Locus 1184

Sequence ID	X_DroMel_CAF1
Location	3,527,704 – 3,527,799
Length	95
Max. P	0.995489

overview

Window 7

Location	3,527,704 – 3,527,799
Length	95
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	72.86
Mean single sequence MFE	-27.48
Consensus MFE	-11.48
Energy contribution	-13.02
Covariance contribution	1.54
Combinations/Pair	1.00
Mean z-score	-2.82
Structure conservation index	0.42
SVM decision value	2.58
SVM RNA-class probability	0.995489
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3527704 95 + 22224390
GG----AGGGGGUGGUGGUGC-UGGGGGCUUAAAUGCAUAAAGCAAAGCGAAAAUUAUGCAUG-AAAUGUGGCAUAAAAGUUG-------CAUAUCGUUGCCUCCGCA
..----.((((((..((((((-(....((......))....)))...((((...((((((...-.......))))))...)))-------)..))))..))))))... ( -31.70)
>DroSec_CAF1 35959 89 + 1
G-----GGGAGGU----GUGC-UGGGGGCUUAAAUGCAUA-AGCAAAGCGAAAAUUAUGCAUG-AAAUGUGGCAUAAAAGUUG-------CAUAUCGUUGCCUCCGCA
(-----.((((((----.(((-(....(((((......))-)))..))))..........(((-(.(((..((......))..-------))).)))).)))))).). ( -30.40)
>DroSim_CAF1 37184 91 + 1
GG----GGGAGGU----GUGC-UGGGGGCUUAAAUGCAUAAAGCAAAGCGAAAAUUAUGCAUG-AAAUGUGGCAUAAAAGUUG-------CAUAUCGUUGCCUCCGCA
.(----.((((((----.(((-(....((......))....))))..((((...((((((...-.......))))))...)))-------)........)))))).). ( -29.50)
>DroEre_CAF1 39746 79 + 1
UC----CGGGG--------GUUGGGGGGCUUAAAUGCAUAAGGCAAAGCAAAAAUUAUGCAUGGAAAUGUGGCAUAAAAGUU-----------------ACCUCCGCA
..----(((((--------((......((((...(((.....))))))).....((((((((......)).)))))).....-----------------))))))).. ( -20.30)
>DroYak_CAF1 35733 91 + 1
AU----AGGGG----UGGAGU-UGGGGGCUUGAAUGCAUAAAGCAAAGCGAAAAUUAUGCAUG-AAAUGUGGCAUUAAAGUUG-------CAUAUCGUUGCCUCCGCA
..----.....----....((-.((((((....((((((((.((...)).....))))))))(-(.(((..((......))..-------))).))...)))))))). ( -26.90)
>DroAna_CAF1 61989 96 + 1
GGGGGUGGGGGGUGGAUGUGC-CAA----CAGAAUGCUAAAAACAAAACGAAAAUUAUGCAUG-AAAAGUGGCAUACUAGUUUUUCCAUUCAUUUCAUUCUC------
((((((((.((((((((((((-((.----....((((.....................)))).-.....)))))))........)))))))...))))))))------ ( -26.10)
>consensus
GG____GGGGGGU____GUGC_UGGGGGCUUAAAUGCAUAAAGCAAAGCGAAAAUUAUGCAUG_AAAUGUGGCAUAAAAGUUG_______CAUAUCGUUGCCUCCGCA
.......................((((((.....(((.....))).........((((((((......)).))))))......................))))))... (-11.48 = -13.02 +   1.54)

alignment

secondary structure

dotplot

Window 8

Location	3,527,704 – 3,527,799
Length	95
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	72.86
Mean single sequence MFE	-17.45
Consensus MFE	-8.98
Energy contribution	-9.90
Covariance contribution	0.92
Combinations/Pair	1.14
Mean z-score	-1.66
Structure conservation index	0.51
SVM decision value	0.35
SVM RNA-class probability	0.700801
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3527704 95 - 22224390
UGCGGAGGCAACGAUAUG-------CAACUUUUAUGCCACAUUU-CAUGCAUAAUUUUCGCUUUGCUUUAUGCAUUUAAGCCCCCA-GCACCACCACCCCCU----CC
...(((((........((-------(.....((((((.......-...)))))).....(((((((.....)))...)))).....-))).........)))----)) ( -18.53)
>DroSec_CAF1 35959 89 - 1
UGCGGAGGCAACGAUAUG-------CAACUUUUAUGCCACAUUU-CAUGCAUAAUUUUCGCUUUGCU-UAUGCAUUUAAGCCCCCA-GCAC----ACCUCCC-----C
...(((((......((((-------((......(((...)))..-..))))))......(((..(((-((......)))))....)-))..----.))))).-----. ( -19.60)
>DroSim_CAF1 37184 91 - 1
UGCGGAGGCAACGAUAUG-------CAACUUUUAUGCCACAUUU-CAUGCAUAAUUUUCGCUUUGCUUUAUGCAUUUAAGCCCCCA-GCAC----ACCUCCC----CC
(((((.(((........(-------(.....((((((.......-...)))))).....))..(((.....))).....))).)).-))).----.......----.. ( -18.50)
>DroEre_CAF1 39746 79 - 1
UGCGGAGGU-----------------AACUUUUAUGCCACAUUUCCAUGCAUAAUUUUUGCUUUGCCUUAUGCAUUUAAGCCCCCCAAC--------CCCCG----GA
..(((.(((-----------------.....((((((...........)))))).....(((((((.....)))...))))......))--------).)))----.. ( -15.30)
>DroYak_CAF1 35733 91 - 1
UGCGGAGGCAACGAUAUG-------CAACUUUAAUGCCACAUUU-CAUGCAUAAUUUUCGCUUUGCUUUAUGCAUUCAAGCCCCCA-ACUCCA----CCCCU----AU
...((((.......((((-------((.....((((...)))).-..))))))......(((((((.....)))...)))).....-.)))).----.....----.. ( -17.20)
>DroAna_CAF1 61989 96 - 1
------GAGAAUGAAAUGAAUGGAAAAACUAGUAUGCCACUUUU-CAUGCAUAAUUUUCGUUUUGUUUUUAGCAUUCUG----UUG-GCACAUCCACCCCCCACCCCC
------.((((((....(((..(((.......(((((.......-...))))).......)))..)))....)))))).----.((-(.....)))............ ( -15.54)
>consensus
UGCGGAGGCAACGAUAUG_______CAACUUUUAUGCCACAUUU_CAUGCAUAAUUUUCGCUUUGCUUUAUGCAUUUAAGCCCCCA_GCAC____ACCCCCC____CC
...((.(((......................((((((...........)))))).........(((.....))).....))).))....................... ( -8.98 =  -9.90 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:17 2006