Locus 6439

Sequence ID 3R_DroMel_CAF1
Location 16,869,419 – 16,869,554
Length 135
Max. P 0.883793
window10493 window10494 window10495

overview

Window 3

Location 16,869,419 – 16,869,519
Length 100
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 82.45
Mean single sequence MFE -22.89
Consensus MFE -15.25
Energy contribution -14.97
Covariance contribution -0.27
Combinations/Pair 1.23
Mean z-score -2.38
Structure conservation index 0.67
SVM decision value 0.53
SVM RNA-class probability 0.773078
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16869419 100 + 27905053
GUAACACCAUCCAAGUAAAUCAU--UUGUAUUUCCCAUAAUUUGUAACCCCUUUUUAUGGAAACUACAAGCGCAGGCGCGAUUAACAAGUGGUUGUAAACAA
...(((((((....((.((((..--(((((.((.((((((...(......)...)))))).)).)))))(((....))))))).))..)))).)))...... ( -21.20)
>DroSec_CAF1 22308 100 + 1
GUAACACCAUCCAAGUAAAUCAU--UCGUAUUUCCCAUAAUUUGUAACCCCUUUUUAUGGAAACUACAAGCGCAGGCGCGAUUAACAAGUGGUUGUAAACAA
...(((((((....((.((((..--..(((.((.((((((...(......)...)))))).)).)))..(((....))))))).))..)))).)))...... ( -19.70)
>DroSim_CAF1 21965 100 + 1
GUAACACCAUCCAAGUAAAUCAU--UCGUAUUUCCCAUAAUUUGGAACCCCUUUUUAUGGAAACUAAAAGCGCAGGCGCGAUUAACAAGUGGUUGUAAACAA
...(((((((....((.((((..--.........((((((...((....))...)))))).........(((....))))))).))..)))).)))...... ( -21.10)
>DroEre_CAF1 23056 100 + 1
CUAGCACCAUCCAAGUAAAUCAU--UCGUAGUUCCCAUAAUUUGUAGCCCCUUGUUAUGGAAACUGCAAGCGCAAGCGCGAUUAACAAGUGGUUGUAAACAA
...(((((((....((.((((..--..((((((.(((((((..(......)..))))))).))))))..((....))..)))).))..)))).)))...... ( -28.80)
>DroYak_CAF1 26859 100 + 1
GUAACACCAUCCAGGUAAAUCAU--UCUUAGUUCCCAUAAUUUGUAACCCCUUGUUAUGGAAACUCGAAGCGCAAGCGCGAUUAACAGGUGGUUGUCAACAA
((.((((((((...((.((((.(--((..((((.(((((((..(......)..))))))).)))).)))((....))..)))).)).))))).)))..)).. ( -27.30)
>DroPer_CAF1 31917 97 + 1
CCCACCCUAUCC----AAAACAUAAACACAGCUUCUAUAAAAAAU-ACCCAUUUUUAUAGCAACCCCAAGCGCAGGCGCCUGCAACACGUGGCGGUAAAAUA
...(((((((..----..............(((((((((((((..-.....))))))))).......))))((((....)))).....)))).)))...... ( -19.21)
>consensus
GUAACACCAUCCAAGUAAAUCAU__UCGUAGUUCCCAUAAUUUGUAACCCCUUUUUAUGGAAACUACAAGCGCAGGCGCGAUUAACAAGUGGUUGUAAACAA
...(((((((....((.((((.............((((((..............)))))).........(((....))))))).))..)))).)))...... (-15.25 = -14.97 +  -0.27)

