AutoCloner

Multiple sequence alignment - TraesCS2A01G430100

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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	TraesCS2A01G430100	chr2A	100.000	7623	0	0	1	7623	683504951	683512573	0.000000e+00	14078.0
1	TraesCS2A01G430100	chr2A	83.117	77	3	7	929	1005	375036990	375037056	2.300000e-05	62.1
2	TraesCS2A01G430100	chr2D	95.585	4145	127	33	1978	6084	539871309	539875435	0.000000e+00	6589.0
3	TraesCS2A01G430100	chr2D	89.992	1209	65	23	771	1966	539870069	539871234	0.000000e+00	1511.0
4	TraesCS2A01G430100	chr2D	95.382	693	25	5	6245	6934	539875632	539876320	0.000000e+00	1096.0
5	TraesCS2A01G430100	chr2D	89.815	756	56	6	27	779	539868245	539868982	0.000000e+00	950.0
6	TraesCS2A01G430100	chr2D	86.264	182	18	4	7373	7551	539876699	539876876	2.810000e-44	191.0
7	TraesCS2A01G430100	chr2B	94.197	3843	143	33	766	4560	644144439	644148249	0.000000e+00	5788.0
8	TraesCS2A01G430100	chr2B	91.419	1142	67	17	4960	6084	644148640	644149767	0.000000e+00	1537.0
9	TraesCS2A01G430100	chr2B	93.822	696	35	8	6245	6934	644149965	644150658	0.000000e+00	1040.0
10	TraesCS2A01G430100	chr2B	95.935	369	11	1	4548	4916	644148273	644148637	5.090000e-166	595.0
11	TraesCS2A01G430100	chr1B	90.859	2702	176	35	2159	4828	591440143	591437481	0.000000e+00	3555.0
12	TraesCS2A01G430100	chr1B	93.419	775	42	3	4998	5763	591437368	591436594	0.000000e+00	1140.0
13	TraesCS2A01G430100	chr1B	88.235	272	22	7	6246	6508	591436291	591436021	4.440000e-82	316.0
14	TraesCS2A01G430100	chr1B	91.266	229	11	3	985	1213	591440818	591440599	3.460000e-78	303.0
15	TraesCS2A01G430100	chr1B	92.453	53	1	1	6565	6614	591435997	591435945	1.060000e-08	73.1
16	TraesCS2A01G430100	chr1B	92.500	40	3	0	5687	5726	591436634	591436595	2.970000e-04	58.4
17	TraesCS2A01G430100	chr1D	89.847	2738	167	42	2153	4828	436623183	436620495	0.000000e+00	3413.0
18	TraesCS2A01G430100	chr1D	89.255	940	61	14	4860	5763	436620496	436619561	0.000000e+00	1140.0
19	TraesCS2A01G430100	chr1D	87.586	290	25	6	6227	6506	436619354	436619066	7.380000e-85	326.0
20	TraesCS2A01G430100	chr1D	90.086	232	10	6	985	1213	436623839	436623618	9.680000e-74	289.0
21	TraesCS2A01G430100	chr1D	98.000	50	1	0	6565	6614	436619040	436618991	3.790000e-13	87.9
22	TraesCS2A01G430100	chr1D	90.909	44	4	0	5810	5853	436619574	436619531	8.260000e-05	60.2
23	TraesCS2A01G430100	chr1D	92.500	40	3	0	5687	5726	436619601	436619562	2.970000e-04	58.4
24	TraesCS2A01G430100	chr1A	89.551	1914	130	25	2683	4560	533702144	533700265	0.000000e+00	2362.0
