Clone validation report

Sample status

This table gives the status of each sample, either completed successfully or the reason the assembly failed. If applicable the mean quality for the whole construct has been provided, derived by Medaka from aligning the reads to the consensus.

The assembly was generated using Flye. The assemblies and/or inserts were aligned with provided references and marked as expected if they meet both the acceptance criteria defined by the expected_coverage and expected_identity parameters which have been set to 95.0% and 99.0% respectively.

Sample	Assembly completed / failed reason	Length	Mean Quality	Expected insert	Expected Assembly
sample01	Failed due to insufficient reads	N/A	N/A	❌	❌
sample02	Completed successfully	2871	52.79	✅	❌
sample03	Completed successfully	3096	48.08	✅	✅
sample04	Completed successfully	3097	41.88	✅	✅
sample05	Completed successfully	3036	52.23	✅	✅
sample06	Completed successfully	3037	39.08	✅	✅
sample07	Completed successfully	3096	46.94	✅	✅
sample08	Completed successfully	3096	46.46	✅	✅
sample09	Completed successfully	3036	47.16	✅	✅
sample10	Completed successfully	3036	50.27	✅	✅
sample11	Completed successfully	3096	44.41	✅	✅
sample12	Completed successfully	3096	47.78	✅	✅

Plannotate

The Plasmid annotation plot and feature table are produced using pLannotate

A pLannotate plot is shown for each assembly. A feature table provides descriptions of the annotated sequence. Unfilled features on the plannotate plots are incomplete features; the sequence match in the plasmid covers less than 95% of the full length of the feature in the database. These elements may be leftover fragments from earlier cloning steps used to create a plasmid. If they include only a small fraction of the feature, they likely do not still have the annotated function. However, even small feature fragments may affect plasmid function if they result in cryptic gene expression or are inadvertently combined with other elements during later cloning steps. The plannotate plot may have overlapping annotation labels, use the zoom and hover tools to decipher the labels.

Feature	Database	Identity	Match Length	Description	Start Location	End Location	Length	Strand
csgG	swissprot	100.0%	100.0%	CSGG_ECO57 - Experimental evidence at protein level: Swiss-Prot protein existence level 1. May be involved in the biogenesis of curli organelles. From Escherichia coli O157:H7.	765	1596	831	-
rhaB promoter	snapgene	100.0%	100.0%	promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006)	1659	1778	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	1874	1965	91	+
CloDF13 ori	snapgene	100.0%	92.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2743	554	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	687	735	48	-
KanR	snapgene	99.3%	65.7%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	1965	2501	536	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	1842	1874	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	560	590	30	-
kanMX	snapgene	99.0%	37.3%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	1995	2501	506	+
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	2741	2844	103	-
KanR	snapgene	99.1%	14.2%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	2501	2616	115	+
CloDF13 ori	snapgene	99.0%	13.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2622	2719	98	+
kanMX	snapgene	99.1%	8.5%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	2501	2616	115	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	1884	1966	82	+

Feature	Database	Identity	Match Length	Description	Start Location	End Location	Length	Strand
TXL_EISFE	swissprot	100.0%	100.0%	Experimental evidence at protein level: Swiss-Prot protein existence level 1. Pore-forming toxin that defensively acts against parasitic microorganisms by forming pores in sphingomyelin-containing membranes. Has hemolytic activity and is also cytotoxic to spermatozoa of some species of invertebrates and many species of vertebrates and to amphibian larvae, guinea pig polymorphonuclear leukocytes, chicken fibroblasts, normal spleen cells and various tumor cells. Is lethal for various species of reptiles, amphibian, birds and mammals. Induces smooth muscle contraction. It binds sphingomyelin and induces hemolysis in the same manner as lysenin-related protein 2, and is 10-fold more effective than lysenin-related protein 1.	909	1800	891	-
rhaB promoter	snapgene	100.0%	100.0%	promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006)	1863	1982	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	2078	2169	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	2169	2985	816	+
CloDF13 ori	snapgene	100.0%	92.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	16	698	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	831	879	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	2199	2985	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	2046	2078	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	704	734	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	14	117	103	-
CloDF13 ori	snapgene	99.0%	13.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2991	3088	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	2088	2170	82	+

Feature	Database	Identity	Match Length	Description	Start Location	End Location	Length	Strand
TXL_EISFE	swissprot	100.0%	100.0%	Experimental evidence at protein level: Swiss-Prot protein existence level 1. Pore-forming toxin that defensively acts against parasitic microorganisms by forming pores in sphingomyelin-containing membranes. Has hemolytic activity and is also cytotoxic to spermatozoa of some species of invertebrates and many species of vertebrates and to amphibian larvae, guinea pig polymorphonuclear leukocytes, chicken fibroblasts, normal spleen cells and various tumor cells. Is lethal for various species of reptiles, amphibian, birds and mammals. Induces smooth muscle contraction. It binds sphingomyelin and induces hemolysis in the same manner as lysenin-related protein 2, and is 10-fold more effective than lysenin-related protein 1.	909	1800	891	-
rhaB promoter	snapgene	100.0%	100.0%	promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006)	1863	1982	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	2078	2169	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	2169	2985	816	+
CloDF13 ori	snapgene	100.0%	92.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	16	698	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	831	879	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	2199	2985	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	2046	2078	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	704	734	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	14	117	103	-
CloDF13 ori	snapgene	100.0%	13.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2991	3089	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	2088	2170	82	+

Feature	Database	Identity	Match Length	Description	Start Location	End Location	Length	Strand
csgG	swissprot	100.0%	100.0%	CSGG_ECO57 - Experimental evidence at protein level: Swiss-Prot protein existence level 1. May be involved in the biogenesis of curli organelles. From Escherichia coli O157:H7.	765	1596	831	-
rhaB promoter	snapgene	100.0%	100.0%	promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006)	1659	1778	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	1874	1965	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	1965	2781	816	+
CloDF13 ori	snapgene	100.0%	92.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2908	554	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	687	735	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	1995	2781	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	1842	1874	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	560	590	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	2906	3009	103	-
CloDF13 ori	snapgene	99.0%	13.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2787	2884	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	1884	1966	82	+

Feature	Database	Identity	Match Length	Description	Start Location	End Location	Length	Strand
csgG	swissprot	100.0%	100.0%	CSGG_ECO57 - Experimental evidence at protein level: Swiss-Prot protein existence level 1. May be involved in the biogenesis of curli organelles. From Escherichia coli O157:H7.	765	1596	831	-
rhaB promoter	snapgene	100.0%	100.0%	promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006)	1659	1778	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	1874	1965	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	1965	2781	816	+
CloDF13 ori	snapgene	100.0%	92.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2909	554	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	687	735	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	1995	2781	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	1842	1874	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	560	590	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	2907	3010	103	-
CloDF13 ori	snapgene	100.0%	13.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2787	2885	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	1884	1966	82	+

