AutoCloner

Multiple sequence alignment - TraesCS6A01G065000

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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	TraesCS6A01G065000	chr6A	100.000	2705	0	0	1	2705	34393550	34390846	0.000000e+00	4996.0
1	TraesCS6A01G065000	chr6A	97.910	2680	33	5	29	2705	34280935	34278276	0.000000e+00	4617.0
2	TraesCS6A01G065000	chr6A	93.895	2113	89	11	571	2679	34275564	34273488	0.000000e+00	3151.0
3	TraesCS6A01G065000	chr6A	88.916	2039	151	26	116	2134	34282832	34280849	0.000000e+00	2444.0
4	TraesCS6A01G065000	chr6A	90.960	354	23	6	117	463	34275934	34275583	4.080000e-128	468.0
5	TraesCS6A01G065000	chr6A	94.382	89	5	0	29	117	34282954	34282866	1.310000e-28	137.0
6	TraesCS6A01G065000	chr6A	93.103	87	6	0	29	115	34276057	34275971	7.860000e-26	128.0
7	TraesCS6A01G065000	chrUn	96.601	2148	46	8	576	2705	101989846	101987708	0.000000e+00	3537.0
8	TraesCS6A01G065000	chrUn	85.817	1114	132	19	724	1830	101984262	101983168	0.000000e+00	1158.0
9	TraesCS6A01G065000	chrUn	90.284	422	24	10	117	534	101990509	101990101	1.100000e-148	536.0
10	TraesCS6A01G065000	chrUn	100.000	143	0	0	2563	2705	476643204	476643062	5.740000e-67	265.0
11	TraesCS6A01G065000	chrUn	95.238	84	3	1	2623	2705	101984429	101984346	6.080000e-27	132.0
12	TraesCS6A01G065000	chrUn	82.178	101	16	2	479	578	41698809	41698908	4.800000e-13	86.1
13	TraesCS6A01G065000	chr6B	93.051	1842	111	3	479	2311	62691231	62689398	0.000000e+00	2676.0
14	TraesCS6A01G065000	chr6B	89.226	1318	121	10	479	1792	62634416	62633116	0.000000e+00	1628.0
15	TraesCS6A01G065000	chr6B	92.271	414	23	5	2296	2705	62689453	62689045	1.810000e-161	579.0
16	TraesCS6A01G065000	chr6B	90.184	163	13	2	117	276	62691505	62691343	2.730000e-50	209.0
17	TraesCS6A01G065000	chr6B	89.634	164	12	4	117	276	62634698	62634536	1.270000e-48	204.0
18	TraesCS6A01G065000	chr6B	96.296	81	3	0	2604	2684	62630860	62630780	1.690000e-27	134.0
19	TraesCS6A01G065000	chr6B	93.258	89	6	0	29	117	62634821	62634733	6.080000e-27	132.0
20	TraesCS6A01G065000	chr6B	95.062	81	4	0	2604	2684	62676575	62676495	7.860000e-26	128.0
21	TraesCS6A01G065000	chr6B	92.135	89	7	0	29	117	62691628	62691540	2.830000e-25	126.0
22	TraesCS6A01G065000	chr6B	100.000	29	0	0	435	463	62634447	62634419	1.000000e-03	54.7
23	TraesCS6A01G065000	chr3D	83.407	1579	211	35	682	2241	583289991	583288445	0.000000e+00	1417.0
24	TraesCS6A01G065000	chr3D	85.094	1335	138	36	835	2147	583169951	583168656	0.000000e+00	1306.0
25	TraesCS6A01G065000	chr3D	81.531	1489	204	43	401	1858	583223323	583221875	0.000000e+00	1160.0
26	TraesCS6A01G065000	chr3D	81.684	1485	188	45	401	1858	583185845	583184418	0.000000e+00	1158.0
