Locus 1128

Sequence ID 3R_DroMel_CAF1
Location 3,391,507 – 3,391,705
Length 198
Max. P 0.984603
window1848 window1849 window1850 window1851 window1852

overview

Window 8

Location 3,391,507 – 3,391,627
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.61
Mean single sequence MFE -28.17
Consensus MFE -25.63
Energy contribution -25.63
Covariance contribution 0.00
Combinations/Pair 1.09
Mean z-score -1.93
Structure conservation index 0.91
SVM decision value 0.46
SVM RNA-class probability 0.746585
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3391507 120 + 27905053
UACUUACAUAUUUAGAUUUCUGGAUAUUUUAAGUGUACGCUUUAUGGUCAUGCAGAAGGUUGGAUGAAUUCGUUUCUCGCCUUCGCCGUCUAAUGACAAUCAAAUUAGCGCCAUUUUCCU
((((((.((((((((....))))))))..))))))..((((...((((...((.((((((.(((..........))).)))))))).(((....))).))))....)))).......... ( -28.90)
>DroSim_CAF1 368 120 + 1
UACUUAUAUAUUAAGAUUUCUGCAUAUUUUAAGUGUACGCAUUAUGGUCAUGCAGAAGGUUGGAUGAAUUUGUUUCUCGCCUUCGCCGUCUAAUGACAAUCAAAUUAGCGCCAUUUUCCU
..((((.....))))..(((((((((((...((((....))))..))).))))))))((.(((...((((((......((....)).(((....)))...))))))....)))....)). ( -24.20)
>DroYak_CAF1 4081 120 + 1
UACUUUUAUAUUUAGAGUUCUAAAUAUUUUAAGUGUACGCAUUAUGUUCAUGCAGAAGGUUGGAUGAAUUUGUUUCUCGCCUUCGCUGUCUAAUGACAAUCAAAUUAGCGGCAUUUUCCU
(((((..((((((((....))))))))...)))))...((((.......)))).((((((.(((..........))).))))))((((.(((((.........)))))))))........ ( -31.40)
>consensus
UACUUAUAUAUUUAGAUUUCUGAAUAUUUUAAGUGUACGCAUUAUGGUCAUGCAGAAGGUUGGAUGAAUUUGUUUCUCGCCUUCGCCGUCUAAUGACAAUCAAAUUAGCGCCAUUUUCCU
(((((..((((((((....))))))))...)))))........(((((...((.((((((.(((..........))).))))))...(((....)))..........)))))))...... (-25.63 = -25.63 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 3,391,547 – 3,391,667
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -27.71
Consensus MFE -26.70
Energy contribution -26.81
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.70
Structure conservation index 0.96
SVM decision value 0.38
SVM RNA-class probability 0.711190
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3391547 120 + 27905053
UUUAUGGUCAUGCAGAAGGUUGGAUGAAUUCGUUUCUCGCCUUCGCCGUCUAAUGACAAUCAAAUUAGCGCCAUUUUCCUUGGCGCCAAAAACUUUUUCCAUUAAACGUGCAAUUUUUUC
..........((((((((((.(((..........))).))))))..(((.(((((............((((((.......)))))).............))))).)))))))........ ( -29.61)
>DroSim_CAF1 408 120 + 1
AUUAUGGUCAUGCAGAAGGUUGGAUGAAUUUGUUUCUCGCCUUCGCCGUCUAAUGACAAUCAAAUUAGCGCCAUUUUCCUUGGCGCCAAAAACUUUUUCCAUUAAACGUGCAAUUUUUUC
..........((((((((((.(((..........))).))))))..(((.(((((............((((((.......)))))).............))))).)))))))........ ( -29.61)
>DroYak_CAF1 4121 120 + 1
AUUAUGUUCAUGCAGAAGGUUGGAUGAAUUUGUUUCUCGCCUUCGCUGUCUAAUGACAAUCAAAUUAGCGGCAUUUUCCUUGGCGCCAAAAACUUUUUCCAUUAAACGUGCAAUUUUUUC
..........((((((((((.(((..........))).))))))..((((....)))).........(((.((.......)).)))......................))))........ ( -23.90)
>consensus
AUUAUGGUCAUGCAGAAGGUUGGAUGAAUUUGUUUCUCGCCUUCGCCGUCUAAUGACAAUCAAAUUAGCGCCAUUUUCCUUGGCGCCAAAAACUUUUUCCAUUAAACGUGCAAUUUUUUC
..........((((((((((.(((..........))).))))))..(((.(((((............((((((.......)))))).............))))).)))))))........ (-26.70 = -26.81 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 3,391,547 – 3,391,667
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -32.80
Consensus MFE -31.43
Energy contribution -32.10
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.91
Structure conservation index 0.96
SVM decision value 1.88
SVM RNA-class probability 0.981272
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3391547 120 - 27905053
GAAAAAAUUGCACGUUUAAUGGAAAAAGUUUUUGGCGCCAAGGAAAAUGGCGCUAAUUUGAUUGUCAUUAGACGGCGAAGGCGAGAAACGAAUUCAUCCAACCUUCUGCAUGACCAUAAA
........((((((((((((((....((((.(((((((((.......)))))))))...)))).))))))))))..(((((.(((((.....))).))...))))))))).......... ( -35.90)
>DroSim_CAF1 408 120 - 1
