AutoCloner

Multiple sequence alignment - TraesCS2A01G281300

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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	TraesCS2A01G281300	chr2A	100.000	3181	0	0	1	3181	469818033	469821213	0.000000e+00	5875.0
1	TraesCS2A01G281300	chr2A	78.632	468	83	14	293	750	694444383	694443923	8.630000e-76	294.0
2	TraesCS2A01G281300	chr6B	98.393	2302	23	2	1	2289	650650242	650652542	0.000000e+00	4034.0
3	TraesCS2A01G281300	chr5A	97.848	1208	12	2	1100	2293	55272841	55274048	0.000000e+00	2074.0
4	TraesCS2A01G281300	chr5A	99.004	1104	11	0	1	1104	55266412	55267515	0.000000e+00	1978.0
5	TraesCS2A01G281300	chr5A	94.240	625	17	7	907	1518	592034664	592035282	0.000000e+00	937.0
6	TraesCS2A01G281300	chr5A	92.467	531	26	2	1519	2036	592035792	592036321	0.000000e+00	747.0
7	TraesCS2A01G281300	chr5A	84.466	309	42	2	907	1215	592123043	592123345	1.850000e-77	300.0
8	TraesCS2A01G281300	chr3A	93.541	1316	55	6	62	1366	497760860	497759564	0.000000e+00	1932.0
9	TraesCS2A01G281300	chr3A	90.253	790	41	7	1519	2295	497759452	497758686	0.000000e+00	1000.0
10	TraesCS2A01G281300	chr4D	94.147	803	44	1	62	864	47895819	47895020	0.000000e+00	1219.0
11	TraesCS2A01G281300	chr4D	98.413	63	1	0	847	909	47894965	47894903	9.330000e-21	111.0
12	TraesCS2A01G281300	chr4D	92.105	76	5	1	1	76	47895987	47895913	4.340000e-19	106.0
13	TraesCS2A01G281300	chr4A	92.638	815	51	5	59	864	549819571	549820385	0.000000e+00	1164.0
14	TraesCS2A01G281300	chr4A	96.970	66	2	0	844	909	549820437	549820502	9.330000e-21	111.0
15	TraesCS2A01G281300	chr4A	92.105	76	5	1	1	76	549819406	549819480	4.340000e-19	106.0
16	TraesCS2A01G281300	chr2D	92.795	805	49	6	2383	3179	351997802	351998605	0.000000e+00	1157.0
17	TraesCS2A01G281300	chr2D	78.419	468	84	13	293	750	553992060	553991600	4.010000e-74	289.0
18	TraesCS2A01G281300	chr4B	91.563	806	59	4	62	864	70551961	70551162	0.000000e+00	1103.0
19	TraesCS2A01G281300	chr4B	95.364	302	13	1	64	365	310972962	310972662	2.220000e-131	479.0
20	TraesCS2A01G281300	chr4B	98.413	63	1	0	847	909	70551107	70551045	9.330000e-21	111.0
21	TraesCS2A01G281300	chr4B	92.105	76	5	1	1	76	310973132	310973058	4.340000e-19	106.0
22	TraesCS2A01G281300	chr4B	89.189	74	7	1	1	74	70552129	70552057	1.220000e-14	91.6
23	TraesCS2A01G281300	chr2B	89.583	720	58	3	2476	3179	418283544	418284262	0.000000e+00	898.0
24	TraesCS2A01G281300	chr2B	78.205	468	85	13	293	750	660114947	660114487	1.870000e-72	283.0
25	TraesCS2A01G281300	chr2B	81.897	232	10	11	2292	2491	418282566	418282797	1.960000e-37	167.0
26	TraesCS2A01G281300	chr5B	94.128	596	24	2	907	1498	579520762	579521350	0.000000e+00	896.0
27	TraesCS2A01G281300	chr5B	93.309	538	22	2	1523	2047	579521649	579522185	0.000000e+00	782.0
28	TraesCS2A01G281300	chr5B	96.026	302	12	0	64	365	663519747	663519446	2.850000e-135	492.0
29	TraesCS2A01G281300	chr5B	87.543	289	28	5	907	1194	579808053	579808334	8.510000e-86	327.0
