Locus 8356

Sequence ID X_DroMel_CAF1
Location 20,737,871 – 20,737,978
Length 107
Max. P 0.995164
window13720 window13721 window13722 window13723

overview

Window 0

Location 20,737,871 – 20,737,967
Length 96
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 79.32
Mean single sequence MFE -29.72
Consensus MFE -21.31
Energy contribution -22.00
Covariance contribution 0.70
Combinations/Pair 1.04
Mean z-score -2.94
Structure conservation index 0.72
SVM decision value 1.71
SVM RNA-class probability 0.973205
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20737871 96 + 22224390
GCCAAC-----------GUGCAGCCG-G--A--AAACUGCAAUGUGCAAAACUCCGGGCAUGCGAUUUGAAAAUUGUGUCGUCAGCUUGACACAAUUUUCCAGAAAAUGCGC
((...(-----------((((..(((-(--(--....(((.....)))....))))))))))......(((((((((((((......)))))))))))))........)).. ( -33.10)
>DroPse_CAF1 88034 81 + 1
-----------------CUGCAGCAG-GGAA--AAACUGCA---------ACUCCGGGCAUGCGAUUUGAAAAUUGUGUCGUCAGCUUGACACAAUUUUCCAGA--AUGCGC
-----------------.(((.((((-....--...)))).---------.(....)))).(((.((((((((((((((((......)))))))))))).))))--.))).. ( -27.00)
>DroWil_CAF1 91451 96 + 1
GCCUACGAAAGCAGCAGCUGCAGCUG-UGAA--AAACUGCA---------ACUCCGGGCAUGCGAUUUGAAAAUUGUG---UCAGCUUGACACAAUUUUCCAGA-UAUGCGA
((((......((((((((....))))-....--...)))).---------.....)))).((((((((((((((((((---((.....))))))))))).))))-).)))). ( -33.71)
>DroMoj_CAF1 120212 81 + 1
-------------------GUUUUUG-GGAAGCCAACUGCA---------ACUCCGGGCAUGCGAUUUGAAAAUUGUGUCGUCAGCUUGACACAAUUUUCCAGA--AUGCGC
-------------------((..(((-(....))))..)).---------...........(((.((((((((((((((((......)))))))))))).))))--.))).. ( -26.40)
>DroAna_CAF1 1756 87 + 1
AGUAGC-----------AGGCAGCUGGG--A--AAACUGCA---------ACUCCGGGCAUGCGAUUUGAAAAUUGUGUCGUCAGCUUGACACAAUUUUCCAGA-AAUGCGC
....((-----------(.((((((.((--(--........---------..))).))).))).....(((((((((((((......)))))))))))))....-..))).. ( -31.10)
>DroPer_CAF1 90133 81 + 1
-----------------CUGCAGCAG-GGAA--AAACUGCA---------ACUCCGGGCAUGCGAUUUGAAAAUUGUGUCGUCAGCUUGACACAAUUUUCCAGA--AUGCGC
-----------------.(((.((((-....--...)))).---------.(....)))).(((.((((((((((((((((......)))))))))))).))))--.))).. ( -27.00)
>consensus
_________________CUGCAGCUG_GGAA__AAACUGCA_________ACUCCGGGCAUGCGAUUUGAAAAUUGUGUCGUCAGCUUGACACAAUUUUCCAGA__AUGCGC
...................((((.............)))).................((((....((((((((((((((((......)))))))))))).))))..)))).. (-21.31 = -22.00 +   0.70)

