Locus 4596

Sequence ID 3R_DroMel_CAF1
Location 12,086,239 – 12,086,358
Length 119
Max. P 0.999633
window7552 window7553 window7554

overview

Window 2

Location 12,086,239 – 12,086,342
Length 103
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 76.93
Mean single sequence MFE -29.75
Consensus MFE -20.81
Energy contribution -22.12
Covariance contribution 1.31
Combinations/Pair 1.16
Mean z-score -1.55
Structure conservation index 0.70
SVM decision value 0.19
SVM RNA-class probability 0.625432
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12086239 103 + 27905053
A---------------UUUUAGUGCUGCCGUUACUUGUAAAAUAUUUCUCUAGGUUCGGGUCUCUGCUACACAAAGCAGUUUACACUGCUUGUCUAGUGGAUGCACCCGAUAAGCUAG-
.---------------.......((((((.......................)))(((((((((..(((.((((.(((((....))))))))).)))..)).).))))))..)))...- ( -30.10)
>DroSec_CAF1 22895 119 + 1
AUUUUCCCAGCCUGCAUUUUAGUGUGGCCGUUACGUGUAAAAUAUUUCUUUAGGGUCGGGUCUCUGCUGUACAAAGCAGUUUACACUGCUUGUCUAGUGGAUGCACCGGAUAAACUUAC
.....(((.(((.((((....)))))))..(((....)))............)))((((((.((..(((.((((.(((((....))))))))).)))..)).)).)))).......... ( -33.50)
>DroSim_CAF1 23072 118 + 1
AUUUUCCCAGCCUGUGUUUUAGUGUGGCCGUUACUUGUAAAAUAUUUCUUUAGGUACGGGUCUCUGCUAUACAAAGCAGUUUACACUGCUUGUCUAGUGGAUGCACCGGAUAAACUUG-
..........((.((((.((.(((((((.(..(((((((...((......))..)))))))..).))))))).(((((((....)))))))........)).)))).)).........- ( -31.40)
>DroYak_CAF1 25411 107 + 1
AUCUUCCCAAACUGUACUUUAGUGUGACCAUUAC-----------UUCUUUAGGUUCGAUUCCCCGCUACACAAAGCAGUGUACACUGCUUGUCUGGUGGAAGCACCCGAUAAAAAUG-
.....................((((((((.....-----------.......)))).......((((((.((((.(((((....))))))))).))))))..))))............- ( -24.00)
>consensus
AUUUUCCCAGCCUGUAUUUUAGUGUGGCCGUUACUUGUAAAAUAUUUCUUUAGGUUCGGGUCUCUGCUACACAAAGCAGUUUACACUGCUUGUCUAGUGGAUGCACCCGAUAAACUUG_
.................((..((((((((...(((((.............)))))...))))(((((((.((((.(((((....))))))))).))))))).))))..))......... (-20.81 = -22.12 +   1.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,086,263 – 12,086,358
Length 95
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 74.75
Mean single sequence MFE -33.45
Consensus MFE -21.89
Energy contribution -22.70
Covariance contribution 0.81
Combinations/Pair 1.09
Mean z-score -2.80
Structure conservation index 0.65
SVM decision value 3.81
SVM RNA-class probability 0.999633
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12086263 95 + 27905053
AAAUAUUUCUCUAGGUUCGGGUCUCUGCUACACAAAGCAGUUUACACUGCUUGUCUAGUGGAUGCACCCGAUAAGCUAG--C----------------------UUGGUGUUCUUAAAA-
.((((((...((((.((((((((((..(((.((((.(((((....))))))))).)))..)).).))))))..).))))--.----------------------..)))))).......- ( -32.60)
>DroSec_CAF1 22934 119 + 1
AAAUAUUUCUUUAGGGUCGGGUCUCUGCUGUACAAAGCAGUUUACACUGCUUGUCUAGUGGAUGCACCGGAUAAACUUACACUCAUAUAAAGGGUCACACUUUGUUGGGGCUUUUAAAA-
