Locus 3350

Sequence ID	2L_DroMel_CAF1
Location	9,711,826 – 9,711,967
Length	141
Max. P	0.990908

overview

Window 2

Location	9,711,826 – 9,711,932
Length	106
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	92.09
Mean single sequence MFE	-23.80
Consensus MFE	-21.20
Energy contribution	-21.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.89
SVM decision value	1.22
SVM RNA-class probability	0.932747
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9711826 106 + 22407834
UUGAGUGUCUGCUUGAGUGAUUCUUCUGAGCUUUCAAAGCCUUGUUAACGGUUCGAUGUAAAUGUAUCUGUAUCUGCAUUUGCAUCUGCAUCUUGCAGCUGCAUCU
....(((.((((..((((.........(((((..(((....))).....)))))((((((((((((........)))))))))))).)).))..)))).))).... ( -27.30)
>DroSec_CAF1 2822 93 + 1
UUGAGUGUCUGCUUGAGUGAUUCUUCUGAGCUUUCAAAGCCUUGUUAACGGUUCGAUGUAAAUGUAUCUGUAUCUGCAUUUGCAUCUGC-------------AUCC
(((((.....(((((((......))).)))).)))))((((........)))).((((((((((((........))))))))))))...-------------.... ( -21.20)
>DroSim_CAF1 2815 93 + 1
UUGAGUGUCUGCUUGAGUGAUUCUUCUGAGCUUUCAAAGCCUUGUUAACGGUUCGAUGUAAAUGUAUCUGUAUCUGCAUUUGCAUCUGC-------------AUCU
(((((.....(((((((......))).)))).)))))((((........)))).((((((((((((........))))))))))))...-------------.... ( -21.20)
>DroEre_CAF1 2811 99 + 1
UUGAGUGUCUGCUUGAGUAAUUCUUCUGAGCUUUCAAAGCCUUGUUAACGGUUCGAUGUAAAUGUAUCUGCAUCUGCAUUUGCAUCUGCAUC-UGC------AUCU
(((((.....(((((((......))).)))).)))))((((........)))).((((((.(((((..((((........))))..))))).-)))------))). ( -23.90)
>DroYak_CAF1 2823 99 + 1
UUGAGUGUCUGCUUGAGUAAUUCUUCUGAGCUUUCAAAGCCUUGUUAACGGUUCGAUGUAAAUGUAUCUGUAUCUGCAUUUGCAUCUGCAUU-UGC------AUCU
(((((.....(((((((......))).)))).)))))((((........)))).((((((((((((..((((........))))..))))))-)))------))). ( -25.40)
>consensus
UUGAGUGUCUGCUUGAGUGAUUCUUCUGAGCUUUCAAAGCCUUGUUAACGGUUCGAUGUAAAUGUAUCUGUAUCUGCAUUUGCAUCUGCAU__UGC______AUCU
(((((.....(((((((......))).)))).)))))((((........)))).((((((((((((........)))))))))))).................... (-21.20 = -21.20 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	9,711,866 – 9,711,967
Length	101
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	89.31
Mean single sequence MFE	-25.76
Consensus MFE	-20.76
Energy contribution	-20.76
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.56
Structure conservation index	0.81
SVM decision value	2.24
SVM RNA-class probability	0.990908
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9711866 101 + 22407834
CUUGUUAACGGUUCGAUGUAAAUGUAUCUGUAUCUGCAUUUGCAUCUGCAUCUUGCAGCUGCAUCUC-----GCAUCCUGCAUCUGAGUGUGGUUUGUUGUAUAUU
.....((((((..(((((((((((((........)))))))))))).(((((.(((((.(((.....-----)))..)))))...)).))))..))))))...... ( -28.20)
>DroSec_CAF1 2862 88 + 1
CUUGUUAACGGUUCGAUGUAAAUGUAUCUGUAUCUGCAUUUGCAUCUGC-------------AUCCC-----GCAUCCUGCAUCUGAGUGUGGUUUGUUGUAUAUU
..............((((((((((((........)))))))))))).((-------------(..((-----(((..(.......)..)))))..)))........ ( -24.40)
>DroSim_CAF1 2855 88 + 1
CUUGUUAACGGUUCGAUGUAAAUGUAUCUGUAUCUGCAUUUGCAUCUGC-------------AUCUC-----GCAUCCUGCAUCUGAGUGUGGUUUGUUGUAUAUU
..............((((((((((((........))))))))))))(((-------------(....-----(((..(..(((....)))..)..))))))).... ( -22.30)
>DroEre_CAF1 2851 94 + 1
CUUGUUAACGGUUCGAUGUAAAUGUAUCUGCAUCUGCAUUUGCAUCUGCAUC-UGC------AUCUA-----GCAUCCUGCAUCUGAGUGUGGUUUGUUGUAUAUU
..............((((((.(((((..((((........))))..))))).-)))------)))((-----(((..(..(((....)))..)..)))))...... ( -25.60)
>DroYak_CAF1 2863 99 + 1
CUUGUUAACGGUUCGAUGUAAAUGUAUCUGUAUCUGCAUUUGCAUCUGCAUU-UGC------AUCUGCAUCUGCAUGCUGCAUCUGAGUGUGGUUUGUUGUAUAUU
.......(((.((.((((((.(((((..((((..((((..(((....)))..-)))------)..))))..)))))..)))))).)).)))............... ( -28.30)
>consensus
CUUGUUAACGGUUCGAUGUAAAUGUAUCUGUAUCUGCAUUUGCAUCUGCAU__UGC______AUCUC_____GCAUCCUGCAUCUGAGUGUGGUUUGUUGUAUAUU
..............((((((((((((........))))))))))))..........................(((..(..(((....)))..)..)))........ (-20.76 = -20.76 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:25 2006