AutoCloner

Multiple sequence alignment - TraesCS6D01G170300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS6D01G170300	chr6D	100.000	2653	0	0	1	2653	157157067	157154415	0.000000e+00	4900.0
1	TraesCS6D01G170300	chr6A	90.696	1494	102	18	566	2048	211924105	211925572	0.000000e+00	1954.0
2	TraesCS6D01G170300	chr6A	87.332	742	80	10	1919	2653	569406993	569407727	0.000000e+00	837.0
3	TraesCS6D01G170300	chr6B	94.577	1051	45	7	878	1922	279907310	279906266	0.000000e+00	1615.0
4	TraesCS6D01G170300	chr6B	85.349	744	92	10	1922	2653	141664336	141665074	0.000000e+00	754.0
5	TraesCS6D01G170300	chr6B	88.691	619	53	6	1	605	279908584	279907969	0.000000e+00	739.0
6	TraesCS6D01G170300	chr6B	82.973	740	108	10	1922	2653	136361886	136362615	0.000000e+00	652.0
7	TraesCS6D01G170300	chr6B	93.939	132	8	0	633	764	279907637	279907506	1.610000e-47	200.0
8	TraesCS6D01G170300	chr6B	90.476	105	2	6	762	865	279907392	279907295	5.960000e-27	132.0
9	TraesCS6D01G170300	chr2B	85.464	743	80	16	1922	2653	638762609	638763334	0.000000e+00	749.0
10	TraesCS6D01G170300	chr4D	85.210	737	90	11	1920	2653	13045443	13046163	0.000000e+00	739.0
11	TraesCS6D01G170300	chr3B	85.125	679	81	17	1985	2653	2268850	2269518	0.000000e+00	676.0
12	TraesCS6D01G170300	chr5B	85.388	657	73	14	2009	2653	390551924	390551279	0.000000e+00	660.0
13	TraesCS6D01G170300	chr2A	85.038	655	84	8	2011	2653	717176823	717177475	0.000000e+00	654.0
14	TraesCS6D01G170300	chr7D	83.042	743	103	16	1920	2653	65617080	65616352	0.000000e+00	652.0
15	TraesCS6D01G170300	chr4B	85.149	101	9	5	367	465	94767319	94767223	6.040000e-17	99.0
16	TraesCS6D01G170300	chr7A	77.931	145	17	10	389	525	511538100	511538237	2.830000e-10	76.8

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS6D01G170300	chr6D	157154415	157157067	2652	True	4900.0	4900	100.00000	1	2653	1	chr6D.!!$R1	2652
1	TraesCS6D01G170300	chr6A	211924105	211925572	1467	False	1954.0	1954	90.69600	566	2048	1	chr6A.!!$F1	1482
2	TraesCS6D01G170300	chr6A	569406993	569407727	734	False	837.0	837	87.33200	1919	2653	1	chr6A.!!$F2	734
3	TraesCS6D01G170300	chr6B	141664336	141665074	738	False	754.0	754	85.34900	1922	2653	1	chr6B.!!$F2	731
4	TraesCS6D01G170300	chr6B	279906266	279908584	2318	True	671.5	1615	91.92075	1	1922	4	chr6B.!!$R1	1921
5	TraesCS6D01G170300	chr6B	136361886	136362615	729	False	652.0	652	82.97300	1922	2653	1	chr6B.!!$F1	731
6	TraesCS6D01G170300	chr2B	638762609	638763334	725	False	749.0	749	85.46400	1922	2653	1	chr2B.!!$F1	731
7	TraesCS6D01G170300	chr4D	13045443	13046163	720	False	739.0	739	85.21000	1920	2653	1	chr4D.!!$F1	733
