Locus 3186

Sequence ID	2R_DroMel_CAF1
Location	10,882,167 – 10,882,306
Length	139
Max. P	0.996718

overview

Window 3

Location	10,882,167 – 10,882,267
Length	100
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	86.32
Mean single sequence MFE	-26.92
Consensus MFE	-21.29
Energy contribution	-21.97
Covariance contribution	0.68
Combinations/Pair	1.07
Mean z-score	-2.88
Structure conservation index	0.79
SVM decision value	2.44
SVM RNA-class probability	0.994000
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10882167 100 - 20766785
UGUUUGUUGGAUUAGUUAUCUUUGGAAACAAAUAGUGAUUUGUCACUGGAAACAGGGUGAAGUUAGGU----------AAAACUGGCAAAACUUUUAAAA-------ACUCAACGGA
..((((((((((.((((((.((((....))))..)))))).))).(((....)))(((...(((((..----------....)))))...))).......-------...))))))) ( -25.30)
>DroSec_CAF1 13794 100 - 1
UGUUUGUUGGAUAAGUUAUCUUUGGAAACAAAUAGUGAUUUGUCACUGGAAACAGGGUGAAGGUAGGU----------GAAACUGGCAAAACUUUUAAAA-------ACUCAACGGA
..(((((((((((((((((.((((....))))..)))))))))).(((....)))(((...(.(((..----------....))).)...))).......-------...))))))) ( -26.90)
>DroSim_CAF1 10410 100 - 1
UGUUUGUUGGAUAAGUUAUCUUUGGAAACAAAUAGUGAUUUGUCACUGGAAACAGGGUGAAGGUAGGU----------GAAACUGGCAAAACUUUUAAAA-------ACUCAACGGA
..(((((((((((((((((.((((....))))..)))))))))).(((....)))(((...(.(((..----------....))).)...))).......-------...))))))) ( -26.90)
>DroEre_CAF1 10514 107 - 1
UGUUUGUUGGAUAAGUUAUCUUUGGAAACAAAUAGUGAUUUGUCACUGGAAACAGGGUGAAGAUAGGU----------GAAACUGGGAAAACUUACAAAACGAAUACGUUCAACGGA
((((((((...((((((.((((((....))).((((.(((((((.(((....)))......)))))))----------...))))))).))))))...))))))))((.....)).. ( -26.80)
>DroYak_CAF1 14485 115 - 1
UGUUUGUUGGAUAAGUCAUCUUUGGAAACAAAUAGUGAUUUGUCACUGGAAACGGGGUGAAGAUAGGUGAAGUUGGGUGAAACUGGGAAAACUUUCAAAACGGAUACAUUAAACU--
((((((((.((((((((((.((((....))))..)))))))))).(((....)))..(((((........((((......))))........))))).)))))))).........-- ( -28.69)
>consensus
UGUUUGUUGGAUAAGUUAUCUUUGGAAACAAAUAGUGAUUUGUCACUGGAAACAGGGUGAAGAUAGGU__________GAAACUGGCAAAACUUUUAAAA_______ACUCAACGGA
..(((((((((((((((((.((((....))))..)))))))))).(((....)))(((.....(((................))).....))).................))))))) (-21.29 = -21.97 +   0.68)

alignment

secondary structure

dotplot

Window 4

Location	10,882,198 – 10,882,306
Length	108
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	94.29
Mean single sequence MFE	-27.38
Consensus MFE	-26.54
Energy contribution	-26.42
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-1.72
Structure conservation index	0.97
SVM decision value	2.74
SVM RNA-class probability	0.996718
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10882198 108 - 20766785
UAACAAACUUUGCAGGUGGUUCAGUUCUUAGGUGUUACUUGUUUGUUGGAUUAGUUAUCUUUGGAAACAAAUAGUGAUUUGUCACUGGAAACAGGGUGAAGUUAGGU----------A
...(.(((((..(..((..((((((...((((.....)))).......(((.((((((.((((....))))..)))))).))))))))).))...)..))))).)..----------. ( -24.90)
>DroSec_CAF1 13825 108 - 1
UAACAAACUUUGCAGGUGGUUCAGUUCUUAGGUGUUACUUGUUUGUUGGAUAAGUUAUCUUUGGAAACAAAUAGUGAUUUGUCACUGGAAACAGGGUGAAGGUAGGU----------G
..((..(((((((((((((..(.........)..))))))))......((((((((((.((((....))))..)))))))))).(((....)))....)))))..))----------. ( -27.00)
>DroSim_CAF1 10441 108 - 1
UAACAAACUUUGCAGGUGGUUCAGUUCUUAGGUGUUACUUGUUUGUUGGAUAAGUUAUCUUUGGAAACAAAUAGUGAUUUGUCACUGGAAACAGGGUGAAGGUAGGU----------G
..((..(((((((((((((..(.........)..))))))))......((((((((((.((((....))))..)))))))))).(((....)))....)))))..))----------. ( -27.00)
>DroEre_CAF1 10552 108 - 1
UAACAAACUUUGCAGGUGGUUCAGUUCUUAGGUGUUACUUGUUUGUUGGAUAAGUUAUCUUUGGAAACAAAUAGUGAUUUGUCACUGGAAACAGGGUGAAGAUAGGU----------G
((((((.....((((((((..(.........)..))))))))))))))((((((((((.((((....))))..)))))))))).(((....))).............----------. ( -26.50)
>DroYak_CAF1 14521 118 - 1
UAACAAACUUUGCAGGUGGUUCAGUUCUUAGGUGUUACUUGUUUGUUGGAUAAGUCAUCUUUGGAAACAAAUAGUGAUUUGUCACUGGAAACGGGGUGAAGAUAGGUGAAGUUGGGUG
..((.(((((..(..((..((((.(((..(((.....)))((((.(..((((((((((.((((....))))..))))))))))...).))))))).)))).))..)..)))))..)). ( -31.50)
>consensus
UAACAAACUUUGCAGGUGGUUCAGUUCUUAGGUGUUACUUGUUUGUUGGAUAAGUUAUCUUUGGAAACAAAUAGUGAUUUGUCACUGGAAACAGGGUGAAGAUAGGU__________G
((((((.....((((((((..(.........)..))))))))))))))((((((((((.((((....))))..)))))))))).(((....)))........................ (-26.54 = -26.42 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:33 2006