Locus 540

Sequence ID	3R_DroMel_CAF1
Location	1,996,625 – 1,996,903
Length	278
Max. P	0.983231

overview

Window 7

Location	1,996,625 – 1,996,729
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	66.93
Mean single sequence MFE	-32.74
Consensus MFE	-15.68
Energy contribution	-15.92
Covariance contribution	0.24
Combinations/Pair	1.36
Mean z-score	-2.21
Structure conservation index	0.48
SVM decision value	1.94
SVM RNA-class probability	0.983231
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1996625 104 + 27905053
ACAUUCUACAUUAU-UGCGUGCCGCCUUCUUGCGGAAGCUGAUAGAAACACUUGUCCAGUGGCACCUCUU---GGAUUUAUGU----AUCUCUACAUUUAGACGGCGCUAUU--------
..............-...((((((.((((..((....)).)).(((.(((...((((((.(....).).)---))))...)))----.)))........)).))))))....-------- ( -25.20)
>DroSec_CAF1 145742 112 + 1
ACAUUCUACAUUUU-UGCCUGCUGCCAUCUCGCGGAAGCGAGGAGAAGAACUUGUCCAGUGGCACCUCUA---GUAUUUAUGU----GACUUUUCAUCUAGAUGGCGGUAUUUGAGCAAG
.............(-((((((((((((((((((....))))..(((.(((...(((((...((.......---)).....)).----)))..))).))).))))))))))...).)))). ( -33.80)
>DroSim_CAF1 150955 103 + 1
ACAUUCUACAUUCU----------ACAUCUUGCGGAAGCGAGGAGAAUAACUUGUCCAGUAGCACCACUA---GUAUUUAUGU----GACUUUUCAUCUAGAUGGCGCUAUUUGAGCAAG
.........(((((----------...((((((....)))))))))))..((((..(((((((.((((((---(.......((----((....)))))))).))).)))).)))..)))) ( -31.91)
>DroEre_CAF1 149012 91 + 1
ACAUUCUACAUUGUGUGCCUAUCGCCAUCUUGCGGAAGCAGACAGAAGCACGUGGCAAGUGUCGCCUCU---------------------UGUACAGGUAGAUGGCGGUACU--------
((((........))))...((((((((((((((....)))((((...((.....))...))))((((..---------------------.....)))))))))))))))..-------- ( -30.30)
>DroYak_CAF1 152882 112 + 1
GCAUUCUACAUCAUGUGCCUAUCGCCAUCUUGCGGAAGCAGACAGAAACACUUGUCGAGUGGCUCUGCUACUUAGGUGUUUGUAUCGGAAGGUACAUGUAGAUGGCGCUACU--------
((((..........))))....(((((((((((....))).(((.((((((((...(((((((...)))))))))))))))(((((....))))).))))))))))).....-------- ( -42.50)
>consensus
ACAUUCUACAUUAU_UGCCUACCGCCAUCUUGCGGAAGCAGACAGAAACACUUGUCCAGUGGCACCUCUA___GGAUUUAUGU____GACUGUACAUCUAGAUGGCGCUAUU________
......................(((((((((((....))))............(((....))).....................................)))))))............. (-15.68 = -15.92 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	1,996,729 – 1,996,830
Length	101
Sequences	3
Columns	116
Reading direction	reverse
Mean pairwise identity	81.03
Mean single sequence MFE	-27.97
Consensus MFE	-21.42
Energy contribution	-22.10
Covariance contribution	0.68
Combinations/Pair	1.18
Mean z-score	-1.72
Structure conservation index	0.77
SVM decision value	0.50
SVM RNA-class probability	0.759680
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1996729 101 - 27905053
UCGACUGUAUGUGAAGCGAAUUCGAUUGGUAAAAACAAACCAAAUUCGCCUGAAUUUGAAGCGAAUUCGAAUCUUUUGAGUUUACAUUAUAAACUGUACGU---------------
......((((..((..((((((((.(((.......)))..(((((((....)))))))...))))))))..)).....((((((.....))))))))))..--------------- ( -22.30)
>DroSec_CAF1 145854 116 - 1
UCGACUAUAUGUGAAGCGAGUUCGAUUGGUAAAAUUAAACAGAAUUUGCCUGUAUGUGAAGCGAAUUCGAAUGGUUUGAGUUUACAUCAUCGCAUGUAGUUUUACUCGCAUGUGUG
..((((((((((((.((((((((..(((((...)))))...)))))))).((.(((((((.((((((.....))))))..))))))))))))))))))))).....(((....))) ( -30.80)
>DroSim_CAF1 151058 116 - 1
UCGACUAUAUGUGAAGCGAAUUCGAUUGGUAAAAUUAAACAGAAUUUGCCUGUAUGUGAAGCGAAUUCGAAUGGUUUGAGUUUACAUCAUCGCAUGUAGUUUUACUCGCAUGUGUG
..((((((((((((.((((((((..(((((...)))))...)))))))).((.(((((((.((((((.....))))))..))))))))))))))))))))).....(((....))) ( -30.80)
>consensus
UCGACUAUAUGUGAAGCGAAUUCGAUUGGUAAAAUUAAACAGAAUUUGCCUGUAUGUGAAGCGAAUUCGAAUGGUUUGAGUUUACAUCAUCGCAUGUAGUUUUACUCGCAUGUGUG
..((((((((((((.((((((((..(((.......)))...)))))))).......(((.(..(((((((.....)))))))..).)))))))))))))))............... (-21.42 = -22.10 +   0.68)

