Locus 7547

Sequence ID 3L_DroMel_CAF1
Location 20,253,353 – 20,253,671
Length 318
Max. P 0.956909
window12264 window12265 window12266 window12267 window12268

overview

Window 4

Location 20,253,353 – 20,253,471
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.32
Mean single sequence MFE -29.15
Consensus MFE -25.43
Energy contribution -26.06
Covariance contribution 0.63
Combinations/Pair 1.12
Mean z-score -1.87
Structure conservation index 0.87
SVM decision value 0.97
SVM RNA-class probability 0.891481
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20253353 118 + 23771897
AUGCCCAAGUUUGUGACUGCCACAGAUUUCACUCUUAAGGGAGUCCUCAUCCAGGUGACAGAACUUCUAAAUCCAAUCUGGAAAU--ACAUUUGUAAAUAACUUCUAAUUCUAGAUGGGC
..(((((((((((((.....))))))))..........((((((.....(((((((...................)))))))..(--((....)))....)))))).........))))) ( -27.11)
>DroSec_CAF1 5658 118 + 1
AUGCCCAAGUUUGUGACUGCCACAGAUUUCACUCUUAAGGGAGUCCUCAUCCAGGUGCGAGAACUUCUAAAUCCAAUCUGGAAAU--ACAUUUGUAAAUAACUUCUAAUUCUAGAUGGGC
..(((((((((((((.....))))))))..........((((((.....(((((((...((.....)).......)))))))..(--((....)))....)))))).........))))) ( -27.80)
>DroSim_CAF1 5634 118 + 1
AUGCCCAAGUUUGUGACUGCCACAGAUUUCACUCUUAAGGGAGUCCUCAUCCAGGUGCGAGAACUUCUAAAUCCAAUCUGGAAAU--ACAUUUGUAAAUAACUUCUAAUUCUAGAUGGGC
..(((((((((((((.....))))))))..........((((((.....(((((((...((.....)).......)))))))..(--((....)))....)))))).........))))) ( -27.80)
>DroYak_CAF1 6176 119 + 1
AUGCCCAAGUUUGUCACUUCCACAGAUUUCACUCUUAAGGAAGUCCUUAUCGAGGUGGGAGAACUUCUAAAUCUAAUCUGGACCUUAAUAUUUG-AAAUACAUUUCGAUUCCAGAUGGGC
..((((..........(((((((.(....).(((.(((((....)))))..))))))))))..............(((((((.........(((-(((....)))))).))))))))))) ( -33.90)
>consensus
AUGCCCAAGUUUGUGACUGCCACAGAUUUCACUCUUAAGGGAGUCCUCAUCCAGGUGCGAGAACUUCUAAAUCCAAUCUGGAAAU__ACAUUUGUAAAUAACUUCUAAUUCUAGAUGGGC
..(((((((((((((.....))))))))).........((((((((((((....))))).).)))))).......((((((((.........................)))))))))))) (-25.43 = -26.06 +   0.63)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,253,471 – 20,253,591
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.72
Mean single sequence MFE -43.70
Consensus MFE -39.62
Energy contribution -40.06
Covariance contribution 0.44
Combinations/Pair 1.06
Mean z-score -1.67
Structure conservation index 0.91
SVM decision value 0.50
SVM RNA-class probability 0.758981
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20253471 120 + 23771897
AUUCGCGAUCUGUUCGACGAGAAUACAGCCAACCUGGACCGAAUGUCUUCCGGCUUGUUUGCCAAGCUGGUCGUCCACUCAACCAAGAUCAUUGUGGACGAACAGGGAACCACGGCGGGA
.(((((((.....))).)))).......((..(((((.((.........((((((((.....))))))))((((((((...............))))))))...))...))).))..)). ( -41.16)
>DroSec_CAF1 5776 120 + 1
AUUCGCGAUCUGUUCGACGAGAAUACCGCCAACCUGAACCGAAUGUCGUCCGGCUUGUUUGCCAAGCUGGUCGUCCACUCAACCAAGAUCAUUGUGGACGAGCAGGGAACCACGGCGGGA
.(((((((.....))).))))....(((((.........((.....))((((((......)))...(((.((((((((...............)))))))).)))))).....))))).. ( -44.66)
>DroSim_CAF1 5752 120 + 1
AUUCGCGAUCUGUUCGACGAGAAUACCGCCAACCUGAACCGAAUGUCGUCCGGCUUGUUUGCCAAGCUGGUCGUCCACUCAACCAAGAUCAUUGUGGACGAGCAGGGAACCACGGCGGGA
