Locus 4040

Sequence ID	3R_DroMel_CAF1
Location	11,033,164 – 11,033,284
Length	120
Max. P	0.797762

overview

Window 8

Location	11,033,164 – 11,033,284
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.42
Mean single sequence MFE	-44.80
Consensus MFE	-37.86
Energy contribution	-38.14
Covariance contribution	0.28
Combinations/Pair	1.11
Mean z-score	-1.34
Structure conservation index	0.85
SVM decision value	0.22
SVM RNA-class probability	0.641076
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11033164 120 + 27905053
CGCUCGUUAAUGAAGAAUGGCUUCAAGGCGGUCUCCUCCACCUUGAACUGGCUGAGCCACUGGCCCUUCAUGUAGGCGGCGUUGGCCAGCACCAACAUGGUGUGGGGUGUGAUCUCCUCG
..........(((((.....)))))(((.((((.((((((((.((.....((((.((((.((.((((......))).).)).)))))))).....)).)))).))))...)))).))).. ( -44.70)
>DroSec_CAF1 8463 120 + 1
CGCUCGUUUAUGAAGAACGGCUUCAAGGCGGUCUCCUCCACCUUGAACUGGCUGAGCCACUGGCCCUUCAUGUAGGCGGCGUUGGCCAGCACCAACAUGGUGCGGGAUGUGAUCUCCUGG
.(((....(((((((..(((((((((((.((......)).))))))...))))).(((...))).)))))))..)))(((....))).(((((.....)))))((((.......)))).. ( -45.70)
>DroSim_CAF1 9148 120 + 1
CGCUCGUUUAUGAAGAACGGCUUCGAGGCGGUCUCCUCCACCUUAAACUGGCUGAGCCACUGGCCCUUCAUGUAGGCGGCGUUGGCCAGCACCAACAUGGUGCGGGAUGUGAUCUCCUGG
.((.(((((.....)))))))..(.(((.((((((((.((((........((((.((((.((.((((......))).).)).))))))))........)))).))))...)))).))).) ( -45.29)
>DroEre_CAF1 11227 120 + 1
UGCUCGUUUAUGAAAAACGGCUUCAAGGAGGUUUCCUCCACCUUGAACUGGUUGAGCCACUGGCCCUUCAUGUAGGCGGCGUUGCCCAGCACCAACAUGGUACGGGAAUUGAUCUCCUCG
.((.(((((.....)))))))....((((((((((((..(((.((.....((((.((.((.(.((((......))).).))).)).)))).....)).)))..))))...)))))))).. ( -35.70)
>DroYak_CAF1 8635 120 + 1
UACUCGUUUAUGUAGAAGGGCUUCAAGGAGGUUUCCUCCACCUUGAACUGGCUGAGCCACUGGCCCUUCAUGUAGGCGGCGUUUCCCAGCACCAUCAUGGUGCGGGAAUUGAUCUCUUUG
...((((((((((.((((((((((((((.((......)).))))))..((((...))))..))))))))))))))))))((.(((((.(((((.....)))))))))).))......... ( -52.60)
>consensus
CGCUCGUUUAUGAAGAACGGCUUCAAGGCGGUCUCCUCCACCUUGAACUGGCUGAGCCACUGGCCCUUCAUGUAGGCGGCGUUGGCCAGCACCAACAUGGUGCGGGAUGUGAUCUCCUCG
(((.(((((((...(((.((((((((((.((......)).))))))..((((...))))..)))).)))..))))))))))....((.(((((.....))))).)).............. (-37.86 = -38.14 +   0.28)

alignment

secondary structure

dotplot

Window 9

Location	11,033,164 – 11,033,284
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.42
Mean single sequence MFE	-43.33
Consensus MFE	-35.66
Energy contribution	-36.94
Covariance contribution	1.28
Combinations/Pair	1.05
Mean z-score	-1.56
Structure conservation index	0.82
SVM decision value	0.61
SVM RNA-class probability	0.797762
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11033164 120 - 27905053
CGAGGAGAUCACACCCCACACCAUGUUGGUGCUGGCCAACGCCGCCUACAUGAAGGGCCAGUGGCUCAGCCAGUUCAAGGUGGAGGAGACCGCCUUGAAGCCAUUCUUCAUUAACGAGCG
.((((((..............(((((.((((.((.....)).)))).)))))...(((...((((...)))).((((((((((......))))))))))))).))))))........... ( -41.70)
>DroSec_CAF1 8463 120 - 1
CCAGGAGAUCACAUCCCGCACCAUGUUGGUGCUGGCCAACGCCGCCUACAUGAAGGGCCAGUGGCUCAGCCAGUUCAAGGUGGAGGAGACCGCCUUGAAGCCGUUCUUCAUAAACGAGCG
(((((.(((...)))))(((((.....))))))))....(((((.....(((((((((...((((...)))).((((((((((......))))))))))...)))))))))...)).))) ( -44.80)
>DroSim_CAF1 9148 120 - 1
CCAGGAGAUCACAUCCCGCACCAUGUUGGUGCUGGCCAACGCCGCCUACAUGAAGGGCCAGUGGCUCAGCCAGUUUAAGGUGGAGGAGACCGCCUCGAAGCCGUUCUUCAUAAACGAGCG
....(((.((((..((((((((.....))))).(((....)))...........)))...))))))).((..(((((((((((......)))))).((((.....)))).)))))..)). ( -41.60)
>DroEre_CAF1 11227 120 - 1
CGAGGAGAUCAAUUCCCGUACCAUGUUGGUGCUGGGCAACGCCGCCUACAUGAAGGGCCAGUGGCUCAACCAGUUCAAGGUGGAGGAAACCUCCUUGAAGCCGUUUUUCAUAAACGAGCA
(((((((.......((((((((.....))))).)))...(.((((((...(((((((((...)))))......)))))))))).).....)))))))..(((((((.....))))).)). ( -43.20)
>DroYak_CAF1 8635 120 - 1
CAAAGAGAUCAAUUCCCGCACCAUGAUGGUGCUGGGAAACGCCGCCUACAUGAAGGGCCAGUGGCUCAGCCAGUUCAAGGUGGAGGAAACCUCCUUGAAGCCCUUCUACAUAAACGAGUA
............((((((((((.....))))).)))))..((((.......(((((((...((((...)))).(((((((.((......)).))))))))))))))........)).)). ( -45.36)
>consensus
CCAGGAGAUCACAUCCCGCACCAUGUUGGUGCUGGCCAACGCCGCCUACAUGAAGGGCCAGUGGCUCAGCCAGUUCAAGGUGGAGGAGACCGCCUUGAAGCCGUUCUUCAUAAACGAGCG
....(((.((((..(((....(((((.((((.((.....)).)))).)))))..)))...)))))))......((((((((((......))))))))))((((((.......)))).)). (-35.66 = -36.94 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:29 2006