Locus 2054

Sequence ID 2L_DroMel_CAF1
Location 5,553,662 – 5,553,851
Length 189
Max. P 0.999071
window3303 window3304 window3305

overview

Window 3

Location 5,553,662 – 5,553,777
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.98
Mean single sequence MFE -39.68
Consensus MFE -33.20
Energy contribution -33.32
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -3.11
Structure conservation index 0.84
SVM decision value 3.36
SVM RNA-class probability 0.999071
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5553662 115 + 22407834
UAAUUGUCAAACUCCAAUACGCUAAAGUCCACGCUCUUUCCCUGGGUGGCCAUCUU-----AGUCCUACUGCUGUGUGGUGUGGAUGGACUUCAGCCAAGAGCAGGUUCCUGCUCCUCUU
....................(((.((((((((((((.......)))))(((((..(-----(((......)))).))))).....))))))).)))...((((((....))))))..... ( -36.70)
>DroSec_CAF1 5826 115 + 1
UAAUUGUCGAACUCCAAUACGCUGAAGUCCACGCUCUUUCCCUGGGUGGCCAUACU-----AAUCCUACUGCUGUGUGGUGUGGAUGGACUUCAGCCAAGAGCAGAUUCCUGCUCCUUUG
....................((((((((((((((((.......))))).(((((((-----(....(((....))))))))))).)))))))))))...((((((....))))))..... ( -43.60)
>DroSim_CAF1 5943 115 + 1
UAAUUGUCAAACUCCAAUACGCUGAAGUCCACGCUCUUUCCCUGGGUGGCCAUACU-----AAUCCUACUGCUGUGUGGUGUGGAUGGACUUCAGCCAAGAGCAGGUUCCUGCUCCUUGG
.............((((...((((((((((((((((.......))))).(((((((-----(....(((....))))))))))).)))))))))))...((((((....)))))).)))) ( -47.00)
>DroEre_CAF1 6016 115 + 1
UAGUUGUCAAACUCCAAUACGCUGAAGUCCACGUUCUUUCCCUGUGAGCCCAUUCUGCUGCAAUCCUACUGCU----GGUGUGGAUGGACUUCAGCCAAGAGCAGGUCCUUGCUC-UUUG
.((((....)))).......(((((((((((.((((.........))))((((.((...(((.......))).----)).)))).))))))))))).((((((((....))))))-)).. ( -38.40)
>DroYak_CAF1 6155 110 + 1
UAGUUGUCAAACUCCAAUACGCUGAAGUCCACAUUCUUUCCCUGUGAGCCCAUCCU-----AAUCCUACUGCU----GGUGUAGAUGGACUUCAGCCAAGAGCAGGUCCUUGCUC-UUUG
.((((....)))).......((((((((((((((.........)))..........-----.......((((.----...)))).))))))))))).((((((((....))))))-)).. ( -32.70)
>consensus
UAAUUGUCAAACUCCAAUACGCUGAAGUCCACGCUCUUUCCCUGGGUGGCCAUACU_____AAUCCUACUGCUGUGUGGUGUGGAUGGACUUCAGCCAAGAGCAGGUUCCUGCUCCUUUG
..((((........))))..((((((((((((((((.......))))).................((((.(((....))))))).)))))))))))...((((((....))))))..... (-33.20 = -33.32 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 5,553,662 – 5,553,777
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.98
Mean single sequence MFE -36.28
Consensus MFE -29.86
Energy contribution -30.34
Covariance contribution 0.48
Combinations/Pair 1.07
Mean z-score -1.72
Structure conservation index 0.82
SVM decision value 0.74
SVM RNA-class probability 0.838479
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5553662 115 - 22407834
AAGAGGAGCAGGAACCUGCUCUUGGCUGAAGUCCAUCCACACCACACAGCAGUAGGACU-----AAGAUGGCCACCCAGGGAAAGAGCGUGGACUUUAGCGUAUUGGAGUUUGACAAUUA
...((((((((....)))))))).((((((((((((.(...((((......)).)).((-----....(((....))).)).....).))))))))))))..((((........)))).. ( -36.70)
>DroSec_CAF1 5826 115 - 1
CAAAGGAGCAGGAAUCUGCUCUUGGCUGAAGUCCAUCCACACCACACAGCAGUAGGAUU-----AGUAUGGCCACCCAGGGAAAGAGCGUGGACUUCAGCGUAUUGGAGUUCGACAAUUA
...((((((((....)))))))).((((((((((((.(...((((......)).))...-----....(((....)))........).))))))))))))..((((........)))).. ( -36.50)
>DroSim_CAF1 5943 115 - 1