.(((((((.....))).))))....(((((.........((.....))((((((......)))...(((.((((((((...............)))))))).)))))).....))))).. ( -44.66)
>DroYak_CAF1 6295 120 + 1
AUUCGCGAUCUGUUUGACGAGAACAAUGCCAACCUAAGCCGGAUGUCGUCCGGCUUGUUUGCCAAGCUGGUCGUCCACUCGACCAAGAUCAUCGUGGACGAGCAGGGAACCACGGCGGGA
.(((((((((((((((.((((.............((((((((((...)))))))))))))).)))))((((((......)))))))))))..(((((.(......)...)))))))))). ( -44.31)
>consensus
AUUCGCGAUCUGUUCGACGAGAAUACCGCCAACCUGAACCGAAUGUCGUCCGGCUUGUUUGCCAAGCUGGUCGUCCACUCAACCAAGAUCAUUGUGGACGAGCAGGGAACCACGGCGGGA
.(((((((.....))).))))....(((((..((((.............((((((((.....))))))))((((((((...............)))))))).))))(.....)))))).. (-39.62 = -40.06 +   0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,253,511 – 20,253,631
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 97.08
Mean single sequence MFE -50.64
Consensus MFE -49.47
Energy contribution -49.53
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -1.79
Structure conservation index 0.98
SVM decision value 0.66
SVM RNA-class probability 0.815556
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20253511 120 + 23771897
GAAUGUCUUCCGGCUUGUUUGCCAAGCUGGUCGUCCACUCAACCAAGAUCAUUGUGGACGAACAGGGAACCACGGCGGGAGCCGUCACGGAGGCAGCGCUGGCCAACAAGGCCACACCGC
...(((((((((((......)))...(((.((((((((...............)))))))).)))))).(((((((....)))))...)))))))(((.(((((.....)))))...))) ( -50.66)
>DroSec_CAF1 5816 120 + 1
GAAUGUCGUCCGGCUUGUUUGCCAAGCUGGUCGUCCACUCAACCAAGAUCAUUGUGGACGAGCAGGGAACCACGGCGGGAGCCGUCACGGAGGCAGCGCUGGCCAACAAGGCCACACCGC
...((((.((((((......)))...(((.((((((((...............)))))))).)))))).(((((((....)))))...)).))))(((.(((((.....)))))...))) ( -52.56)
>DroSim_CAF1 5792 120 + 1
GAAUGUCGUCCGGCUUGUUUGCCAAGCUGGUCGUCCACUCAACCAAGAUCAUUGUGGACGAGCAGGGAACCACGGCGGGAGCCGUCACGGAGGCAGCGCUGGCCAACAAGGCCACACCGC
...((((.((((((......)))...(((.((((((((...............)))))))).)))))).(((((((....)))))...)).))))(((.(((((.....)))))...))) ( -52.56)
>DroYak_CAF1 6335 120 + 1
GGAUGUCGUCCGGCUUGUUUGCCAAGCUGGUCGUCCACUCGACCAAGAUCAUCGUGGACGAGCAGGGAACCACGGCGGGAGCUGUCACGGAGGCAGCGCUGUCCAACAAGGCCACACCGC
((((...))))((((((((.(((...(((.((((((((..((......))...)))))))).)))(....)..)))(((.((((((.....))))))....)))))))).)))....... ( -46.80)
>consensus
GAAUGUCGUCCGGCUUGUUUGCCAAGCUGGUCGUCCACUCAACCAAGAUCAUUGUGGACGAGCAGGGAACCACGGCGGGAGCCGUCACGGAGGCAGCGCUGGCCAACAAGGCCACACCGC
...((((.((((((......)))...(((.((((((((...............)))))))).)))))).(((((((....)))))...)).))))(((.(((((.....)))))...))) (-49.47 = -49.53 +   0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,253,551 – 20,253,671
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.53
Mean single sequence MFE -46.18
Consensus MFE -43.30
Energy contribution -44.05
Covariance contribution 0.75
Combinations/Pair 1.03
Mean z-score -1.85
Structure conservation index 0.94
SVM decision value 0.71
SVM RNA-class probability 0.830825
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20253551 120 + 23771897
AACCAAGAUCAUUGUGGACGAACAGGGAACCACGGCGGGAGCCGUCACGGAGGCAGCGCUGGCCAACAAGGCCACACCGCCCAAGUUCCUGCUCAACCGGCCCUUCCAGUACAUGAUCGU
