Locus 543

Sequence ID 2L_DroMel_CAF1
Location 1,677,855 – 1,677,968
Length 113
Max. P 0.919533
window876 window877

overview

Window 6

Location 1,677,855 – 1,677,968
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.69
Mean single sequence MFE -33.77
Consensus MFE -24.17
Energy contribution -24.05
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -1.73
Structure conservation index 0.72
SVM decision value 0.37
SVM RNA-class probability 0.709359
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1677855 113 + 22407834
GCCCAU-------CGCCCACUCCAAUCCACUAUACGCUUUUCCCCCCCAGCUUGUUGUGUAUUUUUGCAAUAAACCAGGAAAAAGCAGACUGGGACAGUAGAGCUGGCCAUGCGUACCUU
((.(((-------.(((..(((.............((((((.((.....(.((((((((......)))))))).)..)).))))))..((((...)))).)))..))).))).))..... ( -23.80)
>DroSec_CAF1 4223 104 + 1
C--------------UCCACUCCACUCUACUACACGC--UUUUCCCCCAGCUUGUUGUGUAUUUUUGCAAUAAACCAGGAAAAAGCAGGCUGGGACAGUGGAGCUGGCCAUGCGUACCUU
.--------------.((((((((((...(.....).--......(((((((((((.....((((((........))))))..)))))))))))..))))))).)))............. ( -30.50)
>DroSim_CAF1 5214 120 + 1
GCCCAUCGCCCAUCGCCCACUCCACUCCACUACACGCUCUUUUCCCCCAGCUUGUUGUGUAUUUUUGCAAUAAACCAGGGAAAAGCAGGCUGGGACAGUGGAGCUGGCCAUGCGUACCUU
.......((.(((.(((..(((((((...(((...(((((((((((...(.((((((((......)))))))).)..))))))))..))))))...)))))))..))).))).))..... ( -38.90)
>DroYak_CAF1 5294 113 + 1
GCCCAU-------GGCCCACUCCACCUCACUGCACGCUUUUCCCCCGCAGCUUGUUGUGUAUUUUUGCAAUAAAGCAGGGAAAAGCAGGCUGGGAUAGCAGAGCUGGCCAUGCGUACCUU
((.(((-------((((..(((....((...((..(((((((((..((...((((((((......)))))))).)).)))))))))..))...)).....)))..))))))).))..... ( -41.90)
>consensus
GCCCAU_______CGCCCACUCCACUCCACUACACGCUUUUCCCCCCCAGCUUGUUGUGUAUUUUUGCAAUAAACCAGGAAAAAGCAGGCUGGGACAGUAGAGCUGGCCAUGCGUACCUU
.................................((((........(((((((((((.....((((((........))))))..))))))))))).((((...)))).....))))..... (-24.17 = -24.05 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,677,855 – 1,677,968
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.69
Mean single sequence MFE -41.90
Consensus MFE -29.62
Energy contribution -29.00
Covariance contribution -0.62
Combinations/Pair 1.26
Mean z-score -2.30
Structure conservation index 0.71
SVM decision value 1.13
SVM RNA-class probability 0.919533
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1677855 113 - 22407834
AAGGUACGCAUGGCCAGCUCUACUGUCCCAGUCUGCUUUUUCCUGGUUUAUUGCAAAAAUACACAACAAGCUGGGGGGGAAAAGCGUAUAGUGGAUUGGAGUGGGCG-------AUGGGC
......(.(((.(((.((((((..(((((.((.((((((((((((((((.(((..........))).)))))...))))))))))).)).).)))))))))).))).-------))).). ( -39.50)
>DroSec_CAF1 4223 104 - 1
AAGGUACGCAUGGCCAGCUCCACUGUCCCAGCCUGCUUUUUCCUGGUUUAUUGCAAAAAUACACAACAAGCUGGGGGAAAA--GCGUGUAGUAGAGUGGAGUGGA--------------G
..(((.......))).((((((((.(.(..((.((((((((((..((((.(((..........))).))))..).))))))--))).)).).).))))))))...--------------. ( -33.40)
>DroSim_CAF1 5214 120 - 1
AAGGUACGCAUGGCCAGCUCCACUGUCCCAGCCUGCUUUUCCCUGGUUUAUUGCAAAAAUACACAACAAGCUGGGGGAAAAGAGCGUGUAGUGGAGUGGAGUGGGCGAUGGGCGAUGGGC
......(.(((.(((.(((((((..((((.((.((((((((((..((((.(((..........))).))))..)))))...))))).)).).)))))))))).))).))).)........ ( -46.70)
>DroYak_CAF1 5294 113 - 1
AAGGUACGCAUGGCCAGCUCUGCUAUCCCAGCCUGCUUUUCCCUGCUUUAUUGCAAAAAUACACAACAAGCUGCGGGGGAAAAGCGUGCAGUGAGGUGGAGUGGGCC-------AUGGGC
......(.(((((((.((((..((.((.(.((.(((((((((((((......)).......(.((......)).)))))))))))).)).).))))..)))).))))-------))).). ( -48.00)
>consensus
AAGGUACGCAUGGCCAGCUCCACUGUCCCAGCCUGCUUUUCCCUGGUUUAUUGCAAAAAUACACAACAAGCUGGGGGAAAAAAGCGUGUAGUGGAGUGGAGUGGGCG_______AUGGGC
............(((.((((((((.((.(.((.((((((((((((((((.(((..........))).)))))))))))))...))).)).).)))))))))).))).............. (-29.62 = -29.00 +  -0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:54 2006