Locus 8690

Sequence ID	3L_DroMel_CAF1
Location	22,533,221 – 22,533,390
Length	169
Max. P	0.911052

overview

Window 1

Location	22,533,221 – 22,533,311
Length	90
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	81.18
Mean single sequence MFE	-21.98
Consensus MFE	-12.08
Energy contribution	-12.36
Covariance contribution	0.28
Combinations/Pair	1.32
Mean z-score	-2.47
Structure conservation index	0.55
SVM decision value	1.07
SVM RNA-class probability	0.911052
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22533221 90 + 23771897
AAAGCGAAAGACAAAUAAGUGACGAGGAAAAAGCAGGGAAAUGCUUUUAAAUCGUGCAGCACGAGUACAGUAAAAUAU-------------UCCUGCUUGUUA
.........(((((....((.((((...(((((((......)))))))...)))))).(((.(((((........)))-------------)).)))))))). ( -21.10)
>DroSec_CAF1 16679 89 + 1
AAAGCGAAAGACAAACAAGUGACGAGGAA-AAGCAGGGAAAUGCUUUUAAAUCGUGCAGCACGAGCACAGUAAAAUAU-------------UCCUGCUUGUUA
...((....).).(((((((...((..((-(((((......)))))))...))((((.......))))..........-------------....))))))). ( -22.30)
>DroSim_CAF1 17541 89 + 1
AAAGCGAAAGACAAACAAGUGACGAGGAA-AAGCAGGGAAAUGCUUUUAAAUCGUUCAGCACGAGCACAGUAAAAUAU-------------UCCUGCUUGUUA
...((....).).((((((((((((..((-(((((......)))))))...)))))..((....))............-------------....))))))). ( -21.90)
>DroEre_CAF1 15634 89 + 1
AAGACGAAAGAUAAACAAGGGACGGGGAA-AAGCAGGGAAAUGCUUUUAAAUCGUGCAGCACGAGUACAGUAAAAUAU-------------UCCUGCUUGUUA
....(....)...(((((.(.((((..((-(((((......)))))))...)))).).(((.(((((........)))-------------)).)))))))). ( -22.90)
>DroAna_CAF1 46180 96 + 1
AACGUGAAAGACAAACA-GUCGGGAAGAA-AAGCAGGAAAAAGCUUUUAAAUCUUAUAGCG-----ACUGUAUUAUAUGCUCGUGUAUUGCUGCCGCUUGUUA
...(((..((.((((((-(((((((..((-((((........))))))...))).....))-----)))))..(((((....))))))))))..)))...... ( -21.70)
>consensus
AAAGCGAAAGACAAACAAGUGACGAGGAA_AAGCAGGGAAAUGCUUUUAAAUCGUGCAGCACGAGCACAGUAAAAUAU_____________UCCUGCUUGUUA
....(....)...(((((((.((((.....(((((......))))).....))))...((....)).............................))))))). (-12.08 = -12.36 +   0.28)

alignment

secondary structure

dotplot

Window 2

Location	22,533,221 – 22,533,311
Length	90
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	81.18
Mean single sequence MFE	-18.76
Consensus MFE	-10.32
Energy contribution	-11.80
Covariance contribution	1.48
Combinations/Pair	1.10
Mean z-score	-2.13
Structure conservation index	0.55
SVM decision value	0.44
SVM RNA-class probability	0.735507
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22533221 90 - 23771897
UAACAAGCAGGA-------------AUAUUUUACUGUACUCGUGCUGCACGAUUUAAAAGCAUUUCCCUGCUUUUUCCUCGUCACUUAUUUGUCUUUCGCUUU
..(((((((.((-------------.(((......))).)).)))((.((((...(((((((......)))))))...)))))).....)))).......... ( -18.00)
>DroSec_CAF1 16679 89 - 1
UAACAAGCAGGA-------------AUAUUUUACUGUGCUCGUGCUGCACGAUUUAAAAGCAUUUCCCUGCUU-UUCCUCGUCACUUGUUUGUCUUUCGCUUU
..(((((((((.-------------..........((((.......))))(((..(((((((......)))))-))....))).))))))))).......... ( -22.10)
>DroSim_CAF1 17541 89 - 1
UAACAAGCAGGA-------------AUAUUUUACUGUGCUCGUGCUGAACGAUUUAAAAGCAUUUCCCUGCUU-UUCCUCGUCACUUGUUUGUCUUUCGCUUU
..(((((((((.-------------............((....))(((.(((...(((((((......)))))-))..))))))))))))))).......... ( -20.30)
>DroEre_CAF1 15634 89 - 1
UAACAAGCAGGA-------------AUAUUUUACUGUACUCGUGCUGCACGAUUUAAAAGCAUUUCCCUGCUU-UUCCCCGUCCCUUGUUUAUCUUUCGUCUU
.((((((..(((-------------..............(((((...)))))...(((((((......)))))-)).....)))))))))............. ( -15.40)
>DroAna_CAF1 46180 96 - 1
UAACAAGCGGCAGCAAUACACGAGCAUAUAAUACAGU-----CGCUAUAAGAUUUAAAAGCUUUUUCCUGCUU-UUCUUCCCGAC-UGUUUGUCUUUCACGUU
.(((..((....)).......(((...((((.(((((-----((....((((....(((((........))))-)))))..))))-)))))))..)))..))) ( -18.00)
>consensus
UAACAAGCAGGA_____________AUAUUUUACUGUACUCGUGCUGCACGAUUUAAAAGCAUUUCCCUGCUU_UUCCUCGUCACUUGUUUGUCUUUCGCUUU
..(((((((((........................(((....)))...((((.....(((((......))))).....))))..))))))))).......... (-10.32 = -11.80 +   1.48)

