Locus 952

Sequence ID 3R_DroMel_CAF1
Location 3,132,524 – 3,132,655
Length 131
Max. P 0.999156
window1520 window1521 window1522

overview

Window 0

Location 3,132,524 – 3,132,624
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.66
Mean single sequence MFE -38.35
Consensus MFE -20.07
Energy contribution -20.77
Covariance contribution 0.70
Combinations/Pair 1.19
Mean z-score -2.67
Structure conservation index 0.52
SVM decision value 1.96
SVM RNA-class probability 0.983960
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3132524 100 - 27905053
CUUUCUCUCUUC--GGGGA--AAGCAAGAGCACC-----GCAAAACG-------GAGAGAUCUCUUGU-UUCGAGUGGGUUUUA---AUGGUAAAACGCUCAAGCUUUUGCGUCGCUUUU
((((((((....--)))))--))).((((((..(-----((((((.(-------(((....)))).((-((.(((((..((...---.....))..))))))))))))))))..)))))) ( -32.70)
>DroSec_CAF1 7925 100 - 1
CUUCCUCUCUUU--GGGGA--AAGCAAGAGCGCC-----GCAAAAAG-------GAGAGAGCUCUUGU-UUCGAGUGGGUUUUU---GGAGGAAAACGCUCAAGCUUUUGCGUCGCUUUU
.((((((.....--)))))--)...(((((((.(-----((((((((-------(((....)))))((-((.(((((..((((.---...))))..)))))))))))))))).))))))) ( -37.60)
>DroSim_CAF1 8549 100 - 1
CUUCCUCUCUUU--GGGGA--AAGCAAGAGCGCC-----GCAAAAAG-------GAGAGAGCUCUAGU-UUCGAGUGGGUUUUU---AGGGGAAAACGCUCAAGCUUUUGCGUCGCUUUU
.((((((.....--)))))--)...(((((((.(-----((((((.(-------(((....)))).((-((.(((((..((((.---...))))..)))))))))))))))).))))))) ( -37.20)
>DroPer_CAF1 6702 120 - 1
CCCGCUCUCUUAUGGGGGAGUGUGUAAGAGUGCCUGAGCGCCAGAGGGCAGUGGAAGAGAGCGAGUGCUUUCGAGUGGCAUUUUUCGGGGGAAAAACACUCAAGCUUUGGCGGGGGGAUU
((((((((((....)))))))..........(((.(((((((....))).......((((((....))))))(((((...((((((....)))))))))))..)))).))))))...... ( -45.30)
>DroEre_CAF1 8323 100 - 1
CCUUUUCUCUUU--GGCGC--AUGCAAGAGCGCG-----CCCAA-AA-------GAGAGAGCUCUUGUUUUGGAGUGGUUUUUU---GGGGGAAAACGCUCAAGCUUUUGCGUCGCUCUU
............--(((((--(.((..(((((..-----(((..-((-------((((..(((((......)))))..))))))---..)))....)))))..))...))))))...... ( -36.90)
>DroYak_CAF1 8335 101 - 1
CGUCUUCUCUUU--GGGGA--AUGCAAGAGCGCC-----CCCAAAAA-------GAGAGAGCUCAUGGGUUCGAGUGGUUUUUU---GGGGGAAAACGCUCAAGCUUUUGCGUCGCUCUU
.((.(((((...--.))))--).))(((((((((-----((((((((-------(...(((((....)))))......))))))---)))))...((((..........))))))))))) ( -40.40)
>consensus
CUUCCUCUCUUU__GGGGA__AAGCAAGAGCGCC_____GCAAAAAG_______GAGAGAGCUCUUGU_UUCGAGUGGGUUUUU___GGGGGAAAACGCUCAAGCUUUUGCGUCGCUUUU
.....(((((....)))))....((((((((.......................(((....)))........(((((..(((((.....)))))..)))))..))))))))......... (-20.07 = -20.77 +   0.70)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,132,561 – 3,132,655
Length 94
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.17
Mean single sequence MFE -36.71
Consensus MFE -11.98
Energy contribution -13.60
Covariance contribution 1.62
Combinations/Pair 1.24
Mean z-score -4.09
Structure conservation index 0.33
SVM decision value 3.18
SVM RNA-class probability 0.998656
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3132561 94 + 27905053
ACCCACUCGAA-ACAAGAGAUCUCUC-------CGUUUUGC-----GGUGCUCUUGCUU--UCCCC--GAAGAGAGAAAG---------AGAGAGCUCUUUCACUGACGCUCUUCGAGUU
....(((((((-(((((((......(-------((.....)-----))..)))))).))--))...--((((((.(((((---------((....))))))).......)))))))))). ( -31.30)
>DroSec_CAF1 7962 92 + 1
ACCCACUCGAA-ACAAGAGCUCUCUC-------CUUUUUGC-----GGCGCUCUUGCUU--UCCCC--AAAGAGAGGAAG---------AGAGAGCUCUUUC--UCACGCUCUUCGAGUU
....(((((((-..((((((((((((-------(((((((.-----((.((....))..--.)).)--)))))).....)---------)))))))))))..--........))))))). ( -33.40)
>DroSim_CAF1 8586 92 + 1
ACCCACUCGAA-ACUAGAGCUCUCUC-------CUUUUUGC-----GGCGCUCUUGCUU--UCCCC--AAAGAGAGGAAG---------AGAGAGCUCUUUC--UCGCGCUCUUCGAGUU
