Locus 4825

Sequence ID	X_DroMel_CAF1
Location	12,526,360 – 12,526,485
Length	125
Max. P	0.999024

overview

Window 4

Location	12,526,360 – 12,526,454
Length	94
Sequences	4
Columns	105
Reading direction	reverse
Mean pairwise identity	73.47
Mean single sequence MFE	-42.50
Consensus MFE	-24.50
Energy contribution	-25.25
Covariance contribution	0.75
Combinations/Pair	1.27
Mean z-score	-1.90
Structure conservation index	0.58
SVM decision value	0.87
SVM RNA-class probability	0.871845
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12526360 94 - 22224390
---CAUGCCAAUAAUGUGGCUGGUCUGCAGCCGCCGGUGGCCAAUAUGGGGACGGGUGGUGGUGUUCAACCAGGUGGAGCUGCUGGG----CAACAGGU----CA
---...((((......)))).(..(((((((((((....((((...((....))..))))(((.....))).))))..)))))..(.----...)))..----). ( -34.80)
>DroSec_CAF1 55973 94 - 1
---CACGCCAAUAAUGUGGCGGGCCUGCAGCCGCCGGUGGCCAAUAUGGUGCCGGGUGGUGGUGUCCAACCCGGUGGUGCUCCAGGC----CCACAGGU----CA
---...((((......))))(((((((.(((.(((....(((.....)))(((((((((......)).))))))))))))).)))))----))......----.. ( -47.80)
>DroEre_CAF1 56088 85 - 1
---CAUGCCAAUAAUGUGGCGGGCCUCCAGCCGCCGGCGGCCAAUAUGGUGGCGGCUGGAG---------CCGCUGGAGCUCCGGGC----CAGCAGCU----CA
---...((((......))))((((((((((((((((.((.......)).))))))))))))---------..(((((..(....).)----)))).)))----). ( -46.40)
>DroYak_CAF1 56827 96 - 1
GGUCAUGCCAAUAAUGUGGCCGGCCUACAGCCGCCGGUGGGCAAUAUGGUGGCUGGUGGCG---------CUGGUGGUGCUGGUGGUGUCCAAGCGGGUGGAACA
.((..((((....(..(.((((((((((.(((((((((.(.(.....).).))))))))).---------...)))).)))))).)..).......))))..)). ( -41.00)
>consensus
___CAUGCCAAUAAUGUGGCGGGCCUGCAGCCGCCGGUGGCCAAUAUGGUGGCGGGUGGUG_________CCGGUGGAGCUCCUGGC____CAACAGGU____CA
......((((......))))((((((((.((((((.((.(((.....))).)).))))))(((.....)))..)))).))))....................... (-24.50 = -25.25 +   0.75)

alignment

secondary structure

dotplot

Window 5

Location	12,526,389 – 12,526,485
Length	96
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	69.94
Mean single sequence MFE	-38.38
Consensus MFE	-14.96
Energy contribution	-16.48
Covariance contribution	1.52
Combinations/Pair	1.26
Mean z-score	-2.45
Structure conservation index	0.39
SVM decision value	2.45
SVM RNA-class probability	0.994097
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12526389 96 + 22224390
UGAACACCACCACCC---GUCCCCAUAUUGGCCACCGGCGGCUGCAGAC---CAGCCACAUUAUUGGCAUG------------------ACCACCAUGUCCAUGUCCAUGGCCAUGGAAU
...............---....(((...((((((..((((((((.....---))))).......(((((((------------------.....)))).))).)))..)))))))))... ( -30.40)
>DroSec_CAF1 56002 96 + 1
UGGACACCACCACCC---GGCACCAUAUUGGCCACCGGCGGCUGCAGGC---CCGCCACAUUAUUGGCGUG------------------ACCUCCAUGUCCAUGUCCAUGUCCGUGGAAU
((((((...((..((---((..((.....))...)))).)).((.((((---.(((((......))))).)------------------.))).))))))))..(((((....))))).. ( -33.10)
>DroEre_CAF1 56115 89 + 1
-------CUCCAGCC---GCCACCAUAUUGGCCGCCGGCGGCUGGAGGC---CCGCCACAUUAUUGGCAUG------------------GCCGCCAUGUCCAUGGCCAUGGCCGUGGAAC
-------.(((((((---(((.((.....)).....))))))))))(((---(.((((......))))..)------------------)))......((((((((....)))))))).. ( -50.00)
>DroYak_CAF1 56862 92 + 1
-------CGCCACCA---GCCACCAUAUUGCCCACCGGCGGCUGUAGGC---CGGCCACAUUAUUGGCAUGACC---------------GCCGCCAUGUCCGUGUCCAUGGCCGUGGAAU
-------.(((..((---(((.((............)).)))))..)))---..((((......))))....((---------------((.((((((........)))))).))))... ( -37.60)
>DroAna_CAF1 66488 114 + 1
UGUCCUCCACCGCCCAGUGGCACCA------CCACCGGCGGCUGCAGGCUGCCACCCACAUUGUUGGCAUGACCACCGACGACUCCACUGCCGCCACUGCCACUGCCACUGCUGGGGAAG
.....(((.(((..((((((((...------.((..((((((.((.....))........(((((((........))))))).......))))))..))....)))))))).)))))).. ( -40.80)
>consensus
UG__C_CCACCACCC___GCCACCAUAUUGGCCACCGGCGGCUGCAGGC___CAGCCACAUUAUUGGCAUG__________________GCCGCCAUGUCCAUGUCCAUGGCCGUGGAAU
..............................((((...(.(((((........))))).).....)))).........................(((((.((((....)))).)))))... (-14.96 = -16.48 +   1.52)

