Locus 6612

Sequence ID	3L_DroMel_CAF1
Location	17,577,492 – 17,577,590
Length	98
Max. P	0.982963

overview

Window 0

Location	17,577,492 – 17,577,590
Length	98
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	80.55
Mean single sequence MFE	-33.14
Consensus MFE	-20.60
Energy contribution	-21.64
Covariance contribution	1.04
Combinations/Pair	1.23
Mean z-score	-2.68
Structure conservation index	0.62
SVM decision value	1.93
SVM RNA-class probability	0.982963
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17577492 98 + 23771897
UUCAUUACGCCAGCGCUCACAUACGCAC----ACACAUGCAAACAC----ACAUGUGUGUGCGUGCGUUUCGAGGUGCAUUGCAUUGCAUGGCGAGACCUCAACUA
.......((((....(((((.(((((((----(((((((.......----.)))))))))))))).))...)))(((((......)))))))))............ ( -39.20)
>DroSec_CAF1 13904 104 + 1
UUCAUUACUCUAGCGCUCACAUACACAC--ACACACAUGACAACACAUGCACGCAUGUAUGCGUGCGUUUCGAGGUGCAUUGUAUUGCAUGGCGAGACCUCAACUA
............................--.......(((........(((((((....)))))))((((((..(((((......)))))..)))))).))).... ( -27.20)
>DroSim_CAF1 16206 106 + 1
UUCAUUACGCCAGCGCUCACAUACACACACACACACAUGACAACACAUGCACGCAUGUAUGCGUGCGUUUCGAGGUGCAUUGCAUUGCAUGGCGAGACCUCAACUA
.......((((((((((.....((............(((......)))(((((((....))))))))).....)))))..(((...))))))))............ ( -28.00)
>DroEre_CAF1 22672 102 + 1
UCCAUUACGGCAGUGUGUACAGGCACAGACAGGCACACGCC----UGGGCACACAAGUGUGCGUGCGUUUCGAGGUGCAUUGCAUUGCAUGGCGAGACCUCAACUA
...........(((........((((...(((((....)))----)).(((((....)))))))))((((((..(((((......)))))..))))))....))). ( -38.10)
>DroYak_CAF1 23562 102 + 1
UCCAUUACGCCAGUGUGCUCACACACACACACCAACACAUA----CACGCACAUAAGUGUGCGUGCGUUUCGAGGUGCAUUGCAUUGCAUGGCGAGACCUCAACUA
............(((((......))))).............----((((((((....)))))))).((((((..(((((......)))))..))))))........ ( -33.20)
>consensus
UUCAUUACGCCAGCGCUCACAUACACACACACACACAUGACAACACAUGCACACAUGUGUGCGUGCGUUUCGAGGUGCAUUGCAUUGCAUGGCGAGACCUCAACUA
............(((........)))...................((((((((....)))))))).((((((..(((((......)))))..))))))........ (-20.60 = -21.64 +   1.04)

alignment

secondary structure

dotplot

Window 1

Location	17,577,492 – 17,577,590
Length	98
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	80.55
Mean single sequence MFE	-37.52
Consensus MFE	-22.50
Energy contribution	-23.26
Covariance contribution	0.76
Combinations/Pair	1.31
Mean z-score	-2.46
Structure conservation index	0.60
SVM decision value	1.43
SVM RNA-class probability	0.952925
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17577492 98 - 23771897
UAGUUGAGGUCUCGCCAUGCAAUGCAAUGCACCUCGAAACGCACGCACACACAUGU----GUGUUUGCAUGUGU----GUGCGUAUGUGAGCGCUGGCGUAAUGAA
...(((((((...((..(((...)))..))))))))).((((((((((((((((((----......))))))))----))))))..((....))..))))...... ( -39.40)
>DroSec_CAF1 13904 104 - 1
UAGUUGAGGUCUCGCCAUGCAAUACAAUGCACCUCGAAACGCACGCAUACAUGCGUGCAUGUGUUGUCAUGUGUGU--GUGUGUAUGUGAGCGCUAGAGUAAUGAA
...(((((((........(((......))))))))))..(((.((((((((((((..((((((....))))))..)--))))))))))).)))............. ( -38.50)
>DroSim_CAF1 16206 106 - 1
UAGUUGAGGUCUCGCCAUGCAAUGCAAUGCACCUCGAAACGCACGCAUACAUGCGUGCAUGUGUUGUCAUGUGUGUGUGUGUGUAUGUGAGCGCUGGCGUAAUGAA
........((..(((((.((..(((...))).((((....(((((((((((((((((((.....)).)))))))))))))))))...)))).)))))))..))... ( -40.50)
>DroEre_CAF1 22672 102 - 1
UAGUUGAGGUCUCGCCAUGCAAUGCAAUGCACCUCGAAACGCACGCACACUUGUGUGCCCA----GGCGUGUGCCUGUCUGUGCCUGUACACACUGCCGUAAUGGA
...(((((((...((..(((...)))..)))))))))...(((((((....)))))))(((----(((((((((..((....))..))))))...)))....))). ( -31.10)
>DroYak_CAF1 23562 102 - 1
UAGUUGAGGUCUCGCCAUGCAAUGCAAUGCACCUCGAAACGCACGCACACUUAUGUGCGUG----UAUGUGUUGGUGUGUGUGUGUGAGCACACUGGCGUAAUGGA
...(((((((...((..(((...)))..))))))))).(((((((((((....))))))))----)....((..((((((........))))))..))))...... ( -38.10)
>consensus
UAGUUGAGGUCUCGCCAUGCAAUGCAAUGCACCUCGAAACGCACGCACACAUGUGUGCAUGUGUUGGCAUGUGUGUGUGUGUGUAUGUGAGCGCUGGCGUAAUGAA
((((((((((...((..(((...)))..))))))))....(((((((((((((((((..........)))))))))))))))))........)))).......... (-22.50 = -23.26 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:39 2006