Locus 7515

Sequence ID 3L_DroMel_CAF1
Location 20,202,280 – 20,202,422
Length 142
Max. P 0.999920
window12221 window12222 window12223

overview

Window 1

Location 20,202,280 – 20,202,400
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.33
Mean single sequence MFE -29.92
Consensus MFE -14.54
Energy contribution -17.66
Covariance contribution 3.12
Combinations/Pair 1.12
Mean z-score -2.52
Structure conservation index 0.49
SVM decision value 1.98
SVM RNA-class probability 0.984744
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20202280 120 - 23771897
AAGUUUCACUAGGAAAAGUAAUUAAAUUACUUUUCUUAGGGAAACUAGACAUACUACUCGCAGUGCCGAAAAUAUUUAUCCUACUUUCCAGAGUGUAAAGUUCUUUUUUGCUGAGAUCAU
.((((((.((((((((((((((...)))))))))))))).))))))..........(((((((....(((....(((((...((((....))))))))).)))....)))).)))..... ( -31.40)
>DroSec_CAF1 16188 120 - 1
AAGAUUCGCUAGGAAAAGUACAUAGAUUUCUUUUCUUAGGGAAUCUAGACAUACUACUCGCAGUGCCGAAAAUAUUGCUCCUACUCUUCAGAGUGUAGAGUUCUUUUUUUCUGAGAUCGU
.((((((.((((((((((...........)))))))))).))))))..........(((((...)).(((((....((((.(((((....)))))..)))).....))))).)))..... ( -32.50)
>DroSim_CAF1 11145 120 - 1
AAUUUUCGCUAGGAAAAGUACAUAGAUUUCUUUUCUUAGGGAAUCUAGACAUACUACUCGCAGUGCCGAAAAUAUUGCUCCUACUCUUCAGAGUGUAGAGUUCUUUUUUCCUGAGAUCGU
.....((..((((((((((...((((((((((.....)))))))))).)).....((((((((((.......))))))...(((((....)))))..))))....)))))))).)).... ( -31.40)
>DroEre_CAF1 11463 99 - 1
UAGUUUCCCUAGGAAAAUUAGUUAAAUUACUUGUCUUAG---------------------CAUUGCCGAAAAGAGUUAUGCUACUUUCCAGAGAGUAUAGUUCUUUUUUGCCGAGAUCGU
((((((..((((.....))))..))))))...((((..(---------------------((.....(((((((..((((((.(((....)))))))))..))))))))))..))))... ( -24.50)
>DroYak_CAF1 24784 120 - 1
UAGUUUCCCUAGGCAAAGUAGUUAAGUUACUCGUCUUAGGGAAACUAUUAGUAUUACAUGCAUGGCUGAAAAUUUUUGUCGUACUUUCCAAAGAGUAAAGUUCUUUUUUGCUGAGAUCGU
(((((((((((((...(((((.....)))))...)))))))))))))((((((......(((((((...........)))))((((......))))...)).......))))))...... ( -29.82)
>consensus
AAGUUUCCCUAGGAAAAGUACUUAAAUUACUUUUCUUAGGGAAACUAGACAUACUACUCGCAGUGCCGAAAAUAUUUAUCCUACUUUCCAGAGUGUAAAGUUCUUUUUUGCUGAGAUCGU
.((((((.(((((((((((((.....))))))))))))).))))))....................(((.............(((((.(.....).)))))((((.......))))))). (-14.54 = -17.66 +   3.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,202,320 – 20,202,422
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 73.67
Mean single sequence MFE -23.76
Consensus MFE -10.90
Energy contribution -14.82
Covariance contribution 3.92
Combinations/Pair 1.16
Mean z-score -3.27
Structure conservation index 0.46
SVM decision value 4.26
SVM RNA-class probability 0.999853
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20202320 102 + 23771897
GAUAAAUAUUUUCGGCACUGCGAGUAGUAUGUCUAGUUUCCCUAAGAAAAGUAAUUUAAUUACUUUUCCUAGUGAAACUUAAUCAUAUUACUCAUAUCCAAA
((((..........((...))((((((((((...((((((.(((.((((((((((...)))))))))).))).))))))....)))))))))).)))).... ( -32.30)
>DroSec_CAF1 16228 101 + 1
GAGCAAUAUUUUCGGCACUGCGAGUAGUAUGUCUAGAUUCCCUAAGAAAAGAAAUCUAUGUACUUUUCCUAGCGAAUCUUAGUC-UAUUACUCAUCUCCGAA
