACAUUCUGUCUGCUCAUUGUAGCCAACCUGAUUUGACUUGGAAAACGAUUCAAAUUGAAU
..((((((((.((((((--..((.(((((((((((....)))))))))..........((.((((.....)))).))....))..))...)))))).))))))))....... ( -40.10)
>DroSim_CAF1 13786 112 + 1
CAUUGAAUCGUUUUCCAAAUGCAUUCGGCGACACUAUCGUGUGUCGCCGCCCACAUUCUGUCUGCUCAUUGUGGCCAACCUGAUUUGACUUGGAAAACGAUUCAAAUUGAAU
..((((((((((((((((...((.((((((((((......))))))))(.(((((....(....)....))))).).....))..))..))))))))))))))))....... ( -46.30)
>DroEre_CAF1 25858 112 + 1
UAUUGAAUUGUUUUCCAAAUGUAUCCGGCGACACCAUACGGUAUCGCCGCCCACAUUGUGUCUGCUCAUUGUUGCAGACCUGAUAUGACUUGGAAAACGCUUCAAAUUUGAU
..(((((.((((((((((..(((((((((((.(((....))).))))))..........((((((........))))))..)))))...)))))))))).)))))....... ( -42.60)
>DroYak_CAF1 12310 112 + 1
CAUUGAACUGUUUUCCAAAUGUAUCCGGCGAACCAAUCUGGUAUCGCCGCCCACAUUUUGUCUGCUCCUUGUGGCAGGCCUGAUUUGACUUGGAAAACGGUUCAAAUCCAAU
..((((((((((((((((.......(((((((((.....))).))))))..((.(((..(((((((......)))))))..))).))..))))))))))))))))....... ( -46.70)
>consensus
CAUUGAAUCGUUUUCCAAAUGCAUCCGGCGACACUAUCUGGUAUCGCCGCCCACAUUCUGUCUGCUCAUUGUGGCAAACCUGAUUUGACUUGGAAAACGAUUCAAAUUGAAU
..((((((((((((((((.......(((((((((......)))))))))..((.(((..((((((........))))))..))).))..))))))))))))))))....... (-40.51 = -42.33 +   1.81)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,111,286 – 16,111,396
Length 110
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 85.71
Mean single sequence MFE -47.38
Consensus MFE -43.59
Energy contribution -45.02
Covariance contribution 1.44
Combinations/Pair 1.14
Mean z-score -6.17
Structure conservation index 0.92
SVM decision value 1.72
SVM RNA-class probability 0.973950
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16111286 110 - 22224390
AUUCAAUUUGAAUCGUUUUCCAAGUCAAAUCAGGUUGGCUACAAUGAGCAGACAGAAUGUGGGCGGCGACACCAGAUAGUGUCGCCGAAUGCA--UGGAAAGCGAUUCAAUG
.......((((((((((((((..(((...(((..(((....))))))...)))...(((((..(((((((((......)))))))))..))))--))))))))))))))).. ( -48.00)
>DroSim_CAF1 13786 112 - 1
AUUCAAUUUGAAUCGUUUUCCAAGUCAAAUCAGGUUGGCCACAAUGAGCAGACAGAAUGUGGGCGGCGACACACGAUAGUGUCGCCGAAUGCAUUUGGAAAACGAUUCAAUG
.......((((((((((((((..(((...(((..(((....))))))...))).(((((((..(((((((((......)))))))))..))))))))))))))))))))).. ( -50.70)
>DroEre_CAF1 25858 112 - 1
AUCAAAUUUGAAGCGUUUUCCAAGUCAUAUCAGGUCUGCAACAAUGAGCAGACACAAUGUGGGCGGCGAUACCGUAUGGUGUCGCCGGAUACAUUUGGAAAACAAUUCAAUA
.......(((((..((((((((((((((((...((((((........))))))...)))))..((((((((((....)))))))))).....)))))))))))..))))).. ( -48.70)
>DroYak_CAF1 12310 112 - 1
AUUGGAUUUGAACCGUUUUCCAAGUCAAAUCAGGCCUGCCACAAGGAGCAGACAAAAUGUGGGCGGCGAUACCAGAUUGGUUCGCCGGAUACAUUUGGAAAACAGUUCAAUG
.......((((((.(((((((..(((......)))((((........))))...(((((((..((((((.(((.....)))))))))..)))))))))))))).)))))).. ( -42.10)
>consensus
AUUCAAUUUGAAUCGUUUUCCAAGUCAAAUCAGGUCGGCCACAAUGAGCAGACAGAAUGUGGGCGGCGACACCAGAUAGUGUCGCCGAAUACAUUUGGAAAACAAUUCAAUG
.......(((((((((((((((...........((((((........))))))..((((((..(((((((((......)))))))))..))))))))))))))))))))).. (-43.59 = -45.02 +   1.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,111,318 – 16,111,433
Length 115
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 86.67
Mean single sequence MFE -26.45
Consensus MFE -20.80
Energy contribution -22.43
Covariance contribution 1.63
Combinations/Pair 1.15
Mean z-score -1.39
Structure conservation index 0.79
SVM decision value -0.03
SVM RNA-class probability 0.516830
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16111318 115 + 22224390
UAUCUGGUGUCGCCGCCCACAUUCUGUCUGCUCAUUGUAGCCAACCUGAUUUGACUUGGAAAACGAUUCAAAUUGAAUUCGGUGAACCGAAUGCAUACUUUUUUUAAUUACCACU
....(((((((.............((.((((.....)))).))....(((((((.(((.....))).)))))))))((((((....))))))................))))).. ( -23.80)
>DroSim_CAF1 13820 115 + 1
UAUCGUGUGUCGCCGCCCACAUUCUGUCUGCUCAUUGUGGCCAACCUGAUUUGACUUGGAAAACGAUUCAAAUUGAAUUCGGUGAACCGAAUGCAUACUUUUUUUAAUUGUCACU
....((((((....(.(((((....(....)....))))).).....(((((((.(((.....))).)))))))..((((((....))))))))))))................. ( -27.10)
>DroEre_CAF1 25892 115 + 1
CAUACGGUAUCGCCGCCCACAUUGUGUCUGCUCAUUGUUGCAGACCUGAUAUGACUUGGAAAACGCUUCAAAUUUGAUUCGGUGAACCGAAUUCAAACUUUUUUUAAUUAACACU
....((((.((((((..((.((((.((((((........)))))).)))).))..(((((......)))))........)))))))))).......................... ( -27.20)
>DroYak_CAF1 12344 110 + 1
AAUCUGGUAUCGCCGCCCACAUUUUGUCUGCUCCUUGUGGCAGGCCUGAUUUGACUUGGAAAACGGUUCAAAUCCAAUUCGGUAAACCGAAUGCAUACUUUUUUUAA-----ACU
.....(((((((((..(((((....(....)....)))))..)))..(((((((.(((.....))).)))))))..((((((....))))))).)))))........-----... ( -27.70)
>consensus
UAUCUGGUAUCGCCGCCCACAUUCUGUCUGCUCAUUGUGGCAAACCUGAUUUGACUUGGAAAACGAUUCAAAUUGAAUUCGGUGAACCGAAUGCAUACUUUUUUUAAUUA_CACU
....((((.((((((..........((((((........))))))..(((((((.(((.....))).))))))).....)))))))))).......................... (-20.80 = -22.43 +   1.63)

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 12:13:22 2006