Locus 4483

Sequence ID	3R_DroMel_CAF1
Location	11,865,944 – 11,866,050
Length	106
Max. P	0.834361

overview

Window 3

Location	11,865,944 – 11,866,050
Length	106
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	75.74
Mean single sequence MFE	-38.98
Consensus MFE	-23.81
Energy contribution	-23.92
Covariance contribution	0.11
Combinations/Pair	1.14
Mean z-score	-1.37
Structure conservation index	0.61
SVM decision value	0.16
SVM RNA-class probability	0.613043
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11865944 106 + 27905053
GCCAUGGCUGGCGGAGCGGCCAGUGAACUGGCUGGCUACCAUCACCAGCACAACGUCAUCCAGGCAGCCAAACUGAUGGCCACCUCGUAAAGUUAAAAAUC-------UGGAC
.(((..(((((.(((((((((((....)))))).))).))....)))))..(((.....(.(((..((((......))))..))).)....))).......-------))).. ( -36.90)
>DroPse_CAF1 35345 102 + 1
GCCAUGGCGGGGGGAGCGGCCAGUGAGUUGGCCGGAUAUCACCAUCAGCACAAUGUCAUACAGGCGGCCAAGCUGAUGGCCACCUCCUAAGGGCCAUCCCUU-----------
((....)).((((((..((((((.(((.(((((((......))((((((....((((.....)))).....))))))))))).)))))...)))).))))))----------- ( -44.40)
>DroWil_CAF1 23893 93 + 1
GCCAUGGCAGGCGGAGGAGCCAGCGAUUUGGCCGGCUAUCAUCAUCAGCAUAAUGUCAUCCAGGCAGCCAAACUAAUGGCGUCUUCUUGAA--------------------AC
(((......)))((((((((((....((((((..(((.........)))....((((.....))))))))))....)))).))))))....--------------------.. ( -29.20)
>DroYak_CAF1 23414 113 + 1
GCCAUGGCAGGCGGAGCGGCCAGUGAACUGGCAGGCUACCAUCACCAGCACAACGUCAUCCAGGCAGCCAAGCUGAUGGCCACCUCGUAAGGCUAGAACUUUGGGCUCCGGAC
(((......)))(((((.(((((....)))))..))).))..................(((.((.((((.......(((((.........)))))........))))))))). ( -40.06)
>DroAna_CAF1 23328 101 + 1
GCCAUGGCGGGCGGAGCUGCCAGCGAACUGGCCGGCUACCAUCACCAGCACAACGUCAUCCAGGCGGCCAAGUUGAUGGCCACCUCGUAAGG-----AAUC-------GCGGA
((..(((.((..(((((((((((....)))).))))).)).)).)))))....(((..((((((.(((((......))))).))).....))-----)...-------))).. ( -38.20)
>DroPer_CAF1 35448 102 + 1
GCCAUGGCGGGGGGAGCGGCCAGCGAGUUGGCCGGAUAUCACCAUCAGCACAAUGUCAUCCAGGCGGCCAAGCUGAUGGCCACCUCCUAAGGGCCAUCCCUU-----------
((....))((((((..(((((((....))))))).......((((((((....((((.....)))).....))))))))...))))))(((((....)))))----------- ( -45.10)
>consensus
GCCAUGGCGGGCGGAGCGGCCAGCGAACUGGCCGGCUACCAUCACCAGCACAACGUCAUCCAGGCAGCCAAGCUGAUGGCCACCUCGUAAGG___A_ACUU__________AC
((....))..(((..(.(((((......(((((((......))...........(((.....))))))))......))))).)..)))......................... (-23.81 = -23.92 +   0.11)

alignment

secondary structure

dotplot

Window 4

Location	11,865,944 – 11,866,050
Length	106
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	75.74
Mean single sequence MFE	-42.17
Consensus MFE	-27.09
Energy contribution	-26.53
Covariance contribution	-0.55
Combinations/Pair	1.31
Mean z-score	-1.51
Structure conservation index	0.64
SVM decision value	0.73
SVM RNA-class probability	0.834361
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11865944 106 - 27905053
GUCCA-------GAUUUUUAACUUUACGAGGUGGCCAUCAGUUUGGCUGCCUGGAUGACGUUGUGCUGGUGAUGGUAGCCAGCCAGUUCACUGGCCGCUCCGCCAGCCAUGGC
..(((-------......((((.((((.(((..((((......))))..))).).))).)))).(((((((..((..(((((........)))))..)).)))))))..))). ( -44.20)
>DroPse_CAF1 35345 102 - 1
-----------AAGGGAUGGCCCUUAGGAGGUGGCCAUCAGCUUGGCCGCCUGUAUGACAUUGUGCUGAUGGUGAUAUCCGGCCAACUCACUGGCCGCUCCCCCCGCCAUGGC
-----------(((((....))))).(.(((((((((......))))))))).)..........(((.((((((.....((((((......)))))).......))))))))) ( -42.50)
>DroWil_CAF1 23893 93 - 1
GU--------------------UUCAAGAAGACGCCAUUAGUUUGGCUGCCUGGAUGACAUUAUGCUGAUGAUGAUAGCCGGCCAAAUCGCUGGCUCCUCCGCCUGCCAUGGC
((--------------------((.....))))(((((..(((((((((.(((.....((((((....)))))).))).))))))))).((.(((......))).)).))))) ( -28.90)
>DroYak_CAF1 23414 113 - 1
GUCCGGAGCCCAAAGUUCUAGCCUUACGAGGUGGCCAUCAGCUUGGCUGCCUGGAUGACGUUGUGCUGGUGAUGGUAGCCUGCCAGUUCACUGGCCGCUCCGCCUGCCAUGGC
....(((((.........((((.((((.(((..((((......))))..))).).))).)))).((..((((((((.....))))..))))..)).)))))(((......))) ( -46.60)
>DroAna_CAF1 23328 101 - 1
UCCGC-------GAUU-----CCUUACGAGGUGGCCAUCAACUUGGCCGCCUGGAUGACGUUGUGCUGGUGAUGGUAGCCGGCCAGUUCGCUGGCAGCUCCGCCCGCCAUGGC
.((((-------(...-----(.((((.(((((((((......))))))))).).))).)...)))(((((.(((.(((..(((((....))))).))))))..))))).)). ( -45.70)
>DroPer_CAF1 35448 102 - 1
-----------AAGGGAUGGCCCUUAGGAGGUGGCCAUCAGCUUGGCCGCCUGGAUGACAUUGUGCUGAUGGUGAUAUCCGGCCAACUCGCUGGCCGCUCCCCCCGCCAUGGC
-----------..(((..(((.......(((((((((......)))))))))(((((.(((..(....)..))).)))))(((((......))))))))..))).((....)) ( -45.10)
>consensus
GU__________AAGU_U___CCUUACGAGGUGGCCAUCAGCUUGGCCGCCUGGAUGACAUUGUGCUGAUGAUGAUAGCCGGCCAAUUCACUGGCCGCUCCGCCCGCCAUGGC
..........................((.((((((((.....(((((((.(((.....(((..(....)..))).))).))))))).....)))))))).))...((....)) (-27.09 = -26.53 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:33 2006