AutoCloner

Multiple sequence alignment - TraesCS6B01G304200

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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	TraesCS6B01G304200	chr6B	100.000	7662	0	0	1	7662	545215920	545223581	0.000000e+00	14150.0
1	TraesCS6B01G304200	chr6B	97.122	139	4	0	1767	1905	555720943	555721081	1.290000e-57	235.0
2	TraesCS6B01G304200	chr6B	96.479	142	5	0	1767	1908	680405579	680405720	1.290000e-57	235.0
3	TraesCS6B01G304200	chr6B	95.238	147	6	1	1767	1913	103700489	103700344	1.660000e-56	231.0
4	TraesCS6B01G304200	chr6B	95.041	121	5	1	3472	3591	379820008	379820128	1.010000e-43	189.0
5	TraesCS6B01G304200	chr6B	88.742	151	16	1	1767	1917	556794954	556795103	4.720000e-42	183.0
6	TraesCS6B01G304200	chr6A	95.669	4272	135	36	2713	6969	503763211	503767447	0.000000e+00	6818.0
7	TraesCS6B01G304200	chr6A	92.395	1591	69	26	189	1770	503760768	503762315	0.000000e+00	2220.0
8	TraesCS6B01G304200	chr6A	88.221	832	41	13	1905	2710	503762325	503763125	0.000000e+00	941.0
9	TraesCS6B01G304200	chr6A	85.511	352	23	10	6966	7291	503767527	503767876	7.360000e-90	342.0
10	TraesCS6B01G304200	chr6D	93.449	4152	153	50	1905	5982	363055512	363059618	0.000000e+00	6050.0
11	TraesCS6B01G304200	chr6D	95.466	1213	36	5	553	1764	363054302	363055496	0.000000e+00	1917.0
12	TraesCS6B01G304200	chr6D	90.467	1091	68	15	6079	7146	363059767	363060844	0.000000e+00	1406.0
13	TraesCS6B01G304200	chr6D	88.078	562	53	6	1	557	363041123	363041675	0.000000e+00	654.0
14	TraesCS6B01G304200	chr6D	94.815	135	6	1	1222	1356	42401438	42401305	7.790000e-50	209.0
15	TraesCS6B01G304200	chr6D	85.606	132	17	2	173	303	336208383	336208253	3.730000e-28	137.0
16	TraesCS6B01G304200	chr6D	83.221	149	21	4	2575	2721	346830428	346830574	4.820000e-27	134.0
17	TraesCS6B01G304200	chr3A	93.519	1543	83	11	2751	4282	136004998	136003462	0.000000e+00	2279.0
18	TraesCS6B01G304200	chr3A	84.211	684	47	23	1905	2578	136005622	136004990	6.570000e-170	608.0
19	TraesCS6B01G304200	chr3A	90.052	382	36	2	1230	1610	136006080	136005700	1.920000e-135	494.0
20	TraesCS6B01G304200	chr3A	94.977	219	10	1	7445	7662	468004995	468005213	7.360000e-90	342.0
21	TraesCS6B01G304200	chr3A	96.454	141	5	0	1767	1907	285775275	285775135	4.620000e-57	233.0
22	TraesCS6B01G304200	chr3A	95.172	145	6	1	1767	1911	688892726	688892583	2.150000e-55	228.0
23	TraesCS6B01G304200	chr3A	90.196	51	5	0	252	302	744267242	744267192	4.960000e-07	67.6
24	TraesCS6B01G304200	chr3A	100.000	31	0	0	252	282	744287525	744287495	2.990000e-04	58.4
25	TraesCS6B01G304200	chr1B	94.786	863	37	6	3076	3935	374013486	374012629	0.000000e+00	1338.0
26	TraesCS6B01G304200	chr1B	83.971	680	43	18	1905	2573	374014484	374013860	6.620000e-165	592.0
27	TraesCS6B01G304200	chr1B	92.749	331	17	4	2751	3076	374013863	374013535	9.000000e-129	472.0
28	TraesCS6B01G304200	chr5D	87.709	358	41	3	1222	1578	540196783	540196428	1.540000e-111	414.0
