AutoCloner

Multiple sequence alignment - TraesCS2D01G423100

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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	TraesCS2D01G423100	chr2D	100.000	5951	0	0	1	5951	536228679	536222729	0.000000e+00	10990.0
1	TraesCS2D01G423100	chr2D	86.053	2065	238	29	2453	4504	536157303	536155276	0.000000e+00	2172.0
2	TraesCS2D01G423100	chr2D	77.094	1755	312	64	2451	4155	536509011	536507297	0.000000e+00	931.0
3	TraesCS2D01G423100	chr2D	84.205	994	99	33	789	1760	536158958	536158001	0.000000e+00	913.0
4	TraesCS2D01G423100	chr2D	77.609	1121	208	30	2486	3585	539310363	539309265	1.810000e-179	640.0
5	TraesCS2D01G423100	chr2D	86.320	519	70	1	1933	2451	536157765	536157248	1.120000e-156	564.0
6	TraesCS2D01G423100	chr2D	77.430	926	167	26	2676	3585	536384319	536383420	1.140000e-141	514.0
7	TraesCS2D01G423100	chr2D	98.031	254	4	1	61	313	621659354	621659607	1.970000e-119	440.0
8	TraesCS2D01G423100	chr2D	80.739	514	95	3	1941	2451	599948756	599948244	1.200000e-106	398.0
9	TraesCS2D01G423100	chr2D	82.313	441	64	12	1944	2376	536385388	536384954	2.620000e-98	370.0
10	TraesCS2D01G423100	chr2D	96.610	118	4	0	5076	5193	87030974	87031091	4.710000e-46	196.0
11	TraesCS2D01G423100	chr2D	98.165	109	2	0	5076	5184	87035731	87035839	2.190000e-44	191.0
12	TraesCS2D01G423100	chr2D	76.025	317	72	4	4599	4913	12129240	12129554	1.720000e-35	161.0
13	TraesCS2D01G423100	chr2D	76.534	277	59	6	1096	1369	536510327	536510054	4.810000e-31	147.0
14	TraesCS2D01G423100	chr2D	89.474	95	8	1	4157	4251	536223476	536223384	1.050000e-22	119.0
15	TraesCS2D01G423100	chr2D	89.474	95	8	1	5204	5296	536224523	536224429	1.050000e-22	119.0
16	TraesCS2D01G423100	chr2D	100.000	58	0	0	2394	2451	536226229	536226172	2.270000e-19	108.0
17	TraesCS2D01G423100	chr2B	93.686	2059	121	8	2451	4506	638264355	638262303	0.000000e+00	3073.0
18	TraesCS2D01G423100	chr2B	92.826	2063	120	17	2451	4506	637767375	637765334	0.000000e+00	2964.0
19	TraesCS2D01G423100	chr2B	91.793	1584	99	16	314	1884	637769480	637767915	0.000000e+00	2176.0
20	TraesCS2D01G423100	chr2B	91.981	1459	84	16	3056	4506	637995121	637993688	0.000000e+00	2015.0
21	TraesCS2D01G423100	chr2B	89.806	1599	112	31	314	1884	638266470	638264895	0.000000e+00	2002.0
22	TraesCS2D01G423100	chr2B	88.738	1616	116	36	314	1884	637999572	637997978	0.000000e+00	1916.0
23	TraesCS2D01G423100	chr2B	76.887	1722	308	64	2470	4144	638757692	638756014	0.000000e+00	893.0
24	TraesCS2D01G423100	chr2B	94.435	575	30	2	4507	5080	638262254	638261681	0.000000e+00	883.0
25	TraesCS2D01G423100	chr2B	93.772	578	31	4	4507	5080	637765274	637764698	0.000000e+00	863.0
26	TraesCS2D01G423100	chr2B	92.919	579	37	3	4507	5082	637993639	637993062	0.000000e+00	839.0
27	TraesCS2D01G423100	chr2B	90.507	611	45	6	2451	3060	637997438	637996840	0.000000e+00	795.0
