Locus 2498

Sequence ID	X_DroMel_CAF1
Location	6,636,248 – 6,636,340
Length	92
Max. P	0.917257

overview

Window 5

Location	6,636,248 – 6,636,340
Length	92
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	72.22
Mean single sequence MFE	-12.50
Consensus MFE	-0.40
Energy contribution	-1.20
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.95
Structure conservation index	0.03
SVM decision value	0.97
SVM RNA-class probability	0.892184
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6636248 92 + 22224390
CUA-----ACACUUUUGGCCUGCCACUCUCAG--UGCAAUUUCUUUCACUUUUCAAGUGCAAUUU--GGCGC-UCUUUU---CUUU-GAUUUUUC-AUCAUCCAUCC---
...-----.......(((....))).....((--(((.........((((.....))))......--.))))-).....---...(-(((.....-)))).......--- ( -10.29)
>DroSec_CAF1 30159 93 + 1
CUA-----ACACUUU-UGCCUG-CACUUUCGG--UGCAAUAUCUUUCACUUUUCAAGUGCAAUUU--GGCGC-UCUUUU---CUUU-GAUUUUUC-ACCAUCCAUCAAUC
...-----.......-.(((((-(((((..((--((.((.....))))))....)))))))....--)))..-......---...(-((....))-)............. ( -14.30)
>DroEre_CAF1 23769 83 + 1
CAA-----ACACUUU-G--CUG-CACUUUCAG--UGCAAUUUCUUUCACUU-UCAAGAGCAAUUU--GGCGC-UCUUUU---CUUUGCAUUUUU--UUCA-CCA------
...-----......(-(--(((-(((.....)--)))).............-..((((((.....--...))-))))..---....))).....--....-...------ ( -15.40)
>DroYak_CAF1 26043 95 + 1
CAC-----ACACUUU-G--CUG-CACUUCCAG--GGCAAUUUCUUUCACUU-UCAAGUGCAAUUUUCUGCGC-UCGUUUUUCCUUUUGAUUUUUC-ACCA-CCAUCAAUC
...-----.....((-(--((.-.........--)))))............-...((((((......)))))-)...........(((((.....-....-..))))).. (  -9.40)
>DroAna_CAF1 31710 90 + 1
CAAUAACCGCACUUU-G--UUG-CACUUUCUGUGUGCAAUUUCUUUCGCUU-UCAAGAGCAAUUU--CCACCAGAUUUU---CUAUCUAUAUUUCUUUUU----------
...............-(--(((-(((.......))))))).......((((-....)))).....--.....((((...---..))))............---------- ( -13.10)
>consensus
CAA_____ACACUUU_G__CUG_CACUUUCAG__UGCAAUUUCUUUCACUU_UCAAGUGCAAUUU__GGCGC_UCUUUU___CUUU_GAUUUUUC_AUCA_CCAUC____
........................................................((((........))))...................................... ( -0.40 =  -1.20 +   0.80)

alignment

secondary structure

dotplot

Window 6

Location	6,636,248 – 6,636,340
Length	92
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	72.22
Mean single sequence MFE	-17.16
Consensus MFE	-5.04
Energy contribution	-5.40
Covariance contribution	0.36
Combinations/Pair	1.25
Mean z-score	-2.00
Structure conservation index	0.29
SVM decision value	1.11
SVM RNA-class probability	0.917257
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6636248 92 - 22224390
---GGAUGGAUGAU-GAAAAAUC-AAAG---AAAAGA-GCGCC--AAAUUGCACUUGAAAAGUGAAAGAAAUUGCA--CUGAGAGUGGCAGGCCAAAAGUGU-----UAG
---.......((((-.....)))-)...---.....(-((((.--...((((((((....((((.((....)).))--))..)))).)))).......))))-----).. ( -17.40)
>DroSec_CAF1 30159 93 - 1
GAUUGAUGGAUGGU-GAAAAAUC-AAAG---AAAAGA-GCGCC--AAAUUGCACUUGAAAAGUGAAAGAUAUUGCA--CCGAAAGUG-CAGGCA-AAAGUGU-----UAG
..(((((.......-.....)))-))..---......-..(((--..(((.((((.....))))...)))..((((--.(....)))-))))).-.......-----... ( -16.70)
>DroEre_CAF1 23769 83 - 1
------UGG-UGAA--AAAAAUGCAAAG---AAAAGA-GCGCC--AAAUUGCUCUUGA-AAGUGAAAGAAAUUGCA--CUGAAAGUG-CAG--C-AAAGUGU-----UUG
------...-....--..((((((....---..((((-(((..--....)))))))..-............(((((--(.....)))-)))--.-...))))-----)). ( -17.60)
>DroYak_CAF1 26043 95 - 1
GAUUGAUGG-UGGU-GAAAAAUCAAAAGGAAAAACGA-GCGCAGAAAAUUGCACUUGA-AAGUGAAAGAAAUUGCC--CUGGAAGUG-CAG--C-AAAGUGU-----GUG
..(((((..-(...-..)..)))))............-(((((.....((((((((..-.((.(.((....)).).--))..)))))-)))--.-....)))-----)). ( -17.20)
>DroAna_CAF1 31710 90 - 1
----------AAAAAGAAAUAUAGAUAG---AAAAUCUGGUGG--AAAUUGCUCUUGA-AAGCGAAAGAAAUUGCACACAGAAAGUG-CAA--C-AAAGUGCGGUUAUUG
----------...........(((((..---...)))))....--.((((((.(((..-...(....)...((((((.......)))-)))--.-.))).)))))).... ( -16.90)
>consensus
____GAUGG_UGAU_GAAAAAUC_AAAG___AAAAGA_GCGCC__AAAUUGCACUUGA_AAGUGAAAGAAAUUGCA__CUGAAAGUG_CAG__C_AAAGUGU_____UUG
......................................((((......((((((((.....((((......)))).......))))).))).......))))........ ( -5.04 =  -5.40 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:18 2006