Locus 1114

Sequence ID 2R_DroMel_CAF1
Location 4,452,658 – 4,452,779
Length 121
Max. P 0.891274
window1966 window1967

overview

Window 6

Location 4,452,658 – 4,452,751
Length 93
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 77.15
Mean single sequence MFE -29.57
Consensus MFE -19.11
Energy contribution -18.89
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -1.42
Structure conservation index 0.65
SVM decision value 0.42
SVM RNA-class probability 0.729621
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4452658 93 + 20766785
-----UAGCGAUCGGUCC----UCCGCGACCGAUGUGUUGCCAAAGGCGGCUGCUU--CCC-CUCGAGCUCUGCAAUCCAGC-GAACCAAAGGCAGCAUUC---UCCAC
-----.....(((((((.----.....)))))))((((((((....((((..((((--...-...)))).))))..((....-))......))))))))..---..... ( -29.30)
>DroPse_CAF1 29308 102 + 1
GCUACUGCUGAUCGG-CC----AAUAUGGUCGAUGUGUUGCCAAAGGCGCCUGCUU--UUCUUUCGAGCUCUGCAAAGUAGCAGAACCAAAGGCAGCAUUUAAUUUAAC
((....))..(((((-((----.....)))))))((((((((((((((....))))--)).........(((((......)))))......)))))))).......... ( -33.30)
>DroEre_CAF1 847 93 + 1
-----UAGCGAUCGGUCC----UACACGGCCGAUGUGUUGCCAAAGGCGGCUGCUU--UCC-UUCGAGCUCUGCAACCCAGC-GAACCAAAGGCAGCAUUG---UCCAC
-----.(((((((((((.----.....))))))).))))(((...))).(((((((--(..-((((....(((.....))))-)))...))))))))....---..... ( -27.80)
>DroYak_CAF1 419 93 + 1
-----UAGCGAUCGGACC----UCCACGGCCGAUGUGUUGCCAAAGGCGGAUGCUU--UUC-UUCGAGCUCUGCAAUUCAGC-GAACCAAAGGCAGCAUUC---UCCAC
-----.....(((((.((----.....)))))))((((((((....(((((.((((--...-...)))))))))..(((...-))).....))))))))..---..... ( -29.70)
>DroAna_CAF1 758 95 + 1
--------AGAUCGGAGUCCCAUUUAUGACCGAUGUGUUGCCAAAGGCGCCUGCUUUUUUC-UUCGA-UUCUGCAAAGUAGC-GAACCAAAGGCAGCAUAA---ACAAU
--------..(((((..((........)))))))((((((((((((((....))))))...-((((.-..((....))...)-))).....))))))))..---..... ( -24.00)
>DroPer_CAF1 30236 102 + 1
GCUACUGCUGAUCGG-CC----AAUAUGGUCGAUGUGUUGCCAAAGGCGCCUGCUU--UUCUUUCGAGCUCUGCAAAGUAGCAGAACCAAAGGCAGCAUUUAAUUUAAC
((....))..(((((-((----.....)))))))((((((((((((((....))))--)).........(((((......)))))......)))))))).......... ( -33.30)
>consensus
_____UAGCGAUCGG_CC____UACACGGCCGAUGUGUUGCCAAAGGCGCCUGCUU__UUC_UUCGAGCUCUGCAAAGCAGC_GAACCAAAGGCAGCAUUC___UCAAC
..........(((((..............)))))((((((((..((((....)))).............((.((......)).))......)))))))).......... (-19.11 = -18.89 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,452,683 – 4,452,779
Length 96
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 78.20
Mean single sequence MFE -20.80
Consensus MFE -15.27
Energy contribution -15.27
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.59
Structure conservation index 0.73
SVM decision value 0.97
SVM RNA-class probability 0.891274
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4452683 96 + 20766785
GUGUUGCCAAAGGCGGCUGCUU--CCC-CUCGAGCUCUGCAAUCCAGC-GAACCAAAGGCAGCAUUC---UCCACA---CCCAAACUC--ACACACAAACAUCACAAU
((((((((....((((..((((--...-...)))).))))..((....-))......))))))))..---......---.........--.................. ( -19.20)
>DroPse_CAF1 29337 97 + 1
GUGUUGCCAAAGGCGCCUGCUU--UUCUUUCGAGCUCUGCAAAGUAGCAGAACCAAAGGCAGCAUUUAAUUUAACC---CACAUACAC--AUACA----CAUCAUAAU
((((((((((((((....))))--)).........(((((......)))))......))))))))...........---.........--.....----......... ( -22.10)
>DroEre_CAF1 872 92 + 1
GUGUUGCCAAAGGCGGCUGCUU--UCC-UUCGAGCUCUGCAACCCAGC-GAACCAAAGGCAGCAUUG---UCCACU---CCUAAACUC--ACGCAC----AUCACAAU
((((((((...))))(((((((--(..-((((....(((.....))))-)))...))))))))....---......---.........--..))))----........ ( -20.70)
>DroYak_CAF1 444 89 + 1
GUGUUGCCAAAGGCGGAUGCUU--UUC-UUCGAGCUCUGCAAUUCAGC-GAACCAAAGGCAGCAUUC---UCCACU---CCUAAACUC--ACGCAC----AUCA---U
((((((((....(((((.((((--...-...)))))))))..(((...-))).....))))))))..---......---.........--......----....---. ( -21.00)
>DroAna_CAF1 784 98 + 1
GUGUUGCCAAAGGCGCCUGCUUUUUUC-UUCGA-UUCUGCAAAGUAGC-GAACCAAAGGCAGCAUAA---ACAAUGUACUUUAAACUUUCACCCA----CAUCACAAU
((((((((((((((....))))))...-((((.-..((....))...)-))).....))))))))..---.........................----......... ( -19.70)
>DroPer_CAF1 30265 97 + 1
GUGUUGCCAAAGGCGCCUGCUU--UUCUUUCGAGCUCUGCAAAGUAGCAGAACCAAAGGCAGCAUUUAAUUUAACC---CACAUACAC--AUACA----CAUCAUAAU
((((((((((((((....))))--)).........(((((......)))))......))))))))...........---.........--.....----......... ( -22.10)
>consensus
GUGUUGCCAAAGGCGCCUGCUU__UUC_UUCGAGCUCUGCAAAGCAGC_GAACCAAAGGCAGCAUUC___UCAACC___CCCAAACUC__ACACA____CAUCACAAU
((((((((..((((....)))).............((.((......)).))......))))))))........................................... (-15.27 = -15.27 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:51 2006