AutoCloner

Multiple sequence alignment - TraesCS3A01G468400

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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	TraesCS3A01G468400	chr3A	100.000	3085	0	0	1	3085	701220331	701217247	0.000000e+00	5698.0
1	TraesCS3A01G468400	chr3A	82.560	711	121	3	1362	2072	735981617	735980910	9.390000e-175	623.0
2	TraesCS3A01G468400	chr3A	82.410	722	117	7	1358	2074	735976095	735975379	3.380000e-174	621.0
3	TraesCS3A01G468400	chr3A	79.674	674	130	6	1359	2030	735846386	735847054	2.150000e-131	479.0
4	TraesCS3A01G468400	chr3B	89.824	1592	115	26	658	2239	755805359	755806913	0.000000e+00	1999.0
5	TraesCS3A01G468400	chr3B	90.598	585	49	3	2494	3073	759351918	759352501	0.000000e+00	771.0
6	TraesCS3A01G468400	chr3B	80.952	714	127	6	1362	2072	812726760	812726053	9.660000e-155	556.0
7	TraesCS3A01G468400	chr3B	90.446	157	10	5	223	374	136809656	136809500	5.220000e-48	202.0
8	TraesCS3A01G468400	chr3D	91.707	1435	79	18	889	2301	566080501	566081917	0.000000e+00	1954.0
9	TraesCS3A01G468400	chr3D	82.684	693	113	6	1358	2048	604968076	604967389	2.630000e-170	608.0
10	TraesCS3A01G468400	chr3D	80.839	715	134	2	1358	2072	605026832	605026121	2.690000e-155	558.0
11	TraesCS3A01G468400	chr3D	90.338	207	14	2	656	856	566080300	566080506	1.820000e-67	267.0
12	TraesCS3A01G468400	chr3D	84.135	208	22	6	393	597	566078555	566078754	1.130000e-44	191.0
13	TraesCS3A01G468400	chr1B	90.769	585	44	5	2495	3073	93856339	93855759	0.000000e+00	773.0
14	TraesCS3A01G468400	chr1B	79.454	696	126	13	1361	2049	14138310	14138995	7.740000e-131	477.0
15	TraesCS3A01G468400	chr7A	90.582	584	49	3	2494	3073	389344720	389345301	0.000000e+00	769.0
16	TraesCS3A01G468400	chr5D	90.427	585	51	2	2493	3073	70888222	70887639	0.000000e+00	765.0
17	TraesCS3A01G468400	chr4D	90.582	584	41	2	2494	3073	419212414	419211841	0.000000e+00	761.0
18	TraesCS3A01G468400	chr4D	79.580	715	135	9	1362	2072	485043041	485042334	4.590000e-138	501.0
19	TraesCS3A01G468400	chr4D	94.030	67	4	0	1199	1265	485043333	485043267	5.440000e-18	102.0
20	TraesCS3A01G468400	chr4D	94.030	67	4	0	1199	1265	485065276	485065210	5.440000e-18	102.0
21	TraesCS3A01G468400	chr4D	93.939	66	4	0	1199	1264	484934220	484934155	1.960000e-17	100.0
22	TraesCS3A01G468400	chr4D	93.939	66	4	0	1199	1264	484952140	484952075	1.960000e-17	100.0
23	TraesCS3A01G468400	chr1A	90.240	584	52	2	2494	3073	504658852	504659434	0.000000e+00	758.0
24	TraesCS3A01G468400	chr1A	78.970	699	124	16	1361	2049	11555172	11555857	3.630000e-124	455.0
25	TraesCS3A01G468400	chr4B	90.306	588	39	4	2490	3073	517125188	517124615	0.000000e+00	754.0
