Locus 8040

Sequence ID X_DroMel_CAF1
Location 19,987,037 – 19,987,179
Length 142
Max. P 0.984233
window13193 window13194 window13195

overview

Window 3

Location 19,987,037 – 19,987,129
Length 92
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 73.51
Mean single sequence MFE -30.38
Consensus MFE -19.40
Energy contribution -19.72
Covariance contribution 0.32
Combinations/Pair 1.13
Mean z-score -1.67
Structure conservation index 0.64
SVM decision value 0.86
SVM RNA-class probability 0.868252
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19987037 92 + 22224390
GAACAGUCUGCGGGGAAUGGAAGUAGCUCGGAUUCCCUGCUCCAUG-------------------------AUGUUCCCUGCUGCCGCCCCAAGGACACCGGAUUCUUUUCCAUUCA
(((..((((..((((...((.(((((...(((....(........)-------------------------....)))))))).)).))))..))))...(((......))).))). ( -26.20)
>DroSec_CAF1 24629 117 + 1
GAACAGUCUACGGGGAGUGUAAGGAGCUCGGAUUCCCUGCUCCCUGCUCCCUGCUCCCUGCUCCAUGCACCAUGUUCCCUGCUGCCGCCCCAAGGACUCCGGAUUCUUUUCCAUUCA
(((.(((((..((((.(((((.(((((..(((......((.....)).......)))..))))).)))))...((.....)).....))))..)))))..(((......))).))). ( -36.42)
>DroSim_CAF1 17815 103 + 1
GAACAGUCUACGGGGAGUGUAAGGAGCUCGGAUUCCCUGCUCCC--------------UGCUCCAUGCACCAUGUUCCCUGCUGCCGCCCCAAGGACUCCGGAUUCUUUUCCAUUCA
(((.(((((..((((.(((((.(((((..(((........))).--------------.))))).)))))...((.....)).....))))..)))))..(((......))).))). ( -34.60)
>DroEre_CAF1 19488 75 + 1
GAACAGUCCACGGGGAGUGGAAGGAGCUCGGAUUCCCUGCUC------------------------------------------ACGCCCCAAGGACUCGGGAUUCUUUUCCAUUCA
(((.(((((...(((.(((....((((..((....)).))))------------------------------------------.))))))..))))).((((.....)))).))). ( -27.30)
>DroYak_CAF1 17483 75 + 1
GAACAGUCUACGGGGAGUGGAAGGAGCUCGGAUUCCUUGCUC------------------------------------------CCGCCUCAAGGACUCUGGAUUCUUUUCCAUUCA
......((....))((((((((((((..((((.((((((...------------------------------------------......)))))).))))..))).))))))))). ( -27.40)
>consensus
GAACAGUCUACGGGGAGUGGAAGGAGCUCGGAUUCCCUGCUCC____________________________AUGUUCCCUGCUGCCGCCCCAAGGACUCCGGAUUCUUUUCCAUUCA
(((..((((..((((.......(((((..((....)).)))))..............................((.....)).....))))..))))...(((......))).))). (-19.40 = -19.72 +   0.32)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,987,089 – 19,987,179
Length 90
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 86.38
Mean single sequence MFE -34.88
Consensus MFE -27.16
Energy contribution -28.85
Covariance contribution 1.69
Combinations/Pair 1.07
Mean z-score -2.88
Structure conservation index 0.78
SVM decision value 1.97
SVM RNA-class probability 0.984233
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19987089 90 + 22224390
CCUGCUGCCGCCCCAAGGACACCGGAUUCUUUUCCAUUCAUGUUCCUGGGGAGCCGAA------GCAGUUGCGAUUCCCUUUGGGCGUGUUGCAGA
