Locus 3744

Sequence ID	2L_DroMel_CAF1
Location	10,891,770 – 10,891,893
Length	123
Max. P	0.807037

overview

Window 4

Location	10,891,770 – 10,891,868
Length	98
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	83.64
Mean single sequence MFE	-27.48
Consensus MFE	-21.73
Energy contribution	-21.95
Covariance contribution	0.22
Combinations/Pair	1.03
Mean z-score	-1.93
Structure conservation index	0.79
SVM decision value	0.43
SVM RNA-class probability	0.732339
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10891770 98 + 22407834
----------GGCUGAUUUACCAAUUGAAAGUUCAUUUCAGCUGUCAUUUGGCGGUUAAUUGUGAAAACUUGAUUAACAUCGGUUAAUUGACAGUUUGGAAACG-GU-----UA
----------(((((.(((.((((.(((((.....)))))(((((((.(((((.(((((((((....))..)))))))....))))).))))))))))))))))-))-----). ( -28.50)
>DroSec_CAF1 31343 108 + 1
GAUUUCGGGUGGCUGAUUUACCAAUUGAAAGUUCAUUUCAGCUGUCAUUUGGCGGUUAAUUGUGAAAACUUGAUUAACAUCGGUUAAUUGACAGUUUGGAAACG-GU-----UA
.........((((((.(((.((((.(((((.....)))))(((((((.(((((.(((((((((....))..)))))))....))))).))))))))))))))))-))-----)) ( -29.00)
>DroSim_CAF1 31740 108 + 1
GAUUUCGGGUGGCUGAUUUACCAAUUGAAAGUUCAUUUCAGCUGUCAUUUGGCGGUUAAUUGUGAAAACUUGAUUAACAUCGGUUAAUUGACAGUUUGGAAACG-GU-----UA
.........((((((.(((.((((.(((((.....)))))(((((((.(((((.(((((((((....))..)))))))....))))).))))))))))))))))-))-----)) ( -29.00)
>DroEre_CAF1 31489 109 + 1
GAAUUCGGGUGGCUGA-UUACCAAUUGAAAGUUCAUUUCAGCUGUCAUUUGGCGGUUAAUUGUGAAAACUUGAUUAACGUCGGUUAAUUGACAGUUUGGCAACA----ACAGUA
...........((((.-........(((((.....)))))(((((((.((((((.((((((((....))..)))))))))))).....)))))))(((....))----))))). ( -26.40)
>DroYak_CAF1 32274 102 + 1
------------AUGAUUUACCAAUCGAAAGUUCAUUUCAGCUGUCAUUUGGCGGUUAAUUGUGAAAACUUGAUUAACAUCGGUUAAUUGACAGUUGGGAAACUGGAUACACUC
------------........(((..(....)....(..(((((((((.(((((.(((((((((....))..)))))))....))))).)))))))))..)...)))........ ( -28.70)
>DroAna_CAF1 34494 108 + 1
GAGUGAAGCCUGUUGAUAUACCGAUUGAAAAUUUAUUUCAGCUGUCAUUUGGCGGUUAAUUGCGUAAACCUGAUUAACAUCGGUUAAUUGACAGUUUGGAAAUU-GA-----AC
...(.((((.(((..((..(((((((((((.....)))))((((.....)))).((((((((.(....).))))))))))))))..))..))))))).).....-..-----.. ( -23.30)
>consensus
GA_UUCGGGUGGCUGAUUUACCAAUUGAAAGUUCAUUUCAGCUGUCAUUUGGCGGUUAAUUGUGAAAACUUGAUUAACAUCGGUUAAUUGACAGUUUGGAAACG_GU_____UA
....................((((.(((((.....)))))(((((((.(((((.((((((((........))))))))....))))).)))))))))))............... (-21.73 = -21.95 +   0.22)

alignment

secondary structure

dotplot

Window 5

Location	10,891,800 – 10,891,893
Length	93
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	83.21
Mean single sequence MFE	-22.20
Consensus MFE	-17.49
Energy contribution	-17.22
Covariance contribution	-0.28
Combinations/Pair	1.14
Mean z-score	-2.11
Structure conservation index	0.79
SVM decision value	0.64
SVM RNA-class probability	0.807037
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10891800 93 + 22407834
GCUGUCAUUUGGCGGUUAAUUGUGAAAACUUGAUUAACAUCGGUUAAUUGACAGUUUGGAAACG-GU-----UAAAUAAUUGUAUUUUUCUUCAUUUUA
(((((((.(((((.(((((((((....))..)))))))....))))).)))))))..(....)(-(.-----.(((((....)))))..))........ ( -20.50)
>DroSec_CAF1 31383 93 + 1
GCUGUCAUUUGGCGGUUAAUUGUGAAAACUUGAUUAACAUCGGUUAAUUGACAGUUUGGAAACG-GU-----UAAAUAAUUGUAUUUUUCAUCGUUUUA
(((((((.(((((.(((((((((....))..)))))))....))))).)))))))...((((((-((-----.(((((....)))))...)))))))). ( -25.10)
>DroSim_CAF1 31780 93 + 1
GCUGUCAUUUGGCGGUUAAUUGUGAAAACUUGAUUAACAUCGGUUAAUUGACAGUUUGGAAACG-GU-----UAAAUAAUUGUAUUUUUCAUCGUUUUA
(((((((.(((((.(((((((((....))..)))))))....))))).)))))))...((((((-((-----.(((((....)))))...)))))))). ( -25.10)
>DroEre_CAF1 31528 95 + 1
GCUGUCAUUUGGCGGUUAAUUGUGAAAACUUGAUUAACGUCGGUUAAUUGACAGUUUGGCAACA----ACAGUAAAUAAAUGUUUUUUUCAACGUUUUG
(((((((.((((((.((((((((....))..)))))))))))).....)))))))(((....))----)........(((((((......))))))).. ( -22.10)
>DroYak_CAF1 32302 96 + 1
GCUGUCAUUUGGCGGUUAAUUGUGAAAACUUGAUUAACAUCGGUUAAUUGACAGUUGGGAAACUGGAUACACUCA---UUUGUUUUUUGCGUCGUUUUA
(((((((.(((((.(((((((((....))..)))))))....))))).)))))))(..(((((..((.....)).---...)))))..).......... ( -21.40)
>DroAna_CAF1 34534 80 + 1
GCUGUCAUUUGGCGGUUAAUUGCGUAAACCUGAUUAACAUCGGUUAAUUGACAGUUUGGAAAUU-GA-----ACAACAAUUGU-------------UUA
(((((((.(((((.((((((((.(....).))))))))....))))).)))))))........(-((-----(((.....)))-------------))) ( -19.00)
>consensus
GCUGUCAUUUGGCGGUUAAUUGUGAAAACUUGAUUAACAUCGGUUAAUUGACAGUUUGGAAACG_GU_____UAAAUAAUUGUAUUUUUCAUCGUUUUA
(((((((.(((((.((((((((........))))))))....))))).))))))).((....))................................... (-17.49 = -17.22 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:58 2006