Locus 3406

Sequence ID X_DroMel_CAF1
Location 9,120,619 – 9,120,710
Length 91
Max. P 0.971859
window5570 window5571

overview

Window 0

Location 9,120,619 – 9,120,710
Length 91
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 66.77
Mean single sequence MFE -27.10
Consensus MFE -11.85
Energy contribution -11.72
Covariance contribution -0.13
Combinations/Pair 1.12
Mean z-score -2.50
Structure conservation index 0.44
SVM decision value 1.68
SVM RNA-class probability 0.971859
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9120619 91 + 22224390
GUGAGUCUGUGGCACUUGAAAGUAUAUCUGU-------AAUGUGGCAGGUAAU---UGACUUUUACAAGCAAACAGUAC---------------CAUUGCCACACCCC-CACAUUUA
(((.(..(((((((..(((((((.(((((((-------......)))))))..---..)))))))...((.....))..---------------...)))))))..).-)))..... ( -25.90)
>DroSec_CAF1 1886 79 + 1
GUGAGCCUGUGGC---------------UGU-------ACUGUGGCAGGUAAUUAUUGCCUUUUACAAGCAAACAGUUC---------------CAUUGCCACACCCC-UAUAUUUA
(((.((.((..((---------------(((-------.((((((.(((((.....))))).)))).))...)))))..---------------))..))))).....-........ ( -20.40)
>DroEre_CAF1 1952 105 + 1
GUGGGAAUGUGGCGCUUCAAAGUAUAUUUUU-------AACGUGGCAGGUAAU---UGACU--UACAAGCAAGAAGUUCUAAAGAACGCGAACCUAUUGCCACACCCCACACACUUC
(((((..(((((((((....)))........-------..(((.((..((((.---....)--)))..)).....((((....)))))))........)))))).)))))....... ( -29.30)
>DroYak_CAF1 1957 114 + 1
GUGAGGAUGUGGCGCUUGAAAUUAUACUUUUUUUAUACUAUGUGGCAGGUAAU---UGACUUUUACAAGCAACAAGUUCUAAAGAACGCGAAUCCAUUGCCACACCUCACACGUUUA
((((((.(((((((..((......................(((.((..((((.---......))))..)).))).((((....)))).......)).)))))))))))))....... ( -32.80)
>consensus
GUGAGAAUGUGGCGCUUGAAAGUAUAUUUGU_______AAUGUGGCAGGUAAU___UGACUUUUACAAGCAAAAAGUUC_______________CAUUGCCACACCCC_CACAUUUA
(((....((((((............................((((.((...........)).))))..((.....)).....................)))))).....)))..... (-11.85 = -11.72 +  -0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 9,120,619 – 9,120,710
Length 91
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 66.77
Mean single sequence MFE -26.70
Consensus MFE -12.71
Energy contribution -15.03
Covariance contribution 2.31
Combinations/Pair 1.15
Mean z-score -1.98
Structure conservation index 0.48
SVM decision value 1.05
SVM RNA-class probability 0.906690
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9120619 91 - 22224390
UAAAUGUG-GGGGUGUGGCAAUG---------------GUACUGUUUGCUUGUAAAAGUCA---AUUACCUGCCACAUU-------ACAGAUAUACUUUCAAGUGCCACAGACUCAC
....((((-(.(((((((((..(---------------(((..(((.((((....)))).)---)))))))))))))))-------.......((((....)))))))))....... ( -26.80)
>DroSec_CAF1 1886 79 - 1
UAAAUAUA-GGGGUGUGGCAAUG---------------GAACUGUUUGCUUGUAAAAGGCAAUAAUUACCUGCCACAGU-------ACA---------------GCCACAGGCUCAC
........-(.(.(((((((..(---------------(......((((((.....))))))......))))))))).)-------.)(---------------(((...))))... ( -21.60)
>DroEre_CAF1 1952 105 - 1
GAAGUGUGUGGGGUGUGGCAAUAGGUUCGCGUUCUUUAGAACUUCUUGCUUGUA--AGUCA---AUUACCUGCCACGUU-------AAAAAUAUACUUUGAAGCGCCACAUUCCCAC
.....(((.((((((((((...((((....((((....))))..((((....))--))...---...))))((....((-------(((.......))))).))))))))))))))) ( -28.80)
>DroYak_CAF1 1957 114 - 1
UAAACGUGUGAGGUGUGGCAAUGGAUUCGCGUUCUUUAGAACUUGUUGCUUGUAAAAGUCA---AUUACCUGCCACAUAGUAUAAAAAAAGUAUAAUUUCAAGCGCCACAUCCUCAC
.......((((((((((((..((((...((((((....)))).(((.((..((((......---.))))..)).))).............)).....))))...)))))).)))))) ( -29.60)
>consensus
UAAAUGUG_GGGGUGUGGCAAUG_______________GAACUGUUUGCUUGUAAAAGUCA___AUUACCUGCCACAUU_______AAAAAUAUACUUUCAAGCGCCACAGACUCAC
.........((((((((((...........((((....)))).....((..((((..........))))..))...............................)))))).)))).. (-12.71 = -15.03 +   2.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:33 2006