Locus 9183

Sequence ID	3R_DroMel_CAF1
Location	24,494,899 – 24,495,098
Length	199
Max. P	0.915320

overview

Window 7

Location	24,494,899 – 24,495,018
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.39
Mean single sequence MFE	-25.45
Consensus MFE	-18.55
Energy contribution	-20.55
Covariance contribution	2.00
Combinations/Pair	1.11
Mean z-score	-1.95
Structure conservation index	0.73
SVM decision value	0.65
SVM RNA-class probability	0.811161
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24494899 119 + 27905053
GUUUCUCUUUAAGCUUAUUU-UUCGAUAUCUUCAGUUCUACUUUCAAGCUUGUACCAUGAAGAUGCACGAGCUACGAUAUCUAAUUAUUACUUUGAGCUUGUUCCUAAGUAAGCUCAAGG
......((((.(((((((((-...((((((((((....(((..........)))...)))))))).(((((((.(((...............))))))))))))..))))))))).)))) ( -26.66)
>DroSec_CAF1 37875 120 + 1
UUUUCUAUUUAAGCUUAUUUUUUCAAUAUCUUCAGUUCUACUUUCAAGCUCGUACCAUGAAGAUGCACGAGCUACGAUAUCUAAUUAUUACUUUGAGCUUGUUCCUAAGUGAGCUUAAGG
.......(((((((((((((......((((((((....(((..........)))...)))))))).(((((((.(((...............))))))))))....))))))))))))). ( -27.86)
>DroSim_CAF1 49731 120 + 1
UUUUCUAUUUAAGCUUAUUUUUUCAAUAUCUUCAGUUCUACUUUCAAGCUCGUACCAUGAAGAUGCACGAGCUACGAUAUCUAAUUAUUACUUUGAGUUUGUUCCUAAGUGAGCUUAAGG
.......(((((((((((((....((((..(((((...........(((((((..(((....))).)))))))..((((......))))...)))))..))))...))))))))))))). ( -27.30)
>DroEre_CAF1 44287 120 + 1
GUCUCUCAAUAACCCAAUUGCUCUGCUACCUUCAGUACUUCCUUCAAGCUCAAACCAUGAAGAUGCACGAGCUACGAUAUCUACUUAUUACUCUGAGCCUGUUUCUGAGUGAGCAUAAAG
.((.((((..(((......(((((((...(((((.......................)))))..))).))))...........((((......))))...)))..)))).))........ ( -20.00)
>consensus
GUUUCUAUUUAAGCUUAUUUUUUCAAUAUCUUCAGUUCUACUUUCAAGCUCGUACCAUGAAGAUGCACGAGCUACGAUAUCUAAUUAUUACUUUGAGCUUGUUCCUAAGUGAGCUUAAGG
.......(((((((((((((....((((..(((((...........(((((((..(((....))).)))))))..((((......))))...)))))..))))...))))))))))))). (-18.55 = -20.55 +   2.00)

alignment

secondary structure

dotplot

Window 8

Location	24,494,978 – 24,495,098
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.67
Mean single sequence MFE	-31.93
Consensus MFE	-25.39
Energy contribution	-26.33
Covariance contribution	0.94
Combinations/Pair	1.22
Mean z-score	-2.12
Structure conservation index	0.80
SVM decision value	1.10
SVM RNA-class probability	0.915320
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24494978 120 + 27905053
CUAAUUAUUACUUUGAGCUUGUUCCUAAGUAAGCUCAAGGACGAUAAGAUUCUUUGGUGAACUAAUGUGACAAUCAUUUCUUGCAGCUGUGGGAAAUGUCAAGUCCUUUUGCCAGAUCAC
....(((((.(((((((((((........)))))))))))..)))))((((...(((..((.....(.(((...(((((((..(....)..)))))))....)))).))..))))))).. ( -35.00)
>DroSec_CAF1 37955 120 + 1
CUAAUUAUUACUUUGAGCUUGUUCCUAAGUGAGCUUAAGGACAAUAAGACUCUUUGGCCAACUAAUGUGACAAUCAUUUCUUGCAGCUGUGGGAAAUGCCAAGUCCUUUUGCCAGAUCAC
....(((((.(((((((((..(......)..)))))))))..))))).....((((((..((....))(((...(((((((..(....)..)))))))....))).....)))))).... ( -31.50)
>DroSim_CAF1 49811 120 + 1
CUAAUUAUUACUUUGAGUUUGUUCCUAAGUGAGCUUAAGGACGAUAAGACUCUUUGGCCAACUAAUUUGACAAUCAUUUCUUGCAGCUGUGGGAAAUGUCAAGUCCAUAUGCCAGAUCAC
....(((((.(((((((((..(......)..)))))))))..))))).....((((((......((((((((....(((((..(....)..)))))))))))))......)))))).... ( -32.00)
>DroEre_CAF1 44367 116 + 1
CUACUUAUUACUCUGAGCCUGUUUCUGAGUGAGCAUAAAGACCUCAG----UUCGGGUCAACCAAAGUGACAAUCAUUUCUUGCAGCUGUGGGAAAUGCCAAGUCCUAUUGCCAGAUCAC
.......((((((.(((.....))).))))))(((....(((((...----...)))))......((.(((...(((((((..(....)..)))))))....)))))..)))........ ( -29.20)
>consensus
CUAAUUAUUACUUUGAGCUUGUUCCUAAGUGAGCUUAAGGACGAUAAGACUCUUUGGCCAACUAAUGUGACAAUCAUUUCUUGCAGCUGUGGGAAAUGCCAAGUCCUUUUGCCAGAUCAC
..........((((((((((..(....)..))))))))))............((((((.....((((.(((...(((((((..(....)..)))))))....))))))).)))))).... (-25.39 = -26.33 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:28:23 2006