Locus 4167

Sequence ID	3R_DroMel_CAF1
Location	11,329,131 – 11,329,240
Length	109
Max. P	0.737680

overview

Window 4

Location	11,329,131 – 11,329,240
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.70
Mean single sequence MFE	-27.28
Consensus MFE	-19.42
Energy contribution	-20.22
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.71
SVM decision value	0.11
SVM RNA-class probability	0.587806
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11329131 109 + 27905053
UGACUGCUUUCGCC-------UUUCGCAGGCGAAUCAAUGUCACACAUCAGCAAUUUUCAGAAGCUCGACAAAGUUGCAAAUUUAUUGAAAUUUUCUGCGCAGCAGAAAGCAAUCA----
.((.(((.((((((-------(.....)))))))((((((.....)....((((((((..(.....)...))))))))......)))))...(((((((...)))))))))).)).---- ( -27.80)
>DroSec_CAF1 68284 109 + 1
UGACUGCUUUCGCU-------CCUCGCUGGCGAAUCAAUGUCACACAUCAGCACUUUUCAGCAGCUCGGAAAAGUUGCAAAUUUAUCGAAAUUUUCCGCAAAGCAGAAAGCAAUCA----
.((.((((((((((-------....(.(((((......))))))......((........((((((......))))))((((((....))))))...))..))).))))))).)).---- ( -25.60)
>DroSim_CAF1 66480 109 + 1
UGACUGCUUUCGCU-------CCUCGCUGGCGAAUCAAUGUCACACAUCAGCACUUUUCAGCAGCUCGGAAAAGUUGCAAAUUUAUUGAAAUUUUCCGCAAAGCAGAAAGCAAUCA----
.((.(((((((...-------....(((((.((.....((........))....)).))))).((((((((((....(((.....)))...)))))))...))).))))))).)).---- ( -28.00)
>DroEre_CAF1 63807 112 + 1
UGACUGCUUUCGUC-------CUUCGCAGGCGCAUCAAUGUCACACAUCAGCAAUUUUC-GCAGCUCGUCAAAGUUGCAACUUUAUUGAAAUUUUCGGAAAAGCAGAAAGCAAUCAGGUA
(((.(((((((.((-------(...((....)).((((((.....)....((((((((.-((.....)).))))))))......))))).......)))......))))))).))).... ( -25.30)
>DroYak_CAF1 65618 115 + 1
UGACUACUUUCGCCUUUUGCCUUUCGCAGGCGCAUCAGUGUCACACAUCAGCAGUUUUC-GCAGCUCGACAAAGUUGCAAAUUUAUUAAAAUUCGCUGAGAAGCAGAAAGCAAUCA----
...........((.((((((..(((...(((((....))))).....(((((.......-((((((......)))))).(((((....))))).)))))))))))))).)).....---- ( -29.70)
>consensus
UGACUGCUUUCGCC_______CUUCGCAGGCGAAUCAAUGUCACACAUCAGCAAUUUUCAGCAGCUCGACAAAGUUGCAAAUUUAUUGAAAUUUUCCGCAAAGCAGAAAGCAAUCA____
(((.(((((((.................((((......))))........((........((((((......))))))((((((....))))))........)).))))))).))).... (-19.42 = -20.22 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	11,329,131 – 11,329,240
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.70
Mean single sequence MFE	-35.32
Consensus MFE	-21.30
Energy contribution	-21.86
Covariance contribution	0.56
Combinations/Pair	1.24
Mean z-score	-2.65
Structure conservation index	0.60
SVM decision value	0.44
SVM RNA-class probability	0.737680
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11329131 109 - 27905053
----UGAUUGCUUUCUGCUGCGCAGAAAAUUUCAAUAAAUUUGCAACUUUGUCGAGCUUCUGAAAAUUGCUGAUGUGUGACAUUGAUUCGCCUGCGAAA-------GGCGAAAGCAGUCA
----.((((((((((.(((.(((((.((((((....))))))(((((..(((((.((.((...........)).)).)))))..).)).)))))))...-------))))))))))))). ( -34.50)
>DroSec_CAF1 68284 109 - 1
----UGAUUGCUUUCUGCUUUGCGGAAAAUUUCGAUAAAUUUGCAACUUUUCCGAGCUGCUGAAAAGUGCUGAUGUGUGACAUUGAUUCGCCAGCGAGG-------AGCGAAAGCAGUCA
----.((((((((((.(((((.(((((((.(((((.....))).)).))))))).((((.((((.(((((........).))))..)))).))))..))-------))))))))))))). ( -38.50)
>DroSim_CAF1 66480 109 - 1
----UGAUUGCUUUCUGCUUUGCGGAAAAUUUCAAUAAAUUUGCAACUUUUCCGAGCUGCUGAAAAGUGCUGAUGUGUGACAUUGAUUCGCCAGCGAGG-------AGCGAAAGCAGUCA
----.((((((((((.(((((.(((((((.(((((.....))).)).))))))).((((.((((.(((((........).))))..)))).))))..))-------))))))))))))). ( -38.80)
>DroEre_CAF1 63807 112 - 1
UACCUGAUUGCUUUCUGCUUUUCCGAAAAUUUCAAUAAAGUUGCAACUUUGACGAGCUGC-GAAAAUUGCUGAUGUGUGACAUUGAUGCGCCUGCGAAG-------GACGAAAGCAGUCA
.....((((((((((..(((((.((......(((((....(((((.(((....))).)))-))...(..(......)..).)))))......)).))))-------)..)))))))))). ( -27.90)
>DroYak_CAF1 65618 115 - 1
----UGAUUGCUUUCUGCUUCUCAGCGAAUUUUAAUAAAUUUGCAACUUUGUCGAGCUGC-GAAAACUGCUGAUGUGUGACACUGAUGCGCCUGCGAAAGGCAAAAGGCGAAAGUAGUCA
----.((((((((((.((((.(((((((((((....)))))))).....(((((.((.((-(.....)))....)).))))).)))...((((.....))))...)))))))))))))). ( -36.90)
>consensus
____UGAUUGCUUUCUGCUUUGCAGAAAAUUUCAAUAAAUUUGCAACUUUGCCGAGCUGCUGAAAAGUGCUGAUGUGUGACAUUGAUUCGCCUGCGAAG_______GGCGAAAGCAGUCA
.....((((((((((.((((.(((((......(((.....)))....))))).))))...........(((((((.....))))..((((....))))........))))))))))))). (-21.30 = -21.86 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:04 2006