Locus 3939

Sequence ID	2R_DroMel_CAF1
Location	13,006,369 – 13,006,529
Length	160
Max. P	0.740625

overview

Window 9

Location	13,006,369 – 13,006,489
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.17
Mean single sequence MFE	-36.62
Consensus MFE	-21.70
Energy contribution	-21.48
Covariance contribution	-0.22
Combinations/Pair	1.40
Mean z-score	-1.43
Structure conservation index	0.59
SVM decision value	-0.01
SVM RNA-class probability	0.527707
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13006369 120 + 20766785
GUAAUCUGGACCUAAGCAAGGUUCCCCAACUGAAGGCCACUUGGCACUUGGCUAACUCCGCCAUUCUGGAGACCAAUGGCACUAAGGUCGGUGUCAUAGGUUAUUUGACUCCAGAUACCA
.......((((((.....))))))........((((((....))).)))(((.......)))..((((((((((.((((((((......)))))))).))).......)))))))..... ( -38.51)
>DroPse_CAF1 14748 120 + 1
GCAAUCUGGAUAUGAGGAAAGUGCCCGAGUUGGCUGCCACCAAACAUUUGGUUCCCUCUACGAUCCUGGAGACCCAGGGCACCAAGAUAGGUGUGAUUGGCUAUUUGACGCCAGAUACUA
...((((((....((((.....(((......)))....(((((....)))))..))))..(((((((((....)))).(((((......))))))))))...........)))))).... ( -36.40)
>DroGri_CAF1 19469 120 + 1
GUAAUUUGGAUCUUACUAAUGAGCCCGAAAUGGCUGCCACUAAGCAUUUGGCCAAUUCGACAAUAAUUGAAACAAAUGGUACUAAAAUUGCUGUAAUCGGAUAUGUGACGCCAGAUACGA
(((.(((((...((((...(((...((((.(((((((......))....))))).))))................((((((.......))))))..))).....))))..)))))))).. ( -22.70)
>DroEre_CAF1 16182 120 + 1
GCAAUCUGGACCUUAGCAAGGUGCCCCAACUGGAGGCCACCAAGCACUUGGCUCACUCCGCCAUCCUGGAGGCCAAUGGCACUAGUAUCGGUGUCAUAGGUUAUUUGACACCGGAUACCA
((....(((.((((.((..((((((((....)).)).))))..))...((((.......)))).....)))))))...))....((((((((((((.........))))))).))))).. ( -44.20)
>DroYak_CAF1 16775 120 + 1
GUAAUCUGGAUCUGAGCAAGGUUCCCCAACUGAAGGCCACCAAGCACUUGGCUCACUCCGCCAUCCUGGAGACCAAUGGCACUAAGAUCGGUGUCAUUGGUUACUUGACCCCGGAUACCA
...((((((...(((((..((....)).....(((((......)).))).)))))(((((......)))))((((((((((((......)))))))))))).........)))))).... ( -39.70)
>DroAna_CAF1 23921 120 + 1
GUAAUCUGGAUCUGAGCAAAGUGCCCGAACUCAAGGCCACAAAGCACUUGGCCCACUCUGCCAUCCUGGAGGCUAAUGGCACCAAGAUCGGUGUGAUUGGCUACCUCACUCCCGACACCA
....((.(((..((((((.((((...(....)..(((((.........))))))))).)))......((.(((((((.(((((......))))).))))))).))))).))).))..... ( -38.20)
>consensus
GUAAUCUGGAUCUGAGCAAGGUGCCCCAACUGAAGGCCACCAAGCACUUGGCUCACUCCGCCAUCCUGGAGACCAAUGGCACUAAGAUCGGUGUCAUUGGUUAUUUGACGCCAGAUACCA
...((((((...........(((((.........(((((.........)))))..(((((......)))))......)))))..........((((.........)))).)))))).... (-21.70 = -21.48 +  -0.22)

alignment

secondary structure

dotplot

Window 0

Location	13,006,409 – 13,006,529
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.56
Mean single sequence MFE	-37.25
Consensus MFE	-27.22
Energy contribution	-28.20
Covariance contribution	0.98
Combinations/Pair	1.31
Mean z-score	-1.96
Structure conservation index	0.73
SVM decision value	0.45
SVM RNA-class probability	0.740625
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13006409 120 + 20766785
UUGGCACUUGGCUAACUCCGCCAUUCUGGAGACCAAUGGCACUAAGGUCGGUGUCAUAGGUUAUUUGACUCCAGAUACCAAAAAACUUACUCUCAACAUGGAUGUGGAGUUCAACGAGGA
......((((...((((((((...((((((((((.((((((((......)))))))).))).......)))))))..(((..................)))..))))))))...)))).. ( -38.68)
>DroSim_CAF1 16466 120 + 1
CAAGCACUUGGCUCACUCCGCCAUCCUUGAGACCAAUGGCACUAAGGUCGGUGUCAUAGGUUAUUUGACACCAGAUACCAAAAAACUUACUCUCAACAUGGAUGUGGAGUUCAACGAAGA
......(((.(...(((((((.((((((((((...((((((((......)))))))).(((.(((((....))))))))...........))))))...)))))))))))....).))). ( -37.80)
>DroEre_CAF1 16222 120 + 1
CAAGCACUUGGCUCACUCCGCCAUCCUGGAGGCCAAUGGCACUAGUAUCGGUGUCAUAGGUUAUUUGACACCGGAUACCAAAAAGCUGACAUUGAACAUGGAUGUGGAAUUUAACGAGGA
......((((......(((((.((((....(..(((((.((((.((((((((((((.........))))))).))))).....)).)).)))))..)..)))))))))......)))).. ( -35.80)
>DroYak_CAF1 16815 120 + 1
CAAGCACUUGGCUCACUCCGCCAUCCUGGAGACCAAUGGCACUAAGAUCGGUGUCAUUGGUUACUUGACCCCGGAUACCAAAAAGCUUACGCUCAACAUGGAUGUGGAGUUUAACGAGGA
......((((....(((((((.(((((((.(((((((((((((......)))))))))))))......(....)...)))...(((....)))......)))))))))))....)))).. ( -42.00)
>DroAna_CAF1 23961 120 + 1
AAAGCACUUGGCCCACUCUGCCAUCCUGGAGGCUAAUGGCACCAAGAUCGGUGUGAUUGGCUACCUCACUCCCGACACCAAGAAACUUACUCUCCAUAUGGAUGUGGACUUUAACGAGGA
......((((......((..(.(((((((((((((((.(((((......))))).))))))....((......))................)))))...)))))..))......)))).. ( -34.10)
>DroPer_CAF1 14734 120 + 1
CAAACAUUUGGUUCCCUCUACGAUCCUGGAGACCCAGGGCACCAAGAUAGGUGUGAUUGGCUAUUUGACGCCAGAUACUAAACAGCUUACCCUCCAGAGUGAGGUGGAGUUCUACGAGGA
..............((((......(((((....)))))(((((......)))))....(((........)))(((.(((...((.(((((.(....).))))).)).))))))..)))). ( -35.10)
>consensus
CAAGCACUUGGCUCACUCCGCCAUCCUGGAGACCAAUGGCACUAAGAUCGGUGUCAUAGGUUAUUUGACACCAGAUACCAAAAAACUUACUCUCAACAUGGAUGUGGAGUUCAACGAGGA
......((((....(((((((.((((..((((((.((((((((......)))))))).)))((((((....))))))..............))).....)))))))))))....)))).. (-27.22 = -28.20 +   0.98)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:49 2006