Locus 989

Sequence ID	3R_DroMel_CAF1
Location	3,168,411 – 3,168,570
Length	159
Max. P	0.881569

overview

Window 2

Location	3,168,411 – 3,168,530
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.47
Mean single sequence MFE	-27.27
Consensus MFE	-21.85
Energy contribution	-22.41
Covariance contribution	0.56
Combinations/Pair	1.16
Mean z-score	-2.34
Structure conservation index	0.80
SVM decision value	0.92
SVM RNA-class probability	0.881569
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3168411 119 + 27905053
UAAAUUCAAAUUCUUGGCGUUGA-ACUGAUUAAAAAAGCGCUCGAACUUAUUUAGCCAUAUUCGAUGCGAAUCAGCUCUAAUUACCAUUAACAUUCUGGGCUGGCCAGCAUCUGAAUUUC
.(((((((..(((..((((((..-............)))))).))).................(((((...(((((((...................)))))))...)))))))))))). ( -26.45)
>DroSec_CAF1 16524 119 + 1
UAAAUUAAAUUUCUUUGCGUUGA-AUUGAUUAAAAAAGCGCCCCAACUUAUUUAGCCAUAUUCGAUGCGAAUCAGCUCUAAUUACCAUUAACAUUCUGGGCUGGCCAGCAUCUGAAUUUC
..........(((((((((((((-((((..((((.(((........))).))))..)).))))))))))))(((((((...................))))))).........))).... ( -23.81)
>DroSim_CAF1 19250 119 + 1
UAAAUUCAAUUUCUUCGCGUUGA-AUUGAUUAAAAAAGCGCUCCAACUUAUUUAGCCAUAUUCGAUGCGAAUCAGCCCUAAUUACCAUUAACAUUCUGGGCUGGCCAGCAUCUGAAUUUC
.(((((((.....((((((((((-((((..((((.(((........))).))))..)).))))))))))))(((((((...................)))))))........))))))). ( -32.61)
>DroEre_CAF1 8193 120 + 1
UAAAUGCGAUUUCUUCUCAUUGAGAUUGAUUUAACCAGCGCUCCAACUUAUUUAGCCAUAUUCGAUGCGAUUCAGCCUUAAUUACCAUUAACAUUCUGGGCUGGCCAGCAUCUGAAUUUC
(((((.(((((((........))))))))))))....(.(((...........))))..(((((((((...(((((((...................)))))))...))))).))))... ( -26.21)
>consensus
UAAAUUCAAUUUCUUCGCGUUGA_AUUGAUUAAAAAAGCGCUCCAACUUAUUUAGCCAUAUUCGAUGCGAAUCAGCCCUAAUUACCAUUAACAUUCUGGGCUGGCCAGCAUCUGAAUUUC
.(((((((......(((((((((...((..((((.(((........))).))))..))...))))))))).(((((((...................)))))))........))))))). (-21.85 = -22.41 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	3,168,450 – 3,168,570
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.42
Mean single sequence MFE	-25.88
Consensus MFE	-25.16
Energy contribution	-24.54
Covariance contribution	-0.62
Combinations/Pair	1.12
Mean z-score	-1.65
Structure conservation index	0.97
SVM decision value	0.69
SVM RNA-class probability	0.824015
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3168450 120 + 27905053
CUCGAACUUAUUUAGCCAUAUUCGAUGCGAAUCAGCUCUAAUUACCAUUAACAUUCUGGGCUGGCCAGCAUCUGAAUUUCCAAUUCGGCUUGAAACAAGCUUUCUUUGUGCGCAUCUUAA
..............((((((((((((((...(((((((...................)))))))...))))).)))..........((((((...)))))).....)))).))....... ( -27.01)
>DroSec_CAF1 16563 120 + 1
CCCCAACUUAUUUAGCCAUAUUCGAUGCGAAUCAGCUCUAAUUACCAUUAACAUUCUGGGCUGGCCAGCAUCUGAAUUUCCAAUUCGGCCUUAAACAAGCUUUCUUUGUGCGCAUUUUAA
......(((.(((((((......(((((...(((((((...................)))))))...))))).((((.....)))))))..)))).)))..................... ( -23.31)
>DroSim_CAF1 19289 120 + 1
CUCCAACUUAUUUAGCCAUAUUCGAUGCGAAUCAGCCCUAAUUACCAUUAACAUUCUGGGCUGGCCAGCAUCUGAAUUUCCAAUUCGGCCUGAAACAAGCUUUCUUUGUGCGCAUUUUAA
..........(((((((......(((((...(((((((...................)))))))...))))).((((.....)))))).)))))(((((.....)))))........... ( -27.31)
>DroEre_CAF1 8233 120 + 1
CUCCAACUUAUUUAGCCAUAUUCGAUGCGAUUCAGCCUUAAUUACCAUUAACAUUCUGGGCUGGCCAGCAUCUGAAUUUCCGAUUCGGCAAGAAACAAGCUUUCUUUGUGCGCAUUUUAA
..............(((......(((((...(((((((...................)))))))...))))).(((((...))))))))((((((.....)))))).............. ( -25.91)
>consensus
CUCCAACUUAUUUAGCCAUAUUCGAUGCGAAUCAGCCCUAAUUACCAUUAACAUUCUGGGCUGGCCAGCAUCUGAAUUUCCAAUUCGGCCUGAAACAAGCUUUCUUUGUGCGCAUUUUAA
..............(((......(((((...(((((((...................)))))))...))))).(((((...)))))))).....(((((.....)))))........... (-25.16 = -24.54 +  -0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:45 2006