AutoCloner

Multiple sequence alignment - TraesCS6D01G286500

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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	TraesCS6D01G286500	chr6D	100.000	5255	0	0	1	5255	394932426	394937680	0.000000e+00	9705.0
1	TraesCS6D01G286500	chr6D	95.229	524	23	2	4733	5255	395014144	395014666	0.000000e+00	828.0
2	TraesCS6D01G286500	chr6D	78.919	370	69	9	332	698	437960271	437960634	5.260000e-60	243.0
3	TraesCS6D01G286500	chr6A	94.933	2250	65	13	736	2961	541414355	541416579	0.000000e+00	3478.0
4	TraesCS6D01G286500	chr6A	96.696	1362	39	5	3367	4728	541416576	541417931	0.000000e+00	2261.0
5	TraesCS6D01G286500	chr6B	96.454	1946	51	6	1019	2961	591248119	591250049	0.000000e+00	3195.0
6	TraesCS6D01G286500	chr6B	95.598	1363	29	9	3367	4728	591250046	591251378	0.000000e+00	2156.0
7	TraesCS6D01G286500	chr6B	78.193	509	71	28	195	675	474816304	474815808	6.660000e-74	289.0
8	TraesCS6D01G286500	chr6B	81.449	345	40	15	339	666	688467328	688467665	1.450000e-65	261.0
9	TraesCS6D01G286500	chr6B	84.977	213	13	4	767	978	591247420	591247614	1.150000e-46	198.0
10	TraesCS6D01G286500	chr3D	94.307	527	29	1	4729	5255	375269808	375270333	0.000000e+00	806.0
11	TraesCS6D01G286500	chr3D	94.129	528	29	2	4729	5255	375252987	375253513	0.000000e+00	802.0
12	TraesCS6D01G286500	chr3D	92.381	525	39	1	4729	5253	295154834	295155357	0.000000e+00	747.0
13	TraesCS6D01G286500	chr3D	92.395	526	37	2	4729	5253	295180731	295181254	0.000000e+00	747.0
14	TraesCS6D01G286500	chr3D	90.227	440	39	4	2954	3389	554048278	554048717	5.900000e-159	571.0
15	TraesCS6D01G286500	chr3D	90.887	417	37	1	2956	3371	368224711	368224295	4.600000e-155	558.0
16	TraesCS6D01G286500	chr3D	81.973	294	36	14	393	675	84804050	84803763	3.160000e-57	233.0
17	TraesCS6D01G286500	chr3D	81.818	187	28	5	260	444	545322069	545322251	9.110000e-33	152.0
18	TraesCS6D01G286500	chr3D	76.699	206	29	14	20	213	42749440	42749242	4.330000e-16	97.1
19	TraesCS6D01G286500	chr7D	94.084	524	30	1	4732	5255	261075922	261075400	0.000000e+00	795.0
20	TraesCS6D01G286500	chr7D	92.060	529	40	2	4728	5255	261112833	261112306	0.000000e+00	743.0
21	TraesCS6D01G286500	chr2D	92.762	525	37	1	4732	5255	471708880	471708356	0.000000e+00	758.0
22	TraesCS6D01G286500	chr2D	80.328	183	27	9	116	293	547770354	547770532	4.270000e-26	130.0
23	TraesCS6D01G286500	chr1D	92.015	526	40	2	4732	5255	335345446	335344921	0.000000e+00	737.0
24	TraesCS6D01G286500	chr1D	85.128	195	18	8	261	444	435798266	435798460	6.950000e-44	189.0
25	TraesCS6D01G286500	chr1D	81.683	202	23	11	250	444	483256069	483255875	7.050000e-34	156.0
26	TraesCS6D01G286500	chr2A	92.892	408	27	2	2968	3373	584516792	584516385	4.530000e-165	592.0
27	TraesCS6D01G286500	chr2A	92.099	405	31	1	2968	3371	367647427	367647831	2.120000e-158	569.0
28	TraesCS6D01G286500	chr2A	91.106	416	36	1	2955	3369	121288833	121289248	3.550000e-156	562.0
