Locus 1672

Sequence ID 2R_DroMel_CAF1
Location 6,333,195 – 6,333,289
Length 94
Max. P 0.877566
window2791 window2792

overview

Window 1

Location 6,333,195 – 6,333,289
Length 94
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 78.36
Mean single sequence MFE -34.90
Consensus MFE -21.84
Energy contribution -22.02
Covariance contribution 0.17
Combinations/Pair 1.31
Mean z-score -1.89
Structure conservation index 0.63
SVM decision value 0.90
SVM RNA-class probability 0.877566
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6333195 94 + 20766785
UC--CGC-----CCUUGGAUGGGGAUUAUAAG---GUGGCGAUAAGGAAGAAAGCUGGCGCUUGCUCUCCUGUUCGCUGUCCCUUUCCAUGAUCAGGGUGGUUU
.(--(((-----(((((((.((((((......---..(((((..((((((.((((....)))).)).))))..))))))))))).)))).....)))))))... ( -40.50)
>DroSim_CAF1 3226 94 + 1
UC--CGC-----UCUUGGAUGGGGAUUAUAAG---GUGGCGAUAAGGAAGAAAGCUGUUGCUUGCCCUCCUGUUCGCUGUCCCUUUCCAUGAUCAGUGUGGUUU
.(--(((-----.((((((.((((((......---..(((((..((((.(.((((....))))..).))))..))))))))))).)))).....)).))))... ( -34.20)
>DroEre_CAF1 3244 94 + 1
UC--CGG-----UCUUGGAUGGGGAUUAUAGG---GUGGCGAUAAGGAAGAAAGCUGGUGCUUGCCCUCCUGUUCGCUGUCCCUUUCCAUGAUCAGUGUGGUUU
..--.((-----((.((((.((((((......---..(((((..((((.(.((((....))))..).))))..))))))))))).)))).)))).......... ( -35.10)
>DroYak_CAF1 3258 94 + 1
UC--UGC-----UCUAGGAUGGGGAUUAUAGG---GUGGCGAUAAGGAAGAAAGCUGGUGCUUGCCCUCCUGUUCGCUGUCCCUUUCCAUGAUCAGUGUGGUUU
.(--..(-----.((..(((.((((....(((---(((((((..((((.(.((((....))))..).))))..)))))).)))).))).).))))).)..)... ( -31.90)
>DroMoj_CAF1 3222 102 + 1
UCUCUGGAGUGUACAUGGAUG--GAUUACUUUGCUCUGGCGACAGGGAGCAGAGCUGGCGUUUAUUCUCCUGCUCGUUGUCUCGCUCCAUGAUGAGAGUGGUCU
(((.((.......)).))).(--(((((((((...(((....)))(((((.((((.((.(......).)).))))(......))))))......)))))))))) ( -31.90)
>DroAna_CAF1 4478 94 + 1
UC--GGG-----UCUGGUGUUGGGCUUGUAGG---GCGGGGAAAGCGAGGACAGCUGGUGCUUGUUCUCCUGCUCGCUAUCCCGCUCCAUGAUCAGAGUGGUCU
.(--.(.-----((((((..(((((..(...(---(((((...((.(((((((((....)).))))))))).))))))..)..)).)))..)))))).).)... ( -35.80)
>consensus
UC__CGC_____UCUUGGAUGGGGAUUAUAGG___GUGGCGAUAAGGAAGAAAGCUGGUGCUUGCCCUCCUGUUCGCUGUCCCUUUCCAUGAUCAGUGUGGUUU
................(((.((((((...........(((((..((((...((((....))))....))))..))))))))))).)))..((((.....)))). (-21.84 = -22.02 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 6,333,195 – 6,333,289
Length 94
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 78.36
Mean single sequence MFE -28.60
Consensus MFE -11.59
Energy contribution -13.93
Covariance contribution 2.34
Combinations/Pair 1.09
Mean z-score -2.64
Structure conservation index 0.41
SVM decision value 0.69
SVM RNA-class probability 0.823387
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6333195 94 - 20766785
AAACCACCCUGAUCAUGGAAAGGGACAGCGAACAGGAGAGCAAGCGCCAGCUUUCUUCCUUAUCGCCAC---CUUAUAAUCCCCAUCCAAGG-----GCG--GA
...((.((((.....((((..((((..((((..((((.((.((((....)))).))))))..))))...---.......))))..)))))))-----).)--). ( -31.20)
>DroSim_CAF1 3226 94 - 1
AAACCACACUGAUCAUGGAAAGGGACAGCGAACAGGAGGGCAAGCAACAGCUUUCUUCCUUAUCGCCAC---CUUAUAAUCCCCAUCCAAGA-----GCG--GA
........(((.((.((((..((((..((((..(((((((.((((....)))))))))))..))))...---.......))))..)))).))-----.))--). ( -30.40)
>DroEre_CAF1 3244 94 - 1
AAACCACACUGAUCAUGGAAAGGGACAGCGAACAGGAGGGCAAGCACCAGCUUUCUUCCUUAUCGCCAC---CCUAUAAUCCCCAUCCAAGA-----CCG--GA
........(((.((.((((..((((..((((..(((((((.((((....)))))))))))..))))...---.......))))..)))).))-----.))--). ( -30.40)
>DroYak_CAF1 3258 94 - 1
AAACCACACUGAUCAUGGAAAGGGACAGCGAACAGGAGGGCAAGCACCAGCUUUCUUCCUUAUCGCCAC---CCUAUAAUCCCCAUCCUAGA-----GCA--GA
........(((.((..(((..((((..((((..(((((((.((((....)))))))))))..))))...---.......))))..)))..))-----.))--). ( -28.70)
>DroMoj_CAF1 3222 102 - 1
AGACCACUCUCAUCAUGGAGCGAGACAACGAGCAGGAGAAUAAACGCCAGCUCUGCUCCCUGUCGCCAGAGCAAAGUAAUC--CAUCCAUGUACACUCCAGAGA
......((((...((((((..((((((..((((((.((............))))))))..))))((....)).......))--..))))))........)))). ( -25.20)
>DroAna_CAF1 4478 94 - 1
AGACCACUCUGAUCAUGGAGCGGGAUAGCGAGCAGGAGAACAAGCACCAGCUGUCCUCGCUUUCCCCGC---CCUACAAGCCCAACACCAGA-----CCC--GA
.......((((....(((.((((((.((((((.....((...(((....))).)))))))).)))).(.---....)..)))))....))))-----...--.. ( -25.70)
>consensus
AAACCACACUGAUCAUGGAAAGGGACAGCGAACAGGAGAGCAAGCACCAGCUUUCUUCCUUAUCGCCAC___CCUAUAAUCCCCAUCCAAGA_____CCG__GA
............((.((((..((((..((((..(((((...((((....))))..)))))..)))).............))))..)))).))............ (-11.59 = -13.93 +   2.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:19 2006