Feature	Database	Identity	Match Length	Description	Start Location	End Location	Length	Strand
TXL_EISFE	swissprot	100.0%	100.0%	Experimental evidence at protein level: Swiss-Prot protein existence level 1. Pore-forming toxin that defensively acts against parasitic microorganisms by forming pores in sphingomyelin-containing membranes. Has hemolytic activity and is also cytotoxic to spermatozoa of some species of invertebrates and many species of vertebrates and to amphibian larvae, guinea pig polymorphonuclear leukocytes, chicken fibroblasts, normal spleen cells and various tumor cells. Is lethal for various species of reptiles, amphibian, birds and mammals. Induces smooth muscle contraction. It binds sphingomyelin and induces hemolysis in the same manner as lysenin-related protein 2, and is 10-fold more effective than lysenin-related protein 1.	909	1800	891	-
rhaB promoter	snapgene	100.0%	100.0%	promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006)	1863	1982	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	2078	2169	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	2169	2985	816	+
CloDF13 ori	snapgene	100.0%	92.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	16	698	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	831	879	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	2199	2985	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	2046	2078	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	704	734	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	14	117	103	-
CloDF13 ori	snapgene	99.0%	13.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2991	3088	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	2088	2170	82	+

Feature	Database	Identity	Match Length	Description	Start Location	End Location	Length	Strand
TXL_EISFE	swissprot	100.0%	100.0%	Experimental evidence at protein level: Swiss-Prot protein existence level 1. Pore-forming toxin that defensively acts against parasitic microorganisms by forming pores in sphingomyelin-containing membranes. Has hemolytic activity and is also cytotoxic to spermatozoa of some species of invertebrates and many species of vertebrates and to amphibian larvae, guinea pig polymorphonuclear leukocytes, chicken fibroblasts, normal spleen cells and various tumor cells. Is lethal for various species of reptiles, amphibian, birds and mammals. Induces smooth muscle contraction. It binds sphingomyelin and induces hemolysis in the same manner as lysenin-related protein 2, and is 10-fold more effective than lysenin-related protein 1.	909	1800	891	-
rhaB promoter	snapgene	100.0%	100.0%	promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006)	1863	1982	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	2078	2169	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	2169	2985	816	+
CloDF13 ori	snapgene	100.0%	92.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	16	698	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	831	879	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	2199	2985	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	2046	2078	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	704	734	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	14	117	103	-
CloDF13 ori	snapgene	99.0%	13.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2991	3088	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	2088	2170	82	+

Feature	Database	Identity	Match Length	Description	Start Location	End Location	Length	Strand
csgG	swissprot	100.0%	100.0%	CSGG_ECO57 - Experimental evidence at protein level: Swiss-Prot protein existence level 1. May be involved in the biogenesis of curli organelles. From Escherichia coli O157:H7.	765	1596	831	-
rhaB promoter	snapgene	100.0%	100.0%	promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006)	1659	1778	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	1874	1965	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	1965	2781	816	+
CloDF13 ori	snapgene	100.0%	92.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2908	554	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	687	735	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	1995	2781	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	1842	1874	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	560	590	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	2906	3009	103	-
CloDF13 ori	snapgene	99.0%	13.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2787	2884	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	1884	1966	82	+

Feature	Database	Identity	Match Length	Description	Start Location	End Location	Length	Strand
csgG	swissprot	100.0%	100.0%	CSGG_ECO57 - Experimental evidence at protein level: Swiss-Prot protein existence level 1. May be involved in the biogenesis of curli organelles. From Escherichia coli O157:H7.	765	1596	831	-
rhaB promoter	snapgene	100.0%	100.0%	promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006)	1659	1778	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	1874	1965	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	1965	2781	816	+
CloDF13 ori	snapgene	100.0%	92.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2908	554	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	687	735	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	1995	2781	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	1842	1874	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	560	590	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	2906	3009	103	-
CloDF13 ori	snapgene	99.0%	13.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	2787	2884	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	1884	1966	82	+

Feature	Database	Identity	Match Length	Description	Start Location	End Location	Length	Strand
TXL_EISFE	swissprot	100.0%	100.0%	Experimental evidence at protein level: Swiss-Prot protein existence level 1. Pore-forming toxin that defensively acts against parasitic microorganisms by forming pores in sphingomyelin-containing membranes. Has hemolytic activity and is also cytotoxic to spermatozoa of some species of invertebrates and many species of vertebrates and to amphibian larvae, guinea pig polymorphonuclear leukocytes, chicken fibroblasts, normal spleen cells and various tumor cells. Is lethal for various species of reptiles, amphibian, birds and mammals. Induces smooth muscle contraction. It binds sphingomyelin and induces hemolysis in the same manner as lysenin-related protein 2, and is 10-fold more effective than lysenin-related protein 1.	928	1819	891	-
rhaB promoter	snapgene	100.0%	100.0%	promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006)	1882	2001	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	2097	2188	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	2188	3004	816	+
CloDF13 ori	snapgene	100.0%	92.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	35	717	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	850	898	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	2218	3004	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	2065	2097	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	723	753	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	33	136	103	-
CloDF13 ori	snapgene	99.0%	13.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	3010	11	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	2107	2189	82	+

Feature	Database	Identity	Match Length	Description	Start Location	End Location	Length	Strand
TXL_EISFE	swissprot	100.0%	100.0%	Experimental evidence at protein level: Swiss-Prot protein existence level 1. Pore-forming toxin that defensively acts against parasitic microorganisms by forming pores in sphingomyelin-containing membranes. Has hemolytic activity and is also cytotoxic to spermatozoa of some species of invertebrates and many species of vertebrates and to amphibian larvae, guinea pig polymorphonuclear leukocytes, chicken fibroblasts, normal spleen cells and various tumor cells. Is lethal for various species of reptiles, amphibian, birds and mammals. Induces smooth muscle contraction. It binds sphingomyelin and induces hemolysis in the same manner as lysenin-related protein 2, and is 10-fold more effective than lysenin-related protein 1.	928	1819	891	-
rhaB promoter	snapgene	100.0%	100.0%	promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006)	1882	2001	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	2097	2188	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	2188	3004	816	+
CloDF13 ori	snapgene	100.0%	92.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	35	717	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	850	898	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	2218	3004	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	2065	2097	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	723	753	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	33	136	103	-
CloDF13 ori	snapgene	99.0%	13.3%	Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins.	3010	11	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	2107	2189	82	+

Read Counts

Number of reads per sample.

Read stats

Read count

1,334

Read count

1,332

Read count

203

Insert sequences

This table shows which primers were found in the consensus sequence of each sample and where the inserts were found.

Sample	start	end	primer	strand	Insert length
sample02	526	1655	pRham	-	1129
sample05	526	1655	pRham	-	1129
sample06	526	1655	pRham	-	1129
sample09	526	1655	pRham	-	1129
sample10	526	1655	pRham	-	1129

This table shows which primers were found in the consensus sequence of each sample and where the inserts were found.

