Locus 8381

Sequence ID	X_DroMel_CAF1
Location	20,809,748 – 20,809,903
Length	155
Max. P	0.825107

overview

Window 4

Location	20,809,748 – 20,809,865
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.35
Mean single sequence MFE	-24.34
Consensus MFE	-22.96
Energy contribution	-22.71
Covariance contribution	-0.25
Combinations/Pair	1.05
Mean z-score	-1.81
Structure conservation index	0.94
SVM decision value	0.69
SVM RNA-class probability	0.825107
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20809748 117 + 22224390
GGAAA-CU--GGGAAACUGUGCGCAGCAUAACGGAACAACAAAGCGCACCAGGCACGAGUGCAAAAGUACAAUAAAAUUGCAUACGAAAGCAGUUUACUGCAGACGAAAAAAUUAAAUUA
.....-((--((....).((((((...................)))))))))...((.((((((.............)))))).))...((((....))))................... ( -24.73)
>DroSim_CAF1 5435 117 + 1
GGAAA-CU--GGGAAACUGUGCGCAGCAUAACGGAACAACAAAGCGCACCAGGCACGAGUGCAAAAGUACAAUAAAAUUGCAUACGAAAGCAGUUUACUGCAGACGAAAAAAUUAAAUUA
.....-((--((....).((((((...................)))))))))...((.((((((.............)))))).))...((((....))))................... ( -24.73)
>DroEre_CAF1 1749 118 + 1
GGAAAACU--GGGAAACUGUGCGCAGCAUAACGGAACAACAAAGCGCACCAGGCACGAGUACAGAAGUACAAUAAAAUUGCAUACGAAAGCAGUUUGCUGCAGACGAAAAAAUUAAAUUA
......((--((....).((((((...................)))))))))((((..((((....))))....(((((((........)))))))).)))................... ( -24.51)
>DroYak_CAF1 5908 120 + 1
GGAAAAUGGGGGGAAACUGUGCGCAGCAUAACGGAACAACAAAGCGCACCAGGCACGAGUACAAAAGUACAAUAAAAUUGCAUACGAAAGCAGUUUACUGCAGACGAAAAAAUUAAAUUA
......(((.((....)).(((((...................)))))))).(((...((((....))))....(((((((........)))))))..)))................... ( -23.41)
>consensus
GGAAA_CU__GGGAAACUGUGCGCAGCAUAACGGAACAACAAAGCGCACCAGGCACGAGUACAAAAGUACAAUAAAAUUGCAUACGAAAGCAGUUUACUGCAGACGAAAAAAUUAAAUUA
..........((....))((((((...................))))))...(((...((((....))))....(((((((........)))))))..)))................... (-22.96 = -22.71 +  -0.25)

alignment

secondary structure

dotplot

Window 5

Location	20,809,785 – 20,809,903
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.20
Mean single sequence MFE	-23.01
Consensus MFE	-19.60
Energy contribution	-19.35
Covariance contribution	-0.25
Combinations/Pair	1.04
Mean z-score	-1.88
Structure conservation index	0.85
SVM decision value	-0.02
SVM RNA-class probability	0.524039
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20809785 118 + 22224390
AAAGCGCACCAGGCACGAGUGCAAAAGUACAAUAAAAUUGCAUACGAAAGCAGUUUACUGCAGACGAAAAAAUUAAAUUAAUGAAGAAAAAUGGUAAUAAAGCGUUAGUCACGUGU--GC
...((((((..(((.((.((((((.............)))))).))...((((....)))).((((.....((((.(((..........)))..))))....)))).)))..))))--)) ( -24.02)
>DroSim_CAF1 5472 118 + 1
AAAGCGCACCAGGCACGAGUGCAAAAGUACAAUAAAAUUGCAUACGAAAGCAGUUUACUGCAGACGAAAAAAUUAAAUUAAUGAAGAAAAAUGGUAAUAAAGCGUUAGUCACGUGU--GC
...((((((..(((.((.((((((.............)))))).))...((((....)))).((((.....((((.(((..........)))..))))....)))).)))..))))--)) ( -24.02)
>DroEre_CAF1 1787 120 + 1
AAAGCGCACCAGGCACGAGUACAGAAGUACAAUAAAAUUGCAUACGAAAGCAGUUUGCUGCAGACGAAAAAAUUAAAUUAAUGAAGAAAAAUGGUAAUAAAGCGUUAGUCACGUGUGUGU
...(.((.....)).)..((((....)))).........(((((((...((((....))))........................((..((((.(.....).))))..)).))))))).. ( -22.50)
>DroYak_CAF1 5948 118 + 1
AAAGCGCACCAGGCACGAGUACAAAAGUACAAUAAAAUUGCAUACGAAAGCAGUUUACUGCAGACGAAAAAAUUAAAUUAAUGAAGAAAAAUGGUAAUAAAGCGUUAGUCACGUGU--GU
...(.((.....)).)..((((....)))).........(((((((...((((....))))........................((..((((.(.....).))))..)).)))))--)) ( -21.50)
>consensus
AAAGCGCACCAGGCACGAGUACAAAAGUACAAUAAAAUUGCAUACGAAAGCAGUUUACUGCAGACGAAAAAAUUAAAUUAAUGAAGAAAAAUGGUAAUAAAGCGUUAGUCACGUGU__GC
...((((.....))....((((....)))).........))(((((...((((....))))........................((..((((.(.....).))))..)).))))).... (-19.60 = -19.35 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:02:34 2006