Locus 7771

Sequence ID 3L_DroMel_CAF1
Location 20,735,018 – 20,735,191
Length 173
Max. P 0.994888
window12651 window12652 window12653 window12654

overview

Window 1

Location 20,735,018 – 20,735,111
Length 93
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.10
Mean single sequence MFE -30.27
Consensus MFE -25.75
Energy contribution -25.38
Covariance contribution -0.38
Combinations/Pair 1.09
Mean z-score -1.46
Structure conservation index 0.85
SVM decision value 0.13
SVM RNA-class probability 0.598022
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20735018 93 + 23771897
UGGUAUUCACGCCAGCUGUCAAGGCUGUGAGUGACUCCUUCAUGGACAUCACGCCAUUGGGAUUUACUGAUCCCAAUCCUGCUGCUCCCG---------------------------CUC
.(((..(((((((.........))).))))((((.(((.....)))..)))))))(((((((((....)))))))))......((....)---------------------------).. ( -29.00)
>DroSec_CAF1 10482 93 + 1
UGGUAUUCACGCCAGCUGUCAAGGCUGUGAGUGACUCCUUCAUGGACAUCACGCCAUUGGGGUUUACUGAUCCCACUCCUGCUGCUCCUG---------------------------CUC
((((..(((((((.........))).))))((((.(((.....)))..)))))))).(((((((....)))))))........((....)---------------------------).. ( -27.80)
>DroSim_CAF1 13612 93 + 1
UGGUAUUCACGCCAGCUGUCAAGGCUGUGAGUGACUCCUUCAUGGACAUCACGCCAUUGGGAUUUACUGAUCCCACUCCUGCUGCUCCUG---------------------------CUC
((((..(((((((.........))).))))((((.(((.....)))..)))))))).(((((((....)))))))........((....)---------------------------).. ( -28.40)
>DroYak_CAF1 12267 120 + 1
GGGUACACACCCCAGCGGUCAAGGCUGUGAGUGACUCCUUCAUGGACAUCACGCCAUUGGGAUUUACUGAUCCUACUCCUGCUGCUCCUGCUCAUGCUGCUCCCGCUCCGGUUUCCGCUC
((((....)))).(((((...((((((.(((((..(((.....)))......((...(((((((....))))))).....((.((....))....)).))...)))))))))))))))). ( -35.90)
>consensus
UGGUAUUCACGCCAGCUGUCAAGGCUGUGAGUGACUCCUUCAUGGACAUCACGCCAUUGGGAUUUACUGAUCCCACUCCUGCUGCUCCUG___________________________CUC
............((((......(((.((((.((..(((.....))))))))))))..(((((((....))))))).....)))).................................... (-25.75 = -25.38 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,735,058 – 20,735,151
Length 93
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.32
Mean single sequence MFE -19.97
Consensus MFE -14.38
Energy contribution -14.25
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -1.60
Structure conservation index 0.72
SVM decision value 0.15
SVM RNA-class probability 0.609196
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20735058 93 + 23771897
CAUGGACAUCACGCCAUUGGGAUUUACUGAUCCCAAUCCUGCUGCUCCCG---------------------------CUCCAGCUCCAGUUGCAACUCUAUAUCCUCCAACUCAACAAAG
..((((.........(((((((((....)))))))))..(((.(((...(---------------------------(....))...))).)))...........))))........... ( -20.70)
>DroSec_CAF1 10522 93 + 1
CAUGGACAUCACGCCAUUGGGGUUUACUGAUCCCACUCCUGCUGCUCCUG---------------------------CUCCAGCUCCAGUUGAAACUGUAUAUCCUCCAACUCAACAAAG
..((((...........(((((((....)))))))...(((..((....)---------------------------)..))).))))(((((..................))))).... ( -19.47)
>DroSim_CAF1 13652 93 + 1
CAUGGACAUCACGCCAUUGGGAUUUACUGAUCCCACUCCUGCUGCUCCUG---------------------------CUCCAGCUCCAGUUGUAACUCUAUAUCCUCCAACUCAACAAAG
..((((............((((((....))))))((..(((..(((....---------------------------....)))..)))..))............))))........... ( -18.70)
>DroYak_CAF1 12307 120 + 1
CAUGGACAUCACGCCAUUGGGAUUUACUGAUCCUACUCCUGCUGCUCCUGCUCAUGCUGCUCCCGCUCCGGUUUCCGCUCCAGCUCCUGUUACAACUCUGUAUCCUCCAGCUCAACAAAG
..((((......(((..(((((((....))))))).....((.((....((....)).))....))...)))......))))(((.....((((....))))......)))......... ( -21.00)
>consensus
CAUGGACAUCACGCCAUUGGGAUUUACUGAUCCCACUCCUGCUGCUCCUG___________________________CUCCAGCUCCAGUUGCAACUCUAUAUCCUCCAACUCAACAAAG
..((((......((...(((((((....))))))).....))......................................((((....)))).............))))........... (-14.38 = -14.25 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,735,098 – 20,735,191
