Locus 6784

Sequence ID	3L_DroMel_CAF1
Location	18,222,829 – 18,222,933
Length	104
Max. P	0.733368

overview

Window 2

Location	18,222,829 – 18,222,933
Length	104
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	88.02
Mean single sequence MFE	-20.16
Consensus MFE	-14.66
Energy contribution	-14.94
Covariance contribution	0.28
Combinations/Pair	1.13
Mean z-score	-1.94
Structure conservation index	0.73
SVM decision value	0.43
SVM RNA-class probability	0.733368
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18222829 104 + 23771897
CUUCCCAUUCCCACUUUUAAACCACUGGUCUUUACUUCCUUGAAAUGUGGGCCCACCCACAAAUCUCUCACACUCAGUGUUGUCCGUUG---UGGAUCCAAAAGCAA
.............(((((...(((((((.(..((((....(((..((((((....))))))......))).....))))..).)))..)---)))....)))))... ( -20.20)
>DroSec_CAF1 5363 100 + 1
CUUCCCAUUCCCACUUUUAAACCACUGGUCUUUACUUCCUUGAAAUGUGGGCCCACCCACAAAUCUCUC----UCAGUGUUGUCAGUUG---UGGAUCCAAAAGCAA
..........((((.........(((((.(..((((.....((..((((((....))))))..))....----..))))..)))))).)---)))............ ( -20.30)
>DroSim_CAF1 11835 104 + 1
CUUCCCAUUCCCACUUUUAAACCACUGGUCUUUACUUCCUUGAAAUGUGGGCCCACCCACAAACCUCUCACACUUAGUGUUGUCAGUUG---UGGAUCCAAAAGCAA
..........((((.........(((((.(..((((....(((..((((((....))))))......))).....))))..)))))).)---)))............ ( -19.00)
>DroEre_CAF1 5341 104 + 1
CUUCCCAUUCCCACUUUCAAACCACUGGUCUUAACUUCCUUGAAAUGUGGGCCCACCCACAAAUCUUUCAUACUCAGUGUUGUCGGUUG---UGGAACCCAAAACGA
....((((..((.....(((..(((((((...........(((((((((((....))))))....))))).)).))))))))..))..)---)))............ ( -22.20)
>DroYak_CAF1 12186 106 + 1
CUUCCCACUCCCUCU-GCAAACCACUGGUCUUUACUUCCUUGAAAUGUGGGCCCACCCACAAAUCCCGCACCCUCAGUGCUGUCAGUUCAGUUAGAUUCAAAAUAAA
...............-..........(((((..(((...((((..((((((....))))))......((((.....))))..))))...))).)))))......... ( -19.10)
>consensus
CUUCCCAUUCCCACUUUUAAACCACUGGUCUUUACUUCCUUGAAAUGUGGGCCCACCCACAAAUCUCUCACACUCAGUGUUGUCAGUUG___UGGAUCCAAAAGCAA
....(((.....(((..(((..((((((((...........))..((((((....))))))............)))))))))..))).....)))............ (-14.66 = -14.94 +   0.28)

alignment

secondary structure

dotplot

Window 3

Location	18,222,829 – 18,222,933
Length	104
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	88.02
Mean single sequence MFE	-30.04
Consensus MFE	-21.25
Energy contribution	-21.25
Covariance contribution	0.00
Combinations/Pair	1.15
Mean z-score	-2.01
Structure conservation index	0.71
SVM decision value	0.34
SVM RNA-class probability	0.694522
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18222829 104 - 23771897
UUGCUUUUGGAUCCA---CAACGGACAACACUGAGUGUGAGAGAUUUGUGGGUGGGCCCACAUUUCAAGGAAGUAAAGACCAGUGGUUUAAAAGUGGGAAUGGGAAG
(..((((((((.(((---(...((....(((.....)))...((..((((((....))))))..)).............)).))))))))))))..).......... ( -31.00)
>DroSec_CAF1 5363 100 - 1
UUGCUUUUGGAUCCA---CAACUGACAACACUGA----GAGAGAUUUGUGGGUGGGCCCACAUUUCAAGGAAGUAAAGACCAGUGGUUUAAAAGUGGGAAUGGGAAG
(..((((((((.(((---(...............----....((..((((((....))))))..))..((.........)).))))))))))))..).......... ( -28.30)
>DroSim_CAF1 11835 104 - 1
UUGCUUUUGGAUCCA---CAACUGACAACACUAAGUGUGAGAGGUUUGUGGGUGGGCCCACAUUUCAAGGAAGUAAAGACCAGUGGUUUAAAAGUGGGAAUGGGAAG
(..((((((((.(((---(..((.(((........))).)).((((((((((....)))))(((((...)))))..))))).))))))))))))..).......... ( -32.70)
>DroEre_CAF1 5341 104 - 1
UCGUUUUGGGUUCCA---CAACCGACAACACUGAGUAUGAAAGAUUUGUGGGUGGGCCCACAUUUCAAGGAAGUUAAGACCAGUGGUUUGAAAGUGGGAAUGGGAAG
...((((.(.(((((---(...(((...(((((.........((..((((((....))))))..))......((....)))))))..)))...)))))).).)))). ( -27.80)
>DroYak_CAF1 12186 106 - 1
UUUAUUUUGAAUCUAACUGAACUGACAGCACUGAGGGUGCGGGAUUUGUGGGUGGGCCCACAUUUCAAGGAAGUAAAGACCAGUGGUUUGC-AGAGGGAGUGGGAAG
....((((.(.(((..(((.(((..(.((((.....))))..((..((((((....))))))..))..)..)))..(((((...))))).)-))..))).).)))). ( -30.40)
>consensus
UUGCUUUUGGAUCCA___CAACUGACAACACUGAGUGUGAGAGAUUUGUGGGUGGGCCCACAUUUCAAGGAAGUAAAGACCAGUGGUUUAAAAGUGGGAAUGGGAAG
...(((((.(.(((.........(((..(((((.........((..((((((....))))))..))......((....))))))))))........))).).))))) (-21.25 = -21.25 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:29:53 2006