Locus 4130

Sequence ID 2R_DroMel_CAF1
Location 13,575,195 – 13,575,328
Length 133
Max. P 0.940060
window6650 window6651

overview

Window 0

Location 13,575,195 – 13,575,293
Length 98
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 73.59
Mean single sequence MFE -30.76
Consensus MFE -15.82
Energy contribution -17.32
Covariance contribution 1.50
Combinations/Pair 1.06
Mean z-score -2.06
Structure conservation index 0.51
SVM decision value 1.31
SVM RNA-class probability 0.940060
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13575195 98 - 20766785
---GG-GUGCCGCAUCCAGGGGCAAUUAAACGCCCACCGAAAAGCCGAUGGUGCUGUUCG---------UACUGUUGGUUCUGCUGGUGGGGCAUAAAUCACACAAAACUA
---..-(((((.((.((((((((........)))).......((((((((((((.....)---------)))))))))))...)))))).)))))................ ( -38.70)
>DroSec_CAF1 122165 93 - 1
---GG-GUGCCGCAUCCACGGGCAAUUAAGCGCCCACCGAAAAGCCGAUGGUACUGUUGG---------UACUGUUCGUUCUGCUG-----GCAUAAAUCACACAAAACUA
---..-((((((((.....((((........))))..((((..((((((......)))))---------)....))))...))).)-----))))................ ( -26.90)
>DroSim_CAF1 126670 89 - 1
---GG-GUGCCGCAUCCAGGGGCAAUUAAACGCCCACCGAAAAGUGGAUGGUAC------------------UGUUCGUUCUGCUGGUGGGGCAUAAAUCACACAAAACUA
---..-(((((.((.((((((((........))))..((((.((((.....)))------------------).)))).....)))))).)))))................ ( -29.90)
>DroEre_CAF1 124034 80 - 1
---GG-GUGCCGCAUCCAGGGGCAAUUAAACGCCCACCGAAAUGCCGAUGGUGCU---------------------------GUUGGUGGGGCAUAAAUCACACAAAACUA
---..-(((((.((.((((.((((.........(((.((......)).)))))))---------------------------.)))))).)))))................ ( -24.50)
>DroYak_CAF1 127911 107 - 1
---GG-GUGCCGCAUCCAGGGGCAAUUAAACGCCCACCGAAAUACCGAUGGUGCUGUUGGUGAUGAUGGUGCUGUUGGUGCUGUUGGUGGGGCAUAAAUCACACAAAACUA
---..-(((((.(((((((((((........)))).......(((((((((..(((((......)))))..))))))))))))..)))).)))))................ ( -40.80)
>DroAna_CAF1 121392 92 - 1
AUAAACUUCCAACAUCCAGGGGCAAUCAAACGCCCACCGGAUUUC----GGUGCGGUACA---------CACA--UGCC----UCGGCGGAGCAUAAAUCACACAAAACUA
..............(((.((((((.......((((((((.....)----)))).)))...---------....--))))----))...))).................... ( -23.74)
>consensus
___GG_GUGCCGCAUCCAGGGGCAAUUAAACGCCCACCGAAAAGCCGAUGGUGCUGUU_G_________UACUGUUGGUUCUGCUGGUGGGGCAUAAAUCACACAAAACUA
......(((((.((.((((((((........))))(((...........)))...............................)))))).)))))................ (-15.82 = -17.32 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

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Window 1

Location 13,575,226 – 13,575,328
Length 102
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.02
Mean single sequence MFE -37.68
Consensus MFE -22.32
Energy contribution -23.27
Covariance contribution 0.95
Combinations/Pair 1.21
Mean z-score -1.68
Structure conservation index 0.59
SVM decision value 0.91
SVM RNA-class probability 0.878794
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13575226 102 + 20766785
AACCAACAGUA---------CGAACAGCACCAUCGGCUUUUCGGUGGGCGUUUAAUUGCCCCUGGAUGCGGCAC-CC--------AAUGUGGCUGGGAAUGCGGCAGUGGAUGUGCGUCA
...........---------.((...((((.(((.((..(((((.(((((......))))))))))(((.((((-((--------(.......))))..))).))))).))))))).)). ( -39.20)
>DroSec_CAF1 122191 102 + 1
AACGAACAGUA---------CCAACAGUACCAUCGGCUUUUCGGUGGGCGCUUAAUUGCCCGUGGAUGCGGCAC-CC--------AAUGUGGCUGGGAAUGCGGCGGUGGAUGUGCGUCA
.(((.(((.((---------((.......((((.(((..((.(((....))).))..))).))))..((.((((-((--------(.......))))..))).))))))..))).))).. ( -34.60)
>DroSim_CAF1 126701 93 + 1
AACGAACA------------------GUACCAUCCACUUUUCGGUGGGCGUUUAAUUGCCCCUGGAUGCGGCAC-CC--------AAUGUGGCUGGGAAUGCGGCGGUGGAUGUGCGUCA
...((...------------------((((.(((((((.(((((.(((((......)))))))))).((.((((-((--------(.......))))..))).))))))))))))).)). ( -40.90)
>DroEre_CAF1 124063 86 + 1
-------------------------AGCACCAUCGGCAUUUCGGUGGGCGUUUAAUUGCCCCUGGAUGCGGCAC-CC--------AAUGUGGCUGGGAAUGCGGCGGUGGAUGUGCGUCA
-------------------------.((((.(((.((..(((((.(((((......))))))))))(((.((((-((--------(.......))))..))).))))).))))))).... ( -37.50)
>DroYak_CAF1 127942 111 + 1
CACCAACAGCACCAUCAUCACCAACAGCACCAUCGGUAUUUCGGUGGGCGUUUAAUUGCCCCUGGAUGCGGCAC-CC--------AAUGUGGCUGGGAAUGCGGCGGUGGAUGUGCGUCA
........((((.(((..((((.................(((((.(((((......)))))))))).((.((((-((--------(.......))))..))).))))))))))))).... ( -38.80)
>DroAna_CAF1 121420 98 + 1
-GGCA--UGUG---------UGUACCGCACC----GAAAUCCGGUGGGCGUUUGAUUGCCCCUGGAUGUUGGAAGUUUAUAUAUAAGCAUGGCUGGGAAUG------UGAAUUUGCGUCA
-.((.--((((---------((((.....((----((.((((((.(((((......))))))))))).)))).....)))))))).)).((((.(.((((.------...)))).))))) ( -35.10)
>consensus
AACCAACAGUA_________C_AACAGCACCAUCGGCAUUUCGGUGGGCGUUUAAUUGCCCCUGGAUGCGGCAC_CC________AAUGUGGCUGGGAAUGCGGCGGUGGAUGUGCGUCA
..........................((((.(((.((..(((((.(((((......)))))))))).....................(((.((.......)).))))).))))))).... (-22.32 = -23.27 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:33 2006