Locus 783

Sequence ID 2R_DroMel_CAF1
Location 3,746,740 – 3,746,976
Length 236
Max. P 0.799631
window1373 window1374

overview

Window 3

Location 3,746,740 – 3,746,860
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.54
Mean single sequence MFE -38.57
Consensus MFE -35.91
Energy contribution -35.70
Covariance contribution -0.21
Combinations/Pair 1.10
Mean z-score -1.64
Structure conservation index 0.93
SVM decision value 0.09
SVM RNA-class probability 0.578556
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3746740 120 + 20766785
GACGAGGGGAAACCUGAGUGAAGUGUGCGGUCUGCGGGGCAUUAGAAGUCGUGACGGGCCGCCCAACUAUUUGAUUGUUUUUCUUCCUGCUGUGGGAGAUUUCAUUUUUAUGAAUUUGAU
((((((((....)))(((((...((.((((((((((.(((.......))).)).)))))))).))..)))))..)))))..((((((......)))))).(((((....)))))...... ( -38.90)
>DroSim_CAF1 9565 118 + 1
GACGAGGGGAAACCUGAGUGAAGUGUGCGGUCUGCGGGGCAUUAGAAGUCGUGACGGGCCGCCCAACUAUUUGAUUGUU--UCUUCCUGCUGUGGGAGAUUUCAUUUUUAUGAAUUUGAU
((((((((....)))(((((...((.((((((((((.(((.......))).)).)))))))).))..)))))..)))))--((((((......)))))).(((((....)))))...... ( -38.90)
>DroYak_CAF1 9314 117 + 1
AGCGAGGGGAAAUCCGAGUGAAGUGUGCGGUCUGCGGGGCAUUAGAAGUCGUGACGGGCCGCCCAACUAUUUGAUUGUUU---UUCCUGCUGUGGGAGAUUUCAUUUUUAUGAAUUUGAU
(((.(((..((((.((((((...((.((((((((((.(((.......))).)).)))))))).))..))))))...))))---..))))))......((.(((((....))))).))... ( -37.90)
>consensus
GACGAGGGGAAACCUGAGUGAAGUGUGCGGUCUGCGGGGCAUUAGAAGUCGUGACGGGCCGCCCAACUAUUUGAUUGUUU_UCUUCCUGCUGUGGGAGAUUUCAUUUUUAUGAAUUUGAU
((((((((....)))(((((...((.((((((((((.(((.......))).)).)))))))).))..)))))..)))))..((((((......)))))).(((((....)))))...... (-35.91 = -35.70 +  -0.21) 

alignment

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secondary structure

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dotplot

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Window 4

Location 3,746,860 – 3,746,976
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.55
Mean single sequence MFE -29.40
Consensus MFE -22.01
Energy contribution -21.57
Covariance contribution -0.44
Combinations/Pair 1.09
Mean z-score -2.44
Structure conservation index 0.75
SVM decision value 0.61
SVM RNA-class probability 0.799631
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3746860 116 + 20766785
AAAUGGCCAGCCAGGAGUCGGGCUAAUAACUGGAAAGUUCUUUCUGACAGACUCCAAAAAGGGGGAAAAGUGUU-UUCACCCAAAAAAAACAAAAGAUGCAAUAAUUUAUAUGCUG---A
.......((((..((((((...(.((.((((....)))).))...)...)))))).....((((((((....))-))).)))..............................))))---. ( -26.70)
>DroSim_CAF1 9683 117 + 1
AAAUGGCCAGCCAGGAGUCGGGCUAAUAACUGGAAAGUUCUUUCUGACAGACUCCAAAAAGGGGGAUAUGCAUUCUUCACCCAAAAAAAGCAAAUGAUGCCAUAAUUUAUAUGCUG---A
...(((....)))((((((...(.((.((((....)))).))...)...)))))).....(((.((..........)).)))......((((.((((.........)))).)))).---. ( -26.60)
>DroYak_CAF1 9431 114 + 1
AAAUGGCCAGCCAGGAGUCGGGCUAAUAACUGGAAAGUUCUUUCUGCCAGACUCCAAAAAGGGGAAAAAGUAUUUUUCCCCCAAAAAA------CAAUUCUAUAAUUUAUAUGUUGUCGA
...(((....)))((((((.(((.((.((((....)))).))...))).)))))).....((((((((.....)))))))).......------....((.(((((......))))).)) ( -34.90)
>consensus
AAAUGGCCAGCCAGGAGUCGGGCUAAUAACUGGAAAGUUCUUUCUGACAGACUCCAAAAAGGGGGAAAAGUAUU_UUCACCCAAAAAAA_CAAAAGAUGCAAUAAUUUAUAUGCUG___A
.......((((..((((((((........))(((((....)))))....)))))).....((((((.........))).)))..............................)))).... (-22.01 = -21.57 +  -0.44) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:16 2006