..........(((((......((((((((.(.((((((((.(((.((((((...........)))))).))).))))).))).)-))))))))....))))) ( -27.50)
>DroSim_CAF1 11185 101 + 1
GAGCAAUAUUUUCGGCACUGCGAGUAGUAUGUCUAGAUUCCCUAAGAAAAGAAAUCUAUGUACUUUUCCUAGCGAAAAUUAGUC-UAUUACUCAUCUCCGAA
..........(((((......((((((((.(.((((.(((.(((.((((((...........)))))).))).)))..)))).)-))))))))....))))) ( -22.40)
>DroEre_CAF1 11503 80 + 1
CAUAACUCUUUUCGGCAAUG---------------------CUAAGACAAGUAAUUUAACUAAUUUUCCUAGGGAAACUAAGUC-UAUUACUCUUCUGAGAA
.....(((.....(((...)---------------------)).(((..((((((...(((.(.(((((...))))).).))).-.))))))..)))))).. ( -13.30)
>DroYak_CAF1 24824 101 + 1
GACAAAAAUUUUCAGCCAUGCAUGUAAUACUAAUAGUUUCCCUAAGACGAGUAACUUAACUACUUUGCCUAGGGAAACUAAGUC-UAUUACUUUUAUCAAGA
((.((((.......((...))..((((((....(((((((((((.(..(((((.......)))))..).)))))))))))....-)))))))))).)).... ( -23.30)
>consensus
GAGAAAUAUUUUCGGCACUGCGAGUAGUAUGUCUAGAUUCCCUAAGAAAAGUAAUUUAACUACUUUUCCUAGCGAAACUUAGUC_UAUUACUCAUCUCCGAA
.....................((((((((.....((((((.(((.((((((((.......)))))))).))).))))))......))))))))......... (-10.90 = -14.82 +   3.92)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,202,320 – 20,202,422
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 73.67
Mean single sequence MFE -27.56
Consensus MFE -13.13
Energy contribution -17.81
Covariance contribution 4.68
Combinations/Pair 1.14
Mean z-score -3.52
Structure conservation index 0.48
SVM decision value 4.56
SVM RNA-class probability 0.999920
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20202320 102 - 23771897
UUUGGAUAUGAGUAAUAUGAUUAAGUUUCACUAGGAAAAGUAAUUAAAUUACUUUUCUUAGGGAAACUAGACAUACUACUCGCAGUGCCGAAAAUAUUUAUC
(((((.(.((((((.((((.((.((((((.((((((((((((((...)))))))))))))).)))))).)))))).)))))).)...))))).......... ( -35.20)
>DroSec_CAF1 16228 101 - 1
UUCGGAGAUGAGUAAUA-GACUAAGAUUCGCUAGGAAAAGUACAUAGAUUUCUUUUCUUAGGGAAUCUAGACAUACUACUCGCAGUGCCGAAAAUAUUGCUC
(((((...((((((.((-..(((.(((((.((((((((((...........)))))))))).))))))))...)).)))))).....))))).......... ( -31.90)
>DroSim_CAF1 11185 101 - 1
UUCGGAGAUGAGUAAUA-GACUAAUUUUCGCUAGGAAAAGUACAUAGAUUUCUUUUCUUAGGGAAUCUAGACAUACUACUCGCAGUGCCGAAAAUAUUGCUC
(((((...((((((.((-..(((...(((.((((((((((...........)))))))))).)))..)))...)).)))))).....))))).......... ( -27.10)
>DroEre_CAF1 11503 80 - 1
UUCUCAGAAGAGUAAUA-GACUUAGUUUCCCUAGGAAAAUUAGUUAAAUUACUUGUCUUAG---------------------CAUUGCCGAAAAGAGUUAUG
..((.(((.(((((((.-((((...(((((...)))))...))))..))))))).))).))---------------------(((.(((.....).)).))) ( -14.80)
>DroYak_CAF1 24824 101 - 1
UCUUGAUAAAAGUAAUA-GACUUAGUUUCCCUAGGCAAAGUAGUUAAGUUACUCGUCUUAGGGAAACUAUUAGUAUUACAUGCAUGGCUGAAAAUUUUUGUC
....(((((((((((((-....(((((((((((((...(((((.....)))))...)))))))))))))....))))))..((...)).......))))))) ( -28.80)
>consensus
UUCGGAGAUGAGUAAUA_GACUAAGUUUCCCUAGGAAAAGUACUUAAAUUACUUUUCUUAGGGAAACUAGACAUACUACUCGCAGUGCCGAAAAUAUUUAUC
(((((....(((((.........((((((.(((((((((((((.....))))))))))))).))))))........)))))......))))).......... (-13.13 = -17.81 +   4.68)

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 12:49:14 2006