Locus 4497

Sequence ID 2L_DroMel_CAF1
Location 12,890,278 – 12,890,372
Length 94
Max. P 0.976405
window7073 window7074

overview

Window 3

Location 12,890,278 – 12,890,372
Length 94
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 77.85
Mean single sequence MFE -24.69
Consensus MFE -15.01
Energy contribution -15.03
Covariance contribution 0.03
Combinations/Pair 1.08
Mean z-score -1.88
Structure conservation index 0.61
SVM decision value 0.87
SVM RNA-class probability 0.870405
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12890278 94 + 22407834
GGCGGGUGG------AUAUGGAUGUGGAUAUGGAAGGCACCAUAAGCAGUUGGAAAAUUUAUGACCAAGGGCAAUGGCAAAUGGCCAUGUGAAUGAGUCC
(((..((..------((((((.(((.(.(((((......))))).((..((((...........))))..))..).))).....))))))..))..))). ( -20.90)
>DroPse_CAF1 81819 84 + 1
GCC---UGG------ACUGAG----AGAUGUCGAAAGACCCAUAAGCAGUUGGAAAAUUUAUGGCCAAGGGCAUUGGCAAAUGGCCAUGUGAAUGGG---
.((---(.(------((((..----....(((....))).......))))).)......((((((((...((....))...)))))))).....)).--- ( -26.12)
>DroSec_CAF1 69346 94 + 1
GGCGGUUGG------AUAUGGAUGUGGAUGUGGAAGGCACCAUAAGCAGUUGGAAAAUUUAUGGCCAAGGGCAAUGGCAAAUGGCCAUGUGAAUGAGUCC
(((..((.(------((.((..(((((.(((.....))))))))..))))).)).....((((((((...((....))...)))))))).......))). ( -23.80)
>DroEre_CAF1 74919 100 + 1
GGCGGGUGGAUAAGGAUGUGGAUGUGGAUGUGGAAGGCGCCAUAAGCAGUUGGAAAAUUUAUGGCCAAGGGCAAUGGCAAAUGGCCAUGUGAAUGAGCCC
...((((..((.....(((...(((((.(((.....)))))))).)))...........((((((((...((....))...))))))))...))..)))) ( -26.80)
>DroAna_CAF1 92185 75 + 1
CGCGGG-------------------------GCAAAGAGCCAUAAGCAGUUGGAAAAUUUAUGGCUAAGGGCAAUGGCAAAUGGCCAUGUGAAUGGGCCC
....((-------------------------((....((((((((...(((....)))))))))))....(((.((((.....)))))))......)))) ( -24.40)
>DroPer_CAF1 101654 84 + 1
GCC---UGG------ACUGAG----AGAUGUCGAAAGACCCAUAAGCAGUUGGAAAAUUUAUGGCCAAGGGCAUUGGCAAAUGGCCAUGUGAAUGGG---
.((---(.(------((((..----....(((....))).......))))).)......((((((((...((....))...)))))))).....)).--- ( -26.12)
>consensus
GGCGGGUGG______AUAUGG____GGAUGUGGAAAGAACCAUAAGCAGUUGGAAAAUUUAUGGCCAAGGGCAAUGGCAAAUGGCCAUGUGAAUGAG_CC
.......................................(((........)))......((((((((...((....))...))))))))........... (-15.01 = -15.03 +   0.03)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,890,278 – 12,890,372
Length 94
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 77.85
Mean single sequence MFE -18.66
Consensus MFE -11.99
Energy contribution -12.02
Covariance contribution 0.03
Combinations/Pair 1.08
Mean z-score -2.49
Structure conservation index 0.64
SVM decision value 1.77
SVM RNA-class probability 0.976405
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12890278 94 - 22407834
GGACUCAUUCACAUGGCCAUUUGCCAUUGCCCUUGGUCAUAAAUUUUCCAACUGCUUAUGGUGCCUUCCAUAUCCACAUCCAUAU------CCACCCGCC
(((.........(((((((...((....))...)))))))............((..(((((......)))))..))..)))....------......... ( -18.10)
>DroPse_CAF1 81819 84 - 1
---CCCAUUCACAUGGCCAUUUGCCAAUGCCCUUGGCCAUAAAUUUUCCAACUGCUUAUGGGUCUUUCGACAUCU----CUCAGU------CCA---GGC
---.((......(((((((...((....))...)))))))..........((((.......(((....)))....----..))))------...---)). ( -18.22)
>DroSec_CAF1 69346 94 - 1
GGACUCAUUCACAUGGCCAUUUGCCAUUGCCCUUGGCCAUAAAUUUUCCAACUGCUUAUGGUGCCUUCCACAUCCACAUCCAUAU------CCAACCGCC
((..........(((((((...((....))...)))))))............((..(((((((.............)).))))).------.)).))... ( -18.72)
>DroEre_CAF1 74919 100 - 1
GGGCUCAUUCACAUGGCCAUUUGCCAUUGCCCUUGGCCAUAAAUUUUCCAACUGCUUAUGGCGCCUUCCACAUCCACAUCCACAUCCUUAUCCACCCGCC
((((........(((((((...((....))...))))))).............((.....)))))).................................. ( -19.00)
>DroAna_CAF1 92185 75 - 1
GGGCCCAUUCACAUGGCCAUUUGCCAUUGCCCUUAGCCAUAAAUUUUCCAACUGCUUAUGGCUCUUUGC-------------------------CCCGCG
((((........(((((.....))))).......((((((((.............))))))))....))-------------------------)).... ( -19.72)
>DroPer_CAF1 101654 84 - 1
---CCCAUUCACAUGGCCAUUUGCCAAUGCCCUUGGCCAUAAAUUUUCCAACUGCUUAUGGGUCUUUCGACAUCU----CUCAGU------CCA---GGC
---.((......(((((((...((....))...)))))))..........((((.......(((....)))....----..))))------...---)). ( -18.22)
>consensus
GG_CCCAUUCACAUGGCCAUUUGCCAUUGCCCUUGGCCAUAAAUUUUCCAACUGCUUAUGGCGCCUUCCACAUCC____CCAAAU______CCACCCGCC
............(((((((...((....))...))))))).......(((........)))....................................... (-11.99 = -12.02 +   0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:14 2006