AutoCloner

Multiple sequence alignment - TraesCS7A01G511100

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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	TraesCS7A01G511100	chr7A	100.000	6382	0	0	1	6382	698761353	698767734	0.000000e+00	11786
1	TraesCS7A01G511100	chr7A	98.202	4839	72	5	1547	6382	698849935	698854761	0.000000e+00	8440
2	TraesCS7A01G511100	chr7A	98.858	3940	41	4	2445	6382	699020776	699024713	0.000000e+00	7023
3	TraesCS7A01G511100	chr7A	96.171	2455	73	8	1	2447	699018098	699020539	0.000000e+00	3993
4	TraesCS7A01G511100	chr7A	95.745	1551	52	5	1	1549	698848092	698849630	0.000000e+00	2486
5	TraesCS7A01G511100	chr7D	93.354	4935	252	26	1458	6382	606700348	606705216	0.000000e+00	7227
6	TraesCS7A01G511100	chr7D	89.658	1083	85	12	867	1930	607505527	607504453	0.000000e+00	1354
7	TraesCS7A01G511100	chr7D	91.068	918	33	18	522	1417	606699461	606700351	0.000000e+00	1195
8	TraesCS7A01G511100	chr7D	91.841	527	39	4	1	525	330090439	330090963	0.000000e+00	732
9	TraesCS7A01G511100	chr7D	91.445	526	40	5	1	524	412233332	412232810	0.000000e+00	717
10	TraesCS7A01G511100	chr7D	85.788	387	31	8	5863	6249	141230795	141230433	7.760000e-104	388
11	TraesCS7A01G511100	chrUn	94.524	4565	232	11	1829	6382	92707977	92703420	0.000000e+00	7029
12	TraesCS7A01G511100	chrUn	91.228	4195	321	28	1681	5858	33119434	33123598	0.000000e+00	5664
13	TraesCS7A01G511100	chrUn	88.907	1199	81	19	747	1914	33118267	33119444	0.000000e+00	1430
14	TraesCS7A01G511100	chrUn	87.500	656	33	16	544	1177	92708680	92708052	0.000000e+00	712
15	TraesCS7A01G511100	chrUn	92.821	195	10	4	523	713	33118072	33118266	4.870000e-71	279
16	TraesCS7A01G511100	chr7B	93.457	4646	269	16	1766	6382	691022456	691027095	0.000000e+00	6863
17	TraesCS7A01G511100	chr7B	88.020	1369	99	28	544	1884	690915322	690916653	0.000000e+00	1559
18	TraesCS7A01G511100	chr7B	93.864	880	48	1	913	1792	691021726	691022599	0.000000e+00	1321
19	TraesCS7A01G511100	chr7B	88.124	581	26	13	544	1107	690948789	690949343	0.000000e+00	651
20	TraesCS7A01G511100	chr7B	91.898	432	33	2	5952	6382	650132142	650131712	2.550000e-168	603
21	TraesCS7A01G511100	chr3B	90.385	5169	398	41	747	5867	760056083	760050966	0.000000e+00	6700
22	TraesCS7A01G511100	chr3B	88.269	520	42	7	5863	6382	436511338	436511838	7.080000e-169	604
23	TraesCS7A01G511100	chr3B	91.724	435	35	1	5949	6382	661541451	661541885	2.550000e-168	603
24	TraesCS7A01G511100	chr3B	92.821	195	9	4	522	713	760056276	760056084	1.750000e-70	278
25	TraesCS7A01G511100	chr3A	90.831	3959	318	30	1681	5618	704694754	704690820	0.000000e+00	5258
26	TraesCS7A01G511100	chr3A	90.599	3957	331	22	1681	5618	704780518	704776584	0.000000e+00	5208
27	TraesCS7A01G511100	chr3A	89.967	3957	335	30	1681	5618	704840574	704836661	0.000000e+00	5051
