Locus 5079

Sequence ID	X_DroMel_CAF1
Location	13,278,671 – 13,278,824
Length	153
Max. P	0.791151

overview

Window 4

Location	13,278,671 – 13,278,784
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.26
Mean single sequence MFE	-40.14
Consensus MFE	-30.18
Energy contribution	-30.74
Covariance contribution	0.56
Combinations/Pair	1.11
Mean z-score	-1.66
Structure conservation index	0.75
SVM decision value	0.19
SVM RNA-class probability	0.624243
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13278671 113 - 22224390
CAUUG--UUCGAGUGCGAGUGAGAUGGGAGUGAGCGGGAAUUUUGAGUGAGUUGUAGGUUUUUUACUCAUUUCCGCUGGCACUUC-----CGACGUCGUCCUGGGCCAAGGAAGUUGUAG
..(..--((((....))))..)..((((((((((((((((...((((((((..........))))))))))))))))..))))))-----))(((...((((......))))...))).. ( -38.80)
>DroSec_CAF1 24882 113 - 1
CUUCG--CUCGAGUGCGAGUGAGACGGGAGUGAGCGGGAAUUUUGAGUGAGUUGUAGGUUUUUUACUCAUUUCCGCUGGCACUUC-----CGACGUCGUCCUGGGCCAAGGAAGUUGUAG
.((((--((((....)))))))).((((((((((((((((...((((((((..........))))))))))))))))..))))))-----))(((...((((......))))...))).. ( -46.50)
>DroSim_CAF1 23501 113 - 1
CUUUG--CUCGAGUGCGAGUGAGACGGGAGUGAGCGGGAAUUUUGAGUGAGUUGUAGGUUUUUUACUCAUUUCCGCUGGCACUUC-----CGACGUCGUCCUGGGCCAAGGAAGUUGUAG
.((..--((((....))))..)).((((((((((((((((...((((((((..........))))))))))))))))..))))))-----))(((...((((......))))...))).. ( -44.10)
>DroEre_CAF1 24698 112 - 1
CUGUACACGCGAGUGCGAGUGAGGCG--AGUGAGCGGGAAUUUUGAGUGAGUUGUAGGUU-UUUACUCAUUUCCGCUGGCACUUC-----CGACGUCGUCCUGGGCCAAGGAAGUUGUAG
((.(((.(((....))).)))))(((--(((.((((((((...((((((((.........-)))))))))))))))).)).((((-----(...(((......)))...))))))))).. ( -37.70)
>DroYak_CAF1 24365 108 - 1
---------CGGGUGCGAGUGAGACG--GAUGAGUGGGACUUUUGAGUGAGUUGUAGGUU-UUUACUCAUUUCCGCUGGCACUUCCGUUCCGUCGUCGUCCUGGGCCAAGGAAGUUGUAG
---------((((.((((....((((--((..(((((((....((((((((.........-)))))))).)))))))((.....))..)))))).))))))))................. ( -33.60)
>consensus
CUUUG__CUCGAGUGCGAGUGAGACGGGAGUGAGCGGGAAUUUUGAGUGAGUUGUAGGUUUUUUACUCAUUUCCGCUGGCACUUC_____CGACGUCGUCCUGGGCCAAGGAAGUUGUAG
.............(((((.(..((((((((((((((((((...((((((((..........))))))))))))))))..))))))........)))).((((......))))).))))). (-30.18 = -30.74 +   0.56)

