Locus 4327

Sequence ID	3L_DroMel_CAF1
Location	12,723,000 – 12,723,105
Length	105
Max. P	0.997413

overview

Window 0

Location	12,723,000 – 12,723,105
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	75.76
Mean single sequence MFE	-26.08
Consensus MFE	-14.69
Energy contribution	-15.01
Covariance contribution	0.32
Combinations/Pair	1.10
Mean z-score	-2.67
Structure conservation index	0.56
SVM decision value	2.85
SVM RNA-class probability	0.997413
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12723000 105 + 23771897
--------------AAACAAAUUCCAGUUCAUUC-AAUUAUGUUUUCUAAUUGGAAACUAAUGGUGGAAGCAUAUUCGAUUUAUAUCGAAUACUGUGCUUUGAAAACUUUCUUUUAUUUA
--------------...........(((((((..-.((((.((((((.....)))))))))).)))((((((((((((((....)))))))...)))))))...))))............ ( -20.20)
>DroSec_CAF1 3335 119 + 1
UCAGAUUAUCCGCUUAACAAAUUCCAGUUCACUG-AAUGAUGUUUUCCAAUUGGAAACUAAAGGUGGAUGCAUAUUCGAUUUAUAUCGAAUACUAUGCUUUGAAGACUUUCUUUUAUUUA
(((((..((((((((((((.((((.((....)))-)))..))))((((....)))).....))))))))(((((((((((....))))))...))))))))))................. ( -28.20)
>DroSim_CAF1 3710 119 + 1
UCAGAUUAUCCGCUUAACAAAUUCCAGUUCAGUC-AAUGAUGUUUUCCAAUUGGAAACUAAAGGUGGAAGCAUAUUCGAUUUAUAUCGAAUACUUUGCUUUGAAGACUUUCUUUUAUUUA
(((((...(((((((......((((((((....(-(....))......)))))))).....))))))).(((((((((((....))))))))...))))))))................. ( -25.10)
>DroEre_CAF1 3318 119 + 1
UCAGAAUCUACGCUCAACAAAAUCCAAUUGAGUACGAACA-AGUGUCCAAUUGGAAAAUACGGAUAAAAGUAUAUUCGAUUUAUAUCGAAUACGCUGCUUGUAAGCCUUUCCUUUAUUUA
......................((((((((..(((.....-.)))..))))))))(((((.(((....((..((((((((....))))))))..))(((....)))...)))..))))). ( -28.80)
>DroYak_CAF1 3167 108 + 1
UCAGA------------UAAAAUCCAAUUGAGUUUGAACUCAACUUCCAAUUGGAAAAUAAGGAUGAAAGUAUAUUCGAUUUAUAUCGAAUACGGCGCUUGCAAGCCUUUCUUUUAUUUA
..(((------------((((((((..((((((....)))))).((((....)))).....))))((((...((((((((....)))))))).(((........))))))).))))))). ( -28.10)
>consensus
UCAGA_U_U_CGCUUAACAAAUUCCAGUUCAGUC_AAUCAUGUUUUCCAAUUGGAAACUAAAGGUGGAAGCAUAUUCGAUUUAUAUCGAAUACUGUGCUUUGAAGACUUUCUUUUAUUUA
......................(((((((...................)))))))...........((((((((((((((....))))))))...))))))................... (-14.69 = -15.01 +   0.32)

alignment

secondary structure

dotplot

Window 1

Location	12,723,000 – 12,723,105
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	75.76
Mean single sequence MFE	-25.66
Consensus MFE	-11.42
Energy contribution	-11.90
Covariance contribution	0.48
Combinations/Pair	1.10
Mean z-score	-2.51
Structure conservation index	0.45
SVM decision value	2.27
SVM RNA-class probability	0.991548
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12723000 105 - 23771897
UAAAUAAAAGAAAGUUUUCAAAGCACAGUAUUCGAUAUAAAUCGAAUAUGCUUCCACCAUUAGUUUCCAAUUAGAAAACAUAAUU-GAAUGAACUGGAAUUUGUUU--------------
.(((((((............(((((...((((((((....)))))))))))))......(((((((.((((((.......)))))-)...)))))))..)))))))-------------- ( -19.10)
>DroSec_CAF1 3335 119 - 1
UAAAUAAAAGAAAGUCUUCAAAGCAUAGUAUUCGAUAUAAAUCGAAUAUGCAUCCACCUUUAGUUUCCAAUUGGAAAACAUCAUU-CAGUGAACUGGAAUUUGUUAAGCGGAUAAUCUGA
........(((...........(((((...((((((....)))))))))))((((.........((((....))))((((...((-(((....)))))...))))....))))..))).. ( -26.50)
>DroSim_CAF1 3710 119 - 1
UAAAUAAAAGAAAGUCUUCAAAGCAAAGUAUUCGAUAUAAAUCGAAUAUGCUUCCACCUUUAGUUUCCAAUUGGAAAACAUCAUU-GACUGAACUGGAAUUUGUUAAGCGGAUAAUCUGA
........(((..((((.(..(((((((((((((((....)))))))))..(((((..((((((((((....))))..((....)-))))))).)))))))))))..).))))..))).. ( -26.70)
>DroEre_CAF1 3318 119 - 1
UAAAUAAAGGAAAGGCUUACAAGCAGCGUAUUCGAUAUAAAUCGAAUAUACUUUUAUCCGUAUUUUCCAAUUGGACACU-UGUUCGUACUCAAUUGGAUUUUGUUGAGCGUAGAUUCUGA
........(((((.(((((((((.((..((((((((....))))))))..)).............(((((((((..((.-.....))..))))))))).)))).))))).)...)))).. ( -27.30)
>DroYak_CAF1 3167 108 - 1
UAAAUAAAAGAAAGGCUUGCAAGCGCCGUAUUCGAUAUAAAUCGAAUAUACUUUCAUCCUUAUUUUCCAAUUGGAAGUUGAGUUCAAACUCAAUUGGAUUUUA------------UCUGA
...((((((((((((((....)))...(((((((((....))))))))).))))).(((......(((....)))((((((((....))))))))))))))))------------).... ( -28.70)
>consensus
UAAAUAAAAGAAAGUCUUCAAAGCACAGUAUUCGAUAUAAAUCGAAUAUGCUUCCACCCUUAGUUUCCAAUUGGAAAACAUCAUU_GACUGAACUGGAAUUUGUUAAGCG_A_A_UCUGA
..((((((...................(((((((((....)))))))))..............(((((....)))))......................))))))............... (-11.42 = -11.90 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:45 2006