Locus 1367

Sequence ID	3R_DroMel_CAF1
Location	4,004,318 – 4,004,472
Length	154
Max. P	0.895509

overview

Window 4

Location	4,004,318 – 4,004,432
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.04
Mean single sequence MFE	-38.02
Consensus MFE	-26.50
Energy contribution	-28.12
Covariance contribution	1.62
Combinations/Pair	1.08
Mean z-score	-2.26
Structure conservation index	0.70
SVM decision value	0.99
SVM RNA-class probability	0.895509
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4004318 114 + 27905053
GCGGUG------GGCUGUUCGUGGUGGGUGGUAAUGCACGCCCACGCACUCCGUAAAAUACCAACCAGAGCGGCAACUAUCAGAGGAGCACACCCCCGCCAAAAUACAUUCAUUAAAAAC
((((.(------((.(((((((((((((((........))))))).))).((((...............))))............)))))..)))))))..................... ( -36.86)
>DroSec_CAF1 9914 114 + 1
GCGGUG------GGCCACUCGUGGUGGGUGGUAAUGCACGCCCACGCACUCCGUAAAAUACCAACCAGAGCGGGAACUAUCAGAGGGGCACACCCCCGCCAAAAUACAUUCAUUAAAAAC
((((.(------((((.(((((((((((((........))))))).)))(((((...............)))))........))).)))...)).))))..................... ( -38.16)
>DroSim_CAF1 10490 114 + 1
GCGGUG------GGCCACUCGUGGUGGGUGGUAAUGCACGCCCACGCACUCCGUAAAAUACCAACCAGAGCGGGAACUAUCAGAGGGACACACCCCCGCCAAAAUACAUUCAUUAAAAAC
((((.(------((((.(((((((((((((........))))))).)))(((((...............)))))........))))).....)))))))..................... ( -37.16)
>DroYak_CAF1 9904 105 + 1
GCGGUUUCUGGUGGGUGGUGGUGGUGGGUGGUAAUGCACGCCCACGCACUCCGUAAAACACCAACCAGUGCGGCA---------------AACCCCCGCCAAACUACAUUCAUUAAAAAC
(..(((..(((((((.((((((((((((((........))))))).))))(((((.............)))))..---------------.)))))))))))))..)............. ( -39.92)
>consensus
GCGGUG______GGCCACUCGUGGUGGGUGGUAAUGCACGCCCACGCACUCCGUAAAAUACCAACCAGAGCGGCAACUAUCAGAGGGGCACACCCCCGCCAAAAUACAUUCAUUAAAAAC
..((((.......(((.(((((((((((((........))))))).))).((((...............)))).........))).))).......)))).................... (-26.50 = -28.12 +   1.62)

alignment

secondary structure

dotplot

Window 5

Location	4,004,352 – 4,004,472
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.56
Mean single sequence MFE	-33.58
Consensus MFE	-28.74
Energy contribution	-29.30
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.46
Structure conservation index	0.86
SVM decision value	0.17
SVM RNA-class probability	0.616446
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4004352 120 - 27905053
GUUACCCCUUGAACAUUUGUUCUAAUGUCAUUUCUAAUGCGUUUUUAAUGAAUGUAUUUUGGCGGGGGUGUGCUCCUCUGAUAGUUGCCGCUCUGGUUGGUAUUUUACGGAGUGCGUGGG
...((((((.((((....))))....((((.....(((((((((.....))))))))).))))))))))(..((((...((((.(.(((.....))).).))))....))))..)..... ( -37.70)
>DroSec_CAF1 9948 120 - 1
GUUACCCCUUGAACAUUUGUUCUAAUGUCAUUUCUAAUGCGUUUUUAAUGAAUGUAUUUUGGCGGGGGUGUGCCCCUCUGAUAGUUCCCGCUCUGGUUGGUAUUUUACGGAGUGCGUGGG
..(((((((.((((....))))....((((.....(((((((((.....))))))))).)))))))))))...(((.(.((....)).(((((((............))))))).).))) ( -34.30)
>DroSim_CAF1 10524 120 - 1
GUUACCCCUUGGACAUUUGUUCUAAUGUCAUUUCUAAUGCGUUUUUAAUGAAUGUAUUUUGGCGGGGGUGUGUCCCUCUGAUAGUUCCCGCUCUGGUUGGUAUUUUACGGAGUGCGUGGG
.....(((.((.((.(((((...(((..((...(((((((((((.....))))))))...((((((..(.((((.....)))))..)))))).))).))..)))..))))))).)).))) ( -33.90)
>DroYak_CAF1 9944 105 - 1
GUUACCCCUUGAACAUUUGUUCUAAUGUCAUUUCUAAUGCGUUUUUAAUGAAUGUAGUUUGGCGGGGGUU---------------UGCCGCACUGGUUGGUGUUUUACGGAGUGCGUGGG
((.((((((.((((....))))....((((.......(((((((.....)))))))...)))))))))).---------------.))((((((..(((........))))))))).... ( -28.40)
>consensus
GUUACCCCUUGAACAUUUGUUCUAAUGUCAUUUCUAAUGCGUUUUUAAUGAAUGUAUUUUGGCGGGGGUGUGCCCCUCUGAUAGUUCCCGCUCUGGUUGGUAUUUUACGGAGUGCGUGGG
..(((((((.((((....))))....((((.....(((((((((.....))))))))).)))))))))))..................(((((((............)))))))...... (-28.74 = -29.30 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:18 2006