Locus 1717

Sequence ID X_DroMel_CAF1
Location 4,780,769 – 4,780,917
Length 148
Max. P 0.999550
window2816 window2817 window2818 window2819

overview

Window 6

Location 4,780,769 – 4,780,877
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 85.43
Mean single sequence MFE -27.93
Consensus MFE -22.51
Energy contribution -23.07
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -1.77
Structure conservation index 0.81
SVM decision value 0.16
SVM RNA-class probability 0.613164
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4780769 108 + 22224390
GCCAACUGACGAAACUGACGAAAAUCGACUAGAGGUGGUGGAGA---------AACAUCGAUGCCAAACAUCGAUAUUUUCGAAAAAUCACAUAAAUUGGUG---UUUUUUGAUGAAUAU
..(((..(((........((.....))(((((..(((((...((---------((.(((((((.....)))))))..)))).....))))).....))))))---))..)))........ ( -20.00)
>DroSec_CAF1 20359 117 + 1
GCCAACUGGCGAAACUGACGAAAAUCGACUAGAGGUGGAGAAAAAUUGAUGCCAACAUCGAUGUCAAACAUCGAUAUUUUCGAAGAAUCACAAACAUCGGUG---UUUUUCGAGGAAUCA
(((....))).....((((.....((.((.....)).)).....(((((((....)))))))))))......(((.(((((((((((.(((........)))---)))))))))))))). ( -31.00)
>DroSim_CAF1 14495 120 + 1
GCCAACUGGCGAAACUGACGAAAAUCGACUAGAGGUGGAGAAAAAUUGAUGCCAACAUCGAUGUCAAACAUCGAUAUUUUCGAAGAAUCACAAACAUCGGUUUGUUUUUUCGAGGAAUCA
(((....))).....((((.....((.((.....)).)).....(((((((....)))))))))))......(((.(((((((((((..((((((....)))))))))))))))))))). ( -32.80)
>consensus
GCCAACUGGCGAAACUGACGAAAAUCGACUAGAGGUGGAGAAAAAUUGAUGCCAACAUCGAUGUCAAACAUCGAUAUUUUCGAAGAAUCACAAACAUCGGUG___UUUUUCGAGGAAUCA
.(((.(((((((............))).))))...)))..................(((((((.....))))))).(((((((((((.(((........)))...))))))))))).... (-22.51 = -23.07 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,780,769 – 4,780,877
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.43
Mean single sequence MFE -26.27
Consensus MFE -21.26
Energy contribution -20.60
Covariance contribution -0.66
Combinations/Pair 1.11
Mean z-score -1.58
Structure conservation index 0.81
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4780769 108 - 22224390
AUAUUCAUCAAAAAA---CACCAAUUUAUGUGAUUUUUCGAAAAUAUCGAUGUUUGGCAUCGAUGUU---------UCUCCACCACCUCUAGUCGAUUUUCGUCAGUUUCGUCAGUUGGC
...............---..((((((.(((.((((...((((((((((((((.....))))))))).---------..((.((........)).)).)))))..)))).))).)))))). ( -22.20)
>DroSec_CAF1 20359 117 - 1
UGAUUCCUCGAAAAA---CACCGAUGUUUGUGAUUCUUCGAAAAUAUCGAUGUUUGACAUCGAUGUUGGCAUCAAUUUUUCUCCACCUCUAGUCGAUUUUCGUCAGUUUCGCCAGUUGGC
((((.(((((((.((---(((........))).)).))))).((((((((((.....)))))))))))).)))).................(((((((..((.......))..))))))) ( -26.90)
>DroSim_CAF1 14495 120 - 1
UGAUUCCUCGAAAAAACAAACCGAUGUUUGUGAUUCUUCGAAAAUAUCGAUGUUUGACAUCGAUGUUGGCAUCAAUUUUUCUCCACCUCUAGUCGAUUUUCGUCAGUUUCGCCAGUUGGC
((((.(((((((...((((((....)))))).....))))).((((((((((.....)))))))))))).)))).................(((((((..((.......))..))))))) ( -29.70)
>consensus
UGAUUCCUCGAAAAA___CACCGAUGUUUGUGAUUCUUCGAAAAUAUCGAUGUUUGACAUCGAUGUUGGCAUCAAUUUUUCUCCACCUCUAGUCGAUUUUCGUCAGUUUCGCCAGUUGGC
....................(((((....((((..((.((((((((((((((.....))))))))))....................((.....))..))))..))..))))..))))). (-21.26 = -20.60 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,780,809 – 4,780,917
