Locus 4305

Sequence ID	2R_DroMel_CAF1
Location	14,157,437 – 14,157,532
Length	95
Max. P	0.899484

overview

Window 0

Location	14,157,437 – 14,157,532
Length	95
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	81.11
Mean single sequence MFE	-35.92
Consensus MFE	-25.70
Energy contribution	-26.12
Covariance contribution	0.42
Combinations/Pair	1.16
Mean z-score	-2.35
Structure conservation index	0.72
SVM decision value	1.01
SVM RNA-class probability	0.899484
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14157437 95 + 20766785
CUGUAGACGGGAUGCUGCAGGAACAGGCUGUUGGUGUCCAUGGGGCAGUCAUCCUGCAGCACACCAUUCAGCACGAGCACCAUC----CUGGC------UGUCUG
...(((((((..((((((((((...(((((((((...)))....)))))).))))))))))..))....(((..((......))----...))------)))))) ( -38.20)
>DroVir_CAF1 3206 95 + 1
CUAUAGACAGGAUGCUGCAGGAACAGGCUGUUUGUAUCCAUCGGGCAGUCAUCCUGCAGCACACCGUUCAGCACAAGCACCAUC----CUGGU------CGUUUC
.....(((((((((((((((((...(((((((((.......))))))))).)))))))))..........((....))...)))----)).))------)..... ( -38.70)
>DroPse_CAF1 1869 93 + 1
CGGUAGACGGGAUGCUGCAGGAACAGGCUGUUGGUGUCCAUCGGGCAAUCAUCCUGCAGCACGCCAUUCAGCACUAGGACCAUC----CUGGC------U--CCG
(((.((.(((((((((((((((...(.(((.(((...))).))).).....)))))))))..((......)).........)))----))).)------)--))) ( -36.10)
>DroWil_CAF1 1235 90 + 1
CUAUACACGGGAUGCUGUAGAAACAAACUGUUGGUGUCCAUGGGGCAGUCAUCCUGCAGAACACCAUUCAAUACGAGCACCAUU----CUCCC------U-----
........(((((((((((..(((.....)))(((((.(.....((((.....)))).).)))))......))).)))).....----.))))------.----- ( -20.80)
>DroMoj_CAF1 3076 105 + 1
CUGUAGACGGGAUGCUGCAGGAACAGGCUGUUCGUGUCCAUGGGGCAGUCAUCCUGCAGCACACCAUUCAGCACUAGCACCAUUGCUCUUGCUAUCCAACGUCUC
....((((((..((((((((((...((((((((.........)))))))).))))))))))..))....((((..((((....))))..)))).......)))). ( -44.90)
>DroAna_CAF1 3699 94 + 1
CUGUAGACGGGAUGCUGCAGGAACAGGCUGUUGGUGUCCAUGGGACAGUCGUCCUGCAGCACUCCAUUCAAAACGAGCACCAUU----GUGGC------UGGCU-
........((..((((((((((...(((((((((...)))....)))))).))))))))))..))..........(((.((...----..)).------..)))- ( -36.80)
>consensus
CUGUAGACGGGAUGCUGCAGGAACAGGCUGUUGGUGUCCAUGGGGCAGUCAUCCUGCAGCACACCAUUCAGCACGAGCACCAUC____CUGGC______UGUCU_
........((..((((((((((...(((((((...........))))))).))))))))))..))........................................ (-25.70 = -26.12 +   0.42)

alignment

secondary structure

dotplot

Window 1

Location	14,157,437 – 14,157,532
Length	95
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	81.11
Mean single sequence MFE	-33.51
Consensus MFE	-23.01
Energy contribution	-22.93
Covariance contribution	-0.08
Combinations/Pair	1.27
Mean z-score	-1.37
Structure conservation index	0.69
SVM decision value	0.07
SVM RNA-class probability	0.571147
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14157437 95 - 20766785
CAGACA------GCCAG----GAUGGUGCUCGUGCUGAAUGGUGUGCUGCAGGAUGACUGCCCCAUGGACACCAACAGCCUGUUCCUGCAGCAUCCCGUCUACAG
.((((.------..(((----.(((.....))).)))...((..((((((((((.(.(((.....(((...))).))).)...))))))))))..)))))).... ( -34.90)
>DroVir_CAF1 3206 95 - 1
GAAACG------ACCAG----GAUGGUGCUUGUGCUGAACGGUGUGCUGCAGGAUGACUGCCCGAUGGAUACAAACAGCCUGUUCCUGCAGCAUCCUGUCUAUAG
.....(------((.((----((((.(((..(.((((....((((.(.((((.....)))).....).))))...)))).....)..))).)))))))))..... ( -30.80)
>DroPse_CAF1 1869 93 - 1
CGG--A------GCCAG----GAUGGUCCUAGUGCUGAAUGGCGUGCUGCAGGAUGAUUGCCCGAUGGACACCAACAGCCUGUUCCUGCAGCAUCCCGUCUACCG
(((--(------(((((----(.....))).).)))..((((.(((((((((((.....((..(.(((...))).).))....))))))))))).))))...))) ( -35.20)
>DroWil_CAF1 1235 90 - 1
-----A------GGGAG----AAUGGUGCUCGUAUUGAAUGGUGUUCUGCAGGAUGACUGCCCCAUGGACACCAACAGUUUGUUUCUACAGCAUCCCGUGUAUAG
-----.------((((.----..((.....((.((((..((((((((.((((.....)))).....)))))))).)))).))......))...))))........ ( -26.90)
>DroMoj_CAF1 3076 105 - 1
GAGACGUUGGAUAGCAAGAGCAAUGGUGCUAGUGCUGAAUGGUGUGCUGCAGGAUGACUGCCCCAUGGACACGAACAGCCUGUUCCUGCAGCAUCCCGUCUACAG
.((((......(((((..((((....))))..)))))...((..((((((((((.(.(((...............))).)...))))))))))..)))))).... ( -40.16)
>DroAna_CAF1 3699 94 - 1
-AGCCA------GCCAC----AAUGGUGCUCGUUUUGAAUGGAGUGCUGCAGGACGACUGUCCCAUGGACACCAACAGCCUGUUCCUGCAGCAUCCCGUCUACAG
-(((..------(((..----...)))))).((...((.(((..((((((((((((.((((....(((...)))))))..)).))))))))))..))))).)).. ( -33.10)
>consensus
_AGACA______GCCAG____AAUGGUGCUCGUGCUGAAUGGUGUGCUGCAGGAUGACUGCCCCAUGGACACCAACAGCCUGUUCCUGCAGCAUCCCGUCUACAG
............((((.......))))...........((((..((((((((((.(.(((...............))).)...))))))))))..))))...... (-23.01 = -22.93 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:42 2006