29	TraesCS6B01G304200	chr5D	91.053	190	16	1	1219	1408	44956890	44956702	9.870000e-64	255.0
30	TraesCS6B01G304200	chr5D	92.000	150	11	1	1767	1915	505463851	505463702	7.790000e-50	209.0
31	TraesCS6B01G304200	chr5D	85.075	134	18	2	2578	2710	44784362	44784494	1.340000e-27	135.0
32	TraesCS6B01G304200	chr5D	84.559	136	19	2	2579	2713	542696937	542696803	4.820000e-27	134.0
33	TraesCS6B01G304200	chr5D	96.667	60	2	0	2780	2839	403644270	403644211	4.890000e-17	100.0
34	TraesCS6B01G304200	chr7D	98.157	217	4	0	7446	7662	70150989	70150773	5.610000e-101	379.0
35	TraesCS6B01G304200	chr7D	85.385	130	17	2	175	303	30913288	30913416	4.820000e-27	134.0
36	TraesCS6B01G304200	chr4D	98.157	217	4	0	7446	7662	28848595	28848811	5.610000e-101	379.0
37	TraesCS6B01G304200	chr4D	97.706	218	4	1	7446	7662	401416711	401416494	2.610000e-99	374.0
38	TraesCS6B01G304200	chr4D	85.496	262	25	10	1222	1473	12041266	12041008	2.120000e-65	261.0
39	TraesCS6B01G304200	chr2B	96.330	218	8	0	7445	7662	379119042	379118825	7.310000e-95	359.0
40	TraesCS6B01G304200	chr2B	92.857	196	13	1	7468	7662	32631924	32632119	4.530000e-72	283.0
41	TraesCS6B01G304200	chr2B	82.734	139	21	3	173	309	131581007	131581144	3.760000e-23	121.0
42	TraesCS6B01G304200	chr7A	91.204	216	16	1	7447	7662	634478916	634478704	2.700000e-74	291.0
43	TraesCS6B01G304200	chr4B	88.745	231	25	1	1222	1451	580717672	580717442	1.630000e-71	281.0
44	TraesCS6B01G304200	chr4B	97.842	139	3	0	1767	1905	45773777	45773639	2.760000e-59	241.0
45	TraesCS6B01G304200	chr5B	93.923	181	10	1	1219	1399	648850992	648851171	9.800000e-69	272.0
46	TraesCS6B01G304200	chr5B	85.714	133	18	1	2578	2710	44657220	44657351	1.040000e-28	139.0
47	TraesCS6B01G304200	chr5B	84.397	141	17	5	2576	2715	509171383	509171519	4.820000e-27	134.0
48	TraesCS6B01G304200	chr5A	93.785	177	10	1	3415	3590	592001312	592001488	1.640000e-66	265.0
49	TraesCS6B01G304200	chr3D	95.238	168	7	1	7495	7662	395669524	395669690	1.640000e-66	265.0
50	TraesCS6B01G304200	chr7B	98.582	141	2	0	1767	1907	671719095	671719235	4.590000e-62	250.0
51	TraesCS6B01G304200	chr7B	97.842	139	3	0	1767	1905	227282569	227282707	2.760000e-59	241.0
52	TraesCS6B01G304200	chr7B	96.479	142	5	0	7444	7585	537841954	537842095	1.290000e-57	235.0
53	TraesCS6B01G304200	chr4A	96.403	139	5	0	1767	1905	696374879	696375017	5.980000e-56	230.0
54	TraesCS6B01G304200	chr3B	90.667	150	12	2	1770	1918	367582261	367582113	1.690000e-46	198.0
55	TraesCS6B01G304200	chr1A	85.714	140	18	2	2576	2713	202093227	202093088	6.200000e-31	147.0
56	TraesCS6B01G304200	chr1A	83.916	143	20	3	2568	2709	285535994	285535854	4.820000e-27	134.0
57	TraesCS6B01G304200	chr2D	81.609	174	24	7	2580	2747	22120398	22120227	3.730000e-28	137.0

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	TraesCS6B01G304200	chr6B	545215920	545223581	7661	False	14150.000000	14150	100.000000	1	7662	1	chr6B.!!$F2	7661
