Locus 4977

Sequence ID 2R_DroMel_CAF1
Location 16,223,408 – 16,223,548
Length 140
Max. P 0.997937
window7966 window7967 window7968 window7969 window7970

overview

Window 6

Location 16,223,408 – 16,223,498
Length 90
Sequences 4
Columns 90
Reading direction forward
Mean pairwise identity 84.88
Mean single sequence MFE -24.12
Consensus MFE -16.61
Energy contribution -17.80
Covariance contribution 1.19
Combinations/Pair 1.12
Mean z-score -1.54
Structure conservation index 0.69
SVM decision value 0.05
SVM RNA-class probability 0.560658
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16223408 90 + 20766785
GCGAAAGUUGUCAGGCAGUUAAUAAGCCGACUCUUUUGUGGUAGUUGGUUGUAGCUCAGCAGCUCAGUAGCUCAGUAGCUCAGUAGCUGU
((....))......(.(((((...((((((((((.....)).)))))))).)))))).((((((....((((....))))....)))))) ( -26.20)
>DroSec_CAF1 4440 82 + 1
GCGAAAGUUGUCAGGCAGUUAAUAAGCUGACUCUUUUGUGGUAGUUGGCUGUAGCUC--------AGUUGCUCAGUAGCUUAGUAGCUGU
((....))......(((((((.((((((((((((.....)).)))).((((.(((..--------....))))))))))))).))))))) ( -26.50)
>DroSim_CAF1 4488 82 + 1
GCGAAAGUUGUCAGGCAGUUAAUAAGCUGACUCUUUUGUGGUAGUUGGCUGUAGCUC--------AGUUGCUCAGUAGCUCAGUAGCUGU
((....))........(((((...(((..(((((.....)).)))..))).)))))(--------(((((((.((...)).)))))))). ( -23.70)
>DroYak_CAF1 15677 73 + 1
GCGAAAGUUGUCAGGCAGUUAAUAAGCUGACUCUUUUGUGGUAGUUGGUAGUUGG-----------------UAGUAGCUCAGUAGCUGC
(((((((..(((((............))))).))))))).(((((((.((((((.-----------------...))))).).))))))) ( -20.10)
>consensus
GCGAAAGUUGUCAGGCAGUUAAUAAGCUGACUCUUUUGUGGUAGUUGGCUGUAGCUC________AGUUGCUCAGUAGCUCAGUAGCUGU
((....))......(((((((...((((((((((.....)).))))))))((((((.........))))))............))))))) (-16.61 = -17.80 +   1.19)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,223,443 – 16,223,533
Length 90
Sequences 4
Columns 90
Reading direction forward
Mean pairwise identity 85.47
Mean single sequence MFE -32.50
Consensus MFE -26.30
Energy contribution -26.17
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -3.97
Structure conservation index 0.81
SVM decision value 2.83
SVM RNA-class probability 0.997259
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16223443 90 + 20766785
UUGUGGUAGUUGGUUGUAGCUCAGCAGCUCAGUAGCUCAGUAGCUCAGUAGCUGUUGCAGCCGAGAGGCAAUUUGCAGUUGGCUUAACAU
.(((...((((..((((((..((((((((....((((....))))....))))))))..(((....)))...))))))..))))..))). ( -32.30)
>DroSec_CAF1 4475 82 + 1
UUGUGGUAGUUGGCUGUAGCUC--------AGUUGCUCAGUAGCUUAGUAGCUGUUGCAGCCGAGAGGCAAUUUGCAGUUGGCUUAACAU
.(((...(((..((((((((.(--------(((((((.((...)).))))))))..)).(((....)))....))))))..)))..))). ( -35.20)
>DroSim_CAF1 4523 82 + 1
UUGUGGUAGUUGGCUGUAGCUC--------AGUUGCUCAGUAGCUCAGUAGCUGUUGCAGCCGAGAGGCAAUUUGCAGUUGGCUUAACAU
.(((...(((..((((((((.(--------(((((((.((...)).))))))))..)).(((....)))....))))))..)))..))). ( -35.20)