8	TraesCS6D01G170300	chr3B	2268850	2269518	668	False	676.0	676	85.12500	1985	2653	1	chr3B.!!$F1	668
9	TraesCS6D01G170300	chr5B	390551279	390551924	645	True	660.0	660	85.38800	2009	2653	1	chr5B.!!$R1	644
10	TraesCS6D01G170300	chr2A	717176823	717177475	652	False	654.0	654	85.03800	2011	2653	1	chr2A.!!$F1	642
11	TraesCS6D01G170300	chr7D	65616352	65617080	728	True	652.0	652	83.04200	1920	2653	1	chr7D.!!$R1	733

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
621	636	1.06424	TGCTCCTGCATTCATGGATGT	60.064	47.619	15.55	0.0	45.31	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2460	2979	0.458669	GATCCGGTCTAGGCGTGAAA	59.541	55.0	0.0	0.0	0.0	2.69	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	1.291877	CGTCCGCCTTGGTCTTCTTG	61.292	60.000	0.00	0.00	39.52	3.02
50	51	4.467795	TGGTCTTCTTGGACTAGGATGAAG	59.532	45.833	0.00	1.99	36.55	3.02
79	93	3.050275	GCTTCGTGCCTCCACCAC	61.050	66.667	0.00	0.00	38.79	4.16
98	112	3.228688	GAGATTTGGCCGCGATCGC	62.229	63.158	29.80	29.80	37.85	4.58
126	140	4.418328	GGCGGCACACCCATACCA	62.418	66.667	3.07	0.00	0.00	3.25
136	150	4.488136	CCATACCAGCGGCAGCCA	62.488	66.667	13.30	0.00	46.67	4.75
176	190	4.530857	GGTGCGACGAGATGGGGG	62.531	72.222	0.00	0.00	0.00	5.40
246	260	2.391389	GGTGCGTAAGACTGGCTGC	61.391	63.158	0.00	0.00	43.02	5.25
247	261	2.432456	TGCGTAAGACTGGCTGCG	60.432	61.111	3.74	3.74	43.02	5.18
271	285	2.443577	GTAGGGTCGGGGGAGTCC	60.444	72.222	0.00	0.00	0.00	3.85
346	360	2.360350	CCGCATGACAGTTGGGCT	60.360	61.111	0.00	0.00	0.00	5.19
360	374	3.788766	GGCTTTCGTGCGACGCAT	61.789	61.111	27.23	0.00	41.91	4.73
361	375	2.173382	GCTTTCGTGCGACGCATT	59.827	55.556	27.23	0.00	41.91	3.56
364	378	3.587342	TTTCGTGCGACGCATTGCC	62.587	57.895	27.23	12.02	41.91	4.52
375	389	1.075542	CGCATTGCCACTTTACTCGA	58.924	50.000	2.41	0.00	0.00	4.04
383	397	2.503375	CTTTACTCGACCGCGCGT	60.503	61.111	29.95	17.00	39.09	6.01
479	493	6.467677	CATCTATCATTTATTGGAGGGACGT	58.532	40.000	0.00	0.00	0.00	4.34
490	505	1.546099	GGAGGGACGTTTTTGGCCTTA	60.546	52.381	3.32	0.00	0.00	2.69
539	554	8.392124	CATCATCTATTAGTGATGCTCTTACG	57.608	38.462	16.36	0.00	43.45	3.18
540	555	7.745620	TCATCTATTAGTGATGCTCTTACGA	57.254	36.000	0.00	0.00	40.59	3.43
547	562	7.667043	TTAGTGATGCTCTTACGAAAACATT	57.333	32.000	0.00	0.00	0.00	2.71
548	563	8.766000	TTAGTGATGCTCTTACGAAAACATTA	57.234	30.769	0.00	0.00	0.00	1.90
605	620	5.182001	TGAAGGTGCTTAAATCTTCTTGCTC	59.818	40.000	2.65	0.00	37.21	4.26
606	621	4.013050	AGGTGCTTAAATCTTCTTGCTCC	58.987	43.478	0.00	0.00	35.22	4.70
