Locus 620

Sequence ID	2L_DroMel_CAF1
Location	1,831,691 – 1,831,781
Length	90
Max. P	0.998724

overview

Window 4

Location	1,831,691 – 1,831,781
Length	90
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	89.29
Mean single sequence MFE	-23.16
Consensus MFE	-16.78
Energy contribution	-16.94
Covariance contribution	0.16
Combinations/Pair	1.16
Mean z-score	-3.05
Structure conservation index	0.72
SVM decision value	1.53
SVM RNA-class probability	0.961331
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1831691 90 + 22407834
UUGCACU-GAAUA-UCCCCUUCAGUUAGCUUGGAAGUAAAUUACUAGUUUCUGUGAAUAAUAUUUUAUUGCCAAGCUAAGAAAACGGGAUAU
.......-..(((-((((.(((..(((((((((.((((((((((........)))).......)))))).))))))))))))...))))))) ( -24.31)
>DroSec_CAF1 51695 90 + 1
UUGCACU-GAAUA-UCCCCUUCAGUUAGCUUGGAAGUAAGUUACUAGUUUCUGUGAAUAAUAUUUUAUUGCCAAGCAAAGAAAACGGGAUAU
.......-..(((-((((.........((((((.((((((((((........)))).......)))))).)))))).........))))))) ( -19.98)
>DroSim_CAF1 32261 91 + 1
UUGCACU-GAAUAAUUCCCUUCAGUUAGCUUGGAAGUAAAUUACUAGUUUCUGUGAAUAAUAUUUUAUUGCCAAGCUAAGAAAACGGGAUAU
.......-.......(((((((..(((((((((.((((((((((........)))).......)))))).))))))))))))...))))... ( -21.01)
>DroEre_CAF1 42135 87 + 1
--GCAGU-GAAUA-UCCCCUUUAGUUGGCUUGGAAUUAAAUUACUAGU-UCGAUGAAUAAUAUUUUAUUGCCAAGCUAAGAAAAUGGGAUAU
--.....-..(((-((((.(((..((((((((((((((......))))-)(((((((......))))))))))))))))..))).))))))) ( -25.90)
>DroYak_CAF1 16710 89 + 1
--GUUGUAGAAUA-UCCACUUCAGUUAGCUUGGAAGUAAAUUACUAGUUUCAAUCAACAAUAUUUUAUUGCCAAGCUAACAAAAUGGGAUAU
--........(((-(((......((((((((((.((((((.((...(((......)))..)).)))))).))))))))))......)))))) ( -24.60)
>consensus
UUGCACU_GAAUA_UCCCCUUCAGUUAGCUUGGAAGUAAAUUACUAGUUUCUGUGAAUAAUAUUUUAUUGCCAAGCUAAGAAAACGGGAUAU
..............((((......(((((((((.((((((.......................)))))).)))))))))......))))... (-16.78 = -16.94 +   0.16)

alignment

secondary structure

dotplot

Window 5

Location	1,831,691 – 1,831,781
Length	90
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	89.29
Mean single sequence MFE	-23.36
Consensus MFE	-18.42
Energy contribution	-19.10
Covariance contribution	0.68
Combinations/Pair	1.08
Mean z-score	-3.95
Structure conservation index	0.79
SVM decision value	3.20
SVM RNA-class probability	0.998724
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1831691 90 - 22407834
AUAUCCCGUUUUCUUAGCUUGGCAAUAAAAUAUUAUUCACAGAAACUAGUAAUUUACUUCCAAGCUAACUGAAGGGGA-UAUUC-AGUGCAA
(((((((.(((..(((((((((...((((.((((((((...)))..))))).))))...)))))))))..))).))))-)))..-....... ( -26.90)
>DroSec_CAF1 51695 90 - 1
AUAUCCCGUUUUCUUUGCUUGGCAAUAAAAUAUUAUUCACAGAAACUAGUAACUUACUUCCAAGCUAACUGAAGGGGA-UAUUC-AGUGCAA
(((((((.(((..((.((((((...(((..((((((((...)))..)))))..)))...)))))).))..))).))))-)))..-....... ( -20.60)
>DroSim_CAF1 32261 91 - 1
AUAUCCCGUUUUCUUAGCUUGGCAAUAAAAUAUUAUUCACAGAAACUAGUAAUUUACUUCCAAGCUAACUGAAGGGAAUUAUUC-AGUGCAA
...((((.(((..(((((((((...((((.((((((((...)))..))))).))))...)))))))))..))))))).......-....... ( -21.70)
>DroEre_CAF1 42135 87 - 1
AUAUCCCAUUUUCUUAGCUUGGCAAUAAAAUAUUAUUCAUCGA-ACUAGUAAUUUAAUUCCAAGCCAACUAAAGGGGA-UAUUC-ACUGC--
(((((((.(((..((.((((((...((((.((((((((...))-).))))).))))...)))))).))..))).))))-)))..-.....-- ( -21.00)
>DroYak_CAF1 16710 89 - 1
AUAUCCCAUUUUGUUAGCUUGGCAAUAAAAUAUUGUUGAUUGAAACUAGUAAUUUACUUCCAAGCUAACUGAAGUGGA-UAUUCUACAAC--
((((((.(((((((((((((((...((((.(((((((......))).)))).))))...)))))))))).))))))))-)))........-- ( -26.60)
>consensus
AUAUCCCGUUUUCUUAGCUUGGCAAUAAAAUAUUAUUCACAGAAACUAGUAAUUUACUUCCAAGCUAACUGAAGGGGA_UAUUC_AGUGCAA
...((((.(((..(((((((((...((((.(((((...........))))).))))...)))))))))..))).)))).............. (-18.42 = -19.10 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:10 2006