alignment

secondary structure

dotplot

Window 9

Location	1,996,754 – 1,996,867
Length	113
Sequences	3
Columns	113
Reading direction	forward
Mean pairwise identity	90.56
Mean single sequence MFE	-24.46
Consensus MFE	-20.34
Energy contribution	-20.23
Covariance contribution	-0.10
Combinations/Pair	1.12
Mean z-score	-3.08
Structure conservation index	0.83
SVM decision value	1.22
SVM RNA-class probability	0.932050
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1996754 113 + 27905053
AAAGAUUCGAAUUCGCUUCAAAUUCAGGCGAAUUUGGUUUGUUUUUACCAAUCGAAUUCGCUUCACAUACAGUCGAAUUCGAUUUGAUUUUACUUUAUUACACGAGUCAAAUU
......(((((((((((........((((((((((((((.((....)).)))))))))))))).......)).)))))))))((((((((.............)))))))).. ( -31.98)
>DroSec_CAF1 145894 112 + 1
AACCAUUCGAAUUCGCUUCACAUACAGGCAAAUUCUGUUUAAUUUUACCAAUCGAACUCGCUUCACAUAUAGUCGA-UUCGGUUUGAUUUUACAUUAUUACACGAGUUAAAUU
....(((((((((.((((.......)))).)))))(((..((((..(((((((((.((............))))))-)).)))..))))..))).........))))...... ( -20.10)
>DroSim_CAF1 151098 113 + 1
AACCAUUCGAAUUCGCUUCACAUACAGGCAAAUUCUGUUUAAUUUUACCAAUCGAAUUCGCUUCACAUAUAGUCGAAUUCGGUUUUAUUUUACAUUAUUACACGAGUUAAAUU
....(((((((((.((((.......)))).)))))(((..(((......(((((((((((((........)).)))))))))))..)))..))).........))))...... ( -21.30)
>consensus
AACCAUUCGAAUUCGCUUCACAUACAGGCAAAUUCUGUUUAAUUUUACCAAUCGAAUUCGCUUCACAUAUAGUCGAAUUCGGUUUGAUUUUACAUUAUUACACGAGUUAAAUU
....(((((((((.((((.......)))).)))))(((..((((.....(((((((((((((........)).))))))))))).))))..))).........))))...... (-20.34 = -20.23 +  -0.10)

alignment

secondary structure

dotplot

Window 0

Location	1,996,794 – 1,996,903
Length	109
Sequences	3
Columns	113
Reading direction	forward
Mean pairwise identity	81.68
Mean single sequence MFE	-15.60
Consensus MFE	-14.49
Energy contribution	-14.60
Covariance contribution	0.11
Combinations/Pair	1.06
Mean z-score	-0.99
Structure conservation index	0.93
SVM decision value	0.87
SVM RNA-class probability	0.871468
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1996794 109 + 27905053
GUUUUUACCAAUCGAAUUCGCUUCACAUACAGUCGAAUUCGAUUUGAUUUUACUUUAUUACACGAGUCAAAUUACGUGCAUAUAUAUA----GACCUCCUUCGACCAUAUAUA
.........(((((((((((((........)).)))))))))))((((((.((((........)))).)))))).....((((((...----((......))....)))))). ( -18.10)
>DroSec_CAF1 145934 102 + 1
AAUUUUACCAAUCGAACUCGCUUCACAUAUAGUCGA-UUCGGUUUGAUUUUACAUUAUUACACGAGUUAAAUUACGUGCGUACUUAUA--------UCCUUUGACUAU--UUA
.........((((((((.((..((((.....)).))-..))))))))))...............(((((((..(..((......))..--------)..)))))))..--... ( -12.50)
>DroSim_CAF1 151138 107 + 1
AAUUUUACCAAUCGAAUUCGCUUCACAUAUAGUCGAAUUCGGUUUUAUUUUACAUUAUUACACGAGUUAAAUUACGUGCGUACUUAUAUUUAUUUAUCCUUUGACU------A
.........(((((((((((((........)).)))))))))))....................(((((((.((.(((.(((....))).))).))...)))))))------. ( -16.20)
>consensus
AAUUUUACCAAUCGAAUUCGCUUCACAUAUAGUCGAAUUCGGUUUGAUUUUACAUUAUUACACGAGUUAAAUUACGUGCGUACUUAUA________UCCUUUGACUAU___UA
.........(((((((((((((........)).)))))))))))................((((..........))))................................... (-14.49 = -14.60 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:34 2006