Locus 2260

Sequence ID	3L_DroMel_CAF1
Location	6,293,154 – 6,293,251
Length	97
Max. P	0.947925

overview

Window 3

Location	6,293,154 – 6,293,251
Length	97
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	85.78
Mean single sequence MFE	-33.58
Consensus MFE	-28.27
Energy contribution	-28.10
Covariance contribution	-0.17
Combinations/Pair	1.07
Mean z-score	-2.79
Structure conservation index	0.84
SVM decision value	1.38
SVM RNA-class probability	0.947925
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6293154 97 + 23771897
AAAGGCAUUUCAUGCUCAUCAAAU---GCGUUGACAUUGAACAAUUGCGCGUAAUGUUGUCGUACACUUGACAAGCGCGCAAAUUGUAGU---GCUACCUGUA----------------
...((((((((((((.........---))).)))......((((((((((((....((((((......)))))))))))).)))))))))---))).......---------------- ( -28.20)
>DroVir_CAF1 72381 97 + 1
UGUAGCAUUUCAUGCCCAUCAAAU---GCAUUGACAUUGAACAAUUGCGCGUAAUGUUGUCGUACACUUGACAAGCGCGCAAAUUGUAGU---GCUACCUGUG----------------
.((((((((((((((.........---))).)))......((((((((((((....((((((......)))))))))))).)))))))))---))))).....---------------- ( -31.20)
>DroPse_CAF1 86373 119 + 1
AGUGGCAUUUCAUGCUCAUCAAAUGCUGCGUUGACAUUGAACAAUUGCGCGUAAUGUUGUCGUACACUUGACAAGCGCGCAAAUUGUAGUGCUGCUACCUGUAGCUGUAGCUGUAGCUG
.(((((((...)))).))).....(((((((((.((....((((((((((((....((((((......)))))))))))).))))))...(((((.....))))))))))).))))).. ( -39.40)
>DroGri_CAF1 63049 97 + 1
UGUAGCAUUUCAUGCCCAUCAAAU---GCAUUGACAUUGAACAAUUGCGCGUAAUGUUGUCGUACACUUGACAAGCGCGCAAAUUGUAGU---GCUACCUGUG----------------
.((((((((((((((.........---))).)))......((((((((((((....((((((......)))))))))))).)))))))))---))))).....---------------- ( -31.20)
>DroMoj_CAF1 69956 97 + 1
UGUAGCAUUUCAUGCCCAUCAAAU---GCAUUGACAUUGAACAAUUGCGCGUAAUGUUGUCGUACACUUGACAAGCGCGCAAAUUGUAGU---GCUACCUGUG----------------
.((((((((((((((.........---))).)))......((((((((((((....((((((......)))))))))))).)))))))))---))))).....---------------- ( -31.20)
>DroPer_CAF1 89805 119 + 1
UGUGGCAUUUCAUGCUCAUCAAAUGCUGCGUUGACAUUGAACAAUUGCGCGUAAUGUUGUCGUACACUUGACAAGCGCGCAAAUUGUAGAGCUGCUACCUGUAGCUGUAGCUGUAGCUG
.(((((((...)))).))).....(((((((((.......((((((((((((....((((((......)))))))))))).))))))..((((((.....)))))).)))).))))).. ( -40.30)
>consensus
UGUAGCAUUUCAUGCCCAUCAAAU___GCAUUGACAUUGAACAAUUGCGCGUAAUGUUGUCGUACACUUGACAAGCGCGCAAAUUGUAGU___GCUACCUGUA________________
.(((((...((((((............))).)))......((((((((((((....((((((......)))))))))))).))))))......)))))..................... (-28.27 = -28.10 +  -0.17)

alignment

secondary structure

dotplot

Window 4

Location	6,293,154 – 6,293,251
Length	97
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	85.78
Mean single sequence MFE	-29.57
Consensus MFE	-23.27
Energy contribution	-22.77
Covariance contribution	-0.50
Combinations/Pair	1.08
Mean z-score	-2.17
Structure conservation index	0.79
SVM decision value	0.29
SVM RNA-class probability	0.669694
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6293154 97 - 23771897
----------------UACAGGUAGC---ACUACAAUUUGCGCGCUUGUCAAGUGUACGACAACAUUACGCGCAAUUGUUCAAUGUCAACGC---AUUUGAUGAGCAUGAAAUGCCUUU
----------------...(((((((---.(........).))(((..((((((((..((((.....(((......)))....))))...))---))))))..)))......))))).. ( -27.40)
>DroVir_CAF1 72381 97 - 1
----------------CACAGGUAGC---ACUACAAUUUGCGCGCUUGUCAAGUGUACGACAACAUUACGCGCAAUUGUUCAAUGUCAAUGC---AUUUGAUGGGCAUGAAAUGCUACA
----------------.....(((((---(...(((((.(((((.(((((........))))).....))))))))))((((.((((....(---....)...)))))))).)))))). ( -28.30)
>DroPse_CAF1 86373 119 - 1
CAGCUACAGCUACAGCUACAGGUAGCAGCACUACAAUUUGCGCGCUUGUCAAGUGUACGACAACAUUACGCGCAAUUGUUCAAUGUCAACGCAGCAUUUGAUGAGCAUGAAAUGCCACU
.((((........))))...((((((.(((........)))))(((..((((((((.((...(((((..(((....)))..)))))...))..))))))))..)))......))))... ( -32.30)
>DroGri_CAF1 63049 97 - 1
----------------CACAGGUAGC---ACUACAAUUUGCGCGCUUGUCAAGUGUACGACAACAUUACGCGCAAUUGUUCAAUGUCAAUGC---AUUUGAUGGGCAUGAAAUGCUACA
----------------.....(((((---(...(((((.(((((.(((((........))))).....))))))))))((((.((((....(---....)...)))))))).)))))). ( -28.30)
>DroMoj_CAF1 69956 97 - 1
----------------CACAGGUAGC---ACUACAAUUUGCGCGCUUGUCAAGUGUACGACAACAUUACGCGCAAUUGUUCAAUGUCAAUGC---AUUUGAUGGGCAUGAAAUGCUACA
----------------.....(((((---(...(((((.(((((.(((((........))))).....))))))))))((((.((((....(---....)...)))))))).)))))). ( -28.30)
>DroPer_CAF1 89805 119 - 1
CAGCUACAGCUACAGCUACAGGUAGCAGCUCUACAAUUUGCGCGCUUGUCAAGUGUACGACAACAUUACGCGCAAUUGUUCAAUGUCAACGCAGCAUUUGAUGAGCAUGAAAUGCCACA
.((((........))))...((((.((((((.((((((.(((((.(((((........))))).....)))))))))))(((((((.......))).)))).)))).))...))))... ( -32.80)
>consensus
________________CACAGGUAGC___ACUACAAUUUGCGCGCUUGUCAAGUGUACGACAACAUUACGCGCAAUUGUUCAAUGUCAACGC___AUUUGAUGAGCAUGAAAUGCCACA
....................((((.............(((((((.(((((........))))).....))))))).((((((...((((........)))))))))).....))))... (-23.27 = -22.77 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:04 2006