Locus 3735

Sequence ID 3L_DroMel_CAF1
Location 10,824,442 – 10,824,595
Length 153
Max. P 0.999817
window5832 window5833 window5834 window5835

overview

Window 2

Location 10,824,442 – 10,824,555
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 91.56
Mean single sequence MFE -33.02
Consensus MFE -29.98
Energy contribution -29.82
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -2.63
Structure conservation index 0.91
SVM decision value 4.15
SVM RNA-class probability 0.999817
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10824442 113 + 23771897
CGGGUAACUGCAUGAAUAAUUAUUAAGUUAUUCGAGGAGGGUCGUAAAAUGAGGGGUAUGCAGAUGUACUGCACUCACUCGCACUCACCCCAAAAAUUUAUGGGAUUUCUCCC
(((((((((..((((....))))..))))))))).((((((.........(((((((..((((.....)))))))).)))........((((........))))..)))))). ( -31.40)
>DroSec_CAF1 33493 112 + 1
CGGGUAACUGCAUGAAUAAUUAUUAAGUUAUUCGAGGAGGGUCAUAAAAUGAGGGGUAUGCAGAAGUACUGCACUCACUCGCACUCACCCCAA-AAUUUAUGGGUUUUCUCCC
.((((((((..((((....))))..))))))))(((((((.(((((((.(..(((((.(((((.....)))))(......).....)))))..-).))))))).))))))).. ( -32.70)
>DroSim_CAF1 35101 112 + 1
CGGGUAACUGCAUGAAUAAUUAUUAAGUUAUUCGAGGAGGGUCAUAAAAUGAGGGGUAUGCAGAAGUACUGCACUCACUCGCACUCACCCCAA-AAUUUAUGGGUUUUCUCCC
.((((((((..((((....))))..))))))))(((((((.(((((((.(..(((((.(((((.....)))))(......).....)))))..-).))))))).))))))).. ( -32.70)
>DroEre_CAF1 34881 102 + 1
CGGGUAACUGCAUGAAUAAUUAUUAAGUUAUUCGAGGAGGGUCAUAAAACGAGGGGUAUGCAGAAGUGCUGCACU----------CACCCCAA-AAUUUAUGGGAUUUCUCCC
.((((((((..((((....))))..))))))))((((((..(((((((....(((((.(((((.....)))))..----------.)))))..-..)))))))..)))))).. ( -33.70)
>DroYak_CAF1 34189 102 + 1
CGGGUAACUGCAUGAAUAAUUAUUAAGUUAUUCGAGGAGGGUCAUAAAAUAGGGGGUAUGCAGAAGUACUGCACU----------CACCCCAA-AAUUUAUGGGAUUUCUCCC
.((((((((..((((....))))..))))))))((((((..(((((((....(((((.(((((.....)))))..----------.)))))..-..)))))))..)))))).. ( -34.60)
>consensus
CGGGUAACUGCAUGAAUAAUUAUUAAGUUAUUCGAGGAGGGUCAUAAAAUGAGGGGUAUGCAGAAGUACUGCACUCACUCGCACUCACCCCAA_AAUUUAUGGGAUUUCUCCC
(((((((((..((((....))))..))))))))).(((((((((((((....(((((.(((((.....))))).............))))).....)))))))...)))))). (-29.98 = -29.82 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,824,442 – 10,824,555
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 91.56
Mean single sequence MFE -33.54
Consensus MFE -25.76
Energy contribution -27.76
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -3.49
Structure conservation index 0.77
SVM decision value 2.37
SVM RNA-class probability 0.993099
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10824442 113 - 23771897
GGGAGAAAUCCCAUAAAUUUUUGGGGUGAGUGCGAGUGAGUGCAGUACAUCUGCAUACCCCUCAUUUUACGACCCUCCUCGAAUAACUUAAUAAUUAUUCAUGCAGUUACCCG
((((....))))...........((((((.(((((((((((((((.....))))).....))))))).............((((((........))))))..))).)))))). ( -38.00)
