Locus 2317

Sequence ID 3L_DroMel_CAF1
Location 6,509,313 – 6,509,446
Length 133
Max. P 0.835366
window3576 window3577 window3578

overview

Window 6

Location 6,509,313 – 6,509,406
Length 93
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 86.90
Mean single sequence MFE -19.93
Consensus MFE -14.27
Energy contribution -14.52
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.72
SVM decision value 0.73
SVM RNA-class probability 0.835366
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6509313 93 + 23771897
UCUGGCUCACAUGGCUCCUCCUUCUCUUCCUCCUUCACCUCCAAC---UGACCAAGUCAGCAGUUUUUCCCGACCACACCGCCUGCAGUCGGCCAA
..(((((.((..(((.............................(---((((...)))))..(((......)))......)))....)).))))). ( -16.30)
>DroSec_CAF1 860 93 + 1
UCUGGCUCACAUGGCUCCUCCUUCUCUUCCGCCUUCACCUCCAAC---UGACCAAGUCAGCAGUUUUUCCCGACCACACUGCCUGCAGUCGGCCAA
..(((((.((..(((...............)))............---.......((..(((((.............)))))..)).)).))))). ( -17.38)
>DroSim_CAF1 857 90 + 1
UCUGGCUCACAUGGCUUCUCCUCCUC---CUCCUUUACCUCCAAC---UGACCAAGUCAGCAGUUUUUCCCGACCACACUGCCUGCAGUCGGCCAA
..(((((.((..(((...........---...............(---((((...)))))..(((......)))......)))....)).))))). ( -16.00)
>DroEre_CAF1 866 87 + 1
UCUGGCUCACAUGGCUUCG---------CCUGCUUCACCUCCAACUGCUGACCAAGUCAGCAGUUUUUCCCAAGCACACUGCCUGCAGUUGGCCAC
..(((((.((..(((....---------..(((((.......((((((((((...))))))))))......)))))....)))....)).))))). ( -30.02)
>consensus
UCUGGCUCACAUGGCUCCUCCUUCUC__CCUCCUUCACCUCCAAC___UGACCAAGUCAGCAGUUUUUCCCGACCACACUGCCUGCAGUCGGCCAA
..(((((.((...((.................................((((...))))(((((.............)))))..)).)).))))). (-14.27 = -14.52 +   0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,509,313 – 6,509,406
Length 93
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 86.90
Mean single sequence MFE -27.58
Consensus MFE -20.65
Energy contribution -20.53
Covariance contribution -0.12
Combinations/Pair 1.05
Mean z-score -1.60
Structure conservation index 0.75
SVM decision value 0.24
SVM RNA-class probability 0.647649
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6509313 93 - 23771897
UUGGCCGACUGCAGGCGGUGUGGUCGGGAAAAACUGCUGACUUGGUCA---GUUGGAGGUGAAGGAGGAAGAGAAGGAGGAGCCAUGUGAGCCAGA
(((((((((..((.....))..))))((.....((.((..(((..(((---.(....).)))..)))..))...))......))......))))). ( -26.20)
>DroSec_CAF1 860 93 - 1
UUGGCCGACUGCAGGCAGUGUGGUCGGGAAAAACUGCUGACUUGGUCA---GUUGGAGGUGAAGGCGGAAGAGAAGGAGGAGCCAUGUGAGCCAGA
(((((((((..((.....))..)))).......(.((((((...))))---)).)........(((...............)))......))))). ( -25.56)
>DroSim_CAF1 857 90 - 1
UUGGCCGACUGCAGGCAGUGUGGUCGGGAAAAACUGCUGACUUGGUCA---GUUGGAGGUAAAGGAG---GAGGAGGAGAAGCCAUGUGAGCCAGA
(((((((((..((.....))..)))).......(.((((((...))))---)).)..(((.......---...........)))......))))). ( -22.77)
>DroEre_CAF1 866 87 - 1
GUGGCCAACUGCAGGCAGUGUGCUUGGGAAAAACUGCUGACUUGGUCAGCAGUUGGAGGUGAAGCAGG---------CGAAGCCAUGUGAGCCAGA
.((((..((....(((.((.(((((.(....((((((((((...)))))))))).....).))))).)---------)...)))..))..)))).. ( -35.80)
>consensus
UUGGCCGACUGCAGGCAGUGUGGUCGGGAAAAACUGCUGACUUGGUCA___GUUGGAGGUGAAGGAGG__GAGAAGGAGAAGCCAUGUGAGCCAGA
....(((((((((.....)))))))))......(((((.((.((((...................................)))).)).)).))). (-20.65 = -20.53 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,509,338 – 6,509,446
Length 108
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 89.92
Mean single sequence MFE -32.45
Consensus MFE -22.14
Energy contribution -22.32
Covariance contribution 0.19
Combinations/Pair 1.10
Mean z-score -2.01
Structure conservation index 0.68
SVM decision value 0.05
SVM RNA-class probability 0.560143
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6509338 108 + 23771897
CUUCCUCCUUCACCUCCAAC---UGACCAAGUCAGCAGUUUUUCCCGACCACACCGCCUGCAGUCGGCCAACAAAGUGCUGAACUUCAAGUAGGAGUUGAGUCCCUUGGGG
....((((((((.((((.((---(....(((((((((.(((...(((((..((.....))..))))).....))).))))).))))..))).)))).))))......)))) ( -31.70)
>DroSec_CAF1 885 108 + 1
CUUCCGCCUUCACCUCCAAC---UGACCAAGUCAGCAGUUUUUCCCGACCACACUGCCUGCAGUCGGCCAACAAACUGCUGAACUUCAAGGAGUAGUUGAGUCCCUUGGGA
..............(((((.---.((((((.((((((((((...(((((..((.....))..))))).....))))))))))((((....))))..))).)))..))))). ( -32.30)
>DroSim_CAF1 882 105 + 1
C---CUCCUUUACCUCCAAC---UGACCAAGUCAGCAGUUUUUCCCGACCACACUGCCUGCAGUCGGCCAACAAAGUGCUGAACUUCAAGGAGGAGUUGAGUCCCUUGGGG
.---(((..((.(((((...---(((.....((((((.(((...(((((..((.....))..))))).....))).))))))...))).)))))))..))).((....)). ( -30.50)
>DroEre_CAF1 885 108 + 1
---CCUGCUUCACCUCCAACUGCUGACCAAGUCAGCAGUUUUUCCCAAGCACACUGCCUGCAGUUGGCCACCAAAGUGCUGAACUUCAAGGAGCAGUUGAGUCCCUUAGGU
---.(((((((......((((((((((...)))))))))).......(((((((((....))))(((...)))..))))).........)))))))............... ( -35.30)
>consensus
C__CCUCCUUCACCUCCAAC___UGACCAAGUCAGCAGUUUUUCCCGACCACACUGCCUGCAGUCGGCCAACAAAGUGCUGAACUUCAAGGAGGAGUUGAGUCCCUUGGGG
....(((((((.....((.....))...(((((((((.(((...(((((..((.....))..))))).....))).))))).))))...)))))))......((....)). (-22.14 = -22.32 +   0.19)

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 10:29:24 2006