Locus 4093

Sequence ID	2R_DroMel_CAF1
Location	13,485,801 – 13,485,900
Length	99
Max. P	0.731153

overview

Window 1

Location	13,485,801 – 13,485,900
Length	99
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.06
Mean single sequence MFE	-19.92
Consensus MFE	-12.21
Energy contribution	-11.77
Covariance contribution	-0.44
Combinations/Pair	1.17
Mean z-score	-1.70
Structure conservation index	0.61
SVM decision value	0.08
SVM RNA-class probability	0.572558
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13485801 99 + 20766785
UGUGCCGGGUC-UGAAUACGAAAUAUUUGUUUAUUUCUAGUUCAUAC-CGCUCAUGUGCGCUACACUUGUUUCCCUUUCACUUCGUCCUGACCCCGACCAC-------------------
((..(.(((((-(((((..((((((......))))))..)))))...-(((......))).............................))))).)..)).------------------- ( -19.30)
>DroSec_CAF1 34410 100 + 1
UGUGCCGGGGCUUGAAUACGAAAUAUUUGUUUAUUUCUAGUUCAUAU-CUCUCAUGUGCGCUACACUUGUUUCCCUUUCACUACGCCCUGCCCCCCAGCAC-------------------
.((((.(((((........((((((......))))))((((.(((((-.....))))).))))..........................)))))...))))------------------- ( -23.70)
>DroSim_CAF1 34560 100 + 1
UGUGCCGGGUC-UGAAUACGAAAUAUUUGUUUAUUUCUAGUUCAUAUUCUUUCAUGUGCGUUACACUUGUUUCCUUUUCAAAACUUCCAAUCCCCCACCAC-------------------
.(((..(((..-(((((..((((((......))))))..)))))........((.(((.....))).))........................)))..)))------------------- ( -13.80)
>DroEre_CAF1 34755 92 + 1
UGUGCCGGGUC-GGAAUACGAAAUAUUUGUUUAUUUCUAGUUCAUAU-CUCUCAUGUGCGCUACACUUGUUUCCCUUUCACUUCGUCCUGCCCC--------------------------
......((((.-(((....((((((......))))))((((.(((((-.....))))).))))......................))).)))).-------------------------- ( -19.50)
>DroYak_CAF1 36025 98 + 1
UGUGCCGGGUC-UGAAUACGAAAUAUUUGUUUAUUUCUAGUUCAUAU-CUCUCAUGUGCGCUACACUUGUUUCCCUUUCACUUGGUCCUGCCCCCU-CCCC-------------------
...((.((..(-((((...((((((..(((........(((.(((((-.....))))).))))))..))))))...))))...)..)).)).....-....------------------- ( -18.30)
>DroAna_CAF1 36094 116 + 1
UUUUGCGAGCC-UGAAUACGAAAUAUUUGUUUAUUUCUAGUUCAUAU-CUUUCAUGUGCGCUACACUUGUUUCCCUUUCAUUUCGCUUU--CCCCAGCCACAUGACACAUGAGGCAUACU
....(((((..-((((...((((((..(((........(((.(((((-.....))))).))))))..))))))...)))).)))))...--.....(((.((((...)))).)))..... ( -24.90)
>consensus
UGUGCCGGGUC_UGAAUACGAAAUAUUUGUUUAUUUCUAGUUCAUAU_CUCUCAUGUGCGCUACACUUGUUUCCCUUUCACUUCGUCCUGCCCCCCACCAC___________________
......(((...((((...((((((..(((........(((.(((((......))))).))))))..))))))...)))).....)))................................ (-12.21 = -11.77 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	13,485,801 – 13,485,900
Length	99
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.06
Mean single sequence MFE	-26.12
Consensus MFE	-13.92
Energy contribution	-14.45
Covariance contribution	0.53
Combinations/Pair	1.05
Mean z-score	-2.45
Structure conservation index	0.53
SVM decision value	0.42
SVM RNA-class probability	0.731153
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13485801 99 - 20766785
-------------------GUGGUCGGGGUCAGGACGAAGUGAAAGGGAAACAAGUGUAGCGCACAUGAGCG-GUAUGAACUAGAAAUAAACAAAUAUUUCGUAUUCA-GACCCGGCACA
-------------------(((.(((((......((((((((....(....).((((((.(((......)))-.)))..))).............)))))))).....-..)))))))). ( -28.42)
>DroSec_CAF1 34410 100 - 1
-------------------GUGCUGGGGGGCAGGGCGUAGUGAAAGGGAAACAAGUGUAGCGCACAUGAGAG-AUAUGAACUAGAAAUAAACAAAUAUUUCGUAUUCAAGCCCCGGCACA
-------------------(((((((((..((..((((..((....(....)...))..))))...))....-...((((...((((((......))))))...))))..))))))))). ( -33.50)
>DroSim_CAF1 34560 100 - 1
-------------------GUGGUGGGGGAUUGGAAGUUUUGAAAAGGAAACAAGUGUAACGCACAUGAAAGAAUAUGAACUAGAAAUAAACAAAUAUUUCGUAUUCA-GACCCGGCACA
-------------------(((.((((.........(((((......)))))..(((.....)))......(((((((((.((............)).))))))))).-..)))).))). ( -24.40)
>DroEre_CAF1 34755 92 - 1
--------------------------GGGGCAGGACGAAGUGAAAGGGAAACAAGUGUAGCGCACAUGAGAG-AUAUGAACUAGAAAUAAACAAAUAUUUCGUAUUCC-GACCCGGCACA
--------------------------.(((..((((((((((....(....)..(((.....))).......-......................)))))))...)))-..)))...... ( -19.70)
>DroYak_CAF1 36025 98 - 1
-------------------GGGG-AGGGGGCAGGACCAAGUGAAAGGGAAACAAGUGUAGCGCACAUGAGAG-AUAUGAACUAGAAAUAAACAAAUAUUUCGUAUUCA-GACCCGGCACA
-------------------....-...((......))..(((...(((...((.(((.....))).))....-...((((...((((((......))))))...))))-..)))..))). ( -21.10)
>DroAna_CAF1 36094 116 - 1
AGUAUGCCUCAUGUGUCAUGUGGCUGGGG--AAAGCGAAAUGAAAGGGAAACAAGUGUAGCGCACAUGAAAG-AUAUGAACUAGAAAUAAACAAAUAUUUCGUAUUCA-GGCUCGCAAAA
.((..((((((((((((((.(.(((....--..))).).))))...(....)..........)))))))...-...((((...((((((......))))))...))))-)))..)).... ( -29.60)
>consensus
___________________GUGGUGGGGGGCAGGACGAAGUGAAAGGGAAACAAGUGUAGCGCACAUGAGAG_AUAUGAACUAGAAAUAAACAAAUAUUUCGUAUUCA_GACCCGGCACA
.......................................(((...(((...((.(((.....))).)).........(((...((((((......))))))...)))....)))..))). (-13.92 = -14.45 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:37 2006