25	TraesCS2A01G430100	chr1A	88.374	1402	105	21	2318	3685	81358711	81357334	0.000000e+00	1633.0
26	TraesCS2A01G430100	chr1A	90.217	920	65	9	4860	5763	533699958	533699048	0.000000e+00	1177.0
27	TraesCS2A01G430100	chr1A	96.441	281	10	0	4548	4828	533700237	533699957	1.500000e-126	464.0
28	TraesCS2A01G430100	chr1A	83.085	402	29	28	835	1228	533703799	533703429	5.700000e-86	329.0
29	TraesCS2A01G430100	chr1A	86.986	292	26	7	6227	6508	533698841	533698552	1.230000e-82	318.0
30	TraesCS2A01G430100	chr1A	93.642	173	11	0	2507	2679	533702553	533702381	7.590000e-65	259.0
31	TraesCS2A01G430100	chr1A	89.542	153	14	2	2156	2307	81364311	81364160	7.810000e-45	193.0
32	TraesCS2A01G430100	chr1A	94.000	50	3	0	6565	6614	533698528	533698479	8.200000e-10	76.8
33	TraesCS2A01G430100	chr1A	92.683	41	3	0	5813	5853	533699058	533699018	8.260000e-05	60.2
34	TraesCS2A01G430100	chr5D	86.207	116	7	5	918	1033	433038094	433038200	4.830000e-22	117.0
35	TraesCS2A01G430100	chr7B	95.556	45	2	0	3	47	269670000	269669956	1.060000e-08	73.1
36	TraesCS2A01G430100	chr7B	91.489	47	4	0	1	47	677116440	677116394	1.780000e-06	65.8
37	TraesCS2A01G430100	chr7B	89.362	47	5	0	1	47	4018649	4018695	8.260000e-05	60.2
38	TraesCS2A01G430100	chr4D	93.333	45	3	0	3	47	384685998	384686042	4.940000e-07	67.6

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	TraesCS2A01G430100	chr2A	683504951	683512573	7622	False	14078.000000	14078	100.000000	1	7623	1	chr2A.!!$F2	7622
1	TraesCS2A01G430100	chr2D	539868245	539876876	8631	False	2067.400000	6589	91.407600	27	7551	5	chr2D.!!$F1	7524
2	TraesCS2A01G430100	chr2B	644144439	644150658	6219	False	2240.000000	5788	93.843250	766	6934	4	chr2B.!!$F1	6168
3	TraesCS2A01G430100	chr1B	591435945	591440818	4873	True	907.583333	3555	91.455333	985	6614	6	chr1B.!!$R1	5629
4	TraesCS2A01G430100	chr1D	436618991	436623839	4848	True	767.785714	3413	91.169000	985	6614	7	chr1D.!!$R1	5629
5	TraesCS2A01G430100	chr1A	81357334	81358711	1377	True	1633.000000	1633	88.374000	2318	3685	1	chr1A.!!$R1	1367
6	TraesCS2A01G430100	chr1A	533698479	533703799	5320	True	630.750000	2362	90.825625	835	6614	8	chr1A.!!$R3	5779

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
252	253	0.540365	CCAACTGACAGTGGGCCAAT	60.540	55.000	16.30	3.05	31.40	3.16	F
436	439	0.813610	TCGCAAACACTCACCCACAG	60.814	55.000	0.00	0.00	0.00	3.66	F
1165	2293	1.003573	ATGTGAGACCCCTCCCCTC	59.996	63.158	0.00	0.00	38.66	4.30	F
1483	2622	0.179034	GATTCCTGGGATTCAGCGCT	60.179	55.000	2.64	2.64	42.05	5.92	F
