Template:BerkiGEM2007 ArthurSequencingFiles

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'''[[Template:BerkiGEM2007_ArthurSequencingFiles#Start 26|Skip to 26 Start]]'''
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'''[[Template:BerkiGEM2007_ArthurSequencingFiles#Start 51|Skip to 51 Start]]'''
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|AY028||070507||I716008 (Ptet-rbs-wbbL-rbs-neuS)||J2||ca998||wbbL or neuS not cloned. only Ptet.||[[BerkiGEM2007-Sequencing-AY028 | AY028]]
|AY028||070507||I716008 (Ptet-rbs-wbbL-rbs-neuS)||J2||ca998||wbbL or neuS not cloned. only Ptet.||[[BerkiGEM2007-Sequencing-AY028 | AY028]]
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|AY029||070507||I716008 (Ptet-rbs-wbbL-rbs-neuS)||J3||ca998||Ptet and wbbL were successfully cloned. neuS, unsure||[[BerkiGEM2007-Sequencing-AY029 | AY029]]
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|AY029||070507||I716008 (Ptet-rbs-wbbL-rbs-neuS)||J3||ca998||Ptet and wbbL were successfully cloned. neuS, unsure. Possibly neuS is gone since there could be a BamHI site right after wbbL in sequence file.||[[BerkiGEM2007-Sequencing-AY029 | AY029]]
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|AY030||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY030 | AY030]]
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|AY030||071107||I716012 (101-008)||1||ca998||Could not amplify||[[BerkiGEM2007-Sequencing-AY030 | AY030]]
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|AY031||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY031 | AY031]]
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|AY031||071107||I716012 (101-008)||2||ca998||Could not amplify||[[BerkiGEM2007-Sequencing-AY031 | AY031]]
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|AY032||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY032 | AY032]]
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|AY032||071207||I716013 (pBca9145-yfbE-rbs-ATG)||1||ca998||V>A right after BglII site. Amino acid change is bad.||[[BerkiGEM2007-Sequencing-AY032 | AY032]]
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|AY033||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY033 | AY033]]
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|AY033||071207||I716013 (pBca9145-yfbE-rbs-ATG)||3||ca998||Perfection||[[BerkiGEM2007-Sequencing-AY033 | AY033]]
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|AY034||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY034 | AY034]]
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|AY034||071207||I716014 (pBca9145-yfbE_solo)||1||ca998||Perfection||[[BerkiGEM2007-Sequencing-AY034 | AY034]]
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|AY035||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY035 | AY035]]
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|AY035||071207||I716014 (pBca9145-yfbE_solo)||2||ca998||Perfection||[[BerkiGEM2007-Sequencing-AY035 | AY035]]
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|AY036||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY036 | AY036]]
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|AY036||071207||I716014 (pBca9145-yfbE_solo)||3||ca998||Perfection||[[BerkiGEM2007-Sequencing-AY036 | AY036]]
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|AY037||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY037 | AY037]]
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|AY037||071307||I716015 (RFP no ATG)||1||ca998||Perfection||[[BerkiGEM2007-Sequencing-AY037 | AY037]]
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|-
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|AY038||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY038 | AY038]]
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|AY038||071307||I716015 (RFP no ATG)||2||ca998||Perfection||[[BerkiGEM2007-Sequencing-AY038 | AY038]]
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|-
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|AY039||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY039 | AY039]]
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|AY039||071307||I716015 (RFP no ATG)||3||ca998||Perfection||[[BerkiGEM2007-Sequencing-AY039 | AY039]]
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|AY040||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY040 | AY040]]
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|AY040||071307||I716008 Ptet-wbbL-neuS||lib||ca998||really weird I think it's missing half of Ptet||[[BerkiGEM2007-Sequencing-AY040 | AY040]]
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|AY041||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY041 | AY041]]
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|AY041||071707||I716008 Ptet-wbbL-neuS||lib||ca998||really weird I think it's missing half of Ptet AGAIN - but the sequencing is extremely mixed.||[[BerkiGEM2007-Sequencing-AY041 | AY041]]
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|AY042||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY042 | AY042]]
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|AY042||071907||I716019 (t7-rbs-cytB5-rbs-cytB5red-dblterm)||lib||ca998||T7 promoter, CytB5 and the first part of CytB5Red cloned successfully. 591 it is ambiguous if the base is right or not (CytB5Red) but data from Austin's I716011 sequence suggests that it is good.||[[BerkiGEM2007-Sequencing-AY042 | AY042]]
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|AY043||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY043 | AY043]]
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|AY043||071907||I716019 (t7-rbs-cytB5-rbs-cytB5red-dblterm)||lib||G01001||dblTerm and the rest of CytB5Red was cloned successfully.||[[BerkiGEM2007-Sequencing-AY043 | AY043]]
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|AY044||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY044 | AY044]]