1	TraesCS6B01G304200	chr6A	503760768	503767876	7108	False	2580.250000	6818	90.449000	189	7291	4	chr6A.!!$F1	7102
2	TraesCS6B01G304200	chr6D	363054302	363060844	6542	False	3124.333333	6050	93.127333	553	7146	3	chr6D.!!$F3	6593
3	TraesCS6B01G304200	chr6D	363041123	363041675	552	False	654.000000	654	88.078000	1	557	1	chr6D.!!$F2	556
4	TraesCS6B01G304200	chr3A	136003462	136006080	2618	True	1127.000000	2279	89.260667	1230	4282	3	chr3A.!!$R5	3052
5	TraesCS6B01G304200	chr1B	374012629	374014484	1855	True	800.666667	1338	90.502000	1905	3935	3	chr1B.!!$R1	2030

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	Hairpin	End Stability	Orientation
223	224	0.167251	CCCGTCGTTTTTCATTCCGG	59.833	55.000	0.00	5.14	F
1779	1807	0.250295	TCTCCCGCCTTGTTCTGTTG	60.250	55.000	0.00	3.33	F
1866	1894	0.031817	CCAATCCTTGCCAATCCCCT	60.032	55.000	0.00	4.79	F
1871	1899	0.031817	CCTTGCCAATCCCCTCCAAT	60.032	55.000	0.00	3.16	F
1873	1901	0.032217	TTGCCAATCCCCTCCAATCC	60.032	55.000	0.00	3.01	F
1875	1903	0.178978	GCCAATCCCCTCCAATCCTC	60.179	60.000	0.00	3.71	F
2226	2279	0.392706	TGAAGAAGCAGGTCAAGCGA	59.607	50.000	37.01	4.93	F
4956	5164	1.517832	CGGAGGAGAACTGCCGAAT	59.482	57.895	40.22	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1852	1880	0.031817	ATTGGAGGGGATTGGCAAGG	60.032	55.000	5.96	0.00	0.00	3.61	R
2677	2731	0.172578	TTACACGGAGAGACATGCGG	59.827	55.000	0.00	0.00	38.46	5.69	R
3297	3493	1.331756	GTCCTGCATTCCATTACAGCG	59.668	52.381	0.00	0.00	0.00	5.18	R
3455	3651	1.541379	AAACCCCGTGCCAAATACTC	58.459	50.000	0.00	0.00	0.00	2.59	R
4922	5130	0.107993	TCCGCTCAGCATCCTTCTTG	60.108	55.000	0.00	0.00	0.00	3.02	R
5008	5216	5.343249	ACAAGCTACAAACTTTGCAAAGAG	58.657	37.500	38.78	28.69	39.31	2.85	R
5138	5346	0.595095	CTGTGCTTTCCTCCAACTGC	59.405	55.000	0.00	0.00	0.00	4.40	R
7293	7723	0.032615	TCCCACCACAAGCAAAACCT	60.033	50.000	0.00	0.00	0.00	3.50	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
36	37	3.767806	TGCAGCAGCGGAGAGAGG	61.768	66.667	0.00	0.00	46.23	3.69
38	39	2.757508	CAGCAGCGGAGAGAGGGA	60.758	66.667	0.00	0.00	0.00	4.20
54	55	2.040464	GATGGGCTCAGGGGAGGA	60.040	66.667	0.00	0.00	41.67	3.71
58	59	2.693017	GGCTCAGGGGAGGAGAGA	59.307	66.667	0.00	0.00	41.67	3.10
178	179	2.281276	ACCCGTCTGCCCGTTTTC	60.281	61.111	0.00	0.00	0.00	2.29
187	188	3.361977	CCCGTTTTCTGGCCGGTG	61.362	66.667	12.43	0.00	40.10	4.94
194	195	2.396590	TTTCTGGCCGGTGAAGATAC	57.603	50.000	12.43	0.00	0.00	2.24
195	196	1.568504	TTCTGGCCGGTGAAGATACT	58.431	50.000	12.43	0.00	0.00	2.12
209	210	1.133730	AGATACTGACCTCCTCCCGTC	60.134	57.143	0.00	0.00	0.00	4.79
223	224	0.167251	CCCGTCGTTTTTCATTCCGG	59.833	55.000	0.00	0.00	0.00	5.14
224	225	1.149987	CCGTCGTTTTTCATTCCGGA	58.850	50.000	0.00	0.00	36.12	5.14
305	307	3.070576	GCCATTCCAAGCGGGCTT	61.071	61.111	0.00	0.00	43.09	4.35
323	325	6.034150	GCGGGCTTTAAAATGTGTTTACATAC	59.966	38.462	0.00	0.00	46.54	2.39
324	326	7.309920	CGGGCTTTAAAATGTGTTTACATACT	58.690	34.615	0.00	0.00	46.54	2.12