27	TraesCS6A01G065000	chr3D	80.973	226	34	7	402	622	583179625	583179404	1.290000e-38	171.0
28	TraesCS6A01G065000	chr3D	79.147	211	32	8	401	606	583179854	583179651	4.700000e-28	135.0
29	TraesCS6A01G065000	chr3D	88.764	89	8	1	29	115	583276890	583276802	1.020000e-19	108.0
30	TraesCS6A01G065000	chr3D	84.158	101	14	2	479	578	583027243	583027144	2.220000e-16	97.1
31	TraesCS6A01G065000	chr3D	86.517	89	10	1	29	115	583168757	583168669	2.220000e-16	97.1
32	TraesCS6A01G065000	chr3D	85.714	91	11	2	29	117	583288641	583288551	7.970000e-16	95.3
33	TraesCS6A01G065000	chr3B	83.407	1579	189	42	682	2241	780355613	780354089	0.000000e+00	1397.0
34	TraesCS6A01G065000	chr3B	87.435	1146	117	18	835	1962	780301925	780300789	0.000000e+00	1293.0
35	TraesCS6A01G065000	chr3B	86.061	1155	115	13	835	1968	780316019	780314890	0.000000e+00	1199.0
36	TraesCS6A01G065000	chr3B	86.061	1155	115	13	835	1968	780321393	780320264	0.000000e+00	1199.0
37	TraesCS6A01G065000	chr3B	86.061	1155	115	13	835	1968	780325998	780324869	0.000000e+00	1199.0
38	TraesCS6A01G065000	chr3B	82.048	1426	194	37	401	1792	780339378	780337981	0.000000e+00	1158.0
39	TraesCS6A01G065000	chr3B	85.393	1157	120	15	836	1968	780329734	780328603	0.000000e+00	1155.0
40	TraesCS6A01G065000	chr3B	81.170	1402	176	47	483	1858	780300249	780298910	0.000000e+00	1046.0
41	TraesCS6A01G065000	chr3B	83.488	430	43	9	1540	1968	780340174	780339772	2.540000e-100	375.0
42	TraesCS6A01G065000	chr3B	82.110	218	19	8	2508	2705	780339415	780339198	4.630000e-38	169.0
43	TraesCS6A01G065000	chr3B	85.714	91	11	1	29	117	780354285	780354195	7.970000e-16	95.3
44	TraesCS6A01G065000	chr3B	86.420	81	11	0	133	213	780339584	780339504	3.710000e-14	89.8
45	TraesCS6A01G065000	chr3B	83.750	80	13	0	134	213	780314690	780314611	2.890000e-10	76.8
46	TraesCS6A01G065000	chr3B	83.750	80	13	0	134	213	780320064	780319985	2.890000e-10	76.8
47	TraesCS6A01G065000	chr7D	81.548	672	92	18	1201	1857	264082493	264083147	2.390000e-145	525.0
48	TraesCS6A01G065000	chr7B	81.773	406	53	12	1457	1857	244426563	244426952	1.210000e-83	320.0
49	TraesCS6A01G065000	chr7B	84.444	90	11	3	2465	2553	244635265	244635352	4.800000e-13	86.1

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	TraesCS6A01G065000	chr6A	34390846	34393550	2704	True	4996.000000	4996	100.000000	1	2705	1	chr6A.!!$R1	2704
1	TraesCS6A01G065000	chr6A	34273488	34282954	9466	True	1824.166667	4617	93.194333	29	2705	6	chr6A.!!$R2	2676
2	TraesCS6A01G065000	chrUn	101983168	101990509	7341	True	1340.750000	3537	91.985000	117	2705	4	chrUn.!!$R2	2588
3	TraesCS6A01G065000	chr6B	62689045	62691628	2583	True	897.500000	2676	91.910250	29	2705	4	chr6B.!!$R3	2676
