Locus 7886

Sequence ID 3L_DroMel_CAF1
Location 21,034,628 – 21,034,828
Length 200
Max. P 0.772800
window12831 window12832 window12833 window12834

overview

Window 1

Location 21,034,628 – 21,034,748
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.79
Mean single sequence MFE -31.93
Consensus MFE -27.90
Energy contribution -28.23
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.49
Structure conservation index 0.87
SVM decision value 0.29
SVM RNA-class probability 0.672453
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21034628 120 + 23771897
GCAUUCGUUUUUGCAUUGACUCGUGUAUAUUUGGAUUUUUUUUUUUUAAAGUGCCUUUCAAUCUUGGCUGGCGCUUGGAAGUCAUUUCCUGCCCGAAUCACCGGAUGGGCAGAUGACUCA
..(((((..(.(((((......))))).)..)))))............(((((((..(((....)))..))))))).((.((((((((((..(((......)))..))).))))))))). ( -33.90)
>DroSec_CAF1 89747 115 + 1
GCAUUUGUUUUUGCAUUGAGUUGUGUAUUUUUGGAUUUU-----UUUAAUGUCCCUUUCAAUCUUGGCUGGCGCUUGGAAGUCAUUUCCUGCCCGAAUCGCCGGAUGGGCAGAUGACUCA
(((........)))..(((((..(.........((((((-----(.....((.((..(((....)))..)).))..))))))).....((((((..(((....))))))))))..))))) ( -29.40)
>DroEre_CAF1 11313 106 + 1
GCAUUUGUUUUUGCAGUGUGUUGUGUCCAUUUG--------------AAUGUGCCUUUCAAUCUUGGUUGGCGCUUGGAAGUCAUUUCCUGCCCGAAUUGCCGGAUGGGCAGAUGACUCA
(((((.((....)))))))......((((....--------------...(((((..(((....)))..))))).))))(((((((((((..(((......)))..))).)))))))).. ( -32.50)
>consensus
GCAUUUGUUUUUGCAUUGAGUUGUGUAUAUUUGGAUUUU_____UUUAAUGUGCCUUUCAAUCUUGGCUGGCGCUUGGAAGUCAUUUCCUGCCCGAAUCGCCGGAUGGGCAGAUGACUCA
(((........)))....................................(((((..(((....)))..)))))...((.((((((((((..(((......)))..))).))))))))). (-27.90 = -28.23 +   0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,034,668 – 21,034,788
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 92.70
Mean single sequence MFE -32.00
Consensus MFE -30.25
Energy contribution -30.37
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.75
Structure conservation index 0.95
SVM decision value 0.53
SVM RNA-class probability 0.772800
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21034668 120 + 23771897
UUUUUUUAAAGUGCCUUUCAAUCUUGGCUGGCGCUUGGAAGUCAUUUCCUGCCCGAAUCACCGGAUGGGCAGAUGACUCAAAAUGGGUUAAUUAAAAACCAUCUAGCAGUGAUUUUAUUU
........(((((((..(((....)))..))))))).(((((((((.(((((((..(((....))))))))).((((((.....))))))...............).))))))))).... ( -34.60)
>DroSec_CAF1 89786 116 + 1
----UUUAAUGUCCCUUUCAAUCUUGGCUGGCGCUUGGAAGUCAUUUCCUGCCCGAAUCGCCGGAUGGGCAGAUGACUCAAAAUGGGUUAAUUAAAAACCAUCUAGCAGUGAUUUUAUUU
----((((((..(((......(((.(((....))).)))(((((((((((..(((......)))..))).))))))))......)))...))))))........................ ( -29.30)
>DroEre_CAF1 11346 112 + 1
-------AAUGUGCCUUUCAAUCUUGGUUGGCGCUUGGAAGUCAUUUCCUGCCCGAAUUGCCGGAUGGGCAGAUGACUCAA-AUGGGUUAAUUAAAAACCAUCUAGCAGUGAUUUUAUUU
-------...(((((..(((....)))..)))))((((((((((((((((..(((......)))..))).))))))))...-...((((.......)))).))))).............. ( -32.10)
>consensus
____UUUAAUGUGCCUUUCAAUCUUGGCUGGCGCUUGGAAGUCAUUUCCUGCCCGAAUCGCCGGAUGGGCAGAUGACUCAAAAUGGGUUAAUUAAAAACCAUCUAGCAGUGAUUUUAUUU
..........(((((..(((....)))..)))))...(((((((((.(((((((..(((....))))))))).((((((.....))))))...............).))))))))).... (-30.25 = -30.37 +   0.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,034,708 – 21,034,828
