Locus 2741

Sequence ID 2L_DroMel_CAF1
Location 7,714,112 – 7,714,392
Length 280
Max. P 0.896363
window4354 window4355 window4356 window4357

overview

Window 4

Location 7,714,112 – 7,714,232
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.81
Mean single sequence MFE -37.70
Consensus MFE -27.29
Energy contribution -28.60
Covariance contribution 1.31
Combinations/Pair 1.21
Mean z-score -1.43
Structure conservation index 0.72
SVM decision value 0.00
SVM RNA-class probability 0.533828
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7714112 120 - 22407834
GGAGCGUCUAAAGCGCUCCUGCCGACCCACAGAUUGGUAUCCGGUUGAGAUGAAACAUCGUCAGCAUUACGGGGAUCGUGUCGGAAAUAUUGAGAUGACCGACCAUCUUUUCAAUGGUAU
(((((((.....)))))))(((((......((((.(((..((((((((((((...)))).)))))....)))((.((((.((((.....)))).)))))).)))))))......))))). ( -38.40)
>DroSec_CAF1 3105 120 - 1
GGAGCGUCUAAAACGCUCCUGCCGACCCACAGAUUGGUAUCCGGUUGAUGUGAAACAUCCUCAGCAUUACGGGGAUCUCGUCGGAAACAUUGAGAUGACAGACCAUCUUUCUAAUGGUAC
(((((((.....)))))))..(((((.((((((((((...))))))..))))....((((((........))))))...)))))...((((((((((......))))))...)))).... ( -38.90)
>DroSim_CAF1 3109 120 - 1
GGAGCGUCUAAAACGCUCCUGCCGACCCACAGAUUGGUAUCCAGUUGAGAUGAAACAUCGCCAGCAUUACGGGGAUCUCGUCGGAAACAUUGAGAUGACAGACCAUCUUUGUAAUGGUAC
(((((((.....)))))))(((((...((.((((.(((.....((((.((((...))))..))))......(..((((((..(....)..))))))..)..))))))).))...))))). ( -39.50)
>DroEre_CAF1 3231 120 - 1
CGAGCGCCUAAAACGCGCAUGUCGACCCACGGAUUGGUAUCCGUCUGAGAUGAAACACCGUCAGCACUACGGGGACCUUAUAGGCCACAUUGAGAUGACCGACCAUCUAUUCGAUGGUAC
((.((((.......))))..((((.....(((((....)))))(((..((((.....((((.......))))((.((.....)))).)))).)))))))))((((((.....)))))).. ( -34.00)
>consensus
GGAGCGUCUAAAACGCUCCUGCCGACCCACAGAUUGGUAUCCGGUUGAGAUGAAACAUCGUCAGCAUUACGGGGAUCUCGUCGGAAACAUUGAGAUGACAGACCAUCUUUUCAAUGGUAC
(((((((.....)))))))(((((......((((.(((.....(((((((((...)))).)))))....(((..((((((..(....)..))))))..))))))))))......))))). (-27.29 = -28.60 +   1.31)