Length 93
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.69
Mean single sequence MFE -32.44
Consensus MFE -23.29
Energy contribution -23.60
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -2.18
Structure conservation index 0.72
SVM decision value 1.27
SVM RNA-class probability 0.938760
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20735098 93 + 23771897
GCUGCUCCCG---------------------------CUCCAGCUCCAGUUGCAACUCUAUAUCCUCCAACUCAACAAAGUUUAAUGGAGCUCGAAGAGGACAGCAUUGUAAGGGAGAUG
....((((((---------------------------(....))....((((...((((.....((((((((......)))....))))).....))))..)))).......)))))... ( -24.40)
>DroSec_CAF1 10562 93 + 1
GCUGCUCCUG---------------------------CUCCAGCUCCAGUUGAAACUGUAUAUCCUCCAACUCAACAAAGUUUAAUGGAGCUGGAAGAGGACAGCAUUGUAAGGGAGAUG
((((.((((.---------------------------.((((((((((....(((((.....................)))))..))))))))))..))))))))............... ( -34.70)
>DroSim_CAF1 13692 93 + 1
GCUGCUCCUG---------------------------CUCCAGCUCCAGUUGUAACUCUAUAUCCUCCAACUCAACAAAGUUUAAUGGAGCUGGAAGAGGACAGCAUUGUGAGGGAGAUG
((((.((((.---------------------------.((((((((((.....((((.....................))))...))))))))))..))))))))............... ( -31.90)
>DroYak_CAF1 12347 120 + 1
GCUGCUCCUGCUCAUGCUGCUCCCGCUCCGGUUUCCGCUCCAGCUCCUGUUACAACUCUGUAUCCUCCAGCUCAACAAAGUUCAAUGGAGCUGGAAGACGACAGCAUUGUGAGGGAGAUG
((.((....))....))..((((((((..(((....)))..))).....((((((..((((.((.((((((((..............)))))))).))..))))..)))))))))))... ( -38.74)
>consensus
GCUGCUCCUG___________________________CUCCAGCUCCAGUUGCAACUCUAUAUCCUCCAACUCAACAAAGUUUAAUGGAGCUGGAAGAGGACAGCAUUGUAAGGGAGAUG
....(((((.............................((((((((((.....((((.....................))))...)))))))))).....((......))..)))))... (-23.29 = -23.60 +   0.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,735,098 – 20,735,191
Length 93
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.69
Mean single sequence MFE -36.56
Consensus MFE -25.27
Energy contribution -25.89
Covariance contribution 0.62
Combinations/Pair 1.07
Mean z-score -2.95
Structure conservation index 0.69
SVM decision value 2.52
SVM RNA-class probability 0.994888
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20735098 93 - 23771897
CAUCUCCCUUACAAUGCUGUCCUCUUCGAGCUCCAUUAAACUUUGUUGAGUUGGAGGAUAUAGAGUUGCAACUGGAGCUGGAG---------------------------CGGGAGCAGC
...............((((((((.(((.(((((((...((((((((.............)))))))).....))))))).)))---------------------------.)))).)))) ( -31.42)
>DroSec_CAF1 10562 93 - 1
CAUCUCCCUUACAAUGCUGUCCUCUUCCAGCUCCAUUAAACUUUGUUGAGUUGGAGGAUAUACAGUUUCAACUGGAGCUGGAG---------------------------CAGGAGCAGC
...............((((((((.((((((((((......(......)((((((((.........))))))))))))))))))---------------------------.)))).)))) ( -34.30)
>DroSim_CAF1 13692 93 - 1
CAUCUCCCUCACAAUGCUGUCCUCUUCCAGCUCCAUUAAACUUUGUUGAGUUGGAGGAUAUAGAGUUACAACUGGAGCUGGAG---------------------------CAGGAGCAGC
...............((((((((.(((((((((((...((((((((.............)))))))).....)))))))))))---------------------------.)))).)))) ( -34.72)
>DroYak_CAF1 12347 120 - 1
CAUCUCCCUCACAAUGCUGUCGUCUUCCAGCUCCAUUGAACUUUGUUGAGCUGGAGGAUACAGAGUUGUAACAGGAGCUGGAGCGGAAACCGGAGCGGGAGCAGCAUGAGCAGGAGCAGC
...((((...(((((.((((.((((((((((((.((........)).)))))))))))))))).))))).......(((.(.(((....)....((....)).)).).))).)))).... ( -45.80)
>consensus
CAUCUCCCUCACAAUGCUGUCCUCUUCCAGCUCCAUUAAACUUUGUUGAGUUGGAGGAUAUAGAGUUGCAACUGGAGCUGGAG___________________________CAGGAGCAGC
...............((((((((.(((((((((((...((((((((.............)))))))).....)))))))))))............................)))).)))) (-25.27 = -25.89 +   0.62)

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 12:56:34 2006