AutoCloner

Multiple sequence alignment - TraesCS1A01G151300

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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	TraesCS1A01G151300	chr1A	100.000	2264	0	0	1	2264	259894126	259891863	0.000000e+00	4181.0
1	TraesCS1A01G151300	chr3D	91.263	1671	132	8	603	2261	230694418	230696086	0.000000e+00	2265.0
2	TraesCS1A01G151300	chr3D	89.451	948	89	7	1323	2261	230710467	230711412	0.000000e+00	1186.0
3	TraesCS1A01G151300	chr3D	89.103	881	82	8	1389	2261	230593240	230594114	0.000000e+00	1083.0
4	TraesCS1A01G151300	chr3D	84.567	473	44	12	99	544	230647956	230648426	2.060000e-120	442.0
5	TraesCS1A01G151300	chr3D	84.277	477	49	9	93	544	230706765	230707240	2.060000e-120	442.0
6	TraesCS1A01G151300	chr3D	76.128	532	69	26	32	525	55540019	55540530	2.260000e-55	226.0
7	TraesCS1A01G151300	chr3D	88.398	181	21	0	2084	2264	486671366	486671186	3.790000e-53	219.0
8	TraesCS1A01G151300	chr3D	86.726	113	15	0	433	545	605963174	605963286	2.360000e-25	126.0
9	TraesCS1A01G151300	chr3D	100.000	28	0	0	517	544	552281502	552281475	4.000000e-03	52.8
10	TraesCS1A01G151300	chr4B	90.545	1523	124	5	544	2064	612515298	612513794	0.000000e+00	1997.0
11	TraesCS1A01G151300	chr4B	87.750	400	22	9	30	409	612516037	612515645	2.060000e-120	442.0
12	TraesCS1A01G151300	chr5D	93.867	1125	53	10	582	1691	527486551	527487674	0.000000e+00	1681.0
13	TraesCS1A01G151300	chr5D	82.594	586	45	21	1	550	527485919	527486483	4.400000e-127	464.0
14	TraesCS1A01G151300	chr7B	87.668	1411	144	16	394	1781	65835376	65836779	0.000000e+00	1615.0
15	TraesCS1A01G151300	chr7B	91.618	680	53	4	560	1237	685956034	685956711	0.000000e+00	937.0
16	TraesCS1A01G151300	chr7B	85.075	469	41	14	1	444	685906417	685906881	3.430000e-123	451.0
17	TraesCS1A01G151300	chr7B	83.871	310	35	9	30	333	65834864	65835164	4.760000e-72	281.0
18	TraesCS1A01G151300	chr7B	87.336	229	28	1	2036	2264	685957403	685957630	6.200000e-66	261.0
19	TraesCS1A01G151300	chr5A	91.833	1151	83	6	541	1691	588455334	588454195	0.000000e+00	1594.0
20	TraesCS1A01G151300	chr5A	88.583	254	14	11	92	333	484667840	484667590	6.120000e-76	294.0
21	TraesCS1A01G151300	chr6D	89.034	1304	116	13	970	2263	43206468	43205182	0.000000e+00	1591.0
22	TraesCS1A01G151300	chr6D	83.934	361	46	8	559	913	421593106	421593460	3.600000e-88	335.0
23	TraesCS1A01G151300	chr6D	91.061	179	8	3	157	333	380049211	380049039	3.760000e-58	235.0
24	TraesCS1A01G151300	chr6D	76.173	554	64	33	32	542	347348252	347347724	1.750000e-56	230.0
25	TraesCS1A01G151300	chr6D	82.313	147	26	0	398	544	421592851	421592997	6.560000e-26	128.0
26	TraesCS1A01G151300	chr4A	91.778	1119	76	6	576	1691	598516195	598517300	0.000000e+00	1543.0
27	TraesCS1A01G151300	chr4A	88.889	108	8	2	32	135	651402203	651402310	1.820000e-26	130.0
