Locus 5272

Sequence ID 3L_DroMel_CAF1
Location 14,563,836 – 14,563,976
Length 140
Max. P 0.704734
window8338 window8339

overview

Window 8

Location 14,563,836 – 14,563,944
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.62
Mean single sequence MFE -54.97
Consensus MFE -24.58
Energy contribution -24.58
Covariance contribution 0.00
Combinations/Pair 1.37
Mean z-score -1.99
Structure conservation index 0.45
SVM decision value 0.06
SVM RNA-class probability 0.566073
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14563836 108 + 23771897
UCGCAUGGGCAUGGACAUCCGCGAAGCCAUUGCUCAUGGCCGCCG------------CCAAAUGAUGACGUUGAGCCGCCGACGGGGGACUUCCCUGGGCGGCGGCCGCAAAACUAUGAU
..((((((((((((.(.((...)).)))).)))))))((((((((------------((.........(((((......)))))((((....)))).))))))))))))........... ( -51.50)
>DroVir_CAF1 43525 117 + 1
UCGCAUGUGCAUGAACAUCGGCAAAUCCAUUGCUCAGACCUGCGGCAGCCGCUGCGGCCAAAUGAUGGCG---UGCCGCCGACGGCGGACUGCUCUGGGAGGCAGCCGCAAAACUGUGAU
(((((..(((..(.....)(((...(((...((........))(((((((((((((((...(((....))---)...)))).)))))).)))))...)))....))))))....))))). ( -44.40)
>DroGri_CAF1 44633 120 + 1
UCGCAUGCGCAUGCACAUCAGCGAAACCAUUGCUCAAGCCCGCUGCAGCUGCAGCGGCCAAAUGGUGACGCUGUGCCGCCGACGGCGGACUGCCCUGGGCGGCGGCAGCGAAACUAUGAU
((((.(((..........(((((..((((((((....))(((((((....)))))))...))))))..)))))(((((((.(.(((.....))).).))))))))))))))......... ( -58.20)
>DroWil_CAF1 187444 120 + 1
UGGCAUGAGCAUGGACAUCGGCGAAUCCGUUGCUCAGGCCAGCCGCUGCCGCUGCAGCAAGAUGGUGUCUCUGCGCUGCUGACGGCGGACUUCCCUGGGUGGCGGCGGCGAAGGUAUGGU
((((.((((((((((..........)))).)))))).))))(((((((((((((((((.(((.......)))..)))))...(((.((....)))))))))))))))))........... ( -59.30)
>DroMoj_CAF1 49654 120 + 1
UCGCAUGUGCAUGAACAUCGGCGAAUCCAUUGCUCAGUCCCGCGGCAGCCGCUGCGGCCAGGUGAUGGCGCUGCGCCGCCGACGGCGGGCUGCUCUGGGAGGCAGCGGCGAAGCUGUGAU
((((((((......)))).(((....((.(((((...(((((.(((((((((.(((.(((.....)))))).))((((....)))).))))))).)))))))))).))....))))))). ( -55.90)
>DroAna_CAF1 35889 108 + 1
UCGCAUGGGCGUGGACAUCCGCGAAUCCAUUGCUCAUGGCCGCCG------------CCAAAUGGUGGCGCUGGGCCGCCGACGGGGGCGAUCCCUGGGCGGCCGCCGCGAAGCUGUGAU
..((((((.(((((....)))))...))).)))(((((((.((((------------((....))))))((.((((((((..(((((.....)))))))))))).).))...))))))). ( -60.50)
>consensus
UCGCAUGGGCAUGGACAUCGGCGAAUCCAUUGCUCAGGCCCGCCGCAGCCGCUGCGGCCAAAUGAUGGCGCUGCGCCGCCGACGGCGGACUGCCCUGGGCGGCGGCCGCGAAACUAUGAU
..((....((.....((((.((((.....))))........((.((.......)).)).....))))......(((((((.(.(((.....))).).))))))))).))........... (-24.58 = -24.58 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 14,563,876 – 14,563,976
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.36
Mean single sequence MFE -48.63
Consensus MFE -25.75
Energy contribution -26.28
Covariance contribution 0.53
Combinations/Pair 1.46
Mean z-score -1.69
Structure conservation index 0.53
SVM decision value 0.36
SVM RNA-class probability 0.704734
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14563876 100 + 23771897
CGCCG------------CCAAAUGAUGACGUUGAGCCGCCGACGGGGGACUUCCCUGGGCGGCGGCCGCAAAACUAUGAUGGCGCAUAUACGGAUUUAUCAGAUCCAUCUC------G--
.((.(------------(((..(.(((...(((.(((((((.(.((((....)))).).)))))))..)))...))).)))))))......(((((.....))))).....------.-- ( -39.70)
>DroVir_CAF1 43565 109 + 1
UGCGGCAGCCGCUGCGGCCAAAUGAUGGCG---UGCCGCCGACGGCGGACUGCUCUGGGAGGCAGCCGCAAAACUGUGAUGGCGCAUAUAGGGAUUGAUGAGAUCCAUGUC------C--
.(((((....))))).((((.....))))(---(((((.((...((((.(((((......))))))))).......)).))))))......(((((.....))))).....------.-- ( -42.60)
>DroGri_CAF1 44673 114 + 1
CGCUGCAGCUGCAGCGGCCAAAUGGUGACGCUGUGCCGCCGACGGCGGACUGCCCUGGGCGGCGGCAGCGAAACUAUGAUGCCGCAUAUAGGGAUUGAUGAGAUCCAUCUC------CGU
.(((((....)))))(((...(((((..((((((((((((.(.(((.....))).).)))))).))))))..)))))...)))........(((..((((.....))))))------).. ( -55.20)
>DroWil_CAF1 187484 112 + 1
AGCCGCUGCCGCUGCAGCAAGAUGGUGUCUCUGCGCUGCUGACGGCGGACUUCCCUGGGUGGCGGCGGCGAAGGUAUGGUGUCUCAUAUACGGAUUUAUCAGAUCCAUUUC------U--
.(((((((((((((((((.(((.......)))..)))))...(((.((....)))))))))))))))))((((((((((....))))))..(((((.....))))).))))------.-- ( -50.10)
>DroMoj_CAF1 49694 112 + 1
CGCGGCAGCCGCUGCGGCCAGGUGAUGGCGCUGCGCCGCCGACGGCGGGCUGCUCUGGGAGGCAGCGGCGAAGCUGUGAUGGCGCAUGUAGGGAUUUAUUAGAUCCAUGUC------G--
((((((.((((((((.((((.....))))((.((.(((((...))))))).))........))))))))...))))))..((((.......(((((.....))))).))))------.-- ( -52.90)
>DroAna_CAF1 35929 106 + 1
CGCCG------------CCAAAUGGUGGCGCUGGGCCGCCGACGGGGGCGAUCCCUGGGCGGCCGCCGCGAAGCUGUGAUGCCGCAUAUACGGAUUGAUCAGAUCCAUGUCCACCGGC--
(((((------------((....)))))))...(((((((..(((((.....))))))))))))((((((..((......)))))......(((((.....))))).........)))-- ( -51.30)
>consensus
CGCCGCAGCCGCUGCGGCCAAAUGAUGGCGCUGCGCCGCCGACGGCGGACUGCCCUGGGCGGCGGCCGCGAAACUAUGAUGGCGCAUAUACGGAUUGAUCAGAUCCAUGUC______C__
.(((((.(((.....)))...............(((((((.(.(((.....))).).)))))))))))).....((((......))))...(((((.....))))).............. (-25.75 = -26.28 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:05 2006