alignment

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secondary structure

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Window 4

Location 16,869,456 – 16,869,554
Length 98
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 80.66
Mean single sequence MFE -28.53
Consensus MFE -17.25
Energy contribution -19.42
Covariance contribution 2.17
Combinations/Pair 1.12
Mean z-score -2.49
Structure conservation index 0.60
SVM decision value 0.93
SVM RNA-class probability 0.883793
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16869456 98 + 27905053
AUUUGUAACCCCUUUUUAUGGAAACU-ACAAGCGCAGGCGCGAUUAACAAGUGGUUGUAAACAAA--ACAGUCACCUGUUGCCACGAUAGCAACAAGGUGC
.(((((((((.(((.(((.(....).-....(((....)))...))).))).)))))))))....--.....((((((((((.......))))).))))). ( -25.60)
>DroVir_CAF1 25533 88 + 1
AGUAGU-UGCCGUUUUUAUGGUAAAUAUGUGGCGCAGGCGCCA----------GCCAUAAACAAA--ACAAAUAACUGUUGCGCCAAGGGCAACAUUGUUG
....((-((((.....((((.....))))((((((.(((....----------)))........(--(((......))))))))))..))))))....... ( -27.80)
>DroSec_CAF1 22345 98 + 1
AUUUGUAACCCCUUUUUAUGGAAACU-ACAAGCGCAGGCGCGAUUAACAAGUGGUUGUAAACAAA--GUAGUCACCUGUUGCCACGAUAGCAACAAGGUGC
.(((((((((.(((.(((.(....).-....(((....)))...))).))).)))))))))....--.....((((((((((.......))))).))))). ( -25.60)
>DroSim_CAF1 22002 98 + 1
AUUUGGAACCCCUUUUUAUGGAAACU-AAAAGCGCAGGCGCGAUUAACAAGUGGUUGUAAACAAA--GUAGUCACCUGUUGCCACGAUAGCAACAAGGUGC
.((((.((((.(((.(((.(....).-....(((....)))...))).))).)))).))))....--.....((((((((((.......))))).))))). ( -26.30)
>DroEre_CAF1 23093 99 + 1
AUUUGUAGCCCCUUGUUAUGGAAACU-GCAAGCGCAAGCGCGAUUAACAAGUGGUUGUAAACAAAA-AAAGCCACCUGUUGCCACGAAAGCAACAAGGUGC
.(((((((((.(((((((.(....)(-((..((....)))))..))))))).))))))))).....-.....((((((((((.......))))).))))). ( -32.70)
>DroYak_CAF1 26896 100 + 1
AUUUGUAACCCCUUGUUAUGGAAACU-CGAAGCGCAAGCGCGAUUAACAGGUGGUUGUCAACAAAAAAAAGUCACCUGUUGCCACGAUAGCAACAAGGUGC
..((((((((.(((((((.(....)(-((..((....)).))).))))))).))))).)))...........((((((((((.......))))).))))). ( -33.20)
>consensus
AUUUGUAACCCCUUUUUAUGGAAACU_ACAAGCGCAGGCGCGAUUAACAAGUGGUUGUAAACAAA__AAAGUCACCUGUUGCCACGAUAGCAACAAGGUGC
.(((((((((.(((.....(....)......(((....))).......))).)))))))))...........((((((((((.......)))))).)))). (-17.25 = -19.42 +   2.17)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,869,456 – 16,869,554
Length 98
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 80.66
Mean single sequence MFE -25.97
Consensus MFE -16.38
Energy contribution -17.05
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.62
Structure conservation index 0.63
SVM decision value 0.16
SVM RNA-class probability 0.611812
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16869456 98 - 27905053
GCACCUUGUUGCUAUCGUGGCAACAGGUGACUGU--UUUGUUUACAACCACUUGUUAAUCGCGCCUGCGCUUGU-AGUUUCCAUAAAAAGGGGUUACAAAU
.(((((.((((((.....))))))))))).....--...(((.((((....)))).))).(((....)))((((-((..((........))..)))))).. ( -24.60)
>DroVir_CAF1 25533 88 - 1
CAACAAUGUUGCCCUUGGCGCAACAGUUAUUUGU--UUUGUUUAUGGC----------UGGCGCCUGCGCCACAUAUUUACCAUAAAAACGGCA-ACUACU
.......((((((....(((.(((((....))))--).)))((((((.----------(((((....)))))........))))))....))))-)).... ( -24.20)
>DroSec_CAF1 22345 98 - 1
GCACCUUGUUGCUAUCGUGGCAACAGGUGACUAC--UUUGUUUACAACCACUUGUUAAUCGCGCCUGCGCUUGU-AGUUUCCAUAAAAAGGGGUUACAAAU
...((((((((((.....)))))).((.((((((--...(((.((((....)))).))).(((....)))..))-)))).)).....)))).......... ( -25.30)
>DroSim_CAF1 22002 98 - 1
GCACCUUGUUGCUAUCGUGGCAACAGGUGACUAC--UUUGUUUACAACCACUUGUUAAUCGCGCCUGCGCUUUU-AGUUUCCAUAAAAAGGGGUUCCAAAU
.(((((.((((((.....))))))))))).....--...((((..((((.....((((..(((....)))..))-))...((.......))))))..)))) ( -23.50)
>DroEre_CAF1 23093 99 - 1
GCACCUUGUUGCUUUCGUGGCAACAGGUGGCUUU-UUUUGUUUACAACCACUUGUUAAUCGCGCUUGCGCUUGC-AGUUUCCAUAACAAGGGGCUACAAAU
.(((((.((((((.....))))))))))).....-.(((((......((.(((((((.....(((.((....))-))).....)))))))))...))))). ( -29.20)
>DroYak_CAF1 26896 100 - 1
GCACCUUGUUGCUAUCGUGGCAACAGGUGACUUUUUUUUGUUGACAACCACCUGUUAAUCGCGCUUGCGCUUCG-AGUUUCCAUAACAAGGGGUUACAAAU
.(((((.((((((.....))))))))))).......(((((....((((.(((((((.....(((((.....))-))).....)))).)))))))))))). ( -29.00)
>consensus
GCACCUUGUUGCUAUCGUGGCAACAGGUGACUAU__UUUGUUUACAACCACUUGUUAAUCGCGCCUGCGCUUGU_AGUUUCCAUAAAAAGGGGUUACAAAU
.((((.(((((((.....)))))))))))...............................(((....)))..........((........))......... (-16.38 = -17.05 +   0.67)

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 12:21:35 2006