Sample	start	end	primer	strand	Insert length
sample03	670	1859	pRham	-	1189
sample04	670	1859	pRham	-	1189
sample07	670	1859	pRham	-	1189
sample08	670	1859	pRham	-	1189
sample11	689	1878	pRham	-	1189
sample12	689	1878	pRham	-	1189

Multiple Sequence Alignment

This section shows the inserts aligned with each other or a reference sequence if provided.

Reference GACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTATAAGAAGGAGATATACATATGCAGCGTCTGTTTCTGCTG
sample02  GACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTATAAGAAGGAGATATACATATGCAGCGTCTGTTTCTGCTG
sample05  GACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTATAAGAAGGAGATATACATATGCAGCGTCTGTTTCTGCTG
sample06  GACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTATAAGAAGGAGATATACATATGCAGCGTCTGTTTCTGCTG
sample09  GACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTATAAGAAGGAGATATACATATGCAGCGTCTGTTTCTGCTG
sample10  GACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTATAAGAAGGAGATATACATATGCAGCGTCTGTTTCTGCTG

Reference GTCGCGGTGATGCTGCTGAGTGGTTGTCTGACCGCACCGCCGAAAGAAGCGGCACGTCCGACCCTGATGCCGCGTGCACA
sample02  GTCGCGGTGATGCTGCTGAGTGGTTGTCTGACCGCACCGCCGAAAGAAGCGGCACGTCCGACCCTGATGCCGCGTGCACA
sample05  GTCGCGGTGATGCTGCTGAGTGGTTGTCTGACCGCACCGCCGAAAGAAGCGGCACGTCCGACCCTGATGCCGCGTGCACA
sample06  GTCGCGGTGATGCTGCTGAGTGGTTGTCTGACCGCACCGCCGAAAGAAGCGGCACGTCCGACCCTGATGCCGCGTGCACA
sample09  GTCGCGGTGATGCTGCTGAGTGGTTGTCTGACCGCACCGCCGAAAGAAGCGGCACGTCCGACCCTGATGCCGCGTGCACA
sample10  GTCGCGGTGATGCTGCTGAGTGGTTGTCTGACCGCACCGCCGAAAGAAGCGGCACGTCCGACCCTGATGCCGCGTGCACA

Reference GTCTTATAAAGATCTGACCCATCTGCCGGCTCCGACGGGCAAAATTTTTGTTAGCGTCTATAACATCCAGGACGAAACCG
sample02  GTCTTATAAAGATCTGACCCATCTGCCGGCTCCGACGGGCAAAATTTTTGTTAGCGTCTATAACATCCAGGACGAAACCG
sample05  GTCTTATAAAGATCTGACCCATCTGCCGGCTCCGACGGGCAAAATTTTTGTTAGCGTCTATAACATCCAGGACGAAACCG
sample06  GTCTTATAAAGATCTGACCCATCTGCCGGCTCCGACGGGCAAAATTTTTGTTAGCGTCTATAACATCCAGGACGAAACCG
sample09  GTCTTATAAAGATCTGACCCATCTGCCGGCTCCGACGGGCAAAATTTTTGTTAGCGTCTATAACATCCAGGACGAAACCG
sample10  GTCTTATAAAGATCTGACCCATCTGCCGGCTCCGACGGGCAAAATTTTTGTTAGCGTCTATAACATCCAGGACGAAACCG

Reference GTCAATTTAAACCGTACCCGGCGAGTAATTTCTCCACGGCCGTTCCGCAGAGTGCAACCGCTATGCTGGTCACGGCACTG
sample02  GTCAATTTAAACCGTACCCGGCGAGTAATTTCTCCACGGCCGTTCCGCAGAGTGCAACCGCTATGCTGGTCACGGCACTG
sample05  GTCAATTTAAACCGTACCCGGCGAGTAATTTCTCCACGGCCGTTCCGCAGAGTGCAACCGCTATGCTGGTCACGGCACTG
sample06  GTCAATTTAAACCGTACCCGGCGAGTAATTTCTCCACGGCCGTTCCGCAGAGTGCAACCGCTATGCTGGTCACGGCACTG
sample09  GTCAATTTAAACCGTACCCGGCGAGTAATTTCTCCACGGCCGTTCCGCAGAGTGCAACCGCTATGCTGGTCACGGCACTG
sample10  GTCAATTTAAACCGTACCCGGCGAGTAATTTCTCCACGGCCGTTCCGCAGAGTGCAACCGCTATGCTGGTCACGGCACTG

Reference AAAGATTCCCGTTGGTTCATTCCGCTGGAACGCCAGGGCCTGCAAAACCTGCTGAATGAACGTAAAATTATCCGCGCAGC
sample02  AAAGATTCCCGTTGGTTCATTCCGCTGGAACGCCAGGGCCTGCAAAACCTGCTGAATGAACGTAAAATTATCCGCGCAGC
sample05  AAAGATTCCCGTTGGTTCATTCCGCTGGAACGCCAGGGCCTGCAAAACCTGCTGAATGAACGTAAAATTATCCGCGCAGC
sample06  AAAGATTCCCGTTGGTTCATTCCGCTGGAACGCCAGGGCCTGCAAAACCTGCTGAATGAACGTAAAATTATCCGCGCAGC
sample09  AAAGATTCCCGTTGGTTCATTCCGCTGGAACGCCAGGGCCTGCAAAACCTGCTGAATGAACGTAAAATTATCCGCGCAGC
sample10  AAAGATTCCCGTTGGTTCATTCCGCTGGAACGCCAGGGCCTGCAAAACCTGCTGAATGAACGTAAAATTATCCGCGCAGC

Reference TCAGGAAAACGGTACCGTGGCCATTAACAATCGTATTCCGCTGCAAAGCCTGACCGCCGCAAACATCATGGTTGAAGGCT
sample02  TCAGGAAAACGGTACCGTGGCCATTAACAATCGTATTCCGCTGCAAAGCCTGACCGCCGCAAACATCATGGTTGAAGGCT
sample05  TCAGGAAAACGGTACCGTGGCCATTAACAATCGTATTCCGCTGCAAAGCCTGACCGCCGCAAACATCATGGTTGAAGGCT
sample06  TCAGGAAAACGGTACCGTGGCCATTAACAATCGTATTCCGCTGCAAAGCCTGACCGCCGCAAACATCATGGTTGAAGGCT
sample09  TCAGGAAAACGGTACCGTGGCCATTAACAATCGTATTCCGCTGCAAAGCCTGACCGCCGCAAACATCATGGTTGAAGGCT
sample10  TCAGGAAAACGGTACCGTGGCCATTAACAATCGTATTCCGCTGCAAAGCCTGACCGCCGCAAACATCATGGTTGAAGGCT

