Locus 5804

Sequence ID	3L_DroMel_CAF1
Location	15,708,762 – 15,708,868
Length	106
Max. P	0.736753

overview

Window 3

Location	15,708,762 – 15,708,868
Length	106
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	74.39
Mean single sequence MFE	-35.77
Consensus MFE	-18.52
Energy contribution	-21.52
Covariance contribution	3.00
Combinations/Pair	1.23
Mean z-score	-1.76
Structure conservation index	0.52
SVM decision value	0.44
SVM RNA-class probability	0.736753
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15708762 106 + 23771897
AUUCAGUUUAGUCCACGCCACUGCACCUACAACAACUAGUGCCGUCAAGUGGUAG----AUGGG---GGGGGUGGUGCUGGUGCUGGUUUGUGGUGCAGGAGCCACUGGAA-AG
.((((((....(((.((((((.(((((..((...(((..(.(((((........)----)))).---)..)))..))..)))))......))))))..)))...)))))).-.. ( -37.50)
>DroSec_CAF1 24288 84 + 1
AUUCAGUUUAGUCCGCGCCACUGCACCUACAACAACUAGUGCCGUCAAGU-----------------------------GGUGCUGGUUUGUGGUACAGGAGCCACUGGAA-AG
.((((((...(....)((..(((.(((.((((..(((((..(((.....)-----------------------------))..)))))))))))).)))..)).)))))).-.. ( -28.90)
>DroSim_CAF1 24744 102 + 1
AUUCAGUUUAGUCCACGCCACUGCACCUACAACAACUAGUACCGUCAAGUGGUUG----AUGGG---AGGGG----GGUGGUGCUGGAUUGUGGUACAGGAGCCACUGGAA-AG
.((((((.((((((((((((((.(.(((.((.((((((.(.......).))))))----.))..---)))).----))))))).))))))).(((......))))))))).-.. ( -39.80)
>DroEre_CAF1 15623 103 + 1
AUUCAGUUUAGUCCACGCCACUGCACCUACAACAACUC---CUGUCAAGGGGGGC----AGGGGCAGAGAGG----GGAGGUGCUGGUUUGUGGUGCAGGAGGCACUGGAAAAG
.((((((.(..(((.((((((.((((((.(.....(((---(((((......)))----))))).......)----..))))))......))))))..))).).)))))).... ( -38.00)
>DroYak_CAF1 61190 110 + 1
AUUCAGUUUAGUCUACGCCACUGCACCUACAACAACUAGUGCCGUCAAGGGGGGUGAAAGGGGGCCGAAGGG----GGUGGUGCUGGUUUGUGGUGCAGGAGGCACUGGAAAAG
.((((((...(....)(((.(((((((.((((..(((((..((..(......(((........)))......----)..))..))))))))))))))))..))))))))).... ( -43.00)
>DroAna_CAF1 21690 84 + 1
AUUCAGUUUAGUCCACGCCAGUGCACCUACAACAACUAGUCCUGUCGGGG----A----AGGGGC---------------------AACUGCGGUGCAGGAGUCGGCGGGA-AG
...........(((.((((..((((((........((..((((....)))----)----..))((---------------------....))))))))(....))))))))-.. ( -27.40)
>consensus
AUUCAGUUUAGUCCACGCCACUGCACCUACAACAACUAGUGCCGUCAAGGGG__G____AGGGG___AGGGG____GGUGGUGCUGGUUUGUGGUGCAGGAGCCACUGGAA_AG
...........((((.((..(((((((.((((..(((((((((....................................))))))))))))))))))))..))...)))).... (-18.52 = -21.52 +   3.00)

alignment

secondary structure

dotplot

Window 4

Location	15,708,762 – 15,708,868
Length	106
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	74.39
Mean single sequence MFE	-27.47
Consensus MFE	-16.76
Energy contribution	-17.35
Covariance contribution	0.59
Combinations/Pair	1.22
Mean z-score	-1.29
Structure conservation index	0.61
SVM decision value	0.10
SVM RNA-class probability	0.582508
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15708762 106 - 23771897
CU-UUCCAGUGGCUCCUGCACCACAAACCAGCACCAGCACCACCCCC---CCCAU----CUACCACUUGACGGCACUAGUUGUUGUAGGUGCAGUGGCGUGGACUAAACUGAAU
..-...((((.(((..(((...........)))..))).((((((.(---..(((----((((.....((((((....)))))))))))))..).)).)))).....))))... ( -29.20)
>DroSec_CAF1 24288 84 - 1
CU-UUCCAGUGGCUCCUGUACCACAAACCAGCACC-----------------------------ACUUGACGGCACUAGUUGUUGUAGGUGCAGUGGCGCGGACUAAACUGAAU
..-...((((.....(((..((((......(((((-----------------------------...(((((((....)))))))..))))).))))..))).....))))... ( -26.20)
>DroSim_CAF1 24744 102 - 1
CU-UUCCAGUGGCUCCUGUACCACAAUCCAGCACCACC----CCCCU---CCCAU----CAACCACUUGACGGUACUAGUUGUUGUAGGUGCAGUGGCGUGGACUAAACUGAAU
..-.((((...((..(((((((((((..((((......----.....---.((.(----(((....)))).)).....)))))))).)))))))..)).))))........... ( -24.33)
>DroEre_CAF1 15623 103 - 1
CUUUUCCAGUGCCUCCUGCACCACAAACCAGCACCUCC----CCUCUCUGCCCCU----GCCCCCCUUGACAG---GAGUUGUUGUAGGUGCAGUGGCGUGGACUAAACUGAAU
....((((.((((..(((((((......(((((.((((----..((.........----.........))..)---))).)))))..))))))).))))))))........... ( -32.57)
>DroYak_CAF1 61190 110 - 1
CUUUUCCAGUGCCUCCUGCACCACAAACCAGCACCACC----CCCUUCGGCCCCCUUUCACCCCCCUUGACGGCACUAGUUGUUGUAGGUGCAGUGGCGUAGACUAAACUGAAU
......((((.....((((.((((......(((((...----..(....)..................((((((....))))))...))))).)))).)))).....))))... ( -27.00)
>DroAna_CAF1 21690 84 - 1
CU-UCCCGCCGACUCCUGCACCGCAGUU---------------------GCCCCU----U----CCCCGACAGGACUAGUUGUUGUAGGUGCACUGGCGUGGACUAAACUGAAU
..-((((((((.....((((((((((..---------------------((....----(----((......)))...))..)))).)))))).))))).)))........... ( -25.50)
>consensus
CU_UUCCAGUGGCUCCUGCACCACAAACCAGCACCACC____CCCCU___CCCCU____C__CCACUUGACGGCACUAGUUGUUGUAGGUGCAGUGGCGUGGACUAAACUGAAU
....((((.((.((.(((((((((((..((((..............................................)))))))).))))))).))))))))........... (-16.76 = -17.35 +   0.59)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:23 2006