Locus 3499

Sequence ID 2R_DroMel_CAF1
Location 11,734,466 – 11,734,623
Length 157
Max. P 0.999331
window5699 window5700 window5701

overview

Window 9

Location 11,734,466 – 11,734,586
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 73.33
Mean single sequence MFE -33.87
Consensus MFE -26.57
Energy contribution -26.90
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.40
Structure conservation index 0.78
SVM decision value 1.47
SVM RNA-class probability 0.957140
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11734466 120 + 20766785
ACUAAGGACACACUUUAGUCACCUUCCAGACAAGUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAACUUUUUUGCCUAA
(((((((.....)))))))..(((.((((((((........)))))...)))..)))...(((((.......)))))(((((((((.......)))))...((....)).....)))).. ( -36.90)
>DroSim_CAF1 20925 120 + 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAAGUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAACUUUUUUGCCUAA
..................................(((((((.(((((........))))).((((.((..((((((.....))))))..))...)))))))))))............... ( -28.80)
>DroAna_CAF1 20508 120 + 1
ACAAGUAGACAGUUUAACCGCAUGGGUCUUCAAGUACCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAACGUUUAUUGUUAA
...(((((((......(((....((((((((....(((((........)))))...))..(((((.......)))))))))))(((.......))))))...(....))))))))..... ( -35.90)
>consensus
AC_A_________UU_A_____________CAAGUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAACUUUUUUGCCUAA
..................................(((((((.(((((........))))).((((.((..((((((.....))))))..))...)))))))))))............... (-26.57 = -26.90 +   0.33)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,734,466 – 11,734,586
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 73.33
Mean single sequence MFE -34.80
Consensus MFE -27.67
Energy contribution -28.00
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.80
SVM decision value 3.52
SVM RNA-class probability 0.999331
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11734466 120 - 20766785
UUAGGCAAAAAAGUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUUGUCUGGAAGGUGACUAAAGUGUGUCCUUAGU
...(((........(((((.....)))))((..((((((.....))))))..)))))(((((..((.....((((((((........)))))))).((....))..))..)))))..... ( -44.70)
>DroSim_CAF1 20925 120 - 1
UUAGGCAAAAAAGUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUUGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
...............(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....))))))).................................. ( -29.90)
>DroAna_CAF1 20508 120 - 1
UUAACAAUAAACGUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGUACUUGAAGACCCAUGCGGUUAAACUGUCUACUUGU
(((((......((.(((((.....))))).)).....(((.(((((.(((....))).)........((((.((.....))))))....)))).))).....)))))............. ( -29.80)
>consensus
UUAGGCAAAAAAGUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUUG_____________U_AA_________U_GU
...............(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....))))))).................................. (-27.67 = -28.00 +   0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,734,506 – 11,734,623
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.44
Mean single sequence MFE -30.20
Consensus MFE -21.57
Energy contribution -22.57
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.91
Structure conservation index 0.71
SVM decision value 2.81
SVM RNA-class probability 0.997145
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11734506 117 - 20766785
UAACCCUCUGAUGGUAACAAAUAAA---AAAAAAGCGAAAUUAGGCAAAAAAGUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAU
......((((.((((..........---...............(((........(((((.....)))))((..((((((.....))))))..)))))((....))..)))).)))).... ( -33.80)
>DroSim_CAF1 20965 120 - 1
UAACCCCCUAAGGGAAAAAAACAAAAUAAAAAAAGGAAAUUUAGGCAAAAAAGUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAU
...(((.....)))...................((((.((((.(((........(((((.....)))))((..((((((.....))))))..))))))))).)))).............. ( -33.90)
>DroAna_CAF1 20548 107 - 1
-------------GAUAAAAAGCCAAGAGUAAUAACAAAGUUAACAAUAAACGUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAU
-------------((((....(((..(.((..((((...))))........((.(((((.....))))).)).)))..)))..(((((.(....))))))))))................ ( -22.90)
>consensus
UAACCC_CU_A_GGAAAAAAACAAAA_AAAAAAAGCAAAAUUAGGCAAAAAAGUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAU
...........................................(((........(((((.....)))))((..((((((.....))))))..)))))((....))............... (-21.57 = -22.57 +   1.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:00 2006