Locus 3052

Sequence ID	2L_DroMel_CAF1
Location	8,715,372 – 8,715,509
Length	137
Max. P	0.987092

overview

Window 7

Location	8,715,372 – 8,715,489
Length	117
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	85.22
Mean single sequence MFE	-30.26
Consensus MFE	-19.76
Energy contribution	-20.68
Covariance contribution	0.92
Combinations/Pair	1.21
Mean z-score	-1.89
Structure conservation index	0.65
SVM decision value	0.09
SVM RNA-class probability	0.578278
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8715372 117 + 22407834
UAAAUGCAGAUUAUCUUUUUGUCAUGAUUGUAUGUUC-CUUGAGUAUUCCAAGUCUAUGCUCCCAAUUUCUGGCAACACAGACUAGCUGGCUGUGAAACAACUCAAGACCAAGUGCAG
...(((((((.......)))).)))...(((((....-(((((((.(((..((((...(((.......((((......))))..))).))))..)))...))))))).....))))). ( -24.10)
>DroSec_CAF1 27940 117 + 1
UAACUGCAGACUAUCUAUUUGUCAAGAUUGUCUGUUC-CUUGAGUAUUCCAAGUCUGUGCUCCCAAUUUCUGGCAACACAGACUAGCUGGCUAUGAAACAACUCAAGACCAAGUGCAG
...((((((((.((((........)))).))))....-(((((((......((((((((...(((.....)))...))))))))((....))........))))))).......)))) ( -34.20)
>DroSim_CAF1 28648 117 + 1
UAACUGCAGACUAUCUAUUUGUCAAGAUUGUCUGUUC-CUUGAGUAUUCCAAGUCUGUGCUCCCAAUUUCUGGCAACACAGACUAGCUGGCUAUGAAACAACUCAAGACCAAGUGCAG
...((((((((.((((........)))).))))....-(((((((......((((((((...(((.....)))...))))))))((....))........))))))).......)))) ( -34.20)
>DroEre_CAF1 30369 113 + 1
UAAAUACAGACUAUCAUUCC-----UGUUGCAUGUUUUCUUAGCUGCUCCAAGUCUGUGCUCCCAAUUUCUGGCAACACAGACUAGUUGGCUGUGGAACAACUCAAGACCAAGUGCAG
.....((((..........)-----)))(((((....((((((.((.((((((((((((...(((.....)))...))))))))((....)).)))).)).)).))))....))))). ( -29.80)
>DroYak_CAF1 28227 118 + 1
UAAGUGGAGACUAUCAUUCCUUCAAUGUUGUAUGAUUUCUGAUAUACUCCAAGUCUGUGCUCCCAAUUUCUGGCUACGCAGACAAGUUGGCUGUGAAACAACUCAAGACCAAGUGCAG
....(((((..(((((.....(((........)))....)))))..))))).(((((((...(((.....)))...))))))).(.((((((.(((......))))).)))).).... ( -29.00)
>consensus
UAAAUGCAGACUAUCUUUUUGUCAAGAUUGUAUGUUC_CUUGAGUAUUCCAAGUCUGUGCUCCCAAUUUCUGGCAACACAGACUAGCUGGCUGUGAAACAACUCAAGACCAAGUGCAG
............................(((((.....(((((((((.(((((((((((...(((.....)))...))))))))...)))..))......))))))).....))))). (-19.76 = -20.68 +   0.92)

