Locus 8288

Sequence ID	3L_DroMel_CAF1
Location	21,738,798 – 21,739,078
Length	280
Max. P	0.968848

overview

Window 3

Location	21,738,798 – 21,738,918
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.31
Mean single sequence MFE	-31.30
Consensus MFE	-28.86
Energy contribution	-29.30
Covariance contribution	0.44
Combinations/Pair	1.05
Mean z-score	-1.10
Structure conservation index	0.92
SVM decision value	0.07
SVM RNA-class probability	0.569299
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21738798 120 - 23771897
GACAGGCCUCGUCUCACCUCAAGACAUUCACAGCCCGGAUAAAUCACACAGCGAUGAAUUUGCAUAACUCCCGGUGCAGAUCGGUCGAGUAAUUUGUUCUGCUUAAGAGGAAACUAGUUU
(((((.((((((((.......))))......(((..((((((((.((....((((..((((((((........))))))))..)))).)).)))))))).)))...))))...)).))). ( -32.20)
>DroSec_CAF1 20694 120 - 1
GACAGGCCUCGUCUCACCUCAAGACAUUCCCAGCCCGGAUAAAUCACACAGCGAUGAAUUUGCAUAACUCUCGGUGCAGAUCGGUCGAGUAAUUUGUUCUGCUUAAGAGGAAACUAGUUU
(((((.((((((((.......))))......(((..((((((((.((....((((..((((((((........))))))))..)))).)).)))))))).)))...))))...)).))). ( -32.20)
>DroSim_CAF1 25586 120 - 1
GACAGGCCUCGUCUCACCUCAAGACAUUCCCAGCCCGGAUAAAUCACACAGCGAUGAAUUUGCAUAACUCCCGGUGCAGAUCGGUCGAGUAAUUUGUUCUGCUUAAGAGGAAACUAGUUU
(((((.((((((((.......))))......(((..((((((((.((....((((..((((((((........))))))))..)))).)).)))))))).)))...))))...)).))). ( -32.20)
>DroEre_CAF1 6773 116 - 1
GACAGGCCUCGUCUC---CCAAGACAUUCCCAGCCCGAAUAAAUCACACAGCGAUGAAUUUGCAUAACUCCUGGUGCAGAUCGGUCGAGUAAUUUGUUCUGCUUAGC-AGAAACUAGUUU
(((.((..((((((.---...))))......(((..((((((((.((....((((..((((((((........))))))))..)))).)).)))))))).)))....-.))..)).))). ( -27.00)
>DroYak_CAF1 78347 116 - 1
GACAGGCUUCGUCUC---CCAAGACAUUCCCAGCCCGAAUAAAUCACACAGCGAUGAAUUUGCAUAACUCCCGGUGCAGAUCAGUCGAGUAAUUUGUUCUGCUUAAG-GGAAACUAGUUU
(((((.....((((.---...)))).((((((((..((((((((.((....((((..((((((((........))))))))..)))).)).)))))))).)))...)-)))).)).))). ( -32.90)
>consensus
GACAGGCCUCGUCUCACCUCAAGACAUUCCCAGCCCGGAUAAAUCACACAGCGAUGAAUUUGCAUAACUCCCGGUGCAGAUCGGUCGAGUAAUUUGUUCUGCUUAAGAGGAAACUAGUUU
(((((.((((((((.......))))......(((..((((((((.((....((((..((((((((........))))))))..)))).)).)))))))).)))...))))...)).))). (-28.86 = -29.30 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	21,738,918 – 21,739,038
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.66
Mean single sequence MFE	-43.70
Consensus MFE	-36.06
Energy contribution	-36.50
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.46
Structure conservation index	0.83
SVM decision value	0.37
SVM RNA-class probability	0.706872
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21738918 120 - 23771897
CUGGCUCCCGGCCCUUGACUUUGACACUUCAUAAAGGUGUCGACGCGAGGGAAGAUCCGUCGGCGUCCUGGCAAGGACAAUAGACGGGCCGACCGUUUCAGUUGCCUCACUUUAUGCGAG
((((....(((((((((.(.(((((((((.....))))))))).)))))))..(..(((((...(((((....)))))....)))))..)..)))..))))....(((.(.....).))) ( -44.30)
>DroSec_CAF1 20814 119 - 1
CUGGCUCCCGGCCCUUGACUUUGACACUUCAUAAAGGUGUCGACGCGAGGGAAGAGCCGUCGGCAUCCU-GCAAGGACAAUAACCGGGCUGUCCGUUUCAGUUGCCUCACUUUAUGCGAG
..(((((....((((((.(.(((((((((.....))))))))).)))))))..)))))...((((..((-(...(((((..........)))))....))).)))).............. ( -44.20)
>DroSim_CAF1 25706 119 - 1
CUGGCUCCCGGCCCUUGACUUUGACACUUCAUAAAGGUGUCGACGCGAGGGAAGAGCCGUCGGCAUCCU-GCAAGGACAAUAACCGGGCUGCCCGUUUCAGUUGCCUCACUUUAUGCGAG
..(((((....((((((.(.(((((((((.....))))))))).)))))))..)))))....((((...-(..(((.((((((.((((...)))).))..)))))))..)...))))... ( -43.40)
>DroEre_CAF1 6889 120 - 1
CUCGCUCCCGGCCCUUGACUUUGACACUUCAUAAAGGUGUCGACGCGAGGGAAGAGCAGUCGGCAUCCUGGCAAGGACAAUGAACGGGCUGCUCGUUUCAUUUGCCUCACUUUAUGCGGG
......((((.((((((.(.(((((((((.....))))))))).)))))))..((((((((.(((((((....))))...))..).))))))))......................)))) ( -44.20)
>DroYak_CAF1 78463 111 - 1
CUCGCUCCCGGCCCUUGACUUUGACACUUCAUAAAGGUGUCGACGCGAGGGAAGAGCAGUUGGCAUCCUGACAAGGACAACAGCCGGGCU---------AUUUGCCUCACUUUAUGCGAG
(((((...(((((((((.(.(((((((((.....))))))))).))))))........((((...((((....)))))))).))))(((.---------....))).........))))) ( -42.40)
>consensus
CUGGCUCCCGGCCCUUGACUUUGACACUUCAUAAAGGUGUCGACGCGAGGGAAGAGCCGUCGGCAUCCUGGCAAGGACAAUAACCGGGCUGCCCGUUUCAGUUGCCUCACUUUAUGCGAG
.((((((....((((((.(.(((((((((.....))))))))).)))))))..))))))...(((((((....))))........((((..............)))).......)))... (-36.06 = -36.50 +   0.44)

