Locus 6409

Sequence ID 2L_DroMel_CAF1
Location 17,993,205 – 17,993,341
Length 136
Max. P 0.984905
window10227 window10228

overview

Window 7

Location 17,993,205 – 17,993,311
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.02
Mean single sequence MFE -29.60
Consensus MFE -19.07
Energy contribution -18.60
Covariance contribution -0.47
Combinations/Pair 1.22
Mean z-score -2.54
Structure conservation index 0.64
SVM decision value 1.99
SVM RNA-class probability 0.984905
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17993205 106 + 22407834
UACGGGAAAAG--------GUCCCUG-GCCUCGUG---CGUACAUG--UACAUGCUAAAUUUAUGCGCAAUGAAGAGUGAAAAGCAAUAAGCUCUGCCAAGUUGUGCAUGAAAGGGAAAU
...........--------.((((((-((...(((---((....))--)))..)))...((((((((((((..(((((............))))).....)))))))))))))))))... ( -31.90)
>DroVir_CAF1 269668 87 + 1
---------------------------AUAUCAUG---CGUAU-UG--UAUAUGCUAAAUUUAUGCGCAAUGAAGAGUAAAAAGCAAUAAGCUCUGUUAAGUUGUGCAUAAAAGGGAAAU
---------------------------...((..(---(((((-..--.))))))....((((((((((((..(((((............))))).....))))))))))))...))... ( -22.30)
>DroGri_CAF1 285548 92 + 1
---------------------------ACAUCAUGCUGCGCAU-UGUGUGUAUGCUAAAUUUAUGCGCACUGAAGAGUGAAAAGCAAUAAGCUCUGUUAAGUUGUGCAUAAAAGGGAAAU
---------------------------...((..(((((((..-...))))).))....((((((((((((..(((((............)))))....)).))))))))))...))... ( -24.40)
>DroEre_CAF1 199849 105 + 1
GCCGGGA-AAG--------GUCCCUG-GCCUCUUG---CGUACAUG--UACAUGCUAAAUUUAUGCGCAAUGAAGAGUGAAAAGCAAUAAGCUCUGCCAAGUUGUGCAUGAAAGGGAAAU
((((((.-...--------...))))-))((((((---(((.....--...)))).....(((((((((((..(((((............))))).....)))))))))))))))).... ( -33.90)
>DroYak_CAF1 215127 105 + 1
GUCGUGA-AAG--------GUCCCUG-GCCUCUUG---CGUACAUG--UACAUGCUAAAUUUAUGCGCAAUGAAGAGUGAAAAGCAAUAAGCUCUGCCAAGUUGUGCAUGAAAGGGAAAU
((((..(-.((--------((.....-)))).)..---)).))...--......((...((((((((((((..(((((............))))).....))))))))))))..)).... ( -30.30)
>DroAna_CAF1 199376 114 + 1
UCUGGGAGGGGAGCGACUUAUCGCUGGGACCCCUG---GGUAUG-G--UGUAUGCUGAAUUUAUGCGCAAUGAAGAGUGAAAAGCAAUAAGCUCUGCCAAGUUGUGCAUGAAAGGGAAAU
(((...((((((((((....)))))....))))).---((((((-.--..))))))...((((((((((((..(((((............))))).....))))))))))))..)))... ( -34.80)
>consensus
__CGGGA_AAG________GUCCCUG_GCCUCAUG___CGUACAUG__UACAUGCUAAAUUUAUGCGCAAUGAAGAGUGAAAAGCAAUAAGCUCUGCCAAGUUGUGCAUGAAAGGGAAAU
.............................(((.......(((......)))........((((((((((((..(((((............))))).....)))))))))))).))).... (-19.07 = -18.60 +  -0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

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Window 8

Location 17,993,233 – 17,993,341
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.80
Mean single sequence MFE -28.17
Consensus MFE -20.63
Energy contribution -20.91
Covariance contribution 0.28
Combinations/Pair 1.05
Mean z-score -1.71
Structure conservation index 0.73
SVM decision value 0.22
SVM RNA-class probability 0.640221
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17993233 108 + 22407834
UACAUG--UACAUGCUAAAUUUAUGCGCAAUGAAGAGUGAAAAGCAAUAAGCUCUGCCAAGUUGUGCAUGAAAGGGAAAUUGGCA--UUGAAAUGGGCCCG----U--UGG-CAACCCG-
......--....((((((.((((((((((((..(((((............))))).....)))))))))))).(((..(((....--....)))...))).----)--)))-)).....- ( -30.50)
>DroVir_CAF1 269678 99 + 1
UAU-UG--UAUAUGCUAAAUUUAUGCGCAAUGAAGAGUAAAAAGCAAUAAGCUCUGUUAAGUUGUGCAUAAAAGGGAAAUUGGCA--UUGACAUGGGGCCAGGG----------------
...-((--(..(((((((.((((((((((((..(((((............))))).....)))))))))))).......))))))--)..)))...........---------------- ( -23.80)
>DroGri_CAF1 285561 116 + 1
CAU-UGUGUGUAUGCUAAAUUUAUGCGCACUGAAGAGUGAAAAGCAAUAAGCUCUGUUAAGUUGUGCAUAAAAGGGAAAUAGGCAUAUUGACAUGGGCCCAUCAAC--UGA-CAACUAGC
((.-(((((.(((.((...((((((((((((..(((((............)))))....)).))))))))))..))..))).))))).))..(((....)))....--...-........ ( -26.40)
>DroEre_CAF1 199876 108 + 1
UACAUG--UACAUGCUAAAUUUAUGCGCAAUGAAGAGUGAAAAGCAAUAAGCUCUGCCAAGUUGUGCAUGAAAGGGAAAUUGGCA--UUAAAAUGGGCCCG---A---UGG-CAGCCCG-
......--....(((((..((((((((((((..(((((............))))).....)))))))))))).(((..(((....--....)))...))).---.---)))-)).....- ( -29.70)
>DroYak_CAF1 215154 108 + 1
UACAUG--UACAUGCUAAAUUUAUGCGCAAUGAAGAGUGAAAAGCAAUAAGCUCUGCCAAGUUGUGCAUGAAAGGGAAAUUGGCA--UUGAAAUGGGCCCG---A---UGG-CAACCCG-
......--...........((((((((((((..(((((............))))).....)))))))))))).(((...(((.((--(((.........))---)---)).-)))))).- ( -29.90)
>DroAna_CAF1 199413 113 + 1
UAUG-G--UGUAUGCUGAAUUUAUGCGCAAUGAAGAGUGAAAAGCAAUAAGCUCUGCCAAGUUGUGCAUGAAAGGGAAAUUGGCA--UUGACAUGGGCCCCCG-AAUAUGGAGGAAUCG-
....-(--(((((((..(.((((((((((((..(((((............))))).....)))))))))))).......)..)))--)..))))((..((((.-.....)).))..)).- ( -28.70)
>consensus
UACAUG__UACAUGCUAAAUUUAUGCGCAAUGAAGAGUGAAAAGCAAUAAGCUCUGCCAAGUUGUGCAUGAAAGGGAAAUUGGCA__UUGAAAUGGGCCCG___A___UGG_CAACCCG_
...................((((((((((((..(((((............))))).....)))))))))))).(((.......(.....).......))).................... (-20.63 = -20.91 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:18 2006