AutoCloner

Multiple sequence alignment - TraesCS3B01G466000

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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	TraesCS3B01G466000	chr3B	100.000	3030	0	0	1	3030	708521879	708518850	0.000000e+00	5596.0
1	TraesCS3B01G466000	chr3B	100.000	2954	0	0	3322	6275	708518558	708515605	0.000000e+00	5456.0
2	TraesCS3B01G466000	chr3B	95.327	321	13	2	1	320	733909939	733909620	5.610000e-140	508.0
3	TraesCS3B01G466000	chr3B	95.327	321	14	1	1	320	750115477	750115797	5.610000e-140	508.0
4	TraesCS3B01G466000	chr3B	94.720	322	15	2	1	320	35488833	35489154	3.380000e-137	499.0
5	TraesCS3B01G466000	chr3B	82.353	459	49	10	5533	5969	708940975	708940527	2.760000e-98	370.0
6	TraesCS3B01G466000	chr3B	90.351	114	11	0	3570	3683	495475486	495475599	3.920000e-32	150.0
7	TraesCS3B01G466000	chr3B	82.946	129	16	6	3563	3687	43186396	43186522	1.850000e-20	111.0
8	TraesCS3B01G466000	chr3D	92.880	1854	94	11	4144	5969	536331136	536332979	0.000000e+00	2658.0
9	TraesCS3B01G466000	chr3D	94.661	1461	45	11	679	2124	536327034	536328476	0.000000e+00	2235.0
10	TraesCS3B01G466000	chr3D	87.390	682	30	14	2383	3030	536329619	536330278	0.000000e+00	732.0
11	TraesCS3B01G466000	chr3D	92.489	466	32	3	3322	3786	536330329	536330792	0.000000e+00	664.0
12	TraesCS3B01G466000	chr3D	83.002	453	51	11	5533	5969	536426524	536426082	2.740000e-103	387.0
13	TraesCS3B01G466000	chr3D	86.842	228	28	1	3922	4149	536330811	536331036	2.900000e-63	254.0
14	TraesCS3B01G466000	chr3D	91.667	168	13	1	514	681	536325182	536325348	1.360000e-56	231.0
15	TraesCS3B01G466000	chr3D	88.710	186	13	2	2129	2306	536329022	536329207	2.940000e-53	220.0
16	TraesCS3B01G466000	chr3D	84.167	240	21	9	6012	6249	536332948	536333172	3.810000e-52	217.0
17	TraesCS3B01G466000	chr3D	90.351	114	11	0	3570	3683	379826346	379826233	3.920000e-32	150.0
18	TraesCS3B01G466000	chr3A	90.424	1838	91	35	516	2306	671731503	671733302	0.000000e+00	2340.0
19	TraesCS3B01G466000	chr3A	91.524	1581	97	12	3922	5489	671738967	671740523	0.000000e+00	2143.0
20	TraesCS3B01G466000	chr3A	90.499	621	28	6	2420	3030	671737733	671738332	0.000000e+00	791.0
21	TraesCS3B01G466000	chr3A	86.722	482	42	12	3322	3798	671738383	671738847	3.350000e-142	516.0
22	TraesCS3B01G466000	chr3A	84.352	409	42	8	5564	5960	671740930	671741328	1.280000e-101	381.0
23	TraesCS3B01G466000	chr3A	82.667	450	52	10	5533	5966	672076234	672075795	5.940000e-100	375.0
24	TraesCS3B01G466000	chr3A	89.516	248	13	3	6034	6275	671741333	671741573	1.020000e-77	302.0
25	TraesCS3B01G466000	chr3A	90.351	114	11	0	3570	3683	503822288	503822401	3.920000e-32	150.0
26	TraesCS3B01G466000	chr7B	86.156	874	101	13	4553	5412	507139531	507138664	0.000000e+00	926.0