>DroSec_CAF1 33493 112 - 1
GGGAGAAAACCCAUAAAUU-UUGGGGUGAGUGCGAGUGAGUGCAGUACUUCUGCAUACCCCUCAUUUUAUGACCCUCCUCGAAUAACUUAAUAAUUAUUCAUGCAGUUACCCG
(((......))).......-...((((((.((((((.((((((((.....)))))......((((...))))..))))))((((((........))))))..))).)))))). ( -35.10)
>DroSim_CAF1 35101 112 - 1
GGGAGAAAACCCAUAAAUU-UUGGGGUGAGUGCGAGUGAGUGCAGUACUUCUGCAUACCCCUCAUUUUAUGACCCUCCUCGAAUAACUUAAUAAUUAUUCAUGCAGUUACCCG
(((......))).......-...((((((.((((((.((((((((.....)))))......((((...))))..))))))((((((........))))))..))).)))))). ( -35.10)
>DroEre_CAF1 34881 102 - 1
GGGAGAAAUCCCAUAAAUU-UUGGGGUG----------AGUGCAGCACUUCUGCAUACCCCUCGUUUUAUGACCCUCCUCGAAUAACUUAAUAAUUAUUCAUGCAGUUACCCG
((((....)))).......-...(((((----------(.(((((((....)))..........................((((((........)))))).)))).)))))). ( -30.10)
>DroYak_CAF1 34189 102 - 1
GGGAGAAAUCCCAUAAAUU-UUGGGGUG----------AGUGCAGUACUUCUGCAUACCCCCUAUUUUAUGACCCUCCUCGAAUAACUUAAUAAUUAUUCAUGCAGUUACCCG
(((........((((((..-..((((.(----------.((((((.....)))))).)))))...)))))).........((((((........)))))).........))). ( -29.40)
>consensus
GGGAGAAAUCCCAUAAAUU_UUGGGGUGAGUGCGAGUGAGUGCAGUACUUCUGCAUACCCCUCAUUUUAUGACCCUCCUCGAAUAACUUAAUAAUUAUUCAUGCAGUUACCCG
((((....))))...........((((((.(((......((((((.....))))))........................((((((........))))))..))).)))))). (-25.76 = -27.76 +   2.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,824,481 – 10,824,595
Length 114
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 91.28
Mean single sequence MFE -24.56
Consensus MFE -22.28
Energy contribution -22.36
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -1.21
Structure conservation index 0.91
SVM decision value 0.20
SVM RNA-class probability 0.631546
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10824481 114 + 23771897
GGUCGUAAAAUGAGGGGUAUGCAGAUGUACUGCACUCACUCGCACUCACCCCAAAAAUUUAUGGGAUUUCUCCCUGAUAUCCGACUUAUUUUUAGACGUGCUCAAUCAUUUCUU
.......((((((((((..(((((.....)))))..).)))((((((.....((((((...(.((((.((.....)).)))).)...)))))).)).))))....))))))... ( -24.90)
>DroSec_CAF1 33532 113 + 1
GGUCAUAAAAUGAGGGGUAUGCAGAAGUACUGCACUCACUCGCACUCACCCCAA-AAUUUAUGGGUUUUCUCCCUGAUAUCCGACUUAUUUUUAGACGUGCUCAAUCAUUUCUU
.(((..((((((((((((((.(((......(((........))).....((((.-......))))........)))))))))..))))))))..)))................. ( -23.20)
>DroSim_CAF1 35140 113 + 1
GGUCAUAAAAUGAGGGGUAUGCAGAAGUACUGCACUCACUCGCACUCACCCCAA-AAUUUAUGGGUUUUCUCCCUGAUAUCCGACUUAUUUUUAGACGUGCUCAAUCAUUUCUU
.(((..((((((((((((((.(((......(((........))).....((((.-......))))........)))))))))..))))))))..)))................. ( -23.20)
>DroEre_CAF1 34920 103 + 1
GGUCAUAAAACGAGGGGUAUGCAGAAGUGCUGCACU----------CACCCCAA-AAUUUAUGGGAUUUCUCCCUGAUAUCCGACUUAUUUUUAGACGUGCUCAAUCAUUUCUU
