Locus 2228

Sequence ID	X_DroMel_CAF1
Location	6,003,722 – 6,003,830
Length	108
Max. P	0.873671

overview

Window 3

Location	6,003,722 – 6,003,830
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	71.20
Mean single sequence MFE	-36.14
Consensus MFE	-14.74
Energy contribution	-18.38
Covariance contribution	3.64
Combinations/Pair	1.05
Mean z-score	-1.90
Structure conservation index	0.41
SVM decision value	0.75
SVM RNA-class probability	0.840328
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6003722 108 + 22224390
GGCCGCAUUUCCCCACUUACCCACAUCCCACUCCCUUUCAGGCCAAUUGGCCGUGUCGUGGUGCACCGUAAAAUAGGCAACGCUUGUGGGGGGGAGGAGGAUGCGGGU
..................((((.(((((..((((((..((((((....)))).....(((.(((............))).)))...))..))))))..))))).)))) ( -45.80)
>DroSec_CAF1 23790 103 + 1
--CCCCACUUUCCCACUUUCCCACAUCCCAUCCCCCUUCAUGCCAAUUGGCCGUGUCGCGGUGCACUGUAAAAUAGGCAACGCUUGUGGUGGGG---GGGAUGCGGGA
--................((((.((((((.((((((..((((((....)).))))..(((.(((.((((...))))))).)))....)).))))---)))))).)))) ( -41.30)
>DroSim_CAF1 20439 90 + 1
--CCCCACU--------UUCCCACAUCCCAUCCCCCUUCAGGCCAAUUGGCCGUGUCGCGGUGCACUGUAAAAUAGGCAACGCUUGUG-----G---GGGAUGCGGGC
--.......--------........(((((((((((..((((((....)))).....(((.(((.((((...))))))).))).)).)-----)---)))))).))). ( -37.80)
>DroEre_CAF1 18452 83 + 1
--CACCUU----GCACUUUGCC-------ACC--CCAACAGGCCAAUUGGCCGUGUCGCGGUGCAC-GUAAGCUAGACUCCGCUUGUGGU---------GUUGCAGGC
--...(((----(((...((((-------((.--...(((((((....)))).))).((((.((..-....))......))))..)))))---------).)))))). ( -29.10)
>DroYak_CAF1 20859 86 + 1
--UGCCAC----CCACAUUCCC-------ACCCUCCAUCAGGGCAAUUGGCCGUGUCGCGGUGCACUGCAAAAUAGGCAACGCUUGUGGU---------AAUGCAGGC
--.(((((----((((((..((-------(((((.....))))....)))..)))).).)))(((.(((...((((((...)))))).))---------).))).))) ( -26.70)
>consensus
__CCCCACU___CCACUUUCCCACAUCCCACCCCCCUUCAGGCCAAUUGGCCGUGUCGCGGUGCACUGUAAAAUAGGCAACGCUUGUGGU___G____GGAUGCGGGC
...................(((.((((((...........((((....)))).....(((.(((.(((.....)))))).)))..............)))))).))). (-14.74 = -18.38 +   3.64)

alignment

secondary structure

dotplot

Window 4

Location	6,003,722 – 6,003,830
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	71.20
Mean single sequence MFE	-38.14
Consensus MFE	-19.30
Energy contribution	-22.10
Covariance contribution	2.80
Combinations/Pair	1.17
Mean z-score	-1.86
Structure conservation index	0.51
SVM decision value	0.88
SVM RNA-class probability	0.873671
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6003722 108 - 22224390
ACCCGCAUCCUCCUCCCCCCCACAAGCGUUGCCUAUUUUACGGUGCACCACGACACGGCCAAUUGGCCUGAAAGGGAGUGGGAUGUGGGUAAGUGGGGAAAUGCGGCC
((((((((((..(((((.........((((((((.......)).)))..))).((.((((....))))))...)))))..)))))))))).................. ( -42.70)
>DroSec_CAF1 23790 103 - 1
UCCCGCAUCCC---CCCCACCACAAGCGUUGCCUAUUUUACAGUGCACCGCGACACGGCCAAUUGGCAUGAAGGGGGAUGGGAUGUGGGAAAGUGGGAAAGUGGGG--
(((((((((((---.(((.((....(((.(((((.......)).))).)))......(((....))).....)))))..)))))))))))................-- ( -42.60)
>DroSim_CAF1 20439 90 - 1
GCCCGCAUCCC---C-----CACAAGCGUUGCCUAUUUUACAGUGCACCGCGACACGGCCAAUUGGCCUGAAGGGGGAUGGGAUGUGGGAA--------AGUGGGG--
.((((((((((---(-----(....(((.(((((.......)).))).)))..((.((((....))))))..)))))).....))))))..--------.......-- ( -38.10)
>DroEre_CAF1 18452 83 - 1
GCCUGCAAC---------ACCACAAGCGGAGUCUAGCUUAC-GUGCACCGCGACACGGCCAAUUGGCCUGUUGG--GGU-------GGCAAAGUGC----AAGGUG--
(((((((.(---------((...((((........))))..-)))((((.(((((.((((....))))))))).--)))-------)......)))----.)))).-- ( -35.30)
>DroYak_CAF1 20859 86 - 1
GCCUGCAUU---------ACCACAAGCGUUGCCUAUUUUGCAGUGCACCGCGACACGGCCAAUUGCCCUGAUGGAGGGU-------GGGAAUGUGG----GUGGCA--
(((..((((---------.((((..(((((((.......))))))).((.(.(((.(((.....))).)).).).))))-------)).))))..)----))....-- ( -32.00)
>consensus
GCCCGCAUCC____C___ACCACAAGCGUUGCCUAUUUUACAGUGCACCGCGACACGGCCAAUUGGCCUGAAGGGGGGUGGGAUGUGGGAAAGUGG___AGUGGGG__
.((((((((((..............(((.(((((.......)).))).)))..((.((((....)))))).........))))))))))................... (-19.30 = -22.10 +   2.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:18 2006