Locus 4160

Sequence ID	2L_DroMel_CAF1
Location	11,959,785 – 11,959,894
Length	109
Max. P	0.999943

overview

Window 6

Location	11,959,785 – 11,959,894
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.82
Mean single sequence MFE	-38.97
Consensus MFE	-30.56
Energy contribution	-30.80
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.36
Structure conservation index	0.78
SVM decision value	1.35
SVM RNA-class probability	0.945253
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11959785 109 + 22407834
GUGAAAUGCAUGCGUUCAUUAAAUUAAUGCGCAUGGGGCAUGUGGAGCCGGGCAGAUAAUUAAAUGCGUGUUUUGUGGCAUGGGCGC-------UGGGCGC----AAGAGGUGCCCGUAA
((.(...(((((((((.....(((((.(((.(....(((.......)))).)))..))))).)))))))))....).))((((((((-------(...(..----..).))))))))).. ( -36.70)
>DroSec_CAF1 179136 109 + 1
GUGAAAUGCAUGCGUUCAUUAAAUUAAUGCGCAUGGGGCAUGUGGUGCCGGGCAGAUAAUUAAAUGCGUGUUUUAUGGCAUGGGCGC-------UGGGCGC----AUGAGGUGCCCGUAA
........(((((((.............)))))))((((((.(.(((((.(((..((......)).((((((....))))))...))-------).)))))----...).)))))).... ( -38.32)
>DroSim_CAF1 145585 109 + 1
GUGAAAUGCAUGCGUUCAUUAAAUUAAUGCGCAUGGGGCAUGUGGUGCCGGGCAGAUAAUUAAAUGCGUGUUUUGUGGCAUGGGCGC-------UGGGCGC----AUGAGGUGCCCGUAA
........(((((((.............)))))))((((((.(.(((((.(((..((......)).((((((....))))))...))-------).)))))----...).)))))).... ( -38.32)
>DroEre_CAF1 154104 119 + 1
GUGAAAUGCAUGCGUUCAUUAAAUUAAUGCGCAUGGGGCAUGUGGAGACGGGCAGAUAAUUAAAUGCGUGUU-UGUGGCAUGGGCGCUACGCGCUGGGCGCUCGUAAGAGGUGCCCGUAA
......(.(((((((.............))))))).).(((((.((((((.(((..........))).))))-).).)))))(((((...)))))((((((((....)).)))))).... ( -44.12)
>DroYak_CAF1 149916 108 + 1
GUGAAAUGCAUGCGUUCAUUAAAUUAAUGCGCAUGGGGCAUGUGGAGCCGGGCAGAUAAUUAAAUGCGUGUU-UGUGGCAUGGGCGC-------UGGGCGC----AAGAGGUGCCCGUAA
((.(...(((((((((.....(((((.(((.(....(((.......)))).)))..))))).))))))))).-..).))((((((((-------(...(..----..).))))))))).. ( -37.40)
>consensus
GUGAAAUGCAUGCGUUCAUUAAAUUAAUGCGCAUGGGGCAUGUGGAGCCGGGCAGAUAAUUAAAUGCGUGUUUUGUGGCAUGGGCGC_______UGGGCGC____AAGAGGUGCCCGUAA
......(((..(((((((.........(((.((((((((((.((....)).(((..........)))))))))))))))))))))))........((((((.........))))))))). (-30.56 = -30.80 +   0.24)

alignment

secondary structure

dotplot

Window 7

Location	11,959,785 – 11,959,894
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.82
Mean single sequence MFE	-27.45
Consensus MFE	-25.44
Energy contribution	-25.64
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.77
Structure conservation index	0.93
SVM decision value	4.73
SVM RNA-class probability	0.999943
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11959785 109 - 22407834
UUACGGGCACCUCUU----GCGCCCA-------GCGCCCAUGCCACAAAACACGCAUUUAAUUAUCUGCCCGGCUCCACAUGCCCCAUGCGCAUUAAUUUAAUGAACGCAUGCAUUUCAC
....(((((......----((((...-------))))..((((..........)))).........)))))(((.......))).(((((((((((...)))))..))))))........ ( -26.90)
>DroSec_CAF1 179136 109 - 1
UUACGGGCACCUCAU----GCGCCCA-------GCGCCCAUGCCAUAAAACACGCAUUUAAUUAUCUGCCCGGCACCACAUGCCCCAUGCGCAUUAAUUUAAUGAACGCAUGCAUUUCAC
....(((((......----((((...-------))))..((((..........)))).........)))))((((.....)))).(((((((((((...)))))..))))))........ ( -27.40)
>DroSim_CAF1 145585 109 - 1
UUACGGGCACCUCAU----GCGCCCA-------GCGCCCAUGCCACAAAACACGCAUUUAAUUAUCUGCCCGGCACCACAUGCCCCAUGCGCAUUAAUUUAAUGAACGCAUGCAUUUCAC
....(((((......----((((...-------))))..((((..........)))).........)))))((((.....)))).(((((((((((...)))))..))))))........ ( -27.40)
>DroEre_CAF1 154104 119 - 1
UUACGGGCACCUCUUACGAGCGCCCAGCGCGUAGCGCCCAUGCCACA-AACACGCAUUUAAUUAUCUGCCCGUCUCCACAUGCCCCAUGCGCAUUAAUUUAAUGAACGCAUGCAUUUCAC
..(((((((.....((((.((.....)).))))(((...........-....)))...........)))))))............(((((((((((...)))))..))))))........ ( -28.56)
>DroYak_CAF1 149916 108 - 1
UUACGGGCACCUCUU----GCGCCCA-------GCGCCCAUGCCACA-AACACGCAUUUAAUUAUCUGCCCGGCUCCACAUGCCCCAUGCGCAUUAAUUUAAUGAACGCAUGCAUUUCAC
....(((((......----((((...-------))))..((((....-.....)))).........)))))(((.......))).(((((((((((...)))))..))))))........ ( -27.00)
>consensus
UUACGGGCACCUCUU____GCGCCCA_______GCGCCCAUGCCACAAAACACGCAUUUAAUUAUCUGCCCGGCUCCACAUGCCCCAUGCGCAUUAAUUUAAUGAACGCAUGCAUUUCAC
....(((((..........((((..........))))..((((..........)))).........)))))(((.......))).(((((((((((...)))))..))))))........ (-25.44 = -25.64 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:08 2006