Locus 4051

Sequence ID 3L_DroMel_CAF1
Location 11,799,646 – 11,799,782
Length 136
Max. P 0.967683
window6309 window6310 window6311 window6312

overview

Window 9

Location 11,799,646 – 11,799,745
Length 99
Sequences 3
Columns 103
Reading direction forward
Mean pairwise identity 82.84
Mean single sequence MFE -24.30
Consensus MFE -19.18
Energy contribution -19.73
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.62
Structure conservation index 0.79
SVM decision value 1.61
SVM RNA-class probability 0.967683
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11799646 99 + 23771897
CACCAAUCGUAUAAGGGCAAAACAUUUAUAAUCGAUAGUUUUCUAUCGAUUAUAAAGCAAUCGCGGGCUUUGCAUUCAC----UGUUAUUCAGGCAUUCAUUG
........((......(((((.(.((((((((((((((....))))))))))))))((....))..).))))).....(----((.....)))))........ ( -24.30)
>DroSec_CAF1 9182 97 + 1
CAACACUCGUAUUAGGGCAAAACAUUUAUAAUCGAUAGUUGUCUAUCGAUUUUGAAGCAAUCGCUGGUUUUGCUAUCGCAUUGCGUUAU------AUCCUCUG
.............(((..(.(((.((((.(((((((((....))))))))).))))(((((((.(((.....))).)).)))))))).)------..)))... ( -25.50)
>DroSim_CAF1 8777 97 + 1
CACCACUCGUAUUAGGGCAAAACAUUUAUAAUCGAUAGUUUUCUAUCGAUUUUCAAGCAAUCGCUGGUUUUGCUAUCACACUGCGUUAU------AUUCUCUG
.......((((....((((((((......(((((((((....)))))))))....(((....))).)))))))).......))))....------........ ( -23.10)
>consensus
CACCACUCGUAUUAGGGCAAAACAUUUAUAAUCGAUAGUUUUCUAUCGAUUUUAAAGCAAUCGCUGGUUUUGCUAUCACA_UGCGUUAU______AUUCUCUG
................(((((((.((((.(((((((((....))))))))).))))((....))..))))))).............................. (-19.18 = -19.73 +   0.56)