27	TraesCS3B01G466000	chr7B	93.121	596	33	4	1044	1638	507141176	507140588	0.000000e+00	867.0
28	TraesCS3B01G466000	chr7B	90.909	110	10	0	3570	3679	357651589	357651480	1.410000e-31	148.0
29	TraesCS3B01G466000	chr7B	96.667	60	2	0	5979	6038	394399415	394399474	4.000000e-17	100.0
30	TraesCS3B01G466000	chr7B	94.643	56	2	1	3874	3928	731191034	731191089	1.120000e-12	86.1
31	TraesCS3B01G466000	chr7D	87.407	810	95	5	4553	5356	481696074	481695266	0.000000e+00	924.0
32	TraesCS3B01G466000	chr7D	93.624	596	30	4	1044	1638	481697562	481696974	0.000000e+00	883.0
33	TraesCS3B01G466000	chr7D	90.351	114	11	0	3561	3674	310990309	310990196	3.920000e-32	150.0
34	TraesCS3B01G466000	chr7A	93.109	595	33	4	1044	1637	548585886	548585299	0.000000e+00	865.0
35	TraesCS3B01G466000	chr7A	87.746	710	87	0	4553	5262	548584326	548583617	0.000000e+00	830.0
36	TraesCS3B01G466000	chr4D	86.387	595	69	4	1043	1637	40401135	40401717	1.910000e-179	640.0
37	TraesCS3B01G466000	chr4D	81.591	679	119	5	4591	5266	40402029	40402704	1.980000e-154	556.0
38	TraesCS3B01G466000	chr4D	90.244	82	4	4	3784	3864	300285014	300284936	3.090000e-18	104.0
39	TraesCS3B01G466000	chr4D	88.750	80	2	5	3782	3860	41219350	41219423	2.410000e-14	91.6
40	TraesCS3B01G466000	chr4D	88.158	76	3	3	3785	3860	455925214	455925283	1.120000e-12	86.1
41	TraesCS3B01G466000	chr4B	86.172	593	70	6	1043	1635	58955482	58956062	1.150000e-176	630.0
42	TraesCS3B01G466000	chr4B	95.639	321	13	1	1	320	124767106	124766786	1.210000e-141	514.0
43	TraesCS3B01G466000	chr2D	86.027	594	71	9	1043	1636	71621678	71622259	1.490000e-175	627.0
44	TraesCS3B01G466000	chr2D	88.506	87	4	3	3781	3862	377154994	377155079	4.000000e-17	100.0
45	TraesCS3B01G466000	chr2A	85.859	594	72	9	1043	1636	70674302	70674883	6.910000e-174	621.0
46	TraesCS3B01G466000	chr2A	89.744	117	11	1	3566	3682	205917709	205917594	1.410000e-31	148.0
47	TraesCS3B01G466000	chr4A	81.591	679	119	6	4591	5266	559486874	559486199	1.980000e-154	556.0
48	TraesCS3B01G466000	chr1B	95.016	321	15	1	1	320	297437144	297437464	2.610000e-138	503.0
49	TraesCS3B01G466000	chr1B	95.385	65	3	0	5974	6038	99705741	99705677	3.090000e-18	104.0
50	TraesCS3B01G466000	chr1B	96.667	60	2	0	5979	6038	5708923	5708864	4.000000e-17	100.0
51	TraesCS3B01G466000	chr1B	93.103	58	2	2	3872	3928	589768937	589768993	4.030000e-12	84.2
52	TraesCS3B01G466000	chrUn	94.737	323	13	4	1	320	38831287	38830966	3.380000e-137	499.0
53	TraesCS3B01G466000	chrUn	91.549	71	3	2	5971	6038	109126597	109126527	1.860000e-15	95.3
54	TraesCS3B01G466000	chr5B	94.737	323	13	4	1	320	438527316	438527637	3.380000e-137	499.0
55	TraesCS3B01G466000	chr5B	94.393	321	16	2	1	320	214668234	214667915	5.650000e-135	492.0
56	TraesCS3B01G466000	chr5B	92.105	76	4	2	3785	3860	102640546	102640619	8.600000e-19	106.0
