Locus 5127

Sequence ID	X_DroMel_CAF1
Location	13,391,856 – 13,391,954
Length	98
Max. P	0.992146

overview

Window 2

Location	13,391,856 – 13,391,954
Length	98
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	72.32
Mean single sequence MFE	-26.08
Consensus MFE	-13.98
Energy contribution	-15.02
Covariance contribution	1.04
Combinations/Pair	1.05
Mean z-score	-1.86
Structure conservation index	0.54
SVM decision value	0.93
SVM RNA-class probability	0.883980
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13391856 98 + 22224390
UUCAUG----GGGGUG---CGGCAAUAAACUUG-UUUUUAUUGCCGAAAAUGUUGUUAAAGGGUUAACAAGGUGGCAACGGGGGGGAGGUUGUUUCUUAGCCCUUA
....((----(((((.---.((.(((((.(((.-((((..(((((....((.(((((((....))))))).)))))))..)))).))).))))).))..))))))) ( -29.90)
>DroSim_CAF1 7956 92 + 1
UUCAUG----GGGGUG---CGGCAAUAAACUUG-UUUUUAUUGCCGAAAAUGUUGUUAAAGGGUUAACAAGGAG-----GGGGAGGUGUUUGCUUCUUAGCCCUA-
......----(((((.---((((((((((....-..))))))))))....(.(((((((....))))))).)..-----.(((((((....))))))).))))).- ( -29.60)
>DroEre_CAF1 7358 81 + 1
UUCAUG----GGGGUG---CGGCAAUAAACUUG-CUUUUAUUGCCGAAAAUGUUGUUAAAGGGUUAACAAGAG----------------CGGCUCCUUAGCCCAA-
.....(----(((.((---((((((((((....-..))))))))).....(.(((((((....))))))).))----------------)).)))).........- ( -25.90)
>DroYak_CAF1 4923 84 + 1
UUCAUG----GGGGUG---CGGCAAUAAACUAG-CUUUCAUUGCCCCAAAUGUUGUUAAAGGGUUAACAAGAAGC-------------CCUGCUCCUUGGCUCAA-
.(((.(----((((((---.((((((.((....-..)).)))))).)............((((((.......)))-------------)))))))))))).....- ( -20.80)
>DroAna_CAF1 4828 89 + 1
UUCAUGGAAGGGGGUGUCCCGACUAUAAAGUUGUCUUUUAUUGCCAUAGAUGGUGUUAAAGGUUUUACAAGCC----------------UCGGUGACUGGGCCAA-
...((((..(((.....)))..))))...((...((((((..((((....))))..))))))....))..(((----------------(.(....).))))...- ( -24.20)
>consensus
UUCAUG____GGGGUG___CGGCAAUAAACUUG_CUUUUAUUGCCGAAAAUGUUGUUAAAGGGUUAACAAGAAG_______________UUGCUCCUUAGCCCAA_
...........((((.....(((((((((.......))))))))).......(((((((....))))))).............................))))... (-13.98 = -15.02 +   1.04)

alignment

secondary structure

dotplot

Window 3

Location	13,391,856 – 13,391,954
Length	98
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	72.32
Mean single sequence MFE	-19.38
Consensus MFE	-12.22
Energy contribution	-12.90
Covariance contribution	0.68
Combinations/Pair	1.11
Mean z-score	-2.18
Structure conservation index	0.63
SVM decision value	2.31
SVM RNA-class probability	0.992146
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13391856 98 - 22224390
UAAGGGCUAAGAAACAACCUCCCCCCCGUUGCCACCUUGUUAACCCUUUAACAACAUUUUCGGCAAUAAAAA-CAAGUUUAUUGCCG---CACCCC----CAUGAA
...(((....((((((((.........)))).....(((((((....)))))))...))))(((((((((..-....))))))))).---....))----)..... ( -20.70)
>DroSim_CAF1 7956 92 - 1
-UAGGGCUAAGAAGCAAACACCUCCCC-----CUCCUUGUUAACCCUUUAACAACAUUUUCGGCAAUAAAAA-CAAGUUUAUUGCCG---CACCCC----CAUGAA
-..(((.....................-----....(((((((....)))))))......((((((((((..-....))))))))))---....))----)..... ( -19.30)
>DroEre_CAF1 7358 81 - 1
-UUGGGCUAAGGAGCCG----------------CUCUUGUUAACCCUUUAACAACAUUUUCGGCAAUAAAAG-CAAGUUUAUUGCCG---CACCCC----CAUGAA
-.((((....((.((..----------------...(((((((....))))))).......(((((((((..-....))))))))))---).))))----)).... ( -22.00)
>DroYak_CAF1 4923 84 - 1
-UUGAGCCAAGGAGCAGG-------------GCUUCUUGUUAACCCUUUAACAACAUUUGGGGCAAUGAAAG-CUAGUUUAUUGCCG---CACCCC----CAUGAA
-.((..(....)..))((-------------(....(((((((....)))))))....((.(((((((((..-....))))))))).---))..))----)..... ( -21.70)
>DroAna_CAF1 4828 89 - 1
-UUGGCCCAGUCACCGA----------------GGCUUGUAAAACCUUUAACACCAUCUAUGGCAAUAAAAGACAACUUUAUAGUCGGGACACCCCCUUCCAUGAA
-..((((..(....)..----------------)))).....................(((((........(((.........)))(((.....)))..))))).. ( -13.20)
>consensus
_UUGGGCUAAGAAGCAA_______________CUCCUUGUUAACCCUUUAACAACAUUUUCGGCAAUAAAAG_CAAGUUUAUUGCCG___CACCCC____CAUGAA
...(((..............................(((((((....))))))).......(((((((((.......)))))))))......)))........... (-12.22 = -12.90 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:41 2006