4	TraesCS6A01G065000	chr6B	62630780	62634821	4041	True	430.540000	1628	93.682800	29	2684	5	chr6B.!!$R2	2655
5	TraesCS6A01G065000	chr3D	583221875	583223323	1448	True	1160.000000	1160	81.531000	401	1858	1	chr3D.!!$R3	1457
6	TraesCS6A01G065000	chr3D	583184418	583185845	1427	True	1158.000000	1158	81.684000	401	1858	1	chr3D.!!$R2	1457
7	TraesCS6A01G065000	chr3D	583288445	583289991	1546	True	756.150000	1417	84.560500	29	2241	2	chr3D.!!$R7	2212
8	TraesCS6A01G065000	chr3D	583168656	583169951	1295	True	701.550000	1306	85.805500	29	2147	2	chr3D.!!$R5	2118
9	TraesCS6A01G065000	chr3B	780298910	780301925	3015	True	1169.500000	1293	84.302500	483	1962	2	chr3B.!!$R1	1479
10	TraesCS6A01G065000	chr3B	780314611	780329734	15123	True	817.600000	1199	85.179333	134	1968	6	chr3B.!!$R2	1834
11	TraesCS6A01G065000	chr3B	780354089	780355613	1524	True	746.150000	1397	84.560500	29	2241	2	chr3B.!!$R4	2212
12	TraesCS6A01G065000	chr3B	780337981	780340174	2193	True	447.950000	1158	83.516500	133	2705	4	chr3B.!!$R3	2572
13	TraesCS6A01G065000	chr7D	264082493	264083147	654	False	525.000000	525	81.548000	1201	1857	1	chr7D.!!$F1	656

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
25	26	2.158623	TGAAGATGTGCTTGTGTTCCCT	60.159	45.455	0.00	0.0	36.83	4.20	F
1351	12361	1.143684	GGAAAGGGGATGATGCAGCTA	59.856	52.381	2.53	0.0	0.00	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1470	12480	1.039856	GCAGAGGGACAGAGATCTCC	58.960	60.000	19.3	4.58	0.0	3.71	R
2588	21646	2.501723	AGATCCATGTTAGCGGTTCAGT	59.498	45.455	0.0	0.00	0.0	3.41	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
22	23	4.558538	ACTTGAAGATGTGCTTGTGTTC	57.441	40.909	0.00	0.00	36.83	3.18
23	24	3.316308	ACTTGAAGATGTGCTTGTGTTCC	59.684	43.478	0.00	0.00	36.83	3.62
24	25	2.229792	TGAAGATGTGCTTGTGTTCCC	58.770	47.619	0.00	0.00	36.83	3.97
25	26	2.158623	TGAAGATGTGCTTGTGTTCCCT	60.159	45.455	0.00	0.00	36.83	4.20
27	28	2.233271	AGATGTGCTTGTGTTCCCTTG	58.767	47.619	0.00	0.00	0.00	3.61
65	66	8.836413	GCAGTCTGGCACTACAATTAATTATAA	58.164	33.333	0.00	0.00	32.21	0.98
97	98	8.699749	GTTTCATACAACAAAGTCCAAATTAGC	58.300	33.333	0.00	0.00	0.00	3.09
98	99	7.517614	TCATACAACAAAGTCCAAATTAGCA	57.482	32.000	0.00	0.00	0.00	3.49
386	2526	3.438781	ACACAACAAAAGCTCGTTTCTCA	59.561	39.130	0.00	0.00	0.00	3.27
463	2647	3.196901	ACGCTGAACCACTAACATGGATA	59.803	43.478	0.00	0.00	43.02	2.59
464	2648	4.188462	CGCTGAACCACTAACATGGATAA	58.812	43.478	0.00	0.00	43.02	1.75
465	2649	4.816385	CGCTGAACCACTAACATGGATAAT	59.184	41.667	0.00	0.00	43.02	1.28
466	2650	5.989168	CGCTGAACCACTAACATGGATAATA	59.011	40.000	0.00	0.00	43.02	0.98
467	2651	6.481976	CGCTGAACCACTAACATGGATAATAA	59.518	38.462	0.00	0.00	43.02	1.40