28	TraesCS1A01G151300	chr2B	89.183	1248	114	15	541	1777	40122405	40123642	0.000000e+00	1537.0
29	TraesCS1A01G151300	chr2B	88.758	765	83	2	1501	2264	730044157	730044919	0.000000e+00	933.0
30	TraesCS1A01G151300	chr1D	91.097	1067	87	4	1040	2099	465920717	465921782	0.000000e+00	1437.0
31	TraesCS1A01G151300	chr1D	80.588	510	63	22	32	532	25685059	25685541	5.940000e-96	361.0
32	TraesCS1A01G151300	chr1D	83.069	189	27	5	2078	2263	465921791	465921977	1.390000e-37	167.0
33	TraesCS1A01G151300	chr1D	93.069	101	5	2	36	135	465920603	465920702	1.810000e-31	147.0
34	TraesCS1A01G151300	chr7A	87.063	773	79	11	1482	2244	188643381	188644142	0.000000e+00	854.0
35	TraesCS1A01G151300	chr5B	83.613	476	34	18	1	447	415419861	415419401	7.530000e-110	407.0
36	TraesCS1A01G151300	chr5B	88.571	105	11	1	32	135	379355481	379355585	2.360000e-25	126.0
37	TraesCS1A01G151300	chr5B	90.789	76	6	1	470	544	338721190	338721265	1.430000e-17	100.0
38	TraesCS1A01G151300	chr3B	85.000	400	21	17	31	409	677722454	677722835	9.880000e-99	370.0
39	TraesCS1A01G151300	chr3B	74.805	385	65	25	32	390	21414527	21414149	6.520000e-31	145.0
40	TraesCS1A01G151300	chr3B	80.357	168	27	6	380	544	217319566	217319730	3.050000e-24	122.0
41	TraesCS1A01G151300	chr1B	86.544	327	37	5	557	882	282148665	282148985	9.950000e-94	353.0
42	TraesCS1A01G151300	chr1B	86.544	327	37	5	557	882	282156196	282156516	9.950000e-94	353.0
43	TraesCS1A01G151300	chr7D	82.493	377	44	8	188	544	564827321	564826947	6.070000e-81	311.0
44	TraesCS1A01G151300	chr3A	87.500	48	4	2	2030	2076	22510097	22510051	1.000000e-03	54.7
45	TraesCS1A01G151300	chr3A	87.234	47	6	0	2049	2095	713938897	713938851	1.000000e-03	54.7
46	TraesCS1A01G151300	chr2D	100.000	28	0	0	517	544	627340360	627340387	4.000000e-03	52.8

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	TraesCS1A01G151300	chr1A	259891863	259894126	2263	True	4181.000000	4181	100.000000	1	2264	1	chr1A.!!$R1	2263
1	TraesCS1A01G151300	chr3D	230694418	230696086	1668	False	2265.000000	2265	91.263000	603	2261	1	chr3D.!!$F4	1658
2	TraesCS1A01G151300	chr3D	230593240	230594114	874	False	1083.000000	1083	89.103000	1389	2261	1	chr3D.!!$F2	872
3	TraesCS1A01G151300	chr3D	230706765	230711412	4647	False	814.000000	1186	86.864000	93	2261	2	chr3D.!!$F6	2168
4	TraesCS1A01G151300	chr3D	55540019	55540530	511	False	226.000000	226	76.128000	32	525	1	chr3D.!!$F1	493
5	TraesCS1A01G151300	chr4B	612513794	612516037	2243	True	1219.500000	1997	89.147500	30	2064	2	chr4B.!!$R1	2034
6	TraesCS1A01G151300	chr5D	527485919	527487674	1755	False	1072.500000	1681	88.230500	1	1691	2	chr5D.!!$F1	1690
7	TraesCS1A01G151300	chr7B	65834864	65836779	1915	False	948.000000	1615	85.769500	30	1781	2	chr7B.!!$F2	1751
8	TraesCS1A01G151300	chr7B	685956034	685957630	1596	False	599.000000	937	89.477000	560	2264	2	chr7B.!!$F3	1704
