Locus 7506

Sequence ID X_DroMel_CAF1
Location 18,715,070 – 18,715,221
Length 151
Max. P 0.998761
window12311 window12312 window12313 window12314

overview

Window 1

Location 18,715,070 – 18,715,181
Length 111
Sequences 3
Columns 111
Reading direction forward
Mean pairwise identity 77.71
Mean single sequence MFE -26.37
Consensus MFE -13.57
Energy contribution -14.13
Covariance contribution 0.56
Combinations/Pair 1.13
Mean z-score -3.26
Structure conservation index 0.51
SVM decision value 1.52
SVM RNA-class probability 0.961043
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18715070 111 + 22224390
AGAAACCGAUUAUAAAGCGAAUAUAUAAAUGAAAUUACAUCGAAUCCAGACCGAUUUCGAUUUCGAUUUCGAUUUGGAUUUGGAUUUCGGACUCAGAUUCGAAUUCUGAAA
.....(((((((((.........)))))...........(((((((((((.(((..(((....)))..))).)))))))))))...))))..(((((.......))))).. ( -30.00)
>DroSec_CAF1 16388 92 + 1
AGAAACCGAUUAUAAAGCGAAUAUAUAAAUGAAAUUACAUCGAAUCCAGGCCGAUU------------------UGGAUUUGGAU-UCGGAUUCGGAUUCGAGUUCUGAAA
.(((.(((((((((.........)))))...........(((((((((((((....------------------.)).)))))))-))))..)))).)))........... ( -22.30)
>DroYak_CAF1 15970 90 + 1
AGAAUCCGAUUAUAAUGCG--UAUAUAAAUGAAAUUACAUCGAGUCCAUACCGAUU------------------UCGAUGUGGAU-UCAAAUUCGGAUUCGAGUUUUGUAA
.((((((((.........(--((............)))...(((((((((.((...------------------.)).)))))))-))....))))))))........... ( -26.80)
>consensus
AGAAACCGAUUAUAAAGCGAAUAUAUAAAUGAAAUUACAUCGAAUCCAGACCGAUU__________________UGGAUUUGGAU_UCGGAUUCGGAUUCGAGUUCUGAAA
.(((.(((((((((.........)))))...........((((((((((((((...((((........))))..))).))))))).))))..)))).)))........... (-13.57 = -14.13 +   0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,715,070 – 18,715,181
Length 111
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 77.71
Mean single sequence MFE -24.33
Consensus MFE -14.37
Energy contribution -14.59
Covariance contribution 0.23
Combinations/Pair 1.08
Mean z-score -3.55
Structure conservation index 0.59
SVM decision value 3.22
SVM RNA-class probability 0.998761
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18715070 111 - 22224390
UUUCAGAAUUCGAAUCUGAGUCCGAAAUCCAAAUCCAAAUCGAAAUCGAAAUCGAAAUCGGUCUGGAUUCGAUGUAAUUUCAUUUAUAUAUUCGCUUUAUAAUCGGUUUCU
.((((((.......))))))...(((((((.((((((.(((((..(((....)))..))))).)))))).)((((((......))))))...............)))))). ( -26.00)
>DroSec_CAF1 16388 92 - 1
UUUCAGAACUCGAAUCCGAAUCCGA-AUCCAAAUCCA------------------AAUCGGCCUGGAUUCGAUGUAAUUUCAUUUAUAUAUUCGCUUUAUAAUCGGUUUCU
...........(((.((((...(((-(((((...((.------------------....))..))))))))((((((......)))))).............)))).))). ( -22.10)
>DroYak_CAF1 15970 90 - 1
UUACAAAACUCGAAUCCGAAUUUGA-AUCCACAUCGA------------------AAUCGGUAUGGACUCGAUGUAAUUUCAUUUAUAUA--CGCAUUAUAAUCGGAUUCU
...........((((((((...(((-.((((.((((.------------------...)))).)))).)))((((((......)))))).--..........)))))))). ( -24.90)
>consensus
UUUCAGAACUCGAAUCCGAAUCCGA_AUCCAAAUCCA__________________AAUCGGUCUGGAUUCGAUGUAAUUUCAUUUAUAUAUUCGCUUUAUAAUCGGUUUCU
...........(((.((((...(((.(((((.(((........................))).))))))))((((((......)))))).............)))).))). (-14.37 = -14.59 +   0.23)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,715,101 – 18,715,221