>DroYak_CAF1 15712 73 + 1
UUGUGGUAGUUGGUAGUUGG-----------------UAGUAGCUCAGUAGCUGCUGCAGCCGAGAGGCAAUUUGCAGUUGGCUUAACAU
.(((...(((..(..((..(-----------------((((((((....))))))))).(((....))).....))..)..)))..))). ( -27.30)
>consensus
UUGUGGUAGUUGGCUGUAGCUC________AGUUGCUCAGUAGCUCAGUAGCUGUUGCAGCCGAGAGGCAAUUUGCAGUUGGCUUAACAU
.(((...(((..(((((((..................((((((((....))))))))..(((....)))...)))))))..)))..))). (-26.30 = -26.17 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,223,443 – 16,223,533
Length 90
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 85.47
Mean single sequence MFE -16.88
Consensus MFE -11.46
Energy contribution -11.27
Covariance contribution -0.19
Combinations/Pair 1.08
Mean z-score -1.60
Structure conservation index 0.68
SVM decision value 0.09
SVM RNA-class probability 0.580539
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16223443 90 - 20766785
AUGUUAAGCCAACUGCAAAUUGCCUCUCGGCUGCAACAGCUACUGAGCUACUGAGCUACUGAGCUGCUGAGCUACAACCAACUACCACAA
.(((..(((((..((((....(((....))))))).(((((....((((....))))....))))).)).)))))).............. ( -22.10)
>DroSec_CAF1 4475 82 - 1
AUGUUAAGCCAACUGCAAAUUGCCUCUCGGCUGCAACAGCUACUAAGCUACUGAGCAACU--------GAGCUACAGCCAACUACCACAA
..(((.((((....((.....)).....))))..)))((((....)))).((((((....--------..))).)))............. ( -16.50)
>DroSim_CAF1 4523 82 - 1
AUGUUAAGCCAACUGCAAAUUGCCUCUCGGCUGCAACAGCUACUGAGCUACUGAGCAACU--------GAGCUACAGCCAACUACCACAA
..(((.((((....((.....)).....))))..)))((((....)))).((((((....--------..))).)))............. ( -16.60)
>DroYak_CAF1 15712 73 - 1
AUGUUAAGCCAACUGCAAAUUGCCUCUCGGCUGCAGCAGCUACUGAGCUACUA-----------------CCAACUACCAACUACCACAA
..(((.......(((((....(((....)))))))).((((....))))....-----------------..)))............... ( -12.30)
>consensus
AUGUUAAGCCAACUGCAAAUUGCCUCUCGGCUGCAACAGCUACUGAGCUACUGAGCAACU________GAGCUACAACCAACUACCACAA
..(((.((((....((.....)).....))))..)))((((....))))......................................... (-11.46 = -11.27 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,223,458 – 16,223,548
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 85.53
Mean single sequence MFE -30.06
Consensus MFE -26.18
Energy contribution -25.78
Covariance contribution -0.40
Combinations/Pair 1.09
Mean z-score -2.77
Structure conservation index 0.87
SVM decision value 2.97
SVM RNA-class probability 0.997937
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16223458 90 + 20766785
GUAGCUCAGCAGCUCAGUAGCUCAGUAGCUCAGUAGCUGUUGCAGCCGAGAGGCAAUUUGCAGUUGGCUUAACAUGCCUCGAUGGCUGUU
......((((((((....((((....))))....))))))))((((((.((((((....((.....))......))))))..)))))).. ( -34.00)
>DroSec_CAF1 4490 82 + 1
GUAGCUC--------AGUUGCUCAGUAGCUUAGUAGCUGUUGCAGCCGAGAGGCAAUUUGCAGUUGGCUUAACAUGCCUCGAUGGCUGUU