28	TraesCS2D01G423100	chr2B	92.021	564	44	1	1889	2451	637767881	637767318	0.000000e+00	791.0
29	TraesCS2D01G423100	chr2B	82.766	911	105	25	800	1693	637707245	637706370	0.000000e+00	765.0
30	TraesCS2D01G423100	chr2B	90.603	564	52	1	1889	2451	638264861	638264298	0.000000e+00	747.0
31	TraesCS2D01G423100	chr2B	90.071	564	55	1	1889	2451	637997944	637997381	0.000000e+00	730.0
32	TraesCS2D01G423100	chr2B	78.565	1143	198	36	2470	3585	637932880	637931758	0.000000e+00	710.0
33	TraesCS2D01G423100	chr2B	82.713	752	98	18	3710	4458	637681198	637680476	1.810000e-179	640.0
34	TraesCS2D01G423100	chr2B	86.318	497	66	2	3208	3704	637696701	637696207	1.890000e-149	540.0
35	TraesCS2D01G423100	chr2B	89.637	386	35	3	4525	4907	637582922	637582539	2.490000e-133	486.0
36	TraesCS2D01G423100	chr2B	82.136	515	86	5	1941	2451	729901774	729901262	2.550000e-118	436.0
37	TraesCS2D01G423100	chr2B	94.872	234	12	0	5184	5417	637993065	637992832	3.390000e-97	366.0
38	TraesCS2D01G423100	chr2B	79.600	500	94	8	1957	2451	638758150	638757654	9.490000e-93	351.0
39	TraesCS2D01G423100	chr2B	90.837	251	22	1	5275	5524	637707741	637707491	9.560000e-88	335.0
40	TraesCS2D01G423100	chr2B	93.013	229	16	0	5189	5417	638261677	638261449	9.560000e-88	335.0
41	TraesCS2D01G423100	chr2B	96.809	94	3	0	5189	5282	637764694	637764601	2.220000e-34	158.0
42	TraesCS2D01G423100	chr2B	90.526	95	7	1	5204	5296	637765673	637765579	2.250000e-24	124.0
43	TraesCS2D01G423100	chr2B	80.000	160	25	7	559	714	733725636	733725792	1.750000e-20	111.0
44	TraesCS2D01G423100	chr2B	87.368	95	10	1	5204	5296	637994037	637993943	2.270000e-19	108.0
45	TraesCS2D01G423100	chr2B	86.316	95	11	1	5204	5296	638262652	638262558	1.060000e-17	102.0
46	TraesCS2D01G423100	chr2A	86.326	2055	229	33	2453	4493	678969256	678967240	0.000000e+00	2191.0
47	TraesCS2D01G423100	chr2A	84.985	979	92	31	800	1756	678970902	678969957	0.000000e+00	942.0
48	TraesCS2D01G423100	chr2A	76.799	1737	313	64	2470	4155	679265489	679263792	0.000000e+00	893.0
49	TraesCS2D01G423100	chr2A	86.679	563	71	3	1889	2451	678969759	678969201	6.550000e-174	621.0
50	TraesCS2D01G423100	chr2A	75.589	1401	258	58	2470	3825	733685263	733683902	3.050000e-172	616.0
51	TraesCS2D01G423100	chr2A	87.980	391	38	7	4572	4956	678966973	678966586	2.530000e-123	453.0
52	TraesCS2D01G423100	chr2A	71.622	888	190	46	2470	3337	756952892	756952047	2.830000e-43	187.0
53	TraesCS2D01G423100	chr2A	97.222	108	3	0	5079	5186	115096208	115096101	3.660000e-42	183.0
54	TraesCS2D01G423100	chr2A	75.394	317	74	4	4599	4913	12742015	12742329	3.720000e-32	150.0
55	TraesCS2D01G423100	chr2A	76.534	277	57	6	1096	1368	679266996	679266724	1.730000e-30	145.0
56	TraesCS2D01G423100	chr6D	98.069	259	3	2	61	318	90353268	90353011	3.270000e-122	449.0
57	TraesCS2D01G423100	chr6D	97.308	260	6	1	61	319	131058454	131058195	1.970000e-119	440.0