325	327	7.272515	CGGGCTTTAAAATGTGTTTACATACTG	59.727	37.037	0.00	0.00	46.54	2.74
326	328	8.085909	GGGCTTTAAAATGTGTTTACATACTGT	58.914	33.333	0.00	0.00	46.54	3.55
344	346	9.725019	ACATACTGTACATCTGAATCAGAAAAA	57.275	29.630	17.59	2.52	44.04	1.94
400	410	0.678366	AACAAACACCGCACCACTCA	60.678	50.000	0.00	0.00	0.00	3.41
416	426	3.004734	CCACTCAGATTTTCCAAAAGCGT	59.995	43.478	0.00	0.00	39.15	5.07
428	438	3.452990	TCCAAAAGCGTACCATCTCCATA	59.547	43.478	0.00	0.00	0.00	2.74
460	470	0.727122	GACCGTTGACAGTCCGTACG	60.727	60.000	8.69	8.69	0.00	3.67
517	527	0.947180	GGCAACGGCGAGACTGTTTA	60.947	55.000	16.62	0.00	46.01	2.01
658	673	2.198304	GACTCAATCCCCTGCCGGTT	62.198	60.000	1.90	0.00	0.00	4.44
672	687	0.678684	CCGGTTCTGCCCCGTTTTAT	60.679	55.000	0.00	0.00	43.98	1.40
679	694	2.823154	TCTGCCCCGTTTTATTTCCAAG	59.177	45.455	0.00	0.00	0.00	3.61

Showing 1 to 25 of 457 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	1.685517	CTGCTGCAGATGGCTACTCTA	59.314	52.381	24.88	0.00	45.15	2.43
19	20	3.767806	CCTCTCTCCGCTGCTGCA	61.768	66.667	16.29	0.88	39.64	4.41
36	37	3.174265	CCTCCCCTGAGCCCATCC	61.174	72.222	0.00	0.00	37.29	3.51
38	39	2.040043	CTCCTCCCCTGAGCCCAT	60.040	66.667	0.00	0.00	37.29	4.00
54	55	7.398904	AGAGATACTTCCTAAAGCAAACTCTCT	59.601	37.037	0.00	0.00	35.81	3.10
58	59	9.825109	GATTAGAGATACTTCCTAAAGCAAACT	57.175	33.333	0.00	0.00	35.81	2.66
119	120	5.665459	CTCATTTCGGTCTCTAGATGGTTT	58.335	41.667	0.00	0.00	0.00	3.27
123	124	4.313277	TGCTCATTTCGGTCTCTAGATG	57.687	45.455	0.00	0.00	0.00	2.90
126	127	7.539712	TTTATTTGCTCATTTCGGTCTCTAG	57.460	36.000	0.00	0.00	0.00	2.43
134	135	7.043854	CCTTAGTGCATTTATTTGCTCATTTCG	60.044	37.037	0.00	0.00	43.18	3.46
160	161	2.281276	AAAACGGGCAGACGGGTC	60.281	61.111	0.00	0.00	38.39	4.46
162	163	2.032071	AGAAAACGGGCAGACGGG	59.968	61.111	0.00	0.00	38.39	5.28
178	179	0.824109	TCAGTATCTTCACCGGCCAG	59.176	55.000	0.00	0.00	0.00	4.85
187	188	1.957877	CGGGAGGAGGTCAGTATCTTC	59.042	57.143	0.00	0.00	0.00	2.87
194	195	1.533469	AAACGACGGGAGGAGGTCAG	61.533	60.000	0.00	0.00	32.74	3.51
195	196	1.117142	AAAACGACGGGAGGAGGTCA	61.117	55.000	0.00	0.00	32.74	4.02
209	210	5.460419	TGATTTTTGTCCGGAATGAAAAACG	59.540	36.000	22.66	0.00	31.88	3.60
223	224	5.650543	ACAGGTCAACACTTGATTTTTGTC	58.349	37.500	0.00	0.00	42.47	3.18
224	225	5.659440	ACAGGTCAACACTTGATTTTTGT	57.341	34.783	0.00	0.00	42.47	2.83
400	410	5.010282	AGATGGTACGCTTTTGGAAAATCT	58.990	37.500	0.00	0.00	0.00	2.40
416	426	6.534475	ACGTTTGTAAGTATGGAGATGGTA	57.466	37.500	0.00	0.00	0.00	3.25
475	485	4.824166	CCGGTAGTGACGACGGCG	62.824	72.222	10.39	10.39	39.85	6.46
478	488	3.678717	CTGGCCGGTAGTGACGACG	62.679	68.421	2.29	0.00	0.00	5.12
482	492	2.264794	CCACTGGCCGGTAGTGAC	59.735	66.667	30.37	4.45	46.52	3.67
537	552	1.512926	GTGAGGTCGTGACATGCTTT	58.487	50.000	2.00	0.00	0.00	3.51

Showing 1 to 25 of 419 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.