AutoCloner

Multiple sequence alignment - TraesCS7D01G101400

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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	TraesCS7D01G101400	chr7D	100.000	3143	0	0	1	3143	60593872	60590730	0.000000e+00	5805.0
1	TraesCS7D01G101400	chr7D	90.877	559	22	10	2481	3016	29778101	29778653	0.000000e+00	723.0
2	TraesCS7D01G101400	chr7D	93.766	401	11	1	2630	3016	544988850	544989250	9.710000e-165	590.0
3	TraesCS7D01G101400	chr7D	97.736	265	6	0	2752	3016	623036333	623036069	1.030000e-124	457.0
4	TraesCS7D01G101400	chr7D	92.230	296	13	5	2490	2776	500234133	500233839	8.110000e-111	411.0
5	TraesCS7D01G101400	chr7D	86.316	190	20	5	2004	2193	29577229	29577412	5.320000e-48	202.0
6	TraesCS7D01G101400	chr7D	94.355	124	7	0	112	235	605154643	605154520	1.150000e-44	191.0
7	TraesCS7D01G101400	chr7D	90.769	130	12	0	106	235	263891122	263891251	1.160000e-39	174.0
8	TraesCS7D01G101400	chr7D	93.478	46	2	1	707	752	106022100	106022144	2.020000e-07	67.6
9	TraesCS7D01G101400	chr7A	89.748	1229	61	20	801	2000	64738579	64737387	0.000000e+00	1511.0
10	TraesCS7D01G101400	chr7A	87.778	90	10	1	2108	2197	227094276	227094364	1.540000e-18	104.0
11	TraesCS7D01G101400	chr2D	90.973	565	17	5	2486	3016	572790115	572790679	0.000000e+00	730.0
12	TraesCS7D01G101400	chr2D	98.400	125	2	0	3019	3143	30187348	30187472	1.470000e-53	220.0
13	TraesCS7D01G101400	chr2D	96.241	133	4	1	3011	3143	534953290	534953159	1.900000e-52	217.0
14	TraesCS7D01G101400	chr2D	95.161	124	6	0	111	234	613232023	613232146	2.470000e-46	196.0
15	TraesCS7D01G101400	chr1D	91.439	549	19	4	2490	3016	66767159	66766617	0.000000e+00	728.0
16	TraesCS7D01G101400	chr1D	97.600	125	3	0	3019	3143	66765698	66765574	6.830000e-52	215.0
17	TraesCS7D01G101400	chr5D	92.711	439	13	9	2597	3016	374629344	374628906	1.600000e-172	616.0
18	TraesCS7D01G101400	chr5D	96.981	265	8	0	2752	3016	332784517	332784253	2.220000e-121	446.0
19	TraesCS7D01G101400	chr5D	92.053	302	14	5	2484	2776	84379649	84379949	1.740000e-112	416.0
20	TraesCS7D01G101400	chr5D	92.230	296	13	4	2490	2776	385444075	385443781	8.110000e-111	411.0
21	TraesCS7D01G101400	chr5D	97.600	125	3	0	3019	3143	84381766	84381890	6.830000e-52	215.0
22	TraesCS7D01G101400	chr5D	97.600	125	3	0	3019	3143	423273398	423273274	6.830000e-52	215.0
23	TraesCS7D01G101400	chr5D	86.310	168	16	4	2026	2193	422005476	422005316	3.220000e-40	176.0
24	TraesCS7D01G101400	chr5D	86.792	159	11	4	2305	2461	441215854	441216004	5.390000e-38	169.0
25	TraesCS7D01G101400	chr7B	87.638	542	45	13	2490	3016	701282728	701283262	7.450000e-171	610.0
26	TraesCS7D01G101400	chr7B	86.555	238	8	10	1758	1992	2952391	2952175	1.130000e-59	241.0
27	TraesCS7D01G101400	chr7B	90.449	178	8	5	870	1043	2952566	2952394	3.150000e-55	226.0
