Locus 8952

Sequence ID	3R_DroMel_CAF1
Location	24,010,027 – 24,010,124
Length	97
Max. P	0.999282

overview

Window 8

Location	24,010,027 – 24,010,124
Length	97
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	70.81
Mean single sequence MFE	-38.28
Consensus MFE	-13.82
Energy contribution	-16.51
Covariance contribution	2.69
Combinations/Pair	1.32
Mean z-score	-2.87
Structure conservation index	0.36
SVM decision value	3.48
SVM RNA-class probability	0.999282
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24010027 97 + 27905053
-------GGAAC----AGAGGUCUGAGUCCUG-----CGGGCGACUCGGGAGUGUGGA-UUCCCAAAGGACACCAACCAACUGGUCGCUUGCAGGACAAAUCGAAUGCAUCCAG
-------(((.(----((....))).((((((-----((((((((.(((..(..(((.-.(((....)))..)))..)..)))))))))))))))))............))).. ( -44.20)
>DroSec_CAF1 204211 97 + 1
-------GGAAC----AGAGGUCUGAGUCCUG-----CGGGCGGUUCGGGAGUGGGGA-UUCCCAAAGGACACCAACCAAGUGGUCGCCUGCAGGAAGAAUCGAAUGCAUCCAG
-------(((.(----((....)))..(((((-----((((((((((((((((....)-)))))...))))((((......))))))))))))))).............))).. ( -40.90)
>DroSim_CAF1 202891 97 + 1
-------GGAAC----AGAGGUCUGAGUCCUG-----CGGGCGGCUCGGGAGUGGGGA-UUCCCAAAGGACACCAACCAAGUGGUCGCCUACAGGACGAAUCGAAUGCAUCCAG
-------(((.(----((....))).((((((-----..((((((..((((((....)-)))))......(((.......)))))))))..))))))............))).. ( -40.30)
>DroEre_CAF1 212873 83 + 1
-------GGAAC----AAAGGUCUGAGUCCUG-----CG-GCGACUCGGGAGUGGCUAAGUCCCAAAGGACUCCCACC--------------AGGACAAAUCGAAUGCAUCCAG
-------(((..----...(((..(((((((.-----.(-(.((((..(......)..))))))..)))))))..)))--------------..((....)).......))).. ( -27.10)
>DroAna_CAF1 215650 113 + 1
AUUGGGGGGAAUAGGAAGAGGCAUGGGGCAAGAGGCACGAGCCACCAGGGAGGGGAUA-UCCUGCAGGGAGCCCCAGCAAGUGGUGCGUUGAAUGACAAAUGAAAUGCAUCUAU
....................((.((((((....(((....))).((..(.((((....-)))).)..)).))))))))....((((((((..((.....))..))))))))... ( -38.90)
>consensus
_______GGAAC____AGAGGUCUGAGUCCUG_____CGGGCGACUCGGGAGUGGGGA_UUCCCAAAGGACACCAACCAAGUGGUCGCCUGCAGGACAAAUCGAAUGCAUCCAG
.......(((.........(((....((((((.....(((((((((.(((((.......)))))...((...))........)))))))))))))))..))).......))).. (-13.82 = -16.51 +   2.69)

alignment

secondary structure

dotplot

Window 9

Location	24,010,027 – 24,010,124
Length	97
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	70.81
Mean single sequence MFE	-31.70
Consensus MFE	-12.46
Energy contribution	-13.22
Covariance contribution	0.76
Combinations/Pair	1.42
Mean z-score	-1.86
Structure conservation index	0.39
SVM decision value	0.61
SVM RNA-class probability	0.797878
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24010027 97 - 27905053
CUGGAUGCAUUCGAUUUGUCCUGCAAGCGACCAGUUGGUUGGUGUCCUUUGGGAA-UCCACACUCCCGAGUCGCCCG-----CAGGACUCAGACCUCU----GUUCC-------
..(((............(((((((..(((((..(..((((((..(((....))).-.))).)))..)..)))))..)-----)))))).(((....))----).)))------- ( -34.60)
>DroSec_CAF1 204211 97 - 1
CUGGAUGCAUUCGAUUCUUCCUGCAGGCGACCACUUGGUUGGUGUCCUUUGGGAA-UCCCCACUCCCGAACCGCCCG-----CAGGACUCAGACCUCU----GUUCC-------
..(((.............((((((.((((((((......))))....(((((((.-.......))))))).)))).)-----)))))..(((....))----).)))------- ( -32.40)
>DroSim_CAF1 202891 97 - 1
CUGGAUGCAUUCGAUUCGUCCUGUAGGCGACCACUUGGUUGGUGUCCUUUGGGAA-UCCCCACUCCCGAGCCGCCCG-----CAGGACUCAGACCUCU----GUUCC-------
..(((............((((((..(((((((....))))(((.....((((((.-.......))))))))))))..-----)))))).(((....))----).)))------- ( -35.00)
>DroEre_CAF1 212873 83 - 1
CUGGAUGCAUUCGAUUUGUCCU--------------GGUGGGAGUCCUUUGGGACUUAGCCACUCCCGAGUCGC-CG-----CAGGACUCAGACCUUU----GUUCC-------
..((((...........)))).--------------(((..(((((((.(((((((..(......)..)))).)-))-----.)))))))..)))...----.....------- ( -28.60)
>DroAna_CAF1 215650 113 - 1
AUAGAUGCAUUUCAUUUGUCAUUCAACGCACCACUUGCUGGGGCUCCCUGCAGGA-UAUCCCCUCCCUGGUGGCUCGUGCCUCUUGCCCCAUGCCUCUUCCUAUUCCCCCCAAU
..(((.((((.................(((.....))).(((((.....(((.((-...((((.....)).)).)).))).....))))))))).)))................ ( -27.90)
>consensus
CUGGAUGCAUUCGAUUUGUCCUGCAAGCGACCACUUGGUUGGUGUCCUUUGGGAA_UCCCCACUCCCGAGUCGCCCG_____CAGGACUCAGACCUCU____GUUCC_______
(((((.....)).....((((((.....((((....))))((((...(((((((.........))))))).)))).......)))))).)))...................... (-12.46 = -13.22 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:23:24 2006