621	636	1.064240	TGCTCCTGCATTCATGGATGT	60.064	47.619	15.55	0.00	45.31	3.06
624	639	1.210234	TCCTGCATTCATGGATGTCGT	59.790	47.619	15.55	0.00	0.00	4.34
627	642	3.461061	CTGCATTCATGGATGTCGTACT	58.539	45.455	15.55	0.00	0.00	2.73
676	995	2.239654	CCTCTGTCCAAAGGGAGCAATA	59.760	50.000	0.00	0.00	46.12	1.90
687	1006	7.760470	CCAAAGGGAGCAATATGGTTAAACCA	61.760	42.308	0.00	0.00	45.36	3.67
722	1041	4.075963	AGCAACAGCCAAAAATGTCATT	57.924	36.364	0.00	0.00	0.00	2.57
841	1277	3.983988	ACATGATATTGACATCGCTCGAC	59.016	43.478	0.00	0.00	0.00	4.20
855	1291	3.495894	GCTCGACGATCTTGCAATTAG	57.504	47.619	0.00	0.00	0.00	1.73
856	1292	2.219674	GCTCGACGATCTTGCAATTAGG	59.780	50.000	0.00	0.00	0.00	2.69
857	1293	2.201732	TCGACGATCTTGCAATTAGGC	58.798	47.619	0.00	0.00	0.00	3.93
858	1294	1.933181	CGACGATCTTGCAATTAGGCA	59.067	47.619	0.00	0.00	43.19	4.75
859	1295	2.033407	CGACGATCTTGCAATTAGGCAG	60.033	50.000	0.00	0.00	45.88	4.85
860	1296	2.939103	GACGATCTTGCAATTAGGCAGT	59.061	45.455	0.00	0.00	45.88	4.40
861	1297	4.119862	GACGATCTTGCAATTAGGCAGTA	58.880	43.478	0.00	0.00	45.88	2.74
862	1298	4.513442	ACGATCTTGCAATTAGGCAGTAA	58.487	39.130	0.00	0.00	45.88	2.24
863	1299	5.126067	ACGATCTTGCAATTAGGCAGTAAT	58.874	37.500	0.00	0.00	45.88	1.89
864	1300	5.590259	ACGATCTTGCAATTAGGCAGTAATT	59.410	36.000	0.00	0.00	45.88	1.40
865	1301	6.095440	ACGATCTTGCAATTAGGCAGTAATTT	59.905	34.615	0.00	0.00	45.88	1.82
866	1302	6.974622	CGATCTTGCAATTAGGCAGTAATTTT	59.025	34.615	0.00	0.00	45.88	1.82
867	1303	7.489113	CGATCTTGCAATTAGGCAGTAATTTTT	59.511	33.333	0.00	0.00	45.88	1.94
923	1359	8.258708	GCTTACCTTATCCTACCAACCATATAG	58.741	40.741	0.00	0.00	0.00	1.31
987	1451	2.876550	TCCCGTCTACATGATCTACACG	59.123	50.000	0.00	0.00	0.00	4.49
1065	1529	0.878416	GTGCTCGCCACCATTTGTTA	59.122	50.000	0.00	0.00	38.55	2.41
1126	1590	2.587194	CGCCCATCTTGCTCCTCG	60.587	66.667	0.00	0.00	0.00	4.63
1455	1922	1.962822	CGCTGAGGCAGTGCTTCAA	60.963	57.895	27.44	13.61	43.63	2.69
1594	2061	6.398918	AGCTAATAAGGATTAATGTCGCGAT	58.601	36.000	14.06	0.00	32.17	4.58
1763	2235	3.285745	GAACACACGACAAATTTCGGAC	58.714	45.455	4.68	0.00	43.58	4.79
1769	2241	3.723764	CACGACAAATTTCGGACACTTTG	59.276	43.478	4.68	0.00	43.58	2.77
1963	2435	0.246360	CAAATTCGGCCCCTCAAACC	59.754	55.000	0.00	0.00	0.00	3.27
2074	2557	8.849168	CATCCTTAAATCCATACAAAGCATGTA	58.151	33.333	5.04	5.04	43.63	2.29
2075	2558	8.815565	TCCTTAAATCCATACAAAGCATGTAA	57.184	30.769	6.48	0.00	43.63	2.41
2185	2675	2.439104	GCTCCGGCTCATCCTCCTT	61.439	63.158	0.00	0.00	35.22	3.36
2255	2746	0.617413	CTTGTGCCTCCATCTCCTGT	59.383	55.000	0.00	0.00	0.00	4.00