29	TraesCS6D01G286500	chr2A	83.898	118	13	5	82	194	53992519	53992635	2.000000e-19	108.0
30	TraesCS6D01G286500	chr7B	91.587	416	33	2	2958	3371	570461950	570462365	1.640000e-159	573.0
31	TraesCS6D01G286500	chr7B	80.882	204	25	13	225	424	135994666	135994859	1.180000e-31	148.0
32	TraesCS6D01G286500	chr7B	85.714	91	8	5	214	299	526861049	526860959	2.020000e-14	91.6
33	TraesCS6D01G286500	chr2B	92.079	404	31	1	2968	3371	366019431	366019029	7.640000e-158	568.0
34	TraesCS6D01G286500	chr4D	90.931	419	37	1	2952	3369	296443397	296443815	3.550000e-156	562.0
35	TraesCS6D01G286500	chr3B	89.498	438	40	6	2956	3390	734539580	734539146	2.770000e-152	549.0
36	TraesCS6D01G286500	chr3B	82.143	112	11	5	189	293	351983478	351983587	2.610000e-13	87.9
37	TraesCS6D01G286500	chr1B	80.899	356	62	6	325	675	520971168	520971522	5.180000e-70	276.0
38	TraesCS6D01G286500	chr4B	77.621	496	75	20	209	675	584948191	584948679	8.670000e-68	268.0
39	TraesCS6D01G286500	chr5A	79.941	339	56	8	349	675	502392091	502392429	6.800000e-59	239.0
40	TraesCS6D01G286500	chr5A	75.192	391	59	21	86	444	546506368	546505984	3.280000e-32	150.0
41	TraesCS6D01G286500	chr7A	81.973	294	40	11	391	675	732930905	732930616	2.450000e-58	237.0
42	TraesCS6D01G286500	chr4A	78.857	350	66	7	332	675	648414734	648414387	4.090000e-56	230.0
43	TraesCS6D01G286500	chr4A	77.255	255	38	11	181	423	627740655	627740409	1.190000e-26	132.0
44	TraesCS6D01G286500	chr4A	78.947	209	29	8	108	303	34268749	34268543	1.540000e-25	128.0
45	TraesCS6D01G286500	chrUn	79.762	336	43	21	332	649	95603964	95604292	2.460000e-53	220.0
46	TraesCS6D01G286500	chr5D	81.905	210	23	8	250	445	495141981	495141773	4.210000e-36	163.0
47	TraesCS6D01G286500	chr5D	79.279	222	28	11	102	309	30684980	30685197	7.100000e-29	139.0
48	TraesCS6D01G286500	chr5D	78.199	211	32	9	129	327	43247028	43247236	7.150000e-24	122.0
49	TraesCS6D01G286500	chr5D	87.129	101	12	1	96	195	345077805	345077905	4.300000e-21	113.0
50	TraesCS6D01G286500	chr5B	85.000	120	14	4	96	213	705365486	705365603	9.240000e-23	119.0
51	TraesCS6D01G286500	chr5B	78.173	197	28	10	103	290	447550776	447550966	1.550000e-20	111.0

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	TraesCS6D01G286500	chr6D	394932426	394937680	5254	False	9705.000000	9705	100.0000	1	5255	1	chr6D.!!$F1	5254
1	TraesCS6D01G286500	chr6D	395014144	395014666	522	False	828.000000	828	95.2290	4733	5255	1	chr6D.!!$F2	522
2	TraesCS6D01G286500	chr6A	541414355	541417931	3576	False	2869.500000	3478	95.8145	736	4728	2	chr6A.!!$F1	3992
3	TraesCS6D01G286500	chr6B	591247420	591251378	3958	False	1849.666667	3195	92.3430	767	4728	3	chr6B.!!$F2	3961
4	TraesCS6D01G286500	chr3D	375269808	375270333	525	False	806.000000	806	94.3070	4729	5255	1	chr3D.!!$F4	526
5	TraesCS6D01G286500	chr3D	375252987	375253513	526	False	802.000000	802	94.1290	4729	5255	1	chr3D.!!$F3	526
6	TraesCS6D01G286500	chr3D	295154834	295155357	523	False	747.000000	747	92.3810	4729	5253	1	chr3D.!!$F1	524