Reference CTATCATCGGTTACGAATCAAACGTCAAATCGGGCGGTGTGGGCGCACGTTATTTTGGCATTGGTGCTGATACCCAGTAC
sample02  CTATCATCGGTTACGAATCAAACGTCAAATCGGGCGGTGTGGGCGCACGTTATTTTGGCATTGGTGCTGATACCCAGTAC
sample05  CTATCATCGGTTACGAATCAAACGTCAAATCGGGCGGTGTGGGCGCACGTTATTTTGGCATTGGTGCTGATACCCAGTAC
sample06  CTATCATCGGTTACGAATCAAACGTCAAATCGGGCGGTGTGGGCGCACGTTATTTTGGCATTGGTGCTGATACCCAGTAC
sample09  CTATCATCGGTTACGAATCAAACGTCAAATCGGGCGGTGTGGGCGCACGTTATTTTGGCATTGGTGCTGATACCCAGTAC
sample10  CTATCATCGGTTACGAATCAAACGTCAAATCGGGCGGTGTGGGCGCACGTTATTTTGGCATTGGTGCTGATACCCAGTAC

Reference CAACTGGACCAGATCGCAGTTAACCTGCGCGTGGTTAATGTCAGCACCGGCGAAATTCTGAGCTCTGTGAATACCAGCAA
sample02  CAACTGGACCAGATCGCAGTTAACCTGCGCGTGGTTAATGTCAGCACCGGCGAAATTCTGAGCTCTGTGAATACCAGCAA
sample05  CAACTGGACCAGATCGCAGTTAACCTGCGCGTGGTTAATGTCAGCACCGGCGAAATTCTGAGCTCTGTGAATACCAGCAA
sample06  CAACTGGACCAGATCGCAGTTAACCTGCGCGTGGTTAATGTCAGCACCGGCGAAATTCTGAGCTCTGTGAATACCAGCAA
sample09  CAACTGGACCAGATCGCAGTTAACCTGCGCGTGGTTAATGTCAGCACCGGCGAAATTCTGAGCTCTGTGAATACCAGCAA
sample10  CAACTGGACCAGATCGCAGTTAACCTGCGCGTGGTTAATGTCAGCACCGGCGAAATTCTGAGCTCTGTGAATACCAGCAA

Reference AACGATCCTGTCTTACGAAGTGCAGGCTGGTGTTTTTCGTTTCATTGATTATCAACGCCTGCTGGAAGGCGAAGTCGGTT
sample02  AACGATCCTGTCTTACGAAGTGCAGGCTGGTGTTTTTCGTTTCATTGATTATCAACGCCTGCTGGAAGGCGAAGTCGGTT
sample05  AACGATCCTGTCTTACGAAGTGCAGGCTGGTGTTTTTCGTTTCATTGATTATCAACGCCTGCTGGAAGGCGAAGTCGGTT
sample06  AACGATCCTGTCTTACGAAGTGCAGGCTGGTGTTTTTCGTTTCATTGATTATCAACGCCTGCTGGAAGGCGAAGTCGGTT
sample09  AACGATCCTGTCTTACGAAGTGCAGGCTGGTGTTTTTCGTTTCATTGATTATCAACGCCTGCTGGAAGGCGAAGTCGGTT
sample10  AACGATCCTGTCTTACGAAGTGCAGGCTGGTGTTTTTCGTTTCATTGATTATCAACGCCTGCTGGAAGGCGAAGTCGGTT

Reference ACACCTCAAACGAACCGGTGATGCTGTGTCTGATGTCGGCGATTGAAACGGGTGTTATTTTCCTGATCAATGATGGCATC
sample02  ACACCTCAAACGAACCGGTGATGCTGTGTCTGATGTCGGCGATTGAAACGGGTGTTATTTTCCTGATCAATGATGGCATC
sample05  ACACCTCAAACGAACCGGTGATGCTGTGTCTGATGTCGGCGATTGAAACGGGTGTTATTTTCCTGATCAATGATGGCATC
sample06  ACACCTCAAACGAACCGGTGATGCTGTGTCTGATGTCGGCGATTGAAACGGGTGTTATTTTCCTGATCAATGATGGCATC
sample09  ACACCTCAAACGAACCGGTGATGCTGTGTCTGATGTCGGCGATTGAAACGGGTGTTATTTTCCTGATCAATGATGGCATC
sample10  ACACCTCAAACGAACCGGTGATGCTGTGTCTGATGTCGGCGATTGAAACGGGTGTTATTTTCCTGATCAATGATGGCATC

Reference GACCGTGGTCTGTGGGATCTGCAGAACAAAGCCGAACGTCAAAATGACATTCTGGTGAAATACCGCCACATGAGTGTTCC
sample02  GACCGTGGTCTGTGGGATCTGCAGAACAAAGCCGAACGTCAAAATGACATTCTGGTGAAATACCGCCACATGAGTGTTCC
sample05  GACCGTGGTCTGTGGGATCTGCAGAACAAAGCCGAACGTCAAAATGACATTCTGGTGAAATACCGCCACATGAGTGTTCC
sample06  GACCGTGGTCTGTGGGATCTGCAGAACAAAGCCGAACGTCAAAATGACATTCTGGTGAAATACCGCCACATGAGTGTTCC
sample09  GACCGTGGTCTGTGGGATCTGCAGAACAAAGCCGAACGTCAAAATGACATTCTGGTGAAATACCGCCACATGAGTGTTCC
sample10  GACCGTGGTCTGTGGGATCTGCAGAACAAAGCCGAACGTCAAAATGACATTCTGGTGAAATACCGCCACATGAGTGTTCC

Reference ACCAGAATCCTAATGAGCAGCAGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGG
sample02  ACCAGAATCCTAATGAGCAGCAGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGG
sample05  ACCAGAATCCTAATGAGCAGCAGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGG
sample06  ACCAGAATCCTAATGAGCAGCAGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGG
sample09  ACCAGAATCCTAATGAGCAGCAGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGG
sample10  ACCAGAATCCTAATGAGCAGCAGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGG

Reference GTTTTTTGCTGAAAGGAGGAACTATATCCGGGTAACGAATTCAAGCTTGATATCATTCAGGACGAGCCTCAGACTCCAGC
sample02  GTTTTTTGCTGAAAGGAGGAACTATATCCGGGTAACGAATTCAAGCTTGATATCATTCAGGACGAGCCTCAGACTCCAGC
sample05  GTTTTTTGCTGAAAGGAGGAACTATATCCGGGTAACGAATTCAAGCTTGATATCATTCAGGACGAGCCTCAGACTCCAGC
sample06  GTTTTTTGCTGAAAGGAGGAACTATATCCGGGTAACGAATTCAAGCTTGATATCATTCAGGACGAGCCTCAGACTCCAGC
sample09  GTTTTTTGCTGAAAGGAGGAACTATATCCGGGTAACGAATTCAAGCTTGATATCATTCAGGACGAGCCTCAGACTCCAGC
sample10  GTTTTTTGCTGAAAGGAGGAACTATATCCGGGTAACGAATTCAAGCTTGATATCATTCAGGACGAGCCTCAGACTCCAGC

