AutoCloner

Multiple sequence alignment - TraesCS6A01G081000

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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	TraesCS6A01G081000	chr6A	100.000	2312	0	0	1	2312	49549925	49552236	0.000000e+00	4270.0
1	TraesCS6A01G081000	chr6A	85.010	1481	118	42	814	2233	49483658	49485095	0.000000e+00	1410.0
2	TraesCS6A01G081000	chr6A	87.442	1290	80	33	704	1961	49499535	49500774	0.000000e+00	1410.0
3	TraesCS6A01G081000	chr6A	87.236	1183	90	30	814	1968	49196657	49197806	0.000000e+00	1291.0
4	TraesCS6A01G081000	chr6A	86.373	954	67	32	860	1793	49201970	49202880	0.000000e+00	983.0
5	TraesCS6A01G081000	chr6A	82.073	820	99	32	1532	2312	49192800	49193610	0.000000e+00	656.0
6	TraesCS6A01G081000	chr6A	87.782	532	45	7	1786	2312	49202918	49203434	2.540000e-169	604.0
7	TraesCS6A01G081000	chr6A	77.289	863	87	49	11	785	49195820	49196661	7.690000e-110	407.0
8	TraesCS6A01G081000	chr6A	87.770	278	22	4	516	785	49483389	49483662	4.800000e-82	315.0
9	TraesCS6A01G081000	chr6A	86.598	291	20	8	1954	2233	49197832	49198114	1.040000e-78	303.0
10	TraesCS6A01G081000	chr6A	84.071	226	17	6	538	753	49201432	49201648	1.400000e-47	200.0
11	TraesCS6A01G081000	chr6A	82.036	167	12	8	118	283	49483152	49483301	2.410000e-25	126.0
12	TraesCS6A01G081000	chr6D	89.387	1696	119	33	650	2312	37933764	37935431	0.000000e+00	2078.0
13	TraesCS6A01G081000	chr6D	86.960	1135	91	27	650	1751	37927516	37928626	0.000000e+00	1223.0
14	TraesCS6A01G081000	chr6D	88.077	931	70	14	814	1718	38119716	38120631	0.000000e+00	1066.0
15	TraesCS6A01G081000	chr6D	81.576	825	99	33	1532	2312	37923622	37924437	1.170000e-177	632.0
16	TraesCS6A01G081000	chr6D	84.542	524	52	19	116	619	37926907	37927421	2.060000e-135	492.0
17	TraesCS6A01G081000	chr6D	83.014	418	35	25	118	521	38119012	38119407	1.700000e-91	346.0
18	TraesCS6A01G081000	chr6D	88.000	100	8	2	11	106	37926770	37926869	5.220000e-22	115.0
19	TraesCS6A01G081000	chr6D	90.805	87	7	1	700	785	38119634	38119720	5.220000e-22	115.0
20	TraesCS6A01G081000	chr6D	78.788	165	26	7	245	402	429049708	429049546	4.060000e-18	102.0
21	TraesCS6A01G081000	chr6B	90.177	1018	51	16	650	1651	88735836	88736820	0.000000e+00	1280.0
22	TraesCS6A01G081000	chr6B	83.924	1157	111	39	757	1874	88717282	88718402	0.000000e+00	1037.0
23	TraesCS6A01G081000	chr6B	86.943	965	70	18	1381	2312	88816852	88817793	0.000000e+00	1033.0
24	TraesCS6A01G081000	chr6B	89.721	574	41	9	814	1385	88781204	88781761	0.000000e+00	717.0
25	TraesCS6A01G081000	chr6B	82.010	806	101	27	1532	2312	88714139	88714925	0.000000e+00	645.0
26	TraesCS6A01G081000	chr6B	84.434	424	39	12	118	517	88778858	88779278	2.150000e-105	392.0
27	TraesCS6A01G081000	chr6B	84.277	318	38	9	118	424	88735286	88735602	1.340000e-77	300.0
