Locus 4379

Sequence ID 3R_DroMel_CAF1
Location 11,570,542 – 11,570,662
Length 120
Max. P 0.992709
window7154 window7155

overview

Window 4

Location 11,570,542 – 11,570,662
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.83
Mean single sequence MFE -41.60
Consensus MFE -37.44
Energy contribution -37.33
Covariance contribution -0.11
Combinations/Pair 1.23
Mean z-score -2.00
Structure conservation index 0.90
SVM decision value 1.71
SVM RNA-class probability 0.973392
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11570542 120 + 27905053
UCCGAAUUGGGCAUCUUCUUUCCGGAUUGCUUCGAACGCGUCAGCGGUCAUUGCAACAAGAAGAAUCCCGGCAAUGUCCAGAAUCUCCACAUCCUGGCCCAUCGGGUGAUGCCCAAAUUC
...((((((((((((((((((...(.((((...((.(((....))).))...)))))..)))))).(((((....(.((((............)))))...))))).))))))).))))) ( -38.90)
>DroSec_CAF1 99712 120 + 1
UCCGAACUGGGCAUCUUCUUUCCGGAUUGCUUCGAACGCGUCAGCGGACAUUGCAACAAGAAGAAUCCCGGCAAUGUCCAGAAUCUGCACAUCCUGGCCCAUCGGGUUAUGCCCAAGUUC
...((((((((((..........((((((((((....((....))(((((((((.....((....))...))))))))).)))...))).))))((((((...))))))))))).))))) ( -43.40)
>DroSim_CAF1 103573 120 + 1
UCUGAACUGGGCAUCUUCUUCCCGGAUUGCUUCGAACGCGUCAGCGGGCAUUGCAACAAGAAGAAUCCCGGCAAUGUCCAGAAUCUGCACAUCCUGGCCCAUCGGGUUAUGCCCAAGUUC
...((((((((((..........((((((((((....((....))(((((((((.....((....))...))))))))).)))...))).))))((((((...))))))))))).))))) ( -42.50)
>DroEre_CAF1 102815 120 + 1
UCCGAAUUGGGCAUCUUCUUUCCGGAUUGCUUCGAACGCGUCAGCGGGCACUGCAACAAGAAGAAUCCCGGCAAUGUCCAGAAUCUGCACAUCCUGGCCCACCGGGUGAUGCCCAAAUUC
...((((((((((((((((((...(.((((...(..(((....)))..)...)))))..)))))).(((((....(.((((............)))))...))))).))))))).))))) ( -42.00)
>DroYak_CAF1 100573 120 + 1
UCCGAGUUGGGCAUCUUCUUUCCGGAUUGCUUCGAACGCGUCGGCGGGCAUUGCAACAAGAAGAAUCCCGGCAAUGUCCAGAACCUGCACAUUCUGGCCCACCGGGUGAUGCCCAAGUUC
...((.(((((((((((((((...(.((((...(..(((....)))..)...)))))..)))))).(((((....(.((((((........)))))))...))))).))))))))).)). ( -45.10)
>DroAna_CAF1 185701 120 + 1
AUAGAGCUAGGCUUCUUUUUUCCGGGCUGCUUUGAGCGCGUCAGCGGCCAUUGCACCAAGAAGAAUCCCGGAAAUGUCCAGAGCCUUCACAUCCUGGCCCACCGGGUGAUGCCCAAGUUU
...(((((((((((....((((((((...((((...(((....)))((....)).....))))...))))))))......))))))...((.(((((....))))))).......))))) ( -37.70)
>consensus
UCCGAACUGGGCAUCUUCUUUCCGGAUUGCUUCGAACGCGUCAGCGGGCAUUGCAACAAGAAGAAUCCCGGCAAUGUCCAGAAUCUGCACAUCCUGGCCCACCGGGUGAUGCCCAAGUUC
...((((((((((((.....(((((...(((..((..((....))(((((((((.....((....))...)))))))))............))..)))...))))).))))))).))))) (-37.44 = -37.33 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,570,542 – 11,570,662