Reference GTAACTGGACTGCAATCAACTCACTGGCTCACCTTCACGGGTGGGCCTTTCTTCGGGATCCGCGCTGCGGACACATACAA
sample02  GTAACTGGACTGCAATCAACTCACTGGCTCACCTTCACGGGTGGGCCTTTCTTCGGGATCCGCGCTGCGGACACATACAA
sample05  GTAACTGGACTGCAATCAACTCACTGGCTCACCTTCACGGGTGGGCCTTTCTTCGGGATCCGCGCTGCGGACACATACAA
sample06  GTAACTGGACTGCAATCAACTCACTGGCTCACCTTCACGGGTGGGCCTTTCTTCGGGATCCGCGCTGCGGACACATACAA
sample09  GTAACTGGACTGCAATCAACTCACTGGCTCACCTTCACGGGTGGGCCTTTCTTCGGGATCCGCGCTGCGGACACATACAA
sample10  GTAACTGGACTGCAATCAACTCACTGGCTCACCTTCACGGGTGGGCCTTTCTTCGGGATCCGCGCTGCGGACACATACAA

Reference AGTTACCCA
sample02  AGTTACCCA
sample05  AGTTACCCA
sample06  AGTTACCCA
sample09  AGTTACCCA
sample10  AGTTACCCA

Reference GACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTATAAGAAGGAGATATACATATGAGTGCGAAGGCTGCTGAA
sample03  GACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTATAAGAAGGAGATATACATATGAGTGCGAAGGCTGCTGAA
sample04  GACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTATAAGAAGGAGATATACATATGAGTGCGAAGGCTGCTGAA
sample07  GACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTATAAGAAGGAGATATACATATGAGTGCGAAGGCTGCTGAA
sample08  GACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTATAAGAAGGAGATATACATATGAGTGCGAAGGCTGCTGAA
sample11  GACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTATAAGAAGGAGATATACATATGAGTGCGAAGGCTGCTGAA
sample12  GACCACAACGGTTTCCCTCTAGAAATAATTTTGTTTAACTATAAGAAGGAGATATACATATGAGTGCGAAGGCTGCTGAA

Reference GGTTATGAACAAATCGAAGTTGATGTGGTTGCTGTGTGGAAGGAAGGTTATGTGTATGAAAATCGTGGTAGTACCTCCGT
sample03  GGTTATGAACAAATCGAAGTTGATGTGGTTGCTGTGTGGAAGGAAGGTTATGTGTATGAAAATCGTGGTAGTACCTCCGT
sample04  GGTTATGAACAAATCGAAGTTGATGTGGTTGCTGTGTGGAAGGAAGGTTATGTGTATGAAAATCGTGGTAGTACCTCCGT
sample07  GGTTATGAACAAATCGAAGTTGATGTGGTTGCTGTGTGGAAGGAAGGTTATGTGTATGAAAATCGTGGTAGTACCTCCGT
sample08  GGTTATGAACAAATCGAAGTTGATGTGGTTGCTGTGTGGAAGGAAGGTTATGTGTATGAAAATCGTGGTAGTACCTCCGT
sample11  GGTTATGAACAAATCGAAGTTGATGTGGTTGCTGTGTGGAAGGAAGGTTATGTGTATGAAAATCGTGGTAGTACCTCCGT
sample12  GGTTATGAACAAATCGAAGTTGATGTGGTTGCTGTGTGGAAGGAAGGTTATGTGTATGAAAATCGTGGTAGTACCTCCGT

Reference GGATCAAAAAATTACCATCACGAAAGGCATGAAGAACGTTAATAGCGAAACCCGTACGGTCACCGCGACGCATTCTATTG
sample03  GGATCAAAAAATTACCATCACGAAAGGCATGAAGAACGTTAATAGCGAAACCCGTACGGTCACCGCGACGCATTCTATTG
sample04  GGATCAAAAAATTACCATCACGAAAGGCATGAAGAACGTTAATAGCGAAACCCGTACGGTCACCGCGACGCATTCTATTG
sample07  GGATCAAAAAATTACCATCACGAAAGGCATGAAGAACGTTAATAGCGAAACCCGTACGGTCACCGCGACGCATTCTATTG
sample08  GGATCAAAAAATTACCATCACGAAAGGCATGAAGAACGTTAATAGCGAAACCCGTACGGTCACCGCGACGCATTCTATTG
sample11  GGATCAAAAAATTACCATCACGAAAGGCATGAAGAACGTTAATAGCGAAACCCGTACGGTCACCGCGACGCATTCTATTG
sample12  GGATCAAAAAATTACCATCACGAAAGGCATGAAGAACGTTAATAGCGAAACCCGTACGGTCACCGCGACGCATTCTATTG

Reference GCAGTACCATCTCCACGGGTGACGCCTTTGAAATCGGCTCCGTGGAAGTTTCATATTCGCATAGCCACGAAGAATCACAA
sample03  GCAGTACCATCTCCACGGGTGACGCCTTTGAAATCGGCTCCGTGGAAGTTTCATATTCGCATAGCCACGAAGAATCACAA
sample04  GCAGTACCATCTCCACGGGTGACGCCTTTGAAATCGGCTCCGTGGAAGTTTCATATTCGCATAGCCACGAAGAATCACAA
sample07  GCAGTACCATCTCCACGGGTGACGCCTTTGAAATCGGCTCCGTGGAAGTTTCATATTCGCATAGCCACGAAGAATCACAA
sample08  GCAGTACCATCTCCACGGGTGACGCCTTTGAAATCGGCTCCGTGGAAGTTTCATATTCGCATAGCCACGAAGAATCACAA
sample11  GCAGTACCATCTCCACGGGTGACGCCTTTGAAATCGGCTCCGTGGAAGTTTCATATTCGCATAGCCACGAAGAATCACAA
sample12  GCAGTACCATCTCCACGGGTGACGCCTTTGAAATCGGCTCCGTGGAAGTTTCATATTCGCATAGCCACGAAGAATCACAA

Reference GTTTCGATGACCGAAACGGAAGTCTACGAATCAAAAGTGATTGAACACACCATTACGATCCCGCCGACCTCGAAGTTCAC
sample03  GTTTCGATGACCGAAACGGAAGTCTACGAATCAAAAGTGATTGAACACACCATTACGATCCCGCCGACCTCGAAGTTCAC
sample04  GTTTCGATGACCGAAACGGAAGTCTACGAATCAAAAGTGATTGAACACACCATTACGATCCCGCCGACCTCGAAGTTCAC
sample07  GTTTCGATGACCGAAACGGAAGTCTACGAATCAAAAGTGATTGAACACACCATTACGATCCCGCCGACCTCGAAGTTCAC
sample08  GTTTCGATGACCGAAACGGAAGTCTACGAATCAAAAGTGATTGAACACACCATTACGATCCCGCCGACCTCGAAGTTCAC
sample11  GTTTCGATGACCGAAACGGAAGTCTACGAATCAAAAGTGATTGAACACACCATTACGATCCCGCCGACCTCGAAGTTCAC
sample12  GTTTCGATGACCGAAACGGAAGTCTACGAATCAAAAGTGATTGAACACACCATTACGATCCCGCCGACCTCGAAGTTCAC

