Locus 1926

Sequence ID 3R_DroMel_CAF1
Location 5,445,963 – 5,446,141
Length 178
Max. P 0.816691
window3167 window3168

overview

Window 7

Location 5,445,963 – 5,446,069
Length 106
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.86
Mean single sequence MFE -24.00
Consensus MFE -19.63
Energy contribution -18.97
Covariance contribution -0.66
Combinations/Pair 1.12
Mean z-score -2.33
Structure conservation index 0.82
SVM decision value 0.67
SVM RNA-class probability 0.816691
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5445963 106 + 27905053
CACUUGGCCGUAAAUUACCAUAAAUUCCAUUCCGCAGAACAGUUUGAUAUUUAUAAUUUUAAAUCACGAGCACGACUGUCUGCAACU--------------UUAUAGUUGGCCAUAAAAA
....(((((........................(((((.(((((((..(((((......)))))......)).))))))))))((((--------------....)))))))))...... ( -23.40)
>DroEre_CAF1 33114 120 + 1
CACUUGGCCGUAAAUUACCAUAAAUUCCAUUCCGCGGAACAGUUUAAUAUUUAUAAUUCUAAAUCACGAGCACGACUGUCUGCAGCUUUGUAUGUACUCGUACAUAGUUGGCCAUAAAAA
....(((((........................(((((.((((.....(((((......)))))..((....)))))))))))((((.((((((....)))))).)))))))))...... ( -27.90)
>DroYak_CAF1 33771 106 + 1
CACUUGGCCGUAAAUUACCAUAAAUUCCAUUCCGCAGAACAGUUUAAUAUUUAUAAUUCUAAAUCACGAGCACGACUGUCUGCAGCU--------------AUAUGGUUGGCCAUAAAAA
....((((((......(((((((((...)))..(((((.((((.....(((((......)))))..((....)))))))))))....--------------.))))))))))))...... ( -20.70)
>consensus
CACUUGGCCGUAAAUUACCAUAAAUUCCAUUCCGCAGAACAGUUUAAUAUUUAUAAUUCUAAAUCACGAGCACGACUGUCUGCAGCU______________AUAUAGUUGGCCAUAAAAA
....(((((........................(((((.((((.....(((((......)))))..((....)))))))))))((((..................)))))))))...... (-19.63 = -18.97 +  -0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 5,446,043 – 5,446,141
Length 98
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 80.53
Mean single sequence MFE -28.95
Consensus MFE -25.07
Energy contribution -25.30
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -0.95
Structure conservation index 0.87
SVM decision value 0.09
SVM RNA-class probability 0.577216
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5446043 98 - 27905053
ACGAGGUGUUUUAGCCAA----CUGCAGGCGCGUUCUGGCUCUAAUCUAAUC---GCUGUGGCCAUUUUGCGGUUCUGAUUUUUAUGGCCAACUAUAA--------------AGUUGCA
..((...(((..(((((.----.(((....)))...)))))..)))....))---((...((((((....((....))......))))))((((....--------------)))))). ( -22.00)
>DroEre_CAF1 33194 115 - 1
ACGAGGUGUUUUAGCCAA----CUGCAGGCGCUUUCUGGCUGUAAUCUAAUCUAAGCUGUGGCUAUUUUGCGGCUCUGAUUUUUAUGGCCAACUAUGUACGAGUACAUACAAAGCUGCA
....(((......)))..----......(((((((.(((((((((...((((..(((((..(.....)..)))))..)))).)))))))))..((((((....)))))).))))).)). ( -36.50)
>DroYak_CAF1 33851 105 - 1
UCGAGGUGUUUUGGCCAACUAACUGCAAGCGAGUUCUGGCUGUAAUCUAAUCUAAGCUGUGGCUAUUUUGCGGUUCUGAUUUUUAUGGCCAACCAUAU--------------AGCUGCA
....(((......)))........(((.((......(((((((((...((((..(((((..(.....)..)))))..)))).))))))))).......--------------.))))). ( -28.34)
>consensus
ACGAGGUGUUUUAGCCAA____CUGCAGGCGCGUUCUGGCUGUAAUCUAAUCUAAGCUGUGGCUAUUUUGCGGUUCUGAUUUUUAUGGCCAACUAUAU______________AGCUGCA
....(((......)))........(((.(((....)(((((((((...((((..(((((..(.....)..)))))..)))).)))))))))......................))))). (-25.07 = -25.30 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:03 2006