9	TraesCS1A01G151300	chr5A	588454195	588455334	1139	True	1594.000000	1594	91.833000	541	1691	1	chr5A.!!$R2	1150
10	TraesCS1A01G151300	chr6D	43205182	43206468	1286	True	1591.000000	1591	89.034000	970	2263	1	chr6D.!!$R1	1293
11	TraesCS1A01G151300	chr6D	421592851	421593460	609	False	231.500000	335	83.123500	398	913	2	chr6D.!!$F1	515
12	TraesCS1A01G151300	chr6D	347347724	347348252	528	True	230.000000	230	76.173000	32	542	1	chr6D.!!$R2	510
13	TraesCS1A01G151300	chr4A	598516195	598517300	1105	False	1543.000000	1543	91.778000	576	1691	1	chr4A.!!$F1	1115
14	TraesCS1A01G151300	chr2B	40122405	40123642	1237	False	1537.000000	1537	89.183000	541	1777	1	chr2B.!!$F1	1236
15	TraesCS1A01G151300	chr2B	730044157	730044919	762	False	933.000000	933	88.758000	1501	2264	1	chr2B.!!$F2	763
16	TraesCS1A01G151300	chr1D	465920603	465921977	1374	False	583.666667	1437	89.078333	36	2263	3	chr1D.!!$F2	2227
17	TraesCS1A01G151300	chr7A	188643381	188644142	761	False	854.000000	854	87.063000	1482	2244	1	chr7A.!!$F1	762

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
21	22	0.10741	GGTATGGCGTCATCCCAACA	60.107	55.0	5.39	0.0	35.67	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1986	5064	0.389948	AGGCGCTGCAGTACTGTTAC	60.39	55.0	23.44	11.98	0.0	2.5	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
21	22	0.107410	GGTATGGCGTCATCCCAACA	60.107	55.000	5.39	0.00	35.67	3.33
27	28	0.665835	GCGTCATCCCAACACAACAA	59.334	50.000	0.00	0.00	0.00	2.83
34	35	1.205893	TCCCAACACAACAAAGCAACC	59.794	47.619	0.00	0.00	0.00	3.77
77	80	3.083997	GGGAGGTGAGATGCCGGT	61.084	66.667	1.90	0.00	0.00	5.28
85	88	3.249189	AGATGCCGGTGTGGTGGT	61.249	61.111	1.90	0.00	41.21	4.16
114	133	6.556874	AGGAAGAAGAAGAAGAAGAGAGGAAA	59.443	38.462	0.00	0.00	0.00	3.13
156	190	2.231215	GCTCGATGCAATAGACCACT	57.769	50.000	0.00	0.00	42.31	4.00
230	290	5.527214	TGACTATGTGTTTTGGACAACTCTG	59.473	40.000	0.00	0.00	40.65	3.35
245	305	4.184629	CAACTCTGTGTGCTATAACTCCC	58.815	47.826	0.00	0.00	0.00	4.30
347	446	2.577700	ACTATGCGAACCACAAAACCA	58.422	42.857	0.00	0.00	0.00	3.67
383	567	5.182001	GGTATTTGAAATCAGCAGACAGTGT	59.818	40.000	0.00	0.00	0.00	3.55
412	596	4.030452	GTTGGGCGCTGCACTGTC	62.030	66.667	7.64	0.00	30.56	3.51
456	690	1.476891	CGCTGCACCCTTACTTAGAGA	59.523	52.381	0.00	0.00	0.00	3.10
485	873	3.758554	GGCAAGAAAAGCTACTGGAATCA	59.241	43.478	0.00	0.00	0.00	2.57
565	1047	1.485066	GTAGCAACTAAGGGCTAGGCA	59.515	52.381	19.14	0.00	42.80	4.75
591	1073	2.252747	CATGTTAATGTGCAACGCCTG	58.747	47.619	0.00	0.00	42.39	4.85
635	1117	1.127567	TGTCACTTAGGCTGCACCCT	61.128	55.000	5.73	5.73	40.58	4.34
794	1789	2.610873	GTAATCTCCTCCGATCCCCTT	58.389	52.381	0.00	0.00	0.00	3.95
971	1980	7.611467	ACCTATGTACATGTCAATGTGTTGAAT	59.389	33.333	18.81	0.00	46.66	2.57
975	1984	8.939201	TGTACATGTCAATGTGTTGAATTTTT	57.061	26.923	0.00	0.00	46.66	1.94