2310	2801	2.733590	CGGAGGGAATCGAGGATGA	58.266	57.895	0.00	0.00	0.00	2.92
2472	2991	1.480954	GATCCAGGTTTCACGCCTAGA	59.519	52.381	0.00	0.00	34.45	2.43
2499	3018	3.292656	CTCAAGGAGCTCGAGCCA	58.707	61.111	32.94	9.87	43.38	4.75
2627	3148	7.463618	AGGAGGAAAATATGGATGGATGATAGT	59.536	37.037	0.00	0.00	0.00	2.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	3.119096	GAAGACCAAGGCGGACGC	61.119	66.667	8.39	8.39	38.63	5.19
20	21	1.125093	TCCAAGAAGACCAAGGCGGA	61.125	55.000	0.00	0.00	38.63	5.54
37	38	0.249657	CCGCAGCTTCATCCTAGTCC	60.250	60.000	0.00	0.00	0.00	3.85
67	81	0.321653	AAATCTCGTGGTGGAGGCAC	60.322	55.000	0.00	0.00	34.74	5.01
79	93	2.931386	GATCGCGGCCAAATCTCG	59.069	61.111	6.13	0.00	0.00	4.04
98	112	2.125147	TGCCGCCGATGAAGAAGG	60.125	61.111	0.00	0.00	0.00	3.46
112	126	2.824041	CGCTGGTATGGGTGTGCC	60.824	66.667	0.00	0.00	0.00	5.01
145	159	0.667184	CGCACCAGATTTGTTTGGGC	60.667	55.000	0.00	0.00	38.82	5.36
149	163	1.531149	CTCGTCGCACCAGATTTGTTT	59.469	47.619	0.00	0.00	0.00	2.83
151	165	0.317160	TCTCGTCGCACCAGATTTGT	59.683	50.000	0.00	0.00	0.00	2.83
196	210	4.660938	GCCACGGCTCCCACCTTT	62.661	66.667	0.00	0.00	38.26	3.11
232	246	3.188786	GCCGCAGCCAGTCTTACG	61.189	66.667	0.00	0.00	0.00	3.18
346	360	2.127421	GCAATGCGTCGCACGAAA	60.127	55.556	24.34	0.00	46.05	3.46
359	373	1.722011	CGGTCGAGTAAAGTGGCAAT	58.278	50.000	0.00	0.00	0.00	3.56
360	374	0.947180	GCGGTCGAGTAAAGTGGCAA	60.947	55.000	0.00	0.00	0.00	4.52
361	375	1.373748	GCGGTCGAGTAAAGTGGCA	60.374	57.895	0.00	0.00	0.00	4.92
364	378	2.774951	CGCGCGGTCGAGTAAAGTG	61.775	63.158	24.84	0.00	38.10	3.16
365	379	2.503375	CGCGCGGTCGAGTAAAGT	60.503	61.111	24.84	0.00	38.10	2.66
366	380	2.503375	ACGCGCGGTCGAGTAAAG	60.503	61.111	35.22	1.22	46.46	1.85
375	389	2.000215	TACATCATCAGACGCGCGGT	62.000	55.000	35.22	19.76	0.00	5.68
454	468	5.352569	CGTCCCTCCAATAAATGATAGATGC	59.647	44.000	0.00	0.00	0.00	3.91
458	472	7.568199	AAAACGTCCCTCCAATAAATGATAG	57.432	36.000	0.00	0.00	0.00	2.08
467	481	0.966179	GCCAAAAACGTCCCTCCAAT	59.034	50.000	0.00	0.00	0.00	3.16
471	485	1.810755	CTAAGGCCAAAAACGTCCCTC	59.189	52.381	5.01	0.00	0.00	4.30
605	620	1.671979	ACGACATCCATGAATGCAGG	58.328	50.000	0.00	0.00	0.00	4.85
606	621	3.246936	CAGTACGACATCCATGAATGCAG	59.753	47.826	0.00	0.00	0.00	4.41
612	627	3.445805	TGCTTACAGTACGACATCCATGA	59.554	43.478	0.00	0.00	0.00	3.07
616	631	3.062234	GCTTTGCTTACAGTACGACATCC	59.938	47.826	0.00	0.00	0.00	3.51
621	636	3.653539	TGAGCTTTGCTTACAGTACGA	57.346	42.857	0.00	0.00	39.88	3.43
624	639	4.685169	GCAATGAGCTTTGCTTACAGTA	57.315	40.909	14.55	0.00	46.66	2.74
