Locus 7451

Sequence ID	3L_DroMel_CAF1
Location	20,005,486 – 20,005,623
Length	137
Max. P	0.976292

overview

Window 8

Location	20,005,486 – 20,005,590
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.87
Mean single sequence MFE	-33.38
Consensus MFE	-23.30
Energy contribution	-24.02
Covariance contribution	0.72
Combinations/Pair	1.04
Mean z-score	-1.94
Structure conservation index	0.70
SVM decision value	0.28
SVM RNA-class probability	0.665184
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20005486 104 - 23771897
GACCAUCUGCAUUAUGCAUGAGGUUCACUGCUCCGCAUUUGGAGCAGUCUGGC-----AGGACU----------CUCGG-CAUCCUUUUGUAAGCAAGUGCGAAAGUUUUAUUUAACAAU
(((..((.(((((.(((.(((((((((((((((((....))))))))).....-----.)))).----------))))(-((......)))..))))))))))..)))............ ( -30.20)
>DroSec_CAF1 95737 104 - 1
GACCAUCUGCAUCAUCCAUGAGGUUCACUGCUCCGUAUUUGGAGCAGUCUGGC-----CGGACU----------CACGG-CAUCCUUUUGUUGGCAAGUGCGAAACUUUUAUUUAACUAU
.......(((((...(((.((((...(((((((((....)))))))))...((-----((....----------..)))-)..))))....)))...))))).................. ( -33.10)
>DroSim_CAF1 54713 104 - 1
GACCAUCUGCAUUAUGCAUGAGGUUCACUGCUCCGCAUUUGGAGCAGUCUGGC-----CGGACU----------CACGG-CAUCCUUUUGUUGGCAAGUGCGAAACUUUUAUUUAACUAU
..(((..(((.....(((.((((...(((((((((....)))))))))...((-----((....----------..)))-)..)))).)))..)))..)).).................. ( -32.90)
>DroEre_CAF1 46062 120 - 1
GAGCAACUGCAUUAUGCAUGAGGUUCACUGCUCCGCAUUUGGAGCAGUCUGCCGCACUCGGACUCGGACUCGAACUCGGACAGCCUUUUGUGAGCAAGUGGGAAGCUUUUAUUUAACAAU
((((..((.((((.(((....(((..(((((((((....)))))))))..))).(((..((..((.((.......)).))...))....))).)))))))))..))))............ ( -34.30)
>DroYak_CAF1 51928 104 - 1
GACCAACUGCAUUAUGCAUGAGGUUCACUGCUCCGCAUUUGGAGCAGUCUGGC-----CGGACU----------CUCGG-CAGCCUUUUGUAAGCAAGUGAGAAACUUGUAUUUAACAAU
..............((((.((((((.(((((((((....)))))))))...((-----(((...----------.))))-))))))).)))).((((((.....)))))).......... ( -36.40)
>consensus
GACCAUCUGCAUUAUGCAUGAGGUUCACUGCUCCGCAUUUGGAGCAGUCUGGC_____CGGACU__________CUCGG_CAUCCUUUUGUAAGCAAGUGCGAAACUUUUAUUUAACAAU
...((..(((....((((.((((.....(((((((....)))))))(((((.......)))))....................)))).)))).)))..)).................... (-23.30 = -24.02 +   0.72)

alignment

secondary structure

dotplot

Window 9

Location	20,005,526 – 20,005,623
Length	97
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	87.43
Mean single sequence MFE	-39.74
Consensus MFE	-29.48
Energy contribution	-29.60
Covariance contribution	0.12
Combinations/Pair	1.08
Mean z-score	-2.84
Structure conservation index	0.74
SVM decision value	1.77
SVM RNA-class probability	0.976292
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20005526 97 + 23771897
-CCGAG----------AGUCCU-----GCCAGACUGCUCCAAAUGCGGAGCAGUGAACCUCAUGCAUAAUGCAGAUGGUCGGACAUGCAGCCAUCUCGCUGAGGAGAUUACAG
-((...----------.((((.-----((((.((((((((......)))))))).....((.(((.....))))))))).))))...((((......)))).))......... ( -35.60)
>DroSec_CAF1 95777 97 + 1
-CCGUG----------AGUCCG-----GCCAGACUGCUCCAAAUACGGAGCAGUGAACCUCAUGGAUGAUGCAGAUGGUCGGACAUGCAGUCAUCUCGCUGAGCAGAUUACAG
-..(((----------.(((((-----((((.((((((((......))))))))...((....))..........))))))))).))).((.((((.((...)))))).)).. ( -38.40)
>DroSim_CAF1 54753 97 + 1
-CCGUG----------AGUCCG-----GCCAGACUGCUCCAAAUGCGGAGCAGUGAACCUCAUGCAUAAUGCAGAUGGUCGGACAUGCAGCCAUCUCGCUGAGCAGAUUACAG
-..(((----------((((((-----((((.((((((((......)))))))).....((.(((.....))))))))))))))...((((......))))......)))).. ( -41.40)
>DroEre_CAF1 46102 113 + 1
UCCGAGUUCGAGUCCGAGUCCGAGUGCGGCAGACUGCUCCAAAUGCGGAGCAGUGAACCUCAUGCAUAAUGCAGUUGCUCGGACUUGCAGCCAUCUCGCCGAGGAGAUUACAG
...(.((((((((((((((....(((.((...((((((((......))))))))...)).)))((.....))....))))))))))).))))(((((......)))))..... ( -44.20)
>DroYak_CAF1 51968 97 + 1
-CCGAG----------AGUCCG-----GCCAGACUGCUCCAAAUGCGGAGCAGUGAACCUCAUGCAUAAUGCAGUUGGUCGGACAUGCAGCCAACUCGCUGAAGAGAUUACCG
-.....----------.(((((-----(((((((((((((......))))))))........(((.....))).))))))))))...((((......))))............ ( -39.10)
>consensus
_CCGAG__________AGUCCG_____GCCAGACUGCUCCAAAUGCGGAGCAGUGAACCUCAUGCAUAAUGCAGAUGGUCGGACAUGCAGCCAUCUCGCUGAGGAGAUUACAG
.................(((((.....((((.((((((((......))))))))........(((.....)))..)))))))))...((((......))))............ (-29.48 = -29.60 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:47:27 2006