1615	2771	1.159285	CTTTCATGTCTGCGCTTGGA	58.841	50.000	9.73	1.07	0.00	3.53	F
1765	2927	1.957113	GCCTGCCCTGTGCTAAGAAAT	60.957	52.381	0.00	0.00	42.00	2.17	F
3398	4990	1.134371	GGTCAGTCCAACCCTGATAGC	60.134	57.143	0.00	0.00	40.79	2.97	F
3512	5104	0.109781	CAAATGGAAACGCTCACCCG	60.110	55.000	0.00	0.00	0.00	5.28	F
5196	6901	1.661617	TCGGACGTTGTTGACTTTGTG	59.338	47.619	0.00	0.00	0.00	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1177	2305	0.381801	TAACGCGGGAAGGATACGAC	59.618	55.000	12.47	0.00	46.39	4.34	R
1434	2573	1.088340	CAGATCAGAGCCAAGCCACG	61.088	60.000	0.00	0.00	0.00	4.94	R
2205	3446	1.664659	CATACAAGCTCTCACTGCAGC	59.335	52.381	15.27	0.00	35.73	5.25	R
3368	4960	0.482887	TGGACTGACCAGGAGTCTGA	59.517	55.000	7.97	0.00	46.46	3.27	R
3398	4990	1.068474	CGACTGGTAAAGCTGAACCG	58.932	55.000	11.93	9.51	38.70	4.44	R
3512	5104	2.165030	CACTGCCTCATTTGGATCAACC	59.835	50.000	0.00	0.00	39.54	3.77	R
5340	7045	4.774124	CATCCAGAATACCAGAAGCAAGA	58.226	43.478	0.00	0.00	0.00	3.02	R
5526	7231	0.182775	ACTTCGGCACTTCCAGGTTT	59.817	50.000	0.00	0.00	34.01	3.27	R
7050	8871	0.035439	ACTTCATACAAGCCGGGGTG	60.035	55.000	2.18	0.00	0.00	4.61	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
105	106	4.667420	GTGTGAACACGTCCGGAT	57.333	55.556	7.81	0.00	37.10	4.18
162	163	4.158209	TCAACCGATGCATCAAAATGACAT	59.842	37.500	25.70	0.00	34.61	3.06
171	172	6.850555	TGCATCAAAATGACATCAAATCGTA	58.149	32.000	0.00	0.00	34.61	3.43
180	181	6.793492	TGACATCAAATCGTAACAACATGA	57.207	33.333	0.00	0.00	0.00	3.07
229	230	0.867753	CACGAGCTATGAGGACACGC	60.868	60.000	0.00	0.00	0.00	5.34
252	253	0.540365	CCAACTGACAGTGGGCCAAT	60.540	55.000	16.30	3.05	31.40	3.16
261	262	1.545582	CAGTGGGCCAATCGAAATGTT	59.454	47.619	8.40	0.00	0.00	2.71
262	263	1.818674	AGTGGGCCAATCGAAATGTTC	59.181	47.619	8.40	0.00	0.00	3.18
294	295	7.311992	CCTCTAAATCTCCCCTAGGTTTTCTTT	60.312	40.741	8.29	4.78	39.34	2.52
303	304	8.222138	TCCCCTAGGTTTTCTTTAGATTTGTA	57.778	34.615	8.29	0.00	0.00	2.41
322	323	9.995003	GATTTGTAGGAATTCAGACATCTAGAT	57.005	33.333	7.93	0.00	0.00	1.98
332	333	4.777366	TCAGACATCTAGATTGGTCCACAA	59.223	41.667	15.95	0.00	44.54	3.33
334	335	6.070021	TCAGACATCTAGATTGGTCCACAAAT	60.070	38.462	15.95	0.00	43.46	2.32
430	433	6.311935	TGGTATAATTAGTCGCAAACACTCAC	59.688	38.462	0.00	0.00	0.00	3.51
435	438	1.092921	GTCGCAAACACTCACCCACA	61.093	55.000	0.00	0.00	0.00	4.17
436	439	0.813610	TCGCAAACACTCACCCACAG	60.814	55.000	0.00	0.00	0.00	3.66
442	445	1.956170	CACTCACCCACAGACGCAC	60.956	63.158	0.00	0.00	0.00	5.34
