Locus 5159

Sequence ID	2L_DroMel_CAF1
Location	14,621,366 – 14,621,519
Length	153
Max. P	0.912970

overview

Window 6

Location	14,621,366 – 14,621,479
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.98
Mean single sequence MFE	-41.30
Consensus MFE	-23.33
Energy contribution	-25.89
Covariance contribution	2.56
Combinations/Pair	1.27
Mean z-score	-2.07
Structure conservation index	0.56
SVM decision value	0.90
SVM RNA-class probability	0.877055
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14621366 113 - 22407834
GCAGGCCGAGAGUUAUAUAGUCUCUGGCCCGAGACAACAAGUCGGCCAUACAAAUGGGACUUGGCUUUCAGAGCUUCAAAG------UCUGAGAGCG-GUCUUGGCGGGCAAGGGGUAUU
((.((((((((.(.....).)))).))))((((((..((((((..((((....))))))))))(((((((((.((....))------))))))))).-)))))))).............. ( -45.80)
>DroPse_CAF1 4425 90 - 1
GGAGACGGAGA-----------------CGGAGUCUACGAGUCGGCCAUACAAAUGGGUCUGGGCUUUUAAGACUCGAUCG------UCUCUGUGUGUGUGUUUGUGGA-------UUGU
..(.(((((((-----------------((((((((..(((((((((.........))))..)))))...))))))...))------))))))).).............-------.... ( -29.40)
>DroSec_CAF1 3557 113 - 1
GCAGGCCGAGAGUUGUAUAGUCUCAGGCCCGAGACAACGAGUCGGCCAUACAAAUGGGACUUGGCUUUCAGAGCUUCAAAG------UCUGAGAGCG-GUCUUGGCGGGCAAGGGGUAUU
((.((((((((.(.....).)))).))))((((((..((((((..((((....))))))))))(((((((((.((....))------))))))))).-)))))))).............. ( -45.50)
>DroSim_CAF1 3568 113 - 1
GCAGGCCGAGAGUUGUAUAGUCUCAGGCCCGAGACAACGAGUCGGCCAUACAAAUGGGACUUGGCUUUCAGAGCUUCAAAG------UCUGAGAGCG-GUCUUGGCGGGCAAGGGGUAUU
((.((((((((.(.....).)))).))))((((((..((((((..((((....))))))))))(((((((((.((....))------))))))))).-)))))))).............. ( -45.50)
>DroEre_CAF1 3637 113 - 1
UCGGUCCCCGAGUUAUAUAGUUUCAGGCCCGAGACAACGGGUCGGCCAUACAAAUGGGACUUGGCUUACAGAGCUUCAAAG------UUUGAGAGCG-GGUUUGGCGGGCAAGGGGUAUU
.....(((((((.........)))..(((((.(((..((((((..((((....))))))))))((((...(((((....))------)))..)))).-.)))...)))))..)))).... ( -36.10)
>DroYak_CAF1 3727 119 - 1
GCGGGCCCAGAGUUAUAUAGUUUCAGGCCCGAGACAACGAGUCGGCCAUACAAAUGGGACUUGGCUUUCCGAGCUUCAAAGCCUGAGCUUGAGAGCG-GACUUGGCGGGCCAGGGGUAUU
....((((.(((.........))).((((((...(((((((((..((((....))))))))))((((((.((((((........)))))))))))).-...))).))))))..))))... ( -45.50)
>consensus
GCAGGCCGAGAGUUAUAUAGUCUCAGGCCCGAGACAACGAGUCGGCCAUACAAAUGGGACUUGGCUUUCAGAGCUUCAAAG______UCUGAGAGCG_GUCUUGGCGGGCAAGGGGUAUU
((..(((((((........(((((......)))))..((((((..((((....))))))))))(((((((((...............)))))))))...)))))))..)).......... (-23.33 = -25.89 +   2.56)

alignment

secondary structure

dotplot

Window 7

Location	14,621,399 – 14,621,519
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.17
Mean single sequence MFE	-37.52
Consensus MFE	-32.80
Energy contribution	-33.08
Covariance contribution	0.28
Combinations/Pair	1.12
Mean z-score	-1.53
Structure conservation index	0.87
SVM decision value	1.09
SVM RNA-class probability	0.912970
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14621399 120 - 22407834
CUCCAAGCUCCACAUCGGUGUCUCAGUCAAAAUCUGAAUCGCAGGCCGAGAGUUAUAUAGUCUCUGGCCCGAGACAACAAGUCGGCCAUACAAAUGGGACUUGGCUUUCAGAGCUUCAAA
....((((((....((((((..((((.......))))..))).((((((((.(.....).)))).)))))))((...((((((..((((....))))))))))....)).)))))).... ( -38.80)
>DroSec_CAF1 3590 120 - 1
CUCCAAGCUCCACAUCGGUGUCUCAGUCAAAAUCUGAAUCGCAGGCCGAGAGUUGUAUAGUCUCAGGCCCGAGACAACGAGUCGGCCAUACAAAUGGGACUUGGCUUUCAGAGCUUCAAA
....((((((....((((((..((((.......))))..))).((((((((.(.....).)))).)))))))((...((((((..((((....))))))))))....)).)))))).... ( -38.50)
>DroSim_CAF1 3601 120 - 1
CUCCAAGCUCCACAUCGGUGUCUCAGUCAAAAUCUGAAUCGCAGGCCGAGAGUUGUAUAGUCUCAGGCCCGAGACAACGAGUCGGCCAUACAAAUGGGACUUGGCUUUCAGAGCUUCAAA
....((((((....((((((..((((.......))))..))).((((((((.(.....).)))).)))))))((...((((((..((((....))))))))))....)).)))))).... ( -38.50)
>DroEre_CAF1 3670 120 - 1
CUCCGAGCUCCGCAUCGGUGUCUCAGUCAAAAUCGGAAUCUCGGUCCCCGAGUUAUAUAGUUUCAGGCCCGAGACAACGGGUCGGCCAUACAAAUGGGACUUGGCUUACAGAGCUUCAAA
....((((.(((...))).).)))...........(((.(((.((..(((((((...........((((((......))))))..((((....)))))))))))...)).))).)))... ( -34.70)
>DroYak_CAF1 3766 120 - 1
CUCCAAGCUCCGCAUCGGUGUCUCAGUCAAAAUCUGAAUCGCGGGCCCAGAGUUAUAUAGUUUCAGGCCCGAGACAACGAGUCGGCCAUACAAAUGGGACUUGGCUUUCCGAGCUUCAAA
...........((.((((((((((..(((.....))).....(((((..(((.........))).))))))))))).((((((..((((....)))))))))).....))))))...... ( -37.10)
>consensus
CUCCAAGCUCCACAUCGGUGUCUCAGUCAAAAUCUGAAUCGCAGGCCGAGAGUUAUAUAGUCUCAGGCCCGAGACAACGAGUCGGCCAUACAAAUGGGACUUGGCUUUCAGAGCUUCAAA
....((((((........((((((..(((.....)))......((((((((.(.....).)))).)))).)))))).((((((..((((....)))))))))).......)))))).... (-32.80 = -33.08 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:31 2006