28	TraesCS7D01G101400	chr7B	97.619	42	1	0	2250	2291	2952144	2952103	4.350000e-09	73.1
29	TraesCS7D01G101400	chrUn	85.923	547	51	15	2490	3016	82492069	82491529	7.610000e-156	560.0
30	TraesCS7D01G101400	chrUn	97.600	125	3	0	3019	3143	20485591	20485715	6.830000e-52	215.0
31	TraesCS7D01G101400	chrUn	86.528	193	19	5	2004	2196	22548436	22548251	4.110000e-49	206.0
32	TraesCS7D01G101400	chr5B	87.500	488	48	5	278	761	54587998	54587520	4.580000e-153	551.0
33	TraesCS7D01G101400	chr5B	91.209	273	16	3	2751	3016	21546712	21546983	6.410000e-97	364.0
34	TraesCS7D01G101400	chr5B	85.237	359	30	13	2677	3016	339093687	339094041	6.450000e-92	348.0
35	TraesCS7D01G101400	chr5B	94.595	111	6	0	125	235	54588979	54588869	4.170000e-39	172.0
36	TraesCS7D01G101400	chr2A	85.634	536	56	11	2491	3016	718483256	718482732	7.670000e-151	544.0
37	TraesCS7D01G101400	chr2A	92.857	266	18	1	2751	3016	685491332	685491068	4.920000e-103	385.0
38	TraesCS7D01G101400	chr1A	90.168	417	29	7	2608	3016	582751686	582752098	1.660000e-147	532.0
39	TraesCS7D01G101400	chr1A	91.566	83	7	0	110	192	567982550	567982632	7.120000e-22	115.0
40	TraesCS7D01G101400	chr3D	85.880	517	51	12	233	732	574293439	574292928	5.970000e-147	531.0
41	TraesCS7D01G101400	chr3D	92.282	298	11	5	2490	2776	80217783	80218079	2.260000e-111	412.0
42	TraesCS7D01G101400	chr3D	98.400	125	2	0	3019	3143	602048427	602048303	1.470000e-53	220.0
43	TraesCS7D01G101400	chr3D	97.600	125	3	0	3019	3143	80219877	80220001	6.830000e-52	215.0
44	TraesCS7D01G101400	chr3D	89.394	132	7	1	111	235	574294174	574294043	3.240000e-35	159.0
45	TraesCS7D01G101400	chr6A	91.729	266	15	2	2751	3016	560104886	560105144	2.300000e-96	363.0
46	TraesCS7D01G101400	chr3B	86.667	240	26	4	500	735	23403008	23403245	8.650000e-66	261.0
47	TraesCS7D01G101400	chr3B	88.718	195	13	3	278	472	23402825	23403010	2.440000e-56	230.0
48	TraesCS7D01G101400	chr3B	91.200	125	11	0	111	235	23401923	23402047	1.500000e-38	171.0
49	TraesCS7D01G101400	chr3A	98.400	125	2	0	3019	3143	461844478	461844354	1.470000e-53	220.0
50	TraesCS7D01G101400	chr3A	98.387	124	2	0	112	235	681061289	681061166	5.280000e-53	219.0
51	TraesCS7D01G101400	chr3A	96.078	102	4	0	663	764	681060122	681060021	1.940000e-37	167.0
52	TraesCS7D01G101400	chr6B	88.506	174	10	4	2305	2476	159953899	159953734	5.320000e-48	202.0
53	TraesCS7D01G101400	chr4A	85.204	196	22	3	2004	2199	490960063	490959875	8.890000e-46	195.0
54	TraesCS7D01G101400	chr1B	84.211	190	21	4	2005	2194	31973900	31974080	3.220000e-40	176.0
55	TraesCS7D01G101400	chr5A	93.243	74	5	0	125	198	634810432	634810505	3.310000e-20	110.0

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	TraesCS7D01G101400	chr7D	60590730	60593872	3142	True	5805.000000	5805	100.000000	1	3143	1	chr7D.!!$R1	3142
