# Tab-separated file containing the ladders Geneious will try to match against

# Genescan is from ABI  https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=602825
# Genflo is from CHIMERx  http://www.chimerx.com/store/dna-markers-and-ladders
# GGF is from Georgia Genomics Facility http://dna.uga.edu/products/dye-labeled-size-standard/

# home made ladders because people don't want to pay the above corporations -- see "Universal method for producing ROX-labeled size standards suitable for automated genotyping" by DeWoody et al  http://www.agriculture.purdue.edu/fnr/html/faculty/DeWoody/DeWoodyweb/documents/ROX.pdf
pBS II SK	78	89	104	130	150	181	200	253	305	336	361	424	485	508	559	597	673	738	798
pUC-19	79	90	105	131	151	182	201	254	306	337	362	425	486	509	560	598	674	739	799	902	1007

#LIZ
GeneScan 120	15	20	25	35	50	62	80	110	120
GeneScan 600	20	40	60	80	100	114	120	140	160	180	200	214	220	240	250	260	280	300	314	320	340	360	380	400	414	420	440	460	480	500	514	520	540	560	580	600
GeneScan 1200	20	30	40	60	80	100	114	120	140	160	180	200	214	220	240	250	260	280	300	314	320	340	360	380	400	414	420	440	460	480	500	514	520	540	560	580	600	614	620	640	660	680	700	714	720	740	760	780	800	820	840	850	860	880	900	920	940	960	980	1000	1020	1040	1060	1080	1100	1120	1160	1200

#ROX
GeneScan 400HD	50	90	100	120	150	160	180	190	200	220	240	260	280	290	300	320	340	360	380	400
# "Under denaturing conditions the two strands of the doubly-labeled GeneScan-1000 size standard fragments migrate at different rates, appearing as split peaks. To ensure size-calling precision and a reliable size standard definition, you must explicitly define one peak from each split peak pair in the size standard definition."
# from http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_040961.pdf
# currently Geneious should call both these peaks and not be able to fit a ladder, so the user will have to manually delete one of them.
GeneScan 1000	47	51	55	82	85	93	99	126	136	262	293	317	439	557	692	695	946
Genflo 1000	400	425	450	475	500	525	550	560	575	600	625	650	675	700	725	750	775	800	825	835	850	875	900	925	950	975	1000
GGF 500	88	99	114	138	160	192	210	263	315	346	371	435
GGF 1000	88	99	114	138	160	192	210	263	315	346	371	435	518	570	607	683	747	806	911	1016
Gel Company 500	70	80	90	100	120	140	160	180	190	200	220	240	260	280	300	320	340	360	380	400	425	450	475	490	500

# ROX or TAMRA
GeneScan 350	35	50	75	100	139	150	160	200	250	300	340	350
Genflo 625	50	75	100	125	129	150	175	200	225	250	275	300	325	350	375	400	425	429	450	475	500	525	550	575	600	625

# LIZ, ROX or TAMRA
GeneScan 500	35	50	75	100	139	150	160	200	250	300	340	350	400	450	490	500
GeneScan 500 - no 250bp peak	35	50	75	100	139	150	160	200	300	340	350	400	450	490	500
