Locus 6705

Sequence ID 3R_DroMel_CAF1
Location 17,638,512 – 17,638,639
Length 127
Max. P 0.996511
window10897 window10898

overview

Window 7

Location 17,638,512 – 17,638,602
Length 90
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 75.81
Mean single sequence MFE -20.92
Consensus MFE -10.34
Energy contribution -11.15
Covariance contribution 0.81
Combinations/Pair 1.15
Mean z-score -2.00
Structure conservation index 0.49
SVM decision value 0.66
SVM RNA-class probability 0.814759
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17638512 90 - 27905053
CAC----------CACCCGCAUGAUGCGUUGGAAAACUGACGAUUAUGGGGGAGCUGGGCUG--CUAGACCACUUAAUUACUUUUCAAUUUAAAUCAAAUUA
...----------..(((.((((((.(((..(....)..))))))))).)))(((......)--)).................................... ( -21.40)
>DroSec_CAF1 33390 90 - 1
CUC----------CACCCGCAUGAUGCGUUGGAAAACUGACGAUUAUGUGGGAGAUGGGCUG--CUAGACCACUUAAUUACUUUUCAAUUUAAAUCAAAUUA
...----------..((((((((((.(((..(....)..)))))))))))))((.(((....--.....)))))............................ ( -22.80)
>DroSim_CAF1 33207 90 - 1
CUC----------CACCCGCAUGAUGCGUUGGAAAACUGACGAUUAUGUGGGAGAUGGGCUG--CUAGACCACUUAAUUACUUUUCAAUUUAAAUCAAAUUA
...----------..((((((((((.(((..(....)..)))))))))))))((.(((....--.....)))))............................ ( -22.80)
>DroEre_CAF1 35251 82 - 1
CAG----------CACCCGCAUAAUGCGUUCCAAAAGUGACGAUUAUGGGGGAGAUGG----------ACCACUUAAUUACUUUUCAAUUUAAGUCAAAUUA
((.----------(.(((.((((((.(((..(....)..))))))))).))).).)).----------...((((((............))))))....... ( -18.40)
>DroYak_CAF1 38148 93 - 1
CAC-------CAUCACCCGCAUAAUGCGUUCAAAAACUGACGAUUAUGGGGGAGAUGGACUG--ACAGACCACUUAAUUACUUUUCAAUUUAAAUCAAAUUA
..(-------((((.(((.((((((.((((........)))))))))).))).)))))....--...................................... ( -23.80)
>DroAna_CAF1 41862 94 - 1
CAGGAAAAUACGCUUCCCGCAUAAAGCUUUACAG---GGAGAACUACUCCACA-----GCUACUCCACAACACUUAAUUAGUUUUCCGUUUAAAUCAAAUAU
..(((((((..((.....))....((((......---((((.....))))..)-----)))...................)))))))............... ( -16.30)
>consensus
CAC__________CACCCGCAUAAUGCGUUGGAAAACUGACGAUUAUGGGGGAGAUGGGCUG__CUAGACCACUUAAUUACUUUUCAAUUUAAAUCAAAUUA
...............(((.((((((.((((........)))))))))).))).................................................. (-10.34 = -11.15 +   0.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,638,534 – 17,638,639
Length 105
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 78.91
Mean single sequence MFE -32.96
Consensus MFE -20.29
Energy contribution -21.16
Covariance contribution 0.87
Combinations/Pair 1.07
Mean z-score -2.90
Structure conservation index 0.62
SVM decision value 2.71
SVM RNA-class probability 0.996511
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17638534 105 - 27905053
AAUGCCCGCUGAA-AUGGGUGGG-GAAAAACUAGGAGAACAC---CACCCGCAUGAUGCGUUGGAAAACUGACGAUUAUGGGGGAGCUGGGCUGCUAGACCACUUAAUUA
..(.((((((...-...))))))-.)....((((.((..((.---(.(((.((((((.(((..(....)..))))))))).))).).))..)).))))............ ( -38.90)
>DroSec_CAF1 33412 106 - 1
AAUGCCCGCUGAA-GUGGGUGGGGGGAAAACUAGGAGAGCUC---CACCCGCAUGAUGCGUUGGAAAACUGACGAUUAUGUGGGAGAUGGGCUGCUAGACCACUUAAUUA
...((((((....-))))))(((((.....((((...(((.(---((((((((((((.(((..(....)..)))))))))))))...)))))).)))).)).)))..... ( -40.50)
>DroSim_CAF1 33229 106 - 1
AAUGCCCGCUGAA-GUGGGUGGGGGAAAAACUAGGAGAGCUC---CACCCGCAUGAUGCGUUGGAAAACUGACGAUUAUGUGGGAGAUGGGCUGCUAGACCACUUAAUUA
...((((((....-))))))(((((.....((((...(((.(---((((((((((((.(((..(....)..)))))))))))))...)))))).)))).)).)))..... ( -39.40)
>DroEre_CAF1 35273 79 - 1
AA-------------UG-------UGAAAACUAGGAGCGCAG---CACCCGCAUAAUGCGUUCCAAAAGUGACGAUUAUGGGGGAGAUGG--------ACCACUUAAUUA
..-------------.(-------(....))..((..(.((.---(.(((.((((((.(((..(....)..))))))))).))).).)))--------.))......... ( -19.20)
>DroYak_CAF1 38170 98 - 1
AAUG-----UGAAAAUG-------UGAAAACUAGGAGAGCACCAUCACCCGCAUAAUGCGUUCAAAAACUGACGAUUAUGGGGGAGAUGGACUGACAGACCACUUAAUUA
...(-----((.....(-------(....))..........(((((.(((.((((((.((((........)))))))))).))).)))))..........)))....... ( -26.80)
>consensus
AAUGCCCGCUGAA_AUGGGUGGG_GGAAAACUAGGAGAGCAC___CACCCGCAUGAUGCGUUGGAAAACUGACGAUUAUGGGGGAGAUGGGCUGCUAGACCACUUAAUUA
....((((((.......))))))........((((............(((.((((((.((((((....)))))))))))).)))...(((.........))))))).... (-20.29 = -21.16 +   0.87)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:01 2006