Locus 9526

Sequence ID	3R_DroMel_CAF1
Location	25,174,895 – 25,174,999
Length	104
Max. P	0.997535

overview

Window 1

Location	25,174,895 – 25,174,999
Length	104
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	90.15
Mean single sequence MFE	-39.38
Consensus MFE	-34.62
Energy contribution	-34.82
Covariance contribution	0.20
Combinations/Pair	1.03
Mean z-score	-3.28
Structure conservation index	0.88
SVM decision value	2.88
SVM RNA-class probability	0.997535
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25174895 104 + 27905053
ACAACCGCAGGACAUUGUAUUGUGUUACACAAAAGAUUGCCAGCACCGAGCCACCCAA-AGGAUUCGAUGGAUUCAAUGGGUGGCCCGGUGGGCGUCC-CCCUACC
.........((((......(((((...)))))......(((..(((((.((((((((.-.(((((.....)))))..)))))))).))))))))))))-....... ( -42.80)
>DroSec_CAF1 33441 105 + 1
ACAACCGCAGGACAUUGUAUUGUGUUACACAAAAGAUUGCCAGCACCGAGCCACCCAA-AGGAUUCGAUGGAUUCAAUGGGUGGCCCGGUGGGCUUCCCCCCAACC
......((.((.((.(.(.(((((...))))).).).)))).))((((.((((((((.-.(((((.....)))))..)))))))).))))(((......))).... ( -39.10)
>DroSim_CAF1 33626 104 + 1
ACAACCGCAGGACAUUGUAUUGUGUUACACAAAAGAUUGCCAGCACCGAGCCACCCAA-AGGAUUCGAUGGAUUCAAUGGGUGGCCCGGUGGGCUUCC-CCCAACC
......((.((.((.(.(.(((((...))))).).).)))).))((((.((((((((.-.(((((.....)))))..)))))))).))))(((.....-))).... ( -38.90)
>DroEre_CAF1 34189 91 + 1
ACAACCGCAGGACAUUGUAUUGUGUUACACAAAAGAUUGCCAGCACCGAGCCACCCAA-AGGAUUCGAUGGAUUCAAUGGGUGGC-CGGUGGG-------------
....((((.((.((.(.(.(((((...))))).).).)))).))((((.((((((((.-.(((((.....)))))..))))))))-)))))).------------- ( -37.50)
>DroYak_CAF1 35329 105 + 1
ACAACCGCAGGACAUUGUAUUGUGUUACACAAAAGAUUGCCAGCACCGAGCCACCCAA-AGGAUUCGAUGGAUUCAAUGGGUGGCCCGGUGGGUACCCAUCCCAUC
......((.((.((.(.(.(((((...))))).).).)))).))((((.((((((((.-.(((((.....)))))..)))))))).))))(((.......)))... ( -39.40)
>DroAna_CAF1 31200 104 + 1
ACAACCGCAGGACAUUGUAUUGUGUUACACAAAAGAUUGCCAGCGCCGUGCCACCCAAAAGGAUUCGAUGGAUUCAAUGGGUGACUGGGUGGCUGGCG--GCUACC
....((((.((.((.(.(.(((((...))))).).).)))).))((((.(((((((....(((((.....)))))...((....))))))))))))))--)..... ( -38.60)
>consensus
ACAACCGCAGGACAUUGUAUUGUGUUACACAAAAGAUUGCCAGCACCGAGCCACCCAA_AGGAUUCGAUGGAUUCAAUGGGUGGCCCGGUGGGCGUCC_CCCAACC
....((((.((.((.(.(.(((((...))))).).).)))).))((((.((((((((...(((((.....)))))..)))))))).)))))).............. (-34.62 = -34.82 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	25,174,895 – 25,174,999
Length	104
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	90.15
Mean single sequence MFE	-41.40
Consensus MFE	-33.92
Energy contribution	-34.45
Covariance contribution	0.53
Combinations/Pair	1.03
Mean z-score	-3.32
Structure conservation index	0.82
SVM decision value	1.68
SVM RNA-class probability	0.971589
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25174895 104 - 27905053
GGUAGGG-GGACGCCCACCGGGCCACCCAUUGAAUCCAUCGAAUCCU-UUGGGUGGCUCGGUGCUGGCAAUCUUUUGUGUAACACAAUACAAUGUCCUGCGGUUGU
....(.(-(((((((((((((((((((((..((.((....)).))..-.))))))))))))))..)))......((((((......)))))).))))).)...... ( -48.30)
>DroSec_CAF1 33441 105 - 1
GGUUGGGGGGAAGCCCACCGGGCCACCCAUUGAAUCCAUCGAAUCCU-UUGGGUGGCUCGGUGCUGGCAAUCUUUUGUGUAACACAAUACAAUGUCCUGCGGUUGU
.....(.((((.(((((((((((((((((..((.((....)).))..-.))))))))))))))..)))......((((((......))))))..)))).)...... ( -44.60)
>DroSim_CAF1 33626 104 - 1
GGUUGGG-GGAAGCCCACCGGGCCACCCAUUGAAUCCAUCGAAUCCU-UUGGGUGGCUCGGUGCUGGCAAUCUUUUGUGUAACACAAUACAAUGUCCUGCGGUUGU
((..(.(-(((.(((((((((((((((((..((.((....)).))..-.))))))))))))))..)))......((((((......))))))..)))).)..)).. ( -45.20)
>DroEre_CAF1 34189 91 - 1
-------------CCCACCG-GCCACCCAUUGAAUCCAUCGAAUCCU-UUGGGUGGCUCGGUGCUGGCAAUCUUUUGUGUAACACAAUACAAUGUCCUGCGGUUGU
-------------.((((((-((((((((..((.((....)).))..-.)))))))).))))((.((((.....(((((...))))).....))))..)))).... ( -33.60)
>DroYak_CAF1 35329 105 - 1
GAUGGGAUGGGUACCCACCGGGCCACCCAUUGAAUCCAUCGAAUCCU-UUGGGUGGCUCGGUGCUGGCAAUCUUUUGUGUAACACAAUACAAUGUCCUGCGGUUGU
...(((((..((...((((((((((((((..((.((....)).))..-.))))))))))))))...))......((((((......)))))).)))))........ ( -40.40)
>DroAna_CAF1 31200 104 - 1
GGUAGC--CGCCAGCCACCCAGUCACCCAUUGAAUCCAUCGAAUCCUUUUGGGUGGCACGGCGCUGGCAAUCUUUUGUGUAACACAAUACAAUGUCCUGCGGUUGU
..((((--((((.(((((((((.......((((.....))))......)))))))))..)))((.((((.....(((((...))))).....))))..))))))). ( -36.32)
>consensus
GGUAGGG_GGAAGCCCACCGGGCCACCCAUUGAAUCCAUCGAAUCCU_UUGGGUGGCUCGGUGCUGGCAAUCUUUUGUGUAACACAAUACAAUGUCCUGCGGUUGU
..............(((((((((((((((..((.((....)).))....)))))))))))))((.((((.....(((((...))))).....))))..)))).... (-33.92 = -34.45 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:36:29 2006