28	TraesCS6A01G081000	chr6B	92.481	133	9	1	345	476	88716808	88716940	3.030000e-44	189.0
29	TraesCS6A01G081000	chr6B	89.781	137	10	4	1689	1824	88752205	88752338	3.050000e-39	172.0
30	TraesCS6A01G081000	chr6B	89.412	85	7	1	645	727	88717198	88717282	3.140000e-19	106.0
31	TraesCS6A01G081000	chr6B	93.443	61	3	1	2173	2233	88754962	88755021	3.160000e-14	89.8
32	TraesCS6A01G081000	chr7A	79.263	1085	127	49	913	1934	679004356	679003307	0.000000e+00	667.0
33	TraesCS6A01G081000	chr7A	83.197	732	77	32	676	1388	511011968	511012672	1.510000e-176	628.0
34	TraesCS6A01G081000	chr7A	78.610	187	25	13	225	400	14915431	14915613	2.430000e-20	110.0
35	TraesCS6A01G081000	chr2B	83.094	627	88	12	1700	2312	156918788	156918166	2.600000e-154	555.0
36	TraesCS6A01G081000	chr2B	77.387	199	31	12	213	402	396194864	396195057	3.140000e-19	106.0
37	TraesCS6A01G081000	chr7D	83.201	631	71	19	676	1304	587150435	587149838	1.560000e-151	545.0
38	TraesCS6A01G081000	chr7B	77.951	449	60	19	1512	1930	658243430	658242991	6.380000e-61	244.0
39	TraesCS6A01G081000	chr2A	78.916	166	24	7	245	402	563219865	563220027	4.060000e-18	102.0
40	TraesCS6A01G081000	chr1A	78.788	165	24	7	246	402	450594436	450594275	1.460000e-17	100.0

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	TraesCS6A01G081000	chr6A	49549925	49552236	2311	False	4270.000000	4270	100.000000	1	2312	1	chr6A.!!$F2	2311
1	TraesCS6A01G081000	chr6A	49499535	49500774	1239	False	1410.000000	1410	87.442000	704	1961	1	chr6A.!!$F1	1257
2	TraesCS6A01G081000	chr6A	49192800	49203434	10634	False	634.857143	1291	84.488857	11	2312	7	chr6A.!!$F3	2301
3	TraesCS6A01G081000	chr6A	49483152	49485095	1943	False	617.000000	1410	84.938667	118	2233	3	chr6A.!!$F4	2115
4	TraesCS6A01G081000	chr6D	37933764	37935431	1667	False	2078.000000	2078	89.387000	650	2312	1	chr6D.!!$F1	1662
5	TraesCS6A01G081000	chr6D	37923622	37928626	5004	False	615.500000	1223	85.269500	11	2312	4	chr6D.!!$F2	2301
6	TraesCS6A01G081000	chr6D	38119012	38120631	1619	False	509.000000	1066	87.298667	118	1718	3	chr6D.!!$F3	1600
7	TraesCS6A01G081000	chr6B	88816852	88817793	941	False	1033.000000	1033	86.943000	1381	2312	1	chr6B.!!$F1	931
8	TraesCS6A01G081000	chr6B	88735286	88736820	1534	False	790.000000	1280	87.227000	118	1651	2	chr6B.!!$F3	1533
9	TraesCS6A01G081000	chr6B	88778858	88781761	2903	False	554.500000	717	87.077500	118	1385	2	chr6B.!!$F5	1267
10	TraesCS6A01G081000	chr6B	88714139	88718402	4263	False	494.250000	1037	86.956750	345	2312	4	chr6B.!!$F2	1967
11	TraesCS6A01G081000	chr7A	679003307	679004356	1049	True	667.000000	667	79.263000	913	1934	1	chr7A.!!$R1	1021
12	TraesCS6A01G081000	chr7A	511011968	511012672	704	False	628.000000	628	83.197000	676	1388	1	chr7A.!!$F2	712
13	TraesCS6A01G081000	chr2B	156918166	156918788	622	True	555.000000	555	83.094000	1700	2312	1	chr2B.!!$R1	612