28	TraesCS7A01G511100	chr3A	91.219	3371	282	12	2496	5858	704578363	704581727	0.000000e+00	4573
29	TraesCS7A01G511100	chr3A	86.862	1431	104	33	522	1914	704570859	704572243	0.000000e+00	1524
30	TraesCS7A01G511100	chr3A	89.040	1177	82	18	770	1914	704695905	704694744	0.000000e+00	1415
31	TraesCS7A01G511100	chr3A	88.040	1204	85	20	747	1914	704781801	704780621	0.000000e+00	1371
32	TraesCS7A01G511100	chr3A	87.552	1205	90	22	747	1914	704841745	704840564	0.000000e+00	1339
33	TraesCS7A01G511100	chr3A	90.000	530	51	2	1	528	747049254	747049783	0.000000e+00	684
34	TraesCS7A01G511100	chr3A	91.795	195	13	3	522	713	704696114	704695920	1.050000e-67	268
35	TraesCS7A01G511100	chr4D	90.840	524	45	3	1	522	110624217	110624739	0.000000e+00	699
36	TraesCS7A01G511100	chr3D	90.512	527	42	7	1	522	56413710	56414233	0.000000e+00	689
37	TraesCS7A01G511100	chr6D	90.323	527	48	3	1	525	396998255	396998780	0.000000e+00	688
38	TraesCS7A01G511100	chr4A	90.304	526	48	3	1	525	236056447	236055924	0.000000e+00	686
39	TraesCS7A01G511100	chr2A	89.060	521	50	6	5863	6382	694758322	694758836	1.940000e-179	640
40	TraesCS7A01G511100	chr2B	92.130	432	33	1	5952	6382	592808066	592807635	5.470000e-170	608
41	TraesCS7A01G511100	chr5A	87.229	415	35	10	5864	6278	546150526	546150130	2.100000e-124	457

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	TraesCS7A01G511100	chr7A	698761353	698767734	6381	False	11786.000000	11786	100.000000	1	6382	1	chr7A.!!$F1	6381
1	TraesCS7A01G511100	chr7A	699018098	699024713	6615	False	5508.000000	7023	97.514500	1	6382	2	chr7A.!!$F3	6381
2	TraesCS7A01G511100	chr7A	698848092	698854761	6669	False	5463.000000	8440	96.973500	1	6382	2	chr7A.!!$F2	6381
3	TraesCS7A01G511100	chr7D	606699461	606705216	5755	False	4211.000000	7227	92.211000	522	6382	2	chr7D.!!$F2	5860
4	TraesCS7A01G511100	chr7D	607504453	607505527	1074	True	1354.000000	1354	89.658000	867	1930	1	chr7D.!!$R3	1063
5	TraesCS7A01G511100	chr7D	330090439	330090963	524	False	732.000000	732	91.841000	1	525	1	chr7D.!!$F1	524
6	TraesCS7A01G511100	chr7D	412232810	412233332	522	True	717.000000	717	91.445000	1	524	1	chr7D.!!$R2	523
7	TraesCS7A01G511100	chrUn	92703420	92708680	5260	True	3870.500000	7029	91.012000	544	6382	2	chrUn.!!$R1	5838
8	TraesCS7A01G511100	chrUn	33118072	33123598	5526	False	2457.666667	5664	90.985333	523	5858	3	chrUn.!!$F1	5335
9	TraesCS7A01G511100	chr7B	691021726	691027095	5369	False	4092.000000	6863	93.660500	913	6382	2	chr7B.!!$F3	5469
10	TraesCS7A01G511100	chr7B	690915322	690916653	1331	False	1559.000000	1559	88.020000	544	1884	1	chr7B.!!$F1	1340
11	TraesCS7A01G511100	chr7B	690948789	690949343	554	False	651.000000	651	88.124000	544	1107	1	chr7B.!!$F2	563
