Locus 2780

Sequence ID 2R_DroMel_CAF1
Location 9,720,810 – 9,720,920
Length 110
Max. P 0.560462
window4599 window4600

overview

Window 9

Location 9,720,810 – 9,720,920
Length 110
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.57
Mean single sequence MFE -26.28
Consensus MFE -23.71
Energy contribution -23.88
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.10
Structure conservation index 0.90
SVM decision value 0.05
SVM RNA-class probability 0.560462
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9720810 110 + 20766785
C--CUG--CUUAGCCAUGGCCCUGAU------UUUAAAAUAGGACACAUACAGUGGCCGGUAAGUUGGCAUUUUUAUGCGCGCAAAAUGUCAACAUCUUUGCAAAAUGCCACAUAUUCCA
.--..(--((((.((..(((((((..------..................))).)))))))))))(((((((((.......((((((((....))).))))))))))))))......... ( -26.76)
>DroVir_CAF1 38128 112 + 1
CAGCUU--CUUAGCCAUGGCCCUGAU------UUUAAAAUAGGACACAUACAGUGGCCGGUAAGUUGGCAUUUUUAUGCGCGCAAAAUGUCAACAUCUUUGCAAAAUGCCACAUAUUCCA
..(((.--...)))...(((((((..------..................))).))))((.....(((((((((.......((((((((....))).))))))))))))))......)). ( -26.66)
>DroGri_CAF1 39287 114 + 1
CAGCGUCUCUUAGCCAUGGCCCUGAU------UUUAAAAUAGGACACAUACAGUGGCCGGUAAGUUGGCAUUUUUAUGCGCGCAAAAUGUCAACAUCUUUGCAAAAUGCCACAUAUUCCA
..((........))...(((((((..------..................))).))))((.....(((((((((.......((((((((....))).))))))))))))))......)). ( -25.96)
>DroSim_CAF1 29898 110 + 1
C--CUG--CUUAGCCAUGGCCCUGAU------UUUAAAAUAGGACACAUACAGUGGCCGGUAAGUUGGGAUUUUUAUGCGCGCAAAAUGUCAACAUCUUUGCAAAAUGCCACAUAUUCCA
.--(.(--((((.((..(((((((..------..................))).))))))))))).)(((....((((.(.(((...((.(((.....)))))...)))).)))).))). ( -23.65)
>DroWil_CAF1 32125 113 + 1
-----G--CUUAGCCAUGGCCCUGAUUUUGAUUUUAAAAUAGGACACAUACAGUGGCCGGUAAGUUGGCAUUUUUAUGCGCGCAAAAUGUCAACAUCUUUGCAAAAUGCCACAUAUUCCA
-----(--((((.((..(((((((((((((....)))))).(....)...))).)))))))))))(((((((((.......((((((((....))).))))))))))))))......... ( -28.51)
>DroMoj_CAF1 38880 112 + 1
CAGCGU--CUUAGCCAUGGCCCUGAU------UUUAAAAUAGGACACAUACAGUGGCCGGUAAGUUGGCAUUUUUAUGCGCGCAAAAUGUCAACAUCUUUGCAAAAUGCCACAUAUUCCA
..((..--....))...(((((((..------..................))).))))((.....(((((((((.......((((((((....))).))))))))))))))......)). ( -26.16)
>consensus
C__CUG__CUUAGCCAUGGCCCUGAU______UUUAAAAUAGGACACAUACAGUGGCCGGUAAGUUGGCAUUUUUAUGCGCGCAAAAUGUCAACAUCUUUGCAAAAUGCCACAUAUUCCA
........((((.((..(((((((..........................))).)))))))))).(((((((((.......((((((((....))).))))))))))))))......... (-23.71 = -23.88 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 9,720,810 – 9,720,920
Length 110
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.57
Mean single sequence MFE -29.13
Consensus MFE -26.35
Energy contribution -26.51
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.06
Structure conservation index 0.90
SVM decision value 0.01
SVM RNA-class probability 0.538018
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9720810 110 - 20766785
UGGAAUAUGUGGCAUUUUGCAAAGAUGUUGACAUUUUGCGCGCAUAAAAAUGCCAACUUACCGGCCACUGUAUGUGUCCUAUUUUAAA------AUCAGGGCCAUGGCUAAG--CAG--G
.((......(((((((((((.((((((....))))))..)).....))))))))).....))(((((.....((.((((((((....)------)).))))))))))))...--...--. ( -28.40)
>DroVir_CAF1 38128 112 - 1
UGGAAUAUGUGGCAUUUUGCAAAGAUGUUGACAUUUUGCGCGCAUAAAAAUGCCAACUUACCGGCCACUGUAUGUGUCCUAUUUUAAA------AUCAGGGCCAUGGCUAAG--AAGCUG
.((......(((((((((((.((((((....))))))..)).....))))))))).....))((((.(((....((........))..------..)))))))..((((...--.)))). ( -30.70)
>DroGri_CAF1 39287 114 - 1
UGGAAUAUGUGGCAUUUUGCAAAGAUGUUGACAUUUUGCGCGCAUAAAAAUGCCAACUUACCGGCCACUGUAUGUGUCCUAUUUUAAA------AUCAGGGCCAUGGCUAAGAGACGCUG
.((......(((((((((((.((((((....))))))..)).....))))))))).....))((((.(((....((........))..------..)))))))..(((........))). ( -29.50)
>DroSim_CAF1 29898 110 - 1
UGGAAUAUGUGGCAUUUUGCAAAGAUGUUGACAUUUUGCGCGCAUAAAAAUCCCAACUUACCGGCCACUGUAUGUGUCCUAUUUUAAA------AUCAGGGCCAUGGCUAAG--CAG--G
.....(((((((((...(((((.....))).))...))).))))))......((..((((((((((.(((....((........))..------..)))))))..)).))))--..)--) ( -26.10)
>DroWil_CAF1 32125 113 - 1
UGGAAUAUGUGGCAUUUUGCAAAGAUGUUGACAUUUUGCGCGCAUAAAAAUGCCAACUUACCGGCCACUGUAUGUGUCCUAUUUUAAAAUCAAAAUCAGGGCCAUGGCUAAG--C-----
.((......(((((((((((.((((((....))))))..)).....))))))))).....))(((((.....((.((((((((((......))))).))))))))))))...--.----- ( -30.40)
>DroMoj_CAF1 38880 112 - 1
UGGAAUAUGUGGCAUUUUGCAAAGAUGUUGACAUUUUGCGCGCAUAAAAAUGCCAACUUACCGGCCACUGUAUGUGUCCUAUUUUAAA------AUCAGGGCCAUGGCUAAG--ACGCUG
.((......(((((((((((.((((((....))))))..)).....))))))))).....))((((.(((....((........))..------..)))))))..(((....--..))). ( -29.70)
>consensus
UGGAAUAUGUGGCAUUUUGCAAAGAUGUUGACAUUUUGCGCGCAUAAAAAUGCCAACUUACCGGCCACUGUAUGUGUCCUAUUUUAAA______AUCAGGGCCAUGGCUAAG__AAG__G
.((......(((((((((((.((((((....))))))..)).....))))))))).....))(((((.....((.(((((.................))))))))))))........... (-26.35 = -26.51 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:16 2006