Locus 1430

Sequence ID 3L_DroMel_CAF1
Location 4,150,619 – 4,150,804
Length 185
Max. P 0.966880
window2224 window2225 window2226

overview

Window 4

Location 4,150,619 – 4,150,729
Length 110
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.86
Mean single sequence MFE -28.71
Consensus MFE -25.55
Energy contribution -27.66
Covariance contribution 2.11
Combinations/Pair 1.04
Mean z-score -1.87
Structure conservation index 0.89
SVM decision value 0.59
SVM RNA-class probability 0.793672
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4150619 110 + 23771897
CGUCGCGCGAACAAGUUAAGCGACUUCU----------GUUUCUCGGUUAUCCCCACACCCGUCUCUGUUCUUUUUUCUUUUCGGAUCUCGAGAUCGUAAGAUCUUCAGAUCUUAACGGU
.(((((...((....))..)))))..((----------(((....((......))............................((((((.((((((....)))))).)))))).))))). ( -27.50)
>DroSim_CAF1 260 106 + 1
CGUCGCGCGAACAAGUUAAGCGACUUCU----------GUUUCUCGGUUAUCCCCACACCCGUCUCUUUUCUUUC----UUUGGGAUCUCGAGAUCGUAAGAUCUUCAGAUCUUAACGGU
.(((((...((....))..)))))....----------.......((......))....((((............----..((((((((.((((((....)))))).)))))))))))). ( -29.13)
>DroYak_CAF1 271 116 + 1
UGUCGCACGAACAAGUUAAGCGACUUCUCGGUUUCUCGGUUUCUCGGCUAUCCCCAUACCCGUCUCUUUUCUUUC----UUUGGGAUCUCGAGAUCGUAAGAUCUUCAGAUCUUAACGGU
.(((((((......))...))))).((((((..((((((.....(((.(((....))).))).............----.))))))..))))))((((((((((....)))))).)))). ( -29.51)
>consensus
CGUCGCGCGAACAAGUUAAGCGACUUCU__________GUUUCUCGGUUAUCCCCACACCCGUCUCUUUUCUUUC____UUUGGGAUCUCGAGAUCGUAAGAUCUUCAGAUCUUAACGGU
.(((((((......))...))))).....................((......))....((((..................((((((((.((((((....)))))).)))))))))))). (-25.55 = -27.66 +   2.11)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,150,649 – 4,150,764
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.31
Mean single sequence MFE -36.23
Consensus MFE -25.77
Energy contribution -28.33
Covariance contribution 2.56
Combinations/Pair 1.06
Mean z-score -3.36
Structure conservation index 0.71
SVM decision value 0.60
SVM RNA-class probability 0.794246
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4150649 115 + 23771897
UUCUCGGUUAUCCCCACACCCGUCUCUGUUCUUUUUUCUUUUCGGAUCUCGAGAUCGUAAGAUCUUCAGAUCUUAACGGUAUGUUUGCAGA-CGCCUAACUGU--GAGCUGG--CAGCCA
.....((((..(.(((((...((.(((((........((.((.((((((.((((((....)))))).)))))).)).)).......)))))-.)).....)))--).)..).--.)))). ( -31.76)
>DroSim_CAF1 290 111 + 1
UUCUCGGUUAUCCCCACACCCGUCUCUUUUCUUUC----UUUGGGAUCUCGAGAUCGUAAGAUCUUCAGAUCUUAACGGUAUGUUCGCAGA-CGCCUAACUGU--GAGCUGG--CAGCCA
.....((((....(((...((((............----..((((((((.((((((....)))))).))))))))))))...((((((((.-.......))))--)))))))--.)))). ( -35.93)
>DroYak_CAF1 311 116 + 1
UUCUCGGCUAUCCCCAUACCCGUCUCUUUUCUUUC----UUUGGGAUCUCGAGAUCGUAAGAUCUUCAGAUCUUAACGGUAUGUUUGCAUACCGCCUAACUGUGUGUGCUGGCGCAGCCA
.....((((..((.((((((.((............----.(((((((((.((((((....)))))).)))))))))(((((((....)))))))....)).).)))))..))...)))). ( -41.00)
>consensus
UUCUCGGUUAUCCCCACACCCGUCUCUUUUCUUUC____UUUGGGAUCUCGAGAUCGUAAGAUCUUCAGAUCUUAACGGUAUGUUUGCAGA_CGCCUAACUGU__GAGCUGG__CAGCCA
.....((((....(((...((((..................((((((((.((((((....)))))).))))))))))))...((((((((.........))))..)))))))...)))). (-25.77 = -28.33 +   2.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,150,689 – 4,150,804
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.42
Mean single sequence MFE -39.23
Consensus MFE -34.71
Energy contribution -35.10
Covariance contribution 0.39
Combinations/Pair 1.06
Mean z-score -2.99
Structure conservation index 0.88
SVM decision value 1.60
SVM RNA-class probability 0.966880
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4150689 115 - 23771897
UCUAGUUAGAAGUGGGUCUCCGGAUCGAUACCAAUUCUCCUGGCUG--CCAGCUC--ACAGUUAGGCG-UCUGCAAACAUACCGUUAAGAUCUGAAGAUCUUACGAUCUCGAGAUCCGAA
............((((((((.((((((.........(.((((((((--.......--.)))))))).)-................(((((((....))))))))))))).)))))))).. ( -37.60)
>DroSim_CAF1 326 115 - 1
UCUAGCUAGAAGUGGGUCUCCAGAUCGAUGGCAAUUCUCCUGGCUG--CCAGCUC--ACAGUUAGGCG-UCUGCGAACAUACCGUUAAGAUCUGAAGAUCUUACGAUCUCGAGAUCCCAA
...........(.(((((((.((((((...(((...(.((((((((--.......--.)))))))).)-..)))...........(((((((....))))))))))))).)))))))).. ( -41.30)
>DroYak_CAF1 347 120 - 1
ACUAGUUAAAAGUGGGUUUCCGAAUCGAUAGCAAUUCUCCUGGCUGCGCCAGCACACACAGUUAGGCGGUAUGCAAACAUACCGUUAAGAUCUGAAGAUCUUACGAUCUCGAGAUCCCAA
............((((.(..(((((((...........((((((((.(........).))))))))(((((((....))))))).(((((((....))))))))))).)))..).)))). ( -38.80)
>consensus
UCUAGUUAGAAGUGGGUCUCCGGAUCGAUAGCAAUUCUCCUGGCUG__CCAGCUC__ACAGUUAGGCG_UCUGCAAACAUACCGUUAAGAUCUGAAGAUCUUACGAUCUCGAGAUCCCAA
.............(((((((.((((((...(((...(.((((((((.(........).)))))))).)...)))...........(((((((....))))))))))))).)))))))... (-34.71 = -35.10 +   0.39)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:21 2006