alignment

secondary structure

dotplot

Window 8

Location	8,715,372 – 8,715,489
Length	117
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	85.22
Mean single sequence MFE	-39.42
Consensus MFE	-25.88
Energy contribution	-26.32
Covariance contribution	0.44
Combinations/Pair	1.11
Mean z-score	-3.68
Structure conservation index	0.66
SVM decision value	2.07
SVM RNA-class probability	0.987092
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8715372 117 - 22407834
CUGCACUUGGUCUUGAGUUGUUUCACAGCCAGCUAGUCUGUGUUGCCAGAAAUUGGGAGCAUAGACUUGGAAUACUCAAG-GAACAUACAAUCAUGACAAAAAGAUAAUCUGCAUUUA
.((((.....((((((((.((((((.((....))((((((((((.((((...)))).)))))))))))))))))))))))-)..(((......)))..............)))).... ( -33.20)
>DroSec_CAF1 27940 117 - 1
CUGCACUUGGUCUUGAGUUGUUUCAUAGCCAGCUAGUCUGUGUUGCCAGAAAUUGGGAGCACAGACUUGGAAUACUCAAG-GAACAGACAAUCUUGACAAAUAGAUAGUCUGCAGUUA
((((......((((((((.(((((((((....)))(((((((((.((((...)))).))))))))).)))))))))))))-)...((((.((((........)))).))))))))... ( -45.30)
>DroSim_CAF1 28648 117 - 1
CUGCACUUGGUCUUGAGUUGUUUCAUAGCCAGCUAGUCUGUGUUGCCAGAAAUUGGGAGCACAGACUUGGAAUACUCAAG-GAACAGACAAUCUUGACAAAUAGAUAGUCUGCAGUUA
((((......((((((((.(((((((((....)))(((((((((.((((...)))).))))))))).)))))))))))))-)...((((.((((........)))).))))))))... ( -45.30)
>DroEre_CAF1 30369 113 - 1
CUGCACUUGGUCUUGAGUUGUUCCACAGCCAACUAGUCUGUGUUGCCAGAAAUUGGGAGCACAGACUUGGAGCAGCUAAGAAAACAUGCAACA-----GGAAUGAUAGUCUGUAUUUA
.((((..(..((((.((((((((((.........((((((((((.((((...)))).))))))))))))))))))))))))..)..))))(((-----((........)))))..... ( -42.80)
>DroYak_CAF1 28227 118 - 1
CUGCACUUGGUCUUGAGUUGUUUCACAGCCAACUUGUCUGCGUAGCCAGAAAUUGGGAGCACAGACUUGGAGUAUAUCAGAAAUCAUACAACAUUGAAGGAAUGAUAGUCUCCACUUA
......(((((..((((....))))..)))))...(((((.((..((((...))))..)).))))).(((((..(((((....(((........))).....)))))..))))).... ( -30.50)
>consensus
CUGCACUUGGUCUUGAGUUGUUUCACAGCCAGCUAGUCUGUGUUGCCAGAAAUUGGGAGCACAGACUUGGAAUACUCAAG_GAACAUACAAUCUUGACAAAAAGAUAGUCUGCAGUUA
.((((.(((((..((((....))))..)))))(.((((((((((.((((...)))).)))))))))).).........................................)))).... (-25.88 = -26.32 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	8,715,411 – 8,715,509
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	92.45
Mean single sequence MFE	-31.64
Consensus MFE	-28.34
Energy contribution	-28.82
Covariance contribution	0.48
Combinations/Pair	1.06
Mean z-score	-1.73
Structure conservation index	0.90
SVM decision value	1.90
SVM RNA-class probability	0.981914
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8715411 98 - 22407834
UAGACAAGUUUGACCGCCGUCUGCACUUGGUCUUGAGUUGUUUCACAGCCAGCUAGUCUGUGUUGCCAGAAAUUGGGAGCAUAGACUUGGAAUACUCA
.((((((((..(((....)))...)))).))))(((((.((((((.((....))((((((((((.((((...)))).))))))))))))))))))))) ( -32.50)
>DroSec_CAF1 27979 98 - 1
UAGACAAGUUUGACCGCCGCCUGCACUUGGUCUUGAGUUGUUUCAUAGCCAGCUAGUCUGUGUUGCCAGAAAUUGGGAGCACAGACUUGGAAUACUCA
...........(((((..(....)...))))).(((((.(((((((((....)))(((((((((.((((...)))).))))))))).))))))))))) ( -32.10)
>DroSim_CAF1 28687 98 - 1
UAGACAAGUUUGACCGCCGCCUGCACUUGGUCUUGAGUUGUUUCAUAGCCAGCUAGUCUGUGUUGCCAGAAAUUGGGAGCACAGACUUGGAAUACUCA
...........(((((..(....)...))))).(((((.(((((((((....)))(((((((((.((((...)))).))))))))).))))))))))) ( -32.10)
>DroEre_CAF1 30404 98 - 1
UAGACGAGUUUGACCGCCGCCUGCACUUGGUCUUGAGUUGUUCCACAGCCAACUAGUCUGUGUUGCCAGAAAUUGGGAGCACAGACUUGGAGCAGCUA
....((((.(..(..((.....))..)..).))))((((((((((.........((((((((((.((((...)))).)))))))))))))))))))). ( -36.80)
>DroYak_CAF1 28267 98 - 1
UAGACAAGUUUGACCGCCGCCUGCACUUGGUCUUGAGUUGUUUCACAGCCAACUUGUCUGCGUAGCCAGAAAUUGGGAGCACAGACUUGGAGUAUAUC
....((((((((...(((((..(((.(((((..((((....))))..)))))..)))..)))...((((...))))..)).))))))))......... ( -24.70)
>consensus
UAGACAAGUUUGACCGCCGCCUGCACUUGGUCUUGAGUUGUUUCACAGCCAGCUAGUCUGUGUUGCCAGAAAUUGGGAGCACAGACUUGGAAUACUCA
.((((((.((.(((((..(....)...)))))..)).)))))).....(((...((((((((((.((((...)))).)))))))))))))........ (-28.34 = -28.82 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:11 2006