GAAAAAAUUGCACGUUUAAUGGAAAAAGUUUUUGGCGCCAAGGAAAAUGGCGCUAAUUUGAUUGUCAUUAGACGGCGAAGGCGAGAAACAAAUUCAUCCAACCUUCUGCAUGACCAUAAU
........((((((((((((((....((((.(((((((((.......)))))))))...)))).))))))))))..(((((.(((((.....))).))...))))))))).......... ( -35.90)
>DroYak_CAF1 4121 120 - 1
GAAAAAAUUGCACGUUUAAUGGAAAAAGUUUUUGGCGCCAAGGAAAAUGCCGCUAAUUUGAUUGUCAUUAGACAGCGAAGGCGAGAAACAAAUUCAUCCAACCUUCUGCAUGAACAUAAU
........((((.(((((((((....((((.((((((.((.......)).))))))...)))).)))))))))...(((((.(((((.....))).))...))))))))).......... ( -26.60)
>consensus
GAAAAAAUUGCACGUUUAAUGGAAAAAGUUUUUGGCGCCAAGGAAAAUGGCGCUAAUUUGAUUGUCAUUAGACGGCGAAGGCGAGAAACAAAUUCAUCCAACCUUCUGCAUGACCAUAAU
........((((((((((((((....((((.(((((((((.......)))))))))...)))).))))))))))..(((((.(((((.....))).))...))))))))).......... (-31.43 = -32.10 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 3,391,587 – 3,391,705
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.62
Mean single sequence MFE -16.74
Consensus MFE -15.93
Energy contribution -16.04
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -2.27
Structure conservation index 0.95
SVM decision value 1.47
SVM RNA-class probability 0.956570
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3391587 118 + 27905053
CUUCGCCGUCUAAUGACAAUCAAAUUAGCGCCAUUUUCCUUGGCGCCAAAAACUUUUUCCAUUAAACGUGCAAUUUUUUCUUUGUAUACAUUUUU--UUUUUAACUUGCCUCAAUAAAUU
....(((((.(((((............((((((.......)))))).............))))).))).))........................--....................... ( -19.01)
>DroSim_CAF1 448 120 + 1
CUUCGCCGUCUAAUGACAAUCAAAUUAGCGCCAUUUUCCUUGGCGCCAAAAACUUUUUCCAUUAAACGUGCAAUUUUUUCUUUGUAUACAUUUUUAUUUUUUAACUUGCCUCAAUAAAUU
....(((((.(((((............((((((.......)))))).............))))).))).))................................................. ( -19.01)
>DroYak_CAF1 4161 111 + 1
CUUCGCUGUCUAAUGACAAUCAAAUUAGCGGCAUUUUCCUUGGCGCCAAAAACUUUUUCCAUUAAACGUGCAAUUUUUUCUUCAUUUA--UUUUU--UUU-----UUCCCUCAAUAAAUU
....(((((.(((((............(((.((.......)).))).............))))).))).)).................--.....--...-----............... ( -12.21)
>consensus
CUUCGCCGUCUAAUGACAAUCAAAUUAGCGCCAUUUUCCUUGGCGCCAAAAACUUUUUCCAUUAAACGUGCAAUUUUUUCUUUGUAUACAUUUUU__UUUUUAACUUGCCUCAAUAAAUU
....(((((.(((((............((((((.......)))))).............))))).))).))................................................. (-15.93 = -16.04 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 3,391,587 – 3,391,705
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.62
Mean single sequence MFE -28.21
Consensus MFE -25.90
Energy contribution -26.57
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.99
Structure conservation index 0.92
SVM decision value 1.98
SVM RNA-class probability 0.984603
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3391587 118 - 27905053
AAUUUAUUGAGGCAAGUUAAAAA--AAAAAUGUAUACAAAGAAAAAAUUGCACGUUUAAUGGAAAAAGUUUUUGGCGCCAAGGAAAAUGGCGCUAAUUUGAUUGUCAUUAGACGGCGAAG
..(((.(((..(((..((.....--.))..)))...))).)))....((((.((((((((((....((((.(((((((((.......)))))))))...)))).)))))))))))))).. ( -32.00)
>DroSim_CAF1 448 120 - 1
AAUUUAUUGAGGCAAGUUAAAAAAUAAAAAUGUAUACAAAGAAAAAAUUGCACGUUUAAUGGAAAAAGUUUUUGGCGCCAAGGAAAAUGGCGCUAAUUUGAUUGUCAUUAGACGGCGAAG
..(((.(((..(((..((........))..)))...))).)))....((((.((((((((((....((((.(((((((((.......)))))))))...)))).)))))))))))))).. ( -31.80)
>DroYak_CAF1 4161 111 - 1
AAUUUAUUGAGGGAA-----AAA--AAAAA--UAAAUGAAGAAAAAAUUGCACGUUUAAUGGAAAAAGUUUUUGGCGCCAAGGAAAAUGCCGCUAAUUUGAUUGUCAUUAGACAGCGAAG
.(((((((.......-----...--...))--)))))..........((((..(((((((((....((((.((((((.((.......)).))))))...)))).))))))))).)))).. ( -20.82)
>consensus
AAUUUAUUGAGGCAAGUUAAAAA__AAAAAUGUAUACAAAGAAAAAAUUGCACGUUUAAUGGAAAAAGUUUUUGGCGCCAAGGAAAAUGGCGCUAAUUUGAUUGUCAUUAGACGGCGAAG
...............................................((((.((((((((((....((((.(((((((((.......)))))))))...)))).)))))))))))))).. (-25.90 = -26.57 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:42 2006