57	TraesCS3B01G466000	chr5B	96.154	52	1	1	3878	3928	429121985	429122036	4.030000e-12	84.2
58	TraesCS3B01G466000	chr6B	94.704	321	13	4	1	320	707047698	707047381	4.370000e-136	496.0
59	TraesCS3B01G466000	chr6B	89.610	77	4	3	3784	3860	10731471	10731399	1.860000e-15	95.3
60	TraesCS3B01G466000	chr6B	86.667	75	8	1	4045	4119	473084455	473084383	1.450000e-11	82.4
61	TraesCS3B01G466000	chr6A	76.306	536	94	23	1087	1606	449667563	449668081	8.070000e-64	255.0
62	TraesCS3B01G466000	chr6A	94.545	55	1	2	3876	3928	395248882	395248936	4.030000e-12	84.2
63	TraesCS3B01G466000	chr6A	94.545	55	2	1	3875	3928	601207346	601207292	4.030000e-12	84.2
64	TraesCS3B01G466000	chr6D	90.351	114	10	1	3570	3682	391925880	391925993	1.410000e-31	148.0
65	TraesCS3B01G466000	chr6D	96.774	62	2	0	5977	6038	28474460	28474399	3.090000e-18	104.0
66	TraesCS3B01G466000	chr6D	85.000	80	10	2	3782	3860	21613025	21613103	5.210000e-11	80.5
67	TraesCS3B01G466000	chr1D	97.143	70	2	0	5969	6038	81365641	81365572	1.110000e-22	119.0
68	TraesCS3B01G466000	chr1D	93.421	76	4	1	3785	3860	402437785	402437859	1.850000e-20	111.0
69	TraesCS3B01G466000	chr1D	95.238	63	2	1	5977	6038	323273252	323273190	1.440000e-16	99.0
70	TraesCS3B01G466000	chr1D	79.630	108	14	7	3986	4089	29694818	29694715	3.140000e-08	71.3
71	TraesCS3B01G466000	chr5D	88.764	89	3	4	3779	3867	63616064	63615983	1.110000e-17	102.0
72	TraesCS3B01G466000	chr5D	95.161	62	3	0	5977	6038	466574136	466574075	1.440000e-16	99.0
73	TraesCS3B01G466000	chr5D	96.078	51	1	1	3879	3928	532749820	532749770	1.450000e-11	82.4
74	TraesCS3B01G466000	chr5A	95.161	62	3	0	5977	6038	691397993	691397932	1.440000e-16	99.0
75	TraesCS3B01G466000	chr5A	96.226	53	1	1	3877	3928	639187335	639187387	1.120000e-12	86.1
76	TraesCS3B01G466000	chr5A	92.857	42	3	0	2344	2385	249848333	249848374	1.890000e-05	62.1
77	TraesCS3B01G466000	chr2B	94.915	59	1	2	3872	3928	788660484	788660426	2.410000e-14	91.6
78	TraesCS3B01G466000	chr1A	94.643	56	1	2	3875	3928	539977697	539977642	1.120000e-12	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	TraesCS3B01G466000	chr3B	708515605	708521879	6274	True	5526.000	5596	100.00000	1	6275	2	chr3B.!!$R3	6274
1	TraesCS3B01G466000	chr3D	536325182	536333172	7990	False	901.375	2658	89.85075	514	6249	8	chr3D.!!$F1	5735
2	TraesCS3B01G466000	chr3A	671731503	671733302	1799	False	2340.000	2340	90.42400	516	2306	1	chr3A.!!$F2	1790
3	TraesCS3B01G466000	chr3A	671737733	671741573	3840	False	826.600	2143	88.52260	2420	6275	5	chr3A.!!$F3	3855
4	TraesCS3B01G466000	chr7B	507138664	507141176	2512	True	896.500	926	89.63850	1044	5412	2	chr7B.!!$R2	4368
5	TraesCS3B01G466000	chr7D	481695266	481697562	2296	True	903.500	924	90.51550	1044	5356	2	chr7D.!!$R2	4312