Reference GCGCTGGCAGCTGAACGCAGATGTCGGCGGTGCTGACATTGAATATATGTACCTGATCGATGAAGTTACCCCGATTGGCG
sample03  GCGCTGGCAGCTGAACGCAGATGTCGGCGGTGCTGACATTGAATATATGTACCTGATCGATGAAGTTACCCCGATTGGCG
sample04  GCGCTGGCAGCTGAACGCAGATGTCGGCGGTGCTGACATTGAATATATGTACCTGATCGATGAAGTTACCCCGATTGGCG
sample07  GCGCTGGCAGCTGAACGCAGATGTCGGCGGTGCTGACATTGAATATATGTACCTGATCGATGAAGTTACCCCGATTGGCG
sample08  GCGCTGGCAGCTGAACGCAGATGTCGGCGGTGCTGACATTGAATATATGTACCTGATCGATGAAGTTACCCCGATTGGCG
sample11  GCGCTGGCAGCTGAACGCAGATGTCGGCGGTGCTGACATTGAATATATGTACCTGATCGATGAAGTTACCCCGATTGGCG
sample12  GCGCTGGCAGCTGAACGCAGATGTCGGCGGTGCTGACATTGAATATATGTACCTGATCGATGAAGTTACCCCGATTGGCG

Reference GTACGCAGAGTATTCCGCAAGTGATCACCTCCCGTGCAAAAATTATCGTTGGTCGCCAGATTATCCTGGGCAAGACCGAA
sample03  GTACGCAGAGTATTCCGCAAGTGATCACCTCCCGTGCAAAAATTATCGTTGGTCGCCAGATTATCCTGGGCAAGACCGAA
sample04  GTACGCAGAGTATTCCGCAAGTGATCACCTCCCGTGCAAAAATTATCGTTGGTCGCCAGATTATCCTGGGCAAGACCGAA
sample07  GTACGCAGAGTATTCCGCAAGTGATCACCTCCCGTGCAAAAATTATCGTTGGTCGCCAGATTATCCTGGGCAAGACCGAA
sample08  GTACGCAGAGTATTCCGCAAGTGATCACCTCCCGTGCAAAAATTATCGTTGGTCGCCAGATTATCCTGGGCAAGACCGAA
sample11  GTACGCAGAGTATTCCGCAAGTGATCACCTCCCGTGCAAAAATTATCGTTGGTCGCCAGATTATCCTGGGCAAGACCGAA
sample12  GTACGCAGAGTATTCCGCAAGTGATCACCTCCCGTGCAAAAATTATCGTTGGTCGCCAGATTATCCTGGGCAAGACCGAA

Reference ATTCGTATCAAACATGCTGAACGCAAGGAATATATGACCGTGGTTAGCCGTAAATCTTGGCCGGCGGCCACGCTGGGTCA
sample03  ATTCGTATCAAACATGCTGAACGCAAGGAATATATGACCGTGGTTAGCCGTAAATCTTGGCCGGCGGCCACGCTGGGTCA
sample04  ATTCGTATCAAACATGCTGAACGCAAGGAATATATGACCGTGGTTAGCCGTAAATCTTGGCCGGCGGCCACGCTGGGTCA
sample07  ATTCGTATCAAACATGCTGAACGCAAGGAATATATGACCGTGGTTAGCCGTAAATCTTGGCCGGCGGCCACGCTGGGTCA
sample08  ATTCGTATCAAACATGCTGAACGCAAGGAATATATGACCGTGGTTAGCCGTAAATCTTGGCCGGCGGCCACGCTGGGTCA
sample11  ATTCGTATCAAACATGCTGAACGCAAGGAATATATGACCGTGGTTAGCCGTAAATCTTGGCCGGCGGCCACGCTGGGTCA
sample12  ATTCGTATCAAACATGCTGAACGCAAGGAATATATGACCGTGGTTAGCCGTAAATCTTGGCCGGCGGCCACGCTGGGTCA

Reference CAGTAAACTGTTTAAGTTCGTGCTGTACGAAGATTGGGGCGGTTTTCGCATCAAAACCCTGAATACGATGTATTCTGGTT
sample03  CAGTAAACTGTTTAAGTTCGTGCTGTACGAAGATTGGGGCGGTTTTCGCATCAAAACCCTGAATACGATGTATTCTGGTT
sample04  CAGTAAACTGTTTAAGTTCGTGCTGTACGAAGATTGGGGCGGTTTTCGCATCAAAACCCTGAATACGATGTATTCTGGTT
sample07  CAGTAAACTGTTTAAGTTCGTGCTGTACGAAGATTGGGGCGGTTTTCGCATCAAAACCCTGAATACGATGTATTCTGGTT
sample08  CAGTAAACTGTTTAAGTTCGTGCTGTACGAAGATTGGGGCGGTTTTCGCATCAAAACCCTGAATACGATGTATTCTGGTT
sample11  CAGTAAACTGTTTAAGTTCGTGCTGTACGAAGATTGGGGCGGTTTTCGCATCAAAACCCTGAATACGATGTATTCTGGTT
sample12  CAGTAAACTGTTTAAGTTCGTGCTGTACGAAGATTGGGGCGGTTTTCGCATCAAAACCCTGAATACGATGTATTCTGGTT

Reference ATGAATACGCGTATAGCTCTGACCAGGGCGGTATCTACTTCGATCAAGGCACCGACAACCCGAAACAGCGTTGGGCCATT
sample03  ATGAATACGCGTATAGCTCTGACCAGGGCGGTATCTACTTCGATCAAGGCACCGACAACCCGAAACAGCGTTGGGCCATT
sample04  ATGAATACGCGTATAGCTCTGACCAGGGCGGTATCTACTTCGATCAAGGCACCGACAACCCGAAACAGCGTTGGGCCATT
sample07  ATGAATACGCGTATAGCTCTGACCAGGGCGGTATCTACTTCGATCAAGGCACCGACAACCCGAAACAGCGTTGGGCCATT
sample08  ATGAATACGCGTATAGCTCTGACCAGGGCGGTATCTACTTCGATCAAGGCACCGACAACCCGAAACAGCGTTGGGCCATT
sample11  ATGAATACGCGTATAGCTCTGACCAGGGCGGTATCTACTTCGATCAAGGCACCGACAACCCGAAACAGCGTTGGGCCATT
sample12  ATGAATACGCGTATAGCTCTGACCAGGGCGGTATCTACTTCGATCAAGGCACCGACAACCCGAAACAGCGTTGGGCCATT