alignment

secondary structure

dotplot

Window 5

Location	13,278,706 – 13,278,824
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.88
Mean single sequence MFE	-26.75
Consensus MFE	-17.56
Energy contribution	-18.79
Covariance contribution	1.23
Combinations/Pair	1.04
Mean z-score	-1.94
Structure conservation index	0.66
SVM decision value	0.30
SVM RNA-class probability	0.679759
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13278706 118 + 22224390
GCCAGCGGAAAUGAGUAAAAAACCUACAACUCACUCAAAAUUCCCGCUCACUCCCAUCUCACUCGCACUCGAA--CAAUGGGAAAUUCCGUUUCGAGUGAAAUUUUGUGCCACAAACGAA
...(((((.(((((((................)))))...)).)))))..............(((((((((((--..(((((....)))))))))))))....((((.....))))))). ( -24.99)
>DroSec_CAF1 24917 117 + 1
GCCAGCGGAAAUGAGUAAAAAACCUACAACUCACUCAAAAUUCCCGCUCACUCCCGUCUCACUCGCACUCGAG--CGAAGGGAAAUUCCGUUUCGAGUGAAAUU-CGGGCCACACACGAA
...(((((.(((((((................)))))...)).)))))....((((..((((((((......)--)((((((.....)).))))))))))....-))))........... ( -29.39)
>DroSim_CAF1 23536 117 + 1
GCCAGCGGAAAUGAGUAAAAAACCUACAACUCACUCAAAAUUCCCGCUCACUCCCGUCUCACUCGCACUCGAG--CAAAGGGAAAUUCCGUUUCGAGUGGAAUU-CGGGCCACACACGAA
((((((((((.(((((............))))).......(((((((((.....((.......)).....)))--)...))))).))))))).(((((...)))-))))).......... ( -28.20)
>DroEre_CAF1 24733 116 + 1
GCCAGCGGAAAUGAGUAAA-AACCUACAACUCACUCAAAAUUCCCGCUCACU--CGCCUCACUCGCACUCGCGUGUACAGGGUAAUUCCACUUCGAGUGAAACU-CAGGCCGCACACGAA
(((.((((.(((((((...-............)))))...)).))))(((((--((....((.(((....))).))...(((....)))....)))))))....-..))).......... ( -29.86)
>DroYak_CAF1 24405 97 + 1
GCCAGCGGAAAUGAGUAAA-AACCUACAACUCACUCAAAAGUCCCACUCAUC--CGUCUCACUCGCACCCG-------------------UUCCGAGUGAAACU-CAGGCCACACACGAA
(((.(((((..(((((...-.........................)))))))--))).(((((((......-------------------...)))))))....-..))).......... ( -21.29)
>consensus
GCCAGCGGAAAUGAGUAAAAAACCUACAACUCACUCAAAAUUCCCGCUCACUCCCGUCUCACUCGCACUCGAG__CAAAGGGAAAUUCCGUUUCGAGUGAAAUU_CGGGCCACACACGAA
((((((((...(((((................)))))......))))).................((((((((......(((....)))..))))))))........))).......... (-17.56 = -18.79 +   1.23)

alignment

secondary structure

dotplot

Window 6

Location	13,278,706 – 13,278,824
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.88
Mean single sequence MFE	-39.28
Consensus MFE	-28.49
Energy contribution	-29.01
Covariance contribution	0.52
Combinations/Pair	1.10
Mean z-score	-1.93
Structure conservation index	0.73
SVM decision value	0.59
SVM RNA-class probability	0.791151
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13278706 118 - 22224390
UUCGUUUGUGGCACAAAAUUUCACUCGAAACGGAAUUUCCCAUUG--UUCGAGUGCGAGUGAGAUGGGAGUGAGCGGGAAUUUUGAGUGAGUUGUAGGUUUUUUACUCAUUUCCGCUGGC
(((((((((((.........))))...)))))))...(((((((.--((((....))))...)))))))((.((((((((...((((((((..........)))))))))))))))).)) ( -37.60)
>DroSec_CAF1 24917 117 - 1
UUCGUGUGUGGCCCG-AAUUUCACUCGAAACGGAAUUUCCCUUCG--CUCGAGUGCGAGUGAGACGGGAGUGAGCGGGAAUUUUGAGUGAGUUGUAGGUUUUUUACUCAUUUCCGCUGGC
...........((((-..(((((((((((..((.....)).)))(--(......)))))))))))))).((.((((((((...((((((((..........)))))))))))))))).)) ( -41.70)
>DroSim_CAF1 23536 117 - 1
UUCGUGUGUGGCCCG-AAUUCCACUCGAAACGGAAUUUCCCUUUG--CUCGAGUGCGAGUGAGACGGGAGUGAGCGGGAAUUUUGAGUGAGUUGUAGGUUUUUUACUCAUUUCCGCUGGC
(((((..((((....-....)))).....)))))...((((((..--((((....))))..))..))))((.((((((((...((((((((..........)))))))))))))))).)) ( -41.00)
>DroEre_CAF1 24733 116 - 1
UUCGUGUGCGGCCUG-AGUUUCACUCGAAGUGGAAUUACCCUGUACACGCGAGUGCGAGUGAGGCG--AGUGAGCGGGAAUUUUGAGUGAGUUGUAGGUU-UUUACUCAUUUCCGCUGGC
..((....))(((..-.((((((((((.((.((.....))))...(((....))))))))))))).--....((((((((...((((((((.........-))))))))))))))))))) ( -42.40)
>DroYak_CAF1 24405 97 - 1
UUCGUGUGUGGCCUG-AGUUUCACUCGGAA-------------------CGGGUGCGAGUGAGACG--GAUGAGUGGGACUUUUGAGUGAGUUGUAGGUU-UUUACUCAUUUCCGCUGGC
..........(((..-.((((((((((.(.-------------------....).)))))))))).--....(((((((....((((((((.........-)))))))).)))))))))) ( -33.70)
>consensus
UUCGUGUGUGGCCCG_AAUUUCACUCGAAACGGAAUUUCCCUUUG__CUCGAGUGCGAGUGAGACGGGAGUGAGCGGGAAUUUUGAGUGAGUUGUAGGUUUUUUACUCAUUUCCGCUGGC
..........(((....((((((((((............................)))))))))).......((((((((...((((((((..........))))))))))))))))))) (-28.49 = -29.01 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:33 2006