30	TraesCS2A01G281300	chr5B	93.839	211	12	1	2082	2291	663520094	663520304	1.840000e-82	316.0
31	TraesCS2A01G281300	chr5B	92.537	67	5	0	1	67	663519917	663519851	2.610000e-16	97.1
32	TraesCS2A01G281300	chr5D	94.350	531	16	2	1519	2036	472522210	472522739	0.000000e+00	802.0
33	TraesCS2A01G281300	chr5D	90.346	549	23	11	907	1431	472521031	472521573	0.000000e+00	693.0
34	TraesCS2A01G281300	chr5D	92.000	225	16	2	2070	2293	387823701	387823924	6.620000e-82	315.0
35	TraesCS2A01G281300	chr5D	85.113	309	40	2	907	1215	472569164	472569466	8.570000e-81	311.0
36	TraesCS2A01G281300	chr5D	90.129	233	22	1	2068	2299	387815305	387815073	5.160000e-78	302.0
37	TraesCS2A01G281300	chr5D	89.362	94	3	4	1429	1520	472521599	472521687	9.330000e-21	111.0
38	TraesCS2A01G281300	chr3D	95.440	307	14	0	59	365	32388004	32388310	1.030000e-134	490.0
39	TraesCS2A01G281300	chr3D	93.421	76	4	1	1	76	32387839	32387913	9.330000e-21	111.0
40	TraesCS2A01G281300	chr6A	95.154	227	10	1	2068	2293	66266834	66266608	1.090000e-94	357.0
41	TraesCS2A01G281300	chr6A	94.419	215	11	1	2082	2295	66269447	66269661	2.370000e-86	329.0
42	TraesCS2A01G281300	chr6A	92.105	76	5	1	1	76	66269270	66269196	4.340000e-19	106.0
43	TraesCS2A01G281300	chr3B	95.872	218	7	2	2081	2296	42176067	42176284	5.050000e-93	351.0
44	TraesCS2A01G281300	chr1D	91.111	225	17	3	2077	2300	359696765	359696543	5.160000e-78	302.0
45	TraesCS2A01G281300	chr7A	79.661	236	34	14	2930	3158	512183974	512183746	1.180000e-34	158.0

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	TraesCS2A01G281300	chr2A	469818033	469821213	3180	False	5875.000000	5875	100.000000	1	3181	1	chr2A.!!$F1	3180
1	TraesCS2A01G281300	chr6B	650650242	650652542	2300	False	4034.000000	4034	98.393000	1	2289	1	chr6B.!!$F1	2288
2	TraesCS2A01G281300	chr5A	55272841	55274048	1207	False	2074.000000	2074	97.848000	1100	2293	1	chr5A.!!$F2	1193
3	TraesCS2A01G281300	chr5A	55266412	55267515	1103	False	1978.000000	1978	99.004000	1	1104	1	chr5A.!!$F1	1103
4	TraesCS2A01G281300	chr5A	592034664	592036321	1657	False	842.000000	937	93.353500	907	2036	2	chr5A.!!$F4	1129
5	TraesCS2A01G281300	chr3A	497758686	497760860	2174	True	1466.000000	1932	91.897000	62	2295	2	chr3A.!!$R1	2233
6	TraesCS2A01G281300	chr4D	47894903	47895987	1084	True	478.666667	1219	94.888333	1	909	3	chr4D.!!$R1	908
7	TraesCS2A01G281300	chr4A	549819406	549820502	1096	False	460.333333	1164	93.904333	1	909	3	chr4A.!!$F1	908
8	TraesCS2A01G281300	chr2D	351997802	351998605	803	False	1157.000000	1157	92.795000	2383	3179	1	chr2D.!!$F1	796
9	TraesCS2A01G281300	chr4B	70551045	70552129	1084	True	435.200000	1103	93.055000	1	909	3	chr4B.!!$R1	908
10	TraesCS2A01G281300	chr2B	418282566	418284262	1696	False	532.500000	898	85.740000	2292	3179	2	chr2B.!!$F1	887
11	TraesCS2A01G281300	chr5B	579520762	579522185	1423	False	839.000000	896	93.718500	907	2047	2	chr5B.!!$F3	1140
12	TraesCS2A01G281300	chr5D	472521031	472522739	1708	False	535.333333	802	91.352667	907	2036	3	chr5D.!!$F3	1129
