Locus 3346

Sequence ID	2R_DroMel_CAF1
Location	11,362,870 – 11,363,062
Length	192
Max. P	0.795572

overview

Window 0

Location	11,362,870 – 11,362,969
Length	99
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	81.61
Mean single sequence MFE	-32.40
Consensus MFE	-10.92
Energy contribution	-10.32
Covariance contribution	-0.60
Combinations/Pair	1.29
Mean z-score	-2.50
Structure conservation index	0.34
SVM decision value	0.30
SVM RNA-class probability	0.680453
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11362870 99 + 20766785
AGCAACAAAUAUUUGC------UAGUGGCAUCCAAAAUGUGUUUCGAAAAACCGUUGA------CUGUAGCAAUUACCUGCUGUCAGCUAGCUUGGAGCGUCGCAGCAGUG
............((((------(.(((((.(((((...(.((((....)))))(((((------(.((((.......)))).))))))....)))))..)))))))))).. ( -28.90)
>DroSec_CAF1 21032 97 + 1
AGCAACAAAUAUUUGC------UAGUGGCAUCUAAA--GUGUUUCAAAAAACCGUUGG------CUGUAGCAAUUACCAGCUGUCAGCUAGCUCGGAGCAUCACAGCAGUG
............((((------(.((((..(((...--(.((((....)))))(((((------(((((((........)))).))))))))..)))...))))))))).. ( -26.80)
>DroSim_CAF1 20777 97 + 1
AGCAACAAAUAUUUGC------AAGUGGCAUCUAAA--GUGUUUCAAAAAACCGUUGG------CUGUAGCAACUACCUGCUGUCAGCUAGCUCGGAGCGUCACAGCAGUG
.((((.......))))------..(((((.(((...--(.((((....)))))(((((------((((((((......))))).))))))))..)))..)))))....... ( -29.50)
>DroEre_CAF1 23258 103 + 1
AGCAACAAAUAUUCGC------UGCUGACAGCUAAA--GCAAUUCAAAAAACCGUUGAAGCGGACUGUAGCAGGUACCUGCUGUCAGCUUGCGCGGACUGUCGCAGCAGUG
..............((------(((.(((((((...--((((.........((((....)))).(((((((((....)))))).))).))))..)).)))))))))).... ( -38.80)
>DroYak_CAF1 21446 109 + 1
AGCAACAAAUAUUUGCUUUAGCUAUUGACAUCUAAA--GUAAUUUGAAAAACCGUUGAAGCGCUCUGUAGCAGUUAGCUGGUGUCAGCUUGCUCGGAGCGUCGCAGCAGUG
.....(((((...((((((((..........)))))--))))))))....((.((((..((((((((.((((...(((((....)))))))))))))))))..)))).)). ( -38.00)
>consensus
AGCAACAAAUAUUUGC______UAGUGGCAUCUAAA__GUGUUUCAAAAAACCGUUGA______CUGUAGCAAUUACCUGCUGUCAGCUAGCUCGGAGCGUCGCAGCAGUG
.((.(((..................((.....)).........((((.......)))).......))).))......(((((((..(((.......)))...))))))).. (-10.92 = -10.32 +  -0.60)

alignment

secondary structure

dotplot

Window 1

Location	11,362,969 – 11,363,062
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	74.54
Mean single sequence MFE	-27.04
Consensus MFE	-10.18
Energy contribution	-10.30
Covariance contribution	0.12
Combinations/Pair	1.37
Mean z-score	-1.91
Structure conservation index	0.38
SVM decision value	0.60
SVM RNA-class probability	0.795572
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11362969 93 + 20766785
AGCAGCUCACAGCGUGCAACAUAGCUAAUAGCUUUUGUGCGUAUGCGAUGGGCAUCACUGUUUGCUUGCUGCGCUCAAUUGGAUUCUGAUUGA
.(((((.....((((((.(((.(((.....)))..)))..))))))...(((((........))))))))))..(((((..(...)..))))) ( -30.80)
>DroSec_CAF1 21129 84 + 1
AGCAGCUCACAGCGUGCGUCAUAGCUAAAAGCUUUUGUGCGUAUGCGAUGGGCAUCAUUGUU---------CGCUCAAUCGGAUUCUGAUUGA
....(((((..((((((((((.(((.....)))..)).))))))))..))))).........---------...((((((((...)))))))) ( -29.80)
>DroSim_CAF1 20874 84 + 1
AGCAGCUCACAGCGUGCGUCAUAGCUAAAAGCUUUUGUGCGUGUGCGAUGGGCAUCAUUGUU---------CGCUCAAUCGGAUUCUGAUUGA
....(((((..(((..(((((.(((.....)))..)).)))..)))..))))).........---------...((((((((...)))))))) ( -28.40)
>DroEre_CAF1 23361 78 + 1
AGCAAUCCAC-GCGUGCUUCGUAGCUAAUAGCUUUAGUCCUCGUGCGAUGGGCAUCAUUGUUUGCCCGUU--------------UCUGAUUGG
..((((((((-(.(..((....(((.....)))..))..).)))).((((((((........))))))))--------------...))))). ( -25.80)
>DroYak_CAF1 21555 93 + 1
AGCAAUGCACAGCGCGCUUUAUAGCUUAUAACUUUAGUCUCUAUGCGAUGGGCAGCACUGUUUGCUUGCUUCGCUAAAUAGAAUUCUGAUUGG
(((((.((((((.((((((....((.....((....))......))...)))).)).))))..)))))))...((((.(((....))).)))) ( -20.40)
>consensus
AGCAGCUCACAGCGUGCGUCAUAGCUAAUAGCUUUUGUGCGUAUGCGAUGGGCAUCAUUGUUUGC__G_U_CGCUCAAUCGGAUUCUGAUUGA
(((((......(((((((....(((.....)))..)))))))((((.....))))..)))))............................... (-10.18 = -10.30 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:16 2006