Locus 5842

Sequence ID	3R_DroMel_CAF1
Location	15,296,493 – 15,296,588
Length	95
Max. P	0.999091

overview

Window 0

Location	15,296,493 – 15,296,588
Length	95
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	75.26
Mean single sequence MFE	-13.02
Consensus MFE	-3.12
Energy contribution	-3.40
Covariance contribution	0.28
Combinations/Pair	1.12
Mean z-score	-1.98
Structure conservation index	0.24
SVM decision value	1.05
SVM RNA-class probability	0.907685
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15296493 95 + 27905053
C---UUGCUGGAAACUGGUUUUCCCAGGCAUUUCCCCGUGC--UUCAGACAUUCCUCUCUACCAUUUACAUACAUAUAUACAUUCAUAUACAUAUAUUCA
.---.(((((((..((((.....))))((((......))))--))))).))..................(((..(((((......)))))..)))..... ( -12.60)
>DroSec_CAF1 49285 92 + 1
C---UUGCUGGAAACGGGUUUUCCCAGGCUUUUCCCC-UGC--CUCAGACAUUCCUCUCUACCUUUUACAUACACAUAUACAUUCAUAUA--UAUAUUCA
.---.....((((..(((....)))((((........-.))--))......))))...................................--........ ( -12.60)
>DroSim_CAF1 50355 92 + 1
C---UUGCUGGAAACUGGUUUUCCCAGGCUUUUCCCC-UGC--CUCAGACAUUCCUCUCUACCAUUUACUUACACAUAUACAUUCAUAUA--UAUAUUCA
.---.((.((((....((...((..((((........-.))--))..))....))..)))).))..........................--........ (  -9.30)
>DroEre_CAF1 44978 85 + 1
C---UUGCUCGAAACGGGUUUUCCCAGGCUUUUCCCC-UGC--UUC-GACAUUCCUCUCUACCACAUAUACA----UAUAC--UCAUACA--UAUAUUCA
.---.((.(((((.((((....)))(((.......))-)).--)))-)))).....................----.....--.......--........ ( -10.10)
>DroAna_CAF1 47822 83 + 1
UGUAUUGGGGGAAACAGGUUUUCCCCAUGUUUUCCCCCUCCGACCC-AGCAUUCCUGCCUCUC--------------AUACAUUUAUUUC--UAUAUGCA
(((((.((((((((((((......)).))))))))))....((..(-((.....)))..))..--------------)))))........--........ ( -20.50)
>consensus
C___UUGCUGGAAACGGGUUUUCCCAGGCUUUUCCCC_UGC__CUCAGACAUUCCUCUCUACCAUUUACAUACA_AUAUACAUUCAUAUA__UAUAUUCA
......((((((((.....)))))..)))....................................................................... ( -3.12 =  -3.40 +   0.28)

alignment

secondary structure

dotplot

Window 1

Location	15,296,493 – 15,296,588
Length	95
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	75.26
Mean single sequence MFE	-22.62
Consensus MFE	-7.54
Energy contribution	-7.50
Covariance contribution	-0.04
Combinations/Pair	1.27
Mean z-score	-2.95
Structure conservation index	0.33
SVM decision value	3.37
SVM RNA-class probability	0.999091
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15296493 95 - 27905053
UGAAUAUAUGUAUAUGAAUGUAUAUAUGUAUGUAAAUGGUAGAGAGGAAUGUCUGAA--GCACGGGGAAAUGCCUGGGAAAACCAGUUUCCAGCAA---G
...((((((((((((....))))))))))))........((((.(....).))))..--((....(((((...((((.....))))))))).))..---. ( -22.10)
>DroSec_CAF1 49285 92 - 1
UGAAUAUA--UAUAUGAAUGUAUAUGUGUAUGUAAAAGGUAGAGAGGAAUGUCUGAG--GCA-GGGGAAAAGCCUGGGAAAACCCGUUUCCAGCAA---G
...(((((--((((((....)))))))))))......(.(.((((((....(((.((--((.-........)))).)))....)).)))).).)..---. ( -21.50)
>DroSim_CAF1 50355 92 - 1
UGAAUAUA--UAUAUGAAUGUAUAUGUGUAAGUAAAUGGUAGAGAGGAAUGUCUGAG--GCA-GGGGAAAAGCCUGGGAAAACCAGUUUCCAGCAA---G
...(((((--(((((....)))))))))).......(((.(((..((....(((.((--((.-........)))).)))...))..))))))....---. ( -21.60)
>DroEre_CAF1 44978 85 - 1
UGAAUAUA--UGUAUGA--GUAUA----UGUAUAUGUGGUAGAGAGGAAUGUC-GAA--GCA-GGGGAAAAGCCUGGGAAAACCCGUUUCGAGCAA---G
....((((--(((((..--.....----.)))))))))...........((((-(((--((.-(((......)))(((....)))))))))).)).---. ( -20.70)
>DroAna_CAF1 47822 83 - 1
UGCAUAUA--GAAAUAAAUGUAU--------------GAGAGGCAGGAAUGCU-GGGUCGGAGGGGGAAAACAUGGGGAAAACCUGUUUCCCCCAAUACA
(((((.((--....)).)))))(--------------((..((((....))))-...)))..((((((((.((.((......))))))))))))...... ( -27.20)
>consensus
UGAAUAUA__UAUAUGAAUGUAUAU_UGUAUGUAAAUGGUAGAGAGGAAUGUCUGAG__GCA_GGGGAAAAGCCUGGGAAAACCAGUUUCCAGCAA___G
...........................................................((....(((((...((((.....))))))))).))...... ( -7.54 =  -7.50 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:01 2006