Locus 2429

Sequence ID	2R_DroMel_CAF1
Location	8,730,528 – 8,730,672
Length	144
Max. P	0.990771

overview

Window 8

Location	8,730,528 – 8,730,632
Length	104
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	73.64
Mean single sequence MFE	-36.27
Consensus MFE	-19.37
Energy contribution	-19.27
Covariance contribution	-0.11
Combinations/Pair	1.10
Mean z-score	-2.66
Structure conservation index	0.53
SVM decision value	2.23
SVM RNA-class probability	0.990771
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8730528 104 - 20766785
ACGGUACCUAAAGCGAAUCAGC-------UGCUUAUCGAUAAGUCAGGUGCCAAUCGAUACAUGG---------CAGUGCUGCCCAGUAUCGCACAGCAAGGUGCGUUUAAAUUUUGAAA
..(((((((..(((......))-------)(((((....))))).)))))))..(((((((..((---------((....))))..)))))((((......))))...........)).. ( -33.70)
>DroSim_CAF1 537 111 - 1
ACGGUACCUAAAGCGAAUCAGC-------UGCUUAACGAUAAGCCAGGUGCCAAUCGAUAUAUGGGCCACGUGCCAGUGCUGCCCA-UAUCGCACAGCAAAGUGCGUAUA-AUUUUGAAA
..(((((((..(((......))-------)(((((....))))).)))))))..((((.(((((((((((......)))..)))))-)))(((((......)))))....-...)))).. ( -40.30)
>DroYak_CAF1 559 105 - 1
ACGGUACCUAAAGCCAAUCAGCUGGCAGCUGUCUAUCGAUAAGCCAGGUGCCGC---------------CGUGCCAGUGCUGCCCAGCGUAGCUCAGCAAACUGCGGUUACUUUUUGAAA
.((((((((...((((......)))).((((((....))).))).)))))))).---------------.(((((.(.(((((.....))))).).((.....)))).)))......... ( -34.80)
>consensus
ACGGUACCUAAAGCGAAUCAGC_______UGCUUAUCGAUAAGCCAGGUGCCAAUCGAUA_AUGG____CGUGCCAGUGCUGCCCAGUAUCGCACAGCAAAGUGCGUUUA_AUUUUGAAA
..(((((((...((......))........(((((....))))).))))))).........................(((((..(......)..)))))..................... (-19.37 = -19.27 +  -0.11)

alignment

secondary structure

dotplot

Window 9

Location	8,730,568 – 8,730,672
Length	104
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	77.36
Mean single sequence MFE	-28.93
Consensus MFE	-20.11
Energy contribution	-20.33
Covariance contribution	0.23
Combinations/Pair	1.08
Mean z-score	-1.94
Structure conservation index	0.69
SVM decision value	1.43
SVM RNA-class probability	0.953132
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8730568 104 - 20766785
UUACAAAUAUGCCUUGCAUAAUAAACAAAUGCACGUUUAAACGGUACCUAAAGCGAAUCAGC-------UGCUUAUCGAUAAGUCAGGUGCCAAUCGAUACAUGG---------CAGUGC
.........((((.(((((.........))))).........(((((((..(((......))-------)(((((....))))).)))))))...........))---------)).... ( -25.40)
>DroSim_CAF1 575 113 - 1
UUACUAAUAUGCCUUGCAUAAUAAACAAAUGCACGUUUAAACGGUACCUAAAGCGAAUCAGC-------UGCUUAACGAUAAGCCAGGUGCCAAUCGAUAUAUGGGCCACGUGCCAGUGC
.......(((((...)))))..........((((........(((((((..(((......))-------)(((((....))))).)))))))............(((.....))).)))) ( -29.70)
>DroYak_CAF1 599 105 - 1
UUACUAACAUGCCUUGCAUAAUAAACAAACGCACGUGUGAACGGUACCUAAAGCCAAUCAGCUGGCAGCUGUCUAUCGAUAAGCCAGGUGCCGC---------------CGUGCCAGUGC
.((((...((((...))))...........(((((.(....((((((((...((((......)))).((((((....))).))).)))))))))---------------))))).)))). ( -31.70)
>consensus
UUACUAAUAUGCCUUGCAUAAUAAACAAAUGCACGUUUAAACGGUACCUAAAGCGAAUCAGC_______UGCUUAUCGAUAAGCCAGGUGCCAAUCGAUA_AUGG____CGUGCCAGUGC
.......(((((...)))))..........((((((....))(((((((...((......))........(((((....))))).)))))))........................)))) (-20.11 = -20.33 +   0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:54 2006