6	TraesCS3B01G466000	chr7A	548583617	548585886	2269	True	847.500	865	90.42750	1044	5262	2	chr7A.!!$R1	4218
7	TraesCS3B01G466000	chr4D	40401135	40402704	1569	False	598.000	640	83.98900	1043	5266	2	chr4D.!!$F3	4223
8	TraesCS3B01G466000	chr4B	58955482	58956062	580	False	630.000	630	86.17200	1043	1635	1	chr4B.!!$F1	592
9	TraesCS3B01G466000	chr2D	71621678	71622259	581	False	627.000	627	86.02700	1043	1636	1	chr2D.!!$F1	593
10	TraesCS3B01G466000	chr2A	70674302	70674883	581	False	621.000	621	85.85900	1043	1636	1	chr2A.!!$F1	593
11	TraesCS3B01G466000	chr4A	559486199	559486874	675	True	556.000	556	81.59100	4591	5266	1	chr4A.!!$R1	675
12	TraesCS3B01G466000	chr6A	449667563	449668081	518	False	255.000	255	76.30600	1087	1606	1	chr6A.!!$F2	519

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	End Stability	Orientation
407	408	0.033781	TTGCGTGGGGTGTACAGTAC	59.966	55.0	3.49	3.49	2.73	F
984	2687	0.112606	AACCGAGTCCAGTCTCCAGA	59.887	55.0	0.00	0.00	3.86	F
2415	5158	0.176680	CTGCGCCAATCTCCACTACT	59.823	55.0	4.18	0.00	2.57	F
2576	5335	0.524862	CTGAGGCATTTGTCCAGCAC	59.475	55.0	0.00	0.00	4.40	F
3800	6584	0.338814	AACTACTCCCTCCGTCCCAT	59.661	55.0	0.00	0.00	4.00	F
3982	6883	0.396435	ATTGACTGGTCTCGGCAACA	59.604	50.0	2.38	0.00	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2333	5014	1.070443	CAAACGGATGTTTACACGCGT	60.070	47.619	5.58	5.58	46.33	6.01	R
2602	5361	0.036010	AAAGATGGCTGTCACTCCGG	60.036	55.000	0.00	0.00	0.00	5.14	R
3354	6131	0.390603	TTGTACAGATTGTCCGGGCG	60.391	55.000	0.00	0.00	0.00	6.13	R
4121	7029	1.011333	AACAAAACAGACACGACCGG	58.989	50.000	0.00	0.00	0.00	5.28	R
5118	8375	0.904649	TGTTCCTCCTCATCGTGCAT	59.095	50.000	0.00	0.00	0.00	3.96	R
5890	9520	1.016627	TCACACAAGCACTTGACTGC	58.983	50.000	16.95	0.00	42.93	4.40	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
22	23	3.940852	TGAAACCATGATGAAGGTGATCG	59.059	43.478	38.37	3.69
23	24	2.627515	ACCATGATGAAGGTGATCGG	57.372	50.000	36.60	4.18
24	25	2.118679	ACCATGATGAAGGTGATCGGA	58.881	47.619	36.60	4.55
25	26	2.505407	ACCATGATGAAGGTGATCGGAA	59.495	45.455	36.60	4.30
26	27	3.054434	ACCATGATGAAGGTGATCGGAAA	60.054	43.478	36.60	3.13
27	28	3.947196	CCATGATGAAGGTGATCGGAAAA	59.053	43.478	0.00	2.29
28	29	4.398988	CCATGATGAAGGTGATCGGAAAAA	59.601	41.667	0.00	1.94
29	30	5.068198	CCATGATGAAGGTGATCGGAAAAAT	59.932	40.000	0.00	1.82
30	31	5.818136	TGATGAAGGTGATCGGAAAAATC	57.182	39.130	0.00	2.17
31	32	4.332543	TGATGAAGGTGATCGGAAAAATCG	59.667	41.667	0.00	3.34
32	33	2.418628	TGAAGGTGATCGGAAAAATCGC	59.581	45.455	33.78	4.58
33	34	2.107950	AGGTGATCGGAAAAATCGCA	57.892	45.000	35.75	5.10
34	35	2.432444	AGGTGATCGGAAAAATCGCAA	58.568	42.857	35.75	4.85
35	36	2.161609	AGGTGATCGGAAAAATCGCAAC	59.838	45.455	35.75	4.17
