Locus 1264

Sequence ID	2L_DroMel_CAF1
Location	3,363,971 – 3,364,079
Length	108
Max. P	0.888869

overview

Window 8

Location	3,363,971 – 3,364,079
Length	108
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	80.86
Mean single sequence MFE	-42.74
Consensus MFE	-27.80
Energy contribution	-29.05
Covariance contribution	1.25
Combinations/Pair	1.29
Mean z-score	-2.29
Structure conservation index	0.65
SVM decision value	0.86
SVM RNA-class probability	0.869573
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3363971 108 + 22407834
AACUGGCACUGGCCAGCGAUUGAGCGGCU---UCUGCCGCUGCUACGGCGGCCGAGUUAGAAGCCGUGCUAACCUUCUUCUCCGCACUCAUCUUGUCGCUGCCACUGCCGC
....((((.((((.((((((.((..((((---(((((((((((....)))).)).).))))))))((((..............))))...))..)))))))))).)))).. ( -50.74)
>DroSec_CAF1 54694 108 + 1
AACUGGCACUGGCCAGCGUUUGAGCGGCU---GCUGCCGCUGCUACUGCGGCCGAGUUCGAAGCCGUGCUAACCUUCUUCGCCGCACUCAUCUUGUCGCUGCCACUGCCGC
....((((.((((.((((....((((((.---...)))))).....((((((.(((.....(((...)))......))).))))))..........)))))))).)))).. ( -45.20)
>DroSim_CAF1 50748 108 + 1
AACUGGCACUGGCCAGCGUUUGAGCGGCU---GCUGCCGCUGCUACAGCGGCCGAGUUCGAAGCCGUGCUAACCUUCUUCUCUGCGCUCAUCUUGUCGCUGCCACUGCCGC
....((((.((((.((((..(((((((((---((((.........))))))))(((...((((..((....))))))..)))...)))))......)))))))).)))).. ( -47.10)
>DroEre_CAF1 49155 108 + 1
AACUGGCACUGGCCUGUGAUUGGGCGGCU---GCUGCAGCCGCCACUGCGGCCGAGUUAGAAACCGUGCUAACCUUCUUCUCCGCACUCAUCUUGUCGCUGCCACUGCCGC
....((((.((((..(((((..(((((((---(...))))))))..(((((..(((((((........)))))..))....)))))........))))).)))).)))).. ( -44.80)
>DroYak_CAF1 50395 108 + 1
AACUGGCACUGGCCUGUGAUUGGGCUGCU---GUUGCAGCCGCCACUGCGGCCGAGUUAGAAACCGUACUAACCUUCUUCUCCGCACUCAUUUUGUCGCUGCCACUGCCGC
....((((.((((..(((((..((((((.---...)))))).....(((((..(((((((........)))))..))....)))))........))))).)))).)))).. ( -41.00)
>DroAna_CAF1 58832 111 + 1
AAGUGCCAGCUACGUGGGACACUGAGGCCGUCCCGGCCGUCGCUGCUGCCCCUGAACUGGAAACCGUACUUAUUUUCUUUUCUGCACUCUUCUUAUCGCUGCCACCUGCAG
..(((.((((..((.(((.((.((((((((...))))).))).))...))).)).((.(....).))..............................)))).)))...... ( -27.60)
>consensus
AACUGGCACUGGCCAGCGAUUGAGCGGCU___GCUGCCGCCGCUACUGCGGCCGAGUUAGAAACCGUGCUAACCUUCUUCUCCGCACUCAUCUUGUCGCUGCCACUGCCGC
...(((((.((((..(((((..((((((.......))))))......((((..(((((((........)))))..))....)))).........))))).)))).))))). (-27.80 = -29.05 +   1.25)

alignment

secondary structure

dotplot

Window 9

Location	3,363,971 – 3,364,079
Length	108
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	80.86
Mean single sequence MFE	-45.43
Consensus MFE	-33.47
Energy contribution	-33.14
Covariance contribution	-0.33
Combinations/Pair	1.38
Mean z-score	-2.12
Structure conservation index	0.74
SVM decision value	0.95
SVM RNA-class probability	0.888869
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3363971 108 - 22407834
GCGGCAGUGGCAGCGACAAGAUGAGUGCGGAGAAGAAGGUUAGCACGGCUUCUAACUCGGCCGCCGUAGCAGCGGCAGA---AGCCGCUCAAUCGCUGGCCAGUGCCAGUU
..((((.(((((((((........((((..............))))(((((((......(((((.......))))))))---))))......))))).)))).)))).... ( -48.14)
>DroSec_CAF1 54694 108 - 1
GCGGCAGUGGCAGCGACAAGAUGAGUGCGGCGAAGAAGGUUAGCACGGCUUCGAACUCGGCCGCAGUAGCAGCGGCAGC---AGCCGCUCAAACGCUGGCCAGUGCCAGUU
..((((.((((((((........(.((((((((((..(.......)..))))(....).)))))).).(.((((((...---.)))))))...)))).)))).)))).... ( -49.80)
>DroSim_CAF1 50748 108 - 1
GCGGCAGUGGCAGCGACAAGAUGAGCGCAGAGAAGAAGGUUAGCACGGCUUCGAACUCGGCCGCUGUAGCAGCGGCAGC---AGCCGCUCAAACGCUGGCCAGUGCCAGUU
..((((.((((((((......(((((((.(((..((((.(......).))))...))).(((((((...)))))))...---.).))))))..)))).)))).)))).... ( -49.50)
>DroEre_CAF1 49155 108 - 1
GCGGCAGUGGCAGCGACAAGAUGAGUGCGGAGAAGAAGGUUAGCACGGUUUCUAACUCGGCCGCAGUGGCGGCUGCAGC---AGCCGCCCAAUCACAGGCCAGUGCCAGUU
..((((.((((.(((......(((((....(((((..(.......)..))))).)))))..))).(.((((((((...)---))))))))........)))).)))).... ( -44.90)
>DroYak_CAF1 50395 108 - 1
GCGGCAGUGGCAGCGACAAAAUGAGUGCGGAGAAGAAGGUUAGUACGGUUUCUAACUCGGCCGCAGUGGCGGCUGCAAC---AGCAGCCCAAUCACAGGCCAGUGCCAGUU
..((((.((((..............(((((....((..(((((........)))))))..)))))((((.((((((...---.))))))...))))..)))).)))).... ( -44.00)
>DroAna_CAF1 58832 111 - 1
CUGCAGGUGGCAGCGAUAAGAAGAGUGCAGAAAAGAAAAUAAGUACGGUUUCCAGUUCAGGGGCAGCAGCGACGGCCGGGACGGCCUCAGUGUCCCACGUAGCUGGCACUU
....(((((.((((((...((((.((((..............))))..))))....)).((((((.(...((.(((((...))))))).))))))).....)))).))))) ( -36.24)
>consensus
GCGGCAGUGGCAGCGACAAGAUGAGUGCGGAGAAGAAGGUUAGCACGGCUUCUAACUCGGCCGCAGUAGCAGCGGCAGC___AGCCGCUCAAUCGCAGGCCAGUGCCAGUU
..((((.((((.((.((.......((((..............))))((((........))))...)).))((((((.......)))))).........)))).)))).... (-33.47 = -33.14 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:07 2006