1	TraesCS7D01G101400	chr7D	29778101	29778653	552	False	723.000000	723	90.877000	2481	3016	1	chr7D.!!$F2	535
2	TraesCS7D01G101400	chr7A	64737387	64738579	1192	True	1511.000000	1511	89.748000	801	2000	1	chr7A.!!$R1	1199
3	TraesCS7D01G101400	chr2D	572790115	572790679	564	False	730.000000	730	90.973000	2486	3016	1	chr2D.!!$F2	530
4	TraesCS7D01G101400	chr1D	66765574	66767159	1585	True	471.500000	728	94.519500	2490	3143	2	chr1D.!!$R1	653
5	TraesCS7D01G101400	chr5D	84379649	84381890	2241	False	315.500000	416	94.826500	2484	3143	2	chr5D.!!$F2	659
6	TraesCS7D01G101400	chr7B	701282728	701283262	534	False	610.000000	610	87.638000	2490	3016	1	chr7B.!!$F1	526
7	TraesCS7D01G101400	chrUn	82491529	82492069	540	True	560.000000	560	85.923000	2490	3016	1	chrUn.!!$R2	526
8	TraesCS7D01G101400	chr5B	54587520	54588979	1459	True	361.500000	551	91.047500	125	761	2	chr5B.!!$R1	636
9	TraesCS7D01G101400	chr2A	718482732	718483256	524	True	544.000000	544	85.634000	2491	3016	1	chr2A.!!$R2	525
10	TraesCS7D01G101400	chr3D	574292928	574294174	1246	True	345.000000	531	87.637000	111	732	2	chr3D.!!$R2	621
11	TraesCS7D01G101400	chr3D	80217783	80220001	2218	False	313.500000	412	94.941000	2490	3143	2	chr3D.!!$F1	653
12	TraesCS7D01G101400	chr3B	23401923	23403245	1322	False	220.666667	261	88.861667	111	735	3	chr3B.!!$F1	624

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
64	65	0.039180	TCCTCCTCACCAAGTCGCTA	59.961	55.0	0.0	0.0	0.0	4.26	F
772	1714	0.041312	CCGCACTCTTCAAACAACGG	60.041	55.0	0.0	0.0	0.0	4.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2023	2992	0.106918	TCCTTCGGTGCCAAAACAGT	60.107	50.0	0.0	0.0	0.0	3.55	R
2429	3398	0.032267	CGGAGAAAGATAGGCGGACC	59.968	60.0	0.0	0.0	0.0	4.46	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
26	27	9.737844	AAAACCTAACATAAATTACTAACCGGA	57.262	29.630	9.46	0.00	0.00	5.14
27	28	8.953368	AACCTAACATAAATTACTAACCGGAG	57.047	34.615	9.46	0.00	0.00	4.63
28	29	6.988580	ACCTAACATAAATTACTAACCGGAGC	59.011	38.462	9.46	0.00	0.00	4.70
29	30	5.978934	AACATAAATTACTAACCGGAGCG	57.021	39.130	9.46	0.00	0.00	5.03
40	41	2.487428	CGGAGCGGAGACACTGAG	59.513	66.667	0.00	0.00	0.00	3.35
41	42	2.041115	CGGAGCGGAGACACTGAGA	61.041	63.158	0.00	0.00	0.00	3.27
42	43	1.380403	CGGAGCGGAGACACTGAGAT	61.380	60.000	0.00	0.00	0.00	2.75
43	44	0.820871	GGAGCGGAGACACTGAGATT	59.179	55.000	0.00	0.00	0.00	2.40
44	45	1.202359	GGAGCGGAGACACTGAGATTC	60.202	57.143	0.00	0.00	0.00	2.52
45	46	1.748493	GAGCGGAGACACTGAGATTCT	59.252	52.381	0.00	0.00	0.00	2.40
46	47	1.748493	AGCGGAGACACTGAGATTCTC	59.252	52.381	6.73	6.73	35.92	2.87
51	52	3.631250	GAGACACTGAGATTCTCCTCCT	58.369	50.000	11.12	1.86	31.26	3.69
52	53	3.631250	AGACACTGAGATTCTCCTCCTC	58.369	50.000	11.12	1.68	32.32	3.71
53	54	3.011144	AGACACTGAGATTCTCCTCCTCA	59.989	47.826	11.12	0.00	35.81	3.86