26	TraesCS3A01G468400	chr4B	92.308	78	6	0	225	302	416118576	416118499	9.040000e-21	111.0
27	TraesCS3A01G468400	chr4B	95.455	66	3	0	1199	1264	618241345	618241280	4.210000e-19	106.0
28	TraesCS3A01G468400	chr2A	90.020	501	43	4	2578	3073	534598340	534598838	2.590000e-180	641.0
29	TraesCS3A01G468400	chr2B	87.879	462	51	2	2616	3073	792203183	792203643	3.500000e-149	538.0
30	TraesCS3A01G468400	chr2B	75.115	655	123	30	1395	2029	443147939	443147305	1.410000e-68	270.0
31	TraesCS3A01G468400	chr2B	75.115	655	123	30	1395	2029	443224081	443224715	1.410000e-68	270.0
32	TraesCS3A01G468400	chr1D	78.174	701	126	18	1361	2049	9745190	9745875	3.680000e-114	422.0
33	TraesCS3A01G468400	chr1D	78.512	121	23	2	222	339	458129041	458129161	3.300000e-10	76.8
34	TraesCS3A01G468400	chr4A	82.938	422	61	9	2666	3084	645587805	645587392	1.350000e-98	370.0
35	TraesCS3A01G468400	chr7D	86.709	158	18	3	2489	2645	159698496	159698341	4.090000e-39	172.0
36	TraesCS3A01G468400	chr6D	84.615	169	20	4	2477	2641	225838465	225838299	2.460000e-36	163.0

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	TraesCS3A01G468400	chr3A	701217247	701220331	3084	True	5698.0	5698	100.000000	1	3085	1	chr3A.!!$R1	3084
1	TraesCS3A01G468400	chr3A	735980910	735981617	707	True	623.0	623	82.560000	1362	2072	1	chr3A.!!$R3	710
2	TraesCS3A01G468400	chr3A	735975379	735976095	716	True	621.0	621	82.410000	1358	2074	1	chr3A.!!$R2	716
3	TraesCS3A01G468400	chr3A	735846386	735847054	668	False	479.0	479	79.674000	1359	2030	1	chr3A.!!$F1	671
4	TraesCS3A01G468400	chr3B	755805359	755806913	1554	False	1999.0	1999	89.824000	658	2239	1	chr3B.!!$F1	1581
5	TraesCS3A01G468400	chr3B	759351918	759352501	583	False	771.0	771	90.598000	2494	3073	1	chr3B.!!$F2	579
6	TraesCS3A01G468400	chr3B	812726053	812726760	707	True	556.0	556	80.952000	1362	2072	1	chr3B.!!$R2	710
7	TraesCS3A01G468400	chr3D	566078555	566081917	3362	False	804.0	1954	88.726667	393	2301	3	chr3D.!!$F1	1908
8	TraesCS3A01G468400	chr3D	604967389	604968076	687	True	608.0	608	82.684000	1358	2048	1	chr3D.!!$R1	690
9	TraesCS3A01G468400	chr3D	605026121	605026832	711	True	558.0	558	80.839000	1358	2072	1	chr3D.!!$R2	714
10	TraesCS3A01G468400	chr1B	93855759	93856339	580	True	773.0	773	90.769000	2495	3073	1	chr1B.!!$R1	578
11	TraesCS3A01G468400	chr1B	14138310	14138995	685	False	477.0	477	79.454000	1361	2049	1	chr1B.!!$F1	688
12	TraesCS3A01G468400	chr7A	389344720	389345301	581	False	769.0	769	90.582000	2494	3073	1	chr7A.!!$F1	579
13	TraesCS3A01G468400	chr5D	70887639	70888222	583	True	765.0	765	90.427000	2493	3073	1	chr5D.!!$R1	580
