Locus 8782

Sequence ID	3R_DroMel_CAF1
Location	23,461,999 – 23,462,137
Length	138
Max. P	0.967800

overview

Window 7

Location	23,461,999 – 23,462,110
Length	111
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	77.60
Mean single sequence MFE	-33.24
Consensus MFE	-14.98
Energy contribution	-16.70
Covariance contribution	1.72
Combinations/Pair	1.19
Mean z-score	-2.27
Structure conservation index	0.45
SVM decision value	1.19
SVM RNA-class probability	0.928847
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23461999 111 - 27905053
UACAAUUGGCACUUAAAAAUCAGCUAGACUUGGCGUGAAA------AAAGAGAGCGGGUAGUCCAGCUCCGCUCUCUCGAAACUGACAAGCAGUGCUGCAAAAGGUGCAGGGCUCAG
........((.........(((((((....)))).)))..------..(((((((((((......)).)))))))))............))(((.(((((.....))))).)))... ( -33.60)
>DroSec_CAF1 61411 111 - 1
UACAAUUGGCACUAAAAAAUAAACUAGACUUGUCGGGAAA------AAAGAGAGCGGGUAGUCCAGCUCCGCUCUCUCGAAACUGACAAGCAGUGUUGCAAAAGUUGCAGGGCUAAG
.....(((((............(((.(.((((((((....------..(((((((((((......)).))))))))).....)))))))))))).(((((.....))))).))))). ( -39.00)
>DroSim_CAF1 54092 111 - 1
UACAAUUGGCACUAAAAAAUAAACUAGACUUGGCGGGAAA------AAAGAGAGCGGGUAGUCCAGCUCCGCUCUCUCGAAACUGACAAGCAGUGUUGCAAAAGUUGCAGGGCUAAG
.....(((((............(((.(.((((.(((....------..(((((((((((......)).))))))))).....))).)))))))).(((((.....))))).))))). ( -34.00)
>DroEre_CAF1 52136 117 - 1
UACAACUGGCGCCUUAAAAUCAGCCUGAUUUGGCGGGCAAAUAUGAAAUGAGAACUGGCAGUUCAGCUCCGCUCUCUUGAAAGUGACAAGCAGUGUUGCAAAACGCGCACUGCAUAG
....(((..(((((..(((((.....)))))...))))...........((((..(((.((.....))))).))))..)..))).....(((((((.((.....))))))))).... ( -31.50)
>DroYak_CAF1 52804 100 - 1
UGCAAUUUGCACCUUGAAGUCAGACAGAUUUAGCGGUGAA------AAUGAACACUGGC-----------GCUCUCUCGAAACUGACAAGCAGUGUUGCAAAAGGAGCACUGCAAAG
(((.....))).......(((((...((...(((((((..------......)))...)-----------)))...))....)))))..((((((((.(....).)))))))).... ( -28.10)
>consensus
UACAAUUGGCACUUAAAAAUCAGCUAGACUUGGCGGGAAA______AAAGAGAGCGGGUAGUCCAGCUCCGCUCUCUCGAAACUGACAAGCAGUGUUGCAAAAGGUGCAGGGCUAAG
........((.............((.(......).))............((((((((((......)).)))))))).............)).((.((((.......)))).)).... (-14.98 = -16.70 +   1.72)

alignment

secondary structure

dotplot

Window 8

Location	23,462,036 – 23,462,137
Length	101
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	73.15
Mean single sequence MFE	-27.02
Consensus MFE	-17.90
Energy contribution	-18.77
Covariance contribution	0.88
Combinations/Pair	1.32
Mean z-score	-1.90
Structure conservation index	0.66
SVM decision value	1.62
SVM RNA-class probability	0.967800
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23462036 101 + 27905053
UCGAGAGAGCGGAGCUGGACUACCCGCUCUCUUUUUUCACGCCAAGUCUAGCUGAUUUUUAAGUGCCAAUUGUAAAAAAAAGUUUAUUUUAGUUUUGGAA-------------A
..((((((((((.(........)))))))))))........(((((.((((..(((((((...(((.....)))...)))))))....)))).)))))..-------------. ( -26.20)
>DroSec_CAF1 61448 111 + 1
UCGAGAGAGCGGAGCUGGACUACCCGCUCUCUUUUUUCCCGACAAGUCUAGUUUAUUUUUUAGUGCCAAUUGUAAAAAUAAGUUGGAAAUAGUUUUGGAAC---UUAAAAAAAA
..((((((((((.(........)))))))))))..((((.(((...((((..((((((((((((....)))).))))))))..))))....)))..)))).---.......... ( -30.20)
>DroSim_CAF1 54129 109 + 1
UCGAGAGAGCGGAGCUGGACUACCCGCUCUCUUUUUUCCCGCCAAGUCUAGUUUAUUUUUUAGUGCCAAUUGUAAAAAUAAGUUGGAAAUAGUUUUGGAAC---UUAAAAAA--
..((((((((((.(........)))))))))))..((((.((....((((..((((((((((((....)))).))))))))..))))....))...)))).---........-- ( -29.20)
>DroYak_CAF1 52841 103 + 1
UCGAGAGAGC-----------GCCAGUGUUCAUUUUCACCGCUAAAUCUGUCUGACUUCAAGGUGCAAAUUGCAACAAUAAGUUGGAUAUGGUUAUGGAAUAUUUUAAAAAAGC
..((((((((-----------(....)))))..)))).(((...((((((((..((((.....(((.....))).....))))..)))).)))).)))................ ( -22.50)
>consensus
UCGAGAGAGCGGAGCUGGACUACCCGCUCUCUUUUUUCCCGCCAAGUCUAGCUGAUUUUUAAGUGCCAAUUGUAAAAAUAAGUUGGAAAUAGUUUUGGAAC___UUAAAAAA_A
..((((((((((...........))))))))))........(((((.(((.(((((((.....(((.....))).....)))))))...))).)))))................ (-17.90 = -18.77 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:39 2006