Reference AATAAGAGCCTGCCGCTGCGCCATGGTGATGTCGTGACCTTTATGAACAAATACTTCACGCGTTCTGGTCTGTGCTATGA
sample03  AATAAGAGCCTGCCGCTGCGCCATGGTGATGTCGTGACCTTTATGAACAAATACTTCACGCGTTCTGGTCTGTGCTATGA
sample04  AATAAGAGCCTGCCGCTGCGCCATGGTGATGTCGTGACCTTTATGAACAAATACTTCACGCGTTCTGGTCTGTGCTATGA
sample07  AATAAGAGCCTGCCGCTGCGCCATGGTGATGTCGTGACCTTTATGAACAAATACTTCACGCGTTCTGGTCTGTGCTATGA
sample08  AATAAGAGCCTGCCGCTGCGCCATGGTGATGTCGTGACCTTTATGAACAAATACTTCACGCGTTCTGGTCTGTGCTATGA
sample11  AATAAGAGCCTGCCGCTGCGCCATGGTGATGTCGTGACCTTTATGAACAAATACTTCACGCGTTCTGGTCTGTGCTATGA
sample12  AATAAGAGCCTGCCGCTGCGCCATGGTGATGTCGTGACCTTTATGAACAAATACTTCACGCGTTCTGGTCTGTGCTATGA

Reference TGACGGCCCGGCGACCAATGTGTATTGTCTGGATAAACGCGAAGACAAGTGGATTCTGGAAGTTGTCGGATAATGAGCAG
sample03  TGACGGCCCGGCGACCAATGTGTATTGTCTGGATAAACGCGAAGACAAGTGGATTCTGGAAGTTGTCGGATAATGAGCAG
sample04  TGACGGCCCGGCGACCAATGTGTATTGTCTGGATAAACGCGAAGACAAGTGGATTCTGGAAGTTGTCGGATAATGAGCAG
sample07  TGACGGCCCGGCGACCAATGTGTATTGTCTGGATAAACGCGAAGACAAGTGGATTCTGGAAGTTGTCGGATAATGAGCAG
sample08  TGACGGCCCGGCGACCAATGTGTATTGTCTGGATAAACGCGAAGACAAGTGGATTCTGGAAGTTGTCGGATAATGAGCAG
sample11  TGACGGCCCGGCGACCAATGTGTATTGTCTGGATAAACGCGAAGACAAGTGGATTCTGGAAGTTGTCGGATAATGAGCAG
sample12  TGACGGCCCGGCGACCAATGTGTATTGTCTGGATAAACGCGAAGACAAGTGGATTCTGGAAGTTGTCGGATAATGAGCAG

Reference CAGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCTGAAAGGAGGA
sample03  CAGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCTGAAAGGAGGA
sample04  CAGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCTGAAAGGAGGA
sample07  CAGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCTGAAAGGAGGA
sample08  CAGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCTGAAAGGAGGA
sample11  CAGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCTGAAAGGAGGA
sample12  CAGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCTGAAAGGAGGA

Reference ACTATATCCGGGTAACGAATTCAAGCTTGATATCATTCAGGACGAGCCTCAGACTCCAGCGTAACTGGACTGCAATCAAC
sample03  ACTATATCCGGGTAACGAATTCAAGCTTGATATCATTCAGGACGAGCCTCAGACTCCAGCGTAACTGGACTGCAATCAAC
sample04  ACTATATCCGGGTAACGAATTCAAGCTTGATATCATTCAGGACGAGCCTCAGACTCCAGCGTAACTGGACTGCAATCAAC
sample07  ACTATATCCGGGTAACGAATTCAAGCTTGATATCATTCAGGACGAGCCTCAGACTCCAGCGTAACTGGACTGCAATCAAC
sample08  ACTATATCCGGGTAACGAATTCAAGCTTGATATCATTCAGGACGAGCCTCAGACTCCAGCGTAACTGGACTGCAATCAAC
sample11  ACTATATCCGGGTAACGAATTCAAGCTTGATATCATTCAGGACGAGCCTCAGACTCCAGCGTAACTGGACTGCAATCAAC
sample12  ACTATATCCGGGTAACGAATTCAAGCTTGATATCATTCAGGACGAGCCTCAGACTCCAGCGTAACTGGACTGCAATCAAC

Reference TCACTGGCTCACCTTCACGGGTGGGCCTTTCTTCGGGATCCGCGCTGCGGACACATACAAAGTTACCCA
sample03  TCACTGGCTCACCTTCACGGGTGGGCCTTTCTTCGGGATCCGCGCTGCGGACACATACAAAGTTACCCA
sample04  TCACTGGCTCACCTTCACGGGTGGGCCTTTCTTCGGGATCCGCGCTGCGGACACATACAAAGTTACCCA
sample07  TCACTGGCTCACCTTCACGGGTGGGCCTTTCTTCGGGATCCGCGCTGCGGACACATACAAAGTTACCCA
sample08  TCACTGGCTCACCTTCACGGGTGGGCCTTTCTTCGGGATCCGCGCTGCGGACACATACAAAGTTACCCA
sample11  TCACTGGCTCACCTTCACGGGTGGGCCTTTCTTCGGGATCCGCGCTGCGGACACATACAAAGTTACCCA
sample12  TCACTGGCTCACCTTCACGGGTGGGCCTTTCTTCGGGATCCGCGCTGCGGACACATACAAAGTTACCCA

Insert QC

This section can be used to ensure the provided insert reference matches the insert found in the assembly. The table belows shows coverage and BLAST identity between the two. Reference coverage is the percentage of the provided insert reference sequence covered in the alignment with the assembled construct. Assembly coverage is the percentage of the assembled insert sequence covered in the alignment with the provided insert reference. BLAST identity is calculated as: (length - ins - del - sub) / length. If both coverage and identity are 0, the assembled insert did not align with the provided insert reference.

Sample name	Reference coverage	Assembly coverage	BLAST Identity
sample02	100.0	100.0	100.0
sample03	100.0	100.0	100.0
sample04	100.0	100.0	100.0
sample05	100.0	100.0	100.0
sample06	100.0	100.0	100.0
sample07	100.0	100.0	100.0
sample08	100.0	100.0	100.0
sample09	100.0	100.0	100.0
sample10	100.0	100.0	100.0
sample11	100.0	100.0	100.0
sample12	100.0	100.0	100.0

Insert variants

The following tables and figures are output from bcftools from finding any variants between the consensus insert and the provided reference insert.