58	TraesCS2D01G423100	chr7D	98.419	253	4	0	61	313	29931887	29932139	4.230000e-121	446.0
59	TraesCS2D01G423100	chr7D	98.425	254	3	1	61	313	597974827	597974574	4.230000e-121	446.0
60	TraesCS2D01G423100	chr7D	97.683	259	5	1	61	318	159998444	159998702	1.520000e-120	444.0
61	TraesCS2D01G423100	chr3D	98.425	254	3	1	61	313	79111091	79110838	4.230000e-121	446.0
62	TraesCS2D01G423100	chr3D	98.031	254	4	1	61	313	7734046	7733793	1.970000e-119	440.0
63	TraesCS2D01G423100	chr4D	98.039	255	4	1	61	314	73304767	73305021	5.470000e-120	442.0
64	TraesCS2D01G423100	chr5A	95.833	120	3	2	5079	5196	69844788	69844907	6.090000e-45	193.0
65	TraesCS2D01G423100	chr5A	92.969	128	7	2	5079	5206	580937840	580937715	1.020000e-42	185.0
66	TraesCS2D01G423100	chr1A	95.122	123	5	1	5072	5193	343396688	343396810	6.090000e-45	193.0
67	TraesCS2D01G423100	chr1A	95.763	118	4	1	5076	5193	587607300	587607416	7.870000e-44	189.0
68	TraesCS2D01G423100	chr1A	95.763	118	4	1	5076	5193	587610182	587610298	7.870000e-44	189.0
69	TraesCS2D01G423100	chr1A	85.057	87	9	3	632	717	28618276	28618193	1.060000e-12	86.1
70	TraesCS2D01G423100	chr4A	95.763	118	5	0	5077	5194	132996259	132996376	2.190000e-44	191.0
71	TraesCS2D01G423100	chr4A	80.120	166	28	5	562	724	734892579	734892416	1.050000e-22	119.0
72	TraesCS2D01G423100	chr4A	97.619	42	1	0	4834	4875	215225726	215225685	8.270000e-09	73.1
73	TraesCS2D01G423100	chr6B	79.245	159	29	4	559	714	391070270	391070427	2.270000e-19	108.0
74	TraesCS2D01G423100	chrUn	77.059	170	33	6	555	720	269319789	269319622	6.350000e-15	93.5
75	TraesCS2D01G423100	chr4B	77.301	163	31	6	558	717	517369328	517369487	2.280000e-14	91.6
76	TraesCS2D01G423100	chr1B	100.000	38	0	0	314	351	59461453	59461490	2.980000e-08	71.3

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	TraesCS2D01G423100	chr2D	536222729	536228679	5950	True	10990.000000	10990	100.000000	1	5951	1	chr2D.!!$R1	5950
1	TraesCS2D01G423100	chr2D	536155276	536158958	3682	True	1216.333333	2172	85.526000	789	4504	3	chr2D.!!$R4	3715
2	TraesCS2D01G423100	chr2D	539309265	539310363	1098	True	640.000000	640	77.609000	2486	3585	1	chr2D.!!$R2	1099
3	TraesCS2D01G423100	chr2D	536507297	536510327	3030	True	539.000000	931	76.814000	1096	4155	2	chr2D.!!$R7	3059
4	TraesCS2D01G423100	chr2D	536383420	536385388	1968	True	442.000000	514	79.871500	1944	3585	2	chr2D.!!$R6	1641
5	TraesCS2D01G423100	chr2D	599948244	599948756	512	True	398.000000	398	80.739000	1941	2451	1	chr2D.!!$R3	510
6	TraesCS2D01G423100	chr2B	638261449	638266470	5021	True	1190.333333	3073	91.309833	314	5417	6	chr2B.!!$R9	5103
7	TraesCS2D01G423100	chr2B	637764601	637769480	4879	True	1179.333333	2964	92.957833	314	5296	6	chr2B.!!$R7	4982
8	TraesCS2D01G423100	chr2B	637992832	637999572	6740	True	967.000000	2015	90.922286	314	5417	7	chr2B.!!$R8	5103
