Locus 8021

Sequence ID	3L_DroMel_CAF1
Location	21,134,531 – 21,134,678
Length	147
Max. P	0.710084

overview

Window 1

Location	21,134,531 – 21,134,646
Length	115
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	88.99
Mean single sequence MFE	-26.85
Consensus MFE	-24.80
Energy contribution	-24.55
Covariance contribution	-0.25
Combinations/Pair	1.05
Mean z-score	-1.44
Structure conservation index	0.92
SVM decision value	0.37
SVM RNA-class probability	0.710084
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21134531 115 - 23771897
AAAUGUUGUCACUGAGGCUCGAAGAUUCUCGCUGGGCUUUCGCCCGGCACGUCGCUUCACCCAUAACCCAUAACCCAUACCACCAUACCCAUGCCCACAUCCACAUCGAGCUCCG
.............(..((((((((......(((((((....)))))))......)))).........................(((....)))..............))))..). ( -25.70)
>DroSec_CAF1 5745 107 - 1
AAAUGUUGUCACCAAGGCUCGAAGAUUCUCGCUGGGCUUUCGCCCGGCACGUCGCUUCACCCAUAAC--------CAUACCACCAUACCCAUGCCCACAUCCACAUCGAGCUCCG
...............(((((((((......(((((((....)))))))......)))).........--------........(((....)))..............)))))... ( -24.40)
>DroEre_CAF1 2348 99 - 1
AAAUGUUGUCACUGAGGCUCGAAGAUUCUCGCUGGGCUUUCGCCCGGCACGUCGCUUCACCCAUAGC--------CAUA--------CCCGUGCCCACAUCCACACCGAGCUCCG
.............(..(((((............((((....))))((((((..(((........)))--------....--------..))))))...........)))))..). ( -28.80)
>DroYak_CAF1 5763 104 - 1
AAAUGUUGUCACUGAGGCUCGAAGAUUCUCGCUGGGCUUUCGCCCGGCACGUCGCUUCACCCAUAAC--------CAUAAC---AAUCCCGUGCCCACAUCCACAUCGAGCUCCG
.............(..((((((((......(((((((....)))))))......)))).........--------......---......(((........)))...))))..). ( -28.50)
>consensus
AAAUGUUGUCACUGAGGCUCGAAGAUUCUCGCUGGGCUUUCGCCCGGCACGUCGCUUCACCCAUAAC________CAUACC___AUACCCAUGCCCACAUCCACAUCGAGCUCCG
...............(((((((((......(((((((....)))))))......))))................................(((....))).......)))))... (-24.80 = -24.55 +  -0.25)

alignment

secondary structure

dotplot

Window 2

Location	21,134,571 – 21,134,678
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.37
Mean single sequence MFE	-40.68
Consensus MFE	-26.96
Energy contribution	-28.04
Covariance contribution	1.08
Combinations/Pair	1.09
Mean z-score	-1.69
Structure conservation index	0.66
SVM decision value	0.22
SVM RNA-class probability	0.640841
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21134571 107 + 23771897
GGUUAUGGGUUAUGGGUGAAGCGACGUGCCGGGCGAAAGCCCAGCGAGAAUCUUCGA-----GCCUCAGUGACAACAUUUCGCCCAGAGGCGCCGCCGCGG--GG---CUCCAAAUG---
.....((((((((((((((((.....(((.((((....)))).))).....))))..-----))))..)))))........((((...(((...)))...)--))---).)))....--- ( -41.20)
>DroSec_CAF1 5785 100 + 1
--------GUUAUGGGUGAAGCGACGUGCCGGGCGAAAGCCCAGCGAGAAUCUUCGA-----GCCUUGGUGACAACAUUUCGCCCAGAGGCGUCGCCGCGGG-GG---CUCAAAAAA---
--------.........((((.....(((.((((....)))).))).....))))((-----(((((((((((........(((....))))))))))...)-))---)))......--- ( -40.70)
>DroEre_CAF1 2380 100 + 1
--------GCUAUGGGUGAAGCGACGUGCCGGGCGAAAGCCCAGCGAGAAUCUUCGA-----GCCUCAGUGACAACAUUUCGCCCAGAGGCGCCGCCGCAGG-GG---UUCCAAAAA---
--------....(((((((((.(..((((.((((....)))).))(((..((...))-----..)))....))..).)))))))))(..((.((......))-.)---)..).....--- ( -37.70)
>DroYak_CAF1 5800 101 + 1
--------GUUAUGGGUGAAGCGACGUGCCGGGCGAAAGCCCAGCGAGAAUCUUCGA-----GCCUCAGUGACAACAUUUCGCCCAGAGCCGCUGCCGCAGGGGG---UUCAAAAAA---
--------....(((((((((.(..((((.((((....)))).))(((..((...))-----..)))....))..).)))))))))(((((.((......)).))---)))......--- ( -40.40)
>DroAna_CAF1 24466 103 + 1
----------------CGACGCCAAAAGCCGGGCGAAAGCCCAGCAAGAAUCUUCAAUCGGCGCGGCGGUGACAACAUUUCGCCCAGAGGCGGCGCCGCGGG-GGUGCUUCGAAAAAUGA
----------------(((((((....(((((((....)))).....((....))....)))((((((....)......(((((....))))).)))))...-))))..)))........ ( -43.40)
>consensus
________GUUAUGGGUGAAGCGACGUGCCGGGCGAAAGCCCAGCGAGAAUCUUCGA_____GCCUCAGUGACAACAUUUCGCCCAGAGGCGCCGCCGCGGG_GG___UUCAAAAAA___
..............(((((((.....(((.((((....)))).))).....)))).......(((((.((((.......))))...)))))...)))....................... (-26.96 = -28.04 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:04:04 2006