alignment

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secondary structure

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Window 1

Location 20,737,871 – 20,737,967
Length 96
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 79.32
Mean single sequence MFE -29.70
Consensus MFE -21.17
Energy contribution -22.12
Covariance contribution 0.95
Combinations/Pair 1.09
Mean z-score -3.10
Structure conservation index 0.71
SVM decision value 1.75
SVM RNA-class probability 0.975702
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20737871 96 - 22224390
GCGCAUUUUCUGGAAAAUUGUGUCAAGCUGACGACACAAUUUUCAAAUCGCAUGCCCGGAGUUUUGCACAUUGCAGUUU--U--C-CGGCUGCAC-----------GUUGGC
(((.((((....((((((((((((........))))))))))))))))))).(((((((((..((((.....))))..)--)--)-)))..))).-----------...... ( -35.60)
>DroPse_CAF1 88034 81 - 1
GCGCAU--UCUGGAAAAUUGUGUCAAGCUGACGACACAAUUUUCAAAUCGCAUGCCCGGAGU---------UGCAGUUU--UUCC-CUGCUGCAG-----------------
(((.((--(...((((((((((((........)))))))))))).))))))...........---------((((((..--....-..)))))).----------------- ( -27.70)
>DroWil_CAF1 91451 96 - 1
UCGCAUA-UCUGGAAAAUUGUGUCAAGCUGA---CACAAUUUUCAAAUCGCAUGCCCGGAGU---------UGCAGUUU--UUCA-CAGCUGCAGCUGCUGCUUUCGUAGGC
..((((.-....((((((((((((.....))---)))))))))).......))))..(.(((---------(((((((.--....-.)))))))))).).((((....)))) ( -35.20)
>DroMoj_CAF1 120212 81 - 1
GCGCAU--UCUGGAAAAUUGUGUCAAGCUGACGACACAAUUUUCAAAUCGCAUGCCCGGAGU---------UGCAGUUGGCUUCC-CAAAAAC-------------------
(((.((--((((((((((((((((........)))))))))))).....(....).))))))---------)))..((((....)-)))....------------------- ( -24.40)
>DroAna_CAF1 1756 87 - 1
GCGCAUU-UCUGGAAAAUUGUGUCAAGCUGACGACACAAUUUUCAAAUCGCAUGCCCGGAGU---------UGCAGUUU--U--CCCAGCUGCCU-----------GCUACU
(((.(((-(...((((((((((((........)))))))))))))))))))........(((---------.((((((.--.--...))))))..-----------)))... ( -27.60)
>DroPer_CAF1 90133 81 - 1
GCGCAU--UCUGGAAAAUUGUGUCAAGCUGACGACACAAUUUUCAAAUCGCAUGCCCGGAGU---------UGCAGUUU--UUCC-CUGCUGCAG-----------------
(((.((--(...((((((((((((........)))))))))))).))))))...........---------((((((..--....-..)))))).----------------- ( -27.70)
>consensus
GCGCAU__UCUGGAAAAUUGUGUCAAGCUGACGACACAAUUUUCAAAUCGCAUGCCCGGAGU_________UGCAGUUU__UUCC_CAGCUGCAG_________________
..((((......((((((((((((........)))))))))))).......)))).................((((((.........))))))................... (-21.17 = -22.12 +   0.95)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,737,888 – 20,737,978
Length 90
Sequences 6
Columns 91
Reading direction forward
Mean pairwise identity 87.41
Mean single sequence MFE -31.80
Consensus MFE -26.60
Energy contribution -27.43
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -4.65
Structure conservation index 0.84
SVM decision value 2.55
SVM RNA-class probability 0.995164
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20737888 90 + 22224390
-AAACUGCAAUGUGCAAAACUCCGGGCAUGCGAUUUGAAAAUUGUGUCGUCAGCUUGACACAAUUUUCCAGAAAAUGCGCCUGGAAUGGAG
-....(((.....)))....(((((((..(((.((((((((((((((((......)))))))))))))...))).))))))))))...... ( -32.00)
>DroVir_CAF1 78364 80 + 1
CCAACUGCA---------ACUCCGGGCAUGCGAUUUGAAAAUUGUGUCGUCAGCUUGACACAAUUUUCCAGA--AUGCGCCUGGAACGUAG
