Locus 82

Sequence ID	3R_DroMel_CAF1
Location	510,716 – 510,916
Length	200
Max. P	0.739464

overview

Window 9

Location	510,716 – 510,836
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	90.00
Mean single sequence MFE	-30.70
Consensus MFE	-23.67
Energy contribution	-23.79
Covariance contribution	0.12
Combinations/Pair	1.15
Mean z-score	-2.54
Structure conservation index	0.77
SVM decision value	0.45
SVM RNA-class probability	0.739464
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 510716 120 - 27905053
AUGCAAAAUACUUUUGCUCUCAUACCUUGAGAGAGCCAACGAAGCAUUCAAUUCUAGCUUGGCCGCGAUCCCCUUUAUUCACACGCACUACGCCCCUAAAGGGGGAAGCUAGGCAAAAAU
..(((((.....)))))(((((.....)))))..(((..(.((((...........)))).)..((..(((((((((.......((.....))...)))))))))..))..)))...... ( -31.80)
>DroSim_CAF1 37516 120 - 1
AUGCAAAAUACCUUUGCUCUCAUACCUUGAGAGACCCAACGAAGCAUUCAAUUAUAGCUUGGCCGCGAUCCCCUUCAUUCACACGCACUACGCCCCUAAAAGGGGGAACUUGGCAACAAU
..(((((.....)))))(((((.....))))).........((((...........)))).((((.(.(((((((.........((.....)).......))))))).).))))...... ( -27.39)
>DroEre_CAF1 41743 120 - 1
ACUCAAAAUACUUUUGCUCUCAUACCUUGAGAGACCCAACGAAGCAUUUAAUUCUAGCUGGGUCGCUAUCCCCUUUAUUUACAGGCACUACGCCCCUAAAAGGGGAAACUUUGCAACAAU
.............(((((((((.....)))))((((((..(((........)))....))))))....((((((((...((..(((.....)))..))))))))))......)))).... ( -32.90)
>consensus
AUGCAAAAUACUUUUGCUCUCAUACCUUGAGAGACCCAACGAAGCAUUCAAUUCUAGCUUGGCCGCGAUCCCCUUUAUUCACACGCACUACGCCCCUAAAAGGGGAAACUUGGCAACAAU
................((((((.....)))))).......................(((((((.(((................)))......((((.....))))..)))))))...... (-23.67 = -23.79 +   0.12)

alignment

secondary structure

dotplot

Window 0

Location	510,756 – 510,876
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	87.64
Mean single sequence MFE	-28.47
Consensus MFE	-18.52
Energy contribution	-18.97
Covariance contribution	0.45
Combinations/Pair	1.04
Mean z-score	-2.79
Structure conservation index	0.65
SVM decision value	0.24
SVM RNA-class probability	0.649602
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 510756 120 - 27905053
UUCUCACUCCCCACGUCCGCUGCCCGCCCCCACAGUUGGCAUGCAAAAUACUUUUGCUCUCAUACCUUGAGAGAGCCAACGAAGCAUUCAAUUCUAGCUUGGCCGCGAUCCCCUUUAUUC
.................(((.(((..........((((((..(((((.....)))))(((((.....)))))..)))))).((((...........))))))).)))............. ( -30.80)
>DroSim_CAF1 37556 116 - 1
UGCUCACUCCCCACGUCCGCUGC----CCCCACAGUUGGCAUGCAAAAUACCUUUGCUCUCAUACCUUGAGAGACCCAACGAAGCAUUCAAUUAUAGCUUGGCCGCGAUCCCCUUCAUUC
.................(((.((----(......(((((...(((((.....)))))(((((.....)))))...))))).((((...........))))))).)))............. ( -26.40)
>DroEre_CAF1 41783 116 - 1
UUCUUACUCCCCAAGCGCGCAGC----CCCCACAGUUGGAACUCAAAAUACUUUUGCUCUCAUACCUUGAGAGACCCAACGAAGCAUUUAAUUCUAGCUGGGUCGCUAUCCCCUUUAUUU
.............(((((.((((----.......(((((....((((.....))))((((((.....))))))..)))))(((........)))..)))).).))))............. ( -28.20)
>consensus
UUCUCACUCCCCACGUCCGCUGC____CCCCACAGUUGGCAUGCAAAAUACUUUUGCUCUCAUACCUUGAGAGACCCAACGAAGCAUUCAAUUCUAGCUUGGCCGCGAUCCCCUUUAUUC
.................(((.((...........(((((....((((.....))))((((((.....))))))..))))).((((...........)))).)).)))............. (-18.52 = -18.97 +   0.45)

alignment

secondary structure

dotplot

Window 1

Location	510,796 – 510,916
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.54
Mean single sequence MFE	-24.27
Consensus MFE	-17.33
Energy contribution	-17.33
Covariance contribution	-0.00
Combinations/Pair	1.21
Mean z-score	-1.68
Structure conservation index	0.71
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 510796 120 - 27905053
AUGCCAUUAUUACAUGAGAUAACUGCAACCUAAAGGUAUCUUCUCACUCCCCACGUCCGCUGCCCGCCCCCACAGUUGGCAUGCAAAAUACUUUUGCUCUCAUACCUUGAGAGAGCCAAC
.(((..(((((......)))))..))).......(((.....................((((((.((.......)).)))).))............((((((.....)))))).)))... ( -24.50)
>DroSec_CAF1 37516 116 - 1
GUGCCAUUAUUACUUGAGUUAACUGCAACCUAAAGGUAUCUGCUCACUCCCCACGUCCGCUGC----CCCCACAGUUGGCAUGCAAAAUACCUUUGCUCUCAUACCUUGAGAGACCCAAC
((((((.........((((.....((((((....)))...)))..)))).........((((.----.....))))))))))(((((.....)))))(((((.....)))))........ ( -25.50)
>DroSim_CAF1 37596 116 - 1
GUGCCAUUAUUACAUGAGUUAACUGCAACCUAAAGGUAUCUGCUCACUCCCCACGUCCGCUGC----CCCCACAGUUGGCAUGCAAAAUACCUUUGCUCUCAUACCUUGAGAGACCCAAC
((((((.........((((.....((((((....)))...)))..)))).........((((.----.....))))))))))(((((.....)))))(((((.....)))))........ ( -25.50)
>DroEre_CAF1 41823 114 - 1
GUGCUUUUAUUACAUGAG-UAACUGCAACCUAAA-GUAUCUUCUUACUCCCCAAGCGCGCAGC----CCCCACAGUUGGAACUCAAAAUACUUUUGCUCUCAUACCUUGAGAGACCCAAC
((((((...((((....)-)))...........(-(((......))))....)))))).....----.......(((((....((((.....))))((((((.....))))))..))))) ( -21.60)
>consensus
GUGCCAUUAUUACAUGAGUUAACUGCAACCUAAAGGUAUCUGCUCACUCCCCACGUCCGCUGC____CCCCACAGUUGGCAUGCAAAAUACCUUUGCUCUCAUACCUUGAGAGACCCAAC
((((((........(((((....(((.........)))...)))))............((((..........))))))))))..............((((((.....))))))....... (-17.33 = -17.33 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:35 2006