36	37	2.161609	GGTGATCGGAAAAATCGCAACT	59.838	45.455	35.75	3.16
37	38	3.365969	GGTGATCGGAAAAATCGCAACTT	60.366	43.478	35.75	2.66
38	39	3.846335	GTGATCGGAAAAATCGCAACTTC	59.154	43.478	34.51	3.01
39	40	3.751175	TGATCGGAAAAATCGCAACTTCT	59.249	39.130	0.00	2.85
40	41	3.806316	TCGGAAAAATCGCAACTTCTC	57.194	42.857	0.00	2.87
41	42	2.482721	TCGGAAAAATCGCAACTTCTCC	59.517	45.455	0.00	3.71
42	43	2.225491	CGGAAAAATCGCAACTTCTCCA	59.775	45.455	0.00	3.86
43	44	3.304391	CGGAAAAATCGCAACTTCTCCAA	60.304	43.478	0.00	3.53
44	45	4.615912	CGGAAAAATCGCAACTTCTCCAAT	60.616	41.667	0.00	3.16
45	46	5.391523	CGGAAAAATCGCAACTTCTCCAATA	60.392	40.000	0.00	1.90
46	47	6.386654	GGAAAAATCGCAACTTCTCCAATAA	58.613	36.000	0.00	1.40

Showing 1 to 25 of 592 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.940852	CGATCACCTTCATCATGGTTTCA	59.059	43.478	0.00	0.00	33.75	2.69
1	2	3.313526	CCGATCACCTTCATCATGGTTTC	59.686	47.826	0.00	0.00	33.75	2.78
2	3	3.054434	TCCGATCACCTTCATCATGGTTT	60.054	43.478	0.00	0.00	33.75	3.27
3	4	2.505407	TCCGATCACCTTCATCATGGTT	59.495	45.455	0.00	0.00	33.75	3.67
5	6	2.916702	TCCGATCACCTTCATCATGG	57.083	50.000	0.00	0.00	0.00	3.66
6	7	5.565592	TTTTTCCGATCACCTTCATCATG	57.434	39.130	0.00	0.00	0.00	3.07
7	8	5.008019	CGATTTTTCCGATCACCTTCATCAT	59.992	40.000	0.00	0.00	0.00	2.45
8	9	4.332543	CGATTTTTCCGATCACCTTCATCA	59.667	41.667	0.00	0.00	0.00	3.07
9	10	4.786609	GCGATTTTTCCGATCACCTTCATC	60.787	45.833	0.00	0.00	0.00	2.92
10	11	3.065371	GCGATTTTTCCGATCACCTTCAT	59.935	43.478	0.00	0.00	0.00	2.57
11	12	2.418628	GCGATTTTTCCGATCACCTTCA	59.581	45.455	0.00	0.00	0.00	3.02
12	13	2.418628	TGCGATTTTTCCGATCACCTTC	59.581	45.455	0.00	0.00	0.00	3.46
13	14	2.432444	TGCGATTTTTCCGATCACCTT	58.568	42.857	0.00	0.00	0.00	3.50
14	15	2.107950	TGCGATTTTTCCGATCACCT	57.892	45.000	0.00	0.00	0.00	4.00
15	16	2.161609	AGTTGCGATTTTTCCGATCACC	59.838	45.455	0.00	0.00	0.00	4.02
16	17	3.471495	AGTTGCGATTTTTCCGATCAC	57.529	42.857	0.00	0.00	0.00	3.06
17	18	3.751175	AGAAGTTGCGATTTTTCCGATCA	59.249	39.130	0.00	0.00	0.00	2.92
18	19	4.335272	GAGAAGTTGCGATTTTTCCGATC	58.665	43.478	0.00	0.00	0.00	3.69
19	20	3.127030	GGAGAAGTTGCGATTTTTCCGAT	59.873	43.478	3.36	0.00	0.00	4.18
20	21	2.482721	GGAGAAGTTGCGATTTTTCCGA	59.517	45.455	3.36	0.00	0.00	4.55
21	22	2.225491	TGGAGAAGTTGCGATTTTTCCG	59.775	45.455	12.46	0.00	30.94	4.30
22	23	3.915437	TGGAGAAGTTGCGATTTTTCC	57.085	42.857	10.87	10.87	0.00	3.13
23	24	7.084486	ACTTATTGGAGAAGTTGCGATTTTTC	58.916	34.615	0.00	0.00	33.25	2.29
24	25	6.981722	ACTTATTGGAGAAGTTGCGATTTTT	58.018	32.000	0.00	0.00	33.25	1.94
25	26	6.575162	ACTTATTGGAGAAGTTGCGATTTT	57.425	33.333	0.00	0.00	33.25	1.82

Showing 1 to 25 of 635 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.