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 76.40
Mean single sequence MFE -26.13
Consensus MFE -17.24
Energy contribution -17.47
Covariance contribution 0.23
Combinations/Pair 1.10
Mean z-score -2.92
Structure conservation index 0.66
SVM decision value 3.71
SVM RNA-class probability 0.999550
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4780809 108 + 22224390
GAGA---------AACAUCGAUGCCAAACAUCGAUAUUUUCGAAAAAUCACAUAAAUUGGUG---UUUUUUGAUGAAUAUUCAUUUUUGAUGUAUAUUCAAAUUUCUGAUGAAUCAUUGU
.(((---------((.(((((((.....)))))))....((((((((.(((........)))---))))))))(((((((.((((...)))).)))))))..)))))............. ( -23.90)
>DroSec_CAF1 20399 116 + 1
AAAAAUUGAUGCCAACAUCGAUGUCAAACAUCGAUAUUUUCGAAGAAUCACAAACAUCGGUG---UUUUUCGAGGAAUCAUCGUAUAAAUUGUAAGUACAAAUUAAUUUUGCAU-AUCUU
.(((((((((....(((((((((.....))))))).(((((((((((.(((........)))---)))))))))))...................))....)))))))))....-..... ( -26.20)
>DroSim_CAF1 14535 119 + 1
AAAAAUUGAUGCCAACAUCGAUGUCAAACAUCGAUAUUUUCGAAGAAUCACAAACAUCGGUUUGUUUUUUCGAGGAAUCAUCGUAUAAAUUGUAAGAACAAAUUAAUUUUGCAU-AUCUU
.......((((.....(((((((.....))))))).(((((((((((..((((((....)))))))))))))))))..))))........(((((((.........))))))).-..... ( -28.30)
>consensus
AAAAAUUGAUGCCAACAUCGAUGUCAAACAUCGAUAUUUUCGAAGAAUCACAAACAUCGGUG___UUUUUCGAGGAAUCAUCGUAUAAAUUGUAAGUACAAAUUAAUUUUGCAU_AUCUU
................(((((((.....))))))).(((((((((((.(((........)))...)))))))))))............................................ (-17.24 = -17.47 +   0.23)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,780,809 – 4,780,917
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 76.40
Mean single sequence MFE -24.53
Consensus MFE -13.39
Energy contribution -14.17
Covariance contribution 0.78
Combinations/Pair 1.11
Mean z-score -2.43
Structure conservation index 0.55
SVM decision value 1.08
SVM RNA-class probability 0.911529
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4780809 108 - 22224390
ACAAUGAUUCAUCAGAAAUUUGAAUAUACAUCAAAAAUGAAUAUUCAUCAAAAAA---CACCAAUUUAUGUGAUUUUUCGAAAAUAUCGAUGUUUGGCAUCGAUGUU---------UCUC
....................(((((((.(((.....))).)))))))((.(((((---(((........))).))))).))(((((((((((.....))))))))))---------)... ( -21.50)
>DroSec_CAF1 20399 116 - 1
AAGAU-AUGCAAAAUUAAUUUGUACUUACAAUUUAUACGAUGAUUCCUCGAAAAA---CACCGAUGUUUGUGAUUCUUCGAAAAUAUCGAUGUUUGACAUCGAUGUUGGCAUCAAUUUUU
.....-.((((((.....))))))................((((.(((((((.((---(((........))).)).))))).((((((((((.....)))))))))))).))))...... ( -24.60)
>DroSim_CAF1 14535 119 - 1
AAGAU-AUGCAAAAUUAAUUUGUUCUUACAAUUUAUACGAUGAUUCCUCGAAAAAACAAACCGAUGUUUGUGAUUCUUCGAAAAUAUCGAUGUUUGACAUCGAUGUUGGCAUCAAUUUUU
((((.-..(((((.....))))))))).............((((.(((((((...((((((....)))))).....))))).((((((((((.....)))))))))))).))))...... ( -27.50)
>consensus
AAGAU_AUGCAAAAUUAAUUUGUACUUACAAUUUAUACGAUGAUUCCUCGAAAAA___CACCGAUGUUUGUGAUUCUUCGAAAAUAUCGAUGUUUGACAUCGAUGUUGGCAUCAAUUUUU
.......((((((.....)))))).............(((.((.((..((((..............)))).)).)).)))..((((((((((.....))))))))))............. (-13.39 = -14.17 +   0.78)

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 10:17:23 2006