7	TraesCS6D01G286500	chr3D	295180731	295181254	523	False	747.000000	747	92.3950	4729	5253	1	chr3D.!!$F2	524
8	TraesCS6D01G286500	chr7D	261075400	261075922	522	True	795.000000	795	94.0840	4732	5255	1	chr7D.!!$R1	523
9	TraesCS6D01G286500	chr7D	261112306	261112833	527	True	743.000000	743	92.0600	4728	5255	1	chr7D.!!$R2	527
10	TraesCS6D01G286500	chr2D	471708356	471708880	524	True	758.000000	758	92.7620	4732	5255	1	chr2D.!!$R1	523
11	TraesCS6D01G286500	chr1D	335344921	335345446	525	True	737.000000	737	92.0150	4732	5255	1	chr1D.!!$R1	523

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	Hairpin	End Stability	Orientation
172	173	0.036306	GTGCCTCTCGGAAAGGGAAA	59.964	55.000	35.86	3.13	F
410	411	0.036732	TGAGAGGCACGGATTTGCTT	59.963	50.000	42.56	3.91	F
592	593	0.037605	ACGGTTCGAGATTGGGACAC	60.038	55.000	39.29	3.67	F
593	594	0.037697	CGGTTCGAGATTGGGACACA	60.038	55.000	39.29	3.72	F
686	687	0.179116	CGCACATGAGGAGGTGAGAG	60.179	60.000	35.94	3.20	F
692	693	0.780637	TGAGGAGGTGAGAGTGGTCT	59.219	55.000	34.86	3.85	F
693	694	1.148027	TGAGGAGGTGAGAGTGGTCTT	59.852	52.381	30.97	3.01	F
696	697	1.971357	GGAGGTGAGAGTGGTCTTTGA	59.029	52.381	30.97	2.69	F
702	703	2.037772	TGAGAGTGGTCTTTGAAGCCTC	59.962	50.000	30.97	4.70	F
983	994	2.299297	GGAGAAGAGAAACCCGAACAGA	59.701	50.000	0.00	3.41	F
2989	3476	0.322975	GGACTGCTCTGCTCCTTCAA	59.677	55.000	0.00	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1670	2154	2.476241	GCAAACTTTTCAAGGGCAATCG	59.524	45.455	0.00	0.00	3.34	R
1849	2335	3.068560	TGGTACACACGATTAAACCAGC	58.931	45.455	0.00	33.28	4.85	R
2497	2983	1.679032	GGAGTGTATGGCCCTGTCAAC	60.679	57.143	0.00	0.00	3.18	R
2613	3099	0.685097	TAATATGCGGTCTGGGCCTC	59.315	55.000	4.53	0.00	4.70	R
2652	3138	5.927954	TGGTAACACGAAATAAGTTGACC	57.072	39.130	0.00	46.17	4.02	R
2957	3444	4.681624	AGTCCCAACTGGCCCTTA	57.318	55.556	0.00	33.32	2.69	R
2970	3457	0.322975	TTGAAGGAGCAGAGCAGTCC	59.677	55.000	0.00	0.00	3.85	R
2975	3462	2.159407	GCTGAATTTGAAGGAGCAGAGC	60.159	50.000	0.00	0.00	4.09	R
2980	3467	1.399791	CGGAGCTGAATTTGAAGGAGC	59.600	52.381	0.00	0.00	4.70	R
3023	3510	0.037232	GCATATCGTGGAGCTACCCC	60.037	60.000	0.00	38.00	4.95	R
4966	5454	0.755698	ATGACCGACCGTAGCCATCT	60.756	55.000	0.00	0.00	2.90	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
27	28	5.204409	GGTTTTTCCCGGTATTTTTGACT	57.796	39.130	0.00	3.41
28	29	5.603596	GGTTTTTCCCGGTATTTTTGACTT	58.396	37.500	0.00	3.01
29	30	6.050432	GGTTTTTCCCGGTATTTTTGACTTT	58.950	36.000	0.00	2.66
30	31	6.539464	GGTTTTTCCCGGTATTTTTGACTTTT	59.461	34.615	0.00	2.27
31	32	7.254522	GGTTTTTCCCGGTATTTTTGACTTTTC	60.255	37.037	0.00	2.29
32	33	4.752661	TCCCGGTATTTTTGACTTTTCG	57.247	40.909	0.00	3.46
33	34	3.502979	TCCCGGTATTTTTGACTTTTCGG	59.497	43.478	35.33	4.30
34	35	3.253921	CCCGGTATTTTTGACTTTTCGGT	59.746	43.478	33.93	4.69
35	36	4.261698	CCCGGTATTTTTGACTTTTCGGTT	60.262	41.667	33.93	4.44
36	37	5.283294	CCGGTATTTTTGACTTTTCGGTTT	58.717	37.500	0.00	3.27