1045	3690	1.946267	CCACCGTGTGCTAACCAAC	59.054	57.895	0.00	0.00	31.34	3.77
1056	3701	1.885887	GCTAACCAACAAGACATGCCA	59.114	47.619	0.00	0.00	0.00	4.92
1072	3717	1.179174	GCCAAACAAGTGGGAGGACC	61.179	60.000	0.00	0.00	39.26	4.46
1073	3718	0.478507	CCAAACAAGTGGGAGGACCT	59.521	55.000	0.00	0.00	41.11	3.85
1181	3826	3.614150	CGAAAGAAGTCATGGACGGAAGA	60.614	47.826	0.00	0.00	37.67	2.87
1185	3830	0.820871	AGTCATGGACGGAAGAGAGC	59.179	55.000	0.00	0.00	37.67	4.09
1216	3861	8.972458	TTTTGTATGCCTGAACTATGCTTATA	57.028	30.769	0.00	0.00	0.00	0.98
1254	3899	1.298340	CGCCTATGACCAACCACCA	59.702	57.895	0.00	0.00	0.00	4.17
1419	4483	0.462759	ATTGTCTTAGGAGCCAGCGC	60.463	55.000	0.00	0.00	0.00	5.92
1611	4675	2.158667	ACGTGACAAGAAGGGGAAATGT	60.159	45.455	0.00	0.00	0.00	2.71
1653	4717	1.291184	TTCGCTTCGGTGCACTCATG	61.291	55.000	17.98	6.92	0.00	3.07
1687	4751	7.092716	GGATGTATCCATGCCATATTTTTCAC	58.907	38.462	6.03	0.00	46.38	3.18
1757	4828	7.065324	CGTAGTAGGCCTAAATTTGTCATTTCA	59.935	37.037	15.83	0.00	0.00	2.69
1778	4849	6.852858	TCAAATGAATGTGTCGTGAACTTA	57.147	33.333	0.00	0.00	0.00	2.24
1799	4870	9.905713	AACTTATGAGGTTATGTGATATGTTGT	57.094	29.630	0.00	0.00	0.00	3.32
1832	4903	5.856126	GTAGTGTGCTACTTATGTTTGCA	57.144	39.130	0.00	5.45	43.14	4.08
1877	4949	8.853077	ATTGTCTTAAGTGATGAACTCATTGA	57.147	30.769	1.63	0.00	38.56	2.57
1966	5044	9.199982	CAAGTGAATTGAAATTGCTATCAACTT	57.800	29.630	0.00	3.68	41.83	2.66
1977	5055	7.733402	ATTGCTATCAACTTTGTTTTTGCAT	57.267	28.000	0.00	0.00	34.60	3.96
1983	5061	9.771915	CTATCAACTTTGTTTTTGCATTTTTGT	57.228	25.926	0.00	0.00	0.00	2.83
1986	5064	8.233190	TCAACTTTGTTTTTGCATTTTTGTAGG	58.767	29.630	0.00	0.00	0.00	3.18
2005	5083	0.389948	GTAACAGTACTGCAGCGCCT	60.390	55.000	22.90	3.89	0.00	5.52
2006	5084	0.108804	TAACAGTACTGCAGCGCCTC	60.109	55.000	22.90	0.00	0.00	4.70
2010	5088	2.750237	TACTGCAGCGCCTCGAGA	60.750	61.111	15.71	0.00	0.00	4.04
2128	5276	1.999648	TTTGGCAAGATCAGGCACTT	58.000	45.000	12.87	0.00	41.56	3.16
2178	5326	0.456653	CCAAATGTGCAACGCCTAGC	60.457	55.000	0.00	0.00	42.39	3.42
2199	5347	2.413837	CCATAGGCGCTACACAATACC	58.586	52.381	7.64	0.00	0.00	2.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	1.066573	TGGTTGCTTTGTTGTGTTGGG	60.067	47.619	0.00	0.00	0.00	4.12
21	22	2.102925	CCCTTCATGGTTGCTTTGTTGT	59.897	45.455	0.00	0.00	0.00	3.32
27	28	0.542702	CACCCCCTTCATGGTTGCTT	60.543	55.000	0.00	0.00	30.70	3.91
34	35	1.207488	TGTCCTCCACCCCCTTCATG	61.207	60.000	0.00	0.00	0.00	3.07
77	80	2.158219	TCTTCTTCCTCCTACCACCACA	60.158	50.000	0.00	0.00	0.00	4.17
85	88	6.795590	TCTCTTCTTCTTCTTCTTCCTCCTA	58.204	40.000	0.00	0.00	0.00	2.94
114	133	4.816048	AGGTCCTTTTCCCTTCTTCTTT	57.184	40.909	0.00	0.00	0.00	2.52
152	186	1.308998	GGTTCACAAGGTCACAGTGG	58.691	55.000	0.00	0.00	34.17	4.00
156	190	3.766591	ACATTTTGGTTCACAAGGTCACA	59.233	39.130	0.00	0.00	40.82	3.58