468	2652	7.307396	CGCTGAACCACTAACATGGATAATAAG	60.307	40.741	0.00	0.00	43.02	1.73
469	2653	7.041098	GCTGAACCACTAACATGGATAATAAGG	60.041	40.741	0.00	0.00	43.02	2.69
470	2654	7.867921	TGAACCACTAACATGGATAATAAGGT	58.132	34.615	0.00	0.00	43.02	3.50
471	2655	7.773224	TGAACCACTAACATGGATAATAAGGTG	59.227	37.037	0.00	0.00	43.02	4.00
472	2656	7.446106	ACCACTAACATGGATAATAAGGTGA	57.554	36.000	0.00	0.00	43.02	4.02
473	2657	8.045720	ACCACTAACATGGATAATAAGGTGAT	57.954	34.615	0.00	0.00	43.02	3.06
474	2658	9.166222	ACCACTAACATGGATAATAAGGTGATA	57.834	33.333	0.00	0.00	43.02	2.15
522	2707	3.245754	CAGCTCTGATCATCGAAGCTTTC	59.754	47.826	15.42	0.00	0.00	2.62
582	2980	6.906157	CCTGATTAAATACAGGCATTCCAT	57.094	37.500	11.74	0.00	45.30	3.41
1142	7316	1.323271	TGCGATGGTCTCAGGAGTCC	61.323	60.000	0.00	0.00	37.19	3.85
1289	12299	3.372954	GCATCATGCAAGAGATCTTTGC	58.627	45.455	24.03	24.03	44.26	3.68
1291	12301	3.076079	TCATGCAAGAGATCTTTGCCA	57.924	42.857	26.00	18.89	33.11	4.92
1351	12361	1.143684	GGAAAGGGGATGATGCAGCTA	59.856	52.381	2.53	0.00	0.00	3.32
1368	12378	2.559440	GCTACTCAAGCCAAGATCCAG	58.441	52.381	0.00	0.00	46.25	3.86
1415	12425	5.184671	AGGCCAAGAATCATTTCAAGAAGAC	59.815	40.000	5.01	0.00	34.08	3.01
1417	12427	5.634896	CCAAGAATCATTTCAAGAAGACCG	58.365	41.667	0.00	0.00	34.08	4.79
1429	12439	1.614413	AGAAGACCGCGAAGAAGACTT	59.386	47.619	8.23	1.66	39.24	3.01
1479	12489	0.693767	CCAAGGCCAGGGAGATCTCT	60.694	60.000	21.81	0.23	0.00	3.10
1481	12491	0.043940	AAGGCCAGGGAGATCTCTGT	59.956	55.000	21.81	7.09	0.00	3.41
1483	12493	1.406860	GGCCAGGGAGATCTCTGTCC	61.407	65.000	21.81	14.57	34.00	4.02
1501	12511	1.294780	CCTCTGCTGGAGTCCACAC	59.705	63.158	8.12	3.97	40.30	3.82
1602	12615	2.555325	CTGCAAGGAAGAGCAATTGTCA	59.445	45.455	7.40	0.00	40.73	3.58
1744	15344	1.330655	ACGACCTCCGATTGGCATCT	61.331	55.000	0.00	0.00	41.76	2.90
1777	18167	8.618702	AAGGAATAGCTGATCTTCATACAATG	57.381	34.615	0.00	0.00	0.00	2.82
2235	21246	9.203421	CATGCTCTACGTATTAACAATAATCCA	57.797	33.333	0.00	0.00	33.75	3.41
2242	21253	7.703328	ACGTATTAACAATAATCCAAGCAAGG	58.297	34.615	0.00	0.00	33.75	3.61
2259	21270	3.084039	CAAGGCCTGATCTAAACTTGCA	58.916	45.455	5.69	0.00	0.00	4.08
2377	21428	7.483307	ACAATCGATGCTTTACATGCTTATTT	58.517	30.769	0.00	0.00	39.84	1.40
2378	21429	7.975616	ACAATCGATGCTTTACATGCTTATTTT	59.024	29.630	0.00	0.00	39.84	1.82
2596	21654	9.681062	AAATAATGGGGATAATATACTGAACCG	57.319	33.333	0.00	0.00	0.00	4.44
2691	25322	0.324738	TGCCCACCAAGGAAAACACA	60.325	50.000	0.00	0.00	41.22	3.72

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	2.508526	AGGGAACACAAGCACATCTTC	58.491	47.619	0.00	0.00	31.27	2.87
