Locus 1688

Sequence ID X_DroMel_CAF1
Location 4,711,507 – 4,711,614
Length 107
Max. P 0.972570
window2775 window2776

overview

Window 5

Location 4,711,507 – 4,711,614
Length 107
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 82.66
Mean single sequence MFE -30.93
Consensus MFE -20.96
Energy contribution -24.40
Covariance contribution 3.44
Combinations/Pair 1.06
Mean z-score -2.60
Structure conservation index 0.68
SVM decision value 1.70
SVM RNA-class probability 0.972570
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4711507 107 + 22224390
UGGUGCAUGCAGGGGAAUUGACAUGCCGCAACUUGGCGGCAAAAGUACACAAUAAAUUUGCAUGCCACAUGCACAUUCGUAUACGAGUAUGUAUGCACUCGGUCUCA
..(.(((((((((...((((((.((((((......))))))...))...))))...)))))))))).((((((.(((((....))))).))))))............ ( -35.10)
>DroSec_CAF1 4677 98 + 1
-GUUGCAUGCAGGGGAAUUGACAUGCCGCAACUUGGCGGCAAAAGUACACAAUAAAUUUGCAUGCCACAUGCACAUUCGUAUAGGAGUAUGUAUGCAC--------A
-...(((((((((...((((((.((((((......))))))...))...))))...)))))))))..((((((.((((......)))).))))))...--------. ( -32.20)
>DroEre_CAF1 5610 97 + 1
-G---CGUGCAGGGGAGUUGACAUGCCGCAACUUGGCGGCAAAAGUACACAAUAAAUUUGCAUGCCACAUGCACACUCGUAU------GUGUAUGCACUCGCUCACA
-.---.(((..((.((((.....((((((......))))))..................((((((.((((((......))))------)))))))))))).))))). ( -35.10)
>DroYak_CAF1 5544 83 + 1
-G--------AGGGG-AUUGACAUGCCGCAACUUGGCGGCAAAAGUACACAAUAAAUUUGCAUGCCACAUGCACAUUCGUAU------AUGUAUGCACA--------
-.--------.....-.......((((((......)))))).................(((((((...((((......))))------..)))))))..-------- ( -21.30)
>consensus
_G___CAUGCAGGGGAAUUGACAUGCCGCAACUUGGCGGCAAAAGUACACAAUAAAUUUGCAUGCCACAUGCACAUUCGUAU______AUGUAUGCACU_______A
....(((((((((...((((((.((((((......))))))...))...))))...)))))))))..((((((.((((......)))).))))))............ (-20.96 = -24.40 +   3.44)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 6

Location 4,711,507 – 4,711,614
Length 107
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 82.66
Mean single sequence MFE -29.00
Consensus MFE -21.69
Energy contribution -21.50
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.06
Structure conservation index 0.75
SVM decision value 1.04
SVM RNA-class probability 0.905325
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4711507 107 - 22224390
UGAGACCGAGUGCAUACAUACUCGUAUACGAAUGUGCAUGUGGCAUGCAAAUUUAUUGUGUACUUUUGCCGCCAAGUUGCGGCAUGUCAAUUCCCCUGCAUGCACCA
.......(.((((((.((.....((((((((...((((((...))))))......))))))))...((((((......))))))............)).))))))). ( -32.50)
>DroSec_CAF1 4677 98 - 1
U--------GUGCAUACAUACUCCUAUACGAAUGUGCAUGUGGCAUGCAAAUUUAUUGUGUACUUUUGCCGCCAAGUUGCGGCAUGUCAAUUCCCCUGCAUGCAAC-
.--------..((((.((((.((......)).)))).)))).(((((((.....((((...((...((((((......)))))).)))))).....)))))))...- ( -29.00)
>DroEre_CAF1 5610 97 - 1
UGUGAGCGAGUGCAUACAC------AUACGAGUGUGCAUGUGGCAUGCAAAUUUAUUGUGUACUUUUGCCGCCAAGUUGCGGCAUGUCAACUCCCCUGCACG---C-
.(((((.((((((((((((------(...((((.((((((...)))))).))))..))))))....((((((......)))))))))..))))..)).))).---.- ( -31.70)
>DroYak_CAF1 5544 83 - 1
--------UGUGCAUACAU------AUACGAAUGUGCAUGUGGCAUGCAAAUUUAUUGUGUACUUUUGCCGCCAAGUUGCGGCAUGUCAAU-CCCCU--------C-
--------((.((((((((------(...((((.((((((...)))))).))))..))))))....((((((......)))))))))))..-.....--------.- ( -22.80)
>consensus
U_______AGUGCAUACAU______AUACGAAUGUGCAUGUGGCAUGCAAAUUUAUUGUGUACUUUUGCCGCCAAGUUGCGGCAUGUCAAUUCCCCUGCAUG___C_
.........(((((((...........(..(((.((((((...)))))).)))..))))))))...((((((......))))))....................... (-21.69 = -21.50 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:43 2006