Locus 6470

Sequence ID	2L_DroMel_CAF1
Location	18,182,608 – 18,182,742
Length	134
Max. P	0.994739

overview

Window 8

Location	18,182,608 – 18,182,715
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	93.46
Mean single sequence MFE	-29.98
Consensus MFE	-25.24
Energy contribution	-25.84
Covariance contribution	0.60
Combinations/Pair	1.10
Mean z-score	-2.11
Structure conservation index	0.84
SVM decision value	2.08
SVM RNA-class probability	0.987392
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18182608 107 + 22407834
AGGGGGCACAAGGUGCCGGCAGAUCCCUUCUGCCCACCAGAACCCCAAAGUCACCCAAAACCCCCGCAGAACGGGCACUUAAGUACACAACUACCCUCUCCAGAGUU
.((((......((((..((((((.....))))))))))....))))................((((.....))))....................(((....))).. ( -29.70)
>DroSec_CAF1 25365 107 + 1
AGAGGGCACAAGGUGCCGGCAGAUCCCUUCUGCCCACCAGAACCCCAAAGUCACCCAAAACCCCCGCAGAACGGGCACUUAAGUACACAACCACCCUCUGCAGAGUU
((((((.....((((..((((((.....))))))))))........................((((.....))))..................))))))........ ( -30.40)
>DroSim_CAF1 26005 107 + 1
AGAGGGCACAAGGUGCCGGCAGAUCCCUUCUGCCCACCAGAACCCCAAAGUCACCCAAAACCCCCGCAGAACGGGCACUUAAGUACACAACCACCCUCUGCAGAGUU
((((((.....((((..((((((.....))))))))))........................((((.....))))..................))))))........ ( -30.40)
>DroEre_CAF1 25465 106 + 1
AGAGGGCACAAGGUGCCAGCAGU-CCCUUCUGCCCGCCAGAGCCCCAAAGUCGCCCAAAACUCCCGCAGAACGGGCACUUAAGUACUCAACUACCCUCUCCAGAAUU
((((((.....((((...((((.-.....)))).)))).(((..(..((((.((((................))))))))..)..))).....))))))........ ( -31.69)
>DroYak_CAF1 25398 107 + 1
AGAGGGCACAAGGUGCCAGCAGUUCCCUUCUGCCCGCCAGAGCCCCAAAGUCACCCAAAACUGCCGCAGAACGGGCACUUAAGUACACAACUACCCUCUCCAGAGCU
((((((......((((....(((.(((((((((..((....)).....(((........)))...)))))).))).)))...)))).......))))))........ ( -27.72)
>consensus
AGAGGGCACAAGGUGCCGGCAGAUCCCUUCUGCCCACCAGAACCCCAAAGUCACCCAAAACCCCCGCAGAACGGGCACUUAAGUACACAACUACCCUCUCCAGAGUU
((((((.....((((..((((((.....))))))))))........................((((.....))))..................))))))........ (-25.24 = -25.84 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	18,182,608 – 18,182,715
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	93.46
Mean single sequence MFE	-44.48
Consensus MFE	-37.90
Energy contribution	-36.94
Covariance contribution	-0.96
Combinations/Pair	1.19
Mean z-score	-2.23
Structure conservation index	0.85
SVM decision value	2.51
SVM RNA-class probability	0.994739
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18182608 107 - 22407834
AACUCUGGAGAGGGUAGUUGUGUACUUAAGUGCCCGUUCUGCGGGGGUUUUGGGUGACUUUGGGGUUCUGGUGGGCAGAAGGGAUCUGCCGGCACCUUGUGCCCCCU
..(((((.((((((((.(((......))).)))))..))).))))).....((....))..(((((...((((((((((.....))))))..))))....))))).. ( -44.90)
>DroSec_CAF1 25365 107 - 1
AACUCUGCAGAGGGUGGUUGUGUACUUAAGUGCCCGUUCUGCGGGGGUUUUGGGUGACUUUGGGGUUCUGGUGGGCAGAAGGGAUCUGCCGGCACCUUGUGCCCUCU
..((((((((((((((.(((......))).)))))..))))))))).....((....))..(((((...((((((((((.....))))))..))))....))))).. ( -45.90)
>DroSim_CAF1 26005 107 - 1
AACUCUGCAGAGGGUGGUUGUGUACUUAAGUGCCCGUUCUGCGGGGGUUUUGGGUGACUUUGGGGUUCUGGUGGGCAGAAGGGAUCUGCCGGCACCUUGUGCCCUCU
..((((((((((((((.(((......))).)))))..))))))))).....((....))..(((((...((((((((((.....))))))..))))....))))).. ( -45.90)
>DroEre_CAF1 25465 106 - 1
AAUUCUGGAGAGGGUAGUUGAGUACUUAAGUGCCCGUUCUGCGGGAGUUUUGGGCGACUUUGGGGCUCUGGCGGGCAGAAGGG-ACUGCUGGCACCUUGUGCCCUCU
......((((.(((((.((((....)))).))))).))))((.(((((((..((....))..))))))).))(((((.((((.-.(.....)..)))).)))))... ( -45.20)
>DroYak_CAF1 25398 107 - 1
AGCUCUGGAGAGGGUAGUUGUGUACUUAAGUGCCCGUUCUGCGGCAGUUUUGGGUGACUUUGGGGCUCUGGCGGGCAGAAGGGAACUGCUGGCACCUUGUGCCCUCU
(((((..(((.(((((.(((......))).)))))(..(.((....))...)..)..)))..)))))..((.(((((.((((...(....)...)))).))))).)) ( -40.50)
>consensus
AACUCUGGAGAGGGUAGUUGUGUACUUAAGUGCCCGUUCUGCGGGGGUUUUGGGUGACUUUGGGGUUCUGGUGGGCAGAAGGGAUCUGCCGGCACCUUGUGCCCUCU
..(((((.((((((((.(((......))).)))))..))).))))).....((....))..(((((.(..((.(((((.......))))).)).....).))))).. (-37.90 = -36.94 +  -0.96)

