Locus 8500

Sequence ID X_DroMel_CAF1
Location 21,068,217 – 21,068,367
Length 150
Max. P 0.970546
window13995 window13996 window13997

overview

Window 5

Location 21,068,217 – 21,068,327
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.23
Mean single sequence MFE -33.15
Consensus MFE -19.67
Energy contribution -20.80
Covariance contribution 1.13
Combinations/Pair 1.07
Mean z-score -2.56
Structure conservation index 0.59
SVM decision value 0.66
SVM RNA-class probability 0.813710
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21068217 110 + 22224390
GUCGGGGGAUUUCCCGCAUUUCCCCCGUUCGCUAU---GCGCUUUUCAGUUGAUUUGGCACUUUUCAUGUGCUGCUAAGUGAUUUCCCAAAAUCAU-------UGCUUGGUAUUUUUACA
..(((((((...........)))))))...((((.---((((...((....))...(((((.......)))))))..((((((((....)))))))-------))).))))......... ( -29.90)
>DroSim_CAF1 24344 110 + 1
GUCGGGGGAUUUCCCGCACUUCCCCCGUUCGCUGU---GCGCUUUUCAGCUGAUUUGGCACUUUUCAUGUGCUGCUAAGUGAUUUUCCAAAAUCAU-------UGCUUGGUAUUUUUGCA
..(((((((...........)))))))...((((.---........))))......(((((.......)))))((((((((((((....)))))..-------.)))))))......... ( -31.50)
>DroEre_CAF1 38713 116 + 1
GCCGGGGUCC-UUCCACAUUUCCCUCGAUGCCCCU---GCGCUUUUCAGCUGAUUUGGCACUUUUCAUGUGCUGCUAAGUGAUUUCCCAAAAUCAUUUGGAUGUGCUUGGUGUUUUUGCA
((.(((((..-.((............)).))))).---))((......((..(...(((((.......))))).(((((((((((....)))))))))))......)..))......)). ( -31.30)
>DroYak_CAF1 44466 120 + 1
GUCGGGGGCUUUUCCACACUUGCCCCCUUCGCCUUUUCGCGCUUUUCAGCUGAUUUGGCACUUUUCAUGUGCAGCUAAGUGAUUUCCCAAAAUCAUUUAGAUGUGCUUGGUAUUUUUUCA
...((((((............))))))...(((...(((.(((....))))))...))).....(((.(..((.(((((((((((....))))))))))).))..).))).......... ( -39.90)
>consensus
GUCGGGGGAUUUCCCACACUUCCCCCGUUCGCCAU___GCGCUUUUCAGCUGAUUUGGCACUUUUCAUGUGCUGCUAAGUGAUUUCCCAAAAUCAU_______UGCUUGGUAUUUUUGCA
..(((((((...........))))))).............(((....)))......(((((.......)))))((((((((((((....)))))..........)))))))......... (-19.67 = -20.80 +   1.13)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,068,217 – 21,068,327
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.23
Mean single sequence MFE -29.10
Consensus MFE -19.17
Energy contribution -20.67
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -1.86
Structure conservation index 0.66
SVM decision value 0.34
SVM RNA-class probability 0.696815
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21068217 110 - 22224390
UGUAAAAAUACCAAGCA-------AUGAUUUUGGGAAAUCACUUAGCAGCACAUGAAAAGUGCCAAAUCAACUGAAAAGCGC---AUAGCGAACGGGGGAAAUGCGGGAAAUCCCCCGAC
..............((.-------.((((((.((.....(((((..((.....))..))))))))))))).((....)).))---........(((((((...........))))))).. ( -26.10)
>DroSim_CAF1 24344 110 - 1
UGCAAAAAUACCAAGCA-------AUGAUUUUGGAAAAUCACUUAGCAGCACAUGAAAAGUGCCAAAUCAGCUGAAAAGCGC---ACAGCGAACGGGGGAAGUGCGGGAAAUCCCCCGAC
