Locus 959

Sequence ID 2R_DroMel_CAF1
Location 4,104,626 – 4,104,742
Length 116
Max. P 0.692237
window1710 window1711

overview

Window 0

Location 4,104,626 – 4,104,742
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.47
Mean single sequence MFE -27.86
Consensus MFE -19.25
Energy contribution -18.75
Covariance contribution -0.50
Combinations/Pair 1.26
Mean z-score -1.68
Structure conservation index 0.69
SVM decision value 0.23
SVM RNA-class probability 0.645677
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4104626 116 + 20766785
AUUUUUCCCCAUUGCUUCAGUUAUUUGCCUUUAUUCCUGGCUAGUGGCGUACUCUUUUUACGCCGCCUUAGGAGGACCUCUCUUCAUCUGAAUGUGAUCCAUUGCCAAGUA----AUAAA
...................((((((((.(.....((((((...((((((((.......)))))))).))))))(((..((.((((....))).).)))))...).))))))----))... ( -26.80)
>DroSec_CAF1 8784 116 + 1
AUUAUUUCCCAAUACUUUAGUUGUAUGCCUUUAUUUCUGGCUAGUGGCGUACUCCUUUUACGCCGCCUUGGGAGGACCUCUCUUCAUCUGAAUGCGAUCCUUUGCAAAGUA----AUAAA
....(((((((((((.......))))(((.........)))..((((((((.......))))))))..))))))).................(((((....))))).....----..... ( -29.10)
>DroSim_CAF1 12578 116 + 1
AUUAUUUCCCAAUACUUUAGUUGUAUGCAUUUAUUUCUGGCUAGUGGCGUACUCCUUUUACGCCGCCUUAGGAGGACCUCUCUUCAUCUGAAUGCGAUCCUUUGCAAAGUA----AUAAA
(((((((..((((((.......))))(((((((.......(((((((((((.......))))))))..)))(((((....)))))...))))))).......))..)))))----))... ( -27.50)
>DroYak_CAF1 1680 120 + 1
ACUGUUUUCGACUUCCUCAGUUAUAUGUCUAUAUUUCUGGCUGGUGGCAUACUCUUUUUACGCCGCCUUAGGAGGCCCGCUAUUCAUCUGAAGGGGAUCCUCUACCAAGAAGCUAUUGAA
......(((((......(((..((((....))))..)))(((((((((.............))))))...((((((((....(((....))).)))..))))).......)))..))))) ( -28.02)
>consensus
AUUAUUUCCCAAUACUUCAGUUAUAUGCCUUUAUUUCUGGCUAGUGGCGUACUCCUUUUACGCCGCCUUAGGAGGACCUCUCUUCAUCUGAAUGCGAUCCUUUGCAAAGUA____AUAAA
............(((.((((.............(((((((...((((((((.......)))))))).))))))).............)))).(((((....)))))..)))......... (-19.25 = -18.75 +  -0.50) 

alignment

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secondary structure

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dotplot

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Window 1

Location 4,104,626 – 4,104,742
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.47
Mean single sequence MFE -29.42
Consensus MFE -20.31
Energy contribution -20.50
Covariance contribution 0.19
Combinations/Pair 1.14
Mean z-score -1.75
Structure conservation index 0.69
SVM decision value 0.33
SVM RNA-class probability 0.692237
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4104626 116 - 20766785
UUUAU----UACUUGGCAAUGGAUCACAUUCAGAUGAAGAGAGGUCCUCCUAAGGCGGCGUAAAAAGAGUACGCCACUAGCCAGGAAUAAAGGCAAAUAACUGAAGCAAUGGGGAAAAAU
(((((----(.((((((...(((((.(.(((....)))..).)))))......((.((((((.......)))))).)).))))))))))))............................. ( -29.90)
>DroSec_CAF1 8784 116 - 1
UUUAU----UACUUUGCAAAGGAUCGCAUUCAGAUGAAGAGAGGUCCUCCCAAGGCGGCGUAAAAGGAGUACGCCACUAGCCAGAAAUAAAGGCAUACAACUAAAGUAUUGGGAAAUAAU
.((((----(..........(((((...(((....)))....)))))((((((.((((((((.......))))))....(((.........)))...........)).))))))))))). ( -31.90)
>DroSim_CAF1 12578 116 - 1
UUUAU----UACUUUGCAAAGGAUCGCAUUCAGAUGAAGAGAGGUCCUCCUAAGGCGGCGUAAAAGGAGUACGCCACUAGCCAGAAAUAAAUGCAUACAACUAAAGUAUUGGGAAAUAAU
((((.----(((((((((.((((((...(((....)))....)))))).....(((((((((.......))))))....))).........))))........))))).))))....... ( -26.40)
>DroYak_CAF1 1680 120 - 1
UUCAAUAGCUUCUUGGUAGAGGAUCCCCUUCAGAUGAAUAGCGGGCCUCCUAAGGCGGCGUAAAAAGAGUAUGCCACCAGCCAGAAAUAUAGACAUAUAACUGAGGAAGUCGAAAACAGU
.......((((((((((.((((..(((((((....))..)).)))))))....((.((((((.......)))))).)).))).....((((....))))....))))))).......... ( -29.50)
>consensus
UUUAU____UACUUGGCAAAGGAUCGCAUUCAGAUGAAGAGAGGUCCUCCUAAGGCGGCGUAAAAAGAGUACGCCACUAGCCAGAAAUAAAGGCAUACAACUAAAGUAUUGGGAAAUAAU
............(((((...(((((...(((....)))....)))))......((.((((((.......)))))).)).))))).................................... (-20.31 = -20.50 +   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 09:52:47 2006