14	TraesCS3A01G468400	chr4D	419211841	419212414	573	True	761.0	761	90.582000	2494	3073	1	chr4D.!!$R1	579
15	TraesCS3A01G468400	chr4D	485042334	485043333	999	True	301.5	501	86.805000	1199	2072	2	chr4D.!!$R5	873
16	TraesCS3A01G468400	chr1A	504658852	504659434	582	False	758.0	758	90.240000	2494	3073	1	chr1A.!!$F2	579
17	TraesCS3A01G468400	chr1A	11555172	11555857	685	False	455.0	455	78.970000	1361	2049	1	chr1A.!!$F1	688
18	TraesCS3A01G468400	chr4B	517124615	517125188	573	True	754.0	754	90.306000	2490	3073	1	chr4B.!!$R2	583
19	TraesCS3A01G468400	chr2B	443147305	443147939	634	True	270.0	270	75.115000	1395	2029	1	chr2B.!!$R1	634
20	TraesCS3A01G468400	chr2B	443224081	443224715	634	False	270.0	270	75.115000	1395	2029	1	chr2B.!!$F1	634
21	TraesCS3A01G468400	chr1D	9745190	9745875	685	False	422.0	422	78.174000	1361	2049	1	chr1D.!!$F1	688

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
624	2064	0.031721	ACGTTCCAGACAGAACCGTC	59.968	55.0	0.0	0.0	42.63	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2458	4136	0.037419	GGCGGGCACATGTTTGAATT	60.037	50.0	0.0	0.0	0.0	2.17	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
67	68	9.860898	AAATGTTTTTCTGCTCAGATTAATACC	57.139	29.630	0.00	0.00	37.29	2.73
68	69	7.072177	TGTTTTTCTGCTCAGATTAATACCG	57.928	36.000	0.00	0.00	37.29	4.02
69	70	6.093495	TGTTTTTCTGCTCAGATTAATACCGG	59.907	38.462	0.00	0.00	37.29	5.28
70	71	5.607939	TTTCTGCTCAGATTAATACCGGA	57.392	39.130	9.46	0.00	37.29	5.14
71	72	4.585955	TCTGCTCAGATTAATACCGGAC	57.414	45.455	9.46	0.00	31.41	4.79
72	73	4.215908	TCTGCTCAGATTAATACCGGACT	58.784	43.478	9.46	0.00	31.41	3.85
73	74	4.649674	TCTGCTCAGATTAATACCGGACTT	59.350	41.667	9.46	3.07	31.41	3.01
74	75	5.128827	TCTGCTCAGATTAATACCGGACTTT	59.871	40.000	9.46	0.33	31.41	2.66
75	76	5.741011	TGCTCAGATTAATACCGGACTTTT	58.259	37.500	9.46	0.00	0.00	2.27
76	77	5.815740	TGCTCAGATTAATACCGGACTTTTC	59.184	40.000	9.46	2.24	0.00	2.29
77	78	6.049790	GCTCAGATTAATACCGGACTTTTCT	58.950	40.000	9.46	4.49	0.00	2.52
78	79	6.539103	GCTCAGATTAATACCGGACTTTTCTT	59.461	38.462	9.46	0.00	0.00	2.52
79	80	7.466050	GCTCAGATTAATACCGGACTTTTCTTG	60.466	40.741	9.46	0.00	0.00	3.02
80	81	7.391620	TCAGATTAATACCGGACTTTTCTTGT	58.608	34.615	9.46	0.00	0.00	3.16
81	82	7.881232	TCAGATTAATACCGGACTTTTCTTGTT	59.119	33.333	9.46	0.00	0.00	2.83
82	83	7.962918	CAGATTAATACCGGACTTTTCTTGTTG	59.037	37.037	9.46	0.00	0.00	3.33
83	84	7.664318	AGATTAATACCGGACTTTTCTTGTTGT	59.336	33.333	9.46	0.00	0.00	3.32
84	85	5.684550	AATACCGGACTTTTCTTGTTGTC	57.315	39.130	9.46	0.00	0.00	3.18