......((((((.((((..((.((((((.....(((((..(((........)))...(.(((((.....)))))).)))))....)))))).))..))((.....))...)))))))).. ( -44.20)
>DroSec_CAF1 5856 120 + 1
AACCAAGAUCAUUGUGGACGAGCAGGGAACCACGGCGGGAGCCGUCACGGAGGCAGCGCUGGCCAACAAGGCCACACCGCCCAAGUUCCUGCUCAACCGGCCCUUCCAGUAUAUGAUCGU
......((((((...((..(((((((((.....(((((..(((........)))...(.(((((.....)))))).)))))....)))))))))..))((.....)).....)))))).. ( -49.70)
>DroSim_CAF1 5832 120 + 1
AACCAAGAUCAUUGUGGACGAGCAGGGAACCACGGCGGGAGCCGUCACGGAGGCAGCGCUGGCCAACAAGGCCACACCGCCCAAGUUCCUGCUCAACCGGCCCUUCCAGUAUAUGAUCGU
......((((((...((..(((((((((.....(((((..(((........)))...(.(((((.....)))))).)))))....)))))))))..))((.....)).....)))))).. ( -49.70)
>DroYak_CAF1 6375 120 + 1
GACCAAGAUCAUCGUGGACGAGCAGGGAACCACGGCGGGAGCUGUCACGGAGGCAGCGCUGUCCAACAAGGCCACACCGCCCAAGUUCCAGCUGAACCGGCCCUUCCAGUACAUGAUCGU
......((((((..((((.(.....(((((...(((((..((((((.....))))))(.((.((.....)).))).)))))...))))).((((...)))).).))))....)))))).. ( -41.10)
>consensus
AACCAAGAUCAUUGUGGACGAGCAGGGAACCACGGCGGGAGCCGUCACGGAGGCAGCGCUGGCCAACAAGGCCACACCGCCCAAGUUCCUGCUCAACCGGCCCUUCCAGUACAUGAUCGU
......((((((.((((..(((((((((.....(((((..((.(((.....))).))(.(((((.....)))))).)))))....)))))))))..))((.....))...)))))))).. (-43.30 = -44.05 +   0.75)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,253,551 – 20,253,671
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.53
Mean single sequence MFE -55.10
Consensus MFE -51.31
Energy contribution -52.12
Covariance contribution 0.81
Combinations/Pair 1.02
Mean z-score -2.43
Structure conservation index 0.93
SVM decision value 1.47
SVM RNA-class probability 0.956909
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20253551 120 - 23771897
ACGAUCAUGUACUGGAAGGGCCGGUUGAGCAGGAACUUGGGCGGUGUGGCCUUGUUGGCCAGCGCUGCCUCCGUGACGGCUCCCGCCGUGGUUCCCUGUUCGUCCACAAUGAUCUUGGUU
..((((((((...((.....))((.((((((((((((.(((((((((((((.....))))).)))))))).....(((((....))))))))).)))))))).)))).))))))...... ( -55.90)
>DroSec_CAF1 5856 120 - 1
ACGAUCAUAUACUGGAAGGGCCGGUUGAGCAGGAACUUGGGCGGUGUGGCCUUGUUGGCCAGCGCUGCCUCCGUGACGGCUCCCGCCGUGGUUCCCUGCUCGUCCACAAUGAUCUUGGUU
..((((((.....((.....))((.((((((((((((.(((((((((((((.....))))).)))))))).....(((((....))))))))).)))))))).))...))))))...... ( -57.80)
>DroSim_CAF1 5832 120 - 1
ACGAUCAUAUACUGGAAGGGCCGGUUGAGCAGGAACUUGGGCGGUGUGGCCUUGUUGGCCAGCGCUGCCUCCGUGACGGCUCCCGCCGUGGUUCCCUGCUCGUCCACAAUGAUCUUGGUU
..((((((.....((.....))((.((((((((((((.(((((((((((((.....))))).)))))))).....(((((....))))))))).)))))))).))...))))))...... ( -57.80)
>DroYak_CAF1 6375 120 - 1
ACGAUCAUGUACUGGAAGGGCCGGUUCAGCUGGAACUUGGGCGGUGUGGCCUUGUUGGACAGCGCUGCCUCCGUGACAGCUCCCGCCGUGGUUCCCUGCUCGUCCACGAUGAUCUUGGUC
..((((((....((((.((((((((..(((((..((..(((((((((..((.....))...)))))))))..))..)))))...)))).((...)).)))).))))..))))))...... ( -48.90)
>consensus
ACGAUCAUAUACUGGAAGGGCCGGUUGAGCAGGAACUUGGGCGGUGUGGCCUUGUUGGCCAGCGCUGCCUCCGUGACGGCUCCCGCCGUGGUUCCCUGCUCGUCCACAAUGAUCUUGGUU
..((((((.....((.....))((.((((((((((((.(((((((((((((.....))))).)))))))).....(((((....))))))))).)))))))).))...))))))...... (-51.31 = -52.12 +   0.81)

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 12:49:58 2006