Locus 2852

Sequence ID	2L_DroMel_CAF1
Location	8,170,966 – 8,171,108
Length	142
Max. P	0.885526

overview

Window 6

Location	8,170,966 – 8,171,068
Length	102
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	81.47
Mean single sequence MFE	-31.52
Consensus MFE	-21.10
Energy contribution	-22.06
Covariance contribution	0.96
Combinations/Pair	1.05
Mean z-score	-2.12
Structure conservation index	0.67
SVM decision value	0.94
SVM RNA-class probability	0.885526
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8170966 102 - 22407834
GAAUGGCACACGUGUUGCUUCUAUGCU-UUGG-GGCUUGAUUAUGGGCCUACACAGACAUUCCAAGGCACACACACACACACACACCCCCCUUUUU--GGGGAACC
...........(((((((((..(((((-.(((-(((((......)))))).)).)).)))....))))).)))).............((((.....--)))).... ( -27.50)
>DroSec_CAF1 10683 91 - 1
GAAUGGCACACGUGUUGCUUCUAUGCUUUUAG-GGCGUGAUUAUGGGCCUGCACAGGCAUUUCAAGGCACA------------CACCCCCCUUUUU--GGGGAACC
...........((((.((((..((((((...(-(((.(......).))))....))))))....)))))))------------)...((((.....--)))).... ( -28.30)
>DroSim_CAF1 11317 91 - 1
GAAUGGCACACGUGUUGCUUCUAUGCUCUUGG-GGCUUGAUUAUGGGCCUGCACAGGCAUUCCAAGGCACA------------CACCCCCCUUUUU--GGGGAACC
...........((((.((((..(((((..(((-(((((......)))))).))..)))))....)))))))------------)...((((.....--)))).... ( -30.10)
>DroEre_CAF1 11192 86 - 1
GAAUGGGACACGUGUUGCUUCUAUGCUU--GG-GGCUUGAUUAUGGGCCUG--CAGGCAUUCCAAAGCACA------------CACCCCCUUUUU---GGGGAACC
....((.....((((.((((..((((((--((-(((((......)))))).--)))))))....)))))))------------)..((((.....---))))..)) ( -33.50)
>DroYak_CAF1 11156 86 - 1
GAAUGGGACACGUGUUGCUUCUAUGCUU--UGGGGC----CUUUGAGCCUA--AAGGCAUUCCAAAGCACA------------CACCCCCCUUUUUUGGGGGGAAU
(((.(.(((....))).))))..(((((--(((.((----(((((....))--)))))...))))))))..------------..((((((......))))))... ( -38.20)
>consensus
GAAUGGCACACGUGUUGCUUCUAUGCUUUUGG_GGCUUGAUUAUGGGCCUGCACAGGCAUUCCAAGGCACA____________CACCCCCCUUUUU__GGGGAACC
...........(((((......((((((.....(((((......))))).....)))))).....)))))................((((........)))).... (-21.10 = -22.06 +   0.96)

alignment

secondary structure

dotplot

Window 7

Location	8,170,999 – 8,171,108
Length	109
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	83.55
Mean single sequence MFE	-38.31
Consensus MFE	-23.80
Energy contribution	-25.64
Covariance contribution	1.84
Combinations/Pair	1.22
Mean z-score	-2.48
Structure conservation index	0.62
SVM decision value	0.90
SVM RNA-class probability	0.877128
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8170999 109 - 22407834
GGAGAGAGAGCGACACGUCUCCAUCGUUCCAUCAAAAAUCGAAUGGCACACGUGUUGCUUCUAUGCU-UUGG-GGCUUGAUUAUGGGCCUACACAGACAUUCCAAGGCACA
....(((.((((((((((..((((((.............)).))))...))))))))))))).((((-((((-(((((......)))))............)))))))).. ( -35.02)
>DroSec_CAF1 10704 109 - 1
GGAAAGGAAGCGACAAGUCUGCAUUGUUCCAUCAA-AAUCGAAUGGCACACGUGUUGCUUCUAUGCUUUUAG-GGCGUGAUUAUGGGCCUGCACAGGCAUUUCAAGGCACA
.((((((((((((((.((.(((...((((.((...-.)).)))).))).)).)))))))))).(((((...(-(((.(......).))))....)))))))))........ ( -32.90)
>DroSim_CAF1 11338 108 - 1
GGAAAGGGAGCGACACGUCU-CAUGGUUCCAUCAA-AAUCGAAUGGCACACGUGUUGCUUCUAUGCUCUUGG-GGCUUGAUUAUGGGCCUGCACAGGCAUUCCAAGGCACA
.....(((((((((((((..-....((.(((((..-....).)))).))))))))))))))).(((.(((((-(((((......)))))(((....)))..)))))))).. ( -39.90)
>DroEre_CAF1 11212 105 - 1
GGAAAGAGAAGGGUUCGUCUCCAUCGUUCCAUCAA-AAUCGAAUGGGACACGUGUUGCUUCUAUGCUU--GG-GGCUUGAUUAUGGGCCUG--CAGGCAUUCCAAAGCACA
.((..((((........))))..))((((((((..-....).)))))))..(((((......((((((--((-(((((......)))))).--))))))).....))))). ( -34.50)
>DroYak_CAF1 11179 102 - 1
GGAUGGAGAGCGGCACGUCCCCAUCGUCCCAUCGA-AAUCGAAUGGGACACGUGUUGCUUCUAUGCUU--UGGGGC----CUUUGAGCCUA--AAGGCAUUCCAAAGCACA
..(((((.((((((((((.......(((((((((.-...)).))))))))))))))))))))))((((--(((.((----(((((....))--)))))...)))))))... ( -49.21)
>consensus
GGAAAGAGAGCGACACGUCUCCAUCGUUCCAUCAA_AAUCGAAUGGCACACGUGUUGCUUCUAUGCUUUUGG_GGCUUGAUUAUGGGCCUGCACAGGCAUUCCAAGGCACA
(((((((.((((((((((.(((..(((((.((.....)).)))))))).))))))))))))).(((((.....(((((......))))).....)))))))))........ (-23.80 = -25.64 +   1.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:56 2006