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.

Sample	Assembly completed / failed reason	Length	Mean Quality
sample02	Completed successfully	3037	37.67
sample03	Completed successfully	3096	40.54
sample04	Completed successfully	3096	52.02
sample05	Completed successfully	3036	52.18
sample06	Completed successfully	3037	35.65
sample07	Completed successfully	3096	44.4
sample08	Completed successfully	3096	45.99
sample09	Completed successfully	3036	48.27
sample10	Completed successfully	3036	45.87
sample11	Completed successfully	3096	48.94

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.	430	1261	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)	248	367	119	+
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	61	152	91	-
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	2282	61	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.	1472	2154	682	-
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	1291	1339	48	+
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	2282	31	786	-
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	152	184	32	-
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	1436	1466	30	+
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	2051	2154	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.	2178	2276	98	-
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	60	142	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.	2976	771	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)	834	953	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	1049	1140	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	1140	1956	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.	2083	2765	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	2898	2946	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	1170	1956	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	1017	1049	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	2771	2801	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	2081	2184	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.	1962	2059	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	1059	1141	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.	2571	366	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)	2389	2508	119	+
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	2202	2293	91	-
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	1386	2202	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.	577	1259	682	-
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	396	444	48	+
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	1386	2172	786	-
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	2293	2325	32	-
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	541	571	30	+
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	1156	1259	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.	1283	1380	98	-
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	2201	2283	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.	764	1595	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)	1658	1777	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	1873	1964	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	1964	2780	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.	2907	553	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	686	734	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	1994	2780	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	1841	1873	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	559	589	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	2905	3008	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.	2786	2883	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	1883	1965	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.	1698	2529	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)	2592	2711	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	2807	2898	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	2898	677	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.	805	1487	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	1620	1668	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	2928	677	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	2775	2807	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	1493	1523	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	803	906	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.	683	781	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	2817	2899	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.	2950	745	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)	808	927	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	1023	1114	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	1114	1930	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.	2057	2739	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	2872	2920	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	1144	1930	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	991	1023	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	2745	2775	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	2055	2158	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.	1936	2033	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	1033	1115	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.	2137	3028	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)	3091	114	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	210	301	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	301	1117	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.	1244	1926	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	2059	2107	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	331	1117	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	178	210	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	1932	1962	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	1242	1345	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.	1123	1220	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	220	302	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.	2117	2948	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)	3011	94	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	190	281	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	281	1097	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.	1224	1906	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	2039	2087	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	311	1097	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	158	190	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	1912	1942	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	1222	1325	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.	1103	1200	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	200	282	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.	2849	644	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)	707	826	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	922	1013	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	1013	1829	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.	1956	2638	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	2771	2819	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	1043	1829	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	890	922	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	2644	2674	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	1954	2057	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.	1835	1932	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	932	1014	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.	2117	3008	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)	3071	94	119	-
cat promoter	snapgene	100.0%	100.0%	promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase	190	281	91	+
KanR	snapgene	99.4%	100.0%	aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes	281	1097	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.	1224	1906	682	+
T7 terminator	snapgene	100.0%	100.0%	transcription terminator for bacteriophage T7 RNA polymerase	2039	2087	48	-
kanMX	snapgene	99.2%	57.9%	yeast selectable marker conferring kanamycin resistance (Wach et al., 1994)	311	1097	786	+
tonB terminator	snapgene	100.0%	100.0%	bidirectional E. coli tonB-P14 transcription terminator	158	190	32	+
T3Te terminator	snapgene	100.0%	100.0%	phage T3 early transcription terminator	1912	1942	30	-
RNAI	Rfam	100.0%	99.0%	Accession: RF00106 - RNAI	1222	1325	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.	1103	1200	98	+
PDK intron	snapgene	100.0%	5.1%	pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0	200	282	82	+

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	outputs/out_dir/
approx_size	7000
assm_coverage	60
analyse_unclassified	False
large_construct	False
trim_length	0
min_quality	9
flye_quality	nano-hq
non_uniform_coverage	False
assembly_tool	flye
canu_fast	False
cutsite_mismatch	1
primer_mismatch	2
expected_coverage	95
expected_identity	99
threads	4
fastq	data/input/fastq/fastq
sample_sheet	data/input/sample_sheet/sample_sheet.csv
store_dir	None
bam	None
db_directory	None
host_reference	None
regions_bedfile	None
prefix	None
primers	None
insert_reference	None
sample	None
override_basecaller_cfg	None
medaka_model_path	None
full_reference	None
client_fields	None