...........((((.((((((.((..(((.((((.(((((....))))))))).)))..)).)).)))).....))))..((((.((((((.......))))))))))..........- ( -32.60)
>DroSim_CAF1 23111 117 + 1
AAAUAUUUCUUUAGGUACGGGUCUCUGCUAUACAAAGCAGUUUACACUGCUUGUCUAGUGGAUGCACCGGAUAAACUUG--CUCAUAUAAAGGGUCACACUUUUUAGGUGCUUUUUAAA-
...........(((((.(((((.((..(((.((((.(((((....))))))))).)))..)).)).))).....)))))--......(((((((.(((.((....))))))))))))..- ( -32.40)
>DroEre_CAF1 25041 108 + 1
------UUCUUGAGGUUCGGGUCCCUGCUGCACAAAGCAGUUUACACUGCUUGUGUGGUGGAAGCACCCGAUAAGCUUG--G--GUAUAAAGGGUUACACUUUUUGC-U-UUUUUGAAAU
------..((..((.((((((((.(..(..(((((.(((((....))))))))))..)..)..).))))))..).))..--)--)..(((((((.....))))))).-.-.......... ( -36.20)
>consensus
AAAUAUUUCUUUAGGUUCGGGUCUCUGCUACACAAAGCAGUUUACACUGCUUGUCUAGUGGAUGCACCCGAUAAACUUG__C__AUAUAAAGGGUCACACUUUUUUGGUGCUUUUAAAA_
..............((((((((.((..(((.((((.(((((....))))))))).)))..)).)).))))))................................................ (-21.89 = -22.70 +   0.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,086,263 – 12,086,358
Length 95
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 74.75
Mean single sequence MFE -26.38
Consensus MFE -17.31
Energy contribution -18.62
Covariance contribution 1.31
Combinations/Pair 1.05
Mean z-score -1.88
Structure conservation index 0.66
SVM decision value 1.22
SVM RNA-class probability 0.932677
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12086263 95 - 27905053
-UUUUAAGAACACCAA----------------------G--CUAGCUUAUCGGGUGCAUCCACUAGACAAGCAGUGUAAACUGCUUUGUGUAGCAGAGACCCGAACCUAGAGAAAUAUUU
-...............----------------------.--((((....((((((...((..(((.(((((((((....))))).)))).)))..)).))))))..)))).......... ( -28.00)
>DroSec_CAF1 22934 119 - 1
-UUUUAAAAGCCCCAACAAAGUGUGACCCUUUAUAUGAGUGUAAGUUUAUCCGGUGCAUCCACUAGACAAGCAGUGUAAACUGCUUUGUACAGCAGAGACCCGACCCUAAAGAAAUAUUU
-......((((....(((..((((((....))))))...)))..))))...(((.(..((..((..(((((((((....))))).))))..))..))..))))................. ( -21.20)
>DroSim_CAF1 23111 117 - 1
-UUUAAAAAGCACCUAAAAAGUGUGACCCUUUAUAUGAG--CAAGUUUAUCCGGUGCAUCCACUAGACAAGCAGUGUAAACUGCUUUGUAUAGCAGAGACCCGUACCUAAAGAAAUAUUU
-........((((.......))))....(((((.(((((--....)))))..(((((.((..(((.(((((((((....))))).)))).)))..)).....))))))))))........ ( -23.40)
>DroEre_CAF1 25041 108 - 1
AUUUCAAAAA-A-GCAAAAAGUGUAACCCUUUAUAC--C--CAAGCUUAUCGGGUGCUUCCACCACACAAGCAGUGUAAACUGCUUUGUGCAGCAGGGACCCGAACCUCAAGAA------
..(((....(-(-((.....((((((....))))))--.--...)))).((((((.(((.(..((((.(((((((....)))))))))))..).))).)))))).......)))------ ( -32.90)
>consensus
_UUUUAAAAACACCAAAAAAGUGUGACCCUUUAUAU__G__CAAGCUUAUCCGGUGCAUCCACUAGACAAGCAGUGUAAACUGCUUUGUACAGCAGAGACCCGAACCUAAAGAAAUAUUU
.................................................((((((.(.((..(((.(((((((((....))))).)))).)))..)))))))))................ (-17.31 = -18.62 +   1.31)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:07 2006