Locus 6

Sequence ID	2R_DroMel_CAF1
Location	847,442 – 847,602
Length	160
Max. P	0.833083

overview

Window 3

Location	847,442 – 847,562
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.53
Mean single sequence MFE	-30.38
Consensus MFE	-21.42
Energy contribution	-22.05
Covariance contribution	0.63
Combinations/Pair	1.22
Mean z-score	-1.51
Structure conservation index	0.71
SVM decision value	0.06
SVM RNA-class probability	0.561727
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 847442 120 - 20766785
AUUGAAUUAUUUGAUAAGCUUUCUUUGCGCUUUAACGAACGAAUUUUGUUUAUUAAAGACGUAAUUGGGCCAAGUGAAAUCUGCUGCUGGUCAUUUUACGGACACGGAAAAAAAGUAGCU
......(((((((....((((...(((((((((((..(((((...)))))..)))))).)))))..))))))))))).....((((((.....((((.((....)).))))..)))))). ( -29.50)
>DroSim_CAF1 307 120 - 1
AUUGAACUAUUUGAUAAGCUUUCGUUGCGCUUUAAUGAACGAAUUUUGUUCAUUAAAGAUGUAAUUGGACCCAGUGAAAUCUGCUGCUGGUCAUUUUACGGACAUGGAAAAAAAGUAGCU
.......................(((((.(((((((((((((...))))))))))))).(((((...((((((((.......))))..))))...)))))..............))))). ( -30.10)
>DroYak_CAF1 34998 120 - 1
AUUGAACUAUUUGAUAAGCUUUCUUUGCGCUUUAAUGAACGAAUUUUGUUCAUUAAAGACGUAAUUGGACCUAGUGAAAUCUGUUGCUGGUCAUUUUACGGACACGGCAAAAAAGUGGCU
.................(((((.(((((.(((((((((((((...))))))))))))).(((((...((((.((..(......)..))))))...)))))......)))))))))).... ( -35.80)
>DroMoj_CAF1 2387 120 - 1
AUUGAACUGUUCGACAAGCUAUCGUUGCGCUUCAACGAACGAAUACUUUUUAUUAAGGACGUCAUCGGUCCAAGUGAGAUCUGUUGCUGGUCCUUCUAUGGUCAUGGCAAGAAAGUAGCG
.......((((((..((((.........))))...))))))..((((((((.....((((.......)))).............((((((.((......)).).)))))))))))))... ( -26.10)
>consensus
AUUGAACUAUUUGAUAAGCUUUCGUUGCGCUUUAACGAACGAAUUUUGUUCAUUAAAGACGUAAUUGGACCAAGUGAAAUCUGCUGCUGGUCAUUUUACGGACACGGAAAAAAAGUAGCU
............(((..((((((((((((((((((((((((.....)))))))))))).))))).))))...)))...))).((((((.(((........)))..........)))))). (-21.42 = -22.05 +   0.63)