alignment

secondary structure

dotplot

Window 5

Location	21,738,958 – 21,739,078
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.16
Mean single sequence MFE	-39.28
Consensus MFE	-34.24
Energy contribution	-35.20
Covariance contribution	0.96
Combinations/Pair	1.05
Mean z-score	-1.83
Structure conservation index	0.87
SVM decision value	1.63
SVM RNA-class probability	0.968848
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21738958 120 - 23771897
UUGAGCGUUUCAAGAUCACGGAUCAUGUCAAAUUAAUGAACUGGCUCCCGGCCCUUGACUUUGACACUUCAUAAAGGUGUCGACGCGAGGGAAGAUCCGUCGGCGUCCUGGCAAGGACAA
(((((...)))))(.(((((((((................((((...))))((((((.(.(((((((((.....))))))))).)))))))..))))))).)))(((((....))))).. ( -41.50)
>DroSec_CAF1 20854 119 - 1
UUGAGCGUUUCAAGAUCACGGAUCAUGUCAAAUUAAUGAACUGGCUCCCGGCCCUUGACUUUGACACUUCAUAAAGGUGUCGACGCGAGGGAAGAGCCGUCGGCAUCCU-GCAAGGACAA
(((((...)))))((((...)))).((((.......(((...(((((....((((((.(.(((((((((.....))))))))).)))))))..))))).)))((.....-))...)))). ( -38.10)
>DroSim_CAF1 25746 119 - 1
UUGAGCGUUUCAAGAUCACGGAUCAUGUCAAAUUAAUGAACUGGCUCCCGGCCCUUGACUUUGACACUUCAUAAAGGUGUCGACGCGAGGGAAGAGCCGUCGGCAUCCU-GCAAGGACAA
(((((...)))))((((...)))).((((.......(((...(((((....((((((.(.(((((((((.....))))))))).)))))))..))))).)))((.....-))...)))). ( -38.10)
>DroEre_CAF1 6929 120 - 1
UUGAGCGUUUCAAGAUCACGGAUCAUGUCACAUUAAUGAACUCGCUCCCGGCCCUUGACUUUGACACUUCAUAAAGGUGUCGACGCGAGGGAAGAGCAGUCGGCAUCCUGGCAAGGACAA
....((((..((.((((...)))).))..)).....(((.((.((((....((((((.(.(((((((((.....))))))))).)))))))..))))))))))).((((....))))... ( -38.60)
>DroYak_CAF1 78494 120 - 1
UUGAGCCUUUCAAGAUCACGGAUCAUAUCAAAUUAAUGAACUCGCUCCCGGCCCUUGACUUUGACACUUCAUAAAGGUGUCGACGCGAGGGAAGAGCAGUUGGCAUCCUGACAAGGACAA
....(((......((((...))))..............((((.((((....((((((.(.(((((((((.....))))))))).)))))))..))))))))))).((((....))))... ( -40.10)
>consensus
UUGAGCGUUUCAAGAUCACGGAUCAUGUCAAAUUAAUGAACUGGCUCCCGGCCCUUGACUUUGACACUUCAUAAAGGUGUCGACGCGAGGGAAGAGCCGUCGGCAUCCUGGCAAGGACAA
(((((...)))))((((...)))).((((.............(((((....((((((.(.(((((((((.....))))))))).)))))))..)))))(((((....)))))...)))). (-34.24 = -35.20 +   0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:11:30 2006