Locus 835

Sequence ID 3L_DroMel_CAF1
Location 2,533,755 – 2,533,921
Length 166
Max. P 0.844292
window1284 window1285 window1286

overview

Window 4

Location 2,533,755 – 2,533,857
Length 102
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 83.68
Mean single sequence MFE -16.67
Consensus MFE -11.90
Energy contribution -11.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.71
SVM decision value 0.01
SVM RNA-class probability 0.540506
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2533755 102 + 23771897
AAAAACUUGUUAAUUAAGAAAUUAACAACGUUGCAUUACAUUAUGUUAACAUAUAGUGUGGGAAAUAUAGUGAAACAUUUCCACUCUUCUGCCUUAUAAUUC
...((((((((((((....))))))))).)))(((.((((((((((....))))))))))((((((..........)))))).......))).......... ( -20.20)
>DroSec_CAF1 156607 82 + 1
AAAAACUUGUUAAUUAAGAAAUUAACAACGUUGCAUUACAUUAUGUUAACAUACAGUGUGGGAAA---UGUG-----------------UGCCUUAUAAUUC
...((((((((((((....))))))))).)))((((.(((((...(..((((...))))..).))---))))-----------------))).......... ( -14.10)
>DroSim_CAF1 154176 84 + 1
AAAAACUUGUUAAUUAAGAAAUUAACAACGUUGCAUUACAUUAUGUUAACAUACAGUGUGGGAAU-ACAGUG-----------------UGCCUUAUAAUUC
...((((((((((((....))))))))).))).......((((((....(((((.((((....))-)).)))-----------------))...)))))).. ( -15.70)
>consensus
AAAAACUUGUUAAUUAAGAAAUUAACAACGUUGCAUUACAUUAUGUUAACAUACAGUGUGGGAAA_A_AGUG_________________UGCCUUAUAAUUC
...((((((((((((....))))))))).)))...((((((((((....))))..))))))......................................... (-11.90 = -11.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,533,817 – 2,533,921
Length 104
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 83.33
Mean single sequence MFE -17.65
Consensus MFE -16.40
Energy contribution -16.73
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -0.54
Structure conservation index 0.93
SVM decision value 0.09
SVM RNA-class probability 0.577821
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2533817 104 + 23771897
AAAUAUAGUGAAACAUUUCCACUCUUCUGCCUUAUAAUUCCCAACUAGCCAUUUCGUUUGACUUAUUAAGGGAAGUAAUCCUCUUUUGUUCAGAGGGUUAAACG
......((((.........))))((((..((((((((.((..(((..........))).)).))).)))))))))(((((((((.......))))))))).... ( -17.10)
>DroSec_CAF1 156669 84 + 1
AAA---UGUG-----------------UGCCUUAUAAUUCCCAACUAGCCAUUUCGUUCGACUUAUUAAGGGAAGUAAUCCUCUGUUGUUCAGAGGGUUAAACG
...---....-----------------..........(((((...........................))))).((((((((((.....)))))))))).... ( -17.93)
>DroSim_CAF1 154238 86 + 1
AAU-ACAGUG-----------------UGCCUUAUAAUUCCCAACUAGCCAUUUCGUUCGACUUAUUAAGGGAAGUAAUCCUCUGUUGUUCAGAGGGUUAAACG
...-......-----------------..........(((((...........................))))).((((((((((.....)))))))))).... ( -17.93)
>consensus
AAA_A_AGUG_________________UGCCUUAUAAUUCCCAACUAGCCAUUUCGUUCGACUUAUUAAGGGAAGUAAUCCUCUGUUGUUCAGAGGGUUAAACG
.....................................(((((...........................))))).((((((((((.....)))))))))).... (-16.40 = -16.73 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,533,817 – 2,533,921
Length 104
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 83.33
Mean single sequence MFE -20.40
Consensus MFE -18.42
Energy contribution -18.53
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.45
Structure conservation index 0.90
SVM decision value 0.76
SVM RNA-class probability 0.844292
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2533817 104 - 23771897
CGUUUAACCCUCUGAACAAAAGAGGAUUACUUCCCUUAAUAAGUCAAACGAAAUGGCUAGUUGGGAAUUAUAAGGCAGAAGAGUGGAAAUGUUUCACUAUAUUU
.((((...(((((.......))))).....(((((..(((.(((((.......))))).)))))))).....)))).....((((((.....))))))...... ( -22.80)
>DroSec_CAF1 156669 84 - 1
CGUUUAACCCUCUGAACAACAGAGGAUUACUUCCCUUAAUAAGUCGAACGAAAUGGCUAGUUGGGAAUUAUAAGGCA-----------------CACA---UUU
.((((...((((((.....)))))).....(((((..(((.(((((.......))))).)))))))).....)))).-----------------....---... ( -19.20)
>DroSim_CAF1 154238 86 - 1
CGUUUAACCCUCUGAACAACAGAGGAUUACUUCCCUUAAUAAGUCGAACGAAAUGGCUAGUUGGGAAUUAUAAGGCA-----------------CACUGU-AUU
.((((...((((((.....)))))).....(((((..(((.(((((.......))))).)))))))).....)))).-----------------......-... ( -19.20)
>consensus
CGUUUAACCCUCUGAACAACAGAGGAUUACUUCCCUUAAUAAGUCGAACGAAAUGGCUAGUUGGGAAUUAUAAGGCA_________________CACU_U_UUU
.((((...((((((.....)))))).....(((((..(((.(((((.......))))).)))))))).....))))............................ (-18.42 = -18.53 +   0.11)

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 09:52:22 2006