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|AY044||072307||I716008||R1||ca998||half of ptet missing||[[BerkiGEM2007-Sequencing-AY044 | AY044]]
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|AY045||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY045 | AY045]]
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|AY045||072307||I716008||R2||ca998||half of ptet missing||[[BerkiGEM2007-Sequencing-AY045 | AY045]]
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|AY046||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY046 | AY046]]
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|AY046||072307||I716008||R3||ca998||half of ptet missing||[[BerkiGEM2007-Sequencing-AY046 | AY046]]
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|AY047||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY047 | AY047]]
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|AY047||072307||I716008||R4||ca998||Ptet intact. RBS appears garbled but it's because N's were not placed in the I716008 for the library. Need to map to check for neuS.||[[BerkiGEM2007-Sequencing-AY047 | AY047]]
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|AY048||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY048 | AY048]]
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|AY048||072307||I716008||R5||ca998||wtf is this lol||[[BerkiGEM2007-Sequencing-AY048 | AY048]]
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|AY049||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY049 | AY049]]
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|AY049||072307||I716008||R6||ca998||half of ptet is missing||[[BerkiGEM2007-Sequencing-AY049 | AY049]]
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|AY050||???||???||???||???||???||[[BerkiGEM2007-Sequencing-AY050 | AY050]]
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|AY050||072307||I716008||R7||ca998||wtf is this||[[BerkiGEM2007-Sequencing-AY050 | AY050]]
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|}
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===Start 51===
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{|
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|AY051||072307||I716008||R8||ca998||half ptet missing||[[BerkiGEM2007-Sequencing-AY051 | AY051]]
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|-
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|AY052||072307||I716008||r9||ca998||wtf||[[BerkiGEM2007-Sequencing-AY052 | AY052]]
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|-
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|AY053||072607||I716012|| ||ca998||M.I.A.||[[BerkiGEM2007-Sequencing-AY053 | AY053]]
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|-
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|AY054||080607||I716026||V1||ca998||Great||[[BerkiGEM2007-Sequencing-AY054 | AY054]]
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|-
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|AY055||080607||I716026||V2||ca998||Great||[[BerkiGEM2007-Sequencing-AY055 | AY055]]
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|AY056||080607||I716026||V3||ca998||A -> G  at position 136 in the sequence file||[[BerkiGEM2007-Sequencing-AY056 | AY056]]
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|AY057||080607||I716028||W1||ca998||T->C @ 269, G->T @ 539||[[BerkiGEM2007-Sequencing-AY057 | AY057]]
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|AY058||080607||I716028||W2||ca998||deletions and stuff, whoa||[[BerkiGEM2007-Sequencing-AY058 | AY058]]
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|-
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|AY059||080607||I716028||W3||ca998||Great||[[BerkiGEM2007-Sequencing-AY059 | AY059]]
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|-
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|AY060||080607||I716029||X1||ca998||Great||[[BerkiGEM2007-Sequencing-AY060 | AY060]]
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|-
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|AY061||080607||I716029||X2||ca998||A->G @ 531||[[BerkiGEM2007-Sequencing-AY061 | AY061]]
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|-
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|AY062||080607||I716029||X3||ca998||Great||[[BerkiGEM2007-Sequencing-AY062 | AY062]]
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|-
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|AY063||080707||I716024 VHb basic part||1||ca998||Great||[[BerkiGEM2007-Sequencing-AY063 | AY063]]
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|-
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|AY064||080707||I716024 VHb basic part||2||ca998||restriction sites in front are funny||[[BerkiGEM2007-Sequencing-AY064 | AY064]]
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|-
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|AY065||080707||I716024 VHb basic part||3||ca998||Great||[[BerkiGEM2007-Sequencing-AY065 | AY065]]
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|-
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|AY066||081407||I716033 (ptet-wbbL-neuS)(F-CmR-F)||1||ca998||lol||[[BerkiGEM2007-Sequencing-AY066 | AY066]]
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|-
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|AY067||081407||I716033 (ptet-wbbL-neuS)(F-CmR-F)||2||ca998||lol||[[BerkiGEM2007-Sequencing-AY067 | AY067]]
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|-
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|AY068||081407||I716033 (ptet-wbbL-neuS)(F-CmR-F)||3||ca998||lol||[[BerkiGEM2007-Sequencing-AY068 | AY068]]
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|-
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|AY069||081407||I716033 (ptet-wbbL-neuS)(F-CmR-F)||4||ca998||lol||[[BerkiGEM2007-Sequencing-AY069 | AY069]]
|}
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Latest revision as of 19:30, 16 August 2007