......(--------(((((((.((...)).))))))))..(((((((.((((((....((.....))......))))))..))))))). ( -30.10)
>DroSim_CAF1 4538 82 + 1
GUAGCUC--------AGUUGCUCAGUAGCUCAGUAGCUGUUGCAGCCGAGAGGCAAUUUGCAGUUGGCUUAACAUGCCUCGAUGGCUGUU
......(--------(((((((.((...)).))))))))..(((((((.((((((....((.....))......))))))..))))))). ( -30.10)
>DroEre_CAF1 9237 71 + 1
--UGG-----------------UAGUAGCUCAGUAGCUGUUGCAGCCGAGAGGCAAUUUGCAGUUGGCUUAACAUGCCUCGAUGGCUGUU
--..(-----------------((((((((....)))))))))(((((.((((((....((.....))......))))))..)))))... ( -25.40)
>DroYak_CAF1 15727 73 + 1
GUUGG-----------------UAGUAGCUCAGUAGCUGCUGCAGCCGAGAGGCAAUUUGCAGUUGGCUUAACAUGCCUCGAUGGCUGUU
....(-----------------((((((((....)))))))))(((((.((((((....((.....))......))))))..)))))... ( -30.70)
>consensus
GUAGCUC________AGU_GCUCAGUAGCUCAGUAGCUGUUGCAGCCGAGAGGCAAUUUGCAGUUGGCUUAACAUGCCUCGAUGGCUGUU
......................((((((((....))))))))((((((.((((((....((.....))......))))))..)))))).. (-26.18 = -25.78 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,223,458 – 16,223,548
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 85.53
Mean single sequence MFE -24.56
Consensus MFE -20.98
Energy contribution -20.98
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.78
Structure conservation index 0.85
SVM decision value 2.86
SVM RNA-class probability 0.997422
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16223458 90 - 20766785
AACAGCCAUCGAGGCAUGUUAAGCCAACUGCAAAUUGCCUCUCGGCUGCAACAGCUACUGAGCUACUGAGCUACUGAGCUGCUGAGCUAC
..(((((...((((((......((.....))....))))))..)))))((.(((((....((((....))))....))))).))...... ( -31.00)
>DroSec_CAF1 4490 82 - 1
AACAGCCAUCGAGGCAUGUUAAGCCAACUGCAAAUUGCCUCUCGGCUGCAACAGCUACUAAGCUACUGAGCAACU--------GAGCUAC
..(((((...((((((......((.....))....))))))..)))))....((((.....(((....)))....--------.)))).. ( -24.40)
>DroSim_CAF1 4538 82 - 1
AACAGCCAUCGAGGCAUGUUAAGCCAACUGCAAAUUGCCUCUCGGCUGCAACAGCUACUGAGCUACUGAGCAACU--------GAGCUAC
..(((((...((((((......((.....))....))))))..)))))....((((.....(((....)))....--------.)))).. ( -24.40)
>DroEre_CAF1 9237 71 - 1
AACAGCCAUCGAGGCAUGUUAAGCCAACUGCAAAUUGCCUCUCGGCUGCAACAGCUACUGAGCUACUA-----------------CCA--
..(((((...((((((......((.....))....))))))..)))))....((((....))))....-----------------...-- ( -21.00)
>DroYak_CAF1 15727 73 - 1
AACAGCCAUCGAGGCAUGUUAAGCCAACUGCAAAUUGCCUCUCGGCUGCAGCAGCUACUGAGCUACUA-----------------CCAAC
..(((((...((((((......((.....))....))))))..))))).((.((((....)))).)).-----------------..... ( -22.00)
>consensus
AACAGCCAUCGAGGCAUGUUAAGCCAACUGCAAAUUGCCUCUCGGCUGCAACAGCUACUGAGCUACUGAGC_ACU________GAGCUAC
..(((((...((((((......((.....))....))))))..)))))....((((....)))).......................... (-20.98 = -20.98 +   0.00)

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 11:33:37 2006