....((((.---------..(((((((..(((.((((((((((((((((......)))))))))))).))))--.))))))))))..)))) ( -34.70)
>DroGri_CAF1 84275 76 + 1
-CAAUUGCA---------ACUCCGGGCAUGCGAUUCGAAAAUUGUGUCGUCAGCUUGACACAAUUUUCCAGA--AUGCGCCUGGAACG---
-........---------..(((((((..((.(((((((((((((((((......)))))))))))))..))--)))))))))))...--- ( -32.00)
>DroWil_CAF1 91481 76 + 1
-AAACUGCA---------ACUCCGGGCAUGCGAUUUGAAAAUUGUG---UCAGCUUGACACAAUUUUCCAGA-UAUGCGACUGGAAAUGG-
-......((---------..(((((...((((((((((((((((((---((.....))))))))))).))))-).)))).)))))..)).- ( -27.20)
>DroMoj_CAF1 120224 80 + 1
CCAACUGCA---------ACUCCGGGCAUGCGAUUUGAAAAUUGUGUCGUCAGCUUGACACAAUUUUCCAGA--AUGCGCCUGGAACGCAC
.....(((.---------..(((((((..(((.((((((((((((((((......)))))))))))).))))--.))))))))))..))). ( -34.20)
>DroAna_CAF1 1774 80 + 1
-AAACUGCA---------ACUCCGGGCAUGCGAUUUGAAAAUUGUGUCGUCAGCUUGACACAAUUUUCCAGA-AAUGCGCCUGGAAUGGAA
-........---------..(((((((..(((.((((((((((((((((......)))))))))))))..))-).))))))))))...... ( -30.70)
>consensus
_AAACUGCA_________ACUCCGGGCAUGCGAUUUGAAAAUUGUGUCGUCAGCUUGACACAAUUUUCCAGA__AUGCGCCUGGAACGGA_
....................(((((((..(((.((((((((((((((((......)))))))))))).))))...))))))))))...... (-26.60 = -27.43 +   0.83)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,737,888 – 20,737,978
Length 90
Sequences 6
Columns 91
Reading direction reverse
Mean pairwise identity 87.41
Mean single sequence MFE -26.43
Consensus MFE -23.30
Energy contribution -23.80
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.96
Structure conservation index 0.88
SVM decision value 2.22
SVM RNA-class probability 0.990597
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20737888 90 - 22224390
CUCCAUUCCAGGCGCAUUUUCUGGAAAAUUGUGUCAAGCUGACGACACAAUUUUCAAAUCGCAUGCCCGGAGUUUUGCACAUUGCAGUUU-
....(((((.((.((((......((((((((((((........)))))))))))).......))))))))))).((((.....))))...- ( -29.32)
>DroVir_CAF1 78364 80 - 1
CUACGUUCCAGGCGCAU--UCUGGAAAAUUGUGUCAAGCUGACGACACAAUUUUCAAAUCGCAUGCCCGGAGU---------UGCAGUUGG
.....((((.(((((((--(...((((((((((((........)))))))))))).))).))..))).)))).---------......... ( -25.50)
>DroGri_CAF1 84275 76 - 1
---CGUUCCAGGCGCAU--UCUGGAAAAUUGUGUCAAGCUGACGACACAAUUUUCGAAUCGCAUGCCCGGAGU---------UGCAAUUG-
---..((((.(((((((--((..((((((((((((........)))))))))))))))).))..))).)))).---------........- ( -27.40)
>DroWil_CAF1 91481 76 - 1
-CCAUUUCCAGUCGCAUA-UCUGGAAAAUUGUGUCAAGCUGA---CACAAUUUUCAAAUCGCAUGCCCGGAGU---------UGCAGUUU-
-............(((..-((((((((((((((((.....))---)))))))))).....(....).))))..---------))).....- ( -22.10)
>DroMoj_CAF1 120224 80 - 1
GUGCGUUCCAGGCGCAU--UCUGGAAAAUUGUGUCAAGCUGACGACACAAUUUUCAAAUCGCAUGCCCGGAGU---------UGCAGUUGG
.(((..(((.(((((((--(...((((((((((((........)))))))))))).))).))..))).)))..---------.)))..... ( -27.60)
>DroAna_CAF1 1774 80 - 1
UUCCAUUCCAGGCGCAUU-UCUGGAAAAUUGUGUCAAGCUGACGACACAAUUUUCAAAUCGCAUGCCCGGAGU---------UGCAGUUU-
....(((((.((((....-....((((((((((((........))))))))))))........)))).)))))---------........- ( -26.69)
>consensus
_UCCGUUCCAGGCGCAU__UCUGGAAAAUUGUGUCAAGCUGACGACACAAUUUUCAAAUCGCAUGCCCGGAGU_________UGCAGUUG_
.....((((.((.((((......((((((((((((........)))))))))))).......))))))))))................... (-23.30 = -23.80 +   0.50)

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 13:01:57 2006