alignment

secondary structure

dotplot

Window 4

Location	847,482 – 847,602
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.39
Mean single sequence MFE	-25.65
Consensus MFE	-18.36
Energy contribution	-17.80
Covariance contribution	-0.56
Combinations/Pair	1.24
Mean z-score	-1.65
Structure conservation index	0.72
SVM decision value	0.24
SVM RNA-class probability	0.649255
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 847482 120 + 20766785
AUUUCACUUGGCCCAAUUACGUCUUUAAUAAACAAAAUUCGUUCGUUAAAGCGCAAAGAAAGCUUAUCAAAUAAUUCAAUAUUUUUUAAUAAGUUGUCGUCUGAUGUACUUGUGUACGAA
...(((..((((.......((.((((((..(((.......)))..)))))))).......(((((((.(((.(((.....))).))).)))))))))))..)))(((((....))))).. ( -21.70)
>DroSim_CAF1 347 120 + 1
AUUUCACUGGGUCCAAUUACAUCUUUAAUGAACAAAAUUCGUUCAUUAAAGCGCAACGAAAGCUUAUCAAAUAGUUCAAUAUUUUUUAAUAAGUUGUCGUCUGAUGUACUUGUGUACGAA
..........((((((.((((((((((((((((.......)))))))))).....((((.(((((((.(((.(((.....))).))).))))))).))))..)))))).))).).))... ( -27.20)
>DroYak_CAF1 35038 120 + 1
AUUUCACUAGGUCCAAUUACGUCUUUAAUGAACAAAAUUCGUUCAUUAAAGCGCAAAGAAAGCUUAUCAAAUAGUUCAAUAUUUUUUAAUAAGUUGUCAUCUGAUGUACUUGUGUAUGAA
....(((.((((.((....((.(((((((((((.......)))))))))))))....((.(((((((.(((.(((.....))).))).))))))).))......)).)))))))...... ( -25.40)
>DroMoj_CAF1 2427 120 + 1
AUCUCACUUGGACCGAUGACGUCCUUAAUAAAAAGUAUUCGUUCGUUGAAGCGCAACGAUAGCUUGUCGAACAGUUCAAUAUUCUUGAGCAAAUUAUCAUCCGAUGUGCUUGUGUACGAG
..(((..(((((..(((((.....................(((((...((((.........))))..))))).((((((.....))))))...))))).))))).((((....))))))) ( -28.30)
>consensus
AUUUCACUUGGUCCAAUUACGUCUUUAAUAAACAAAAUUCGUUCAUUAAAGCGCAAAGAAAGCUUAUCAAAUAGUUCAAUAUUUUUUAAUAAGUUGUCAUCUGAUGUACUUGUGUACGAA
..(((........((....((.(((((((((((.......)))))))))))))....((.(((((((.(((.(((.....))).))).))))))).))...))..((((....))))))) (-18.36 = -17.80 +  -0.56)

alignment

secondary structure

dotplot

Window 5

Location	847,482 – 847,602
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.39
Mean single sequence MFE	-26.28
Consensus MFE	-20.60
Energy contribution	-21.35
Covariance contribution	0.75
Combinations/Pair	1.26
Mean z-score	-1.89
Structure conservation index	0.78
SVM decision value	0.72
SVM RNA-class probability	0.833083
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 847482 120 - 20766785
UUCGUACACAAGUACAUCAGACGACAACUUAUUAAAAAAUAUUGAAUUAUUUGAUAAGCUUUCUUUGCGCUUUAACGAACGAAUUUUGUUUAUUAAAGACGUAAUUGGGCCAAGUGAAAU
...((((....)))).(((.........((((((((.(((.....))).))))))))((((...(((((((((((..(((((...)))))..)))))).)))))..))))....)))... ( -24.70)
>DroSim_CAF1 347 120 - 1
UUCGUACACAAGUACAUCAGACGACAACUUAUUAAAAAAUAUUGAACUAUUUGAUAAGCUUUCGUUGCGCUUUAAUGAACGAAUUUUGUUCAUUAAAGAUGUAAUUGGACCCAGUGAAAU
...((((....))))....(((((...(((((((((.............)))))))))...)))))((((((((((((((((...))))))))))))).))).((((....))))..... ( -28.92)
>DroYak_CAF1 35038 120 - 1
UUCAUACACAAGUACAUCAGAUGACAACUUAUUAAAAAAUAUUGAACUAUUUGAUAAGCUUUCUUUGCGCUUUAAUGAACGAAUUUUGUUCAUUAAAGACGUAAUUGGACCUAGUGAAAU
......(((((((..((((((((......((((....))))......))))))))..))))(((((((((((((((((((((...))))))))))))).)))))..)))....))).... ( -28.80)
>DroMoj_CAF1 2427 120 - 1
CUCGUACACAAGCACAUCGGAUGAUAAUUUGCUCAAGAAUAUUGAACUGUUCGACAAGCUAUCGUUGCGCUUCAACGAACGAAUACUUUUUAUUAAGGACGUCAUCGGUCCAAGUGAGAU
.((((.....(((...((((((((((.(((.....))).)))).....))))))...))).((((((.....)))))))))).....(((((((..((((.......)))).))))))). ( -22.70)
>consensus
UUCGUACACAAGUACAUCAGACGACAACUUAUUAAAAAAUAUUGAACUAUUUGAUAAGCUUUCGUUGCGCUUUAACGAACGAAUUUUGUUCAUUAAAGACGUAAUUGGACCAAGUGAAAU
......(((.(((..((((((((......((((....))))......))))))))..)))(((((((((((((((((((((.....)))))))))))).))))).))))....))).... (-20.60 = -21.35 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:23:13 2006