alignment

secondary structure

dotplot

Window 0

Location	18,182,641 – 18,182,742
Length	101
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	76.99
Mean single sequence MFE	-38.71
Consensus MFE	-23.91
Energy contribution	-24.37
Covariance contribution	0.46
Combinations/Pair	1.35
Mean z-score	-2.66
Structure conservation index	0.62
SVM decision value	2.08
SVM RNA-class probability	0.987467
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18182641 101 - 22407834
CCCAGUGUUUGAAGGGAAUCCGUCC--AGAACUCUGGAGAGGGUAGUUGUGUACUUAAGUGCCCGUUCUGCGGGGG-UUUUGGGUGACUUUGGGGUUCUGGUGG
.((((..(((.((((.....(..((--((((((((.(((((((((.(((......))).)))))..))).).))))-))))))..).)))).)))..))))... ( -37.40)
>DroPse_CAF1 27639 81 - 1
------------GGGGAAA-UAUGGUGGGAGGGCAAGGCAAGGCAGUUAUGUACUUAAGUGCCCUUGCUGUGGGCGGCACCGUGUG-CUUUGUGC---------
------------((((..(-((((((..(((((((.......(((....))).......)))))))((((....))))))))))).-))))....--------- ( -26.74)
>DroSec_CAF1 25398 101 - 1
ACCAGUGCUUGAAGGGAAUCCGUCC--AGAACUCUGCAGAGGGUGGUUGUGUACUUAAGUGCCCGUUCUGCGGGGG-UUUUGGGUGACUUUGGGGUUCUGGUGG
(((((.((((.((((.....(..((--((((((((((((((((((.(((......))).)))))..))))).))))-))))))..).)))).)))).))))).. ( -44.60)
>DroSim_CAF1 26038 101 - 1
CCCAGUGCUUGAAGGGAAUCCGUCC--AAAACUCUGCAGAGGGUGGUUGUGUACUUAAGUGCCCGUUCUGCGGGGG-UUUUGGGUGACUUUGGGGUUCUGGUGG
.((((.((((.((((.....(..((--((((((((((((((((((.(((......))).)))))..))))).))))-))))))..).)))).)))).))))... ( -43.00)
>DroEre_CAF1 25497 101 - 1
CCCAGUGCUUGAAGGGAAACCGUCG--AGAAUUCUGGAGAGGGUAGUUGAGUACUUAAGUGCCCGUUCUGCGGGAG-UUUUGGGCGACUUUGGGGCUCUGGCGG
.((((..(((((.((....)).)))--))....))))...(((((.((((....)))).)))))...((((.((((-(((..((....))..))))))).)))) ( -44.20)
>DroYak_CAF1 25431 101 - 1
CCCAGUGUUUGAAGGGAAACCGUGG--AGAGCUCUGGAGAGGGUAGUUGUGUACUUAAGUGCCCGUUCUGCGGCAG-UUUUGGGUGACUUUGGGGCUCUGGCGG
(((((.((((.((((...(((....--(((((((((.((((((((.(((......))).)))))..))).))).))-)))).)))..)))).)))).)))).). ( -36.30)
>consensus
CCCAGUGCUUGAAGGGAAACCGUCC__AGAACUCUGGAGAGGGUAGUUGUGUACUUAAGUGCCCGUUCUGCGGGGG_UUUUGGGUGACUUUGGGGUUCUGGUGG
.((((.((((.((((....(((.........(((((.((((((((.(((......))).)))))..))).))))).....)))....)))).)))).))))... (-23.91 = -24.37 +   0.46)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:00 2006