Locus 4099

Sequence ID	2L_DroMel_CAF1
Location	11,786,691 – 11,786,883
Length	192
Max. P	0.995573

overview

Window 3

Location	11,786,691 – 11,786,804
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.46
Mean single sequence MFE	-31.72
Consensus MFE	-28.28
Energy contribution	-28.36
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.69
Structure conservation index	0.89
SVM decision value	1.48
SVM RNA-class probability	0.957842
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11786691 113 + 22407834
-------UGUGUGCAGUCGUGUGUUAUUUGGUGUAAAUUAUAUGGCCGAAAGAUGCAAAAUUAGCCAAAUAAUGGCUGCCUAAUGUGCCGGAAAGCUGGCGAGCAAAAGUUAAUGGCGAA
-------....((((((((((((((((.....))))..))))))))(....).)))).....(((((.....)))))(((.....((((((....))))))(((....)))...)))... ( -29.70)
>DroSec_CAF1 44441 118 + 1
--GUGUGUGUGUGCAGUCGUGUGUUAUUUGGUGUAAAUUAUAUGGCCGAAAGAUGCAAAAUUAGCCAAAUAAUGGCUGCCUAAUGUGCCGGAAAGCUGGCGAGCAAAAGUUAAUGGCGAA
--.........((((((((((((((((.....))))..))))))))(....).)))).....(((((.....)))))(((.....((((((....))))))(((....)))...)))... ( -29.70)
>DroSim_CAF1 43648 116 + 1
--G--UGUGUGUGCAGUCGUGUGUUAUUUGGUGUAAAUUAUAUGGCCGAAAGAUGCAAAAUUAGCCAAAUAAUGGCUGCCUAAUGUGCCGGAAAGCUGGCGAGCAAAAGUUAAUGGCGAA
--.--......((((((((((((((((.....))))..))))))))(....).)))).....(((((.....)))))(((.....((((((....))))))(((....)))...)))... ( -29.70)
>DroEre_CAF1 54850 120 + 1
GGGUAUGUGUGUGCAGUCGUGUGUUAUUUGGUGUAAAUUGUAUGGCCGAAAGAUGCAAAAUUAGCCAAAUAAUGGCUGCCUAAUGUGCCGGAAAGCUGGCGAGCAAAAGUUAAUGGCGAA
.(((((((....((((((((....((((((((.....((((((...(....))))))).....))))))))))))))))...))))))).....((((...(((....)))..))))... ( -35.90)
>DroYak_CAF1 46494 118 + 1
--GUGUGUGUGUGCAGUCGUGUGUUAUUUGGUGUAAAUUAUAUGGCUGAAAGAUGCAAAAUUAGCCAAAUAAUGGCUGCCUAAUGUGCCGGAAAGCUGGCGAGCAAAAGUUAAUGGCGAA
--.(((((.(...((((((((((((((.....))))..))))))))))..).))))).....(((((.....)))))(((.....((((((....))))))(((....)))...)))... ( -33.60)
>consensus
__GU_UGUGUGUGCAGUCGUGUGUUAUUUGGUGUAAAUUAUAUGGCCGAAAGAUGCAAAAUUAGCCAAAUAAUGGCUGCCUAAUGUGCCGGAAAGCUGGCGAGCAAAAGUUAAUGGCGAA
...........(((((((((((.((((.....))))...)))))))(....).)))).....(((((.....)))))(((.....((((((....))))))(((....)))...)))... (-28.28 = -28.36 +   0.08)

alignment

secondary structure

dotplot

Window 4

Location	11,786,764 – 11,786,883
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.41
Mean single sequence MFE	-34.30
Consensus MFE	-32.10
Energy contribution	-31.94
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-2.10
Structure conservation index	0.94
SVM decision value	2.59
SVM RNA-class probability	0.995573
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11786764 119 - 22407834
UUAGCAAAUAUGUGCCGCUGUCGAUUUGCUUUUAGUGGCUCCGUUUUAUGUUUUCAUUAUGGUG-GGGGACUAAAGGAUUUUCGCCAUUAACUUUUGCUCGCCAGCUUUCCGGCACAUUA
.........(((((((((((.(((...((..((((((((.((((...(((....))).))))((-(....)))..........)))))))).....))))).)))).....))))))).. ( -34.50)
>DroSec_CAF1 44519 119 - 1
UUAGCAAAUAUGUGCCGCUGUCGAUUUGCUUUUAGUGGCUCCGUUUUAUGUUUUCAUUAUGGUG-GGGGACUAAAGGAUUUUCGCCAUUAACUUUUGCUCGCCAGCUUUCCGGCACAUUA
.........(((((((((((.(((...((..((((((((.((((...(((....))).))))((-(....)))..........)))))))).....))))).)))).....))))))).. ( -34.50)
>DroSim_CAF1 43724 119 - 1
UUAGCAAAUAUGUGCCGCUGUCGAUUUGCUUUUAGUGGCUCCGUUUUAUGUUUUCAUUAUGGUG-GGGGACUAAAGGAUUUUCGCCAUUAACUUUUGCUCGCCAGCUUUCCGGCACAUUA
.........(((((((((((.(((...((..((((((((.((((...(((....))).))))((-(....)))..........)))))))).....))))).)))).....))))))).. ( -34.50)
>DroEre_CAF1 54930 119 - 1
UUAGCAAAUAUGUGCCGCUGUCGAUUUGCUUUUAGUGGCUCCGUUUUAUGUUUUCAUUAUGGAG-GGGGACUAAAGGAUUUUCGCCAUUAACUUUUGCUCGCCAGCUUUCCGGCACAUUA
.........(((((((((((.(((...((..(((((((((((((...(((....))).)))))(-(....))...........)))))))).....))))).)))).....))))))).. ( -35.60)
>DroYak_CAF1 46572 120 - 1
UUAGCAACUAUGUGCCGCUGUCGAUUUGCUUUUAGUGGCUUCGUUUUAUGUUUUCAUUAUGGGGAGGGGACUAAAGGAUUUUCGCCAUUAACUUUUGCUCGCCAGCUUUCCGGCACAUUA
.........(((((((((((.(((...((..(((((((((((((...(((....))).)))))(((((..(....)..))))))))))))).....))))).)))).....))))))).. ( -32.40)
>consensus
UUAGCAAAUAUGUGCCGCUGUCGAUUUGCUUUUAGUGGCUCCGUUUUAUGUUUUCAUUAUGGUG_GGGGACUAAAGGAUUUUCGCCAUUAACUUUUGCUCGCCAGCUUUCCGGCACAUUA
.........(((((((((((.(((...((..((((((((.((((...(((....))).))))...(..(((.....).))..))))))))).....))))).)))).....))))))).. (-32.10 = -31.94 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:24 2006