Locus 6339

Sequence ID	2L_DroMel_CAF1
Location	17,704,624 – 17,704,717
Length	93
Max. P	0.858693

overview

Window 5

Location	17,704,624 – 17,704,717
Length	93
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	80.52
Mean single sequence MFE	-24.35
Consensus MFE	-13.05
Energy contribution	-12.85
Covariance contribution	-0.19
Combinations/Pair	1.10
Mean z-score	-2.11
Structure conservation index	0.54
SVM decision value	0.17
SVM RNA-class probability	0.617526
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17704624 93 + 22407834
UUCUGCAUUCUGCAUUAGUUUUUUUC-AC-AACGCCCUCCUUA--UUCGUGGACUUUC--ACCAAGGGCUUAGCACACACUUGGAAGGCGUGCAAAAAU
...(((.....)))......(((((.-..-.(((((.(((...--...(((..((...--.(....)....))..)))....))).)))))..))))). ( -18.90)
>DroPse_CAF1 32072 95 + 1
UUCUGCAUUUUGCAUUAGUUU-UUUU-UUGUUUUGCCUCUCGC--UUGCUGGCCCUUCCAUCCGAGGGCUUAGCACACACUUGGAAGGCGUGCAAAAAU
...(((.....))).......-.(((-((((..(((((..((.--.(((((((((((......)))))).)))))......))..))))).))))))). ( -29.70)
>DroEre_CAF1 16530 92 + 1
CCCUGCAUUUUGCAUUAGUUU-UUUC-AA-AACGCCCUCCUUA--GUCCUGGACUUUC--ACCAAGGGCUUAGCACACACUUGGAAGGCGUGCAAAAAU
.......((((((((..((((-....-.)-)))(((.(((..(--(((((((......--.)).))))))............))).))))))))))).. ( -24.64)
>DroYak_CAF1 8499 92 + 1
UUCUGCAUUUUGCAUUAGUUU-UUUC-AA-AACGCCCUCCUUA--GUCCUGGACUUUC--ACCAAGGGCUUAGCACACACUUGGAAGGCGUGCAAGAAU
.......((((((((..((((-....-.)-)))(((.(((..(--(((((((......--.)).))))))............))).))))))))))).. ( -24.74)
>DroAna_CAF1 16821 88 + 1
CUCUGCAUUUUGCAUUAGUUU-CC--------CGCCCUGUCUCCCACUUUGGACUUUC--ACCAAGGGCUUAGCACACACUUGGAAGGCGUGCAAAAAU
.......((((((((...(((-((--------.....(((((....((((((......--.))))))....)).))).....)))))..)))))))).. ( -19.90)
>DroPer_CAF1 32589 96 + 1
UUCUGCAUUUUGCAUUAGUUU-UUUUUUUUUUUUGCCUCUCGC--CGGCUGGCCCUUCCAUCCGAGGGCUUAGCACACACUUGGAAGGCGUGCAAAAAU
...(((.....))).......-.......(((((((....(((--(.((((((((((......)))))).)))).((....))...)))).))))))). ( -28.20)
>consensus
UUCUGCAUUUUGCAUUAGUUU_UUUC_AA_AACGCCCUCCCUA__GUCCUGGACUUUC__ACCAAGGGCUUAGCACACACUUGGAAGGCGUGCAAAAAU
.......((((((((..((((..............((.............)).........(((((.((...)).....))))).)))))))))))).. (-13.05 = -12.85 +  -0.19)

alignment

secondary structure

dotplot

Window 6

Location	17,704,624 – 17,704,717
Length	93
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	80.52
Mean single sequence MFE	-27.15
Consensus MFE	-16.59
Energy contribution	-17.26
Covariance contribution	0.67
Combinations/Pair	1.06
Mean z-score	-2.30
Structure conservation index	0.61
SVM decision value	0.82
SVM RNA-class probability	0.858693
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17704624 93 - 22407834
AUUUUUGCACGCCUUCCAAGUGUGUGCUAAGCCCUUGGU--GAAAGUCCACGAA--UAAGGAGGGCGUU-GU-GAAAAAAACUAAUGCAGAAUGCAGAA
.((((..((((((((((...((((..((..(((...)))--...))..))))..--...)))))))).)-).-.)))).......(((.....)))... ( -31.80)
>DroPse_CAF1 32072 95 - 1
AUUUUUGCACGCCUUCCAAGUGUGUGCUAAGCCCUCGGAUGGAAGGGCCAGCAA--GCGAGAGGCAAAACAA-AAAA-AAACUAAUGCAAAAUGCAGAA
.((((((...(((((....((...((((..(((((........))))).)))).--))..)))))....)))-))).-.......(((.....)))... ( -25.20)
>DroEre_CAF1 16530 92 - 1
AUUUUUGCACGCCUUCCAAGUGUGUGCUAAGCCCUUGGU--GAAAGUCCAGGAC--UAAGGAGGGCGUU-UU-GAAA-AAACUAAUGCAAAAUGCAGGG
..(((((((((((((((.(((....))).....((((((--....).)))))..--...)))))))))(-((-....-))).....))))))....... ( -27.40)
>DroYak_CAF1 8499 92 - 1
AUUCUUGCACGCCUUCCAAGUGUGUGCUAAGCCCUUGGU--GAAAGUCCAGGAC--UAAGGAGGGCGUU-UU-GAAA-AAACUAAUGCAAAAUGCAGAA
.(((....(((((((((.(((....))).....((((((--....).)))))..--...))))))))).-..-))).-.......(((.....)))... ( -26.10)
>DroAna_CAF1 16821 88 - 1
AUUUUUGCACGCCUUCCAAGUGUGUGCUAAGCCCUUGGU--GAAAGUCCAAAGUGGGAGACAGGGCG--------GG-AAACUAAUGCAAAAUGCAGAG
......((((((((....)).))))))...(((((((((--....).))))....(....).))))(--------(.-...))..(((.....)))... ( -26.60)
>DroPer_CAF1 32589 96 - 1
AUUUUUGCACGCCUUCCAAGUGUGUGCUAAGCCCUCGGAUGGAAGGGCCAGCCG--GCGAGAGGCAAAAAAAAAAAA-AAACUAAUGCAAAAUGCAGAA
.(((((((...(((((((..((.(.((...)).).))..)))))))(((....)--)).....))))))).......-.......(((.....)))... ( -25.80)
>consensus
AUUUUUGCACGCCUUCCAAGUGUGUGCUAAGCCCUUGGU__GAAAGUCCAGGAA__GAAAGAGGGCGUU_AU_GAAA_AAACUAAUGCAAAAUGCAGAA
......((((((((....)).))))))...((((((........................))))))...................(((.....)))... (-16.59 = -17.26 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:45 2006