Locus 5363

Sequence ID X_DroMel_CAF1
Location 13,959,509 – 13,959,737
Length 228
Max. P 0.901615
window8704 window8705 window8706 window8707

overview

Window 4

Location 13,959,509 – 13,959,617
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.87
Mean single sequence MFE -35.62
Consensus MFE -26.48
Energy contribution -26.23
Covariance contribution -0.25
Combinations/Pair 1.10
Mean z-score -2.24
Structure conservation index 0.74
SVM decision value 1.02
SVM RNA-class probability 0.901615
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13959509 108 - 22224390
AAAUCGCCAGUUGGCGAUGGU------------GGACAACGGGGCGUAUGUGUGUAUUCCCCAAUGCAUAUGCAUAUGGAUAUGGAUAUGGAUAUAGAUGCGUGUCGAUGCGCUGACCAA
..((((((....))))))(((------------((.((.(((.((((((.(((((..((((((((((....)))).)))....))).....))))).)))))).))).))..)).))).. ( -38.30)
>DroSec_CAF1 11008 97 - 1
-AAUCGUCAGUUGGCGGUGGU------------GGACAACGGGGCGUAU----GUAUUCCCCAAUGCAUAUGCAUAUGGAU------AUGGAUAUAGAUGCGUGUCGAUGCGCUGACCAA
-.((((((....))))))(((------------((.((.(((.((((((----.(((((((((((((....)))).)))..------..))).))).)))))).))).))..)).))).. ( -33.00)
>DroSim_CAF1 11655 100 - 1
AAAUCGUCAGUUGGCGGUGGU------------GGACAACGGGGCGUAUG--UGUAUUCCCCAAUGCAUAUGCAUAUGGAU------AUGGAUAUAGAUGCGUGUCGAUGCGCUGACCAA
..((((((....))))))(((------------((.((.(((.((((((.--(((((((.(((((((....)))).)))..------..))))))).)))))).))).))..)).))).. ( -35.70)
>DroYak_CAF1 11463 117 - 1
AAAUCGGUUGUUGGCGGUGGUUUGGUGGUGGUGGGACAACGGGGCGUAUG--UGUAUUCCCCAAUGCAUAUGCAUAUGGAUAUGG-UAUGGAUAUAGAUGCGUGUCGAUGCGCUGACCAA
..........(((((((((((((.(......).))))..(((.((((((.--(((((((.(((((.((((....)))).)).)))-...))))))).)))))).)))...))))).)))) ( -35.50)
>consensus
AAAUCGUCAGUUGGCGGUGGU____________GGACAACGGGGCGUAUG__UGUAUUCCCCAAUGCAUAUGCAUAUGGAU______AUGGAUAUAGAUGCGUGUCGAUGCGCUGACCAA
..((((((....))))))(((...............((..((((.((((....)))).)))).((((....)))).))................(((.(((((....))))))))))).. (-26.48 = -26.23 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,959,549 – 13,959,657
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.89
Mean single sequence MFE -28.67
Consensus MFE -25.30
Energy contribution -25.30
Covariance contribution 0.00
Combinations/Pair 1.11
Mean z-score -1.80
Structure conservation index 0.88
SVM decision value 0.93
SVM RNA-class probability 0.883130
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13959549 108 - 22224390
GUUGCCUUUGUAAUUAAAAAGGAAAAGGAAAAUACGACAAAAAUCGCCAGUUGGCGAUGGU------------GGACAACGGGGCGUAUGUGUGUAUUCCCCAAUGCAUAUGCAUAUGGA
(((((((((........)))))............(.((....((((((....)))))).))------------.).))))((((.((((....)))).)))).((((....))))..... ( -32.60)
>DroSec_CAF1 11042 93 - 1
GUUGCCUUUGUAAUUAAAAAGGAAAAGGAA-----------AAUCGUCAGUUGGCGGUGGU------------GGACAACGGGGCGUAU----GUAUUCCCCAAUGCAUAUGCAUAUGGA
(((((((((........)))))........-----------.((((((....))))))...------------...))))...((((((----(((((....)))))))))))....... ( -25.90)
>DroSim_CAF1 11689 106 - 1
GUUGCCUUUGUAAUUAAAAAGGAAAAGGAAAAUACGACAAAAAUCGUCAGUUGGCGGUGGU------------GGACAACGGGGCGUAUG--UGUAUUCCCCAAUGCAUAUGCAUAUGGA
(((((((((........)))))............(.((....((((((....)))))).))------------.).))))((((.(((..--..))).)))).((((....))))..... ( -27.80)
>DroYak_CAF1 11502 112 - 1
GUUUCCUUUGUAAUUAAAAAGGAA------AAUACGACAAAAAUCGGUUGUUGGCGGUGGUUUGGUGGUGGUGGGACAACGGGGCGUAUG--UGUAUUCCCCAAUGCAUAUGCAUAUGGA
.((((((((........)))))))------)...((((((.......)))))).(.(((((((.((.((......)).)).))))(((((--((((((....))))))))))).))).). ( -28.40)
>consensus
GUUGCCUUUGUAAUUAAAAAGGAAAAGGAAAAUACGACAAAAAUCGUCAGUUGGCGGUGGU____________GGACAACGGGGCGUAUG__UGUAUUCCCCAAUGCAUAUGCAUAUGGA
(((((((((........)))))....................((((((....))))))..................))))((((.((((....)))).)))).((((....))))..... (-25.30 = -25.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,959,589 – 13,959,697
