Locus 612

Sequence ID	2R_DroMel_CAF1
Location	3,111,482 – 3,111,581
Length	99
Max. P	0.951690

overview

Window 2

Location	3,111,482 – 3,111,581
Length	99
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	80.26
Mean single sequence MFE	-29.73
Consensus MFE	-20.06
Energy contribution	-21.46
Covariance contribution	1.40
Combinations/Pair	1.25
Mean z-score	-2.26
Structure conservation index	0.67
SVM decision value	1.41
SVM RNA-class probability	0.951690
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3111482 99 + 20766785
CGCAUUCAUCUGGGUUUUCCCUGAAGAAUUUCCCGCGGAUUACGCAGCAGCGGCGGUGGGAUUUUUCUUUGUGGAAACCCCUUUCAGGUAGAAAAUCA----U--
....((((((((((.(((((.(((((((..((((((.(....(((....))).).))))))...))))))).))))).)))....)))).))).....----.-- ( -34.90)
>DroSec_CAF1 6903 97 + 1
CGCAUUCAUCUGGGUUUUCCACGAAGAAUUUCCCGCGGAUUACGCAGCAA--GCGUUGGGAUUUUUCCUUGCGGAAACCCUUUCCAGGUAGAAAAUCA----U--
....((((((((((.(((((.(((.(((..(((((((.....)))(((..--..)))))))...))).))).))))).....))))))).))).....----.-- ( -30.10)
>DroSim_CAF1 6171 97 + 1
CGGAUUCAUCUGGGUUUUCCACGAAGAAUUUCCCGCGGAUUACGCAGCAA--GCGUUGGGAUUUUUCUUUGCGGAAACCCUUUCCAGGUAGAAAAUCA----U--
....((((((((((.(((((.(((((((..(((((((.....)))(((..--..)))))))...))))))).))))).....))))))).))).....----.-- ( -34.20)
>DroEre_CAF1 6835 103 + 1
CGCAUUAAUCUGGGUUUACCUUGGGAAAUUUCCCGCAUAUUAUGCAGCAA--UCGGUGGGAUUUUUCUUAAUGGAAACCCUUUCCAGCUAGCAAAUCUCUCAAAG
.((........((((((.((((((((((..((((((..(((.......))--)..))))))..)))))))).))))))))..........))............. ( -28.47)
>DroYak_CAF1 6868 95 + 1
GGCAUUAAUCUGGGU-UACCUCGGAAAAUUUU-CGCAAAUUACGCUGUAA--UCGG--GGACUUUUCCUUAUGGAAACCCUUUUCAGGUAGAAAAUCA----UAG
...........((((-(.((..((((((((..-((...(((((...))))--))).--.)).))))))....)).)))))(((((.....)))))...----... ( -21.00)
>consensus
CGCAUUCAUCUGGGUUUUCCACGAAGAAUUUCCCGCGGAUUACGCAGCAA__GCGGUGGGAUUUUUCUUUGUGGAAACCCUUUCCAGGUAGAAAAUCA____U__
...........((((((.((.(((((((..(((((((.....))).((....))...))))...))))))).))))))))......................... (-20.06 = -21.46 +   1.40)

alignment

secondary structure

dotplot

Window 3

Location	3,111,482 – 3,111,581
Length	99
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	80.26
Mean single sequence MFE	-26.72
Consensus MFE	-18.50
Energy contribution	-18.90
Covariance contribution	0.40
Combinations/Pair	1.30
Mean z-score	-1.63
Structure conservation index	0.69
SVM decision value	0.22
SVM RNA-class probability	0.641952
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3111482 99 - 20766785
--A----UGAUUUUCUACCUGAAAGGGGUUUCCACAAAGAAAAAUCCCACCGCCGCUGCUGCGUAAUCCGCGGGAAAUUCUUCAGGGAAAACCCAGAUGAAUGCG
--.----...(((((.....)))))((((((((...(((((...((((...((....)).(((.....)))))))..)))))...)).))))))........... ( -26.40)
>DroSec_CAF1 6903 97 - 1
--A----UGAUUUUCUACCUGGAAAGGGUUUCCGCAAGGAAAAAUCCCAACGC--UUGCUGCGUAAUCCGCGGGAAAUUCUUCGUGGAAAACCCAGAUGAAUGCG
--.----.(...(((...((((...((((((((....)))))...))).((((--.....))))..((((((((......))))))))....))))..)))..). ( -32.60)
>DroSim_CAF1 6171 97 - 1
--A----UGAUUUUCUACCUGGAAAGGGUUUCCGCAAAGAAAAAUCCCAACGC--UUGCUGCGUAAUCCGCGGGAAAUUCUUCGUGGAAAACCCAGAUGAAUCCG
--.----.((((((((.(((....))).(((((((.(((((...((((...(.--...).(((.....)))))))..))))).)))))))....))).))))).. ( -29.20)
>DroEre_CAF1 6835 103 - 1
CUUUGAGAGAUUUGCUAGCUGGAAAGGGUUUCCAUUAAGAAAAAUCCCACCGA--UUGCUGCAUAAUAUGCGGGAAAUUUCCCAAGGUAAACCCAGAUUAAUGCG
.............((...((((...(((((((......))))...)))(((..--.....((((...))))((((....))))..)))....))))......)). ( -23.00)
>DroYak_CAF1 6868 95 - 1
CUA----UGAUUUUCUACCUGAAAAGGGUUUCCAUAAGGAAAAGUCC--CCGA--UUACAGCGUAAUUUGCG-AAAAUUUUCCGAGGUA-ACCCAGAUUAAUGCC
...----...(((((.....)))))(((((.((....((((((.((.--(.((--((((...)))))).).)-)...))))))..)).)-))))........... ( -22.40)
>consensus
__A____UGAUUUUCUACCUGGAAAGGGUUUCCACAAAGAAAAAUCCCACCGC__UUGCUGCGUAAUCCGCGGGAAAUUCUUCGAGGAAAACCCAGAUGAAUGCG
..........(((((.....)))))((((((((.(.(((((...((((...(......).(((.....)))))))..))))).).)).))))))........... (-18.50 = -18.90 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:50 2006