9	TraesCS2D01G423100	chr2B	637931758	637932880	1122	True	710.000000	710	78.565000	2470	3585	1	chr2B.!!$R4	1115
10	TraesCS2D01G423100	chr2B	637680476	637681198	722	True	640.000000	640	82.713000	3710	4458	1	chr2B.!!$R2	748
11	TraesCS2D01G423100	chr2B	638756014	638758150	2136	True	622.000000	893	78.243500	1957	4144	2	chr2B.!!$R10	2187
12	TraesCS2D01G423100	chr2B	637706370	637707741	1371	True	550.000000	765	86.801500	800	5524	2	chr2B.!!$R6	4724
13	TraesCS2D01G423100	chr2B	729901262	729901774	512	True	436.000000	436	82.136000	1941	2451	1	chr2B.!!$R5	510
14	TraesCS2D01G423100	chr2A	678966586	678970902	4316	True	1051.750000	2191	86.492500	800	4956	4	chr2A.!!$R4	4156
15	TraesCS2D01G423100	chr2A	733683902	733685263	1361	True	616.000000	616	75.589000	2470	3825	1	chr2A.!!$R2	1355
16	TraesCS2D01G423100	chr2A	679263792	679266996	3204	True	519.000000	893	76.666500	1096	4155	2	chr2A.!!$R5	3059

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	Hairpin	End Stability	Orientation
76	77	0.035056	AAATCAGCCTTCTGTCCCGG	60.035	55.000	0.00	41.10	5.73	F
1058	1122	0.035739	GGTGCGGTTTGAGGGACTTA	59.964	55.000	0.00	41.55	2.24	F
1283	1347	0.460284	CCAAATGGACTCCTCCGTCG	60.460	60.000	0.00	39.88	5.12	F
1762	1861	0.758685	TGGGTTTTTGGGACTGGCTG	60.759	55.000	0.00	0.00	4.85	F
2374	2728	0.991146	TGGACATGGCATACAGGTGT	59.009	50.000	0.00	45.39	4.16	F
2610	3006	1.203212	TCCTCGGGTACTTCCTTTGGA	60.203	52.381	0.00	36.25	3.53	F
3206	5733	1.293924	CTGAATCAGGCCATGTCGTC	58.706	55.000	5.01	0.00	4.20	F
4631	7409	0.258484	CAGAGAGAGAGCAGGGAGGA	59.742	60.000	0.00	0.00	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1742	1841	0.469892	AGCCAGTCCCAAAAACCCAG	60.470	55.000	0.00	0.00	0.00	4.45	R
2280	2634	1.755179	ATCCACCAATGAAAGCCGAG	58.245	50.000	0.00	0.00	0.00	4.63	R
3029	3815	2.093869	TCTTGTGGCCTATACGTTCCAC	60.094	50.000	3.32	5.05	46.78	4.02	R
3362	5900	1.250840	ATTCCCTTTCGCCCAACTGC	61.251	55.000	0.00	0.00	0.00	4.40	R
3876	6444	0.250234	GTAGCCACTGCAGATGGACA	59.750	55.000	28.64	17.02	39.87	4.02	R
4481	7056	1.743958	ACATGAGTCCGTCTTCTACCG	59.256	52.381	0.00	0.00	0.00	4.02	R
4863	7641	0.304705	CATTAACCGCGCTCACCATC	59.695	55.000	5.56	0.00	0.00	3.51	R
5476	8258	0.035317	AGCTTGCGAACATCACAGGA	59.965	50.000	0.00	0.00	0.00	3.86	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	Hairpin	End Stability
24	25	1.290203	CCAGTTGGCTGCTGTATACG	58.710	55.000	41.26	3.06
25	26	1.405526	CCAGTTGGCTGCTGTATACGT	60.406	52.381	41.26	3.57
26	27	1.660607	CAGTTGGCTGCTGTATACGTG	59.339	52.381	35.77	4.49
27	28	1.275291	AGTTGGCTGCTGTATACGTGT	59.725	47.619	0.00	4.49
28	29	1.393539	GTTGGCTGCTGTATACGTGTG	59.606	52.381	0.00	3.82
30	31	0.999406	GGCTGCTGTATACGTGTGTG	59.001	55.000	0.00	3.82
31	32	1.403647	GGCTGCTGTATACGTGTGTGA	60.404	52.381	0.00	3.58
32	33	1.920574	GCTGCTGTATACGTGTGTGAG	59.079	52.381	0.00	3.51
33	34	2.415491	GCTGCTGTATACGTGTGTGAGA	60.415	50.000	0.00	3.27