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 79.82
Mean single sequence MFE -29.33
Consensus MFE -22.11
Energy contribution -22.42
Covariance contribution 0.31
Combinations/Pair 1.14
Mean z-score -1.60
Structure conservation index 0.75
SVM decision value 0.28
SVM RNA-class probability 0.666139
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13959589 108 - 22224390
GAGGGAUUUGGAAGGCGGCAAAUAGCGCUGCAUCCUUCUUGUUGCCUUUGUAAUUAAAAAGGAAAAGGAAAAUACGACAAAAAUCGCCAGUUGGCGAUGGU------------GGACAAC
(((((((.......(((((.......))))))))))))(((((.(((((........)))))...............((...((((((....))))))..)------------)))))). ( -32.01)
>DroSec_CAF1 11078 97 - 1
GAGGGAAUCGGUGGGCGGAAAAGAGCGCUGCAUCCUUCUUGUUGCCUUUGUAAUUAAAAAGGAAAAGGAA-----------AAUCGUCAGUUGGCGGUGGU------------GGACAAC
((((((..(((((..(......)..)))))..))))))(((((.(((((........)))))........-----------.((((((....))))))...------------.))))). ( -26.80)
>DroSim_CAF1 11727 108 - 1
GAGGGAAUCGGUGGGCGGAAGAGAGCGCUGCAUCCUUCUUGUUGCCUUUGUAAUUAAAAAGGAAAAGGAAAAUACGACAAAAAUCGUCAGUUGGCGGUGGU------------GGACAAC
((((((..(((((..(....)....)))))..))))))(((((.(((((........)))))...............((...((((((....))))))..)------------)))))). ( -29.40)
>DroYak_CAF1 11540 110 - 1
GAGGGAAUCG----GCGAAAAAGAGCGCUGCAUCCUUCUUGUUUCCUUUGUAAUUAAAAAGGAA------AAUACGACAAAAAUCGGUUGUUGGCGGUGGUUUGGUGGUGGUGGGACAAC
((((((..((----(((........)))))..))))))(((((((((((........)))))).------..(((.(((((.((((.(....).))))..))).)).)))....))))). ( -29.10)
>consensus
GAGGGAAUCGGUGGGCGGAAAAGAGCGCUGCAUCCUUCUUGUUGCCUUUGUAAUUAAAAAGGAAAAGGAAAAUACGACAAAAAUCGUCAGUUGGCGGUGGU____________GGACAAC
((((((..((((..((........))))))..))))))(((((.(((((........)))))....................((((((....))))))................))))). (-22.11 = -22.42 +   0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,959,617 – 13,959,737
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.86
Mean single sequence MFE -30.35
Consensus MFE -20.99
Energy contribution -21.55
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.65
Structure conservation index 0.69
SVM decision value 0.20
SVM RNA-class probability 0.632076
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13959617 120 - 22224390
GCCGCCCACCGGAAAAUAUAUGUGCACAAAUAGCGAGCGAGAGGGAUUUGGAAGGCGGCAAAUAGCGCUGCAUCCUUCUUGUUGCCUUUGUAAUUAAAAAGGAAAAGGAAAAUACGACAA
.(((.....)))........(((((.......)).((((((((((((.......(((((.......))))))))))))))))).(((((........)))))..............))). ( -28.81)
>DroSec_CAF1 11105 110 - 1
GCUACCCACCGGAAAAUAUAUGUGGAGAAAUAGCGAGCGAGAGGGAAUCGGUGGGCGGAAAAGAGCGCUGCAUCCUUCUUGUUGCCUUUGUAAUUAAAAAGGAAAAGGAA----------
(((((((((............)))).)...)))).(((((((((((..(((((..(......)..)))))..))))))))))).(((((........)))))........---------- ( -31.50)
>DroSim_CAF1 11755 120 - 1
GCUGCCCACCGGAAAAUAUAUGUGCACAAAUAGCGAGCGAGAGGGAAUCGGUGGGCGGAAGAGAGCGCUGCAUCCUUCUUGUUGCCUUUGUAAUUAAAAAGGAAAAGGAAAAUACGACAA
.(((((((((((..........(((.......)))..(....)....))))))))))).................(((((....(((((........)))))...))))).......... ( -31.50)
>DroYak_CAF1 11580 110 - 1
ACCUCCCACCGGAAAAUAUAUGUGCACAAAUUGAGAGCGAGAGGGAAUCG----GCGAAAAAGAGCGCUGCAUCCUUCUUGUUUCCUUUGUAAUUAAAAAGGAA------AAUACGACAA
...(((....))).......((((............((((((((((..((----(((........)))))..))))))))))(((((((........)))))))------..)))).... ( -29.60)
>consensus
GCCGCCCACCGGAAAAUAUAUGUGCACAAAUAGCGAGCGAGAGGGAAUCGGUGGGCGGAAAAGAGCGCUGCAUCCUUCUUGUUGCCUUUGUAAUUAAAAAGGAAAAGGAAAAUACGACAA
...................................(((((((((((..((((..((........))))))..))))))))))).(((((........))))).................. (-20.99 = -21.55 +   0.56)

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 11:46:13 2006