Variant counts per sample. See output bcf file for info on individual variants.

filename	id	MNPs	SNPs	indels	multiallelic SNP sites	multiallelic sites	no-ALTs	others	records
sample02.insert.stats	sample02.insert.stats	0	0	0	0	0	0	0	0
sample03.insert.stats	sample03.insert.stats	0	0	0	0	0	0	0	0
sample04.insert.stats	sample04.insert.stats	0	0	0	0	0	0	0	0
sample05.insert.stats	sample05.insert.stats	0	0	0	0	0	0	0	0
sample06.insert.stats	sample06.insert.stats	0	0	0	0	0	0	0	0
sample07.insert.stats	sample07.insert.stats	0	0	0	0	0	0	0	0
sample08.insert.stats	sample08.insert.stats	0	0	0	0	0	0	0	0
sample09.insert.stats	sample09.insert.stats	0	0	0	0	0	0	0	0
sample10.insert.stats	sample10.insert.stats	0	0	0	0	0	0	0	0
sample11.insert.stats	sample11.insert.stats	0	0	0	0	0	0	0	0
sample12.insert.stats	sample12.insert.stats	0	0	0	0	0	0	0	0

Trans counts per sample. See output bcf file for info on individual transitions.

filename	id	ts	tv	ts/tv	ts (1st ALT)	tv (1st ALT)	ts/tv (1st ALT)
sample02.insert.stats	sample02.insert.stats	0	0	0.0	0	0	0.0
sample03.insert.stats	sample03.insert.stats	0	0	0.0	0	0	0.0
sample04.insert.stats	sample04.insert.stats	0	0	0.0	0	0	0.0
sample05.insert.stats	sample05.insert.stats	0	0	0.0	0	0	0.0
sample06.insert.stats	sample06.insert.stats	0	0	0.0	0	0	0.0
sample07.insert.stats	sample07.insert.stats	0	0	0.0	0	0	0.0
sample08.insert.stats	sample08.insert.stats	0	0	0.0	0	0	0.0
sample09.insert.stats	sample09.insert.stats	0	0	0.0	0	0	0.0
sample10.insert.stats	sample10.insert.stats	0	0	0.0	0	0	0.0
sample11.insert.stats	sample11.insert.stats	0	0	0.0	0	0	0.0
sample12.insert.stats	sample12.insert.stats	0	0	0.0	0	0	0.0

Full construct QC

This section can be used to ensure the provided reference matches the assembly. The table belows shows coverage and BLAST identity between the provided reference and assembly. Reference coverage is the percentage of the provided reference sequence covered in the alignment with the assembled construct. Assembly coverage is the percentage of assembled contruct sequence covered in the alignment with the provided reference. BLAST Identity is calculated as: (length - ins - del - sub) / length. If both coverage and identity are 0, the assembly did not align with the provided reference.

Sample name	Reference coverage	Assembly coverage	BLAST Identity
sample02	100.0	100.0	94.57
sample03	99.3825	98.7726	100.0
sample04	99.3825	98.773	99.97
sample05	100.0	100.0	100.0
sample06	100.0	100.0	99.97
sample07	99.3825	98.7726	100.0
sample08	99.3825	98.7726	100.0
sample09	100.0	100.0	100.0
sample10	100.0	100.0	100.0
sample11	99.3825	98.7726	100.0
sample12	99.3825	98.7726	100.0

Additionally, BCFtools was used to report any variants between the provided reference and assembly.

Variant counts per sample. See output bcf file for info on individual variants.

filename	id	MNPs	SNPs	indels	multiallelic SNP sites	multiallelic sites	no-ALTs	others	records
sample02.full_construct.stats	sample02.full_construct.stats	0	0	0	0	0	0	0	0
sample03.full_construct.stats	sample03.full_construct.stats	0	0	0	0	0	0	0	0
sample04.full_construct.stats	sample04.full_construct.stats	0	0	0	0	0	0	0	0
sample05.full_construct.stats	sample05.full_construct.stats	0	0	0	0	0	0	0	0
sample06.full_construct.stats	sample06.full_construct.stats	0	0	0	0	0	0	0	0
sample07.full_construct.stats	sample07.full_construct.stats	0	0	0	0	0	0	0	0
sample08.full_construct.stats	sample08.full_construct.stats	0	0	0	0	0	0	0	0
sample09.full_construct.stats	sample09.full_construct.stats	0	0	0	0	0	0	0	0
sample10.full_construct.stats	sample10.full_construct.stats	0	0	0	0	0	0	0	0
sample11.full_construct.stats	sample11.full_construct.stats	0	0	0	0	0	0	0	0
sample12.full_construct.stats	sample12.full_construct.stats	0	0	0	0	0	0	0	0

Trans counts per sample. See output bcf file for info on individual transitions.

filename	id	ts	tv	ts/tv	ts (1st ALT)	tv (1st ALT)	ts/tv (1st ALT)
sample02.full_construct.stats	sample02.full_construct.stats	0	0	0.0	0	0	0.0
sample03.full_construct.stats	sample03.full_construct.stats	0	0	0.0	0	0	0.0
sample04.full_construct.stats	sample04.full_construct.stats	0	0	0.0	0	0	0.0
sample05.full_construct.stats	sample05.full_construct.stats	0	0	0.0	0	0	0.0
sample06.full_construct.stats	sample06.full_construct.stats	0	0	0.0	0	0	0.0
sample07.full_construct.stats	sample07.full_construct.stats	0	0	0.0	0	0	0.0
sample08.full_construct.stats	sample08.full_construct.stats	0	0	0.0	0	0	0.0
sample09.full_construct.stats	sample09.full_construct.stats	0	0	0.0	0	0	0.0
sample10.full_construct.stats	sample10.full_construct.stats	0	0	0.0	0	0	0.0
sample11.full_construct.stats	sample11.full_construct.stats	0	0	0.0	0	0	0.0
sample12.full_construct.stats	sample12.full_construct.stats	0	0	0.0	0	0	0.0

Dot plots

These dot plots have been created by aligning the assembly to itself to reveal any repeats or repetitive regions. Black is for repeats found in the forward strand and red for repeats found in the reverse complement. This was done using last

Software versions

Name	Version
medaka	2.0.0
flye	2.9.4-b1799
minimap2	2.28-r1209
samtools	1.19.2
seqkit	v2.4.0
Trycycler	v0.5.5
bedtools	v2.31.0
fastcat	0.18.6
rasusa	0.7.1
spoa	0.0.10
pandas	1.3.5
plannotate	1.2.0
bokeh	3.1.1

Workflow parameters

Key	Value
out_dir	wf-clone-validation
store_dir	wf-clone-validation/store_dir
fastq	wf-clone-validation/data/clone_val_test/fastq
primers	wf-clone-validation/data/clone_val_test/primers.tsv
host_reference	wf-clone-validation/data/clone_val_test/host_reference.fa.gz
regions_bedfile	wf-clone-validation/data/clone_val_test/reference.bed
sample_sheet	wf-clone-validation/data/clone_val_test/sample_sheet.csv
override_basecaller_cfg	dna_r10.4.1_e8.2_400bps_hac@v4.2.0
bam	None
db_directory	None
threads	4
approx_size	7000
assm_coverage	60
trim_length	150
prefix	None
insert_reference	None
sample	None
analyse_unclassified	False
medaka_model_path	None
flye_quality	nano-hq
non_uniform_coverage	False
large_construct	False
full_reference	None
cutsite_mismatch	1
primer_mismatch	2
expected_coverage	95
expected_identity	99
assembly_tool	flye
canu_fast	False
client_fields	None