Locus 1016

Sequence ID 3R_DroMel_CAF1
Location 3,206,973 – 3,207,069
Length 96
Max. P 0.523225
window1642

overview

Window 2

Location 3,206,973 – 3,207,069
Length 96
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 79.65
Mean single sequence MFE -18.65
Consensus MFE -11.00
Energy contribution -11.67
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.59
SVM decision value -0.02
SVM RNA-class probability 0.523225
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3206973 96 + 27905053
CCCGGGCAUAAAAAAGG----------------GGAAAAGAAAAAAGAAUUAUUUCAAGCAGUUUCGAAGCCAUAAAAAACUGCAUUUGGCAGCCGUUGCCAAAAC-CUAUAA
(((............))----------------)............(((....)))..(((((((............))))))).((((((((...))))))))..-...... ( -18.80)
>DroVir_CAF1 34244 112 + 1
CCCAGCUCUAAAAAAAUAGCAAAAAAAAACGCAGCAAUGAGAACAAAAAGUAUUUGAAGCAGCUUCGAAGCCAUAAAAAACUGCAUUUGGCAGUUGUCGCCAA-AGGCAAACU
....(((.......................((((...((....))....(..(((((((...)))))))..)........)))).((((((.......)))))-))))..... ( -18.10)
>DroGri_CAF1 27923 100 + 1
CCCAGCAAUAAAAA-----------AAAUA--UGGAAAGAGAACAAAAAGUAUUUCAAACAGCUUCGAAGCCAUAAAAAACUGCAUUUGGCAGUUGUCGCCAAAAAGCAAACU
....((........-----------...((--((....((((((.....)).)))).....(((....)))))))...((((((.....))))))...........))..... ( -14.30)
>DroSec_CAF1 26362 96 + 1
CCCGGGCAUAAAAAAGG----------------GGAAAAGGAAAAAGAAUUAUUUCAAGCAGUUUCGAAGCCAUAAAAAACUGCAUUUGGCAGCCGUUGCCAAAAC-CUAUAU
(((............))----------------)....(((.....(((....)))..(((((((............))))))).((((((((...)))))))).)-)).... ( -21.30)
>DroSim_CAF1 33203 96 + 1
CCCGGGCAUAAAAAAGG----------------GGAAAAGGAAAAAGAAUUAUUUCAAGCAGUUUCGAAGCCAUAAAAAACUGCAUUUGGCAGCCGUUGCCAAAAC-CUAUAU
(((............))----------------)....(((.....(((....)))..(((((((............))))))).((((((((...)))))))).)-)).... ( -21.30)
>DroEre_CAF1 25878 95 + 1
CCCGGGCAUAAAAAAGG----------------GGA-AAGCAAAAAGAAUUAUAUCAAGCAGUUUCGAAGCCAUAAAAAACUGCAUUUGGCAGCCGUUGCCAAAAC-CUAUAU
(((............))----------------)..-.....................(((((((............))))))).((((((((...))))))))..-...... ( -18.10)
>consensus
CCCGGGCAUAAAAAAGG________________GGAAAAGGAAAAAGAAUUAUUUCAAGCAGUUUCGAAGCCAUAAAAAACUGCAUUUGGCAGCCGUUGCCAAAAC_CUAUAU
..........................................................(((((((............))))))).((((((.......))))))......... (-11.00 = -11.67 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:23 2006