456	459	4.084888	GCACGCGCACAACCCTAC	62.085	66.667	5.73	0.00	38.36	3.18
464	467	1.535462	CGCACAACCCTACCTTTTGAG	59.465	52.381	0.00	0.00	0.00	3.02
471	474	2.177016	ACCCTACCTTTTGAGCACCTTT	59.823	45.455	0.00	0.00	0.00	3.11
472	475	2.558359	CCCTACCTTTTGAGCACCTTTG	59.442	50.000	0.00	0.00	0.00	2.77
475	478	4.022849	CCTACCTTTTGAGCACCTTTGAAG	60.023	45.833	0.00	0.00	0.00	3.02
480	483	5.499139	TTTTGAGCACCTTTGAAGTACTG	57.501	39.130	0.00	0.00	0.00	2.74
485	488	2.813754	GCACCTTTGAAGTACTGCATCA	59.186	45.455	3.81	0.00	0.00	3.07
493	496	3.247411	TGAAGTACTGCATCAACACAACG	59.753	43.478	0.00	0.00	0.00	4.10

Showing 1 to 25 of 471 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
36	37	6.206395	TGTTGGAGTTGCAATTATACCATG	57.794	37.500	0.59	0.00	3.66
89	90	0.598942	CACATCCGGACGTGTTCACA	60.599	55.000	22.21	0.00	3.58
91	92	1.743391	ACACATCCGGACGTGTTCA	59.257	52.632	29.47	43.71	3.18
97	98	1.222300	TTTGTGAACACATCCGGACG	58.778	50.000	6.12	41.52	4.79
127	128	2.488204	TCGGTTGAATGATTGGCTCA	57.512	45.000	0.00	38.53	4.26
162	163	6.552859	ACACATCATGTTGTTACGATTTGA	57.447	33.333	6.68	38.98	2.69
229	230	1.301716	CCCACTGTCAGTTGGACCG	60.302	63.158	16.53	46.38	4.79
261	262	2.424523	GGGGAGATTTAGAGGAGTCCGA	60.425	54.545	2.76	0.00	4.55
262	263	1.964933	GGGGAGATTTAGAGGAGTCCG	59.035	57.143	2.76	0.00	4.79
303	304	6.183361	GGACCAATCTAGATGTCTGAATTCCT	60.183	42.308	17.94	0.00	3.36
320	321	6.586082	GTGTATCAAACATTTGTGGACCAATC	59.414	38.462	0.00	41.10	2.67
322	323	5.506483	CGTGTATCAAACATTTGTGGACCAA	60.506	40.000	0.00	41.10	3.67
332	333	3.417101	TCCAAGCCGTGTATCAAACATT	58.583	40.909	0.00	41.10	2.71
334	335	2.552599	TCCAAGCCGTGTATCAAACA	57.447	45.000	0.00	35.06	2.83
406	409	6.238022	GGTGAGTGTTTGCGACTAATTATACC	60.238	42.308	0.00	0.00	2.73
415	418	0.814010	GTGGGTGAGTGTTTGCGACT	60.814	55.000	0.00	0.00	4.18
423	426	2.421739	GCGTCTGTGGGTGAGTGT	59.578	61.111	0.00	0.00	3.55
442	445	1.512156	AAAAGGTAGGGTTGTGCGCG	61.512	55.000	0.00	34.93	6.86
456	459	4.580580	AGTACTTCAAAGGTGCTCAAAAGG	59.419	41.667	0.00	0.00	3.11
464	467	2.813754	TGATGCAGTACTTCAAAGGTGC	59.186	45.455	0.00	34.12	5.01
471	474	3.247411	CGTTGTGTTGATGCAGTACTTCA	59.753	43.478	0.00	0.00	3.02
472	475	3.363970	CCGTTGTGTTGATGCAGTACTTC	60.364	47.826	0.00	0.00	3.01
475	478	1.871039	ACCGTTGTGTTGATGCAGTAC	59.129	47.619	0.00	0.00	2.73
480	483	2.032799	TCTCAAACCGTTGTGTTGATGC	59.967	45.455	0.00	36.07	3.91
485	488	4.571580	TCGTAAATCTCAAACCGTTGTGTT	59.428	37.500	0.00	36.07	3.32

Showing 1 to 25 of 471 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.