13	TraesCS2A01G281300	chr6A	66266608	66269270	2662	True	231.500000	357	93.629500	1	2293	2	chr6A.!!$R1	2292

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
368	499	0.528466	GCCGAGATGAGCACGATGAA	60.528	55.0	0.0	0.0	31.96	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2364	4690	0.904649	TGGCCAGTCATACCACTCTG	59.095	55.0	0.0	0.0	0.0	3.35	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
82	198	3.215245	GCTCGTCCAGCTCCATCT	58.785	61.111	0.00	0.00	45.83	2.90
368	499	0.528466	GCCGAGATGAGCACGATGAA	60.528	55.000	0.00	0.00	31.96	2.57
2070	4383	5.470047	ACAGTAGTTTCCAGTAGAAGTGG	57.530	43.478	0.00	0.00	40.10	4.00
2234	4549	4.213564	TGGTTTGGTCAAGTTTTGCAAT	57.786	36.364	0.00	0.00	0.00	3.56
2364	4690	0.037790	AGCTTTCTGCACCTCGAGTC	60.038	55.000	12.31	0.60	45.94	3.36
2372	4698	1.528292	GCACCTCGAGTCAGAGTGGT	61.528	60.000	12.31	0.00	36.56	4.16
2414	4758	2.368875	CTCTACCGGTTGCTCCCAATAT	59.631	50.000	15.04	0.00	32.75	1.28
2608	5718	7.218204	ACGCGAAATTTCAAGTTATTATTGAGC	59.782	33.333	15.93	6.88	37.91	4.26
2653	5763	9.973246	CAAACATAGTGTATTTGTAAGCTACAG	57.027	33.333	0.00	0.00	40.24	2.74
2656	5766	9.587772	ACATAGTGTATTTGTAAGCTACAGAAG	57.412	33.333	0.00	0.00	40.24	2.85
2660	5770	8.754080	AGTGTATTTGTAAGCTACAGAAGAGAT	58.246	33.333	0.00	0.00	40.24	2.75
2675	5785	6.705381	ACAGAAGAGATTCAACTTGAACTCTG	59.295	38.462	23.22	20.32	40.50	3.35
2676	5786	6.927936	CAGAAGAGATTCAACTTGAACTCTGA	59.072	38.462	23.22	1.02	40.50	3.27
2686	5796	8.594881	TCAACTTGAACTCTGATTCTTAGTTC	57.405	34.615	17.62	17.62	45.99	3.01
2693	5803	6.677781	ACTCTGATTCTTAGTTCTCTCTCG	57.322	41.667	0.00	0.00	0.00	4.04
2704	5814	3.690139	AGTTCTCTCTCGCTATTCGTTCA	59.310	43.478	0.00	0.00	39.67	3.18
2754	5864	6.928492	TGTTATTGAGTTTGGCCTTCAAATTC	59.072	34.615	3.32	3.38	45.79	2.17
2850	5960	6.527423	TCTACTACAAGGTTGTTTTCCGAAT	58.473	36.000	0.00	0.00	42.35	3.34
2851	5961	6.993902	TCTACTACAAGGTTGTTTTCCGAATT	59.006	34.615	0.00	0.00	42.35	2.17
2889	6014	2.240500	GCCGTCGATCTGCCATGAC	61.241	63.158	0.00	0.00	0.00	3.06
2899	6024	2.272146	GCCATGACCCGGACACAT	59.728	61.111	0.73	2.22	0.00	3.21
2916	6041	5.004922	ACACATGTTTCCACGAAAATTGT	57.995	34.783	0.00	0.00	33.14	2.71
2920	6045	5.293079	ACATGTTTCCACGAAAATTGTTTGG	59.707	36.000	0.00	0.00	33.14	3.28
2921	6046	5.073311	TGTTTCCACGAAAATTGTTTGGA	57.927	34.783	0.00	0.00	33.14	3.53
2951	6076	6.659242	GGATGGAAATTCTGAACTACCTGAAA	59.341	38.462	0.00	0.00	0.00	2.69
2954	6079	6.831353	TGGAAATTCTGAACTACCTGAAAACA	59.169	34.615	0.00	0.00	0.00	2.83
2992	6117	9.667989	GTGTTTATTTTGTACAAATACTTCCGT	57.332	29.630	21.17	4.20	32.00	4.69
3032	6157	5.287992	GTCTTTCTACCTGTGCGTATGTTAC	59.712	44.000	0.00	0.00	0.00	2.50
3069	6194	4.602340	ACATACTCTGTTCCACGAGTTT	57.398	40.909	0.00	0.00	40.67	2.66
3079	6204	1.009675	CACGAGTTTGCCACACTGC	60.010	57.895	0.00	0.00	0.00	4.40
3097	6222	4.392445	CACTGCTCATCTTCTTCTTCCTTG	59.608	45.833	0.00	0.00	0.00	3.61
3112	6237	2.626785	TCCTTGGTCCATGTCCTGTTA	58.373	47.619	0.00	0.00	0.00	2.41