687	1006	4.036852	GGCTGTTGCTTCTACAAACTTCTT	59.963	41.667	0.00	0.00	39.59	2.52
722	1041	6.072175	GCTTTGGTGTATTTTGGTCTACATCA	60.072	38.462	0.00	0.00	37.23	3.07
812	1248	7.099120	AGCGATGTCAATATCATGTGCTAATA	58.901	34.615	0.00	0.00	34.28	0.98
841	1277	5.679734	ATTACTGCCTAATTGCAAGATCG	57.320	39.130	4.94	0.00	41.51	3.69
865	1301	4.517453	ACTGCCTAATTGTCGTAGCAAAAA	59.483	37.500	0.00	0.00	31.63	1.94
866	1302	4.069304	ACTGCCTAATTGTCGTAGCAAAA	58.931	39.130	0.00	0.00	31.63	2.44
867	1303	3.670625	ACTGCCTAATTGTCGTAGCAAA	58.329	40.909	0.00	0.00	31.63	3.68
868	1304	3.328382	ACTGCCTAATTGTCGTAGCAA	57.672	42.857	0.00	0.00	0.00	3.91
869	1305	4.459390	TTACTGCCTAATTGTCGTAGCA	57.541	40.909	0.00	0.00	0.00	3.49
870	1306	5.522460	TCAATTACTGCCTAATTGTCGTAGC	59.478	40.000	17.32	0.00	46.64	3.58
871	1307	7.358435	CGATCAATTACTGCCTAATTGTCGTAG	60.358	40.741	21.78	11.44	46.64	3.51
872	1308	6.419710	CGATCAATTACTGCCTAATTGTCGTA	59.580	38.462	21.78	10.15	46.64	3.43
873	1309	5.234329	CGATCAATTACTGCCTAATTGTCGT	59.766	40.000	21.78	13.26	46.64	4.34
874	1310	5.670097	CGATCAATTACTGCCTAATTGTCG	58.330	41.667	17.32	18.66	46.64	4.35
875	1311	5.237344	AGCGATCAATTACTGCCTAATTGTC	59.763	40.000	17.32	14.11	46.64	3.18
876	1312	5.126067	AGCGATCAATTACTGCCTAATTGT	58.874	37.500	17.32	9.48	46.64	2.71
987	1451	3.743396	CGATTTATAGAGGGCAGCAGAAC	59.257	47.826	0.00	0.00	0.00	3.01
1032	1496	2.266554	CGAGCACAACTGATCTTCTCC	58.733	52.381	0.00	0.00	29.98	3.71
1166	1630	8.095169	TCTGAAGGAAAGACAGAAGGTATTTAC	58.905	37.037	0.00	0.00	40.79	2.01
1260	1727	1.638467	GCGTCATCACCTTCATCGC	59.362	57.895	0.00	0.00	35.86	4.58
1455	1922	3.414136	TTGCAGTTGGGGCAGACGT	62.414	57.895	0.00	0.00	43.05	4.34
1612	2079	3.938963	ACGACATGATACGCTTTTCCATT	59.061	39.130	0.00	0.00	0.00	3.16
1763	2235	5.005740	TCTGTCCAAATCCATCTCAAAGTG	58.994	41.667	0.00	0.00	0.00	3.16
1769	2241	4.440880	CTGACTCTGTCCAAATCCATCTC	58.559	47.826	0.00	0.00	0.00	2.75
1863	2335	0.890996	GGTGCCTTTGAGGTCCACAG	60.891	60.000	0.00	0.00	37.80	3.66
1864	2336	1.150536	GGTGCCTTTGAGGTCCACA	59.849	57.895	0.00	0.00	37.80	4.17
1963	2435	2.461110	CCCGAACATTTCCGCGGAG	61.461	63.158	29.20	19.58	46.29	4.63
2185	2675	3.298686	ACATGGATGAGGTCGAGTAGA	57.701	47.619	0.00	0.00	0.00	2.59
2449	2968	1.741770	GCGTGAAACCTGGATCGCT	60.742	57.895	0.00	0.00	40.39	4.93
2460	2979	0.458669	GATCCGGTCTAGGCGTGAAA	59.541	55.000	0.00	0.00	0.00	2.69
2472	2991	2.206635	CTCCTTGAGCAGATCCGGT	58.793	57.895	0.00	0.00	0.00	5.28
2499	3018	2.172483	ATTTCTGACACCGGAGCGCT	62.172	55.000	11.27	11.27	0.00	5.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.