37	38	5.749588	CCGGTATTTTTGACTTTTCGGTTTT	59.250	36.000	0.00	2.43
38	39	6.256104	CCGGTATTTTTGACTTTTCGGTTTTT	59.744	34.615	0.00	1.94
39	40	7.331792	CGGTATTTTTGACTTTTCGGTTTTTC	58.668	34.615	0.00	2.29
40	41	7.009357	CGGTATTTTTGACTTTTCGGTTTTTCA	59.991	33.333	0.00	2.69
41	42	8.822855	GGTATTTTTGACTTTTCGGTTTTTCAT	58.177	29.630	0.00	2.57
42	43	9.843874	GTATTTTTGACTTTTCGGTTTTTCATC	57.156	29.630	0.00	2.92
43	44	6.561945	TTTTGACTTTTCGGTTTTTCATCG	57.438	33.333	0.00	3.84
44	45	4.217754	TGACTTTTCGGTTTTTCATCGG	57.782	40.909	0.00	4.18
45	46	3.628487	TGACTTTTCGGTTTTTCATCGGT	59.372	39.130	0.00	4.69
46	47	4.216731	GACTTTTCGGTTTTTCATCGGTC	58.783	43.478	0.00	4.79
47	48	3.881089	ACTTTTCGGTTTTTCATCGGTCT	59.119	39.130	0.00	3.85
48	49	4.337274	ACTTTTCGGTTTTTCATCGGTCTT	59.663	37.500	0.00	3.01
49	50	4.904253	TTTCGGTTTTTCATCGGTCTTT	57.096	36.364	0.00	2.52
50	51	4.904253	TTCGGTTTTTCATCGGTCTTTT	57.096	36.364	0.00	2.27
51	52	4.477302	TCGGTTTTTCATCGGTCTTTTC	57.523	40.909	0.00	2.29

Showing 1 to 25 of 624 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
6	7	7.515528	CGAAAAGTCAAAAATACCGGGAAAAAC	60.516	37.037	6.32	0.00	2.43
7	8	6.476053	CGAAAAGTCAAAAATACCGGGAAAAA	59.524	34.615	6.32	0.00	1.94
8	9	5.978322	CGAAAAGTCAAAAATACCGGGAAAA	59.022	36.000	6.32	0.00	2.29
9	10	5.507650	CCGAAAAGTCAAAAATACCGGGAAA	60.508	40.000	6.32	0.00	3.13
10	11	4.023021	CCGAAAAGTCAAAAATACCGGGAA	60.023	41.667	6.32	0.00	3.97
11	12	3.502979	CCGAAAAGTCAAAAATACCGGGA	59.497	43.478	6.32	0.00	5.14
12	13	3.253921	ACCGAAAAGTCAAAAATACCGGG	59.746	43.478	6.32	38.79	5.73
13	14	4.492791	ACCGAAAAGTCAAAAATACCGG	57.507	40.909	0.00	40.15	5.28
14	15	6.815672	AAAACCGAAAAGTCAAAAATACCG	57.184	33.333	0.00	0.00	4.02
15	16	8.187354	TGAAAAACCGAAAAGTCAAAAATACC	57.813	30.769	0.00	0.00	2.73
16	17	9.843874	GATGAAAAACCGAAAAGTCAAAAATAC	57.156	29.630	0.00	0.00	1.89
17	18	8.747666	CGATGAAAAACCGAAAAGTCAAAAATA	58.252	29.630	0.00	0.00	1.40
18	19	7.254286	CCGATGAAAAACCGAAAAGTCAAAAAT	60.254	33.333	0.00	0.00	1.82
19	20	6.035112	CCGATGAAAAACCGAAAAGTCAAAAA	59.965	34.615	0.00	0.00	1.94
20	21	5.517054	CCGATGAAAAACCGAAAAGTCAAAA	59.483	36.000	0.00	0.00	2.44
21	22	5.038033	CCGATGAAAAACCGAAAAGTCAAA	58.962	37.500	0.00	0.00	2.69
22	23	4.096682	ACCGATGAAAAACCGAAAAGTCAA	59.903	37.500	0.00	0.00	3.18
23	24	3.628487	ACCGATGAAAAACCGAAAAGTCA	59.372	39.130	0.00	0.00	3.41
24	25	4.024302	AGACCGATGAAAAACCGAAAAGTC	60.024	41.667	0.00	0.00	3.01
25	26	3.881089	AGACCGATGAAAAACCGAAAAGT	59.119	39.130	0.00	0.00	2.66
26	27	4.483476	AGACCGATGAAAAACCGAAAAG	57.517	40.909	0.00	0.00	2.27
27	28	4.904253	AAGACCGATGAAAAACCGAAAA	57.096	36.364	0.00	0.00	2.29
28	29	4.904253	AAAGACCGATGAAAAACCGAAA	57.096	36.364	0.00	0.00	3.46
29	30	4.577283	AGAAAAGACCGATGAAAAACCGAA	59.423	37.500	0.00	0.00	4.30
30	31	4.131596	AGAAAAGACCGATGAAAAACCGA	58.868	39.130	0.00	0.00	4.69

Showing 1 to 25 of 652 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.