Locus 6424

Sequence ID	2R_DroMel_CAF1
Location	20,065,408 – 20,065,509
Length	101
Max. P	0.993482

overview

Window 0

Location	20,065,408 – 20,065,509
Length	101
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	74.43
Mean single sequence MFE	-18.94
Consensus MFE	-8.24
Energy contribution	-8.08
Covariance contribution	-0.16
Combinations/Pair	1.11
Mean z-score	-2.17
Structure conservation index	0.44
SVM decision value	1.45
SVM RNA-class probability	0.955173
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20065408 101 + 20766785
---------UUUUUGUUAAAUUC----CUCAAUAAUCCUCGAACUGUUGAGCUCGUAUUU-UUUGAGCAAACAAACAGAACAAGAUUUUGAGAACAAUAAUUUUUGUGAUAUAUU
---------..............----(((((.((((......(((((..(((((.....-..))))).....))))).....))))))))).((((......))))........ ( -17.20)
>DroSec_CAF1 2427 84 + 1
---------CUUUUUUAAAAUU-------UAAUAAUCCUCCAACUGGUGAGCUCGUAUUU-UUUGAGCAAACAGU------------UU--GAACAAUAAUUUUUGUGAUAUAUU
---------.............-------.....(((.((.(((((....(((((.....-..)))))...))))------------).--))((((......)))))))..... ( -13.50)
>DroSim_CAF1 2439 87 + 1
---------CUUUUUUAAAAUUU----CUUAAUAAUCCUUCAACUGGUGAGCUCGUAUUU-UUUGAGCAAACAGG------------UU--GAACAAUAAUUUUUGUGAUAUAUU
---------..............----.......(((..((((((.((..(((((.....-..)))))..)).))------------))--))((((......)))))))..... ( -16.40)
>DroEre_CAF1 2506 96 + 1
UUCGAAACUCGUUUUUCAAGUUU----CUGAGUAAUUUUCUAACUGUUGUGCUCGUAUUU-UUUGAGCAUAUCGG------------UU--GAACAAUAAUUUUUGUGCUAUAUU
...((((((.(.....).)))))----)..(((.......((((((.((((((((.....-..)))))))).)))------------))--).((((......)))))))..... ( -23.20)
>DroYak_CAF1 2436 101 + 1
UUCUAAACUCUUUUUUCAAAUUACAUACUUAGUAAUUUUCUAACUGGUGUGCUCGUAUUUUUUUGAGCAAACCGG------------UU--GAGCAAUAAUUUUUGUGAAAUAUU
.............(((((((((((.......)))))))..((((((((.((((((........)))))).)))))------------))--).((((......)))))))).... ( -24.40)
>consensus
_________CUUUUUUAAAAUUU____CUUAAUAAUCCUCCAACUGGUGAGCUCGUAUUU_UUUGAGCAAACAGG____________UU__GAACAAUAAUUUUUGUGAUAUAUU
..................................................(((((........))))).........................((((......))))........ ( -8.24 =  -8.08 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	20,065,408 – 20,065,509
Length	101
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	74.43
Mean single sequence MFE	-17.30
Consensus MFE	-4.30
Energy contribution	-4.30
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.47
Structure conservation index	0.25
SVM decision value	2.40
SVM RNA-class probability	0.993482
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20065408 101 - 20766785
AAUAUAUCACAAAAAUUAUUGUUCUCAAAAUCUUGUUCUGUUUGUUUGCUCAAA-AAAUACGAGCUCAACAGUUCGAGGAUUAUUGAG----GAAUUUAACAAAAA---------
...............(((...((((((((((((((..(((((.(...((((...-......)))).))))))..).)))))).)))))----))...)))......--------- ( -21.50)
>DroSec_CAF1 2427 84 - 1
AAUAUAUCACAAAAAUUAUUGUUC--AA------------ACUGUUUGCUCAAA-AAAUACGAGCUCACCAGUUGGAGGAUUAUUA-------AAUUUUAAAAAAG---------
.............(((.(((.(((--((------------.(((...((((...-......))))....)))))))).))).))).-------.............--------- ( -12.90)
>DroSim_CAF1 2439 87 - 1
AAUAUAUCACAAAAAUUAUUGUUC--AA------------CCUGUUUGCUCAAA-AAAUACGAGCUCACCAGUUGAAGGAUUAUUAAG----AAAUUUUAAAAAAG---------
.............(((.(((.(((--((------------(..((..((((...-......))))..))..)))))).))).)))...----..............--------- ( -14.80)
>DroEre_CAF1 2506 96 - 1
AAUAUAGCACAAAAAUUAUUGUUC--AA------------CCGAUAUGCUCAAA-AAAUACGAGCACAACAGUUAGAAAAUUACUCAG----AAACUUGAAAAACGAGUUUCGAA
....((((........(((((...--..------------.)))))(((((...-......))))).....))))............(----(((((((.....))))))))... ( -17.30)
>DroYak_CAF1 2436 101 - 1
AAUAUUUCACAAAAAUUAUUGCUC--AA------------CCGGUUUGCUCAAAAAAAUACGAGCACACCAGUUAGAAAAUUACUAAGUAUGUAAUUUGAAAAAAGAGUUUAGAA
....................((((--((------------(.(((.(((((..........))))).))).)))...(((((((.......))))))).......))))...... ( -20.00)
>consensus
AAUAUAUCACAAAAAUUAUUGUUC__AA____________CCUGUUUGCUCAAA_AAAUACGAGCUCACCAGUUAGAGGAUUAUUAAG____AAAUUUGAAAAAAG_________
...............................................((((..........)))).................................................. ( -4.30 =  -4.30 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:40 2006