alignment

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secondary structure

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Window 0

Location 11,799,646 – 11,799,745
Length 99
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 82.84
Mean single sequence MFE -24.30
Consensus MFE -17.75
Energy contribution -17.53
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -2.37
Structure conservation index 0.73
SVM decision value 1.08
SVM RNA-class probability 0.912471
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11799646 99 - 23771897
CAAUGAAUGCCUGAAUAACA----GUGAAUGCAAAGCCCGCGAUUGCUUUAUAAUCGAUAGAAAACUAUCGAUUAUAAAUGUUUUGCCCUUAUACGAUUGGUG
........(((..(((....----((((..(((((((..((....))((((((((((((((....)))))))))))))).)))))))..))))...)))))). ( -25.60)
>DroSec_CAF1 9182 97 - 1
CAGAGGAU------AUAACGCAAUGCGAUAGCAAAACCAGCGAUUGCUUCAAAAUCGAUAGACAACUAUCGAUUAUAAAUGUUUUGCCCUAAUACGAGUGUUG
...(((..------....(((...)))...(((((((.(((....)))....(((((((((....)))))))))......))))))))))............. ( -22.70)
>DroSim_CAF1 8777 97 - 1
CAGAGAAU------AUAACGCAGUGUGAUAGCAAAACCAGCGAUUGCUUGAAAAUCGAUAGAAAACUAUCGAUUAUAAAUGUUUUGCCCUAAUACGAGUGGUG
........------....(((.((((....(((((((.(((....)))....(((((((((....)))))))))......)))))))....))))..)))... ( -24.60)
>consensus
CAGAGAAU______AUAACGCA_UGUGAUAGCAAAACCAGCGAUUGCUUCAAAAUCGAUAGAAAACUAUCGAUUAUAAAUGUUUUGCCCUAAUACGAGUGGUG
..............................(((((((..((....)).....(((((((((....)))))))))......)))))))................ (-17.75 = -17.53 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,799,673 – 11,799,782
Length 109
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 78.95
Mean single sequence MFE -23.93
Consensus MFE -13.98
Energy contribution -15.54
Covariance contribution 1.56
Combinations/Pair 1.09
Mean z-score -2.11
Structure conservation index 0.58
SVM decision value 0.42
SVM RNA-class probability 0.729875
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11799673 109 + 23771897
AUAAUCGAUAGUUUUCUAUCGAUUAUAAAGCAAUCGCGGGCUUUGCAUUCAC----UGUUAUUCAGGCAUUCAUUGUUA---UCCUAAAACAGUUAAUAAAAAGGAAAAGAAAAAU
(((((((((((....)))))))))))...((....))...((((..(((.((----((((....(((.((........)---))))..)))))).)))..))))............ ( -22.80)
>DroSec_CAF1 9209 110 + 1
AUAAUCGAUAGUUGUCUAUCGAUUUUGAAGCAAUCGCUGGUUUUGCUAUCGCAUUGCGUUAU------AUCCUCUGUUUUUUGCUUAGAAUAAUUAAUAAAAAGAAGCAGAAAAUU
..(((((((((....))))))))).....(((((((.(((.....))).)).))))).....------....((((((((((..(((..........))).))))))))))..... ( -26.90)
>DroSim_CAF1 8804 110 + 1
AUAAUCGAUAGUUUUCUAUCGAUUUUCAAGCAAUCGCUGGUUUUGCUAUCACACUGCGUUAU------AUUCUCUGUUUUUUGCUUAGAACAAUUAAUAAAAAGAAGCAGAAAAUU
..(((((((((....)))))))))....(((((.........)))))......((((.((.(------(((...((((((......))))))...)))).))....))))...... ( -22.10)
>consensus
AUAAUCGAUAGUUUUCUAUCGAUUUUAAAGCAAUCGCUGGUUUUGCUAUCACA_UGCGUUAU______AUUCUCUGUUUUUUGCUUAGAACAAUUAAUAAAAAGAAGCAGAAAAUU
..(((((((((....))))))))).....((((.........))))..........................((((((((((...................))))))))))..... (-13.98 = -15.54 +   1.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,799,673 – 11,799,782
Length 109
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 78.95
Mean single sequence MFE -21.67
Consensus MFE -13.75
Energy contribution -13.87
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -1.86
Structure conservation index 0.63
SVM decision value 0.48
SVM RNA-class probability 0.752894
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11799673 109 - 23771897
AUUUUUCUUUUCCUUUUUAUUAACUGUUUUAGGA---UAACAAUGAAUGCCUGAAUAACA----GUGAAUGCAAAGCCCGCGAUUGCUUUAUAAUCGAUAGAAAACUAUCGAUUAU
............((((.((((.((((((((((((---(........)).)))))..))))----)).)))).))))...((....))...(((((((((((....))))))))))) ( -23.90)
>DroSec_CAF1 9209 110 - 1
AAUUUUCUGCUUCUUUUUAUUAAUUAUUCUAAGCAAAAAACAGAGGAU------AUAACGCAAUGCGAUAGCAAAACCAGCGAUUGCUUCAAAAUCGAUAGACAACUAUCGAUUAU
.((((((((....(((((.(((.......)))..))))).))))))))------..........(((((.((.......)).))))).....(((((((((....))))))))).. ( -20.90)
>DroSim_CAF1 8804 110 - 1
AAUUUUCUGCUUCUUUUUAUUAAUUGUUCUAAGCAAAAAACAGAGAAU------AUAACGCAGUGUGAUAGCAAAACCAGCGAUUGCUUGAAAAUCGAUAGAAAACUAUCGAUUAU
.((((((((....(((((.(((.......)))..))))).))))))))------......(((.(..((.((.......)).))..))))..(((((((((....))))))))).. ( -20.20)
>consensus
AAUUUUCUGCUUCUUUUUAUUAAUUGUUCUAAGCAAAAAACAGAGAAU______AUAACGCA_UGUGAUAGCAAAACCAGCGAUUGCUUCAAAAUCGAUAGAAAACUAUCGAUUAU
................................................................(((((.((.......)).))))).....(((((((((....))))))))).. (-13.75 = -13.87 +   0.11)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:23 2006