36	37	3.254903	TGCTGTATACGTGTGTGAGAGTT	59.745	43.478	0.00	3.01
37	38	3.608506	GCTGTATACGTGTGTGAGAGTTG	59.391	47.826	0.00	3.16
38	39	4.795268	CTGTATACGTGTGTGAGAGTTGT	58.205	43.478	0.00	3.32
39	40	4.542735	TGTATACGTGTGTGAGAGTTGTG	58.457	43.478	0.00	3.33
40	41	1.847818	TACGTGTGTGAGAGTTGTGC	58.152	50.000	0.00	4.57
41	42	1.145759	ACGTGTGTGAGAGTTGTGCG	61.146	55.000	0.00	5.34
43	44	1.006832	GTGTGTGAGAGTTGTGCGTT	58.993	50.000	0.00	4.84
44	45	1.396996	GTGTGTGAGAGTTGTGCGTTT	59.603	47.619	0.00	3.60
45	46	1.663643	TGTGTGAGAGTTGTGCGTTTC	59.336	47.619	0.00	2.78
46	47	1.933853	GTGTGAGAGTTGTGCGTTTCT	59.066	47.619	0.00	2.52
47	48	1.933181	TGTGAGAGTTGTGCGTTTCTG	59.067	47.619	0.00	3.02
51	52	0.040958	GAGTTGTGCGTTTCTGGCTG	60.041	55.000	0.00	4.85
52	53	1.008538	GTTGTGCGTTTCTGGCTGG	60.009	57.895	0.00	4.85
53	54	1.453015	TTGTGCGTTTCTGGCTGGT	60.453	52.632	0.00	4.00
54	55	1.723608	TTGTGCGTTTCTGGCTGGTG	61.724	55.000	0.00	4.17
55	56	2.594303	TGCGTTTCTGGCTGGTGG	60.594	61.111	0.00	4.61

Showing 1 to 25 of 733 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
5	6	1.290203	CGTATACAGCAGCCAACTGG	58.710	55.000	3.32	44.63	4.00
8	9	1.393539	CACACGTATACAGCAGCCAAC	59.606	52.381	3.32	0.00	3.77
9	10	1.001520	ACACACGTATACAGCAGCCAA	59.998	47.619	3.32	0.00	4.52
12	13	1.920574	CTCACACACGTATACAGCAGC	59.079	52.381	3.32	0.00	5.25
13	14	3.119814	ACTCTCACACACGTATACAGCAG	60.120	47.826	3.32	0.00	4.24
14	15	2.817844	ACTCTCACACACGTATACAGCA	59.182	45.455	3.32	0.00	4.41
16	17	4.617223	CACAACTCTCACACACGTATACAG	59.383	45.833	3.32	0.00	2.74
17	18	4.542735	CACAACTCTCACACACGTATACA	58.457	43.478	3.32	0.00	2.29
18	19	3.364023	GCACAACTCTCACACACGTATAC	59.636	47.826	0.00	0.00	1.47
20	21	2.404215	GCACAACTCTCACACACGTAT	58.596	47.619	0.00	0.00	3.06
21	22	1.847818	GCACAACTCTCACACACGTA	58.152	50.000	0.00	0.00	3.57
22	23	1.145759	CGCACAACTCTCACACACGT	61.146	55.000	0.00	0.00	4.49
23	24	1.145759	ACGCACAACTCTCACACACG	61.146	55.000	0.00	0.00	4.49
24	25	1.006832	AACGCACAACTCTCACACAC	58.993	50.000	0.00	0.00	3.82
25	26	1.663643	GAAACGCACAACTCTCACACA	59.336	47.619	0.00	0.00	3.72
26	27	1.933853	AGAAACGCACAACTCTCACAC	59.066	47.619	0.00	0.00	3.82
27	28	1.933181	CAGAAACGCACAACTCTCACA	59.067	47.619	0.00	0.00	3.58
28	29	1.261619	CCAGAAACGCACAACTCTCAC	59.738	52.381	0.00	0.00	3.51
30	31	0.235926	GCCAGAAACGCACAACTCTC	59.764	55.000	0.00	0.00	3.20
31	32	0.179045	AGCCAGAAACGCACAACTCT	60.179	50.000	0.00	0.00	3.24
32	33	0.040958	CAGCCAGAAACGCACAACTC	60.041	55.000	0.00	0.00	3.01
33	34	1.447317	CCAGCCAGAAACGCACAACT	61.447	55.000	0.00	0.00	3.16
36	37	2.186160	CACCAGCCAGAAACGCACA	61.186	57.895	0.00	0.00	4.57
37	38	2.639286	CACCAGCCAGAAACGCAC	59.361	61.111	0.00	0.00	5.34
38	39	2.046009	TACCACCAGCCAGAAACGCA	62.046	55.000	0.00	0.00	5.24

Showing 1 to 25 of 696 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.