Skip to 26 Start
Skip to 51 Start

SampleDatePlasmidClonePrimerResultFile Link
AY001060407 pBca9145-Bca1145#1ca998Probably good. Long, ambiguous long AAAAAAA. AY001
AY002060407 pBca9145-Bca1145#2ca998Good. AY002
AY003061207pBca9145-HPI/katG (I716253)A1ca998super wrong. Seems like only half of HPI/katG, from the AY004.Sal.katG.HPI-Fx "mutate GAT>GAC (BglII)" til the end, was cloned. AY003
AY004061207pBca9145-HPI/katG (I716253)A3ca998generally OK. There is one extra G at 584 in the goal plasmid in the calls file. There is low confidence, but I am not sure what to make of it. Possibly should send for recheck at this point; may be necessary to check the mutation point @1308, and the end portion as well. But based on the miniprep digest run yesterday, this guy has a high chance of being the right one. DECISION: sent as AY007 with G01001 for a reverse check. AY004
AY005061207pBca9145-HPI/katG (I716253)A4ca998crazy :( there are big gaps AY005
AY006061207pBca9145-wbbL (I716000)B1ca998also crazy AY006
AY007061307pBca9145-HPI/katG (I716???)A3G01001Looks good actually, only notable thing is silent point mutation @ 1782 TCG > TCA still S. but the mutation point was just missed by sequencing. I don't think it's necessary to recheck; i have faith the primers worked right. well.. idk. major concern still is the possible addition mutation of a G AY007
AY008061307pBca9145-neuS (I716001)C1ca998Forward. Looks great! AY008
AY009061307pBca9145-neuS (I716001)C1G01001Reverse. Looks great! AY009
AY010061407I716002 (pBca9145-yfbE_promote)D1ca998Perfect promoter cloned region. @ 443 there is a deletion of ttgcag. Point mutation @631, T > C AY010
AY011061407I716002 (pBca9145-yfbE_promote)D1G01001Mixed DNA tube (contamination) AY011
AY012061407I716002 (pBca9145-yfbE_promote)D4ca998Perfect promoter cloned region. @ 443 there is a deletion of ttgcag. Point mutation @631, T > C. @640 addition of a C AY012
AY013061407I716002 (pBca9145-yfbE_promote)D4G01001Mixed DNA tube (contamination) AY013
AY014061507I716000 (pBca9145-wbbL)E1ca998long stretch of t's at 696, sequencing got an extra one. Likely read error. Missing a T @ 812, but read quality is low here. Lack of agttgca right after insert?? maybe not?? AY014
AY015061507I716000 (pBca9145-wbbL)E2ca998long stretch of t's at 696, sequencing got an extra one. Likely read error. Missing a T at 801. Lack of agttgca right after insert?? maybe not?? AY015
AY016061807I716000 (pBca9145-wbbL)E1G01001good AY016
AY017061807I716000 (pBca9145-wbbL)E2G01001good AY017
AY018061807I716253 (pBca9145-HPI/katG)A3ay007good AY018
AY019062107I716006 (pBca9145-Bca9203 B5red)G1ca998fail, mixed sample?? I believe it's quintara's fault AY019
AY020062107I716006 (pBca9145-Bca9203 B5red)G3ca998fail, mixed sample?? I believe it's quintara's fault AY020
AY021062507I716006 (pBca9145-Bca9203 B5red)G1ca998looks good AY021
AY022062507I716006 (pBca9145-Bca9203 B5red)H3ca998looks good AY022
AY023062507I716005 (pBca9145-Bca9229 cytoB5)H3ca998looks good AY023
AY024062507I716005 (pBca9145-Bca9229 cytoB5)H4ca998looks good AY024
AY025062807I716002 (pBca9145-yfbE_promote)IBca998our proprietary yfbE was cloned successfully AY025