14	TraesCS6A01G081000	chr7D	587149838	587150435	597	True	545.000000	545	83.201000	676	1304	1	chr7D.!!$R1	628

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
72	3086	0.250295	GGTGGAGCTACACACAAGCA	60.25	55.0	29.89	0.0	43.08	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1877	12567	0.871057	GCTTGAGCACAGTTGTCTCC	59.129	55.0	0.0	0.0	41.59	3.71	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
51	3065	2.224523	TGGGAGCTTCACTTAACACAGG	60.225	50.000	0.00	0.00	0.00	4.00
72	3086	0.250295	GGTGGAGCTACACACAAGCA	60.250	55.000	29.89	0.00	43.08	3.91
75	3089	2.357637	GTGGAGCTACACACAAGCAAAA	59.642	45.455	24.69	0.00	42.62	2.44
76	3090	3.004734	GTGGAGCTACACACAAGCAAAAT	59.995	43.478	24.69	0.00	42.62	1.82
83	3097	5.277779	GCTACACACAAGCAAAATAGTGTCA	60.278	40.000	0.00	0.00	42.79	3.58
87	3103	5.048504	CACACAAGCAAAATAGTGTCATCCT	60.049	40.000	0.00	0.00	42.79	3.24
175	3212	8.810652	TCGGAAAATTCTGAAAACAAAATAGG	57.189	30.769	2.21	0.00	39.51	2.57
176	3213	8.634444	TCGGAAAATTCTGAAAACAAAATAGGA	58.366	29.630	2.21	0.00	39.51	2.94
342	3384	8.492673	ACAATGAACAATATCTTGTACACGAT	57.507	30.769	17.81	17.81	44.83	3.73
343	3385	8.390354	ACAATGAACAATATCTTGTACACGATG	58.610	33.333	21.61	11.39	44.83	3.84
344	3386	8.603181	CAATGAACAATATCTTGTACACGATGA	58.397	33.333	21.61	8.84	44.83	2.92
345	3387	8.716646	ATGAACAATATCTTGTACACGATGAA	57.283	30.769	21.61	6.25	44.83	2.57
347	3389	9.161629	TGAACAATATCTTGTACACGATGAATT	57.838	29.630	21.61	12.91	44.83	2.17
348	3390	9.988350	GAACAATATCTTGTACACGATGAATTT	57.012	29.630	21.61	11.28	44.83	1.82
424	3754	3.626977	TGTATTGTGCAGCGAACTTTTG	58.373	40.909	0.00	0.00	0.00	2.44
525	3939	4.036852	GGAAAAGAACCAGAAACCACAGAG	59.963	45.833	0.00	0.00	0.00	3.35
619	5669	0.390603	CTGTCGAATTGGCCCGTGTA	60.391	55.000	0.00	0.00	0.00	2.90
625	5692	2.422127	CGAATTGGCCCGTGTAAAATCT	59.578	45.455	0.00	0.00	0.00	2.40
706	5851	2.262423	GGATCCCGATTTCCTCCAAG	57.738	55.000	0.00	0.00	0.00	3.61
1085	6304	1.063811	GCGTAGTAGCCGTCAGGAC	59.936	63.158	0.00	0.00	41.02	3.85
1252	11755	1.073199	CTGGCCTTGAAGAACGGGT	59.927	57.895	3.32	0.00	0.00	5.28
1362	11899	6.203530	TCTCATCTCATTGTCCAATTATTCGC	59.796	38.462	0.00	0.00	0.00	4.70
1598	12195	7.380536	TCTGTATGAAAATTTGATTGCTGCTT	58.619	30.769	0.00	0.00	0.00	3.91
1613	12216	2.509845	GCTTTCCAGCAGCGTTTTG	58.490	52.632	0.00	0.00	46.49	2.44
1658	12264	5.850557	TTCTTTGTGACATGTCAATGGTT	57.149	34.783	29.42	0.00	41.85	3.67
1659	12265	5.185668	TCTTTGTGACATGTCAATGGTTG	57.814	39.130	29.42	16.72	41.85	3.77
1675	12282	2.687425	TGGTTGTATGGCATATGCACAC	59.313	45.455	28.07	20.68	44.36	3.82
1692	12300	4.679197	TGCACACGCTTTTGATTTATGTTC	59.321	37.500	0.00	0.00	39.64	3.18
1757	12396	6.092259	GTGACTACCAGTTTGATGTATCCAAC	59.908	42.308	1.71	1.71	33.89	3.77