alignment

secondary structure

dotplot

Window 3

Location	22,533,295 – 22,533,390
Length	95
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	83.30
Mean single sequence MFE	-30.06
Consensus MFE	-18.52
Energy contribution	-20.96
Covariance contribution	2.44
Combinations/Pair	1.04
Mean z-score	-2.15
Structure conservation index	0.62
SVM decision value	0.45
SVM RNA-class probability	0.742387
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22533295 95 - 23771897
-GAGGAGCAGUUCUUCCCCGCUUGGGCUUUUACCGAUUAUUGAUCGCCCGGUUGACAUUGCAUCAAUAUCUGGCGAAAGUUAACAAGCAGGA-------------AUAU
-((((((...))))))((.(((((.(((((..(((..(((((((.((...(....)...)))))))))..)))..)))))...))))).)).-------------.... ( -29.70)
>DroSec_CAF1 16752 95 - 1
-GAGGAGCAGUUCUUCUCCGCUUGGGCUUUUACCGAUUAUUGAUCGCCCGGUUGACAUUGCAUCAAUAUCUGGCGAAAGUUAACAAGCAGGA-------------AUAU
-((((((...))))))((((((((.(((((..(((..(((((((.((...(....)...)))))))))..)))..)))))...))))).)))-------------.... ( -30.50)
>DroSim_CAF1 17614 95 - 1
-GAGGAGCAGUUCUUCUCCGCUUGGGCUUUUACCGAUUAUUGAUCGCCCGGUUGACAUUGCAUCAAUAUCUGGCGAAAGUUAACAAGCAGGA-------------AUAU
-((((((...))))))((((((((.(((((..(((..(((((((.((...(....)...)))))))))..)))..)))))...))))).)))-------------.... ( -30.50)
>DroEre_CAF1 15707 95 - 1
-GAGGAGAGCUUCUUCUCCGCUUGGGCUUUUACCGAUUAUUGAUCGGCCGAUUGACAUUGCAUCAAUAUCUGGCGAAAGUUAACAAGCAGGA-------------AUAU
-..((((((....))))))(((((.(((((..(((..(((((((..((.(((....))))))))))))..)))..)))))...)))))....-------------.... ( -29.50)
>DroAna_CAF1 46247 100 - 1
CGACGAGCUGUGUUU----GAGUUGGCUU-----GCUUAUUGAUCGCCCGAUUGACAUUGCAUCAAUUUCGGGCCAAAGUUAACAAGCGGCAGCAAUACACGAGCAUAU
........(((((((----(.((..((((-----((((.(((((.((((((((((.......))))..))))))....))))).)))))..)))...)).)))))))). ( -30.10)
>consensus
_GAGGAGCAGUUCUUCUCCGCUUGGGCUUUUACCGAUUAUUGAUCGCCCGGUUGACAUUGCAUCAAUAUCUGGCGAAAGUUAACAAGCAGGA_____________AUAU
.((((((.....)))))).(((((.(((((..(((..(((((((.((............)))))))))..)))..)))))...)))))..................... (-18.52 = -20.96 +   2.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:24 2006