12	TraesCS7A01G511100	chr3B	760050966	760056276	5310	True	3489.000000	6700	91.603000	522	5867	2	chr3B.!!$R1	5345
13	TraesCS7A01G511100	chr3B	436511338	436511838	500	False	604.000000	604	88.269000	5863	6382	1	chr3B.!!$F1	519
14	TraesCS7A01G511100	chr3A	704578363	704581727	3364	False	4573.000000	4573	91.219000	2496	5858	1	chr3A.!!$F2	3362
15	TraesCS7A01G511100	chr3A	704776584	704781801	5217	True	3289.500000	5208	89.319500	747	5618	2	chr3A.!!$R2	4871
16	TraesCS7A01G511100	chr3A	704836661	704841745	5084	True	3195.000000	5051	88.759500	747	5618	2	chr3A.!!$R3	4871
17	TraesCS7A01G511100	chr3A	704690820	704696114	5294	True	2313.666667	5258	90.555333	522	5618	3	chr3A.!!$R1	5096
18	TraesCS7A01G511100	chr3A	704570859	704572243	1384	False	1524.000000	1524	86.862000	522	1914	1	chr3A.!!$F1	1392
19	TraesCS7A01G511100	chr3A	747049254	747049783	529	False	684.000000	684	90.000000	1	528	1	chr3A.!!$F3	527
20	TraesCS7A01G511100	chr4D	110624217	110624739	522	False	699.000000	699	90.840000	1	522	1	chr4D.!!$F1	521
21	TraesCS7A01G511100	chr3D	56413710	56414233	523	False	689.000000	689	90.512000	1	522	1	chr3D.!!$F1	521
22	TraesCS7A01G511100	chr6D	396998255	396998780	525	False	688.000000	688	90.323000	1	525	1	chr6D.!!$F1	524
23	TraesCS7A01G511100	chr4A	236055924	236056447	523	True	686.000000	686	90.304000	1	525	1	chr4A.!!$R1	524
24	TraesCS7A01G511100	chr2A	694758322	694758836	514	False	640.000000	640	89.060000	5863	6382	1	chr2A.!!$F1	519

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
483	487	1.003839	TCAGCGGCCGAAAAGTCAT	60.004	52.632	33.48	0.00	0.00	3.06	F
1083	1201	0.032540	AAAGGTTACGCGTCCTCGTT	59.967	50.000	18.63	12.34	43.15	3.85	F
1693	2283	0.032678	CACTCTTCCGATCGGATGGG	59.967	60.000	35.90	35.90	44.74	4.00	F
1718	2308	1.076923	GGTAGGAGAGCGGAGGTGA	60.077	63.158	0.00	0.00	39.88	4.02	F
1809	2770	1.439228	CGTCTGATGGATGGCGACT	59.561	57.895	0.00	0.00	0.00	4.18	F
3753	5340	2.054453	GCCATCCACAGAAAGCCCC	61.054	63.158	0.00	0.00	0.00	5.80	F
4437	6036	2.972625	TCACGAACATGGAAGATGGAC	58.027	47.619	0.00	0.00	0.00	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1801	2762	0.757188	CTCTCCTACCCAGTCGCCAT	60.757	60.000	0.00	0.00	0.00	4.40	R
2853	4429	1.100510	CGTGGTCCTCTCGTCCAATA	58.899	55.000	0.00	0.00	32.82	1.90	R
3345	4929	5.600696	AGACGGAAAAGCATTTCAATGTTT	58.399	33.333	15.63	4.36	45.53	2.83	R
3753	5340	1.268184	CGCAATTGTCCATGTCATCCG	60.268	52.381	7.40	0.00	0.00	4.18	R
4437	6036	3.051210	TGTCGCCAGAGGACACAG	58.949	61.111	0.00	0.00	39.36	3.66	R
4623	6222	2.086094	TGTTGTCGTATAGGCTGACGA	58.914	47.619	18.79	18.79	45.28	4.20	R
6265	7870	3.087031	CCACTTGAGTACGGAGGTCTTA	58.913	50.000	0.00	0.00	0.00	2.10	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
95	96	1.823899	GCTGGGGGTCGGCTTTATG	60.824	63.158	0.00	0.00	44.20	1.90