Start 26

AY026062807I716002 (pBca9145-yfbE_promote)IDca998our proprietary yfbE was cloned successfully AY026
AY027070507I716008 (Ptet-rbs-wbbL-rbs-neuS)J1ca998wbbL or neuS not cloned. only Ptet. AY027
AY028070507I716008 (Ptet-rbs-wbbL-rbs-neuS)J2ca998wbbL or neuS not cloned. only Ptet. AY028
AY029070507I716008 (Ptet-rbs-wbbL-rbs-neuS)J3ca998Ptet and wbbL were successfully cloned. neuS, unsure. Possibly neuS is gone since there could be a BamHI site right after wbbL in sequence file. AY029
AY030071107I716012 (101-008)1ca998Could not amplify AY030
AY031071107I716012 (101-008)2ca998Could not amplify AY031
AY032071207I716013 (pBca9145-yfbE-rbs-ATG)1ca998V>A right after BglII site. Amino acid change is bad. AY032
AY033071207I716013 (pBca9145-yfbE-rbs-ATG)3ca998Perfection AY033
AY034071207I716014 (pBca9145-yfbE_solo)1ca998Perfection AY034
AY035071207I716014 (pBca9145-yfbE_solo)2ca998Perfection AY035
AY036071207I716014 (pBca9145-yfbE_solo)3ca998Perfection AY036
AY037071307I716015 (RFP no ATG)1ca998Perfection AY037
AY038071307I716015 (RFP no ATG)2ca998Perfection AY038
AY039071307I716015 (RFP no ATG)3ca998Perfection AY039
AY040071307I716008 Ptet-wbbL-neuSlibca998really weird I think it's missing half of Ptet AY040
AY041071707I716008 Ptet-wbbL-neuSlibca998really weird I think it's missing half of Ptet AGAIN - but the sequencing is extremely mixed. AY041
AY042071907I716019 (t7-rbs-cytB5-rbs-cytB5red-dblterm)libca998T7 promoter, CytB5 and the first part of CytB5Red cloned successfully. 591 it is ambiguous if the base is right or not (CytB5Red) but data from Austin's I716011 sequence suggests that it is good. AY042
AY043071907I716019 (t7-rbs-cytB5-rbs-cytB5red-dblterm)libG01001dblTerm and the rest of CytB5Red was cloned successfully. AY043
AY044072307I716008R1ca998half of ptet missing AY044
AY045072307I716008R2ca998half of ptet missing AY045
AY046072307I716008R3ca998half of ptet missing AY046
AY047072307I716008R4ca998Ptet intact. RBS appears garbled but it's because N's were not placed in the I716008 for the library. Need to map to check for neuS. AY047
AY048072307I716008R5ca998wtf is this lol AY048
AY049072307I716008R6ca998half of ptet is missing AY049
AY050072307I716008R7ca998wtf is this AY050

Start 51

AY051072307I716008R8ca998half ptet missing AY051
AY052072307I716008r9ca998wtf AY052
AY053072607I716012 ca998M.I.A. AY053
AY054080607I716026V1ca998Great AY054
AY055080607I716026V2ca998Great AY055
AY056080607I716026V3ca998A -> G at position 136 in the sequence file AY056
AY057080607I716028W1ca998T->C @ 269, G->T @ 539 AY057
AY058080607I716028W2ca998deletions and stuff, whoa AY058
AY059080607I716028W3ca998Great AY059
AY060080607I716029X1ca998Great AY060
AY061080607I716029X2ca998A->G @ 531 AY061
AY062080607I716029X3ca998Great AY062
AY063080707I716024 VHb basic part1ca998Great AY063
AY064080707I716024 VHb basic part2ca998restriction sites in front are funny AY064
AY065080707I716024 VHb basic part3ca998Great AY065
AY066081407I716033 (ptet-wbbL-neuS)(F-CmR-F)1ca998lol AY066
AY067081407I716033 (ptet-wbbL-neuS)(F-CmR-F)2ca998lol AY067
AY068081407I716033 (ptet-wbbL-neuS)(F-CmR-F)3ca998lol AY068
AY069081407I716033 (ptet-wbbL-neuS)(F-CmR-F)4ca998lol AY069
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