1817	12507	7.665690	TCCACTCTTCTGCAATCTCTATATTC	58.334	38.462	0.00	0.00	0.00	1.75
1878	12568	2.268999	TGTGCAGCCACATTCATGG	58.731	52.632	0.00	0.00	46.51	3.66
1879	12569	0.251253	TGTGCAGCCACATTCATGGA	60.251	50.000	0.00	0.00	46.51	3.41
1918	12608	4.321452	GCAAGAGAATGCAAGGATGTCAAA	60.321	41.667	0.00	0.00	45.70	2.69
1945	12637	3.009723	CCGAGTGTATTGGTTCTTGCAT	58.990	45.455	0.00	0.00	0.00	3.96
1961	12653	3.719268	TGCATTGGTGGTAAGACTGAT	57.281	42.857	0.00	0.00	0.00	2.90
1992	12684	2.605580	GCTGCTGCAAAGGTGTTCTTAC	60.606	50.000	11.11	0.00	39.41	2.34
2031	12728	7.095017	GCTTTAAACCTATCATCTAGCATGGTC	60.095	40.741	0.00	0.00	0.00	4.02
2034	12731	5.417754	ACCTATCATCTAGCATGGTCATG	57.582	43.478	0.00	5.55	41.60	3.07
2037	12736	6.498303	ACCTATCATCTAGCATGGTCATGTAA	59.502	38.462	0.00	0.00	40.80	2.41
2039	12738	8.045507	CCTATCATCTAGCATGGTCATGTAATT	58.954	37.037	0.00	0.00	40.80	1.40
2107	12807	6.092944	TGTCGGCTATGTATTTTGTAACTTGG	59.907	38.462	0.00	0.00	0.00	3.61
2123	12823	7.191551	TGTAACTTGGAGAGTACGATTATTCG	58.808	38.462	5.51	5.51	43.98	3.34
2275	12989	1.082690	GCTTCTCCTGCAGCACTAAC	58.917	55.000	8.66	0.00	35.95	2.34
2306	13020	7.982354	GGGCTAGTATTATTATCATGACAGGTC	59.018	40.741	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	2.164624	GTCAGTTGAGACATAGGCGACT	59.835	50.000	0.00	0.00	40.51	4.18
5	6	2.164624	AGTCAGTTGAGACATAGGCGAC	59.835	50.000	0.00	0.00	40.98	5.19
6	7	2.423892	GAGTCAGTTGAGACATAGGCGA	59.576	50.000	0.00	0.00	40.98	5.54
7	8	2.425312	AGAGTCAGTTGAGACATAGGCG	59.575	50.000	0.00	0.00	40.98	5.52
8	9	4.464069	AAGAGTCAGTTGAGACATAGGC	57.536	45.455	0.00	0.00	40.98	3.93
9	10	5.174395	CCAAAGAGTCAGTTGAGACATAGG	58.826	45.833	7.87	0.00	40.98	2.57
11	12	4.838423	TCCCAAAGAGTCAGTTGAGACATA	59.162	41.667	7.87	0.00	40.98	2.29
12	13	3.648067	TCCCAAAGAGTCAGTTGAGACAT	59.352	43.478	7.87	0.00	40.98	3.06
13	14	3.038280	TCCCAAAGAGTCAGTTGAGACA	58.962	45.455	7.87	0.00	40.98	3.41
14	15	3.658709	CTCCCAAAGAGTCAGTTGAGAC	58.341	50.000	7.87	0.00	37.87	3.36
15	16	2.037772	GCTCCCAAAGAGTCAGTTGAGA	59.962	50.000	7.87	0.65	45.21	3.27
16	17	2.038295	AGCTCCCAAAGAGTCAGTTGAG	59.962	50.000	7.87	1.46	45.21	3.02
18	19	2.557920	AGCTCCCAAAGAGTCAGTTG	57.442	50.000	0.00	0.00	45.21	3.16
19	20	2.439507	TGAAGCTCCCAAAGAGTCAGTT	59.560	45.455	0.00	0.00	45.21	3.16
20	21	2.050144	TGAAGCTCCCAAAGAGTCAGT	58.950	47.619	0.00	0.00	45.21	3.41
51	3065	1.512926	CTTGTGTGTAGCTCCACCAC	58.487	55.000	7.00	6.09	34.35	4.16
56	3070	3.923017	ATTTTGCTTGTGTGTAGCTCC	57.077	42.857	0.00	0.00	39.38	4.70
107	3123	0.657840	GTTCGGTGCACCATAGATGC	59.342	55.000	34.16	15.36	43.68	3.91
151	3188	8.699749	GTCCTATTTTGTTTTCAGAATTTTCCG	58.300	33.333	0.00	0.00	36.32	4.30
167	3204	9.726232	CATTGATATTGTGAGTGTCCTATTTTG	57.274	33.333	0.00	0.00	0.00	2.44
168	3205	9.466497	ACATTGATATTGTGAGTGTCCTATTTT	57.534	29.630	0.00	0.00	0.00	1.82
