Locus 2145

Sequence ID	2L_DroMel_CAF1
Location	5,786,349 – 5,786,472
Length	123
Max. P	0.719763

overview

Window 7

Location	5,786,349 – 5,786,455
Length	106
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.87
Mean single sequence MFE	-23.70
Consensus MFE	-7.82
Energy contribution	-9.82
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-2.87
Structure conservation index	0.33
SVM decision value	0.25
SVM RNA-class probability	0.653618
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5786349 106 + 22407834
GAAUGUGUGCGAAU---GAGUAU--AAAA--CAAUACAUUCG-----AAAGCAAAC-CGAAAGUCAUUGCG-AGAGAAAUCUGUGCAAAUGAAGAAAAGGUGUCAAGAACUUUAUUGACA
...(((...(((((---(.((..--....--..)).))))))-----...))).((-(.....((((((((-(((....))).))).)))))......)))(((((........))))). ( -27.10)
>DroVir_CAF1 35269 111 + 1
GUGUGUGCUAAGAG---AAAUAA--AAAG--GAAAACCCUCGAACAGAAAGCAAAG-UUAAAGUCAUGUCG-AGAGAAAUCUGAGCAAAUGAAGUAAAGGUGUCAAGAACUUUAUUGACA
.....((((.(((.---......--...(--(....))(((((.((((.(((...)-))....)).)))))-)).....))).)))).............((((((........)))))) ( -17.30)
>DroSec_CAF1 23427 106 + 1
GAAUGUUUUCGAAU---GAGUAU--AAAA--CAAUACAGUCG-----AAAGCAAAC-CGAAAGUCAUUGCG-AGAGAAAUCUGUGCAAAUGAAGAAAAGGUGUCAAGAACUUUAUUGACA
...(((((((((..---..((((--....--..))))..)))-----)))))).((-(.....((((((((-(((....))).))).)))))......)))(((((........))))). ( -30.20)
>DroSim_CAF1 24201 106 + 1
GAAUGUGUUCGAAU---GAGUAU--AAAA--CAAUACAGUCG-----AAAGCAAAC-CGAAAGUCAUUGCG-AGAGAAAUCUGUGCAAAUGAAGAAAAGGUGUCAAGAACUUUAUUGACA
...(((.(((((..---..((((--....--..))))..)))-----)).))).((-(.....((((((((-(((....))).))).)))))......)))(((((........))))). ( -27.00)
>DroWil_CAF1 44524 108 + 1
GCAUGUGCUAAAAGCCAAAGUAU--AAAAAACGAAGCAU----------GGCAAAUCUUAAAGUCAUGCCAAAGAGAAAUCUGAGCAAAUGAAGUAAAGGUGUCAAGAACUUUAUUGACA
.(((.((((..............--..........((((----------(((..........)))))))...(((....))).)))).))).........((((((........)))))) ( -22.50)
>DroMoj_CAF1 42969 113 + 1
GUGUUUGUUAAGUA---AAAUAAAAAAAG--GAAAACCCUCGAACAGAAAGCAAUG-CUAAAGUCAUGUCG-AGAGAAAUCUGAGCAAAUGAAGUAAAGGUGUCAAGAACUUUAUUGACA
..(((((((.((..---...........(--(....))(((((.((((.(((...)-))....)).)))))-))......)).)))))))..........((((((........)))))) ( -18.10)
>consensus
GAAUGUGUUAAAAU___AAGUAU__AAAA__CAAAACACUCG_____AAAGCAAAC_CGAAAGUCAUGGCG_AGAGAAAUCUGAGCAAAUGAAGAAAAGGUGUCAAGAACUUUAUUGACA
...............................................................((((.....(((....)))......))))........((((((........)))))) ( -7.82 =  -9.82 +   2.00)

alignment

secondary structure

dotplot

Window 8

Location	5,786,382 – 5,786,472
Length	90
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	84.40
Mean single sequence MFE	-22.20
Consensus MFE	-13.36
Energy contribution	-16.80
Covariance contribution	3.44
Combinations/Pair	1.05
Mean z-score	-2.34
Structure conservation index	0.60
SVM decision value	0.40
SVM RNA-class probability	0.719763
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5786382 90 + 22407834
CG-----AAAGCAAAC-CGAAAGUCAUUGCG-AGAGAAAUCUGUGCAAAUGAAGAAAAGGUGUCAAGAACUUUAUUGACAAGCAGUCCUCAAGCUGC---
..-----.......((-(.....((((((((-(((....))).))).)))))......)))(((((........)))))..(((((......)))))--- ( -23.40)
>DroVir_CAF1 35302 90 + 1
CGAACAGAAAGCAAAG-UUAAAGUCAUGUCG-AGAGAAAUCUGAGCAAAUGAAGUAAAGGUGUCAAGAACUUUAUUGACAGG----CUUCAAGCUG----
.........(((....-.........(((..-(((....)))..)))..((((((.....((((((........)))))).)----))))).))).---- ( -20.30)
>DroSec_CAF1 23460 90 + 1
CG-----AAAGCAAAC-CGAAAGUCAUUGCG-AGAGAAAUCUGUGCAAAUGAAGAAAAGGUGUCAAGAACUUUAUUGACAAGCAGUCCUCAAGCUGC---
..-----.......((-(.....((((((((-(((....))).))).)))))......)))(((((........)))))..(((((......)))))--- ( -23.40)
>DroSim_CAF1 24234 90 + 1
CG-----AAAGCAAAC-CGAAAGUCAUUGCG-AGAGAAAUCUGUGCAAAUGAAGAAAAGGUGUCAAGAACUUUAUUGACAAGCAGUCCUCAAGCUGC---
..-----.......((-(.....((((((((-(((....))).))).)))))......)))(((((........)))))..(((((......)))))--- ( -23.40)
>DroWil_CAF1 44561 87 + 1
---------GGCAAAUCUUAAAGUCAUGCCAAAGAGAAAUCUGAGCAAAUGAAGUAAAGGUGUCAAGAACUUUAUUGACAGG----CCUCAAGCUGCUGG
---------(((..(((((.(..((((((...(((....)))..)))..)))..).)))))(((((........)))))..)----))............ ( -20.50)
>consensus
CG_____AAAGCAAAC_CGAAAGUCAUUGCG_AGAGAAAUCUGUGCAAAUGAAGAAAAGGUGUCAAGAACUUUAUUGACAAGCAGUCCUCAAGCUGC___
.........(((..............(((((.(((....))).))))).(((.((.....((((((........)))))).....)).))).)))..... (-13.36 = -16.80 +   3.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:47 2006