Locus 7808

Sequence ID 3L_DroMel_CAF1
Location 20,887,479 – 20,887,580
Length 101
Max. P 0.976070
window12705 window12706

overview

Window 5

Location 20,887,479 – 20,887,580
Length 101
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 77.21
Mean single sequence MFE -30.90
Consensus MFE -17.41
Energy contribution -17.60
Covariance contribution 0.19
Combinations/Pair 1.11
Mean z-score -1.62
Structure conservation index 0.56
SVM decision value 0.13
SVM RNA-class probability 0.597388
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20887479 101 + 23771897
GC-GAGAAACUGGAGACCACCUGGCGUCUGCAGACCCCGCUAAUUGCAUUGUGGGUACGCA-G--GGCACAAAGGA-AAGU--UGCCAGGUGAUGAUAUCAGCAUGAU
((-..((....(....)((((((((((((((.(..(((((..........)))))..))))-.--)))((......-..))--.))))))))......)).))..... ( -31.70)
>DroVir_CAF1 178783 91 + 1
--------AGAGGAGACCACCUGGCGUCAGCGGA---GGCUAAUUGCAUUGAAGGCAACGC-U--GGCACAAAGAA-AUGU--UGCCAGGUGAUGAUAUCAGCAUGAU
--------.(((....)(((((((((((((((..---.(((............)))..)))-)--)))(((.....-.)))--.))))))))......))........ ( -32.40)
>DroGri_CAF1 163740 102 + 1
GAUGGAGAAGAGGAGACCACCUGGCGUCUGCAGA---CGCUAAUUGCAUUGAAGGCAACA--GCAGACACAAAGAA-AUGUUUUGCCAGGUGAUGAUAUCAGCAUGAU
((((.......(....)((((((((((((((...---.((.....))......(....).--))))))(((.....-.)))...))))))))....))))........ ( -33.60)
>DroWil_CAF1 196278 101 + 1
GA-GAGUAA--AGAGACCACCUGGCGUUUGCAGAGAACACUAAUUGCAUUGAUGGUCCGUGUG--GGCACAAAGGAAAAGU--UACCAGGUGAUGAUAUCAGCAUGAU
..-......--......(((((((....((((.((....))...)))).((((..(((...((--....))..)))...))--)))))))))................ ( -21.50)
>DroMoj_CAF1 173482 101 + 1
GACGUAGCAGAGGAGACCACCUGGCGUUCGCGGA---GGCUAAUUGCAUUGAAGGCAACUC-UCAGGCACAAAGAA-AUGC--UGCCAGGUGAUGAUAUCAGCAUGAU
..(((.((.(((....)(((((((((...(((..---..((...(((.((((((....)).-)))))))...))..-.)))--)))))))))......)).))))).. ( -31.50)
>DroAna_CAF1 143443 101 + 1
GG-CGAAGCCCGAAGACCACCUGGCGGCCGCAGAGCCCGCUAAUUGCAUUGUGGGUACGCA-G--GGCACAAAGGA-AAGU--UGCCAGGUGAUGAUAUCAGCAUGAU
((-(...))).......(((((((((((..(.(.((((((.....))..((((....))))-)--))).)....).-..))--)))))))))................ ( -34.70)
>consensus
GA_GAAAAAGAGGAGACCACCUGGCGUCUGCAGA___CGCUAAUUGCAUUGAAGGCAACCA_G__GGCACAAAGAA_AAGU__UGCCAGGUGAUGAUAUCAGCAUGAU
.................(((((((((...((.......((.....)).(((...((..........)).))).......))..)))))))))................ (-17.41 = -17.60 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

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Window 6

Location 20,887,479 – 20,887,580
Length 101
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 77.21
Mean single sequence MFE -29.70
Consensus MFE -18.24
Energy contribution -18.16
Covariance contribution -0.08
Combinations/Pair 1.19
Mean z-score -2.40
Structure conservation index 0.61
SVM decision value 1.76
SVM RNA-class probability 0.976070
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20887479 101 - 23771897
AUCAUGCUGAUAUCAUCACCUGGCA--ACUU-UCCUUUGUGCC--C-UGCGUACCCACAAUGCAAUUAGCGGGGUCUGCAGACGCCAGGUGGUCUCCAGUUUCUC-GC
.....((((.....((((((((((.--((..-......))...--(-((((.((((....(((.....))))))).)))))..))))))))))...)))).....-.. ( -34.50)
>DroVir_CAF1 178783 91 - 1
AUCAUGCUGAUAUCAUCACCUGGCA--ACAU-UUCUUUGUGCC--A-GCGUUGCCUUCAAUGCAAUUAGCC---UCCGCUGACGCCAGGUGGUCUCCUCU--------
..............((((((((((.--(((.-.....)))...--.-((((((....))))))..(((((.---...))))).)))))))))).......-------- ( -28.20)
>DroGri_CAF1 163740 102 - 1
AUCAUGCUGAUAUCAUCACCUGGCAAAACAU-UUCUUUGUGUCUGC--UGUUGCCUUCAAUGCAAUUAGCG---UCUGCAGACGCCAGGUGGUCUCCUCUUCUCCAUC
...(((..((....((((((((((...(((.-.....)))((((((--.(((((.......))))).....---...)))))))))))))))).......))..))). ( -31.60)
>DroWil_CAF1 196278 101 - 1
AUCAUGCUGAUAUCAUCACCUGGUA--ACUUUUCCUUUGUGCC--CACACGGACCAUCAAUGCAAUUAGUGUUCUCUGCAAACGCCAGGUGGUCUCU--UUACUC-UC
..............((((((((((.--........((((((..--..)))))).......((((...((....)).))))...))))))))))....--......-.. ( -21.50)
>DroMoj_CAF1 173482 101 - 1
AUCAUGCUGAUAUCAUCACCUGGCA--GCAU-UUCUUUGUGCCUGA-GAGUUGCCUUCAAUGCAAUUAGCC---UCCGCGAACGCCAGGUGGUCUCCUCUGCUACGUC
.....((.((....((((((((((.--((((-......))))..((-(((((((.......))))))...)---)).......))))))))))....)).))...... ( -29.90)
>DroAna_CAF1 143443 101 - 1
AUCAUGCUGAUAUCAUCACCUGGCA--ACUU-UCCUUUGUGCC--C-UGCGUACCCACAAUGCAAUUAGCGGGCUCUGCGGCCGCCAGGUGGUCUUCGGGCUUCG-CC
.....((.........((((((((.--....-.....(((...--.-(((((.......)))))....)))((((....))))))))))))(((....)))...)-). ( -32.50)
>consensus
AUCAUGCUGAUAUCAUCACCUGGCA__ACAU_UCCUUUGUGCC__C_GACGUACCUUCAAUGCAAUUAGCG___UCUGCAGACGCCAGGUGGUCUCCUCUUCUCC_UC
..............((((((((((...............(((...................)))....(((.....)))....))))))))))............... (-18.24 = -18.16 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:57:26 2006