248	249	3.609175	CGGCAACTTTGACATTGATTCGT	60.609	43.478	0.00	0.00	35.35	3.85
251	252	5.156355	GCAACTTTGACATTGATTCGTCAT	58.844	37.500	0.00	0.00	41.55	3.06
314	315	2.604686	AGTCGCTGGCAAGGAGGA	60.605	61.111	0.00	0.00	0.00	3.71
319	320	3.322466	CTGGCAAGGAGGACCCGT	61.322	66.667	0.00	0.00	40.87	5.28
352	353	2.262303	AAAAACGATTCGCCCGGCA	61.262	52.632	10.77	0.00	0.00	5.69
435	437	1.890174	CCGGTGAAAATTGAGCCCC	59.110	57.895	0.00	0.00	0.00	5.80
483	487	1.003839	TCAGCGGCCGAAAAGTCAT	60.004	52.632	33.48	0.00	0.00	3.06
542	547	7.023575	GCTCTAACATTTGTGTCCAACATTAG	58.976	38.462	0.00	0.00	38.99	1.73
550	555	6.707440	TTGTGTCCAACATTAGACATTTGT	57.293	33.333	0.00	0.00	44.34	2.83
1066	1184	1.541670	CGGAGGACAAGTTTCCCGAAA	60.542	52.381	0.00	0.00	39.31	3.46
1083	1201	0.032540	AAAGGTTACGCGTCCTCGTT	59.967	50.000	18.63	12.34	43.15	3.85
1579	2153	7.556275	AGGACGATTTTATGAAACCACATACAT	59.444	33.333	0.00	0.00	33.31	2.29
1679	2269	2.496470	GTCCCATCTAACCGTTCACTCT	59.504	50.000	0.00	0.00	0.00	3.24
1693	2283	0.032678	CACTCTTCCGATCGGATGGG	59.967	60.000	35.90	35.90	44.74	4.00
1718	2308	1.076923	GGTAGGAGAGCGGAGGTGA	60.077	63.158	0.00	0.00	39.88	4.02
1807	2768	2.814604	CCGTCTGATGGATGGCGA	59.185	61.111	10.50	0.00	43.30	5.54
1808	2769	1.592669	CCGTCTGATGGATGGCGAC	60.593	63.158	10.50	0.00	43.30	5.19
1809	2770	1.439228	CGTCTGATGGATGGCGACT	59.561	57.895	0.00	0.00	0.00	4.18
1964	3267	5.798132	ACATGGATAGCACGTGATTATGAT	58.202	37.500	22.23	2.44	0.00	2.45
2129	3436	9.088512	GGCGTATTTATGGACTATCTAGAATTG	57.911	37.037	0.00	0.00	0.00	2.32
2214	3521	2.545526	CACTATCCACATGTTCGATGGC	59.454	50.000	13.26	0.00	33.20	4.40
2853	4429	9.847224	ATTAATTTATGGAAACTATCACCGAGT	57.153	29.630	0.00	0.00	0.00	4.18
3753	5340	2.054453	GCCATCCACAGAAAGCCCC	61.054	63.158	0.00	0.00	0.00	5.80
4115	5707	5.289675	CAGTCAAAGCTCTAGTAATGGAACG	59.710	44.000	0.00	0.00	0.00	3.95
4437	6036	2.972625	TCACGAACATGGAAGATGGAC	58.027	47.619	0.00	0.00	0.00	4.02
4576	6175	6.855403	ATCGTAGAATGCCAAAGTATGTTGGA	60.855	38.462	8.13	0.00	46.18	3.53
4623	6222	0.846693	ACAGGTTTTGCTGACCCTCT	59.153	50.000	0.00	0.00	37.93	3.69
5718	7320	6.408869	GGTAACAAGGCACACTTTATACCTA	58.591	40.000	0.00	0.00	40.92	3.08
5943	7546	0.111446	CATTGGTGGTGGTGGTGGTA	59.889	55.000	0.00	0.00	0.00	3.25
6133	7738	1.374947	CGGTGATGGTGGTGGAAGT	59.625	57.895	0.00	0.00	0.00	3.01
6240	7845	3.706373	GCAACCGGAGAGCCCTCA	61.706	66.667	9.46	0.00	41.20	3.86
6265	7870	1.417890	CTTGTCTGTGTTGAGGACCCT	59.582	52.381	0.00	0.00	0.00	4.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
223	224	1.130955	CAATGTCAAAGTTGCCGTGC	58.869	50.000	0.00	0.00	0.00	5.34
224	225	2.772568	TCAATGTCAAAGTTGCCGTG	57.227	45.000	0.00	0.00	0.00	4.94
225	226	3.609175	CGAATCAATGTCAAAGTTGCCGT	60.609	43.478	0.00	0.00	0.00	5.68