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.83
Mean single sequence MFE -49.53
Consensus MFE -42.75
Energy contribution -42.92
Covariance contribution 0.17
Combinations/Pair 1.19
Mean z-score -3.01
Structure conservation index 0.86
SVM decision value 2.35
SVM RNA-class probability 0.992709
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11570542 120 - 27905053
GAAUUUGGGCAUCACCCGAUGGGCCAGGAUGUGGAGAUUCUGGACAUUGCCGGGAUUCUUCUUGUUGCAAUGACCGCUGACGCGUUCGAAGCAAUCCGGAAAGAAGAUGCCCAAUUCGGA
(((((.(((((((.(((((((..(((((((......))))))).)))...)))).(((((((.(((((..(((.(((....))).)))..)))))..)).)))))))))))))))))... ( -48.60)
>DroSec_CAF1 99712 120 - 1
GAACUUGGGCAUAACCCGAUGGGCCAGGAUGUGCAGAUUCUGGACAUUGCCGGGAUUCUUCUUGUUGCAAUGUCCGCUGACGCGUUCGAAGCAAUCCGGAAAGAAGAUGCCCAGUUCGGA
(((((.((((((..((.(((..((..((((((((((....(((((((((((((((....)))))..))))))))))))).)))))))...)).))).)).......)))))))))))... ( -50.90)
>DroSim_CAF1 103573 120 - 1
GAACUUGGGCAUAACCCGAUGGGCCAGGAUGUGCAGAUUCUGGACAUUGCCGGGAUUCUUCUUGUUGCAAUGCCCGCUGACGCGUUCGAAGCAAUCCGGGAAGAAGAUGCCCAGUUCAGA
(((((.((((((..(((((((..(((((((......))))))).)))...)))).(((((((((((((..((..(((....)))..))..))))..))))))))).)))))))))))... ( -50.60)
>DroEre_CAF1 102815 120 - 1
GAAUUUGGGCAUCACCCGGUGGGCCAGGAUGUGCAGAUUCUGGACAUUGCCGGGAUUCUUCUUGUUGCAGUGCCCGCUGACGCGUUCGAAGCAAUCCGGAAAGAAGAUGCCCAAUUCGGA
(((((.(((((((.(((((..(.(((((((......)))))))...)..))))).(((((((.(((((..((..(((....)))..))..)))))..)).)))))))))))))))))... ( -55.40)
>DroYak_CAF1 100573 120 - 1
GAACUUGGGCAUCACCCGGUGGGCCAGAAUGUGCAGGUUCUGGACAUUGCCGGGAUUCUUCUUGUUGCAAUGCCCGCCGACGCGUUCGAAGCAAUCCGGAAAGAAGAUGCCCAACUCGGA
((..(((((((((.(((((..(.(((((((......)))))))...)..))))).(((((((.(((((..((..(((....)))..))..)))))..)).)))))))))))))).))... ( -52.20)
>DroAna_CAF1 185701 120 - 1
AAACUUGGGCAUCACCCGGUGGGCCAGGAUGUGAAGGCUCUGGACAUUUCCGGGAUUCUUCUUGGUGCAAUGGCCGCUGACGCGCUCAAAGCAGCCCGGAAAAAAGAAGCCUAGCUCUAU
......((((.((((((((....)).))..))))(((((((.....((((((((..((.....))(((..((..(((....)))..))..))).))))))))..)).))))).))))... ( -39.50)
>consensus
GAACUUGGGCAUCACCCGAUGGGCCAGGAUGUGCAGAUUCUGGACAUUGCCGGGAUUCUUCUUGUUGCAAUGCCCGCUGACGCGUUCGAAGCAAUCCGGAAAGAAGAUGCCCAAUUCGGA
(((((.(((((((.(((((((..(((((((......))))))).)))...)))).(((((((.(((((..((..(((....)))..))..)))))..))).))))))))))))))))... (-42.75 = -42.92 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:39 2006