CCAAGGAGCAGGAACCUGCUCUUGGCUGAAGUCCAUCCACACCACACAGCAGUAGGAUU-----AGUAUGGCCACCCAGGGAAAGAGCGUGGACUUCAGCGUAUUGGAGUUUGACAAUUA
(((((((((((....)))))))).((((((((((((.(...((((......)).))...-----....(((....)))........).))))))))))))....)))............. ( -39.90)
>DroEre_CAF1 6016 115 - 1
CAAA-GAGCAAGGACCUGCUCUUGGCUGAAGUCCAUCCACACC----AGCAGUAGGAUUGCAGCAGAAUGGGCUCACAGGGAAAGAACGUGGACUUCAGCGUAUUGGAGUUUGACAACUA
..((-(((((......))))))).((((((((((((.....((----.(((((...)))))(((.......)))....))........)))))))))))).......((((....)))). ( -35.82)
>DroYak_CAF1 6155 110 - 1
CAAA-GAGCAAGGACCUGCUCUUGGCUGAAGUCCAUCUACACC----AGCAGUAGGAUU-----AGGAUGGGCUCACAGGGAAAGAAUGUGGACUUCAGCGUAUUGGAGUUUGACAACUA
..((-(((((......))))))).((((((((((((((((...----....))))....-----....((......))..........)))))))))))).......((((....)))). ( -32.50)
>consensus
CAAAGGAGCAGGAACCUGCUCUUGGCUGAAGUCCAUCCACACCACACAGCAGUAGGAUU_____AGGAUGGCCACCCAGGGAAAGAGCGUGGACUUCAGCGUAUUGGAGUUUGACAAUUA
...((((((((....)))))))).((((((((((((((((...........)).)))...........((......))...........)))))))))))...(((........)))... (-29.86 = -30.34 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 5,553,737 – 5,553,851
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.02
Mean single sequence MFE -23.27
Consensus MFE -18.52
Energy contribution -18.92
Covariance contribution 0.40
Combinations/Pair 1.11
Mean z-score -2.43
Structure conservation index 0.80
SVM decision value 1.86
SVM RNA-class probability 0.980311
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5553737 114 - 22407834
UAACACACAACACAAACACACACUCUUUUAA------AUAUAACACUUACACAUUAAAAGGGACUUUUUCCUGAACCACAAAGAGGAGCAGGAACCUGCUCUUGGCUGAAGUCCAUCCAC
........................(((((((------................)))))))(((((((..((((.....))...((((((((....))))))))))..)))))))...... ( -25.09)
>DroSec_CAF1 5901 109 - 1
-A--ACACGACACAAACA--CACUCUUUUAA------AUAUAACACUCACACAUUAGAAGGGGCUUUUUUCUGAACCGCACAAAGGAGCAGGAAUCUGCUCUUGGCUGAAGUCCAUCCAC
-.--....(((.......--..(((((((((------................)))))))))...............((....((((((((....)))))))).))....)))....... ( -22.29)
>DroSim_CAF1 6018 112 - 1
UAACACACGACACAAACA--CACUCUUUUUA------AUAUAACACUUACACAUUAGAAAGGACUUUUUCCUGAACCACACCAAGGAGCAGGAACCUGCUCUUGGCUGAAGUCCAUCCAC
..................--.....((((((------((.............))))))))(((((((..((((........))((((((((....))))))))))..)))))))...... ( -24.82)
>DroEre_CAF1 6092 106 - 1
UGGCACACGGC--AAAUA--CACUU-UUUAA------ACACAACACUCACACUC--GCAGGGGCUUUUUCCUGAACCACACAAA-GAGCAAGGACCUGCUCUUGGCUGAAGUCCAUCCAC
(((.((.((((--.....--.....-.....------.................--.((((((....)))))).........((-(((((......))))))).))))..)))))..... ( -22.00)
>DroYak_CAF1 6226 112 - 1
UAGCACACGAC--AAAUA--CACUU-CUUUAUGAAUUAAAAAACACUCACACAU--AAAGGGGCUUUUUCCUGAACCACACAAA-GAGCAAGGACCUGCUCUUGGCUGAAGUCCAUCUAC
...........--.....--.....-(((((((..................)))--))))(((((((..((((.....))..((-(((((......)))))))))..)))))))...... ( -22.17)
>consensus
UAACACACGACACAAACA__CACUCUUUUAA______AUAUAACACUCACACAUUAGAAGGGGCUUUUUCCUGAACCACACAAAGGAGCAGGAACCUGCUCUUGGCUGAAGUCCAUCCAC
............................................................(((((((..((((.....))...((((((((....))))))))))..)))))))...... (-18.52 = -18.92 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:09 2006