Locus 6993

Sequence ID 2L_DroMel_CAF1
Location 19,448,067 – 19,448,212
Length 145
Max. P 0.896601
window11152 window11153

overview

Window 2

Location 19,448,067 – 19,448,187
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.78
Mean single sequence MFE -37.94
Consensus MFE -25.82
Energy contribution -26.35
Covariance contribution 0.53
Combinations/Pair 1.50
Mean z-score -2.32
Structure conservation index 0.68
SVM decision value 0.99
SVM RNA-class probability 0.896601
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19448067 120 - 22407834
AUCGAACAGAUGUACCAGAAGAAGUCGCAGCUGGAGCACAUCCUGCUGCGACCCGACUCGUACAUCGGAUCCGUGGAGUUCACCAAGGAGCUGAUGUGGGUGUAUGACAACUCCCAAAAC
(((.....(((((((.((..(..((((((((.(((.....))).)))))))).)..)).)))))))((.(((.(((......))).))).))))).((((.((......)).)))).... ( -45.70)
>DroVir_CAF1 4840 120 - 1
AUCGAACAGAUGUACCAGAAGAAAUCGCAGCUGGAGCAUAUUCUCUUGCGUCCGGAUUCGUAUAUUGGAUCCGUGGAGUUUACCAAGGAGCUAAUGUGGGUACAUGAUGUCGAAAAGAAU
.((((.((.(((((((.........((...((((((((........))).)))))...))((((((((.(((.(((......))).))).)))))))))))))))..))))))....... ( -39.60)
>DroGri_CAF1 4067 120 - 1
AUCGAACAGAUGUACCAGAAGAAAUCGCAGCUGGAGCACAUUCUGUUGCGACCGGACUCGUAUAUUGGUUCCGUUGAGUUUACCAAGGAGCUGAUGUGGGUUCUUGAUCUUGAGAAAAAU
.((((((((((((.((((..(....)....)))).)))...)))))).)))..((((((..((((..(((((.(((.(....)))))))))..))))))))))................. ( -35.60)
>DroWil_CAF1 4342 120 - 1
AUCGAGCAGAUGUAUCAGAAGAAGACCCAAUUGGAGCAUAUUCUACUACGUCCCGAUUCGUAUAUUGGCUCCGUUGAGUAUACCAAAGAGCUAAUGUGGGUCUAUGAUUUCGAAAACAAU
.(((((.......((((.....((((((((((((..(.((......)).)..))))))...((((((((((..(((.(....)))).)))))))))))))))).)))))))))....... ( -31.71)
>DroMoj_CAF1 4076 120 - 1
AUCGAGCAGAUGUAUCAGAAAAAAUCGCAAUUGGAGCACAUCUUGUUGCGUCCAGAUUCGUACAUUGGCUCGGUGGAAUUUACAAAGGAGUUAAUGUGGGUACACGAUGCAGAAAAGAAU
.((..(((..((((((.(((.....((((((.(((.....))).))))))......))).(((((((((((..((.......))...)))))))))))))))))...))).))....... ( -34.10)
>DroAna_CAF1 3976 120 - 1
AUCGAACAGAUGUACCAGAAAAAGUCCCAGCUGGAACACAUCCUGCUGCGACCGGACUCGUACAUUGGCUCUGUGGAGUACACCAAGGAGCUGAUGUGGGUGUAUGACUUUGAGAAGAAC
.(((((...(((((((......(((((((((.(((.....))).)))).....)))))..(((((..(((((.(((......))).)))))..))))))))))))...)))))....... ( -40.90)
>consensus
AUCGAACAGAUGUACCAGAAGAAAUCGCAGCUGGAGCACAUCCUGCUGCGACCGGACUCGUACAUUGGCUCCGUGGAGUUUACCAAGGAGCUAAUGUGGGUACAUGAUGUCGAAAAGAAU
.((((....(((((((........(((((((.(((.....))).))))))).........((((((((((((...(......)...)))))))))))))))))))....))))....... (-25.82 = -26.35 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 19,448,107 – 19,448,212
Length 105
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.39
Mean single sequence MFE -34.75
Consensus MFE -21.17
Energy contribution -20.70
Covariance contribution -0.47
Combinations/Pair 1.41
Mean z-score -1.47
Structure conservation index 0.61
SVM decision value 0.32
SVM RNA-class probability 0.686486
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19448107 105 - 22407834
GGAGAACGGAAACAAG---G------------CCCUGUCCAUCGAACAGAUGUACCAGAAGAAGUCGCAGCUGGAGCACAUCCUGCUGCGACCCGACUCGUACAUCGGAUCCGUGGAGUU
((.(...(....)...---.------------)))..(((((.((.(.(((((((.((..(..((((((((.(((.....))).)))))))).)..)).))))))).).)).)))))... ( -40.70)
>DroVir_CAF1 4880 108 - 1
GGAGAAUGGUAAAGGUAAAG------------GCAUGUCCAUCGAACAGAUGUACCAGAAGAAAUCGCAGCUGGAGCAUAUUCUCUUGCGUCCGGAUUCGUAUAUUGGAUCCGUGGAGUU
((((((((((..........------------.......((((.....))))..((((..(....)....)))).)).)))))))).((..(((((((((.....)))))))).)..)). ( -28.20)
>DroGri_CAF1 4107 105 - 1
GCAGAACGGUAAAAAC---G------------CCAUGUCCAUCGAACAGAUGUACCAGAAGAAAUCGCAGCUGGAGCACAUUCUGUUGCGACCGGACUCGUAUAUUGGUUCCGUUGAGUU
((.(((((((......---)------------))..((((.((((((((((((.((((..(....)....)))).)))...)))))).)))..))))..........)))).))...... ( -29.20)
>DroWil_CAF1 4382 114 - 1
GGAAAACGGUAGCGGA---AAAUCUGGUG---GAAUGUCCAUCGAGCAGAUGUAUCAGAAGAAGACCCAAUUGGAGCAUAUUCUACUACGUCCCGAUUCGUAUAUUGGCUCCGUUGAGUA
....(((((.(((.((---......((((---(.....)))))((((.((((((..((((...(..((....))..)...))))..))))))..).))).....)).))))))))..... ( -29.90)
>DroMoj_CAF1 4116 105 - 1
GGAGAACGGCAAAGGC---G------------CCAUGUCCAUCGAGCAGAUGUAUCAGAAAAAAUCGCAAUUGGAGCACAUCUUGUUGCGUCCAGAUUCGUACAUUGGCUCGGUGGAAUU
.......(((......---)------------))...((((((((((.(((((((..(((.....((((((.(((.....))).))))))......)))))))))).))))))))))... ( -40.00)
>DroAna_CAF1 4016 117 - 1
GGAGAACGGCAGCAAG---GCCUCUGGCGGGGCCAUGUCCAUCGAACAGAUGUACCAGAAAAAGUCCCAGCUGGAACACAUCCUGCUGCGACCGGACUCGUACAUUGGCUCUGUGGAGUA
........((.....(---(((((....))))))...(((((.((.(.(((((((.((.....(((.((((.(((.....))).)))).)))....)).))))))).).)).))))))). ( -40.50)
>consensus
GGAGAACGGUAAAAAC___G____________CCAUGUCCAUCGAACAGAUGUACCAGAAGAAAUCGCAGCUGGAGCACAUCCUGCUGCGACCGGACUCGUACAUUGGCUCCGUGGAGUU
.....................................(((((.((.(.(((((((.((......(((((((.(((.....))).))))))).....)).))))))).).)).)))))... (-21.17 = -20.70 +  -0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:45 2006