3138	6263	5.443431	GCTCTTATGTTCGAGTTCTGTTTCG	60.443	44.000	0.00	0.00	38.13	3.46
3159	6284	5.997385	TCGTCCTCTTCTTTTTACATTTGC	58.003	37.500	0.00	0.00	0.00	3.68
3179	6304	1.957877	CTTCCCTCTACGTCATCTCCC	59.042	57.143	0.00	0.00	0.00	4.30
3180	6305	0.185416	TCCCTCTACGTCATCTCCCC	59.815	60.000	0.00	0.00	0.00	4.81

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	198	1.594833	CGATCGACAAGGGGTTCCA	59.405	57.895	10.26	0.00	34.83	3.53
349	480	0.528466	TTCATCGTGCTCATCTCGGC	60.528	55.000	0.00	0.00	32.98	5.54
368	499	1.220206	CAGCCGATGAAGACCAGCT	59.780	57.895	0.00	0.00	0.00	4.24
1759	3861	1.227943	CCATCCCGAACGGCATCAT	60.228	57.895	7.80	0.00	0.00	2.45
2070	4383	1.906105	TATCAACCCGCAGTCACCCC	61.906	60.000	0.00	0.00	0.00	4.95
2234	4549	5.476599	CCAGTGTGATGATTTAGTCCCAAAA	59.523	40.000	0.00	0.00	0.00	2.44
2322	4639	3.065655	GTCAGCCAGCAAGATAGCATAG	58.934	50.000	0.00	0.00	36.85	2.23
2364	4690	0.904649	TGGCCAGTCATACCACTCTG	59.095	55.000	0.00	0.00	0.00	3.35
2372	4698	2.571653	GCTACCCATATGGCCAGTCATA	59.428	50.000	16.97	0.00	37.83	2.15
2653	5763	7.903995	ATCAGAGTTCAAGTTGAATCTCTTC	57.096	36.000	28.89	19.13	39.97	2.87
2656	5766	7.903995	AGAATCAGAGTTCAAGTTGAATCTC	57.096	36.000	25.14	25.14	38.79	2.75
2660	5770	8.964476	AACTAAGAATCAGAGTTCAAGTTGAA	57.036	30.769	14.35	14.35	36.29	2.69
2675	5785	6.795114	CGAATAGCGAGAGAGAACTAAGAATC	59.205	42.308	0.00	0.00	44.57	2.52
2676	5786	6.261381	ACGAATAGCGAGAGAGAACTAAGAAT	59.739	38.462	0.00	0.00	44.57	2.40
2686	5796	4.800993	ACAAATGAACGAATAGCGAGAGAG	59.199	41.667	0.00	0.00	44.57	3.20
2693	5803	5.106317	TGGAAGGAACAAATGAACGAATAGC	60.106	40.000	0.00	0.00	0.00	2.97
2704	5814	7.601705	TTTGAGAGAAATGGAAGGAACAAAT	57.398	32.000	0.00	0.00	0.00	2.32
2885	6010	1.613255	GGAAACATGTGTCCGGGTCAT	60.613	52.381	19.43	1.03	0.00	3.06
2889	6014	1.573829	CGTGGAAACATGTGTCCGGG	61.574	60.000	26.65	18.11	46.14	5.73
2899	6024	5.073311	TCCAAACAATTTTCGTGGAAACA	57.927	34.783	0.00	0.00	35.45	2.83
2916	6041	7.313740	TCAGAATTTCCATCCATTTTCCAAA	57.686	32.000	0.00	0.00	0.00	3.28
2920	6045	7.976175	GGTAGTTCAGAATTTCCATCCATTTTC	59.024	37.037	0.00	0.00	0.00	2.29
2921	6046	7.675619	AGGTAGTTCAGAATTTCCATCCATTTT	59.324	33.333	4.44	0.00	0.00	1.82
2992	6117	5.021458	AGAAAGACGTATAAGAAGGGTCCA	58.979	41.667	0.00	0.00	0.00	4.02
3032	6157	1.834188	ATGTAACAGAAAAGGGGGCG	58.166	50.000	0.00	0.00	0.00	6.13
3034	6159	5.186198	CAGAGTATGTAACAGAAAAGGGGG	58.814	45.833	0.00	0.00	0.00	5.40
3069	6194	0.689055	AGAAGATGAGCAGTGTGGCA	59.311	50.000	0.00	0.00	35.83	4.92
3079	6204	4.019860	TGGACCAAGGAAGAAGAAGATGAG	60.020	45.833	0.00	0.00	0.00	2.90
3097	6222	2.171448	AGAGCATAACAGGACATGGACC	59.829	50.000	0.00	0.00	0.00	4.46
3112	6237	5.078411	ACAGAACTCGAACATAAGAGCAT	57.922	39.130	0.00	0.00	37.99	3.79
3138	6263	6.863645	GGAAGCAAATGTAAAAAGAAGAGGAC	59.136	38.462	0.00	0.00	0.00	3.85
3159	6284	1.957877	GGGAGATGACGTAGAGGGAAG	59.042	57.143	0.00	0.00	0.00	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.