Locus 7110

Sequence ID	3R_DroMel_CAF1
Location	18,746,636 – 18,746,832
Length	196
Max. P	0.883944

overview

Window 8

Location	18,746,636 – 18,746,752
Length	116
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	83.68
Mean single sequence MFE	-31.43
Consensus MFE	-21.14
Energy contribution	-22.82
Covariance contribution	1.69
Combinations/Pair	1.06
Mean z-score	-2.21
Structure conservation index	0.67
SVM decision value	0.93
SVM RNA-class probability	0.883944
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18746636 116 - 27905053
CUACUCUUUUCUACGAUUU-UUUCCGCCACUUUCUGGCCUGCACU--GUCAAUGGCAUUGUUGCUUGGCACGCACUCGCACUGCGAAAAAAAUUGUAUCAAUUUUCGUUAAUAUCCAUC
...........((((((((-(((.(((((.....))))..(((.(--((((..((((....))))))))).((....))..)))).)))))))))))...................... ( -24.40)
>DroSec_CAF1 5425 117 - 1
CUACACUUUUCUGCGAUUU-UUUCCGCCAGUUGCUGGCCUGCACUGUGUCAAUGGCAUUGUUGCUUGGCACGCACUCGCACUGU-AAAAAAAUUGUAUCAAUUAUCGUUGAUAUCCAUC
............(((((((-(((..(((((...))))).((((..((((((..((((....))))))))))((....))..)))-)))))))))))((((((....))))))....... ( -29.80)
>DroSim_CAF1 5441 119 - 1
CUACGCUUUUCUACGAUUUUUUUCCGCCAGUUGCUGGCCUGCACUGUGUCAAUGGCAUUGUUGCUUGGCACGCACUCGCACUGCGAAAAAAAUUGUAUAAAUUUUCGUUGAUAUUCAUC
(.(((..(((.(((((((((((((.(((((...)))))..(((..((((((..((((....))))))))))((....))..)))))))))))))))).)))....))).)......... ( -35.00)
>DroEre_CAF1 5440 112 - 1
CUACAGCCCUCGCCGAGUU-UUUCCGCCAAUUGCCGGCCAGCA--GUGUCAAUGGCAUUGUUGCUUGGCACGCACUCGCACUGCGAAAAAAAAUGCAGCAAUAU----CGGCAUGGAAC
.......((..(((((...-.....((....((((((.(((((--((((.....))))))))).)))))).)).......(((((........))))).....)----))))..))... ( -36.50)
>consensus
CUACACUUUUCUACGAUUU_UUUCCGCCAGUUGCUGGCCUGCACUGUGUCAAUGGCAUUGUUGCUUGGCACGCACUCGCACUGCGAAAAAAAUUGUAUCAAUUUUCGUUGAUAUCCAUC
...........((((((((.((((.((((.....))))..(((..((((((..((((....))))))))))((....))..))))))).))))))))...................... (-21.14 = -22.82 +   1.69)

alignment

secondary structure

dotplot

Window 9

Location	18,746,713 – 18,746,832
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.54
Mean single sequence MFE	-27.87
Consensus MFE	-21.01
Energy contribution	-22.32
Covariance contribution	1.31
Combinations/Pair	1.14
Mean z-score	-1.57
Structure conservation index	0.75
SVM decision value	0.11
SVM RNA-class probability	0.589176
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18746713 119 + 27905053
AGGCCAGAAAGUGGCGGAAA-AAAUCGUAGAAAAGAGUAGAGCAGUUUCCCAUCCAAUGAAAAGCUCUAUAUAUUUUUCAACGCUUUUAAAUAAAAUUCCCGAGGAAGUUGGUUGGAAAA
.((((((((((((((((...-...)))).((((((.(((((((..((((.........)))).)))))))...))))))..)))))))........((((...))))..)))))...... ( -26.90)
>DroSec_CAF1 5503 119 + 1
AGGCCAGCAACUGGCGGAAA-AAAUCGCAGAAAAGUGUAGAGCAGUUUCCCAUCCAAUGAAAAGCUCUAUAUAUUUUUCAACGCUUUUAAAUAAAAUUCCCGAGGAAGUUGGUUGGAAAA
.(((((((..((.(.(((((-(((.((..((((((((((((((..((((.........)))).)))))))))..)))))..)).))))........))))).))...)))))))...... ( -29.80)
>DroSim_CAF1 5520 120 + 1
AGGCCAGCAACUGGCGGAAAAAAAUCGUAGAAAAGCGUAGAGCAGUUUCCCAUCCAAUGAAAAGCUCUAUAUAUUUUUCAACGCUUUUAAAUAAAAUUCCCGAGGAAGUUGGUUGGAAAA
.(((((((..((.(.((((.((((.(((.((((((.(((((((..((((.........)))).)))))))...)))))).))).))))........))))).))...)))))))...... ( -28.80)
>DroEre_CAF1 5513 114 + 1
UGGCCGGCAAUUGGCGGAAA-AACUCGGCGAGGGCUGUAG----GCUUCCCAUCCAAUGAAAACCUCUAUAUAUUUUUCAACGCUUUUAAAUAAAAUUCCCAAGCAAGUUGGCUGGAAA-
.(((((((.(((((.((((.-..((((((....)))).))----..))))...)))))........................((((...............))))..))))))).....- ( -25.96)
>consensus
AGGCCAGCAACUGGCGGAAA_AAAUCGUAGAAAAGUGUAGAGCAGUUUCCCAUCCAAUGAAAAGCUCUAUAUAUUUUUCAACGCUUUUAAAUAAAAUUCCCGAGGAAGUUGGUUGGAAAA
.(((((((....((((((......))...((((((((((((((..((((.........)))).))))))))..))))))..))))...........((((...)))))))))))...... (-21.01 = -22.32 +   1.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:35 2006