226	227	2.910482	CGAATCAATGTCAAAGTTGCCG	59.090	45.455	0.00	0.00	0.00	5.69
228	229	4.536065	TGACGAATCAATGTCAAAGTTGC	58.464	39.130	0.00	0.00	41.82	4.17
236	237	4.662145	GTTTCCCATGACGAATCAATGTC	58.338	43.478	0.00	0.00	38.69	3.06
237	238	3.126858	CGTTTCCCATGACGAATCAATGT	59.873	43.478	0.00	0.00	41.53	2.71
248	249	0.461870	CATCGCCTCGTTTCCCATGA	60.462	55.000	0.00	0.00	0.00	3.07
251	252	1.218047	CTCATCGCCTCGTTTCCCA	59.782	57.895	0.00	0.00	0.00	4.37
296	297	2.125350	CCTCCTTGCCAGCGACTC	60.125	66.667	0.00	0.00	0.00	3.36
467	471	1.021390	CAGATGACTTTTCGGCCGCT	61.021	55.000	23.51	5.10	0.00	5.52
470	474	0.804989	CACCAGATGACTTTTCGGCC	59.195	55.000	0.00	0.00	0.00	6.13
483	487	2.520458	CCAACAAGGCCCACCAGA	59.480	61.111	0.00	0.00	39.06	3.86
508	512	7.293731	GACACAAATGTTAGAGCATCTCCAGT	61.294	42.308	0.00	0.00	39.99	4.00
542	547	7.899841	GCTTTTGTTCTTTTCTCAACAAATGTC	59.100	33.333	17.42	10.51	46.60	3.06
1066	1184	1.080974	CAACGAGGACGCGTAACCT	60.081	57.895	18.55	18.55	44.86	3.50
1579	2153	3.222173	AGAGTGTGGGTTTTGTGCATA	57.778	42.857	0.00	0.00	0.00	3.14
1693	2283	2.128507	CGCTCTCCTACCCCACTCC	61.129	68.421	0.00	0.00	0.00	3.85
1718	2308	4.081420	CCTCTACTAACTCATGTGCCACTT	60.081	45.833	0.00	0.00	0.00	3.16
1799	2616	1.749334	CTCCTACCCAGTCGCCATCC	61.749	65.000	0.00	0.00	0.00	3.51
1801	2762	0.757188	CTCTCCTACCCAGTCGCCAT	60.757	60.000	0.00	0.00	0.00	4.40
1802	2763	1.379977	CTCTCCTACCCAGTCGCCA	60.380	63.158	0.00	0.00	0.00	5.69
1803	2764	2.787567	GCTCTCCTACCCAGTCGCC	61.788	68.421	0.00	0.00	0.00	5.54
1805	2766	2.482333	CCGCTCTCCTACCCAGTCG	61.482	68.421	0.00	0.00	0.00	4.18
1807	2768	1.076632	CTCCGCTCTCCTACCCAGT	60.077	63.158	0.00	0.00	0.00	4.00
1808	2769	1.830408	CCTCCGCTCTCCTACCCAG	60.830	68.421	0.00	0.00	0.00	4.45
1809	2770	2.279073	CCTCCGCTCTCCTACCCA	59.721	66.667	0.00	0.00	0.00	4.51
2853	4429	1.100510	CGTGGTCCTCTCGTCCAATA	58.899	55.000	0.00	0.00	32.82	1.90
3345	4929	5.600696	AGACGGAAAAGCATTTCAATGTTT	58.399	33.333	15.63	4.36	45.53	2.83
3753	5340	1.268184	CGCAATTGTCCATGTCATCCG	60.268	52.381	7.40	0.00	0.00	4.18
4437	6036	3.051210	TGTCGCCAGAGGACACAG	58.949	61.111	0.00	0.00	39.36	3.66
4576	6175	2.230508	TCTCGCATCTGACGGTAGTTTT	59.769	45.455	0.00	0.00	0.00	2.43
4623	6222	2.086094	TGTTGTCGTATAGGCTGACGA	58.914	47.619	18.79	18.79	45.28	4.20
5718	7320	3.181423	TGGGCCAGAAACAAGTTTATCCT	60.181	43.478	0.00	0.00	32.11	3.24
5943	7546	4.599500	ACCCCTCCCACTGCCACT	62.599	66.667	0.00	0.00	0.00	4.00
6133	7738	5.191124	GGGGAGGACCTCAACTTTTTCTATA	59.809	44.000	23.06	0.00	40.03	1.31
6240	7845	5.063880	GGTCCTCAACACAGACAAGTTTAT	58.936	41.667	0.00	0.00	31.99	1.40
6265	7870	3.087031	CCACTTGAGTACGGAGGTCTTA	58.913	50.000	0.00	0.00	0.00	2.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.