Locus 3178

Sequence ID	3L_DroMel_CAF1
Location	9,259,969 – 9,260,066
Length	97
Max. P	0.979796

overview

Window 5

Location	9,259,969 – 9,260,066
Length	97
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	82.20
Mean single sequence MFE	-19.66
Consensus MFE	-10.30
Energy contribution	-13.00
Covariance contribution	2.70
Combinations/Pair	1.18
Mean z-score	-3.26
Structure conservation index	0.52
SVM decision value	1.85
SVM RNA-class probability	0.979796
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9259969 97 + 23771897
AAGUAAUUUGAAAAUUAAAUUUCAAUUUCGAUUUCCAAAGUGAAAAUGCGAGGAAAAUGCGUUGAAAAAUGCAUAGCUCGCGUUGAGAAUAAAAUGG
.......((((((......))))))((((...(((......)))((((((((....(((((((....)))))))..))))))))))))......... ( -22.00)
>DroSec_CAF1 106746 89 + 1
AAGUAAUUUGAAAAUUAAAC--------CGAUUUCAAAAGUGAAAAUGCGAUGAAAAUGCGUUGAAAAAUGAAUAGCUCGCGUUGAGAACAAAAUUG
......(((((((.......--------...))))))).((...(((((((.(......((((....)))).....))))))))....))....... ( -15.00)
>DroSim_CAF1 106997 88 + 1
AAGUAAUUUGAAAAUUAAAC--------CGUUUUCAAAAGUGAAAAUGCGAGG-AAAUGCGCUGAAAAAUGCAUGGCUCGCGUUGAGAACAAAAUUG
......(((((((((.....--------.))))))))).((...((((((((.-..(((((.(....).)))))..))))))))....))....... ( -23.60)
>DroEre_CAF1 129526 88 + 1
AAGUAGUUUGAAAAU--AAG-------CAGAUUUUAAAAGUGAAAAUGCGAGAAAAAUGCGUUGAAAAAUGCAUAGCGCACUUUCAGAGAGAAAUGG
....((((((.....--...-------)))))).......(((((.((((......(((((((....)))))))..)))).)))))........... ( -18.20)
>DroYak_CAF1 124752 89 + 1
AAGUAAUUUGAAAAUUAAAG-------CAAAU-GCAAAAGUGAAAAUGCGCGAAAAAUGCGUUGAAAAAUGCAUAGCGCACUUUGGGAGCAAAAUUG
......((((....((((((-------(....-))...........(((((.....(((((((....))))))).))))).)))))...)))).... ( -19.50)
>consensus
AAGUAAUUUGAAAAUUAAAC________CGAUUUCAAAAGUGAAAAUGCGAGGAAAAUGCGUUGAAAAAUGCAUAGCUCGCGUUGAGAACAAAAUUG
.......................................((...((((((((....(((((((....)))))))..))))))))....))....... (-10.30 = -13.00 +   2.70)

alignment

secondary structure

dotplot

Window 6

Location	9,259,969 – 9,260,066
Length	97
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	82.20
Mean single sequence MFE	-13.37
Consensus MFE	-7.50
Energy contribution	-7.62
Covariance contribution	0.12
Combinations/Pair	1.22
Mean z-score	-2.49
Structure conservation index	0.56
SVM decision value	0.89
SVM RNA-class probability	0.875621
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9259969 97 - 23771897
CCAUUUUAUUCUCAACGCGAGCUAUGCAUUUUUCAACGCAUUUUCCUCGCAUUUUCACUUUGGAAAUCGAAAUUGAAAUUUAAUUUUCAAAUUACUU
........(((.....(((((..((((..........))))....)))))((((((.....)))))).))).((((((......))))))....... ( -17.00)
>DroSec_CAF1 106746 89 - 1
CAAUUUUGUUCUCAACGCGAGCUAUUCAUUUUUCAACGCAUUUUCAUCGCAUUUUCACUUUUGAAAUCG--------GUUUAAUUUUCAAAUUACUU
................((((..........................)))).........(((((((...--------.......)))))))...... (  -6.77)
>DroSim_CAF1 106997 88 - 1
CAAUUUUGUUCUCAACGCGAGCCAUGCAUUUUUCAGCGCAUUU-CCUCGCAUUUUCACUUUUGAAAACG--------GUUUAAUUUUCAAAUUACUU
................(((((..((((..........))))..-.))))).........((((((((..--------......))))))))...... ( -14.70)
>DroEre_CAF1 129526 88 - 1
CCAUUUCUCUCUGAAAGUGCGCUAUGCAUUUUUCAACGCAUUUUUCUCGCAUUUUCACUUUUAAAAUCUG-------CUU--AUUUUCAAACUACUU
...........((((((((((..((((..........))))......)))))))))).............-------...--............... ( -13.60)
>DroYak_CAF1 124752 89 - 1
CAAUUUUGCUCCCAAAGUGCGCUAUGCAUUUUUCAACGCAUUUUUCGCGCAUUUUCACUUUUGC-AUUUG-------CUUUAAUUUUCAAAUUACUU
(((...(((....(((((((((.((((..........)))).....))))))))).......))-).)))-------.................... ( -14.80)
>consensus
CAAUUUUGUUCUCAACGCGAGCUAUGCAUUUUUCAACGCAUUUUCCUCGCAUUUUCACUUUUGAAAUCG________CUUUAAUUUUCAAAUUACUU
................(((((..((((..........))))....)))))............................................... ( -7.50 =  -7.62 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:27 2006