((((.........(((((.(((((.....)))))..----------.)))))..-........((((.((.....)).)))))))).......(((.(((......))).))). ( -26.00)
>DroYak_CAF1 34228 103 + 1
GGUCAUAAAAUAGGGGGUAUGCAGAAGUACUGCACU----------CACCCCAA-AAUUUAUGGGAUUUCUCCCUGAUAUCCGACUUAUUUUUAAACGUGCUCAAUCAUUUCUU
(((((((((....(((((.(((((.....)))))..----------.)))))..-..))))).((((.((.....)).))))))))............................ ( -25.50)
>consensus
GGUCAUAAAAUGAGGGGUAUGCAGAAGUACUGCACUCACUCGCACUCACCCCAA_AAUUUAUGGGAUUUCUCCCUGAUAUCCGACUUAUUUUUAGACGUGCUCAAUCAUUUCUU
.(((..((((((((((((((((((.....))))................((((........))))...........))))))..))))))))..)))................. (-22.28 = -22.36 +   0.08)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,824,481 – 10,824,595
Length 114
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 91.28
Mean single sequence MFE -29.54
Consensus MFE -26.42
Energy contribution -26.54
Covariance contribution 0.12
Combinations/Pair 1.10
Mean z-score -1.92
Structure conservation index 0.89
SVM decision value 2.33
SVM RNA-class probability 0.992422
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10824481 114 - 23771897
AAGAAAUGAUUGAGCACGUCUAAAAAUAAGUCGGAUAUCAGGGAGAAAUCCCAUAAAUUUUUGGGGUGAGUGCGAGUGAGUGCAGUACAUCUGCAUACCCCUCAUUUUACGACC
..(((((((.(((...((.((.......)).))....)))((((....))))..........((((((...((......))((((.....)))).)))))))))))))...... ( -31.60)
>DroSec_CAF1 33532 113 - 1
AAGAAAUGAUUGAGCACGUCUAAAAAUAAGUCGGAUAUCAGGGAGAAAACCCAUAAAUU-UUGGGGUGAGUGCGAGUGAGUGCAGUACUUCUGCAUACCCCUCAUUUUAUGACC
..(((((((.(((...((.((.......)).))....)))(((......))).......-..((((((...((......))((((.....)))).)))))))))))))...... ( -27.40)
>DroSim_CAF1 35140 113 - 1
AAGAAAUGAUUGAGCACGUCUAAAAAUAAGUCGGAUAUCAGGGAGAAAACCCAUAAAUU-UUGGGGUGAGUGCGAGUGAGUGCAGUACUUCUGCAUACCCCUCAUUUUAUGACC
..(((((((.(((...((.((.......)).))....)))(((......))).......-..((((((...((......))((((.....)))).)))))))))))))...... ( -27.40)
>DroEre_CAF1 34920 103 - 1
AAGAAAUGAUUGAGCACGUCUAAAAAUAAGUCGGAUAUCAGGGAGAAAUCCCAUAAAUU-UUGGGGUG----------AGUGCAGCACUUCUGCAUACCCCUCGUUUUAUGACC
..(((((((.(((...((.((.......)).))....)))((((....)))).......-..(((((.----------.((((((.....))))))))))))))))))...... ( -31.50)
>DroYak_CAF1 34228 103 - 1
AAGAAAUGAUUGAGCACGUUUAAAAAUAAGUCGGAUAUCAGGGAGAAAUCCCAUAAAUU-UUGGGGUG----------AGUGCAGUACUUCUGCAUACCCCCUAUUUUAUGACC
...(((((........)))))........(((........((((....))))(((((..-..((((.(----------.((((((.....)))))).)))))...)))))))). ( -29.80)
>consensus
AAGAAAUGAUUGAGCACGUCUAAAAAUAAGUCGGAUAUCAGGGAGAAAUCCCAUAAAUU_UUGGGGUGAGUGCGAGUGAGUGCAGUACUUCUGCAUACCCCUCAUUUUAUGACC
..(((((((.(((...((.((.......)).))....)))((((....))))..........(((((............((((((.....))))))))))))))))))...... (-26.42 = -26.54 +   0.12)

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 11:05:30 2006