7	8	2.233271	CAAGGGAACACAAGCACATCT	58.767	47.619	0.00	0.00	0.00	2.90
9	10	0.675633	GCAAGGGAACACAAGCACAT	59.324	50.000	0.00	0.00	0.00	3.21
10	11	0.682532	TGCAAGGGAACACAAGCACA	60.683	50.000	0.00	0.00	0.00	4.57
11	12	0.249031	GTGCAAGGGAACACAAGCAC	60.249	55.000	0.00	0.00	44.31	4.40
17	18	1.181098	AGCCATGTGCAAGGGAACAC	61.181	55.000	8.58	0.00	44.83	3.32
19	20	1.181098	ACAGCCATGTGCAAGGGAAC	61.181	55.000	8.58	0.00	44.83	3.62
20	21	1.153524	ACAGCCATGTGCAAGGGAA	59.846	52.632	8.58	0.00	44.83	3.97
21	22	2.845784	ACAGCCATGTGCAAGGGA	59.154	55.556	8.58	0.00	44.83	4.20
65	66	6.549364	TGGACTTTGTTGTATGAAACCAGAAT	59.451	34.615	0.00	0.00	0.00	2.40
138	174	9.860898	GGTCTTGCTCAGATTATTGTTAATTTT	57.139	29.630	0.00	0.00	32.60	1.82
139	175	9.247861	AGGTCTTGCTCAGATTATTGTTAATTT	57.752	29.630	0.00	0.00	32.60	1.82
386	2526	5.079643	GCCACCCACCATTTCATATCTAAT	58.920	41.667	0.00	0.00	0.00	1.73
522	2707	1.238439	ACCCTTGCGAATCACAAGTG	58.762	50.000	9.76	1.54	42.41	3.16
542	2727	2.107366	CAGGTGTTTTCTTTGGTGGGT	58.893	47.619	0.00	0.00	0.00	4.51
623	3023	3.457234	GCATAATTGCTTACCAAAGGCC	58.543	45.455	0.00	0.00	45.77	5.19
765	6909	6.767902	GCATAGACATTGGAATCCTAAAGTCA	59.232	38.462	16.78	7.71	0.00	3.41
1142	7316	3.525537	AGACCATCGTAGATGTTTGCAG	58.474	45.455	8.91	0.00	45.12	4.41
1351	12361	2.264455	AGACTGGATCTTGGCTTGAGT	58.736	47.619	0.00	0.00	31.62	3.41
1368	12378	3.574780	GCCAAGCGGGTGTAAGAC	58.425	61.111	0.00	0.00	39.65	3.01
1429	12439	3.106827	TGACCATCCTGCAATCTACAGA	58.893	45.455	0.00	0.00	37.32	3.41
1433	12443	2.440627	AGCATGACCATCCTGCAATCTA	59.559	45.455	0.00	0.00	39.92	1.98
1470	12480	1.039856	GCAGAGGGACAGAGATCTCC	58.960	60.000	19.30	4.58	0.00	3.71
1501	12511	2.154854	TGCTTTGACAAGAGACGGAG	57.845	50.000	0.00	0.00	30.57	4.63
1505	12515	7.561556	CATTTCAATTTGCTTTGACAAGAGAC	58.438	34.615	0.00	0.00	35.42	3.36
1602	12615	5.672503	TCTACGATACTGCACTCTAACTCT	58.327	41.667	0.00	0.00	0.00	3.24
1744	15344	6.006275	AGATCAGCTATTCCTTAAAAGGCA	57.994	37.500	3.73	0.00	46.06	4.75
2027	21025	3.248024	TGTGGTAGTGGTGGAGAATCTT	58.752	45.455	0.00	0.00	33.73	2.40
2058	21067	7.986085	ATATATTCAATTGTAGTGCCAGACC	57.014	36.000	5.13	0.00	0.00	3.85
2235	21246	3.728385	AGTTTAGATCAGGCCTTGCTT	57.272	42.857	0.00	0.00	0.00	3.91
2242	21253	3.671702	GCACTTGCAAGTTTAGATCAGGC	60.672	47.826	29.23	20.82	41.59	4.85
2399	21453	4.000331	CTGATACTCCGGAATCAGCATT	58.000	45.455	25.80	0.00	41.80	3.56
2573	21631	6.442564	AGCGGTTCAGTATATTATCCCCATTA	59.557	38.462	0.00	0.00	0.00	1.90
2588	21646	2.501723	AGATCCATGTTAGCGGTTCAGT	59.498	45.455	0.00	0.00	0.00	3.41
2596	21654	3.808728	TGGTAGCAAGATCCATGTTAGC	58.191	45.455	12.35	12.35	34.05	3.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.