Locus 377

Sequence ID 2R_DroMel_CAF1
Location 2,359,957 – 2,360,068
Length 111
Max. P 0.911999
window743 window744

overview

Window 3

Location 2,359,957 – 2,360,068
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.75
Mean single sequence MFE -33.26
Consensus MFE -25.72
Energy contribution -24.96
Covariance contribution -0.76
Combinations/Pair 1.16
Mean z-score -1.76
Structure conservation index 0.77
SVM decision value 0.51
SVM RNA-class probability 0.764636
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2359957 111 + 20766785
GUAAGGGUUUUAAUAUGGCCAAAUCGUCGGUCUGGCGUUUAUUAAAUUUUAUUUGUGAGC---------AGCGCACAACAAACUUUUGUGUUGUGCUGUAUGGCUCACUGCAUGUGCAGU
(((...(((((((((..((((.((.....)).))))...)))))))........((((((---------.((((((((((........)))))))).))...)))))).))...)))... ( -33.30)
>DroSec_CAF1 9417 111 + 1
GUAAGGGUUUUAAUAUGGCCAAAUCGCCGGUCUGGCGUUUAUUAAAUUUCAUUUGUGAGC---------AGCGCACAGCAAACUUUUGUGUUGUGCUCUAUGGCUCACUGCAUGUGCAGU
....(((.(((((((..((((.((.....)).))))...))))))).)))....((((((---------((.((((((((........)))))))).))...))))))(((....))).. ( -34.50)
>DroSim_CAF1 9528 111 + 1
GUAAGGGUUUUAAUAUGGCCAAAUCGCCGGUCUGGCGUUUAUUAAAUUUCAUUUGUGAGC---------AGCGCACAGCAAACUUUUGUGUUGUGCUCUAUGGCUCACUGCAUUUGCAGU
....(((.(((((((..((((.((.....)).))))...))))))).)))....((((((---------((.((((((((........)))))))).))...))))))(((....))).. ( -34.50)
>DroEre_CAF1 9551 111 + 1
GUAAGGGUUUUAAUACGGCGAAAUCGCUGCUCUGGCGUUUAUUAAAUUUUAUUUGCGAGC---------AGCGCACAGCAAACUUUUGUAUUGUGCUCUAUGGCUUACUGCAUGUGCAGU
((.(((((..(((((((((.....((((((((..(((..((........))..)))))))---------))))....)).......))))))).)))))...))..(((((....))))) ( -32.41)
>DroYak_CAF1 8938 120 + 1
GUAAGGGUUUUAAUAUGGCGAACUCGCUGGUCUGGCGUUUAUUAAAUUUUAUUUGCGAGCACAGUUUGCAGGGCACAGCAAACUUUUGUAUUGUGCUGUAUGGCUUACUGCAUGUGCAGU
(((((...(((((((.((((....)))).(.....)...))))))).....)))))..(((((...((((((((((((((.((....))....))))))...)))..))))))))))... ( -31.60)
>consensus
GUAAGGGUUUUAAUAUGGCCAAAUCGCCGGUCUGGCGUUUAUUAAAUUUUAUUUGUGAGC_________AGCGCACAGCAAACUUUUGUGUUGUGCUCUAUGGCUCACUGCAUGUGCAGU
(((((.(((......((((......))))....))).)))))..............((((.........((((((..((((....))))..)))))).....))))(((((....))))) (-25.72 = -24.96 +  -0.76)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,359,957 – 2,360,068
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.75
Mean single sequence MFE -27.99
Consensus MFE -20.35
Energy contribution -20.87
Covariance contribution 0.52
Combinations/Pair 1.07
Mean z-score -2.75
Structure conservation index 0.73
SVM decision value 1.08
SVM RNA-class probability 0.911999
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2359957 111 - 20766785
ACUGCACAUGCAGUGAGCCAUACAGCACAACACAAAAGUUUGUUGUGCGCU---------GCUCACAAAUAAAAUUUAAUAAACGCCAGACCGACGAUUUGGCCAUAUUAAAACCCUUAC
..(((....)))((((((......((((((((........))))))))...---------))))))........(((((((...((((((.......))))))..)))))))........ ( -31.90)
>DroSec_CAF1 9417 111 - 1
ACUGCACAUGCAGUGAGCCAUAGAGCACAACACAAAAGUUUGCUGUGCGCU---------GCUCACAAAUGAAAUUUAAUAAACGCCAGACCGGCGAUUUGGCCAUAUUAAAACCCUUAC
..(((....)))((((((...((.(((((.((........)).))))).))---------))))))........(((((((...((((((.......))))))..)))))))........ ( -29.00)
>DroSim_CAF1 9528 111 - 1
ACUGCAAAUGCAGUGAGCCAUAGAGCACAACACAAAAGUUUGCUGUGCGCU---------GCUCACAAAUGAAAUUUAAUAAACGCCAGACCGGCGAUUUGGCCAUAUUAAAACCCUUAC
..(((....)))((((((...((.(((((.((........)).))))).))---------))))))........(((((((...((((((.......))))))..)))))))........ ( -29.00)
>DroEre_CAF1 9551 111 - 1
ACUGCACAUGCAGUAAGCCAUAGAGCACAAUACAAAAGUUUGCUGUGCGCU---------GCUCGCAAAUAAAAUUUAAUAAACGCCAGAGCAGCGAUUUCGCCGUAUUAAAACCCUUAC
(((((....)))))..((......(((((..((....))....)))))(((---------((((((..................))..)))))))......))................. ( -25.67)
>DroYak_CAF1 8938 120 - 1
ACUGCACAUGCAGUAAGCCAUACAGCACAAUACAAAAGUUUGCUGUGCCCUGCAAACUGUGCUCGCAAAUAAAAUUUAAUAAACGCCAGACCAGCGAGUUCGCCAUAUUAAAACCCUUAC
...((((((((((...((...((((((.(((......))))))))))).)))))...)))))............(((((((..(....)....(((....)))..)))))))........ ( -24.40)
>consensus
ACUGCACAUGCAGUGAGCCAUAGAGCACAACACAAAAGUUUGCUGUGCGCU_________GCUCACAAAUAAAAUUUAAUAAACGCCAGACCGGCGAUUUGGCCAUAUUAAAACCCUUAC
..(((....)))((((((......(((((.((........)).)))))............))))))........(((((((...((((((.......))))))..)))))))........ (-20.35 = -20.87 +   0.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:55 2006