Locus 776

Sequence ID	2R_DroMel_CAF1
Location	3,738,612 – 3,738,772
Length	160
Max. P	0.961482

overview

Window 7

Location	3,738,612 – 3,738,732
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.56
Mean single sequence MFE	-30.40
Consensus MFE	-29.23
Energy contribution	-28.13
Covariance contribution	-1.10
Combinations/Pair	1.13
Mean z-score	-2.42
Structure conservation index	0.96
SVM decision value	1.53
SVM RNA-class probability	0.961482
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3738612 120 + 20766785
CGAAUAACUCUAUUGUAAGCAGGAGAAUUUGUCUGUGGGAAAAUCAGUGCCAGAGUUUUUGAAUUUUUGGCAAGUUAAUUUGUUAAAUGACAAUUAAAUAUGCCAAAGUCCCAAAGACAA
.......((((..((....))))))...((((((.(((((...((((.((....))..))))..((((((((.(((...(((((....)))))...))).))))))))))))).)))))) ( -31.60)
>DroSim_CAF1 1375 120 + 1
CGAAUAACUCUAUUGUAAGCAGGGGAAUUUGUCUGUGGGAAAAUCAGUGCCAGAGUUUUUGAAUUUUUGGCAAGUUAAUUUGUUAAAUGACAAUUAAAUAUGCCGGAGACCCAAAGACAA
........(((.(((....))).)))..((((((.((((....((((.((....))..)))).(((((((((.(((...(((((....)))))...))).))))))))))))).)))))) ( -30.30)
>DroYak_CAF1 1364 120 + 1
CGAAUAAUUCUAUUGUAAGCAGGGGAAUUUGUCUGUGGGAAAAUCAGUGCCGGAGUUUUUGAAUUUUUGGCAAAUUAAUUUGUUAAAUGACAAUUAAAUAUGCCGGAGUUCCAAAGACAA
.....((((((.(((....))).))))))(((((.(((((...((((.((....))..))))..((((((((.(((...(((((....)))))...))).))))))))))))).))))). ( -29.30)
>consensus
CGAAUAACUCUAUUGUAAGCAGGGGAAUUUGUCUGUGGGAAAAUCAGUGCCAGAGUUUUUGAAUUUUUGGCAAGUUAAUUUGUUAAAUGACAAUUAAAUAUGCCGGAGUCCCAAAGACAA
........(((.(((....))).)))..((((((.((((....((((.((....))..))))..((((((((.(((...(((((....)))))...))).)))))))).)))).)))))) (-29.23 = -28.13 +  -1.10)

alignment

secondary structure

dotplot

Window 8

Location	3,738,612 – 3,738,732
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	95.56
Mean single sequence MFE	-22.75
Consensus MFE	-19.58
Energy contribution	-19.70
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.22
Structure conservation index	0.86
SVM decision value	0.37
SVM RNA-class probability	0.708905
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3738612 120 - 20766785
UUGUCUUUGGGACUUUGGCAUAUUUAAUUGUCAUUUAACAAAUUAACUUGCCAAAAAUUCAAAAACUCUGGCACUGAUUUUCCCACAGACAAAUUCUCCUGCUUACAAUAGAGUUAUUCG
.(((((.(((((...(((((........)))))......((((((...(((((...............))))).))))))))))).)))))((((((..((....))..))))))..... ( -26.96)
>DroSim_CAF1 1375 120 - 1
UUGUCUUUGGGUCUCCGGCAUAUUUAAUUGUCAUUUAACAAAUUAACUUGCCAAAAAUUCAAAAACUCUGGCACUGAUUUUCCCACAGACAAAUUCCCCUGCUUACAAUAGAGUUAUUCG
((((((.((((.....((((........)))).......((((((...(((((...............))))).)))))).)))).))))))........((((......))))...... ( -22.96)
>DroYak_CAF1 1364 120 - 1
UUGUCUUUGGAACUCCGGCAUAUUUAAUUGUCAUUUAACAAAUUAAUUUGCCAAAAAUUCAAAAACUCCGGCACUGAUUUUCCCACAGACAAAUUCCCCUGCUUACAAUAGAAUUAUUCG
((((((.(((......((((........)))).......((((((...((((.................)))).))))))..))).))))))............................ ( -18.33)
>consensus
UUGUCUUUGGGACUCCGGCAUAUUUAAUUGUCAUUUAACAAAUUAACUUGCCAAAAAUUCAAAAACUCUGGCACUGAUUUUCCCACAGACAAAUUCCCCUGCUUACAAUAGAGUUAUUCG
.(((((.((((.....((((........)))).......((((((...((((.................)))).)))))).)))).)))))(((((...((....))...)))))..... (-19.58 = -19.70 +   0.11)

alignment

secondary structure

dotplot

Window 9

Location	3,738,652 – 3,738,772
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	94.44
Mean single sequence MFE	-29.33
Consensus MFE	-28.96
Energy contribution	-28.30
Covariance contribution	-0.66
Combinations/Pair	1.09
Mean z-score	-2.17
Structure conservation index	0.99
SVM decision value	1.49
SVM RNA-class probability	0.958464
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3738652 120 + 20766785
AAAUCAGUGCCAGAGUUUUUGAAUUUUUGGCAAGUUAAUUUGUUAAAUGACAAUUAAAUAUGCCAAAGUCCCAAAGACAAAGAACUAAGGGGGCGCUAAGACGAAUUCUGUUAAUAACGC
.....((((((..(((((((.....(((((((.(((...(((((....)))))...))).)))))))(((.....))).))))))).....))))))..((((.....))))........ ( -29.60)
>DroSim_CAF1 1415 120 + 1
AAAUCAGUGCCAGAGUUUUUGAAUUUUUGGCAAGUUAAUUUGUUAAAUGACAAUUAAAUAUGCCGGAGACCCAAAGACAAAGCACUAAGGGGGCGCUAAGACGAUUUCUGUUAAUAAUGC
.....(((((....(((((((..(((((((((.(((...(((((....)))))...))).)))))))))..)))))))...))))).((..(.((......)).)..))........... ( -30.30)
>DroYak_CAF1 1404 120 + 1
AAAUCAGUGCCGGAGUUUUUGAAUUUUUGGCAAAUUAAUUUGUUAAAUGACAAUUAAAUAUGCCGGAGUUCCAAAGACAAAGAACUAAGGGGGCGCUAAGACGAUUUCUGUUAAUAAUGG
.....((((((...(((((((...((((((((.(((...(((((....)))))...))).))))))))...)))))))......(....).))))))..((((.....))))........ ( -28.10)
>consensus
AAAUCAGUGCCAGAGUUUUUGAAUUUUUGGCAAGUUAAUUUGUUAAAUGACAAUUAAAUAUGCCGGAGUCCCAAAGACAAAGAACUAAGGGGGCGCUAAGACGAUUUCUGUUAAUAAUGC
.....((((((...(((((((...((((((((.(((...(((((....)))))...))).))))))))...)))))))......(....).))))))..((((.....))))........ (-28.96 = -28.30 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:02 2006