alignment

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secondary structure

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Window 5

Location 7,714,192 – 7,714,312
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.44
Mean single sequence MFE -34.28
Consensus MFE -26.92
Energy contribution -27.30
Covariance contribution 0.38
Combinations/Pair 1.21
Mean z-score -1.78
Structure conservation index 0.79
SVM decision value 0.49
SVM RNA-class probability 0.755541
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7714192 120 + 22407834
AUACCAAUCUGUGGGUCGGCAGGAGCGCUUUAGACGCUCCAAAAAGGUGCCAGGACUCUGUCUCAGGUAGUAAAAUCCAUAACCAGGUAUUGCCAAAAAGGGCAACACGACAAGUAUAAU
.((((....(((((((..((.(((((((....).)))))).......((((.((((...))))..))))))...)))))))....))))(((((......)))))............... ( -34.70)
>DroSec_CAF1 3185 120 + 1
AUACCAAUCUGUGGGUCGGCAGGAGCGUUUUAGACGCUCCAAAAAGGUGCCAGGACUCUGUUUUAGGUAGUAAAAUGCAUAACCAGGUAUUGCCAGAAAGGGUAACACAACAAGUACAAU
.((((..(((..(((((((((((((((((...)))))))).......))))..))))).......(((((((...((......))..))))))))))...))))................ ( -35.01)
>DroSim_CAF1 3189 120 + 1
AUACCAAUCUGUGGGUCGGCAGGAGCGUUUUAGACGCUCCAAAAAGGUGCCAGGACUCUGUUUUAGGUAGUAAUAUCCAUAACCAGGUAUUGCCAAAAAGGGUAACACUACAAGUAUAAU
.((((.(((((.(((((((((((((((((...)))))))).......))))..))))).....))))).((((((((........)))))))).......))))................ ( -33.81)
>DroEre_CAF1 3311 120 + 1
AUACCAAUCCGUGGGUCGACAUGCGCGUUUUAGGCGCUCGGAAAAGGUUCCAGUGCUAUUUUUUAGGUAGUAGAAUCCAUAACCAGGUAUUGCCAGAAAGGGUAGCCCCACAAGUAUAAU
..........(((((...((..((((.......))))..((((....)))).))((((((((((.(((((((....((.......)))))))))..)))))))))))))))......... ( -33.60)
>consensus
AUACCAAUCUGUGGGUCGGCAGGAGCGUUUUAGACGCUCCAAAAAGGUGCCAGGACUCUGUUUUAGGUAGUAAAAUCCAUAACCAGGUAUUGCCAAAAAGGGUAACACAACAAGUAUAAU
.((((....(((((((..((.(((((((.....))))))).......((((((((.....)))).))))))...)))))))....))))(((((......)))))............... (-26.92 = -27.30 +   0.38)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,714,272 – 7,714,392
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.14
Mean single sequence MFE -26.43
Consensus MFE -21.15
Energy contribution -21.27
Covariance contribution 0.13
Combinations/Pair 1.23
Mean z-score -1.54
Structure conservation index 0.80
SVM decision value 0.26
SVM RNA-class probability 0.658874
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7714272 120 + 22407834
AACCAGGUAUUGCCAAAAAGGGCAACACGACAAGUAUAAUGCCUAGUACGAGGAACACUUCCUUAAAGAAGAAGUGAACUCGUAUGCACUCGAUUAUGCCCAAUAUCUAAAAGGAAAAGC
..((.((.....)).....(((((..((.....))....(((...(((((((...((((((.........))))))..))))))))))........)))))...........))...... ( -30.30)
>DroSec_CAF1 3265 120 + 1
AACCAGGUAUUGCCAGAAAGGGUAACACAACAAGUACAAUGCCUAGUACGAGAAAGACUUCCUUAAAGAAGGAGUGACCUCGUAUGCACUCGAUUAUGCCCAAUAUCUAAUAGGAAAAGC
..((.((.....)).....(((((..((.....))....(((...(((((((....(((.((((....)))))))...))))))))))........)))))...........))...... ( -25.30)
>DroSim_CAF1 3269 120 + 1
AACCAGGUAUUGCCAAAAAGGGUAACACUACAAGUAUAAUGCCCAAUACAAGGAACACUUCCAUAAAAAAGGAGUGACCUCGUAUGCACUCGAUUAUGCCCAAUAUCUAAUAGGAAAAGC
..((((((((((.......(((((..((.....))....))))).((((.(((..((((.((........)))))).))).))))(((........))).))))))))....))...... ( -24.80)
>DroEre_CAF1 3391 120 + 1
AACCAGGUAUUGCCAGAAAGGGUAGCCCCACAAGUAUAAUCGCCAGUGCAAAGAACACUUCACGGUAGUAGAAGUGAGAAUACAUGAUUUCUUUUAUGCCGUAUACCUAGUCAGUCAAUC
.((.((((((.((.((((((((....))).((.((((..((((....))......((((((((....)).)))))).)))))).)).))))).....))...)))))).))......... ( -25.30)
>consensus
AACCAGGUAUUGCCAAAAAGGGUAACACAACAAGUAUAAUGCCCAGUACAAGGAACACUUCCUUAAAGAAGAAGUGACCUCGUAUGCACUCGAUUAUGCCCAAUAUCUAAUAGGAAAAGC
....((((((((((......)))))........(((((((.....(((((((...((((((.........))))))..))))))).......)))))))....)))))............ (-21.15 = -21.27 +   0.13)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,714,272 – 7,714,392
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.14
Mean single sequence MFE -33.74
Consensus MFE -19.16
Energy contribution -20.60
Covariance contribution 1.44
Combinations/Pair 1.24
Mean z-score -2.43
Structure conservation index 0.57
SVM decision value 0.99
SVM RNA-class probability 0.896363
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7714272 120 - 22407834
GCUUUUCCUUUUAGAUAUUGGGCAUAAUCGAGUGCAUACGAGUUCACUUCUUCUUUAAGGAAGUGUUCCUCGUACUAGGCAUUAUACUUGUCGUGUUGCCCUUUUUGGCAAUACCUGGUU
..........((((......((((......(((((.((((((..((((((((.....))))))))...))))))....))))).....))))((((((((......)))))))))))).. ( -37.00)
>DroSec_CAF1 3265 120 - 1
GCUUUUCCUAUUAGAUAUUGGGCAUAAUCGAGUGCAUACGAGGUCACUCCUUCUUUAAGGAAGUCUUUCUCGUACUAGGCAUUGUACUUGUUGUGUUACCCUUUCUGGCAAUACCUGGUU
.........(((((.((((((((((((.(((((((((((((((..(((((((....)))).)))...)))))))........)))))))))))))))..((.....))))))).))))). ( -33.20)
>DroSim_CAF1 3269 120 - 1
GCUUUUCCUAUUAGAUAUUGGGCAUAAUCGAGUGCAUACGAGGUCACUCCUUUUUUAUGGAAGUGUUCCUUGUAUUGGGCAUUAUACUUGUAGUGUUACCCUUUUUGGCAAUACCUGGUU
.........(((((.(((((.((((......))))((((((((.((((((........)).))))..)))))))).(((((((((....))))))...))).......))))).))))). ( -31.70)
>DroEre_CAF1 3391 120 - 1
GAUUGACUGACUAGGUAUACGGCAUAAAAGAAAUCAUGUAUUCUCACUUCUACUACCGUGAAGUGUUCUUUGCACUGGCGAUUAUACUUGUGGGGCUACCCUUUCUGGCAAUACCUGGUU
........((((((((((...((.....(((((....(((..(((((.........(((..(((((.....))))).))).........)))))..)))..))))).)).)))))))))) ( -33.07)
>consensus
GCUUUUCCUAUUAGAUAUUGGGCAUAAUCGAGUGCAUACGAGGUCACUCCUUCUUUAAGGAAGUGUUCCUCGUACUAGGCAUUAUACUUGUAGUGUUACCCUUUCUGGCAAUACCUGGUU
.........(((((.(((((((((......(((((.((((((..(((((((.......)))))))...))))))....))))).....)))).......((.....))))))).))))). (-19.16 = -20.60 +   1.44)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:04 2006