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 81.23
Mean single sequence MFE -28.10
Consensus MFE -17.15
Energy contribution -17.60
Covariance contribution 0.45
Combinations/Pair 1.14
Mean z-score -2.02
Structure conservation index 0.61
SVM decision value 0.15
SVM RNA-class probability 0.608093
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18715101 120 + 22224390
AAAUUACAUCGAAUCCAGACCGAUUUCGAUUUCGAUUUCGAUUUGGAUUUGGAUUUCGGACUCAGAUUCGAAUUCUGAAAGCAAUCGCGUAAUUUGUAAACUUUUAGUAGGCAGUGUUUU
(((((((.(((((((((((.(((..(((....)))..))).))))))))))).(((((((.((......))..)))))))((....)))))))))((..((.....))..))........ ( -32.90)
>DroSec_CAF1 16419 101 + 1
AAAUUACAUCGAAUCCAGGCCGAUU------------------UGGAUUUGGAU-UCGGAUUCGGAUUCGAGUUCUGAAAGCAAUCGCGUAAUUUGUAAACUUUUAGUAGGCAGUGUUUU
(((((((.(((((((((((((....------------------.)).)))))))-)))).((((((.......)))))).((....)))))))))((..((.....))..))........ ( -26.80)
>DroYak_CAF1 15999 101 + 1
AAAUUACAUCGAGUCCAUACCGAUU------------------UCGAUGUGGAU-UCAAAUUCGGAUUCGAGUUUUGUAAGCAAUCGCGUUAUUUGUAAACUUUUAGUAGGCAGUGUUUU
...(((((..(((((((((.((...------------------.)).)))))))-))(((((((....))))))))))))((....)).....((((..((.....))..))))...... ( -24.60)
>consensus
AAAUUACAUCGAAUCCAGACCGAUU__________________UGGAUUUGGAU_UCGGAUUCGGAUUCGAGUUCUGAAAGCAAUCGCGUAAUUUGUAAACUUUUAGUAGGCAGUGUUUU
(((((((...((((((((((((...((((........))))..))).))))))).))(((((((....))))))).....((....)))))))))((..((.....))..))........ (-17.15 = -17.60 +   0.45)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,715,101 – 18,715,221
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 81.23
Mean single sequence MFE -21.12
Consensus MFE -15.18
Energy contribution -15.18
Covariance contribution 0.01
Combinations/Pair 1.14
Mean z-score -1.84
Structure conservation index 0.72
SVM decision value 0.51
SVM RNA-class probability 0.765153
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18715101 120 - 22224390
AAAACACUGCCUACUAAAAGUUUACAAAUUACGCGAUUGCUUUCAGAAUUCGAAUCUGAGUCCGAAAUCCAAAUCCAAAUCGAAAUCGAAAUCGAAAUCGGUCUGGAUUCGAUGUAAUUU
.........................((((((((((((((..((((((.......))))))..))).......(((((.(((((..(((....)))..))))).)))))))).)))))))) ( -27.50)
>DroSec_CAF1 16419 101 - 1
AAAACACUGCCUACUAAAAGUUUACAAAUUACGCGAUUGCUUUCAGAACUCGAAUCCGAAUCCGA-AUCCAAAUCCA------------------AAUCGGCCUGGAUUCGAUGUAAUUU
.........................(((((((((....)).........(((((((((...((((-...........------------------..))))..))))))))).))))))) ( -19.72)
>DroYak_CAF1 15999 101 - 1
AAAACACUGCCUACUAAAAGUUUACAAAUAACGCGAUUGCUUACAAAACUCGAAUCCGAAUUUGA-AUCCACAUCGA------------------AAUCGGUAUGGACUCGAUGUAAUUU
.....................(((((.....((.((((..............))))))...((((-.((((.((((.------------------...)))).)))).)))))))))... ( -16.14)
>consensus
AAAACACUGCCUACUAAAAGUUUACAAAUUACGCGAUUGCUUUCAGAACUCGAAUCCGAAUCCGA_AUCCAAAUCCA__________________AAUCGGUCUGGAUUCGAUGUAAUUU
.........................(((((((((....)).........(((((((((...((((................................))))..))))))))).))))))) (-15.18 = -15.18 +   0.01)

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 12:40:38 2006