Locus 8471

Sequence ID 3L_DroMel_CAF1
Location 22,273,235 – 22,273,340
Length 105
Max. P 0.977712
window13856 window13857

overview

Window 6

Location 22,273,235 – 22,273,340
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.30
Mean single sequence MFE -27.10
Consensus MFE -18.82
Energy contribution -18.26
Covariance contribution -0.56
Combinations/Pair 1.14
Mean z-score -2.57
Structure conservation index 0.69
SVM decision value 1.80
SVM RNA-class probability 0.977712
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22273235 105 + 23771897
AAAAAGAAAACAAAAGGCUGUACAAAGCAAAUACACAUACAUAUAC----AGGCUGAAGCAGUGGCAGCAGCCCGAAAGUGUGCUACACAAAUGUAUUCGCAUGAUUCU-----------
....((((........(((......))).......(((.(..((((----((((((..((....))..))))).....(((.....)))...)))))..).))).))))----------- ( -22.50)
>DroSec_CAF1 31645 120 + 1
AAAAAGAAAACAAAAGGCUGCACAAAGCAAAUACACAUACGUAUACAGACAGGCAGGAGCAGUGGCAGCAGUCCAAAAGUGUGCUACACAAAUGUAUUCGCACGAUUCUGGACCAGAAUU
................(((((.((..((..((((......)))).(.....)......))..))))))).(((((.((.(((((((((....))))...))))).)).)))))....... ( -27.10)
>DroSim_CAF1 23211 120 + 1
AAAAAGAAAACAAAAGGCUGCACAAAGCAAAUACACAUACGUAUACAGACAGGCAGGAGCAGUGGCAGCAGUCCAAAAGUGUGCUACACAAAUGUAUUCGCACGAUUCUGGACCAGAAUU
................(((((.((..((..((((......)))).(.....)......))..))))))).(((((.((.(((((((((....))))...))))).)).)))))....... ( -27.10)
>DroEre_CAF1 30437 103 + 1
AA-AAGAAAACAAAA-GCUGCACAAAGCAAAUACAUAU------G----CAGGCCAAAGCAGUGGCAGCAGCCCGAAAGUGUGCUACACAAAUGUGUACGCACGAUUCUGGU-----GAU
..-............-(((((.....(((........)------)----)..((((......)))).)))))(((((.(((((.(((((....))))))))))..))).)).-----... ( -31.70)
>consensus
AAAAAGAAAACAAAAGGCUGCACAAAGCAAAUACACAUACGUAUAC___CAGGCAGAAGCAGUGGCAGCAGCCCAAAAGUGUGCUACACAAAUGUAUUCGCACGAUUCUGGA_____AUU
....((((........(((((.((..((..............................))..))))))).........(((((.((((....))))..)))))..))))........... (-18.82 = -18.26 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 22,273,235 – 22,273,340
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.30
Mean single sequence MFE -31.52
Consensus MFE -18.58
Energy contribution -18.70
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -2.96
Structure conservation index 0.59
SVM decision value 1.56
SVM RNA-class probability 0.963769
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22273235 105 - 23771897
-----------AGAAUCAUGCGAAUACAUUUGUGUAGCACACUUUCGGGCUGCUGCCACUGCUUCAGCCU----GUAUAUGUAUGUGUAUUUGCUUUGUACAGCCUUUUGUUUUCUUUUU
-----------........((((((((((.((..((.........(((((((..((....))..))))))----)..))..)).)))))))))).......................... ( -27.20)
>DroSec_CAF1 31645 120 - 1
AAUUCUGGUCCAGAAUCGUGCGAAUACAUUUGUGUAGCACACUUUUGGACUGCUGCCACUGCUCCUGCCUGUCUGUAUACGUAUGUGUAUUUGCUUUGUGCAGCCUUUUGUUUUCUUUUU
......(((((((((..((((..((((....)))).))))..)))))))))(((((((..((....))..((..((((((....))))))..))..)).)))))................ ( -34.40)
>DroSim_CAF1 23211 120 - 1
AAUUCUGGUCCAGAAUCGUGCGAAUACAUUUGUGUAGCACACUUUUGGACUGCUGCCACUGCUCCUGCCUGUCUGUAUACGUAUGUGUAUUUGCUUUGUGCAGCCUUUUGUUUUCUUUUU
......(((((((((..((((..((((....)))).))))..)))))))))(((((((..((....))..((..((((((....))))))..))..)).)))))................ ( -34.40)
>DroEre_CAF1 30437 103 - 1
AUC-----ACCAGAAUCGUGCGUACACAUUUGUGUAGCACACUUUCGGGCUGCUGCCACUGCUUUGGCCUG----C------AUAUGUAUUUGCUUUGUGCAGC-UUUUGUUUUCUU-UU
...-----.((.(((..((((.(((((....)))))))))...)))))(((((.((((......))))..(----(------(........))).....)))))-............-.. ( -30.10)
>consensus
AAU_____UCCAGAAUCGUGCGAAUACAUUUGUGUAGCACACUUUCGGACUGCUGCCACUGCUCCUGCCUG___GUAUACGUAUGUGUAUUUGCUUUGUGCAGCCUUUUGUUUUCUUUUU
...........((((....((((((((((.((.((((((..(.....)..))))))))..((....))................)))))))))).....((((....)))).)))).... (-18.58 = -18.70 +   0.12)

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 13:16:18 2006