85	86	2.993937	ACCGGACTTTTCTTGTTGTCA	58.006	42.857	9.46	0.00	0.00	3.58
86	87	3.349022	ACCGGACTTTTCTTGTTGTCAA	58.651	40.909	9.46	0.00	0.00	3.18
87	88	3.951680	ACCGGACTTTTCTTGTTGTCAAT	59.048	39.130	9.46	0.00	32.82	2.57
88	89	4.401202	ACCGGACTTTTCTTGTTGTCAATT	59.599	37.500	9.46	0.00	32.82	2.32
89	90	5.105513	ACCGGACTTTTCTTGTTGTCAATTT	60.106	36.000	9.46	0.00	32.82	1.82
90	91	5.810074	CCGGACTTTTCTTGTTGTCAATTTT	59.190	36.000	0.00	0.00	32.82	1.82
91	92	6.312672	CCGGACTTTTCTTGTTGTCAATTTTT	59.687	34.615	0.00	0.00	32.82	1.94

Showing 1 to 25 of 330 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	9.860898	GGTATTAATCTGAGCAGAAAAACATTT	57.139	29.630	4.06	0.00	41.36	2.32
42	43	8.184192	CGGTATTAATCTGAGCAGAAAAACATT	58.816	33.333	4.06	0.00	41.36	2.71
43	44	7.201732	CCGGTATTAATCTGAGCAGAAAAACAT	60.202	37.037	4.06	0.00	41.36	2.71
44	45	6.093495	CCGGTATTAATCTGAGCAGAAAAACA	59.907	38.462	4.06	0.00	41.36	2.83
45	46	6.315393	TCCGGTATTAATCTGAGCAGAAAAAC	59.685	38.462	0.00	0.01	41.36	2.43
46	47	6.315393	GTCCGGTATTAATCTGAGCAGAAAAA	59.685	38.462	0.00	2.76	41.36	1.94
47	48	5.815740	GTCCGGTATTAATCTGAGCAGAAAA	59.184	40.000	0.00	3.10	41.36	2.29
48	49	5.128827	AGTCCGGTATTAATCTGAGCAGAAA	59.871	40.000	0.00	0.00	41.36	2.52
49	50	4.649674	AGTCCGGTATTAATCTGAGCAGAA	59.350	41.667	0.00	0.00	41.36	3.02
50	51	4.215908	AGTCCGGTATTAATCTGAGCAGA	58.784	43.478	0.00	2.23	42.37	4.26
51	52	4.592485	AGTCCGGTATTAATCTGAGCAG	57.408	45.455	0.00	0.00	0.00	4.24
52	53	5.353394	AAAGTCCGGTATTAATCTGAGCA	57.647	39.130	0.00	0.00	0.00	4.26
53	54	6.049790	AGAAAAGTCCGGTATTAATCTGAGC	58.950	40.000	0.00	0.00	0.00	4.26
54	55	7.549488	ACAAGAAAAGTCCGGTATTAATCTGAG	59.451	37.037	0.00	5.26	0.00	3.35
55	56	7.391620	ACAAGAAAAGTCCGGTATTAATCTGA	58.608	34.615	0.00	0.00	0.00	3.27
56	57	7.611213	ACAAGAAAAGTCCGGTATTAATCTG	57.389	36.000	0.00	0.00	0.00	2.90
57	58	7.664318	ACAACAAGAAAAGTCCGGTATTAATCT	59.336	33.333	0.00	2.96	0.00	2.40
58	59	7.813645	ACAACAAGAAAAGTCCGGTATTAATC	58.186	34.615	0.00	0.68	0.00	1.75
59	60	7.446013	TGACAACAAGAAAAGTCCGGTATTAAT	59.554	33.333	0.00	0.00	0.00	1.40
60	61	6.766944	TGACAACAAGAAAAGTCCGGTATTAA	59.233	34.615	0.00	0.00	0.00	1.40
61	62	6.289834	TGACAACAAGAAAAGTCCGGTATTA	58.710	36.000	0.00	0.00	0.00	0.98
62	63	5.127491	TGACAACAAGAAAAGTCCGGTATT	58.873	37.500	0.00	0.00	0.00	1.89
63	64	4.710324	TGACAACAAGAAAAGTCCGGTAT	58.290	39.130	0.00	0.00	0.00	2.73
64	65	4.139859	TGACAACAAGAAAAGTCCGGTA	57.860	40.909	0.00	0.00	0.00	4.02
65	66	2.993937	TGACAACAAGAAAAGTCCGGT	58.006	42.857	0.00	0.00	0.00	5.28

Showing 1 to 25 of 325 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.