alignment

secondary structure

dotplot

Window 6

Location	12,526,389 – 12,526,485
Length	96
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	69.94
Mean single sequence MFE	-47.34
Consensus MFE	-19.62
Energy contribution	-20.78
Covariance contribution	1.16
Combinations/Pair	1.40
Mean z-score	-2.78
Structure conservation index	0.41
SVM decision value	3.33
SVM RNA-class probability	0.999024
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12526389 96 - 22224390
AUUCCAUGGCCAUGGACAUGGACAUGGUGGU------------------CAUGCCAAUAAUGUGGCUG---GUCUGCAGCCGCCGGUGGCCAAUAUGGGGAC---GGGUGGUGGUGUUCA
...(((((.((((....)))).))))).(..------------------((.((((......))))))---..).((.((((((.((..((.....))..))---.)))))).))..... ( -37.20)
>DroSec_CAF1 56002 96 - 1
AUUCCACGGACAUGGACAUGGACAUGGAGGU------------------CACGCCAAUAAUGUGGCGG---GCCUGCAGCCGCCGGUGGCCAAUAUGGUGCC---GGGUGGUGGUGUCCA
..((((......))))..((((((((.((((------------------(.(((((......))))))---)))).).((((((.(..(((.....)))..)---.)))))).))))))) ( -45.80)
>DroEre_CAF1 56115 89 - 1
GUUCCACGGCCAUGGCCAUGGACAUGGCGGC------------------CAUGCCAAUAAUGUGGCGG---GCCUCCAGCCGCCGGCGGCCAAUAUGGUGGC---GGCUGGAG-------
..((((.(((....))).))))......(((------------------(.(((((......))))))---)))(((((((((((.((.......)).))))---))))))).------- ( -50.70)
>DroYak_CAF1 56862 92 - 1
AUUCCACGGCCAUGGACACGGACAUGGCGGC---------------GGUCAUGCCAAUAAUGUGGCCG---GCCUACAGCCGCCGGUGGGCAAUAUGGUGGC---UGGUGGCG-------
......((((((((.....((.((((((...---------------.)))))))).....))))))))---(((..(((((((((..........)))))))---))..))).------- ( -45.30)
>DroAna_CAF1 66488 114 - 1
CUUCCCCAGCAGUGGCAGUGGCAGUGGCGGCAGUGGAGUCGUCGGUGGUCAUGCCAACAAUGUGGGUGGCAGCCUGCAGCCGCCGGUGG------UGGUGCCACUGGGCGGUGGAGGACA
(((((((..((((((((.((.((.(((((((.........((.(((......))).))..((..(((....)))..))))))))).)).------)).))))))))...)).)))))... ( -57.70)
>consensus
AUUCCACGGCCAUGGACAUGGACAUGGCGGC__________________CAUGCCAAUAAUGUGGCGG___GCCUGCAGCCGCCGGUGGCCAAUAUGGUGCC___GGGUGGUGG_G__CA
...(((((((((((........))))))(((.....................))).....))))).............((((((.((.(((.....))).))....))))))........ (-19.62 = -20.78 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:57 2006