....(((((((-...(((((((((((-------(((((((.-----((.((....))..--.)).)--)))))).....)---------))))))))))...--........))))))). ( -33.04)
>DroPer_CAF1 6742 118 + 1
UGCCACUCGAAAGCACUCGCUCUCUUCCACUGCCCUCUGGCGCUCAGGCACUCUUACACACUCCCCCAUAAGAGAGCGGGGGGUGUGUGUGUGUGCUCUUUC--AUUUGCUCUUCGUGUU
....((.((((((((................(((....))).....(((((.(.(((((((((((((........).)))))))))))).).))))).....--...)))).)))).)). ( -41.60)
>DroEre_CAF1 8360 92 + 1
AACCACUCCAAAACAAGAGCUCUCUC-------UU-UUGGG-----CGCGCUCUUGCAU--GCGCC--AAAGAGAAAAGG---------AGAGAGCCCUUUC--UCUCGCUCUUCGAGUU
....((((......((((((..((((-------((-...((-----(((((....))..--)))))--.))))))....(---------((((((....)))--)))))))))).)))). ( -34.80)
>DroYak_CAF1 8372 97 + 1
AACCACUCGAACCCAUGAGCUCUCUC-------UUUUUGGG-----GGCGCUCUUGCAU--UCCCC--AAAGAGAAGACG-----AGAGAGAGAGCCCUUUC--UCUCGCUCUUCGAGUU
....(((((((.....(((((((.((-------((((((((-----((.((....))..--)))))--)))))))))).(-----((((((((....)))))--))))))))))))))). ( -46.10)
>consensus
ACCCACUCGAA_ACAAGAGCUCUCUC_______CUUUUGGC_____GGCGCUCUUGCAU__UCCCC__AAAGAGAGGAAG_________AGAGAGCUCUUUC__UCUCGCUCUUCGAGUU
....(((((((...(((.(((((((........(((((.((......)).(((((..............))))).))))).........))))))).)))............))))))). (-11.98 = -13.60 +   1.62)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,132,561 – 3,132,655
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 73.17
Mean single sequence MFE -38.57
Consensus MFE -17.30
Energy contribution -18.86
Covariance contribution 1.56
Combinations/Pair 1.12
Mean z-score -3.48
Structure conservation index 0.45
SVM decision value 3.40
SVM RNA-class probability 0.999156
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3132561 94 - 27905053
AACUCGAAGAGCGUCAGUGAAAGAGCUCUCU---------CUUUCUCUCUUC--GGGGA--AAGCAAGAGCACC-----GCAAAACG-------GAGAGAUCUCUUGU-UUCGAGUGGGU
.((((((((((.(((.........(((((..---------((((((((....--)))))--)))..))))).((-----(.....))-------)...)))))))...-.)))))).... ( -32.50)
>DroSec_CAF1 7962 92 - 1
AACUCGAAGAGCGUGA--GAAAGAGCUCUCU---------CUUCCUCUCUUU--GGGGA--AAGCAAGAGCGCC-----GCAAAAAG-------GAGAGAGCUCUUGU-UUCGAGUGGGU
.((((((((..(....--).(((((((((((---------(((((((.....--)))))--..((....))...-----.......)-------)))))))))))).)-))))))).... ( -40.00)
>DroSim_CAF1 8586 92 - 1
AACUCGAAGAGCGCGA--GAAAGAGCUCUCU---------CUUCCUCUCUUU--GGGGA--AAGCAAGAGCGCC-----GCAAAAAG-------GAGAGAGCUCUAGU-UUCGAGUGGGU
.((((((((..(....--)..((((((((((---------(((((((.....--)))))--..((....))...-----.......)-------)))))))))))..)-))))))).... ( -38.60)
>DroPer_CAF1 6742 118 - 1
AACACGAAGAGCAAAU--GAAAGAGCACACACACACACCCCCCGCUCUCUUAUGGGGGAGUGUGUAAGAGUGCCUGAGCGCCAGAGGGCAGUGGAAGAGAGCGAGUGCUUUCGAGUGGCA
..(((.....((....--(..((.((((.(..((((((((((((........)))))).))))))..).))))))...)(((....))).))....((((((....))))))..)))... ( -42.60)
>DroEre_CAF1 8360 92 - 1
AACUCGAAGAGCGAGA--GAAAGGGCUCUCU---------CCUUUUCUCUUU--GGCGC--AUGCAAGAGCGCG-----CCCAA-AA-------GAGAGAGCUCUUGUUUUGGAGUGGUU
.((((.((((((((((--((......)))))---------)..(((((((((--(((((--..((....)))))-----))..)-))-------))))))))))).....).)))).... ( -37.00)
>DroYak_CAF1 8372 97 - 1
AACUCGAAGAGCGAGA--GAAAGGGCUCUCUCUCU-----CGUCUUCUCUUU--GGGGA--AUGCAAGAGCGCC-----CCCAAAAA-------GAGAGAGCUCAUGGGUUCGAGUGGUU
.((((((((((.((((--((......)))))).))-----)(..((((((((--((((.--.(((....))).)-----))))..))-------)))))..).......))))))).... ( -40.70)
>consensus
AACUCGAAGAGCGAGA__GAAAGAGCUCUCU_________CUUCCUCUCUUU__GGGGA__AAGCAAGAGCGCC_____GCAAAAAG_______GAGAGAGCUCUUGU_UUCGAGUGGGU
.(((((((............((((((((((...............(((((....)))))....((....)).........................))))))))))...))))))).... (-17.30 = -18.86 +   1.56)

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 09:56:26 2006