230	290	5.523916	CACACATAAGGGAGTTATAGCACAC	59.476	44.000	0.00	0.00	29.54	3.82
447	681	9.965824	CTTTTCTTGCCAAAATTTCTCTAAGTA	57.034	29.630	0.00	0.00	0.00	2.24
456	690	5.759763	CCAGTAGCTTTTCTTGCCAAAATTT	59.240	36.000	0.00	0.00	0.00	1.82
485	873	2.027377	CCTGTCCAGAGAGCAACAGAAT	60.027	50.000	3.06	0.00	41.26	2.40
551	1033	2.732619	GCGGTGCCTAGCCCTTAGT	61.733	63.158	0.00	0.00	0.00	2.24
645	1453	4.203543	TGTGGGGTGGGGTGGGTA	62.204	66.667	0.00	0.00	0.00	3.69
815	1811	2.025887	AGCAGGATTTGAGGTAAGGTGG	60.026	50.000	0.00	0.00	0.00	4.61
819	1815	5.355350	CCAAACTAGCAGGATTTGAGGTAAG	59.645	44.000	4.74	0.00	35.73	2.34
1045	3690	2.546373	CCCACTTGTTTGGCATGTCTTG	60.546	50.000	0.00	0.00	35.00	3.02
1056	3701	3.532102	AGATAGGTCCTCCCACTTGTTT	58.468	45.455	0.00	0.00	34.66	2.83
1072	3717	5.046304	TCTCCTTCACCTTGTCCAAAGATAG	60.046	44.000	0.00	0.00	0.00	2.08
1073	3718	4.844085	TCTCCTTCACCTTGTCCAAAGATA	59.156	41.667	0.00	0.00	0.00	1.98
1181	3826	7.123247	AGTTCAGGCATACAAAATATTTGCTCT	59.877	33.333	0.39	0.00	33.86	4.09
1185	3830	8.971321	GCATAGTTCAGGCATACAAAATATTTG	58.029	33.333	0.39	1.47	32.98	2.32
1216	3861	2.350388	CGTTAGTTGGAAGCGCACAATT	60.350	45.455	11.47	11.19	0.00	2.32
1419	4483	4.678509	TCAAAATGATTCTTCGAACCGG	57.321	40.909	0.00	0.00	0.00	5.28
1575	4639	2.278857	CGTGCCGAATCCTCCTCG	60.279	66.667	0.00	0.00	36.06	4.63
1611	4675	1.464734	CCTACTGAGTCGAGCAAGGA	58.535	55.000	0.00	0.00	0.00	3.36
1757	4828	7.361201	CCTCATAAGTTCACGACACATTCATTT	60.361	37.037	0.00	0.00	0.00	2.32
1778	4849	8.677300	GTTCAACAACATATCACATAACCTCAT	58.323	33.333	0.00	0.00	32.14	2.90
1824	4895	9.248291	CAAACATTACTAGAACTTTGCAAACAT	57.752	29.630	8.05	0.00	0.00	2.71
1966	5044	8.547967	TGTTACCTACAAAAATGCAAAAACAA	57.452	26.923	0.00	0.00	32.64	2.83
1977	5055	5.237779	GCTGCAGTACTGTTACCTACAAAAA	59.762	40.000	23.44	0.00	36.02	1.94
1983	5061	1.135199	GCGCTGCAGTACTGTTACCTA	60.135	52.381	23.44	3.84	0.00	3.08
1986	5064	0.389948	AGGCGCTGCAGTACTGTTAC	60.390	55.000	23.44	11.98	0.00	2.50
2005	5083	0.969149	AGTGCAACACCTGATCTCGA	59.031	50.000	0.00	0.00	41.43	4.04
2006	5084	2.654749	TAGTGCAACACCTGATCTCG	57.345	50.000	0.00	0.00	41.43	4.04
2010	5088	4.507710	CACAGTATAGTGCAACACCTGAT	58.492	43.478	7.51	0.00	41.43	2.90
2125	5273	3.549794	AGAGCAACAGAAGCTTTGAAGT	58.450	40.909	0.00	0.00	43.58	3.01
2128	5276	3.136763	CAGAGAGCAACAGAAGCTTTGA	58.863	45.455	0.00	0.00	43.58	2.69
2162	5310	2.046285	GGGCTAGGCGTTGCACATT	61.046	57.895	14.42	0.00	32.02	2.71
2178	5326	2.413837	GTATTGTGTAGCGCCTATGGG	58.586	52.381	2.29	0.00	0.00	4.00
2194	5342	1.623811	AGTCAGGCTTCACACGGTATT	59.376	47.619	0.00	0.00	0.00	1.89
2199	5347	0.583438	CAACAGTCAGGCTTCACACG	59.417	55.000	0.00	0.00	0.00	4.49
2244	5392	3.372730	GCAACGCCCATGCCTCAA	61.373	61.111	0.00	0.00	37.85	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.