.((((.(((((((.((((.....(((......))).(((..(((((...))))).)))------((....)).....)))).))))).)).)))). ( -33.60)
>DroSec_CAF1 24706 90 + 1
CCUGCUGCCGCCCCAAGGACUCCGGAUUCUUUUCCAUUCAUGUUCCUUGGGAGCAGAU------GCAGUUGCAAUUCCCUUUGGGCGUGCUGCAGA
.((((.(((((((.((((.....(((......)))..((.((((((...))))))))(------((....)))....)))).))))).)).)))). ( -37.40)
>DroSim_CAF1 17878 90 + 1
CCUGCUGCCGCCCCAAGGACUCCGGAUUCUUUUCCAUUCAUGUUCCUGGGGAGCAGAU------GCAGUUGCAAUUCCCUUUGGGCGUGCUACAGA
.(((..(((((((.((((.....(((......)))..((.((((((...))))))))(------((....)))....)))).))))).))..))). ( -34.10)
>DroEre_CAF1 19530 89 + 1
-------ACGCCCCAAGGACUCGGGAUUCUUUUCCAUUCAUGUUCCUGAGGAGCAGAUGCAGAUGCAGAUGCAAUUCCUUUUGGGCGUGUUGCAGA
-------((((((.((((((((((((.................)))))))..(((..(((....)))..)))...)))))..))))))........ ( -34.43)
>consensus
CCUGCUGCCGCCCCAAGGACUCCGGAUUCUUUUCCAUUCAUGUUCCUGGGGAGCAGAU______GCAGUUGCAAUUCCCUUUGGGCGUGCUGCAGA
.((((.(((((((.((((.....(((......)))..((.((((((...)))))))).......((....)).....)))).))))).)).)))). (-27.16 = -28.85 +   1.69)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,987,089 – 19,987,179
Length 90
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 86.38
Mean single sequence MFE -32.66
Consensus MFE -23.26
Energy contribution -25.02
Covariance contribution 1.75
Combinations/Pair 1.08
Mean z-score -2.42
Structure conservation index 0.71
SVM decision value 1.10
SVM RNA-class probability 0.914894
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19987089 90 - 22224390
UCUGCAACACGCCCAAAGGGAAUCGCAACUGC------UUCGGCUCCCCAGGAACAUGAAUGGAAAAGAAUCCGGUGUCCUUGGGGCGGCAGCAGG
.((((..(.(((((...((((..((.......------..))..))))((((.((((...((((......)))))))).))))))))))..)))). ( -33.00)
>DroSec_CAF1 24706 90 - 1
UCUGCAGCACGCCCAAAGGGAAUUGCAACUGC------AUCUGCUCCCAAGGAACAUGAAUGGAAAAGAAUCCGGAGUCCUUGGGGCGGCAGCAGG
..(((((....(((...)))..))))).((((------..((((.((((((((.......((((......))))...))))))))))))..)))). ( -36.60)
>DroSim_CAF1 17878 90 - 1
UCUGUAGCACGCCCAAAGGGAAUUGCAACUGC------AUCUGCUCCCCAGGAACAUGAAUGGAAAAGAAUCCGGAGUCCUUGGGGCGGCAGCAGG
.((((.((.(((((.((((....(((....))------)...(((((.((......))...(((......)))))))))))).))))))).)))). ( -34.40)
>DroEre_CAF1 19530 89 - 1
UCUGCAACACGCCCAAAAGGAAUUGCAUCUGCAUCUGCAUCUGCUCCUCAGGAACAUGAAUGGAAAAGAAUCCCGAGUCCUUGGGGCGU-------
........((((((..(((((...(((..(((....)))..)))..(((.(((.................))).)))))))).))))))------- ( -26.63)
>consensus
UCUGCAACACGCCCAAAGGGAAUUGCAACUGC______AUCUGCUCCCCAGGAACAUGAAUGGAAAAGAAUCCGGAGUCCUUGGGGCGGCAGCAGG
.((((.((.(((((...((((...(((..............))))))).((((.......((((......))))...))))..))))))).)))). (-23.26 = -25.02 +   1.75)

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 12:53:53 2006