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -35.20
Consensus MFE -30.97
Energy contribution -31.63
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.12
Structure conservation index 0.88
SVM decision value 0.38
SVM RNA-class probability 0.714304
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21034708 120 + 23771897
GUCAUUUCCUGCCCGAAUCACCGGAUGGGCAGAUGACUCAAAAUGGGUUAAUUAAAAACCAUCUAGCAGUGAUUUUAUUUGGGCCGAUGUAAAGUCAUGUGCCCAAAAGAGUUGUUCUCA
((((((((((..(((......)))..))).)))))))........((((.......))))....((.((..(((((.(((((((..(((......)))..))))))))))))..)))).. ( -34.90)
>DroSec_CAF1 89822 120 + 1
GUCAUUUCCUGCCCGAAUCGCCGGAUGGGCAGAUGACUCAAAAUGGGUUAAUUAAAAACCAUCUAGCAGUGAUUUUAUUUGGGCCGAUGUAAAGUCAUGUGCCCAAAAGAGUUGUUCUCA
((((((((((..(((......)))..))).)))))))........((((.......))))....((.((..(((((.(((((((..(((......)))..))))))))))))..)))).. ( -34.90)
>DroEre_CAF1 11379 119 + 1
GUCAUUUCCUGCCCGAAUUGCCGGAUGGGCAGAUGACUCAA-AUGGGUUAAUUAAAAACCAUCUAGCAGUGAUUUUAUUUGGCCCGAUGAAAAGUCAUGUGCCCAAAACAGUUGUUCCCA
........(((.(((......))).((((((.((((((...-.((((((((.(((((..(((......))).))))).))))))))......)))))).))))))...)))......... ( -35.80)
>consensus
GUCAUUUCCUGCCCGAAUCGCCGGAUGGGCAGAUGACUCAAAAUGGGUUAAUUAAAAACCAUCUAGCAGUGAUUUUAUUUGGGCCGAUGUAAAGUCAUGUGCCCAAAAGAGUUGUUCUCA
((((((((((..(((......)))..))).)))))))........((((.......)))).......((..(((((.(((((((..(((......)))..))))))))))))..)).... (-30.97 = -31.63 +   0.67)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,034,708 – 21,034,828
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -32.57
Consensus MFE -28.96
Energy contribution -28.74
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.82
Structure conservation index 0.89
SVM decision value 0.05
SVM RNA-class probability 0.557975
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21034708 120 - 23771897
UGAGAACAACUCUUUUGGGCACAUGACUUUACAUCGGCCCAAAUAAAAUCACUGCUAGAUGGUUUUUAAUUAACCCAUUUUGAGUCAUCUGCCCAUCCGGUGAUUCGGGCAGGAAAUGAC
.(((.....))).(((((((..(((......)))..))))))).....((.(((((((((((.((......)).))))))(((((((((.........))))))))))))))))...... ( -32.60)
>DroSec_CAF1 89822 120 - 1
UGAGAACAACUCUUUUGGGCACAUGACUUUACAUCGGCCCAAAUAAAAUCACUGCUAGAUGGUUUUUAAUUAACCCAUUUUGAGUCAUCUGCCCAUCCGGCGAUUCGGGCAGGAAAUGAC
.(((.....))).(((((((..(((......)))..))))))).....((.((((((((((..((..(((......)))..))..)))))(((.....)))......)))))))...... ( -31.30)
>DroEre_CAF1 11379 119 - 1
UGGGAACAACUGUUUUGGGCACAUGACUUUUCAUCGGGCCAAAUAAAAUCACUGCUAGAUGGUUUUUAAUUAACCCAU-UUGAGUCAUCUGCCCAUCCGGCAAUUCGGGCAGGAAAUGAC
((....)).((((..((((((.(((((((......(((......(((((((........))))))).......)))..-..))))))).)))))).((((....))))))))........ ( -33.82)
>consensus
UGAGAACAACUCUUUUGGGCACAUGACUUUACAUCGGCCCAAAUAAAAUCACUGCUAGAUGGUUUUUAAUUAACCCAUUUUGAGUCAUCUGCCCAUCCGGCGAUUCGGGCAGGAAAUGAC
...............((((((.(((((((...((.((.......(((((((........))))))).......)).))...))))))).))))))(((.((.......)).)))...... (-28.96 = -28.74 +  -0.22)

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 12:59:29 2006