54	55	3.096092	ACACTGAGATTCTCCTCCTCAC	58.904	50.000	11.12	0.00	33.80	3.51
55	56	2.430332	CACTGAGATTCTCCTCCTCACC	59.570	54.545	11.12	0.00	33.80	4.02
56	57	2.043664	ACTGAGATTCTCCTCCTCACCA	59.956	50.000	11.12	0.00	33.80	4.17
57	58	3.102972	CTGAGATTCTCCTCCTCACCAA	58.897	50.000	11.12	0.00	33.80	3.67
58	59	3.102972	TGAGATTCTCCTCCTCACCAAG	58.897	50.000	11.12	0.00	32.57	3.61
59	60	3.103742	GAGATTCTCCTCCTCACCAAGT	58.896	50.000	1.97	0.00	0.00	3.16
60	61	3.103742	AGATTCTCCTCCTCACCAAGTC	58.896	50.000	0.00	0.00	0.00	3.01
61	62	1.257743	TTCTCCTCCTCACCAAGTCG	58.742	55.000	0.00	0.00	0.00	4.18
62	63	1.216710	CTCCTCCTCACCAAGTCGC	59.783	63.158	0.00	0.00	0.00	5.19
63	64	1.228894	TCCTCCTCACCAAGTCGCT	60.229	57.895	0.00	0.00	0.00	4.93
64	65	0.039180	TCCTCCTCACCAAGTCGCTA	59.961	55.000	0.00	0.00	0.00	4.26

Showing 1 to 25 of 573 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	9.737844	TCCGGTTAGTAATTTATGTTAGGTTTT	57.262	29.630	0.00	0.00	0.00	2.43
2	3	7.496920	GCTCCGGTTAGTAATTTATGTTAGGTT	59.503	37.037	0.00	0.00	0.00	3.50
3	4	6.988580	GCTCCGGTTAGTAATTTATGTTAGGT	59.011	38.462	0.00	0.00	0.00	3.08
5	6	6.145048	CCGCTCCGGTTAGTAATTTATGTTAG	59.855	42.308	0.00	0.00	42.73	2.34
7	8	4.812626	CCGCTCCGGTTAGTAATTTATGTT	59.187	41.667	0.00	0.00	42.73	2.71
8	9	4.374399	CCGCTCCGGTTAGTAATTTATGT	58.626	43.478	0.00	0.00	42.73	2.29
9	10	4.985044	CCGCTCCGGTTAGTAATTTATG	57.015	45.455	0.00	0.00	42.73	1.90
23	24	1.380403	ATCTCAGTGTCTCCGCTCCG	61.380	60.000	0.00	0.00	0.00	4.63
24	25	0.820871	AATCTCAGTGTCTCCGCTCC	59.179	55.000	0.00	0.00	0.00	4.70
25	26	1.748493	AGAATCTCAGTGTCTCCGCTC	59.252	52.381	0.00	0.00	0.00	5.03
26	27	1.748493	GAGAATCTCAGTGTCTCCGCT	59.252	52.381	5.22	0.00	33.16	5.52
27	28	1.202359	GGAGAATCTCAGTGTCTCCGC	60.202	57.143	12.79	0.00	45.95	5.54
28	29	2.861462	GGAGAATCTCAGTGTCTCCG	57.139	55.000	12.79	0.00	45.95	4.63
30	31	3.631250	AGGAGGAGAATCTCAGTGTCTC	58.369	50.000	12.79	8.50	37.63	3.36
31	32	3.011144	TGAGGAGGAGAATCTCAGTGTCT	59.989	47.826	12.79	0.00	35.58	3.41
32	33	3.130340	GTGAGGAGGAGAATCTCAGTGTC	59.870	52.174	12.79	4.10	38.09	3.67
33	34	3.096092	GTGAGGAGGAGAATCTCAGTGT	58.904	50.000	12.79	0.00	38.09	3.55
34	35	2.430332	GGTGAGGAGGAGAATCTCAGTG	59.570	54.545	12.79	0.00	38.09	3.66
35	36	2.043664	TGGTGAGGAGGAGAATCTCAGT	59.956	50.000	12.79	0.00	38.09	3.41
36	37	2.744760	TGGTGAGGAGGAGAATCTCAG	58.255	52.381	12.79	0.00	38.09	3.35
37	38	2.928036	TGGTGAGGAGGAGAATCTCA	57.072	50.000	12.79	0.00	35.58	3.27
38	39	3.103742	ACTTGGTGAGGAGGAGAATCTC	58.896	50.000	0.71	0.71	33.73	2.75
39	40	3.103742	GACTTGGTGAGGAGGAGAATCT	58.896	50.000	0.00	0.00	33.73	2.40
40	41	2.159170	CGACTTGGTGAGGAGGAGAATC	60.159	54.545	0.00	0.00	0.00	2.52
41	42	1.827969	CGACTTGGTGAGGAGGAGAAT	59.172	52.381	0.00	0.00	0.00	2.40

Showing 1 to 25 of 595 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.