Locus 6083

Sequence ID	2R_DroMel_CAF1
Location	19,148,206 – 19,148,309
Length	103
Max. P	0.898212

overview

Window 8

Location	19,148,206 – 19,148,309
Length	103
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.04
Mean single sequence MFE	-30.73
Consensus MFE	-20.89
Energy contribution	-22.12
Covariance contribution	1.22
Combinations/Pair	1.10
Mean z-score	-2.11
Structure conservation index	0.68
SVM decision value	1.00
SVM RNA-class probability	0.898212
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19148206 103 + 20766785
AUCCAC-----UUGCACCAGCCACAUUAAAGCGGCACAAAUUCGUUGUGCAUUAAUUAGACAUUUUAUAGGUGCAAGUUGGCAUGGCCUGCAUGCCGCCGCUUUCCGU------------
....((-----(((((((.((.........)).((((((.....))))))...................))))))))).((((((.....))))))............------------ ( -32.00)
>DroSec_CAF1 32048 103 + 1
AUCCAC-----UUGCACCAGCCACAUUAAAGCGGCACAAAUUCGUUGUGCAUUAAUUAGACAUUUUAUAGGUGCAAGUUGGCAUGGCCUGCAUGCCGCCGCUUUCCGC------------
....((-----(((((((.((.........)).((((((.....))))))...................))))))))).((((((.....))))))............------------ ( -32.00)
>DroEre_CAF1 40209 112 + 1
AUCCAC-----UUGCACCAGCCACAUUAAAGCGGCACAAAUUCGUUGUGCAUUAAUUAGACAUUUUAUAGGUGCAAGUUGGCAUGGCCUGUAUGCCG---CUUUCGGUUGCCAGUUGCCA
....((-----(((((((.((.........)).((((((.....))))))...................)))))))))(((((((((......((((---....)))).))))..))))) ( -36.50)
>DroYak_CAF1 38731 110 + 1
AUCCAC-----UUGCAACCGCCACAUUAAAGCGGCACAAAUUCGUUGUGCAUUAAUUAGACAUUUUAUAGGUGCAAGUUGGCAUGGCCUGCAUGCCG---CUUUUCGUUGGCCGUUGC--
......-----..(((((.((((....(((((((((.......((..(((..(((((.(.((((.....))))).))))))))..)).....)))))---))))....)))).)))))-- ( -36.70)
>DroAna_CAF1 41323 82 + 1
A-------------CACCAGCAACAUUAAAGCGGCACAAAUUCGUUGUGCAUUAAUUAGACAUUUUAUAGGUGCAAGUUGGCAUGGCCUGCAUGC-------------------------
.-------------((((.((.........)).((((((.....))))))...................)))).......(((((.....)))))------------------------- ( -17.80)
>DroPer_CAF1 41290 102 + 1
AACGACUGCAGAGGCAGCAGCAACAA-AAAGCGGCACAAAUUCGUUGUGCAUUAAUUAGACAUUUUAUAGGUGCAAGUUGGCAUGGCCUGCAUGUACCUG------GU-G----------
...(.((((....))))).((.....-...)).((((((.....)))))).................((((((((.((.(((...))).)).))))))))------..-.---------- ( -29.40)
>consensus
AUCCAC_____UUGCACCAGCCACAUUAAAGCGGCACAAAUUCGUUGUGCAUUAAUUAGACAUUUUAUAGGUGCAAGUUGGCAUGGCCUGCAUGCCG___CUUUCCGU____________
...........(((((((.((.........)).((((((.....))))))...................)))))))...((((((.....))))))........................ (-20.89 = -22.12 +   1.22)

alignment

secondary structure

dotplot

Window 9

Location	19,148,206 – 19,148,309
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.04
Mean single sequence MFE	-30.45
Consensus MFE	-18.28
Energy contribution	-20.12
Covariance contribution	1.83
Combinations/Pair	1.00
Mean z-score	-1.86
Structure conservation index	0.60
SVM decision value	0.38
SVM RNA-class probability	0.714523
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19148206 103 - 20766785
------------ACGGAAAGCGGCGGCAUGCAGGCCAUGCCAACUUGCACCUAUAAAAUGUCUAAUUAAUGCACAACGAAUUUGUGCCGCUUUAAUGUGGCUGGUGCAA-----GUGGAU
------------............((((((.....)))))).(((((((((.....................((((.....))))(((((......))))).)))))))-----)).... ( -33.20)
>DroSec_CAF1 32048 103 - 1
------------GCGGAAAGCGGCGGCAUGCAGGCCAUGCCAACUUGCACCUAUAAAAUGUCUAAUUAAUGCACAACGAAUUUGUGCCGCUUUAAUGUGGCUGGUGCAA-----GUGGAU
------------((.(....).))((((((.....)))))).(((((((((.....................((((.....))))(((((......))))).)))))))-----)).... ( -35.40)
>DroEre_CAF1 40209 112 - 1
UGGCAACUGGCAACCGAAAG---CGGCAUACAGGCCAUGCCAACUUGCACCUAUAAAAUGUCUAAUUAAUGCACAACGAAUUUGUGCCGCUUUAAUGUGGCUGGUGCAA-----GUGGAU
(((((..((((..(((....---))).......)))))))))(((((((((.....................((((.....))))(((((......))))).)))))))-----)).... ( -37.90)
>DroYak_CAF1 38731 110 - 1
--GCAACGGCCAACGAAAAG---CGGCAUGCAGGCCAUGCCAACUUGCACCUAUAAAAUGUCUAAUUAAUGCACAACGAAUUUGUGCCGCUUUAAUGUGGCGGUUGCAA-----GUGGAU
--(((((.((((....((((---(((((((((((.........)))))..........((((........).)))........))))))))))....)))).)))))..-----...... ( -38.10)
>DroAna_CAF1 41323 82 - 1
-------------------------GCAUGCAGGCCAUGCCAACUUGCACCUAUAAAAUGUCUAAUUAAUGCACAACGAAUUUGUGCCGCUUUAAUGUUGCUGGUG-------------U
-------------------------(((((.....)))))......(((((...................((((((.....)))))).((.........)).))))-------------) ( -17.60)
>DroPer_CAF1 41290 102 - 1
----------C-AC------CAGGUACAUGCAGGCCAUGCCAACUUGCACCUAUAAAAUGUCUAAUUAAUGCACAACGAAUUUGUGCCGCUUU-UUGUUGCUGCUGCCUCUGCAGUCGUU
----------.-..------.((((.((.(..(((...)))..).)).))))..................((((((.....))))))......-.....((.(((((....))))).)). ( -20.50)
>consensus
____________ACGGAAAG___CGGCAUGCAGGCCAUGCCAACUUGCACCUAUAAAAUGUCUAAUUAAUGCACAACGAAUUUGUGCCGCUUUAAUGUGGCUGGUGCAA_____GUGGAU
........................((((((.....))))))....((((((.....................((((.....))))(((((......))))).))))))............ (-18.28 = -20.12 +   1.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:24 2006