Locus 84

Sequence ID	2L_DroMel_CAF1
Location	297,288 – 297,383
Length	95
Max. P	0.999479

overview

Window 6

Location	297,288 – 297,383
Length	95
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	93.61
Mean single sequence MFE	-25.67
Consensus MFE	-22.24
Energy contribution	-22.05
Covariance contribution	-0.19
Combinations/Pair	1.16
Mean z-score	-2.87
Structure conservation index	0.87
SVM decision value	2.53
SVM RNA-class probability	0.994937
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 297288 95 + 22407834
AGAAAACAAAAUCAUUGAUAAAUGUCUGCCUAAUUGAUUUACGCAGACGGGUGGAGUAGGCUCCAAACGUCAUGGUCCUUAUUUUCUUACUACAA
((((((.((.(((((.(((....((((((.(((.....))).))))))(..(((((....)))))..)))))))))..)).))))))........ ( -27.00)
>DroSec_CAF1 1950 95 + 1
AGAAAAAAAAAUCAUUGAUAAAUGUCUGCCUAAUUGUUUUACGCAGACGGGUGGAGUAGGCUCCAAACGUCAUGGUCCUUAUUUUCUUACUACAA
((((((.((.(((((.(((....((((((.(((.....))).))))))(..(((((....)))))..)))))))))..)).))))))........ ( -27.00)
>DroSim_CAF1 1929 95 + 1
AGAAAACAAAAUCAUUGAUAAAUGUCUGCCUAAUUGUUUUACGCAGACGGGUGGAGUAGGCUCCAAACGUCAUGGUCCUUAUUUUCUUACUACAA
((((((.((.(((((.(((....((((((.(((.....))).))))))(..(((((....)))))..)))))))))..)).))))))........ ( -27.00)
>DroEre_CAF1 1914 95 + 1
AGGAAACAAAGUAAUUGAUAAACGUCUGCCUAAUUGAUUUACGCAGAUGAGUGAAGUAGGCUCCAAACGUCAUGGUCCUUAUUUUCUUACUACAA
.(....)..(((((........(((((((.(((.....))).)))))))...((((((((..(((.......)))..)))))))).))))).... ( -22.90)
>DroYak_CAF1 1907 95 + 1
AGGAAACAAAAUCAUUGAUAAACAUCUGCCUAAUUGAUUUACGCAGAUGGGUGGAGUAGGCUCCAAACGUCAUGGUCCUUAUUUUCUUACUACAA
((((((.((.(((((.(((...(((((((.(((.....))).)))))))..(((((....)))))...))))))))..)).))))))........ ( -25.00)
>DroAna_CAF1 2496 94 + 1
AGAAUAUAAAAUCAUUGAUAAAUGUCUGCCUAGUUGAUUUACGCAGACGGAUGGAGUAGGCUCCA-ACGUCAAGGUCCUUAUUUUCUUACUACAA
((((.((((.(((.(((((...(((((((.(((.....))).)))))))..(((((....)))))-..))))))))..)))).))))........ ( -25.10)
>consensus
AGAAAACAAAAUCAUUGAUAAAUGUCUGCCUAAUUGAUUUACGCAGACGGGUGGAGUAGGCUCCAAACGUCAUGGUCCUUAUUUUCUUACUACAA
((((((.((.(((((.(((....((((((.(((.....))).))))))(..(((((....)))))..)))))))))..)).))))))........ (-22.24 = -22.05 +  -0.19)

alignment

secondary structure

dotplot

Window 7

Location	297,288 – 297,383
Length	95
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	93.61
Mean single sequence MFE	-23.62
Consensus MFE	-22.59
Energy contribution	-22.98
Covariance contribution	0.39
Combinations/Pair	1.14
Mean z-score	-2.18
Structure conservation index	0.96
SVM decision value	3.64
SVM RNA-class probability	0.999479
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 297288 95 - 22407834
UUGUAGUAAGAAAAUAAGGACCAUGACGUUUGGAGCCUACUCCACCCGUCUGCGUAAAUCAAUUAGGCAGACAUUUAUCAAUGAUUUUGUUUUCU
........(((((((((((..(((((.(..(((((....)))))..)((((((.(((.....))).)))))).....)).))).))))))))))) ( -26.90)
>DroSec_CAF1 1950 95 - 1
UUGUAGUAAGAAAAUAAGGACCAUGACGUUUGGAGCCUACUCCACCCGUCUGCGUAAAACAAUUAGGCAGACAUUUAUCAAUGAUUUUUUUUUCU
........((((((.(((((.(((((.(..(((((....)))))..)((((((.(((.....))).)))))).....)).))).))))))))))) ( -24.80)
>DroSim_CAF1 1929 95 - 1
UUGUAGUAAGAAAAUAAGGACCAUGACGUUUGGAGCCUACUCCACCCGUCUGCGUAAAACAAUUAGGCAGACAUUUAUCAAUGAUUUUGUUUUCU
........(((((((((((..(((((.(..(((((....)))))..)((((((.(((.....))).)))))).....)).))).))))))))))) ( -26.90)
>DroEre_CAF1 1914 95 - 1
UUGUAGUAAGAAAAUAAGGACCAUGACGUUUGGAGCCUACUUCACUCAUCUGCGUAAAUCAAUUAGGCAGACGUUUAUCAAUUACUUUGUUUCCU
........((.((((((((....(((.(..(((((....)))))..).(((((.(((.....))).)))))......)))....)))))))).)) ( -17.70)
>DroYak_CAF1 1907 95 - 1
UUGUAGUAAGAAAAUAAGGACCAUGACGUUUGGAGCCUACUCCACCCAUCUGCGUAAAUCAAUUAGGCAGAUGUUUAUCAAUGAUUUUGUUUCCU
.........((((...((((.(((((....(((((....)))))..(((((((.(((.....))).)))))))....)).))).)))).)))).. ( -21.80)
>DroAna_CAF1 2496 94 - 1
UUGUAGUAAGAAAAUAAGGACCUUGACGU-UGGAGCCUACUCCAUCCGUCUGCGUAAAUCAACUAGGCAGACAUUUAUCAAUGAUUUUAUAUUCU
........((((.((((((.(.((((...-(((((....)))))...((((((.((.......)).)))))).....)))).).)))))).)))) ( -23.60)
>consensus
UUGUAGUAAGAAAAUAAGGACCAUGACGUUUGGAGCCUACUCCACCCGUCUGCGUAAAUCAAUUAGGCAGACAUUUAUCAAUGAUUUUGUUUUCU
........(((((((((((....(((.(..(((((....)))))..)((((((.(((.....))).)))))).....)))....))))))))))) (-22.59 = -22.98 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:25:18 2006