173	3210	9.466497	AAAATACATTGATATTGTGAGTGTCCT	57.534	29.630	0.00	0.00	0.00	3.85
174	3211	9.507280	CAAAATACATTGATATTGTGAGTGTCC	57.493	33.333	0.00	0.00	33.25	4.02
315	3357	9.594478	TCGTGTACAAGATATTGTTCATTGTAT	57.406	29.630	11.55	0.00	38.28	2.29
316	3358	8.989653	TCGTGTACAAGATATTGTTCATTGTA	57.010	30.769	11.55	0.00	35.31	2.41
317	3359	7.899178	TCGTGTACAAGATATTGTTCATTGT	57.101	32.000	11.55	0.00	35.31	2.71
318	3360	8.603181	TCATCGTGTACAAGATATTGTTCATTG	58.397	33.333	21.52	11.17	35.31	2.82
319	3361	8.716646	TCATCGTGTACAAGATATTGTTCATT	57.283	30.769	21.52	0.00	35.31	2.57
320	3362	8.716646	TTCATCGTGTACAAGATATTGTTCAT	57.283	30.769	21.52	0.00	35.31	2.57
321	3363	8.716646	ATTCATCGTGTACAAGATATTGTTCA	57.283	30.769	21.52	9.74	36.44	3.18
322	3364	9.988350	AAATTCATCGTGTACAAGATATTGTTC	57.012	29.630	21.52	6.96	36.44	3.18
487	3867	6.403200	GGTTCTTTTCCTTTTTCTGTTTTGGC	60.403	38.462	0.00	0.00	0.00	4.52
539	3959	4.944249	GCAGTTTCTTGCGGGTTC	57.056	55.556	0.00	0.00	33.90	3.62
604	5654	2.422127	AGATTTTACACGGGCCAATTCG	59.578	45.455	4.39	0.10	0.00	3.34
606	5656	2.495669	CCAGATTTTACACGGGCCAATT	59.504	45.455	4.39	0.00	0.00	2.32
706	5851	5.249336	TCTTGAAAAATTTCGCGAAATGC	57.751	34.783	39.07	28.54	40.57	3.56
1085	6304	4.112341	GCCGCTTCAGCTTGCAGG	62.112	66.667	0.00	0.00	39.32	4.85
1228	11731	2.437359	CTTCAAGGCCAGCTCCGG	60.437	66.667	5.01	0.00	0.00	5.14
1240	11743	4.792087	GGCAGACCCGTTCTTCAA	57.208	55.556	0.00	0.00	28.96	2.69
1362	11899	4.322198	CCAATCCAACCAAATCTTGTCCAG	60.322	45.833	0.00	0.00	0.00	3.86
1562	12153	9.903682	CAAATTTTCATACAGAAGACATGAGTT	57.096	29.630	0.00	0.00	37.57	3.01
1563	12154	9.288576	TCAAATTTTCATACAGAAGACATGAGT	57.711	29.630	0.00	0.00	37.57	3.41
1658	12264	0.943673	GCGTGTGCATATGCCATACA	59.056	50.000	24.54	18.65	42.15	2.29
1659	12265	1.229428	AGCGTGTGCATATGCCATAC	58.771	50.000	24.54	16.30	46.23	2.39
1675	12282	9.994432	ATAGAAGAAGAACATAAATCAAAAGCG	57.006	29.630	0.00	0.00	0.00	4.68
1757	12396	1.808945	CTTGCAACTACTGGCTCCAAG	59.191	52.381	0.00	0.00	0.00	3.61
1846	12536	3.252701	GGCTGCACATTCATGGAGATTAG	59.747	47.826	0.50	0.00	40.28	1.73
1875	12565	2.775890	CTTGAGCACAGTTGTCTCCAT	58.224	47.619	0.00	0.00	0.00	3.41
1876	12566	1.811558	GCTTGAGCACAGTTGTCTCCA	60.812	52.381	0.00	0.00	41.59	3.86
1877	12567	0.871057	GCTTGAGCACAGTTGTCTCC	59.129	55.000	0.00	0.00	41.59	3.71
1918	12608	4.906618	AGAACCAATACACTCGGTCAATT	58.093	39.130	0.00	0.00	30.91	2.32
1945	12637	4.346709	TGAAGTCATCAGTCTTACCACCAA	59.653	41.667	0.00	0.00	33.04	3.67
1992	12684	6.650427	AGGTTTAAAGCTTCTTACCAAAGG	57.350	37.500	14.07	0.00	31.69	3.11
2009	12703	6.994421	TGACCATGCTAGATGATAGGTTTA	57.006	37.500	0.00	0.00	0.00	2.01
2275	12989	9.035607	GTCATGATAATAATACTAGCCCATTCG	57.964	37.037	0.00	0.00	0.00	3.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.