Locus 705

Sequence ID 2L_DroMel_CAF1
Location 2,038,830 – 2,038,960
Length 130
Max. P 0.825206
window1153 window1154

overview

Window 3

Location 2,038,830 – 2,038,934
Length 104
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 88.06
Mean single sequence MFE -28.32
Consensus MFE -18.88
Energy contribution -20.76
Covariance contribution 1.88
Combinations/Pair 1.10
Mean z-score -2.83
Structure conservation index 0.67
SVM decision value 0.69
SVM RNA-class probability 0.825206
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2038830 104 - 22407834
AAGAAAACGGCAAGUGAAUUCGGUUUCAAUUGUUGAAUGGCUAUUGCAUAUUGAUUGUGUGCAGGAAGCAACAUGGCCGAUAUGGCGAUACACAAGCCCACAAA-----
.......((((((.((((......)))).))))))...(((((((((((((((.(..(((((.....)).)))..).)))))).))))).....))))......----- ( -28.00)
>DroSec_CAF1 56248 104 - 1
AAGAAAACGGCAAGUGAAUUCGGUUUCAAUUGUUGAAUGGCUAUUGCACAUUGAUUGUGUGCAGGAAGCAACAUGGCCGAUAUGGCGAUACACAAGCCAAGAAA-----
.......((((((.((((......)))).))))))..(((((.((((((((.....))))))))........((.(((.....))).)).....))))).....----- ( -30.30)
>DroSim_CAF1 54709 104 - 1
AAGAAAACGGCAAGUGAAUUCGGUUUCAAUUGUUGAAUGGCUAUUGCAUAUUGAUUGUGUGCAGGAAGCAACAUGGCCGAUAUGGCGAUACACAAGCCAAGAAA-----
.......((((((.((((......)))).))))))..((((((((((((((((.(..(((((.....)).)))..).)))))).))))).....))))).....----- ( -29.90)
>DroEre_CAF1 55036 98 - 1
AAGAAAACGGCAAGUGAAUUCAGUUUCAAUUGUUGA-UAGCUAAAGCACAUUGAUUGUGCGUAGGAAAC---------GAUAUAGCGAUACACAAACCAAGAAACACA-
.......((((((.((((......)))).)))))).-..((((..(((((.....)))))...(....)---------....))))......................- ( -22.00)
>DroYak_CAF1 58393 109 - 1
AAGAAAACGGCAAGUGAAUUCAGUUUCAAUUGUUGAAUGGCUAUUGCAUAUUGAUUGUGUGCAGGAAACAACAUGGUCGAUAUGGCGAUACACAAACCAAGAAAUACAA
.......((((((.((((......)))).))))))..((..((((((((((((((..(((...(....).)))..)))))))).))))))..))............... ( -31.40)
>consensus
AAGAAAACGGCAAGUGAAUUCGGUUUCAAUUGUUGAAUGGCUAUUGCAUAUUGAUUGUGUGCAGGAAGCAACAUGGCCGAUAUGGCGAUACACAAGCCAAGAAA_____
.......((((((.((((......)))).))))))..((((((((((((((.....)))))))(....)...)))))))...((((.........)))).......... (-18.88 = -20.76 +   1.88)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,038,865 – 2,038,960
Length 95
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 81.44
Mean single sequence MFE -22.87
Consensus MFE -15.42
Energy contribution -15.98
Covariance contribution 0.56
Combinations/Pair 1.23
Mean z-score -1.79
Structure conservation index 0.67
SVM decision value 0.39
SVM RNA-class probability 0.715996
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2038865 95 - 22407834
AUGUGAGUCA---UCGGCUCAACGCGAA----AAAG---AAAACGGCAAGUGAAUUCGGUUUCAAUUGUUGAAUGGCUAUUGCAUAUUGAUUGUGUGCAGGAAGC
...(((((..---...))))).......----....---....((((((.((((......)))).))))))....(((.((((((((.....))))))))..))) ( -24.30)
>DroSec_CAF1 56283 93 - 1
AUGUGAGUCA---UCGA--CAACACGAA----AAAG---AAAACGGCAAGUGAAUUCGGUUUCAAUUGUUGAAUGGCUAUUGCACAUUGAUUGUGUGCAGGAAGC
.....(((((---((((--(((...(((----(..(---((.((.....))...)))..))))..)))))).)))))).((((((((.....))))))))..... ( -26.60)
>DroSim_CAF1 54744 93 - 1
AUGUGAGUCA---UCGA--CAACACGAA----AAAG---AAAACGGCAAGUGAAUUCGGUUUCAAUUGUUGAAUGGCUAUUGCAUAUUGAUUGUGUGCAGGAAGC
.....(((((---((((--(((...(((----(..(---((.((.....))...)))..))))..)))))).)))))).((((((((.....))))))))..... ( -24.70)
>DroEre_CAF1 55066 95 - 1
AUGUGAGUCAUCAUCGA--CCGCACGAA----AAAG---AAAACGGCAAGUGAAUUCAGUUUCAAUUGUUGA-UAGCUAAAGCACAUUGAUUGUGCGUAGGAAAC
.((((.(((......))--)))))....----....---....((((((.((((......)))).)))))).-...(((..(((((.....))))).)))..... ( -22.60)
>DroYak_CAF1 58433 92 - 1
AUGUGAGUCA---UCGA--CAACACGAA-----AAG---AAAACGGCAAGUGAAUUCAGUUUCAAUUGUUGAAUGGCUAUUGCAUAUUGAUUGUGUGCAGGAAAC
.....(((((---((((--(((...(((-----(.(---((.((.....))...)))..))))..)))))).)))))).((((((((.....))))))))..... ( -22.10)
>DroAna_CAF1 53315 93 - 1
AUGUGACUCA---UCAG--CAAAAUAAAGGAAACUGAACGGAACGGUAAACGAAUAAAAUUUCAGUUGUUGAAUGGGAAUUGCAUAUUGAUUG---GCAAG----
(((..(((((---((((--(((.....((....))................(((......)))..)))))).)))))..)..)))........---.....---- ( -16.90)
>consensus
AUGUGAGUCA___UCGA__CAACACGAA____AAAG___AAAACGGCAAGUGAAUUCAGUUUCAAUUGUUGAAUGGCUAUUGCAUAUUGAUUGUGUGCAGGAAGC
.....(((((...(((........)))................((((((.((((......)))).))))))..))))).((((((((.....))))))))..... (-15.42 = -15.98 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:23 2006