Locus 5088

Sequence ID 2R_DroMel_CAF1
Location 16,536,329 – 16,536,425
Length 96
Max. P 0.876491
window8135 window8136

overview

Window 5

Location 16,536,329 – 16,536,425
Length 96
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 88.38
Mean single sequence MFE -24.88
Consensus MFE -18.69
Energy contribution -19.12
Covariance contribution 0.44
Combinations/Pair 1.11
Mean z-score -2.20
Structure conservation index 0.75
SVM decision value 0.89
SVM RNA-class probability 0.876491
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16536329 96 + 20766785
AUCCGAGGAAGAAGACGGCGGAUGGAAACAAAUGAAGUGAUUGAAUGCGUUGCGCAGACGCAG----UUGGGUGGGAGGUUUACAUAUAG-----AUAUGUAAAU
((((((........((..((..((....))..))..)).......((((((.....)))))).----)))))).....(((((((((...-----.))))))))) ( -23.10)
>DroSec_CAF1 3371 93 + 1
AUCCG---AAGAAGACGGCGGAUGGAAACAAAUGAAGUGAUUGAAUGCGUUGCGCAGACGCAG----UUGGGUGGGAGGUUUACAUACAG-----AUAUGUAAAU
(((((---(.....((..((..((....))..))..)).......((((((.....)))))).----)))))).....(((((((((...-----.))))))))) ( -22.90)
>DroEre_CAF1 3373 96 + 1
AUCCG---AAGAAGACUGCGGAUGGAAACAAAUGAAGUGAUUGAAUGCGUUGCGCAGACGCAGUCAGUCGGGUGGGAGGCUUACGUACU------AUAUGUAAAU
(((((---(....(((((((..((....))...............((((...))))..)))))))..)))))).......(((((((..------.))))))).. ( -28.40)
>DroYak_CAF1 3403 98 + 1
AUCCA---AAGAAGACUGCGGAUGGAAACAAAUGAAGUGAUUGAAUGCGUUGCGCAGACGCAG----UUGGGUGGGAGGUAUACAUACAUAUUUCUUAUGUAAAU
.((((---.....(((((((..((....))...............((((...))))..)))))----))...)))).........((((((.....))))))... ( -25.10)
>consensus
AUCCG___AAGAAGACGGCGGAUGGAAACAAAUGAAGUGAUUGAAUGCGUUGCGCAGACGCAG____UUGGGUGGGAGGUUUACAUACAG_____AUAUGUAAAU
(((((.........(((.((..((....))..)).))).......((((((.....))))))......))))).....(((((((((.........))))))))) (-18.69 = -19.12 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 16,536,329 – 16,536,425
Length 96
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 88.38
Mean single sequence MFE -15.07
Consensus MFE -10.94
Energy contribution -11.20
Covariance contribution 0.25
Combinations/Pair 1.17
Mean z-score -1.49
Structure conservation index 0.73
SVM decision value 0.02
SVM RNA-class probability 0.544556
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16536329 96 - 20766785
AUUUACAUAU-----CUAUAUGUAAACCUCCCACCCAA----CUGCGUCUGCGCAACGCAUUCAAUCACUUCAUUUGUUUCCAUCCGCCGUCUUCUUCCUCGGAU
.((((((((.-----...))))))))............----.((((....))))...........................(((((..(.......)..))))) ( -12.90)
>DroSec_CAF1 3371 93 - 1
AUUUACAUAU-----CUGUAUGUAAACCUCCCACCCAA----CUGCGUCUGCGCAACGCAUUCAAUCACUUCAUUUGUUUCCAUCCGCCGUCUUCUU---CGGAU
.((((((((.-----...))))))))............----.((((....))))...........................(((((..(....)..---))))) ( -13.70)
>DroEre_CAF1 3373 96 - 1
AUUUACAUAU------AGUACGUAAGCCUCCCACCCGACUGACUGCGUCUGCGCAACGCAUUCAAUCACUUCAUUUGUUUCCAUCCGCAGUCUUCUU---CGGAU
.(((((....------.....)))))........((((..(((((((..((.(.((((.................)))).)))..)))))))....)---))).. ( -19.03)
>DroYak_CAF1 3403 98 - 1
AUUUACAUAAGAAAUAUGUAUGUAUACCUCCCACCCAA----CUGCGUCUGCGCAACGCAUUCAAUCACUUCAUUUGUUUCCAUCCGCAGUCUUCUU---UGGAU
...((((((.....))))))........(((......(----(((((..((.(.((((.................)))).)))..))))))......---.))). ( -14.65)
>consensus
AUUUACAUAU_____CUGUAUGUAAACCUCCCACCCAA____CUGCGUCUGCGCAACGCAUUCAAUCACUUCAUUUGUUUCCAUCCGCAGUCUUCUU___CGGAU
.(((((((((.......))))))))).................((((....))))...........................(((((.............))))) (-10.94 = -11.20 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:14 2006