(((..............-------.((((((.((.....(((((..((.....))..)))))))))))))(((....)))))---).......(((((((...........))))))).. ( -30.70)
>DroEre_CAF1 38713 116 - 1
UGCAAAAACACCAAGCACAUCCAAAUGAUUUUGGGAAAUCACUUAGCAGCACAUGAAAAGUGCCAAAUCAGCUGAAAAGCGC---AGGGGCAUCGAGGGAAAUGUGGAA-GGACCCCGGC
..........((..((.........((((((.((.....(((((..((.....))..)))))))))))))(((....)))))---.(((((.((.(.(....).).)).-.).)))))). ( -26.90)
>DroYak_CAF1 44466 120 - 1
UGAAAAAAUACCAAGCACAUCUAAAUGAUUUUGGGAAAUCACUUAGCUGCACAUGAAAAGUGCCAAAUCAGCUGAAAAGCGCGAAAAGGCGAAGGGGGCAAGUGUGGAAAAGCCCCCGAC
..............(((...((((.((((((....)))))).)))).)))..........((((...((.(((....)))..))...))))..((((((............))))))... ( -32.70)
>consensus
UGCAAAAAUACCAAGCA_______AUGAUUUUGGGAAAUCACUUAGCAGCACAUGAAAAGUGCCAAAUCAGCUGAAAAGCGC___AAAGCGAACGGGGGAAAUGCGGAAAAGCCCCCGAC
..............((.........((((((.((.....(((((..((.....))..)))))))))))))(((....)))))...........((((((.............)))))).. (-19.17 = -20.67 +   1.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,068,254 – 21,068,367
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.20
Mean single sequence MFE -32.45
Consensus MFE -25.19
Energy contribution -25.50
Covariance contribution 0.31
Combinations/Pair 1.06
Mean z-score -3.10
Structure conservation index 0.78
SVM decision value 1.66
SVM RNA-class probability 0.970546
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21068254 113 + 22224390
GCUUUUCAGUUGAUUUGGCACUUUUCAUGUGCUGCUAAGUGAUUUCCCAAAAUCAU-------UGCUUGGUAUUUUUACAACGUUCCCCCGCAUUUUGUGCUAAUAUUGGAGAAGCCUUU
(((((((.((((....(((((.......)))))((((((((((((....)))))..-------.))))))).......))))........((((...))))........))))))).... ( -28.90)
>DroSim_CAF1 24381 113 + 1
GCUUUUCAGCUGAUUUGGCACUUUUCAUGUGCUGCUAAGUGAUUUUCCAAAAUCAU-------UGCUUGGUAUUUUUGCAACGUUCCCCCGCAUUUUGCGCUAAUAUCAGAGAAGCCUUU
((((((((((......(((((.......)))))....((((((((....)))))))-------))))(((((((..(((((.((........)).)))))..)))))))))))))).... ( -30.90)
>DroEre_CAF1 38749 120 + 1
GCUUUUCAGCUGAUUUGGCACUUUUCAUGUGCUGCUAAGUGAUUUCCCAAAAUCAUUUGGAUGUGCUUGGUGUUUUUGCAGCGUUCCCUCGCAUUCUCCGCUAAUAUCCGAGAAGCCUUU
(((((((.((((....((((((......(..(..(((((((((((....)))))))))))..)..)..))))))....))))........((.......))........))))))).... ( -35.00)
>DroYak_CAF1 44506 120 + 1
GCUUUUCAGCUGAUUUGGCACUUUUCAUGUGCAGCUAAGUGAUUUCCCAAAAUCAUUUAGAUGUGCUUGGUAUUUUUUCAGCACUCCCUCGCAUUUUGCGCUAAUAUCCGAGAAGCCUUU
(((((((.(((((...((.(((......(..((.(((((((((((....))))))))))).))..)..))).))...))))).......(((.....))).........))))))).... ( -35.00)
>consensus
GCUUUUCAGCUGAUUUGGCACUUUUCAUGUGCUGCUAAGUGAUUUCCCAAAAUCAU_______UGCUUGGUAUUUUUGCAACGUUCCCCCGCAUUUUGCGCUAAUAUCCGAGAAGCCUUU
(((((((.((((....(((((.......)))))((((((((((((....)))))..........))))))).......)))).......(((.....))).........))))))).... (-25.19 = -25.50 +   0.31)

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 13:05:59 2006