Locus 6292

Sequence ID	2R_DroMel_CAF1
Location	19,745,296 – 19,745,457
Length	161
Max. P	0.974373

overview

Window 8

Location	19,745,296 – 19,745,387
Length	91
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.36
Mean single sequence MFE	-29.62
Consensus MFE	-15.63
Energy contribution	-14.23
Covariance contribution	-1.40
Combinations/Pair	1.24
Mean z-score	-2.20
Structure conservation index	0.53
SVM decision value	1.73
SVM RNA-class probability	0.974373
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19745296 91 + 20766785
----------GGGUUCGG----------UUUUUCCCCGAUUCCUGCCUGCGGA----UGGCUUAAUAACGUUAUUUUUCUCUGGUCAUUGUACUUUUAAUGGCCA-GUGGCAGCAG----
----------((..((((----------.......))))..))(((.((((((----((((........)))))))..(.((((((((((......)))))))))-).))))))).---- ( -31.00)
>DroPse_CAF1 6442 101 + 1
UGUUGUUAUAGGGUUUAG----CUUUCAUUGGUUGCUGGUGCCUGCUU--GGA----UGGCUUAAUAACGUUAUUUUUCUCUGGUCAUUGUACUUUUAAUGGUCAAGCAGC---------
.((((((((((.(((.((----((.((...(((.((....))..))).--.))----.))))....))).)))).......((..(((((......)))))..))))))))--------- ( -24.60)
>DroSim_CAF1 615 91 + 1
----------UGGUUCGG----------UUUUUCCCUGAUUCCUGCCUGCGGA----UGGCUUAAUAACGUUAUUUUUCUCUGGUCAUUGUACUUUUAAUGGCCA-GUGGCAGCAG----
----------.(..((((----------.......))))..)((((.((((((----((((........)))))))..(.((((((((((......)))))))))-).))))))))---- ( -27.10)
>DroYak_CAF1 531 109 + 1
----------GGGUUCGGUUCGCUUUGGUUUUUCCCUGAUUCCUGCCUGCGGAUGGAUGGCUUAAUAACGUUAUUUUUCUCUGGUCAUUGUACUUUUAAUGGCCA-GUGGCAGCAGGAGC
----------(((.((((......)))).....)))...(((((((.((((((..((((((........))))))..)))((((((((((......)))))))))-)..)))))))))). ( -37.60)
>DroPer_CAF1 6444 107 + 1
UGUUGUUAUAGGGUUUAG----CUUUCAUUGGUUGCUGGUGCCUGCUU--GGA----UGGCUUAAUAACGUUAUUUUUCUCUGGUCAUUGUACUUUUAAUGGUCAAGCAGC---AGCAGC
(((((((...((((((((----(..(.....)..))))).))))((((--(((----((((........)))))))......(..(((((......)))))..))))))))---)))).. ( -27.80)
>consensus
__________GGGUUCGG____CUUU__UUUUUCCCUGAUUCCUGCCUGCGGA____UGGCUUAAUAACGUUAUUUUUCUCUGGUCAUUGUACUUUUAAUGGCCA_GUGGCAGCAG____
..........((..((((.................))))..)).(((...(((....((((........))))....))).(((((((((......)))))))))...)))......... (-15.63 = -14.23 +  -1.40)

alignment

secondary structure

dotplot

Window 9

Location	19,745,352 – 19,745,457
Length	105
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	87.69
Mean single sequence MFE	-40.81
Consensus MFE	-26.87
Energy contribution	-29.53
Covariance contribution	2.67
Combinations/Pair	1.00
Mean z-score	-2.80
Structure conservation index	0.66
SVM decision value	0.30
SVM RNA-class probability	0.677940
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19745352 105 + 20766785
CUGGUCAUUGUACUUUUAAUGGCCAGUGGCAGCAG---------GAGCAGCAAACAAAUCAAACGCAGACGCCGUUUUGCCUUCGGGCCAGCUUCUUCUGCUCUGCUCAGAUGC
((((((((((......))))))))))(((((((((---------(((.(((.........((((((....).))))).(((....)))..))).)))))))..))).))..... ( -39.90)
>DroSim_CAF1 671 105 + 1
CUGGUCAUUGUACUUUUAAUGGCCAGUGGCAGCAG---------GAGCAGCAAACAAAUCAAACGCAGACGCCGUUUUGCCUUCGGGCCAGCUUGUUCUGCGCUGCUCAGCUGC
((((((((((......))))))))))..(((((..---------(((((((.............(((((.((.(((..(((....))).)))..)))))))))))))).))))) ( -45.71)
>DroYak_CAF1 601 109 + 1
CUGGUCAUUGUACUUUUAAUGGCCAGUGGCAGCAGGAGCAGCAGGAGCAGCAAACAAAUCAAACGCAGACGCCGUUUUGCCUUAGGGCCAGCUUGUUCAGCUCGGCUC-----U
((((((((((......)))))))))).(((((.(.(.((.((....)).((.............))....))).).)))))..((((((((((.....)))).)))))-----) ( -36.82)
>consensus
CUGGUCAUUGUACUUUUAAUGGCCAGUGGCAGCAG_________GAGCAGCAAACAAAUCAAACGCAGACGCCGUUUUGCCUUCGGGCCAGCUUGUUCUGCUCUGCUCAG_UGC
((((((((((......))))))))))..................((((.((((((((...((((((....).))))).(((....)))....))))).)))...))))...... (-26.87 = -29.53 +   2.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:32 2006